Multiple sequence alignment - TraesCS5A01G323900

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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 TraesCS5A01G323900 chr5A 100.000 5242 0 0 1 5242 535532477 535527236 0.000000e+00 9681.0
1 TraesCS5A01G323900 chr5A 84.841 1260 185 3 2862 4120 535521009 535519755 0.000000e+00 1264.0
2 TraesCS5A01G323900 chr5A 79.868 909 170 10 989 1892 535522958 535522058 0.000000e+00 652.0
3 TraesCS5A01G323900 chr5A 86.207 319 38 4 2339 2656 535521475 535521162 1.810000e-89 340.0
4 TraesCS5A01G323900 chr5A 82.215 298 53 0 3602 3899 535572072 535571775 1.870000e-64 257.0
5 TraesCS5A01G323900 chr5A 82.609 92 13 3 2676 2765 487357360 487357450 1.570000e-10 78.7
6 TraesCS5A01G323900 chr5B 91.739 2070 135 21 2756 4808 508682011 508679961 0.000000e+00 2843.0
7 TraesCS5A01G323900 chr5B 88.529 1142 127 2 755 1896 508683994 508682857 0.000000e+00 1380.0
8 TraesCS5A01G323900 chr5B 83.632 1338 202 8 2775 4103 508676720 508675391 0.000000e+00 1242.0
9 TraesCS5A01G323900 chr5B 84.894 940 135 5 2863 3801 508781301 508780368 0.000000e+00 942.0
10 TraesCS5A01G323900 chr5B 90.948 696 46 3 3 681 508685073 508684378 0.000000e+00 920.0
11 TraesCS5A01G323900 chr5B 78.924 911 172 10 999 1896 508678515 508677612 7.510000e-168 601.0
12 TraesCS5A01G323900 chr5B 81.266 758 88 25 1951 2679 508682739 508682007 9.850000e-157 564.0
13 TraesCS5A01G323900 chr5B 79.789 757 128 14 999 1743 508783897 508783154 1.290000e-145 527.0
14 TraesCS5A01G323900 chr5B 87.346 324 32 6 2339 2656 508677102 508676782 3.860000e-96 363.0
15 TraesCS5A01G323900 chr5B 81.602 337 57 5 2913 3248 508729989 508729657 1.860000e-69 274.0
16 TraesCS5A01G323900 chr5B 86.047 86 10 2 2675 2758 399811641 399811556 2.010000e-14 91.6
17 TraesCS5A01G323900 chr5D 93.956 1605 82 8 2996 4599 421992898 421991308 0.000000e+00 2412.0
18 TraesCS5A01G323900 chr5D 94.974 1174 51 6 725 1896 421995704 421994537 0.000000e+00 1834.0
19 TraesCS5A01G323900 chr5D 92.909 1100 39 15 1900 2961 421994496 421993398 0.000000e+00 1563.0
20 TraesCS5A01G323900 chr5D 84.826 1351 188 11 2762 4103 421987357 421986015 0.000000e+00 1343.0
21 TraesCS5A01G323900 chr5D 83.333 1218 197 5 2913 4128 422001401 422000188 0.000000e+00 1120.0
22 TraesCS5A01G323900 chr5D 83.052 1186 177 12 2760 3935 422012090 422010919 0.000000e+00 1055.0
23 TraesCS5A01G323900 chr5D 89.112 698 42 6 1 681 421996724 421996044 0.000000e+00 837.0
24 TraesCS5A01G323900 chr5D 79.093 904 173 13 999 1894 421989162 421988267 4.490000e-170 608.0
25 TraesCS5A01G323900 chr5D 80.306 589 74 26 2117 2677 422012663 422012089 1.760000e-109 407.0
26 TraesCS5A01G323900 chr5D 86.567 335 37 6 2339 2671 421987692 421987364 3.860000e-96 363.0
27 TraesCS5A01G323900 chr5D 88.276 290 33 1 4953 5241 480853192 480852903 3.890000e-91 346.0
28 TraesCS5A01G323900 chr5D 75.319 235 54 4 3229 3461 446876368 446876136 5.550000e-20 110.0
29 TraesCS5A01G323900 chr3A 84.818 685 88 15 1 678 66796453 66797128 0.000000e+00 675.0
30 TraesCS5A01G323900 chr3A 83.865 564 78 7 124 678 18797894 18797335 4.650000e-145 525.0
31 TraesCS5A01G323900 chr1A 83.895 683 106 4 1 681 256951360 256950680 0.000000e+00 649.0
32 TraesCS5A01G323900 chr1D 83.564 651 95 9 30 678 334245674 334246314 2.700000e-167 599.0
33 TraesCS5A01G323900 chr1D 88.215 297 33 2 4946 5241 33841481 33841776 2.320000e-93 353.0
34 TraesCS5A01G323900 chr2B 85.140 572 80 5 1 569 474349960 474349391 9.790000e-162 580.0
35 TraesCS5A01G323900 chr2B 87.213 305 35 4 4939 5241 377519256 377518954 1.400000e-90 344.0
36 TraesCS5A01G323900 chr2B 89.552 67 6 1 2695 2760 320343959 320344025 3.360000e-12 84.2
37 TraesCS5A01G323900 chr2D 86.640 509 67 1 171 678 327757288 327756780 3.540000e-156 562.0
38 TraesCS5A01G323900 chr2D 88.176 296 31 3 4948 5241 325339622 325339915 3.000000e-92 350.0
39 TraesCS5A01G323900 chr4D 83.670 594 86 10 1 589 46491475 46492062 2.760000e-152 549.0
40 TraesCS5A01G323900 chr4D 87.625 299 36 1 4944 5241 97780818 97781116 3.890000e-91 346.0
41 TraesCS5A01G323900 chr3D 90.365 301 25 4 4945 5242 433435591 433435292 4.920000e-105 392.0
42 TraesCS5A01G323900 chr7D 89.420 293 30 1 4950 5241 53629411 53629703 8.290000e-98 368.0
43 TraesCS5A01G323900 chr7D 76.601 765 110 42 1950 2664 104547782 104548527 1.800000e-94 357.0
44 TraesCS5A01G323900 chr7D 94.737 38 2 0 2725 2762 46911457 46911420 5.670000e-05 60.2
45 TraesCS5A01G323900 chr4B 88.963 299 32 1 4944 5241 172375012 172374714 8.290000e-98 368.0
46 TraesCS5A01G323900 chr1B 89.153 295 30 2 4948 5241 497149865 497149572 2.980000e-97 366.0
47 TraesCS5A01G323900 chr1B 84.783 92 9 3 2674 2760 317581135 317581044 2.600000e-13 87.9
48 TraesCS5A01G323900 chr4A 76.378 762 113 42 1950 2664 592497127 592497868 1.080000e-91 348.0
49 TraesCS5A01G323900 chr4A 76.378 762 113 43 1950 2664 593064013 593064754 1.080000e-91 348.0
50 TraesCS5A01G323900 chr2A 81.579 190 31 2 1 190 485778196 485778381 2.530000e-33 154.0
51 TraesCS5A01G323900 chr6D 80.667 150 23 3 1035 1184 29376648 29376505 1.540000e-20 111.0
52 TraesCS5A01G323900 chr6D 86.207 87 10 2 2676 2760 38155306 38155392 5.590000e-15 93.5
53 TraesCS5A01G323900 chr6D 89.796 49 1 4 2725 2773 79823333 79823377 5.670000e-05 60.2
54 TraesCS5A01G323900 chr7B 85.393 89 8 3 2676 2759 733368693 733368605 2.600000e-13 87.9


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 TraesCS5A01G323900 chr5A 535527236 535532477 5241 True 9681.000000 9681 100.000000 1 5242 1 chr5A.!!$R1 5241
1 TraesCS5A01G323900 chr5A 535519755 535522958 3203 True 752.000000 1264 83.638667 989 4120 3 chr5A.!!$R3 3131
2 TraesCS5A01G323900 chr5B 508675391 508685073 9682 True 1130.428571 2843 86.054857 3 4808 7 chr5B.!!$R3 4805
3 TraesCS5A01G323900 chr5B 508780368 508783897 3529 True 734.500000 942 82.341500 999 3801 2 chr5B.!!$R4 2802
4 TraesCS5A01G323900 chr5D 421986015 422001401 15386 True 1260.000000 2412 88.096250 1 4599 8 chr5D.!!$R3 4598
5 TraesCS5A01G323900 chr5D 422010919 422012663 1744 True 731.000000 1055 81.679000 2117 3935 2 chr5D.!!$R4 1818
6 TraesCS5A01G323900 chr3A 66796453 66797128 675 False 675.000000 675 84.818000 1 678 1 chr3A.!!$F1 677
7 TraesCS5A01G323900 chr3A 18797335 18797894 559 True 525.000000 525 83.865000 124 678 1 chr3A.!!$R1 554
8 TraesCS5A01G323900 chr1A 256950680 256951360 680 True 649.000000 649 83.895000 1 681 1 chr1A.!!$R1 680
9 TraesCS5A01G323900 chr1D 334245674 334246314 640 False 599.000000 599 83.564000 30 678 1 chr1D.!!$F2 648
10 TraesCS5A01G323900 chr2B 474349391 474349960 569 True 580.000000 580 85.140000 1 569 1 chr2B.!!$R2 568
11 TraesCS5A01G323900 chr2D 327756780 327757288 508 True 562.000000 562 86.640000 171 678 1 chr2D.!!$R1 507
12 TraesCS5A01G323900 chr4D 46491475 46492062 587 False 549.000000 549 83.670000 1 589 1 chr4D.!!$F1 588
13 TraesCS5A01G323900 chr7D 104547782 104548527 745 False 357.000000 357 76.601000 1950 2664 1 chr7D.!!$F2 714
14 TraesCS5A01G323900 chr4A 592497127 592497868 741 False 348.000000 348 76.378000 1950 2664 1 chr4A.!!$F1 714
15 TraesCS5A01G323900 chr4A 593064013 593064754 741 False 348.000000 348 76.378000 1950 2664 1 chr4A.!!$F2 714

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
23 4702 0.110056 CACAAGAGCGTTGCCATCAC 60.110 55.000 2.08 0.0 0.00 3.06 F
1248 6262 0.381089 GCATCTCAGCATCAAGTGGC 59.619 55.000 0.00 0.0 0.00 5.01 F
1506 6524 0.531974 CGTGTGTTGGTGTAGGCTGT 60.532 55.000 0.00 0.0 0.00 4.40 F
1887 6922 1.614317 GGTGGATGCACAGGCTAGTTT 60.614 52.381 19.67 0.0 41.91 2.66 F
3422 10049 0.602905 AGGTGCCTTTGCTCGTGTAC 60.603 55.000 0.00 0.0 38.71 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 6443 0.036388 ACCCTGTCGCATACCTTGTG 60.036 55.000 0.00 0.00 37.17 3.33 R
2928 9063 2.749621 AGGCGCATAAAAGTCTTCCTTG 59.250 45.455 10.83 0.00 32.32 3.61 R
3194 9821 3.438781 TGCGTGTGGAGTCAAAATTATCC 59.561 43.478 0.00 0.00 0.00 2.59 R
3782 10409 1.370609 TCCTAGTCAGAAGCTCGACG 58.629 55.000 0.00 0.00 37.23 5.12 R
5030 12791 0.177373 AGAAAATACGAGGGCCCGTC 59.823 55.000 18.44 13.57 43.20 4.79 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
23 4702 0.110056 CACAAGAGCGTTGCCATCAC 60.110 55.000 2.08 0.00 0.00 3.06
28 4707 3.799755 GCGTTGCCATCACCCGAC 61.800 66.667 0.00 0.00 0.00 4.79
60 4739 2.525105 GGTTTCCCCCAAAGATAGCA 57.475 50.000 0.00 0.00 0.00 3.49
91 4770 1.137872 GGAGCTTCACCTCGATGATGT 59.862 52.381 0.00 0.00 32.57 3.06
137 4817 1.995066 ATCACCATCACCGGCTCCA 60.995 57.895 0.00 0.00 0.00 3.86
196 4877 4.392138 GTCCTAAGAAAATCCAACCGACAG 59.608 45.833 0.00 0.00 0.00 3.51
228 4910 4.394712 AGACCGCCTCAAAGCCCG 62.395 66.667 0.00 0.00 0.00 6.13
280 4962 1.953686 ACAACAACACTACCACCATGC 59.046 47.619 0.00 0.00 0.00 4.06
330 5013 2.124942 GCTACCACTGGAGCCTGC 60.125 66.667 0.71 0.00 32.25 4.85
579 5262 1.681666 CTGCCACCAGTCACATCCT 59.318 57.895 0.00 0.00 34.31 3.24
643 5342 3.190849 CACTGATCGGCCAGCACG 61.191 66.667 2.24 0.00 37.68 5.34
732 5710 5.768164 ACGCAAATCCGGGAGATAAATAAAT 59.232 36.000 0.00 0.00 33.66 1.40
735 5713 8.458843 CGCAAATCCGGGAGATAAATAAATATT 58.541 33.333 0.00 0.00 33.66 1.28
772 5781 9.748708 TTATTTGCAAGGTTAGCATATCATTTC 57.251 29.630 0.00 0.00 42.33 2.17
806 5815 7.333672 AGGTTACTTCCGTTTGATGTAAATCTC 59.666 37.037 0.00 0.00 42.13 2.75
913 5922 9.823647 AGACAATTAAGAAGTGATAACATCGAT 57.176 29.630 0.00 0.00 0.00 3.59
1153 6162 1.394917 CTGGCTGTGCTATCGAACAAC 59.605 52.381 0.00 0.00 0.00 3.32
1243 6252 4.080695 AGGTTCTAAGCATCTCAGCATCAA 60.081 41.667 0.00 0.00 36.85 2.57
1248 6262 0.381089 GCATCTCAGCATCAAGTGGC 59.619 55.000 0.00 0.00 0.00 5.01
1365 6383 3.423776 CGTATCGGATCTCTAACTCGCAG 60.424 52.174 0.00 0.00 0.00 5.18
1425 6443 5.622770 ACATCTACAACACCGAAAAATCC 57.377 39.130 0.00 0.00 0.00 3.01
1506 6524 0.531974 CGTGTGTTGGTGTAGGCTGT 60.532 55.000 0.00 0.00 0.00 4.40
1665 6683 3.119743 TCAACTCCGAGTACATAACCACG 60.120 47.826 0.26 0.00 0.00 4.94
1757 6792 1.845809 GAGGTGGCACGCAGAAACAG 61.846 60.000 12.17 0.00 43.02 3.16
1759 6794 3.286751 TGGCACGCAGAAACAGGC 61.287 61.111 0.00 0.00 0.00 4.85
1887 6922 1.614317 GGTGGATGCACAGGCTAGTTT 60.614 52.381 19.67 0.00 41.91 2.66
1896 6931 2.838202 CACAGGCTAGTTTCTCCCCTTA 59.162 50.000 0.00 0.00 0.00 2.69
1897 6932 3.456277 CACAGGCTAGTTTCTCCCCTTAT 59.544 47.826 0.00 0.00 0.00 1.73
1921 6999 6.491714 TTCAAAAGGATTTGTGGAATGGAA 57.508 33.333 1.69 0.00 45.02 3.53
1995 7110 6.660521 TGTGGATTTTATCTCTTGAGCAATGT 59.339 34.615 0.00 0.00 0.00 2.71
2092 7360 3.710209 AGGAAATGGAGAACAGACCAG 57.290 47.619 0.00 0.00 39.62 4.00
2100 7368 6.963083 ATGGAGAACAGACCAGTATACTAC 57.037 41.667 4.74 0.73 39.62 2.73
2111 7391 9.141400 CAGACCAGTATACTACAACTCTTTTTC 57.859 37.037 4.74 0.00 0.00 2.29
2193 7473 7.012704 CCATCTCACTTCCATCGTTGATTAAAT 59.987 37.037 0.00 0.00 0.00 1.40
2195 7475 9.784531 ATCTCACTTCCATCGTTGATTAAATAT 57.215 29.630 0.00 0.00 0.00 1.28
2196 7476 9.045223 TCTCACTTCCATCGTTGATTAAATATG 57.955 33.333 0.00 0.00 0.00 1.78
2683 8810 6.673839 ATCTTTATTGGCTAGTACTCCCTC 57.326 41.667 0.00 0.00 0.00 4.30
2715 8844 2.834574 AGAGCGTTCAGATCACTACG 57.165 50.000 1.01 8.56 37.82 3.51
2720 8849 2.530700 GCGTTCAGATCACTACGTTAGC 59.469 50.000 0.00 0.00 36.45 3.09
2723 8852 3.946308 TCAGATCACTACGTTAGCGAG 57.054 47.619 5.81 1.50 42.00 5.03
2725 8854 2.032302 CAGATCACTACGTTAGCGAGCT 59.968 50.000 5.81 2.25 42.00 4.09
2964 9591 2.869801 TGCGCCTAACTGTTACATATGC 59.130 45.455 4.18 0.00 0.00 3.14
2965 9592 3.131396 GCGCCTAACTGTTACATATGCT 58.869 45.455 1.58 0.00 0.00 3.79
2968 9595 5.333111 GCGCCTAACTGTTACATATGCTTAC 60.333 44.000 1.58 0.00 0.00 2.34
2969 9596 5.983720 CGCCTAACTGTTACATATGCTTACT 59.016 40.000 1.58 0.00 0.00 2.24
2978 9605 8.856153 TGTTACATATGCTTACTTTTTCAGGA 57.144 30.769 1.58 0.00 0.00 3.86
3194 9821 3.751175 TGGATGAGTTAGAAAAGGCAACG 59.249 43.478 0.00 0.00 46.39 4.10
3332 9959 9.861138 CAAAGAGAGATCGATCAATTCATAAAC 57.139 33.333 26.47 6.41 0.00 2.01
3422 10049 0.602905 AGGTGCCTTTGCTCGTGTAC 60.603 55.000 0.00 0.00 38.71 2.90
3782 10409 7.124347 TGTTTACAGTTTCGGTGTGATAATC 57.876 36.000 0.00 0.00 0.00 1.75
3812 10439 1.550976 CTGACTAGGAAGAAGCCGGTT 59.449 52.381 1.90 0.00 0.00 4.44
3823 10450 3.230976 AGAAGCCGGTTTTCCTCAATTT 58.769 40.909 4.57 0.00 37.95 1.82
3886 10513 7.331934 TCAGATGCTACAAGATAACACTTTGAC 59.668 37.037 0.00 0.00 0.00 3.18
3887 10514 7.118245 CAGATGCTACAAGATAACACTTTGACA 59.882 37.037 0.00 0.00 0.00 3.58
3896 10523 6.692486 AGATAACACTTTGACAGAGATCGTT 58.308 36.000 0.00 3.39 0.00 3.85
3926 10553 0.038526 TTCTCGAGGAAGGCAACGAC 60.039 55.000 13.56 0.00 46.39 4.34
3936 10563 0.969149 AGGCAACGACAGACAGATCA 59.031 50.000 0.00 0.00 46.39 2.92
4029 10656 1.153208 CTTAGGCTGCAGCTCCTGG 60.153 63.158 35.82 19.02 41.70 4.45
4073 10700 1.183549 AACACGGGTTAGAGAGCGAT 58.816 50.000 0.00 0.00 34.87 4.58
4114 10741 5.124776 TGTTACCTTCAAACTGTTCCACTTG 59.875 40.000 0.00 0.00 0.00 3.16
4127 10754 3.838244 TCCACTTGTTTCAGTGCTAGT 57.162 42.857 0.00 0.00 42.63 2.57
4128 10755 3.728845 TCCACTTGTTTCAGTGCTAGTC 58.271 45.455 0.00 0.00 42.63 2.59
4157 10784 1.066573 CGGCATGGTGAGTTCTTCTCT 60.067 52.381 0.00 0.00 43.13 3.10
4257 10885 3.945285 TCGCTGAATTTTAATGGACTCCC 59.055 43.478 0.00 0.00 0.00 4.30
4277 10905 6.240060 ACTCCCTTAGTTTGCTATGGTAACAA 60.240 38.462 0.00 0.00 44.30 2.83
4325 10953 2.749621 GGATTGGTGTGCTTCGATTTCT 59.250 45.455 0.00 0.00 0.00 2.52
4355 10984 4.685169 TTCAATCTCCGAGTTGCAATTC 57.315 40.909 11.69 11.69 0.00 2.17
4435 11064 4.217983 AGACGTCGTAATCTGAAAGGTCTT 59.782 41.667 10.46 0.00 0.00 3.01
4436 11065 4.483311 ACGTCGTAATCTGAAAGGTCTTC 58.517 43.478 0.00 0.00 0.00 2.87
4437 11066 4.217983 ACGTCGTAATCTGAAAGGTCTTCT 59.782 41.667 0.00 0.00 0.00 2.85
4438 11067 4.794246 CGTCGTAATCTGAAAGGTCTTCTC 59.206 45.833 0.00 0.00 0.00 2.87
4497 11126 9.249053 TGGTTTTGTGAATTTCTAGCCATAATA 57.751 29.630 0.00 0.00 0.00 0.98
4498 11127 9.736023 GGTTTTGTGAATTTCTAGCCATAATAG 57.264 33.333 0.00 0.00 0.00 1.73
4504 11134 9.472361 GTGAATTTCTAGCCATAATAGTTACGA 57.528 33.333 0.00 0.00 0.00 3.43
4535 11165 6.998074 TGATATTTGCTCCGAATAATTCCTGT 59.002 34.615 0.00 0.00 0.00 4.00
4589 11219 2.093973 TGCTAGTAGTTCCTGAGCAAGC 60.094 50.000 0.00 0.00 40.07 4.01
4601 11286 1.072806 TGAGCAAGCCAAGTCTCATGT 59.927 47.619 0.00 0.00 31.35 3.21
4602 11287 1.736681 GAGCAAGCCAAGTCTCATGTC 59.263 52.381 0.00 0.00 0.00 3.06
4625 11314 6.037172 GTCTTAGTGTGCAGTTTCAGAAGAAA 59.963 38.462 0.00 0.00 41.26 2.52
4644 11333 6.463995 AGAAACCAACAAATAAACAGCTGA 57.536 33.333 23.35 0.00 0.00 4.26
4662 11351 4.648307 AGCTGATCCTTCAATTCCCAAATC 59.352 41.667 0.00 0.00 0.00 2.17
4664 11353 5.451520 GCTGATCCTTCAATTCCCAAATCTG 60.452 44.000 0.00 0.00 0.00 2.90
4733 11422 1.133199 TGGAGTCCAAAAACCAGGCAT 60.133 47.619 10.20 0.00 0.00 4.40
4756 11445 5.760484 TTATATATGTGCCCATCTCTGCA 57.240 39.130 0.00 0.00 34.54 4.41
4803 11506 2.281484 GTTTGAGCTGGCGGTGGA 60.281 61.111 0.00 0.00 0.00 4.02
4820 11523 1.340502 TGGACGGCAGCAAATTATCCA 60.341 47.619 0.00 0.00 32.39 3.41
4829 11532 4.970003 GCAGCAAATTATCCATAACACGAC 59.030 41.667 0.00 0.00 0.00 4.34
4835 11538 8.342634 GCAAATTATCCATAACACGACTTGTAT 58.657 33.333 0.00 0.00 37.51 2.29
4866 11931 5.739752 TGTTTCTCAACATCTGTGAACTG 57.260 39.130 0.00 0.00 38.03 3.16
4871 11936 6.791887 TCTCAACATCTGTGAACTGAAATC 57.208 37.500 0.00 0.00 0.00 2.17
4876 11941 4.872691 ACATCTGTGAACTGAAATCGGATC 59.127 41.667 0.00 0.00 0.00 3.36
4884 11949 6.963805 GTGAACTGAAATCGGATCTGAATTTC 59.036 38.462 20.89 20.89 33.30 2.17
4887 11952 6.176183 ACTGAAATCGGATCTGAATTTCTGT 58.824 36.000 25.39 25.39 38.03 3.41
4897 11962 7.095229 CGGATCTGAATTTCTGTGACAAAGTAA 60.095 37.037 0.00 0.00 0.00 2.24
4903 11968 7.434897 TGAATTTCTGTGACAAAGTAAATGCAC 59.565 33.333 0.00 0.00 0.00 4.57
4906 11971 7.503521 TTCTGTGACAAAGTAAATGCACATA 57.496 32.000 0.00 0.00 35.69 2.29
4911 11976 9.008965 TGTGACAAAGTAAATGCACATAGTATT 57.991 29.630 0.00 0.00 33.26 1.89
4912 11977 9.840427 GTGACAAAGTAAATGCACATAGTATTT 57.160 29.630 0.00 0.00 43.59 1.40
4923 11988 9.445786 AATGCACATAGTATTTAATTTACACGC 57.554 29.630 0.00 0.00 0.00 5.34
4925 11990 8.119845 TGCACATAGTATTTAATTTACACGCAG 58.880 33.333 0.00 0.00 0.00 5.18
4950 12015 8.452989 GTGTTTATCACAATGAAAGCCTTAAG 57.547 34.615 0.00 0.00 45.51 1.85
4951 12016 8.296713 GTGTTTATCACAATGAAAGCCTTAAGA 58.703 33.333 3.36 0.00 45.51 2.10
4952 12017 8.514594 TGTTTATCACAATGAAAGCCTTAAGAG 58.485 33.333 3.36 0.00 29.87 2.85
4953 12018 5.573337 ATCACAATGAAAGCCTTAAGAGC 57.427 39.130 3.36 5.95 0.00 4.09
4954 12019 4.397420 TCACAATGAAAGCCTTAAGAGCA 58.603 39.130 15.45 2.99 0.00 4.26
4969 12034 2.674796 GAGCATCTACAACCGGACTT 57.325 50.000 9.46 0.00 0.00 3.01
4970 12035 2.271800 GAGCATCTACAACCGGACTTG 58.728 52.381 9.46 5.71 0.00 3.16
4971 12036 1.066143 AGCATCTACAACCGGACTTGG 60.066 52.381 9.46 0.00 0.00 3.61
4976 12041 2.159382 CTACAACCGGACTTGGCAAAT 58.841 47.619 9.46 0.00 0.00 2.32
4977 12042 1.408969 ACAACCGGACTTGGCAAATT 58.591 45.000 9.46 0.00 0.00 1.82
4979 12044 0.596082 AACCGGACTTGGCAAATTCG 59.404 50.000 9.46 1.67 0.00 3.34
4980 12045 1.241315 ACCGGACTTGGCAAATTCGG 61.241 55.000 25.60 25.60 0.00 4.30
4981 12046 1.154035 CGGACTTGGCAAATTCGGC 60.154 57.895 0.51 0.00 0.00 5.54
4987 12052 2.362375 GGCAAATTCGGCCCCTCA 60.362 61.111 9.40 0.00 45.87 3.86
4988 12053 1.981853 GGCAAATTCGGCCCCTCAA 60.982 57.895 9.40 0.00 45.87 3.02
4989 12054 1.512694 GCAAATTCGGCCCCTCAAG 59.487 57.895 0.00 0.00 0.00 3.02
4990 12055 1.512694 CAAATTCGGCCCCTCAAGC 59.487 57.895 0.00 0.00 0.00 4.01
4991 12056 2.046285 AAATTCGGCCCCTCAAGCG 61.046 57.895 0.00 0.00 0.00 4.68
4993 12058 3.682292 ATTCGGCCCCTCAAGCGTC 62.682 63.158 0.00 0.00 0.00 5.19
5040 12801 4.554036 GCATCTGGACGGGCCCTC 62.554 72.222 22.43 16.12 34.97 4.30
5051 12827 1.003928 ACGGGCCCTCGTATTTTCTTT 59.996 47.619 22.43 0.00 41.98 2.52
5052 12828 1.669265 CGGGCCCTCGTATTTTCTTTC 59.331 52.381 22.43 0.00 0.00 2.62
5054 12830 1.669265 GGCCCTCGTATTTTCTTTCGG 59.331 52.381 0.00 0.00 0.00 4.30
5055 12831 1.669265 GCCCTCGTATTTTCTTTCGGG 59.331 52.381 0.00 0.00 0.00 5.14
5057 12833 3.679639 GCCCTCGTATTTTCTTTCGGGTA 60.680 47.826 0.00 0.00 33.00 3.69
5058 12834 4.700700 CCCTCGTATTTTCTTTCGGGTAT 58.299 43.478 0.00 0.00 0.00 2.73
5059 12835 4.748600 CCCTCGTATTTTCTTTCGGGTATC 59.251 45.833 0.00 0.00 0.00 2.24
5060 12836 4.748600 CCTCGTATTTTCTTTCGGGTATCC 59.251 45.833 0.00 0.00 0.00 2.59
5061 12837 5.341872 TCGTATTTTCTTTCGGGTATCCA 57.658 39.130 0.00 0.00 0.00 3.41
5062 12838 5.111293 TCGTATTTTCTTTCGGGTATCCAC 58.889 41.667 0.00 0.00 0.00 4.02
5063 12839 4.871557 CGTATTTTCTTTCGGGTATCCACA 59.128 41.667 0.00 0.00 0.00 4.17
5065 12841 6.702723 CGTATTTTCTTTCGGGTATCCACATA 59.297 38.462 0.00 0.00 0.00 2.29
5067 12843 7.745620 ATTTTCTTTCGGGTATCCACATATC 57.254 36.000 0.00 0.00 0.00 1.63
5068 12844 6.494666 TTTCTTTCGGGTATCCACATATCT 57.505 37.500 0.00 0.00 0.00 1.98
5069 12845 5.723672 TCTTTCGGGTATCCACATATCTC 57.276 43.478 0.00 0.00 0.00 2.75
5070 12846 5.144832 TCTTTCGGGTATCCACATATCTCA 58.855 41.667 0.00 0.00 0.00 3.27
5071 12847 5.600898 TCTTTCGGGTATCCACATATCTCAA 59.399 40.000 0.00 0.00 0.00 3.02
5072 12848 5.880164 TTCGGGTATCCACATATCTCAAA 57.120 39.130 0.00 0.00 0.00 2.69
5073 12849 6.433847 TTCGGGTATCCACATATCTCAAAT 57.566 37.500 0.00 0.00 0.00 2.32
5074 12850 7.547697 TTCGGGTATCCACATATCTCAAATA 57.452 36.000 0.00 0.00 0.00 1.40
5075 12851 6.931838 TCGGGTATCCACATATCTCAAATAC 58.068 40.000 0.00 0.00 0.00 1.89
5076 12852 5.805486 CGGGTATCCACATATCTCAAATACG 59.195 44.000 0.00 0.00 0.00 3.06
5078 12854 6.070995 GGGTATCCACATATCTCAAATACGGA 60.071 42.308 0.00 0.00 0.00 4.69
5080 12856 6.672266 ATCCACATATCTCAAATACGGACT 57.328 37.500 0.00 0.00 0.00 3.85
5083 12859 6.016192 TCCACATATCTCAAATACGGACTCTC 60.016 42.308 0.00 0.00 0.00 3.20
5084 12860 6.239036 CCACATATCTCAAATACGGACTCTCA 60.239 42.308 0.00 0.00 0.00 3.27
5086 12862 7.706607 CACATATCTCAAATACGGACTCTCAAA 59.293 37.037 0.00 0.00 0.00 2.69
5087 12863 8.424918 ACATATCTCAAATACGGACTCTCAAAT 58.575 33.333 0.00 0.00 0.00 2.32
5088 12864 8.920665 CATATCTCAAATACGGACTCTCAAATC 58.079 37.037 0.00 0.00 0.00 2.17
5090 12866 5.186992 TCTCAAATACGGACTCTCAAATCCA 59.813 40.000 0.00 0.00 34.35 3.41
5092 12868 7.069455 TCTCAAATACGGACTCTCAAATCCATA 59.931 37.037 0.00 0.00 34.35 2.74
5094 12870 6.479972 AATACGGACTCTCAAATCCATACA 57.520 37.500 0.00 0.00 34.35 2.29
5095 12871 4.819105 ACGGACTCTCAAATCCATACAA 57.181 40.909 0.00 0.00 34.35 2.41
5096 12872 5.160607 ACGGACTCTCAAATCCATACAAA 57.839 39.130 0.00 0.00 34.35 2.83
5097 12873 5.745227 ACGGACTCTCAAATCCATACAAAT 58.255 37.500 0.00 0.00 34.35 2.32
5098 12874 6.884832 ACGGACTCTCAAATCCATACAAATA 58.115 36.000 0.00 0.00 34.35 1.40
5099 12875 6.761714 ACGGACTCTCAAATCCATACAAATAC 59.238 38.462 0.00 0.00 34.35 1.89
5100 12876 6.761242 CGGACTCTCAAATCCATACAAATACA 59.239 38.462 0.00 0.00 34.35 2.29
5101 12877 7.442364 CGGACTCTCAAATCCATACAAATACAT 59.558 37.037 0.00 0.00 34.35 2.29
5102 12878 8.562892 GGACTCTCAAATCCATACAAATACATG 58.437 37.037 0.00 0.00 34.87 3.21
5103 12879 7.934457 ACTCTCAAATCCATACAAATACATGC 58.066 34.615 0.00 0.00 0.00 4.06
5104 12880 7.557358 ACTCTCAAATCCATACAAATACATGCA 59.443 33.333 0.00 0.00 0.00 3.96
5106 12882 6.493978 TCAAATCCATACAAATACATGCACG 58.506 36.000 0.00 0.00 0.00 5.34
5107 12883 6.094742 TCAAATCCATACAAATACATGCACGT 59.905 34.615 0.00 0.00 0.00 4.49
5109 12885 3.553917 TCCATACAAATACATGCACGTCG 59.446 43.478 0.00 0.00 0.00 5.12
5110 12886 3.553917 CCATACAAATACATGCACGTCGA 59.446 43.478 0.00 0.00 0.00 4.20
5112 12888 3.925688 ACAAATACATGCACGTCGATC 57.074 42.857 0.00 0.00 0.00 3.69
5113 12889 3.258228 ACAAATACATGCACGTCGATCA 58.742 40.909 0.00 0.00 0.00 2.92
5125 13809 2.159667 ACGTCGATCATGCAACACAATG 60.160 45.455 0.00 0.00 0.00 2.82
5126 13810 2.159667 CGTCGATCATGCAACACAATGT 60.160 45.455 0.00 0.00 0.00 2.71
5127 13811 3.419915 GTCGATCATGCAACACAATGTC 58.580 45.455 0.00 0.00 0.00 3.06
5128 13812 2.094099 TCGATCATGCAACACAATGTCG 59.906 45.455 0.00 0.00 33.30 4.35
5129 13813 2.179589 GATCATGCAACACAATGTCGC 58.820 47.619 0.00 0.00 0.00 5.19
5132 13816 0.385849 ATGCAACACAATGTCGCACG 60.386 50.000 0.00 0.00 35.02 5.34
5134 13818 0.233590 GCAACACAATGTCGCACGTA 59.766 50.000 0.00 0.00 0.00 3.57
5135 13819 1.333347 GCAACACAATGTCGCACGTAA 60.333 47.619 0.00 0.00 0.00 3.18
5137 13821 3.550561 CAACACAATGTCGCACGTAAAT 58.449 40.909 0.00 0.00 0.00 1.40
5139 13823 4.577687 ACACAATGTCGCACGTAAATAG 57.422 40.909 0.00 0.00 0.00 1.73
5140 13824 3.181524 ACACAATGTCGCACGTAAATAGC 60.182 43.478 0.00 0.00 0.00 2.97
5142 13826 3.433957 ACAATGTCGCACGTAAATAGCAA 59.566 39.130 0.00 0.00 0.00 3.91
5143 13827 4.094294 ACAATGTCGCACGTAAATAGCAAT 59.906 37.500 0.00 0.00 0.00 3.56
5144 13828 4.875544 ATGTCGCACGTAAATAGCAATT 57.124 36.364 0.00 0.00 0.00 2.32
5146 13830 3.433957 TGTCGCACGTAAATAGCAATTGT 59.566 39.130 7.40 0.00 0.00 2.71
5147 13831 4.083749 TGTCGCACGTAAATAGCAATTGTT 60.084 37.500 7.40 3.27 0.00 2.83
5149 13833 3.541916 CGCACGTAAATAGCAATTGTTGG 59.458 43.478 7.40 0.00 0.00 3.77
5150 13834 4.481463 GCACGTAAATAGCAATTGTTGGT 58.519 39.130 7.40 0.00 44.64 3.67
5151 13835 5.632959 GCACGTAAATAGCAATTGTTGGTA 58.367 37.500 7.40 4.34 46.32 3.25
5152 13836 5.510323 GCACGTAAATAGCAATTGTTGGTAC 59.490 40.000 7.40 4.87 45.25 3.34
5153 13837 6.025280 CACGTAAATAGCAATTGTTGGTACC 58.975 40.000 4.43 4.43 45.25 3.34
5154 13838 5.706369 ACGTAAATAGCAATTGTTGGTACCA 59.294 36.000 11.60 11.60 45.25 3.25
5156 13840 6.745450 CGTAAATAGCAATTGTTGGTACCAAG 59.255 38.462 27.77 16.17 45.25 3.61
5157 13841 4.718940 ATAGCAATTGTTGGTACCAAGC 57.281 40.909 27.77 24.45 45.25 4.01
5158 13842 2.315176 AGCAATTGTTGGTACCAAGCA 58.685 42.857 27.77 22.89 40.04 3.91
5159 13843 2.899256 AGCAATTGTTGGTACCAAGCAT 59.101 40.909 27.77 18.49 40.04 3.79
5161 13845 4.158394 AGCAATTGTTGGTACCAAGCATAG 59.842 41.667 27.77 17.62 40.04 2.23
5162 13846 4.157656 GCAATTGTTGGTACCAAGCATAGA 59.842 41.667 27.77 13.36 36.52 1.98
5163 13847 5.163519 GCAATTGTTGGTACCAAGCATAGAT 60.164 40.000 27.77 14.79 36.52 1.98
5165 13849 7.642669 CAATTGTTGGTACCAAGCATAGATAG 58.357 38.462 27.77 8.02 36.52 2.08
5169 14424 3.386726 TGGTACCAAGCATAGATAGCGTT 59.613 43.478 13.60 0.00 37.01 4.84
5171 14426 5.069383 TGGTACCAAGCATAGATAGCGTTTA 59.931 40.000 13.60 0.00 37.01 2.01
5174 14429 5.611374 ACCAAGCATAGATAGCGTTTACAT 58.389 37.500 0.00 0.00 37.01 2.29
5219 14474 4.425577 CAAGCATTGTCTCCTTGGTTAC 57.574 45.455 0.00 0.00 42.34 2.50
5220 14475 3.073274 AGCATTGTCTCCTTGGTTACC 57.927 47.619 0.00 0.00 0.00 2.85
5226 15585 3.750371 TGTCTCCTTGGTTACCATTGTG 58.250 45.455 4.38 0.80 31.53 3.33
5233 15592 1.202952 TGGTTACCATTGTGGGTCCAC 60.203 52.381 12.89 12.89 43.37 4.02
5241 15600 4.500265 GTGGGTCCACATGTGCTT 57.500 55.556 20.81 0.00 45.53 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 4693 1.602323 GTTGGTCGGGTGATGGCAA 60.602 57.895 0.00 0.00 0.00 4.52
15 4694 2.033448 GTTGGTCGGGTGATGGCA 59.967 61.111 0.00 0.00 0.00 4.92
23 4702 0.392998 CCCTTGATCAGTTGGTCGGG 60.393 60.000 0.00 0.00 0.00 5.14
52 4731 2.122768 CCCAACTCCTCCTGCTATCTT 58.877 52.381 0.00 0.00 0.00 2.40
55 4734 1.799933 CTCCCAACTCCTCCTGCTAT 58.200 55.000 0.00 0.00 0.00 2.97
60 4739 0.178891 TGAAGCTCCCAACTCCTCCT 60.179 55.000 0.00 0.00 0.00 3.69
137 4817 2.249413 CTGATCTTCGGCTGGTGGCT 62.249 60.000 0.00 0.00 41.46 4.75
196 4877 2.042831 GTCTGGATGGTGCACAGGC 61.043 63.158 20.43 4.46 41.68 4.85
228 4910 1.899142 GGATCTGGGTGGCTAGATCTC 59.101 57.143 0.00 0.00 45.43 2.75
301 4984 0.606401 GTGGTAGCACACACAGGCAT 60.606 55.000 19.87 0.00 40.99 4.40
590 5273 4.109675 GGCCATGGCTACGGTGGT 62.110 66.667 34.70 0.00 41.60 4.16
629 5328 4.451150 GGTCGTGCTGGCCGATCA 62.451 66.667 0.00 0.00 35.56 2.92
643 5342 1.444553 CGACGTGGAAGAGCAGGTC 60.445 63.158 0.00 0.00 34.16 3.85
706 5439 1.116308 TATCTCCCGGATTTGCGTCA 58.884 50.000 0.73 0.00 35.98 4.35
737 5715 8.580720 TGCTAACCTTGCAAATAAAACATAAGA 58.419 29.630 0.00 0.00 37.51 2.10
748 5726 7.784037 TGAAATGATATGCTAACCTTGCAAAT 58.216 30.769 0.00 0.00 44.01 2.32
750 5728 6.772360 TGAAATGATATGCTAACCTTGCAA 57.228 33.333 0.00 0.00 44.01 4.08
772 5781 3.915437 ACGGAAGTAACCTTGCAAATG 57.085 42.857 0.00 0.00 46.88 2.32
806 5815 0.323725 CAGGGGTTGGATGGGTTCAG 60.324 60.000 0.00 0.00 0.00 3.02
1153 6162 1.481019 CTGCAGCTGATCTCGAAGCG 61.481 60.000 20.43 0.00 44.34 4.68
1186 6195 0.689623 AATGGCCTCTCGATCCCATC 59.310 55.000 3.32 0.00 37.09 3.51
1243 6252 0.112412 AAAACTCGGGATTGGCCACT 59.888 50.000 3.88 0.00 38.95 4.00
1248 6262 3.505680 TGAACATCAAAACTCGGGATTGG 59.494 43.478 0.00 0.00 0.00 3.16
1356 6374 6.148645 TGCTTATGAATTTGTTCTGCGAGTTA 59.851 34.615 0.00 0.00 0.00 2.24
1360 6378 5.565592 ATGCTTATGAATTTGTTCTGCGA 57.434 34.783 0.00 0.00 0.00 5.10
1425 6443 0.036388 ACCCTGTCGCATACCTTGTG 60.036 55.000 0.00 0.00 37.17 3.33
1506 6524 2.112297 GGGACGGTGTTCTGGCAA 59.888 61.111 0.00 0.00 0.00 4.52
1665 6683 6.145338 TCGTAGGTATCATTGAACCTCTTC 57.855 41.667 18.04 11.87 42.60 2.87
1757 6792 1.656441 CGGCATGCATAAGAAGGCC 59.344 57.895 21.36 12.32 38.04 5.19
1759 6794 1.233019 CTCCGGCATGCATAAGAAGG 58.767 55.000 21.36 10.26 0.00 3.46
1887 6922 7.016296 ACAAATCCTTTTGAAATAAGGGGAGA 58.984 34.615 5.52 0.00 44.11 3.71
1896 6931 7.077050 TCCATTCCACAAATCCTTTTGAAAT 57.923 32.000 5.52 0.87 44.11 2.17
1897 6932 6.491714 TCCATTCCACAAATCCTTTTGAAA 57.508 33.333 5.52 0.00 44.11 2.69
1953 7065 4.810345 TCCACAGTTTAACCCCTGATTTT 58.190 39.130 0.00 0.00 32.93 1.82
1995 7110 6.767524 ATATAAAAGTTGATTTGCGACCCA 57.232 33.333 0.00 0.00 0.00 4.51
2033 7289 6.987992 GTGGTTTCCATTAATATCCGTCTACA 59.012 38.462 0.00 0.00 35.28 2.74
2100 7368 7.655490 ACATGAGATGGAAAGAAAAAGAGTTG 58.345 34.615 0.00 0.00 33.60 3.16
2111 7391 8.033038 ACAATTTGATCAACATGAGATGGAAAG 58.967 33.333 20.80 0.40 33.60 2.62
2115 7395 8.245491 TGTAACAATTTGATCAACATGAGATGG 58.755 33.333 20.80 7.33 33.60 3.51
2336 7669 2.751166 ATCTGAACCCAAGTGAGTCG 57.249 50.000 0.00 0.00 0.00 4.18
2622 8748 8.629158 TGCTACTCTCAACAAAACACAAAATAT 58.371 29.630 0.00 0.00 0.00 1.28
2751 8880 8.521176 ACAAGCCTATTATACATTAGTACTCCG 58.479 37.037 0.00 0.00 31.96 4.63
2759 8888 9.325198 CAACAGTGACAAGCCTATTATACATTA 57.675 33.333 0.00 0.00 0.00 1.90
2821 8951 3.053170 TGCTCTGGTCCCAGTATACACTA 60.053 47.826 12.88 0.00 43.96 2.74
2928 9063 2.749621 AGGCGCATAAAAGTCTTCCTTG 59.250 45.455 10.83 0.00 32.32 3.61
2964 9591 8.846211 TCCAATAACAACTCCTGAAAAAGTAAG 58.154 33.333 0.00 0.00 0.00 2.34
2965 9592 8.626526 GTCCAATAACAACTCCTGAAAAAGTAA 58.373 33.333 0.00 0.00 0.00 2.24
2968 9595 7.277174 AGTCCAATAACAACTCCTGAAAAAG 57.723 36.000 0.00 0.00 0.00 2.27
2969 9596 8.754991 TTAGTCCAATAACAACTCCTGAAAAA 57.245 30.769 0.00 0.00 0.00 1.94
2973 9600 5.248477 AGCTTAGTCCAATAACAACTCCTGA 59.752 40.000 0.00 0.00 0.00 3.86
2978 9605 4.504858 CGGAGCTTAGTCCAATAACAACT 58.495 43.478 0.00 0.00 36.23 3.16
3194 9821 3.438781 TGCGTGTGGAGTCAAAATTATCC 59.561 43.478 0.00 0.00 0.00 2.59
3332 9959 6.308524 TGATTTGTGATAAAATTGCAAGCTCG 59.691 34.615 4.94 0.00 29.89 5.03
3782 10409 1.370609 TCCTAGTCAGAAGCTCGACG 58.629 55.000 0.00 0.00 37.23 5.12
3812 10439 3.216187 TCACACCGGAAATTGAGGAAA 57.784 42.857 9.46 0.00 0.00 3.13
3823 10450 2.096248 AGTTTTGCTTTTCACACCGGA 58.904 42.857 9.46 0.00 0.00 5.14
3863 10490 7.331934 TCTGTCAAAGTGTTATCTTGTAGCATC 59.668 37.037 0.00 0.00 0.00 3.91
3886 10513 5.636965 AGAACTTGAACATCAACGATCTCTG 59.363 40.000 0.00 0.00 32.21 3.35
3887 10514 5.788450 AGAACTTGAACATCAACGATCTCT 58.212 37.500 0.00 0.00 32.21 3.10
3896 10523 4.560128 CTTCCTCGAGAACTTGAACATCA 58.440 43.478 15.71 0.00 0.00 3.07
3926 10553 2.431419 AGCCATCTCAGTGATCTGTCTG 59.569 50.000 0.00 0.77 41.91 3.51
3936 10563 1.302285 CAAGGGCAGCCATCTCAGT 59.698 57.895 15.19 0.00 0.00 3.41
3976 10603 0.467659 GGTAGGCCGCTCTTCTCCTA 60.468 60.000 0.00 0.00 0.00 2.94
4029 10656 0.479815 TCCATCATCATCTTGCCCCC 59.520 55.000 0.00 0.00 0.00 5.40
4060 10687 2.815478 CTTCACCATCGCTCTCTAACC 58.185 52.381 0.00 0.00 0.00 2.85
4114 10741 0.320697 ACCGGGACTAGCACTGAAAC 59.679 55.000 6.32 0.00 0.00 2.78
4257 10885 9.906660 TCAAAATTGTTACCATAGCAAACTAAG 57.093 29.630 0.00 0.00 32.67 2.18
4325 10953 4.703897 ACTCGGAGATTGAAACAAAGTCA 58.296 39.130 12.86 0.00 33.89 3.41
4355 10984 8.627403 GCCTGACATATATCCCAATCAAATATG 58.373 37.037 0.00 0.00 36.84 1.78
4435 11064 5.365619 GGGTAAGTTGTTTCACAGAAGAGA 58.634 41.667 0.00 0.00 0.00 3.10
4436 11065 4.515567 GGGGTAAGTTGTTTCACAGAAGAG 59.484 45.833 0.00 0.00 0.00 2.85
4437 11066 4.457466 GGGGTAAGTTGTTTCACAGAAGA 58.543 43.478 0.00 0.00 0.00 2.87
4438 11067 3.568430 GGGGGTAAGTTGTTTCACAGAAG 59.432 47.826 0.00 0.00 0.00 2.85
4497 11126 7.472543 GGAGCAAATATCACAAAATCGTAACT 58.527 34.615 0.00 0.00 0.00 2.24
4498 11127 6.410914 CGGAGCAAATATCACAAAATCGTAAC 59.589 38.462 0.00 0.00 0.00 2.50
4535 11165 1.918262 ACAAATGCAGGAGGAGATGGA 59.082 47.619 0.00 0.00 0.00 3.41
4589 11219 3.681897 GCACACTAAGACATGAGACTTGG 59.318 47.826 0.00 6.77 35.01 3.61
4601 11286 5.276461 TCTTCTGAAACTGCACACTAAGA 57.724 39.130 0.00 0.00 0.00 2.10
4602 11287 5.991328 TTCTTCTGAAACTGCACACTAAG 57.009 39.130 0.00 0.00 0.00 2.18
4625 11314 5.079643 AGGATCAGCTGTTTATTTGTTGGT 58.920 37.500 14.67 0.00 0.00 3.67
4644 11333 5.336102 ACACAGATTTGGGAATTGAAGGAT 58.664 37.500 0.00 0.00 0.00 3.24
4662 11351 0.662619 TTCAGCGAGCCAAAACACAG 59.337 50.000 0.00 0.00 0.00 3.66
4664 11353 1.401539 GGATTCAGCGAGCCAAAACAC 60.402 52.381 0.00 0.00 0.00 3.32
4733 11422 6.125589 TGCAGAGATGGGCACATATATAAA 57.874 37.500 0.00 0.00 37.47 1.40
4751 11440 0.324614 TTTCCGATGGCTCTTGCAGA 59.675 50.000 0.00 0.00 41.91 4.26
4756 11445 3.339141 GAGAAGTTTTCCGATGGCTCTT 58.661 45.455 0.00 0.00 0.00 2.85
4766 11469 2.038837 CCGGCCGGAGAAGTTTTCC 61.039 63.158 41.82 2.22 37.50 3.13
4803 11506 3.951037 TGTTATGGATAATTTGCTGCCGT 59.049 39.130 0.00 0.00 0.00 5.68
4839 11542 7.121168 AGTTCACAGATGTTGAGAAACAAGAAA 59.879 33.333 0.00 0.00 37.98 2.52
4844 11547 5.427378 TCAGTTCACAGATGTTGAGAAACA 58.573 37.500 0.00 0.00 37.98 2.83
4845 11548 5.991328 TCAGTTCACAGATGTTGAGAAAC 57.009 39.130 0.00 0.00 37.98 2.78
4848 11551 5.406477 CGATTTCAGTTCACAGATGTTGAGA 59.594 40.000 0.00 0.00 0.00 3.27
4849 11552 5.390251 CCGATTTCAGTTCACAGATGTTGAG 60.390 44.000 0.00 0.00 0.00 3.02
4850 11553 4.452114 CCGATTTCAGTTCACAGATGTTGA 59.548 41.667 0.00 0.00 0.00 3.18
4851 11554 4.452114 TCCGATTTCAGTTCACAGATGTTG 59.548 41.667 0.00 0.00 0.00 3.33
4852 11555 4.641396 TCCGATTTCAGTTCACAGATGTT 58.359 39.130 0.00 0.00 0.00 2.71
4853 11556 4.271696 TCCGATTTCAGTTCACAGATGT 57.728 40.909 0.00 0.00 0.00 3.06
4854 11557 5.006455 CAGATCCGATTTCAGTTCACAGATG 59.994 44.000 0.00 0.00 0.00 2.90
4857 11922 4.498241 TCAGATCCGATTTCAGTTCACAG 58.502 43.478 0.00 0.00 0.00 3.66
4866 11931 6.092670 TGTCACAGAAATTCAGATCCGATTTC 59.907 38.462 13.86 13.86 0.00 2.17
4871 11936 5.180117 ACTTTGTCACAGAAATTCAGATCCG 59.820 40.000 0.00 0.00 0.00 4.18
4876 11941 7.648908 TGCATTTACTTTGTCACAGAAATTCAG 59.351 33.333 0.00 0.00 0.00 3.02
4884 11949 6.902341 ACTATGTGCATTTACTTTGTCACAG 58.098 36.000 0.00 0.00 35.86 3.66
4897 11962 9.445786 GCGTGTAAATTAAATACTATGTGCATT 57.554 29.630 0.00 0.00 0.00 3.56
4903 11968 9.982291 AACACTGCGTGTAAATTAAATACTATG 57.018 29.630 13.33 0.00 46.79 2.23
4911 11976 7.862648 TGTGATAAACACTGCGTGTAAATTAA 58.137 30.769 13.33 3.30 46.79 1.40
4912 11977 7.422878 TGTGATAAACACTGCGTGTAAATTA 57.577 32.000 13.33 9.64 46.79 1.40
4914 11979 5.933187 TGTGATAAACACTGCGTGTAAAT 57.067 34.783 13.33 10.24 46.79 1.40
4915 11980 5.736486 TTGTGATAAACACTGCGTGTAAA 57.264 34.783 13.33 6.62 46.79 2.01
4917 11982 4.991687 TCATTGTGATAAACACTGCGTGTA 59.008 37.500 13.33 1.74 46.79 2.90
4928 11993 7.176515 TGCTCTTAAGGCTTTCATTGTGATAAA 59.823 33.333 4.45 0.00 0.00 1.40
4929 11994 6.658816 TGCTCTTAAGGCTTTCATTGTGATAA 59.341 34.615 4.45 0.00 0.00 1.75
4930 11995 6.179756 TGCTCTTAAGGCTTTCATTGTGATA 58.820 36.000 4.45 0.00 0.00 2.15
4931 11996 5.012239 TGCTCTTAAGGCTTTCATTGTGAT 58.988 37.500 4.45 0.00 0.00 3.06
4933 11998 4.771590 TGCTCTTAAGGCTTTCATTGTG 57.228 40.909 4.45 0.00 0.00 3.33
4934 11999 5.259632 AGATGCTCTTAAGGCTTTCATTGT 58.740 37.500 4.45 0.00 0.00 2.71
4936 12001 6.418101 TGTAGATGCTCTTAAGGCTTTCATT 58.582 36.000 4.45 0.00 0.00 2.57
4937 12002 5.994250 TGTAGATGCTCTTAAGGCTTTCAT 58.006 37.500 4.45 1.90 0.00 2.57
4938 12003 5.420725 TGTAGATGCTCTTAAGGCTTTCA 57.579 39.130 4.45 0.00 0.00 2.69
4939 12004 5.065346 GGTTGTAGATGCTCTTAAGGCTTTC 59.935 44.000 4.45 11.64 0.00 2.62
4940 12005 4.944317 GGTTGTAGATGCTCTTAAGGCTTT 59.056 41.667 4.45 5.15 0.00 3.51
4941 12006 4.518249 GGTTGTAGATGCTCTTAAGGCTT 58.482 43.478 4.58 4.58 0.00 4.35
4942 12007 3.430929 CGGTTGTAGATGCTCTTAAGGCT 60.431 47.826 14.45 0.00 0.00 4.58
4943 12008 2.866762 CGGTTGTAGATGCTCTTAAGGC 59.133 50.000 1.85 5.85 0.00 4.35
4944 12009 3.132289 TCCGGTTGTAGATGCTCTTAAGG 59.868 47.826 0.00 0.00 0.00 2.69
4946 12011 3.767673 AGTCCGGTTGTAGATGCTCTTAA 59.232 43.478 0.00 0.00 0.00 1.85
4947 12012 3.362706 AGTCCGGTTGTAGATGCTCTTA 58.637 45.455 0.00 0.00 0.00 2.10
4948 12013 2.180276 AGTCCGGTTGTAGATGCTCTT 58.820 47.619 0.00 0.00 0.00 2.85
4949 12014 1.853963 AGTCCGGTTGTAGATGCTCT 58.146 50.000 0.00 0.00 0.00 4.09
4950 12015 2.271800 CAAGTCCGGTTGTAGATGCTC 58.728 52.381 0.00 0.00 0.00 4.26
4951 12016 1.066143 CCAAGTCCGGTTGTAGATGCT 60.066 52.381 0.00 0.00 0.00 3.79
4952 12017 1.369625 CCAAGTCCGGTTGTAGATGC 58.630 55.000 0.00 0.00 0.00 3.91
4953 12018 1.338674 TGCCAAGTCCGGTTGTAGATG 60.339 52.381 0.00 0.00 0.00 2.90
4954 12019 0.981183 TGCCAAGTCCGGTTGTAGAT 59.019 50.000 0.00 0.00 0.00 1.98
4957 12022 2.279935 ATTTGCCAAGTCCGGTTGTA 57.720 45.000 0.00 0.00 0.00 2.41
4958 12023 1.339929 GAATTTGCCAAGTCCGGTTGT 59.660 47.619 0.00 0.00 0.00 3.32
4960 12025 0.596082 CGAATTTGCCAAGTCCGGTT 59.404 50.000 0.00 0.00 0.00 4.44
4961 12026 1.241315 CCGAATTTGCCAAGTCCGGT 61.241 55.000 0.00 0.00 0.00 5.28
4971 12036 1.512694 CTTGAGGGGCCGAATTTGC 59.487 57.895 0.00 0.00 0.00 3.68
4976 12041 4.388499 GACGCTTGAGGGGCCGAA 62.388 66.667 0.00 0.00 0.00 4.30
5026 12787 2.866523 AATACGAGGGCCCGTCCAGA 62.867 60.000 18.44 0.69 43.20 3.86
5030 12791 0.177373 AGAAAATACGAGGGCCCGTC 59.823 55.000 18.44 13.57 43.20 4.79
5032 12793 1.669265 GAAAGAAAATACGAGGGCCCG 59.331 52.381 18.44 8.21 0.00 6.13
5033 12794 1.669265 CGAAAGAAAATACGAGGGCCC 59.331 52.381 16.46 16.46 0.00 5.80
5034 12795 1.669265 CCGAAAGAAAATACGAGGGCC 59.331 52.381 0.00 0.00 0.00 5.80
5037 12798 4.748600 GGATACCCGAAAGAAAATACGAGG 59.251 45.833 0.00 0.00 0.00 4.63
5038 12799 5.233689 GTGGATACCCGAAAGAAAATACGAG 59.766 44.000 0.00 0.00 34.29 4.18
5040 12801 4.871557 TGTGGATACCCGAAAGAAAATACG 59.128 41.667 0.00 0.00 34.29 3.06
5051 12827 6.349860 CGTATTTGAGATATGTGGATACCCGA 60.350 42.308 0.00 0.00 34.29 5.14
5052 12828 5.805486 CGTATTTGAGATATGTGGATACCCG 59.195 44.000 0.00 0.00 34.29 5.28
5054 12830 6.812160 GTCCGTATTTGAGATATGTGGATACC 59.188 42.308 0.00 0.00 0.00 2.73
5055 12831 7.603651 AGTCCGTATTTGAGATATGTGGATAC 58.396 38.462 0.00 0.00 0.00 2.24
5057 12833 6.495181 AGAGTCCGTATTTGAGATATGTGGAT 59.505 38.462 0.00 0.00 0.00 3.41
5058 12834 5.833667 AGAGTCCGTATTTGAGATATGTGGA 59.166 40.000 0.00 0.00 0.00 4.02
5059 12835 6.090483 AGAGTCCGTATTTGAGATATGTGG 57.910 41.667 0.00 0.00 0.00 4.17
5060 12836 6.739112 TGAGAGTCCGTATTTGAGATATGTG 58.261 40.000 0.00 0.00 0.00 3.21
5061 12837 6.961360 TGAGAGTCCGTATTTGAGATATGT 57.039 37.500 0.00 0.00 0.00 2.29
5062 12838 8.824159 ATTTGAGAGTCCGTATTTGAGATATG 57.176 34.615 0.00 0.00 0.00 1.78
5063 12839 8.091449 GGATTTGAGAGTCCGTATTTGAGATAT 58.909 37.037 0.00 0.00 0.00 1.63
5065 12841 6.127054 TGGATTTGAGAGTCCGTATTTGAGAT 60.127 38.462 0.00 0.00 37.32 2.75
5067 12843 5.419542 TGGATTTGAGAGTCCGTATTTGAG 58.580 41.667 0.00 0.00 37.32 3.02
5068 12844 5.414789 TGGATTTGAGAGTCCGTATTTGA 57.585 39.130 0.00 0.00 37.32 2.69
5069 12845 6.761242 TGTATGGATTTGAGAGTCCGTATTTG 59.239 38.462 0.00 0.00 38.06 2.32
5070 12846 6.884832 TGTATGGATTTGAGAGTCCGTATTT 58.115 36.000 0.00 0.00 38.06 1.40
5071 12847 6.479972 TGTATGGATTTGAGAGTCCGTATT 57.520 37.500 0.00 0.00 38.06 1.89
5072 12848 6.479972 TTGTATGGATTTGAGAGTCCGTAT 57.520 37.500 0.00 0.00 38.06 3.06
5073 12849 5.925506 TTGTATGGATTTGAGAGTCCGTA 57.074 39.130 0.00 0.00 37.32 4.02
5074 12850 4.819105 TTGTATGGATTTGAGAGTCCGT 57.181 40.909 0.00 0.00 37.32 4.69
5075 12851 6.761242 TGTATTTGTATGGATTTGAGAGTCCG 59.239 38.462 0.00 0.00 37.32 4.79
5076 12852 8.562892 CATGTATTTGTATGGATTTGAGAGTCC 58.437 37.037 0.00 0.00 35.02 3.85
5078 12854 7.557358 TGCATGTATTTGTATGGATTTGAGAGT 59.443 33.333 0.00 0.00 0.00 3.24
5080 12856 7.467131 CGTGCATGTATTTGTATGGATTTGAGA 60.467 37.037 0.00 0.00 0.00 3.27
5083 12859 6.264832 ACGTGCATGTATTTGTATGGATTTG 58.735 36.000 10.57 0.00 0.00 2.32
5084 12860 6.449635 ACGTGCATGTATTTGTATGGATTT 57.550 33.333 10.57 0.00 0.00 2.17
5086 12862 4.211164 CGACGTGCATGTATTTGTATGGAT 59.789 41.667 12.53 0.00 0.00 3.41
5087 12863 3.553917 CGACGTGCATGTATTTGTATGGA 59.446 43.478 12.53 0.00 0.00 3.41
5088 12864 3.553917 TCGACGTGCATGTATTTGTATGG 59.446 43.478 12.53 0.00 0.00 2.74
5090 12866 5.047188 TGATCGACGTGCATGTATTTGTAT 58.953 37.500 12.53 0.00 0.00 2.29
5092 12868 3.258228 TGATCGACGTGCATGTATTTGT 58.742 40.909 12.53 0.00 0.00 2.83
5094 12870 4.457433 CATGATCGACGTGCATGTATTT 57.543 40.909 12.53 0.00 35.78 1.40
5103 12879 0.789601 TGTGTTGCATGATCGACGTG 59.210 50.000 0.00 0.00 38.43 4.49
5104 12880 1.507562 TTGTGTTGCATGATCGACGT 58.492 45.000 0.00 0.00 0.00 4.34
5106 12882 3.419915 GACATTGTGTTGCATGATCGAC 58.580 45.455 0.00 0.00 0.00 4.20
5107 12883 2.094099 CGACATTGTGTTGCATGATCGA 59.906 45.455 0.00 0.00 0.00 3.59
5125 13809 3.998522 ACAATTGCTATTTACGTGCGAC 58.001 40.909 5.05 0.00 0.00 5.19
5126 13810 4.399112 CAACAATTGCTATTTACGTGCGA 58.601 39.130 5.05 0.00 0.00 5.10
5127 13811 3.541916 CCAACAATTGCTATTTACGTGCG 59.458 43.478 5.05 0.00 0.00 5.34
5128 13812 4.481463 ACCAACAATTGCTATTTACGTGC 58.519 39.130 5.05 0.00 0.00 5.34
5129 13813 6.025280 GGTACCAACAATTGCTATTTACGTG 58.975 40.000 7.15 0.00 0.00 4.49
5132 13816 6.530181 GCTTGGTACCAACAATTGCTATTTAC 59.470 38.462 23.69 1.24 0.00 2.01
5134 13818 5.011533 TGCTTGGTACCAACAATTGCTATTT 59.988 36.000 26.77 0.00 0.00 1.40
5135 13819 4.526262 TGCTTGGTACCAACAATTGCTATT 59.474 37.500 26.77 0.00 0.00 1.73
5137 13821 3.491342 TGCTTGGTACCAACAATTGCTA 58.509 40.909 26.77 15.77 0.00 3.49
5139 13823 2.810439 TGCTTGGTACCAACAATTGC 57.190 45.000 23.69 23.00 0.00 3.56
5140 13824 5.895636 TCTATGCTTGGTACCAACAATTG 57.104 39.130 23.69 18.18 0.00 2.32
5142 13826 5.765182 GCTATCTATGCTTGGTACCAACAAT 59.235 40.000 23.69 19.89 0.00 2.71
5143 13827 5.123227 GCTATCTATGCTTGGTACCAACAA 58.877 41.667 23.69 14.44 0.00 2.83
5144 13828 4.703897 GCTATCTATGCTTGGTACCAACA 58.296 43.478 23.69 23.47 0.00 3.33
5146 13830 3.386726 ACGCTATCTATGCTTGGTACCAA 59.613 43.478 25.58 25.58 0.00 3.67
5147 13831 2.963101 ACGCTATCTATGCTTGGTACCA 59.037 45.455 11.60 11.60 0.00 3.25
5149 13833 5.981315 TGTAAACGCTATCTATGCTTGGTAC 59.019 40.000 0.00 0.00 0.00 3.34
5150 13834 6.151663 TGTAAACGCTATCTATGCTTGGTA 57.848 37.500 0.00 0.00 0.00 3.25
5151 13835 5.018539 TGTAAACGCTATCTATGCTTGGT 57.981 39.130 0.00 0.00 0.00 3.67
5152 13836 7.652300 TTATGTAAACGCTATCTATGCTTGG 57.348 36.000 0.00 0.00 0.00 3.61
5183 14438 6.825610 ACAATGCTTGATTTCCCACTTAAAA 58.174 32.000 3.37 0.00 0.00 1.52
5186 14441 5.324409 AGACAATGCTTGATTTCCCACTTA 58.676 37.500 3.37 0.00 0.00 2.24
5187 14442 4.154942 AGACAATGCTTGATTTCCCACTT 58.845 39.130 3.37 0.00 0.00 3.16
5190 14445 3.091545 GGAGACAATGCTTGATTTCCCA 58.908 45.455 3.37 0.00 0.00 4.37
5199 14454 3.181434 TGGTAACCAAGGAGACAATGCTT 60.181 43.478 0.00 0.00 40.78 3.91
5200 14455 2.375174 TGGTAACCAAGGAGACAATGCT 59.625 45.455 0.00 0.00 0.00 3.79
5202 14457 4.766891 ACAATGGTAACCAAGGAGACAATG 59.233 41.667 0.00 0.00 36.95 2.82
5204 14459 4.141287 CACAATGGTAACCAAGGAGACAA 58.859 43.478 0.00 0.00 36.95 3.18
5206 14461 3.081804 CCACAATGGTAACCAAGGAGAC 58.918 50.000 0.00 0.00 36.95 3.36
5207 14462 2.041081 CCCACAATGGTAACCAAGGAGA 59.959 50.000 0.00 0.00 36.95 3.71
5209 14464 1.783979 ACCCACAATGGTAACCAAGGA 59.216 47.619 0.00 0.00 36.95 3.36
5210 14465 2.167662 GACCCACAATGGTAACCAAGG 58.832 52.381 0.00 0.00 39.24 3.61
5211 14466 2.167662 GGACCCACAATGGTAACCAAG 58.832 52.381 0.00 0.00 39.24 3.61
5213 14468 1.149986 TGGACCCACAATGGTAACCA 58.850 50.000 0.00 0.00 39.24 3.67
5214 14469 1.541379 GTGGACCCACAATGGTAACC 58.459 55.000 13.92 0.00 45.53 2.85


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

AutoCloner maintained by Alex Coulton.