Multiple sequence alignment - TraesCS4D01G099500

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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 TraesCS4D01G099500 chr4D 100.000 3422 0 0 1 3422 76625991 76622570 0.000000e+00 6320.0
1 TraesCS4D01G099500 chr4D 95.512 1827 81 1 933 2758 77016804 77018630 0.000000e+00 2918.0
2 TraesCS4D01G099500 chr4D 87.106 667 75 7 2753 3414 77022882 77023542 0.000000e+00 745.0
3 TraesCS4D01G099500 chr4B 92.702 2494 162 13 933 3414 109053122 109050637 0.000000e+00 3579.0
4 TraesCS4D01G099500 chr4B 77.344 128 23 4 2721 2842 453888087 453887960 1.700000e-08 71.3
5 TraesCS4D01G099500 chr4A 94.959 1726 84 1 939 2664 511036915 511038637 0.000000e+00 2702.0
6 TraesCS4D01G099500 chr4A 87.185 437 55 1 2900 3336 511077607 511078042 2.370000e-136 496.0
7 TraesCS4D01G099500 chr4A 78.295 129 20 6 2721 2842 129361634 129361761 3.660000e-10 76.8
8 TraesCS4D01G099500 chr6A 87.519 665 74 6 166 822 93621301 93621964 0.000000e+00 760.0
9 TraesCS4D01G099500 chr6D 87.037 594 74 3 231 822 77858078 77858670 0.000000e+00 667.0
10 TraesCS4D01G099500 chr7D 88.486 469 48 5 356 822 364369170 364369634 2.310000e-156 562.0
11 TraesCS4D01G099500 chr7D 88.380 284 29 1 81 360 364368747 364369030 4.230000e-89 339.0
12 TraesCS4D01G099500 chr7D 78.864 317 40 8 495 808 572186602 572186894 4.510000e-44 189.0
13 TraesCS4D01G099500 chr3A 85.045 448 65 2 377 822 24209932 24209485 4.030000e-124 455.0
14 TraesCS4D01G099500 chr6B 78.417 139 23 6 2710 2842 487136237 487136100 2.190000e-12 84.2
15 TraesCS4D01G099500 chr1B 83.333 96 11 3 3319 3414 356961585 356961675 2.190000e-12 84.2
16 TraesCS4D01G099500 chr5D 76.978 139 25 6 2710 2842 125588482 125588345 4.740000e-09 73.1
17 TraesCS4D01G099500 chr1A 77.686 121 21 5 2721 2835 92032869 92032989 6.130000e-08 69.4
18 TraesCS4D01G099500 chr5B 88.462 52 4 2 2792 2842 668104404 668104354 1.030000e-05 62.1


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 TraesCS4D01G099500 chr4D 76622570 76625991 3421 True 6320.0 6320 100.000 1 3422 1 chr4D.!!$R1 3421
1 TraesCS4D01G099500 chr4D 77016804 77018630 1826 False 2918.0 2918 95.512 933 2758 1 chr4D.!!$F1 1825
2 TraesCS4D01G099500 chr4D 77022882 77023542 660 False 745.0 745 87.106 2753 3414 1 chr4D.!!$F2 661
3 TraesCS4D01G099500 chr4B 109050637 109053122 2485 True 3579.0 3579 92.702 933 3414 1 chr4B.!!$R1 2481
4 TraesCS4D01G099500 chr4A 511036915 511038637 1722 False 2702.0 2702 94.959 939 2664 1 chr4A.!!$F2 1725
5 TraesCS4D01G099500 chr6A 93621301 93621964 663 False 760.0 760 87.519 166 822 1 chr6A.!!$F1 656
6 TraesCS4D01G099500 chr6D 77858078 77858670 592 False 667.0 667 87.037 231 822 1 chr6D.!!$F1 591
7 TraesCS4D01G099500 chr7D 364368747 364369634 887 False 450.5 562 88.433 81 822 2 chr7D.!!$F2 741

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
848 1002 0.032952 GGACAGCCGACAAGTACACA 59.967 55.0 0.00 0.0 0.0 3.72 F
930 1084 0.037512 CCAAATCCCAAACGCATGCA 60.038 50.0 19.57 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1898 0.036010 AGGTCAACCTCATGCCGAAG 60.036 55.0 0.0 0.00 44.77 3.79 R
2913 3080 0.698238 TATCACCTTGGCTGCTTGGT 59.302 50.0 0.0 2.78 0.00 3.67 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
18 19 1.659233 TCACGCTGCAACCATTTGG 59.341 52.632 0.00 0.00 42.17 3.28
19 20 1.373246 CACGCTGCAACCATTTGGG 60.373 57.895 0.00 0.00 44.81 4.12
20 21 1.530419 ACGCTGCAACCATTTGGGA 60.530 52.632 0.00 0.00 41.15 4.37
21 22 0.899717 ACGCTGCAACCATTTGGGAT 60.900 50.000 0.00 0.00 41.15 3.85
22 23 0.179129 CGCTGCAACCATTTGGGATC 60.179 55.000 0.00 0.00 41.15 3.36
23 24 1.188863 GCTGCAACCATTTGGGATCT 58.811 50.000 0.96 0.00 41.15 2.75
24 25 1.551883 GCTGCAACCATTTGGGATCTT 59.448 47.619 0.96 0.00 41.15 2.40
25 26 2.760092 GCTGCAACCATTTGGGATCTTA 59.240 45.455 0.96 0.00 41.15 2.10
26 27 3.385755 GCTGCAACCATTTGGGATCTTAT 59.614 43.478 0.96 0.00 41.15 1.73
27 28 4.738541 GCTGCAACCATTTGGGATCTTATG 60.739 45.833 0.96 0.00 41.15 1.90
28 29 3.132646 TGCAACCATTTGGGATCTTATGC 59.867 43.478 0.96 0.00 41.15 3.14
29 30 3.132646 GCAACCATTTGGGATCTTATGCA 59.867 43.478 0.96 0.00 41.15 3.96
30 31 4.685924 CAACCATTTGGGATCTTATGCAC 58.314 43.478 0.96 0.00 41.15 4.57
31 32 3.979911 ACCATTTGGGATCTTATGCACA 58.020 40.909 0.96 0.00 41.15 4.57
32 33 3.701040 ACCATTTGGGATCTTATGCACAC 59.299 43.478 0.96 0.00 41.15 3.82
33 34 3.700539 CCATTTGGGATCTTATGCACACA 59.299 43.478 0.00 0.00 40.01 3.72
34 35 4.202080 CCATTTGGGATCTTATGCACACAG 60.202 45.833 0.00 0.00 40.01 3.66
35 36 3.719268 TTGGGATCTTATGCACACAGT 57.281 42.857 0.00 0.00 0.00 3.55
36 37 3.266510 TGGGATCTTATGCACACAGTC 57.733 47.619 0.00 0.00 0.00 3.51
37 38 2.092968 TGGGATCTTATGCACACAGTCC 60.093 50.000 0.00 0.00 0.00 3.85
38 39 2.205074 GGATCTTATGCACACAGTCCG 58.795 52.381 0.00 0.00 0.00 4.79
39 40 2.205074 GATCTTATGCACACAGTCCGG 58.795 52.381 0.00 0.00 0.00 5.14
40 41 0.391130 TCTTATGCACACAGTCCGGC 60.391 55.000 0.00 0.00 0.00 6.13
41 42 1.369091 CTTATGCACACAGTCCGGCC 61.369 60.000 0.00 0.00 0.00 6.13
42 43 3.657448 TATGCACACAGTCCGGCCG 62.657 63.158 21.04 21.04 0.00 6.13
57 58 4.457496 CCGCTGTCTGGCCGTGAT 62.457 66.667 0.00 0.00 0.00 3.06
58 59 2.887568 CGCTGTCTGGCCGTGATC 60.888 66.667 0.00 0.00 0.00 2.92
59 60 2.581354 GCTGTCTGGCCGTGATCT 59.419 61.111 0.00 0.00 0.00 2.75
60 61 1.816537 GCTGTCTGGCCGTGATCTA 59.183 57.895 0.00 0.00 0.00 1.98
61 62 0.175760 GCTGTCTGGCCGTGATCTAA 59.824 55.000 0.00 0.00 0.00 2.10
62 63 1.202580 GCTGTCTGGCCGTGATCTAAT 60.203 52.381 0.00 0.00 0.00 1.73
63 64 2.477825 CTGTCTGGCCGTGATCTAATG 58.522 52.381 0.00 0.00 0.00 1.90
64 65 2.101415 CTGTCTGGCCGTGATCTAATGA 59.899 50.000 0.00 0.00 0.00 2.57
65 66 2.700371 TGTCTGGCCGTGATCTAATGAT 59.300 45.455 0.00 0.00 35.26 2.45
66 67 3.134623 TGTCTGGCCGTGATCTAATGATT 59.865 43.478 0.00 0.00 32.19 2.57
67 68 3.496130 GTCTGGCCGTGATCTAATGATTG 59.504 47.826 0.00 0.00 32.19 2.67
68 69 3.387699 TCTGGCCGTGATCTAATGATTGA 59.612 43.478 0.00 0.00 32.19 2.57
69 70 4.040829 TCTGGCCGTGATCTAATGATTGAT 59.959 41.667 0.00 0.00 32.19 2.57
70 71 5.245977 TCTGGCCGTGATCTAATGATTGATA 59.754 40.000 0.00 0.00 32.19 2.15
71 72 5.237815 TGGCCGTGATCTAATGATTGATAC 58.762 41.667 0.00 0.00 32.19 2.24
72 73 5.221621 TGGCCGTGATCTAATGATTGATACA 60.222 40.000 0.00 0.00 32.19 2.29
73 74 5.877012 GGCCGTGATCTAATGATTGATACAT 59.123 40.000 0.00 0.00 32.19 2.29
74 75 6.183360 GGCCGTGATCTAATGATTGATACATG 60.183 42.308 0.00 0.00 32.19 3.21
75 76 6.369890 GCCGTGATCTAATGATTGATACATGT 59.630 38.462 2.69 2.69 32.19 3.21
76 77 7.095060 GCCGTGATCTAATGATTGATACATGTT 60.095 37.037 2.30 0.00 32.19 2.71
77 78 8.225777 CCGTGATCTAATGATTGATACATGTTG 58.774 37.037 2.30 0.00 32.19 3.33
78 79 8.225777 CGTGATCTAATGATTGATACATGTTGG 58.774 37.037 2.30 0.00 32.19 3.77
79 80 8.509690 GTGATCTAATGATTGATACATGTTGGG 58.490 37.037 2.30 0.00 32.19 4.12
86 87 5.593909 TGATTGATACATGTTGGGAATGGTC 59.406 40.000 2.30 0.00 0.00 4.02
101 102 6.071616 TGGGAATGGTCACTTAATTTACTTGC 60.072 38.462 0.00 0.00 0.00 4.01
104 105 8.736244 GGAATGGTCACTTAATTTACTTGCTAA 58.264 33.333 0.00 0.00 0.00 3.09
128 129 2.156917 CAATGACACAGTGCAGGACAT 58.843 47.619 0.00 0.00 0.00 3.06
131 132 1.151668 GACACAGTGCAGGACATGAC 58.848 55.000 0.00 0.00 0.00 3.06
154 155 3.003394 TCATGTTGATTTGGCGGATCT 57.997 42.857 0.00 0.00 0.00 2.75
164 165 0.760567 TGGCGGATCTGGAGCATACT 60.761 55.000 3.14 0.00 0.00 2.12
170 171 3.319405 CGGATCTGGAGCATACTTACAGT 59.681 47.826 0.00 0.00 34.55 3.55
224 225 6.866010 AAAAATTTCTGTTGATTTCCTGCC 57.134 33.333 0.00 0.00 0.00 4.85
235 236 3.751175 TGATTTCCTGCCAAGTTACTTCG 59.249 43.478 0.00 0.00 0.00 3.79
252 257 2.281484 GGTTGCGGCTGTCAAGGA 60.281 61.111 0.00 0.00 0.00 3.36
259 264 2.169561 TGCGGCTGTCAAGGATATACAA 59.830 45.455 0.00 0.00 0.00 2.41
268 273 7.303182 TGTCAAGGATATACAATACTGAGGG 57.697 40.000 0.00 0.00 0.00 4.30
276 281 9.751542 GGATATACAATACTGAGGGAATTATCG 57.248 37.037 0.00 0.00 0.00 2.92
282 287 2.706190 ACTGAGGGAATTATCGAAGGGG 59.294 50.000 0.00 0.00 0.00 4.79
372 522 2.659063 CCTCCCGTGCATCAGGTGA 61.659 63.158 0.00 0.00 0.00 4.02
373 523 1.524002 CTCCCGTGCATCAGGTGAT 59.476 57.895 0.00 0.00 34.56 3.06
413 563 2.570415 TTTTAGTGGGCGATGGTTCA 57.430 45.000 0.00 0.00 0.00 3.18
443 593 3.131223 CAGGTGTGATCCTACGAAGACAT 59.869 47.826 0.00 0.00 35.87 3.06
470 620 3.318017 GAGTGTTATCTTCGCGGCATAT 58.682 45.455 6.13 0.00 0.00 1.78
471 621 3.728845 AGTGTTATCTTCGCGGCATATT 58.271 40.909 6.13 0.00 0.00 1.28
490 640 7.920682 GGCATATTGGGTTTTATTCAACTGTAG 59.079 37.037 0.00 0.00 0.00 2.74
507 657 5.942961 ACTGTAGTAATGCTCTAGAGGCTA 58.057 41.667 21.23 5.59 34.47 3.93
515 665 4.927978 TGCTCTAGAGGCTAAGATTCAC 57.072 45.455 21.23 0.62 0.00 3.18
572 722 1.103398 CGGAGGGCCCAATCATTGTC 61.103 60.000 27.56 9.99 34.14 3.18
577 727 1.560505 GGCCCAATCATTGTCCAGTT 58.439 50.000 0.00 0.00 0.00 3.16
591 741 4.578871 TGTCCAGTTTGATTCATCGACAT 58.421 39.130 0.00 0.00 0.00 3.06
608 758 3.005155 CGACATCACTGGCATCTCTCATA 59.995 47.826 0.00 0.00 0.00 2.15
628 778 2.795329 AGGTGATTGTTTGGATCGCTT 58.205 42.857 0.00 0.00 35.07 4.68
651 801 4.261801 AGCGTATGGTCATTTAGTTGCTT 58.738 39.130 0.00 0.00 0.00 3.91
689 841 6.716628 TGATGCTTGACAAGGAGTTTATTCTT 59.283 34.615 16.80 0.00 30.29 2.52
690 842 7.882791 TGATGCTTGACAAGGAGTTTATTCTTA 59.117 33.333 16.80 0.00 30.29 2.10
726 878 7.067494 GTCATGAACAAAATAGGGTAGCAGATT 59.933 37.037 0.00 0.00 0.00 2.40
743 896 6.423182 AGCAGATTTTTGGCTGGTTATAGTA 58.577 36.000 0.00 0.00 39.60 1.82
748 901 7.556635 AGATTTTTGGCTGGTTATAGTAGAACC 59.443 37.037 18.07 18.07 45.64 3.62
765 918 7.424001 AGTAGAACCGAGTGTAATACTATTGC 58.576 38.462 0.00 0.00 40.53 3.56
768 921 7.948357 AGAACCGAGTGTAATACTATTGCATA 58.052 34.615 3.25 0.00 40.53 3.14
769 922 7.866393 AGAACCGAGTGTAATACTATTGCATAC 59.134 37.037 3.25 1.34 40.53 2.39
776 929 9.144298 AGTGTAATACTATTGCATACCTACACT 57.856 33.333 13.32 13.32 41.10 3.55
786 939 3.366396 CATACCTACACTGTGGACCTCT 58.634 50.000 13.09 0.00 0.00 3.69
793 946 5.010112 CCTACACTGTGGACCTCTATGTATG 59.990 48.000 13.09 5.45 0.00 2.39
797 950 4.079154 ACTGTGGACCTCTATGTATGGAGA 60.079 45.833 6.79 0.00 37.57 3.71
822 976 6.177310 TCTTTTGCTACTTACTGTAACCCA 57.823 37.500 0.00 0.00 0.00 4.51
823 977 6.593807 TCTTTTGCTACTTACTGTAACCCAA 58.406 36.000 0.00 0.00 0.00 4.12
824 978 7.055378 TCTTTTGCTACTTACTGTAACCCAAA 58.945 34.615 0.00 2.18 0.00 3.28
825 979 7.556996 TCTTTTGCTACTTACTGTAACCCAAAA 59.443 33.333 14.85 14.85 35.25 2.44
826 980 7.642082 TTTGCTACTTACTGTAACCCAAAAA 57.358 32.000 0.00 0.00 0.00 1.94
841 995 3.505835 AAAAAGGGACAGCCGACAA 57.494 47.368 0.00 0.00 33.83 3.18
842 996 1.318576 AAAAAGGGACAGCCGACAAG 58.681 50.000 0.00 0.00 33.83 3.16
843 997 0.182775 AAAAGGGACAGCCGACAAGT 59.817 50.000 0.00 0.00 33.83 3.16
844 998 1.053424 AAAGGGACAGCCGACAAGTA 58.947 50.000 0.00 0.00 33.83 2.24
845 999 0.320697 AAGGGACAGCCGACAAGTAC 59.679 55.000 0.00 0.00 33.83 2.73
846 1000 0.830444 AGGGACAGCCGACAAGTACA 60.830 55.000 0.00 0.00 33.83 2.90
847 1001 0.669625 GGGACAGCCGACAAGTACAC 60.670 60.000 0.00 0.00 33.83 2.90
848 1002 0.032952 GGACAGCCGACAAGTACACA 59.967 55.000 0.00 0.00 0.00 3.72
849 1003 1.337823 GGACAGCCGACAAGTACACAT 60.338 52.381 0.00 0.00 0.00 3.21
850 1004 2.413837 GACAGCCGACAAGTACACATT 58.586 47.619 0.00 0.00 0.00 2.71
851 1005 2.806244 GACAGCCGACAAGTACACATTT 59.194 45.455 0.00 0.00 0.00 2.32
852 1006 3.211045 ACAGCCGACAAGTACACATTTT 58.789 40.909 0.00 0.00 0.00 1.82
853 1007 3.250040 ACAGCCGACAAGTACACATTTTC 59.750 43.478 0.00 0.00 0.00 2.29
854 1008 3.498397 CAGCCGACAAGTACACATTTTCT 59.502 43.478 0.00 0.00 0.00 2.52
855 1009 3.498397 AGCCGACAAGTACACATTTTCTG 59.502 43.478 0.00 0.00 0.00 3.02
856 1010 3.250040 GCCGACAAGTACACATTTTCTGT 59.750 43.478 0.00 0.00 39.20 3.41
885 1039 7.934855 AATGATGAAGAAAATGTAGTGCTCT 57.065 32.000 0.00 0.00 0.00 4.09
886 1040 6.732531 TGATGAAGAAAATGTAGTGCTCTG 57.267 37.500 0.00 0.00 0.00 3.35
887 1041 6.233434 TGATGAAGAAAATGTAGTGCTCTGT 58.767 36.000 0.00 0.00 0.00 3.41
888 1042 6.712095 TGATGAAGAAAATGTAGTGCTCTGTT 59.288 34.615 0.00 0.00 0.00 3.16
889 1043 6.942532 TGAAGAAAATGTAGTGCTCTGTTT 57.057 33.333 0.00 0.00 0.00 2.83
890 1044 6.959361 TGAAGAAAATGTAGTGCTCTGTTTC 58.041 36.000 0.00 3.85 0.00 2.78
891 1045 6.767902 TGAAGAAAATGTAGTGCTCTGTTTCT 59.232 34.615 0.00 5.84 0.00 2.52
892 1046 7.283127 TGAAGAAAATGTAGTGCTCTGTTTCTT 59.717 33.333 19.76 19.76 0.00 2.52
893 1047 6.963796 AGAAAATGTAGTGCTCTGTTTCTTG 58.036 36.000 0.00 0.00 0.00 3.02
894 1048 5.695851 AAATGTAGTGCTCTGTTTCTTGG 57.304 39.130 0.00 0.00 0.00 3.61
895 1049 4.623932 ATGTAGTGCTCTGTTTCTTGGA 57.376 40.909 0.00 0.00 0.00 3.53
896 1050 3.728845 TGTAGTGCTCTGTTTCTTGGAC 58.271 45.455 0.00 0.00 0.00 4.02
897 1051 1.871080 AGTGCTCTGTTTCTTGGACG 58.129 50.000 0.00 0.00 0.00 4.79
898 1052 1.139058 AGTGCTCTGTTTCTTGGACGT 59.861 47.619 0.00 0.00 0.00 4.34
899 1053 1.261619 GTGCTCTGTTTCTTGGACGTG 59.738 52.381 0.00 0.00 0.00 4.49
900 1054 1.138069 TGCTCTGTTTCTTGGACGTGA 59.862 47.619 0.00 0.00 0.00 4.35
901 1055 2.224281 TGCTCTGTTTCTTGGACGTGAT 60.224 45.455 0.00 0.00 0.00 3.06
902 1056 2.158449 GCTCTGTTTCTTGGACGTGATG 59.842 50.000 0.00 0.00 0.00 3.07
903 1057 2.143122 TCTGTTTCTTGGACGTGATGC 58.857 47.619 0.00 0.00 0.00 3.91
905 1059 1.144969 GTTTCTTGGACGTGATGCGA 58.855 50.000 0.00 0.00 44.77 5.10
906 1060 1.732259 GTTTCTTGGACGTGATGCGAT 59.268 47.619 0.00 0.00 44.77 4.58
907 1061 1.358877 TTCTTGGACGTGATGCGATG 58.641 50.000 0.00 0.00 44.77 3.84
908 1062 1.083806 TCTTGGACGTGATGCGATGC 61.084 55.000 0.00 0.00 44.77 3.91
909 1063 1.360931 CTTGGACGTGATGCGATGCA 61.361 55.000 0.00 0.00 44.86 3.96
919 1073 2.417978 TGCGATGCATCCAAATCCC 58.582 52.632 20.87 1.95 31.71 3.85
920 1074 0.395448 TGCGATGCATCCAAATCCCA 60.395 50.000 20.87 4.38 31.71 4.37
921 1075 0.746063 GCGATGCATCCAAATCCCAA 59.254 50.000 20.87 0.00 0.00 4.12
922 1076 1.136695 GCGATGCATCCAAATCCCAAA 59.863 47.619 20.87 0.00 0.00 3.28
923 1077 2.813061 CGATGCATCCAAATCCCAAAC 58.187 47.619 20.87 0.00 0.00 2.93
924 1078 2.795681 CGATGCATCCAAATCCCAAACG 60.796 50.000 20.87 1.11 0.00 3.60
925 1079 0.246086 TGCATCCAAATCCCAAACGC 59.754 50.000 0.00 0.00 0.00 4.84
926 1080 0.246086 GCATCCAAATCCCAAACGCA 59.754 50.000 0.00 0.00 0.00 5.24
927 1081 1.134729 GCATCCAAATCCCAAACGCAT 60.135 47.619 0.00 0.00 0.00 4.73
928 1082 2.542597 CATCCAAATCCCAAACGCATG 58.457 47.619 0.00 0.00 0.00 4.06
929 1083 0.246086 TCCAAATCCCAAACGCATGC 59.754 50.000 7.91 7.91 0.00 4.06
930 1084 0.037512 CCAAATCCCAAACGCATGCA 60.038 50.000 19.57 0.00 0.00 3.96
931 1085 1.405797 CCAAATCCCAAACGCATGCAT 60.406 47.619 19.57 0.00 0.00 3.96
932 1086 2.159128 CCAAATCCCAAACGCATGCATA 60.159 45.455 19.57 0.00 0.00 3.14
933 1087 3.493002 CCAAATCCCAAACGCATGCATAT 60.493 43.478 19.57 0.00 0.00 1.78
934 1088 4.121317 CAAATCCCAAACGCATGCATATT 58.879 39.130 19.57 5.73 0.00 1.28
935 1089 4.405116 AATCCCAAACGCATGCATATTT 57.595 36.364 19.57 11.80 0.00 1.40
936 1090 3.162202 TCCCAAACGCATGCATATTTG 57.838 42.857 22.82 22.82 32.89 2.32
937 1091 2.757314 TCCCAAACGCATGCATATTTGA 59.243 40.909 27.81 14.44 34.62 2.69
942 1096 5.960683 CCAAACGCATGCATATTTGATTTTG 59.039 36.000 27.81 16.83 34.62 2.44
947 1101 3.523606 TGCATATTTGATTTTGCCGCT 57.476 38.095 0.00 0.00 34.20 5.52
961 1115 4.697756 CGCTGGCTTTCCCGTCCA 62.698 66.667 0.00 0.00 35.87 4.02
1012 1166 0.392706 CTAGCATATGTGGACGGGCA 59.607 55.000 4.29 0.00 0.00 5.36
1090 1244 2.801631 CGCCTCCTCCAGGTCCATC 61.802 68.421 0.00 0.00 45.61 3.51
1195 1349 4.323477 TCCCCGCTTCCACCGTTG 62.323 66.667 0.00 0.00 0.00 4.10
1228 1382 2.756283 CCCTCCGCCTCTTCTCGT 60.756 66.667 0.00 0.00 0.00 4.18
1380 1534 2.863153 GTTGCATGCTCGCTCGTT 59.137 55.556 20.33 0.00 0.00 3.85
1554 1708 1.079127 GGTGAGGGATGTGGTGTCG 60.079 63.158 0.00 0.00 0.00 4.35
1572 1726 1.226717 GTGGACGACGCTCATCTCC 60.227 63.158 0.00 0.00 0.00 3.71
1581 1735 0.038159 CGCTCATCTCCGGGTTATCC 60.038 60.000 0.00 0.00 0.00 2.59
1608 1762 1.604593 GTGCCACTGGGATGCTGTT 60.605 57.895 0.00 0.00 35.59 3.16
1626 1780 2.040278 TGTTGAGGTCTTCAGGGGATTG 59.960 50.000 0.00 0.00 37.07 2.67
1646 1800 2.197324 GGTGGACAACAAGGGGCA 59.803 61.111 0.00 0.00 0.00 5.36
1677 1831 0.673333 CCACATTGGTCAGCGTGCTA 60.673 55.000 0.00 0.00 31.35 3.49
1692 1846 1.133025 GTGCTATCGGCTTGTGCAAAT 59.867 47.619 0.00 0.00 42.39 2.32
1725 1879 4.966787 GGGCTTGCGGTTGGGACA 62.967 66.667 0.00 0.00 0.00 4.02
1737 1891 3.050275 GGGACAGCTGTTCACGCC 61.050 66.667 26.38 18.88 0.00 5.68
1743 1897 1.270839 ACAGCTGTTCACGCCTATGTT 60.271 47.619 15.25 0.00 0.00 2.71
1744 1898 1.394917 CAGCTGTTCACGCCTATGTTC 59.605 52.381 5.25 0.00 0.00 3.18
1818 1972 3.391296 TGTATGGGAAGTATGGGAAGCTC 59.609 47.826 0.00 0.00 0.00 4.09
1881 2035 1.993370 GTCTGTACGTGGAATGCACTC 59.007 52.381 2.94 0.00 0.00 3.51
2111 2265 1.213182 TGTTGTGGACCTGTTAAGCCA 59.787 47.619 0.00 0.00 0.00 4.75
2178 2332 3.572584 CTTTTTGCCTGATGCTTCTGTC 58.427 45.455 0.88 0.00 42.00 3.51
2295 2449 2.876550 CGACCGGTATGTGACTATCAGA 59.123 50.000 7.34 0.00 0.00 3.27
2388 2542 0.892814 AGAAGACAGCAGGGCAAAGC 60.893 55.000 0.00 0.00 0.00 3.51
2479 2633 4.935808 GGACTACCGTTTGTTTCTCATGAT 59.064 41.667 0.00 0.00 0.00 2.45
2485 2639 7.214467 ACCGTTTGTTTCTCATGATTTGTAT 57.786 32.000 0.00 0.00 0.00 2.29
2600 2758 2.289010 GGGTCACCTTTGATTTGCAAGG 60.289 50.000 0.00 0.00 37.87 3.61
2618 2776 3.942130 AGGTTGCAAAAAGGCAGTATC 57.058 42.857 0.00 0.00 45.88 2.24
2639 2797 5.689383 TCAGGAAAAGCACAGAATTGTAC 57.311 39.130 0.00 0.00 35.25 2.90
2740 2901 5.444663 AGATTCTTTGCAAGAGGTTTGAC 57.555 39.130 0.00 0.00 39.03 3.18
2869 3034 9.284968 TCTTTTAAATCAAAGAGTCCCTAACAG 57.715 33.333 0.00 0.00 37.77 3.16
2905 3072 7.277174 AGATTGTCCAGTTTAACCAAAAGAG 57.723 36.000 0.00 0.00 0.00 2.85
2913 3080 8.808092 TCCAGTTTAACCAAAAGAGAAAGAAAA 58.192 29.630 0.00 0.00 0.00 2.29
2961 3128 3.372206 CAGTTCTCCATTGTTTAGCTCCG 59.628 47.826 0.00 0.00 0.00 4.63
3052 3219 1.395635 TGTGTCATCTACCGCCGTAT 58.604 50.000 0.00 0.00 0.00 3.06
3059 3226 3.069016 TCATCTACCGCCGTATGTCAAAT 59.931 43.478 0.00 0.00 0.00 2.32
3094 3261 0.040514 TGCACGTTTGAATTCCTGCG 60.041 50.000 2.27 7.00 0.00 5.18
3162 3329 1.964448 CGTAGGTGTCTGGCACTCA 59.036 57.895 12.66 0.00 46.86 3.41
3169 3336 2.997315 TCTGGCACTCAGGACCCG 60.997 66.667 0.00 0.00 43.53 5.28
3177 3344 1.971695 CTCAGGACCCGGCCAAAAC 60.972 63.158 2.24 0.00 0.00 2.43
3178 3345 2.989253 CAGGACCCGGCCAAAACC 60.989 66.667 2.24 0.06 0.00 3.27
3189 3357 1.541672 CCAAAACCCCACCCAGAGT 59.458 57.895 0.00 0.00 0.00 3.24
3192 3360 1.726192 AAAACCCCACCCAGAGTCCC 61.726 60.000 0.00 0.00 0.00 4.46
3202 3370 1.486726 CCCAGAGTCCCGCTTTTATCT 59.513 52.381 0.00 0.00 0.00 1.98
3252 3421 2.359214 GCATAGTCTGAGACCGATGTCA 59.641 50.000 19.99 0.00 44.33 3.58
3255 3424 0.888619 GTCTGAGACCGATGTCACCA 59.111 55.000 0.00 0.00 44.33 4.17
3275 3444 0.321653 CTACACCAACCACTCAGCCC 60.322 60.000 0.00 0.00 0.00 5.19
3320 3489 2.894126 CGCTCCCTGGATGTAGACTAAT 59.106 50.000 0.00 0.00 0.00 1.73
3336 3505 4.400884 AGACTAATCACATGTCTCGAAGCT 59.599 41.667 0.00 0.00 36.45 3.74
3360 3529 1.880027 GTCAAGTTTGCTACTGGGGTG 59.120 52.381 0.00 0.00 37.12 4.61
3361 3530 0.598065 CAAGTTTGCTACTGGGGTGC 59.402 55.000 0.00 0.00 37.12 5.01
3362 3531 0.184933 AAGTTTGCTACTGGGGTGCA 59.815 50.000 0.00 0.00 37.12 4.57
3363 3532 0.405585 AGTTTGCTACTGGGGTGCAT 59.594 50.000 0.00 0.00 35.19 3.96
3373 3542 1.136961 TGGGGTGCATGGTCAAGGTA 61.137 55.000 0.00 0.00 0.00 3.08
3406 3575 3.643792 AGTACTTGAGAGAACCAACTGCT 59.356 43.478 0.00 0.00 0.00 4.24
3414 3583 3.072184 AGAGAACCAACTGCTGAAGACAT 59.928 43.478 0.00 0.00 0.00 3.06
3415 3584 3.144506 AGAACCAACTGCTGAAGACATG 58.855 45.455 0.00 0.00 0.00 3.21
3416 3585 1.242076 ACCAACTGCTGAAGACATGC 58.758 50.000 0.00 0.00 0.00 4.06
3417 3586 1.241165 CCAACTGCTGAAGACATGCA 58.759 50.000 0.00 0.00 35.30 3.96
3418 3587 1.816835 CCAACTGCTGAAGACATGCAT 59.183 47.619 0.00 0.00 36.07 3.96
3419 3588 3.011818 CCAACTGCTGAAGACATGCATA 58.988 45.455 0.00 0.00 36.07 3.14
3420 3589 3.441222 CCAACTGCTGAAGACATGCATAA 59.559 43.478 0.00 0.00 36.07 1.90
3421 3590 4.409570 CAACTGCTGAAGACATGCATAAC 58.590 43.478 0.00 0.00 36.07 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.659233 CCAAATGGTTGCAGCGTGA 59.341 52.632 0.00 0.00 33.01 4.35
1 2 1.373246 CCCAAATGGTTGCAGCGTG 60.373 57.895 0.00 0.00 33.01 5.34
2 3 0.899717 ATCCCAAATGGTTGCAGCGT 60.900 50.000 0.00 0.00 33.01 5.07
3 4 0.179129 GATCCCAAATGGTTGCAGCG 60.179 55.000 0.00 0.00 33.01 5.18
5 6 4.738541 GCATAAGATCCCAAATGGTTGCAG 60.739 45.833 0.00 0.00 33.01 4.41
7 8 3.132646 TGCATAAGATCCCAAATGGTTGC 59.867 43.478 0.00 0.00 33.01 4.17
8 9 4.160065 TGTGCATAAGATCCCAAATGGTTG 59.840 41.667 0.00 0.00 34.77 3.77
9 10 4.160252 GTGTGCATAAGATCCCAAATGGTT 59.840 41.667 0.00 0.00 34.77 3.67
10 11 3.701040 GTGTGCATAAGATCCCAAATGGT 59.299 43.478 0.00 0.00 34.77 3.55
11 12 3.700539 TGTGTGCATAAGATCCCAAATGG 59.299 43.478 0.00 0.00 0.00 3.16
12 13 4.400251 ACTGTGTGCATAAGATCCCAAATG 59.600 41.667 0.00 0.00 0.00 2.32
13 14 4.603131 ACTGTGTGCATAAGATCCCAAAT 58.397 39.130 0.00 0.00 0.00 2.32
14 15 4.009675 GACTGTGTGCATAAGATCCCAAA 58.990 43.478 0.00 0.00 0.00 3.28
15 16 3.609853 GACTGTGTGCATAAGATCCCAA 58.390 45.455 0.00 0.00 0.00 4.12
16 17 2.092968 GGACTGTGTGCATAAGATCCCA 60.093 50.000 0.00 0.00 0.00 4.37
17 18 2.565841 GGACTGTGTGCATAAGATCCC 58.434 52.381 0.00 0.00 0.00 3.85
18 19 2.205074 CGGACTGTGTGCATAAGATCC 58.795 52.381 0.00 0.00 0.00 3.36
19 20 2.205074 CCGGACTGTGTGCATAAGATC 58.795 52.381 0.00 0.00 0.00 2.75
20 21 1.743772 GCCGGACTGTGTGCATAAGAT 60.744 52.381 5.05 0.00 0.00 2.40
21 22 0.391130 GCCGGACTGTGTGCATAAGA 60.391 55.000 5.05 0.00 0.00 2.10
22 23 1.369091 GGCCGGACTGTGTGCATAAG 61.369 60.000 5.05 0.00 0.00 1.73
23 24 1.376683 GGCCGGACTGTGTGCATAA 60.377 57.895 5.05 0.00 0.00 1.90
24 25 2.267642 GGCCGGACTGTGTGCATA 59.732 61.111 5.05 0.00 0.00 3.14
40 41 4.457496 ATCACGGCCAGACAGCGG 62.457 66.667 2.24 0.00 38.89 5.52
41 42 2.004808 TAGATCACGGCCAGACAGCG 62.005 60.000 2.24 0.00 0.00 5.18
42 43 0.175760 TTAGATCACGGCCAGACAGC 59.824 55.000 2.24 0.00 0.00 4.40
43 44 2.101415 TCATTAGATCACGGCCAGACAG 59.899 50.000 2.24 0.00 0.00 3.51
44 45 2.107366 TCATTAGATCACGGCCAGACA 58.893 47.619 2.24 0.00 0.00 3.41
45 46 2.890808 TCATTAGATCACGGCCAGAC 57.109 50.000 2.24 0.00 0.00 3.51
46 47 3.387699 TCAATCATTAGATCACGGCCAGA 59.612 43.478 2.24 0.00 31.90 3.86
47 48 3.732212 TCAATCATTAGATCACGGCCAG 58.268 45.455 2.24 0.00 31.90 4.85
48 49 3.836365 TCAATCATTAGATCACGGCCA 57.164 42.857 2.24 0.00 31.90 5.36
49 50 5.237815 TGTATCAATCATTAGATCACGGCC 58.762 41.667 0.00 0.00 31.90 6.13
50 51 6.369890 ACATGTATCAATCATTAGATCACGGC 59.630 38.462 0.00 0.00 31.90 5.68
51 52 7.895975 ACATGTATCAATCATTAGATCACGG 57.104 36.000 0.00 0.00 31.90 4.94
52 53 8.225777 CCAACATGTATCAATCATTAGATCACG 58.774 37.037 0.00 0.00 31.90 4.35
53 54 8.509690 CCCAACATGTATCAATCATTAGATCAC 58.490 37.037 0.00 0.00 31.90 3.06
54 55 8.439172 TCCCAACATGTATCAATCATTAGATCA 58.561 33.333 0.00 0.00 31.90 2.92
55 56 8.853077 TCCCAACATGTATCAATCATTAGATC 57.147 34.615 0.00 0.00 31.90 2.75
56 57 9.818270 ATTCCCAACATGTATCAATCATTAGAT 57.182 29.630 0.00 0.00 35.53 1.98
57 58 9.070179 CATTCCCAACATGTATCAATCATTAGA 57.930 33.333 0.00 0.00 0.00 2.10
58 59 8.301720 CCATTCCCAACATGTATCAATCATTAG 58.698 37.037 0.00 0.00 0.00 1.73
59 60 7.784073 ACCATTCCCAACATGTATCAATCATTA 59.216 33.333 0.00 0.00 0.00 1.90
60 61 6.612456 ACCATTCCCAACATGTATCAATCATT 59.388 34.615 0.00 0.00 0.00 2.57
61 62 6.138263 ACCATTCCCAACATGTATCAATCAT 58.862 36.000 0.00 0.00 0.00 2.45
62 63 5.517924 ACCATTCCCAACATGTATCAATCA 58.482 37.500 0.00 0.00 0.00 2.57
63 64 5.593909 TGACCATTCCCAACATGTATCAATC 59.406 40.000 0.00 0.00 0.00 2.67
64 65 5.360714 GTGACCATTCCCAACATGTATCAAT 59.639 40.000 0.00 0.00 0.00 2.57
65 66 4.704540 GTGACCATTCCCAACATGTATCAA 59.295 41.667 0.00 0.00 0.00 2.57
66 67 4.018506 AGTGACCATTCCCAACATGTATCA 60.019 41.667 0.00 0.00 0.00 2.15
67 68 4.526970 AGTGACCATTCCCAACATGTATC 58.473 43.478 0.00 0.00 0.00 2.24
68 69 4.591321 AGTGACCATTCCCAACATGTAT 57.409 40.909 0.00 0.00 0.00 2.29
69 70 4.380843 AAGTGACCATTCCCAACATGTA 57.619 40.909 0.00 0.00 0.00 2.29
70 71 2.978156 AGTGACCATTCCCAACATGT 57.022 45.000 0.00 0.00 0.00 3.21
71 72 5.920193 ATTAAGTGACCATTCCCAACATG 57.080 39.130 0.00 0.00 0.00 3.21
72 73 6.933514 AAATTAAGTGACCATTCCCAACAT 57.066 33.333 0.00 0.00 0.00 2.71
73 74 7.007723 AGTAAATTAAGTGACCATTCCCAACA 58.992 34.615 0.00 0.00 0.00 3.33
74 75 7.462571 AGTAAATTAAGTGACCATTCCCAAC 57.537 36.000 0.00 0.00 0.00 3.77
75 76 7.524698 GCAAGTAAATTAAGTGACCATTCCCAA 60.525 37.037 0.00 0.00 0.00 4.12
76 77 6.071616 GCAAGTAAATTAAGTGACCATTCCCA 60.072 38.462 0.00 0.00 0.00 4.37
77 78 6.152831 AGCAAGTAAATTAAGTGACCATTCCC 59.847 38.462 0.00 0.00 0.00 3.97
78 79 7.158099 AGCAAGTAAATTAAGTGACCATTCC 57.842 36.000 0.00 0.00 0.00 3.01
101 102 4.163458 TGCACTGTGTCATTGCATTTAG 57.837 40.909 9.86 0.00 43.21 1.85
104 105 1.271379 CCTGCACTGTGTCATTGCATT 59.729 47.619 13.36 0.00 45.94 3.56
111 112 0.758123 TCATGTCCTGCACTGTGTCA 59.242 50.000 9.86 7.14 0.00 3.58
128 129 3.367190 CCGCCAAATCAACATGATTGTCA 60.367 43.478 0.00 0.00 45.57 3.58
131 132 3.507103 TCCGCCAAATCAACATGATTG 57.493 42.857 0.00 0.37 45.57 2.67
164 165 5.127845 TCCTTGCCATGAACAAAAACTGTAA 59.872 36.000 0.00 0.00 37.23 2.41
170 171 3.134442 AGCTTCCTTGCCATGAACAAAAA 59.866 39.130 0.00 0.00 0.00 1.94
202 203 5.927819 TGGCAGGAAATCAACAGAAATTTT 58.072 33.333 0.00 0.00 0.00 1.82
224 225 0.110373 GCCGCAACCGAAGTAACTTG 60.110 55.000 0.00 0.00 36.29 3.16
235 236 0.392461 TATCCTTGACAGCCGCAACC 60.392 55.000 0.00 0.00 0.00 3.77
259 264 4.532521 CCCCTTCGATAATTCCCTCAGTAT 59.467 45.833 0.00 0.00 0.00 2.12
268 273 6.729187 CAAGACATTTCCCCTTCGATAATTC 58.271 40.000 0.00 0.00 0.00 2.17
276 281 1.821216 TCGCAAGACATTTCCCCTTC 58.179 50.000 0.00 0.00 45.01 3.46
342 348 3.661648 GGGAGGTGGTGGCCATGT 61.662 66.667 9.72 0.00 35.28 3.21
363 513 2.679837 CCACCGAAAGAATCACCTGATG 59.320 50.000 0.00 0.00 34.49 3.07
372 522 1.561542 AGCTCCATCCACCGAAAGAAT 59.438 47.619 0.00 0.00 0.00 2.40
373 523 0.984230 AGCTCCATCCACCGAAAGAA 59.016 50.000 0.00 0.00 0.00 2.52
397 547 1.220749 GCTGAACCATCGCCCACTA 59.779 57.895 0.00 0.00 0.00 2.74
426 576 4.302455 CCATCATGTCTTCGTAGGATCAC 58.698 47.826 0.00 0.00 0.00 3.06
443 593 2.481276 CGCGAAGATAACACTCCCATCA 60.481 50.000 0.00 0.00 0.00 3.07
470 620 8.301002 GCATTACTACAGTTGAATAAAACCCAA 58.699 33.333 0.00 0.00 0.00 4.12
471 621 7.668052 AGCATTACTACAGTTGAATAAAACCCA 59.332 33.333 0.00 0.00 0.00 4.51
490 640 6.866248 GTGAATCTTAGCCTCTAGAGCATTAC 59.134 42.308 14.73 1.00 0.00 1.89
492 642 5.508825 CGTGAATCTTAGCCTCTAGAGCATT 60.509 44.000 14.73 4.36 0.00 3.56
507 657 1.155889 TGCATCAACGCGTGAATCTT 58.844 45.000 14.98 0.00 40.50 2.40
572 722 4.633126 AGTGATGTCGATGAATCAAACTGG 59.367 41.667 9.22 0.00 34.70 4.00
577 727 2.938451 GCCAGTGATGTCGATGAATCAA 59.062 45.455 9.22 0.00 34.70 2.57
591 741 2.697229 CACCTATGAGAGATGCCAGTGA 59.303 50.000 0.00 0.00 0.00 3.41
608 758 2.496899 AGCGATCCAAACAATCACCT 57.503 45.000 0.00 0.00 0.00 4.00
628 778 5.018539 AGCAACTAAATGACCATACGCTA 57.981 39.130 0.00 0.00 0.00 4.26
662 812 7.395489 AGAATAAACTCCTTGTCAAGCATCAAT 59.605 33.333 7.09 0.00 0.00 2.57
726 878 5.046448 TCGGTTCTACTATAACCAGCCAAAA 60.046 40.000 5.89 0.00 45.59 2.44
743 896 6.216801 TGCAATAGTATTACACTCGGTTCT 57.783 37.500 0.00 0.00 38.80 3.01
748 901 8.294577 TGTAGGTATGCAATAGTATTACACTCG 58.705 37.037 0.00 0.00 38.80 4.18
765 918 3.366396 AGAGGTCCACAGTGTAGGTATG 58.634 50.000 0.00 0.00 0.00 2.39
768 921 3.245658 ACATAGAGGTCCACAGTGTAGGT 60.246 47.826 0.00 0.00 0.00 3.08
769 922 3.366396 ACATAGAGGTCCACAGTGTAGG 58.634 50.000 0.00 0.02 0.00 3.18
776 929 4.536295 TCTCCATACATAGAGGTCCACA 57.464 45.455 0.00 0.00 0.00 4.17
793 946 8.657729 GTTACAGTAAGTAGCAAAAGATTCTCC 58.342 37.037 0.00 0.00 34.42 3.71
797 950 7.228590 TGGGTTACAGTAAGTAGCAAAAGATT 58.771 34.615 0.00 0.00 35.81 2.40
823 977 1.318576 CTTGTCGGCTGTCCCTTTTT 58.681 50.000 0.00 0.00 0.00 1.94
824 978 0.182775 ACTTGTCGGCTGTCCCTTTT 59.817 50.000 0.00 0.00 0.00 2.27
825 979 1.053424 TACTTGTCGGCTGTCCCTTT 58.947 50.000 0.00 0.00 0.00 3.11
826 980 0.320697 GTACTTGTCGGCTGTCCCTT 59.679 55.000 0.00 0.00 0.00 3.95
827 981 0.830444 TGTACTTGTCGGCTGTCCCT 60.830 55.000 0.00 0.00 0.00 4.20
828 982 0.669625 GTGTACTTGTCGGCTGTCCC 60.670 60.000 0.00 0.00 0.00 4.46
829 983 0.032952 TGTGTACTTGTCGGCTGTCC 59.967 55.000 0.00 0.00 0.00 4.02
830 984 2.080286 ATGTGTACTTGTCGGCTGTC 57.920 50.000 0.00 0.00 0.00 3.51
831 985 2.543777 AATGTGTACTTGTCGGCTGT 57.456 45.000 0.00 0.00 0.00 4.40
832 986 3.498397 AGAAAATGTGTACTTGTCGGCTG 59.502 43.478 0.00 0.00 0.00 4.85
833 987 3.498397 CAGAAAATGTGTACTTGTCGGCT 59.502 43.478 0.00 0.00 0.00 5.52
834 988 3.250040 ACAGAAAATGTGTACTTGTCGGC 59.750 43.478 0.00 0.00 41.91 5.54
859 1013 9.453572 AGAGCACTACATTTTCTTCATCATTTA 57.546 29.630 0.00 0.00 0.00 1.40
860 1014 8.242053 CAGAGCACTACATTTTCTTCATCATTT 58.758 33.333 0.00 0.00 0.00 2.32
861 1015 7.392673 ACAGAGCACTACATTTTCTTCATCATT 59.607 33.333 0.00 0.00 0.00 2.57
862 1016 6.883217 ACAGAGCACTACATTTTCTTCATCAT 59.117 34.615 0.00 0.00 0.00 2.45
863 1017 6.233434 ACAGAGCACTACATTTTCTTCATCA 58.767 36.000 0.00 0.00 0.00 3.07
864 1018 6.734104 ACAGAGCACTACATTTTCTTCATC 57.266 37.500 0.00 0.00 0.00 2.92
865 1019 7.446625 AGAAACAGAGCACTACATTTTCTTCAT 59.553 33.333 0.00 0.00 0.00 2.57
866 1020 6.767902 AGAAACAGAGCACTACATTTTCTTCA 59.232 34.615 0.00 0.00 0.00 3.02
867 1021 7.195839 AGAAACAGAGCACTACATTTTCTTC 57.804 36.000 0.00 0.00 0.00 2.87
868 1022 7.420800 CAAGAAACAGAGCACTACATTTTCTT 58.579 34.615 12.23 12.23 0.00 2.52
869 1023 6.016777 CCAAGAAACAGAGCACTACATTTTCT 60.017 38.462 0.00 0.00 0.00 2.52
870 1024 6.017109 TCCAAGAAACAGAGCACTACATTTTC 60.017 38.462 0.00 0.00 0.00 2.29
871 1025 5.827797 TCCAAGAAACAGAGCACTACATTTT 59.172 36.000 0.00 0.00 0.00 1.82
872 1026 5.239525 GTCCAAGAAACAGAGCACTACATTT 59.760 40.000 0.00 0.00 0.00 2.32
873 1027 4.757149 GTCCAAGAAACAGAGCACTACATT 59.243 41.667 0.00 0.00 0.00 2.71
874 1028 4.319177 GTCCAAGAAACAGAGCACTACAT 58.681 43.478 0.00 0.00 0.00 2.29
875 1029 3.728845 GTCCAAGAAACAGAGCACTACA 58.271 45.455 0.00 0.00 0.00 2.74
876 1030 2.731976 CGTCCAAGAAACAGAGCACTAC 59.268 50.000 0.00 0.00 0.00 2.73
877 1031 2.364324 ACGTCCAAGAAACAGAGCACTA 59.636 45.455 0.00 0.00 0.00 2.74
878 1032 1.139058 ACGTCCAAGAAACAGAGCACT 59.861 47.619 0.00 0.00 0.00 4.40
879 1033 1.261619 CACGTCCAAGAAACAGAGCAC 59.738 52.381 0.00 0.00 0.00 4.40
880 1034 1.138069 TCACGTCCAAGAAACAGAGCA 59.862 47.619 0.00 0.00 0.00 4.26
881 1035 1.865865 TCACGTCCAAGAAACAGAGC 58.134 50.000 0.00 0.00 0.00 4.09
882 1036 2.158449 GCATCACGTCCAAGAAACAGAG 59.842 50.000 0.00 0.00 0.00 3.35
883 1037 2.143122 GCATCACGTCCAAGAAACAGA 58.857 47.619 0.00 0.00 0.00 3.41
884 1038 1.136252 CGCATCACGTCCAAGAAACAG 60.136 52.381 0.00 0.00 36.87 3.16
885 1039 0.865111 CGCATCACGTCCAAGAAACA 59.135 50.000 0.00 0.00 36.87 2.83
886 1040 1.144969 TCGCATCACGTCCAAGAAAC 58.855 50.000 0.00 0.00 44.19 2.78
887 1041 1.731709 CATCGCATCACGTCCAAGAAA 59.268 47.619 0.00 0.00 44.19 2.52
888 1042 1.358877 CATCGCATCACGTCCAAGAA 58.641 50.000 0.00 0.00 44.19 2.52
889 1043 1.083806 GCATCGCATCACGTCCAAGA 61.084 55.000 0.00 0.00 44.19 3.02
890 1044 1.349627 GCATCGCATCACGTCCAAG 59.650 57.895 0.00 0.00 44.19 3.61
891 1045 1.375268 TGCATCGCATCACGTCCAA 60.375 52.632 0.00 0.00 44.19 3.53
892 1046 2.264166 TGCATCGCATCACGTCCA 59.736 55.556 0.00 0.00 44.19 4.02
901 1055 0.395448 TGGGATTTGGATGCATCGCA 60.395 50.000 20.15 15.77 44.86 5.10
902 1056 0.746063 TTGGGATTTGGATGCATCGC 59.254 50.000 20.15 13.43 33.90 4.58
903 1057 2.795681 CGTTTGGGATTTGGATGCATCG 60.796 50.000 20.15 0.90 0.00 3.84
904 1058 2.813061 CGTTTGGGATTTGGATGCATC 58.187 47.619 18.81 18.81 0.00 3.91
905 1059 1.134729 GCGTTTGGGATTTGGATGCAT 60.135 47.619 0.00 0.00 0.00 3.96
906 1060 0.246086 GCGTTTGGGATTTGGATGCA 59.754 50.000 0.00 0.00 0.00 3.96
907 1061 0.246086 TGCGTTTGGGATTTGGATGC 59.754 50.000 0.00 0.00 0.00 3.91
908 1062 2.542597 CATGCGTTTGGGATTTGGATG 58.457 47.619 0.00 0.00 0.00 3.51
909 1063 1.134729 GCATGCGTTTGGGATTTGGAT 60.135 47.619 0.00 0.00 0.00 3.41
910 1064 0.246086 GCATGCGTTTGGGATTTGGA 59.754 50.000 0.00 0.00 0.00 3.53
911 1065 0.037512 TGCATGCGTTTGGGATTTGG 60.038 50.000 14.09 0.00 0.00 3.28
912 1066 2.012937 ATGCATGCGTTTGGGATTTG 57.987 45.000 14.09 0.00 0.00 2.32
913 1067 4.405116 AATATGCATGCGTTTGGGATTT 57.595 36.364 19.31 0.00 0.00 2.17
914 1068 4.121317 CAAATATGCATGCGTTTGGGATT 58.879 39.130 19.31 8.36 0.00 3.01
915 1069 3.384146 TCAAATATGCATGCGTTTGGGAT 59.616 39.130 27.79 12.68 33.55 3.85
916 1070 2.757314 TCAAATATGCATGCGTTTGGGA 59.243 40.909 27.79 16.44 33.55 4.37
917 1071 3.162202 TCAAATATGCATGCGTTTGGG 57.838 42.857 27.79 14.95 33.55 4.12
918 1072 5.721876 AAATCAAATATGCATGCGTTTGG 57.278 34.783 27.79 17.10 33.55 3.28
919 1073 5.449748 GCAAAATCAAATATGCATGCGTTTG 59.550 36.000 25.04 25.04 38.63 2.93
920 1074 5.447548 GGCAAAATCAAATATGCATGCGTTT 60.448 36.000 19.31 13.20 40.51 3.60
921 1075 4.034279 GGCAAAATCAAATATGCATGCGTT 59.966 37.500 19.31 8.03 40.51 4.84
922 1076 3.556775 GGCAAAATCAAATATGCATGCGT 59.443 39.130 18.07 18.07 40.51 5.24
923 1077 3.362207 CGGCAAAATCAAATATGCATGCG 60.362 43.478 14.09 0.00 40.51 4.73
924 1078 3.605231 GCGGCAAAATCAAATATGCATGC 60.605 43.478 11.82 11.82 40.51 4.06
925 1079 3.805422 AGCGGCAAAATCAAATATGCATG 59.195 39.130 10.16 0.00 40.51 4.06
926 1080 3.805422 CAGCGGCAAAATCAAATATGCAT 59.195 39.130 3.79 3.79 40.51 3.96
927 1081 3.188492 CAGCGGCAAAATCAAATATGCA 58.812 40.909 1.45 0.00 40.51 3.96
928 1082 2.540931 CCAGCGGCAAAATCAAATATGC 59.459 45.455 1.45 0.00 38.06 3.14
947 1101 2.281208 CGTTGGACGGGAAAGCCA 60.281 61.111 0.00 0.00 38.08 4.75
972 1126 3.141488 GAAGCCGGCGAGAGGAGA 61.141 66.667 23.20 0.00 0.00 3.71
1012 1166 3.073101 GGCGAAGGAGTACGGGGT 61.073 66.667 0.00 0.00 0.00 4.95
1090 1244 2.041405 GGAGGTGAGGAGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
1456 1610 0.687757 AGCATGGCGTTAGAGGAGGA 60.688 55.000 0.00 0.00 0.00 3.71
1508 1662 3.525537 CGCTCAAAGAATTCTCTAGCCA 58.474 45.455 21.59 1.95 0.00 4.75
1554 1708 1.226717 GGAGATGAGCGTCGTCCAC 60.227 63.158 0.00 1.05 32.93 4.02
1572 1726 0.843984 ACCCATTCCTGGATAACCCG 59.156 55.000 0.00 0.00 46.37 5.28
1581 1735 1.679977 CCAGTGGCACCCATTCCTG 60.680 63.158 15.27 3.79 35.28 3.86
1608 1762 2.040278 CAACAATCCCCTGAAGACCTCA 59.960 50.000 0.00 0.00 0.00 3.86
1677 1831 1.617850 TCCAAATTTGCACAAGCCGAT 59.382 42.857 12.92 0.00 41.13 4.18
1692 1846 1.383799 CCCCTCAGCACCATCCAAA 59.616 57.895 0.00 0.00 0.00 3.28
1719 1873 2.280797 GCGTGAACAGCTGTCCCA 60.281 61.111 21.95 18.02 0.00 4.37
1725 1879 1.276421 AGAACATAGGCGTGAACAGCT 59.724 47.619 0.00 0.00 34.52 4.24
1737 1891 3.185246 ACCTCATGCCGAAGAACATAG 57.815 47.619 0.00 0.00 0.00 2.23
1743 1897 0.036388 GGTCAACCTCATGCCGAAGA 60.036 55.000 0.00 0.00 0.00 2.87
1744 1898 0.036010 AGGTCAACCTCATGCCGAAG 60.036 55.000 0.00 0.00 44.77 3.79
1818 1972 3.305398 AAAGCTCTCCTACAACAGTCG 57.695 47.619 0.00 0.00 0.00 4.18
1881 2035 1.483827 TGATTAGCCAGTGCAGAGAGG 59.516 52.381 0.00 0.00 41.13 3.69
2013 2167 4.371681 ACCAGTATAACCCAATCTCCACT 58.628 43.478 0.00 0.00 0.00 4.00
2111 2265 1.392589 CTCCATAAAACGGCCAGCAT 58.607 50.000 2.24 0.00 0.00 3.79
2388 2542 2.679837 AGAGCTGTGAAACACAACACTG 59.320 45.455 0.00 0.00 45.67 3.66
2556 2712 5.120519 CCGCACAATGCAGTGAATAAAAATT 59.879 36.000 22.73 0.00 45.36 1.82
2600 2758 3.255642 TCCTGATACTGCCTTTTTGCAAC 59.744 43.478 0.00 0.00 41.51 4.17
2618 2776 5.455392 CAGTACAATTCTGTGCTTTTCCTG 58.545 41.667 0.00 0.00 45.15 3.86
2793 2954 9.590451 GTTGTTTGATTTGTATGATGAATCCAT 57.410 29.630 0.00 0.00 35.29 3.41
2794 2955 8.034215 GGTTGTTTGATTTGTATGATGAATCCA 58.966 33.333 0.00 0.00 0.00 3.41
2905 3072 2.888834 TGGCTGCTTGGTTTTCTTTC 57.111 45.000 0.00 0.00 0.00 2.62
2913 3080 0.698238 TATCACCTTGGCTGCTTGGT 59.302 50.000 0.00 2.78 0.00 3.67
3042 3209 2.542597 GACATTTGACATACGGCGGTA 58.457 47.619 13.24 6.59 0.00 4.02
3052 3219 2.172505 ACTGGTCTGTGGACATTTGACA 59.827 45.455 0.00 0.00 43.77 3.58
3094 3261 0.803117 GCCAGCTTTACTTCCGGTTC 59.197 55.000 0.00 0.00 0.00 3.62
3124 3291 2.125512 GCGGCTGTTCGGACATCT 60.126 61.111 0.00 0.00 34.72 2.90
3162 3329 4.295199 GGGTTTTGGCCGGGTCCT 62.295 66.667 2.18 0.00 0.00 3.85
3169 3336 2.922503 CTGGGTGGGGTTTTGGCC 60.923 66.667 0.00 0.00 0.00 5.36
3189 3357 1.407979 GACGGAGAGATAAAAGCGGGA 59.592 52.381 0.00 0.00 0.00 5.14
3192 3360 1.409427 AGGGACGGAGAGATAAAAGCG 59.591 52.381 0.00 0.00 0.00 4.68
3202 3370 0.908180 GAAAGGGGAAGGGACGGAGA 60.908 60.000 0.00 0.00 0.00 3.71
3252 3421 1.416401 CTGAGTGGTTGGTGTAGTGGT 59.584 52.381 0.00 0.00 0.00 4.16
3255 3424 0.396811 GGCTGAGTGGTTGGTGTAGT 59.603 55.000 0.00 0.00 0.00 2.73
3320 3489 2.760650 ACCATAGCTTCGAGACATGTGA 59.239 45.455 1.15 0.00 0.00 3.58
3336 3505 3.308117 CCCCAGTAGCAAACTTGACCATA 60.308 47.826 0.00 0.00 35.76 2.74
3360 3529 3.509575 TGGTTCAAATACCTTGACCATGC 59.490 43.478 0.00 0.00 43.90 4.06
3361 3530 5.009631 TCTGGTTCAAATACCTTGACCATG 58.990 41.667 0.00 0.00 43.90 3.66
3362 3531 5.222130 ACTCTGGTTCAAATACCTTGACCAT 60.222 40.000 0.00 0.00 43.90 3.55
3363 3532 4.104102 ACTCTGGTTCAAATACCTTGACCA 59.896 41.667 0.00 0.00 43.90 4.02
3373 3542 6.672266 TCTCTCAAGTACTCTGGTTCAAAT 57.328 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.