Multiple sequence alignment - TraesCS5D01G115200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G115200 chr5D 100.000 4178 0 0 1 4178 134914642 134918819 0.000000e+00 7716.0
1 TraesCS5D01G115200 chr5D 82.540 315 44 9 3670 3982 263367551 263367246 2.480000e-67 267.0
2 TraesCS5D01G115200 chr5B 94.202 2018 52 26 1684 3638 146365578 146367593 0.000000e+00 3018.0
3 TraesCS5D01G115200 chr5B 95.597 954 19 7 739 1681 146364598 146365539 0.000000e+00 1507.0
4 TraesCS5D01G115200 chr5B 91.437 689 44 3 1 689 146363914 146364587 0.000000e+00 931.0
5 TraesCS5D01G115200 chr5B 85.554 713 82 7 1 710 535390289 535389595 0.000000e+00 726.0
6 TraesCS5D01G115200 chr5B 98.901 182 1 1 3998 4178 146367587 146367768 1.450000e-84 324.0
7 TraesCS5D01G115200 chr5B 100.000 28 0 0 723 750 656019927 656019954 8.000000e-03 52.8
8 TraesCS5D01G115200 chr5A 93.810 937 27 13 1938 2843 159533418 159534354 0.000000e+00 1380.0
9 TraesCS5D01G115200 chr5A 96.384 802 23 2 2840 3638 159534383 159535181 0.000000e+00 1315.0
10 TraesCS5D01G115200 chr5A 95.216 648 17 7 807 1444 159532767 159533410 0.000000e+00 1013.0
11 TraesCS5D01G115200 chr5A 97.790 181 4 0 3998 4178 159535175 159535355 3.140000e-81 313.0
12 TraesCS5D01G115200 chr6D 87.815 714 63 13 1 710 462687611 462688304 0.000000e+00 815.0
13 TraesCS5D01G115200 chr6D 87.552 715 69 11 1 710 61103039 61103738 0.000000e+00 809.0
14 TraesCS5D01G115200 chr6D 82.848 309 46 5 3641 3949 328503782 328504083 1.910000e-68 270.0
15 TraesCS5D01G115200 chr6D 96.552 87 3 0 1853 1939 122992191 122992105 1.210000e-30 145.0
16 TraesCS5D01G115200 chr6D 100.000 28 0 0 723 750 378734544 378734571 8.000000e-03 52.8
17 TraesCS5D01G115200 chr3D 87.065 719 73 13 1 710 281081283 281081990 0.000000e+00 795.0
18 TraesCS5D01G115200 chr3D 83.810 735 81 16 1 710 85024325 85023604 0.000000e+00 664.0
19 TraesCS5D01G115200 chr3D 91.143 350 22 7 3639 3987 133543920 133544261 2.270000e-127 466.0
20 TraesCS5D01G115200 chr3D 86.744 347 24 14 3661 3997 56681541 56681207 2.370000e-97 366.0
21 TraesCS5D01G115200 chr3D 94.444 90 5 0 1849 1938 326697044 326696955 5.630000e-29 139.0
22 TraesCS5D01G115200 chr7D 85.655 718 79 15 1 710 424489598 424488897 0.000000e+00 734.0
23 TraesCS5D01G115200 chr7D 88.286 350 28 9 3639 3987 433174889 433174552 1.400000e-109 407.0
24 TraesCS5D01G115200 chr7D 95.402 87 3 1 1853 1939 131468367 131468452 2.030000e-28 137.0
25 TraesCS5D01G115200 chr7D 100.000 29 0 0 723 751 117578451 117578479 2.000000e-03 54.7
26 TraesCS5D01G115200 chr1D 85.854 714 61 10 4 710 223469325 223468645 0.000000e+00 723.0
27 TraesCS5D01G115200 chr1D 83.119 622 71 25 1 611 6323024 6322426 1.710000e-148 536.0
28 TraesCS5D01G115200 chr1D 96.875 32 1 0 720 751 447450901 447450932 2.000000e-03 54.7
29 TraesCS5D01G115200 chr6B 83.894 714 89 18 1 710 261572407 261571716 0.000000e+00 658.0
30 TraesCS5D01G115200 chr6B 85.795 352 28 12 3640 3981 321255738 321256077 1.850000e-93 353.0
31 TraesCS5D01G115200 chr2B 83.450 713 93 14 1 710 673089960 673090650 1.270000e-179 640.0
32 TraesCS5D01G115200 chr1B 89.157 332 25 7 3665 3994 327829973 327830295 1.810000e-108 403.0
33 TraesCS5D01G115200 chr1B 92.473 93 5 2 1853 1945 495412951 495412861 9.420000e-27 132.0
34 TraesCS5D01G115200 chr1B 100.000 29 0 0 723 751 410313331 410313359 2.000000e-03 54.7
35 TraesCS5D01G115200 chr6A 86.232 276 30 6 3676 3950 335787573 335787841 4.090000e-75 292.0
36 TraesCS5D01G115200 chr6A 95.556 90 3 1 1853 1941 548408060 548408149 4.350000e-30 143.0
37 TraesCS5D01G115200 chr6A 94.118 34 2 0 718 751 531403536 531403569 8.000000e-03 52.8
38 TraesCS5D01G115200 chr4B 80.627 351 49 14 3641 3981 551000928 551000587 1.930000e-63 254.0
39 TraesCS5D01G115200 chr4B 100.000 29 0 0 3646 3674 15902596 15902624 2.000000e-03 54.7
40 TraesCS5D01G115200 chr2A 95.455 88 4 0 1851 1938 385002702 385002789 1.570000e-29 141.0
41 TraesCS5D01G115200 chr2A 100.000 29 0 0 723 751 698649824 698649852 2.000000e-03 54.7
42 TraesCS5D01G115200 chr4A 93.617 94 4 2 1845 1938 625404770 625404861 5.630000e-29 139.0
43 TraesCS5D01G115200 chr7B 93.333 90 6 0 1849 1938 153326932 153326843 2.620000e-27 134.0
44 TraesCS5D01G115200 chrUn 100.000 28 0 0 723 750 362216547 362216574 8.000000e-03 52.8
45 TraesCS5D01G115200 chrUn 100.000 28 0 0 723 750 362218596 362218623 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G115200 chr5D 134914642 134918819 4177 False 7716.00 7716 100.00000 1 4178 1 chr5D.!!$F1 4177
1 TraesCS5D01G115200 chr5B 146363914 146367768 3854 False 1445.00 3018 95.03425 1 4178 4 chr5B.!!$F2 4177
2 TraesCS5D01G115200 chr5B 535389595 535390289 694 True 726.00 726 85.55400 1 710 1 chr5B.!!$R1 709
3 TraesCS5D01G115200 chr5A 159532767 159535355 2588 False 1005.25 1380 95.80000 807 4178 4 chr5A.!!$F1 3371
4 TraesCS5D01G115200 chr6D 462687611 462688304 693 False 815.00 815 87.81500 1 710 1 chr6D.!!$F4 709
5 TraesCS5D01G115200 chr6D 61103039 61103738 699 False 809.00 809 87.55200 1 710 1 chr6D.!!$F1 709
6 TraesCS5D01G115200 chr3D 281081283 281081990 707 False 795.00 795 87.06500 1 710 1 chr3D.!!$F2 709
7 TraesCS5D01G115200 chr3D 85023604 85024325 721 True 664.00 664 83.81000 1 710 1 chr3D.!!$R2 709
8 TraesCS5D01G115200 chr7D 424488897 424489598 701 True 734.00 734 85.65500 1 710 1 chr7D.!!$R1 709
9 TraesCS5D01G115200 chr1D 223468645 223469325 680 True 723.00 723 85.85400 4 710 1 chr1D.!!$R2 706
10 TraesCS5D01G115200 chr1D 6322426 6323024 598 True 536.00 536 83.11900 1 611 1 chr1D.!!$R1 610
11 TraesCS5D01G115200 chr6B 261571716 261572407 691 True 658.00 658 83.89400 1 710 1 chr6B.!!$R1 709
12 TraesCS5D01G115200 chr2B 673089960 673090650 690 False 640.00 640 83.45000 1 710 1 chr2B.!!$F1 709

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
712 791 0.032952 TCGTGCGCTAGAGTTGGTTT 59.967 50.0 9.73 0.0 0.0 3.27 F
1477 1572 0.528017 TGGCGTGCTCTCTTCTACTG 59.472 55.0 0.00 0.0 0.0 2.74 F
1514 1609 0.669318 GACGATGTCTTGCGGGTGAA 60.669 55.0 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1870 0.322975 AGCATCGCAAAGACAGAGGT 59.677 50.000 0.0 0.0 0.0 3.85 R
2760 2921 1.555075 GGGTCTGAAGCTGATGTACCA 59.445 52.381 0.0 0.0 0.0 3.25 R
3184 3378 4.012374 CTGAAGGTTGCAAGGACACATAT 58.988 43.478 0.0 0.0 0.0 1.78 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
82 93 1.392534 GGAGGAGGTGAGGGAGGAA 59.607 63.158 0.00 0.00 0.00 3.36
343 394 1.210931 CGACCTTACTGGCGACGAA 59.789 57.895 0.00 0.00 40.22 3.85
570 647 4.940905 TTTTATATCACGTCCATCCCGA 57.059 40.909 0.00 0.00 0.00 5.14
653 730 2.747177 TGGATGACTCCATTACCGTCT 58.253 47.619 0.00 0.00 46.95 4.18
654 731 3.905968 TGGATGACTCCATTACCGTCTA 58.094 45.455 0.00 0.00 46.95 2.59
657 734 5.365605 TGGATGACTCCATTACCGTCTAAAT 59.634 40.000 0.00 0.00 46.95 1.40
661 738 5.301045 TGACTCCATTACCGTCTAAATCGAT 59.699 40.000 0.00 0.00 0.00 3.59
710 789 0.246635 AATCGTGCGCTAGAGTTGGT 59.753 50.000 9.73 0.00 0.00 3.67
711 790 0.246635 ATCGTGCGCTAGAGTTGGTT 59.753 50.000 9.73 0.00 0.00 3.67
712 791 0.032952 TCGTGCGCTAGAGTTGGTTT 59.967 50.000 9.73 0.00 0.00 3.27
713 792 1.270274 TCGTGCGCTAGAGTTGGTTTA 59.730 47.619 9.73 0.00 0.00 2.01
714 793 2.063266 CGTGCGCTAGAGTTGGTTTAA 58.937 47.619 9.73 0.00 0.00 1.52
715 794 2.092211 CGTGCGCTAGAGTTGGTTTAAG 59.908 50.000 9.73 0.00 0.00 1.85
716 795 2.073816 TGCGCTAGAGTTGGTTTAAGC 58.926 47.619 9.73 0.00 0.00 3.09
717 796 2.073816 GCGCTAGAGTTGGTTTAAGCA 58.926 47.619 0.00 0.00 0.00 3.91
718 797 2.678336 GCGCTAGAGTTGGTTTAAGCAT 59.322 45.455 0.00 0.00 0.00 3.79
719 798 3.485877 GCGCTAGAGTTGGTTTAAGCATG 60.486 47.826 0.00 0.00 0.00 4.06
720 799 3.932710 CGCTAGAGTTGGTTTAAGCATGA 59.067 43.478 0.00 0.00 0.00 3.07
721 800 4.391830 CGCTAGAGTTGGTTTAAGCATGAA 59.608 41.667 0.00 0.00 0.00 2.57
722 801 5.065218 CGCTAGAGTTGGTTTAAGCATGAAT 59.935 40.000 0.00 0.00 0.00 2.57
723 802 6.403636 CGCTAGAGTTGGTTTAAGCATGAATT 60.404 38.462 0.00 0.00 0.00 2.17
724 803 6.749118 GCTAGAGTTGGTTTAAGCATGAATTG 59.251 38.462 0.00 0.00 0.00 2.32
725 804 6.029346 AGAGTTGGTTTAAGCATGAATTGG 57.971 37.500 0.00 0.00 0.00 3.16
726 805 5.774690 AGAGTTGGTTTAAGCATGAATTGGA 59.225 36.000 0.00 0.00 0.00 3.53
727 806 6.438425 AGAGTTGGTTTAAGCATGAATTGGAT 59.562 34.615 0.00 0.00 0.00 3.41
728 807 6.633856 AGTTGGTTTAAGCATGAATTGGATC 58.366 36.000 0.00 0.00 0.00 3.36
729 808 5.247507 TGGTTTAAGCATGAATTGGATCG 57.752 39.130 0.00 0.00 0.00 3.69
730 809 4.097741 TGGTTTAAGCATGAATTGGATCGG 59.902 41.667 0.00 0.00 0.00 4.18
731 810 3.988379 TTAAGCATGAATTGGATCGGC 57.012 42.857 0.00 0.00 0.00 5.54
732 811 0.664761 AAGCATGAATTGGATCGGCG 59.335 50.000 0.00 0.00 0.00 6.46
733 812 1.370900 GCATGAATTGGATCGGCGC 60.371 57.895 0.00 0.00 0.00 6.53
734 813 1.082561 CATGAATTGGATCGGCGCG 60.083 57.895 0.00 0.00 0.00 6.86
735 814 1.523711 ATGAATTGGATCGGCGCGT 60.524 52.632 8.43 0.00 0.00 6.01
736 815 1.095228 ATGAATTGGATCGGCGCGTT 61.095 50.000 8.43 0.00 0.00 4.84
737 816 1.297598 GAATTGGATCGGCGCGTTG 60.298 57.895 8.43 0.00 0.00 4.10
738 817 2.646799 GAATTGGATCGGCGCGTTGG 62.647 60.000 8.43 0.00 0.00 3.77
739 818 3.673956 ATTGGATCGGCGCGTTGGA 62.674 57.895 8.43 2.80 0.00 3.53
740 819 4.812476 TGGATCGGCGCGTTGGAG 62.812 66.667 8.43 0.00 0.00 3.86
741 820 4.814294 GGATCGGCGCGTTGGAGT 62.814 66.667 8.43 0.00 0.00 3.85
742 821 2.813908 GATCGGCGCGTTGGAGTT 60.814 61.111 8.43 0.00 0.00 3.01
756 835 4.846137 CGTTGGAGTTGCTCTTATTTTTCG 59.154 41.667 0.00 0.00 0.00 3.46
837 925 3.965539 CTGACTTGCAGGCCCTCCG 62.966 68.421 0.00 0.00 41.07 4.63
847 935 4.157120 GCCCTCCGCGGCTTTCTA 62.157 66.667 23.51 0.00 46.10 2.10
848 936 2.107141 CCCTCCGCGGCTTTCTAG 59.893 66.667 23.51 11.70 0.00 2.43
984 1076 1.600916 AGCCAAGGACCAACGAAGC 60.601 57.895 0.00 0.00 0.00 3.86
1324 1419 2.578940 TGGGTTCAGGGTTTATCGGATT 59.421 45.455 0.00 0.00 0.00 3.01
1477 1572 0.528017 TGGCGTGCTCTCTTCTACTG 59.472 55.000 0.00 0.00 0.00 2.74
1478 1573 0.804156 GGCGTGCTCTCTTCTACTGC 60.804 60.000 0.00 0.00 0.00 4.40
1479 1574 1.136872 GCGTGCTCTCTTCTACTGCG 61.137 60.000 0.00 0.00 0.00 5.18
1509 1604 2.456119 GCCAGACGATGTCTTGCGG 61.456 63.158 7.18 2.99 41.37 5.69
1510 1605 1.811266 CCAGACGATGTCTTGCGGG 60.811 63.158 0.00 0.00 41.37 6.13
1511 1606 1.079819 CAGACGATGTCTTGCGGGT 60.080 57.895 0.00 0.00 41.37 5.28
1512 1607 1.079819 AGACGATGTCTTGCGGGTG 60.080 57.895 0.00 0.00 40.28 4.61
1513 1608 1.080093 GACGATGTCTTGCGGGTGA 60.080 57.895 0.00 0.00 0.00 4.02
1514 1609 0.669318 GACGATGTCTTGCGGGTGAA 60.669 55.000 0.00 0.00 0.00 3.18
1515 1610 0.670546 ACGATGTCTTGCGGGTGAAG 60.671 55.000 0.00 0.00 0.00 3.02
1561 1656 2.036862 GACGGGTTAGGAATAAGCGGAT 59.963 50.000 10.46 0.00 33.74 4.18
1633 1728 1.339438 GGCTGAATTCCTGCTCTGTCA 60.339 52.381 16.54 0.00 39.38 3.58
1681 1776 3.574354 TGATACAACTGCATGGCCATA 57.426 42.857 20.30 2.28 0.00 2.74
1769 1900 6.536941 TGTCTTTGCGATGCTGTATTATGTAA 59.463 34.615 0.00 0.00 0.00 2.41
1783 1914 9.811995 CTGTATTATGTAAGTAACAACAGCCTA 57.188 33.333 0.00 0.00 42.70 3.93
1816 1947 8.306038 CAAATTCCATTTTCTTGTCCAGTATGA 58.694 33.333 0.00 0.00 39.69 2.15
1845 1976 7.896496 AGAATCCTAACCTCTCTTTGTTCTCTA 59.104 37.037 0.00 0.00 0.00 2.43
1855 1986 9.403583 CCTCTCTTTGTTCTCTAGTTATCTACT 57.596 37.037 0.00 0.00 41.04 2.57
1874 2005 4.423625 ACTCCCTCCGATCCAAAATAAG 57.576 45.455 0.00 0.00 0.00 1.73
1940 2071 7.393796 ACTTATTATGGATCGGAGGTAGTACAG 59.606 40.741 2.06 0.00 0.00 2.74
1975 2106 3.073798 TGGAGGAAACTTACCATCAGCAA 59.926 43.478 0.00 0.00 44.43 3.91
2038 2169 4.697514 CAACGGTTCCTATGATGACATCT 58.302 43.478 16.25 5.06 37.87 2.90
2062 2193 6.698008 TTGTGGTATCTGCAATTTATCTGG 57.302 37.500 0.00 0.00 0.00 3.86
2097 2228 3.771479 AGACTGCTCTATCAACCACATCA 59.229 43.478 0.00 0.00 0.00 3.07
2144 2275 2.851824 GCAACAAGTGTTTTTCCACTCG 59.148 45.455 0.00 0.00 44.74 4.18
2226 2359 3.054434 TGTCTGACCATTCCGATTCCAAT 60.054 43.478 5.17 0.00 0.00 3.16
2308 2467 6.093219 CACATCCTGTTTCAGAAATCACCTAG 59.907 42.308 0.00 0.00 32.44 3.02
2469 2629 6.999950 TCTCCTTGTGTACTTTATGCTTGTA 58.000 36.000 0.00 0.00 0.00 2.41
2676 2837 8.668353 TCATGCAATATCTTGTTCTGTTTAGAC 58.332 33.333 0.00 0.00 34.69 2.59
2760 2921 7.606456 ACGTATTTCTTTCCAACATCTATGTGT 59.394 33.333 0.00 0.00 41.61 3.72
3059 3253 4.514401 AGCCGGTTCTGAAGGTATTTTAG 58.486 43.478 1.90 0.00 0.00 1.85
3074 3268 8.009622 AGGTATTTTAGCCTACTTGAGTAGTC 57.990 38.462 15.07 4.55 44.88 2.59
3184 3378 2.513317 TGGCAGATGGGGTAAATCATCA 59.487 45.455 0.00 0.00 41.45 3.07
3316 3510 5.803237 AACTGTACTGTTAAGTAGCCACT 57.197 39.130 15.65 0.00 39.60 4.00
3342 3536 6.321690 GCCTGTCTAAGTCTAAGTAGGATTGA 59.678 42.308 0.00 0.00 0.00 2.57
3638 3835 8.911247 ACAAAACTTCAATTGTGACTTCTTAC 57.089 30.769 5.13 0.00 38.29 2.34
3639 3836 8.739972 ACAAAACTTCAATTGTGACTTCTTACT 58.260 29.630 5.13 0.00 38.29 2.24
3640 3837 9.013490 CAAAACTTCAATTGTGACTTCTTACTG 57.987 33.333 5.13 0.00 31.90 2.74
3641 3838 6.867662 ACTTCAATTGTGACTTCTTACTGG 57.132 37.500 5.13 0.00 31.90 4.00
3642 3839 5.239525 ACTTCAATTGTGACTTCTTACTGGC 59.760 40.000 5.13 0.00 31.90 4.85
3643 3840 3.745975 TCAATTGTGACTTCTTACTGGCG 59.254 43.478 5.13 0.00 0.00 5.69
3644 3841 2.902705 TTGTGACTTCTTACTGGCGT 57.097 45.000 0.00 0.00 0.00 5.68
3645 3842 2.902705 TGTGACTTCTTACTGGCGTT 57.097 45.000 0.00 0.00 0.00 4.84
3646 3843 3.188159 TGTGACTTCTTACTGGCGTTT 57.812 42.857 0.00 0.00 0.00 3.60
3647 3844 3.537580 TGTGACTTCTTACTGGCGTTTT 58.462 40.909 0.00 0.00 0.00 2.43
3648 3845 3.311322 TGTGACTTCTTACTGGCGTTTTG 59.689 43.478 0.00 0.00 0.00 2.44
3649 3846 2.875933 TGACTTCTTACTGGCGTTTTGG 59.124 45.455 0.00 0.00 0.00 3.28
3650 3847 1.607148 ACTTCTTACTGGCGTTTTGGC 59.393 47.619 0.00 0.00 45.12 4.52
3651 3848 1.880027 CTTCTTACTGGCGTTTTGGCT 59.120 47.619 0.00 0.00 45.14 4.75
3652 3849 1.519408 TCTTACTGGCGTTTTGGCTC 58.481 50.000 0.00 0.00 45.14 4.70
3653 3850 0.521735 CTTACTGGCGTTTTGGCTCC 59.478 55.000 0.00 0.00 45.14 4.70
3654 3851 0.891904 TTACTGGCGTTTTGGCTCCC 60.892 55.000 0.00 0.00 45.14 4.30
3655 3852 3.737172 CTGGCGTTTTGGCTCCCG 61.737 66.667 0.00 0.00 45.14 5.14
3659 3856 2.746277 CGTTTTGGCTCCCGGGAG 60.746 66.667 41.29 41.29 44.56 4.30
3676 3873 2.361104 GCATTTGCTCCCGGGTGA 60.361 61.111 26.61 3.85 38.21 4.02
3677 3874 1.976474 GCATTTGCTCCCGGGTGAA 60.976 57.895 26.61 13.82 38.21 3.18
3678 3875 1.883021 CATTTGCTCCCGGGTGAAC 59.117 57.895 26.61 11.90 0.00 3.18
3679 3876 0.893270 CATTTGCTCCCGGGTGAACA 60.893 55.000 26.61 9.56 0.00 3.18
3680 3877 0.609131 ATTTGCTCCCGGGTGAACAG 60.609 55.000 26.61 14.30 0.00 3.16
3681 3878 1.990160 TTTGCTCCCGGGTGAACAGT 61.990 55.000 26.61 0.00 0.00 3.55
3682 3879 1.122632 TTGCTCCCGGGTGAACAGTA 61.123 55.000 26.61 9.89 0.00 2.74
3683 3880 1.122632 TGCTCCCGGGTGAACAGTAA 61.123 55.000 26.61 3.32 0.00 2.24
3684 3881 0.672711 GCTCCCGGGTGAACAGTAAC 60.673 60.000 26.61 1.70 0.00 2.50
3685 3882 0.682852 CTCCCGGGTGAACAGTAACA 59.317 55.000 22.86 0.00 0.00 2.41
3686 3883 0.393820 TCCCGGGTGAACAGTAACAC 59.606 55.000 22.86 0.00 36.44 3.32
3687 3884 0.947180 CCCGGGTGAACAGTAACACG 60.947 60.000 14.18 4.32 42.80 4.49
3688 3885 0.032403 CCGGGTGAACAGTAACACGA 59.968 55.000 11.60 0.00 46.01 4.35
3689 3886 1.538634 CCGGGTGAACAGTAACACGAA 60.539 52.381 11.60 0.00 46.01 3.85
3690 3887 2.203401 CGGGTGAACAGTAACACGAAA 58.797 47.619 5.22 0.00 46.01 3.46
3691 3888 2.608546 CGGGTGAACAGTAACACGAAAA 59.391 45.455 5.22 0.00 46.01 2.29
3692 3889 3.063725 CGGGTGAACAGTAACACGAAAAA 59.936 43.478 5.22 0.00 46.01 1.94
3753 3950 8.785329 TTGTAGATGATTGTATTAGTGTTGCA 57.215 30.769 0.00 0.00 0.00 4.08
3754 3951 8.785329 TGTAGATGATTGTATTAGTGTTGCAA 57.215 30.769 0.00 0.00 0.00 4.08
3755 3952 9.225436 TGTAGATGATTGTATTAGTGTTGCAAA 57.775 29.630 0.00 0.00 0.00 3.68
3771 3968 5.752892 TTGCAAACATGCATGACAATTTT 57.247 30.435 32.75 18.50 44.94 1.82
3772 3969 5.345609 TGCAAACATGCATGACAATTTTC 57.654 34.783 32.75 16.53 40.23 2.29
3773 3970 4.814771 TGCAAACATGCATGACAATTTTCA 59.185 33.333 32.75 18.73 40.23 2.69
3774 3971 5.470437 TGCAAACATGCATGACAATTTTCAT 59.530 32.000 32.75 3.33 40.23 2.57
3782 3979 4.862329 CATGACAATTTTCATGCGAAACG 58.138 39.130 18.86 0.00 44.83 3.60
3783 3980 3.304257 TGACAATTTTCATGCGAAACGG 58.696 40.909 0.00 0.00 40.84 4.44
3784 3981 3.003793 TGACAATTTTCATGCGAAACGGA 59.996 39.130 0.00 0.00 40.84 4.69
3785 3982 3.564511 ACAATTTTCATGCGAAACGGAG 58.435 40.909 0.00 0.00 40.84 4.63
3786 3983 2.262572 ATTTTCATGCGAAACGGAGC 57.737 45.000 0.00 0.00 40.84 4.70
3787 3984 1.234821 TTTTCATGCGAAACGGAGCT 58.765 45.000 0.00 0.00 40.84 4.09
3788 3985 0.516877 TTTCATGCGAAACGGAGCTG 59.483 50.000 0.00 0.00 36.19 4.24
3789 3986 1.911293 TTCATGCGAAACGGAGCTGC 61.911 55.000 0.00 0.00 0.00 5.25
3790 3987 3.490759 ATGCGAAACGGAGCTGCG 61.491 61.111 26.95 26.95 0.00 5.18
3793 3990 3.777925 CGAAACGGAGCTGCGGTG 61.778 66.667 31.29 10.83 0.00 4.94
3794 3991 2.665185 GAAACGGAGCTGCGGTGT 60.665 61.111 31.29 15.77 0.00 4.16
3795 3992 2.203153 AAACGGAGCTGCGGTGTT 60.203 55.556 31.29 18.59 0.00 3.32
3796 3993 1.782028 GAAACGGAGCTGCGGTGTTT 61.782 55.000 31.29 21.69 35.61 2.83
3797 3994 1.782028 AAACGGAGCTGCGGTGTTTC 61.782 55.000 31.29 0.00 0.00 2.78
3798 3995 3.777925 CGGAGCTGCGGTGTTTCG 61.778 66.667 21.08 0.00 0.00 3.46
3799 3996 2.665185 GGAGCTGCGGTGTTTCGT 60.665 61.111 0.00 0.00 0.00 3.85
3800 3997 2.668280 GGAGCTGCGGTGTTTCGTC 61.668 63.158 0.00 0.00 0.00 4.20
3801 3998 3.000080 GAGCTGCGGTGTTTCGTCG 62.000 63.158 0.00 0.00 0.00 5.12
3802 3999 4.072088 GCTGCGGTGTTTCGTCGG 62.072 66.667 0.00 0.00 0.00 4.79
3803 4000 4.072088 CTGCGGTGTTTCGTCGGC 62.072 66.667 0.00 0.00 0.00 5.54
3804 4001 4.893601 TGCGGTGTTTCGTCGGCA 62.894 61.111 0.00 0.00 37.51 5.69
3805 4002 3.641986 GCGGTGTTTCGTCGGCAA 61.642 61.111 0.00 0.00 0.00 4.52
3806 4003 3.015677 CGGTGTTTCGTCGGCAAA 58.984 55.556 0.00 0.00 0.00 3.68
3807 4004 1.352404 CGGTGTTTCGTCGGCAAAA 59.648 52.632 0.00 0.00 0.00 2.44
3808 4005 0.248134 CGGTGTTTCGTCGGCAAAAA 60.248 50.000 0.00 0.00 0.00 1.94
3835 4032 6.790282 CAAACAAATTTGGGGTAACTTTTGG 58.210 36.000 21.74 0.00 41.39 3.28
3836 4033 5.702065 ACAAATTTGGGGTAACTTTTGGT 57.298 34.783 21.74 0.00 31.04 3.67
3837 4034 5.432645 ACAAATTTGGGGTAACTTTTGGTG 58.567 37.500 21.74 0.00 31.04 4.17
3838 4035 5.045505 ACAAATTTGGGGTAACTTTTGGTGT 60.046 36.000 21.74 0.00 31.04 4.16
3839 4036 5.702065 AATTTGGGGTAACTTTTGGTGTT 57.298 34.783 0.00 0.00 0.00 3.32
3840 4037 4.739587 TTTGGGGTAACTTTTGGTGTTC 57.260 40.909 0.00 0.00 0.00 3.18
3841 4038 2.299521 TGGGGTAACTTTTGGTGTTCG 58.700 47.619 0.00 0.00 0.00 3.95
3842 4039 2.092538 TGGGGTAACTTTTGGTGTTCGA 60.093 45.455 0.00 0.00 0.00 3.71
3843 4040 3.151554 GGGGTAACTTTTGGTGTTCGAT 58.848 45.455 0.00 0.00 0.00 3.59
3844 4041 3.570975 GGGGTAACTTTTGGTGTTCGATT 59.429 43.478 0.00 0.00 0.00 3.34
3845 4042 4.038282 GGGGTAACTTTTGGTGTTCGATTT 59.962 41.667 0.00 0.00 0.00 2.17
3846 4043 4.979815 GGGTAACTTTTGGTGTTCGATTTG 59.020 41.667 0.00 0.00 0.00 2.32
3847 4044 5.450826 GGGTAACTTTTGGTGTTCGATTTGT 60.451 40.000 0.00 0.00 0.00 2.83
3848 4045 6.037726 GGTAACTTTTGGTGTTCGATTTGTT 58.962 36.000 0.00 0.00 0.00 2.83
3849 4046 7.194962 GGTAACTTTTGGTGTTCGATTTGTTA 58.805 34.615 0.00 0.00 0.00 2.41
3850 4047 7.863877 GGTAACTTTTGGTGTTCGATTTGTTAT 59.136 33.333 0.00 0.00 0.00 1.89
3851 4048 9.240159 GTAACTTTTGGTGTTCGATTTGTTATT 57.760 29.630 0.00 0.00 0.00 1.40
3852 4049 8.710835 AACTTTTGGTGTTCGATTTGTTATTT 57.289 26.923 0.00 0.00 0.00 1.40
3853 4050 8.710835 ACTTTTGGTGTTCGATTTGTTATTTT 57.289 26.923 0.00 0.00 0.00 1.82
3854 4051 9.157104 ACTTTTGGTGTTCGATTTGTTATTTTT 57.843 25.926 0.00 0.00 0.00 1.94
3855 4052 9.419737 CTTTTGGTGTTCGATTTGTTATTTTTG 57.580 29.630 0.00 0.00 0.00 2.44
3856 4053 8.480643 TTTGGTGTTCGATTTGTTATTTTTGT 57.519 26.923 0.00 0.00 0.00 2.83
3857 4054 9.582431 TTTGGTGTTCGATTTGTTATTTTTGTA 57.418 25.926 0.00 0.00 0.00 2.41
3858 4055 8.563289 TGGTGTTCGATTTGTTATTTTTGTAC 57.437 30.769 0.00 0.00 0.00 2.90
3859 4056 8.188799 TGGTGTTCGATTTGTTATTTTTGTACA 58.811 29.630 0.00 0.00 0.00 2.90
3860 4057 9.021863 GGTGTTCGATTTGTTATTTTTGTACAA 57.978 29.630 3.59 3.59 0.00 2.41
3862 4059 8.747666 TGTTCGATTTGTTATTTTTGTACAAGC 58.252 29.630 8.56 0.00 33.74 4.01
3863 4060 7.861176 TCGATTTGTTATTTTTGTACAAGCC 57.139 32.000 8.56 0.00 33.74 4.35
3864 4061 7.426410 TCGATTTGTTATTTTTGTACAAGCCA 58.574 30.769 8.56 0.00 33.74 4.75
3865 4062 7.921214 TCGATTTGTTATTTTTGTACAAGCCAA 59.079 29.630 8.56 4.12 33.74 4.52
3866 4063 8.543774 CGATTTGTTATTTTTGTACAAGCCAAA 58.456 29.630 8.56 7.35 33.74 3.28
3869 4066 9.994432 TTTGTTATTTTTGTACAAGCCAAAATG 57.006 25.926 19.34 0.00 40.39 2.32
3870 4067 8.723942 TGTTATTTTTGTACAAGCCAAAATGT 57.276 26.923 19.34 4.80 40.39 2.71
3871 4068 9.167311 TGTTATTTTTGTACAAGCCAAAATGTT 57.833 25.926 19.34 4.27 40.39 2.71
3872 4069 9.995957 GTTATTTTTGTACAAGCCAAAATGTTT 57.004 25.926 19.34 4.00 40.39 2.83
3883 4080 9.676195 ACAAGCCAAAATGTTTAATATTTTTGC 57.324 25.926 20.13 20.13 42.12 3.68
3884 4081 9.127006 CAAGCCAAAATGTTTAATATTTTTGCC 57.873 29.630 22.36 11.57 42.46 4.52
3885 4082 8.634335 AGCCAAAATGTTTAATATTTTTGCCT 57.366 26.923 22.36 12.94 42.46 4.75
3886 4083 8.729756 AGCCAAAATGTTTAATATTTTTGCCTC 58.270 29.630 22.36 8.04 42.46 4.70
3887 4084 8.510505 GCCAAAATGTTTAATATTTTTGCCTCA 58.489 29.630 18.28 0.00 38.86 3.86
3898 4095 4.897025 TTTTTGCCTCAAAATTTGCAGG 57.103 36.364 15.26 15.26 41.89 4.85
3899 4096 3.557228 TTTGCCTCAAAATTTGCAGGT 57.443 38.095 18.47 0.00 34.81 4.00
3900 4097 4.679373 TTTGCCTCAAAATTTGCAGGTA 57.321 36.364 18.47 14.22 34.81 3.08
3901 4098 3.940209 TGCCTCAAAATTTGCAGGTAG 57.060 42.857 18.47 5.60 33.36 3.18
3902 4099 2.029110 TGCCTCAAAATTTGCAGGTAGC 60.029 45.455 18.47 9.02 45.96 3.58
3903 4100 7.423799 TTTGCCTCAAAATTTGCAGGTAGCA 62.424 40.000 18.47 10.80 40.01 3.49
3904 4101 8.643385 TTTGCCTCAAAATTTGCAGGTAGCAT 62.643 38.462 18.47 0.00 40.79 3.79
3913 4110 2.857592 GCAGGTAGCATTTGGATGTG 57.142 50.000 0.00 0.00 44.79 3.21
3914 4111 2.368439 GCAGGTAGCATTTGGATGTGA 58.632 47.619 0.00 0.00 44.79 3.58
3915 4112 2.098117 GCAGGTAGCATTTGGATGTGAC 59.902 50.000 0.00 0.00 44.79 3.67
3916 4113 3.614092 CAGGTAGCATTTGGATGTGACT 58.386 45.455 0.00 0.00 35.63 3.41
3917 4114 4.769688 CAGGTAGCATTTGGATGTGACTA 58.230 43.478 0.00 0.00 35.63 2.59
3918 4115 5.185454 CAGGTAGCATTTGGATGTGACTAA 58.815 41.667 0.00 0.00 35.63 2.24
3919 4116 5.295292 CAGGTAGCATTTGGATGTGACTAAG 59.705 44.000 0.00 0.00 35.63 2.18
3920 4117 5.045578 AGGTAGCATTTGGATGTGACTAAGT 60.046 40.000 0.00 0.00 35.63 2.24
3921 4118 6.156256 AGGTAGCATTTGGATGTGACTAAGTA 59.844 38.462 0.00 0.00 35.63 2.24
3922 4119 6.258068 GGTAGCATTTGGATGTGACTAAGTAC 59.742 42.308 0.00 0.00 35.63 2.73
3923 4120 5.804639 AGCATTTGGATGTGACTAAGTACA 58.195 37.500 0.00 0.00 35.63 2.90
3924 4121 5.643777 AGCATTTGGATGTGACTAAGTACAC 59.356 40.000 0.00 0.00 35.63 2.90
3936 4133 9.347934 TGTGACTAAGTACACAAACAAATTTTG 57.652 29.630 7.59 7.59 42.72 2.44
3937 4134 9.349145 GTGACTAAGTACACAAACAAATTTTGT 57.651 29.630 8.97 8.97 42.75 2.83
3938 4135 9.562583 TGACTAAGTACACAAACAAATTTTGTC 57.437 29.630 14.80 1.60 44.59 3.18
3939 4136 9.783256 GACTAAGTACACAAACAAATTTTGTCT 57.217 29.630 14.80 0.00 44.59 3.41
3943 4140 9.651913 AAGTACACAAACAAATTTTGTCTTGAT 57.348 25.926 26.13 19.98 44.59 2.57
3944 4141 9.651913 AGTACACAAACAAATTTTGTCTTGATT 57.348 25.926 26.13 19.19 44.59 2.57
3988 4185 2.573340 GCCACGGGAGCCAAATTG 59.427 61.111 0.00 0.00 0.00 2.32
3989 4186 1.976474 GCCACGGGAGCCAAATTGA 60.976 57.895 0.00 0.00 0.00 2.57
3990 4187 1.883021 CCACGGGAGCCAAATTGAC 59.117 57.895 0.00 0.00 0.00 3.18
3991 4188 0.609131 CCACGGGAGCCAAATTGACT 60.609 55.000 0.00 0.00 0.00 3.41
3992 4189 1.247567 CACGGGAGCCAAATTGACTT 58.752 50.000 0.00 0.00 0.00 3.01
3993 4190 1.613437 CACGGGAGCCAAATTGACTTT 59.387 47.619 0.00 0.00 0.00 2.66
3994 4191 1.886542 ACGGGAGCCAAATTGACTTTC 59.113 47.619 0.00 0.00 0.00 2.62
3995 4192 1.202348 CGGGAGCCAAATTGACTTTCC 59.798 52.381 0.00 0.00 0.00 3.13
3996 4193 1.202348 GGGAGCCAAATTGACTTTCCG 59.798 52.381 0.00 0.00 0.00 4.30
3997 4194 1.402852 GGAGCCAAATTGACTTTCCGC 60.403 52.381 0.00 0.00 0.00 5.54
3998 4195 1.541588 GAGCCAAATTGACTTTCCGCT 59.458 47.619 0.00 0.00 33.96 5.52
3999 4196 1.963515 AGCCAAATTGACTTTCCGCTT 59.036 42.857 0.00 0.00 29.26 4.68
4000 4197 2.029918 AGCCAAATTGACTTTCCGCTTC 60.030 45.455 0.00 0.00 29.26 3.86
4001 4198 2.029918 GCCAAATTGACTTTCCGCTTCT 60.030 45.455 0.00 0.00 0.00 2.85
4002 4199 3.552890 GCCAAATTGACTTTCCGCTTCTT 60.553 43.478 0.00 0.00 0.00 2.52
4141 4338 5.400485 CGGAAGCTTGTTTTCTTTTGATCAG 59.600 40.000 2.10 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
398 455 1.835121 AACAAAAGAAAAGCGTCGCC 58.165 45.000 14.86 0.00 0.00 5.54
552 628 3.224269 TGTTCGGGATGGACGTGATATA 58.776 45.455 0.00 0.00 0.00 0.86
553 629 2.036387 TGTTCGGGATGGACGTGATAT 58.964 47.619 0.00 0.00 0.00 1.63
554 630 1.476477 TGTTCGGGATGGACGTGATA 58.524 50.000 0.00 0.00 0.00 2.15
570 647 0.823356 GCCGCACCCCATATCATGTT 60.823 55.000 0.00 0.00 0.00 2.71
647 724 4.159879 ACCTCTTTCATCGATTTAGACGGT 59.840 41.667 0.00 5.99 0.00 4.83
653 730 6.647481 TCGTTTTGACCTCTTTCATCGATTTA 59.353 34.615 0.00 0.00 0.00 1.40
654 731 5.468746 TCGTTTTGACCTCTTTCATCGATTT 59.531 36.000 0.00 0.00 0.00 2.17
657 734 3.985008 TCGTTTTGACCTCTTTCATCGA 58.015 40.909 0.00 0.00 0.00 3.59
661 738 3.264104 ACGTTCGTTTTGACCTCTTTCA 58.736 40.909 0.00 0.00 0.00 2.69
691 770 0.246635 ACCAACTCTAGCGCACGATT 59.753 50.000 11.47 0.00 0.00 3.34
692 771 0.246635 AACCAACTCTAGCGCACGAT 59.753 50.000 11.47 0.00 0.00 3.73
710 789 3.243035 CGCCGATCCAATTCATGCTTAAA 60.243 43.478 0.00 0.00 0.00 1.52
711 790 2.290367 CGCCGATCCAATTCATGCTTAA 59.710 45.455 0.00 0.00 0.00 1.85
712 791 1.872952 CGCCGATCCAATTCATGCTTA 59.127 47.619 0.00 0.00 0.00 3.09
713 792 0.664761 CGCCGATCCAATTCATGCTT 59.335 50.000 0.00 0.00 0.00 3.91
714 793 1.789078 GCGCCGATCCAATTCATGCT 61.789 55.000 0.00 0.00 0.00 3.79
715 794 1.370900 GCGCCGATCCAATTCATGC 60.371 57.895 0.00 0.00 0.00 4.06
716 795 1.082561 CGCGCCGATCCAATTCATG 60.083 57.895 0.00 0.00 0.00 3.07
717 796 1.095228 AACGCGCCGATCCAATTCAT 61.095 50.000 5.73 0.00 0.00 2.57
718 797 1.743623 AACGCGCCGATCCAATTCA 60.744 52.632 5.73 0.00 0.00 2.57
719 798 1.297598 CAACGCGCCGATCCAATTC 60.298 57.895 5.73 0.00 0.00 2.17
720 799 2.760159 CCAACGCGCCGATCCAATT 61.760 57.895 5.73 0.00 0.00 2.32
721 800 3.202001 CCAACGCGCCGATCCAAT 61.202 61.111 5.73 0.00 0.00 3.16
722 801 4.380781 TCCAACGCGCCGATCCAA 62.381 61.111 5.73 0.00 0.00 3.53
723 802 4.812476 CTCCAACGCGCCGATCCA 62.812 66.667 5.73 0.00 0.00 3.41
724 803 4.814294 ACTCCAACGCGCCGATCC 62.814 66.667 5.73 0.00 0.00 3.36
725 804 2.813908 AACTCCAACGCGCCGATC 60.814 61.111 5.73 0.00 0.00 3.69
726 805 3.118454 CAACTCCAACGCGCCGAT 61.118 61.111 5.73 0.00 0.00 4.18
729 808 4.090057 GAGCAACTCCAACGCGCC 62.090 66.667 5.73 0.00 0.00 6.53
730 809 1.289109 TAAGAGCAACTCCAACGCGC 61.289 55.000 5.73 0.00 0.00 6.86
731 810 1.359848 ATAAGAGCAACTCCAACGCG 58.640 50.000 3.53 3.53 0.00 6.01
732 811 3.831715 AAATAAGAGCAACTCCAACGC 57.168 42.857 0.00 0.00 0.00 4.84
733 812 4.846137 CGAAAAATAAGAGCAACTCCAACG 59.154 41.667 0.00 0.00 0.00 4.10
734 813 5.997385 TCGAAAAATAAGAGCAACTCCAAC 58.003 37.500 0.00 0.00 0.00 3.77
735 814 6.627395 TTCGAAAAATAAGAGCAACTCCAA 57.373 33.333 0.00 0.00 0.00 3.53
736 815 6.262273 ACTTTCGAAAAATAAGAGCAACTCCA 59.738 34.615 12.41 0.00 0.00 3.86
737 816 6.669278 ACTTTCGAAAAATAAGAGCAACTCC 58.331 36.000 12.41 0.00 0.00 3.85
738 817 7.532209 CAGACTTTCGAAAAATAAGAGCAACTC 59.468 37.037 12.41 0.00 0.00 3.01
739 818 7.012421 ACAGACTTTCGAAAAATAAGAGCAACT 59.988 33.333 12.41 0.00 0.00 3.16
740 819 7.132863 ACAGACTTTCGAAAAATAAGAGCAAC 58.867 34.615 12.41 0.00 0.00 4.17
741 820 7.011950 TGACAGACTTTCGAAAAATAAGAGCAA 59.988 33.333 12.41 0.00 0.00 3.91
742 821 6.481976 TGACAGACTTTCGAAAAATAAGAGCA 59.518 34.615 12.41 1.60 0.00 4.26
756 835 6.060028 TGCAGTTTAACATGACAGACTTTC 57.940 37.500 0.00 0.00 0.00 2.62
796 884 5.580691 AGCCTTTCTTTTTAACACAAACAGC 59.419 36.000 0.00 0.00 0.00 4.40
837 925 3.068307 TGGAGATTCTACTAGAAAGCCGC 59.932 47.826 2.56 0.00 37.82 6.53
846 934 4.371681 AGGGGCTTTTGGAGATTCTACTA 58.628 43.478 0.00 0.00 0.00 1.82
847 935 3.193782 AGGGGCTTTTGGAGATTCTACT 58.806 45.455 0.00 0.00 0.00 2.57
848 936 3.201045 AGAGGGGCTTTTGGAGATTCTAC 59.799 47.826 0.00 0.00 0.00 2.59
984 1076 1.141881 CATCGTCAACTCCCTCCCG 59.858 63.158 0.00 0.00 0.00 5.14
1324 1419 0.108804 GCAGTCTCGAAACCGATCCA 60.109 55.000 0.00 0.00 35.31 3.41
1453 1548 1.808945 AGAAGAGAGCACGCCATTTTG 59.191 47.619 0.00 0.00 0.00 2.44
1477 1572 3.615496 TCGTCTGGCTCTAAAAATAACGC 59.385 43.478 0.00 0.00 0.00 4.84
1478 1573 5.291128 ACATCGTCTGGCTCTAAAAATAACG 59.709 40.000 0.00 0.00 0.00 3.18
1479 1574 6.535508 AGACATCGTCTGGCTCTAAAAATAAC 59.464 38.462 0.00 0.00 40.02 1.89
1527 1622 0.935194 ACCCGTCTATCCTTCCTCCT 59.065 55.000 0.00 0.00 0.00 3.69
1561 1656 2.030007 GCAAATTGTCTTACAGCCTGCA 60.030 45.455 0.00 0.00 31.83 4.41
1611 1706 1.094073 CAGAGCAGGAATTCAGCCCG 61.094 60.000 15.85 4.32 0.00 6.13
1613 1708 1.339438 TGACAGAGCAGGAATTCAGCC 60.339 52.381 15.85 9.39 0.00 4.85
1633 1728 5.804639 TGCAGACCAACTAATTCAGTACAT 58.195 37.500 0.00 0.00 36.04 2.29
1681 1776 9.471702 CCTAGCATCAATATTTGGGAAGAATAT 57.528 33.333 0.00 0.00 32.51 1.28
1739 1870 0.322975 AGCATCGCAAAGACAGAGGT 59.677 50.000 0.00 0.00 0.00 3.85
1769 1900 3.838317 TGTCCAGATAGGCTGTTGTTACT 59.162 43.478 0.00 0.00 43.33 2.24
1845 1976 3.398292 TGGATCGGAGGGAGTAGATAACT 59.602 47.826 0.00 0.00 42.80 2.24
1855 1986 3.521937 ACACTTATTTTGGATCGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
1874 2005 3.243068 ACTCCAGTTCAAAATTGCGACAC 60.243 43.478 0.00 0.00 0.00 3.67
1940 2071 3.915575 CTCCAGTGAGGCCATTGC 58.084 61.111 5.01 0.00 37.29 3.56
2019 2150 5.007039 CACAAAGATGTCATCATAGGAACCG 59.993 44.000 15.20 0.00 37.82 4.44
2038 2169 6.405731 GCCAGATAAATTGCAGATACCACAAA 60.406 38.462 0.00 0.00 0.00 2.83
2062 2193 5.118642 AGAGCAGTCTGAAAATTTGAAGC 57.881 39.130 3.32 0.00 0.00 3.86
2097 2228 4.633126 CACAATCTGCTAAGTGTACATGCT 59.367 41.667 0.00 0.00 0.00 3.79
2144 2275 5.813672 TGAACCGCCTTATGATAAGTACAAC 59.186 40.000 10.98 0.21 0.00 3.32
2287 2446 5.071788 ACACTAGGTGATTTCTGAAACAGGA 59.928 40.000 4.73 0.00 36.96 3.86
2308 2467 6.357198 CAGCACAATCATTTTAGCAAAACAC 58.643 36.000 0.00 0.00 32.37 3.32
2469 2629 5.003804 ACGACTGCATCCTGAACTTTATTT 58.996 37.500 0.00 0.00 0.00 1.40
2676 2837 6.149308 TGTTGTTAAGAGATGTAAGTGCATGG 59.851 38.462 0.00 0.00 0.00 3.66
2760 2921 1.555075 GGGTCTGAAGCTGATGTACCA 59.445 52.381 0.00 0.00 0.00 3.25
3184 3378 4.012374 CTGAAGGTTGCAAGGACACATAT 58.988 43.478 0.00 0.00 0.00 1.78
3316 3510 5.188988 TCCTACTTAGACTTAGACAGGCA 57.811 43.478 0.00 0.00 29.16 4.75
3638 3835 3.737172 CGGGAGCCAAAACGCCAG 61.737 66.667 0.00 0.00 0.00 4.85
3642 3839 2.746277 CTCCCGGGAGCCAAAACG 60.746 66.667 36.90 12.91 35.31 3.60
3659 3856 1.976474 TTCACCCGGGAGCAAATGC 60.976 57.895 32.02 0.00 42.49 3.56
3660 3857 0.893270 TGTTCACCCGGGAGCAAATG 60.893 55.000 32.02 14.65 0.00 2.32
3661 3858 0.609131 CTGTTCACCCGGGAGCAAAT 60.609 55.000 32.02 0.00 0.00 2.32
3662 3859 1.228124 CTGTTCACCCGGGAGCAAA 60.228 57.895 32.02 12.52 0.00 3.68
3663 3860 1.122632 TACTGTTCACCCGGGAGCAA 61.123 55.000 32.02 13.72 0.00 3.91
3664 3861 1.122632 TTACTGTTCACCCGGGAGCA 61.123 55.000 32.02 18.12 0.00 4.26
3665 3862 0.672711 GTTACTGTTCACCCGGGAGC 60.673 60.000 32.02 14.25 0.00 4.70
3666 3863 0.682852 TGTTACTGTTCACCCGGGAG 59.317 55.000 32.02 21.98 0.00 4.30
3667 3864 0.393820 GTGTTACTGTTCACCCGGGA 59.606 55.000 32.02 1.07 0.00 5.14
3668 3865 0.947180 CGTGTTACTGTTCACCCGGG 60.947 60.000 22.25 22.25 0.00 5.73
3669 3866 0.032403 TCGTGTTACTGTTCACCCGG 59.968 55.000 0.00 0.00 0.00 5.73
3670 3867 1.855513 TTCGTGTTACTGTTCACCCG 58.144 50.000 9.15 0.92 0.00 5.28
3671 3868 4.619437 TTTTTCGTGTTACTGTTCACCC 57.381 40.909 9.15 0.00 0.00 4.61
3727 3924 9.225436 TGCAACACTAATACAATCATCTACAAA 57.775 29.630 0.00 0.00 0.00 2.83
3728 3925 8.785329 TGCAACACTAATACAATCATCTACAA 57.215 30.769 0.00 0.00 0.00 2.41
3729 3926 8.785329 TTGCAACACTAATACAATCATCTACA 57.215 30.769 0.00 0.00 0.00 2.74
3730 3927 9.490663 GTTTGCAACACTAATACAATCATCTAC 57.509 33.333 0.00 0.00 0.00 2.59
3731 3928 9.225436 TGTTTGCAACACTAATACAATCATCTA 57.775 29.630 0.00 0.00 36.25 1.98
3732 3929 8.109705 TGTTTGCAACACTAATACAATCATCT 57.890 30.769 0.00 0.00 36.25 2.90
3733 3930 8.800972 CATGTTTGCAACACTAATACAATCATC 58.199 33.333 0.00 0.00 45.50 2.92
3734 3931 8.692110 CATGTTTGCAACACTAATACAATCAT 57.308 30.769 0.00 0.00 45.50 2.45
3751 3948 5.792962 CATGAAAATTGTCATGCATGTTTGC 59.207 36.000 22.60 16.94 46.14 3.68
3761 3958 3.919804 CCGTTTCGCATGAAAATTGTCAT 59.080 39.130 5.20 5.20 45.22 3.06
3762 3959 3.003793 TCCGTTTCGCATGAAAATTGTCA 59.996 39.130 0.00 0.00 45.22 3.58
3763 3960 3.560503 TCCGTTTCGCATGAAAATTGTC 58.439 40.909 0.00 0.00 45.22 3.18
3764 3961 3.564511 CTCCGTTTCGCATGAAAATTGT 58.435 40.909 0.00 0.00 45.22 2.71
3765 3962 2.342354 GCTCCGTTTCGCATGAAAATTG 59.658 45.455 0.00 0.00 45.22 2.32
3766 3963 2.228822 AGCTCCGTTTCGCATGAAAATT 59.771 40.909 0.00 0.00 45.22 1.82
3767 3964 1.812571 AGCTCCGTTTCGCATGAAAAT 59.187 42.857 0.00 0.00 45.22 1.82
3768 3965 1.069296 CAGCTCCGTTTCGCATGAAAA 60.069 47.619 0.00 0.00 45.22 2.29
3769 3966 0.516877 CAGCTCCGTTTCGCATGAAA 59.483 50.000 0.00 0.00 41.69 2.69
3770 3967 1.911293 GCAGCTCCGTTTCGCATGAA 61.911 55.000 0.00 0.00 0.00 2.57
3771 3968 2.390599 GCAGCTCCGTTTCGCATGA 61.391 57.895 0.00 0.00 0.00 3.07
3772 3969 2.099062 GCAGCTCCGTTTCGCATG 59.901 61.111 0.00 0.00 0.00 4.06
3773 3970 3.490759 CGCAGCTCCGTTTCGCAT 61.491 61.111 0.00 0.00 0.00 4.73
3776 3973 3.777925 CACCGCAGCTCCGTTTCG 61.778 66.667 0.00 0.00 0.00 3.46
3777 3974 1.782028 AAACACCGCAGCTCCGTTTC 61.782 55.000 0.00 0.00 0.00 2.78
3778 3975 1.782028 GAAACACCGCAGCTCCGTTT 61.782 55.000 0.00 3.38 32.72 3.60
3779 3976 2.203153 AAACACCGCAGCTCCGTT 60.203 55.556 0.00 0.00 0.00 4.44
3780 3977 2.665185 GAAACACCGCAGCTCCGT 60.665 61.111 0.00 0.00 0.00 4.69
3781 3978 3.777925 CGAAACACCGCAGCTCCG 61.778 66.667 0.00 0.00 0.00 4.63
3782 3979 2.665185 ACGAAACACCGCAGCTCC 60.665 61.111 0.00 0.00 0.00 4.70
3783 3980 2.853914 GACGAAACACCGCAGCTC 59.146 61.111 0.00 0.00 0.00 4.09
3784 3981 3.036084 CGACGAAACACCGCAGCT 61.036 61.111 0.00 0.00 0.00 4.24
3785 3982 4.072088 CCGACGAAACACCGCAGC 62.072 66.667 0.00 0.00 0.00 5.25
3786 3983 4.072088 GCCGACGAAACACCGCAG 62.072 66.667 0.00 0.00 0.00 5.18
3787 3984 4.893601 TGCCGACGAAACACCGCA 62.894 61.111 0.00 0.00 0.00 5.69
3788 3985 2.649843 TTTTGCCGACGAAACACCGC 62.650 55.000 0.00 0.00 0.00 5.68
3789 3986 0.248134 TTTTTGCCGACGAAACACCG 60.248 50.000 0.00 0.00 0.00 4.94
3790 3987 3.626154 TTTTTGCCGACGAAACACC 57.374 47.368 0.00 0.00 0.00 4.16
3806 4003 8.410673 AAGTTACCCCAAATTTGTTTGTTTTT 57.589 26.923 16.73 1.94 0.00 1.94
3807 4004 8.410673 AAAGTTACCCCAAATTTGTTTGTTTT 57.589 26.923 16.73 6.11 33.38 2.43
3808 4005 8.300286 CAAAAGTTACCCCAAATTTGTTTGTTT 58.700 29.630 16.73 4.80 34.79 2.83
3809 4006 7.094162 CCAAAAGTTACCCCAAATTTGTTTGTT 60.094 33.333 16.73 0.00 34.79 2.83
3810 4007 6.375736 CCAAAAGTTACCCCAAATTTGTTTGT 59.624 34.615 16.73 12.21 34.79 2.83
3811 4008 6.375736 ACCAAAAGTTACCCCAAATTTGTTTG 59.624 34.615 16.73 15.55 34.79 2.93
3812 4009 6.375736 CACCAAAAGTTACCCCAAATTTGTTT 59.624 34.615 16.73 6.21 34.79 2.83
3813 4010 5.883115 CACCAAAAGTTACCCCAAATTTGTT 59.117 36.000 16.73 3.76 34.79 2.83
3814 4011 5.045505 ACACCAAAAGTTACCCCAAATTTGT 60.046 36.000 16.73 1.39 34.79 2.83
3815 4012 5.432645 ACACCAAAAGTTACCCCAAATTTG 58.567 37.500 11.40 11.40 34.79 2.32
3816 4013 5.702065 ACACCAAAAGTTACCCCAAATTT 57.298 34.783 0.00 0.00 36.02 1.82
3817 4014 5.676552 GAACACCAAAAGTTACCCCAAATT 58.323 37.500 0.00 0.00 0.00 1.82
3818 4015 4.202172 CGAACACCAAAAGTTACCCCAAAT 60.202 41.667 0.00 0.00 0.00 2.32
3819 4016 3.130693 CGAACACCAAAAGTTACCCCAAA 59.869 43.478 0.00 0.00 0.00 3.28
3820 4017 2.688958 CGAACACCAAAAGTTACCCCAA 59.311 45.455 0.00 0.00 0.00 4.12
3821 4018 2.092538 TCGAACACCAAAAGTTACCCCA 60.093 45.455 0.00 0.00 0.00 4.96
3822 4019 2.574450 TCGAACACCAAAAGTTACCCC 58.426 47.619 0.00 0.00 0.00 4.95
3823 4020 4.841443 AATCGAACACCAAAAGTTACCC 57.159 40.909 0.00 0.00 0.00 3.69
3824 4021 5.584442 ACAAATCGAACACCAAAAGTTACC 58.416 37.500 0.00 0.00 0.00 2.85
3825 4022 8.791355 ATAACAAATCGAACACCAAAAGTTAC 57.209 30.769 0.00 0.00 0.00 2.50
3826 4023 9.804758 AAATAACAAATCGAACACCAAAAGTTA 57.195 25.926 0.00 0.00 0.00 2.24
3827 4024 8.710835 AAATAACAAATCGAACACCAAAAGTT 57.289 26.923 0.00 0.00 0.00 2.66
3828 4025 8.710835 AAAATAACAAATCGAACACCAAAAGT 57.289 26.923 0.00 0.00 0.00 2.66
3829 4026 9.419737 CAAAAATAACAAATCGAACACCAAAAG 57.580 29.630 0.00 0.00 0.00 2.27
3830 4027 8.936864 ACAAAAATAACAAATCGAACACCAAAA 58.063 25.926 0.00 0.00 0.00 2.44
3831 4028 8.480643 ACAAAAATAACAAATCGAACACCAAA 57.519 26.923 0.00 0.00 0.00 3.28
3832 4029 9.021863 GTACAAAAATAACAAATCGAACACCAA 57.978 29.630 0.00 0.00 0.00 3.67
3833 4030 8.188799 TGTACAAAAATAACAAATCGAACACCA 58.811 29.630 0.00 0.00 0.00 4.17
3834 4031 8.563289 TGTACAAAAATAACAAATCGAACACC 57.437 30.769 0.00 0.00 0.00 4.16
3836 4033 8.747666 GCTTGTACAAAAATAACAAATCGAACA 58.252 29.630 10.03 0.00 33.05 3.18
3837 4034 8.211838 GGCTTGTACAAAAATAACAAATCGAAC 58.788 33.333 10.03 0.00 33.05 3.95
3838 4035 7.921214 TGGCTTGTACAAAAATAACAAATCGAA 59.079 29.630 10.03 0.00 33.05 3.71
3839 4036 7.426410 TGGCTTGTACAAAAATAACAAATCGA 58.574 30.769 10.03 0.00 33.05 3.59
3840 4037 7.630470 TGGCTTGTACAAAAATAACAAATCG 57.370 32.000 10.03 0.00 33.05 3.34
3843 4040 9.994432 CATTTTGGCTTGTACAAAAATAACAAA 57.006 25.926 10.03 11.01 46.88 2.83
3844 4041 9.167311 ACATTTTGGCTTGTACAAAAATAACAA 57.833 25.926 10.03 6.08 46.88 2.83
3845 4042 8.723942 ACATTTTGGCTTGTACAAAAATAACA 57.276 26.923 10.03 0.28 46.88 2.41
3846 4043 9.995957 AAACATTTTGGCTTGTACAAAAATAAC 57.004 25.926 10.03 0.00 46.88 1.89
3857 4054 9.676195 GCAAAAATATTAAACATTTTGGCTTGT 57.324 25.926 20.46 3.38 43.98 3.16
3872 4069 8.728833 CCTGCAAATTTTGAGGCAAAAATATTA 58.271 29.630 13.26 0.00 44.68 0.98
3873 4070 7.231115 ACCTGCAAATTTTGAGGCAAAAATATT 59.769 29.630 13.26 3.59 44.68 1.28
3874 4071 6.716173 ACCTGCAAATTTTGAGGCAAAAATAT 59.284 30.769 13.26 0.00 44.68 1.28
3875 4072 6.060788 ACCTGCAAATTTTGAGGCAAAAATA 58.939 32.000 13.26 0.00 44.68 1.40
3876 4073 4.888823 ACCTGCAAATTTTGAGGCAAAAAT 59.111 33.333 13.26 5.40 44.68 1.82
3877 4074 4.268359 ACCTGCAAATTTTGAGGCAAAAA 58.732 34.783 13.26 1.32 44.68 1.94
3878 4075 3.883669 ACCTGCAAATTTTGAGGCAAAA 58.116 36.364 13.26 7.66 45.41 2.44
3879 4076 3.557228 ACCTGCAAATTTTGAGGCAAA 57.443 38.095 13.26 0.00 35.59 3.68
3880 4077 3.554752 GCTACCTGCAAATTTTGAGGCAA 60.555 43.478 13.26 7.75 42.31 4.52
3881 4078 2.029110 GCTACCTGCAAATTTTGAGGCA 60.029 45.455 13.26 6.48 42.31 4.75
3882 4079 2.610433 GCTACCTGCAAATTTTGAGGC 58.390 47.619 13.26 2.38 42.31 4.70
3894 4091 2.098117 GTCACATCCAAATGCTACCTGC 59.902 50.000 0.00 0.00 43.25 4.85
3895 4092 3.614092 AGTCACATCCAAATGCTACCTG 58.386 45.455 0.00 0.00 36.26 4.00
3896 4093 5.045578 ACTTAGTCACATCCAAATGCTACCT 60.046 40.000 0.00 0.00 36.26 3.08
3897 4094 5.186198 ACTTAGTCACATCCAAATGCTACC 58.814 41.667 0.00 0.00 36.26 3.18
3898 4095 6.816640 TGTACTTAGTCACATCCAAATGCTAC 59.183 38.462 0.00 0.00 36.26 3.58
3899 4096 6.816640 GTGTACTTAGTCACATCCAAATGCTA 59.183 38.462 9.07 0.00 36.26 3.49
3900 4097 5.643777 GTGTACTTAGTCACATCCAAATGCT 59.356 40.000 9.07 0.00 36.26 3.79
3901 4098 5.411361 TGTGTACTTAGTCACATCCAAATGC 59.589 40.000 11.54 0.00 39.23 3.56
3902 4099 7.433708 TTGTGTACTTAGTCACATCCAAATG 57.566 36.000 14.72 0.00 42.77 2.32
3903 4100 7.500892 TGTTTGTGTACTTAGTCACATCCAAAT 59.499 33.333 14.72 0.00 42.77 2.32
3904 4101 6.824196 TGTTTGTGTACTTAGTCACATCCAAA 59.176 34.615 14.72 10.24 42.77 3.28
3905 4102 6.350103 TGTTTGTGTACTTAGTCACATCCAA 58.650 36.000 14.72 7.17 42.77 3.53
3906 4103 5.919755 TGTTTGTGTACTTAGTCACATCCA 58.080 37.500 14.72 12.14 42.77 3.41
3907 4104 6.854496 TTGTTTGTGTACTTAGTCACATCC 57.146 37.500 14.72 10.48 42.77 3.51
3908 4105 9.730420 AAATTTGTTTGTGTACTTAGTCACATC 57.270 29.630 14.72 12.21 42.77 3.06
3910 4107 9.347934 CAAAATTTGTTTGTGTACTTAGTCACA 57.652 29.630 11.54 11.54 41.81 3.58
3911 4108 9.349145 ACAAAATTTGTTTGTGTACTTAGTCAC 57.651 29.630 5.41 0.00 42.22 3.67
3912 4109 9.562583 GACAAAATTTGTTTGTGTACTTAGTCA 57.437 29.630 13.00 0.00 45.52 3.41
3913 4110 9.783256 AGACAAAATTTGTTTGTGTACTTAGTC 57.217 29.630 13.00 0.00 45.52 2.59
3917 4114 9.651913 ATCAAGACAAAATTTGTTTGTGTACTT 57.348 25.926 13.00 6.82 45.52 2.24
3918 4115 9.651913 AATCAAGACAAAATTTGTTTGTGTACT 57.348 25.926 13.00 0.75 45.52 2.73
3971 4168 1.976474 TCAATTTGGCTCCCGTGGC 60.976 57.895 0.00 0.00 0.00 5.01
3972 4169 0.609131 AGTCAATTTGGCTCCCGTGG 60.609 55.000 0.00 0.00 0.00 4.94
3973 4170 1.247567 AAGTCAATTTGGCTCCCGTG 58.752 50.000 3.58 0.00 26.08 4.94
3974 4171 1.886542 GAAAGTCAATTTGGCTCCCGT 59.113 47.619 3.58 0.00 26.08 5.28
3975 4172 1.202348 GGAAAGTCAATTTGGCTCCCG 59.798 52.381 3.58 0.00 26.08 5.14
3976 4173 1.202348 CGGAAAGTCAATTTGGCTCCC 59.798 52.381 3.58 7.95 26.08 4.30
3977 4174 1.402852 GCGGAAAGTCAATTTGGCTCC 60.403 52.381 3.58 1.72 26.08 4.70
3978 4175 1.541588 AGCGGAAAGTCAATTTGGCTC 59.458 47.619 3.58 0.00 34.00 4.70
3979 4176 1.620822 AGCGGAAAGTCAATTTGGCT 58.379 45.000 0.00 0.00 34.22 4.75
3980 4177 2.029918 AGAAGCGGAAAGTCAATTTGGC 60.030 45.455 0.00 0.00 0.00 4.52
3981 4178 3.923017 AGAAGCGGAAAGTCAATTTGG 57.077 42.857 0.00 0.00 0.00 3.28
3982 4179 6.863126 ACAATAAGAAGCGGAAAGTCAATTTG 59.137 34.615 0.00 0.00 0.00 2.32
3983 4180 6.981722 ACAATAAGAAGCGGAAAGTCAATTT 58.018 32.000 0.00 0.00 0.00 1.82
3984 4181 6.575162 ACAATAAGAAGCGGAAAGTCAATT 57.425 33.333 0.00 0.00 0.00 2.32
3985 4182 6.575162 AACAATAAGAAGCGGAAAGTCAAT 57.425 33.333 0.00 0.00 0.00 2.57
3986 4183 6.385649 AAACAATAAGAAGCGGAAAGTCAA 57.614 33.333 0.00 0.00 0.00 3.18
3987 4184 6.385649 AAAACAATAAGAAGCGGAAAGTCA 57.614 33.333 0.00 0.00 0.00 3.41
3988 4185 8.965986 AATAAAACAATAAGAAGCGGAAAGTC 57.034 30.769 0.00 0.00 0.00 3.01
3989 4186 8.793592 AGAATAAAACAATAAGAAGCGGAAAGT 58.206 29.630 0.00 0.00 0.00 2.66
3993 4190 9.607988 TCATAGAATAAAACAATAAGAAGCGGA 57.392 29.630 0.00 0.00 0.00 5.54
4141 4338 1.210155 GTGACCAAACTGCATCGCC 59.790 57.895 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.