Multiple sequence alignment - TraesCS3D01G119800

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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 TraesCS3D01G119800 chr3D 100.000 2281 0 0 1 2281 75354673 75356953 0.000000e+00 4213.0
1 TraesCS3D01G119800 chr3D 100.000 1279 0 0 2842 4120 75357514 75358792 0.000000e+00 2362.0
2 TraesCS3D01G119800 chr3D 79.021 858 153 24 1157 2002 291765522 291766364 2.780000e-156 562.0
3 TraesCS3D01G119800 chr3B 94.681 1805 62 20 489 2281 121575327 121577109 0.000000e+00 2771.0
4 TraesCS3D01G119800 chr3B 94.741 1293 39 18 2842 4120 121577754 121579031 0.000000e+00 1984.0
5 TraesCS3D01G119800 chr3B 78.596 855 162 19 1157 2002 384909929 384910771 2.800000e-151 545.0
6 TraesCS3D01G119800 chr3B 92.353 170 10 3 219 386 121575119 121575287 5.320000e-59 239.0
7 TraesCS3D01G119800 chr3A 94.245 1668 49 19 533 2187 88854183 88855816 0.000000e+00 2505.0
8 TraesCS3D01G119800 chr3A 93.281 893 38 11 2842 3718 88856373 88857259 0.000000e+00 1297.0
9 TraesCS3D01G119800 chr3A 76.429 1137 222 34 1157 2281 384320000 384321102 1.280000e-159 573.0
10 TraesCS3D01G119800 chr3A 93.846 195 12 0 1 195 180419134 180419328 1.120000e-75 294.0
11 TraesCS3D01G119800 chr3A 91.351 185 8 2 278 461 88852597 88852774 3.180000e-61 246.0
12 TraesCS3D01G119800 chr3A 85.000 160 7 10 3837 3990 88857357 88857505 3.320000e-31 147.0
13 TraesCS3D01G119800 chr3A 97.561 82 2 0 4039 4120 88857503 88857584 1.540000e-29 141.0
14 TraesCS3D01G119800 chr1B 83.162 1069 156 20 1084 2141 181218282 181217227 0.000000e+00 955.0
15 TraesCS3D01G119800 chr1B 89.286 84 6 3 3933 4013 20174201 20174284 7.290000e-18 102.0
16 TraesCS3D01G119800 chr1A 83.397 1048 151 19 1104 2141 131521574 131520540 0.000000e+00 950.0
17 TraesCS3D01G119800 chr1A 92.228 193 15 0 3 195 6622227 6622035 1.460000e-69 274.0
18 TraesCS3D01G119800 chr1A 89.848 197 20 0 1 197 6535341 6535145 1.900000e-63 254.0
19 TraesCS3D01G119800 chr1D 83.349 1045 153 17 1106 2141 119010784 119009752 0.000000e+00 946.0
20 TraesCS3D01G119800 chr6B 76.228 896 175 36 1130 2006 134000298 133999422 1.360000e-119 440.0
21 TraesCS3D01G119800 chr6B 88.764 89 6 4 3931 4017 601883870 601883784 5.630000e-19 106.0
22 TraesCS3D01G119800 chr6D 92.821 195 14 0 1 195 446535390 446535584 2.420000e-72 283.0
23 TraesCS3D01G119800 chr6D 88.506 87 6 4 3931 4015 305190214 305190130 7.290000e-18 102.0
24 TraesCS3D01G119800 chr4D 91.327 196 17 0 1 196 469305648 469305453 6.790000e-68 268.0
25 TraesCS3D01G119800 chr2A 91.371 197 15 2 1 196 103345615 103345810 6.790000e-68 268.0
26 TraesCS3D01G119800 chr2A 90.355 197 19 0 1 197 136969775 136969579 4.090000e-65 259.0
27 TraesCS3D01G119800 chr7A 91.237 194 16 1 3 195 686002029 686002222 3.160000e-66 263.0
28 TraesCS3D01G119800 chrUn 89.848 197 20 0 1 197 406710673 406710869 1.900000e-63 254.0
29 TraesCS3D01G119800 chrUn 88.636 88 6 4 3933 4016 9847632 9847545 2.030000e-18 104.0
30 TraesCS3D01G119800 chrUn 85.882 85 10 2 3932 4015 11032315 11032398 5.670000e-14 89.8
31 TraesCS3D01G119800 chr5D 88.636 88 7 3 3933 4017 516792140 516792227 2.030000e-18 104.0
32 TraesCS3D01G119800 chr6A 86.364 88 8 3 3931 4017 547829636 547829552 4.390000e-15 93.5


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 TraesCS3D01G119800 chr3D 75354673 75358792 4119 False 3287.500000 4213 100.0000 1 4120 2 chr3D.!!$F2 4119
1 TraesCS3D01G119800 chr3D 291765522 291766364 842 False 562.000000 562 79.0210 1157 2002 1 chr3D.!!$F1 845
2 TraesCS3D01G119800 chr3B 121575119 121579031 3912 False 1664.666667 2771 93.9250 219 4120 3 chr3B.!!$F2 3901
3 TraesCS3D01G119800 chr3B 384909929 384910771 842 False 545.000000 545 78.5960 1157 2002 1 chr3B.!!$F1 845
4 TraesCS3D01G119800 chr3A 88852597 88857584 4987 False 867.200000 2505 92.2876 278 4120 5 chr3A.!!$F3 3842
5 TraesCS3D01G119800 chr3A 384320000 384321102 1102 False 573.000000 573 76.4290 1157 2281 1 chr3A.!!$F2 1124
6 TraesCS3D01G119800 chr1B 181217227 181218282 1055 True 955.000000 955 83.1620 1084 2141 1 chr1B.!!$R1 1057
7 TraesCS3D01G119800 chr1A 131520540 131521574 1034 True 950.000000 950 83.3970 1104 2141 1 chr1A.!!$R3 1037
8 TraesCS3D01G119800 chr1D 119009752 119010784 1032 True 946.000000 946 83.3490 1106 2141 1 chr1D.!!$R1 1035
9 TraesCS3D01G119800 chr6B 133999422 134000298 876 True 440.000000 440 76.2280 1130 2006 1 chr6B.!!$R1 876

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
19 20 0.398696 AGTGTGGTCCGGTGCATAAA 59.601 50.000 0.0 0.0 0.0 1.40 F
21 22 0.398696 TGTGGTCCGGTGCATAAAGT 59.601 50.000 0.0 0.0 0.0 2.66 F
194 195 0.684153 GCCACCATTGTACATGCCCT 60.684 55.000 0.0 0.0 0.0 5.19 F
949 2339 1.079438 ACTCCACTCCACTCCCCTC 59.921 63.158 0.0 0.0 0.0 4.30 F
950 2340 1.390125 CTCCACTCCACTCCCCTCT 59.610 63.158 0.0 0.0 0.0 3.69 F
1006 2409 2.250031 CTGGAGGAGATGAGATGAGGG 58.750 57.143 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1006 2409 2.409651 CAGGAGTAGCGCGAGTCC 59.590 66.667 30.56 30.56 39.00 3.85 R
2198 3604 1.144936 GATGGTGGAGGCGGAGAAG 59.855 63.158 0.00 0.00 0.00 2.85 R
2244 3650 2.125106 GGTGGTGGAGATGGCGAC 60.125 66.667 0.00 0.00 0.00 5.19 R
2996 4486 1.290009 GGACACAGGTGGCAATTGC 59.710 57.895 22.47 22.47 41.42 3.56 R
2998 4488 1.603455 CGGGACACAGGTGGCAATT 60.603 57.895 7.68 0.00 41.42 2.32 R
3143 4638 5.447778 ACCATGTCTTCCTTCAGATGATT 57.552 39.130 0.00 0.00 31.83 2.57 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
17 18 3.800188 AGTGTGGTCCGGTGCATA 58.200 55.556 0.00 0.00 0.00 3.14
18 19 2.062922 AGTGTGGTCCGGTGCATAA 58.937 52.632 0.00 0.00 0.00 1.90
19 20 0.398696 AGTGTGGTCCGGTGCATAAA 59.601 50.000 0.00 0.00 0.00 1.40
20 21 0.802494 GTGTGGTCCGGTGCATAAAG 59.198 55.000 0.00 0.00 0.00 1.85
21 22 0.398696 TGTGGTCCGGTGCATAAAGT 59.601 50.000 0.00 0.00 0.00 2.66
22 23 1.202830 TGTGGTCCGGTGCATAAAGTT 60.203 47.619 0.00 0.00 0.00 2.66
23 24 1.199097 GTGGTCCGGTGCATAAAGTTG 59.801 52.381 0.00 0.00 0.00 3.16
24 25 0.808755 GGTCCGGTGCATAAAGTTGG 59.191 55.000 0.00 0.00 0.00 3.77
25 26 1.612199 GGTCCGGTGCATAAAGTTGGA 60.612 52.381 0.00 0.00 0.00 3.53
26 27 2.156098 GTCCGGTGCATAAAGTTGGAA 58.844 47.619 0.00 0.00 0.00 3.53
27 28 2.554893 GTCCGGTGCATAAAGTTGGAAA 59.445 45.455 0.00 0.00 0.00 3.13
28 29 3.004944 GTCCGGTGCATAAAGTTGGAAAA 59.995 43.478 0.00 0.00 0.00 2.29
29 30 3.254657 TCCGGTGCATAAAGTTGGAAAAG 59.745 43.478 0.00 0.00 0.00 2.27
30 31 3.005367 CCGGTGCATAAAGTTGGAAAAGT 59.995 43.478 0.00 0.00 0.00 2.66
31 32 4.500716 CCGGTGCATAAAGTTGGAAAAGTT 60.501 41.667 0.00 0.00 0.00 2.66
32 33 5.278561 CCGGTGCATAAAGTTGGAAAAGTTA 60.279 40.000 0.00 0.00 0.00 2.24
33 34 6.210078 CGGTGCATAAAGTTGGAAAAGTTAA 58.790 36.000 0.00 0.00 0.00 2.01
34 35 6.697892 CGGTGCATAAAGTTGGAAAAGTTAAA 59.302 34.615 0.00 0.00 0.00 1.52
35 36 7.096230 CGGTGCATAAAGTTGGAAAAGTTAAAG 60.096 37.037 0.00 0.00 0.00 1.85
36 37 7.709182 GGTGCATAAAGTTGGAAAAGTTAAAGT 59.291 33.333 0.00 0.00 0.00 2.66
37 38 8.539674 GTGCATAAAGTTGGAAAAGTTAAAGTG 58.460 33.333 0.00 0.00 0.00 3.16
38 39 8.470805 TGCATAAAGTTGGAAAAGTTAAAGTGA 58.529 29.630 0.00 0.00 0.00 3.41
39 40 9.308318 GCATAAAGTTGGAAAAGTTAAAGTGAA 57.692 29.630 0.00 0.00 0.00 3.18
43 44 7.334844 AGTTGGAAAAGTTAAAGTGAAGAGG 57.665 36.000 0.00 0.00 0.00 3.69
44 45 7.116736 AGTTGGAAAAGTTAAAGTGAAGAGGA 58.883 34.615 0.00 0.00 0.00 3.71
45 46 7.283354 AGTTGGAAAAGTTAAAGTGAAGAGGAG 59.717 37.037 0.00 0.00 0.00 3.69
46 47 6.062095 TGGAAAAGTTAAAGTGAAGAGGAGG 58.938 40.000 0.00 0.00 0.00 4.30
47 48 5.473846 GGAAAAGTTAAAGTGAAGAGGAGGG 59.526 44.000 0.00 0.00 0.00 4.30
48 49 5.906772 AAAGTTAAAGTGAAGAGGAGGGA 57.093 39.130 0.00 0.00 0.00 4.20
49 50 6.455690 AAAGTTAAAGTGAAGAGGAGGGAT 57.544 37.500 0.00 0.00 0.00 3.85
50 51 5.428184 AGTTAAAGTGAAGAGGAGGGATG 57.572 43.478 0.00 0.00 0.00 3.51
51 52 2.797177 AAAGTGAAGAGGAGGGATGC 57.203 50.000 0.00 0.00 0.00 3.91
52 53 1.661463 AAGTGAAGAGGAGGGATGCA 58.339 50.000 0.00 0.00 0.00 3.96
53 54 1.890552 AGTGAAGAGGAGGGATGCAT 58.109 50.000 0.00 0.00 0.00 3.96
54 55 1.489649 AGTGAAGAGGAGGGATGCATG 59.510 52.381 2.46 0.00 0.00 4.06
55 56 1.211457 GTGAAGAGGAGGGATGCATGT 59.789 52.381 2.46 0.00 0.00 3.21
56 57 1.211212 TGAAGAGGAGGGATGCATGTG 59.789 52.381 2.46 0.00 0.00 3.21
57 58 1.211457 GAAGAGGAGGGATGCATGTGT 59.789 52.381 2.46 0.00 0.00 3.72
58 59 2.180946 AGAGGAGGGATGCATGTGTA 57.819 50.000 2.46 0.00 0.00 2.90
59 60 2.045524 AGAGGAGGGATGCATGTGTAG 58.954 52.381 2.46 0.00 0.00 2.74
60 61 1.765314 GAGGAGGGATGCATGTGTAGT 59.235 52.381 2.46 0.00 0.00 2.73
61 62 1.487976 AGGAGGGATGCATGTGTAGTG 59.512 52.381 2.46 0.00 0.00 2.74
62 63 1.486310 GGAGGGATGCATGTGTAGTGA 59.514 52.381 2.46 0.00 0.00 3.41
63 64 2.484417 GGAGGGATGCATGTGTAGTGAG 60.484 54.545 2.46 0.00 0.00 3.51
64 65 2.432146 GAGGGATGCATGTGTAGTGAGA 59.568 50.000 2.46 0.00 0.00 3.27
65 66 2.433604 AGGGATGCATGTGTAGTGAGAG 59.566 50.000 2.46 0.00 0.00 3.20
66 67 2.169352 GGGATGCATGTGTAGTGAGAGT 59.831 50.000 2.46 0.00 0.00 3.24
67 68 3.452474 GGATGCATGTGTAGTGAGAGTC 58.548 50.000 2.46 0.00 0.00 3.36
68 69 3.118992 GGATGCATGTGTAGTGAGAGTCA 60.119 47.826 2.46 0.00 0.00 3.41
69 70 4.442612 GGATGCATGTGTAGTGAGAGTCAT 60.443 45.833 2.46 0.00 0.00 3.06
70 71 4.541973 TGCATGTGTAGTGAGAGTCATT 57.458 40.909 0.00 0.00 0.00 2.57
71 72 4.898320 TGCATGTGTAGTGAGAGTCATTT 58.102 39.130 0.00 0.00 0.00 2.32
72 73 5.308014 TGCATGTGTAGTGAGAGTCATTTT 58.692 37.500 0.00 0.00 0.00 1.82
73 74 5.409520 TGCATGTGTAGTGAGAGTCATTTTC 59.590 40.000 0.00 0.00 0.00 2.29
74 75 5.641209 GCATGTGTAGTGAGAGTCATTTTCT 59.359 40.000 0.00 0.00 0.00 2.52
75 76 6.813649 GCATGTGTAGTGAGAGTCATTTTCTA 59.186 38.462 0.00 0.00 0.00 2.10
76 77 7.493971 GCATGTGTAGTGAGAGTCATTTTCTAT 59.506 37.037 0.00 0.00 0.00 1.98
77 78 9.376075 CATGTGTAGTGAGAGTCATTTTCTATT 57.624 33.333 0.00 0.00 0.00 1.73
78 79 8.988064 TGTGTAGTGAGAGTCATTTTCTATTC 57.012 34.615 0.00 0.00 0.00 1.75
79 80 8.807118 TGTGTAGTGAGAGTCATTTTCTATTCT 58.193 33.333 0.00 0.00 0.00 2.40
80 81 9.646427 GTGTAGTGAGAGTCATTTTCTATTCTT 57.354 33.333 0.00 0.00 0.00 2.52
92 93 9.973661 TCATTTTCTATTCTTTAATGAGGTCCA 57.026 29.630 0.00 0.00 32.10 4.02
94 95 9.981460 ATTTTCTATTCTTTAATGAGGTCCACT 57.019 29.630 0.00 0.00 0.00 4.00
97 98 8.840200 TCTATTCTTTAATGAGGTCCACTAGT 57.160 34.615 0.00 0.00 0.00 2.57
98 99 8.696374 TCTATTCTTTAATGAGGTCCACTAGTG 58.304 37.037 16.34 16.34 0.00 2.74
99 100 6.928348 TTCTTTAATGAGGTCCACTAGTGA 57.072 37.500 24.68 7.64 0.00 3.41
100 101 7.496346 TTCTTTAATGAGGTCCACTAGTGAT 57.504 36.000 24.68 5.56 0.00 3.06
101 102 8.603898 TTCTTTAATGAGGTCCACTAGTGATA 57.396 34.615 24.68 9.06 0.00 2.15
102 103 8.239038 TCTTTAATGAGGTCCACTAGTGATAG 57.761 38.462 24.68 7.85 0.00 2.08
103 104 4.946478 AATGAGGTCCACTAGTGATAGC 57.054 45.455 24.68 19.26 0.00 2.97
104 105 3.671740 TGAGGTCCACTAGTGATAGCT 57.328 47.619 24.68 23.18 0.00 3.32
105 106 3.982516 TGAGGTCCACTAGTGATAGCTT 58.017 45.455 24.68 10.60 0.00 3.74
106 107 4.353777 TGAGGTCCACTAGTGATAGCTTT 58.646 43.478 24.68 6.64 0.00 3.51
107 108 4.402793 TGAGGTCCACTAGTGATAGCTTTC 59.597 45.833 24.68 14.46 0.00 2.62
108 109 4.353777 AGGTCCACTAGTGATAGCTTTCA 58.646 43.478 24.68 2.39 0.00 2.69
109 110 4.965532 AGGTCCACTAGTGATAGCTTTCAT 59.034 41.667 24.68 2.92 0.00 2.57
110 111 5.426833 AGGTCCACTAGTGATAGCTTTCATT 59.573 40.000 24.68 8.64 0.00 2.57
111 112 5.525378 GGTCCACTAGTGATAGCTTTCATTG 59.475 44.000 24.68 2.63 0.00 2.82
112 113 5.525378 GTCCACTAGTGATAGCTTTCATTGG 59.475 44.000 24.68 10.33 0.00 3.16
113 114 5.425217 TCCACTAGTGATAGCTTTCATTGGA 59.575 40.000 24.68 17.39 0.00 3.53
114 115 5.757320 CCACTAGTGATAGCTTTCATTGGAG 59.243 44.000 24.68 10.49 0.00 3.86
115 116 6.344500 CACTAGTGATAGCTTTCATTGGAGT 58.656 40.000 18.45 8.93 0.00 3.85
116 117 6.257411 CACTAGTGATAGCTTTCATTGGAGTG 59.743 42.308 18.45 15.28 0.00 3.51
117 118 5.426689 AGTGATAGCTTTCATTGGAGTGA 57.573 39.130 10.18 0.00 0.00 3.41
118 119 5.809001 AGTGATAGCTTTCATTGGAGTGAA 58.191 37.500 10.18 0.00 36.38 3.18
119 120 6.240894 AGTGATAGCTTTCATTGGAGTGAAA 58.759 36.000 10.18 2.55 43.66 2.69
120 121 6.716628 AGTGATAGCTTTCATTGGAGTGAAAA 59.283 34.615 10.18 0.00 44.76 2.29
121 122 7.231317 AGTGATAGCTTTCATTGGAGTGAAAAA 59.769 33.333 10.18 0.00 44.76 1.94
143 144 8.851541 AAAAATCAACACATATGCCTCAAATT 57.148 26.923 1.58 0.00 0.00 1.82
144 145 9.941325 AAAAATCAACACATATGCCTCAAATTA 57.059 25.926 1.58 0.00 0.00 1.40
145 146 8.931385 AAATCAACACATATGCCTCAAATTAC 57.069 30.769 1.58 0.00 0.00 1.89
146 147 7.886629 ATCAACACATATGCCTCAAATTACT 57.113 32.000 1.58 0.00 0.00 2.24
147 148 7.701539 TCAACACATATGCCTCAAATTACTT 57.298 32.000 1.58 0.00 0.00 2.24
148 149 8.121305 TCAACACATATGCCTCAAATTACTTT 57.879 30.769 1.58 0.00 0.00 2.66
149 150 8.584157 TCAACACATATGCCTCAAATTACTTTT 58.416 29.630 1.58 0.00 0.00 2.27
150 151 9.206870 CAACACATATGCCTCAAATTACTTTTT 57.793 29.630 1.58 0.00 0.00 1.94
151 152 8.761575 ACACATATGCCTCAAATTACTTTTTG 57.238 30.769 1.58 0.00 37.83 2.44
152 153 8.367156 ACACATATGCCTCAAATTACTTTTTGT 58.633 29.630 1.58 0.00 37.73 2.83
153 154 8.863049 CACATATGCCTCAAATTACTTTTTGTC 58.137 33.333 1.58 0.00 37.73 3.18
154 155 8.584157 ACATATGCCTCAAATTACTTTTTGTCA 58.416 29.630 1.58 0.00 37.73 3.58
155 156 9.590451 CATATGCCTCAAATTACTTTTTGTCAT 57.410 29.630 0.00 0.00 37.73 3.06
156 157 7.894376 ATGCCTCAAATTACTTTTTGTCATG 57.106 32.000 0.00 0.00 37.73 3.07
157 158 7.048629 TGCCTCAAATTACTTTTTGTCATGA 57.951 32.000 0.00 0.00 37.73 3.07
158 159 7.147312 TGCCTCAAATTACTTTTTGTCATGAG 58.853 34.615 0.00 0.00 37.73 2.90
159 160 6.587608 GCCTCAAATTACTTTTTGTCATGAGG 59.412 38.462 12.43 12.43 37.73 3.86
160 161 6.587608 CCTCAAATTACTTTTTGTCATGAGGC 59.412 38.462 0.00 0.00 37.73 4.70
161 162 7.048629 TCAAATTACTTTTTGTCATGAGGCA 57.951 32.000 0.00 0.00 37.73 4.75
162 163 7.669427 TCAAATTACTTTTTGTCATGAGGCAT 58.331 30.769 0.00 0.00 37.73 4.40
163 164 8.801299 TCAAATTACTTTTTGTCATGAGGCATA 58.199 29.630 0.00 0.00 37.73 3.14
164 165 8.863049 CAAATTACTTTTTGTCATGAGGCATAC 58.137 33.333 0.00 0.00 32.99 2.39
165 166 4.685169 ACTTTTTGTCATGAGGCATACG 57.315 40.909 0.00 0.00 0.00 3.06
166 167 4.072131 ACTTTTTGTCATGAGGCATACGT 58.928 39.130 0.00 0.00 0.00 3.57
167 168 5.242434 ACTTTTTGTCATGAGGCATACGTA 58.758 37.500 0.00 0.00 0.00 3.57
168 169 5.880332 ACTTTTTGTCATGAGGCATACGTAT 59.120 36.000 1.14 1.14 0.00 3.06
169 170 6.374333 ACTTTTTGTCATGAGGCATACGTATT 59.626 34.615 5.03 0.00 0.00 1.89
170 171 5.984233 TTTGTCATGAGGCATACGTATTC 57.016 39.130 5.03 0.05 0.00 1.75
171 172 4.664150 TGTCATGAGGCATACGTATTCA 57.336 40.909 5.03 8.09 0.00 2.57
172 173 5.213891 TGTCATGAGGCATACGTATTCAT 57.786 39.130 13.17 13.17 0.00 2.57
173 174 6.339587 TGTCATGAGGCATACGTATTCATA 57.660 37.500 16.89 4.12 0.00 2.15
174 175 6.935167 TGTCATGAGGCATACGTATTCATAT 58.065 36.000 16.89 2.76 0.00 1.78
175 176 6.813152 TGTCATGAGGCATACGTATTCATATG 59.187 38.462 16.89 12.32 32.83 1.78
180 181 4.600012 GCATACGTATTCATATGCCACC 57.400 45.455 5.03 0.00 45.24 4.61
181 182 4.000325 GCATACGTATTCATATGCCACCA 59.000 43.478 5.03 0.00 45.24 4.17
182 183 4.635765 GCATACGTATTCATATGCCACCAT 59.364 41.667 5.03 0.00 45.24 3.55
183 184 5.123820 GCATACGTATTCATATGCCACCATT 59.876 40.000 5.03 0.00 45.24 3.16
184 185 6.545508 CATACGTATTCATATGCCACCATTG 58.454 40.000 5.03 0.00 32.85 2.82
185 186 4.460263 ACGTATTCATATGCCACCATTGT 58.540 39.130 0.00 0.00 32.85 2.71
186 187 5.616270 ACGTATTCATATGCCACCATTGTA 58.384 37.500 0.00 0.00 32.85 2.41
187 188 5.468746 ACGTATTCATATGCCACCATTGTAC 59.531 40.000 0.00 0.00 32.85 2.90
188 189 5.468409 CGTATTCATATGCCACCATTGTACA 59.532 40.000 0.00 0.00 32.85 2.90
189 190 6.149308 CGTATTCATATGCCACCATTGTACAT 59.851 38.462 0.00 0.00 32.85 2.29
190 191 5.771153 TTCATATGCCACCATTGTACATG 57.229 39.130 0.00 0.00 32.85 3.21
191 192 3.569277 TCATATGCCACCATTGTACATGC 59.431 43.478 0.00 0.00 32.85 4.06
192 193 1.113788 ATGCCACCATTGTACATGCC 58.886 50.000 0.00 0.00 0.00 4.40
193 194 0.969917 TGCCACCATTGTACATGCCC 60.970 55.000 0.00 0.00 0.00 5.36
194 195 0.684153 GCCACCATTGTACATGCCCT 60.684 55.000 0.00 0.00 0.00 5.19
195 196 1.851304 CCACCATTGTACATGCCCTT 58.149 50.000 0.00 0.00 0.00 3.95
196 197 2.948147 GCCACCATTGTACATGCCCTTA 60.948 50.000 0.00 0.00 0.00 2.69
197 198 3.565307 CCACCATTGTACATGCCCTTAT 58.435 45.455 0.00 0.00 0.00 1.73
198 199 4.724399 CCACCATTGTACATGCCCTTATA 58.276 43.478 0.00 0.00 0.00 0.98
199 200 4.518970 CCACCATTGTACATGCCCTTATAC 59.481 45.833 0.00 0.00 0.00 1.47
200 201 5.129634 CACCATTGTACATGCCCTTATACA 58.870 41.667 0.00 0.00 0.00 2.29
201 202 5.008613 CACCATTGTACATGCCCTTATACAC 59.991 44.000 0.00 0.00 0.00 2.90
202 203 4.518970 CCATTGTACATGCCCTTATACACC 59.481 45.833 0.00 0.00 0.00 4.16
203 204 3.849563 TGTACATGCCCTTATACACCC 57.150 47.619 0.00 0.00 0.00 4.61
204 205 3.116174 TGTACATGCCCTTATACACCCA 58.884 45.455 0.00 0.00 0.00 4.51
205 206 3.523972 TGTACATGCCCTTATACACCCAA 59.476 43.478 0.00 0.00 0.00 4.12
206 207 3.971468 ACATGCCCTTATACACCCAAT 57.029 42.857 0.00 0.00 0.00 3.16
207 208 3.565307 ACATGCCCTTATACACCCAATG 58.435 45.455 0.00 0.00 0.00 2.82
208 209 3.204158 ACATGCCCTTATACACCCAATGA 59.796 43.478 0.00 0.00 0.00 2.57
209 210 4.214310 CATGCCCTTATACACCCAATGAA 58.786 43.478 0.00 0.00 0.00 2.57
210 211 3.897239 TGCCCTTATACACCCAATGAAG 58.103 45.455 0.00 0.00 0.00 3.02
211 212 3.268334 TGCCCTTATACACCCAATGAAGT 59.732 43.478 0.00 0.00 0.00 3.01
212 213 4.475381 TGCCCTTATACACCCAATGAAGTA 59.525 41.667 0.00 0.00 0.00 2.24
213 214 5.133660 TGCCCTTATACACCCAATGAAGTAT 59.866 40.000 0.00 0.00 0.00 2.12
214 215 5.705905 GCCCTTATACACCCAATGAAGTATC 59.294 44.000 0.00 0.00 0.00 2.24
215 216 6.465894 GCCCTTATACACCCAATGAAGTATCT 60.466 42.308 0.00 0.00 0.00 1.98
216 217 7.256547 GCCCTTATACACCCAATGAAGTATCTA 60.257 40.741 0.00 0.00 0.00 1.98
217 218 8.826765 CCCTTATACACCCAATGAAGTATCTAT 58.173 37.037 0.00 0.00 0.00 1.98
238 239 9.720769 ATCTATTTTATGTATAAGGTTGGTCCG 57.279 33.333 0.00 0.00 41.99 4.79
260 261 7.769507 GTCCGGGAGTTTAGAATTTCTTTCTAT 59.230 37.037 0.00 0.00 44.47 1.98
272 273 3.793797 TCTTTCTATGATTCCGTGCGA 57.206 42.857 0.00 0.00 0.00 5.10
289 290 1.935933 CGACCCACCTTAATTCCTCG 58.064 55.000 0.00 0.00 0.00 4.63
535 585 6.904463 TTACTCCATCCCAAAGGTAAAAAC 57.096 37.500 0.00 0.00 0.00 2.43
804 2185 4.435970 CTAAACCCCACCCGCCCC 62.436 72.222 0.00 0.00 0.00 5.80
833 2218 2.461637 CCCTTCCTCCCCTTCCCT 59.538 66.667 0.00 0.00 0.00 4.20
909 2294 1.216678 TGTCCTCCTCCTCCTCATCTC 59.783 57.143 0.00 0.00 0.00 2.75
941 2331 4.631740 TCCCCGCACTCCACTCCA 62.632 66.667 0.00 0.00 0.00 3.86
945 2335 2.262915 CGCACTCCACTCCACTCC 59.737 66.667 0.00 0.00 0.00 3.85
948 2338 1.229336 CACTCCACTCCACTCCCCT 60.229 63.158 0.00 0.00 0.00 4.79
949 2339 1.079438 ACTCCACTCCACTCCCCTC 59.921 63.158 0.00 0.00 0.00 4.30
950 2340 1.390125 CTCCACTCCACTCCCCTCT 59.610 63.158 0.00 0.00 0.00 3.69
1006 2409 2.250031 CTGGAGGAGATGAGATGAGGG 58.750 57.143 0.00 0.00 0.00 4.30
1695 3101 3.353836 CACAACACCTTCGGCGGG 61.354 66.667 7.21 3.35 0.00 6.13
2208 3614 4.394712 CCGTTGCCTTCTCCGCCT 62.395 66.667 0.00 0.00 0.00 5.52
2244 3650 4.227134 CCATCACCTCCTCCGCCG 62.227 72.222 0.00 0.00 0.00 6.46
2885 4375 2.597217 CCGCCAAAGCCAGTCCAA 60.597 61.111 0.00 0.00 34.57 3.53
2996 4486 2.826003 GCCACCCTATTACCCCGGG 61.826 68.421 15.80 15.80 43.79 5.73
2997 4487 2.826003 CCACCCTATTACCCCGGGC 61.826 68.421 17.73 0.00 41.86 6.13
2998 4488 2.073716 CACCCTATTACCCCGGGCA 61.074 63.158 17.73 0.70 41.86 5.36
3214 4709 1.135721 GGATGGCAAGCTCACCAAATC 59.864 52.381 11.38 6.01 39.96 2.17
3293 4788 4.041198 TGAAGAGTTAGTTGTAAGGTGGGG 59.959 45.833 0.00 0.00 0.00 4.96
3393 4888 3.950395 AGGCTACAGATTGAAGGCAAATC 59.050 43.478 0.00 0.00 37.59 2.17
3564 5069 4.888326 AGAGCAAGAGATTCAGAGTGTT 57.112 40.909 0.00 0.00 0.00 3.32
3565 5070 5.991933 AGAGCAAGAGATTCAGAGTGTTA 57.008 39.130 0.00 0.00 0.00 2.41
3569 5074 8.535335 AGAGCAAGAGATTCAGAGTGTTATTTA 58.465 33.333 0.00 0.00 0.00 1.40
3643 5148 8.801715 TTTTAGTCAGCATTCTTTTAGCTTTG 57.198 30.769 0.00 0.00 36.26 2.77
3674 5179 7.359262 TGTTAAGTGTTCTAATCCAATCACG 57.641 36.000 0.00 0.00 0.00 4.35
3741 5247 4.578928 GTGATGGTACTTGTTTCTTGTGGT 59.421 41.667 0.00 0.00 0.00 4.16
3920 5456 9.268282 AGTCTAATACTCCCTCTGTATCAAAAA 57.732 33.333 0.00 0.00 30.33 1.94
3931 5467 8.213679 CCCTCTGTATCAAAAATCTAGAATCCA 58.786 37.037 0.00 0.00 0.00 3.41
3940 5476 8.432805 TCAAAAATCTAGAATCCATACTCCTCC 58.567 37.037 0.00 0.00 0.00 4.30
3941 5477 6.597832 AAATCTAGAATCCATACTCCTCCG 57.402 41.667 0.00 0.00 0.00 4.63
3942 5478 4.726035 TCTAGAATCCATACTCCTCCGT 57.274 45.455 0.00 0.00 0.00 4.69
3943 5479 5.837770 TCTAGAATCCATACTCCTCCGTA 57.162 43.478 0.00 0.00 0.00 4.02
3946 5482 4.999310 AGAATCCATACTCCTCCGTATCA 58.001 43.478 0.00 0.00 0.00 2.15
3958 5500 7.391620 ACTCCTCCGTATCAAAATGTAAGAAA 58.608 34.615 0.00 0.00 0.00 2.52
4075 5623 3.446161 TCCTACGTTTATGAGTGTCCTGG 59.554 47.826 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.398696 TTTATGCACCGGACCACACT 59.601 50.000 9.46 0.00 0.00 3.55
2 3 0.398696 ACTTTATGCACCGGACCACA 59.601 50.000 9.46 0.00 0.00 4.17
3 4 1.199097 CAACTTTATGCACCGGACCAC 59.801 52.381 9.46 0.00 0.00 4.16
4 5 1.529226 CAACTTTATGCACCGGACCA 58.471 50.000 9.46 4.56 0.00 4.02
6 7 1.816074 TCCAACTTTATGCACCGGAC 58.184 50.000 9.46 0.00 0.00 4.79
7 8 2.570415 TTCCAACTTTATGCACCGGA 57.430 45.000 9.46 0.00 0.00 5.14
8 9 3.005367 ACTTTTCCAACTTTATGCACCGG 59.995 43.478 0.00 0.00 0.00 5.28
9 10 4.237349 ACTTTTCCAACTTTATGCACCG 57.763 40.909 0.00 0.00 0.00 4.94
10 11 7.709182 ACTTTAACTTTTCCAACTTTATGCACC 59.291 33.333 0.00 0.00 0.00 5.01
11 12 8.539674 CACTTTAACTTTTCCAACTTTATGCAC 58.460 33.333 0.00 0.00 0.00 4.57
12 13 8.470805 TCACTTTAACTTTTCCAACTTTATGCA 58.529 29.630 0.00 0.00 0.00 3.96
13 14 8.865590 TCACTTTAACTTTTCCAACTTTATGC 57.134 30.769 0.00 0.00 0.00 3.14
17 18 8.251026 CCTCTTCACTTTAACTTTTCCAACTTT 58.749 33.333 0.00 0.00 0.00 2.66
18 19 7.614192 TCCTCTTCACTTTAACTTTTCCAACTT 59.386 33.333 0.00 0.00 0.00 2.66
19 20 7.116736 TCCTCTTCACTTTAACTTTTCCAACT 58.883 34.615 0.00 0.00 0.00 3.16
20 21 7.329588 TCCTCTTCACTTTAACTTTTCCAAC 57.670 36.000 0.00 0.00 0.00 3.77
21 22 6.546034 CCTCCTCTTCACTTTAACTTTTCCAA 59.454 38.462 0.00 0.00 0.00 3.53
22 23 6.062095 CCTCCTCTTCACTTTAACTTTTCCA 58.938 40.000 0.00 0.00 0.00 3.53
23 24 5.473846 CCCTCCTCTTCACTTTAACTTTTCC 59.526 44.000 0.00 0.00 0.00 3.13
24 25 6.296803 TCCCTCCTCTTCACTTTAACTTTTC 58.703 40.000 0.00 0.00 0.00 2.29
25 26 6.262056 TCCCTCCTCTTCACTTTAACTTTT 57.738 37.500 0.00 0.00 0.00 2.27
26 27 5.906772 TCCCTCCTCTTCACTTTAACTTT 57.093 39.130 0.00 0.00 0.00 2.66
27 28 5.804771 GCATCCCTCCTCTTCACTTTAACTT 60.805 44.000 0.00 0.00 0.00 2.66
28 29 4.323868 GCATCCCTCCTCTTCACTTTAACT 60.324 45.833 0.00 0.00 0.00 2.24
29 30 3.942115 GCATCCCTCCTCTTCACTTTAAC 59.058 47.826 0.00 0.00 0.00 2.01
30 31 3.587061 TGCATCCCTCCTCTTCACTTTAA 59.413 43.478 0.00 0.00 0.00 1.52
31 32 3.181329 TGCATCCCTCCTCTTCACTTTA 58.819 45.455 0.00 0.00 0.00 1.85
32 33 1.988107 TGCATCCCTCCTCTTCACTTT 59.012 47.619 0.00 0.00 0.00 2.66
33 34 1.661463 TGCATCCCTCCTCTTCACTT 58.339 50.000 0.00 0.00 0.00 3.16
34 35 1.489649 CATGCATCCCTCCTCTTCACT 59.510 52.381 0.00 0.00 0.00 3.41
35 36 1.211457 ACATGCATCCCTCCTCTTCAC 59.789 52.381 0.00 0.00 0.00 3.18
36 37 1.211212 CACATGCATCCCTCCTCTTCA 59.789 52.381 0.00 0.00 0.00 3.02
37 38 1.211457 ACACATGCATCCCTCCTCTTC 59.789 52.381 0.00 0.00 0.00 2.87
38 39 1.293062 ACACATGCATCCCTCCTCTT 58.707 50.000 0.00 0.00 0.00 2.85
39 40 2.045524 CTACACATGCATCCCTCCTCT 58.954 52.381 0.00 0.00 0.00 3.69
40 41 1.765314 ACTACACATGCATCCCTCCTC 59.235 52.381 0.00 0.00 0.00 3.71
41 42 1.487976 CACTACACATGCATCCCTCCT 59.512 52.381 0.00 0.00 0.00 3.69
42 43 1.486310 TCACTACACATGCATCCCTCC 59.514 52.381 0.00 0.00 0.00 4.30
43 44 2.432146 TCTCACTACACATGCATCCCTC 59.568 50.000 0.00 0.00 0.00 4.30
44 45 2.433604 CTCTCACTACACATGCATCCCT 59.566 50.000 0.00 0.00 0.00 4.20
45 46 2.169352 ACTCTCACTACACATGCATCCC 59.831 50.000 0.00 0.00 0.00 3.85
46 47 3.118992 TGACTCTCACTACACATGCATCC 60.119 47.826 0.00 0.00 0.00 3.51
47 48 4.115401 TGACTCTCACTACACATGCATC 57.885 45.455 0.00 0.00 0.00 3.91
48 49 4.750021 ATGACTCTCACTACACATGCAT 57.250 40.909 0.00 0.00 0.00 3.96
49 50 4.541973 AATGACTCTCACTACACATGCA 57.458 40.909 0.00 0.00 0.00 3.96
50 51 5.641209 AGAAAATGACTCTCACTACACATGC 59.359 40.000 0.00 0.00 0.00 4.06
51 52 8.939201 ATAGAAAATGACTCTCACTACACATG 57.061 34.615 0.00 0.00 0.00 3.21
52 53 9.593134 GAATAGAAAATGACTCTCACTACACAT 57.407 33.333 0.00 0.00 0.00 3.21
53 54 8.807118 AGAATAGAAAATGACTCTCACTACACA 58.193 33.333 0.00 0.00 0.00 3.72
54 55 9.646427 AAGAATAGAAAATGACTCTCACTACAC 57.354 33.333 0.00 0.00 0.00 2.90
66 67 9.973661 TGGACCTCATTAAAGAATAGAAAATGA 57.026 29.630 0.00 0.00 35.76 2.57
68 69 9.981460 AGTGGACCTCATTAAAGAATAGAAAAT 57.019 29.630 0.00 0.00 0.00 1.82
71 72 9.268282 ACTAGTGGACCTCATTAAAGAATAGAA 57.732 33.333 0.00 0.00 0.00 2.10
72 73 8.696374 CACTAGTGGACCTCATTAAAGAATAGA 58.304 37.037 15.49 0.00 0.00 1.98
73 74 8.696374 TCACTAGTGGACCTCATTAAAGAATAG 58.304 37.037 22.48 0.00 0.00 1.73
74 75 8.603898 TCACTAGTGGACCTCATTAAAGAATA 57.396 34.615 22.48 0.00 0.00 1.75
75 76 7.496346 TCACTAGTGGACCTCATTAAAGAAT 57.504 36.000 22.48 0.00 0.00 2.40
76 77 6.928348 TCACTAGTGGACCTCATTAAAGAA 57.072 37.500 22.48 0.00 0.00 2.52
77 78 7.201920 GCTATCACTAGTGGACCTCATTAAAGA 60.202 40.741 22.48 0.00 0.00 2.52
78 79 6.926272 GCTATCACTAGTGGACCTCATTAAAG 59.074 42.308 22.48 3.96 0.00 1.85
79 80 6.611642 AGCTATCACTAGTGGACCTCATTAAA 59.388 38.462 22.48 0.00 0.00 1.52
80 81 6.136857 AGCTATCACTAGTGGACCTCATTAA 58.863 40.000 22.48 0.00 0.00 1.40
81 82 5.706447 AGCTATCACTAGTGGACCTCATTA 58.294 41.667 22.48 0.13 0.00 1.90
82 83 4.551671 AGCTATCACTAGTGGACCTCATT 58.448 43.478 22.48 0.00 0.00 2.57
83 84 4.191804 AGCTATCACTAGTGGACCTCAT 57.808 45.455 22.48 10.01 0.00 2.90
84 85 3.671740 AGCTATCACTAGTGGACCTCA 57.328 47.619 22.48 2.45 0.00 3.86
85 86 4.402793 TGAAAGCTATCACTAGTGGACCTC 59.597 45.833 22.48 10.59 0.00 3.85
86 87 4.353777 TGAAAGCTATCACTAGTGGACCT 58.646 43.478 22.48 10.93 0.00 3.85
87 88 4.737855 TGAAAGCTATCACTAGTGGACC 57.262 45.455 22.48 8.94 0.00 4.46
88 89 5.525378 CCAATGAAAGCTATCACTAGTGGAC 59.475 44.000 22.48 9.67 30.82 4.02
89 90 5.425217 TCCAATGAAAGCTATCACTAGTGGA 59.575 40.000 22.48 10.25 31.87 4.02
90 91 5.674525 TCCAATGAAAGCTATCACTAGTGG 58.325 41.667 22.48 8.08 30.82 4.00
91 92 6.257411 CACTCCAATGAAAGCTATCACTAGTG 59.743 42.308 17.17 17.17 30.82 2.74
92 93 6.155221 TCACTCCAATGAAAGCTATCACTAGT 59.845 38.462 0.00 0.00 30.82 2.57
93 94 6.577103 TCACTCCAATGAAAGCTATCACTAG 58.423 40.000 0.00 0.00 30.82 2.57
94 95 6.544928 TCACTCCAATGAAAGCTATCACTA 57.455 37.500 0.00 0.00 30.82 2.74
95 96 5.426689 TCACTCCAATGAAAGCTATCACT 57.573 39.130 0.00 0.00 30.82 3.41
96 97 6.500684 TTTCACTCCAATGAAAGCTATCAC 57.499 37.500 0.00 0.00 42.32 3.06
97 98 7.523293 TTTTTCACTCCAATGAAAGCTATCA 57.477 32.000 0.00 0.00 46.44 2.15
118 119 8.851541 AATTTGAGGCATATGTGTTGATTTTT 57.148 26.923 4.29 0.00 0.00 1.94
119 120 9.369904 GTAATTTGAGGCATATGTGTTGATTTT 57.630 29.630 4.29 0.00 0.00 1.82
120 121 8.752187 AGTAATTTGAGGCATATGTGTTGATTT 58.248 29.630 4.29 0.00 0.00 2.17
121 122 8.297470 AGTAATTTGAGGCATATGTGTTGATT 57.703 30.769 4.29 1.96 0.00 2.57
122 123 7.886629 AGTAATTTGAGGCATATGTGTTGAT 57.113 32.000 4.29 0.00 0.00 2.57
123 124 7.701539 AAGTAATTTGAGGCATATGTGTTGA 57.298 32.000 4.29 0.00 0.00 3.18
124 125 8.761575 AAAAGTAATTTGAGGCATATGTGTTG 57.238 30.769 4.29 0.00 0.00 3.33
125 126 9.206870 CAAAAAGTAATTTGAGGCATATGTGTT 57.793 29.630 4.29 0.00 41.73 3.32
126 127 8.367156 ACAAAAAGTAATTTGAGGCATATGTGT 58.633 29.630 4.29 0.00 41.73 3.72
127 128 8.761575 ACAAAAAGTAATTTGAGGCATATGTG 57.238 30.769 4.29 0.00 41.73 3.21
128 129 8.584157 TGACAAAAAGTAATTTGAGGCATATGT 58.416 29.630 4.29 0.00 41.73 2.29
129 130 8.984891 TGACAAAAAGTAATTTGAGGCATATG 57.015 30.769 6.76 0.00 41.73 1.78
130 131 9.590451 CATGACAAAAAGTAATTTGAGGCATAT 57.410 29.630 8.15 0.00 41.73 1.78
131 132 8.801299 TCATGACAAAAAGTAATTTGAGGCATA 58.199 29.630 8.15 0.00 41.73 3.14
132 133 7.669427 TCATGACAAAAAGTAATTTGAGGCAT 58.331 30.769 6.76 3.81 41.73 4.40
133 134 7.048629 TCATGACAAAAAGTAATTTGAGGCA 57.951 32.000 6.76 0.00 41.73 4.75
134 135 6.587608 CCTCATGACAAAAAGTAATTTGAGGC 59.412 38.462 6.76 0.00 41.73 4.70
135 136 6.587608 GCCTCATGACAAAAAGTAATTTGAGG 59.412 38.462 11.42 11.42 41.73 3.86
136 137 7.147312 TGCCTCATGACAAAAAGTAATTTGAG 58.853 34.615 6.76 0.00 41.73 3.02
137 138 7.048629 TGCCTCATGACAAAAAGTAATTTGA 57.951 32.000 6.76 0.00 41.73 2.69
138 139 7.894376 ATGCCTCATGACAAAAAGTAATTTG 57.106 32.000 0.00 0.00 44.11 2.32
139 140 7.754924 CGTATGCCTCATGACAAAAAGTAATTT 59.245 33.333 0.00 0.00 0.00 1.82
140 141 7.094377 ACGTATGCCTCATGACAAAAAGTAATT 60.094 33.333 0.00 0.00 0.00 1.40
141 142 6.374333 ACGTATGCCTCATGACAAAAAGTAAT 59.626 34.615 0.00 0.00 0.00 1.89
142 143 5.703592 ACGTATGCCTCATGACAAAAAGTAA 59.296 36.000 0.00 0.00 0.00 2.24
143 144 5.242434 ACGTATGCCTCATGACAAAAAGTA 58.758 37.500 0.00 0.00 0.00 2.24
144 145 4.072131 ACGTATGCCTCATGACAAAAAGT 58.928 39.130 0.00 0.00 0.00 2.66
145 146 4.685169 ACGTATGCCTCATGACAAAAAG 57.315 40.909 0.00 0.00 0.00 2.27
146 147 6.372937 TGAATACGTATGCCTCATGACAAAAA 59.627 34.615 9.24 0.00 0.00 1.94
147 148 5.877564 TGAATACGTATGCCTCATGACAAAA 59.122 36.000 9.24 0.00 0.00 2.44
148 149 5.423886 TGAATACGTATGCCTCATGACAAA 58.576 37.500 9.24 0.00 0.00 2.83
149 150 5.017294 TGAATACGTATGCCTCATGACAA 57.983 39.130 9.24 0.00 0.00 3.18
150 151 4.664150 TGAATACGTATGCCTCATGACA 57.336 40.909 9.24 0.00 0.00 3.58
151 152 7.226757 CATATGAATACGTATGCCTCATGAC 57.773 40.000 22.76 5.02 38.57 3.06
160 161 6.149308 ACAATGGTGGCATATGAATACGTATG 59.851 38.462 9.24 0.00 44.34 2.39
161 162 6.237901 ACAATGGTGGCATATGAATACGTAT 58.762 36.000 6.97 1.14 0.00 3.06
162 163 5.616270 ACAATGGTGGCATATGAATACGTA 58.384 37.500 6.97 0.00 0.00 3.57
163 164 4.460263 ACAATGGTGGCATATGAATACGT 58.540 39.130 6.97 0.00 0.00 3.57
164 165 5.468409 TGTACAATGGTGGCATATGAATACG 59.532 40.000 6.97 0.00 0.00 3.06
165 166 6.875948 TGTACAATGGTGGCATATGAATAC 57.124 37.500 6.97 1.49 0.00 1.89
166 167 6.072008 GCATGTACAATGGTGGCATATGAATA 60.072 38.462 6.97 0.00 0.00 1.75
167 168 5.279106 GCATGTACAATGGTGGCATATGAAT 60.279 40.000 6.97 0.00 0.00 2.57
168 169 4.037803 GCATGTACAATGGTGGCATATGAA 59.962 41.667 6.97 0.00 0.00 2.57
169 170 3.569277 GCATGTACAATGGTGGCATATGA 59.431 43.478 6.97 0.00 0.00 2.15
170 171 3.305539 GGCATGTACAATGGTGGCATATG 60.306 47.826 14.01 0.00 37.14 1.78
171 172 2.892852 GGCATGTACAATGGTGGCATAT 59.107 45.455 14.01 0.00 37.14 1.78
172 173 2.305928 GGCATGTACAATGGTGGCATA 58.694 47.619 14.01 0.00 37.14 3.14
173 174 1.113788 GGCATGTACAATGGTGGCAT 58.886 50.000 14.01 0.00 37.14 4.40
174 175 0.969917 GGGCATGTACAATGGTGGCA 60.970 55.000 18.87 0.00 38.72 4.92
175 176 0.684153 AGGGCATGTACAATGGTGGC 60.684 55.000 11.25 11.25 36.52 5.01
176 177 1.851304 AAGGGCATGTACAATGGTGG 58.149 50.000 0.00 0.00 0.00 4.61
177 178 5.008613 GTGTATAAGGGCATGTACAATGGTG 59.991 44.000 0.00 0.00 0.00 4.17
178 179 5.130350 GTGTATAAGGGCATGTACAATGGT 58.870 41.667 0.00 0.00 0.00 3.55
179 180 4.518970 GGTGTATAAGGGCATGTACAATGG 59.481 45.833 0.00 0.00 0.00 3.16
180 181 4.518970 GGGTGTATAAGGGCATGTACAATG 59.481 45.833 0.00 0.12 0.00 2.82
181 182 4.167113 TGGGTGTATAAGGGCATGTACAAT 59.833 41.667 0.00 0.00 0.00 2.71
182 183 3.523972 TGGGTGTATAAGGGCATGTACAA 59.476 43.478 0.00 0.00 0.00 2.41
183 184 3.116174 TGGGTGTATAAGGGCATGTACA 58.884 45.455 0.00 0.00 0.00 2.90
184 185 3.849563 TGGGTGTATAAGGGCATGTAC 57.150 47.619 0.00 0.00 0.00 2.90
185 186 4.413851 TCATTGGGTGTATAAGGGCATGTA 59.586 41.667 0.00 0.00 0.00 2.29
186 187 3.204158 TCATTGGGTGTATAAGGGCATGT 59.796 43.478 0.00 0.00 0.00 3.21
187 188 3.831323 TCATTGGGTGTATAAGGGCATG 58.169 45.455 0.00 0.00 0.00 4.06
188 189 4.079212 ACTTCATTGGGTGTATAAGGGCAT 60.079 41.667 0.00 0.00 0.00 4.40
189 190 3.268334 ACTTCATTGGGTGTATAAGGGCA 59.732 43.478 0.00 0.00 0.00 5.36
190 191 3.898482 ACTTCATTGGGTGTATAAGGGC 58.102 45.455 0.00 0.00 0.00 5.19
191 192 7.079451 AGATACTTCATTGGGTGTATAAGGG 57.921 40.000 0.00 0.00 0.00 3.95
198 199 9.920946 ACATAAAATAGATACTTCATTGGGTGT 57.079 29.630 0.00 0.00 0.00 4.16
212 213 9.720769 CGGACCAACCTTATACATAAAATAGAT 57.279 33.333 0.00 0.00 36.31 1.98
213 214 8.152246 CCGGACCAACCTTATACATAAAATAGA 58.848 37.037 0.00 0.00 36.31 1.98
214 215 7.389607 CCCGGACCAACCTTATACATAAAATAG 59.610 40.741 0.73 0.00 36.31 1.73
215 216 7.072202 TCCCGGACCAACCTTATACATAAAATA 59.928 37.037 0.73 0.00 36.31 1.40
216 217 6.066032 CCCGGACCAACCTTATACATAAAAT 58.934 40.000 0.73 0.00 36.31 1.82
217 218 5.191323 TCCCGGACCAACCTTATACATAAAA 59.809 40.000 0.73 0.00 36.31 1.52
223 224 2.113807 ACTCCCGGACCAACCTTATAC 58.886 52.381 0.73 0.00 36.31 1.47
235 236 6.123045 AGAAAGAAATTCTAAACTCCCGGA 57.877 37.500 0.73 0.00 46.65 5.14
260 261 2.047655 GTGGGTCGCACGGAATCA 60.048 61.111 4.06 0.00 0.00 2.57
266 267 0.725117 GAATTAAGGTGGGTCGCACG 59.275 55.000 13.31 0.00 0.00 5.34
272 273 2.640826 TCAACGAGGAATTAAGGTGGGT 59.359 45.455 0.00 0.00 0.00 4.51
289 290 1.334869 CTTGTTCCTGCACTGGTCAAC 59.665 52.381 0.00 0.00 0.00 3.18
484 488 9.688592 GCAACGACATAAACTATATACTACCTT 57.311 33.333 0.00 0.00 0.00 3.50
485 489 9.075678 AGCAACGACATAAACTATATACTACCT 57.924 33.333 0.00 0.00 0.00 3.08
486 490 9.688592 AAGCAACGACATAAACTATATACTACC 57.311 33.333 0.00 0.00 0.00 3.18
535 585 3.748568 CGAGACCCTTTTTCTCTCCTTTG 59.251 47.826 0.00 0.00 37.89 2.77
704 2083 2.750237 GGCGGCTTTACTGTGGGG 60.750 66.667 0.00 0.00 0.00 4.96
813 2198 1.541620 GGAAGGGGAGGAAGGGTGT 60.542 63.158 0.00 0.00 0.00 4.16
909 2294 1.075600 GGGACAGAGGGAGGGAGAG 60.076 68.421 0.00 0.00 0.00 3.20
941 2331 1.149782 TGTCAGAGGGAGAGGGGAGT 61.150 60.000 0.00 0.00 0.00 3.85
945 2335 2.422231 CGCTGTCAGAGGGAGAGGG 61.422 68.421 3.32 0.00 42.17 4.30
948 2338 3.071206 GGCGCTGTCAGAGGGAGA 61.071 66.667 7.64 0.00 36.74 3.71
949 2339 4.154347 GGGCGCTGTCAGAGGGAG 62.154 72.222 7.64 0.00 36.74 4.30
1006 2409 2.409651 CAGGAGTAGCGCGAGTCC 59.590 66.667 30.56 30.56 39.00 3.85
2193 3599 2.436824 GGAGGCGGAGAAGGCAAC 60.437 66.667 0.00 0.00 39.37 4.17
2194 3600 2.927856 TGGAGGCGGAGAAGGCAA 60.928 61.111 0.00 0.00 39.37 4.52
2195 3601 3.706373 GTGGAGGCGGAGAAGGCA 61.706 66.667 0.00 0.00 39.37 4.75
2196 3602 4.475135 GGTGGAGGCGGAGAAGGC 62.475 72.222 0.00 0.00 0.00 4.35
2197 3603 2.317149 GATGGTGGAGGCGGAGAAGG 62.317 65.000 0.00 0.00 0.00 3.46
2198 3604 1.144936 GATGGTGGAGGCGGAGAAG 59.855 63.158 0.00 0.00 0.00 2.85
2244 3650 2.125106 GGTGGTGGAGATGGCGAC 60.125 66.667 0.00 0.00 0.00 5.19
2841 4247 2.978010 GTGGTGGACTGGCGTTGG 60.978 66.667 0.00 0.00 0.00 3.77
2842 4248 1.961277 GAGTGGTGGACTGGCGTTG 60.961 63.158 0.00 0.00 33.83 4.10
2843 4249 2.426023 GAGTGGTGGACTGGCGTT 59.574 61.111 0.00 0.00 33.83 4.84
2844 4250 2.842462 TGAGTGGTGGACTGGCGT 60.842 61.111 0.00 0.00 33.83 5.68
2845 4251 2.357517 GTGAGTGGTGGACTGGCG 60.358 66.667 0.00 0.00 33.83 5.69
2996 4486 1.290009 GGACACAGGTGGCAATTGC 59.710 57.895 22.47 22.47 41.42 3.56
2997 4487 1.865788 CGGGACACAGGTGGCAATTG 61.866 60.000 7.68 0.00 41.42 2.32
2998 4488 1.603455 CGGGACACAGGTGGCAATT 60.603 57.895 7.68 0.00 41.42 2.32
3143 4638 5.447778 ACCATGTCTTCCTTCAGATGATT 57.552 39.130 0.00 0.00 31.83 2.57
3214 4709 2.621338 AGCATGACAATGACCACGTAG 58.379 47.619 0.00 0.00 35.67 3.51
3293 4788 6.980397 ACAAATCATAATCCAGAAAATTCCGC 59.020 34.615 0.00 0.00 0.00 5.54
3393 4888 7.333423 TCTCAAACTCTTATTATTCACAACCCG 59.667 37.037 0.00 0.00 0.00 5.28
3546 5049 9.323985 AGATAAATAACACTCTGAATCTCTTGC 57.676 33.333 0.00 0.00 0.00 4.01
3569 5074 9.232473 GAAGTAACTGGGATACAAAAAGAAGAT 57.768 33.333 0.00 0.00 39.74 2.40
3575 5080 7.064229 ACCAAGAAGTAACTGGGATACAAAAA 58.936 34.615 0.00 0.00 34.76 1.94
3674 5179 6.142320 GGAAAGACATGACAAAATTCGTCAAC 59.858 38.462 13.00 8.81 45.91 3.18
3904 5440 8.432805 GGATTCTAGATTTTTGATACAGAGGGA 58.567 37.037 0.00 0.00 0.00 4.20
3920 5456 5.263872 ACGGAGGAGTATGGATTCTAGAT 57.736 43.478 0.00 0.00 0.00 1.98
3931 5467 8.246430 TCTTACATTTTGATACGGAGGAGTAT 57.754 34.615 0.00 0.00 39.77 2.12
3933 5469 6.540438 TCTTACATTTTGATACGGAGGAGT 57.460 37.500 0.00 0.00 0.00 3.85
3934 5470 7.843490 TTTCTTACATTTTGATACGGAGGAG 57.157 36.000 0.00 0.00 0.00 3.69
3935 5471 8.801882 AATTTCTTACATTTTGATACGGAGGA 57.198 30.769 0.00 0.00 0.00 3.71
3936 5472 9.855021 AAAATTTCTTACATTTTGATACGGAGG 57.145 29.630 0.00 0.00 33.47 4.30
3946 5482 9.034544 GCAGTGTCAGAAAATTTCTTACATTTT 57.965 29.630 21.11 10.67 43.45 1.82
3995 5537 9.476928 ACTGATGTACTACCTCTGTAACTTAAT 57.523 33.333 0.00 0.00 0.00 1.40
3996 5538 8.874744 ACTGATGTACTACCTCTGTAACTTAA 57.125 34.615 0.00 0.00 0.00 1.85
3997 5539 9.388506 GTACTGATGTACTACCTCTGTAACTTA 57.611 37.037 10.67 0.00 44.08 2.24
3998 5540 7.886970 TGTACTGATGTACTACCTCTGTAACTT 59.113 37.037 10.67 0.00 46.70 2.66
3999 5541 7.400439 TGTACTGATGTACTACCTCTGTAACT 58.600 38.462 10.67 0.00 46.70 2.24
4000 5542 7.621428 TGTACTGATGTACTACCTCTGTAAC 57.379 40.000 10.67 7.68 46.70 2.50
4001 5543 8.640063 TTTGTACTGATGTACTACCTCTGTAA 57.360 34.615 10.67 0.64 46.70 2.41
4011 5553 5.611374 ACAGTTGCTTTGTACTGATGTACT 58.389 37.500 9.03 0.00 46.70 2.73
4018 5560 2.348872 CGCAGACAGTTGCTTTGTACTG 60.349 50.000 0.00 0.00 45.61 2.74
4024 5566 1.867233 CAGTACGCAGACAGTTGCTTT 59.133 47.619 6.27 0.00 41.90 3.51
4075 5623 5.405797 GGCAAATGAAAAGGAACTCAGATC 58.594 41.667 0.00 0.00 38.49 2.75


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

AutoCloner maintained by Alex Coulton.