Multiple sequence alignment - TraesCS6A01G304200

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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 TraesCS6A01G304200 chr6A 100.000 3161 0 0 1 3161 537021500 537018340 0.000000e+00 5838.0
1 TraesCS6A01G304200 chr6A 92.143 420 30 3 208 625 2082734 2083152 9.770000e-165 590.0
2 TraesCS6A01G304200 chr6B 93.177 2257 107 19 623 2871 583723609 583725826 0.000000e+00 3271.0
3 TraesCS6A01G304200 chr6B 91.706 422 33 2 203 623 447958615 447958195 4.540000e-163 584.0
4 TraesCS6A01G304200 chr6B 94.737 114 6 0 2849 2962 583725878 583725991 9.010000e-41 178.0
5 TraesCS6A01G304200 chr6D 92.003 2376 109 21 818 3161 390486338 390484012 0.000000e+00 3260.0
6 TraesCS6A01G304200 chr6D 93.119 2020 107 15 818 2826 390781137 390779139 0.000000e+00 2931.0
7 TraesCS6A01G304200 chr6D 92.522 1618 99 9 831 2438 390729446 390727841 0.000000e+00 2298.0
8 TraesCS6A01G304200 chr6D 95.477 398 17 1 2474 2871 390727542 390727146 4.450000e-178 634.0
9 TraesCS6A01G304200 chr6D 94.485 272 10 1 2890 3161 390778986 390778720 6.310000e-112 414.0
10 TraesCS6A01G304200 chr6D 90.968 310 16 8 2852 3161 390727065 390726768 1.060000e-109 407.0
11 TraesCS6A01G304200 chr6D 91.753 194 12 4 13 203 390781498 390781306 1.870000e-67 267.0
12 TraesCS6A01G304200 chr6D 89.103 156 13 2 623 775 390781292 390781138 1.160000e-44 191.0
13 TraesCS6A01G304200 chr6D 92.683 123 8 1 635 757 390729589 390729468 3.240000e-40 176.0
14 TraesCS6A01G304200 chr6D 88.889 144 12 2 635 775 390486481 390486339 1.170000e-39 174.0
15 TraesCS6A01G304200 chr6D 100.000 30 0 0 784 813 390729470 390729441 4.400000e-04 56.5
16 TraesCS6A01G304200 chr7A 96.235 425 15 1 201 625 33981889 33982312 0.000000e+00 695.0
17 TraesCS6A01G304200 chr7A 91.706 422 33 2 203 623 516511131 516510711 4.540000e-163 584.0
18 TraesCS6A01G304200 chr7A 73.956 1221 278 26 1183 2379 79334993 79333789 1.030000e-124 457.0
19 TraesCS6A01G304200 chr5A 96.437 421 15 0 203 623 576281005 576281425 0.000000e+00 695.0
20 TraesCS6A01G304200 chr2B 92.290 428 30 3 203 628 48796338 48796764 3.490000e-169 604.0
21 TraesCS6A01G304200 chr2A 92.180 422 31 2 203 623 740399339 740398919 2.100000e-166 595.0
22 TraesCS6A01G304200 chr2A 91.726 423 33 2 202 623 76870971 76870550 1.260000e-163 586.0
23 TraesCS6A01G304200 chr2A 91.121 428 37 1 196 623 88726910 88726484 2.110000e-161 579.0
24 TraesCS6A01G304200 chr7B 74.713 1218 271 21 1183 2379 20721521 20720320 2.810000e-140 508.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G304200 chr6A 537018340 537021500 3160 True 5838.00 5838 100.000 1 3161 1 chr6A.!!$R1 3160
1 TraesCS6A01G304200 chr6B 583723609 583725991 2382 False 1724.50 3271 93.957 623 2962 2 chr6B.!!$F1 2339
2 TraesCS6A01G304200 chr6D 390484012 390486481 2469 True 1717.00 3260 90.446 635 3161 2 chr6D.!!$R1 2526
3 TraesCS6A01G304200 chr6D 390778720 390781498 2778 True 950.75 2931 92.115 13 3161 4 chr6D.!!$R3 3148
4 TraesCS6A01G304200 chr6D 390726768 390729589 2821 True 714.30 2298 94.330 635 3161 5 chr6D.!!$R2 2526
5 TraesCS6A01G304200 chr7A 79333789 79334993 1204 True 457.00 457 73.956 1183 2379 1 chr7A.!!$R1 1196
6 TraesCS6A01G304200 chr7B 20720320 20721521 1201 True 508.00 508 74.713 1183 2379 1 chr7B.!!$R1 1196

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
230 233 0.042731 TCAAGTCCTCCCACCCCTAG 59.957 60.0 0.0 0.0 0.0 3.02 F
747 759 0.109597 TTCGTCTTCTCGCCGGTTAC 60.110 55.0 1.9 0.0 0.0 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1164 0.250901 ATATTCTCCATGGGCGGTGC 60.251 55.0 13.02 0.0 0.00 5.01 R
2319 2363 1.484038 TGGCCAGGTGCAATAAATCC 58.516 50.0 0.00 0.0 43.89 3.01 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
46 47 5.229887 CGAACACAACAAATCCTGACAAAAG 59.770 40.000 0.00 0.00 0.00 2.27
77 78 2.432510 TGAAAACCGTTCATTTTGCCCT 59.567 40.909 0.00 0.00 29.44 5.19
80 81 2.812358 ACCGTTCATTTTGCCCTTTC 57.188 45.000 0.00 0.00 0.00 2.62
91 92 4.871933 TTTGCCCTTTCTCAAGAAATCC 57.128 40.909 5.69 0.00 42.44 3.01
102 103 2.036733 TCAAGAAATCCGTCGTTCCACT 59.963 45.455 0.00 0.00 0.00 4.00
109 110 2.338984 GTCGTTCCACTGACGGCT 59.661 61.111 0.00 0.00 41.54 5.52
118 119 0.798776 CACTGACGGCTGAATTCACC 59.201 55.000 3.38 10.12 0.00 4.02
129 130 2.163613 CTGAATTCACCGCTTTTACCCC 59.836 50.000 3.38 0.00 0.00 4.95
130 131 1.475280 GAATTCACCGCTTTTACCCCC 59.525 52.381 0.00 0.00 0.00 5.40
158 159 5.163416 GCCATAATTTAGCACCATTTGACCT 60.163 40.000 0.00 0.00 0.00 3.85
159 160 6.275335 CCATAATTTAGCACCATTTGACCTG 58.725 40.000 0.00 0.00 0.00 4.00
161 162 3.517296 TTTAGCACCATTTGACCTGGA 57.483 42.857 0.00 0.00 37.22 3.86
162 163 2.787473 TAGCACCATTTGACCTGGAG 57.213 50.000 0.00 0.00 37.22 3.86
190 193 1.078143 GCTTGTTGCCCTCTCGGAT 60.078 57.895 0.00 0.00 35.15 4.18
209 212 4.016706 CCGCCAGTCCGGGAAAGT 62.017 66.667 0.00 0.00 44.46 2.66
210 213 2.652095 CCGCCAGTCCGGGAAAGTA 61.652 63.158 0.00 0.00 44.46 2.24
211 214 1.520666 CGCCAGTCCGGGAAAGTAT 59.479 57.895 0.00 0.00 34.06 2.12
212 215 0.529992 CGCCAGTCCGGGAAAGTATC 60.530 60.000 0.00 0.00 34.06 2.24
213 216 0.539986 GCCAGTCCGGGAAAGTATCA 59.460 55.000 0.00 0.00 34.06 2.15
214 217 1.065709 GCCAGTCCGGGAAAGTATCAA 60.066 52.381 0.00 0.00 34.06 2.57
215 218 2.906354 CCAGTCCGGGAAAGTATCAAG 58.094 52.381 0.00 0.00 0.00 3.02
216 219 2.236395 CCAGTCCGGGAAAGTATCAAGT 59.764 50.000 0.00 0.00 0.00 3.16
217 220 3.522553 CAGTCCGGGAAAGTATCAAGTC 58.477 50.000 0.00 0.00 0.00 3.01
218 221 2.500504 AGTCCGGGAAAGTATCAAGTCC 59.499 50.000 0.00 0.00 0.00 3.85
219 222 2.500504 GTCCGGGAAAGTATCAAGTCCT 59.499 50.000 0.00 0.00 0.00 3.85
220 223 2.764572 TCCGGGAAAGTATCAAGTCCTC 59.235 50.000 0.00 0.00 0.00 3.71
221 224 2.158943 CCGGGAAAGTATCAAGTCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
222 225 2.158943 CGGGAAAGTATCAAGTCCTCCC 60.159 54.545 0.00 0.00 38.14 4.30
223 226 2.844348 GGGAAAGTATCAAGTCCTCCCA 59.156 50.000 0.00 0.00 40.72 4.37
224 227 3.370633 GGGAAAGTATCAAGTCCTCCCAC 60.371 52.174 0.00 0.00 40.72 4.61
225 228 3.370633 GGAAAGTATCAAGTCCTCCCACC 60.371 52.174 0.00 0.00 0.00 4.61
226 229 1.880941 AGTATCAAGTCCTCCCACCC 58.119 55.000 0.00 0.00 0.00 4.61
227 230 0.837940 GTATCAAGTCCTCCCACCCC 59.162 60.000 0.00 0.00 0.00 4.95
228 231 0.722676 TATCAAGTCCTCCCACCCCT 59.277 55.000 0.00 0.00 0.00 4.79
229 232 0.722676 ATCAAGTCCTCCCACCCCTA 59.277 55.000 0.00 0.00 0.00 3.53
230 233 0.042731 TCAAGTCCTCCCACCCCTAG 59.957 60.000 0.00 0.00 0.00 3.02
231 234 0.983378 CAAGTCCTCCCACCCCTAGG 60.983 65.000 0.06 0.06 40.04 3.02
309 312 2.572191 AAAATGCAGCACATCGATGG 57.428 45.000 28.09 17.84 38.34 3.51
310 313 1.753930 AAATGCAGCACATCGATGGA 58.246 45.000 28.09 4.89 38.34 3.41
311 314 1.753930 AATGCAGCACATCGATGGAA 58.246 45.000 28.09 6.44 38.34 3.53
312 315 1.019673 ATGCAGCACATCGATGGAAC 58.980 50.000 28.09 16.72 31.52 3.62
313 316 1.679640 ATGCAGCACATCGATGGAACA 60.680 47.619 28.09 18.06 37.22 3.18
314 317 3.008230 ATGCAGCACATCGATGGAACAT 61.008 45.455 28.09 19.30 37.60 2.71
315 318 4.848152 ATGCAGCACATCGATGGAACATC 61.848 47.826 28.09 13.14 37.60 3.06
327 330 3.961480 TGGAACATCGATGTCTCTTGT 57.039 42.857 30.06 14.44 40.80 3.16
328 331 3.849911 TGGAACATCGATGTCTCTTGTC 58.150 45.455 30.06 21.40 40.80 3.18
329 332 3.258123 TGGAACATCGATGTCTCTTGTCA 59.742 43.478 30.06 17.69 40.80 3.58
330 333 3.614616 GGAACATCGATGTCTCTTGTCAC 59.385 47.826 30.06 13.06 40.80 3.67
331 334 3.942130 ACATCGATGTCTCTTGTCACA 57.058 42.857 25.18 0.00 35.87 3.58
332 335 4.257267 ACATCGATGTCTCTTGTCACAA 57.743 40.909 25.18 0.00 35.87 3.33
333 336 4.631131 ACATCGATGTCTCTTGTCACAAA 58.369 39.130 25.18 0.00 35.87 2.83
334 337 5.056480 ACATCGATGTCTCTTGTCACAAAA 58.944 37.500 25.18 0.00 35.87 2.44
335 338 5.702670 ACATCGATGTCTCTTGTCACAAAAT 59.297 36.000 25.18 0.00 35.87 1.82
336 339 6.205464 ACATCGATGTCTCTTGTCACAAAATT 59.795 34.615 25.18 0.00 35.87 1.82
337 340 6.618287 TCGATGTCTCTTGTCACAAAATTT 57.382 33.333 0.00 0.00 0.00 1.82
338 341 6.658831 TCGATGTCTCTTGTCACAAAATTTC 58.341 36.000 0.00 0.00 0.00 2.17
339 342 6.259829 TCGATGTCTCTTGTCACAAAATTTCA 59.740 34.615 0.00 0.00 0.00 2.69
340 343 6.912051 CGATGTCTCTTGTCACAAAATTTCAA 59.088 34.615 0.00 0.00 0.00 2.69
341 344 7.431960 CGATGTCTCTTGTCACAAAATTTCAAA 59.568 33.333 0.00 0.00 0.00 2.69
342 345 9.252962 GATGTCTCTTGTCACAAAATTTCAAAT 57.747 29.630 0.00 0.00 0.00 2.32
343 346 8.633075 TGTCTCTTGTCACAAAATTTCAAATC 57.367 30.769 0.00 0.00 0.00 2.17
344 347 8.249638 TGTCTCTTGTCACAAAATTTCAAATCA 58.750 29.630 0.00 0.00 0.00 2.57
345 348 9.086336 GTCTCTTGTCACAAAATTTCAAATCAA 57.914 29.630 0.00 0.00 0.00 2.57
346 349 9.650539 TCTCTTGTCACAAAATTTCAAATCAAA 57.349 25.926 0.00 0.00 0.00 2.69
351 354 9.699985 TGTCACAAAATTTCAAATCAAAATTCG 57.300 25.926 0.00 0.00 35.75 3.34
352 355 9.913451 GTCACAAAATTTCAAATCAAAATTCGA 57.087 25.926 0.00 0.00 35.75 3.71
360 363 8.765044 TTTCAAATCAAAATTCGAAACATTGC 57.235 26.923 0.00 0.00 0.00 3.56
361 364 7.712264 TCAAATCAAAATTCGAAACATTGCT 57.288 28.000 0.00 0.00 0.00 3.91
362 365 7.786114 TCAAATCAAAATTCGAAACATTGCTC 58.214 30.769 0.00 0.00 0.00 4.26
363 366 5.997732 ATCAAAATTCGAAACATTGCTCG 57.002 34.783 0.00 3.07 36.39 5.03
364 367 5.102020 TCAAAATTCGAAACATTGCTCGA 57.898 34.783 0.00 7.21 42.05 4.04
365 368 5.146460 TCAAAATTCGAAACATTGCTCGAG 58.854 37.500 8.45 8.45 44.25 4.04
366 369 5.049749 TCAAAATTCGAAACATTGCTCGAGA 60.050 36.000 18.75 0.00 44.25 4.04
367 370 5.551760 AAATTCGAAACATTGCTCGAGAT 57.448 34.783 18.75 0.00 44.25 2.75
368 371 6.662414 AAATTCGAAACATTGCTCGAGATA 57.338 33.333 18.75 2.54 44.25 1.98
369 372 6.851222 AATTCGAAACATTGCTCGAGATAT 57.149 33.333 18.75 5.17 44.25 1.63
370 373 7.946655 AATTCGAAACATTGCTCGAGATATA 57.053 32.000 18.75 0.00 44.25 0.86
371 374 7.946655 ATTCGAAACATTGCTCGAGATATAA 57.053 32.000 18.75 5.47 44.25 0.98
372 375 7.764695 TTCGAAACATTGCTCGAGATATAAA 57.235 32.000 18.75 2.00 44.25 1.40
373 376 7.764695 TCGAAACATTGCTCGAGATATAAAA 57.235 32.000 18.75 0.13 39.07 1.52
374 377 8.192068 TCGAAACATTGCTCGAGATATAAAAA 57.808 30.769 18.75 0.00 39.07 1.94
375 378 8.826710 TCGAAACATTGCTCGAGATATAAAAAT 58.173 29.630 18.75 0.84 39.07 1.82
376 379 8.886080 CGAAACATTGCTCGAGATATAAAAATG 58.114 33.333 18.75 14.25 37.23 2.32
377 380 9.935682 GAAACATTGCTCGAGATATAAAAATGA 57.064 29.630 18.75 0.00 0.00 2.57
378 381 9.722056 AAACATTGCTCGAGATATAAAAATGAC 57.278 29.630 18.75 0.00 0.00 3.06
379 382 8.437360 ACATTGCTCGAGATATAAAAATGACA 57.563 30.769 18.75 0.00 0.00 3.58
380 383 8.892723 ACATTGCTCGAGATATAAAAATGACAA 58.107 29.630 18.75 6.18 0.00 3.18
381 384 9.720667 CATTGCTCGAGATATAAAAATGACAAA 57.279 29.630 18.75 0.00 0.00 2.83
405 408 8.891671 AATTTAACATCAATGTGATAATGGGC 57.108 30.769 0.00 0.00 41.61 5.36
406 409 4.942761 AACATCAATGTGATAATGGGCC 57.057 40.909 0.00 0.00 41.61 5.80
407 410 3.913509 ACATCAATGTGATAATGGGCCA 58.086 40.909 9.61 9.61 40.03 5.36
408 411 4.288398 ACATCAATGTGATAATGGGCCAA 58.712 39.130 11.89 0.00 40.03 4.52
409 412 4.715792 ACATCAATGTGATAATGGGCCAAA 59.284 37.500 11.89 1.34 40.03 3.28
410 413 5.367352 ACATCAATGTGATAATGGGCCAAAT 59.633 36.000 11.89 7.49 40.03 2.32
411 414 5.534207 TCAATGTGATAATGGGCCAAATC 57.466 39.130 11.89 17.28 0.00 2.17
412 415 5.210430 TCAATGTGATAATGGGCCAAATCT 58.790 37.500 24.45 9.19 0.00 2.40
413 416 6.372104 TCAATGTGATAATGGGCCAAATCTA 58.628 36.000 24.45 17.05 0.00 1.98
414 417 6.838090 TCAATGTGATAATGGGCCAAATCTAA 59.162 34.615 24.45 16.42 0.00 2.10
415 418 7.344093 TCAATGTGATAATGGGCCAAATCTAAA 59.656 33.333 24.45 14.65 0.00 1.85
416 419 6.713762 TGTGATAATGGGCCAAATCTAAAG 57.286 37.500 24.45 0.00 0.00 1.85
417 420 5.068987 TGTGATAATGGGCCAAATCTAAAGC 59.931 40.000 24.45 14.04 0.00 3.51
418 421 5.302823 GTGATAATGGGCCAAATCTAAAGCT 59.697 40.000 24.45 0.00 0.00 3.74
419 422 5.536161 TGATAATGGGCCAAATCTAAAGCTC 59.464 40.000 24.45 6.19 0.00 4.09
420 423 2.897271 TGGGCCAAATCTAAAGCTCA 57.103 45.000 2.13 0.00 32.05 4.26
421 424 3.168035 TGGGCCAAATCTAAAGCTCAA 57.832 42.857 2.13 0.00 31.42 3.02
422 425 2.825532 TGGGCCAAATCTAAAGCTCAAC 59.174 45.455 2.13 0.00 31.42 3.18
423 426 3.092301 GGGCCAAATCTAAAGCTCAACT 58.908 45.455 4.39 0.00 0.00 3.16
424 427 3.511540 GGGCCAAATCTAAAGCTCAACTT 59.488 43.478 4.39 0.00 41.70 2.66
425 428 4.705023 GGGCCAAATCTAAAGCTCAACTTA 59.295 41.667 4.39 0.00 37.75 2.24
426 429 5.360999 GGGCCAAATCTAAAGCTCAACTTAT 59.639 40.000 4.39 0.00 37.75 1.73
427 430 6.268566 GGCCAAATCTAAAGCTCAACTTATG 58.731 40.000 0.00 0.00 37.75 1.90
428 431 6.127619 GGCCAAATCTAAAGCTCAACTTATGT 60.128 38.462 0.00 0.00 37.75 2.29
429 432 7.315890 GCCAAATCTAAAGCTCAACTTATGTT 58.684 34.615 0.00 0.00 37.75 2.71
430 433 8.458843 GCCAAATCTAAAGCTCAACTTATGTTA 58.541 33.333 0.00 0.00 37.75 2.41
441 444 9.893305 AGCTCAACTTATGTTATGTACAAAAAC 57.107 29.630 14.45 14.45 40.89 2.43
442 445 9.893305 GCTCAACTTATGTTATGTACAAAAACT 57.107 29.630 19.39 11.13 40.89 2.66
461 464 9.232082 CAAAAACTTGTCATTTTTGTATCTCGA 57.768 29.630 13.01 0.00 45.57 4.04
462 465 9.450807 AAAAACTTGTCATTTTTGTATCTCGAG 57.549 29.630 5.93 5.93 37.74 4.04
463 466 6.170675 ACTTGTCATTTTTGTATCTCGAGC 57.829 37.500 7.81 0.00 0.00 5.03
464 467 5.700832 ACTTGTCATTTTTGTATCTCGAGCA 59.299 36.000 7.81 0.00 0.00 4.26
465 468 6.204688 ACTTGTCATTTTTGTATCTCGAGCAA 59.795 34.615 7.81 3.53 0.00 3.91
466 469 6.741992 TGTCATTTTTGTATCTCGAGCAAT 57.258 33.333 7.81 0.00 0.00 3.56
467 470 6.545508 TGTCATTTTTGTATCTCGAGCAATG 58.454 36.000 7.81 7.21 0.00 2.82
468 471 6.149308 TGTCATTTTTGTATCTCGAGCAATGT 59.851 34.615 7.81 0.00 0.00 2.71
469 472 7.023575 GTCATTTTTGTATCTCGAGCAATGTT 58.976 34.615 7.81 0.00 0.00 2.71
470 473 7.538678 GTCATTTTTGTATCTCGAGCAATGTTT 59.461 33.333 7.81 0.00 0.00 2.83
471 474 7.750458 TCATTTTTGTATCTCGAGCAATGTTTC 59.250 33.333 7.81 0.00 0.00 2.78
472 475 4.840401 TTGTATCTCGAGCAATGTTTCG 57.160 40.909 7.81 3.56 38.13 3.46
473 476 4.104696 TGTATCTCGAGCAATGTTTCGA 57.895 40.909 7.81 10.47 42.91 3.71
474 477 4.490743 TGTATCTCGAGCAATGTTTCGAA 58.509 39.130 7.81 0.00 44.25 3.71
475 478 5.109210 TGTATCTCGAGCAATGTTTCGAAT 58.891 37.500 7.81 10.43 44.25 3.34
476 479 5.580691 TGTATCTCGAGCAATGTTTCGAATT 59.419 36.000 7.81 6.31 44.25 2.17
477 480 5.551760 ATCTCGAGCAATGTTTCGAATTT 57.448 34.783 7.81 0.00 44.25 1.82
478 481 5.356882 TCTCGAGCAATGTTTCGAATTTT 57.643 34.783 7.81 0.00 44.25 1.82
479 482 5.146460 TCTCGAGCAATGTTTCGAATTTTG 58.854 37.500 7.81 4.87 44.25 2.44
480 483 5.049749 TCTCGAGCAATGTTTCGAATTTTGA 60.050 36.000 7.81 4.60 44.25 2.69
481 484 5.698832 TCGAGCAATGTTTCGAATTTTGAT 58.301 33.333 15.39 10.93 42.27 2.57
482 485 6.836953 TCGAGCAATGTTTCGAATTTTGATA 58.163 32.000 15.39 0.00 42.27 2.15
483 486 7.471721 TCGAGCAATGTTTCGAATTTTGATAT 58.528 30.769 15.39 0.00 42.27 1.63
484 487 7.429051 TCGAGCAATGTTTCGAATTTTGATATG 59.571 33.333 15.39 8.24 42.27 1.78
485 488 7.429051 CGAGCAATGTTTCGAATTTTGATATGA 59.571 33.333 15.39 0.00 39.06 2.15
486 489 8.984891 AGCAATGTTTCGAATTTTGATATGAA 57.015 26.923 15.39 0.00 0.00 2.57
487 490 9.421806 AGCAATGTTTCGAATTTTGATATGAAA 57.578 25.926 15.39 0.00 0.00 2.69
508 511 8.546597 TGAAATTTTGTGATAAGAGACATCGA 57.453 30.769 0.00 0.00 0.00 3.59
509 512 9.166173 TGAAATTTTGTGATAAGAGACATCGAT 57.834 29.630 0.00 0.00 0.00 3.59
510 513 9.430838 GAAATTTTGTGATAAGAGACATCGATG 57.569 33.333 23.68 23.68 0.00 3.84
511 514 8.498054 AATTTTGTGATAAGAGACATCGATGT 57.502 30.769 30.37 30.37 45.16 3.06
512 515 7.905604 TTTTGTGATAAGAGACATCGATGTT 57.094 32.000 30.46 20.01 41.95 2.71
513 516 7.525688 TTTGTGATAAGAGACATCGATGTTC 57.474 36.000 30.46 25.63 41.95 3.18
514 517 5.592054 TGTGATAAGAGACATCGATGTTCC 58.408 41.667 30.46 23.29 41.95 3.62
515 518 4.677378 GTGATAAGAGACATCGATGTTCCG 59.323 45.833 30.46 5.28 41.95 4.30
516 519 4.338400 TGATAAGAGACATCGATGTTCCGT 59.662 41.667 30.46 22.94 41.95 4.69
517 520 3.594603 AAGAGACATCGATGTTCCGTT 57.405 42.857 30.46 18.44 41.95 4.44
518 521 4.713824 AAGAGACATCGATGTTCCGTTA 57.286 40.909 30.46 0.00 41.95 3.18
519 522 4.713824 AGAGACATCGATGTTCCGTTAA 57.286 40.909 30.46 0.00 41.95 2.01
520 523 5.263968 AGAGACATCGATGTTCCGTTAAT 57.736 39.130 30.46 5.77 41.95 1.40
521 524 5.043903 AGAGACATCGATGTTCCGTTAATG 58.956 41.667 30.46 2.45 41.95 1.90
522 525 4.755411 AGACATCGATGTTCCGTTAATGT 58.245 39.130 30.46 6.02 41.95 2.71
523 526 4.566759 AGACATCGATGTTCCGTTAATGTG 59.433 41.667 30.46 1.76 41.95 3.21
524 527 3.063452 ACATCGATGTTCCGTTAATGTGC 59.937 43.478 25.18 0.00 37.90 4.57
525 528 2.967362 TCGATGTTCCGTTAATGTGCT 58.033 42.857 0.00 0.00 0.00 4.40
526 529 2.670905 TCGATGTTCCGTTAATGTGCTG 59.329 45.455 0.00 0.00 0.00 4.41
527 530 2.415168 CGATGTTCCGTTAATGTGCTGT 59.585 45.455 0.00 0.00 0.00 4.40
528 531 3.615056 CGATGTTCCGTTAATGTGCTGTA 59.385 43.478 0.00 0.00 0.00 2.74
529 532 4.270084 CGATGTTCCGTTAATGTGCTGTAT 59.730 41.667 0.00 0.00 0.00 2.29
530 533 5.220586 CGATGTTCCGTTAATGTGCTGTATT 60.221 40.000 0.00 0.00 0.00 1.89
531 534 5.950758 TGTTCCGTTAATGTGCTGTATTT 57.049 34.783 0.00 0.00 0.00 1.40
532 535 6.320494 TGTTCCGTTAATGTGCTGTATTTT 57.680 33.333 0.00 0.00 0.00 1.82
533 536 6.740110 TGTTCCGTTAATGTGCTGTATTTTT 58.260 32.000 0.00 0.00 0.00 1.94
572 575 9.267096 TGAACAATTTAAAAATGTTTTTCGTGC 57.733 25.926 18.31 8.79 40.53 5.34
573 576 9.267096 GAACAATTTAAAAATGTTTTTCGTGCA 57.733 25.926 18.31 0.00 40.53 4.57
574 577 9.780413 AACAATTTAAAAATGTTTTTCGTGCAT 57.220 22.222 13.87 0.00 40.53 3.96
575 578 9.780413 ACAATTTAAAAATGTTTTTCGTGCATT 57.220 22.222 6.73 0.00 40.53 3.56
578 581 9.994432 ATTTAAAAATGTTTTTCGTGCATTTGA 57.006 22.222 6.73 0.00 40.58 2.69
579 582 9.825972 TTTAAAAATGTTTTTCGTGCATTTGAA 57.174 22.222 6.73 0.00 40.58 2.69
580 583 7.951706 AAAAATGTTTTTCGTGCATTTGAAG 57.048 28.000 0.00 0.00 40.58 3.02
581 584 4.713854 ATGTTTTTCGTGCATTTGAAGC 57.286 36.364 0.00 0.00 0.00 3.86
582 585 3.515630 TGTTTTTCGTGCATTTGAAGCA 58.484 36.364 0.00 0.00 40.19 3.91
583 586 4.118410 TGTTTTTCGTGCATTTGAAGCAT 58.882 34.783 0.00 0.00 44.79 3.79
584 587 4.208873 TGTTTTTCGTGCATTTGAAGCATC 59.791 37.500 0.00 0.00 44.79 3.91
585 588 2.245795 TTCGTGCATTTGAAGCATCG 57.754 45.000 0.00 0.00 44.79 3.84
586 589 0.447406 TCGTGCATTTGAAGCATCGG 59.553 50.000 0.00 0.00 44.79 4.18
587 590 0.523968 CGTGCATTTGAAGCATCGGG 60.524 55.000 0.00 0.00 44.79 5.14
588 591 0.810648 GTGCATTTGAAGCATCGGGA 59.189 50.000 0.00 0.00 44.79 5.14
589 592 1.097232 TGCATTTGAAGCATCGGGAG 58.903 50.000 0.00 0.00 37.02 4.30
590 593 1.098050 GCATTTGAAGCATCGGGAGT 58.902 50.000 0.00 0.00 0.00 3.85
591 594 2.288666 GCATTTGAAGCATCGGGAGTA 58.711 47.619 0.00 0.00 0.00 2.59
592 595 2.032178 GCATTTGAAGCATCGGGAGTAC 59.968 50.000 0.00 0.00 0.00 2.73
593 596 2.396590 TTTGAAGCATCGGGAGTACC 57.603 50.000 0.00 0.00 0.00 3.34
603 606 2.998949 GGAGTACCCCAAGCCTGG 59.001 66.667 0.00 0.00 43.10 4.45
613 616 2.160721 CCAAGCCTGGGAGTACTAGA 57.839 55.000 0.00 0.00 39.30 2.43
614 617 2.683768 CCAAGCCTGGGAGTACTAGAT 58.316 52.381 0.00 0.00 39.30 1.98
615 618 3.845860 CCAAGCCTGGGAGTACTAGATA 58.154 50.000 0.00 0.00 39.30 1.98
616 619 3.574826 CCAAGCCTGGGAGTACTAGATAC 59.425 52.174 0.00 0.00 39.30 2.24
617 620 4.693058 CCAAGCCTGGGAGTACTAGATACT 60.693 50.000 0.00 0.45 39.33 2.12
618 621 4.817874 AGCCTGGGAGTACTAGATACTT 57.182 45.455 0.00 0.00 44.64 2.24
619 622 5.145513 AGCCTGGGAGTACTAGATACTTT 57.854 43.478 0.00 0.00 44.64 2.66
620 623 5.141910 AGCCTGGGAGTACTAGATACTTTC 58.858 45.833 0.00 0.00 44.64 2.62
621 624 4.281435 GCCTGGGAGTACTAGATACTTTCC 59.719 50.000 0.00 7.54 44.64 3.13
631 634 4.470304 ACTAGATACTTTCCCCACTTCCAC 59.530 45.833 0.00 0.00 0.00 4.02
637 640 2.127651 TTCCCCACTTCCACTAACCT 57.872 50.000 0.00 0.00 0.00 3.50
673 685 0.698818 AACCACCCTCTGAATCCCAC 59.301 55.000 0.00 0.00 0.00 4.61
681 693 0.687757 TCTGAATCCCACTAGCGCCT 60.688 55.000 2.29 0.00 0.00 5.52
747 759 0.109597 TTCGTCTTCTCGCCGGTTAC 60.110 55.000 1.90 0.00 0.00 2.50
809 827 4.143333 TTGTAGCGCGGAGGAGGC 62.143 66.667 8.83 0.00 0.00 4.70
906 924 1.073025 AGCACACCGCAAGATTCCA 59.927 52.632 0.00 0.00 46.13 3.53
957 975 2.654079 CGACTTGAGCAGGCCCTCT 61.654 63.158 0.00 0.00 33.02 3.69
1015 1035 0.833834 CCCGATGGAGGCCTGTATCT 60.834 60.000 12.00 0.00 0.00 1.98
1033 1053 7.039923 CCTGTATCTTAATAAGGAGCTTACGGA 60.040 40.741 0.00 0.00 0.00 4.69
1034 1054 7.883217 TGTATCTTAATAAGGAGCTTACGGAG 58.117 38.462 0.00 0.00 0.00 4.63
1044 1064 3.661745 CTTACGGAGCTTACGGCAT 57.338 52.632 14.86 0.00 44.79 4.40
1144 1164 2.928757 CTCAGCAAATTCAGAGGAGACG 59.071 50.000 0.00 0.00 0.00 4.18
1146 1166 1.002430 AGCAAATTCAGAGGAGACGCA 59.998 47.619 0.00 0.00 0.00 5.24
1269 1295 0.971959 CAGGCTCTGTCTGCTCCTCT 60.972 60.000 0.00 0.00 0.00 3.69
1275 1301 2.125350 GTCTGCTCCTCTTGGCGG 60.125 66.667 0.00 0.00 36.28 6.13
1394 1420 0.322008 GCTTGCCTCTACAGCCTTGT 60.322 55.000 0.00 0.00 41.39 3.16
1413 1439 2.175931 TGTGGAAAAGAGGGCCTACAAA 59.824 45.455 5.73 0.00 0.00 2.83
1726 1759 6.855763 TCAAGGCATATTTGTTTCCTGATT 57.144 33.333 0.00 0.00 0.00 2.57
1812 1845 2.852075 GGGGACTGTGGGTGGACA 60.852 66.667 0.00 0.00 0.00 4.02
1839 1872 1.406887 CCACCGGGTTGGAACTATCAG 60.407 57.143 6.32 0.00 42.00 2.90
1954 1987 1.168714 GGTTCTGGGTGACATGAAGC 58.831 55.000 0.00 0.00 32.16 3.86
2194 2238 9.408760 CTGTGTCTCAGTGTGGAAGAATATCCA 62.409 44.444 0.00 0.00 41.70 3.41
2224 2268 4.408182 AGCAAACTGTGTCTACTTCACT 57.592 40.909 0.00 0.00 36.83 3.41
2227 2271 4.025647 GCAAACTGTGTCTACTTCACTGAC 60.026 45.833 9.22 0.00 37.87 3.51
2294 2338 5.523438 AGGCGTTCTAAATTTGGAAAACA 57.477 34.783 17.39 0.00 29.23 2.83
2319 2363 1.470098 CAGGGAAGAAATTGTGCCTCG 59.530 52.381 0.00 0.00 32.44 4.63
2531 2856 5.064198 GTGTTAAATTACTGCCGCTGTCATA 59.936 40.000 6.13 0.00 0.00 2.15
2584 2909 5.069781 CCAAGGTCCTTGTGGAAATGTTAAA 59.930 40.000 26.52 0.00 45.18 1.52
2591 2916 6.547880 TCCTTGTGGAAATGTTAAAGCAACTA 59.452 34.615 0.00 0.00 39.87 2.24
2665 2990 6.369615 GGTACTTTGAGACGCTTAATTTGGTA 59.630 38.462 0.00 0.00 0.00 3.25
3048 3566 5.584251 CCAGCATGTTTTGTTTTTGTTAGGT 59.416 36.000 0.00 0.00 0.00 3.08
3087 3605 4.286032 AGGTATTGCAGAAGTGAGGTTACA 59.714 41.667 0.00 0.00 0.00 2.41
3131 3649 6.569179 TTGTAGGTTTTTGCTACAAGATCC 57.431 37.500 0.00 0.00 38.26 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.574830 CAGGATTTGTTGTGTTCGTGAAAAA 59.425 36.000 0.00 0.00 0.00 1.94
16 17 5.098893 CAGGATTTGTTGTGTTCGTGAAAA 58.901 37.500 0.00 0.00 0.00 2.29
21 22 3.275143 TGTCAGGATTTGTTGTGTTCGT 58.725 40.909 0.00 0.00 0.00 3.85
23 24 6.329496 TCTTTTGTCAGGATTTGTTGTGTTC 58.671 36.000 0.00 0.00 0.00 3.18
46 47 4.854399 TGAACGGTTTTCATGTGTCAATC 58.146 39.130 0.00 0.00 0.00 2.67
77 78 3.744426 GGAACGACGGATTTCTTGAGAAA 59.256 43.478 8.48 8.48 46.60 2.52
80 81 2.412089 GTGGAACGACGGATTTCTTGAG 59.588 50.000 0.00 0.00 0.00 3.02
102 103 2.032634 GCGGTGAATTCAGCCGTCA 61.033 57.895 31.50 4.52 40.99 4.35
109 110 2.164338 GGGGTAAAAGCGGTGAATTCA 58.836 47.619 3.38 3.38 0.00 2.57
118 119 1.182385 TGGCAAAGGGGGTAAAAGCG 61.182 55.000 0.00 0.00 0.00 4.68
120 121 5.692115 AATTATGGCAAAGGGGGTAAAAG 57.308 39.130 0.00 0.00 0.00 2.27
129 130 4.734398 TGGTGCTAAATTATGGCAAAGG 57.266 40.909 0.00 0.00 37.73 3.11
130 131 6.817641 TCAAATGGTGCTAAATTATGGCAAAG 59.182 34.615 0.00 0.00 37.73 2.77
203 206 3.370633 GGTGGGAGGACTTGATACTTTCC 60.371 52.174 0.00 0.00 0.00 3.13
204 207 3.370633 GGGTGGGAGGACTTGATACTTTC 60.371 52.174 0.00 0.00 0.00 2.62
206 209 2.197465 GGGTGGGAGGACTTGATACTT 58.803 52.381 0.00 0.00 0.00 2.24
207 210 1.625508 GGGGTGGGAGGACTTGATACT 60.626 57.143 0.00 0.00 0.00 2.12
208 211 0.837940 GGGGTGGGAGGACTTGATAC 59.162 60.000 0.00 0.00 0.00 2.24
209 212 0.722676 AGGGGTGGGAGGACTTGATA 59.277 55.000 0.00 0.00 0.00 2.15
210 213 0.722676 TAGGGGTGGGAGGACTTGAT 59.277 55.000 0.00 0.00 0.00 2.57
211 214 0.042731 CTAGGGGTGGGAGGACTTGA 59.957 60.000 0.00 0.00 0.00 3.02
212 215 0.983378 CCTAGGGGTGGGAGGACTTG 60.983 65.000 0.00 0.00 0.00 3.16
213 216 1.396594 CCTAGGGGTGGGAGGACTT 59.603 63.158 0.00 0.00 0.00 3.01
214 217 3.120191 CCTAGGGGTGGGAGGACT 58.880 66.667 0.00 0.00 0.00 3.85
240 243 8.915922 AAAAATATTTTTCAGCATGGGTGCACC 61.916 37.037 28.57 28.57 43.84 5.01
241 244 6.072563 AAAAATATTTTTCAGCATGGGTGCAC 60.073 34.615 18.40 8.80 43.84 4.57
242 245 6.002704 AAAAATATTTTTCAGCATGGGTGCA 58.997 32.000 18.40 0.00 43.84 4.57
243 246 6.499234 AAAAATATTTTTCAGCATGGGTGC 57.501 33.333 18.40 0.00 42.73 5.01
289 292 2.492881 TCCATCGATGTGCTGCATTTTT 59.507 40.909 23.27 0.00 38.06 1.94
290 293 2.093890 TCCATCGATGTGCTGCATTTT 58.906 42.857 23.27 0.00 38.06 1.82
291 294 1.753930 TCCATCGATGTGCTGCATTT 58.246 45.000 23.27 0.00 38.06 2.32
292 295 1.402968 GTTCCATCGATGTGCTGCATT 59.597 47.619 23.27 0.00 38.06 3.56
293 296 1.019673 GTTCCATCGATGTGCTGCAT 58.980 50.000 23.27 0.00 41.24 3.96
294 297 0.321475 TGTTCCATCGATGTGCTGCA 60.321 50.000 23.27 11.81 0.00 4.41
295 298 1.003116 GATGTTCCATCGATGTGCTGC 60.003 52.381 23.27 9.57 0.00 5.25
296 299 1.259770 CGATGTTCCATCGATGTGCTG 59.740 52.381 23.27 8.71 43.59 4.41
297 300 1.136891 TCGATGTTCCATCGATGTGCT 59.863 47.619 23.27 4.01 44.42 4.40
298 301 1.570813 TCGATGTTCCATCGATGTGC 58.429 50.000 23.27 13.13 44.42 4.57
304 307 3.361794 AGAGACATCGATGTTCCATCG 57.638 47.619 30.46 17.96 41.95 3.84
305 308 4.437239 ACAAGAGACATCGATGTTCCATC 58.563 43.478 30.46 23.35 41.95 3.51
306 309 4.081476 TGACAAGAGACATCGATGTTCCAT 60.081 41.667 30.46 17.35 41.95 3.41
307 310 3.258123 TGACAAGAGACATCGATGTTCCA 59.742 43.478 30.46 17.94 41.95 3.53
308 311 3.614616 GTGACAAGAGACATCGATGTTCC 59.385 47.826 30.46 23.29 41.95 3.62
309 312 4.237724 TGTGACAAGAGACATCGATGTTC 58.762 43.478 30.46 25.63 41.95 3.18
310 313 4.257267 TGTGACAAGAGACATCGATGTT 57.743 40.909 30.46 20.01 41.95 2.71
311 314 3.942130 TGTGACAAGAGACATCGATGT 57.058 42.857 30.37 30.37 45.16 3.06
312 315 5.596268 TTTTGTGACAAGAGACATCGATG 57.404 39.130 23.68 23.68 0.00 3.84
313 316 6.808008 AATTTTGTGACAAGAGACATCGAT 57.192 33.333 0.00 0.00 0.00 3.59
314 317 6.259829 TGAAATTTTGTGACAAGAGACATCGA 59.740 34.615 0.00 0.00 0.00 3.59
315 318 6.429624 TGAAATTTTGTGACAAGAGACATCG 58.570 36.000 0.00 0.00 0.00 3.84
316 319 8.633075 TTTGAAATTTTGTGACAAGAGACATC 57.367 30.769 0.00 0.00 0.00 3.06
317 320 9.252962 GATTTGAAATTTTGTGACAAGAGACAT 57.747 29.630 0.00 0.00 0.00 3.06
318 321 8.249638 TGATTTGAAATTTTGTGACAAGAGACA 58.750 29.630 0.00 0.00 0.00 3.41
319 322 8.633075 TGATTTGAAATTTTGTGACAAGAGAC 57.367 30.769 0.00 0.00 0.00 3.36
320 323 9.650539 TTTGATTTGAAATTTTGTGACAAGAGA 57.349 25.926 0.00 0.00 0.00 3.10
325 328 9.699985 CGAATTTTGATTTGAAATTTTGTGACA 57.300 25.926 0.00 0.00 36.96 3.58
326 329 9.913451 TCGAATTTTGATTTGAAATTTTGTGAC 57.087 25.926 0.00 0.00 36.96 3.67
334 337 9.384682 GCAATGTTTCGAATTTTGATTTGAAAT 57.615 25.926 14.33 0.00 42.52 2.17
335 338 8.610896 AGCAATGTTTCGAATTTTGATTTGAAA 58.389 25.926 15.39 9.40 40.00 2.69
336 339 8.140677 AGCAATGTTTCGAATTTTGATTTGAA 57.859 26.923 15.39 0.00 33.42 2.69
337 340 7.358270 CGAGCAATGTTTCGAATTTTGATTTGA 60.358 33.333 15.39 0.00 39.06 2.69
338 341 6.728854 CGAGCAATGTTTCGAATTTTGATTTG 59.271 34.615 15.39 7.74 39.06 2.32
339 342 6.640499 TCGAGCAATGTTTCGAATTTTGATTT 59.360 30.769 15.39 4.36 42.27 2.17
340 343 6.148948 TCGAGCAATGTTTCGAATTTTGATT 58.851 32.000 15.39 6.14 42.27 2.57
341 344 5.698832 TCGAGCAATGTTTCGAATTTTGAT 58.301 33.333 15.39 10.93 42.27 2.57
342 345 5.049749 TCTCGAGCAATGTTTCGAATTTTGA 60.050 36.000 7.81 4.60 44.25 2.69
343 346 5.146460 TCTCGAGCAATGTTTCGAATTTTG 58.854 37.500 7.81 4.87 44.25 2.44
344 347 5.356882 TCTCGAGCAATGTTTCGAATTTT 57.643 34.783 7.81 0.00 44.25 1.82
345 348 5.551760 ATCTCGAGCAATGTTTCGAATTT 57.448 34.783 7.81 0.00 44.25 1.82
346 349 6.851222 ATATCTCGAGCAATGTTTCGAATT 57.149 33.333 7.81 6.31 44.25 2.17
347 350 7.946655 TTATATCTCGAGCAATGTTTCGAAT 57.053 32.000 7.81 10.43 44.25 3.34
348 351 7.764695 TTTATATCTCGAGCAATGTTTCGAA 57.235 32.000 7.81 0.00 44.25 3.71
349 352 7.764695 TTTTATATCTCGAGCAATGTTTCGA 57.235 32.000 7.81 10.47 42.91 3.71
350 353 8.886080 CATTTTTATATCTCGAGCAATGTTTCG 58.114 33.333 7.81 3.56 38.13 3.46
351 354 9.935682 TCATTTTTATATCTCGAGCAATGTTTC 57.064 29.630 7.81 0.00 0.00 2.78
352 355 9.722056 GTCATTTTTATATCTCGAGCAATGTTT 57.278 29.630 7.81 0.00 0.00 2.83
353 356 8.892723 TGTCATTTTTATATCTCGAGCAATGTT 58.107 29.630 7.81 0.00 0.00 2.71
354 357 8.437360 TGTCATTTTTATATCTCGAGCAATGT 57.563 30.769 7.81 0.00 0.00 2.71
355 358 9.720667 TTTGTCATTTTTATATCTCGAGCAATG 57.279 29.630 7.81 7.21 0.00 2.82
379 382 9.328845 GCCCATTATCACATTGATGTTAAATTT 57.671 29.630 0.00 0.00 39.39 1.82
380 383 7.933033 GGCCCATTATCACATTGATGTTAAATT 59.067 33.333 0.00 0.00 39.39 1.82
381 384 7.070946 TGGCCCATTATCACATTGATGTTAAAT 59.929 33.333 0.00 0.00 39.39 1.40
382 385 6.382282 TGGCCCATTATCACATTGATGTTAAA 59.618 34.615 0.00 0.00 39.39 1.52
383 386 5.896106 TGGCCCATTATCACATTGATGTTAA 59.104 36.000 0.00 0.00 39.39 2.01
384 387 5.453158 TGGCCCATTATCACATTGATGTTA 58.547 37.500 0.00 0.00 39.39 2.41
385 388 4.288398 TGGCCCATTATCACATTGATGTT 58.712 39.130 0.00 0.00 39.39 2.71
386 389 3.913509 TGGCCCATTATCACATTGATGT 58.086 40.909 0.00 0.00 42.84 3.06
387 390 4.940905 TTGGCCCATTATCACATTGATG 57.059 40.909 0.00 0.00 37.70 3.07
388 391 5.842328 AGATTTGGCCCATTATCACATTGAT 59.158 36.000 0.00 0.00 40.72 2.57
389 392 5.210430 AGATTTGGCCCATTATCACATTGA 58.790 37.500 0.00 0.00 0.00 2.57
390 393 5.540400 AGATTTGGCCCATTATCACATTG 57.460 39.130 0.00 0.00 0.00 2.82
391 394 7.673641 TTTAGATTTGGCCCATTATCACATT 57.326 32.000 0.00 0.00 0.00 2.71
392 395 6.239402 GCTTTAGATTTGGCCCATTATCACAT 60.239 38.462 0.00 0.00 0.00 3.21
393 396 5.068987 GCTTTAGATTTGGCCCATTATCACA 59.931 40.000 0.00 0.00 0.00 3.58
394 397 5.302823 AGCTTTAGATTTGGCCCATTATCAC 59.697 40.000 0.00 0.00 0.00 3.06
395 398 5.457686 AGCTTTAGATTTGGCCCATTATCA 58.542 37.500 0.00 0.00 0.00 2.15
396 399 5.536161 TGAGCTTTAGATTTGGCCCATTATC 59.464 40.000 0.00 0.00 0.00 1.75
397 400 5.457686 TGAGCTTTAGATTTGGCCCATTAT 58.542 37.500 0.00 0.00 0.00 1.28
398 401 4.865905 TGAGCTTTAGATTTGGCCCATTA 58.134 39.130 0.00 0.00 0.00 1.90
399 402 3.711863 TGAGCTTTAGATTTGGCCCATT 58.288 40.909 0.00 0.00 0.00 3.16
400 403 3.386932 TGAGCTTTAGATTTGGCCCAT 57.613 42.857 0.00 0.00 0.00 4.00
401 404 2.825532 GTTGAGCTTTAGATTTGGCCCA 59.174 45.455 0.00 0.00 0.00 5.36
402 405 3.092301 AGTTGAGCTTTAGATTTGGCCC 58.908 45.455 0.00 0.00 0.00 5.80
403 406 4.790765 AAGTTGAGCTTTAGATTTGGCC 57.209 40.909 0.00 0.00 32.57 5.36
404 407 6.856895 ACATAAGTTGAGCTTTAGATTTGGC 58.143 36.000 0.00 0.00 38.57 4.52
415 418 9.893305 GTTTTTGTACATAACATAAGTTGAGCT 57.107 29.630 13.55 0.00 38.10 4.09
416 419 9.893305 AGTTTTTGTACATAACATAAGTTGAGC 57.107 29.630 18.23 0.00 38.10 4.26
436 439 9.450807 CTCGAGATACAAAAATGACAAGTTTTT 57.549 29.630 6.58 0.00 38.82 1.94
437 440 7.591426 GCTCGAGATACAAAAATGACAAGTTTT 59.409 33.333 18.75 0.00 34.05 2.43
438 441 7.078228 GCTCGAGATACAAAAATGACAAGTTT 58.922 34.615 18.75 0.00 0.00 2.66
439 442 6.204688 TGCTCGAGATACAAAAATGACAAGTT 59.795 34.615 18.75 0.00 0.00 2.66
440 443 5.700832 TGCTCGAGATACAAAAATGACAAGT 59.299 36.000 18.75 0.00 0.00 3.16
441 444 6.169419 TGCTCGAGATACAAAAATGACAAG 57.831 37.500 18.75 0.00 0.00 3.16
442 445 6.552859 TTGCTCGAGATACAAAAATGACAA 57.447 33.333 18.75 2.82 0.00 3.18
443 446 6.149308 ACATTGCTCGAGATACAAAAATGACA 59.851 34.615 18.75 0.00 0.00 3.58
444 447 6.546395 ACATTGCTCGAGATACAAAAATGAC 58.454 36.000 18.75 0.00 0.00 3.06
445 448 6.741992 ACATTGCTCGAGATACAAAAATGA 57.258 33.333 18.75 0.00 0.00 2.57
446 449 7.253092 CGAAACATTGCTCGAGATACAAAAATG 60.253 37.037 18.75 14.25 37.23 2.32
447 450 6.742718 CGAAACATTGCTCGAGATACAAAAAT 59.257 34.615 18.75 0.84 37.23 1.82
448 451 6.073494 TCGAAACATTGCTCGAGATACAAAAA 60.073 34.615 18.75 0.00 39.07 1.94
449 452 5.407084 TCGAAACATTGCTCGAGATACAAAA 59.593 36.000 18.75 0.13 39.07 2.44
450 453 4.926832 TCGAAACATTGCTCGAGATACAAA 59.073 37.500 18.75 2.00 39.07 2.83
451 454 4.490743 TCGAAACATTGCTCGAGATACAA 58.509 39.130 18.75 11.56 39.07 2.41
452 455 4.104696 TCGAAACATTGCTCGAGATACA 57.895 40.909 18.75 1.12 39.07 2.29
453 456 5.643339 ATTCGAAACATTGCTCGAGATAC 57.357 39.130 18.75 0.00 44.25 2.24
454 457 6.662414 AAATTCGAAACATTGCTCGAGATA 57.338 33.333 18.75 2.54 44.25 1.98
455 458 5.551760 AAATTCGAAACATTGCTCGAGAT 57.448 34.783 18.75 0.00 44.25 2.75
456 459 5.049749 TCAAAATTCGAAACATTGCTCGAGA 60.050 36.000 18.75 0.00 44.25 4.04
457 460 5.146460 TCAAAATTCGAAACATTGCTCGAG 58.854 37.500 8.45 8.45 44.25 4.04
458 461 5.102020 TCAAAATTCGAAACATTGCTCGA 57.898 34.783 0.00 7.21 42.05 4.04
459 462 5.997732 ATCAAAATTCGAAACATTGCTCG 57.002 34.783 0.00 3.07 36.39 5.03
460 463 8.619146 TCATATCAAAATTCGAAACATTGCTC 57.381 30.769 0.00 0.00 0.00 4.26
461 464 8.984891 TTCATATCAAAATTCGAAACATTGCT 57.015 26.923 0.00 2.54 0.00 3.91
482 485 9.166173 TCGATGTCTCTTATCACAAAATTTCAT 57.834 29.630 0.00 0.00 0.00 2.57
483 486 8.546597 TCGATGTCTCTTATCACAAAATTTCA 57.453 30.769 0.00 0.00 0.00 2.69
484 487 9.430838 CATCGATGTCTCTTATCACAAAATTTC 57.569 33.333 17.50 0.00 0.00 2.17
485 488 8.950210 ACATCGATGTCTCTTATCACAAAATTT 58.050 29.630 25.18 0.00 35.87 1.82
486 489 8.498054 ACATCGATGTCTCTTATCACAAAATT 57.502 30.769 25.18 0.00 35.87 1.82
487 490 8.498054 AACATCGATGTCTCTTATCACAAAAT 57.502 30.769 30.06 6.94 40.80 1.82
488 491 7.064609 GGAACATCGATGTCTCTTATCACAAAA 59.935 37.037 30.06 0.00 40.80 2.44
489 492 6.535150 GGAACATCGATGTCTCTTATCACAAA 59.465 38.462 30.06 0.00 40.80 2.83
490 493 6.042777 GGAACATCGATGTCTCTTATCACAA 58.957 40.000 30.06 0.00 40.80 3.33
491 494 5.592054 GGAACATCGATGTCTCTTATCACA 58.408 41.667 30.06 0.00 40.80 3.58
492 495 4.677378 CGGAACATCGATGTCTCTTATCAC 59.323 45.833 30.06 14.94 40.80 3.06
493 496 4.338400 ACGGAACATCGATGTCTCTTATCA 59.662 41.667 30.06 0.00 40.80 2.15
494 497 4.861210 ACGGAACATCGATGTCTCTTATC 58.139 43.478 30.06 21.40 40.80 1.75
495 498 4.920640 ACGGAACATCGATGTCTCTTAT 57.079 40.909 30.06 14.44 40.80 1.73
496 499 4.713824 AACGGAACATCGATGTCTCTTA 57.286 40.909 30.06 0.00 40.80 2.10
497 500 3.594603 AACGGAACATCGATGTCTCTT 57.405 42.857 30.06 15.59 40.80 2.85
498 501 4.713824 TTAACGGAACATCGATGTCTCT 57.286 40.909 30.06 15.98 40.80 3.10
499 502 4.804139 ACATTAACGGAACATCGATGTCTC 59.196 41.667 30.06 25.22 40.80 3.36
500 503 4.566759 CACATTAACGGAACATCGATGTCT 59.433 41.667 30.06 19.72 40.80 3.41
501 504 4.782195 GCACATTAACGGAACATCGATGTC 60.782 45.833 30.06 21.59 40.80 3.06
502 505 3.063452 GCACATTAACGGAACATCGATGT 59.937 43.478 25.18 25.18 44.20 3.06
503 506 3.309682 AGCACATTAACGGAACATCGATG 59.690 43.478 23.68 23.68 0.00 3.84
504 507 3.309682 CAGCACATTAACGGAACATCGAT 59.690 43.478 0.00 0.00 0.00 3.59
505 508 2.670905 CAGCACATTAACGGAACATCGA 59.329 45.455 0.00 0.00 0.00 3.59
506 509 2.415168 ACAGCACATTAACGGAACATCG 59.585 45.455 0.00 0.00 0.00 3.84
507 510 5.734855 ATACAGCACATTAACGGAACATC 57.265 39.130 0.00 0.00 0.00 3.06
508 511 6.509418 AAATACAGCACATTAACGGAACAT 57.491 33.333 0.00 0.00 0.00 2.71
509 512 5.950758 AAATACAGCACATTAACGGAACA 57.049 34.783 0.00 0.00 0.00 3.18
546 549 9.267096 GCACGAAAAACATTTTTAAATTGTTCA 57.733 25.926 15.32 0.00 40.21 3.18
547 550 9.267096 TGCACGAAAAACATTTTTAAATTGTTC 57.733 25.926 15.32 5.90 40.21 3.18
548 551 9.780413 ATGCACGAAAAACATTTTTAAATTGTT 57.220 22.222 10.87 10.87 40.21 2.83
549 552 9.780413 AATGCACGAAAAACATTTTTAAATTGT 57.220 22.222 2.39 0.08 40.21 2.71
552 555 9.994432 TCAAATGCACGAAAAACATTTTTAAAT 57.006 22.222 2.39 0.00 40.94 1.40
553 556 9.825972 TTCAAATGCACGAAAAACATTTTTAAA 57.174 22.222 2.39 0.00 40.94 1.52
554 557 9.483062 CTTCAAATGCACGAAAAACATTTTTAA 57.517 25.926 2.39 0.00 40.94 1.52
555 558 7.637907 GCTTCAAATGCACGAAAAACATTTTTA 59.362 29.630 2.39 0.00 40.94 1.52
556 559 6.468637 GCTTCAAATGCACGAAAAACATTTTT 59.531 30.769 2.00 2.00 40.94 1.94
557 560 5.964751 GCTTCAAATGCACGAAAAACATTTT 59.035 32.000 0.00 0.00 40.94 1.82
558 561 5.064452 TGCTTCAAATGCACGAAAAACATTT 59.936 32.000 0.00 0.00 43.01 2.32
559 562 4.569966 TGCTTCAAATGCACGAAAAACATT 59.430 33.333 0.00 0.00 35.31 2.71
560 563 4.118410 TGCTTCAAATGCACGAAAAACAT 58.882 34.783 0.00 0.00 35.31 2.71
561 564 3.515630 TGCTTCAAATGCACGAAAAACA 58.484 36.364 0.00 0.00 35.31 2.83
562 565 4.661402 CGATGCTTCAAATGCACGAAAAAC 60.661 41.667 0.00 0.00 43.59 2.43
563 566 3.424861 CGATGCTTCAAATGCACGAAAAA 59.575 39.130 0.00 0.00 43.59 1.94
564 567 2.979151 CGATGCTTCAAATGCACGAAAA 59.021 40.909 0.00 0.00 43.59 2.29
565 568 2.583739 CGATGCTTCAAATGCACGAAA 58.416 42.857 0.00 0.00 43.59 3.46
566 569 1.135717 CCGATGCTTCAAATGCACGAA 60.136 47.619 0.00 0.00 43.59 3.85
567 570 0.447406 CCGATGCTTCAAATGCACGA 59.553 50.000 0.00 0.00 43.59 4.35
568 571 0.523968 CCCGATGCTTCAAATGCACG 60.524 55.000 0.00 0.00 43.59 5.34
569 572 0.810648 TCCCGATGCTTCAAATGCAC 59.189 50.000 0.00 0.00 43.59 4.57
570 573 1.097232 CTCCCGATGCTTCAAATGCA 58.903 50.000 0.00 0.00 44.95 3.96
571 574 1.098050 ACTCCCGATGCTTCAAATGC 58.902 50.000 0.08 0.00 0.00 3.56
572 575 2.614057 GGTACTCCCGATGCTTCAAATG 59.386 50.000 0.08 0.00 0.00 2.32
573 576 2.421529 GGGTACTCCCGATGCTTCAAAT 60.422 50.000 0.08 0.00 44.74 2.32
574 577 1.065709 GGGTACTCCCGATGCTTCAAA 60.066 52.381 0.08 0.00 44.74 2.69
575 578 0.539986 GGGTACTCCCGATGCTTCAA 59.460 55.000 0.08 0.00 44.74 2.69
576 579 2.208527 GGGTACTCCCGATGCTTCA 58.791 57.895 0.08 0.00 44.74 3.02
586 589 2.998949 CCAGGCTTGGGGTACTCC 59.001 66.667 4.21 4.21 41.05 3.85
594 597 2.160721 TCTAGTACTCCCAGGCTTGG 57.839 55.000 8.15 8.15 44.60 3.61
595 598 4.475345 AGTATCTAGTACTCCCAGGCTTG 58.525 47.826 0.00 0.00 39.46 4.01
596 599 4.817874 AGTATCTAGTACTCCCAGGCTT 57.182 45.455 0.00 0.00 39.46 4.35
597 600 4.817874 AAGTATCTAGTACTCCCAGGCT 57.182 45.455 0.00 0.00 42.83 4.58
598 601 4.281435 GGAAAGTATCTAGTACTCCCAGGC 59.719 50.000 0.00 0.00 42.83 4.85
599 602 4.833938 GGGAAAGTATCTAGTACTCCCAGG 59.166 50.000 0.00 0.00 42.96 4.45
600 603 4.833938 GGGGAAAGTATCTAGTACTCCCAG 59.166 50.000 19.76 0.00 44.23 4.45
601 604 4.233521 TGGGGAAAGTATCTAGTACTCCCA 59.766 45.833 19.76 18.57 45.66 4.37
602 605 4.588106 GTGGGGAAAGTATCTAGTACTCCC 59.412 50.000 0.00 14.74 42.83 4.30
603 606 5.456779 AGTGGGGAAAGTATCTAGTACTCC 58.543 45.833 0.00 0.00 42.83 3.85
604 607 6.040729 GGAAGTGGGGAAAGTATCTAGTACTC 59.959 46.154 0.00 0.00 42.83 2.59
605 608 5.898397 GGAAGTGGGGAAAGTATCTAGTACT 59.102 44.000 0.00 0.00 45.56 2.73
606 609 5.659971 TGGAAGTGGGGAAAGTATCTAGTAC 59.340 44.000 0.00 0.00 0.00 2.73
607 610 5.659971 GTGGAAGTGGGGAAAGTATCTAGTA 59.340 44.000 0.00 0.00 0.00 1.82
608 611 4.470304 GTGGAAGTGGGGAAAGTATCTAGT 59.530 45.833 0.00 0.00 0.00 2.57
609 612 4.717280 AGTGGAAGTGGGGAAAGTATCTAG 59.283 45.833 0.00 0.00 0.00 2.43
610 613 4.695606 AGTGGAAGTGGGGAAAGTATCTA 58.304 43.478 0.00 0.00 0.00 1.98
611 614 3.532102 AGTGGAAGTGGGGAAAGTATCT 58.468 45.455 0.00 0.00 0.00 1.98
612 615 5.183969 GTTAGTGGAAGTGGGGAAAGTATC 58.816 45.833 0.00 0.00 0.00 2.24
613 616 4.018688 GGTTAGTGGAAGTGGGGAAAGTAT 60.019 45.833 0.00 0.00 0.00 2.12
614 617 3.328637 GGTTAGTGGAAGTGGGGAAAGTA 59.671 47.826 0.00 0.00 0.00 2.24
615 618 2.107726 GGTTAGTGGAAGTGGGGAAAGT 59.892 50.000 0.00 0.00 0.00 2.66
616 619 2.375509 AGGTTAGTGGAAGTGGGGAAAG 59.624 50.000 0.00 0.00 0.00 2.62
617 620 2.424793 AGGTTAGTGGAAGTGGGGAAA 58.575 47.619 0.00 0.00 0.00 3.13
618 621 2.127651 AGGTTAGTGGAAGTGGGGAA 57.872 50.000 0.00 0.00 0.00 3.97
619 622 2.127651 AAGGTTAGTGGAAGTGGGGA 57.872 50.000 0.00 0.00 0.00 4.81
620 623 3.118000 GGATAAGGTTAGTGGAAGTGGGG 60.118 52.174 0.00 0.00 0.00 4.96
621 624 3.118000 GGGATAAGGTTAGTGGAAGTGGG 60.118 52.174 0.00 0.00 0.00 4.61
631 634 1.692519 CGGACTGGGGGATAAGGTTAG 59.307 57.143 0.00 0.00 0.00 2.34
724 736 2.564975 GGCGAGAAGACGAACGGA 59.435 61.111 0.00 0.00 35.09 4.69
747 759 2.094675 CCAAGGCCCAAGATGTGTAAG 58.905 52.381 0.00 0.00 0.00 2.34
906 924 4.662278 TCCAAATCCGAATCCAGAAAACT 58.338 39.130 0.00 0.00 0.00 2.66
957 975 3.096092 AGGCAAGAAAGACAAACCAACA 58.904 40.909 0.00 0.00 0.00 3.33
1033 1053 1.889829 CCTAGCTAGATGCCGTAAGCT 59.110 52.381 22.70 0.95 46.58 3.74
1034 1054 1.670380 GCCTAGCTAGATGCCGTAAGC 60.670 57.143 22.70 9.50 44.23 3.09
1035 1055 1.613925 TGCCTAGCTAGATGCCGTAAG 59.386 52.381 22.70 3.00 44.23 2.34
1036 1056 1.340248 GTGCCTAGCTAGATGCCGTAA 59.660 52.381 22.70 0.00 44.23 3.18
1037 1057 0.959553 GTGCCTAGCTAGATGCCGTA 59.040 55.000 22.70 1.42 44.23 4.02
1038 1058 1.742768 GTGCCTAGCTAGATGCCGT 59.257 57.895 22.70 0.00 44.23 5.68
1039 1059 1.005630 GGTGCCTAGCTAGATGCCG 60.006 63.158 22.70 5.97 44.23 5.69
1040 1060 1.373059 GGGTGCCTAGCTAGATGCC 59.627 63.158 22.70 18.00 44.23 4.40
1041 1061 1.005630 CGGGTGCCTAGCTAGATGC 60.006 63.158 22.70 17.45 43.29 3.91
1044 1064 1.822613 CGTCGGGTGCCTAGCTAGA 60.823 63.158 22.70 0.00 0.00 2.43
1144 1164 0.250901 ATATTCTCCATGGGCGGTGC 60.251 55.000 13.02 0.00 0.00 5.01
1146 1166 0.401738 CCATATTCTCCATGGGCGGT 59.598 55.000 13.02 0.00 39.49 5.68
1269 1295 2.029369 GTGTACACCGACCGCCAA 59.971 61.111 15.42 0.00 0.00 4.52
1394 1420 3.825908 ATTTGTAGGCCCTCTTTTCCA 57.174 42.857 0.00 0.00 0.00 3.53
1413 1439 2.136026 GGTGGATCAGGGAGGGTTAAT 58.864 52.381 0.00 0.00 0.00 1.40
1538 1564 3.018149 AGAGTAATCACTGACGGGAGAC 58.982 50.000 0.00 0.00 34.21 3.36
1726 1759 2.472695 ATGTAGCTTCCTGTTTGCGA 57.527 45.000 0.00 0.00 0.00 5.10
1824 1857 2.952310 GCATTCCTGATAGTTCCAACCC 59.048 50.000 0.00 0.00 0.00 4.11
1839 1872 3.817647 GACCATCCTTGTAGATGCATTCC 59.182 47.826 0.00 0.00 41.98 3.01
2169 2213 5.337571 GGATATTCTTCCACACTGAGACACA 60.338 44.000 0.00 0.00 35.72 3.72
2194 2238 5.329035 AGACACAGTTTGCTTTCAATTGT 57.671 34.783 5.13 0.00 33.46 2.71
2258 2302 4.799678 AGAACGCCTATATCACGATGAAG 58.200 43.478 0.00 0.00 0.00 3.02
2259 2303 4.848562 AGAACGCCTATATCACGATGAA 57.151 40.909 0.00 0.00 0.00 2.57
2275 2319 5.107875 GCTGCTGTTTTCCAAATTTAGAACG 60.108 40.000 0.00 0.00 0.00 3.95
2294 2338 1.891150 CACAATTTCTTCCCTGCTGCT 59.109 47.619 0.00 0.00 0.00 4.24
2319 2363 1.484038 TGGCCAGGTGCAATAAATCC 58.516 50.000 0.00 0.00 43.89 3.01
2354 2398 2.615912 GCATCATTCTAAGACTGGGTGC 59.384 50.000 0.00 0.00 0.00 5.01
2531 2856 3.698040 CCATCTAAGCTCCAACTTTGCAT 59.302 43.478 0.00 0.00 0.00 3.96
2584 2909 5.865085 TCTTCCTTGTACAACATAGTTGCT 58.135 37.500 3.59 1.10 0.00 3.91
2591 2916 8.812972 TCAGTAACTATCTTCCTTGTACAACAT 58.187 33.333 3.59 0.00 0.00 2.71
2850 3341 8.840833 TGGAAACCAAATAAAATCCTAAAAGC 57.159 30.769 0.00 0.00 0.00 3.51
2956 3468 8.912988 CAAAAAGGCAGGGAACATAATCTAATA 58.087 33.333 0.00 0.00 0.00 0.98
3110 3628 4.436986 GCGGATCTTGTAGCAAAAACCTAC 60.437 45.833 0.00 0.00 36.55 3.18
3131 3649 4.034394 TCATTAGTGCAGCTTCAAATAGCG 59.966 41.667 0.00 0.00 45.82 4.26


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

AutoCloner maintained by Alex Coulton.