Multiple sequence alignment - TraesCS1A01G331800

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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 TraesCS1A01G331800 chr1A 100.000 5433 0 0 1 5433 520569276 520574708 0.000000e+00 10033.0
1 TraesCS1A01G331800 chr1A 92.708 96 4 2 2252 2344 241914879 241914974 9.490000e-28 135.0
2 TraesCS1A01G331800 chr1A 92.708 96 4 2 2252 2344 369167916 369168011 9.490000e-28 135.0
3 TraesCS1A01G331800 chr1D 94.429 2208 89 21 2342 4538 424729236 424731420 0.000000e+00 3365.0
4 TraesCS1A01G331800 chr1D 91.128 2288 77 53 1 2254 424727038 424729233 0.000000e+00 2985.0
5 TraesCS1A01G331800 chr1D 84.605 734 53 32 4619 5336 424731445 424732134 0.000000e+00 675.0
6 TraesCS1A01G331800 chr1B 89.736 2309 87 70 1 2254 573857669 573859882 0.000000e+00 2813.0
7 TraesCS1A01G331800 chr1B 92.949 1404 68 20 3518 4915 573861014 573862392 0.000000e+00 2015.0
8 TraesCS1A01G331800 chr1B 94.384 1104 57 3 2342 3444 573859885 573860984 0.000000e+00 1690.0
9 TraesCS1A01G331800 chr1B 88.718 390 24 7 4995 5368 573862438 573862823 4.960000e-125 459.0
10 TraesCS1A01G331800 chr1B 95.238 42 2 0 5392 5433 599243562 599243603 3.510000e-07 67.6
11 TraesCS1A01G331800 chr3B 81.972 649 107 9 3790 4433 543467857 543467214 4.790000e-150 542.0
12 TraesCS1A01G331800 chr3B 76.638 946 184 27 2436 3368 543469452 543468531 6.330000e-134 488.0
13 TraesCS1A01G331800 chr3B 76.000 750 97 38 1052 1767 543470781 543470081 1.470000e-80 311.0
14 TraesCS1A01G331800 chr3B 81.150 313 57 2 3804 4115 665444 665755 3.250000e-62 250.0
15 TraesCS1A01G331800 chr3D 81.202 649 112 9 3790 4433 417160810 417160167 1.040000e-141 514.0
16 TraesCS1A01G331800 chr3D 76.874 947 179 26 2436 3368 417162369 417161449 2.920000e-137 499.0
17 TraesCS1A01G331800 chr3D 77.019 644 83 35 1052 1679 417163870 417163276 5.290000e-80 309.0
18 TraesCS1A01G331800 chr3D 74.382 445 91 19 2938 3366 535744413 535744850 9.360000e-38 169.0
19 TraesCS1A01G331800 chr3A 81.202 649 112 10 3787 4433 533661709 533662349 1.040000e-141 514.0
20 TraesCS1A01G331800 chr3A 78.679 530 95 12 2849 3368 533660528 533661049 2.420000e-88 337.0
21 TraesCS1A01G331800 chr3A 86.802 197 22 3 1484 1678 533659018 533659212 3.300000e-52 217.0
22 TraesCS1A01G331800 chr3A 81.439 264 33 9 1052 1314 533658610 533658858 9.230000e-48 202.0
23 TraesCS1A01G331800 chr3A 92.708 96 4 2 2252 2344 441498556 441498461 9.490000e-28 135.0
24 TraesCS1A01G331800 chr5D 79.881 671 119 12 3775 4433 478163970 478163304 1.370000e-130 477.0
25 TraesCS1A01G331800 chr5D 74.760 416 69 23 1048 1429 478166309 478165896 2.620000e-33 154.0
26 TraesCS1A01G331800 chr5D 90.476 105 5 4 2260 2361 448145014 448145116 3.410000e-27 134.0
27 TraesCS1A01G331800 chr5A 80.526 647 104 16 3804 4433 597290118 597289477 1.370000e-130 477.0
28 TraesCS1A01G331800 chr5A 75.802 405 72 19 1048 1429 597292367 597291966 1.200000e-41 182.0
29 TraesCS1A01G331800 chr5B 79.851 670 111 19 3783 4433 585752606 585751942 8.240000e-128 468.0
30 TraesCS1A01G331800 chr5B 74.519 416 70 22 1048 1429 585754845 585754432 1.220000e-31 148.0
31 TraesCS1A01G331800 chr4B 85.371 458 15 17 765 1211 628227110 628227526 1.400000e-115 427.0
32 TraesCS1A01G331800 chr4B 84.279 458 20 18 765 1211 628257580 628257996 3.050000e-107 399.0
33 TraesCS1A01G331800 chr4B 100.000 28 0 0 1176 1203 628227074 628227047 1.000000e-02 52.8
34 TraesCS1A01G331800 chr4B 100.000 28 0 0 1176 1203 628257544 628257517 1.000000e-02 52.8
35 TraesCS1A01G331800 chr4A 74.376 441 92 17 2941 3366 741259136 741258702 9.360000e-38 169.0
36 TraesCS1A01G331800 chr4A 94.118 51 1 2 5381 5430 696105632 696105583 5.840000e-10 76.8
37 TraesCS1A01G331800 chr4A 94.444 36 2 0 5392 5427 668234145 668234180 7.600000e-04 56.5
38 TraesCS1A01G331800 chr4A 96.875 32 1 0 5396 5427 668183812 668183843 3.000000e-03 54.7
39 TraesCS1A01G331800 chr4A 96.875 32 1 0 5396 5427 668191693 668191724 3.000000e-03 54.7
40 TraesCS1A01G331800 chr4A 96.875 32 1 0 5396 5427 668210596 668210627 3.000000e-03 54.7
41 TraesCS1A01G331800 chrUn 74.023 435 92 17 2947 3366 221213140 221213568 2.030000e-34 158.0
42 TraesCS1A01G331800 chrUn 92.982 57 3 1 5378 5433 316546243 316546187 1.250000e-11 82.4
43 TraesCS1A01G331800 chr7A 93.684 95 3 2 2258 2350 94450200 94450107 7.340000e-29 139.0
44 TraesCS1A01G331800 chr7A 92.708 96 4 2 2252 2344 81178185 81178090 9.490000e-28 135.0
45 TraesCS1A01G331800 chr7A 83.846 130 14 6 2221 2348 5487174 5487298 3.440000e-22 117.0
46 TraesCS1A01G331800 chr6A 95.455 88 2 1 2258 2343 548412701 548412788 7.340000e-29 139.0
47 TraesCS1A01G331800 chr2A 92.708 96 3 3 2252 2344 235516624 235516530 9.490000e-28 135.0
48 TraesCS1A01G331800 chr2A 97.059 34 1 0 5400 5433 714645503 714645470 2.110000e-04 58.4
49 TraesCS1A01G331800 chr6B 86.154 65 8 1 5370 5433 404376043 404375979 9.760000e-08 69.4


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 TraesCS1A01G331800 chr1A 520569276 520574708 5432 False 10033.000000 10033 100.000000 1 5433 1 chr1A.!!$F3 5432
1 TraesCS1A01G331800 chr1D 424727038 424732134 5096 False 2341.666667 3365 90.054000 1 5336 3 chr1D.!!$F1 5335
2 TraesCS1A01G331800 chr1B 573857669 573862823 5154 False 1744.250000 2813 91.446750 1 5368 4 chr1B.!!$F2 5367
3 TraesCS1A01G331800 chr3B 543467214 543470781 3567 True 447.000000 542 78.203333 1052 4433 3 chr3B.!!$R1 3381
4 TraesCS1A01G331800 chr3D 417160167 417163870 3703 True 440.666667 514 78.365000 1052 4433 3 chr3D.!!$R1 3381
5 TraesCS1A01G331800 chr3A 533658610 533662349 3739 False 317.500000 514 82.030500 1052 4433 4 chr3A.!!$F1 3381
6 TraesCS1A01G331800 chr5D 478163304 478166309 3005 True 315.500000 477 77.320500 1048 4433 2 chr5D.!!$R1 3385
7 TraesCS1A01G331800 chr5A 597289477 597292367 2890 True 329.500000 477 78.164000 1048 4433 2 chr5A.!!$R1 3385
8 TraesCS1A01G331800 chr5B 585751942 585754845 2903 True 308.000000 468 77.185000 1048 4433 2 chr5B.!!$R1 3385

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
476 505 0.103208 ACGTTGATCTCATCTCGCCC 59.897 55.0 0.0 0.0 33.40 6.13 F
1873 2659 0.043940 AGAGTGGGGGAAGATGCTCT 59.956 55.0 0.0 0.0 0.00 4.09 F
1955 2741 0.034059 AGCTCTCCAACCACAACTCG 59.966 55.0 0.0 0.0 0.00 4.18 F
1963 2750 0.670546 AACCACAACTCGGATGCTCG 60.671 55.0 0.0 0.0 0.00 5.03 F
3686 4691 0.254462 TCCATGCCGGCACATCTTTA 59.746 50.0 35.5 6.2 33.14 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2663 0.107017 CCGAATCCCCAGAATGCAGT 60.107 55.000 0.00 0.00 31.97 4.40 R
3668 4621 0.664761 CTAAAGATGTGCCGGCATGG 59.335 55.000 35.23 13.96 42.50 3.66 R
3673 4626 5.360591 AGATAAGAACTAAAGATGTGCCGG 58.639 41.667 0.00 0.00 0.00 6.13 R
3741 5032 6.153340 AGGCCAATTATCCATACATGCATTAC 59.847 38.462 5.01 0.00 0.00 1.89 R
5348 7047 0.586802 GAACTGGACGACAAGGCAAC 59.413 55.000 0.00 0.00 0.00 4.17 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
47 48 4.642437 TGTCCATTTGTCTGTTTAGTTGCA 59.358 37.500 0.00 0.00 0.00 4.08
48 49 5.215160 GTCCATTTGTCTGTTTAGTTGCAG 58.785 41.667 0.00 0.00 0.00 4.41
67 68 3.057174 GCAGAGATACTAATCCTGTCCCG 60.057 52.174 0.00 0.00 34.99 5.14
121 122 6.146898 CCTTTTGTTGTTTACCACGGATTAG 58.853 40.000 0.00 0.00 0.00 1.73
122 123 6.238814 CCTTTTGTTGTTTACCACGGATTAGT 60.239 38.462 0.00 0.00 0.00 2.24
123 124 7.041235 CCTTTTGTTGTTTACCACGGATTAGTA 60.041 37.037 0.00 0.00 0.00 1.82
245 252 2.978010 CGTAATCCGCCCCCATGC 60.978 66.667 0.00 0.00 0.00 4.06
246 253 2.194597 GTAATCCGCCCCCATGCA 59.805 61.111 0.00 0.00 0.00 3.96
476 505 0.103208 ACGTTGATCTCATCTCGCCC 59.897 55.000 0.00 0.00 33.40 6.13
477 506 0.936764 CGTTGATCTCATCTCGCCCG 60.937 60.000 0.00 0.00 0.00 6.13
478 507 1.068083 TTGATCTCATCTCGCCCGC 59.932 57.895 0.00 0.00 0.00 6.13
479 508 2.048690 GATCTCATCTCGCCCGCC 60.049 66.667 0.00 0.00 0.00 6.13
480 509 2.839632 ATCTCATCTCGCCCGCCA 60.840 61.111 0.00 0.00 0.00 5.69
492 521 4.878878 CCGCCAGGGAGGAAATAC 57.121 61.111 1.29 0.00 41.22 1.89
493 522 1.912220 CCGCCAGGGAGGAAATACA 59.088 57.895 1.29 0.00 41.22 2.29
494 523 0.463833 CCGCCAGGGAGGAAATACAC 60.464 60.000 1.29 0.00 41.22 2.90
495 524 0.810031 CGCCAGGGAGGAAATACACG 60.810 60.000 0.00 0.00 41.22 4.49
496 525 0.463833 GCCAGGGAGGAAATACACGG 60.464 60.000 0.00 0.00 41.22 4.94
497 526 0.463833 CCAGGGAGGAAATACACGGC 60.464 60.000 0.00 0.00 41.22 5.68
498 527 0.810031 CAGGGAGGAAATACACGGCG 60.810 60.000 4.80 4.80 0.00 6.46
499 528 0.974010 AGGGAGGAAATACACGGCGA 60.974 55.000 16.62 0.00 0.00 5.54
500 529 0.106149 GGGAGGAAATACACGGCGAT 59.894 55.000 16.62 3.31 0.00 4.58
501 530 1.499049 GGAGGAAATACACGGCGATC 58.501 55.000 16.62 1.44 0.00 3.69
502 531 1.068741 GGAGGAAATACACGGCGATCT 59.931 52.381 16.62 0.00 0.00 2.75
503 532 2.395654 GAGGAAATACACGGCGATCTC 58.604 52.381 16.62 4.53 0.00 2.75
504 533 1.129326 GGAAATACACGGCGATCTCG 58.871 55.000 16.62 0.00 43.27 4.04
505 534 1.129326 GAAATACACGGCGATCTCGG 58.871 55.000 16.62 0.00 40.23 4.63
570 599 1.860078 CTGCTCGTTTCGGTTCACC 59.140 57.895 0.00 0.00 0.00 4.02
571 600 0.600255 CTGCTCGTTTCGGTTCACCT 60.600 55.000 0.00 0.00 0.00 4.00
572 601 0.179067 TGCTCGTTTCGGTTCACCTT 60.179 50.000 0.00 0.00 0.00 3.50
573 602 0.234884 GCTCGTTTCGGTTCACCTTG 59.765 55.000 0.00 0.00 0.00 3.61
574 603 1.860676 CTCGTTTCGGTTCACCTTGA 58.139 50.000 0.00 0.00 0.00 3.02
731 779 1.469308 GGAGCTCGTATCGTATCCTGG 59.531 57.143 7.83 0.00 0.00 4.45
732 780 2.424557 GAGCTCGTATCGTATCCTGGA 58.575 52.381 0.00 0.00 0.00 3.86
733 781 2.152830 AGCTCGTATCGTATCCTGGAC 58.847 52.381 0.00 0.00 0.00 4.02
734 782 1.199558 GCTCGTATCGTATCCTGGACC 59.800 57.143 0.00 0.00 0.00 4.46
735 783 2.780714 CTCGTATCGTATCCTGGACCT 58.219 52.381 0.00 0.00 0.00 3.85
736 784 2.484651 CTCGTATCGTATCCTGGACCTG 59.515 54.545 0.00 0.00 0.00 4.00
778 826 1.376037 GGTGAGCTGTTCTTCCCCG 60.376 63.158 0.00 0.00 0.00 5.73
837 885 2.681778 CTCTGGCGGGTGTCTCCT 60.682 66.667 0.00 0.00 36.25 3.69
838 886 2.680352 TCTGGCGGGTGTCTCCTC 60.680 66.667 0.00 0.00 36.25 3.71
840 888 4.631740 TGGCGGGTGTCTCCTCCA 62.632 66.667 0.00 0.00 36.82 3.86
845 893 1.229209 GGGTGTCTCCTCCAGTCCA 60.229 63.158 0.00 0.00 36.25 4.02
846 894 1.261238 GGGTGTCTCCTCCAGTCCAG 61.261 65.000 0.00 0.00 36.25 3.86
899 949 0.600255 CTATGAGCGGGTAAAGCGGG 60.600 60.000 0.00 0.00 40.04 6.13
906 956 3.777910 GGTAAAGCGGGGCCGAGA 61.778 66.667 0.00 0.00 42.83 4.04
944 996 4.335647 CTTCGTGGGCTGCCTGGT 62.336 66.667 19.68 0.00 0.00 4.00
945 997 3.850098 CTTCGTGGGCTGCCTGGTT 62.850 63.158 19.68 0.00 0.00 3.67
946 998 4.641645 TCGTGGGCTGCCTGGTTG 62.642 66.667 19.68 4.72 0.00 3.77
947 999 4.641645 CGTGGGCTGCCTGGTTGA 62.642 66.667 19.68 0.00 0.00 3.18
948 1000 2.674380 GTGGGCTGCCTGGTTGAG 60.674 66.667 19.68 0.00 0.00 3.02
952 1004 2.045536 GCTGCCTGGTTGAGGAGG 60.046 66.667 0.00 0.00 46.33 4.30
978 1030 2.358860 CTGCTGCTGCTGCTGTCT 60.359 61.111 27.67 0.00 39.81 3.41
979 1031 2.668550 TGCTGCTGCTGCTGTCTG 60.669 61.111 27.67 6.08 39.81 3.51
981 1033 3.432588 CTGCTGCTGCTGTCTGCC 61.433 66.667 17.00 0.00 42.00 4.85
1772 1939 3.320541 CGAGAGGTAAGCTCCAATCATCT 59.679 47.826 0.00 0.00 0.00 2.90
1773 1940 4.630111 GAGAGGTAAGCTCCAATCATCTG 58.370 47.826 0.00 0.00 0.00 2.90
1775 1942 2.158696 AGGTAAGCTCCAATCATCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
1776 1943 2.225467 GTAAGCTCCAATCATCTGCCC 58.775 52.381 0.00 0.00 0.00 5.36
1825 2108 2.279120 GGAGCTCCACGATGCGAG 60.279 66.667 28.43 0.00 35.64 5.03
1872 2658 1.414550 GTAGAGTGGGGGAAGATGCTC 59.585 57.143 0.00 0.00 0.00 4.26
1873 2659 0.043940 AGAGTGGGGGAAGATGCTCT 59.956 55.000 0.00 0.00 0.00 4.09
1875 2661 0.043940 AGTGGGGGAAGATGCTCTCT 59.956 55.000 0.00 0.00 34.96 3.10
1876 2662 0.179936 GTGGGGGAAGATGCTCTCTG 59.820 60.000 0.00 0.00 33.29 3.35
1877 2663 0.043183 TGGGGGAAGATGCTCTCTGA 59.957 55.000 0.00 0.00 33.29 3.27
1878 2664 0.467804 GGGGGAAGATGCTCTCTGAC 59.532 60.000 0.00 0.00 33.29 3.51
1879 2665 1.494960 GGGGAAGATGCTCTCTGACT 58.505 55.000 0.00 0.00 33.29 3.41
1880 2666 1.138661 GGGGAAGATGCTCTCTGACTG 59.861 57.143 0.00 0.00 33.29 3.51
1881 2667 1.473080 GGGAAGATGCTCTCTGACTGC 60.473 57.143 0.00 0.00 33.29 4.40
1882 2668 1.206610 GGAAGATGCTCTCTGACTGCA 59.793 52.381 2.93 2.93 41.13 4.41
1955 2741 0.034059 AGCTCTCCAACCACAACTCG 59.966 55.000 0.00 0.00 0.00 4.18
1963 2750 0.670546 AACCACAACTCGGATGCTCG 60.671 55.000 0.00 0.00 0.00 5.03
1964 2751 2.456119 CCACAACTCGGATGCTCGC 61.456 63.158 0.00 0.00 0.00 5.03
1965 2752 1.446792 CACAACTCGGATGCTCGCT 60.447 57.895 0.00 0.00 0.00 4.93
1966 2753 1.153745 ACAACTCGGATGCTCGCTC 60.154 57.895 0.00 0.00 0.00 5.03
2095 2882 8.920665 CATATCATCTCTACTTTCTTTAAGGCG 58.079 37.037 0.00 0.00 38.23 5.52
2127 2914 4.985538 TCCAAATCTCGGACTAGAAGTC 57.014 45.455 0.00 0.00 44.32 3.01
2182 2969 3.201487 AGGCATGTGATTGGAGATCAAGA 59.799 43.478 0.00 0.00 38.95 3.02
2197 2984 6.416631 AGATCAAGATGTCAAGCTATAGCA 57.583 37.500 26.07 5.82 45.16 3.49
2198 2985 6.824553 AGATCAAGATGTCAAGCTATAGCAA 58.175 36.000 26.07 8.80 45.16 3.91
2199 2986 6.705381 AGATCAAGATGTCAAGCTATAGCAAC 59.295 38.462 26.07 19.49 45.16 4.17
2234 3023 4.571176 GGGAAGTGGCTAAGAAAAGATACG 59.429 45.833 0.00 0.00 0.00 3.06
2257 3051 8.603242 ACGTACTAAAATTCAATCAACTGTCT 57.397 30.769 0.00 0.00 0.00 3.41
2258 3052 9.701098 ACGTACTAAAATTCAATCAACTGTCTA 57.299 29.630 0.00 0.00 0.00 2.59
2259 3053 9.953825 CGTACTAAAATTCAATCAACTGTCTAC 57.046 33.333 0.00 0.00 0.00 2.59
2265 3059 8.779354 AAATTCAATCAACTGTCTACTACTCC 57.221 34.615 0.00 0.00 0.00 3.85
2266 3060 5.916661 TCAATCAACTGTCTACTACTCCC 57.083 43.478 0.00 0.00 0.00 4.30
2267 3061 5.580998 TCAATCAACTGTCTACTACTCCCT 58.419 41.667 0.00 0.00 0.00 4.20
2268 3062 5.652891 TCAATCAACTGTCTACTACTCCCTC 59.347 44.000 0.00 0.00 0.00 4.30
2269 3063 4.931027 TCAACTGTCTACTACTCCCTCT 57.069 45.455 0.00 0.00 0.00 3.69
2270 3064 4.590918 TCAACTGTCTACTACTCCCTCTG 58.409 47.826 0.00 0.00 0.00 3.35
2271 3065 4.043059 TCAACTGTCTACTACTCCCTCTGT 59.957 45.833 0.00 0.00 0.00 3.41
2272 3066 4.224991 ACTGTCTACTACTCCCTCTGTC 57.775 50.000 0.00 0.00 0.00 3.51
2273 3067 3.054213 ACTGTCTACTACTCCCTCTGTCC 60.054 52.174 0.00 0.00 0.00 4.02
2274 3068 2.241685 TGTCTACTACTCCCTCTGTCCC 59.758 54.545 0.00 0.00 0.00 4.46
2275 3069 2.241685 GTCTACTACTCCCTCTGTCCCA 59.758 54.545 0.00 0.00 0.00 4.37
2276 3070 2.510382 TCTACTACTCCCTCTGTCCCAG 59.490 54.545 0.00 0.00 0.00 4.45
2277 3071 1.085715 ACTACTCCCTCTGTCCCAGT 58.914 55.000 0.00 0.00 32.61 4.00
2278 3072 2.285707 ACTACTCCCTCTGTCCCAGTA 58.714 52.381 0.00 0.00 32.61 2.74
2279 3073 2.860041 ACTACTCCCTCTGTCCCAGTAT 59.140 50.000 0.00 0.00 32.61 2.12
2280 3074 4.052922 ACTACTCCCTCTGTCCCAGTATA 58.947 47.826 0.00 0.00 32.61 1.47
2281 3075 4.481280 ACTACTCCCTCTGTCCCAGTATAA 59.519 45.833 0.00 0.00 32.61 0.98
2282 3076 3.917300 ACTCCCTCTGTCCCAGTATAAG 58.083 50.000 0.00 0.00 32.61 1.73
2283 3077 3.532232 ACTCCCTCTGTCCCAGTATAAGA 59.468 47.826 0.00 0.00 32.61 2.10
2284 3078 4.016479 ACTCCCTCTGTCCCAGTATAAGAA 60.016 45.833 0.00 0.00 32.61 2.52
2285 3079 4.287552 TCCCTCTGTCCCAGTATAAGAAC 58.712 47.826 0.00 0.00 32.61 3.01
2286 3080 4.030913 CCCTCTGTCCCAGTATAAGAACA 58.969 47.826 0.00 0.00 32.61 3.18
2287 3081 4.656112 CCCTCTGTCCCAGTATAAGAACAT 59.344 45.833 0.00 0.00 32.61 2.71
2288 3082 5.131142 CCCTCTGTCCCAGTATAAGAACATT 59.869 44.000 0.00 0.00 32.61 2.71
2289 3083 6.353082 CCCTCTGTCCCAGTATAAGAACATTT 60.353 42.308 0.00 0.00 32.61 2.32
2290 3084 7.112779 CCTCTGTCCCAGTATAAGAACATTTT 58.887 38.462 0.00 0.00 32.61 1.82
2291 3085 7.611855 CCTCTGTCCCAGTATAAGAACATTTTT 59.388 37.037 0.00 0.00 32.61 1.94
2292 3086 8.335532 TCTGTCCCAGTATAAGAACATTTTTG 57.664 34.615 0.00 0.00 32.61 2.44
2293 3087 8.160765 TCTGTCCCAGTATAAGAACATTTTTGA 58.839 33.333 0.00 0.00 32.61 2.69
2294 3088 8.106247 TGTCCCAGTATAAGAACATTTTTGAC 57.894 34.615 0.00 0.00 0.00 3.18
2295 3089 7.721842 TGTCCCAGTATAAGAACATTTTTGACA 59.278 33.333 0.00 0.00 0.00 3.58
2296 3090 8.021396 GTCCCAGTATAAGAACATTTTTGACAC 58.979 37.037 0.00 0.00 0.00 3.67
2297 3091 7.942341 TCCCAGTATAAGAACATTTTTGACACT 59.058 33.333 0.00 0.00 0.00 3.55
2298 3092 9.226606 CCCAGTATAAGAACATTTTTGACACTA 57.773 33.333 0.00 0.00 0.00 2.74
2333 3127 9.609950 TTAAAAACGTTCTTATATTTTGGGACG 57.390 29.630 0.00 0.00 0.00 4.79
2334 3128 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
2335 3129 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
2336 3130 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
2337 3131 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
2338 3132 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
2339 3133 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
2340 3134 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
2367 3162 8.990163 AGTACACTTCTTTTGGGAAATCTTAA 57.010 30.769 0.00 0.00 0.00 1.85
2370 3165 7.066781 ACACTTCTTTTGGGAAATCTTAAGGA 58.933 34.615 1.85 0.00 0.00 3.36
2373 3168 9.997172 ACTTCTTTTGGGAAATCTTAAGGATAT 57.003 29.630 1.85 0.00 33.71 1.63
2411 3206 6.867662 AAGAACACTAGTCCAATTCAGTTG 57.132 37.500 0.00 0.00 37.57 3.16
2658 3453 3.570975 TCAAATCAGCAATGAACTGCAGT 59.429 39.130 15.25 15.25 45.18 4.40
2724 3519 2.115291 GCCACAGGCGGATTTCCTC 61.115 63.158 0.00 0.00 39.62 3.71
2752 3547 1.207811 CCATGCCCCATTTCAAGGTTC 59.792 52.381 0.00 0.00 0.00 3.62
2777 3572 3.585862 TCGACTGACCAATTCTTACTGC 58.414 45.455 0.00 0.00 0.00 4.40
2790 3585 8.730680 CCAATTCTTACTGCTGTAGTTGTATTT 58.269 33.333 3.17 0.00 40.89 1.40
2810 3605 9.844790 TGTATTTCTGCTTCAATTATTTGACAG 57.155 29.630 9.86 9.86 41.50 3.51
2815 3610 7.587629 TCTGCTTCAATTATTTGACAGTCAAG 58.412 34.615 15.61 4.09 41.50 3.02
2854 3668 3.899734 TCTGACAAAATTCAATGTGCGG 58.100 40.909 0.00 0.00 0.00 5.69
3414 4237 5.304101 TGAAAGTTAAAATGTCCAGCCATGT 59.696 36.000 0.00 0.00 0.00 3.21
3415 4238 6.491745 TGAAAGTTAAAATGTCCAGCCATGTA 59.508 34.615 0.00 0.00 0.00 2.29
3416 4239 7.178274 TGAAAGTTAAAATGTCCAGCCATGTAT 59.822 33.333 0.00 0.00 0.00 2.29
3426 4249 5.356751 TGTCCAGCCATGTATGTTTATTCAC 59.643 40.000 0.00 0.00 0.00 3.18
3592 4538 6.875972 ACATTCACCCTCTTATACTCAAGT 57.124 37.500 0.00 0.00 0.00 3.16
3612 4558 4.307432 AGTAGTCGTCAATTTCCACACAG 58.693 43.478 0.00 0.00 0.00 3.66
3618 4564 5.229260 GTCGTCAATTTCCACACAGAAAAAC 59.771 40.000 0.00 0.00 39.11 2.43
3644 4597 7.910683 CCTTTTTCAGTTCACTTGAAGTAGAAC 59.089 37.037 21.89 21.89 36.94 3.01
3668 4621 7.717568 ACTATTGACATATATCCTACCGCATC 58.282 38.462 0.00 0.00 0.00 3.91
3686 4691 0.254462 TCCATGCCGGCACATCTTTA 59.746 50.000 35.50 6.20 33.14 1.85
3741 5032 1.851666 GCCATTTTGTCGTGTGTTGTG 59.148 47.619 0.00 0.00 0.00 3.33
3769 5071 6.255287 TGCATGTATGGATAATTGGCCTAAT 58.745 36.000 3.32 0.00 0.00 1.73
4123 5748 4.699522 ACCAAGAAGTCGGGCCGC 62.700 66.667 23.83 16.81 0.00 6.53
4167 5801 3.470567 CGTCGAGAAGCACACCGC 61.471 66.667 0.00 0.00 42.91 5.68
4168 5802 2.355837 GTCGAGAAGCACACCGCA 60.356 61.111 0.00 0.00 46.13 5.69
4396 6036 2.182030 GGCGTCTCCTTCCTCGTG 59.818 66.667 0.00 0.00 0.00 4.35
4433 6073 2.029844 GGCGAGCAAGTGGAGTGAC 61.030 63.158 0.00 0.00 0.00 3.67
4486 6130 1.136280 CGACGGCGGTTATTTTTCGTT 60.136 47.619 13.24 0.00 0.00 3.85
4529 6173 1.156736 CTCTGTAAAGGGTGGCAACG 58.843 55.000 0.00 0.00 42.51 4.10
4530 6174 0.470766 TCTGTAAAGGGTGGCAACGT 59.529 50.000 0.00 0.00 42.51 3.99
4531 6175 0.872388 CTGTAAAGGGTGGCAACGTC 59.128 55.000 0.00 0.00 42.51 4.34
4532 6176 0.470766 TGTAAAGGGTGGCAACGTCT 59.529 50.000 0.00 0.00 42.51 4.18
4533 6177 0.872388 GTAAAGGGTGGCAACGTCTG 59.128 55.000 0.00 0.00 42.51 3.51
4534 6178 0.759959 TAAAGGGTGGCAACGTCTGA 59.240 50.000 0.00 0.00 42.51 3.27
4535 6179 0.110486 AAAGGGTGGCAACGTCTGAT 59.890 50.000 0.00 0.00 42.51 2.90
4536 6180 0.606401 AAGGGTGGCAACGTCTGATG 60.606 55.000 0.00 0.00 42.51 3.07
4537 6181 2.690778 GGGTGGCAACGTCTGATGC 61.691 63.158 0.00 1.24 42.66 3.91
4542 6186 1.499056 GCAACGTCTGATGCCTGTG 59.501 57.895 0.00 0.00 37.89 3.66
4657 6312 9.760926 TGTGGAGAATGTAGATAGATATAGCTT 57.239 33.333 0.00 0.00 0.00 3.74
4680 6335 7.627300 GCTTTGGATCATCATCATCATCATCAG 60.627 40.741 0.00 0.00 0.00 2.90
4714 6371 4.824289 AGACGCTTTTATTCTTTCGGGTA 58.176 39.130 0.00 0.00 0.00 3.69
4800 6457 0.464735 TGACGGGTGGTCCTTTGTTG 60.465 55.000 0.00 0.00 45.46 3.33
4802 6459 1.826054 CGGGTGGTCCTTTGTTGCA 60.826 57.895 0.00 0.00 0.00 4.08
4872 6537 5.041951 TGTACTTTTTGCCACGATCAATC 57.958 39.130 0.00 0.00 0.00 2.67
4873 6538 4.517075 TGTACTTTTTGCCACGATCAATCA 59.483 37.500 0.00 0.00 0.00 2.57
4874 6539 4.164822 ACTTTTTGCCACGATCAATCAG 57.835 40.909 0.00 0.00 0.00 2.90
4875 6540 3.569701 ACTTTTTGCCACGATCAATCAGT 59.430 39.130 0.00 0.00 0.00 3.41
4910 6575 3.051081 ACATGTTCAGCTCTTCACCTC 57.949 47.619 0.00 0.00 0.00 3.85
4912 6577 3.260740 CATGTTCAGCTCTTCACCTCTC 58.739 50.000 0.00 0.00 0.00 3.20
4914 6579 2.298446 TGTTCAGCTCTTCACCTCTCTG 59.702 50.000 0.00 0.00 0.00 3.35
4918 6583 2.562298 CAGCTCTTCACCTCTCTGTCTT 59.438 50.000 0.00 0.00 0.00 3.01
4981 6646 5.502079 TCTGGATGATAGTAGGCTAGTAGC 58.498 45.833 14.09 14.09 41.46 3.58
5131 6813 6.541969 GTTGCTTGTTTGTTTGCTTATTTGT 58.458 32.000 0.00 0.00 0.00 2.83
5133 6815 7.138692 TGCTTGTTTGTTTGCTTATTTGTTT 57.861 28.000 0.00 0.00 0.00 2.83
5134 6816 7.020010 TGCTTGTTTGTTTGCTTATTTGTTTG 58.980 30.769 0.00 0.00 0.00 2.93
5220 6907 0.107508 CAGTCCATGTGGAGGCGAAT 60.108 55.000 1.07 0.00 46.49 3.34
5224 6911 0.758734 CCATGTGGAGGCGAATAGGA 59.241 55.000 0.00 0.00 37.39 2.94
5251 6941 2.814336 CAGTGCTAGGTTTTCTTGGACC 59.186 50.000 0.00 0.00 39.52 4.46
5255 6945 2.483106 GCTAGGTTTTCTTGGACCGTTC 59.517 50.000 0.00 0.00 40.89 3.95
5280 6975 1.005294 CGTTGCATGTTCTTGCCTGC 61.005 55.000 7.92 0.00 42.06 4.85
5331 7030 7.598759 TCAGAAACTAACTAACCACTTCTCT 57.401 36.000 0.00 0.00 0.00 3.10
5336 7035 6.726490 ACTAACTAACCACTTCTCTGTCAA 57.274 37.500 0.00 0.00 0.00 3.18
5339 7038 5.153950 ACTAACCACTTCTCTGTCAATCC 57.846 43.478 0.00 0.00 0.00 3.01
5341 7040 1.971357 ACCACTTCTCTGTCAATCCGT 59.029 47.619 0.00 0.00 0.00 4.69
5348 7047 2.489722 TCTCTGTCAATCCGTCAGTCAG 59.510 50.000 0.00 0.00 33.12 3.51
5363 7062 0.531974 GTCAGTTGCCTTGTCGTCCA 60.532 55.000 0.00 0.00 0.00 4.02
5368 7067 0.179234 TTGCCTTGTCGTCCAGTTCA 59.821 50.000 0.00 0.00 0.00 3.18
5369 7068 0.396435 TGCCTTGTCGTCCAGTTCAT 59.604 50.000 0.00 0.00 0.00 2.57
5370 7069 1.079503 GCCTTGTCGTCCAGTTCATC 58.920 55.000 0.00 0.00 0.00 2.92
5371 7070 1.726853 CCTTGTCGTCCAGTTCATCC 58.273 55.000 0.00 0.00 0.00 3.51
5372 7071 1.276421 CCTTGTCGTCCAGTTCATCCT 59.724 52.381 0.00 0.00 0.00 3.24
5373 7072 2.611518 CTTGTCGTCCAGTTCATCCTC 58.388 52.381 0.00 0.00 0.00 3.71
5374 7073 0.895530 TGTCGTCCAGTTCATCCTCC 59.104 55.000 0.00 0.00 0.00 4.30
5375 7074 1.187087 GTCGTCCAGTTCATCCTCCT 58.813 55.000 0.00 0.00 0.00 3.69
5376 7075 1.550976 GTCGTCCAGTTCATCCTCCTT 59.449 52.381 0.00 0.00 0.00 3.36
5377 7076 2.028020 GTCGTCCAGTTCATCCTCCTTT 60.028 50.000 0.00 0.00 0.00 3.11
5378 7077 3.194968 GTCGTCCAGTTCATCCTCCTTTA 59.805 47.826 0.00 0.00 0.00 1.85
5379 7078 4.030913 TCGTCCAGTTCATCCTCCTTTAT 58.969 43.478 0.00 0.00 0.00 1.40
5380 7079 4.469945 TCGTCCAGTTCATCCTCCTTTATT 59.530 41.667 0.00 0.00 0.00 1.40
5381 7080 5.659525 TCGTCCAGTTCATCCTCCTTTATTA 59.340 40.000 0.00 0.00 0.00 0.98
5382 7081 5.753921 CGTCCAGTTCATCCTCCTTTATTAC 59.246 44.000 0.00 0.00 0.00 1.89
5383 7082 6.407074 CGTCCAGTTCATCCTCCTTTATTACT 60.407 42.308 0.00 0.00 0.00 2.24
5384 7083 6.987404 GTCCAGTTCATCCTCCTTTATTACTC 59.013 42.308 0.00 0.00 0.00 2.59
5385 7084 6.099845 TCCAGTTCATCCTCCTTTATTACTCC 59.900 42.308 0.00 0.00 0.00 3.85
5386 7085 6.100424 CCAGTTCATCCTCCTTTATTACTCCT 59.900 42.308 0.00 0.00 0.00 3.69
5387 7086 7.366011 CCAGTTCATCCTCCTTTATTACTCCTT 60.366 40.741 0.00 0.00 0.00 3.36
5388 7087 8.049721 CAGTTCATCCTCCTTTATTACTCCTTT 58.950 37.037 0.00 0.00 0.00 3.11
5389 7088 8.268605 AGTTCATCCTCCTTTATTACTCCTTTC 58.731 37.037 0.00 0.00 0.00 2.62
5390 7089 7.749377 TCATCCTCCTTTATTACTCCTTTCA 57.251 36.000 0.00 0.00 0.00 2.69
5391 7090 8.337118 TCATCCTCCTTTATTACTCCTTTCAT 57.663 34.615 0.00 0.00 0.00 2.57
5392 7091 8.781951 TCATCCTCCTTTATTACTCCTTTCATT 58.218 33.333 0.00 0.00 0.00 2.57
5393 7092 9.061435 CATCCTCCTTTATTACTCCTTTCATTC 57.939 37.037 0.00 0.00 0.00 2.67
5394 7093 8.393959 TCCTCCTTTATTACTCCTTTCATTCT 57.606 34.615 0.00 0.00 0.00 2.40
5395 7094 8.267894 TCCTCCTTTATTACTCCTTTCATTCTG 58.732 37.037 0.00 0.00 0.00 3.02
5396 7095 8.267894 CCTCCTTTATTACTCCTTTCATTCTGA 58.732 37.037 0.00 0.00 0.00 3.27
5397 7096 9.672673 CTCCTTTATTACTCCTTTCATTCTGAA 57.327 33.333 0.00 0.00 34.03 3.02
5405 7104 9.793259 TTACTCCTTTCATTCTGAATTACTTGT 57.207 29.630 0.00 0.00 36.11 3.16
5406 7105 8.329203 ACTCCTTTCATTCTGAATTACTTGTC 57.671 34.615 0.00 0.00 36.11 3.18
5407 7106 7.118390 ACTCCTTTCATTCTGAATTACTTGTCG 59.882 37.037 0.00 0.00 36.11 4.35
5408 7107 7.158697 TCCTTTCATTCTGAATTACTTGTCGA 58.841 34.615 0.00 0.00 36.11 4.20
5409 7108 7.659799 TCCTTTCATTCTGAATTACTTGTCGAA 59.340 33.333 0.00 0.00 36.11 3.71
5410 7109 8.289618 CCTTTCATTCTGAATTACTTGTCGAAA 58.710 33.333 0.00 4.54 36.11 3.46
5411 7110 9.663904 CTTTCATTCTGAATTACTTGTCGAAAA 57.336 29.630 0.00 0.00 36.11 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.304356 TCTCTGCAACTAAACAGACAAATG 57.696 37.500 0.00 0.00 37.99 2.32
47 48 3.500654 CCCGGGACAGGATTAGTATCTCT 60.501 52.174 18.48 0.00 0.00 3.10
48 49 2.826725 CCCGGGACAGGATTAGTATCTC 59.173 54.545 18.48 0.00 0.00 2.75
67 68 1.605712 CGGCCGAATCTCTGAATACCC 60.606 57.143 24.07 0.00 0.00 3.69
121 122 4.017271 CGCGATTCCATTAACAAACGTAC 58.983 43.478 0.00 0.00 0.00 3.67
122 123 3.062369 CCGCGATTCCATTAACAAACGTA 59.938 43.478 8.23 0.00 0.00 3.57
123 124 2.159626 CCGCGATTCCATTAACAAACGT 60.160 45.455 8.23 0.00 0.00 3.99
245 252 1.248101 GGTGGGAAATTCGGGGTGTG 61.248 60.000 0.00 0.00 0.00 3.82
246 253 1.076014 GGTGGGAAATTCGGGGTGT 59.924 57.895 0.00 0.00 0.00 4.16
309 328 4.758251 TACGTGCTGCATGCCGCT 62.758 61.111 30.24 15.95 43.06 5.52
310 329 4.228097 CTACGTGCTGCATGCCGC 62.228 66.667 25.25 25.25 42.00 6.53
311 330 1.482621 CTACTACGTGCTGCATGCCG 61.483 60.000 21.11 14.92 42.00 5.69
312 331 1.766143 GCTACTACGTGCTGCATGCC 61.766 60.000 21.11 0.28 42.00 4.40
313 332 1.083806 TGCTACTACGTGCTGCATGC 61.084 55.000 21.11 11.82 43.25 4.06
314 333 1.325640 CTTGCTACTACGTGCTGCATG 59.674 52.381 19.72 19.72 33.50 4.06
476 505 0.810031 CGTGTATTTCCTCCCTGGCG 60.810 60.000 0.00 0.00 35.26 5.69
477 506 0.463833 CCGTGTATTTCCTCCCTGGC 60.464 60.000 0.00 0.00 35.26 4.85
478 507 0.463833 GCCGTGTATTTCCTCCCTGG 60.464 60.000 0.00 0.00 37.10 4.45
479 508 0.810031 CGCCGTGTATTTCCTCCCTG 60.810 60.000 0.00 0.00 0.00 4.45
480 509 0.974010 TCGCCGTGTATTTCCTCCCT 60.974 55.000 0.00 0.00 0.00 4.20
483 512 2.395654 GAGATCGCCGTGTATTTCCTC 58.604 52.381 0.00 0.00 0.00 3.71
484 513 1.269102 CGAGATCGCCGTGTATTTCCT 60.269 52.381 2.96 0.00 0.00 3.36
485 514 1.129326 CGAGATCGCCGTGTATTTCC 58.871 55.000 2.96 0.00 0.00 3.13
486 515 1.129326 CCGAGATCGCCGTGTATTTC 58.871 55.000 9.14 0.00 38.18 2.17
487 516 0.874607 GCCGAGATCGCCGTGTATTT 60.875 55.000 9.14 0.00 38.18 1.40
488 517 1.299926 GCCGAGATCGCCGTGTATT 60.300 57.895 9.14 0.00 38.18 1.89
489 518 2.335369 GCCGAGATCGCCGTGTAT 59.665 61.111 9.14 0.00 38.18 2.29
490 519 3.896133 GGCCGAGATCGCCGTGTA 61.896 66.667 9.14 0.00 38.18 2.90
495 524 4.524318 TTTCGGGCCGAGATCGCC 62.524 66.667 29.30 1.71 37.14 5.54
496 525 3.262686 GTTTCGGGCCGAGATCGC 61.263 66.667 29.30 14.15 37.14 4.58
497 526 1.878522 CTGTTTCGGGCCGAGATCG 60.879 63.158 29.30 15.25 37.14 3.69
498 527 2.174319 GCTGTTTCGGGCCGAGATC 61.174 63.158 29.30 21.55 37.14 2.75
499 528 2.125106 GCTGTTTCGGGCCGAGAT 60.125 61.111 29.30 0.00 37.14 2.75
500 529 4.735132 CGCTGTTTCGGGCCGAGA 62.735 66.667 29.30 22.90 37.14 4.04
505 534 3.011760 CTTCGACGCTGTTTCGGGC 62.012 63.158 0.00 0.00 37.09 6.13
506 535 3.011760 GCTTCGACGCTGTTTCGGG 62.012 63.158 6.65 0.00 37.09 5.14
518 547 1.662446 GTTTGGACGGACGCTTCGA 60.662 57.895 0.00 0.00 0.00 3.71
731 779 3.119709 CTCGCTCTCGCTCCAGGTC 62.120 68.421 0.00 0.00 35.26 3.85
732 780 3.137459 CTCGCTCTCGCTCCAGGT 61.137 66.667 0.00 0.00 35.26 4.00
733 781 4.567385 GCTCGCTCTCGCTCCAGG 62.567 72.222 0.00 0.00 35.26 4.45
734 782 4.903355 CGCTCGCTCTCGCTCCAG 62.903 72.222 0.00 0.00 35.26 3.86
736 784 4.605967 CTCGCTCGCTCTCGCTCC 62.606 72.222 0.00 0.00 35.26 4.70
817 865 3.941657 GAGACACCCGCCAGAGCAC 62.942 68.421 0.00 0.00 39.83 4.40
832 880 2.780693 CCCCTGGACTGGAGGAGA 59.219 66.667 0.00 0.00 31.48 3.71
833 881 2.366167 CCCCCTGGACTGGAGGAG 60.366 72.222 0.00 0.00 31.48 3.69
899 949 1.681486 CTTCCTCCTCCTTCTCGGCC 61.681 65.000 0.00 0.00 0.00 6.13
906 956 1.978361 ATGGCTTCTTCCTCCTCCTT 58.022 50.000 0.00 0.00 0.00 3.36
944 996 0.401738 CAGCCAAGAACCCTCCTCAA 59.598 55.000 0.00 0.00 0.00 3.02
945 997 2.069776 CAGCCAAGAACCCTCCTCA 58.930 57.895 0.00 0.00 0.00 3.86
946 998 1.377856 GCAGCCAAGAACCCTCCTC 60.378 63.158 0.00 0.00 0.00 3.71
947 999 1.849823 AGCAGCCAAGAACCCTCCT 60.850 57.895 0.00 0.00 0.00 3.69
948 1000 1.676967 CAGCAGCCAAGAACCCTCC 60.677 63.158 0.00 0.00 0.00 4.30
952 1004 2.960170 CAGCAGCAGCCAAGAACC 59.040 61.111 0.00 0.00 43.56 3.62
1438 1563 2.664185 CGGCATCTCGGGCATCTG 60.664 66.667 0.00 0.00 0.00 2.90
1773 1940 2.418083 CGATTGGGAAGCAAGGGGC 61.418 63.158 0.00 0.00 45.30 5.80
1775 1942 1.133976 AGATCGATTGGGAAGCAAGGG 60.134 52.381 0.00 0.00 0.00 3.95
1776 1943 2.338577 AGATCGATTGGGAAGCAAGG 57.661 50.000 0.00 0.00 0.00 3.61
1817 2100 1.299468 GGCTGTCCTACTCGCATCG 60.299 63.158 0.00 0.00 0.00 3.84
1821 2104 2.892784 ATTTAGGCTGTCCTACTCGC 57.107 50.000 0.00 0.00 44.36 5.03
1825 2108 4.489306 ACTGGAATTTAGGCTGTCCTAC 57.511 45.455 0.00 0.00 44.36 3.18
1872 2658 0.907486 TCCCCAGAATGCAGTCAGAG 59.093 55.000 17.53 5.65 31.97 3.35
1873 2659 1.588239 ATCCCCAGAATGCAGTCAGA 58.412 50.000 17.53 7.72 31.97 3.27
1875 2661 1.407299 CGAATCCCCAGAATGCAGTCA 60.407 52.381 17.53 0.00 31.97 3.41
1876 2662 1.303309 CGAATCCCCAGAATGCAGTC 58.697 55.000 5.91 5.91 31.97 3.51
1877 2663 0.107017 CCGAATCCCCAGAATGCAGT 60.107 55.000 0.00 0.00 31.97 4.40
1878 2664 0.820891 CCCGAATCCCCAGAATGCAG 60.821 60.000 0.00 0.00 31.97 4.41
1879 2665 1.227102 CCCGAATCCCCAGAATGCA 59.773 57.895 0.00 0.00 31.97 3.96
1880 2666 0.395724 AACCCGAATCCCCAGAATGC 60.396 55.000 0.00 0.00 31.97 3.56
1881 2667 3.214328 CTTAACCCGAATCCCCAGAATG 58.786 50.000 0.00 0.00 0.00 2.67
1882 2668 2.422945 GCTTAACCCGAATCCCCAGAAT 60.423 50.000 0.00 0.00 0.00 2.40
1883 2669 1.064979 GCTTAACCCGAATCCCCAGAA 60.065 52.381 0.00 0.00 0.00 3.02
1955 2741 1.299014 CGTCAGAGAGCGAGCATCC 60.299 63.158 0.00 0.00 0.00 3.51
1963 2750 0.718343 GCACATCAACGTCAGAGAGC 59.282 55.000 0.00 0.00 0.00 4.09
1964 2751 2.257894 GAGCACATCAACGTCAGAGAG 58.742 52.381 0.00 0.00 0.00 3.20
1965 2752 1.401539 CGAGCACATCAACGTCAGAGA 60.402 52.381 0.00 0.00 0.00 3.10
1966 2753 0.987715 CGAGCACATCAACGTCAGAG 59.012 55.000 0.00 0.00 0.00 3.35
2095 2882 6.483640 AGTCCGAGATTTGGATTAATAAGTGC 59.516 38.462 0.00 0.00 37.93 4.40
2182 2969 5.878406 AGTAGGTTGCTATAGCTTGACAT 57.122 39.130 24.61 18.71 42.66 3.06
2197 2984 4.770531 GCCACTTCCCAAATTAAGTAGGTT 59.229 41.667 0.00 0.00 34.23 3.50
2198 2985 4.044191 AGCCACTTCCCAAATTAAGTAGGT 59.956 41.667 0.00 0.00 34.23 3.08
2199 2986 4.600062 AGCCACTTCCCAAATTAAGTAGG 58.400 43.478 0.00 0.00 34.23 3.18
2254 3048 2.241685 TGGGACAGAGGGAGTAGTAGAC 59.758 54.545 0.00 0.00 0.00 2.59
2269 3063 7.721842 TGTCAAAAATGTTCTTATACTGGGACA 59.278 33.333 0.00 0.00 0.00 4.02
2270 3064 8.021396 GTGTCAAAAATGTTCTTATACTGGGAC 58.979 37.037 0.00 0.00 0.00 4.46
2271 3065 7.942341 AGTGTCAAAAATGTTCTTATACTGGGA 59.058 33.333 0.00 0.00 0.00 4.37
2272 3066 8.110860 AGTGTCAAAAATGTTCTTATACTGGG 57.889 34.615 0.00 0.00 0.00 4.45
2307 3101 9.609950 CGTCCCAAAATATAAGAACGTTTTTAA 57.390 29.630 14.41 5.85 0.00 1.52
2308 3102 8.235905 CCGTCCCAAAATATAAGAACGTTTTTA 58.764 33.333 13.02 13.02 0.00 1.52
2309 3103 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
2310 3104 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
2311 3105 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
2312 3106 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
2313 3107 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
2314 3108 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
2315 3109 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
2316 3110 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
2317 3111 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
2318 3112 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
2319 3113 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
2320 3114 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
2321 3115 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
2322 3116 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2323 3117 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2324 3118 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
2325 3119 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2326 3120 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2327 3121 0.257039 GTACTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
2328 3122 0.257039 TGTACTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
2329 3123 1.064832 AGTGTACTACTCCCTCCGTCC 60.065 57.143 0.00 0.00 33.17 4.79
2330 3124 2.416680 AGTGTACTACTCCCTCCGTC 57.583 55.000 0.00 0.00 33.17 4.79
2331 3125 2.308275 AGAAGTGTACTACTCCCTCCGT 59.692 50.000 0.00 0.00 39.18 4.69
2332 3126 3.002038 AGAAGTGTACTACTCCCTCCG 57.998 52.381 0.00 0.00 39.18 4.63
2333 3127 5.480205 CAAAAGAAGTGTACTACTCCCTCC 58.520 45.833 0.00 0.00 39.18 4.30
2334 3128 5.480205 CCAAAAGAAGTGTACTACTCCCTC 58.520 45.833 0.00 0.00 39.18 4.30
2335 3129 4.286291 CCCAAAAGAAGTGTACTACTCCCT 59.714 45.833 0.00 0.00 39.18 4.20
2336 3130 4.285260 TCCCAAAAGAAGTGTACTACTCCC 59.715 45.833 0.00 0.00 39.18 4.30
2337 3131 5.479124 TCCCAAAAGAAGTGTACTACTCC 57.521 43.478 0.00 0.00 39.18 3.85
2338 3132 7.878644 AGATTTCCCAAAAGAAGTGTACTACTC 59.121 37.037 0.00 0.00 39.18 2.59
2339 3133 7.746703 AGATTTCCCAAAAGAAGTGTACTACT 58.253 34.615 0.00 0.00 42.89 2.57
2340 3134 7.981102 AGATTTCCCAAAAGAAGTGTACTAC 57.019 36.000 0.00 0.00 0.00 2.73
2373 3168 9.968870 ACTAGTGTTCTTTTTACAACAACAAAA 57.031 25.926 0.00 0.00 0.00 2.44
2385 3180 7.881775 ACTGAATTGGACTAGTGTTCTTTTT 57.118 32.000 0.00 0.00 0.00 1.94
2411 3206 6.980397 CAGGCATCCAAATGAAATAAGTTACC 59.020 38.462 0.00 0.00 34.61 2.85
2752 3547 2.638556 AGAATTGGTCAGTCGAGTCG 57.361 50.000 6.09 6.09 0.00 4.18
2790 3585 7.509141 TTGACTGTCAAATAATTGAAGCAGA 57.491 32.000 20.14 0.00 46.66 4.26
2810 3605 7.965107 CAGAAAAACATAACTGATAGGCTTGAC 59.035 37.037 0.00 0.00 32.90 3.18
2815 3610 7.377766 TGTCAGAAAAACATAACTGATAGGC 57.622 36.000 0.00 0.00 40.61 3.93
2854 3668 3.787001 CGTCCTTCCCCTGGAGGC 61.787 72.222 0.00 0.00 33.58 4.70
3426 4249 7.327032 GGCTTCTTGCAGAAAACTACATTTTAG 59.673 37.037 0.00 0.00 41.20 1.85
3566 4512 8.258708 ACTTGAGTATAAGAGGGTGAATGTAAC 58.741 37.037 0.00 0.00 0.00 2.50
3574 4520 5.589452 ACGACTACTTGAGTATAAGAGGGTG 59.411 44.000 0.00 0.00 39.06 4.61
3575 4521 5.753716 ACGACTACTTGAGTATAAGAGGGT 58.246 41.667 0.00 0.00 39.06 4.34
3577 4523 6.922247 TGACGACTACTTGAGTATAAGAGG 57.078 41.667 0.00 0.00 39.06 3.69
3579 4525 9.784680 GAAATTGACGACTACTTGAGTATAAGA 57.215 33.333 0.00 0.00 39.06 2.10
3592 4538 4.594123 TCTGTGTGGAAATTGACGACTA 57.406 40.909 0.00 0.00 0.00 2.59
3618 4564 7.553881 TCTACTTCAAGTGAACTGAAAAAGG 57.446 36.000 0.00 0.00 0.00 3.11
3644 4597 7.148641 GGATGCGGTAGGATATATGTCAATAG 58.851 42.308 1.63 0.00 0.00 1.73
3668 4621 0.664761 CTAAAGATGTGCCGGCATGG 59.335 55.000 35.23 13.96 42.50 3.66
3673 4626 5.360591 AGATAAGAACTAAAGATGTGCCGG 58.639 41.667 0.00 0.00 0.00 6.13
3675 4628 8.045176 ACAAAGATAAGAACTAAAGATGTGCC 57.955 34.615 0.00 0.00 0.00 5.01
3686 4691 8.170730 ACAAATTAGGGGACAAAGATAAGAACT 58.829 33.333 0.00 0.00 0.00 3.01
3741 5032 6.153340 AGGCCAATTATCCATACATGCATTAC 59.847 38.462 5.01 0.00 0.00 1.89
4123 5748 4.824515 AGGTCGCCCTCGGAGGAG 62.825 72.222 25.60 17.70 35.62 3.69
4147 5772 2.089349 GGTGTGCTTCTCGACGAGC 61.089 63.158 20.11 10.22 0.00 5.03
4167 5801 2.746671 CCCTCTGCTGCTGCTGTG 60.747 66.667 17.00 15.65 40.48 3.66
4168 5802 3.247648 ACCCTCTGCTGCTGCTGT 61.248 61.111 17.00 3.71 40.48 4.40
4396 6036 1.369321 GATCAGGTCGAGGCCCATC 59.631 63.158 0.00 0.00 0.00 3.51
4433 6073 2.032290 CGCTGCTGTCATGGTATCAATG 60.032 50.000 0.00 0.00 0.00 2.82
4486 6130 1.908619 TCCTCTGATGCCTGCAAAGTA 59.091 47.619 0.00 0.00 0.00 2.24
4529 6173 0.731417 GCATCACACAGGCATCAGAC 59.269 55.000 0.00 0.00 0.00 3.51
4530 6174 0.616891 AGCATCACACAGGCATCAGA 59.383 50.000 0.00 0.00 0.00 3.27
4531 6175 1.460504 AAGCATCACACAGGCATCAG 58.539 50.000 0.00 0.00 0.00 2.90
4532 6176 2.290197 TGTAAGCATCACACAGGCATCA 60.290 45.455 0.00 0.00 0.00 3.07
4533 6177 2.353889 CTGTAAGCATCACACAGGCATC 59.646 50.000 0.00 0.00 36.79 3.91
4534 6178 2.362736 CTGTAAGCATCACACAGGCAT 58.637 47.619 0.00 0.00 36.79 4.40
4535 6179 1.812235 CTGTAAGCATCACACAGGCA 58.188 50.000 0.00 0.00 36.79 4.75
4538 6182 2.234661 TCCTCCTGTAAGCATCACACAG 59.765 50.000 0.00 0.00 39.50 3.66
4539 6183 2.256306 TCCTCCTGTAAGCATCACACA 58.744 47.619 0.00 0.00 0.00 3.72
4542 6186 2.284190 GCTTCCTCCTGTAAGCATCAC 58.716 52.381 0.00 0.00 45.89 3.06
4605 6260 0.623723 TTTGTATGCTCCAGACCCCC 59.376 55.000 0.00 0.00 0.00 5.40
4606 6261 1.282157 AGTTTGTATGCTCCAGACCCC 59.718 52.381 0.00 0.00 0.00 4.95
4607 6262 2.027192 TCAGTTTGTATGCTCCAGACCC 60.027 50.000 0.00 0.00 0.00 4.46
4614 6269 5.412594 TCTCCACATTTCAGTTTGTATGCTC 59.587 40.000 0.00 0.00 0.00 4.26
4615 6270 5.316167 TCTCCACATTTCAGTTTGTATGCT 58.684 37.500 0.00 0.00 0.00 3.79
4657 6312 7.016153 TCTGATGATGATGATGATGATCCAA 57.984 36.000 0.00 0.00 0.00 3.53
4680 6335 1.003233 AGCGTCTCCCAGGCTTTTC 60.003 57.895 0.00 0.00 44.04 2.29
4800 6457 4.515191 TGAAGGTAAAGTCTGTCAACATGC 59.485 41.667 0.00 0.00 0.00 4.06
4802 6459 7.502226 TCATTTGAAGGTAAAGTCTGTCAACAT 59.498 33.333 0.00 0.00 0.00 2.71
4918 6583 9.303116 TGCATAAGAATTACTACAAGGGAAAAA 57.697 29.630 0.00 0.00 30.46 1.94
4923 6588 8.454106 GCATATGCATAAGAATTACTACAAGGG 58.546 37.037 22.84 0.00 41.59 3.95
4927 6592 8.506437 GCAAGCATATGCATAAGAATTACTACA 58.494 33.333 28.62 0.00 45.70 2.74
4928 6593 8.886816 GCAAGCATATGCATAAGAATTACTAC 57.113 34.615 28.62 1.10 45.70 2.73
4973 6638 4.750598 GCCACTTAATACAAGGCTACTAGC 59.249 45.833 0.00 0.00 42.01 3.42
4974 6639 5.914033 TGCCACTTAATACAAGGCTACTAG 58.086 41.667 0.00 0.00 45.42 2.57
4976 6641 4.770795 CTGCCACTTAATACAAGGCTACT 58.229 43.478 0.00 0.00 45.42 2.57
4977 6642 3.312697 GCTGCCACTTAATACAAGGCTAC 59.687 47.826 0.00 0.00 45.42 3.58
4981 6646 4.009675 TGAAGCTGCCACTTAATACAAGG 58.990 43.478 0.00 0.00 0.00 3.61
4982 6647 4.455533 TGTGAAGCTGCCACTTAATACAAG 59.544 41.667 17.15 0.00 35.66 3.16
4984 6649 4.014569 TGTGAAGCTGCCACTTAATACA 57.985 40.909 17.15 0.00 35.66 2.29
4986 6651 5.105797 CCATTTGTGAAGCTGCCACTTAATA 60.106 40.000 17.15 0.00 35.66 0.98
4992 6670 0.961019 TCCATTTGTGAAGCTGCCAC 59.039 50.000 11.39 11.39 35.23 5.01
4993 6671 1.250328 CTCCATTTGTGAAGCTGCCA 58.750 50.000 0.00 0.00 0.00 4.92
5102 6784 3.306703 AGCAAACAAACAAGCAACGAATG 59.693 39.130 0.00 0.00 0.00 2.67
5131 6813 1.835121 CGATAGCGACACGGATCAAA 58.165 50.000 0.00 0.00 40.82 2.69
5175 6857 2.203625 GCCAAGCCCAGGGACAAA 60.204 61.111 10.89 0.00 0.00 2.83
5193 6875 2.361757 CTCCACATGGACTGCTCTCTAG 59.638 54.545 0.00 0.00 39.78 2.43
5220 6907 3.170991 ACCTAGCACTGTGAGTTCCTA 57.829 47.619 12.86 2.13 0.00 2.94
5224 6911 4.423625 AGAAAACCTAGCACTGTGAGTT 57.576 40.909 12.86 6.10 0.00 3.01
5255 6945 1.069022 CAAGAACATGCAACGTCAGGG 60.069 52.381 0.00 0.00 0.00 4.45
5280 6975 2.691409 TCGCCAGTTGGAAGATAAGG 57.309 50.000 1.45 0.00 37.39 2.69
5331 7030 2.754472 CAACTGACTGACGGATTGACA 58.246 47.619 0.00 0.00 0.00 3.58
5348 7047 0.586802 GAACTGGACGACAAGGCAAC 59.413 55.000 0.00 0.00 0.00 4.17
5363 7062 7.757242 AAGGAGTAATAAAGGAGGATGAACT 57.243 36.000 0.00 0.00 0.00 3.01
5368 7067 9.008584 AGAATGAAAGGAGTAATAAAGGAGGAT 57.991 33.333 0.00 0.00 0.00 3.24
5369 7068 8.267894 CAGAATGAAAGGAGTAATAAAGGAGGA 58.732 37.037 0.00 0.00 39.69 3.71
5370 7069 8.267894 TCAGAATGAAAGGAGTAATAAAGGAGG 58.732 37.037 0.00 0.00 45.97 4.30


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

AutoCloner maintained by Alex Coulton.