Multiple sequence alignment - TraesCS3B01G275900

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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 TraesCS3B01G275900 chr3B 100.000 3289 0 0 1 3289 445601399 445598111 0.000000e+00 6074.0
1 TraesCS3B01G275900 chr3A 91.497 1129 53 21 95 1182 457482426 457483552 0.000000e+00 1513.0
2 TraesCS3B01G275900 chr3A 91.582 594 26 9 2678 3260 457483902 457484482 0.000000e+00 798.0
3 TraesCS3B01G275900 chr3A 86.957 391 23 14 2282 2655 457483534 457483913 6.570000e-112 414.0
4 TraesCS3B01G275900 chr3D 91.477 1056 46 22 156 1177 346316209 346315164 0.000000e+00 1411.0
5 TraesCS3B01G275900 chr3D 91.910 581 24 9 2686 3260 346314794 346314231 0.000000e+00 791.0
6 TraesCS3B01G275900 chr3D 89.863 365 22 6 2306 2655 346315155 346314791 3.870000e-124 455.0
7 TraesCS3B01G275900 chr3D 90.476 42 4 0 3248 3289 402471981 402472022 4.580000e-04 56.5
8 TraesCS3B01G275900 chr2A 88.669 1112 122 3 1183 2291 379292524 379293634 0.000000e+00 1352.0
9 TraesCS3B01G275900 chr5D 87.882 1114 129 4 1183 2292 447219645 447218534 0.000000e+00 1304.0
10 TraesCS3B01G275900 chr5B 81.558 1117 195 8 1183 2293 603983104 603984215 0.000000e+00 911.0
11 TraesCS3B01G275900 chr5B 82.234 985 170 5 1192 2174 3875185 3874204 0.000000e+00 845.0
12 TraesCS3B01G275900 chr5B 80.483 1117 203 12 1183 2291 364109306 364110415 0.000000e+00 841.0
13 TraesCS3B01G275900 chr5B 89.130 46 2 3 3244 3289 550556562 550556604 2.000000e-03 54.7
14 TraesCS3B01G275900 chr7B 72.954 281 69 7 1183 1460 517874530 517874806 1.260000e-14 91.6
15 TraesCS3B01G275900 chr7B 97.143 35 0 1 3251 3285 552029581 552029548 1.270000e-04 58.4
16 TraesCS3B01G275900 chr4D 97.500 40 1 0 2357 2396 32061568 32061607 5.890000e-08 69.4
17 TraesCS3B01G275900 chr6D 100.000 33 0 0 3257 3289 2404746 2404778 9.850000e-06 62.1
18 TraesCS3B01G275900 chr7A 97.143 35 1 0 3251 3285 222941727 222941761 3.540000e-05 60.2
19 TraesCS3B01G275900 chr4B 94.872 39 1 1 3251 3289 392367899 392367936 3.540000e-05 60.2
20 TraesCS3B01G275900 chr1D 97.143 35 1 0 3255 3289 484565404 484565438 3.540000e-05 60.2
21 TraesCS3B01G275900 chr2D 94.737 38 1 1 3250 3287 114520409 114520373 1.270000e-04 58.4
22 TraesCS3B01G275900 chr7D 89.362 47 2 3 3245 3289 30842266 30842221 4.580000e-04 56.5


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 TraesCS3B01G275900 chr3B 445598111 445601399 3288 True 6074.000000 6074 100.000000 1 3289 1 chr3B.!!$R1 3288
1 TraesCS3B01G275900 chr3A 457482426 457484482 2056 False 908.333333 1513 90.012000 95 3260 3 chr3A.!!$F1 3165
2 TraesCS3B01G275900 chr3D 346314231 346316209 1978 True 885.666667 1411 91.083333 156 3260 3 chr3D.!!$R1 3104
3 TraesCS3B01G275900 chr2A 379292524 379293634 1110 False 1352.000000 1352 88.669000 1183 2291 1 chr2A.!!$F1 1108
4 TraesCS3B01G275900 chr5D 447218534 447219645 1111 True 1304.000000 1304 87.882000 1183 2292 1 chr5D.!!$R1 1109
5 TraesCS3B01G275900 chr5B 603983104 603984215 1111 False 911.000000 911 81.558000 1183 2293 1 chr5B.!!$F3 1110
6 TraesCS3B01G275900 chr5B 3874204 3875185 981 True 845.000000 845 82.234000 1192 2174 1 chr5B.!!$R1 982
7 TraesCS3B01G275900 chr5B 364109306 364110415 1109 False 841.000000 841 80.483000 1183 2291 1 chr5B.!!$F1 1108

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
42 43 0.026803 GCGACGGACAAATGCATCTC 59.973 55.0 0.00 0.0 0.0 2.75 F
333 344 0.385473 GGTTGGATTTGACGTGCGTG 60.385 55.0 0.67 0.0 0.0 5.34 F
1991 2041 0.249741 CCGCCCTTTATACTGGTCCG 60.250 60.0 0.00 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1850 0.165295 CGCTGCATCAGTGTTCAGTG 59.835 55.0 0.00 1.62 37.23 3.66 R
2099 2149 0.240411 CCTGAGCAGCAGCAAACTTC 59.760 55.0 3.17 0.00 45.49 3.01 R
3263 3350 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.0 0.00 0.00 0.00 4.30 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
39 40 3.187058 GGCGACGGACAAATGCAT 58.813 55.556 0.00 0.00 0.00 3.96
40 41 1.062525 GGCGACGGACAAATGCATC 59.937 57.895 0.00 0.00 0.00 3.91
41 42 1.369091 GGCGACGGACAAATGCATCT 61.369 55.000 0.00 0.00 0.00 2.90
42 43 0.026803 GCGACGGACAAATGCATCTC 59.973 55.000 0.00 0.00 0.00 2.75
43 44 1.645034 CGACGGACAAATGCATCTCT 58.355 50.000 0.00 0.00 0.00 3.10
44 45 1.590238 CGACGGACAAATGCATCTCTC 59.410 52.381 0.00 0.00 0.00 3.20
45 46 2.736719 CGACGGACAAATGCATCTCTCT 60.737 50.000 0.00 0.00 0.00 3.10
46 47 2.863137 GACGGACAAATGCATCTCTCTC 59.137 50.000 0.00 0.00 0.00 3.20
47 48 2.208431 CGGACAAATGCATCTCTCTCC 58.792 52.381 0.00 0.00 0.00 3.71
48 49 2.158986 CGGACAAATGCATCTCTCTCCT 60.159 50.000 0.00 0.00 0.00 3.69
49 50 3.465871 GGACAAATGCATCTCTCTCCTC 58.534 50.000 0.00 0.00 0.00 3.71
50 51 3.134442 GGACAAATGCATCTCTCTCCTCT 59.866 47.826 0.00 0.00 0.00 3.69
51 52 4.383989 GGACAAATGCATCTCTCTCCTCTT 60.384 45.833 0.00 0.00 0.00 2.85
52 53 4.768583 ACAAATGCATCTCTCTCCTCTTC 58.231 43.478 0.00 0.00 0.00 2.87
53 54 4.470664 ACAAATGCATCTCTCTCCTCTTCT 59.529 41.667 0.00 0.00 0.00 2.85
54 55 4.942761 AATGCATCTCTCTCCTCTTCTC 57.057 45.455 0.00 0.00 0.00 2.87
55 56 2.665165 TGCATCTCTCTCCTCTTCTCC 58.335 52.381 0.00 0.00 0.00 3.71
56 57 2.244510 TGCATCTCTCTCCTCTTCTCCT 59.755 50.000 0.00 0.00 0.00 3.69
57 58 3.299503 GCATCTCTCTCCTCTTCTCCTT 58.700 50.000 0.00 0.00 0.00 3.36
58 59 3.706086 GCATCTCTCTCCTCTTCTCCTTT 59.294 47.826 0.00 0.00 0.00 3.11
59 60 4.202151 GCATCTCTCTCCTCTTCTCCTTTC 60.202 50.000 0.00 0.00 0.00 2.62
60 61 3.976015 TCTCTCTCCTCTTCTCCTTTCC 58.024 50.000 0.00 0.00 0.00 3.13
61 62 3.596046 TCTCTCTCCTCTTCTCCTTTCCT 59.404 47.826 0.00 0.00 0.00 3.36
62 63 4.045334 TCTCTCTCCTCTTCTCCTTTCCTT 59.955 45.833 0.00 0.00 0.00 3.36
63 64 4.757692 TCTCTCCTCTTCTCCTTTCCTTT 58.242 43.478 0.00 0.00 0.00 3.11
64 65 4.530161 TCTCTCCTCTTCTCCTTTCCTTTG 59.470 45.833 0.00 0.00 0.00 2.77
65 66 3.008485 TCTCCTCTTCTCCTTTCCTTTGC 59.992 47.826 0.00 0.00 0.00 3.68
66 67 2.040412 TCCTCTTCTCCTTTCCTTTGCC 59.960 50.000 0.00 0.00 0.00 4.52
67 68 2.079925 CTCTTCTCCTTTCCTTTGCCG 58.920 52.381 0.00 0.00 0.00 5.69
68 69 0.523519 CTTCTCCTTTCCTTTGCCGC 59.476 55.000 0.00 0.00 0.00 6.53
69 70 1.234615 TTCTCCTTTCCTTTGCCGCG 61.235 55.000 0.00 0.00 0.00 6.46
70 71 1.966451 CTCCTTTCCTTTGCCGCGT 60.966 57.895 4.92 0.00 0.00 6.01
71 72 1.912371 CTCCTTTCCTTTGCCGCGTC 61.912 60.000 4.92 0.00 0.00 5.19
72 73 2.561373 CTTTCCTTTGCCGCGTCC 59.439 61.111 4.92 0.00 0.00 4.79
73 74 3.308878 CTTTCCTTTGCCGCGTCCG 62.309 63.158 4.92 0.00 0.00 4.79
90 91 4.324991 GGCGTCCCGTTCCCAAGT 62.325 66.667 0.00 0.00 0.00 3.16
91 92 2.658422 GCGTCCCGTTCCCAAGTA 59.342 61.111 0.00 0.00 0.00 2.24
92 93 1.739196 GCGTCCCGTTCCCAAGTAC 60.739 63.158 0.00 0.00 0.00 2.73
93 94 1.969862 CGTCCCGTTCCCAAGTACT 59.030 57.895 0.00 0.00 0.00 2.73
101 102 2.098117 CGTTCCCAAGTACTAGTACGGG 59.902 54.545 27.85 27.85 40.80 5.28
121 122 1.216710 GAGTGGAGGAAGCACGGAG 59.783 63.158 0.00 0.00 0.00 4.63
191 201 0.736325 CCCCGACGATAATGCCGATC 60.736 60.000 0.00 0.00 0.00 3.69
225 235 2.419739 GCCAACAACCACCAACCGT 61.420 57.895 0.00 0.00 0.00 4.83
327 338 2.017049 GAGATGGGGTTGGATTTGACG 58.983 52.381 0.00 0.00 0.00 4.35
330 341 1.175983 TGGGGTTGGATTTGACGTGC 61.176 55.000 0.00 0.00 0.00 5.34
331 342 1.209127 GGGTTGGATTTGACGTGCG 59.791 57.895 0.00 0.00 0.00 5.34
333 344 0.385473 GGTTGGATTTGACGTGCGTG 60.385 55.000 0.67 0.00 0.00 5.34
334 345 0.996727 GTTGGATTTGACGTGCGTGC 60.997 55.000 0.67 0.00 0.00 5.34
359 380 8.344831 GCAATTGCACAATAATGATCTACTGTA 58.655 33.333 25.36 0.00 41.59 2.74
379 400 3.339713 AAGGGTTAGTATGGGATCGGA 57.660 47.619 0.00 0.00 0.00 4.55
428 453 6.365789 CACAATTCATGGTGCGTTATTTTTCT 59.634 34.615 0.00 0.00 0.00 2.52
429 454 6.928492 ACAATTCATGGTGCGTTATTTTTCTT 59.072 30.769 0.00 0.00 0.00 2.52
430 455 7.116233 ACAATTCATGGTGCGTTATTTTTCTTC 59.884 33.333 0.00 0.00 0.00 2.87
451 477 4.574892 TCTCTACAACGATGATTTTGCCA 58.425 39.130 0.00 0.00 0.00 4.92
482 508 4.181578 GCAACACGTGATTGTATAGTCCT 58.818 43.478 25.01 0.00 0.00 3.85
506 532 9.961265 CCTACTCATTTTCATCACGTACTAATA 57.039 33.333 0.00 0.00 0.00 0.98
542 568 1.066215 TGACATACTCGCACTTGCCAT 60.066 47.619 0.00 0.00 37.91 4.40
543 569 1.328680 GACATACTCGCACTTGCCATG 59.671 52.381 0.00 0.00 37.91 3.66
603 640 0.666274 CAGCTGTCTCGCGGTTGTAA 60.666 55.000 6.13 0.00 34.40 2.41
749 788 5.911378 AGATGGAAAGAAAAAGATGGAGC 57.089 39.130 0.00 0.00 0.00 4.70
788 827 2.029838 AAGGGCGAGAACATGATCAC 57.970 50.000 0.00 0.00 0.00 3.06
791 833 1.293924 GGCGAGAACATGATCACAGG 58.706 55.000 0.00 0.00 0.00 4.00
804 846 4.529897 TGATCACAGGCTCAATTATGCTT 58.470 39.130 0.00 0.00 0.00 3.91
818 860 7.377398 TCAATTATGCTTAGCAAAAGCTTTCA 58.623 30.769 12.08 4.52 43.62 2.69
966 1014 4.382577 CCAAATTAAATGCCCCGCTAGTTT 60.383 41.667 0.00 0.00 0.00 2.66
1064 1113 8.349983 AGACCAAAATGTATTGTGTTTGTAGAC 58.650 33.333 0.00 0.00 30.61 2.59
1114 1163 1.134521 GCGGAGATGTTGGTGGTATGA 60.135 52.381 0.00 0.00 0.00 2.15
1137 1186 7.739295 TGAATTAACGACTAGCAATTCTTGAC 58.261 34.615 0.00 0.00 37.94 3.18
1139 1188 6.706055 TTAACGACTAGCAATTCTTGACAG 57.294 37.500 0.00 0.00 0.00 3.51
1214 1263 2.358898 CTGGGACATTATTTGGAAGGCG 59.641 50.000 0.00 0.00 38.20 5.52
1220 1269 3.443681 ACATTATTTGGAAGGCGAAGGTG 59.556 43.478 0.00 0.00 0.00 4.00
1232 1281 1.541588 GCGAAGGTGCCTCAGAAAATT 59.458 47.619 0.00 0.00 0.00 1.82
1238 1287 6.538742 CGAAGGTGCCTCAGAAAATTAAGATA 59.461 38.462 0.00 0.00 0.00 1.98
1256 1305 4.561752 AGATATTTGGGTGGAGAGTAGCT 58.438 43.478 0.00 0.00 0.00 3.32
1266 1315 3.695060 GTGGAGAGTAGCTACTTGCACTA 59.305 47.826 30.46 19.03 45.94 2.74
1277 1326 4.034510 GCTACTTGCACTATGGCTACAAAG 59.965 45.833 0.00 0.00 42.31 2.77
1361 1410 5.525012 CGAGGAAGATGAATTTCATGCTGTA 59.475 40.000 16.41 0.00 37.20 2.74
1381 1430 2.693797 ATTTCGTGCACAAAGAGCAG 57.306 45.000 18.64 0.00 43.63 4.24
1443 1492 4.810191 AGCGAGGAAAAACTCAGATACT 57.190 40.909 0.00 0.00 37.34 2.12
1460 1509 2.414994 ACTCAGGTGATGATTGGCTG 57.585 50.000 0.00 0.00 37.28 4.85
1466 1515 1.607628 GGTGATGATTGGCTGCAGATC 59.392 52.381 20.43 12.41 0.00 2.75
1472 1521 0.924823 ATTGGCTGCAGATCCTCCTT 59.075 50.000 20.43 0.00 0.00 3.36
1484 1533 3.269381 AGATCCTCCTTAACCCATGCAAA 59.731 43.478 0.00 0.00 0.00 3.68
1492 1541 2.610438 AACCCATGCAAACCAGAGAT 57.390 45.000 0.00 0.00 0.00 2.75
1499 1548 4.201851 CCATGCAAACCAGAGATTAGAACG 60.202 45.833 0.00 0.00 0.00 3.95
1503 1552 5.529430 TGCAAACCAGAGATTAGAACGAAAA 59.471 36.000 0.00 0.00 0.00 2.29
1532 1581 3.030652 CTGTGGCGGTGTTGGTTC 58.969 61.111 0.00 0.00 0.00 3.62
1535 1584 2.112297 TGGCGGTGTTGGTTCCTC 59.888 61.111 0.00 0.00 0.00 3.71
1574 1623 1.504275 ATGCAGGGAAGGAGCTGGTT 61.504 55.000 0.00 0.00 0.00 3.67
1585 1634 2.967615 GCTGGTTAGCCGATCCGC 60.968 66.667 0.00 0.00 44.33 5.54
1610 1659 7.095523 GCTATGTTCTTAAAACAGTACGTGGAA 60.096 37.037 0.00 0.00 33.18 3.53
1627 1676 1.405661 GGAAGAACTAACCTGCGGAGG 60.406 57.143 22.94 22.94 46.21 4.30
1630 1679 0.460459 GAACTAACCTGCGGAGGCTC 60.460 60.000 24.53 5.78 44.33 4.70
1648 1697 1.689273 CTCGGGGGAGGAAACTGATAG 59.311 57.143 0.00 0.00 44.43 2.08
1649 1698 1.007963 TCGGGGGAGGAAACTGATAGT 59.992 52.381 0.00 0.00 44.43 2.12
1655 1704 3.391626 GGGAGGAAACTGATAGTAAGGGG 59.608 52.174 0.00 0.00 44.43 4.79
1698 1747 2.597510 GTGCTTTGGCGAAGGGGT 60.598 61.111 16.10 0.00 42.25 4.95
1712 1761 0.400594 AGGGGTTTTCTCTGTTCCCG 59.599 55.000 0.00 0.00 39.31 5.14
1742 1791 4.078571 ACAGGGATAGATGGACAAGAGGTA 60.079 45.833 0.00 0.00 0.00 3.08
1772 1821 2.350522 GTGGATCACACCATCAGTCAC 58.649 52.381 0.00 0.00 44.49 3.67
1801 1850 0.462047 CCTATGGCGGGAACAGTCAC 60.462 60.000 0.00 0.00 0.00 3.67
1829 1878 3.315191 ACACTGATGCAGCGTTTTTAACT 59.685 39.130 0.00 0.00 34.37 2.24
1863 1912 2.031919 ACTCGGGTGCAATTGCGA 59.968 55.556 24.58 14.62 45.83 5.10
1871 1920 1.089920 GTGCAATTGCGAGAGACCAT 58.910 50.000 24.58 0.00 45.83 3.55
1873 1922 1.338960 TGCAATTGCGAGAGACCATGA 60.339 47.619 24.58 0.12 45.83 3.07
1874 1923 1.945394 GCAATTGCGAGAGACCATGAT 59.055 47.619 15.87 0.00 0.00 2.45
1910 1959 1.275010 TCGCTGTCTGAACATGGCTTA 59.725 47.619 0.00 0.00 34.13 3.09
1959 2009 1.303888 CAGGCATTGCTGACAGGGT 60.304 57.895 8.82 0.00 30.17 4.34
1988 2038 1.575419 TGTCCGCCCTTTATACTGGT 58.425 50.000 0.00 0.00 0.00 4.00
1991 2041 0.249741 CCGCCCTTTATACTGGTCCG 60.250 60.000 0.00 0.00 0.00 4.79
2016 2066 1.271379 TCGCGGAAACAGACTGTATGT 59.729 47.619 8.91 1.56 0.00 2.29
2063 2113 2.095567 CACCAGTAGTTTGTCTGCATGC 60.096 50.000 11.82 11.82 0.00 4.06
2099 2149 0.107456 ATATCAAGGTGGAGCTGGCG 59.893 55.000 0.00 0.00 0.00 5.69
2135 2185 1.059098 AGGTCCAACATGTCAGCAGA 58.941 50.000 0.00 0.00 0.00 4.26
2147 2197 5.981315 ACATGTCAGCAGAAATCAAAACAAG 59.019 36.000 0.00 0.00 0.00 3.16
2196 2246 6.064717 GCTAGGAAAATGGATGGAATGTACT 58.935 40.000 0.00 0.00 0.00 2.73
2215 2265 2.508663 GGTAGCGAGTGTTCCGGC 60.509 66.667 0.00 0.00 0.00 6.13
2224 2274 0.534412 AGTGTTCCGGCTGATCTGAG 59.466 55.000 0.00 0.00 0.00 3.35
2264 2314 3.118038 ACCTTGTGTTGGCTGAAGAGTAA 60.118 43.478 0.00 0.00 0.00 2.24
2579 2637 2.187163 GACTCCGGGCTTACCAGC 59.813 66.667 0.00 0.00 46.52 4.85
2623 2696 2.940158 TGGATCAATAGCAGCAGCAAT 58.060 42.857 3.17 0.00 45.49 3.56
2655 2728 3.376859 TGAAACTGACAACGTGATGCTTT 59.623 39.130 0.00 0.00 0.00 3.51
2656 2729 4.142491 TGAAACTGACAACGTGATGCTTTT 60.142 37.500 0.00 0.00 0.00 2.27
2657 2730 4.370364 AACTGACAACGTGATGCTTTTT 57.630 36.364 0.00 0.00 0.00 1.94
2658 2731 3.952535 ACTGACAACGTGATGCTTTTTC 58.047 40.909 0.00 0.00 0.00 2.29
2659 2732 3.627577 ACTGACAACGTGATGCTTTTTCT 59.372 39.130 0.00 0.00 0.00 2.52
2660 2733 4.096382 ACTGACAACGTGATGCTTTTTCTT 59.904 37.500 0.00 0.00 0.00 2.52
2661 2734 4.597079 TGACAACGTGATGCTTTTTCTTC 58.403 39.130 0.00 0.00 0.00 2.87
2662 2735 4.335315 TGACAACGTGATGCTTTTTCTTCT 59.665 37.500 0.00 0.00 0.00 2.85
2663 2736 5.163663 TGACAACGTGATGCTTTTTCTTCTT 60.164 36.000 0.00 0.00 0.00 2.52
2664 2737 5.650543 ACAACGTGATGCTTTTTCTTCTTT 58.349 33.333 0.00 0.00 0.00 2.52
2665 2738 6.099341 ACAACGTGATGCTTTTTCTTCTTTT 58.901 32.000 0.00 0.00 0.00 2.27
2666 2739 6.589907 ACAACGTGATGCTTTTTCTTCTTTTT 59.410 30.769 0.00 0.00 0.00 1.94
2683 2756 4.237445 TTTTTGCGGGGAACGTGA 57.763 50.000 0.00 0.00 46.52 4.35
2684 2757 2.721945 TTTTTGCGGGGAACGTGAT 58.278 47.368 0.00 0.00 46.52 3.06
2685 2758 0.312416 TTTTTGCGGGGAACGTGATG 59.688 50.000 0.00 0.00 46.52 3.07
2686 2759 2.136196 TTTTGCGGGGAACGTGATGC 62.136 55.000 0.00 0.00 46.52 3.91
2687 2760 3.545124 TTGCGGGGAACGTGATGCT 62.545 57.895 0.00 0.00 46.52 3.79
2688 2761 2.746277 GCGGGGAACGTGATGCTT 60.746 61.111 0.00 0.00 46.52 3.91
2755 2831 5.680619 TCTCTACAACACAACAATGGAACT 58.319 37.500 0.00 0.00 0.00 3.01
2819 2895 2.604139 TGGGAAATTTCAAGGGGACAC 58.396 47.619 19.49 0.00 0.00 3.67
2850 2927 0.596082 GCCTTTCGCTTGCTAACCAA 59.404 50.000 0.00 0.00 0.00 3.67
3044 3124 3.308401 TGGCTGAGAGAAGCATGGTATA 58.692 45.455 0.00 0.00 45.43 1.47
3124 3211 7.781324 AAAAGAAAGCTCATGATTAAAGGGA 57.219 32.000 0.00 0.00 0.00 4.20
3125 3212 7.781324 AAAGAAAGCTCATGATTAAAGGGAA 57.219 32.000 0.00 0.00 0.00 3.97
3126 3213 7.781324 AAGAAAGCTCATGATTAAAGGGAAA 57.219 32.000 0.00 0.00 0.00 3.13
3127 3214 7.781324 AGAAAGCTCATGATTAAAGGGAAAA 57.219 32.000 0.00 0.00 0.00 2.29
3128 3215 7.834803 AGAAAGCTCATGATTAAAGGGAAAAG 58.165 34.615 0.00 0.00 0.00 2.27
3129 3216 6.535963 AAGCTCATGATTAAAGGGAAAAGG 57.464 37.500 0.00 0.00 0.00 3.11
3130 3217 5.831103 AGCTCATGATTAAAGGGAAAAGGA 58.169 37.500 0.00 0.00 0.00 3.36
3137 3224 4.594123 TTAAAGGGAAAAGGAAAAGGCG 57.406 40.909 0.00 0.00 0.00 5.52
3151 3238 1.851267 AGGCGTTCCCTTTTCCCTT 59.149 52.632 0.00 0.00 43.06 3.95
3152 3239 0.187606 AGGCGTTCCCTTTTCCCTTT 59.812 50.000 0.00 0.00 43.06 3.11
3153 3240 1.045407 GGCGTTCCCTTTTCCCTTTT 58.955 50.000 0.00 0.00 0.00 2.27
3154 3241 2.158430 AGGCGTTCCCTTTTCCCTTTTA 60.158 45.455 0.00 0.00 43.06 1.52
3174 3261 2.192664 TTTAGTGAAGCGATTGGGCA 57.807 45.000 0.00 0.00 34.64 5.36
3186 3273 3.525537 CGATTGGGCATAGCTGTATAGG 58.474 50.000 0.00 0.00 0.00 2.57
3271 3358 9.638176 TCTTATAATATTATACTCCCTCCGTCC 57.362 37.037 13.63 0.00 0.00 4.79
3272 3359 6.956202 ATAATATTATACTCCCTCCGTCCG 57.044 41.667 6.16 0.00 0.00 4.79
3273 3360 2.965671 ATTATACTCCCTCCGTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
3274 3361 2.734755 TTATACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
3275 3362 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
3276 3363 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3277 3364 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
3278 3365 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
3279 3366 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
3280 3367 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
3281 3368 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
3282 3369 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3283 3370 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
3284 3371 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
3285 3372 0.941542 CCGTCCGAAAAAGCTTGTCA 59.058 50.000 0.00 0.00 0.00 3.58
3286 3373 1.333791 CCGTCCGAAAAAGCTTGTCAC 60.334 52.381 0.00 0.00 0.00 3.67
3287 3374 1.597663 CGTCCGAAAAAGCTTGTCACT 59.402 47.619 0.00 0.00 0.00 3.41
3288 3375 2.348591 CGTCCGAAAAAGCTTGTCACTC 60.349 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.226974 TCGCCGCTAGCTGCTTAAG 60.227 57.895 25.70 12.43 40.39 1.85
9 10 1.518572 GTCGCCGCTAGCTGCTTAA 60.519 57.895 25.70 10.79 40.39 1.85
10 11 2.104331 GTCGCCGCTAGCTGCTTA 59.896 61.111 25.70 13.08 40.39 3.09
16 17 4.789075 TTGTCCGTCGCCGCTAGC 62.789 66.667 4.06 4.06 38.52 3.42
17 18 1.518572 ATTTGTCCGTCGCCGCTAG 60.519 57.895 0.00 0.00 0.00 3.42
18 19 1.807981 CATTTGTCCGTCGCCGCTA 60.808 57.895 0.00 0.00 0.00 4.26
19 20 3.118454 CATTTGTCCGTCGCCGCT 61.118 61.111 0.00 0.00 0.00 5.52
20 21 4.811761 GCATTTGTCCGTCGCCGC 62.812 66.667 0.00 0.00 0.00 6.53
21 22 2.631696 GATGCATTTGTCCGTCGCCG 62.632 60.000 0.00 0.00 0.00 6.46
22 23 1.062525 GATGCATTTGTCCGTCGCC 59.937 57.895 0.00 0.00 0.00 5.54
23 24 0.026803 GAGATGCATTTGTCCGTCGC 59.973 55.000 0.00 0.00 0.00 5.19
24 25 1.590238 GAGAGATGCATTTGTCCGTCG 59.410 52.381 0.00 0.00 0.00 5.12
25 26 2.863137 GAGAGAGATGCATTTGTCCGTC 59.137 50.000 10.38 0.19 0.00 4.79
26 27 2.419297 GGAGAGAGATGCATTTGTCCGT 60.419 50.000 10.38 0.00 0.00 4.69
27 28 2.158986 AGGAGAGAGATGCATTTGTCCG 60.159 50.000 10.38 0.00 0.00 4.79
28 29 3.134442 AGAGGAGAGAGATGCATTTGTCC 59.866 47.826 10.38 11.49 0.00 4.02
29 30 4.405116 AGAGGAGAGAGATGCATTTGTC 57.595 45.455 6.28 6.28 0.00 3.18
30 31 4.470664 AGAAGAGGAGAGAGATGCATTTGT 59.529 41.667 0.00 0.00 0.00 2.83
31 32 5.026038 AGAAGAGGAGAGAGATGCATTTG 57.974 43.478 0.00 0.00 0.00 2.32
32 33 4.101430 GGAGAAGAGGAGAGAGATGCATTT 59.899 45.833 0.00 0.00 0.00 2.32
33 34 3.642848 GGAGAAGAGGAGAGAGATGCATT 59.357 47.826 0.00 0.00 0.00 3.56
34 35 3.117016 AGGAGAAGAGGAGAGAGATGCAT 60.117 47.826 0.00 0.00 0.00 3.96
35 36 2.244510 AGGAGAAGAGGAGAGAGATGCA 59.755 50.000 0.00 0.00 0.00 3.96
36 37 2.949447 AGGAGAAGAGGAGAGAGATGC 58.051 52.381 0.00 0.00 0.00 3.91
37 38 4.342092 GGAAAGGAGAAGAGGAGAGAGATG 59.658 50.000 0.00 0.00 0.00 2.90
38 39 4.232820 AGGAAAGGAGAAGAGGAGAGAGAT 59.767 45.833 0.00 0.00 0.00 2.75
39 40 3.596046 AGGAAAGGAGAAGAGGAGAGAGA 59.404 47.826 0.00 0.00 0.00 3.10
40 41 3.981212 AGGAAAGGAGAAGAGGAGAGAG 58.019 50.000 0.00 0.00 0.00 3.20
41 42 4.412060 AAGGAAAGGAGAAGAGGAGAGA 57.588 45.455 0.00 0.00 0.00 3.10
42 43 4.831107 CAAAGGAAAGGAGAAGAGGAGAG 58.169 47.826 0.00 0.00 0.00 3.20
43 44 3.008485 GCAAAGGAAAGGAGAAGAGGAGA 59.992 47.826 0.00 0.00 0.00 3.71
44 45 3.342719 GCAAAGGAAAGGAGAAGAGGAG 58.657 50.000 0.00 0.00 0.00 3.69
45 46 2.040412 GGCAAAGGAAAGGAGAAGAGGA 59.960 50.000 0.00 0.00 0.00 3.71
46 47 2.441410 GGCAAAGGAAAGGAGAAGAGG 58.559 52.381 0.00 0.00 0.00 3.69
47 48 2.079925 CGGCAAAGGAAAGGAGAAGAG 58.920 52.381 0.00 0.00 0.00 2.85
48 49 1.882352 GCGGCAAAGGAAAGGAGAAGA 60.882 52.381 0.00 0.00 0.00 2.87
49 50 0.523519 GCGGCAAAGGAAAGGAGAAG 59.476 55.000 0.00 0.00 0.00 2.85
50 51 1.234615 CGCGGCAAAGGAAAGGAGAA 61.235 55.000 0.00 0.00 0.00 2.87
51 52 1.671054 CGCGGCAAAGGAAAGGAGA 60.671 57.895 0.00 0.00 0.00 3.71
52 53 1.912371 GACGCGGCAAAGGAAAGGAG 61.912 60.000 7.34 0.00 0.00 3.69
53 54 1.964373 GACGCGGCAAAGGAAAGGA 60.964 57.895 7.34 0.00 0.00 3.36
54 55 2.561373 GACGCGGCAAAGGAAAGG 59.439 61.111 7.34 0.00 0.00 3.11
55 56 2.561373 GGACGCGGCAAAGGAAAG 59.439 61.111 17.00 0.00 0.00 2.62
56 57 3.350612 CGGACGCGGCAAAGGAAA 61.351 61.111 17.00 0.00 0.00 3.13
75 76 6.211799 GTACTAGTACTTGGGAACGGGACG 62.212 54.167 23.17 0.00 44.97 4.79
76 77 2.174360 ACTAGTACTTGGGAACGGGAC 58.826 52.381 0.00 0.00 0.00 4.46
77 78 2.610438 ACTAGTACTTGGGAACGGGA 57.390 50.000 0.00 0.00 0.00 5.14
78 79 2.098117 CGTACTAGTACTTGGGAACGGG 59.902 54.545 26.36 7.07 34.04 5.28
79 80 2.098117 CCGTACTAGTACTTGGGAACGG 59.902 54.545 26.36 22.80 42.12 4.44
80 81 2.098117 CCCGTACTAGTACTTGGGAACG 59.902 54.545 29.02 18.00 38.32 3.95
81 82 3.356290 TCCCGTACTAGTACTTGGGAAC 58.644 50.000 31.24 10.96 40.45 3.62
82 83 3.266772 TCTCCCGTACTAGTACTTGGGAA 59.733 47.826 31.94 24.21 41.78 3.97
83 84 2.846206 TCTCCCGTACTAGTACTTGGGA 59.154 50.000 31.13 31.13 40.84 4.37
84 85 3.212685 CTCTCCCGTACTAGTACTTGGG 58.787 54.545 27.85 27.85 37.78 4.12
85 86 3.626670 CACTCTCCCGTACTAGTACTTGG 59.373 52.174 26.36 24.51 34.04 3.61
86 87 3.626670 CCACTCTCCCGTACTAGTACTTG 59.373 52.174 26.36 18.18 34.04 3.16
87 88 3.521126 TCCACTCTCCCGTACTAGTACTT 59.479 47.826 26.36 3.74 34.04 2.24
88 89 3.110705 TCCACTCTCCCGTACTAGTACT 58.889 50.000 26.36 0.00 34.04 2.73
89 90 3.465871 CTCCACTCTCCCGTACTAGTAC 58.534 54.545 21.06 21.06 0.00 2.73
90 91 2.437281 CCTCCACTCTCCCGTACTAGTA 59.563 54.545 0.00 0.00 0.00 1.82
91 92 1.212441 CCTCCACTCTCCCGTACTAGT 59.788 57.143 0.00 0.00 0.00 2.57
92 93 1.489649 TCCTCCACTCTCCCGTACTAG 59.510 57.143 0.00 0.00 0.00 2.57
93 94 1.588239 TCCTCCACTCTCCCGTACTA 58.412 55.000 0.00 0.00 0.00 1.82
101 102 1.216710 CCGTGCTTCCTCCACTCTC 59.783 63.158 0.00 0.00 0.00 3.20
191 201 2.105128 GCTGGTCCTGGTCGATCG 59.895 66.667 9.36 9.36 0.00 3.69
333 344 7.198390 ACAGTAGATCATTATTGTGCAATTGC 58.802 34.615 23.69 23.69 42.50 3.56
359 380 2.970640 GTCCGATCCCATACTAACCCTT 59.029 50.000 0.00 0.00 0.00 3.95
379 400 3.446516 GGTTGGAGTGTCTCTTATACGGT 59.553 47.826 0.00 0.00 0.00 4.83
428 453 5.000591 TGGCAAAATCATCGTTGTAGAGAA 58.999 37.500 0.00 0.00 0.00 2.87
429 454 4.391830 GTGGCAAAATCATCGTTGTAGAGA 59.608 41.667 0.00 0.00 0.00 3.10
430 455 4.154015 TGTGGCAAAATCATCGTTGTAGAG 59.846 41.667 0.00 0.00 0.00 2.43
451 477 3.921119 ATCACGTGTTGCATCAATTGT 57.079 38.095 16.51 0.00 0.00 2.71
506 532 9.405587 CGAGTATGTCACAAAAATATTGGTTTT 57.594 29.630 0.00 0.00 32.94 2.43
542 568 1.221466 CTTTTCTGACGGCAGCGACA 61.221 55.000 15.33 0.00 42.01 4.35
543 569 1.493311 CTTTTCTGACGGCAGCGAC 59.507 57.895 15.33 0.00 42.01 5.19
584 621 0.666274 TTACAACCGCGAGACAGCTG 60.666 55.000 13.48 13.48 34.40 4.24
597 634 3.925913 TCCGTTACGCATTACCTTACAAC 59.074 43.478 0.00 0.00 0.00 3.32
603 640 3.814005 AGAATCCGTTACGCATTACCT 57.186 42.857 0.00 0.00 0.00 3.08
706 745 9.018582 CCATCTTCTCTTTTATTCAAGGAAAGT 57.981 33.333 0.00 0.00 33.32 2.66
707 746 9.236006 TCCATCTTCTCTTTTATTCAAGGAAAG 57.764 33.333 0.00 0.00 0.00 2.62
730 769 5.739935 GCTTTGCTCCATCTTTTTCTTTCCA 60.740 40.000 0.00 0.00 0.00 3.53
749 788 2.710096 TATTCCCTCCCTTCGCTTTG 57.290 50.000 0.00 0.00 0.00 2.77
788 827 4.906065 TTGCTAAGCATAATTGAGCCTG 57.094 40.909 0.00 0.00 38.76 4.85
791 833 5.632445 GCTTTTGCTAAGCATAATTGAGC 57.368 39.130 16.10 0.00 42.56 4.26
818 860 3.131933 AGATATCTTGCGTGAGTTCAGCT 59.868 43.478 0.00 0.00 0.00 4.24
966 1014 2.420372 TGCTGCGTCGCCATTTTTATAA 59.580 40.909 15.88 0.00 0.00 0.98
980 1028 1.680735 TCAACCAAAAATCTGCTGCGT 59.319 42.857 0.00 0.00 0.00 5.24
1064 1113 3.371898 TGCTTGATGTAGATGCAAACTCG 59.628 43.478 0.00 0.00 0.00 4.18
1214 1263 6.765915 ATCTTAATTTTCTGAGGCACCTTC 57.234 37.500 0.00 0.00 0.00 3.46
1220 1269 7.922811 CACCCAAATATCTTAATTTTCTGAGGC 59.077 37.037 0.00 0.00 0.00 4.70
1232 1281 6.143915 AGCTACTCTCCACCCAAATATCTTA 58.856 40.000 0.00 0.00 0.00 2.10
1238 1287 3.725634 AGTAGCTACTCTCCACCCAAAT 58.274 45.455 20.95 0.00 0.00 2.32
1256 1305 5.414789 TCTTTGTAGCCATAGTGCAAGTA 57.585 39.130 0.00 0.00 0.00 2.24
1266 1315 5.774690 TCCATTTGTTCTTCTTTGTAGCCAT 59.225 36.000 0.00 0.00 0.00 4.40
1277 1326 2.287547 TGTGCGCTTCCATTTGTTCTTC 60.288 45.455 9.73 0.00 0.00 2.87
1361 1410 2.287788 CCTGCTCTTTGTGCACGAAATT 60.288 45.455 19.89 0.00 36.37 1.82
1381 1430 4.517285 TCTCATTTCATGTCTTAGTGCCC 58.483 43.478 0.00 0.00 0.00 5.36
1408 1457 0.671251 CTCGCTAGGTAGCTCCCAAG 59.329 60.000 0.00 0.00 46.85 3.61
1409 1458 0.755698 CCTCGCTAGGTAGCTCCCAA 60.756 60.000 0.00 0.00 46.85 4.12
1434 1483 5.539979 CCAATCATCACCTGAGTATCTGAG 58.460 45.833 0.00 0.00 37.28 3.35
1443 1492 0.328926 TGCAGCCAATCATCACCTGA 59.671 50.000 0.00 0.00 38.53 3.86
1460 1509 2.856222 CATGGGTTAAGGAGGATCTGC 58.144 52.381 0.00 0.00 33.73 4.26
1466 1515 1.824852 GGTTTGCATGGGTTAAGGAGG 59.175 52.381 0.00 0.00 0.00 4.30
1472 1521 3.737559 ATCTCTGGTTTGCATGGGTTA 57.262 42.857 0.00 0.00 0.00 2.85
1484 1533 9.503399 AGTAAAATTTTCGTTCTAATCTCTGGT 57.497 29.630 6.72 0.00 0.00 4.00
1492 1541 6.855914 CAGCAGCAGTAAAATTTTCGTTCTAA 59.144 34.615 6.72 0.00 0.00 2.10
1499 1548 3.429881 GCCACAGCAGCAGTAAAATTTTC 59.570 43.478 6.72 0.00 39.53 2.29
1503 1552 0.523072 CGCCACAGCAGCAGTAAAAT 59.477 50.000 0.00 0.00 39.83 1.82
1532 1581 1.026718 GGGTGCAATCGTCTTGGAGG 61.027 60.000 0.00 0.00 0.00 4.30
1535 1584 2.036958 TATGGGTGCAATCGTCTTGG 57.963 50.000 0.00 0.00 0.00 3.61
1585 1634 7.878477 TCCACGTACTGTTTTAAGAACATAG 57.122 36.000 0.00 0.00 0.00 2.23
1627 1676 1.627297 ATCAGTTTCCTCCCCCGAGC 61.627 60.000 0.00 0.00 34.49 5.03
1630 1679 1.497161 ACTATCAGTTTCCTCCCCCG 58.503 55.000 0.00 0.00 0.00 5.73
1634 1683 4.296056 TCCCCTTACTATCAGTTTCCTCC 58.704 47.826 0.00 0.00 0.00 4.30
1648 1697 0.744771 CGCCTTCTGCTTCCCCTTAC 60.745 60.000 0.00 0.00 38.05 2.34
1649 1698 1.602237 CGCCTTCTGCTTCCCCTTA 59.398 57.895 0.00 0.00 38.05 2.69
1680 1729 3.373565 CCCCTTCGCCAAAGCACC 61.374 66.667 0.00 0.00 39.83 5.01
1681 1730 1.744320 AAACCCCTTCGCCAAAGCAC 61.744 55.000 0.00 0.00 39.83 4.40
1698 1747 1.140052 TGACAGCGGGAACAGAGAAAA 59.860 47.619 0.00 0.00 0.00 2.29
1712 1761 2.435805 TCCATCTATCCCTGTTGACAGC 59.564 50.000 5.62 0.00 42.47 4.40
1742 1791 0.837691 TGTGATCCACAGTGGCTCCT 60.838 55.000 18.90 2.66 39.62 3.69
1759 1808 0.979665 CCTCCAGTGACTGATGGTGT 59.020 55.000 15.33 0.00 37.84 4.16
1760 1809 0.392193 GCCTCCAGTGACTGATGGTG 60.392 60.000 15.33 0.00 37.84 4.17
1765 1814 2.607750 GGGGCCTCCAGTGACTGA 60.608 66.667 15.33 0.00 32.44 3.41
1796 1845 2.158914 TGCATCAGTGTTCAGTGTGACT 60.159 45.455 7.39 0.00 0.00 3.41
1801 1850 0.165295 CGCTGCATCAGTGTTCAGTG 59.835 55.000 0.00 1.62 37.23 3.66
1811 1860 2.621055 ACCAGTTAAAAACGCTGCATCA 59.379 40.909 0.00 0.00 36.23 3.07
1829 1878 1.600107 GTGGGAATCACCGCTACCA 59.400 57.895 0.00 0.00 40.39 3.25
1871 1920 3.677148 GCGAGAAGATGACAGAACCATCA 60.677 47.826 0.00 0.00 42.03 3.07
1873 1922 2.499289 AGCGAGAAGATGACAGAACCAT 59.501 45.455 0.00 0.00 0.00 3.55
1874 1923 1.895798 AGCGAGAAGATGACAGAACCA 59.104 47.619 0.00 0.00 0.00 3.67
1879 1928 2.163211 TCAGACAGCGAGAAGATGACAG 59.837 50.000 0.00 0.00 38.85 3.51
1925 1974 2.046892 TGCGCTTCAGCTTCCTCC 60.047 61.111 9.73 0.00 39.32 4.30
1955 2005 1.227853 GGACAAGTGTCGCAACCCT 60.228 57.895 5.40 0.00 45.65 4.34
1959 2009 2.970324 GGCGGACAAGTGTCGCAA 60.970 61.111 21.21 0.00 45.65 4.85
1991 2041 1.590238 CAGTCTGTTTCCGCGATCATC 59.410 52.381 8.23 0.00 0.00 2.92
2016 2066 2.093500 ACCTGAGCTCATTCGCAATGTA 60.093 45.455 18.63 0.00 39.87 2.29
2063 2113 6.404184 CCTTGATATCAGCGAGTACTGGATAG 60.404 46.154 9.33 0.00 38.26 2.08
2099 2149 0.240411 CCTGAGCAGCAGCAAACTTC 59.760 55.000 3.17 0.00 45.49 3.01
2147 2197 0.320247 CCGCCAGTAGATGAGCCATC 60.320 60.000 6.98 6.98 40.80 3.51
2196 2246 1.290955 CCGGAACACTCGCTACCAA 59.709 57.895 0.00 0.00 0.00 3.67
2303 2356 9.716507 CGTTTGCTTTACTTTTATATACAGCAT 57.283 29.630 0.00 0.00 36.00 3.79
2304 2357 7.694784 GCGTTTGCTTTACTTTTATATACAGCA 59.305 33.333 0.00 0.00 38.39 4.41
2318 2371 4.143824 CGTTTCTTCATGCGTTTGCTTTAC 60.144 41.667 0.00 0.00 43.34 2.01
2323 2376 1.708680 GACGTTTCTTCATGCGTTTGC 59.291 47.619 0.00 0.00 37.71 3.68
2335 2388 1.096416 TTTTGCCCGTTGACGTTTCT 58.904 45.000 2.63 0.00 37.74 2.52
2430 2483 4.171103 ATACCCAGTTCCGCGCCC 62.171 66.667 0.00 0.00 0.00 6.13
2431 2484 2.588034 GATACCCAGTTCCGCGCC 60.588 66.667 0.00 0.00 0.00 6.53
2598 2671 1.776063 TGCTGCTATTGATCCATCCCA 59.224 47.619 0.00 0.00 0.00 4.37
2666 2739 0.312416 CATCACGTTCCCCGCAAAAA 59.688 50.000 0.00 0.00 41.42 1.94
2667 2740 1.953017 CATCACGTTCCCCGCAAAA 59.047 52.632 0.00 0.00 41.42 2.44
2668 2741 2.622011 GCATCACGTTCCCCGCAAA 61.622 57.895 0.00 0.00 41.42 3.68
2669 2742 3.053291 GCATCACGTTCCCCGCAA 61.053 61.111 0.00 0.00 41.42 4.85
2670 2743 3.545124 AAGCATCACGTTCCCCGCA 62.545 57.895 0.00 0.00 41.42 5.69
2671 2744 2.746277 AAGCATCACGTTCCCCGC 60.746 61.111 0.00 0.00 41.42 6.13
2672 2745 0.953471 TTCAAGCATCACGTTCCCCG 60.953 55.000 0.00 0.00 44.03 5.73
2673 2746 0.521735 GTTCAAGCATCACGTTCCCC 59.478 55.000 0.00 0.00 0.00 4.81
2674 2747 0.165944 CGTTCAAGCATCACGTTCCC 59.834 55.000 0.00 0.00 0.00 3.97
2675 2748 1.126846 CTCGTTCAAGCATCACGTTCC 59.873 52.381 0.00 0.00 35.40 3.62
2676 2749 2.058798 TCTCGTTCAAGCATCACGTTC 58.941 47.619 0.00 0.00 35.40 3.95
2677 2750 2.061773 CTCTCGTTCAAGCATCACGTT 58.938 47.619 0.00 0.00 35.40 3.99
2678 2751 1.269723 TCTCTCGTTCAAGCATCACGT 59.730 47.619 0.00 0.00 35.40 4.49
2679 2752 1.916651 CTCTCTCGTTCAAGCATCACG 59.083 52.381 0.00 0.00 35.18 4.35
2680 2753 3.223423 TCTCTCTCGTTCAAGCATCAC 57.777 47.619 0.00 0.00 0.00 3.06
2681 2754 3.942130 TTCTCTCTCGTTCAAGCATCA 57.058 42.857 0.00 0.00 0.00 3.07
2682 2755 4.489810 TCTTTCTCTCTCGTTCAAGCATC 58.510 43.478 0.00 0.00 0.00 3.91
2683 2756 4.219507 TCTCTTTCTCTCTCGTTCAAGCAT 59.780 41.667 0.00 0.00 0.00 3.79
2684 2757 3.570125 TCTCTTTCTCTCTCGTTCAAGCA 59.430 43.478 0.00 0.00 0.00 3.91
2685 2758 4.167554 TCTCTTTCTCTCTCGTTCAAGC 57.832 45.455 0.00 0.00 0.00 4.01
2686 2759 6.477033 TGTTTTCTCTTTCTCTCTCGTTCAAG 59.523 38.462 0.00 0.00 0.00 3.02
2687 2760 6.338146 TGTTTTCTCTTTCTCTCTCGTTCAA 58.662 36.000 0.00 0.00 0.00 2.69
2688 2761 5.902681 TGTTTTCTCTTTCTCTCTCGTTCA 58.097 37.500 0.00 0.00 0.00 3.18
2755 2831 3.469008 AACCGTGATCAAGTTCAGACA 57.531 42.857 7.88 0.00 0.00 3.41
2819 2895 3.665173 GCGAAAGGCAATCACTAAGAG 57.335 47.619 0.00 0.00 42.87 2.85
2914 2994 7.288810 TGAAGGACAAGCAATTGATTAACTT 57.711 32.000 8.90 12.76 0.00 2.66
3012 3092 0.599558 TCTCAGCCATGCACAAAAGC 59.400 50.000 0.00 0.00 0.00 3.51
3124 3211 2.082140 AGGGAACGCCTTTTCCTTTT 57.918 45.000 2.90 0.00 44.16 2.27
3125 3212 2.082140 AAGGGAACGCCTTTTCCTTT 57.918 45.000 0.07 0.00 44.16 3.11
3126 3213 2.082140 AAAGGGAACGCCTTTTCCTT 57.918 45.000 0.07 0.07 44.16 3.36
3127 3214 2.082140 AAAAGGGAACGCCTTTTCCT 57.918 45.000 11.23 0.00 42.06 3.36
3130 3217 1.045407 GGGAAAAGGGAACGCCTTTT 58.955 50.000 15.50 15.50 44.49 2.27
3137 3224 8.185506 TCACTAAATAAAAGGGAAAAGGGAAC 57.814 34.615 0.00 0.00 0.00 3.62
3149 3236 5.743872 GCCCAATCGCTTCACTAAATAAAAG 59.256 40.000 0.00 0.00 0.00 2.27
3151 3238 4.702612 TGCCCAATCGCTTCACTAAATAAA 59.297 37.500 0.00 0.00 0.00 1.40
3152 3239 4.265893 TGCCCAATCGCTTCACTAAATAA 58.734 39.130 0.00 0.00 0.00 1.40
3153 3240 3.879998 TGCCCAATCGCTTCACTAAATA 58.120 40.909 0.00 0.00 0.00 1.40
3154 3241 2.722094 TGCCCAATCGCTTCACTAAAT 58.278 42.857 0.00 0.00 0.00 1.40
3186 3273 2.028883 GGACGCGCTACAGAAATACAAC 59.971 50.000 5.73 0.00 0.00 3.32
3260 3347 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
3261 3348 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
3262 3349 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
3263 3350 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3264 3351 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
3265 3352 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
3266 3353 0.941542 TGACAAGCTTTTTCGGACGG 59.058 50.000 0.00 0.00 0.00 4.79
3267 3354 1.597663 AGTGACAAGCTTTTTCGGACG 59.402 47.619 0.00 0.00 0.00 4.79
3268 3355 3.254827 GAGTGACAAGCTTTTTCGGAC 57.745 47.619 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.