Multiple sequence alignment - TraesCS2D01G019500

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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 TraesCS2D01G019500 chr2D 100.000 3461 0 0 1 3461 9379447 9382907 0.000000e+00 6392.0
1 TraesCS2D01G019500 chr2D 87.382 1276 155 5 937 2210 9251968 9253239 0.000000e+00 1459.0
2 TraesCS2D01G019500 chr2D 81.449 1601 252 25 999 2580 8683372 8684946 0.000000e+00 1269.0
3 TraesCS2D01G019500 chr2D 82.197 1438 215 22 930 2360 8479409 8478006 0.000000e+00 1199.0
4 TraesCS2D01G019500 chr2D 87.705 488 43 8 2357 2838 9334202 9334678 1.400000e-153 553.0
5 TraesCS2D01G019500 chr2D 91.727 278 21 2 3180 3455 9334850 9335127 5.420000e-103 385.0
6 TraesCS2D01G019500 chr2D 86.735 196 18 7 2959 3150 9382596 9382405 9.730000e-51 211.0
7 TraesCS2D01G019500 chr2D 100.000 31 0 0 3382 3412 9335139 9335169 1.340000e-04 58.4
8 TraesCS2D01G019500 chr2A 93.814 1859 102 7 923 2779 8630882 8632729 0.000000e+00 2784.0
9 TraesCS2D01G019500 chr2A 82.141 1607 240 23 930 2503 9395056 9396648 0.000000e+00 1334.0
10 TraesCS2D01G019500 chr2A 82.078 1607 241 23 930 2503 9847533 9849125 0.000000e+00 1328.0
11 TraesCS2D01G019500 chr2A 81.586 1564 262 20 922 2475 9111194 9109647 0.000000e+00 1269.0
12 TraesCS2D01G019500 chr2A 81.368 1535 264 14 999 2524 9944092 9945613 0.000000e+00 1230.0
13 TraesCS2D01G019500 chr2B 87.314 1277 154 7 937 2210 11725336 11724065 0.000000e+00 1454.0
14 TraesCS2D01G019500 chr2B 81.938 1600 245 22 930 2520 11226497 11224933 0.000000e+00 1314.0
15 TraesCS2D01G019500 chr2B 80.013 1536 255 25 998 2503 138993293 138991780 0.000000e+00 1088.0
16 TraesCS2D01G019500 chr2B 88.160 701 72 7 2138 2838 11568741 11568052 0.000000e+00 824.0
17 TraesCS2D01G019500 chr2B 77.367 433 90 7 471 899 693847759 693847331 2.060000e-62 250.0
18 TraesCS2D01G019500 chr2B 91.275 149 13 0 921 1069 11567813 11567665 1.630000e-48 204.0
19 TraesCS2D01G019500 chr2B 81.325 166 19 5 2998 3151 250533932 250533767 1.300000e-24 124.0
20 TraesCS2D01G019500 chr4D 81.812 1600 264 19 926 2514 464204536 464206119 0.000000e+00 1317.0
21 TraesCS2D01G019500 chr3D 82.412 904 151 7 1 899 152680433 152679533 0.000000e+00 782.0
22 TraesCS2D01G019500 chr5A 75.965 907 205 13 1 900 568738860 568739760 4.070000e-124 455.0
23 TraesCS2D01G019500 chr1B 76.227 917 184 27 1 906 629758759 629757866 4.070000e-124 455.0
24 TraesCS2D01G019500 chr6D 75.725 828 175 23 1 815 433165208 433164394 3.240000e-105 392.0
25 TraesCS2D01G019500 chr1D 84.712 399 48 7 496 894 49572788 49573173 1.510000e-103 387.0
26 TraesCS2D01G019500 chr1D 80.525 457 79 9 1 452 49572334 49572785 3.310000e-90 342.0
27 TraesCS2D01G019500 chr6A 72.639 826 193 28 1 807 524827883 524828694 3.450000e-60 243.0
28 TraesCS2D01G019500 chr6A 72.518 826 194 28 1 807 524826149 524826960 1.610000e-58 237.0
29 TraesCS2D01G019500 chr4A 93.805 113 7 0 3040 3152 469239494 469239382 1.650000e-38 171.0
30 TraesCS2D01G019500 chr7D 87.681 138 15 2 768 904 169459451 169459315 3.580000e-35 159.0
31 TraesCS2D01G019500 chr7D 85.915 71 10 0 829 899 632113168 632113238 3.700000e-10 76.8
32 TraesCS2D01G019500 chr5D 89.189 111 11 1 3044 3153 70394828 70394938 1.680000e-28 137.0
33 TraesCS2D01G019500 chr5D 85.714 119 15 2 3039 3156 70394434 70394317 1.300000e-24 124.0
34 TraesCS2D01G019500 chr5D 86.207 116 15 1 3040 3154 447988125 447988240 1.300000e-24 124.0
35 TraesCS2D01G019500 chr5D 84.884 86 9 4 2959 3042 447988236 447988153 2.210000e-12 84.2
36 TraesCS2D01G019500 chr3A 87.629 97 12 0 3057 3153 649605046 649605142 2.820000e-21 113.0
37 TraesCS2D01G019500 chr6B 88.298 94 10 1 3044 3136 61998558 61998465 1.020000e-20 111.0
38 TraesCS2D01G019500 chr6B 95.918 49 2 0 2997 3045 61998489 61998537 2.860000e-11 80.5


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 TraesCS2D01G019500 chr2D 9379447 9382907 3460 False 6392.000000 6392 100.0000 1 3461 1 chr2D.!!$F3 3460
1 TraesCS2D01G019500 chr2D 9251968 9253239 1271 False 1459.000000 1459 87.3820 937 2210 1 chr2D.!!$F2 1273
2 TraesCS2D01G019500 chr2D 8683372 8684946 1574 False 1269.000000 1269 81.4490 999 2580 1 chr2D.!!$F1 1581
3 TraesCS2D01G019500 chr2D 8478006 8479409 1403 True 1199.000000 1199 82.1970 930 2360 1 chr2D.!!$R1 1430
4 TraesCS2D01G019500 chr2D 9334202 9335169 967 False 332.133333 553 93.1440 2357 3455 3 chr2D.!!$F4 1098
5 TraesCS2D01G019500 chr2A 8630882 8632729 1847 False 2784.000000 2784 93.8140 923 2779 1 chr2A.!!$F1 1856
6 TraesCS2D01G019500 chr2A 9395056 9396648 1592 False 1334.000000 1334 82.1410 930 2503 1 chr2A.!!$F2 1573
7 TraesCS2D01G019500 chr2A 9847533 9849125 1592 False 1328.000000 1328 82.0780 930 2503 1 chr2A.!!$F3 1573
8 TraesCS2D01G019500 chr2A 9109647 9111194 1547 True 1269.000000 1269 81.5860 922 2475 1 chr2A.!!$R1 1553
9 TraesCS2D01G019500 chr2A 9944092 9945613 1521 False 1230.000000 1230 81.3680 999 2524 1 chr2A.!!$F4 1525
10 TraesCS2D01G019500 chr2B 11724065 11725336 1271 True 1454.000000 1454 87.3140 937 2210 1 chr2B.!!$R2 1273
11 TraesCS2D01G019500 chr2B 11224933 11226497 1564 True 1314.000000 1314 81.9380 930 2520 1 chr2B.!!$R1 1590
12 TraesCS2D01G019500 chr2B 138991780 138993293 1513 True 1088.000000 1088 80.0130 998 2503 1 chr2B.!!$R3 1505
13 TraesCS2D01G019500 chr2B 11567665 11568741 1076 True 514.000000 824 89.7175 921 2838 2 chr2B.!!$R6 1917
14 TraesCS2D01G019500 chr4D 464204536 464206119 1583 False 1317.000000 1317 81.8120 926 2514 1 chr4D.!!$F1 1588
15 TraesCS2D01G019500 chr3D 152679533 152680433 900 True 782.000000 782 82.4120 1 899 1 chr3D.!!$R1 898
16 TraesCS2D01G019500 chr5A 568738860 568739760 900 False 455.000000 455 75.9650 1 900 1 chr5A.!!$F1 899
17 TraesCS2D01G019500 chr1B 629757866 629758759 893 True 455.000000 455 76.2270 1 906 1 chr1B.!!$R1 905
18 TraesCS2D01G019500 chr6D 433164394 433165208 814 True 392.000000 392 75.7250 1 815 1 chr6D.!!$R1 814
19 TraesCS2D01G019500 chr1D 49572334 49573173 839 False 364.500000 387 82.6185 1 894 2 chr1D.!!$F1 893
20 TraesCS2D01G019500 chr6A 524826149 524828694 2545 False 240.000000 243 72.5785 1 807 2 chr6A.!!$F1 806

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
706 714 0.036388 CTACCAGAGCCCAAAAGCGA 60.036 55.0 0.0 0.0 38.01 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2693 3787 3.834489 ATCTGGCTAAGTCTGTGGATG 57.166 47.619 0.0 0.0 0.0 3.51 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
46 47 1.381463 GGCGAGTAGGGAAGAGGGT 60.381 63.158 0.00 0.00 0.00 4.34
90 91 4.277552 CCTCCGATCTGGTGGCTA 57.722 61.111 10.38 0.00 44.10 3.93
129 130 1.140134 TAGGGTTCCTTTGGGCAGCT 61.140 55.000 0.00 0.00 34.61 4.24
243 249 3.832237 CTGACCGCTGCCACTTGGT 62.832 63.158 0.00 0.00 37.44 3.67
283 291 4.827087 CCGAGCAGCATGGCGTCT 62.827 66.667 0.00 0.00 39.27 4.18
287 295 4.783621 GCAGCATGGCGTCTCCCA 62.784 66.667 0.00 0.00 39.65 4.37
327 335 3.006728 CGGTGCCCCAACCCTAGA 61.007 66.667 0.00 0.00 36.84 2.43
331 339 4.176752 GCCCCAACCCTAGAGCCG 62.177 72.222 0.00 0.00 0.00 5.52
337 345 4.541648 ACCCTAGAGCCGGGCGAT 62.542 66.667 14.39 8.86 46.04 4.58
448 456 3.550431 GCATCCGGGGCTGCTAGA 61.550 66.667 14.75 0.00 34.78 2.43
452 460 0.764369 ATCCGGGGCTGCTAGATCAA 60.764 55.000 0.00 0.00 0.00 2.57
453 461 1.227674 CCGGGGCTGCTAGATCAAC 60.228 63.158 0.00 0.00 0.00 3.18
455 463 1.915228 GGGGCTGCTAGATCAACCA 59.085 57.895 0.00 0.00 0.00 3.67
458 466 1.340017 GGGCTGCTAGATCAACCAACA 60.340 52.381 0.00 0.00 0.00 3.33
467 475 3.276091 CAACCAACAGCGGACGCA 61.276 61.111 19.48 0.00 44.88 5.24
471 479 4.988598 CAACAGCGGACGCAGGGT 62.989 66.667 19.48 10.74 44.88 4.34
489 497 1.969589 TCGTCGACCTAGCAGCACA 60.970 57.895 10.58 0.00 0.00 4.57
490 498 1.080772 CGTCGACCTAGCAGCACAA 60.081 57.895 10.58 0.00 0.00 3.33
513 521 2.765807 CACCCCCGCCTGAGATCT 60.766 66.667 0.00 0.00 0.00 2.75
523 531 1.158484 CCTGAGATCTACGCCGACGA 61.158 60.000 0.00 0.00 43.93 4.20
618 626 2.674754 GAAATCCCCCACCGAGCA 59.325 61.111 0.00 0.00 0.00 4.26
619 627 1.749258 GAAATCCCCCACCGAGCAC 60.749 63.158 0.00 0.00 0.00 4.40
658 666 2.102357 CCCTCACCATCGTCGACG 59.898 66.667 31.30 31.30 41.45 5.12
659 667 2.579787 CCTCACCATCGTCGACGC 60.580 66.667 32.19 0.00 39.60 5.19
665 673 2.104132 CATCGTCGACGCCATCCA 59.896 61.111 32.19 15.14 39.60 3.41
670 678 2.362503 TCGACGCCATCCACCTCT 60.363 61.111 0.00 0.00 0.00 3.69
676 684 1.144936 GCCATCCACCTCTTCCTCG 59.855 63.158 0.00 0.00 0.00 4.63
688 696 2.231540 CTTCCTCGGACTCCTCCCCT 62.232 65.000 0.00 0.00 31.93 4.79
689 697 0.922738 TTCCTCGGACTCCTCCCCTA 60.923 60.000 0.00 0.00 31.93 3.53
706 714 0.036388 CTACCAGAGCCCAAAAGCGA 60.036 55.000 0.00 0.00 38.01 4.93
709 717 0.036388 CCAGAGCCCAAAAGCGACTA 60.036 55.000 0.00 0.00 38.01 2.59
720 728 3.450115 GCGACTACCGGACCAGCT 61.450 66.667 9.46 0.00 39.04 4.24
721 729 2.490217 CGACTACCGGACCAGCTG 59.510 66.667 9.46 6.78 33.91 4.24
724 732 3.077556 CTACCGGACCAGCTGCCT 61.078 66.667 9.46 0.00 0.00 4.75
853 861 4.293648 CCCGTGTCGCACTCACCA 62.294 66.667 8.07 0.00 32.86 4.17
860 868 2.887568 CGCACTCACCATCGCCTC 60.888 66.667 0.00 0.00 0.00 4.70
862 870 2.187946 CACTCACCATCGCCTCCC 59.812 66.667 0.00 0.00 0.00 4.30
894 902 1.218316 GTACAGGAGCCGTTGGAGG 59.782 63.158 0.00 0.00 0.00 4.30
904 912 1.826385 CCGTTGGAGGCATCTTTTCT 58.174 50.000 0.00 0.00 0.00 2.52
905 913 1.740025 CCGTTGGAGGCATCTTTTCTC 59.260 52.381 0.00 0.00 0.00 2.87
906 914 1.740025 CGTTGGAGGCATCTTTTCTCC 59.260 52.381 0.00 0.00 45.36 3.71
907 915 2.616510 CGTTGGAGGCATCTTTTCTCCT 60.617 50.000 0.00 0.00 45.36 3.69
908 916 2.751806 GTTGGAGGCATCTTTTCTCCTG 59.248 50.000 0.00 0.00 45.36 3.86
909 917 1.283029 TGGAGGCATCTTTTCTCCTGG 59.717 52.381 0.00 0.00 45.36 4.45
910 918 1.409381 GGAGGCATCTTTTCTCCTGGG 60.409 57.143 0.00 0.00 42.70 4.45
911 919 1.283321 GAGGCATCTTTTCTCCTGGGT 59.717 52.381 0.00 0.00 0.00 4.51
912 920 1.005215 AGGCATCTTTTCTCCTGGGTG 59.995 52.381 0.00 0.00 0.00 4.61
913 921 1.272147 GGCATCTTTTCTCCTGGGTGT 60.272 52.381 0.00 0.00 0.00 4.16
914 922 1.815003 GCATCTTTTCTCCTGGGTGTG 59.185 52.381 0.00 0.00 0.00 3.82
915 923 2.815589 GCATCTTTTCTCCTGGGTGTGT 60.816 50.000 0.00 0.00 0.00 3.72
916 924 3.490348 CATCTTTTCTCCTGGGTGTGTT 58.510 45.455 0.00 0.00 0.00 3.32
917 925 3.208747 TCTTTTCTCCTGGGTGTGTTC 57.791 47.619 0.00 0.00 0.00 3.18
918 926 2.777692 TCTTTTCTCCTGGGTGTGTTCT 59.222 45.455 0.00 0.00 0.00 3.01
919 927 3.202151 TCTTTTCTCCTGGGTGTGTTCTT 59.798 43.478 0.00 0.00 0.00 2.52
920 928 2.638480 TTCTCCTGGGTGTGTTCTTG 57.362 50.000 0.00 0.00 0.00 3.02
928 936 1.230324 GGTGTGTTCTTGTCTCTGCC 58.770 55.000 0.00 0.00 0.00 4.85
967 975 6.016610 GCCAGTCTAGTTAAATTTGTCCACAA 60.017 38.462 0.00 0.00 0.00 3.33
977 986 1.668101 TTGTCCACAAACGGCCAACC 61.668 55.000 2.24 0.00 32.11 3.77
1049 1058 1.865865 GAACTCGTGAGCCAGTTCAA 58.134 50.000 7.37 0.00 45.38 2.69
1074 1083 4.761739 TCCTTCCTAATGAACAAGTGCAAG 59.238 41.667 0.00 0.00 0.00 4.01
1111 1132 2.836981 CAATCAGAGGAGGAGAAGGTGT 59.163 50.000 0.00 0.00 0.00 4.16
1145 1166 0.535797 CACCTGCTGATGAGAGCTGA 59.464 55.000 0.00 0.00 39.58 4.26
1169 1190 1.949847 ATCGTTGAGGAGGCGGACAG 61.950 60.000 0.00 0.00 0.00 3.51
1245 1266 2.082140 TGTACCGAGGATATGGTGCT 57.918 50.000 0.00 0.00 40.95 4.40
1280 1301 1.122632 TACCGTGCCCTCCAAGACAA 61.123 55.000 0.00 0.00 0.00 3.18
1346 1376 4.550831 CGGATTGTATTTAGTCAAGCGCTG 60.551 45.833 12.58 5.47 31.84 5.18
1445 1484 6.633856 ACATGGCAGAATTTATTGTTCTTCC 58.366 36.000 0.00 0.00 38.82 3.46
1447 1486 5.083122 TGGCAGAATTTATTGTTCTTCCCA 58.917 37.500 2.89 2.73 37.95 4.37
1689 1807 2.675348 CTCACGCTTCTCCTCCATTTTC 59.325 50.000 0.00 0.00 0.00 2.29
1733 1925 6.227522 TCTTGACGATACTTGACAATGGAAA 58.772 36.000 0.00 0.00 0.00 3.13
1769 2334 8.768397 AGGAATGATGTTGGTAGTTATTGAGTA 58.232 33.333 0.00 0.00 0.00 2.59
2031 2910 1.203052 GCCATGTTAGTGCACAATGCT 59.797 47.619 21.04 0.00 45.31 3.79
2167 3049 3.818210 CTCCAGATATAGCAGTGTCGACT 59.182 47.826 17.92 0.00 0.00 4.18
2169 3051 3.364465 CCAGATATAGCAGTGTCGACTCG 60.364 52.174 17.92 10.54 0.00 4.18
2314 3199 3.257624 ACTTCTAACAGACCCTACCGTTG 59.742 47.826 0.00 0.00 0.00 4.10
2559 3649 8.739972 GGCCATATAAAGTATTTTATGGAGTGG 58.260 37.037 17.00 14.33 43.72 4.00
2595 3685 7.123160 TCGACTAAACATATGAGAGATCTCG 57.877 40.000 16.97 4.39 45.72 4.04
2693 3787 0.321653 CACAGTAGTGCCTCCCCAAC 60.322 60.000 0.00 0.00 39.21 3.77
2703 3797 0.035056 CCTCCCCAACATCCACAGAC 60.035 60.000 0.00 0.00 0.00 3.51
2850 4018 1.363744 GGATCTCCGCACTTGACTTG 58.636 55.000 0.00 0.00 0.00 3.16
2856 4024 1.572085 CCGCACTTGACTTGAGCCAG 61.572 60.000 0.00 0.00 0.00 4.85
2903 4071 3.775654 GGTGCTAGGTGCTCGGCT 61.776 66.667 0.00 0.00 43.37 5.52
2951 4119 3.302344 GCCGCCATGGTGGTTTGT 61.302 61.111 38.24 0.00 46.72 2.83
2965 4133 4.262036 GGTGGTTTGTGGAAGGAGAAAATC 60.262 45.833 0.00 0.00 0.00 2.17
2966 4134 4.584743 GTGGTTTGTGGAAGGAGAAAATCT 59.415 41.667 0.00 0.00 0.00 2.40
2967 4135 5.069119 GTGGTTTGTGGAAGGAGAAAATCTT 59.931 40.000 0.00 0.00 0.00 2.40
2968 4136 6.264518 GTGGTTTGTGGAAGGAGAAAATCTTA 59.735 38.462 0.00 0.00 0.00 2.10
2969 4137 7.010160 TGGTTTGTGGAAGGAGAAAATCTTAT 58.990 34.615 0.00 0.00 0.00 1.73
2972 4140 7.843490 TTGTGGAAGGAGAAAATCTTATACG 57.157 36.000 0.00 0.00 0.00 3.06
2976 4144 6.383147 TGGAAGGAGAAAATCTTATACGACCT 59.617 38.462 0.00 0.00 0.00 3.85
2978 4146 6.163135 AGGAGAAAATCTTATACGACCTGG 57.837 41.667 0.00 0.00 0.00 4.45
2979 4147 5.661759 AGGAGAAAATCTTATACGACCTGGT 59.338 40.000 0.00 0.00 0.00 4.00
2980 4148 6.156429 AGGAGAAAATCTTATACGACCTGGTT 59.844 38.462 0.00 0.00 0.00 3.67
2981 4149 6.258068 GGAGAAAATCTTATACGACCTGGTTG 59.742 42.308 12.66 12.66 0.00 3.77
2982 4150 6.708285 AGAAAATCTTATACGACCTGGTTGT 58.292 36.000 22.70 22.70 34.24 3.32
2983 4151 7.844009 AGAAAATCTTATACGACCTGGTTGTA 58.156 34.615 25.27 25.27 36.91 2.41
2984 4152 7.763071 AGAAAATCTTATACGACCTGGTTGTAC 59.237 37.037 25.51 11.89 35.55 2.90
2985 4153 4.621068 TCTTATACGACCTGGTTGTACG 57.379 45.455 25.51 15.34 35.55 3.67
2986 4154 4.009675 TCTTATACGACCTGGTTGTACGT 58.990 43.478 25.51 19.83 35.55 3.57
2987 4155 5.182487 TCTTATACGACCTGGTTGTACGTA 58.818 41.667 25.51 21.16 42.06 3.57
2988 4156 5.822519 TCTTATACGACCTGGTTGTACGTAT 59.177 40.000 25.51 25.23 46.57 3.06
2989 4157 2.927553 ACGACCTGGTTGTACGTATC 57.072 50.000 18.20 0.00 35.49 2.24
2990 4158 1.474077 ACGACCTGGTTGTACGTATCC 59.526 52.381 18.20 3.09 35.49 2.59
2991 4159 1.747355 CGACCTGGTTGTACGTATCCT 59.253 52.381 0.00 0.00 0.00 3.24
2992 4160 2.223433 CGACCTGGTTGTACGTATCCTC 60.223 54.545 0.00 0.00 0.00 3.71
2993 4161 3.022406 GACCTGGTTGTACGTATCCTCT 58.978 50.000 0.00 0.00 0.00 3.69
2994 4162 3.022406 ACCTGGTTGTACGTATCCTCTC 58.978 50.000 0.00 0.00 0.00 3.20
2995 4163 3.021695 CCTGGTTGTACGTATCCTCTCA 58.978 50.000 0.00 0.00 0.00 3.27
2996 4164 3.637229 CCTGGTTGTACGTATCCTCTCAT 59.363 47.826 0.00 0.00 0.00 2.90
2997 4165 4.499865 CCTGGTTGTACGTATCCTCTCATG 60.500 50.000 0.00 0.00 0.00 3.07
2998 4166 4.274978 TGGTTGTACGTATCCTCTCATGA 58.725 43.478 0.00 0.00 0.00 3.07
2999 4167 4.338400 TGGTTGTACGTATCCTCTCATGAG 59.662 45.833 17.07 17.07 39.92 2.90
3000 4168 4.579340 GGTTGTACGTATCCTCTCATGAGA 59.421 45.833 23.75 23.75 42.73 3.27
3001 4169 5.505985 GGTTGTACGTATCCTCTCATGAGAC 60.506 48.000 21.67 11.04 42.73 3.36
3002 4170 4.135306 TGTACGTATCCTCTCATGAGACC 58.865 47.826 21.67 6.45 42.73 3.85
3003 4171 2.588620 ACGTATCCTCTCATGAGACCC 58.411 52.381 21.67 6.77 42.73 4.46
3004 4172 1.889829 CGTATCCTCTCATGAGACCCC 59.110 57.143 21.67 7.10 42.73 4.95
3005 4173 2.753168 CGTATCCTCTCATGAGACCCCA 60.753 54.545 21.67 6.02 42.73 4.96
3006 4174 2.811322 ATCCTCTCATGAGACCCCAT 57.189 50.000 21.67 8.02 42.73 4.00
3007 4175 2.094100 TCCTCTCATGAGACCCCATC 57.906 55.000 21.67 0.00 42.73 3.51
3008 4176 0.678395 CCTCTCATGAGACCCCATCG 59.322 60.000 21.67 9.84 42.73 3.84
3009 4177 1.697284 CTCTCATGAGACCCCATCGA 58.303 55.000 21.67 0.00 42.73 3.59
3010 4178 2.246469 CTCTCATGAGACCCCATCGAT 58.754 52.381 21.67 0.00 42.73 3.59
3011 4179 1.966354 TCTCATGAGACCCCATCGATG 59.034 52.381 21.67 18.76 31.41 3.84
3012 4180 1.966354 CTCATGAGACCCCATCGATGA 59.034 52.381 26.86 5.01 32.89 2.92
3013 4181 2.566279 CTCATGAGACCCCATCGATGAT 59.434 50.000 26.86 11.50 33.23 2.45
3014 4182 3.766051 CTCATGAGACCCCATCGATGATA 59.234 47.826 26.86 5.01 33.23 2.15
3015 4183 4.356436 TCATGAGACCCCATCGATGATAT 58.644 43.478 26.86 10.76 30.34 1.63
3016 4184 4.161001 TCATGAGACCCCATCGATGATATG 59.839 45.833 26.86 16.83 30.34 1.78
3017 4185 3.778265 TGAGACCCCATCGATGATATGA 58.222 45.455 26.86 0.61 0.00 2.15
3018 4186 3.511540 TGAGACCCCATCGATGATATGAC 59.488 47.826 26.86 13.31 0.00 3.06
3019 4187 3.510459 AGACCCCATCGATGATATGACA 58.490 45.455 26.86 0.00 0.00 3.58
3020 4188 3.259374 AGACCCCATCGATGATATGACAC 59.741 47.826 26.86 9.08 0.00 3.67
3021 4189 2.029020 ACCCCATCGATGATATGACACG 60.029 50.000 26.86 6.27 0.00 4.49
3022 4190 2.029020 CCCCATCGATGATATGACACGT 60.029 50.000 26.86 0.00 0.00 4.49
3023 4191 2.989166 CCCATCGATGATATGACACGTG 59.011 50.000 26.86 15.48 0.00 4.49
3024 4192 2.989166 CCATCGATGATATGACACGTGG 59.011 50.000 26.86 2.46 0.00 4.94
3025 4193 2.134201 TCGATGATATGACACGTGGC 57.866 50.000 21.57 19.24 0.00 5.01
3026 4194 1.681264 TCGATGATATGACACGTGGCT 59.319 47.619 24.38 10.78 0.00 4.75
3027 4195 2.100749 TCGATGATATGACACGTGGCTT 59.899 45.455 24.38 19.39 0.00 4.35
3028 4196 2.472861 CGATGATATGACACGTGGCTTC 59.527 50.000 24.38 16.66 0.00 3.86
3029 4197 3.457234 GATGATATGACACGTGGCTTCA 58.543 45.455 24.38 21.51 0.00 3.02
3030 4198 2.616960 TGATATGACACGTGGCTTCAC 58.383 47.619 24.38 13.78 38.00 3.18
3031 4199 2.028567 TGATATGACACGTGGCTTCACA 60.029 45.455 24.38 16.10 41.27 3.58
3032 4200 2.535012 TATGACACGTGGCTTCACAA 57.465 45.000 24.38 0.00 41.27 3.33
3033 4201 1.674359 ATGACACGTGGCTTCACAAA 58.326 45.000 24.38 0.00 41.27 2.83
3034 4202 1.674359 TGACACGTGGCTTCACAAAT 58.326 45.000 24.38 0.00 41.27 2.32
3035 4203 1.601903 TGACACGTGGCTTCACAAATC 59.398 47.619 24.38 5.73 41.27 2.17
3036 4204 1.873591 GACACGTGGCTTCACAAATCT 59.126 47.619 21.57 0.00 41.27 2.40
3037 4205 1.873591 ACACGTGGCTTCACAAATCTC 59.126 47.619 21.57 0.00 41.27 2.75
3038 4206 1.872952 CACGTGGCTTCACAAATCTCA 59.127 47.619 7.95 0.00 41.27 3.27
3039 4207 2.290367 CACGTGGCTTCACAAATCTCAA 59.710 45.455 7.95 0.00 41.27 3.02
3040 4208 2.948979 ACGTGGCTTCACAAATCTCAAA 59.051 40.909 0.00 0.00 41.27 2.69
3041 4209 3.003689 ACGTGGCTTCACAAATCTCAAAG 59.996 43.478 0.00 0.00 41.27 2.77
3042 4210 3.311966 GTGGCTTCACAAATCTCAAAGC 58.688 45.455 0.00 0.00 40.91 3.51
3043 4211 2.957680 TGGCTTCACAAATCTCAAAGCA 59.042 40.909 7.59 0.00 43.15 3.91
3044 4212 3.005050 TGGCTTCACAAATCTCAAAGCAG 59.995 43.478 7.59 0.00 43.15 4.24
3045 4213 3.254166 GGCTTCACAAATCTCAAAGCAGA 59.746 43.478 7.59 0.00 43.15 4.26
3046 4214 4.261741 GGCTTCACAAATCTCAAAGCAGAA 60.262 41.667 7.59 0.00 43.15 3.02
3047 4215 4.916249 GCTTCACAAATCTCAAAGCAGAAG 59.084 41.667 0.00 0.00 41.46 2.85
3048 4216 5.278169 GCTTCACAAATCTCAAAGCAGAAGA 60.278 40.000 0.00 0.00 41.46 2.87
3049 4217 5.679734 TCACAAATCTCAAAGCAGAAGAC 57.320 39.130 0.00 0.00 0.00 3.01
3050 4218 4.212004 TCACAAATCTCAAAGCAGAAGACG 59.788 41.667 0.00 0.00 0.00 4.18
3051 4219 4.212004 CACAAATCTCAAAGCAGAAGACGA 59.788 41.667 0.00 0.00 0.00 4.20
3052 4220 4.999950 ACAAATCTCAAAGCAGAAGACGAT 59.000 37.500 0.00 0.00 0.00 3.73
3053 4221 5.106791 ACAAATCTCAAAGCAGAAGACGATG 60.107 40.000 0.00 0.00 0.00 3.84
3054 4222 2.341257 TCTCAAAGCAGAAGACGATGC 58.659 47.619 0.00 0.00 42.87 3.91
3059 4227 2.743195 GCAGAAGACGATGCGTTCT 58.257 52.632 0.00 0.00 41.37 3.01
3060 4228 1.071605 GCAGAAGACGATGCGTTCTT 58.928 50.000 0.00 0.00 41.37 2.52
3061 4229 1.461127 GCAGAAGACGATGCGTTCTTT 59.539 47.619 0.00 0.00 41.37 2.52
3062 4230 2.723010 GCAGAAGACGATGCGTTCTTTG 60.723 50.000 0.00 0.00 41.37 2.77
3063 4231 2.476619 CAGAAGACGATGCGTTCTTTGT 59.523 45.455 0.00 0.00 41.37 2.83
3064 4232 3.059597 CAGAAGACGATGCGTTCTTTGTT 60.060 43.478 0.00 0.00 41.37 2.83
3065 4233 2.949714 AGACGATGCGTTCTTTGTTG 57.050 45.000 0.00 0.00 41.37 3.33
3066 4234 1.069906 AGACGATGCGTTCTTTGTTGC 60.070 47.619 0.00 0.00 41.37 4.17
3067 4235 0.944386 ACGATGCGTTCTTTGTTGCT 59.056 45.000 0.00 0.00 36.35 3.91
3068 4236 1.333619 ACGATGCGTTCTTTGTTGCTT 59.666 42.857 0.00 0.00 36.35 3.91
3069 4237 2.223479 ACGATGCGTTCTTTGTTGCTTT 60.223 40.909 0.00 0.00 36.35 3.51
3070 4238 2.151736 CGATGCGTTCTTTGTTGCTTTG 59.848 45.455 0.00 0.00 0.00 2.77
3071 4239 2.929531 TGCGTTCTTTGTTGCTTTGA 57.070 40.000 0.00 0.00 0.00 2.69
3072 4240 2.796304 TGCGTTCTTTGTTGCTTTGAG 58.204 42.857 0.00 0.00 0.00 3.02
3073 4241 2.421775 TGCGTTCTTTGTTGCTTTGAGA 59.578 40.909 0.00 0.00 0.00 3.27
3074 4242 3.066621 TGCGTTCTTTGTTGCTTTGAGAT 59.933 39.130 0.00 0.00 0.00 2.75
3075 4243 4.044426 GCGTTCTTTGTTGCTTTGAGATT 58.956 39.130 0.00 0.00 0.00 2.40
3076 4244 4.504097 GCGTTCTTTGTTGCTTTGAGATTT 59.496 37.500 0.00 0.00 0.00 2.17
3077 4245 5.555069 GCGTTCTTTGTTGCTTTGAGATTTG 60.555 40.000 0.00 0.00 0.00 2.32
3078 4246 5.516339 CGTTCTTTGTTGCTTTGAGATTTGT 59.484 36.000 0.00 0.00 0.00 2.83
3079 4247 6.506827 CGTTCTTTGTTGCTTTGAGATTTGTG 60.507 38.462 0.00 0.00 0.00 3.33
3080 4248 6.206395 TCTTTGTTGCTTTGAGATTTGTGA 57.794 33.333 0.00 0.00 0.00 3.58
3081 4249 6.629128 TCTTTGTTGCTTTGAGATTTGTGAA 58.371 32.000 0.00 0.00 0.00 3.18
3082 4250 6.753279 TCTTTGTTGCTTTGAGATTTGTGAAG 59.247 34.615 0.00 0.00 0.00 3.02
3083 4251 4.362279 TGTTGCTTTGAGATTTGTGAAGC 58.638 39.130 0.00 0.00 42.19 3.86
3084 4252 3.648339 TGCTTTGAGATTTGTGAAGCC 57.352 42.857 4.20 0.00 41.40 4.35
3085 4253 2.957680 TGCTTTGAGATTTGTGAAGCCA 59.042 40.909 4.20 0.00 41.40 4.75
3086 4254 3.243501 TGCTTTGAGATTTGTGAAGCCAC 60.244 43.478 4.20 0.00 41.40 5.01
3087 4255 3.558505 CTTTGAGATTTGTGAAGCCACG 58.441 45.455 0.00 0.00 46.06 4.94
3088 4256 2.254546 TGAGATTTGTGAAGCCACGT 57.745 45.000 0.00 0.00 46.06 4.49
3089 4257 1.872952 TGAGATTTGTGAAGCCACGTG 59.127 47.619 9.08 9.08 46.06 4.49
3090 4258 1.873591 GAGATTTGTGAAGCCACGTGT 59.126 47.619 15.65 0.00 46.06 4.49
3091 4259 1.873591 AGATTTGTGAAGCCACGTGTC 59.126 47.619 15.65 0.10 46.06 3.67
3092 4260 1.601903 GATTTGTGAAGCCACGTGTCA 59.398 47.619 15.65 9.07 46.06 3.58
3093 4261 1.674359 TTTGTGAAGCCACGTGTCAT 58.326 45.000 15.65 0.00 46.06 3.06
3094 4262 1.225855 TTGTGAAGCCACGTGTCATC 58.774 50.000 15.65 4.62 46.06 2.92
3095 4263 0.392706 TGTGAAGCCACGTGTCATCT 59.607 50.000 15.65 3.00 46.06 2.90
3096 4264 1.616374 TGTGAAGCCACGTGTCATCTA 59.384 47.619 15.65 0.70 46.06 1.98
3097 4265 2.036604 TGTGAAGCCACGTGTCATCTAA 59.963 45.455 15.65 0.00 46.06 2.10
3098 4266 3.262420 GTGAAGCCACGTGTCATCTAAT 58.738 45.455 15.65 0.00 33.10 1.73
3099 4267 3.307242 GTGAAGCCACGTGTCATCTAATC 59.693 47.826 15.65 2.09 33.10 1.75
3100 4268 2.209838 AGCCACGTGTCATCTAATCG 57.790 50.000 15.65 0.00 0.00 3.34
3101 4269 1.749063 AGCCACGTGTCATCTAATCGA 59.251 47.619 15.65 0.00 0.00 3.59
3102 4270 2.362397 AGCCACGTGTCATCTAATCGAT 59.638 45.455 15.65 0.00 0.00 3.59
3112 4280 3.919216 CATCTAATCGATGGGGTCTCAC 58.081 50.000 0.00 0.00 44.69 3.51
3113 4281 1.954382 TCTAATCGATGGGGTCTCACG 59.046 52.381 0.00 0.00 0.00 4.35
3114 4282 1.954382 CTAATCGATGGGGTCTCACGA 59.046 52.381 0.00 0.00 37.39 4.35
3115 4283 0.747255 AATCGATGGGGTCTCACGAG 59.253 55.000 0.00 0.00 36.49 4.18
3116 4284 0.106669 ATCGATGGGGTCTCACGAGA 60.107 55.000 0.00 0.00 36.49 4.04
3123 4291 4.535425 GTCTCACGAGACGGTGTG 57.465 61.111 11.23 0.00 46.93 3.82
3124 4292 1.653115 GTCTCACGAGACGGTGTGT 59.347 57.895 11.23 0.00 46.93 3.72
3125 4293 0.870393 GTCTCACGAGACGGTGTGTA 59.130 55.000 11.23 0.00 46.93 2.90
3126 4294 0.870393 TCTCACGAGACGGTGTGTAC 59.130 55.000 0.00 0.00 39.00 2.90
3127 4295 0.452287 CTCACGAGACGGTGTGTACG 60.452 60.000 0.00 0.00 39.00 3.67
3128 4296 0.879839 TCACGAGACGGTGTGTACGA 60.880 55.000 0.00 0.00 39.00 3.43
3129 4297 0.723790 CACGAGACGGTGTGTACGAC 60.724 60.000 0.00 0.00 35.44 4.34
3130 4298 1.154338 CGAGACGGTGTGTACGACC 60.154 63.158 4.14 4.14 34.03 4.79
3131 4299 1.844771 CGAGACGGTGTGTACGACCA 61.845 60.000 12.94 0.00 34.03 4.02
3132 4300 0.109873 GAGACGGTGTGTACGACCAG 60.110 60.000 12.94 8.62 32.45 4.00
3133 4301 1.080974 GACGGTGTGTACGACCAGG 60.081 63.158 12.94 0.00 32.45 4.45
3134 4302 1.799258 GACGGTGTGTACGACCAGGT 61.799 60.000 12.94 0.00 32.45 4.00
3135 4303 1.080974 CGGTGTGTACGACCAGGTC 60.081 63.158 9.92 9.92 32.45 3.85
3151 4319 7.466193 GACCAGGTCGTATAAGATTTTCTTC 57.534 40.000 3.05 0.00 37.89 2.87
3152 4320 6.346896 ACCAGGTCGTATAAGATTTTCTTCC 58.653 40.000 0.00 0.00 37.89 3.46
3153 4321 6.070424 ACCAGGTCGTATAAGATTTTCTTCCA 60.070 38.462 0.00 0.00 37.89 3.53
3154 4322 6.821665 CCAGGTCGTATAAGATTTTCTTCCAA 59.178 38.462 0.00 0.00 37.89 3.53
3155 4323 7.011482 CCAGGTCGTATAAGATTTTCTTCCAAG 59.989 40.741 0.00 0.00 37.89 3.61
3156 4324 7.764443 CAGGTCGTATAAGATTTTCTTCCAAGA 59.236 37.037 0.00 0.00 37.89 3.02
3157 4325 7.982354 AGGTCGTATAAGATTTTCTTCCAAGAG 59.018 37.037 0.00 0.00 37.89 2.85
3158 4326 7.980099 GGTCGTATAAGATTTTCTTCCAAGAGA 59.020 37.037 0.00 0.00 37.89 3.10
3159 4327 9.535878 GTCGTATAAGATTTTCTTCCAAGAGAT 57.464 33.333 0.00 0.00 37.89 2.75
3163 4331 6.847421 AAGATTTTCTTCCAAGAGATTGGG 57.153 37.500 7.15 0.00 42.32 4.12
3164 4332 5.267587 AGATTTTCTTCCAAGAGATTGGGG 58.732 41.667 7.15 1.83 42.32 4.96
3165 4333 2.514458 TTCTTCCAAGAGATTGGGGC 57.486 50.000 7.15 0.00 42.32 5.80
3215 4392 0.331616 ATTGGGCCCAACTGGAGTAC 59.668 55.000 39.44 0.00 38.88 2.73
3217 4394 2.267961 GGCCCAACTGGAGTACGG 59.732 66.667 0.00 0.00 37.39 4.02
3252 4429 2.097825 GTCCCACACGTCATAGGTACT 58.902 52.381 0.00 0.00 46.37 2.73
3255 4432 2.758979 CCCACACGTCATAGGTACTCTT 59.241 50.000 0.00 0.00 41.75 2.85
3260 4438 6.100004 CACACGTCATAGGTACTCTTGAAAT 58.900 40.000 0.00 0.00 41.75 2.17
3265 4443 7.760340 ACGTCATAGGTACTCTTGAAATTCTTC 59.240 37.037 0.00 0.00 41.75 2.87
3266 4444 7.759886 CGTCATAGGTACTCTTGAAATTCTTCA 59.240 37.037 0.00 0.00 41.75 3.02
3293 4471 1.550976 GAAATGGACTCCGACTCCAGT 59.449 52.381 3.53 0.00 41.24 4.00
3328 4506 5.296531 ACAAGCGCCATTTTCTTTTTGAAAT 59.703 32.000 2.29 0.00 43.34 2.17
3329 4507 5.347012 AGCGCCATTTTCTTTTTGAAATG 57.653 34.783 2.29 0.00 43.34 2.32
3333 4511 6.857451 GCGCCATTTTCTTTTTGAAATGAAAT 59.143 30.769 14.40 6.33 43.34 2.17
3383 4562 6.633500 TTTCGTGATTGACTCCAAGATTTT 57.367 33.333 0.00 0.00 35.48 1.82
3457 4636 4.805744 ACTCTCTCCGTCCCATATTAGTT 58.194 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 0.745468 GATCCGACGCTAGGGTTTCT 59.255 55.000 14.33 0.00 0.00 2.52
129 130 4.522022 GGAGCGGGTATTTAACTAGCTCTA 59.478 45.833 16.79 0.00 46.70 2.43
189 190 1.554822 CCAGGGTCTTTAGGGGACTGA 60.555 57.143 0.00 0.00 43.88 3.41
233 239 4.150994 GTTTCGGACCAAGTGGCA 57.849 55.556 0.00 0.00 39.32 4.92
243 249 0.896940 ACTACTGGCTCGGTTTCGGA 60.897 55.000 0.00 0.00 36.95 4.55
312 320 2.272471 GCTCTAGGGTTGGGGCAC 59.728 66.667 0.00 0.00 0.00 5.01
313 321 3.015145 GGCTCTAGGGTTGGGGCA 61.015 66.667 0.00 0.00 0.00 5.36
445 453 1.403647 CGTCCGCTGTTGGTTGATCTA 60.404 52.381 0.00 0.00 0.00 1.98
448 456 2.325082 GCGTCCGCTGTTGGTTGAT 61.325 57.895 4.10 0.00 38.26 2.57
452 460 4.988598 CCTGCGTCCGCTGTTGGT 62.989 66.667 13.31 0.00 42.51 3.67
455 463 4.681978 GACCCTGCGTCCGCTGTT 62.682 66.667 13.31 1.77 42.51 3.16
471 479 1.520600 TTGTGCTGCTAGGTCGACGA 61.521 55.000 9.92 0.00 0.00 4.20
474 482 1.080772 CGTTGTGCTGCTAGGTCGA 60.081 57.895 0.00 0.00 0.00 4.20
480 488 4.978863 TGGCGCGTTGTGCTGCTA 62.979 61.111 8.43 0.00 43.27 3.49
497 505 1.457831 GTAGATCTCAGGCGGGGGT 60.458 63.158 0.00 0.00 0.00 4.95
502 510 2.050895 CGGCGTAGATCTCAGGCG 60.051 66.667 24.16 24.16 45.35 5.52
510 518 3.593794 GCCCTCGTCGGCGTAGAT 61.594 66.667 10.18 0.00 39.64 1.98
561 569 3.319198 GGGGTTCGCTCCACTCCA 61.319 66.667 0.00 0.00 37.80 3.86
562 570 4.097361 GGGGGTTCGCTCCACTCC 62.097 72.222 0.00 0.00 40.41 3.85
649 657 2.104331 GTGGATGGCGTCGACGAT 59.896 61.111 39.74 25.55 43.02 3.73
658 666 1.144936 CGAGGAAGAGGTGGATGGC 59.855 63.158 0.00 0.00 0.00 4.40
659 667 0.687757 TCCGAGGAAGAGGTGGATGG 60.688 60.000 0.00 0.00 0.00 3.51
665 673 0.033894 GAGGAGTCCGAGGAAGAGGT 60.034 60.000 2.76 0.00 0.00 3.85
670 678 0.922738 TAGGGGAGGAGTCCGAGGAA 60.923 60.000 2.76 0.00 45.05 3.36
676 684 0.105913 CTCTGGTAGGGGAGGAGTCC 60.106 65.000 0.00 0.00 43.05 3.85
688 696 0.321298 GTCGCTTTTGGGCTCTGGTA 60.321 55.000 0.00 0.00 0.00 3.25
689 697 1.600916 GTCGCTTTTGGGCTCTGGT 60.601 57.895 0.00 0.00 0.00 4.00
706 714 3.391382 GGCAGCTGGTCCGGTAGT 61.391 66.667 17.12 0.00 0.00 2.73
840 848 2.432456 GCGATGGTGAGTGCGACA 60.432 61.111 0.00 0.00 0.00 4.35
841 849 3.188786 GGCGATGGTGAGTGCGAC 61.189 66.667 0.00 0.00 0.00 5.19
865 873 4.849329 CCTGTACGGAGCGGCGAC 62.849 72.222 12.98 3.05 33.16 5.19
887 895 2.751806 CAGGAGAAAAGATGCCTCCAAC 59.248 50.000 9.92 0.00 46.74 3.77
894 902 1.815003 CACACCCAGGAGAAAAGATGC 59.185 52.381 0.00 0.00 0.00 3.91
899 907 3.287222 CAAGAACACACCCAGGAGAAAA 58.713 45.455 0.00 0.00 0.00 2.29
900 908 2.241176 ACAAGAACACACCCAGGAGAAA 59.759 45.455 0.00 0.00 0.00 2.52
901 909 1.843851 ACAAGAACACACCCAGGAGAA 59.156 47.619 0.00 0.00 0.00 2.87
902 910 1.416401 GACAAGAACACACCCAGGAGA 59.584 52.381 0.00 0.00 0.00 3.71
903 911 1.417890 AGACAAGAACACACCCAGGAG 59.582 52.381 0.00 0.00 0.00 3.69
904 912 1.416401 GAGACAAGAACACACCCAGGA 59.584 52.381 0.00 0.00 0.00 3.86
905 913 1.417890 AGAGACAAGAACACACCCAGG 59.582 52.381 0.00 0.00 0.00 4.45
906 914 2.487934 CAGAGACAAGAACACACCCAG 58.512 52.381 0.00 0.00 0.00 4.45
907 915 1.475034 GCAGAGACAAGAACACACCCA 60.475 52.381 0.00 0.00 0.00 4.51
908 916 1.230324 GCAGAGACAAGAACACACCC 58.770 55.000 0.00 0.00 0.00 4.61
909 917 1.230324 GGCAGAGACAAGAACACACC 58.770 55.000 0.00 0.00 0.00 4.16
910 918 1.869767 CTGGCAGAGACAAGAACACAC 59.130 52.381 9.42 0.00 0.00 3.82
911 919 1.762370 TCTGGCAGAGACAAGAACACA 59.238 47.619 14.43 0.00 0.00 3.72
912 920 2.533266 TCTGGCAGAGACAAGAACAC 57.467 50.000 14.43 0.00 0.00 3.32
967 975 0.820482 GGTGTAAGTGGTTGGCCGTT 60.820 55.000 0.00 0.00 37.67 4.44
977 986 2.684881 GCCAGGATTGATGGTGTAAGTG 59.315 50.000 0.00 0.00 40.17 3.16
1049 1058 4.202461 TGCACTTGTTCATTAGGAAGGAGT 60.202 41.667 0.00 0.00 35.82 3.85
1074 1083 0.685458 ATTGGGCATGCCTCAAGGAC 60.685 55.000 34.70 17.52 37.39 3.85
1145 1166 1.296715 GCCTCCTCAACGATGGTGT 59.703 57.895 0.00 0.00 0.00 4.16
1169 1190 3.378339 CCGGAGTTGGTTATGTATCGTC 58.622 50.000 0.00 0.00 0.00 4.20
1245 1266 1.542492 GGTACCTCGAGTTGTCCAGA 58.458 55.000 12.31 0.00 0.00 3.86
1280 1301 3.441290 CCTCGTCGAAGCCTCCGT 61.441 66.667 0.00 0.00 0.00 4.69
1346 1376 4.083003 TGGCCTTATCATTTGTTGTTCGAC 60.083 41.667 3.32 0.00 0.00 4.20
1466 1505 3.857157 AAACATCATATGGCCTACGGT 57.143 42.857 3.32 0.00 33.60 4.83
1689 1807 4.983053 AGAGGCTATCTCCATTCAATTGG 58.017 43.478 5.42 0.00 43.44 3.16
1733 1925 5.192522 ACCAACATCATTCCTTCCATAGTCT 59.807 40.000 0.00 0.00 0.00 3.24
1769 2334 4.926140 TCGTCATCTACATCAGAAGCAT 57.074 40.909 0.00 0.00 36.67 3.79
2031 2910 4.350368 TGCTGAGGTAAGTGAACATTGA 57.650 40.909 0.00 0.00 0.00 2.57
2086 2968 4.614555 TGCTACGCCAAAACTGAATATG 57.385 40.909 0.00 0.00 0.00 1.78
2167 3049 4.699637 CCTTGTTGTATAAGTATGGCCGA 58.300 43.478 0.00 0.00 0.00 5.54
2169 3051 4.830826 GCCTTGTTGTATAAGTATGGCC 57.169 45.455 0.00 0.00 32.50 5.36
2314 3199 9.597170 AACTATAATAAAGTCTCCTTTTCGTCC 57.403 33.333 0.00 0.00 41.18 4.79
2693 3787 3.834489 ATCTGGCTAAGTCTGTGGATG 57.166 47.619 0.00 0.00 0.00 3.51
2703 3797 7.066404 GGTTTCCTTCTCTAAAATCTGGCTAAG 59.934 40.741 0.00 0.00 0.00 2.18
2756 3850 0.601311 GTGCTCTGCCAGTTCTTCGT 60.601 55.000 0.00 0.00 0.00 3.85
2951 4119 6.383147 AGGTCGTATAAGATTTTCTCCTTCCA 59.617 38.462 0.00 0.00 0.00 3.53
2965 4133 4.361451 ACGTACAACCAGGTCGTATAAG 57.639 45.455 2.27 0.00 33.04 1.73
2966 4134 5.008613 GGATACGTACAACCAGGTCGTATAA 59.991 44.000 19.09 0.76 44.06 0.98
2967 4135 4.515191 GGATACGTACAACCAGGTCGTATA 59.485 45.833 19.09 0.00 44.06 1.47
2968 4136 3.316308 GGATACGTACAACCAGGTCGTAT 59.684 47.826 19.13 19.13 45.76 3.06
2969 4137 2.682856 GGATACGTACAACCAGGTCGTA 59.317 50.000 12.33 12.33 40.32 3.43
2972 4140 3.022406 AGAGGATACGTACAACCAGGTC 58.978 50.000 14.68 6.52 46.39 3.85
2976 4144 4.274978 TCATGAGAGGATACGTACAACCA 58.725 43.478 14.68 3.35 46.39 3.67
2978 4146 5.505985 GGTCTCATGAGAGGATACGTACAAC 60.506 48.000 25.76 9.46 42.34 3.32
2979 4147 4.579340 GGTCTCATGAGAGGATACGTACAA 59.421 45.833 25.76 0.00 42.34 2.41
2980 4148 4.135306 GGTCTCATGAGAGGATACGTACA 58.865 47.826 25.76 0.00 42.34 2.90
2981 4149 3.502979 GGGTCTCATGAGAGGATACGTAC 59.497 52.174 25.76 10.87 42.34 3.67
2982 4150 3.498121 GGGGTCTCATGAGAGGATACGTA 60.498 52.174 25.76 0.00 42.34 3.57
2983 4151 2.588620 GGGTCTCATGAGAGGATACGT 58.411 52.381 25.76 0.00 42.34 3.57
2984 4152 1.889829 GGGGTCTCATGAGAGGATACG 59.110 57.143 25.76 0.00 42.34 3.06
2985 4153 2.964209 TGGGGTCTCATGAGAGGATAC 58.036 52.381 25.76 13.73 42.34 2.24
2986 4154 3.784178 GATGGGGTCTCATGAGAGGATA 58.216 50.000 25.76 13.00 42.34 2.59
2987 4155 2.618794 GATGGGGTCTCATGAGAGGAT 58.381 52.381 25.76 14.22 42.34 3.24
2988 4156 1.755621 CGATGGGGTCTCATGAGAGGA 60.756 57.143 25.76 10.13 42.34 3.71
2989 4157 0.678395 CGATGGGGTCTCATGAGAGG 59.322 60.000 25.76 0.00 42.34 3.69
2990 4158 1.697284 TCGATGGGGTCTCATGAGAG 58.303 55.000 25.76 12.13 43.48 3.20
2991 4159 1.966354 CATCGATGGGGTCTCATGAGA 59.034 52.381 21.67 21.67 34.56 3.27
2992 4160 1.966354 TCATCGATGGGGTCTCATGAG 59.034 52.381 24.61 17.07 0.00 2.90
2993 4161 2.086610 TCATCGATGGGGTCTCATGA 57.913 50.000 24.61 0.00 0.00 3.07
2994 4162 4.161001 TCATATCATCGATGGGGTCTCATG 59.839 45.833 24.61 15.60 0.00 3.07
2995 4163 4.161189 GTCATATCATCGATGGGGTCTCAT 59.839 45.833 24.61 11.52 0.00 2.90
2996 4164 3.511540 GTCATATCATCGATGGGGTCTCA 59.488 47.826 24.61 4.33 0.00 3.27
2997 4165 3.511540 TGTCATATCATCGATGGGGTCTC 59.488 47.826 24.61 12.18 0.00 3.36
2998 4166 3.259374 GTGTCATATCATCGATGGGGTCT 59.741 47.826 24.61 7.84 0.00 3.85
2999 4167 3.589988 GTGTCATATCATCGATGGGGTC 58.410 50.000 24.61 11.25 0.00 4.46
3000 4168 2.029020 CGTGTCATATCATCGATGGGGT 60.029 50.000 24.61 13.57 0.00 4.95
3001 4169 2.029020 ACGTGTCATATCATCGATGGGG 60.029 50.000 24.61 11.90 0.00 4.96
3002 4170 2.989166 CACGTGTCATATCATCGATGGG 59.011 50.000 24.61 12.23 0.00 4.00
3003 4171 2.989166 CCACGTGTCATATCATCGATGG 59.011 50.000 24.61 9.17 0.00 3.51
3004 4172 2.409715 GCCACGTGTCATATCATCGATG 59.590 50.000 19.61 19.61 0.00 3.84
3005 4173 2.297315 AGCCACGTGTCATATCATCGAT 59.703 45.455 15.65 0.00 0.00 3.59
3006 4174 1.681264 AGCCACGTGTCATATCATCGA 59.319 47.619 15.65 0.00 0.00 3.59
3007 4175 2.140065 AGCCACGTGTCATATCATCG 57.860 50.000 15.65 0.00 0.00 3.84
3008 4176 3.246226 GTGAAGCCACGTGTCATATCATC 59.754 47.826 15.65 2.09 33.10 2.92
3009 4177 3.198068 GTGAAGCCACGTGTCATATCAT 58.802 45.455 15.65 0.00 33.10 2.45
3010 4178 2.028567 TGTGAAGCCACGTGTCATATCA 60.029 45.455 15.65 8.53 46.06 2.15
3011 4179 2.616960 TGTGAAGCCACGTGTCATATC 58.383 47.619 15.65 6.02 46.06 1.63
3012 4180 2.760634 TGTGAAGCCACGTGTCATAT 57.239 45.000 15.65 0.00 46.06 1.78
3013 4181 2.535012 TTGTGAAGCCACGTGTCATA 57.465 45.000 15.65 7.38 46.06 2.15
3014 4182 1.674359 TTTGTGAAGCCACGTGTCAT 58.326 45.000 15.65 0.00 46.06 3.06
3015 4183 1.601903 GATTTGTGAAGCCACGTGTCA 59.398 47.619 15.65 9.07 46.06 3.58
3016 4184 1.873591 AGATTTGTGAAGCCACGTGTC 59.126 47.619 15.65 0.10 46.06 3.67
3017 4185 1.873591 GAGATTTGTGAAGCCACGTGT 59.126 47.619 15.65 0.00 46.06 4.49
3018 4186 1.872952 TGAGATTTGTGAAGCCACGTG 59.127 47.619 9.08 9.08 46.06 4.49
3019 4187 2.254546 TGAGATTTGTGAAGCCACGT 57.745 45.000 0.00 0.00 46.06 4.49
3020 4188 3.558505 CTTTGAGATTTGTGAAGCCACG 58.441 45.455 0.00 0.00 46.06 4.94
3021 4189 3.243501 TGCTTTGAGATTTGTGAAGCCAC 60.244 43.478 4.20 0.00 41.40 5.01
3022 4190 2.957680 TGCTTTGAGATTTGTGAAGCCA 59.042 40.909 4.20 0.00 41.40 4.75
3023 4191 3.254166 TCTGCTTTGAGATTTGTGAAGCC 59.746 43.478 4.20 0.00 41.40 4.35
3024 4192 4.494350 TCTGCTTTGAGATTTGTGAAGC 57.506 40.909 0.00 0.00 42.19 3.86
3025 4193 6.141462 GTCTTCTGCTTTGAGATTTGTGAAG 58.859 40.000 0.00 0.00 0.00 3.02
3026 4194 5.277490 CGTCTTCTGCTTTGAGATTTGTGAA 60.277 40.000 0.00 0.00 0.00 3.18
3027 4195 4.212004 CGTCTTCTGCTTTGAGATTTGTGA 59.788 41.667 0.00 0.00 0.00 3.58
3028 4196 4.212004 TCGTCTTCTGCTTTGAGATTTGTG 59.788 41.667 0.00 0.00 0.00 3.33
3029 4197 4.380531 TCGTCTTCTGCTTTGAGATTTGT 58.619 39.130 0.00 0.00 0.00 2.83
3030 4198 4.997905 TCGTCTTCTGCTTTGAGATTTG 57.002 40.909 0.00 0.00 0.00 2.32
3031 4199 4.142730 GCATCGTCTTCTGCTTTGAGATTT 60.143 41.667 0.00 0.00 35.49 2.17
3032 4200 3.373439 GCATCGTCTTCTGCTTTGAGATT 59.627 43.478 0.00 0.00 35.49 2.40
3033 4201 2.935201 GCATCGTCTTCTGCTTTGAGAT 59.065 45.455 0.00 0.00 35.49 2.75
3034 4202 2.341257 GCATCGTCTTCTGCTTTGAGA 58.659 47.619 0.00 0.00 35.49 3.27
3035 4203 1.060266 CGCATCGTCTTCTGCTTTGAG 59.940 52.381 0.00 0.00 36.23 3.02
3036 4204 1.070821 CGCATCGTCTTCTGCTTTGA 58.929 50.000 0.00 0.00 36.23 2.69
3037 4205 0.792640 ACGCATCGTCTTCTGCTTTG 59.207 50.000 0.00 0.00 33.69 2.77
3038 4206 1.461127 GAACGCATCGTCTTCTGCTTT 59.539 47.619 0.00 0.00 39.99 3.51
3039 4207 1.071605 GAACGCATCGTCTTCTGCTT 58.928 50.000 0.00 0.00 39.99 3.91
3040 4208 0.244994 AGAACGCATCGTCTTCTGCT 59.755 50.000 0.00 0.00 39.99 4.24
3041 4209 1.071605 AAGAACGCATCGTCTTCTGC 58.928 50.000 0.00 0.00 39.99 4.26
3042 4210 2.476619 ACAAAGAACGCATCGTCTTCTG 59.523 45.455 0.00 3.61 39.99 3.02
3043 4211 2.755650 ACAAAGAACGCATCGTCTTCT 58.244 42.857 0.00 0.00 39.99 2.85
3044 4212 3.218398 CAACAAAGAACGCATCGTCTTC 58.782 45.455 0.00 0.00 39.99 2.87
3045 4213 2.602217 GCAACAAAGAACGCATCGTCTT 60.602 45.455 0.00 0.00 39.99 3.01
3046 4214 1.069906 GCAACAAAGAACGCATCGTCT 60.070 47.619 0.00 0.00 39.99 4.18
3047 4215 1.069906 AGCAACAAAGAACGCATCGTC 60.070 47.619 0.00 0.00 39.99 4.20
3048 4216 0.944386 AGCAACAAAGAACGCATCGT 59.056 45.000 0.00 0.00 43.97 3.73
3049 4217 2.036556 AAGCAACAAAGAACGCATCG 57.963 45.000 0.00 0.00 0.00 3.84
3050 4218 3.371168 TCAAAGCAACAAAGAACGCATC 58.629 40.909 0.00 0.00 0.00 3.91
3051 4219 3.066621 TCTCAAAGCAACAAAGAACGCAT 59.933 39.130 0.00 0.00 0.00 4.73
3052 4220 2.421775 TCTCAAAGCAACAAAGAACGCA 59.578 40.909 0.00 0.00 0.00 5.24
3053 4221 3.065019 TCTCAAAGCAACAAAGAACGC 57.935 42.857 0.00 0.00 0.00 4.84
3054 4222 5.516339 ACAAATCTCAAAGCAACAAAGAACG 59.484 36.000 0.00 0.00 0.00 3.95
3055 4223 6.531240 TCACAAATCTCAAAGCAACAAAGAAC 59.469 34.615 0.00 0.00 0.00 3.01
3056 4224 6.629128 TCACAAATCTCAAAGCAACAAAGAA 58.371 32.000 0.00 0.00 0.00 2.52
3057 4225 6.206395 TCACAAATCTCAAAGCAACAAAGA 57.794 33.333 0.00 0.00 0.00 2.52
3058 4226 6.509039 GCTTCACAAATCTCAAAGCAACAAAG 60.509 38.462 0.00 0.00 41.46 2.77
3059 4227 5.291614 GCTTCACAAATCTCAAAGCAACAAA 59.708 36.000 0.00 0.00 41.46 2.83
3060 4228 4.805192 GCTTCACAAATCTCAAAGCAACAA 59.195 37.500 0.00 0.00 41.46 2.83
3061 4229 4.362279 GCTTCACAAATCTCAAAGCAACA 58.638 39.130 0.00 0.00 41.46 3.33
3062 4230 3.737774 GGCTTCACAAATCTCAAAGCAAC 59.262 43.478 7.59 0.00 43.15 4.17
3063 4231 3.384146 TGGCTTCACAAATCTCAAAGCAA 59.616 39.130 7.59 0.00 43.15 3.91
3064 4232 2.957680 TGGCTTCACAAATCTCAAAGCA 59.042 40.909 7.59 0.00 43.15 3.91
3065 4233 3.311966 GTGGCTTCACAAATCTCAAAGC 58.688 45.455 0.00 0.00 40.91 3.51
3066 4234 3.003689 ACGTGGCTTCACAAATCTCAAAG 59.996 43.478 0.00 0.00 41.27 2.77
3067 4235 2.948979 ACGTGGCTTCACAAATCTCAAA 59.051 40.909 0.00 0.00 41.27 2.69
3068 4236 2.290367 CACGTGGCTTCACAAATCTCAA 59.710 45.455 7.95 0.00 41.27 3.02
3069 4237 1.872952 CACGTGGCTTCACAAATCTCA 59.127 47.619 7.95 0.00 41.27 3.27
3070 4238 1.873591 ACACGTGGCTTCACAAATCTC 59.126 47.619 21.57 0.00 41.27 2.75
3071 4239 1.873591 GACACGTGGCTTCACAAATCT 59.126 47.619 21.57 0.00 41.27 2.40
3072 4240 1.601903 TGACACGTGGCTTCACAAATC 59.398 47.619 24.38 5.73 41.27 2.17
3073 4241 1.674359 TGACACGTGGCTTCACAAAT 58.326 45.000 24.38 0.00 41.27 2.32
3074 4242 1.601903 GATGACACGTGGCTTCACAAA 59.398 47.619 27.41 5.08 41.27 2.83
3075 4243 1.202639 AGATGACACGTGGCTTCACAA 60.203 47.619 31.85 9.61 41.27 3.33
3076 4244 0.392706 AGATGACACGTGGCTTCACA 59.607 50.000 31.85 16.74 41.27 3.58
3077 4245 2.363788 TAGATGACACGTGGCTTCAC 57.636 50.000 31.85 16.93 38.00 3.18
3078 4246 3.521560 GATTAGATGACACGTGGCTTCA 58.478 45.455 31.85 21.61 30.28 3.02
3079 4247 2.535984 CGATTAGATGACACGTGGCTTC 59.464 50.000 25.65 25.65 0.00 3.86
3080 4248 2.165641 TCGATTAGATGACACGTGGCTT 59.834 45.455 24.38 17.40 0.00 4.35
3081 4249 1.749063 TCGATTAGATGACACGTGGCT 59.251 47.619 24.38 14.43 0.00 4.75
3082 4250 2.203800 TCGATTAGATGACACGTGGC 57.796 50.000 21.57 19.24 0.00 5.01
3091 4259 5.817700 TCGTGAGACCCCATCGATTAGATG 61.818 50.000 0.00 0.17 45.44 2.90
3092 4260 2.558795 CGTGAGACCCCATCGATTAGAT 59.441 50.000 0.00 0.00 41.01 1.98
3093 4261 1.954382 CGTGAGACCCCATCGATTAGA 59.046 52.381 0.00 0.00 0.00 2.10
3094 4262 1.954382 TCGTGAGACCCCATCGATTAG 59.046 52.381 0.00 0.00 33.31 1.73
3095 4263 1.954382 CTCGTGAGACCCCATCGATTA 59.046 52.381 0.00 0.00 35.39 1.75
3096 4264 0.747255 CTCGTGAGACCCCATCGATT 59.253 55.000 0.00 0.00 35.39 3.34
3097 4265 0.106669 TCTCGTGAGACCCCATCGAT 60.107 55.000 0.00 0.00 35.39 3.59
3098 4266 1.301954 TCTCGTGAGACCCCATCGA 59.698 57.895 0.00 0.00 35.39 3.59
3099 4267 3.920031 TCTCGTGAGACCCCATCG 58.080 61.111 0.00 0.00 35.39 3.84
3107 4275 0.870393 GTACACACCGTCTCGTGAGA 59.130 55.000 0.00 0.00 37.20 3.27
3108 4276 0.452287 CGTACACACCGTCTCGTGAG 60.452 60.000 0.00 0.00 37.20 3.51
3109 4277 0.879839 TCGTACACACCGTCTCGTGA 60.880 55.000 0.00 0.00 37.20 4.35
3110 4278 0.723790 GTCGTACACACCGTCTCGTG 60.724 60.000 0.00 0.00 39.75 4.35
3111 4279 1.571460 GTCGTACACACCGTCTCGT 59.429 57.895 0.00 0.00 0.00 4.18
3112 4280 1.154338 GGTCGTACACACCGTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3113 4281 0.109873 CTGGTCGTACACACCGTCTC 60.110 60.000 6.52 0.00 36.61 3.36
3114 4282 1.521450 CCTGGTCGTACACACCGTCT 61.521 60.000 6.52 0.00 36.61 4.18
3115 4283 1.080974 CCTGGTCGTACACACCGTC 60.081 63.158 6.52 0.00 36.61 4.79
3116 4284 1.799258 GACCTGGTCGTACACACCGT 61.799 60.000 11.71 0.25 36.61 4.83
3117 4285 1.080974 GACCTGGTCGTACACACCG 60.081 63.158 11.71 2.51 36.61 4.94
3118 4286 4.981415 GACCTGGTCGTACACACC 57.019 61.111 11.71 4.30 0.00 4.16
3126 4294 6.040878 AAGAAAATCTTATACGACCTGGTCG 58.959 40.000 39.25 39.25 46.77 4.79
3127 4295 6.479331 GGAAGAAAATCTTATACGACCTGGTC 59.521 42.308 16.99 16.99 36.73 4.02
3128 4296 6.070424 TGGAAGAAAATCTTATACGACCTGGT 60.070 38.462 0.00 0.00 36.73 4.00
3129 4297 6.346096 TGGAAGAAAATCTTATACGACCTGG 58.654 40.000 0.00 0.00 36.73 4.45
3130 4298 7.764443 TCTTGGAAGAAAATCTTATACGACCTG 59.236 37.037 0.00 0.00 36.73 4.00
3131 4299 7.848128 TCTTGGAAGAAAATCTTATACGACCT 58.152 34.615 0.00 0.00 36.73 3.85
3132 4300 7.980099 TCTCTTGGAAGAAAATCTTATACGACC 59.020 37.037 0.00 0.00 36.73 4.79
3133 4301 8.928270 TCTCTTGGAAGAAAATCTTATACGAC 57.072 34.615 0.00 0.00 36.73 4.34
3152 4320 2.216898 GAATCGAGCCCCAATCTCTTG 58.783 52.381 0.00 0.00 0.00 3.02
3153 4321 1.839994 TGAATCGAGCCCCAATCTCTT 59.160 47.619 0.00 0.00 0.00 2.85
3154 4322 1.500474 TGAATCGAGCCCCAATCTCT 58.500 50.000 0.00 0.00 0.00 3.10
3155 4323 2.421619 GATGAATCGAGCCCCAATCTC 58.578 52.381 0.00 0.00 0.00 2.75
3156 4324 2.557920 GATGAATCGAGCCCCAATCT 57.442 50.000 0.00 0.00 0.00 2.40
3191 4359 2.035626 AGTTGGGCCCAATGGTCG 59.964 61.111 39.03 0.00 36.99 4.79
3255 4432 6.041865 TCCATTTCTTGGCTTGAAGAATTTCA 59.958 34.615 0.00 0.00 46.01 2.69
3260 4438 4.473444 AGTCCATTTCTTGGCTTGAAGAA 58.527 39.130 0.00 0.00 46.01 2.52
3265 4443 1.470098 CGGAGTCCATTTCTTGGCTTG 59.530 52.381 10.49 0.00 46.01 4.01
3266 4444 1.351017 TCGGAGTCCATTTCTTGGCTT 59.649 47.619 10.49 0.00 46.01 4.35
3284 4462 1.275291 TGCCTAGGAAAACTGGAGTCG 59.725 52.381 14.75 0.00 0.00 4.18
3293 4471 2.253513 GCGCTTGTGCCTAGGAAAA 58.746 52.632 14.75 0.00 35.36 2.29
3363 4542 5.180117 AGTGAAAATCTTGGAGTCAATCACG 59.820 40.000 0.00 0.00 40.25 4.35


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

AutoCloner maintained by Alex Coulton.