Multiple sequence alignment - TraesCS1B01G271500

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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 TraesCS1B01G271500 chr1B 100.000 2318 0 0 1 2318 477129790 477127473 0.000000e+00 4281
1 TraesCS1B01G271500 chr1A 91.357 1157 80 13 395 1538 454742663 454741514 0.000000e+00 1565
2 TraesCS1B01G271500 chr1A 89.950 398 31 7 1 393 454743210 454742817 2.660000e-139 505
3 TraesCS1B01G271500 chr1D 91.263 1156 70 14 395 1536 355147115 355145977 0.000000e+00 1546
4 TraesCS1B01G271500 chr1D 85.742 519 64 6 1634 2145 355145777 355145262 7.290000e-150 540
5 TraesCS1B01G271500 chr1D 90.932 397 19 5 1 392 355147602 355147218 3.410000e-143 518
6 TraesCS1B01G271500 chr5A 81.524 525 75 12 1642 2157 408178575 408179086 1.660000e-111 412
7 TraesCS1B01G271500 chr4B 82.255 479 67 12 1688 2157 572152931 572153400 4.640000e-107 398
8 TraesCS1B01G271500 chr7D 81.616 495 69 12 1675 2157 511689833 511690317 7.770000e-105 390
9 TraesCS1B01G271500 chr7D 87.209 172 19 1 2150 2318 437201809 437201638 2.350000e-45 193
10 TraesCS1B01G271500 chr7D 88.199 161 19 0 2150 2310 467537613 467537453 2.350000e-45 193
11 TraesCS1B01G271500 chr7D 87.578 161 20 0 2150 2310 543087174 543087014 1.090000e-43 187
12 TraesCS1B01G271500 chr4A 80.730 493 78 9 1672 2157 629464088 629464570 3.640000e-98 368
13 TraesCS1B01G271500 chr2B 81.978 455 58 10 1711 2157 488912310 488911872 4.710000e-97 364
14 TraesCS1B01G271500 chr5B 80.364 494 74 13 1672 2157 680626755 680626277 1.020000e-93 353
15 TraesCS1B01G271500 chr5B 86.928 153 20 0 2150 2302 290113608 290113760 3.060000e-39 172
16 TraesCS1B01G271500 chr7A 81.903 431 56 13 1743 2157 584200470 584200046 6.130000e-91 344
17 TraesCS1B01G271500 chr4D 80.605 397 53 18 1669 2056 82517782 82518163 3.770000e-73 285
18 TraesCS1B01G271500 chr2D 89.941 169 17 0 2150 2318 416931461 416931293 3.880000e-53 219
19 TraesCS1B01G271500 chr2D 87.578 161 20 0 2150 2310 317599807 317599967 1.090000e-43 187
20 TraesCS1B01G271500 chr3B 86.628 172 20 1 2150 2318 821434340 821434169 1.090000e-43 187
21 TraesCS1B01G271500 chr3B 86.047 172 21 1 2150 2318 821284916 821284745 5.090000e-42 182
22 TraesCS1B01G271500 chr5D 85.465 172 22 1 2150 2318 256219601 256219772 2.370000e-40 176


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 TraesCS1B01G271500 chr1B 477127473 477129790 2317 True 4281 4281 100.000000 1 2318 1 chr1B.!!$R1 2317
1 TraesCS1B01G271500 chr1A 454741514 454743210 1696 True 1035 1565 90.653500 1 1538 2 chr1A.!!$R1 1537
2 TraesCS1B01G271500 chr1D 355145262 355147602 2340 True 868 1546 89.312333 1 2145 3 chr1D.!!$R1 2144
3 TraesCS1B01G271500 chr5A 408178575 408179086 511 False 412 412 81.524000 1642 2157 1 chr5A.!!$F1 515

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
495 658 0.031917 TAGCACCCCACCCGATAAGA 60.032 55.0 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 2455 0.179124 CGCTCGAGGAAAAGAGGGAG 60.179 60.0 15.58 0.0 46.32 4.3 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
88 90 4.380531 ACCATAGAGATATGCAAACACGG 58.619 43.478 0.00 0.00 0.00 4.94
105 109 3.479269 GCGCGCGCCTATGTATCC 61.479 66.667 42.83 12.59 34.56 2.59
136 140 1.675801 CTGCTCTCTGAACCCAGCA 59.324 57.895 0.00 0.00 40.20 4.41
137 141 0.252479 CTGCTCTCTGAACCCAGCAT 59.748 55.000 0.00 0.00 41.00 3.79
193 198 0.247537 CGGTCGCCTTGTTTAATCGC 60.248 55.000 0.00 0.00 0.00 4.58
194 199 0.247537 GGTCGCCTTGTTTAATCGCG 60.248 55.000 0.00 0.00 44.00 5.87
231 238 1.226379 GCACGATGCATGGTTTCCG 60.226 57.895 12.10 6.64 44.26 4.30
232 239 1.429021 CACGATGCATGGTTTCCGG 59.571 57.895 12.10 0.00 0.00 5.14
233 240 2.406616 ACGATGCATGGTTTCCGGC 61.407 57.895 8.73 0.00 0.00 6.13
234 241 2.807622 GATGCATGGTTTCCGGCC 59.192 61.111 2.46 0.00 0.00 6.13
239 246 4.419921 ATGGTTTCCGGCCGGTCC 62.420 66.667 41.57 36.02 36.47 4.46
264 272 6.458232 ACTATCGTTAGCTTGATCTTGTCT 57.542 37.500 0.00 0.00 0.00 3.41
267 275 3.679980 TCGTTAGCTTGATCTTGTCTTGC 59.320 43.478 0.00 0.00 0.00 4.01
393 404 6.426025 GGCCATTACCGGAAACTAATTACTAG 59.574 42.308 9.46 0.00 0.00 2.57
458 621 7.633789 ACAGGGCATAATTATACTCCATTAGG 58.366 38.462 0.00 0.00 0.00 2.69
461 624 9.346515 AGGGCATAATTATACTCCATTAGGTAA 57.653 33.333 0.00 0.00 35.89 2.85
495 658 0.031917 TAGCACCCCACCCGATAAGA 60.032 55.000 0.00 0.00 0.00 2.10
527 693 0.246635 AGACGAGATTGTTGGACGGG 59.753 55.000 0.00 0.00 0.00 5.28
540 706 3.153270 GACGGGCGGGATTCTCTCC 62.153 68.421 0.00 0.00 44.11 3.71
584 752 4.884668 ACCTTAACAAGACTGAATCGGA 57.115 40.909 0.00 0.00 0.00 4.55
620 788 0.671472 CTCGTCTGCTTGCATCACCA 60.671 55.000 0.00 0.00 0.00 4.17
622 790 0.952497 CGTCTGCTTGCATCACCAGT 60.952 55.000 0.00 0.00 0.00 4.00
682 851 3.098555 CCAAAGCGCCCGATACAC 58.901 61.111 2.29 0.00 0.00 2.90
748 917 1.078708 AATTGGCCGACGGGTACAG 60.079 57.895 17.22 0.00 34.97 2.74
771 940 1.613317 CGCATCCGGGGCATCCTATA 61.613 60.000 17.27 0.00 0.00 1.31
827 1002 1.678101 GTATCTGTCCTTGGCCATTGC 59.322 52.381 6.09 0.00 0.00 3.56
846 1021 2.187946 CCGCCCGAATTCAGAGCT 59.812 61.111 6.22 0.00 0.00 4.09
852 1027 3.471680 GCCCGAATTCAGAGCTATCTTT 58.528 45.455 6.22 0.00 31.64 2.52
853 1028 3.496507 GCCCGAATTCAGAGCTATCTTTC 59.503 47.826 6.22 0.00 31.64 2.62
860 1035 7.171167 CGAATTCAGAGCTATCTTTCATCACAT 59.829 37.037 6.22 0.00 31.64 3.21
864 1039 5.177142 CAGAGCTATCTTTCATCACATTCCG 59.823 44.000 0.00 0.00 31.64 4.30
870 1045 3.189080 TCTTTCATCACATTCCGTTGCAG 59.811 43.478 0.00 0.00 0.00 4.41
898 1073 1.630878 CAAGCCCTTCTGGTTAGTCCT 59.369 52.381 0.00 0.00 37.07 3.85
940 1115 3.941573 TGTCTGCTGCTGATACAATCAA 58.058 40.909 12.42 0.00 39.11 2.57
984 1159 0.322456 CTCCGCTTGGAATTGGGACA 60.322 55.000 0.00 0.00 42.58 4.02
1004 1183 1.226859 TCCACGCCGATCGAATGTC 60.227 57.895 18.66 0.00 41.67 3.06
1014 1193 1.428219 TCGAATGTCGACGGAGAGC 59.572 57.895 11.62 0.00 44.82 4.09
1022 1201 3.760035 GACGGAGAGCAGGGCGAA 61.760 66.667 0.00 0.00 0.00 4.70
1035 1214 2.881352 GCGAAGAGGAGCGGTTCG 60.881 66.667 1.50 1.50 44.63 3.95
1272 1451 4.874977 GTCCTACTCGCGCTGGCC 62.875 72.222 5.56 0.00 35.02 5.36
1325 1504 0.389817 TCGTGCCATTGAAGAGGACG 60.390 55.000 5.20 5.20 33.09 4.79
1326 1505 0.389817 CGTGCCATTGAAGAGGACGA 60.390 55.000 5.57 0.00 33.38 4.20
1352 1531 3.887716 GCGGTAGTAGGAGTGGAGAAATA 59.112 47.826 0.00 0.00 0.00 1.40
1413 1597 4.159693 ACTGCTAACACGATCCATGTAGAA 59.840 41.667 0.00 0.00 0.00 2.10
1424 1608 5.757320 CGATCCATGTAGAAAAATCAGAGCT 59.243 40.000 0.00 0.00 0.00 4.09
1517 1702 8.549338 AGAAACTAGGATTTGTAAGTGTTAGC 57.451 34.615 0.00 0.00 0.00 3.09
1518 1703 7.606839 AGAAACTAGGATTTGTAAGTGTTAGCC 59.393 37.037 0.00 0.00 0.00 3.93
1519 1704 6.622427 ACTAGGATTTGTAAGTGTTAGCCT 57.378 37.500 0.00 0.00 0.00 4.58
1538 1723 2.239654 CCTTGAGTTAGGCCATCTCCAA 59.760 50.000 5.01 2.47 0.00 3.53
1539 1724 3.539604 CTTGAGTTAGGCCATCTCCAAG 58.460 50.000 5.01 9.09 0.00 3.61
1540 1725 1.839994 TGAGTTAGGCCATCTCCAAGG 59.160 52.381 5.01 0.00 0.00 3.61
1541 1726 1.141858 GAGTTAGGCCATCTCCAAGGG 59.858 57.143 5.01 0.00 0.00 3.95
1545 1730 4.692930 GCCATCTCCAAGGGCAAT 57.307 55.556 0.00 0.00 46.92 3.56
1548 1733 0.820891 CCATCTCCAAGGGCAATCCG 60.821 60.000 0.00 0.00 41.52 4.18
1549 1734 0.107017 CATCTCCAAGGGCAATCCGT 60.107 55.000 0.00 0.00 41.52 4.69
1556 1741 3.835395 TCCAAGGGCAATCCGTAAATTTT 59.165 39.130 0.00 0.00 41.52 1.82
1557 1742 3.932089 CCAAGGGCAATCCGTAAATTTTG 59.068 43.478 0.00 0.00 41.52 2.44
1559 1744 4.450082 AGGGCAATCCGTAAATTTTGTC 57.550 40.909 0.00 0.00 41.52 3.18
1561 1746 3.517602 GGCAATCCGTAAATTTTGTCCC 58.482 45.455 0.00 0.00 0.00 4.46
1570 1755 4.093703 CGTAAATTTTGTCCCGCATCTGTA 59.906 41.667 0.00 0.00 0.00 2.74
1571 1756 5.220777 CGTAAATTTTGTCCCGCATCTGTAT 60.221 40.000 0.00 0.00 0.00 2.29
1573 1758 6.959639 AAATTTTGTCCCGCATCTGTATAT 57.040 33.333 0.00 0.00 0.00 0.86
1574 1759 6.959639 AATTTTGTCCCGCATCTGTATATT 57.040 33.333 0.00 0.00 0.00 1.28
1577 1762 4.681074 TGTCCCGCATCTGTATATTCAA 57.319 40.909 0.00 0.00 0.00 2.69
1578 1763 4.377021 TGTCCCGCATCTGTATATTCAAC 58.623 43.478 0.00 0.00 0.00 3.18
1579 1764 3.428870 GTCCCGCATCTGTATATTCAACG 59.571 47.826 0.00 0.00 0.00 4.10
1580 1765 2.157668 CCCGCATCTGTATATTCAACGC 59.842 50.000 0.00 0.00 0.00 4.84
1581 1766 3.059884 CCGCATCTGTATATTCAACGCT 58.940 45.455 0.00 0.00 0.00 5.07
1583 1768 4.864806 CCGCATCTGTATATTCAACGCTAT 59.135 41.667 0.00 0.00 0.00 2.97
1584 1769 5.004821 CCGCATCTGTATATTCAACGCTATC 59.995 44.000 0.00 0.00 0.00 2.08
1585 1770 5.004821 CGCATCTGTATATTCAACGCTATCC 59.995 44.000 0.00 0.00 0.00 2.59
1586 1771 6.102663 GCATCTGTATATTCAACGCTATCCT 58.897 40.000 0.00 0.00 0.00 3.24
1587 1772 6.035435 GCATCTGTATATTCAACGCTATCCTG 59.965 42.308 0.00 0.00 0.00 3.86
1588 1773 6.650427 TCTGTATATTCAACGCTATCCTGT 57.350 37.500 0.00 0.00 0.00 4.00
1590 1775 8.349568 TCTGTATATTCAACGCTATCCTGTAT 57.650 34.615 0.00 0.00 0.00 2.29
1598 1783 2.686915 ACGCTATCCTGTATATACCCGC 59.313 50.000 10.38 3.50 0.00 6.13
1600 1785 3.028850 GCTATCCTGTATATACCCGCCA 58.971 50.000 10.38 0.00 0.00 5.69
1603 1788 5.396436 GCTATCCTGTATATACCCGCCAAAT 60.396 44.000 10.38 0.00 0.00 2.32
1604 1789 6.183360 GCTATCCTGTATATACCCGCCAAATA 60.183 42.308 10.38 0.00 0.00 1.40
1605 1790 5.670792 TCCTGTATATACCCGCCAAATAG 57.329 43.478 10.38 0.00 0.00 1.73
1606 1791 4.468510 TCCTGTATATACCCGCCAAATAGG 59.531 45.833 10.38 7.02 41.84 2.57
1617 1802 2.951229 CCAAATAGGCGGGTATTCCT 57.049 50.000 0.00 0.00 36.51 3.36
1618 1803 2.779506 CCAAATAGGCGGGTATTCCTC 58.220 52.381 0.00 0.00 34.02 3.71
1621 1806 2.417719 ATAGGCGGGTATTCCTCCTT 57.582 50.000 7.72 0.00 37.63 3.36
1622 1807 2.185663 TAGGCGGGTATTCCTCCTTT 57.814 50.000 7.72 0.00 37.63 3.11
1623 1808 2.185663 AGGCGGGTATTCCTCCTTTA 57.814 50.000 0.00 0.00 34.74 1.85
1624 1809 2.484602 AGGCGGGTATTCCTCCTTTAA 58.515 47.619 0.00 0.00 34.74 1.52
1625 1810 2.848071 AGGCGGGTATTCCTCCTTTAAA 59.152 45.455 0.00 0.00 34.74 1.52
1626 1811 3.267551 AGGCGGGTATTCCTCCTTTAAAA 59.732 43.478 0.00 0.00 34.74 1.52
1627 1812 4.018490 GGCGGGTATTCCTCCTTTAAAAA 58.982 43.478 0.00 0.00 0.00 1.94
1628 1813 4.647853 GGCGGGTATTCCTCCTTTAAAAAT 59.352 41.667 0.00 0.00 0.00 1.82
1629 1814 5.829391 GGCGGGTATTCCTCCTTTAAAAATA 59.171 40.000 0.00 0.00 0.00 1.40
1631 1816 7.014905 GGCGGGTATTCCTCCTTTAAAAATAAT 59.985 37.037 0.00 0.00 0.00 1.28
1632 1817 9.070179 GCGGGTATTCCTCCTTTAAAAATAATA 57.930 33.333 0.00 0.00 0.00 0.98
1710 2003 1.807139 CATGTCCGATCACCACAACA 58.193 50.000 0.00 0.00 0.00 3.33
1756 2055 7.490079 AGTTTTTACCCGAATTCAAAAGAACAC 59.510 33.333 6.22 0.91 0.00 3.32
1757 2056 3.619233 ACCCGAATTCAAAAGAACACG 57.381 42.857 6.22 0.00 0.00 4.49
1761 2060 4.261031 CCCGAATTCAAAAGAACACGAGTT 60.261 41.667 6.22 0.00 41.64 3.01
1770 2069 3.802948 AGAACACGAGTTTGACAGTCT 57.197 42.857 1.31 0.00 38.30 3.24
1800 2099 2.361610 CCTGCTGGACCGGCAATT 60.362 61.111 27.73 0.00 45.60 2.32
1803 2102 2.044946 GCTGGACCGGCAATTCCT 60.045 61.111 20.97 0.00 35.55 3.36
1868 2170 4.671590 TCCGCCTCCTCGTCCACA 62.672 66.667 0.00 0.00 0.00 4.17
1869 2171 3.691342 CCGCCTCCTCGTCCACAA 61.691 66.667 0.00 0.00 0.00 3.33
1873 2175 2.571216 CCTCCTCGTCCACAACCGT 61.571 63.158 0.00 0.00 0.00 4.83
1883 2185 2.049802 ACAACCGTGTACGCCTCG 60.050 61.111 0.00 0.00 35.72 4.63
1928 2230 3.589988 CGCCAACTACTGATCTTTCTGT 58.410 45.455 0.00 0.00 37.70 3.41
1950 2252 1.078497 TGCAACATCTGGTAGCGGG 60.078 57.895 0.00 0.00 0.00 6.13
1992 2294 2.190578 CGGCATCCAAGGAGTCCC 59.809 66.667 5.25 0.00 0.00 4.46
2022 2324 0.329261 CAACATCTTGGCCTCCTCCA 59.671 55.000 3.32 0.00 0.00 3.86
2029 2331 1.434513 TTGGCCTCCTCCACATTGGT 61.435 55.000 3.32 0.00 39.03 3.67
2058 2360 1.071605 CACCTTCTTTTCCTCGAGCG 58.928 55.000 6.99 0.19 0.00 5.03
2060 2362 1.891150 ACCTTCTTTTCCTCGAGCGTA 59.109 47.619 6.99 0.00 0.00 4.42
2115 2417 2.815647 GCTTGAGCTTCCCGTCCG 60.816 66.667 0.00 0.00 38.21 4.79
2116 2418 2.657237 CTTGAGCTTCCCGTCCGT 59.343 61.111 0.00 0.00 0.00 4.69
2117 2419 1.446272 CTTGAGCTTCCCGTCCGTC 60.446 63.158 0.00 0.00 0.00 4.79
2118 2420 3.277211 TTGAGCTTCCCGTCCGTCG 62.277 63.158 0.00 0.00 39.52 5.12
2122 2424 4.493747 CTTCCCGTCCGTCGCCTC 62.494 72.222 0.00 0.00 38.35 4.70
2126 2428 4.143333 CCGTCCGTCGCCTCCATT 62.143 66.667 0.00 0.00 38.35 3.16
2127 2429 2.777972 CCGTCCGTCGCCTCCATTA 61.778 63.158 0.00 0.00 38.35 1.90
2128 2430 1.140161 CGTCCGTCGCCTCCATTAA 59.860 57.895 0.00 0.00 0.00 1.40
2129 2431 0.249322 CGTCCGTCGCCTCCATTAAT 60.249 55.000 0.00 0.00 0.00 1.40
2130 2432 1.001048 CGTCCGTCGCCTCCATTAATA 60.001 52.381 0.00 0.00 0.00 0.98
2131 2433 2.673833 GTCCGTCGCCTCCATTAATAG 58.326 52.381 0.00 0.00 0.00 1.73
2132 2434 2.035576 GTCCGTCGCCTCCATTAATAGT 59.964 50.000 0.00 0.00 0.00 2.12
2133 2435 2.696707 TCCGTCGCCTCCATTAATAGTT 59.303 45.455 0.00 0.00 0.00 2.24
2134 2436 3.133362 TCCGTCGCCTCCATTAATAGTTT 59.867 43.478 0.00 0.00 0.00 2.66
2135 2437 3.247648 CCGTCGCCTCCATTAATAGTTTG 59.752 47.826 0.00 0.00 0.00 2.93
2136 2438 4.116961 CGTCGCCTCCATTAATAGTTTGA 58.883 43.478 0.00 0.00 0.00 2.69
2137 2439 4.569162 CGTCGCCTCCATTAATAGTTTGAA 59.431 41.667 0.00 0.00 0.00 2.69
2138 2440 5.501897 CGTCGCCTCCATTAATAGTTTGAAC 60.502 44.000 0.00 0.00 0.00 3.18
2139 2441 4.879545 TCGCCTCCATTAATAGTTTGAACC 59.120 41.667 0.00 0.00 0.00 3.62
2140 2442 4.881850 CGCCTCCATTAATAGTTTGAACCT 59.118 41.667 0.00 0.00 0.00 3.50
2141 2443 5.007724 CGCCTCCATTAATAGTTTGAACCTC 59.992 44.000 0.00 0.00 0.00 3.85
2142 2444 6.122964 GCCTCCATTAATAGTTTGAACCTCT 58.877 40.000 0.00 0.00 0.00 3.69
2143 2445 6.261158 GCCTCCATTAATAGTTTGAACCTCTC 59.739 42.308 0.00 0.00 0.00 3.20
2144 2446 6.768381 CCTCCATTAATAGTTTGAACCTCTCC 59.232 42.308 0.00 0.00 0.00 3.71
2145 2447 6.346096 TCCATTAATAGTTTGAACCTCTCCG 58.654 40.000 0.00 0.00 0.00 4.63
2146 2448 5.007724 CCATTAATAGTTTGAACCTCTCCGC 59.992 44.000 0.00 0.00 0.00 5.54
2147 2449 2.693267 ATAGTTTGAACCTCTCCGCC 57.307 50.000 0.00 0.00 0.00 6.13
2148 2450 1.640917 TAGTTTGAACCTCTCCGCCT 58.359 50.000 0.00 0.00 0.00 5.52
2149 2451 0.765510 AGTTTGAACCTCTCCGCCTT 59.234 50.000 0.00 0.00 0.00 4.35
2150 2452 1.157585 GTTTGAACCTCTCCGCCTTC 58.842 55.000 0.00 0.00 0.00 3.46
2151 2453 1.056660 TTTGAACCTCTCCGCCTTCT 58.943 50.000 0.00 0.00 0.00 2.85
2152 2454 1.056660 TTGAACCTCTCCGCCTTCTT 58.943 50.000 0.00 0.00 0.00 2.52
2153 2455 0.608640 TGAACCTCTCCGCCTTCTTC 59.391 55.000 0.00 0.00 0.00 2.87
2154 2456 0.899019 GAACCTCTCCGCCTTCTTCT 59.101 55.000 0.00 0.00 0.00 2.85
2155 2457 0.899019 AACCTCTCCGCCTTCTTCTC 59.101 55.000 0.00 0.00 0.00 2.87
2156 2458 0.973496 ACCTCTCCGCCTTCTTCTCC 60.973 60.000 0.00 0.00 0.00 3.71
2157 2459 1.681486 CCTCTCCGCCTTCTTCTCCC 61.681 65.000 0.00 0.00 0.00 4.30
2158 2460 0.686112 CTCTCCGCCTTCTTCTCCCT 60.686 60.000 0.00 0.00 0.00 4.20
2159 2461 0.684805 TCTCCGCCTTCTTCTCCCTC 60.685 60.000 0.00 0.00 0.00 4.30
2160 2462 0.686112 CTCCGCCTTCTTCTCCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
2161 2463 0.252284 TCCGCCTTCTTCTCCCTCTT 60.252 55.000 0.00 0.00 0.00 2.85
2162 2464 0.615850 CCGCCTTCTTCTCCCTCTTT 59.384 55.000 0.00 0.00 0.00 2.52
2163 2465 1.003696 CCGCCTTCTTCTCCCTCTTTT 59.996 52.381 0.00 0.00 0.00 2.27
2164 2466 2.351455 CGCCTTCTTCTCCCTCTTTTC 58.649 52.381 0.00 0.00 0.00 2.29
2165 2467 2.717390 GCCTTCTTCTCCCTCTTTTCC 58.283 52.381 0.00 0.00 0.00 3.13
2166 2468 2.307392 GCCTTCTTCTCCCTCTTTTCCT 59.693 50.000 0.00 0.00 0.00 3.36
2167 2469 3.621214 GCCTTCTTCTCCCTCTTTTCCTC 60.621 52.174 0.00 0.00 0.00 3.71
2168 2470 3.368948 CCTTCTTCTCCCTCTTTTCCTCG 60.369 52.174 0.00 0.00 0.00 4.63
2169 2471 3.170991 TCTTCTCCCTCTTTTCCTCGA 57.829 47.619 0.00 0.00 0.00 4.04
2170 2472 3.093057 TCTTCTCCCTCTTTTCCTCGAG 58.907 50.000 5.13 5.13 0.00 4.04
2171 2473 1.187087 TCTCCCTCTTTTCCTCGAGC 58.813 55.000 6.99 0.00 0.00 5.03
2172 2474 0.179124 CTCCCTCTTTTCCTCGAGCG 60.179 60.000 6.99 0.19 0.00 5.03
2173 2475 1.811679 CCCTCTTTTCCTCGAGCGC 60.812 63.158 6.99 0.00 0.00 5.92
2174 2476 2.161486 CCTCTTTTCCTCGAGCGCG 61.161 63.158 6.99 2.41 39.35 6.86
2175 2477 2.126071 TCTTTTCCTCGAGCGCGG 60.126 61.111 10.69 0.00 38.28 6.46
2176 2478 3.854459 CTTTTCCTCGAGCGCGGC 61.854 66.667 10.69 0.00 38.28 6.53
2188 2490 2.815647 CGCGGCCTTCCTGTCTTC 60.816 66.667 0.00 0.00 0.00 2.87
2189 2491 2.815647 GCGGCCTTCCTGTCTTCG 60.816 66.667 0.00 0.00 0.00 3.79
2190 2492 2.125512 CGGCCTTCCTGTCTTCGG 60.126 66.667 0.00 0.00 0.00 4.30
2191 2493 2.943978 CGGCCTTCCTGTCTTCGGT 61.944 63.158 0.00 0.00 0.00 4.69
2192 2494 1.079057 GGCCTTCCTGTCTTCGGTC 60.079 63.158 0.00 0.00 0.00 4.79
2193 2495 1.671742 GCCTTCCTGTCTTCGGTCA 59.328 57.895 0.00 0.00 0.00 4.02
2194 2496 0.250513 GCCTTCCTGTCTTCGGTCAT 59.749 55.000 0.00 0.00 0.00 3.06
2195 2497 2.009042 GCCTTCCTGTCTTCGGTCATG 61.009 57.143 0.00 0.00 0.00 3.07
2196 2498 1.406069 CCTTCCTGTCTTCGGTCATGG 60.406 57.143 0.00 0.00 0.00 3.66
2197 2499 1.276421 CTTCCTGTCTTCGGTCATGGT 59.724 52.381 0.00 0.00 0.00 3.55
2198 2500 0.895530 TCCTGTCTTCGGTCATGGTC 59.104 55.000 0.00 0.00 0.00 4.02
2199 2501 0.608130 CCTGTCTTCGGTCATGGTCA 59.392 55.000 0.00 0.00 0.00 4.02
2200 2502 1.208052 CCTGTCTTCGGTCATGGTCAT 59.792 52.381 0.00 0.00 0.00 3.06
2201 2503 2.544685 CTGTCTTCGGTCATGGTCATC 58.455 52.381 0.00 0.00 0.00 2.92
2202 2504 1.207089 TGTCTTCGGTCATGGTCATCC 59.793 52.381 0.00 0.00 0.00 3.51
2203 2505 1.482593 GTCTTCGGTCATGGTCATCCT 59.517 52.381 0.00 0.00 34.23 3.24
2204 2506 1.757118 TCTTCGGTCATGGTCATCCTC 59.243 52.381 0.00 0.00 34.23 3.71
2205 2507 1.759445 CTTCGGTCATGGTCATCCTCT 59.241 52.381 0.00 0.00 34.23 3.69
2206 2508 1.403814 TCGGTCATGGTCATCCTCTC 58.596 55.000 0.00 0.00 34.23 3.20
2207 2509 1.063642 TCGGTCATGGTCATCCTCTCT 60.064 52.381 0.00 0.00 34.23 3.10
2208 2510 1.759445 CGGTCATGGTCATCCTCTCTT 59.241 52.381 0.00 0.00 34.23 2.85
2209 2511 2.223923 CGGTCATGGTCATCCTCTCTTC 60.224 54.545 0.00 0.00 34.23 2.87
2210 2512 2.223923 GGTCATGGTCATCCTCTCTTCG 60.224 54.545 0.00 0.00 34.23 3.79
2211 2513 2.690497 GTCATGGTCATCCTCTCTTCGA 59.310 50.000 0.00 0.00 34.23 3.71
2212 2514 2.954989 TCATGGTCATCCTCTCTTCGAG 59.045 50.000 0.00 0.00 39.57 4.04
2213 2515 1.107114 TGGTCATCCTCTCTTCGAGC 58.893 55.000 0.00 0.00 38.49 5.03
2214 2516 1.341482 TGGTCATCCTCTCTTCGAGCT 60.341 52.381 0.00 0.00 38.49 4.09
2215 2517 1.754226 GGTCATCCTCTCTTCGAGCTT 59.246 52.381 0.00 0.00 38.49 3.74
2216 2518 2.481104 GGTCATCCTCTCTTCGAGCTTG 60.481 54.545 0.00 0.00 38.49 4.01
2217 2519 2.425312 GTCATCCTCTCTTCGAGCTTGA 59.575 50.000 0.00 0.00 38.49 3.02
2218 2520 2.687425 TCATCCTCTCTTCGAGCTTGAG 59.313 50.000 3.32 2.55 38.49 3.02
2219 2521 0.814457 TCCTCTCTTCGAGCTTGAGC 59.186 55.000 3.32 0.00 38.49 4.26
2230 2532 2.873288 CTTGAGCTTCTTGCCCGC 59.127 61.111 0.00 0.00 44.23 6.13
2261 2563 0.468226 ACAGTTTGAACCTCTCCGCA 59.532 50.000 0.00 0.00 0.00 5.69
2271 2573 1.118838 CCTCTCCGCATTCTTCTCCT 58.881 55.000 0.00 0.00 0.00 3.69
2272 2574 2.311463 CCTCTCCGCATTCTTCTCCTA 58.689 52.381 0.00 0.00 0.00 2.94
2273 2575 2.035321 CCTCTCCGCATTCTTCTCCTAC 59.965 54.545 0.00 0.00 0.00 3.18
2274 2576 2.955660 CTCTCCGCATTCTTCTCCTACT 59.044 50.000 0.00 0.00 0.00 2.57
2275 2577 3.366396 TCTCCGCATTCTTCTCCTACTT 58.634 45.455 0.00 0.00 0.00 2.24
2276 2578 3.131223 TCTCCGCATTCTTCTCCTACTTG 59.869 47.826 0.00 0.00 0.00 3.16
2277 2579 3.096852 TCCGCATTCTTCTCCTACTTGA 58.903 45.455 0.00 0.00 0.00 3.02
2278 2580 3.706594 TCCGCATTCTTCTCCTACTTGAT 59.293 43.478 0.00 0.00 0.00 2.57
2279 2581 3.806521 CCGCATTCTTCTCCTACTTGATG 59.193 47.826 0.00 0.00 0.00 3.07
2280 2582 4.437239 CGCATTCTTCTCCTACTTGATGT 58.563 43.478 0.00 0.00 0.00 3.06
2281 2583 4.505922 CGCATTCTTCTCCTACTTGATGTC 59.494 45.833 0.00 0.00 0.00 3.06
2282 2584 4.813697 GCATTCTTCTCCTACTTGATGTCC 59.186 45.833 0.00 0.00 0.00 4.02
2283 2585 4.720649 TTCTTCTCCTACTTGATGTCCG 57.279 45.455 0.00 0.00 0.00 4.79
2284 2586 3.964411 TCTTCTCCTACTTGATGTCCGA 58.036 45.455 0.00 0.00 0.00 4.55
2285 2587 3.695060 TCTTCTCCTACTTGATGTCCGAC 59.305 47.826 0.00 0.00 0.00 4.79
2286 2588 2.376109 TCTCCTACTTGATGTCCGACC 58.624 52.381 0.00 0.00 0.00 4.79
2287 2589 1.065701 CTCCTACTTGATGTCCGACCG 59.934 57.143 0.00 0.00 0.00 4.79
2288 2590 0.527817 CCTACTTGATGTCCGACCGC 60.528 60.000 0.00 0.00 0.00 5.68
2289 2591 0.456221 CTACTTGATGTCCGACCGCT 59.544 55.000 0.00 0.00 0.00 5.52
2290 2592 0.892755 TACTTGATGTCCGACCGCTT 59.107 50.000 0.00 0.00 0.00 4.68
2291 2593 0.389948 ACTTGATGTCCGACCGCTTC 60.390 55.000 0.00 0.00 0.00 3.86
2292 2594 0.389817 CTTGATGTCCGACCGCTTCA 60.390 55.000 0.00 0.00 0.00 3.02
2293 2595 0.669318 TTGATGTCCGACCGCTTCAC 60.669 55.000 0.00 0.00 0.00 3.18
2294 2596 2.126071 ATGTCCGACCGCTTCACG 60.126 61.111 0.00 0.00 43.15 4.35
2297 2599 4.063967 TCCGACCGCTTCACGCAT 62.064 61.111 0.00 0.00 41.76 4.73
2298 2600 3.853330 CCGACCGCTTCACGCATG 61.853 66.667 0.00 0.00 41.76 4.06
2299 2601 4.505217 CGACCGCTTCACGCATGC 62.505 66.667 7.91 7.91 41.76 4.06
2300 2602 4.166011 GACCGCTTCACGCATGCC 62.166 66.667 13.15 0.00 41.76 4.40
2301 2603 4.704833 ACCGCTTCACGCATGCCT 62.705 61.111 13.15 0.00 41.76 4.75
2302 2604 4.170062 CCGCTTCACGCATGCCTG 62.170 66.667 13.15 11.44 41.76 4.85
2303 2605 4.824166 CGCTTCACGCATGCCTGC 62.824 66.667 13.15 3.57 45.31 4.85
2304 2606 3.437795 GCTTCACGCATGCCTGCT 61.438 61.111 13.15 0.00 46.65 4.24
2305 2607 2.789917 CTTCACGCATGCCTGCTC 59.210 61.111 13.15 0.00 46.65 4.26
2306 2608 2.747460 TTCACGCATGCCTGCTCC 60.747 61.111 13.15 0.00 46.65 4.70
2307 2609 3.258228 TTCACGCATGCCTGCTCCT 62.258 57.895 13.15 0.00 46.65 3.69
2308 2610 2.749044 CACGCATGCCTGCTCCTT 60.749 61.111 13.15 0.00 46.65 3.36
2309 2611 2.437359 ACGCATGCCTGCTCCTTC 60.437 61.111 13.15 0.00 46.65 3.46
2310 2612 3.570638 CGCATGCCTGCTCCTTCG 61.571 66.667 13.15 0.00 46.65 3.79
2311 2613 3.885521 GCATGCCTGCTCCTTCGC 61.886 66.667 6.36 0.00 45.32 4.70
2312 2614 3.207669 CATGCCTGCTCCTTCGCC 61.208 66.667 0.00 0.00 0.00 5.54
2313 2615 3.720601 ATGCCTGCTCCTTCGCCA 61.721 61.111 0.00 0.00 0.00 5.69
2314 2616 3.272364 ATGCCTGCTCCTTCGCCAA 62.272 57.895 0.00 0.00 0.00 4.52
2315 2617 3.130160 GCCTGCTCCTTCGCCAAG 61.130 66.667 0.00 0.00 0.00 3.61
2316 2618 2.665000 CCTGCTCCTTCGCCAAGA 59.335 61.111 0.00 0.00 0.00 3.02
2317 2619 1.222936 CCTGCTCCTTCGCCAAGAT 59.777 57.895 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.081061 GCATATTGGACGGGATTGCATA 58.919 45.455 0.00 0.00 0.00 3.14
88 90 2.537792 TAGGATACATAGGCGCGCGC 62.538 60.000 44.40 44.40 41.41 6.86
100 104 2.288186 GCAGCGGCTTTTCTTAGGATAC 59.712 50.000 0.00 0.00 36.96 2.24
136 140 4.965119 TCGTATCAGCGTATCAGCATAT 57.035 40.909 0.00 0.00 40.15 1.78
137 141 4.965119 ATCGTATCAGCGTATCAGCATA 57.035 40.909 0.00 0.00 40.15 3.14
193 198 1.069703 CATGCACCGGATATTTCTGCG 60.070 52.381 9.46 0.00 0.00 5.18
194 199 1.335324 GCATGCACCGGATATTTCTGC 60.335 52.381 14.21 6.16 0.00 4.26
217 222 2.807622 GGCCGGAAACCATGCATC 59.192 61.111 5.05 0.00 0.00 3.91
242 249 6.292061 GCAAGACAAGATCAAGCTAACGATAG 60.292 42.308 0.00 0.00 46.19 2.08
447 610 7.700846 AGATAGCTAGCTTACCTAATGGAGTA 58.299 38.462 24.88 0.00 37.04 2.59
495 658 2.228059 TCTCGTCTCGTGGTCTCTTTT 58.772 47.619 0.00 0.00 0.00 2.27
620 788 0.112995 TGATGGCTGCTTTTCCCACT 59.887 50.000 0.00 0.00 0.00 4.00
622 790 1.619827 CTTTGATGGCTGCTTTTCCCA 59.380 47.619 0.00 0.00 0.00 4.37
695 864 1.272147 GGCAGACCCTGAAGATTTGGT 60.272 52.381 0.00 0.00 32.44 3.67
765 934 0.536687 CGAGTGCGGGGTCTATAGGA 60.537 60.000 0.00 0.00 0.00 2.94
768 937 3.440151 GCGAGTGCGGGGTCTATA 58.560 61.111 0.00 0.00 38.16 1.31
827 1002 3.264897 CTCTGAATTCGGGCGGCG 61.265 66.667 14.33 0.51 0.00 6.46
846 1021 4.940654 TGCAACGGAATGTGATGAAAGATA 59.059 37.500 0.00 0.00 0.00 1.98
852 1027 0.804364 GCTGCAACGGAATGTGATGA 59.196 50.000 0.00 0.00 0.00 2.92
853 1028 0.522626 TGCTGCAACGGAATGTGATG 59.477 50.000 0.00 0.00 0.00 3.07
860 1035 0.533978 TGCTACTTGCTGCAACGGAA 60.534 50.000 11.69 0.00 43.37 4.30
864 1039 0.387750 GGCTTGCTACTTGCTGCAAC 60.388 55.000 11.69 2.22 43.17 4.17
870 1045 0.807496 CAGAAGGGCTTGCTACTTGC 59.193 55.000 7.54 0.00 43.25 4.01
898 1073 7.756272 CAGACAACTTGTACGTGGTACATATAA 59.244 37.037 9.20 0.00 46.36 0.98
940 1115 1.517832 GAGTATGTCCGCCACTGCT 59.482 57.895 0.00 0.00 34.43 4.24
945 1120 1.447140 GCAACGAGTATGTCCGCCA 60.447 57.895 0.00 0.00 0.00 5.69
984 1159 1.226974 CATTCGATCGGCGTGGACT 60.227 57.895 16.41 0.00 41.80 3.85
1014 1193 4.521062 CCGCTCCTCTTCGCCCTG 62.521 72.222 0.00 0.00 0.00 4.45
1022 1201 3.082579 GCCATCGAACCGCTCCTCT 62.083 63.158 0.00 0.00 0.00 3.69
1072 1251 4.360405 CCCCACCCGTTTCCCCTG 62.360 72.222 0.00 0.00 0.00 4.45
1325 1504 2.327244 CTCCTACTACCGCGCGTC 59.673 66.667 29.95 0.00 0.00 5.19
1326 1505 2.437359 ACTCCTACTACCGCGCGT 60.437 61.111 29.95 18.85 0.00 6.01
1385 1569 5.703592 ACATGGATCGTGTTAGCAGTTAAAA 59.296 36.000 0.00 0.00 28.11 1.52
1386 1570 5.242434 ACATGGATCGTGTTAGCAGTTAAA 58.758 37.500 0.00 0.00 28.11 1.52
1413 1597 9.559958 CACGTGATTAAATAAAGCTCTGATTTT 57.440 29.630 10.90 0.00 0.00 1.82
1424 1608 3.679025 ACGGTCGCACGTGATTAAATAAA 59.321 39.130 22.23 0.00 46.64 1.40
1492 1676 7.606839 GGCTAACACTTACAAATCCTAGTTTCT 59.393 37.037 0.00 0.00 0.00 2.52
1517 1702 1.839994 TGGAGATGGCCTAACTCAAGG 59.160 52.381 19.82 0.00 39.87 3.61
1518 1703 3.539604 CTTGGAGATGGCCTAACTCAAG 58.460 50.000 19.82 15.97 33.00 3.02
1519 1704 2.239654 CCTTGGAGATGGCCTAACTCAA 59.760 50.000 19.82 10.62 33.00 3.02
1529 1714 0.820891 CGGATTGCCCTTGGAGATGG 60.821 60.000 0.00 0.00 0.00 3.51
1533 1718 2.122783 TTTACGGATTGCCCTTGGAG 57.877 50.000 0.00 0.00 0.00 3.86
1538 1723 3.194755 GGACAAAATTTACGGATTGCCCT 59.805 43.478 0.00 0.00 0.00 5.19
1539 1724 3.517602 GGACAAAATTTACGGATTGCCC 58.482 45.455 0.00 0.00 0.00 5.36
1540 1725 3.517602 GGGACAAAATTTACGGATTGCC 58.482 45.455 0.00 0.00 0.00 4.52
1541 1726 3.175929 CGGGACAAAATTTACGGATTGC 58.824 45.455 0.00 0.00 0.00 3.56
1542 1727 3.175929 GCGGGACAAAATTTACGGATTG 58.824 45.455 0.00 0.00 0.00 2.67
1543 1728 2.820787 TGCGGGACAAAATTTACGGATT 59.179 40.909 0.00 0.00 0.00 3.01
1545 1730 1.893544 TGCGGGACAAAATTTACGGA 58.106 45.000 0.00 0.00 0.00 4.69
1548 1733 4.434713 ACAGATGCGGGACAAAATTTAC 57.565 40.909 0.00 0.00 0.00 2.01
1549 1734 8.458573 AATATACAGATGCGGGACAAAATTTA 57.541 30.769 0.00 0.00 0.00 1.40
1556 1741 4.377021 GTTGAATATACAGATGCGGGACA 58.623 43.478 0.00 0.00 0.00 4.02
1557 1742 3.428870 CGTTGAATATACAGATGCGGGAC 59.571 47.826 0.00 0.00 0.00 4.46
1559 1744 2.157668 GCGTTGAATATACAGATGCGGG 59.842 50.000 0.00 0.00 0.00 6.13
1561 1746 5.004821 GGATAGCGTTGAATATACAGATGCG 59.995 44.000 0.00 0.00 0.00 4.73
1570 1755 8.639761 GGGTATATACAGGATAGCGTTGAATAT 58.360 37.037 14.70 0.00 0.00 1.28
1571 1756 7.201758 CGGGTATATACAGGATAGCGTTGAATA 60.202 40.741 14.70 0.00 0.00 1.75
1573 1758 5.106038 CGGGTATATACAGGATAGCGTTGAA 60.106 44.000 14.70 0.00 0.00 2.69
1574 1759 4.397103 CGGGTATATACAGGATAGCGTTGA 59.603 45.833 14.70 0.00 0.00 3.18
1577 1762 2.686915 GCGGGTATATACAGGATAGCGT 59.313 50.000 14.70 0.00 0.00 5.07
1578 1763 2.034305 GGCGGGTATATACAGGATAGCG 59.966 54.545 14.70 0.00 0.00 4.26
1579 1764 3.028850 TGGCGGGTATATACAGGATAGC 58.971 50.000 14.70 9.29 0.00 2.97
1580 1765 5.670792 TTTGGCGGGTATATACAGGATAG 57.329 43.478 14.70 0.81 0.00 2.08
1581 1766 6.325545 CCTATTTGGCGGGTATATACAGGATA 59.674 42.308 14.70 2.89 0.00 2.59
1583 1768 4.468510 CCTATTTGGCGGGTATATACAGGA 59.531 45.833 14.70 0.00 0.00 3.86
1584 1769 4.766375 CCTATTTGGCGGGTATATACAGG 58.234 47.826 14.70 5.62 0.00 4.00
1598 1783 2.779506 GAGGAATACCCGCCTATTTGG 58.220 52.381 0.00 0.00 40.87 3.28
1606 1791 5.847111 ATTTTTAAAGGAGGAATACCCGC 57.153 39.130 0.00 0.00 40.87 6.13
1656 1948 6.804295 GCGTTGTGTGGATCAAAATACATTTA 59.196 34.615 0.00 0.00 0.00 1.40
1664 1956 0.317436 GCGCGTTGTGTGGATCAAAA 60.317 50.000 8.43 0.00 0.00 2.44
1667 1959 3.047280 GGCGCGTTGTGTGGATCA 61.047 61.111 8.43 0.00 0.00 2.92
1722 2015 7.754625 TGAATTCGGGTAAAAACTAAGCATAC 58.245 34.615 0.04 0.00 0.00 2.39
1756 2055 1.570813 TGCACAGACTGTCAAACTCG 58.429 50.000 4.74 0.00 0.00 4.18
1757 2056 4.274459 AGAAATGCACAGACTGTCAAACTC 59.726 41.667 4.74 0.56 0.00 3.01
1761 2060 2.291465 GCAGAAATGCACAGACTGTCAA 59.709 45.455 4.74 0.00 34.41 3.18
1770 2069 1.228644 AGCAGGGCAGAAATGCACA 60.229 52.632 5.15 0.00 41.47 4.57
1800 2099 1.979155 CAGGGAGCAGACGACAGGA 60.979 63.158 0.00 0.00 0.00 3.86
1803 2102 0.611896 TGATCAGGGAGCAGACGACA 60.612 55.000 0.00 0.00 0.00 4.35
1826 2125 3.222354 CTATACAGCGGCGGGACCC 62.222 68.421 9.78 0.00 33.26 4.46
1838 2137 3.138625 GCGGAGGCTGCCTATACA 58.861 61.111 23.44 0.00 31.76 2.29
1868 2170 4.729856 GCCGAGGCGTACACGGTT 62.730 66.667 16.21 0.00 46.95 4.44
1928 2230 0.740868 GCTACCAGATGTTGCAGCGA 60.741 55.000 0.00 0.00 43.93 4.93
1950 2252 0.940126 AGAATCATCGTGCAATCCGC 59.060 50.000 0.00 0.00 42.89 5.54
1960 2262 1.273887 GCCGACGCAAGAATCATCG 59.726 57.895 0.00 0.00 43.62 3.84
1985 2287 0.991920 TGACCTTGAATGGGGACTCC 59.008 55.000 0.00 0.00 0.00 3.85
1992 2294 3.367703 GCCAAGATGTTGACCTTGAATGG 60.368 47.826 3.74 0.00 41.56 3.16
2022 2324 1.382522 GTGATGATCGCCACCAATGT 58.617 50.000 6.13 0.00 0.00 2.71
2037 2339 2.675317 CGCTCGAGGAAAAGAAGGTGAT 60.675 50.000 15.58 0.00 0.00 3.06
2058 2360 4.640789 TGATCGAAGAGAGAAAGGCTAC 57.359 45.455 0.00 0.00 43.63 3.58
2060 2362 3.181467 CCATGATCGAAGAGAGAAAGGCT 60.181 47.826 0.00 0.00 43.63 4.58
2109 2411 2.287457 TTAATGGAGGCGACGGACGG 62.287 60.000 1.66 0.00 42.83 4.79
2110 2412 0.249322 ATTAATGGAGGCGACGGACG 60.249 55.000 0.00 0.00 45.66 4.79
2111 2413 2.035576 ACTATTAATGGAGGCGACGGAC 59.964 50.000 5.74 0.00 0.00 4.79
2112 2414 2.313317 ACTATTAATGGAGGCGACGGA 58.687 47.619 5.74 0.00 0.00 4.69
2113 2415 2.814280 ACTATTAATGGAGGCGACGG 57.186 50.000 5.74 0.00 0.00 4.79
2114 2416 4.116961 TCAAACTATTAATGGAGGCGACG 58.883 43.478 5.74 0.00 0.00 5.12
2115 2417 5.220796 GGTTCAAACTATTAATGGAGGCGAC 60.221 44.000 5.74 0.00 0.00 5.19
2116 2418 4.879545 GGTTCAAACTATTAATGGAGGCGA 59.120 41.667 5.74 0.00 0.00 5.54
2117 2419 4.881850 AGGTTCAAACTATTAATGGAGGCG 59.118 41.667 5.74 0.00 0.00 5.52
2118 2420 6.122964 AGAGGTTCAAACTATTAATGGAGGC 58.877 40.000 5.74 0.00 0.00 4.70
2119 2421 6.768381 GGAGAGGTTCAAACTATTAATGGAGG 59.232 42.308 5.74 0.00 0.00 4.30
2120 2422 6.480320 CGGAGAGGTTCAAACTATTAATGGAG 59.520 42.308 5.74 0.00 0.00 3.86
2121 2423 6.346096 CGGAGAGGTTCAAACTATTAATGGA 58.654 40.000 5.74 0.00 0.00 3.41
2122 2424 5.007724 GCGGAGAGGTTCAAACTATTAATGG 59.992 44.000 0.00 0.00 0.00 3.16
2123 2425 5.007724 GGCGGAGAGGTTCAAACTATTAATG 59.992 44.000 0.00 0.00 0.00 1.90
2124 2426 5.104485 AGGCGGAGAGGTTCAAACTATTAAT 60.104 40.000 0.00 0.00 0.00 1.40
2125 2427 4.224370 AGGCGGAGAGGTTCAAACTATTAA 59.776 41.667 0.00 0.00 0.00 1.40
2126 2428 3.773119 AGGCGGAGAGGTTCAAACTATTA 59.227 43.478 0.00 0.00 0.00 0.98
2127 2429 2.572104 AGGCGGAGAGGTTCAAACTATT 59.428 45.455 0.00 0.00 0.00 1.73
2128 2430 2.188817 AGGCGGAGAGGTTCAAACTAT 58.811 47.619 0.00 0.00 0.00 2.12
2129 2431 1.640917 AGGCGGAGAGGTTCAAACTA 58.359 50.000 0.00 0.00 0.00 2.24
2130 2432 0.765510 AAGGCGGAGAGGTTCAAACT 59.234 50.000 0.00 0.00 0.00 2.66
2131 2433 1.157585 GAAGGCGGAGAGGTTCAAAC 58.842 55.000 0.00 0.00 0.00 2.93
2132 2434 1.056660 AGAAGGCGGAGAGGTTCAAA 58.943 50.000 0.00 0.00 0.00 2.69
2133 2435 1.002087 GAAGAAGGCGGAGAGGTTCAA 59.998 52.381 0.00 0.00 0.00 2.69
2134 2436 0.608640 GAAGAAGGCGGAGAGGTTCA 59.391 55.000 0.00 0.00 0.00 3.18
2135 2437 0.899019 AGAAGAAGGCGGAGAGGTTC 59.101 55.000 0.00 0.00 0.00 3.62
2136 2438 0.899019 GAGAAGAAGGCGGAGAGGTT 59.101 55.000 0.00 0.00 0.00 3.50
2137 2439 0.973496 GGAGAAGAAGGCGGAGAGGT 60.973 60.000 0.00 0.00 0.00 3.85
2138 2440 1.681486 GGGAGAAGAAGGCGGAGAGG 61.681 65.000 0.00 0.00 0.00 3.69
2139 2441 0.686112 AGGGAGAAGAAGGCGGAGAG 60.686 60.000 0.00 0.00 0.00 3.20
2140 2442 0.684805 GAGGGAGAAGAAGGCGGAGA 60.685 60.000 0.00 0.00 0.00 3.71
2141 2443 0.686112 AGAGGGAGAAGAAGGCGGAG 60.686 60.000 0.00 0.00 0.00 4.63
2142 2444 0.252284 AAGAGGGAGAAGAAGGCGGA 60.252 55.000 0.00 0.00 0.00 5.54
2143 2445 0.615850 AAAGAGGGAGAAGAAGGCGG 59.384 55.000 0.00 0.00 0.00 6.13
2144 2446 2.351455 GAAAAGAGGGAGAAGAAGGCG 58.649 52.381 0.00 0.00 0.00 5.52
2145 2447 2.307392 AGGAAAAGAGGGAGAAGAAGGC 59.693 50.000 0.00 0.00 0.00 4.35
2146 2448 3.368948 CGAGGAAAAGAGGGAGAAGAAGG 60.369 52.174 0.00 0.00 0.00 3.46
2147 2449 3.511934 TCGAGGAAAAGAGGGAGAAGAAG 59.488 47.826 0.00 0.00 0.00 2.85
2148 2450 3.507411 TCGAGGAAAAGAGGGAGAAGAA 58.493 45.455 0.00 0.00 0.00 2.52
2149 2451 3.093057 CTCGAGGAAAAGAGGGAGAAGA 58.907 50.000 3.91 0.00 0.00 2.87
2150 2452 2.418060 GCTCGAGGAAAAGAGGGAGAAG 60.418 54.545 15.58 0.00 35.19 2.85
2151 2453 1.550976 GCTCGAGGAAAAGAGGGAGAA 59.449 52.381 15.58 0.00 35.19 2.87
2152 2454 1.187087 GCTCGAGGAAAAGAGGGAGA 58.813 55.000 15.58 0.00 35.19 3.71
2153 2455 0.179124 CGCTCGAGGAAAAGAGGGAG 60.179 60.000 15.58 0.00 46.32 4.30
2154 2456 1.890894 CGCTCGAGGAAAAGAGGGA 59.109 57.895 15.58 0.00 46.32 4.20
2155 2457 1.811679 GCGCTCGAGGAAAAGAGGG 60.812 63.158 15.58 5.35 46.20 4.30
2156 2458 2.161486 CGCGCTCGAGGAAAAGAGG 61.161 63.158 15.58 0.00 38.10 3.69
2157 2459 2.161486 CCGCGCTCGAGGAAAAGAG 61.161 63.158 15.58 0.00 37.24 2.85
2158 2460 2.126071 CCGCGCTCGAGGAAAAGA 60.126 61.111 15.58 0.00 37.24 2.52
2159 2461 3.854459 GCCGCGCTCGAGGAAAAG 61.854 66.667 15.58 0.00 37.24 2.27
2171 2473 2.815647 GAAGACAGGAAGGCCGCG 60.816 66.667 0.00 0.00 39.96 6.46
2172 2474 2.815647 CGAAGACAGGAAGGCCGC 60.816 66.667 0.00 0.00 39.96 6.53
2173 2475 2.125512 CCGAAGACAGGAAGGCCG 60.126 66.667 0.00 0.00 39.96 6.13
2174 2476 1.079057 GACCGAAGACAGGAAGGCC 60.079 63.158 0.00 0.00 0.00 5.19
2175 2477 0.250513 ATGACCGAAGACAGGAAGGC 59.749 55.000 0.00 0.00 0.00 4.35
2176 2478 1.406069 CCATGACCGAAGACAGGAAGG 60.406 57.143 0.00 0.00 0.00 3.46
2177 2479 1.276421 ACCATGACCGAAGACAGGAAG 59.724 52.381 0.00 0.00 0.00 3.46
2178 2480 1.275291 GACCATGACCGAAGACAGGAA 59.725 52.381 0.00 0.00 0.00 3.36
2179 2481 0.895530 GACCATGACCGAAGACAGGA 59.104 55.000 0.00 0.00 0.00 3.86
2180 2482 0.608130 TGACCATGACCGAAGACAGG 59.392 55.000 0.00 0.00 0.00 4.00
2181 2483 2.544685 GATGACCATGACCGAAGACAG 58.455 52.381 0.00 0.00 0.00 3.51
2182 2484 1.207089 GGATGACCATGACCGAAGACA 59.793 52.381 0.00 0.00 35.97 3.41
2183 2485 1.482593 AGGATGACCATGACCGAAGAC 59.517 52.381 0.00 0.00 38.94 3.01
2184 2486 1.757118 GAGGATGACCATGACCGAAGA 59.243 52.381 0.00 0.00 38.94 2.87
2185 2487 1.759445 AGAGGATGACCATGACCGAAG 59.241 52.381 0.00 0.00 38.94 3.79
2186 2488 1.757118 GAGAGGATGACCATGACCGAA 59.243 52.381 0.00 0.00 38.94 4.30
2187 2489 1.063642 AGAGAGGATGACCATGACCGA 60.064 52.381 0.00 0.00 38.94 4.69
2188 2490 1.407936 AGAGAGGATGACCATGACCG 58.592 55.000 0.00 0.00 38.94 4.79
2189 2491 2.223923 CGAAGAGAGGATGACCATGACC 60.224 54.545 0.00 0.00 38.94 4.02
2190 2492 2.690497 TCGAAGAGAGGATGACCATGAC 59.310 50.000 0.00 0.00 38.94 3.06
2191 2493 3.018423 TCGAAGAGAGGATGACCATGA 57.982 47.619 0.00 0.00 38.94 3.07
2230 2532 0.523072 CAAACTGTTGATGGAGGCGG 59.477 55.000 0.00 0.00 36.83 6.13
2261 2563 4.956700 TCGGACATCAAGTAGGAGAAGAAT 59.043 41.667 0.00 0.00 0.00 2.40
2271 2573 0.892755 AAGCGGTCGGACATCAAGTA 59.107 50.000 10.76 0.00 0.00 2.24
2272 2574 0.389948 GAAGCGGTCGGACATCAAGT 60.390 55.000 10.76 0.00 0.00 3.16
2273 2575 0.389817 TGAAGCGGTCGGACATCAAG 60.390 55.000 10.76 0.00 0.00 3.02
2274 2576 0.669318 GTGAAGCGGTCGGACATCAA 60.669 55.000 10.76 0.00 0.00 2.57
2275 2577 1.080093 GTGAAGCGGTCGGACATCA 60.080 57.895 10.76 5.86 0.00 3.07
2276 2578 2.158959 CGTGAAGCGGTCGGACATC 61.159 63.158 10.76 3.37 36.85 3.06
2277 2579 2.126071 CGTGAAGCGGTCGGACAT 60.126 61.111 10.76 0.00 36.85 3.06
2295 2597 3.207669 GGCGAAGGAGCAGGCATG 61.208 66.667 0.00 0.00 39.27 4.06
2296 2598 3.272364 TTGGCGAAGGAGCAGGCAT 62.272 57.895 0.00 0.00 40.12 4.40
2297 2599 3.907260 CTTGGCGAAGGAGCAGGCA 62.907 63.158 0.00 0.00 39.27 4.75
2298 2600 2.883267 ATCTTGGCGAAGGAGCAGGC 62.883 60.000 8.73 0.00 39.27 4.85
2299 2601 1.222936 ATCTTGGCGAAGGAGCAGG 59.777 57.895 8.73 0.00 39.27 4.85
2300 2602 4.950479 ATCTTGGCGAAGGAGCAG 57.050 55.556 8.73 0.00 39.27 4.24


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

AutoCloner maintained by Alex Coulton.