Multiple sequence alignment - TraesCS2D01G507600

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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 TraesCS2D01G507600 chr2D 100.000 6279 0 0 1 6279 601200718 601206996 0.000000e+00 11596.0
1 TraesCS2D01G507600 chr2D 80.033 601 81 33 5640 6217 601244984 601245568 5.860000e-110 409.0
2 TraesCS2D01G507600 chr2D 92.157 102 8 0 5803 5904 601398803 601398904 1.820000e-30 145.0
3 TraesCS2D01G507600 chr2D 87.736 106 13 0 3521 3626 601203305 601203410 2.380000e-24 124.0
4 TraesCS2D01G507600 chr2D 87.736 106 13 0 2588 2693 601204238 601204343 2.380000e-24 124.0
5 TraesCS2D01G507600 chr2A 92.478 2898 150 38 2491 5365 734626292 734629144 0.000000e+00 4082.0
6 TraesCS2D01G507600 chr2A 91.805 2294 114 37 786 3032 734523487 734521221 0.000000e+00 3127.0
7 TraesCS2D01G507600 chr2A 93.086 1620 67 20 886 2477 734624508 734626110 0.000000e+00 2329.0
8 TraesCS2D01G507600 chr2A 90.549 455 28 7 5501 5954 734629139 734629579 7.010000e-164 588.0
9 TraesCS2D01G507600 chr2A 87.658 316 20 9 5983 6279 734629638 734629953 3.600000e-92 350.0
10 TraesCS2D01G507600 chr2A 88.571 140 12 3 786 924 734624330 734624466 3.890000e-37 167.0
11 TraesCS2D01G507600 chr2A 83.815 173 20 5 5780 5947 734634073 734634242 2.340000e-34 158.0
12 TraesCS2D01G507600 chr2B 91.657 1666 100 20 4562 6217 731342516 731344152 0.000000e+00 2270.0
13 TraesCS2D01G507600 chr2B 88.903 1577 102 34 754 2287 731339790 731341336 0.000000e+00 1875.0
14 TraesCS2D01G507600 chr2B 78.855 681 89 42 5614 6253 731460470 731461136 5.860000e-110 409.0
15 TraesCS2D01G507600 chr2B 84.080 402 50 10 3868 4259 731341794 731342191 5.940000e-100 375.0
16 TraesCS2D01G507600 chr2B 84.977 213 29 2 2979 3188 731461988 731462200 4.930000e-51 213.0
17 TraesCS2D01G507600 chr2B 79.054 148 27 4 2332 2477 181060281 181060136 1.440000e-16 99.0
18 TraesCS2D01G507600 chr2B 87.500 88 8 1 3624 3708 731457216 731457303 1.440000e-16 99.0
19 TraesCS2D01G507600 chr5D 98.977 684 7 0 1 684 445495441 445494758 0.000000e+00 1225.0
20 TraesCS2D01G507600 chr5D 98.684 684 9 0 1 684 482739925 482740608 0.000000e+00 1214.0
21 TraesCS2D01G507600 chr3D 98.977 684 7 0 1 684 547907025 547907708 0.000000e+00 1225.0
22 TraesCS2D01G507600 chr3D 98.830 684 8 0 1 684 577170760 577171443 0.000000e+00 1219.0
23 TraesCS2D01G507600 chr3D 98.829 683 8 0 1 683 155358439 155359121 0.000000e+00 1218.0
24 TraesCS2D01G507600 chr3D 98.682 683 9 0 1 683 612684400 612683718 0.000000e+00 1212.0
25 TraesCS2D01G507600 chr1D 98.975 683 7 0 1 683 467952665 467953347 0.000000e+00 1223.0
26 TraesCS2D01G507600 chr1D 92.683 41 3 0 2726 2766 9868128 9868168 6.800000e-05 60.2
27 TraesCS2D01G507600 chr4D 98.549 689 10 0 1 689 488790603 488791291 0.000000e+00 1218.0
28 TraesCS2D01G507600 chr4D 80.420 143 28 0 2718 2860 430881801 430881943 6.660000e-20 110.0
29 TraesCS2D01G507600 chr6D 98.406 690 10 1 1 690 420901765 420901077 0.000000e+00 1212.0
30 TraesCS2D01G507600 chr6D 85.965 114 13 3 2743 2855 38154316 38154205 1.110000e-22 119.0
31 TraesCS2D01G507600 chr6D 77.660 188 38 4 2292 2477 339854063 339853878 1.850000e-20 111.0
32 TraesCS2D01G507600 chr7B 75.847 236 49 5 2292 2521 268063874 268063641 5.140000e-21 113.0
33 TraesCS2D01G507600 chr5B 75.966 233 48 5 2293 2519 506578762 506578532 5.140000e-21 113.0
34 TraesCS2D01G507600 chr5B 76.064 188 41 4 2292 2477 253888082 253888267 1.860000e-15 95.3
35 TraesCS2D01G507600 chr5B 82.955 88 13 2 2776 2862 502472994 502473080 1.880000e-10 78.7
36 TraesCS2D01G507600 chr7D 77.005 187 39 4 2293 2477 225707256 225707072 3.100000e-18 104.0
37 TraesCS2D01G507600 chr4B 75.431 232 48 6 2294 2519 106355793 106356021 3.100000e-18 104.0


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 TraesCS2D01G507600 chr2D 601200718 601206996 6278 False 3948.000000 11596 91.824000 1 6279 3 chr2D.!!$F3 6278
1 TraesCS2D01G507600 chr2D 601244984 601245568 584 False 409.000000 409 80.033000 5640 6217 1 chr2D.!!$F1 577
2 TraesCS2D01G507600 chr2A 734521221 734523487 2266 True 3127.000000 3127 91.805000 786 3032 1 chr2A.!!$R1 2246
3 TraesCS2D01G507600 chr2A 734624330 734629953 5623 False 1503.200000 4082 90.468400 786 6279 5 chr2A.!!$F2 5493
4 TraesCS2D01G507600 chr2B 731339790 731344152 4362 False 1506.666667 2270 88.213333 754 6217 3 chr2B.!!$F1 5463
5 TraesCS2D01G507600 chr2B 731457216 731462200 4984 False 240.333333 409 83.777333 2979 6253 3 chr2B.!!$F2 3274
6 TraesCS2D01G507600 chr5D 445494758 445495441 683 True 1225.000000 1225 98.977000 1 684 1 chr5D.!!$R1 683
7 TraesCS2D01G507600 chr5D 482739925 482740608 683 False 1214.000000 1214 98.684000 1 684 1 chr5D.!!$F1 683
8 TraesCS2D01G507600 chr3D 547907025 547907708 683 False 1225.000000 1225 98.977000 1 684 1 chr3D.!!$F2 683
9 TraesCS2D01G507600 chr3D 577170760 577171443 683 False 1219.000000 1219 98.830000 1 684 1 chr3D.!!$F3 683
10 TraesCS2D01G507600 chr3D 155358439 155359121 682 False 1218.000000 1218 98.829000 1 683 1 chr3D.!!$F1 682
11 TraesCS2D01G507600 chr3D 612683718 612684400 682 True 1212.000000 1212 98.682000 1 683 1 chr3D.!!$R1 682
12 TraesCS2D01G507600 chr1D 467952665 467953347 682 False 1223.000000 1223 98.975000 1 683 1 chr1D.!!$F2 682
13 TraesCS2D01G507600 chr4D 488790603 488791291 688 False 1218.000000 1218 98.549000 1 689 1 chr4D.!!$F2 688
14 TraesCS2D01G507600 chr6D 420901077 420901765 688 True 1212.000000 1212 98.406000 1 690 1 chr6D.!!$R3 689

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
707 708 0.037326 CGCGCACACCATATCCCTAT 60.037 55.0 8.75 0.0 0.00 2.57 F
847 854 0.039978 ACAGCGTCGAACACTCTCAG 60.040 55.0 0.00 0.0 0.00 3.35 F
2034 2159 0.174162 GGTGCATGCCATGTCCTTTC 59.826 55.0 16.68 0.0 0.00 2.62 F
2720 3032 0.523546 CATATCTACTAGCCGCGCCG 60.524 60.0 0.00 0.0 0.00 6.46 F
3183 3495 0.036010 CCGCCACTGACCAGAAAGAT 60.036 55.0 3.76 0.0 0.00 2.40 F
3501 3813 1.006813 ACCCATATTTGGTGCTCCCA 58.993 50.0 1.59 0.0 41.91 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2501 0.033228 CCAATTCGTGGGCAAGCAAA 59.967 50.000 0.00 0.0 44.64 3.68 R
2700 3012 0.526662 GGCGCGGCTAGTAGATATGT 59.473 55.000 27.05 0.0 0.00 2.29 R
3006 3318 1.002087 GGTCTGCCAATCGGGTATAGG 59.998 57.143 0.00 0.0 39.65 2.57 R
3621 3933 1.108132 GTACCTAGAGTGCCCCCTCG 61.108 65.000 0.00 0.0 36.56 4.63 R
4888 6832 0.179103 AAACAGCACAAACAGCAGCC 60.179 50.000 0.00 0.0 0.00 4.85 R
5445 8087 0.036306 ACCAGTTGGATGGAACGGTC 59.964 55.000 4.92 0.0 43.57 4.79 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
299 300 7.959658 ACCTTTGTGATCATTTGAATGGATA 57.040 32.000 0.00 0.00 37.03 2.59
575 576 1.408702 GGCCACGAACCGGTACTAATA 59.591 52.381 8.00 0.00 0.00 0.98
689 690 4.496341 CCATTTTTCTACTAGTGGCATGCG 60.496 45.833 12.44 0.00 0.00 4.73
690 691 1.651987 TTTCTACTAGTGGCATGCGC 58.348 50.000 12.44 0.00 37.44 6.09
691 692 0.527600 TTCTACTAGTGGCATGCGCG 60.528 55.000 12.44 0.00 39.92 6.86
692 693 2.584970 TACTAGTGGCATGCGCGC 60.585 61.111 27.26 27.26 39.92 6.86
693 694 3.363844 TACTAGTGGCATGCGCGCA 62.364 57.895 38.27 38.27 39.92 6.09
694 695 4.228097 CTAGTGGCATGCGCGCAC 62.228 66.667 39.05 24.98 39.92 5.34
700 701 3.875039 GCATGCGCGCACACCATA 61.875 61.111 39.05 12.65 0.00 2.74
701 702 3.024784 CATGCGCGCACACCATAT 58.975 55.556 39.05 16.81 0.00 1.78
702 703 1.082561 CATGCGCGCACACCATATC 60.083 57.895 39.05 0.00 0.00 1.63
703 704 2.253758 ATGCGCGCACACCATATCC 61.254 57.895 39.05 0.00 0.00 2.59
704 705 3.649986 GCGCGCACACCATATCCC 61.650 66.667 29.10 0.00 0.00 3.85
705 706 2.108976 CGCGCACACCATATCCCT 59.891 61.111 8.75 0.00 0.00 4.20
706 707 1.365999 CGCGCACACCATATCCCTA 59.634 57.895 8.75 0.00 0.00 3.53
707 708 0.037326 CGCGCACACCATATCCCTAT 60.037 55.000 8.75 0.00 0.00 2.57
708 709 1.442769 GCGCACACCATATCCCTATG 58.557 55.000 0.30 0.00 35.47 2.23
709 710 1.001974 GCGCACACCATATCCCTATGA 59.998 52.381 0.30 0.00 37.51 2.15
710 711 2.688507 CGCACACCATATCCCTATGAC 58.311 52.381 0.00 0.00 37.51 3.06
711 712 2.037121 CGCACACCATATCCCTATGACA 59.963 50.000 0.00 0.00 37.51 3.58
712 713 3.494223 CGCACACCATATCCCTATGACAA 60.494 47.826 0.00 0.00 37.51 3.18
713 714 4.067896 GCACACCATATCCCTATGACAAG 58.932 47.826 0.00 0.00 37.51 3.16
714 715 4.444876 GCACACCATATCCCTATGACAAGT 60.445 45.833 0.00 0.00 37.51 3.16
715 716 5.300752 CACACCATATCCCTATGACAAGTC 58.699 45.833 0.00 0.00 37.51 3.01
716 717 5.070981 CACACCATATCCCTATGACAAGTCT 59.929 44.000 1.53 0.00 37.51 3.24
717 718 5.667626 ACACCATATCCCTATGACAAGTCTT 59.332 40.000 1.53 0.00 37.51 3.01
718 719 5.994054 CACCATATCCCTATGACAAGTCTTG 59.006 44.000 11.17 11.17 37.51 3.02
719 720 5.905331 ACCATATCCCTATGACAAGTCTTGA 59.095 40.000 19.53 0.00 37.51 3.02
720 721 6.386927 ACCATATCCCTATGACAAGTCTTGAA 59.613 38.462 19.53 7.32 37.51 2.69
721 722 7.092444 ACCATATCCCTATGACAAGTCTTGAAA 60.092 37.037 19.53 6.97 37.51 2.69
722 723 7.775093 CCATATCCCTATGACAAGTCTTGAAAA 59.225 37.037 19.53 4.54 37.51 2.29
723 724 9.177608 CATATCCCTATGACAAGTCTTGAAAAA 57.822 33.333 19.53 2.14 37.51 1.94
724 725 9.927081 ATATCCCTATGACAAGTCTTGAAAAAT 57.073 29.630 19.53 8.87 0.00 1.82
726 727 8.792830 TCCCTATGACAAGTCTTGAAAAATAG 57.207 34.615 19.53 16.36 0.00 1.73
727 728 7.829211 TCCCTATGACAAGTCTTGAAAAATAGG 59.171 37.037 19.53 22.06 35.10 2.57
728 729 7.415653 CCCTATGACAAGTCTTGAAAAATAGGC 60.416 40.741 19.53 0.00 34.63 3.93
729 730 5.356882 TGACAAGTCTTGAAAAATAGGCG 57.643 39.130 19.53 0.00 0.00 5.52
730 731 5.060506 TGACAAGTCTTGAAAAATAGGCGA 58.939 37.500 19.53 0.00 0.00 5.54
731 732 5.705441 TGACAAGTCTTGAAAAATAGGCGAT 59.295 36.000 19.53 0.00 0.00 4.58
732 733 6.876789 TGACAAGTCTTGAAAAATAGGCGATA 59.123 34.615 19.53 0.00 0.00 2.92
733 734 7.552687 TGACAAGTCTTGAAAAATAGGCGATAT 59.447 33.333 19.53 0.00 0.00 1.63
734 735 7.697691 ACAAGTCTTGAAAAATAGGCGATATG 58.302 34.615 19.53 0.00 0.00 1.78
735 736 7.552687 ACAAGTCTTGAAAAATAGGCGATATGA 59.447 33.333 19.53 0.00 0.00 2.15
736 737 7.721286 AGTCTTGAAAAATAGGCGATATGAG 57.279 36.000 0.00 0.00 0.00 2.90
737 738 7.275920 AGTCTTGAAAAATAGGCGATATGAGT 58.724 34.615 0.00 0.00 0.00 3.41
738 739 7.770897 AGTCTTGAAAAATAGGCGATATGAGTT 59.229 33.333 0.00 0.00 0.00 3.01
739 740 7.852945 GTCTTGAAAAATAGGCGATATGAGTTG 59.147 37.037 0.00 0.00 0.00 3.16
740 741 6.618287 TGAAAAATAGGCGATATGAGTTGG 57.382 37.500 0.00 0.00 0.00 3.77
741 742 6.119536 TGAAAAATAGGCGATATGAGTTGGT 58.880 36.000 0.00 0.00 0.00 3.67
742 743 7.276658 TGAAAAATAGGCGATATGAGTTGGTA 58.723 34.615 0.00 0.00 0.00 3.25
743 744 7.225931 TGAAAAATAGGCGATATGAGTTGGTAC 59.774 37.037 0.00 0.00 0.00 3.34
744 745 6.420913 AAATAGGCGATATGAGTTGGTACT 57.579 37.500 0.00 0.00 37.31 2.73
761 762 4.873827 TGGTACTCGAATCAATTGTTAGCC 59.126 41.667 5.13 0.00 0.00 3.93
804 805 1.774639 AAGCAAAATCAAGCAGCGTG 58.225 45.000 1.21 1.21 0.00 5.34
840 847 3.421741 CAAAGAAAAACAGCGTCGAACA 58.578 40.909 0.00 0.00 0.00 3.18
844 851 1.935933 AAAACAGCGTCGAACACTCT 58.064 45.000 0.00 0.00 0.00 3.24
845 852 1.488527 AAACAGCGTCGAACACTCTC 58.511 50.000 0.00 0.00 0.00 3.20
846 853 0.384309 AACAGCGTCGAACACTCTCA 59.616 50.000 0.00 0.00 0.00 3.27
847 854 0.039978 ACAGCGTCGAACACTCTCAG 60.040 55.000 0.00 0.00 0.00 3.35
945 1037 2.356313 CCGCGTGTCAGCTTCACT 60.356 61.111 4.92 0.00 34.14 3.41
1023 1117 2.019272 TCCTCTCTCCCCTACCCCC 61.019 68.421 0.00 0.00 0.00 5.40
1487 1581 7.944554 TCAAGATGGTATTGGAGTTTCTTTCTT 59.055 33.333 0.00 0.00 0.00 2.52
1503 1597 3.297134 TTCTTGCCAACACTTCTTCCT 57.703 42.857 0.00 0.00 0.00 3.36
1520 1614 5.007682 TCTTCCTTTTACTCGGATTTTGGG 58.992 41.667 0.00 0.00 0.00 4.12
1521 1615 3.086282 TCCTTTTACTCGGATTTTGGGC 58.914 45.455 0.00 0.00 0.00 5.36
1522 1616 2.159435 CCTTTTACTCGGATTTTGGGCG 60.159 50.000 0.00 0.00 0.00 6.13
1529 1623 1.001158 TCGGATTTTGGGCGTTTTCAC 60.001 47.619 0.00 0.00 0.00 3.18
1652 1749 4.321156 GCAATGCAGGTAACACATTTCAGA 60.321 41.667 0.00 0.00 41.86 3.27
1661 1758 7.770433 CAGGTAACACATTTCAGAATCAGGATA 59.230 37.037 0.00 0.00 41.41 2.59
1713 1810 3.635331 ACCGATATCGATGGTTAACACG 58.365 45.455 26.32 9.89 43.02 4.49
1753 1868 6.989759 TCAGTGTATCATGTTGTTAAGTGTGT 59.010 34.615 0.00 0.00 0.00 3.72
1758 1873 5.940192 TCATGTTGTTAAGTGTGTCCATC 57.060 39.130 0.00 0.00 0.00 3.51
1778 1900 5.591472 CCATCTTTGCAACAGGAGATATTGA 59.409 40.000 10.31 0.00 0.00 2.57
1797 1919 3.930336 TGAGCTGACATACCTGTTTGAG 58.070 45.455 0.00 0.00 35.14 3.02
1811 1933 7.881775 ACCTGTTTGAGACTTTAGATTGTTT 57.118 32.000 0.00 0.00 0.00 2.83
1812 1934 7.931275 ACCTGTTTGAGACTTTAGATTGTTTC 58.069 34.615 0.00 0.00 0.00 2.78
1817 1939 9.600646 GTTTGAGACTTTAGATTGTTTCTTAGC 57.399 33.333 0.00 0.00 35.79 3.09
1818 1940 9.561069 TTTGAGACTTTAGATTGTTTCTTAGCT 57.439 29.630 0.00 0.00 35.79 3.32
1832 1954 6.537660 TGTTTCTTAGCTCTGATCATGACATG 59.462 38.462 9.28 9.28 0.00 3.21
1905 2028 9.743057 TTTCCTTTCTGTTAATATGTGTGTTTG 57.257 29.630 0.00 0.00 0.00 2.93
1911 2034 6.429692 TCTGTTAATATGTGTGTTTGTCTGGG 59.570 38.462 0.00 0.00 0.00 4.45
1924 2047 3.159213 TGTCTGGGATGAATGCAGTTT 57.841 42.857 0.00 0.00 0.00 2.66
2006 2131 7.601073 TGTTTTCTATGAACATGTCTGCTAG 57.399 36.000 0.00 0.00 32.44 3.42
2023 2148 1.321805 TAGGTGCCAATGGTGCATGC 61.322 55.000 11.82 11.82 41.46 4.06
2031 2156 1.308666 ATGGTGCATGCCATGTCCT 59.691 52.632 16.68 5.47 46.63 3.85
2032 2157 0.324923 ATGGTGCATGCCATGTCCTT 60.325 50.000 16.68 11.01 46.63 3.36
2033 2158 0.542467 TGGTGCATGCCATGTCCTTT 60.542 50.000 16.68 0.00 32.81 3.11
2034 2159 0.174162 GGTGCATGCCATGTCCTTTC 59.826 55.000 16.68 0.00 0.00 2.62
2035 2160 1.180029 GTGCATGCCATGTCCTTTCT 58.820 50.000 16.68 0.00 0.00 2.52
2036 2161 1.547372 GTGCATGCCATGTCCTTTCTT 59.453 47.619 16.68 0.00 0.00 2.52
2037 2162 2.754552 GTGCATGCCATGTCCTTTCTTA 59.245 45.455 16.68 0.00 0.00 2.10
2038 2163 3.018856 TGCATGCCATGTCCTTTCTTAG 58.981 45.455 16.68 0.00 0.00 2.18
2039 2164 3.282021 GCATGCCATGTCCTTTCTTAGA 58.718 45.455 6.36 0.00 0.00 2.10
2040 2165 3.696051 GCATGCCATGTCCTTTCTTAGAA 59.304 43.478 6.36 0.00 0.00 2.10
2041 2166 4.201990 GCATGCCATGTCCTTTCTTAGAAG 60.202 45.833 6.36 0.00 0.00 2.85
2188 2322 1.171308 CCTGATGCTCAAACCAGGTG 58.829 55.000 0.00 0.00 40.84 4.00
2251 2389 7.175104 TGAAAACTAGATGGTAGCATTTTCCT 58.825 34.615 19.93 11.61 34.96 3.36
2266 2404 5.738783 GCATTTTCCTTAACACTTGAGCCAA 60.739 40.000 0.00 0.00 0.00 4.52
2301 2439 2.825532 CCAAGACAAGGGGTATGTTTGG 59.174 50.000 0.00 0.00 35.12 3.28
2326 2464 2.478292 AGCCTAGCTTTACCCTAGCAA 58.522 47.619 0.00 0.00 41.11 3.91
2409 2551 8.514594 CATTGGCAAGAAAAGTGAACTAGATTA 58.485 33.333 5.96 0.00 0.00 1.75
2529 2840 2.757868 CAAACACACCCAAGGTTTCTGA 59.242 45.455 0.00 0.00 31.02 3.27
2530 2841 3.312736 AACACACCCAAGGTTTCTGAT 57.687 42.857 0.00 0.00 31.02 2.90
2531 2842 2.863809 ACACACCCAAGGTTTCTGATC 58.136 47.619 0.00 0.00 31.02 2.92
2632 2944 2.289002 GCAATGTCCCGATGTTGATCTC 59.711 50.000 0.00 0.00 0.00 2.75
2700 3012 2.438021 ACCAGACAGCAAGGAAACACTA 59.562 45.455 0.00 0.00 0.00 2.74
2720 3032 0.523546 CATATCTACTAGCCGCGCCG 60.524 60.000 0.00 0.00 0.00 6.46
2784 3096 1.061812 AGAGGCATGTAGATGGGAGGT 60.062 52.381 1.57 0.00 0.00 3.85
2812 3124 2.429907 GCTCATCGGCGGAGATCG 60.430 66.667 15.84 1.79 42.76 3.69
2820 3132 2.203365 GCGGAGATCGAGGGGAGA 60.203 66.667 0.00 0.00 42.43 3.71
2844 3156 2.633488 GCTTTGCCCTAGTCACCTTAG 58.367 52.381 0.00 0.00 0.00 2.18
2900 3212 3.309682 ACATTATCTTGACGGCATCAACG 59.690 43.478 0.00 0.00 42.62 4.10
2901 3213 2.951457 TATCTTGACGGCATCAACGA 57.049 45.000 0.00 0.00 42.62 3.85
2916 3228 3.031013 TCAACGATTATCAGGGAGAGCA 58.969 45.455 0.00 0.00 0.00 4.26
2932 3244 2.092592 AGAGCATGGACATCATTGCTCA 60.093 45.455 25.03 0.88 46.81 4.26
2935 3247 2.927028 CATGGACATCATTGCTCAGGA 58.073 47.619 0.00 0.00 32.92 3.86
3006 3318 1.881973 TGGCTGATCAGACAAGCAAAC 59.118 47.619 29.30 5.73 44.93 2.93
3024 3336 2.097110 ACCTATACCCGATTGGCAGA 57.903 50.000 0.00 0.00 37.83 4.26
3040 3352 1.079543 AGACCAGTCAGCATGTCGC 60.080 57.895 0.00 0.00 42.91 5.19
3069 3381 3.817647 GTCAAGATGATAATGGCTCACCC 59.182 47.826 0.00 0.00 33.59 4.61
3070 3382 3.152341 CAAGATGATAATGGCTCACCCC 58.848 50.000 0.00 0.00 33.59 4.95
3183 3495 0.036010 CCGCCACTGACCAGAAAGAT 60.036 55.000 3.76 0.00 0.00 2.40
3205 3517 3.446161 TGGATAGGTTACGTCCAAGACTG 59.554 47.826 0.00 0.00 38.99 3.51
3206 3518 3.446516 GGATAGGTTACGTCCAAGACTGT 59.553 47.826 0.00 0.00 32.23 3.55
3207 3519 2.814280 AGGTTACGTCCAAGACTGTG 57.186 50.000 0.00 0.00 0.00 3.66
3212 3524 2.440539 ACGTCCAAGACTGTGTGATC 57.559 50.000 0.00 0.00 0.00 2.92
3245 3557 9.219603 GCAGCTTTAGTATACAATCCATGAATA 57.780 33.333 5.50 0.00 0.00 1.75
3271 3583 8.289939 TGATCTGTATTCCTTACGTCTTAACT 57.710 34.615 0.00 0.00 33.15 2.24
3272 3584 8.746530 TGATCTGTATTCCTTACGTCTTAACTT 58.253 33.333 0.00 0.00 33.15 2.66
3273 3585 9.583765 GATCTGTATTCCTTACGTCTTAACTTT 57.416 33.333 0.00 0.00 33.15 2.66
3274 3586 9.939802 ATCTGTATTCCTTACGTCTTAACTTTT 57.060 29.630 0.00 0.00 33.15 2.27
3314 3626 2.386935 GGAGGGGGTGAGGGAATGG 61.387 68.421 0.00 0.00 0.00 3.16
3350 3662 1.341285 TGATCTGATGCCCAAACCAGG 60.341 52.381 0.00 0.00 0.00 4.45
3368 3680 1.918957 AGGTGGCTGCTTCTCCTAATT 59.081 47.619 0.00 0.00 0.00 1.40
3374 3686 3.956848 GGCTGCTTCTCCTAATTCCAAAT 59.043 43.478 0.00 0.00 0.00 2.32
3432 3744 6.775234 TGGTATAGTCTATAGTGTCTCCCA 57.225 41.667 0.00 0.35 0.00 4.37
3452 3764 4.520492 CCCATAATACCTAAGCCAGCTTTG 59.480 45.833 10.64 8.51 37.47 2.77
3463 3775 2.757314 AGCCAGCTTTGCTTCTTTATCC 59.243 45.455 1.60 0.00 36.40 2.59
3477 3789 8.109634 TGCTTCTTTATCCAAGATAAGGTTTCT 58.890 33.333 6.42 0.00 41.42 2.52
3478 3790 8.961634 GCTTCTTTATCCAAGATAAGGTTTCTT 58.038 33.333 6.42 0.00 41.42 2.52
3500 3812 1.402787 CACCCATATTTGGTGCTCCC 58.597 55.000 7.97 0.00 46.13 4.30
3501 3813 1.006813 ACCCATATTTGGTGCTCCCA 58.993 50.000 1.59 0.00 41.91 4.37
3569 3881 6.320171 CAATGTCCAAATGTTGATCTCTGTC 58.680 40.000 0.00 0.00 0.00 3.51
3581 3893 1.379044 CTCTGTCCCCATGCCAACC 60.379 63.158 0.00 0.00 0.00 3.77
3592 3904 3.167485 CCATGCCAACCAGCCAATATAT 58.833 45.455 0.00 0.00 0.00 0.86
3621 3933 2.097825 AGATTTGATTGGCCAGACAGC 58.902 47.619 5.11 0.00 0.00 4.40
3645 3957 1.065636 GGGGCACTCTAGGTACCAAAC 60.066 57.143 15.94 0.00 33.04 2.93
3653 3965 6.091437 CACTCTAGGTACCAAACTAAACTCG 58.909 44.000 15.94 0.00 0.00 4.18
3704 4024 3.687125 TCCTCATTGTGACTACTCGACT 58.313 45.455 0.00 0.00 0.00 4.18
3726 4046 7.363205 ACTACTCGTCTAGAACTAGAAACAC 57.637 40.000 12.30 1.81 43.12 3.32
3811 4131 6.619744 TGAACAATGGTAAACATGCTGTATG 58.380 36.000 4.09 4.09 40.44 2.39
3889 4264 6.368791 TGTTTTTAGAAGTGGATGAGTGATCG 59.631 38.462 0.00 0.00 30.87 3.69
4062 4441 7.388500 AGGTATCGTTATCAGTAGCTACTTCTC 59.612 40.741 23.94 11.36 33.46 2.87
4067 4446 6.512091 CGTTATCAGTAGCTACTTCTCCTGTC 60.512 46.154 23.94 8.79 33.46 3.51
4075 4454 5.817784 AGCTACTTCTCCTGTCTGTACTAA 58.182 41.667 0.00 0.00 0.00 2.24
4089 4468 8.424274 TGTCTGTACTAATGCATAATCAAGTG 57.576 34.615 0.00 0.00 0.00 3.16
4097 4476 9.113838 ACTAATGCATAATCAAGTGTCCTAAAG 57.886 33.333 0.00 0.00 0.00 1.85
4180 4562 5.112129 AGGTGGTTGTGAAAGTAGAAAGT 57.888 39.130 0.00 0.00 0.00 2.66
4236 4618 2.017049 GTCTTGTTGTTCACTGGCACT 58.983 47.619 0.00 0.00 0.00 4.40
4470 4903 8.977267 TTTCAGAAAAATGAAACATCCCATTT 57.023 26.923 0.00 0.00 42.68 2.32
4725 5600 9.685276 ATTTAATCTTCATCTACACACATCCAA 57.315 29.630 0.00 0.00 0.00 3.53
4874 6818 5.860941 TTTCAGAATTTGTGGGCTTGTAA 57.139 34.783 0.00 0.00 0.00 2.41
4886 6830 5.071653 TGTGGGCTTGTAATGAGCTGATATA 59.928 40.000 0.00 0.00 40.01 0.86
4888 6832 6.093219 GTGGGCTTGTAATGAGCTGATATATG 59.907 42.308 0.00 0.00 40.01 1.78
4896 6840 2.636403 TGAGCTGATATATGGCTGCTGT 59.364 45.455 12.71 0.00 39.04 4.40
4974 6918 6.478344 GTGGTCTGAAGCTCTTATAACATGAG 59.522 42.308 0.00 0.00 0.00 2.90
4983 6927 7.268586 AGCTCTTATAACATGAGTTCGACATT 58.731 34.615 0.00 0.00 39.15 2.71
4985 6929 7.306866 GCTCTTATAACATGAGTTCGACATTCC 60.307 40.741 0.00 0.00 39.15 3.01
4995 6939 5.160607 AGTTCGACATTCCCAAACATAGA 57.839 39.130 0.00 0.00 0.00 1.98
4997 6941 6.180472 AGTTCGACATTCCCAAACATAGAAT 58.820 36.000 0.00 0.00 0.00 2.40
4998 6942 6.316390 AGTTCGACATTCCCAAACATAGAATC 59.684 38.462 0.00 0.00 0.00 2.52
5009 6953 7.336931 TCCCAAACATAGAATCTAAAAGAGCAC 59.663 37.037 0.00 0.00 0.00 4.40
5144 7452 7.558444 AGGTTTTGTCCACTTTTACTTGTATCA 59.442 33.333 0.00 0.00 0.00 2.15
5182 7492 7.792364 TTGGAGACCTCTGATTTAAGTAGAA 57.208 36.000 0.00 0.00 0.00 2.10
5215 7525 3.644966 TTGGGGCTGAGTAGTTAATGG 57.355 47.619 0.00 0.00 0.00 3.16
5222 7532 4.251268 GCTGAGTAGTTAATGGACCGTTT 58.749 43.478 3.77 0.00 0.00 3.60
5227 7537 6.938030 TGAGTAGTTAATGGACCGTTTCATTT 59.062 34.615 3.77 0.00 35.50 2.32
5239 7549 4.393062 ACCGTTTCATTTCATCTGTAGCAG 59.607 41.667 0.00 0.00 0.00 4.24
5240 7550 4.337763 CGTTTCATTTCATCTGTAGCAGC 58.662 43.478 0.00 0.00 0.00 5.25
5241 7551 4.142838 CGTTTCATTTCATCTGTAGCAGCA 60.143 41.667 0.00 0.00 0.00 4.41
5242 7552 5.448225 CGTTTCATTTCATCTGTAGCAGCAT 60.448 40.000 0.00 0.00 0.00 3.79
5246 7556 9.511272 TTTCATTTCATCTGTAGCAGCATATAT 57.489 29.630 0.00 0.00 0.00 0.86
5276 7587 6.442952 TGAAAAGGATAAATGTGGTGTTTCG 58.557 36.000 0.00 0.00 0.00 3.46
5356 7998 7.771183 ACTATCTGAACTCTCTTGTCTGATTC 58.229 38.462 0.00 0.00 0.00 2.52
5384 8026 3.445096 ACTTGATGCAAGCCTGGATTAAC 59.555 43.478 0.00 0.00 44.43 2.01
5385 8027 2.016318 TGATGCAAGCCTGGATTAACG 58.984 47.619 0.00 0.00 33.05 3.18
5389 8031 1.392589 CAAGCCTGGATTAACGCCAT 58.607 50.000 0.00 0.00 34.33 4.40
5390 8032 1.066002 CAAGCCTGGATTAACGCCATG 59.934 52.381 0.00 0.00 34.33 3.66
5409 8051 5.559417 GCCATGTTTTTCTTCGTTAACTCGA 60.559 40.000 3.71 0.00 38.08 4.04
5440 8082 2.931969 GGGCATTTTGCTTGCAATAGAC 59.068 45.455 8.93 4.49 44.28 2.59
5443 8085 5.039333 GGCATTTTGCTTGCAATAGACTAG 58.961 41.667 8.93 0.00 44.28 2.57
5445 8087 5.970023 GCATTTTGCTTGCAATAGACTAGAG 59.030 40.000 8.93 0.00 40.96 2.43
5521 8164 8.172352 ACTACACATGGAAGTAGTAGATCATC 57.828 38.462 19.77 0.00 46.56 2.92
5522 8165 7.780271 ACTACACATGGAAGTAGTAGATCATCA 59.220 37.037 19.77 0.00 46.56 3.07
5545 8188 8.867112 TCACCATCGTACTTATACTGAAAATC 57.133 34.615 0.00 0.00 0.00 2.17
5620 8268 5.854866 CACCATATACGTACGTTCATACAGG 59.145 44.000 27.92 22.56 0.00 4.00
5667 8315 1.937546 GAAGCCGCTTTGGTGGATGG 61.938 60.000 7.16 0.00 45.39 3.51
5668 8316 2.361104 GCCGCTTTGGTGGATGGA 60.361 61.111 0.00 0.00 45.39 3.41
5669 8317 1.754234 GCCGCTTTGGTGGATGGAT 60.754 57.895 0.00 0.00 45.39 3.41
5670 8318 1.728490 GCCGCTTTGGTGGATGGATC 61.728 60.000 0.00 0.00 45.39 3.36
5711 8360 1.531883 GCGAATTCGTGATTTCTGGCC 60.532 52.381 27.24 0.00 42.22 5.36
5907 8559 4.677584 GGAGTAGTACTCATCTGCAGTTG 58.322 47.826 27.41 17.14 46.79 3.16
5915 8567 3.001414 CTCATCTGCAGTTGAGTTCCAG 58.999 50.000 32.94 16.82 37.20 3.86
5955 8609 7.538575 CACTCGTTCCAAAGGAATCATAATTT 58.461 34.615 1.30 0.00 44.04 1.82
5980 8670 9.447040 TTTAGTCTTATTGATTGATCTCGTACG 57.553 33.333 9.53 9.53 0.00 3.67
5981 8671 7.028926 AGTCTTATTGATTGATCTCGTACGT 57.971 36.000 16.05 0.00 0.00 3.57
6089 8793 0.320771 TTTCAAGCCGTCAGCCTCTC 60.321 55.000 0.00 0.00 45.47 3.20
6109 8816 5.316167 TCTCAACATGTATCCAGTTTTGCT 58.684 37.500 0.00 0.00 0.00 3.91
6172 8886 1.234821 CGCAGGTCTTGGTTTTGCTA 58.765 50.000 0.00 0.00 32.80 3.49
6199 8913 1.621672 CCTCCCACTGCTTCTCCTCC 61.622 65.000 0.00 0.00 0.00 4.30
6221 8935 1.594310 GACCAGTCCTCCTGTGAGC 59.406 63.158 0.00 0.00 39.74 4.26
6227 8948 1.625818 AGTCCTCCTGTGAGCGAAATT 59.374 47.619 0.00 0.00 37.29 1.82
6228 8949 2.039084 AGTCCTCCTGTGAGCGAAATTT 59.961 45.455 0.00 0.00 37.29 1.82
6259 8987 3.758554 TCAAGGTGAAATTAAGCTCAGGC 59.241 43.478 0.00 0.00 39.06 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.401931 CCGTCGTAACCACAGTCGATT 60.402 52.381 0.00 0.00 34.93 3.34
299 300 1.428912 TGTCAAGATTTGAAGGCCCCT 59.571 47.619 0.00 0.00 42.15 4.79
689 690 1.001974 TCATAGGGATATGGTGTGCGC 59.998 52.381 0.00 0.00 0.00 6.09
690 691 2.037121 TGTCATAGGGATATGGTGTGCG 59.963 50.000 0.00 0.00 0.00 5.34
691 692 3.769739 TGTCATAGGGATATGGTGTGC 57.230 47.619 0.00 0.00 0.00 4.57
692 693 5.070981 AGACTTGTCATAGGGATATGGTGTG 59.929 44.000 3.49 0.00 0.00 3.82
693 694 5.219739 AGACTTGTCATAGGGATATGGTGT 58.780 41.667 3.49 0.00 0.00 4.16
694 695 5.815233 AGACTTGTCATAGGGATATGGTG 57.185 43.478 3.49 0.00 0.00 4.17
695 696 5.905331 TCAAGACTTGTCATAGGGATATGGT 59.095 40.000 14.75 0.00 0.00 3.55
696 697 6.425210 TCAAGACTTGTCATAGGGATATGG 57.575 41.667 14.75 0.00 0.00 2.74
697 698 8.737168 TTTTCAAGACTTGTCATAGGGATATG 57.263 34.615 14.75 0.00 0.00 1.78
698 699 9.927081 ATTTTTCAAGACTTGTCATAGGGATAT 57.073 29.630 14.75 0.00 0.00 1.63
700 701 9.401058 CTATTTTTCAAGACTTGTCATAGGGAT 57.599 33.333 14.75 3.45 0.00 3.85
701 702 7.829211 CCTATTTTTCAAGACTTGTCATAGGGA 59.171 37.037 21.82 2.53 30.97 4.20
702 703 7.415653 GCCTATTTTTCAAGACTTGTCATAGGG 60.416 40.741 25.72 18.13 32.85 3.53
703 704 7.475840 GCCTATTTTTCAAGACTTGTCATAGG 58.524 38.462 23.39 23.39 33.95 2.57
704 705 7.064609 TCGCCTATTTTTCAAGACTTGTCATAG 59.935 37.037 14.75 13.79 0.00 2.23
705 706 6.876789 TCGCCTATTTTTCAAGACTTGTCATA 59.123 34.615 14.75 6.64 0.00 2.15
706 707 5.705441 TCGCCTATTTTTCAAGACTTGTCAT 59.295 36.000 14.75 5.92 0.00 3.06
707 708 5.060506 TCGCCTATTTTTCAAGACTTGTCA 58.939 37.500 14.75 0.75 0.00 3.58
708 709 5.607119 TCGCCTATTTTTCAAGACTTGTC 57.393 39.130 14.75 0.00 0.00 3.18
709 710 7.552687 TCATATCGCCTATTTTTCAAGACTTGT 59.447 33.333 14.75 0.00 0.00 3.16
710 711 7.919690 TCATATCGCCTATTTTTCAAGACTTG 58.080 34.615 9.03 9.03 0.00 3.16
711 712 7.770897 ACTCATATCGCCTATTTTTCAAGACTT 59.229 33.333 0.00 0.00 0.00 3.01
712 713 7.275920 ACTCATATCGCCTATTTTTCAAGACT 58.724 34.615 0.00 0.00 0.00 3.24
713 714 7.484035 ACTCATATCGCCTATTTTTCAAGAC 57.516 36.000 0.00 0.00 0.00 3.01
714 715 7.012327 CCAACTCATATCGCCTATTTTTCAAGA 59.988 37.037 0.00 0.00 0.00 3.02
715 716 7.134815 CCAACTCATATCGCCTATTTTTCAAG 58.865 38.462 0.00 0.00 0.00 3.02
716 717 6.601613 ACCAACTCATATCGCCTATTTTTCAA 59.398 34.615 0.00 0.00 0.00 2.69
717 718 6.119536 ACCAACTCATATCGCCTATTTTTCA 58.880 36.000 0.00 0.00 0.00 2.69
718 719 6.619801 ACCAACTCATATCGCCTATTTTTC 57.380 37.500 0.00 0.00 0.00 2.29
719 720 7.280356 AGTACCAACTCATATCGCCTATTTTT 58.720 34.615 0.00 0.00 0.00 1.94
720 721 6.827727 AGTACCAACTCATATCGCCTATTTT 58.172 36.000 0.00 0.00 0.00 1.82
721 722 6.420913 AGTACCAACTCATATCGCCTATTT 57.579 37.500 0.00 0.00 0.00 1.40
735 736 6.092259 GCTAACAATTGATTCGAGTACCAACT 59.908 38.462 13.59 0.00 39.21 3.16
736 737 6.248631 GCTAACAATTGATTCGAGTACCAAC 58.751 40.000 13.59 0.00 0.00 3.77
737 738 5.353123 GGCTAACAATTGATTCGAGTACCAA 59.647 40.000 13.59 0.00 0.00 3.67
738 739 4.873827 GGCTAACAATTGATTCGAGTACCA 59.126 41.667 13.59 0.00 0.00 3.25
739 740 4.873827 TGGCTAACAATTGATTCGAGTACC 59.126 41.667 13.59 1.75 0.00 3.34
740 741 6.417191 TTGGCTAACAATTGATTCGAGTAC 57.583 37.500 13.59 0.00 33.18 2.73
776 777 7.645340 CGCTGCTTGATTTTGCTTATATTTAGT 59.355 33.333 0.00 0.00 0.00 2.24
840 847 5.563475 CGATTGGAAATTTGCAACTGAGAGT 60.563 40.000 24.92 9.39 41.30 3.24
844 851 4.844998 TCGATTGGAAATTTGCAACTGA 57.155 36.364 24.92 21.20 41.30 3.41
845 852 5.162794 TGATCGATTGGAAATTTGCAACTG 58.837 37.500 24.92 19.53 41.30 3.16
846 853 5.389859 TGATCGATTGGAAATTTGCAACT 57.610 34.783 24.92 14.97 41.30 3.16
847 854 5.443170 CGTTGATCGATTGGAAATTTGCAAC 60.443 40.000 24.92 17.39 41.30 4.17
900 992 1.628846 GGTTCAGTGGGTATGGTCTGT 59.371 52.381 0.00 0.00 0.00 3.41
905 997 3.153024 CACGGTTCAGTGGGTATGG 57.847 57.895 0.00 0.00 38.40 2.74
945 1037 0.676736 GGATTGGTGGTTTTGGCGAA 59.323 50.000 0.00 0.00 0.00 4.70
1487 1581 4.532834 AGTAAAAGGAAGAAGTGTTGGCA 58.467 39.130 0.00 0.00 0.00 4.92
1503 1597 2.506444 ACGCCCAAAATCCGAGTAAAA 58.494 42.857 0.00 0.00 0.00 1.52
1520 1614 0.536460 TCTCCCCCAAGTGAAAACGC 60.536 55.000 0.00 0.00 0.00 4.84
1521 1615 1.071699 TCTCTCCCCCAAGTGAAAACG 59.928 52.381 0.00 0.00 0.00 3.60
1522 1616 2.951229 TCTCTCCCCCAAGTGAAAAC 57.049 50.000 0.00 0.00 0.00 2.43
1529 1623 1.298953 TTCCCATTCTCTCCCCCAAG 58.701 55.000 0.00 0.00 0.00 3.61
1652 1749 9.165057 AGTTTCTATTCTTAGCCTATCCTGATT 57.835 33.333 0.00 0.00 0.00 2.57
1713 1810 3.679389 ACACTGACCATTTCATCACTCC 58.321 45.455 0.00 0.00 32.17 3.85
1753 1868 3.726557 ATCTCCTGTTGCAAAGATGGA 57.273 42.857 9.96 9.74 0.00 3.41
1758 1873 4.639310 AGCTCAATATCTCCTGTTGCAAAG 59.361 41.667 0.00 0.97 0.00 2.77
1778 1900 3.580458 AGTCTCAAACAGGTATGTCAGCT 59.420 43.478 0.00 0.00 39.29 4.24
1797 1919 8.764524 TCAGAGCTAAGAAACAATCTAAAGTC 57.235 34.615 0.00 0.00 37.42 3.01
1811 1933 5.866159 ACATGTCATGATCAGAGCTAAGA 57.134 39.130 19.77 0.00 0.00 2.10
1812 1934 6.922247 AAACATGTCATGATCAGAGCTAAG 57.078 37.500 19.77 0.00 0.00 2.18
1817 1939 7.856398 GCTCATAAAAACATGTCATGATCAGAG 59.144 37.037 19.77 15.11 0.00 3.35
1818 1940 7.555195 AGCTCATAAAAACATGTCATGATCAGA 59.445 33.333 19.77 6.80 0.00 3.27
1832 1954 7.985634 TGTTCAGTTTGAAGCTCATAAAAAC 57.014 32.000 0.00 0.00 37.00 2.43
1898 2020 2.557924 GCATTCATCCCAGACAAACACA 59.442 45.455 0.00 0.00 0.00 3.72
1905 2028 3.084039 TGAAACTGCATTCATCCCAGAC 58.916 45.455 0.00 0.00 34.50 3.51
1911 2034 4.227512 TGTGTGTGAAACTGCATTCATC 57.772 40.909 6.05 4.29 41.09 2.92
1924 2047 2.035704 GGCATGACCAATTTGTGTGTGA 59.964 45.455 0.00 0.00 38.86 3.58
1966 2089 6.354039 AGAAAACAAGCAGCAAGAAAAATG 57.646 33.333 0.00 0.00 0.00 2.32
2006 2131 2.125431 GCATGCACCATTGGCACC 60.125 61.111 14.21 0.00 45.23 5.01
2023 2148 8.097662 AGTTCTAACTTCTAAGAAAGGACATGG 58.902 37.037 0.00 0.00 35.21 3.66
2031 2156 8.812972 TGCAGGATAGTTCTAACTTCTAAGAAA 58.187 33.333 0.00 0.00 40.37 2.52
2032 2157 8.362464 TGCAGGATAGTTCTAACTTCTAAGAA 57.638 34.615 0.00 0.00 40.37 2.52
2033 2158 7.416890 GCTGCAGGATAGTTCTAACTTCTAAGA 60.417 40.741 17.12 0.00 40.37 2.10
2034 2159 6.699642 GCTGCAGGATAGTTCTAACTTCTAAG 59.300 42.308 17.12 0.00 40.37 2.18
2035 2160 6.381420 AGCTGCAGGATAGTTCTAACTTCTAA 59.619 38.462 17.12 0.00 40.37 2.10
2036 2161 5.894393 AGCTGCAGGATAGTTCTAACTTCTA 59.106 40.000 17.12 0.00 40.37 2.10
2037 2162 4.714308 AGCTGCAGGATAGTTCTAACTTCT 59.286 41.667 17.12 0.00 40.37 2.85
2038 2163 5.017294 AGCTGCAGGATAGTTCTAACTTC 57.983 43.478 17.12 0.00 40.37 3.01
2039 2164 6.739331 ATAGCTGCAGGATAGTTCTAACTT 57.261 37.500 17.12 0.00 40.37 2.66
2040 2165 7.007723 ACTATAGCTGCAGGATAGTTCTAACT 58.992 38.462 17.12 1.49 42.91 2.24
2041 2166 7.222000 ACTATAGCTGCAGGATAGTTCTAAC 57.778 40.000 17.12 0.00 33.56 2.34
2116 2245 4.355889 ACCCCTACAACCCAATACTTCTTT 59.644 41.667 0.00 0.00 0.00 2.52
2119 2248 4.263594 TGAACCCCTACAACCCAATACTTC 60.264 45.833 0.00 0.00 0.00 3.01
2130 2264 2.990284 TCCATTCCTTGAACCCCTACAA 59.010 45.455 0.00 0.00 0.00 2.41
2188 2322 0.107165 AAGAATTAGGTGAGGCGGCC 60.107 55.000 12.11 12.11 0.00 6.13
2243 2381 5.452078 TGGCTCAAGTGTTAAGGAAAATG 57.548 39.130 0.00 0.00 0.00 2.32
2301 2439 4.815308 GCTAGGGTAAAGCTAGGCTAAAAC 59.185 45.833 0.00 0.00 38.25 2.43
2358 2500 1.539929 CCAATTCGTGGGCAAGCAAAA 60.540 47.619 0.00 0.00 44.64 2.44
2359 2501 0.033228 CCAATTCGTGGGCAAGCAAA 59.967 50.000 0.00 0.00 44.64 3.68
2360 2502 1.664873 CCAATTCGTGGGCAAGCAA 59.335 52.632 0.00 0.00 44.64 3.91
2361 2503 3.364442 CCAATTCGTGGGCAAGCA 58.636 55.556 0.00 0.00 44.64 3.91
2409 2551 5.016173 TGGCATGCCAATACTTCTTTTACT 58.984 37.500 36.95 0.00 44.12 2.24
2529 2840 3.309296 AGGACCGAATACTGGTGATGAT 58.691 45.455 0.00 0.00 40.63 2.45
2530 2841 2.693591 GAGGACCGAATACTGGTGATGA 59.306 50.000 0.00 0.00 40.63 2.92
2531 2842 2.224066 GGAGGACCGAATACTGGTGATG 60.224 54.545 0.00 0.00 40.63 3.07
2632 2944 2.236146 TGGCTGGTTGGTATGAGTACAG 59.764 50.000 0.00 0.00 32.25 2.74
2700 3012 0.526662 GGCGCGGCTAGTAGATATGT 59.473 55.000 27.05 0.00 0.00 2.29
2720 3032 0.915364 AATCCTGGGACCTCAGCTTC 59.085 55.000 0.00 0.00 33.64 3.86
2784 3096 1.143838 CGATGAGCCCGTGGATTCA 59.856 57.895 0.00 0.00 0.00 2.57
2812 3124 0.967887 GGCAAAGCCTTTCTCCCCTC 60.968 60.000 0.00 0.00 46.69 4.30
2820 3132 3.899208 AGGTGACTAGGGCAAAGCCTTT 61.899 50.000 8.08 0.00 44.69 3.11
2844 3156 2.226674 CGTGCTTTTCTTTCCCCTCTTC 59.773 50.000 0.00 0.00 0.00 2.87
2900 3212 3.326006 TGTCCATGCTCTCCCTGATAATC 59.674 47.826 0.00 0.00 0.00 1.75
2901 3213 3.321039 TGTCCATGCTCTCCCTGATAAT 58.679 45.455 0.00 0.00 0.00 1.28
2916 3228 3.657398 TTCCTGAGCAATGATGTCCAT 57.343 42.857 0.00 0.00 36.99 3.41
2932 3244 1.068333 GCATGCACGACACATTTTCCT 60.068 47.619 14.21 0.00 0.00 3.36
2935 3247 1.881973 AGAGCATGCACGACACATTTT 59.118 42.857 21.98 0.00 0.00 1.82
2988 3300 2.157738 AGGTTTGCTTGTCTGATCAGC 58.842 47.619 18.36 13.24 0.00 4.26
3006 3318 1.002087 GGTCTGCCAATCGGGTATAGG 59.998 57.143 0.00 0.00 39.65 2.57
3024 3336 2.046892 GGCGACATGCTGACTGGT 60.047 61.111 0.00 0.00 45.43 4.00
3040 3352 4.458295 GCCATTATCATCTTGACTGGATGG 59.542 45.833 0.00 0.00 40.44 3.51
3165 3477 1.081892 CATCTTTCTGGTCAGTGGCG 58.918 55.000 0.00 0.00 0.00 5.69
3183 3495 3.446161 CAGTCTTGGACGTAACCTATCCA 59.554 47.826 0.00 0.00 40.83 3.41
3205 3517 2.906691 AGCTGCAGGATAGATCACAC 57.093 50.000 17.12 0.00 0.00 3.82
3206 3518 3.920231 AAAGCTGCAGGATAGATCACA 57.080 42.857 17.12 0.00 0.00 3.58
3207 3519 4.954875 ACTAAAGCTGCAGGATAGATCAC 58.045 43.478 17.12 0.00 0.00 3.06
3212 3524 7.547370 GGATTGTATACTAAAGCTGCAGGATAG 59.453 40.741 17.12 1.19 0.00 2.08
3245 3557 8.915036 AGTTAAGACGTAAGGAATACAGATCAT 58.085 33.333 0.00 0.00 46.39 2.45
3269 3581 9.939802 ATCTCTATGGTTTCTTTACGTAAAAGT 57.060 29.630 20.47 5.71 44.27 2.66
3271 3583 9.158233 CCATCTCTATGGTTTCTTTACGTAAAA 57.842 33.333 20.47 9.82 46.68 1.52
3272 3584 8.712285 CCATCTCTATGGTTTCTTTACGTAAA 57.288 34.615 19.12 19.12 46.68 2.01
3314 3626 7.699812 GCATCAGATCAAACCAAAATAGTCTTC 59.300 37.037 0.00 0.00 0.00 2.87
3350 3662 2.293170 GGAATTAGGAGAAGCAGCCAC 58.707 52.381 0.00 0.00 0.00 5.01
3368 3680 8.517062 AAACAAAATGACAATTCCAATTTGGA 57.483 26.923 14.24 14.24 46.61 3.53
3416 3728 9.750783 TTAGGTATTATGGGAGACACTATAGAC 57.249 37.037 6.78 0.00 0.00 2.59
3432 3744 5.053978 AGCAAAGCTGGCTTAGGTATTAT 57.946 39.130 8.30 0.00 38.81 1.28
3463 3775 9.799106 ATATGGGTGATAAGAAACCTTATCTTG 57.201 33.333 19.66 0.00 46.39 3.02
3509 3821 5.063312 ACGCAATAAGCATTAAATTTGCCAC 59.937 36.000 0.00 0.00 46.13 5.01
3539 3851 5.273674 TCAACATTTGGACATTGCAAAGA 57.726 34.783 8.96 0.00 40.88 2.52
3569 3881 4.700448 TGGCTGGTTGGCATGGGG 62.700 66.667 0.00 0.00 46.76 4.96
3581 3893 9.419297 CAAATCTGATGGAAAATATATTGGCTG 57.581 33.333 0.00 0.00 0.00 4.85
3592 3904 4.531339 TGGCCAATCAAATCTGATGGAAAA 59.469 37.500 0.61 0.00 41.66 2.29
3621 3933 1.108132 GTACCTAGAGTGCCCCCTCG 61.108 65.000 0.00 0.00 36.56 4.63
3645 3957 5.935789 TCATAGGGGTGAAAAACGAGTTTAG 59.064 40.000 1.32 0.00 31.63 1.85
3653 3965 3.096092 TGCCATCATAGGGGTGAAAAAC 58.904 45.455 0.00 0.00 0.00 2.43
3704 4024 7.976135 AAGTGTTTCTAGTTCTAGACGAGTA 57.024 36.000 8.81 0.00 33.27 2.59
3811 4131 5.927954 ATTGAAATGCCACATGTTTTCAC 57.072 34.783 18.51 0.00 37.69 3.18
4062 4441 7.712639 ACTTGATTATGCATTAGTACAGACAGG 59.287 37.037 3.54 0.00 0.00 4.00
4067 4446 7.712639 AGGACACTTGATTATGCATTAGTACAG 59.287 37.037 3.54 0.00 0.00 2.74
4075 4454 5.829924 CCCTTTAGGACACTTGATTATGCAT 59.170 40.000 3.79 3.79 38.24 3.96
4180 4562 7.994425 TTGTAAAACAAGCATATCTTCCTCA 57.006 32.000 0.00 0.00 32.34 3.86
4214 4596 2.358898 GTGCCAGTGAACAACAAGACAT 59.641 45.455 0.00 0.00 0.00 3.06
4217 4599 2.418368 AGTGCCAGTGAACAACAAGA 57.582 45.000 0.00 0.00 0.00 3.02
4236 4618 5.212745 ACCCAAGGTGGTTTCAAGATTAAA 58.787 37.500 0.00 0.00 33.91 1.52
4393 4823 3.407424 TTCAGGACAGGACACATTCAG 57.593 47.619 0.00 0.00 0.00 3.02
4725 5600 9.730705 TCAAGAGATAAACAGACAGAATTGAAT 57.269 29.630 0.00 0.00 0.00 2.57
4874 6818 3.263681 ACAGCAGCCATATATCAGCTCAT 59.736 43.478 4.16 0.00 33.70 2.90
4886 6830 1.111116 ACAGCACAAACAGCAGCCAT 61.111 50.000 0.00 0.00 0.00 4.40
4888 6832 0.179103 AAACAGCACAAACAGCAGCC 60.179 50.000 0.00 0.00 0.00 4.85
4896 6840 4.114073 CTGCTCAAATGAAACAGCACAAA 58.886 39.130 0.00 0.00 36.96 2.83
4974 6918 5.873179 TTCTATGTTTGGGAATGTCGAAC 57.127 39.130 0.00 0.00 0.00 3.95
4983 6927 7.336931 GTGCTCTTTTAGATTCTATGTTTGGGA 59.663 37.037 0.00 0.00 0.00 4.37
4985 6929 8.180267 CAGTGCTCTTTTAGATTCTATGTTTGG 58.820 37.037 0.00 0.00 0.00 3.28
4995 6939 4.292186 TCCAGCAGTGCTCTTTTAGATT 57.708 40.909 16.58 0.00 36.40 2.40
4997 6941 3.769739 TTCCAGCAGTGCTCTTTTAGA 57.230 42.857 16.58 2.59 36.40 2.10
4998 6942 5.382618 AAATTCCAGCAGTGCTCTTTTAG 57.617 39.130 16.58 2.38 36.40 1.85
5009 6953 2.762745 AGCTTTGCAAAATTCCAGCAG 58.237 42.857 18.10 3.39 39.72 4.24
5182 7492 2.568509 CAGCCCCAAAATCCAGTGAAAT 59.431 45.455 0.00 0.00 0.00 2.17
5193 7503 4.043561 TCCATTAACTACTCAGCCCCAAAA 59.956 41.667 0.00 0.00 0.00 2.44
5215 7525 4.391830 TGCTACAGATGAAATGAAACGGTC 59.608 41.667 0.00 0.00 0.00 4.79
5246 7556 9.747898 ACACCACATTTATCCTTTTCATACTTA 57.252 29.630 0.00 0.00 0.00 2.24
5249 7559 9.353999 GAAACACCACATTTATCCTTTTCATAC 57.646 33.333 0.00 0.00 0.00 2.39
5251 7561 7.090173 CGAAACACCACATTTATCCTTTTCAT 58.910 34.615 0.00 0.00 0.00 2.57
5276 7587 4.813697 GGAGTTCAGATAGTTCATGGAAGC 59.186 45.833 0.00 0.00 0.00 3.86
5384 8026 4.533222 AGTTAACGAAGAAAAACATGGCG 58.467 39.130 0.00 0.00 0.00 5.69
5385 8027 4.611366 CGAGTTAACGAAGAAAAACATGGC 59.389 41.667 0.00 0.00 35.09 4.40
5409 8051 2.634453 AGCAAAATGCCCAGCTAAACTT 59.366 40.909 0.00 0.00 46.52 2.66
5418 8060 2.566279 TCTATTGCAAGCAAAATGCCCA 59.434 40.909 11.89 0.00 46.52 5.36
5440 8082 2.761208 AGTTGGATGGAACGGTCTCTAG 59.239 50.000 0.00 0.00 0.00 2.43
5443 8085 1.676014 CCAGTTGGATGGAACGGTCTC 60.676 57.143 0.00 0.00 43.57 3.36
5445 8087 0.036306 ACCAGTTGGATGGAACGGTC 59.964 55.000 4.92 0.00 43.57 4.79
5520 8163 8.471609 TGATTTTCAGTATAAGTACGATGGTGA 58.528 33.333 0.00 0.00 35.92 4.02
5521 8164 8.642908 TGATTTTCAGTATAAGTACGATGGTG 57.357 34.615 0.00 0.00 35.92 4.17
5522 8165 9.314321 CTTGATTTTCAGTATAAGTACGATGGT 57.686 33.333 0.00 0.00 35.92 3.55
5587 8235 4.555313 CGTACGTATATGGTGGTGTACTGG 60.555 50.000 7.22 0.00 32.20 4.00
5711 8360 4.813161 CCTGTCTGACCATGTTATAGCTTG 59.187 45.833 5.17 0.00 0.00 4.01
5907 8559 3.555139 CGATGAGATCTTTGCTGGAACTC 59.445 47.826 0.00 0.00 34.58 3.01
5915 8567 1.257415 CGAGTGCGATGAGATCTTTGC 59.743 52.381 0.00 0.00 40.82 3.68
5955 8609 8.618677 ACGTACGAGATCAATCAATAAGACTAA 58.381 33.333 24.41 0.00 0.00 2.24
6109 8816 1.475571 CCACGATGATCCATTCCAGCA 60.476 52.381 0.00 0.00 0.00 4.41
6255 8983 0.248498 CTGAATTGCAGCATCGCCTG 60.248 55.000 0.00 0.00 37.90 4.85
6257 8985 4.704007 CTGAATTGCAGCATCGCC 57.296 55.556 0.00 0.00 37.90 5.54


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

AutoCloner maintained by Alex Coulton.