Multiple sequence alignment - TraesCS2D01G219400

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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 TraesCS2D01G219400 chr2D 100.000 3303 0 0 1312 4614 186313387 186316689 0.000000e+00 6100.0
1 TraesCS2D01G219400 chr2D 100.000 1009 0 0 1 1009 186312076 186313084 0.000000e+00 1864.0
2 TraesCS2D01G219400 chr2D 90.588 85 4 1 2037 2121 518804289 518804209 4.880000e-20 110.0
3 TraesCS2D01G219400 chr2D 92.647 68 2 1 3694 3758 186315715 186315782 1.370000e-15 95.3
4 TraesCS2D01G219400 chr2D 92.647 68 2 1 3640 3707 186315769 186315833 1.370000e-15 95.3
5 TraesCS2D01G219400 chr2A 92.863 2494 78 34 2159 4612 198744174 198746607 0.000000e+00 3528.0
6 TraesCS2D01G219400 chr2A 93.391 696 26 11 1312 2006 198743494 198744170 0.000000e+00 1013.0
7 TraesCS2D01G219400 chr2A 96.059 609 19 4 86 692 198742405 198743010 0.000000e+00 987.0
8 TraesCS2D01G219400 chr2A 97.030 202 6 0 808 1009 198743254 198743455 1.590000e-89 340.0
9 TraesCS2D01G219400 chr2A 87.195 164 21 0 86 249 701861358 701861521 2.190000e-43 187.0
10 TraesCS2D01G219400 chr2A 94.309 123 4 3 692 814 198743172 198743291 7.880000e-43 185.0
11 TraesCS2D01G219400 chr2A 92.647 68 2 1 3694 3758 198745661 198745728 1.370000e-15 95.3
12 TraesCS2D01G219400 chr2B 90.455 1561 69 38 2135 3645 239507820 239509350 0.000000e+00 1984.0
13 TraesCS2D01G219400 chr2B 89.770 479 32 9 1558 2030 239507333 239507800 8.540000e-167 597.0
14 TraesCS2D01G219400 chr2B 82.047 635 72 21 4008 4612 239509816 239510438 1.920000e-138 503.0
15 TraesCS2D01G219400 chr2B 90.358 363 22 8 655 1009 239506737 239507094 9.040000e-127 464.0
16 TraesCS2D01G219400 chr2B 85.549 346 21 11 248 569 239506403 239506743 7.400000e-88 335.0
17 TraesCS2D01G219400 chr2B 96.429 196 7 0 1312 1507 239507143 239507338 1.600000e-84 324.0
18 TraesCS2D01G219400 chr2B 82.566 304 27 12 3726 4006 239509353 239509653 1.280000e-60 244.0
19 TraesCS2D01G219400 chr2B 90.698 86 4 1 2037 2122 73555164 73555083 1.360000e-20 111.0
20 TraesCS2D01G219400 chr3D 91.716 169 12 2 86 253 555188200 555188367 2.780000e-57 233.0
21 TraesCS2D01G219400 chr3D 96.522 115 4 0 1 115 555188065 555188179 1.690000e-44 191.0
22 TraesCS2D01G219400 chr3D 91.304 115 10 0 1 115 460254708 460254822 1.720000e-34 158.0
23 TraesCS2D01G219400 chr7D 90.303 165 14 2 86 249 483692234 483692071 1.010000e-51 215.0
24 TraesCS2D01G219400 chr7D 91.525 118 10 0 1 118 483692369 483692252 3.690000e-36 163.0
25 TraesCS2D01G219400 chr4D 89.881 168 15 2 86 253 461778219 461778384 1.010000e-51 215.0
26 TraesCS2D01G219400 chr4D 93.913 115 6 1 1 115 461778085 461778198 6.140000e-39 172.0
27 TraesCS2D01G219400 chr6A 89.697 165 16 1 86 249 557142873 557142709 4.680000e-50 209.0
28 TraesCS2D01G219400 chr5A 88.415 164 18 1 86 249 650094191 650094353 3.640000e-46 196.0
29 TraesCS2D01G219400 chr6D 87.805 164 20 0 86 249 401670817 401670980 4.710000e-45 193.0
30 TraesCS2D01G219400 chr6D 87.059 170 14 3 86 254 408696686 408696524 7.880000e-43 185.0
31 TraesCS2D01G219400 chr6D 88.696 115 7 4 1 115 291390726 291390834 8.050000e-28 135.0
32 TraesCS2D01G219400 chr3A 96.522 115 4 0 1 115 230987080 230987194 1.690000e-44 191.0
33 TraesCS2D01G219400 chr3A 92.920 113 8 0 1 113 114585733 114585845 1.030000e-36 165.0
34 TraesCS2D01G219400 chr4A 94.783 115 6 0 1 115 528552682 528552796 3.670000e-41 180.0
35 TraesCS2D01G219400 chr1D 94.068 118 7 0 1 118 463924934 463924817 3.670000e-41 180.0
36 TraesCS2D01G219400 chr1D 86.000 100 8 6 2037 2133 279945331 279945235 8.170000e-18 102.0
37 TraesCS2D01G219400 chr3B 90.805 87 6 1 2037 2123 450376637 450376553 1.050000e-21 115.0
38 TraesCS2D01G219400 chr7A 89.130 92 6 1 2029 2120 82512405 82512318 1.360000e-20 111.0
39 TraesCS2D01G219400 chr5B 90.588 85 4 2 2037 2121 583172444 583172524 4.880000e-20 110.0
40 TraesCS2D01G219400 chr1B 89.773 88 5 2 2037 2124 527834246 527834329 4.880000e-20 110.0
41 TraesCS2D01G219400 chr1B 87.234 94 8 1 2028 2121 586056804 586056715 2.270000e-18 104.0
42 TraesCS2D01G219400 chr5D 86.000 100 8 3 2023 2120 434549301 434549396 8.170000e-18 102.0


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 TraesCS2D01G219400 chr2D 186312076 186316689 4613 False 2038.650000 6100 96.323500 1 4614 4 chr2D.!!$F1 4613
1 TraesCS2D01G219400 chr2A 198742405 198746607 4202 False 1024.716667 3528 94.383167 86 4612 6 chr2A.!!$F2 4526
2 TraesCS2D01G219400 chr2B 239506403 239510438 4035 False 635.857143 1984 88.167714 248 4612 7 chr2B.!!$F1 4364

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
75 76 0.036164 TCCAGGCGTAGTTTGCATGT 59.964 50.0 0.00 0.0 42.19 3.21 F
776 987 0.103937 TGTGTGTGATGTGTGCGAGA 59.896 50.0 0.00 0.0 0.00 4.04 F
1909 2156 0.116342 TCCAGGGCTCACTGTTCCTA 59.884 55.0 0.00 0.0 36.75 2.94 F
2178 2430 0.040781 TTAGCGCAAGTTCGTTTGGC 60.041 50.0 11.47 0.0 41.68 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2156 0.541863 GTTGACGGATCCAGGGTCAT 59.458 55.000 18.21 0.0 40.10 3.06 R
2125 2377 0.096454 CGAGATCAGACGTACACGCA 59.904 55.000 0.85 0.0 44.43 5.24 R
3264 3577 1.247419 CCTCAGCACTCTGACGGACT 61.247 60.000 0.00 0.0 43.95 3.85 R
4112 4619 1.346722 GACGAGAAGAAAGGGTGGGAA 59.653 52.381 0.00 0.0 0.00 3.97 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 3.902515 CTCCTCGGCATGTAGATGG 57.097 57.895 1.57 0.00 0.00 3.51
24 25 3.337619 GCATGTAGATGGCAGGCG 58.662 61.111 1.57 0.00 34.04 5.52
25 26 2.256591 GCATGTAGATGGCAGGCGG 61.257 63.158 1.57 0.00 34.04 6.13
26 27 2.111878 ATGTAGATGGCAGGCGGC 59.888 61.111 0.00 0.00 43.74 6.53
27 28 3.814615 ATGTAGATGGCAGGCGGCG 62.815 63.158 0.51 0.51 46.16 6.46
52 53 3.528370 CGTAGCAGGGCTAGGCGT 61.528 66.667 10.58 8.10 42.11 5.68
53 54 2.191513 CGTAGCAGGGCTAGGCGTA 61.192 63.158 11.50 0.00 42.11 4.42
54 55 1.660917 GTAGCAGGGCTAGGCGTAG 59.339 63.158 11.50 9.11 42.11 3.51
55 56 1.108132 GTAGCAGGGCTAGGCGTAGT 61.108 60.000 11.50 4.51 42.11 2.73
56 57 0.396695 TAGCAGGGCTAGGCGTAGTT 60.397 55.000 11.50 7.02 40.44 2.24
57 58 1.227292 GCAGGGCTAGGCGTAGTTC 60.227 63.158 11.50 7.62 0.00 3.01
58 59 1.442148 CAGGGCTAGGCGTAGTTCC 59.558 63.158 11.50 15.05 0.00 3.62
59 60 1.001248 AGGGCTAGGCGTAGTTCCA 59.999 57.895 21.32 0.00 0.00 3.53
60 61 1.043673 AGGGCTAGGCGTAGTTCCAG 61.044 60.000 21.32 0.33 0.00 3.86
61 62 1.442148 GGCTAGGCGTAGTTCCAGG 59.558 63.158 14.52 0.00 0.00 4.45
62 63 1.227292 GCTAGGCGTAGTTCCAGGC 60.227 63.158 14.52 0.00 0.00 4.85
63 64 1.065928 CTAGGCGTAGTTCCAGGCG 59.934 63.158 5.25 0.00 35.47 5.52
64 65 1.664321 CTAGGCGTAGTTCCAGGCGT 61.664 60.000 5.25 0.00 35.47 5.68
65 66 0.394216 TAGGCGTAGTTCCAGGCGTA 60.394 55.000 0.00 0.00 35.47 4.42
66 67 1.226888 GGCGTAGTTCCAGGCGTAG 60.227 63.158 0.00 0.00 0.00 3.51
67 68 1.509923 GCGTAGTTCCAGGCGTAGT 59.490 57.895 0.00 0.00 0.00 2.73
68 69 0.108945 GCGTAGTTCCAGGCGTAGTT 60.109 55.000 0.00 0.00 0.00 2.24
69 70 1.670967 GCGTAGTTCCAGGCGTAGTTT 60.671 52.381 0.00 0.00 0.00 2.66
70 71 1.990563 CGTAGTTCCAGGCGTAGTTTG 59.009 52.381 0.00 0.00 0.00 2.93
71 72 1.730612 GTAGTTCCAGGCGTAGTTTGC 59.269 52.381 0.00 0.00 0.00 3.68
72 73 0.107831 AGTTCCAGGCGTAGTTTGCA 59.892 50.000 0.00 0.00 0.00 4.08
73 74 1.165270 GTTCCAGGCGTAGTTTGCAT 58.835 50.000 0.00 0.00 0.00 3.96
74 75 1.135689 GTTCCAGGCGTAGTTTGCATG 60.136 52.381 0.00 0.00 43.28 4.06
75 76 0.036164 TCCAGGCGTAGTTTGCATGT 59.964 50.000 0.00 0.00 42.19 3.21
76 77 0.881118 CCAGGCGTAGTTTGCATGTT 59.119 50.000 0.00 0.00 42.19 2.71
77 78 1.269448 CCAGGCGTAGTTTGCATGTTT 59.731 47.619 0.00 0.00 42.19 2.83
78 79 2.486203 CCAGGCGTAGTTTGCATGTTTA 59.514 45.455 0.00 0.00 42.19 2.01
79 80 3.128589 CCAGGCGTAGTTTGCATGTTTAT 59.871 43.478 0.00 0.00 42.19 1.40
80 81 4.342772 CAGGCGTAGTTTGCATGTTTATC 58.657 43.478 0.00 0.00 39.15 1.75
81 82 4.094887 CAGGCGTAGTTTGCATGTTTATCT 59.905 41.667 0.00 0.00 39.15 1.98
82 83 4.094887 AGGCGTAGTTTGCATGTTTATCTG 59.905 41.667 0.00 0.00 0.00 2.90
83 84 4.142687 GGCGTAGTTTGCATGTTTATCTGT 60.143 41.667 0.00 0.00 0.00 3.41
84 85 5.390613 GCGTAGTTTGCATGTTTATCTGTT 58.609 37.500 0.00 0.00 0.00 3.16
113 114 8.279800 TGTACAAATTTCTATGAAATATCGCCG 58.720 33.333 6.04 0.00 0.00 6.46
121 122 0.158928 GAAATATCGCCGACTTCGCG 59.841 55.000 0.00 0.00 39.11 5.87
128 129 2.020016 CCGACTTCGCGCGATTTG 59.980 61.111 35.21 26.54 38.18 2.32
159 160 3.047877 GGGCGTCAACTGGGAACG 61.048 66.667 0.00 0.00 0.00 3.95
162 163 3.725819 CGTCAACTGGGAACGCAA 58.274 55.556 0.00 0.00 0.00 4.85
327 329 2.042831 GCAGTGCAGTTGGCTAGGG 61.043 63.158 11.09 0.00 45.15 3.53
344 346 1.356624 GGGCATCTCGATTTTGGCG 59.643 57.895 8.98 0.00 36.84 5.69
366 368 2.253392 CGCAAGAAAATGTCAGGCTC 57.747 50.000 0.00 0.00 43.02 4.70
594 619 0.531974 TGGATCGATTTGCTACGGCC 60.532 55.000 0.00 0.00 37.74 6.13
772 983 1.875514 AGTGATGTGTGTGATGTGTGC 59.124 47.619 0.00 0.00 0.00 4.57
773 984 0.867086 TGATGTGTGTGATGTGTGCG 59.133 50.000 0.00 0.00 0.00 5.34
774 985 1.147473 GATGTGTGTGATGTGTGCGA 58.853 50.000 0.00 0.00 0.00 5.10
775 986 1.127397 GATGTGTGTGATGTGTGCGAG 59.873 52.381 0.00 0.00 0.00 5.03
776 987 0.103937 TGTGTGTGATGTGTGCGAGA 59.896 50.000 0.00 0.00 0.00 4.04
777 988 0.786581 GTGTGTGATGTGTGCGAGAG 59.213 55.000 0.00 0.00 0.00 3.20
778 989 0.673437 TGTGTGATGTGTGCGAGAGA 59.327 50.000 0.00 0.00 0.00 3.10
779 990 1.336240 TGTGTGATGTGTGCGAGAGAG 60.336 52.381 0.00 0.00 0.00 3.20
780 991 1.068264 GTGTGATGTGTGCGAGAGAGA 60.068 52.381 0.00 0.00 0.00 3.10
781 992 1.200948 TGTGATGTGTGCGAGAGAGAG 59.799 52.381 0.00 0.00 0.00 3.20
782 993 1.470494 GTGATGTGTGCGAGAGAGAGA 59.530 52.381 0.00 0.00 0.00 3.10
783 994 1.742268 TGATGTGTGCGAGAGAGAGAG 59.258 52.381 0.00 0.00 0.00 3.20
784 995 2.013400 GATGTGTGCGAGAGAGAGAGA 58.987 52.381 0.00 0.00 0.00 3.10
785 996 1.447945 TGTGTGCGAGAGAGAGAGAG 58.552 55.000 0.00 0.00 0.00 3.20
786 997 1.002544 TGTGTGCGAGAGAGAGAGAGA 59.997 52.381 0.00 0.00 0.00 3.10
787 998 1.665679 GTGTGCGAGAGAGAGAGAGAG 59.334 57.143 0.00 0.00 0.00 3.20
788 999 1.552792 TGTGCGAGAGAGAGAGAGAGA 59.447 52.381 0.00 0.00 0.00 3.10
789 1000 2.205074 GTGCGAGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
790 1001 2.107366 TGCGAGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
791 1002 2.101415 TGCGAGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
792 1003 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
793 1004 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
794 1005 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
795 1006 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
796 1007 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
797 1008 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
798 1009 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
799 1010 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
800 1011 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
801 1012 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
802 1013 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
803 1014 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
804 1015 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
805 1016 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1439 1668 2.935201 GCTTCAGCACATTCTCGAAGAT 59.065 45.455 0.00 0.00 41.59 2.40
1530 1759 1.075748 ATGCCCATCCTTTGCTCCC 60.076 57.895 0.00 0.00 0.00 4.30
1534 1763 2.124151 CATCCTTTGCTCCCCGGG 60.124 66.667 15.80 15.80 0.00 5.73
1596 1825 2.226437 CCTCGCACTTACTTTGCACAAT 59.774 45.455 0.00 0.00 40.20 2.71
1735 1978 3.938963 CGTGGTTTATCTAACTGGTGCAT 59.061 43.478 0.00 0.00 36.93 3.96
1788 2031 2.569059 CGCATGGAGAAAGACATGGAT 58.431 47.619 0.00 0.00 43.50 3.41
1806 2049 2.892425 GAGGCGGTGAAGATGGCG 60.892 66.667 0.00 0.00 0.00 5.69
1829 2072 4.754114 GCGGATCATGAAAGAGAAGCTAAT 59.246 41.667 0.00 0.00 0.00 1.73
1902 2149 1.073444 CATGCATATCCAGGGCTCACT 59.927 52.381 0.00 0.00 0.00 3.41
1909 2156 0.116342 TCCAGGGCTCACTGTTCCTA 59.884 55.000 0.00 0.00 36.75 2.94
1929 2176 1.153628 GACCCTGGATCCGTCAACG 60.154 63.158 7.39 0.00 39.44 4.10
1950 2197 3.521560 GCTGTCCATCATCACGTAAGAA 58.478 45.455 0.00 0.00 43.62 2.52
1951 2198 3.932710 GCTGTCCATCATCACGTAAGAAA 59.067 43.478 0.00 0.00 43.62 2.52
1952 2199 4.033358 GCTGTCCATCATCACGTAAGAAAG 59.967 45.833 0.00 0.00 43.62 2.62
1953 2200 5.400066 TGTCCATCATCACGTAAGAAAGA 57.600 39.130 0.00 0.00 43.62 2.52
1966 2213 7.492669 TCACGTAAGAAAGATCTTGATCCATTC 59.507 37.037 9.17 14.00 45.47 2.67
1990 2242 7.890515 TCATCTGTGTAGCTTAATCATCTAGG 58.109 38.462 0.00 0.00 0.00 3.02
2015 2267 7.095270 GGTATGTTAACTGCTACTGTAGTTGT 58.905 38.462 15.71 11.60 46.03 3.32
2030 2282 8.278729 ACTGTAGTTGTTAGTCTACCAGATAC 57.721 38.462 0.00 0.00 36.63 2.24
2032 2284 9.610705 CTGTAGTTGTTAGTCTACCAGATACTA 57.389 37.037 0.00 0.00 36.63 1.82
2033 2285 9.610705 TGTAGTTGTTAGTCTACCAGATACTAG 57.389 37.037 0.00 0.00 36.63 2.57
2034 2286 9.612066 GTAGTTGTTAGTCTACCAGATACTAGT 57.388 37.037 0.00 0.00 32.83 2.57
2036 2288 9.612066 AGTTGTTAGTCTACCAGATACTAGTAC 57.388 37.037 4.31 0.00 0.00 2.73
2038 2290 8.329346 TGTTAGTCTACCAGATACTAGTACCT 57.671 38.462 4.31 0.00 0.00 3.08
2040 2292 8.650490 GTTAGTCTACCAGATACTAGTACCTCT 58.350 40.741 4.31 2.33 0.00 3.69
2041 2293 7.069877 AGTCTACCAGATACTAGTACCTCTG 57.930 44.000 20.02 20.02 35.88 3.35
2042 2294 6.616548 AGTCTACCAGATACTAGTACCTCTGT 59.383 42.308 22.99 13.85 34.62 3.41
2043 2295 7.788867 AGTCTACCAGATACTAGTACCTCTGTA 59.211 40.741 22.99 14.15 34.62 2.74
2044 2296 8.428063 GTCTACCAGATACTAGTACCTCTGTAA 58.572 40.741 22.99 14.12 34.62 2.41
2045 2297 8.996655 TCTACCAGATACTAGTACCTCTGTAAA 58.003 37.037 22.99 12.44 34.62 2.01
2046 2298 9.275398 CTACCAGATACTAGTACCTCTGTAAAG 57.725 40.741 22.99 16.06 34.62 1.85
2047 2299 7.870027 ACCAGATACTAGTACCTCTGTAAAGA 58.130 38.462 22.99 0.00 34.62 2.52
2048 2300 8.334734 ACCAGATACTAGTACCTCTGTAAAGAA 58.665 37.037 22.99 0.00 34.62 2.52
2049 2301 9.186837 CCAGATACTAGTACCTCTGTAAAGAAA 57.813 37.037 22.99 0.00 34.62 2.52
2079 2331 8.608844 AGAGTGTTTAGGTCACTTCTTTAATG 57.391 34.615 0.00 0.00 44.68 1.90
2080 2332 8.429641 AGAGTGTTTAGGTCACTTCTTTAATGA 58.570 33.333 0.00 0.00 44.68 2.57
2081 2333 9.220767 GAGTGTTTAGGTCACTTCTTTAATGAT 57.779 33.333 0.00 0.00 44.68 2.45
2082 2334 9.220767 AGTGTTTAGGTCACTTCTTTAATGATC 57.779 33.333 0.00 0.00 42.50 2.92
2083 2335 9.220767 GTGTTTAGGTCACTTCTTTAATGATCT 57.779 33.333 0.00 0.00 37.56 2.75
2088 2340 8.480643 AGGTCACTTCTTTAATGATCTAAACG 57.519 34.615 0.00 0.00 31.95 3.60
2089 2341 7.064728 AGGTCACTTCTTTAATGATCTAAACGC 59.935 37.037 0.00 0.00 31.95 4.84
2090 2342 7.064728 GGTCACTTCTTTAATGATCTAAACGCT 59.935 37.037 0.00 0.00 0.00 5.07
2091 2343 8.111224 GTCACTTCTTTAATGATCTAAACGCTC 58.889 37.037 0.00 0.00 0.00 5.03
2092 2344 8.035394 TCACTTCTTTAATGATCTAAACGCTCT 58.965 33.333 0.00 0.00 0.00 4.09
2093 2345 8.660373 CACTTCTTTAATGATCTAAACGCTCTT 58.340 33.333 0.00 0.00 0.00 2.85
2094 2346 9.871238 ACTTCTTTAATGATCTAAACGCTCTTA 57.129 29.630 0.00 0.00 0.00 2.10
2104 2356 9.477484 TGATCTAAACGCTCTTATATTCCTTTC 57.523 33.333 0.00 0.00 0.00 2.62
2105 2357 9.699703 GATCTAAACGCTCTTATATTCCTTTCT 57.300 33.333 0.00 0.00 0.00 2.52
2107 2359 9.886132 TCTAAACGCTCTTATATTCCTTTCTTT 57.114 29.630 0.00 0.00 0.00 2.52
2111 2363 8.608844 ACGCTCTTATATTCCTTTCTTTATGG 57.391 34.615 0.00 0.00 0.00 2.74
2112 2364 8.429641 ACGCTCTTATATTCCTTTCTTTATGGA 58.570 33.333 0.00 0.00 0.00 3.41
2113 2365 8.930760 CGCTCTTATATTCCTTTCTTTATGGAG 58.069 37.037 0.00 0.00 32.16 3.86
2114 2366 9.225436 GCTCTTATATTCCTTTCTTTATGGAGG 57.775 37.037 0.00 0.00 32.16 4.30
2115 2367 9.732130 CTCTTATATTCCTTTCTTTATGGAGGG 57.268 37.037 0.00 0.00 32.16 4.30
2116 2368 9.460413 TCTTATATTCCTTTCTTTATGGAGGGA 57.540 33.333 0.00 0.00 32.16 4.20
2117 2369 9.732130 CTTATATTCCTTTCTTTATGGAGGGAG 57.268 37.037 0.00 0.00 32.16 4.30
2118 2370 7.713704 ATATTCCTTTCTTTATGGAGGGAGT 57.286 36.000 0.00 0.00 32.16 3.85
2119 2371 8.814448 ATATTCCTTTCTTTATGGAGGGAGTA 57.186 34.615 0.00 0.00 32.16 2.59
2120 2372 6.963117 TTCCTTTCTTTATGGAGGGAGTAA 57.037 37.500 0.00 0.00 32.16 2.24
2121 2373 7.525158 TTCCTTTCTTTATGGAGGGAGTAAT 57.475 36.000 0.00 0.00 32.16 1.89
2122 2374 7.525158 TCCTTTCTTTATGGAGGGAGTAATT 57.475 36.000 0.00 0.00 0.00 1.40
2123 2375 7.574607 TCCTTTCTTTATGGAGGGAGTAATTC 58.425 38.462 0.00 0.00 0.00 2.17
2124 2376 6.773200 CCTTTCTTTATGGAGGGAGTAATTCC 59.227 42.308 0.00 0.00 46.00 3.01
2125 2377 7.366913 CCTTTCTTTATGGAGGGAGTAATTCCT 60.367 40.741 0.00 0.00 45.98 3.36
2126 2378 6.500589 TCTTTATGGAGGGAGTAATTCCTG 57.499 41.667 0.00 0.00 45.98 3.86
2127 2379 4.706842 TTATGGAGGGAGTAATTCCTGC 57.293 45.455 1.34 1.34 45.98 4.85
2128 2380 0.830648 TGGAGGGAGTAATTCCTGCG 59.169 55.000 4.42 0.00 45.98 5.18
2129 2381 0.831307 GGAGGGAGTAATTCCTGCGT 59.169 55.000 0.00 0.00 45.98 5.24
2130 2382 1.473434 GGAGGGAGTAATTCCTGCGTG 60.473 57.143 0.00 0.00 45.98 5.34
2131 2383 1.207329 GAGGGAGTAATTCCTGCGTGT 59.793 52.381 0.00 0.00 45.98 4.49
2132 2384 2.429610 GAGGGAGTAATTCCTGCGTGTA 59.570 50.000 0.00 0.00 45.98 2.90
2133 2385 2.167900 AGGGAGTAATTCCTGCGTGTAC 59.832 50.000 0.00 0.00 45.98 2.90
2151 2403 3.749609 TGTACGTCTGATCTCGAGAAACA 59.250 43.478 20.91 19.98 0.00 2.83
2178 2430 0.040781 TTAGCGCAAGTTCGTTTGGC 60.041 50.000 11.47 0.00 41.68 4.52
2206 2458 8.073768 CGGTCAATTAAAAACAGTTCATACAGT 58.926 33.333 0.00 0.00 0.00 3.55
2213 2465 6.635030 AAAACAGTTCATACAGTCCTTTCC 57.365 37.500 0.00 0.00 0.00 3.13
2214 2466 5.568620 AACAGTTCATACAGTCCTTTCCT 57.431 39.130 0.00 0.00 0.00 3.36
2215 2467 5.568620 ACAGTTCATACAGTCCTTTCCTT 57.431 39.130 0.00 0.00 0.00 3.36
2216 2468 5.552178 ACAGTTCATACAGTCCTTTCCTTC 58.448 41.667 0.00 0.00 0.00 3.46
2219 2471 4.207891 TCATACAGTCCTTTCCTTCAGC 57.792 45.455 0.00 0.00 0.00 4.26
2246 2498 4.215613 AGGGTGAAATTTGACTAGCGTTTC 59.784 41.667 7.72 0.00 0.00 2.78
2298 2550 8.791675 AGCTTAAGGAAAGAAAGAAAGATCTTG 58.208 33.333 9.17 0.00 39.82 3.02
2320 2572 4.142447 TGAGGTGTGCTTATCTAACTCGAC 60.142 45.833 0.00 0.00 0.00 4.20
2330 2582 6.584563 GCTTATCTAACTCGACATCCATCTTC 59.415 42.308 0.00 0.00 0.00 2.87
2335 2592 2.167281 ACTCGACATCCATCTTCTGTGG 59.833 50.000 0.00 0.00 38.11 4.17
2366 2623 5.968387 ATTAAAGATCTTTCGGTGTAGCG 57.032 39.130 23.70 0.00 34.23 4.26
2373 2630 4.913335 TCTTTCGGTGTAGCGATCTAAT 57.087 40.909 7.02 0.00 0.00 1.73
2460 2720 4.597507 AGGATTTTCACAGGTGAGGAACTA 59.402 41.667 2.01 0.00 41.55 2.24
2527 2787 1.094785 GTGTATGAATGGCCTTGCGT 58.905 50.000 3.32 0.00 0.00 5.24
2631 2892 2.983136 GCATCATGCTAGCTGTACTACG 59.017 50.000 17.23 0.00 40.96 3.51
2655 2916 4.383931 CTACACTAGGTAGGAGGGCATA 57.616 50.000 9.39 0.00 44.77 3.14
2659 2920 3.904339 CACTAGGTAGGAGGGCATACATT 59.096 47.826 0.00 0.00 33.13 2.71
2660 2921 3.904339 ACTAGGTAGGAGGGCATACATTG 59.096 47.826 0.00 0.00 33.13 2.82
2753 3016 2.159234 GCAGATGTTTGAGCACAGAGTC 59.841 50.000 0.00 0.00 0.00 3.36
2944 3211 1.139654 CCATGGATCTCGGCAAGAAGA 59.860 52.381 5.56 0.00 37.61 2.87
2945 3212 2.420547 CCATGGATCTCGGCAAGAAGAA 60.421 50.000 5.56 0.00 37.61 2.52
2948 3215 1.601430 GGATCTCGGCAAGAAGAATGC 59.399 52.381 0.00 0.00 43.08 3.56
2969 3239 2.622942 CTGAGGTGCAAAAGGTAAGCAA 59.377 45.455 0.00 0.00 40.35 3.91
2984 3254 8.738645 AAGGTAAGCAATCTTCTTGGTTATAG 57.261 34.615 11.39 0.00 42.12 1.31
3264 3577 5.188434 TGAAAAATGAAAATGTGGTGCCAA 58.812 33.333 0.00 0.00 0.00 4.52
3298 3611 4.457496 AGGCCCGTGCACGATCTG 62.457 66.667 39.10 23.74 43.02 2.90
3334 3647 2.027751 GTGCGCGATCTAGGGTCC 59.972 66.667 12.10 0.00 0.00 4.46
3339 3652 1.107538 CGCGATCTAGGGTCCAGGAA 61.108 60.000 0.00 0.00 0.00 3.36
3717 4039 0.647925 GAGATGCTTTTCTCGACCGC 59.352 55.000 0.00 0.00 33.35 5.68
3794 4116 0.531974 TGTTGCACTCCTTCGGACAC 60.532 55.000 0.00 0.00 0.00 3.67
3815 4150 3.119101 ACAGCCACACTATAGAGAAACCG 60.119 47.826 6.78 0.00 0.00 4.44
3935 4278 5.335191 CGAGTAGTACTACCCGAAAAACACT 60.335 44.000 27.19 8.50 39.20 3.55
4104 4611 5.782893 ATATCCTCTTTCTCTTCAGGTCG 57.217 43.478 0.00 0.00 0.00 4.79
4105 4612 2.877866 TCCTCTTTCTCTTCAGGTCGT 58.122 47.619 0.00 0.00 0.00 4.34
4106 4613 3.231818 TCCTCTTTCTCTTCAGGTCGTT 58.768 45.455 0.00 0.00 0.00 3.85
4107 4614 4.404640 TCCTCTTTCTCTTCAGGTCGTTA 58.595 43.478 0.00 0.00 0.00 3.18
4108 4615 4.831155 TCCTCTTTCTCTTCAGGTCGTTAA 59.169 41.667 0.00 0.00 0.00 2.01
4109 4616 5.480772 TCCTCTTTCTCTTCAGGTCGTTAAT 59.519 40.000 0.00 0.00 0.00 1.40
4110 4617 6.662234 TCCTCTTTCTCTTCAGGTCGTTAATA 59.338 38.462 0.00 0.00 0.00 0.98
4111 4618 7.342284 TCCTCTTTCTCTTCAGGTCGTTAATAT 59.658 37.037 0.00 0.00 0.00 1.28
4112 4619 7.982354 CCTCTTTCTCTTCAGGTCGTTAATATT 59.018 37.037 0.00 0.00 0.00 1.28
4264 4793 7.825681 TCTCTTACTCACTCATTCTCTCTTTG 58.174 38.462 0.00 0.00 0.00 2.77
4283 4812 6.217294 TCTTTGAAGTTTTCACCGTTGTTTT 58.783 32.000 0.00 0.00 39.87 2.43
4359 4897 1.539827 GTATTGCCTTCACACCACCAC 59.460 52.381 0.00 0.00 0.00 4.16
4439 4994 1.657556 CAACGCGGGGACACATTTT 59.342 52.632 12.47 0.00 0.00 1.82
4479 5034 2.280524 CCGCGTGGACAGAAACCA 60.281 61.111 10.20 0.00 37.49 3.67
4514 5069 2.463653 CGACACATTTTGCGTTTGTCTG 59.536 45.455 0.00 0.00 35.46 3.51
4526 5084 3.303725 GCGTTTGTCTGTTTATGTCTGCA 60.304 43.478 0.00 0.00 0.00 4.41
4598 5157 3.545481 CAGACGCGTCGCATGTCC 61.545 66.667 31.56 7.95 33.09 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320247 GCCATCTACATGCCGAGGAG 60.320 60.000 0.00 0.00 0.00 3.69
1 2 1.048160 TGCCATCTACATGCCGAGGA 61.048 55.000 0.00 0.00 0.00 3.71
2 3 0.602106 CTGCCATCTACATGCCGAGG 60.602 60.000 0.00 0.00 0.00 4.63
3 4 0.602106 CCTGCCATCTACATGCCGAG 60.602 60.000 0.00 0.00 0.00 4.63
4 5 1.447217 CCTGCCATCTACATGCCGA 59.553 57.895 0.00 0.00 0.00 5.54
5 6 2.256591 GCCTGCCATCTACATGCCG 61.257 63.158 0.00 0.00 0.00 5.69
6 7 2.256591 CGCCTGCCATCTACATGCC 61.257 63.158 0.00 0.00 0.00 4.40
7 8 2.256591 CCGCCTGCCATCTACATGC 61.257 63.158 0.00 0.00 0.00 4.06
8 9 2.256591 GCCGCCTGCCATCTACATG 61.257 63.158 0.00 0.00 0.00 3.21
9 10 2.111878 GCCGCCTGCCATCTACAT 59.888 61.111 0.00 0.00 0.00 2.29
10 11 4.529219 CGCCGCCTGCCATCTACA 62.529 66.667 0.00 0.00 36.24 2.74
31 32 4.951963 CTAGCCCTGCTACGCCGC 62.952 72.222 0.00 0.00 40.44 6.53
32 33 4.286320 CCTAGCCCTGCTACGCCG 62.286 72.222 0.00 0.00 40.44 6.46
33 34 4.610714 GCCTAGCCCTGCTACGCC 62.611 72.222 5.99 0.00 40.44 5.68
34 35 4.951963 CGCCTAGCCCTGCTACGC 62.952 72.222 6.92 6.92 40.44 4.42
35 36 2.131294 CTACGCCTAGCCCTGCTACG 62.131 65.000 5.04 5.04 40.44 3.51
36 37 1.108132 ACTACGCCTAGCCCTGCTAC 61.108 60.000 0.00 0.00 40.44 3.58
37 38 0.396695 AACTACGCCTAGCCCTGCTA 60.397 55.000 0.00 0.00 40.44 3.49
38 39 1.677637 GAACTACGCCTAGCCCTGCT 61.678 60.000 0.00 0.00 43.41 4.24
39 40 1.227292 GAACTACGCCTAGCCCTGC 60.227 63.158 0.00 0.00 0.00 4.85
40 41 1.327690 TGGAACTACGCCTAGCCCTG 61.328 60.000 0.00 0.00 0.00 4.45
41 42 1.001248 TGGAACTACGCCTAGCCCT 59.999 57.895 0.00 0.00 0.00 5.19
42 43 1.442148 CTGGAACTACGCCTAGCCC 59.558 63.158 0.00 0.00 0.00 5.19
43 44 1.442148 CCTGGAACTACGCCTAGCC 59.558 63.158 0.00 0.00 0.00 3.93
44 45 1.227292 GCCTGGAACTACGCCTAGC 60.227 63.158 0.00 0.00 0.00 3.42
45 46 1.065928 CGCCTGGAACTACGCCTAG 59.934 63.158 0.00 0.00 0.00 3.02
46 47 0.394216 TACGCCTGGAACTACGCCTA 60.394 55.000 0.00 0.00 0.00 3.93
47 48 1.664321 CTACGCCTGGAACTACGCCT 61.664 60.000 0.00 0.00 0.00 5.52
48 49 1.226888 CTACGCCTGGAACTACGCC 60.227 63.158 0.00 0.00 0.00 5.68
49 50 0.108945 AACTACGCCTGGAACTACGC 60.109 55.000 0.00 0.00 0.00 4.42
50 51 1.990563 CAAACTACGCCTGGAACTACG 59.009 52.381 0.00 0.00 0.00 3.51
51 52 1.730612 GCAAACTACGCCTGGAACTAC 59.269 52.381 0.00 0.00 0.00 2.73
52 53 1.345089 TGCAAACTACGCCTGGAACTA 59.655 47.619 0.00 0.00 0.00 2.24
53 54 0.107831 TGCAAACTACGCCTGGAACT 59.892 50.000 0.00 0.00 0.00 3.01
54 55 1.135689 CATGCAAACTACGCCTGGAAC 60.136 52.381 0.00 0.00 0.00 3.62
55 56 1.164411 CATGCAAACTACGCCTGGAA 58.836 50.000 0.00 0.00 0.00 3.53
56 57 0.036164 ACATGCAAACTACGCCTGGA 59.964 50.000 0.00 0.00 30.26 3.86
57 58 0.881118 AACATGCAAACTACGCCTGG 59.119 50.000 0.00 0.00 30.26 4.45
58 59 2.704725 AAACATGCAAACTACGCCTG 57.295 45.000 0.00 0.00 0.00 4.85
59 60 4.094887 CAGATAAACATGCAAACTACGCCT 59.905 41.667 0.00 0.00 0.00 5.52
60 61 4.142687 ACAGATAAACATGCAAACTACGCC 60.143 41.667 0.00 0.00 0.00 5.68
61 62 4.969816 ACAGATAAACATGCAAACTACGC 58.030 39.130 0.00 0.00 0.00 4.42
62 63 7.851822 AAAACAGATAAACATGCAAACTACG 57.148 32.000 0.00 0.00 0.00 3.51
63 64 9.030301 ACAAAAACAGATAAACATGCAAACTAC 57.970 29.630 0.00 0.00 0.00 2.73
65 66 9.030301 GTACAAAAACAGATAAACATGCAAACT 57.970 29.630 0.00 0.00 0.00 2.66
66 67 8.812329 TGTACAAAAACAGATAAACATGCAAAC 58.188 29.630 0.00 0.00 0.00 2.93
67 68 8.932945 TGTACAAAAACAGATAAACATGCAAA 57.067 26.923 0.00 0.00 0.00 3.68
68 69 8.932945 TTGTACAAAAACAGATAAACATGCAA 57.067 26.923 5.64 0.00 0.00 4.08
69 70 8.932945 TTTGTACAAAAACAGATAAACATGCA 57.067 26.923 18.54 0.00 0.00 3.96
113 114 2.399611 CCCAAATCGCGCGAAGTC 59.600 61.111 38.07 0.00 0.00 3.01
121 122 3.861263 GGTCGTCGCCCAAATCGC 61.861 66.667 0.00 0.00 0.00 4.58
228 229 3.567797 GCATCTCCAGCCGTTCGC 61.568 66.667 0.00 0.00 37.98 4.70
327 329 1.356624 CCGCCAAAATCGAGATGCC 59.643 57.895 0.00 0.00 0.00 4.40
344 346 1.401539 GCCTGACATTTTCTTGCGACC 60.402 52.381 0.00 0.00 0.00 4.79
594 619 2.060050 AGTGGAGTAGATCGGTGAGG 57.940 55.000 0.00 0.00 0.00 3.86
772 983 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
773 984 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
774 985 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
775 986 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
776 987 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
777 988 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
778 989 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
779 990 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
780 991 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
781 992 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
782 993 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
783 994 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
784 995 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
785 996 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
786 997 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
787 998 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
788 999 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
789 1000 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
790 1001 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
791 1002 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
792 1003 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
793 1004 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
794 1005 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
795 1006 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
796 1007 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
797 1008 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
798 1009 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
799 1010 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
800 1011 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
801 1012 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
802 1013 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
803 1014 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
804 1015 3.708631 CACCTCTCTCTCTCTCTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
805 1016 3.181461 CCACCTCTCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
1439 1668 1.725665 CGTCGAGAACTGGCGGATA 59.274 57.895 0.00 0.00 0.00 2.59
1494 1723 2.605366 GCATGAGCGTTTCTCTTACCTC 59.395 50.000 0.00 0.00 42.38 3.85
1530 1759 3.213402 AAACACGTTGTGGCCCGG 61.213 61.111 0.00 0.00 37.94 5.73
1596 1825 2.489073 GGTGGGGAGAAAGAAGAGCAAA 60.489 50.000 0.00 0.00 0.00 3.68
1788 2031 2.268920 GCCATCTTCACCGCCTCA 59.731 61.111 0.00 0.00 0.00 3.86
1806 2049 2.559440 AGCTTCTCTTTCATGATCCGC 58.441 47.619 0.00 0.00 0.00 5.54
1829 2072 1.945819 GCACGCCTTGGAAGATTCTGA 60.946 52.381 0.00 0.00 0.00 3.27
1902 2149 2.408565 GGATCCAGGGTCATAGGAACA 58.591 52.381 6.95 0.00 34.62 3.18
1909 2156 0.541863 GTTGACGGATCCAGGGTCAT 59.458 55.000 18.21 0.00 40.10 3.06
1929 2176 3.165058 TCTTACGTGATGATGGACAGC 57.835 47.619 0.00 0.00 35.25 4.40
1950 2197 6.660800 ACACAGATGAATGGATCAAGATCTT 58.339 36.000 0.88 0.88 42.54 2.40
1951 2198 6.249911 ACACAGATGAATGGATCAAGATCT 57.750 37.500 9.69 0.00 42.54 2.75
1952 2199 6.147492 GCTACACAGATGAATGGATCAAGATC 59.853 42.308 1.40 1.40 42.54 2.75
1953 2200 5.996513 GCTACACAGATGAATGGATCAAGAT 59.003 40.000 0.00 0.00 42.54 2.40
1966 2213 7.095910 CCCTAGATGATTAAGCTACACAGATG 58.904 42.308 0.00 0.00 0.00 2.90
1990 2242 7.095270 ACAACTACAGTAGCAGTTAACATACC 58.905 38.462 8.61 0.00 33.29 2.73
2015 2267 8.649591 CAGAGGTACTAGTATCTGGTAGACTAA 58.350 40.741 20.51 0.00 41.55 2.24
2053 2305 9.057089 CATTAAAGAAGTGACCTAAACACTCTT 57.943 33.333 0.00 0.00 46.01 2.85
2054 2306 8.429641 TCATTAAAGAAGTGACCTAAACACTCT 58.570 33.333 0.00 0.00 46.01 3.24
2055 2307 8.603242 TCATTAAAGAAGTGACCTAAACACTC 57.397 34.615 0.00 0.00 46.01 3.51
2057 2309 9.220767 AGATCATTAAAGAAGTGACCTAAACAC 57.779 33.333 0.00 0.00 38.38 3.32
2062 2314 9.582431 CGTTTAGATCATTAAAGAAGTGACCTA 57.418 33.333 0.00 0.00 0.00 3.08
2063 2315 7.064728 GCGTTTAGATCATTAAAGAAGTGACCT 59.935 37.037 0.00 0.00 0.00 3.85
2064 2316 7.064728 AGCGTTTAGATCATTAAAGAAGTGACC 59.935 37.037 0.00 0.00 0.00 4.02
2065 2317 7.965045 AGCGTTTAGATCATTAAAGAAGTGAC 58.035 34.615 0.00 0.00 0.00 3.67
2066 2318 8.035394 AGAGCGTTTAGATCATTAAAGAAGTGA 58.965 33.333 0.00 0.00 37.82 3.41
2067 2319 8.190888 AGAGCGTTTAGATCATTAAAGAAGTG 57.809 34.615 0.00 0.00 37.82 3.16
2068 2320 8.779354 AAGAGCGTTTAGATCATTAAAGAAGT 57.221 30.769 0.00 0.00 37.82 3.01
2078 2330 9.477484 GAAAGGAATATAAGAGCGTTTAGATCA 57.523 33.333 0.00 0.00 37.82 2.92
2079 2331 9.699703 AGAAAGGAATATAAGAGCGTTTAGATC 57.300 33.333 0.00 0.00 35.01 2.75
2081 2333 9.886132 AAAGAAAGGAATATAAGAGCGTTTAGA 57.114 29.630 0.00 0.00 0.00 2.10
2085 2337 9.057089 CCATAAAGAAAGGAATATAAGAGCGTT 57.943 33.333 0.00 0.00 0.00 4.84
2086 2338 8.429641 TCCATAAAGAAAGGAATATAAGAGCGT 58.570 33.333 0.00 0.00 0.00 5.07
2087 2339 8.833231 TCCATAAAGAAAGGAATATAAGAGCG 57.167 34.615 0.00 0.00 0.00 5.03
2088 2340 9.225436 CCTCCATAAAGAAAGGAATATAAGAGC 57.775 37.037 0.00 0.00 0.00 4.09
2089 2341 9.732130 CCCTCCATAAAGAAAGGAATATAAGAG 57.268 37.037 0.00 0.00 0.00 2.85
2090 2342 9.460413 TCCCTCCATAAAGAAAGGAATATAAGA 57.540 33.333 0.00 0.00 0.00 2.10
2091 2343 9.732130 CTCCCTCCATAAAGAAAGGAATATAAG 57.268 37.037 0.00 0.00 0.00 1.73
2092 2344 9.237706 ACTCCCTCCATAAAGAAAGGAATATAA 57.762 33.333 0.00 0.00 0.00 0.98
2093 2345 8.814448 ACTCCCTCCATAAAGAAAGGAATATA 57.186 34.615 0.00 0.00 0.00 0.86
2094 2346 7.713704 ACTCCCTCCATAAAGAAAGGAATAT 57.286 36.000 0.00 0.00 0.00 1.28
2095 2347 8.632731 TTACTCCCTCCATAAAGAAAGGAATA 57.367 34.615 0.00 0.00 0.00 1.75
2096 2348 7.525158 TTACTCCCTCCATAAAGAAAGGAAT 57.475 36.000 0.00 0.00 0.00 3.01
2097 2349 6.963117 TTACTCCCTCCATAAAGAAAGGAA 57.037 37.500 0.00 0.00 0.00 3.36
2098 2350 7.366551 GGAATTACTCCCTCCATAAAGAAAGGA 60.367 40.741 0.00 0.00 38.44 3.36
2099 2351 6.773200 GGAATTACTCCCTCCATAAAGAAAGG 59.227 42.308 0.00 0.00 38.44 3.11
2100 2352 7.500559 CAGGAATTACTCCCTCCATAAAGAAAG 59.499 40.741 0.00 0.00 46.81 2.62
2101 2353 7.346471 CAGGAATTACTCCCTCCATAAAGAAA 58.654 38.462 0.00 0.00 46.81 2.52
2102 2354 6.634955 GCAGGAATTACTCCCTCCATAAAGAA 60.635 42.308 0.00 0.00 46.81 2.52
2103 2355 5.163195 GCAGGAATTACTCCCTCCATAAAGA 60.163 44.000 0.00 0.00 46.81 2.52
2104 2356 5.066593 GCAGGAATTACTCCCTCCATAAAG 58.933 45.833 0.00 0.00 46.81 1.85
2105 2357 4.444306 CGCAGGAATTACTCCCTCCATAAA 60.444 45.833 0.00 0.00 46.81 1.40
2106 2358 3.071023 CGCAGGAATTACTCCCTCCATAA 59.929 47.826 0.00 0.00 46.81 1.90
2107 2359 2.632996 CGCAGGAATTACTCCCTCCATA 59.367 50.000 0.00 0.00 46.81 2.74
2108 2360 1.417890 CGCAGGAATTACTCCCTCCAT 59.582 52.381 0.00 0.00 46.81 3.41
2109 2361 0.830648 CGCAGGAATTACTCCCTCCA 59.169 55.000 0.00 0.00 46.81 3.86
2110 2362 0.831307 ACGCAGGAATTACTCCCTCC 59.169 55.000 0.00 0.00 46.81 4.30
2111 2363 1.207329 ACACGCAGGAATTACTCCCTC 59.793 52.381 0.00 0.00 46.81 4.30
2112 2364 1.276622 ACACGCAGGAATTACTCCCT 58.723 50.000 0.00 0.00 46.81 4.20
2113 2365 2.547826 GTACACGCAGGAATTACTCCC 58.452 52.381 0.00 0.00 46.81 4.30
2114 2366 2.190981 CGTACACGCAGGAATTACTCC 58.809 52.381 0.00 0.00 45.81 3.85
2115 2367 2.850647 GACGTACACGCAGGAATTACTC 59.149 50.000 0.85 0.00 44.43 2.59
2116 2368 2.490903 AGACGTACACGCAGGAATTACT 59.509 45.455 0.85 0.00 44.43 2.24
2117 2369 2.597305 CAGACGTACACGCAGGAATTAC 59.403 50.000 0.85 0.00 44.43 1.89
2118 2370 2.488937 TCAGACGTACACGCAGGAATTA 59.511 45.455 0.85 0.00 44.43 1.40
2119 2371 1.271379 TCAGACGTACACGCAGGAATT 59.729 47.619 0.85 0.00 44.43 2.17
2120 2372 0.885879 TCAGACGTACACGCAGGAAT 59.114 50.000 0.85 0.00 44.43 3.01
2121 2373 0.885879 ATCAGACGTACACGCAGGAA 59.114 50.000 0.85 0.00 44.43 3.36
2122 2374 0.450583 GATCAGACGTACACGCAGGA 59.549 55.000 0.85 0.00 44.43 3.86
2123 2375 0.452184 AGATCAGACGTACACGCAGG 59.548 55.000 0.85 0.00 44.43 4.85
2124 2376 1.816370 GAGATCAGACGTACACGCAG 58.184 55.000 0.85 0.00 44.43 5.18
2125 2377 0.096454 CGAGATCAGACGTACACGCA 59.904 55.000 0.85 0.00 44.43 5.24
2126 2378 0.372679 TCGAGATCAGACGTACACGC 59.627 55.000 0.85 0.00 44.43 5.34
2127 2379 1.925185 TCTCGAGATCAGACGTACACG 59.075 52.381 12.08 0.00 46.33 4.49
2128 2380 4.090034 GTTTCTCGAGATCAGACGTACAC 58.910 47.826 17.44 0.00 0.00 2.90
2129 2381 3.749609 TGTTTCTCGAGATCAGACGTACA 59.250 43.478 17.44 7.78 0.00 2.90
2130 2382 4.090034 GTGTTTCTCGAGATCAGACGTAC 58.910 47.826 17.44 5.05 0.00 3.67
2131 2383 4.001652 AGTGTTTCTCGAGATCAGACGTA 58.998 43.478 17.44 0.00 0.00 3.57
2132 2384 2.814919 AGTGTTTCTCGAGATCAGACGT 59.185 45.455 17.44 0.00 0.00 4.34
2133 2385 3.167425 CAGTGTTTCTCGAGATCAGACG 58.833 50.000 17.44 7.66 0.00 4.18
2178 2430 4.283678 TGAACTGTTTTTAATTGACCGCG 58.716 39.130 0.00 0.00 0.00 6.46
2213 2465 5.234972 GTCAAATTTCACCCTTTTGCTGAAG 59.765 40.000 0.00 0.00 31.88 3.02
2214 2466 5.104982 AGTCAAATTTCACCCTTTTGCTGAA 60.105 36.000 0.00 0.00 31.88 3.02
2215 2467 4.405358 AGTCAAATTTCACCCTTTTGCTGA 59.595 37.500 0.00 0.00 31.88 4.26
2216 2468 4.696455 AGTCAAATTTCACCCTTTTGCTG 58.304 39.130 0.00 0.00 31.88 4.41
2219 2471 4.917415 CGCTAGTCAAATTTCACCCTTTTG 59.083 41.667 0.00 0.00 0.00 2.44
2246 2498 0.249120 TCAGTGCCCTGTAATGACCG 59.751 55.000 0.00 0.00 39.82 4.79
2298 2550 4.142447 TGTCGAGTTAGATAAGCACACCTC 60.142 45.833 0.00 0.00 0.00 3.85
2320 2572 3.697542 TGATTTGCCACAGAAGATGGATG 59.302 43.478 0.00 0.00 39.87 3.51
2330 2582 8.767478 AAGATCTTTAATTTGATTTGCCACAG 57.233 30.769 0.88 0.00 0.00 3.66
2335 2592 8.375465 CACCGAAAGATCTTTAATTTGATTTGC 58.625 33.333 20.51 3.23 32.11 3.68
2366 2623 0.861837 CAACAGGCGCGGATTAGATC 59.138 55.000 8.83 0.00 0.00 2.75
2460 2720 8.720562 CAAAATGAAGAAAGTTGAACCAAGTTT 58.279 29.630 11.06 11.06 45.81 2.66
2628 2889 4.345257 CCCTCCTACCTAGTGTAGTACGTA 59.655 50.000 13.87 0.00 44.66 3.57
2629 2890 3.135530 CCCTCCTACCTAGTGTAGTACGT 59.864 52.174 13.87 0.00 44.66 3.57
2630 2891 3.737850 CCCTCCTACCTAGTGTAGTACG 58.262 54.545 13.87 0.00 44.66 3.67
2631 2892 3.117738 TGCCCTCCTACCTAGTGTAGTAC 60.118 52.174 13.87 0.00 44.66 2.73
2655 2916 3.508793 CAGTGAGATGGGAAAAGCAATGT 59.491 43.478 0.00 0.00 0.00 2.71
2659 2920 1.538047 GCAGTGAGATGGGAAAAGCA 58.462 50.000 0.00 0.00 0.00 3.91
2660 2921 0.813821 GGCAGTGAGATGGGAAAAGC 59.186 55.000 0.00 0.00 0.00 3.51
2661 2922 2.205022 TGGCAGTGAGATGGGAAAAG 57.795 50.000 0.00 0.00 0.00 2.27
2944 3211 1.708341 ACCTTTTGCACCTCAGCATT 58.292 45.000 0.00 0.00 45.19 3.56
2945 3212 2.584835 TACCTTTTGCACCTCAGCAT 57.415 45.000 0.00 0.00 45.19 3.79
2948 3215 2.229792 TGCTTACCTTTTGCACCTCAG 58.770 47.619 0.00 0.00 0.00 3.35
2969 3239 5.597182 TGCGGTCTACTATAACCAAGAAGAT 59.403 40.000 0.00 0.00 35.13 2.40
2984 3254 3.403277 CTGCTGCATGCGGTCTAC 58.597 61.111 26.79 11.32 46.63 2.59
3264 3577 1.247419 CCTCAGCACTCTGACGGACT 61.247 60.000 0.00 0.00 43.95 3.85
3334 3647 2.290122 ATCTCCTCGCGCAGTTCCTG 62.290 60.000 8.75 0.00 34.12 3.86
3339 3652 2.755876 TCCATCTCCTCGCGCAGT 60.756 61.111 8.75 0.00 0.00 4.40
3346 3659 2.158971 GCTTTGTCTCCTCCATCTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
3717 4039 2.031508 AGCAAATACGTGTTGGGAAACG 60.032 45.455 13.65 0.00 45.15 3.60
3794 4116 3.130516 TCGGTTTCTCTATAGTGTGGCTG 59.869 47.826 0.00 0.00 0.00 4.85
3815 4150 5.303845 ACCTACCCCTCGATAATTTACACTC 59.696 44.000 0.00 0.00 0.00 3.51
4082 4589 5.205056 ACGACCTGAAGAGAAAGAGGATAT 58.795 41.667 0.00 0.00 0.00 1.63
4094 4601 6.110707 GTGGGAAATATTAACGACCTGAAGA 58.889 40.000 0.00 0.00 0.00 2.87
4095 4602 5.296035 GGTGGGAAATATTAACGACCTGAAG 59.704 44.000 13.04 0.00 0.00 3.02
4096 4603 5.187687 GGTGGGAAATATTAACGACCTGAA 58.812 41.667 13.04 0.00 0.00 3.02
4097 4604 4.384427 GGGTGGGAAATATTAACGACCTGA 60.384 45.833 17.19 0.00 0.00 3.86
4098 4605 3.881089 GGGTGGGAAATATTAACGACCTG 59.119 47.826 17.19 0.00 0.00 4.00
4099 4606 3.784202 AGGGTGGGAAATATTAACGACCT 59.216 43.478 17.19 7.29 0.00 3.85
4100 4607 4.160642 AGGGTGGGAAATATTAACGACC 57.839 45.455 12.30 12.30 0.00 4.79
4101 4608 5.884232 AGAAAGGGTGGGAAATATTAACGAC 59.116 40.000 0.00 0.00 0.00 4.34
4102 4609 6.069705 AGAAAGGGTGGGAAATATTAACGA 57.930 37.500 0.00 0.00 0.00 3.85
4103 4610 6.602009 AGAAGAAAGGGTGGGAAATATTAACG 59.398 38.462 0.00 0.00 0.00 3.18
4104 4611 7.201705 CGAGAAGAAAGGGTGGGAAATATTAAC 60.202 40.741 0.00 0.00 0.00 2.01
4105 4612 6.826741 CGAGAAGAAAGGGTGGGAAATATTAA 59.173 38.462 0.00 0.00 0.00 1.40
4106 4613 6.069847 ACGAGAAGAAAGGGTGGGAAATATTA 60.070 38.462 0.00 0.00 0.00 0.98
4107 4614 5.193679 CGAGAAGAAAGGGTGGGAAATATT 58.806 41.667 0.00 0.00 0.00 1.28
4108 4615 4.227527 ACGAGAAGAAAGGGTGGGAAATAT 59.772 41.667 0.00 0.00 0.00 1.28
4109 4616 3.585732 ACGAGAAGAAAGGGTGGGAAATA 59.414 43.478 0.00 0.00 0.00 1.40
4110 4617 2.375509 ACGAGAAGAAAGGGTGGGAAAT 59.624 45.455 0.00 0.00 0.00 2.17
4111 4618 1.772453 ACGAGAAGAAAGGGTGGGAAA 59.228 47.619 0.00 0.00 0.00 3.13
4112 4619 1.346722 GACGAGAAGAAAGGGTGGGAA 59.653 52.381 0.00 0.00 0.00 3.97
4264 4793 6.199531 GGGATAAAAACAACGGTGAAAACTTC 59.800 38.462 7.88 0.00 0.00 3.01
4283 4812 5.192522 AGAGAGCAGAAAATTGAGGGGATAA 59.807 40.000 0.00 0.00 0.00 1.75
4359 4897 3.118738 GGGGTCCTAATATGGATACGCTG 60.119 52.174 0.00 0.00 38.52 5.18
4439 4994 1.601903 AGAAATGAACGCGAGCAAACA 59.398 42.857 15.93 3.57 0.00 2.83
4479 5034 2.125269 GTCGCCGCATTAGGGTGT 60.125 61.111 0.00 0.00 36.45 4.16
4514 5069 1.084289 GGGTCCGTGCAGACATAAAC 58.916 55.000 8.22 0.00 38.59 2.01


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

AutoCloner maintained by Alex Coulton.