Multiple sequence alignment - TraesCS1B01G054200

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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 TraesCS1B01G054200 chr1B 100.000 8187 0 0 1 8187 35126542 35134728 0.000000e+00 15119.0
1 TraesCS1B01G054200 chr1B 94.229 4072 164 23 2015 6054 35702530 35698498 0.000000e+00 6152.0
2 TraesCS1B01G054200 chr1B 95.641 803 34 1 6827 7628 35689386 35688584 0.000000e+00 1288.0
3 TraesCS1B01G054200 chr1B 91.232 901 53 14 562 1455 35705695 35704814 0.000000e+00 1203.0
4 TraesCS1B01G054200 chr1B 89.369 602 33 6 1446 2017 35703176 35702576 0.000000e+00 728.0
5 TraesCS1B01G054200 chr1B 94.406 429 24 0 6398 6826 35698356 35697928 0.000000e+00 660.0
6 TraesCS1B01G054200 chr1B 88.987 454 38 5 7743 8184 35688376 35687923 1.200000e-152 551.0
7 TraesCS1B01G054200 chr1B 90.798 326 25 3 5 329 35706013 35705692 1.630000e-116 431.0
8 TraesCS1B01G054200 chr1B 90.432 324 26 3 7 329 35797306 35796987 9.820000e-114 422.0
9 TraesCS1B01G054200 chr1B 82.353 102 14 2 7638 7735 35688517 35688416 1.460000e-12 86.1
10 TraesCS1B01G054200 chr4A 93.644 5035 220 38 2278 7279 591847066 591852033 0.000000e+00 7433.0
11 TraesCS1B01G054200 chr4A 83.683 1336 107 51 948 2218 591845789 591847078 0.000000e+00 1157.0
12 TraesCS1B01G054200 chr4A 87.723 896 76 19 3 884 591844914 591845789 0.000000e+00 1014.0
13 TraesCS1B01G054200 chr4A 83.784 444 32 16 4267 4696 109426939 109427356 1.290000e-102 385.0
14 TraesCS1B01G054200 chr4A 84.925 398 40 13 5638 6027 109429835 109430220 1.290000e-102 385.0
15 TraesCS1B01G054200 chr4A 89.600 125 11 2 7275 7397 591852508 591852632 3.060000e-34 158.0
16 TraesCS1B01G054200 chr4A 100.000 28 0 0 3626 3653 109426540 109426567 1.500000e-02 52.8
17 TraesCS1B01G054200 chr1D 94.803 4233 166 17 2139 6334 21457819 21453604 0.000000e+00 6549.0
18 TraesCS1B01G054200 chr1D 89.598 1442 75 24 689 2082 21459703 21458289 0.000000e+00 1762.0
19 TraesCS1B01G054200 chr1D 93.425 1019 48 4 6398 7415 21453601 21452601 0.000000e+00 1493.0
20 TraesCS1B01G054200 chr1D 88.553 463 35 10 7743 8187 21451906 21451444 5.590000e-151 545.0
21 TraesCS1B01G054200 chr1D 90.526 380 32 3 144 523 21460078 21459703 4.410000e-137 499.0
22 TraesCS1B01G054200 chr1D 87.766 376 44 2 287 662 106962552 106962925 9.760000e-119 438.0
23 TraesCS1B01G054200 chr1D 94.022 184 11 0 7442 7625 21452299 21452116 6.260000e-71 279.0
24 TraesCS1B01G054200 chr1A 94.101 4238 176 23 2143 6334 23008188 23003979 0.000000e+00 6373.0
25 TraesCS1B01G054200 chr1A 92.885 1012 51 7 6398 7409 23003976 23002986 0.000000e+00 1450.0
26 TraesCS1B01G054200 chr1A 92.078 871 53 9 356 1220 23010287 23009427 0.000000e+00 1212.0
27 TraesCS1B01G054200 chr1A 86.836 904 45 21 1268 2122 23009442 23008564 0.000000e+00 942.0
28 TraesCS1B01G054200 chr1A 87.174 460 44 6 7743 8187 23002185 23001726 7.330000e-140 508.0
29 TraesCS1B01G054200 chr1A 94.030 201 8 1 7429 7625 23002595 23002395 1.340000e-77 302.0
30 TraesCS1B01G054200 chr1A 82.524 103 12 4 7638 7735 23002326 23002225 1.460000e-12 86.1
31 TraesCS1B01G054200 chr4D 91.067 4041 222 64 866 4819 10967544 10971532 0.000000e+00 5334.0
32 TraesCS1B01G054200 chr4D 92.948 2198 126 14 5447 7633 10972316 10974495 0.000000e+00 3173.0
33 TraesCS1B01G054200 chr4D 95.211 710 29 2 4818 5524 10971614 10972321 0.000000e+00 1118.0
34 TraesCS1B01G054200 chr4D 89.238 669 59 5 2 667 10965229 10965887 0.000000e+00 824.0
35 TraesCS1B01G054200 chr4D 90.179 448 38 4 7743 8184 10975843 10976290 5.510000e-161 579.0
36 TraesCS1B01G054200 chr4D 95.455 44 2 0 7638 7681 10974746 10974789 4.100000e-08 71.3
37 TraesCS1B01G054200 chr5A 89.261 4237 255 93 341 4493 622208116 622203996 0.000000e+00 5120.0
38 TraesCS1B01G054200 chr5A 91.950 2907 160 30 4534 7420 622203853 622201001 0.000000e+00 4004.0
39 TraesCS1B01G054200 chr5A 88.930 271 23 5 7371 7639 622200958 622200693 2.200000e-85 327.0
40 TraesCS1B01G054200 chr5A 93.182 88 6 0 7967 8054 622199172 622199085 6.670000e-26 130.0
41 TraesCS1B01G054200 chr4B 93.785 3395 160 15 4227 7586 20720019 20723397 0.000000e+00 5053.0
42 TraesCS1B01G054200 chr4B 86.693 2773 222 67 2 2716 20715735 20718418 0.000000e+00 2940.0
43 TraesCS1B01G054200 chr4B 94.471 850 33 10 2785 3629 20718418 20719258 0.000000e+00 1297.0
44 TraesCS1B01G054200 chr4B 93.704 683 31 4 3627 4304 20719381 20720056 0.000000e+00 1013.0
45 TraesCS1B01G054200 chr4B 88.147 464 46 7 4860 5319 439317101 439316643 2.010000e-150 544.0
46 TraesCS1B01G054200 chr4B 88.889 414 38 4 7749 8155 20723737 20724149 3.410000e-138 503.0
47 TraesCS1B01G054200 chr4B 79.464 112 7 2 7638 7733 20723580 20723691 1.910000e-06 65.8
48 TraesCS1B01G054200 chrUn 93.159 2339 99 15 3740 6054 328886668 328888969 0.000000e+00 3376.0
49 TraesCS1B01G054200 chrUn 96.154 1092 39 2 2145 3234 440910307 440909217 0.000000e+00 1781.0
50 TraesCS1B01G054200 chrUn 89.369 602 33 6 1446 2017 465907243 465906643 0.000000e+00 728.0
51 TraesCS1B01G054200 chrUn 90.909 484 30 8 562 1045 379145608 379145139 8.960000e-179 638.0
52 TraesCS1B01G054200 chrUn 90.909 484 30 8 562 1045 379147396 379146927 8.960000e-179 638.0
53 TraesCS1B01G054200 chrUn 94.541 403 22 0 6398 6800 328889111 328889513 2.510000e-174 623.0
54 TraesCS1B01G054200 chrUn 91.814 452 25 6 1011 1455 356845362 356844916 3.250000e-173 619.0
55 TraesCS1B01G054200 chrUn 91.814 452 25 6 1011 1455 356896950 356896504 3.250000e-173 619.0
56 TraesCS1B01G054200 chrUn 91.814 452 25 6 1011 1455 474797292 474796846 3.250000e-173 619.0
57 TraesCS1B01G054200 chrUn 91.104 326 24 3 5 329 379145926 379145605 3.510000e-118 436.0
58 TraesCS1B01G054200 chrUn 90.798 326 25 3 5 329 379147714 379147393 1.630000e-116 431.0
59 TraesCS1B01G054200 chrUn 92.000 300 19 3 5 303 480481682 480481387 4.570000e-112 416.0
60 TraesCS1B01G054200 chrUn 99.145 117 1 0 2015 2131 465906597 465906481 2.320000e-50 211.0
61 TraesCS1B01G054200 chr7B 89.216 102 5 4 8059 8155 121778292 121778192 1.120000e-23 122.0
62 TraesCS1B01G054200 chr6A 86.726 113 10 1 8058 8165 586845902 586845790 4.010000e-23 121.0
63 TraesCS1B01G054200 chr6D 85.714 119 8 7 8058 8168 457522266 457522149 5.190000e-22 117.0
64 TraesCS1B01G054200 chr2D 85.714 112 10 4 8059 8164 544568270 544568159 6.720000e-21 113.0
65 TraesCS1B01G054200 chr7D 84.167 120 13 4 8054 8168 37794037 37793919 2.420000e-20 111.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G054200 chr1B 35126542 35134728 8186 False 15119.000000 15119 100.000000 1 8187 1 chr1B.!!$F1 8186
1 TraesCS1B01G054200 chr1B 35697928 35706013 8085 True 1834.800000 6152 92.006800 5 6826 5 chr1B.!!$R3 6821
2 TraesCS1B01G054200 chr1B 35687923 35689386 1463 True 641.700000 1288 88.993667 6827 8184 3 chr1B.!!$R2 1357
3 TraesCS1B01G054200 chr4A 591844914 591852632 7718 False 2440.500000 7433 88.662500 3 7397 4 chr4A.!!$F2 7394
4 TraesCS1B01G054200 chr4A 109426540 109430220 3680 False 274.266667 385 89.569667 3626 6027 3 chr4A.!!$F1 2401
5 TraesCS1B01G054200 chr1D 21451444 21460078 8634 True 1854.500000 6549 91.821167 144 8187 6 chr1D.!!$R1 8043
6 TraesCS1B01G054200 chr1A 23001726 23010287 8561 True 1553.300000 6373 89.946857 356 8187 7 chr1A.!!$R1 7831
7 TraesCS1B01G054200 chr4D 10965229 10976290 11061 False 1849.883333 5334 92.349667 2 8184 6 chr4D.!!$F1 8182
8 TraesCS1B01G054200 chr5A 622199085 622208116 9031 True 2395.250000 5120 90.830750 341 8054 4 chr5A.!!$R1 7713
9 TraesCS1B01G054200 chr4B 20715735 20724149 8414 False 1811.966667 5053 89.501000 2 8155 6 chr4B.!!$F1 8153
10 TraesCS1B01G054200 chrUn 328886668 328889513 2845 False 1999.500000 3376 93.850000 3740 6800 2 chrUn.!!$F1 3060
11 TraesCS1B01G054200 chrUn 440909217 440910307 1090 True 1781.000000 1781 96.154000 2145 3234 1 chrUn.!!$R3 1089
12 TraesCS1B01G054200 chrUn 379145139 379147714 2575 True 535.750000 638 90.930000 5 1045 4 chrUn.!!$R6 1040
13 TraesCS1B01G054200 chrUn 465906481 465907243 762 True 469.500000 728 94.257000 1446 2131 2 chrUn.!!$R7 685

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
318 322 0.375454 TTGACGTGAAACACCAAGCG 59.625 50.000 0.00 0.00 35.74 4.68 F
1236 4508 1.077644 CGAGGACGAGGAGGAGGAA 60.078 63.158 0.00 0.00 42.66 3.36 F
1262 4549 0.634465 GAGGAAGAGGAGGAGGAGGT 59.366 60.000 0.00 0.00 0.00 3.85 F
2373 7876 0.603569 CGGGATCTTGCGGCTAGTAT 59.396 55.000 11.06 4.15 0.00 2.12 F
3559 9078 1.386748 CTCAGCACACACACGATTACG 59.613 52.381 0.00 0.00 45.75 3.18 F
4955 11605 0.978146 AGCCCAGCCGAACTATCACT 60.978 55.000 0.00 0.00 0.00 3.41 F
6112 14089 0.109532 TTTGTTCATCAGCCCGGTCA 59.890 50.000 0.00 0.00 0.00 4.02 F
6865 14857 1.830477 AGATGACCTTGAGAGTCAGGC 59.170 52.381 0.00 0.00 46.76 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 4549 0.177604 GTCCTCCTCGTCCTCGTCTA 59.822 60.0 0.00 0.00 38.33 2.59 R
2272 7775 1.151668 CCTGCTTGTCACTTTCCTCG 58.848 55.0 0.00 0.00 0.00 4.63 R
2600 8105 1.305219 TAACAAGCCAGCCACATCGC 61.305 55.0 0.00 0.00 0.00 4.58 R
4061 9748 2.093500 GTGTGAGGATGCACCACTGATA 60.093 50.0 10.18 0.00 42.04 2.15 R
5299 11965 2.093235 AGTGCATAGGAGAAGCTTCCAC 60.093 50.0 22.81 19.42 39.84 4.02 R
6854 14846 0.247460 CATCAACCGCCTGACTCTCA 59.753 55.0 0.00 0.00 0.00 3.27 R
7003 15002 0.601311 GCTGCCGAGATGTATCCCAC 60.601 60.0 0.00 0.00 0.00 4.61 R
7999 19146 0.944386 AACTGCCACACGAACATGAC 59.056 50.0 0.00 0.00 0.00 3.06 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
96 100 4.701651 TGATGTCATGGAAATGGAAGACAC 59.298 41.667 0.00 0.00 38.62 3.67
98 102 5.497464 TGTCATGGAAATGGAAGACACTA 57.503 39.130 0.00 0.00 31.72 2.74
163 167 1.600023 TCACAAAAGGGGTAAGTGCG 58.400 50.000 0.00 0.00 0.00 5.34
183 187 6.037940 AGTGCGTCGATTCAGACTTAATACTA 59.962 38.462 0.00 0.00 38.90 1.82
237 241 3.623863 ACCAAAGTCACATTAAAACGCG 58.376 40.909 3.53 3.53 0.00 6.01
263 267 5.688176 GGAGCGTGTCTCTTTGACTAATATC 59.312 44.000 0.00 0.00 45.54 1.63
268 272 7.644490 CGTGTCTCTTTGACTAATATCTAGCT 58.356 38.462 0.00 0.00 45.54 3.32
278 282 6.879993 TGACTAATATCTAGCTCTAACCGAGG 59.120 42.308 0.00 0.00 40.25 4.63
315 319 6.035112 GCTTTTTATTTGACGTGAAACACCAA 59.965 34.615 1.24 0.00 35.74 3.67
318 322 0.375454 TTGACGTGAAACACCAAGCG 59.625 50.000 0.00 0.00 35.74 4.68
331 335 4.585879 ACACCAAGCGTTCCATTAACTAT 58.414 39.130 0.00 0.00 35.81 2.12
339 343 4.777463 CGTTCCATTAACTATTGGGTCCT 58.223 43.478 0.00 0.00 35.81 3.85
361 365 3.892284 TCAATATTACCGGCCACAACAT 58.108 40.909 0.00 0.00 0.00 2.71
457 461 6.833416 AGCTAGTAGATGAGCAGGGATATTAG 59.167 42.308 0.00 0.00 41.36 1.73
463 467 7.811482 AGATGAGCAGGGATATTAGAAAGAT 57.189 36.000 0.00 0.00 0.00 2.40
469 473 7.678837 AGCAGGGATATTAGAAAGATGAGAAG 58.321 38.462 0.00 0.00 0.00 2.85
530 542 4.175787 TGAACTTAGCTTCTCGGAAGAC 57.824 45.455 15.23 8.21 35.39 3.01
615 628 2.675844 CGTGATGAAAATAACTCGGCCA 59.324 45.455 2.24 0.00 0.00 5.36
640 654 1.613836 AAACTCTTCAGCAAGCCTGG 58.386 50.000 0.00 0.00 42.05 4.45
712 733 9.272901 GTTTTTAAACAGGATTGCAAGTTTTTC 57.727 29.630 16.67 4.42 38.74 2.29
713 734 8.785329 TTTTAAACAGGATTGCAAGTTTTTCT 57.215 26.923 16.67 0.00 35.90 2.52
714 735 9.877178 TTTTAAACAGGATTGCAAGTTTTTCTA 57.123 25.926 16.67 0.57 35.90 2.10
715 736 9.528018 TTTAAACAGGATTGCAAGTTTTTCTAG 57.472 29.630 16.67 4.47 35.90 2.43
719 740 7.781056 ACAGGATTGCAAGTTTTTCTAGAAAA 58.219 30.769 23.65 23.65 38.40 2.29
720 741 7.706607 ACAGGATTGCAAGTTTTTCTAGAAAAC 59.293 33.333 26.47 20.65 39.70 2.43
733 1856 7.576861 TTTCTAGAAAACGAAAAAGGACCAT 57.423 32.000 15.57 0.00 0.00 3.55
856 2351 1.145156 GTGTGGGTGGGGTTTTTGC 59.855 57.895 0.00 0.00 0.00 3.68
1188 4445 1.305046 GGAGGACGACCAGGAGGAA 60.305 63.158 6.71 0.00 38.69 3.36
1232 4504 2.271497 GGACGAGGACGAGGAGGA 59.729 66.667 0.00 0.00 42.66 3.71
1236 4508 1.077644 CGAGGACGAGGAGGAGGAA 60.078 63.158 0.00 0.00 42.66 3.36
1241 4513 2.226149 GACGAGGAGGAGGAAGGGGA 62.226 65.000 0.00 0.00 0.00 4.81
1242 4514 1.758906 CGAGGAGGAGGAAGGGGAC 60.759 68.421 0.00 0.00 0.00 4.46
1243 4515 1.758906 GAGGAGGAGGAAGGGGACG 60.759 68.421 0.00 0.00 0.00 4.79
1244 4516 2.226149 GAGGAGGAGGAAGGGGACGA 62.226 65.000 0.00 0.00 0.00 4.20
1245 4517 1.758906 GGAGGAGGAAGGGGACGAG 60.759 68.421 0.00 0.00 0.00 4.18
1246 4518 1.758906 GAGGAGGAAGGGGACGAGG 60.759 68.421 0.00 0.00 0.00 4.63
1247 4519 2.226149 GAGGAGGAAGGGGACGAGGA 62.226 65.000 0.00 0.00 0.00 3.71
1248 4520 1.305887 GGAGGAAGGGGACGAGGAA 60.306 63.158 0.00 0.00 0.00 3.36
1249 4521 1.331399 GGAGGAAGGGGACGAGGAAG 61.331 65.000 0.00 0.00 0.00 3.46
1262 4549 0.634465 GAGGAAGAGGAGGAGGAGGT 59.366 60.000 0.00 0.00 0.00 3.85
1550 6526 1.862123 CACGTTGTGCTCGATGCTT 59.138 52.632 8.07 0.00 43.37 3.91
1573 6552 2.780414 TGAATCCTCCTCCATCCATGT 58.220 47.619 0.00 0.00 0.00 3.21
1607 6588 1.511613 TCCTGGGGAACATCCATCTC 58.488 55.000 0.00 0.00 38.64 2.75
1715 6705 9.541884 AATCTGTTATTACAACTGGGGTTTAAT 57.458 29.630 0.00 0.00 32.92 1.40
1718 6708 7.379750 TGTTATTACAACTGGGGTTTAATTGC 58.620 34.615 0.00 0.00 32.73 3.56
1719 6709 7.015292 TGTTATTACAACTGGGGTTTAATTGCA 59.985 33.333 0.00 0.00 32.73 4.08
1720 6710 5.871396 TTACAACTGGGGTTTAATTGCAA 57.129 34.783 0.00 0.00 32.73 4.08
1721 6711 4.066646 ACAACTGGGGTTTAATTGCAAC 57.933 40.909 0.00 0.00 32.73 4.17
1722 6712 3.056304 CAACTGGGGTTTAATTGCAACG 58.944 45.455 0.00 0.00 32.73 4.10
1723 6713 1.000394 ACTGGGGTTTAATTGCAACGC 60.000 47.619 0.00 0.00 36.58 4.84
1788 6778 9.990360 TTTACAACTGACTACTGTGAATATGAA 57.010 29.630 0.00 0.00 0.00 2.57
1842 6864 4.726021 GCAACTGCTTATCGTGAACATGAG 60.726 45.833 0.00 0.00 38.21 2.90
1857 6879 7.899841 CGTGAACATGAGACTTTAATGTACATG 59.100 37.037 23.60 23.60 38.94 3.21
1961 6997 4.401925 ACATGCTCCCTTGGAATTATAGC 58.598 43.478 0.00 0.00 0.00 2.97
1972 7008 7.822334 CCCTTGGAATTATAGCAATATCGTGTA 59.178 37.037 0.00 0.00 0.00 2.90
1991 7027 8.827177 TCGTGTAGTCTTAATGTTCAATCTTT 57.173 30.769 0.00 0.00 0.00 2.52
2088 7178 5.307196 GCAACTAATACCTAAGGGATCCAGA 59.693 44.000 15.23 0.00 36.25 3.86
2157 7660 9.206870 CAATAAAGTTGGTTTAGCAATGAATGT 57.793 29.630 0.00 0.00 34.01 2.71
2272 7775 2.150397 CGGATAACACGGATCCTTCC 57.850 55.000 10.75 5.56 40.77 3.46
2340 7843 2.907892 TGAGGATCAGTGGGAAGAGTT 58.092 47.619 0.00 0.00 42.56 3.01
2373 7876 0.603569 CGGGATCTTGCGGCTAGTAT 59.396 55.000 11.06 4.15 0.00 2.12
2414 7917 7.934855 ATGGTATTTATCTGCATCATTCTCC 57.065 36.000 0.00 0.00 0.00 3.71
2446 7949 7.051000 AGGATGTCTTTCTTCTATAGGTTTGC 58.949 38.462 0.00 0.00 0.00 3.68
2609 8114 3.374745 CTGGATTTTAATGCGATGTGGC 58.625 45.455 0.00 0.00 0.00 5.01
2815 8320 5.614324 TTGCTGGTGATAGCTACTTGTAT 57.386 39.130 0.00 0.00 44.01 2.29
2817 8322 5.989477 TGCTGGTGATAGCTACTTGTATTT 58.011 37.500 0.00 0.00 44.01 1.40
2878 8383 7.938490 ACAAACATTTTAAATGGAAGAATGGCT 59.062 29.630 20.00 0.00 33.25 4.75
3324 8834 4.586001 ACTGTCATGGAGCAATTGTTTCTT 59.414 37.500 7.40 0.00 0.00 2.52
3466 8985 6.528072 GCCATTTGACAAGCTGTTTACTATTC 59.472 38.462 0.00 0.00 0.00 1.75
3518 9037 9.864034 GTGAAATTTAAGTCGTATATCATGTGG 57.136 33.333 0.00 0.00 0.00 4.17
3529 9048 9.509855 GTCGTATATCATGTGGAATAGATCTTC 57.490 37.037 0.00 0.00 0.00 2.87
3559 9078 1.386748 CTCAGCACACACACGATTACG 59.613 52.381 0.00 0.00 45.75 3.18
3561 9080 1.386748 CAGCACACACACGATTACGAG 59.613 52.381 0.00 0.00 42.66 4.18
3603 9122 8.129161 TGTTCTTGAATTTGTGCAATTTGTAG 57.871 30.769 0.00 0.00 35.02 2.74
3673 9317 6.294453 CCACATGCAAAACTACACATCCTTAA 60.294 38.462 0.00 0.00 0.00 1.85
3703 9350 7.555914 ACATGTTACATGCATACCTACATTTGA 59.444 33.333 23.43 0.00 0.00 2.69
3767 9414 6.573664 AAATGCTTGAACATACAGCACTTA 57.426 33.333 2.47 0.00 38.37 2.24
3812 9461 5.710513 ACTGTGTTAGTCGGTTATGTACA 57.289 39.130 0.00 0.00 33.17 2.90
3819 9468 9.734620 GTGTTAGTCGGTTATGTACATATGTTA 57.265 33.333 14.77 4.29 0.00 2.41
3820 9469 9.734620 TGTTAGTCGGTTATGTACATATGTTAC 57.265 33.333 14.77 10.95 0.00 2.50
3821 9470 9.956720 GTTAGTCGGTTATGTACATATGTTACT 57.043 33.333 14.77 17.32 0.00 2.24
3921 9604 4.718961 ACTTGGAGAAGCTGCTTTCTAAA 58.281 39.130 17.10 8.52 37.53 1.85
3922 9605 4.517075 ACTTGGAGAAGCTGCTTTCTAAAC 59.483 41.667 17.10 2.29 37.53 2.01
3963 9647 5.144692 TGAGAACTGAGAAGTTCCATCTG 57.855 43.478 13.54 0.00 46.74 2.90
4050 9737 6.239317 CCCGAGATAGTTGGAATGAGTATTGA 60.239 42.308 0.00 0.00 0.00 2.57
4093 9780 4.036734 TGCATCCTCACACAGTTTTTCTTC 59.963 41.667 0.00 0.00 0.00 2.87
4187 9876 2.004583 TCTTTCACGTATTCTGCGGG 57.995 50.000 0.00 0.00 0.00 6.13
4263 9952 4.090786 TCGTATATGCAACTTGTTGTGACG 59.909 41.667 13.97 14.46 0.00 4.35
4628 10494 9.219603 CTATATCCATGTTATCCGAACAATGTT 57.780 33.333 0.00 0.00 33.42 2.71
4634 10500 7.545265 CCATGTTATCCGAACAATGTTGAATTT 59.455 33.333 2.20 0.00 33.42 1.82
4643 10509 6.292274 CGAACAATGTTGAATTTTCCTTGGTG 60.292 38.462 2.20 0.00 0.00 4.17
4845 10869 9.820229 TTTGCTTATCGTTCTACAATTACTTTG 57.180 29.630 0.00 0.00 41.36 2.77
4955 11605 0.978146 AGCCCAGCCGAACTATCACT 60.978 55.000 0.00 0.00 0.00 3.41
5234 11896 9.349713 AGGTATGTTGAACTAACTTGAAATTCA 57.650 29.630 0.00 0.00 40.05 2.57
5351 12017 7.064490 CCATTCCAAAATGCAAGGTGTATTAAC 59.936 37.037 0.00 0.00 40.85 2.01
5462 12128 7.475137 TGGAGGGAGTATTTGGTAAATTTTG 57.525 36.000 0.00 0.00 32.38 2.44
5515 12575 3.138468 ACCTAAGGGCCTGTTTGGATATC 59.862 47.826 20.05 0.00 37.63 1.63
5572 12635 3.650281 TTATGGGCTGAATGCTGAAGA 57.350 42.857 0.00 0.00 42.39 2.87
5715 13528 7.081857 TCTAGGCAAAGTTTAGGTCCTTAAA 57.918 36.000 0.00 0.00 0.00 1.52
5765 13579 8.956426 GTTGTTTTCCAATAATATGGTCTGAGA 58.044 33.333 0.00 0.00 41.46 3.27
5830 13648 2.568956 AGGACTGTAGCTGCATTTCTCA 59.431 45.455 4.51 0.00 0.00 3.27
5926 13746 7.768240 ACCTTTTTCTTAACACGTTTCAGATT 58.232 30.769 0.00 0.00 0.00 2.40
5930 13750 6.928979 TTCTTAACACGTTTCAGATTGGAA 57.071 33.333 0.00 0.00 0.00 3.53
5934 13754 7.444183 TCTTAACACGTTTCAGATTGGAATCTT 59.556 33.333 0.00 0.00 42.96 2.40
5937 13757 6.438763 ACACGTTTCAGATTGGAATCTTTTC 58.561 36.000 0.00 0.00 42.96 2.29
5941 13761 7.809806 ACGTTTCAGATTGGAATCTTTTCATTC 59.190 33.333 0.00 0.00 42.96 2.67
5986 13809 7.394359 AGAATTATCAGCCATACACTGTGTTTT 59.606 33.333 19.73 4.50 36.50 2.43
6058 14034 2.742053 TCAAGTCGCCTGATAAAGTTGC 59.258 45.455 0.00 0.00 0.00 4.17
6112 14089 0.109532 TTTGTTCATCAGCCCGGTCA 59.890 50.000 0.00 0.00 0.00 4.02
6119 14096 2.503765 TCATCAGCCCGGTCAAATTCTA 59.496 45.455 0.00 0.00 0.00 2.10
6293 14280 2.158475 TCCTTGCCTCTTCCACATTTGT 60.158 45.455 0.00 0.00 0.00 2.83
6319 14306 8.203485 TCAAACTTCACCTTGCATTAATTCTTT 58.797 29.630 0.00 0.00 0.00 2.52
6385 14373 8.539770 TTCACTTGAAAGATCTGTAGATTCAC 57.460 34.615 6.33 0.00 34.37 3.18
6389 14377 6.915544 TGAAAGATCTGTAGATTCACATGC 57.084 37.500 0.00 0.00 34.37 4.06
6396 14384 6.484364 TCTGTAGATTCACATGCAGGAATA 57.516 37.500 4.84 0.00 34.06 1.75
6535 14523 3.133003 CCTAAGATATCCCATGGTAGGCG 59.867 52.174 11.73 0.00 0.00 5.52
6626 14618 7.169645 ACGACTTGAAATCAATGTTTCCATTTG 59.830 33.333 0.00 0.00 39.28 2.32
6640 14632 3.088532 TCCATTTGGTGCCATTACAGTC 58.911 45.455 0.00 0.00 36.34 3.51
6670 14662 8.895845 CAGTCTTTCAATTGTTTCAGATTTACG 58.104 33.333 5.13 0.00 0.00 3.18
6723 14715 4.042884 AGAGATCCCTGATGATGACCAAA 58.957 43.478 0.00 0.00 0.00 3.28
6759 14751 9.314321 CACTTTGGAGTATCTTATCGTGTATTT 57.686 33.333 0.00 0.00 33.90 1.40
6854 14846 2.681976 CGGCCTCATCAAAGATGACCTT 60.682 50.000 0.00 0.00 38.69 3.50
6865 14857 1.830477 AGATGACCTTGAGAGTCAGGC 59.170 52.381 0.00 0.00 46.76 4.85
6935 14927 6.516739 TGGATATCGAGATGTGTATCCTTC 57.483 41.667 17.26 0.00 41.92 3.46
7102 15101 4.973856 TCCTTCTTCATGGAGAGATGGATT 59.026 41.667 14.72 0.00 0.00 3.01
7106 15105 3.766068 TCATGGAGAGATGGATTGAGC 57.234 47.619 0.00 0.00 0.00 4.26
7165 15164 0.749649 CTCGGAAGGTGCTGAGCTAT 59.250 55.000 5.83 0.00 34.76 2.97
7176 15175 1.407989 GCTGAGCTATTGCCAGAAGGT 60.408 52.381 17.11 0.00 38.72 3.50
7341 15825 6.770785 ACTACTGCAACCTGTAAAGAAAATCA 59.229 34.615 0.00 0.00 0.00 2.57
7344 15828 4.340666 TGCAACCTGTAAAGAAAATCAGCA 59.659 37.500 0.00 0.00 0.00 4.41
7415 15991 2.621526 GGGTGGTGGTACAGTTCTTTTG 59.378 50.000 0.00 0.00 41.80 2.44
7416 15992 2.621526 GGTGGTGGTACAGTTCTTTTGG 59.378 50.000 0.00 0.00 41.80 3.28
7417 15993 2.621526 GTGGTGGTACAGTTCTTTTGGG 59.378 50.000 0.00 0.00 41.80 4.12
7589 16542 5.221441 CCAGTTTTCTCTTACTTTTTGGGGG 60.221 44.000 0.00 0.00 0.00 5.40
7600 16553 5.607939 ACTTTTTGGGGGAAAAACTGTAG 57.392 39.130 0.00 0.00 38.38 2.74
7633 16586 1.952296 GAATCAAATCGCCTGCCATCT 59.048 47.619 0.00 0.00 0.00 2.90
7689 17178 7.462571 ACTGGTGTTAAAAGTTTGACTTTCT 57.537 32.000 6.53 1.52 46.78 2.52
7739 18178 9.810231 CAAAACTGGCACAATATAAAAATTCAC 57.190 29.630 0.00 0.00 38.70 3.18
7740 18179 9.553064 AAAACTGGCACAATATAAAAATTCACA 57.447 25.926 0.00 0.00 38.70 3.58
7741 18180 8.532977 AACTGGCACAATATAAAAATTCACAC 57.467 30.769 0.00 0.00 38.70 3.82
7848 18319 5.193099 ACCCAAGGTTCAGTGCTATTAAT 57.807 39.130 0.00 0.00 27.29 1.40
7874 18983 5.705609 TTTTTATTGAAGCAGGACTGGTC 57.294 39.130 4.32 0.14 40.87 4.02
7924 19045 3.194968 AGGTCGGTCAGGTGTAATTAGTG 59.805 47.826 0.00 0.00 0.00 2.74
7978 19125 6.553953 ACAATTTAGGTTTTTGAGTTGGGT 57.446 33.333 0.00 0.00 0.00 4.51
8008 19156 7.830217 TTTCAAGTTTAAATCGTCATGTTCG 57.170 32.000 0.00 0.00 0.00 3.95
8069 19222 2.676471 GTGGAGGCGGCAATGGTT 60.676 61.111 13.08 0.00 0.00 3.67
8085 19244 0.250553 GGTTGTTCGGTGGTCCATGA 60.251 55.000 0.00 0.00 0.00 3.07
8087 19246 2.159382 GTTGTTCGGTGGTCCATGAAT 58.841 47.619 11.40 0.00 0.00 2.57
8095 19254 2.103094 GGTGGTCCATGAATCTCGATGA 59.897 50.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 132 8.798402 CCCTTTTGTGATTATTTGGTTACACTA 58.202 33.333 0.00 0.00 0.00 2.74
163 167 8.575565 TTGCATAGTATTAAGTCTGAATCGAC 57.424 34.615 0.00 0.00 0.00 4.20
237 241 1.704070 GTCAAAGAGACACGCTCCTC 58.296 55.000 0.00 0.00 46.77 3.71
263 267 1.655329 CCGCCTCGGTTAGAGCTAG 59.345 63.158 0.00 0.00 45.54 3.42
278 282 8.047859 CGTCAAATAAAAAGCATTTATAACCGC 58.952 33.333 7.64 0.00 37.28 5.68
290 294 5.517054 TGGTGTTTCACGTCAAATAAAAAGC 59.483 36.000 0.00 0.00 34.83 3.51
315 319 4.196971 GACCCAATAGTTAATGGAACGCT 58.803 43.478 0.00 0.00 43.37 5.07
318 322 6.184789 TGAAGGACCCAATAGTTAATGGAAC 58.815 40.000 0.00 0.00 39.12 3.62
331 335 3.686120 GCCGGTAATATTGAAGGACCCAA 60.686 47.826 1.90 0.00 0.00 4.12
339 343 3.687125 TGTTGTGGCCGGTAATATTGAA 58.313 40.909 1.90 0.00 0.00 2.69
361 365 3.095912 TCTTCCCCGAGATGTAAGTGA 57.904 47.619 0.00 0.00 0.00 3.41
457 461 7.556733 AGATTGATGCTTCTTCTCATCTTTC 57.443 36.000 0.88 0.00 39.69 2.62
491 503 6.910536 AGTTCAAGCTATAAATGGACTTCG 57.089 37.500 0.00 0.00 28.32 3.79
530 542 2.887568 GTGCACCTCTCGGCATCG 60.888 66.667 5.22 0.00 42.75 3.84
615 628 5.645497 CAGGCTTGCTGAAGAGTTTAGTATT 59.355 40.000 0.00 0.00 0.00 1.89
640 654 5.520376 ACTTTGGCCATGATAAATGCTAC 57.480 39.130 6.09 0.00 0.00 3.58
669 683 8.685427 GTTTAAAAACTTACAACCCAGGTAGAA 58.315 33.333 0.00 0.00 36.03 2.10
671 685 7.998580 TGTTTAAAAACTTACAACCCAGGTAG 58.001 34.615 7.09 0.00 39.59 3.18
712 733 6.426937 TGAGATGGTCCTTTTTCGTTTTCTAG 59.573 38.462 0.00 0.00 0.00 2.43
713 734 6.292923 TGAGATGGTCCTTTTTCGTTTTCTA 58.707 36.000 0.00 0.00 0.00 2.10
714 735 5.130350 TGAGATGGTCCTTTTTCGTTTTCT 58.870 37.500 0.00 0.00 0.00 2.52
715 736 5.432885 TGAGATGGTCCTTTTTCGTTTTC 57.567 39.130 0.00 0.00 0.00 2.29
719 740 2.637872 TCCTGAGATGGTCCTTTTTCGT 59.362 45.455 0.00 0.00 0.00 3.85
720 741 3.334583 TCCTGAGATGGTCCTTTTTCG 57.665 47.619 0.00 0.00 0.00 3.46
804 2299 4.659172 TTTCACAGGGCCGGGCTG 62.659 66.667 28.80 23.98 0.00 4.85
805 2300 3.868200 CTTTTCACAGGGCCGGGCT 62.868 63.158 28.80 11.20 0.00 5.19
856 2351 4.318546 GCGTAGGTCTGGTTTATAATTGCG 60.319 45.833 0.00 0.00 0.00 4.85
939 2467 1.010793 AGGAGAGGAGAGGAGAGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
1066 2664 4.851179 GTGATCGGGGCCGGTTCC 62.851 72.222 16.72 5.24 40.25 3.62
1232 4504 0.324830 CTCTTCCTCGTCCCCTTCCT 60.325 60.000 0.00 0.00 0.00 3.36
1236 4508 1.308326 CTCCTCTTCCTCGTCCCCT 59.692 63.158 0.00 0.00 0.00 4.79
1241 4513 0.257616 CTCCTCCTCCTCTTCCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
1242 4514 0.467290 CCTCCTCCTCCTCTTCCTCG 60.467 65.000 0.00 0.00 0.00 4.63
1243 4515 0.634465 ACCTCCTCCTCCTCTTCCTC 59.366 60.000 0.00 0.00 0.00 3.71
1244 4516 1.856920 CTACCTCCTCCTCCTCTTCCT 59.143 57.143 0.00 0.00 0.00 3.36
1245 4517 1.854280 TCTACCTCCTCCTCCTCTTCC 59.146 57.143 0.00 0.00 0.00 3.46
1246 4518 2.747135 CGTCTACCTCCTCCTCCTCTTC 60.747 59.091 0.00 0.00 0.00 2.87
1247 4519 1.213430 CGTCTACCTCCTCCTCCTCTT 59.787 57.143 0.00 0.00 0.00 2.85
1248 4520 0.841289 CGTCTACCTCCTCCTCCTCT 59.159 60.000 0.00 0.00 0.00 3.69
1249 4521 0.838608 TCGTCTACCTCCTCCTCCTC 59.161 60.000 0.00 0.00 0.00 3.71
1262 4549 0.177604 GTCCTCCTCGTCCTCGTCTA 59.822 60.000 0.00 0.00 38.33 2.59
1339 4644 2.123854 CGAGTCGGGGAGATGGGA 60.124 66.667 4.10 0.00 0.00 4.37
1382 4707 1.059657 CGAGCGACGCAAAAACCATG 61.060 55.000 23.70 0.00 34.51 3.66
1550 6526 3.135161 TGGATGGAGGAGGATTCAAGA 57.865 47.619 0.00 0.00 0.00 3.02
1573 6552 1.630369 CCAGGAATTCACCCTCTGTCA 59.370 52.381 7.93 0.00 0.00 3.58
1715 6705 2.721231 GCTCCACAAGCGTTGCAA 59.279 55.556 0.00 0.00 42.21 4.08
1723 6713 6.317789 TCTAAGAAACAATTGCTCCACAAG 57.682 37.500 5.05 0.00 42.87 3.16
1768 6758 7.030165 CGAGTTTCATATTCACAGTAGTCAGT 58.970 38.462 0.00 0.00 0.00 3.41
1787 6777 2.851195 ACTCCAGTTGCATTCGAGTTT 58.149 42.857 0.00 0.00 29.59 2.66
1788 6778 2.550830 ACTCCAGTTGCATTCGAGTT 57.449 45.000 0.00 0.00 29.59 3.01
1842 6864 6.375377 TGCGAAAACCATGTACATTAAAGTC 58.625 36.000 5.37 0.91 0.00 3.01
1972 7008 8.695456 ACAACCAAAAGATTGAACATTAAGACT 58.305 29.630 0.00 0.00 38.94 3.24
1991 7027 6.007936 GTGACTGCACATAATTACAACCAA 57.992 37.500 0.00 0.00 44.51 3.67
2088 7178 3.251484 TCACCTGAACTCTTCCTCCAAT 58.749 45.455 0.00 0.00 0.00 3.16
2132 7222 9.777297 AACATTCATTGCTAAACCAACTTTATT 57.223 25.926 0.00 0.00 0.00 1.40
2157 7660 4.641094 ACAACCAGGTCGTTTTGATAACAA 59.359 37.500 0.00 0.00 0.00 2.83
2272 7775 1.151668 CCTGCTTGTCACTTTCCTCG 58.848 55.000 0.00 0.00 0.00 4.63
2276 7779 2.262423 AGACCCTGCTTGTCACTTTC 57.738 50.000 4.17 0.00 35.15 2.62
2340 7843 2.238646 AGATCCCGCAGAATACAACCAA 59.761 45.455 0.00 0.00 0.00 3.67
2373 7876 6.808321 ATACCATAAGTTCTGCTTGAGGTA 57.192 37.500 11.73 11.73 44.40 3.08
2428 7931 8.956426 TGTTTATGGCAAACCTATAGAAGAAAG 58.044 33.333 0.00 0.00 36.63 2.62
2446 7949 2.290071 ACGGTCCACCTTCTGTTTATGG 60.290 50.000 0.00 0.00 0.00 2.74
2600 8105 1.305219 TAACAAGCCAGCCACATCGC 61.305 55.000 0.00 0.00 0.00 4.58
2609 8114 6.352516 ACTCCTAATTGATCTAACAAGCCAG 58.647 40.000 0.00 0.00 33.22 4.85
2817 8322 9.681692 GCATGTTATTATGACATAAGCATTCAA 57.318 29.630 13.15 0.00 36.04 2.69
2878 8383 8.685838 AAATACTTTTGACTTACTGCAACCTA 57.314 30.769 0.00 0.00 0.00 3.08
3324 8834 5.011586 TCAGAAAGGCATTTGACATGATCA 58.988 37.500 0.00 0.00 34.65 2.92
3466 8985 6.349944 GGGATGAAATATCTTGCAATGCTAGG 60.350 42.308 15.92 2.02 32.69 3.02
3518 9037 7.325097 GCTGAGCTAAACTACGAAGATCTATTC 59.675 40.741 0.00 0.00 0.00 1.75
3529 9048 2.408704 GTGTGTGCTGAGCTAAACTACG 59.591 50.000 5.83 0.00 0.00 3.51
3596 9115 2.849943 TGGGTATCTGGCCACTACAAAT 59.150 45.455 18.12 3.18 0.00 2.32
3603 9122 2.435372 TTGAATGGGTATCTGGCCAC 57.565 50.000 0.00 0.00 0.00 5.01
3673 9317 7.053498 TGTAGGTATGCATGTAACATGTGATT 58.947 34.615 10.16 0.00 0.00 2.57
3703 9350 6.267471 ACAACTTGTGATTGATTGGGTATGTT 59.733 34.615 0.00 0.00 0.00 2.71
3819 9468 4.916424 AGCTCCTATCCCCAAATGATTAGT 59.084 41.667 0.00 0.00 0.00 2.24
3820 9469 5.511386 AGCTCCTATCCCCAAATGATTAG 57.489 43.478 0.00 0.00 0.00 1.73
3821 9470 6.562608 ACTTAGCTCCTATCCCCAAATGATTA 59.437 38.462 0.00 0.00 0.00 1.75
3822 9471 5.373854 ACTTAGCTCCTATCCCCAAATGATT 59.626 40.000 0.00 0.00 0.00 2.57
3823 9472 4.916424 ACTTAGCTCCTATCCCCAAATGAT 59.084 41.667 0.00 0.00 0.00 2.45
3824 9473 4.307259 ACTTAGCTCCTATCCCCAAATGA 58.693 43.478 0.00 0.00 0.00 2.57
3825 9474 4.713792 ACTTAGCTCCTATCCCCAAATG 57.286 45.455 0.00 0.00 0.00 2.32
3829 9494 6.841781 AAATTTACTTAGCTCCTATCCCCA 57.158 37.500 0.00 0.00 0.00 4.96
3881 9548 7.390440 TCTCCAAGTTTTGAACATCGACAATAT 59.610 33.333 0.00 0.00 0.00 1.28
3921 9604 5.009710 TCTCATTGTCTACAACTCAGAACGT 59.990 40.000 0.00 0.00 38.86 3.99
3922 9605 5.461526 TCTCATTGTCTACAACTCAGAACG 58.538 41.667 0.00 0.00 38.86 3.95
4014 9698 5.484715 CAACTATCTCGGGGTGTAAGAAAA 58.515 41.667 0.00 0.00 0.00 2.29
4015 9699 4.081309 CCAACTATCTCGGGGTGTAAGAAA 60.081 45.833 0.00 0.00 0.00 2.52
4050 9737 6.528537 TGCACCACTGATAAAATTTAGCAT 57.471 33.333 4.06 0.00 0.00 3.79
4061 9748 2.093500 GTGTGAGGATGCACCACTGATA 60.093 50.000 10.18 0.00 42.04 2.15
4093 9780 2.639286 GCAGCCAACAACCTGTCG 59.361 61.111 0.00 0.00 0.00 4.35
4187 9876 8.475639 TGTAGAATTATCTGTCTTCCCAACTAC 58.524 37.037 0.00 0.00 37.10 2.73
4263 9952 7.663664 CATATACGAATTCAGTACAATACGCC 58.336 38.462 6.22 0.00 0.00 5.68
4628 10494 5.477984 CCTCATTCTCACCAAGGAAAATTCA 59.522 40.000 0.00 0.00 0.00 2.57
4634 10500 2.305927 GGACCTCATTCTCACCAAGGAA 59.694 50.000 0.00 0.00 0.00 3.36
4725 10612 8.367911 ACATGTTTCTCAAGAGTATCAACTGTA 58.632 33.333 0.00 0.00 37.82 2.74
4839 10863 5.165961 AGGCTTTCACTGCTATCAAAGTA 57.834 39.130 0.00 0.00 0.00 2.24
4845 10869 6.975197 GGAAAATAAAGGCTTTCACTGCTATC 59.025 38.462 17.13 5.55 33.96 2.08
4975 11625 8.470002 GGAAATTTTTCAGCTGAACCATAGTAT 58.530 33.333 28.46 10.25 38.92 2.12
4976 11626 7.450014 TGGAAATTTTTCAGCTGAACCATAGTA 59.550 33.333 28.46 9.66 38.92 1.82
5056 11715 3.005554 AGGAAGTCAATGATCTGCAACG 58.994 45.455 0.00 0.00 0.00 4.10
5299 11965 2.093235 AGTGCATAGGAGAAGCTTCCAC 60.093 50.000 22.81 19.42 39.84 4.02
5515 12575 6.429385 GCCATAAATCTCCAGAGAAATACCAG 59.571 42.308 0.66 0.00 41.36 4.00
5572 12635 4.798882 TCCTTACACAACTGTTTTGGGAT 58.201 39.130 11.02 0.00 0.00 3.85
5678 13491 7.617041 ACTTTGCCTAGAAGACATGAAATAC 57.383 36.000 0.00 0.00 0.00 1.89
5715 13528 0.179062 GGCCGCATCTCAGAAGACAT 60.179 55.000 0.00 0.00 33.32 3.06
5765 13579 9.719355 AAGGCGGAATGTAAGAAATTTAAAATT 57.281 25.926 0.00 0.00 0.00 1.82
5830 13648 2.180276 AGAAGGGTTATCGCAGTGACT 58.820 47.619 0.00 0.00 0.00 3.41
5926 13746 6.094048 GTGAAGGATCGAATGAAAAGATTCCA 59.906 38.462 0.00 0.00 34.49 3.53
5930 13750 6.881065 TGAAGTGAAGGATCGAATGAAAAGAT 59.119 34.615 0.00 0.00 0.00 2.40
5934 13754 5.355071 CCATGAAGTGAAGGATCGAATGAAA 59.645 40.000 0.00 0.00 0.00 2.69
5937 13757 4.445453 TCCATGAAGTGAAGGATCGAATG 58.555 43.478 0.00 0.00 0.00 2.67
5941 13761 4.128925 TCTTCCATGAAGTGAAGGATCG 57.871 45.455 8.88 0.00 40.24 3.69
5986 13809 4.335315 GGTCATTCGATGTCATTGCCTTTA 59.665 41.667 0.00 0.00 0.00 1.85
6119 14096 7.669427 TGCATTTCTTCCAAAATGTATGAACT 58.331 30.769 10.14 0.00 44.72 3.01
6293 14280 7.288810 AGAATTAATGCAAGGTGAAGTTTGA 57.711 32.000 0.00 0.00 0.00 2.69
6319 14306 1.061546 GTTGTAGGGTGGGGACTCAA 58.938 55.000 0.00 0.00 0.00 3.02
6385 14373 3.441222 TGCTTGACTTGTATTCCTGCATG 59.559 43.478 0.00 0.00 0.00 4.06
6389 14377 4.012374 ACCATGCTTGACTTGTATTCCTG 58.988 43.478 0.22 0.00 0.00 3.86
6396 14384 7.394359 AGAATACAATTACCATGCTTGACTTGT 59.606 33.333 0.22 7.47 0.00 3.16
6626 14618 2.292267 CTGGATGACTGTAATGGCACC 58.708 52.381 0.00 0.00 0.00 5.01
6640 14632 6.973843 TCTGAAACAATTGAAAGACTGGATG 58.026 36.000 13.59 0.00 0.00 3.51
6670 14662 1.208293 CAAGTAGGCTCTCCAGGAACC 59.792 57.143 0.00 0.00 33.74 3.62
6723 14715 3.895232 ACTCCAAAGTGCATATCGAGT 57.105 42.857 0.00 0.00 33.32 4.18
6759 14751 2.553602 CAGTATCTTGCACTTGTGCCAA 59.446 45.455 21.01 14.24 0.00 4.52
6775 14767 2.496470 GACGAGGAGTTCAACCCAGTAT 59.504 50.000 0.00 0.00 0.00 2.12
6776 14768 1.891150 GACGAGGAGTTCAACCCAGTA 59.109 52.381 0.00 0.00 0.00 2.74
6803 14795 2.429250 TGAGAACAGAGACACAAACCGA 59.571 45.455 0.00 0.00 0.00 4.69
6854 14846 0.247460 CATCAACCGCCTGACTCTCA 59.753 55.000 0.00 0.00 0.00 3.27
6865 14857 5.107065 GGTGTTAACTTCTCTTCATCAACCG 60.107 44.000 7.22 0.00 0.00 4.44
6999 14998 1.338200 GCCGAGATGTATCCCACCATC 60.338 57.143 0.00 0.00 38.17 3.51
7003 15002 0.601311 GCTGCCGAGATGTATCCCAC 60.601 60.000 0.00 0.00 0.00 4.61
7102 15101 0.906756 CCTGGGAGGACTTCTGCTCA 60.907 60.000 0.00 0.00 37.67 4.26
7106 15105 1.492133 TTGCCCTGGGAGGACTTCTG 61.492 60.000 19.27 0.00 37.67 3.02
7165 15164 2.032528 CGGAGCACCTTCTGGCAA 59.967 61.111 0.00 0.00 36.63 4.52
7271 15272 2.084546 GACTCCCGGTTCCAAAATCAG 58.915 52.381 0.00 0.00 0.00 2.90
7341 15825 4.689983 GCCCCTAGTTAATCTCCATTTGCT 60.690 45.833 0.00 0.00 0.00 3.91
7344 15828 5.388654 CATGCCCCTAGTTAATCTCCATTT 58.611 41.667 0.00 0.00 0.00 2.32
7417 15993 1.227973 GCAATCGGACATCTCCCCC 60.228 63.158 0.00 0.00 31.93 5.40
7589 16542 5.278022 CCAGTCAAAGAGGCTACAGTTTTTC 60.278 44.000 0.00 0.00 0.00 2.29
7858 18966 2.439507 AGAAAGACCAGTCCTGCTTCAA 59.560 45.455 0.00 0.00 0.00 2.69
7953 19075 7.398829 ACCCAACTCAAAAACCTAAATTGTTT 58.601 30.769 0.00 0.00 37.52 2.83
7999 19146 0.944386 AACTGCCACACGAACATGAC 59.056 50.000 0.00 0.00 0.00 3.06
8008 19156 4.024387 TGAATAACTCGAAAACTGCCACAC 60.024 41.667 0.00 0.00 0.00 3.82
8056 19209 2.625823 CGAACAACCATTGCCGCCT 61.626 57.895 0.00 0.00 0.00 5.52
8069 19222 1.628340 AGATTCATGGACCACCGAACA 59.372 47.619 9.75 0.00 39.42 3.18
8109 19268 8.617290 AAGATTCACCGAAAGTATAAAACACT 57.383 30.769 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.