Multiple sequence alignment - TraesCS5D01G090100

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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 TraesCS5D01G090100 chr5D 100.000 5816 0 0 1 5816 97273773 97279588 0.000000e+00 10741.0
1 TraesCS5D01G090100 chr5D 94.688 753 25 6 5076 5816 398821246 398821995 0.000000e+00 1155.0
2 TraesCS5D01G090100 chr5D 91.788 755 47 11 5075 5816 35118192 35118944 0.000000e+00 1037.0
3 TraesCS5D01G090100 chr5D 81.651 872 140 18 3453 4311 97325152 97326016 0.000000e+00 706.0
4 TraesCS5D01G090100 chr5D 75.362 552 101 27 2062 2590 97323771 97324310 3.500000e-57 233.0
5 TraesCS5D01G090100 chr5D 84.049 163 24 2 2717 2878 97324454 97324615 7.800000e-34 156.0
6 TraesCS5D01G090100 chr5D 86.364 110 13 2 2235 2343 97043444 97043552 1.020000e-22 119.0
7 TraesCS5D01G090100 chr5D 88.333 60 6 1 1183 1242 439643613 439643671 2.910000e-08 71.3
8 TraesCS5D01G090100 chr5B 94.891 3543 152 16 1539 5073 103471071 103474592 0.000000e+00 5513.0
9 TraesCS5D01G090100 chr5B 94.352 3541 148 21 1539 5073 105710356 105713850 0.000000e+00 5384.0
10 TraesCS5D01G090100 chr5B 85.304 1218 64 53 1 1190 103469568 103470698 0.000000e+00 1151.0
11 TraesCS5D01G090100 chr5B 81.860 871 133 19 3453 4306 105769860 105770722 0.000000e+00 710.0
12 TraesCS5D01G090100 chr5B 88.385 551 16 16 609 1145 105701714 105702230 2.300000e-173 619.0
13 TraesCS5D01G090100 chr5B 83.929 616 37 26 2 609 105700803 105701364 3.090000e-147 532.0
14 TraesCS5D01G090100 chr5B 86.059 373 47 5 3942 4311 103572170 103572540 4.220000e-106 396.0
15 TraesCS5D01G090100 chr5B 83.372 433 61 9 3453 3882 103571596 103572020 1.970000e-104 390.0
16 TraesCS5D01G090100 chr5B 81.121 339 52 9 3018 3352 103571196 103571526 1.610000e-65 261.0
17 TraesCS5D01G090100 chr5B 75.725 552 96 30 2062 2590 103570220 103570756 5.820000e-60 243.0
18 TraesCS5D01G090100 chr5B 83.951 243 28 6 1239 1473 105709992 105710231 7.590000e-54 222.0
19 TraesCS5D01G090100 chr5B 74.499 549 96 32 2062 2590 105768497 105769021 1.280000e-46 198.0
20 TraesCS5D01G090100 chr5B 85.629 167 21 3 2720 2885 103570906 103571070 7.750000e-39 172.0
21 TraesCS5D01G090100 chr5B 85.276 163 22 2 2717 2878 105769163 105769324 3.600000e-37 167.0
22 TraesCS5D01G090100 chr5B 94.340 53 0 2 1190 1242 278886775 278886824 1.740000e-10 78.7
23 TraesCS5D01G090100 chr5A 93.980 3555 174 20 1539 5073 92443366 92446900 0.000000e+00 5343.0
24 TraesCS5D01G090100 chr5A 91.111 1215 76 19 1 1200 92441809 92443006 0.000000e+00 1616.0
25 TraesCS5D01G090100 chr5A 88.102 353 40 2 3960 4311 106748637 106748286 9.010000e-113 418.0
26 TraesCS5D01G090100 chr5A 83.028 436 61 9 3453 3882 106749163 106748735 3.290000e-102 383.0
27 TraesCS5D01G090100 chr5A 85.507 207 23 3 1275 1474 92443042 92443248 5.910000e-50 209.0
28 TraesCS5D01G090100 chr5A 78.249 354 55 16 2254 2590 106750352 106750004 2.120000e-49 207.0
29 TraesCS5D01G090100 chr5A 84.756 164 22 3 2723 2885 106749855 106749694 1.680000e-35 161.0
30 TraesCS5D01G090100 chr5A 82.759 87 12 2 2068 2152 106750522 106750437 2.250000e-09 75.0
31 TraesCS5D01G090100 chr2D 96.653 747 16 1 5079 5816 8149538 8150284 0.000000e+00 1232.0
32 TraesCS5D01G090100 chr2D 96.390 748 18 1 5078 5816 182772453 182773200 0.000000e+00 1223.0
33 TraesCS5D01G090100 chr2D 94.913 747 22 3 5079 5816 69971065 69970326 0.000000e+00 1155.0
34 TraesCS5D01G090100 chr2D 92.573 754 41 11 5075 5816 573488496 573487746 0.000000e+00 1068.0
35 TraesCS5D01G090100 chr2D 90.885 757 50 15 5076 5816 483625497 483624744 0.000000e+00 998.0
36 TraesCS5D01G090100 chr2D 94.521 73 3 1 5076 5147 14966615 14966687 1.710000e-20 111.0
37 TraesCS5D01G090100 chr4D 96.272 751 16 3 5078 5816 499723794 499723044 0.000000e+00 1221.0
38 TraesCS5D01G090100 chr4D 95.890 73 1 2 5076 5147 480137147 480137076 3.680000e-22 117.0
39 TraesCS5D01G090100 chr1D 96.144 752 18 3 5076 5816 74411401 74410650 0.000000e+00 1218.0
40 TraesCS5D01G090100 chr1D 91.469 633 42 5 5077 5699 490374600 490373970 0.000000e+00 859.0
41 TraesCS5D01G090100 chr1D 92.727 55 2 1 1188 1242 347215401 347215349 1.740000e-10 78.7
42 TraesCS5D01G090100 chr6D 96.128 749 19 2 5077 5816 448364806 448364059 0.000000e+00 1214.0
43 TraesCS5D01G090100 chr6D 95.467 750 22 6 5079 5816 100489979 100489230 0.000000e+00 1186.0
44 TraesCS5D01G090100 chr7D 95.745 752 20 3 5076 5816 223868449 223867699 0.000000e+00 1201.0
45 TraesCS5D01G090100 chr3D 95.594 749 20 5 5079 5816 149913930 149913184 0.000000e+00 1188.0
46 TraesCS5D01G090100 chr3D 92.430 753 45 8 5074 5816 582732859 582732109 0.000000e+00 1064.0
47 TraesCS5D01G090100 chr7A 81.699 153 22 3 321 467 487716470 487716318 7.910000e-24 122.0
48 TraesCS5D01G090100 chr7B 100.000 46 0 0 1195 1240 687328918 687328963 1.040000e-12 86.1
49 TraesCS5D01G090100 chr3A 97.959 49 0 1 1194 1242 45603357 45603310 3.730000e-12 84.2
50 TraesCS5D01G090100 chr2B 100.000 44 0 0 1199 1242 505494876 505494919 1.340000e-11 82.4
51 TraesCS5D01G090100 chr2B 89.655 58 5 1 1183 1240 1835136 1835080 8.080000e-09 73.1
52 TraesCS5D01G090100 chr6B 91.228 57 3 2 1188 1242 646750157 646750101 6.250000e-10 76.8
53 TraesCS5D01G090100 chr6B 91.228 57 3 2 1188 1242 646750267 646750211 6.250000e-10 76.8
54 TraesCS5D01G090100 chr1A 100.000 34 0 0 3615 3648 377013540 377013573 4.870000e-06 63.9


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 TraesCS5D01G090100 chr5D 97273773 97279588 5815 False 10741.000000 10741 100.000000 1 5816 1 chr5D.!!$F3 5815
1 TraesCS5D01G090100 chr5D 398821246 398821995 749 False 1155.000000 1155 94.688000 5076 5816 1 chr5D.!!$F4 740
2 TraesCS5D01G090100 chr5D 35118192 35118944 752 False 1037.000000 1037 91.788000 5075 5816 1 chr5D.!!$F1 741
3 TraesCS5D01G090100 chr5D 97323771 97326016 2245 False 365.000000 706 80.354000 2062 4311 3 chr5D.!!$F6 2249
4 TraesCS5D01G090100 chr5B 103469568 103474592 5024 False 3332.000000 5513 90.097500 1 5073 2 chr5B.!!$F2 5072
5 TraesCS5D01G090100 chr5B 105709992 105713850 3858 False 2803.000000 5384 89.151500 1239 5073 2 chr5B.!!$F5 3834
6 TraesCS5D01G090100 chr5B 105700803 105702230 1427 False 575.500000 619 86.157000 2 1145 2 chr5B.!!$F4 1143
7 TraesCS5D01G090100 chr5B 105768497 105770722 2225 False 358.333333 710 80.545000 2062 4306 3 chr5B.!!$F6 2244
8 TraesCS5D01G090100 chr5B 103570220 103572540 2320 False 292.400000 396 82.381200 2062 4311 5 chr5B.!!$F3 2249
9 TraesCS5D01G090100 chr5A 92441809 92446900 5091 False 2389.333333 5343 90.199333 1 5073 3 chr5A.!!$F1 5072
10 TraesCS5D01G090100 chr5A 106748286 106750522 2236 True 248.800000 418 83.378800 2068 4311 5 chr5A.!!$R1 2243
11 TraesCS5D01G090100 chr2D 8149538 8150284 746 False 1232.000000 1232 96.653000 5079 5816 1 chr2D.!!$F1 737
12 TraesCS5D01G090100 chr2D 182772453 182773200 747 False 1223.000000 1223 96.390000 5078 5816 1 chr2D.!!$F3 738
13 TraesCS5D01G090100 chr2D 69970326 69971065 739 True 1155.000000 1155 94.913000 5079 5816 1 chr2D.!!$R1 737
14 TraesCS5D01G090100 chr2D 573487746 573488496 750 True 1068.000000 1068 92.573000 5075 5816 1 chr2D.!!$R3 741
15 TraesCS5D01G090100 chr2D 483624744 483625497 753 True 998.000000 998 90.885000 5076 5816 1 chr2D.!!$R2 740
16 TraesCS5D01G090100 chr4D 499723044 499723794 750 True 1221.000000 1221 96.272000 5078 5816 1 chr4D.!!$R2 738
17 TraesCS5D01G090100 chr1D 74410650 74411401 751 True 1218.000000 1218 96.144000 5076 5816 1 chr1D.!!$R1 740
18 TraesCS5D01G090100 chr1D 490373970 490374600 630 True 859.000000 859 91.469000 5077 5699 1 chr1D.!!$R3 622
19 TraesCS5D01G090100 chr6D 448364059 448364806 747 True 1214.000000 1214 96.128000 5077 5816 1 chr6D.!!$R2 739
20 TraesCS5D01G090100 chr6D 100489230 100489979 749 True 1186.000000 1186 95.467000 5079 5816 1 chr6D.!!$R1 737
21 TraesCS5D01G090100 chr7D 223867699 223868449 750 True 1201.000000 1201 95.745000 5076 5816 1 chr7D.!!$R1 740
22 TraesCS5D01G090100 chr3D 149913184 149913930 746 True 1188.000000 1188 95.594000 5079 5816 1 chr3D.!!$R1 737
23 TraesCS5D01G090100 chr3D 582732109 582732859 750 True 1064.000000 1064 92.430000 5074 5816 1 chr3D.!!$R2 742

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
626 1012 0.047176 AGAGGGAGGGAGAGAGGAGA 59.953 60.0 0.0 0.0 0.00 3.71 F
1621 2102 0.037303 AGATGAGGCTGTGGTTGGTG 59.963 55.0 0.0 0.0 0.00 4.17 F
2209 2696 0.461961 CAGGATTCAGACTCCGGGAC 59.538 60.0 0.0 0.0 37.88 4.46 F
2216 2704 0.679505 CAGACTCCGGGACACTTTCA 59.320 55.0 0.0 0.0 0.00 2.69 F
4116 4777 0.750911 CCTGGCTCATCTTTCTGGCC 60.751 60.0 0.0 0.0 42.73 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 2275 0.101040 TGTGCAACTGTTGAGCAAGC 59.899 50.000 23.81 7.94 40.35 4.01 R
2497 3003 3.253921 TGACCATGTTTGAGACAGCAATG 59.746 43.478 0.00 0.00 42.62 2.82 R
4116 4777 0.395312 AGTACCCAAGAACACGGTGG 59.605 55.000 13.48 0.00 0.00 4.61 R
4715 5378 0.108992 ATCATACACGTTGCCGTCGT 60.109 50.000 0.00 0.00 46.28 4.34 R
5732 6428 1.522569 GAATAGGCTGCCCACGTCT 59.477 57.895 16.57 0.00 0.00 4.18 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
73 82 5.700832 TCATACTCACTGTCCAACAATCAAC 59.299 40.000 0.00 0.00 0.00 3.18
74 83 3.884895 ACTCACTGTCCAACAATCAACA 58.115 40.909 0.00 0.00 0.00 3.33
112 121 1.228862 AATGGGGTTCCTGTGTGCC 60.229 57.895 0.00 0.00 0.00 5.01
154 163 0.983378 GGAGAGAAAGGGGGCTGCTA 60.983 60.000 0.00 0.00 0.00 3.49
226 240 0.975040 TGCAGAGAGGAAGAGAGGGC 60.975 60.000 0.00 0.00 0.00 5.19
295 309 2.038557 ACGCCCAGTGTCTAAAACTGAT 59.961 45.455 5.17 0.00 46.55 2.90
296 310 3.259876 ACGCCCAGTGTCTAAAACTGATA 59.740 43.478 5.17 0.00 46.55 2.15
297 311 4.081087 ACGCCCAGTGTCTAAAACTGATAT 60.081 41.667 5.17 0.00 46.55 1.63
298 312 4.876107 CGCCCAGTGTCTAAAACTGATATT 59.124 41.667 5.17 0.00 46.55 1.28
299 313 5.006746 CGCCCAGTGTCTAAAACTGATATTC 59.993 44.000 5.17 0.00 46.55 1.75
341 355 0.537143 CCGGCCATAGCATAAGCCAA 60.537 55.000 2.24 0.00 42.43 4.52
382 410 2.125552 CGCGGTCTGCCTCATTCA 60.126 61.111 0.00 0.00 42.08 2.57
383 411 2.456119 CGCGGTCTGCCTCATTCAC 61.456 63.158 0.00 0.00 42.08 3.18
384 412 2.456119 GCGGTCTGCCTCATTCACG 61.456 63.158 0.00 0.00 37.76 4.35
385 413 1.811266 CGGTCTGCCTCATTCACGG 60.811 63.158 0.00 0.00 0.00 4.94
386 414 2.109126 GGTCTGCCTCATTCACGGC 61.109 63.158 0.00 0.00 46.46 5.68
387 415 2.109126 GTCTGCCTCATTCACGGCC 61.109 63.158 0.00 0.00 45.71 6.13
388 416 2.270205 CTGCCTCATTCACGGCCT 59.730 61.111 0.00 0.00 45.71 5.19
389 417 2.046023 TGCCTCATTCACGGCCTG 60.046 61.111 0.00 0.00 45.71 4.85
390 418 3.512516 GCCTCATTCACGGCCTGC 61.513 66.667 0.00 0.00 40.43 4.85
391 419 2.825836 CCTCATTCACGGCCTGCC 60.826 66.667 0.00 0.00 0.00 4.85
392 420 2.825836 CTCATTCACGGCCTGCCC 60.826 66.667 0.00 0.00 0.00 5.36
567 606 2.782222 GCTCACCTATCGCGACCCA 61.782 63.158 12.93 0.00 0.00 4.51
613 653 8.285891 AGAGATAGAGAAAAGATTACAGAGGGA 58.714 37.037 0.00 0.00 0.00 4.20
615 1001 5.948742 AGAGAAAAGATTACAGAGGGAGG 57.051 43.478 0.00 0.00 0.00 4.30
623 1009 1.227249 TACAGAGGGAGGGAGAGAGG 58.773 60.000 0.00 0.00 0.00 3.69
624 1010 0.553862 ACAGAGGGAGGGAGAGAGGA 60.554 60.000 0.00 0.00 0.00 3.71
626 1012 0.047176 AGAGGGAGGGAGAGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
628 1014 0.998945 AGGGAGGGAGAGAGGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
668 1063 2.507992 CCGCTGCCTTCTCTGTCG 60.508 66.667 0.00 0.00 0.00 4.35
704 1101 2.427506 GTAGCTTTCTGTTCCTGTGGG 58.572 52.381 0.00 0.00 0.00 4.61
705 1102 0.111253 AGCTTTCTGTTCCTGTGGGG 59.889 55.000 0.00 0.00 0.00 4.96
795 1193 4.932105 GGCCCAACCCAACAGCCA 62.932 66.667 0.00 0.00 43.32 4.75
796 1194 3.305516 GCCCAACCCAACAGCCAG 61.306 66.667 0.00 0.00 0.00 4.85
797 1195 3.305516 CCCAACCCAACAGCCAGC 61.306 66.667 0.00 0.00 0.00 4.85
798 1196 3.305516 CCAACCCAACAGCCAGCC 61.306 66.667 0.00 0.00 0.00 4.85
799 1197 3.673484 CAACCCAACAGCCAGCCG 61.673 66.667 0.00 0.00 0.00 5.52
991 1399 0.321564 TTCGACCAAGGTCCATGCTG 60.322 55.000 13.35 0.00 41.76 4.41
1045 1460 2.176546 CATGGCTGCGAACAACCG 59.823 61.111 0.00 0.00 34.53 4.44
1057 1472 0.180406 AACAACCGCTGTCCAAGACT 59.820 50.000 0.00 0.00 37.23 3.24
1097 1512 1.813513 CCACGGTTCTTGCTCTCAAT 58.186 50.000 0.00 0.00 0.00 2.57
1169 1584 7.793927 ATCTTTACCGATTGATCTTTTCTCC 57.206 36.000 0.00 0.00 0.00 3.71
1179 1594 2.814280 TCTTTTCTCCACGTCTGTCC 57.186 50.000 0.00 0.00 0.00 4.02
1181 1596 2.035961 TCTTTTCTCCACGTCTGTCCAG 59.964 50.000 0.00 0.00 0.00 3.86
1190 1605 4.039973 TCCACGTCTGTCCAGTTAATCTTT 59.960 41.667 0.00 0.00 0.00 2.52
1192 1607 6.070995 TCCACGTCTGTCCAGTTAATCTTTAT 60.071 38.462 0.00 0.00 0.00 1.40
1195 1610 7.330946 CACGTCTGTCCAGTTAATCTTTATCAA 59.669 37.037 0.00 0.00 0.00 2.57
1246 1661 6.915349 AGAGTGTTTAGATCACTACTGACAC 58.085 40.000 0.00 0.00 44.68 3.67
1247 1662 5.700846 AGTGTTTAGATCACTACTGACACG 58.299 41.667 0.00 0.00 43.17 4.49
1252 1667 3.357203 AGATCACTACTGACACGGACAT 58.643 45.455 0.00 0.00 0.00 3.06
1257 1672 2.025605 ACTACTGACACGGACATCCCTA 60.026 50.000 0.00 0.00 0.00 3.53
1259 1674 1.272536 ACTGACACGGACATCCCTAGT 60.273 52.381 0.00 0.00 0.00 2.57
1332 1747 4.261614 GGTCTTTCTTGACGCCATTTTTCT 60.262 41.667 0.00 0.00 37.81 2.52
1335 1750 6.524586 GTCTTTCTTGACGCCATTTTTCTATG 59.475 38.462 0.00 0.00 0.00 2.23
1336 1751 4.355543 TCTTGACGCCATTTTTCTATGC 57.644 40.909 0.00 0.00 0.00 3.14
1339 1754 3.023119 TGACGCCATTTTTCTATGCCAT 58.977 40.909 0.00 0.00 0.00 4.40
1341 1756 4.642437 TGACGCCATTTTTCTATGCCATTA 59.358 37.500 0.00 0.00 0.00 1.90
1345 1760 5.984926 CGCCATTTTTCTATGCCATTATGTT 59.015 36.000 0.00 0.00 0.00 2.71
1358 1773 4.141869 GCCATTATGTTTTCTTGGGAGCAT 60.142 41.667 0.00 0.00 0.00 3.79
1364 1779 4.584874 TGTTTTCTTGGGAGCATCGAATA 58.415 39.130 0.00 0.00 34.37 1.75
1375 1790 5.361285 GGGAGCATCGAATAGTATCCTATGT 59.639 44.000 0.00 0.00 32.46 2.29
1385 1800 3.155501 AGTATCCTATGTCTACACGCCC 58.844 50.000 0.00 0.00 0.00 6.13
1412 1827 9.236006 ACCTCAATGATTGGCTATATATTTGTC 57.764 33.333 5.20 0.00 0.00 3.18
1418 1833 7.118723 TGATTGGCTATATATTTGTCCATCCC 58.881 38.462 0.00 0.00 0.00 3.85
1420 1835 6.718593 TGGCTATATATTTGTCCATCCCTT 57.281 37.500 0.00 0.00 0.00 3.95
1422 1837 6.274436 TGGCTATATATTTGTCCATCCCTTCA 59.726 38.462 0.00 0.00 0.00 3.02
1439 1861 2.885135 TCATCCAATCCTGCACACTT 57.115 45.000 0.00 0.00 0.00 3.16
1448 1870 1.224069 CCTGCACACTTGGTCACTCG 61.224 60.000 0.00 0.00 0.00 4.18
1451 1873 1.548973 GCACACTTGGTCACTCGACG 61.549 60.000 0.00 0.00 43.61 5.12
1452 1874 1.299926 ACACTTGGTCACTCGACGC 60.300 57.895 0.00 0.00 43.61 5.19
1474 1907 4.983090 GCACTGTGCACGCATATC 57.017 55.556 26.70 0.00 44.26 1.63
1477 1910 1.064505 GCACTGTGCACGCATATCATT 59.935 47.619 26.70 0.00 44.26 2.57
1481 1914 4.034394 CACTGTGCACGCATATCATTAAGT 59.966 41.667 13.13 2.18 0.00 2.24
1490 1923 5.586243 ACGCATATCATTAAGTTGCTGTCTT 59.414 36.000 0.00 0.00 0.00 3.01
1492 1925 6.630443 CGCATATCATTAAGTTGCTGTCTTTC 59.370 38.462 0.00 0.00 0.00 2.62
1493 1926 6.914757 GCATATCATTAAGTTGCTGTCTTTCC 59.085 38.462 0.00 0.00 0.00 3.13
1500 1933 3.477530 AGTTGCTGTCTTTCCTTGGTAC 58.522 45.455 0.00 0.00 0.00 3.34
1501 1934 3.136626 AGTTGCTGTCTTTCCTTGGTACT 59.863 43.478 0.00 0.00 0.00 2.73
1506 1939 4.747009 GCTGTCTTTCCTTGGTACTCCTTT 60.747 45.833 0.00 0.00 34.23 3.11
1516 1972 3.870559 TGGTACTCCTTTTCCTTCTCCT 58.129 45.455 0.00 0.00 34.23 3.69
1533 1989 5.627499 TCTCCTGAAATGGTTCGAAATTG 57.373 39.130 0.00 0.00 36.46 2.32
1539 1995 3.575965 AATGGTTCGAAATTGCAGGTC 57.424 42.857 0.00 0.00 0.00 3.85
1540 1996 2.270352 TGGTTCGAAATTGCAGGTCT 57.730 45.000 0.00 0.00 0.00 3.85
1541 1997 2.582052 TGGTTCGAAATTGCAGGTCTT 58.418 42.857 0.00 0.00 0.00 3.01
1542 1998 3.745799 TGGTTCGAAATTGCAGGTCTTA 58.254 40.909 0.00 0.00 0.00 2.10
1543 1999 4.331968 TGGTTCGAAATTGCAGGTCTTAT 58.668 39.130 0.00 0.00 0.00 1.73
1544 2000 4.155826 TGGTTCGAAATTGCAGGTCTTATG 59.844 41.667 0.00 0.00 0.00 1.90
1549 2029 4.676546 GAAATTGCAGGTCTTATGCTTCC 58.323 43.478 0.00 0.00 44.17 3.46
1551 2031 3.439857 TTGCAGGTCTTATGCTTCCTT 57.560 42.857 0.00 0.00 44.17 3.36
1552 2032 2.991250 TGCAGGTCTTATGCTTCCTTC 58.009 47.619 0.00 0.00 44.17 3.46
1556 2036 4.383118 GCAGGTCTTATGCTTCCTTCTGTA 60.383 45.833 0.00 0.00 40.59 2.74
1566 2046 4.249661 GCTTCCTTCTGTACTTCTTGGAG 58.750 47.826 0.00 0.00 0.00 3.86
1569 2049 3.006967 TCCTTCTGTACTTCTTGGAGTGC 59.993 47.826 0.00 0.00 33.50 4.40
1577 2057 3.996480 ACTTCTTGGAGTGCTGTCTTAC 58.004 45.455 0.00 0.00 0.00 2.34
1578 2058 3.244249 ACTTCTTGGAGTGCTGTCTTACC 60.244 47.826 0.00 0.00 0.00 2.85
1597 2078 1.612726 CCTGGGAGTTTCAGGCTTCTG 60.613 57.143 0.00 0.00 44.29 3.02
1600 2081 1.339535 GGGAGTTTCAGGCTTCTGGAG 60.340 57.143 0.00 0.00 38.96 3.86
1603 2084 1.627834 AGTTTCAGGCTTCTGGAGGAG 59.372 52.381 0.00 0.00 38.96 3.69
1616 2097 0.980231 GGAGGAGATGAGGCTGTGGT 60.980 60.000 0.00 0.00 0.00 4.16
1621 2102 0.037303 AGATGAGGCTGTGGTTGGTG 59.963 55.000 0.00 0.00 0.00 4.17
1631 2112 1.707989 TGTGGTTGGTGGTCATATGGT 59.292 47.619 2.13 0.00 0.00 3.55
1720 2201 1.006805 CCTCGCCATCGATGACTCC 60.007 63.158 26.86 10.50 44.56 3.85
1723 2204 0.816421 TCGCCATCGATGACTCCGTA 60.816 55.000 26.86 10.14 40.21 4.02
1727 2208 2.228103 GCCATCGATGACTCCGTACATA 59.772 50.000 26.86 0.00 0.00 2.29
1774 2255 2.746472 GCTCAAGGTTAGTATGCCCCAG 60.746 54.545 0.00 0.00 0.00 4.45
1786 2267 1.003233 GCCCCAGTTCTCACCACTC 60.003 63.158 0.00 0.00 0.00 3.51
1787 2268 1.484444 GCCCCAGTTCTCACCACTCT 61.484 60.000 0.00 0.00 0.00 3.24
1788 2269 1.059913 CCCCAGTTCTCACCACTCTT 58.940 55.000 0.00 0.00 0.00 2.85
1789 2270 1.271054 CCCCAGTTCTCACCACTCTTG 60.271 57.143 0.00 0.00 0.00 3.02
1790 2271 1.417890 CCCAGTTCTCACCACTCTTGT 59.582 52.381 0.00 0.00 0.00 3.16
1791 2272 2.548920 CCCAGTTCTCACCACTCTTGTC 60.549 54.545 0.00 0.00 0.00 3.18
1792 2273 2.366916 CCAGTTCTCACCACTCTTGTCT 59.633 50.000 0.00 0.00 0.00 3.41
1793 2274 3.574396 CCAGTTCTCACCACTCTTGTCTA 59.426 47.826 0.00 0.00 0.00 2.59
1794 2275 4.321601 CCAGTTCTCACCACTCTTGTCTAG 60.322 50.000 0.00 0.00 0.00 2.43
1799 2280 2.072298 CACCACTCTTGTCTAGCTTGC 58.928 52.381 0.00 0.00 0.00 4.01
1832 2313 2.219458 CAGTGATGTGATGCCATCCTC 58.781 52.381 1.49 0.00 40.43 3.71
1833 2314 2.125233 AGTGATGTGATGCCATCCTCT 58.875 47.619 1.49 0.00 40.43 3.69
1840 2321 1.992519 GATGCCATCCTCTGCAGGGT 61.993 60.000 13.79 0.00 41.46 4.34
1906 2387 1.134699 TCTGATGACGACTGGATTGGC 60.135 52.381 0.00 0.00 0.00 4.52
1921 2402 0.749818 TTGGCGTGTTTTCTCCTGCA 60.750 50.000 0.00 0.00 0.00 4.41
1952 2433 7.177744 TCAGGTAACAATATCGGTATATCTGCA 59.822 37.037 0.00 0.00 41.41 4.41
1971 2452 2.477825 CACGGAGGCAGATCTATTGTG 58.522 52.381 0.00 0.00 0.00 3.33
1978 2459 5.363101 GAGGCAGATCTATTGTGACATGAA 58.637 41.667 0.00 0.00 0.00 2.57
1979 2460 5.938279 AGGCAGATCTATTGTGACATGAAT 58.062 37.500 0.00 0.00 0.00 2.57
1993 2474 5.882557 GTGACATGAATTCAATCCACCTAGT 59.117 40.000 13.09 0.60 0.00 2.57
1999 2480 6.962182 TGAATTCAATCCACCTAGTCATTCT 58.038 36.000 5.45 0.00 0.00 2.40
2000 2481 7.405292 TGAATTCAATCCACCTAGTCATTCTT 58.595 34.615 5.45 0.00 0.00 2.52
2001 2482 7.890127 TGAATTCAATCCACCTAGTCATTCTTT 59.110 33.333 5.45 0.00 0.00 2.52
2010 2491 4.263462 ACCTAGTCATTCTTTGATGCACCA 60.263 41.667 0.00 0.00 36.54 4.17
2011 2492 4.701651 CCTAGTCATTCTTTGATGCACCAA 59.298 41.667 0.00 0.00 36.54 3.67
2091 2573 3.616956 TCTGCGATCCTGAAAATGAGT 57.383 42.857 0.00 0.00 0.00 3.41
2152 2635 5.306678 AGGTTGGCATTATTTTTCCTGTTCA 59.693 36.000 0.00 0.00 0.00 3.18
2156 2639 7.670009 TGGCATTATTTTTCCTGTTCAATTG 57.330 32.000 0.00 0.00 0.00 2.32
2204 2691 2.968574 TCTATGCCAGGATTCAGACTCC 59.031 50.000 0.00 0.00 0.00 3.85
2209 2696 0.461961 CAGGATTCAGACTCCGGGAC 59.538 60.000 0.00 0.00 37.88 4.46
2216 2704 0.679505 CAGACTCCGGGACACTTTCA 59.320 55.000 0.00 0.00 0.00 2.69
2222 2710 0.802494 CCGGGACACTTTCATTTCGG 59.198 55.000 0.00 0.00 0.00 4.30
2236 2724 7.230712 ACTTTCATTTCGGACATTAACCTTTCT 59.769 33.333 0.00 0.00 0.00 2.52
2361 2849 6.128145 GGGAAGACTTCTCTTTTGCACTATTC 60.128 42.308 14.72 0.00 36.82 1.75
2393 2882 4.019321 TCTGTTGAAGGCAAGGCTATACTT 60.019 41.667 0.00 0.00 34.01 2.24
2848 3384 0.923358 TTCCCCAGCCGGAACATTAT 59.077 50.000 5.05 0.00 36.98 1.28
2911 3455 7.721402 TGCCTATTCTTCTTAAGAGATGAGAC 58.279 38.462 5.12 0.94 39.03 3.36
2973 3523 8.083828 AGAATCTGCTCATAGGTTTTCTTAGA 57.916 34.615 0.00 0.00 0.00 2.10
3004 3554 7.579726 TGTTTTTGTTTTGAATCAAACACCTG 58.420 30.769 8.06 0.00 35.02 4.00
3060 3610 2.988684 GTTGGTTGGCGCCATCCA 60.989 61.111 42.23 42.23 42.18 3.41
3183 3734 9.614792 CCAGCTACTAAGAAATGGTTACTTAAT 57.385 33.333 0.00 0.00 0.00 1.40
3285 3836 2.437281 AGCATCACCTTATCCTGGACAG 59.563 50.000 0.00 0.00 0.00 3.51
3332 3883 9.182214 CATATTTGGAGATATGGGAAAGGTATG 57.818 37.037 0.00 0.00 36.69 2.39
3702 4257 8.428063 AGTATATCATTTCAGAACTTCCTCTGG 58.572 37.037 1.03 0.00 42.68 3.86
3910 4466 1.478510 ACTCAGTGAGGCCATAACTCG 59.521 52.381 23.79 1.47 37.79 4.18
4026 4687 4.214119 TGCATTGCTAACACAGAAGAAGAC 59.786 41.667 10.49 0.00 0.00 3.01
4116 4777 0.750911 CCTGGCTCATCTTTCTGGCC 60.751 60.000 0.00 0.00 42.73 5.36
4715 5378 4.202010 GCTGTTTGAGTACAAGAAAAGCCA 60.202 41.667 0.00 0.00 37.32 4.75
4749 5412 6.818142 ACGTGTATGATCATTTCACAATCTCA 59.182 34.615 27.36 4.16 37.11 3.27
4759 5422 4.545208 TTCACAATCTCACGGGATTACA 57.455 40.909 0.00 0.00 34.59 2.41
4864 5528 3.019564 AGTTGATCTGCTAATGGTTGCC 58.980 45.455 0.00 0.00 0.00 4.52
4888 5552 2.300956 TGTGTGTGGCCCAATACAAT 57.699 45.000 0.00 0.00 0.00 2.71
4936 5600 6.303839 AGAAACTTGTATTGGCTACCTGAAA 58.696 36.000 0.00 0.00 0.00 2.69
5228 5918 1.268352 GCGAAGGCAACATTACACCAA 59.732 47.619 0.00 0.00 39.62 3.67
5308 5999 1.896345 CATCATCGAGTCGTCGTGTT 58.104 50.000 13.12 3.22 46.85 3.32
5627 6323 1.005037 CCTAACTGCACTCCACGCA 60.005 57.895 0.00 0.00 37.88 5.24
5732 6428 4.378563 CCGTTACGTTTTGCCACATTATCA 60.379 41.667 3.52 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.545666 TGTTGGACAGTGAGTATGAAATGTTT 59.454 34.615 0.00 0.00 0.00 2.83
45 54 6.558771 TTGTTGGACAGTGAGTATGAAATG 57.441 37.500 0.00 0.00 0.00 2.32
48 57 5.863965 TGATTGTTGGACAGTGAGTATGAA 58.136 37.500 0.00 0.00 0.00 2.57
53 62 3.884895 TGTTGATTGTTGGACAGTGAGT 58.115 40.909 0.00 0.00 0.00 3.41
73 82 6.073657 CCATTGCTGTTGTTTGGTTCTATTTG 60.074 38.462 0.00 0.00 0.00 2.32
74 83 5.990996 CCATTGCTGTTGTTTGGTTCTATTT 59.009 36.000 0.00 0.00 0.00 1.40
154 163 1.032114 GCCGGCCAAGATAACAAGCT 61.032 55.000 18.11 0.00 0.00 3.74
181 191 1.227089 CCGAGCGATTCTCCTGGTG 60.227 63.158 0.00 0.00 38.62 4.17
295 309 4.468713 TGCCATTGGATCGGAATTGAATA 58.531 39.130 6.95 0.00 0.00 1.75
296 310 3.298619 TGCCATTGGATCGGAATTGAAT 58.701 40.909 6.95 0.00 0.00 2.57
297 311 2.732763 TGCCATTGGATCGGAATTGAA 58.267 42.857 6.95 0.00 0.00 2.69
298 312 2.426738 GTTGCCATTGGATCGGAATTGA 59.573 45.455 6.95 0.00 0.00 2.57
299 313 2.481795 GGTTGCCATTGGATCGGAATTG 60.482 50.000 6.95 0.00 0.00 2.32
474 502 3.480133 GGACGGTGAGGGATGGGG 61.480 72.222 0.00 0.00 0.00 4.96
613 653 2.710826 GCCCCTCTCCTCTCTCCCT 61.711 68.421 0.00 0.00 0.00 4.20
615 1001 1.457455 CAGCCCCTCTCCTCTCTCC 60.457 68.421 0.00 0.00 0.00 3.71
623 1009 4.154347 CGAGGTGCAGCCCCTCTC 62.154 72.222 20.46 1.87 45.29 3.20
624 1010 4.704103 TCGAGGTGCAGCCCCTCT 62.704 66.667 20.46 0.00 45.29 3.69
704 1101 6.465439 TTTCTTTTTCTTTTCTCACCCTCC 57.535 37.500 0.00 0.00 0.00 4.30
705 1102 7.009265 CGTTTTTCTTTTTCTTTTCTCACCCTC 59.991 37.037 0.00 0.00 0.00 4.30
800 1198 4.803426 GAGGACGGTGGCAGCGAG 62.803 72.222 41.06 17.48 42.41 5.03
803 1201 4.767255 CTGGAGGACGGTGGCAGC 62.767 72.222 6.62 6.62 0.00 5.25
804 1202 4.087892 CCTGGAGGACGGTGGCAG 62.088 72.222 0.00 0.00 37.39 4.85
879 1287 2.135581 TTCCAGACCCGACACCGTT 61.136 57.895 0.00 0.00 0.00 4.44
915 1323 1.866496 GTCATCGTTCGCGCGTACT 60.866 57.895 31.58 15.61 41.05 2.73
991 1399 1.336125 GCCAAGAAGCATCCATAGCAC 59.664 52.381 0.00 0.00 0.00 4.40
1045 1460 1.342819 ACTCTCACAGTCTTGGACAGC 59.657 52.381 0.52 0.00 34.60 4.40
1051 1466 1.506493 GTGGCACTCTCACAGTCTTG 58.494 55.000 11.13 0.00 35.39 3.02
1057 1472 2.131067 TGGACGTGGCACTCTCACA 61.131 57.895 16.72 4.78 35.03 3.58
1097 1512 5.538053 TCTTGATCAAATTACCAGGCAAACA 59.462 36.000 9.88 0.00 0.00 2.83
1156 1571 4.307432 GACAGACGTGGAGAAAAGATCAA 58.693 43.478 0.00 0.00 0.00 2.57
1169 1584 6.811665 TGATAAAGATTAACTGGACAGACGTG 59.188 38.462 6.29 0.00 0.00 4.49
1219 1634 9.244292 TGTCAGTAGTGATCTAAACACTCTTAT 57.756 33.333 2.99 0.00 45.58 1.73
1220 1635 8.512956 GTGTCAGTAGTGATCTAAACACTCTTA 58.487 37.037 2.99 0.00 45.58 2.10
1221 1636 7.371936 GTGTCAGTAGTGATCTAAACACTCTT 58.628 38.462 2.99 0.00 45.58 2.85
1222 1637 6.348622 CGTGTCAGTAGTGATCTAAACACTCT 60.349 42.308 2.99 0.00 45.58 3.24
1223 1638 5.795939 CGTGTCAGTAGTGATCTAAACACTC 59.204 44.000 2.99 0.00 45.58 3.51
1225 1640 4.857588 CCGTGTCAGTAGTGATCTAAACAC 59.142 45.833 2.99 5.80 35.44 3.32
1226 1641 4.763279 TCCGTGTCAGTAGTGATCTAAACA 59.237 41.667 2.99 0.00 34.36 2.83
1227 1642 5.094134 GTCCGTGTCAGTAGTGATCTAAAC 58.906 45.833 2.99 0.00 34.36 2.01
1228 1643 4.763279 TGTCCGTGTCAGTAGTGATCTAAA 59.237 41.667 2.99 0.00 34.36 1.85
1229 1644 4.329392 TGTCCGTGTCAGTAGTGATCTAA 58.671 43.478 2.99 0.00 34.36 2.10
1230 1645 3.946606 TGTCCGTGTCAGTAGTGATCTA 58.053 45.455 2.99 0.00 34.36 1.98
1231 1646 2.791655 TGTCCGTGTCAGTAGTGATCT 58.208 47.619 2.99 0.00 34.36 2.75
1232 1647 3.489398 GGATGTCCGTGTCAGTAGTGATC 60.489 52.174 2.99 0.05 34.36 2.92
1233 1648 2.427453 GGATGTCCGTGTCAGTAGTGAT 59.573 50.000 2.99 0.00 34.36 3.06
1234 1649 1.816835 GGATGTCCGTGTCAGTAGTGA 59.183 52.381 0.00 0.00 0.00 3.41
1235 1650 1.135083 GGGATGTCCGTGTCAGTAGTG 60.135 57.143 0.00 0.00 36.71 2.74
1236 1651 1.183549 GGGATGTCCGTGTCAGTAGT 58.816 55.000 0.00 0.00 36.71 2.73
1237 1652 1.475403 AGGGATGTCCGTGTCAGTAG 58.525 55.000 0.00 0.00 41.52 2.57
1272 1687 4.202441 ACTCTGTCAGTGTCAGCATTTTT 58.798 39.130 11.96 0.00 32.26 1.94
1273 1688 3.812053 GACTCTGTCAGTGTCAGCATTTT 59.188 43.478 23.78 0.00 38.30 1.82
1308 1723 1.156736 AATGGCGTCAAGAAAGACCG 58.843 50.000 0.00 0.00 35.07 4.79
1332 1747 5.068987 GCTCCCAAGAAAACATAATGGCATA 59.931 40.000 0.00 0.00 0.00 3.14
1335 1750 3.195396 TGCTCCCAAGAAAACATAATGGC 59.805 43.478 0.00 0.00 0.00 4.40
1336 1751 5.594926 GATGCTCCCAAGAAAACATAATGG 58.405 41.667 0.00 0.00 0.00 3.16
1339 1754 4.584874 TCGATGCTCCCAAGAAAACATAA 58.415 39.130 0.00 0.00 0.00 1.90
1341 1756 3.071874 TCGATGCTCCCAAGAAAACAT 57.928 42.857 0.00 0.00 0.00 2.71
1345 1760 4.487714 ACTATTCGATGCTCCCAAGAAA 57.512 40.909 0.00 0.00 0.00 2.52
1375 1790 0.249120 CATTGAGGTGGGCGTGTAGA 59.751 55.000 0.00 0.00 0.00 2.59
1385 1800 9.017509 ACAAATATATAGCCAATCATTGAGGTG 57.982 33.333 0.00 0.00 0.00 4.00
1412 1827 2.872732 CAGGATTGGATGAAGGGATGG 58.127 52.381 0.00 0.00 0.00 3.51
1416 1831 1.341285 TGTGCAGGATTGGATGAAGGG 60.341 52.381 0.00 0.00 0.00 3.95
1418 1833 2.719739 AGTGTGCAGGATTGGATGAAG 58.280 47.619 0.00 0.00 0.00 3.02
1420 1835 2.439409 CAAGTGTGCAGGATTGGATGA 58.561 47.619 0.00 0.00 0.00 2.92
1422 1837 1.076024 ACCAAGTGTGCAGGATTGGAT 59.924 47.619 23.62 10.23 44.04 3.41
1439 1861 1.299850 CAACTGCGTCGAGTGACCA 60.300 57.895 0.00 0.00 42.37 4.02
1462 1884 3.725740 GCAACTTAATGATATGCGTGCAC 59.274 43.478 6.82 6.82 0.00 4.57
1463 1885 3.627123 AGCAACTTAATGATATGCGTGCA 59.373 39.130 0.00 0.00 41.72 4.57
1464 1886 3.970610 CAGCAACTTAATGATATGCGTGC 59.029 43.478 0.00 0.00 41.72 5.34
1474 1907 5.010012 ACCAAGGAAAGACAGCAACTTAATG 59.990 40.000 0.00 0.00 0.00 1.90
1477 1910 4.164843 ACCAAGGAAAGACAGCAACTTA 57.835 40.909 0.00 0.00 0.00 2.24
1481 1914 3.496160 GGAGTACCAAGGAAAGACAGCAA 60.496 47.826 0.00 0.00 35.97 3.91
1490 1923 4.663592 AGAAGGAAAAGGAGTACCAAGGAA 59.336 41.667 0.00 0.00 38.94 3.36
1492 1925 4.565861 GGAGAAGGAAAAGGAGTACCAAGG 60.566 50.000 0.00 0.00 38.94 3.61
1493 1926 4.287326 AGGAGAAGGAAAAGGAGTACCAAG 59.713 45.833 0.00 0.00 38.94 3.61
1500 1933 4.704057 CCATTTCAGGAGAAGGAAAAGGAG 59.296 45.833 0.00 0.00 41.83 3.69
1501 1934 4.106341 ACCATTTCAGGAGAAGGAAAAGGA 59.894 41.667 13.37 0.00 41.83 3.36
1506 1939 3.326588 TCGAACCATTTCAGGAGAAGGAA 59.673 43.478 0.00 0.00 34.71 3.36
1516 1972 3.320541 ACCTGCAATTTCGAACCATTTCA 59.679 39.130 0.00 0.00 0.00 2.69
1533 1989 2.941720 CAGAAGGAAGCATAAGACCTGC 59.058 50.000 0.00 0.00 39.97 4.85
1539 1995 6.314896 CCAAGAAGTACAGAAGGAAGCATAAG 59.685 42.308 0.00 0.00 0.00 1.73
1540 1996 6.013725 TCCAAGAAGTACAGAAGGAAGCATAA 60.014 38.462 0.00 0.00 0.00 1.90
1541 1997 5.483937 TCCAAGAAGTACAGAAGGAAGCATA 59.516 40.000 0.00 0.00 0.00 3.14
1542 1998 4.287067 TCCAAGAAGTACAGAAGGAAGCAT 59.713 41.667 0.00 0.00 0.00 3.79
1543 1999 3.646162 TCCAAGAAGTACAGAAGGAAGCA 59.354 43.478 0.00 0.00 0.00 3.91
1544 2000 4.249661 CTCCAAGAAGTACAGAAGGAAGC 58.750 47.826 0.00 0.00 0.00 3.86
1549 2029 3.993081 CAGCACTCCAAGAAGTACAGAAG 59.007 47.826 0.00 0.00 0.00 2.85
1551 2031 2.965831 ACAGCACTCCAAGAAGTACAGA 59.034 45.455 0.00 0.00 0.00 3.41
1552 2032 3.006323 AGACAGCACTCCAAGAAGTACAG 59.994 47.826 0.00 0.00 0.00 2.74
1556 2036 3.244249 GGTAAGACAGCACTCCAAGAAGT 60.244 47.826 0.00 0.00 0.00 3.01
1566 2046 0.977395 ACTCCCAGGTAAGACAGCAC 59.023 55.000 0.00 0.00 0.00 4.40
1569 2049 3.307059 CCTGAAACTCCCAGGTAAGACAG 60.307 52.174 0.00 0.00 44.66 3.51
1578 2058 1.612726 CCAGAAGCCTGAAACTCCCAG 60.613 57.143 0.00 0.00 43.02 4.45
1597 2078 0.980231 ACCACAGCCTCATCTCCTCC 60.980 60.000 0.00 0.00 0.00 4.30
1600 2081 0.393537 CCAACCACAGCCTCATCTCC 60.394 60.000 0.00 0.00 0.00 3.71
1603 2084 0.962356 CCACCAACCACAGCCTCATC 60.962 60.000 0.00 0.00 0.00 2.92
1616 2097 3.078097 CGAACAACCATATGACCACCAA 58.922 45.455 3.65 0.00 0.00 3.67
1621 2102 4.472286 CACAAACGAACAACCATATGACC 58.528 43.478 3.65 0.00 0.00 4.02
1631 2112 2.023461 CGCCGCACAAACGAACAA 59.977 55.556 0.00 0.00 34.06 2.83
1696 2177 2.124612 TCGATGGCGAGGGTCGTA 60.125 61.111 0.00 0.00 42.51 3.43
1720 2201 2.036217 TGGGGACGCCTTTATATGTACG 59.964 50.000 10.28 0.00 0.00 3.67
1723 2204 3.486383 CAATGGGGACGCCTTTATATGT 58.514 45.455 10.28 0.00 0.00 2.29
1727 2208 0.629058 ACCAATGGGGACGCCTTTAT 59.371 50.000 10.28 0.00 41.15 1.40
1765 2246 0.618458 GTGGTGAGAACTGGGGCATA 59.382 55.000 0.00 0.00 0.00 3.14
1774 2255 3.257127 AGCTAGACAAGAGTGGTGAGAAC 59.743 47.826 0.00 0.00 0.00 3.01
1786 2267 3.397482 ACTGTTGAGCAAGCTAGACAAG 58.603 45.455 10.07 7.69 0.00 3.16
1787 2268 3.475566 ACTGTTGAGCAAGCTAGACAA 57.524 42.857 10.07 2.09 0.00 3.18
1788 2269 3.133691 CAACTGTTGAGCAAGCTAGACA 58.866 45.455 15.26 2.36 0.00 3.41
1789 2270 2.096019 GCAACTGTTGAGCAAGCTAGAC 60.096 50.000 23.81 0.00 0.00 2.59
1790 2271 2.146342 GCAACTGTTGAGCAAGCTAGA 58.854 47.619 23.81 0.00 0.00 2.43
1791 2272 1.875514 TGCAACTGTTGAGCAAGCTAG 59.124 47.619 23.81 0.00 34.97 3.42
1792 2273 1.603802 GTGCAACTGTTGAGCAAGCTA 59.396 47.619 23.81 0.00 40.35 3.32
1793 2274 0.383231 GTGCAACTGTTGAGCAAGCT 59.617 50.000 23.81 0.00 40.35 3.74
1794 2275 0.101040 TGTGCAACTGTTGAGCAAGC 59.899 50.000 23.81 7.94 40.35 4.01
1832 2313 2.031516 CGCTGTTCTCACCCTGCAG 61.032 63.158 6.78 6.78 0.00 4.41
1833 2314 2.031012 CGCTGTTCTCACCCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
1840 2321 0.888619 CTACCCACTCGCTGTTCTCA 59.111 55.000 0.00 0.00 0.00 3.27
1906 2387 4.358851 TGAAATTTGCAGGAGAAAACACG 58.641 39.130 0.00 0.00 0.00 4.49
1934 2415 4.993905 TCCGTGCAGATATACCGATATTG 58.006 43.478 0.00 0.00 0.00 1.90
1952 2433 2.101582 GTCACAATAGATCTGCCTCCGT 59.898 50.000 5.18 0.00 0.00 4.69
1961 2442 8.843262 TGGATTGAATTCATGTCACAATAGATC 58.157 33.333 9.40 4.56 32.50 2.75
1971 2452 6.115446 TGACTAGGTGGATTGAATTCATGTC 58.885 40.000 9.40 10.46 0.00 3.06
1978 2459 7.405292 TCAAAGAATGACTAGGTGGATTGAAT 58.595 34.615 0.00 0.00 31.50 2.57
1979 2460 6.778821 TCAAAGAATGACTAGGTGGATTGAA 58.221 36.000 0.00 0.00 31.50 2.69
1993 2474 7.558807 AGATCTTATTGGTGCATCAAAGAATGA 59.441 33.333 17.88 12.58 43.67 2.57
1999 2480 6.597672 ACGTAAGATCTTATTGGTGCATCAAA 59.402 34.615 17.88 0.00 43.62 2.69
2000 2481 6.112734 ACGTAAGATCTTATTGGTGCATCAA 58.887 36.000 16.12 16.12 43.62 2.57
2001 2482 5.670485 ACGTAAGATCTTATTGGTGCATCA 58.330 37.500 17.95 0.00 43.62 3.07
2065 2547 0.528466 TTCAGGATCGCAGATCGCAC 60.528 55.000 10.86 0.93 45.12 5.34
2078 2560 2.942804 TGTTGCCACTCATTTTCAGGA 58.057 42.857 0.00 0.00 0.00 3.86
2177 2664 7.013220 AGTCTGAATCCTGGCATAGAACTATA 58.987 38.462 0.00 0.00 0.00 1.31
2204 2691 1.463444 GTCCGAAATGAAAGTGTCCCG 59.537 52.381 0.00 0.00 0.00 5.14
2209 2696 6.254281 AGGTTAATGTCCGAAATGAAAGTG 57.746 37.500 0.00 0.00 0.00 3.16
2216 2704 7.094334 GGAAAGAGAAAGGTTAATGTCCGAAAT 60.094 37.037 0.00 0.00 0.00 2.17
2222 2710 9.674068 AAGATAGGAAAGAGAAAGGTTAATGTC 57.326 33.333 0.00 0.00 0.00 3.06
2236 2724 6.070251 TGGTACTGCAATGAAGATAGGAAAGA 60.070 38.462 0.00 0.00 0.00 2.52
2361 2849 0.320771 CCTTCAACAGACCACCGGAG 60.321 60.000 9.46 0.00 0.00 4.63
2393 2882 4.415881 TGCAGAGAAGTTGAGGTAACAA 57.584 40.909 0.00 0.00 41.88 2.83
2497 3003 3.253921 TGACCATGTTTGAGACAGCAATG 59.746 43.478 0.00 0.00 42.62 2.82
2848 3384 5.643664 GCACATGCTATTTCTGTTGAATGA 58.356 37.500 0.00 0.00 38.21 2.57
2911 3455 5.052567 CGGTGTAAATTCTGAACTACGATCG 60.053 44.000 14.88 14.88 0.00 3.69
3004 3554 5.907207 TCCTACATGTGCAGATTAGAAGTC 58.093 41.667 9.11 0.00 0.00 3.01
3042 3592 3.758931 GGATGGCGCCAACCAACC 61.759 66.667 41.50 29.20 44.39 3.77
3237 3788 5.930837 AGCTATATATCTTGCTCCAGACC 57.069 43.478 0.00 0.00 0.00 3.85
3285 3836 4.630111 TGACAATTTGTTGCAAGGAATCC 58.370 39.130 0.00 0.00 0.00 3.01
3332 3883 5.497474 ACCAAGATGGACAGGTAACATAAC 58.503 41.667 2.85 0.00 40.96 1.89
3340 3895 6.074648 TGAAATAAAACCAAGATGGACAGGT 58.925 36.000 2.85 0.00 40.96 4.00
4116 4777 0.395312 AGTACCCAAGAACACGGTGG 59.605 55.000 13.48 0.00 0.00 4.61
4715 5378 0.108992 ATCATACACGTTGCCGTCGT 60.109 50.000 0.00 0.00 46.28 4.34
4725 5388 7.121911 GTGAGATTGTGAAATGATCATACACG 58.878 38.462 26.18 0.00 40.97 4.49
4749 5412 2.695666 CAGGACATCTCTGTAATCCCGT 59.304 50.000 0.00 0.00 35.14 5.28
4759 5422 0.540923 GAGCAAGCCAGGACATCTCT 59.459 55.000 0.00 0.00 0.00 3.10
4864 5528 1.743321 ATTGGGCCACACACAAACCG 61.743 55.000 5.23 0.00 0.00 4.44
4936 5600 1.825474 CCCGTCTGAATGTACTGGAGT 59.175 52.381 0.00 0.00 0.00 3.85
5228 5918 2.198827 TCTGCGTTGGATGATTTGGT 57.801 45.000 0.00 0.00 0.00 3.67
5308 5999 2.787473 CCAGGTGATGGCTAGACAAA 57.213 50.000 0.13 0.00 43.83 2.83
5331 6022 2.689785 CCTTGGCGCGCATCAAGAA 61.690 57.895 36.02 18.52 41.94 2.52
5732 6428 1.522569 GAATAGGCTGCCCACGTCT 59.477 57.895 16.57 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.