Multiple sequence alignment - TraesCS4A01G337100

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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 TraesCS4A01G337100 chr4A 100.000 1797 0 0 810 2606 619333525 619335321 0.000000e+00 3319.0
1 TraesCS4A01G337100 chr4A 100.000 630 0 0 1 630 619332716 619333345 0.000000e+00 1164.0
2 TraesCS4A01G337100 chr4A 83.376 776 74 33 877 1629 619369937 619370680 0.000000e+00 667.0
3 TraesCS4A01G337100 chr4A 80.527 683 73 32 962 1624 619312298 619312940 1.090000e-128 470.0
4 TraesCS4A01G337100 chr4A 86.139 202 24 4 2248 2447 31396999 31397198 5.650000e-52 215.0
5 TraesCS4A01G337100 chr4A 86.139 202 25 2 2248 2449 286747780 286747582 5.650000e-52 215.0
6 TraesCS4A01G337100 chr4A 86.000 200 26 1 2248 2447 32114627 32114824 2.030000e-51 213.0
7 TraesCS4A01G337100 chr5D 88.854 960 44 28 813 1745 548460412 548461335 0.000000e+00 1122.0
8 TraesCS4A01G337100 chr5D 83.511 843 79 39 812 1629 548479500 548480307 0.000000e+00 732.0
9 TraesCS4A01G337100 chr5D 90.133 375 21 8 1866 2229 548461369 548461738 8.440000e-130 473.0
10 TraesCS4A01G337100 chr5D 86.047 215 10 9 425 627 548460100 548460306 2.030000e-51 213.0
11 TraesCS4A01G337100 chr5D 85.068 221 18 11 414 627 548479195 548479407 7.310000e-51 211.0
12 TraesCS4A01G337100 chr5D 81.100 291 21 11 1328 1618 548374349 548374605 4.400000e-48 202.0
13 TraesCS4A01G337100 chr5D 82.759 116 14 3 31 146 548468173 548468282 5.940000e-17 99.0
14 TraesCS4A01G337100 chr5D 97.826 46 1 0 1708 1753 548368544 548368589 2.150000e-11 80.5
15 TraesCS4A01G337100 chr5D 93.333 45 2 1 169 213 548460033 548460076 6.020000e-07 65.8
16 TraesCS4A01G337100 chr5D 90.909 44 4 0 1708 1751 548374849 548374892 2.800000e-05 60.2
17 TraesCS4A01G337100 chr5B 89.633 762 53 11 1003 1745 692678727 692679481 0.000000e+00 946.0
18 TraesCS4A01G337100 chr5B 83.733 750 64 35 880 1610 692691084 692691794 0.000000e+00 656.0
19 TraesCS4A01G337100 chr5B 88.017 242 21 2 1817 2051 692679477 692679717 1.970000e-71 279.0
20 TraesCS4A01G337100 chr5B 88.210 229 20 3 3 227 692677769 692677994 1.540000e-67 267.0
21 TraesCS4A01G337100 chr5B 87.766 188 21 2 2044 2230 692679746 692679932 4.370000e-53 219.0
22 TraesCS4A01G337100 chr5B 88.415 164 15 4 465 627 692690785 692690945 7.360000e-46 195.0
23 TraesCS4A01G337100 chr5B 87.324 142 18 0 2465 2606 692681145 692681286 2.080000e-36 163.0
24 TraesCS4A01G337100 chr5B 76.159 302 46 16 862 1151 692648702 692648989 4.520000e-28 135.0
25 TraesCS4A01G337100 chr5B 92.771 83 6 0 2147 2229 155715217 155715135 1.270000e-23 121.0
26 TraesCS4A01G337100 chr5B 95.652 46 2 0 1708 1753 692635794 692635839 1.000000e-09 75.0
27 TraesCS4A01G337100 chr5B 100.000 29 0 0 810 838 692691039 692691067 1.000000e-03 54.7
28 TraesCS4A01G337100 chr5A 88.614 202 19 3 2248 2447 388578128 388577929 2.590000e-60 243.0
29 TraesCS4A01G337100 chr5A 86.000 200 26 2 2248 2447 703663990 703663793 2.030000e-51 213.0
30 TraesCS4A01G337100 chr5A 86.792 53 7 0 2447 2499 523936847 523936795 2.800000e-05 60.2
31 TraesCS4A01G337100 chr2A 87.000 200 24 1 2248 2447 65676017 65675820 9.390000e-55 224.0
32 TraesCS4A01G337100 chr6D 86.500 200 25 2 2248 2447 71936506 71936309 4.370000e-53 219.0
33 TraesCS4A01G337100 chr6D 91.954 87 6 1 2144 2229 296197007 296196921 1.270000e-23 121.0
34 TraesCS4A01G337100 chr3A 86.500 200 25 2 2248 2447 627272173 627271976 4.370000e-53 219.0
35 TraesCS4A01G337100 chr1A 86.598 194 24 1 2248 2441 490778266 490778075 2.030000e-51 213.0
36 TraesCS4A01G337100 chr1A 93.827 81 5 0 2148 2228 91162182 91162262 3.520000e-24 122.0
37 TraesCS4A01G337100 chrUn 92.771 83 6 0 2147 2229 90452956 90453038 1.270000e-23 121.0
38 TraesCS4A01G337100 chr6B 91.860 86 7 0 2144 2229 530128963 530129048 1.270000e-23 121.0
39 TraesCS4A01G337100 chr3D 92.771 83 6 0 2147 2229 315480577 315480495 1.270000e-23 121.0
40 TraesCS4A01G337100 chr1D 94.805 77 4 0 2153 2229 289395162 289395086 1.270000e-23 121.0
41 TraesCS4A01G337100 chr2B 91.379 58 5 0 2443 2500 101416714 101416771 2.150000e-11 80.5
42 TraesCS4A01G337100 chr2B 91.379 58 5 0 2443 2500 101430614 101430671 2.150000e-11 80.5
43 TraesCS4A01G337100 chr2B 92.308 52 4 0 2447 2498 101443269 101443320 1.000000e-09 75.0


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 TraesCS4A01G337100 chr4A 619332716 619335321 2605 False 2241.50 3319 100.00000 1 2606 2 chr4A.!!$F5 2605
1 TraesCS4A01G337100 chr4A 619369937 619370680 743 False 667.00 667 83.37600 877 1629 1 chr4A.!!$F4 752
2 TraesCS4A01G337100 chr4A 619312298 619312940 642 False 470.00 470 80.52700 962 1624 1 chr4A.!!$F3 662
3 TraesCS4A01G337100 chr5D 548479195 548480307 1112 False 471.50 732 84.28950 414 1629 2 chr5D.!!$F5 1215
4 TraesCS4A01G337100 chr5D 548460033 548461738 1705 False 468.45 1122 89.59175 169 2229 4 chr5D.!!$F4 2060
5 TraesCS4A01G337100 chr5B 692677769 692681286 3517 False 374.80 946 88.19000 3 2606 5 chr5B.!!$F3 2603
6 TraesCS4A01G337100 chr5B 692690785 692691794 1009 False 301.90 656 90.71600 465 1610 3 chr5B.!!$F4 1145

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
856 955 0.251519 CCTTGCCTTGCTTTCCCTCT 60.252 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1982 0.037232 ACCGGTCTACAGCAAAGCTC 60.037 55.0 0.0 0.0 36.4 4.09 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
34 35 2.038837 GGGTTGGCCACTCGTTAGC 61.039 63.158 3.88 0.00 36.17 3.09
38 39 2.202756 GGCCACTCGTTAGCCTCG 60.203 66.667 0.00 0.00 43.62 4.63
48 49 0.738975 GTTAGCCTCGCCAAAATCCC 59.261 55.000 0.00 0.00 0.00 3.85
49 50 0.746563 TTAGCCTCGCCAAAATCCCG 60.747 55.000 0.00 0.00 0.00 5.14
68 69 2.546373 CCGCCCATTATCAAATTGCTGG 60.546 50.000 0.00 0.00 0.00 4.85
102 103 8.431910 TCATTTGGATGAGATGATGATAGAGA 57.568 34.615 0.00 0.00 37.37 3.10
115 116 6.773638 TGATGATAGAGATAGCCCTTTTTCC 58.226 40.000 0.00 0.00 0.00 3.13
118 119 7.213178 TGATAGAGATAGCCCTTTTTCCTTT 57.787 36.000 0.00 0.00 0.00 3.11
218 223 2.125952 CTGCATGACGCGTCCAGA 60.126 61.111 34.34 18.30 46.97 3.86
227 232 2.456119 CGCGTCCAGAGCATGAACC 61.456 63.158 0.00 0.00 34.19 3.62
228 233 1.375908 GCGTCCAGAGCATGAACCA 60.376 57.895 0.00 0.00 34.19 3.67
233 238 1.704628 TCCAGAGCATGAACCAGGAAA 59.295 47.619 0.00 0.00 0.00 3.13
234 239 1.815003 CCAGAGCATGAACCAGGAAAC 59.185 52.381 0.00 0.00 0.00 2.78
235 240 2.507484 CAGAGCATGAACCAGGAAACA 58.493 47.619 0.00 0.00 0.00 2.83
236 241 3.087031 CAGAGCATGAACCAGGAAACAT 58.913 45.455 0.00 0.00 0.00 2.71
237 242 3.087031 AGAGCATGAACCAGGAAACATG 58.913 45.455 15.62 15.62 41.72 3.21
239 244 2.267188 CATGAACCAGGAAACATGCG 57.733 50.000 0.00 0.00 34.76 4.73
243 248 0.667993 AACCAGGAAACATGCGTGTG 59.332 50.000 13.39 0.97 38.92 3.82
248 290 1.603802 AGGAAACATGCGTGTGTTCAG 59.396 47.619 23.34 0.00 41.22 3.02
251 293 3.434637 GAAACATGCGTGTGTTCAGTTT 58.565 40.909 13.39 0.45 41.22 2.66
257 299 4.530094 TGCGTGTGTTCAGTTTTTCTAG 57.470 40.909 0.00 0.00 0.00 2.43
265 307 7.065923 GTGTGTTCAGTTTTTCTAGGAAGACTT 59.934 37.037 4.18 0.00 34.14 3.01
268 310 6.619801 TCAGTTTTTCTAGGAAGACTTTGC 57.380 37.500 4.18 0.00 0.00 3.68
300 370 3.275143 TCCGCGATAATTTTGGATGTGT 58.725 40.909 8.23 0.00 0.00 3.72
301 371 3.064682 TCCGCGATAATTTTGGATGTGTG 59.935 43.478 8.23 0.00 0.00 3.82
303 373 3.730362 CGCGATAATTTTGGATGTGTGCA 60.730 43.478 0.00 0.00 0.00 4.57
304 374 4.362279 GCGATAATTTTGGATGTGTGCAT 58.638 39.130 0.00 0.00 38.18 3.96
320 392 3.564218 ATCCCGGGATGCAGAGGC 61.564 66.667 35.53 0.00 41.68 4.70
332 404 1.614241 GCAGAGGCCCGGAAGAGTTA 61.614 60.000 0.73 0.00 0.00 2.24
364 442 2.885894 TGTAAAACCATGACCCGGAAAC 59.114 45.455 0.73 0.00 0.00 2.78
367 445 0.887387 AACCATGACCCGGAAACACG 60.887 55.000 0.73 0.00 0.00 4.49
378 456 1.538634 CGGAAACACGTACTCCCACAA 60.539 52.381 0.00 0.00 0.00 3.33
379 457 1.869132 GGAAACACGTACTCCCACAAC 59.131 52.381 0.00 0.00 0.00 3.32
380 458 2.484241 GGAAACACGTACTCCCACAACT 60.484 50.000 0.00 0.00 0.00 3.16
381 459 3.243839 GGAAACACGTACTCCCACAACTA 60.244 47.826 0.00 0.00 0.00 2.24
382 460 4.370917 GAAACACGTACTCCCACAACTAA 58.629 43.478 0.00 0.00 0.00 2.24
383 461 4.612264 AACACGTACTCCCACAACTAAT 57.388 40.909 0.00 0.00 0.00 1.73
384 462 4.612264 ACACGTACTCCCACAACTAATT 57.388 40.909 0.00 0.00 0.00 1.40
385 463 4.964593 ACACGTACTCCCACAACTAATTT 58.035 39.130 0.00 0.00 0.00 1.82
386 464 4.753107 ACACGTACTCCCACAACTAATTTG 59.247 41.667 0.00 0.00 41.49 2.32
387 465 4.992319 CACGTACTCCCACAACTAATTTGA 59.008 41.667 0.00 0.00 38.73 2.69
393 471 4.527944 TCCCACAACTAATTTGACACACA 58.472 39.130 0.00 0.00 38.73 3.72
397 475 5.392487 CCACAACTAATTTGACACACACACA 60.392 40.000 0.00 0.00 38.73 3.72
401 479 4.697828 ACTAATTTGACACACACACACACA 59.302 37.500 0.00 0.00 0.00 3.72
405 483 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
406 484 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
408 486 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
410 488 1.136000 CACACACACACACACACACTG 60.136 52.381 0.00 0.00 0.00 3.66
455 537 4.376819 GCATGACACGACAAAGAGAAAGAG 60.377 45.833 0.00 0.00 0.00 2.85
460 548 4.233789 CACGACAAAGAGAAAGAGGAGAG 58.766 47.826 0.00 0.00 0.00 3.20
491 579 1.153568 GCGTGCTGCATCCACTAGA 60.154 57.895 5.27 0.00 45.45 2.43
494 582 1.068281 CGTGCTGCATCCACTAGAGAT 59.932 52.381 5.27 0.00 0.00 2.75
521 618 1.243342 CGCCAAATCAAGCTCACCCA 61.243 55.000 0.00 0.00 0.00 4.51
522 619 0.529378 GCCAAATCAAGCTCACCCAG 59.471 55.000 0.00 0.00 0.00 4.45
607 704 3.381272 CAGCAACAAGAGAAAGGAAACCA 59.619 43.478 0.00 0.00 0.00 3.67
609 706 3.792124 GCAACAAGAGAAAGGAAACCACG 60.792 47.826 0.00 0.00 0.00 4.94
611 708 1.069906 CAAGAGAAAGGAAACCACGCG 60.070 52.381 3.53 3.53 0.00 6.01
615 714 0.790814 GAAAGGAAACCACGCGAGAG 59.209 55.000 15.93 2.63 0.00 3.20
627 726 3.408150 CACGCGAGAGAAAAGCAATTAC 58.592 45.455 15.93 0.00 0.00 1.89
855 954 0.540597 ACCTTGCCTTGCTTTCCCTC 60.541 55.000 0.00 0.00 0.00 4.30
856 955 0.251519 CCTTGCCTTGCTTTCCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
857 956 1.625511 CTTGCCTTGCTTTCCCTCTT 58.374 50.000 0.00 0.00 0.00 2.85
858 957 1.966354 CTTGCCTTGCTTTCCCTCTTT 59.034 47.619 0.00 0.00 0.00 2.52
875 974 2.124507 TTTTGCTCTCCTCCCGTGGG 62.125 60.000 0.00 0.00 0.00 4.61
920 1019 3.334691 CCAAGAACGCAACTCCATTCTA 58.665 45.455 0.00 0.00 31.20 2.10
923 1026 4.207891 AGAACGCAACTCCATTCTACAT 57.792 40.909 0.00 0.00 29.63 2.29
924 1027 4.184629 AGAACGCAACTCCATTCTACATC 58.815 43.478 0.00 0.00 29.63 3.06
926 1029 4.207891 ACGCAACTCCATTCTACATCTT 57.792 40.909 0.00 0.00 0.00 2.40
1007 1131 2.363795 TCCGGCTCCGATGAAGGT 60.364 61.111 10.28 0.00 42.83 3.50
1093 1217 1.371558 GACCCGCTCCACAAGAAGT 59.628 57.895 0.00 0.00 0.00 3.01
1138 1274 2.606519 CCGACAACCCCTCCTCCA 60.607 66.667 0.00 0.00 0.00 3.86
1146 1282 2.529136 CCCTCCTCCACCACCACA 60.529 66.667 0.00 0.00 0.00 4.17
1151 1290 1.065410 TCCTCCACCACCACAACCAT 61.065 55.000 0.00 0.00 0.00 3.55
1632 1860 1.026584 TTCTCCATTGCCATGCATCG 58.973 50.000 0.00 0.00 38.76 3.84
1638 1866 2.555325 CCATTGCCATGCATCGTAATCT 59.445 45.455 4.72 0.00 38.76 2.40
1648 1876 3.951680 TGCATCGTAATCTACCTCACTCA 59.048 43.478 0.00 0.00 0.00 3.41
1659 1887 1.226267 CTCACTCAGCTCGAGCGAC 60.226 63.158 30.39 6.07 46.63 5.19
1688 1918 1.376553 GCCCAAGACTGACTGAGGC 60.377 63.158 5.28 5.28 39.36 4.70
1762 1992 4.368391 ACGGAGTGAGCTTTGCTG 57.632 55.556 0.00 0.00 42.51 4.41
1763 1993 1.447643 ACGGAGTGAGCTTTGCTGT 59.552 52.632 0.00 0.00 42.51 4.40
1764 1994 0.679505 ACGGAGTGAGCTTTGCTGTA 59.320 50.000 0.00 0.00 42.51 2.74
1765 1995 1.337260 ACGGAGTGAGCTTTGCTGTAG 60.337 52.381 0.00 0.00 42.51 2.74
1766 1996 1.067565 CGGAGTGAGCTTTGCTGTAGA 60.068 52.381 0.00 0.00 39.88 2.59
1767 1997 2.342179 GGAGTGAGCTTTGCTGTAGAC 58.658 52.381 0.00 0.00 39.88 2.59
1768 1998 2.342179 GAGTGAGCTTTGCTGTAGACC 58.658 52.381 0.00 0.00 39.88 3.85
1769 1999 1.071605 GTGAGCTTTGCTGTAGACCG 58.928 55.000 0.00 0.00 39.88 4.79
1770 2000 0.037326 TGAGCTTTGCTGTAGACCGG 60.037 55.000 0.00 0.00 39.88 5.28
1771 2001 0.037232 GAGCTTTGCTGTAGACCGGT 60.037 55.000 6.92 6.92 39.88 5.28
1772 2002 0.320771 AGCTTTGCTGTAGACCGGTG 60.321 55.000 14.63 0.00 37.57 4.94
1773 2003 0.602905 GCTTTGCTGTAGACCGGTGT 60.603 55.000 14.63 12.06 0.00 4.16
1774 2004 1.148310 CTTTGCTGTAGACCGGTGTG 58.852 55.000 14.63 0.00 0.00 3.82
1775 2005 0.466543 TTTGCTGTAGACCGGTGTGT 59.533 50.000 14.63 0.00 0.00 3.72
1776 2006 0.249699 TTGCTGTAGACCGGTGTGTG 60.250 55.000 14.63 3.74 0.00 3.82
1777 2007 1.110518 TGCTGTAGACCGGTGTGTGA 61.111 55.000 14.63 0.00 0.00 3.58
1778 2008 0.666577 GCTGTAGACCGGTGTGTGAC 60.667 60.000 14.63 3.47 0.00 3.67
1779 2009 0.671796 CTGTAGACCGGTGTGTGACA 59.328 55.000 14.63 8.99 0.00 3.58
1780 2010 1.067974 CTGTAGACCGGTGTGTGACAA 59.932 52.381 14.63 0.00 0.00 3.18
1781 2011 1.067974 TGTAGACCGGTGTGTGACAAG 59.932 52.381 14.63 0.00 0.00 3.16
1782 2012 0.677288 TAGACCGGTGTGTGACAAGG 59.323 55.000 14.63 0.00 35.24 3.61
1783 2013 2.203153 ACCGGTGTGTGACAAGGC 60.203 61.111 6.12 0.00 33.23 4.35
1784 2014 3.345808 CCGGTGTGTGACAAGGCG 61.346 66.667 0.00 0.00 0.00 5.52
1785 2015 2.279851 CGGTGTGTGACAAGGCGA 60.280 61.111 0.00 0.00 0.00 5.54
1786 2016 2.594962 CGGTGTGTGACAAGGCGAC 61.595 63.158 0.00 0.00 0.00 5.19
1787 2017 1.522806 GGTGTGTGACAAGGCGACA 60.523 57.895 0.00 0.00 0.00 4.35
1788 2018 1.641677 GTGTGTGACAAGGCGACAC 59.358 57.895 0.00 0.00 40.38 3.67
1789 2019 0.810031 GTGTGTGACAAGGCGACACT 60.810 55.000 0.00 0.00 40.42 3.55
1790 2020 0.107897 TGTGTGACAAGGCGACACTT 60.108 50.000 0.00 0.00 40.42 3.16
1796 2026 3.532138 CAAGGCGACACTTGTGTTG 57.468 52.632 14.87 14.87 42.18 3.33
1797 2027 0.732571 CAAGGCGACACTTGTGTTGT 59.267 50.000 18.84 1.74 42.18 3.32
1798 2028 0.732571 AAGGCGACACTTGTGTTGTG 59.267 50.000 18.84 9.26 40.87 3.33
1799 2029 0.107897 AGGCGACACTTGTGTTGTGA 60.108 50.000 18.84 0.00 38.65 3.58
1800 2030 0.304705 GGCGACACTTGTGTTGTGAG 59.695 55.000 18.84 6.50 38.65 3.51
1801 2031 1.286501 GCGACACTTGTGTTGTGAGA 58.713 50.000 18.84 0.00 38.65 3.27
1802 2032 1.258982 GCGACACTTGTGTTGTGAGAG 59.741 52.381 18.84 3.79 38.65 3.20
1803 2033 1.258982 CGACACTTGTGTTGTGAGAGC 59.741 52.381 7.87 0.00 38.65 4.09
1804 2034 2.279741 GACACTTGTGTTGTGAGAGCA 58.720 47.619 7.87 0.00 38.65 4.26
1805 2035 2.283298 ACACTTGTGTTGTGAGAGCAG 58.717 47.619 0.00 0.00 38.65 4.24
1806 2036 1.600957 CACTTGTGTTGTGAGAGCAGG 59.399 52.381 0.00 0.00 37.60 4.85
1807 2037 0.590195 CTTGTGTTGTGAGAGCAGGC 59.410 55.000 0.00 0.00 0.00 4.85
1808 2038 0.107263 TTGTGTTGTGAGAGCAGGCA 60.107 50.000 0.00 0.00 0.00 4.75
1809 2039 0.109153 TGTGTTGTGAGAGCAGGCAT 59.891 50.000 0.00 0.00 0.00 4.40
1810 2040 0.520404 GTGTTGTGAGAGCAGGCATG 59.480 55.000 0.00 0.00 0.00 4.06
1811 2041 0.607217 TGTTGTGAGAGCAGGCATGG 60.607 55.000 0.00 0.00 0.00 3.66
1812 2042 1.001764 TTGTGAGAGCAGGCATGGG 60.002 57.895 0.00 0.00 0.00 4.00
1813 2043 2.827642 GTGAGAGCAGGCATGGGC 60.828 66.667 0.00 0.00 40.13 5.36
1814 2044 3.332385 TGAGAGCAGGCATGGGCA 61.332 61.111 0.00 0.00 43.71 5.36
1815 2045 2.195139 GAGAGCAGGCATGGGCAT 59.805 61.111 0.00 0.00 43.71 4.40
1832 2062 0.179026 CATGGCTGGCAGCTGTAGAT 60.179 55.000 35.73 18.19 41.99 1.98
1841 2071 2.294791 GGCAGCTGTAGATAGTGTCGAT 59.705 50.000 16.64 0.00 0.00 3.59
1888 2118 6.804295 CGGAGAAGAAGAGAATATATTCGTGG 59.196 42.308 17.69 0.00 41.56 4.94
1893 2123 7.526142 AGAAGAGAATATATTCGTGGCTGTA 57.474 36.000 17.69 0.00 41.56 2.74
1897 2127 6.429078 AGAGAATATATTCGTGGCTGTACGTA 59.571 38.462 17.69 0.00 44.06 3.57
1898 2128 6.376978 AGAATATATTCGTGGCTGTACGTAC 58.623 40.000 18.90 18.90 44.06 3.67
1912 2142 2.126189 GTACTCGCCGTGACACCC 60.126 66.667 0.00 0.00 0.00 4.61
1913 2143 2.282674 TACTCGCCGTGACACCCT 60.283 61.111 0.00 0.00 0.00 4.34
2035 2281 2.218603 CAGAGTTGGCACGTTACCTTT 58.781 47.619 5.98 0.00 0.00 3.11
2104 2386 6.399743 TGATGAATTGATGATGGTGTTTTGG 58.600 36.000 0.00 0.00 0.00 3.28
2122 2404 7.118535 GTGTTTTGGTGAGGTTTGTAACAAATT 59.881 33.333 0.00 0.00 0.00 1.82
2137 2419 2.452366 AAATTGGTGTTCGCGTCGCC 62.452 55.000 22.21 22.21 36.18 5.54
2150 2432 4.812476 TCGCCGCATGGTTCTCCG 62.812 66.667 0.00 0.00 37.67 4.63
2230 2513 9.979270 CTGAAATGAGTGAACAAACATACTATC 57.021 33.333 0.00 0.00 0.00 2.08
2231 2514 9.725019 TGAAATGAGTGAACAAACATACTATCT 57.275 29.630 0.00 0.00 0.00 1.98
2234 2517 7.812309 TGAGTGAACAAACATACTATCTTCG 57.188 36.000 0.00 0.00 0.00 3.79
2236 2519 6.931838 AGTGAACAAACATACTATCTTCGGA 58.068 36.000 0.00 0.00 0.00 4.55
2237 2520 7.383687 AGTGAACAAACATACTATCTTCGGAA 58.616 34.615 0.00 0.00 0.00 4.30
2238 2521 7.331193 AGTGAACAAACATACTATCTTCGGAAC 59.669 37.037 0.00 0.00 0.00 3.62
2239 2522 6.592607 TGAACAAACATACTATCTTCGGAACC 59.407 38.462 0.00 0.00 0.00 3.62
2240 2523 5.425630 ACAAACATACTATCTTCGGAACCC 58.574 41.667 0.00 0.00 0.00 4.11
2241 2524 5.189145 ACAAACATACTATCTTCGGAACCCT 59.811 40.000 0.00 0.00 0.00 4.34
2243 2526 5.952347 ACATACTATCTTCGGAACCCTTT 57.048 39.130 0.00 0.00 0.00 3.11
2244 2527 6.309389 ACATACTATCTTCGGAACCCTTTT 57.691 37.500 0.00 0.00 0.00 2.27
2245 2528 6.718294 ACATACTATCTTCGGAACCCTTTTT 58.282 36.000 0.00 0.00 0.00 1.94
2246 2529 6.598064 ACATACTATCTTCGGAACCCTTTTTG 59.402 38.462 0.00 0.00 0.00 2.44
2249 2532 3.284793 TCTTCGGAACCCTTTTTGTGA 57.715 42.857 0.00 0.00 0.00 3.58
2250 2533 2.946990 TCTTCGGAACCCTTTTTGTGAC 59.053 45.455 0.00 0.00 0.00 3.67
2252 2535 3.842007 TCGGAACCCTTTTTGTGACTA 57.158 42.857 0.00 0.00 0.00 2.59
2254 2537 4.525024 TCGGAACCCTTTTTGTGACTAAA 58.475 39.130 0.00 0.00 0.00 1.85
2255 2538 5.134661 TCGGAACCCTTTTTGTGACTAAAT 58.865 37.500 0.00 0.00 0.00 1.40
2256 2539 5.595133 TCGGAACCCTTTTTGTGACTAAATT 59.405 36.000 0.00 0.00 0.00 1.82
2257 2540 6.097129 TCGGAACCCTTTTTGTGACTAAATTT 59.903 34.615 0.00 0.00 0.00 1.82
2258 2541 7.284944 TCGGAACCCTTTTTGTGACTAAATTTA 59.715 33.333 0.00 0.00 0.00 1.40
2259 2542 8.085909 CGGAACCCTTTTTGTGACTAAATTTAT 58.914 33.333 0.00 0.00 0.00 1.40
2287 2570 6.743575 AGAAATACCAACATCAACAGTAGC 57.256 37.500 0.00 0.00 0.00 3.58
2289 2572 6.714810 AGAAATACCAACATCAACAGTAGCAA 59.285 34.615 0.00 0.00 0.00 3.91
2290 2573 6.892658 AATACCAACATCAACAGTAGCAAA 57.107 33.333 0.00 0.00 0.00 3.68
2291 2574 7.466746 AATACCAACATCAACAGTAGCAAAT 57.533 32.000 0.00 0.00 0.00 2.32
2292 2575 8.574251 AATACCAACATCAACAGTAGCAAATA 57.426 30.769 0.00 0.00 0.00 1.40
2293 2576 8.752005 ATACCAACATCAACAGTAGCAAATAT 57.248 30.769 0.00 0.00 0.00 1.28
2294 2577 9.845740 ATACCAACATCAACAGTAGCAAATATA 57.154 29.630 0.00 0.00 0.00 0.86
2350 2633 9.377312 TCTAACAATATTGATTTGACATCGTGA 57.623 29.630 22.16 0.78 0.00 4.35
2351 2634 9.986833 CTAACAATATTGATTTGACATCGTGAA 57.013 29.630 22.16 0.00 0.00 3.18
2353 2636 8.845942 ACAATATTGATTTGACATCGTGAATG 57.154 30.769 22.16 0.00 41.48 2.67
2397 3055 9.047947 AGAAGTTGGGTCAAAGTATAGATAGTT 57.952 33.333 0.00 0.00 0.00 2.24
2422 3080 8.725405 TTGACTTCGGATAAAACTTATATGCA 57.275 30.769 0.00 0.00 0.00 3.96
2424 3082 9.168451 TGACTTCGGATAAAACTTATATGCAAA 57.832 29.630 0.00 0.00 0.00 3.68
2437 3095 9.884636 AACTTATATGCAAATTAAAAAGGACCC 57.115 29.630 0.00 0.00 0.00 4.46
2438 3096 8.194769 ACTTATATGCAAATTAAAAAGGACCCG 58.805 33.333 0.00 0.00 0.00 5.28
2439 3097 6.783708 ATATGCAAATTAAAAAGGACCCGA 57.216 33.333 0.00 0.00 0.00 5.14
2440 3098 4.513198 TGCAAATTAAAAAGGACCCGAG 57.487 40.909 0.00 0.00 0.00 4.63
2442 3100 3.368013 GCAAATTAAAAAGGACCCGAGGG 60.368 47.826 6.63 6.63 42.03 4.30
2443 3101 4.083565 CAAATTAAAAAGGACCCGAGGGA 58.916 43.478 16.26 0.00 38.96 4.20
2456 3732 1.477295 CCGAGGGAGTAAGTTGAGGTC 59.523 57.143 0.00 0.00 0.00 3.85
2459 3735 2.498078 GAGGGAGTAAGTTGAGGTCTGG 59.502 54.545 0.00 0.00 0.00 3.86
2465 3741 2.736670 AAGTTGAGGTCTGGCAAAGT 57.263 45.000 0.00 0.00 0.00 2.66
2466 3742 1.972872 AGTTGAGGTCTGGCAAAGTG 58.027 50.000 0.00 0.00 0.00 3.16
2467 3743 1.212935 AGTTGAGGTCTGGCAAAGTGT 59.787 47.619 0.00 0.00 0.00 3.55
2468 3744 1.334869 GTTGAGGTCTGGCAAAGTGTG 59.665 52.381 0.00 0.00 0.00 3.82
2469 3745 0.179020 TGAGGTCTGGCAAAGTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
2505 3781 1.145571 ACCAAACAGCCCCTAAGTCA 58.854 50.000 0.00 0.00 0.00 3.41
2508 3784 1.145571 AAACAGCCCCTAAGTCACCA 58.854 50.000 0.00 0.00 0.00 4.17
2512 3788 2.038837 GCCCCTAAGTCACCAACGC 61.039 63.158 0.00 0.00 0.00 4.84
2513 3789 1.376812 CCCCTAAGTCACCAACGCC 60.377 63.158 0.00 0.00 0.00 5.68
2530 3806 1.469940 CGCCAAGAAGTATCGAGCACT 60.470 52.381 0.00 0.00 0.00 4.40
2539 3815 0.037697 TATCGAGCACTGCAAACCGT 60.038 50.000 3.30 0.00 0.00 4.83
2541 3817 1.956170 CGAGCACTGCAAACCGTCT 60.956 57.895 3.30 0.00 0.00 4.18
2554 3830 4.194640 CAAACCGTCTGATTGGAGATGAT 58.805 43.478 5.98 0.00 31.50 2.45
2556 3832 3.033909 ACCGTCTGATTGGAGATGATCA 58.966 45.455 0.00 0.00 31.50 2.92
2571 3847 1.805943 TGATCATTGACACGGCAGTTG 59.194 47.619 0.00 0.00 0.00 3.16
2593 3869 2.159037 GCCACTAAGAAACGGTAAGTGC 59.841 50.000 0.00 0.00 36.96 4.40
2597 3873 0.584876 AAGAAACGGTAAGTGCGTGC 59.415 50.000 0.00 0.00 0.00 5.34
2601 3877 2.430244 CGGTAAGTGCGTGCGAGT 60.430 61.111 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.565307 CAACCCAACCACCTGCATATAT 58.435 45.455 0.00 0.00 0.00 0.86
1 2 2.357673 CCAACCCAACCACCTGCATATA 60.358 50.000 0.00 0.00 0.00 0.86
34 35 3.518068 GGCGGGATTTTGGCGAGG 61.518 66.667 0.00 0.00 0.00 4.63
38 39 1.000843 GATAATGGGCGGGATTTTGGC 59.999 52.381 0.00 0.00 0.00 4.52
48 49 2.101249 ACCAGCAATTTGATAATGGGCG 59.899 45.455 0.00 0.00 32.86 6.13
49 50 3.118665 ACACCAGCAATTTGATAATGGGC 60.119 43.478 0.00 0.00 31.95 5.36
68 69 8.442632 TCATCTCATCCAAATGAAATCTACAC 57.557 34.615 0.00 0.00 41.33 2.90
98 99 6.209589 GTGAAAAAGGAAAAAGGGCTATCTCT 59.790 38.462 0.00 0.00 0.00 3.10
102 103 6.493189 TTGTGAAAAAGGAAAAAGGGCTAT 57.507 33.333 0.00 0.00 0.00 2.97
104 105 4.769688 CTTGTGAAAAAGGAAAAAGGGCT 58.230 39.130 0.00 0.00 0.00 5.19
227 232 1.333308 TGAACACACGCATGTTTCCTG 59.667 47.619 6.36 0.00 42.89 3.86
228 233 1.603802 CTGAACACACGCATGTTTCCT 59.396 47.619 6.36 0.00 42.89 3.36
233 238 3.128589 AGAAAAACTGAACACACGCATGT 59.871 39.130 0.00 0.00 40.80 3.21
234 239 3.694734 AGAAAAACTGAACACACGCATG 58.305 40.909 0.00 0.00 0.00 4.06
235 240 4.024048 CCTAGAAAAACTGAACACACGCAT 60.024 41.667 0.00 0.00 0.00 4.73
236 241 3.311322 CCTAGAAAAACTGAACACACGCA 59.689 43.478 0.00 0.00 0.00 5.24
237 242 3.558418 TCCTAGAAAAACTGAACACACGC 59.442 43.478 0.00 0.00 0.00 5.34
239 244 6.539103 AGTCTTCCTAGAAAAACTGAACACAC 59.461 38.462 0.00 0.00 30.65 3.82
243 248 6.913132 GCAAAGTCTTCCTAGAAAAACTGAAC 59.087 38.462 0.00 0.00 30.65 3.18
248 290 7.731882 ACTAGCAAAGTCTTCCTAGAAAAAC 57.268 36.000 19.43 0.00 30.33 2.43
265 307 3.458163 CGGAGCCCGGACTAGCAA 61.458 66.667 0.73 0.00 44.15 3.91
303 373 3.564218 GCCTCTGCATCCCGGGAT 61.564 66.667 31.20 31.20 37.47 3.85
309 379 3.764160 CTTCCGGGCCTCTGCATCC 62.764 68.421 0.84 0.00 40.13 3.51
320 392 0.912968 AAGGGGGTAACTCTTCCGGG 60.913 60.000 0.00 0.00 37.10 5.73
342 414 2.188062 TCCGGGTCATGGTTTTACAC 57.812 50.000 0.00 0.00 0.00 2.90
343 415 2.885894 GTTTCCGGGTCATGGTTTTACA 59.114 45.455 0.00 0.00 0.00 2.41
364 442 4.992319 TCAAATTAGTTGTGGGAGTACGTG 59.008 41.667 0.00 0.00 38.47 4.49
367 445 5.761234 TGTGTCAAATTAGTTGTGGGAGTAC 59.239 40.000 0.00 0.00 38.47 2.73
378 456 4.697828 TGTGTGTGTGTGTGTCAAATTAGT 59.302 37.500 0.00 0.00 0.00 2.24
379 457 5.027737 GTGTGTGTGTGTGTGTCAAATTAG 58.972 41.667 0.00 0.00 0.00 1.73
380 458 4.455877 TGTGTGTGTGTGTGTGTCAAATTA 59.544 37.500 0.00 0.00 0.00 1.40
381 459 3.254411 TGTGTGTGTGTGTGTGTCAAATT 59.746 39.130 0.00 0.00 0.00 1.82
382 460 2.816672 TGTGTGTGTGTGTGTGTCAAAT 59.183 40.909 0.00 0.00 0.00 2.32
383 461 2.031595 GTGTGTGTGTGTGTGTGTCAAA 60.032 45.455 0.00 0.00 0.00 2.69
384 462 1.533299 GTGTGTGTGTGTGTGTGTCAA 59.467 47.619 0.00 0.00 0.00 3.18
385 463 1.152510 GTGTGTGTGTGTGTGTGTCA 58.847 50.000 0.00 0.00 0.00 3.58
386 464 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
387 465 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
393 471 1.270571 TGTCAGTGTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
397 475 2.093500 AGTGATGTCAGTGTGTGTGTGT 60.093 45.455 0.00 0.00 0.00 3.72
401 479 1.134431 TGCAGTGATGTCAGTGTGTGT 60.134 47.619 16.72 0.00 46.30 3.72
405 483 0.601046 CGGTGCAGTGATGTCAGTGT 60.601 55.000 16.72 0.00 46.30 3.55
408 486 2.393768 GCCGGTGCAGTGATGTCAG 61.394 63.158 1.90 0.00 37.47 3.51
410 488 3.127533 GGCCGGTGCAGTGATGTC 61.128 66.667 1.90 0.00 40.13 3.06
455 537 2.266554 CGCACACAAAGAGATCTCTCC 58.733 52.381 25.29 7.45 43.88 3.71
460 548 1.136141 CAGCACGCACACAAAGAGATC 60.136 52.381 0.00 0.00 0.00 2.75
491 579 1.202639 TGATTTGGCGCCATCGTATCT 60.203 47.619 33.25 9.76 38.14 1.98
494 582 1.013596 CTTGATTTGGCGCCATCGTA 58.986 50.000 33.25 13.29 38.14 3.43
607 704 3.326747 AGTAATTGCTTTTCTCTCGCGT 58.673 40.909 5.77 0.00 0.00 6.01
855 954 0.674895 CCACGGGAGGAGAGCAAAAG 60.675 60.000 0.00 0.00 0.00 2.27
856 955 1.374947 CCACGGGAGGAGAGCAAAA 59.625 57.895 0.00 0.00 0.00 2.44
857 956 2.592993 CCCACGGGAGGAGAGCAAA 61.593 63.158 0.00 0.00 37.50 3.68
858 957 3.003173 CCCACGGGAGGAGAGCAA 61.003 66.667 0.00 0.00 37.50 3.91
875 974 2.589890 CGTGTCTTATAGCCACGGC 58.410 57.895 0.00 0.00 45.97 5.68
920 1019 6.446909 AGGAGGAGAAAGAAAGAAAGATGT 57.553 37.500 0.00 0.00 0.00 3.06
923 1026 4.589374 ACGAGGAGGAGAAAGAAAGAAAGA 59.411 41.667 0.00 0.00 0.00 2.52
924 1027 4.888917 ACGAGGAGGAGAAAGAAAGAAAG 58.111 43.478 0.00 0.00 0.00 2.62
926 1029 3.895656 TGACGAGGAGGAGAAAGAAAGAA 59.104 43.478 0.00 0.00 0.00 2.52
1074 1198 1.371183 CTTCTTGTGGAGCGGGTCA 59.629 57.895 9.66 0.00 0.00 4.02
1112 1248 2.626780 GGGTTGTCGGCCTGCTTTC 61.627 63.158 0.00 0.00 0.00 2.62
1138 1274 2.597217 CGCCATGGTTGTGGTGGT 60.597 61.111 14.67 0.00 44.23 4.16
1294 1474 2.747855 CTTGGCCTTGTCCTCGCC 60.748 66.667 3.32 0.00 43.32 5.54
1393 1579 4.682563 TCCTCTTCATCTTCTTCCTCACT 58.317 43.478 0.00 0.00 0.00 3.41
1395 1581 4.940483 TCTCCTCTTCATCTTCTTCCTCA 58.060 43.478 0.00 0.00 0.00 3.86
1560 1776 4.935495 CCGGGGTCCATGGCGATG 62.935 72.222 6.96 1.01 0.00 3.84
1632 1860 3.878103 TCGAGCTGAGTGAGGTAGATTAC 59.122 47.826 0.00 0.00 29.84 1.89
1648 1876 4.421479 CGGTTGGTCGCTCGAGCT 62.421 66.667 32.88 0.00 42.49 4.09
1659 1887 3.058160 CTTGGGCAGAGCGGTTGG 61.058 66.667 0.00 0.00 0.00 3.77
1688 1918 0.321653 GGGTGCTACACAGTCTTGGG 60.322 60.000 0.00 0.00 35.86 4.12
1745 1975 0.679505 TACAGCAAAGCTCACTCCGT 59.320 50.000 0.00 0.00 36.40 4.69
1746 1976 1.067565 TCTACAGCAAAGCTCACTCCG 60.068 52.381 0.00 0.00 36.40 4.63
1747 1977 2.342179 GTCTACAGCAAAGCTCACTCC 58.658 52.381 0.00 0.00 36.40 3.85
1748 1978 2.342179 GGTCTACAGCAAAGCTCACTC 58.658 52.381 0.00 0.00 36.40 3.51
1749 1979 1.337260 CGGTCTACAGCAAAGCTCACT 60.337 52.381 0.00 0.00 36.40 3.41
1750 1980 1.071605 CGGTCTACAGCAAAGCTCAC 58.928 55.000 0.00 0.00 36.40 3.51
1751 1981 0.037326 CCGGTCTACAGCAAAGCTCA 60.037 55.000 0.00 0.00 36.40 4.26
1752 1982 0.037232 ACCGGTCTACAGCAAAGCTC 60.037 55.000 0.00 0.00 36.40 4.09
1753 1983 0.320771 CACCGGTCTACAGCAAAGCT 60.321 55.000 2.59 0.00 40.77 3.74
1754 1984 0.602905 ACACCGGTCTACAGCAAAGC 60.603 55.000 2.59 0.00 0.00 3.51
1755 1985 1.148310 CACACCGGTCTACAGCAAAG 58.852 55.000 2.59 0.00 0.00 2.77
1756 1986 0.466543 ACACACCGGTCTACAGCAAA 59.533 50.000 2.59 0.00 0.00 3.68
1757 1987 0.249699 CACACACCGGTCTACAGCAA 60.250 55.000 2.59 0.00 0.00 3.91
1758 1988 1.110518 TCACACACCGGTCTACAGCA 61.111 55.000 2.59 0.00 0.00 4.41
1759 1989 0.666577 GTCACACACCGGTCTACAGC 60.667 60.000 2.59 0.00 0.00 4.40
1760 1990 0.671796 TGTCACACACCGGTCTACAG 59.328 55.000 2.59 0.00 0.00 2.74
1761 1991 1.067974 CTTGTCACACACCGGTCTACA 59.932 52.381 2.59 1.61 0.00 2.74
1762 1992 1.604693 CCTTGTCACACACCGGTCTAC 60.605 57.143 2.59 0.00 0.00 2.59
1763 1993 0.677288 CCTTGTCACACACCGGTCTA 59.323 55.000 2.59 0.00 0.00 2.59
1764 1994 1.445942 CCTTGTCACACACCGGTCT 59.554 57.895 2.59 0.00 0.00 3.85
1765 1995 2.251642 GCCTTGTCACACACCGGTC 61.252 63.158 2.59 0.00 0.00 4.79
1766 1996 2.203153 GCCTTGTCACACACCGGT 60.203 61.111 0.00 0.00 0.00 5.28
1767 1997 3.345808 CGCCTTGTCACACACCGG 61.346 66.667 0.00 0.00 0.00 5.28
1768 1998 2.279851 TCGCCTTGTCACACACCG 60.280 61.111 0.00 0.00 0.00 4.94
1769 1999 1.522806 TGTCGCCTTGTCACACACC 60.523 57.895 0.00 0.00 0.00 4.16
1770 2000 0.810031 AGTGTCGCCTTGTCACACAC 60.810 55.000 4.39 0.00 42.48 3.82
1771 2001 0.107897 AAGTGTCGCCTTGTCACACA 60.108 50.000 4.39 0.00 42.48 3.72
1772 2002 0.304705 CAAGTGTCGCCTTGTCACAC 59.695 55.000 0.00 0.00 38.83 3.82
1773 2003 2.689083 CAAGTGTCGCCTTGTCACA 58.311 52.632 0.00 0.00 38.83 3.58
1778 2008 0.732571 ACAACACAAGTGTCGCCTTG 59.267 50.000 6.28 3.58 44.13 3.61
1779 2009 0.732571 CACAACACAAGTGTCGCCTT 59.267 50.000 6.28 0.00 44.13 4.35
1780 2010 0.107897 TCACAACACAAGTGTCGCCT 60.108 50.000 6.28 0.00 44.13 5.52
1781 2011 0.304705 CTCACAACACAAGTGTCGCC 59.695 55.000 6.28 0.00 44.13 5.54
1782 2012 1.258982 CTCTCACAACACAAGTGTCGC 59.741 52.381 6.28 0.00 44.13 5.19
1783 2013 1.258982 GCTCTCACAACACAAGTGTCG 59.741 52.381 6.28 0.00 44.13 4.35
1784 2014 2.279741 TGCTCTCACAACACAAGTGTC 58.720 47.619 6.28 0.00 44.13 3.67
1786 2016 1.600957 CCTGCTCTCACAACACAAGTG 59.399 52.381 0.00 0.00 38.32 3.16
1787 2017 1.959042 CCTGCTCTCACAACACAAGT 58.041 50.000 0.00 0.00 0.00 3.16
1788 2018 0.590195 GCCTGCTCTCACAACACAAG 59.410 55.000 0.00 0.00 0.00 3.16
1789 2019 0.107263 TGCCTGCTCTCACAACACAA 60.107 50.000 0.00 0.00 0.00 3.33
1790 2020 0.109153 ATGCCTGCTCTCACAACACA 59.891 50.000 0.00 0.00 0.00 3.72
1791 2021 0.520404 CATGCCTGCTCTCACAACAC 59.480 55.000 0.00 0.00 0.00 3.32
1792 2022 0.607217 CCATGCCTGCTCTCACAACA 60.607 55.000 0.00 0.00 0.00 3.33
1793 2023 1.310933 CCCATGCCTGCTCTCACAAC 61.311 60.000 0.00 0.00 0.00 3.32
1794 2024 1.001764 CCCATGCCTGCTCTCACAA 60.002 57.895 0.00 0.00 0.00 3.33
1795 2025 2.672908 CCCATGCCTGCTCTCACA 59.327 61.111 0.00 0.00 0.00 3.58
1796 2026 2.827642 GCCCATGCCTGCTCTCAC 60.828 66.667 0.00 0.00 0.00 3.51
1797 2027 2.686572 ATGCCCATGCCTGCTCTCA 61.687 57.895 0.00 0.00 36.33 3.27
1798 2028 2.194212 CATGCCCATGCCTGCTCTC 61.194 63.158 0.00 0.00 36.33 3.20
1799 2029 2.123854 CATGCCCATGCCTGCTCT 60.124 61.111 0.00 0.00 36.33 4.09
1800 2030 3.224324 CCATGCCCATGCCTGCTC 61.224 66.667 2.75 0.00 37.49 4.26
1803 2033 3.536917 CAGCCATGCCCATGCCTG 61.537 66.667 5.05 5.05 37.83 4.85
1804 2034 4.853142 CCAGCCATGCCCATGCCT 62.853 66.667 2.75 0.00 37.49 4.75
1807 2037 3.536917 CTGCCAGCCATGCCCATG 61.537 66.667 1.28 1.28 38.51 3.66
1812 2042 2.438975 TACAGCTGCCAGCCATGC 60.439 61.111 14.25 0.00 43.77 4.06
1813 2043 0.179026 ATCTACAGCTGCCAGCCATG 60.179 55.000 14.25 8.83 43.77 3.66
1814 2044 1.347050 CTATCTACAGCTGCCAGCCAT 59.653 52.381 14.25 4.11 43.77 4.40
1815 2045 0.755079 CTATCTACAGCTGCCAGCCA 59.245 55.000 14.25 0.00 43.77 4.75
1816 2046 0.755686 ACTATCTACAGCTGCCAGCC 59.244 55.000 14.25 0.00 43.77 4.85
1817 2047 1.137872 ACACTATCTACAGCTGCCAGC 59.862 52.381 15.27 9.13 42.84 4.85
1818 2048 2.542618 CGACACTATCTACAGCTGCCAG 60.543 54.545 15.27 11.70 0.00 4.85
1819 2049 1.405463 CGACACTATCTACAGCTGCCA 59.595 52.381 15.27 0.20 0.00 4.92
1820 2050 1.676529 TCGACACTATCTACAGCTGCC 59.323 52.381 15.27 0.00 0.00 4.85
1832 2062 0.107993 ACTCGTCCGGATCGACACTA 60.108 55.000 20.37 5.25 33.71 2.74
1888 2118 1.866496 CACGGCGAGTACGTACAGC 60.866 63.158 27.30 27.30 43.58 4.40
1893 2123 2.253452 GTGTCACGGCGAGTACGT 59.747 61.111 16.62 0.00 46.82 3.57
1897 2127 3.681835 GAGGGTGTCACGGCGAGT 61.682 66.667 16.62 0.00 0.00 4.18
1898 2128 4.778415 CGAGGGTGTCACGGCGAG 62.778 72.222 16.62 5.72 0.00 5.03
1912 2142 0.742281 CCCACTGTTGCAGGATCGAG 60.742 60.000 0.00 0.00 35.51 4.04
1913 2143 1.296392 CCCACTGTTGCAGGATCGA 59.704 57.895 0.00 0.00 35.51 3.59
1952 2189 4.212716 ACCAGATCATAATTGTGCAGCAT 58.787 39.130 0.00 0.00 0.00 3.79
1991 2234 2.236766 ACAAGAAGCAGCAGCAGATTT 58.763 42.857 3.17 0.00 45.49 2.17
2035 2281 6.154534 AGAGTTATATACACAAGCACAGGTCA 59.845 38.462 0.00 0.00 0.00 4.02
2074 2356 8.563123 ACACCATCATCAATTCATCATCTATC 57.437 34.615 0.00 0.00 0.00 2.08
2104 2386 5.656480 ACACCAATTTGTTACAAACCTCAC 58.344 37.500 13.01 0.00 0.00 3.51
2137 2419 0.744414 AATGGACGGAGAACCATGCG 60.744 55.000 0.00 0.00 43.73 4.73
2145 2427 7.119709 TCTTATATTTGTGAATGGACGGAGA 57.880 36.000 0.00 0.00 0.00 3.71
2201 2484 8.345565 AGTATGTTTGTTCACTCATTTCAGTTC 58.654 33.333 0.00 0.00 0.00 3.01
2202 2485 8.225603 AGTATGTTTGTTCACTCATTTCAGTT 57.774 30.769 0.00 0.00 0.00 3.16
2230 2513 2.949644 AGTCACAAAAAGGGTTCCGAAG 59.050 45.455 0.00 0.00 0.00 3.79
2231 2514 3.007473 AGTCACAAAAAGGGTTCCGAA 57.993 42.857 0.00 0.00 0.00 4.30
2233 2516 4.904253 TTTAGTCACAAAAAGGGTTCCG 57.096 40.909 0.00 0.00 0.00 4.30
2261 2544 8.726988 GCTACTGTTGATGTTGGTATTTCTTAA 58.273 33.333 0.00 0.00 0.00 1.85
2263 2546 6.714810 TGCTACTGTTGATGTTGGTATTTCTT 59.285 34.615 0.00 0.00 0.00 2.52
2267 2550 6.892658 TTTGCTACTGTTGATGTTGGTATT 57.107 33.333 0.00 0.00 0.00 1.89
2268 2551 8.752005 ATATTTGCTACTGTTGATGTTGGTAT 57.248 30.769 0.00 0.00 0.00 2.73
2269 2552 9.674068 TTATATTTGCTACTGTTGATGTTGGTA 57.326 29.630 0.00 0.00 0.00 3.25
2270 2553 8.574251 TTATATTTGCTACTGTTGATGTTGGT 57.426 30.769 0.00 0.00 0.00 3.67
2324 2607 9.377312 TCACGATGTCAAATCAATATTGTTAGA 57.623 29.630 14.97 6.45 0.00 2.10
2325 2608 9.986833 TTCACGATGTCAAATCAATATTGTTAG 57.013 29.630 14.97 4.38 0.00 2.34
2328 2611 8.461222 ACATTCACGATGTCAAATCAATATTGT 58.539 29.630 14.97 0.43 45.88 2.71
2329 2612 8.845942 ACATTCACGATGTCAAATCAATATTG 57.154 30.769 9.29 9.29 45.88 1.90
2371 2654 8.611051 ACTATCTATACTTTGACCCAACTTCT 57.389 34.615 0.00 0.00 0.00 2.85
2375 2658 8.880750 GTCAAACTATCTATACTTTGACCCAAC 58.119 37.037 16.45 2.34 43.35 3.77
2381 2664 8.963725 TCCGAAGTCAAACTATCTATACTTTGA 58.036 33.333 0.00 0.00 32.45 2.69
2395 2678 9.434559 GCATATAAGTTTTATCCGAAGTCAAAC 57.565 33.333 0.00 0.00 0.00 2.93
2397 3055 8.725405 TGCATATAAGTTTTATCCGAAGTCAA 57.275 30.769 0.00 0.00 0.00 3.18
2415 3073 7.013846 CCTCGGGTCCTTTTTAATTTGCATATA 59.986 37.037 0.00 0.00 0.00 0.86
2422 3080 4.202641 ACTCCCTCGGGTCCTTTTTAATTT 60.203 41.667 1.18 0.00 36.47 1.82
2424 3082 2.917600 ACTCCCTCGGGTCCTTTTTAAT 59.082 45.455 1.18 0.00 36.47 1.40
2425 3083 2.341695 ACTCCCTCGGGTCCTTTTTAA 58.658 47.619 1.18 0.00 36.47 1.52
2427 3085 2.034436 TACTCCCTCGGGTCCTTTTT 57.966 50.000 1.18 0.00 36.47 1.94
2428 3086 1.907255 CTTACTCCCTCGGGTCCTTTT 59.093 52.381 1.18 0.00 36.47 2.27
2431 3089 0.412640 AACTTACTCCCTCGGGTCCT 59.587 55.000 1.18 0.00 36.47 3.85
2432 3090 0.535797 CAACTTACTCCCTCGGGTCC 59.464 60.000 1.18 0.00 36.47 4.46
2433 3091 1.477295 CTCAACTTACTCCCTCGGGTC 59.523 57.143 1.18 0.00 36.47 4.46
2434 3092 1.558233 CTCAACTTACTCCCTCGGGT 58.442 55.000 1.18 0.00 36.47 5.28
2435 3093 0.824759 CCTCAACTTACTCCCTCGGG 59.175 60.000 0.00 0.00 0.00 5.14
2437 3095 2.164624 CAGACCTCAACTTACTCCCTCG 59.835 54.545 0.00 0.00 0.00 4.63
2438 3096 2.498078 CCAGACCTCAACTTACTCCCTC 59.502 54.545 0.00 0.00 0.00 4.30
2439 3097 2.541466 CCAGACCTCAACTTACTCCCT 58.459 52.381 0.00 0.00 0.00 4.20
2440 3098 1.066071 GCCAGACCTCAACTTACTCCC 60.066 57.143 0.00 0.00 0.00 4.30
2442 3100 3.402628 TTGCCAGACCTCAACTTACTC 57.597 47.619 0.00 0.00 0.00 2.59
2443 3101 3.136626 ACTTTGCCAGACCTCAACTTACT 59.863 43.478 0.00 0.00 0.00 2.24
2456 3732 0.461135 AACTTGCCACACTTTGCCAG 59.539 50.000 0.00 0.00 0.00 4.85
2459 3735 1.280066 CACAACTTGCCACACTTTGC 58.720 50.000 0.00 0.00 0.00 3.68
2465 3741 0.682532 TCAAGCCACAACTTGCCACA 60.683 50.000 0.00 0.00 45.43 4.17
2466 3742 0.459489 TTCAAGCCACAACTTGCCAC 59.541 50.000 0.00 0.00 45.43 5.01
2467 3743 1.134848 GTTTCAAGCCACAACTTGCCA 60.135 47.619 0.00 0.00 45.43 4.92
2468 3744 1.570813 GTTTCAAGCCACAACTTGCC 58.429 50.000 0.00 0.00 45.43 4.52
2469 3745 1.134848 TGGTTTCAAGCCACAACTTGC 60.135 47.619 0.00 0.00 45.43 4.01
2470 3746 2.957491 TGGTTTCAAGCCACAACTTG 57.043 45.000 0.00 0.00 46.86 3.16
2471 3747 3.007398 TGTTTGGTTTCAAGCCACAACTT 59.993 39.130 14.68 0.00 35.46 2.66
2472 3748 2.564947 TGTTTGGTTTCAAGCCACAACT 59.435 40.909 14.68 0.00 35.46 3.16
2473 3749 2.929398 CTGTTTGGTTTCAAGCCACAAC 59.071 45.455 0.00 2.32 35.46 3.32
2474 3750 2.676463 GCTGTTTGGTTTCAAGCCACAA 60.676 45.455 0.00 0.00 35.46 3.33
2505 3781 1.274167 TCGATACTTCTTGGCGTTGGT 59.726 47.619 0.00 0.00 0.00 3.67
2508 3784 1.067142 TGCTCGATACTTCTTGGCGTT 60.067 47.619 0.00 0.00 0.00 4.84
2512 3788 1.929836 GCAGTGCTCGATACTTCTTGG 59.070 52.381 8.18 0.00 0.00 3.61
2513 3789 2.610433 TGCAGTGCTCGATACTTCTTG 58.390 47.619 17.60 0.00 0.00 3.02
2530 3806 1.071542 TCTCCAATCAGACGGTTTGCA 59.928 47.619 0.00 0.00 0.00 4.08
2539 3815 6.053650 GTGTCAATGATCATCTCCAATCAGA 58.946 40.000 9.06 0.00 35.49 3.27
2541 3817 4.812626 CGTGTCAATGATCATCTCCAATCA 59.187 41.667 9.06 0.00 36.40 2.57
2554 3830 1.514678 GCCAACTGCCGTGTCAATGA 61.515 55.000 0.00 0.00 0.00 2.57
2556 3832 3.354678 GCCAACTGCCGTGTCAAT 58.645 55.556 0.00 0.00 0.00 2.57
2571 3847 2.740447 CACTTACCGTTTCTTAGTGGCC 59.260 50.000 0.00 0.00 34.14 5.36
2577 3853 1.794116 GCACGCACTTACCGTTTCTTA 59.206 47.619 0.00 0.00 36.69 2.10
2578 3854 0.584876 GCACGCACTTACCGTTTCTT 59.415 50.000 0.00 0.00 36.69 2.52


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

AutoCloner maintained by Alex Coulton.