Multiple sequence alignment - TraesCS3D01G483900

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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 TraesCS3D01G483900 chr3D 100.000 2455 0 0 1 2455 581060932 581058478 0.000000e+00 4534.0
1 TraesCS3D01G483900 chr3D 82.099 972 98 41 393 1320 581014059 581013120 0.000000e+00 761.0
2 TraesCS3D01G483900 chr3D 77.563 985 121 57 694 1621 581069544 581068603 1.010000e-138 503.0
3 TraesCS3D01G483900 chr3D 80.552 689 64 24 393 1080 580994940 580994321 1.330000e-127 466.0
4 TraesCS3D01G483900 chr3D 88.800 375 20 9 777 1137 580918854 580918488 8.060000e-120 440.0
5 TraesCS3D01G483900 chr3D 82.262 451 51 20 531 955 580974144 580973697 1.790000e-96 363.0
6 TraesCS3D01G483900 chr3D 83.541 401 31 15 393 784 580919649 580919275 2.340000e-90 342.0
7 TraesCS3D01G483900 chr3D 83.651 367 27 11 1326 1682 580912029 580911686 5.100000e-82 315.0
8 TraesCS3D01G483900 chr3D 93.158 190 13 0 1133 1322 580912257 580912068 1.860000e-71 279.0
9 TraesCS3D01G483900 chr3D 81.948 349 41 11 1339 1681 581013066 581012734 2.400000e-70 276.0
10 TraesCS3D01G483900 chr3D 84.328 268 22 8 1075 1325 580994176 580993912 6.780000e-61 244.0
11 TraesCS3D01G483900 chr3D 86.432 199 14 5 393 580 581084600 581084404 3.200000e-49 206.0
12 TraesCS3D01G483900 chr3D 91.228 114 9 1 281 393 581014284 581014171 1.180000e-33 154.0
13 TraesCS3D01G483900 chr3D 84.828 145 20 1 621 763 581084397 581084253 7.080000e-31 145.0
14 TraesCS3D01G483900 chr3D 97.297 37 1 0 357 393 581084748 581084712 2.040000e-06 63.9
15 TraesCS3D01G483900 chr3B 87.753 939 64 20 393 1329 777653625 777654514 0.000000e+00 1050.0
16 TraesCS3D01G483900 chr3B 84.662 828 89 21 233 1050 777754993 777755792 0.000000e+00 791.0
17 TraesCS3D01G483900 chr3B 86.876 541 36 13 245 782 777690753 777691261 7.610000e-160 573.0
18 TraesCS3D01G483900 chr3B 84.492 374 26 14 1324 1681 777756640 777756997 8.410000e-90 340.0
19 TraesCS3D01G483900 chr3B 83.862 378 30 12 1324 1682 777654555 777654920 5.060000e-87 331.0
20 TraesCS3D01G483900 chr3B 79.934 304 34 15 1041 1325 777756301 777756596 5.350000e-47 198.0
21 TraesCS3D01G483900 chr3B 86.111 180 16 7 783 961 777745484 777745655 4.170000e-43 185.0
22 TraesCS3D01G483900 chr3A 84.276 1043 99 26 244 1256 716791968 716792975 0.000000e+00 957.0
23 TraesCS3D01G483900 chr3A 90.283 741 55 4 594 1325 716806872 716807604 0.000000e+00 953.0
24 TraesCS3D01G483900 chr3A 81.193 771 74 31 389 1125 716794502 716795235 2.760000e-154 555.0
25 TraesCS3D01G483900 chr3A 87.071 495 40 11 249 742 716790296 716790767 2.780000e-149 538.0
26 TraesCS3D01G483900 chr3A 82.836 536 54 14 1163 1681 716795234 716795748 1.730000e-121 446.0
27 TraesCS3D01G483900 chr3A 88.142 253 29 1 1746 1998 551727569 551727318 1.430000e-77 300.0
28 TraesCS3D01G483900 chr3A 92.228 193 5 3 749 933 716787066 716787256 5.210000e-67 265.0
29 TraesCS3D01G483900 chr3A 81.369 263 26 12 1217 1460 716777778 716778036 2.490000e-45 193.0
30 TraesCS3D01G483900 chr3A 89.333 150 15 1 244 393 716786436 716786584 1.160000e-43 187.0
31 TraesCS3D01G483900 chr6B 86.732 716 81 5 1746 2455 712622421 712621714 0.000000e+00 784.0
32 TraesCS3D01G483900 chr6B 96.708 243 6 2 1 243 663857553 663857313 1.060000e-108 403.0
33 TraesCS3D01G483900 chr6B 95.833 192 6 2 1 192 692608126 692608315 2.370000e-80 309.0
34 TraesCS3D01G483900 chr7B 85.376 718 95 4 1743 2455 637028358 637029070 0.000000e+00 736.0
35 TraesCS3D01G483900 chr2D 84.283 579 83 3 1882 2455 77373939 77374514 2.130000e-155 558.0
36 TraesCS3D01G483900 chr5A 84.831 534 67 11 1745 2271 504763936 504764462 2.160000e-145 525.0
37 TraesCS3D01G483900 chr2B 87.786 393 41 5 1744 2136 147484279 147484664 1.040000e-123 453.0
38 TraesCS3D01G483900 chr2B 86.170 188 20 5 2267 2449 147486178 147486364 5.350000e-47 198.0
39 TraesCS3D01G483900 chr2B 81.818 132 14 6 2313 2439 119593609 119593735 4.320000e-18 102.0
40 TraesCS3D01G483900 chr7D 87.805 369 37 4 2093 2455 575464159 575464525 2.260000e-115 425.0
41 TraesCS3D01G483900 chr7D 87.749 351 39 2 1747 2097 575442865 575443211 8.170000e-110 407.0
42 TraesCS3D01G483900 chr1A 96.311 244 7 2 1 243 6334409 6334651 1.370000e-107 399.0
43 TraesCS3D01G483900 chr1A 82.051 195 32 3 1747 1941 99048605 99048414 1.950000e-36 163.0
44 TraesCS3D01G483900 chr1D 92.400 250 9 3 1 243 440711472 440711226 5.020000e-92 348.0
45 TraesCS3D01G483900 chr7A 89.256 242 8 4 11 244 20188958 20188727 1.110000e-73 287.0
46 TraesCS3D01G483900 chr2A 89.212 241 8 4 11 243 755405512 755405742 4.000000e-73 285.0
47 TraesCS3D01G483900 chr2A 87.603 242 27 3 1746 1986 137928207 137927968 6.690000e-71 278.0
48 TraesCS3D01G483900 chr2A 87.097 186 7 2 75 243 706213778 706213593 6.930000e-46 195.0
49 TraesCS3D01G483900 chr2A 87.097 93 5 4 142 232 554430599 554430686 5.590000e-17 99.0


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 TraesCS3D01G483900 chr3D 581058478 581060932 2454 True 4534.000000 4534 100.000000 1 2455 1 chr3D.!!$R2 2454
1 TraesCS3D01G483900 chr3D 581068603 581069544 941 True 503.000000 503 77.563000 694 1621 1 chr3D.!!$R3 927
2 TraesCS3D01G483900 chr3D 581012734 581014284 1550 True 397.000000 761 85.091667 281 1681 3 chr3D.!!$R7 1400
3 TraesCS3D01G483900 chr3D 580918488 580919649 1161 True 391.000000 440 86.170500 393 1137 2 chr3D.!!$R5 744
4 TraesCS3D01G483900 chr3D 580993912 580994940 1028 True 355.000000 466 82.440000 393 1325 2 chr3D.!!$R6 932
5 TraesCS3D01G483900 chr3D 580911686 580912257 571 True 297.000000 315 88.404500 1133 1682 2 chr3D.!!$R4 549
6 TraesCS3D01G483900 chr3B 777653625 777654920 1295 False 690.500000 1050 85.807500 393 1682 2 chr3B.!!$F3 1289
7 TraesCS3D01G483900 chr3B 777690753 777691261 508 False 573.000000 573 86.876000 245 782 1 chr3B.!!$F1 537
8 TraesCS3D01G483900 chr3B 777754993 777756997 2004 False 443.000000 791 83.029333 233 1681 3 chr3B.!!$F4 1448
9 TraesCS3D01G483900 chr3A 716806872 716807604 732 False 953.000000 953 90.283000 594 1325 1 chr3A.!!$F2 731
10 TraesCS3D01G483900 chr3A 716786436 716795748 9312 False 491.333333 957 86.156167 244 1681 6 chr3A.!!$F3 1437
11 TraesCS3D01G483900 chr6B 712621714 712622421 707 True 784.000000 784 86.732000 1746 2455 1 chr6B.!!$R2 709
12 TraesCS3D01G483900 chr7B 637028358 637029070 712 False 736.000000 736 85.376000 1743 2455 1 chr7B.!!$F1 712
13 TraesCS3D01G483900 chr2D 77373939 77374514 575 False 558.000000 558 84.283000 1882 2455 1 chr2D.!!$F1 573
14 TraesCS3D01G483900 chr5A 504763936 504764462 526 False 525.000000 525 84.831000 1745 2271 1 chr5A.!!$F1 526
15 TraesCS3D01G483900 chr2B 147484279 147486364 2085 False 325.500000 453 86.978000 1744 2449 2 chr2B.!!$F2 705

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
707 6400 0.102481 CACCTCGAATCGAATCCGGT 59.898 55.0 6.84 7.65 34.74 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 11423 0.033504 AGCGCTTTCTTCCTTGTCGA 59.966 50.0 2.64 0.0 0.0 4.2 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
63 64 4.287781 TCCGCGGTCGCAAGTCAA 62.288 61.111 27.15 0.00 42.06 3.18
64 65 3.342627 CCGCGGTCGCAAGTCAAA 61.343 61.111 19.50 0.00 42.06 2.69
65 66 2.170985 CGCGGTCGCAAGTCAAAG 59.829 61.111 15.68 0.00 42.06 2.77
66 67 2.556287 GCGGTCGCAAGTCAAAGG 59.444 61.111 10.67 0.00 41.49 3.11
67 68 2.966309 GCGGTCGCAAGTCAAAGGG 61.966 63.158 10.67 0.00 41.49 3.95
68 69 2.325082 CGGTCGCAAGTCAAAGGGG 61.325 63.158 0.00 0.00 39.48 4.79
69 70 1.072505 GGTCGCAAGTCAAAGGGGA 59.927 57.895 0.00 0.00 39.48 4.81
70 71 0.536460 GGTCGCAAGTCAAAGGGGAA 60.536 55.000 0.00 0.00 39.48 3.97
71 72 1.314730 GTCGCAAGTCAAAGGGGAAA 58.685 50.000 0.00 0.00 39.48 3.13
72 73 1.679153 GTCGCAAGTCAAAGGGGAAAA 59.321 47.619 0.00 0.00 39.48 2.29
73 74 1.953686 TCGCAAGTCAAAGGGGAAAAG 59.046 47.619 0.00 0.00 39.48 2.27
74 75 1.000274 CGCAAGTCAAAGGGGAAAAGG 60.000 52.381 0.00 0.00 0.00 3.11
75 76 2.316108 GCAAGTCAAAGGGGAAAAGGA 58.684 47.619 0.00 0.00 0.00 3.36
76 77 2.899900 GCAAGTCAAAGGGGAAAAGGAT 59.100 45.455 0.00 0.00 0.00 3.24
77 78 3.324846 GCAAGTCAAAGGGGAAAAGGATT 59.675 43.478 0.00 0.00 0.00 3.01
78 79 4.561530 GCAAGTCAAAGGGGAAAAGGATTC 60.562 45.833 0.00 0.00 0.00 2.52
79 80 4.749048 AGTCAAAGGGGAAAAGGATTCT 57.251 40.909 0.00 0.00 0.00 2.40
80 81 4.411013 AGTCAAAGGGGAAAAGGATTCTG 58.589 43.478 0.00 0.00 0.00 3.02
81 82 3.511540 GTCAAAGGGGAAAAGGATTCTGG 59.488 47.826 0.00 0.00 0.00 3.86
82 83 3.401002 TCAAAGGGGAAAAGGATTCTGGA 59.599 43.478 0.00 0.00 0.00 3.86
83 84 3.746792 AAGGGGAAAAGGATTCTGGAG 57.253 47.619 0.00 0.00 0.00 3.86
84 85 2.648838 AGGGGAAAAGGATTCTGGAGT 58.351 47.619 0.00 0.00 0.00 3.85
85 86 2.310052 AGGGGAAAAGGATTCTGGAGTG 59.690 50.000 0.00 0.00 0.00 3.51
86 87 2.041755 GGGGAAAAGGATTCTGGAGTGT 59.958 50.000 0.00 0.00 0.00 3.55
87 88 3.084786 GGGAAAAGGATTCTGGAGTGTG 58.915 50.000 0.00 0.00 0.00 3.82
88 89 3.084786 GGAAAAGGATTCTGGAGTGTGG 58.915 50.000 0.00 0.00 0.00 4.17
89 90 3.244911 GGAAAAGGATTCTGGAGTGTGGA 60.245 47.826 0.00 0.00 0.00 4.02
90 91 3.710209 AAAGGATTCTGGAGTGTGGAG 57.290 47.619 0.00 0.00 0.00 3.86
91 92 2.334006 AGGATTCTGGAGTGTGGAGT 57.666 50.000 0.00 0.00 0.00 3.85
92 93 2.625639 AGGATTCTGGAGTGTGGAGTT 58.374 47.619 0.00 0.00 0.00 3.01
93 94 2.304180 AGGATTCTGGAGTGTGGAGTTG 59.696 50.000 0.00 0.00 0.00 3.16
94 95 2.616510 GGATTCTGGAGTGTGGAGTTGG 60.617 54.545 0.00 0.00 0.00 3.77
95 96 1.507140 TTCTGGAGTGTGGAGTTGGT 58.493 50.000 0.00 0.00 0.00 3.67
96 97 1.048601 TCTGGAGTGTGGAGTTGGTC 58.951 55.000 0.00 0.00 0.00 4.02
97 98 0.319900 CTGGAGTGTGGAGTTGGTCG 60.320 60.000 0.00 0.00 0.00 4.79
98 99 1.668151 GGAGTGTGGAGTTGGTCGC 60.668 63.158 0.00 0.00 0.00 5.19
99 100 1.367840 GAGTGTGGAGTTGGTCGCT 59.632 57.895 0.00 0.00 0.00 4.93
100 101 0.946221 GAGTGTGGAGTTGGTCGCTG 60.946 60.000 0.00 0.00 0.00 5.18
101 102 2.280797 TGTGGAGTTGGTCGCTGC 60.281 61.111 0.00 0.00 0.00 5.25
102 103 2.280797 GTGGAGTTGGTCGCTGCA 60.281 61.111 0.00 0.00 31.96 4.41
103 104 1.672356 GTGGAGTTGGTCGCTGCAT 60.672 57.895 0.00 0.00 36.72 3.96
104 105 1.375908 TGGAGTTGGTCGCTGCATC 60.376 57.895 0.00 0.00 29.44 3.91
105 106 2.109126 GGAGTTGGTCGCTGCATCC 61.109 63.158 0.00 1.60 0.00 3.51
106 107 1.375908 GAGTTGGTCGCTGCATCCA 60.376 57.895 8.38 8.38 0.00 3.41
107 108 1.364626 GAGTTGGTCGCTGCATCCAG 61.365 60.000 11.48 0.00 42.13 3.86
108 109 2.046023 TTGGTCGCTGCATCCAGG 60.046 61.111 11.48 0.00 39.54 4.45
114 115 4.119363 GCTGCATCCAGGGCTCCA 62.119 66.667 0.00 0.00 39.54 3.86
115 116 2.192443 CTGCATCCAGGGCTCCAG 59.808 66.667 0.00 0.00 35.38 3.86
116 117 3.414193 TGCATCCAGGGCTCCAGG 61.414 66.667 0.00 0.00 0.00 4.45
117 118 4.891037 GCATCCAGGGCTCCAGGC 62.891 72.222 0.00 0.00 40.90 4.85
118 119 3.414193 CATCCAGGGCTCCAGGCA 61.414 66.667 2.16 0.00 44.01 4.75
119 120 2.369291 ATCCAGGGCTCCAGGCAT 60.369 61.111 2.16 0.00 44.01 4.40
120 121 2.459086 ATCCAGGGCTCCAGGCATC 61.459 63.158 2.16 0.00 44.01 3.91
121 122 4.559063 CCAGGGCTCCAGGCATCG 62.559 72.222 2.16 0.00 44.01 3.84
122 123 3.790437 CAGGGCTCCAGGCATCGT 61.790 66.667 2.16 0.00 44.01 3.73
123 124 2.041922 AGGGCTCCAGGCATCGTA 60.042 61.111 2.16 0.00 44.01 3.43
124 125 2.136878 AGGGCTCCAGGCATCGTAG 61.137 63.158 2.16 0.00 44.01 3.51
125 126 2.134287 GGGCTCCAGGCATCGTAGA 61.134 63.158 2.16 0.00 44.01 2.59
126 127 1.068250 GGCTCCAGGCATCGTAGAC 59.932 63.158 0.00 0.00 44.01 2.59
127 128 1.395826 GGCTCCAGGCATCGTAGACT 61.396 60.000 0.00 0.00 44.01 3.24
128 129 1.319541 GCTCCAGGCATCGTAGACTA 58.680 55.000 0.00 0.00 42.51 2.59
129 130 1.268352 GCTCCAGGCATCGTAGACTAG 59.732 57.143 0.00 0.00 42.51 2.57
130 131 2.577700 CTCCAGGCATCGTAGACTAGT 58.422 52.381 0.00 0.00 42.51 2.57
131 132 2.550606 CTCCAGGCATCGTAGACTAGTC 59.449 54.545 15.41 15.41 42.51 2.59
132 133 2.092592 TCCAGGCATCGTAGACTAGTCA 60.093 50.000 24.44 8.16 42.51 3.41
133 134 2.887783 CCAGGCATCGTAGACTAGTCAT 59.112 50.000 24.44 12.01 42.51 3.06
134 135 4.072839 CCAGGCATCGTAGACTAGTCATA 58.927 47.826 24.44 11.07 42.51 2.15
135 136 4.155099 CCAGGCATCGTAGACTAGTCATAG 59.845 50.000 24.44 14.09 42.51 2.23
136 137 4.757657 CAGGCATCGTAGACTAGTCATAGT 59.242 45.833 24.44 6.62 45.16 2.12
137 138 5.239744 CAGGCATCGTAGACTAGTCATAGTT 59.760 44.000 24.44 6.24 42.46 2.24
138 139 5.239744 AGGCATCGTAGACTAGTCATAGTTG 59.760 44.000 24.44 17.77 42.46 3.16
139 140 5.238868 GGCATCGTAGACTAGTCATAGTTGA 59.761 44.000 24.44 12.82 42.46 3.18
140 141 6.072397 GGCATCGTAGACTAGTCATAGTTGAT 60.072 42.308 24.44 14.31 42.46 2.57
141 142 7.119407 GGCATCGTAGACTAGTCATAGTTGATA 59.881 40.741 24.44 3.05 42.46 2.15
142 143 8.504815 GCATCGTAGACTAGTCATAGTTGATAA 58.495 37.037 24.44 0.00 42.46 1.75
144 145 9.781633 ATCGTAGACTAGTCATAGTTGATAAGT 57.218 33.333 24.44 1.87 42.46 2.24
145 146 9.043079 TCGTAGACTAGTCATAGTTGATAAGTG 57.957 37.037 24.44 0.86 42.46 3.16
146 147 8.283992 CGTAGACTAGTCATAGTTGATAAGTGG 58.716 40.741 24.44 0.00 42.46 4.00
147 148 7.589958 AGACTAGTCATAGTTGATAAGTGGG 57.410 40.000 24.44 0.00 42.46 4.61
148 149 6.041069 AGACTAGTCATAGTTGATAAGTGGGC 59.959 42.308 24.44 0.00 42.46 5.36
149 150 4.423625 AGTCATAGTTGATAAGTGGGCC 57.576 45.455 0.00 0.00 33.56 5.80
150 151 4.040755 AGTCATAGTTGATAAGTGGGCCT 58.959 43.478 4.53 0.00 33.56 5.19
151 152 4.130118 GTCATAGTTGATAAGTGGGCCTG 58.870 47.826 4.53 0.00 33.56 4.85
152 153 3.780294 TCATAGTTGATAAGTGGGCCTGT 59.220 43.478 4.53 0.00 0.00 4.00
153 154 2.496899 AGTTGATAAGTGGGCCTGTG 57.503 50.000 4.53 0.00 0.00 3.66
154 155 1.004745 AGTTGATAAGTGGGCCTGTGG 59.995 52.381 4.53 0.00 0.00 4.17
155 156 0.331278 TTGATAAGTGGGCCTGTGGG 59.669 55.000 4.53 0.00 0.00 4.61
169 170 4.623932 CCTGTGGGCTGTATGTATACAT 57.376 45.455 21.57 21.57 41.92 2.29
170 171 5.738619 CCTGTGGGCTGTATGTATACATA 57.261 43.478 19.51 19.51 41.92 2.29
171 172 5.724328 CCTGTGGGCTGTATGTATACATAG 58.276 45.833 23.03 16.30 41.92 2.23
172 173 5.337571 CCTGTGGGCTGTATGTATACATAGG 60.338 48.000 23.03 18.86 41.92 2.57
173 174 4.530553 TGTGGGCTGTATGTATACATAGGG 59.469 45.833 23.03 18.57 41.92 3.53
174 175 4.081087 GTGGGCTGTATGTATACATAGGGG 60.081 50.000 23.03 16.58 41.92 4.79
175 176 4.101856 GGGCTGTATGTATACATAGGGGT 58.898 47.826 23.03 2.93 41.92 4.95
176 177 5.222589 TGGGCTGTATGTATACATAGGGGTA 60.223 44.000 23.03 2.96 41.92 3.69
177 178 5.363005 GGGCTGTATGTATACATAGGGGTAG 59.637 48.000 23.03 16.53 41.92 3.18
178 179 5.956563 GGCTGTATGTATACATAGGGGTAGT 59.043 44.000 23.03 0.81 41.92 2.73
179 180 7.121382 GGCTGTATGTATACATAGGGGTAGTA 58.879 42.308 23.03 0.85 41.92 1.82
180 181 7.616935 GGCTGTATGTATACATAGGGGTAGTAA 59.383 40.741 23.03 0.14 41.92 2.24
181 182 9.028284 GCTGTATGTATACATAGGGGTAGTAAA 57.972 37.037 23.03 0.00 41.92 2.01
230 231 4.278513 CAGGTTGGCCCCCACGAA 62.279 66.667 10.93 0.00 30.78 3.85
231 232 3.966543 AGGTTGGCCCCCACGAAG 61.967 66.667 10.93 0.00 30.78 3.79
233 234 4.660938 GTTGGCCCCCACGAAGCT 62.661 66.667 0.00 0.00 30.78 3.74
234 235 4.344865 TTGGCCCCCACGAAGCTC 62.345 66.667 0.00 0.00 30.78 4.09
242 243 3.777925 CACGAAGCTCCGCCGTTG 61.778 66.667 0.00 0.00 33.96 4.10
252 253 1.080093 CCGCCGTTGTCTGCTAGAA 60.080 57.895 0.00 0.00 0.00 2.10
264 265 3.950395 GTCTGCTAGAAATGCCCTTGATT 59.050 43.478 0.00 0.00 0.00 2.57
265 266 3.949754 TCTGCTAGAAATGCCCTTGATTG 59.050 43.478 0.00 0.00 0.00 2.67
324 325 0.731514 TGCTTCGTCTCCGTTAAGCG 60.732 55.000 0.00 0.00 43.19 4.68
340 341 2.548295 GCGGGTCCAAAAGTGCGAA 61.548 57.895 0.00 0.00 0.00 4.70
420 4386 0.846693 AACAGCAGTCAGAAAGGGGT 59.153 50.000 0.00 0.00 0.00 4.95
467 4447 6.146021 GCATCTGATCTTTAGCTAGCTTTCTC 59.854 42.308 24.88 13.03 0.00 2.87
468 4448 6.155475 TCTGATCTTTAGCTAGCTTTCTCC 57.845 41.667 24.88 8.94 0.00 3.71
469 4449 4.938080 TGATCTTTAGCTAGCTTTCTCCG 58.062 43.478 24.88 6.21 0.00 4.63
470 4450 3.802948 TCTTTAGCTAGCTTTCTCCGG 57.197 47.619 24.88 0.00 0.00 5.14
482 4462 4.208686 CTCCGGCCGGTCAGCTAC 62.209 72.222 41.57 0.00 36.47 3.58
543 4523 4.529219 CGTGCATGGCCGGCTAGA 62.529 66.667 28.56 11.36 0.00 2.43
566 6237 0.453782 TCGATCACTGTACGTGCGTG 60.454 55.000 17.45 17.45 43.46 5.34
588 6281 3.819337 GCCATGTCGATCACTACCTAGTA 59.181 47.826 0.00 0.00 34.13 1.82
589 6282 4.083217 GCCATGTCGATCACTACCTAGTAG 60.083 50.000 0.23 0.23 41.43 2.57
590 6283 4.083217 CCATGTCGATCACTACCTAGTAGC 60.083 50.000 1.69 0.00 39.51 3.58
591 6284 4.418973 TGTCGATCACTACCTAGTAGCT 57.581 45.455 1.69 0.00 39.51 3.32
592 6285 5.541953 TGTCGATCACTACCTAGTAGCTA 57.458 43.478 1.69 0.00 39.51 3.32
614 6307 2.733552 GTGTGTGTGTGTCTATCTGCTG 59.266 50.000 0.00 0.00 0.00 4.41
707 6400 0.102481 CACCTCGAATCGAATCCGGT 59.898 55.000 6.84 7.65 34.74 5.28
745 6438 3.716006 CGTGGCGTGGTCTGCAAG 61.716 66.667 0.00 0.00 0.00 4.01
759 6455 1.065410 TGCAAGGGTGGGGAGAGAAA 61.065 55.000 0.00 0.00 0.00 2.52
1145 10415 2.257894 CTGCAGTGTCGTCTTCAGATC 58.742 52.381 5.25 0.00 32.13 2.75
1167 10451 1.929169 GATAAACGTACCCCGAGTTGC 59.071 52.381 0.00 0.00 40.70 4.17
1186 10472 0.601558 CTGGCTTGTTTGCTCATGCT 59.398 50.000 11.86 0.00 40.48 3.79
1197 10485 0.886563 GCTCATGCTTGTGCCTTTCT 59.113 50.000 13.92 0.00 36.57 2.52
1201 10489 2.694628 TCATGCTTGTGCCTTTCTTGTT 59.305 40.909 0.00 0.00 38.71 2.83
1350 10717 4.455877 CCACCTCCTTTGTAACTTGCTTAG 59.544 45.833 0.00 0.00 0.00 2.18
1371 10738 1.179152 TGTCGCTAGTGATTTCCGGA 58.821 50.000 9.64 0.00 0.00 5.14
1391 10761 5.590259 CCGGACTGATAATGGTCTGAATTTT 59.410 40.000 0.00 0.00 40.21 1.82
1395 10765 4.671377 TGATAATGGTCTGAATTTTGCGC 58.329 39.130 0.00 0.00 0.00 6.09
1463 10839 4.287781 TGCGACTGACCGGCGAAA 62.288 61.111 9.30 0.00 0.00 3.46
1517 10909 6.986231 TGCCTATGAAGAACATACACATACAG 59.014 38.462 0.00 0.00 40.07 2.74
1519 10911 7.383572 GCCTATGAAGAACATACACATACAGAG 59.616 40.741 0.00 0.00 40.07 3.35
1657 11073 8.135529 GTCACACCTATAATCAATTTTAAGGCC 58.864 37.037 0.00 0.00 0.00 5.19
1682 11098 5.882557 CCAAATTATCAGGCTACTGTTGAGT 59.117 40.000 0.00 0.00 45.14 3.41
1683 11099 6.375455 CCAAATTATCAGGCTACTGTTGAGTT 59.625 38.462 0.00 0.00 45.14 3.01
1684 11100 6.992063 AATTATCAGGCTACTGTTGAGTTG 57.008 37.500 0.00 0.00 45.14 3.16
1685 11101 5.483685 TTATCAGGCTACTGTTGAGTTGT 57.516 39.130 0.00 0.00 45.14 3.32
1686 11102 3.111853 TCAGGCTACTGTTGAGTTGTG 57.888 47.619 0.00 0.00 45.14 3.33
1687 11103 2.434336 TCAGGCTACTGTTGAGTTGTGT 59.566 45.455 0.00 0.00 45.14 3.72
1688 11104 2.545526 CAGGCTACTGTTGAGTTGTGTG 59.454 50.000 0.00 0.00 39.92 3.82
1689 11105 1.264288 GGCTACTGTTGAGTTGTGTGC 59.736 52.381 0.00 0.00 33.21 4.57
1690 11106 1.939934 GCTACTGTTGAGTTGTGTGCA 59.060 47.619 0.00 0.00 33.21 4.57
1691 11107 2.549754 GCTACTGTTGAGTTGTGTGCAT 59.450 45.455 0.00 0.00 33.21 3.96
1692 11108 3.364366 GCTACTGTTGAGTTGTGTGCATC 60.364 47.826 0.00 0.00 33.21 3.91
1693 11109 1.949525 ACTGTTGAGTTGTGTGCATCC 59.050 47.619 0.00 0.00 0.00 3.51
1694 11110 2.224606 CTGTTGAGTTGTGTGCATCCT 58.775 47.619 0.00 0.00 0.00 3.24
1695 11111 3.181455 ACTGTTGAGTTGTGTGCATCCTA 60.181 43.478 0.00 0.00 0.00 2.94
1696 11112 3.814625 TGTTGAGTTGTGTGCATCCTAA 58.185 40.909 0.00 0.00 0.00 2.69
1697 11113 4.203226 TGTTGAGTTGTGTGCATCCTAAA 58.797 39.130 0.00 0.00 0.00 1.85
1698 11114 4.826733 TGTTGAGTTGTGTGCATCCTAAAT 59.173 37.500 0.00 0.00 0.00 1.40
1699 11115 6.000840 TGTTGAGTTGTGTGCATCCTAAATA 58.999 36.000 0.00 0.00 0.00 1.40
1700 11116 6.658816 TGTTGAGTTGTGTGCATCCTAAATAT 59.341 34.615 0.00 0.00 0.00 1.28
1701 11117 6.682423 TGAGTTGTGTGCATCCTAAATATG 57.318 37.500 0.00 0.00 0.00 1.78
1713 11129 5.749596 TCCTAAATATGCAAATCGTGTGG 57.250 39.130 0.00 0.00 0.00 4.17
1714 11130 4.578516 TCCTAAATATGCAAATCGTGTGGG 59.421 41.667 0.00 0.00 0.00 4.61
1715 11131 3.799281 AAATATGCAAATCGTGTGGGG 57.201 42.857 0.00 0.00 0.00 4.96
1716 11132 2.435372 ATATGCAAATCGTGTGGGGT 57.565 45.000 0.00 0.00 0.00 4.95
1717 11133 2.208132 TATGCAAATCGTGTGGGGTT 57.792 45.000 0.00 0.00 0.00 4.11
1718 11134 2.208132 ATGCAAATCGTGTGGGGTTA 57.792 45.000 0.00 0.00 0.00 2.85
1719 11135 2.208132 TGCAAATCGTGTGGGGTTAT 57.792 45.000 0.00 0.00 0.00 1.89
1720 11136 2.088423 TGCAAATCGTGTGGGGTTATC 58.912 47.619 0.00 0.00 0.00 1.75
1721 11137 1.063469 GCAAATCGTGTGGGGTTATCG 59.937 52.381 0.00 0.00 0.00 2.92
1722 11138 2.352388 CAAATCGTGTGGGGTTATCGT 58.648 47.619 0.00 0.00 0.00 3.73
1723 11139 2.304751 AATCGTGTGGGGTTATCGTC 57.695 50.000 0.00 0.00 0.00 4.20
1724 11140 0.462789 ATCGTGTGGGGTTATCGTCC 59.537 55.000 0.00 0.00 0.00 4.79
1725 11141 0.612732 TCGTGTGGGGTTATCGTCCT 60.613 55.000 0.00 0.00 0.00 3.85
1726 11142 0.179119 CGTGTGGGGTTATCGTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
1727 11143 1.192428 GTGTGGGGTTATCGTCCTCT 58.808 55.000 0.00 0.00 0.00 3.69
1728 11144 2.381911 GTGTGGGGTTATCGTCCTCTA 58.618 52.381 0.00 0.00 0.00 2.43
1729 11145 2.762327 GTGTGGGGTTATCGTCCTCTAA 59.238 50.000 0.00 0.00 0.00 2.10
1730 11146 3.196254 GTGTGGGGTTATCGTCCTCTAAA 59.804 47.826 0.00 0.00 0.00 1.85
1731 11147 3.839490 TGTGGGGTTATCGTCCTCTAAAA 59.161 43.478 0.00 0.00 0.00 1.52
1732 11148 4.286549 TGTGGGGTTATCGTCCTCTAAAAA 59.713 41.667 0.00 0.00 0.00 1.94
1733 11149 4.874396 GTGGGGTTATCGTCCTCTAAAAAG 59.126 45.833 0.00 0.00 0.00 2.27
1734 11150 4.080751 TGGGGTTATCGTCCTCTAAAAAGG 60.081 45.833 0.00 0.00 37.81 3.11
1735 11151 4.449131 GGGTTATCGTCCTCTAAAAAGGG 58.551 47.826 0.00 0.00 37.02 3.95
1736 11152 4.080695 GGGTTATCGTCCTCTAAAAAGGGT 60.081 45.833 0.00 0.00 37.02 4.34
1737 11153 5.114780 GGTTATCGTCCTCTAAAAAGGGTC 58.885 45.833 0.00 0.00 37.02 4.46
1738 11154 5.105023 GGTTATCGTCCTCTAAAAAGGGTCT 60.105 44.000 0.00 0.00 37.02 3.85
1739 11155 6.097412 GGTTATCGTCCTCTAAAAAGGGTCTA 59.903 42.308 0.00 0.00 37.02 2.59
1740 11156 7.201983 GGTTATCGTCCTCTAAAAAGGGTCTAT 60.202 40.741 0.00 0.00 37.02 1.98
1741 11157 5.848833 TCGTCCTCTAAAAAGGGTCTATC 57.151 43.478 0.00 0.00 37.02 2.08
1776 11192 6.103997 TGGCGACGATAAAGAGTTTTATTCT 58.896 36.000 0.00 0.00 39.10 2.40
1797 11213 3.627732 ATAGATGCAGAGTTACCGTCG 57.372 47.619 0.00 0.00 0.00 5.12
1801 11217 0.961857 TGCAGAGTTACCGTCGGCTA 60.962 55.000 12.28 0.01 36.26 3.93
1823 11239 2.416547 GCAAAAGCTCAGCGATACAAGA 59.583 45.455 0.00 0.00 0.00 3.02
1852 11268 1.577328 CTGTAGCCAACAAGCCGTGG 61.577 60.000 0.00 0.00 37.74 4.94
1903 11323 2.599082 CGATCGGCTACTCTGTTTTGAC 59.401 50.000 7.38 0.00 0.00 3.18
1919 11339 9.847224 TCTGTTTTGACCTCTAGAAACTTTTAT 57.153 29.630 0.00 0.00 34.12 1.40
1971 11391 6.677781 TGCTTAATCTCCGAAACTAAATGG 57.322 37.500 0.00 0.00 0.00 3.16
1973 11394 5.297029 GCTTAATCTCCGAAACTAAATGGCT 59.703 40.000 0.00 0.00 0.00 4.75
1986 11407 6.363577 ACTAAATGGCTGTATGTCGATTTG 57.636 37.500 0.00 0.00 0.00 2.32
2002 11423 5.864474 GTCGATTTGTCAAGACTATCTGTGT 59.136 40.000 1.53 0.00 0.00 3.72
2003 11424 6.034044 GTCGATTTGTCAAGACTATCTGTGTC 59.966 42.308 1.53 0.00 34.88 3.67
2034 11455 3.932710 AGAAAGCGCTATCGAACAATCAA 59.067 39.130 12.05 0.00 38.10 2.57
2078 11499 1.202114 GATCATTCCAAAGGCAACGCA 59.798 47.619 0.00 0.00 46.39 5.24
2081 11502 1.000385 CATTCCAAAGGCAACGCAAGA 60.000 47.619 0.00 0.00 46.39 3.02
2132 12971 3.060339 CCAAAGCGTCATTGCAGAAAAAC 60.060 43.478 0.00 0.00 37.31 2.43
2170 13009 6.682113 GCAGCAAAAATCATATGTCCATCTGT 60.682 38.462 1.90 0.00 0.00 3.41
2171 13010 7.469043 GCAGCAAAAATCATATGTCCATCTGTA 60.469 37.037 1.90 0.00 0.00 2.74
2177 13016 9.941325 AAAATCATATGTCCATCTGTATCTCTC 57.059 33.333 1.90 0.00 0.00 3.20
2180 13019 7.465116 TCATATGTCCATCTGTATCTCTCAGA 58.535 38.462 1.90 0.00 44.37 3.27
2190 13030 7.911130 TCTGTATCTCTCAGAATCATTCCTT 57.089 36.000 0.00 0.00 38.71 3.36
2192 13032 7.784073 TCTGTATCTCTCAGAATCATTCCTTCT 59.216 37.037 0.00 0.00 38.71 2.85
2216 13056 2.027625 CGACCCGTCTGAGGCAAAC 61.028 63.158 0.00 0.00 0.00 2.93
2256 13096 3.781307 CCCGCCTGACATCCGGAA 61.781 66.667 9.01 0.00 44.55 4.30
2280 13120 0.179037 CCACGATGGAGATGGTGCAT 60.179 55.000 0.00 0.00 40.96 3.96
2320 13160 0.034186 GACCAGCCATCACCCAATGA 60.034 55.000 0.00 0.00 43.13 2.57
2356 13197 4.134379 ACATCTCCTCTGTGCTATGTTG 57.866 45.455 0.00 0.00 0.00 3.33
2373 13214 8.402472 TGCTATGTTGTTTAGCATACCAAATAC 58.598 33.333 1.45 0.00 45.28 1.89
2387 13233 5.968676 ACCAAATACAGGTAGCTATCCAA 57.031 39.130 0.00 0.00 37.67 3.53
2449 13295 0.110056 CACAACATCTGTCCGCAAGC 60.110 55.000 0.00 0.00 35.47 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.793775 TTTGACTTGCGACCGCGGA 62.794 57.895 35.90 6.02 45.51 5.54
47 48 3.295228 CTTTGACTTGCGACCGCGG 62.295 63.158 26.86 26.86 45.51 6.46
48 49 2.170985 CTTTGACTTGCGACCGCG 59.829 61.111 9.91 0.00 45.51 6.46
49 50 2.556287 CCTTTGACTTGCGACCGC 59.444 61.111 7.53 7.53 42.35 5.68
50 51 2.325082 CCCCTTTGACTTGCGACCG 61.325 63.158 0.00 0.00 0.00 4.79
51 52 0.536460 TTCCCCTTTGACTTGCGACC 60.536 55.000 0.00 0.00 0.00 4.79
52 53 1.314730 TTTCCCCTTTGACTTGCGAC 58.685 50.000 0.00 0.00 0.00 5.19
53 54 1.953686 CTTTTCCCCTTTGACTTGCGA 59.046 47.619 0.00 0.00 0.00 5.10
54 55 1.000274 CCTTTTCCCCTTTGACTTGCG 60.000 52.381 0.00 0.00 0.00 4.85
55 56 2.316108 TCCTTTTCCCCTTTGACTTGC 58.684 47.619 0.00 0.00 0.00 4.01
56 57 4.835056 AGAATCCTTTTCCCCTTTGACTTG 59.165 41.667 0.00 0.00 0.00 3.16
57 58 4.835056 CAGAATCCTTTTCCCCTTTGACTT 59.165 41.667 0.00 0.00 0.00 3.01
58 59 4.411013 CAGAATCCTTTTCCCCTTTGACT 58.589 43.478 0.00 0.00 0.00 3.41
59 60 3.511540 CCAGAATCCTTTTCCCCTTTGAC 59.488 47.826 0.00 0.00 0.00 3.18
60 61 3.401002 TCCAGAATCCTTTTCCCCTTTGA 59.599 43.478 0.00 0.00 0.00 2.69
61 62 3.766051 CTCCAGAATCCTTTTCCCCTTTG 59.234 47.826 0.00 0.00 0.00 2.77
62 63 3.402708 ACTCCAGAATCCTTTTCCCCTTT 59.597 43.478 0.00 0.00 0.00 3.11
63 64 2.996742 ACTCCAGAATCCTTTTCCCCTT 59.003 45.455 0.00 0.00 0.00 3.95
64 65 2.310052 CACTCCAGAATCCTTTTCCCCT 59.690 50.000 0.00 0.00 0.00 4.79
65 66 2.041755 ACACTCCAGAATCCTTTTCCCC 59.958 50.000 0.00 0.00 0.00 4.81
66 67 3.084786 CACACTCCAGAATCCTTTTCCC 58.915 50.000 0.00 0.00 0.00 3.97
67 68 3.084786 CCACACTCCAGAATCCTTTTCC 58.915 50.000 0.00 0.00 0.00 3.13
68 69 4.006319 CTCCACACTCCAGAATCCTTTTC 58.994 47.826 0.00 0.00 0.00 2.29
69 70 3.395941 ACTCCACACTCCAGAATCCTTTT 59.604 43.478 0.00 0.00 0.00 2.27
70 71 2.982488 ACTCCACACTCCAGAATCCTTT 59.018 45.455 0.00 0.00 0.00 3.11
71 72 2.625639 ACTCCACACTCCAGAATCCTT 58.374 47.619 0.00 0.00 0.00 3.36
72 73 2.304180 CAACTCCACACTCCAGAATCCT 59.696 50.000 0.00 0.00 0.00 3.24
73 74 2.616510 CCAACTCCACACTCCAGAATCC 60.617 54.545 0.00 0.00 0.00 3.01
74 75 2.039084 ACCAACTCCACACTCCAGAATC 59.961 50.000 0.00 0.00 0.00 2.52
75 76 2.039084 GACCAACTCCACACTCCAGAAT 59.961 50.000 0.00 0.00 0.00 2.40
76 77 1.416401 GACCAACTCCACACTCCAGAA 59.584 52.381 0.00 0.00 0.00 3.02
77 78 1.048601 GACCAACTCCACACTCCAGA 58.951 55.000 0.00 0.00 0.00 3.86
78 79 0.319900 CGACCAACTCCACACTCCAG 60.320 60.000 0.00 0.00 0.00 3.86
79 80 1.745890 CGACCAACTCCACACTCCA 59.254 57.895 0.00 0.00 0.00 3.86
80 81 1.668151 GCGACCAACTCCACACTCC 60.668 63.158 0.00 0.00 0.00 3.85
81 82 0.946221 CAGCGACCAACTCCACACTC 60.946 60.000 0.00 0.00 0.00 3.51
82 83 1.069765 CAGCGACCAACTCCACACT 59.930 57.895 0.00 0.00 0.00 3.55
83 84 2.607892 GCAGCGACCAACTCCACAC 61.608 63.158 0.00 0.00 0.00 3.82
84 85 2.280797 GCAGCGACCAACTCCACA 60.281 61.111 0.00 0.00 0.00 4.17
85 86 1.639298 GATGCAGCGACCAACTCCAC 61.639 60.000 0.00 0.00 0.00 4.02
86 87 1.375908 GATGCAGCGACCAACTCCA 60.376 57.895 0.00 0.00 0.00 3.86
87 88 2.109126 GGATGCAGCGACCAACTCC 61.109 63.158 0.00 0.00 0.00 3.85
88 89 1.364626 CTGGATGCAGCGACCAACTC 61.365 60.000 0.00 0.00 33.14 3.01
89 90 1.376424 CTGGATGCAGCGACCAACT 60.376 57.895 0.00 0.00 33.14 3.16
90 91 2.401766 CCTGGATGCAGCGACCAAC 61.402 63.158 9.03 0.00 33.14 3.77
91 92 2.046023 CCTGGATGCAGCGACCAA 60.046 61.111 9.03 0.00 33.14 3.67
92 93 4.100084 CCCTGGATGCAGCGACCA 62.100 66.667 9.03 9.54 0.00 4.02
94 95 4.479993 AGCCCTGGATGCAGCGAC 62.480 66.667 9.03 0.00 0.00 5.19
95 96 4.166888 GAGCCCTGGATGCAGCGA 62.167 66.667 9.03 0.00 0.00 4.93
97 98 4.119363 TGGAGCCCTGGATGCAGC 62.119 66.667 9.03 0.00 0.00 5.25
98 99 2.192443 CTGGAGCCCTGGATGCAG 59.808 66.667 8.57 8.57 42.83 4.41
99 100 3.414193 CCTGGAGCCCTGGATGCA 61.414 66.667 10.45 0.00 44.09 3.96
100 101 4.891037 GCCTGGAGCCCTGGATGC 62.891 72.222 17.59 0.00 44.09 3.91
101 102 2.693896 GATGCCTGGAGCCCTGGATG 62.694 65.000 17.59 0.00 44.09 3.51
102 103 2.369291 ATGCCTGGAGCCCTGGAT 60.369 61.111 17.59 8.09 44.09 3.41
103 104 3.092511 GATGCCTGGAGCCCTGGA 61.093 66.667 17.59 6.56 44.09 3.86
104 105 4.559063 CGATGCCTGGAGCCCTGG 62.559 72.222 0.00 11.33 44.16 4.45
105 106 2.374830 CTACGATGCCTGGAGCCCTG 62.375 65.000 0.00 0.00 42.71 4.45
106 107 2.041922 TACGATGCCTGGAGCCCT 60.042 61.111 0.00 0.00 42.71 5.19
107 108 2.134287 TCTACGATGCCTGGAGCCC 61.134 63.158 0.00 0.00 42.71 5.19
108 109 1.068250 GTCTACGATGCCTGGAGCC 59.932 63.158 0.00 0.00 42.71 4.70
109 110 1.268352 CTAGTCTACGATGCCTGGAGC 59.732 57.143 0.00 0.00 44.14 4.70
110 111 2.550606 GACTAGTCTACGATGCCTGGAG 59.449 54.545 15.91 0.00 0.00 3.86
111 112 2.092592 TGACTAGTCTACGATGCCTGGA 60.093 50.000 23.01 0.00 0.00 3.86
112 113 2.298610 TGACTAGTCTACGATGCCTGG 58.701 52.381 23.01 0.00 0.00 4.45
113 114 4.757657 ACTATGACTAGTCTACGATGCCTG 59.242 45.833 23.01 5.11 32.56 4.85
114 115 4.975631 ACTATGACTAGTCTACGATGCCT 58.024 43.478 23.01 0.86 32.56 4.75
115 116 5.238868 TCAACTATGACTAGTCTACGATGCC 59.761 44.000 23.01 0.00 37.20 4.40
116 117 6.301687 TCAACTATGACTAGTCTACGATGC 57.698 41.667 23.01 0.00 37.20 3.91
118 119 9.781633 ACTTATCAACTATGACTAGTCTACGAT 57.218 33.333 23.01 16.44 37.20 3.73
119 120 9.043079 CACTTATCAACTATGACTAGTCTACGA 57.957 37.037 23.01 11.30 37.20 3.43
120 121 8.283992 CCACTTATCAACTATGACTAGTCTACG 58.716 40.741 23.01 12.99 37.20 3.51
121 122 8.569641 CCCACTTATCAACTATGACTAGTCTAC 58.430 40.741 23.01 0.00 37.20 2.59
122 123 7.230913 GCCCACTTATCAACTATGACTAGTCTA 59.769 40.741 23.01 10.48 37.20 2.59
123 124 6.041069 GCCCACTTATCAACTATGACTAGTCT 59.959 42.308 23.01 11.45 37.20 3.24
124 125 6.217294 GCCCACTTATCAACTATGACTAGTC 58.783 44.000 16.32 16.32 37.20 2.59
125 126 5.070580 GGCCCACTTATCAACTATGACTAGT 59.929 44.000 0.00 0.00 39.97 2.57
126 127 5.305644 AGGCCCACTTATCAACTATGACTAG 59.694 44.000 0.00 0.00 38.69 2.57
127 128 5.070446 CAGGCCCACTTATCAACTATGACTA 59.930 44.000 0.00 0.00 38.69 2.59
128 129 4.040755 AGGCCCACTTATCAACTATGACT 58.959 43.478 0.00 0.00 38.69 3.41
129 130 4.130118 CAGGCCCACTTATCAACTATGAC 58.870 47.826 0.00 0.00 38.69 3.06
130 131 3.780294 ACAGGCCCACTTATCAACTATGA 59.220 43.478 0.00 0.00 40.57 2.15
131 132 3.879295 CACAGGCCCACTTATCAACTATG 59.121 47.826 0.00 0.00 0.00 2.23
132 133 3.117888 CCACAGGCCCACTTATCAACTAT 60.118 47.826 0.00 0.00 0.00 2.12
133 134 2.238646 CCACAGGCCCACTTATCAACTA 59.761 50.000 0.00 0.00 0.00 2.24
134 135 1.004745 CCACAGGCCCACTTATCAACT 59.995 52.381 0.00 0.00 0.00 3.16
135 136 1.463674 CCACAGGCCCACTTATCAAC 58.536 55.000 0.00 0.00 0.00 3.18
136 137 0.331278 CCCACAGGCCCACTTATCAA 59.669 55.000 0.00 0.00 0.00 2.57
137 138 1.998530 CCCACAGGCCCACTTATCA 59.001 57.895 0.00 0.00 0.00 2.15
138 139 4.986467 CCCACAGGCCCACTTATC 57.014 61.111 0.00 0.00 0.00 1.75
148 149 4.623932 ATGTATACATACAGCCCACAGG 57.376 45.455 16.85 0.00 45.46 4.00
149 150 5.337571 CCCTATGTATACATACAGCCCACAG 60.338 48.000 19.51 9.76 45.46 3.66
150 151 4.530553 CCCTATGTATACATACAGCCCACA 59.469 45.833 19.51 0.90 45.46 4.17
151 152 4.081087 CCCCTATGTATACATACAGCCCAC 60.081 50.000 19.51 0.00 45.46 4.61
152 153 4.101114 CCCCTATGTATACATACAGCCCA 58.899 47.826 19.51 2.25 45.46 5.36
153 154 4.101856 ACCCCTATGTATACATACAGCCC 58.898 47.826 19.51 0.00 45.46 5.19
154 155 5.956563 ACTACCCCTATGTATACATACAGCC 59.043 44.000 19.51 0.00 45.46 4.85
155 156 8.585471 TTACTACCCCTATGTATACATACAGC 57.415 38.462 19.51 0.00 45.46 4.40
213 214 4.278513 TTCGTGGGGGCCAACCTG 62.279 66.667 15.84 9.13 40.03 4.00
214 215 3.966543 CTTCGTGGGGGCCAACCT 61.967 66.667 15.84 0.00 40.03 3.50
216 217 4.660938 AGCTTCGTGGGGGCCAAC 62.661 66.667 4.39 1.53 34.18 3.77
217 218 4.344865 GAGCTTCGTGGGGGCCAA 62.345 66.667 4.39 0.00 34.18 4.52
232 233 1.517257 CTAGCAGACAACGGCGGAG 60.517 63.158 13.24 5.44 41.73 4.63
233 234 1.529152 TTCTAGCAGACAACGGCGGA 61.529 55.000 13.24 0.00 41.73 5.54
234 235 0.669318 TTTCTAGCAGACAACGGCGG 60.669 55.000 13.24 0.00 41.73 6.13
235 236 1.061131 CATTTCTAGCAGACAACGGCG 59.939 52.381 4.80 4.80 41.73 6.46
236 237 1.202076 GCATTTCTAGCAGACAACGGC 60.202 52.381 0.00 0.00 37.48 5.68
237 238 1.398390 GGCATTTCTAGCAGACAACGG 59.602 52.381 0.00 0.00 0.00 4.44
238 239 1.398390 GGGCATTTCTAGCAGACAACG 59.602 52.381 0.00 0.00 0.00 4.10
239 240 2.716217 AGGGCATTTCTAGCAGACAAC 58.284 47.619 0.00 0.00 0.00 3.32
240 241 3.084039 CAAGGGCATTTCTAGCAGACAA 58.916 45.455 0.00 0.00 0.00 3.18
241 242 2.305635 TCAAGGGCATTTCTAGCAGACA 59.694 45.455 0.00 0.00 0.00 3.41
242 243 2.991250 TCAAGGGCATTTCTAGCAGAC 58.009 47.619 0.00 0.00 0.00 3.51
252 253 1.551883 GGCTGTTCAATCAAGGGCATT 59.448 47.619 0.00 0.00 0.00 3.56
324 325 0.526211 GGATTCGCACTTTTGGACCC 59.474 55.000 0.00 0.00 0.00 4.46
340 341 0.114364 AAGTTCAAAAGCCCCGGGAT 59.886 50.000 26.32 7.34 0.00 3.85
420 4386 0.546122 AGCAACCATATTCTCCGGCA 59.454 50.000 0.00 0.00 0.00 5.69
566 6237 2.623889 ACTAGGTAGTGATCGACATGGC 59.376 50.000 0.00 0.00 34.72 4.40
588 6281 4.082517 CAGATAGACACACACACACTAGCT 60.083 45.833 0.00 0.00 31.47 3.32
589 6282 4.169508 CAGATAGACACACACACACTAGC 58.830 47.826 0.00 0.00 0.00 3.42
590 6283 4.082517 AGCAGATAGACACACACACACTAG 60.083 45.833 0.00 0.00 0.00 2.57
591 6284 3.826729 AGCAGATAGACACACACACACTA 59.173 43.478 0.00 0.00 0.00 2.74
592 6285 2.630098 AGCAGATAGACACACACACACT 59.370 45.455 0.00 0.00 0.00 3.55
614 6307 1.821216 TCAATGGCCGAGGTTTCTTC 58.179 50.000 0.00 0.00 0.00 2.87
707 6400 2.163412 GCGGTTGCAGATTGACCATTAA 59.837 45.455 5.40 0.00 42.15 1.40
742 6435 1.068121 AGTTTCTCTCCCCACCCTTG 58.932 55.000 0.00 0.00 0.00 3.61
745 6438 0.771755 ACAAGTTTCTCTCCCCACCC 59.228 55.000 0.00 0.00 0.00 4.61
759 6455 8.572185 CACATAGATAGAGCATAGTACACAAGT 58.428 37.037 0.00 0.00 0.00 3.16
1145 10415 3.184541 CAACTCGGGGTACGTTTATCTG 58.815 50.000 0.00 0.00 44.69 2.90
1167 10451 0.601558 AGCATGAGCAAACAAGCCAG 59.398 50.000 0.00 0.00 45.49 4.85
1186 10472 2.088423 ACACGAACAAGAAAGGCACAA 58.912 42.857 0.00 0.00 0.00 3.33
1197 10485 0.105964 AGTAGCCTGCACACGAACAA 59.894 50.000 0.00 0.00 0.00 2.83
1201 10489 1.601419 GGGTAGTAGCCTGCACACGA 61.601 60.000 11.29 0.00 31.81 4.35
1350 10717 1.659098 CCGGAAATCACTAGCGACAAC 59.341 52.381 0.00 0.00 0.00 3.32
1371 10738 5.677091 GCGCAAAATTCAGACCATTATCAGT 60.677 40.000 0.30 0.00 0.00 3.41
1431 10803 2.796425 CGCAGCACATCTCGCAGAC 61.796 63.158 0.00 0.00 0.00 3.51
1517 10909 3.802948 ACGACTCTCTCTCTCTCTCTC 57.197 52.381 0.00 0.00 0.00 3.20
1519 10911 2.351726 GCAACGACTCTCTCTCTCTCTC 59.648 54.545 0.00 0.00 0.00 3.20
1657 11073 5.192927 TCAACAGTAGCCTGATAATTTGGG 58.807 41.667 0.00 0.00 41.50 4.12
1689 11105 6.144854 CCACACGATTTGCATATTTAGGATG 58.855 40.000 0.00 0.00 0.00 3.51
1690 11106 5.241506 CCCACACGATTTGCATATTTAGGAT 59.758 40.000 0.00 0.00 0.00 3.24
1691 11107 4.578516 CCCACACGATTTGCATATTTAGGA 59.421 41.667 0.00 0.00 0.00 2.94
1692 11108 4.261572 CCCCACACGATTTGCATATTTAGG 60.262 45.833 0.00 0.00 0.00 2.69
1693 11109 4.338118 ACCCCACACGATTTGCATATTTAG 59.662 41.667 0.00 0.00 0.00 1.85
1694 11110 4.274147 ACCCCACACGATTTGCATATTTA 58.726 39.130 0.00 0.00 0.00 1.40
1695 11111 3.096092 ACCCCACACGATTTGCATATTT 58.904 40.909 0.00 0.00 0.00 1.40
1696 11112 2.733956 ACCCCACACGATTTGCATATT 58.266 42.857 0.00 0.00 0.00 1.28
1697 11113 2.435372 ACCCCACACGATTTGCATAT 57.565 45.000 0.00 0.00 0.00 1.78
1698 11114 2.208132 AACCCCACACGATTTGCATA 57.792 45.000 0.00 0.00 0.00 3.14
1699 11115 2.208132 TAACCCCACACGATTTGCAT 57.792 45.000 0.00 0.00 0.00 3.96
1700 11116 2.088423 GATAACCCCACACGATTTGCA 58.912 47.619 0.00 0.00 0.00 4.08
1701 11117 1.063469 CGATAACCCCACACGATTTGC 59.937 52.381 0.00 0.00 0.00 3.68
1702 11118 2.350498 GACGATAACCCCACACGATTTG 59.650 50.000 0.00 0.00 0.00 2.32
1703 11119 2.624636 GACGATAACCCCACACGATTT 58.375 47.619 0.00 0.00 0.00 2.17
1704 11120 1.134610 GGACGATAACCCCACACGATT 60.135 52.381 0.00 0.00 0.00 3.34
1705 11121 0.462789 GGACGATAACCCCACACGAT 59.537 55.000 0.00 0.00 0.00 3.73
1706 11122 0.612732 AGGACGATAACCCCACACGA 60.613 55.000 0.00 0.00 0.00 4.35
1707 11123 0.179119 GAGGACGATAACCCCACACG 60.179 60.000 0.00 0.00 0.00 4.49
1708 11124 1.192428 AGAGGACGATAACCCCACAC 58.808 55.000 0.00 0.00 0.00 3.82
1709 11125 2.832643 TAGAGGACGATAACCCCACA 57.167 50.000 0.00 0.00 0.00 4.17
1710 11126 4.476628 TTTTAGAGGACGATAACCCCAC 57.523 45.455 0.00 0.00 0.00 4.61
1711 11127 4.080751 CCTTTTTAGAGGACGATAACCCCA 60.081 45.833 0.00 0.00 39.25 4.96
1712 11128 4.449131 CCTTTTTAGAGGACGATAACCCC 58.551 47.826 0.00 0.00 39.25 4.95
1713 11129 4.080695 ACCCTTTTTAGAGGACGATAACCC 60.081 45.833 0.00 0.00 39.25 4.11
1714 11130 5.095145 ACCCTTTTTAGAGGACGATAACC 57.905 43.478 0.00 0.00 39.25 2.85
1715 11131 5.975282 AGACCCTTTTTAGAGGACGATAAC 58.025 41.667 0.00 0.00 39.25 1.89
1716 11132 7.783596 AGATAGACCCTTTTTAGAGGACGATAA 59.216 37.037 0.00 0.00 39.25 1.75
1717 11133 7.296098 AGATAGACCCTTTTTAGAGGACGATA 58.704 38.462 0.00 0.00 39.25 2.92
1718 11134 6.137559 AGATAGACCCTTTTTAGAGGACGAT 58.862 40.000 0.00 0.00 39.25 3.73
1719 11135 5.516984 AGATAGACCCTTTTTAGAGGACGA 58.483 41.667 0.00 0.00 39.25 4.20
1720 11136 5.595133 AGAGATAGACCCTTTTTAGAGGACG 59.405 44.000 0.00 0.00 39.25 4.79
1721 11137 7.426606 AAGAGATAGACCCTTTTTAGAGGAC 57.573 40.000 0.00 0.00 39.25 3.85
1722 11138 8.450780 AAAAGAGATAGACCCTTTTTAGAGGA 57.549 34.615 0.00 0.00 39.25 3.71
1753 11169 6.585389 AGAATAAAACTCTTTATCGTCGCC 57.415 37.500 0.00 0.00 36.84 5.54
1776 11192 3.501062 CCGACGGTAACTCTGCATCTATA 59.499 47.826 5.48 0.00 0.00 1.31
1823 11239 2.308570 TGTTGGCTACAGGATTGTCCAT 59.691 45.455 0.00 0.00 39.61 3.41
1852 11268 7.541437 GGCGAATTATGGTAGAATAGAGTGTAC 59.459 40.741 0.00 0.00 0.00 2.90
1887 11303 3.686916 AGAGGTCAAAACAGAGTAGCC 57.313 47.619 0.00 0.00 0.00 3.93
1919 11339 6.099269 ACTTGTTGGTAGAGAGTTTGTTCCTA 59.901 38.462 0.00 0.00 0.00 2.94
1971 11391 4.627467 AGTCTTGACAAATCGACATACAGC 59.373 41.667 8.32 0.00 0.00 4.40
1973 11394 7.702348 CAGATAGTCTTGACAAATCGACATACA 59.298 37.037 8.32 0.00 0.00 2.29
1986 11407 4.421033 TGTCGACACAGATAGTCTTGAC 57.579 45.455 15.76 0.00 33.89 3.18
2002 11423 0.033504 AGCGCTTTCTTCCTTGTCGA 59.966 50.000 2.64 0.00 0.00 4.20
2003 11424 1.710013 TAGCGCTTTCTTCCTTGTCG 58.290 50.000 18.68 0.00 0.00 4.35
2034 11455 4.519906 ACCTTCCGGTGATTATCCAATT 57.480 40.909 0.00 0.00 43.51 2.32
2081 11502 5.396884 GGAACTACATGCAATAAGAGAGGGT 60.397 44.000 0.00 0.00 0.00 4.34
2132 12971 5.484173 TTTTTGCTGCTTACCGATATCTG 57.516 39.130 0.00 0.00 0.00 2.90
2170 13009 7.233144 CAGGAGAAGGAATGATTCTGAGAGATA 59.767 40.741 5.03 0.00 37.14 1.98
2171 13010 6.042322 CAGGAGAAGGAATGATTCTGAGAGAT 59.958 42.308 5.03 0.00 37.14 2.75
2177 13016 3.212685 GGCAGGAGAAGGAATGATTCTG 58.787 50.000 5.03 0.00 37.14 3.02
2180 13019 1.839994 TCGGCAGGAGAAGGAATGATT 59.160 47.619 0.00 0.00 0.00 2.57
2190 13030 4.361971 AGACGGGTCGGCAGGAGA 62.362 66.667 0.00 0.00 37.34 3.71
2192 13032 4.671590 TCAGACGGGTCGGCAGGA 62.672 66.667 0.00 0.00 37.34 3.86
2250 13090 3.000819 ATCGTGGCCTGTTCCGGA 61.001 61.111 0.00 0.00 0.00 5.14
2256 13096 1.524002 CATCTCCATCGTGGCCTGT 59.476 57.895 3.32 0.00 37.47 4.00
2320 13160 8.043710 CAGAGGAGATGTTAAAAGGTAAGATGT 58.956 37.037 0.00 0.00 0.00 3.06
2356 13197 6.766467 AGCTACCTGTATTTGGTATGCTAAAC 59.234 38.462 11.95 0.00 39.89 2.01
2373 13214 6.703607 CAGTTGACTATTTGGATAGCTACCTG 59.296 42.308 0.00 0.00 39.09 4.00
2387 13233 8.918202 TCCAGTACAATTTTCAGTTGACTATT 57.082 30.769 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.