Multiple sequence alignment - TraesCS2D01G147200

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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 TraesCS2D01G147200 chr2D 100.000 3011 0 0 1 3011 88119427 88122437 0.000000e+00 5561.0
1 TraesCS2D01G147200 chr2D 87.195 820 85 1 2186 3005 414408832 414408033 0.000000e+00 915.0
2 TraesCS2D01G147200 chr2D 76.362 863 161 35 1083 1919 87762258 87763103 9.980000e-115 424.0
3 TraesCS2D01G147200 chr2A 96.190 1365 24 5 841 2184 88329163 88330520 0.000000e+00 2207.0
4 TraesCS2D01G147200 chr2A 92.743 565 38 3 279 840 419091256 419090692 0.000000e+00 813.0
5 TraesCS2D01G147200 chr2A 92.174 575 41 4 278 848 139042286 139042860 0.000000e+00 809.0
6 TraesCS2D01G147200 chr2B 96.557 1307 33 4 883 2184 141367262 141368561 0.000000e+00 2154.0
7 TraesCS2D01G147200 chr2B 89.144 829 72 5 2183 3011 677800056 677800866 0.000000e+00 1016.0
8 TraesCS2D01G147200 chr2B 76.778 900 158 38 1083 1952 140852196 140853074 9.840000e-125 457.0
9 TraesCS2D01G147200 chr7D 92.159 829 56 1 2183 3011 607078273 607079092 0.000000e+00 1162.0
10 TraesCS2D01G147200 chr7D 97.007 568 13 4 276 839 459128347 459128914 0.000000e+00 952.0
11 TraesCS2D01G147200 chr7D 82.927 123 21 0 154 276 555670716 555670838 8.820000e-21 111.0
12 TraesCS2D01G147200 chr7D 74.086 301 57 20 1254 1545 126468907 126468619 1.480000e-18 104.0
13 TraesCS2D01G147200 chr3D 90.799 826 67 3 2186 3011 338584040 338583224 0.000000e+00 1096.0
14 TraesCS2D01G147200 chr3D 89.277 830 77 5 2183 3011 447615450 447616268 0.000000e+00 1029.0
15 TraesCS2D01G147200 chr3D 85.006 827 112 5 2186 3011 496509719 496508904 0.000000e+00 830.0
16 TraesCS2D01G147200 chr3B 89.626 829 76 4 2183 3011 513713858 513714676 0.000000e+00 1046.0
17 TraesCS2D01G147200 chr4D 97.691 563 10 3 279 838 437738530 437739092 0.000000e+00 965.0
18 TraesCS2D01G147200 chr6D 97.522 565 11 3 279 840 40770516 40769952 0.000000e+00 963.0
19 TraesCS2D01G147200 chr6D 86.486 111 14 1 160 270 193208940 193209049 1.470000e-23 121.0
20 TraesCS2D01G147200 chr1A 85.766 822 106 4 2186 3006 167986309 167985498 0.000000e+00 859.0
21 TraesCS2D01G147200 chr1A 92.374 577 40 4 276 848 562082459 562083035 0.000000e+00 819.0
22 TraesCS2D01G147200 chr1A 91.851 589 42 5 272 854 12866411 12865823 0.000000e+00 817.0
23 TraesCS2D01G147200 chr1A 87.879 66 5 2 1254 1319 14524350 14524288 1.160000e-09 75.0
24 TraesCS2D01G147200 chr6A 92.267 569 40 4 279 843 611336720 611336152 0.000000e+00 804.0
25 TraesCS2D01G147200 chr4A 91.327 588 47 4 276 859 164036626 164036039 0.000000e+00 800.0
26 TraesCS2D01G147200 chr5B 83.133 830 129 4 2183 3011 317338055 317338874 0.000000e+00 747.0
27 TraesCS2D01G147200 chr5B 82.301 113 18 2 157 268 39775113 39775002 2.470000e-16 97.1
28 TraesCS2D01G147200 chr5B 84.536 97 15 0 180 276 271583230 271583134 2.470000e-16 97.1
29 TraesCS2D01G147200 chr3A 86.239 109 13 2 160 267 152659915 152659808 1.900000e-22 117.0
30 TraesCS2D01G147200 chr3A 84.348 115 18 0 153 267 152661230 152661344 2.450000e-21 113.0
31 TraesCS2D01G147200 chr3A 83.898 118 13 5 154 268 547411114 547411000 1.140000e-19 108.0
32 TraesCS2D01G147200 chr7B 74.434 309 51 24 1254 1545 87138634 87138337 1.140000e-19 108.0
33 TraesCS2D01G147200 chr7A 74.434 309 51 21 1254 1545 127572004 127571707 1.140000e-19 108.0
34 TraesCS2D01G147200 chr7A 81.600 125 16 6 157 276 80533408 80533530 2.470000e-16 97.1
35 TraesCS2D01G147200 chr7A 84.810 79 12 0 189 267 473888286 473888208 2.490000e-11 80.5
36 TraesCS2D01G147200 chr7A 83.146 89 8 6 1204 1290 127371227 127371310 1.160000e-09 75.0


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 TraesCS2D01G147200 chr2D 88119427 88122437 3010 False 5561 5561 100.000 1 3011 1 chr2D.!!$F2 3010
1 TraesCS2D01G147200 chr2D 414408033 414408832 799 True 915 915 87.195 2186 3005 1 chr2D.!!$R1 819
2 TraesCS2D01G147200 chr2D 87762258 87763103 845 False 424 424 76.362 1083 1919 1 chr2D.!!$F1 836
3 TraesCS2D01G147200 chr2A 88329163 88330520 1357 False 2207 2207 96.190 841 2184 1 chr2A.!!$F1 1343
4 TraesCS2D01G147200 chr2A 419090692 419091256 564 True 813 813 92.743 279 840 1 chr2A.!!$R1 561
5 TraesCS2D01G147200 chr2A 139042286 139042860 574 False 809 809 92.174 278 848 1 chr2A.!!$F2 570
6 TraesCS2D01G147200 chr2B 141367262 141368561 1299 False 2154 2154 96.557 883 2184 1 chr2B.!!$F2 1301
7 TraesCS2D01G147200 chr2B 677800056 677800866 810 False 1016 1016 89.144 2183 3011 1 chr2B.!!$F3 828
8 TraesCS2D01G147200 chr2B 140852196 140853074 878 False 457 457 76.778 1083 1952 1 chr2B.!!$F1 869
9 TraesCS2D01G147200 chr7D 607078273 607079092 819 False 1162 1162 92.159 2183 3011 1 chr7D.!!$F3 828
10 TraesCS2D01G147200 chr7D 459128347 459128914 567 False 952 952 97.007 276 839 1 chr7D.!!$F1 563
11 TraesCS2D01G147200 chr3D 338583224 338584040 816 True 1096 1096 90.799 2186 3011 1 chr3D.!!$R1 825
12 TraesCS2D01G147200 chr3D 447615450 447616268 818 False 1029 1029 89.277 2183 3011 1 chr3D.!!$F1 828
13 TraesCS2D01G147200 chr3D 496508904 496509719 815 True 830 830 85.006 2186 3011 1 chr3D.!!$R2 825
14 TraesCS2D01G147200 chr3B 513713858 513714676 818 False 1046 1046 89.626 2183 3011 1 chr3B.!!$F1 828
15 TraesCS2D01G147200 chr4D 437738530 437739092 562 False 965 965 97.691 279 838 1 chr4D.!!$F1 559
16 TraesCS2D01G147200 chr6D 40769952 40770516 564 True 963 963 97.522 279 840 1 chr6D.!!$R1 561
17 TraesCS2D01G147200 chr1A 167985498 167986309 811 True 859 859 85.766 2186 3006 1 chr1A.!!$R3 820
18 TraesCS2D01G147200 chr1A 562082459 562083035 576 False 819 819 92.374 276 848 1 chr1A.!!$F1 572
19 TraesCS2D01G147200 chr1A 12865823 12866411 588 True 817 817 91.851 272 854 1 chr1A.!!$R1 582
20 TraesCS2D01G147200 chr6A 611336152 611336720 568 True 804 804 92.267 279 843 1 chr6A.!!$R1 564
21 TraesCS2D01G147200 chr4A 164036039 164036626 587 True 800 800 91.327 276 859 1 chr4A.!!$R1 583
22 TraesCS2D01G147200 chr5B 317338055 317338874 819 False 747 747 83.133 2183 3011 1 chr5B.!!$F1 828

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
175 176 0.024111 GTGACCGTATTTGTACGCGC 59.976 55.0 5.73 0.0 41.67 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2086 0.457166 TAGGAACGTCGCCAACATCG 60.457 55.0 9.73 0.0 0.0 3.84 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
19 20 2.470057 AACATGGAAAGGTGGTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
20 21 2.470057 ACATGGAAAGGTGGTTGGTT 57.530 45.000 0.00 0.00 0.00 3.67
21 22 3.603965 ACATGGAAAGGTGGTTGGTTA 57.396 42.857 0.00 0.00 0.00 2.85
22 23 3.496331 ACATGGAAAGGTGGTTGGTTAG 58.504 45.455 0.00 0.00 0.00 2.34
23 24 3.139397 ACATGGAAAGGTGGTTGGTTAGA 59.861 43.478 0.00 0.00 0.00 2.10
24 25 3.502123 TGGAAAGGTGGTTGGTTAGAG 57.498 47.619 0.00 0.00 0.00 2.43
25 26 2.781174 TGGAAAGGTGGTTGGTTAGAGT 59.219 45.455 0.00 0.00 0.00 3.24
26 27 3.975312 TGGAAAGGTGGTTGGTTAGAGTA 59.025 43.478 0.00 0.00 0.00 2.59
27 28 4.041198 TGGAAAGGTGGTTGGTTAGAGTAG 59.959 45.833 0.00 0.00 0.00 2.57
28 29 3.697619 AAGGTGGTTGGTTAGAGTAGC 57.302 47.619 0.00 0.00 0.00 3.58
29 30 2.903926 AGGTGGTTGGTTAGAGTAGCT 58.096 47.619 0.00 0.00 0.00 3.32
30 31 3.248888 AGGTGGTTGGTTAGAGTAGCTT 58.751 45.455 0.00 0.00 0.00 3.74
31 32 3.008049 AGGTGGTTGGTTAGAGTAGCTTG 59.992 47.826 0.00 0.00 0.00 4.01
32 33 3.244457 GGTGGTTGGTTAGAGTAGCTTGT 60.244 47.826 0.00 0.00 0.00 3.16
33 34 3.746492 GTGGTTGGTTAGAGTAGCTTGTG 59.254 47.826 0.00 0.00 0.00 3.33
34 35 3.389983 TGGTTGGTTAGAGTAGCTTGTGT 59.610 43.478 0.00 0.00 0.00 3.72
35 36 3.995048 GGTTGGTTAGAGTAGCTTGTGTC 59.005 47.826 0.00 0.00 0.00 3.67
36 37 3.570926 TGGTTAGAGTAGCTTGTGTCG 57.429 47.619 0.00 0.00 0.00 4.35
37 38 2.889045 TGGTTAGAGTAGCTTGTGTCGT 59.111 45.455 0.00 0.00 0.00 4.34
38 39 3.243336 GGTTAGAGTAGCTTGTGTCGTG 58.757 50.000 0.00 0.00 0.00 4.35
39 40 3.057736 GGTTAGAGTAGCTTGTGTCGTGA 60.058 47.826 0.00 0.00 0.00 4.35
40 41 4.543692 GTTAGAGTAGCTTGTGTCGTGAA 58.456 43.478 0.00 0.00 0.00 3.18
41 42 3.014604 AGAGTAGCTTGTGTCGTGAAC 57.985 47.619 0.00 0.00 0.00 3.18
42 43 2.361119 AGAGTAGCTTGTGTCGTGAACA 59.639 45.455 0.00 0.00 34.78 3.18
43 44 3.005897 AGAGTAGCTTGTGTCGTGAACAT 59.994 43.478 0.00 0.00 40.80 2.71
44 45 3.318017 AGTAGCTTGTGTCGTGAACATC 58.682 45.455 0.00 0.00 40.80 3.06
45 46 1.139989 AGCTTGTGTCGTGAACATCG 58.860 50.000 0.00 0.00 40.80 3.84
46 47 0.859232 GCTTGTGTCGTGAACATCGT 59.141 50.000 0.00 0.00 40.80 3.73
47 48 1.260561 GCTTGTGTCGTGAACATCGTT 59.739 47.619 0.00 0.00 40.80 3.85
48 49 2.659291 GCTTGTGTCGTGAACATCGTTC 60.659 50.000 0.00 0.00 40.80 3.95
49 50 1.125270 TGTGTCGTGAACATCGTTCG 58.875 50.000 2.68 0.00 40.80 3.95
50 51 0.179282 GTGTCGTGAACATCGTTCGC 60.179 55.000 9.77 9.77 40.80 4.70
61 62 2.792374 TCGTTCGCGAGTTTGACTC 58.208 52.632 9.59 0.00 45.62 3.36
62 63 0.662374 TCGTTCGCGAGTTTGACTCC 60.662 55.000 9.59 0.00 45.62 3.85
63 64 0.937699 CGTTCGCGAGTTTGACTCCA 60.938 55.000 9.59 0.00 42.12 3.86
64 65 0.784778 GTTCGCGAGTTTGACTCCAG 59.215 55.000 9.59 0.00 42.12 3.86
65 66 0.319555 TTCGCGAGTTTGACTCCAGG 60.320 55.000 9.59 0.00 42.12 4.45
66 67 1.738099 CGCGAGTTTGACTCCAGGG 60.738 63.158 0.00 0.00 42.12 4.45
67 68 1.371558 GCGAGTTTGACTCCAGGGT 59.628 57.895 2.74 0.00 42.12 4.34
68 69 0.951040 GCGAGTTTGACTCCAGGGTG 60.951 60.000 2.74 0.00 42.12 4.61
69 70 0.951040 CGAGTTTGACTCCAGGGTGC 60.951 60.000 2.74 0.00 42.12 5.01
70 71 0.398318 GAGTTTGACTCCAGGGTGCT 59.602 55.000 0.00 0.00 39.28 4.40
71 72 0.846693 AGTTTGACTCCAGGGTGCTT 59.153 50.000 0.00 0.00 0.00 3.91
72 73 1.215423 AGTTTGACTCCAGGGTGCTTT 59.785 47.619 0.00 0.00 0.00 3.51
73 74 1.338020 GTTTGACTCCAGGGTGCTTTG 59.662 52.381 0.00 0.00 0.00 2.77
74 75 0.550914 TTGACTCCAGGGTGCTTTGT 59.449 50.000 0.00 0.00 0.00 2.83
75 76 0.179020 TGACTCCAGGGTGCTTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
76 77 1.518903 GACTCCAGGGTGCTTTGTGC 61.519 60.000 0.00 0.00 43.25 4.57
92 93 7.176285 GCTTTGTGCAAAAATGAATTAGTCA 57.824 32.000 1.65 0.00 42.31 3.41
93 94 7.799784 GCTTTGTGCAAAAATGAATTAGTCAT 58.200 30.769 1.65 0.00 44.62 3.06
94 95 7.742963 GCTTTGTGCAAAAATGAATTAGTCATG 59.257 33.333 1.65 0.00 43.14 3.07
95 96 8.659925 TTTGTGCAAAAATGAATTAGTCATGT 57.340 26.923 0.00 0.00 46.80 3.21
96 97 7.640616 TGTGCAAAAATGAATTAGTCATGTG 57.359 32.000 0.00 0.00 46.80 3.21
97 98 7.208777 TGTGCAAAAATGAATTAGTCATGTGT 58.791 30.769 0.00 0.00 46.80 3.72
98 99 7.381948 TGTGCAAAAATGAATTAGTCATGTGTC 59.618 33.333 0.00 0.00 46.80 3.67
99 100 7.381948 GTGCAAAAATGAATTAGTCATGTGTCA 59.618 33.333 0.00 0.00 46.80 3.58
100 101 8.089597 TGCAAAAATGAATTAGTCATGTGTCAT 58.910 29.630 0.00 0.00 46.80 3.06
101 102 8.589629 GCAAAAATGAATTAGTCATGTGTCATC 58.410 33.333 0.00 0.00 46.80 2.92
102 103 9.628746 CAAAAATGAATTAGTCATGTGTCATCA 57.371 29.630 0.00 0.00 46.80 3.07
103 104 9.630098 AAAAATGAATTAGTCATGTGTCATCAC 57.370 29.630 0.00 0.00 46.80 3.06
104 105 8.571461 AAATGAATTAGTCATGTGTCATCACT 57.429 30.769 0.00 0.00 46.80 3.41
105 106 7.783090 ATGAATTAGTCATGTGTCATCACTC 57.217 36.000 0.00 0.00 45.69 3.51
106 107 6.700352 TGAATTAGTCATGTGTCATCACTCA 58.300 36.000 0.00 0.00 44.14 3.41
107 108 6.591448 TGAATTAGTCATGTGTCATCACTCAC 59.409 38.462 0.00 0.00 44.14 3.51
108 109 5.728637 TTAGTCATGTGTCATCACTCACT 57.271 39.130 0.00 0.00 44.14 3.41
109 110 4.185467 AGTCATGTGTCATCACTCACTC 57.815 45.455 0.00 0.00 44.14 3.51
110 111 3.575687 AGTCATGTGTCATCACTCACTCA 59.424 43.478 0.00 0.00 44.14 3.41
111 112 3.677121 GTCATGTGTCATCACTCACTCAC 59.323 47.826 0.00 0.00 44.14 3.51
112 113 3.575687 TCATGTGTCATCACTCACTCACT 59.424 43.478 0.00 0.00 44.14 3.41
113 114 3.375782 TGTGTCATCACTCACTCACTG 57.624 47.619 0.00 0.00 44.14 3.66
114 115 2.958355 TGTGTCATCACTCACTCACTGA 59.042 45.455 0.00 0.00 44.14 3.41
115 116 3.243535 TGTGTCATCACTCACTCACTGAC 60.244 47.826 0.00 0.00 44.14 3.51
116 117 2.958355 TGTCATCACTCACTCACTGACA 59.042 45.455 0.00 0.00 40.29 3.58
117 118 3.005155 TGTCATCACTCACTCACTGACAG 59.995 47.826 0.00 0.00 38.36 3.51
118 119 2.560105 TCATCACTCACTCACTGACAGG 59.440 50.000 7.51 0.00 0.00 4.00
119 120 1.332195 TCACTCACTCACTGACAGGG 58.668 55.000 7.51 2.02 0.00 4.45
120 121 0.319728 CACTCACTCACTGACAGGGG 59.680 60.000 4.51 0.00 0.00 4.79
121 122 0.833834 ACTCACTCACTGACAGGGGG 60.834 60.000 1.99 1.99 0.00 5.40
138 139 1.615392 GGGGGCAATACATCTTGATGC 59.385 52.381 10.20 0.00 36.31 3.91
139 140 1.267806 GGGGCAATACATCTTGATGCG 59.732 52.381 10.20 0.00 37.88 4.73
140 141 1.949525 GGGCAATACATCTTGATGCGT 59.050 47.619 10.20 0.00 37.88 5.24
141 142 3.138304 GGGCAATACATCTTGATGCGTA 58.862 45.455 10.20 0.00 37.88 4.42
142 143 3.058914 GGGCAATACATCTTGATGCGTAC 60.059 47.826 10.20 0.00 37.88 3.67
143 144 3.362986 GGCAATACATCTTGATGCGTACG 60.363 47.826 11.84 11.84 37.88 3.67
144 145 3.245284 GCAATACATCTTGATGCGTACGT 59.755 43.478 17.90 0.00 0.00 3.57
145 146 4.443063 GCAATACATCTTGATGCGTACGTA 59.557 41.667 17.90 13.65 0.00 3.57
146 147 5.118664 GCAATACATCTTGATGCGTACGTAT 59.881 40.000 19.06 19.06 0.00 3.06
147 148 6.516739 CAATACATCTTGATGCGTACGTATG 58.483 40.000 23.74 11.83 0.00 2.39
148 149 4.041740 ACATCTTGATGCGTACGTATGT 57.958 40.909 23.74 12.49 0.00 2.29
149 150 3.796717 ACATCTTGATGCGTACGTATGTG 59.203 43.478 23.74 14.72 0.00 3.21
150 151 3.497297 TCTTGATGCGTACGTATGTGT 57.503 42.857 23.74 0.00 0.00 3.72
151 152 4.619437 TCTTGATGCGTACGTATGTGTA 57.381 40.909 23.74 3.96 0.00 2.90
152 153 5.177725 TCTTGATGCGTACGTATGTGTAT 57.822 39.130 23.74 0.00 0.00 2.29
153 154 5.584442 TCTTGATGCGTACGTATGTGTATT 58.416 37.500 23.74 0.00 0.00 1.89
154 155 6.037726 TCTTGATGCGTACGTATGTGTATTT 58.962 36.000 23.74 0.00 0.00 1.40
155 156 6.532302 TCTTGATGCGTACGTATGTGTATTTT 59.468 34.615 23.74 0.00 0.00 1.82
156 157 6.026873 TGATGCGTACGTATGTGTATTTTG 57.973 37.500 23.74 0.00 0.00 2.44
157 158 5.577554 TGATGCGTACGTATGTGTATTTTGT 59.422 36.000 23.74 0.00 0.00 2.83
158 159 5.192896 TGCGTACGTATGTGTATTTTGTG 57.807 39.130 17.90 0.00 0.00 3.33
159 160 4.922103 TGCGTACGTATGTGTATTTTGTGA 59.078 37.500 17.90 0.00 0.00 3.58
160 161 5.164070 TGCGTACGTATGTGTATTTTGTGAC 60.164 40.000 17.90 0.00 0.00 3.67
161 162 5.722051 GCGTACGTATGTGTATTTTGTGACC 60.722 44.000 17.90 0.00 0.00 4.02
162 163 4.914312 ACGTATGTGTATTTTGTGACCG 57.086 40.909 0.00 0.00 0.00 4.79
163 164 4.309099 ACGTATGTGTATTTTGTGACCGT 58.691 39.130 0.00 0.00 0.00 4.83
164 165 5.468592 ACGTATGTGTATTTTGTGACCGTA 58.531 37.500 0.00 0.00 0.00 4.02
165 166 6.101332 ACGTATGTGTATTTTGTGACCGTAT 58.899 36.000 0.00 0.00 0.00 3.06
166 167 6.591062 ACGTATGTGTATTTTGTGACCGTATT 59.409 34.615 0.00 0.00 0.00 1.89
167 168 7.118101 ACGTATGTGTATTTTGTGACCGTATTT 59.882 33.333 0.00 0.00 0.00 1.40
168 169 7.424167 CGTATGTGTATTTTGTGACCGTATTTG 59.576 37.037 0.00 0.00 0.00 2.32
169 170 6.621316 TGTGTATTTTGTGACCGTATTTGT 57.379 33.333 0.00 0.00 0.00 2.83
170 171 7.725818 TGTGTATTTTGTGACCGTATTTGTA 57.274 32.000 0.00 0.00 0.00 2.41
171 172 7.574496 TGTGTATTTTGTGACCGTATTTGTAC 58.426 34.615 0.00 0.00 0.00 2.90
172 173 6.733280 GTGTATTTTGTGACCGTATTTGTACG 59.267 38.462 1.27 1.27 42.56 3.67
173 174 3.791993 TTTGTGACCGTATTTGTACGC 57.208 42.857 2.67 0.00 41.67 4.42
174 175 1.338765 TGTGACCGTATTTGTACGCG 58.661 50.000 3.53 3.53 41.67 6.01
175 176 0.024111 GTGACCGTATTTGTACGCGC 59.976 55.000 5.73 0.00 41.67 6.86
176 177 0.109179 TGACCGTATTTGTACGCGCT 60.109 50.000 5.73 0.00 41.67 5.92
177 178 0.296642 GACCGTATTTGTACGCGCTG 59.703 55.000 5.73 1.02 41.67 5.18
178 179 0.388907 ACCGTATTTGTACGCGCTGT 60.389 50.000 5.73 8.05 41.67 4.40
179 180 0.296642 CCGTATTTGTACGCGCTGTC 59.703 55.000 5.73 0.00 41.67 3.51
180 181 0.986270 CGTATTTGTACGCGCTGTCA 59.014 50.000 5.73 0.00 36.62 3.58
181 182 1.387420 CGTATTTGTACGCGCTGTCAA 59.613 47.619 5.73 3.75 36.62 3.18
182 183 2.532193 CGTATTTGTACGCGCTGTCAAG 60.532 50.000 5.73 0.00 36.62 3.02
183 184 1.508632 ATTTGTACGCGCTGTCAAGT 58.491 45.000 5.73 0.59 0.00 3.16
184 185 1.292061 TTTGTACGCGCTGTCAAGTT 58.708 45.000 5.73 0.00 0.00 2.66
185 186 2.137129 TTGTACGCGCTGTCAAGTTA 57.863 45.000 5.73 0.00 0.00 2.24
186 187 2.137129 TGTACGCGCTGTCAAGTTAA 57.863 45.000 5.73 0.00 0.00 2.01
187 188 2.055838 TGTACGCGCTGTCAAGTTAAG 58.944 47.619 5.73 0.00 0.00 1.85
188 189 2.056577 GTACGCGCTGTCAAGTTAAGT 58.943 47.619 5.73 0.00 0.00 2.24
189 190 0.859232 ACGCGCTGTCAAGTTAAGTG 59.141 50.000 5.73 0.00 0.00 3.16
190 191 1.136690 CGCGCTGTCAAGTTAAGTGA 58.863 50.000 5.56 0.00 0.00 3.41
191 192 1.136611 CGCGCTGTCAAGTTAAGTGAC 60.137 52.381 5.56 10.88 44.67 3.67
192 193 1.194772 GCGCTGTCAAGTTAAGTGACC 59.805 52.381 13.93 2.63 43.95 4.02
193 194 2.479837 CGCTGTCAAGTTAAGTGACCA 58.520 47.619 13.93 4.82 43.95 4.02
194 195 3.067106 CGCTGTCAAGTTAAGTGACCAT 58.933 45.455 13.93 0.00 43.95 3.55
195 196 4.242475 CGCTGTCAAGTTAAGTGACCATA 58.758 43.478 13.93 0.00 43.95 2.74
196 197 4.688879 CGCTGTCAAGTTAAGTGACCATAA 59.311 41.667 13.93 0.00 43.95 1.90
197 198 5.178623 CGCTGTCAAGTTAAGTGACCATAAA 59.821 40.000 13.93 0.00 43.95 1.40
198 199 6.128282 CGCTGTCAAGTTAAGTGACCATAAAT 60.128 38.462 13.93 0.00 43.95 1.40
199 200 7.573096 CGCTGTCAAGTTAAGTGACCATAAATT 60.573 37.037 13.93 0.00 43.95 1.82
200 201 7.750903 GCTGTCAAGTTAAGTGACCATAAATTC 59.249 37.037 13.93 0.00 43.95 2.17
201 202 8.684386 TGTCAAGTTAAGTGACCATAAATTCA 57.316 30.769 13.93 0.00 43.95 2.57
202 203 9.295825 TGTCAAGTTAAGTGACCATAAATTCAT 57.704 29.630 13.93 0.00 43.95 2.57
232 233 9.436957 TTTAAAATTTTAGCACCAAACTGAACA 57.563 25.926 10.40 0.00 0.00 3.18
233 234 9.606631 TTAAAATTTTAGCACCAAACTGAACAT 57.393 25.926 10.40 0.00 0.00 2.71
234 235 7.713764 AAATTTTAGCACCAAACTGAACATC 57.286 32.000 0.00 0.00 0.00 3.06
235 236 5.843673 TTTTAGCACCAAACTGAACATCA 57.156 34.783 0.00 0.00 0.00 3.07
236 237 5.843673 TTTAGCACCAAACTGAACATCAA 57.156 34.783 0.00 0.00 0.00 2.57
237 238 3.996150 AGCACCAAACTGAACATCAAG 57.004 42.857 0.00 0.00 0.00 3.02
238 239 2.035066 AGCACCAAACTGAACATCAAGC 59.965 45.455 0.00 0.00 0.00 4.01
239 240 2.863704 GCACCAAACTGAACATCAAGCC 60.864 50.000 0.00 0.00 0.00 4.35
240 241 1.963515 ACCAAACTGAACATCAAGCCC 59.036 47.619 0.00 0.00 0.00 5.19
241 242 2.242043 CCAAACTGAACATCAAGCCCT 58.758 47.619 0.00 0.00 0.00 5.19
242 243 3.181434 ACCAAACTGAACATCAAGCCCTA 60.181 43.478 0.00 0.00 0.00 3.53
243 244 3.441572 CCAAACTGAACATCAAGCCCTAG 59.558 47.826 0.00 0.00 0.00 3.02
244 245 4.074970 CAAACTGAACATCAAGCCCTAGT 58.925 43.478 0.00 0.00 0.00 2.57
245 246 4.373156 AACTGAACATCAAGCCCTAGTT 57.627 40.909 0.00 0.00 0.00 2.24
246 247 3.944087 ACTGAACATCAAGCCCTAGTTC 58.056 45.455 0.00 0.00 39.11 3.01
247 248 3.584848 ACTGAACATCAAGCCCTAGTTCT 59.415 43.478 0.00 0.00 39.33 3.01
248 249 3.937706 CTGAACATCAAGCCCTAGTTCTG 59.062 47.826 0.00 0.00 39.33 3.02
249 250 3.327757 TGAACATCAAGCCCTAGTTCTGT 59.672 43.478 0.00 0.00 39.33 3.41
250 251 3.340814 ACATCAAGCCCTAGTTCTGTG 57.659 47.619 0.00 0.00 0.00 3.66
251 252 2.906389 ACATCAAGCCCTAGTTCTGTGA 59.094 45.455 0.00 0.00 0.00 3.58
252 253 3.265791 CATCAAGCCCTAGTTCTGTGAC 58.734 50.000 0.00 0.00 0.00 3.67
253 254 2.609747 TCAAGCCCTAGTTCTGTGACT 58.390 47.619 0.00 0.00 0.00 3.41
254 255 2.972713 TCAAGCCCTAGTTCTGTGACTT 59.027 45.455 0.00 0.00 0.00 3.01
255 256 3.006967 TCAAGCCCTAGTTCTGTGACTTC 59.993 47.826 0.00 0.00 0.00 3.01
256 257 2.896039 AGCCCTAGTTCTGTGACTTCT 58.104 47.619 0.00 0.00 0.00 2.85
257 258 4.048970 AGCCCTAGTTCTGTGACTTCTA 57.951 45.455 0.00 0.00 0.00 2.10
258 259 4.020543 AGCCCTAGTTCTGTGACTTCTAG 58.979 47.826 0.00 0.00 0.00 2.43
259 260 3.764972 GCCCTAGTTCTGTGACTTCTAGT 59.235 47.826 0.00 0.00 0.00 2.57
260 261 4.381079 GCCCTAGTTCTGTGACTTCTAGTG 60.381 50.000 0.00 0.00 0.00 2.74
261 262 5.010933 CCCTAGTTCTGTGACTTCTAGTGA 58.989 45.833 0.00 0.00 0.00 3.41
262 263 5.654650 CCCTAGTTCTGTGACTTCTAGTGAT 59.345 44.000 0.00 0.00 0.00 3.06
263 264 6.829298 CCCTAGTTCTGTGACTTCTAGTGATA 59.171 42.308 0.00 0.00 0.00 2.15
264 265 7.504238 CCCTAGTTCTGTGACTTCTAGTGATAT 59.496 40.741 0.00 0.00 0.00 1.63
265 266 8.908903 CCTAGTTCTGTGACTTCTAGTGATATT 58.091 37.037 0.00 0.00 0.00 1.28
268 269 9.469097 AGTTCTGTGACTTCTAGTGATATTACT 57.531 33.333 5.39 5.39 34.71 2.24
359 361 7.951591 ACTTACAACTACTCAAAAATGCCATT 58.048 30.769 0.00 0.00 0.00 3.16
365 367 9.421806 CAACTACTCAAAAATGCCATTAATTCA 57.578 29.630 0.00 0.00 0.00 2.57
379 381 6.294342 GCCATTAATTCATGAGATGCTTGCTA 60.294 38.462 1.02 0.00 0.00 3.49
585 588 8.556213 AGTAACCAAGCGAATAATTTTACAGA 57.444 30.769 0.00 0.00 0.00 3.41
772 775 2.557924 TGAAGCGATGGCATTTTTGAGT 59.442 40.909 0.00 0.00 43.41 3.41
880 886 4.935205 CAGGTTGTCATATTTGTCCTCGAA 59.065 41.667 0.00 0.00 0.00 3.71
1011 1031 4.440127 CAAGCAATGGCCGGCACC 62.440 66.667 30.85 12.89 42.56 5.01
1503 1538 2.672098 GACCTCTCCAGATGCTTCCTA 58.328 52.381 0.00 0.00 0.00 2.94
1728 1763 0.693049 GGAGGGAGTTCTTGCCAGAA 59.307 55.000 0.00 0.00 40.38 3.02
2184 2230 6.517605 AGTACTTCTGTTCCTCTTCAAGTTC 58.482 40.000 0.00 0.00 0.00 3.01
2264 2310 3.677527 TCGAGGTTGGTCGAGGAC 58.322 61.111 0.00 0.00 43.91 3.85
2265 2311 2.178521 CGAGGTTGGTCGAGGACG 59.821 66.667 0.00 0.00 42.85 4.79
2266 2312 2.330372 CGAGGTTGGTCGAGGACGA 61.330 63.158 0.00 0.00 46.56 4.20
2298 2344 5.186797 ACAAAGTGTTGTTTTGGAAGGATCA 59.813 36.000 0.00 0.00 46.01 2.92
2334 2380 2.664518 TGTGCAAGACATCGCGCA 60.665 55.556 8.75 0.00 45.76 6.09
2341 2387 1.191868 CAAGACATCGCGCATCTCATC 59.808 52.381 8.75 0.00 0.00 2.92
2410 2456 2.362736 GCACTGGAAGATGAGCAATGA 58.637 47.619 0.00 0.00 37.43 2.57
2457 2503 1.675641 ACATGGCGCTCCTTCAACC 60.676 57.895 7.64 0.00 0.00 3.77
2464 2510 1.033746 CGCTCCTTCAACCCATGCAT 61.034 55.000 0.00 0.00 0.00 3.96
2521 2567 2.157421 GTCGCCTGACAGCTTTCTG 58.843 57.895 0.87 0.43 44.82 3.02
2627 2673 2.373169 ACAGCCATTTGGAGAAGTCTCA 59.627 45.455 10.39 0.00 44.60 3.27
2745 2791 0.600255 GCCTGTTACACGTGTCTGCT 60.600 55.000 27.16 1.98 0.00 4.24
2767 2813 2.303022 GGATGAAGACACTCTGGACCAA 59.697 50.000 0.00 0.00 0.00 3.67
2908 2954 1.153349 GGGCTTCGCGAAGGAAGAT 60.153 57.895 40.64 0.00 44.93 2.40
2910 2956 1.492720 GGCTTCGCGAAGGAAGATAG 58.507 55.000 40.64 21.12 44.93 2.08
2968 3014 3.490933 GGTCACTTTGGAAGCAAAGGAAC 60.491 47.826 1.40 0.00 44.14 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.781174 ACTCTAACCAACCACCTTTCCA 59.219 45.455 0.00 0.00 0.00 3.53
7 8 3.651423 AGCTACTCTAACCAACCACCTTT 59.349 43.478 0.00 0.00 0.00 3.11
8 9 3.248888 AGCTACTCTAACCAACCACCTT 58.751 45.455 0.00 0.00 0.00 3.50
9 10 2.903926 AGCTACTCTAACCAACCACCT 58.096 47.619 0.00 0.00 0.00 4.00
10 11 3.244457 ACAAGCTACTCTAACCAACCACC 60.244 47.826 0.00 0.00 0.00 4.61
11 12 3.746492 CACAAGCTACTCTAACCAACCAC 59.254 47.826 0.00 0.00 0.00 4.16
12 13 3.389983 ACACAAGCTACTCTAACCAACCA 59.610 43.478 0.00 0.00 0.00 3.67
13 14 3.995048 GACACAAGCTACTCTAACCAACC 59.005 47.826 0.00 0.00 0.00 3.77
14 15 3.673809 CGACACAAGCTACTCTAACCAAC 59.326 47.826 0.00 0.00 0.00 3.77
15 16 3.319972 ACGACACAAGCTACTCTAACCAA 59.680 43.478 0.00 0.00 0.00 3.67
16 17 2.889045 ACGACACAAGCTACTCTAACCA 59.111 45.455 0.00 0.00 0.00 3.67
17 18 3.057736 TCACGACACAAGCTACTCTAACC 60.058 47.826 0.00 0.00 0.00 2.85
18 19 4.156664 TCACGACACAAGCTACTCTAAC 57.843 45.455 0.00 0.00 0.00 2.34
19 20 4.037089 TGTTCACGACACAAGCTACTCTAA 59.963 41.667 0.00 0.00 32.00 2.10
20 21 3.566742 TGTTCACGACACAAGCTACTCTA 59.433 43.478 0.00 0.00 32.00 2.43
21 22 2.361119 TGTTCACGACACAAGCTACTCT 59.639 45.455 0.00 0.00 32.00 3.24
22 23 2.739292 TGTTCACGACACAAGCTACTC 58.261 47.619 0.00 0.00 32.00 2.59
23 24 2.882927 TGTTCACGACACAAGCTACT 57.117 45.000 0.00 0.00 32.00 2.57
24 25 2.090658 CGATGTTCACGACACAAGCTAC 59.909 50.000 0.00 0.00 42.04 3.58
25 26 2.287970 ACGATGTTCACGACACAAGCTA 60.288 45.455 0.00 0.00 42.04 3.32
26 27 1.139989 CGATGTTCACGACACAAGCT 58.860 50.000 0.00 0.00 42.04 3.74
27 28 0.859232 ACGATGTTCACGACACAAGC 59.141 50.000 0.00 0.00 42.04 4.01
28 29 2.408487 CGAACGATGTTCACGACACAAG 60.408 50.000 10.01 0.00 42.04 3.16
29 30 1.519343 CGAACGATGTTCACGACACAA 59.481 47.619 10.01 0.00 42.04 3.33
30 31 1.125270 CGAACGATGTTCACGACACA 58.875 50.000 10.01 0.00 42.04 3.72
31 32 0.179282 GCGAACGATGTTCACGACAC 60.179 55.000 10.01 0.00 42.04 3.67
32 33 1.602012 CGCGAACGATGTTCACGACA 61.602 55.000 13.12 0.00 43.93 4.35
33 34 1.055235 CGCGAACGATGTTCACGAC 59.945 57.895 13.12 0.00 43.93 4.34
34 35 1.081972 TCGCGAACGATGTTCACGA 60.082 52.632 16.07 16.07 45.12 4.35
35 36 3.443546 TCGCGAACGATGTTCACG 58.556 55.556 6.20 12.40 45.12 4.35
43 44 0.662374 GGAGTCAAACTCGCGAACGA 60.662 55.000 11.33 0.86 45.96 3.85
44 45 0.937699 TGGAGTCAAACTCGCGAACG 60.938 55.000 11.33 1.10 45.96 3.95
45 46 0.784778 CTGGAGTCAAACTCGCGAAC 59.215 55.000 11.33 4.79 45.96 3.95
46 47 0.319555 CCTGGAGTCAAACTCGCGAA 60.320 55.000 11.33 0.00 45.96 4.70
47 48 1.289066 CCTGGAGTCAAACTCGCGA 59.711 57.895 9.26 9.26 45.96 5.87
48 49 1.738099 CCCTGGAGTCAAACTCGCG 60.738 63.158 0.00 0.00 45.96 5.87
49 50 0.951040 CACCCTGGAGTCAAACTCGC 60.951 60.000 0.00 0.00 45.96 5.03
50 51 0.951040 GCACCCTGGAGTCAAACTCG 60.951 60.000 0.00 0.00 45.96 4.18
51 52 0.398318 AGCACCCTGGAGTCAAACTC 59.602 55.000 0.00 0.00 44.32 3.01
52 53 0.846693 AAGCACCCTGGAGTCAAACT 59.153 50.000 0.00 0.00 0.00 2.66
53 54 1.338020 CAAAGCACCCTGGAGTCAAAC 59.662 52.381 0.00 0.00 0.00 2.93
54 55 1.064017 ACAAAGCACCCTGGAGTCAAA 60.064 47.619 0.00 0.00 0.00 2.69
55 56 0.550914 ACAAAGCACCCTGGAGTCAA 59.449 50.000 0.00 0.00 0.00 3.18
56 57 0.179020 CACAAAGCACCCTGGAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
57 58 1.518903 GCACAAAGCACCCTGGAGTC 61.519 60.000 0.00 0.00 44.79 3.36
58 59 1.529244 GCACAAAGCACCCTGGAGT 60.529 57.895 0.00 0.00 44.79 3.85
59 60 3.359002 GCACAAAGCACCCTGGAG 58.641 61.111 0.00 0.00 44.79 3.86
68 69 7.176285 TGACTAATTCATTTTTGCACAAAGC 57.824 32.000 4.13 0.00 45.96 3.51
69 70 8.767085 ACATGACTAATTCATTTTTGCACAAAG 58.233 29.630 0.00 0.00 42.87 2.77
70 71 8.549548 CACATGACTAATTCATTTTTGCACAAA 58.450 29.630 0.00 0.00 42.87 2.83
71 72 7.710044 ACACATGACTAATTCATTTTTGCACAA 59.290 29.630 0.00 0.00 42.87 3.33
72 73 7.208777 ACACATGACTAATTCATTTTTGCACA 58.791 30.769 0.00 0.00 42.87 4.57
73 74 7.381948 TGACACATGACTAATTCATTTTTGCAC 59.618 33.333 0.00 0.00 42.87 4.57
74 75 7.432059 TGACACATGACTAATTCATTTTTGCA 58.568 30.769 0.00 0.00 42.87 4.08
75 76 7.872163 TGACACATGACTAATTCATTTTTGC 57.128 32.000 0.00 0.00 42.87 3.68
76 77 9.628746 TGATGACACATGACTAATTCATTTTTG 57.371 29.630 0.00 0.00 42.87 2.44
77 78 9.630098 GTGATGACACATGACTAATTCATTTTT 57.370 29.630 0.00 0.00 43.68 1.94
78 79 9.017509 AGTGATGACACATGACTAATTCATTTT 57.982 29.630 0.00 0.00 43.68 1.82
79 80 8.571461 AGTGATGACACATGACTAATTCATTT 57.429 30.769 0.00 0.00 43.68 2.32
80 81 7.825761 TGAGTGATGACACATGACTAATTCATT 59.174 33.333 0.00 0.00 43.68 2.57
81 82 7.279536 GTGAGTGATGACACATGACTAATTCAT 59.720 37.037 0.00 0.00 46.75 2.57
94 95 3.243535 TGTCAGTGAGTGAGTGATGACAC 60.244 47.826 0.00 0.00 41.37 3.67
95 96 2.958355 TGTCAGTGAGTGAGTGATGACA 59.042 45.455 0.00 1.92 43.33 3.58
96 97 3.573598 CTGTCAGTGAGTGAGTGATGAC 58.426 50.000 0.00 0.00 36.38 3.06
97 98 2.560105 CCTGTCAGTGAGTGAGTGATGA 59.440 50.000 0.00 0.00 36.38 2.92
98 99 2.353505 CCCTGTCAGTGAGTGAGTGATG 60.354 54.545 0.00 0.00 36.38 3.07
99 100 1.898472 CCCTGTCAGTGAGTGAGTGAT 59.102 52.381 0.00 0.00 36.38 3.06
100 101 1.332195 CCCTGTCAGTGAGTGAGTGA 58.668 55.000 0.00 0.00 35.13 3.41
101 102 0.319728 CCCCTGTCAGTGAGTGAGTG 59.680 60.000 0.00 0.00 35.13 3.51
102 103 0.833834 CCCCCTGTCAGTGAGTGAGT 60.834 60.000 0.00 0.00 35.13 3.41
103 104 1.978473 CCCCCTGTCAGTGAGTGAG 59.022 63.158 0.00 0.00 35.13 3.51
104 105 4.215370 CCCCCTGTCAGTGAGTGA 57.785 61.111 0.00 0.00 0.00 3.41
118 119 1.615392 GCATCAAGATGTATTGCCCCC 59.385 52.381 11.35 0.00 40.80 5.40
119 120 1.267806 CGCATCAAGATGTATTGCCCC 59.732 52.381 11.35 0.00 40.80 5.80
120 121 1.949525 ACGCATCAAGATGTATTGCCC 59.050 47.619 11.35 0.00 40.80 5.36
121 122 3.362986 CGTACGCATCAAGATGTATTGCC 60.363 47.826 0.52 0.00 40.80 4.52
122 123 3.245284 ACGTACGCATCAAGATGTATTGC 59.755 43.478 16.72 0.00 40.80 3.56
123 124 6.143919 ACATACGTACGCATCAAGATGTATTG 59.856 38.462 16.72 0.00 40.80 1.90
124 125 6.143919 CACATACGTACGCATCAAGATGTATT 59.856 38.462 16.72 0.00 40.80 1.89
125 126 5.629435 CACATACGTACGCATCAAGATGTAT 59.371 40.000 16.72 0.00 40.80 2.29
126 127 4.973663 CACATACGTACGCATCAAGATGTA 59.026 41.667 16.72 0.00 40.80 2.29
127 128 3.796717 CACATACGTACGCATCAAGATGT 59.203 43.478 16.72 10.37 40.80 3.06
128 129 3.796717 ACACATACGTACGCATCAAGATG 59.203 43.478 16.72 9.78 41.60 2.90
129 130 4.041740 ACACATACGTACGCATCAAGAT 57.958 40.909 16.72 0.00 0.00 2.40
130 131 3.497297 ACACATACGTACGCATCAAGA 57.503 42.857 16.72 0.00 0.00 3.02
131 132 5.883328 AATACACATACGTACGCATCAAG 57.117 39.130 16.72 3.92 0.00 3.02
132 133 6.091034 ACAAAATACACATACGTACGCATCAA 59.909 34.615 16.72 0.00 0.00 2.57
133 134 5.577554 ACAAAATACACATACGTACGCATCA 59.422 36.000 16.72 0.00 0.00 3.07
134 135 5.894266 CACAAAATACACATACGTACGCATC 59.106 40.000 16.72 0.00 0.00 3.91
135 136 5.577554 TCACAAAATACACATACGTACGCAT 59.422 36.000 16.72 4.85 0.00 4.73
136 137 4.922103 TCACAAAATACACATACGTACGCA 59.078 37.500 16.72 1.76 0.00 5.24
137 138 5.242877 GTCACAAAATACACATACGTACGC 58.757 41.667 16.72 0.00 0.00 4.42
138 139 5.497439 CGGTCACAAAATACACATACGTACG 60.497 44.000 15.01 15.01 0.00 3.67
139 140 5.345741 ACGGTCACAAAATACACATACGTAC 59.654 40.000 0.00 0.00 0.00 3.67
140 141 5.468592 ACGGTCACAAAATACACATACGTA 58.531 37.500 0.00 0.00 0.00 3.57
141 142 4.309099 ACGGTCACAAAATACACATACGT 58.691 39.130 0.00 0.00 0.00 3.57
142 143 4.914312 ACGGTCACAAAATACACATACG 57.086 40.909 0.00 0.00 0.00 3.06
143 144 8.231837 ACAAATACGGTCACAAAATACACATAC 58.768 33.333 0.00 0.00 0.00 2.39
144 145 8.325421 ACAAATACGGTCACAAAATACACATA 57.675 30.769 0.00 0.00 0.00 2.29
145 146 7.209471 ACAAATACGGTCACAAAATACACAT 57.791 32.000 0.00 0.00 0.00 3.21
146 147 6.621316 ACAAATACGGTCACAAAATACACA 57.379 33.333 0.00 0.00 0.00 3.72
147 148 7.998081 GTACAAATACGGTCACAAAATACAC 57.002 36.000 0.00 0.00 0.00 2.90
162 163 2.410730 ACTTGACAGCGCGTACAAATAC 59.589 45.455 8.43 0.00 0.00 1.89
163 164 2.679450 ACTTGACAGCGCGTACAAATA 58.321 42.857 8.43 0.00 0.00 1.40
164 165 1.508632 ACTTGACAGCGCGTACAAAT 58.491 45.000 8.43 0.00 0.00 2.32
165 166 1.292061 AACTTGACAGCGCGTACAAA 58.708 45.000 8.43 0.00 0.00 2.83
166 167 2.137129 TAACTTGACAGCGCGTACAA 57.863 45.000 8.43 8.80 0.00 2.41
167 168 2.055838 CTTAACTTGACAGCGCGTACA 58.944 47.619 8.43 0.00 0.00 2.90
168 169 2.056577 ACTTAACTTGACAGCGCGTAC 58.943 47.619 8.43 0.00 0.00 3.67
169 170 2.055838 CACTTAACTTGACAGCGCGTA 58.944 47.619 8.43 0.00 0.00 4.42
170 171 0.859232 CACTTAACTTGACAGCGCGT 59.141 50.000 8.43 2.53 0.00 6.01
171 172 1.136611 GTCACTTAACTTGACAGCGCG 60.137 52.381 0.00 0.00 42.58 6.86
172 173 1.194772 GGTCACTTAACTTGACAGCGC 59.805 52.381 0.00 0.00 44.47 5.92
173 174 2.479837 TGGTCACTTAACTTGACAGCG 58.520 47.619 12.44 0.00 44.47 5.18
174 175 6.554334 TTTATGGTCACTTAACTTGACAGC 57.446 37.500 12.44 0.61 44.47 4.40
175 176 8.783093 TGAATTTATGGTCACTTAACTTGACAG 58.217 33.333 12.44 0.00 44.47 3.51
176 177 8.684386 TGAATTTATGGTCACTTAACTTGACA 57.316 30.769 12.44 2.68 44.47 3.58
206 207 9.436957 TGTTCAGTTTGGTGCTAAAATTTTAAA 57.563 25.926 11.62 1.76 0.00 1.52
207 208 9.606631 ATGTTCAGTTTGGTGCTAAAATTTTAA 57.393 25.926 11.62 0.00 0.00 1.52
208 209 9.255304 GATGTTCAGTTTGGTGCTAAAATTTTA 57.745 29.630 10.16 10.16 0.00 1.52
209 210 7.768120 TGATGTTCAGTTTGGTGCTAAAATTTT 59.232 29.630 8.75 8.75 0.00 1.82
210 211 7.271511 TGATGTTCAGTTTGGTGCTAAAATTT 58.728 30.769 0.00 0.00 0.00 1.82
211 212 6.815089 TGATGTTCAGTTTGGTGCTAAAATT 58.185 32.000 0.00 0.00 0.00 1.82
212 213 6.403866 TGATGTTCAGTTTGGTGCTAAAAT 57.596 33.333 0.00 0.00 0.00 1.82
213 214 5.843673 TGATGTTCAGTTTGGTGCTAAAA 57.156 34.783 0.00 0.00 0.00 1.52
214 215 5.735922 GCTTGATGTTCAGTTTGGTGCTAAA 60.736 40.000 0.00 0.00 0.00 1.85
215 216 4.261572 GCTTGATGTTCAGTTTGGTGCTAA 60.262 41.667 0.00 0.00 0.00 3.09
216 217 3.253188 GCTTGATGTTCAGTTTGGTGCTA 59.747 43.478 0.00 0.00 0.00 3.49
217 218 2.035066 GCTTGATGTTCAGTTTGGTGCT 59.965 45.455 0.00 0.00 0.00 4.40
218 219 2.397549 GCTTGATGTTCAGTTTGGTGC 58.602 47.619 0.00 0.00 0.00 5.01
219 220 2.288395 GGGCTTGATGTTCAGTTTGGTG 60.288 50.000 0.00 0.00 0.00 4.17
220 221 1.963515 GGGCTTGATGTTCAGTTTGGT 59.036 47.619 0.00 0.00 0.00 3.67
221 222 2.242043 AGGGCTTGATGTTCAGTTTGG 58.758 47.619 0.00 0.00 0.00 3.28
222 223 4.074970 ACTAGGGCTTGATGTTCAGTTTG 58.925 43.478 0.00 0.00 0.00 2.93
223 224 4.373156 ACTAGGGCTTGATGTTCAGTTT 57.627 40.909 0.00 0.00 0.00 2.66
224 225 4.042187 AGAACTAGGGCTTGATGTTCAGTT 59.958 41.667 0.00 0.00 39.33 3.16
225 226 3.584848 AGAACTAGGGCTTGATGTTCAGT 59.415 43.478 0.00 0.00 39.33 3.41
226 227 3.937706 CAGAACTAGGGCTTGATGTTCAG 59.062 47.826 0.00 0.00 39.33 3.02
227 228 3.327757 ACAGAACTAGGGCTTGATGTTCA 59.672 43.478 0.00 0.00 39.33 3.18
228 229 3.686726 CACAGAACTAGGGCTTGATGTTC 59.313 47.826 0.00 0.00 37.76 3.18
229 230 3.327757 TCACAGAACTAGGGCTTGATGTT 59.672 43.478 0.00 0.00 0.00 2.71
230 231 2.906389 TCACAGAACTAGGGCTTGATGT 59.094 45.455 0.00 0.00 0.00 3.06
231 232 3.055530 AGTCACAGAACTAGGGCTTGATG 60.056 47.826 0.00 0.00 0.00 3.07
232 233 3.177228 AGTCACAGAACTAGGGCTTGAT 58.823 45.455 0.00 0.00 0.00 2.57
233 234 2.609747 AGTCACAGAACTAGGGCTTGA 58.390 47.619 0.00 0.00 0.00 3.02
234 235 3.007398 AGAAGTCACAGAACTAGGGCTTG 59.993 47.826 0.00 0.00 0.00 4.01
235 236 3.243724 AGAAGTCACAGAACTAGGGCTT 58.756 45.455 0.00 0.00 0.00 4.35
236 237 2.896039 AGAAGTCACAGAACTAGGGCT 58.104 47.619 0.00 0.00 0.00 5.19
237 238 3.764972 ACTAGAAGTCACAGAACTAGGGC 59.235 47.826 0.00 0.00 36.06 5.19
238 239 5.010933 TCACTAGAAGTCACAGAACTAGGG 58.989 45.833 0.00 0.00 36.35 3.53
239 240 6.767524 ATCACTAGAAGTCACAGAACTAGG 57.232 41.667 0.00 0.00 36.06 3.02
242 243 9.469097 AGTAATATCACTAGAAGTCACAGAACT 57.531 33.333 0.00 0.00 0.00 3.01
273 274 9.660180 GTGGCATAATGATAAAAACCCTTTTAA 57.340 29.630 0.00 0.00 39.75 1.52
274 275 9.041354 AGTGGCATAATGATAAAAACCCTTTTA 57.959 29.630 0.00 0.00 40.42 1.52
585 588 7.461182 TGATCCCAACATCGTTCTTATTTTT 57.539 32.000 0.00 0.00 0.00 1.94
772 775 6.775629 AGTTTTGCCACTAGGAATTTCAACTA 59.224 34.615 0.00 0.00 36.89 2.24
1108 1128 1.990060 CGCCCAGGGAGAAGAGGAA 60.990 63.158 10.89 0.00 0.00 3.36
1964 1999 1.079503 GACGAACAGCTTGATGTCCC 58.920 55.000 0.00 0.00 31.50 4.46
2050 2085 1.735198 GGAACGTCGCCAACATCGA 60.735 57.895 2.77 0.00 0.00 3.59
2051 2086 0.457166 TAGGAACGTCGCCAACATCG 60.457 55.000 9.73 0.00 0.00 3.84
2052 2087 1.593006 CATAGGAACGTCGCCAACATC 59.407 52.381 9.73 0.00 0.00 3.06
2156 2202 7.943447 ACTTGAAGAGGAACAGAAGTACTAGTA 59.057 37.037 0.00 0.00 0.00 1.82
2157 2203 6.778559 ACTTGAAGAGGAACAGAAGTACTAGT 59.221 38.462 0.00 0.00 0.00 2.57
2158 2204 7.222000 ACTTGAAGAGGAACAGAAGTACTAG 57.778 40.000 0.00 0.00 0.00 2.57
2184 2230 1.153086 AGCATTCCTAGCCCTTGCG 60.153 57.895 0.00 0.00 44.33 4.85
2262 2308 1.001597 ACACTTTGTCTCCTCGTCGTC 60.002 52.381 0.00 0.00 0.00 4.20
2263 2309 1.030457 ACACTTTGTCTCCTCGTCGT 58.970 50.000 0.00 0.00 0.00 4.34
2264 2310 1.787155 CAACACTTTGTCTCCTCGTCG 59.213 52.381 0.00 0.00 0.00 5.12
2265 2311 2.822764 ACAACACTTTGTCTCCTCGTC 58.177 47.619 0.00 0.00 42.67 4.20
2266 2312 2.981859 ACAACACTTTGTCTCCTCGT 57.018 45.000 0.00 0.00 42.67 4.18
2267 2313 4.342772 CAAAACAACACTTTGTCTCCTCG 58.657 43.478 0.00 0.00 45.69 4.63
2268 2314 4.398044 TCCAAAACAACACTTTGTCTCCTC 59.602 41.667 0.00 0.00 45.69 3.71
2269 2315 4.340617 TCCAAAACAACACTTTGTCTCCT 58.659 39.130 0.00 0.00 45.69 3.69
2270 2316 4.712122 TCCAAAACAACACTTTGTCTCC 57.288 40.909 0.00 0.00 45.69 3.71
2298 2344 1.133575 CAGAGTGGCCATGGATCCATT 60.134 52.381 25.20 11.23 33.90 3.16
2341 2387 2.069273 CGTGTTTCTACCAGCTCAAGG 58.931 52.381 0.00 0.00 0.00 3.61
2410 2456 1.595357 GAAGGGGACGTCCAACGAT 59.405 57.895 34.40 20.02 46.05 3.73
2464 2510 1.927487 AGGCAATGGCATGTCTCAAA 58.073 45.000 10.05 0.00 43.71 2.69
2534 2580 3.216800 TGGCAGAATAAGACATGGATGC 58.783 45.455 0.00 0.00 0.00 3.91
2627 2673 2.579860 AGATCTTGCATTTGAGAGGGGT 59.420 45.455 0.00 0.00 0.00 4.95
2694 2740 2.093500 TCTTGCAATCCATGTCTAGCGT 60.093 45.455 0.00 0.00 0.00 5.07
2745 2791 1.902508 GGTCCAGAGTGTCTTCATCCA 59.097 52.381 0.00 0.00 0.00 3.41
2767 2813 4.621274 GCATAACCACATTGCACCAAGATT 60.621 41.667 0.00 0.00 36.40 2.40
2908 2954 0.314935 GGGTGTCGAAACCACGTCTA 59.685 55.000 26.06 0.00 42.47 2.59
2910 2956 1.068585 AGGGTGTCGAAACCACGTC 59.931 57.895 26.06 8.81 42.47 4.34
2968 3014 1.199097 GTTATGTTGAACACCCTGGCG 59.801 52.381 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.