Multiple sequence alignment - TraesCS7A01G254200

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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 TraesCS7A01G254200 chr7A 100.000 2727 0 0 1 2727 240084658 240087384 0.000000e+00 5036.0
1 TraesCS7A01G254200 chr7A 100.000 2558 0 0 3037 5594 240087694 240090251 0.000000e+00 4724.0
2 TraesCS7A01G254200 chr7A 98.901 91 1 0 5231 5321 240089798 240089888 4.480000e-36 163.0
3 TraesCS7A01G254200 chr7A 98.901 91 1 0 5141 5231 240089888 240089978 4.480000e-36 163.0
4 TraesCS7A01G254200 chr7A 80.100 201 27 3 4758 4945 2226214 2226014 2.720000e-28 137.0
5 TraesCS7A01G254200 chr7A 95.000 80 4 0 3037 3116 510162626 510162705 5.880000e-25 126.0
6 TraesCS7A01G254200 chr7A 91.667 84 7 0 3037 3120 166872876 166872959 3.540000e-22 117.0
7 TraesCS7A01G254200 chr7A 90.000 90 7 2 3037 3125 730881809 730881721 1.270000e-21 115.0
8 TraesCS7A01G254200 chr7B 93.974 2705 105 30 1 2663 199494216 199496904 0.000000e+00 4039.0
9 TraesCS7A01G254200 chr7B 95.463 2116 83 10 3116 5229 199496896 199499000 0.000000e+00 3363.0
10 TraesCS7A01G254200 chr7B 90.305 361 35 0 5233 5593 199498914 199499274 1.820000e-129 473.0
11 TraesCS7A01G254200 chr7D 96.693 2117 66 4 3116 5231 228011954 228014067 0.000000e+00 3518.0
12 TraesCS7A01G254200 chr7D 92.878 2022 92 24 681 2663 228009954 228011962 0.000000e+00 2889.0
13 TraesCS7A01G254200 chr7D 93.450 687 34 7 1 685 228007783 228008460 0.000000e+00 1009.0
14 TraesCS7A01G254200 chr7D 91.713 362 29 1 5233 5594 228013980 228014340 8.370000e-138 501.0
15 TraesCS7A01G254200 chr7D 86.957 115 15 0 4757 4871 564063182 564063296 4.550000e-26 130.0
16 TraesCS7A01G254200 chr7D 92.941 85 6 0 3037 3121 463712410 463712326 2.120000e-24 124.0
17 TraesCS7A01G254200 chr7D 96.825 63 2 0 2665 2727 37120415 37120353 7.660000e-19 106.0
18 TraesCS7A01G254200 chr5B 83.281 317 47 5 5283 5594 335370962 335371277 2.550000e-73 287.0
19 TraesCS7A01G254200 chr5B 80.711 197 23 5 4760 4942 466641259 466641064 7.560000e-29 139.0
20 TraesCS7A01G254200 chr5B 82.249 169 16 4 4760 4915 503777825 503777992 3.520000e-27 134.0
21 TraesCS7A01G254200 chr5B 82.482 137 19 5 4939 5071 335370750 335370885 1.270000e-21 115.0
22 TraesCS7A01G254200 chr5D 82.653 196 21 2 4760 4942 7616610 7616415 1.610000e-35 161.0
23 TraesCS7A01G254200 chr5D 96.825 63 2 0 2665 2727 163793598 163793536 7.660000e-19 106.0
24 TraesCS7A01G254200 chr5D 93.023 43 3 0 5029 5071 294162017 294162059 4.680000e-06 63.9
25 TraesCS7A01G254200 chr3D 88.991 109 12 0 4762 4870 291975107 291974999 9.780000e-28 135.0
26 TraesCS7A01G254200 chr3D 95.238 84 3 1 3037 3120 568184645 568184727 1.260000e-26 132.0
27 TraesCS7A01G254200 chr3D 95.000 80 4 0 3037 3116 547450454 547450533 5.880000e-25 126.0
28 TraesCS7A01G254200 chrUn 86.290 124 15 2 4749 4871 19196659 19196537 3.520000e-27 134.0
29 TraesCS7A01G254200 chr4A 96.250 80 3 0 3037 3116 165368324 165368245 1.260000e-26 132.0
30 TraesCS7A01G254200 chr4B 77.193 228 45 4 5367 5590 540730164 540729940 5.880000e-25 126.0
31 TraesCS7A01G254200 chr4D 94.937 79 4 0 3038 3116 278425509 278425431 2.120000e-24 124.0
32 TraesCS7A01G254200 chr4D 93.939 66 2 2 2663 2727 5664166 5664230 1.280000e-16 99.0
33 TraesCS7A01G254200 chr3A 93.902 82 5 0 3037 3118 595440198 595440279 2.120000e-24 124.0
34 TraesCS7A01G254200 chr3A 96.970 66 2 0 2662 2727 505539245 505539180 1.650000e-20 111.0
35 TraesCS7A01G254200 chr2B 96.825 63 1 1 2665 2727 701923269 701923208 2.760000e-18 104.0
36 TraesCS7A01G254200 chr2B 92.000 75 2 4 2656 2727 453342248 453342175 9.910000e-18 102.0
37 TraesCS7A01G254200 chr2B 87.755 49 6 0 4964 5012 549502517 549502565 2.180000e-04 58.4
38 TraesCS7A01G254200 chr1D 96.825 63 1 1 2665 2727 457209462 457209401 2.760000e-18 104.0
39 TraesCS7A01G254200 chr6A 92.857 70 4 1 2658 2727 595931751 595931819 3.570000e-17 100.0
40 TraesCS7A01G254200 chr3B 95.238 63 2 1 2665 2727 764533190 764533251 1.280000e-16 99.0
41 TraesCS7A01G254200 chr5A 84.286 70 9 2 4955 5023 645395055 645395123 3.620000e-07 67.6


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 TraesCS7A01G254200 chr7A 240084658 240090251 5593 False 2521.50 5036 99.450500 1 5594 4 chr7A.!!$F3 5593
1 TraesCS7A01G254200 chr7B 199494216 199499274 5058 False 2625.00 4039 93.247333 1 5593 3 chr7B.!!$F1 5592
2 TraesCS7A01G254200 chr7D 228007783 228014340 6557 False 1979.25 3518 93.683500 1 5594 4 chr7D.!!$F2 5593
3 TraesCS7A01G254200 chr5B 335370750 335371277 527 False 201.00 287 82.881500 4939 5594 2 chr5B.!!$F2 655

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
76 78 0.532862 AGGACAACGACAGTGCAAGG 60.533 55.0 0.00 0.0 0.00 3.61 F
421 424 0.613260 CCAGAATCTTGTGGGACGGA 59.387 55.0 0.00 0.0 37.92 4.69 F
1356 2892 0.036294 GGTAGTGGTTGCTGGGAGAC 60.036 60.0 0.00 0.0 0.00 3.36 F
3063 4633 0.036022 TGCCACGTGTCATCCATCAA 59.964 50.0 15.65 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 2892 0.309612 GTTTTACACTGGCACACCCG 59.690 55.0 0.00 0.00 35.87 5.28 R
1794 3361 1.006832 GTGCGTGACTTGTCAGTTGT 58.993 50.0 3.45 0.00 31.22 3.32 R
3075 4645 0.033405 AGGTCTCACGGGCTAGCTTA 60.033 55.0 15.72 0.00 0.00 3.09 R
4922 6498 0.600057 GGCCTTATGCAATGCTAGGC 59.400 55.0 26.54 26.54 42.69 3.93 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
76 78 0.532862 AGGACAACGACAGTGCAAGG 60.533 55.000 0.00 0.00 0.00 3.61
283 286 7.701924 TCGAATTTGGAATAGAAATGAATGTGC 59.298 33.333 0.00 0.00 0.00 4.57
303 306 4.848299 GTGCTGTTTTCATGTCTTTCGATC 59.152 41.667 0.00 0.00 0.00 3.69
421 424 0.613260 CCAGAATCTTGTGGGACGGA 59.387 55.000 0.00 0.00 37.92 4.69
435 438 2.237893 GGGACGGAAAAGTATCTTGGGA 59.762 50.000 0.00 0.00 0.00 4.37
686 2212 3.134623 TGGGAGCATGGTATGTCTAAGTG 59.865 47.826 0.00 0.00 0.00 3.16
754 2286 1.427435 CGAACCCGCATGCAATTTTT 58.573 45.000 19.57 2.53 0.00 1.94
759 2291 2.807392 ACCCGCATGCAATTTTTCTTTG 59.193 40.909 19.57 0.00 0.00 2.77
882 2416 3.006112 GGGAAAGTGGAAGAATCCCTC 57.994 52.381 1.89 0.00 45.95 4.30
930 2464 1.815421 CCAACGCCTCCAGATTCGG 60.815 63.158 0.00 0.00 0.00 4.30
954 2488 1.978580 GTCTCCTTCTCTTTCCCACCA 59.021 52.381 0.00 0.00 0.00 4.17
1322 2858 4.997395 ACGTGATGCAAAGTAAGAAGTGAT 59.003 37.500 0.00 0.00 0.00 3.06
1356 2892 0.036294 GGTAGTGGTTGCTGGGAGAC 60.036 60.000 0.00 0.00 0.00 3.36
1372 2908 1.070105 GACGGGTGTGCCAGTGTAA 59.930 57.895 0.00 0.00 43.18 2.41
1433 2969 2.670148 GGCCTACCCAGACCTGTGG 61.670 68.421 0.00 0.48 37.34 4.17
1438 2974 1.420138 CTACCCAGACCTGTGGTGTTT 59.580 52.381 15.69 0.00 35.25 2.83
1490 3026 6.314896 AGGTTTCGAAGCTTGATATCTTTGAG 59.685 38.462 2.10 0.00 35.27 3.02
1495 3031 5.689514 CGAAGCTTGATATCTTTGAGATCGT 59.310 40.000 2.10 0.00 36.20 3.73
1500 3036 5.515797 TGATATCTTTGAGATCGTTCGGT 57.484 39.130 3.98 0.00 36.20 4.69
1520 3056 4.454161 CGGTAAGTTTTGTGGATGTCATGA 59.546 41.667 0.00 0.00 0.00 3.07
1521 3057 5.049060 CGGTAAGTTTTGTGGATGTCATGAA 60.049 40.000 0.00 0.00 0.00 2.57
1522 3058 6.514212 CGGTAAGTTTTGTGGATGTCATGAAA 60.514 38.462 0.00 0.00 0.00 2.69
1523 3059 7.206687 GGTAAGTTTTGTGGATGTCATGAAAA 58.793 34.615 0.00 0.00 0.00 2.29
1524 3060 7.872483 GGTAAGTTTTGTGGATGTCATGAAAAT 59.128 33.333 0.00 0.00 0.00 1.82
1554 3090 4.798882 ACCTCCTTTTGTACCAATGAACA 58.201 39.130 0.00 0.00 0.00 3.18
1565 3101 6.177610 TGTACCAATGAACATAGAACTTCCC 58.822 40.000 0.00 0.00 0.00 3.97
1569 3105 7.410174 ACCAATGAACATAGAACTTCCCAATA 58.590 34.615 0.00 0.00 0.00 1.90
1618 3155 5.179555 GCTTAGGGGTTCGCAAAGATATTAG 59.820 44.000 0.00 0.00 0.00 1.73
1736 3275 6.207810 GTGGGTCACATATCTTTGGTTTGTAA 59.792 38.462 0.00 0.00 34.08 2.41
1749 3316 8.592809 TCTTTGGTTTGTAATAAATTGCCTGAT 58.407 29.630 0.00 0.00 0.00 2.90
1775 3342 5.514274 TGAAGGTTGATCCAAGTCAAAAC 57.486 39.130 0.00 0.00 39.61 2.43
1794 3361 2.750637 GAGCTCTCGGTCCGGTCA 60.751 66.667 12.29 0.00 0.00 4.02
1838 3405 3.127548 CCTCATCAACCAATTCAACTCCG 59.872 47.826 0.00 0.00 0.00 4.63
1844 3411 1.003233 ACCAATTCAACTCCGGACTCC 59.997 52.381 0.00 0.00 0.00 3.85
1847 3414 1.645710 ATTCAACTCCGGACTCCAGT 58.354 50.000 0.00 0.00 0.00 4.00
2044 3611 2.231478 GTCTTACTGTGCTCACTAGGCA 59.769 50.000 0.00 0.00 37.36 4.75
2274 3841 0.392998 CGCCCTTAGCAATCCACACT 60.393 55.000 0.00 0.00 44.04 3.55
2474 4044 0.615331 TCTACCCTTTGCCAGCTGAG 59.385 55.000 17.39 6.56 0.00 3.35
2606 4176 5.989477 TCCAACAGTATGAATAGGAACCTG 58.011 41.667 3.36 0.00 39.69 4.00
2654 4224 5.871396 TGGGATTGTACATCCTCTAGAAC 57.129 43.478 18.10 6.16 38.26 3.01
2655 4225 4.654262 TGGGATTGTACATCCTCTAGAACC 59.346 45.833 18.10 2.18 38.26 3.62
2656 4226 4.040584 GGGATTGTACATCCTCTAGAACCC 59.959 50.000 18.10 6.83 38.26 4.11
2657 4227 4.654262 GGATTGTACATCCTCTAGAACCCA 59.346 45.833 13.85 0.00 35.36 4.51
2658 4228 5.130477 GGATTGTACATCCTCTAGAACCCAA 59.870 44.000 13.85 0.00 35.36 4.12
2659 4229 5.677319 TTGTACATCCTCTAGAACCCAAG 57.323 43.478 0.00 0.00 0.00 3.61
2660 4230 4.684724 TGTACATCCTCTAGAACCCAAGT 58.315 43.478 0.00 0.00 0.00 3.16
2661 4231 4.466370 TGTACATCCTCTAGAACCCAAGTG 59.534 45.833 0.00 0.00 0.00 3.16
2662 4232 3.791320 ACATCCTCTAGAACCCAAGTGA 58.209 45.455 0.00 0.00 0.00 3.41
2663 4233 4.366267 ACATCCTCTAGAACCCAAGTGAT 58.634 43.478 0.00 0.00 0.00 3.06
2664 4234 4.163078 ACATCCTCTAGAACCCAAGTGATG 59.837 45.833 0.00 0.00 33.39 3.07
2704 4274 3.984838 GGTCTCATGAGCTAGCAGG 57.015 57.895 18.36 0.00 37.68 4.85
2705 4275 1.118838 GGTCTCATGAGCTAGCAGGT 58.881 55.000 18.36 0.00 37.68 4.00
2706 4276 1.202510 GGTCTCATGAGCTAGCAGGTG 60.203 57.143 18.36 11.83 37.68 4.00
2707 4277 1.753649 GTCTCATGAGCTAGCAGGTGA 59.246 52.381 18.36 15.34 0.00 4.02
2708 4278 2.030371 TCTCATGAGCTAGCAGGTGAG 58.970 52.381 25.21 25.21 35.58 3.51
2709 4279 2.030371 CTCATGAGCTAGCAGGTGAGA 58.970 52.381 26.22 13.22 36.15 3.27
2710 4280 1.753649 TCATGAGCTAGCAGGTGAGAC 59.246 52.381 18.83 0.00 0.00 3.36
2711 4281 1.118838 ATGAGCTAGCAGGTGAGACC 58.881 55.000 18.83 0.00 38.99 3.85
2712 4282 0.972983 TGAGCTAGCAGGTGAGACCC 60.973 60.000 18.83 0.00 39.75 4.46
2713 4283 0.972983 GAGCTAGCAGGTGAGACCCA 60.973 60.000 18.83 0.00 39.75 4.51
2714 4284 1.219393 GCTAGCAGGTGAGACCCAC 59.781 63.158 10.63 0.00 39.75 4.61
2722 4292 1.604378 GTGAGACCCACCCTGATGG 59.396 63.158 0.00 0.00 39.86 3.51
2723 4293 0.909610 GTGAGACCCACCCTGATGGA 60.910 60.000 0.00 0.00 43.02 3.41
2724 4294 0.044702 TGAGACCCACCCTGATGGAT 59.955 55.000 0.00 0.00 43.02 3.41
2725 4295 0.471617 GAGACCCACCCTGATGGATG 59.528 60.000 0.00 0.00 43.02 3.51
2726 4296 0.044702 AGACCCACCCTGATGGATGA 59.955 55.000 0.00 0.00 43.02 2.92
3057 4627 3.822594 TTGTAAATGCCACGTGTCATC 57.177 42.857 13.12 1.09 0.00 2.92
3058 4628 2.080693 TGTAAATGCCACGTGTCATCC 58.919 47.619 13.12 4.88 0.00 3.51
3059 4629 2.080693 GTAAATGCCACGTGTCATCCA 58.919 47.619 13.12 0.69 0.00 3.41
3060 4630 1.838112 AAATGCCACGTGTCATCCAT 58.162 45.000 13.12 4.99 0.00 3.41
3061 4631 1.382522 AATGCCACGTGTCATCCATC 58.617 50.000 13.12 0.00 0.00 3.51
3062 4632 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
3063 4633 0.036022 TGCCACGTGTCATCCATCAA 59.964 50.000 15.65 0.00 0.00 2.57
3064 4634 0.729116 GCCACGTGTCATCCATCAAG 59.271 55.000 15.65 0.00 0.00 3.02
3065 4635 1.675714 GCCACGTGTCATCCATCAAGA 60.676 52.381 15.65 0.00 0.00 3.02
3066 4636 2.910199 CCACGTGTCATCCATCAAGAT 58.090 47.619 15.65 0.00 0.00 2.40
3067 4637 2.610833 CCACGTGTCATCCATCAAGATG 59.389 50.000 15.65 3.07 44.21 2.90
3080 4650 4.970711 CATCAAGATGGGTCTCATAAGCT 58.029 43.478 2.09 0.00 35.97 3.74
3081 4651 6.106648 CATCAAGATGGGTCTCATAAGCTA 57.893 41.667 2.09 0.00 35.97 3.32
3082 4652 5.798125 TCAAGATGGGTCTCATAAGCTAG 57.202 43.478 0.00 0.00 35.97 3.42
3083 4653 4.039730 TCAAGATGGGTCTCATAAGCTAGC 59.960 45.833 6.62 6.62 35.97 3.42
3084 4654 2.903135 AGATGGGTCTCATAAGCTAGCC 59.097 50.000 12.13 0.00 35.97 3.93
3085 4655 1.424638 TGGGTCTCATAAGCTAGCCC 58.575 55.000 12.13 2.16 35.37 5.19
3086 4656 0.318762 GGGTCTCATAAGCTAGCCCG 59.681 60.000 12.13 0.00 0.00 6.13
3087 4657 1.041437 GGTCTCATAAGCTAGCCCGT 58.959 55.000 12.13 0.00 0.00 5.28
3088 4658 1.269831 GGTCTCATAAGCTAGCCCGTG 60.270 57.143 12.13 7.78 0.00 4.94
3089 4659 1.681793 GTCTCATAAGCTAGCCCGTGA 59.318 52.381 12.13 11.77 0.00 4.35
3090 4660 1.957177 TCTCATAAGCTAGCCCGTGAG 59.043 52.381 24.15 24.15 35.58 3.51
3091 4661 1.957177 CTCATAAGCTAGCCCGTGAGA 59.043 52.381 25.15 11.65 36.15 3.27
3092 4662 1.681793 TCATAAGCTAGCCCGTGAGAC 59.318 52.381 12.13 0.00 0.00 3.36
3093 4663 1.041437 ATAAGCTAGCCCGTGAGACC 58.959 55.000 12.13 0.00 0.00 3.85
3094 4664 0.033405 TAAGCTAGCCCGTGAGACCT 60.033 55.000 12.13 0.00 0.00 3.85
3095 4665 1.608717 AAGCTAGCCCGTGAGACCTG 61.609 60.000 12.13 0.00 0.00 4.00
3096 4666 3.082579 GCTAGCCCGTGAGACCTGG 62.083 68.421 2.29 0.00 0.00 4.45
3097 4667 1.682684 CTAGCCCGTGAGACCTGGT 60.683 63.158 0.00 0.00 0.00 4.00
3098 4668 1.668101 CTAGCCCGTGAGACCTGGTC 61.668 65.000 19.20 19.20 0.00 4.02
3099 4669 2.151307 TAGCCCGTGAGACCTGGTCT 62.151 60.000 28.70 28.70 46.42 3.85
3270 4840 8.774586 TCTCTGAGTAAGTAATTTTTGTTGAGC 58.225 33.333 4.32 0.00 0.00 4.26
3356 4927 4.910195 AGATGTTCTGTCATGGCTGTTAA 58.090 39.130 0.00 0.00 0.00 2.01
3359 4930 4.397420 TGTTCTGTCATGGCTGTTAACAT 58.603 39.130 9.13 0.00 0.00 2.71
3370 4941 9.002600 TCATGGCTGTTAACATAATACATGATC 57.997 33.333 22.68 0.00 37.75 2.92
3393 4964 7.227049 TCGATATGCATGACCATTAAGAGTA 57.773 36.000 10.16 0.00 0.00 2.59
3420 4991 7.465353 TGCAGATTTATTCTTCCATTTGTGA 57.535 32.000 0.00 0.00 29.93 3.58
3464 5035 2.364324 ACGGTGAATACATGTATCCGCT 59.636 45.455 30.03 20.11 35.26 5.52
3620 5191 8.469200 TCATTTCAGGTTGATGAATCCATTTAC 58.531 33.333 0.00 0.00 38.90 2.01
3641 5212 2.095853 CCGTTTACACAGATGCACATCC 59.904 50.000 7.01 0.00 38.58 3.51
3654 5225 1.289160 CACATCCCTTCTCCCTTCCA 58.711 55.000 0.00 0.00 0.00 3.53
3704 5275 5.218885 TGATTTGTGACAAACTATTTGCGG 58.781 37.500 13.56 0.00 44.39 5.69
3708 5279 5.098218 TGTGACAAACTATTTGCGGTAAC 57.902 39.130 1.23 0.00 44.39 2.50
3876 5447 9.531942 CAGATTAGCTGGATCATCATATTAGTC 57.468 37.037 12.65 0.00 41.07 2.59
3921 5492 3.314913 TGAGTACAGTAAAACGTCGACCA 59.685 43.478 10.58 0.00 0.00 4.02
4322 5893 2.531685 ACCAGCCCTACAAGCCCA 60.532 61.111 0.00 0.00 0.00 5.36
4374 5945 7.022384 GGATATGTAATCTAGCGTACACAGAC 58.978 42.308 7.31 2.18 33.23 3.51
4786 6358 4.014569 TGTACAATGCAAGGTGCTTAGA 57.985 40.909 9.81 0.00 45.31 2.10
4789 6364 2.040278 ACAATGCAAGGTGCTTAGAGGA 59.960 45.455 0.00 0.00 45.31 3.71
4791 6366 0.615331 TGCAAGGTGCTTAGAGGAGG 59.385 55.000 1.43 0.00 45.31 4.30
4792 6367 0.615850 GCAAGGTGCTTAGAGGAGGT 59.384 55.000 0.00 0.00 40.96 3.85
4793 6368 1.677217 GCAAGGTGCTTAGAGGAGGTG 60.677 57.143 0.00 0.00 40.96 4.00
4794 6369 1.625818 CAAGGTGCTTAGAGGAGGTGT 59.374 52.381 0.00 0.00 0.00 4.16
4800 6375 2.631062 TGCTTAGAGGAGGTGTTTCGAA 59.369 45.455 0.00 0.00 0.00 3.71
4895 6470 1.664874 CGGTGCTTTAGAAAAACCGCC 60.665 52.381 13.09 4.05 46.20 6.13
4915 6491 4.494199 CGCCTTATTTTTCTAAGCACCTCG 60.494 45.833 0.00 0.00 0.00 4.63
4933 6509 0.864455 CGCTAAGAGCCTAGCATTGC 59.136 55.000 0.00 0.00 43.84 3.56
4935 6511 2.502295 GCTAAGAGCCTAGCATTGCAT 58.498 47.619 11.91 0.00 43.25 3.96
4942 6518 1.251251 CCTAGCATTGCATAAGGCCC 58.749 55.000 11.91 0.00 44.22 5.80
5001 6578 3.759618 CCCGGTTAATTAGCAGAAAACCA 59.240 43.478 0.00 0.00 39.66 3.67
5042 6619 0.612732 CCTGCAAAGAGGGCATTCCA 60.613 55.000 0.00 0.00 41.06 3.53
5071 6648 1.536676 CACCCACAGGACCCAAACT 59.463 57.895 0.00 0.00 36.73 2.66
5072 6649 0.106217 CACCCACAGGACCCAAACTT 60.106 55.000 0.00 0.00 36.73 2.66
5078 6655 1.491754 ACAGGACCCAAACTTACCGTT 59.508 47.619 0.00 0.00 37.47 4.44
5112 6706 5.892160 CAATGTCATTGTCATCACCTCTT 57.108 39.130 16.15 0.00 35.57 2.85
5141 6736 0.737715 GCGACTCCGACTTTGATGCT 60.738 55.000 0.00 0.00 38.22 3.79
5197 6792 2.417719 CTTTACTCCAGCAAGCGACTT 58.582 47.619 0.00 0.00 0.00 3.01
5216 6811 2.804090 GACTTCGACGCCACCGAC 60.804 66.667 0.00 0.00 35.61 4.79
5217 6812 4.353437 ACTTCGACGCCACCGACC 62.353 66.667 0.00 0.00 35.61 4.79
5222 6817 4.754667 GACGCCACCGACCCTTCC 62.755 72.222 0.00 0.00 38.29 3.46
5224 6819 4.323477 CGCCACCGACCCTTCCAA 62.323 66.667 0.00 0.00 36.29 3.53
5225 6820 2.114411 GCCACCGACCCTTCCAAA 59.886 61.111 0.00 0.00 0.00 3.28
5226 6821 2.265904 GCCACCGACCCTTCCAAAC 61.266 63.158 0.00 0.00 0.00 2.93
5227 6822 1.964373 CCACCGACCCTTCCAAACG 60.964 63.158 0.00 0.00 0.00 3.60
5228 6823 1.070105 CACCGACCCTTCCAAACGA 59.930 57.895 0.00 0.00 0.00 3.85
5229 6824 0.533308 CACCGACCCTTCCAAACGAA 60.533 55.000 0.00 0.00 0.00 3.85
5230 6825 0.533531 ACCGACCCTTCCAAACGAAC 60.534 55.000 0.00 0.00 0.00 3.95
5231 6826 0.250166 CCGACCCTTCCAAACGAACT 60.250 55.000 0.00 0.00 0.00 3.01
5232 6827 0.865769 CGACCCTTCCAAACGAACTG 59.134 55.000 0.00 0.00 0.00 3.16
5233 6828 0.591659 GACCCTTCCAAACGAACTGC 59.408 55.000 0.00 0.00 0.00 4.40
5234 6829 0.822121 ACCCTTCCAAACGAACTGCC 60.822 55.000 0.00 0.00 0.00 4.85
5235 6830 1.574428 CCTTCCAAACGAACTGCCG 59.426 57.895 0.00 0.00 0.00 5.69
5236 6831 0.882927 CCTTCCAAACGAACTGCCGA 60.883 55.000 0.00 0.00 0.00 5.54
5237 6832 0.234884 CTTCCAAACGAACTGCCGAC 59.765 55.000 0.00 0.00 0.00 4.79
5238 6833 1.161563 TTCCAAACGAACTGCCGACC 61.162 55.000 0.00 0.00 0.00 4.79
5239 6834 2.613506 CCAAACGAACTGCCGACCC 61.614 63.158 0.00 0.00 0.00 4.46
5240 6835 1.597027 CAAACGAACTGCCGACCCT 60.597 57.895 0.00 0.00 0.00 4.34
5241 6836 1.147600 AAACGAACTGCCGACCCTT 59.852 52.632 0.00 0.00 0.00 3.95
5242 6837 0.464916 AAACGAACTGCCGACCCTTT 60.465 50.000 0.00 0.00 0.00 3.11
5243 6838 0.883370 AACGAACTGCCGACCCTTTC 60.883 55.000 0.00 0.00 0.00 2.62
5255 6850 3.682372 GACCCTTTCGAATGAATGAGC 57.318 47.619 12.31 0.00 33.20 4.26
5256 6851 2.356069 GACCCTTTCGAATGAATGAGCC 59.644 50.000 12.31 0.00 33.20 4.70
5257 6852 2.290896 ACCCTTTCGAATGAATGAGCCA 60.291 45.455 12.31 0.00 33.20 4.75
5258 6853 2.954318 CCCTTTCGAATGAATGAGCCAT 59.046 45.455 12.31 0.00 33.20 4.40
5259 6854 3.243301 CCCTTTCGAATGAATGAGCCATG 60.243 47.826 12.31 0.00 33.20 3.66
5260 6855 3.243301 CCTTTCGAATGAATGAGCCATGG 60.243 47.826 7.63 7.63 33.20 3.66
5261 6856 3.280197 TTCGAATGAATGAGCCATGGA 57.720 42.857 18.40 0.00 0.00 3.41
5262 6857 3.280197 TCGAATGAATGAGCCATGGAA 57.720 42.857 18.40 0.00 0.00 3.53
5263 6858 2.945008 TCGAATGAATGAGCCATGGAAC 59.055 45.455 18.40 8.87 0.00 3.62
5264 6859 2.033801 CGAATGAATGAGCCATGGAACC 59.966 50.000 18.40 3.53 0.00 3.62
5265 6860 2.832643 ATGAATGAGCCATGGAACCA 57.167 45.000 18.40 9.82 0.00 3.67
5266 6861 1.838112 TGAATGAGCCATGGAACCAC 58.162 50.000 18.40 0.00 0.00 4.16
5267 6862 1.106285 GAATGAGCCATGGAACCACC 58.894 55.000 18.40 0.00 39.54 4.61
5268 6863 0.706433 AATGAGCCATGGAACCACCT 59.294 50.000 18.40 0.45 39.86 4.00
5269 6864 0.706433 ATGAGCCATGGAACCACCTT 59.294 50.000 18.40 0.00 39.86 3.50
5270 6865 0.482446 TGAGCCATGGAACCACCTTT 59.518 50.000 18.40 0.00 39.86 3.11
5271 6866 1.707989 TGAGCCATGGAACCACCTTTA 59.292 47.619 18.40 0.00 39.86 1.85
5272 6867 2.092323 GAGCCATGGAACCACCTTTAC 58.908 52.381 18.40 0.00 39.86 2.01
5273 6868 1.710809 AGCCATGGAACCACCTTTACT 59.289 47.619 18.40 0.00 39.86 2.24
5274 6869 2.092323 GCCATGGAACCACCTTTACTC 58.908 52.381 18.40 0.00 39.86 2.59
5275 6870 2.723273 CCATGGAACCACCTTTACTCC 58.277 52.381 5.56 0.00 39.86 3.85
5276 6871 2.041081 CCATGGAACCACCTTTACTCCA 59.959 50.000 5.56 0.00 40.36 3.86
5277 6872 3.347216 CATGGAACCACCTTTACTCCAG 58.653 50.000 0.00 0.00 39.47 3.86
5278 6873 1.073284 TGGAACCACCTTTACTCCAGC 59.927 52.381 0.00 0.00 39.86 4.85
5279 6874 1.073284 GGAACCACCTTTACTCCAGCA 59.927 52.381 0.00 0.00 35.41 4.41
5280 6875 2.488347 GGAACCACCTTTACTCCAGCAA 60.488 50.000 0.00 0.00 35.41 3.91
5281 6876 2.568623 ACCACCTTTACTCCAGCAAG 57.431 50.000 0.00 0.00 0.00 4.01
5282 6877 1.168714 CCACCTTTACTCCAGCAAGC 58.831 55.000 0.00 0.00 0.00 4.01
5283 6878 0.798776 CACCTTTACTCCAGCAAGCG 59.201 55.000 0.00 0.00 0.00 4.68
5284 6879 0.685097 ACCTTTACTCCAGCAAGCGA 59.315 50.000 0.00 0.00 0.00 4.93
5285 6880 1.079503 CCTTTACTCCAGCAAGCGAC 58.920 55.000 0.00 0.00 0.00 5.19
5286 6881 1.338200 CCTTTACTCCAGCAAGCGACT 60.338 52.381 0.00 0.00 0.00 4.18
5287 6882 2.417719 CTTTACTCCAGCAAGCGACTT 58.582 47.619 0.00 0.00 0.00 3.01
5288 6883 2.080286 TTACTCCAGCAAGCGACTTC 57.920 50.000 0.00 0.00 0.00 3.01
5289 6884 0.109272 TACTCCAGCAAGCGACTTCG 60.109 55.000 0.00 0.00 43.27 3.79
5290 6885 1.080501 CTCCAGCAAGCGACTTCGA 60.081 57.895 2.02 0.00 43.02 3.71
5291 6886 1.347817 CTCCAGCAAGCGACTTCGAC 61.348 60.000 2.02 0.00 43.02 4.20
5292 6887 1.373497 CCAGCAAGCGACTTCGACT 60.373 57.895 2.02 0.00 43.02 4.18
5293 6888 0.946221 CCAGCAAGCGACTTCGACTT 60.946 55.000 2.02 2.91 43.02 3.01
5294 6889 0.436531 CAGCAAGCGACTTCGACTTC 59.563 55.000 2.02 1.48 43.02 3.01
5295 6890 1.004277 AGCAAGCGACTTCGACTTCG 61.004 55.000 9.92 9.92 43.02 3.79
5358 6953 1.418373 GACCAAAGCCAAACAATCGC 58.582 50.000 0.00 0.00 0.00 4.58
5438 7033 1.678635 GCATGCCTGGCACCTACAA 60.679 57.895 25.99 0.00 43.04 2.41
5460 7055 0.975556 TCCAGACTGCCAATCGCCTA 60.976 55.000 0.00 0.00 36.24 3.93
5465 7060 0.107017 ACTGCCAATCGCCTAGCATT 60.107 50.000 0.00 0.00 36.24 3.56
5475 7070 1.305219 GCCTAGCATTGTTGTCGCCA 61.305 55.000 0.00 0.00 0.00 5.69
5497 7092 1.246056 TAGCCCTACAACGTCGCAGT 61.246 55.000 0.00 0.00 0.00 4.40
5500 7095 0.038526 CCCTACAACGTCGCAGTTCT 60.039 55.000 0.00 0.00 30.96 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 1.376037 CTCGGCCTTCAAGTCCACC 60.376 63.158 0.00 0.00 0.00 4.61
283 286 6.576313 CACAAGATCGAAAGACATGAAAACAG 59.424 38.462 0.00 0.00 46.97 3.16
303 306 8.286800 TGAACACGGAAATAAATTCTACACAAG 58.713 33.333 0.00 0.00 38.18 3.16
337 340 3.827898 CACTCCGAGCGGGTCCTC 61.828 72.222 9.29 0.00 37.00 3.71
421 424 8.028652 TCCACAAATTTTCCCAAGATACTTTT 57.971 30.769 0.00 0.00 0.00 2.27
551 556 9.449719 AGTTCAAGTTTCTCTTCTGAAGTTTTA 57.550 29.630 16.43 0.00 33.63 1.52
644 654 5.049828 CCCAACTCACAAAAGTCAAATTCC 58.950 41.667 0.00 0.00 0.00 3.01
743 2275 9.557338 TTTCTGAAAACAAAGAAAAATTGCATG 57.443 25.926 0.00 0.00 38.98 4.06
882 2416 2.102357 CGTCGATCCGTCCCACTG 59.898 66.667 0.00 0.00 0.00 3.66
904 2438 0.960364 TGGAGGCGTTGGATTGAAGC 60.960 55.000 0.00 0.00 0.00 3.86
930 2464 1.673329 GGGAAAGAGAAGGAGACGTGC 60.673 57.143 0.00 0.00 0.00 5.34
954 2488 3.124066 GGAGAGGGATTTTTAGGGAGGT 58.876 50.000 0.00 0.00 0.00 3.85
1313 2849 7.147672 ACCCAAACAAAATCTTCATCACTTCTT 60.148 33.333 0.00 0.00 0.00 2.52
1322 2858 5.205056 ACCACTACCCAAACAAAATCTTCA 58.795 37.500 0.00 0.00 0.00 3.02
1335 2871 1.462432 TCCCAGCAACCACTACCCA 60.462 57.895 0.00 0.00 0.00 4.51
1356 2892 0.309612 GTTTTACACTGGCACACCCG 59.690 55.000 0.00 0.00 35.87 5.28
1364 2900 4.664150 AACCCAACATGTTTTACACTGG 57.336 40.909 8.77 5.90 0.00 4.00
1372 2908 5.843969 AGAAATCCCTAAACCCAACATGTTT 59.156 36.000 8.77 0.00 39.19 2.83
1433 2969 7.744715 CCTCGTAATAAGAACACAATGAAACAC 59.255 37.037 0.00 0.00 0.00 3.32
1438 2974 6.588756 GTCACCTCGTAATAAGAACACAATGA 59.411 38.462 0.00 0.00 0.00 2.57
1490 3026 3.742369 TCCACAAAACTTACCGAACGATC 59.258 43.478 0.00 0.00 0.00 3.69
1495 3031 4.452825 TGACATCCACAAAACTTACCGAA 58.547 39.130 0.00 0.00 0.00 4.30
1596 3133 6.243216 ACTAATATCTTTGCGAACCCCTAA 57.757 37.500 0.00 0.00 0.00 2.69
1599 3136 5.049612 GCTAACTAATATCTTTGCGAACCCC 60.050 44.000 0.00 0.00 0.00 4.95
1736 3275 7.615365 TCAACCTTCAACTATCAGGCAATTTAT 59.385 33.333 0.00 0.00 0.00 1.40
1749 3316 5.560722 TGACTTGGATCAACCTTCAACTA 57.439 39.130 0.00 0.00 39.86 2.24
1794 3361 1.006832 GTGCGTGACTTGTCAGTTGT 58.993 50.000 3.45 0.00 31.22 3.32
1838 3405 1.118838 CTCTGGATCCACTGGAGTCC 58.881 60.000 11.44 0.73 34.05 3.85
1972 3539 2.355010 CCCAAAGGCCAGGAGATAAG 57.645 55.000 5.01 0.00 0.00 1.73
2044 3611 3.558829 CAGTGCATAGATGAGCAAATCGT 59.441 43.478 0.00 0.00 43.20 3.73
2274 3841 5.481824 TCTTGGATCAGAGAGCAAGTTTCTA 59.518 40.000 0.00 0.00 0.00 2.10
2474 4044 3.181496 GCAGCTAAATAGGAACCTGTTGC 60.181 47.826 3.36 4.42 0.00 4.17
2680 4250 2.665165 CTAGCTCATGAGACCTGGTCT 58.335 52.381 28.70 28.70 46.42 3.85
2681 4251 1.068434 GCTAGCTCATGAGACCTGGTC 59.932 57.143 27.04 19.20 0.00 4.02
2682 4252 1.118838 GCTAGCTCATGAGACCTGGT 58.881 55.000 27.04 7.86 0.00 4.00
2683 4253 1.068895 CTGCTAGCTCATGAGACCTGG 59.931 57.143 27.04 16.58 0.00 4.45
2684 4254 1.068895 CCTGCTAGCTCATGAGACCTG 59.931 57.143 27.04 12.94 0.00 4.00
2685 4255 1.342874 ACCTGCTAGCTCATGAGACCT 60.343 52.381 27.04 16.44 0.00 3.85
2686 4256 1.118838 ACCTGCTAGCTCATGAGACC 58.881 55.000 27.04 9.56 0.00 3.85
2687 4257 1.753649 TCACCTGCTAGCTCATGAGAC 59.246 52.381 27.04 16.75 0.00 3.36
2688 4258 2.030371 CTCACCTGCTAGCTCATGAGA 58.970 52.381 27.04 5.37 36.50 3.27
2689 4259 2.030371 TCTCACCTGCTAGCTCATGAG 58.970 52.381 24.80 24.80 35.87 2.90
2690 4260 1.753649 GTCTCACCTGCTAGCTCATGA 59.246 52.381 17.23 14.48 0.00 3.07
2691 4261 1.202510 GGTCTCACCTGCTAGCTCATG 60.203 57.143 17.23 10.94 34.73 3.07
2692 4262 1.118838 GGTCTCACCTGCTAGCTCAT 58.881 55.000 17.23 0.00 34.73 2.90
2693 4263 0.972983 GGGTCTCACCTGCTAGCTCA 60.973 60.000 17.23 0.00 38.64 4.26
2694 4264 0.972983 TGGGTCTCACCTGCTAGCTC 60.973 60.000 17.23 0.00 38.64 4.09
2695 4265 1.079256 TGGGTCTCACCTGCTAGCT 59.921 57.895 17.23 0.00 38.64 3.32
2696 4266 1.219393 GTGGGTCTCACCTGCTAGC 59.781 63.158 8.10 8.10 40.39 3.42
2704 4274 0.909610 TCCATCAGGGTGGGTCTCAC 60.910 60.000 0.00 0.00 45.34 3.51
2705 4275 0.044702 ATCCATCAGGGTGGGTCTCA 59.955 55.000 0.00 0.00 39.80 3.27
2706 4276 0.471617 CATCCATCAGGGTGGGTCTC 59.528 60.000 0.00 0.00 42.67 3.36
2707 4277 0.044702 TCATCCATCAGGGTGGGTCT 59.955 55.000 0.00 0.00 46.59 3.85
2708 4278 2.620234 TCATCCATCAGGGTGGGTC 58.380 57.895 0.00 0.00 46.59 4.46
2709 4279 4.940571 TCATCCATCAGGGTGGGT 57.059 55.556 0.00 0.00 46.59 4.51
3036 4606 3.057876 GGATGACACGTGGCATTTACAAA 60.058 43.478 36.07 7.37 45.42 2.83
3037 4607 2.486203 GGATGACACGTGGCATTTACAA 59.514 45.455 36.07 8.22 45.42 2.41
3038 4608 2.080693 GGATGACACGTGGCATTTACA 58.919 47.619 36.07 9.07 45.42 2.41
3039 4609 2.080693 TGGATGACACGTGGCATTTAC 58.919 47.619 36.07 27.36 45.42 2.01
3040 4610 2.481289 TGGATGACACGTGGCATTTA 57.519 45.000 36.07 24.74 45.42 1.40
3041 4611 1.745087 GATGGATGACACGTGGCATTT 59.255 47.619 36.07 23.79 45.42 2.32
3042 4612 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
3044 4614 0.036022 TTGATGGATGACACGTGGCA 59.964 50.000 29.28 29.28 37.54 4.92
3045 4615 0.729116 CTTGATGGATGACACGTGGC 59.271 55.000 21.57 19.24 0.00 5.01
3046 4616 2.385013 TCTTGATGGATGACACGTGG 57.615 50.000 21.57 1.66 0.00 4.94
3047 4617 2.610833 CCATCTTGATGGATGACACGTG 59.389 50.000 21.56 15.48 44.01 4.49
3048 4618 2.420547 CCCATCTTGATGGATGACACGT 60.421 50.000 26.19 0.00 44.01 4.49
3049 4619 2.216046 CCCATCTTGATGGATGACACG 58.784 52.381 26.19 7.99 44.01 4.49
3050 4620 3.118112 AGACCCATCTTGATGGATGACAC 60.118 47.826 26.19 12.60 44.01 3.67
3051 4621 3.117745 AGACCCATCTTGATGGATGACA 58.882 45.455 26.19 0.00 44.01 3.58
3052 4622 3.135348 TGAGACCCATCTTGATGGATGAC 59.865 47.826 26.19 16.12 44.01 3.06
3053 4623 3.387012 TGAGACCCATCTTGATGGATGA 58.613 45.455 26.19 7.60 44.01 2.92
3054 4624 3.851458 TGAGACCCATCTTGATGGATG 57.149 47.619 26.19 15.20 44.39 3.51
3055 4625 5.514484 GCTTATGAGACCCATCTTGATGGAT 60.514 44.000 26.19 13.41 44.39 3.41
3056 4626 4.202398 GCTTATGAGACCCATCTTGATGGA 60.202 45.833 26.19 10.10 44.39 3.41
3057 4627 4.070716 GCTTATGAGACCCATCTTGATGG 58.929 47.826 19.73 19.73 41.34 3.51
3058 4628 4.970711 AGCTTATGAGACCCATCTTGATG 58.029 43.478 3.77 3.77 34.34 3.07
3059 4629 5.279910 GCTAGCTTATGAGACCCATCTTGAT 60.280 44.000 7.70 0.00 34.34 2.57
3060 4630 4.039730 GCTAGCTTATGAGACCCATCTTGA 59.960 45.833 7.70 0.00 34.34 3.02
3061 4631 4.314121 GCTAGCTTATGAGACCCATCTTG 58.686 47.826 7.70 0.00 34.34 3.02
3062 4632 3.326297 GGCTAGCTTATGAGACCCATCTT 59.674 47.826 15.72 0.00 34.34 2.40
3063 4633 2.903135 GGCTAGCTTATGAGACCCATCT 59.097 50.000 15.72 0.00 38.15 2.90
3064 4634 2.027653 GGGCTAGCTTATGAGACCCATC 60.028 54.545 15.72 0.00 34.39 3.51
3065 4635 1.981495 GGGCTAGCTTATGAGACCCAT 59.019 52.381 15.72 0.00 34.39 4.00
3066 4636 1.424638 GGGCTAGCTTATGAGACCCA 58.575 55.000 15.72 0.00 34.39 4.51
3067 4637 0.318762 CGGGCTAGCTTATGAGACCC 59.681 60.000 15.72 2.63 37.62 4.46
3068 4638 1.041437 ACGGGCTAGCTTATGAGACC 58.959 55.000 15.72 3.40 37.53 3.85
3069 4639 1.681793 TCACGGGCTAGCTTATGAGAC 59.318 52.381 15.72 0.00 0.00 3.36
3070 4640 1.957177 CTCACGGGCTAGCTTATGAGA 59.043 52.381 25.59 12.99 36.50 3.27
3071 4641 1.957177 TCTCACGGGCTAGCTTATGAG 59.043 52.381 24.61 24.61 35.87 2.90
3072 4642 1.681793 GTCTCACGGGCTAGCTTATGA 59.318 52.381 15.72 13.80 0.00 2.15
3073 4643 1.269831 GGTCTCACGGGCTAGCTTATG 60.270 57.143 15.72 10.21 0.00 1.90
3074 4644 1.041437 GGTCTCACGGGCTAGCTTAT 58.959 55.000 15.72 0.00 0.00 1.73
3075 4645 0.033405 AGGTCTCACGGGCTAGCTTA 60.033 55.000 15.72 0.00 0.00 3.09
3076 4646 1.305381 AGGTCTCACGGGCTAGCTT 60.305 57.895 15.72 0.00 0.00 3.74
3077 4647 2.055042 CAGGTCTCACGGGCTAGCT 61.055 63.158 15.72 0.00 0.00 3.32
3078 4648 2.496817 CAGGTCTCACGGGCTAGC 59.503 66.667 6.04 6.04 0.00 3.42
3079 4649 1.668101 GACCAGGTCTCACGGGCTAG 61.668 65.000 12.94 0.00 0.00 3.42
3080 4650 1.681327 GACCAGGTCTCACGGGCTA 60.681 63.158 12.94 0.00 0.00 3.93
3081 4651 2.997897 GACCAGGTCTCACGGGCT 60.998 66.667 12.94 0.00 0.00 5.19
3082 4652 2.997897 AGACCAGGTCTCACGGGC 60.998 66.667 17.31 0.00 38.71 6.13
3089 4659 8.214364 GGAAAAGAATTATATGAGACCAGGTCT 58.786 37.037 23.18 23.18 46.42 3.85
3090 4660 7.445707 GGGAAAAGAATTATATGAGACCAGGTC 59.554 40.741 12.25 12.25 0.00 3.85
3091 4661 7.290813 GGGAAAAGAATTATATGAGACCAGGT 58.709 38.462 0.00 0.00 0.00 4.00
3092 4662 6.717084 GGGGAAAAGAATTATATGAGACCAGG 59.283 42.308 0.00 0.00 0.00 4.45
3093 4663 7.290061 TGGGGAAAAGAATTATATGAGACCAG 58.710 38.462 0.00 0.00 0.00 4.00
3094 4664 7.219601 TGGGGAAAAGAATTATATGAGACCA 57.780 36.000 0.00 0.00 0.00 4.02
3095 4665 7.780271 ACTTGGGGAAAAGAATTATATGAGACC 59.220 37.037 0.00 0.00 0.00 3.85
3096 4666 8.624776 CACTTGGGGAAAAGAATTATATGAGAC 58.375 37.037 0.00 0.00 0.00 3.36
3097 4667 8.556589 TCACTTGGGGAAAAGAATTATATGAGA 58.443 33.333 0.00 0.00 0.00 3.27
3098 4668 8.752005 TCACTTGGGGAAAAGAATTATATGAG 57.248 34.615 0.00 0.00 0.00 2.90
3099 4669 7.285401 GCTCACTTGGGGAAAAGAATTATATGA 59.715 37.037 0.00 0.00 0.00 2.15
3100 4670 7.286316 AGCTCACTTGGGGAAAAGAATTATATG 59.714 37.037 0.00 0.00 0.00 1.78
3101 4671 7.357471 AGCTCACTTGGGGAAAAGAATTATAT 58.643 34.615 0.00 0.00 0.00 0.86
3102 4672 6.731467 AGCTCACTTGGGGAAAAGAATTATA 58.269 36.000 0.00 0.00 0.00 0.98
3103 4673 5.583932 AGCTCACTTGGGGAAAAGAATTAT 58.416 37.500 0.00 0.00 0.00 1.28
3104 4674 4.998051 AGCTCACTTGGGGAAAAGAATTA 58.002 39.130 0.00 0.00 0.00 1.40
3105 4675 3.849527 AGCTCACTTGGGGAAAAGAATT 58.150 40.909 0.00 0.00 0.00 2.17
3106 4676 3.532641 AGCTCACTTGGGGAAAAGAAT 57.467 42.857 0.00 0.00 0.00 2.40
3107 4677 3.810743 GCTAGCTCACTTGGGGAAAAGAA 60.811 47.826 7.70 0.00 0.00 2.52
3108 4678 2.290323 GCTAGCTCACTTGGGGAAAAGA 60.290 50.000 7.70 0.00 0.00 2.52
3109 4679 2.087646 GCTAGCTCACTTGGGGAAAAG 58.912 52.381 7.70 0.00 0.00 2.27
3110 4680 1.705186 AGCTAGCTCACTTGGGGAAAA 59.295 47.619 12.68 0.00 0.00 2.29
3111 4681 1.362224 AGCTAGCTCACTTGGGGAAA 58.638 50.000 12.68 0.00 0.00 3.13
3112 4682 2.111384 CTAGCTAGCTCACTTGGGGAA 58.889 52.381 23.26 0.00 0.00 3.97
3113 4683 1.689575 CCTAGCTAGCTCACTTGGGGA 60.690 57.143 23.26 0.00 0.00 4.81
3114 4684 0.755686 CCTAGCTAGCTCACTTGGGG 59.244 60.000 23.26 9.21 0.00 4.96
3253 4823 8.560355 AAAACCAAGCTCAACAAAAATTACTT 57.440 26.923 0.00 0.00 0.00 2.24
3270 4840 4.753516 AAAGGGAAGACCAAAAACCAAG 57.246 40.909 0.00 0.00 43.89 3.61
3356 4927 9.038803 GTCATGCATATCGATCATGTATTATGT 57.961 33.333 19.37 0.46 38.82 2.29
3359 4930 7.555087 TGGTCATGCATATCGATCATGTATTA 58.445 34.615 19.37 9.21 38.82 0.98
3370 4941 7.889589 TTACTCTTAATGGTCATGCATATCG 57.110 36.000 0.00 0.00 0.00 2.92
3393 4964 9.158233 CACAAATGGAAGAATAAATCTGCATTT 57.842 29.630 0.00 0.00 38.79 2.32
3420 4991 9.410556 CCGTCAGTTCATGAAATCTTTTAAAAT 57.589 29.630 10.35 0.00 40.43 1.82
3464 5035 3.660970 TTGCTTATGTGCCCATTCCTA 57.339 42.857 0.00 0.00 32.29 2.94
3499 5070 0.240945 GTTGAGACGCCCATTGTTGG 59.759 55.000 0.00 0.00 43.23 3.77
3620 5191 2.095853 GGATGTGCATCTGTGTAAACGG 59.904 50.000 11.39 0.00 37.92 4.44
3641 5212 5.841237 TCTATGAGTAATGGAAGGGAGAAGG 59.159 44.000 0.00 0.00 0.00 3.46
3704 5275 9.594038 CAATAAAATATATGTCGCTGTGGTTAC 57.406 33.333 0.00 0.00 0.00 2.50
3708 5279 7.361201 CCTCCAATAAAATATATGTCGCTGTGG 60.361 40.741 0.00 0.00 0.00 4.17
3914 5485 2.159517 GCATCCATCAAAAGTGGTCGAC 60.160 50.000 7.13 7.13 37.96 4.20
3921 5492 2.799017 TGCAGAGCATCCATCAAAAGT 58.201 42.857 0.00 0.00 33.66 2.66
4617 6188 6.803320 ACAATTTAGCGTCAAAATCATCACAG 59.197 34.615 0.00 0.00 0.00 3.66
4786 6358 7.309194 CCTGATTTATTTTTCGAAACACCTCCT 60.309 37.037 10.79 0.00 0.00 3.69
4789 6364 7.284919 ACCTGATTTATTTTTCGAAACACCT 57.715 32.000 10.79 0.00 0.00 4.00
4915 6491 1.959042 TGCAATGCTAGGCTCTTAGC 58.041 50.000 6.82 0.71 44.97 3.09
4922 6498 0.600057 GGCCTTATGCAATGCTAGGC 59.400 55.000 26.54 26.54 42.69 3.93
5001 6578 3.676540 CGTGTTGTAACAGTTTTCGCTT 58.323 40.909 0.00 0.00 40.05 4.68
5042 6619 2.282180 GTGGGTGCCATGTCGGTT 60.282 61.111 0.00 0.00 35.28 4.44
5071 6648 6.460781 ACATTGTAGACAATCTCAACGGTAA 58.539 36.000 4.90 0.00 44.10 2.85
5072 6649 6.032956 ACATTGTAGACAATCTCAACGGTA 57.967 37.500 4.90 0.00 44.10 4.02
5099 6693 1.552337 GCTGGAGAAGAGGTGATGACA 59.448 52.381 0.00 0.00 0.00 3.58
5112 6706 2.973899 GGAGTCGCTTGCTGGAGA 59.026 61.111 0.00 0.00 0.00 3.71
5157 6752 1.616725 GGTGGTTCCATGGCTCATTCA 60.617 52.381 6.96 0.00 35.97 2.57
5161 6756 0.482446 AAAGGTGGTTCCATGGCTCA 59.518 50.000 6.96 1.91 39.02 4.26
5211 6806 0.533531 GTTCGTTTGGAAGGGTCGGT 60.534 55.000 0.00 0.00 34.69 4.69
5216 6811 1.852067 CGGCAGTTCGTTTGGAAGGG 61.852 60.000 0.00 0.00 34.69 3.95
5217 6812 0.882927 TCGGCAGTTCGTTTGGAAGG 60.883 55.000 0.00 0.00 34.69 3.46
5218 6813 0.234884 GTCGGCAGTTCGTTTGGAAG 59.765 55.000 0.00 0.00 34.69 3.46
5219 6814 1.161563 GGTCGGCAGTTCGTTTGGAA 61.162 55.000 0.00 0.00 0.00 3.53
5220 6815 1.595929 GGTCGGCAGTTCGTTTGGA 60.596 57.895 0.00 0.00 0.00 3.53
5221 6816 2.613506 GGGTCGGCAGTTCGTTTGG 61.614 63.158 0.00 0.00 0.00 3.28
5222 6817 1.164041 AAGGGTCGGCAGTTCGTTTG 61.164 55.000 0.00 0.00 0.00 2.93
5223 6818 0.464916 AAAGGGTCGGCAGTTCGTTT 60.465 50.000 0.00 0.00 0.00 3.60
5224 6819 0.883370 GAAAGGGTCGGCAGTTCGTT 60.883 55.000 0.00 0.00 0.00 3.85
5225 6820 1.301479 GAAAGGGTCGGCAGTTCGT 60.301 57.895 0.00 0.00 0.00 3.85
5226 6821 2.380410 CGAAAGGGTCGGCAGTTCG 61.380 63.158 4.89 4.89 46.45 3.95
5227 6822 3.562635 CGAAAGGGTCGGCAGTTC 58.437 61.111 0.00 0.00 46.45 3.01
5235 6830 2.356069 GGCTCATTCATTCGAAAGGGTC 59.644 50.000 0.00 0.00 34.01 4.46
5236 6831 2.290896 TGGCTCATTCATTCGAAAGGGT 60.291 45.455 0.00 0.00 34.01 4.34
5237 6832 2.368439 TGGCTCATTCATTCGAAAGGG 58.632 47.619 0.00 0.00 34.01 3.95
5238 6833 3.243301 CCATGGCTCATTCATTCGAAAGG 60.243 47.826 0.00 0.00 34.01 3.11
5239 6834 3.628942 TCCATGGCTCATTCATTCGAAAG 59.371 43.478 6.96 0.00 34.01 2.62
5240 6835 3.619419 TCCATGGCTCATTCATTCGAAA 58.381 40.909 6.96 0.00 34.01 3.46
5241 6836 3.280197 TCCATGGCTCATTCATTCGAA 57.720 42.857 6.96 0.00 35.05 3.71
5242 6837 2.945008 GTTCCATGGCTCATTCATTCGA 59.055 45.455 6.96 0.00 0.00 3.71
5243 6838 2.033801 GGTTCCATGGCTCATTCATTCG 59.966 50.000 6.96 0.00 0.00 3.34
5244 6839 3.025978 TGGTTCCATGGCTCATTCATTC 58.974 45.455 6.96 0.00 0.00 2.67
5245 6840 2.762327 GTGGTTCCATGGCTCATTCATT 59.238 45.455 6.96 0.00 0.00 2.57
5246 6841 2.381911 GTGGTTCCATGGCTCATTCAT 58.618 47.619 6.96 0.00 0.00 2.57
5247 6842 1.616725 GGTGGTTCCATGGCTCATTCA 60.617 52.381 6.96 0.00 35.97 2.57
5248 6843 1.106285 GGTGGTTCCATGGCTCATTC 58.894 55.000 6.96 0.00 35.97 2.67
5249 6844 0.706433 AGGTGGTTCCATGGCTCATT 59.294 50.000 6.96 0.00 39.02 2.57
5250 6845 0.706433 AAGGTGGTTCCATGGCTCAT 59.294 50.000 6.96 0.00 39.02 2.90
5251 6846 0.482446 AAAGGTGGTTCCATGGCTCA 59.518 50.000 6.96 1.91 39.02 4.26
5252 6847 2.092323 GTAAAGGTGGTTCCATGGCTC 58.908 52.381 6.96 1.88 39.02 4.70
5253 6848 1.710809 AGTAAAGGTGGTTCCATGGCT 59.289 47.619 6.96 0.00 39.02 4.75
5254 6849 2.092323 GAGTAAAGGTGGTTCCATGGC 58.908 52.381 6.96 0.00 39.02 4.40
5255 6850 2.041081 TGGAGTAAAGGTGGTTCCATGG 59.959 50.000 4.97 4.97 39.02 3.66
5256 6851 3.347216 CTGGAGTAAAGGTGGTTCCATG 58.653 50.000 0.00 0.00 37.32 3.66
5257 6852 2.290960 GCTGGAGTAAAGGTGGTTCCAT 60.291 50.000 0.00 0.00 37.32 3.41
5258 6853 1.073284 GCTGGAGTAAAGGTGGTTCCA 59.927 52.381 0.00 0.00 39.02 3.53
5259 6854 1.073284 TGCTGGAGTAAAGGTGGTTCC 59.927 52.381 0.00 0.00 0.00 3.62
5260 6855 2.561478 TGCTGGAGTAAAGGTGGTTC 57.439 50.000 0.00 0.00 0.00 3.62
5261 6856 2.863809 CTTGCTGGAGTAAAGGTGGTT 58.136 47.619 0.00 0.00 0.00 3.67
5262 6857 1.545651 GCTTGCTGGAGTAAAGGTGGT 60.546 52.381 0.00 0.00 0.00 4.16
5263 6858 1.168714 GCTTGCTGGAGTAAAGGTGG 58.831 55.000 0.00 0.00 0.00 4.61
5264 6859 0.798776 CGCTTGCTGGAGTAAAGGTG 59.201 55.000 0.00 0.00 0.00 4.00
5265 6860 0.685097 TCGCTTGCTGGAGTAAAGGT 59.315 50.000 0.00 0.00 0.00 3.50
5266 6861 1.079503 GTCGCTTGCTGGAGTAAAGG 58.920 55.000 0.00 0.00 0.00 3.11
5267 6862 2.086054 AGTCGCTTGCTGGAGTAAAG 57.914 50.000 0.00 0.00 0.00 1.85
5268 6863 2.413837 GAAGTCGCTTGCTGGAGTAAA 58.586 47.619 0.00 0.00 0.00 2.01
5269 6864 1.668919 CGAAGTCGCTTGCTGGAGTAA 60.669 52.381 0.00 0.00 0.00 2.24
5270 6865 0.109272 CGAAGTCGCTTGCTGGAGTA 60.109 55.000 0.00 0.00 0.00 2.59
5271 6866 1.373497 CGAAGTCGCTTGCTGGAGT 60.373 57.895 0.00 0.00 0.00 3.85
5272 6867 1.080501 TCGAAGTCGCTTGCTGGAG 60.081 57.895 0.00 0.00 39.60 3.86
5273 6868 1.372997 GTCGAAGTCGCTTGCTGGA 60.373 57.895 0.00 0.00 39.60 3.86
5274 6869 0.946221 AAGTCGAAGTCGCTTGCTGG 60.946 55.000 8.79 0.00 39.60 4.85
5275 6870 0.436531 GAAGTCGAAGTCGCTTGCTG 59.563 55.000 12.77 0.00 36.44 4.41
5276 6871 1.004277 CGAAGTCGAAGTCGCTTGCT 61.004 55.000 12.77 0.05 43.02 3.91
5277 6872 1.002250 TCGAAGTCGAAGTCGCTTGC 61.002 55.000 12.81 6.34 46.30 4.01
5278 6873 3.087638 TCGAAGTCGAAGTCGCTTG 57.912 52.632 12.81 7.52 46.30 4.01
5288 6883 4.394078 TCGGTGGCGTCGAAGTCG 62.394 66.667 0.00 0.00 42.81 4.18
5289 6884 2.804090 GTCGGTGGCGTCGAAGTC 60.804 66.667 0.00 0.00 38.42 3.01
5290 6885 4.353437 GGTCGGTGGCGTCGAAGT 62.353 66.667 0.00 0.00 38.42 3.01
5295 6890 4.754667 GGAAGGGTCGGTGGCGTC 62.755 72.222 0.00 0.00 0.00 5.19
5298 6893 4.011517 TTCGGAAGGGTCGGTGGC 62.012 66.667 0.00 0.00 0.00 5.01
5299 6894 2.047560 GTTCGGAAGGGTCGGTGG 60.048 66.667 0.00 0.00 0.00 4.61
5300 6895 2.424705 TTCGTTCGGAAGGGTCGGTG 62.425 60.000 10.23 0.00 0.00 4.94
5301 6896 2.202395 TTCGTTCGGAAGGGTCGGT 61.202 57.895 10.23 0.00 0.00 4.69
5302 6897 1.735559 GTTCGTTCGGAAGGGTCGG 60.736 63.158 10.23 0.00 34.69 4.79
5303 6898 2.084681 CGTTCGTTCGGAAGGGTCG 61.085 63.158 10.23 10.79 36.98 4.79
5334 6929 1.323271 TGTTTGGCTTTGGTCGGCAA 61.323 50.000 0.00 0.00 43.89 4.52
5358 6953 1.139095 GGTCCTCGACGTAGCCAAG 59.861 63.158 0.00 0.00 32.65 3.61
5364 6959 1.065636 AGATGTCTGGTCCTCGACGTA 60.066 52.381 6.59 0.00 32.65 3.57
5438 7033 0.674895 GCGATTGGCAGTCTGGACTT 60.675 55.000 8.43 0.00 40.20 3.01
5460 7055 0.601576 TACGTGGCGACAACAATGCT 60.602 50.000 0.00 0.00 46.06 3.79
5465 7060 2.356553 GGCTACGTGGCGACAACA 60.357 61.111 18.14 0.00 46.06 3.33


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

AutoCloner maintained by Alex Coulton.