Multiple sequence alignment - TraesCS3D01G108200

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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 TraesCS3D01G108200 chr3D 100.000 2791 0 0 1 2791 61661439 61658649 0.000000e+00 5155.0
1 TraesCS3D01G108200 chr3D 81.497 708 110 18 1 700 574347148 574347842 1.880000e-156 562.0
2 TraesCS3D01G108200 chr3D 100.000 45 0 0 658 702 61665562 61665518 1.780000e-12 84.2
3 TraesCS3D01G108200 chr2D 97.292 2105 45 7 692 2791 61252007 61249910 0.000000e+00 3561.0
4 TraesCS3D01G108200 chr2D 97.571 1770 31 6 1024 2791 35814881 35813122 0.000000e+00 3020.0
5 TraesCS3D01G108200 chr2D 86.697 669 67 13 44 702 534419861 534420517 0.000000e+00 723.0
6 TraesCS3D01G108200 chr2D 81.215 708 103 19 1 700 481569824 481570509 6.800000e-151 544.0
7 TraesCS3D01G108200 chr1D 97.283 2098 49 8 698 2791 461375190 461373097 0.000000e+00 3552.0
8 TraesCS3D01G108200 chr7D 97.230 2094 53 3 702 2791 19181758 19183850 0.000000e+00 3541.0
9 TraesCS3D01G108200 chr7D 97.228 2092 49 8 702 2791 617634381 617632297 0.000000e+00 3533.0
10 TraesCS3D01G108200 chr7D 81.690 710 109 18 1 702 5189304 5188608 3.120000e-159 571.0
11 TraesCS3D01G108200 chr7D 92.701 137 10 0 524 660 11791679 11791815 6.100000e-47 198.0
12 TraesCS3D01G108200 chr7D 86.207 58 8 0 443 500 11791634 11791691 2.320000e-06 63.9
13 TraesCS3D01G108200 chr2A 96.466 2094 65 8 703 2791 706910672 706912761 0.000000e+00 3448.0
14 TraesCS3D01G108200 chr2A 92.955 2115 89 27 702 2791 54215533 54217612 0.000000e+00 3025.0
15 TraesCS3D01G108200 chr2A 94.324 828 35 6 703 1521 24524300 24523476 0.000000e+00 1258.0
16 TraesCS3D01G108200 chr6D 95.515 2096 72 16 702 2790 429708204 429706124 0.000000e+00 3330.0
17 TraesCS3D01G108200 chr4A 95.513 2095 62 13 707 2791 667277513 667279585 0.000000e+00 3319.0
18 TraesCS3D01G108200 chr5A 95.357 2089 85 10 707 2791 660241505 660239425 0.000000e+00 3310.0
19 TraesCS3D01G108200 chr7B 88.780 713 61 14 1 702 598168186 598167482 0.000000e+00 856.0
20 TraesCS3D01G108200 chr2B 88.359 713 64 13 1 702 507796653 507795949 0.000000e+00 839.0
21 TraesCS3D01G108200 chr6B 87.169 717 75 12 1 702 707445024 707444310 0.000000e+00 798.0
22 TraesCS3D01G108200 chr6B 80.758 712 114 18 1 700 36782329 36781629 4.090000e-148 534.0
23 TraesCS3D01G108200 chr5B 80.726 716 113 20 1 702 648275274 648275978 4.090000e-148 534.0
24 TraesCS3D01G108200 chrUn 92.701 137 10 0 524 660 269657010 269656874 6.100000e-47 198.0


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 TraesCS3D01G108200 chr3D 61658649 61661439 2790 True 5155 5155 100.000 1 2791 1 chr3D.!!$R1 2790
1 TraesCS3D01G108200 chr3D 574347148 574347842 694 False 562 562 81.497 1 700 1 chr3D.!!$F1 699
2 TraesCS3D01G108200 chr2D 61249910 61252007 2097 True 3561 3561 97.292 692 2791 1 chr2D.!!$R2 2099
3 TraesCS3D01G108200 chr2D 35813122 35814881 1759 True 3020 3020 97.571 1024 2791 1 chr2D.!!$R1 1767
4 TraesCS3D01G108200 chr2D 534419861 534420517 656 False 723 723 86.697 44 702 1 chr2D.!!$F2 658
5 TraesCS3D01G108200 chr2D 481569824 481570509 685 False 544 544 81.215 1 700 1 chr2D.!!$F1 699
6 TraesCS3D01G108200 chr1D 461373097 461375190 2093 True 3552 3552 97.283 698 2791 1 chr1D.!!$R1 2093
7 TraesCS3D01G108200 chr7D 19181758 19183850 2092 False 3541 3541 97.230 702 2791 1 chr7D.!!$F1 2089
8 TraesCS3D01G108200 chr7D 617632297 617634381 2084 True 3533 3533 97.228 702 2791 1 chr7D.!!$R2 2089
9 TraesCS3D01G108200 chr7D 5188608 5189304 696 True 571 571 81.690 1 702 1 chr7D.!!$R1 701
10 TraesCS3D01G108200 chr2A 706910672 706912761 2089 False 3448 3448 96.466 703 2791 1 chr2A.!!$F2 2088
11 TraesCS3D01G108200 chr2A 54215533 54217612 2079 False 3025 3025 92.955 702 2791 1 chr2A.!!$F1 2089
12 TraesCS3D01G108200 chr2A 24523476 24524300 824 True 1258 1258 94.324 703 1521 1 chr2A.!!$R1 818
13 TraesCS3D01G108200 chr6D 429706124 429708204 2080 True 3330 3330 95.515 702 2790 1 chr6D.!!$R1 2088
14 TraesCS3D01G108200 chr4A 667277513 667279585 2072 False 3319 3319 95.513 707 2791 1 chr4A.!!$F1 2084
15 TraesCS3D01G108200 chr5A 660239425 660241505 2080 True 3310 3310 95.357 707 2791 1 chr5A.!!$R1 2084
16 TraesCS3D01G108200 chr7B 598167482 598168186 704 True 856 856 88.780 1 702 1 chr7B.!!$R1 701
17 TraesCS3D01G108200 chr2B 507795949 507796653 704 True 839 839 88.359 1 702 1 chr2B.!!$R1 701
18 TraesCS3D01G108200 chr6B 707444310 707445024 714 True 798 798 87.169 1 702 1 chr6B.!!$R2 701
19 TraesCS3D01G108200 chr6B 36781629 36782329 700 True 534 534 80.758 1 700 1 chr6B.!!$R1 699
20 TraesCS3D01G108200 chr5B 648275274 648275978 704 False 534 534 80.726 1 702 1 chr5B.!!$F1 701

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
420 421 0.037605 ATGTCGACGGTTTGGAGGAC 60.038 55.0 11.62 0.0 0.0 3.85 F
661 662 0.107831 GGGCGCCTGATACCATGTTA 59.892 55.0 28.56 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 1285 0.676151 CCTGCTCTGGTTTGCTCTCC 60.676 60.000 0.0 0.0 0.0 3.71 R
2178 2310 2.131972 CCAACCTTTTGTTTTAGCCGC 58.868 47.619 0.0 0.0 34.0 6.53 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
94 95 4.729856 ACAACGGCGCGGTACTCC 62.730 66.667 21.59 0.00 0.00 3.85
104 105 2.654404 GGTACTCCGCGTCGATGC 60.654 66.667 19.84 19.84 0.00 3.91
199 200 1.812922 CTGCATGACGACCTCCAGC 60.813 63.158 0.00 0.00 0.00 4.85
225 226 2.311463 CGGAGAGATGGTGGAGTACAT 58.689 52.381 0.00 0.00 0.00 2.29
254 255 2.588877 CGGTGTGATCGGCCATCC 60.589 66.667 2.24 0.82 0.00 3.51
255 256 2.911143 GGTGTGATCGGCCATCCT 59.089 61.111 2.24 0.00 0.00 3.24
263 264 2.928988 ATCGGCCATCCTCCACTCGA 62.929 60.000 2.24 0.00 0.00 4.04
302 303 3.403057 CCGTGGCGTTGACGTGAG 61.403 66.667 0.00 0.00 42.22 3.51
303 304 4.059459 CGTGGCGTTGACGTGAGC 62.059 66.667 0.00 0.00 42.22 4.26
304 305 4.059459 GTGGCGTTGACGTGAGCG 62.059 66.667 6.93 6.93 42.22 5.03
309 310 3.470567 GTTGACGTGAGCGCCGAG 61.471 66.667 11.49 0.00 42.83 4.63
310 311 4.717629 TTGACGTGAGCGCCGAGG 62.718 66.667 11.49 3.08 42.83 4.63
315 316 4.742201 GTGAGCGCCGAGGCTGAA 62.742 66.667 12.70 0.00 44.93 3.02
316 317 4.742201 TGAGCGCCGAGGCTGAAC 62.742 66.667 12.70 2.11 44.93 3.18
317 318 4.742201 GAGCGCCGAGGCTGAACA 62.742 66.667 12.70 0.00 44.93 3.18
318 319 4.087892 AGCGCCGAGGCTGAACAT 62.088 61.111 12.70 0.00 42.86 2.71
319 320 3.869272 GCGCCGAGGCTGAACATG 61.869 66.667 12.70 0.00 39.32 3.21
320 321 3.869272 CGCCGAGGCTGAACATGC 61.869 66.667 12.70 0.00 39.32 4.06
326 327 2.359850 GGCTGAACATGCCGACCA 60.360 61.111 0.00 0.00 41.03 4.02
327 328 2.690778 GGCTGAACATGCCGACCAC 61.691 63.158 0.00 0.00 41.03 4.16
328 329 2.690778 GCTGAACATGCCGACCACC 61.691 63.158 0.00 0.00 0.00 4.61
329 330 1.302431 CTGAACATGCCGACCACCA 60.302 57.895 0.00 0.00 0.00 4.17
330 331 0.677731 CTGAACATGCCGACCACCAT 60.678 55.000 0.00 0.00 0.00 3.55
331 332 0.959867 TGAACATGCCGACCACCATG 60.960 55.000 0.00 0.00 43.34 3.66
332 333 2.756400 ACATGCCGACCACCATGT 59.244 55.556 0.00 0.78 45.16 3.21
333 334 1.377202 ACATGCCGACCACCATGTC 60.377 57.895 0.00 0.00 46.56 3.06
341 342 3.578456 CCACCATGTCGAAGTGGC 58.422 61.111 15.27 0.00 44.21 5.01
342 343 2.390599 CCACCATGTCGAAGTGGCG 61.391 63.158 15.27 7.60 44.21 5.69
343 344 2.742372 ACCATGTCGAAGTGGCGC 60.742 61.111 15.27 0.00 39.13 6.53
344 345 3.499737 CCATGTCGAAGTGGCGCC 61.500 66.667 22.73 22.73 0.00 6.53
345 346 3.853330 CATGTCGAAGTGGCGCCG 61.853 66.667 23.90 9.58 0.00 6.46
362 363 2.556287 GCCACTGCGTGTAGTTGC 59.444 61.111 7.68 0.00 33.08 4.17
363 364 2.966309 GCCACTGCGTGTAGTTGCC 61.966 63.158 3.30 0.00 34.31 4.52
364 365 2.667318 CCACTGCGTGTAGTTGCCG 61.667 63.158 7.68 0.00 0.00 5.69
365 366 2.357034 ACTGCGTGTAGTTGCCGG 60.357 61.111 0.00 0.00 0.00 6.13
366 367 3.788766 CTGCGTGTAGTTGCCGGC 61.789 66.667 22.73 22.73 0.00 6.13
369 370 3.179265 CGTGTAGTTGCCGGCGAG 61.179 66.667 23.90 2.46 0.00 5.03
370 371 3.488090 GTGTAGTTGCCGGCGAGC 61.488 66.667 23.90 14.31 0.00 5.03
371 372 3.997397 TGTAGTTGCCGGCGAGCA 61.997 61.111 23.90 16.06 42.17 4.26
372 373 3.188786 GTAGTTGCCGGCGAGCAG 61.189 66.667 23.90 0.04 45.13 4.24
373 374 4.451150 TAGTTGCCGGCGAGCAGG 62.451 66.667 23.90 9.88 45.13 4.85
381 382 4.459089 GGCGAGCAGGTCCAGGAC 62.459 72.222 11.70 11.70 0.00 3.85
382 383 4.803426 GCGAGCAGGTCCAGGACG 62.803 72.222 13.80 1.88 32.65 4.79
383 384 3.062466 CGAGCAGGTCCAGGACGA 61.062 66.667 13.80 0.00 32.65 4.20
384 385 2.574399 GAGCAGGTCCAGGACGAC 59.426 66.667 13.80 5.32 32.65 4.34
385 386 3.343788 GAGCAGGTCCAGGACGACG 62.344 68.421 13.80 5.40 33.30 5.12
386 387 4.436998 GCAGGTCCAGGACGACGG 62.437 72.222 13.80 2.72 33.30 4.79
387 388 3.760035 CAGGTCCAGGACGACGGG 61.760 72.222 13.80 0.00 33.30 5.28
390 391 3.756727 GTCCAGGACGACGGGGAC 61.757 72.222 3.05 12.33 39.86 4.46
413 414 4.565531 GACGGATGTCGACGGTTT 57.434 55.556 11.62 0.00 42.43 3.27
414 415 2.067616 GACGGATGTCGACGGTTTG 58.932 57.895 11.62 2.12 42.43 2.93
415 416 1.349259 GACGGATGTCGACGGTTTGG 61.349 60.000 11.62 0.43 42.43 3.28
416 417 1.080366 CGGATGTCGACGGTTTGGA 60.080 57.895 11.62 0.00 42.43 3.53
417 418 1.076533 CGGATGTCGACGGTTTGGAG 61.077 60.000 11.62 0.00 42.43 3.86
418 419 0.739813 GGATGTCGACGGTTTGGAGG 60.740 60.000 11.62 0.00 0.00 4.30
419 420 0.245539 GATGTCGACGGTTTGGAGGA 59.754 55.000 11.62 0.00 0.00 3.71
420 421 0.037605 ATGTCGACGGTTTGGAGGAC 60.038 55.000 11.62 0.00 0.00 3.85
421 422 1.731969 GTCGACGGTTTGGAGGACG 60.732 63.158 0.00 0.00 0.00 4.79
422 423 2.431942 CGACGGTTTGGAGGACGG 60.432 66.667 0.00 0.00 0.00 4.79
423 424 2.741211 GACGGTTTGGAGGACGGC 60.741 66.667 0.00 0.00 0.00 5.68
424 425 4.675029 ACGGTTTGGAGGACGGCG 62.675 66.667 4.80 4.80 0.00 6.46
426 427 4.324991 GGTTTGGAGGACGGCGGT 62.325 66.667 13.24 0.00 0.00 5.68
427 428 3.047877 GTTTGGAGGACGGCGGTG 61.048 66.667 13.24 0.00 0.00 4.94
428 429 4.323477 TTTGGAGGACGGCGGTGG 62.323 66.667 13.24 0.00 0.00 4.61
442 443 3.450115 GTGGGGACGGACGGAGAG 61.450 72.222 0.00 0.00 0.00 3.20
443 444 4.753662 TGGGGACGGACGGAGAGG 62.754 72.222 0.00 0.00 0.00 3.69
451 452 3.827898 GACGGAGAGGGCGGTGAG 61.828 72.222 0.00 0.00 0.00 3.51
477 478 3.571119 CGCAGCCTGTTGAAGAGG 58.429 61.111 3.64 3.64 0.00 3.69
481 482 3.793144 GCCTGTTGAAGAGGCGCG 61.793 66.667 17.95 0.00 46.47 6.86
482 483 2.357517 CCTGTTGAAGAGGCGCGT 60.358 61.111 8.43 0.27 0.00 6.01
483 484 2.383527 CCTGTTGAAGAGGCGCGTC 61.384 63.158 21.96 21.96 0.00 5.19
484 485 1.664649 CTGTTGAAGAGGCGCGTCA 60.665 57.895 29.61 14.32 33.06 4.35
485 486 1.005037 TGTTGAAGAGGCGCGTCAT 60.005 52.632 29.61 19.93 34.96 3.06
486 487 0.602638 TGTTGAAGAGGCGCGTCATT 60.603 50.000 29.61 20.27 34.96 2.57
487 488 0.179215 GTTGAAGAGGCGCGTCATTG 60.179 55.000 29.61 0.00 34.96 2.82
488 489 0.320334 TTGAAGAGGCGCGTCATTGA 60.320 50.000 29.61 13.60 34.96 2.57
489 490 0.737367 TGAAGAGGCGCGTCATTGAG 60.737 55.000 29.61 0.00 29.81 3.02
490 491 0.458543 GAAGAGGCGCGTCATTGAGA 60.459 55.000 29.61 0.00 0.00 3.27
491 492 0.459237 AAGAGGCGCGTCATTGAGAG 60.459 55.000 29.61 0.00 0.00 3.20
492 493 2.510238 AGGCGCGTCATTGAGAGC 60.510 61.111 15.58 4.47 0.00 4.09
495 496 3.918220 CGCGTCATTGAGAGCGCC 61.918 66.667 19.01 0.00 45.94 6.53
496 497 3.918220 GCGTCATTGAGAGCGCCG 61.918 66.667 2.29 0.00 39.32 6.46
497 498 3.257561 CGTCATTGAGAGCGCCGG 61.258 66.667 2.29 0.00 0.00 6.13
498 499 3.567797 GTCATTGAGAGCGCCGGC 61.568 66.667 19.07 19.07 40.37 6.13
528 529 2.665185 AGCGGCCACGTTGAGAAC 60.665 61.111 2.24 0.00 43.45 3.01
537 538 4.090057 GTTGAGAACGCCAGCGGC 62.090 66.667 17.33 7.97 46.75 6.53
547 548 4.758251 CCAGCGGCACCATCGTCA 62.758 66.667 1.45 0.00 0.00 4.35
548 549 3.190849 CAGCGGCACCATCGTCAG 61.191 66.667 1.45 0.00 0.00 3.51
549 550 3.381983 AGCGGCACCATCGTCAGA 61.382 61.111 1.45 0.00 0.00 3.27
550 551 2.887568 GCGGCACCATCGTCAGAG 60.888 66.667 0.00 0.00 0.00 3.35
551 552 2.202797 CGGCACCATCGTCAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
552 553 2.710902 CGGCACCATCGTCAGAGGA 61.711 63.158 0.00 0.00 0.00 3.71
553 554 1.142748 GGCACCATCGTCAGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69
554 555 1.520342 GCACCATCGTCAGAGGAGC 60.520 63.158 0.00 0.00 0.00 4.70
555 556 1.226802 CACCATCGTCAGAGGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
556 557 2.415010 CCATCGTCAGAGGAGCGG 59.585 66.667 0.00 0.00 0.00 5.52
557 558 2.415010 CATCGTCAGAGGAGCGGG 59.585 66.667 0.00 0.00 0.00 6.13
558 559 2.835431 ATCGTCAGAGGAGCGGGG 60.835 66.667 0.00 0.00 0.00 5.73
559 560 3.360423 ATCGTCAGAGGAGCGGGGA 62.360 63.158 0.00 0.00 0.00 4.81
560 561 3.522731 CGTCAGAGGAGCGGGGAG 61.523 72.222 0.00 0.00 0.00 4.30
561 562 2.043852 GTCAGAGGAGCGGGGAGA 60.044 66.667 0.00 0.00 0.00 3.71
562 563 2.124693 GTCAGAGGAGCGGGGAGAG 61.125 68.421 0.00 0.00 0.00 3.20
563 564 2.043450 CAGAGGAGCGGGGAGAGT 60.043 66.667 0.00 0.00 0.00 3.24
564 565 2.043450 AGAGGAGCGGGGAGAGTG 60.043 66.667 0.00 0.00 0.00 3.51
565 566 3.151022 GAGGAGCGGGGAGAGTGG 61.151 72.222 0.00 0.00 0.00 4.00
566 567 3.663815 GAGGAGCGGGGAGAGTGGA 62.664 68.421 0.00 0.00 0.00 4.02
567 568 3.462678 GGAGCGGGGAGAGTGGAC 61.463 72.222 0.00 0.00 0.00 4.02
568 569 3.827898 GAGCGGGGAGAGTGGACG 61.828 72.222 0.00 0.00 0.00 4.79
572 573 4.716977 GGGGAGAGTGGACGGGGT 62.717 72.222 0.00 0.00 0.00 4.95
573 574 2.606826 GGGAGAGTGGACGGGGTT 60.607 66.667 0.00 0.00 0.00 4.11
574 575 2.663196 GGAGAGTGGACGGGGTTG 59.337 66.667 0.00 0.00 0.00 3.77
575 576 2.214920 GGAGAGTGGACGGGGTTGT 61.215 63.158 0.00 0.00 0.00 3.32
576 577 1.292541 GAGAGTGGACGGGGTTGTC 59.707 63.158 0.00 0.00 38.17 3.18
577 578 2.048503 GAGTGGACGGGGTTGTCG 60.049 66.667 0.00 0.00 39.83 4.35
578 579 2.841044 AGTGGACGGGGTTGTCGT 60.841 61.111 0.00 0.00 44.03 4.34
583 584 2.345991 ACGGGGTTGTCGTCCATG 59.654 61.111 0.00 0.00 35.87 3.66
584 585 2.435938 CGGGGTTGTCGTCCATGG 60.436 66.667 4.97 4.97 0.00 3.66
585 586 2.754375 GGGGTTGTCGTCCATGGT 59.246 61.111 12.58 0.00 0.00 3.55
586 587 1.674322 GGGGTTGTCGTCCATGGTG 60.674 63.158 12.58 6.00 0.00 4.17
587 588 1.674322 GGGTTGTCGTCCATGGTGG 60.674 63.158 12.58 5.00 39.43 4.61
588 589 1.373435 GGTTGTCGTCCATGGTGGA 59.627 57.895 12.58 7.53 45.98 4.02
595 596 3.489636 TCCATGGTGGAAGCGGAA 58.510 55.556 12.58 0.00 45.00 4.30
596 597 1.299648 TCCATGGTGGAAGCGGAAG 59.700 57.895 12.58 0.00 45.00 3.46
630 631 3.977244 CGCCTGCGCAAAAGGGTT 61.977 61.111 13.05 0.00 35.17 4.11
631 632 2.356194 GCCTGCGCAAAAGGGTTG 60.356 61.111 13.05 0.00 35.17 3.77
632 633 2.855514 GCCTGCGCAAAAGGGTTGA 61.856 57.895 13.05 0.00 35.17 3.18
633 634 1.286880 CCTGCGCAAAAGGGTTGAG 59.713 57.895 13.05 0.00 0.00 3.02
634 635 1.372128 CTGCGCAAAAGGGTTGAGC 60.372 57.895 13.05 7.70 43.85 4.26
635 636 2.727544 GCGCAAAAGGGTTGAGCA 59.272 55.556 0.30 0.00 43.22 4.26
636 637 1.372128 GCGCAAAAGGGTTGAGCAG 60.372 57.895 0.30 0.00 43.22 4.24
637 638 1.286880 CGCAAAAGGGTTGAGCAGG 59.713 57.895 0.00 0.00 0.00 4.85
638 639 1.455383 CGCAAAAGGGTTGAGCAGGT 61.455 55.000 0.00 0.00 0.00 4.00
639 640 0.315251 GCAAAAGGGTTGAGCAGGTC 59.685 55.000 0.00 0.00 0.00 3.85
640 641 0.961753 CAAAAGGGTTGAGCAGGTCC 59.038 55.000 0.00 0.00 0.00 4.46
641 642 0.537371 AAAAGGGTTGAGCAGGTCCG 60.537 55.000 0.00 0.00 0.00 4.79
642 643 2.411765 AAAGGGTTGAGCAGGTCCGG 62.412 60.000 0.00 0.00 0.00 5.14
643 644 4.410400 GGGTTGAGCAGGTCCGGG 62.410 72.222 0.00 0.00 0.00 5.73
644 645 4.410400 GGTTGAGCAGGTCCGGGG 62.410 72.222 0.00 0.00 0.00 5.73
654 655 4.603946 GTCCGGGGCGCCTGATAC 62.604 72.222 28.56 15.99 29.82 2.24
657 658 3.941188 CGGGGCGCCTGATACCAT 61.941 66.667 28.56 0.00 29.82 3.55
658 659 2.281761 GGGGCGCCTGATACCATG 60.282 66.667 28.56 0.00 0.00 3.66
659 660 2.510906 GGGCGCCTGATACCATGT 59.489 61.111 28.56 0.00 0.00 3.21
660 661 1.152963 GGGCGCCTGATACCATGTT 60.153 57.895 28.56 0.00 0.00 2.71
661 662 0.107831 GGGCGCCTGATACCATGTTA 59.892 55.000 28.56 0.00 0.00 2.41
662 663 1.476110 GGGCGCCTGATACCATGTTAA 60.476 52.381 28.56 0.00 0.00 2.01
663 664 1.873591 GGCGCCTGATACCATGTTAAG 59.126 52.381 22.15 0.00 0.00 1.85
664 665 1.873591 GCGCCTGATACCATGTTAAGG 59.126 52.381 0.00 0.00 0.00 2.69
665 666 2.484770 GCGCCTGATACCATGTTAAGGA 60.485 50.000 0.00 0.00 0.00 3.36
666 667 3.393800 CGCCTGATACCATGTTAAGGAG 58.606 50.000 0.00 0.00 0.00 3.69
667 668 3.744660 GCCTGATACCATGTTAAGGAGG 58.255 50.000 0.00 0.00 0.00 4.30
668 669 3.391296 GCCTGATACCATGTTAAGGAGGA 59.609 47.826 0.00 0.00 0.00 3.71
669 670 4.141482 GCCTGATACCATGTTAAGGAGGAA 60.141 45.833 0.00 0.00 0.00 3.36
670 671 5.615289 CCTGATACCATGTTAAGGAGGAAG 58.385 45.833 0.00 0.00 0.00 3.46
671 672 5.366768 CCTGATACCATGTTAAGGAGGAAGA 59.633 44.000 0.00 0.00 0.00 2.87
672 673 6.126768 CCTGATACCATGTTAAGGAGGAAGAA 60.127 42.308 0.00 0.00 0.00 2.52
673 674 6.889198 TGATACCATGTTAAGGAGGAAGAAG 58.111 40.000 0.00 0.00 0.00 2.85
674 675 6.672218 TGATACCATGTTAAGGAGGAAGAAGA 59.328 38.462 0.00 0.00 0.00 2.87
675 676 5.428184 ACCATGTTAAGGAGGAAGAAGAG 57.572 43.478 0.00 0.00 0.00 2.85
676 677 5.094387 ACCATGTTAAGGAGGAAGAAGAGA 58.906 41.667 0.00 0.00 0.00 3.10
677 678 5.548056 ACCATGTTAAGGAGGAAGAAGAGAA 59.452 40.000 0.00 0.00 0.00 2.87
678 679 6.216456 ACCATGTTAAGGAGGAAGAAGAGAAT 59.784 38.462 0.00 0.00 0.00 2.40
679 680 6.541641 CCATGTTAAGGAGGAAGAAGAGAATG 59.458 42.308 0.00 0.00 0.00 2.67
680 681 6.054860 TGTTAAGGAGGAAGAAGAGAATGG 57.945 41.667 0.00 0.00 0.00 3.16
681 682 5.045578 TGTTAAGGAGGAAGAAGAGAATGGG 60.046 44.000 0.00 0.00 0.00 4.00
682 683 1.843206 AGGAGGAAGAAGAGAATGGGC 59.157 52.381 0.00 0.00 0.00 5.36
683 684 1.561542 GGAGGAAGAAGAGAATGGGCA 59.438 52.381 0.00 0.00 0.00 5.36
684 685 2.637947 GAGGAAGAAGAGAATGGGCAC 58.362 52.381 0.00 0.00 0.00 5.01
685 686 1.988107 AGGAAGAAGAGAATGGGCACA 59.012 47.619 0.00 0.00 0.00 4.57
686 687 2.376518 AGGAAGAAGAGAATGGGCACAA 59.623 45.455 0.00 0.00 0.00 3.33
687 688 2.489722 GGAAGAAGAGAATGGGCACAAC 59.510 50.000 0.00 0.00 0.00 3.32
688 689 2.957402 AGAAGAGAATGGGCACAACA 57.043 45.000 0.00 0.00 0.00 3.33
689 690 2.508526 AGAAGAGAATGGGCACAACAC 58.491 47.619 0.00 0.00 0.00 3.32
690 691 2.158623 AGAAGAGAATGGGCACAACACA 60.159 45.455 0.00 0.00 0.00 3.72
691 692 1.609208 AGAGAATGGGCACAACACAC 58.391 50.000 0.00 0.00 0.00 3.82
692 693 1.143684 AGAGAATGGGCACAACACACT 59.856 47.619 0.00 0.00 0.00 3.55
693 694 1.956477 GAGAATGGGCACAACACACTT 59.044 47.619 0.00 0.00 0.00 3.16
694 695 1.956477 AGAATGGGCACAACACACTTC 59.044 47.619 0.00 0.00 0.00 3.01
695 696 0.667993 AATGGGCACAACACACTTCG 59.332 50.000 0.00 0.00 0.00 3.79
696 697 0.179032 ATGGGCACAACACACTTCGA 60.179 50.000 0.00 0.00 0.00 3.71
844 846 6.150976 TGCCTAATCCAAAGACACATGTTTAG 59.849 38.462 0.00 0.00 0.00 1.85
1018 1034 4.115199 GCACCCGAGCCCATCCTT 62.115 66.667 0.00 0.00 0.00 3.36
1165 1200 2.283101 GCCCATGACAAGGTGCCA 60.283 61.111 0.00 0.00 0.00 4.92
1250 1285 0.100503 GGCGGGAATTCGTGAAATGG 59.899 55.000 0.00 0.00 0.00 3.16
1956 2084 3.910627 CCAGGCCCATATAGAAGTTAGGT 59.089 47.826 0.00 0.00 0.00 3.08
1975 2103 3.577415 AGGTAGGGCCGAATAGAACATAC 59.423 47.826 0.00 0.00 43.70 2.39
1982 2110 2.368875 CCGAATAGAACATACCCAGGCT 59.631 50.000 0.00 0.00 0.00 4.58
2051 2182 7.867909 GGTCAGTGACATCGATATATCTTTTCA 59.132 37.037 24.20 5.40 33.68 2.69
2178 2310 0.604511 GGTAGGGTCCCGTGTTGTTG 60.605 60.000 0.99 0.00 0.00 3.33
2326 2459 6.039616 TGTGCTATGGTGTTTTCAAAGTTTC 58.960 36.000 0.00 0.00 0.00 2.78
2367 2501 0.555769 AAAGGTTGTGCCCCTCTCAA 59.444 50.000 0.00 0.00 38.26 3.02
2683 2821 9.716507 CCTTACAACATATAGTGCATAAAACAC 57.283 33.333 0.00 0.00 38.35 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.667830 CAAGAGCTTCGCCGACCAA 60.668 57.895 0.00 0.00 0.00 3.67
160 161 2.997897 GAGGACACGGCCCTGACT 60.998 66.667 8.88 6.13 33.36 3.41
199 200 1.440893 CACCATCTCTCCGGAGCTG 59.559 63.158 27.39 21.15 39.31 4.24
225 226 1.958715 CACACCGTCGTGCATTGGA 60.959 57.895 0.00 0.00 44.40 3.53
254 255 4.180946 CCGCGACCTCGAGTGGAG 62.181 72.222 8.23 1.69 43.02 3.86
292 293 3.470567 CTCGGCGCTCACGTCAAC 61.471 66.667 7.64 0.00 46.71 3.18
293 294 4.717629 CCTCGGCGCTCACGTCAA 62.718 66.667 7.64 0.00 46.71 3.18
310 311 2.690778 GGTGGTCGGCATGTTCAGC 61.691 63.158 0.00 0.00 0.00 4.26
311 312 0.677731 ATGGTGGTCGGCATGTTCAG 60.678 55.000 0.00 0.00 0.00 3.02
312 313 0.959867 CATGGTGGTCGGCATGTTCA 60.960 55.000 0.00 0.00 0.00 3.18
313 314 0.960364 ACATGGTGGTCGGCATGTTC 60.960 55.000 0.00 0.00 35.01 3.18
314 315 0.960364 GACATGGTGGTCGGCATGTT 60.960 55.000 0.00 0.00 38.25 2.71
315 316 1.377202 GACATGGTGGTCGGCATGT 60.377 57.895 0.00 0.00 40.49 3.21
316 317 3.501396 GACATGGTGGTCGGCATG 58.499 61.111 0.00 0.00 0.00 4.06
322 323 2.840974 CCACTTCGACATGGTGGTC 58.159 57.895 14.23 0.00 43.72 4.02
325 326 3.168271 CGCCACTTCGACATGGTG 58.832 61.111 14.17 13.14 39.97 4.17
326 327 2.742372 GCGCCACTTCGACATGGT 60.742 61.111 14.17 0.00 38.34 3.55
327 328 3.499737 GGCGCCACTTCGACATGG 61.500 66.667 24.80 9.40 37.45 3.66
328 329 3.853330 CGGCGCCACTTCGACATG 61.853 66.667 28.98 0.98 37.32 3.21
349 350 3.788766 GCCGGCAACTACACGCAG 61.789 66.667 24.80 0.00 0.00 5.18
352 353 3.179265 CTCGCCGGCAACTACACG 61.179 66.667 28.98 7.38 0.00 4.49
353 354 3.488090 GCTCGCCGGCAACTACAC 61.488 66.667 28.98 3.89 0.00 2.90
354 355 3.932580 CTGCTCGCCGGCAACTACA 62.933 63.158 28.98 15.34 41.94 2.74
355 356 3.188786 CTGCTCGCCGGCAACTAC 61.189 66.667 28.98 11.15 41.94 2.73
356 357 4.451150 CCTGCTCGCCGGCAACTA 62.451 66.667 28.98 8.84 41.94 2.24
364 365 4.459089 GTCCTGGACCTGCTCGCC 62.459 72.222 16.14 0.00 0.00 5.54
365 366 4.803426 CGTCCTGGACCTGCTCGC 62.803 72.222 20.68 0.00 0.00 5.03
366 367 3.062466 TCGTCCTGGACCTGCTCG 61.062 66.667 20.68 8.44 0.00 5.03
367 368 2.574399 GTCGTCCTGGACCTGCTC 59.426 66.667 20.68 3.85 0.00 4.26
368 369 3.374402 CGTCGTCCTGGACCTGCT 61.374 66.667 20.68 0.00 33.30 4.24
369 370 4.436998 CCGTCGTCCTGGACCTGC 62.437 72.222 20.68 10.02 33.30 4.85
370 371 3.760035 CCCGTCGTCCTGGACCTG 61.760 72.222 20.68 10.43 33.30 4.00
373 374 3.756727 GTCCCCGTCGTCCTGGAC 61.757 72.222 16.99 16.99 40.40 4.02
376 377 4.415332 CACGTCCCCGTCGTCCTG 62.415 72.222 0.00 0.00 46.28 3.86
377 378 4.648626 TCACGTCCCCGTCGTCCT 62.649 66.667 0.00 0.00 46.28 3.85
378 379 4.410743 GTCACGTCCCCGTCGTCC 62.411 72.222 0.00 0.00 46.28 4.79
379 380 4.748679 CGTCACGTCCCCGTCGTC 62.749 72.222 0.00 0.00 46.28 4.20
381 382 4.748679 GTCGTCACGTCCCCGTCG 62.749 72.222 0.00 0.00 46.28 5.12
382 383 4.748679 CGTCGTCACGTCCCCGTC 62.749 72.222 0.00 0.00 46.28 4.79
385 386 3.446570 ATCCGTCGTCACGTCCCC 61.447 66.667 0.00 0.00 45.17 4.81
386 387 2.202570 CATCCGTCGTCACGTCCC 60.203 66.667 0.00 0.00 45.17 4.46
387 388 1.513586 GACATCCGTCGTCACGTCC 60.514 63.158 0.00 0.00 45.17 4.79
388 389 4.053067 GACATCCGTCGTCACGTC 57.947 61.111 0.00 0.00 45.17 4.34
396 397 1.349259 CCAAACCGTCGACATCCGTC 61.349 60.000 17.16 0.00 39.75 4.79
397 398 1.373748 CCAAACCGTCGACATCCGT 60.374 57.895 17.16 2.52 39.75 4.69
398 399 1.076533 CTCCAAACCGTCGACATCCG 61.077 60.000 17.16 0.65 40.25 4.18
399 400 0.739813 CCTCCAAACCGTCGACATCC 60.740 60.000 17.16 0.00 0.00 3.51
400 401 0.245539 TCCTCCAAACCGTCGACATC 59.754 55.000 17.16 0.00 0.00 3.06
401 402 0.037605 GTCCTCCAAACCGTCGACAT 60.038 55.000 17.16 0.00 0.00 3.06
402 403 1.364901 GTCCTCCAAACCGTCGACA 59.635 57.895 17.16 0.00 0.00 4.35
403 404 1.731969 CGTCCTCCAAACCGTCGAC 60.732 63.158 5.18 5.18 0.00 4.20
404 405 2.646719 CGTCCTCCAAACCGTCGA 59.353 61.111 0.00 0.00 0.00 4.20
405 406 2.431942 CCGTCCTCCAAACCGTCG 60.432 66.667 0.00 0.00 0.00 5.12
406 407 2.741211 GCCGTCCTCCAAACCGTC 60.741 66.667 0.00 0.00 0.00 4.79
407 408 4.675029 CGCCGTCCTCCAAACCGT 62.675 66.667 0.00 0.00 0.00 4.83
409 410 4.324991 ACCGCCGTCCTCCAAACC 62.325 66.667 0.00 0.00 0.00 3.27
410 411 3.047877 CACCGCCGTCCTCCAAAC 61.048 66.667 0.00 0.00 0.00 2.93
411 412 4.323477 CCACCGCCGTCCTCCAAA 62.323 66.667 0.00 0.00 0.00 3.28
425 426 3.450115 CTCTCCGTCCGTCCCCAC 61.450 72.222 0.00 0.00 0.00 4.61
426 427 4.753662 CCTCTCCGTCCGTCCCCA 62.754 72.222 0.00 0.00 0.00 4.96
434 435 3.827898 CTCACCGCCCTCTCCGTC 61.828 72.222 0.00 0.00 0.00 4.79
459 460 2.684843 CCTCTTCAACAGGCTGCGC 61.685 63.158 15.89 0.00 0.00 6.09
460 461 3.571119 CCTCTTCAACAGGCTGCG 58.429 61.111 15.89 6.27 0.00 5.18
465 466 2.357517 ACGCGCCTCTTCAACAGG 60.358 61.111 5.73 0.00 0.00 4.00
466 467 1.016130 ATGACGCGCCTCTTCAACAG 61.016 55.000 5.73 0.00 0.00 3.16
467 468 0.602638 AATGACGCGCCTCTTCAACA 60.603 50.000 5.73 0.00 0.00 3.33
468 469 0.179215 CAATGACGCGCCTCTTCAAC 60.179 55.000 5.73 0.00 0.00 3.18
469 470 0.320334 TCAATGACGCGCCTCTTCAA 60.320 50.000 5.73 0.00 0.00 2.69
470 471 0.737367 CTCAATGACGCGCCTCTTCA 60.737 55.000 5.73 1.44 0.00 3.02
471 472 0.458543 TCTCAATGACGCGCCTCTTC 60.459 55.000 5.73 0.00 0.00 2.87
472 473 0.459237 CTCTCAATGACGCGCCTCTT 60.459 55.000 5.73 0.00 0.00 2.85
473 474 1.140589 CTCTCAATGACGCGCCTCT 59.859 57.895 5.73 0.00 0.00 3.69
474 475 2.520904 GCTCTCAATGACGCGCCTC 61.521 63.158 5.73 0.00 0.00 4.70
475 476 2.510238 GCTCTCAATGACGCGCCT 60.510 61.111 5.73 0.00 0.00 5.52
476 477 3.918220 CGCTCTCAATGACGCGCC 61.918 66.667 5.73 0.00 36.29 6.53
480 481 3.257561 CCGGCGCTCTCAATGACG 61.258 66.667 7.64 0.00 0.00 4.35
481 482 3.567797 GCCGGCGCTCTCAATGAC 61.568 66.667 12.58 0.00 0.00 3.06
509 510 4.680237 TCTCAACGTGGCCGCTGG 62.680 66.667 15.69 1.68 37.70 4.85
510 511 2.664851 TTCTCAACGTGGCCGCTG 60.665 61.111 15.69 10.56 37.70 5.18
511 512 2.665185 GTTCTCAACGTGGCCGCT 60.665 61.111 15.69 0.00 37.70 5.52
520 521 4.090057 GCCGCTGGCGTTCTCAAC 62.090 66.667 13.84 0.00 39.62 3.18
530 531 4.758251 TGACGATGGTGCCGCTGG 62.758 66.667 0.00 0.00 0.00 4.85
531 532 3.190849 CTGACGATGGTGCCGCTG 61.191 66.667 0.00 0.00 0.00 5.18
532 533 3.362399 CTCTGACGATGGTGCCGCT 62.362 63.158 0.00 0.00 0.00 5.52
533 534 2.887568 CTCTGACGATGGTGCCGC 60.888 66.667 0.00 0.00 0.00 6.53
534 535 2.202797 CCTCTGACGATGGTGCCG 60.203 66.667 0.00 0.00 0.00 5.69
535 536 1.142748 CTCCTCTGACGATGGTGCC 59.857 63.158 0.00 0.00 0.00 5.01
536 537 1.520342 GCTCCTCTGACGATGGTGC 60.520 63.158 0.00 0.00 34.07 5.01
537 538 1.226802 CGCTCCTCTGACGATGGTG 60.227 63.158 0.00 0.00 0.00 4.17
538 539 2.418910 CCGCTCCTCTGACGATGGT 61.419 63.158 0.00 0.00 0.00 3.55
539 540 2.415010 CCGCTCCTCTGACGATGG 59.585 66.667 0.00 0.00 0.00 3.51
540 541 2.415010 CCCGCTCCTCTGACGATG 59.585 66.667 0.00 0.00 0.00 3.84
541 542 2.835431 CCCCGCTCCTCTGACGAT 60.835 66.667 0.00 0.00 0.00 3.73
542 543 3.997400 CTCCCCGCTCCTCTGACGA 62.997 68.421 0.00 0.00 0.00 4.20
543 544 3.522731 CTCCCCGCTCCTCTGACG 61.523 72.222 0.00 0.00 0.00 4.35
544 545 2.043852 TCTCCCCGCTCCTCTGAC 60.044 66.667 0.00 0.00 0.00 3.51
545 546 2.277072 CTCTCCCCGCTCCTCTGA 59.723 66.667 0.00 0.00 0.00 3.27
546 547 2.043450 ACTCTCCCCGCTCCTCTG 60.043 66.667 0.00 0.00 0.00 3.35
547 548 2.043450 CACTCTCCCCGCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
548 549 3.151022 CCACTCTCCCCGCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
549 550 3.673597 TCCACTCTCCCCGCTCCT 61.674 66.667 0.00 0.00 0.00 3.69
550 551 3.462678 GTCCACTCTCCCCGCTCC 61.463 72.222 0.00 0.00 0.00 4.70
551 552 3.827898 CGTCCACTCTCCCCGCTC 61.828 72.222 0.00 0.00 0.00 5.03
555 556 4.716977 ACCCCGTCCACTCTCCCC 62.717 72.222 0.00 0.00 0.00 4.81
556 557 2.606826 AACCCCGTCCACTCTCCC 60.607 66.667 0.00 0.00 0.00 4.30
557 558 2.168666 GACAACCCCGTCCACTCTCC 62.169 65.000 0.00 0.00 0.00 3.71
558 559 1.292541 GACAACCCCGTCCACTCTC 59.707 63.158 0.00 0.00 0.00 3.20
559 560 2.571216 CGACAACCCCGTCCACTCT 61.571 63.158 0.00 0.00 31.91 3.24
560 561 2.048503 CGACAACCCCGTCCACTC 60.049 66.667 0.00 0.00 31.91 3.51
561 562 2.841044 ACGACAACCCCGTCCACT 60.841 61.111 0.00 0.00 34.97 4.00
566 567 2.345991 CATGGACGACAACCCCGT 59.654 61.111 0.00 0.00 43.56 5.28
567 568 2.435938 CCATGGACGACAACCCCG 60.436 66.667 5.56 0.00 0.00 5.73
568 569 1.674322 CACCATGGACGACAACCCC 60.674 63.158 21.47 0.00 0.00 4.95
569 570 1.674322 CCACCATGGACGACAACCC 60.674 63.158 21.47 0.00 40.96 4.11
570 571 1.373435 TCCACCATGGACGACAACC 59.627 57.895 21.47 0.00 42.67 3.77
578 579 1.299648 CTTCCGCTTCCACCATGGA 59.700 57.895 21.47 0.00 46.61 3.41
579 580 2.409870 GCTTCCGCTTCCACCATGG 61.410 63.158 11.19 11.19 39.43 3.66
580 581 2.753966 CGCTTCCGCTTCCACCATG 61.754 63.158 0.00 0.00 0.00 3.66
581 582 2.436646 CGCTTCCGCTTCCACCAT 60.437 61.111 0.00 0.00 0.00 3.55
582 583 4.697756 CCGCTTCCGCTTCCACCA 62.698 66.667 0.00 0.00 0.00 4.17
583 584 3.894547 TTCCGCTTCCGCTTCCACC 62.895 63.158 0.00 0.00 0.00 4.61
584 585 2.358247 TTCCGCTTCCGCTTCCAC 60.358 61.111 0.00 0.00 0.00 4.02
585 586 2.047274 CTTCCGCTTCCGCTTCCA 60.047 61.111 0.00 0.00 0.00 3.53
586 587 3.500642 GCTTCCGCTTCCGCTTCC 61.501 66.667 0.00 0.00 0.00 3.46
587 588 2.742372 TGCTTCCGCTTCCGCTTC 60.742 61.111 0.00 0.00 36.97 3.86
588 589 2.731691 TTCTGCTTCCGCTTCCGCTT 62.732 55.000 0.00 0.00 36.97 4.68
589 590 3.240134 TTCTGCTTCCGCTTCCGCT 62.240 57.895 0.00 0.00 36.97 5.52
590 591 2.742372 TTCTGCTTCCGCTTCCGC 60.742 61.111 0.00 0.00 36.97 5.54
591 592 2.391389 GGTTCTGCTTCCGCTTCCG 61.391 63.158 0.00 0.00 36.97 4.30
592 593 2.391389 CGGTTCTGCTTCCGCTTCC 61.391 63.158 0.00 0.00 40.28 3.46
593 594 2.391389 CCGGTTCTGCTTCCGCTTC 61.391 63.158 0.00 0.00 44.63 3.86
594 595 2.358737 CCGGTTCTGCTTCCGCTT 60.359 61.111 0.00 0.00 44.63 4.68
595 596 4.394712 CCCGGTTCTGCTTCCGCT 62.395 66.667 0.00 0.00 44.63 5.52
613 614 3.977244 AACCCTTTTGCGCAGGCG 61.977 61.111 11.31 9.68 44.10 5.52
614 615 2.356194 CAACCCTTTTGCGCAGGC 60.356 61.111 11.31 0.00 40.52 4.85
615 616 1.286880 CTCAACCCTTTTGCGCAGG 59.713 57.895 11.31 11.46 0.00 4.85
616 617 1.372128 GCTCAACCCTTTTGCGCAG 60.372 57.895 11.31 0.00 31.12 5.18
617 618 2.074230 CTGCTCAACCCTTTTGCGCA 62.074 55.000 5.66 5.66 37.74 6.09
618 619 1.372128 CTGCTCAACCCTTTTGCGC 60.372 57.895 0.00 0.00 0.00 6.09
619 620 1.286880 CCTGCTCAACCCTTTTGCG 59.713 57.895 0.00 0.00 0.00 4.85
620 621 0.315251 GACCTGCTCAACCCTTTTGC 59.685 55.000 0.00 0.00 0.00 3.68
621 622 0.961753 GGACCTGCTCAACCCTTTTG 59.038 55.000 0.00 0.00 0.00 2.44
622 623 0.537371 CGGACCTGCTCAACCCTTTT 60.537 55.000 0.00 0.00 0.00 2.27
623 624 1.073199 CGGACCTGCTCAACCCTTT 59.927 57.895 0.00 0.00 0.00 3.11
624 625 2.750350 CGGACCTGCTCAACCCTT 59.250 61.111 0.00 0.00 0.00 3.95
625 626 3.322466 CCGGACCTGCTCAACCCT 61.322 66.667 0.00 0.00 0.00 4.34
626 627 4.410400 CCCGGACCTGCTCAACCC 62.410 72.222 0.73 0.00 0.00 4.11
627 628 4.410400 CCCCGGACCTGCTCAACC 62.410 72.222 0.73 0.00 0.00 3.77
637 638 4.603946 GTATCAGGCGCCCCGGAC 62.604 72.222 26.15 13.33 38.17 4.79
640 641 3.941188 ATGGTATCAGGCGCCCCG 61.941 66.667 26.15 15.87 35.76 5.73
641 642 2.281761 CATGGTATCAGGCGCCCC 60.282 66.667 26.15 17.84 0.00 5.80
642 643 0.107831 TAACATGGTATCAGGCGCCC 59.892 55.000 26.15 7.01 0.00 6.13
643 644 1.873591 CTTAACATGGTATCAGGCGCC 59.126 52.381 21.89 21.89 0.00 6.53
644 645 1.873591 CCTTAACATGGTATCAGGCGC 59.126 52.381 0.00 0.00 0.00 6.53
645 646 3.393800 CTCCTTAACATGGTATCAGGCG 58.606 50.000 3.88 0.00 0.00 5.52
646 647 3.391296 TCCTCCTTAACATGGTATCAGGC 59.609 47.826 3.88 0.00 0.00 4.85
647 648 5.366768 TCTTCCTCCTTAACATGGTATCAGG 59.633 44.000 2.45 2.45 0.00 3.86
648 649 6.485830 TCTTCCTCCTTAACATGGTATCAG 57.514 41.667 0.00 0.00 0.00 2.90
649 650 6.672218 TCTTCTTCCTCCTTAACATGGTATCA 59.328 38.462 0.00 0.00 0.00 2.15
650 651 7.070074 TCTCTTCTTCCTCCTTAACATGGTATC 59.930 40.741 0.00 0.00 0.00 2.24
651 652 6.903534 TCTCTTCTTCCTCCTTAACATGGTAT 59.096 38.462 0.00 0.00 0.00 2.73
652 653 6.261435 TCTCTTCTTCCTCCTTAACATGGTA 58.739 40.000 0.00 0.00 0.00 3.25
653 654 5.094387 TCTCTTCTTCCTCCTTAACATGGT 58.906 41.667 0.00 0.00 0.00 3.55
654 655 5.683876 TCTCTTCTTCCTCCTTAACATGG 57.316 43.478 0.00 0.00 0.00 3.66
655 656 6.541641 CCATTCTCTTCTTCCTCCTTAACATG 59.458 42.308 0.00 0.00 0.00 3.21
656 657 6.353429 CCCATTCTCTTCTTCCTCCTTAACAT 60.353 42.308 0.00 0.00 0.00 2.71
657 658 5.045578 CCCATTCTCTTCTTCCTCCTTAACA 60.046 44.000 0.00 0.00 0.00 2.41
658 659 5.432645 CCCATTCTCTTCTTCCTCCTTAAC 58.567 45.833 0.00 0.00 0.00 2.01
659 660 4.080299 GCCCATTCTCTTCTTCCTCCTTAA 60.080 45.833 0.00 0.00 0.00 1.85
660 661 3.456277 GCCCATTCTCTTCTTCCTCCTTA 59.544 47.826 0.00 0.00 0.00 2.69
661 662 2.240921 GCCCATTCTCTTCTTCCTCCTT 59.759 50.000 0.00 0.00 0.00 3.36
662 663 1.843206 GCCCATTCTCTTCTTCCTCCT 59.157 52.381 0.00 0.00 0.00 3.69
663 664 1.561542 TGCCCATTCTCTTCTTCCTCC 59.438 52.381 0.00 0.00 0.00 4.30
664 665 2.026822 TGTGCCCATTCTCTTCTTCCTC 60.027 50.000 0.00 0.00 0.00 3.71
665 666 1.988107 TGTGCCCATTCTCTTCTTCCT 59.012 47.619 0.00 0.00 0.00 3.36
666 667 2.489722 GTTGTGCCCATTCTCTTCTTCC 59.510 50.000 0.00 0.00 0.00 3.46
667 668 3.057946 GTGTTGTGCCCATTCTCTTCTTC 60.058 47.826 0.00 0.00 0.00 2.87
668 669 2.887152 GTGTTGTGCCCATTCTCTTCTT 59.113 45.455 0.00 0.00 0.00 2.52
669 670 2.158623 TGTGTTGTGCCCATTCTCTTCT 60.159 45.455 0.00 0.00 0.00 2.85
670 671 2.030805 GTGTGTTGTGCCCATTCTCTTC 60.031 50.000 0.00 0.00 0.00 2.87
671 672 1.956477 GTGTGTTGTGCCCATTCTCTT 59.044 47.619 0.00 0.00 0.00 2.85
672 673 1.143684 AGTGTGTTGTGCCCATTCTCT 59.856 47.619 0.00 0.00 0.00 3.10
673 674 1.609208 AGTGTGTTGTGCCCATTCTC 58.391 50.000 0.00 0.00 0.00 2.87
674 675 1.956477 GAAGTGTGTTGTGCCCATTCT 59.044 47.619 0.00 0.00 0.00 2.40
675 676 1.334960 CGAAGTGTGTTGTGCCCATTC 60.335 52.381 0.00 0.00 0.00 2.67
676 677 0.667993 CGAAGTGTGTTGTGCCCATT 59.332 50.000 0.00 0.00 0.00 3.16
677 678 0.179032 TCGAAGTGTGTTGTGCCCAT 60.179 50.000 0.00 0.00 0.00 4.00
678 679 0.179032 ATCGAAGTGTGTTGTGCCCA 60.179 50.000 0.00 0.00 0.00 5.36
679 680 0.951558 AATCGAAGTGTGTTGTGCCC 59.048 50.000 0.00 0.00 0.00 5.36
680 681 3.426159 CCATAATCGAAGTGTGTTGTGCC 60.426 47.826 0.00 0.00 0.00 5.01
681 682 3.426159 CCCATAATCGAAGTGTGTTGTGC 60.426 47.826 0.00 0.00 0.00 4.57
682 683 3.426159 GCCCATAATCGAAGTGTGTTGTG 60.426 47.826 0.00 0.00 0.00 3.33
683 684 2.747446 GCCCATAATCGAAGTGTGTTGT 59.253 45.455 0.00 0.00 0.00 3.32
684 685 2.746904 TGCCCATAATCGAAGTGTGTTG 59.253 45.455 0.00 0.00 0.00 3.33
685 686 3.066291 TGCCCATAATCGAAGTGTGTT 57.934 42.857 0.00 0.00 0.00 3.32
686 687 2.779755 TGCCCATAATCGAAGTGTGT 57.220 45.000 0.00 0.00 0.00 3.72
687 688 4.637483 ATTTGCCCATAATCGAAGTGTG 57.363 40.909 0.00 0.00 0.00 3.82
688 689 4.275936 GCTATTTGCCCATAATCGAAGTGT 59.724 41.667 0.00 0.00 35.15 3.55
689 690 4.516698 AGCTATTTGCCCATAATCGAAGTG 59.483 41.667 0.00 0.00 44.23 3.16
690 691 4.718961 AGCTATTTGCCCATAATCGAAGT 58.281 39.130 0.00 0.00 44.23 3.01
691 692 4.154918 GGAGCTATTTGCCCATAATCGAAG 59.845 45.833 0.00 0.00 44.23 3.79
692 693 4.072131 GGAGCTATTTGCCCATAATCGAA 58.928 43.478 0.00 0.00 44.23 3.71
693 694 3.559171 GGGAGCTATTTGCCCATAATCGA 60.559 47.826 2.53 0.00 44.23 3.59
694 695 2.749621 GGGAGCTATTTGCCCATAATCG 59.250 50.000 2.53 0.00 44.23 3.34
695 696 3.766545 TGGGAGCTATTTGCCCATAATC 58.233 45.455 6.02 0.00 46.57 1.75
696 697 3.901570 TGGGAGCTATTTGCCCATAAT 57.098 42.857 6.02 0.00 46.57 1.28
844 846 1.272781 CGCTCACCTGATTCGAGTTC 58.727 55.000 0.00 0.00 0.00 3.01
1250 1285 0.676151 CCTGCTCTGGTTTGCTCTCC 60.676 60.000 0.00 0.00 0.00 3.71
1956 2084 2.901839 GGGTATGTTCTATTCGGCCCTA 59.098 50.000 0.00 0.00 32.47 3.53
1975 2103 4.952335 ACTTCTTTTATCAATGAGCCTGGG 59.048 41.667 0.00 0.00 0.00 4.45
1982 2110 9.371136 CACTAGCTACACTTCTTTTATCAATGA 57.629 33.333 0.00 0.00 0.00 2.57
2030 2161 7.881643 AGCTGAAAAGATATATCGATGTCAC 57.118 36.000 8.54 0.00 0.00 3.67
2178 2310 2.131972 CCAACCTTTTGTTTTAGCCGC 58.868 47.619 0.00 0.00 34.00 6.53
2250 2382 8.528044 TGGTTGAAATAAACTAGAACCAAACT 57.472 30.769 6.06 0.00 39.83 2.66
2326 2459 2.734670 TCGGTTGAAACACACGAGTAG 58.265 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.