Multiple sequence alignment - TraesCS5A01G556500

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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 TraesCS5A01G556500 chr5A 100.000 6925 0 0 732 7656 707828184 707821260 0.000000e+00 12789.0
1 TraesCS5A01G556500 chr5A 97.210 4875 53 20 2067 6914 659144028 659139210 0.000000e+00 8172.0
2 TraesCS5A01G556500 chr5A 100.000 631 0 0 1 631 707828915 707828285 0.000000e+00 1166.0
3 TraesCS5A01G556500 chr5A 98.418 632 9 1 1 631 258095167 258095798 0.000000e+00 1110.0
4 TraesCS5A01G556500 chr5A 98.259 632 10 1 1 631 585173265 585172634 0.000000e+00 1105.0
5 TraesCS5A01G556500 chr5A 98.254 630 10 1 1 629 205486332 205485703 0.000000e+00 1101.0
6 TraesCS5A01G556500 chr5A 97.136 419 8 1 7238 7656 709674412 709674826 0.000000e+00 704.0
7 TraesCS5A01G556500 chr5A 98.127 267 5 0 732 998 709773394 709773660 4.180000e-127 466.0
8 TraesCS5A01G556500 chr5A 96.043 278 7 3 6922 7199 659138675 659138402 4.210000e-122 449.0
9 TraesCS5A01G556500 chr5A 86.256 422 11 12 7272 7656 659138163 659137752 1.540000e-111 414.0
10 TraesCS5A01G556500 chr5A 99.301 143 1 0 732 874 709773601 709773743 7.620000e-65 259.0
11 TraesCS5A01G556500 chr5A 95.620 137 5 1 1527 1663 659144248 659144113 1.290000e-52 219.0
12 TraesCS5A01G556500 chr5A 96.154 104 4 0 895 998 709773350 709773453 3.670000e-38 171.0
13 TraesCS5A01G556500 chr5A 91.379 116 9 1 7084 7199 709672735 709672849 2.860000e-34 158.0
14 TraesCS5A01G556500 chr5A 95.000 60 3 0 732 791 707827977 707827918 2.270000e-15 95.3
15 TraesCS5A01G556500 chr5A 95.000 60 3 0 939 998 707828184 707828125 2.270000e-15 95.3
16 TraesCS5A01G556500 chr5A 97.436 39 1 0 1151 1189 659144286 659144248 4.960000e-07 67.6
17 TraesCS5A01G556500 chrUn 95.280 5297 156 48 1543 6806 100180376 100175141 0.000000e+00 8311.0
18 TraesCS5A01G556500 chrUn 100.000 631 0 0 1 631 299798845 299798215 0.000000e+00 1166.0
19 TraesCS5A01G556500 chrUn 94.558 147 5 2 1225 1371 100180967 100180824 2.780000e-54 224.0
20 TraesCS5A01G556500 chrUn 92.617 149 7 1 7491 7639 100173322 100173178 2.160000e-50 211.0
21 TraesCS5A01G556500 chrUn 85.377 212 10 12 7208 7405 100173516 100173312 4.690000e-47 200.0
22 TraesCS5A01G556500 chrUn 97.222 36 1 0 1184 1219 100181029 100180994 2.310000e-05 62.1
23 TraesCS5A01G556500 chr4B 93.625 5286 204 53 1547 6772 672111601 672116813 0.000000e+00 7771.0
24 TraesCS5A01G556500 chr4B 94.151 2120 92 16 3294 5397 646316705 646318808 0.000000e+00 3199.0
25 TraesCS5A01G556500 chr4B 93.957 2118 92 12 3294 5397 646333787 646335882 0.000000e+00 3169.0
26 TraesCS5A01G556500 chr4B 93.574 2132 90 16 3294 5397 646274262 646276374 0.000000e+00 3134.0
27 TraesCS5A01G556500 chr4B 93.236 2129 101 14 3297 5397 646361082 646363195 0.000000e+00 3094.0
28 TraesCS5A01G556500 chr4B 93.652 1922 85 12 3297 5196 646307836 646309742 0.000000e+00 2839.0
29 TraesCS5A01G556500 chr4B 92.308 377 25 4 5396 5771 646336042 646336415 4.070000e-147 532.0
30 TraesCS5A01G556500 chr4B 92.063 378 24 5 5396 5771 646276534 646276907 1.890000e-145 527.0
31 TraesCS5A01G556500 chr4B 91.534 378 26 5 5396 5771 646318970 646319343 4.100000e-142 516.0
32 TraesCS5A01G556500 chr4B 90.380 395 27 6 5396 5783 646363355 646363745 6.850000e-140 508.0
33 TraesCS5A01G556500 chr4B 96.296 135 5 0 7517 7651 646366906 646367040 1.000000e-53 222.0
34 TraesCS5A01G556500 chr4B 94.074 135 8 0 7517 7651 646322480 646322614 1.010000e-48 206.0
35 TraesCS5A01G556500 chr4B 93.333 135 9 0 7517 7651 646348020 646348154 4.690000e-47 200.0
36 TraesCS5A01G556500 chr4B 91.333 150 6 6 1226 1371 672110893 672111039 1.690000e-46 198.0
37 TraesCS5A01G556500 chr4B 96.491 114 4 0 7538 7651 646280082 646280195 1.010000e-43 189.0
38 TraesCS5A01G556500 chr4B 86.897 145 16 3 7055 7199 646321816 646321957 7.950000e-35 159.0
39 TraesCS5A01G556500 chr4B 80.258 233 19 6 6991 7199 646347271 646347500 4.790000e-32 150.0
40 TraesCS5A01G556500 chr4B 79.424 243 24 8 6981 7199 646366142 646366382 1.720000e-31 148.0
41 TraesCS5A01G556500 chr4B 79.487 234 22 9 6988 7198 646279338 646279568 8.010000e-30 143.0
42 TraesCS5A01G556500 chr4B 86.486 111 6 5 7208 7318 646279803 646279904 6.280000e-21 113.0
43 TraesCS5A01G556500 chr4B 86.486 111 6 5 7208 7318 646322194 646322295 6.280000e-21 113.0
44 TraesCS5A01G556500 chr4B 86.486 111 6 5 7208 7318 646347738 646347839 6.280000e-21 113.0
45 TraesCS5A01G556500 chr4B 84.545 110 8 5 7209 7318 646366618 646366718 4.890000e-17 100.0
46 TraesCS5A01G556500 chr4B 81.132 106 13 3 1111 1215 672110744 672110843 2.290000e-10 78.7
47 TraesCS5A01G556500 chr2B 95.331 4905 134 35 1547 6430 95353378 95348548 0.000000e+00 7701.0
48 TraesCS5A01G556500 chr2B 84.549 466 24 22 7208 7639 95339915 95339464 1.190000e-112 418.0
49 TraesCS5A01G556500 chr2B 91.418 268 17 2 732 999 95356708 95356447 5.650000e-96 363.0
50 TraesCS5A01G556500 chr2B 91.386 267 17 2 732 998 95357110 95356850 2.030000e-95 361.0
51 TraesCS5A01G556500 chr2B 89.888 267 21 4 732 998 95356909 95356649 9.520000e-89 339.0
52 TraesCS5A01G556500 chr2B 85.660 265 4 9 1151 1385 95354198 95353938 1.650000e-61 248.0
53 TraesCS5A01G556500 chr2B 88.945 199 16 2 800 998 95359172 95358980 2.760000e-59 241.0
54 TraesCS5A01G556500 chr2B 85.532 235 10 2 6988 7199 95341336 95341103 2.780000e-54 224.0
55 TraesCS5A01G556500 chr2B 83.193 238 14 4 6988 7199 95346208 95345971 2.180000e-45 195.0
56 TraesCS5A01G556500 chr2B 84.184 196 14 9 7208 7401 95345751 95345571 2.840000e-39 174.0
57 TraesCS5A01G556500 chr2B 79.038 291 22 20 6549 6810 95348456 95348176 6.150000e-36 163.0
58 TraesCS5A01G556500 chr2B 92.045 88 4 2 6464 6551 95348574 95348490 3.750000e-23 121.0
59 TraesCS5A01G556500 chr6A 98.576 632 8 1 1 631 561695536 561696167 0.000000e+00 1116.0
60 TraesCS5A01G556500 chr3A 98.418 632 9 1 1 631 720576443 720575812 0.000000e+00 1110.0
61 TraesCS5A01G556500 chr3A 97.059 34 1 0 6365 6398 104414432 104414399 2.980000e-04 58.4
62 TraesCS5A01G556500 chr2A 98.418 632 9 1 1 631 382022352 382021721 0.000000e+00 1110.0
63 TraesCS5A01G556500 chr7A 98.098 631 12 0 1 631 356302553 356303183 0.000000e+00 1099.0
64 TraesCS5A01G556500 chr1A 98.101 632 11 1 1 631 134742337 134742968 0.000000e+00 1099.0
65 TraesCS5A01G556500 chr2D 82.098 1201 114 47 1552 2740 602419089 602417978 0.000000e+00 933.0
66 TraesCS5A01G556500 chr2D 83.834 699 58 21 2042 2740 42698422 42697779 1.410000e-171 614.0
67 TraesCS5A01G556500 chr2D 85.470 117 14 3 1263 1378 42700082 42699968 1.350000e-22 119.0
68 TraesCS5A01G556500 chr3B 94.586 314 12 2 2162 2475 47190780 47191088 1.490000e-131 481.0
69 TraesCS5A01G556500 chr3B 92.271 207 11 2 2162 2368 47189861 47189660 9.720000e-74 289.0
70 TraesCS5A01G556500 chr3B 96.552 116 4 0 2405 2520 47189662 47189547 7.840000e-45 193.0
71 TraesCS5A01G556500 chr3D 88.764 267 24 4 2488 2754 129678086 129678346 9.580000e-84 322.0
72 TraesCS5A01G556500 chr5B 92.562 121 8 1 7517 7637 690967405 690967524 1.020000e-38 172.0
73 TraesCS5A01G556500 chr5D 81.308 214 19 16 1180 1378 484041963 484041756 3.700000e-33 154.0
74 TraesCS5A01G556500 chr5D 95.122 41 1 1 6988 7027 78059003 78059043 6.410000e-06 63.9
75 TraesCS5A01G556500 chr4A 89.381 113 11 1 1264 1376 234615541 234615652 2.880000e-29 141.0
76 TraesCS5A01G556500 chr1D 100.000 29 0 0 1257 1285 314700413 314700385 4.000000e-03 54.7


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 TraesCS5A01G556500 chr5A 707821260 707828915 7655 True 3536.400000 12789 97.500000 1 7656 4 chr5A.!!$R4 7655
1 TraesCS5A01G556500 chr5A 659137752 659144286 6534 True 1864.320000 8172 94.513000 1151 7656 5 chr5A.!!$R3 6505
2 TraesCS5A01G556500 chr5A 258095167 258095798 631 False 1110.000000 1110 98.418000 1 631 1 chr5A.!!$F1 630
3 TraesCS5A01G556500 chr5A 585172634 585173265 631 True 1105.000000 1105 98.259000 1 631 1 chr5A.!!$R2 630
4 TraesCS5A01G556500 chr5A 205485703 205486332 629 True 1101.000000 1101 98.254000 1 629 1 chr5A.!!$R1 628
5 TraesCS5A01G556500 chr5A 709672735 709674826 2091 False 431.000000 704 94.257500 7084 7656 2 chr5A.!!$F2 572
6 TraesCS5A01G556500 chrUn 100173178 100181029 7851 True 1801.620000 8311 93.010800 1184 7639 5 chrUn.!!$R2 6455
7 TraesCS5A01G556500 chrUn 299798215 299798845 630 True 1166.000000 1166 100.000000 1 631 1 chrUn.!!$R1 630
8 TraesCS5A01G556500 chr4B 646307836 646309742 1906 False 2839.000000 2839 93.652000 3297 5196 1 chr4B.!!$F1 1899
9 TraesCS5A01G556500 chr4B 672110744 672116813 6069 False 2682.566667 7771 88.696667 1111 6772 3 chr4B.!!$F7 5661
10 TraesCS5A01G556500 chr4B 646333787 646336415 2628 False 1850.500000 3169 93.132500 3294 5771 2 chr4B.!!$F4 2477
11 TraesCS5A01G556500 chr4B 646316705 646322614 5909 False 838.600000 3199 90.628400 3294 7651 5 chr4B.!!$F3 4357
12 TraesCS5A01G556500 chr4B 646274262 646280195 5933 False 821.200000 3134 89.620200 3294 7651 5 chr4B.!!$F2 4357
13 TraesCS5A01G556500 chr4B 646361082 646367040 5958 False 814.400000 3094 88.776200 3297 7651 5 chr4B.!!$F6 4354
14 TraesCS5A01G556500 chr2B 95345571 95359172 13601 True 990.600000 7701 88.108800 732 7401 10 chr2B.!!$R2 6669
15 TraesCS5A01G556500 chr2B 95339464 95341336 1872 True 321.000000 418 85.040500 6988 7639 2 chr2B.!!$R1 651
16 TraesCS5A01G556500 chr6A 561695536 561696167 631 False 1116.000000 1116 98.576000 1 631 1 chr6A.!!$F1 630
17 TraesCS5A01G556500 chr3A 720575812 720576443 631 True 1110.000000 1110 98.418000 1 631 1 chr3A.!!$R2 630
18 TraesCS5A01G556500 chr2A 382021721 382022352 631 True 1110.000000 1110 98.418000 1 631 1 chr2A.!!$R1 630
19 TraesCS5A01G556500 chr7A 356302553 356303183 630 False 1099.000000 1099 98.098000 1 631 1 chr7A.!!$F1 630
20 TraesCS5A01G556500 chr1A 134742337 134742968 631 False 1099.000000 1099 98.101000 1 631 1 chr1A.!!$F1 630
21 TraesCS5A01G556500 chr2D 602417978 602419089 1111 True 933.000000 933 82.098000 1552 2740 1 chr2D.!!$R1 1188
22 TraesCS5A01G556500 chr2D 42697779 42700082 2303 True 366.500000 614 84.652000 1263 2740 2 chr2D.!!$R2 1477

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
840 2574 0.179081 CCGACGGATTCCTTCCTTCC 60.179 60.000 8.64 0.00 42.99 3.46 F
1584 5990 0.033504 ATGCGTCCTGTTCGTCAACT 59.966 50.000 0.00 0.00 33.17 3.16 F
2012 6478 0.404426 GTAACAGGCCCCTTCAGGTT 59.596 55.000 0.00 0.00 0.00 3.50 F
2247 7535 1.081442 GGCAAAGTTAGGTGCACGC 60.081 57.895 11.45 5.63 42.74 5.34 F
3281 8580 1.273606 AGTTGAGACATCGTCAGGGTG 59.726 52.381 0.00 0.00 34.60 4.61 F
4681 10017 5.183140 ACTTGGCTACGTGATTAATTTGCTT 59.817 36.000 0.00 0.00 0.00 3.91 F
5947 11477 0.407528 TGCCTTACATTTGGAGGGCA 59.592 50.000 14.16 14.16 45.81 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 6136 1.153449 TCGCCGCCTTCAACTATGG 60.153 57.895 0.0 0.0 0.00 2.74 R
2588 7879 3.689649 GCAAAACAAGGATAGGACGATGT 59.310 43.478 0.0 0.0 0.00 3.06 R
3281 8580 6.867816 TCCATCAAAATCTACAACACATTTGC 59.132 34.615 0.0 0.0 0.00 3.68 R
3849 9157 6.911250 AACAAAATGAAGGGTACTAAAGGG 57.089 37.500 0.0 0.0 0.00 3.95 R
4681 10017 6.042143 GCAATTGTGGAGAAGAACAGAAAAA 58.958 36.000 7.4 0.0 0.00 1.94 R
6422 11990 0.904865 TTCTCGACCTCACCCTGCAT 60.905 55.000 0.0 0.0 0.00 3.96 R
7346 18269 0.178903 TGCTCTGGTGGGGAACTAGT 60.179 55.000 0.0 0.0 38.48 2.57 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
773 2507 1.640670 TCTTTCCATTCCCTCCCTTGG 59.359 52.381 0.00 0.00 0.00 3.61
826 2560 1.349627 GAGCAATGCATCACCGACG 59.650 57.895 8.35 0.00 0.00 5.12
839 2573 0.535797 ACCGACGGATTCCTTCCTTC 59.464 55.000 23.38 0.00 42.99 3.46
840 2574 0.179081 CCGACGGATTCCTTCCTTCC 60.179 60.000 8.64 0.00 42.99 3.46
841 2575 0.179081 CGACGGATTCCTTCCTTCCC 60.179 60.000 3.76 0.00 42.99 3.97
842 2576 1.205055 GACGGATTCCTTCCTTCCCT 58.795 55.000 0.30 0.00 42.99 4.20
843 2577 1.139256 GACGGATTCCTTCCTTCCCTC 59.861 57.143 0.30 0.00 42.99 4.30
876 2610 6.877236 TCTTGGTGCAAATTTCTTCTCTTTT 58.123 32.000 0.00 0.00 0.00 2.27
887 2621 4.625607 TCTTCTCTTTTCCTTCCTCACC 57.374 45.455 0.00 0.00 0.00 4.02
899 2633 1.734477 CCTCACCGACAAGCACTCG 60.734 63.158 0.00 0.00 0.00 4.18
942 2676 1.354368 TCCTTCCCTTGCTTCGGATTT 59.646 47.619 0.00 0.00 0.00 2.17
945 2679 3.761752 CCTTCCCTTGCTTCGGATTTAAA 59.238 43.478 0.00 0.00 0.00 1.52
947 2681 4.295141 TCCCTTGCTTCGGATTTAAAGA 57.705 40.909 0.00 0.00 0.00 2.52
952 2686 5.412904 CCTTGCTTCGGATTTAAAGAAGTCT 59.587 40.000 13.95 0.00 42.28 3.24
954 2688 4.695455 TGCTTCGGATTTAAAGAAGTCTGG 59.305 41.667 13.95 0.00 42.28 3.86
955 2689 4.695928 GCTTCGGATTTAAAGAAGTCTGGT 59.304 41.667 13.95 0.00 42.28 4.00
957 2691 4.575885 TCGGATTTAAAGAAGTCTGGTGG 58.424 43.478 0.00 0.00 30.50 4.61
966 2700 2.641815 AGAAGTCTGGTGGCATCTTTCT 59.358 45.455 0.00 0.77 0.00 2.52
980 2714 4.723309 CATCTTTCTATTCCCTCCCTTGG 58.277 47.826 0.00 0.00 0.00 3.61
999 2733 1.200020 GGTTCGGATTCAAGGCAGTTG 59.800 52.381 0.00 0.00 37.52 3.16
1000 2734 2.151202 GTTCGGATTCAAGGCAGTTGA 58.849 47.619 0.00 0.00 43.82 3.18
1001 2735 2.749621 GTTCGGATTCAAGGCAGTTGAT 59.250 45.455 1.88 0.00 44.89 2.57
1002 2736 2.358957 TCGGATTCAAGGCAGTTGATG 58.641 47.619 1.88 0.00 44.89 3.07
1013 2747 2.594529 CAGTTGATGCTACGCGTTTT 57.405 45.000 20.78 0.00 0.00 2.43
1048 4301 3.804193 GGCAAAGCCGAAGCCGAG 61.804 66.667 0.00 0.00 39.62 4.63
1049 4302 4.467062 GCAAAGCCGAAGCCGAGC 62.467 66.667 0.00 0.00 41.25 5.03
1050 4303 3.049674 CAAAGCCGAAGCCGAGCA 61.050 61.111 0.00 0.00 41.25 4.26
1052 4305 3.825160 AAAGCCGAAGCCGAGCACA 62.825 57.895 0.00 0.00 41.25 4.57
1055 4308 3.414700 CCGAAGCCGAGCACACAC 61.415 66.667 0.00 0.00 38.22 3.82
1057 4310 2.939022 GAAGCCGAGCACACACAC 59.061 61.111 0.00 0.00 0.00 3.82
1058 4311 1.887242 GAAGCCGAGCACACACACA 60.887 57.895 0.00 0.00 0.00 3.72
1059 4312 1.835483 GAAGCCGAGCACACACACAG 61.835 60.000 0.00 0.00 0.00 3.66
1060 4313 4.017877 GCCGAGCACACACACAGC 62.018 66.667 0.00 0.00 0.00 4.40
1061 4314 3.705638 CCGAGCACACACACAGCG 61.706 66.667 0.00 0.00 0.00 5.18
1062 4315 3.705638 CGAGCACACACACAGCGG 61.706 66.667 0.00 0.00 0.00 5.52
1065 4318 4.318021 GCACACACACAGCGGCAG 62.318 66.667 1.45 0.00 0.00 4.85
1066 4319 4.318021 CACACACACAGCGGCAGC 62.318 66.667 0.00 0.00 45.58 5.25
1078 4331 1.152984 CGGCAGCAACCCATCCATA 60.153 57.895 0.00 0.00 0.00 2.74
1079 4332 0.538057 CGGCAGCAACCCATCCATAT 60.538 55.000 0.00 0.00 0.00 1.78
1080 4333 1.251251 GGCAGCAACCCATCCATATC 58.749 55.000 0.00 0.00 0.00 1.63
1081 4334 1.251251 GCAGCAACCCATCCATATCC 58.749 55.000 0.00 0.00 0.00 2.59
1082 4335 1.479205 GCAGCAACCCATCCATATCCA 60.479 52.381 0.00 0.00 0.00 3.41
1083 4336 2.820485 GCAGCAACCCATCCATATCCAT 60.820 50.000 0.00 0.00 0.00 3.41
1087 4340 5.718130 CAGCAACCCATCCATATCCATATTT 59.282 40.000 0.00 0.00 0.00 1.40
1088 4341 6.211986 CAGCAACCCATCCATATCCATATTTT 59.788 38.462 0.00 0.00 0.00 1.82
1089 4342 6.788957 AGCAACCCATCCATATCCATATTTTT 59.211 34.615 0.00 0.00 0.00 1.94
1090 4343 7.038799 AGCAACCCATCCATATCCATATTTTTC 60.039 37.037 0.00 0.00 0.00 2.29
1098 4903 8.039603 TCCATATCCATATTTTTCGAAATCCG 57.960 34.615 12.12 0.00 40.25 4.18
1132 4952 2.560119 CCTCCATCCTCCTCTCGCG 61.560 68.421 0.00 0.00 0.00 5.87
1375 5257 3.224269 TCCCCTTCCCCTTCCCCT 61.224 66.667 0.00 0.00 0.00 4.79
1391 5273 0.626382 CCCTTCTTCCCTTCCCCTTC 59.374 60.000 0.00 0.00 0.00 3.46
1392 5274 0.626382 CCTTCTTCCCTTCCCCTTCC 59.374 60.000 0.00 0.00 0.00 3.46
1395 5277 1.230314 CTTCCCTTCCCCTTCCCCT 60.230 63.158 0.00 0.00 0.00 4.79
1396 5278 1.543896 TTCCCTTCCCCTTCCCCTG 60.544 63.158 0.00 0.00 0.00 4.45
1397 5279 3.744155 CCCTTCCCCTTCCCCTGC 61.744 72.222 0.00 0.00 0.00 4.85
1398 5280 2.615288 CCTTCCCCTTCCCCTGCT 60.615 66.667 0.00 0.00 0.00 4.24
1399 5281 2.241659 CCTTCCCCTTCCCCTGCTT 61.242 63.158 0.00 0.00 0.00 3.91
1401 5283 2.505364 CTTCCCCTTCCCCTGCTTGG 62.505 65.000 0.00 0.00 0.00 3.61
1403 5285 3.665971 CCCTTCCCCTGCTTGGCT 61.666 66.667 0.00 0.00 0.00 4.75
1404 5286 2.308722 CCCTTCCCCTGCTTGGCTA 61.309 63.158 0.00 0.00 0.00 3.93
1405 5287 1.649271 CCCTTCCCCTGCTTGGCTAT 61.649 60.000 0.00 0.00 0.00 2.97
1406 5288 0.259938 CCTTCCCCTGCTTGGCTATT 59.740 55.000 0.00 0.00 0.00 1.73
1407 5289 1.494721 CCTTCCCCTGCTTGGCTATTA 59.505 52.381 0.00 0.00 0.00 0.98
1408 5290 2.487986 CCTTCCCCTGCTTGGCTATTAG 60.488 54.545 0.00 0.00 0.00 1.73
1409 5291 1.893315 TCCCCTGCTTGGCTATTAGT 58.107 50.000 0.00 0.00 0.00 2.24
1410 5292 2.205342 TCCCCTGCTTGGCTATTAGTT 58.795 47.619 0.00 0.00 0.00 2.24
1413 5295 3.620488 CCCTGCTTGGCTATTAGTTTCA 58.380 45.455 0.00 0.00 0.00 2.69
1414 5296 4.016444 CCCTGCTTGGCTATTAGTTTCAA 58.984 43.478 0.00 0.00 0.00 2.69
1415 5297 4.096984 CCCTGCTTGGCTATTAGTTTCAAG 59.903 45.833 13.91 13.91 38.18 3.02
1416 5298 4.943705 CCTGCTTGGCTATTAGTTTCAAGA 59.056 41.667 18.63 9.32 37.57 3.02
1418 5300 5.804639 TGCTTGGCTATTAGTTTCAAGAGA 58.195 37.500 18.63 8.36 37.57 3.10
1454 5434 4.112341 CTGTCCGTCCGTCCGTCC 62.112 72.222 0.00 0.00 0.00 4.79
1459 5439 3.422303 CGTCCGTCCGTCCGTGTA 61.422 66.667 0.00 0.00 0.00 2.90
1460 5440 2.753966 CGTCCGTCCGTCCGTGTAT 61.754 63.158 0.00 0.00 0.00 2.29
1461 5441 1.063166 GTCCGTCCGTCCGTGTATC 59.937 63.158 0.00 0.00 0.00 2.24
1462 5442 2.023741 CCGTCCGTCCGTGTATCG 59.976 66.667 0.00 0.00 39.52 2.92
1463 5443 2.649975 CGTCCGTCCGTGTATCGC 60.650 66.667 0.00 0.00 38.35 4.58
1464 5444 2.486504 GTCCGTCCGTGTATCGCA 59.513 61.111 0.00 0.00 38.35 5.10
1465 5445 1.153978 GTCCGTCCGTGTATCGCAA 60.154 57.895 0.00 0.00 38.35 4.85
1466 5446 0.526954 GTCCGTCCGTGTATCGCAAT 60.527 55.000 0.00 0.00 38.35 3.56
1467 5447 0.173935 TCCGTCCGTGTATCGCAATT 59.826 50.000 0.00 0.00 38.35 2.32
1468 5448 0.575390 CCGTCCGTGTATCGCAATTC 59.425 55.000 0.00 0.00 38.35 2.17
1469 5449 0.226235 CGTCCGTGTATCGCAATTCG 59.774 55.000 0.00 0.00 38.35 3.34
1470 5450 0.043310 GTCCGTGTATCGCAATTCGC 60.043 55.000 0.00 0.00 38.27 4.70
1471 5451 0.458716 TCCGTGTATCGCAATTCGCA 60.459 50.000 1.75 0.00 42.60 5.10
1472 5452 0.371989 CCGTGTATCGCAATTCGCAA 59.628 50.000 1.75 0.00 42.60 4.85
1473 5453 1.442765 CGTGTATCGCAATTCGCAAC 58.557 50.000 1.75 0.32 42.60 4.17
1474 5454 1.060553 CGTGTATCGCAATTCGCAACT 59.939 47.619 1.75 0.00 42.60 3.16
1478 5458 4.501559 GTGTATCGCAATTCGCAACTAGTA 59.498 41.667 0.00 0.00 42.60 1.82
1494 5474 6.569610 GCAACTAGTAGATGAGATCTGGCTAC 60.570 46.154 11.36 8.86 40.51 3.58
1495 5475 6.448369 ACTAGTAGATGAGATCTGGCTACT 57.552 41.667 22.31 22.31 42.92 2.57
1496 5476 6.848069 ACTAGTAGATGAGATCTGGCTACTT 58.152 40.000 23.19 11.45 41.27 2.24
1497 5477 6.714810 ACTAGTAGATGAGATCTGGCTACTTG 59.285 42.308 23.19 22.51 41.27 3.16
1499 5479 3.036819 AGATGAGATCTGGCTACTTGCA 58.963 45.455 0.00 0.00 38.88 4.08
1500 5480 3.453717 AGATGAGATCTGGCTACTTGCAA 59.546 43.478 0.00 0.00 38.88 4.08
1584 5990 0.033504 ATGCGTCCTGTTCGTCAACT 59.966 50.000 0.00 0.00 33.17 3.16
1747 6202 2.190981 CTACGGCGATTTCACCTACAC 58.809 52.381 16.62 0.00 0.00 2.90
1873 6328 0.595095 CAAGACAAGGCAAGCTCACC 59.405 55.000 0.00 0.00 0.00 4.02
1948 6413 3.375642 GCTCAAACAGTCTGCCTTTTTC 58.624 45.455 0.00 0.00 0.00 2.29
2012 6478 0.404426 GTAACAGGCCCCTTCAGGTT 59.596 55.000 0.00 0.00 0.00 3.50
2033 6499 3.149196 TCTTGACATCAGGGCTTTTGTC 58.851 45.455 3.33 3.33 39.11 3.18
2060 7340 3.688185 GCAATGGTGCTATCATCATCGAT 59.312 43.478 0.00 0.00 42.92 3.59
2242 7530 1.210155 GCAGCGGCAAAGTTAGGTG 59.790 57.895 3.18 0.00 40.72 4.00
2247 7535 1.081442 GGCAAAGTTAGGTGCACGC 60.081 57.895 11.45 5.63 42.74 5.34
2588 7879 8.726870 GGTAAGTACCAGACTATTGCATTAAA 57.273 34.615 2.47 0.00 45.73 1.52
2603 7894 5.680619 TGCATTAAACATCGTCCTATCCTT 58.319 37.500 0.00 0.00 0.00 3.36
3281 8580 1.273606 AGTTGAGACATCGTCAGGGTG 59.726 52.381 0.00 0.00 34.60 4.61
4681 10017 5.183140 ACTTGGCTACGTGATTAATTTGCTT 59.817 36.000 0.00 0.00 0.00 3.91
5126 10466 2.744494 GCAGTTGAGGAGGAGGCTAATG 60.744 54.545 0.00 0.00 0.00 1.90
5163 10506 7.840342 ATATCTGACTGAATCTTGTGTTGAC 57.160 36.000 0.00 0.00 0.00 3.18
5946 11476 1.478105 CTTGCCTTACATTTGGAGGGC 59.522 52.381 8.92 8.92 39.93 5.19
5947 11477 0.407528 TGCCTTACATTTGGAGGGCA 59.592 50.000 14.16 14.16 45.81 5.36
5948 11478 0.817654 GCCTTACATTTGGAGGGCAC 59.182 55.000 10.85 0.00 39.38 5.01
5949 11479 1.616994 GCCTTACATTTGGAGGGCACT 60.617 52.381 10.85 0.00 39.38 4.40
5950 11480 2.356741 GCCTTACATTTGGAGGGCACTA 60.357 50.000 10.85 0.00 39.38 2.74
6420 11988 4.521062 CGGGCGGAAGAGGAGCAG 62.521 72.222 0.00 0.00 0.00 4.24
6421 11989 4.847444 GGGCGGAAGAGGAGCAGC 62.847 72.222 0.00 0.00 0.00 5.25
6422 11990 4.087892 GGCGGAAGAGGAGCAGCA 62.088 66.667 0.00 0.00 0.00 4.41
6423 11991 2.188994 GCGGAAGAGGAGCAGCAT 59.811 61.111 0.00 0.00 0.00 3.79
6424 11992 2.178890 GCGGAAGAGGAGCAGCATG 61.179 63.158 0.00 0.00 40.87 4.06
6435 12003 2.353958 CAGCATGCAGGGTGAGGT 59.646 61.111 25.13 0.00 38.52 3.85
6436 12004 1.748122 CAGCATGCAGGGTGAGGTC 60.748 63.158 25.13 0.00 38.52 3.85
6437 12005 2.821366 GCATGCAGGGTGAGGTCG 60.821 66.667 14.21 0.00 0.00 4.79
6438 12006 2.981302 CATGCAGGGTGAGGTCGA 59.019 61.111 0.00 0.00 0.00 4.20
6439 12007 1.153489 CATGCAGGGTGAGGTCGAG 60.153 63.158 0.00 0.00 0.00 4.04
6440 12008 1.305297 ATGCAGGGTGAGGTCGAGA 60.305 57.895 0.00 0.00 0.00 4.04
6441 12009 0.904865 ATGCAGGGTGAGGTCGAGAA 60.905 55.000 0.00 0.00 0.00 2.87
6442 12010 1.079750 GCAGGGTGAGGTCGAGAAC 60.080 63.158 0.00 0.00 0.00 3.01
6451 12019 3.701454 GTCGAGAACCAGCTCCCT 58.299 61.111 0.00 0.00 0.00 4.20
6452 12020 1.216710 GTCGAGAACCAGCTCCCTG 59.783 63.158 0.00 0.00 38.85 4.45
6453 12021 2.125350 CGAGAACCAGCTCCCTGC 60.125 66.667 0.00 0.00 43.29 4.85
6481 12049 4.821589 GCCGTGGCGAGGAAGAGG 62.822 72.222 0.00 0.00 0.00 3.69
6482 12050 3.068691 CCGTGGCGAGGAAGAGGA 61.069 66.667 0.00 0.00 0.00 3.71
6483 12051 2.492090 CGTGGCGAGGAAGAGGAG 59.508 66.667 0.00 0.00 0.00 3.69
6729 12450 6.544650 TGAGATGAGATGAGATGAGATGAGA 58.455 40.000 0.00 0.00 0.00 3.27
6730 12451 6.431852 TGAGATGAGATGAGATGAGATGAGAC 59.568 42.308 0.00 0.00 0.00 3.36
6732 12453 3.819902 TGAGATGAGATGAGATGAGACGG 59.180 47.826 0.00 0.00 0.00 4.79
6735 12456 2.302260 TGAGATGAGATGAGACGGGAC 58.698 52.381 0.00 0.00 0.00 4.46
6778 12499 2.910199 TGCATTGCTCTAGTGATGACC 58.090 47.619 10.49 0.00 0.00 4.02
6786 12507 3.763902 CTCTAGTGATGACCGACTTGTG 58.236 50.000 0.00 0.00 0.00 3.33
6876 12716 9.361315 GTGAATGAATGAATGAATGAATCACAA 57.639 29.630 0.00 0.00 41.93 3.33
6914 12788 6.533723 TGTTGTTGTTGTTGTTGTTGTTGTTA 59.466 30.769 0.00 0.00 0.00 2.41
6984 15322 1.467190 TTCAATGGTGGGGGTCCCT 60.467 57.895 8.15 0.00 45.70 4.20
6986 15324 2.212761 AATGGTGGGGGTCCCTCA 59.787 61.111 6.30 6.30 45.70 3.86
7121 15483 5.580691 TGTTTTGAGCTGGATATCGTTACAG 59.419 40.000 0.00 0.00 0.00 2.74
7222 16853 8.542497 ACGCTCATTTGAAGTAGTGTTATAAA 57.458 30.769 0.00 0.00 28.65 1.40
7223 16854 9.162764 ACGCTCATTTGAAGTAGTGTTATAAAT 57.837 29.630 0.00 0.00 28.65 1.40
7250 18167 0.337428 AGAGGGGCCATTGATTTGCT 59.663 50.000 4.39 0.00 0.00 3.91
7251 18168 1.570501 AGAGGGGCCATTGATTTGCTA 59.429 47.619 4.39 0.00 0.00 3.49
7252 18169 2.024080 AGAGGGGCCATTGATTTGCTAA 60.024 45.455 4.39 0.00 0.00 3.09
7253 18170 2.765699 GAGGGGCCATTGATTTGCTAAA 59.234 45.455 4.39 0.00 0.00 1.85
7327 18250 1.798223 GTTATGTGCTGACGTTCTGCA 59.202 47.619 12.85 12.85 46.64 4.41
7344 18267 1.341156 GCATGCAGTCCTCCTACCCT 61.341 60.000 14.21 0.00 0.00 4.34
7345 18268 2.034799 GCATGCAGTCCTCCTACCCTA 61.035 57.143 14.21 0.00 0.00 3.53
7346 18269 2.398588 CATGCAGTCCTCCTACCCTAA 58.601 52.381 0.00 0.00 0.00 2.69
7447 18455 1.595382 ACCGCAGCAGTGTTGAGTC 60.595 57.895 11.60 0.00 0.00 3.36
7448 18456 2.320587 CCGCAGCAGTGTTGAGTCC 61.321 63.158 11.60 0.00 0.00 3.85
7449 18457 1.595109 CGCAGCAGTGTTGAGTCCA 60.595 57.895 11.60 0.00 0.00 4.02
7450 18458 1.563435 CGCAGCAGTGTTGAGTCCAG 61.563 60.000 11.60 0.00 0.00 3.86
7451 18459 1.849976 GCAGCAGTGTTGAGTCCAGC 61.850 60.000 11.60 0.00 0.00 4.85
7452 18460 0.533531 CAGCAGTGTTGAGTCCAGCA 60.534 55.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
731 734 2.087646 GCCACCAGACTTCCTTGAATC 58.912 52.381 0.00 0.00 0.00 2.52
734 737 1.003580 GATGCCACCAGACTTCCTTGA 59.996 52.381 0.00 0.00 0.00 3.02
735 738 1.004044 AGATGCCACCAGACTTCCTTG 59.996 52.381 0.00 0.00 0.00 3.61
747 2481 2.027385 GAGGGAATGGAAAGATGCCAC 58.973 52.381 0.00 0.00 38.44 5.01
748 2482 1.063717 GGAGGGAATGGAAAGATGCCA 60.064 52.381 0.00 0.00 40.24 4.92
773 2507 1.087501 GGACTGCCTTGAATCCGAAC 58.912 55.000 0.00 0.00 0.00 3.95
808 2542 1.349627 CGTCGGTGATGCATTGCTC 59.650 57.895 10.49 5.76 0.00 4.26
839 2573 2.367512 CAAGAGGGGAGGGGAGGG 60.368 72.222 0.00 0.00 0.00 4.30
840 2574 2.367512 CCAAGAGGGGAGGGGAGG 60.368 72.222 0.00 0.00 0.00 4.30
841 2575 1.997874 CACCAAGAGGGGAGGGGAG 60.998 68.421 0.00 0.00 42.79 4.30
842 2576 2.124996 CACCAAGAGGGGAGGGGA 59.875 66.667 0.00 0.00 42.79 4.81
843 2577 3.732849 GCACCAAGAGGGGAGGGG 61.733 72.222 0.00 0.00 42.79 4.79
876 2610 1.118965 TGCTTGTCGGTGAGGAAGGA 61.119 55.000 0.00 0.00 0.00 3.36
887 2621 0.318699 TTGAGGACGAGTGCTTGTCG 60.319 55.000 12.04 2.04 43.34 4.35
899 2633 3.181465 TGACTCTGTTGGTTCTTGAGGAC 60.181 47.826 0.00 0.00 0.00 3.85
942 2676 4.640771 AAGATGCCACCAGACTTCTTTA 57.359 40.909 0.00 0.00 28.92 1.85
945 2679 2.641815 AGAAAGATGCCACCAGACTTCT 59.358 45.455 0.00 0.00 0.00 2.85
947 2681 4.851639 ATAGAAAGATGCCACCAGACTT 57.148 40.909 0.00 0.00 0.00 3.01
952 2686 2.852449 AGGGAATAGAAAGATGCCACCA 59.148 45.455 0.00 0.00 0.00 4.17
954 2688 3.481453 GGAGGGAATAGAAAGATGCCAC 58.519 50.000 0.00 0.00 0.00 5.01
955 2689 2.443255 GGGAGGGAATAGAAAGATGCCA 59.557 50.000 0.00 0.00 0.00 4.92
957 2691 4.140536 CAAGGGAGGGAATAGAAAGATGC 58.859 47.826 0.00 0.00 0.00 3.91
966 2700 1.209621 CCGAACCAAGGGAGGGAATA 58.790 55.000 0.00 0.00 0.00 1.75
980 2714 2.151202 TCAACTGCCTTGAATCCGAAC 58.849 47.619 0.00 0.00 35.84 3.95
1003 2737 0.385473 CTGTTGGGCAAAACGCGTAG 60.385 55.000 14.46 7.09 43.84 3.51
1004 2738 1.096386 ACTGTTGGGCAAAACGCGTA 61.096 50.000 14.46 0.00 43.84 4.42
1005 2739 1.939769 AACTGTTGGGCAAAACGCGT 61.940 50.000 5.58 5.58 43.84 6.01
1006 2740 0.804156 AAACTGTTGGGCAAAACGCG 60.804 50.000 3.53 3.53 43.84 6.01
1008 2742 0.649993 GCAAACTGTTGGGCAAAACG 59.350 50.000 11.24 0.00 35.10 3.60
1010 2744 2.706339 ATGCAAACTGTTGGGCAAAA 57.294 40.000 19.56 2.46 40.02 2.44
1012 2746 1.617850 CCTATGCAAACTGTTGGGCAA 59.382 47.619 19.56 10.91 40.02 4.52
1013 2747 1.255882 CCTATGCAAACTGTTGGGCA 58.744 50.000 18.44 18.44 41.00 5.36
1040 4293 1.835483 CTGTGTGTGTGCTCGGCTTC 61.835 60.000 0.00 0.00 0.00 3.86
1042 4295 2.280389 CTGTGTGTGTGCTCGGCT 60.280 61.111 0.00 0.00 0.00 5.52
1046 4299 4.017877 GCCGCTGTGTGTGTGCTC 62.018 66.667 0.00 0.00 0.00 4.26
1047 4300 4.854924 TGCCGCTGTGTGTGTGCT 62.855 61.111 0.00 0.00 0.00 4.40
1048 4301 4.318021 CTGCCGCTGTGTGTGTGC 62.318 66.667 0.00 0.00 0.00 4.57
1049 4302 4.318021 GCTGCCGCTGTGTGTGTG 62.318 66.667 0.00 0.00 0.00 3.82
1050 4303 4.854924 TGCTGCCGCTGTGTGTGT 62.855 61.111 0.70 0.00 36.97 3.72
1052 4305 3.585990 GTTGCTGCCGCTGTGTGT 61.586 61.111 0.70 0.00 36.97 3.72
1053 4306 4.332637 GGTTGCTGCCGCTGTGTG 62.333 66.667 0.70 0.00 36.97 3.82
1057 4310 3.818787 GATGGGTTGCTGCCGCTG 61.819 66.667 0.70 0.00 36.97 5.18
1060 4313 0.538057 ATATGGATGGGTTGCTGCCG 60.538 55.000 0.00 0.00 0.00 5.69
1061 4314 1.251251 GATATGGATGGGTTGCTGCC 58.749 55.000 0.00 0.00 0.00 4.85
1062 4315 1.251251 GGATATGGATGGGTTGCTGC 58.749 55.000 0.00 0.00 0.00 5.25
1065 4318 6.610075 AAAATATGGATATGGATGGGTTGC 57.390 37.500 0.00 0.00 0.00 4.17
1066 4319 7.176515 TCGAAAAATATGGATATGGATGGGTTG 59.823 37.037 0.00 0.00 0.00 3.77
1067 4320 7.237982 TCGAAAAATATGGATATGGATGGGTT 58.762 34.615 0.00 0.00 0.00 4.11
1068 4321 6.789268 TCGAAAAATATGGATATGGATGGGT 58.211 36.000 0.00 0.00 0.00 4.51
1069 4322 7.701539 TTCGAAAAATATGGATATGGATGGG 57.298 36.000 0.00 0.00 0.00 4.00
1070 4323 9.793252 GATTTCGAAAAATATGGATATGGATGG 57.207 33.333 15.66 0.00 35.21 3.51
1071 4324 9.793252 GGATTTCGAAAAATATGGATATGGATG 57.207 33.333 15.66 0.00 35.21 3.51
1072 4325 8.677300 CGGATTTCGAAAAATATGGATATGGAT 58.323 33.333 15.66 0.00 42.43 3.41
1074 4327 8.039603 TCGGATTTCGAAAAATATGGATATGG 57.960 34.615 15.66 0.00 45.86 2.74
1090 4343 4.516698 AGATGGATTTGGATTCGGATTTCG 59.483 41.667 0.00 0.00 40.90 3.46
1098 4903 4.443978 TGGAGGAGATGGATTTGGATTC 57.556 45.455 0.00 0.00 0.00 2.52
1137 4957 3.480133 GGGTCCATGGGGTCGGAG 61.480 72.222 13.02 0.00 34.93 4.63
1146 4976 1.526917 GCCTTCCATCGGGTCCATG 60.527 63.158 0.00 0.00 34.93 3.66
1148 4978 3.781307 CGCCTTCCATCGGGTCCA 61.781 66.667 0.00 0.00 34.93 4.02
1149 4979 3.467226 TCGCCTTCCATCGGGTCC 61.467 66.667 0.00 0.00 34.93 4.46
1375 5257 0.849540 GGGGAAGGGGAAGGGAAGAA 60.850 60.000 0.00 0.00 0.00 2.52
1391 5273 2.736670 AACTAATAGCCAAGCAGGGG 57.263 50.000 0.00 0.00 38.09 4.79
1392 5274 3.620488 TGAAACTAATAGCCAAGCAGGG 58.380 45.455 0.00 0.00 38.09 4.45
1395 5277 5.804639 TCTCTTGAAACTAATAGCCAAGCA 58.195 37.500 10.67 1.64 35.48 3.91
1396 5278 5.220758 GCTCTCTTGAAACTAATAGCCAAGC 60.221 44.000 10.67 0.00 35.48 4.01
1397 5279 5.006165 CGCTCTCTTGAAACTAATAGCCAAG 59.994 44.000 9.75 9.75 36.49 3.61
1398 5280 4.870426 CGCTCTCTTGAAACTAATAGCCAA 59.130 41.667 0.00 0.00 0.00 4.52
1399 5281 4.081642 ACGCTCTCTTGAAACTAATAGCCA 60.082 41.667 0.00 0.00 0.00 4.75
1401 5283 4.268884 CCACGCTCTCTTGAAACTAATAGC 59.731 45.833 0.00 0.00 0.00 2.97
1403 5285 5.654603 TCCACGCTCTCTTGAAACTAATA 57.345 39.130 0.00 0.00 0.00 0.98
1404 5286 4.537135 TCCACGCTCTCTTGAAACTAAT 57.463 40.909 0.00 0.00 0.00 1.73
1405 5287 4.537135 ATCCACGCTCTCTTGAAACTAA 57.463 40.909 0.00 0.00 0.00 2.24
1406 5288 4.537135 AATCCACGCTCTCTTGAAACTA 57.463 40.909 0.00 0.00 0.00 2.24
1407 5289 3.409026 AATCCACGCTCTCTTGAAACT 57.591 42.857 0.00 0.00 0.00 2.66
1408 5290 3.365364 CCAAATCCACGCTCTCTTGAAAC 60.365 47.826 0.00 0.00 0.00 2.78
1409 5291 2.813754 CCAAATCCACGCTCTCTTGAAA 59.186 45.455 0.00 0.00 0.00 2.69
1410 5292 2.426522 CCAAATCCACGCTCTCTTGAA 58.573 47.619 0.00 0.00 0.00 2.69
1413 5295 0.326264 AGCCAAATCCACGCTCTCTT 59.674 50.000 0.00 0.00 0.00 2.85
1414 5296 0.107945 GAGCCAAATCCACGCTCTCT 60.108 55.000 1.14 0.00 44.52 3.10
1415 5297 1.092345 GGAGCCAAATCCACGCTCTC 61.092 60.000 8.08 0.00 46.60 3.20
1416 5298 1.078143 GGAGCCAAATCCACGCTCT 60.078 57.895 8.08 0.00 46.60 4.09
1418 5300 2.044946 GGGAGCCAAATCCACGCT 60.045 61.111 0.00 0.00 41.52 5.07
1449 5429 0.575390 GAATTGCGATACACGGACGG 59.425 55.000 0.00 0.00 42.85 4.79
1450 5430 0.226235 CGAATTGCGATACACGGACG 59.774 55.000 0.00 0.00 42.85 4.79
1451 5431 0.043310 GCGAATTGCGATACACGGAC 60.043 55.000 9.15 0.00 42.85 4.79
1462 5442 5.043903 TCTCATCTACTAGTTGCGAATTGC 58.956 41.667 0.00 0.00 46.70 3.56
1463 5443 7.114670 CAGATCTCATCTACTAGTTGCGAATTG 59.885 40.741 0.00 0.00 37.58 2.32
1464 5444 7.144661 CAGATCTCATCTACTAGTTGCGAATT 58.855 38.462 0.00 0.00 37.58 2.17
1465 5445 6.294453 CCAGATCTCATCTACTAGTTGCGAAT 60.294 42.308 0.00 0.00 37.58 3.34
1466 5446 5.009110 CCAGATCTCATCTACTAGTTGCGAA 59.991 44.000 0.00 0.00 37.58 4.70
1467 5447 4.517075 CCAGATCTCATCTACTAGTTGCGA 59.483 45.833 0.00 0.00 37.58 5.10
1468 5448 4.793071 CCAGATCTCATCTACTAGTTGCG 58.207 47.826 0.00 0.00 37.58 4.85
1469 5449 4.280677 AGCCAGATCTCATCTACTAGTTGC 59.719 45.833 0.00 0.00 37.58 4.17
1470 5450 6.714810 AGTAGCCAGATCTCATCTACTAGTTG 59.285 42.308 18.99 0.00 38.41 3.16
1471 5451 6.848069 AGTAGCCAGATCTCATCTACTAGTT 58.152 40.000 18.99 4.06 38.41 2.24
1472 5452 6.448369 AGTAGCCAGATCTCATCTACTAGT 57.552 41.667 18.99 0.00 38.41 2.57
1473 5453 6.349280 GCAAGTAGCCAGATCTCATCTACTAG 60.349 46.154 19.99 0.00 39.02 2.57
1474 5454 5.475220 GCAAGTAGCCAGATCTCATCTACTA 59.525 44.000 19.99 4.52 39.02 1.82
1478 5458 3.036819 TGCAAGTAGCCAGATCTCATCT 58.963 45.455 0.00 0.00 44.83 2.90
1530 5561 1.771255 GAGAGAGAGAGAGAGAGGGCT 59.229 57.143 0.00 0.00 0.00 5.19
1533 5564 3.963374 TGAGAGAGAGAGAGAGAGAGAGG 59.037 52.174 0.00 0.00 0.00 3.69
1681 6136 1.153449 TCGCCGCCTTCAACTATGG 60.153 57.895 0.00 0.00 0.00 2.74
1873 6328 7.584987 ACGAAATTTATGAGAGAAACAAGTGG 58.415 34.615 0.00 0.00 0.00 4.00
1948 6413 7.019774 TCAAGTTGAGACAAAATCTGTGAAG 57.980 36.000 0.08 0.00 38.84 3.02
2012 6478 3.149196 GACAAAAGCCCTGATGTCAAGA 58.851 45.455 0.00 0.00 41.35 3.02
2060 7340 4.202535 GGGTTTCCTCTTACTCCCTTGAAA 60.203 45.833 0.00 0.00 32.89 2.69
2242 7530 4.752879 TAAGCCACTCCCGCGTGC 62.753 66.667 4.92 0.00 33.60 5.34
2247 7535 1.173043 TTTTGCATAAGCCACTCCCG 58.827 50.000 0.00 0.00 41.13 5.14
2588 7879 3.689649 GCAAAACAAGGATAGGACGATGT 59.310 43.478 0.00 0.00 0.00 3.06
3281 8580 6.867816 TCCATCAAAATCTACAACACATTTGC 59.132 34.615 0.00 0.00 0.00 3.68
3849 9157 6.911250 AACAAAATGAAGGGTACTAAAGGG 57.089 37.500 0.00 0.00 0.00 3.95
4681 10017 6.042143 GCAATTGTGGAGAAGAACAGAAAAA 58.958 36.000 7.40 0.00 0.00 1.94
5163 10506 6.454795 AGTGAAGAAAAGCAGTCTAGAAGAG 58.545 40.000 0.00 0.00 0.00 2.85
5403 10916 7.444183 GCATTATTATCTGCCTTACCTTACACA 59.556 37.037 0.00 0.00 32.15 3.72
5811 11335 3.194116 CCATTGCCTGCACATTTCTTAGT 59.806 43.478 0.00 0.00 0.00 2.24
5812 11336 3.444742 TCCATTGCCTGCACATTTCTTAG 59.555 43.478 0.00 0.00 0.00 2.18
5813 11337 3.429492 TCCATTGCCTGCACATTTCTTA 58.571 40.909 0.00 0.00 0.00 2.10
5814 11338 2.250031 TCCATTGCCTGCACATTTCTT 58.750 42.857 0.00 0.00 0.00 2.52
5815 11339 1.927487 TCCATTGCCTGCACATTTCT 58.073 45.000 0.00 0.00 0.00 2.52
5816 11340 2.747396 TTCCATTGCCTGCACATTTC 57.253 45.000 0.00 0.00 0.00 2.17
5946 11476 6.693545 GCTCTGCATTACTAACTAGTGTAGTG 59.306 42.308 19.50 15.08 39.39 2.74
5947 11477 6.183360 GGCTCTGCATTACTAACTAGTGTAGT 60.183 42.308 16.66 16.66 41.73 2.73
5948 11478 6.039941 AGGCTCTGCATTACTAACTAGTGTAG 59.960 42.308 0.00 3.51 37.10 2.74
5949 11479 5.892119 AGGCTCTGCATTACTAACTAGTGTA 59.108 40.000 0.00 0.00 37.10 2.90
5950 11480 4.712337 AGGCTCTGCATTACTAACTAGTGT 59.288 41.667 0.00 0.00 37.10 3.55
6418 11986 1.748122 GACCTCACCCTGCATGCTG 60.748 63.158 20.33 18.55 0.00 4.41
6419 11987 2.673523 GACCTCACCCTGCATGCT 59.326 61.111 20.33 0.00 0.00 3.79
6420 11988 2.821366 CGACCTCACCCTGCATGC 60.821 66.667 11.82 11.82 0.00 4.06
6421 11989 1.153489 CTCGACCTCACCCTGCATG 60.153 63.158 0.00 0.00 0.00 4.06
6422 11990 0.904865 TTCTCGACCTCACCCTGCAT 60.905 55.000 0.00 0.00 0.00 3.96
6423 11991 1.533033 TTCTCGACCTCACCCTGCA 60.533 57.895 0.00 0.00 0.00 4.41
6424 11992 1.079750 GTTCTCGACCTCACCCTGC 60.080 63.158 0.00 0.00 0.00 4.85
6425 11993 1.592223 GGTTCTCGACCTCACCCTG 59.408 63.158 0.00 0.00 45.55 4.45
6426 11994 4.115270 GGTTCTCGACCTCACCCT 57.885 61.111 0.00 0.00 45.55 4.34
6434 12002 1.216710 CAGGGAGCTGGTTCTCGAC 59.783 63.158 0.00 0.00 33.98 4.20
6435 12003 2.650116 GCAGGGAGCTGGTTCTCGA 61.650 63.158 0.00 0.00 41.15 4.04
6436 12004 2.125350 GCAGGGAGCTGGTTCTCG 60.125 66.667 0.00 0.00 41.15 4.04
6464 12032 4.821589 CCTCTTCCTCGCCACGGC 62.822 72.222 0.00 0.00 37.85 5.68
6465 12033 3.068691 TCCTCTTCCTCGCCACGG 61.069 66.667 0.00 0.00 0.00 4.94
6466 12034 2.492090 CTCCTCTTCCTCGCCACG 59.508 66.667 0.00 0.00 0.00 4.94
6467 12035 2.185608 GCTCCTCTTCCTCGCCAC 59.814 66.667 0.00 0.00 0.00 5.01
6468 12036 3.077556 GGCTCCTCTTCCTCGCCA 61.078 66.667 0.00 0.00 40.41 5.69
6469 12037 2.762043 AGGCTCCTCTTCCTCGCC 60.762 66.667 0.00 0.00 40.99 5.54
6470 12038 2.498726 CAGGCTCCTCTTCCTCGC 59.501 66.667 0.00 0.00 0.00 5.03
6471 12039 2.295472 CTGCAGGCTCCTCTTCCTCG 62.295 65.000 5.57 0.00 0.00 4.63
6472 12040 1.521616 CTGCAGGCTCCTCTTCCTC 59.478 63.158 5.57 0.00 0.00 3.71
6473 12041 1.994507 CCTGCAGGCTCCTCTTCCT 60.995 63.158 22.33 0.00 0.00 3.36
6474 12042 2.588989 CCTGCAGGCTCCTCTTCC 59.411 66.667 22.33 0.00 0.00 3.46
6475 12043 2.588989 CCCTGCAGGCTCCTCTTC 59.411 66.667 28.39 0.00 0.00 2.87
6618 12309 3.043713 TCTTGTTGCTGCTCGCCG 61.044 61.111 0.00 0.00 38.05 6.46
6778 12499 5.387279 ACAAACAAAGTTACACACAAGTCG 58.613 37.500 0.00 0.00 0.00 4.18
6876 12716 2.625790 ACAACAACAACAACACACAGGT 59.374 40.909 0.00 0.00 0.00 4.00
6947 15275 7.040062 CCATTGAACCAACTTACAATTACCTCA 60.040 37.037 0.00 0.00 31.85 3.86
6956 15284 3.226777 CCCACCATTGAACCAACTTACA 58.773 45.455 0.00 0.00 0.00 2.41
6957 15285 2.560981 CCCCACCATTGAACCAACTTAC 59.439 50.000 0.00 0.00 0.00 2.34
6984 15322 5.987953 GCAGAGCTATGTGTTAAGATGATGA 59.012 40.000 10.55 0.00 0.00 2.92
6986 15324 5.071519 AGGCAGAGCTATGTGTTAAGATGAT 59.928 40.000 10.55 0.00 0.00 2.45
7121 15483 7.728847 AGGTCCTTTTTCAAAATGTTTATGC 57.271 32.000 0.00 0.00 0.00 3.14
7187 15554 9.180678 CTACTTCAAATGAGCGTTTACAAATTT 57.819 29.630 0.00 0.00 0.00 1.82
7222 16853 5.402054 TCAATGGCCCCTCTAAACATTAT 57.598 39.130 0.00 0.00 31.19 1.28
7223 16854 4.871871 TCAATGGCCCCTCTAAACATTA 57.128 40.909 0.00 0.00 31.19 1.90
7224 16855 3.756082 TCAATGGCCCCTCTAAACATT 57.244 42.857 0.00 0.00 32.43 2.71
7327 18250 2.022918 AGTTAGGGTAGGAGGACTGCAT 60.023 50.000 0.00 0.00 32.86 3.96
7344 18267 2.185387 GCTCTGGTGGGGAACTAGTTA 58.815 52.381 8.42 0.00 38.48 2.24
7345 18268 0.984995 GCTCTGGTGGGGAACTAGTT 59.015 55.000 8.13 8.13 38.48 2.24
7346 18269 0.178903 TGCTCTGGTGGGGAACTAGT 60.179 55.000 0.00 0.00 38.48 2.57
7447 18455 1.970114 CTTCTGGTGCTGGTGCTGG 60.970 63.158 0.00 0.00 40.48 4.85
7448 18456 2.623915 GCTTCTGGTGCTGGTGCTG 61.624 63.158 0.00 0.00 40.48 4.41
7449 18457 2.282040 GCTTCTGGTGCTGGTGCT 60.282 61.111 0.00 0.00 40.48 4.40
7450 18458 2.595463 TGCTTCTGGTGCTGGTGC 60.595 61.111 0.00 0.00 40.20 5.01
7451 18459 0.535780 TTCTGCTTCTGGTGCTGGTG 60.536 55.000 0.00 0.00 0.00 4.17
7452 18460 0.536006 GTTCTGCTTCTGGTGCTGGT 60.536 55.000 0.00 0.00 0.00 4.00
7494 18524 3.379445 GCCCTCCTCAACGGACGA 61.379 66.667 0.00 0.00 36.69 4.20


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

AutoCloner maintained by Alex Coulton.