Multiple sequence alignment - TraesCS3B01G365500

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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 TraesCS3B01G365500 chr3B 100.000 4637 0 0 1 4637 578278872 578283508 0.000000e+00 8564
1 TraesCS3B01G365500 chr3B 96.244 213 8 0 511 723 662377880 662377668 2.650000e-92 350
2 TraesCS3B01G365500 chr3D 93.472 2696 109 30 929 3584 441128387 441131055 0.000000e+00 3941
3 TraesCS3B01G365500 chr3D 93.593 718 34 7 3921 4635 441132494 441133202 0.000000e+00 1061
4 TraesCS3B01G365500 chr3D 84.087 553 44 16 1 514 441127846 441128393 1.160000e-135 494
5 TraesCS3B01G365500 chr3D 90.152 132 11 2 3701 3832 441131073 441131202 2.220000e-38 171
6 TraesCS3B01G365500 chr3D 87.931 116 13 1 2556 2671 388748272 388748386 8.090000e-28 135
7 TraesCS3B01G365500 chr3D 90.789 76 7 0 3585 3660 123640249 123640324 8.210000e-18 102
8 TraesCS3B01G365500 chr3D 90.667 75 7 0 3586 3660 388748609 388748683 2.950000e-17 100
9 TraesCS3B01G365500 chr3A 91.996 2686 150 38 929 3584 581256886 581259536 0.000000e+00 3709
10 TraesCS3B01G365500 chr3A 88.426 1080 78 16 3590 4637 581259504 581260568 0.000000e+00 1258
11 TraesCS3B01G365500 chr3A 96.209 211 8 0 513 723 647488328 647488538 3.430000e-91 346
12 TraesCS3B01G365500 chr3A 95.305 213 10 0 511 723 71786447 71786659 5.750000e-89 339
13 TraesCS3B01G365500 chr3A 91.748 206 9 4 6 205 581254769 581254972 3.530000e-71 279
14 TraesCS3B01G365500 chr3A 86.940 268 12 8 192 455 581256556 581256804 3.530000e-71 279
15 TraesCS3B01G365500 chr3A 98.611 72 1 0 795 866 71787218 71787289 1.350000e-25 128
16 TraesCS3B01G365500 chr3A 77.880 217 35 8 3585 3799 734848941 734849146 6.300000e-24 122
17 TraesCS3B01G365500 chr3A 77.778 216 37 5 3585 3799 734894357 734894562 6.300000e-24 122
18 TraesCS3B01G365500 chr5B 96.744 215 7 0 509 723 112834369 112834155 4.410000e-95 359
19 TraesCS3B01G365500 chr5B 95.370 216 10 0 508 723 113098237 113098452 1.240000e-90 344
20 TraesCS3B01G365500 chr5B 89.189 111 11 1 2556 2665 374391300 374391190 2.250000e-28 137
21 TraesCS3B01G365500 chr7A 96.244 213 8 0 511 723 116511819 116511607 2.650000e-92 350
22 TraesCS3B01G365500 chr4B 95.305 213 10 0 511 723 87820144 87819932 5.750000e-89 339
23 TraesCS3B01G365500 chr4B 90.090 222 11 1 511 721 189084770 189084549 1.270000e-70 278
24 TraesCS3B01G365500 chr4B 95.205 146 4 1 724 866 87817156 87817011 1.300000e-55 228
25 TraesCS3B01G365500 chr1A 93.897 213 13 0 511 723 290212423 290212635 5.790000e-84 322
26 TraesCS3B01G365500 chr1A 93.836 146 6 1 724 866 290216067 290216212 2.810000e-52 217
27 TraesCS3B01G365500 chr1A 87.069 116 14 1 2556 2671 4372558 4372672 3.770000e-26 130
28 TraesCS3B01G365500 chr1A 87.069 116 14 1 2556 2671 293637832 293637946 3.770000e-26 130
29 TraesCS3B01G365500 chr6D 90.667 225 10 1 508 721 457754365 457754589 5.870000e-74 289
30 TraesCS3B01G365500 chr6D 98.198 111 1 1 2638 2747 7513387 7513277 4.730000e-45 193
31 TraesCS3B01G365500 chr6D 90.789 76 7 0 3585 3660 270569893 270569818 8.210000e-18 102
32 TraesCS3B01G365500 chr5A 74.274 482 89 26 3326 3799 638287512 638287966 2.220000e-38 171
33 TraesCS3B01G365500 chr7D 89.655 116 11 1 2556 2671 602278526 602278412 3.740000e-31 147
34 TraesCS3B01G365500 chr7D 90.789 76 7 0 3585 3660 140747958 140747883 8.210000e-18 102
35 TraesCS3B01G365500 chr5D 90.090 111 10 1 2556 2665 322773296 322773186 4.840000e-30 143
36 TraesCS3B01G365500 chr2A 88.235 119 12 2 2556 2673 256208692 256208809 1.740000e-29 141
37 TraesCS3B01G365500 chr1D 90.789 76 7 0 3585 3660 449228552 449228477 8.210000e-18 102
38 TraesCS3B01G365500 chr4D 90.667 75 7 0 3586 3660 36667209 36667135 2.950000e-17 100


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 TraesCS3B01G365500 chr3B 578278872 578283508 4636 False 8564.00 8564 100.0000 1 4637 1 chr3B.!!$F1 4636
1 TraesCS3B01G365500 chr3D 441127846 441133202 5356 False 1416.75 3941 90.3260 1 4635 4 chr3D.!!$F3 4634
2 TraesCS3B01G365500 chr3A 581254769 581260568 5799 False 1381.25 3709 89.7775 6 4637 4 chr3A.!!$F5 4631
3 TraesCS3B01G365500 chr3A 71786447 71787289 842 False 233.50 339 96.9580 511 866 2 chr3A.!!$F4 355
4 TraesCS3B01G365500 chr4B 87817011 87820144 3133 True 283.50 339 95.2550 511 866 2 chr4B.!!$R2 355
5 TraesCS3B01G365500 chr1A 290212423 290216212 3789 False 269.50 322 93.8665 511 866 2 chr1A.!!$F3 355

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
896 6031 0.320683 TGCTGATGTGGACTCCGTTG 60.321 55.0 0.0 0.0 0.00 4.10 F
1836 6999 0.107017 AGAACGAGCAATCCCCCATG 60.107 55.0 0.0 0.0 0.00 3.66 F
3574 8768 0.035725 TGCAGCAGGATGAACTCAGG 60.036 55.0 0.0 0.0 39.69 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2516 7680 0.249120 CATCTCCAACACGCCCACTA 59.751 55.000 0.00 0.0 0.00 2.74 R
3593 8787 0.040058 TGGGTTCATCCTGCTGCAAT 59.960 50.000 3.02 0.0 36.25 3.56 R
4436 10837 1.971357 AGGAAGCTCCGTGAAGAAGAA 59.029 47.619 0.00 0.0 42.75 2.52 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
28 29 1.944032 CACCTTTTGCTTGCTTGCTT 58.056 45.000 3.47 0.00 0.00 3.91
29 30 2.282407 CACCTTTTGCTTGCTTGCTTT 58.718 42.857 3.47 0.00 0.00 3.51
30 31 2.031191 CACCTTTTGCTTGCTTGCTTTG 59.969 45.455 3.47 0.00 0.00 2.77
31 32 1.600485 CCTTTTGCTTGCTTGCTTTGG 59.400 47.619 3.47 0.00 0.00 3.28
98 99 6.070538 GGATAACTGATGTAGGGCTGATATGT 60.071 42.308 0.00 0.00 0.00 2.29
147 149 0.538287 GCTGGCAGACTTCCAACCTT 60.538 55.000 20.86 0.00 32.41 3.50
216 1819 6.825721 TGCCAACCAAAACAATTGAAGTAAAT 59.174 30.769 13.59 0.00 0.00 1.40
217 1820 7.987458 TGCCAACCAAAACAATTGAAGTAAATA 59.013 29.630 13.59 0.00 0.00 1.40
218 1821 8.831550 GCCAACCAAAACAATTGAAGTAAATAA 58.168 29.630 13.59 0.00 0.00 1.40
331 1955 7.807907 GGTTGGACAGTTAAAAATCATGTGTAG 59.192 37.037 0.00 0.00 0.00 2.74
339 1963 8.357402 AGTTAAAAATCATGTGTAGGTTTGTCC 58.643 33.333 0.00 0.00 0.00 4.02
367 1991 3.484229 GCATCTTCACAACATGTACGAGC 60.484 47.826 0.00 0.00 0.00 5.03
398 2022 5.744666 TTTCGTTACAGGGAAAGAAGTTG 57.255 39.130 0.00 0.00 30.25 3.16
496 2158 1.452108 GCTAGGCTTGGGCGATTGT 60.452 57.895 0.00 0.00 39.81 2.71
640 2302 7.339212 TGACCCTAATAAAGACATGGACATTTG 59.661 37.037 0.00 0.00 0.00 2.32
732 5864 6.183360 GCCATTCATACCAATAAGCAACTTCT 60.183 38.462 0.00 0.00 0.00 2.85
738 5870 7.450014 TCATACCAATAAGCAACTTCTTTCCAA 59.550 33.333 0.00 0.00 0.00 3.53
774 5909 8.592529 TCTTGTAATTTGATTGGATTGGATCA 57.407 30.769 0.00 0.00 0.00 2.92
866 6001 2.795231 ACATGGAGACCAACATGGAG 57.205 50.000 2.85 0.00 46.60 3.86
867 6002 2.269023 ACATGGAGACCAACATGGAGA 58.731 47.619 2.85 0.00 46.60 3.71
868 6003 2.848694 ACATGGAGACCAACATGGAGAT 59.151 45.455 2.85 0.00 46.60 2.75
869 6004 3.118112 ACATGGAGACCAACATGGAGATC 60.118 47.826 2.85 0.00 46.60 2.75
870 6005 2.550175 TGGAGACCAACATGGAGATCA 58.450 47.619 2.85 0.00 40.96 2.92
871 6006 2.502947 TGGAGACCAACATGGAGATCAG 59.497 50.000 2.85 0.00 40.96 2.90
872 6007 2.768527 GGAGACCAACATGGAGATCAGA 59.231 50.000 2.85 0.00 40.96 3.27
873 6008 3.390639 GGAGACCAACATGGAGATCAGAT 59.609 47.826 2.85 0.00 40.96 2.90
874 6009 4.141528 GGAGACCAACATGGAGATCAGATT 60.142 45.833 2.85 0.00 40.96 2.40
875 6010 5.435291 GAGACCAACATGGAGATCAGATTT 58.565 41.667 2.85 0.00 40.96 2.17
876 6011 5.824421 AGACCAACATGGAGATCAGATTTT 58.176 37.500 2.85 0.00 40.96 1.82
877 6012 6.251471 AGACCAACATGGAGATCAGATTTTT 58.749 36.000 2.85 0.00 40.96 1.94
878 6013 6.152323 AGACCAACATGGAGATCAGATTTTTG 59.848 38.462 2.85 0.00 40.96 2.44
879 6014 5.107133 CCAACATGGAGATCAGATTTTTGC 58.893 41.667 0.00 0.00 40.96 3.68
880 6015 5.105473 CCAACATGGAGATCAGATTTTTGCT 60.105 40.000 0.00 0.00 40.96 3.91
881 6016 5.578005 ACATGGAGATCAGATTTTTGCTG 57.422 39.130 0.00 0.00 34.71 4.41
882 6017 5.258841 ACATGGAGATCAGATTTTTGCTGA 58.741 37.500 0.00 0.00 45.52 4.26
889 6024 4.771590 TCAGATTTTTGCTGATGTGGAC 57.228 40.909 0.00 0.00 37.46 4.02
890 6025 4.401022 TCAGATTTTTGCTGATGTGGACT 58.599 39.130 0.00 0.00 37.46 3.85
891 6026 4.456911 TCAGATTTTTGCTGATGTGGACTC 59.543 41.667 0.00 0.00 37.46 3.36
892 6027 3.760684 AGATTTTTGCTGATGTGGACTCC 59.239 43.478 0.00 0.00 0.00 3.85
893 6028 1.522668 TTTTGCTGATGTGGACTCCG 58.477 50.000 0.00 0.00 0.00 4.63
894 6029 0.396435 TTTGCTGATGTGGACTCCGT 59.604 50.000 0.00 0.00 0.00 4.69
895 6030 0.396435 TTGCTGATGTGGACTCCGTT 59.604 50.000 0.00 0.00 0.00 4.44
896 6031 0.320683 TGCTGATGTGGACTCCGTTG 60.321 55.000 0.00 0.00 0.00 4.10
897 6032 1.639298 GCTGATGTGGACTCCGTTGC 61.639 60.000 0.00 0.00 0.00 4.17
898 6033 0.320683 CTGATGTGGACTCCGTTGCA 60.321 55.000 0.00 0.00 0.00 4.08
899 6034 0.320683 TGATGTGGACTCCGTTGCAG 60.321 55.000 0.00 0.00 0.00 4.41
900 6035 1.639298 GATGTGGACTCCGTTGCAGC 61.639 60.000 0.00 0.00 0.00 5.25
901 6036 3.050275 GTGGACTCCGTTGCAGCC 61.050 66.667 0.00 0.00 0.00 4.85
902 6037 3.241530 TGGACTCCGTTGCAGCCT 61.242 61.111 0.00 0.00 0.00 4.58
903 6038 2.743928 GGACTCCGTTGCAGCCTG 60.744 66.667 0.00 0.00 0.00 4.85
904 6039 3.426568 GACTCCGTTGCAGCCTGC 61.427 66.667 10.45 10.45 45.29 4.85
905 6040 3.890936 GACTCCGTTGCAGCCTGCT 62.891 63.158 18.96 0.00 45.31 4.24
906 6041 3.429141 CTCCGTTGCAGCCTGCTG 61.429 66.667 18.96 14.70 45.31 4.41
909 6044 2.749044 CGTTGCAGCCTGCTGGAT 60.749 61.111 18.96 3.57 45.31 3.41
910 6045 1.450134 CGTTGCAGCCTGCTGGATA 60.450 57.895 18.96 6.39 45.31 2.59
911 6046 1.434622 CGTTGCAGCCTGCTGGATAG 61.435 60.000 18.96 10.59 45.31 2.08
912 6047 1.099879 GTTGCAGCCTGCTGGATAGG 61.100 60.000 18.96 0.00 45.31 2.57
913 6048 1.273986 TTGCAGCCTGCTGGATAGGA 61.274 55.000 18.96 0.64 45.31 2.94
914 6049 1.227793 GCAGCCTGCTGGATAGGAC 60.228 63.158 19.88 0.00 43.77 3.85
915 6050 1.694133 GCAGCCTGCTGGATAGGACT 61.694 60.000 19.88 0.00 43.77 3.85
916 6051 1.709578 CAGCCTGCTGGATAGGACTA 58.290 55.000 14.77 0.00 40.17 2.59
917 6052 2.255406 CAGCCTGCTGGATAGGACTAT 58.745 52.381 14.77 0.00 40.17 2.12
918 6053 2.636893 CAGCCTGCTGGATAGGACTATT 59.363 50.000 14.77 0.00 40.17 1.73
919 6054 2.636893 AGCCTGCTGGATAGGACTATTG 59.363 50.000 14.77 0.00 37.52 1.90
920 6055 2.370189 GCCTGCTGGATAGGACTATTGT 59.630 50.000 14.77 0.00 37.52 2.71
921 6056 3.578716 GCCTGCTGGATAGGACTATTGTA 59.421 47.826 14.77 0.00 37.52 2.41
922 6057 4.561734 GCCTGCTGGATAGGACTATTGTAC 60.562 50.000 14.77 0.00 37.52 2.90
923 6058 4.835615 CCTGCTGGATAGGACTATTGTACT 59.164 45.833 2.92 0.00 37.52 2.73
924 6059 5.305644 CCTGCTGGATAGGACTATTGTACTT 59.694 44.000 2.92 0.00 37.52 2.24
925 6060 6.161855 TGCTGGATAGGACTATTGTACTTG 57.838 41.667 0.00 0.00 38.53 3.16
926 6061 4.991687 GCTGGATAGGACTATTGTACTTGC 59.008 45.833 0.00 0.00 38.53 4.01
927 6062 5.221541 GCTGGATAGGACTATTGTACTTGCT 60.222 44.000 0.00 0.00 38.53 3.91
954 6089 2.994995 ATCGACTGGTGCCACCGA 60.995 61.111 9.78 2.70 42.58 4.69
978 6114 2.345760 GGTCGGACCCAACTCGCTA 61.346 63.158 16.55 0.00 30.04 4.26
983 6119 2.283388 ACCCAACTCGCTACCCGA 60.283 61.111 0.00 0.00 45.15 5.14
985 6121 1.294138 CCCAACTCGCTACCCGAAA 59.706 57.895 0.00 0.00 46.81 3.46
1260 6396 4.785453 CCCCGCAGCCTCAAGGTC 62.785 72.222 0.00 0.00 37.57 3.85
1271 6410 4.016706 CAAGGTCCGCCCCGTTCT 62.017 66.667 0.00 0.00 34.57 3.01
1272 6411 3.246880 AAGGTCCGCCCCGTTCTT 61.247 61.111 0.00 0.00 34.57 2.52
1314 6453 5.503498 CGAGTTCGTGTAGAAGGATTCTAG 58.497 45.833 0.00 0.00 45.30 2.43
1315 6454 5.064962 CGAGTTCGTGTAGAAGGATTCTAGT 59.935 44.000 0.00 0.00 45.30 2.57
1316 6455 6.257411 CGAGTTCGTGTAGAAGGATTCTAGTA 59.743 42.308 0.00 0.00 45.30 1.82
1317 6456 7.517101 CGAGTTCGTGTAGAAGGATTCTAGTAG 60.517 44.444 0.00 0.00 45.30 2.57
1341 6480 8.854614 AGTAGCTTTCTGTGATATTTCAGTTT 57.145 30.769 0.00 0.00 33.89 2.66
1394 6546 5.627499 TGGACAGTTGACATTAGCATTTC 57.373 39.130 0.00 0.00 0.00 2.17
1438 6591 5.221263 TGTCTGTGTCCTTAGAGTTTGAGAC 60.221 44.000 0.00 0.00 0.00 3.36
1443 6596 4.039245 TGTCCTTAGAGTTTGAGACTGGTG 59.961 45.833 0.00 0.00 39.19 4.17
1502 6658 7.596749 ATTATCGGGCAAATAGTAATCTTCG 57.403 36.000 0.00 0.00 0.00 3.79
1569 6725 7.374491 GCAATATTCTTGTCGATACTTTTGAGC 59.626 37.037 0.00 0.00 0.00 4.26
1570 6726 8.607459 CAATATTCTTGTCGATACTTTTGAGCT 58.393 33.333 0.00 0.00 0.00 4.09
1571 6727 9.817809 AATATTCTTGTCGATACTTTTGAGCTA 57.182 29.630 0.00 0.00 0.00 3.32
1572 6728 9.988815 ATATTCTTGTCGATACTTTTGAGCTAT 57.011 29.630 0.00 0.00 0.00 2.97
1628 6788 8.534333 TGTAGAATCACAGTTCATTACTTCAC 57.466 34.615 0.00 0.00 33.85 3.18
1641 6801 2.278332 ACTTCACTTTCCCCTTCTGC 57.722 50.000 0.00 0.00 0.00 4.26
1644 6804 1.675641 CACTTTCCCCTTCTGCCCG 60.676 63.158 0.00 0.00 0.00 6.13
1815 6978 3.307242 GGAAATGCTCTACAAGTACTGCG 59.693 47.826 0.00 0.00 0.00 5.18
1836 6999 0.107017 AGAACGAGCAATCCCCCATG 60.107 55.000 0.00 0.00 0.00 3.66
1847 7010 4.096003 CCCCATGAACGGCTCGGT 62.096 66.667 0.00 0.00 0.00 4.69
2124 7287 6.014669 TGTTTATTTTGCCTGCTACAATCCTT 60.015 34.615 0.00 0.00 0.00 3.36
2167 7330 1.608283 GGTCCCTTTTCACACTCTCCG 60.608 57.143 0.00 0.00 0.00 4.63
2170 7333 1.338200 CCCTTTTCACACTCTCCGAGG 60.338 57.143 0.00 0.00 33.35 4.63
2205 7368 5.748630 TGTACAGATAACTGAAATAGCGCTG 59.251 40.000 22.90 4.03 46.03 5.18
2231 7394 0.178068 GGGCCTCTGCACTATCGAAA 59.822 55.000 0.84 0.00 38.13 3.46
2295 7458 4.378874 CGTTTTCCTTCTCAAATGAGCTCC 60.379 45.833 12.15 0.00 41.80 4.70
2321 7484 0.260230 TGTTTGGAAGGTTCAGGCCA 59.740 50.000 5.01 0.00 0.00 5.36
2340 7504 7.784073 TCAGGCCAGATAATCCAAAATATTTCA 59.216 33.333 5.01 0.00 0.00 2.69
2346 7510 9.199982 CAGATAATCCAAAATATTTCACATGCC 57.800 33.333 0.10 0.00 0.00 4.40
2361 7525 2.002586 CATGCCTCTTTCCTGTACACG 58.997 52.381 0.00 0.00 0.00 4.49
2362 7526 1.334160 TGCCTCTTTCCTGTACACGA 58.666 50.000 0.00 0.00 0.00 4.35
2399 7563 8.506168 TCATTTTATGTTAGTCCACTTCATCC 57.494 34.615 0.00 0.00 0.00 3.51
2428 7592 7.823149 GCATCATGCAAAACTCTAAATCTTT 57.177 32.000 4.20 0.00 44.26 2.52
2433 7597 9.414295 TCATGCAAAACTCTAAATCTTTTCATG 57.586 29.630 0.00 0.00 31.84 3.07
2494 7658 0.240145 GAAAACCTAGGCGCAACCAC 59.760 55.000 10.83 0.00 43.14 4.16
2514 7678 4.512944 CCACATCATATAACACAGCAGTCC 59.487 45.833 0.00 0.00 0.00 3.85
2516 7680 5.819379 CACATCATATAACACAGCAGTCCTT 59.181 40.000 0.00 0.00 0.00 3.36
2541 7705 1.648467 GCGTGTTGGAGATGAAGGGC 61.648 60.000 0.00 0.00 0.00 5.19
2917 8108 9.739276 TTTCCTGAATAGGTAAGCCATTATATG 57.261 33.333 0.00 0.00 44.88 1.78
2973 8164 7.011482 GCTGAAATCGATGGAGTTACAAATACT 59.989 37.037 0.00 0.00 29.21 2.12
2974 8165 9.529325 CTGAAATCGATGGAGTTACAAATACTA 57.471 33.333 0.00 0.00 29.21 1.82
2975 8166 9.309516 TGAAATCGATGGAGTTACAAATACTAC 57.690 33.333 0.00 0.00 29.21 2.73
3016 8207 8.650143 AATGTTCTAGTGGTGTCCAATATTTT 57.350 30.769 0.00 0.00 33.54 1.82
3091 8282 5.459536 AGTTTCTCCTTCTTGAAAATGCC 57.540 39.130 0.00 0.00 34.52 4.40
3129 8320 8.695456 TGACTTTTAGCATCTATGTACATCAGA 58.305 33.333 12.68 13.38 0.00 3.27
3189 8380 9.315525 GGATTTTACTCTGTGATAAGGAAGTAC 57.684 37.037 0.00 0.00 0.00 2.73
3295 8486 9.289303 CTTCGGATTTTGTTATTCAGGTTATTG 57.711 33.333 0.00 0.00 0.00 1.90
3329 8520 8.579850 AACATAGTTCTTATTCATTTCCAGCA 57.420 30.769 0.00 0.00 0.00 4.41
3330 8521 7.989826 ACATAGTTCTTATTCATTTCCAGCAC 58.010 34.615 0.00 0.00 0.00 4.40
3331 8522 7.611467 ACATAGTTCTTATTCATTTCCAGCACA 59.389 33.333 0.00 0.00 0.00 4.57
3332 8523 6.259550 AGTTCTTATTCATTTCCAGCACAC 57.740 37.500 0.00 0.00 0.00 3.82
3335 8526 6.985188 TCTTATTCATTTCCAGCACACTAC 57.015 37.500 0.00 0.00 0.00 2.73
3345 8536 1.657594 CAGCACACTACATCAGCTTCG 59.342 52.381 0.00 0.00 32.35 3.79
3353 8544 6.145534 CACACTACATCAGCTTCGAAGTTTAA 59.854 38.462 25.24 11.13 0.00 1.52
3382 8575 9.739276 TTCACTCAAGTATGAATCAATAAACCT 57.261 29.630 0.00 0.00 34.49 3.50
3503 8697 3.395639 CTTGGCAATTGCAGAACACATT 58.604 40.909 30.32 0.00 44.36 2.71
3539 8733 5.581126 ACAGCACTTGATTCTCAAACAAA 57.419 34.783 0.00 0.00 35.73 2.83
3544 8738 4.734854 CACTTGATTCTCAAACAAACACCG 59.265 41.667 0.00 0.00 35.73 4.94
3547 8741 5.766150 TGATTCTCAAACAAACACCGATT 57.234 34.783 0.00 0.00 0.00 3.34
3561 8755 2.093890 ACCGATTGATGAATTGCAGCA 58.906 42.857 0.00 0.00 41.97 4.41
3562 8756 2.098607 ACCGATTGATGAATTGCAGCAG 59.901 45.455 0.00 0.00 44.75 4.24
3563 8757 2.543031 CCGATTGATGAATTGCAGCAGG 60.543 50.000 0.00 0.00 44.75 4.85
3564 8758 2.356695 CGATTGATGAATTGCAGCAGGA 59.643 45.455 0.00 0.00 44.75 3.86
3565 8759 3.004419 CGATTGATGAATTGCAGCAGGAT 59.996 43.478 0.00 0.00 44.75 3.24
3566 8760 3.793797 TTGATGAATTGCAGCAGGATG 57.206 42.857 0.00 0.00 44.75 3.51
3567 8761 3.007473 TGATGAATTGCAGCAGGATGA 57.993 42.857 0.00 0.00 38.12 2.92
3568 8762 3.358118 TGATGAATTGCAGCAGGATGAA 58.642 40.909 0.00 0.00 38.12 2.57
3569 8763 3.129813 TGATGAATTGCAGCAGGATGAAC 59.870 43.478 0.00 0.00 38.12 3.18
3570 8764 2.799017 TGAATTGCAGCAGGATGAACT 58.201 42.857 0.00 0.00 39.69 3.01
3571 8765 2.751259 TGAATTGCAGCAGGATGAACTC 59.249 45.455 0.00 0.00 39.69 3.01
3572 8766 2.502142 ATTGCAGCAGGATGAACTCA 57.498 45.000 0.00 0.00 39.69 3.41
3573 8767 1.817357 TTGCAGCAGGATGAACTCAG 58.183 50.000 0.00 0.00 39.69 3.35
3574 8768 0.035725 TGCAGCAGGATGAACTCAGG 60.036 55.000 0.00 0.00 39.69 3.86
3575 8769 0.251354 GCAGCAGGATGAACTCAGGA 59.749 55.000 0.00 0.00 39.69 3.86
3576 8770 1.134159 GCAGCAGGATGAACTCAGGAT 60.134 52.381 0.00 0.00 39.69 3.24
3577 8771 2.562635 CAGCAGGATGAACTCAGGATG 58.437 52.381 0.00 0.00 39.69 3.51
3578 8772 1.489649 AGCAGGATGAACTCAGGATGG 59.510 52.381 0.00 0.00 39.69 3.51
3579 8773 1.964552 CAGGATGAACTCAGGATGGC 58.035 55.000 0.00 0.00 39.69 4.40
3580 8774 1.489649 CAGGATGAACTCAGGATGGCT 59.510 52.381 0.00 0.00 39.69 4.75
3581 8775 1.489649 AGGATGAACTCAGGATGGCTG 59.510 52.381 0.00 0.00 36.16 4.85
3582 8776 1.476471 GGATGAACTCAGGATGGCTGG 60.476 57.143 0.00 0.00 36.16 4.85
3583 8777 1.487976 GATGAACTCAGGATGGCTGGA 59.512 52.381 0.00 0.00 36.16 3.86
3584 8778 1.361204 TGAACTCAGGATGGCTGGAA 58.639 50.000 0.00 0.00 36.16 3.53
3585 8779 1.704628 TGAACTCAGGATGGCTGGAAA 59.295 47.619 0.00 0.00 36.16 3.13
3586 8780 2.309755 TGAACTCAGGATGGCTGGAAAT 59.690 45.455 0.00 0.00 36.16 2.17
3587 8781 3.245371 TGAACTCAGGATGGCTGGAAATT 60.245 43.478 0.00 0.00 36.16 1.82
3588 8782 3.010200 ACTCAGGATGGCTGGAAATTC 57.990 47.619 0.00 0.00 36.16 2.17
3589 8783 2.309755 ACTCAGGATGGCTGGAAATTCA 59.690 45.455 0.00 0.00 36.16 2.57
3590 8784 3.053095 ACTCAGGATGGCTGGAAATTCAT 60.053 43.478 0.00 0.00 36.16 2.57
3591 8785 3.293337 TCAGGATGGCTGGAAATTCATG 58.707 45.455 0.00 0.00 36.16 3.07
3592 8786 3.053470 TCAGGATGGCTGGAAATTCATGA 60.053 43.478 0.00 0.00 36.16 3.07
3593 8787 3.702548 CAGGATGGCTGGAAATTCATGAA 59.297 43.478 11.26 11.26 0.00 2.57
3594 8788 4.344102 CAGGATGGCTGGAAATTCATGAAT 59.656 41.667 15.36 15.36 0.00 2.57
3595 8789 4.966805 AGGATGGCTGGAAATTCATGAATT 59.033 37.500 24.83 24.83 42.35 2.17
3596 8790 5.054477 GGATGGCTGGAAATTCATGAATTG 58.946 41.667 29.52 19.37 40.57 2.32
3597 8791 3.864243 TGGCTGGAAATTCATGAATTGC 58.136 40.909 29.52 27.48 40.57 3.56
3598 8792 3.261137 TGGCTGGAAATTCATGAATTGCA 59.739 39.130 31.38 23.68 40.57 4.08
3599 8793 3.869246 GGCTGGAAATTCATGAATTGCAG 59.131 43.478 31.38 29.30 40.57 4.41
3600 8794 3.308866 GCTGGAAATTCATGAATTGCAGC 59.691 43.478 33.49 33.49 41.06 5.25
3601 8795 4.500127 CTGGAAATTCATGAATTGCAGCA 58.500 39.130 31.38 22.44 40.57 4.41
3618 8812 1.983224 CAGGATGAACCCAGGACGT 59.017 57.895 0.00 0.00 39.69 4.34
3686 8880 6.937392 TGTTTATTTCCTTTTATTTCGGGGG 58.063 36.000 0.00 0.00 0.00 5.40
3699 8893 1.815421 CGGGGGAGAACAAGATGCG 60.815 63.158 0.00 0.00 0.00 4.73
3714 8908 2.027561 AGATGCGGCTTGTAAAGGTGTA 60.028 45.455 0.00 0.00 46.35 2.90
3720 8914 3.432252 CGGCTTGTAAAGGTGTAACTCTG 59.568 47.826 0.00 0.00 46.35 3.35
3762 8956 6.959639 ACAGAATATATCAATTGCGGGTTT 57.040 33.333 0.00 0.00 0.00 3.27
3764 8958 6.545666 ACAGAATATATCAATTGCGGGTTTGA 59.454 34.615 0.00 0.00 36.38 2.69
3765 8959 7.231317 ACAGAATATATCAATTGCGGGTTTGAT 59.769 33.333 0.00 3.89 43.22 2.57
3766 8960 7.539710 CAGAATATATCAATTGCGGGTTTGATG 59.460 37.037 0.00 0.00 41.42 3.07
3767 8961 2.298411 ATCAATTGCGGGTTTGATGC 57.702 45.000 0.00 0.00 40.22 3.91
3768 8962 0.964700 TCAATTGCGGGTTTGATGCA 59.035 45.000 0.00 0.00 36.72 3.96
3770 8964 2.757314 TCAATTGCGGGTTTGATGCATA 59.243 40.909 0.00 0.00 38.60 3.14
3771 8965 3.117794 CAATTGCGGGTTTGATGCATAG 58.882 45.455 0.00 0.00 38.60 2.23
3775 8969 2.822561 TGCGGGTTTGATGCATAGAAAA 59.177 40.909 0.00 0.00 32.86 2.29
3786 8980 4.842531 TGCATAGAAAAGTGGATCCTCA 57.157 40.909 14.23 0.00 0.00 3.86
3832 9026 3.254166 CCTCTGCATTACAAGCTTGTGTT 59.746 43.478 36.50 22.77 42.31 3.32
3833 9027 4.455533 CCTCTGCATTACAAGCTTGTGTTA 59.544 41.667 36.50 23.33 42.31 2.41
3834 9028 5.048782 CCTCTGCATTACAAGCTTGTGTTAA 60.049 40.000 36.50 25.13 42.31 2.01
3835 9029 6.384258 TCTGCATTACAAGCTTGTGTTAAA 57.616 33.333 36.50 24.80 42.31 1.52
3863 9089 5.438698 TTTGATGAAAATTGGATGGCCAT 57.561 34.783 20.96 20.96 45.46 4.40
3871 9098 4.411256 AATTGGATGGCCATGATTGAAC 57.589 40.909 26.56 6.35 45.46 3.18
3877 9104 1.818060 TGGCCATGATTGAACGGAAAG 59.182 47.619 0.00 0.00 0.00 2.62
3880 9107 2.159198 GCCATGATTGAACGGAAAGCAT 60.159 45.455 0.00 0.00 34.11 3.79
3882 9109 3.119388 CCATGATTGAACGGAAAGCATGT 60.119 43.478 17.89 0.00 45.49 3.21
3891 9118 1.135689 CGGAAAGCATGTTGGTAGTGC 60.136 52.381 0.00 0.00 39.10 4.40
3953 10351 4.465632 TTGGCTCTGCTTTCTAATCGTA 57.534 40.909 0.00 0.00 0.00 3.43
4023 10422 5.255687 TCTTGATAACAACACAGGCATGAT 58.744 37.500 4.84 0.00 32.27 2.45
4035 10434 7.088589 ACACAGGCATGATTTTCAACTATAC 57.911 36.000 4.84 0.00 0.00 1.47
4042 10441 7.365741 GCATGATTTTCAACTATACCCATCAG 58.634 38.462 0.00 0.00 0.00 2.90
4051 10450 7.861629 TCAACTATACCCATCAGAATTGTTCT 58.138 34.615 0.00 0.00 41.70 3.01
4064 10463 6.427853 TCAGAATTGTTCTTACATGGTGACTG 59.572 38.462 0.00 0.00 38.11 3.51
4090 10489 9.055248 GTGATCACTTAACATTTCGAGAAATTG 57.945 33.333 18.83 4.36 38.84 2.32
4145 10546 3.007940 TCCGGCATAGGATCCACAAATAG 59.992 47.826 15.82 0.00 34.92 1.73
4187 10588 9.799106 ATAAAGGTATCTGAAAGTAATGGATGG 57.201 33.333 0.00 0.00 33.76 3.51
4210 10611 4.659172 TGTGGAAGGGCAAGGGCG 62.659 66.667 0.00 0.00 42.47 6.13
4225 10626 1.596934 GGCGATGTCACAGGGAAGA 59.403 57.895 0.00 0.00 0.00 2.87
4229 10630 2.419297 GCGATGTCACAGGGAAGAGAAT 60.419 50.000 0.00 0.00 0.00 2.40
4260 10661 1.691196 CCAGCTTGTCTGTTCCCAAA 58.309 50.000 0.00 0.00 41.25 3.28
4274 10675 1.202879 TCCCAAATGTCCAGCTTTCGT 60.203 47.619 0.00 0.00 0.00 3.85
4341 10742 5.146010 ACAGGTCAGCAAGAAAACAAAAA 57.854 34.783 0.00 0.00 0.00 1.94
4436 10837 7.040201 ACAGTCTGTGATGCTGAATTTACAATT 60.040 33.333 4.21 0.00 34.60 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.600485 CCCAAAGCAAGCAAGCAAAAG 59.400 47.619 3.19 0.00 36.85 2.27
28 29 4.897076 AGATCTAATTGATGCATTGCCCAA 59.103 37.500 6.12 10.65 35.14 4.12
29 30 4.476297 AGATCTAATTGATGCATTGCCCA 58.524 39.130 6.12 1.38 35.14 5.36
30 31 5.391310 CGTAGATCTAATTGATGCATTGCCC 60.391 44.000 3.40 0.00 35.14 5.36
31 32 5.409520 TCGTAGATCTAATTGATGCATTGCC 59.590 40.000 3.40 0.00 35.14 4.52
37 38 6.382608 TGCTACTCGTAGATCTAATTGATGC 58.617 40.000 3.40 6.54 35.14 3.91
98 99 3.678289 CTTGGACATCTCACACCAATGA 58.322 45.455 0.00 0.00 40.78 2.57
216 1819 0.739462 CAGCGACAGCCATCCGTTTA 60.739 55.000 0.00 0.00 46.67 2.01
217 1820 2.034879 CAGCGACAGCCATCCGTTT 61.035 57.895 0.00 0.00 46.67 3.60
218 1821 2.434884 CAGCGACAGCCATCCGTT 60.435 61.111 0.00 0.00 46.67 4.44
219 1822 4.457496 CCAGCGACAGCCATCCGT 62.457 66.667 0.00 0.00 46.67 4.69
339 1963 4.624015 ACATGTTGTGAAGATGCTTTTGG 58.376 39.130 0.00 0.00 35.71 3.28
380 2004 3.219281 TGGCAACTTCTTTCCCTGTAAC 58.781 45.455 0.00 0.00 37.61 2.50
398 2022 2.191128 AGGAAATCACTGTCACTGGC 57.809 50.000 0.00 0.00 0.00 4.85
507 2169 4.445453 TGTGCTATTAACCATGCTCTCAG 58.555 43.478 0.00 0.00 0.00 3.35
508 2170 4.445453 CTGTGCTATTAACCATGCTCTCA 58.555 43.478 0.00 0.00 0.00 3.27
509 2171 3.249559 GCTGTGCTATTAACCATGCTCTC 59.750 47.826 0.00 0.00 0.00 3.20
557 2219 4.457257 GTGGGAAGGCTTTATAGATGATGC 59.543 45.833 0.00 0.00 0.00 3.91
676 2338 3.592059 CTGATTGAAATGGCCACAAAGG 58.408 45.455 8.16 0.00 41.84 3.11
738 5870 9.787532 CAATCAAATTACAAGAACGACCAATAT 57.212 29.630 0.00 0.00 0.00 1.28
846 5981 2.644299 TCTCCATGTTGGTCTCCATGTT 59.356 45.455 0.00 0.00 39.03 2.71
866 6001 5.125097 AGTCCACATCAGCAAAAATCTGATC 59.875 40.000 2.81 0.00 45.31 2.92
868 6003 4.401022 AGTCCACATCAGCAAAAATCTGA 58.599 39.130 0.00 0.00 43.79 3.27
869 6004 4.380233 GGAGTCCACATCAGCAAAAATCTG 60.380 45.833 3.60 0.00 0.00 2.90
870 6005 3.760684 GGAGTCCACATCAGCAAAAATCT 59.239 43.478 3.60 0.00 0.00 2.40
871 6006 3.426695 CGGAGTCCACATCAGCAAAAATC 60.427 47.826 10.49 0.00 0.00 2.17
872 6007 2.489329 CGGAGTCCACATCAGCAAAAAT 59.511 45.455 10.49 0.00 0.00 1.82
873 6008 1.879380 CGGAGTCCACATCAGCAAAAA 59.121 47.619 10.49 0.00 0.00 1.94
874 6009 1.202758 ACGGAGTCCACATCAGCAAAA 60.203 47.619 10.49 0.00 29.74 2.44
875 6010 0.396435 ACGGAGTCCACATCAGCAAA 59.604 50.000 10.49 0.00 29.74 3.68
876 6011 0.396435 AACGGAGTCCACATCAGCAA 59.604 50.000 10.49 0.00 45.00 3.91
877 6012 0.320683 CAACGGAGTCCACATCAGCA 60.321 55.000 10.49 0.00 45.00 4.41
878 6013 1.639298 GCAACGGAGTCCACATCAGC 61.639 60.000 10.49 0.17 45.00 4.26
879 6014 0.320683 TGCAACGGAGTCCACATCAG 60.321 55.000 10.49 0.00 45.00 2.90
880 6015 0.320683 CTGCAACGGAGTCCACATCA 60.321 55.000 10.49 0.64 45.00 3.07
881 6016 1.639298 GCTGCAACGGAGTCCACATC 61.639 60.000 10.49 0.00 45.00 3.06
882 6017 1.672356 GCTGCAACGGAGTCCACAT 60.672 57.895 10.49 0.00 45.00 3.21
883 6018 2.280797 GCTGCAACGGAGTCCACA 60.281 61.111 10.49 0.49 45.00 4.17
884 6019 3.050275 GGCTGCAACGGAGTCCAC 61.050 66.667 10.49 0.00 45.00 4.02
885 6020 3.241530 AGGCTGCAACGGAGTCCA 61.242 61.111 10.49 0.00 45.00 4.02
886 6021 2.743928 CAGGCTGCAACGGAGTCC 60.744 66.667 0.00 0.00 45.00 3.85
887 6022 3.426568 GCAGGCTGCAACGGAGTC 61.427 66.667 33.33 0.49 44.26 3.36
896 6031 1.227793 GTCCTATCCAGCAGGCTGC 60.228 63.158 31.56 31.56 45.46 5.25
897 6032 1.709578 TAGTCCTATCCAGCAGGCTG 58.290 55.000 10.94 10.94 43.26 4.85
898 6033 2.636893 CAATAGTCCTATCCAGCAGGCT 59.363 50.000 0.00 0.00 32.82 4.58
899 6034 2.370189 ACAATAGTCCTATCCAGCAGGC 59.630 50.000 0.00 0.00 32.82 4.85
900 6035 4.835615 AGTACAATAGTCCTATCCAGCAGG 59.164 45.833 0.00 0.00 34.20 4.85
901 6036 6.219473 CAAGTACAATAGTCCTATCCAGCAG 58.781 44.000 0.00 0.00 0.00 4.24
902 6037 5.453339 GCAAGTACAATAGTCCTATCCAGCA 60.453 44.000 0.00 0.00 0.00 4.41
903 6038 4.991687 GCAAGTACAATAGTCCTATCCAGC 59.008 45.833 0.00 0.00 0.00 4.85
904 6039 6.266558 AGAGCAAGTACAATAGTCCTATCCAG 59.733 42.308 0.00 0.00 0.00 3.86
905 6040 6.040955 CAGAGCAAGTACAATAGTCCTATCCA 59.959 42.308 0.00 0.00 0.00 3.41
906 6041 6.265649 TCAGAGCAAGTACAATAGTCCTATCC 59.734 42.308 0.00 0.00 0.00 2.59
907 6042 7.229707 TCTCAGAGCAAGTACAATAGTCCTATC 59.770 40.741 0.00 0.00 0.00 2.08
908 6043 7.063593 TCTCAGAGCAAGTACAATAGTCCTAT 58.936 38.462 0.00 0.00 0.00 2.57
909 6044 6.424032 TCTCAGAGCAAGTACAATAGTCCTA 58.576 40.000 0.00 0.00 0.00 2.94
910 6045 5.265191 TCTCAGAGCAAGTACAATAGTCCT 58.735 41.667 0.00 0.00 0.00 3.85
911 6046 5.126384 ACTCTCAGAGCAAGTACAATAGTCC 59.874 44.000 0.00 0.00 32.04 3.85
912 6047 6.033341 CACTCTCAGAGCAAGTACAATAGTC 58.967 44.000 0.00 0.00 32.04 2.59
913 6048 5.712446 TCACTCTCAGAGCAAGTACAATAGT 59.288 40.000 0.00 0.00 32.04 2.12
914 6049 6.201226 TCACTCTCAGAGCAAGTACAATAG 57.799 41.667 0.00 0.00 32.04 1.73
915 6050 6.458888 CGATCACTCTCAGAGCAAGTACAATA 60.459 42.308 0.00 0.00 32.04 1.90
916 6051 5.659463 GATCACTCTCAGAGCAAGTACAAT 58.341 41.667 0.00 0.00 32.04 2.71
917 6052 4.379918 CGATCACTCTCAGAGCAAGTACAA 60.380 45.833 0.00 0.00 32.04 2.41
918 6053 3.127721 CGATCACTCTCAGAGCAAGTACA 59.872 47.826 0.00 0.00 32.04 2.90
919 6054 3.375610 TCGATCACTCTCAGAGCAAGTAC 59.624 47.826 0.00 0.00 32.04 2.73
920 6055 3.375610 GTCGATCACTCTCAGAGCAAGTA 59.624 47.826 0.00 0.00 32.04 2.24
921 6056 2.163412 GTCGATCACTCTCAGAGCAAGT 59.837 50.000 0.00 0.00 32.04 3.16
922 6057 2.423185 AGTCGATCACTCTCAGAGCAAG 59.577 50.000 0.00 0.00 32.04 4.01
923 6058 2.163211 CAGTCGATCACTCTCAGAGCAA 59.837 50.000 0.00 0.00 30.26 3.91
924 6059 1.742268 CAGTCGATCACTCTCAGAGCA 59.258 52.381 0.00 0.00 30.26 4.26
925 6060 1.065401 CCAGTCGATCACTCTCAGAGC 59.935 57.143 0.00 0.00 30.26 4.09
926 6061 2.097304 CACCAGTCGATCACTCTCAGAG 59.903 54.545 0.00 0.00 30.26 3.35
927 6062 2.087646 CACCAGTCGATCACTCTCAGA 58.912 52.381 0.00 0.00 30.26 3.27
991 6127 3.554692 CGGAAGCATCACGGTCGC 61.555 66.667 0.00 0.00 0.00 5.19
1271 6410 0.753867 TGGATTATACGGCTCGGCAA 59.246 50.000 0.00 0.00 0.00 4.52
1272 6411 0.032952 GTGGATTATACGGCTCGGCA 59.967 55.000 0.00 0.00 0.00 5.69
1301 6440 9.344772 CAGAAAGCTACTACTAGAATCCTTCTA 57.655 37.037 0.00 0.00 41.14 2.10
1314 6453 8.934507 ACTGAAATATCACAGAAAGCTACTAC 57.065 34.615 13.58 0.00 37.54 2.73
1315 6454 9.944376 AAACTGAAATATCACAGAAAGCTACTA 57.056 29.630 13.58 0.00 37.54 1.82
1316 6455 8.854614 AAACTGAAATATCACAGAAAGCTACT 57.145 30.769 13.58 0.00 37.54 2.57
1341 6480 4.215908 ACTGGTGAGAACTGACTGAACTA 58.784 43.478 0.00 0.00 0.00 2.24
1394 6546 4.573900 ACACCTAAGAGACTGAAATGCTG 58.426 43.478 0.00 0.00 0.00 4.41
1502 6658 5.195001 TGAAAATAACACAAAGCAGGGAC 57.805 39.130 0.00 0.00 0.00 4.46
1539 6695 7.948278 AAGTATCGACAAGAATATTGCTACC 57.052 36.000 0.00 0.00 0.00 3.18
1573 6729 8.465999 GCACTCAGCATTAGAGACAGTATATAT 58.534 37.037 0.00 0.00 44.79 0.86
1628 6788 1.377333 GACGGGCAGAAGGGGAAAG 60.377 63.158 0.00 0.00 0.00 2.62
1641 6801 8.830580 CATTATATTAAGAATGCCATAGACGGG 58.169 37.037 0.00 0.00 28.31 5.28
1815 6978 2.115291 GGGGGATTGCTCGTTCTGC 61.115 63.158 0.00 0.00 0.00 4.26
1836 6999 2.533129 CGATAAGTTTACCGAGCCGTTC 59.467 50.000 0.00 0.00 0.00 3.95
1847 7010 5.786311 ACACCAGTAGCAACGATAAGTTTA 58.214 37.500 0.00 0.00 42.02 2.01
2094 7257 2.995258 AGCAGGCAAAATAAACAATGCG 59.005 40.909 0.00 0.00 39.66 4.73
2185 7348 3.362401 CGCAGCGCTATTTCAGTTATCTG 60.362 47.826 10.99 0.00 42.54 2.90
2205 7368 3.461773 TGCAGAGGCCCTCTACGC 61.462 66.667 14.23 14.43 38.99 4.42
2263 7426 6.995511 TTGAGAAGGAAAACGAAAGAAAGA 57.004 33.333 0.00 0.00 0.00 2.52
2295 7458 2.364970 TGAACCTTCCAAACATTGCTGG 59.635 45.455 0.00 0.00 0.00 4.85
2321 7484 9.151177 AGGCATGTGAAATATTTTGGATTATCT 57.849 29.630 1.43 0.00 0.00 1.98
2340 7504 2.612972 CGTGTACAGGAAAGAGGCATGT 60.613 50.000 10.02 0.00 34.38 3.21
2433 7597 2.927553 AAAGGAAATCGCATGACAGC 57.072 45.000 0.00 0.00 0.00 4.40
2442 7606 4.797471 TGCATCACAAGAAAAGGAAATCG 58.203 39.130 0.00 0.00 0.00 3.34
2494 7658 7.170489 CACTAAGGACTGCTGTGTTATATGATG 59.830 40.741 0.00 0.00 0.00 3.07
2514 7678 0.320374 TCTCCAACACGCCCACTAAG 59.680 55.000 0.00 0.00 0.00 2.18
2516 7680 0.249120 CATCTCCAACACGCCCACTA 59.751 55.000 0.00 0.00 0.00 2.74
2541 7705 5.292834 TGCTTTCAGAAATATGAAGCTCGAG 59.707 40.000 8.45 8.45 40.16 4.04
2973 8164 7.689299 AGAACATTAGCATGCCATATTAGGTA 58.311 34.615 15.66 0.00 33.05 3.08
2974 8165 6.546484 AGAACATTAGCATGCCATATTAGGT 58.454 36.000 15.66 0.00 33.05 3.08
2975 8166 7.826252 ACTAGAACATTAGCATGCCATATTAGG 59.174 37.037 15.66 0.00 33.05 2.69
3088 8279 6.349280 GCTAAAAGTCATACAACATCTTGGCA 60.349 38.462 0.00 0.00 0.00 4.92
3091 8282 8.671921 AGATGCTAAAAGTCATACAACATCTTG 58.328 33.333 0.00 0.00 38.79 3.02
3129 8320 3.009695 TGGGGTTCACCGAGTAATCAAAT 59.990 43.478 0.00 0.00 41.60 2.32
3189 8380 5.713861 AGAACCATCCTTGAGATTTGGAAAG 59.286 40.000 0.00 0.00 30.59 2.62
3315 8506 6.413892 TGATGTAGTGTGCTGGAAATGAATA 58.586 36.000 0.00 0.00 0.00 1.75
3317 8508 4.650734 TGATGTAGTGTGCTGGAAATGAA 58.349 39.130 0.00 0.00 0.00 2.57
3318 8509 4.256110 CTGATGTAGTGTGCTGGAAATGA 58.744 43.478 0.00 0.00 0.00 2.57
3319 8510 3.181503 GCTGATGTAGTGTGCTGGAAATG 60.182 47.826 0.00 0.00 0.00 2.32
3320 8511 3.012518 GCTGATGTAGTGTGCTGGAAAT 58.987 45.455 0.00 0.00 0.00 2.17
3321 8512 2.038952 AGCTGATGTAGTGTGCTGGAAA 59.961 45.455 0.00 0.00 32.32 3.13
3322 8513 1.625315 AGCTGATGTAGTGTGCTGGAA 59.375 47.619 0.00 0.00 32.32 3.53
3323 8514 1.269958 AGCTGATGTAGTGTGCTGGA 58.730 50.000 0.00 0.00 32.32 3.86
3324 8515 2.005451 GAAGCTGATGTAGTGTGCTGG 58.995 52.381 0.00 0.00 33.96 4.85
3325 8516 1.657594 CGAAGCTGATGTAGTGTGCTG 59.342 52.381 0.00 0.00 33.96 4.41
3326 8517 1.546029 TCGAAGCTGATGTAGTGTGCT 59.454 47.619 0.00 0.00 35.30 4.40
3327 8518 1.996292 TCGAAGCTGATGTAGTGTGC 58.004 50.000 0.00 0.00 0.00 4.57
3328 8519 3.579709 ACTTCGAAGCTGATGTAGTGTG 58.420 45.455 24.86 0.00 0.00 3.82
3329 8520 3.944055 ACTTCGAAGCTGATGTAGTGT 57.056 42.857 24.86 0.00 0.00 3.55
3330 8521 6.706055 TTAAACTTCGAAGCTGATGTAGTG 57.294 37.500 24.86 0.00 0.00 2.74
3331 8522 7.907214 AATTAAACTTCGAAGCTGATGTAGT 57.093 32.000 24.86 0.00 0.00 2.73
3332 8523 9.267096 GAAAATTAAACTTCGAAGCTGATGTAG 57.733 33.333 24.86 0.00 0.00 2.74
3335 8526 7.805071 AGTGAAAATTAAACTTCGAAGCTGATG 59.195 33.333 24.86 1.38 0.00 3.07
3369 8562 6.500684 TCAGCTTCACAGGTTTATTGATTC 57.499 37.500 0.00 0.00 0.00 2.52
3376 8569 4.127171 GAGTGTTCAGCTTCACAGGTTTA 58.873 43.478 13.50 0.00 37.07 2.01
3382 8575 2.432146 AGTCAGAGTGTTCAGCTTCACA 59.568 45.455 13.50 3.87 37.07 3.58
3503 8697 6.058833 TCAAGTGCTGTTATACCTTGAAACA 58.941 36.000 0.00 0.00 0.00 2.83
3539 8733 2.159338 GCTGCAATTCATCAATCGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
3544 8738 4.037565 TCATCCTGCTGCAATTCATCAATC 59.962 41.667 3.02 0.00 0.00 2.67
3547 8741 3.007473 TCATCCTGCTGCAATTCATCA 57.993 42.857 3.02 0.00 0.00 3.07
3561 8755 1.489649 CAGCCATCCTGAGTTCATCCT 59.510 52.381 0.00 0.00 44.64 3.24
3562 8756 1.476471 CCAGCCATCCTGAGTTCATCC 60.476 57.143 0.00 0.00 44.64 3.51
3563 8757 1.487976 TCCAGCCATCCTGAGTTCATC 59.512 52.381 0.00 0.00 44.64 2.92
3564 8758 1.588239 TCCAGCCATCCTGAGTTCAT 58.412 50.000 0.00 0.00 44.64 2.57
3565 8759 1.361204 TTCCAGCCATCCTGAGTTCA 58.639 50.000 0.00 0.00 44.64 3.18
3566 8760 2.496899 TTTCCAGCCATCCTGAGTTC 57.503 50.000 0.00 0.00 44.64 3.01
3567 8761 3.245371 TGAATTTCCAGCCATCCTGAGTT 60.245 43.478 0.00 0.00 44.64 3.01
3568 8762 2.309755 TGAATTTCCAGCCATCCTGAGT 59.690 45.455 0.00 0.00 44.64 3.41
3569 8763 3.008835 TGAATTTCCAGCCATCCTGAG 57.991 47.619 0.00 0.00 44.64 3.35
3570 8764 3.053470 TCATGAATTTCCAGCCATCCTGA 60.053 43.478 0.00 0.00 44.64 3.86
3571 8765 3.293337 TCATGAATTTCCAGCCATCCTG 58.707 45.455 0.00 0.00 41.41 3.86
3572 8766 3.675348 TCATGAATTTCCAGCCATCCT 57.325 42.857 0.00 0.00 0.00 3.24
3573 8767 4.950205 ATTCATGAATTTCCAGCCATCC 57.050 40.909 15.36 0.00 0.00 3.51
3574 8768 4.510340 GCAATTCATGAATTTCCAGCCATC 59.490 41.667 27.30 7.75 38.84 3.51
3575 8769 4.080807 TGCAATTCATGAATTTCCAGCCAT 60.081 37.500 27.30 4.46 38.84 4.40
3576 8770 3.261137 TGCAATTCATGAATTTCCAGCCA 59.739 39.130 27.30 15.92 38.84 4.75
3577 8771 3.864243 TGCAATTCATGAATTTCCAGCC 58.136 40.909 27.30 14.07 38.84 4.85
3578 8772 3.308866 GCTGCAATTCATGAATTTCCAGC 59.691 43.478 36.92 36.92 45.50 4.85
3579 8773 4.500127 TGCTGCAATTCATGAATTTCCAG 58.500 39.130 31.34 31.34 38.84 3.86
3580 8774 4.500127 CTGCTGCAATTCATGAATTTCCA 58.500 39.130 27.30 23.74 38.84 3.53
3581 8775 3.869246 CCTGCTGCAATTCATGAATTTCC 59.131 43.478 27.30 21.09 38.84 3.13
3582 8776 4.751060 TCCTGCTGCAATTCATGAATTTC 58.249 39.130 27.30 23.44 38.84 2.17
3583 8777 4.811969 TCCTGCTGCAATTCATGAATTT 57.188 36.364 27.30 12.74 38.84 1.82
3584 8778 4.404394 TCATCCTGCTGCAATTCATGAATT 59.596 37.500 24.83 24.83 41.33 2.17
3585 8779 3.958147 TCATCCTGCTGCAATTCATGAAT 59.042 39.130 15.36 15.36 0.00 2.57
3586 8780 3.358118 TCATCCTGCTGCAATTCATGAA 58.642 40.909 11.26 11.26 0.00 2.57
3587 8781 3.007473 TCATCCTGCTGCAATTCATGA 57.993 42.857 3.02 6.13 0.00 3.07
3588 8782 3.444916 GTTCATCCTGCTGCAATTCATG 58.555 45.455 3.02 3.84 0.00 3.07
3589 8783 2.429610 GGTTCATCCTGCTGCAATTCAT 59.570 45.455 3.02 0.00 0.00 2.57
3590 8784 1.820519 GGTTCATCCTGCTGCAATTCA 59.179 47.619 3.02 0.00 0.00 2.57
3591 8785 1.135721 GGGTTCATCCTGCTGCAATTC 59.864 52.381 3.02 0.00 36.25 2.17
3592 8786 1.188863 GGGTTCATCCTGCTGCAATT 58.811 50.000 3.02 0.00 36.25 2.32
3593 8787 0.040058 TGGGTTCATCCTGCTGCAAT 59.960 50.000 3.02 0.00 36.25 3.56
3594 8788 0.609957 CTGGGTTCATCCTGCTGCAA 60.610 55.000 3.02 0.00 36.25 4.08
3595 8789 1.001764 CTGGGTTCATCCTGCTGCA 60.002 57.895 0.88 0.88 36.25 4.41
3596 8790 1.751927 CCTGGGTTCATCCTGCTGC 60.752 63.158 0.00 0.00 36.25 5.25
3597 8791 0.393537 GTCCTGGGTTCATCCTGCTG 60.394 60.000 0.00 0.00 36.25 4.41
3598 8792 1.903877 CGTCCTGGGTTCATCCTGCT 61.904 60.000 0.00 0.00 36.25 4.24
3599 8793 1.450312 CGTCCTGGGTTCATCCTGC 60.450 63.158 0.00 0.00 36.25 4.85
3600 8794 0.108138 GACGTCCTGGGTTCATCCTG 60.108 60.000 3.51 0.00 36.25 3.86
3601 8795 0.252284 AGACGTCCTGGGTTCATCCT 60.252 55.000 13.01 0.00 36.25 3.24
3618 8812 3.969312 TGATTCACATGATAGCCTCCAGA 59.031 43.478 0.00 0.00 0.00 3.86
3681 8875 1.815421 CGCATCTTGTTCTCCCCCG 60.815 63.158 0.00 0.00 0.00 5.73
3686 8880 3.984292 CAAGCCGCATCTTGTTCTC 57.016 52.632 6.74 0.00 38.81 2.87
3699 8893 3.188667 GCAGAGTTACACCTTTACAAGCC 59.811 47.826 0.00 0.00 0.00 4.35
3714 8908 8.669243 GTTTATTCAACTATAAGCTGCAGAGTT 58.331 33.333 20.43 14.77 31.92 3.01
3751 8945 3.023119 TCTATGCATCAAACCCGCAATT 58.977 40.909 0.19 0.00 39.48 2.32
3756 8950 4.414852 CACTTTTCTATGCATCAAACCCG 58.585 43.478 0.19 0.00 0.00 5.28
3762 8956 5.104402 TGAGGATCCACTTTTCTATGCATCA 60.104 40.000 15.82 0.17 0.00 3.07
3764 8958 5.128919 GTGAGGATCCACTTTTCTATGCAT 58.871 41.667 15.82 3.79 34.38 3.96
3765 8959 4.019411 TGTGAGGATCCACTTTTCTATGCA 60.019 41.667 15.82 0.00 37.89 3.96
3766 8960 4.517285 TGTGAGGATCCACTTTTCTATGC 58.483 43.478 15.82 0.00 37.89 3.14
3767 8961 7.959689 CTATGTGAGGATCCACTTTTCTATG 57.040 40.000 15.82 0.00 37.89 2.23
3786 8980 3.655777 TCCTCTTCCCACAAAACCTATGT 59.344 43.478 0.00 0.00 0.00 2.29
3792 8986 3.348119 GAGGATCCTCTTCCCACAAAAC 58.652 50.000 31.11 3.54 39.80 2.43
3822 9016 6.463995 TCAAATGGTCTTTAACACAAGCTT 57.536 33.333 0.00 0.00 0.00 3.74
3832 9026 9.656040 CATCCAATTTTCATCAAATGGTCTTTA 57.344 29.630 0.00 0.00 35.09 1.85
3833 9027 7.608761 CCATCCAATTTTCATCAAATGGTCTTT 59.391 33.333 0.00 0.00 35.09 2.52
3834 9028 7.107542 CCATCCAATTTTCATCAAATGGTCTT 58.892 34.615 0.00 0.00 35.09 3.01
3835 9029 6.646267 CCATCCAATTTTCATCAAATGGTCT 58.354 36.000 0.00 0.00 35.09 3.85
3863 9089 3.305267 CCAACATGCTTTCCGTTCAATCA 60.305 43.478 0.00 0.00 0.00 2.57
3871 9098 1.135689 GCACTACCAACATGCTTTCCG 60.136 52.381 0.00 0.00 36.40 4.30
3877 9104 3.302365 AAATGTGCACTACCAACATGC 57.698 42.857 19.41 0.00 39.88 4.06
3880 9107 4.736168 GCAAGAAAATGTGCACTACCAACA 60.736 41.667 19.41 0.00 40.58 3.33
3882 9109 3.382865 TGCAAGAAAATGTGCACTACCAA 59.617 39.130 19.41 0.00 45.52 3.67
3928 10326 5.880332 ACGATTAGAAAGCAGAGCCAAATTA 59.120 36.000 0.00 0.00 0.00 1.40
3953 10351 3.129988 GGCAGCTGATTAACTTGCATTCT 59.870 43.478 20.43 0.00 0.00 2.40
3967 10365 0.694771 ATTTCAGTCCTGGCAGCTGA 59.305 50.000 20.43 17.49 37.47 4.26
4023 10422 8.877864 ACAATTCTGATGGGTATAGTTGAAAA 57.122 30.769 0.00 0.00 0.00 2.29
4035 10434 5.653769 ACCATGTAAGAACAATTCTGATGGG 59.346 40.000 19.13 10.05 41.57 4.00
4042 10441 6.204688 TCACAGTCACCATGTAAGAACAATTC 59.795 38.462 0.00 0.00 39.58 2.17
4064 10463 9.055248 CAATTTCTCGAAATGTTAAGTGATCAC 57.945 33.333 18.47 18.47 40.57 3.06
4145 10546 3.119137 CCTTTATAACCTTTGCCTGGTGC 60.119 47.826 0.00 0.00 37.93 5.01
4187 10588 3.460478 TTGCCCTTCCACAACCCCC 62.460 63.158 0.00 0.00 0.00 5.40
4210 10611 4.405358 AGAGATTCTCTTCCCTGTGACATC 59.595 45.833 10.50 0.00 37.60 3.06
4225 10626 2.011046 GCTGGCGCTTGAAGAGATTCT 61.011 52.381 7.64 0.00 0.00 2.40
4229 10630 3.063526 AGCTGGCGCTTGAAGAGA 58.936 55.556 7.64 0.00 46.47 3.10
4260 10661 2.026822 AGGAATGACGAAAGCTGGACAT 60.027 45.455 0.00 0.00 0.00 3.06
4274 10675 6.925718 CGCTAAACTTCAGATGATAGGAATGA 59.074 38.462 0.00 0.00 0.00 2.57
4436 10837 1.971357 AGGAAGCTCCGTGAAGAAGAA 59.029 47.619 0.00 0.00 42.75 2.52
4539 10940 7.550196 GGCTTATGAAATTTTGATGGTCATGTT 59.450 33.333 0.00 0.00 31.58 2.71


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

AutoCloner maintained by Alex Coulton.