Multiple sequence alignment - TraesCS6D01G311800

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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 TraesCS6D01G311800 chr6D 100.000 3090 0 0 1 3090 420971337 420968248 0.000000e+00 5707.0
1 TraesCS6D01G311800 chr6D 91.552 2320 124 34 813 3090 421661599 421663888 0.000000e+00 3133.0
2 TraesCS6D01G311800 chr6D 90.767 2307 152 36 813 3090 421679588 421681862 0.000000e+00 3024.0
3 TraesCS6D01G311800 chr6D 92.540 1984 107 19 986 2954 421467998 421466041 0.000000e+00 2806.0
4 TraesCS6D01G311800 chr6D 86.183 1983 183 47 986 2944 422601282 422603197 0.000000e+00 2060.0
5 TraesCS6D01G311800 chr6D 88.588 1516 113 28 986 2483 422215372 422216845 0.000000e+00 1786.0
6 TraesCS6D01G311800 chr6D 92.006 1301 58 19 813 2080 421688927 421690214 0.000000e+00 1784.0
7 TraesCS6D01G311800 chr6D 90.564 1028 72 15 2072 3090 421695315 421696326 0.000000e+00 1338.0
8 TraesCS6D01G311800 chr6D 88.172 279 18 5 3 274 422214650 422214920 4.970000e-83 318.0
9 TraesCS6D01G311800 chr6D 88.087 277 18 6 3 269 422600497 422600768 6.430000e-82 315.0
10 TraesCS6D01G311800 chr6D 86.400 250 14 7 40 274 421688416 421688660 3.950000e-64 255.0
11 TraesCS6D01G311800 chr6D 85.772 246 15 7 40 270 421679077 421679317 3.080000e-60 243.0
12 TraesCS6D01G311800 chr6D 90.244 164 3 4 811 965 421468210 421468051 5.220000e-48 202.0
13 TraesCS6D01G311800 chr6D 92.913 127 7 2 2955 3079 421464187 421464061 1.890000e-42 183.0
14 TraesCS6D01G311800 chr6D 89.032 155 2 2 813 956 422215155 422215305 8.800000e-41 178.0
15 TraesCS6D01G311800 chr6D 91.057 123 4 3 40 155 421652105 421652227 3.190000e-35 159.0
16 TraesCS6D01G311800 chr6D 96.512 86 3 0 813 898 422601040 422601125 3.210000e-30 143.0
17 TraesCS6D01G311800 chr6D 87.500 64 3 2 739 802 422215061 422215119 5.530000e-08 69.4
18 TraesCS6D01G311800 chr6A 91.950 1528 96 13 990 2502 564278871 564277356 0.000000e+00 2115.0
19 TraesCS6D01G311800 chr6A 86.083 1976 179 44 986 2949 565340369 565342260 0.000000e+00 2037.0
20 TraesCS6D01G311800 chr6A 88.380 284 14 8 1 270 564279554 564279276 1.070000e-84 324.0
21 TraesCS6D01G311800 chr6A 85.199 277 33 2 1 274 565317406 565317677 8.440000e-71 278.0
22 TraesCS6D01G311800 chr6A 90.244 164 7 2 811 965 564279101 564278938 4.040000e-49 206.0
23 TraesCS6D01G311800 chr6A 79.769 173 19 6 736 898 565340073 565340239 9.060000e-21 111.0
24 TraesCS6D01G311800 chr6A 89.189 74 3 2 736 808 564279203 564279134 1.530000e-13 87.9
25 TraesCS6D01G311800 chr6B 85.849 1915 198 44 1046 2949 636746185 636748037 0.000000e+00 1967.0
26 TraesCS6D01G311800 chr6B 91.955 1330 87 11 986 2306 634503984 634502666 0.000000e+00 1845.0
27 TraesCS6D01G311800 chr6B 89.051 274 21 3 1 270 636744067 636744335 6.390000e-87 331.0
28 TraesCS6D01G311800 chr6B 86.286 175 4 7 811 965 634504223 634504049 4.100000e-39 172.0
29 TraesCS6D01G311800 chr6B 98.305 59 1 0 813 871 636744463 636744521 1.520000e-18 104.0
30 TraesCS6D01G311800 chr6B 92.000 50 4 0 763 812 634504296 634504247 1.540000e-08 71.3
31 TraesCS6D01G311800 chr2D 99.573 468 2 0 272 739 584804757 584804290 0.000000e+00 854.0
32 TraesCS6D01G311800 chr2A 92.324 469 20 8 272 732 718940940 718940480 0.000000e+00 652.0
33 TraesCS6D01G311800 chr2B 89.474 475 29 11 274 739 705048168 705047706 5.740000e-162 580.0


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 TraesCS6D01G311800 chr6D 420968248 420971337 3089 True 5707.000000 5707 100.000000 1 3090 1 chr6D.!!$R1 3089
1 TraesCS6D01G311800 chr6D 421661599 421663888 2289 False 3133.000000 3133 91.552000 813 3090 1 chr6D.!!$F2 2277
2 TraesCS6D01G311800 chr6D 421679077 421681862 2785 False 1633.500000 3024 88.269500 40 3090 2 chr6D.!!$F4 3050
3 TraesCS6D01G311800 chr6D 421695315 421696326 1011 False 1338.000000 1338 90.564000 2072 3090 1 chr6D.!!$F3 1018
4 TraesCS6D01G311800 chr6D 421464061 421468210 4149 True 1063.666667 2806 91.899000 811 3079 3 chr6D.!!$R2 2268
5 TraesCS6D01G311800 chr6D 421688416 421690214 1798 False 1019.500000 1784 89.203000 40 2080 2 chr6D.!!$F5 2040
6 TraesCS6D01G311800 chr6D 422600497 422603197 2700 False 839.333333 2060 90.260667 3 2944 3 chr6D.!!$F7 2941
7 TraesCS6D01G311800 chr6D 422214650 422216845 2195 False 587.850000 1786 88.323000 3 2483 4 chr6D.!!$F6 2480
8 TraesCS6D01G311800 chr6A 565340073 565342260 2187 False 1074.000000 2037 82.926000 736 2949 2 chr6A.!!$F2 2213
9 TraesCS6D01G311800 chr6A 564277356 564279554 2198 True 683.225000 2115 89.940750 1 2502 4 chr6A.!!$R1 2501
10 TraesCS6D01G311800 chr6B 636744067 636748037 3970 False 800.666667 1967 91.068333 1 2949 3 chr6B.!!$F1 2948
11 TraesCS6D01G311800 chr6B 634502666 634504296 1630 True 696.100000 1845 90.080333 763 2306 3 chr6B.!!$R1 1543

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
671 730 0.033503 GGGGTTGGGTCGAATGGAAT 60.034 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 4316 0.457853 CCTCGGCGTCATCGAAGAAA 60.458 55.0 6.85 0.0 43.58 2.52 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
66 77 3.873801 GCTTCCAGGATTGCCTACTGAAA 60.874 47.826 0.00 0.00 44.80 2.69
104 126 5.505819 CCAAGTTTCTCCGTTTCTCCTTTTC 60.506 44.000 0.00 0.00 0.00 2.29
165 191 1.881973 GCTGCATCCAGAACTTGTTCA 59.118 47.619 14.80 0.00 41.77 3.18
166 192 2.095364 GCTGCATCCAGAACTTGTTCAG 60.095 50.000 14.80 7.46 41.77 3.02
167 193 3.144506 CTGCATCCAGAACTTGTTCAGT 58.855 45.455 14.80 0.00 41.77 3.41
183 209 5.125356 TGTTCAGTTCTTCAAATGCTGAGA 58.875 37.500 0.00 0.00 37.47 3.27
216 242 4.913924 GCTTGAACTGACATGAAACATGAC 59.086 41.667 16.86 11.77 0.00 3.06
223 249 1.194547 ACATGAAACATGACACGCGAC 59.805 47.619 15.93 4.24 0.00 5.19
270 300 3.353836 CGTTGGAACCTGGCCGTG 61.354 66.667 0.00 0.00 0.00 4.94
275 305 3.948719 GAACCTGGCCGTGGTGGA 61.949 66.667 19.25 0.00 42.00 4.02
296 326 4.405762 CGCGAGGCACGGTATAAA 57.594 55.556 0.00 0.00 42.83 1.40
298 328 1.000884 CGCGAGGCACGGTATAAAAA 58.999 50.000 0.00 0.00 42.83 1.94
299 329 1.267186 CGCGAGGCACGGTATAAAAAC 60.267 52.381 0.00 0.00 42.83 2.43
300 330 1.063027 GCGAGGCACGGTATAAAAACC 59.937 52.381 6.44 0.00 42.83 3.27
301 331 1.667212 CGAGGCACGGTATAAAAACCC 59.333 52.381 0.00 0.00 36.03 4.11
303 333 0.734309 GGCACGGTATAAAAACCCGG 59.266 55.000 0.00 0.00 45.85 5.73
304 334 0.099259 GCACGGTATAAAAACCCGGC 59.901 55.000 0.00 0.00 45.85 6.13
305 335 1.741528 CACGGTATAAAAACCCGGCT 58.258 50.000 0.00 0.00 45.85 5.52
307 337 0.932399 CGGTATAAAAACCCGGCTCG 59.068 55.000 0.00 0.00 38.09 5.03
308 338 0.659427 GGTATAAAAACCCGGCTCGC 59.341 55.000 0.00 0.00 33.02 5.03
309 339 1.660167 GTATAAAAACCCGGCTCGCT 58.340 50.000 0.00 0.00 0.00 4.93
311 341 1.092348 ATAAAAACCCGGCTCGCTTC 58.908 50.000 0.00 0.00 0.00 3.86
325 355 2.793322 GCTTCGGCGAAAGAGCGAG 61.793 63.158 23.81 10.89 38.18 5.03
327 357 1.136872 CTTCGGCGAAAGAGCGAGAG 61.137 60.000 23.81 4.34 38.18 3.20
343 373 3.000080 GAGCGACCGCGTTCACAAG 62.000 63.158 4.92 0.00 45.51 3.16
344 374 4.719616 GCGACCGCGTTCACAAGC 62.720 66.667 4.92 0.00 40.36 4.01
345 375 4.072088 CGACCGCGTTCACAAGCC 62.072 66.667 4.92 0.00 0.00 4.35
346 376 3.723348 GACCGCGTTCACAAGCCC 61.723 66.667 4.92 0.00 0.00 5.19
349 379 4.025401 CGCGTTCACAAGCCCCAC 62.025 66.667 0.00 0.00 0.00 4.61
350 380 2.904866 GCGTTCACAAGCCCCACA 60.905 61.111 0.00 0.00 0.00 4.17
351 381 3.030652 CGTTCACAAGCCCCACAC 58.969 61.111 0.00 0.00 0.00 3.82
354 384 3.050354 TTCACAAGCCCCACACGGT 62.050 57.895 0.00 0.00 0.00 4.83
355 385 2.951475 TTCACAAGCCCCACACGGTC 62.951 60.000 0.00 0.00 0.00 4.79
356 386 4.265056 ACAAGCCCCACACGGTCC 62.265 66.667 0.00 0.00 0.00 4.46
360 390 3.324108 GCCCCACACGGTCCCTTA 61.324 66.667 0.00 0.00 0.00 2.69
361 391 2.666812 CCCCACACGGTCCCTTAC 59.333 66.667 0.00 0.00 0.00 2.34
362 392 2.666812 CCCACACGGTCCCTTACC 59.333 66.667 0.00 0.00 45.77 2.85
369 399 2.183555 GGTCCCTTACCTCGCACG 59.816 66.667 0.00 0.00 45.75 5.34
370 400 2.508663 GTCCCTTACCTCGCACGC 60.509 66.667 0.00 0.00 0.00 5.34
371 401 3.766691 TCCCTTACCTCGCACGCC 61.767 66.667 0.00 0.00 0.00 5.68
373 403 2.509336 CCTTACCTCGCACGCCAG 60.509 66.667 0.00 0.00 0.00 4.85
374 404 3.188786 CTTACCTCGCACGCCAGC 61.189 66.667 0.00 0.00 0.00 4.85
376 406 3.932580 TTACCTCGCACGCCAGCAG 62.933 63.158 0.00 0.00 0.00 4.24
379 409 4.731612 CTCGCACGCCAGCAGACT 62.732 66.667 0.00 0.00 0.00 3.24
387 417 2.571757 CCAGCAGACTCGCCGTTA 59.428 61.111 0.00 0.00 0.00 3.18
388 418 1.805945 CCAGCAGACTCGCCGTTAC 60.806 63.158 0.00 0.00 0.00 2.50
390 420 2.879462 GCAGACTCGCCGTTACCG 60.879 66.667 0.00 0.00 0.00 4.02
392 422 4.125695 AGACTCGCCGTTACCGCC 62.126 66.667 0.00 0.00 0.00 6.13
422 452 3.635510 AGGAACTCCGATGGCCTC 58.364 61.111 3.32 0.00 42.08 4.70
423 453 2.066999 AGGAACTCCGATGGCCTCC 61.067 63.158 3.32 0.00 42.08 4.30
424 454 2.367202 GGAACTCCGATGGCCTCCA 61.367 63.158 3.32 0.00 38.19 3.86
425 455 1.153349 GAACTCCGATGGCCTCCAC 60.153 63.158 3.32 0.00 35.80 4.02
426 456 2.595009 GAACTCCGATGGCCTCCACC 62.595 65.000 3.32 0.00 35.80 4.61
427 457 4.227134 CTCCGATGGCCTCCACCG 62.227 72.222 3.32 0.00 40.86 4.94
466 496 4.803426 GCCACTGGCTCGAGGACG 62.803 72.222 15.58 0.00 46.69 4.79
467 497 3.062466 CCACTGGCTCGAGGACGA 61.062 66.667 15.58 0.00 46.56 4.20
492 522 4.593864 GACCTCCGCTCCCGCATC 62.594 72.222 0.00 0.00 35.30 3.91
500 530 3.508840 CTCCCGCATCCGCCAAAC 61.509 66.667 0.00 0.00 33.11 2.93
504 534 3.814268 CGCATCCGCCAAACCCTG 61.814 66.667 0.00 0.00 33.11 4.45
505 535 2.676471 GCATCCGCCAAACCCTGT 60.676 61.111 0.00 0.00 0.00 4.00
506 536 2.993471 GCATCCGCCAAACCCTGTG 61.993 63.158 0.00 0.00 0.00 3.66
507 537 1.303236 CATCCGCCAAACCCTGTGA 60.303 57.895 0.00 0.00 0.00 3.58
508 538 1.002134 ATCCGCCAAACCCTGTGAG 60.002 57.895 0.00 0.00 0.00 3.51
509 539 3.365265 CCGCCAAACCCTGTGAGC 61.365 66.667 0.00 0.00 0.00 4.26
510 540 2.594303 CGCCAAACCCTGTGAGCA 60.594 61.111 0.00 0.00 0.00 4.26
511 541 2.620112 CGCCAAACCCTGTGAGCAG 61.620 63.158 0.00 0.00 42.22 4.24
512 542 2.924105 GCCAAACCCTGTGAGCAGC 61.924 63.158 0.00 0.00 41.26 5.25
513 543 2.270986 CCAAACCCTGTGAGCAGCC 61.271 63.158 0.00 0.00 41.26 4.85
514 544 1.529010 CAAACCCTGTGAGCAGCCA 60.529 57.895 0.00 0.00 41.26 4.75
515 545 1.529244 AAACCCTGTGAGCAGCCAC 60.529 57.895 6.98 6.98 41.26 5.01
516 546 2.983725 AAACCCTGTGAGCAGCCACC 62.984 60.000 10.46 0.00 41.26 4.61
517 547 3.957586 CCCTGTGAGCAGCCACCA 61.958 66.667 10.46 0.00 41.26 4.17
518 548 2.670934 CCTGTGAGCAGCCACCAC 60.671 66.667 10.46 7.24 41.26 4.16
519 549 2.429058 CTGTGAGCAGCCACCACT 59.571 61.111 10.46 0.00 35.77 4.00
520 550 1.670406 CTGTGAGCAGCCACCACTC 60.670 63.158 10.46 0.00 35.77 3.51
521 551 2.359230 GTGAGCAGCCACCACTCC 60.359 66.667 3.30 0.00 0.00 3.85
522 552 2.527624 TGAGCAGCCACCACTCCT 60.528 61.111 0.00 0.00 0.00 3.69
523 553 2.267324 GAGCAGCCACCACTCCTC 59.733 66.667 0.00 0.00 0.00 3.71
524 554 3.322318 GAGCAGCCACCACTCCTCC 62.322 68.421 0.00 0.00 0.00 4.30
525 555 4.416738 GCAGCCACCACTCCTCCC 62.417 72.222 0.00 0.00 0.00 4.30
526 556 2.608988 CAGCCACCACTCCTCCCT 60.609 66.667 0.00 0.00 0.00 4.20
527 557 2.284995 AGCCACCACTCCTCCCTC 60.285 66.667 0.00 0.00 0.00 4.30
528 558 2.607750 GCCACCACTCCTCCCTCA 60.608 66.667 0.00 0.00 0.00 3.86
529 559 2.664081 GCCACCACTCCTCCCTCAG 61.664 68.421 0.00 0.00 0.00 3.35
530 560 2.664081 CCACCACTCCTCCCTCAGC 61.664 68.421 0.00 0.00 0.00 4.26
531 561 1.611851 CACCACTCCTCCCTCAGCT 60.612 63.158 0.00 0.00 0.00 4.24
532 562 1.305718 ACCACTCCTCCCTCAGCTC 60.306 63.158 0.00 0.00 0.00 4.09
533 563 2.063378 CCACTCCTCCCTCAGCTCC 61.063 68.421 0.00 0.00 0.00 4.70
534 564 2.063378 CACTCCTCCCTCAGCTCCC 61.063 68.421 0.00 0.00 0.00 4.30
535 565 2.445654 CTCCTCCCTCAGCTCCCC 60.446 72.222 0.00 0.00 0.00 4.81
536 566 4.095400 TCCTCCCTCAGCTCCCCC 62.095 72.222 0.00 0.00 0.00 5.40
570 600 4.143333 CGTCCCCAGCCCGTACAG 62.143 72.222 0.00 0.00 0.00 2.74
571 601 4.468689 GTCCCCAGCCCGTACAGC 62.469 72.222 0.00 0.00 0.00 4.40
574 604 4.814294 CCCAGCCCGTACAGCGTC 62.814 72.222 0.00 0.00 39.32 5.19
575 605 4.814294 CCAGCCCGTACAGCGTCC 62.814 72.222 0.00 0.00 39.32 4.79
576 606 4.814294 CAGCCCGTACAGCGTCCC 62.814 72.222 0.00 0.00 39.32 4.46
615 645 1.606601 TCGATCGCCTGGGGGATAG 60.607 63.158 17.21 16.80 45.73 2.08
618 648 1.280457 GATCGCCTGGGGGATAGAAT 58.720 55.000 17.21 0.00 45.73 2.40
620 679 1.518367 TCGCCTGGGGGATAGAATTT 58.482 50.000 11.17 0.00 33.58 1.82
621 680 1.420138 TCGCCTGGGGGATAGAATTTC 59.580 52.381 11.17 0.00 33.58 2.17
629 688 2.040412 GGGGATAGAATTTCTGGCGGAT 59.960 50.000 9.22 0.00 0.00 4.18
630 689 3.339141 GGGATAGAATTTCTGGCGGATC 58.661 50.000 9.22 3.76 0.00 3.36
632 691 2.930826 TAGAATTTCTGGCGGATCCC 57.069 50.000 6.06 0.00 0.00 3.85
659 718 3.809013 CCCGGATCTGGGGGTTGG 61.809 72.222 29.94 4.78 46.17 3.77
660 719 3.809013 CCGGATCTGGGGGTTGGG 61.809 72.222 13.34 0.00 0.00 4.12
661 720 3.015145 CGGATCTGGGGGTTGGGT 61.015 66.667 0.00 0.00 0.00 4.51
662 721 3.007542 GGATCTGGGGGTTGGGTC 58.992 66.667 0.00 0.00 0.00 4.46
663 722 2.590092 GATCTGGGGGTTGGGTCG 59.410 66.667 0.00 0.00 0.00 4.79
664 723 1.993391 GATCTGGGGGTTGGGTCGA 60.993 63.158 0.00 0.00 0.00 4.20
665 724 1.540367 ATCTGGGGGTTGGGTCGAA 60.540 57.895 0.00 0.00 0.00 3.71
666 725 0.919289 ATCTGGGGGTTGGGTCGAAT 60.919 55.000 0.00 0.00 0.00 3.34
667 726 1.378514 CTGGGGGTTGGGTCGAATG 60.379 63.158 0.00 0.00 0.00 2.67
668 727 2.044352 GGGGGTTGGGTCGAATGG 60.044 66.667 0.00 0.00 0.00 3.16
669 728 2.608550 GGGGGTTGGGTCGAATGGA 61.609 63.158 0.00 0.00 0.00 3.41
670 729 1.381076 GGGGTTGGGTCGAATGGAA 59.619 57.895 0.00 0.00 0.00 3.53
671 730 0.033503 GGGGTTGGGTCGAATGGAAT 60.034 55.000 0.00 0.00 0.00 3.01
672 731 1.618616 GGGGTTGGGTCGAATGGAATT 60.619 52.381 0.00 0.00 40.93 2.17
673 732 1.476488 GGGTTGGGTCGAATGGAATTG 59.524 52.381 0.00 0.00 36.07 2.32
674 733 2.442413 GGTTGGGTCGAATGGAATTGA 58.558 47.619 0.00 0.00 36.07 2.57
675 734 2.423538 GGTTGGGTCGAATGGAATTGAG 59.576 50.000 0.00 0.00 36.07 3.02
676 735 1.750193 TGGGTCGAATGGAATTGAGC 58.250 50.000 0.00 0.00 36.07 4.26
677 736 0.657840 GGGTCGAATGGAATTGAGCG 59.342 55.000 0.00 0.00 36.07 5.03
678 737 0.657840 GGTCGAATGGAATTGAGCGG 59.342 55.000 0.00 0.00 36.07 5.52
679 738 1.651987 GTCGAATGGAATTGAGCGGA 58.348 50.000 0.00 0.00 36.07 5.54
680 739 2.213499 GTCGAATGGAATTGAGCGGAT 58.787 47.619 0.00 0.00 36.07 4.18
681 740 2.614057 GTCGAATGGAATTGAGCGGATT 59.386 45.455 0.00 0.00 36.07 3.01
682 741 2.613595 TCGAATGGAATTGAGCGGATTG 59.386 45.455 0.00 0.00 36.07 2.67
683 742 2.287188 CGAATGGAATTGAGCGGATTGG 60.287 50.000 0.00 0.00 36.07 3.16
684 743 2.442236 ATGGAATTGAGCGGATTGGT 57.558 45.000 0.00 0.00 0.00 3.67
685 744 2.214376 TGGAATTGAGCGGATTGGTT 57.786 45.000 0.00 0.00 0.00 3.67
686 745 1.818060 TGGAATTGAGCGGATTGGTTG 59.182 47.619 0.00 0.00 0.00 3.77
687 746 2.091541 GGAATTGAGCGGATTGGTTGA 58.908 47.619 0.00 0.00 0.00 3.18
688 747 2.098117 GGAATTGAGCGGATTGGTTGAG 59.902 50.000 0.00 0.00 0.00 3.02
689 748 1.755179 ATTGAGCGGATTGGTTGAGG 58.245 50.000 0.00 0.00 0.00 3.86
690 749 0.322456 TTGAGCGGATTGGTTGAGGG 60.322 55.000 0.00 0.00 0.00 4.30
691 750 2.044946 AGCGGATTGGTTGAGGGC 60.045 61.111 0.00 0.00 0.00 5.19
692 751 2.044946 GCGGATTGGTTGAGGGCT 60.045 61.111 0.00 0.00 0.00 5.19
693 752 1.678970 GCGGATTGGTTGAGGGCTT 60.679 57.895 0.00 0.00 0.00 4.35
694 753 0.393808 GCGGATTGGTTGAGGGCTTA 60.394 55.000 0.00 0.00 0.00 3.09
695 754 1.668419 CGGATTGGTTGAGGGCTTAG 58.332 55.000 0.00 0.00 0.00 2.18
696 755 1.747206 CGGATTGGTTGAGGGCTTAGG 60.747 57.143 0.00 0.00 0.00 2.69
697 756 1.410224 GGATTGGTTGAGGGCTTAGGG 60.410 57.143 0.00 0.00 0.00 3.53
698 757 0.631212 ATTGGTTGAGGGCTTAGGGG 59.369 55.000 0.00 0.00 0.00 4.79
699 758 0.774491 TTGGTTGAGGGCTTAGGGGT 60.774 55.000 0.00 0.00 0.00 4.95
700 759 0.774491 TGGTTGAGGGCTTAGGGGTT 60.774 55.000 0.00 0.00 0.00 4.11
701 760 0.408309 GGTTGAGGGCTTAGGGGTTT 59.592 55.000 0.00 0.00 0.00 3.27
702 761 1.616187 GGTTGAGGGCTTAGGGGTTTC 60.616 57.143 0.00 0.00 0.00 2.78
703 762 0.326927 TTGAGGGCTTAGGGGTTTCG 59.673 55.000 0.00 0.00 0.00 3.46
704 763 1.451567 GAGGGCTTAGGGGTTTCGC 60.452 63.158 0.00 0.00 0.00 4.70
705 764 2.822701 GGGCTTAGGGGTTTCGCG 60.823 66.667 0.00 0.00 0.00 5.87
706 765 2.046604 GGCTTAGGGGTTTCGCGT 60.047 61.111 5.77 0.00 0.00 6.01
707 766 1.218854 GGCTTAGGGGTTTCGCGTA 59.781 57.895 5.77 0.00 0.00 4.42
708 767 0.808847 GGCTTAGGGGTTTCGCGTAG 60.809 60.000 5.77 0.00 0.00 3.51
728 787 4.678743 GGCGGGGGTTCAAGCCTT 62.679 66.667 5.40 0.00 45.67 4.35
729 788 3.062466 GCGGGGGTTCAAGCCTTC 61.062 66.667 5.40 0.00 35.71 3.46
730 789 2.361230 CGGGGGTTCAAGCCTTCC 60.361 66.667 5.40 0.00 35.71 3.46
731 790 2.907179 CGGGGGTTCAAGCCTTCCT 61.907 63.158 5.40 0.00 35.71 3.36
732 791 1.000771 GGGGGTTCAAGCCTTCCTC 60.001 63.158 5.40 0.00 35.71 3.71
733 792 1.501654 GGGGGTTCAAGCCTTCCTCT 61.502 60.000 5.40 0.00 35.71 3.69
734 793 0.034960 GGGGTTCAAGCCTTCCTCTC 60.035 60.000 5.40 0.00 35.71 3.20
982 1675 6.744993 CCAGACGTCATATTAGAATCGATCAG 59.255 42.308 19.50 0.00 0.00 2.90
983 1676 7.361286 CCAGACGTCATATTAGAATCGATCAGA 60.361 40.741 19.50 0.00 0.00 3.27
1050 2687 3.243771 CCATCACCTTCCTCGGTACATAC 60.244 52.174 0.00 0.00 34.94 2.39
1195 2852 0.321122 CCCGAGGGAATGATGCTAGC 60.321 60.000 8.10 8.10 37.50 3.42
1221 2878 1.374252 GTCAAGTCACCGGCGATGT 60.374 57.895 9.30 0.00 0.00 3.06
1311 2970 8.815565 TTAAATATATGGGCTTCAGTTTGTCA 57.184 30.769 0.00 0.00 0.00 3.58
1322 2981 2.024846 TCAGTTTGTCACCCCCTTTGAA 60.025 45.455 0.00 0.00 0.00 2.69
1358 3017 5.638596 TTGATAGATGCATGCATGGAATC 57.361 39.130 36.73 29.71 36.70 2.52
1392 3051 2.912771 CAGGGCGATATGGTGTTTGTA 58.087 47.619 0.00 0.00 0.00 2.41
1542 3206 8.028354 TGCTACACACCAATCAAATCATTAAAG 58.972 33.333 0.00 0.00 0.00 1.85
1580 3244 6.683090 TTTCGTTTGCCTTGAAAATAATCG 57.317 33.333 0.00 0.00 0.00 3.34
1661 3329 4.952957 TCACCAAAGGAGACAACAATTCAA 59.047 37.500 0.00 0.00 0.00 2.69
1888 3557 5.102953 TGTCCAATGCTAACAGCTATCTT 57.897 39.130 0.00 0.00 42.97 2.40
1960 3629 4.293415 GCAAGCACACATTATATTCTGGC 58.707 43.478 0.00 0.00 0.00 4.85
1968 3637 7.535258 GCACACATTATATTCTGGCTAATTTCG 59.465 37.037 0.00 0.00 0.00 3.46
2152 3821 6.017026 TGTTCGTGGTTAAAGTATGCATCAAA 60.017 34.615 0.19 0.00 0.00 2.69
2156 3826 6.375377 GTGGTTAAAGTATGCATCAAACGAA 58.625 36.000 0.19 0.00 0.00 3.85
2349 4032 8.923270 TCTTTGAAAGGTAGATTTTGGTGAAAT 58.077 29.630 4.94 0.00 40.61 2.17
2477 4166 1.377366 TTGGCAACGGCGAGTTTGAA 61.377 50.000 16.62 0.00 42.02 2.69
2491 4180 4.442706 GAGTTTGAATAGCCATCGAAGGA 58.557 43.478 11.67 0.00 0.00 3.36
2506 4195 0.607489 AAGGATCAGCACACACTGGC 60.607 55.000 0.00 0.00 38.26 4.85
2514 4204 1.750930 CACACACTGGCCAGAGAGT 59.249 57.895 39.19 30.68 0.00 3.24
2553 4243 2.223294 CGTTGGATCTGAGGTACGAGTC 60.223 54.545 0.00 0.00 0.00 3.36
2618 4309 1.757306 CCATGGAGCTTAGCCCGAT 59.243 57.895 5.56 0.00 0.00 4.18
2621 4312 1.056700 ATGGAGCTTAGCCCGATGGT 61.057 55.000 0.00 0.00 0.00 3.55
2625 4316 0.397816 AGCTTAGCCCGATGGTCTCT 60.398 55.000 0.00 0.00 0.00 3.10
2629 4320 2.160721 TAGCCCGATGGTCTCTTTCT 57.839 50.000 0.00 0.00 0.00 2.52
2630 4321 1.280457 AGCCCGATGGTCTCTTTCTT 58.720 50.000 0.00 0.00 0.00 2.52
2639 4330 1.921230 GGTCTCTTTCTTCGATGACGC 59.079 52.381 0.00 0.00 39.58 5.19
2821 4513 5.077564 TGTGCTATGGACTCGGTCTTATAT 58.922 41.667 4.41 0.00 32.47 0.86
2824 4516 5.952347 TGCTATGGACTCGGTCTTATATGAT 59.048 40.000 4.41 0.00 32.47 2.45
2900 4592 6.147985 GGTTGACTTTAGAAGCCTTAAGACAG 59.852 42.308 3.36 0.00 36.02 3.51
3003 6548 2.487762 TGTCGATGCCAAGGTGAATTTC 59.512 45.455 0.00 0.00 0.00 2.17
3015 6560 6.552350 CCAAGGTGAATTTCATGGAATAGGAT 59.448 38.462 10.71 0.00 0.00 3.24
3046 6594 9.004717 TCACTATTGAACAACCATCGATAAAAA 57.995 29.630 0.00 0.00 0.00 1.94
3079 6627 8.037758 CGGATCCAAATAGAGCTACAGAAATAT 58.962 37.037 13.41 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 54 1.211457 CAGTAGGCAATCCTGGAAGCT 59.789 52.381 19.62 11.02 44.08 3.74
66 77 0.472734 ACTTGGTGTCTCTGGCCTCT 60.473 55.000 3.32 0.00 0.00 3.69
165 191 4.965814 TCAGTCTCAGCATTTGAAGAACT 58.034 39.130 0.00 0.00 34.81 3.01
166 192 5.238214 AGTTCAGTCTCAGCATTTGAAGAAC 59.762 40.000 0.00 0.00 35.67 3.01
167 193 5.237996 CAGTTCAGTCTCAGCATTTGAAGAA 59.762 40.000 0.00 0.00 34.81 2.52
168 194 4.753610 CAGTTCAGTCTCAGCATTTGAAGA 59.246 41.667 0.00 0.00 34.81 2.87
169 195 4.514441 ACAGTTCAGTCTCAGCATTTGAAG 59.486 41.667 0.00 0.00 34.81 3.02
183 209 2.939103 GTCAGTTCAAGCACAGTTCAGT 59.061 45.455 0.00 0.00 0.00 3.41
216 242 4.259964 GTCGATATACATACATGTCGCGTG 59.740 45.833 5.77 0.00 41.97 5.34
223 249 4.433615 GGCCAGGTCGATATACATACATG 58.566 47.826 0.00 0.00 0.00 3.21
280 310 1.063027 GGTTTTTATACCGTGCCTCGC 59.937 52.381 0.00 0.00 38.35 5.03
282 312 1.667212 CGGGTTTTTATACCGTGCCTC 59.333 52.381 0.00 0.00 42.53 4.70
283 313 1.679640 CCGGGTTTTTATACCGTGCCT 60.680 52.381 0.00 0.00 45.85 4.75
284 314 0.734309 CCGGGTTTTTATACCGTGCC 59.266 55.000 0.00 0.00 45.85 5.01
285 315 0.099259 GCCGGGTTTTTATACCGTGC 59.901 55.000 2.18 0.00 45.85 5.34
286 316 1.667212 GAGCCGGGTTTTTATACCGTG 59.333 52.381 8.00 0.00 45.85 4.94
287 317 1.740043 CGAGCCGGGTTTTTATACCGT 60.740 52.381 8.00 0.00 45.85 4.83
288 318 0.932399 CGAGCCGGGTTTTTATACCG 59.068 55.000 8.00 0.00 46.79 4.02
289 319 0.659427 GCGAGCCGGGTTTTTATACC 59.341 55.000 8.00 0.00 37.47 2.73
290 320 1.660167 AGCGAGCCGGGTTTTTATAC 58.340 50.000 8.00 0.00 0.00 1.47
291 321 2.282407 GAAGCGAGCCGGGTTTTTATA 58.718 47.619 8.00 0.00 0.00 0.98
295 325 3.047877 CGAAGCGAGCCGGGTTTT 61.048 61.111 8.00 2.83 0.00 2.43
307 337 2.793322 CTCGCTCTTTCGCCGAAGC 61.793 63.158 0.00 0.00 0.00 3.86
308 338 1.136872 CTCTCGCTCTTTCGCCGAAG 61.137 60.000 0.00 0.00 0.00 3.79
309 339 1.154016 CTCTCGCTCTTTCGCCGAA 60.154 57.895 0.00 0.00 0.00 4.30
311 341 3.251043 GCTCTCGCTCTTTCGCCG 61.251 66.667 0.00 0.00 0.00 6.46
313 343 2.202492 TCGCTCTCGCTCTTTCGC 60.202 61.111 0.00 0.00 35.26 4.70
314 344 1.870016 GGTCGCTCTCGCTCTTTCG 60.870 63.158 0.00 0.00 35.26 3.46
315 345 1.870016 CGGTCGCTCTCGCTCTTTC 60.870 63.158 0.00 0.00 35.26 2.62
322 352 4.753877 TGAACGCGGTCGCTCTCG 62.754 66.667 20.86 0.39 39.84 4.04
323 353 3.173240 GTGAACGCGGTCGCTCTC 61.173 66.667 29.37 8.72 39.84 3.20
325 355 3.000080 CTTGTGAACGCGGTCGCTC 62.000 63.158 34.65 20.50 39.84 5.03
327 357 4.719616 GCTTGTGAACGCGGTCGC 62.720 66.667 29.89 29.89 39.84 5.19
328 358 4.072088 GGCTTGTGAACGCGGTCG 62.072 66.667 20.86 5.99 42.43 4.79
329 359 3.723348 GGGCTTGTGAACGCGGTC 61.723 66.667 19.40 19.40 0.00 4.79
333 363 2.904866 TGTGGGGCTTGTGAACGC 60.905 61.111 0.00 0.00 0.00 4.84
334 364 2.892334 CGTGTGGGGCTTGTGAACG 61.892 63.158 0.00 0.00 0.00 3.95
335 365 2.551912 CCGTGTGGGGCTTGTGAAC 61.552 63.158 0.00 0.00 0.00 3.18
336 366 2.203280 CCGTGTGGGGCTTGTGAA 60.203 61.111 0.00 0.00 0.00 3.18
337 367 3.469863 GACCGTGTGGGGCTTGTGA 62.470 63.158 0.00 0.00 42.52 3.58
339 369 4.265056 GGACCGTGTGGGGCTTGT 62.265 66.667 0.00 0.00 46.52 3.16
343 373 3.324108 TAAGGGACCGTGTGGGGC 61.324 66.667 0.00 0.00 46.65 5.80
344 374 2.666812 GTAAGGGACCGTGTGGGG 59.333 66.667 0.00 0.00 41.60 4.96
345 375 2.666812 GGTAAGGGACCGTGTGGG 59.333 66.667 0.00 0.00 38.87 4.61
354 384 3.766691 GGCGTGCGAGGTAAGGGA 61.767 66.667 0.00 0.00 0.00 4.20
355 385 4.077184 TGGCGTGCGAGGTAAGGG 62.077 66.667 0.00 0.00 0.00 3.95
356 386 2.509336 CTGGCGTGCGAGGTAAGG 60.509 66.667 0.00 0.00 0.00 2.69
357 387 3.188786 GCTGGCGTGCGAGGTAAG 61.189 66.667 6.01 0.00 0.00 2.34
358 388 3.932580 CTGCTGGCGTGCGAGGTAA 62.933 63.158 6.01 0.00 35.36 2.85
362 392 4.731612 AGTCTGCTGGCGTGCGAG 62.732 66.667 0.00 0.00 35.36 5.03
363 393 4.724602 GAGTCTGCTGGCGTGCGA 62.725 66.667 0.00 0.00 35.36 5.10
369 399 3.642778 TAACGGCGAGTCTGCTGGC 62.643 63.158 16.62 0.44 45.70 4.85
370 400 1.805945 GTAACGGCGAGTCTGCTGG 60.806 63.158 16.62 8.16 45.70 4.85
371 401 1.805945 GGTAACGGCGAGTCTGCTG 60.806 63.158 16.62 12.35 46.83 4.41
395 425 2.573689 GAGTTCCTCGACGACGCG 60.574 66.667 3.53 3.53 39.58 6.01
397 427 1.703438 ATCGGAGTTCCTCGACGACG 61.703 60.000 0.00 0.00 38.25 5.12
398 428 0.248134 CATCGGAGTTCCTCGACGAC 60.248 60.000 0.00 0.00 38.25 4.34
399 429 1.374343 CCATCGGAGTTCCTCGACGA 61.374 60.000 0.00 0.00 38.25 4.20
400 430 1.064296 CCATCGGAGTTCCTCGACG 59.936 63.158 0.00 0.00 38.25 5.12
401 431 1.227002 GCCATCGGAGTTCCTCGAC 60.227 63.158 0.00 0.00 38.25 4.20
402 432 2.423898 GGCCATCGGAGTTCCTCGA 61.424 63.158 0.00 0.00 39.79 4.04
403 433 2.107141 GGCCATCGGAGTTCCTCG 59.893 66.667 0.00 0.00 0.00 4.63
404 434 1.443828 GAGGCCATCGGAGTTCCTC 59.556 63.158 5.01 6.50 36.86 3.71
405 435 2.066999 GGAGGCCATCGGAGTTCCT 61.067 63.158 5.01 0.00 0.00 3.36
406 436 2.367202 TGGAGGCCATCGGAGTTCC 61.367 63.158 5.01 0.00 0.00 3.62
407 437 1.153349 GTGGAGGCCATCGGAGTTC 60.153 63.158 5.01 0.00 35.28 3.01
408 438 2.670148 GGTGGAGGCCATCGGAGTT 61.670 63.158 5.01 0.00 35.28 3.01
409 439 3.083997 GGTGGAGGCCATCGGAGT 61.084 66.667 5.01 0.00 35.28 3.85
450 480 3.062466 TCGTCCTCGAGCCAGTGG 61.062 66.667 6.99 4.20 41.35 4.00
483 513 3.508840 GTTTGGCGGATGCGGGAG 61.509 66.667 9.20 0.00 44.10 4.30
487 517 3.814268 CAGGGTTTGGCGGATGCG 61.814 66.667 0.65 0.65 44.10 4.73
488 518 2.676471 ACAGGGTTTGGCGGATGC 60.676 61.111 0.00 0.00 41.71 3.91
489 519 1.303236 TCACAGGGTTTGGCGGATG 60.303 57.895 0.00 0.00 0.00 3.51
490 520 1.002134 CTCACAGGGTTTGGCGGAT 60.002 57.895 0.00 0.00 0.00 4.18
491 521 2.429930 CTCACAGGGTTTGGCGGA 59.570 61.111 0.00 0.00 0.00 5.54
492 522 3.365265 GCTCACAGGGTTTGGCGG 61.365 66.667 0.00 0.00 0.00 6.13
493 523 2.594303 TGCTCACAGGGTTTGGCG 60.594 61.111 0.00 0.00 0.00 5.69
494 524 2.924105 GCTGCTCACAGGGTTTGGC 61.924 63.158 0.00 0.00 44.63 4.52
495 525 2.270986 GGCTGCTCACAGGGTTTGG 61.271 63.158 0.00 0.00 44.63 3.28
496 526 1.529010 TGGCTGCTCACAGGGTTTG 60.529 57.895 0.00 0.00 44.63 2.93
497 527 1.529244 GTGGCTGCTCACAGGGTTT 60.529 57.895 13.89 0.00 44.63 3.27
498 528 2.113986 GTGGCTGCTCACAGGGTT 59.886 61.111 13.89 0.00 44.63 4.11
499 529 3.958860 GGTGGCTGCTCACAGGGT 61.959 66.667 18.44 0.00 44.63 4.34
500 530 3.957586 TGGTGGCTGCTCACAGGG 61.958 66.667 18.44 0.00 44.63 4.45
501 531 2.670934 GTGGTGGCTGCTCACAGG 60.671 66.667 18.44 0.00 44.63 4.00
503 533 2.427320 GAGTGGTGGCTGCTCACA 59.573 61.111 18.44 5.39 39.27 3.58
504 534 2.359230 GGAGTGGTGGCTGCTCAC 60.359 66.667 11.32 11.32 36.95 3.51
505 535 2.527624 AGGAGTGGTGGCTGCTCA 60.528 61.111 0.00 0.00 31.33 4.26
506 536 2.267324 GAGGAGTGGTGGCTGCTC 59.733 66.667 0.00 0.00 44.39 4.26
507 537 3.325753 GGAGGAGTGGTGGCTGCT 61.326 66.667 0.00 0.00 39.90 4.24
508 538 4.416738 GGGAGGAGTGGTGGCTGC 62.417 72.222 0.00 0.00 0.00 5.25
509 539 2.608988 AGGGAGGAGTGGTGGCTG 60.609 66.667 0.00 0.00 0.00 4.85
510 540 2.284995 GAGGGAGGAGTGGTGGCT 60.285 66.667 0.00 0.00 0.00 4.75
511 541 2.607750 TGAGGGAGGAGTGGTGGC 60.608 66.667 0.00 0.00 0.00 5.01
512 542 2.664081 GCTGAGGGAGGAGTGGTGG 61.664 68.421 0.00 0.00 0.00 4.61
513 543 1.611851 AGCTGAGGGAGGAGTGGTG 60.612 63.158 0.00 0.00 0.00 4.17
514 544 1.305718 GAGCTGAGGGAGGAGTGGT 60.306 63.158 0.00 0.00 0.00 4.16
515 545 2.063378 GGAGCTGAGGGAGGAGTGG 61.063 68.421 0.00 0.00 0.00 4.00
516 546 2.063378 GGGAGCTGAGGGAGGAGTG 61.063 68.421 0.00 0.00 0.00 3.51
517 547 2.366570 GGGAGCTGAGGGAGGAGT 59.633 66.667 0.00 0.00 0.00 3.85
518 548 2.445654 GGGGAGCTGAGGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
519 549 4.095400 GGGGGAGCTGAGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
553 583 4.143333 CTGTACGGGCTGGGGACG 62.143 72.222 0.00 0.00 0.00 4.79
554 584 4.468689 GCTGTACGGGCTGGGGAC 62.469 72.222 3.34 0.00 0.00 4.46
596 626 1.878656 CTATCCCCCAGGCGATCGAC 61.879 65.000 21.57 18.32 0.00 4.20
597 627 1.606601 CTATCCCCCAGGCGATCGA 60.607 63.158 21.57 0.00 0.00 3.59
598 628 1.185618 TTCTATCCCCCAGGCGATCG 61.186 60.000 11.69 11.69 0.00 3.69
599 629 1.280457 ATTCTATCCCCCAGGCGATC 58.720 55.000 0.00 0.00 0.00 3.69
600 630 1.747444 AATTCTATCCCCCAGGCGAT 58.253 50.000 0.00 0.00 0.00 4.58
609 639 2.930826 TCCGCCAGAAATTCTATCCC 57.069 50.000 0.00 0.00 0.00 3.85
610 640 3.339141 GGATCCGCCAGAAATTCTATCC 58.661 50.000 0.00 6.11 36.34 2.59
611 641 3.339141 GGGATCCGCCAGAAATTCTATC 58.661 50.000 5.45 0.00 38.95 2.08
612 642 2.040412 GGGGATCCGCCAGAAATTCTAT 59.960 50.000 17.92 0.00 38.95 1.98
615 645 0.106719 TGGGGATCCGCCAGAAATTC 60.107 55.000 24.83 0.00 41.55 2.17
641 700 4.506255 CAACCCCCAGATCCGGGC 62.506 72.222 8.71 0.00 45.90 6.13
642 701 3.809013 CCAACCCCCAGATCCGGG 61.809 72.222 7.08 7.08 46.94 5.73
643 702 3.809013 CCCAACCCCCAGATCCGG 61.809 72.222 0.00 0.00 0.00 5.14
644 703 3.015145 ACCCAACCCCCAGATCCG 61.015 66.667 0.00 0.00 0.00 4.18
646 705 1.559065 TTCGACCCAACCCCCAGATC 61.559 60.000 0.00 0.00 0.00 2.75
647 706 0.919289 ATTCGACCCAACCCCCAGAT 60.919 55.000 0.00 0.00 0.00 2.90
648 707 1.540367 ATTCGACCCAACCCCCAGA 60.540 57.895 0.00 0.00 0.00 3.86
649 708 1.378514 CATTCGACCCAACCCCCAG 60.379 63.158 0.00 0.00 0.00 4.45
650 709 2.760477 CATTCGACCCAACCCCCA 59.240 61.111 0.00 0.00 0.00 4.96
651 710 2.044352 CCATTCGACCCAACCCCC 60.044 66.667 0.00 0.00 0.00 5.40
652 711 0.033503 ATTCCATTCGACCCAACCCC 60.034 55.000 0.00 0.00 0.00 4.95
653 712 1.476488 CAATTCCATTCGACCCAACCC 59.524 52.381 0.00 0.00 0.00 4.11
654 713 2.423538 CTCAATTCCATTCGACCCAACC 59.576 50.000 0.00 0.00 0.00 3.77
655 714 2.159379 GCTCAATTCCATTCGACCCAAC 60.159 50.000 0.00 0.00 0.00 3.77
656 715 2.091541 GCTCAATTCCATTCGACCCAA 58.908 47.619 0.00 0.00 0.00 4.12
657 716 1.750193 GCTCAATTCCATTCGACCCA 58.250 50.000 0.00 0.00 0.00 4.51
658 717 0.657840 CGCTCAATTCCATTCGACCC 59.342 55.000 0.00 0.00 0.00 4.46
659 718 0.657840 CCGCTCAATTCCATTCGACC 59.342 55.000 0.00 0.00 0.00 4.79
660 719 1.651987 TCCGCTCAATTCCATTCGAC 58.348 50.000 0.00 0.00 0.00 4.20
661 720 2.613595 CAATCCGCTCAATTCCATTCGA 59.386 45.455 0.00 0.00 0.00 3.71
662 721 2.287188 CCAATCCGCTCAATTCCATTCG 60.287 50.000 0.00 0.00 0.00 3.34
663 722 2.689983 ACCAATCCGCTCAATTCCATTC 59.310 45.455 0.00 0.00 0.00 2.67
664 723 2.738743 ACCAATCCGCTCAATTCCATT 58.261 42.857 0.00 0.00 0.00 3.16
665 724 2.428171 CAACCAATCCGCTCAATTCCAT 59.572 45.455 0.00 0.00 0.00 3.41
666 725 1.818060 CAACCAATCCGCTCAATTCCA 59.182 47.619 0.00 0.00 0.00 3.53
667 726 2.091541 TCAACCAATCCGCTCAATTCC 58.908 47.619 0.00 0.00 0.00 3.01
668 727 2.098117 CCTCAACCAATCCGCTCAATTC 59.902 50.000 0.00 0.00 0.00 2.17
669 728 2.094675 CCTCAACCAATCCGCTCAATT 58.905 47.619 0.00 0.00 0.00 2.32
670 729 1.683011 CCCTCAACCAATCCGCTCAAT 60.683 52.381 0.00 0.00 0.00 2.57
671 730 0.322456 CCCTCAACCAATCCGCTCAA 60.322 55.000 0.00 0.00 0.00 3.02
672 731 1.299648 CCCTCAACCAATCCGCTCA 59.700 57.895 0.00 0.00 0.00 4.26
673 732 2.115291 GCCCTCAACCAATCCGCTC 61.115 63.158 0.00 0.00 0.00 5.03
674 733 2.044946 GCCCTCAACCAATCCGCT 60.045 61.111 0.00 0.00 0.00 5.52
675 734 0.393808 TAAGCCCTCAACCAATCCGC 60.394 55.000 0.00 0.00 0.00 5.54
676 735 1.668419 CTAAGCCCTCAACCAATCCG 58.332 55.000 0.00 0.00 0.00 4.18
677 736 1.410224 CCCTAAGCCCTCAACCAATCC 60.410 57.143 0.00 0.00 0.00 3.01
678 737 1.410224 CCCCTAAGCCCTCAACCAATC 60.410 57.143 0.00 0.00 0.00 2.67
679 738 0.631212 CCCCTAAGCCCTCAACCAAT 59.369 55.000 0.00 0.00 0.00 3.16
680 739 0.774491 ACCCCTAAGCCCTCAACCAA 60.774 55.000 0.00 0.00 0.00 3.67
681 740 0.774491 AACCCCTAAGCCCTCAACCA 60.774 55.000 0.00 0.00 0.00 3.67
682 741 0.408309 AAACCCCTAAGCCCTCAACC 59.592 55.000 0.00 0.00 0.00 3.77
683 742 1.835494 GAAACCCCTAAGCCCTCAAC 58.165 55.000 0.00 0.00 0.00 3.18
684 743 0.326927 CGAAACCCCTAAGCCCTCAA 59.673 55.000 0.00 0.00 0.00 3.02
685 744 1.988015 CGAAACCCCTAAGCCCTCA 59.012 57.895 0.00 0.00 0.00 3.86
686 745 1.451567 GCGAAACCCCTAAGCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
687 746 2.675371 GCGAAACCCCTAAGCCCT 59.325 61.111 0.00 0.00 0.00 5.19
688 747 2.242797 TACGCGAAACCCCTAAGCCC 62.243 60.000 15.93 0.00 0.00 5.19
689 748 0.808847 CTACGCGAAACCCCTAAGCC 60.809 60.000 15.93 0.00 0.00 4.35
690 749 1.426816 GCTACGCGAAACCCCTAAGC 61.427 60.000 15.93 3.37 0.00 3.09
691 750 0.808847 GGCTACGCGAAACCCCTAAG 60.809 60.000 15.93 0.00 0.00 2.18
692 751 1.218854 GGCTACGCGAAACCCCTAA 59.781 57.895 15.93 0.00 0.00 2.69
693 752 2.894919 GGCTACGCGAAACCCCTA 59.105 61.111 15.93 0.00 0.00 3.53
694 753 4.446413 CGGCTACGCGAAACCCCT 62.446 66.667 15.93 0.00 0.00 4.79
711 770 4.678743 AAGGCTTGAACCCCCGCC 62.679 66.667 0.00 0.00 42.79 6.13
712 771 3.062466 GAAGGCTTGAACCCCCGC 61.062 66.667 3.46 0.00 0.00 6.13
713 772 2.361230 GGAAGGCTTGAACCCCCG 60.361 66.667 3.46 0.00 0.00 5.73
714 773 1.000771 GAGGAAGGCTTGAACCCCC 60.001 63.158 3.46 0.00 0.00 5.40
715 774 0.034960 GAGAGGAAGGCTTGAACCCC 60.035 60.000 3.46 0.00 0.00 4.95
716 775 0.034960 GGAGAGGAAGGCTTGAACCC 60.035 60.000 3.46 0.00 0.00 4.11
717 776 0.988063 AGGAGAGGAAGGCTTGAACC 59.012 55.000 3.46 0.00 0.00 3.62
718 777 1.339535 CCAGGAGAGGAAGGCTTGAAC 60.340 57.143 3.46 0.00 0.00 3.18
719 778 0.987294 CCAGGAGAGGAAGGCTTGAA 59.013 55.000 3.46 0.00 0.00 2.69
720 779 0.911525 CCCAGGAGAGGAAGGCTTGA 60.912 60.000 3.46 0.00 0.00 3.02
721 780 1.204113 ACCCAGGAGAGGAAGGCTTG 61.204 60.000 3.46 0.00 0.00 4.01
722 781 1.162085 ACCCAGGAGAGGAAGGCTT 59.838 57.895 0.00 0.00 0.00 4.35
723 782 1.614824 CACCCAGGAGAGGAAGGCT 60.615 63.158 0.00 0.00 0.00 4.58
724 783 0.617820 TACACCCAGGAGAGGAAGGC 60.618 60.000 0.00 0.00 0.00 4.35
725 784 1.952621 TTACACCCAGGAGAGGAAGG 58.047 55.000 0.00 0.00 0.00 3.46
726 785 4.141688 GGTAATTACACCCAGGAGAGGAAG 60.142 50.000 17.16 0.00 31.91 3.46
727 786 3.778629 GGTAATTACACCCAGGAGAGGAA 59.221 47.826 17.16 0.00 31.91 3.36
728 787 3.246203 TGGTAATTACACCCAGGAGAGGA 60.246 47.826 17.16 0.00 37.84 3.71
729 788 3.112263 TGGTAATTACACCCAGGAGAGG 58.888 50.000 17.16 0.00 37.84 3.69
730 789 3.430374 CGTGGTAATTACACCCAGGAGAG 60.430 52.174 17.16 0.00 37.84 3.20
731 790 2.498481 CGTGGTAATTACACCCAGGAGA 59.502 50.000 17.16 0.00 37.84 3.71
732 791 2.901249 CGTGGTAATTACACCCAGGAG 58.099 52.381 17.16 0.00 37.84 3.69
733 792 1.065998 GCGTGGTAATTACACCCAGGA 60.066 52.381 17.16 0.00 37.84 3.86
734 793 1.375551 GCGTGGTAATTACACCCAGG 58.624 55.000 17.16 12.16 37.84 4.45
1071 2713 5.227238 AGCAAAATATCAACGCTGAAGAG 57.773 39.130 0.00 0.00 34.49 2.85
1143 2800 1.529438 CAACGCAACGACCATAACTGT 59.471 47.619 0.00 0.00 0.00 3.55
1195 2852 3.932289 GTGACTTGACACCCGTCG 58.068 61.111 0.00 0.00 45.80 5.12
1221 2878 4.963373 TCCATACTTTCTGACAAAACCGA 58.037 39.130 0.00 0.00 0.00 4.69
1291 2948 4.523083 GGTGACAAACTGAAGCCCATATA 58.477 43.478 0.00 0.00 0.00 0.86
1311 2970 0.322187 CGGTCGAATTCAAAGGGGGT 60.322 55.000 6.22 0.00 0.00 4.95
1322 2981 5.807520 GCATCTATCAATATGTCGGTCGAAT 59.192 40.000 0.00 0.00 0.00 3.34
1358 3017 0.877213 GCCCTGCAAAACAAGCACAG 60.877 55.000 0.00 0.00 37.02 3.66
1392 3051 3.225104 AGGTTCATTGCTCATGTTGTGT 58.775 40.909 0.00 0.00 34.06 3.72
1542 3206 8.349983 AGGCAAACGAAATATAACATATGAACC 58.650 33.333 10.38 0.00 0.00 3.62
1560 3224 5.390613 AGACGATTATTTTCAAGGCAAACG 58.609 37.500 0.00 0.00 0.00 3.60
1593 3257 3.943381 TCGATGCTCGTAAACCTAGAGAA 59.057 43.478 0.00 0.00 41.35 2.87
1594 3258 3.538591 TCGATGCTCGTAAACCTAGAGA 58.461 45.455 0.00 0.00 41.35 3.10
1595 3259 3.560481 TCTCGATGCTCGTAAACCTAGAG 59.440 47.826 0.00 0.00 41.35 2.43
1596 3260 3.538591 TCTCGATGCTCGTAAACCTAGA 58.461 45.455 0.00 0.00 41.35 2.43
1661 3329 4.573900 GCATAGAGAAATCGGTCATCCAT 58.426 43.478 0.00 0.00 0.00 3.41
1798 3466 7.396623 ACGGTAGAGCAAGGTATATATAAAGCT 59.603 37.037 8.40 8.40 0.00 3.74
2152 3821 6.361748 GTGTCTTTTACATACTCTTCGTTCGT 59.638 38.462 0.00 0.00 41.10 3.85
2156 3826 7.375834 TGATGTGTCTTTTACATACTCTTCGT 58.624 34.615 0.00 0.00 41.10 3.85
2436 4123 0.957395 CAGAGGCCGAATGTGTGCTT 60.957 55.000 0.00 0.00 0.00 3.91
2467 4156 2.201732 TCGATGGCTATTCAAACTCGC 58.798 47.619 0.00 0.00 0.00 5.03
2477 4166 1.973515 TGCTGATCCTTCGATGGCTAT 59.026 47.619 12.42 2.00 0.00 2.97
2491 4180 1.303074 CTGGCCAGTGTGTGCTGAT 60.303 57.895 25.53 0.00 38.70 2.90
2506 4195 2.223782 GCAGCTGTCATCTACTCTCTGG 60.224 54.545 16.64 0.00 0.00 3.86
2514 4204 1.816537 GTCCCGCAGCTGTCATCTA 59.183 57.895 16.64 0.00 0.00 1.98
2602 4293 1.056700 ACCATCGGGCTAAGCTCCAT 61.057 55.000 0.00 0.00 37.90 3.41
2618 4309 2.671351 GCGTCATCGAAGAAAGAGACCA 60.671 50.000 0.00 0.00 43.58 4.02
2621 4312 1.467543 CGGCGTCATCGAAGAAAGAGA 60.468 52.381 0.00 0.00 43.58 3.10
2625 4316 0.457853 CCTCGGCGTCATCGAAGAAA 60.458 55.000 6.85 0.00 43.58 2.52
2629 4320 2.752640 TCCCTCGGCGTCATCGAA 60.753 61.111 6.85 0.00 39.71 3.71
2630 4321 3.209812 CTCCCTCGGCGTCATCGA 61.210 66.667 6.85 0.00 39.71 3.59
2639 4330 2.907917 CGCTACTCCCTCCCTCGG 60.908 72.222 0.00 0.00 0.00 4.63
2725 4416 1.298413 CCACCTGATACGCGACTCG 60.298 63.158 15.93 5.45 45.38 4.18
2871 4563 8.434392 TCTTAAGGCTTCTAAAGTCAACCTTAA 58.566 33.333 1.30 10.08 42.82 1.85
2985 6530 3.441163 CATGAAATTCACCTTGGCATCG 58.559 45.455 0.00 0.00 0.00 3.84
3015 6560 7.552459 TCGATGGTTGTTCAATAGTGAGATTA 58.448 34.615 0.00 0.00 34.49 1.75
3046 6594 5.440610 AGCTCTATTTGGATCCGAATGTTT 58.559 37.500 30.39 12.98 32.71 2.83
3053 6601 4.855715 TCTGTAGCTCTATTTGGATCCG 57.144 45.455 7.39 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.