Multiple sequence alignment - TraesCS1B01G185400

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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 TraesCS1B01G185400 chr1B 100.000 6350 0 0 1 6350 332162064 332155715 0.000000e+00 11727.0
1 TraesCS1B01G185400 chr1B 92.272 867 26 6 5498 6350 390431152 390430313 0.000000e+00 1192.0
2 TraesCS1B01G185400 chr1B 92.378 328 5 6 5500 5813 169943132 169942811 3.490000e-122 449.0
3 TraesCS1B01G185400 chr1B 91.870 246 6 4 5499 5730 332152948 332153193 1.320000e-86 331.0
4 TraesCS1B01G185400 chr1B 90.244 246 9 5 5499 5730 390428945 390429189 2.220000e-79 307.0
5 TraesCS1B01G185400 chr1B 94.118 68 3 1 3891 3958 211322988 211323054 1.130000e-17 102.0
6 TraesCS1B01G185400 chr1B 94.118 68 3 1 3891 3958 319127190 319127256 1.130000e-17 102.0
7 TraesCS1B01G185400 chr1A 92.613 2667 147 24 2791 5429 306641089 306643733 0.000000e+00 3788.0
8 TraesCS1B01G185400 chr1A 91.167 1551 72 16 735 2284 306639201 306640687 0.000000e+00 2045.0
9 TraesCS1B01G185400 chr1A 93.253 667 23 9 16 665 306637343 306638004 0.000000e+00 963.0
10 TraesCS1B01G185400 chr1A 91.617 334 13 5 5495 5813 483640001 483640334 1.260000e-121 448.0
11 TraesCS1B01G185400 chr1A 91.358 243 14 6 2507 2743 306640850 306641091 6.140000e-85 326.0
12 TraesCS1B01G185400 chr1A 95.567 203 8 1 2321 2522 306640690 306640892 2.210000e-84 324.0
13 TraesCS1B01G185400 chr1A 97.222 72 2 0 5428 5499 306643936 306644007 8.650000e-24 122.0
14 TraesCS1B01G185400 chr1D 92.245 2682 141 30 2791 5429 245979356 245982013 0.000000e+00 3738.0
15 TraesCS1B01G185400 chr1D 92.107 2420 100 24 16 2416 245972690 245975037 0.000000e+00 3326.0
16 TraesCS1B01G185400 chr1D 91.667 240 16 3 2507 2743 245979120 245979358 4.750000e-86 329.0
17 TraesCS1B01G185400 chr1D 96.262 107 3 1 2412 2517 245979051 245979157 2.350000e-39 174.0
18 TraesCS1B01G185400 chr1D 100.000 72 0 0 5428 5499 245982210 245982281 3.990000e-27 134.0
19 TraesCS1B01G185400 chr6B 95.732 867 22 5 5498 6350 631946881 631947746 0.000000e+00 1382.0
20 TraesCS1B01G185400 chr6B 85.871 1182 116 30 4266 5412 119128480 119129645 0.000000e+00 1210.0
21 TraesCS1B01G185400 chr6B 86.660 1057 92 18 2591 3642 119126939 119127951 0.000000e+00 1125.0
22 TraesCS1B01G185400 chr6B 85.181 857 81 22 1267 2107 119125894 119126720 0.000000e+00 837.0
23 TraesCS1B01G185400 chr6B 93.950 281 17 0 3609 3889 119127947 119128227 5.880000e-115 425.0
24 TraesCS1B01G185400 chr6B 87.031 293 28 7 962 1254 119125511 119125793 7.940000e-84 322.0
25 TraesCS1B01G185400 chr6B 87.008 254 20 6 3977 4227 119128241 119128484 2.260000e-69 274.0
26 TraesCS1B01G185400 chr6B 91.979 187 11 3 2276 2461 22426960 22427143 6.320000e-65 259.0
27 TraesCS1B01G185400 chr6A 86.468 1175 115 27 4266 5412 63118956 63120114 0.000000e+00 1249.0
28 TraesCS1B01G185400 chr6A 87.996 1058 84 21 2591 3642 63117401 63118421 0.000000e+00 1210.0
29 TraesCS1B01G185400 chr6A 85.000 600 59 20 962 1542 63116697 63117284 1.190000e-161 580.0
30 TraesCS1B01G185400 chr6A 92.883 281 20 0 3609 3889 63118417 63118697 5.930000e-110 409.0
31 TraesCS1B01G185400 chr6D 86.283 1181 112 32 4266 5412 52339429 52340593 0.000000e+00 1238.0
32 TraesCS1B01G185400 chr6D 87.879 1056 85 20 2591 3642 52337884 52338900 0.000000e+00 1201.0
33 TraesCS1B01G185400 chr6D 85.592 1173 121 21 962 2107 52336518 52337669 0.000000e+00 1186.0
34 TraesCS1B01G185400 chr6D 93.238 281 19 0 3609 3889 52338896 52339176 1.270000e-111 414.0
35 TraesCS1B01G185400 chr3B 95.971 546 19 1 5808 6350 250146231 250145686 0.000000e+00 883.0
36 TraesCS1B01G185400 chr3B 92.513 187 10 2 2276 2461 201514117 201514300 1.360000e-66 265.0
37 TraesCS1B01G185400 chr3B 92.513 187 10 2 2276 2461 201515696 201515879 1.360000e-66 265.0
38 TraesCS1B01G185400 chr3B 91.979 187 11 2 2276 2461 201514654 201514837 6.320000e-65 259.0
39 TraesCS1B01G185400 chr3B 92.778 180 10 1 2282 2461 201515173 201515349 2.270000e-64 257.0
40 TraesCS1B01G185400 chr3B 94.118 68 4 0 3891 3958 438545824 438545757 3.130000e-18 104.0
41 TraesCS1B01G185400 chr3D 94.843 543 25 1 5808 6350 171152667 171152128 0.000000e+00 845.0
42 TraesCS1B01G185400 chr3D 87.946 224 12 2 5499 5708 143611218 143611440 3.800000e-62 250.0
43 TraesCS1B01G185400 chr3A 93.923 543 33 0 5808 6350 208737288 208736746 0.000000e+00 821.0
44 TraesCS1B01G185400 chr3A 95.588 68 3 0 3891 3958 215955020 215955087 6.730000e-20 110.0
45 TraesCS1B01G185400 chr5B 93.921 329 6 4 5499 5813 704280064 704279736 9.570000e-133 484.0
46 TraesCS1B01G185400 chr5B 90.909 88 8 0 5727 5814 667839350 667839437 1.120000e-22 119.0
47 TraesCS1B01G185400 chr5B 94.118 68 3 1 3891 3958 347653276 347653342 1.130000e-17 102.0
48 TraesCS1B01G185400 chr4B 93.114 334 8 5 5495 5813 175550662 175550329 5.760000e-130 475.0
49 TraesCS1B01G185400 chr4B 93.248 311 6 5 5499 5795 564199608 564199299 1.620000e-120 444.0
50 TraesCS1B01G185400 chr4B 91.837 245 6 2 5500 5730 564197113 564197357 4.750000e-86 329.0
51 TraesCS1B01G185400 chr4A 91.870 246 6 1 5499 5730 321128521 321128766 1.320000e-86 331.0
52 TraesCS1B01G185400 chr7B 92.513 187 10 2 2276 2461 45215173 45214990 1.360000e-66 265.0
53 TraesCS1B01G185400 chrUn 91.979 187 11 2 2276 2461 445812047 445811864 6.320000e-65 259.0
54 TraesCS1B01G185400 chr2A 84.871 271 20 6 5479 5730 73282790 73282522 2.940000e-63 254.0
55 TraesCS1B01G185400 chr5D 100.000 87 0 0 5727 5813 529257605 529257691 1.830000e-35 161.0
56 TraesCS1B01G185400 chr5D 94.118 68 3 1 3891 3958 284895003 284895069 1.130000e-17 102.0
57 TraesCS1B01G185400 chr2B 95.588 68 3 0 3891 3958 166470833 166470900 6.730000e-20 110.0
58 TraesCS1B01G185400 chr2D 96.296 54 2 0 423 476 6838258 6838205 8.770000e-14 89.8


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 TraesCS1B01G185400 chr1B 332155715 332162064 6349 True 11727.000000 11727 100.000000 1 6350 1 chr1B.!!$R2 6349
1 TraesCS1B01G185400 chr1B 390430313 390431152 839 True 1192.000000 1192 92.272000 5498 6350 1 chr1B.!!$R3 852
2 TraesCS1B01G185400 chr1A 306637343 306644007 6664 False 1261.333333 3788 93.530000 16 5499 6 chr1A.!!$F2 5483
3 TraesCS1B01G185400 chr1D 245972690 245975037 2347 False 3326.000000 3326 92.107000 16 2416 1 chr1D.!!$F1 2400
4 TraesCS1B01G185400 chr1D 245979051 245982281 3230 False 1093.750000 3738 95.043500 2412 5499 4 chr1D.!!$F2 3087
5 TraesCS1B01G185400 chr6B 631946881 631947746 865 False 1382.000000 1382 95.732000 5498 6350 1 chr6B.!!$F2 852
6 TraesCS1B01G185400 chr6B 119125511 119129645 4134 False 698.833333 1210 87.616833 962 5412 6 chr6B.!!$F3 4450
7 TraesCS1B01G185400 chr6A 63116697 63120114 3417 False 862.000000 1249 88.086750 962 5412 4 chr6A.!!$F1 4450
8 TraesCS1B01G185400 chr6D 52336518 52340593 4075 False 1009.750000 1238 88.248000 962 5412 4 chr6D.!!$F1 4450
9 TraesCS1B01G185400 chr3B 250145686 250146231 545 True 883.000000 883 95.971000 5808 6350 1 chr3B.!!$R1 542
10 TraesCS1B01G185400 chr3B 201514117 201515879 1762 False 261.500000 265 92.445750 2276 2461 4 chr3B.!!$F1 185
11 TraesCS1B01G185400 chr3D 171152128 171152667 539 True 845.000000 845 94.843000 5808 6350 1 chr3D.!!$R1 542
12 TraesCS1B01G185400 chr3A 208736746 208737288 542 True 821.000000 821 93.923000 5808 6350 1 chr3A.!!$R1 542

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
341 350 0.603975 GGTCGAAGGAGCAAGCAACT 60.604 55.0 0.00 0.00 40.40 3.16 F
1240 2395 0.399949 TCCCTGTCACCTGTCCACTT 60.400 55.0 0.00 0.00 0.00 3.16 F
1647 2901 0.463620 GCTGGTTTTGGCAGGTTCAA 59.536 50.0 0.00 0.00 0.00 2.69 F
2715 4050 0.984995 GACCCTTCTACAGGCCTGTT 59.015 55.0 41.69 23.39 41.83 3.16 F
4291 5699 0.034756 TGGACATCATTATCCGCCCG 59.965 55.0 0.00 0.00 37.87 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 2990 0.323178 CTTGGCACTTGAGGCATCCT 60.323 55.000 0.00 0.0 44.02 3.24 R
2887 4236 1.247567 AAGAATTGGTTGGCCTCGTG 58.752 50.000 3.32 0.0 35.27 4.35 R
2926 4275 3.737559 AGGACTGCCAACATGGATAAA 57.262 42.857 0.00 0.0 40.96 1.40 R
4387 5806 0.179215 GTCAGCGAGGCATCAAAACG 60.179 55.000 0.00 0.0 0.00 3.60 R
5959 7629 1.304381 GTGATGGGGCTGGAAAGCA 60.304 57.895 0.00 0.0 36.33 3.91 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
54 55 4.155733 CGCCCTATGTGCGTCCCA 62.156 66.667 0.00 0.00 46.59 4.37
62 63 4.314440 GTGCGTCCCACTGCTCCA 62.314 66.667 0.00 0.00 41.35 3.86
236 245 2.192861 CCGGCTGGTTGTTGCAAGA 61.193 57.895 2.29 0.00 0.00 3.02
237 246 1.732917 CGGCTGGTTGTTGCAAGAA 59.267 52.632 4.66 4.66 0.00 2.52
341 350 0.603975 GGTCGAAGGAGCAAGCAACT 60.604 55.000 0.00 0.00 40.40 3.16
644 666 7.064966 TCACAATGATATGTTTAGTGCAGTCAG 59.935 37.037 0.00 0.00 0.00 3.51
650 672 1.135575 GTTTAGTGCAGTCAGCCATGC 60.136 52.381 0.00 0.00 44.83 4.06
719 1854 7.540400 TGTTTCACGTAAAATTAGCAATGATGG 59.460 33.333 0.00 0.00 0.00 3.51
753 1902 7.012704 GCCAATTTCAAGAAGAGCATATCTGTA 59.987 37.037 0.00 0.00 38.67 2.74
803 1952 5.202765 TGGTCATTCCGGTGTATTCTAGTA 58.797 41.667 0.00 0.00 39.52 1.82
831 1980 4.645588 GGAGCACTAGATACTGGTACTTGT 59.354 45.833 0.00 0.00 0.00 3.16
832 1981 5.221087 GGAGCACTAGATACTGGTACTTGTC 60.221 48.000 0.00 0.00 0.00 3.18
852 2001 7.891183 ACTTGTCCAACAATACCCATGTATTAA 59.109 33.333 0.00 0.00 44.06 1.40
924 2073 7.118101 GCATATTTTGCCTTCAGTTTGAAATCA 59.882 33.333 0.00 0.00 46.15 2.57
927 2076 3.225104 TGCCTTCAGTTTGAAATCAGCT 58.775 40.909 0.00 0.00 35.73 4.24
1023 2172 2.112198 GTCATTTCCGCCGCATCCA 61.112 57.895 0.00 0.00 0.00 3.41
1191 2346 1.956170 CTATGGCGCCACATCCGTC 60.956 63.158 35.50 0.00 32.39 4.79
1240 2395 0.399949 TCCCTGTCACCTGTCCACTT 60.400 55.000 0.00 0.00 0.00 3.16
1314 2557 5.523438 AGCTAGCAGAGTTCCTTATGTAC 57.477 43.478 18.83 0.00 0.00 2.90
1358 2603 3.196685 AGGTCTACTGAGATTTGTCTGCC 59.803 47.826 0.00 0.00 33.14 4.85
1505 2758 3.264450 CAGGTTCCTTCCCTCAAGTACAT 59.736 47.826 0.00 0.00 0.00 2.29
1506 2759 4.469945 CAGGTTCCTTCCCTCAAGTACATA 59.530 45.833 0.00 0.00 0.00 2.29
1530 2783 7.602517 ACTCTGCTTGATTAGTTGTACATTC 57.397 36.000 0.00 0.00 0.00 2.67
1545 2798 6.525121 TGTACATTCTCTTTGTTCGAACTG 57.475 37.500 27.32 17.03 0.00 3.16
1546 2799 4.474226 ACATTCTCTTTGTTCGAACTGC 57.526 40.909 27.32 3.51 0.00 4.40
1550 2803 2.158957 TCTCTTTGTTCGAACTGCCTGT 60.159 45.455 27.32 0.00 0.00 4.00
1606 2859 6.898041 TGTGAATTTCTGTCCTTCGTTATTG 58.102 36.000 0.00 0.00 0.00 1.90
1647 2901 0.463620 GCTGGTTTTGGCAGGTTCAA 59.536 50.000 0.00 0.00 0.00 2.69
1685 2939 3.759086 ACTGATAGTCGAGAGAGCAAACA 59.241 43.478 0.00 0.00 43.49 2.83
1736 2990 3.432749 GCATCAGGAGGAATTAGCTCACA 60.433 47.826 0.00 0.00 0.00 3.58
1859 3115 7.301420 TCCTCCTCATCTTGAGTATGTTATCT 58.699 38.462 4.00 0.00 42.80 1.98
1867 3123 7.348080 TCTTGAGTATGTTATCTCCATCGTT 57.652 36.000 0.00 0.00 0.00 3.85
1877 3133 6.429692 TGTTATCTCCATCGTTGTTGTTTCAT 59.570 34.615 0.00 0.00 0.00 2.57
1932 3200 5.647658 TGAGTTATGACCACTTAAGCCATTG 59.352 40.000 1.29 0.00 0.00 2.82
1980 3253 8.165239 TGTGTTATTAGAAATGAAGCTGTTGT 57.835 30.769 0.00 0.00 0.00 3.32
1991 3264 4.858935 TGAAGCTGTTGTCTGCAAAATAC 58.141 39.130 0.00 0.00 40.25 1.89
2022 3295 1.793532 CTGAAGATGCGAGCTGCTATG 59.206 52.381 0.15 0.00 46.63 2.23
2058 3331 7.603024 ACCTTTGTATTTGTAGTACTCTTCTGC 59.397 37.037 0.00 0.00 0.00 4.26
2087 3360 2.897271 TAAGGCACCCACACATTCAT 57.103 45.000 0.00 0.00 0.00 2.57
2115 3439 2.972713 AGTTTGACCAAGAGCTAGACCA 59.027 45.455 0.00 0.00 0.00 4.02
2257 3581 3.880490 TGTGTGGGCGCCTTATATAAAAG 59.120 43.478 28.56 0.00 0.00 2.27
2267 3591 5.408604 CGCCTTATATAAAAGTGCCTGGTAG 59.591 44.000 0.00 0.00 0.00 3.18
2271 3595 9.490379 CCTTATATAAAAGTGCCTGGTAGTAAG 57.510 37.037 0.00 0.00 0.00 2.34
2280 3604 5.727766 AGTGCCTGGTAGTAAGGGTATTTTA 59.272 40.000 0.00 0.00 35.17 1.52
2317 3641 6.003950 CAGATGGGGAGACTTCAAACTTAAA 58.996 40.000 0.00 0.00 0.00 1.52
2318 3642 6.150140 CAGATGGGGAGACTTCAAACTTAAAG 59.850 42.308 0.00 0.00 0.00 1.85
2319 3643 5.382664 TGGGGAGACTTCAAACTTAAAGT 57.617 39.130 0.00 0.00 38.40 2.66
2333 3657 7.330208 TCAAACTTAAAGTATTAGTCTCCGTGC 59.670 37.037 0.00 0.00 0.00 5.34
2376 3700 2.297701 GTTGAGAGAGTTGCCCAAACA 58.702 47.619 0.00 0.00 41.61 2.83
2416 3740 6.358991 ACCCAGTAAAGCTTACAAGTAAACA 58.641 36.000 0.00 0.00 0.00 2.83
2488 3812 4.030913 CAAGGGTAAGATGACCTGGTCTA 58.969 47.826 26.03 13.79 39.66 2.59
2489 3813 4.561254 AGGGTAAGATGACCTGGTCTAT 57.439 45.455 26.03 17.53 39.66 1.98
2490 3814 4.897051 AGGGTAAGATGACCTGGTCTATT 58.103 43.478 26.03 18.88 39.66 1.73
2491 3815 4.902448 AGGGTAAGATGACCTGGTCTATTC 59.098 45.833 26.03 18.96 39.66 1.75
2492 3816 4.902448 GGGTAAGATGACCTGGTCTATTCT 59.098 45.833 26.03 20.60 39.66 2.40
2493 3817 6.075984 GGGTAAGATGACCTGGTCTATTCTA 58.924 44.000 26.03 6.57 39.66 2.10
2494 3818 6.726764 GGGTAAGATGACCTGGTCTATTCTAT 59.273 42.308 26.03 11.19 39.66 1.98
2495 3819 7.235812 GGGTAAGATGACCTGGTCTATTCTATT 59.764 40.741 26.03 13.68 39.66 1.73
2496 3820 8.652290 GGTAAGATGACCTGGTCTATTCTATTT 58.348 37.037 26.03 13.12 36.47 1.40
2498 3822 8.970859 AAGATGACCTGGTCTATTCTATTTTG 57.029 34.615 26.03 0.00 33.15 2.44
2499 3823 8.324191 AGATGACCTGGTCTATTCTATTTTGA 57.676 34.615 26.03 2.90 33.15 2.69
2500 3824 8.428063 AGATGACCTGGTCTATTCTATTTTGAG 58.572 37.037 26.03 0.00 33.15 3.02
2501 3825 6.889198 TGACCTGGTCTATTCTATTTTGAGG 58.111 40.000 26.03 0.00 33.15 3.86
2502 3826 6.126768 TGACCTGGTCTATTCTATTTTGAGGG 60.127 42.308 26.03 0.00 33.15 4.30
2503 3827 5.970640 ACCTGGTCTATTCTATTTTGAGGGA 59.029 40.000 0.00 0.00 0.00 4.20
2504 3828 6.447084 ACCTGGTCTATTCTATTTTGAGGGAA 59.553 38.462 0.00 0.00 0.00 3.97
2505 3829 7.129504 ACCTGGTCTATTCTATTTTGAGGGAAT 59.870 37.037 0.00 0.00 33.69 3.01
2506 3830 7.663493 CCTGGTCTATTCTATTTTGAGGGAATC 59.337 40.741 0.00 0.00 31.89 2.52
2507 3831 7.518188 TGGTCTATTCTATTTTGAGGGAATCC 58.482 38.462 0.00 0.00 31.89 3.01
2509 3833 7.663493 GGTCTATTCTATTTTGAGGGAATCCTG 59.337 40.741 0.00 0.00 45.05 3.86
2510 3834 7.663493 GTCTATTCTATTTTGAGGGAATCCTGG 59.337 40.741 0.00 0.00 45.05 4.45
2511 3835 5.796502 TTCTATTTTGAGGGAATCCTGGT 57.203 39.130 0.00 0.00 45.05 4.00
2512 3836 5.373812 TCTATTTTGAGGGAATCCTGGTC 57.626 43.478 0.00 0.00 45.05 4.02
2652 3984 4.363999 CCCGTTTCAACAAAATGCTTGTA 58.636 39.130 0.00 0.00 33.28 2.41
2665 3997 8.239314 ACAAAATGCTTGTATGTATGAGAAGTG 58.761 33.333 0.00 0.00 0.00 3.16
2691 4024 4.833390 AGCTCAATTTACCACTACTGGAC 58.167 43.478 0.00 0.00 40.55 4.02
2715 4050 0.984995 GACCCTTCTACAGGCCTGTT 59.015 55.000 41.69 23.39 41.83 3.16
2764 4099 8.313292 GGCCAATTTGCTTATATTATCCAATCA 58.687 33.333 0.00 0.00 0.00 2.57
2773 4108 9.658799 GCTTATATTATCCAATCAGAAGTAGCA 57.341 33.333 0.00 0.00 0.00 3.49
2797 4132 7.373493 CAAAATCAATCTAGCAAACCACTTCT 58.627 34.615 0.00 0.00 0.00 2.85
2801 4136 6.240894 TCAATCTAGCAAACCACTTCTGAAT 58.759 36.000 0.00 0.00 0.00 2.57
2869 4218 3.319405 ACTCCATACTCCATACTTCTGCG 59.681 47.826 0.00 0.00 0.00 5.18
2887 4236 4.394920 TCTGCGATGTTTCATAGTTTTCCC 59.605 41.667 0.00 0.00 0.00 3.97
2907 4256 2.432444 CACGAGGCCAACCAATTCTTA 58.568 47.619 5.01 0.00 39.06 2.10
2926 4275 6.047511 TCTTATCTGCAGAAGCTCTTTCTT 57.952 37.500 22.50 2.10 43.68 2.52
2969 4318 6.989169 CCTAATCCACCATCTTACTTGAGAAG 59.011 42.308 0.00 0.00 0.00 2.85
2980 4329 8.660373 CATCTTACTTGAGAAGTGTGATTAACC 58.340 37.037 0.00 0.00 42.84 2.85
2981 4330 7.732025 TCTTACTTGAGAAGTGTGATTAACCA 58.268 34.615 0.00 0.00 42.84 3.67
2982 4331 8.375506 TCTTACTTGAGAAGTGTGATTAACCAT 58.624 33.333 0.00 0.00 42.84 3.55
2983 4332 9.653287 CTTACTTGAGAAGTGTGATTAACCATA 57.347 33.333 0.00 0.00 42.84 2.74
2984 4333 9.653287 TTACTTGAGAAGTGTGATTAACCATAG 57.347 33.333 0.00 0.00 42.84 2.23
3023 4372 0.843984 GGTATGCATACCCACCACCT 59.156 55.000 36.34 0.00 45.62 4.00
3083 4432 1.089112 CCGTTCCCCGATTTTACACC 58.911 55.000 0.00 0.00 39.56 4.16
3089 4438 1.680860 CCCCGATTTTACACCCAGGTC 60.681 57.143 0.00 0.00 0.00 3.85
3090 4439 1.680860 CCCGATTTTACACCCAGGTCC 60.681 57.143 0.00 0.00 0.00 4.46
3120 4469 3.364889 TCAACCTCGTGAACTACTGTG 57.635 47.619 0.00 0.00 0.00 3.66
3133 4482 1.457303 CTACTGTGACAGTTCGCAAGC 59.543 52.381 24.54 0.00 42.59 4.01
3134 4483 0.179073 ACTGTGACAGTTCGCAAGCT 60.179 50.000 13.33 0.00 42.59 3.74
3299 4649 4.675303 CCTCCCCCTCCACCACCA 62.675 72.222 0.00 0.00 0.00 4.17
3336 4686 5.182760 ACAGAGAAACTTCATTTGGCTGATC 59.817 40.000 0.00 0.00 34.46 2.92
3386 4736 3.587797 TCTGATGTTCGTACCACTTCC 57.412 47.619 0.00 0.00 0.00 3.46
3437 4787 5.609423 TCTTTGCCAAAAGTTTATGTGCAT 58.391 33.333 0.00 0.00 42.91 3.96
3443 4793 7.804712 TGCCAAAAGTTTATGTGCATTTTATG 58.195 30.769 0.00 0.00 0.00 1.90
3478 4831 4.002906 TGATACAAGGAAAGTCAAGCGT 57.997 40.909 0.00 0.00 0.00 5.07
3613 4994 1.136828 ACCCAGTACTGCAGGTGAAA 58.863 50.000 19.49 0.00 0.00 2.69
3760 5142 4.723789 AGGAATTGGCCTCTAGAGATGAAA 59.276 41.667 21.76 9.94 30.76 2.69
3813 5195 8.891720 CCTCAGGAAATAGAGAAAGAGAAATTG 58.108 37.037 0.00 0.00 33.74 2.32
3816 5198 7.121759 CAGGAAATAGAGAAAGAGAAATTGCCA 59.878 37.037 0.00 0.00 0.00 4.92
3875 5257 6.287107 AGACGAATTCAGTATTTTATGCCG 57.713 37.500 6.22 0.00 0.00 5.69
3918 5300 3.007614 TGTGTTTCAACTCTAGCCTACCC 59.992 47.826 0.00 0.00 0.00 3.69
4068 5456 9.764363 ATTACCAATACACAGTGTATGTATCAG 57.236 33.333 24.16 12.84 42.29 2.90
4213 5604 6.929606 GTGGTTGGGTCTATTATGTCACTATC 59.070 42.308 0.00 0.00 0.00 2.08
4226 5617 8.652810 TTATGTCACTATCACACAATGATCAG 57.347 34.615 0.09 0.00 45.52 2.90
4233 5624 2.681344 TCACACAATGATCAGCTGATGC 59.319 45.455 33.33 22.71 34.37 3.91
4234 5625 2.422127 CACACAATGATCAGCTGATGCA 59.578 45.455 33.33 26.88 42.74 3.96
4235 5626 3.066760 CACACAATGATCAGCTGATGCAT 59.933 43.478 33.33 27.70 42.74 3.96
4236 5627 3.699538 ACACAATGATCAGCTGATGCATT 59.300 39.130 33.33 30.71 42.74 3.56
4237 5628 4.044426 CACAATGATCAGCTGATGCATTG 58.956 43.478 39.32 39.32 44.36 2.82
4291 5699 0.034756 TGGACATCATTATCCGCCCG 59.965 55.000 0.00 0.00 37.87 6.13
4293 5701 1.274167 GGACATCATTATCCGCCCGTA 59.726 52.381 0.00 0.00 0.00 4.02
4354 5770 5.070685 AGTCAAGACTTACAAAATGTCCCC 58.929 41.667 0.00 0.00 38.83 4.81
4410 5829 0.950555 TTGATGCCTCGCTGACACAC 60.951 55.000 0.00 0.00 0.00 3.82
4525 5944 8.596781 ACTTCTACTATGTCTTTGGTATGACT 57.403 34.615 0.00 0.00 34.57 3.41
4573 6000 5.970317 TGAAATGTTGATTCTGCACATCT 57.030 34.783 3.38 0.00 0.00 2.90
4638 6065 3.554934 ACAGGATCTGTGTTTGAAAGCA 58.445 40.909 0.00 0.00 43.63 3.91
4670 6097 7.362056 GCTGCAAGATCTGGTTTAAGTATCAAA 60.362 37.037 0.00 0.00 34.07 2.69
4722 6151 8.789825 ATTTTGCTTGTGCCATGATTATAAAA 57.210 26.923 0.00 0.00 38.71 1.52
4723 6152 7.593875 TTTGCTTGTGCCATGATTATAAAAC 57.406 32.000 0.00 0.00 38.71 2.43
4725 6154 6.331845 TGCTTGTGCCATGATTATAAAACAG 58.668 36.000 0.00 0.00 38.71 3.16
4726 6155 5.750067 GCTTGTGCCATGATTATAAAACAGG 59.250 40.000 0.00 0.00 0.00 4.00
4727 6156 5.850557 TGTGCCATGATTATAAAACAGGG 57.149 39.130 16.83 16.83 38.31 4.45
4773 6210 1.376543 ATGATGTTCCTTGCTCTGCG 58.623 50.000 0.00 0.00 0.00 5.18
4781 6218 1.301244 CTTGCTCTGCGTCTGTGGT 60.301 57.895 0.00 0.00 0.00 4.16
4797 6234 6.149633 GTCTGTGGTTCATGGTGAAAATTAC 58.850 40.000 0.00 0.00 38.22 1.89
4810 6247 5.123979 GGTGAAAATTACCGAGAAAGCTGAT 59.876 40.000 0.00 0.00 0.00 2.90
4817 6254 2.549754 ACCGAGAAAGCTGATGTTTGTG 59.450 45.455 0.00 0.00 0.00 3.33
4829 6267 4.464947 TGATGTTTGTGTTGGACCACATA 58.535 39.130 0.00 0.00 44.32 2.29
4833 6271 5.411781 TGTTTGTGTTGGACCACATAAAAC 58.588 37.500 15.35 17.18 44.32 2.43
4839 6277 6.149633 GTGTTGGACCACATAAAACAATCTC 58.850 40.000 0.00 0.00 35.38 2.75
4843 6281 4.770010 GGACCACATAAAACAATCTCCCAA 59.230 41.667 0.00 0.00 0.00 4.12
4887 6325 4.143473 GCGCATTGTTCTGTTTCTGAAATG 60.143 41.667 0.30 3.31 0.00 2.32
4910 6348 1.836166 CTGATCTTGCTCCAGGAAGGA 59.164 52.381 7.87 0.00 46.75 3.36
4958 6396 3.300009 GTTTCCATCTGTTGAACTTGCG 58.700 45.455 0.00 0.00 0.00 4.85
4961 6399 1.400629 CCATCTGTTGAACTTGCGCAG 60.401 52.381 11.31 7.81 0.00 5.18
4985 6423 1.671742 ACTGGTTAGTGACTGCCGG 59.328 57.895 13.07 13.07 35.34 6.13
5089 6530 1.059913 AAAGCTGCTCACTGTACCCT 58.940 50.000 1.00 0.00 0.00 4.34
5132 6575 8.035394 TCTGAAGTAGCAAAGTTATAAGACCAG 58.965 37.037 0.00 0.00 0.00 4.00
5154 6598 4.594491 AGAAAGGGAAAACATTGAATGCCT 59.406 37.500 4.84 0.21 0.00 4.75
5219 6670 8.457238 AATTCCTTATTATTCAGTCCTTGAGC 57.543 34.615 0.00 0.00 37.07 4.26
5241 6692 4.074970 CACCAGAAGTGCTAAAGAATGGT 58.925 43.478 0.00 0.00 40.28 3.55
5243 6694 4.074970 CCAGAAGTGCTAAAGAATGGTGT 58.925 43.478 0.00 0.00 0.00 4.16
5248 6699 4.980573 AGTGCTAAAGAATGGTGTGGTTA 58.019 39.130 0.00 0.00 0.00 2.85
5253 6704 5.648092 GCTAAAGAATGGTGTGGTTACTGAT 59.352 40.000 0.00 0.00 0.00 2.90
5254 6705 6.151144 GCTAAAGAATGGTGTGGTTACTGATT 59.849 38.462 0.00 0.00 0.00 2.57
5340 6791 1.875963 CCCTGCTGCTACCAAAACG 59.124 57.895 0.00 0.00 0.00 3.60
5392 6843 3.069289 CTGATGTGCTGTGAAGCTGTTA 58.931 45.455 0.00 0.00 35.49 2.41
5605 7261 1.845809 CTTGCGCACAGGGTTCACTC 61.846 60.000 11.12 0.00 0.00 3.51
5698 7368 5.769162 GTCGATCCTAGGGTGAATACTACTT 59.231 44.000 9.46 0.00 0.00 2.24
5976 7646 1.000521 CTGCTTTCCAGCCCCATCA 60.001 57.895 0.00 0.00 46.74 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.197790 CAGCCCATTCGCGGACAG 61.198 66.667 6.13 0.00 0.00 3.51
8 9 4.776322 CCAGCCCATTCGCGGACA 62.776 66.667 6.13 0.00 0.00 4.02
644 666 1.948145 CTTCTCTGAATCAGGCATGGC 59.052 52.381 12.14 12.14 31.51 4.40
650 672 8.256605 TCTTCATTACTTCTTCTCTGAATCAGG 58.743 37.037 10.71 1.52 31.51 3.86
688 710 8.912787 TTGCTAATTTTACGTGAAACAAGAAA 57.087 26.923 7.74 6.60 35.74 2.52
691 713 8.500837 TCATTGCTAATTTTACGTGAAACAAG 57.499 30.769 7.74 9.29 35.74 3.16
711 1846 8.890124 TGAAATTGGCAATTATACCATCATTG 57.110 30.769 24.58 0.00 35.42 2.82
719 1854 7.975616 TGCTCTTCTTGAAATTGGCAATTATAC 59.024 33.333 24.58 18.17 0.00 1.47
774 1923 2.227194 ACACCGGAATGACCAAAAGAC 58.773 47.619 9.46 0.00 38.90 3.01
803 1952 4.033709 ACCAGTATCTAGTGCTCCACATT 58.966 43.478 0.00 0.00 36.74 2.71
831 1980 9.922477 TTACATTAATACATGGGTATTGTTGGA 57.078 29.630 9.67 2.68 46.84 3.53
832 1981 9.959749 GTTACATTAATACATGGGTATTGTTGG 57.040 33.333 9.67 1.52 46.84 3.77
877 2026 7.599630 ATGCATGGAAATTCACAACATAAAC 57.400 32.000 0.00 0.00 0.00 2.01
924 2073 3.913107 AGCAACCAAGAGGGAGCT 58.087 55.556 0.00 0.00 43.36 4.09
927 2076 0.108585 GTGACAGCAACCAAGAGGGA 59.891 55.000 0.00 0.00 41.15 4.20
1023 2172 3.322466 CCGGGCAGTGGAGGAAGT 61.322 66.667 0.00 0.00 0.00 3.01
1240 2395 5.906113 TGTAAAACACCAAAGAAAGCAGA 57.094 34.783 0.00 0.00 0.00 4.26
1340 2585 2.544685 CGGGCAGACAAATCTCAGTAG 58.455 52.381 0.00 0.00 30.42 2.57
1358 2603 6.726490 ATACCATATGTATTACCTAGGCGG 57.274 41.667 9.30 0.00 36.77 6.13
1493 2744 4.160439 TCAAGCAGAGTATGTACTTGAGGG 59.840 45.833 4.34 0.00 41.20 4.30
1505 2758 8.531982 AGAATGTACAACTAATCAAGCAGAGTA 58.468 33.333 0.00 0.00 0.00 2.59
1506 2759 7.390027 AGAATGTACAACTAATCAAGCAGAGT 58.610 34.615 0.00 0.00 0.00 3.24
1530 2783 2.032549 CACAGGCAGTTCGAACAAAGAG 60.033 50.000 28.78 17.39 0.00 2.85
1545 2798 6.586082 ACGAAAACAATTCATATTTCACAGGC 59.414 34.615 0.00 0.00 32.64 4.85
1546 2799 7.807433 TCACGAAAACAATTCATATTTCACAGG 59.193 33.333 0.00 0.00 32.64 4.00
1620 2874 1.888436 GCCAAAACCAGCCCTTAGCC 61.888 60.000 0.00 0.00 45.47 3.93
1647 2901 6.206042 ACTATCAGTACTTTCCCAAGGATCT 58.794 40.000 0.00 0.00 33.82 2.75
1685 2939 1.673626 CGCATTCTTGGCATTTGGCTT 60.674 47.619 5.67 0.00 44.01 4.35
1736 2990 0.323178 CTTGGCACTTGAGGCATCCT 60.323 55.000 0.00 0.00 44.02 3.24
1859 3115 5.703978 ATGAATGAAACAACAACGATGGA 57.296 34.783 0.00 0.00 0.00 3.41
1867 3123 8.637099 TGTTGGAAGATAATGAATGAAACAACA 58.363 29.630 0.00 0.00 40.35 3.33
1877 3133 8.884124 AAAGGAAGATGTTGGAAGATAATGAA 57.116 30.769 0.00 0.00 0.00 2.57
1980 3253 8.856153 TCAGTTACTAAATGGTATTTTGCAGA 57.144 30.769 0.00 0.00 0.00 4.26
1991 3264 5.277058 GCTCGCATCTTCAGTTACTAAATGG 60.277 44.000 0.00 0.00 0.00 3.16
2022 3295 5.348164 ACAAATACAAAGGTGAAGTTGCAC 58.652 37.500 0.00 0.00 38.05 4.57
2058 3331 6.119536 TGTGTGGGTGCCTTATATTTTAGAG 58.880 40.000 0.00 0.00 0.00 2.43
2087 3360 4.973168 AGCTCTTGGTCAAACTGAATGTA 58.027 39.130 0.00 0.00 0.00 2.29
2190 3514 9.747898 ACCAATAGTTAGACCAATAAAATGTCA 57.252 29.630 0.00 0.00 0.00 3.58
2232 3556 2.428544 TATAAGGCGCCCACACATTT 57.571 45.000 26.15 11.80 0.00 2.32
2257 3581 4.498894 AAATACCCTTACTACCAGGCAC 57.501 45.455 0.00 0.00 0.00 5.01
2267 3591 9.775854 GGGAGACTTCTTATAAAATACCCTTAC 57.224 37.037 0.00 0.00 0.00 2.34
2271 3595 8.030913 TCTGGGAGACTTCTTATAAAATACCC 57.969 38.462 0.00 0.00 0.00 3.69
2309 3633 7.384477 AGCACGGAGACTAATACTTTAAGTTT 58.616 34.615 1.94 0.81 0.00 2.66
2317 3641 3.312973 CGAAGAGCACGGAGACTAATACT 59.687 47.826 0.00 0.00 0.00 2.12
2318 3642 3.311871 TCGAAGAGCACGGAGACTAATAC 59.688 47.826 0.00 0.00 0.00 1.89
2319 3643 3.538591 TCGAAGAGCACGGAGACTAATA 58.461 45.455 0.00 0.00 0.00 0.98
2333 3657 8.333908 CAACAATTAAGAGATCCATTCGAAGAG 58.666 37.037 3.35 0.00 38.43 2.85
2364 3688 2.863132 TATACCGTGTTTGGGCAACT 57.137 45.000 0.00 0.00 36.21 3.16
2416 3740 2.329267 TGGTCGCCATCTCCATATCTT 58.671 47.619 0.00 0.00 0.00 2.40
2488 3812 6.161170 AGACCAGGATTCCCTCAAAATAGAAT 59.839 38.462 0.00 0.00 42.02 2.40
2489 3813 5.492524 AGACCAGGATTCCCTCAAAATAGAA 59.507 40.000 0.00 0.00 42.02 2.10
2490 3814 5.039645 AGACCAGGATTCCCTCAAAATAGA 58.960 41.667 0.00 0.00 42.02 1.98
2491 3815 5.379706 AGACCAGGATTCCCTCAAAATAG 57.620 43.478 0.00 0.00 42.02 1.73
2492 3816 7.350921 AGAATAGACCAGGATTCCCTCAAAATA 59.649 37.037 0.00 0.00 42.02 1.40
2493 3817 6.161170 AGAATAGACCAGGATTCCCTCAAAAT 59.839 38.462 0.00 0.00 42.02 1.82
2494 3818 5.492524 AGAATAGACCAGGATTCCCTCAAAA 59.507 40.000 0.00 0.00 42.02 2.44
2495 3819 5.039645 AGAATAGACCAGGATTCCCTCAAA 58.960 41.667 0.00 0.00 42.02 2.69
2496 3820 4.635473 AGAATAGACCAGGATTCCCTCAA 58.365 43.478 0.00 0.00 42.02 3.02
2497 3821 4.286813 AGAATAGACCAGGATTCCCTCA 57.713 45.455 0.00 0.00 42.02 3.86
2498 3822 6.943899 AATAGAATAGACCAGGATTCCCTC 57.056 41.667 0.00 0.00 42.02 4.30
2499 3823 7.350921 TCAAAATAGAATAGACCAGGATTCCCT 59.649 37.037 0.00 0.00 45.74 4.20
2500 3824 7.518188 TCAAAATAGAATAGACCAGGATTCCC 58.482 38.462 0.00 0.00 33.34 3.97
2501 3825 7.663493 CCTCAAAATAGAATAGACCAGGATTCC 59.337 40.741 0.00 0.00 33.34 3.01
2502 3826 7.663493 CCCTCAAAATAGAATAGACCAGGATTC 59.337 40.741 0.00 0.00 33.11 2.52
2503 3827 7.350921 TCCCTCAAAATAGAATAGACCAGGATT 59.649 37.037 0.00 0.00 0.00 3.01
2504 3828 6.851836 TCCCTCAAAATAGAATAGACCAGGAT 59.148 38.462 0.00 0.00 0.00 3.24
2505 3829 6.209774 TCCCTCAAAATAGAATAGACCAGGA 58.790 40.000 0.00 0.00 0.00 3.86
2506 3830 6.500589 TCCCTCAAAATAGAATAGACCAGG 57.499 41.667 0.00 0.00 0.00 4.45
2507 3831 7.663493 GGATTCCCTCAAAATAGAATAGACCAG 59.337 40.741 0.00 0.00 0.00 4.00
2508 3832 7.350921 AGGATTCCCTCAAAATAGAATAGACCA 59.649 37.037 0.00 0.00 38.86 4.02
2509 3833 7.663493 CAGGATTCCCTCAAAATAGAATAGACC 59.337 40.741 0.00 0.00 42.02 3.85
2510 3834 7.663493 CCAGGATTCCCTCAAAATAGAATAGAC 59.337 40.741 0.00 0.00 42.02 2.59
2511 3835 7.350921 ACCAGGATTCCCTCAAAATAGAATAGA 59.649 37.037 0.00 0.00 42.02 1.98
2512 3836 7.521669 ACCAGGATTCCCTCAAAATAGAATAG 58.478 38.462 0.00 0.00 42.02 1.73
2618 3949 3.163616 TGAAACGGGGAAAATAAGGCT 57.836 42.857 0.00 0.00 0.00 4.58
2624 3955 4.274705 GCATTTTGTTGAAACGGGGAAAAT 59.725 37.500 0.00 0.00 0.00 1.82
2629 3961 2.524569 AGCATTTTGTTGAAACGGGG 57.475 45.000 0.00 0.00 0.00 5.73
2652 3984 6.782082 TTGAGCTACTCACTTCTCATACAT 57.218 37.500 0.00 0.00 40.46 2.29
2665 3997 6.043411 CCAGTAGTGGTAAATTGAGCTACTC 58.957 44.000 8.59 0.00 39.30 2.59
2715 4050 6.724263 CCATAAACGCTTGCATTGATAACTA 58.276 36.000 0.00 0.00 0.00 2.24
2764 4099 7.928307 TTGCTAGATTGATTTTGCTACTTCT 57.072 32.000 0.00 0.00 0.00 2.85
2771 4106 5.473039 AGTGGTTTGCTAGATTGATTTTGC 58.527 37.500 0.00 0.00 0.00 3.68
2773 4108 7.231317 TCAGAAGTGGTTTGCTAGATTGATTTT 59.769 33.333 0.00 0.00 0.00 1.82
2869 4218 5.163754 CCTCGTGGGAAAACTATGAAACATC 60.164 44.000 0.00 0.00 37.23 3.06
2887 4236 1.247567 AAGAATTGGTTGGCCTCGTG 58.752 50.000 3.32 0.00 35.27 4.35
2907 4256 6.318396 GGATAAAAGAAAGAGCTTCTGCAGAT 59.682 38.462 19.04 1.77 44.00 2.90
2926 4275 3.737559 AGGACTGCCAACATGGATAAA 57.262 42.857 0.00 0.00 40.96 1.40
2969 4318 6.743575 AAAGAGCACTATGGTTAATCACAC 57.256 37.500 0.00 0.00 0.00 3.82
3083 4432 5.264395 AGGTTGAAATTCTAATGGACCTGG 58.736 41.667 0.00 0.00 35.11 4.45
3089 4438 6.149474 AGTTCACGAGGTTGAAATTCTAATGG 59.851 38.462 0.00 0.00 37.24 3.16
3090 4439 7.133891 AGTTCACGAGGTTGAAATTCTAATG 57.866 36.000 0.00 0.00 37.24 1.90
3120 4469 6.249260 CACAAAATAATAGCTTGCGAACTGTC 59.751 38.462 0.00 0.00 0.00 3.51
3183 4533 5.243507 TCATCAAATGCAACACCTGTTACAT 59.756 36.000 0.00 0.00 42.16 2.29
3299 4649 4.530161 AGTTTCTCTGTCATAGAAGGCTGT 59.470 41.667 1.43 0.00 34.59 4.40
3336 4686 5.008911 CCATCTCAGACTCATCACTAGACAG 59.991 48.000 0.00 0.00 0.00 3.51
3443 4793 9.832445 TTTCCTTGTATCAACATCTTCCTATAC 57.168 33.333 0.00 0.00 34.97 1.47
3557 4910 4.583871 ACTTGAAGCTCATTGGGAACTAG 58.416 43.478 0.00 0.00 0.00 2.57
3613 4994 7.872113 ACTTTTGAGTTCTGAGAAAGAATGT 57.128 32.000 0.00 0.00 46.53 2.71
3671 5053 7.147846 CCTTAGGGACAATTTTTATCTGCACAT 60.148 37.037 0.00 0.00 33.58 3.21
3760 5142 7.484324 CGTGGCAAAATGTTTTTCTTCAATTTT 59.516 29.630 0.00 0.00 0.00 1.82
3763 5145 5.503846 GCGTGGCAAAATGTTTTTCTTCAAT 60.504 36.000 0.00 0.00 0.00 2.57
3813 5195 2.489722 GGACAAAATCTCCTCTGTTGGC 59.510 50.000 0.00 0.00 0.00 4.52
3816 5198 4.507512 GGAAGGGACAAAATCTCCTCTGTT 60.508 45.833 0.00 0.00 30.14 3.16
3893 5275 6.043411 GGTAGGCTAGAGTTGAAACACATAG 58.957 44.000 0.00 0.00 0.00 2.23
3918 5300 4.423732 CCTTTCAGTCACAAACAAGTTGG 58.576 43.478 7.96 0.00 41.97 3.77
4068 5456 6.603095 AGAACGAAATTAAGTGAACAGATGC 58.397 36.000 0.00 0.00 0.00 3.91
4122 5513 2.808543 GCTAATAGGAACCATGCTTCCG 59.191 50.000 13.07 1.64 44.12 4.30
4168 5559 3.501828 CACATAACAACTAGCAGCACCAA 59.498 43.478 0.00 0.00 0.00 3.67
4213 5604 2.422127 TGCATCAGCTGATCATTGTGTG 59.578 45.455 26.44 15.10 42.74 3.82
4226 5617 4.178540 ACAAATACAAGCAATGCATCAGC 58.821 39.130 8.35 14.36 42.57 4.26
4306 5721 3.775261 AAAATCAGCATTTGCCCAGTT 57.225 38.095 0.00 0.00 43.38 3.16
4376 5792 7.429920 GCGAGGCATCAAAACGTAATTAAATTA 59.570 33.333 0.00 0.00 0.00 1.40
4387 5806 0.179215 GTCAGCGAGGCATCAAAACG 60.179 55.000 0.00 0.00 0.00 3.60
4410 5829 3.620615 TGCAAAACAGACACAAGCG 57.379 47.368 0.00 0.00 0.00 4.68
4525 5944 3.779444 ACACAGTATTCAGTCTCCCTCA 58.221 45.455 0.00 0.00 0.00 3.86
4573 6000 5.473504 GGTGAGGAAATGAGAAAGCACTAAA 59.526 40.000 0.00 0.00 0.00 1.85
4638 6065 1.214673 ACCAGATCTTGCAGCATCCAT 59.785 47.619 0.00 0.00 0.00 3.41
4749 6185 3.508793 CAGAGCAAGGAACATCATTTGGT 59.491 43.478 0.00 0.00 34.33 3.67
4773 6210 4.853924 ATTTTCACCATGAACCACAGAC 57.146 40.909 0.00 0.00 35.89 3.51
4781 6218 6.569610 GCTTTCTCGGTAATTTTCACCATGAA 60.570 38.462 0.00 0.00 35.67 2.57
4797 6234 2.549754 ACACAAACATCAGCTTTCTCGG 59.450 45.455 0.00 0.00 0.00 4.63
4817 6254 5.336451 GGGAGATTGTTTTATGTGGTCCAAC 60.336 44.000 0.00 0.00 0.00 3.77
4829 6267 7.609532 TGAAACAAAATGTTGGGAGATTGTTTT 59.390 29.630 13.58 1.51 45.60 2.43
4833 6271 7.733402 AATGAAACAAAATGTTGGGAGATTG 57.267 32.000 0.00 0.00 40.14 2.67
4839 6277 6.134040 AGCAAAATGAAACAAAATGTTGGG 57.866 33.333 0.00 0.00 40.14 4.12
4843 6281 5.333263 GCGCTAGCAAAATGAAACAAAATGT 60.333 36.000 16.45 0.00 44.35 2.71
4887 6325 3.269178 CTTCCTGGAGCAAGATCAGAAC 58.731 50.000 0.00 0.00 0.00 3.01
4958 6396 1.961277 ACTAACCAGTGCACGCTGC 60.961 57.895 12.01 3.44 45.29 5.25
5018 6456 6.181908 ACCGTATTTTGGTGGATTAGCTTTA 58.818 36.000 0.00 0.00 38.60 1.85
5019 6457 5.014202 ACCGTATTTTGGTGGATTAGCTTT 58.986 37.500 0.00 0.00 38.60 3.51
5028 6466 3.441222 GGGTTTCTACCGTATTTTGGTGG 59.559 47.826 0.00 0.00 46.04 4.61
5029 6467 3.441222 GGGGTTTCTACCGTATTTTGGTG 59.559 47.826 0.00 0.00 46.04 4.17
5032 6470 5.065988 CAGATGGGGTTTCTACCGTATTTTG 59.934 44.000 0.00 0.00 46.04 2.44
5058 6497 6.798959 CAGTGAGCAGCTTTTGATTTAAGTAC 59.201 38.462 0.00 0.00 0.00 2.73
5063 6504 5.181245 GGTACAGTGAGCAGCTTTTGATTTA 59.819 40.000 0.00 0.00 0.00 1.40
5065 6506 3.503748 GGTACAGTGAGCAGCTTTTGATT 59.496 43.478 0.00 0.00 0.00 2.57
5089 6530 5.414454 ACTTCAGACAAAGTTTGTTAGTGCA 59.586 36.000 21.70 9.90 45.52 4.57
5132 6575 4.898320 AGGCATTCAATGTTTTCCCTTTC 58.102 39.130 0.00 0.00 0.00 2.62
5254 6705 3.679025 CCATGCGCTAAATTCTGCAAAAA 59.321 39.130 9.73 0.00 41.22 1.94
5340 6791 3.198853 AGAATGCAACCTCCTAGGAAGAC 59.801 47.826 14.62 3.97 37.67 3.01
5392 6843 3.823304 GAGAATCTTGGTTGCCAACTCTT 59.177 43.478 7.62 0.00 38.75 2.85
5605 7261 1.596464 GCGAATACGTAGACGGACCAG 60.596 57.143 20.01 0.00 44.95 4.00
5698 7368 2.808919 TGCAAAAATAACCCCGGATCA 58.191 42.857 0.73 0.00 0.00 2.92
5959 7629 1.304381 GTGATGGGGCTGGAAAGCA 60.304 57.895 0.00 0.00 36.33 3.91
6234 7904 4.408821 GTGGAGCATGGCCACGGA 62.409 66.667 8.16 0.00 45.50 4.69
6244 7914 4.662961 CGAGCGTGGTGTGGAGCA 62.663 66.667 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.