Multiple sequence alignment - TraesCS7B01G224900

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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 TraesCS7B01G224900 chr7B 100.000 4234 0 0 1 4234 425156592 425160825 0.000000e+00 7819.0
1 TraesCS7B01G224900 chr7B 84.961 512 68 7 331 835 126999191 126998682 1.050000e-140 510.0
2 TraesCS7B01G224900 chr7B 88.921 343 38 0 1 343 126999568 126999226 1.410000e-114 424.0
3 TraesCS7B01G224900 chr7B 84.956 113 16 1 2540 2652 61627839 61627728 3.460000e-21 113.0
4 TraesCS7B01G224900 chr7B 81.897 116 19 2 2537 2652 61746188 61746075 3.480000e-16 97.1
5 TraesCS7B01G224900 chr7D 94.149 1111 46 6 953 2046 410523667 410522559 0.000000e+00 1674.0
6 TraesCS7B01G224900 chr7D 95.389 1041 35 4 2301 3337 410522566 410521535 0.000000e+00 1644.0
7 TraesCS7B01G224900 chr7A 94.383 1086 43 6 975 2045 471550361 471551443 0.000000e+00 1652.0
8 TraesCS7B01G224900 chr7A 93.004 1115 47 18 2301 3396 471551440 471552542 0.000000e+00 1598.0
9 TraesCS7B01G224900 chr7A 95.167 269 13 0 2036 2304 506291315 506291583 3.910000e-115 425.0
10 TraesCS7B01G224900 chr7A 95.472 265 12 0 2041 2305 599647346 599647082 1.410000e-114 424.0
11 TraesCS7B01G224900 chr7A 95.094 265 13 0 2041 2305 443763914 443763650 6.550000e-113 418.0
12 TraesCS7B01G224900 chr7A 78.976 371 52 15 577 925 718251744 718251378 3.290000e-56 230.0
13 TraesCS7B01G224900 chr7A 84.404 109 17 0 2540 2648 107916705 107916597 1.610000e-19 108.0
14 TraesCS7B01G224900 chr1A 98.759 806 9 1 3430 4234 542174035 542174840 0.000000e+00 1432.0
15 TraesCS7B01G224900 chr1A 79.560 910 135 32 1 875 271579973 271580866 1.680000e-168 603.0
16 TraesCS7B01G224900 chr1A 94.424 269 15 0 2037 2305 88350706 88350974 8.470000e-112 414.0
17 TraesCS7B01G224900 chr1B 98.507 804 12 0 3431 4234 274871095 274870292 0.000000e+00 1419.0
18 TraesCS7B01G224900 chr5B 95.280 805 36 2 3430 4234 658616468 658617270 0.000000e+00 1275.0
19 TraesCS7B01G224900 chr5B 84.864 806 116 5 3431 4234 214440324 214439523 0.000000e+00 808.0
20 TraesCS7B01G224900 chr5B 82.416 563 92 7 339 897 24429949 24430508 6.360000e-133 484.0
21 TraesCS7B01G224900 chr5B 78.850 539 79 14 1 508 59674363 59674897 8.770000e-87 331.0
22 TraesCS7B01G224900 chr5B 81.313 396 67 7 339 728 382225014 382225408 8.840000e-82 315.0
23 TraesCS7B01G224900 chr5B 85.317 252 34 3 1686 1936 372082393 372082144 1.510000e-64 257.0
24 TraesCS7B01G224900 chr5B 79.625 373 58 11 2319 2682 372081688 372081325 7.030000e-63 252.0
25 TraesCS7B01G224900 chr5B 70.942 382 106 5 3840 4219 138787198 138786820 7.540000e-13 86.1
26 TraesCS7B01G224900 chr3B 88.462 806 91 2 3430 4234 814638603 814637799 0.000000e+00 972.0
27 TraesCS7B01G224900 chr6D 85.037 802 116 4 3431 4231 396977595 396978393 0.000000e+00 813.0
28 TraesCS7B01G224900 chr3A 80.952 882 112 27 37 885 382314364 382315222 0.000000e+00 647.0
29 TraesCS7B01G224900 chr3A 95.113 266 12 1 2040 2304 741483461 741483196 6.550000e-113 418.0
30 TraesCS7B01G224900 chr3A 95.113 266 12 1 2040 2304 741557381 741557116 6.550000e-113 418.0
31 TraesCS7B01G224900 chr3A 85.196 331 48 1 331 660 44360200 44359870 5.240000e-89 339.0
32 TraesCS7B01G224900 chr4D 78.492 809 172 2 3428 4234 471227926 471227118 2.900000e-146 529.0
33 TraesCS7B01G224900 chr4D 82.663 398 52 11 535 928 483072447 483072063 1.890000e-88 337.0
34 TraesCS7B01G224900 chr4D 72.513 382 101 4 3840 4219 85729221 85728842 2.070000e-23 121.0
35 TraesCS7B01G224900 chr6B 80.985 589 78 17 105 665 413470958 413470376 1.810000e-118 436.0
36 TraesCS7B01G224900 chr5A 77.926 752 122 29 1 734 575239867 575239142 3.020000e-116 429.0
37 TraesCS7B01G224900 chr5A 78.261 414 72 11 2319 2723 413429412 413429816 2.530000e-62 250.0
38 TraesCS7B01G224900 chr6A 95.113 266 13 0 2043 2308 439231074 439230809 1.820000e-113 420.0
39 TraesCS7B01G224900 chr4A 94.757 267 14 0 2042 2308 78157368 78157634 2.350000e-112 416.0
40 TraesCS7B01G224900 chr2A 93.841 276 17 0 2037 2312 726564676 726564951 2.350000e-112 416.0
41 TraesCS7B01G224900 chr2A 83.988 331 43 5 18 346 728235424 728235102 4.110000e-80 309.0
42 TraesCS7B01G224900 chr5D 87.288 354 43 2 1 352 530494987 530495340 1.830000e-108 403.0
43 TraesCS7B01G224900 chr5D 80.566 530 96 7 342 866 435180994 435180467 6.590000e-108 401.0
44 TraesCS7B01G224900 chr5D 84.463 354 44 6 1 352 232590001 232590345 5.240000e-89 339.0
45 TraesCS7B01G224900 chr5D 84.496 258 38 2 1686 1943 320874621 320874366 1.950000e-63 254.0
46 TraesCS7B01G224900 chr5D 79.088 373 60 11 2319 2682 320873913 320873550 1.520000e-59 241.0
47 TraesCS7B01G224900 chr5D 79.310 348 56 12 393 736 503090041 503089706 3.290000e-56 230.0
48 TraesCS7B01G224900 chr5D 79.904 209 35 6 723 928 519195129 519195333 3.410000e-31 147.0
49 TraesCS7B01G224900 chr2D 85.393 356 39 7 1 350 638618893 638619241 1.450000e-94 357.0
50 TraesCS7B01G224900 chr2D 94.118 68 1 3 3432 3497 83224899 83224833 2.690000e-17 100.0
51 TraesCS7B01G224900 chr2D 80.342 117 14 8 2540 2652 100432469 100432580 3.510000e-11 80.5
52 TraesCS7B01G224900 chr1D 82.583 333 48 9 331 660 222734859 222735184 6.930000e-73 285.0
53 TraesCS7B01G224900 chr2B 79.167 408 72 9 331 735 719761397 719761000 1.940000e-68 270.0
54 TraesCS7B01G224900 chr2B 93.939 66 3 1 3433 3497 73066056 73065991 9.690000e-17 99.0


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 TraesCS7B01G224900 chr7B 425156592 425160825 4233 False 7819.0 7819 100.0000 1 4234 1 chr7B.!!$F1 4233
1 TraesCS7B01G224900 chr7B 126998682 126999568 886 True 467.0 510 86.9410 1 835 2 chr7B.!!$R3 834
2 TraesCS7B01G224900 chr7D 410521535 410523667 2132 True 1659.0 1674 94.7690 953 3337 2 chr7D.!!$R1 2384
3 TraesCS7B01G224900 chr7A 471550361 471552542 2181 False 1625.0 1652 93.6935 975 3396 2 chr7A.!!$F2 2421
4 TraesCS7B01G224900 chr1A 542174035 542174840 805 False 1432.0 1432 98.7590 3430 4234 1 chr1A.!!$F3 804
5 TraesCS7B01G224900 chr1A 271579973 271580866 893 False 603.0 603 79.5600 1 875 1 chr1A.!!$F2 874
6 TraesCS7B01G224900 chr1B 274870292 274871095 803 True 1419.0 1419 98.5070 3431 4234 1 chr1B.!!$R1 803
7 TraesCS7B01G224900 chr5B 658616468 658617270 802 False 1275.0 1275 95.2800 3430 4234 1 chr5B.!!$F4 804
8 TraesCS7B01G224900 chr5B 214439523 214440324 801 True 808.0 808 84.8640 3431 4234 1 chr5B.!!$R2 803
9 TraesCS7B01G224900 chr5B 24429949 24430508 559 False 484.0 484 82.4160 339 897 1 chr5B.!!$F1 558
10 TraesCS7B01G224900 chr5B 59674363 59674897 534 False 331.0 331 78.8500 1 508 1 chr5B.!!$F2 507
11 TraesCS7B01G224900 chr5B 372081325 372082393 1068 True 254.5 257 82.4710 1686 2682 2 chr5B.!!$R3 996
12 TraesCS7B01G224900 chr3B 814637799 814638603 804 True 972.0 972 88.4620 3430 4234 1 chr3B.!!$R1 804
13 TraesCS7B01G224900 chr6D 396977595 396978393 798 False 813.0 813 85.0370 3431 4231 1 chr6D.!!$F1 800
14 TraesCS7B01G224900 chr3A 382314364 382315222 858 False 647.0 647 80.9520 37 885 1 chr3A.!!$F1 848
15 TraesCS7B01G224900 chr4D 471227118 471227926 808 True 529.0 529 78.4920 3428 4234 1 chr4D.!!$R2 806
16 TraesCS7B01G224900 chr6B 413470376 413470958 582 True 436.0 436 80.9850 105 665 1 chr6B.!!$R1 560
17 TraesCS7B01G224900 chr5A 575239142 575239867 725 True 429.0 429 77.9260 1 734 1 chr5A.!!$R1 733
18 TraesCS7B01G224900 chr5D 435180467 435180994 527 True 401.0 401 80.5660 342 866 1 chr5D.!!$R1 524
19 TraesCS7B01G224900 chr5D 320873550 320874621 1071 True 247.5 254 81.7920 1686 2682 2 chr5D.!!$R3 996

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
640 731 0.459078 TGTTGTGGCATTGGTGTGTG 59.541 50.0 0.0 0.0 0.0 3.82 F
1393 1502 0.231279 GGCCACGTATGTTAATCGCG 59.769 55.0 0.0 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1974 1.028868 GCCGCTGAAGCTCCTCAATT 61.029 55.0 0.1 0.0 39.32 2.32 R
3361 3754 0.179040 TTTTCGTCCTCCGCCACTTT 60.179 50.0 0.0 0.0 36.19 2.66 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
20 21 1.986757 GCTCTGGCTGAGGACCTGA 60.987 63.158 20.97 0.00 42.87 3.86
26 27 1.610673 GCTGAGGACCTGACTGGGA 60.611 63.158 0.00 0.00 41.11 4.37
52 53 6.433404 AAGCACTACTACTAGTGTTGCTTCTA 59.567 38.462 22.13 0.00 46.04 2.10
60 61 0.875059 GTGTTGCTTCTAGTGGTGGC 59.125 55.000 0.00 0.00 0.00 5.01
66 67 0.537188 CTTCTAGTGGTGGCGATGGT 59.463 55.000 0.00 0.00 0.00 3.55
170 183 6.583806 GCTTGAAAACTATTTGATGGTCTGTG 59.416 38.462 0.00 0.00 0.00 3.66
188 201 5.408604 GTCTGTGTATTTTAGTGAGGTGGTG 59.591 44.000 0.00 0.00 0.00 4.17
195 208 8.255206 TGTATTTTAGTGAGGTGGTGTATACTG 58.745 37.037 4.17 0.00 0.00 2.74
204 217 2.835764 GTGGTGTATACTGACCCCTCAA 59.164 50.000 9.32 0.00 0.00 3.02
211 224 2.642171 ACTGACCCCTCAAGGTGATA 57.358 50.000 0.00 0.00 41.42 2.15
213 226 3.464828 ACTGACCCCTCAAGGTGATAAT 58.535 45.455 0.00 0.00 41.42 1.28
217 230 4.080356 TGACCCCTCAAGGTGATAATGAAG 60.080 45.833 0.00 0.00 41.42 3.02
218 231 3.217626 CCCCTCAAGGTGATAATGAAGC 58.782 50.000 0.00 0.00 0.00 3.86
277 290 6.223852 GTGGTAGGATGACACCATATTAGTG 58.776 44.000 0.00 1.81 46.15 2.74
292 311 6.823689 CCATATTAGTGCTAGGTTGAACTTGT 59.176 38.462 0.00 0.00 0.00 3.16
298 317 6.062095 AGTGCTAGGTTGAACTTGTTATGTT 58.938 36.000 0.00 0.00 0.00 2.71
336 355 2.593346 ACTATTGCTCTTCTGCTCCG 57.407 50.000 0.00 0.00 0.00 4.63
376 444 3.407424 TTGATCTTGTGCACTGCTAGT 57.593 42.857 19.41 0.00 0.00 2.57
390 459 4.015084 ACTGCTAGTACAAGTGGTATCGT 58.985 43.478 0.00 0.00 33.76 3.73
498 568 1.007580 GTTTAAGAGTAGGCAGGCGC 58.992 55.000 0.00 0.00 37.44 6.53
529 602 4.022416 TGCTTACTCCAAATTTGTGCGAAT 60.022 37.500 16.73 0.28 0.00 3.34
564 640 1.476488 GTGTTGAAGTTGGCAAGGTGT 59.524 47.619 0.00 0.00 0.00 4.16
575 651 1.732259 GGCAAGGTGTATCGTCAGTTG 59.268 52.381 0.00 0.00 0.00 3.16
640 731 0.459078 TGTTGTGGCATTGGTGTGTG 59.541 50.000 0.00 0.00 0.00 3.82
660 751 1.667756 GCGGTGTGATCGTGTGTAAGA 60.668 52.381 0.00 0.00 0.00 2.10
662 753 2.598637 CGGTGTGATCGTGTGTAAGATG 59.401 50.000 0.00 0.00 0.00 2.90
665 756 5.165676 GGTGTGATCGTGTGTAAGATGTAA 58.834 41.667 0.00 0.00 0.00 2.41
684 778 8.156165 AGATGTAATAGTAGTAGGTAAGCTCGT 58.844 37.037 0.00 0.00 0.00 4.18
707 801 6.338937 GTCAAGTAGGGTACAAGGTAATCAG 58.661 44.000 0.00 0.00 0.00 2.90
713 807 5.091552 AGGGTACAAGGTAATCAGAACTCA 58.908 41.667 0.00 0.00 0.00 3.41
721 815 5.593010 AGGTAATCAGAACTCAATACTCGC 58.407 41.667 0.00 0.00 0.00 5.03
759 853 1.201812 GCACTCGTATGAGCACAAACG 60.202 52.381 12.04 0.00 46.69 3.60
818 913 5.028549 ACGATGCAAGAAGAGGATATGTT 57.971 39.130 0.00 0.00 0.00 2.71
829 924 6.600822 AGAAGAGGATATGTTGACAACCAATG 59.399 38.462 15.59 0.00 37.08 2.82
835 930 7.833682 AGGATATGTTGACAACCAATGAACATA 59.166 33.333 15.59 0.00 40.30 2.29
846 941 7.449395 ACAACCAATGAACATATAGATGATGGG 59.551 37.037 3.93 0.00 36.48 4.00
847 942 5.948162 ACCAATGAACATATAGATGATGGGC 59.052 40.000 3.93 0.00 36.48 5.36
866 963 2.624636 GCTTTTTGCCTGCATATGCTT 58.375 42.857 27.13 0.00 37.58 3.91
879 976 3.750599 GCATATGCTTAACCAGGCCCTAA 60.751 47.826 20.64 0.00 38.21 2.69
901 998 3.331150 TGGGACAAGTATGCAAAGTACG 58.669 45.455 0.00 0.00 31.92 3.67
902 999 3.244284 TGGGACAAGTATGCAAAGTACGT 60.244 43.478 0.00 0.00 31.92 3.57
903 1000 4.021280 TGGGACAAGTATGCAAAGTACGTA 60.021 41.667 0.00 0.00 31.92 3.57
904 1001 4.931002 GGGACAAGTATGCAAAGTACGTAA 59.069 41.667 0.00 0.00 0.00 3.18
905 1002 5.409214 GGGACAAGTATGCAAAGTACGTAAA 59.591 40.000 0.00 0.00 0.00 2.01
906 1003 6.073112 GGGACAAGTATGCAAAGTACGTAAAA 60.073 38.462 0.00 0.00 0.00 1.52
907 1004 7.361457 GGGACAAGTATGCAAAGTACGTAAAAT 60.361 37.037 0.00 0.00 0.00 1.82
908 1005 8.019094 GGACAAGTATGCAAAGTACGTAAAATT 58.981 33.333 0.00 0.00 0.00 1.82
909 1006 8.722342 ACAAGTATGCAAAGTACGTAAAATTG 57.278 30.769 0.00 4.44 0.00 2.32
910 1007 8.561212 ACAAGTATGCAAAGTACGTAAAATTGA 58.439 29.630 16.16 5.97 0.00 2.57
911 1008 9.554724 CAAGTATGCAAAGTACGTAAAATTGAT 57.445 29.630 16.16 10.70 0.00 2.57
912 1009 9.554724 AAGTATGCAAAGTACGTAAAATTGATG 57.445 29.630 16.16 3.89 0.00 3.07
913 1010 6.869421 ATGCAAAGTACGTAAAATTGATGC 57.131 33.333 16.16 11.74 0.00 3.91
914 1011 4.848841 TGCAAAGTACGTAAAATTGATGCG 59.151 37.500 16.16 1.39 33.00 4.73
915 1012 5.083389 GCAAAGTACGTAAAATTGATGCGA 58.917 37.500 16.16 0.00 0.00 5.10
916 1013 5.225129 GCAAAGTACGTAAAATTGATGCGAG 59.775 40.000 16.16 0.00 0.00 5.03
917 1014 6.530567 CAAAGTACGTAAAATTGATGCGAGA 58.469 36.000 0.00 0.00 0.00 4.04
918 1015 6.715344 AAGTACGTAAAATTGATGCGAGAA 57.285 33.333 0.00 0.00 0.00 2.87
919 1016 6.715344 AGTACGTAAAATTGATGCGAGAAA 57.285 33.333 0.00 0.00 0.00 2.52
920 1017 7.303634 AGTACGTAAAATTGATGCGAGAAAT 57.696 32.000 0.00 0.00 0.00 2.17
921 1018 7.399523 AGTACGTAAAATTGATGCGAGAAATC 58.600 34.615 0.00 0.00 0.00 2.17
922 1019 5.569413 ACGTAAAATTGATGCGAGAAATCC 58.431 37.500 8.57 0.00 0.00 3.01
923 1020 5.123186 ACGTAAAATTGATGCGAGAAATCCA 59.877 36.000 8.57 0.00 0.00 3.41
924 1021 6.027131 CGTAAAATTGATGCGAGAAATCCAA 58.973 36.000 0.00 0.00 0.00 3.53
925 1022 6.021468 CGTAAAATTGATGCGAGAAATCCAAC 60.021 38.462 0.00 0.00 0.00 3.77
926 1023 5.389859 AAATTGATGCGAGAAATCCAACA 57.610 34.783 0.00 0.00 0.00 3.33
927 1024 3.829886 TTGATGCGAGAAATCCAACAC 57.170 42.857 0.00 0.00 0.00 3.32
928 1025 2.083774 TGATGCGAGAAATCCAACACC 58.916 47.619 0.00 0.00 0.00 4.16
929 1026 2.290260 TGATGCGAGAAATCCAACACCT 60.290 45.455 0.00 0.00 0.00 4.00
930 1027 2.270352 TGCGAGAAATCCAACACCTT 57.730 45.000 0.00 0.00 0.00 3.50
931 1028 2.151202 TGCGAGAAATCCAACACCTTC 58.849 47.619 0.00 0.00 0.00 3.46
932 1029 2.224523 TGCGAGAAATCCAACACCTTCT 60.225 45.455 0.00 0.00 0.00 2.85
933 1030 3.007506 TGCGAGAAATCCAACACCTTCTA 59.992 43.478 0.00 0.00 0.00 2.10
934 1031 4.192317 GCGAGAAATCCAACACCTTCTAT 58.808 43.478 0.00 0.00 0.00 1.98
935 1032 5.105106 TGCGAGAAATCCAACACCTTCTATA 60.105 40.000 0.00 0.00 0.00 1.31
936 1033 5.992217 GCGAGAAATCCAACACCTTCTATAT 59.008 40.000 0.00 0.00 0.00 0.86
937 1034 6.146347 GCGAGAAATCCAACACCTTCTATATC 59.854 42.308 0.00 0.00 0.00 1.63
938 1035 6.363626 CGAGAAATCCAACACCTTCTATATCG 59.636 42.308 0.00 0.00 0.00 2.92
939 1036 7.125792 AGAAATCCAACACCTTCTATATCGT 57.874 36.000 0.00 0.00 0.00 3.73
940 1037 6.986817 AGAAATCCAACACCTTCTATATCGTG 59.013 38.462 0.00 0.00 0.00 4.35
941 1038 6.479972 AATCCAACACCTTCTATATCGTGA 57.520 37.500 0.00 0.00 0.00 4.35
942 1039 6.672266 ATCCAACACCTTCTATATCGTGAT 57.328 37.500 0.00 0.00 0.00 3.06
943 1040 7.776618 ATCCAACACCTTCTATATCGTGATA 57.223 36.000 0.00 0.00 0.00 2.15
944 1041 6.978338 TCCAACACCTTCTATATCGTGATAC 58.022 40.000 0.00 0.00 0.00 2.24
945 1042 6.776116 TCCAACACCTTCTATATCGTGATACT 59.224 38.462 0.00 0.00 0.00 2.12
946 1043 7.940688 TCCAACACCTTCTATATCGTGATACTA 59.059 37.037 0.00 0.00 0.00 1.82
947 1044 8.740906 CCAACACCTTCTATATCGTGATACTAT 58.259 37.037 0.00 0.00 0.00 2.12
955 1052 9.764870 TTCTATATCGTGATACTATTAACGTGC 57.235 33.333 0.00 0.00 37.32 5.34
956 1053 9.159364 TCTATATCGTGATACTATTAACGTGCT 57.841 33.333 0.00 0.00 37.32 4.40
961 1058 9.932699 ATCGTGATACTATTAACGTGCTATATC 57.067 33.333 0.00 0.00 37.32 1.63
962 1059 8.112449 TCGTGATACTATTAACGTGCTATATCG 58.888 37.037 0.00 0.00 37.32 2.92
963 1060 7.901889 CGTGATACTATTAACGTGCTATATCGT 59.098 37.037 0.00 0.00 42.12 3.73
964 1061 8.996933 GTGATACTATTAACGTGCTATATCGTG 58.003 37.037 0.00 0.00 40.19 4.35
965 1062 7.695201 TGATACTATTAACGTGCTATATCGTGC 59.305 37.037 0.00 0.00 40.19 5.34
966 1063 5.159209 ACTATTAACGTGCTATATCGTGCC 58.841 41.667 0.00 0.00 40.19 5.01
967 1064 3.720949 TTAACGTGCTATATCGTGCCT 57.279 42.857 0.00 0.00 40.19 4.75
968 1065 4.834357 TTAACGTGCTATATCGTGCCTA 57.166 40.909 0.00 0.00 40.19 3.93
969 1066 3.936372 AACGTGCTATATCGTGCCTAT 57.064 42.857 0.00 0.00 40.19 2.57
970 1067 3.936372 ACGTGCTATATCGTGCCTATT 57.064 42.857 0.00 0.00 38.85 1.73
971 1068 4.252971 ACGTGCTATATCGTGCCTATTT 57.747 40.909 0.00 0.00 38.85 1.40
972 1069 4.628074 ACGTGCTATATCGTGCCTATTTT 58.372 39.130 0.00 0.00 38.85 1.82
973 1070 5.054477 ACGTGCTATATCGTGCCTATTTTT 58.946 37.500 0.00 0.00 38.85 1.94
1006 1103 3.445805 CCAATCATATGGCTGCATGCATA 59.554 43.478 22.97 11.22 45.15 3.14
1056 1165 2.519063 CCTGGTGGCACTTGCACA 60.519 61.111 18.45 5.46 44.36 4.57
1070 1179 4.275689 CACTTGCACAGATGTAAACAAGGA 59.724 41.667 18.77 0.00 37.15 3.36
1090 1199 4.243007 GACAAGTTCCTGTCCAAAATGG 57.757 45.455 0.00 0.00 39.93 3.16
1146 1255 0.828762 TCTTGTTGCTGGCCAATGCT 60.829 50.000 17.08 0.00 35.55 3.79
1248 1357 4.052229 CCACGCCTTCTCGTCGGT 62.052 66.667 0.00 0.00 41.21 4.69
1361 1470 3.005472 CACTACGTTCTCTGGTCCAAGAA 59.995 47.826 0.00 10.63 0.00 2.52
1369 1478 1.343465 TCTGGTCCAAGAAGTTCGGTC 59.657 52.381 0.00 0.00 0.00 4.79
1393 1502 0.231279 GGCCACGTATGTTAATCGCG 59.769 55.000 0.00 0.00 0.00 5.87
1424 1533 3.650950 ATGACCCGCCTGCCAAGT 61.651 61.111 0.00 0.00 0.00 3.16
1461 1570 2.270434 TTTCCTATCTGCAGGGAGGT 57.730 50.000 25.29 7.82 36.26 3.85
1865 1974 0.744414 GCAAGCGCATCTTCCACCTA 60.744 55.000 11.47 0.00 38.36 3.08
1868 1977 2.684881 CAAGCGCATCTTCCACCTAATT 59.315 45.455 11.47 0.00 31.27 1.40
1922 2031 3.278519 TACCTCTGGGTCCCCGGT 61.279 66.667 15.64 15.64 45.98 5.28
1942 2051 3.118629 GGTAGCCAGTGAGTCATCAATCA 60.119 47.826 0.00 0.00 37.14 2.57
1973 2083 9.253832 TCACCTCACCACAAATTATTTATTCAT 57.746 29.630 0.00 0.00 0.00 2.57
2046 2159 6.488006 TCTCTGTCGTGGTTTAAAGTAGTACT 59.512 38.462 0.00 0.00 0.00 2.73
2048 2161 5.772521 TGTCGTGGTTTAAAGTAGTACTCC 58.227 41.667 2.58 0.60 0.00 3.85
2049 2162 5.164233 GTCGTGGTTTAAAGTAGTACTCCC 58.836 45.833 2.58 0.34 0.00 4.30
2050 2163 5.047731 GTCGTGGTTTAAAGTAGTACTCCCT 60.048 44.000 2.58 0.00 0.00 4.20
2052 2165 5.866092 CGTGGTTTAAAGTAGTACTCCCTTC 59.134 44.000 2.58 0.00 0.00 3.46
2054 2167 5.539955 TGGTTTAAAGTAGTACTCCCTTCGT 59.460 40.000 2.58 0.00 0.00 3.85
2055 2168 6.041979 TGGTTTAAAGTAGTACTCCCTTCGTT 59.958 38.462 2.58 0.00 0.00 3.85
2056 2169 6.931281 GGTTTAAAGTAGTACTCCCTTCGTTT 59.069 38.462 2.58 0.00 0.00 3.60
2057 2170 7.442364 GGTTTAAAGTAGTACTCCCTTCGTTTT 59.558 37.037 2.58 0.00 0.00 2.43
2058 2171 8.830580 GTTTAAAGTAGTACTCCCTTCGTTTTT 58.169 33.333 2.58 0.00 0.00 1.94
2062 2175 9.565090 AAAGTAGTACTCCCTTCGTTTTTATTT 57.435 29.630 2.58 0.00 0.00 1.40
2065 2178 9.645059 GTAGTACTCCCTTCGTTTTTATTTACT 57.355 33.333 0.00 0.00 0.00 2.24
2066 2179 8.768957 AGTACTCCCTTCGTTTTTATTTACTC 57.231 34.615 0.00 0.00 0.00 2.59
2088 2203 7.697352 CTCTGCATATTAGAGTTGACTGAAG 57.303 40.000 5.84 0.00 37.48 3.02
2089 2204 7.175347 TCTGCATATTAGAGTTGACTGAAGT 57.825 36.000 0.00 0.00 0.00 3.01
2090 2205 7.261325 TCTGCATATTAGAGTTGACTGAAGTC 58.739 38.462 3.41 3.41 44.97 3.01
2259 2374 9.634163 CTTGGTTAAAGTTTGTAAAGTTTGACT 57.366 29.630 21.51 3.63 42.59 3.41
2260 2375 9.628746 TTGGTTAAAGTTTGTAAAGTTTGACTC 57.371 29.630 21.51 15.74 42.59 3.36
2261 2376 9.016438 TGGTTAAAGTTTGTAAAGTTTGACTCT 57.984 29.630 21.51 2.85 42.59 3.24
2262 2377 9.285770 GGTTAAAGTTTGTAAAGTTTGACTCTG 57.714 33.333 21.51 0.00 42.59 3.35
2265 2380 6.679327 AGTTTGTAAAGTTTGACTCTGACC 57.321 37.500 0.00 0.00 0.00 4.02
2266 2381 6.177610 AGTTTGTAAAGTTTGACTCTGACCA 58.822 36.000 0.00 0.00 0.00 4.02
2267 2382 6.657541 AGTTTGTAAAGTTTGACTCTGACCAA 59.342 34.615 0.00 0.00 0.00 3.67
2268 2383 7.175990 AGTTTGTAAAGTTTGACTCTGACCAAA 59.824 33.333 0.00 0.00 0.00 3.28
2269 2384 6.677781 TGTAAAGTTTGACTCTGACCAAAG 57.322 37.500 0.00 0.00 33.52 2.77
2270 2385 4.639135 AAAGTTTGACTCTGACCAAAGC 57.361 40.909 0.00 0.00 33.52 3.51
2271 2386 3.567478 AGTTTGACTCTGACCAAAGCT 57.433 42.857 0.00 0.00 33.52 3.74
2272 2387 4.689612 AGTTTGACTCTGACCAAAGCTA 57.310 40.909 0.00 0.00 33.52 3.32
2273 2388 5.036117 AGTTTGACTCTGACCAAAGCTAA 57.964 39.130 0.00 0.00 33.52 3.09
2274 2389 5.625150 AGTTTGACTCTGACCAAAGCTAAT 58.375 37.500 0.00 0.00 33.52 1.73
2275 2390 6.769512 AGTTTGACTCTGACCAAAGCTAATA 58.230 36.000 0.00 0.00 33.52 0.98
2276 2391 7.398024 AGTTTGACTCTGACCAAAGCTAATAT 58.602 34.615 0.00 0.00 33.52 1.28
2277 2392 7.335422 AGTTTGACTCTGACCAAAGCTAATATG 59.665 37.037 0.00 0.00 33.52 1.78
2278 2393 5.118990 TGACTCTGACCAAAGCTAATATGC 58.881 41.667 0.00 0.00 0.00 3.14
2279 2394 4.122776 ACTCTGACCAAAGCTAATATGCG 58.877 43.478 0.00 0.00 38.13 4.73
2281 2396 4.765273 TCTGACCAAAGCTAATATGCGAA 58.235 39.130 0.00 0.00 38.13 4.70
2284 2399 5.666462 TGACCAAAGCTAATATGCGAACTA 58.334 37.500 0.00 0.00 38.13 2.24
2287 2402 7.282224 TGACCAAAGCTAATATGCGAACTAAAT 59.718 33.333 0.00 0.00 38.13 1.40
2289 2404 9.116067 ACCAAAGCTAATATGCGAACTAAATAA 57.884 29.630 0.00 0.00 38.13 1.40
2301 2416 7.142680 TGCGAACTAAATAAAAACAAAGGGAG 58.857 34.615 0.00 0.00 0.00 4.30
2304 2419 9.603298 CGAACTAAATAAAAACAAAGGGAGTAC 57.397 33.333 0.00 0.00 0.00 2.73
2371 2742 3.458163 CGGCTGAACGGGGAGCTA 61.458 66.667 0.00 0.00 35.42 3.32
2443 2814 4.504916 CGGAGGCCGTCAGCAGAG 62.505 72.222 0.00 0.00 46.50 3.35
2671 3048 2.597510 GCCGAGGTTGCCCAAGTT 60.598 61.111 0.00 0.00 0.00 2.66
2678 3055 1.227527 GTTGCCCAAGTTTGTGGCC 60.228 57.895 16.51 0.00 41.12 5.36
2707 3084 4.899239 GCCGCAGATCACCTCCCG 62.899 72.222 0.00 0.00 0.00 5.14
2729 3106 1.518572 CTCGCCGTCGTAAGCCATT 60.519 57.895 0.00 0.00 36.96 3.16
2745 3122 1.600013 CCATTTGACACCGTCGAAACA 59.400 47.619 0.00 0.00 39.09 2.83
2770 3148 4.367023 TCCGGCGCCACTGTACAC 62.367 66.667 28.98 0.00 0.00 2.90
3245 3628 3.717294 CTGTAGGCCGGCTTGGGT 61.717 66.667 28.56 8.68 38.63 4.51
3246 3629 3.253838 TGTAGGCCGGCTTGGGTT 61.254 61.111 28.56 7.81 38.63 4.11
3247 3630 2.035155 GTAGGCCGGCTTGGGTTT 59.965 61.111 28.56 6.00 38.63 3.27
3248 3631 2.034999 TAGGCCGGCTTGGGTTTG 59.965 61.111 28.56 0.00 38.63 2.93
3249 3632 3.577334 TAGGCCGGCTTGGGTTTGG 62.577 63.158 28.56 0.00 38.63 3.28
3337 3730 3.733236 TCGTGCTTCGATTCGGAAT 57.267 47.368 2.19 2.19 44.01 3.01
3338 3731 1.277326 TCGTGCTTCGATTCGGAATG 58.723 50.000 8.18 1.26 44.01 2.67
3340 3733 1.658596 CGTGCTTCGATTCGGAATGAA 59.341 47.619 8.18 10.70 42.86 2.57
3344 3737 3.370978 TGCTTCGATTCGGAATGAAAGTC 59.629 43.478 8.18 8.04 40.71 3.01
3345 3738 3.619038 GCTTCGATTCGGAATGAAAGTCT 59.381 43.478 8.18 0.00 40.71 3.24
3346 3739 4.493220 GCTTCGATTCGGAATGAAAGTCTG 60.493 45.833 8.18 2.54 40.71 3.51
3349 3742 5.340803 TCGATTCGGAATGAAAGTCTGTAG 58.659 41.667 8.18 0.00 38.69 2.74
3351 3744 6.094464 TCGATTCGGAATGAAAGTCTGTAGTA 59.906 38.462 8.18 0.00 38.69 1.82
3358 3751 8.353684 CGGAATGAAAGTCTGTAGTATCTATGT 58.646 37.037 0.00 0.00 31.50 2.29
3399 3792 2.899303 AAATACTTGAGGTGGGGTGG 57.101 50.000 0.00 0.00 0.00 4.61
3400 3793 2.053747 AATACTTGAGGTGGGGTGGA 57.946 50.000 0.00 0.00 0.00 4.02
3401 3794 1.286248 ATACTTGAGGTGGGGTGGAC 58.714 55.000 0.00 0.00 0.00 4.02
3402 3795 0.192566 TACTTGAGGTGGGGTGGACT 59.807 55.000 0.00 0.00 0.00 3.85
3403 3796 1.128188 ACTTGAGGTGGGGTGGACTC 61.128 60.000 0.00 0.00 0.00 3.36
3404 3797 1.074090 TTGAGGTGGGGTGGACTCA 60.074 57.895 0.00 0.00 38.12 3.41
3405 3798 1.415672 TTGAGGTGGGGTGGACTCAC 61.416 60.000 0.00 0.00 39.47 3.51
3406 3799 1.841556 GAGGTGGGGTGGACTCACA 60.842 63.158 0.00 0.00 45.32 3.58
3407 3800 1.831652 GAGGTGGGGTGGACTCACAG 61.832 65.000 0.00 0.00 45.32 3.66
3408 3801 2.750350 GTGGGGTGGACTCACAGG 59.250 66.667 0.00 0.00 45.32 4.00
3409 3802 3.249189 TGGGGTGGACTCACAGGC 61.249 66.667 0.00 0.00 45.32 4.85
3410 3803 2.930562 GGGGTGGACTCACAGGCT 60.931 66.667 0.00 0.00 45.32 4.58
3411 3804 2.348998 GGGTGGACTCACAGGCTG 59.651 66.667 14.16 14.16 45.32 4.85
3412 3805 2.217038 GGGTGGACTCACAGGCTGA 61.217 63.158 23.66 0.00 45.32 4.26
3413 3806 1.557269 GGGTGGACTCACAGGCTGAT 61.557 60.000 23.66 2.23 45.32 2.90
3414 3807 0.392193 GGTGGACTCACAGGCTGATG 60.392 60.000 23.66 15.40 45.32 3.07
3415 3808 0.322975 GTGGACTCACAGGCTGATGT 59.677 55.000 23.66 15.70 43.13 3.06
3420 3813 3.900855 CACAGGCTGATGTGGAGC 58.099 61.111 23.66 0.00 45.53 4.70
3421 3814 1.002990 CACAGGCTGATGTGGAGCA 60.003 57.895 23.66 0.00 45.53 4.26
3422 3815 0.607217 CACAGGCTGATGTGGAGCAA 60.607 55.000 23.66 0.00 45.53 3.91
3423 3816 0.111061 ACAGGCTGATGTGGAGCAAA 59.889 50.000 23.66 0.00 38.27 3.68
3424 3817 0.524862 CAGGCTGATGTGGAGCAAAC 59.475 55.000 9.42 0.00 38.27 2.93
3425 3818 0.403271 AGGCTGATGTGGAGCAAACT 59.597 50.000 0.00 0.00 38.27 2.66
3426 3819 1.630369 AGGCTGATGTGGAGCAAACTA 59.370 47.619 0.00 0.00 38.27 2.24
3427 3820 2.040278 AGGCTGATGTGGAGCAAACTAA 59.960 45.455 0.00 0.00 38.27 2.24
3428 3821 2.819608 GGCTGATGTGGAGCAAACTAAA 59.180 45.455 0.00 0.00 38.27 1.85
3503 3896 6.315393 AGAAAAAGTTTTACAAGAGACGAGCA 59.685 34.615 0.24 0.00 0.00 4.26
3802 4197 1.414919 AGCCACCAGTCGACAAAAGTA 59.585 47.619 19.50 0.00 0.00 2.24
4074 4471 2.290916 CAGCTGTAGGTGATACGATCGT 59.709 50.000 25.94 25.94 45.66 3.73
4156 4553 0.318762 AAGAGAACGTGTCCTCCAGC 59.681 55.000 8.64 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.675038 ACTAGTAGTAGTGCTTTCCCAGT 58.325 43.478 9.52 0.00 38.14 4.00
52 53 2.032528 CACACCATCGCCACCACT 59.967 61.111 0.00 0.00 0.00 4.00
60 61 1.224075 GAGGATCATGCACACCATCG 58.776 55.000 0.00 0.00 33.17 3.84
66 67 1.141665 CCGTCGAGGATCATGCACA 59.858 57.895 6.70 0.00 45.00 4.57
170 183 8.472413 TCAGTATACACCACCTCACTAAAATAC 58.528 37.037 5.50 0.00 0.00 1.89
177 190 3.097614 GGTCAGTATACACCACCTCACT 58.902 50.000 5.50 0.00 32.33 3.41
188 201 3.371965 TCACCTTGAGGGGTCAGTATAC 58.628 50.000 0.00 0.00 40.30 1.47
195 208 4.455606 CTTCATTATCACCTTGAGGGGTC 58.544 47.826 0.00 0.00 40.30 4.46
204 217 2.988010 TCGCAGCTTCATTATCACCT 57.012 45.000 0.00 0.00 0.00 4.00
211 224 1.486310 TCCTACCATCGCAGCTTCATT 59.514 47.619 0.00 0.00 0.00 2.57
213 226 1.123077 ATCCTACCATCGCAGCTTCA 58.877 50.000 0.00 0.00 0.00 3.02
217 230 2.135933 GTGTAATCCTACCATCGCAGC 58.864 52.381 0.00 0.00 0.00 5.25
218 231 2.548067 GGGTGTAATCCTACCATCGCAG 60.548 54.545 0.00 0.00 38.74 5.18
272 285 7.221450 ACATAACAAGTTCAACCTAGCACTAA 58.779 34.615 0.00 0.00 0.00 2.24
277 290 6.313744 ACAACATAACAAGTTCAACCTAGC 57.686 37.500 0.00 0.00 0.00 3.42
292 311 6.887626 AGCATGCATGATCATACAACATAA 57.112 33.333 30.64 0.00 0.00 1.90
298 317 7.361457 GCAATAGTAAGCATGCATGATCATACA 60.361 37.037 30.64 11.03 38.63 2.29
336 355 7.649306 AGATCAATAGTTGAAACAACAAGCAAC 59.351 33.333 15.29 0.00 43.95 4.17
376 444 5.785243 TGATGAACAACGATACCACTTGTA 58.215 37.500 0.00 0.00 0.00 2.41
390 459 0.620556 GGAGCCCTCCTGATGAACAA 59.379 55.000 7.08 0.00 46.16 2.83
419 488 7.174772 TGTTTATTGCAAGCTTCTCATGAACTA 59.825 33.333 4.94 0.00 0.00 2.24
448 517 5.240623 TGGTTGTTGTGCTTGTATCCTAAAG 59.759 40.000 0.00 0.00 0.00 1.85
451 520 4.069304 GTGGTTGTTGTGCTTGTATCCTA 58.931 43.478 0.00 0.00 0.00 2.94
455 524 3.550820 TCTGTGGTTGTTGTGCTTGTAT 58.449 40.909 0.00 0.00 0.00 2.29
498 568 6.071728 ACAAATTTGGAGTAAGCATCTTCTGG 60.072 38.462 21.74 0.00 0.00 3.86
534 607 1.683943 ACTTCAACACTGCTGCATGT 58.316 45.000 1.31 7.32 0.00 3.21
575 651 5.359009 TGAAGATGATGAATTTCTTCAGCCC 59.641 40.000 20.49 15.24 46.28 5.19
586 663 6.427242 CGATGAACTGGATGAAGATGATGAAT 59.573 38.462 0.00 0.00 0.00 2.57
587 664 5.756833 CGATGAACTGGATGAAGATGATGAA 59.243 40.000 0.00 0.00 0.00 2.57
588 665 5.295152 CGATGAACTGGATGAAGATGATGA 58.705 41.667 0.00 0.00 0.00 2.92
640 731 0.713883 CTTACACACGATCACACCGC 59.286 55.000 0.00 0.00 0.00 5.68
660 751 7.935755 TGACGAGCTTACCTACTACTATTACAT 59.064 37.037 0.00 0.00 0.00 2.29
662 753 7.721286 TGACGAGCTTACCTACTACTATTAC 57.279 40.000 0.00 0.00 0.00 1.89
665 756 6.355747 ACTTGACGAGCTTACCTACTACTAT 58.644 40.000 0.00 0.00 0.00 2.12
684 778 6.258354 TCTGATTACCTTGTACCCTACTTGA 58.742 40.000 0.00 0.00 0.00 3.02
707 801 3.485877 GGTTGCATGCGAGTATTGAGTTC 60.486 47.826 14.09 0.00 0.00 3.01
713 807 2.556189 TGTTTGGTTGCATGCGAGTATT 59.444 40.909 14.09 0.00 0.00 1.89
721 815 0.576328 GCACGTTGTTTGGTTGCATG 59.424 50.000 0.00 0.00 0.00 4.06
759 853 0.310543 TGTGTTTGGTTGCTCGCATC 59.689 50.000 0.00 0.00 0.00 3.91
806 901 6.484288 TCATTGGTTGTCAACATATCCTCTT 58.516 36.000 17.29 0.00 38.31 2.85
818 913 9.059260 CATCATCTATATGTTCATTGGTTGTCA 57.941 33.333 0.00 0.00 34.50 3.58
829 924 6.865205 GCAAAAAGCCCATCATCTATATGTTC 59.135 38.462 0.00 0.00 37.23 3.18
846 941 2.304751 AGCATATGCAGGCAAAAAGC 57.695 45.000 28.62 0.80 45.16 3.51
847 942 4.567959 GGTTAAGCATATGCAGGCAAAAAG 59.432 41.667 28.62 0.00 45.16 2.27
879 976 3.938963 CGTACTTTGCATACTTGTCCCAT 59.061 43.478 0.00 0.00 0.00 4.00
897 994 6.627671 GGATTTCTCGCATCAATTTTACGTAC 59.372 38.462 0.00 0.00 0.00 3.67
898 995 6.314152 TGGATTTCTCGCATCAATTTTACGTA 59.686 34.615 0.00 0.00 0.00 3.57
899 996 5.123186 TGGATTTCTCGCATCAATTTTACGT 59.877 36.000 0.00 0.00 0.00 3.57
900 997 5.568482 TGGATTTCTCGCATCAATTTTACG 58.432 37.500 0.00 0.00 0.00 3.18
901 998 6.806249 TGTTGGATTTCTCGCATCAATTTTAC 59.194 34.615 0.00 0.00 0.00 2.01
902 999 6.806249 GTGTTGGATTTCTCGCATCAATTTTA 59.194 34.615 0.00 0.00 0.00 1.52
903 1000 5.634859 GTGTTGGATTTCTCGCATCAATTTT 59.365 36.000 0.00 0.00 0.00 1.82
904 1001 5.163513 GTGTTGGATTTCTCGCATCAATTT 58.836 37.500 0.00 0.00 0.00 1.82
905 1002 4.380867 GGTGTTGGATTTCTCGCATCAATT 60.381 41.667 0.00 0.00 0.00 2.32
906 1003 3.129287 GGTGTTGGATTTCTCGCATCAAT 59.871 43.478 0.00 0.00 0.00 2.57
907 1004 2.487762 GGTGTTGGATTTCTCGCATCAA 59.512 45.455 0.00 0.00 0.00 2.57
908 1005 2.083774 GGTGTTGGATTTCTCGCATCA 58.916 47.619 0.00 0.00 0.00 3.07
909 1006 2.359900 AGGTGTTGGATTTCTCGCATC 58.640 47.619 0.00 0.00 0.00 3.91
910 1007 2.496899 AGGTGTTGGATTTCTCGCAT 57.503 45.000 0.00 0.00 0.00 4.73
911 1008 2.151202 GAAGGTGTTGGATTTCTCGCA 58.849 47.619 0.00 0.00 0.00 5.10
912 1009 2.427506 AGAAGGTGTTGGATTTCTCGC 58.572 47.619 0.00 0.00 0.00 5.03
913 1010 6.363626 CGATATAGAAGGTGTTGGATTTCTCG 59.636 42.308 0.00 0.00 32.54 4.04
914 1011 7.169982 CACGATATAGAAGGTGTTGGATTTCTC 59.830 40.741 0.00 0.00 32.54 2.87
915 1012 6.986817 CACGATATAGAAGGTGTTGGATTTCT 59.013 38.462 0.00 0.00 34.51 2.52
916 1013 6.984474 TCACGATATAGAAGGTGTTGGATTTC 59.016 38.462 0.00 0.00 0.00 2.17
917 1014 6.884832 TCACGATATAGAAGGTGTTGGATTT 58.115 36.000 0.00 0.00 0.00 2.17
918 1015 6.479972 TCACGATATAGAAGGTGTTGGATT 57.520 37.500 0.00 0.00 0.00 3.01
919 1016 6.672266 ATCACGATATAGAAGGTGTTGGAT 57.328 37.500 0.00 0.00 0.00 3.41
920 1017 6.776116 AGTATCACGATATAGAAGGTGTTGGA 59.224 38.462 0.00 0.00 0.00 3.53
921 1018 6.982852 AGTATCACGATATAGAAGGTGTTGG 58.017 40.000 0.00 0.00 0.00 3.77
929 1026 9.764870 GCACGTTAATAGTATCACGATATAGAA 57.235 33.333 17.44 0.00 36.48 2.10
930 1027 9.159364 AGCACGTTAATAGTATCACGATATAGA 57.841 33.333 17.44 0.00 36.48 1.98
935 1032 9.932699 GATATAGCACGTTAATAGTATCACGAT 57.067 33.333 17.44 6.81 36.48 3.73
936 1033 8.112449 CGATATAGCACGTTAATAGTATCACGA 58.888 37.037 17.44 1.01 36.48 4.35
937 1034 7.901889 ACGATATAGCACGTTAATAGTATCACG 59.098 37.037 11.47 11.47 39.75 4.35
938 1035 8.996933 CACGATATAGCACGTTAATAGTATCAC 58.003 37.037 0.00 0.00 40.76 3.06
939 1036 7.695201 GCACGATATAGCACGTTAATAGTATCA 59.305 37.037 0.00 0.00 40.76 2.15
940 1037 7.165483 GGCACGATATAGCACGTTAATAGTATC 59.835 40.741 0.00 0.00 40.76 2.24
941 1038 6.971184 GGCACGATATAGCACGTTAATAGTAT 59.029 38.462 0.00 0.00 40.76 2.12
942 1039 6.149973 AGGCACGATATAGCACGTTAATAGTA 59.850 38.462 0.00 0.00 40.76 1.82
943 1040 5.048224 AGGCACGATATAGCACGTTAATAGT 60.048 40.000 0.00 0.00 40.76 2.12
944 1041 5.399858 AGGCACGATATAGCACGTTAATAG 58.600 41.667 0.00 0.00 40.76 1.73
945 1042 5.381174 AGGCACGATATAGCACGTTAATA 57.619 39.130 0.00 0.00 40.76 0.98
946 1043 4.252971 AGGCACGATATAGCACGTTAAT 57.747 40.909 0.00 0.00 40.76 1.40
947 1044 3.720949 AGGCACGATATAGCACGTTAA 57.279 42.857 0.00 0.00 40.76 2.01
948 1045 5.381174 AATAGGCACGATATAGCACGTTA 57.619 39.130 0.00 0.00 40.76 3.18
949 1046 3.936372 ATAGGCACGATATAGCACGTT 57.064 42.857 0.00 0.00 40.76 3.99
950 1047 3.936372 AATAGGCACGATATAGCACGT 57.064 42.857 0.00 0.00 43.50 4.49
951 1048 5.591643 AAAAATAGGCACGATATAGCACG 57.408 39.130 0.00 0.00 0.00 5.34
970 1067 6.408320 CCATATGATTGGGCCAAGATCAAAAA 60.408 38.462 25.16 13.57 33.89 1.94
971 1068 5.070714 CCATATGATTGGGCCAAGATCAAAA 59.929 40.000 25.16 15.80 33.89 2.44
972 1069 4.589798 CCATATGATTGGGCCAAGATCAAA 59.410 41.667 25.16 8.09 33.89 2.69
973 1070 4.154176 CCATATGATTGGGCCAAGATCAA 58.846 43.478 25.16 14.11 33.89 2.57
1006 1103 7.883311 GCCTATATATAAACACAATGGAGTGGT 59.117 37.037 0.00 0.00 42.26 4.16
1070 1179 3.642141 ACCATTTTGGACAGGAACTTGT 58.358 40.909 0.00 0.00 40.96 3.16
1090 1199 2.292845 GCACTAGGACTATGACCGGTAC 59.707 54.545 7.34 1.38 0.00 3.34
1146 1255 1.070601 CATGAGGCGGTGATCCATACA 59.929 52.381 0.00 0.00 0.00 2.29
1239 1348 1.100510 CATGGAGGTTACCGACGAGA 58.899 55.000 0.00 0.00 0.00 4.04
1361 1470 2.847234 TGGCCCACTGACCGAACT 60.847 61.111 0.00 0.00 0.00 3.01
1369 1478 2.102070 TTAACATACGTGGCCCACTG 57.898 50.000 12.94 6.17 31.34 3.66
1410 1519 4.335647 CAGACTTGGCAGGCGGGT 62.336 66.667 0.00 0.00 30.31 5.28
1416 1525 1.079543 CTCCGGTCAGACTTGGCAG 60.080 63.158 0.00 0.32 0.00 4.85
1419 1528 1.216710 GAGCTCCGGTCAGACTTGG 59.783 63.158 0.87 3.33 0.00 3.61
1442 1551 2.239654 CAACCTCCCTGCAGATAGGAAA 59.760 50.000 30.14 5.33 40.42 3.13
1461 1570 1.541147 CCCGTACCAGTAGACGAACAA 59.459 52.381 0.00 0.00 41.60 2.83
1513 1622 4.783621 GCAGCTCCCGCACCATGA 62.784 66.667 0.00 0.00 39.10 3.07
1673 1782 1.073722 CCTGCCCTTGAGCTTGTCA 59.926 57.895 0.00 0.00 0.00 3.58
1865 1974 1.028868 GCCGCTGAAGCTCCTCAATT 61.029 55.000 0.10 0.00 39.32 2.32
1868 1977 2.999648 AGCCGCTGAAGCTCCTCA 61.000 61.111 0.00 0.00 34.91 3.86
1922 2031 4.824479 TTGATTGATGACTCACTGGCTA 57.176 40.909 0.00 0.00 0.00 3.93
1942 2051 6.916360 ATAATTTGTGGTGAGGTGATGTTT 57.084 33.333 0.00 0.00 0.00 2.83
1998 2111 1.848388 AGGAATGCAGGATCACCATGA 59.152 47.619 0.00 0.00 38.94 3.07
2046 2159 5.998981 TGCAGAGTAAATAAAAACGAAGGGA 59.001 36.000 0.00 0.00 0.00 4.20
2065 2178 7.175347 ACTTCAGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
2066 2179 7.462109 GACTTCAGTCAACTCTAATATGCAG 57.538 40.000 1.86 0.00 44.18 4.41
2233 2348 9.634163 AGTCAAACTTTACAAACTTTAACCAAG 57.366 29.630 0.00 0.00 38.64 3.61
2234 2349 9.628746 GAGTCAAACTTTACAAACTTTAACCAA 57.371 29.630 0.00 0.00 0.00 3.67
2235 2350 9.016438 AGAGTCAAACTTTACAAACTTTAACCA 57.984 29.630 0.00 0.00 0.00 3.67
2236 2351 9.285770 CAGAGTCAAACTTTACAAACTTTAACC 57.714 33.333 0.00 0.00 0.00 2.85
2239 2354 8.671028 GGTCAGAGTCAAACTTTACAAACTTTA 58.329 33.333 0.00 0.00 0.00 1.85
2240 2355 7.175990 TGGTCAGAGTCAAACTTTACAAACTTT 59.824 33.333 0.00 0.00 0.00 2.66
2241 2356 6.657541 TGGTCAGAGTCAAACTTTACAAACTT 59.342 34.615 0.00 0.00 0.00 2.66
2242 2357 6.177610 TGGTCAGAGTCAAACTTTACAAACT 58.822 36.000 0.00 0.00 0.00 2.66
2243 2358 6.431198 TGGTCAGAGTCAAACTTTACAAAC 57.569 37.500 0.00 0.00 0.00 2.93
2244 2359 7.455641 TTTGGTCAGAGTCAAACTTTACAAA 57.544 32.000 0.00 0.00 0.00 2.83
2245 2360 6.404293 GCTTTGGTCAGAGTCAAACTTTACAA 60.404 38.462 0.00 0.00 0.00 2.41
2246 2361 5.065988 GCTTTGGTCAGAGTCAAACTTTACA 59.934 40.000 0.00 0.00 0.00 2.41
2247 2362 5.297029 AGCTTTGGTCAGAGTCAAACTTTAC 59.703 40.000 0.00 0.00 0.00 2.01
2248 2363 5.437060 AGCTTTGGTCAGAGTCAAACTTTA 58.563 37.500 0.00 0.00 0.00 1.85
2249 2364 4.273318 AGCTTTGGTCAGAGTCAAACTTT 58.727 39.130 0.00 0.00 0.00 2.66
2250 2365 3.891049 AGCTTTGGTCAGAGTCAAACTT 58.109 40.909 0.00 0.00 0.00 2.66
2251 2366 3.567478 AGCTTTGGTCAGAGTCAAACT 57.433 42.857 0.00 0.00 0.00 2.66
2252 2367 5.948992 ATTAGCTTTGGTCAGAGTCAAAC 57.051 39.130 0.00 0.00 0.00 2.93
2253 2368 6.094048 GCATATTAGCTTTGGTCAGAGTCAAA 59.906 38.462 0.00 0.00 0.00 2.69
2254 2369 5.586243 GCATATTAGCTTTGGTCAGAGTCAA 59.414 40.000 0.00 0.00 0.00 3.18
2255 2370 5.118990 GCATATTAGCTTTGGTCAGAGTCA 58.881 41.667 0.00 0.00 0.00 3.41
2256 2371 4.210120 CGCATATTAGCTTTGGTCAGAGTC 59.790 45.833 0.00 0.00 0.00 3.36
2257 2372 4.122776 CGCATATTAGCTTTGGTCAGAGT 58.877 43.478 0.00 0.00 0.00 3.24
2258 2373 4.371786 TCGCATATTAGCTTTGGTCAGAG 58.628 43.478 0.00 0.00 0.00 3.35
2259 2374 4.400529 TCGCATATTAGCTTTGGTCAGA 57.599 40.909 0.00 0.00 0.00 3.27
2260 2375 4.572389 AGTTCGCATATTAGCTTTGGTCAG 59.428 41.667 0.00 0.00 0.00 3.51
2261 2376 4.513442 AGTTCGCATATTAGCTTTGGTCA 58.487 39.130 0.00 0.00 0.00 4.02
2262 2377 6.598753 TTAGTTCGCATATTAGCTTTGGTC 57.401 37.500 0.00 0.00 0.00 4.02
2263 2378 6.995511 TTTAGTTCGCATATTAGCTTTGGT 57.004 33.333 0.00 0.00 0.00 3.67
2264 2379 9.944663 TTTATTTAGTTCGCATATTAGCTTTGG 57.055 29.630 0.00 0.00 0.00 3.28
2273 2388 9.581099 CCCTTTGTTTTTATTTAGTTCGCATAT 57.419 29.630 0.00 0.00 0.00 1.78
2274 2389 8.794553 TCCCTTTGTTTTTATTTAGTTCGCATA 58.205 29.630 0.00 0.00 0.00 3.14
2275 2390 7.662897 TCCCTTTGTTTTTATTTAGTTCGCAT 58.337 30.769 0.00 0.00 0.00 4.73
2276 2391 7.040473 TCCCTTTGTTTTTATTTAGTTCGCA 57.960 32.000 0.00 0.00 0.00 5.10
2277 2392 7.143340 ACTCCCTTTGTTTTTATTTAGTTCGC 58.857 34.615 0.00 0.00 0.00 4.70
2278 2393 9.603298 GTACTCCCTTTGTTTTTATTTAGTTCG 57.397 33.333 0.00 0.00 0.00 3.95
2284 2399 7.720957 ACCGTAGTACTCCCTTTGTTTTTATTT 59.279 33.333 0.00 0.00 0.00 1.40
2287 2402 6.173427 ACCGTAGTACTCCCTTTGTTTTTA 57.827 37.500 0.00 0.00 0.00 1.52
2289 2404 4.694760 ACCGTAGTACTCCCTTTGTTTT 57.305 40.909 0.00 0.00 0.00 2.43
2707 3084 2.506345 GCTTACGACGGCGAGCTTC 61.506 63.158 22.49 0.00 41.64 3.86
2729 3106 1.595328 CATGTGTTTCGACGGTGTCAA 59.405 47.619 0.00 0.00 32.09 3.18
2770 3148 3.863396 TCCACGTGTTAAACATTGACG 57.137 42.857 15.65 0.00 0.00 4.35
2927 3310 2.940467 TGGATGGCCAGCAAGGGA 60.940 61.111 24.75 0.00 39.92 4.20
3245 3628 2.828145 GCTGCCAAAAGCCCCAAA 59.172 55.556 0.00 0.00 42.71 3.28
3246 3629 2.985539 TACGCTGCCAAAAGCCCCAA 62.986 55.000 0.00 0.00 42.71 4.12
3247 3630 3.499461 TACGCTGCCAAAAGCCCCA 62.499 57.895 0.00 0.00 42.71 4.96
3248 3631 2.675075 TACGCTGCCAAAAGCCCC 60.675 61.111 0.00 0.00 42.71 5.80
3249 3632 1.923227 GAGTACGCTGCCAAAAGCCC 61.923 60.000 0.00 0.00 42.71 5.19
3250 3633 1.502190 GAGTACGCTGCCAAAAGCC 59.498 57.895 0.00 0.00 42.71 4.35
3251 3634 1.132640 CGAGTACGCTGCCAAAAGC 59.867 57.895 0.00 0.00 44.14 3.51
3320 3713 1.277326 TCATTCCGAATCGAAGCACG 58.723 50.000 3.36 0.00 44.09 5.34
3344 3737 7.078851 CGCCACTTTCTACATAGATACTACAG 58.921 42.308 0.00 0.00 31.40 2.74
3345 3738 6.016527 CCGCCACTTTCTACATAGATACTACA 60.017 42.308 0.00 0.00 31.40 2.74
3346 3739 6.206243 TCCGCCACTTTCTACATAGATACTAC 59.794 42.308 0.00 0.00 31.40 2.73
3349 3742 5.449107 TCCGCCACTTTCTACATAGATAC 57.551 43.478 0.00 0.00 31.40 2.24
3351 3744 3.322254 CCTCCGCCACTTTCTACATAGAT 59.678 47.826 0.00 0.00 31.40 1.98
3358 3751 0.609957 TCGTCCTCCGCCACTTTCTA 60.610 55.000 0.00 0.00 36.19 2.10
3361 3754 0.179040 TTTTCGTCCTCCGCCACTTT 60.179 50.000 0.00 0.00 36.19 2.66
3362 3755 0.179040 TTTTTCGTCCTCCGCCACTT 60.179 50.000 0.00 0.00 36.19 3.16
3396 3789 0.322975 ACATCAGCCTGTGAGTCCAC 59.677 55.000 0.00 0.00 39.07 4.02
3397 3790 2.764007 ACATCAGCCTGTGAGTCCA 58.236 52.632 0.00 0.00 39.07 4.02
3403 3796 0.607217 TTGCTCCACATCAGCCTGTG 60.607 55.000 5.02 5.02 44.92 3.66
3404 3797 0.111061 TTTGCTCCACATCAGCCTGT 59.889 50.000 0.00 0.00 35.89 4.00
3405 3798 0.524862 GTTTGCTCCACATCAGCCTG 59.475 55.000 0.00 0.00 35.89 4.85
3406 3799 0.403271 AGTTTGCTCCACATCAGCCT 59.597 50.000 0.00 0.00 35.89 4.58
3407 3800 2.113860 TAGTTTGCTCCACATCAGCC 57.886 50.000 0.00 0.00 35.89 4.85
3408 3801 4.708726 ATTTAGTTTGCTCCACATCAGC 57.291 40.909 0.00 0.00 37.40 4.26
3409 3802 7.951530 AAAAATTTAGTTTGCTCCACATCAG 57.048 32.000 0.00 0.00 0.00 2.90
3802 4197 4.415150 CACCCCAGCAGCACGGAT 62.415 66.667 2.38 0.00 0.00 4.18
4041 4438 0.036164 TACAGCTGTGGCGATTTGGT 59.964 50.000 29.57 0.00 44.37 3.67
4074 4471 0.911769 CATGAGGCTCAACCAGGGTA 59.088 55.000 22.84 0.00 43.14 3.69
4156 4553 0.528033 CAGTGCCGAGAGATGAGCTG 60.528 60.000 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.