Multiple sequence alignment - TraesCS2D01G337600

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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 TraesCS2D01G337600 chr2D 100.000 3178 0 0 1 3178 431386745 431383568 0.000000e+00 5869
1 TraesCS2D01G337600 chr2D 95.594 1430 43 4 586 2012 431006178 431004766 0.000000e+00 2274
2 TraesCS2D01G337600 chr2D 85.962 1040 82 29 892 1895 431429174 431428163 0.000000e+00 1053
3 TraesCS2D01G337600 chr2D 97.505 521 12 1 2040 2560 431004771 431004252 0.000000e+00 889
4 TraesCS2D01G337600 chr2D 87.732 701 58 14 1882 2559 431425972 431425277 0.000000e+00 793
5 TraesCS2D01G337600 chr2D 96.774 403 12 1 2777 3178 110859126 110859528 0.000000e+00 671
6 TraesCS2D01G337600 chr2D 83.475 587 64 19 1 568 431017038 431016466 1.690000e-142 516
7 TraesCS2D01G337600 chr2D 98.544 206 3 0 2561 2766 520536544 520536749 6.480000e-97 364
8 TraesCS2D01G337600 chr2B 93.682 1662 65 14 913 2560 509575122 509573487 0.000000e+00 2451
9 TraesCS2D01G337600 chr2B 97.238 1086 27 2 903 1986 509997434 509996350 0.000000e+00 1836
10 TraesCS2D01G337600 chr2B 84.681 1756 150 43 859 2559 510062327 510060636 0.000000e+00 1642
11 TraesCS2D01G337600 chr2B 85.332 1493 145 38 890 2342 510350501 510349043 0.000000e+00 1476
12 TraesCS2D01G337600 chr2B 82.602 1253 113 50 1348 2545 509707444 509706242 0.000000e+00 1009
13 TraesCS2D01G337600 chr2B 95.697 581 19 3 1985 2560 509996188 509995609 0.000000e+00 929
14 TraesCS2D01G337600 chr2B 95.533 403 17 1 2777 3178 160199729 160200131 0.000000e+00 643
15 TraesCS2D01G337600 chr2B 94.192 396 22 1 2782 3176 161477394 161476999 1.260000e-168 603
16 TraesCS2D01G337600 chr2B 88.713 505 25 10 859 1355 509713351 509712871 3.530000e-164 588
17 TraesCS2D01G337600 chr2B 91.228 342 27 3 574 913 510052981 510052641 2.230000e-126 462
18 TraesCS2D01G337600 chr2B 89.498 219 15 6 2346 2559 510348954 510348739 1.450000e-68 270
19 TraesCS2D01G337600 chr5D 98.382 618 10 0 2561 3178 254525982 254526599 0.000000e+00 1086
20 TraesCS2D01G337600 chr5D 87.383 428 48 6 8 431 377148337 377147912 1.330000e-133 486
21 TraesCS2D01G337600 chr5D 87.037 432 52 4 2 431 10761532 10761961 4.770000e-133 484
22 TraesCS2D01G337600 chr5D 96.016 251 6 4 2928 3178 513661145 513660899 3.820000e-109 405
23 TraesCS2D01G337600 chr5D 97.059 204 6 0 2561 2764 254527056 254526853 8.440000e-91 344
24 TraesCS2D01G337600 chr2A 85.912 795 77 17 1792 2557 554954160 554954948 0.000000e+00 815
25 TraesCS2D01G337600 chr2A 94.175 412 14 2 2777 3178 107218801 107219212 1.250000e-173 619
26 TraesCS2D01G337600 chr2A 93.333 210 13 1 889 1098 554953002 554953210 3.080000e-80 309
27 TraesCS2D01G337600 chr5B 86.464 591 59 11 1989 2559 100837780 100838369 2.080000e-176 628
28 TraesCS2D01G337600 chr6D 88.018 434 48 4 1 431 61175681 61175249 7.860000e-141 510
29 TraesCS2D01G337600 chr6D 87.298 433 51 4 1 431 336515831 336516261 2.850000e-135 492
30 TraesCS2D01G337600 chr6D 98.467 261 4 0 2918 3178 340107342 340107602 8.030000e-126 460
31 TraesCS2D01G337600 chr7D 95.806 310 12 1 2561 2870 109950538 109950230 1.700000e-137 499
32 TraesCS2D01G337600 chr7D 87.067 433 52 4 1 431 554242091 554241661 1.330000e-133 486
33 TraesCS2D01G337600 chr7D 86.499 437 52 7 1 434 111350619 111350187 1.030000e-129 473
34 TraesCS2D01G337600 chr7D 96.552 232 8 0 2558 2789 109949085 109949316 4.970000e-103 385
35 TraesCS2D01G337600 chr4D 86.792 424 53 3 10 431 93351195 93350773 1.330000e-128 470
36 TraesCS2D01G337600 chr4D 97.585 207 5 0 2560 2766 29363141 29362935 3.900000e-94 355
37 TraesCS2D01G337600 chr4D 97.585 207 5 0 2560 2766 29363744 29363538 3.900000e-94 355
38 TraesCS2D01G337600 chr4D 94.884 215 10 1 2561 2775 30752271 30752058 5.080000e-88 335
39 TraesCS2D01G337600 chr4D 97.826 138 3 0 2795 2932 30751311 30751448 4.100000e-59 239
40 TraesCS2D01G337600 chr1D 86.512 430 55 3 3 430 408823824 408823396 1.330000e-128 470
41 TraesCS2D01G337600 chr1D 97.101 207 5 1 2560 2766 458729601 458729806 6.520000e-92 348


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 TraesCS2D01G337600 chr2D 431383568 431386745 3177 True 5869.0 5869 100.0000 1 3178 1 chr2D.!!$R2 3177
1 TraesCS2D01G337600 chr2D 431004252 431006178 1926 True 1581.5 2274 96.5495 586 2560 2 chr2D.!!$R3 1974
2 TraesCS2D01G337600 chr2D 431425277 431429174 3897 True 923.0 1053 86.8470 892 2559 2 chr2D.!!$R4 1667
3 TraesCS2D01G337600 chr2D 431016466 431017038 572 True 516.0 516 83.4750 1 568 1 chr2D.!!$R1 567
4 TraesCS2D01G337600 chr2B 509573487 509575122 1635 True 2451.0 2451 93.6820 913 2560 1 chr2B.!!$R2 1647
5 TraesCS2D01G337600 chr2B 510060636 510062327 1691 True 1642.0 1642 84.6810 859 2559 1 chr2B.!!$R6 1700
6 TraesCS2D01G337600 chr2B 509995609 509997434 1825 True 1382.5 1836 96.4675 903 2560 2 chr2B.!!$R7 1657
7 TraesCS2D01G337600 chr2B 509706242 509707444 1202 True 1009.0 1009 82.6020 1348 2545 1 chr2B.!!$R3 1197
8 TraesCS2D01G337600 chr2B 510348739 510350501 1762 True 873.0 1476 87.4150 890 2559 2 chr2B.!!$R8 1669
9 TraesCS2D01G337600 chr5D 254525982 254526599 617 False 1086.0 1086 98.3820 2561 3178 1 chr5D.!!$F2 617
10 TraesCS2D01G337600 chr2A 554953002 554954948 1946 False 562.0 815 89.6225 889 2557 2 chr2A.!!$F2 1668
11 TraesCS2D01G337600 chr5B 100837780 100838369 589 False 628.0 628 86.4640 1989 2559 1 chr5B.!!$F1 570
12 TraesCS2D01G337600 chr4D 29362935 29363744 809 True 355.0 355 97.5850 2560 2766 2 chr4D.!!$R3 206

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
328 330 0.178987 ACTCGGACTATCGGCATCCT 60.179 55.0 0.0 0.0 0.0 3.24 F
534 536 0.250467 GCAGACACAGAGGGCAAGAA 60.250 55.0 0.0 0.0 0.0 2.52 F
726 729 0.388006 CCGCACGTACATCTGTGTGA 60.388 55.0 12.1 0.0 46.7 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 4784 0.608308 AAACCGCTAGGCCTTTGTCC 60.608 55.000 12.58 0.00 42.76 4.02 R
2070 5130 6.469782 AGCTGGATCAACAAGAAAGAAAAA 57.530 33.333 0.00 0.00 0.00 1.94 R
2571 5769 2.162408 GCCTCAATTGTGGTACTTCTGC 59.838 50.000 23.73 6.83 0.00 4.26 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
39 41 3.426309 ATGGCAGGGATCTTGGCGG 62.426 63.158 15.60 0.00 0.00 6.13
41 43 4.802051 GCAGGGATCTTGGCGGCA 62.802 66.667 7.97 7.97 0.00 5.69
45 47 3.599704 GGATCTTGGCGGCATGGC 61.600 66.667 22.14 9.69 45.12 4.40
64 66 2.651361 CAGTGGAGACTCGGCGTT 59.349 61.111 6.85 0.00 0.00 4.84
66 68 2.504244 GTGGAGACTCGGCGTTCG 60.504 66.667 6.85 0.00 40.90 3.95
99 101 3.898509 CTCGCGCAGGAGGAGGAG 61.899 72.222 8.75 0.00 0.00 3.69
109 111 1.305718 GAGGAGGAGGCTGTCTGGT 60.306 63.158 0.00 0.00 0.00 4.00
129 131 3.576356 CATGGTGGCGTCGATGGC 61.576 66.667 23.33 23.33 0.00 4.40
132 134 4.451150 GGTGGCGTCGATGGCAGA 62.451 66.667 31.74 10.62 45.88 4.26
140 142 1.681538 GTCGATGGCAGAGAGGTCTA 58.318 55.000 0.00 0.00 0.00 2.59
141 143 2.025155 GTCGATGGCAGAGAGGTCTAA 58.975 52.381 0.00 0.00 0.00 2.10
143 145 1.268794 CGATGGCAGAGAGGTCTAACG 60.269 57.143 0.00 0.00 0.00 3.18
150 152 1.015868 GAGAGGTCTAACGAGGTCGG 58.984 60.000 4.13 0.00 44.95 4.79
162 164 1.505425 GAGGTCGGTGCGTTAGTTTT 58.495 50.000 0.00 0.00 0.00 2.43
171 173 3.545633 GTGCGTTAGTTTTTGCTCTGAG 58.454 45.455 0.00 0.00 0.00 3.35
173 175 2.806244 GCGTTAGTTTTTGCTCTGAGGA 59.194 45.455 6.83 0.00 0.00 3.71
181 183 2.723322 TTGCTCTGAGGATGGATTGG 57.277 50.000 6.83 0.00 0.00 3.16
188 190 2.507058 CTGAGGATGGATTGGTGGAAGA 59.493 50.000 0.00 0.00 0.00 2.87
191 193 1.668419 GATGGATTGGTGGAAGACGG 58.332 55.000 0.00 0.00 0.00 4.79
192 194 0.394352 ATGGATTGGTGGAAGACGGC 60.394 55.000 0.00 0.00 0.00 5.68
202 204 4.814294 AAGACGGCGGCGATGACC 62.814 66.667 38.93 19.24 0.00 4.02
206 208 4.293648 CGGCGGCGATGACCCATA 62.294 66.667 29.19 0.00 0.00 2.74
210 212 0.531974 GCGGCGATGACCCATAAGAA 60.532 55.000 12.98 0.00 0.00 2.52
213 215 2.806745 CGGCGATGACCCATAAGAATGT 60.807 50.000 0.00 0.00 0.00 2.71
214 216 2.549754 GGCGATGACCCATAAGAATGTG 59.450 50.000 0.00 0.00 0.00 3.21
221 223 2.093128 ACCCATAAGAATGTGTCGGACC 60.093 50.000 5.55 0.00 0.00 4.46
222 224 2.093181 CCCATAAGAATGTGTCGGACCA 60.093 50.000 5.55 3.82 0.00 4.02
233 235 0.668401 GTCGGACCAGTTTGTACCCG 60.668 60.000 0.00 0.00 38.41 5.28
238 240 2.563702 GACCAGTTTGTACCCGAAACA 58.436 47.619 9.26 0.00 36.03 2.83
309 311 3.006940 GCGATGTCTGTTTGGTATTGGA 58.993 45.455 0.00 0.00 0.00 3.53
312 314 4.330074 CGATGTCTGTTTGGTATTGGACTC 59.670 45.833 0.00 0.00 0.00 3.36
313 315 3.659786 TGTCTGTTTGGTATTGGACTCG 58.340 45.455 0.00 0.00 0.00 4.18
314 316 3.000727 GTCTGTTTGGTATTGGACTCGG 58.999 50.000 0.00 0.00 0.00 4.63
315 317 2.901192 TCTGTTTGGTATTGGACTCGGA 59.099 45.455 0.00 0.00 0.00 4.55
316 318 3.000727 CTGTTTGGTATTGGACTCGGAC 58.999 50.000 0.00 0.00 0.00 4.79
317 319 2.635915 TGTTTGGTATTGGACTCGGACT 59.364 45.455 0.00 0.00 0.00 3.85
318 320 3.833650 TGTTTGGTATTGGACTCGGACTA 59.166 43.478 0.00 0.00 0.00 2.59
319 321 4.468510 TGTTTGGTATTGGACTCGGACTAT 59.531 41.667 0.00 0.00 0.00 2.12
320 322 4.931661 TTGGTATTGGACTCGGACTATC 57.068 45.455 0.00 0.00 0.00 2.08
321 323 2.882761 TGGTATTGGACTCGGACTATCG 59.117 50.000 0.00 0.00 0.00 2.92
322 324 2.228343 GGTATTGGACTCGGACTATCGG 59.772 54.545 0.00 0.00 0.00 4.18
323 325 0.674534 ATTGGACTCGGACTATCGGC 59.325 55.000 0.00 0.00 0.00 5.54
324 326 0.681887 TTGGACTCGGACTATCGGCA 60.682 55.000 0.00 0.00 0.00 5.69
325 327 0.467474 TGGACTCGGACTATCGGCAT 60.467 55.000 0.00 0.00 0.00 4.40
326 328 0.241481 GGACTCGGACTATCGGCATC 59.759 60.000 0.00 0.00 0.00 3.91
327 329 0.241481 GACTCGGACTATCGGCATCC 59.759 60.000 0.00 0.00 0.00 3.51
328 330 0.178987 ACTCGGACTATCGGCATCCT 60.179 55.000 0.00 0.00 0.00 3.24
329 331 0.962489 CTCGGACTATCGGCATCCTT 59.038 55.000 0.00 0.00 0.00 3.36
330 332 1.341531 CTCGGACTATCGGCATCCTTT 59.658 52.381 0.00 0.00 0.00 3.11
331 333 1.340248 TCGGACTATCGGCATCCTTTC 59.660 52.381 0.00 0.00 0.00 2.62
332 334 1.068588 CGGACTATCGGCATCCTTTCA 59.931 52.381 0.00 0.00 0.00 2.69
333 335 2.289072 CGGACTATCGGCATCCTTTCAT 60.289 50.000 0.00 0.00 0.00 2.57
334 336 3.330267 GGACTATCGGCATCCTTTCATC 58.670 50.000 0.00 0.00 0.00 2.92
335 337 3.244215 GGACTATCGGCATCCTTTCATCA 60.244 47.826 0.00 0.00 0.00 3.07
336 338 4.380531 GACTATCGGCATCCTTTCATCAA 58.619 43.478 0.00 0.00 0.00 2.57
337 339 4.384056 ACTATCGGCATCCTTTCATCAAG 58.616 43.478 0.00 0.00 0.00 3.02
338 340 2.787473 TCGGCATCCTTTCATCAAGT 57.213 45.000 0.00 0.00 0.00 3.16
339 341 2.358957 TCGGCATCCTTTCATCAAGTG 58.641 47.619 0.00 0.00 0.00 3.16
340 342 2.027285 TCGGCATCCTTTCATCAAGTGA 60.027 45.455 0.00 0.00 34.25 3.41
341 343 2.749076 CGGCATCCTTTCATCAAGTGAA 59.251 45.455 0.00 0.00 44.87 3.18
342 344 3.379372 CGGCATCCTTTCATCAAGTGAAT 59.621 43.478 0.00 0.00 45.77 2.57
343 345 4.679662 GGCATCCTTTCATCAAGTGAATG 58.320 43.478 0.00 0.00 45.77 2.67
350 352 6.674694 CTTTCATCAAGTGAATGGGAGTAG 57.325 41.667 0.00 0.00 45.77 2.57
351 353 4.142609 TCATCAAGTGAATGGGAGTAGC 57.857 45.455 0.00 0.00 32.78 3.58
352 354 2.672961 TCAAGTGAATGGGAGTAGCG 57.327 50.000 0.00 0.00 0.00 4.26
353 355 2.176045 TCAAGTGAATGGGAGTAGCGA 58.824 47.619 0.00 0.00 0.00 4.93
354 356 2.094182 TCAAGTGAATGGGAGTAGCGAC 60.094 50.000 0.00 0.00 0.00 5.19
355 357 1.557099 AGTGAATGGGAGTAGCGACA 58.443 50.000 0.00 0.00 0.00 4.35
356 358 1.478510 AGTGAATGGGAGTAGCGACAG 59.521 52.381 0.00 0.00 0.00 3.51
357 359 1.204941 GTGAATGGGAGTAGCGACAGT 59.795 52.381 0.00 0.00 0.00 3.55
358 360 1.899814 TGAATGGGAGTAGCGACAGTT 59.100 47.619 0.00 0.00 0.00 3.16
359 361 2.271800 GAATGGGAGTAGCGACAGTTG 58.728 52.381 0.00 0.00 0.00 3.16
360 362 1.267121 ATGGGAGTAGCGACAGTTGT 58.733 50.000 0.00 0.00 0.00 3.32
361 363 1.045407 TGGGAGTAGCGACAGTTGTT 58.955 50.000 0.00 0.00 0.00 2.83
362 364 1.270094 TGGGAGTAGCGACAGTTGTTG 60.270 52.381 0.00 0.00 0.00 3.33
371 373 3.729526 CGACAGTTGTTGCTAAGATGG 57.270 47.619 0.00 0.00 0.00 3.51
372 374 3.067106 CGACAGTTGTTGCTAAGATGGT 58.933 45.455 0.00 0.00 0.00 3.55
373 375 3.120546 CGACAGTTGTTGCTAAGATGGTG 60.121 47.826 0.00 0.00 0.00 4.17
374 376 3.149196 ACAGTTGTTGCTAAGATGGTGG 58.851 45.455 0.00 0.00 0.00 4.61
375 377 2.095059 CAGTTGTTGCTAAGATGGTGGC 60.095 50.000 0.00 0.00 0.00 5.01
376 378 2.162681 GTTGTTGCTAAGATGGTGGCT 58.837 47.619 0.00 0.00 0.00 4.75
377 379 2.558359 GTTGTTGCTAAGATGGTGGCTT 59.442 45.455 0.00 0.00 0.00 4.35
378 380 2.436417 TGTTGCTAAGATGGTGGCTTC 58.564 47.619 0.00 0.00 0.00 3.86
379 381 2.224744 TGTTGCTAAGATGGTGGCTTCA 60.225 45.455 0.00 0.00 0.00 3.02
380 382 2.408271 TGCTAAGATGGTGGCTTCAG 57.592 50.000 0.00 0.00 0.00 3.02
381 383 1.908619 TGCTAAGATGGTGGCTTCAGA 59.091 47.619 0.00 0.00 0.00 3.27
382 384 2.284190 GCTAAGATGGTGGCTTCAGAC 58.716 52.381 0.00 0.00 0.00 3.51
383 385 2.093235 GCTAAGATGGTGGCTTCAGACT 60.093 50.000 0.00 0.00 0.00 3.24
384 386 3.133003 GCTAAGATGGTGGCTTCAGACTA 59.867 47.826 0.00 0.00 0.00 2.59
385 387 3.618690 AAGATGGTGGCTTCAGACTAC 57.381 47.619 0.00 0.00 0.00 2.73
386 388 1.834263 AGATGGTGGCTTCAGACTACC 59.166 52.381 0.00 0.00 0.00 3.18
387 389 1.834263 GATGGTGGCTTCAGACTACCT 59.166 52.381 0.00 0.00 32.68 3.08
388 390 0.976641 TGGTGGCTTCAGACTACCTG 59.023 55.000 0.00 0.00 44.27 4.00
401 403 7.392494 TCAGACTACCTGATGTACTACTTTG 57.608 40.000 0.00 0.00 46.38 2.77
402 404 6.946583 TCAGACTACCTGATGTACTACTTTGT 59.053 38.462 0.00 0.00 46.38 2.83
403 405 8.105197 TCAGACTACCTGATGTACTACTTTGTA 58.895 37.037 0.00 0.00 46.38 2.41
404 406 8.737175 CAGACTACCTGATGTACTACTTTGTAA 58.263 37.037 0.00 0.00 45.78 2.41
405 407 9.305555 AGACTACCTGATGTACTACTTTGTAAA 57.694 33.333 0.00 0.00 0.00 2.01
406 408 9.570488 GACTACCTGATGTACTACTTTGTAAAG 57.430 37.037 2.94 2.94 41.73 1.85
408 410 9.570488 CTACCTGATGTACTACTTTGTAAAGTC 57.430 37.037 12.84 0.98 45.65 3.01
409 411 8.191534 ACCTGATGTACTACTTTGTAAAGTCT 57.808 34.615 12.84 3.68 45.65 3.24
410 412 9.305555 ACCTGATGTACTACTTTGTAAAGTCTA 57.694 33.333 12.84 2.83 45.65 2.59
448 450 9.512588 AATAAAATGAATATACAGAGGCTGAGG 57.487 33.333 0.00 0.00 35.18 3.86
449 451 5.495926 AATGAATATACAGAGGCTGAGGG 57.504 43.478 0.00 0.00 35.18 4.30
450 452 3.928754 TGAATATACAGAGGCTGAGGGT 58.071 45.455 0.00 0.00 35.18 4.34
451 453 5.074746 TGAATATACAGAGGCTGAGGGTA 57.925 43.478 0.00 0.00 35.18 3.69
452 454 5.464069 TGAATATACAGAGGCTGAGGGTAA 58.536 41.667 0.00 0.00 35.18 2.85
453 455 6.084738 TGAATATACAGAGGCTGAGGGTAAT 58.915 40.000 0.00 0.00 35.18 1.89
454 456 6.211584 TGAATATACAGAGGCTGAGGGTAATC 59.788 42.308 0.00 0.00 35.18 1.75
455 457 2.559381 ACAGAGGCTGAGGGTAATCT 57.441 50.000 0.00 0.00 35.18 2.40
456 458 2.393646 ACAGAGGCTGAGGGTAATCTC 58.606 52.381 0.00 0.00 35.18 2.75
457 459 1.691434 CAGAGGCTGAGGGTAATCTCC 59.309 57.143 0.00 0.00 32.44 3.71
458 460 1.292242 AGAGGCTGAGGGTAATCTCCA 59.708 52.381 0.00 0.00 33.04 3.86
459 461 2.119495 GAGGCTGAGGGTAATCTCCAA 58.881 52.381 0.00 0.00 33.04 3.53
460 462 2.708325 GAGGCTGAGGGTAATCTCCAAT 59.292 50.000 0.00 0.00 33.04 3.16
461 463 3.126453 AGGCTGAGGGTAATCTCCAATT 58.874 45.455 0.00 0.00 33.04 2.32
462 464 3.137360 AGGCTGAGGGTAATCTCCAATTC 59.863 47.826 0.00 0.00 33.04 2.17
463 465 3.117888 GGCTGAGGGTAATCTCCAATTCA 60.118 47.826 0.00 0.00 33.04 2.57
464 466 4.133078 GCTGAGGGTAATCTCCAATTCAG 58.867 47.826 0.00 0.00 36.26 3.02
465 467 4.141620 GCTGAGGGTAATCTCCAATTCAGA 60.142 45.833 12.03 0.00 35.75 3.27
466 468 5.609423 CTGAGGGTAATCTCCAATTCAGAG 58.391 45.833 0.00 0.00 35.75 3.35
467 469 5.280499 TGAGGGTAATCTCCAATTCAGAGA 58.720 41.667 7.08 7.08 44.20 3.10
468 470 5.365025 TGAGGGTAATCTCCAATTCAGAGAG 59.635 44.000 9.85 0.00 43.36 3.20
469 471 5.533112 AGGGTAATCTCCAATTCAGAGAGA 58.467 41.667 9.85 4.30 43.36 3.10
470 472 5.602145 AGGGTAATCTCCAATTCAGAGAGAG 59.398 44.000 9.85 0.00 43.36 3.20
471 473 5.600484 GGGTAATCTCCAATTCAGAGAGAGA 59.400 44.000 9.85 0.00 43.36 3.10
472 474 6.098982 GGGTAATCTCCAATTCAGAGAGAGAA 59.901 42.308 9.85 0.00 43.36 2.87
473 475 7.365117 GGGTAATCTCCAATTCAGAGAGAGAAA 60.365 40.741 9.85 0.00 43.36 2.52
474 476 8.043710 GGTAATCTCCAATTCAGAGAGAGAAAA 58.956 37.037 9.85 0.00 43.36 2.29
475 477 9.612066 GTAATCTCCAATTCAGAGAGAGAAAAT 57.388 33.333 9.85 0.00 43.36 1.82
478 480 9.781633 ATCTCCAATTCAGAGAGAGAAAATATG 57.218 33.333 9.85 0.00 43.36 1.78
479 481 8.985922 TCTCCAATTCAGAGAGAGAAAATATGA 58.014 33.333 1.33 0.00 35.46 2.15
480 482 9.610705 CTCCAATTCAGAGAGAGAAAATATGAA 57.389 33.333 0.00 0.00 32.86 2.57
481 483 9.388506 TCCAATTCAGAGAGAGAAAATATGAAC 57.611 33.333 0.00 0.00 0.00 3.18
482 484 9.393512 CCAATTCAGAGAGAGAAAATATGAACT 57.606 33.333 0.00 0.00 0.00 3.01
484 486 9.612066 AATTCAGAGAGAGAAAATATGAACTCC 57.388 33.333 0.00 0.00 0.00 3.85
485 487 6.800543 TCAGAGAGAGAAAATATGAACTCCG 58.199 40.000 0.00 0.00 0.00 4.63
486 488 6.378564 TCAGAGAGAGAAAATATGAACTCCGT 59.621 38.462 0.00 0.00 0.00 4.69
487 489 6.695278 CAGAGAGAGAAAATATGAACTCCGTC 59.305 42.308 0.00 0.00 0.00 4.79
488 490 6.378564 AGAGAGAGAAAATATGAACTCCGTCA 59.621 38.462 0.00 0.00 0.00 4.35
489 491 6.334202 AGAGAGAAAATATGAACTCCGTCAC 58.666 40.000 0.00 0.00 0.00 3.67
490 492 5.103000 AGAGAAAATATGAACTCCGTCACG 58.897 41.667 0.00 0.00 0.00 4.35
491 493 4.817517 AGAAAATATGAACTCCGTCACGT 58.182 39.130 0.00 0.00 0.00 4.49
492 494 5.957798 AGAAAATATGAACTCCGTCACGTA 58.042 37.500 0.00 0.00 0.00 3.57
493 495 6.570692 AGAAAATATGAACTCCGTCACGTAT 58.429 36.000 0.00 0.00 0.00 3.06
494 496 7.709947 AGAAAATATGAACTCCGTCACGTATA 58.290 34.615 0.00 0.00 0.00 1.47
495 497 8.358148 AGAAAATATGAACTCCGTCACGTATAT 58.642 33.333 0.00 0.00 0.00 0.86
496 498 9.616634 GAAAATATGAACTCCGTCACGTATATA 57.383 33.333 0.00 0.00 0.00 0.86
497 499 9.622004 AAAATATGAACTCCGTCACGTATATAG 57.378 33.333 0.00 0.00 0.00 1.31
498 500 7.918536 ATATGAACTCCGTCACGTATATAGT 57.081 36.000 0.00 0.00 0.00 2.12
499 501 9.440773 AATATGAACTCCGTCACGTATATAGTA 57.559 33.333 0.00 0.00 0.00 1.82
500 502 6.530913 TGAACTCCGTCACGTATATAGTAC 57.469 41.667 0.00 0.00 0.00 2.73
501 503 6.283694 TGAACTCCGTCACGTATATAGTACT 58.716 40.000 0.00 0.00 0.00 2.73
502 504 6.422100 TGAACTCCGTCACGTATATAGTACTC 59.578 42.308 0.00 0.00 0.00 2.59
503 505 5.233988 ACTCCGTCACGTATATAGTACTCC 58.766 45.833 0.00 0.00 0.00 3.85
504 506 4.237724 TCCGTCACGTATATAGTACTCCG 58.762 47.826 0.00 0.00 0.00 4.63
505 507 3.990469 CCGTCACGTATATAGTACTCCGT 59.010 47.826 0.00 0.00 0.00 4.69
506 508 5.048294 TCCGTCACGTATATAGTACTCCGTA 60.048 44.000 0.00 0.00 0.00 4.02
507 509 5.807520 CCGTCACGTATATAGTACTCCGTAT 59.192 44.000 0.00 0.00 0.00 3.06
508 510 6.972901 CCGTCACGTATATAGTACTCCGTATA 59.027 42.308 0.00 0.00 0.00 1.47
509 511 7.488150 CCGTCACGTATATAGTACTCCGTATAA 59.512 40.741 0.00 0.00 0.00 0.98
510 512 8.314635 CGTCACGTATATAGTACTCCGTATAAC 58.685 40.741 0.00 1.32 0.00 1.89
511 513 9.140286 GTCACGTATATAGTACTCCGTATAACA 57.860 37.037 0.00 0.00 0.00 2.41
512 514 9.875691 TCACGTATATAGTACTCCGTATAACAT 57.124 33.333 0.00 0.00 0.00 2.71
519 521 8.859236 ATAGTACTCCGTATAACATAAGCAGA 57.141 34.615 0.00 0.00 0.00 4.26
520 522 6.968250 AGTACTCCGTATAACATAAGCAGAC 58.032 40.000 0.00 0.00 0.00 3.51
521 523 5.847111 ACTCCGTATAACATAAGCAGACA 57.153 39.130 0.00 0.00 0.00 3.41
522 524 5.589192 ACTCCGTATAACATAAGCAGACAC 58.411 41.667 0.00 0.00 0.00 3.67
523 525 5.126545 ACTCCGTATAACATAAGCAGACACA 59.873 40.000 0.00 0.00 0.00 3.72
524 526 5.588240 TCCGTATAACATAAGCAGACACAG 58.412 41.667 0.00 0.00 0.00 3.66
525 527 5.358725 TCCGTATAACATAAGCAGACACAGA 59.641 40.000 0.00 0.00 0.00 3.41
526 528 5.687730 CCGTATAACATAAGCAGACACAGAG 59.312 44.000 0.00 0.00 0.00 3.35
527 529 5.687730 CGTATAACATAAGCAGACACAGAGG 59.312 44.000 0.00 0.00 0.00 3.69
528 530 3.340814 AACATAAGCAGACACAGAGGG 57.659 47.619 0.00 0.00 0.00 4.30
529 531 1.065854 ACATAAGCAGACACAGAGGGC 60.066 52.381 0.00 0.00 0.00 5.19
530 532 1.065926 CATAAGCAGACACAGAGGGCA 60.066 52.381 0.00 0.00 0.00 5.36
531 533 1.055849 TAAGCAGACACAGAGGGCAA 58.944 50.000 0.00 0.00 0.00 4.52
532 534 0.250640 AAGCAGACACAGAGGGCAAG 60.251 55.000 0.00 0.00 0.00 4.01
533 535 1.123861 AGCAGACACAGAGGGCAAGA 61.124 55.000 0.00 0.00 0.00 3.02
534 536 0.250467 GCAGACACAGAGGGCAAGAA 60.250 55.000 0.00 0.00 0.00 2.52
535 537 1.815408 GCAGACACAGAGGGCAAGAAA 60.815 52.381 0.00 0.00 0.00 2.52
536 538 2.575532 CAGACACAGAGGGCAAGAAAA 58.424 47.619 0.00 0.00 0.00 2.29
537 539 2.951642 CAGACACAGAGGGCAAGAAAAA 59.048 45.455 0.00 0.00 0.00 1.94
538 540 2.952310 AGACACAGAGGGCAAGAAAAAC 59.048 45.455 0.00 0.00 0.00 2.43
539 541 2.031870 ACACAGAGGGCAAGAAAAACC 58.968 47.619 0.00 0.00 0.00 3.27
540 542 2.031120 CACAGAGGGCAAGAAAAACCA 58.969 47.619 0.00 0.00 0.00 3.67
541 543 2.430332 CACAGAGGGCAAGAAAAACCAA 59.570 45.455 0.00 0.00 0.00 3.67
542 544 3.070015 CACAGAGGGCAAGAAAAACCAAT 59.930 43.478 0.00 0.00 0.00 3.16
543 545 3.711190 ACAGAGGGCAAGAAAAACCAATT 59.289 39.130 0.00 0.00 0.00 2.32
544 546 4.898861 ACAGAGGGCAAGAAAAACCAATTA 59.101 37.500 0.00 0.00 0.00 1.40
545 547 5.365314 ACAGAGGGCAAGAAAAACCAATTAA 59.635 36.000 0.00 0.00 0.00 1.40
546 548 6.126911 ACAGAGGGCAAGAAAAACCAATTAAA 60.127 34.615 0.00 0.00 0.00 1.52
547 549 6.424812 CAGAGGGCAAGAAAAACCAATTAAAG 59.575 38.462 0.00 0.00 0.00 1.85
548 550 6.099701 AGAGGGCAAGAAAAACCAATTAAAGT 59.900 34.615 0.00 0.00 0.00 2.66
549 551 7.289084 AGAGGGCAAGAAAAACCAATTAAAGTA 59.711 33.333 0.00 0.00 0.00 2.24
550 552 7.797062 AGGGCAAGAAAAACCAATTAAAGTAA 58.203 30.769 0.00 0.00 0.00 2.24
551 553 7.931407 AGGGCAAGAAAAACCAATTAAAGTAAG 59.069 33.333 0.00 0.00 0.00 2.34
552 554 7.929245 GGGCAAGAAAAACCAATTAAAGTAAGA 59.071 33.333 0.00 0.00 0.00 2.10
553 555 9.489084 GGCAAGAAAAACCAATTAAAGTAAGAT 57.511 29.630 0.00 0.00 0.00 2.40
646 648 2.198827 AAACACGATGGCCAATCTGA 57.801 45.000 10.96 0.00 32.61 3.27
650 652 1.153369 CGATGGCCAATCTGACGGT 60.153 57.895 10.96 0.00 32.61 4.83
654 657 1.224592 GGCCAATCTGACGGTCCAT 59.775 57.895 5.55 0.00 0.00 3.41
683 686 3.326981 CGCGCGCACAATCCGATA 61.327 61.111 32.61 0.00 0.00 2.92
707 710 0.897621 AAATTTACAGCCCAGCAGCC 59.102 50.000 0.00 0.00 0.00 4.85
708 711 0.972471 AATTTACAGCCCAGCAGCCC 60.972 55.000 0.00 0.00 0.00 5.19
718 721 4.082523 AGCAGCCCGCACGTACAT 62.083 61.111 0.00 0.00 46.13 2.29
719 722 3.564027 GCAGCCCGCACGTACATC 61.564 66.667 0.00 0.00 41.79 3.06
720 723 2.184322 CAGCCCGCACGTACATCT 59.816 61.111 0.00 0.00 0.00 2.90
721 724 2.167219 CAGCCCGCACGTACATCTG 61.167 63.158 0.00 0.00 0.00 2.90
722 725 2.125673 GCCCGCACGTACATCTGT 60.126 61.111 0.00 0.00 0.00 3.41
723 726 2.452813 GCCCGCACGTACATCTGTG 61.453 63.158 0.00 0.00 39.10 3.66
724 727 1.080093 CCCGCACGTACATCTGTGT 60.080 57.895 0.00 0.00 42.39 3.72
725 728 1.351430 CCCGCACGTACATCTGTGTG 61.351 60.000 5.50 5.50 44.16 3.82
726 729 0.388006 CCGCACGTACATCTGTGTGA 60.388 55.000 12.10 0.00 46.70 3.58
831 834 4.469657 CCATAAGGCCTTGGCTGTATTTA 58.530 43.478 28.77 3.74 38.81 1.40
833 836 3.739401 AAGGCCTTGGCTGTATTTAGT 57.261 42.857 19.73 0.00 38.81 2.24
837 840 2.945668 GCCTTGGCTGTATTTAGTCCAG 59.054 50.000 4.11 0.00 0.00 3.86
922 925 1.545706 GCCTCTGGTCTCCCTCGTTT 61.546 60.000 0.00 0.00 0.00 3.60
923 926 0.533032 CCTCTGGTCTCCCTCGTTTC 59.467 60.000 0.00 0.00 0.00 2.78
924 927 0.533032 CTCTGGTCTCCCTCGTTTCC 59.467 60.000 0.00 0.00 0.00 3.13
1473 1674 3.584406 AGTGAGATTTGATCCTCCACACA 59.416 43.478 0.00 0.00 31.40 3.72
1620 1837 2.353889 CAGTTCGATCCTTCAATGCCTG 59.646 50.000 0.00 0.00 0.00 4.85
1854 2543 2.649516 CCATTGCACGTGTGTACAAAG 58.350 47.619 18.38 9.34 35.10 2.77
1891 4784 4.096984 GGCATATGAGTTCAAGAAGGTTGG 59.903 45.833 6.97 0.00 0.00 3.77
2031 5091 8.798402 AGATAATCTCATCTACTTTACCTTCCG 58.202 37.037 0.00 0.00 33.41 4.30
2487 5682 2.501723 CAGTATTACCTGTGGAGGCACT 59.498 50.000 0.00 0.00 44.33 4.40
2571 5769 3.058983 TGCTGACACAAGAGTTAATTGCG 60.059 43.478 0.00 0.00 0.00 4.85
2982 6783 2.805353 CGTCCGTTCACGCTCCTG 60.805 66.667 0.00 0.00 38.18 3.86
2991 6792 4.704103 ACGCTCCTGGAGGCCTCA 62.704 66.667 33.29 18.37 34.44 3.86
3107 6908 1.380112 GCCTCCTCGACTACCAGGT 60.380 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.456619 CCAAGATCCCTGCCATCAATAAGTA 60.457 44.000 0.00 0.00 0.00 2.24
16 17 2.489619 GCCAAGATCCCTGCCATCAATA 60.490 50.000 0.00 0.00 0.00 1.90
26 27 2.194056 CATGCCGCCAAGATCCCT 59.806 61.111 0.00 0.00 0.00 4.20
39 41 3.503363 GTCTCCACTGCGCCATGC 61.503 66.667 4.18 0.00 46.70 4.06
41 43 2.581354 GAGTCTCCACTGCGCCAT 59.419 61.111 4.18 0.00 30.63 4.40
64 66 3.276846 TCGATCTCCGCGCATCGA 61.277 61.111 22.04 22.04 46.63 3.59
66 68 1.727723 GAGTCGATCTCCGCGCATC 60.728 63.158 8.75 1.15 37.22 3.91
99 101 0.957395 CACCATGACACCAGACAGCC 60.957 60.000 0.00 0.00 0.00 4.85
101 103 0.957395 GCCACCATGACACCAGACAG 60.957 60.000 0.00 0.00 0.00 3.51
109 111 1.447663 CATCGACGCCACCATGACA 60.448 57.895 0.00 0.00 0.00 3.58
129 131 1.666700 CGACCTCGTTAGACCTCTCTG 59.333 57.143 0.00 0.00 34.11 3.35
132 134 0.327591 ACCGACCTCGTTAGACCTCT 59.672 55.000 0.00 0.00 37.74 3.69
140 142 1.080974 CTAACGCACCGACCTCGTT 60.081 57.895 4.69 4.69 46.38 3.85
141 143 1.799258 AACTAACGCACCGACCTCGT 61.799 55.000 0.00 0.00 38.15 4.18
143 145 1.505425 AAAACTAACGCACCGACCTC 58.495 50.000 0.00 0.00 0.00 3.85
150 152 3.545633 CTCAGAGCAAAAACTAACGCAC 58.454 45.455 0.00 0.00 0.00 5.34
162 164 1.918262 ACCAATCCATCCTCAGAGCAA 59.082 47.619 0.00 0.00 0.00 3.91
171 173 1.668419 CGTCTTCCACCAATCCATCC 58.332 55.000 0.00 0.00 0.00 3.51
173 175 0.394352 GCCGTCTTCCACCAATCCAT 60.394 55.000 0.00 0.00 0.00 3.41
181 183 4.814294 ATCGCCGCCGTCTTCCAC 62.814 66.667 0.00 0.00 35.54 4.02
191 193 0.531974 TTCTTATGGGTCATCGCCGC 60.532 55.000 0.00 0.00 0.00 6.53
192 194 1.800586 CATTCTTATGGGTCATCGCCG 59.199 52.381 0.00 0.00 0.00 6.46
202 204 3.198068 CTGGTCCGACACATTCTTATGG 58.802 50.000 0.00 0.00 36.01 2.74
206 208 2.878406 CAAACTGGTCCGACACATTCTT 59.122 45.455 0.00 0.00 0.00 2.52
210 212 2.549349 GGTACAAACTGGTCCGACACAT 60.549 50.000 0.00 0.00 0.00 3.21
213 215 0.393820 GGGTACAAACTGGTCCGACA 59.606 55.000 0.00 0.00 0.00 4.35
214 216 0.668401 CGGGTACAAACTGGTCCGAC 60.668 60.000 0.00 0.00 39.83 4.79
221 223 2.940410 ACTGTGTTTCGGGTACAAACTG 59.060 45.455 8.30 3.10 35.19 3.16
222 224 3.271055 ACTGTGTTTCGGGTACAAACT 57.729 42.857 8.30 0.00 35.19 2.66
233 235 5.107220 CCAACCGAGTTACATACTGTGTTTC 60.107 44.000 0.00 0.00 42.29 2.78
238 240 2.235402 CCCCAACCGAGTTACATACTGT 59.765 50.000 0.00 0.00 37.17 3.55
247 249 3.647771 GGAGGCCCCAACCGAGTT 61.648 66.667 0.00 0.00 34.14 3.01
272 274 0.036765 TCGCACCAAAGCCTAACGAT 60.037 50.000 0.00 0.00 0.00 3.73
273 275 0.036765 ATCGCACCAAAGCCTAACGA 60.037 50.000 0.00 0.00 0.00 3.85
274 276 0.096976 CATCGCACCAAAGCCTAACG 59.903 55.000 0.00 0.00 0.00 3.18
309 311 0.178987 AGGATGCCGATAGTCCGAGT 60.179 55.000 0.00 0.00 37.12 4.18
312 314 1.068588 TGAAAGGATGCCGATAGTCCG 59.931 52.381 0.00 0.00 37.12 4.79
313 315 2.910688 TGAAAGGATGCCGATAGTCC 57.089 50.000 0.00 0.00 0.00 3.85
314 316 3.995199 TGATGAAAGGATGCCGATAGTC 58.005 45.455 0.00 0.00 0.00 2.59
315 317 4.141620 ACTTGATGAAAGGATGCCGATAGT 60.142 41.667 0.00 0.00 40.51 2.12
316 318 4.212847 CACTTGATGAAAGGATGCCGATAG 59.787 45.833 0.00 0.00 40.51 2.08
317 319 4.129380 CACTTGATGAAAGGATGCCGATA 58.871 43.478 0.00 0.00 40.51 2.92
318 320 2.947652 CACTTGATGAAAGGATGCCGAT 59.052 45.455 0.00 0.00 40.51 4.18
319 321 2.027285 TCACTTGATGAAAGGATGCCGA 60.027 45.455 0.00 0.00 40.51 5.54
320 322 2.358957 TCACTTGATGAAAGGATGCCG 58.641 47.619 0.00 0.00 40.51 5.69
330 332 3.430790 CGCTACTCCCATTCACTTGATGA 60.431 47.826 0.00 0.00 34.65 2.92
331 333 2.868583 CGCTACTCCCATTCACTTGATG 59.131 50.000 0.00 0.00 0.00 3.07
332 334 2.766263 TCGCTACTCCCATTCACTTGAT 59.234 45.455 0.00 0.00 0.00 2.57
333 335 2.094182 GTCGCTACTCCCATTCACTTGA 60.094 50.000 0.00 0.00 0.00 3.02
334 336 2.271800 GTCGCTACTCCCATTCACTTG 58.728 52.381 0.00 0.00 0.00 3.16
335 337 1.899814 TGTCGCTACTCCCATTCACTT 59.100 47.619 0.00 0.00 0.00 3.16
336 338 1.478510 CTGTCGCTACTCCCATTCACT 59.521 52.381 0.00 0.00 0.00 3.41
337 339 1.204941 ACTGTCGCTACTCCCATTCAC 59.795 52.381 0.00 0.00 0.00 3.18
338 340 1.557099 ACTGTCGCTACTCCCATTCA 58.443 50.000 0.00 0.00 0.00 2.57
339 341 2.271800 CAACTGTCGCTACTCCCATTC 58.728 52.381 0.00 0.00 0.00 2.67
340 342 1.623811 ACAACTGTCGCTACTCCCATT 59.376 47.619 0.00 0.00 0.00 3.16
341 343 1.267121 ACAACTGTCGCTACTCCCAT 58.733 50.000 0.00 0.00 0.00 4.00
342 344 1.045407 AACAACTGTCGCTACTCCCA 58.955 50.000 0.00 0.00 0.00 4.37
343 345 1.429463 CAACAACTGTCGCTACTCCC 58.571 55.000 0.00 0.00 0.00 4.30
344 346 0.790814 GCAACAACTGTCGCTACTCC 59.209 55.000 0.00 0.00 0.00 3.85
345 347 1.784525 AGCAACAACTGTCGCTACTC 58.215 50.000 0.00 0.00 31.60 2.59
346 348 3.005472 TCTTAGCAACAACTGTCGCTACT 59.995 43.478 1.99 0.00 36.73 2.57
347 349 3.314553 TCTTAGCAACAACTGTCGCTAC 58.685 45.455 1.99 0.00 36.73 3.58
348 350 3.653539 TCTTAGCAACAACTGTCGCTA 57.346 42.857 0.00 0.00 35.93 4.26
349 351 2.526304 TCTTAGCAACAACTGTCGCT 57.474 45.000 0.31 0.31 38.51 4.93
350 352 2.159653 CCATCTTAGCAACAACTGTCGC 60.160 50.000 0.00 0.00 0.00 5.19
351 353 3.067106 ACCATCTTAGCAACAACTGTCG 58.933 45.455 0.00 0.00 0.00 4.35
352 354 3.189287 CCACCATCTTAGCAACAACTGTC 59.811 47.826 0.00 0.00 0.00 3.51
353 355 3.149196 CCACCATCTTAGCAACAACTGT 58.851 45.455 0.00 0.00 0.00 3.55
354 356 2.095059 GCCACCATCTTAGCAACAACTG 60.095 50.000 0.00 0.00 0.00 3.16
355 357 2.162681 GCCACCATCTTAGCAACAACT 58.837 47.619 0.00 0.00 0.00 3.16
356 358 2.162681 AGCCACCATCTTAGCAACAAC 58.837 47.619 0.00 0.00 0.00 3.32
357 359 2.584835 AGCCACCATCTTAGCAACAA 57.415 45.000 0.00 0.00 0.00 2.83
358 360 2.224744 TGAAGCCACCATCTTAGCAACA 60.225 45.455 0.00 0.00 0.00 3.33
359 361 2.421424 CTGAAGCCACCATCTTAGCAAC 59.579 50.000 0.00 0.00 0.00 4.17
360 362 2.305635 TCTGAAGCCACCATCTTAGCAA 59.694 45.455 0.00 0.00 0.00 3.91
361 363 1.908619 TCTGAAGCCACCATCTTAGCA 59.091 47.619 0.00 0.00 0.00 3.49
362 364 2.093235 AGTCTGAAGCCACCATCTTAGC 60.093 50.000 0.00 0.00 0.00 3.09
363 365 3.902881 AGTCTGAAGCCACCATCTTAG 57.097 47.619 0.00 0.00 0.00 2.18
364 366 3.451178 GGTAGTCTGAAGCCACCATCTTA 59.549 47.826 0.00 0.00 0.00 2.10
365 367 2.237392 GGTAGTCTGAAGCCACCATCTT 59.763 50.000 0.00 0.00 0.00 2.40
366 368 1.834263 GGTAGTCTGAAGCCACCATCT 59.166 52.381 0.00 0.00 0.00 2.90
367 369 1.834263 AGGTAGTCTGAAGCCACCATC 59.166 52.381 0.00 0.00 0.00 3.51
368 370 1.556911 CAGGTAGTCTGAAGCCACCAT 59.443 52.381 0.00 0.00 46.18 3.55
369 371 0.976641 CAGGTAGTCTGAAGCCACCA 59.023 55.000 0.00 0.00 46.18 4.17
370 372 3.842869 CAGGTAGTCTGAAGCCACC 57.157 57.895 0.00 0.00 46.18 4.61
378 380 7.159322 ACAAAGTAGTACATCAGGTAGTCTG 57.841 40.000 2.52 0.00 44.68 3.51
379 381 8.874744 TTACAAAGTAGTACATCAGGTAGTCT 57.125 34.615 2.52 0.00 36.94 3.24
380 382 9.570488 CTTTACAAAGTAGTACATCAGGTAGTC 57.430 37.037 2.52 0.00 36.94 2.59
381 383 9.086758 ACTTTACAAAGTAGTACATCAGGTAGT 57.913 33.333 5.56 0.00 46.75 2.73
422 424 9.512588 CCTCAGCCTCTGTATATTCATTTTATT 57.487 33.333 0.00 0.00 32.61 1.40
423 425 8.105829 CCCTCAGCCTCTGTATATTCATTTTAT 58.894 37.037 0.00 0.00 32.61 1.40
424 426 7.072454 ACCCTCAGCCTCTGTATATTCATTTTA 59.928 37.037 0.00 0.00 32.61 1.52
425 427 6.126361 ACCCTCAGCCTCTGTATATTCATTTT 60.126 38.462 0.00 0.00 32.61 1.82
426 428 5.370880 ACCCTCAGCCTCTGTATATTCATTT 59.629 40.000 0.00 0.00 32.61 2.32
427 429 4.910304 ACCCTCAGCCTCTGTATATTCATT 59.090 41.667 0.00 0.00 32.61 2.57
428 430 4.497516 ACCCTCAGCCTCTGTATATTCAT 58.502 43.478 0.00 0.00 32.61 2.57
429 431 3.928754 ACCCTCAGCCTCTGTATATTCA 58.071 45.455 0.00 0.00 32.61 2.57
430 432 6.439058 AGATTACCCTCAGCCTCTGTATATTC 59.561 42.308 0.00 0.00 32.61 1.75
431 433 6.326970 AGATTACCCTCAGCCTCTGTATATT 58.673 40.000 0.00 0.00 32.61 1.28
432 434 5.909760 AGATTACCCTCAGCCTCTGTATAT 58.090 41.667 0.00 0.00 32.61 0.86
433 435 5.326069 GAGATTACCCTCAGCCTCTGTATA 58.674 45.833 0.00 0.00 33.50 1.47
434 436 4.156477 GAGATTACCCTCAGCCTCTGTAT 58.844 47.826 0.00 0.00 33.50 2.29
435 437 3.567397 GAGATTACCCTCAGCCTCTGTA 58.433 50.000 0.00 0.00 33.50 2.74
436 438 2.393646 GAGATTACCCTCAGCCTCTGT 58.606 52.381 0.00 0.00 33.50 3.41
437 439 1.691434 GGAGATTACCCTCAGCCTCTG 59.309 57.143 0.00 0.00 34.94 3.35
438 440 1.292242 TGGAGATTACCCTCAGCCTCT 59.708 52.381 0.00 0.00 34.94 3.69
439 441 1.794714 TGGAGATTACCCTCAGCCTC 58.205 55.000 0.00 0.00 34.94 4.70
440 442 2.270434 TTGGAGATTACCCTCAGCCT 57.730 50.000 0.00 0.00 34.94 4.58
441 443 3.117888 TGAATTGGAGATTACCCTCAGCC 60.118 47.826 0.00 0.00 34.94 4.85
442 444 4.133078 CTGAATTGGAGATTACCCTCAGC 58.867 47.826 0.00 0.00 34.94 4.26
443 445 5.365025 TCTCTGAATTGGAGATTACCCTCAG 59.635 44.000 4.24 0.00 35.25 3.35
444 446 5.280499 TCTCTGAATTGGAGATTACCCTCA 58.720 41.667 4.24 0.00 35.25 3.86
445 447 5.600484 TCTCTCTGAATTGGAGATTACCCTC 59.400 44.000 7.81 0.00 38.85 4.30
446 448 5.533112 TCTCTCTGAATTGGAGATTACCCT 58.467 41.667 7.81 0.00 38.85 4.34
447 449 5.600484 TCTCTCTCTGAATTGGAGATTACCC 59.400 44.000 7.81 0.00 38.85 3.69
448 450 6.723298 TCTCTCTCTGAATTGGAGATTACC 57.277 41.667 7.81 0.00 38.85 2.85
449 451 9.612066 ATTTTCTCTCTCTGAATTGGAGATTAC 57.388 33.333 7.81 0.00 38.85 1.89
452 454 9.781633 CATATTTTCTCTCTCTGAATTGGAGAT 57.218 33.333 7.81 0.00 38.85 2.75
453 455 8.985922 TCATATTTTCTCTCTCTGAATTGGAGA 58.014 33.333 7.30 7.30 38.07 3.71
454 456 9.610705 TTCATATTTTCTCTCTCTGAATTGGAG 57.389 33.333 0.00 0.00 0.00 3.86
455 457 9.388506 GTTCATATTTTCTCTCTCTGAATTGGA 57.611 33.333 0.00 0.00 0.00 3.53
456 458 9.393512 AGTTCATATTTTCTCTCTCTGAATTGG 57.606 33.333 0.00 0.00 0.00 3.16
458 460 9.612066 GGAGTTCATATTTTCTCTCTCTGAATT 57.388 33.333 0.00 0.00 0.00 2.17
459 461 7.925483 CGGAGTTCATATTTTCTCTCTCTGAAT 59.075 37.037 0.00 0.00 31.26 2.57
460 462 7.093727 ACGGAGTTCATATTTTCTCTCTCTGAA 60.094 37.037 0.00 0.00 37.78 3.02
461 463 6.378564 ACGGAGTTCATATTTTCTCTCTCTGA 59.621 38.462 0.00 0.00 37.78 3.27
462 464 6.568869 ACGGAGTTCATATTTTCTCTCTCTG 58.431 40.000 0.00 0.00 37.78 3.35
463 465 6.783708 ACGGAGTTCATATTTTCTCTCTCT 57.216 37.500 0.00 0.00 37.78 3.10
479 481 9.765949 ACGGAGTACTATATACGTGACGGAGTT 62.766 44.444 10.66 0.00 40.88 3.01
480 482 8.401516 ACGGAGTACTATATACGTGACGGAGT 62.402 46.154 10.66 6.93 44.52 3.85
481 483 4.325741 CGGAGTACTATATACGTGACGGAG 59.674 50.000 10.66 0.83 0.00 4.63
482 484 4.237724 CGGAGTACTATATACGTGACGGA 58.762 47.826 10.66 0.00 0.00 4.69
483 485 3.990469 ACGGAGTACTATATACGTGACGG 59.010 47.826 10.66 0.00 41.94 4.79
500 502 5.588240 TGTGTCTGCTTATGTTATACGGAG 58.412 41.667 0.00 0.00 0.00 4.63
501 503 5.358725 TCTGTGTCTGCTTATGTTATACGGA 59.641 40.000 0.00 0.00 0.00 4.69
502 504 5.588240 TCTGTGTCTGCTTATGTTATACGG 58.412 41.667 0.00 0.00 0.00 4.02
503 505 5.687730 CCTCTGTGTCTGCTTATGTTATACG 59.312 44.000 0.00 0.00 0.00 3.06
504 506 5.986135 CCCTCTGTGTCTGCTTATGTTATAC 59.014 44.000 0.00 0.00 0.00 1.47
505 507 5.453339 GCCCTCTGTGTCTGCTTATGTTATA 60.453 44.000 0.00 0.00 0.00 0.98
506 508 4.684485 GCCCTCTGTGTCTGCTTATGTTAT 60.684 45.833 0.00 0.00 0.00 1.89
507 509 3.369471 GCCCTCTGTGTCTGCTTATGTTA 60.369 47.826 0.00 0.00 0.00 2.41
508 510 2.616510 GCCCTCTGTGTCTGCTTATGTT 60.617 50.000 0.00 0.00 0.00 2.71
509 511 1.065854 GCCCTCTGTGTCTGCTTATGT 60.066 52.381 0.00 0.00 0.00 2.29
510 512 1.065926 TGCCCTCTGTGTCTGCTTATG 60.066 52.381 0.00 0.00 0.00 1.90
511 513 1.279496 TGCCCTCTGTGTCTGCTTAT 58.721 50.000 0.00 0.00 0.00 1.73
512 514 1.002430 CTTGCCCTCTGTGTCTGCTTA 59.998 52.381 0.00 0.00 0.00 3.09
513 515 0.250640 CTTGCCCTCTGTGTCTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
514 516 1.123861 TCTTGCCCTCTGTGTCTGCT 61.124 55.000 0.00 0.00 0.00 4.24
515 517 0.250467 TTCTTGCCCTCTGTGTCTGC 60.250 55.000 0.00 0.00 0.00 4.26
516 518 2.260844 TTTCTTGCCCTCTGTGTCTG 57.739 50.000 0.00 0.00 0.00 3.51
517 519 2.952310 GTTTTTCTTGCCCTCTGTGTCT 59.048 45.455 0.00 0.00 0.00 3.41
518 520 2.034685 GGTTTTTCTTGCCCTCTGTGTC 59.965 50.000 0.00 0.00 0.00 3.67
519 521 2.031870 GGTTTTTCTTGCCCTCTGTGT 58.968 47.619 0.00 0.00 0.00 3.72
520 522 2.031120 TGGTTTTTCTTGCCCTCTGTG 58.969 47.619 0.00 0.00 0.00 3.66
521 523 2.452600 TGGTTTTTCTTGCCCTCTGT 57.547 45.000 0.00 0.00 0.00 3.41
522 524 4.341366 AATTGGTTTTTCTTGCCCTCTG 57.659 40.909 0.00 0.00 0.00 3.35
523 525 6.099701 ACTTTAATTGGTTTTTCTTGCCCTCT 59.900 34.615 0.00 0.00 0.00 3.69
524 526 6.288294 ACTTTAATTGGTTTTTCTTGCCCTC 58.712 36.000 0.00 0.00 0.00 4.30
525 527 6.247229 ACTTTAATTGGTTTTTCTTGCCCT 57.753 33.333 0.00 0.00 0.00 5.19
526 528 7.929245 TCTTACTTTAATTGGTTTTTCTTGCCC 59.071 33.333 0.00 0.00 0.00 5.36
527 529 8.880878 TCTTACTTTAATTGGTTTTTCTTGCC 57.119 30.769 0.00 0.00 0.00 4.52
593 595 1.080501 CCTCTTCGTCGCTTCAGCA 60.081 57.895 0.00 0.00 42.21 4.41
595 597 1.784525 AAACCTCTTCGTCGCTTCAG 58.215 50.000 0.00 0.00 0.00 3.02
598 600 1.137513 CGAAAACCTCTTCGTCGCTT 58.862 50.000 0.00 0.00 42.53 4.68
600 602 0.708918 CTCGAAAACCTCTTCGTCGC 59.291 55.000 5.73 0.00 46.49 5.19
637 639 0.179000 AGATGGACCGTCAGATTGGC 59.821 55.000 16.18 0.00 0.00 4.52
644 646 2.265739 GCTGCAGATGGACCGTCA 59.734 61.111 20.43 0.00 0.00 4.35
646 648 2.267006 CTGCTGCAGATGGACCGT 59.733 61.111 24.88 0.00 32.44 4.83
650 652 4.478371 CGGGCTGCTGCAGATGGA 62.478 66.667 32.30 0.00 41.91 3.41
671 674 4.853924 AATTTGGGATATCGGATTGTGC 57.146 40.909 0.00 0.00 0.00 4.57
683 686 2.110578 GCTGGGCTGTAAATTTGGGAT 58.889 47.619 0.00 0.00 0.00 3.85
707 710 0.388006 TCACACAGATGTACGTGCGG 60.388 55.000 0.00 0.00 36.72 5.69
708 711 1.629013 ATCACACAGATGTACGTGCG 58.371 50.000 0.00 0.00 36.72 5.34
711 714 7.724305 AAAACTTTATCACACAGATGTACGT 57.276 32.000 0.00 0.00 36.72 3.57
712 715 9.901724 GATAAAACTTTATCACACAGATGTACG 57.098 33.333 14.55 0.00 45.21 3.67
765 768 0.878086 ACAAATTGCGGCCCGTTTTG 60.878 50.000 19.57 19.57 33.39 2.44
831 834 2.269940 AGGTCAGGCAAATACTGGACT 58.730 47.619 0.00 0.00 36.62 3.85
833 836 3.199946 CCTTAGGTCAGGCAAATACTGGA 59.800 47.826 0.00 0.00 36.62 3.86
837 840 4.216411 TGTCCTTAGGTCAGGCAAATAC 57.784 45.455 0.00 0.00 33.35 1.89
922 925 0.475048 AGGAGTTCCGGGGAAAAGGA 60.475 55.000 0.00 0.00 42.08 3.36
923 926 0.035343 GAGGAGTTCCGGGGAAAAGG 60.035 60.000 0.00 0.00 42.08 3.11
924 927 0.690762 TGAGGAGTTCCGGGGAAAAG 59.309 55.000 0.00 0.00 42.08 2.27
1052 1062 4.404507 TTTGATTCTTACTTGCTGTCGC 57.595 40.909 0.00 0.00 0.00 5.19
1473 1674 9.090692 CAAGAAACAGAACAACAATCTGAAAAT 57.909 29.630 10.27 0.00 45.74 1.82
1620 1837 5.638596 ACAATGGAAAGAAATCGGTAACC 57.361 39.130 0.00 0.00 0.00 2.85
1891 4784 0.608308 AAACCGCTAGGCCTTTGTCC 60.608 55.000 12.58 0.00 42.76 4.02
2029 5089 8.911662 CAAACAGTTTAATTATCCTTTCAACGG 58.088 33.333 0.00 0.00 0.00 4.44
2070 5130 6.469782 AGCTGGATCAACAAGAAAGAAAAA 57.530 33.333 0.00 0.00 0.00 1.94
2487 5682 8.586879 TGTTTTTGGAACATATGATACCATCA 57.413 30.769 10.38 9.29 40.84 3.07
2571 5769 2.162408 GCCTCAATTGTGGTACTTCTGC 59.838 50.000 23.73 6.83 0.00 4.26
2606 5804 6.183360 CGTAAAAATTAGCAATCGTGGTACCT 60.183 38.462 14.36 0.00 37.45 3.08
3028 6829 2.488820 GTCGAGCAGGTACCCGTC 59.511 66.667 8.74 1.78 0.00 4.79


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

AutoCloner maintained by Alex Coulton.