Multiple sequence alignment - TraesCS2D01G571000

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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 TraesCS2D01G571000 chr2D 100.000 4715 0 0 1 4715 637633358 637638072 0.000000e+00 8708.0
1 TraesCS2D01G571000 chr2D 90.000 160 16 0 2912 3071 597847725 597847884 1.720000e-49 207.0
2 TraesCS2D01G571000 chr2D 89.375 160 17 0 2912 3071 641893134 641893293 8.000000e-48 202.0
3 TraesCS2D01G571000 chr2A 86.978 2680 186 58 26 2657 762316525 762313961 0.000000e+00 2865.0
4 TraesCS2D01G571000 chr2A 89.443 2084 159 30 2648 4715 762313906 762311868 0.000000e+00 2573.0
5 TraesCS2D01G571000 chr2B 87.932 2287 146 62 21 2287 795047665 795049841 0.000000e+00 2575.0
6 TraesCS2D01G571000 chr2B 90.238 799 51 13 3288 4077 795050835 795051615 0.000000e+00 1018.0
7 TraesCS2D01G571000 chr2B 89.731 633 55 7 2648 3279 795050111 795050734 0.000000e+00 800.0
8 TraesCS2D01G571000 chr2B 89.386 603 60 4 4114 4715 795051613 795052212 0.000000e+00 756.0
9 TraesCS2D01G571000 chr2B 84.706 340 26 12 1820 2155 523781577 523781260 2.740000e-82 316.0
10 TraesCS2D01G571000 chr2B 81.070 243 22 9 2416 2657 795049836 795050055 6.270000e-39 172.0
11 TraesCS2D01G571000 chr3A 85.366 779 90 14 1 772 610536431 610535670 0.000000e+00 785.0
12 TraesCS2D01G571000 chr3A 84.794 776 97 13 1 772 610535211 610534453 0.000000e+00 760.0
13 TraesCS2D01G571000 chr6A 85.267 767 97 10 1 766 196014394 196013643 0.000000e+00 776.0
14 TraesCS2D01G571000 chr7A 85.032 775 98 11 1 772 580496706 580495947 0.000000e+00 773.0
15 TraesCS2D01G571000 chr7A 83.463 774 110 12 1 772 724002836 724002079 0.000000e+00 704.0
16 TraesCS2D01G571000 chr7A 77.831 627 112 22 4104 4715 666794596 666795210 3.470000e-96 363.0
17 TraesCS2D01G571000 chr5D 84.576 791 82 22 1 772 19106771 19106002 0.000000e+00 749.0
18 TraesCS2D01G571000 chr4A 83.485 769 112 10 1 766 174390514 174391270 0.000000e+00 702.0
19 TraesCS2D01G571000 chr4A 81.497 481 81 6 4082 4559 734579921 734579446 5.720000e-104 388.0
20 TraesCS2D01G571000 chr4A 81.420 479 84 4 4082 4559 735762530 735762056 2.060000e-103 387.0
21 TraesCS2D01G571000 chr4A 76.876 653 117 27 4084 4715 736143986 736143347 5.840000e-89 339.0
22 TraesCS2D01G571000 chr4A 76.683 609 110 27 4114 4715 736806229 736805646 4.580000e-80 309.0
23 TraesCS2D01G571000 chr4A 79.661 354 68 3 4082 4433 736049848 736049497 7.830000e-63 252.0
24 TraesCS2D01G571000 chr4A 83.495 206 32 1 4312 4517 736456599 736456802 1.730000e-44 191.0
25 TraesCS2D01G571000 chr4A 94.545 55 3 0 4660 4714 734579289 734579235 8.410000e-13 86.1
26 TraesCS2D01G571000 chr4A 94.545 55 3 0 4660 4714 735761899 735761845 8.410000e-13 86.1
27 TraesCS2D01G571000 chr1A 85.000 660 74 19 4 655 96732568 96731926 0.000000e+00 647.0
28 TraesCS2D01G571000 chr1A 86.654 547 50 14 1155 1698 168548093 168548619 6.800000e-163 584.0
29 TraesCS2D01G571000 chr1A 84.393 346 27 11 1820 2155 168548644 168548972 9.850000e-82 315.0
30 TraesCS2D01G571000 chr5B 85.584 437 61 1 4091 4527 98514236 98513802 1.550000e-124 457.0
31 TraesCS2D01G571000 chr5B 94.444 54 3 0 4662 4715 98513703 98513650 3.020000e-12 84.2
32 TraesCS2D01G571000 chr7D 82.213 461 72 7 4106 4561 575925167 575925622 5.720000e-104 388.0
33 TraesCS2D01G571000 chr7D 89.627 241 18 4 3801 4034 592269337 592269577 2.760000e-77 300.0
34 TraesCS2D01G571000 chr7D 92.857 56 4 0 4660 4715 5654336 5654391 1.090000e-11 82.4


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 TraesCS2D01G571000 chr2D 637633358 637638072 4714 False 8708.00 8708 100.0000 1 4715 1 chr2D.!!$F2 4714
1 TraesCS2D01G571000 chr2A 762311868 762316525 4657 True 2719.00 2865 88.2105 26 4715 2 chr2A.!!$R1 4689
2 TraesCS2D01G571000 chr2B 795047665 795052212 4547 False 1064.20 2575 87.6714 21 4715 5 chr2B.!!$F1 4694
3 TraesCS2D01G571000 chr3A 610534453 610536431 1978 True 772.50 785 85.0800 1 772 2 chr3A.!!$R1 771
4 TraesCS2D01G571000 chr6A 196013643 196014394 751 True 776.00 776 85.2670 1 766 1 chr6A.!!$R1 765
5 TraesCS2D01G571000 chr7A 580495947 580496706 759 True 773.00 773 85.0320 1 772 1 chr7A.!!$R1 771
6 TraesCS2D01G571000 chr7A 724002079 724002836 757 True 704.00 704 83.4630 1 772 1 chr7A.!!$R2 771
7 TraesCS2D01G571000 chr7A 666794596 666795210 614 False 363.00 363 77.8310 4104 4715 1 chr7A.!!$F1 611
8 TraesCS2D01G571000 chr5D 19106002 19106771 769 True 749.00 749 84.5760 1 772 1 chr5D.!!$R1 771
9 TraesCS2D01G571000 chr4A 174390514 174391270 756 False 702.00 702 83.4850 1 766 1 chr4A.!!$F1 765
10 TraesCS2D01G571000 chr4A 736143347 736143986 639 True 339.00 339 76.8760 4084 4715 1 chr4A.!!$R2 631
11 TraesCS2D01G571000 chr4A 736805646 736806229 583 True 309.00 309 76.6830 4114 4715 1 chr4A.!!$R3 601
12 TraesCS2D01G571000 chr4A 734579235 734579921 686 True 237.05 388 88.0210 4082 4714 2 chr4A.!!$R4 632
13 TraesCS2D01G571000 chr4A 735761845 735762530 685 True 236.55 387 87.9825 4082 4714 2 chr4A.!!$R5 632
14 TraesCS2D01G571000 chr1A 96731926 96732568 642 True 647.00 647 85.0000 4 655 1 chr1A.!!$R1 651
15 TraesCS2D01G571000 chr1A 168548093 168548972 879 False 449.50 584 85.5235 1155 2155 2 chr1A.!!$F1 1000
16 TraesCS2D01G571000 chr5B 98513650 98514236 586 True 270.60 457 90.0140 4091 4715 2 chr5B.!!$R1 624

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
142 155 0.322816 GATCCTGGGTGCTGCTGAAA 60.323 55.0 0.0 0.0 0.00 2.69 F
1065 1584 0.244994 CGCCAACACTAGCAGAGAGT 59.755 55.0 0.0 0.0 0.00 3.24 F
2278 2856 0.323725 GCACCCCATCACTGGTTGAT 60.324 55.0 0.0 0.0 46.75 2.57 F
2581 3160 0.107831 TACTGGCTTTTGTGACCGCT 59.892 50.0 0.0 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2430 0.597568 TTCCGGAAGTTTGCTGCATG 59.402 50.000 14.35 0.00 0.00 4.06 R
2362 2941 0.037447 TTGATGTGGCCACGGATTCA 59.963 50.000 30.07 24.41 0.00 2.57 R
3654 4406 0.114168 TGGTCATTGGTTCTTGGGGG 59.886 55.000 0.00 0.00 0.00 5.40 R
4408 5193 1.072965 CTGGAAGAAGGCCAACTGACT 59.927 52.381 5.01 0.00 34.07 3.41 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
118 131 1.748122 CGGGCAGAGAAGCAAGCAT 60.748 57.895 0.00 0.00 35.83 3.79
130 143 2.307768 AGCAAGCATTCATGATCCTGG 58.692 47.619 0.00 0.00 0.00 4.45
142 155 0.322816 GATCCTGGGTGCTGCTGAAA 60.323 55.000 0.00 0.00 0.00 2.69
195 208 1.328680 GTTCGCGTCATCAATCTGCAT 59.671 47.619 5.77 0.00 0.00 3.96
198 211 3.392882 TCGCGTCATCAATCTGCATAAT 58.607 40.909 5.77 0.00 0.00 1.28
218 231 8.545420 GCATAATTTTGCAAGATGAACATTAGG 58.455 33.333 14.99 0.00 42.31 2.69
219 232 9.806203 CATAATTTTGCAAGATGAACATTAGGA 57.194 29.630 2.81 0.00 0.00 2.94
428 462 1.420514 TCCTCATCCTCCTCGTCGTAT 59.579 52.381 0.00 0.00 0.00 3.06
505 544 4.457496 CGAGCGGGCCATGTCTGT 62.457 66.667 4.39 0.00 0.00 3.41
614 653 2.759973 CCAGGAGAGCCACGCCTA 60.760 66.667 3.76 0.00 46.70 3.93
996 1515 1.480869 CCACCTAGAGCCCCTACTACC 60.481 61.905 0.00 0.00 0.00 3.18
1062 1581 2.103042 GCCGCCAACACTAGCAGAG 61.103 63.158 0.00 0.00 0.00 3.35
1063 1582 1.591703 CCGCCAACACTAGCAGAGA 59.408 57.895 0.00 0.00 0.00 3.10
1064 1583 0.459237 CCGCCAACACTAGCAGAGAG 60.459 60.000 0.00 0.00 0.00 3.20
1065 1584 0.244994 CGCCAACACTAGCAGAGAGT 59.755 55.000 0.00 0.00 0.00 3.24
1066 1585 1.734047 CGCCAACACTAGCAGAGAGTC 60.734 57.143 0.00 0.00 0.00 3.36
1068 1587 1.542030 CCAACACTAGCAGAGAGTCGT 59.458 52.381 0.00 0.00 0.00 4.34
1069 1588 2.414824 CCAACACTAGCAGAGAGTCGTC 60.415 54.545 0.00 0.00 0.00 4.20
1227 1769 2.441164 ACCTGCTCTCGCTCGGAT 60.441 61.111 0.00 0.00 36.97 4.18
1228 1770 2.334653 CCTGCTCTCGCTCGGATC 59.665 66.667 0.00 0.00 36.97 3.36
1229 1771 2.192861 CCTGCTCTCGCTCGGATCT 61.193 63.158 0.00 0.00 36.97 2.75
1230 1772 1.282570 CTGCTCTCGCTCGGATCTC 59.717 63.158 0.00 0.00 36.97 2.75
1231 1773 2.251075 GCTCTCGCTCGGATCTCG 59.749 66.667 0.00 0.00 40.90 4.04
1232 1774 2.251075 CTCTCGCTCGGATCTCGC 59.749 66.667 0.00 0.00 39.05 5.03
1233 1775 3.248630 CTCTCGCTCGGATCTCGCC 62.249 68.421 0.00 0.00 39.05 5.54
1234 1776 3.283684 CTCGCTCGGATCTCGCCT 61.284 66.667 0.00 0.00 39.05 5.52
1235 1777 3.248630 CTCGCTCGGATCTCGCCTC 62.249 68.421 0.00 0.00 39.05 4.70
1236 1778 4.335584 CGCTCGGATCTCGCCTCC 62.336 72.222 0.00 0.00 39.05 4.30
1237 1779 3.219928 GCTCGGATCTCGCCTCCA 61.220 66.667 0.00 0.00 39.05 3.86
1238 1780 3.038280 CTCGGATCTCGCCTCCAG 58.962 66.667 0.00 0.00 39.05 3.86
1239 1781 3.206211 CTCGGATCTCGCCTCCAGC 62.206 68.421 0.00 0.00 39.05 4.85
1240 1782 3.222855 CGGATCTCGCCTCCAGCT 61.223 66.667 0.00 0.00 40.39 4.24
1241 1783 2.790791 CGGATCTCGCCTCCAGCTT 61.791 63.158 0.00 0.00 40.39 3.74
1242 1784 1.227497 GGATCTCGCCTCCAGCTTG 60.227 63.158 0.00 0.00 40.39 4.01
1243 1785 1.227497 GATCTCGCCTCCAGCTTGG 60.227 63.158 0.00 0.00 40.39 3.61
1244 1786 1.680522 GATCTCGCCTCCAGCTTGGA 61.681 60.000 5.03 5.03 45.98 3.53
1289 1833 2.653702 GTGTGTCCGCTCTGCTCT 59.346 61.111 0.00 0.00 0.00 4.09
1290 1834 1.735920 GTGTGTCCGCTCTGCTCTG 60.736 63.158 0.00 0.00 0.00 3.35
1291 1835 2.813042 GTGTCCGCTCTGCTCTGC 60.813 66.667 0.00 0.00 0.00 4.26
1292 1836 2.993840 TGTCCGCTCTGCTCTGCT 60.994 61.111 0.00 0.00 0.00 4.24
1293 1837 2.202730 GTCCGCTCTGCTCTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
1303 1847 2.125753 CTCTGCTCGCAGACCACC 60.126 66.667 17.01 0.00 46.80 4.61
1531 2080 1.741706 GCTGTTGGACTGATGATGGTG 59.258 52.381 0.00 0.00 0.00 4.17
1647 2196 1.884579 ACCATATCGGACGAAGCGTAT 59.115 47.619 0.00 0.00 41.37 3.06
1666 2215 0.679505 TGACAAGCTCGGCAGTAAGT 59.320 50.000 0.00 0.00 0.00 2.24
1673 2222 1.134670 GCTCGGCAGTAAGTTCAGGAT 60.135 52.381 0.00 0.00 0.00 3.24
1674 2223 2.544685 CTCGGCAGTAAGTTCAGGATG 58.455 52.381 0.00 0.00 37.54 3.51
1680 2229 3.242543 GCAGTAAGTTCAGGATGCATTCG 60.243 47.826 0.00 0.00 34.76 3.34
1682 2231 1.098050 AAGTTCAGGATGCATTCGGC 58.902 50.000 0.00 0.00 45.13 5.54
1694 2243 1.810151 GCATTCGGCTTCCAGTTTACA 59.190 47.619 0.00 0.00 40.25 2.41
1695 2244 2.227865 GCATTCGGCTTCCAGTTTACAA 59.772 45.455 0.00 0.00 40.25 2.41
1696 2245 3.670627 GCATTCGGCTTCCAGTTTACAAG 60.671 47.826 0.00 0.00 40.25 3.16
1719 2268 3.434309 AGATGAATTTGGACCCCTTGTG 58.566 45.455 0.00 0.00 0.00 3.33
1737 2286 5.875359 CCTTGTGTACCTCTTGTAGAATTCC 59.125 44.000 0.65 0.00 0.00 3.01
1779 2328 9.467796 AGTTCAGCTTATTCCTTAATTAAAGCT 57.532 29.630 12.11 12.11 43.23 3.74
1782 2331 8.686334 TCAGCTTATTCCTTAATTAAAGCTTGG 58.314 33.333 14.34 5.80 41.23 3.61
1783 2332 8.686334 CAGCTTATTCCTTAATTAAAGCTTGGA 58.314 33.333 14.34 7.76 41.23 3.53
1784 2333 9.426534 AGCTTATTCCTTAATTAAAGCTTGGAT 57.573 29.630 12.11 0.00 41.23 3.41
1791 2350 8.768397 TCCTTAATTAAAGCTTGGATGACTCTA 58.232 33.333 0.00 0.00 33.49 2.43
1836 2395 6.372659 AGTTCAGTTTATCATTTGCACTCGAT 59.627 34.615 0.00 0.00 0.00 3.59
1837 2396 6.349973 TCAGTTTATCATTTGCACTCGATC 57.650 37.500 0.00 0.00 0.00 3.69
1838 2397 5.874261 TCAGTTTATCATTTGCACTCGATCA 59.126 36.000 0.00 0.00 0.00 2.92
1841 2409 7.795734 CAGTTTATCATTTGCACTCGATCATAC 59.204 37.037 0.00 0.00 0.00 2.39
1849 2417 4.871513 TGCACTCGATCATACCATCTAAC 58.128 43.478 0.00 0.00 0.00 2.34
1850 2418 4.584743 TGCACTCGATCATACCATCTAACT 59.415 41.667 0.00 0.00 0.00 2.24
1852 2420 5.631512 GCACTCGATCATACCATCTAACTTC 59.368 44.000 0.00 0.00 0.00 3.01
1861 2430 6.763135 TCATACCATCTAACTTCTGTGCAATC 59.237 38.462 0.00 0.00 0.00 2.67
1862 2431 4.910195 ACCATCTAACTTCTGTGCAATCA 58.090 39.130 0.00 0.00 0.00 2.57
1935 2504 4.650754 ATCGGACGATAAGCAAGTAAGT 57.349 40.909 5.27 0.00 32.36 2.24
1954 2523 1.467734 GTTGCTCATGCTCTGGACTTG 59.532 52.381 0.00 0.00 40.48 3.16
1990 2559 3.141002 GCTTCAACAGGCATACACATG 57.859 47.619 0.00 0.00 35.07 3.21
2039 2608 4.008330 CTCTTTGGCAGTCAGACAATCAT 58.992 43.478 2.66 0.00 46.79 2.45
2075 2644 1.197721 GCCAACATCAAGGTCAGTTCG 59.802 52.381 0.00 0.00 0.00 3.95
2103 2672 9.559732 TTGCTTTACACATGTATGCTAGATTAT 57.440 29.630 0.00 0.00 34.09 1.28
2123 2698 1.059942 GTTTTTGCACACGCTATGGC 58.940 50.000 0.00 0.00 39.64 4.40
2149 2724 5.532406 TGGAATATTGCCAACTAATCTGCTC 59.468 40.000 4.35 0.00 31.13 4.26
2155 2730 4.081406 TGCCAACTAATCTGCTCATGTTT 58.919 39.130 0.00 0.00 0.00 2.83
2275 2853 1.072266 TTAGCACCCCATCACTGGTT 58.928 50.000 0.00 0.00 41.37 3.67
2278 2856 0.323725 GCACCCCATCACTGGTTGAT 60.324 55.000 0.00 0.00 46.75 2.57
2324 2903 1.682854 GCATAGCAGCCCAATTAGCAA 59.317 47.619 2.79 0.00 0.00 3.91
2362 2941 5.839621 AGAACACGCCGAATTAGTATGTAT 58.160 37.500 0.00 0.00 0.00 2.29
2368 2947 5.867716 ACGCCGAATTAGTATGTATGAATCC 59.132 40.000 0.00 0.00 0.00 3.01
2380 2959 0.255604 ATGAATCCGTGGCCACATCA 59.744 50.000 34.16 28.41 0.00 3.07
2386 2965 0.888736 CCGTGGCCACATCAACTTGA 60.889 55.000 34.16 0.00 0.00 3.02
2389 2968 1.680735 GTGGCCACATCAACTTGACAA 59.319 47.619 31.23 0.00 0.00 3.18
2441 3020 6.870769 CATTGGCTGGATATTCTGTTTTTCT 58.129 36.000 0.00 0.00 0.00 2.52
2455 3034 9.950496 ATTCTGTTTTTCTGTCTACAGTCATAT 57.050 29.630 9.81 0.16 44.12 1.78
2484 3063 9.719355 TGCATTATTCTAAGTTTCTAACTGTGA 57.281 29.630 0.00 0.00 41.91 3.58
2497 3076 9.431887 GTTTCTAACTGTGAAGGAATATGTGTA 57.568 33.333 0.00 0.00 0.00 2.90
2512 3091 7.175641 GGAATATGTGTATTCATCTTCCCCTTG 59.824 40.741 10.63 0.00 45.22 3.61
2545 3124 0.835941 CTGGAGCAGCTATTGGGAGT 59.164 55.000 0.00 0.00 0.00 3.85
2547 3126 1.762957 TGGAGCAGCTATTGGGAGTAC 59.237 52.381 0.00 0.00 0.00 2.73
2559 3138 5.537300 ATTGGGAGTACTGCAGTGTATAG 57.463 43.478 29.57 0.00 0.00 1.31
2562 3141 4.775780 TGGGAGTACTGCAGTGTATAGTTT 59.224 41.667 29.57 0.80 0.00 2.66
2563 3142 5.953548 TGGGAGTACTGCAGTGTATAGTTTA 59.046 40.000 29.57 2.44 0.00 2.01
2564 3143 6.127535 TGGGAGTACTGCAGTGTATAGTTTAC 60.128 42.308 29.57 15.43 0.00 2.01
2566 3145 6.973474 GGAGTACTGCAGTGTATAGTTTACTG 59.027 42.308 29.57 0.00 43.49 2.74
2567 3146 6.864342 AGTACTGCAGTGTATAGTTTACTGG 58.136 40.000 29.57 0.00 41.52 4.00
2568 3147 4.504858 ACTGCAGTGTATAGTTTACTGGC 58.495 43.478 20.97 0.00 41.52 4.85
2569 3148 4.223032 ACTGCAGTGTATAGTTTACTGGCT 59.777 41.667 20.97 0.00 41.52 4.75
2570 3149 5.160607 TGCAGTGTATAGTTTACTGGCTT 57.839 39.130 0.00 0.00 41.52 4.35
2571 3150 5.556915 TGCAGTGTATAGTTTACTGGCTTT 58.443 37.500 0.00 0.00 41.52 3.51
2572 3151 6.001460 TGCAGTGTATAGTTTACTGGCTTTT 58.999 36.000 0.00 0.00 41.52 2.27
2573 3152 6.072728 TGCAGTGTATAGTTTACTGGCTTTTG 60.073 38.462 0.00 0.00 41.52 2.44
2574 3153 6.072673 GCAGTGTATAGTTTACTGGCTTTTGT 60.073 38.462 0.00 0.00 41.52 2.83
2575 3154 7.298122 CAGTGTATAGTTTACTGGCTTTTGTG 58.702 38.462 0.00 0.00 38.46 3.33
2576 3155 7.172532 CAGTGTATAGTTTACTGGCTTTTGTGA 59.827 37.037 0.00 0.00 38.46 3.58
2577 3156 7.172703 AGTGTATAGTTTACTGGCTTTTGTGAC 59.827 37.037 0.00 0.00 0.00 3.67
2578 3157 5.959618 ATAGTTTACTGGCTTTTGTGACC 57.040 39.130 0.00 0.00 0.00 4.02
2579 3158 2.616842 AGTTTACTGGCTTTTGTGACCG 59.383 45.455 0.00 0.00 0.00 4.79
2580 3159 0.948678 TTACTGGCTTTTGTGACCGC 59.051 50.000 0.00 0.00 0.00 5.68
2581 3160 0.107831 TACTGGCTTTTGTGACCGCT 59.892 50.000 0.00 0.00 0.00 5.52
2601 3180 3.935828 GCTTAGTAGCTTCCTGGTTTGAG 59.064 47.826 0.00 0.00 44.27 3.02
2607 3186 2.307098 AGCTTCCTGGTTTGAGTAGCAT 59.693 45.455 0.00 0.00 0.00 3.79
2611 3190 5.452078 TTCCTGGTTTGAGTAGCATTTTG 57.548 39.130 0.00 0.00 0.00 2.44
2621 3200 7.452880 TTGAGTAGCATTTTGAGTAAAGCAT 57.547 32.000 0.00 0.00 0.00 3.79
2623 3202 8.560355 TGAGTAGCATTTTGAGTAAAGCATAA 57.440 30.769 0.00 0.00 0.00 1.90
2635 3214 9.547753 TTGAGTAAAGCATAATAGGAATCTCAC 57.452 33.333 0.00 0.00 0.00 3.51
2638 3217 8.085296 AGTAAAGCATAATAGGAATCTCACTCG 58.915 37.037 0.00 0.00 0.00 4.18
2640 3222 4.526262 AGCATAATAGGAATCTCACTCGCT 59.474 41.667 0.00 0.00 0.00 4.93
2647 3229 8.994429 AATAGGAATCTCACTCGCTAAATATG 57.006 34.615 0.00 0.00 0.00 1.78
2648 3230 6.656632 AGGAATCTCACTCGCTAAATATGA 57.343 37.500 0.00 0.00 0.00 2.15
2649 3231 6.451393 AGGAATCTCACTCGCTAAATATGAC 58.549 40.000 0.00 0.00 0.00 3.06
2659 3304 5.466819 TCGCTAAATATGACTATCCAACCG 58.533 41.667 0.00 0.00 0.00 4.44
2661 3306 5.118664 CGCTAAATATGACTATCCAACCGTG 59.881 44.000 0.00 0.00 0.00 4.94
2672 3317 1.202557 TCCAACCGTGTGTAGTTGACC 60.203 52.381 4.52 0.00 44.93 4.02
2679 3324 3.191669 CGTGTGTAGTTGACCAAGTTGA 58.808 45.455 3.87 0.00 0.00 3.18
2690 3335 2.921754 GACCAAGTTGACGAGGAATACG 59.078 50.000 3.87 0.00 0.00 3.06
2694 3339 3.227810 AGTTGACGAGGAATACGGAAC 57.772 47.619 0.00 0.00 34.93 3.62
2697 3342 2.439409 TGACGAGGAATACGGAACTGA 58.561 47.619 0.00 0.00 34.93 3.41
2711 3360 4.161565 ACGGAACTGAGCCAATATAACTGA 59.838 41.667 0.00 0.00 0.00 3.41
2720 3369 9.149225 CTGAGCCAATATAACTGATCACTTATC 57.851 37.037 9.94 0.00 34.93 1.75
2752 3401 1.199327 CTGCTTTCAGAGGCATGTGTG 59.801 52.381 0.00 0.00 42.95 3.82
2781 3430 2.577606 TATTGGTCCTTGGTGTGGTG 57.422 50.000 0.00 0.00 0.00 4.17
2782 3431 0.850100 ATTGGTCCTTGGTGTGGTGA 59.150 50.000 0.00 0.00 0.00 4.02
2783 3432 0.850100 TTGGTCCTTGGTGTGGTGAT 59.150 50.000 0.00 0.00 0.00 3.06
2784 3433 0.850100 TGGTCCTTGGTGTGGTGATT 59.150 50.000 0.00 0.00 0.00 2.57
2785 3434 1.247567 GGTCCTTGGTGTGGTGATTG 58.752 55.000 0.00 0.00 0.00 2.67
2817 3466 5.123979 GCTATTGAAAAGAACGGTCTGGAAT 59.876 40.000 2.28 2.80 33.05 3.01
2822 3471 6.234920 TGAAAAGAACGGTCTGGAATATTGA 58.765 36.000 2.28 0.00 33.05 2.57
2823 3472 6.148811 TGAAAAGAACGGTCTGGAATATTGAC 59.851 38.462 2.28 0.00 33.05 3.18
2827 3477 3.861840 ACGGTCTGGAATATTGACACAG 58.138 45.455 0.00 0.00 32.84 3.66
2848 3498 1.604278 GCTTTCTTCTTCTGTGGCGTT 59.396 47.619 0.00 0.00 0.00 4.84
2860 3510 4.804108 TCTGTGGCGTTAAATGGAAATTG 58.196 39.130 0.00 0.00 0.00 2.32
2873 3523 4.213564 TGGAAATTGCACCTGTTTTGTT 57.786 36.364 0.00 0.00 0.00 2.83
2874 3524 5.344743 TGGAAATTGCACCTGTTTTGTTA 57.655 34.783 0.00 0.00 0.00 2.41
2877 3527 5.334028 GGAAATTGCACCTGTTTTGTTATGC 60.334 40.000 0.00 0.00 0.00 3.14
2935 3585 2.613977 GGTGGGAGACAGATGTGAAGTG 60.614 54.545 0.00 0.00 0.00 3.16
2976 3626 0.591170 ACCGTGAAATTCGTTGGCAG 59.409 50.000 0.00 0.00 0.00 4.85
3019 3669 1.261480 TTTGGGTTGGCGTGCAATAT 58.739 45.000 0.00 0.00 0.00 1.28
3073 3723 4.944962 TGTTCATTCTCAAACTATGGCG 57.055 40.909 0.00 0.00 0.00 5.69
3089 3739 9.569122 AAACTATGGCGGTGATAAATTTATACT 57.431 29.630 10.68 0.00 0.00 2.12
3104 3754 7.625828 AATTTATACTCAGTGCCCAAGTTAC 57.374 36.000 0.00 0.00 0.00 2.50
3134 3784 5.152923 TCTTGCGACTAGTAACGACATAG 57.847 43.478 8.07 6.35 0.00 2.23
3155 3805 5.813513 AGCCTTGGAGAAACAATTCATTT 57.186 34.783 0.00 0.00 38.06 2.32
3196 3846 0.538287 GCTGCAGGGTGAAAGGAGTT 60.538 55.000 17.12 0.00 0.00 3.01
3260 3910 4.187694 GCCAGAGAAAGTGAAGGTAGATG 58.812 47.826 0.00 0.00 0.00 2.90
3262 3912 4.187694 CAGAGAAAGTGAAGGTAGATGCC 58.812 47.826 0.00 0.00 0.00 4.40
3279 3929 4.419537 AGATGCCTACCTACCTTACCTAGT 59.580 45.833 0.00 0.00 0.00 2.57
3280 3930 5.614402 AGATGCCTACCTACCTTACCTAGTA 59.386 44.000 0.00 0.00 0.00 1.82
3281 3931 5.053978 TGCCTACCTACCTTACCTAGTAC 57.946 47.826 0.00 0.00 0.00 2.73
3314 4059 8.820628 TTTTTCATCGCTTCTTATAACATTCG 57.179 30.769 0.00 0.00 0.00 3.34
3316 4061 5.597806 TCATCGCTTCTTATAACATTCGGT 58.402 37.500 0.00 0.00 0.00 4.69
3320 4065 6.103997 TCGCTTCTTATAACATTCGGTCTTT 58.896 36.000 0.00 0.00 0.00 2.52
3369 4114 4.213270 TGGAAGTGTTATTGAGCAGTTTCG 59.787 41.667 0.00 0.00 0.00 3.46
3383 4128 0.179124 GTTTCGTTTGCAGGTTGGCA 60.179 50.000 0.00 0.00 43.19 4.92
3394 4139 1.529713 GGTTGGCAACTTCCCGGAA 60.530 57.895 27.77 0.00 37.61 4.30
3418 4163 3.633986 GGGACCCATTTGATGATGAAGAC 59.366 47.826 5.33 0.00 0.00 3.01
3438 4186 9.074576 TGAAGACGAGATATAGGCAAGTTTATA 57.925 33.333 0.00 0.00 0.00 0.98
3561 4313 7.279615 TGTACTGGCTAGTATTTGTTATGCAT 58.720 34.615 13.51 3.79 41.22 3.96
3562 4314 6.624352 ACTGGCTAGTATTTGTTATGCATG 57.376 37.500 10.16 0.00 34.74 4.06
3578 4330 2.492881 TGCATGTTGTATCAGCAAAGGG 59.507 45.455 0.00 0.00 31.42 3.95
3625 4377 7.696992 TTATGGAGATTACTTTGGGTTCAAC 57.303 36.000 0.00 0.00 31.78 3.18
3648 4400 4.273148 AGTCGCTGGATGACTAAAAAGT 57.727 40.909 0.00 0.00 44.57 2.66
3654 4406 6.312918 TCGCTGGATGACTAAAAAGTTCATAC 59.687 38.462 0.00 0.00 0.00 2.39
3687 4439 2.282180 ACCAAGATTGCGGGCGTT 60.282 55.556 0.00 0.00 0.00 4.84
3708 4460 9.439500 GGCGTTATGGGTATATAAACTTGATAA 57.561 33.333 0.00 0.00 0.00 1.75
3716 4468 9.020731 GGGTATATAAACTTGATAACCATTGGG 57.979 37.037 7.78 0.00 33.73 4.12
3736 4491 5.899631 GGGTTTATATCCAGAAGTACCCA 57.100 43.478 0.00 0.00 42.78 4.51
3793 4548 5.183904 GGAATCAAAGCAGTAACCTGATTGT 59.816 40.000 0.61 0.00 46.14 2.71
3821 4576 8.887717 ACAAGCATTATCTTGAACTTTAGCTAG 58.112 33.333 10.10 0.00 44.61 3.42
3829 4584 3.585862 TGAACTTTAGCTAGCTGAACCG 58.414 45.455 27.68 15.95 0.00 4.44
3905 4661 1.007238 TGCTAGGAGTAGGAGCCACTT 59.993 52.381 0.00 0.00 35.24 3.16
3948 4705 7.565323 TGAAAAATTGCAGCCAAACTTATTT 57.435 28.000 0.00 0.00 34.05 1.40
3964 4721 6.910536 ACTTATTTTCTACGAGGATTGCAG 57.089 37.500 0.00 0.00 0.00 4.41
3997 4754 9.224267 CTACTTATGCTTCTAATACAATGCCAT 57.776 33.333 0.00 0.00 0.00 4.40
4050 4813 5.013704 ACAGGAATGGTCACCAAACATACTA 59.986 40.000 0.00 0.00 36.95 1.82
4077 4840 0.442310 CTTGTAACCACATCGCCACG 59.558 55.000 0.00 0.00 33.76 4.94
4117 4880 5.123186 AGCTGTAGATATGATCGTAGCACTC 59.877 44.000 12.50 0.00 37.07 3.51
4179 4957 3.271586 GCATATGAGCGGCGCACA 61.272 61.111 32.15 32.15 33.26 4.57
4408 5193 1.014044 GTCGCGCCATCTCTGAAACA 61.014 55.000 0.00 0.00 0.00 2.83
4448 5233 7.716799 TCCAGTAAACATTTCCAATAGCAAT 57.283 32.000 0.00 0.00 0.00 3.56
4502 5287 2.305343 GGCTTCAGATCCTGAGCCATAT 59.695 50.000 20.14 0.00 45.28 1.78
4551 5347 6.474751 GGGTTCATTGACTACGTAATGAGTAC 59.525 42.308 10.46 7.84 42.35 2.73
4564 5381 8.997621 ACGTAATGAGTACACATAAATTCAGT 57.002 30.769 6.20 0.00 32.45 3.41
4567 5384 9.973246 GTAATGAGTACACATAAATTCAGTGTG 57.027 33.333 16.29 14.76 45.27 3.82
4631 5496 9.589111 TTAGCGACATAAAATGTATACTGAACA 57.411 29.630 4.17 0.00 45.03 3.18
4632 5497 8.487313 AGCGACATAAAATGTATACTGAACAA 57.513 30.769 4.17 0.00 45.03 2.83
4634 5499 9.158364 GCGACATAAAATGTATACTGAACAATG 57.842 33.333 4.17 4.26 45.03 2.82
4635 5500 9.158364 CGACATAAAATGTATACTGAACAATGC 57.842 33.333 4.17 0.00 45.03 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 77 5.867174 TCGACATGTAATTTACCACACTCTG 59.133 40.000 0.00 0.00 0.00 3.35
118 131 0.394762 GCAGCACCCAGGATCATGAA 60.395 55.000 9.37 0.00 0.00 2.57
130 143 0.877743 GGAGAGTTTTCAGCAGCACC 59.122 55.000 0.00 0.00 0.00 5.01
142 155 3.776969 TGGAGTGCATAATCAGGAGAGTT 59.223 43.478 0.00 0.00 0.00 3.01
220 233 9.734620 GCAGTTCATACTTCAAATGCATTATTA 57.265 29.630 13.39 0.00 41.94 0.98
221 234 8.472413 AGCAGTTCATACTTCAAATGCATTATT 58.528 29.630 13.39 0.00 44.16 1.40
233 246 5.533154 TCTCCTAGCTAGCAGTTCATACTTC 59.467 44.000 18.83 0.00 30.26 3.01
389 414 2.367107 GAGGGGGAGGGGAGGTTC 60.367 72.222 0.00 0.00 0.00 3.62
390 415 4.040198 GGAGGGGGAGGGGAGGTT 62.040 72.222 0.00 0.00 0.00 3.50
392 417 4.179599 GAGGAGGGGGAGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
394 419 4.761304 AGGAGGAGGGGGAGGGGA 62.761 72.222 0.00 0.00 0.00 4.81
395 420 4.179599 GAGGAGGAGGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
396 421 2.687909 GATGAGGAGGAGGGGGAGGG 62.688 70.000 0.00 0.00 0.00 4.30
428 462 2.686106 GAGGCGGGGTACAGGGAA 60.686 66.667 0.00 0.00 0.00 3.97
1047 1566 1.734047 CGACTCTCTGCTAGTGTTGGC 60.734 57.143 0.00 0.00 32.13 4.52
1048 1567 1.542030 ACGACTCTCTGCTAGTGTTGG 59.458 52.381 11.37 4.42 37.40 3.77
1049 1568 2.726373 CGACGACTCTCTGCTAGTGTTG 60.726 54.545 0.00 7.25 38.53 3.33
1050 1569 1.465387 CGACGACTCTCTGCTAGTGTT 59.535 52.381 0.00 0.00 32.13 3.32
1062 1581 2.202146 CCACGACGACGACGACTC 60.202 66.667 25.15 0.78 42.66 3.36
1063 1582 2.947890 GACCACGACGACGACGACT 61.948 63.158 25.15 7.39 42.66 4.18
1064 1583 2.498466 GACCACGACGACGACGAC 60.498 66.667 25.15 7.02 42.66 4.34
1065 1584 2.966537 TGACCACGACGACGACGA 60.967 61.111 25.15 0.25 42.66 4.20
1066 1585 2.794166 GTGACCACGACGACGACG 60.794 66.667 17.60 17.60 42.66 5.12
1068 1587 4.016629 CGGTGACCACGACGACGA 62.017 66.667 15.32 0.00 42.66 4.20
1215 1742 2.251075 GCGAGATCCGAGCGAGAG 59.749 66.667 7.64 0.00 41.76 3.20
1227 1769 2.283894 TCCAAGCTGGAGGCGAGA 60.284 61.111 0.00 0.00 42.67 4.04
1235 1777 4.952071 TTAGAGATGAGATCCAAGCTGG 57.048 45.455 0.00 0.00 39.43 4.85
1236 1778 5.239351 CCATTAGAGATGAGATCCAAGCTG 58.761 45.833 0.00 0.00 0.00 4.24
1237 1779 4.262981 GCCATTAGAGATGAGATCCAAGCT 60.263 45.833 0.00 0.00 0.00 3.74
1238 1780 4.002316 GCCATTAGAGATGAGATCCAAGC 58.998 47.826 0.00 0.00 0.00 4.01
1239 1781 4.244066 CGCCATTAGAGATGAGATCCAAG 58.756 47.826 0.00 0.00 0.00 3.61
1240 1782 3.007290 CCGCCATTAGAGATGAGATCCAA 59.993 47.826 0.00 0.00 0.00 3.53
1241 1783 2.564504 CCGCCATTAGAGATGAGATCCA 59.435 50.000 0.00 0.00 0.00 3.41
1242 1784 2.676463 GCCGCCATTAGAGATGAGATCC 60.676 54.545 0.00 0.00 0.00 3.36
1243 1785 2.615869 GCCGCCATTAGAGATGAGATC 58.384 52.381 0.00 0.00 0.00 2.75
1244 1786 1.067283 CGCCGCCATTAGAGATGAGAT 60.067 52.381 0.00 0.00 0.00 2.75
1289 1833 4.662961 CACGGTGGTCTGCGAGCA 62.663 66.667 0.00 6.39 37.74 4.26
1291 1835 3.633094 CTCCACGGTGGTCTGCGAG 62.633 68.421 25.53 11.53 39.03 5.03
1292 1836 3.680786 CTCCACGGTGGTCTGCGA 61.681 66.667 25.53 5.47 39.03 5.10
1293 1837 4.742201 CCTCCACGGTGGTCTGCG 62.742 72.222 25.53 10.64 39.03 5.18
1303 1847 3.997064 CTCCTTGAGCGCCTCCACG 62.997 68.421 2.29 0.00 0.00 4.94
1458 2005 3.682292 GATGCAGGTGGGGACGGAC 62.682 68.421 0.00 0.00 0.00 4.79
1459 2006 3.399181 GATGCAGGTGGGGACGGA 61.399 66.667 0.00 0.00 0.00 4.69
1462 2009 1.977293 GAGGAGATGCAGGTGGGGAC 61.977 65.000 0.00 0.00 0.00 4.46
1463 2010 1.690633 GAGGAGATGCAGGTGGGGA 60.691 63.158 0.00 0.00 0.00 4.81
1531 2080 1.448013 GCCGGTACCTTCAGAGCAC 60.448 63.158 10.90 0.00 0.00 4.40
1647 2196 0.679505 ACTTACTGCCGAGCTTGTCA 59.320 50.000 0.00 0.00 0.00 3.58
1666 2215 1.382522 GAAGCCGAATGCATCCTGAA 58.617 50.000 0.00 0.00 44.83 3.02
1673 2222 1.810151 GTAAACTGGAAGCCGAATGCA 59.190 47.619 0.00 0.00 44.83 3.96
1674 2223 1.810151 TGTAAACTGGAAGCCGAATGC 59.190 47.619 0.00 0.00 37.60 3.56
1680 2229 5.003804 TCATCTTCTTGTAAACTGGAAGCC 58.996 41.667 0.00 0.00 37.60 4.35
1682 2231 9.403110 CAAATTCATCTTCTTGTAAACTGGAAG 57.597 33.333 0.00 0.00 42.29 3.46
1694 2243 4.682021 AGGGGTCCAAATTCATCTTCTT 57.318 40.909 0.00 0.00 0.00 2.52
1695 2244 4.202716 ACAAGGGGTCCAAATTCATCTTCT 60.203 41.667 0.00 0.00 0.00 2.85
1696 2245 4.082026 CACAAGGGGTCCAAATTCATCTTC 60.082 45.833 0.00 0.00 0.00 2.87
1719 2268 5.422650 ACTCTGGGAATTCTACAAGAGGTAC 59.577 44.000 20.78 0.00 0.00 3.34
1772 2321 7.068839 CCTCTACTAGAGTCATCCAAGCTTTAA 59.931 40.741 11.46 0.00 40.72 1.52
1777 2326 4.465886 TCCTCTACTAGAGTCATCCAAGC 58.534 47.826 11.46 0.00 40.72 4.01
1778 2327 5.690865 ACTCCTCTACTAGAGTCATCCAAG 58.309 45.833 11.46 1.80 40.72 3.61
1779 2328 5.718801 ACTCCTCTACTAGAGTCATCCAA 57.281 43.478 11.46 0.00 40.72 3.53
1831 2390 6.860539 CACAGAAGTTAGATGGTATGATCGAG 59.139 42.308 0.00 0.00 0.00 4.04
1836 2395 5.675684 TGCACAGAAGTTAGATGGTATGA 57.324 39.130 0.00 0.00 0.00 2.15
1837 2396 6.539826 TGATTGCACAGAAGTTAGATGGTATG 59.460 38.462 0.00 0.00 0.00 2.39
1838 2397 6.653020 TGATTGCACAGAAGTTAGATGGTAT 58.347 36.000 0.00 0.00 0.00 2.73
1841 2409 5.817988 CATGATTGCACAGAAGTTAGATGG 58.182 41.667 0.00 0.00 0.00 3.51
1861 2430 0.597568 TTCCGGAAGTTTGCTGCATG 59.402 50.000 14.35 0.00 0.00 4.06
1862 2431 0.883833 CTTCCGGAAGTTTGCTGCAT 59.116 50.000 32.16 0.00 33.87 3.96
1893 2462 2.661718 ACAGGGTTTTTCGACACCATT 58.338 42.857 9.31 0.00 34.36 3.16
1935 2504 1.072806 ACAAGTCCAGAGCATGAGCAA 59.927 47.619 0.00 0.00 45.49 3.91
1939 2508 3.213206 ACAAACAAGTCCAGAGCATGA 57.787 42.857 0.00 0.00 0.00 3.07
1982 2551 5.707298 AGAGTAAACTTGCTTGCATGTGTAT 59.293 36.000 13.52 7.25 0.00 2.29
1984 2553 3.885297 AGAGTAAACTTGCTTGCATGTGT 59.115 39.130 13.52 11.13 0.00 3.72
1985 2554 4.224433 CAGAGTAAACTTGCTTGCATGTG 58.776 43.478 13.52 2.89 0.00 3.21
1986 2555 3.885297 ACAGAGTAAACTTGCTTGCATGT 59.115 39.130 8.09 8.09 0.00 3.21
1987 2556 4.494350 ACAGAGTAAACTTGCTTGCATG 57.506 40.909 6.90 6.90 0.00 4.06
1988 2557 5.300286 AGAAACAGAGTAAACTTGCTTGCAT 59.700 36.000 0.00 0.00 0.00 3.96
1989 2558 4.640201 AGAAACAGAGTAAACTTGCTTGCA 59.360 37.500 0.00 0.00 0.00 4.08
1990 2559 5.175090 AGAAACAGAGTAAACTTGCTTGC 57.825 39.130 0.00 0.00 0.00 4.01
1991 2560 6.555315 ACAAGAAACAGAGTAAACTTGCTTG 58.445 36.000 0.00 0.00 38.42 4.01
1992 2561 6.183360 GGACAAGAAACAGAGTAAACTTGCTT 60.183 38.462 0.00 0.00 38.42 3.91
1993 2562 5.297029 GGACAAGAAACAGAGTAAACTTGCT 59.703 40.000 0.00 0.00 38.42 3.91
1994 2563 5.297029 AGGACAAGAAACAGAGTAAACTTGC 59.703 40.000 0.00 0.00 38.42 4.01
1995 2564 6.763610 AGAGGACAAGAAACAGAGTAAACTTG 59.236 38.462 0.00 0.00 39.98 3.16
1996 2565 6.890293 AGAGGACAAGAAACAGAGTAAACTT 58.110 36.000 0.00 0.00 0.00 2.66
1997 2566 6.487299 AGAGGACAAGAAACAGAGTAAACT 57.513 37.500 0.00 0.00 0.00 2.66
2039 2608 3.088532 GTTGGCACACAATTCCTCCATA 58.911 45.455 0.00 0.00 41.95 2.74
2075 2644 7.072177 TCTAGCATACATGTGTAAAGCAAAC 57.928 36.000 9.11 0.00 37.77 2.93
2103 2672 1.601663 GCCATAGCGTGTGCAAAAACA 60.602 47.619 0.00 0.00 46.23 2.83
2123 2698 6.015688 AGCAGATTAGTTGGCAATATTCCATG 60.016 38.462 1.92 0.00 32.92 3.66
2149 2724 1.676006 GATGACCGGGGCTTAAACATG 59.324 52.381 6.32 0.00 0.00 3.21
2155 2730 0.325296 ACTGAGATGACCGGGGCTTA 60.325 55.000 6.32 0.00 0.00 3.09
2217 2794 6.308766 CGCAGCAAGCTAGACAATAAAAATTT 59.691 34.615 0.00 0.00 42.61 1.82
2305 2884 5.242393 AGTTATTGCTAATTGGGCTGCTATG 59.758 40.000 0.00 0.00 0.00 2.23
2345 2924 5.004440 CGGATTCATACATACTAATTCGGCG 59.996 44.000 0.00 0.00 28.78 6.46
2348 2927 6.183360 GCCACGGATTCATACATACTAATTCG 60.183 42.308 0.00 0.00 36.59 3.34
2362 2941 0.037447 TTGATGTGGCCACGGATTCA 59.963 50.000 30.07 24.41 0.00 2.57
2368 2947 0.238289 GTCAAGTTGATGTGGCCACG 59.762 55.000 30.07 13.70 0.00 4.94
2380 2959 4.023291 AGTTCATGTGGGTTTGTCAAGTT 58.977 39.130 0.00 0.00 0.00 2.66
2386 2965 3.360867 TGTCAAGTTCATGTGGGTTTGT 58.639 40.909 0.00 0.00 0.00 2.83
2389 2968 4.023291 AGTTTGTCAAGTTCATGTGGGTT 58.977 39.130 0.00 0.00 0.00 4.11
2437 3016 7.404671 TGCACTATATGACTGTAGACAGAAA 57.595 36.000 16.44 4.34 46.59 2.52
2441 3020 9.914131 GAATAATGCACTATATGACTGTAGACA 57.086 33.333 0.00 0.00 0.00 3.41
2471 3050 8.324163 ACACATATTCCTTCACAGTTAGAAAC 57.676 34.615 0.00 0.00 0.00 2.78
2474 3053 9.817809 GAATACACATATTCCTTCACAGTTAGA 57.182 33.333 0.00 0.00 40.58 2.10
2475 3054 9.599866 TGAATACACATATTCCTTCACAGTTAG 57.400 33.333 4.94 0.00 44.26 2.34
2477 3056 9.113838 GATGAATACACATATTCCTTCACAGTT 57.886 33.333 4.94 0.00 44.26 3.16
2478 3057 8.489489 AGATGAATACACATATTCCTTCACAGT 58.511 33.333 4.94 0.00 44.26 3.55
2494 3073 4.927267 ACACAAGGGGAAGATGAATACA 57.073 40.909 0.00 0.00 0.00 2.29
2545 3124 5.421056 AGCCAGTAAACTATACACTGCAGTA 59.579 40.000 21.20 5.19 38.67 2.74
2547 3126 4.759782 AGCCAGTAAACTATACACTGCAG 58.240 43.478 13.48 13.48 38.67 4.41
2559 3138 2.857104 GCGGTCACAAAAGCCAGTAAAC 60.857 50.000 0.00 0.00 0.00 2.01
2562 3141 0.107831 AGCGGTCACAAAAGCCAGTA 59.892 50.000 0.00 0.00 0.00 2.74
2563 3142 0.751643 AAGCGGTCACAAAAGCCAGT 60.752 50.000 0.00 0.00 0.00 4.00
2564 3143 1.197721 CTAAGCGGTCACAAAAGCCAG 59.802 52.381 0.00 0.00 0.00 4.85
2566 3145 1.235724 ACTAAGCGGTCACAAAAGCC 58.764 50.000 0.00 0.00 0.00 4.35
2567 3146 2.159693 GCTACTAAGCGGTCACAAAAGC 60.160 50.000 0.00 0.00 39.39 3.51
2568 3147 3.724295 GCTACTAAGCGGTCACAAAAG 57.276 47.619 0.00 0.00 39.39 2.27
2580 3159 5.153950 ACTCAAACCAGGAAGCTACTAAG 57.846 43.478 0.00 0.00 0.00 2.18
2581 3160 5.337330 GCTACTCAAACCAGGAAGCTACTAA 60.337 44.000 0.00 0.00 0.00 2.24
2601 3180 9.884465 CCTATTATGCTTTACTCAAAATGCTAC 57.116 33.333 0.00 0.00 0.00 3.58
2611 3190 9.418045 GAGTGAGATTCCTATTATGCTTTACTC 57.582 37.037 0.00 0.00 0.00 2.59
2623 3202 8.247562 GTCATATTTAGCGAGTGAGATTCCTAT 58.752 37.037 0.00 0.00 0.00 2.57
2632 3211 6.894339 TGGATAGTCATATTTAGCGAGTGA 57.106 37.500 0.00 0.00 0.00 3.41
2635 3214 5.573282 CGGTTGGATAGTCATATTTAGCGAG 59.427 44.000 0.00 0.00 0.00 5.03
2638 3217 5.989777 ACACGGTTGGATAGTCATATTTAGC 59.010 40.000 0.00 0.00 0.00 3.09
2640 3222 6.880484 ACACACGGTTGGATAGTCATATTTA 58.120 36.000 0.00 0.00 0.00 1.40
2645 3227 3.767673 ACTACACACGGTTGGATAGTCAT 59.232 43.478 0.00 0.00 0.00 3.06
2646 3228 3.159472 ACTACACACGGTTGGATAGTCA 58.841 45.455 0.00 0.00 0.00 3.41
2647 3229 3.863142 ACTACACACGGTTGGATAGTC 57.137 47.619 0.00 0.00 0.00 2.59
2648 3230 3.575256 TCAACTACACACGGTTGGATAGT 59.425 43.478 0.00 0.00 41.91 2.12
2649 3231 3.924686 GTCAACTACACACGGTTGGATAG 59.075 47.826 0.00 0.00 41.91 2.08
2659 3304 3.000925 CGTCAACTTGGTCAACTACACAC 59.999 47.826 0.00 0.00 0.00 3.82
2661 3306 3.450578 TCGTCAACTTGGTCAACTACAC 58.549 45.455 0.00 0.00 0.00 2.90
2672 3317 3.226346 TCCGTATTCCTCGTCAACTTG 57.774 47.619 0.00 0.00 0.00 3.16
2679 3324 1.134560 GCTCAGTTCCGTATTCCTCGT 59.865 52.381 0.00 0.00 0.00 4.18
2690 3335 6.203723 GTGATCAGTTATATTGGCTCAGTTCC 59.796 42.308 0.00 0.00 0.00 3.62
2694 3339 9.149225 GATAAGTGATCAGTTATATTGGCTCAG 57.851 37.037 27.98 0.00 37.14 3.35
2697 3342 9.277783 GTTGATAAGTGATCAGTTATATTGGCT 57.722 33.333 27.98 11.62 45.43 4.75
2711 3360 5.395768 GCAGAGTACCCTGTTGATAAGTGAT 60.396 44.000 6.24 0.00 36.57 3.06
2720 3369 3.070018 CTGAAAGCAGAGTACCCTGTTG 58.930 50.000 6.24 0.00 45.17 3.33
2744 3393 7.083875 ACCAATATTTACTACACACACATGC 57.916 36.000 0.00 0.00 0.00 4.06
2752 3401 6.882678 ACACCAAGGACCAATATTTACTACAC 59.117 38.462 0.00 0.00 0.00 2.90
2782 3431 9.132521 CGTTCTTTTCAATAGCAAAGAATCAAT 57.867 29.630 9.71 0.00 44.61 2.57
2783 3432 7.594758 CCGTTCTTTTCAATAGCAAAGAATCAA 59.405 33.333 9.71 0.00 44.61 2.57
2784 3433 7.083858 CCGTTCTTTTCAATAGCAAAGAATCA 58.916 34.615 9.71 0.00 44.61 2.57
2785 3434 7.084486 ACCGTTCTTTTCAATAGCAAAGAATC 58.916 34.615 9.71 4.82 44.61 2.52
2808 3457 2.945668 GCCTGTGTCAATATTCCAGACC 59.054 50.000 2.86 0.00 0.00 3.85
2817 3466 5.702670 CAGAAGAAGAAAGCCTGTGTCAATA 59.297 40.000 0.00 0.00 0.00 1.90
2822 3471 3.209410 CACAGAAGAAGAAAGCCTGTGT 58.791 45.455 11.38 0.00 45.59 3.72
2823 3472 3.892918 CACAGAAGAAGAAAGCCTGTG 57.107 47.619 0.00 0.00 45.48 3.66
2827 3477 0.519077 CGCCACAGAAGAAGAAAGCC 59.481 55.000 0.00 0.00 0.00 4.35
2848 3498 6.352516 ACAAAACAGGTGCAATTTCCATTTA 58.647 32.000 0.00 0.00 0.00 1.40
2860 3510 6.966435 AATATTGCATAACAAAACAGGTGC 57.034 33.333 0.00 0.00 42.86 5.01
2898 3548 7.126573 TGTCTCCCACCTATGACATAAATGTTA 59.873 37.037 0.00 0.00 41.95 2.41
2935 3585 2.045536 CTCTTGGCACCTGGCTCC 60.046 66.667 0.00 0.00 44.01 4.70
3019 3669 1.202915 TGCTTTCCAAGTGGCTCATCA 60.203 47.619 0.00 0.00 34.44 3.07
3073 3723 6.770785 TGGGCACTGAGTATAAATTTATCACC 59.229 38.462 13.95 6.01 0.00 4.02
3089 3739 2.198827 CATGGTAACTTGGGCACTGA 57.801 50.000 0.00 0.00 38.05 3.41
3134 3784 5.759763 ACAAAATGAATTGTTTCTCCAAGGC 59.240 36.000 0.00 0.00 40.52 4.35
3155 3805 2.175202 AGCACCCAACAAGTCAAACAA 58.825 42.857 0.00 0.00 0.00 2.83
3196 3846 2.214181 GAGGGCACTCGAAGAAGCGA 62.214 60.000 0.00 0.00 38.32 4.93
3260 3910 5.317600 AGTACTAGGTAAGGTAGGTAGGC 57.682 47.826 0.00 0.00 0.00 3.93
3297 4042 5.968387 AAGACCGAATGTTATAAGAAGCG 57.032 39.130 0.00 0.00 0.00 4.68
3314 4059 5.570234 TTTTAACCGGATGCATAAAGACC 57.430 39.130 9.46 0.00 0.00 3.85
3316 4061 7.831753 TGAATTTTTAACCGGATGCATAAAGA 58.168 30.769 9.46 1.68 0.00 2.52
3320 4065 5.888724 TCCTGAATTTTTAACCGGATGCATA 59.111 36.000 9.46 0.00 0.00 3.14
3394 4139 4.017222 TCTTCATCATCAAATGGGTCCCTT 60.017 41.667 10.00 0.00 0.00 3.95
3438 4186 3.255642 CCAAAACGATCCACACCAAAGAT 59.744 43.478 0.00 0.00 0.00 2.40
3561 4313 2.290896 CCCTCCCTTTGCTGATACAACA 60.291 50.000 0.00 0.00 0.00 3.33
3562 4314 2.369394 CCCTCCCTTTGCTGATACAAC 58.631 52.381 0.00 0.00 0.00 3.32
3613 4365 2.480419 CAGCGACTAGTTGAACCCAAAG 59.520 50.000 14.70 0.00 33.49 2.77
3625 4377 5.411781 ACTTTTTAGTCATCCAGCGACTAG 58.588 41.667 0.00 0.00 44.53 2.57
3648 4400 3.335183 TCATTGGTTCTTGGGGGTATGAA 59.665 43.478 0.00 0.00 0.00 2.57
3654 4406 0.114168 TGGTCATTGGTTCTTGGGGG 59.886 55.000 0.00 0.00 0.00 5.40
3716 4468 9.239551 AGTTTTTGGGTACTTCTGGATATAAAC 57.760 33.333 0.00 0.00 0.00 2.01
3720 4472 6.070424 TCGAGTTTTTGGGTACTTCTGGATAT 60.070 38.462 0.00 0.00 0.00 1.63
3727 4479 3.562557 TGCTTCGAGTTTTTGGGTACTTC 59.437 43.478 0.00 0.00 0.00 3.01
3728 4480 3.314357 GTGCTTCGAGTTTTTGGGTACTT 59.686 43.478 0.00 0.00 0.00 2.24
3793 4548 7.391554 AGCTAAAGTTCAAGATAATGCTTGTCA 59.608 33.333 0.00 0.00 44.30 3.58
3821 4576 2.677836 TGAATTGCTACATCGGTTCAGC 59.322 45.455 0.00 0.00 34.56 4.26
3865 4621 3.505293 GCAGATTTTCAGTTCTCCTTGCT 59.495 43.478 0.00 0.00 0.00 3.91
3905 4661 4.758773 TCATGGCATCAAGACTGTATCA 57.241 40.909 0.00 0.00 0.00 2.15
3948 4705 5.185249 AGTTTACTCTGCAATCCTCGTAGAA 59.815 40.000 0.00 0.00 34.09 2.10
4050 4813 2.949177 TGTGGTTACAAGCATGTCCT 57.051 45.000 0.00 0.00 41.05 3.85
4077 4840 2.564721 GCTCTGTTGTTGCCACCCC 61.565 63.158 0.00 0.00 0.00 4.95
4179 4957 3.950395 GAGCTGAATGCCATAAAGAAGGT 59.050 43.478 0.00 0.00 44.23 3.50
4408 5193 1.072965 CTGGAAGAAGGCCAACTGACT 59.927 52.381 5.01 0.00 34.07 3.41
4448 5233 5.195940 GGTGATGTATATAGCTACGGGGTA 58.804 45.833 0.00 0.00 0.00 3.69
4502 5287 8.364142 CCCTTGGTTTATATGTTTGTTTCAGAA 58.636 33.333 0.00 0.00 0.00 3.02
4564 5381 6.757897 ATTCAAACTGAAGAGTGAAACACA 57.242 33.333 4.75 0.00 40.05 3.72
4567 5384 5.460091 GCCAATTCAAACTGAAGAGTGAAAC 59.540 40.000 5.11 0.00 40.05 2.78


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

AutoCloner maintained by Alex Coulton.