Multiple sequence alignment - TraesCS5D01G163400

Loading Multiple Alignment...

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 TraesCS5D01G163400 chr5D 100.000 4516 0 0 955 5470 254833256 254837771 0.000000e+00 8340.0
1 TraesCS5D01G163400 chr5D 100.000 576 0 0 1 576 254832302 254832877 0.000000e+00 1064.0
2 TraesCS5D01G163400 chr5D 81.673 251 31 9 1940 2178 370352714 370352467 1.550000e-45 195.0
3 TraesCS5D01G163400 chr5D 100.000 29 0 0 3207 3235 254835466 254835494 3.000000e-03 54.7
4 TraesCS5D01G163400 chr5D 100.000 29 0 0 3165 3193 254835508 254835536 3.000000e-03 54.7
5 TraesCS5D01G163400 chr5A 92.320 3620 177 56 1894 5450 338233925 338237506 0.000000e+00 5051.0
6 TraesCS5D01G163400 chr5A 94.065 556 25 4 1 555 338231859 338232407 0.000000e+00 837.0
7 TraesCS5D01G163400 chr5A 92.326 417 23 7 1482 1891 338233307 338233721 7.900000e-163 584.0
8 TraesCS5D01G163400 chr5A 85.910 511 37 16 955 1447 338232534 338233027 3.780000e-141 512.0
9 TraesCS5D01G163400 chr5A 76.744 258 36 15 1937 2178 472754141 472753892 7.440000e-24 122.0
10 TraesCS5D01G163400 chr5A 100.000 28 0 0 3205 3232 338235213 338235240 1.000000e-02 52.8
11 TraesCS5D01G163400 chr5B 85.540 1971 184 61 1896 3807 287793889 287791961 0.000000e+00 1967.0
12 TraesCS5D01G163400 chr5B 85.654 948 66 25 3809 4717 287791892 287790976 0.000000e+00 933.0
13 TraesCS5D01G163400 chr5B 93.504 585 24 6 1 576 287795008 287794429 0.000000e+00 857.0
14 TraesCS5D01G163400 chr5B 91.005 378 17 7 5081 5450 287790509 287790141 1.370000e-135 494.0
15 TraesCS5D01G163400 chr5B 89.124 331 19 6 955 1275 287794331 287794008 3.970000e-106 396.0
16 TraesCS5D01G163400 chr5B 90.583 223 11 3 4711 4933 287790932 287790720 2.490000e-73 287.0
17 TraesCS5D01G163400 chr5B 77.922 231 31 9 1625 1846 678493189 678493408 5.750000e-25 126.0
18 TraesCS5D01G163400 chr5B 81.197 117 9 5 1312 1427 287794000 287793896 1.260000e-11 82.4
19 TraesCS5D01G163400 chr5B 77.011 174 17 14 1967 2125 541089637 541089802 1.630000e-10 78.7
20 TraesCS5D01G163400 chr2D 83.882 304 42 5 1544 1841 336965936 336965634 3.230000e-72 283.0
21 TraesCS5D01G163400 chr2D 77.604 192 27 10 1598 1776 14887484 14887296 9.690000e-18 102.0
22 TraesCS5D01G163400 chr2A 82.424 330 48 7 1522 1844 447145797 447145471 4.170000e-71 279.0
23 TraesCS5D01G163400 chr2A 90.698 43 2 2 2329 2369 707313232 707313190 7.650000e-04 56.5
24 TraesCS5D01G163400 chr6B 81.180 356 45 16 1466 1806 175714993 175715341 3.250000e-67 267.0
25 TraesCS5D01G163400 chr6B 84.564 149 11 6 1937 2075 682670817 682670963 2.660000e-28 137.0
26 TraesCS5D01G163400 chr7D 80.429 373 48 12 1532 1883 396136492 396136860 1.510000e-65 261.0
27 TraesCS5D01G163400 chr4D 78.093 388 56 22 1523 1901 10100630 10100997 9.230000e-53 219.0
28 TraesCS5D01G163400 chr4D 89.091 55 6 0 1842 1896 58135324 58135270 9.830000e-08 69.4
29 TraesCS5D01G163400 chr4D 100.000 28 0 0 2335 2362 482401697 482401670 1.000000e-02 52.8
30 TraesCS5D01G163400 chr3A 81.679 262 28 11 1935 2178 121652378 121652119 3.340000e-47 200.0
31 TraesCS5D01G163400 chr3A 80.000 170 21 9 2202 2368 121652195 121652036 4.480000e-21 113.0
32 TraesCS5D01G163400 chr3B 80.287 279 38 11 1625 1891 63115026 63115299 1.550000e-45 195.0
33 TraesCS5D01G163400 chr3B 77.778 288 41 18 1532 1801 652733936 652734218 7.340000e-34 156.0
34 TraesCS5D01G163400 chr6D 81.304 230 25 11 1935 2153 112914713 112914491 2.620000e-38 171.0
35 TraesCS5D01G163400 chr6A 81.944 216 25 7 1972 2177 140569030 140568819 2.620000e-38 171.0
36 TraesCS5D01G163400 chr3D 78.889 270 39 11 1616 1870 41693839 41694105 3.390000e-37 167.0
37 TraesCS5D01G163400 chr3D 85.897 156 12 9 1529 1679 490833593 490833743 2.040000e-34 158.0
38 TraesCS5D01G163400 chr3D 78.824 255 37 7 1937 2175 438542094 438541841 7.340000e-34 156.0
39 TraesCS5D01G163400 chr4B 79.026 267 35 9 1541 1789 644867347 644867610 4.380000e-36 163.0
40 TraesCS5D01G163400 chr4A 80.193 207 27 9 1616 1809 673212582 673212377 5.710000e-30 143.0
41 TraesCS5D01G163400 chrUn 79.808 208 28 9 1616 1810 323660977 323660771 7.390000e-29 139.0
42 TraesCS5D01G163400 chrUn 79.808 208 28 9 1616 1810 332112587 332112381 7.390000e-29 139.0
43 TraesCS5D01G163400 chr2B 82.468 154 12 11 1935 2078 109076506 109076654 2.680000e-23 121.0
44 TraesCS5D01G163400 chr2B 82.237 152 12 11 1935 2076 109161418 109161564 3.460000e-22 117.0
45 TraesCS5D01G163400 chr2B 94.118 34 2 0 2335 2368 680580911 680580878 1.000000e-02 52.8
46 TraesCS5D01G163400 chr7B 78.621 145 23 6 2041 2177 184497028 184496884 7.550000e-14 89.8


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 TraesCS5D01G163400 chr5D 254832302 254837771 5469 False 2378.350000 8340 100.000000 1 5470 4 chr5D.!!$F1 5469
1 TraesCS5D01G163400 chr5A 338231859 338237506 5647 False 1407.360000 5051 92.924200 1 5450 5 chr5A.!!$F1 5449
2 TraesCS5D01G163400 chr5B 287790141 287795008 4867 True 716.628571 1967 88.086714 1 5450 7 chr5B.!!$R1 5449

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
516 524 1.835531 GGGAAGGGATAACTTGACCGA 59.164 52.381 0.0 0.0 0.0 4.69 F
1107 1133 0.179225 CGCCGAACCGAAACTTGATG 60.179 55.000 0.0 0.0 0.0 3.07 F
1485 1779 0.685660 ACGTTTTCCTCACCTCCTCC 59.314 55.000 0.0 0.0 0.0 4.30 F
1486 1780 0.977395 CGTTTTCCTCACCTCCTCCT 59.023 55.000 0.0 0.0 0.0 3.69 F
3163 3722 1.228245 TGGTTGGGAGAAGTGCAGC 60.228 57.895 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2040 0.393808 GCACGGGGAGGCAAGATTTA 60.394 55.0 0.00 0.0 0.00 1.40 R
2907 3455 0.179020 CAGACAAGGCCACAAGTCCA 60.179 55.0 5.01 0.0 0.00 4.02 R
3142 3691 0.257328 TGCACTTCTCCCAACCACAA 59.743 50.0 0.00 0.0 0.00 3.33 R
3476 4038 0.674534 GCTGGAATCGTCCCTATCGT 59.325 55.0 0.00 0.0 44.23 3.73 R
4934 5655 0.390124 CCCGGGCGTAAGTGCTATAA 59.610 55.0 8.08 0.0 41.68 0.98 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
48 49 2.285818 TTCACCATACCGGGGGCT 60.286 61.111 6.32 0.00 39.52 5.19
313 314 3.063197 GCGGAGGAGGGAGAGGAGA 62.063 68.421 0.00 0.00 0.00 3.71
369 373 2.533266 TTGGCACACAAGAGAGAGAC 57.467 50.000 0.00 0.00 39.29 3.36
477 485 5.625721 CGTATGTATCGTGTCATCTTCTTCC 59.374 44.000 0.00 0.00 0.00 3.46
515 523 1.838077 AGGGAAGGGATAACTTGACCG 59.162 52.381 0.00 0.00 32.36 4.79
516 524 1.835531 GGGAAGGGATAACTTGACCGA 59.164 52.381 0.00 0.00 0.00 4.69
1072 1090 1.371558 GGCAGGATCCCCGTATGTC 59.628 63.158 8.55 0.00 37.58 3.06
1082 1108 3.315596 TCCCCGTATGTCTCTCTCTCTA 58.684 50.000 0.00 0.00 0.00 2.43
1107 1133 0.179225 CGCCGAACCGAAACTTGATG 60.179 55.000 0.00 0.00 0.00 3.07
1126 1160 4.885907 TGATGTACTACCTGCTACAGTACC 59.114 45.833 8.25 0.00 42.52 3.34
1135 1169 4.969359 ACCTGCTACAGTACCAATTAGGAT 59.031 41.667 0.00 0.00 41.22 3.24
1136 1170 5.428783 ACCTGCTACAGTACCAATTAGGATT 59.571 40.000 0.00 0.00 41.22 3.01
1137 1171 6.614087 ACCTGCTACAGTACCAATTAGGATTA 59.386 38.462 0.00 0.00 41.22 1.75
1138 1172 7.155328 CCTGCTACAGTACCAATTAGGATTAG 58.845 42.308 0.00 0.00 41.22 1.73
1139 1173 7.062749 TGCTACAGTACCAATTAGGATTAGG 57.937 40.000 0.00 0.00 41.22 2.69
1172 1210 1.203262 AGGCCCGGGCATACTAGATTA 60.203 52.381 44.46 0.00 44.11 1.75
1230 1269 4.150897 TGAACTGTACTTTGTTGCCTCT 57.849 40.909 0.00 0.00 0.00 3.69
1232 1271 4.947388 TGAACTGTACTTTGTTGCCTCTTT 59.053 37.500 0.00 0.00 0.00 2.52
1235 1274 6.619801 ACTGTACTTTGTTGCCTCTTTTAG 57.380 37.500 0.00 0.00 0.00 1.85
1253 1292 1.853963 AGATAGTGTGGTTCGGCTCT 58.146 50.000 0.00 0.00 0.00 4.09
1261 1302 2.693591 TGTGGTTCGGCTCTAGATAAGG 59.306 50.000 0.00 0.00 0.00 2.69
1264 1305 3.773119 TGGTTCGGCTCTAGATAAGGTTT 59.227 43.478 0.00 0.00 0.00 3.27
1265 1306 4.120589 GGTTCGGCTCTAGATAAGGTTTG 58.879 47.826 0.00 0.00 0.00 2.93
1266 1307 4.142004 GGTTCGGCTCTAGATAAGGTTTGA 60.142 45.833 0.00 0.00 0.00 2.69
1267 1308 4.650754 TCGGCTCTAGATAAGGTTTGAC 57.349 45.455 0.00 0.00 0.00 3.18
1270 1311 3.492829 GGCTCTAGATAAGGTTTGACGGG 60.493 52.174 0.00 0.00 0.00 5.28
1271 1312 3.132467 GCTCTAGATAAGGTTTGACGGGT 59.868 47.826 0.00 0.00 0.00 5.28
1272 1313 4.683832 CTCTAGATAAGGTTTGACGGGTG 58.316 47.826 0.00 0.00 0.00 4.61
1273 1314 4.346730 TCTAGATAAGGTTTGACGGGTGA 58.653 43.478 0.00 0.00 0.00 4.02
1275 1316 3.170717 AGATAAGGTTTGACGGGTGAGA 58.829 45.455 0.00 0.00 0.00 3.27
1276 1317 3.581332 AGATAAGGTTTGACGGGTGAGAA 59.419 43.478 0.00 0.00 0.00 2.87
1359 1404 1.753903 TTCAATGGGGGTCAGGAAGA 58.246 50.000 0.00 0.00 0.00 2.87
1366 1411 1.177401 GGGGTCAGGAAGATTGTTGC 58.823 55.000 0.00 0.00 0.00 4.17
1372 1417 1.201647 CAGGAAGATTGTTGCAGCCTG 59.798 52.381 0.00 0.00 35.93 4.85
1457 1502 9.869757 ATAAAATAAAGTAAAACCATGTCCTGC 57.130 29.630 0.00 0.00 0.00 4.85
1461 1506 6.909550 AAAGTAAAACCATGTCCTGCATTA 57.090 33.333 0.00 0.00 35.19 1.90
1462 1507 6.909550 AAGTAAAACCATGTCCTGCATTAA 57.090 33.333 0.00 0.00 35.19 1.40
1463 1508 6.267496 AGTAAAACCATGTCCTGCATTAAC 57.733 37.500 0.00 0.00 35.19 2.01
1464 1509 4.535526 AAAACCATGTCCTGCATTAACC 57.464 40.909 0.00 0.00 35.19 2.85
1468 1513 2.872245 CCATGTCCTGCATTAACCTACG 59.128 50.000 0.00 0.00 35.19 3.51
1471 1765 4.010667 TGTCCTGCATTAACCTACGTTT 57.989 40.909 0.00 0.00 33.17 3.60
1484 1778 2.094130 CCTACGTTTTCCTCACCTCCTC 60.094 54.545 0.00 0.00 0.00 3.71
1485 1779 0.685660 ACGTTTTCCTCACCTCCTCC 59.314 55.000 0.00 0.00 0.00 4.30
1486 1780 0.977395 CGTTTTCCTCACCTCCTCCT 59.023 55.000 0.00 0.00 0.00 3.69
1495 1789 1.657162 TCACCTCCTCCTTTCCCCTAT 59.343 52.381 0.00 0.00 0.00 2.57
1502 1796 2.785857 CCTCCTTTCCCCTATGTTGGAT 59.214 50.000 0.00 0.00 0.00 3.41
1540 1834 2.043801 CCCCCTCCTTGGTTTGGAATAA 59.956 50.000 0.00 0.00 32.61 1.40
1570 1864 9.586435 AAATCAAAACAGTACTTTCCTTTCTTG 57.414 29.630 0.00 0.00 0.00 3.02
1571 1865 7.696992 TCAAAACAGTACTTTCCTTTCTTGT 57.303 32.000 0.00 0.00 0.00 3.16
1572 1866 7.758495 TCAAAACAGTACTTTCCTTTCTTGTC 58.242 34.615 0.00 0.00 0.00 3.18
1573 1867 7.610305 TCAAAACAGTACTTTCCTTTCTTGTCT 59.390 33.333 0.00 0.00 0.00 3.41
1578 1873 7.711339 ACAGTACTTTCCTTTCTTGTCTTACTG 59.289 37.037 0.00 0.00 38.96 2.74
1614 1909 7.394077 TCCTGCATTAACTCAATCAAATCTTGA 59.606 33.333 0.00 0.00 45.01 3.02
1684 1979 8.942338 AAACCTCAACTAAATCAAAACTTTCC 57.058 30.769 0.00 0.00 0.00 3.13
1708 2009 6.429385 CCTTGCCTTCTCTTATCCATATCAAC 59.571 42.308 0.00 0.00 0.00 3.18
1710 2011 6.763355 TGCCTTCTCTTATCCATATCAACTC 58.237 40.000 0.00 0.00 0.00 3.01
1723 2024 7.466804 TCCATATCAACTCTTACCAAAACCTT 58.533 34.615 0.00 0.00 0.00 3.50
1757 2058 2.348411 ATAAATCTTGCCTCCCCGTG 57.652 50.000 0.00 0.00 0.00 4.94
1772 2073 2.355197 CCCGTGCACATACTCAAATCA 58.645 47.619 18.64 0.00 0.00 2.57
1862 2163 7.534852 TGAACCATTAGAATATTTATGCCCCT 58.465 34.615 0.00 0.00 0.00 4.79
1884 2185 1.610363 TGCAACTCACGGGCAATTAA 58.390 45.000 0.00 0.00 34.05 1.40
1885 2186 2.166829 TGCAACTCACGGGCAATTAAT 58.833 42.857 0.00 0.00 34.05 1.40
1891 2192 6.238648 GCAACTCACGGGCAATTAATTAGTAT 60.239 38.462 0.00 0.00 0.00 2.12
1892 2193 6.861065 ACTCACGGGCAATTAATTAGTATG 57.139 37.500 0.00 0.00 0.00 2.39
1894 2195 7.224297 ACTCACGGGCAATTAATTAGTATGAT 58.776 34.615 0.00 0.00 0.00 2.45
1947 2450 6.936279 TCCATGATAGTACTAGCTAATTGCC 58.064 40.000 18.38 0.00 44.23 4.52
1956 2459 2.107950 AGCTAATTGCCTGTGCGTTA 57.892 45.000 0.00 0.00 44.23 3.18
1982 2485 6.710597 ACGGTGACATACATATTCTAGTGT 57.289 37.500 0.00 0.00 0.00 3.55
1985 2488 7.491372 ACGGTGACATACATATTCTAGTGTTTG 59.509 37.037 0.00 0.00 34.71 2.93
2081 2594 5.435291 TGCAAAAGATTTGATTTGGTTGGT 58.565 33.333 6.99 0.00 37.09 3.67
2088 2601 2.631160 TGATTTGGTTGGTCGTGTCT 57.369 45.000 0.00 0.00 0.00 3.41
2183 2708 9.287373 ACAAAATATTTGATTTGATTGCCTGTT 57.713 25.926 9.62 0.00 38.50 3.16
2187 2712 4.952071 TTGATTTGATTGCCTGTTTCCA 57.048 36.364 0.00 0.00 0.00 3.53
2218 2743 6.408869 AGCTGGATTGATTTTATTTGGTTGG 58.591 36.000 0.00 0.00 0.00 3.77
2600 3146 5.016173 ACACATATTAAGGTGGTGTGCATT 58.984 37.500 3.93 0.00 41.69 3.56
2638 3184 2.047061 GGGTGATCCTACATGTGCCTA 58.953 52.381 9.11 0.00 0.00 3.93
2722 3269 5.332743 TCAAACTAAATCATCCCAAAGGCT 58.667 37.500 0.00 0.00 0.00 4.58
2788 3336 2.993899 CACCGAGCTACGAAGTCAAATT 59.006 45.455 7.07 0.00 43.93 1.82
2907 3455 3.492829 GGACAGGAGAACTCGTTTCTGTT 60.493 47.826 6.75 0.00 45.24 3.16
2913 3462 4.120589 GAGAACTCGTTTCTGTTGGACTT 58.879 43.478 6.75 0.00 45.24 3.01
3163 3722 1.228245 TGGTTGGGAGAAGTGCAGC 60.228 57.895 0.00 0.00 0.00 5.25
3207 3766 5.120830 CACTTCAGTAAAGATACCACTGTGC 59.879 44.000 1.29 0.00 40.44 4.57
3296 3857 1.889105 CAGTGTGCTTGTGCGAGGT 60.889 57.895 0.00 0.00 43.34 3.85
3325 3886 2.078392 GTCGGCCGAAATTTCTGGTAA 58.922 47.619 32.93 0.00 0.00 2.85
3328 3889 2.443416 GGCCGAAATTTCTGGTAACCT 58.557 47.619 21.84 0.00 0.00 3.50
3475 4037 4.325030 GGAGGATTTGAACCCATGACCTAA 60.325 45.833 0.00 0.00 0.00 2.69
3476 4038 5.261216 GAGGATTTGAACCCATGACCTAAA 58.739 41.667 0.00 0.00 0.00 1.85
3530 4092 1.134699 TCCTCTACTTCGCCTGCAATG 60.135 52.381 0.00 0.00 0.00 2.82
3547 4109 5.433526 TGCAATGTAGGGTAGAAATGTACC 58.566 41.667 0.00 0.00 41.75 3.34
3639 4203 1.397390 CCGTCGGTAACCAGGCCTAT 61.397 60.000 3.98 0.00 0.00 2.57
3742 4306 5.734786 GCTGTCAGAAGAGACTATATGCGTT 60.735 44.000 3.32 0.00 39.27 4.84
3764 4329 1.401905 GGAATTTGATGCCAGGACGTC 59.598 52.381 7.13 7.13 0.00 4.34
3786 4352 6.018262 CGTCTTCTTTGTTGGTTGTCAAGATA 60.018 38.462 0.00 0.00 35.80 1.98
3819 4452 8.301252 TGCTTGGTGACATACTAAATAGACTA 57.699 34.615 0.00 0.00 42.32 2.59
3919 4553 7.391620 AGATTTACTCAAACTGACGGGATTTA 58.608 34.615 0.00 0.00 0.00 1.40
3971 4607 3.318839 TGCATTTCCCTCTGTTGTTTCTG 59.681 43.478 0.00 0.00 0.00 3.02
3979 4615 5.997746 TCCCTCTGTTGTTTCTGTTAATCAG 59.002 40.000 0.00 0.00 44.85 2.90
4061 4697 5.659463 CAGGTGATTGTTGAAAGGTTTTCA 58.341 37.500 0.36 0.36 0.00 2.69
4070 4706 7.654022 TGTTGAAAGGTTTTCAAGGAGTAAT 57.346 32.000 15.12 0.00 38.88 1.89
4191 4827 1.282157 GATTGCAGGTACCTGGTTCCT 59.718 52.381 36.91 18.34 43.77 3.36
4279 4915 1.830338 CTTTTCGTGTTTGTGCGCG 59.170 52.632 0.00 0.00 42.91 6.86
4347 4992 7.890515 TGCACATAAATCCATCTGTTTGTAAA 58.109 30.769 0.00 0.00 0.00 2.01
4489 5134 2.490903 GACATCTGCCTGACTGCAATTT 59.509 45.455 0.00 0.00 41.51 1.82
4490 5135 2.230508 ACATCTGCCTGACTGCAATTTG 59.769 45.455 0.00 0.00 41.51 2.32
4530 5193 5.188751 TCCCAGTGTACATATGTGACATCAA 59.811 40.000 18.81 0.00 0.00 2.57
4615 5286 1.138859 CACATCTGTATTGCTCCCGGA 59.861 52.381 0.73 0.00 0.00 5.14
4662 5333 8.246908 TGTTGTATCACCGAAGTAAACTTATG 57.753 34.615 0.00 0.00 36.11 1.90
4663 5334 6.897259 TGTATCACCGAAGTAAACTTATGC 57.103 37.500 0.00 0.00 36.11 3.14
4754 5475 2.805671 TGTGATGACAAGTAAACGCCTG 59.194 45.455 0.00 0.00 0.00 4.85
4776 5497 2.417933 CTGCTGAGCTGTTGACATTACC 59.582 50.000 5.83 0.00 0.00 2.85
4787 5508 4.826733 TGTTGACATTACCAAGCTCATGTT 59.173 37.500 0.00 0.00 29.81 2.71
4854 5575 1.092921 GTTTGCACGGTGTCCACTCA 61.093 55.000 10.24 0.00 0.00 3.41
4886 5607 1.607148 GTTTGCTTGGAGTAGCGGTTT 59.393 47.619 0.00 0.00 44.18 3.27
4887 5608 2.809696 GTTTGCTTGGAGTAGCGGTTTA 59.190 45.455 0.00 0.00 44.18 2.01
4888 5609 2.380084 TGCTTGGAGTAGCGGTTTAG 57.620 50.000 0.00 0.00 44.18 1.85
4889 5610 1.621814 TGCTTGGAGTAGCGGTTTAGT 59.378 47.619 0.00 0.00 44.18 2.24
4890 5611 2.827322 TGCTTGGAGTAGCGGTTTAGTA 59.173 45.455 0.00 0.00 44.18 1.82
4891 5612 3.119245 TGCTTGGAGTAGCGGTTTAGTAG 60.119 47.826 0.00 0.00 44.18 2.57
4933 5654 2.139917 GACCGTGCACATGTCTACAAA 58.860 47.619 22.65 0.00 0.00 2.83
4934 5655 2.742053 GACCGTGCACATGTCTACAAAT 59.258 45.455 22.65 0.00 0.00 2.32
4935 5656 3.146066 ACCGTGCACATGTCTACAAATT 58.854 40.909 18.64 0.00 0.00 1.82
4936 5657 4.320023 ACCGTGCACATGTCTACAAATTA 58.680 39.130 18.64 0.00 0.00 1.40
4937 5658 4.941263 ACCGTGCACATGTCTACAAATTAT 59.059 37.500 18.64 0.00 0.00 1.28
4938 5659 6.110033 ACCGTGCACATGTCTACAAATTATA 58.890 36.000 18.64 0.00 0.00 0.98
4939 5660 6.257849 ACCGTGCACATGTCTACAAATTATAG 59.742 38.462 18.64 0.00 0.00 1.31
4941 5662 6.238076 CGTGCACATGTCTACAAATTATAGCA 60.238 38.462 18.64 0.00 0.00 3.49
4942 5663 6.907212 GTGCACATGTCTACAAATTATAGCAC 59.093 38.462 13.17 11.64 39.16 4.40
4943 5664 6.823182 TGCACATGTCTACAAATTATAGCACT 59.177 34.615 0.00 0.00 0.00 4.40
4944 5665 7.336679 TGCACATGTCTACAAATTATAGCACTT 59.663 33.333 0.00 0.00 0.00 3.16
4945 5666 8.826710 GCACATGTCTACAAATTATAGCACTTA 58.173 33.333 0.00 0.00 0.00 2.24
4948 5669 7.459394 TGTCTACAAATTATAGCACTTACGC 57.541 36.000 0.00 0.00 0.00 4.42
4949 5670 6.477688 TGTCTACAAATTATAGCACTTACGCC 59.522 38.462 0.00 0.00 0.00 5.68
4950 5671 5.987347 TCTACAAATTATAGCACTTACGCCC 59.013 40.000 0.00 0.00 0.00 6.13
5016 5773 5.184864 TGAAACTGAACTTCAAATGTGGTGT 59.815 36.000 0.00 0.00 29.93 4.16
5059 5818 1.450025 CGGAGTTGGTTAGCCCTTTC 58.550 55.000 0.00 0.00 0.00 2.62
5079 5838 3.659786 TCGATGTCTGATTTTGTCGGTT 58.340 40.909 0.00 0.00 34.65 4.44
5102 5889 4.010349 GGGGACACTGGATTTACAAAGAG 58.990 47.826 0.00 0.00 0.00 2.85
5132 5919 4.975502 TGAGCTGCAAAACGTTTTATCTTG 59.024 37.500 24.79 14.66 0.00 3.02
5134 5921 6.067263 AGCTGCAAAACGTTTTATCTTGTA 57.933 33.333 24.79 12.27 0.00 2.41
5135 5922 6.500041 AGCTGCAAAACGTTTTATCTTGTAA 58.500 32.000 24.79 6.50 0.00 2.41
5261 6049 1.000163 GAAGCTGACCTGACGTTCTCA 60.000 52.381 0.00 0.00 0.00 3.27
5317 6105 1.417517 TGCAGGCATACTAGGATGTGG 59.582 52.381 16.49 7.42 0.00 4.17
5333 6121 4.263331 GGATGTGGTGGAGTTTCCTTTCTA 60.263 45.833 0.00 0.00 37.46 2.10
5352 6140 7.360438 CCTTTCTATTCTTTTTGAGACACGGAG 60.360 40.741 0.00 0.00 33.02 4.63
5355 6143 4.665833 TTCTTTTTGAGACACGGAGAGA 57.334 40.909 0.00 0.00 33.02 3.10
5379 6167 1.609061 GGGAGTCGGATGCCATGTATG 60.609 57.143 0.00 0.00 0.00 2.39
5422 6217 1.538512 TGTCACCGAGAAGTTAGGACG 59.461 52.381 0.00 0.00 0.00 4.79
5426 6221 2.683867 CACCGAGAAGTTAGGACGAGAT 59.316 50.000 0.00 0.00 0.00 2.75
5434 6229 6.320944 AGAAGTTAGGACGAGATAACGAAAC 58.679 40.000 0.00 0.00 37.06 2.78
5437 6232 2.086869 AGGACGAGATAACGAAACCGA 58.913 47.619 0.00 0.00 37.03 4.69
5450 6245 0.541863 AAACCGATGCACTAGGAGGG 59.458 55.000 10.47 0.00 0.00 4.30
5451 6246 0.325296 AACCGATGCACTAGGAGGGA 60.325 55.000 10.47 0.00 0.00 4.20
5452 6247 0.757188 ACCGATGCACTAGGAGGGAG 60.757 60.000 10.47 0.00 0.00 4.30
5453 6248 1.467678 CCGATGCACTAGGAGGGAGG 61.468 65.000 0.00 0.00 0.00 4.30
5454 6249 1.751563 GATGCACTAGGAGGGAGGC 59.248 63.158 0.00 0.00 0.00 4.70
5455 6250 1.003442 ATGCACTAGGAGGGAGGCA 59.997 57.895 0.00 0.00 35.54 4.75
5456 6251 1.341156 ATGCACTAGGAGGGAGGCAC 61.341 60.000 0.00 0.00 33.67 5.01
5457 6252 3.082579 GCACTAGGAGGGAGGCACG 62.083 68.421 0.00 0.00 0.00 5.34
5458 6253 2.760385 ACTAGGAGGGAGGCACGC 60.760 66.667 0.00 0.00 0.00 5.34
5459 6254 3.905678 CTAGGAGGGAGGCACGCG 61.906 72.222 3.53 3.53 36.53 6.01
5460 6255 4.435970 TAGGAGGGAGGCACGCGA 62.436 66.667 15.93 0.00 36.53 5.87
5461 6256 3.733507 TAGGAGGGAGGCACGCGAT 62.734 63.158 15.93 0.00 36.53 4.58
5462 6257 4.899239 GGAGGGAGGCACGCGATG 62.899 72.222 15.93 8.90 36.53 3.84
5463 6258 4.899239 GAGGGAGGCACGCGATGG 62.899 72.222 15.93 2.40 36.53 3.51
5465 6260 4.241555 GGGAGGCACGCGATGGAT 62.242 66.667 15.93 0.00 0.00 3.41
5466 6261 2.969238 GGAGGCACGCGATGGATG 60.969 66.667 15.93 0.00 0.00 3.51
5467 6262 2.969238 GAGGCACGCGATGGATGG 60.969 66.667 15.93 0.00 0.00 3.51
5468 6263 3.445518 GAGGCACGCGATGGATGGA 62.446 63.158 15.93 0.00 0.00 3.41
5469 6264 2.281070 GGCACGCGATGGATGGAT 60.281 61.111 15.93 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.499563 CCCTACCACCAATTCAACTTCCA 60.500 47.826 0.00 0.00 0.00 3.53
197 198 3.648067 ACCTCATCTCCAAGAACAAGTCA 59.352 43.478 0.00 0.00 0.00 3.41
299 300 0.553862 TCCACTCTCCTCTCCCTCCT 60.554 60.000 0.00 0.00 0.00 3.69
305 306 1.091537 CACGACTCCACTCTCCTCTC 58.908 60.000 0.00 0.00 0.00 3.20
306 307 0.322997 CCACGACTCCACTCTCCTCT 60.323 60.000 0.00 0.00 0.00 3.69
307 308 1.316706 CCCACGACTCCACTCTCCTC 61.317 65.000 0.00 0.00 0.00 3.71
313 314 2.283966 CCTCCCCACGACTCCACT 60.284 66.667 0.00 0.00 0.00 4.00
369 373 1.002544 AGACCGGGCTTCTTCTTCTTG 59.997 52.381 2.12 0.00 0.00 3.02
406 410 0.940833 GCCGACGGGTAGTAGTAGAC 59.059 60.000 17.22 0.00 34.97 2.59
515 523 3.189287 AGATTGTTGTCAATGGCGAAGTC 59.811 43.478 0.00 0.00 43.33 3.01
516 524 3.149196 AGATTGTTGTCAATGGCGAAGT 58.851 40.909 0.00 0.00 43.33 3.01
1072 1090 2.028839 TCGGCGAGGTATAGAGAGAGAG 60.029 54.545 4.99 0.00 0.00 3.20
1082 1108 0.459063 GTTTCGGTTCGGCGAGGTAT 60.459 55.000 10.46 0.00 0.00 2.73
1107 1133 5.848833 ATTGGTACTGTAGCAGGTAGTAC 57.151 43.478 17.89 0.00 43.66 2.73
1172 1210 2.154462 CAATCAAAGAGGTCGGTTGCT 58.846 47.619 0.00 0.00 0.00 3.91
1230 1269 4.222145 AGAGCCGAACCACACTATCTAAAA 59.778 41.667 0.00 0.00 0.00 1.52
1232 1271 3.362706 AGAGCCGAACCACACTATCTAA 58.637 45.455 0.00 0.00 0.00 2.10
1235 1274 2.950309 TCTAGAGCCGAACCACACTATC 59.050 50.000 0.00 0.00 0.00 2.08
1253 1292 4.346730 TCTCACCCGTCAAACCTTATCTA 58.653 43.478 0.00 0.00 0.00 1.98
1303 1344 7.700656 GCTGAAAAACTTGACAAGTAAAAGCTA 59.299 33.333 20.85 4.75 41.91 3.32
1304 1345 6.531594 GCTGAAAAACTTGACAAGTAAAAGCT 59.468 34.615 20.85 1.67 41.91 3.74
1305 1346 6.531594 AGCTGAAAAACTTGACAAGTAAAAGC 59.468 34.615 20.85 21.38 41.91 3.51
1306 1347 7.542130 ACAGCTGAAAAACTTGACAAGTAAAAG 59.458 33.333 23.35 14.28 41.91 2.27
1309 1350 6.321717 CACAGCTGAAAAACTTGACAAGTAA 58.678 36.000 23.35 4.70 41.91 2.24
1359 1404 0.958091 TTTACGCAGGCTGCAACAAT 59.042 45.000 35.94 18.86 45.36 2.71
1381 1426 5.432885 TCAACTTAAGCACTTAACCTTGC 57.567 39.130 1.29 0.00 39.16 4.01
1399 1444 4.086457 ACACCCTGGTTATGGATTTCAAC 58.914 43.478 0.00 0.00 0.00 3.18
1441 1486 5.185056 AGGTTAATGCAGGACATGGTTTTAC 59.815 40.000 0.00 0.00 39.60 2.01
1442 1487 5.329399 AGGTTAATGCAGGACATGGTTTTA 58.671 37.500 0.00 0.00 39.60 1.52
1447 1492 2.872245 CGTAGGTTAATGCAGGACATGG 59.128 50.000 0.00 0.00 39.60 3.66
1448 1493 3.531538 ACGTAGGTTAATGCAGGACATG 58.468 45.455 0.00 0.00 39.60 3.21
1449 1494 3.906720 ACGTAGGTTAATGCAGGACAT 57.093 42.857 0.00 0.00 42.30 3.06
1450 1495 3.688694 AACGTAGGTTAATGCAGGACA 57.311 42.857 0.00 0.00 33.72 4.02
1451 1496 4.142752 GGAAAACGTAGGTTAATGCAGGAC 60.143 45.833 0.43 0.00 34.62 3.85
1452 1497 4.004982 GGAAAACGTAGGTTAATGCAGGA 58.995 43.478 0.43 0.00 34.62 3.86
1454 1499 4.693566 TGAGGAAAACGTAGGTTAATGCAG 59.306 41.667 0.43 0.00 34.62 4.41
1455 1500 4.453136 GTGAGGAAAACGTAGGTTAATGCA 59.547 41.667 0.43 0.00 34.62 3.96
1456 1501 4.142752 GGTGAGGAAAACGTAGGTTAATGC 60.143 45.833 0.43 0.00 34.62 3.56
1457 1502 5.243207 AGGTGAGGAAAACGTAGGTTAATG 58.757 41.667 0.43 0.00 34.62 1.90
1461 1506 2.038164 GGAGGTGAGGAAAACGTAGGTT 59.962 50.000 0.00 0.00 38.22 3.50
1462 1507 1.622312 GGAGGTGAGGAAAACGTAGGT 59.378 52.381 0.00 0.00 0.00 3.08
1463 1508 1.900486 AGGAGGTGAGGAAAACGTAGG 59.100 52.381 0.00 0.00 0.00 3.18
1464 1509 2.094130 GGAGGAGGTGAGGAAAACGTAG 60.094 54.545 0.00 0.00 0.00 3.51
1468 1513 3.413327 GAAAGGAGGAGGTGAGGAAAAC 58.587 50.000 0.00 0.00 0.00 2.43
1471 1765 1.657804 GGAAAGGAGGAGGTGAGGAA 58.342 55.000 0.00 0.00 0.00 3.36
1567 1861 5.765182 AGGACATGGTTTTCAGTAAGACAAG 59.235 40.000 0.00 0.00 0.00 3.16
1568 1862 5.530915 CAGGACATGGTTTTCAGTAAGACAA 59.469 40.000 0.00 0.00 0.00 3.18
1570 1864 4.083271 GCAGGACATGGTTTTCAGTAAGAC 60.083 45.833 0.00 0.00 0.00 3.01
1571 1865 4.072131 GCAGGACATGGTTTTCAGTAAGA 58.928 43.478 0.00 0.00 0.00 2.10
1572 1866 3.820467 TGCAGGACATGGTTTTCAGTAAG 59.180 43.478 0.00 0.00 0.00 2.34
1573 1867 3.826524 TGCAGGACATGGTTTTCAGTAA 58.173 40.909 0.00 0.00 0.00 2.24
1578 1873 5.048083 TGAGTTAATGCAGGACATGGTTTTC 60.048 40.000 0.00 0.00 39.60 2.29
1614 1909 4.588528 AGTTAATGCAGGACATGGTTTTGT 59.411 37.500 0.00 0.00 39.60 2.83
1620 1915 4.641541 TGATTGAGTTAATGCAGGACATGG 59.358 41.667 0.00 0.00 39.60 3.66
1674 1969 4.926140 AGAGAAGGCAAGGAAAGTTTTG 57.074 40.909 0.00 0.00 0.00 2.44
1676 1971 5.712446 GGATAAGAGAAGGCAAGGAAAGTTT 59.288 40.000 0.00 0.00 0.00 2.66
1684 1979 7.222872 AGTTGATATGGATAAGAGAAGGCAAG 58.777 38.462 0.00 0.00 0.00 4.01
1732 2033 5.897250 ACGGGGAGGCAAGATTTATTTATTT 59.103 36.000 0.00 0.00 0.00 1.40
1735 2036 4.204012 CACGGGGAGGCAAGATTTATTTA 58.796 43.478 0.00 0.00 0.00 1.40
1738 2039 1.750682 GCACGGGGAGGCAAGATTTAT 60.751 52.381 0.00 0.00 0.00 1.40
1739 2040 0.393808 GCACGGGGAGGCAAGATTTA 60.394 55.000 0.00 0.00 0.00 1.40
1793 2094 9.342308 CACATACTTTACATCCACCATATTCTT 57.658 33.333 0.00 0.00 0.00 2.52
1812 2113 4.631377 CACAAATCATGTCCGACACATACT 59.369 41.667 2.57 0.00 44.60 2.12
1858 2159 2.260869 CCGTGAGTTGCAACAGGGG 61.261 63.158 30.11 20.37 38.08 4.79
1862 2163 1.106351 ATTGCCCGTGAGTTGCAACA 61.106 50.000 30.11 9.08 45.46 3.33
1891 2192 7.177216 AGTTCTCAAATTTGGTGCTTCATATCA 59.823 33.333 17.90 0.00 0.00 2.15
1892 2193 7.487189 CAGTTCTCAAATTTGGTGCTTCATATC 59.513 37.037 17.90 0.00 0.00 1.63
1894 2195 6.680810 CAGTTCTCAAATTTGGTGCTTCATA 58.319 36.000 17.90 0.00 0.00 2.15
1956 2459 6.978659 CACTAGAATATGTATGTCACCGTTGT 59.021 38.462 0.00 0.00 0.00 3.32
1995 2498 4.098349 GGTGTAAGGTATATGTCGGACACA 59.902 45.833 13.92 1.15 38.11 3.72
2081 2594 5.126384 TGTTCCATGTATATGTCAGACACGA 59.874 40.000 5.05 0.00 29.41 4.35
2116 2629 7.248437 GGTGTAAGGTAATTGCATAACTCAAC 58.752 38.462 0.00 0.00 35.84 3.18
2152 2666 8.594687 GCAATCAAATCAAATATTTTGTAGCGT 58.405 29.630 0.00 0.00 35.01 5.07
2153 2667 8.057742 GGCAATCAAATCAAATATTTTGTAGCG 58.942 33.333 0.00 0.00 35.01 4.26
2154 2668 9.101655 AGGCAATCAAATCAAATATTTTGTAGC 57.898 29.630 0.00 1.75 35.01 3.58
2156 2670 9.941325 ACAGGCAATCAAATCAAATATTTTGTA 57.059 25.926 0.00 0.00 35.01 2.41
2157 2671 8.851541 ACAGGCAATCAAATCAAATATTTTGT 57.148 26.923 0.00 0.00 35.01 2.83
2163 2677 7.002250 TGGAAACAGGCAATCAAATCAAATA 57.998 32.000 0.00 0.00 35.01 1.40
2218 2743 5.419471 TGGGTGTAAGGTAATTGCATTAACC 59.581 40.000 16.28 16.28 35.84 2.85
2297 2824 1.274703 TGAAGCATCCCCTCTCCCAC 61.275 60.000 0.00 0.00 0.00 4.61
2600 3146 1.211212 CCCCAGACTCTGCATCAATCA 59.789 52.381 0.00 0.00 0.00 2.57
2638 3184 8.239314 CACAATCACTACAACTTAGAAATGCAT 58.761 33.333 0.00 0.00 0.00 3.96
2703 3250 6.183360 GCATTTAGCCTTTGGGATGATTTAGT 60.183 38.462 0.00 0.00 37.23 2.24
2722 3269 7.002250 TCTGAATTGTGGAATTTGGCATTTA 57.998 32.000 0.00 0.00 31.58 1.40
2730 3277 5.170748 GGCGATTTCTGAATTGTGGAATTT 58.829 37.500 0.00 0.00 31.58 1.82
2788 3336 5.023452 AGGTGTGGTGACTAGTGATATGAA 58.977 41.667 0.00 0.00 0.00 2.57
2907 3455 0.179020 CAGACAAGGCCACAAGTCCA 60.179 55.000 5.01 0.00 0.00 4.02
2913 3462 1.827789 GGCAACAGACAAGGCCACA 60.828 57.895 5.01 0.00 45.70 4.17
2995 3544 4.720902 CCCCATGCACGCAGTCCA 62.721 66.667 0.00 0.00 41.61 4.02
3142 3691 0.257328 TGCACTTCTCCCAACCACAA 59.743 50.000 0.00 0.00 0.00 3.33
3145 3694 1.228245 GCTGCACTTCTCCCAACCA 60.228 57.895 0.00 0.00 0.00 3.67
3146 3695 2.328099 CGCTGCACTTCTCCCAACC 61.328 63.158 0.00 0.00 0.00 3.77
3241 3802 2.843730 TGGGGCTGTATATGTGTTCAGT 59.156 45.455 0.00 0.00 0.00 3.41
3325 3886 2.936032 GGGGAGGGCAGTTCAGGT 60.936 66.667 0.00 0.00 0.00 4.00
3328 3889 2.610859 GAGGGGGAGGGCAGTTCA 60.611 66.667 0.00 0.00 0.00 3.18
3394 3956 9.393249 ACATATTTGATGTAGTTTTGAACGTTG 57.607 29.630 5.00 0.00 36.23 4.10
3475 4037 1.068741 GCTGGAATCGTCCCTATCGTT 59.931 52.381 0.00 0.00 44.23 3.85
3476 4038 0.674534 GCTGGAATCGTCCCTATCGT 59.325 55.000 0.00 0.00 44.23 3.73
3530 4092 6.070938 ACAGAACAGGTACATTTCTACCCTAC 60.071 42.308 0.00 0.00 37.49 3.18
3547 4109 9.748708 TGAATTCAATTTTTAAGGACAGAACAG 57.251 29.630 5.45 0.00 0.00 3.16
3594 4158 9.722184 GTTACAGGGAATCTAGATATTTTACCC 57.278 37.037 5.46 11.56 35.53 3.69
3639 4203 5.404466 TTTTTCTATCGGAGGGTTAACGA 57.596 39.130 0.00 0.00 41.20 3.85
3665 4229 7.314393 ACTAGGTCTTCTTTTTACTGATCGAC 58.686 38.462 0.00 0.00 0.00 4.20
3680 4244 5.500645 AAAACAGCACAAACTAGGTCTTC 57.499 39.130 0.00 0.00 0.00 2.87
3682 4246 8.730680 CATATAAAAACAGCACAAACTAGGTCT 58.269 33.333 0.00 0.00 0.00 3.85
3683 4247 8.512138 ACATATAAAAACAGCACAAACTAGGTC 58.488 33.333 0.00 0.00 0.00 3.85
3684 4248 8.296713 CACATATAAAAACAGCACAAACTAGGT 58.703 33.333 0.00 0.00 0.00 3.08
3742 4306 1.818060 CGTCCTGGCATCAAATTCCAA 59.182 47.619 0.00 0.00 0.00 3.53
3764 4329 9.533253 AAAATATCTTGACAACCAACAAAGAAG 57.467 29.630 0.00 0.00 0.00 2.85
3786 4352 6.594788 AGTATGTCACCAAGCATGAAAAAT 57.405 33.333 0.00 0.00 0.00 1.82
3819 4452 6.662865 ACTTCTCCATATTCATCGTCTCAT 57.337 37.500 0.00 0.00 0.00 2.90
3825 4458 9.708222 CTTTGTTTTACTTCTCCATATTCATCG 57.292 33.333 0.00 0.00 0.00 3.84
3919 4553 5.537300 TTGTCAGAGTCTAGAAGTTGCTT 57.463 39.130 0.00 0.00 0.00 3.91
3971 4607 9.039870 CAAACAGAGATACTCCATCTGATTAAC 57.960 37.037 8.32 0.00 44.41 2.01
3979 4615 9.096160 CATATATGCAAACAGAGATACTCCATC 57.904 37.037 0.00 0.00 0.00 3.51
4191 4827 2.730990 CCCAACTGGCATGTCACAA 58.269 52.632 0.00 0.00 0.00 3.33
4279 4915 2.034221 GGTCTGGGGCAAGGTGTC 59.966 66.667 0.00 0.00 0.00 3.67
4530 5193 9.502091 TGCTACACTTAACATTTAACAAGAGAT 57.498 29.630 0.00 0.00 0.00 2.75
4630 5301 5.790593 ACTTCGGTGATACAACAATACAGT 58.209 37.500 0.00 0.00 0.00 3.55
4787 5508 1.720805 AAGCAATGACGCATGTACGA 58.279 45.000 0.00 0.00 36.70 3.43
4819 5540 6.018542 CGTGCAAACATGACGATAATAACAA 58.981 36.000 0.00 0.00 35.05 2.83
4823 5544 4.033472 CACCGTGCAAACATGACGATAATA 59.967 41.667 0.00 0.00 35.05 0.98
4824 5545 3.006940 ACCGTGCAAACATGACGATAAT 58.993 40.909 0.00 0.00 35.05 1.28
4825 5546 2.158645 CACCGTGCAAACATGACGATAA 59.841 45.455 0.00 0.00 35.05 1.75
4826 5547 1.729517 CACCGTGCAAACATGACGATA 59.270 47.619 0.00 0.00 35.05 2.92
4854 5575 6.585416 ACTCCAAGCAAACTCATTTTGAAAT 58.415 32.000 0.91 0.00 46.76 2.17
4887 5608 9.398538 CTCCAAGACAACTCTTATAGTACTACT 57.601 37.037 4.31 0.00 37.50 2.57
4888 5609 9.393512 TCTCCAAGACAACTCTTATAGTACTAC 57.606 37.037 4.31 0.00 37.50 2.73
4889 5610 9.393512 GTCTCCAAGACAACTCTTATAGTACTA 57.606 37.037 4.77 4.77 44.45 1.82
4890 5611 7.339976 GGTCTCCAAGACAACTCTTATAGTACT 59.660 40.741 9.16 0.00 46.79 2.73
4891 5612 7.482474 GGTCTCCAAGACAACTCTTATAGTAC 58.518 42.308 9.16 0.00 46.79 2.73
4933 5654 1.001633 CCCGGGCGTAAGTGCTATAAT 59.998 52.381 8.08 0.00 41.68 1.28
4934 5655 0.390124 CCCGGGCGTAAGTGCTATAA 59.610 55.000 8.08 0.00 41.68 0.98
4935 5656 1.466025 CCCCGGGCGTAAGTGCTATA 61.466 60.000 17.73 0.00 41.68 1.31
4936 5657 2.803817 CCCCGGGCGTAAGTGCTAT 61.804 63.158 17.73 0.00 41.68 2.97
4937 5658 3.463585 CCCCGGGCGTAAGTGCTA 61.464 66.667 17.73 0.00 41.68 3.49
4941 5662 2.303282 AAATCCCCCGGGCGTAAGT 61.303 57.895 17.73 0.00 41.68 2.24
4942 5663 1.822186 CAAATCCCCCGGGCGTAAG 60.822 63.158 17.73 0.00 43.44 2.34
4943 5664 1.270414 TACAAATCCCCCGGGCGTAA 61.270 55.000 17.73 0.00 34.68 3.18
4944 5665 1.688269 CTACAAATCCCCCGGGCGTA 61.688 60.000 17.73 1.73 34.68 4.42
4945 5666 3.010314 TACAAATCCCCCGGGCGT 61.010 61.111 17.73 7.05 34.68 5.68
4946 5667 2.203153 CTACAAATCCCCCGGGCG 60.203 66.667 17.73 6.99 34.68 6.13
4948 5669 2.194868 GGCTACAAATCCCCCGGG 59.805 66.667 15.80 15.80 0.00 5.73
4949 5670 2.194868 GGGCTACAAATCCCCCGG 59.805 66.667 0.00 0.00 36.50 5.73
5049 5808 4.487714 AATCAGACATCGAAAGGGCTAA 57.512 40.909 0.00 0.00 0.00 3.09
5059 5818 3.424829 CCAACCGACAAAATCAGACATCG 60.425 47.826 0.00 0.00 0.00 3.84
5079 5838 3.396276 TCTTTGTAAATCCAGTGTCCCCA 59.604 43.478 0.00 0.00 0.00 4.96
5240 6028 0.039074 AGAACGTCAGGTCAGCTTCG 60.039 55.000 0.00 0.00 36.28 3.79
5317 6105 8.630037 TCAAAAAGAATAGAAAGGAAACTCCAC 58.370 33.333 0.00 0.00 42.68 4.02
5333 6121 5.215252 TCTCTCCGTGTCTCAAAAAGAAT 57.785 39.130 0.00 0.00 35.21 2.40
5352 6140 0.249657 GCATCCGACTCCCACATCTC 60.250 60.000 0.00 0.00 0.00 2.75
5355 6143 1.348008 ATGGCATCCGACTCCCACAT 61.348 55.000 0.00 0.00 0.00 3.21
5404 6195 2.082231 CTCGTCCTAACTTCTCGGTGA 58.918 52.381 0.00 0.00 0.00 4.02
5405 6196 2.082231 TCTCGTCCTAACTTCTCGGTG 58.918 52.381 0.00 0.00 0.00 4.94
5406 6197 2.486472 TCTCGTCCTAACTTCTCGGT 57.514 50.000 0.00 0.00 0.00 4.69
5407 6198 4.552378 CGTTATCTCGTCCTAACTTCTCGG 60.552 50.000 0.00 0.00 0.00 4.63
5408 6199 4.269603 TCGTTATCTCGTCCTAACTTCTCG 59.730 45.833 0.00 0.00 0.00 4.04
5409 6200 5.731599 TCGTTATCTCGTCCTAACTTCTC 57.268 43.478 0.00 0.00 0.00 2.87
5422 6217 3.187700 AGTGCATCGGTTTCGTTATCTC 58.812 45.455 0.00 0.00 37.69 2.75
5426 6221 2.492881 TCCTAGTGCATCGGTTTCGTTA 59.507 45.455 0.00 0.00 37.69 3.18
5434 6229 1.467678 CCTCCCTCCTAGTGCATCGG 61.468 65.000 0.00 0.00 0.00 4.18
5437 6232 1.003442 TGCCTCCCTCCTAGTGCAT 59.997 57.895 0.00 0.00 0.00 3.96
5450 6245 2.721971 ATCCATCCATCGCGTGCCTC 62.722 60.000 5.77 0.00 0.00 4.70
5451 6246 2.811514 ATCCATCCATCGCGTGCCT 61.812 57.895 5.77 0.00 0.00 4.75
5452 6247 2.281070 ATCCATCCATCGCGTGCC 60.281 61.111 5.77 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.