Multiple sequence alignment - TraesCS1D01G202700

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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 TraesCS1D01G202700 chr1D 100.000 5274 0 0 1 5274 286088512 286093785 0.000000e+00 9740.0
1 TraesCS1D01G202700 chr1D 85.070 355 37 8 417 760 22602143 22601794 1.090000e-91 348.0
2 TraesCS1D01G202700 chr1A 93.132 3800 123 53 605 4337 357414634 357418362 0.000000e+00 5445.0
3 TraesCS1D01G202700 chr1A 89.062 192 14 3 4390 4578 357418375 357418562 1.140000e-56 231.0
4 TraesCS1D01G202700 chr1A 93.836 146 8 1 4595 4740 357418616 357418760 8.890000e-53 219.0
5 TraesCS1D01G202700 chr1A 80.479 292 50 6 51 340 511011368 511011654 3.200000e-52 217.0
6 TraesCS1D01G202700 chr1A 72.250 400 93 15 1335 1725 463290549 463290159 2.010000e-19 108.0
7 TraesCS1D01G202700 chr1B 92.046 2967 152 41 388 3296 388381460 388384400 0.000000e+00 4095.0
8 TraesCS1D01G202700 chr1B 91.667 828 41 9 3773 4578 388384923 388385744 0.000000e+00 1122.0
9 TraesCS1D01G202700 chr1B 90.086 464 22 11 3321 3776 388384397 388384844 9.850000e-162 580.0
10 TraesCS1D01G202700 chr1B 92.042 377 21 6 4776 5146 388385957 388386330 6.050000e-144 521.0
11 TraesCS1D01G202700 chr1B 88.182 330 22 5 441 757 263981351 263981676 1.390000e-100 377.0
12 TraesCS1D01G202700 chr1B 86.994 346 30 6 423 756 583978843 583979185 4.990000e-100 375.0
13 TraesCS1D01G202700 chr1B 83.954 349 47 8 1 344 388381370 388381714 5.090000e-85 326.0
14 TraesCS1D01G202700 chr1B 89.831 177 10 3 4595 4763 388385796 388385972 2.470000e-53 220.0
15 TraesCS1D01G202700 chr1B 93.617 141 9 0 5134 5274 388386346 388386486 1.490000e-50 211.0
16 TraesCS1D01G202700 chr1B 89.474 57 6 0 1519 1575 487495854 487495798 7.330000e-09 73.1
17 TraesCS1D01G202700 chr3D 85.347 389 39 12 382 757 384530361 384530744 2.300000e-103 387.0
18 TraesCS1D01G202700 chr3D 81.787 291 43 7 52 338 347629312 347629028 8.830000e-58 235.0
19 TraesCS1D01G202700 chr4D 85.946 370 34 6 402 759 215458107 215457744 3.850000e-101 379.0
20 TraesCS1D01G202700 chr5D 83.461 393 48 13 382 761 409448132 409448520 3.020000e-92 350.0
21 TraesCS1D01G202700 chr5D 83.784 296 42 4 54 344 409448100 409448394 5.200000e-70 276.0
22 TraesCS1D01G202700 chr7B 84.384 365 40 8 402 753 614233653 614234013 5.060000e-90 342.0
23 TraesCS1D01G202700 chr4A 85.156 256 34 4 92 344 395025868 395026122 5.240000e-65 259.0
24 TraesCS1D01G202700 chrUn 82.131 291 46 6 58 344 35220895 35220607 1.470000e-60 244.0
25 TraesCS1D01G202700 chr7D 81.605 299 44 6 52 341 188360852 188361148 2.460000e-58 237.0
26 TraesCS1D01G202700 chr5B 81.818 297 41 7 53 344 576087945 576088233 2.460000e-58 237.0
27 TraesCS1D01G202700 chr3B 81.379 290 48 4 58 344 12097109 12097395 1.140000e-56 231.0
28 TraesCS1D01G202700 chr3B 82.682 179 24 6 382 558 526735614 526735787 9.150000e-33 152.0
29 TraesCS1D01G202700 chr7A 86.792 53 5 2 1335 1386 663536886 663536835 2.050000e-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 TraesCS1D01G202700 chr1D 286088512 286093785 5273 False 9740.000000 9740 100.000000 1 5274 1 chr1D.!!$F1 5273
1 TraesCS1D01G202700 chr1A 357414634 357418760 4126 False 1965.000000 5445 92.010000 605 4740 3 chr1A.!!$F2 4135
2 TraesCS1D01G202700 chr1B 388381370 388386486 5116 False 1010.714286 4095 90.463286 1 5274 7 chr1B.!!$F3 5273

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
468 474 0.036765 TAAACAAGGATGCGAGGCGT 60.037 50.0 0.0 0.0 0.00 5.68 F
470 476 0.178068 AACAAGGATGCGAGGCGTAT 59.822 50.0 0.0 0.0 34.49 3.06 F
2047 2088 0.108186 ACGCAGCTCCAATCGATGAA 60.108 50.0 0.0 0.0 0.00 2.57 F
2657 2718 0.108520 CATGCGTACCTACCACGGTT 60.109 55.0 0.0 0.0 39.75 4.44 F
3401 3481 0.384725 CGCTCGGTGTTTTGCTCAAG 60.385 55.0 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2065 0.108186 TTCATCGATTGGAGCTGCGT 60.108 50.000 0.0 0.0 0.00 5.24 R
2172 2213 1.080501 CGTTCTCCAGCTCGCTTGA 60.081 57.895 0.0 0.0 0.00 3.02 R
3355 3434 0.302288 TTTTCGCTTTCACCACGTCG 59.698 50.000 0.0 0.0 0.00 5.12 R
4161 4344 0.661483 GACGAGCAAAGCAAAGCACC 60.661 55.000 0.0 0.0 0.00 5.01 R
4790 5039 0.029300 CCAAGTCAAGTGTTGCACCG 59.971 55.000 0.0 0.0 34.49 4.94 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 0.324943 GGACAGTTTAGGGAGCTGCA 59.675 55.000 7.79 0.00 39.95 4.41
31 32 3.039252 AGGGAGCTGCAGTAACTCTAT 57.961 47.619 16.64 3.92 0.00 1.98
36 37 6.782988 AGGGAGCTGCAGTAACTCTATAATTA 59.217 38.462 16.64 0.00 0.00 1.40
65 66 6.183360 GGATAAAACTCGAGAATGGCGTTTTA 60.183 38.462 21.68 17.35 41.43 1.52
77 78 1.672145 GGCGTTTTAGCTCTCGTCCTT 60.672 52.381 0.00 0.00 37.29 3.36
78 79 2.416431 GGCGTTTTAGCTCTCGTCCTTA 60.416 50.000 0.00 0.00 37.29 2.69
176 181 2.764010 ACAAGGATGTGAGGCGTATGTA 59.236 45.455 0.00 0.00 38.69 2.29
194 200 9.929722 GCGTATGTATGTAAAATTTCAAGATGA 57.070 29.630 0.00 0.00 0.00 2.92
210 216 6.664515 TCAAGATGAAACACGTTGAAATACC 58.335 36.000 0.00 0.00 0.00 2.73
213 219 5.763204 AGATGAAACACGTTGAAATACCACT 59.237 36.000 0.00 0.00 0.00 4.00
217 223 6.315642 TGAAACACGTTGAAATACCACTTGTA 59.684 34.615 0.00 0.00 0.00 2.41
218 224 6.870971 AACACGTTGAAATACCACTTGTAT 57.129 33.333 0.00 0.00 42.06 2.29
253 259 6.370186 TTCATGATCTGGGAGGATGAATAG 57.630 41.667 0.00 0.00 30.05 1.73
259 265 7.194761 TGATCTGGGAGGATGAATAGTATCAT 58.805 38.462 0.00 0.00 42.62 2.45
260 266 6.864151 TCTGGGAGGATGAATAGTATCATG 57.136 41.667 0.00 0.00 40.08 3.07
261 267 6.326161 TCTGGGAGGATGAATAGTATCATGT 58.674 40.000 0.00 0.00 40.08 3.21
262 268 6.212187 TCTGGGAGGATGAATAGTATCATGTG 59.788 42.308 0.00 0.00 40.08 3.21
263 269 5.846164 TGGGAGGATGAATAGTATCATGTGT 59.154 40.000 0.00 0.00 40.08 3.72
264 270 6.329986 TGGGAGGATGAATAGTATCATGTGTT 59.670 38.462 0.00 0.00 40.08 3.32
265 271 7.512402 TGGGAGGATGAATAGTATCATGTGTTA 59.488 37.037 0.00 0.00 40.08 2.41
266 272 8.375506 GGGAGGATGAATAGTATCATGTGTTAA 58.624 37.037 0.00 0.00 40.08 2.01
267 273 9.778741 GGAGGATGAATAGTATCATGTGTTAAA 57.221 33.333 0.00 0.00 40.08 1.52
278 284 9.950496 AGTATCATGTGTTAAAAGACTCAAGAT 57.050 29.630 0.00 0.00 36.26 2.40
281 287 9.903682 ATCATGTGTTAAAAGACTCAAGATTTG 57.096 29.630 0.00 0.00 31.41 2.32
282 288 8.902806 TCATGTGTTAAAAGACTCAAGATTTGT 58.097 29.630 0.00 0.00 0.00 2.83
283 289 9.173939 CATGTGTTAAAAGACTCAAGATTTGTC 57.826 33.333 0.00 0.00 0.00 3.18
284 290 8.506168 TGTGTTAAAAGACTCAAGATTTGTCT 57.494 30.769 0.00 0.00 42.12 3.41
290 296 6.455360 AAGACTCAAGATTTGTCTTTTGCA 57.545 33.333 0.00 0.00 45.32 4.08
291 297 5.825507 AGACTCAAGATTTGTCTTTTGCAC 58.174 37.500 0.00 0.00 37.76 4.57
292 298 5.357878 AGACTCAAGATTTGTCTTTTGCACA 59.642 36.000 0.00 0.00 37.76 4.57
293 299 5.964758 ACTCAAGATTTGTCTTTTGCACAA 58.035 33.333 0.00 0.00 31.76 3.33
294 300 6.576185 ACTCAAGATTTGTCTTTTGCACAAT 58.424 32.000 0.00 0.00 33.76 2.71
295 301 6.698766 ACTCAAGATTTGTCTTTTGCACAATC 59.301 34.615 0.00 0.00 33.76 2.67
296 302 5.984926 TCAAGATTTGTCTTTTGCACAATCC 59.015 36.000 0.00 0.00 33.76 3.01
297 303 5.796424 AGATTTGTCTTTTGCACAATCCT 57.204 34.783 0.00 0.00 33.76 3.24
298 304 5.776744 AGATTTGTCTTTTGCACAATCCTC 58.223 37.500 0.00 0.00 33.76 3.71
299 305 4.998671 TTTGTCTTTTGCACAATCCTCA 57.001 36.364 0.00 0.00 33.76 3.86
300 306 5.534207 TTTGTCTTTTGCACAATCCTCAT 57.466 34.783 0.00 0.00 33.76 2.90
301 307 5.534207 TTGTCTTTTGCACAATCCTCATT 57.466 34.783 0.00 0.00 0.00 2.57
302 308 5.534207 TGTCTTTTGCACAATCCTCATTT 57.466 34.783 0.00 0.00 0.00 2.32
303 309 5.531634 TGTCTTTTGCACAATCCTCATTTC 58.468 37.500 0.00 0.00 0.00 2.17
304 310 4.618489 GTCTTTTGCACAATCCTCATTTCG 59.382 41.667 0.00 0.00 0.00 3.46
305 311 4.518590 TCTTTTGCACAATCCTCATTTCGA 59.481 37.500 0.00 0.00 0.00 3.71
306 312 3.829886 TTGCACAATCCTCATTTCGAC 57.170 42.857 0.00 0.00 0.00 4.20
307 313 2.777094 TGCACAATCCTCATTTCGACA 58.223 42.857 0.00 0.00 0.00 4.35
308 314 3.346315 TGCACAATCCTCATTTCGACAT 58.654 40.909 0.00 0.00 0.00 3.06
309 315 4.512484 TGCACAATCCTCATTTCGACATA 58.488 39.130 0.00 0.00 0.00 2.29
310 316 5.125356 TGCACAATCCTCATTTCGACATAT 58.875 37.500 0.00 0.00 0.00 1.78
311 317 5.589855 TGCACAATCCTCATTTCGACATATT 59.410 36.000 0.00 0.00 0.00 1.28
312 318 6.095300 TGCACAATCCTCATTTCGACATATTT 59.905 34.615 0.00 0.00 0.00 1.40
313 319 6.634436 GCACAATCCTCATTTCGACATATTTC 59.366 38.462 0.00 0.00 0.00 2.17
314 320 7.679400 GCACAATCCTCATTTCGACATATTTCA 60.679 37.037 0.00 0.00 0.00 2.69
315 321 8.347771 CACAATCCTCATTTCGACATATTTCAT 58.652 33.333 0.00 0.00 0.00 2.57
316 322 8.562892 ACAATCCTCATTTCGACATATTTCATC 58.437 33.333 0.00 0.00 0.00 2.92
317 323 8.781196 CAATCCTCATTTCGACATATTTCATCT 58.219 33.333 0.00 0.00 0.00 2.90
318 324 8.915057 ATCCTCATTTCGACATATTTCATCTT 57.085 30.769 0.00 0.00 0.00 2.40
320 326 9.830975 TCCTCATTTCGACATATTTCATCTTAA 57.169 29.630 0.00 0.00 0.00 1.85
341 347 2.869233 AAAATTCACGCTTGTGCACT 57.131 40.000 19.41 0.00 43.51 4.40
342 348 3.980646 AAAATTCACGCTTGTGCACTA 57.019 38.095 19.41 9.94 43.51 2.74
343 349 4.503741 AAAATTCACGCTTGTGCACTAT 57.496 36.364 19.41 0.00 43.51 2.12
344 350 4.503741 AAATTCACGCTTGTGCACTATT 57.496 36.364 19.41 0.00 43.51 1.73
345 351 4.503741 AATTCACGCTTGTGCACTATTT 57.496 36.364 19.41 0.00 43.51 1.40
346 352 5.621197 AATTCACGCTTGTGCACTATTTA 57.379 34.783 19.41 0.00 43.51 1.40
347 353 5.621197 ATTCACGCTTGTGCACTATTTAA 57.379 34.783 19.41 2.12 43.51 1.52
348 354 5.425577 TTCACGCTTGTGCACTATTTAAA 57.574 34.783 19.41 1.33 43.51 1.52
349 355 5.425577 TCACGCTTGTGCACTATTTAAAA 57.574 34.783 19.41 0.54 43.51 1.52
350 356 5.822278 TCACGCTTGTGCACTATTTAAAAA 58.178 33.333 19.41 0.00 43.51 1.94
386 392 4.533919 TTTTTCACAAATCCATGCCGAT 57.466 36.364 0.00 0.00 0.00 4.18
387 393 4.533919 TTTTCACAAATCCATGCCGATT 57.466 36.364 0.00 0.00 33.84 3.34
388 394 4.533919 TTTCACAAATCCATGCCGATTT 57.466 36.364 4.61 4.61 41.98 2.17
389 395 4.533919 TTCACAAATCCATGCCGATTTT 57.466 36.364 7.08 0.00 39.82 1.82
390 396 4.533919 TCACAAATCCATGCCGATTTTT 57.466 36.364 7.08 0.33 39.82 1.94
462 468 7.810766 AATTGTACAAATAAACAAGGATGCG 57.189 32.000 13.23 0.00 38.87 4.73
463 469 6.561737 TTGTACAAATAAACAAGGATGCGA 57.438 33.333 5.64 0.00 32.11 5.10
464 470 6.176975 TGTACAAATAAACAAGGATGCGAG 57.823 37.500 0.00 0.00 0.00 5.03
465 471 4.701956 ACAAATAAACAAGGATGCGAGG 57.298 40.909 0.00 0.00 0.00 4.63
466 472 3.119495 ACAAATAAACAAGGATGCGAGGC 60.119 43.478 0.00 0.00 0.00 4.70
467 473 1.299541 ATAAACAAGGATGCGAGGCG 58.700 50.000 0.00 0.00 0.00 5.52
468 474 0.036765 TAAACAAGGATGCGAGGCGT 60.037 50.000 0.00 0.00 0.00 5.68
469 475 0.036765 AAACAAGGATGCGAGGCGTA 60.037 50.000 0.00 0.00 0.00 4.42
470 476 0.178068 AACAAGGATGCGAGGCGTAT 59.822 50.000 0.00 0.00 34.49 3.06
471 477 0.530650 ACAAGGATGCGAGGCGTATG 60.531 55.000 0.00 0.00 31.55 2.39
472 478 0.530650 CAAGGATGCGAGGCGTATGT 60.531 55.000 0.00 0.00 31.55 2.29
473 479 0.178068 AAGGATGCGAGGCGTATGTT 59.822 50.000 0.00 0.00 31.55 2.71
474 480 0.178068 AGGATGCGAGGCGTATGTTT 59.822 50.000 0.00 0.00 31.55 2.83
475 481 0.304705 GGATGCGAGGCGTATGTTTG 59.695 55.000 0.00 0.00 31.55 2.93
476 482 1.006832 GATGCGAGGCGTATGTTTGT 58.993 50.000 0.00 0.00 31.55 2.83
477 483 2.198406 GATGCGAGGCGTATGTTTGTA 58.802 47.619 0.00 0.00 31.55 2.41
478 484 2.081725 TGCGAGGCGTATGTTTGTAA 57.918 45.000 0.00 0.00 0.00 2.41
479 485 2.414806 TGCGAGGCGTATGTTTGTAAA 58.585 42.857 0.00 0.00 0.00 2.01
480 486 2.806818 TGCGAGGCGTATGTTTGTAAAA 59.193 40.909 0.00 0.00 0.00 1.52
481 487 3.437395 TGCGAGGCGTATGTTTGTAAAAT 59.563 39.130 0.00 0.00 0.00 1.82
482 488 4.083217 TGCGAGGCGTATGTTTGTAAAATT 60.083 37.500 0.00 0.00 0.00 1.82
483 489 4.854839 GCGAGGCGTATGTTTGTAAAATTT 59.145 37.500 0.00 0.00 0.00 1.82
484 490 5.003121 GCGAGGCGTATGTTTGTAAAATTTC 59.997 40.000 0.00 0.00 0.00 2.17
485 491 6.081049 CGAGGCGTATGTTTGTAAAATTTCA 58.919 36.000 0.00 0.00 0.00 2.69
486 492 6.248420 CGAGGCGTATGTTTGTAAAATTTCAG 59.752 38.462 0.00 0.00 0.00 3.02
487 493 7.209471 AGGCGTATGTTTGTAAAATTTCAGA 57.791 32.000 0.00 0.00 0.00 3.27
488 494 7.826690 AGGCGTATGTTTGTAAAATTTCAGAT 58.173 30.769 0.00 0.00 0.00 2.90
489 495 7.754924 AGGCGTATGTTTGTAAAATTTCAGATG 59.245 33.333 0.00 0.00 0.00 2.90
490 496 7.753132 GGCGTATGTTTGTAAAATTTCAGATGA 59.247 33.333 0.00 0.00 0.00 2.92
491 497 9.123709 GCGTATGTTTGTAAAATTTCAGATGAA 57.876 29.630 0.00 0.00 0.00 2.57
504 510 5.469373 TTCAGATGAAATGCGACATGTAC 57.531 39.130 0.00 0.00 0.00 2.90
505 511 4.502962 TCAGATGAAATGCGACATGTACA 58.497 39.130 0.00 0.00 0.00 2.90
506 512 4.934602 TCAGATGAAATGCGACATGTACAA 59.065 37.500 0.00 0.00 0.00 2.41
507 513 5.411053 TCAGATGAAATGCGACATGTACAAA 59.589 36.000 0.00 0.00 0.00 2.83
508 514 6.072783 TCAGATGAAATGCGACATGTACAAAA 60.073 34.615 0.00 0.00 0.00 2.44
509 515 6.581919 CAGATGAAATGCGACATGTACAAAAA 59.418 34.615 0.00 0.00 0.00 1.94
531 537 7.698836 AAAAGACAAATTCATGGTTTCGAAG 57.301 32.000 0.00 0.00 0.00 3.79
532 538 5.376854 AGACAAATTCATGGTTTCGAAGG 57.623 39.130 0.00 0.00 0.00 3.46
533 539 5.070001 AGACAAATTCATGGTTTCGAAGGA 58.930 37.500 0.00 0.00 0.00 3.36
534 540 5.711976 AGACAAATTCATGGTTTCGAAGGAT 59.288 36.000 0.00 0.00 0.00 3.24
535 541 5.713025 ACAAATTCATGGTTTCGAAGGATG 58.287 37.500 0.00 2.59 0.00 3.51
536 542 5.476599 ACAAATTCATGGTTTCGAAGGATGA 59.523 36.000 10.23 10.23 0.00 2.92
537 543 6.015519 ACAAATTCATGGTTTCGAAGGATGAA 60.016 34.615 21.20 21.20 37.42 2.57
538 544 6.780457 AATTCATGGTTTCGAAGGATGAAT 57.220 33.333 22.80 22.80 42.72 2.57
539 545 7.880160 AATTCATGGTTTCGAAGGATGAATA 57.120 32.000 25.73 12.25 40.97 1.75
540 546 6.925610 TTCATGGTTTCGAAGGATGAATAG 57.074 37.500 17.71 0.00 30.05 1.73
541 547 5.989477 TCATGGTTTCGAAGGATGAATAGT 58.011 37.500 11.35 0.00 0.00 2.12
542 548 7.119709 TCATGGTTTCGAAGGATGAATAGTA 57.880 36.000 11.35 0.00 0.00 1.82
543 549 7.735917 TCATGGTTTCGAAGGATGAATAGTAT 58.264 34.615 11.35 0.00 0.00 2.12
544 550 7.872993 TCATGGTTTCGAAGGATGAATAGTATC 59.127 37.037 11.35 0.00 0.00 2.24
545 551 7.119709 TGGTTTCGAAGGATGAATAGTATCA 57.880 36.000 0.00 0.00 0.00 2.15
546 552 7.735917 TGGTTTCGAAGGATGAATAGTATCAT 58.264 34.615 0.00 0.00 42.62 2.45
574 580 9.598517 TGTTAAAAAGCATCAGATTTGTCTTTT 57.401 25.926 0.00 0.00 32.90 2.27
602 608 4.153475 CACAACCCTCATTTCGACGTATTT 59.847 41.667 0.00 0.00 0.00 1.40
604 610 3.184541 ACCCTCATTTCGACGTATTTCG 58.815 45.455 0.00 0.00 46.00 3.46
729 735 0.462789 GCATTTGGAGGCCTTCATGG 59.537 55.000 16.58 8.68 39.35 3.66
844 851 5.430886 TCTAGCCTACGAACTACACATACA 58.569 41.667 0.00 0.00 0.00 2.29
854 861 5.539048 GAACTACACATACAACCTCACACT 58.461 41.667 0.00 0.00 0.00 3.55
973 988 2.011548 GCTCACGCCACCATCATAACA 61.012 52.381 0.00 0.00 0.00 2.41
1051 1066 1.683365 CCCCCTGCATTTCCACCAG 60.683 63.158 0.00 0.00 0.00 4.00
1586 1601 2.703798 CCGGGACATGTACGACCGT 61.704 63.158 20.26 0.00 42.81 4.83
1992 2029 2.430244 AAGTTCGTCATCGCGCGT 60.430 55.556 30.98 14.63 36.96 6.01
2027 2064 2.882324 GGAGACGCTCTTCAAGTAAGG 58.118 52.381 6.78 0.00 35.75 2.69
2028 2065 2.492484 GGAGACGCTCTTCAAGTAAGGA 59.508 50.000 6.78 0.00 35.75 3.36
2047 2088 0.108186 ACGCAGCTCCAATCGATGAA 60.108 50.000 0.00 0.00 0.00 2.57
2050 2091 2.799562 CGCAGCTCCAATCGATGAACTA 60.800 50.000 0.00 0.00 0.00 2.24
2070 2111 5.817988 ACTAAAGTTTTGCTTTTCCTCGTC 58.182 37.500 0.00 0.00 44.41 4.20
2117 2158 2.888998 GCGGTTGCTCGTTTCCGTT 61.889 57.895 0.00 0.00 44.07 4.44
2261 2302 1.982660 TCCTAGAGATCGACGGCATT 58.017 50.000 0.00 0.00 0.00 3.56
2305 2346 4.431131 CAACGCCATGCCCCCTCT 62.431 66.667 0.00 0.00 0.00 3.69
2346 2387 2.606272 CAGGAGTAATTTTACGTCGCCC 59.394 50.000 0.00 0.00 38.65 6.13
2372 2418 5.595542 ACGCATACTACTAGGGTACAAATCA 59.404 40.000 0.00 0.00 0.00 2.57
2386 2432 8.903820 AGGGTACAAATCAGCTGAAATAATAAC 58.096 33.333 22.50 12.00 0.00 1.89
2453 2504 0.978146 CCTGTCTCCATCCGGGTTCT 60.978 60.000 0.00 0.00 38.11 3.01
2623 2681 2.542020 TTTCACCTCAACTGCGATCA 57.458 45.000 0.00 0.00 0.00 2.92
2643 2701 1.190833 AGAGGAGGATAGGCCATGCG 61.191 60.000 5.01 0.00 40.02 4.73
2657 2718 0.108520 CATGCGTACCTACCACGGTT 60.109 55.000 0.00 0.00 39.75 4.44
2927 2988 1.415672 TTCCTTGGGTTCAGACGGCT 61.416 55.000 0.00 0.00 0.00 5.52
2958 3019 2.335712 CGCCTGGAAAAGCTGGGTC 61.336 63.158 0.00 0.00 0.00 4.46
3184 3257 2.589720 TGTCCTTGTTCTCCTCGTACA 58.410 47.619 0.00 0.00 0.00 2.90
3233 3306 7.318141 TGTGAGAGTTTTACGGGATAAAGTAG 58.682 38.462 0.00 0.00 34.22 2.57
3332 3405 3.231889 CTGTCACCACTCGGCAGCT 62.232 63.158 0.00 0.00 34.57 4.24
3335 3408 4.363990 CACCACTCGGCAGCTCGT 62.364 66.667 0.00 0.00 34.57 4.18
3336 3409 4.057428 ACCACTCGGCAGCTCGTC 62.057 66.667 0.00 0.00 34.57 4.20
3380 3460 1.333619 TGGTGAAAGCGAAAAGAGTGC 59.666 47.619 0.00 0.00 36.92 4.40
3381 3461 1.660333 GGTGAAAGCGAAAAGAGTGCG 60.660 52.381 0.00 0.00 0.00 5.34
3386 3466 2.094724 CGAAAAGAGTGCGCGCTC 59.905 61.111 37.36 37.36 35.82 5.03
3387 3467 2.094724 GAAAAGAGTGCGCGCTCG 59.905 61.111 37.16 0.00 40.26 5.03
3388 3468 3.354499 GAAAAGAGTGCGCGCTCGG 62.354 63.158 37.16 0.00 40.26 4.63
3389 3469 4.664677 AAAGAGTGCGCGCTCGGT 62.665 61.111 37.16 28.57 40.26 4.69
3395 3475 4.306471 TGCGCGCTCGGTGTTTTG 62.306 61.111 33.29 0.00 35.95 2.44
3398 3478 2.127232 GCGCTCGGTGTTTTGCTC 60.127 61.111 0.00 0.00 0.00 4.26
3399 3479 2.892334 GCGCTCGGTGTTTTGCTCA 61.892 57.895 0.00 0.00 0.00 4.26
3400 3480 1.646540 CGCTCGGTGTTTTGCTCAA 59.353 52.632 0.00 0.00 0.00 3.02
3401 3481 0.384725 CGCTCGGTGTTTTGCTCAAG 60.385 55.000 0.00 0.00 0.00 3.02
3402 3482 0.663153 GCTCGGTGTTTTGCTCAAGT 59.337 50.000 0.00 0.00 0.00 3.16
3403 3483 1.871039 GCTCGGTGTTTTGCTCAAGTA 59.129 47.619 0.00 0.00 0.00 2.24
3404 3484 2.349532 GCTCGGTGTTTTGCTCAAGTAC 60.350 50.000 0.00 0.00 0.00 2.73
3405 3485 2.869801 CTCGGTGTTTTGCTCAAGTACA 59.130 45.455 0.00 0.00 0.00 2.90
3406 3486 2.869801 TCGGTGTTTTGCTCAAGTACAG 59.130 45.455 0.00 0.00 0.00 2.74
3407 3487 2.612212 CGGTGTTTTGCTCAAGTACAGT 59.388 45.455 0.00 0.00 0.00 3.55
3408 3488 3.805422 CGGTGTTTTGCTCAAGTACAGTA 59.195 43.478 0.00 0.00 0.00 2.74
3409 3489 4.084537 CGGTGTTTTGCTCAAGTACAGTAG 60.085 45.833 0.00 0.00 0.00 2.57
3410 3490 4.814771 GGTGTTTTGCTCAAGTACAGTAGT 59.185 41.667 0.00 0.00 0.00 2.73
3411 3491 5.987347 GGTGTTTTGCTCAAGTACAGTAGTA 59.013 40.000 0.00 0.00 0.00 1.82
3547 3641 2.171701 GGCGTAAAACGTCGTGGC 59.828 61.111 0.00 0.00 44.73 5.01
3624 3720 6.978080 TGGTCAATTCTTTTCTTTCTTTTCCG 59.022 34.615 0.00 0.00 0.00 4.30
3666 3762 5.998981 TCTTTAACCGCTGTAAAGAAATGGA 59.001 36.000 9.59 0.00 37.02 3.41
3679 3775 6.484364 AAAGAAATGGACACTGTTTTGGAT 57.516 33.333 0.00 0.00 0.00 3.41
4133 4316 1.304134 TCACCCTGCTGCTCGACTA 60.304 57.895 0.00 0.00 0.00 2.59
4274 4470 7.320399 TGTAGAATATATTGTATGAGCCGTGG 58.680 38.462 1.78 0.00 0.00 4.94
4367 4567 6.597672 TCTGTTCGTATTTACAGATTGCCAAT 59.402 34.615 0.00 0.00 44.20 3.16
4423 4626 7.020827 TCTGAGTAGGATTTCAAGTTGGATT 57.979 36.000 2.34 0.00 0.00 3.01
4424 4627 7.461749 TCTGAGTAGGATTTCAAGTTGGATTT 58.538 34.615 2.34 0.00 0.00 2.17
4425 4628 7.944554 TCTGAGTAGGATTTCAAGTTGGATTTT 59.055 33.333 2.34 0.00 0.00 1.82
4453 4657 0.698818 CCACCTTCTAGGCCCTGTTT 59.301 55.000 0.00 0.00 39.63 2.83
4477 4681 4.326766 CACGCGGGCAAACCACAG 62.327 66.667 12.47 0.00 40.22 3.66
4490 4694 5.106515 GGCAAACCACAGAAATTCTAGAGAC 60.107 44.000 0.00 0.00 35.26 3.36
4494 4698 6.672266 ACCACAGAAATTCTAGAGACAGAA 57.328 37.500 0.00 0.00 38.84 3.02
4525 4729 2.576648 GGAGGTAGGACCACAATTCCTT 59.423 50.000 0.00 0.00 40.95 3.36
4533 4737 3.386402 GGACCACAATTCCTTTGTTCCAA 59.614 43.478 4.93 0.00 46.51 3.53
4543 4747 1.415659 CTTTGTTCCAAATGGCACCCA 59.584 47.619 0.00 0.00 38.19 4.51
4561 4765 4.396166 CACCCAAAATATCAGACACTCCAC 59.604 45.833 0.00 0.00 0.00 4.02
4591 4802 5.650266 TCATATGTTGCCCGTACTTTGATTT 59.350 36.000 1.90 0.00 0.00 2.17
4592 4803 3.634568 TGTTGCCCGTACTTTGATTTG 57.365 42.857 0.00 0.00 0.00 2.32
4593 4804 2.287909 TGTTGCCCGTACTTTGATTTGC 60.288 45.455 0.00 0.00 0.00 3.68
4629 4870 1.456196 TTAGGCCTCCTCGATCGCAG 61.456 60.000 9.68 8.81 34.61 5.18
4636 4877 1.521681 CCTCGATCGCAGGGTTTCC 60.522 63.158 19.76 0.00 0.00 3.13
4645 4886 0.319813 GCAGGGTTTCCACAATGCAC 60.320 55.000 0.00 0.00 36.42 4.57
4711 4959 6.198403 GTGGTCTTTTTCCGCTTTCTTTTTAG 59.802 38.462 0.00 0.00 33.26 1.85
4728 4976 2.691409 TAGGATTTCTCTTGGGCGTG 57.309 50.000 0.00 0.00 0.00 5.34
4741 4990 1.654220 GGCGTGTTGTGATGTTGCT 59.346 52.632 0.00 0.00 0.00 3.91
4810 5059 1.102978 GGTGCAACACTTGACTTGGT 58.897 50.000 0.00 0.00 39.98 3.67
4822 5071 4.576053 ACTTGACTTGGTTACCCGTAAAAC 59.424 41.667 0.00 0.00 0.00 2.43
4825 5074 4.946157 TGACTTGGTTACCCGTAAAACAAA 59.054 37.500 0.00 0.00 0.00 2.83
4830 5079 5.192176 TGGTTACCCGTAAAACAAAAGACT 58.808 37.500 0.00 0.00 0.00 3.24
4831 5080 5.651576 TGGTTACCCGTAAAACAAAAGACTT 59.348 36.000 0.00 0.00 0.00 3.01
4839 5088 6.034150 CCGTAAAACAAAAGACTTGGTTGTTC 59.966 38.462 15.14 5.87 42.96 3.18
4906 5155 8.353423 AGCTTGTTTCAGGACATAAATACATT 57.647 30.769 0.00 0.00 0.00 2.71
4950 5203 6.968131 TGAATTCTATAGGATTATGTGCGC 57.032 37.500 6.23 0.00 0.00 6.09
4954 5207 3.692593 TCTATAGGATTATGTGCGCGCTA 59.307 43.478 33.29 21.51 0.00 4.26
4966 5219 3.037324 GTGCGCGCTAAAGTTTGTTTTA 58.963 40.909 33.29 2.73 0.00 1.52
5024 5277 9.351570 GAGATTTGAGTGAATGGAATTTTCTTC 57.648 33.333 0.00 0.00 36.07 2.87
5055 5308 9.709495 ACATAATGCAAAAGAATGCTAAGAAAA 57.291 25.926 0.00 0.00 46.54 2.29
5098 5353 7.383029 TCCTACAAGTCAAACAACTTACATACG 59.617 37.037 0.00 0.00 37.38 3.06
5106 5361 9.698617 GTCAAACAACTTACATACGATTATTCC 57.301 33.333 0.00 0.00 0.00 3.01
5167 5450 7.797121 AATCCTTTGACTTGGTAAATTCCAT 57.203 32.000 0.00 0.00 37.33 3.41
5177 5460 9.921637 GACTTGGTAAATTCCATTGATTTTACA 57.078 29.630 18.48 8.32 43.04 2.41
5178 5461 9.927668 ACTTGGTAAATTCCATTGATTTTACAG 57.072 29.630 18.48 13.34 43.04 2.74
5189 5472 7.996066 TCCATTGATTTTACAGATTCGGGATAA 59.004 33.333 0.00 0.00 0.00 1.75
5197 5480 4.708177 ACAGATTCGGGATAACCAAGATG 58.292 43.478 0.00 0.00 40.22 2.90
5224 5507 4.897509 AGGAGTGTCATGTCATCTTGAA 57.102 40.909 0.00 0.00 31.27 2.69
5253 5536 9.265901 CTAGTATATGGTTGTTGATTCCAAGAG 57.734 37.037 0.00 0.00 34.80 2.85
5270 5553 5.104277 TCCAAGAGGTTAGAGTGGTTGAAAA 60.104 40.000 0.00 0.00 35.89 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.059913 ACTGCAGCTCCCTAAACTGT 58.940 50.000 15.27 0.00 33.87 3.55
17 18 9.950496 ATCCCATTAATTATAGAGTTACTGCAG 57.050 33.333 13.48 13.48 0.00 4.41
36 37 4.580580 GCCATTCTCGAGTTTTATCCCATT 59.419 41.667 13.13 0.00 0.00 3.16
148 153 2.227388 GCCTCACATCCTTGTTCACTTG 59.773 50.000 0.00 0.00 32.34 3.16
176 181 9.528018 AACGTGTTTCATCTTGAAATTTTACAT 57.472 25.926 6.01 0.00 46.55 2.29
194 200 5.570234 ACAAGTGGTATTTCAACGTGTTT 57.430 34.783 0.00 0.00 0.00 2.83
197 203 9.666626 TTTTTATACAAGTGGTATTTCAACGTG 57.333 29.630 0.00 0.00 42.63 4.49
226 232 5.382616 TCATCCTCCCAGATCATGAAATTG 58.617 41.667 0.00 0.00 0.00 2.32
229 235 5.658198 ATTCATCCTCCCAGATCATGAAA 57.342 39.130 0.00 0.00 37.11 2.69
238 244 6.013898 ACACATGATACTATTCATCCTCCCAG 60.014 42.308 0.00 0.00 34.09 4.45
259 265 8.506168 AGACAAATCTTGAGTCTTTTAACACA 57.494 30.769 0.00 0.00 39.45 3.72
268 274 5.357878 TGTGCAAAAGACAAATCTTGAGTCT 59.642 36.000 0.00 0.00 44.82 3.24
269 275 5.581605 TGTGCAAAAGACAAATCTTGAGTC 58.418 37.500 0.00 0.00 44.82 3.36
270 276 5.581126 TGTGCAAAAGACAAATCTTGAGT 57.419 34.783 0.00 0.00 44.82 3.41
271 277 6.145048 GGATTGTGCAAAAGACAAATCTTGAG 59.855 38.462 0.00 0.00 44.82 3.02
272 278 5.984926 GGATTGTGCAAAAGACAAATCTTGA 59.015 36.000 0.00 0.00 44.82 3.02
273 279 5.987347 AGGATTGTGCAAAAGACAAATCTTG 59.013 36.000 0.00 0.00 44.82 3.02
275 281 5.302568 TGAGGATTGTGCAAAAGACAAATCT 59.697 36.000 0.00 0.00 36.42 2.40
276 282 5.531634 TGAGGATTGTGCAAAAGACAAATC 58.468 37.500 0.00 0.00 0.00 2.17
277 283 5.534207 TGAGGATTGTGCAAAAGACAAAT 57.466 34.783 0.00 0.00 0.00 2.32
278 284 4.998671 TGAGGATTGTGCAAAAGACAAA 57.001 36.364 0.00 0.00 0.00 2.83
279 285 5.534207 AATGAGGATTGTGCAAAAGACAA 57.466 34.783 0.00 0.00 0.00 3.18
280 286 5.531634 GAAATGAGGATTGTGCAAAAGACA 58.468 37.500 0.00 0.00 0.00 3.41
281 287 4.618489 CGAAATGAGGATTGTGCAAAAGAC 59.382 41.667 0.00 0.00 0.00 3.01
282 288 4.518590 TCGAAATGAGGATTGTGCAAAAGA 59.481 37.500 0.00 0.00 0.00 2.52
283 289 4.618489 GTCGAAATGAGGATTGTGCAAAAG 59.382 41.667 0.00 0.00 0.00 2.27
284 290 4.037327 TGTCGAAATGAGGATTGTGCAAAA 59.963 37.500 0.00 0.00 0.00 2.44
285 291 3.567585 TGTCGAAATGAGGATTGTGCAAA 59.432 39.130 0.00 0.00 0.00 3.68
286 292 3.145286 TGTCGAAATGAGGATTGTGCAA 58.855 40.909 0.00 0.00 0.00 4.08
287 293 2.777094 TGTCGAAATGAGGATTGTGCA 58.223 42.857 0.00 0.00 0.00 4.57
288 294 5.679734 ATATGTCGAAATGAGGATTGTGC 57.320 39.130 0.00 0.00 0.00 4.57
289 295 7.696755 TGAAATATGTCGAAATGAGGATTGTG 58.303 34.615 0.00 0.00 0.00 3.33
290 296 7.864108 TGAAATATGTCGAAATGAGGATTGT 57.136 32.000 0.00 0.00 0.00 2.71
291 297 8.781196 AGATGAAATATGTCGAAATGAGGATTG 58.219 33.333 0.00 0.00 0.00 2.67
292 298 8.915057 AGATGAAATATGTCGAAATGAGGATT 57.085 30.769 0.00 0.00 0.00 3.01
293 299 8.915057 AAGATGAAATATGTCGAAATGAGGAT 57.085 30.769 0.00 0.00 0.00 3.24
294 300 9.830975 TTAAGATGAAATATGTCGAAATGAGGA 57.169 29.630 0.00 0.00 0.00 3.71
321 327 3.163630 AGTGCACAAGCGTGAATTTTT 57.836 38.095 21.04 0.00 46.80 1.94
322 328 2.869233 AGTGCACAAGCGTGAATTTT 57.131 40.000 21.04 0.00 46.80 1.82
323 329 4.503741 AATAGTGCACAAGCGTGAATTT 57.496 36.364 21.04 0.00 46.80 1.82
324 330 4.503741 AAATAGTGCACAAGCGTGAATT 57.496 36.364 21.04 2.70 46.80 2.17
325 331 5.621197 TTAAATAGTGCACAAGCGTGAAT 57.379 34.783 21.04 0.00 46.80 2.57
326 332 5.425577 TTTAAATAGTGCACAAGCGTGAA 57.574 34.783 21.04 2.58 46.80 3.18
327 333 5.425577 TTTTAAATAGTGCACAAGCGTGA 57.574 34.783 21.04 0.00 46.80 4.35
365 371 4.533919 ATCGGCATGGATTTGTGAAAAA 57.466 36.364 0.00 0.00 0.00 1.94
366 372 4.533919 AATCGGCATGGATTTGTGAAAA 57.466 36.364 0.00 0.00 32.89 2.29
367 373 4.533919 AAATCGGCATGGATTTGTGAAA 57.466 36.364 8.58 0.00 43.16 2.69
368 374 4.533919 AAAATCGGCATGGATTTGTGAA 57.466 36.364 9.76 0.00 43.81 3.18
369 375 4.533919 AAAAATCGGCATGGATTTGTGA 57.466 36.364 9.76 0.00 43.81 3.58
436 442 8.707839 CGCATCCTTGTTTATTTGTACAATTTT 58.292 29.630 9.56 0.45 0.00 1.82
437 443 8.085296 TCGCATCCTTGTTTATTTGTACAATTT 58.915 29.630 9.56 3.03 0.00 1.82
438 444 7.598278 TCGCATCCTTGTTTATTTGTACAATT 58.402 30.769 9.56 8.67 0.00 2.32
439 445 7.151999 TCGCATCCTTGTTTATTTGTACAAT 57.848 32.000 9.56 2.67 0.00 2.71
440 446 6.348950 CCTCGCATCCTTGTTTATTTGTACAA 60.349 38.462 3.59 3.59 0.00 2.41
441 447 5.123186 CCTCGCATCCTTGTTTATTTGTACA 59.877 40.000 0.00 0.00 0.00 2.90
442 448 5.569413 CCTCGCATCCTTGTTTATTTGTAC 58.431 41.667 0.00 0.00 0.00 2.90
443 449 4.095782 GCCTCGCATCCTTGTTTATTTGTA 59.904 41.667 0.00 0.00 0.00 2.41
444 450 3.119495 GCCTCGCATCCTTGTTTATTTGT 60.119 43.478 0.00 0.00 0.00 2.83
445 451 3.438360 GCCTCGCATCCTTGTTTATTTG 58.562 45.455 0.00 0.00 0.00 2.32
446 452 2.097466 CGCCTCGCATCCTTGTTTATTT 59.903 45.455 0.00 0.00 0.00 1.40
447 453 1.670811 CGCCTCGCATCCTTGTTTATT 59.329 47.619 0.00 0.00 0.00 1.40
448 454 1.299541 CGCCTCGCATCCTTGTTTAT 58.700 50.000 0.00 0.00 0.00 1.40
449 455 0.036765 ACGCCTCGCATCCTTGTTTA 60.037 50.000 0.00 0.00 0.00 2.01
450 456 0.036765 TACGCCTCGCATCCTTGTTT 60.037 50.000 0.00 0.00 0.00 2.83
451 457 0.178068 ATACGCCTCGCATCCTTGTT 59.822 50.000 0.00 0.00 0.00 2.83
452 458 0.530650 CATACGCCTCGCATCCTTGT 60.531 55.000 0.00 0.00 0.00 3.16
453 459 0.530650 ACATACGCCTCGCATCCTTG 60.531 55.000 0.00 0.00 0.00 3.61
454 460 0.178068 AACATACGCCTCGCATCCTT 59.822 50.000 0.00 0.00 0.00 3.36
455 461 0.178068 AAACATACGCCTCGCATCCT 59.822 50.000 0.00 0.00 0.00 3.24
456 462 0.304705 CAAACATACGCCTCGCATCC 59.695 55.000 0.00 0.00 0.00 3.51
457 463 1.006832 ACAAACATACGCCTCGCATC 58.993 50.000 0.00 0.00 0.00 3.91
458 464 2.303163 TACAAACATACGCCTCGCAT 57.697 45.000 0.00 0.00 0.00 4.73
459 465 2.081725 TTACAAACATACGCCTCGCA 57.918 45.000 0.00 0.00 0.00 5.10
460 466 3.458779 TTTTACAAACATACGCCTCGC 57.541 42.857 0.00 0.00 0.00 5.03
461 467 6.081049 TGAAATTTTACAAACATACGCCTCG 58.919 36.000 0.00 0.00 0.00 4.63
462 468 7.302524 TCTGAAATTTTACAAACATACGCCTC 58.697 34.615 0.00 0.00 0.00 4.70
463 469 7.209471 TCTGAAATTTTACAAACATACGCCT 57.791 32.000 0.00 0.00 0.00 5.52
464 470 7.753132 TCATCTGAAATTTTACAAACATACGCC 59.247 33.333 0.00 0.00 0.00 5.68
465 471 8.667987 TCATCTGAAATTTTACAAACATACGC 57.332 30.769 0.00 0.00 0.00 4.42
481 487 5.411053 TGTACATGTCGCATTTCATCTGAAA 59.589 36.000 0.00 7.74 46.60 2.69
482 488 4.934602 TGTACATGTCGCATTTCATCTGAA 59.065 37.500 0.00 0.00 0.00 3.02
483 489 4.502962 TGTACATGTCGCATTTCATCTGA 58.497 39.130 0.00 0.00 0.00 3.27
484 490 4.863152 TGTACATGTCGCATTTCATCTG 57.137 40.909 0.00 0.00 0.00 2.90
485 491 5.878332 TTTGTACATGTCGCATTTCATCT 57.122 34.783 0.00 0.00 0.00 2.90
486 492 6.926280 TTTTTGTACATGTCGCATTTCATC 57.074 33.333 0.00 0.00 0.00 2.92
506 512 7.224557 CCTTCGAAACCATGAATTTGTCTTTTT 59.775 33.333 0.00 0.00 0.00 1.94
507 513 6.701400 CCTTCGAAACCATGAATTTGTCTTTT 59.299 34.615 0.00 0.00 0.00 2.27
508 514 6.040391 TCCTTCGAAACCATGAATTTGTCTTT 59.960 34.615 0.00 0.00 0.00 2.52
509 515 5.534654 TCCTTCGAAACCATGAATTTGTCTT 59.465 36.000 0.00 0.00 0.00 3.01
510 516 5.070001 TCCTTCGAAACCATGAATTTGTCT 58.930 37.500 0.00 0.00 0.00 3.41
511 517 5.371115 TCCTTCGAAACCATGAATTTGTC 57.629 39.130 0.00 0.00 0.00 3.18
512 518 5.476599 TCATCCTTCGAAACCATGAATTTGT 59.523 36.000 0.00 0.00 0.00 2.83
513 519 5.953183 TCATCCTTCGAAACCATGAATTTG 58.047 37.500 0.00 0.00 0.00 2.32
514 520 6.588719 TTCATCCTTCGAAACCATGAATTT 57.411 33.333 16.48 0.00 30.30 1.82
515 521 6.780457 ATTCATCCTTCGAAACCATGAATT 57.220 33.333 21.85 12.85 39.92 2.17
516 522 7.056635 ACTATTCATCCTTCGAAACCATGAAT 58.943 34.615 26.30 26.30 43.42 2.57
517 523 6.414732 ACTATTCATCCTTCGAAACCATGAA 58.585 36.000 20.14 20.14 37.75 2.57
518 524 5.989477 ACTATTCATCCTTCGAAACCATGA 58.011 37.500 0.00 4.39 0.00 3.07
519 525 7.657354 TGATACTATTCATCCTTCGAAACCATG 59.343 37.037 0.00 1.95 0.00 3.66
520 526 7.735917 TGATACTATTCATCCTTCGAAACCAT 58.264 34.615 0.00 0.00 0.00 3.55
521 527 7.119709 TGATACTATTCATCCTTCGAAACCA 57.880 36.000 0.00 0.00 0.00 3.67
522 528 7.657761 ACATGATACTATTCATCCTTCGAAACC 59.342 37.037 0.00 0.00 34.09 3.27
523 529 8.491152 CACATGATACTATTCATCCTTCGAAAC 58.509 37.037 0.00 0.00 34.09 2.78
524 530 8.204160 ACACATGATACTATTCATCCTTCGAAA 58.796 33.333 0.00 0.00 34.09 3.46
525 531 7.726216 ACACATGATACTATTCATCCTTCGAA 58.274 34.615 0.00 0.00 34.09 3.71
526 532 7.290110 ACACATGATACTATTCATCCTTCGA 57.710 36.000 0.00 0.00 34.09 3.71
527 533 7.953158 AACACATGATACTATTCATCCTTCG 57.047 36.000 0.00 0.00 34.09 3.79
538 544 9.665719 TCTGATGCTTTTTAACACATGATACTA 57.334 29.630 0.00 0.00 0.00 1.82
539 545 8.565896 TCTGATGCTTTTTAACACATGATACT 57.434 30.769 0.00 0.00 0.00 2.12
540 546 9.793252 AATCTGATGCTTTTTAACACATGATAC 57.207 29.630 0.00 0.00 0.00 2.24
542 548 9.146984 CAAATCTGATGCTTTTTAACACATGAT 57.853 29.630 0.00 0.00 0.00 2.45
543 549 8.143193 ACAAATCTGATGCTTTTTAACACATGA 58.857 29.630 0.00 0.00 0.00 3.07
544 550 8.301730 ACAAATCTGATGCTTTTTAACACATG 57.698 30.769 0.00 0.00 0.00 3.21
545 551 8.362639 AGACAAATCTGATGCTTTTTAACACAT 58.637 29.630 0.00 0.00 32.29 3.21
546 552 7.715657 AGACAAATCTGATGCTTTTTAACACA 58.284 30.769 0.00 0.00 32.29 3.72
574 580 2.690497 TCGAAATGAGGGTTGTGCAAAA 59.310 40.909 0.00 0.00 0.00 2.44
575 581 2.034053 GTCGAAATGAGGGTTGTGCAAA 59.966 45.455 0.00 0.00 0.00 3.68
576 582 1.606668 GTCGAAATGAGGGTTGTGCAA 59.393 47.619 0.00 0.00 0.00 4.08
577 583 1.234821 GTCGAAATGAGGGTTGTGCA 58.765 50.000 0.00 0.00 0.00 4.57
602 608 7.411274 CACAAGTGTGTAAATTTTTAGGACGA 58.589 34.615 3.17 0.00 40.96 4.20
718 724 2.739996 CCGAGCTCCATGAAGGCCT 61.740 63.158 8.47 0.00 37.29 5.19
729 735 0.320771 TGCTTTTGGAGACCGAGCTC 60.321 55.000 2.73 2.73 34.56 4.09
815 822 5.742926 GTGTAGTTCGTAGGCTAGATTTGTC 59.257 44.000 0.00 0.00 0.00 3.18
844 851 1.755393 GACCCGGACAGTGTGAGGTT 61.755 60.000 0.73 0.00 0.00 3.50
854 861 1.609580 GCACAAAGTATGACCCGGACA 60.610 52.381 0.73 2.81 0.00 4.02
973 988 3.626924 GTGGAGCGTGGGAGTGGT 61.627 66.667 0.00 0.00 0.00 4.16
2027 2064 0.528466 TCATCGATTGGAGCTGCGTC 60.528 55.000 0.00 0.26 0.00 5.19
2028 2065 0.108186 TTCATCGATTGGAGCTGCGT 60.108 50.000 0.00 0.00 0.00 5.24
2050 2091 7.904489 CGACGACGAGGAAAAGCAAAACTTT 62.904 44.000 0.00 0.00 45.62 2.66
2117 2158 2.668632 GGCCGGATGAACCTGTCA 59.331 61.111 5.05 0.00 41.67 3.58
2172 2213 1.080501 CGTTCTCCAGCTCGCTTGA 60.081 57.895 0.00 0.00 0.00 3.02
2174 2215 2.262915 CCGTTCTCCAGCTCGCTT 59.737 61.111 0.00 0.00 0.00 4.68
2261 2302 3.323774 AGGATAACGGGATGTACCTCA 57.676 47.619 0.41 0.00 38.98 3.86
2346 2387 6.624352 TTTGTACCCTAGTAGTATGCGTAG 57.376 41.667 0.00 0.00 0.00 3.51
2453 2504 3.306917 TTAGGCACAAGACGATTTCGA 57.693 42.857 7.01 0.00 43.02 3.71
2565 2616 0.673644 GAGCTGGAACCAAAGCGCTA 60.674 55.000 12.05 0.00 44.34 4.26
2623 2681 1.063183 GCATGGCCTATCCTCCTCTT 58.937 55.000 3.32 0.00 35.26 2.85
2643 2701 1.260544 ACTCCAACCGTGGTAGGTAC 58.739 55.000 0.00 0.00 45.21 3.34
2657 2718 2.233676 TCGAAAGATGCTTGCTACTCCA 59.766 45.455 0.00 0.00 33.31 3.86
2659 2720 2.280183 CGTCGAAAGATGCTTGCTACTC 59.720 50.000 0.00 0.00 45.19 2.59
2958 3019 0.317938 CCGGCGTTACAGCTAGCTAG 60.318 60.000 18.86 16.84 37.29 3.42
3192 3265 3.190849 CATCAGCACGGCGTCTGG 61.191 66.667 27.04 13.74 0.00 3.86
3303 3376 2.807045 GTGACAGCGCGTGGAGAG 60.807 66.667 8.43 0.00 0.00 3.20
3353 3432 4.072088 CGCTTTCACCACGTCGCC 62.072 66.667 0.00 0.00 0.00 5.54
3354 3433 2.096481 TTTCGCTTTCACCACGTCGC 62.096 55.000 0.00 0.00 0.00 5.19
3355 3434 0.302288 TTTTCGCTTTCACCACGTCG 59.698 50.000 0.00 0.00 0.00 5.12
3356 3435 1.595794 TCTTTTCGCTTTCACCACGTC 59.404 47.619 0.00 0.00 0.00 4.34
3357 3436 1.597663 CTCTTTTCGCTTTCACCACGT 59.402 47.619 0.00 0.00 0.00 4.49
3358 3437 1.597663 ACTCTTTTCGCTTTCACCACG 59.402 47.619 0.00 0.00 0.00 4.94
3380 3460 3.911155 GAGCAAAACACCGAGCGCG 62.911 63.158 0.00 0.00 37.24 6.86
3381 3461 2.127232 GAGCAAAACACCGAGCGC 60.127 61.111 0.00 0.00 0.00 5.92
3382 3462 0.384725 CTTGAGCAAAACACCGAGCG 60.385 55.000 0.00 0.00 0.00 5.03
3383 3463 0.663153 ACTTGAGCAAAACACCGAGC 59.337 50.000 0.00 0.00 0.00 5.03
3384 3464 2.869801 TGTACTTGAGCAAAACACCGAG 59.130 45.455 0.00 0.00 0.00 4.63
3386 3466 2.612212 ACTGTACTTGAGCAAAACACCG 59.388 45.455 0.00 0.00 0.00 4.94
3387 3467 4.814771 ACTACTGTACTTGAGCAAAACACC 59.185 41.667 0.00 0.00 0.00 4.16
3388 3468 5.986004 ACTACTGTACTTGAGCAAAACAC 57.014 39.130 0.00 0.00 0.00 3.32
3401 3481 6.237969 GCGTACTTGGAGTAGTACTACTGTAC 60.238 46.154 34.67 31.68 45.63 2.90
3402 3482 5.812642 GCGTACTTGGAGTAGTACTACTGTA 59.187 44.000 34.67 26.06 45.63 2.74
3403 3483 4.633565 GCGTACTTGGAGTAGTACTACTGT 59.366 45.833 34.67 26.95 45.63 3.55
3404 3484 4.633126 TGCGTACTTGGAGTAGTACTACTG 59.367 45.833 34.67 23.43 45.63 2.74
3406 3486 5.747951 ATGCGTACTTGGAGTAGTACTAC 57.252 43.478 23.03 23.03 45.30 2.73
3407 3487 6.017605 GCTAATGCGTACTTGGAGTAGTACTA 60.018 42.308 1.88 0.00 45.30 1.82
3408 3488 5.221009 GCTAATGCGTACTTGGAGTAGTACT 60.221 44.000 1.37 1.37 45.30 2.73
3409 3489 4.974888 GCTAATGCGTACTTGGAGTAGTAC 59.025 45.833 0.00 0.00 44.47 2.73
3410 3490 4.641541 TGCTAATGCGTACTTGGAGTAGTA 59.358 41.667 0.00 0.00 43.34 1.82
3411 3491 3.446161 TGCTAATGCGTACTTGGAGTAGT 59.554 43.478 0.00 0.00 43.34 2.73
3412 3492 4.041740 TGCTAATGCGTACTTGGAGTAG 57.958 45.455 0.00 0.00 43.34 2.57
3413 3493 3.181479 CCTGCTAATGCGTACTTGGAGTA 60.181 47.826 0.00 0.00 43.34 2.59
3414 3494 2.418746 CCTGCTAATGCGTACTTGGAGT 60.419 50.000 0.00 0.00 43.34 3.85
3415 3495 2.205074 CCTGCTAATGCGTACTTGGAG 58.795 52.381 0.00 0.00 43.34 3.86
3416 3496 1.134521 CCCTGCTAATGCGTACTTGGA 60.135 52.381 0.00 0.00 43.34 3.53
3417 3497 1.134521 TCCCTGCTAATGCGTACTTGG 60.135 52.381 0.00 0.00 43.34 3.61
3547 3641 1.026584 AAACGAACCACCCTTTTCCG 58.973 50.000 0.00 0.00 0.00 4.30
3624 3720 2.966050 AGAGAAGAATCGACTGTTGCC 58.034 47.619 0.00 0.00 0.00 4.52
3666 3762 3.562557 GGACGTACAATCCAAAACAGTGT 59.437 43.478 8.06 0.00 36.15 3.55
3679 3775 1.269883 ACGTGAGCATTGGACGTACAA 60.270 47.619 17.13 17.13 44.14 2.41
3899 4082 1.452833 GTACTCCGCCCCGTACTCT 60.453 63.158 0.00 0.00 34.59 3.24
4116 4299 1.153745 GTAGTCGAGCAGCAGGGTG 60.154 63.158 0.00 0.00 0.00 4.61
4161 4344 0.661483 GACGAGCAAAGCAAAGCACC 60.661 55.000 0.00 0.00 0.00 5.01
4225 4421 9.582648 ACATATGGCATAATACATGCATATCAT 57.417 29.630 11.86 7.49 46.21 2.45
4274 4470 4.592485 ACGATGATGACAAGTAGGATCC 57.408 45.455 2.48 2.48 0.00 3.36
4345 4541 5.455525 GCATTGGCAATCTGTAAATACGAAC 59.544 40.000 10.36 0.00 40.72 3.95
4367 4567 8.962679 ACGTATAAAATTTAGGAATCCAAAGCA 58.037 29.630 0.61 0.00 0.00 3.91
4391 4591 7.171678 ACTTGAAATCCTACTCAGAAGAAAACG 59.828 37.037 0.00 0.00 0.00 3.60
4397 4597 6.467677 TCCAACTTGAAATCCTACTCAGAAG 58.532 40.000 0.00 0.00 0.00 2.85
4400 4600 7.693969 AAATCCAACTTGAAATCCTACTCAG 57.306 36.000 0.00 0.00 0.00 3.35
4423 4626 5.074804 GCCTAGAAGGTGGTTAAGGAAAAA 58.925 41.667 0.00 0.00 37.80 1.94
4424 4627 4.507869 GGCCTAGAAGGTGGTTAAGGAAAA 60.508 45.833 0.00 0.00 37.80 2.29
4425 4628 3.009805 GGCCTAGAAGGTGGTTAAGGAAA 59.990 47.826 0.00 0.00 37.80 3.13
4457 4661 4.858680 TGGTTTGCCCGCGTGACA 62.859 61.111 4.92 0.00 35.15 3.58
4490 4694 5.412904 GTCCTACCTCCTGTTTTCATTTCTG 59.587 44.000 0.00 0.00 0.00 3.02
4494 4698 3.655777 TGGTCCTACCTCCTGTTTTCATT 59.344 43.478 0.00 0.00 39.58 2.57
4525 4729 1.500474 TTGGGTGCCATTTGGAACAA 58.500 45.000 9.93 1.70 46.04 2.83
4533 4737 4.160252 GTGTCTGATATTTTGGGTGCCATT 59.840 41.667 0.00 0.00 31.53 3.16
4543 4747 4.020573 TGTCCGTGGAGTGTCTGATATTTT 60.021 41.667 0.00 0.00 0.00 1.82
4591 4802 1.656587 ATCGGCTAATCCCTATGGCA 58.343 50.000 0.00 0.00 0.00 4.92
4592 4803 2.789409 AATCGGCTAATCCCTATGGC 57.211 50.000 0.00 0.00 0.00 4.40
4593 4804 4.408182 CCTAATCGGCTAATCCCTATGG 57.592 50.000 0.00 0.00 0.00 2.74
4629 4870 0.671251 TTCGTGCATTGTGGAAACCC 59.329 50.000 0.00 0.00 0.00 4.11
4636 4877 5.579384 ATTTTTCATGTTCGTGCATTGTG 57.421 34.783 0.00 0.00 0.00 3.33
4645 4886 9.655769 CAAGTCATCCTATATTTTTCATGTTCG 57.344 33.333 0.00 0.00 0.00 3.95
4711 4959 1.200020 CAACACGCCCAAGAGAAATCC 59.800 52.381 0.00 0.00 0.00 3.01
4766 5015 9.262358 CCGAAAATAAAATAGTTTTCCCACAAA 57.738 29.630 0.00 0.00 39.81 2.83
4767 5016 8.422566 ACCGAAAATAAAATAGTTTTCCCACAA 58.577 29.630 0.00 0.00 39.81 3.33
4768 5017 7.868415 CACCGAAAATAAAATAGTTTTCCCACA 59.132 33.333 0.00 0.00 39.81 4.17
4769 5018 7.148705 GCACCGAAAATAAAATAGTTTTCCCAC 60.149 37.037 0.00 0.00 39.81 4.61
4770 5019 6.869388 GCACCGAAAATAAAATAGTTTTCCCA 59.131 34.615 0.00 0.00 39.81 4.37
4771 5020 6.869388 TGCACCGAAAATAAAATAGTTTTCCC 59.131 34.615 0.00 0.00 39.81 3.97
4772 5021 7.876896 TGCACCGAAAATAAAATAGTTTTCC 57.123 32.000 0.00 0.00 39.81 3.13
4773 5022 8.756864 TGTTGCACCGAAAATAAAATAGTTTTC 58.243 29.630 0.00 0.00 39.66 2.29
4774 5023 8.544597 GTGTTGCACCGAAAATAAAATAGTTTT 58.455 29.630 0.00 0.00 36.67 2.43
4775 5024 7.923878 AGTGTTGCACCGAAAATAAAATAGTTT 59.076 29.630 0.00 0.00 34.49 2.66
4776 5025 7.430441 AGTGTTGCACCGAAAATAAAATAGTT 58.570 30.769 0.00 0.00 34.49 2.24
4777 5026 6.977213 AGTGTTGCACCGAAAATAAAATAGT 58.023 32.000 0.00 0.00 34.49 2.12
4778 5027 7.593273 TCAAGTGTTGCACCGAAAATAAAATAG 59.407 33.333 0.00 0.00 34.49 1.73
4779 5028 7.380065 GTCAAGTGTTGCACCGAAAATAAAATA 59.620 33.333 0.00 0.00 34.49 1.40
4780 5029 6.200097 GTCAAGTGTTGCACCGAAAATAAAAT 59.800 34.615 0.00 0.00 34.49 1.82
4781 5030 5.517054 GTCAAGTGTTGCACCGAAAATAAAA 59.483 36.000 0.00 0.00 34.49 1.52
4782 5031 5.038033 GTCAAGTGTTGCACCGAAAATAAA 58.962 37.500 0.00 0.00 34.49 1.40
4783 5032 4.336993 AGTCAAGTGTTGCACCGAAAATAA 59.663 37.500 0.00 0.00 34.49 1.40
4784 5033 3.880490 AGTCAAGTGTTGCACCGAAAATA 59.120 39.130 0.00 0.00 34.49 1.40
4785 5034 2.687935 AGTCAAGTGTTGCACCGAAAAT 59.312 40.909 0.00 0.00 34.49 1.82
4786 5035 2.088423 AGTCAAGTGTTGCACCGAAAA 58.912 42.857 0.00 0.00 34.49 2.29
4787 5036 1.745232 AGTCAAGTGTTGCACCGAAA 58.255 45.000 0.00 0.00 34.49 3.46
4788 5037 1.400142 CAAGTCAAGTGTTGCACCGAA 59.600 47.619 0.00 0.00 34.49 4.30
4789 5038 1.013596 CAAGTCAAGTGTTGCACCGA 58.986 50.000 0.00 0.00 34.49 4.69
4790 5039 0.029300 CCAAGTCAAGTGTTGCACCG 59.971 55.000 0.00 0.00 34.49 4.94
4791 5040 1.102978 ACCAAGTCAAGTGTTGCACC 58.897 50.000 0.00 0.00 34.49 5.01
4810 5059 5.651576 ACCAAGTCTTTTGTTTTACGGGTAA 59.348 36.000 0.00 0.00 0.00 2.85
4822 5071 3.127895 TGTCCGAACAACCAAGTCTTTTG 59.872 43.478 0.00 0.00 30.70 2.44
4825 5074 2.702592 TGTCCGAACAACCAAGTCTT 57.297 45.000 0.00 0.00 30.70 3.01
4830 5079 2.644676 TCAACATGTCCGAACAACCAA 58.355 42.857 0.00 0.00 39.30 3.67
4831 5080 2.333688 TCAACATGTCCGAACAACCA 57.666 45.000 0.00 0.00 39.30 3.67
4869 5118 0.249911 AACAAGCTTTCGCCTCTCGT 60.250 50.000 0.00 0.00 39.67 4.18
4871 5120 1.873591 TGAAACAAGCTTTCGCCTCTC 59.126 47.619 0.00 0.00 36.60 3.20
4872 5121 1.876156 CTGAAACAAGCTTTCGCCTCT 59.124 47.619 0.00 0.00 36.60 3.69
4875 5124 0.951558 TCCTGAAACAAGCTTTCGCC 59.048 50.000 0.00 0.00 36.60 5.54
4945 5198 1.472990 AAACAAACTTTAGCGCGCAC 58.527 45.000 35.10 4.34 0.00 5.34
4950 5203 6.202937 TCATGGTGTAAAACAAACTTTAGCG 58.797 36.000 0.00 0.00 0.00 4.26
4998 5251 9.351570 GAAGAAAATTCCATTCACTCAAATCTC 57.648 33.333 0.00 0.00 0.00 2.75
5005 5258 8.137437 TGTTTCAGAAGAAAATTCCATTCACTC 58.863 33.333 0.00 0.00 44.75 3.51
5024 5277 7.591006 AGCATTCTTTTGCATTATGTTTCAG 57.409 32.000 0.00 0.00 45.23 3.02
5106 5361 7.554118 TGTTGGAGCCATAGAATCTTTAGAAAG 59.446 37.037 0.00 0.00 37.36 2.62
5167 5450 7.113437 TGGTTATCCCGAATCTGTAAAATCAA 58.887 34.615 0.00 0.00 35.15 2.57
5177 5460 3.136443 TGCATCTTGGTTATCCCGAATCT 59.864 43.478 0.00 0.00 35.15 2.40
5178 5461 3.476552 TGCATCTTGGTTATCCCGAATC 58.523 45.455 0.00 0.00 35.15 2.52
5189 5472 4.263462 TGACACTCCTAAATGCATCTTGGT 60.263 41.667 0.00 0.00 0.00 3.67
5197 5480 5.121811 AGATGACATGACACTCCTAAATGC 58.878 41.667 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.