Multiple sequence alignment - TraesCS5D01G525900

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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 TraesCS5D01G525900 chr5D 100.000 6377 0 0 1 6377 543844098 543837722 0.000000e+00 11777.0
1 TraesCS5D01G525900 chr5D 83.665 1610 208 25 4078 5660 544286114 544284533 0.000000e+00 1465.0
2 TraesCS5D01G525900 chr5D 84.421 1303 156 15 4078 5377 543858529 543857271 0.000000e+00 1238.0
3 TraesCS5D01G525900 chr5D 95.017 582 29 0 3495 4076 77670995 77671576 0.000000e+00 915.0
4 TraesCS5D01G525900 chr5D 80.593 742 113 19 2767 3494 544286832 544286108 1.560000e-150 544.0
5 TraesCS5D01G525900 chr5B 91.808 2063 109 25 4077 6082 685992830 685990771 0.000000e+00 2819.0
6 TraesCS5D01G525900 chr5B 94.461 1318 68 2 4077 5391 685648833 685650148 0.000000e+00 2025.0
7 TraesCS5D01G525900 chr5B 83.738 1525 205 26 4077 5568 685951229 685949715 0.000000e+00 1402.0
8 TraesCS5D01G525900 chr5B 91.599 988 63 10 2286 3260 685994375 685993395 0.000000e+00 1347.0
9 TraesCS5D01G525900 chr5B 82.627 1462 188 26 4078 5534 686050896 686049496 0.000000e+00 1232.0
10 TraesCS5D01G525900 chr5B 81.626 1464 202 27 4078 5535 686212090 686210688 0.000000e+00 1151.0
11 TraesCS5D01G525900 chr5B 94.378 587 32 1 3491 4077 504330281 504330866 0.000000e+00 900.0
12 TraesCS5D01G525900 chr5B 91.501 553 39 6 2947 3494 685993372 685992823 0.000000e+00 754.0
13 TraesCS5D01G525900 chr5B 94.118 272 12 3 5427 5695 685650151 685650421 1.650000e-110 411.0
14 TraesCS5D01G525900 chr5B 94.961 258 12 1 6079 6335 685990669 685990412 2.770000e-108 403.0
15 TraesCS5D01G525900 chr5B 88.050 318 28 8 1692 2001 685994885 685994570 1.010000e-97 368.0
16 TraesCS5D01G525900 chr5B 91.635 263 17 4 1354 1613 686007771 686007511 6.080000e-95 359.0
17 TraesCS5D01G525900 chr5B 95.652 161 5 1 3336 3494 685648680 685648840 2.280000e-64 257.0
18 TraesCS5D01G525900 chr5B 80.682 352 21 10 5701 6006 685650476 685650826 4.970000e-56 230.0
19 TraesCS5D01G525900 chr5B 84.322 236 21 6 508 731 101900960 101900729 3.870000e-52 217.0
20 TraesCS5D01G525900 chr5B 89.881 168 11 3 6214 6375 685651009 685651176 1.800000e-50 211.0
21 TraesCS5D01G525900 chr5B 82.625 259 25 12 2205 2455 685952430 685952184 1.800000e-50 211.0
22 TraesCS5D01G525900 chr5B 85.492 193 20 3 2247 2435 686051781 686051593 1.810000e-45 195.0
23 TraesCS5D01G525900 chr5B 89.542 153 15 1 358 509 101901144 101900992 6.520000e-45 193.0
24 TraesCS5D01G525900 chr5B 91.304 115 10 0 855 969 101900670 101900556 2.380000e-34 158.0
25 TraesCS5D01G525900 chr5B 100.000 30 0 0 2118 2147 685994472 685994443 8.930000e-04 56.5
26 TraesCS5D01G525900 chr4A 96.059 1624 22 6 5 1615 625238979 625240573 0.000000e+00 2606.0
27 TraesCS5D01G525900 chr4A 95.296 1318 59 1 4077 5391 625248237 625249554 0.000000e+00 2087.0
28 TraesCS5D01G525900 chr4A 95.537 1210 47 4 2286 3494 625247041 625248244 0.000000e+00 1929.0
29 TraesCS5D01G525900 chr4A 83.251 1612 210 29 4078 5660 624982401 624983981 0.000000e+00 1426.0
30 TraesCS5D01G525900 chr4A 83.653 1462 174 24 4078 5535 625176848 625178248 0.000000e+00 1315.0
31 TraesCS5D01G525900 chr4A 84.942 518 33 19 5699 6178 625249829 625250339 3.460000e-132 483.0
32 TraesCS5D01G525900 chr4A 80.617 583 92 16 2769 3344 624977644 624978212 1.270000e-116 431.0
33 TraesCS5D01G525900 chr4A 93.902 246 15 0 1790 2035 625243071 625243316 7.810000e-99 372.0
34 TraesCS5D01G525900 chr4A 92.216 167 13 0 6209 6375 625250331 625250497 2.970000e-58 237.0
35 TraesCS5D01G525900 chr4A 93.464 153 8 1 5545 5695 625249624 625249776 6.430000e-55 226.0
36 TraesCS5D01G525900 chr4A 88.235 153 15 1 2286 2435 625175671 625175823 5.080000e-41 180.0
37 TraesCS5D01G525900 chr4A 100.000 37 0 0 5427 5463 625249557 625249593 1.150000e-07 69.4
38 TraesCS5D01G525900 chr6A 94.924 591 26 3 3491 4080 520101560 520100973 0.000000e+00 922.0
39 TraesCS5D01G525900 chr7A 95.197 583 24 3 3494 4076 730584383 730584961 0.000000e+00 918.0
40 TraesCS5D01G525900 chr7A 94.558 588 30 2 3492 4079 176569873 176570458 0.000000e+00 907.0
41 TraesCS5D01G525900 chr7A 81.293 294 49 6 1737 2028 699387246 699386957 3.840000e-57 233.0
42 TraesCS5D01G525900 chr7A 81.416 226 26 10 519 732 10416992 10416771 3.060000e-38 171.0
43 TraesCS5D01G525900 chr2B 94.863 584 28 2 3495 4076 734294061 734294644 0.000000e+00 911.0
44 TraesCS5D01G525900 chr5A 94.701 585 27 4 3495 4078 677952081 677952662 0.000000e+00 905.0
45 TraesCS5D01G525900 chr7B 94.674 582 30 1 3495 4076 289954910 289954330 0.000000e+00 902.0
46 TraesCS5D01G525900 chr7B 83.259 448 54 13 75 509 595544993 595544554 5.990000e-105 392.0
47 TraesCS5D01G525900 chr7B 83.516 273 35 7 1730 1997 692828385 692828118 4.940000e-61 246.0
48 TraesCS5D01G525900 chr7B 79.933 299 55 5 1730 2026 692928813 692928518 1.390000e-51 215.0
49 TraesCS5D01G525900 chr3D 94.683 583 28 3 3495 4077 51958529 51957950 0.000000e+00 902.0
50 TraesCS5D01G525900 chr3D 81.639 305 27 13 234 509 209465914 209465610 6.430000e-55 226.0
51 TraesCS5D01G525900 chr3D 91.304 115 10 0 855 969 209465322 209465208 2.380000e-34 158.0
52 TraesCS5D01G525900 chr3D 80.804 224 16 13 508 731 209465577 209465381 3.980000e-32 150.0
53 TraesCS5D01G525900 chr3D 94.118 51 3 0 1499 1549 480413071 480413121 1.910000e-10 78.7
54 TraesCS5D01G525900 chr1D 84.199 443 61 6 75 509 45407578 45407137 7.640000e-114 422.0
55 TraesCS5D01G525900 chr1B 80.793 479 48 11 958 1425 266922703 266923148 1.020000e-87 335.0
56 TraesCS5D01G525900 chr1B 94.118 136 7 1 857 992 266922570 266922704 8.380000e-49 206.0
57 TraesCS5D01G525900 chr1B 88.489 139 14 1 733 869 266921036 266921174 3.950000e-37 167.0
58 TraesCS5D01G525900 chr7D 82.867 286 43 6 1728 2011 606955971 606956252 1.060000e-62 252.0
59 TraesCS5D01G525900 chr7D 82.034 295 48 5 1737 2029 606946123 606946414 4.940000e-61 246.0
60 TraesCS5D01G525900 chr7D 82.657 271 39 6 1730 1996 606973427 606973693 3.840000e-57 233.0
61 TraesCS5D01G525900 chr7D 79.412 340 53 15 1718 2044 606967659 606967994 2.310000e-54 224.0
62 TraesCS5D01G525900 chr3B 84.388 237 20 9 507 731 789487248 789487017 3.870000e-52 217.0
63 TraesCS5D01G525900 chr3B 83.544 237 22 8 507 731 777720402 777720171 8.380000e-49 206.0
64 TraesCS5D01G525900 chr3B 88.961 154 15 2 358 509 777720585 777720432 8.440000e-44 189.0
65 TraesCS5D01G525900 chr3B 88.514 148 15 2 364 509 789487425 789487278 1.830000e-40 178.0
66 TraesCS5D01G525900 chr3B 93.043 115 8 0 855 969 789486966 789486852 1.100000e-37 169.0
67 TraesCS5D01G525900 chr3B 93.103 58 4 0 912 969 777693548 777693491 1.140000e-12 86.1
68 TraesCS5D01G525900 chr3B 92.857 56 4 0 855 910 777720120 777720065 1.470000e-11 82.4
69 TraesCS5D01G525900 chr3B 94.000 50 3 0 1500 1549 640969051 640969100 6.860000e-10 76.8
70 TraesCS5D01G525900 chr3B 96.875 32 0 1 1566 1596 758403077 758403046 1.200000e-02 52.8
71 TraesCS5D01G525900 chrUn 83.966 237 21 11 507 731 41733787 41733556 1.800000e-50 211.0
72 TraesCS5D01G525900 chrUn 89.189 148 14 2 364 509 41733964 41733817 3.930000e-42 183.0
73 TraesCS5D01G525900 chrUn 93.043 115 8 0 855 969 41733505 41733391 1.100000e-37 169.0
74 TraesCS5D01G525900 chr6B 83.898 236 21 7 508 731 92347079 92346849 6.480000e-50 209.0
75 TraesCS5D01G525900 chr6B 88.235 153 17 1 358 509 92347263 92347111 1.410000e-41 182.0
76 TraesCS5D01G525900 chr6B 91.304 115 10 0 855 969 92346790 92346676 2.380000e-34 158.0
77 TraesCS5D01G525900 chr1A 81.858 226 25 9 519 732 571931814 571931593 6.570000e-40 176.0
78 TraesCS5D01G525900 chr2D 81.416 226 26 9 519 732 25879379 25879158 3.060000e-38 171.0
79 TraesCS5D01G525900 chr2A 80.973 226 27 9 519 732 767487401 767487180 1.420000e-36 165.0
80 TraesCS5D01G525900 chr3A 96.875 32 0 1 1566 1596 646288592 646288623 1.200000e-02 52.8


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 TraesCS5D01G525900 chr5D 543837722 543844098 6376 True 11777.000000 11777 100.0000 1 6377 1 chr5D.!!$R1 6376
1 TraesCS5D01G525900 chr5D 543857271 543858529 1258 True 1238.000000 1238 84.4210 4078 5377 1 chr5D.!!$R2 1299
2 TraesCS5D01G525900 chr5D 544284533 544286832 2299 True 1004.500000 1465 82.1290 2767 5660 2 chr5D.!!$R3 2893
3 TraesCS5D01G525900 chr5D 77670995 77671576 581 False 915.000000 915 95.0170 3495 4076 1 chr5D.!!$F1 581
4 TraesCS5D01G525900 chr5B 686210688 686212090 1402 True 1151.000000 1151 81.6260 4078 5535 1 chr5B.!!$R2 1457
5 TraesCS5D01G525900 chr5B 685990412 685994885 4473 True 957.916667 2819 92.9865 1692 6335 6 chr5B.!!$R5 4643
6 TraesCS5D01G525900 chr5B 504330281 504330866 585 False 900.000000 900 94.3780 3491 4077 1 chr5B.!!$F1 586
7 TraesCS5D01G525900 chr5B 685949715 685952430 2715 True 806.500000 1402 83.1815 2205 5568 2 chr5B.!!$R4 3363
8 TraesCS5D01G525900 chr5B 686049496 686051781 2285 True 713.500000 1232 84.0595 2247 5534 2 chr5B.!!$R6 3287
9 TraesCS5D01G525900 chr5B 685648680 685651176 2496 False 626.800000 2025 90.9588 3336 6375 5 chr5B.!!$F2 3039
10 TraesCS5D01G525900 chr4A 624982401 624983981 1580 False 1426.000000 1426 83.2510 4078 5660 1 chr4A.!!$F2 1582
11 TraesCS5D01G525900 chr4A 625238979 625250497 11518 False 1001.175000 2606 93.9270 5 6375 8 chr4A.!!$F4 6370
12 TraesCS5D01G525900 chr4A 625175671 625178248 2577 False 747.500000 1315 85.9440 2286 5535 2 chr4A.!!$F3 3249
13 TraesCS5D01G525900 chr4A 624977644 624978212 568 False 431.000000 431 80.6170 2769 3344 1 chr4A.!!$F1 575
14 TraesCS5D01G525900 chr6A 520100973 520101560 587 True 922.000000 922 94.9240 3491 4080 1 chr6A.!!$R1 589
15 TraesCS5D01G525900 chr7A 730584383 730584961 578 False 918.000000 918 95.1970 3494 4076 1 chr7A.!!$F2 582
16 TraesCS5D01G525900 chr7A 176569873 176570458 585 False 907.000000 907 94.5580 3492 4079 1 chr7A.!!$F1 587
17 TraesCS5D01G525900 chr2B 734294061 734294644 583 False 911.000000 911 94.8630 3495 4076 1 chr2B.!!$F1 581
18 TraesCS5D01G525900 chr5A 677952081 677952662 581 False 905.000000 905 94.7010 3495 4078 1 chr5A.!!$F1 583
19 TraesCS5D01G525900 chr7B 289954330 289954910 580 True 902.000000 902 94.6740 3495 4076 1 chr7B.!!$R1 581
20 TraesCS5D01G525900 chr3D 51957950 51958529 579 True 902.000000 902 94.6830 3495 4077 1 chr3D.!!$R1 582
21 TraesCS5D01G525900 chr1B 266921036 266923148 2112 False 236.000000 335 87.8000 733 1425 3 chr1B.!!$F1 692

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
229 230 1.699083 TGCAACTCTCTGGGTCATTCA 59.301 47.619 0.00 0.00 0.00 2.57 F
1648 4756 0.689745 TGGAGCATTACCCGGCTACT 60.690 55.000 0.00 0.00 41.67 2.57 F
2192 9556 0.031212 ATCCCCGATGGCCCAATTTT 60.031 50.000 0.00 0.00 0.00 1.82 F
2233 9597 0.109272 GACGGATTCACAGTCGCAGA 60.109 55.000 0.00 0.00 34.50 4.26 F
2246 9610 0.690192 TCGCAGAGACCAATTTGGGA 59.310 50.000 19.39 2.61 43.37 4.37 F
2438 9816 0.899019 GCTCGTCTCTCCTTTTCCCT 59.101 55.000 0.00 0.00 0.00 4.20 F
3963 11938 0.466543 TTTCGGTCCATATCGGGTGG 59.533 55.000 0.00 0.00 38.11 4.61 F
4469 12459 1.075659 GCCCTATCAAGCCCATCCC 59.924 63.158 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 9537 0.031212 AAAATTGGGCCATCGGGGAT 60.031 50.000 7.26 0.0 40.01 3.85 R
3195 10717 0.179073 TAGCATGCTCCGCTTCTTCC 60.179 55.000 26.57 0.0 40.96 3.46 R
3225 10747 3.207474 AGTGATGATTTTGCTTGACGC 57.793 42.857 0.00 0.0 39.77 5.19 R
3892 11867 4.096532 CGATATGTCCACCGATATAGCACT 59.903 45.833 0.00 0.0 30.33 4.40 R
3930 11905 5.475719 TGGACCGAAATATCAACCGATATC 58.524 41.667 0.00 0.0 42.83 1.63 R
4404 12394 0.535102 CTGGTTTCAAGTGGAGCGGT 60.535 55.000 0.00 0.0 0.00 5.68 R
5332 13328 1.198759 GGGAACACCCAGAGGCTACA 61.199 60.000 0.00 0.0 43.00 2.74 R
5649 13698 2.389962 TTGTCCGCAATAGTACCCAC 57.610 50.000 0.00 0.0 0.00 4.61 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
26 27 4.322080 TTGGTACATGCCTCTCTTATCG 57.678 45.455 0.00 0.00 39.30 2.92
40 41 6.066054 TCTCTTATCGCACTCTCTACATTG 57.934 41.667 0.00 0.00 0.00 2.82
105 106 5.721000 TGAAATTTCAGGACCATAATGCCTT 59.279 36.000 16.91 0.00 32.50 4.35
109 110 2.092429 TCAGGACCATAATGCCTTCCAC 60.092 50.000 0.00 0.00 0.00 4.02
220 221 2.827800 TCAAGGTCTGCAACTCTCTG 57.172 50.000 0.00 0.00 0.00 3.35
229 230 1.699083 TGCAACTCTCTGGGTCATTCA 59.301 47.619 0.00 0.00 0.00 2.57
303 304 9.950680 CAGTATTAAGTTTTGTCATTCTGTTGT 57.049 29.630 0.00 0.00 0.00 3.32
314 315 9.959749 TTTGTCATTCTGTTGTTTATTTCTACC 57.040 29.630 0.00 0.00 0.00 3.18
315 316 8.918202 TGTCATTCTGTTGTTTATTTCTACCT 57.082 30.769 0.00 0.00 0.00 3.08
316 317 8.783093 TGTCATTCTGTTGTTTATTTCTACCTG 58.217 33.333 0.00 0.00 0.00 4.00
317 318 7.750903 GTCATTCTGTTGTTTATTTCTACCTGC 59.249 37.037 0.00 0.00 0.00 4.85
318 319 6.569179 TTCTGTTGTTTATTTCTACCTGCC 57.431 37.500 0.00 0.00 0.00 4.85
319 320 5.626142 TCTGTTGTTTATTTCTACCTGCCA 58.374 37.500 0.00 0.00 0.00 4.92
320 321 5.705441 TCTGTTGTTTATTTCTACCTGCCAG 59.295 40.000 0.00 0.00 0.00 4.85
321 322 5.626142 TGTTGTTTATTTCTACCTGCCAGA 58.374 37.500 0.00 0.00 0.00 3.86
322 323 6.245408 TGTTGTTTATTTCTACCTGCCAGAT 58.755 36.000 0.00 0.00 0.00 2.90
323 324 6.374333 TGTTGTTTATTTCTACCTGCCAGATC 59.626 38.462 0.00 0.00 0.00 2.75
324 325 6.061022 TGTTTATTTCTACCTGCCAGATCA 57.939 37.500 0.00 0.00 0.00 2.92
325 326 6.480763 TGTTTATTTCTACCTGCCAGATCAA 58.519 36.000 0.00 0.00 0.00 2.57
326 327 6.945435 TGTTTATTTCTACCTGCCAGATCAAA 59.055 34.615 0.00 0.00 0.00 2.69
327 328 7.615365 TGTTTATTTCTACCTGCCAGATCAAAT 59.385 33.333 0.00 0.00 0.00 2.32
328 329 9.120538 GTTTATTTCTACCTGCCAGATCAAATA 57.879 33.333 0.00 0.00 0.00 1.40
329 330 8.908786 TTATTTCTACCTGCCAGATCAAATAG 57.091 34.615 0.00 0.00 0.00 1.73
381 382 1.917872 TGTCCAGGCAACCAATAACC 58.082 50.000 0.00 0.00 37.17 2.85
1412 2867 7.557719 ACATATGTTTATTGTCCAAGAGAAGGG 59.442 37.037 1.41 0.00 0.00 3.95
1414 2869 4.017126 GTTTATTGTCCAAGAGAAGGGGG 58.983 47.826 0.00 0.00 0.00 5.40
1485 2941 3.264193 TCAGACCCTATCAACATGCTTGT 59.736 43.478 0.00 0.00 37.82 3.16
1534 2990 1.671328 TGTCACAACGATCGCCAAAAA 59.329 42.857 16.60 0.00 0.00 1.94
1625 4733 3.686016 AGTTTCATATGGACGTTTGCCT 58.314 40.909 2.13 0.00 0.00 4.75
1629 4737 7.224297 AGTTTCATATGGACGTTTGCCTATAT 58.776 34.615 2.13 0.00 0.00 0.86
1630 4738 7.173218 AGTTTCATATGGACGTTTGCCTATATG 59.827 37.037 2.13 10.33 33.28 1.78
1632 4740 5.247337 TCATATGGACGTTTGCCTATATGGA 59.753 40.000 14.32 3.95 38.35 3.41
1633 4741 3.469008 TGGACGTTTGCCTATATGGAG 57.531 47.619 0.00 0.00 38.35 3.86
1635 4743 2.484770 GGACGTTTGCCTATATGGAGCA 60.485 50.000 0.00 0.00 38.35 4.26
1637 4745 3.815401 GACGTTTGCCTATATGGAGCATT 59.185 43.478 0.00 0.00 38.35 3.56
1638 4746 4.968259 ACGTTTGCCTATATGGAGCATTA 58.032 39.130 3.72 0.00 38.35 1.90
1640 4748 4.154195 CGTTTGCCTATATGGAGCATTACC 59.846 45.833 3.72 0.00 38.35 2.85
1641 4749 4.301072 TTGCCTATATGGAGCATTACCC 57.699 45.455 3.72 0.00 38.35 3.69
1642 4750 2.236146 TGCCTATATGGAGCATTACCCG 59.764 50.000 0.00 0.00 38.35 5.28
1643 4751 2.420129 GCCTATATGGAGCATTACCCGG 60.420 54.545 0.00 0.00 38.35 5.73
1645 4753 1.362224 ATATGGAGCATTACCCGGCT 58.638 50.000 0.00 0.00 44.48 5.52
1648 4756 0.689745 TGGAGCATTACCCGGCTACT 60.690 55.000 0.00 0.00 41.67 2.57
1649 4757 1.335145 GGAGCATTACCCGGCTACTA 58.665 55.000 0.00 0.00 41.22 1.82
1650 4758 1.690352 GGAGCATTACCCGGCTACTAA 59.310 52.381 0.00 0.00 41.22 2.24
1653 4761 2.704065 AGCATTACCCGGCTACTAATGT 59.296 45.455 15.29 2.34 38.90 2.71
1654 4762 2.806244 GCATTACCCGGCTACTAATGTG 59.194 50.000 15.29 0.00 32.59 3.21
1655 4763 3.399330 CATTACCCGGCTACTAATGTGG 58.601 50.000 0.00 0.00 0.00 4.17
1657 4765 1.227853 CCCGGCTACTAATGTGGGC 60.228 63.158 0.00 0.00 44.61 5.36
1660 4768 1.227853 GGCTACTAATGTGGGCCCG 60.228 63.158 19.37 3.48 42.82 6.13
1661 4769 1.525442 GCTACTAATGTGGGCCCGT 59.475 57.895 19.37 10.37 0.00 5.28
1664 4772 0.828022 TACTAATGTGGGCCCGTCTG 59.172 55.000 19.37 7.54 0.00 3.51
1665 4773 1.819632 CTAATGTGGGCCCGTCTGC 60.820 63.158 19.37 5.20 0.00 4.26
1666 4774 2.257409 CTAATGTGGGCCCGTCTGCT 62.257 60.000 19.37 1.31 0.00 4.24
1668 4776 3.925630 ATGTGGGCCCGTCTGCTTG 62.926 63.158 19.37 0.00 0.00 4.01
1677 4785 4.731503 GTCTGCTTGCACGCGCTG 62.732 66.667 5.73 5.02 39.64 5.18
1690 4798 2.932083 GCGCTGGCGATACATGTCG 61.932 63.158 19.31 1.26 44.14 4.35
1723 5526 7.653311 GGATGAACATAATATGGTTTTCAAGGC 59.347 37.037 5.16 1.55 30.08 4.35
1756 5560 9.892130 TTTTATTTTATTTTGGTTGGAGTGTGT 57.108 25.926 0.00 0.00 0.00 3.72
1764 5568 1.217882 GTTGGAGTGTGTCTGTTCCG 58.782 55.000 0.00 0.00 32.27 4.30
1776 5580 2.030185 GTCTGTTCCGAAGCAGTAGTGA 60.030 50.000 0.42 0.00 0.00 3.41
1983 5795 2.228822 CCTGCGTCCACTTTTATTGCTT 59.771 45.455 0.00 0.00 0.00 3.91
1992 5804 4.280677 CCACTTTTATTGCTTCCTGAACCA 59.719 41.667 0.00 0.00 0.00 3.67
2019 5831 3.444742 TCCTCAGGTGCAAAAGCAATATG 59.555 43.478 0.00 0.00 0.00 1.78
2020 5832 3.444742 CCTCAGGTGCAAAAGCAATATGA 59.555 43.478 0.00 0.00 0.00 2.15
2030 5842 6.138761 GCAAAAGCAATATGAGACTATTCCG 58.861 40.000 0.00 0.00 0.00 4.30
2044 5872 5.361285 AGACTATTCCGACAAGTCAAGCTAT 59.639 40.000 10.51 0.00 41.69 2.97
2045 5873 6.546403 AGACTATTCCGACAAGTCAAGCTATA 59.454 38.462 10.51 0.00 41.69 1.31
2046 5874 7.231722 AGACTATTCCGACAAGTCAAGCTATAT 59.768 37.037 10.51 0.00 41.69 0.86
2047 5875 7.148641 ACTATTCCGACAAGTCAAGCTATATG 58.851 38.462 0.72 0.00 0.00 1.78
2048 5876 5.592104 TTCCGACAAGTCAAGCTATATGA 57.408 39.130 0.72 0.00 0.00 2.15
2051 5879 5.985530 TCCGACAAGTCAAGCTATATGATTG 59.014 40.000 0.72 0.00 42.86 2.67
2054 5882 6.642540 CGACAAGTCAAGCTATATGATTGCTA 59.357 38.462 0.72 0.00 41.42 3.49
2055 5883 7.148836 CGACAAGTCAAGCTATATGATTGCTAG 60.149 40.741 0.72 0.00 41.42 3.42
2056 5884 7.730084 ACAAGTCAAGCTATATGATTGCTAGA 58.270 34.615 0.00 0.00 41.42 2.43
2057 5885 8.206867 ACAAGTCAAGCTATATGATTGCTAGAA 58.793 33.333 0.00 0.00 41.42 2.10
2072 9432 9.730420 TGATTGCTAGAACTAGAAAAACAAAAC 57.270 29.630 12.33 6.47 34.57 2.43
2077 9437 5.578776 AGAACTAGAAAAACAAAACGCTGG 58.421 37.500 0.00 0.00 0.00 4.85
2079 9439 3.697542 ACTAGAAAAACAAAACGCTGGGT 59.302 39.130 0.00 0.00 0.00 4.51
2080 9440 4.883006 ACTAGAAAAACAAAACGCTGGGTA 59.117 37.500 0.00 0.00 0.00 3.69
2084 9444 2.061509 AACAAAACGCTGGGTAGGTT 57.938 45.000 0.00 0.75 0.00 3.50
2085 9445 2.934886 ACAAAACGCTGGGTAGGTTA 57.065 45.000 0.00 0.00 0.00 2.85
2086 9446 3.428413 ACAAAACGCTGGGTAGGTTAT 57.572 42.857 0.00 0.00 0.00 1.89
2087 9447 3.758425 ACAAAACGCTGGGTAGGTTATT 58.242 40.909 0.00 0.00 0.00 1.40
2088 9448 4.146564 ACAAAACGCTGGGTAGGTTATTT 58.853 39.130 0.00 0.00 0.00 1.40
2089 9449 4.585581 ACAAAACGCTGGGTAGGTTATTTT 59.414 37.500 0.00 0.00 0.00 1.82
2090 9450 5.069383 ACAAAACGCTGGGTAGGTTATTTTT 59.931 36.000 0.00 0.00 0.00 1.94
2091 9451 6.264970 ACAAAACGCTGGGTAGGTTATTTTTA 59.735 34.615 0.00 0.00 0.00 1.52
2092 9452 6.505044 AAACGCTGGGTAGGTTATTTTTAG 57.495 37.500 0.00 0.00 0.00 1.85
2094 9454 3.881089 CGCTGGGTAGGTTATTTTTAGGG 59.119 47.826 0.00 0.00 0.00 3.53
2110 9473 2.612746 GGGGGCTGGGTAGGTGAA 60.613 66.667 0.00 0.00 0.00 3.18
2159 9523 3.524346 GGAACCCAACCAACAAGGA 57.476 52.632 0.00 0.00 41.22 3.36
2160 9524 2.009681 GGAACCCAACCAACAAGGAT 57.990 50.000 0.00 0.00 41.22 3.24
2161 9525 3.163616 GGAACCCAACCAACAAGGATA 57.836 47.619 0.00 0.00 41.22 2.59
2163 9527 2.194201 ACCCAACCAACAAGGATACG 57.806 50.000 0.00 0.00 46.39 3.06
2172 9536 1.520787 CAAGGATACGACGGCCCAC 60.521 63.158 0.00 0.00 46.39 4.61
2173 9537 1.985662 AAGGATACGACGGCCCACA 60.986 57.895 0.00 0.00 46.39 4.17
2183 9547 4.586235 GGCCCACATCCCCGATGG 62.586 72.222 6.58 0.00 43.60 3.51
2185 9549 4.586235 CCCACATCCCCGATGGCC 62.586 72.222 0.00 0.00 43.60 5.36
2186 9550 4.586235 CCACATCCCCGATGGCCC 62.586 72.222 0.00 0.00 43.60 5.80
2189 9553 2.394506 ACATCCCCGATGGCCCAAT 61.395 57.895 0.00 0.00 43.60 3.16
2190 9554 1.152483 CATCCCCGATGGCCCAATT 60.152 57.895 0.00 0.00 36.51 2.32
2191 9555 0.760189 CATCCCCGATGGCCCAATTT 60.760 55.000 0.00 0.00 36.51 1.82
2192 9556 0.031212 ATCCCCGATGGCCCAATTTT 60.031 50.000 0.00 0.00 0.00 1.82
2194 9558 1.685355 CCCCGATGGCCCAATTTTCC 61.685 60.000 0.00 0.00 0.00 3.13
2195 9559 0.687427 CCCGATGGCCCAATTTTCCT 60.687 55.000 0.00 0.00 0.00 3.36
2196 9560 1.410932 CCCGATGGCCCAATTTTCCTA 60.411 52.381 0.00 0.00 0.00 2.94
2197 9561 2.597455 CCGATGGCCCAATTTTCCTAT 58.403 47.619 0.00 0.00 0.00 2.57
2198 9562 2.558359 CCGATGGCCCAATTTTCCTATC 59.442 50.000 0.00 0.00 0.00 2.08
2199 9563 2.226437 CGATGGCCCAATTTTCCTATCG 59.774 50.000 0.00 0.00 0.00 2.92
2200 9564 1.398692 TGGCCCAATTTTCCTATCGC 58.601 50.000 0.00 0.00 0.00 4.58
2201 9565 1.341482 TGGCCCAATTTTCCTATCGCA 60.341 47.619 0.00 0.00 0.00 5.10
2202 9566 1.754226 GGCCCAATTTTCCTATCGCAA 59.246 47.619 0.00 0.00 0.00 4.85
2203 9567 2.365293 GGCCCAATTTTCCTATCGCAAT 59.635 45.455 0.00 0.00 0.00 3.56
2215 9579 3.248363 CCTATCGCAATTCGCAAAGATGA 59.752 43.478 1.75 0.00 42.60 2.92
2218 9582 1.538276 GCAATTCGCAAAGATGACGG 58.462 50.000 0.00 0.00 41.79 4.79
2232 9596 0.388520 TGACGGATTCACAGTCGCAG 60.389 55.000 0.00 0.00 44.40 5.18
2233 9597 0.109272 GACGGATTCACAGTCGCAGA 60.109 55.000 0.00 0.00 34.50 4.26
2246 9610 0.690192 TCGCAGAGACCAATTTGGGA 59.310 50.000 19.39 2.61 43.37 4.37
2249 9613 1.610624 GCAGAGACCAATTTGGGACGA 60.611 52.381 19.39 0.00 43.37 4.20
2386 9764 3.521529 AAGACGCCGCTCACAGCTT 62.522 57.895 0.00 0.00 39.60 3.74
2390 9768 2.047844 GCCGCTCACAGCTTCAGA 60.048 61.111 0.00 0.00 39.60 3.27
2438 9816 0.899019 GCTCGTCTCTCCTTTTCCCT 59.101 55.000 0.00 0.00 0.00 4.20
2548 9960 6.418057 AGTGAAATTTCCAGTATTTTGGCA 57.582 33.333 15.48 0.00 38.16 4.92
2599 10011 8.974060 TGACAGGTGATATTTAGGGTATTTTC 57.026 34.615 0.00 0.00 0.00 2.29
2705 10161 5.627499 TCAGTTGTTGATAACTCCATTGC 57.373 39.130 0.00 0.00 38.78 3.56
2734 10190 8.477419 TGATGAGGGAAATAGTTTCAGTTTTT 57.523 30.769 4.98 0.00 41.43 1.94
2764 10229 8.523915 AATTGCAATGTAGATGAGTATTCCAA 57.476 30.769 13.82 0.00 0.00 3.53
3032 10546 4.021016 AGGAGCGTCTTCCATTATATCACC 60.021 45.833 5.72 0.00 39.84 4.02
3074 10588 3.616317 GCACGCTTGGGTTGGATAAAATT 60.616 43.478 0.00 0.00 0.00 1.82
3195 10717 4.808077 ATGATCGCTATGCAAGTTTCTG 57.192 40.909 0.00 0.00 0.00 3.02
3225 10747 2.542411 GGAGCATGCTATTCCGCTTTTG 60.542 50.000 22.74 0.00 34.12 2.44
3612 11585 9.915629 ATATATCGGAGAAAACATGTCTAGTTC 57.084 33.333 0.00 1.20 43.58 3.01
3619 11592 7.798982 GGAGAAAACATGTCTAGTTCTTTTTCG 59.201 37.037 0.00 0.00 36.85 3.46
3930 11905 3.316588 ACATATCGGGCTAGATATCAGCG 59.683 47.826 16.08 7.78 40.68 5.18
3963 11938 0.466543 TTTCGGTCCATATCGGGTGG 59.533 55.000 0.00 0.00 38.11 4.61
4347 12337 1.274167 CTTGCATTCATTGGCACCTGT 59.726 47.619 0.00 0.00 40.23 4.00
4348 12338 1.340088 TGCATTCATTGGCACCTGTT 58.660 45.000 0.00 0.00 34.58 3.16
4404 12394 2.290832 TGTGCATACATTCAGCTTCCCA 60.291 45.455 0.00 0.00 0.00 4.37
4469 12459 1.075659 GCCCTATCAAGCCCATCCC 59.924 63.158 0.00 0.00 0.00 3.85
4600 12590 7.418483 GCTCATATGGGTATCTTATCTTCTCCC 60.418 44.444 4.11 0.00 0.00 4.30
4629 12619 1.204704 CACTGCCTCCTTGTCGATGTA 59.795 52.381 0.00 0.00 0.00 2.29
4689 12679 4.868734 CCTAACAACGATCTTGGGTACTTC 59.131 45.833 0.00 0.00 0.00 3.01
4695 12685 2.496070 CGATCTTGGGTACTTCTGTGGA 59.504 50.000 0.00 0.00 0.00 4.02
4773 12766 3.698040 GAGATTCCATGTTTGAGTGGCAT 59.302 43.478 0.00 0.00 35.43 4.40
4851 12844 7.092712 ATCTATCAGATTGTGTCCTTCAAAGGA 60.093 37.037 7.41 7.41 41.62 3.36
4901 12894 2.464865 GCTCCACGCTATACACTTCAG 58.535 52.381 0.00 0.00 35.14 3.02
4913 12906 5.762179 ATACACTTCAGACCTCAATTCCA 57.238 39.130 0.00 0.00 0.00 3.53
4954 12947 6.969993 TTAAAAAGGAGTTTGTGCCTATGT 57.030 33.333 0.00 0.00 33.20 2.29
4989 12982 1.802960 GTCTGTGGTGACATGCTTCTG 59.197 52.381 0.00 0.00 46.14 3.02
5077 13070 1.403514 GCCTCAACTTCTCTGTCGAGG 60.404 57.143 0.00 0.00 42.43 4.63
5109 13102 2.421619 GTGAAGTTGGAGAAGCTGGAG 58.578 52.381 0.00 0.00 0.00 3.86
5380 13376 7.484993 TTAGTTTATGGTTCTGGCTAGTACA 57.515 36.000 9.00 1.92 0.00 2.90
5423 13466 2.131183 CTGCCTAGCGTTTATCTCAGC 58.869 52.381 0.00 0.00 0.00 4.26
5463 13506 6.715347 AGCTGTAATGGTTTTCTGACTTTT 57.285 33.333 0.00 0.00 0.00 2.27
5465 13508 6.321181 AGCTGTAATGGTTTTCTGACTTTTGA 59.679 34.615 0.00 0.00 0.00 2.69
5466 13509 6.417930 GCTGTAATGGTTTTCTGACTTTTGAC 59.582 38.462 0.00 0.00 0.00 3.18
5468 13511 5.930837 AATGGTTTTCTGACTTTTGACCA 57.069 34.783 0.00 0.00 39.71 4.02
5470 13513 5.930837 TGGTTTTCTGACTTTTGACCAAT 57.069 34.783 0.00 0.00 33.15 3.16
5473 13516 7.841956 TGGTTTTCTGACTTTTGACCAATTTA 58.158 30.769 0.00 0.00 33.15 1.40
5485 13529 7.778470 TTTGACCAATTTATTTGTGTCCAAC 57.222 32.000 0.00 0.00 35.95 3.77
5662 13711 5.352016 TCAAATGTAACGTGGGTACTATTGC 59.648 40.000 0.00 0.00 0.00 3.56
5697 13760 3.949754 CGTGTATTCTACTGTACCTCCCA 59.050 47.826 0.00 0.00 0.00 4.37
5716 13814 4.646040 TCCCATGGATCATTCATTGTTGAC 59.354 41.667 15.22 0.00 0.00 3.18
5736 13834 8.052141 TGTTGACCTGAATGAATGTATTGGATA 58.948 33.333 0.00 0.00 0.00 2.59
5755 13859 4.020662 GGATAATGGTGGTTTTCTTGCCAA 60.021 41.667 0.00 0.00 36.41 4.52
5853 13969 3.945921 TCGTAGGAATGTACTGTCCTCTG 59.054 47.826 17.94 12.94 43.44 3.35
6221 14551 2.723322 CAATCTTGGAGGCCATCTCA 57.277 50.000 5.01 0.00 44.19 3.27
6262 14592 4.690184 TCAGCATGATCAAACATCACAC 57.310 40.909 0.00 0.00 42.56 3.82
6265 14595 4.021229 AGCATGATCAAACATCACACCAT 58.979 39.130 0.00 0.00 0.00 3.55
6332 14663 4.513318 GCAGGGCAAATATAGAAGAGTCAC 59.487 45.833 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.944087 AGAGAGGCATGTACCAAAGAAC 58.056 45.455 0.00 0.00 0.00 3.01
1 2 4.640771 AAGAGAGGCATGTACCAAAGAA 57.359 40.909 0.00 0.00 0.00 2.52
3 4 4.747108 CGATAAGAGAGGCATGTACCAAAG 59.253 45.833 0.00 0.00 0.00 2.77
26 27 2.160417 GCACAACCAATGTAGAGAGTGC 59.840 50.000 0.00 0.00 41.46 4.40
105 106 0.251297 CAGCAACCCCTTGATGTGGA 60.251 55.000 0.00 0.00 38.71 4.02
109 110 2.133281 TGATCAGCAACCCCTTGATG 57.867 50.000 0.00 0.00 43.87 3.07
302 303 7.391148 TTTGATCTGGCAGGTAGAAATAAAC 57.609 36.000 15.73 0.00 0.00 2.01
303 304 9.342308 CTATTTGATCTGGCAGGTAGAAATAAA 57.658 33.333 15.73 3.82 0.00 1.40
304 305 7.939039 CCTATTTGATCTGGCAGGTAGAAATAA 59.061 37.037 15.73 4.78 0.00 1.40
305 306 7.453393 CCTATTTGATCTGGCAGGTAGAAATA 58.547 38.462 15.73 16.76 0.00 1.40
306 307 6.302269 CCTATTTGATCTGGCAGGTAGAAAT 58.698 40.000 15.73 16.54 0.00 2.17
307 308 5.397899 CCCTATTTGATCTGGCAGGTAGAAA 60.398 44.000 15.73 10.53 0.00 2.52
308 309 4.103153 CCCTATTTGATCTGGCAGGTAGAA 59.897 45.833 15.73 6.20 0.00 2.10
309 310 3.648067 CCCTATTTGATCTGGCAGGTAGA 59.352 47.826 15.73 0.00 0.00 2.59
310 311 3.392616 ACCCTATTTGATCTGGCAGGTAG 59.607 47.826 15.73 0.59 0.00 3.18
311 312 3.393687 ACCCTATTTGATCTGGCAGGTA 58.606 45.455 15.73 0.00 0.00 3.08
312 313 2.208872 ACCCTATTTGATCTGGCAGGT 58.791 47.619 15.73 7.54 0.00 4.00
313 314 3.303351 AACCCTATTTGATCTGGCAGG 57.697 47.619 15.73 0.00 0.00 4.85
314 315 6.966534 ATAAAACCCTATTTGATCTGGCAG 57.033 37.500 8.58 8.58 0.00 4.85
315 316 8.058847 AGTTATAAAACCCTATTTGATCTGGCA 58.941 33.333 0.00 0.00 36.15 4.92
316 317 8.465273 AGTTATAAAACCCTATTTGATCTGGC 57.535 34.615 0.00 0.00 36.15 4.85
317 318 9.067986 GGAGTTATAAAACCCTATTTGATCTGG 57.932 37.037 0.00 0.00 36.15 3.86
318 319 9.853177 AGGAGTTATAAAACCCTATTTGATCTG 57.147 33.333 0.00 0.00 35.64 2.90
328 329 9.964354 AAACGTTTATAGGAGTTATAAAACCCT 57.036 29.630 12.83 6.74 42.76 4.34
351 352 4.556233 GTTGCCTGGACAAATAAGGAAAC 58.444 43.478 0.00 0.00 41.36 2.78
381 382 2.191802 CGACTTGACAGCTATGCTCTG 58.808 52.381 0.00 0.00 36.40 3.35
472 473 2.028876 GGCAAAAACACACCCTGTAGT 58.971 47.619 0.00 0.00 30.51 2.73
668 669 1.335597 ACTCGAACGTCAGAAATCGCA 60.336 47.619 0.32 0.00 35.39 5.10
1388 2843 7.062957 CCCCTTCTCTTGGACAATAAACATAT 58.937 38.462 0.00 0.00 0.00 1.78
1412 2867 6.882768 AAATCTGAGTAGATGATATCCCCC 57.117 41.667 0.00 0.00 42.80 5.40
1414 2869 7.418483 GGGCTAAATCTGAGTAGATGATATCCC 60.418 44.444 0.00 0.00 42.80 3.85
1459 2915 4.018960 AGCATGTTGATAGGGTCTGACTTT 60.019 41.667 7.85 0.00 0.00 2.66
1479 2935 0.106769 TGCACCAGGAAGAACAAGCA 60.107 50.000 0.00 0.00 0.00 3.91
1485 2941 2.373169 AGAAGACATGCACCAGGAAGAA 59.627 45.455 0.00 0.00 0.00 2.52
1534 2990 0.608035 AACGTCCATTCCACGGCATT 60.608 50.000 0.00 0.00 41.73 3.56
1537 2993 1.209127 CAAACGTCCATTCCACGGC 59.791 57.895 0.00 0.00 41.73 5.68
1568 3024 3.584250 CTTGAGGCGTGCTTGTGCG 62.584 63.158 0.00 0.00 43.34 5.34
1591 3047 0.111639 TGAAACTAGGGGTTGGGTGC 59.888 55.000 0.00 0.00 38.29 5.01
1625 4733 2.546899 AGCCGGGTAATGCTCCATATA 58.453 47.619 3.10 0.00 30.33 0.86
1629 4737 0.689745 AGTAGCCGGGTAATGCTCCA 60.690 55.000 16.36 0.00 39.00 3.86
1630 4738 1.335145 TAGTAGCCGGGTAATGCTCC 58.665 55.000 22.88 6.25 39.00 4.70
1632 4740 2.704065 ACATTAGTAGCCGGGTAATGCT 59.296 45.455 22.88 14.64 37.57 3.79
1633 4741 2.806244 CACATTAGTAGCCGGGTAATGC 59.194 50.000 22.88 7.74 37.57 3.56
1635 4743 2.370849 CCCACATTAGTAGCCGGGTAAT 59.629 50.000 18.49 18.49 0.00 1.89
1637 4745 1.416243 CCCACATTAGTAGCCGGGTA 58.584 55.000 9.87 9.87 0.00 3.69
1638 4746 1.979619 GCCCACATTAGTAGCCGGGT 61.980 60.000 12.58 12.58 35.99 5.28
1640 4748 1.227853 GGCCCACATTAGTAGCCGG 60.228 63.158 0.00 0.00 36.84 6.13
1641 4749 1.227853 GGGCCCACATTAGTAGCCG 60.228 63.158 19.95 0.00 43.73 5.52
1642 4750 1.227853 CGGGCCCACATTAGTAGCC 60.228 63.158 24.92 0.00 42.67 3.93
1643 4751 0.532196 GACGGGCCCACATTAGTAGC 60.532 60.000 24.92 0.00 0.00 3.58
1645 4753 0.828022 CAGACGGGCCCACATTAGTA 59.172 55.000 24.92 0.00 0.00 1.82
1648 4756 1.847798 AAGCAGACGGGCCCACATTA 61.848 55.000 24.92 0.00 0.00 1.90
1649 4757 3.210012 AAGCAGACGGGCCCACATT 62.210 57.895 24.92 1.36 0.00 2.71
1650 4758 3.650950 AAGCAGACGGGCCCACAT 61.651 61.111 24.92 6.17 0.00 3.21
1660 4768 4.731503 CAGCGCGTGCAAGCAGAC 62.732 66.667 24.79 12.65 46.23 3.51
1672 4780 2.931386 GACATGTATCGCCAGCGC 59.069 61.111 7.27 0.00 39.59 5.92
1673 4781 1.299089 TCGACATGTATCGCCAGCG 60.299 57.895 5.50 5.50 41.97 5.18
1674 4782 0.527600 TGTCGACATGTATCGCCAGC 60.528 55.000 15.76 0.00 41.97 4.85
1675 4783 1.788886 CATGTCGACATGTATCGCCAG 59.211 52.381 38.55 18.45 46.40 4.85
1685 4793 3.333029 TGTTCATCCACATGTCGACAT 57.667 42.857 25.18 25.18 36.96 3.06
1686 4794 2.829741 TGTTCATCCACATGTCGACA 57.170 45.000 22.48 22.48 0.00 4.35
1687 4795 5.991328 ATTATGTTCATCCACATGTCGAC 57.009 39.130 9.11 9.11 37.93 4.20
1688 4796 6.650390 CCATATTATGTTCATCCACATGTCGA 59.350 38.462 0.00 0.00 37.93 4.20
1690 4798 7.750229 ACCATATTATGTTCATCCACATGTC 57.250 36.000 0.00 0.00 37.93 3.06
1702 5505 8.474831 GGTTAGCCTTGAAAACCATATTATGTT 58.525 33.333 3.10 0.00 41.89 2.71
1747 5551 1.068588 CTTCGGAACAGACACACTCCA 59.931 52.381 0.00 0.00 0.00 3.86
1756 5560 2.235891 TCACTACTGCTTCGGAACAGA 58.764 47.619 19.88 8.55 37.35 3.41
1764 5568 2.096218 CCAAGCGTTTCACTACTGCTTC 60.096 50.000 0.00 0.00 43.51 3.86
1776 5580 2.157834 TATGTGTCGTCCAAGCGTTT 57.842 45.000 0.00 0.00 0.00 3.60
1983 5795 0.487325 TGAGGAGAGGTGGTTCAGGA 59.513 55.000 0.00 0.00 0.00 3.86
2019 5831 3.860536 GCTTGACTTGTCGGAATAGTCTC 59.139 47.826 16.83 7.10 39.18 3.36
2020 5832 3.511934 AGCTTGACTTGTCGGAATAGTCT 59.488 43.478 16.83 0.74 39.18 3.24
2030 5842 6.857777 AGCAATCATATAGCTTGACTTGTC 57.142 37.500 0.00 0.00 34.37 3.18
2046 5874 9.730420 GTTTTGTTTTTCTAGTTCTAGCAATCA 57.270 29.630 2.31 1.92 0.00 2.57
2047 5875 8.892905 CGTTTTGTTTTTCTAGTTCTAGCAATC 58.107 33.333 2.31 0.00 0.00 2.67
2048 5876 7.378728 GCGTTTTGTTTTTCTAGTTCTAGCAAT 59.621 33.333 2.31 0.00 0.00 3.56
2051 5879 6.357240 CAGCGTTTTGTTTTTCTAGTTCTAGC 59.643 38.462 2.31 0.00 0.00 3.42
2054 5882 5.449999 CCCAGCGTTTTGTTTTTCTAGTTCT 60.450 40.000 0.00 0.00 0.00 3.01
2055 5883 4.738252 CCCAGCGTTTTGTTTTTCTAGTTC 59.262 41.667 0.00 0.00 0.00 3.01
2056 5884 4.158949 ACCCAGCGTTTTGTTTTTCTAGTT 59.841 37.500 0.00 0.00 0.00 2.24
2057 5885 3.697542 ACCCAGCGTTTTGTTTTTCTAGT 59.302 39.130 0.00 0.00 0.00 2.57
2072 9432 3.881089 CCCTAAAAATAACCTACCCAGCG 59.119 47.826 0.00 0.00 0.00 5.18
2094 9454 2.675371 GTTCACCTACCCAGCCCC 59.325 66.667 0.00 0.00 0.00 5.80
2099 9462 1.151899 AGCCAGGTTCACCTACCCA 60.152 57.895 0.00 0.00 46.65 4.51
2107 9470 3.970410 CCAGCCCAGCCAGGTTCA 61.970 66.667 0.00 0.00 34.66 3.18
2147 9511 1.730064 CCGTCGTATCCTTGTTGGTTG 59.270 52.381 0.00 0.00 37.07 3.77
2149 9513 0.390735 GCCGTCGTATCCTTGTTGGT 60.391 55.000 0.00 0.00 37.07 3.67
2150 9514 1.087771 GGCCGTCGTATCCTTGTTGG 61.088 60.000 0.00 0.00 37.10 3.77
2151 9515 1.087771 GGGCCGTCGTATCCTTGTTG 61.088 60.000 0.00 0.00 0.00 3.33
2152 9516 1.219935 GGGCCGTCGTATCCTTGTT 59.780 57.895 0.00 0.00 0.00 2.83
2153 9517 1.985662 TGGGCCGTCGTATCCTTGT 60.986 57.895 0.00 0.00 0.00 3.16
2154 9518 1.520787 GTGGGCCGTCGTATCCTTG 60.521 63.158 0.00 0.00 0.00 3.61
2155 9519 1.335132 ATGTGGGCCGTCGTATCCTT 61.335 55.000 0.00 0.00 0.00 3.36
2156 9520 1.745320 GATGTGGGCCGTCGTATCCT 61.745 60.000 0.00 0.00 0.00 3.24
2157 9521 1.300697 GATGTGGGCCGTCGTATCC 60.301 63.158 0.00 0.00 0.00 2.59
2158 9522 1.300697 GGATGTGGGCCGTCGTATC 60.301 63.158 0.00 0.00 0.00 2.24
2159 9523 2.803817 GGGATGTGGGCCGTCGTAT 61.804 63.158 0.00 0.00 0.00 3.06
2160 9524 3.463585 GGGATGTGGGCCGTCGTA 61.464 66.667 0.00 0.00 0.00 3.43
2172 9536 0.760189 AAATTGGGCCATCGGGGATG 60.760 55.000 7.26 0.00 40.01 3.51
2173 9537 0.031212 AAAATTGGGCCATCGGGGAT 60.031 50.000 7.26 0.00 40.01 3.85
2179 9543 2.029918 GCGATAGGAAAATTGGGCCATC 60.030 50.000 7.26 0.57 0.00 3.51
2199 9563 1.130373 TCCGTCATCTTTGCGAATTGC 59.870 47.619 0.00 0.00 46.70 3.56
2200 9564 3.680642 ATCCGTCATCTTTGCGAATTG 57.319 42.857 0.00 0.00 0.00 2.32
2201 9565 3.689161 TGAATCCGTCATCTTTGCGAATT 59.311 39.130 0.00 0.00 0.00 2.17
2202 9566 3.063997 GTGAATCCGTCATCTTTGCGAAT 59.936 43.478 0.00 0.00 38.90 3.34
2203 9567 2.415168 GTGAATCCGTCATCTTTGCGAA 59.585 45.455 0.00 0.00 38.90 4.70
2215 9579 0.109086 CTCTGCGACTGTGAATCCGT 60.109 55.000 0.00 0.00 0.00 4.69
2218 9582 1.067565 TGGTCTCTGCGACTGTGAATC 60.068 52.381 0.00 0.00 42.44 2.52
2232 9596 1.679032 CCCTCGTCCCAAATTGGTCTC 60.679 57.143 11.52 0.25 35.17 3.36
2233 9597 0.328258 CCCTCGTCCCAAATTGGTCT 59.672 55.000 11.52 0.00 35.17 3.85
2238 9602 1.196104 TCCGTCCCTCGTCCCAAATT 61.196 55.000 0.00 0.00 37.94 1.82
2240 9604 2.203669 TCCGTCCCTCGTCCCAAA 60.204 61.111 0.00 0.00 37.94 3.28
2241 9605 2.993264 GTCCGTCCCTCGTCCCAA 60.993 66.667 0.00 0.00 37.94 4.12
2267 9632 3.011760 GCGCACGACTACTGGTTGC 62.012 63.158 0.30 0.00 32.66 4.17
2268 9633 2.380410 GGCGCACGACTACTGGTTG 61.380 63.158 10.83 0.00 35.50 3.77
2273 9641 3.075005 ATGGGGCGCACGACTACT 61.075 61.111 10.83 0.00 0.00 2.57
2380 9758 0.035630 GGGTGCAGATCTGAAGCTGT 60.036 55.000 27.90 0.00 41.09 4.40
2386 9764 1.267574 GGGTGAGGGTGCAGATCTGA 61.268 60.000 27.04 8.75 0.00 3.27
2390 9768 1.852157 TTGGGGTGAGGGTGCAGAT 60.852 57.895 0.00 0.00 0.00 2.90
2438 9816 8.378172 ACGAAGATGTGTGAAAGATAAAAGAA 57.622 30.769 0.00 0.00 0.00 2.52
2489 9867 2.482142 GCAAGATTACTGACTCTCCCGG 60.482 54.545 0.00 0.00 0.00 5.73
2599 10011 7.494625 AGTCAATTATACCACCACTAATTCACG 59.505 37.037 0.00 0.00 0.00 4.35
2734 10190 9.851686 AATACTCATCTACATTGCAATTAAGGA 57.148 29.630 9.83 6.42 0.00 3.36
2761 10226 1.342174 ACAGTTCAAGGCAGCAATTGG 59.658 47.619 7.72 0.00 0.00 3.16
2764 10229 0.316204 GCACAGTTCAAGGCAGCAAT 59.684 50.000 0.00 0.00 0.00 3.56
3032 10546 6.643845 CGTGCAACACTCTTAATCATATCAG 58.356 40.000 0.00 0.00 35.74 2.90
3074 10588 4.638421 CCAAACGAACAAGAGGCCATATAA 59.362 41.667 5.01 0.00 0.00 0.98
3195 10717 0.179073 TAGCATGCTCCGCTTCTTCC 60.179 55.000 26.57 0.00 40.96 3.46
3225 10747 3.207474 AGTGATGATTTTGCTTGACGC 57.793 42.857 0.00 0.00 39.77 5.19
3510 11481 5.509163 CCAAACTGATACGAACCCGATATCT 60.509 44.000 0.34 0.00 39.50 1.98
3892 11867 4.096532 CGATATGTCCACCGATATAGCACT 59.903 45.833 0.00 0.00 30.33 4.40
3930 11905 5.475719 TGGACCGAAATATCAACCGATATC 58.524 41.667 0.00 0.00 42.83 1.63
4347 12337 3.663176 GCAGCACGCCAAGAGCAA 61.663 61.111 0.00 0.00 44.04 3.91
4348 12338 4.933563 TGCAGCACGCCAAGAGCA 62.934 61.111 0.00 0.00 44.04 4.26
4404 12394 0.535102 CTGGTTTCAAGTGGAGCGGT 60.535 55.000 0.00 0.00 0.00 5.68
4492 12482 6.299141 AGTTTTTCTTGCTAGGATCACTGAA 58.701 36.000 0.00 0.00 0.00 3.02
4600 12590 0.109342 AGGAGGCAGTGAACCTTGTG 59.891 55.000 0.00 0.00 37.77 3.33
4629 12619 3.682718 GCATCACCTTGCTACCAGTGTAT 60.683 47.826 0.00 0.00 39.57 2.29
4689 12679 3.393800 CGTAAGGATGCCTATTCCACAG 58.606 50.000 0.00 0.00 35.59 3.66
4773 12766 2.025793 TGACCAGGAGTTTGTTCCAACA 60.026 45.455 0.00 0.00 39.84 3.33
4901 12894 3.940209 TTTGCATGTGGAATTGAGGTC 57.060 42.857 0.00 0.00 0.00 3.85
4954 12947 2.038426 CACAGACCACCAACCATGAGTA 59.962 50.000 0.00 0.00 0.00 2.59
4989 12982 3.760684 AGCTGAACCTTTGGTCAATCATC 59.239 43.478 0.00 0.00 33.12 2.92
5077 13070 1.537202 CAACTTCACCCACTTAGCTGC 59.463 52.381 0.00 0.00 0.00 5.25
5109 13102 5.358160 AGGGCTAACAAACAGAGCATAATTC 59.642 40.000 0.00 0.00 37.98 2.17
5332 13328 1.198759 GGGAACACCCAGAGGCTACA 61.199 60.000 0.00 0.00 43.00 2.74
5423 13466 4.310769 ACAGCTACAGAACTAGTTGCAAG 58.689 43.478 14.14 8.92 39.61 4.01
5463 13506 6.723298 AGTTGGACACAAATAAATTGGTCA 57.277 33.333 0.00 0.00 43.66 4.02
5465 13508 6.487331 TCGTAGTTGGACACAAATAAATTGGT 59.513 34.615 0.00 0.00 43.66 3.67
5466 13509 6.904498 TCGTAGTTGGACACAAATAAATTGG 58.096 36.000 0.00 0.00 43.66 3.16
5473 13516 7.606456 ACAGATTAATCGTAGTTGGACACAAAT 59.394 33.333 9.78 0.00 38.54 2.32
5485 13529 5.063944 GCATGCCCATACAGATTAATCGTAG 59.936 44.000 6.36 12.32 0.00 3.51
5649 13698 2.389962 TTGTCCGCAATAGTACCCAC 57.610 50.000 0.00 0.00 0.00 4.61
5662 13711 5.164119 GTAGAATACACGACAAGTTTGTCCG 60.164 44.000 16.88 14.23 46.60 4.79
5697 13760 5.512298 TCAGGTCAACAATGAATGATCCAT 58.488 37.500 0.00 0.00 37.30 3.41
5716 13814 8.301720 CACCATTATCCAATACATTCATTCAGG 58.698 37.037 0.00 0.00 0.00 3.86
5736 13834 4.436113 AATTGGCAAGAAAACCACCATT 57.564 36.364 5.96 0.00 35.10 3.16
5755 13859 8.565896 TCTGTCAGCACATTATCAACTAAAAT 57.434 30.769 0.00 0.00 0.00 1.82
5853 13969 4.068599 GGCTGGAGATAATAAACTGGAGC 58.931 47.826 0.00 0.00 0.00 4.70
6221 14551 5.777802 CTGAGTATGCGAATGGACTTAGAT 58.222 41.667 0.00 0.00 29.44 1.98
6262 14592 8.729756 TGTTTGTTCAGATGATGTAAACTATGG 58.270 33.333 13.44 0.00 33.55 2.74
6265 14595 9.944663 GTTTGTTTGTTCAGATGATGTAAACTA 57.055 29.630 13.44 7.37 33.55 2.24
6332 14663 4.892655 TGAGAATTGCAAATAAGCGTACG 58.107 39.130 11.84 11.84 37.31 3.67


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

AutoCloner maintained by Alex Coulton.