Multiple sequence alignment - TraesCS5D01G251500

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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 TraesCS5D01G251500 chr5D 100.000 1644 0 0 1961 3604 357076891 357075248 0.000000e+00 3037
1 TraesCS5D01G251500 chr5D 100.000 1201 0 0 1 1201 357078851 357077651 0.000000e+00 2218
2 TraesCS5D01G251500 chr5D 94.633 913 45 4 1961 2871 287811370 287810460 0.000000e+00 1411
3 TraesCS5D01G251500 chr5D 94.059 909 46 3 1961 2868 326744023 326744924 0.000000e+00 1373
4 TraesCS5D01G251500 chr5D 93.860 912 36 5 1961 2868 14740355 14741250 0.000000e+00 1356
5 TraesCS5D01G251500 chr5D 90.850 918 52 7 1961 2868 434724415 434725310 0.000000e+00 1201
6 TraesCS5D01G251500 chr5D 88.000 275 17 5 919 1178 444747592 444747319 9.720000e-81 311
7 TraesCS5D01G251500 chr5D 86.957 276 27 7 930 1201 326743007 326743277 5.850000e-78 302
8 TraesCS5D01G251500 chr5D 85.153 229 28 3 231 457 357063684 357063460 2.800000e-56 230
9 TraesCS5D01G251500 chr1D 95.516 892 35 3 1980 2870 479343128 479342241 0.000000e+00 1421
10 TraesCS5D01G251500 chr1D 88.235 272 17 4 917 1173 13229704 13229433 9.720000e-81 311
11 TraesCS5D01G251500 chr1D 86.572 283 24 9 919 1193 396219898 396219622 2.100000e-77 300
12 TraesCS5D01G251500 chr1D 85.714 287 30 8 921 1200 11881909 11881627 3.520000e-75 292
13 TraesCS5D01G251500 chr1D 86.822 258 21 8 919 1168 328891951 328891699 3.540000e-70 276
14 TraesCS5D01G251500 chr3D 94.860 895 40 5 1979 2871 526482033 526481143 0.000000e+00 1393
15 TraesCS5D01G251500 chr3D 88.629 299 19 6 917 1201 545071961 545071664 2.060000e-92 350
16 TraesCS5D01G251500 chr3D 87.636 275 20 6 919 1181 264139360 264139088 1.260000e-79 307
17 TraesCS5D01G251500 chrUn 93.005 915 56 5 1961 2871 108949081 108948171 0.000000e+00 1328
18 TraesCS5D01G251500 chrUn 92.982 912 53 7 1961 2870 79926039 79925137 0.000000e+00 1319
19 TraesCS5D01G251500 chrUn 86.957 276 23 6 918 1181 105429061 105428787 7.560000e-77 298
20 TraesCS5D01G251500 chrUn 84.589 292 27 10 915 1190 108949801 108949512 1.270000e-69 274
21 TraesCS5D01G251500 chr7D 93.505 893 46 5 1982 2872 147577048 147576166 0.000000e+00 1317
22 TraesCS5D01G251500 chr7D 92.598 716 50 2 2884 3599 565949618 565948906 0.000000e+00 1026
23 TraesCS5D01G251500 chr7D 86.149 296 26 8 907 1189 464032866 464033159 4.520000e-79 305
24 TraesCS5D01G251500 chr1A 92.514 895 57 6 1978 2870 421910061 421910947 0.000000e+00 1273
25 TraesCS5D01G251500 chr1A 86.207 290 23 13 911 1190 586521455 586521737 7.560000e-77 298
26 TraesCS5D01G251500 chr2D 93.759 721 36 3 2884 3604 435209599 435210310 0.000000e+00 1074
27 TraesCS5D01G251500 chr2D 88.772 285 22 6 916 1192 6719984 6719702 1.240000e-89 340
28 TraesCS5D01G251500 chr4B 93.223 723 46 2 2882 3604 251255859 251256578 0.000000e+00 1061
29 TraesCS5D01G251500 chr4B 92.372 721 48 4 2884 3604 648647876 648648589 0.000000e+00 1020
30 TraesCS5D01G251500 chr4B 92.233 721 51 2 2884 3604 648655064 648655779 0.000000e+00 1016
31 TraesCS5D01G251500 chr4B 92.233 721 49 3 2884 3604 648640650 648641363 0.000000e+00 1014
32 TraesCS5D01G251500 chr2B 92.192 730 50 3 2875 3604 485690844 485691566 0.000000e+00 1026
33 TraesCS5D01G251500 chr5A 92.233 721 51 4 2884 3604 28960259 28959544 0.000000e+00 1016
34 TraesCS5D01G251500 chr5A 93.114 668 40 6 1 666 458329652 458328989 0.000000e+00 974
35 TraesCS5D01G251500 chr5A 80.753 478 72 12 1 469 458318856 458318390 4.430000e-94 355
36 TraesCS5D01G251500 chr5A 89.815 216 20 2 670 884 458324440 458324226 3.540000e-70 276
37 TraesCS5D01G251500 chr3A 91.918 730 47 5 2877 3604 164803407 164802688 0.000000e+00 1011
38 TraesCS5D01G251500 chr3A 87.542 297 21 10 916 1201 9515436 9515727 2.680000e-86 329
39 TraesCS5D01G251500 chr5B 91.716 676 39 6 1 673 421859971 421859310 0.000000e+00 922
40 TraesCS5D01G251500 chr5B 79.589 632 97 20 1 622 421836490 421835881 1.200000e-114 424
41 TraesCS5D01G251500 chr4D 87.925 265 19 5 915 1168 76607763 76608025 2.100000e-77 300
42 TraesCS5D01G251500 chr4D 85.911 291 29 7 919 1201 314523182 314522896 2.100000e-77 300
43 TraesCS5D01G251500 chr4D 88.142 253 23 3 914 1159 210460219 210460471 9.790000e-76 294
44 TraesCS5D01G251500 chr4D 85.816 282 23 6 916 1181 4679064 4678784 2.120000e-72 283
45 TraesCS5D01G251500 chr4D 85.932 263 26 7 920 1173 94418221 94417961 1.650000e-68 270
46 TraesCS5D01G251500 chr4D 86.111 252 25 7 919 1163 414041101 414041349 2.760000e-66 263
47 TraesCS5D01G251500 chr4D 86.975 238 21 6 916 1146 439785583 439785817 3.570000e-65 259
48 TraesCS5D01G251500 chr4D 86.555 238 22 7 916 1145 503478901 503479136 1.660000e-63 254
49 TraesCS5D01G251500 chr4D 83.566 286 28 13 916 1187 84236341 84236621 2.150000e-62 250
50 TraesCS5D01G251500 chr6D 86.111 288 24 9 923 1201 18024094 18023814 2.720000e-76 296
51 TraesCS5D01G251500 chr6D 87.405 262 22 6 908 1159 427314838 427315098 1.270000e-74 291
52 TraesCS5D01G251500 chr6A 85.374 294 28 10 917 1201 9522130 9522417 1.270000e-74 291
53 TraesCS5D01G251500 chr6A 86.121 281 22 6 917 1181 146537208 146537487 1.640000e-73 287


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 TraesCS5D01G251500 chr5D 357075248 357078851 3603 True 2627.5 3037 100.000 1 3604 2 chr5D.!!$R4 3603
1 TraesCS5D01G251500 chr5D 287810460 287811370 910 True 1411.0 1411 94.633 1961 2871 1 chr5D.!!$R1 910
2 TraesCS5D01G251500 chr5D 14740355 14741250 895 False 1356.0 1356 93.860 1961 2868 1 chr5D.!!$F1 907
3 TraesCS5D01G251500 chr5D 434724415 434725310 895 False 1201.0 1201 90.850 1961 2868 1 chr5D.!!$F2 907
4 TraesCS5D01G251500 chr5D 326743007 326744924 1917 False 837.5 1373 90.508 930 2868 2 chr5D.!!$F3 1938
5 TraesCS5D01G251500 chr1D 479342241 479343128 887 True 1421.0 1421 95.516 1980 2870 1 chr1D.!!$R5 890
6 TraesCS5D01G251500 chr3D 526481143 526482033 890 True 1393.0 1393 94.860 1979 2871 1 chr3D.!!$R2 892
7 TraesCS5D01G251500 chrUn 79925137 79926039 902 True 1319.0 1319 92.982 1961 2870 1 chrUn.!!$R1 909
8 TraesCS5D01G251500 chrUn 108948171 108949801 1630 True 801.0 1328 88.797 915 2871 2 chrUn.!!$R3 1956
9 TraesCS5D01G251500 chr7D 147576166 147577048 882 True 1317.0 1317 93.505 1982 2872 1 chr7D.!!$R1 890
10 TraesCS5D01G251500 chr7D 565948906 565949618 712 True 1026.0 1026 92.598 2884 3599 1 chr7D.!!$R2 715
11 TraesCS5D01G251500 chr1A 421910061 421910947 886 False 1273.0 1273 92.514 1978 2870 1 chr1A.!!$F1 892
12 TraesCS5D01G251500 chr2D 435209599 435210310 711 False 1074.0 1074 93.759 2884 3604 1 chr2D.!!$F1 720
13 TraesCS5D01G251500 chr4B 251255859 251256578 719 False 1061.0 1061 93.223 2882 3604 1 chr4B.!!$F1 722
14 TraesCS5D01G251500 chr4B 648647876 648648589 713 False 1020.0 1020 92.372 2884 3604 1 chr4B.!!$F3 720
15 TraesCS5D01G251500 chr4B 648655064 648655779 715 False 1016.0 1016 92.233 2884 3604 1 chr4B.!!$F4 720
16 TraesCS5D01G251500 chr4B 648640650 648641363 713 False 1014.0 1014 92.233 2884 3604 1 chr4B.!!$F2 720
17 TraesCS5D01G251500 chr2B 485690844 485691566 722 False 1026.0 1026 92.192 2875 3604 1 chr2B.!!$F1 729
18 TraesCS5D01G251500 chr5A 28959544 28960259 715 True 1016.0 1016 92.233 2884 3604 1 chr5A.!!$R1 720
19 TraesCS5D01G251500 chr5A 458328989 458329652 663 True 974.0 974 93.114 1 666 1 chr5A.!!$R4 665
20 TraesCS5D01G251500 chr3A 164802688 164803407 719 True 1011.0 1011 91.918 2877 3604 1 chr3A.!!$R1 727
21 TraesCS5D01G251500 chr5B 421859310 421859971 661 True 922.0 922 91.716 1 673 1 chr5B.!!$R2 672
22 TraesCS5D01G251500 chr5B 421835881 421836490 609 True 424.0 424 79.589 1 622 1 chr5B.!!$R1 621

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
846 861 0.107456 AAGGTGCGCATCCATAGGAG 59.893 55.0 19.01 0.0 34.05 3.69 F
854 869 0.250038 CATCCATAGGAGCCACCACG 60.250 60.0 0.47 0.0 42.04 4.94 F
2013 2052 0.321346 TGATGGCGCTGAAGAAGACA 59.679 50.0 7.64 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2042 0.034896 GCCCTTCGGTGTCTTCTTCA 59.965 55.000 0.0 0.0 0.0 3.02 R
2058 2097 0.400815 ACTCCACACCCCAGTTACCA 60.401 55.000 0.0 0.0 0.0 3.25 R
3438 3490 1.333619 CAATTGCCCCGATTCTTACCG 59.666 52.381 0.0 0.0 0.0 4.02 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
110 111 1.743958 AGGTACTCCGTCAACGATCTG 59.256 52.381 3.71 0.00 43.02 2.90
146 147 2.195683 CCATGGCGCCCTTGGTAT 59.804 61.111 28.74 12.43 41.98 2.73
152 153 2.449450 GCGCCCTTGGTATACCCCT 61.449 63.158 19.42 0.00 34.29 4.79
186 187 7.884354 AGGTAATTAACGGGTGTTCAGAAATAA 59.116 33.333 0.00 0.00 39.54 1.40
191 192 8.618702 TTAACGGGTGTTCAGAAATAAACATA 57.381 30.769 0.00 0.00 39.54 2.29
237 242 9.330063 TCAGATATAATGTGTGTTTTGATCCTC 57.670 33.333 0.00 0.00 0.00 3.71
401 407 0.890996 CTTTCCTCAAGGGCGTGCTT 60.891 55.000 0.00 0.00 35.41 3.91
433 440 4.819630 TGACATCCCAAACTAAGTTGTGTC 59.180 41.667 0.00 0.00 35.32 3.67
453 464 2.548057 TCATTTGGACGCTCACTTGTTC 59.452 45.455 0.00 0.00 0.00 3.18
484 498 7.448161 TGTGTTCTGATAATGTTGGATTGACTT 59.552 33.333 0.00 0.00 0.00 3.01
499 513 2.461695 TGACTTCCTCTCCATCCTCAC 58.538 52.381 0.00 0.00 0.00 3.51
503 517 4.624913 ACTTCCTCTCCATCCTCACAATA 58.375 43.478 0.00 0.00 0.00 1.90
624 639 4.103365 TGTTGTTCACATTGAAAAGCGT 57.897 36.364 0.00 0.00 38.22 5.07
625 640 5.236655 TGTTGTTCACATTGAAAAGCGTA 57.763 34.783 0.00 0.00 38.22 4.42
626 641 5.641709 TGTTGTTCACATTGAAAAGCGTAA 58.358 33.333 0.00 0.00 38.22 3.18
627 642 6.093404 TGTTGTTCACATTGAAAAGCGTAAA 58.907 32.000 0.00 0.00 38.22 2.01
628 643 6.754209 TGTTGTTCACATTGAAAAGCGTAAAT 59.246 30.769 0.00 0.00 38.22 1.40
629 644 6.746104 TGTTCACATTGAAAAGCGTAAATG 57.254 33.333 0.00 0.00 38.22 2.32
630 645 5.174761 TGTTCACATTGAAAAGCGTAAATGC 59.825 36.000 0.00 0.00 38.22 3.56
631 646 5.402270 GTTCACATTGAAAAGCGTAAATGCT 59.598 36.000 0.00 0.00 38.22 3.79
638 653 1.501741 AGCGTAAATGCTTGTGCCG 59.498 52.632 0.00 0.00 44.46 5.69
639 654 1.514014 GCGTAAATGCTTGTGCCGG 60.514 57.895 0.00 0.00 38.71 6.13
640 655 1.917782 GCGTAAATGCTTGTGCCGGA 61.918 55.000 5.05 0.00 38.71 5.14
641 656 0.732571 CGTAAATGCTTGTGCCGGAT 59.267 50.000 5.05 0.00 38.71 4.18
642 657 1.937223 CGTAAATGCTTGTGCCGGATA 59.063 47.619 5.05 0.00 38.71 2.59
643 658 2.032894 CGTAAATGCTTGTGCCGGATAG 60.033 50.000 5.05 0.00 38.71 2.08
644 659 1.392589 AAATGCTTGTGCCGGATAGG 58.607 50.000 5.05 0.00 44.97 2.57
653 668 4.924019 CCGGATAGGCACGTTTGA 57.076 55.556 0.00 0.00 0.00 2.69
654 669 3.146783 CCGGATAGGCACGTTTGAA 57.853 52.632 0.00 0.00 0.00 2.69
655 670 1.663695 CCGGATAGGCACGTTTGAAT 58.336 50.000 0.00 0.00 0.00 2.57
656 671 2.014128 CCGGATAGGCACGTTTGAATT 58.986 47.619 0.00 0.00 0.00 2.17
657 672 2.422127 CCGGATAGGCACGTTTGAATTT 59.578 45.455 0.00 0.00 0.00 1.82
658 673 3.119637 CCGGATAGGCACGTTTGAATTTT 60.120 43.478 0.00 0.00 0.00 1.82
659 674 4.095185 CCGGATAGGCACGTTTGAATTTTA 59.905 41.667 0.00 0.00 0.00 1.52
660 675 5.392165 CCGGATAGGCACGTTTGAATTTTAA 60.392 40.000 0.00 0.00 0.00 1.52
661 676 6.262601 CGGATAGGCACGTTTGAATTTTAAT 58.737 36.000 0.00 0.00 0.00 1.40
662 677 6.413818 CGGATAGGCACGTTTGAATTTTAATC 59.586 38.462 0.00 0.00 0.00 1.75
663 678 7.480810 GGATAGGCACGTTTGAATTTTAATCT 58.519 34.615 0.00 0.00 0.00 2.40
664 679 7.973944 GGATAGGCACGTTTGAATTTTAATCTT 59.026 33.333 0.00 0.00 0.00 2.40
665 680 9.997482 GATAGGCACGTTTGAATTTTAATCTTA 57.003 29.630 0.00 0.00 0.00 2.10
667 682 6.806739 AGGCACGTTTGAATTTTAATCTTAGC 59.193 34.615 0.00 0.00 0.00 3.09
668 683 6.237201 GGCACGTTTGAATTTTAATCTTAGCG 60.237 38.462 0.00 0.00 0.00 4.26
669 684 6.304683 GCACGTTTGAATTTTAATCTTAGCGT 59.695 34.615 0.00 0.00 0.00 5.07
670 685 7.479291 GCACGTTTGAATTTTAATCTTAGCGTA 59.521 33.333 0.00 0.00 0.00 4.42
671 686 9.485591 CACGTTTGAATTTTAATCTTAGCGTAT 57.514 29.630 0.00 0.00 0.00 3.06
682 697 6.830114 AATCTTAGCGTATTCTTCTTTCGG 57.170 37.500 0.00 0.00 0.00 4.30
683 698 4.679662 TCTTAGCGTATTCTTCTTTCGGG 58.320 43.478 0.00 0.00 0.00 5.14
684 699 2.311124 AGCGTATTCTTCTTTCGGGG 57.689 50.000 0.00 0.00 0.00 5.73
685 700 1.829222 AGCGTATTCTTCTTTCGGGGA 59.171 47.619 0.00 0.00 0.00 4.81
686 701 1.931841 GCGTATTCTTCTTTCGGGGAC 59.068 52.381 0.00 0.00 0.00 4.46
687 702 2.675889 GCGTATTCTTCTTTCGGGGACA 60.676 50.000 0.00 0.00 0.00 4.02
688 703 2.928116 CGTATTCTTCTTTCGGGGACAC 59.072 50.000 0.00 0.00 0.00 3.67
689 704 3.615592 CGTATTCTTCTTTCGGGGACACA 60.616 47.826 0.00 0.00 0.00 3.72
690 705 3.721087 ATTCTTCTTTCGGGGACACAT 57.279 42.857 0.00 0.00 0.00 3.21
691 706 2.762535 TCTTCTTTCGGGGACACATC 57.237 50.000 0.00 0.00 0.00 3.06
692 707 1.278127 TCTTCTTTCGGGGACACATCC 59.722 52.381 0.00 0.00 45.42 3.51
709 724 7.649306 GGACACATCCAATAATATTCAAACTGC 59.351 37.037 0.00 0.00 45.47 4.40
710 725 8.297470 ACACATCCAATAATATTCAAACTGCT 57.703 30.769 0.00 0.00 0.00 4.24
711 726 8.408601 ACACATCCAATAATATTCAAACTGCTC 58.591 33.333 0.00 0.00 0.00 4.26
712 727 8.627403 CACATCCAATAATATTCAAACTGCTCT 58.373 33.333 0.00 0.00 0.00 4.09
713 728 9.193806 ACATCCAATAATATTCAAACTGCTCTT 57.806 29.630 0.00 0.00 0.00 2.85
714 729 9.674824 CATCCAATAATATTCAAACTGCTCTTC 57.325 33.333 0.00 0.00 0.00 2.87
715 730 8.806429 TCCAATAATATTCAAACTGCTCTTCA 57.194 30.769 0.00 0.00 0.00 3.02
716 731 8.677300 TCCAATAATATTCAAACTGCTCTTCAC 58.323 33.333 0.00 0.00 0.00 3.18
717 732 8.680903 CCAATAATATTCAAACTGCTCTTCACT 58.319 33.333 0.00 0.00 0.00 3.41
720 735 4.843220 ATTCAAACTGCTCTTCACTTGG 57.157 40.909 0.00 0.00 0.00 3.61
721 736 3.281727 TCAAACTGCTCTTCACTTGGT 57.718 42.857 0.00 0.00 0.00 3.67
722 737 3.620488 TCAAACTGCTCTTCACTTGGTT 58.380 40.909 0.00 0.00 0.00 3.67
723 738 4.016444 TCAAACTGCTCTTCACTTGGTTT 58.984 39.130 0.00 0.00 0.00 3.27
724 739 4.462483 TCAAACTGCTCTTCACTTGGTTTT 59.538 37.500 0.00 0.00 0.00 2.43
725 740 5.650266 TCAAACTGCTCTTCACTTGGTTTTA 59.350 36.000 0.00 0.00 0.00 1.52
726 741 5.500645 AACTGCTCTTCACTTGGTTTTAC 57.499 39.130 0.00 0.00 0.00 2.01
727 742 3.883489 ACTGCTCTTCACTTGGTTTTACC 59.117 43.478 0.00 0.00 39.22 2.85
740 755 5.231702 TGGTTTTACCAGACCGAATAACT 57.768 39.130 0.00 0.00 44.79 2.24
741 756 5.623169 TGGTTTTACCAGACCGAATAACTT 58.377 37.500 0.00 0.00 44.79 2.66
742 757 5.702209 TGGTTTTACCAGACCGAATAACTTC 59.298 40.000 0.00 0.00 44.79 3.01
743 758 5.936372 GGTTTTACCAGACCGAATAACTTCT 59.064 40.000 0.00 0.00 38.42 2.85
744 759 6.128363 GGTTTTACCAGACCGAATAACTTCTG 60.128 42.308 0.00 0.00 38.42 3.02
745 760 5.733620 TTACCAGACCGAATAACTTCTGT 57.266 39.130 0.00 0.00 34.79 3.41
746 761 6.839124 TTACCAGACCGAATAACTTCTGTA 57.161 37.500 0.00 0.00 34.79 2.74
747 762 5.934402 ACCAGACCGAATAACTTCTGTAT 57.066 39.130 0.00 0.00 34.79 2.29
748 763 6.295719 ACCAGACCGAATAACTTCTGTATT 57.704 37.500 0.00 0.00 34.79 1.89
749 764 7.414222 ACCAGACCGAATAACTTCTGTATTA 57.586 36.000 0.00 0.00 34.79 0.98
750 765 8.019656 ACCAGACCGAATAACTTCTGTATTAT 57.980 34.615 0.00 0.00 34.79 1.28
751 766 8.142551 ACCAGACCGAATAACTTCTGTATTATC 58.857 37.037 0.00 0.00 34.79 1.75
752 767 8.361139 CCAGACCGAATAACTTCTGTATTATCT 58.639 37.037 0.00 0.00 34.79 1.98
753 768 9.400638 CAGACCGAATAACTTCTGTATTATCTC 57.599 37.037 0.00 0.00 30.07 2.75
754 769 9.132923 AGACCGAATAACTTCTGTATTATCTCA 57.867 33.333 0.00 0.00 30.07 3.27
755 770 9.182933 GACCGAATAACTTCTGTATTATCTCAC 57.817 37.037 0.00 0.00 30.07 3.51
756 771 8.915036 ACCGAATAACTTCTGTATTATCTCACT 58.085 33.333 0.00 0.00 28.35 3.41
757 772 9.751542 CCGAATAACTTCTGTATTATCTCACTT 57.248 33.333 0.00 0.00 0.00 3.16
787 802 8.484214 AGTATTAGCATTTATCCTGAGAGACA 57.516 34.615 0.00 0.00 0.00 3.41
788 803 8.584157 AGTATTAGCATTTATCCTGAGAGACAG 58.416 37.037 0.00 0.00 45.36 3.51
789 804 6.798427 TTAGCATTTATCCTGAGAGACAGT 57.202 37.500 0.00 0.00 44.40 3.55
790 805 5.275067 AGCATTTATCCTGAGAGACAGTC 57.725 43.478 0.00 0.00 44.40 3.51
791 806 4.047822 GCATTTATCCTGAGAGACAGTCG 58.952 47.826 0.00 0.00 44.40 4.18
792 807 4.615949 CATTTATCCTGAGAGACAGTCGG 58.384 47.826 0.00 0.00 44.40 4.79
793 808 3.646736 TTATCCTGAGAGACAGTCGGA 57.353 47.619 0.00 0.00 44.40 4.55
794 809 2.746279 ATCCTGAGAGACAGTCGGAT 57.254 50.000 1.98 1.98 44.40 4.18
795 810 2.516227 TCCTGAGAGACAGTCGGATT 57.484 50.000 0.00 0.00 44.40 3.01
796 811 2.808919 TCCTGAGAGACAGTCGGATTT 58.191 47.619 0.00 0.00 44.40 2.17
797 812 2.493675 TCCTGAGAGACAGTCGGATTTG 59.506 50.000 0.00 0.00 44.40 2.32
798 813 2.232452 CCTGAGAGACAGTCGGATTTGT 59.768 50.000 0.00 0.00 44.40 2.83
799 814 3.506810 CTGAGAGACAGTCGGATTTGTC 58.493 50.000 14.22 14.22 43.08 3.18
800 815 2.890945 TGAGAGACAGTCGGATTTGTCA 59.109 45.455 20.48 5.15 44.72 3.58
801 816 3.320826 TGAGAGACAGTCGGATTTGTCAA 59.679 43.478 20.48 7.05 44.72 3.18
802 817 3.654414 AGAGACAGTCGGATTTGTCAAC 58.346 45.455 20.48 15.44 44.72 3.18
803 818 2.404215 AGACAGTCGGATTTGTCAACG 58.596 47.619 20.48 0.00 44.72 4.10
804 819 2.035449 AGACAGTCGGATTTGTCAACGA 59.965 45.455 20.48 0.00 44.72 3.85
805 820 2.993899 GACAGTCGGATTTGTCAACGAT 59.006 45.455 16.12 0.00 42.47 3.73
806 821 2.736721 ACAGTCGGATTTGTCAACGATG 59.263 45.455 0.00 0.00 37.69 3.84
807 822 2.094258 CAGTCGGATTTGTCAACGATGG 59.906 50.000 0.00 0.00 37.69 3.51
808 823 2.028476 AGTCGGATTTGTCAACGATGGA 60.028 45.455 0.00 0.00 37.69 3.41
809 824 2.093783 GTCGGATTTGTCAACGATGGAC 59.906 50.000 0.00 0.00 37.69 4.02
810 825 1.396996 CGGATTTGTCAACGATGGACC 59.603 52.381 0.00 0.00 34.36 4.46
811 826 1.743394 GGATTTGTCAACGATGGACCC 59.257 52.381 0.00 0.00 34.36 4.46
812 827 1.743394 GATTTGTCAACGATGGACCCC 59.257 52.381 0.00 0.00 34.36 4.95
813 828 0.250989 TTTGTCAACGATGGACCCCC 60.251 55.000 0.00 0.00 34.36 5.40
824 839 0.548989 TGGACCCCCATCAAATACGG 59.451 55.000 0.00 0.00 37.58 4.02
825 840 0.822121 GGACCCCCATCAAATACGGC 60.822 60.000 0.00 0.00 0.00 5.68
826 841 0.822121 GACCCCCATCAAATACGGCC 60.822 60.000 0.00 0.00 0.00 6.13
827 842 1.228793 CCCCCATCAAATACGGCCA 59.771 57.895 2.24 0.00 0.00 5.36
828 843 0.396417 CCCCCATCAAATACGGCCAA 60.396 55.000 2.24 0.00 0.00 4.52
829 844 1.032014 CCCCATCAAATACGGCCAAG 58.968 55.000 2.24 0.00 0.00 3.61
830 845 1.032014 CCCATCAAATACGGCCAAGG 58.968 55.000 2.24 0.00 0.00 3.61
831 846 1.684869 CCCATCAAATACGGCCAAGGT 60.685 52.381 2.24 0.00 0.00 3.50
832 847 1.405105 CCATCAAATACGGCCAAGGTG 59.595 52.381 2.24 0.00 0.00 4.00
833 848 1.102978 ATCAAATACGGCCAAGGTGC 58.897 50.000 2.24 0.00 0.00 5.01
834 849 1.136565 CAAATACGGCCAAGGTGCG 59.863 57.895 2.24 0.00 0.00 5.34
835 850 2.696759 AAATACGGCCAAGGTGCGC 61.697 57.895 2.24 0.00 0.00 6.09
836 851 3.910914 AATACGGCCAAGGTGCGCA 62.911 57.895 5.66 5.66 0.00 6.09
837 852 3.697439 ATACGGCCAAGGTGCGCAT 62.697 57.895 15.91 0.00 0.00 4.73
841 856 3.142838 GCCAAGGTGCGCATCCAT 61.143 61.111 19.01 8.99 0.00 3.41
842 857 1.823470 GCCAAGGTGCGCATCCATA 60.823 57.895 19.01 0.00 0.00 2.74
843 858 1.789078 GCCAAGGTGCGCATCCATAG 61.789 60.000 19.01 11.44 0.00 2.23
844 859 1.168407 CCAAGGTGCGCATCCATAGG 61.168 60.000 19.01 16.13 0.00 2.57
845 860 0.179048 CAAGGTGCGCATCCATAGGA 60.179 55.000 19.01 0.00 35.55 2.94
846 861 0.107456 AAGGTGCGCATCCATAGGAG 59.893 55.000 19.01 0.00 34.05 3.69
847 862 1.963338 GGTGCGCATCCATAGGAGC 60.963 63.158 15.91 0.00 34.05 4.70
848 863 1.963338 GTGCGCATCCATAGGAGCC 60.963 63.158 15.91 0.00 34.05 4.70
849 864 2.427320 GCGCATCCATAGGAGCCA 59.573 61.111 0.30 0.00 34.05 4.75
850 865 1.963338 GCGCATCCATAGGAGCCAC 60.963 63.158 0.30 0.00 34.05 5.01
851 866 1.302033 CGCATCCATAGGAGCCACC 60.302 63.158 0.00 0.00 34.05 4.61
852 867 1.839191 GCATCCATAGGAGCCACCA 59.161 57.895 0.47 0.00 42.04 4.17
853 868 0.536006 GCATCCATAGGAGCCACCAC 60.536 60.000 0.47 0.00 42.04 4.16
854 869 0.250038 CATCCATAGGAGCCACCACG 60.250 60.000 0.47 0.00 42.04 4.94
855 870 0.691078 ATCCATAGGAGCCACCACGT 60.691 55.000 0.47 0.00 42.04 4.49
856 871 1.144057 CCATAGGAGCCACCACGTC 59.856 63.158 0.00 0.00 42.04 4.34
857 872 1.144057 CATAGGAGCCACCACGTCC 59.856 63.158 0.00 0.00 42.04 4.79
858 873 1.001760 ATAGGAGCCACCACGTCCT 59.998 57.895 0.00 0.00 43.43 3.85
859 874 0.617820 ATAGGAGCCACCACGTCCTT 60.618 55.000 0.00 0.00 41.21 3.36
860 875 1.255667 TAGGAGCCACCACGTCCTTC 61.256 60.000 0.00 0.00 41.21 3.46
861 876 2.432628 GAGCCACCACGTCCTTCG 60.433 66.667 0.00 0.00 46.00 3.79
875 890 5.686159 CGTCCTTCGTACCTAGATTACAT 57.314 43.478 0.00 0.00 34.52 2.29
876 891 6.069684 CGTCCTTCGTACCTAGATTACATT 57.930 41.667 0.00 0.00 34.52 2.71
877 892 5.913514 CGTCCTTCGTACCTAGATTACATTG 59.086 44.000 0.00 0.00 34.52 2.82
878 893 6.238566 CGTCCTTCGTACCTAGATTACATTGA 60.239 42.308 0.00 0.00 34.52 2.57
879 894 6.916932 GTCCTTCGTACCTAGATTACATTGAC 59.083 42.308 0.00 0.00 0.00 3.18
880 895 6.604396 TCCTTCGTACCTAGATTACATTGACA 59.396 38.462 0.00 0.00 0.00 3.58
881 896 7.287005 TCCTTCGTACCTAGATTACATTGACAT 59.713 37.037 0.00 0.00 0.00 3.06
882 897 8.573885 CCTTCGTACCTAGATTACATTGACATA 58.426 37.037 0.00 0.00 0.00 2.29
883 898 9.961265 CTTCGTACCTAGATTACATTGACATAA 57.039 33.333 0.00 0.00 0.00 1.90
978 1000 6.998968 TTAAACCGTCTAAGGTCAAAAACA 57.001 33.333 0.00 0.00 45.21 2.83
1002 1024 2.364324 GCTCCAACAGACGGTCCATATA 59.636 50.000 4.14 0.00 0.00 0.86
1056 1078 3.651206 TGTAAAATACAACACCTCGCGA 58.349 40.909 9.26 9.26 35.38 5.87
1102 1124 2.597510 GTCCAAAACCAGCCGCCT 60.598 61.111 0.00 0.00 0.00 5.52
1124 1146 3.656045 CGAACACCCAACCGCCAC 61.656 66.667 0.00 0.00 0.00 5.01
1128 1150 2.203280 CACCCAACCGCCACTTCA 60.203 61.111 0.00 0.00 0.00 3.02
1132 1154 0.678950 CCCAACCGCCACTTCATTTT 59.321 50.000 0.00 0.00 0.00 1.82
2003 2042 4.218578 CCGCTCTCTGATGGCGCT 62.219 66.667 7.64 0.00 46.29 5.92
2013 2052 0.321346 TGATGGCGCTGAAGAAGACA 59.679 50.000 7.64 0.00 0.00 3.41
2087 2126 1.080705 GTGTGGAGTTCTCCGACGG 60.081 63.158 7.84 7.84 0.00 4.79
2107 2146 0.394216 CGGAAGGCATTGGTGGATCA 60.394 55.000 0.00 0.00 0.00 2.92
2196 2235 1.671379 GTCGCACCTCAACTTCCCC 60.671 63.158 0.00 0.00 0.00 4.81
2439 2478 1.316706 CGAAGAAGGAGGACGAGGCT 61.317 60.000 0.00 0.00 0.00 4.58
2471 2510 1.123928 GTGATCCCCATCGAGTCCTT 58.876 55.000 0.00 0.00 0.00 3.36
2473 2512 1.762957 TGATCCCCATCGAGTCCTTTC 59.237 52.381 0.00 0.00 0.00 2.62
2475 2514 1.144057 CCCCATCGAGTCCTTTCCG 59.856 63.158 0.00 0.00 0.00 4.30
2476 2515 1.327690 CCCCATCGAGTCCTTTCCGA 61.328 60.000 0.00 0.00 36.72 4.55
2555 2599 0.178929 ACGAAGGAGGAGTTCTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
2558 2602 1.831652 AAGGAGGAGTTCTGGGTGCG 61.832 60.000 0.00 0.00 0.00 5.34
2675 2719 6.985188 TTGAACTATGTTGAATGGACTAGC 57.015 37.500 0.00 0.00 0.00 3.42
2690 2734 5.647589 TGGACTAGCAGTATGTCGTTTTAG 58.352 41.667 0.00 0.00 39.31 1.85
2874 2919 7.795534 ATCTATTGGAGATGCTCTTAGTCAT 57.204 36.000 0.00 0.00 43.71 3.06
2875 2920 7.609097 TCTATTGGAGATGCTCTTAGTCATT 57.391 36.000 0.00 0.00 0.00 2.57
2876 2921 8.712228 TCTATTGGAGATGCTCTTAGTCATTA 57.288 34.615 0.00 0.00 0.00 1.90
2877 2922 9.147732 TCTATTGGAGATGCTCTTAGTCATTAA 57.852 33.333 0.00 0.00 0.00 1.40
2878 2923 9.941325 CTATTGGAGATGCTCTTAGTCATTAAT 57.059 33.333 0.00 0.00 0.00 1.40
3068 3113 1.011333 GCGGCAAAGACGGCTAATTA 58.989 50.000 0.00 0.00 32.98 1.40
3232 3283 4.858680 GGCGGTGGGAAGCTAGCC 62.859 72.222 12.13 0.00 37.61 3.93
3413 3465 0.974383 ACCGAGGAACCAGAATCGTT 59.026 50.000 0.00 0.00 33.43 3.85
3438 3490 1.351430 TACGTGTGCAGCGAGAATGC 61.351 55.000 16.16 0.00 44.11 3.56
3572 3624 4.012374 GGCCAAGACTCTGATGAATGAAA 58.988 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.653151 GCTTCGTGATGGGTAGGTTC 58.347 55.000 0.00 0.00 0.00 3.62
146 147 0.040058 TTACCTCGCTGTCAGGGGTA 59.960 55.000 16.21 9.01 35.01 3.69
152 153 2.417651 CCCGTTAATTACCTCGCTGTCA 60.418 50.000 0.00 0.00 0.00 3.58
219 224 6.005823 TCATCAGAGGATCAAAACACACATT 58.994 36.000 0.00 0.00 37.82 2.71
227 232 8.698210 CCCATTAATTTCATCAGAGGATCAAAA 58.302 33.333 0.00 0.00 37.82 2.44
228 233 7.288389 CCCCATTAATTTCATCAGAGGATCAAA 59.712 37.037 0.00 0.00 37.82 2.69
237 242 5.187576 ACCACAACCCCATTAATTTCATCAG 59.812 40.000 0.00 0.00 0.00 2.90
401 407 1.133181 TTGGGATGTCAGCTGGTGGA 61.133 55.000 15.13 0.00 0.00 4.02
433 440 2.290367 TGAACAAGTGAGCGTCCAAATG 59.710 45.455 0.00 0.00 0.00 2.32
453 464 6.912082 TCCAACATTATCAGAACACACAATG 58.088 36.000 0.00 0.00 0.00 2.82
484 498 5.667172 TGATTTATTGTGAGGATGGAGAGGA 59.333 40.000 0.00 0.00 0.00 3.71
499 513 7.526608 AGTTGTGTGTAACCGATGATTTATTG 58.473 34.615 0.00 0.00 34.36 1.90
503 517 6.038825 TCAAAGTTGTGTGTAACCGATGATTT 59.961 34.615 0.00 0.00 34.36 2.17
620 635 1.501741 CGGCACAAGCATTTACGCT 59.498 52.632 0.00 0.00 46.67 5.07
621 636 1.514014 CCGGCACAAGCATTTACGC 60.514 57.895 0.00 0.00 44.61 4.42
622 637 0.732571 ATCCGGCACAAGCATTTACG 59.267 50.000 0.00 0.00 44.61 3.18
623 638 2.290641 CCTATCCGGCACAAGCATTTAC 59.709 50.000 0.00 0.00 44.61 2.01
624 639 2.571212 CCTATCCGGCACAAGCATTTA 58.429 47.619 0.00 0.00 44.61 1.40
625 640 1.392589 CCTATCCGGCACAAGCATTT 58.607 50.000 0.00 0.00 44.61 2.32
626 641 3.100545 CCTATCCGGCACAAGCATT 57.899 52.632 0.00 0.00 44.61 3.56
627 642 4.885426 CCTATCCGGCACAAGCAT 57.115 55.556 0.00 0.00 44.61 3.79
636 651 1.663695 ATTCAAACGTGCCTATCCGG 58.336 50.000 0.00 0.00 0.00 5.14
637 652 3.757745 AAATTCAAACGTGCCTATCCG 57.242 42.857 0.00 0.00 0.00 4.18
638 653 7.480810 AGATTAAAATTCAAACGTGCCTATCC 58.519 34.615 0.00 0.00 0.00 2.59
639 654 8.911247 AAGATTAAAATTCAAACGTGCCTATC 57.089 30.769 0.00 0.00 0.00 2.08
641 656 7.966204 GCTAAGATTAAAATTCAAACGTGCCTA 59.034 33.333 0.00 0.00 0.00 3.93
642 657 6.806739 GCTAAGATTAAAATTCAAACGTGCCT 59.193 34.615 0.00 0.00 0.00 4.75
643 658 6.237201 CGCTAAGATTAAAATTCAAACGTGCC 60.237 38.462 0.00 0.00 0.00 5.01
644 659 6.304683 ACGCTAAGATTAAAATTCAAACGTGC 59.695 34.615 0.00 0.00 0.00 5.34
645 660 7.775729 ACGCTAAGATTAAAATTCAAACGTG 57.224 32.000 0.00 0.00 0.00 4.49
656 671 8.814235 CCGAAAGAAGAATACGCTAAGATTAAA 58.186 33.333 0.00 0.00 0.00 1.52
657 672 7.437267 CCCGAAAGAAGAATACGCTAAGATTAA 59.563 37.037 0.00 0.00 0.00 1.40
658 673 6.921857 CCCGAAAGAAGAATACGCTAAGATTA 59.078 38.462 0.00 0.00 0.00 1.75
659 674 5.753921 CCCGAAAGAAGAATACGCTAAGATT 59.246 40.000 0.00 0.00 0.00 2.40
660 675 5.290386 CCCGAAAGAAGAATACGCTAAGAT 58.710 41.667 0.00 0.00 0.00 2.40
661 676 4.441079 CCCCGAAAGAAGAATACGCTAAGA 60.441 45.833 0.00 0.00 0.00 2.10
662 677 3.802685 CCCCGAAAGAAGAATACGCTAAG 59.197 47.826 0.00 0.00 0.00 2.18
663 678 3.448301 TCCCCGAAAGAAGAATACGCTAA 59.552 43.478 0.00 0.00 0.00 3.09
664 679 3.025978 TCCCCGAAAGAAGAATACGCTA 58.974 45.455 0.00 0.00 0.00 4.26
665 680 1.829222 TCCCCGAAAGAAGAATACGCT 59.171 47.619 0.00 0.00 0.00 5.07
666 681 1.931841 GTCCCCGAAAGAAGAATACGC 59.068 52.381 0.00 0.00 0.00 4.42
667 682 2.928116 GTGTCCCCGAAAGAAGAATACG 59.072 50.000 0.00 0.00 0.00 3.06
668 683 3.934068 TGTGTCCCCGAAAGAAGAATAC 58.066 45.455 0.00 0.00 0.00 1.89
669 684 4.383770 GGATGTGTCCCCGAAAGAAGAATA 60.384 45.833 0.00 0.00 38.69 1.75
670 685 3.610911 GATGTGTCCCCGAAAGAAGAAT 58.389 45.455 0.00 0.00 0.00 2.40
671 686 2.290071 GGATGTGTCCCCGAAAGAAGAA 60.290 50.000 0.00 0.00 38.69 2.52
672 687 1.278127 GGATGTGTCCCCGAAAGAAGA 59.722 52.381 0.00 0.00 38.69 2.87
673 688 1.003118 TGGATGTGTCCCCGAAAGAAG 59.997 52.381 0.00 0.00 44.41 2.85
674 689 1.060729 TGGATGTGTCCCCGAAAGAA 58.939 50.000 0.00 0.00 44.41 2.52
675 690 1.060729 TTGGATGTGTCCCCGAAAGA 58.939 50.000 0.00 0.00 44.41 2.52
676 691 2.128771 ATTGGATGTGTCCCCGAAAG 57.871 50.000 0.00 0.00 44.41 2.62
677 692 3.722908 TTATTGGATGTGTCCCCGAAA 57.277 42.857 0.00 0.00 44.41 3.46
678 693 3.943671 ATTATTGGATGTGTCCCCGAA 57.056 42.857 0.00 0.00 44.41 4.30
679 694 5.072464 TGAATATTATTGGATGTGTCCCCGA 59.928 40.000 0.00 0.00 44.41 5.14
680 695 5.312895 TGAATATTATTGGATGTGTCCCCG 58.687 41.667 0.00 0.00 44.41 5.73
681 696 7.287696 AGTTTGAATATTATTGGATGTGTCCCC 59.712 37.037 0.00 0.00 44.41 4.81
682 697 8.137437 CAGTTTGAATATTATTGGATGTGTCCC 58.863 37.037 0.00 0.00 44.41 4.46
683 698 7.649306 GCAGTTTGAATATTATTGGATGTGTCC 59.351 37.037 0.00 0.00 45.31 4.02
684 699 8.408601 AGCAGTTTGAATATTATTGGATGTGTC 58.591 33.333 0.00 0.00 0.00 3.67
685 700 8.297470 AGCAGTTTGAATATTATTGGATGTGT 57.703 30.769 0.00 0.00 0.00 3.72
686 701 8.627403 AGAGCAGTTTGAATATTATTGGATGTG 58.373 33.333 0.00 0.00 0.00 3.21
687 702 8.757982 AGAGCAGTTTGAATATTATTGGATGT 57.242 30.769 0.00 0.00 0.00 3.06
688 703 9.674824 GAAGAGCAGTTTGAATATTATTGGATG 57.325 33.333 0.00 0.00 0.00 3.51
689 704 9.412460 TGAAGAGCAGTTTGAATATTATTGGAT 57.588 29.630 0.00 0.00 0.00 3.41
690 705 8.677300 GTGAAGAGCAGTTTGAATATTATTGGA 58.323 33.333 0.00 0.00 0.00 3.53
691 706 8.680903 AGTGAAGAGCAGTTTGAATATTATTGG 58.319 33.333 0.00 0.00 0.00 3.16
694 709 8.680903 CCAAGTGAAGAGCAGTTTGAATATTAT 58.319 33.333 0.00 0.00 38.07 1.28
695 710 7.665559 ACCAAGTGAAGAGCAGTTTGAATATTA 59.334 33.333 0.00 0.00 38.07 0.98
696 711 6.491403 ACCAAGTGAAGAGCAGTTTGAATATT 59.509 34.615 0.00 0.00 38.07 1.28
697 712 6.006449 ACCAAGTGAAGAGCAGTTTGAATAT 58.994 36.000 0.00 0.00 38.07 1.28
698 713 5.376625 ACCAAGTGAAGAGCAGTTTGAATA 58.623 37.500 0.00 0.00 38.07 1.75
699 714 4.210331 ACCAAGTGAAGAGCAGTTTGAAT 58.790 39.130 0.00 0.00 38.07 2.57
700 715 3.620488 ACCAAGTGAAGAGCAGTTTGAA 58.380 40.909 0.00 0.00 38.07 2.69
701 716 3.281727 ACCAAGTGAAGAGCAGTTTGA 57.718 42.857 0.00 0.00 38.07 2.69
702 717 4.376340 AAACCAAGTGAAGAGCAGTTTG 57.624 40.909 0.00 0.00 38.07 2.93
703 718 5.163550 GGTAAAACCAAGTGAAGAGCAGTTT 60.164 40.000 0.00 0.00 38.07 2.66
704 719 4.338400 GGTAAAACCAAGTGAAGAGCAGTT 59.662 41.667 0.00 0.00 40.77 3.16
705 720 3.883489 GGTAAAACCAAGTGAAGAGCAGT 59.117 43.478 0.00 0.00 38.42 4.40
706 721 4.489679 GGTAAAACCAAGTGAAGAGCAG 57.510 45.455 0.00 0.00 38.42 4.24
717 732 7.906385 AGAAGTTATTCGGTCTGGTAAAACCAA 60.906 37.037 0.00 0.00 43.34 3.67
718 733 6.464749 AGAAGTTATTCGGTCTGGTAAAACCA 60.465 38.462 0.00 0.00 42.48 3.67
719 734 5.936372 AGAAGTTATTCGGTCTGGTAAAACC 59.064 40.000 0.00 0.00 40.58 3.27
720 735 6.426025 ACAGAAGTTATTCGGTCTGGTAAAAC 59.574 38.462 4.69 0.00 39.26 2.43
721 736 6.527423 ACAGAAGTTATTCGGTCTGGTAAAA 58.473 36.000 4.69 0.00 39.26 1.52
722 737 6.105397 ACAGAAGTTATTCGGTCTGGTAAA 57.895 37.500 4.69 0.00 39.26 2.01
723 738 5.733620 ACAGAAGTTATTCGGTCTGGTAA 57.266 39.130 4.69 0.00 39.26 2.85
724 739 7.414222 AATACAGAAGTTATTCGGTCTGGTA 57.586 36.000 4.69 0.00 41.99 3.25
725 740 5.934402 ATACAGAAGTTATTCGGTCTGGT 57.066 39.130 4.69 0.00 41.99 4.00
726 741 8.361139 AGATAATACAGAAGTTATTCGGTCTGG 58.639 37.037 4.69 0.00 41.99 3.86
727 742 9.400638 GAGATAATACAGAAGTTATTCGGTCTG 57.599 37.037 0.00 0.00 41.99 3.51
728 743 9.132923 TGAGATAATACAGAAGTTATTCGGTCT 57.867 33.333 0.00 0.00 41.99 3.85
729 744 9.182933 GTGAGATAATACAGAAGTTATTCGGTC 57.817 37.037 0.00 0.00 41.99 4.79
730 745 8.915036 AGTGAGATAATACAGAAGTTATTCGGT 58.085 33.333 0.00 0.00 44.54 4.69
731 746 9.751542 AAGTGAGATAATACAGAAGTTATTCGG 57.248 33.333 0.00 0.00 40.58 4.30
761 776 9.588096 TGTCTCTCAGGATAAATGCTAATACTA 57.412 33.333 0.00 0.00 0.00 1.82
762 777 8.484214 TGTCTCTCAGGATAAATGCTAATACT 57.516 34.615 0.00 0.00 0.00 2.12
763 778 8.755696 CTGTCTCTCAGGATAAATGCTAATAC 57.244 38.462 0.00 0.00 40.23 1.89
779 794 2.890945 TGACAAATCCGACTGTCTCTCA 59.109 45.455 6.21 0.00 42.06 3.27
780 795 3.577649 TGACAAATCCGACTGTCTCTC 57.422 47.619 6.21 0.00 42.06 3.20
781 796 3.654414 GTTGACAAATCCGACTGTCTCT 58.346 45.455 6.21 0.00 42.06 3.10
782 797 2.408704 CGTTGACAAATCCGACTGTCTC 59.591 50.000 6.21 0.00 42.06 3.36
783 798 2.035449 TCGTTGACAAATCCGACTGTCT 59.965 45.455 6.21 0.00 42.06 3.41
784 799 2.400399 TCGTTGACAAATCCGACTGTC 58.600 47.619 0.00 0.00 41.93 3.51
785 800 2.519377 TCGTTGACAAATCCGACTGT 57.481 45.000 0.00 0.00 0.00 3.55
786 801 2.094258 CCATCGTTGACAAATCCGACTG 59.906 50.000 1.95 3.19 31.43 3.51
787 802 2.028476 TCCATCGTTGACAAATCCGACT 60.028 45.455 1.95 0.00 31.43 4.18
788 803 2.093783 GTCCATCGTTGACAAATCCGAC 59.906 50.000 1.95 0.00 32.91 4.79
789 804 2.343101 GTCCATCGTTGACAAATCCGA 58.657 47.619 2.36 2.36 32.91 4.55
790 805 1.396996 GGTCCATCGTTGACAAATCCG 59.603 52.381 0.00 0.00 34.36 4.18
791 806 1.743394 GGGTCCATCGTTGACAAATCC 59.257 52.381 0.00 0.00 34.36 3.01
792 807 1.743394 GGGGTCCATCGTTGACAAATC 59.257 52.381 0.00 0.00 34.36 2.17
793 808 1.615919 GGGGGTCCATCGTTGACAAAT 60.616 52.381 0.00 0.00 34.36 2.32
794 809 0.250989 GGGGGTCCATCGTTGACAAA 60.251 55.000 0.00 0.00 34.36 2.83
795 810 1.377229 GGGGGTCCATCGTTGACAA 59.623 57.895 0.00 0.00 34.36 3.18
796 811 1.843832 TGGGGGTCCATCGTTGACA 60.844 57.895 0.00 0.00 38.32 3.58
797 812 3.074281 TGGGGGTCCATCGTTGAC 58.926 61.111 0.00 0.00 38.32 3.18
806 821 0.822121 GCCGTATTTGATGGGGGTCC 60.822 60.000 0.00 0.00 34.34 4.46
807 822 0.822121 GGCCGTATTTGATGGGGGTC 60.822 60.000 0.00 0.00 34.34 4.46
808 823 1.229076 GGCCGTATTTGATGGGGGT 59.771 57.895 0.00 0.00 34.34 4.95
809 824 0.396417 TTGGCCGTATTTGATGGGGG 60.396 55.000 0.00 0.00 34.34 5.40
810 825 1.032014 CTTGGCCGTATTTGATGGGG 58.968 55.000 0.00 0.00 34.34 4.96
811 826 1.032014 CCTTGGCCGTATTTGATGGG 58.968 55.000 0.00 0.00 34.34 4.00
812 827 1.405105 CACCTTGGCCGTATTTGATGG 59.595 52.381 0.00 0.00 37.27 3.51
813 828 1.202290 GCACCTTGGCCGTATTTGATG 60.202 52.381 0.00 0.00 0.00 3.07
814 829 1.102978 GCACCTTGGCCGTATTTGAT 58.897 50.000 0.00 0.00 0.00 2.57
815 830 1.302383 CGCACCTTGGCCGTATTTGA 61.302 55.000 0.00 0.00 0.00 2.69
816 831 1.136565 CGCACCTTGGCCGTATTTG 59.863 57.895 0.00 0.00 0.00 2.32
817 832 2.696759 GCGCACCTTGGCCGTATTT 61.697 57.895 0.30 0.00 0.00 1.40
818 833 3.131478 GCGCACCTTGGCCGTATT 61.131 61.111 0.30 0.00 0.00 1.89
819 834 3.697439 ATGCGCACCTTGGCCGTAT 62.697 57.895 14.90 0.00 0.00 3.06
820 835 4.402528 ATGCGCACCTTGGCCGTA 62.403 61.111 14.90 0.00 0.00 4.02
824 839 1.789078 CTATGGATGCGCACCTTGGC 61.789 60.000 14.90 0.00 0.00 4.52
825 840 1.168407 CCTATGGATGCGCACCTTGG 61.168 60.000 14.90 15.48 0.00 3.61
826 841 0.179048 TCCTATGGATGCGCACCTTG 60.179 55.000 14.90 10.19 0.00 3.61
827 842 0.107456 CTCCTATGGATGCGCACCTT 59.893 55.000 14.90 16.43 0.00 3.50
828 843 1.750930 CTCCTATGGATGCGCACCT 59.249 57.895 14.90 0.00 0.00 4.00
829 844 1.963338 GCTCCTATGGATGCGCACC 60.963 63.158 14.90 17.25 0.00 5.01
830 845 1.963338 GGCTCCTATGGATGCGCAC 60.963 63.158 14.90 6.86 30.49 5.34
831 846 2.427320 GGCTCCTATGGATGCGCA 59.573 61.111 14.96 14.96 30.49 6.09
832 847 1.963338 GTGGCTCCTATGGATGCGC 60.963 63.158 0.00 0.00 30.49 6.09
833 848 1.302033 GGTGGCTCCTATGGATGCG 60.302 63.158 0.00 0.00 30.49 4.73
834 849 0.536006 GTGGTGGCTCCTATGGATGC 60.536 60.000 7.19 0.00 37.07 3.91
835 850 0.250038 CGTGGTGGCTCCTATGGATG 60.250 60.000 7.19 0.00 37.07 3.51
836 851 0.691078 ACGTGGTGGCTCCTATGGAT 60.691 55.000 7.19 0.00 37.07 3.41
837 852 1.305802 ACGTGGTGGCTCCTATGGA 60.306 57.895 7.19 0.00 37.07 3.41
838 853 1.144057 GACGTGGTGGCTCCTATGG 59.856 63.158 7.19 0.00 37.07 2.74
839 854 1.144057 GGACGTGGTGGCTCCTATG 59.856 63.158 7.19 2.04 37.07 2.23
840 855 0.617820 AAGGACGTGGTGGCTCCTAT 60.618 55.000 7.19 0.00 32.93 2.57
841 856 1.229082 AAGGACGTGGTGGCTCCTA 60.229 57.895 7.19 0.00 32.93 2.94
842 857 2.526873 AAGGACGTGGTGGCTCCT 60.527 61.111 7.19 0.00 35.83 3.69
843 858 2.047179 GAAGGACGTGGTGGCTCC 60.047 66.667 0.00 0.00 0.00 4.70
844 859 2.432628 CGAAGGACGTGGTGGCTC 60.433 66.667 0.00 0.00 37.22 4.70
854 869 6.916932 GTCAATGTAATCTAGGTACGAAGGAC 59.083 42.308 0.00 0.00 0.00 3.85
855 870 6.604396 TGTCAATGTAATCTAGGTACGAAGGA 59.396 38.462 0.00 0.00 0.00 3.36
856 871 6.802608 TGTCAATGTAATCTAGGTACGAAGG 58.197 40.000 0.00 0.00 0.00 3.46
857 872 9.961265 TTATGTCAATGTAATCTAGGTACGAAG 57.039 33.333 0.00 0.00 0.00 3.79
902 917 8.643324 GGAGATGCTCTAAGGTCTAAGAAATAA 58.357 37.037 0.00 0.00 0.00 1.40
903 918 7.785028 TGGAGATGCTCTAAGGTCTAAGAAATA 59.215 37.037 0.00 0.00 0.00 1.40
904 919 6.613271 TGGAGATGCTCTAAGGTCTAAGAAAT 59.387 38.462 0.00 0.00 0.00 2.17
905 920 5.958380 TGGAGATGCTCTAAGGTCTAAGAAA 59.042 40.000 0.00 0.00 0.00 2.52
906 921 5.519808 TGGAGATGCTCTAAGGTCTAAGAA 58.480 41.667 0.00 0.00 0.00 2.52
907 922 5.130705 TGGAGATGCTCTAAGGTCTAAGA 57.869 43.478 0.00 0.00 0.00 2.10
908 923 5.860941 TTGGAGATGCTCTAAGGTCTAAG 57.139 43.478 0.00 0.00 0.00 2.18
909 924 7.298374 TCTATTGGAGATGCTCTAAGGTCTAA 58.702 38.462 0.00 0.00 34.66 2.10
910 925 6.853490 TCTATTGGAGATGCTCTAAGGTCTA 58.147 40.000 0.00 0.00 34.66 2.59
911 926 5.710646 TCTATTGGAGATGCTCTAAGGTCT 58.289 41.667 0.00 0.00 34.66 3.85
912 927 6.603940 ATCTATTGGAGATGCTCTAAGGTC 57.396 41.667 0.00 0.00 43.71 3.85
944 966 9.177608 ACCTTAGACGGTTTAAAAGTTAGTTTT 57.822 29.630 3.18 3.18 36.71 2.43
945 967 8.737168 ACCTTAGACGGTTTAAAAGTTAGTTT 57.263 30.769 0.00 0.00 31.94 2.66
957 979 4.701171 TGTGTTTTTGACCTTAGACGGTTT 59.299 37.500 0.00 0.00 37.42 3.27
966 988 2.733956 TGGAGCTGTGTTTTTGACCTT 58.266 42.857 0.00 0.00 0.00 3.50
978 1000 1.367840 GACCGTCTGTTGGAGCTGT 59.632 57.895 0.00 0.00 0.00 4.40
1012 1034 2.444140 AGGAGGCCGCGGTCTAAT 60.444 61.111 35.72 21.96 0.00 1.73
1034 1056 4.056740 TCGCGAGGTGTTGTATTTTACAA 58.943 39.130 3.71 0.00 45.66 2.41
1056 1078 4.675146 GCACCTCGTGATGTAAATTTGCAT 60.675 41.667 20.00 20.00 35.23 3.96
1102 1124 4.629523 GGTTGGGTGTTCGCGGGA 62.630 66.667 6.13 0.00 0.00 5.14
1112 1134 0.469144 AAATGAAGTGGCGGTTGGGT 60.469 50.000 0.00 0.00 0.00 4.51
1124 1146 1.135402 CGGGCGGGAAAGAAAATGAAG 60.135 52.381 0.00 0.00 0.00 3.02
1128 1150 2.696759 CGCGGGCGGGAAAGAAAAT 61.697 57.895 4.92 0.00 35.56 1.82
2003 2042 0.034896 GCCCTTCGGTGTCTTCTTCA 59.965 55.000 0.00 0.00 0.00 3.02
2058 2097 0.400815 ACTCCACACCCCAGTTACCA 60.401 55.000 0.00 0.00 0.00 3.25
2087 2126 1.728490 GATCCACCAATGCCTTCCGC 61.728 60.000 0.00 0.00 38.31 5.54
2096 2135 1.406887 GGTACGTGCTGATCCACCAAT 60.407 52.381 3.01 0.00 32.10 3.16
2446 2485 2.421739 GATGGGGATCACCGTCGG 59.578 66.667 20.44 10.48 41.60 4.79
2471 2510 2.291043 GCCCAGTCCTCCTTCGGAA 61.291 63.158 0.00 0.00 34.20 4.30
2473 2512 3.003173 TGCCCAGTCCTCCTTCGG 61.003 66.667 0.00 0.00 0.00 4.30
2475 2514 0.907230 AGTCTGCCCAGTCCTCCTTC 60.907 60.000 0.00 0.00 0.00 3.46
2476 2515 0.474660 AAGTCTGCCCAGTCCTCCTT 60.475 55.000 0.00 0.00 0.00 3.36
2625 2669 9.773328 ACATCAAATTCAACATAGTTTCATACG 57.227 29.630 0.00 0.00 0.00 3.06
2690 2734 8.040132 TGGTCCAAAATGATGATGTAAATTTCC 58.960 33.333 0.00 0.00 0.00 3.13
2876 2921 9.019656 GGCAAAAGGATAATTAACCCAAAAATT 57.980 29.630 8.09 0.00 0.00 1.82
2877 2922 7.613801 GGGCAAAAGGATAATTAACCCAAAAAT 59.386 33.333 8.09 0.00 34.82 1.82
2878 2923 6.943146 GGGCAAAAGGATAATTAACCCAAAAA 59.057 34.615 8.09 0.00 34.82 1.94
2879 2924 6.273495 AGGGCAAAAGGATAATTAACCCAAAA 59.727 34.615 8.09 0.00 37.28 2.44
3055 3100 6.157211 CGGTCTGAATATAATTAGCCGTCTT 58.843 40.000 7.05 0.00 32.99 3.01
3192 3243 3.624861 GTGCTCTCTCTCTCTCTCTCTTG 59.375 52.174 0.00 0.00 0.00 3.02
3193 3244 3.679917 CGTGCTCTCTCTCTCTCTCTCTT 60.680 52.174 0.00 0.00 0.00 2.85
3413 3465 1.728074 CGCTGCACACGTAGAACGA 60.728 57.895 6.44 0.00 46.05 3.85
3438 3490 1.333619 CAATTGCCCCGATTCTTACCG 59.666 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.