Multiple sequence alignment - TraesCS3B01G518900

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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 TraesCS3B01G518900 chr3B 100.000 6789 0 0 1 6789 761932260 761939048 0.000000e+00 12538.0
1 TraesCS3B01G518900 chr3B 87.650 1085 134 0 4666 5750 761902263 761903347 0.000000e+00 1262.0
2 TraesCS3B01G518900 chr3B 82.392 744 111 14 996 1729 761901020 761901753 1.240000e-176 630.0
3 TraesCS3B01G518900 chr3B 78.750 320 41 19 6448 6760 448564812 448564513 8.990000e-44 189.0
4 TraesCS3B01G518900 chr3B 82.249 169 15 7 2813 2981 762488097 762488250 1.540000e-26 132.0
5 TraesCS3B01G518900 chr3D 94.205 2226 113 12 4573 6789 572046120 572043902 0.000000e+00 3382.0
6 TraesCS3B01G518900 chr3D 90.209 2053 114 26 1897 3909 572048347 572046342 0.000000e+00 2597.0
7 TraesCS3B01G518900 chr3D 93.772 1734 75 16 17 1743 572050347 572048640 0.000000e+00 2573.0
8 TraesCS3B01G518900 chr3D 89.350 1108 118 0 4643 5750 572085521 572084414 0.000000e+00 1393.0
9 TraesCS3B01G518900 chr3D 88.126 1078 128 0 4666 5743 572101787 572100710 0.000000e+00 1282.0
10 TraesCS3B01G518900 chr3D 90.963 841 62 5 883 1714 572088789 572087954 0.000000e+00 1120.0
11 TraesCS3B01G518900 chr3D 89.562 891 73 4 3034 3904 543807379 543806489 0.000000e+00 1112.0
12 TraesCS3B01G518900 chr3D 91.939 521 32 7 1 519 572096261 572095749 0.000000e+00 721.0
13 TraesCS3B01G518900 chr3D 81.900 779 117 18 966 1729 572103041 572102272 2.670000e-178 636.0
14 TraesCS3B01G518900 chr3D 93.525 139 9 0 3904 4042 572046286 572046148 2.480000e-49 207.0
15 TraesCS3B01G518900 chr3D 79.149 235 42 7 6451 6684 29814443 29814215 9.120000e-34 156.0
16 TraesCS3B01G518900 chr3D 86.260 131 12 3 657 783 572090875 572090747 3.300000e-28 137.0
17 TraesCS3B01G518900 chr3D 92.857 70 4 1 1737 1806 455007466 455007398 4.330000e-17 100.0
18 TraesCS3B01G518900 chr3D 100.000 38 0 0 841 878 572090661 572090624 3.400000e-08 71.3
19 TraesCS3B01G518900 chr3A 92.455 2240 139 15 4568 6789 706922765 706924992 0.000000e+00 3173.0
20 TraesCS3B01G518900 chr3A 95.212 1107 41 6 646 1743 706911012 706912115 0.000000e+00 1740.0
21 TraesCS3B01G518900 chr3A 88.018 1085 130 0 4666 5750 706851422 706852506 0.000000e+00 1284.0
22 TraesCS3B01G518900 chr3A 89.853 887 67 8 841 1711 706899495 706900374 0.000000e+00 1118.0
23 TraesCS3B01G518900 chr3A 91.650 503 39 3 2134 2635 706919302 706919802 0.000000e+00 693.0
24 TraesCS3B01G518900 chr3A 88.095 546 44 8 17 556 706910483 706911013 4.470000e-176 628.0
25 TraesCS3B01G518900 chr3A 86.159 289 15 10 1802 2089 706912114 706912378 8.610000e-74 289.0
26 TraesCS3B01G518900 chr3A 91.935 186 13 2 36 219 706857011 706857196 6.750000e-65 259.0
27 TraesCS3B01G518900 chr3A 88.038 209 12 5 2620 2816 706922390 706922597 1.140000e-57 235.0
28 TraesCS3B01G518900 chr2B 85.620 1064 150 1 4691 5751 390925520 390926583 0.000000e+00 1114.0
29 TraesCS3B01G518900 chr1D 92.112 786 61 1 3107 3892 494347926 494347142 0.000000e+00 1107.0
30 TraesCS3B01G518900 chr1D 77.861 402 71 13 6355 6754 95790540 95790925 4.090000e-57 233.0
31 TraesCS3B01G518900 chr1D 92.647 68 3 2 1737 1802 297127263 297127196 5.600000e-16 97.1
32 TraesCS3B01G518900 chr5A 89.241 883 80 3 3037 3904 703350476 703351358 0.000000e+00 1090.0
33 TraesCS3B01G518900 chr2D 85.230 1063 154 1 4692 5751 323076868 323077930 0.000000e+00 1090.0
34 TraesCS3B01G518900 chr2D 91.214 626 53 1 3286 3909 322854566 322855191 0.000000e+00 850.0
35 TraesCS3B01G518900 chr2D 77.447 235 37 13 6444 6670 7618754 7618980 7.150000e-25 126.0
36 TraesCS3B01G518900 chr2A 89.165 886 81 3 3033 3904 498109415 498110299 0.000000e+00 1090.0
37 TraesCS3B01G518900 chr2A 84.962 1064 157 1 4691 5751 407740548 407739485 0.000000e+00 1075.0
38 TraesCS3B01G518900 chr2A 89.853 818 83 0 3087 3904 544284111 544283294 0.000000e+00 1051.0
39 TraesCS3B01G518900 chr2A 87.406 532 67 0 4031 4562 73547037 73547568 4.500000e-171 612.0
40 TraesCS3B01G518900 chr2A 86.517 534 70 2 4031 4563 654383529 654384061 2.730000e-163 586.0
41 TraesCS3B01G518900 chr2A 78.733 221 32 12 6542 6762 702241676 702241881 4.270000e-27 134.0
42 TraesCS3B01G518900 chr6A 89.915 823 82 1 3087 3909 85028325 85027504 0.000000e+00 1059.0
43 TraesCS3B01G518900 chr6A 90.467 535 48 3 4031 4564 537731628 537732160 0.000000e+00 702.0
44 TraesCS3B01G518900 chr6A 90.789 76 4 3 1735 1807 426607715 426607640 1.560000e-16 99.0
45 TraesCS3B01G518900 chr1A 88.588 701 66 4 3037 3723 32294928 32295628 0.000000e+00 839.0
46 TraesCS3B01G518900 chr1A 85.542 166 10 2 2820 2985 460081398 460081247 1.960000e-35 161.0
47 TraesCS3B01G518900 chr1A 94.118 68 2 2 1737 1802 44540254 44540187 1.200000e-17 102.0
48 TraesCS3B01G518900 chr1A 94.118 68 2 2 1737 1802 44598263 44598196 1.200000e-17 102.0
49 TraesCS3B01G518900 chr5B 92.322 534 38 3 4040 4572 482180226 482179695 0.000000e+00 756.0
50 TraesCS3B01G518900 chr5B 89.844 512 52 0 4031 4542 442784143 442784654 0.000000e+00 658.0
51 TraesCS3B01G518900 chr5B 85.294 170 10 4 2813 2982 458154894 458154740 1.960000e-35 161.0
52 TraesCS3B01G518900 chr5B 82.716 81 14 0 5894 5974 322890330 322890250 9.440000e-09 73.1
53 TraesCS3B01G518900 chr7D 90.347 518 44 4 4050 4567 4249316 4248805 0.000000e+00 675.0
54 TraesCS3B01G518900 chr7D 81.277 235 39 4 6363 6597 535951040 535950811 1.160000e-42 185.0
55 TraesCS3B01G518900 chr7D 84.971 173 11 3 2810 2982 115023057 115023214 1.960000e-35 161.0
56 TraesCS3B01G518900 chr7D 95.122 41 2 0 5900 5940 599503945 599503905 1.580000e-06 65.8
57 TraesCS3B01G518900 chr4A 87.617 533 61 5 4031 4562 96026421 96026949 1.250000e-171 614.0
58 TraesCS3B01G518900 chr6D 86.891 534 70 0 4031 4564 48674795 48675328 3.500000e-167 599.0
59 TraesCS3B01G518900 chr6D 92.647 68 3 2 1737 1802 457453407 457453474 5.600000e-16 97.1
60 TraesCS3B01G518900 chr5D 86.355 535 71 2 4031 4564 311608919 311609452 3.530000e-162 582.0
61 TraesCS3B01G518900 chr5D 78.370 319 48 15 6449 6759 450609204 450609509 3.230000e-43 187.0
62 TraesCS3B01G518900 chr5D 79.476 229 37 8 6448 6674 380524366 380524146 3.280000e-33 154.0
63 TraesCS3B01G518900 chr5D 92.754 69 2 3 1737 1802 169581114 169581182 5.600000e-16 97.1
64 TraesCS3B01G518900 chr5D 82.979 94 11 5 5900 5991 75921465 75921375 5.640000e-11 80.5
65 TraesCS3B01G518900 chrUn 85.294 170 10 3 2813 2982 259872084 259871930 1.960000e-35 161.0
66 TraesCS3B01G518900 chrUn 73.508 419 85 18 6355 6766 429101564 429101963 1.190000e-27 135.0
67 TraesCS3B01G518900 chr1B 82.822 163 14 3 2822 2984 10546854 10546706 4.270000e-27 134.0
68 TraesCS3B01G518900 chr1B 81.977 172 16 7 2813 2984 107593987 107593831 1.540000e-26 132.0
69 TraesCS3B01G518900 chr1B 77.108 166 12 13 2817 2980 650456094 650456235 9.440000e-09 73.1
70 TraesCS3B01G518900 chr4D 92.857 70 3 2 1737 1804 28889119 28889188 4.330000e-17 100.0
71 TraesCS3B01G518900 chr4D 92.647 68 3 2 1737 1802 405589090 405589157 5.600000e-16 97.1
72 TraesCS3B01G518900 chr7B 93.617 47 3 0 5894 5940 678740491 678740537 3.400000e-08 71.3
73 TraesCS3B01G518900 chr7B 95.455 44 2 0 5889 5932 678838906 678838863 3.400000e-08 71.3
74 TraesCS3B01G518900 chr7B 97.436 39 1 0 5894 5932 678838170 678838132 4.390000e-07 67.6
75 TraesCS3B01G518900 chr7B 97.436 39 1 0 5894 5932 678839626 678839588 4.390000e-07 67.6
76 TraesCS3B01G518900 chr7B 84.375 64 8 2 259 321 80087259 80087321 2.040000e-05 62.1


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 TraesCS3B01G518900 chr3B 761932260 761939048 6788 False 12538.000000 12538 100.000000 1 6789 1 chr3B.!!$F1 6788
1 TraesCS3B01G518900 chr3B 761901020 761903347 2327 False 946.000000 1262 85.021000 996 5750 2 chr3B.!!$F3 4754
2 TraesCS3B01G518900 chr3D 572043902 572050347 6445 True 2189.750000 3382 92.927750 17 6789 4 chr3D.!!$R5 6772
3 TraesCS3B01G518900 chr3D 543806489 543807379 890 True 1112.000000 1112 89.562000 3034 3904 1 chr3D.!!$R3 870
4 TraesCS3B01G518900 chr3D 572100710 572103041 2331 True 959.000000 1282 85.013000 966 5743 2 chr3D.!!$R7 4777
5 TraesCS3B01G518900 chr3D 572095749 572096261 512 True 721.000000 721 91.939000 1 519 1 chr3D.!!$R4 518
6 TraesCS3B01G518900 chr3D 572084414 572090875 6461 True 680.325000 1393 91.643250 657 5750 4 chr3D.!!$R6 5093
7 TraesCS3B01G518900 chr3A 706919302 706924992 5690 False 1367.000000 3173 90.714333 2134 6789 3 chr3A.!!$F5 4655
8 TraesCS3B01G518900 chr3A 706851422 706852506 1084 False 1284.000000 1284 88.018000 4666 5750 1 chr3A.!!$F1 1084
9 TraesCS3B01G518900 chr3A 706899495 706900374 879 False 1118.000000 1118 89.853000 841 1711 1 chr3A.!!$F3 870
10 TraesCS3B01G518900 chr3A 706910483 706912378 1895 False 885.666667 1740 89.822000 17 2089 3 chr3A.!!$F4 2072
11 TraesCS3B01G518900 chr2B 390925520 390926583 1063 False 1114.000000 1114 85.620000 4691 5751 1 chr2B.!!$F1 1060
12 TraesCS3B01G518900 chr1D 494347142 494347926 784 True 1107.000000 1107 92.112000 3107 3892 1 chr1D.!!$R2 785
13 TraesCS3B01G518900 chr5A 703350476 703351358 882 False 1090.000000 1090 89.241000 3037 3904 1 chr5A.!!$F1 867
14 TraesCS3B01G518900 chr2D 323076868 323077930 1062 False 1090.000000 1090 85.230000 4692 5751 1 chr2D.!!$F3 1059
15 TraesCS3B01G518900 chr2D 322854566 322855191 625 False 850.000000 850 91.214000 3286 3909 1 chr2D.!!$F2 623
16 TraesCS3B01G518900 chr2A 498109415 498110299 884 False 1090.000000 1090 89.165000 3033 3904 1 chr2A.!!$F2 871
17 TraesCS3B01G518900 chr2A 407739485 407740548 1063 True 1075.000000 1075 84.962000 4691 5751 1 chr2A.!!$R1 1060
18 TraesCS3B01G518900 chr2A 544283294 544284111 817 True 1051.000000 1051 89.853000 3087 3904 1 chr2A.!!$R2 817
19 TraesCS3B01G518900 chr2A 73547037 73547568 531 False 612.000000 612 87.406000 4031 4562 1 chr2A.!!$F1 531
20 TraesCS3B01G518900 chr2A 654383529 654384061 532 False 586.000000 586 86.517000 4031 4563 1 chr2A.!!$F3 532
21 TraesCS3B01G518900 chr6A 85027504 85028325 821 True 1059.000000 1059 89.915000 3087 3909 1 chr6A.!!$R1 822
22 TraesCS3B01G518900 chr6A 537731628 537732160 532 False 702.000000 702 90.467000 4031 4564 1 chr6A.!!$F1 533
23 TraesCS3B01G518900 chr1A 32294928 32295628 700 False 839.000000 839 88.588000 3037 3723 1 chr1A.!!$F1 686
24 TraesCS3B01G518900 chr5B 482179695 482180226 531 True 756.000000 756 92.322000 4040 4572 1 chr5B.!!$R3 532
25 TraesCS3B01G518900 chr5B 442784143 442784654 511 False 658.000000 658 89.844000 4031 4542 1 chr5B.!!$F1 511
26 TraesCS3B01G518900 chr7D 4248805 4249316 511 True 675.000000 675 90.347000 4050 4567 1 chr7D.!!$R1 517
27 TraesCS3B01G518900 chr4A 96026421 96026949 528 False 614.000000 614 87.617000 4031 4562 1 chr4A.!!$F1 531
28 TraesCS3B01G518900 chr6D 48674795 48675328 533 False 599.000000 599 86.891000 4031 4564 1 chr6D.!!$F1 533
29 TraesCS3B01G518900 chr5D 311608919 311609452 533 False 582.000000 582 86.355000 4031 4564 1 chr5D.!!$F2 533

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
75 76 0.458669 GATCATGCCACCTTTGCCTG 59.541 55.000 0.00 0.00 0.00 4.85 F
186 189 0.994263 GTTGGCACGTCCGTGTATAC 59.006 55.000 19.67 11.61 46.90 1.47 F
1084 2998 1.007734 GTCGTCTTCACCTGCGTCA 60.008 57.895 0.00 0.00 0.00 4.35 F
1841 3947 1.272490 GGCAAGCCCCACTTTACTTTC 59.728 52.381 0.00 0.00 36.04 2.62 F
3297 9988 0.176680 GCTCGAGAGAATGGCCAGAA 59.823 55.000 18.75 0.00 41.32 3.02 F
5170 12001 0.384669 ACTTCTATGCGCCCGTACTC 59.615 55.000 4.18 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 3980 1.372004 CAGCCGCCAATTGTGTGTG 60.372 57.895 4.43 0.00 0.00 3.82 R
1878 3984 2.126228 CAGCAGCCGCCAATTGTG 60.126 61.111 4.43 0.00 39.83 3.33 R
2302 6315 0.596082 CAACTAAACCCACAAGCCCG 59.404 55.000 0.00 0.00 0.00 6.13 R
3469 10160 0.103026 TCAGGATGATCGCACTTCGG 59.897 55.000 0.00 0.00 42.56 4.30 R
5290 12121 2.839098 CCACCCTGCAGGAACAGT 59.161 61.111 34.91 20.11 39.89 3.55 R
6231 13068 0.252197 ACCGTGTTTATCTGCTCCCC 59.748 55.000 0.00 0.00 0.00 4.81 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.592898 ATGATACTGTCTTGCACGTCA 57.407 42.857 0.00 0.00 0.00 4.35
75 76 0.458669 GATCATGCCACCTTTGCCTG 59.541 55.000 0.00 0.00 0.00 4.85
86 87 3.511146 CACCTTTGCCTGTCAATTGGTAT 59.489 43.478 5.42 0.00 38.75 2.73
120 121 1.340017 ACACGATCAAACCCATCCTGG 60.340 52.381 0.00 0.00 37.25 4.45
156 157 5.066593 CCTCTGGGGCACTATTTATTCTTC 58.933 45.833 0.00 0.00 0.00 2.87
186 189 0.994263 GTTGGCACGTCCGTGTATAC 59.006 55.000 19.67 11.61 46.90 1.47
225 230 3.181440 ACCAAAGCACTCATGGAAGAGAA 60.181 43.478 8.88 0.00 38.98 2.87
226 231 4.015084 CCAAAGCACTCATGGAAGAGAAT 58.985 43.478 0.00 0.00 38.98 2.40
239 244 3.759086 GGAAGAGAATGAGTTTGTTCCCC 59.241 47.826 0.00 0.00 0.00 4.81
240 245 4.398319 GAAGAGAATGAGTTTGTTCCCCA 58.602 43.478 0.00 0.00 0.00 4.96
287 292 2.548920 GGTTGCAGATCGGCTAGCTAAT 60.549 50.000 20.07 8.38 34.87 1.73
295 300 4.827835 AGATCGGCTAGCTAATTACAGTCA 59.172 41.667 15.72 0.00 0.00 3.41
322 327 6.600032 ACAGAGTCTACTACTGTTGTATGGAG 59.400 42.308 2.71 0.00 41.21 3.86
336 341 3.401342 TGTATGGAGGCATAGAGGTCCTA 59.599 47.826 0.00 0.00 0.00 2.94
337 342 3.637821 ATGGAGGCATAGAGGTCCTAA 57.362 47.619 0.00 0.00 0.00 2.69
352 357 4.096081 AGGTCCTAAGTGTATCGAGAAACG 59.904 45.833 0.00 0.00 44.09 3.60
368 373 5.470047 AGAAACGAGTACCTCTCAATTGT 57.530 39.130 5.13 0.00 42.88 2.71
369 374 6.585695 AGAAACGAGTACCTCTCAATTGTA 57.414 37.500 5.13 0.00 42.88 2.41
370 375 6.989659 AGAAACGAGTACCTCTCAATTGTAA 58.010 36.000 5.13 0.00 42.88 2.41
371 376 6.867293 AGAAACGAGTACCTCTCAATTGTAAC 59.133 38.462 5.13 0.00 42.88 2.50
372 377 5.069501 ACGAGTACCTCTCAATTGTAACC 57.930 43.478 5.13 0.00 42.88 2.85
373 378 4.081807 ACGAGTACCTCTCAATTGTAACCC 60.082 45.833 5.13 0.00 42.88 4.11
374 379 4.159879 CGAGTACCTCTCAATTGTAACCCT 59.840 45.833 5.13 0.00 42.88 4.34
375 380 5.420409 GAGTACCTCTCAATTGTAACCCTG 58.580 45.833 5.13 0.00 42.34 4.45
376 381 4.844655 AGTACCTCTCAATTGTAACCCTGT 59.155 41.667 5.13 0.00 0.00 4.00
377 382 4.724279 ACCTCTCAATTGTAACCCTGTT 57.276 40.909 5.13 0.00 0.00 3.16
378 383 5.836024 ACCTCTCAATTGTAACCCTGTTA 57.164 39.130 5.13 0.00 0.00 2.41
575 584 6.094186 TGACTTGCGTTGCACCAATATATAAA 59.906 34.615 0.00 0.00 38.71 1.40
601 610 4.097863 CCGGCGGCGAAAAGGAAC 62.098 66.667 34.49 0.00 0.00 3.62
611 620 2.737252 GCGAAAAGGAACTAGTGACTGG 59.263 50.000 0.00 0.00 38.49 4.00
612 621 2.737252 CGAAAAGGAACTAGTGACTGGC 59.263 50.000 0.00 0.00 38.49 4.85
613 622 3.555168 CGAAAAGGAACTAGTGACTGGCT 60.555 47.826 0.00 0.00 38.49 4.75
614 623 3.409026 AAAGGAACTAGTGACTGGCTG 57.591 47.619 0.00 0.00 38.49 4.85
615 624 2.310779 AGGAACTAGTGACTGGCTGA 57.689 50.000 0.00 0.00 36.02 4.26
616 625 1.896465 AGGAACTAGTGACTGGCTGAC 59.104 52.381 0.00 0.00 36.02 3.51
617 626 1.896465 GGAACTAGTGACTGGCTGACT 59.104 52.381 0.00 0.00 0.00 3.41
618 627 2.353208 GGAACTAGTGACTGGCTGACTG 60.353 54.545 0.00 0.00 0.00 3.51
643 652 1.276989 TGGTTAGTGGTTAGGGCTTCG 59.723 52.381 0.00 0.00 0.00 3.79
655 664 5.220796 GGTTAGGGCTTCGTTTAGCTTATTG 60.221 44.000 0.00 0.00 40.99 1.90
782 863 3.788797 GCAACTGGAAAGAGAAACACGTG 60.789 47.826 15.48 15.48 0.00 4.49
805 886 9.114965 CGTGTATAAACGAAGACTAATATCCAG 57.885 37.037 10.01 0.00 46.49 3.86
884 965 3.769300 TGTGGAATAAGCAGACTGAGCTA 59.231 43.478 6.65 0.00 42.53 3.32
1084 2998 1.007734 GTCGTCTTCACCTGCGTCA 60.008 57.895 0.00 0.00 0.00 4.35
1257 3173 2.435586 CTGCTCCAGGCCTTCACG 60.436 66.667 0.00 0.00 40.92 4.35
1278 3194 2.360726 TCACTCTACCTCGCCGCA 60.361 61.111 0.00 0.00 0.00 5.69
1561 3486 9.120538 GGCTGATTCACTTACCTATTTCAATTA 57.879 33.333 0.00 0.00 0.00 1.40
1602 3569 7.285172 TCAAGTTAACATCACAATCCCATATGG 59.715 37.037 15.41 15.41 0.00 2.74
1744 3850 8.764287 GGTTGTGCCTTGATTATTATTTATTGC 58.236 33.333 0.00 0.00 0.00 3.56
1745 3851 9.533253 GTTGTGCCTTGATTATTATTTATTGCT 57.467 29.630 0.00 0.00 0.00 3.91
1747 3853 9.531942 TGTGCCTTGATTATTATTTATTGCTTG 57.468 29.630 0.00 0.00 0.00 4.01
1748 3854 8.490355 GTGCCTTGATTATTATTTATTGCTTGC 58.510 33.333 0.00 0.00 0.00 4.01
1749 3855 7.656948 TGCCTTGATTATTATTTATTGCTTGCC 59.343 33.333 0.00 0.00 0.00 4.52
1750 3856 7.656948 GCCTTGATTATTATTTATTGCTTGCCA 59.343 33.333 0.00 0.00 0.00 4.92
1751 3857 8.981647 CCTTGATTATTATTTATTGCTTGCCAC 58.018 33.333 0.00 0.00 0.00 5.01
1752 3858 9.531942 CTTGATTATTATTTATTGCTTGCCACA 57.468 29.630 0.00 0.00 0.00 4.17
1754 3860 9.695526 TGATTATTATTTATTGCTTGCCACATC 57.304 29.630 0.00 0.00 0.00 3.06
1755 3861 9.695526 GATTATTATTTATTGCTTGCCACATCA 57.304 29.630 0.00 0.00 0.00 3.07
1757 3863 9.695526 TTATTATTTATTGCTTGCCACATCATC 57.304 29.630 0.00 0.00 0.00 2.92
1758 3864 5.864418 ATTTATTGCTTGCCACATCATCT 57.136 34.783 0.00 0.00 0.00 2.90
1759 3865 6.964807 ATTTATTGCTTGCCACATCATCTA 57.035 33.333 0.00 0.00 0.00 1.98
1760 3866 6.964807 TTTATTGCTTGCCACATCATCTAT 57.035 33.333 0.00 0.00 0.00 1.98
1761 3867 6.964807 TTATTGCTTGCCACATCATCTATT 57.035 33.333 0.00 0.00 0.00 1.73
1762 3868 5.864418 ATTGCTTGCCACATCATCTATTT 57.136 34.783 0.00 0.00 0.00 1.40
1763 3869 5.664294 TTGCTTGCCACATCATCTATTTT 57.336 34.783 0.00 0.00 0.00 1.82
1764 3870 6.772360 TTGCTTGCCACATCATCTATTTTA 57.228 33.333 0.00 0.00 0.00 1.52
1765 3871 6.964807 TGCTTGCCACATCATCTATTTTAT 57.035 33.333 0.00 0.00 0.00 1.40
1766 3872 6.973843 TGCTTGCCACATCATCTATTTTATC 58.026 36.000 0.00 0.00 0.00 1.75
1767 3873 6.774170 TGCTTGCCACATCATCTATTTTATCT 59.226 34.615 0.00 0.00 0.00 1.98
1768 3874 7.938490 TGCTTGCCACATCATCTATTTTATCTA 59.062 33.333 0.00 0.00 0.00 1.98
1769 3875 8.449397 GCTTGCCACATCATCTATTTTATCTAG 58.551 37.037 0.00 0.00 0.00 2.43
1770 3876 9.716531 CTTGCCACATCATCTATTTTATCTAGA 57.283 33.333 0.00 0.00 0.00 2.43
1794 3900 8.366401 AGATATGTCTGATGTTACTCTCATTGG 58.634 37.037 0.00 0.00 32.13 3.16
1795 3901 5.089970 TGTCTGATGTTACTCTCATTGGG 57.910 43.478 0.00 0.00 0.00 4.12
1796 3902 4.532126 TGTCTGATGTTACTCTCATTGGGT 59.468 41.667 0.00 0.00 0.00 4.51
1797 3903 5.719563 TGTCTGATGTTACTCTCATTGGGTA 59.280 40.000 0.00 0.00 0.00 3.69
1798 3904 6.127338 TGTCTGATGTTACTCTCATTGGGTAG 60.127 42.308 0.00 0.00 0.00 3.18
1799 3905 5.958380 TCTGATGTTACTCTCATTGGGTAGT 59.042 40.000 0.00 0.00 0.00 2.73
1800 3906 6.096987 TCTGATGTTACTCTCATTGGGTAGTC 59.903 42.308 0.00 0.00 0.00 2.59
1801 3907 5.958380 TGATGTTACTCTCATTGGGTAGTCT 59.042 40.000 0.00 0.00 0.00 3.24
1802 3908 6.440647 TGATGTTACTCTCATTGGGTAGTCTT 59.559 38.462 0.00 0.00 0.00 3.01
1841 3947 1.272490 GGCAAGCCCCACTTTACTTTC 59.728 52.381 0.00 0.00 36.04 2.62
1842 3948 2.239400 GCAAGCCCCACTTTACTTTCT 58.761 47.619 0.00 0.00 36.04 2.52
1843 3949 3.418047 GCAAGCCCCACTTTACTTTCTA 58.582 45.455 0.00 0.00 36.04 2.10
1844 3950 3.190744 GCAAGCCCCACTTTACTTTCTAC 59.809 47.826 0.00 0.00 36.04 2.59
1845 3951 4.652822 CAAGCCCCACTTTACTTTCTACT 58.347 43.478 0.00 0.00 36.04 2.57
1848 3954 5.070685 AGCCCCACTTTACTTTCTACTTTG 58.929 41.667 0.00 0.00 0.00 2.77
1849 3955 5.067954 GCCCCACTTTACTTTCTACTTTGA 58.932 41.667 0.00 0.00 0.00 2.69
1850 3956 5.710567 GCCCCACTTTACTTTCTACTTTGAT 59.289 40.000 0.00 0.00 0.00 2.57
1851 3957 6.882678 GCCCCACTTTACTTTCTACTTTGATA 59.117 38.462 0.00 0.00 0.00 2.15
1852 3958 7.392393 GCCCCACTTTACTTTCTACTTTGATAA 59.608 37.037 0.00 0.00 0.00 1.75
1853 3959 9.462606 CCCCACTTTACTTTCTACTTTGATAAT 57.537 33.333 0.00 0.00 0.00 1.28
1858 3964 9.121658 CTTTACTTTCTACTTTGATAATCCCCC 57.878 37.037 0.00 0.00 0.00 5.40
1879 3985 4.866224 CGCCCCACCACACACACA 62.866 66.667 0.00 0.00 0.00 3.72
1880 3986 3.216292 GCCCCACCACACACACAC 61.216 66.667 0.00 0.00 0.00 3.82
1916 4221 3.192844 TGCAGGAACCGTGTTAAAACAAA 59.807 39.130 0.00 0.00 41.21 2.83
2064 6064 4.821805 ACTGAACTTAACAAGGGTGTCATG 59.178 41.667 0.00 0.00 36.80 3.07
2177 6183 4.564782 ACTTGTGAGTCACATCCATGAT 57.435 40.909 25.97 4.93 44.16 2.45
2187 6193 4.214119 GTCACATCCATGATTTGATACCCG 59.786 45.833 0.00 0.00 32.52 5.28
2193 6199 7.505585 ACATCCATGATTTGATACCCGTAAAAT 59.494 33.333 0.00 0.00 0.00 1.82
2302 6315 1.507141 CGGTGTGCCTCACTTGTTCC 61.507 60.000 8.60 0.00 45.50 3.62
2319 6332 1.074248 CCGGGCTTGTGGGTTTAGT 59.926 57.895 0.00 0.00 0.00 2.24
2322 6335 0.317160 GGGCTTGTGGGTTTAGTTGC 59.683 55.000 0.00 0.00 0.00 4.17
2342 6355 7.671302 AGTTGCATGTATCCTCTATTTACGAT 58.329 34.615 0.00 0.00 0.00 3.73
2360 6373 2.625314 CGATGAGCATCTCTTGTCCCTA 59.375 50.000 8.66 0.00 35.72 3.53
2363 6376 3.378512 TGAGCATCTCTTGTCCCTATGT 58.621 45.455 0.00 0.00 34.92 2.29
2366 6379 5.184892 AGCATCTCTTGTCCCTATGTTTT 57.815 39.130 0.00 0.00 0.00 2.43
2378 6391 3.899360 CCCTATGTTTTGGGCATCATCAT 59.101 43.478 0.00 0.00 36.61 2.45
2677 9293 8.807581 CATTTCTTCATTTTATTTACTTCGGGC 58.192 33.333 0.00 0.00 0.00 6.13
2689 9305 1.775039 CTTCGGGCCATGCATGTACG 61.775 60.000 24.58 22.82 0.00 3.67
2693 9309 2.534019 GGCCATGCATGTACGGACG 61.534 63.158 24.58 9.02 0.00 4.79
2706 9322 2.201022 CGGACGGGGGAGGAGTATG 61.201 68.421 0.00 0.00 0.00 2.39
2711 9339 1.839894 GGGGGAGGAGTATGCTTGG 59.160 63.158 0.00 0.00 36.27 3.61
2799 9436 1.202417 CGGGGAGCTAGTACACATGTG 60.202 57.143 24.25 24.25 0.00 3.21
2814 9455 3.666253 GTGTTTTCACGGGCCGGG 61.666 66.667 31.78 28.82 41.13 5.73
2841 9482 5.651139 CCTAGCCAGGATTATCAATCATTGG 59.349 44.000 13.28 13.28 45.91 3.16
2842 9483 4.413760 AGCCAGGATTATCAATCATTGGG 58.586 43.478 16.73 5.29 41.10 4.12
2843 9484 4.140853 AGCCAGGATTATCAATCATTGGGT 60.141 41.667 15.08 15.08 43.70 4.51
2844 9485 5.074929 AGCCAGGATTATCAATCATTGGGTA 59.925 40.000 17.48 0.00 45.15 3.69
2883 9524 3.391296 AGAGTGGGTTCAGTTCTTTGCTA 59.609 43.478 0.00 0.00 0.00 3.49
2896 9537 8.314751 TCAGTTCTTTGCTAAGTCTTAAGCTAT 58.685 33.333 7.77 0.00 32.98 2.97
2927 9568 6.303054 TCTACAAGGGACATGTCAAATTTCA 58.697 36.000 26.47 5.72 40.40 2.69
2928 9569 6.947733 TCTACAAGGGACATGTCAAATTTCAT 59.052 34.615 26.47 3.57 40.40 2.57
2929 9570 6.423776 ACAAGGGACATGTCAAATTTCATT 57.576 33.333 26.47 9.57 33.94 2.57
2930 9571 6.225318 ACAAGGGACATGTCAAATTTCATTG 58.775 36.000 26.47 21.23 33.94 2.82
2931 9572 5.410355 AGGGACATGTCAAATTTCATTGG 57.590 39.130 26.47 0.00 0.00 3.16
2932 9573 4.223477 AGGGACATGTCAAATTTCATTGGG 59.777 41.667 26.47 0.00 0.00 4.12
2933 9574 4.020307 GGGACATGTCAAATTTCATTGGGT 60.020 41.667 26.47 0.00 0.00 4.51
2934 9575 5.512921 GGGACATGTCAAATTTCATTGGGTT 60.513 40.000 26.47 0.00 0.00 4.11
2935 9576 5.639082 GGACATGTCAAATTTCATTGGGTTC 59.361 40.000 26.47 0.00 0.00 3.62
2936 9577 6.172136 ACATGTCAAATTTCATTGGGTTCA 57.828 33.333 0.00 0.00 0.00 3.18
3026 9667 5.167121 TGTTGGTTTTCGGCATGATATTTG 58.833 37.500 0.00 0.00 0.00 2.32
3041 9698 7.201548 GCATGATATTTGGTGGTCATGTTTTTC 60.202 37.037 13.67 0.00 45.95 2.29
3052 9709 2.432510 TCATGTTTTTCTTTTGCGGGGT 59.567 40.909 0.00 0.00 0.00 4.95
3080 9737 6.496338 GGAAGTTTTATTCCACAACGAGAT 57.504 37.500 0.64 0.00 46.77 2.75
3093 9778 3.000727 CAACGAGATGGTTACAAGTCCC 58.999 50.000 0.00 0.00 0.00 4.46
3095 9780 1.470979 CGAGATGGTTACAAGTCCCCG 60.471 57.143 0.00 0.00 0.00 5.73
3105 9790 2.308722 AAGTCCCCGCACCATGGAT 61.309 57.895 21.47 0.00 0.00 3.41
3126 9811 4.545208 TGAATCGAGTTCAACCATACCA 57.455 40.909 7.53 0.00 43.64 3.25
3131 9816 2.736721 CGAGTTCAACCATACCACAGTG 59.263 50.000 0.00 0.00 0.00 3.66
3136 9821 2.158682 TCAACCATACCACAGTGCAAGT 60.159 45.455 0.00 0.00 0.00 3.16
3156 9841 3.446161 AGTTTCAGTGCGGCTATAGTGTA 59.554 43.478 0.00 0.00 0.00 2.90
3169 9854 6.055588 GGCTATAGTGTACCAATTGATGTGT 58.944 40.000 7.12 0.00 0.00 3.72
3187 9872 9.913310 TTGATGTGTTACCCTATTTTGATATCA 57.087 29.630 0.00 0.00 0.00 2.15
3277 9968 1.280421 GGCTGACCTGGAGAGATTGTT 59.720 52.381 0.00 0.00 0.00 2.83
3297 9988 0.176680 GCTCGAGAGAATGGCCAGAA 59.823 55.000 18.75 0.00 41.32 3.02
3347 10038 3.772387 TGGGCAGTCCAAATGTTGAATA 58.228 40.909 0.00 0.00 43.84 1.75
3349 10040 3.763897 GGGCAGTCCAAATGTTGAATAGT 59.236 43.478 0.00 0.00 35.00 2.12
3373 10064 3.652869 AGTGCCATACCCTGCATAATAGT 59.347 43.478 0.00 0.00 40.07 2.12
3375 10066 4.935808 GTGCCATACCCTGCATAATAGTAC 59.064 45.833 0.00 0.00 40.07 2.73
3724 10417 5.991606 TCTCATTCTTCCCGTGCTTTATATG 59.008 40.000 0.00 0.00 0.00 1.78
3744 10437 7.765695 ATATGATTTCGGAGTTGCCAAATAT 57.234 32.000 0.00 0.00 35.94 1.28
3785 10478 2.037367 TCCCTGGTCTGGTCCGAG 59.963 66.667 0.00 0.00 0.00 4.63
3805 10498 4.549458 GAGCATTTTGAAAGTAGCTGCAA 58.451 39.130 4.12 0.00 31.61 4.08
3834 10527 3.444388 GTCCTTACCAGAGTCCACTAGTG 59.556 52.174 16.34 16.34 0.00 2.74
3866 10559 3.737172 AACGGCCAGATTGCACGC 61.737 61.111 2.24 0.00 0.00 5.34
3910 10643 2.082366 GCGTGCATGAAAACTGCCG 61.082 57.895 10.93 0.00 38.89 5.69
3933 10687 5.106791 CGATCTATTCATCTTCAACCATGGC 60.107 44.000 13.04 0.00 0.00 4.40
4001 10755 1.035932 TAGCCCGTGGAGCTGTAGAC 61.036 60.000 10.86 0.00 41.71 2.59
4009 10763 3.522553 GTGGAGCTGTAGACCATGTTAC 58.477 50.000 0.00 0.00 36.09 2.50
4059 10830 4.636206 GGTCTACTCAGTTTTGCCATTAGG 59.364 45.833 0.00 0.00 38.23 2.69
4140 10912 9.699985 CATTAGATATCTCAAAAATAGCATCGC 57.300 33.333 8.95 0.00 0.00 4.58
4141 10913 6.734104 AGATATCTCAAAAATAGCATCGCC 57.266 37.500 0.00 0.00 0.00 5.54
4162 10935 7.047891 TCGCCTCATTAGATGTTTACTCAAAT 58.952 34.615 0.00 0.00 0.00 2.32
4258 11031 4.338964 ACATGTCAGCTCTCTGTATCTCAG 59.661 45.833 0.00 0.00 44.85 3.35
4293 11066 1.697982 ACCCCACTTGTCAGGAGTAAC 59.302 52.381 0.00 0.00 0.00 2.50
4299 11072 2.438021 ACTTGTCAGGAGTAACCAAGCA 59.562 45.455 0.00 0.00 42.04 3.91
4389 11162 7.301420 AGATAGAGGGAGAACTGACATATTGA 58.699 38.462 0.00 0.00 0.00 2.57
4390 11163 7.786943 AGATAGAGGGAGAACTGACATATTGAA 59.213 37.037 0.00 0.00 0.00 2.69
4457 11230 4.399618 GCTGAGAGTAATGGTGTCTAGTGA 59.600 45.833 0.00 0.00 0.00 3.41
4475 11249 2.468777 GTGACATTTTTGAGCTTGTGCG 59.531 45.455 0.00 0.00 45.42 5.34
4557 11332 6.032775 CGAAACACAACTGATGTCATAAATGC 59.967 38.462 0.00 0.00 41.46 3.56
4564 11339 9.630098 ACAACTGATGTCATAAATGCTAAAAAG 57.370 29.630 0.00 0.00 37.96 2.27
4569 11344 5.636837 TGTCATAAATGCTAAAAAGCCGAC 58.363 37.500 0.00 0.00 0.00 4.79
4601 11376 6.228258 ACATTGAGTGATTACTTTGGTACGT 58.772 36.000 0.00 0.00 37.25 3.57
4837 11660 3.305064 GCACTAACAAAATCAAAGGCGGA 60.305 43.478 0.00 0.00 0.00 5.54
4891 11719 1.153289 GCCTGCGGTGATCATCACT 60.153 57.895 17.46 0.00 46.19 3.41
5167 11998 0.818938 TCAACTTCTATGCGCCCGTA 59.181 50.000 4.18 0.00 0.00 4.02
5170 12001 0.384669 ACTTCTATGCGCCCGTACTC 59.615 55.000 4.18 0.00 0.00 2.59
5897 12728 3.954258 ACTGCAGGGAAAATAGTTATGGC 59.046 43.478 19.93 0.00 0.00 4.40
5902 12733 3.791545 AGGGAAAATAGTTATGGCCAGGA 59.208 43.478 13.05 0.00 0.00 3.86
5907 12738 1.879575 TAGTTATGGCCAGGAGTGCT 58.120 50.000 13.05 5.95 0.00 4.40
5933 12764 1.136305 GTTAGCTATCCACGTGCCAGA 59.864 52.381 10.91 2.25 0.00 3.86
5934 12765 1.480789 TAGCTATCCACGTGCCAGAA 58.519 50.000 10.91 0.00 0.00 3.02
5935 12766 0.833287 AGCTATCCACGTGCCAGAAT 59.167 50.000 10.91 0.68 0.00 2.40
5940 12777 0.392863 TCCACGTGCCAGAATCATGG 60.393 55.000 10.91 0.00 43.72 3.66
5944 12781 1.280710 ACGTGCCAGAATCATGGGTTA 59.719 47.619 0.00 0.00 40.97 2.85
5947 12784 3.003689 CGTGCCAGAATCATGGGTTAATC 59.996 47.826 0.00 0.00 40.97 1.75
5950 12787 4.646040 TGCCAGAATCATGGGTTAATCTTG 59.354 41.667 0.00 0.00 40.97 3.02
5954 12791 6.377996 CCAGAATCATGGGTTAATCTTGTGAA 59.622 38.462 0.00 0.00 36.64 3.18
5958 12795 7.781324 ATCATGGGTTAATCTTGTGAACTTT 57.219 32.000 0.00 0.00 0.00 2.66
5982 12819 4.890581 TGGGTTTCAGCTCTAGTCTATCTC 59.109 45.833 0.00 0.00 0.00 2.75
5984 12821 5.361285 GGGTTTCAGCTCTAGTCTATCTCAA 59.639 44.000 0.00 0.00 0.00 3.02
6010 12847 5.282510 TGTTGTTGTTAAATAAGTTGCCGG 58.717 37.500 0.00 0.00 0.00 6.13
6016 12853 8.358148 TGTTGTTAAATAAGTTGCCGGAAATTA 58.642 29.630 5.05 7.31 0.00 1.40
6074 12911 0.678684 CATGTGCTCATGGCCACTGA 60.679 55.000 18.85 12.59 45.30 3.41
6142 12979 3.031812 GCGCTAGCAAATGAAGATTTCG 58.968 45.455 16.45 0.00 44.35 3.46
6163 13000 5.105063 TCGCAGATCAATCGAATCCATATC 58.895 41.667 0.00 0.00 0.00 1.63
6211 13048 4.713792 AGAGCTCCCTTCTTTTCTTTGA 57.286 40.909 10.93 0.00 0.00 2.69
6213 13050 4.824537 AGAGCTCCCTTCTTTTCTTTGAAC 59.175 41.667 10.93 0.00 0.00 3.18
6228 13065 2.940994 TGAACCCGTGAATCCAAAGA 57.059 45.000 0.00 0.00 0.00 2.52
6231 13068 3.505680 TGAACCCGTGAATCCAAAGATTG 59.494 43.478 0.00 0.00 42.93 2.67
6252 13089 1.066430 GGGAGCAGATAAACACGGTCA 60.066 52.381 0.00 0.00 0.00 4.02
6256 13093 5.279306 GGGAGCAGATAAACACGGTCATATA 60.279 44.000 0.00 0.00 0.00 0.86
6272 13110 6.465084 GGTCATATATTTTAGAGCGGAACCT 58.535 40.000 0.00 0.00 0.00 3.50
6274 13112 6.308282 GTCATATATTTTAGAGCGGAACCTCG 59.692 42.308 0.00 0.00 36.95 4.63
6279 13117 1.248785 TAGAGCGGAACCTCGTGCTT 61.249 55.000 0.00 0.00 37.91 3.91
6289 13127 2.303175 ACCTCGTGCTTGGCTTTAAAA 58.697 42.857 0.00 0.00 0.00 1.52
6306 13144 2.693267 AAATGAGGCCCTTACGAGTC 57.307 50.000 0.00 0.00 0.00 3.36
6352 13190 9.614792 AGAAATGAAAATAAGTACGATAAGCCT 57.385 29.630 0.00 0.00 0.00 4.58
6355 13193 6.053005 TGAAAATAAGTACGATAAGCCTGGG 58.947 40.000 0.00 0.00 0.00 4.45
6377 13215 0.960364 GCGGCTGTTCTGATCCCAAA 60.960 55.000 0.00 0.00 0.00 3.28
6378 13216 0.804989 CGGCTGTTCTGATCCCAAAC 59.195 55.000 0.00 0.00 0.00 2.93
6498 13336 8.780846 TTTGATAGCTTGCAAAATTTCATCAT 57.219 26.923 0.00 0.00 31.64 2.45
6519 13357 8.997323 CATCATCAGATAACATTTAGGGAGAAC 58.003 37.037 0.00 0.00 31.88 3.01
6523 13361 6.070995 TCAGATAACATTTAGGGAGAACGTGT 60.071 38.462 0.00 0.00 0.00 4.49
6565 13403 8.658609 CGATGCTCCAAAATGTTATTTTCAAAT 58.341 29.630 0.00 0.00 0.00 2.32
6569 13407 7.747357 GCTCCAAAATGTTATTTTCAAATGCAG 59.253 33.333 0.00 0.00 0.00 4.41
6649 13503 9.932207 ATGATGAAATTCTGCAAGTTATCAAAA 57.068 25.926 0.00 0.00 33.76 2.44
6738 13594 3.443681 TGTTCACACGAGCTCATATGAGA 59.556 43.478 32.38 9.61 44.74 3.27
6756 13612 5.614324 TGAGATCGGGATTAGAACAACAT 57.386 39.130 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 7.119846 GTGATATAAGGCCTGATACCAATTGAC 59.880 40.741 12.45 0.00 0.00 3.18
86 87 3.895041 TGATCGTGTGATATAAGGCCTGA 59.105 43.478 5.69 0.00 34.09 3.86
120 121 1.670791 CCAGAGGAGTCCGACTAGAC 58.329 60.000 2.76 0.00 37.01 2.59
156 157 3.131396 GACGTGCCAACATATTCCTAGG 58.869 50.000 0.82 0.82 0.00 3.02
186 189 1.872952 TGGTTTTCACTGCGAGATGTG 59.127 47.619 0.00 0.00 35.68 3.21
255 260 5.410067 CCGATCTGCAACCATATTTTGTTT 58.590 37.500 0.00 0.00 0.00 2.83
265 270 1.153369 GCTAGCCGATCTGCAACCA 60.153 57.895 11.93 0.00 0.00 3.67
287 292 8.319881 ACAGTAGTAGACTCTGTATGACTGTAA 58.680 37.037 9.37 0.00 42.25 2.41
295 300 8.272889 TCCATACAACAGTAGTAGACTCTGTAT 58.727 37.037 12.25 8.45 41.13 2.29
319 324 2.630580 CACTTAGGACCTCTATGCCTCC 59.369 54.545 0.00 0.00 33.28 4.30
322 327 4.082679 CGATACACTTAGGACCTCTATGCC 60.083 50.000 0.00 0.00 0.00 4.40
356 361 4.724279 AACAGGGTTACAATTGAGAGGT 57.276 40.909 13.59 0.00 0.00 3.85
369 374 9.936329 ATTCCATGATAAGTTAATAACAGGGTT 57.064 29.630 5.89 0.00 33.04 4.11
428 433 1.068417 TGACCAGCGCGTTAAGTGT 59.932 52.632 8.43 0.00 0.00 3.55
432 437 1.705256 CTAAGTGACCAGCGCGTTAA 58.295 50.000 8.43 0.00 0.00 2.01
601 610 3.432517 GCAGTCAGCCAGTCACTAG 57.567 57.895 0.00 0.00 37.23 2.57
611 620 0.035458 ACTAACCAGTGGCAGTCAGC 59.965 55.000 9.78 0.00 44.65 4.26
634 643 3.875134 GCAATAAGCTAAACGAAGCCCTA 59.125 43.478 0.00 0.00 43.86 3.53
643 652 8.907685 TCAAACAAATAACGCAATAAGCTAAAC 58.092 29.630 0.00 0.00 42.61 2.01
655 664 5.282076 GGTACGTGAATCAAACAAATAACGC 59.718 40.000 0.00 0.00 33.31 4.84
669 678 2.626266 TGTCAGTGTCTGGTACGTGAAT 59.374 45.455 0.00 0.00 31.51 2.57
719 728 3.468071 TGTAGTCAGTACTCCCACCAT 57.532 47.619 0.00 0.00 37.15 3.55
805 886 0.462375 GGTGGTGGGTTGGTCAAAAC 59.538 55.000 0.00 0.00 0.00 2.43
1257 3173 1.716826 CGGCGAGGTAGAGTGAGGAC 61.717 65.000 0.00 0.00 0.00 3.85
1278 3194 1.884444 GAAGAAGGAGGCGACGAGT 59.116 57.895 0.00 0.00 0.00 4.18
1530 3455 3.944087 AGGTAAGTGAATCAGCCTGTTC 58.056 45.455 0.00 0.00 0.00 3.18
1743 3849 7.211966 AGATAAAATAGATGATGTGGCAAGC 57.788 36.000 0.00 0.00 0.00 4.01
1744 3850 9.716531 TCTAGATAAAATAGATGATGTGGCAAG 57.283 33.333 0.00 0.00 0.00 4.01
1768 3874 8.366401 CCAATGAGAGTAACATCAGACATATCT 58.634 37.037 0.00 0.00 34.57 1.98
1769 3875 7.601886 CCCAATGAGAGTAACATCAGACATATC 59.398 40.741 0.00 0.00 0.00 1.63
1770 3876 7.071698 ACCCAATGAGAGTAACATCAGACATAT 59.928 37.037 0.00 0.00 0.00 1.78
1771 3877 6.384015 ACCCAATGAGAGTAACATCAGACATA 59.616 38.462 0.00 0.00 0.00 2.29
1772 3878 5.190528 ACCCAATGAGAGTAACATCAGACAT 59.809 40.000 0.00 0.00 0.00 3.06
1773 3879 4.532126 ACCCAATGAGAGTAACATCAGACA 59.468 41.667 0.00 0.00 0.00 3.41
1774 3880 5.091261 ACCCAATGAGAGTAACATCAGAC 57.909 43.478 0.00 0.00 0.00 3.51
1775 3881 5.958380 ACTACCCAATGAGAGTAACATCAGA 59.042 40.000 0.00 0.00 0.00 3.27
1776 3882 6.097554 AGACTACCCAATGAGAGTAACATCAG 59.902 42.308 0.00 0.00 0.00 2.90
1777 3883 5.958380 AGACTACCCAATGAGAGTAACATCA 59.042 40.000 0.00 0.00 0.00 3.07
1778 3884 6.472686 AGACTACCCAATGAGAGTAACATC 57.527 41.667 0.00 0.00 0.00 3.06
1779 3885 6.875972 AAGACTACCCAATGAGAGTAACAT 57.124 37.500 0.00 0.00 0.00 2.71
1780 3886 7.786046 TTAAGACTACCCAATGAGAGTAACA 57.214 36.000 0.00 0.00 0.00 2.41
1783 3889 9.931698 TCTAATTAAGACTACCCAATGAGAGTA 57.068 33.333 0.00 0.00 0.00 2.59
1784 3890 8.840200 TCTAATTAAGACTACCCAATGAGAGT 57.160 34.615 0.00 0.00 0.00 3.24
1792 3898 9.670442 AGGACATAATCTAATTAAGACTACCCA 57.330 33.333 0.00 0.00 36.93 4.51
1793 3899 9.930693 CAGGACATAATCTAATTAAGACTACCC 57.069 37.037 0.00 0.00 36.93 3.69
1794 3900 9.425577 GCAGGACATAATCTAATTAAGACTACC 57.574 37.037 0.00 0.00 36.93 3.18
1795 3901 9.130312 CGCAGGACATAATCTAATTAAGACTAC 57.870 37.037 0.00 0.00 36.93 2.73
1863 3969 3.216292 GTGTGTGTGTGGTGGGGC 61.216 66.667 0.00 0.00 0.00 5.80
1871 3977 1.732917 CCGCCAATTGTGTGTGTGT 59.267 52.632 4.43 0.00 0.00 3.72
1874 3980 1.372004 CAGCCGCCAATTGTGTGTG 60.372 57.895 4.43 0.00 0.00 3.82
1875 3981 3.041701 CAGCCGCCAATTGTGTGT 58.958 55.556 4.43 0.00 0.00 3.72
1876 3982 2.431260 GCAGCCGCCAATTGTGTG 60.431 61.111 4.43 2.85 0.00 3.82
1877 3983 2.598394 AGCAGCCGCCAATTGTGT 60.598 55.556 4.43 0.00 39.83 3.72
1878 3984 2.126228 CAGCAGCCGCCAATTGTG 60.126 61.111 4.43 0.00 39.83 3.33
1879 3985 4.060038 GCAGCAGCCGCCAATTGT 62.060 61.111 4.43 0.00 39.83 2.71
1880 3986 3.982372 CTGCAGCAGCCGCCAATTG 62.982 63.158 10.14 0.00 41.13 2.32
1916 4221 8.845413 TTTCCATTAGCTTTAATTGTTTGCAT 57.155 26.923 0.00 0.00 0.00 3.96
2064 6064 8.588789 AGTTTACGCTTCACATTTTTGTTAAAC 58.411 29.630 0.00 0.00 0.00 2.01
2193 6199 7.272244 CCACCTCACAAAGTCATACATGTATA 58.728 38.462 17.86 4.74 0.00 1.47
2302 6315 0.596082 CAACTAAACCCACAAGCCCG 59.404 55.000 0.00 0.00 0.00 6.13
2319 6332 7.666623 TCATCGTAAATAGAGGATACATGCAA 58.333 34.615 0.00 0.00 41.41 4.08
2322 6335 7.315890 TGCTCATCGTAAATAGAGGATACATG 58.684 38.462 0.00 0.00 41.41 3.21
2339 6352 1.411977 AGGGACAAGAGATGCTCATCG 59.588 52.381 4.41 0.00 42.48 3.84
2342 6355 3.378512 ACATAGGGACAAGAGATGCTCA 58.621 45.455 0.00 0.00 32.06 4.26
2378 6391 0.871722 GACACTAACGCAATGTGGCA 59.128 50.000 0.00 0.00 39.36 4.92
2384 6397 2.433868 AGACGTGACACTAACGCAAT 57.566 45.000 3.68 0.00 44.80 3.56
2599 6612 9.553064 CTCTTTTCATTTCTGCCTACATATACT 57.447 33.333 0.00 0.00 0.00 2.12
2677 9293 1.887242 CCCGTCCGTACATGCATGG 60.887 63.158 29.41 12.86 0.00 3.66
2689 9305 2.508751 GCATACTCCTCCCCCGTCC 61.509 68.421 0.00 0.00 0.00 4.79
2693 9309 0.694444 TCCAAGCATACTCCTCCCCC 60.694 60.000 0.00 0.00 0.00 5.40
2740 9377 1.880027 CAGGAGTGGCAGTTTTGTACC 59.120 52.381 0.00 0.00 0.00 3.34
2790 9427 1.604755 GCCCGTGAAAACACATGTGTA 59.395 47.619 30.75 13.43 44.13 2.90
2799 9436 3.666253 CACCCGGCCCGTGAAAAC 61.666 66.667 11.43 0.00 32.77 2.43
2814 9455 3.492102 TTGATAATCCTGGCTAGGCAC 57.508 47.619 16.16 4.33 44.22 5.01
2819 9460 5.074929 ACCCAATGATTGATAATCCTGGCTA 59.925 40.000 6.76 0.00 38.02 3.93
2841 9482 5.148651 TCTTTAGTTGAGCTGAACCTACC 57.851 43.478 12.75 0.00 0.00 3.18
2842 9483 5.635700 CACTCTTTAGTTGAGCTGAACCTAC 59.364 44.000 12.75 0.00 35.12 3.18
2843 9484 5.279506 CCACTCTTTAGTTGAGCTGAACCTA 60.280 44.000 12.75 2.16 35.12 3.08
2844 9485 4.503991 CCACTCTTTAGTTGAGCTGAACCT 60.504 45.833 12.75 3.11 35.12 3.50
2896 9537 6.774673 TGACATGTCCCTTGTAGATTTACAA 58.225 36.000 22.85 8.42 45.15 2.41
2907 9548 5.640357 CCAATGAAATTTGACATGTCCCTTG 59.360 40.000 22.85 13.86 31.22 3.61
2927 9568 3.586429 AGTGAACCCAATTGAACCCAAT 58.414 40.909 7.12 0.00 44.38 3.16
2928 9569 3.039252 AGTGAACCCAATTGAACCCAA 57.961 42.857 7.12 0.00 36.61 4.12
2929 9570 2.765689 AGTGAACCCAATTGAACCCA 57.234 45.000 7.12 0.00 0.00 4.51
3026 9667 3.245048 CGCAAAAGAAAAACATGACCACC 59.755 43.478 0.00 0.00 0.00 4.61
3041 9698 1.000274 CTTCCTTTCACCCCGCAAAAG 60.000 52.381 0.00 0.00 0.00 2.27
3052 9709 6.319152 TCGTTGTGGAATAAAACTTCCTTTCA 59.681 34.615 4.63 0.00 44.27 2.69
3080 9737 1.071814 GTGCGGGGACTTGTAACCA 59.928 57.895 0.00 0.00 0.00 3.67
3093 9778 0.532640 TCGATTCATCCATGGTGCGG 60.533 55.000 12.58 0.00 0.00 5.69
3095 9780 1.959042 ACTCGATTCATCCATGGTGC 58.041 50.000 12.58 0.00 0.00 5.01
3105 9790 4.250464 GTGGTATGGTTGAACTCGATTCA 58.750 43.478 0.00 6.28 45.92 2.57
3126 9811 0.378257 CGCACTGAAACTTGCACTGT 59.622 50.000 0.00 0.00 38.76 3.55
3131 9816 0.804989 ATAGCCGCACTGAAACTTGC 59.195 50.000 0.00 0.00 35.26 4.01
3136 9821 3.429822 GGTACACTATAGCCGCACTGAAA 60.430 47.826 0.00 0.00 0.00 2.69
3156 9841 7.453126 TCAAAATAGGGTAACACATCAATTGGT 59.547 33.333 5.42 0.00 39.74 3.67
3187 9872 7.228906 GGAAGTTTGTTCCTCTAAAAGTTAGCT 59.771 37.037 0.00 0.00 35.73 3.32
3277 9968 0.972471 TCTGGCCATTCTCTCGAGCA 60.972 55.000 5.51 0.00 0.00 4.26
3297 9988 9.635520 GATTGTTCAATCAGATTCTTCAAATGT 57.364 29.630 17.31 0.00 0.00 2.71
3325 10016 1.327303 TCAACATTTGGACTGCCCAC 58.673 50.000 0.00 0.00 46.62 4.61
3373 10064 2.939640 GCCCTGGAAGCAGAAATTCGTA 60.940 50.000 0.00 0.00 0.00 3.43
3375 10066 0.453390 GCCCTGGAAGCAGAAATTCG 59.547 55.000 0.00 0.00 0.00 3.34
3469 10160 0.103026 TCAGGATGATCGCACTTCGG 59.897 55.000 0.00 0.00 42.56 4.30
3553 10244 6.780706 AGTGTGTAAAAACTACAGAATCCG 57.219 37.500 0.00 0.00 0.00 4.18
3724 10417 4.044426 GCATATTTGGCAACTCCGAAATC 58.956 43.478 0.00 0.00 41.47 2.17
3744 10437 4.681074 TGGTAATTATGACGATCTGGCA 57.319 40.909 0.00 0.00 0.00 4.92
3778 10471 3.426292 GCTACTTTCAAAATGCTCGGACC 60.426 47.826 0.00 0.00 0.00 4.46
3785 10478 5.289434 GGTATTGCAGCTACTTTCAAAATGC 59.711 40.000 8.03 0.00 0.00 3.56
3805 10498 3.630311 GGACTCTGGTAAGGACTGGGTAT 60.630 52.174 0.00 0.00 0.00 2.73
3834 10527 1.021390 CCGTTGCCTGATGACTCACC 61.021 60.000 0.00 0.00 0.00 4.02
3866 10559 1.515521 GACGTGTTTGGGAGGGCTTG 61.516 60.000 0.00 0.00 0.00 4.01
3894 10587 1.470098 AGATCGGCAGTTTTCATGCAC 59.530 47.619 0.00 0.00 45.68 4.57
3910 10643 5.766670 TGCCATGGTTGAAGATGAATAGATC 59.233 40.000 14.67 0.00 0.00 2.75
3933 10687 6.142480 TGTTATTTTTGGCGTTCGTTGTAATG 59.858 34.615 0.00 0.00 0.00 1.90
3963 10717 0.178891 AGGCGGGGATCTGGATGTAT 60.179 55.000 0.00 0.00 0.00 2.29
3966 10720 1.978473 CTAGGCGGGGATCTGGATG 59.022 63.158 0.00 0.00 0.00 3.51
3988 10742 2.770164 AACATGGTCTACAGCTCCAC 57.230 50.000 0.00 0.00 33.91 4.02
4001 10755 3.263425 AGAGTGGTAACCCAGTAACATGG 59.737 47.826 0.00 0.00 44.77 3.66
4009 10763 4.256920 CATTCTCAAGAGTGGTAACCCAG 58.743 47.826 0.00 0.00 42.94 4.45
4059 10830 9.508567 GATGGCATTTTTGAGAAGTTATAACTC 57.491 33.333 18.28 11.66 38.57 3.01
4129 10900 5.555017 ACATCTAATGAGGCGATGCTATTT 58.445 37.500 0.00 0.00 38.42 1.40
4133 10905 3.482156 AACATCTAATGAGGCGATGCT 57.518 42.857 0.00 0.00 38.42 3.79
4134 10906 4.752101 AGTAAACATCTAATGAGGCGATGC 59.248 41.667 0.00 0.00 38.42 3.91
4214 10987 8.061304 ACATGTGGGTATAGAAGGATTTTCATT 58.939 33.333 0.00 0.00 0.00 2.57
4258 11031 3.644966 TGGGGTCCACACTTATCATTC 57.355 47.619 0.00 0.00 0.00 2.67
4457 11230 2.869233 ACGCACAAGCTCAAAAATGT 57.131 40.000 0.00 0.00 39.10 2.71
4475 11249 5.379003 TCAAAAATGACATCGCTTCGTTAC 58.621 37.500 0.00 0.00 0.00 2.50
4557 11332 8.973378 TCAATGTTTTTAATGTCGGCTTTTTAG 58.027 29.630 0.00 0.00 0.00 1.85
4564 11339 5.457140 TCACTCAATGTTTTTAATGTCGGC 58.543 37.500 0.00 0.00 0.00 5.54
4891 11719 3.282745 GAGGAAGAGTGCGCCGACA 62.283 63.158 4.18 0.00 0.00 4.35
5170 12001 3.368531 CCTTGAAACCTAGGGTCTCGAAG 60.369 52.174 14.81 9.40 33.12 3.79
5290 12121 2.839098 CCACCCTGCAGGAACAGT 59.161 61.111 34.91 20.11 39.89 3.55
5873 12704 4.339247 CCATAACTATTTTCCCTGCAGTGG 59.661 45.833 13.81 13.59 0.00 4.00
5897 12728 2.485814 GCTAACTTTCAAGCACTCCTGG 59.514 50.000 0.00 0.00 38.63 4.45
5902 12733 4.938226 GTGGATAGCTAACTTTCAAGCACT 59.062 41.667 0.00 0.00 41.32 4.40
5907 12738 3.682858 GCACGTGGATAGCTAACTTTCAA 59.317 43.478 18.88 0.00 0.00 2.69
5933 12764 7.781324 AAGTTCACAAGATTAACCCATGATT 57.219 32.000 0.00 0.00 0.00 2.57
5934 12765 7.781324 AAAGTTCACAAGATTAACCCATGAT 57.219 32.000 0.00 0.00 0.00 2.45
5935 12766 7.432869 CAAAAGTTCACAAGATTAACCCATGA 58.567 34.615 0.00 0.00 0.00 3.07
5940 12777 6.156748 ACCCAAAAGTTCACAAGATTAACC 57.843 37.500 0.00 0.00 0.00 2.85
5944 12781 6.293004 TGAAACCCAAAAGTTCACAAGATT 57.707 33.333 0.00 0.00 0.00 2.40
5947 12784 3.865164 GCTGAAACCCAAAAGTTCACAAG 59.135 43.478 0.00 0.00 0.00 3.16
5950 12787 3.381590 AGAGCTGAAACCCAAAAGTTCAC 59.618 43.478 0.00 0.00 0.00 3.18
5954 12791 4.103311 AGACTAGAGCTGAAACCCAAAAGT 59.897 41.667 0.00 0.00 0.00 2.66
5958 12795 5.273208 AGATAGACTAGAGCTGAAACCCAA 58.727 41.667 0.00 0.00 0.00 4.12
5982 12819 9.432077 GGCAACTTATTTAACAACAACAAATTG 57.568 29.630 0.00 0.00 41.98 2.32
5984 12821 7.042389 CCGGCAACTTATTTAACAACAACAAAT 60.042 33.333 0.00 0.00 0.00 2.32
5997 12834 6.207810 TCACACTAATTTCCGGCAACTTATTT 59.792 34.615 0.00 0.00 0.00 1.40
6001 12838 3.482436 TCACACTAATTTCCGGCAACTT 58.518 40.909 0.00 0.00 0.00 2.66
6010 12847 6.223138 TCGTGTTGTGATCACACTAATTTC 57.777 37.500 27.88 12.59 46.07 2.17
6016 12853 1.412710 ACCTCGTGTTGTGATCACACT 59.587 47.619 27.88 4.31 46.07 3.55
6074 12911 3.034635 ACACCTGTCAGAAGTCAGAACT 58.965 45.455 0.00 0.00 37.32 3.01
6142 12979 5.426504 AGGATATGGATTCGATTGATCTGC 58.573 41.667 0.00 0.00 0.00 4.26
6163 13000 4.796231 CCGACCCAACGCTCGAGG 62.796 72.222 15.58 6.97 31.24 4.63
6179 13016 3.536075 AGGGAGCTCTATTAGAGGACC 57.464 52.381 19.78 1.76 42.54 4.46
6228 13065 2.643551 CGTGTTTATCTGCTCCCCAAT 58.356 47.619 0.00 0.00 0.00 3.16
6231 13068 0.252197 ACCGTGTTTATCTGCTCCCC 59.748 55.000 0.00 0.00 0.00 4.81
6233 13070 2.380084 TGACCGTGTTTATCTGCTCC 57.620 50.000 0.00 0.00 0.00 4.70
6252 13089 6.157211 CACGAGGTTCCGCTCTAAAATATAT 58.843 40.000 0.00 0.00 0.00 0.86
6256 13093 2.618053 CACGAGGTTCCGCTCTAAAAT 58.382 47.619 0.00 0.00 0.00 1.82
6269 13107 1.975660 TTTAAAGCCAAGCACGAGGT 58.024 45.000 0.00 0.00 0.00 3.85
6272 13110 3.057596 CCTCATTTTAAAGCCAAGCACGA 60.058 43.478 0.00 0.00 0.00 4.35
6274 13112 2.995939 GCCTCATTTTAAAGCCAAGCAC 59.004 45.455 0.00 0.00 0.00 4.40
6279 13117 2.621556 AGGGCCTCATTTTAAAGCCA 57.378 45.000 15.08 0.00 45.72 4.75
6306 13144 5.165961 TCTCTGGATCTACCTTTTGTTGG 57.834 43.478 0.00 0.00 39.86 3.77
6352 13190 4.680237 CAGAACAGCCGCGTCCCA 62.680 66.667 4.92 0.00 0.00 4.37
6355 13193 2.167861 GGATCAGAACAGCCGCGTC 61.168 63.158 4.92 0.00 0.00 5.19
6498 13336 6.070995 ACACGTTCTCCCTAAATGTTATCTGA 60.071 38.462 0.00 0.00 0.00 3.27
6511 13349 3.553828 TTTTTCTGACACGTTCTCCCT 57.446 42.857 0.00 0.00 0.00 4.20
6565 13403 4.038282 ACAAGATCAATGCTTCAAACTGCA 59.962 37.500 0.00 0.00 43.67 4.41
6569 13407 8.134905 AGAAAAACAAGATCAATGCTTCAAAC 57.865 30.769 0.00 0.00 0.00 2.93
6738 13594 5.065988 CCGAAAATGTTGTTCTAATCCCGAT 59.934 40.000 0.00 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.