Multiple sequence alignment - TraesCS3D01G015900

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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 TraesCS3D01G015900 chr3D 100.000 4114 0 0 1 4114 5648356 5652469 0.000000e+00 7598.0
1 TraesCS3D01G015900 chr3A 89.418 3109 190 69 351 3380 15620677 15617629 0.000000e+00 3790.0
2 TraesCS3D01G015900 chr3A 89.379 499 29 13 3385 3878 15617585 15617106 1.260000e-169 606.0
3 TraesCS3D01G015900 chr3A 84.400 500 45 16 2457 2939 11620361 11619878 1.040000e-125 460.0
4 TraesCS3D01G015900 chr3A 85.468 406 49 7 1065 1461 17226115 17225711 8.230000e-112 414.0
5 TraesCS3D01G015900 chr3A 90.747 281 17 5 2935 3210 11617582 11617306 2.340000e-97 366.0
6 TraesCS3D01G015900 chr3A 93.525 139 7 2 3977 4114 15616662 15616525 5.390000e-49 206.0
7 TraesCS3D01G015900 chr3A 90.217 92 5 2 189 276 15620780 15620689 2.600000e-22 117.0
8 TraesCS3D01G015900 chr3A 100.000 37 0 0 1459 1495 17225695 17225659 7.380000e-08 69.4
9 TraesCS3D01G015900 chrUn 91.281 2741 161 44 1029 3737 260890839 260888145 0.000000e+00 3666.0
10 TraesCS3D01G015900 chrUn 91.281 2741 161 44 1029 3737 263767926 263770620 0.000000e+00 3666.0
11 TraesCS3D01G015900 chrUn 93.736 2187 92 18 1543 3717 319812508 319810355 0.000000e+00 3238.0
12 TraesCS3D01G015900 chrUn 89.636 1650 139 22 1677 3304 382717510 382719149 0.000000e+00 2071.0
13 TraesCS3D01G015900 chrUn 86.500 800 64 21 438 1199 35834600 35833807 0.000000e+00 839.0
14 TraesCS3D01G015900 chrUn 83.231 811 54 28 215 962 260891774 260890983 0.000000e+00 669.0
15 TraesCS3D01G015900 chrUn 83.231 811 54 28 215 962 263766991 263767782 0.000000e+00 669.0
16 TraesCS3D01G015900 chrUn 87.918 389 37 8 3732 4114 260886795 260886411 2.260000e-122 449.0
17 TraesCS3D01G015900 chrUn 87.918 389 37 8 3732 4114 263771970 263772354 2.260000e-122 449.0
18 TraesCS3D01G015900 chrUn 87.661 389 38 8 3732 4114 36008096 36007712 1.050000e-120 444.0
19 TraesCS3D01G015900 chrUn 85.926 405 27 18 3334 3737 36009862 36009487 4.950000e-109 405.0
20 TraesCS3D01G015900 chrUn 80.913 241 14 14 215 441 35835095 35834873 1.180000e-35 161.0
21 TraesCS3D01G015900 chr3B 90.424 2715 171 52 1034 3717 12304980 12302324 0.000000e+00 3491.0
22 TraesCS3D01G015900 chr3B 92.563 1748 102 11 1542 3272 27873574 27875310 0.000000e+00 2483.0
23 TraesCS3D01G015900 chr3B 87.115 1754 161 28 1298 3014 12121675 12123400 0.000000e+00 1927.0
24 TraesCS3D01G015900 chr3B 89.809 1521 125 20 1968 3467 12141663 12143174 0.000000e+00 1923.0
25 TraesCS3D01G015900 chr3B 86.726 678 57 8 1298 1949 12140911 12141581 0.000000e+00 723.0
26 TraesCS3D01G015900 chr3B 88.006 642 27 15 3268 3904 27877244 27877840 0.000000e+00 713.0
27 TraesCS3D01G015900 chr3B 92.365 406 23 7 996 1397 27872779 27873180 4.610000e-159 571.0
28 TraesCS3D01G015900 chr3B 89.438 445 34 7 3465 3904 12143254 12143690 2.160000e-152 549.0
29 TraesCS3D01G015900 chr3B 85.159 566 35 22 309 825 12120459 12121024 6.050000e-148 534.0
30 TraesCS3D01G015900 chr3B 85.159 566 35 22 309 825 12139442 12140007 6.050000e-148 534.0
31 TraesCS3D01G015900 chr3B 86.715 414 27 17 3334 3746 12298048 12297662 6.320000e-118 435.0
32 TraesCS3D01G015900 chr3B 86.933 375 39 6 3745 4113 12297308 12296938 2.960000e-111 412.0
33 TraesCS3D01G015900 chr3B 81.087 497 47 26 507 962 27872176 27872666 1.820000e-93 353.0
34 TraesCS3D01G015900 chr3B 78.995 557 44 46 461 962 12305676 12305138 3.090000e-81 313.0
35 TraesCS3D01G015900 chr3B 85.374 294 22 11 189 465 12306352 12306063 6.730000e-73 285.0
36 TraesCS3D01G015900 chr3B 94.268 157 6 2 3959 4114 27877841 27877995 1.910000e-58 237.0
37 TraesCS3D01G015900 chr3B 93.082 159 6 2 3959 4114 12143691 12143847 1.150000e-55 228.0
38 TraesCS3D01G015900 chr3B 80.755 265 19 19 189 436 27871513 27871762 1.180000e-40 178.0
39 TraesCS3D01G015900 chr3B 87.302 126 10 2 843 962 12121138 12121263 5.550000e-29 139.0
40 TraesCS3D01G015900 chr3B 87.302 126 10 2 843 962 12140121 12140246 5.550000e-29 139.0
41 TraesCS3D01G015900 chr5D 85.885 503 71 0 1601 2103 557947623 557947121 1.680000e-148 536.0
42 TraesCS3D01G015900 chr5D 90.049 412 37 3 1041 1450 557948154 557947745 7.830000e-147 531.0
43 TraesCS3D01G015900 chr5B 89.499 419 39 4 1035 1451 705055330 705054915 3.640000e-145 525.0
44 TraesCS3D01G015900 chr4A 88.863 422 47 0 1029 1450 610034527 610034948 1.690000e-143 520.0
45 TraesCS3D01G015900 chr4A 94.915 59 3 0 767 825 559496146 559496088 4.380000e-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 TraesCS3D01G015900 chr3D 5648356 5652469 4113 False 7598.000000 7598 100.000000 1 4114 1 chr3D.!!$F1 4113
1 TraesCS3D01G015900 chr3A 15616525 15620780 4255 True 1179.750000 3790 90.634750 189 4114 4 chr3A.!!$R2 3925
2 TraesCS3D01G015900 chr3A 11617306 11620361 3055 True 413.000000 460 87.573500 2457 3210 2 chr3A.!!$R1 753
3 TraesCS3D01G015900 chrUn 319810355 319812508 2153 True 3238.000000 3238 93.736000 1543 3717 1 chrUn.!!$R1 2174
4 TraesCS3D01G015900 chrUn 382717510 382719149 1639 False 2071.000000 2071 89.636000 1677 3304 1 chrUn.!!$F1 1627
5 TraesCS3D01G015900 chrUn 260886411 260891774 5363 True 1594.666667 3666 87.476667 215 4114 3 chrUn.!!$R4 3899
6 TraesCS3D01G015900 chrUn 263766991 263772354 5363 False 1594.666667 3666 87.476667 215 4114 3 chrUn.!!$F2 3899
7 TraesCS3D01G015900 chrUn 35833807 35835095 1288 True 500.000000 839 83.706500 215 1199 2 chrUn.!!$R2 984
8 TraesCS3D01G015900 chrUn 36007712 36009862 2150 True 424.500000 444 86.793500 3334 4114 2 chrUn.!!$R3 780
9 TraesCS3D01G015900 chr3B 12302324 12306352 4028 True 1363.000000 3491 84.931000 189 3717 3 chr3B.!!$R2 3528
10 TraesCS3D01G015900 chr3B 12120459 12123400 2941 False 866.666667 1927 86.525333 309 3014 3 chr3B.!!$F1 2705
11 TraesCS3D01G015900 chr3B 27871513 27877995 6482 False 755.833333 2483 88.174000 189 4114 6 chr3B.!!$F3 3925
12 TraesCS3D01G015900 chr3B 12139442 12143847 4405 False 682.666667 1923 88.586000 309 4114 6 chr3B.!!$F2 3805
13 TraesCS3D01G015900 chr3B 12296938 12298048 1110 True 423.500000 435 86.824000 3334 4113 2 chr3B.!!$R1 779
14 TraesCS3D01G015900 chr5D 557947121 557948154 1033 True 533.500000 536 87.967000 1041 2103 2 chr5D.!!$R1 1062

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
206 207 0.318784 GATCAACCTACGGCGGCTAG 60.319 60.0 13.24 4.54 0.0 3.42 F
1377 3047 0.850883 ACAACCCCATCATCACCCCT 60.851 55.0 0.00 0.00 0.0 4.79 F
2124 4190 0.871722 TTACGCTGCCACATGAACAC 59.128 50.0 0.00 0.00 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 3597 1.546323 CCAACCTCCAGTGTCTGCAAT 60.546 52.381 0.00 0.00 0.00 3.56 R
2250 4322 0.033796 CCACTGGCCATTGGATCAGT 60.034 55.000 33.16 19.81 38.52 3.41 R
3885 11946 0.524862 CGAGATTGCTGGCAAAAGCT 59.475 50.000 12.06 9.62 43.90 3.74 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
25 26 8.897872 GGGTCTTTCTAATCCGACATTATAAA 57.102 34.615 0.00 0.00 0.00 1.40
26 27 9.333724 GGGTCTTTCTAATCCGACATTATAAAA 57.666 33.333 0.00 0.00 0.00 1.52
50 51 9.521503 AAAAATTCAAGTTCTTAGTGCTTTCTC 57.478 29.630 0.00 0.00 0.00 2.87
51 52 8.457238 AAATTCAAGTTCTTAGTGCTTTCTCT 57.543 30.769 0.00 0.00 0.00 3.10
52 53 7.665561 ATTCAAGTTCTTAGTGCTTTCTCTC 57.334 36.000 0.00 0.00 0.00 3.20
53 54 5.223382 TCAAGTTCTTAGTGCTTTCTCTCG 58.777 41.667 0.00 0.00 0.00 4.04
54 55 3.580731 AGTTCTTAGTGCTTTCTCTCGC 58.419 45.455 0.00 0.00 0.00 5.03
55 56 3.005897 AGTTCTTAGTGCTTTCTCTCGCA 59.994 43.478 0.00 0.00 0.00 5.10
56 57 3.660501 TCTTAGTGCTTTCTCTCGCAA 57.339 42.857 0.00 0.00 37.97 4.85
57 58 3.990092 TCTTAGTGCTTTCTCTCGCAAA 58.010 40.909 0.00 0.00 37.97 3.68
58 59 3.990469 TCTTAGTGCTTTCTCTCGCAAAG 59.010 43.478 0.00 0.00 37.97 2.77
66 67 5.536554 CTTTCTCTCGCAAAGCTAAATCA 57.463 39.130 0.00 0.00 0.00 2.57
67 68 5.931532 CTTTCTCTCGCAAAGCTAAATCAA 58.068 37.500 0.00 0.00 0.00 2.57
68 69 6.500684 TTTCTCTCGCAAAGCTAAATCAAT 57.499 33.333 0.00 0.00 0.00 2.57
69 70 5.725110 TCTCTCGCAAAGCTAAATCAATC 57.275 39.130 0.00 0.00 0.00 2.67
70 71 5.178061 TCTCTCGCAAAGCTAAATCAATCA 58.822 37.500 0.00 0.00 0.00 2.57
71 72 5.643348 TCTCTCGCAAAGCTAAATCAATCAA 59.357 36.000 0.00 0.00 0.00 2.57
72 73 5.872635 TCTCGCAAAGCTAAATCAATCAAG 58.127 37.500 0.00 0.00 0.00 3.02
73 74 4.414852 TCGCAAAGCTAAATCAATCAAGC 58.585 39.130 0.00 0.00 35.16 4.01
74 75 4.156556 TCGCAAAGCTAAATCAATCAAGCT 59.843 37.500 0.00 0.00 46.96 3.74
75 76 4.498323 CGCAAAGCTAAATCAATCAAGCTC 59.502 41.667 0.00 0.00 44.30 4.09
76 77 5.648572 GCAAAGCTAAATCAATCAAGCTCT 58.351 37.500 0.00 0.00 44.30 4.09
77 78 6.457392 CGCAAAGCTAAATCAATCAAGCTCTA 60.457 38.462 0.00 0.00 44.30 2.43
78 79 6.911511 GCAAAGCTAAATCAATCAAGCTCTAG 59.088 38.462 0.00 0.00 44.30 2.43
79 80 7.416022 CAAAGCTAAATCAATCAAGCTCTAGG 58.584 38.462 0.00 0.00 44.30 3.02
80 81 6.245890 AGCTAAATCAATCAAGCTCTAGGT 57.754 37.500 0.00 0.00 41.35 3.08
81 82 6.657875 AGCTAAATCAATCAAGCTCTAGGTT 58.342 36.000 0.00 0.00 41.35 3.50
82 83 7.796054 AGCTAAATCAATCAAGCTCTAGGTTA 58.204 34.615 0.00 0.00 41.35 2.85
83 84 7.930865 AGCTAAATCAATCAAGCTCTAGGTTAG 59.069 37.037 0.00 0.00 41.35 2.34
84 85 7.713073 GCTAAATCAATCAAGCTCTAGGTTAGT 59.287 37.037 0.00 0.00 33.98 2.24
86 87 8.950208 AAATCAATCAAGCTCTAGGTTAGTAC 57.050 34.615 0.00 0.00 33.98 2.73
87 88 7.661536 ATCAATCAAGCTCTAGGTTAGTACA 57.338 36.000 0.00 0.00 33.98 2.90
88 89 6.864342 TCAATCAAGCTCTAGGTTAGTACAC 58.136 40.000 0.00 0.00 33.98 2.90
89 90 4.959596 TCAAGCTCTAGGTTAGTACACG 57.040 45.455 0.00 0.00 33.98 4.49
90 91 4.330250 TCAAGCTCTAGGTTAGTACACGT 58.670 43.478 0.00 0.00 33.98 4.49
91 92 5.491070 TCAAGCTCTAGGTTAGTACACGTA 58.509 41.667 0.00 0.00 33.98 3.57
92 93 5.352569 TCAAGCTCTAGGTTAGTACACGTAC 59.647 44.000 0.00 0.00 33.98 3.67
93 94 3.868077 AGCTCTAGGTTAGTACACGTACG 59.132 47.826 15.01 15.01 40.80 3.67
94 95 3.865745 GCTCTAGGTTAGTACACGTACGA 59.134 47.826 24.41 0.00 40.80 3.43
95 96 4.330074 GCTCTAGGTTAGTACACGTACGAA 59.670 45.833 24.41 0.80 40.80 3.85
96 97 5.163854 GCTCTAGGTTAGTACACGTACGAAA 60.164 44.000 24.41 3.39 40.80 3.46
97 98 6.457528 GCTCTAGGTTAGTACACGTACGAAAT 60.458 42.308 24.41 9.05 40.80 2.17
98 99 7.377766 TCTAGGTTAGTACACGTACGAAATT 57.622 36.000 24.41 5.93 40.80 1.82
99 100 7.816640 TCTAGGTTAGTACACGTACGAAATTT 58.183 34.615 24.41 6.91 40.80 1.82
100 101 6.695292 AGGTTAGTACACGTACGAAATTTG 57.305 37.500 24.41 11.87 40.80 2.32
101 102 6.215845 AGGTTAGTACACGTACGAAATTTGT 58.784 36.000 24.41 17.32 40.80 2.83
102 103 6.701400 AGGTTAGTACACGTACGAAATTTGTT 59.299 34.615 24.41 3.95 40.80 2.83
103 104 7.865385 AGGTTAGTACACGTACGAAATTTGTTA 59.135 33.333 24.41 2.97 40.80 2.41
104 105 8.484008 GGTTAGTACACGTACGAAATTTGTTAA 58.516 33.333 24.41 8.81 40.80 2.01
105 106 9.842444 GTTAGTACACGTACGAAATTTGTTAAA 57.158 29.630 24.41 7.55 40.80 1.52
106 107 9.842444 TTAGTACACGTACGAAATTTGTTAAAC 57.158 29.630 24.41 10.27 40.80 2.01
107 108 7.056800 AGTACACGTACGAAATTTGTTAAACG 58.943 34.615 24.41 5.81 40.80 3.60
108 109 6.030379 ACACGTACGAAATTTGTTAAACGA 57.970 33.333 24.41 0.00 33.59 3.85
109 110 6.473521 ACACGTACGAAATTTGTTAAACGAA 58.526 32.000 24.41 0.00 33.59 3.85
110 111 6.624526 ACACGTACGAAATTTGTTAAACGAAG 59.375 34.615 24.41 7.90 33.59 3.79
111 112 6.840292 CACGTACGAAATTTGTTAAACGAAGA 59.160 34.615 24.41 0.00 33.59 2.87
112 113 7.056450 CACGTACGAAATTTGTTAAACGAAGAG 59.944 37.037 24.41 0.00 33.59 2.85
113 114 6.513991 CGTACGAAATTTGTTAAACGAAGAGG 59.486 38.462 10.44 0.00 0.00 3.69
114 115 5.209977 ACGAAATTTGTTAAACGAAGAGGC 58.790 37.500 0.00 0.00 0.00 4.70
115 116 5.209240 CGAAATTTGTTAAACGAAGAGGCA 58.791 37.500 0.00 0.00 0.00 4.75
116 117 5.115021 CGAAATTTGTTAAACGAAGAGGCAC 59.885 40.000 0.00 0.00 0.00 5.01
117 118 3.595709 TTTGTTAAACGAAGAGGCACG 57.404 42.857 0.00 0.00 0.00 5.34
118 119 2.228138 TGTTAAACGAAGAGGCACGT 57.772 45.000 0.00 0.00 44.57 4.49
119 120 1.862201 TGTTAAACGAAGAGGCACGTG 59.138 47.619 12.28 12.28 42.43 4.49
120 121 0.863144 TTAAACGAAGAGGCACGTGC 59.137 50.000 32.15 32.15 42.43 5.34
121 122 1.279527 TAAACGAAGAGGCACGTGCG 61.280 55.000 32.35 20.31 42.43 5.34
124 125 3.121030 GAAGAGGCACGTGCGCAT 61.121 61.111 32.35 21.44 43.26 4.73
125 126 3.372676 GAAGAGGCACGTGCGCATG 62.373 63.158 32.35 27.53 43.26 4.06
136 137 3.126879 GCGCATGCAGCTACCACA 61.127 61.111 19.57 0.00 42.61 4.17
137 138 3.095911 CGCATGCAGCTACCACAG 58.904 61.111 19.57 0.00 42.61 3.66
138 139 2.466982 CGCATGCAGCTACCACAGG 61.467 63.158 19.57 0.00 42.61 4.00
139 140 1.078214 GCATGCAGCTACCACAGGA 60.078 57.895 14.21 0.00 41.15 3.86
140 141 0.677731 GCATGCAGCTACCACAGGAA 60.678 55.000 14.21 0.00 41.15 3.36
141 142 1.825090 CATGCAGCTACCACAGGAAA 58.175 50.000 0.00 0.00 0.00 3.13
142 143 1.470098 CATGCAGCTACCACAGGAAAC 59.530 52.381 0.00 0.00 0.00 2.78
143 144 0.472044 TGCAGCTACCACAGGAAACA 59.528 50.000 0.00 0.00 0.00 2.83
144 145 1.073763 TGCAGCTACCACAGGAAACAT 59.926 47.619 0.00 0.00 0.00 2.71
145 146 1.740025 GCAGCTACCACAGGAAACATC 59.260 52.381 0.00 0.00 0.00 3.06
146 147 2.002586 CAGCTACCACAGGAAACATCG 58.997 52.381 0.00 0.00 0.00 3.84
147 148 1.623811 AGCTACCACAGGAAACATCGT 59.376 47.619 0.00 0.00 0.00 3.73
148 149 2.829720 AGCTACCACAGGAAACATCGTA 59.170 45.455 0.00 0.00 0.00 3.43
149 150 3.451178 AGCTACCACAGGAAACATCGTAT 59.549 43.478 0.00 0.00 0.00 3.06
150 151 4.647853 AGCTACCACAGGAAACATCGTATA 59.352 41.667 0.00 0.00 0.00 1.47
151 152 4.743644 GCTACCACAGGAAACATCGTATAC 59.256 45.833 0.00 0.00 0.00 1.47
152 153 4.133013 ACCACAGGAAACATCGTATACC 57.867 45.455 0.00 0.00 0.00 2.73
153 154 3.773119 ACCACAGGAAACATCGTATACCT 59.227 43.478 0.00 0.00 0.00 3.08
154 155 4.957954 ACCACAGGAAACATCGTATACCTA 59.042 41.667 0.00 0.00 0.00 3.08
155 156 5.163478 ACCACAGGAAACATCGTATACCTAC 60.163 44.000 0.00 0.00 0.00 3.18
156 157 5.163488 CCACAGGAAACATCGTATACCTACA 60.163 44.000 0.00 0.00 0.00 2.74
157 158 6.462487 CCACAGGAAACATCGTATACCTACAT 60.462 42.308 0.00 0.00 0.00 2.29
158 159 6.420903 CACAGGAAACATCGTATACCTACATG 59.579 42.308 0.00 0.00 0.00 3.21
159 160 5.405571 CAGGAAACATCGTATACCTACATGC 59.594 44.000 0.00 0.00 0.00 4.06
160 161 5.069914 AGGAAACATCGTATACCTACATGCA 59.930 40.000 0.00 0.00 0.00 3.96
161 162 5.932303 GGAAACATCGTATACCTACATGCAT 59.068 40.000 0.00 0.00 0.00 3.96
162 163 7.039293 AGGAAACATCGTATACCTACATGCATA 60.039 37.037 0.00 0.00 0.00 3.14
163 164 7.764443 GGAAACATCGTATACCTACATGCATAT 59.236 37.037 0.00 0.00 0.00 1.78
164 165 9.151471 GAAACATCGTATACCTACATGCATATT 57.849 33.333 0.00 0.00 0.00 1.28
165 166 8.703604 AACATCGTATACCTACATGCATATTC 57.296 34.615 0.00 0.00 0.00 1.75
166 167 7.836842 ACATCGTATACCTACATGCATATTCA 58.163 34.615 0.00 0.00 0.00 2.57
167 168 8.478066 ACATCGTATACCTACATGCATATTCAT 58.522 33.333 0.00 0.00 0.00 2.57
168 169 8.758715 CATCGTATACCTACATGCATATTCATG 58.241 37.037 13.01 13.01 46.86 3.07
183 184 6.549061 CATATTCATGTATGCATTCCGAAGG 58.451 40.000 3.54 0.00 41.16 3.46
184 185 2.849942 TCATGTATGCATTCCGAAGGG 58.150 47.619 3.54 0.00 40.42 3.95
185 186 2.437651 TCATGTATGCATTCCGAAGGGA 59.562 45.455 3.54 0.00 43.84 4.20
186 187 2.810274 CATGTATGCATTCCGAAGGGAG 59.190 50.000 3.54 0.00 41.11 4.30
187 188 4.362407 CATGTATGCATTCCGAAGGGAGG 61.362 52.174 3.54 0.00 41.11 4.30
206 207 0.318784 GATCAACCTACGGCGGCTAG 60.319 60.000 13.24 4.54 0.00 3.42
324 354 0.869730 GTGGCACGTACGGTCAAATT 59.130 50.000 21.06 0.00 0.00 1.82
445 776 1.004610 CATGCGTGCGTTCTTATCCAG 60.005 52.381 0.00 0.00 0.00 3.86
502 1232 3.631346 GGAACCCTAGGATCTCAGTCCTT 60.631 52.174 11.48 0.00 46.45 3.36
503 1233 3.786213 ACCCTAGGATCTCAGTCCTTT 57.214 47.619 11.48 0.00 46.45 3.11
508 1613 3.601443 AGGATCTCAGTCCTTTGTTCG 57.399 47.619 0.00 0.00 46.45 3.95
587 1709 2.244486 TTGCTCACTCATCTCCTCCT 57.756 50.000 0.00 0.00 0.00 3.69
588 1710 1.482954 TGCTCACTCATCTCCTCCTG 58.517 55.000 0.00 0.00 0.00 3.86
589 1711 1.006400 TGCTCACTCATCTCCTCCTGA 59.994 52.381 0.00 0.00 0.00 3.86
609 1750 5.419760 TGATCCTTCGAGTACGTAGAATG 57.580 43.478 0.00 0.00 38.78 2.67
632 1773 1.085715 AGGGTGTACTCCTGAGAGGT 58.914 55.000 13.44 0.00 45.11 3.85
646 1787 2.025416 TGAGAGGTTGAGAGGAGAGGAG 60.025 54.545 0.00 0.00 0.00 3.69
855 2104 7.969536 ATATATCCTCTGCATGTTTGTGTAC 57.030 36.000 0.00 0.00 0.00 2.90
860 2109 2.741517 TCTGCATGTTTGTGTACCATCG 59.258 45.455 0.00 0.00 0.00 3.84
865 2114 4.320202 GCATGTTTGTGTACCATCGTCTTT 60.320 41.667 0.00 0.00 0.00 2.52
929 2190 2.508526 GCATTGACCTATCCCATGACC 58.491 52.381 0.00 0.00 0.00 4.02
962 2223 3.753294 ATCAGATCCCAATGGTACGTC 57.247 47.619 0.00 0.00 0.00 4.34
963 2224 2.747177 TCAGATCCCAATGGTACGTCT 58.253 47.619 0.00 0.00 0.00 4.18
965 2238 3.889538 TCAGATCCCAATGGTACGTCTAG 59.110 47.826 0.00 0.00 0.00 2.43
972 2245 6.186957 TCCCAATGGTACGTCTAGTAACTAA 58.813 40.000 0.00 0.00 43.35 2.24
975 2248 8.295288 CCCAATGGTACGTCTAGTAACTAATAG 58.705 40.741 0.00 0.00 43.35 1.73
977 2250 8.347771 CAATGGTACGTCTAGTAACTAATAGCA 58.652 37.037 0.00 0.00 43.35 3.49
1007 2374 8.137437 GTGGATATATATATTTTGCATGGCACC 58.863 37.037 6.69 0.38 38.71 5.01
1377 3047 0.850883 ACAACCCCATCATCACCCCT 60.851 55.000 0.00 0.00 0.00 4.79
1816 3819 4.373116 ACCGCGGAGTTGCACGAT 62.373 61.111 35.90 0.68 34.15 3.73
2124 4190 0.871722 TTACGCTGCCACATGAACAC 59.128 50.000 0.00 0.00 0.00 3.32
2126 4193 1.100463 ACGCTGCCACATGAACACAA 61.100 50.000 0.00 0.00 0.00 3.33
2380 4452 2.596338 TGCAGTCGGACGTGGAGA 60.596 61.111 0.00 0.00 0.00 3.71
2617 4689 4.020039 TGTGTAATGACCCGACAAGGTAAT 60.020 41.667 0.00 0.00 41.42 1.89
2655 4730 6.013725 ACTCACTAAAGTCACATTACATGGGA 60.014 38.462 0.00 0.00 41.19 4.37
2656 4731 6.406370 TCACTAAAGTCACATTACATGGGAG 58.594 40.000 0.00 0.00 44.71 4.30
2811 4915 1.002366 CCAAGACCAAGAAGATCGCG 58.998 55.000 0.00 0.00 0.00 5.87
2814 4918 0.459237 AGACCAAGAAGATCGCGCTG 60.459 55.000 5.56 0.00 0.00 5.18
3181 7621 4.386350 GCTAGCTAGCTTATTAGTTTCGCC 59.614 45.833 33.71 3.53 45.62 5.54
3219 7659 4.460731 AGGAGAGGCTGAAGTTAAAAATGC 59.539 41.667 0.00 0.00 0.00 3.56
3244 7684 1.836999 TACACTTGCTGCCCACGGAT 61.837 55.000 0.00 0.00 0.00 4.18
3245 7685 2.360350 ACTTGCTGCCCACGGATG 60.360 61.111 0.00 0.00 0.00 3.51
3246 7686 3.136123 CTTGCTGCCCACGGATGG 61.136 66.667 0.00 0.00 46.81 3.51
3304 9691 3.693085 GCCTTGAAGAATTGCAGATCAGA 59.307 43.478 0.00 0.00 0.00 3.27
3535 10078 6.183360 ACCAGCAATAGGTTGAAATTTGTGAA 60.183 34.615 0.00 0.00 35.33 3.18
3539 10082 6.202570 GCAATAGGTTGAAATTTGTGAAAGCA 59.797 34.615 0.00 0.00 37.53 3.91
3598 10145 1.670406 CATGGCGGCTGGAGCTATC 60.670 63.158 11.43 0.00 41.70 2.08
3655 10202 1.002888 CTTGAAGCTCTGGCCTTGAGA 59.997 52.381 24.01 10.27 39.73 3.27
3656 10203 0.612229 TGAAGCTCTGGCCTTGAGAG 59.388 55.000 24.01 19.00 40.10 3.20
3777 11829 1.330234 GGAGACCGGATCTAGGGTTC 58.670 60.000 9.46 0.00 38.00 3.62
3778 11830 1.330234 GAGACCGGATCTAGGGTTCC 58.670 60.000 9.46 0.00 38.00 3.62
3842 11899 2.732289 TGCCTTCAACAAGGGAAGC 58.268 52.632 2.98 0.00 46.64 3.86
3846 11903 1.613836 CTTCAACAAGGGAAGCTGCT 58.386 50.000 0.00 0.00 35.77 4.24
3851 11908 2.622942 CAACAAGGGAAGCTGCTTGTAA 59.377 45.455 21.25 0.00 38.85 2.41
3885 11946 3.385384 CTCCAGCCTCGGAGCACA 61.385 66.667 0.00 0.00 45.95 4.57
3909 11970 2.899339 GCCAGCAATCTCGCCCTC 60.899 66.667 0.00 0.00 0.00 4.30
3921 11982 2.770130 GCCCTCCCAAACCCATGA 59.230 61.111 0.00 0.00 0.00 3.07
3951 12012 0.692419 CCATCCAGCCTACCACCTCT 60.692 60.000 0.00 0.00 0.00 3.69
3952 12013 0.467384 CATCCAGCCTACCACCTCTG 59.533 60.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.897872 TTTATAATGTCGGATTAGAAAGACCC 57.102 34.615 4.69 0.00 33.04 4.46
24 25 9.521503 GAGAAAGCACTAAGAACTTGAATTTTT 57.478 29.630 0.00 0.00 0.00 1.94
25 26 8.907885 AGAGAAAGCACTAAGAACTTGAATTTT 58.092 29.630 0.00 0.00 0.00 1.82
26 27 8.457238 AGAGAAAGCACTAAGAACTTGAATTT 57.543 30.769 0.00 0.00 0.00 1.82
27 28 7.095439 CGAGAGAAAGCACTAAGAACTTGAATT 60.095 37.037 0.00 0.00 0.00 2.17
28 29 6.367422 CGAGAGAAAGCACTAAGAACTTGAAT 59.633 38.462 0.00 0.00 0.00 2.57
29 30 5.692204 CGAGAGAAAGCACTAAGAACTTGAA 59.308 40.000 0.00 0.00 0.00 2.69
30 31 5.223382 CGAGAGAAAGCACTAAGAACTTGA 58.777 41.667 0.00 0.00 0.00 3.02
31 32 4.143221 GCGAGAGAAAGCACTAAGAACTTG 60.143 45.833 0.00 0.00 0.00 3.16
32 33 3.991121 GCGAGAGAAAGCACTAAGAACTT 59.009 43.478 0.00 0.00 0.00 2.66
33 34 3.005897 TGCGAGAGAAAGCACTAAGAACT 59.994 43.478 0.00 0.00 38.59 3.01
34 35 3.318017 TGCGAGAGAAAGCACTAAGAAC 58.682 45.455 0.00 0.00 38.59 3.01
35 36 3.660501 TGCGAGAGAAAGCACTAAGAA 57.339 42.857 0.00 0.00 38.59 2.52
36 37 3.660501 TTGCGAGAGAAAGCACTAAGA 57.339 42.857 0.00 0.00 43.69 2.10
37 38 3.424170 GCTTTGCGAGAGAAAGCACTAAG 60.424 47.826 12.21 0.00 45.22 2.18
38 39 2.480419 GCTTTGCGAGAGAAAGCACTAA 59.520 45.455 12.21 0.00 45.22 2.24
39 40 2.069273 GCTTTGCGAGAGAAAGCACTA 58.931 47.619 12.21 0.00 45.22 2.74
40 41 0.871057 GCTTTGCGAGAGAAAGCACT 59.129 50.000 12.21 0.00 45.22 4.40
41 42 0.871057 AGCTTTGCGAGAGAAAGCAC 59.129 50.000 17.61 0.00 46.71 4.40
42 43 2.455674 TAGCTTTGCGAGAGAAAGCA 57.544 45.000 17.61 4.56 46.71 3.91
43 44 3.813529 TTTAGCTTTGCGAGAGAAAGC 57.186 42.857 9.75 9.75 45.72 3.51
44 45 5.536554 TGATTTAGCTTTGCGAGAGAAAG 57.463 39.130 0.00 0.00 33.97 2.62
45 46 5.940192 TTGATTTAGCTTTGCGAGAGAAA 57.060 34.783 0.00 0.00 0.00 2.52
46 47 5.643348 TGATTGATTTAGCTTTGCGAGAGAA 59.357 36.000 0.00 0.00 0.00 2.87
47 48 5.178061 TGATTGATTTAGCTTTGCGAGAGA 58.822 37.500 0.00 0.00 0.00 3.10
48 49 5.475273 TGATTGATTTAGCTTTGCGAGAG 57.525 39.130 0.00 0.00 0.00 3.20
49 50 5.674569 GCTTGATTGATTTAGCTTTGCGAGA 60.675 40.000 0.00 0.00 0.00 4.04
50 51 4.498323 GCTTGATTGATTTAGCTTTGCGAG 59.502 41.667 0.00 0.00 0.00 5.03
51 52 4.156556 AGCTTGATTGATTTAGCTTTGCGA 59.843 37.500 0.00 0.00 40.91 5.10
52 53 4.418392 AGCTTGATTGATTTAGCTTTGCG 58.582 39.130 0.00 0.00 40.91 4.85
53 54 5.648572 AGAGCTTGATTGATTTAGCTTTGC 58.351 37.500 0.00 0.00 43.57 3.68
54 55 7.066766 ACCTAGAGCTTGATTGATTTAGCTTTG 59.933 37.037 0.00 0.00 43.57 2.77
55 56 7.115414 ACCTAGAGCTTGATTGATTTAGCTTT 58.885 34.615 0.00 0.00 43.57 3.51
56 57 6.657875 ACCTAGAGCTTGATTGATTTAGCTT 58.342 36.000 0.00 0.00 43.57 3.74
57 58 6.245890 ACCTAGAGCTTGATTGATTTAGCT 57.754 37.500 0.00 0.00 46.02 3.32
58 59 6.934048 AACCTAGAGCTTGATTGATTTAGC 57.066 37.500 0.00 0.00 0.00 3.09
61 62 8.540388 TGTACTAACCTAGAGCTTGATTGATTT 58.460 33.333 0.00 0.00 0.00 2.17
62 63 7.982354 GTGTACTAACCTAGAGCTTGATTGATT 59.018 37.037 0.00 0.00 0.00 2.57
63 64 7.493367 GTGTACTAACCTAGAGCTTGATTGAT 58.507 38.462 0.00 0.00 0.00 2.57
64 65 6.404403 CGTGTACTAACCTAGAGCTTGATTGA 60.404 42.308 0.00 0.00 0.00 2.57
65 66 5.744345 CGTGTACTAACCTAGAGCTTGATTG 59.256 44.000 0.00 0.00 0.00 2.67
66 67 5.418209 ACGTGTACTAACCTAGAGCTTGATT 59.582 40.000 0.00 0.00 0.00 2.57
67 68 4.948621 ACGTGTACTAACCTAGAGCTTGAT 59.051 41.667 0.00 0.00 0.00 2.57
68 69 4.330250 ACGTGTACTAACCTAGAGCTTGA 58.670 43.478 0.00 0.00 0.00 3.02
69 70 4.698583 ACGTGTACTAACCTAGAGCTTG 57.301 45.455 0.00 0.00 0.00 4.01
70 71 4.331168 CGTACGTGTACTAACCTAGAGCTT 59.669 45.833 7.22 0.00 34.04 3.74
71 72 3.868077 CGTACGTGTACTAACCTAGAGCT 59.132 47.826 7.22 0.00 34.04 4.09
72 73 3.865745 TCGTACGTGTACTAACCTAGAGC 59.134 47.826 16.05 0.00 34.04 4.09
73 74 6.408858 TTTCGTACGTGTACTAACCTAGAG 57.591 41.667 16.05 0.00 34.04 2.43
74 75 6.985188 ATTTCGTACGTGTACTAACCTAGA 57.015 37.500 16.05 0.00 34.04 2.43
75 76 7.538678 ACAAATTTCGTACGTGTACTAACCTAG 59.461 37.037 16.05 0.00 34.04 3.02
76 77 7.367285 ACAAATTTCGTACGTGTACTAACCTA 58.633 34.615 16.05 0.00 34.04 3.08
77 78 6.215845 ACAAATTTCGTACGTGTACTAACCT 58.784 36.000 16.05 0.00 34.04 3.50
78 79 6.452244 ACAAATTTCGTACGTGTACTAACC 57.548 37.500 16.05 0.00 34.04 2.85
79 80 9.842444 TTTAACAAATTTCGTACGTGTACTAAC 57.158 29.630 16.05 0.00 34.04 2.34
80 81 9.842444 GTTTAACAAATTTCGTACGTGTACTAA 57.158 29.630 16.05 5.73 34.04 2.24
81 82 8.204646 CGTTTAACAAATTTCGTACGTGTACTA 58.795 33.333 16.05 0.00 34.04 1.82
82 83 7.043722 TCGTTTAACAAATTTCGTACGTGTACT 60.044 33.333 16.05 0.62 34.04 2.73
83 84 7.054398 TCGTTTAACAAATTTCGTACGTGTAC 58.946 34.615 16.05 6.27 0.00 2.90
84 85 7.154668 TCGTTTAACAAATTTCGTACGTGTA 57.845 32.000 16.05 2.15 0.00 2.90
85 86 6.030379 TCGTTTAACAAATTTCGTACGTGT 57.970 33.333 16.05 8.92 0.00 4.49
86 87 6.840292 TCTTCGTTTAACAAATTTCGTACGTG 59.160 34.615 16.05 8.23 0.00 4.49
87 88 6.932051 TCTTCGTTTAACAAATTTCGTACGT 58.068 32.000 16.05 0.00 0.00 3.57
88 89 6.513991 CCTCTTCGTTTAACAAATTTCGTACG 59.486 38.462 9.53 9.53 0.00 3.67
89 90 6.301607 GCCTCTTCGTTTAACAAATTTCGTAC 59.698 38.462 0.00 0.00 0.00 3.67
90 91 6.018098 TGCCTCTTCGTTTAACAAATTTCGTA 60.018 34.615 0.00 0.00 0.00 3.43
91 92 5.209977 GCCTCTTCGTTTAACAAATTTCGT 58.790 37.500 0.00 0.00 0.00 3.85
92 93 5.115021 GTGCCTCTTCGTTTAACAAATTTCG 59.885 40.000 0.00 0.00 0.00 3.46
93 94 5.115021 CGTGCCTCTTCGTTTAACAAATTTC 59.885 40.000 0.00 0.00 0.00 2.17
94 95 4.973663 CGTGCCTCTTCGTTTAACAAATTT 59.026 37.500 0.00 0.00 0.00 1.82
95 96 4.035909 ACGTGCCTCTTCGTTTAACAAATT 59.964 37.500 0.00 0.00 36.93 1.82
96 97 3.562557 ACGTGCCTCTTCGTTTAACAAAT 59.437 39.130 0.00 0.00 36.93 2.32
97 98 2.937799 ACGTGCCTCTTCGTTTAACAAA 59.062 40.909 0.00 0.00 36.93 2.83
98 99 2.285756 CACGTGCCTCTTCGTTTAACAA 59.714 45.455 0.82 0.00 38.23 2.83
99 100 1.862201 CACGTGCCTCTTCGTTTAACA 59.138 47.619 0.82 0.00 38.23 2.41
100 101 1.398071 GCACGTGCCTCTTCGTTTAAC 60.398 52.381 30.12 0.00 38.23 2.01
101 102 0.863144 GCACGTGCCTCTTCGTTTAA 59.137 50.000 30.12 0.00 38.23 1.52
102 103 1.279527 CGCACGTGCCTCTTCGTTTA 61.280 55.000 33.23 0.00 38.23 2.01
103 104 2.594962 CGCACGTGCCTCTTCGTTT 61.595 57.895 33.23 0.00 38.23 3.60
104 105 3.036084 CGCACGTGCCTCTTCGTT 61.036 61.111 33.23 0.00 38.23 3.85
107 108 3.121030 ATGCGCACGTGCCTCTTC 61.121 61.111 33.23 17.52 37.91 2.87
108 109 3.425713 CATGCGCACGTGCCTCTT 61.426 61.111 33.23 19.85 37.91 2.85
114 115 3.489868 TAGCTGCATGCGCACGTG 61.490 61.111 27.63 12.28 45.36 4.49
115 116 3.490759 GTAGCTGCATGCGCACGT 61.491 61.111 27.63 15.09 45.36 4.49
116 117 4.228097 GGTAGCTGCATGCGCACG 62.228 66.667 27.63 5.23 45.36 5.34
117 118 3.126879 TGGTAGCTGCATGCGCAC 61.127 61.111 27.63 22.61 45.36 5.34
121 122 0.677731 TTCCTGTGGTAGCTGCATGC 60.678 55.000 11.82 11.82 43.29 4.06
122 123 1.470098 GTTTCCTGTGGTAGCTGCATG 59.530 52.381 3.61 0.00 0.00 4.06
123 124 1.073763 TGTTTCCTGTGGTAGCTGCAT 59.926 47.619 3.61 0.00 0.00 3.96
124 125 0.472044 TGTTTCCTGTGGTAGCTGCA 59.528 50.000 3.61 0.00 0.00 4.41
125 126 1.740025 GATGTTTCCTGTGGTAGCTGC 59.260 52.381 0.00 0.00 0.00 5.25
126 127 2.002586 CGATGTTTCCTGTGGTAGCTG 58.997 52.381 0.00 0.00 0.00 4.24
127 128 1.623811 ACGATGTTTCCTGTGGTAGCT 59.376 47.619 0.00 0.00 0.00 3.32
128 129 2.094762 ACGATGTTTCCTGTGGTAGC 57.905 50.000 0.00 0.00 0.00 3.58
129 130 5.068723 AGGTATACGATGTTTCCTGTGGTAG 59.931 44.000 0.00 0.00 0.00 3.18
130 131 4.957954 AGGTATACGATGTTTCCTGTGGTA 59.042 41.667 0.00 0.00 0.00 3.25
131 132 3.773119 AGGTATACGATGTTTCCTGTGGT 59.227 43.478 0.00 0.00 0.00 4.16
132 133 4.402056 AGGTATACGATGTTTCCTGTGG 57.598 45.455 0.00 0.00 0.00 4.17
133 134 5.898174 TGTAGGTATACGATGTTTCCTGTG 58.102 41.667 0.00 0.00 34.39 3.66
134 135 6.513180 CATGTAGGTATACGATGTTTCCTGT 58.487 40.000 0.00 0.00 34.39 4.00
135 136 5.405571 GCATGTAGGTATACGATGTTTCCTG 59.594 44.000 0.00 0.00 34.39 3.86
136 137 5.069914 TGCATGTAGGTATACGATGTTTCCT 59.930 40.000 0.00 0.00 34.39 3.36
137 138 5.294356 TGCATGTAGGTATACGATGTTTCC 58.706 41.667 0.00 0.00 34.39 3.13
138 139 8.703604 ATATGCATGTAGGTATACGATGTTTC 57.296 34.615 10.16 0.00 34.39 2.78
139 140 9.151471 GAATATGCATGTAGGTATACGATGTTT 57.849 33.333 10.16 0.00 34.39 2.83
140 141 8.311109 TGAATATGCATGTAGGTATACGATGTT 58.689 33.333 10.16 0.00 34.39 2.71
141 142 7.836842 TGAATATGCATGTAGGTATACGATGT 58.163 34.615 10.16 0.00 34.39 3.06
142 143 8.758715 CATGAATATGCATGTAGGTATACGATG 58.241 37.037 14.81 0.00 40.52 3.84
143 144 8.877808 CATGAATATGCATGTAGGTATACGAT 57.122 34.615 14.81 0.00 40.52 3.73
159 160 6.403964 CCCTTCGGAATGCATACATGAATATG 60.404 42.308 0.00 0.00 36.36 1.78
160 161 5.649395 CCCTTCGGAATGCATACATGAATAT 59.351 40.000 0.00 0.00 36.36 1.28
161 162 5.003160 CCCTTCGGAATGCATACATGAATA 58.997 41.667 0.00 0.00 36.36 1.75
162 163 3.822735 CCCTTCGGAATGCATACATGAAT 59.177 43.478 0.00 0.00 36.36 2.57
163 164 3.118075 TCCCTTCGGAATGCATACATGAA 60.118 43.478 0.00 1.57 36.36 2.57
164 165 2.437651 TCCCTTCGGAATGCATACATGA 59.562 45.455 0.00 0.00 36.36 3.07
165 166 2.810274 CTCCCTTCGGAATGCATACATG 59.190 50.000 0.00 0.00 37.86 3.21
166 167 2.224621 CCTCCCTTCGGAATGCATACAT 60.225 50.000 0.00 0.00 37.86 2.29
167 168 1.140852 CCTCCCTTCGGAATGCATACA 59.859 52.381 0.00 0.00 37.86 2.29
168 169 1.416401 TCCTCCCTTCGGAATGCATAC 59.584 52.381 0.00 0.00 37.86 2.39
169 170 1.801242 TCCTCCCTTCGGAATGCATA 58.199 50.000 0.00 0.00 37.86 3.14
170 171 1.072965 GATCCTCCCTTCGGAATGCAT 59.927 52.381 0.00 0.00 37.86 3.96
171 172 0.469917 GATCCTCCCTTCGGAATGCA 59.530 55.000 0.00 0.00 37.86 3.96
172 173 0.469917 TGATCCTCCCTTCGGAATGC 59.530 55.000 0.00 0.00 37.86 3.56
173 174 2.565841 GTTGATCCTCCCTTCGGAATG 58.434 52.381 0.00 0.00 37.86 2.67
174 175 1.490910 GGTTGATCCTCCCTTCGGAAT 59.509 52.381 0.00 0.00 37.86 3.01
175 176 0.909623 GGTTGATCCTCCCTTCGGAA 59.090 55.000 0.00 0.00 37.86 4.30
176 177 0.042731 AGGTTGATCCTCCCTTCGGA 59.957 55.000 0.00 0.00 44.42 4.55
177 178 1.413077 GTAGGTTGATCCTCCCTTCGG 59.587 57.143 0.80 0.00 44.42 4.30
178 179 1.067212 CGTAGGTTGATCCTCCCTTCG 59.933 57.143 6.92 6.92 44.42 3.79
179 180 1.413077 CCGTAGGTTGATCCTCCCTTC 59.587 57.143 0.80 0.00 44.42 3.46
180 181 1.497161 CCGTAGGTTGATCCTCCCTT 58.503 55.000 0.80 0.00 44.42 3.95
181 182 3.225608 CCGTAGGTTGATCCTCCCT 57.774 57.895 0.00 0.00 44.42 4.20
324 354 4.393155 CAGCCAGCCAGCGGTACA 62.393 66.667 0.00 0.00 38.01 2.90
502 1232 2.761559 CAGTACACATGGGACGAACAA 58.238 47.619 0.00 0.00 0.00 2.83
503 1233 1.606994 GCAGTACACATGGGACGAACA 60.607 52.381 0.00 0.00 0.00 3.18
508 1613 3.118408 TGGATAAGCAGTACACATGGGAC 60.118 47.826 0.00 0.00 0.00 4.46
587 1709 4.261072 GCATTCTACGTACTCGAAGGATCA 60.261 45.833 10.70 0.00 40.62 2.92
588 1710 4.220572 GCATTCTACGTACTCGAAGGATC 58.779 47.826 10.70 0.00 40.62 3.36
589 1711 3.303857 CGCATTCTACGTACTCGAAGGAT 60.304 47.826 10.70 0.00 40.62 3.24
609 1750 0.739561 CTCAGGAGTACACCCTACGC 59.260 60.000 5.63 0.00 31.64 4.42
632 1773 1.062581 CCCCATCTCCTCTCCTCTCAA 60.063 57.143 0.00 0.00 0.00 3.02
829 1982 9.658799 GTACACAAACATGCAGAGGATATATAT 57.341 33.333 0.00 0.00 0.00 0.86
830 1983 8.094548 GGTACACAAACATGCAGAGGATATATA 58.905 37.037 0.00 0.00 0.00 0.86
833 1986 5.126067 GGTACACAAACATGCAGAGGATAT 58.874 41.667 0.00 0.00 0.00 1.63
834 1987 4.019771 TGGTACACAAACATGCAGAGGATA 60.020 41.667 0.00 0.00 0.00 2.59
853 2102 2.481185 GCCGTTGAAAAAGACGATGGTA 59.519 45.455 0.00 0.00 41.53 3.25
855 2104 1.401018 GGCCGTTGAAAAAGACGATGG 60.401 52.381 0.00 0.00 41.53 3.51
860 2109 2.403259 CAATGGGCCGTTGAAAAAGAC 58.597 47.619 30.53 0.00 32.66 3.01
865 2114 0.825425 TGAGCAATGGGCCGTTGAAA 60.825 50.000 36.48 20.18 46.50 2.69
929 2190 2.414559 GGATCTGATTGGTTGTTGCGTG 60.415 50.000 0.00 0.00 0.00 5.34
989 2262 3.552684 GCACGGTGCCATGCAAAATATAT 60.553 43.478 22.19 0.00 41.47 0.86
1007 2374 2.810650 AGCTAGGTTTAGAATCGCACG 58.189 47.619 0.00 0.00 0.00 5.34
1377 3047 3.047280 GCGTTGATGCCGTGGTCA 61.047 61.111 0.00 0.00 0.00 4.02
1588 3586 7.154656 TCCAGTGTCTGCAATATATCATGTAC 58.845 38.462 0.00 0.00 0.00 2.90
1591 3589 5.642491 CCTCCAGTGTCTGCAATATATCATG 59.358 44.000 0.00 0.00 0.00 3.07
1592 3590 5.309020 ACCTCCAGTGTCTGCAATATATCAT 59.691 40.000 0.00 0.00 0.00 2.45
1594 3592 5.220710 ACCTCCAGTGTCTGCAATATATC 57.779 43.478 0.00 0.00 0.00 1.63
1595 3593 5.371526 CAACCTCCAGTGTCTGCAATATAT 58.628 41.667 0.00 0.00 0.00 0.86
1596 3594 4.384098 CCAACCTCCAGTGTCTGCAATATA 60.384 45.833 0.00 0.00 0.00 0.86
1597 3595 3.614092 CAACCTCCAGTGTCTGCAATAT 58.386 45.455 0.00 0.00 0.00 1.28
1598 3596 2.290260 CCAACCTCCAGTGTCTGCAATA 60.290 50.000 0.00 0.00 0.00 1.90
1599 3597 1.546323 CCAACCTCCAGTGTCTGCAAT 60.546 52.381 0.00 0.00 0.00 3.56
1816 3819 3.220999 CTCCTCGGCCACAACACGA 62.221 63.158 2.24 0.00 35.14 4.35
2250 4322 0.033796 CCACTGGCCATTGGATCAGT 60.034 55.000 33.16 19.81 38.52 3.41
2380 4452 0.322322 TTCCTGATGGTAAACGCCGT 59.678 50.000 0.00 0.00 34.23 5.68
2388 4460 2.335681 TGTCCAGGTTCCTGATGGTA 57.664 50.000 19.12 0.01 36.24 3.25
2454 4526 1.599071 TGCGAGTTGAACTTCTTGCAG 59.401 47.619 0.00 0.00 43.44 4.41
2811 4915 2.953466 TACGTACCAATGTCCTCAGC 57.047 50.000 0.00 0.00 0.00 4.26
2814 4918 9.565213 GTTACATATATACGTACCAATGTCCTC 57.435 37.037 17.11 9.00 0.00 3.71
3114 7543 2.593725 CCTCGATCGTCCGGGCTA 60.594 66.667 15.94 0.00 0.00 3.93
3181 7621 4.620332 GCCTCTCCTAATTGATCCATCTCG 60.620 50.000 0.00 0.00 0.00 4.04
3219 7659 0.593128 GGGCAGCAAGTGTACAACTG 59.407 55.000 0.00 4.65 39.81 3.16
3244 7684 5.081032 CCACTAAAACCTTTATTCACCCCA 58.919 41.667 0.00 0.00 0.00 4.96
3245 7685 5.326900 TCCACTAAAACCTTTATTCACCCC 58.673 41.667 0.00 0.00 0.00 4.95
3246 7686 6.661805 TCATCCACTAAAACCTTTATTCACCC 59.338 38.462 0.00 0.00 0.00 4.61
3247 7687 7.393515 ACTCATCCACTAAAACCTTTATTCACC 59.606 37.037 0.00 0.00 0.00 4.02
3248 7688 8.336801 ACTCATCCACTAAAACCTTTATTCAC 57.663 34.615 0.00 0.00 0.00 3.18
3304 9691 6.642707 TTGTCGAACAAAAAGGGACATAAT 57.357 33.333 0.00 0.00 37.46 1.28
3535 10078 7.043656 GCAGAAATTTTACGTTACAGTTTGCTT 60.044 33.333 0.00 0.00 0.00 3.91
3539 10082 5.910723 CCGCAGAAATTTTACGTTACAGTTT 59.089 36.000 0.00 0.00 0.00 2.66
3598 10145 5.954296 AACTGATGATGTTCAACCTTCAG 57.046 39.130 7.66 7.66 37.79 3.02
3655 10202 5.653255 ACAAGATTATCAGGGGTTATGCT 57.347 39.130 0.00 0.00 0.00 3.79
3656 10203 6.296026 TGTACAAGATTATCAGGGGTTATGC 58.704 40.000 0.00 0.00 0.00 3.14
3717 10265 2.713770 CATGCATCCACGCTGCTC 59.286 61.111 0.00 0.00 40.34 4.26
3794 11846 1.774300 GCCCTCCCCTTCTTTTCCA 59.226 57.895 0.00 0.00 0.00 3.53
3846 11903 3.192230 CGATGGCGGCGCTTACAA 61.192 61.111 32.30 12.67 0.00 2.41
3885 11946 0.524862 CGAGATTGCTGGCAAAAGCT 59.475 50.000 12.06 9.62 43.90 3.74
3899 11960 2.680370 GGGTTTGGGAGGGCGAGAT 61.680 63.158 0.00 0.00 0.00 2.75
3909 11970 1.984026 GCAGGGTCATGGGTTTGGG 60.984 63.158 0.00 0.00 0.00 4.12
3921 11982 2.287117 TGGATGGGATGGCAGGGT 60.287 61.111 0.00 0.00 0.00 4.34
3951 12012 1.006220 AAGATGCTCACGTGTCGCA 60.006 52.632 27.71 27.71 38.14 5.10
3952 12013 1.417592 CAAGATGCTCACGTGTCGC 59.582 57.895 16.51 18.83 0.00 5.19
4067 12472 9.158233 GTGTTGCAATTATTAGTAGGTTAGTCA 57.842 33.333 0.59 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.