Multiple sequence alignment - TraesCS5B01G068500

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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 TraesCS5B01G068500 chr5B 100.000 3598 0 0 1 3598 77926727 77923130 0.000000e+00 6645.0
1 TraesCS5B01G068500 chr5B 81.720 93 14 2 1 93 712011916 712011827 1.390000e-09 75.0
2 TraesCS5B01G068500 chr5B 81.720 93 14 2 1 93 712029368 712029279 1.390000e-09 75.0
3 TraesCS5B01G068500 chr5B 81.429 70 13 0 2210 2279 700936792 700936723 1.400000e-04 58.4
4 TraesCS5B01G068500 chr5D 94.424 2152 78 10 763 2897 74418479 74420605 0.000000e+00 3271.0
5 TraesCS5B01G068500 chr5D 89.088 724 32 18 2900 3598 26461859 26461158 0.000000e+00 856.0
6 TraesCS5B01G068500 chr5D 87.883 718 47 23 2892 3598 394988240 394988928 0.000000e+00 808.0
7 TraesCS5B01G068500 chr5D 86.245 269 25 9 11 268 74414890 74415157 7.610000e-72 281.0
8 TraesCS5B01G068500 chr5D 90.625 128 12 0 383 510 182165754 182165627 1.720000e-38 171.0
9 TraesCS5B01G068500 chr5D 89.764 127 12 1 383 509 355116981 355117106 1.030000e-35 161.0
10 TraesCS5B01G068500 chr5D 97.727 88 1 1 643 729 446918257 446918170 2.240000e-32 150.0
11 TraesCS5B01G068500 chr5D 96.512 86 3 0 307 392 74418163 74418248 3.740000e-30 143.0
12 TraesCS5B01G068500 chr5A 94.902 1981 71 9 755 2712 69544979 69546952 0.000000e+00 3072.0
13 TraesCS5B01G068500 chr5A 87.361 269 25 3 1 261 69533317 69533584 2.100000e-77 300.0
14 TraesCS5B01G068500 chr5A 98.000 100 1 1 296 394 69533792 69533891 4.780000e-39 172.0
15 TraesCS5B01G068500 chr3D 88.388 732 39 18 2893 3598 380961446 380962157 0.000000e+00 839.0
16 TraesCS5B01G068500 chr3D 89.831 59 6 0 1 59 296026202 296026144 3.850000e-10 76.8
17 TraesCS5B01G068500 chr6A 86.740 724 57 15 2894 3598 116793080 116793783 0.000000e+00 769.0
18 TraesCS5B01G068500 chr7A 87.725 668 53 15 2941 3598 684924221 684923573 0.000000e+00 752.0
19 TraesCS5B01G068500 chr4B 86.313 716 64 14 2896 3598 620232303 620232997 0.000000e+00 749.0
20 TraesCS5B01G068500 chr1B 82.638 743 70 21 2894 3598 637307033 637306312 1.430000e-168 603.0
21 TraesCS5B01G068500 chr1B 94.681 94 4 1 642 734 133451840 133451747 1.040000e-30 145.0
22 TraesCS5B01G068500 chr1B 96.512 86 2 1 645 729 151363657 151363742 1.350000e-29 141.0
23 TraesCS5B01G068500 chrUn 79.126 709 96 21 2903 3590 99750660 99749983 3.300000e-120 442.0
24 TraesCS5B01G068500 chr6B 87.293 362 29 5 3244 3596 487766026 487766379 7.240000e-107 398.0
25 TraesCS5B01G068500 chr6B 88.474 321 18 3 2901 3202 487765712 487766032 1.580000e-98 370.0
26 TraesCS5B01G068500 chr3B 87.353 340 25 10 2905 3228 819699154 819698817 1.220000e-99 374.0
27 TraesCS5B01G068500 chr3B 91.597 119 10 0 391 509 820514767 820514649 7.990000e-37 165.0
28 TraesCS5B01G068500 chr3B 92.857 98 3 4 642 737 2309000 2308905 4.840000e-29 139.0
29 TraesCS5B01G068500 chr3B 94.231 52 3 0 1 52 179126901 179126952 2.980000e-11 80.5
30 TraesCS5B01G068500 chr3B 100.000 30 0 0 2293 2322 588694552 588694523 5.020000e-04 56.5
31 TraesCS5B01G068500 chr4A 82.960 223 22 7 3 210 4014610 4014389 1.710000e-43 187.0
32 TraesCS5B01G068500 chr4A 96.703 91 2 1 640 729 704436866 704436776 2.240000e-32 150.0
33 TraesCS5B01G068500 chr4A 92.079 101 6 2 630 729 684976097 684976196 1.350000e-29 141.0
34 TraesCS5B01G068500 chr4A 72.188 320 51 26 2214 2508 620932947 620932641 3.000000e-06 63.9
35 TraesCS5B01G068500 chr4D 91.339 127 11 0 383 509 36723317 36723191 1.330000e-39 174.0
36 TraesCS5B01G068500 chr4D 90.625 128 11 1 383 509 375224223 375224350 6.180000e-38 169.0
37 TraesCS5B01G068500 chr4D 89.062 128 13 1 383 509 98657228 98657101 1.340000e-34 158.0
38 TraesCS5B01G068500 chr7D 90.551 127 12 0 383 509 192763060 192762934 6.180000e-38 169.0
39 TraesCS5B01G068500 chr7D 90.551 127 11 1 383 509 567065353 567065228 2.220000e-37 167.0
40 TraesCS5B01G068500 chr7D 96.629 89 2 1 642 729 167548507 167548419 2.890000e-31 147.0
41 TraesCS5B01G068500 chr7D 85.135 74 10 1 4 76 85279649 85279576 1.390000e-09 75.0
42 TraesCS5B01G068500 chr7D 97.674 43 1 0 2852 2894 398002970 398003012 1.390000e-09 75.0
43 TraesCS5B01G068500 chr1D 89.764 127 13 0 383 509 487323406 487323280 2.870000e-36 163.0
44 TraesCS5B01G068500 chr2A 96.667 90 2 1 641 729 539325666 539325577 8.050000e-32 148.0
45 TraesCS5B01G068500 chr2A 91.262 103 6 3 645 746 78805761 78805661 1.740000e-28 137.0
46 TraesCS5B01G068500 chr2A 86.441 59 3 4 2842 2895 677493721 677493779 3.880000e-05 60.2
47 TraesCS5B01G068500 chr2B 78.099 242 40 8 1 232 76541750 76541988 1.350000e-29 141.0
48 TraesCS5B01G068500 chr6D 81.197 117 15 4 2 111 296639672 296639556 1.780000e-13 87.9
49 TraesCS5B01G068500 chr2D 100.000 33 0 0 2853 2885 189843483 189843515 1.080000e-05 62.1
50 TraesCS5B01G068500 chr3A 100.000 30 0 0 2293 2322 589824550 589824521 5.020000e-04 56.5


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 TraesCS5B01G068500 chr5B 77923130 77926727 3597 True 6645.000000 6645 100.000000 1 3598 1 chr5B.!!$R1 3597
1 TraesCS5B01G068500 chr5D 74414890 74420605 5715 False 1231.666667 3271 92.393667 11 2897 3 chr5D.!!$F3 2886
2 TraesCS5B01G068500 chr5D 26461158 26461859 701 True 856.000000 856 89.088000 2900 3598 1 chr5D.!!$R1 698
3 TraesCS5B01G068500 chr5D 394988240 394988928 688 False 808.000000 808 87.883000 2892 3598 1 chr5D.!!$F2 706
4 TraesCS5B01G068500 chr5A 69544979 69546952 1973 False 3072.000000 3072 94.902000 755 2712 1 chr5A.!!$F1 1957
5 TraesCS5B01G068500 chr5A 69533317 69533891 574 False 236.000000 300 92.680500 1 394 2 chr5A.!!$F2 393
6 TraesCS5B01G068500 chr3D 380961446 380962157 711 False 839.000000 839 88.388000 2893 3598 1 chr3D.!!$F1 705
7 TraesCS5B01G068500 chr6A 116793080 116793783 703 False 769.000000 769 86.740000 2894 3598 1 chr6A.!!$F1 704
8 TraesCS5B01G068500 chr7A 684923573 684924221 648 True 752.000000 752 87.725000 2941 3598 1 chr7A.!!$R1 657
9 TraesCS5B01G068500 chr4B 620232303 620232997 694 False 749.000000 749 86.313000 2896 3598 1 chr4B.!!$F1 702
10 TraesCS5B01G068500 chr1B 637306312 637307033 721 True 603.000000 603 82.638000 2894 3598 1 chr1B.!!$R2 704
11 TraesCS5B01G068500 chrUn 99749983 99750660 677 True 442.000000 442 79.126000 2903 3590 1 chrUn.!!$R1 687
12 TraesCS5B01G068500 chr6B 487765712 487766379 667 False 384.000000 398 87.883500 2901 3596 2 chr6B.!!$F1 695

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
444 3422 0.041312 CACCAAACGCTCAAACCGAG 60.041 55.0 0.0 0.0 45.37 4.63 F
445 3423 0.179067 ACCAAACGCTCAAACCGAGA 60.179 50.0 0.0 0.0 45.45 4.04 F
446 3424 0.234884 CCAAACGCTCAAACCGAGAC 59.765 55.0 0.0 0.0 45.45 3.36 F
470 3448 0.392998 ATTCTGGTGGGCTAACTGCG 60.393 55.0 0.0 0.0 44.05 5.18 F
503 3481 0.606096 TGCCAACTAAGCTACGCTCA 59.394 50.0 0.0 0.0 38.25 4.26 F
734 3716 0.615331 TACGGAGGGAGTACGTCACT 59.385 55.0 0.0 0.0 44.05 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 5144 0.319813 GCAGCCGCATTGTTTCCTTT 60.320 50.000 0.00 0.00 38.36 3.11 R
2433 5439 2.443577 TTGCAGCAGGTTGGCCAA 60.444 55.556 16.05 16.05 37.19 4.52 R
2488 5494 2.025767 CTCCTCCATGCTCAGGTCCG 62.026 65.000 4.10 0.00 0.00 4.79 R
2516 5522 3.898627 CTTCCTGCGCGTCGACAGT 62.899 63.158 17.16 0.00 32.39 3.55 R
2579 5585 0.908910 ATCAGGTCATGGCGGTGTAA 59.091 50.000 0.00 0.00 0.00 2.41 R
2791 5797 0.036164 TACAAATCCGCAGCCACACT 59.964 50.000 0.00 0.00 0.00 3.55 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
140 152 7.250569 AGACACGCATTGGTCTTTTATTTATG 58.749 34.615 0.00 0.00 41.40 1.90
151 163 8.632679 TGGTCTTTTATTTATGGAATGCTCATC 58.367 33.333 0.00 0.00 0.00 2.92
155 167 9.903682 CTTTTATTTATGGAATGCTCATCGATT 57.096 29.630 0.00 0.00 0.00 3.34
210 222 3.952931 AGAATCTGCTCTTGCACTTCAT 58.047 40.909 0.00 0.00 45.31 2.57
211 223 3.940221 AGAATCTGCTCTTGCACTTCATC 59.060 43.478 0.00 0.00 45.31 2.92
237 249 9.404348 CTATATATGTTAGAGCATGGCGATAAG 57.596 37.037 0.00 0.00 0.00 1.73
242 254 6.988522 TGTTAGAGCATGGCGATAAGTTATA 58.011 36.000 0.00 0.00 0.00 0.98
275 287 8.926092 AGAAAAGATTAGGAGCTTAGTTTTGT 57.074 30.769 0.00 0.00 29.85 2.83
276 288 9.004717 AGAAAAGATTAGGAGCTTAGTTTTGTC 57.995 33.333 0.00 0.00 29.85 3.18
277 289 6.969828 AAGATTAGGAGCTTAGTTTTGTCG 57.030 37.500 0.00 0.00 27.75 4.35
278 290 6.282199 AGATTAGGAGCTTAGTTTTGTCGA 57.718 37.500 0.00 0.00 0.00 4.20
279 291 6.334202 AGATTAGGAGCTTAGTTTTGTCGAG 58.666 40.000 0.00 0.00 0.00 4.04
280 292 2.689646 AGGAGCTTAGTTTTGTCGAGC 58.310 47.619 0.00 0.00 0.00 5.03
284 296 4.268884 GGAGCTTAGTTTTGTCGAGCTATG 59.731 45.833 0.00 0.00 43.22 2.23
289 301 6.520104 GCTTAGTTTTGTCGAGCTATGTTTTC 59.480 38.462 0.00 0.00 0.00 2.29
291 303 4.510340 AGTTTTGTCGAGCTATGTTTTCGT 59.490 37.500 0.00 0.00 35.90 3.85
292 304 5.007332 AGTTTTGTCGAGCTATGTTTTCGTT 59.993 36.000 0.00 0.00 35.90 3.85
314 3292 6.476051 GTTGAGCCGTAATAAGCTTAGTTTC 58.524 40.000 12.23 5.40 40.11 2.78
392 3370 1.908619 TGCATGTCATGACTACCCTGT 59.091 47.619 25.55 1.83 0.00 4.00
394 3372 2.679837 GCATGTCATGACTACCCTGTTG 59.320 50.000 25.55 11.28 0.00 3.33
395 3373 3.273434 CATGTCATGACTACCCTGTTGG 58.727 50.000 25.55 0.98 41.37 3.77
396 3374 1.003118 TGTCATGACTACCCTGTTGGC 59.997 52.381 25.55 0.00 37.83 4.52
397 3375 1.003118 GTCATGACTACCCTGTTGGCA 59.997 52.381 18.83 0.00 37.83 4.92
400 3378 2.969821 TGACTACCCTGTTGGCATTT 57.030 45.000 0.00 0.00 37.83 2.32
401 3379 3.237268 TGACTACCCTGTTGGCATTTT 57.763 42.857 0.00 0.00 37.83 1.82
402 3380 3.571590 TGACTACCCTGTTGGCATTTTT 58.428 40.909 0.00 0.00 37.83 1.94
426 3404 6.053632 TCATAGAAGAAAACTCCATGAGCA 57.946 37.500 0.00 0.00 32.04 4.26
429 3407 2.957402 AGAAAACTCCATGAGCACCA 57.043 45.000 0.00 0.00 32.04 4.17
430 3408 3.228188 AGAAAACTCCATGAGCACCAA 57.772 42.857 0.00 0.00 32.04 3.67
432 3410 3.319122 AGAAAACTCCATGAGCACCAAAC 59.681 43.478 0.00 0.00 32.04 2.93
433 3411 1.238439 AACTCCATGAGCACCAAACG 58.762 50.000 0.00 0.00 32.04 3.60
434 3412 1.237285 ACTCCATGAGCACCAAACGC 61.237 55.000 0.00 0.00 32.04 4.84
441 3419 1.733526 AGCACCAAACGCTCAAACC 59.266 52.632 0.00 0.00 33.35 3.27
442 3420 1.657181 GCACCAAACGCTCAAACCG 60.657 57.895 0.00 0.00 0.00 4.44
443 3421 2.018544 CACCAAACGCTCAAACCGA 58.981 52.632 0.00 0.00 0.00 4.69
444 3422 0.041312 CACCAAACGCTCAAACCGAG 60.041 55.000 0.00 0.00 45.37 4.63
445 3423 0.179067 ACCAAACGCTCAAACCGAGA 60.179 50.000 0.00 0.00 45.45 4.04
446 3424 0.234884 CCAAACGCTCAAACCGAGAC 59.765 55.000 0.00 0.00 45.45 3.36
447 3425 1.217882 CAAACGCTCAAACCGAGACT 58.782 50.000 0.00 0.00 45.45 3.24
449 3427 2.798283 CAAACGCTCAAACCGAGACTTA 59.202 45.455 0.00 0.00 45.45 2.24
450 3428 2.806608 ACGCTCAAACCGAGACTTAA 57.193 45.000 0.00 0.00 45.45 1.85
451 3429 3.102052 ACGCTCAAACCGAGACTTAAA 57.898 42.857 0.00 0.00 45.45 1.52
452 3430 3.660865 ACGCTCAAACCGAGACTTAAAT 58.339 40.909 0.00 0.00 45.45 1.40
453 3431 4.062991 ACGCTCAAACCGAGACTTAAATT 58.937 39.130 0.00 0.00 45.45 1.82
454 3432 4.151867 ACGCTCAAACCGAGACTTAAATTC 59.848 41.667 0.00 0.00 45.45 2.17
455 3433 4.389077 CGCTCAAACCGAGACTTAAATTCT 59.611 41.667 0.00 0.00 45.45 2.40
456 3434 5.622378 GCTCAAACCGAGACTTAAATTCTG 58.378 41.667 0.00 0.00 45.45 3.02
457 3435 5.390991 GCTCAAACCGAGACTTAAATTCTGG 60.391 44.000 0.00 0.00 45.45 3.86
458 3436 5.617252 TCAAACCGAGACTTAAATTCTGGT 58.383 37.500 0.00 0.00 0.00 4.00
459 3437 5.468746 TCAAACCGAGACTTAAATTCTGGTG 59.531 40.000 0.00 0.00 29.97 4.17
460 3438 3.939066 ACCGAGACTTAAATTCTGGTGG 58.061 45.455 0.00 0.00 0.00 4.61
461 3439 3.270877 CCGAGACTTAAATTCTGGTGGG 58.729 50.000 0.00 0.00 0.00 4.61
462 3440 2.678336 CGAGACTTAAATTCTGGTGGGC 59.322 50.000 0.00 0.00 0.00 5.36
463 3441 3.619979 CGAGACTTAAATTCTGGTGGGCT 60.620 47.826 0.00 0.00 0.00 5.19
464 3442 4.382685 CGAGACTTAAATTCTGGTGGGCTA 60.383 45.833 0.00 0.00 0.00 3.93
465 3443 5.497474 GAGACTTAAATTCTGGTGGGCTAA 58.503 41.667 0.00 0.00 0.00 3.09
466 3444 5.254115 AGACTTAAATTCTGGTGGGCTAAC 58.746 41.667 0.00 0.00 0.00 2.34
467 3445 5.014228 AGACTTAAATTCTGGTGGGCTAACT 59.986 40.000 0.00 0.00 0.00 2.24
468 3446 5.010282 ACTTAAATTCTGGTGGGCTAACTG 58.990 41.667 0.00 0.00 0.00 3.16
469 3447 1.839424 AATTCTGGTGGGCTAACTGC 58.161 50.000 0.00 0.00 41.94 4.40
470 3448 0.392998 ATTCTGGTGGGCTAACTGCG 60.393 55.000 0.00 0.00 44.05 5.18
471 3449 1.476845 TTCTGGTGGGCTAACTGCGA 61.477 55.000 0.00 0.00 44.05 5.10
472 3450 1.003839 CTGGTGGGCTAACTGCGAA 60.004 57.895 0.00 0.00 44.05 4.70
473 3451 1.298859 CTGGTGGGCTAACTGCGAAC 61.299 60.000 0.00 0.00 44.05 3.95
474 3452 1.003718 GGTGGGCTAACTGCGAACT 60.004 57.895 0.00 0.00 44.05 3.01
475 3453 1.019805 GGTGGGCTAACTGCGAACTC 61.020 60.000 0.00 0.00 44.05 3.01
476 3454 1.019805 GTGGGCTAACTGCGAACTCC 61.020 60.000 0.00 0.00 44.05 3.85
477 3455 1.449778 GGGCTAACTGCGAACTCCC 60.450 63.158 0.00 0.00 44.05 4.30
478 3456 1.810030 GGCTAACTGCGAACTCCCG 60.810 63.158 0.00 0.00 44.05 5.14
493 3471 3.053291 CCGCGCCTTGCCAACTAA 61.053 61.111 0.00 0.00 42.08 2.24
494 3472 2.480555 CGCGCCTTGCCAACTAAG 59.519 61.111 0.00 0.00 42.08 2.18
495 3473 2.179267 GCGCCTTGCCAACTAAGC 59.821 61.111 0.00 0.00 37.76 3.09
496 3474 2.335712 GCGCCTTGCCAACTAAGCT 61.336 57.895 0.00 0.00 37.76 3.74
497 3475 1.024579 GCGCCTTGCCAACTAAGCTA 61.025 55.000 0.00 0.00 37.76 3.32
498 3476 0.727398 CGCCTTGCCAACTAAGCTAC 59.273 55.000 0.00 0.00 0.00 3.58
499 3477 0.727398 GCCTTGCCAACTAAGCTACG 59.273 55.000 0.00 0.00 0.00 3.51
500 3478 0.727398 CCTTGCCAACTAAGCTACGC 59.273 55.000 0.00 0.00 0.00 4.42
501 3479 1.676014 CCTTGCCAACTAAGCTACGCT 60.676 52.381 0.00 0.00 42.56 5.07
502 3480 1.661112 CTTGCCAACTAAGCTACGCTC 59.339 52.381 0.00 0.00 38.25 5.03
503 3481 0.606096 TGCCAACTAAGCTACGCTCA 59.394 50.000 0.00 0.00 38.25 4.26
504 3482 1.281899 GCCAACTAAGCTACGCTCAG 58.718 55.000 0.00 0.00 38.25 3.35
505 3483 1.404315 GCCAACTAAGCTACGCTCAGT 60.404 52.381 0.00 0.00 39.05 3.41
506 3484 2.931320 GCCAACTAAGCTACGCTCAGTT 60.931 50.000 0.00 0.00 46.77 3.16
507 3485 2.924290 CCAACTAAGCTACGCTCAGTTC 59.076 50.000 1.51 0.00 42.82 3.01
551 3529 5.923733 AGGGCCTAAATGAGTATAGATCG 57.076 43.478 2.82 0.00 0.00 3.69
574 3552 4.262894 GGAGATGTTTGACTGGTCCAACTA 60.263 45.833 15.34 6.04 36.52 2.24
601 3583 6.463995 AAAAGATGCTTGACTGGTTAAACA 57.536 33.333 0.00 0.00 0.00 2.83
607 3589 4.336993 TGCTTGACTGGTTAAACACGATTT 59.663 37.500 0.00 0.00 0.00 2.17
611 3593 6.236017 TGACTGGTTAAACACGATTTCATC 57.764 37.500 0.00 0.00 0.00 2.92
649 3631 9.442047 TTGTTAACAGACTACTACTAGTACTCC 57.558 37.037 8.56 0.00 32.96 3.85
650 3632 8.820831 TGTTAACAGACTACTACTAGTACTCCT 58.179 37.037 3.59 0.00 32.96 3.69
651 3633 9.313118 GTTAACAGACTACTACTAGTACTCCTC 57.687 40.741 0.00 0.00 32.96 3.71
653 3635 7.116075 ACAGACTACTACTAGTACTCCTCTG 57.884 44.000 0.00 15.28 32.96 3.35
655 3637 7.838696 ACAGACTACTACTAGTACTCCTCTGTA 59.161 40.741 18.46 9.69 32.96 2.74
656 3638 8.694540 CAGACTACTACTAGTACTCCTCTGTAA 58.305 40.741 0.00 0.00 32.96 2.41
657 3639 9.265862 AGACTACTACTAGTACTCCTCTGTAAA 57.734 37.037 0.00 0.00 32.96 2.01
659 3641 9.265862 ACTACTACTAGTACTCCTCTGTAAAGA 57.734 37.037 0.00 0.00 30.81 2.52
662 3644 9.978336 ACTACTAGTACTCCTCTGTAAAGAAAT 57.022 33.333 0.00 0.00 0.00 2.17
671 3653 8.138712 ACTCCTCTGTAAAGAAATATAAGAGCG 58.861 37.037 0.00 0.00 0.00 5.03
673 3655 8.475639 TCCTCTGTAAAGAAATATAAGAGCGTT 58.524 33.333 0.00 0.00 0.00 4.84
674 3656 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
714 3696 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
719 3701 8.810427 TCTAAACGCTCTTATATTTGTTTACGG 58.190 33.333 0.00 0.00 32.41 4.02
720 3702 7.599630 AAACGCTCTTATATTTGTTTACGGA 57.400 32.000 0.00 0.00 0.00 4.69
721 3703 6.823678 ACGCTCTTATATTTGTTTACGGAG 57.176 37.500 0.00 0.00 0.00 4.63
722 3704 5.751990 ACGCTCTTATATTTGTTTACGGAGG 59.248 40.000 0.00 0.00 0.00 4.30
723 3705 5.176958 CGCTCTTATATTTGTTTACGGAGGG 59.823 44.000 0.00 0.00 0.00 4.30
724 3706 6.285990 GCTCTTATATTTGTTTACGGAGGGA 58.714 40.000 0.00 0.00 0.00 4.20
725 3707 6.424207 GCTCTTATATTTGTTTACGGAGGGAG 59.576 42.308 0.00 0.00 0.00 4.30
726 3708 7.427989 TCTTATATTTGTTTACGGAGGGAGT 57.572 36.000 0.00 0.00 0.00 3.85
727 3709 8.537728 TCTTATATTTGTTTACGGAGGGAGTA 57.462 34.615 0.00 0.00 0.00 2.59
728 3710 8.416329 TCTTATATTTGTTTACGGAGGGAGTAC 58.584 37.037 0.00 0.00 0.00 2.73
729 3711 3.302365 TTTGTTTACGGAGGGAGTACG 57.698 47.619 0.00 0.00 0.00 3.67
730 3712 1.909700 TGTTTACGGAGGGAGTACGT 58.090 50.000 0.00 0.00 43.88 3.57
731 3713 1.812571 TGTTTACGGAGGGAGTACGTC 59.187 52.381 0.00 0.00 41.53 4.34
732 3714 1.812571 GTTTACGGAGGGAGTACGTCA 59.187 52.381 0.00 0.00 41.53 4.35
733 3715 1.453155 TTACGGAGGGAGTACGTCAC 58.547 55.000 0.00 0.00 41.53 3.67
734 3716 0.615331 TACGGAGGGAGTACGTCACT 59.385 55.000 0.00 0.00 44.05 3.41
735 3717 0.615331 ACGGAGGGAGTACGTCACTA 59.385 55.000 0.00 0.00 39.97 2.74
736 3718 1.211457 ACGGAGGGAGTACGTCACTAT 59.789 52.381 0.00 0.00 39.97 2.12
737 3719 1.602851 CGGAGGGAGTACGTCACTATG 59.397 57.143 0.00 0.00 39.97 2.23
738 3720 2.652590 GGAGGGAGTACGTCACTATGT 58.347 52.381 0.00 0.00 39.97 2.29
739 3721 3.742327 CGGAGGGAGTACGTCACTATGTA 60.742 52.174 0.00 0.00 39.97 2.29
740 3722 3.814283 GGAGGGAGTACGTCACTATGTAG 59.186 52.174 0.00 0.00 39.97 2.74
741 3723 3.814283 GAGGGAGTACGTCACTATGTAGG 59.186 52.174 0.00 0.00 39.97 3.18
742 3724 3.457380 AGGGAGTACGTCACTATGTAGGA 59.543 47.826 0.00 0.00 37.04 2.94
743 3725 3.814283 GGGAGTACGTCACTATGTAGGAG 59.186 52.174 0.00 0.00 37.72 3.69
744 3726 4.450053 GGAGTACGTCACTATGTAGGAGT 58.550 47.826 0.00 0.00 37.72 3.85
745 3727 5.453903 GGGAGTACGTCACTATGTAGGAGTA 60.454 48.000 0.00 0.00 37.72 2.59
746 3728 5.465056 GGAGTACGTCACTATGTAGGAGTAC 59.535 48.000 0.00 0.00 37.72 2.73
747 3729 6.232581 AGTACGTCACTATGTAGGAGTACT 57.767 41.667 0.00 0.00 38.76 2.73
748 3730 6.047870 AGTACGTCACTATGTAGGAGTACTG 58.952 44.000 0.00 0.00 41.03 2.74
749 3731 5.095145 ACGTCACTATGTAGGAGTACTGA 57.905 43.478 0.00 0.00 0.00 3.41
750 3732 5.117584 ACGTCACTATGTAGGAGTACTGAG 58.882 45.833 0.00 0.00 0.00 3.35
751 3733 5.117584 CGTCACTATGTAGGAGTACTGAGT 58.882 45.833 0.00 0.00 0.00 3.41
752 3734 6.127225 ACGTCACTATGTAGGAGTACTGAGTA 60.127 42.308 0.00 0.00 0.00 2.59
753 3735 6.200665 CGTCACTATGTAGGAGTACTGAGTAC 59.799 46.154 14.69 14.69 39.10 2.73
761 3743 5.986501 AGGAGTACTGAGTACCTGAAAAG 57.013 43.478 18.45 0.00 39.58 2.27
814 3797 7.754924 ACAAAACACTTATCTGCATATTTTCCG 59.245 33.333 0.00 0.00 0.00 4.30
816 3799 8.500753 AAACACTTATCTGCATATTTTCCGTA 57.499 30.769 0.00 0.00 0.00 4.02
843 3826 2.043227 CTGAGGGGAATCAGGACCTAC 58.957 57.143 0.00 0.00 42.52 3.18
844 3827 1.651770 TGAGGGGAATCAGGACCTACT 59.348 52.381 0.00 0.00 32.42 2.57
845 3828 2.863238 TGAGGGGAATCAGGACCTACTA 59.137 50.000 0.00 0.00 32.42 1.82
904 3887 7.067981 ACCTTTCATGCTTTGGATAGAGAAATC 59.932 37.037 0.00 0.00 0.00 2.17
924 3907 4.425180 TCTGTTACAGCCAACCACTTTA 57.575 40.909 7.61 0.00 0.00 1.85
997 3999 1.566404 CAAGGCCAAAACGTTTCCAC 58.434 50.000 15.01 6.30 0.00 4.02
1434 4436 1.984570 CACCGAGCTCTTCTCCCCA 60.985 63.158 12.85 0.00 38.62 4.96
1604 4606 3.755628 GTGGTCGGGCTGCTACGA 61.756 66.667 14.00 14.00 36.68 3.43
1744 4746 1.815421 CGGAGGATGAAGCGGTTGG 60.815 63.158 3.70 0.00 0.00 3.77
1800 4802 3.800863 GAGCACGACGAGGAGCGA 61.801 66.667 0.00 0.00 44.57 4.93
1904 4910 3.119096 GAAGGCGAGACGGTTGGC 61.119 66.667 0.00 0.00 35.16 4.52
2113 5119 2.748058 GAAGAAAGCGACCTGGCCCA 62.748 60.000 0.00 0.00 0.00 5.36
2138 5144 1.717791 CCTACATCGACGCCGTGGTA 61.718 60.000 0.00 0.00 37.05 3.25
2220 5226 4.063967 CACTGGTCGCCGGCTACA 62.064 66.667 29.71 21.02 32.02 2.74
2369 5375 2.047465 CACTTCGAGCTGCTGCCT 60.047 61.111 7.01 0.00 40.80 4.75
2516 5522 1.825341 CATGGAGGAGCATGTCGGA 59.175 57.895 0.00 0.00 0.00 4.55
2630 5636 3.062504 GCATGCAAAATCAATTTCCCGAC 59.937 43.478 14.21 0.00 0.00 4.79
2705 5711 1.542915 CAGCCACACCATCTTTCCTTG 59.457 52.381 0.00 0.00 0.00 3.61
2706 5712 1.145738 AGCCACACCATCTTTCCTTGT 59.854 47.619 0.00 0.00 0.00 3.16
2727 5733 0.603569 TCTCTCAAGAACCCTGCGTC 59.396 55.000 0.00 0.00 0.00 5.19
2748 5754 0.872021 CGACTAGCGAGTGATTGCCC 60.872 60.000 3.45 0.00 44.57 5.36
2750 5756 0.176680 ACTAGCGAGTGATTGCCCAG 59.823 55.000 0.00 0.00 33.41 4.45
2788 5794 3.129287 CAGCACCTGAGTTGTTTGTTTCT 59.871 43.478 0.00 0.00 32.44 2.52
2789 5795 4.335315 CAGCACCTGAGTTGTTTGTTTCTA 59.665 41.667 0.00 0.00 32.44 2.10
2790 5796 4.576463 AGCACCTGAGTTGTTTGTTTCTAG 59.424 41.667 0.00 0.00 0.00 2.43
2791 5797 4.574828 GCACCTGAGTTGTTTGTTTCTAGA 59.425 41.667 0.00 0.00 0.00 2.43
2825 5831 5.684626 CGGATTTGTACGTACCATTACTCTC 59.315 44.000 22.43 8.04 0.00 3.20
2832 5838 8.206325 TGTACGTACCATTACTCTCTTTCTAG 57.794 38.462 22.43 0.00 0.00 2.43
2857 5863 8.567948 AGAAAAATTCATGATAACACGTGTCTT 58.432 29.630 23.61 12.52 0.00 3.01
3104 6131 1.451504 CCCACTCTCAGCCACACAA 59.548 57.895 0.00 0.00 0.00 3.33
3119 6146 2.097466 CACACAAACCACTCCACTTCAC 59.903 50.000 0.00 0.00 0.00 3.18
3215 6243 4.162690 GGCGAAGAGGATGCGGGT 62.163 66.667 0.00 0.00 0.00 5.28
3288 6341 3.084786 GTGGAAGCCTCAAATAGCAAGT 58.915 45.455 0.00 0.00 0.00 3.16
3300 6353 2.480555 GCAAGTGGCGGTCGATTG 59.519 61.111 0.00 0.00 0.00 2.67
3301 6354 3.039202 GCAAGTGGCGGTCGATTGG 62.039 63.158 0.00 0.00 0.00 3.16
3372 6448 2.651455 CTGTGGGTGTACGAGGATCTA 58.349 52.381 0.00 0.00 0.00 1.98
3489 6565 1.667830 CGGGAGCTGCGTTCAGAAA 60.668 57.895 0.00 0.00 42.95 2.52
3570 6653 0.747283 CACCAGAGCTCTTCATGGCC 60.747 60.000 15.27 0.00 36.21 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 152 4.889832 AGTGAAAATCGATGAGCATTCC 57.110 40.909 0.00 0.00 0.00 3.01
173 185 6.210185 AGCAGATTCTACAAAAGCCTCAATTT 59.790 34.615 0.00 0.00 0.00 1.82
175 187 5.259632 AGCAGATTCTACAAAAGCCTCAAT 58.740 37.500 0.00 0.00 0.00 2.57
210 222 7.588497 ATCGCCATGCTCTAACATATATAGA 57.412 36.000 0.00 0.00 0.00 1.98
211 223 9.404348 CTTATCGCCATGCTCTAACATATATAG 57.596 37.037 0.00 0.00 0.00 1.31
264 276 5.532025 AACATAGCTCGACAAAACTAAGC 57.468 39.130 0.00 0.00 0.00 3.09
265 277 6.732392 CGAAAACATAGCTCGACAAAACTAAG 59.268 38.462 0.00 0.00 34.52 2.18
268 280 4.510340 ACGAAAACATAGCTCGACAAAACT 59.490 37.500 0.00 0.00 36.45 2.66
269 281 4.769215 ACGAAAACATAGCTCGACAAAAC 58.231 39.130 0.00 0.00 36.45 2.43
271 283 4.508492 TCAACGAAAACATAGCTCGACAAA 59.492 37.500 0.00 0.00 36.45 2.83
272 284 4.052608 TCAACGAAAACATAGCTCGACAA 58.947 39.130 0.00 0.00 36.45 3.18
273 285 3.644823 TCAACGAAAACATAGCTCGACA 58.355 40.909 0.00 0.00 36.45 4.35
274 286 3.482112 GCTCAACGAAAACATAGCTCGAC 60.482 47.826 0.00 0.00 36.45 4.20
275 287 2.666508 GCTCAACGAAAACATAGCTCGA 59.333 45.455 0.00 0.00 36.45 4.04
276 288 2.222819 GGCTCAACGAAAACATAGCTCG 60.223 50.000 0.00 0.00 38.53 5.03
277 289 2.222819 CGGCTCAACGAAAACATAGCTC 60.223 50.000 0.00 0.00 35.47 4.09
278 290 1.732259 CGGCTCAACGAAAACATAGCT 59.268 47.619 0.00 0.00 35.47 3.32
279 291 1.463444 ACGGCTCAACGAAAACATAGC 59.537 47.619 0.00 0.00 37.61 2.97
280 292 4.914312 TTACGGCTCAACGAAAACATAG 57.086 40.909 0.00 0.00 37.61 2.23
284 296 4.086574 GCTTATTACGGCTCAACGAAAAC 58.913 43.478 0.00 0.00 37.61 2.43
289 301 4.110482 ACTAAGCTTATTACGGCTCAACG 58.890 43.478 6.64 0.00 37.87 4.10
291 303 5.290158 CGAAACTAAGCTTATTACGGCTCAA 59.710 40.000 6.64 0.00 37.87 3.02
292 304 4.802039 CGAAACTAAGCTTATTACGGCTCA 59.198 41.667 6.64 0.00 37.87 4.26
314 3292 7.352739 ACTAAGAACAAAAACATAGCTCAACG 58.647 34.615 0.00 0.00 0.00 4.10
400 3378 7.448161 TGCTCATGGAGTTTTCTTCTATGAAAA 59.552 33.333 0.00 0.00 41.75 2.29
401 3379 6.942005 TGCTCATGGAGTTTTCTTCTATGAAA 59.058 34.615 0.00 0.00 34.55 2.69
402 3380 6.372659 GTGCTCATGGAGTTTTCTTCTATGAA 59.627 38.462 0.00 0.00 31.39 2.57
403 3381 5.877012 GTGCTCATGGAGTTTTCTTCTATGA 59.123 40.000 0.00 2.15 31.39 2.15
404 3382 5.065731 GGTGCTCATGGAGTTTTCTTCTATG 59.934 44.000 0.00 0.00 31.39 2.23
406 3384 4.041567 TGGTGCTCATGGAGTTTTCTTCTA 59.958 41.667 0.00 0.00 31.39 2.10
407 3385 3.181440 TGGTGCTCATGGAGTTTTCTTCT 60.181 43.478 0.00 0.00 31.39 2.85
409 3387 3.228188 TGGTGCTCATGGAGTTTTCTT 57.772 42.857 0.00 0.00 31.39 2.52
410 3388 2.957402 TGGTGCTCATGGAGTTTTCT 57.043 45.000 0.00 0.00 31.39 2.52
411 3389 3.642705 GTTTGGTGCTCATGGAGTTTTC 58.357 45.455 0.00 0.00 31.39 2.29
412 3390 2.034558 CGTTTGGTGCTCATGGAGTTTT 59.965 45.455 0.00 0.00 31.39 2.43
413 3391 1.608590 CGTTTGGTGCTCATGGAGTTT 59.391 47.619 0.00 0.00 31.39 2.66
414 3392 1.238439 CGTTTGGTGCTCATGGAGTT 58.762 50.000 0.00 0.00 31.39 3.01
415 3393 1.237285 GCGTTTGGTGCTCATGGAGT 61.237 55.000 0.00 0.00 31.39 3.85
416 3394 0.957395 AGCGTTTGGTGCTCATGGAG 60.957 55.000 0.00 0.00 38.62 3.86
417 3395 1.073025 AGCGTTTGGTGCTCATGGA 59.927 52.632 0.00 0.00 38.62 3.41
418 3396 3.672293 AGCGTTTGGTGCTCATGG 58.328 55.556 0.00 0.00 38.62 3.66
424 3402 1.657181 CGGTTTGAGCGTTTGGTGC 60.657 57.895 0.00 0.00 33.95 5.01
426 3404 0.179067 TCTCGGTTTGAGCGTTTGGT 60.179 50.000 0.00 0.00 44.86 3.67
429 3407 1.949465 AAGTCTCGGTTTGAGCGTTT 58.051 45.000 0.00 0.00 44.86 3.60
430 3408 2.806608 TAAGTCTCGGTTTGAGCGTT 57.193 45.000 0.00 0.00 44.86 4.84
432 3410 4.389077 AGAATTTAAGTCTCGGTTTGAGCG 59.611 41.667 0.00 0.00 44.86 5.03
433 3411 5.390991 CCAGAATTTAAGTCTCGGTTTGAGC 60.391 44.000 0.00 0.00 44.86 4.26
434 3412 5.701290 ACCAGAATTTAAGTCTCGGTTTGAG 59.299 40.000 9.49 0.00 46.72 3.02
437 3415 4.760204 CCACCAGAATTTAAGTCTCGGTTT 59.240 41.667 11.62 0.00 29.52 3.27
440 3418 3.270877 CCCACCAGAATTTAAGTCTCGG 58.729 50.000 8.52 8.52 0.00 4.63
441 3419 2.678336 GCCCACCAGAATTTAAGTCTCG 59.322 50.000 0.00 0.00 0.00 4.04
442 3420 3.956744 AGCCCACCAGAATTTAAGTCTC 58.043 45.455 0.00 0.00 0.00 3.36
443 3421 5.014228 AGTTAGCCCACCAGAATTTAAGTCT 59.986 40.000 0.00 0.00 0.00 3.24
444 3422 5.123979 CAGTTAGCCCACCAGAATTTAAGTC 59.876 44.000 0.00 0.00 0.00 3.01
445 3423 5.010282 CAGTTAGCCCACCAGAATTTAAGT 58.990 41.667 0.00 0.00 0.00 2.24
446 3424 4.142381 GCAGTTAGCCCACCAGAATTTAAG 60.142 45.833 0.00 0.00 37.23 1.85
447 3425 3.761752 GCAGTTAGCCCACCAGAATTTAA 59.238 43.478 0.00 0.00 37.23 1.52
449 3427 2.171003 GCAGTTAGCCCACCAGAATTT 58.829 47.619 0.00 0.00 37.23 1.82
450 3428 1.839424 GCAGTTAGCCCACCAGAATT 58.161 50.000 0.00 0.00 37.23 2.17
451 3429 0.392998 CGCAGTTAGCCCACCAGAAT 60.393 55.000 0.00 0.00 41.38 2.40
452 3430 1.003839 CGCAGTTAGCCCACCAGAA 60.004 57.895 0.00 0.00 41.38 3.02
453 3431 1.476845 TTCGCAGTTAGCCCACCAGA 61.477 55.000 0.00 0.00 41.38 3.86
454 3432 1.003839 TTCGCAGTTAGCCCACCAG 60.004 57.895 0.00 0.00 41.38 4.00
455 3433 1.302192 GTTCGCAGTTAGCCCACCA 60.302 57.895 0.00 0.00 41.38 4.17
456 3434 1.003718 AGTTCGCAGTTAGCCCACC 60.004 57.895 0.00 0.00 41.38 4.61
457 3435 1.019805 GGAGTTCGCAGTTAGCCCAC 61.020 60.000 0.00 0.00 41.38 4.61
458 3436 1.295423 GGAGTTCGCAGTTAGCCCA 59.705 57.895 0.00 0.00 41.38 5.36
459 3437 1.449778 GGGAGTTCGCAGTTAGCCC 60.450 63.158 0.00 0.00 41.38 5.19
460 3438 1.810030 CGGGAGTTCGCAGTTAGCC 60.810 63.158 0.00 0.00 41.38 3.93
461 3439 3.782042 CGGGAGTTCGCAGTTAGC 58.218 61.111 0.00 0.00 40.87 3.09
476 3454 3.039202 CTTAGTTGGCAAGGCGCGG 62.039 63.158 8.83 0.00 43.84 6.46
477 3455 2.480555 CTTAGTTGGCAAGGCGCG 59.519 61.111 0.00 0.00 43.84 6.86
478 3456 1.024579 TAGCTTAGTTGGCAAGGCGC 61.025 55.000 0.00 0.00 41.28 6.53
479 3457 0.727398 GTAGCTTAGTTGGCAAGGCG 59.273 55.000 0.00 0.00 0.00 5.52
480 3458 0.727398 CGTAGCTTAGTTGGCAAGGC 59.273 55.000 0.00 3.21 0.00 4.35
527 3505 6.334202 CGATCTATACTCATTTAGGCCCTTC 58.666 44.000 0.00 0.00 0.00 3.46
551 3529 2.814336 GTTGGACCAGTCAAACATCTCC 59.186 50.000 12.27 0.00 41.88 3.71
584 3562 2.907634 TCGTGTTTAACCAGTCAAGCA 58.092 42.857 0.00 0.00 0.00 3.91
585 3563 4.483476 AATCGTGTTTAACCAGTCAAGC 57.517 40.909 0.00 0.00 0.00 4.01
586 3564 6.055231 TGAAATCGTGTTTAACCAGTCAAG 57.945 37.500 0.00 0.00 0.00 3.02
601 3583 8.964476 ACAATTATTGGAGTAGATGAAATCGT 57.036 30.769 9.88 0.00 41.32 3.73
636 3618 9.978336 ATTTCTTTACAGAGGAGTACTAGTAGT 57.022 33.333 10.09 10.09 0.00 2.73
645 3627 8.138712 CGCTCTTATATTTCTTTACAGAGGAGT 58.861 37.037 0.00 0.00 0.00 3.85
647 3629 8.008513 ACGCTCTTATATTTCTTTACAGAGGA 57.991 34.615 0.00 0.00 0.00 3.71
648 3630 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
688 3670 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
693 3675 8.810427 CCGTAAACAAATATAAGAGCGTTTAGA 58.190 33.333 0.00 0.00 31.53 2.10
694 3676 8.810427 TCCGTAAACAAATATAAGAGCGTTTAG 58.190 33.333 0.00 0.00 31.53 1.85
695 3677 8.700722 TCCGTAAACAAATATAAGAGCGTTTA 57.299 30.769 0.00 0.00 0.00 2.01
696 3678 7.201582 CCTCCGTAAACAAATATAAGAGCGTTT 60.202 37.037 0.00 0.00 0.00 3.60
697 3679 6.257193 CCTCCGTAAACAAATATAAGAGCGTT 59.743 38.462 0.00 0.00 0.00 4.84
698 3680 5.751990 CCTCCGTAAACAAATATAAGAGCGT 59.248 40.000 0.00 0.00 0.00 5.07
699 3681 5.176958 CCCTCCGTAAACAAATATAAGAGCG 59.823 44.000 0.00 0.00 0.00 5.03
700 3682 6.285990 TCCCTCCGTAAACAAATATAAGAGC 58.714 40.000 0.00 0.00 0.00 4.09
701 3683 7.498443 ACTCCCTCCGTAAACAAATATAAGAG 58.502 38.462 0.00 0.00 0.00 2.85
702 3684 7.427989 ACTCCCTCCGTAAACAAATATAAGA 57.572 36.000 0.00 0.00 0.00 2.10
703 3685 7.380602 CGTACTCCCTCCGTAAACAAATATAAG 59.619 40.741 0.00 0.00 0.00 1.73
704 3686 7.147915 ACGTACTCCCTCCGTAAACAAATATAA 60.148 37.037 0.00 0.00 32.22 0.98
705 3687 6.321181 ACGTACTCCCTCCGTAAACAAATATA 59.679 38.462 0.00 0.00 32.22 0.86
706 3688 5.127682 ACGTACTCCCTCCGTAAACAAATAT 59.872 40.000 0.00 0.00 32.22 1.28
707 3689 4.462483 ACGTACTCCCTCCGTAAACAAATA 59.538 41.667 0.00 0.00 32.22 1.40
708 3690 3.259123 ACGTACTCCCTCCGTAAACAAAT 59.741 43.478 0.00 0.00 32.22 2.32
709 3691 2.627699 ACGTACTCCCTCCGTAAACAAA 59.372 45.455 0.00 0.00 32.22 2.83
710 3692 2.228822 GACGTACTCCCTCCGTAAACAA 59.771 50.000 0.00 0.00 34.51 2.83
711 3693 1.812571 GACGTACTCCCTCCGTAAACA 59.187 52.381 0.00 0.00 34.51 2.83
712 3694 1.812571 TGACGTACTCCCTCCGTAAAC 59.187 52.381 0.00 0.00 34.51 2.01
713 3695 1.812571 GTGACGTACTCCCTCCGTAAA 59.187 52.381 0.00 0.00 34.51 2.01
714 3696 1.003580 AGTGACGTACTCCCTCCGTAA 59.996 52.381 0.00 0.00 33.17 3.18
715 3697 0.615331 AGTGACGTACTCCCTCCGTA 59.385 55.000 0.00 0.00 33.17 4.02
716 3698 0.615331 TAGTGACGTACTCCCTCCGT 59.385 55.000 0.00 0.00 40.89 4.69
717 3699 1.602851 CATAGTGACGTACTCCCTCCG 59.397 57.143 0.00 0.00 40.89 4.63
718 3700 2.652590 ACATAGTGACGTACTCCCTCC 58.347 52.381 0.00 0.00 40.89 4.30
719 3701 3.814283 CCTACATAGTGACGTACTCCCTC 59.186 52.174 0.00 0.00 40.89 4.30
720 3702 3.457380 TCCTACATAGTGACGTACTCCCT 59.543 47.826 0.00 0.00 40.89 4.20
721 3703 3.813443 TCCTACATAGTGACGTACTCCC 58.187 50.000 0.00 0.00 40.89 4.30
722 3704 4.450053 ACTCCTACATAGTGACGTACTCC 58.550 47.826 0.00 0.00 40.89 3.85
723 3705 6.200665 CAGTACTCCTACATAGTGACGTACTC 59.799 46.154 0.00 0.00 40.89 2.59
724 3706 6.047870 CAGTACTCCTACATAGTGACGTACT 58.952 44.000 0.00 0.00 43.56 2.73
725 3707 6.045318 TCAGTACTCCTACATAGTGACGTAC 58.955 44.000 0.00 0.00 0.00 3.67
726 3708 6.127225 ACTCAGTACTCCTACATAGTGACGTA 60.127 42.308 0.00 0.00 29.66 3.57
727 3709 5.095145 TCAGTACTCCTACATAGTGACGT 57.905 43.478 0.00 0.00 0.00 4.34
728 3710 5.117584 ACTCAGTACTCCTACATAGTGACG 58.882 45.833 0.00 0.00 29.66 4.35
729 3711 6.482973 GGTACTCAGTACTCCTACATAGTGAC 59.517 46.154 14.75 0.00 38.85 3.67
730 3712 6.386342 AGGTACTCAGTACTCCTACATAGTGA 59.614 42.308 14.75 0.00 38.85 3.41
731 3713 6.483974 CAGGTACTCAGTACTCCTACATAGTG 59.516 46.154 14.75 0.00 38.85 2.74
732 3714 6.386342 TCAGGTACTCAGTACTCCTACATAGT 59.614 42.308 14.75 0.00 38.85 2.12
733 3715 6.828788 TCAGGTACTCAGTACTCCTACATAG 58.171 44.000 14.75 0.00 38.85 2.23
734 3716 6.819947 TCAGGTACTCAGTACTCCTACATA 57.180 41.667 14.75 0.00 38.85 2.29
735 3717 5.712084 TCAGGTACTCAGTACTCCTACAT 57.288 43.478 14.75 0.00 38.85 2.29
736 3718 5.509832 TTCAGGTACTCAGTACTCCTACA 57.490 43.478 14.75 0.00 38.85 2.74
737 3719 6.127675 CCTTTTCAGGTACTCAGTACTCCTAC 60.128 46.154 14.75 0.00 38.85 3.18
738 3720 5.950549 CCTTTTCAGGTACTCAGTACTCCTA 59.049 44.000 14.75 0.00 38.85 2.94
739 3721 4.773149 CCTTTTCAGGTACTCAGTACTCCT 59.227 45.833 14.75 1.43 38.85 3.69
740 3722 4.771054 TCCTTTTCAGGTACTCAGTACTCC 59.229 45.833 14.75 0.00 41.69 3.85
741 3723 5.336610 GGTCCTTTTCAGGTACTCAGTACTC 60.337 48.000 14.75 5.26 41.69 2.59
742 3724 4.527427 GGTCCTTTTCAGGTACTCAGTACT 59.473 45.833 14.75 0.00 41.69 2.73
743 3725 4.527427 AGGTCCTTTTCAGGTACTCAGTAC 59.473 45.833 6.40 6.40 41.69 2.73
744 3726 4.527038 CAGGTCCTTTTCAGGTACTCAGTA 59.473 45.833 0.00 0.00 41.69 2.74
745 3727 3.325135 CAGGTCCTTTTCAGGTACTCAGT 59.675 47.826 0.00 0.00 41.69 3.41
746 3728 3.325135 ACAGGTCCTTTTCAGGTACTCAG 59.675 47.826 0.00 0.00 41.69 3.35
747 3729 3.314693 ACAGGTCCTTTTCAGGTACTCA 58.685 45.455 0.00 0.00 41.69 3.41
748 3730 3.579151 AGACAGGTCCTTTTCAGGTACTC 59.421 47.826 0.00 0.00 41.69 2.59
749 3731 3.579151 GAGACAGGTCCTTTTCAGGTACT 59.421 47.826 0.00 0.00 41.69 2.73
750 3732 3.306849 GGAGACAGGTCCTTTTCAGGTAC 60.307 52.174 0.00 0.00 41.69 3.34
751 3733 2.904434 GGAGACAGGTCCTTTTCAGGTA 59.096 50.000 0.00 0.00 41.69 3.08
752 3734 1.700186 GGAGACAGGTCCTTTTCAGGT 59.300 52.381 0.00 0.00 41.69 4.00
753 3735 1.981495 AGGAGACAGGTCCTTTTCAGG 59.019 52.381 0.00 0.00 45.39 3.86
761 3743 1.304217 TCCACGAGGAGACAGGTCC 60.304 63.158 0.00 0.00 39.61 4.46
789 3771 7.754924 ACGGAAAATATGCAGATAAGTGTTTTG 59.245 33.333 0.00 0.00 0.00 2.44
790 3772 7.826690 ACGGAAAATATGCAGATAAGTGTTTT 58.173 30.769 0.00 0.00 0.00 2.43
791 3773 7.391148 ACGGAAAATATGCAGATAAGTGTTT 57.609 32.000 0.00 0.00 0.00 2.83
814 3797 0.846693 ATTCCCCTCAGCCCATGTAC 59.153 55.000 0.00 0.00 0.00 2.90
816 3799 0.920763 TGATTCCCCTCAGCCCATGT 60.921 55.000 0.00 0.00 0.00 3.21
843 3826 6.015504 GTGTTTGTGTCTTTGCGATACATAG 58.984 40.000 0.00 0.00 42.32 2.23
844 3827 5.106869 GGTGTTTGTGTCTTTGCGATACATA 60.107 40.000 0.00 0.00 42.32 2.29
845 3828 4.320202 GGTGTTTGTGTCTTTGCGATACAT 60.320 41.667 0.00 0.00 42.32 2.29
889 3872 6.823689 GGCTGTAACAGATTTCTCTATCCAAA 59.176 38.462 0.00 0.00 32.44 3.28
904 3887 3.880490 TGTAAAGTGGTTGGCTGTAACAG 59.120 43.478 0.00 0.00 32.22 3.16
924 3907 6.039717 AGCATTTTCAGTGTAGTTTGTGATGT 59.960 34.615 0.00 0.00 0.00 3.06
997 3999 3.319405 AGTGTCGGTATGAGCTCCATTAG 59.681 47.826 12.15 0.04 36.71 1.73
1010 4012 2.986290 CCATGGGCAGTGTCGGTA 59.014 61.111 2.85 0.00 0.00 4.02
1495 4497 4.096558 GCCGCGGCATTCGAACAA 62.097 61.111 43.55 0.00 42.43 2.83
1744 4746 0.390735 AACCGATCGTACACCTTGCC 60.391 55.000 15.09 0.00 0.00 4.52
1904 4910 2.096069 CCTTGCTTCTGTTGATGACGTG 60.096 50.000 0.00 0.00 0.00 4.49
1910 4916 2.157738 GTGAGCCTTGCTTCTGTTGAT 58.842 47.619 0.00 0.00 39.88 2.57
2113 5119 2.125961 GCGTCGATGTAGGGGAGGT 61.126 63.158 6.48 0.00 0.00 3.85
2138 5144 0.319813 GCAGCCGCATTGTTTCCTTT 60.320 50.000 0.00 0.00 38.36 3.11
2433 5439 2.443577 TTGCAGCAGGTTGGCCAA 60.444 55.556 16.05 16.05 37.19 4.52
2488 5494 2.025767 CTCCTCCATGCTCAGGTCCG 62.026 65.000 4.10 0.00 0.00 4.79
2516 5522 3.898627 CTTCCTGCGCGTCGACAGT 62.899 63.158 17.16 0.00 32.39 3.55
2579 5585 0.908910 ATCAGGTCATGGCGGTGTAA 59.091 50.000 0.00 0.00 0.00 2.41
2630 5636 0.518636 CAGTCGATTGCACCAACTGG 59.481 55.000 0.00 0.00 42.17 4.00
2705 5711 1.801178 CGCAGGGTTCTTGAGAGAAAC 59.199 52.381 0.00 0.00 46.72 2.78
2706 5712 1.416401 ACGCAGGGTTCTTGAGAGAAA 59.584 47.619 0.00 0.00 43.21 2.52
2748 5754 2.485814 GCTGTGCTAGGAAAAAGACCTG 59.514 50.000 0.00 0.00 38.31 4.00
2750 5756 2.226674 GTGCTGTGCTAGGAAAAAGACC 59.773 50.000 0.00 0.00 0.00 3.85
2788 5794 0.613260 AAATCCGCAGCCACACTCTA 59.387 50.000 0.00 0.00 0.00 2.43
2789 5795 0.957395 CAAATCCGCAGCCACACTCT 60.957 55.000 0.00 0.00 0.00 3.24
2790 5796 1.237285 ACAAATCCGCAGCCACACTC 61.237 55.000 0.00 0.00 0.00 3.51
2791 5797 0.036164 TACAAATCCGCAGCCACACT 59.964 50.000 0.00 0.00 0.00 3.55
2832 5838 8.728088 AAGACACGTGTTATCATGAATTTTTC 57.272 30.769 24.26 3.64 34.90 2.29
2879 5885 7.104326 TCCGTAGTTTTTACGTGATTTGTAC 57.896 36.000 0.00 0.00 39.09 2.90
3104 6131 1.716028 GGGGGTGAAGTGGAGTGGTT 61.716 60.000 0.00 0.00 0.00 3.67
3353 6429 2.651455 CTAGATCCTCGTACACCCACA 58.349 52.381 0.00 0.00 0.00 4.17
3354 6430 1.337387 GCTAGATCCTCGTACACCCAC 59.663 57.143 0.00 0.00 0.00 4.61
3372 6448 1.080434 GAAGCAGACGACGAAGGCT 60.080 57.895 0.00 3.84 36.13 4.58
3414 6490 0.111061 ATGTTGCTCTGGACCAAGCA 59.889 50.000 20.62 20.62 46.31 3.91
3570 6653 2.972505 GCAGGACACACACACCCG 60.973 66.667 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.