Multiple sequence alignment - TraesCS3B01G217200

Loading Multiple Alignment...

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 TraesCS3B01G217200 chr3B 100.000 3710 0 0 1 3710 259369644 259373353 0.000000e+00 6852.0
1 TraesCS3B01G217200 chr3D 94.907 3024 133 9 214 3228 181103053 181106064 0.000000e+00 4711.0
2 TraesCS3B01G217200 chr3D 89.697 330 31 3 3230 3557 181106359 181106687 5.730000e-113 418.0
3 TraesCS3B01G217200 chr3D 88.235 119 12 1 6 122 109842454 109842572 1.390000e-29 141.0
4 TraesCS3B01G217200 chr3A 94.000 2500 135 8 740 3228 227923657 227921162 0.000000e+00 3771.0
5 TraesCS3B01G217200 chr3A 96.018 452 15 2 243 693 227924100 227923651 0.000000e+00 732.0
6 TraesCS3B01G217200 chr3A 85.758 330 29 8 3230 3557 227920913 227920600 2.140000e-87 333.0
7 TraesCS3B01G217200 chr3A 94.958 119 5 1 3527 3645 227920550 227920433 6.330000e-43 185.0
8 TraesCS3B01G217200 chr3A 78.814 118 14 5 3380 3486 58949201 58949084 6.650000e-08 69.4
9 TraesCS3B01G217200 chr7D 90.189 2171 192 13 717 2878 576333005 576335163 0.000000e+00 2809.0
10 TraesCS3B01G217200 chr7D 76.675 403 48 26 2987 3381 576335189 576335553 8.180000e-42 182.0
11 TraesCS3B01G217200 chr7D 89.412 85 7 2 354 437 576332553 576332636 5.070000e-19 106.0
12 TraesCS3B01G217200 chr7B 90.923 1994 165 6 740 2727 639083168 639085151 0.000000e+00 2665.0
13 TraesCS3B01G217200 chr7B 90.826 109 10 0 14 122 221894 221786 2.990000e-31 147.0
14 TraesCS3B01G217200 chr7B 74.790 357 53 21 3029 3381 704093201 704092878 3.890000e-25 126.0
15 TraesCS3B01G217200 chr7B 93.617 47 3 0 391 437 639082740 639082786 1.850000e-08 71.3
16 TraesCS3B01G217200 chr7A 89.353 2057 176 29 1094 3143 667475058 667477078 0.000000e+00 2545.0
17 TraesCS3B01G217200 chr7A 91.429 105 9 0 14 118 498582837 498582733 1.070000e-30 145.0
18 TraesCS3B01G217200 chr7A 84.000 125 12 7 3257 3381 667477143 667477259 3.030000e-21 113.0
19 TraesCS3B01G217200 chr7A 100.000 30 0 0 3352 3381 705142176 705142147 5.180000e-04 56.5
20 TraesCS3B01G217200 chr6A 90.741 108 10 0 14 121 605212183 605212076 1.070000e-30 145.0
21 TraesCS3B01G217200 chr6A 90.090 111 9 2 14 123 58764665 58764556 3.860000e-30 143.0
22 TraesCS3B01G217200 chr6A 89.286 112 10 1 6 115 195270216 195270327 5.000000e-29 139.0
23 TraesCS3B01G217200 chr5D 88.696 115 13 0 14 128 412510334 412510220 1.390000e-29 141.0
24 TraesCS3B01G217200 chr2D 88.793 116 11 1 6 119 12588401 12588516 1.390000e-29 141.0
25 TraesCS3B01G217200 chr2D 90.566 106 10 0 14 119 142440982 142441087 1.390000e-29 141.0
26 TraesCS3B01G217200 chr6D 85.714 84 7 5 3536 3615 269124201 269124119 2.370000e-12 84.2
27 TraesCS3B01G217200 chr5A 78.226 124 15 4 3374 3486 567961288 567961166 6.650000e-08 69.4


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 TraesCS3B01G217200 chr3B 259369644 259373353 3709 False 6852.000000 6852 100.000000 1 3710 1 chr3B.!!$F1 3709
1 TraesCS3B01G217200 chr3D 181103053 181106687 3634 False 2564.500000 4711 92.302000 214 3557 2 chr3D.!!$F2 3343
2 TraesCS3B01G217200 chr3A 227920433 227924100 3667 True 1255.250000 3771 92.683500 243 3645 4 chr3A.!!$R2 3402
3 TraesCS3B01G217200 chr7D 576332553 576335553 3000 False 1032.333333 2809 85.425333 354 3381 3 chr7D.!!$F1 3027
4 TraesCS3B01G217200 chr7B 639082740 639085151 2411 False 1368.150000 2665 92.270000 391 2727 2 chr7B.!!$F1 2336
5 TraesCS3B01G217200 chr7A 667475058 667477259 2201 False 1329.000000 2545 86.676500 1094 3381 2 chr7A.!!$F1 2287

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
128 129 0.036306 AACACCCCCTAAGTCAAGCG 59.964 55.0 0.0 0.0 0.00 4.68 F
132 133 0.177373 CCCCCTAAGTCAAGCGGTAC 59.823 60.0 0.0 0.0 0.00 3.34 F
1740 1885 0.313987 CTGTGTCGTGGACAGCACTA 59.686 55.0 0.0 0.0 43.57 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1954 0.399833 TGTCATTAGGCCTGCACACA 59.600 50.000 17.99 10.43 0.00 3.72 R
2011 2156 1.145738 AGAAACCAGGTCCTTGCACAT 59.854 47.619 0.00 0.00 0.00 3.21 R
3490 3941 0.179084 AGATGGGTACAATCCACGCG 60.179 55.000 3.53 3.53 37.08 6.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.538666 CATTGGGAGGGGCCTAAGG 59.461 63.158 0.84 0.00 40.79 2.69
19 20 0.993509 CATTGGGAGGGGCCTAAGGA 60.994 60.000 0.84 0.00 40.89 3.36
20 21 0.994050 ATTGGGAGGGGCCTAAGGAC 60.994 60.000 0.84 0.00 40.79 3.85
21 22 2.132946 TTGGGAGGGGCCTAAGGACT 62.133 60.000 0.84 0.00 31.35 3.85
22 23 1.307953 GGGAGGGGCCTAAGGACTT 60.308 63.158 0.84 0.00 36.66 3.01
23 24 0.919780 GGGAGGGGCCTAAGGACTTT 60.920 60.000 0.84 0.00 36.66 2.66
24 25 1.000496 GGAGGGGCCTAAGGACTTTT 59.000 55.000 0.84 0.00 0.00 2.27
25 26 2.202707 GGAGGGGCCTAAGGACTTTTA 58.797 52.381 0.84 0.00 0.00 1.52
26 27 2.172930 GGAGGGGCCTAAGGACTTTTAG 59.827 54.545 0.84 0.00 0.00 1.85
27 28 1.564818 AGGGGCCTAAGGACTTTTAGC 59.435 52.381 0.84 0.00 30.84 3.09
28 29 1.283905 GGGGCCTAAGGACTTTTAGCA 59.716 52.381 0.84 0.00 30.84 3.49
29 30 2.291346 GGGGCCTAAGGACTTTTAGCAA 60.291 50.000 0.84 0.00 30.84 3.91
30 31 3.427573 GGGCCTAAGGACTTTTAGCAAA 58.572 45.455 0.84 0.00 30.84 3.68
31 32 3.830178 GGGCCTAAGGACTTTTAGCAAAA 59.170 43.478 0.84 0.00 30.84 2.44
32 33 4.282449 GGGCCTAAGGACTTTTAGCAAAAA 59.718 41.667 0.84 0.00 33.58 1.94
65 66 8.496707 AAAAGTTTCATCTTGTTTGATTTGCT 57.503 26.923 0.00 0.00 0.00 3.91
66 67 9.598517 AAAAGTTTCATCTTGTTTGATTTGCTA 57.401 25.926 0.00 0.00 0.00 3.49
67 68 8.807667 AAGTTTCATCTTGTTTGATTTGCTAG 57.192 30.769 0.00 0.00 0.00 3.42
68 69 7.373493 AGTTTCATCTTGTTTGATTTGCTAGG 58.627 34.615 0.00 0.00 0.00 3.02
69 70 5.902613 TCATCTTGTTTGATTTGCTAGGG 57.097 39.130 0.00 0.00 0.00 3.53
70 71 5.569355 TCATCTTGTTTGATTTGCTAGGGA 58.431 37.500 0.00 0.00 0.00 4.20
71 72 5.415701 TCATCTTGTTTGATTTGCTAGGGAC 59.584 40.000 0.00 0.00 0.00 4.46
72 73 4.985538 TCTTGTTTGATTTGCTAGGGACT 58.014 39.130 0.00 0.00 46.37 3.85
73 74 5.385198 TCTTGTTTGATTTGCTAGGGACTT 58.615 37.500 0.00 0.00 41.75 3.01
74 75 5.833131 TCTTGTTTGATTTGCTAGGGACTTT 59.167 36.000 0.00 0.00 41.75 2.66
75 76 5.705609 TGTTTGATTTGCTAGGGACTTTC 57.294 39.130 0.00 0.00 41.75 2.62
76 77 5.385198 TGTTTGATTTGCTAGGGACTTTCT 58.615 37.500 0.00 0.00 41.75 2.52
77 78 5.473504 TGTTTGATTTGCTAGGGACTTTCTC 59.526 40.000 0.00 0.00 41.75 2.87
78 79 5.505181 TTGATTTGCTAGGGACTTTCTCT 57.495 39.130 0.00 0.00 41.75 3.10
79 80 6.620877 TTGATTTGCTAGGGACTTTCTCTA 57.379 37.500 0.00 0.00 41.75 2.43
80 81 6.620877 TGATTTGCTAGGGACTTTCTCTAA 57.379 37.500 0.00 0.00 41.75 2.10
81 82 7.200434 TGATTTGCTAGGGACTTTCTCTAAT 57.800 36.000 0.00 0.00 41.75 1.73
82 83 7.275920 TGATTTGCTAGGGACTTTCTCTAATC 58.724 38.462 0.00 0.00 41.75 1.75
83 84 5.615925 TTGCTAGGGACTTTCTCTAATCC 57.384 43.478 0.00 0.00 41.75 3.01
90 91 4.906618 GGACTTTCTCTAATCCCAACACA 58.093 43.478 0.00 0.00 0.00 3.72
91 92 5.313712 GGACTTTCTCTAATCCCAACACAA 58.686 41.667 0.00 0.00 0.00 3.33
92 93 5.768164 GGACTTTCTCTAATCCCAACACAAA 59.232 40.000 0.00 0.00 0.00 2.83
93 94 6.264518 GGACTTTCTCTAATCCCAACACAAAA 59.735 38.462 0.00 0.00 0.00 2.44
94 95 7.201875 GGACTTTCTCTAATCCCAACACAAAAA 60.202 37.037 0.00 0.00 0.00 1.94
113 114 4.465632 AAAAGTCCCTGAAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
114 115 2.067365 AGTCCCTGAAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
115 116 1.037493 GTCCCTGAAACCAAACACCC 58.963 55.000 0.00 0.00 0.00 4.61
116 117 0.105913 TCCCTGAAACCAAACACCCC 60.106 55.000 0.00 0.00 0.00 4.95
117 118 1.118965 CCCTGAAACCAAACACCCCC 61.119 60.000 0.00 0.00 0.00 5.40
118 119 0.105709 CCTGAAACCAAACACCCCCT 60.106 55.000 0.00 0.00 0.00 4.79
119 120 1.146152 CCTGAAACCAAACACCCCCTA 59.854 52.381 0.00 0.00 0.00 3.53
120 121 2.425102 CCTGAAACCAAACACCCCCTAA 60.425 50.000 0.00 0.00 0.00 2.69
121 122 2.890945 CTGAAACCAAACACCCCCTAAG 59.109 50.000 0.00 0.00 0.00 2.18
122 123 2.245287 TGAAACCAAACACCCCCTAAGT 59.755 45.455 0.00 0.00 0.00 2.24
123 124 2.670019 AACCAAACACCCCCTAAGTC 57.330 50.000 0.00 0.00 0.00 3.01
124 125 1.525175 ACCAAACACCCCCTAAGTCA 58.475 50.000 0.00 0.00 0.00 3.41
125 126 1.854280 ACCAAACACCCCCTAAGTCAA 59.146 47.619 0.00 0.00 0.00 3.18
126 127 2.158519 ACCAAACACCCCCTAAGTCAAG 60.159 50.000 0.00 0.00 0.00 3.02
127 128 1.886542 CAAACACCCCCTAAGTCAAGC 59.113 52.381 0.00 0.00 0.00 4.01
128 129 0.036306 AACACCCCCTAAGTCAAGCG 59.964 55.000 0.00 0.00 0.00 4.68
129 130 1.078426 CACCCCCTAAGTCAAGCGG 60.078 63.158 0.00 0.00 0.00 5.52
130 131 1.538135 ACCCCCTAAGTCAAGCGGT 60.538 57.895 0.00 0.00 0.00 5.68
131 132 0.252375 ACCCCCTAAGTCAAGCGGTA 60.252 55.000 0.00 0.00 0.00 4.02
132 133 0.177373 CCCCCTAAGTCAAGCGGTAC 59.823 60.000 0.00 0.00 0.00 3.34
152 153 4.335647 CAGTGGGCGCCAGTTCCT 62.336 66.667 30.85 12.68 34.53 3.36
153 154 2.606519 AGTGGGCGCCAGTTCCTA 60.607 61.111 30.85 1.53 32.53 2.94
154 155 2.221299 AGTGGGCGCCAGTTCCTAA 61.221 57.895 30.85 0.00 32.53 2.69
155 156 1.302993 GTGGGCGCCAGTTCCTAAA 60.303 57.895 30.85 0.00 32.34 1.85
156 157 1.302993 TGGGCGCCAGTTCCTAAAC 60.303 57.895 30.85 6.94 35.50 2.01
157 158 2.044555 GGGCGCCAGTTCCTAAACC 61.045 63.158 30.85 1.22 35.92 3.27
158 159 2.396157 GGCGCCAGTTCCTAAACCG 61.396 63.158 24.80 0.00 35.92 4.44
159 160 2.396157 GCGCCAGTTCCTAAACCGG 61.396 63.158 0.00 0.00 36.22 5.28
161 162 2.396157 GCCAGTTCCTAAACCGGCG 61.396 63.158 0.00 0.00 46.19 6.46
162 163 2.396157 CCAGTTCCTAAACCGGCGC 61.396 63.158 0.00 0.00 35.92 6.53
163 164 1.669760 CAGTTCCTAAACCGGCGCA 60.670 57.895 10.83 0.00 35.92 6.09
164 165 1.024579 CAGTTCCTAAACCGGCGCAT 61.025 55.000 10.83 0.00 35.92 4.73
165 166 0.538118 AGTTCCTAAACCGGCGCATA 59.462 50.000 10.83 0.00 35.92 3.14
166 167 1.065998 AGTTCCTAAACCGGCGCATAA 60.066 47.619 10.83 0.00 35.92 1.90
167 168 1.738908 GTTCCTAAACCGGCGCATAAA 59.261 47.619 10.83 0.00 0.00 1.40
168 169 1.658994 TCCTAAACCGGCGCATAAAG 58.341 50.000 10.83 0.00 0.00 1.85
169 170 1.065998 TCCTAAACCGGCGCATAAAGT 60.066 47.619 10.83 0.00 0.00 2.66
170 171 1.063469 CCTAAACCGGCGCATAAAGTG 59.937 52.381 10.83 0.00 0.00 3.16
182 183 3.675467 CATAAAGTGCCGTTTAGGAGC 57.325 47.619 0.00 0.00 45.00 4.70
183 184 3.270877 CATAAAGTGCCGTTTAGGAGCT 58.729 45.455 0.00 0.00 45.00 4.09
184 185 1.809684 AAAGTGCCGTTTAGGAGCTC 58.190 50.000 4.71 4.71 45.00 4.09
185 186 0.977395 AAGTGCCGTTTAGGAGCTCT 59.023 50.000 14.64 2.18 45.00 4.09
186 187 0.977395 AGTGCCGTTTAGGAGCTCTT 59.023 50.000 14.64 8.96 45.00 2.85
187 188 1.079503 GTGCCGTTTAGGAGCTCTTG 58.920 55.000 14.64 0.00 45.00 3.02
188 189 0.673644 TGCCGTTTAGGAGCTCTTGC 60.674 55.000 14.64 5.91 45.00 4.01
205 206 2.987547 CTGTGCAGCCCAACAGGG 60.988 66.667 3.83 0.00 46.03 4.45
332 333 1.113517 GCTGCTCCTACGGTCCCATA 61.114 60.000 0.00 0.00 0.00 2.74
340 341 2.326428 CTACGGTCCCATATCCAAGGT 58.674 52.381 0.00 0.00 0.00 3.50
654 673 8.668510 TGATTTGGTATTAGAAAGCATCTCTC 57.331 34.615 0.00 0.00 39.71 3.20
754 891 5.643664 CACAGTACTATTACTAACCGTGCA 58.356 41.667 0.00 0.00 36.31 4.57
813 950 4.609018 AGCTTGGCGTGCAGTCGT 62.609 61.111 4.46 0.00 0.00 4.34
1045 1190 2.280797 GTGGCACGACTTCCTGCA 60.281 61.111 0.00 0.00 34.90 4.41
1055 1200 1.166531 ACTTCCTGCACTTGCCGTTC 61.167 55.000 0.00 0.00 41.18 3.95
1187 1332 1.375523 GCACTCACTTACCACCCGG 60.376 63.158 0.00 0.00 38.77 5.73
1246 1391 2.294233 GCATTGAGAGTTTTGCACCTCA 59.706 45.455 9.24 4.52 35.22 3.86
1331 1476 1.688772 ATGCATGACATCTTGGGAGC 58.311 50.000 0.00 0.00 31.52 4.70
1355 1500 6.252599 TCAGTTAGGAAATCATGGTATGCT 57.747 37.500 0.00 0.00 0.00 3.79
1412 1557 5.576447 AATACAGAGCAAATTTTACCCGG 57.424 39.130 0.00 0.00 0.00 5.73
1665 1810 6.817641 CCTCTCTGATTAGCTTATATGCAAGG 59.182 42.308 12.65 0.00 34.99 3.61
1683 1828 1.230324 GGTGTTGTCAGCTGGAGAAC 58.770 55.000 15.13 14.96 46.89 3.01
1713 1858 4.687483 CAGGTTTTTCAGAACATGCCAATC 59.313 41.667 0.00 0.00 35.01 2.67
1740 1885 0.313987 CTGTGTCGTGGACAGCACTA 59.686 55.000 0.00 0.00 43.57 2.74
1809 1954 1.273759 TTCAGCTGATGAGGCAGTCT 58.726 50.000 19.04 0.00 39.68 3.24
1935 2080 2.607180 GGGTTTTGATTTGTGTGTGCAC 59.393 45.455 10.75 10.75 45.44 4.57
2004 2149 6.811634 ATTGAGGCCCAATCAATATTTGAA 57.188 33.333 15.19 0.00 43.75 2.69
2011 2156 6.991531 GGCCCAATCAATATTTGAAAGCATTA 59.008 34.615 0.00 0.00 43.95 1.90
2078 2223 3.818787 GCATGGCCTTGCTGACCG 61.819 66.667 30.87 1.16 39.57 4.79
2115 2260 3.362870 AAAGAAATGGAGGAGGAGCAG 57.637 47.619 0.00 0.00 0.00 4.24
2211 2356 1.135199 CGCTGCTTCAAGGCAATGATT 60.135 47.619 0.00 0.00 41.94 2.57
2265 2410 3.288964 CTCGTGTATGGTAGACCTCCTT 58.711 50.000 0.00 0.00 36.82 3.36
2358 2503 2.350514 GGTTCTCTGCTGGCTGCT 59.649 61.111 17.45 0.00 43.37 4.24
2433 2578 3.052082 CTGGAGCCAGGTTGTGCG 61.052 66.667 8.69 0.00 40.17 5.34
2457 2602 4.670221 GCAACTCATGTACAGCTAGCAAAC 60.670 45.833 18.83 11.96 0.00 2.93
2559 2704 3.748083 TGGATGCAGCTGGATAGAAATC 58.252 45.455 21.70 8.22 0.00 2.17
2651 2796 0.644331 CTTGACTGCTTGCGATCTCG 59.356 55.000 0.00 0.00 43.27 4.04
2720 2865 6.636454 TGACCCTCAATAGTTCAAGGTAAT 57.364 37.500 0.00 0.00 0.00 1.89
2733 2878 6.429385 AGTTCAAGGTAATTTTGAGCTCTGAG 59.571 38.462 16.19 0.00 40.60 3.35
2754 2899 9.434275 TCTGAGTAAAGTATTGGGAGATGATAA 57.566 33.333 0.00 0.00 0.00 1.75
2757 2904 8.019656 AGTAAAGTATTGGGAGATGATAACGT 57.980 34.615 0.00 0.00 0.00 3.99
2909 3060 1.512926 CAGAGTTTTCCCACCTGACG 58.487 55.000 0.00 0.00 0.00 4.35
2973 3124 4.851558 CGCACTTGATGTTTTAAACTAGGC 59.148 41.667 9.33 3.13 0.00 3.93
2980 3131 7.667043 TGATGTTTTAAACTAGGCTACACTG 57.333 36.000 9.33 0.00 0.00 3.66
2981 3132 7.221450 TGATGTTTTAAACTAGGCTACACTGT 58.779 34.615 9.33 0.00 0.00 3.55
3094 3245 8.555361 GCTTGATTGACTAGATAAGGTTTGATC 58.445 37.037 0.00 0.00 0.00 2.92
3125 3281 5.726980 TTCTCTGCTATTTTGCATTGGTT 57.273 34.783 0.00 0.00 42.48 3.67
3198 3356 6.258230 TCTTGATTGCAACTTATGGTCAAG 57.742 37.500 22.17 22.17 41.28 3.02
3200 3358 5.627499 TGATTGCAACTTATGGTCAAGTC 57.373 39.130 0.00 0.00 37.78 3.01
3211 3369 6.160459 ACTTATGGTCAAGTCAATCCCCTAAT 59.840 38.462 0.00 0.00 33.41 1.73
3214 3372 3.467803 GTCAAGTCAATCCCCTAATCGG 58.532 50.000 0.00 0.00 0.00 4.18
3228 3386 5.648092 CCCCTAATCGGCCTTCTAATAATTG 59.352 44.000 0.00 0.00 0.00 2.32
3267 3718 8.879342 TTCTTGTGGTTATGTTTATGGTTTTG 57.121 30.769 0.00 0.00 0.00 2.44
3283 3734 5.725362 TGGTTTTGTCCTTTTAGTGGTTTG 58.275 37.500 0.00 0.00 0.00 2.93
3285 3736 5.579119 GGTTTTGTCCTTTTAGTGGTTTGTG 59.421 40.000 0.00 0.00 0.00 3.33
3337 3788 8.532186 TCCTATATTTTGCTTATTGCTTTCCA 57.468 30.769 0.00 0.00 43.37 3.53
3338 3789 8.413229 TCCTATATTTTGCTTATTGCTTTCCAC 58.587 33.333 0.00 0.00 43.37 4.02
3397 3848 2.075979 AAGGCTTCGTTCGGTTAGAC 57.924 50.000 0.00 0.00 0.00 2.59
3408 3859 4.105553 GTTAGACCCCACCCCGCC 62.106 72.222 0.00 0.00 0.00 6.13
3441 3892 2.437716 CCCCATGGTTTCGTCCCG 60.438 66.667 11.73 0.00 0.00 5.14
3445 3896 3.642503 ATGGTTTCGTCCCGCCCA 61.643 61.111 0.00 0.00 0.00 5.36
3457 3908 3.411517 CGCCCAGGGTTCCATCCT 61.412 66.667 7.55 0.00 34.39 3.24
3462 3913 1.221840 CAGGGTTCCATCCTGGTCG 59.778 63.158 2.40 0.00 45.95 4.79
3490 3941 1.239296 GGTGTGTTCGGTTAAGCCCC 61.239 60.000 0.00 0.00 0.00 5.80
3503 3954 3.199891 GCCCCGCGTGGATTGTAC 61.200 66.667 18.79 0.00 37.49 2.90
3506 3957 2.266372 CCGCGTGGATTGTACCCA 59.734 61.111 10.20 0.00 37.49 4.51
3508 3959 1.157870 CCGCGTGGATTGTACCCATC 61.158 60.000 10.20 0.00 37.49 3.51
3511 3962 1.134521 GCGTGGATTGTACCCATCTCA 60.135 52.381 0.00 0.00 35.91 3.27
3512 3963 2.485479 GCGTGGATTGTACCCATCTCAT 60.485 50.000 0.00 0.00 35.91 2.90
3515 3966 4.931601 CGTGGATTGTACCCATCTCATATG 59.068 45.833 0.00 0.00 35.91 1.78
3516 3967 5.279456 CGTGGATTGTACCCATCTCATATGA 60.279 44.000 5.07 5.07 35.91 2.15
3518 3969 7.170965 GTGGATTGTACCCATCTCATATGAAT 58.829 38.462 6.90 1.17 35.91 2.57
3523 3976 7.806409 TGTACCCATCTCATATGAATTGTTG 57.194 36.000 6.90 1.35 0.00 3.33
3575 4108 5.376854 ACACAGAGCACATTGGTAAATTC 57.623 39.130 0.00 0.00 0.00 2.17
3577 4110 5.536161 ACACAGAGCACATTGGTAAATTCTT 59.464 36.000 0.00 0.00 0.00 2.52
3578 4111 6.040842 ACACAGAGCACATTGGTAAATTCTTT 59.959 34.615 0.00 0.00 0.00 2.52
3642 4175 2.701073 GCATCAGCATATGAACTGCC 57.299 50.000 6.97 0.00 42.53 4.85
3645 4178 3.366070 GCATCAGCATATGAACTGCCATC 60.366 47.826 6.97 0.00 42.53 3.51
3646 4179 3.564053 TCAGCATATGAACTGCCATCA 57.436 42.857 6.97 0.00 40.56 3.07
3647 4180 3.888583 TCAGCATATGAACTGCCATCAA 58.111 40.909 6.97 0.00 40.56 2.57
3648 4181 4.271661 TCAGCATATGAACTGCCATCAAA 58.728 39.130 6.97 0.00 40.56 2.69
3649 4182 4.096833 TCAGCATATGAACTGCCATCAAAC 59.903 41.667 6.97 0.00 40.56 2.93
3650 4183 3.382546 AGCATATGAACTGCCATCAAACC 59.617 43.478 6.97 0.00 40.56 3.27
3651 4184 3.491447 GCATATGAACTGCCATCAAACCC 60.491 47.826 6.97 0.00 33.44 4.11
3652 4185 2.307496 ATGAACTGCCATCAAACCCA 57.693 45.000 0.00 0.00 0.00 4.51
3653 4186 2.079170 TGAACTGCCATCAAACCCAA 57.921 45.000 0.00 0.00 0.00 4.12
3654 4187 2.607499 TGAACTGCCATCAAACCCAAT 58.393 42.857 0.00 0.00 0.00 3.16
3655 4188 3.772387 TGAACTGCCATCAAACCCAATA 58.228 40.909 0.00 0.00 0.00 1.90
3656 4189 4.155709 TGAACTGCCATCAAACCCAATAA 58.844 39.130 0.00 0.00 0.00 1.40
3657 4190 4.220382 TGAACTGCCATCAAACCCAATAAG 59.780 41.667 0.00 0.00 0.00 1.73
3658 4191 4.046286 ACTGCCATCAAACCCAATAAGA 57.954 40.909 0.00 0.00 0.00 2.10
3659 4192 4.019174 ACTGCCATCAAACCCAATAAGAG 58.981 43.478 0.00 0.00 0.00 2.85
3660 4193 4.019174 CTGCCATCAAACCCAATAAGAGT 58.981 43.478 0.00 0.00 0.00 3.24
3661 4194 4.016444 TGCCATCAAACCCAATAAGAGTC 58.984 43.478 0.00 0.00 0.00 3.36
3662 4195 3.065371 GCCATCAAACCCAATAAGAGTCG 59.935 47.826 0.00 0.00 0.00 4.18
3663 4196 3.065371 CCATCAAACCCAATAAGAGTCGC 59.935 47.826 0.00 0.00 0.00 5.19
3664 4197 2.343101 TCAAACCCAATAAGAGTCGCG 58.657 47.619 0.00 0.00 0.00 5.87
3665 4198 2.073816 CAAACCCAATAAGAGTCGCGT 58.926 47.619 5.77 0.00 0.00 6.01
3666 4199 1.722011 AACCCAATAAGAGTCGCGTG 58.278 50.000 5.77 0.00 0.00 5.34
3667 4200 0.892755 ACCCAATAAGAGTCGCGTGA 59.107 50.000 5.77 0.00 0.00 4.35
3668 4201 1.274167 ACCCAATAAGAGTCGCGTGAA 59.726 47.619 5.77 0.00 0.00 3.18
3669 4202 2.093658 ACCCAATAAGAGTCGCGTGAAT 60.094 45.455 5.77 0.00 0.00 2.57
3670 4203 2.285220 CCCAATAAGAGTCGCGTGAATG 59.715 50.000 2.56 0.00 0.00 2.67
3671 4204 2.285220 CCAATAAGAGTCGCGTGAATGG 59.715 50.000 2.56 0.00 0.00 3.16
3672 4205 1.571919 ATAAGAGTCGCGTGAATGGC 58.428 50.000 2.56 0.00 0.00 4.40
3680 4213 4.214383 CGTGAATGGCGCTCGCTG 62.214 66.667 7.64 0.00 41.60 5.18
3681 4214 3.869272 GTGAATGGCGCTCGCTGG 61.869 66.667 7.64 0.00 41.60 4.85
3689 4222 4.147449 CGCTCGCTGGGTGATCCA 62.147 66.667 0.00 0.00 44.79 3.41
3690 4223 2.512515 GCTCGCTGGGTGATCCAC 60.513 66.667 0.00 0.00 41.46 4.02
3691 4224 2.202797 CTCGCTGGGTGATCCACG 60.203 66.667 1.16 1.16 41.46 4.94
3692 4225 4.451150 TCGCTGGGTGATCCACGC 62.451 66.667 7.13 7.13 45.53 5.34
3697 4230 4.218722 GGGTGATCCACGCGATTT 57.781 55.556 15.93 0.00 37.54 2.17
3698 4231 2.477880 GGGTGATCCACGCGATTTT 58.522 52.632 15.93 0.00 37.54 1.82
3699 4232 1.658994 GGGTGATCCACGCGATTTTA 58.341 50.000 15.93 0.00 37.54 1.52
3700 4233 1.329599 GGGTGATCCACGCGATTTTAC 59.670 52.381 15.93 4.29 37.54 2.01
3701 4234 2.277084 GGTGATCCACGCGATTTTACT 58.723 47.619 15.93 0.00 34.83 2.24
3702 4235 2.030457 GGTGATCCACGCGATTTTACTG 59.970 50.000 15.93 0.00 34.83 2.74
3703 4236 2.671396 GTGATCCACGCGATTTTACTGT 59.329 45.455 15.93 0.00 0.00 3.55
3704 4237 2.670905 TGATCCACGCGATTTTACTGTG 59.329 45.455 15.93 0.00 0.00 3.66
3705 4238 0.793861 TCCACGCGATTTTACTGTGC 59.206 50.000 15.93 0.00 0.00 4.57
3706 4239 0.179200 CCACGCGATTTTACTGTGCC 60.179 55.000 15.93 0.00 0.00 5.01
3707 4240 0.518355 CACGCGATTTTACTGTGCCG 60.518 55.000 15.93 0.00 0.00 5.69
3708 4241 0.668096 ACGCGATTTTACTGTGCCGA 60.668 50.000 15.93 0.00 0.00 5.54
3709 4242 0.650512 CGCGATTTTACTGTGCCGAT 59.349 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.993509 TCCTTAGGCCCCTCCCAATG 60.994 60.000 0.00 0.00 34.51 2.82
1 2 0.994050 GTCCTTAGGCCCCTCCCAAT 60.994 60.000 0.00 0.00 34.51 3.16
3 4 2.042261 GTCCTTAGGCCCCTCCCA 59.958 66.667 0.00 0.00 34.51 4.37
4 5 0.919780 AAAGTCCTTAGGCCCCTCCC 60.920 60.000 0.00 0.00 34.51 4.30
5 6 1.000496 AAAAGTCCTTAGGCCCCTCC 59.000 55.000 0.00 0.00 0.00 4.30
6 7 2.421670 GCTAAAAGTCCTTAGGCCCCTC 60.422 54.545 0.00 0.00 30.79 4.30
7 8 1.564818 GCTAAAAGTCCTTAGGCCCCT 59.435 52.381 0.00 0.00 30.79 4.79
8 9 1.283905 TGCTAAAAGTCCTTAGGCCCC 59.716 52.381 0.00 0.00 30.79 5.80
10 11 5.462530 TTTTTGCTAAAAGTCCTTAGGCC 57.537 39.130 0.00 0.00 30.79 5.19
39 40 9.598517 AGCAAATCAAACAAGATGAAACTTTTA 57.401 25.926 0.00 0.00 0.00 1.52
40 41 8.496707 AGCAAATCAAACAAGATGAAACTTTT 57.503 26.923 0.00 0.00 0.00 2.27
41 42 9.252962 CTAGCAAATCAAACAAGATGAAACTTT 57.747 29.630 0.00 0.00 0.00 2.66
42 43 7.869429 CCTAGCAAATCAAACAAGATGAAACTT 59.131 33.333 0.00 0.00 0.00 2.66
43 44 7.373493 CCTAGCAAATCAAACAAGATGAAACT 58.627 34.615 0.00 0.00 0.00 2.66
44 45 6.587608 CCCTAGCAAATCAAACAAGATGAAAC 59.412 38.462 0.00 0.00 0.00 2.78
45 46 6.493115 TCCCTAGCAAATCAAACAAGATGAAA 59.507 34.615 0.00 0.00 0.00 2.69
46 47 6.009589 TCCCTAGCAAATCAAACAAGATGAA 58.990 36.000 0.00 0.00 0.00 2.57
47 48 5.415701 GTCCCTAGCAAATCAAACAAGATGA 59.584 40.000 0.00 0.00 0.00 2.92
48 49 5.416952 AGTCCCTAGCAAATCAAACAAGATG 59.583 40.000 0.00 0.00 0.00 2.90
49 50 5.574188 AGTCCCTAGCAAATCAAACAAGAT 58.426 37.500 0.00 0.00 0.00 2.40
50 51 4.985538 AGTCCCTAGCAAATCAAACAAGA 58.014 39.130 0.00 0.00 0.00 3.02
51 52 5.712152 AAGTCCCTAGCAAATCAAACAAG 57.288 39.130 0.00 0.00 0.00 3.16
52 53 5.833131 AGAAAGTCCCTAGCAAATCAAACAA 59.167 36.000 0.00 0.00 0.00 2.83
53 54 5.385198 AGAAAGTCCCTAGCAAATCAAACA 58.615 37.500 0.00 0.00 0.00 2.83
54 55 5.707764 AGAGAAAGTCCCTAGCAAATCAAAC 59.292 40.000 0.00 0.00 0.00 2.93
55 56 5.880901 AGAGAAAGTCCCTAGCAAATCAAA 58.119 37.500 0.00 0.00 0.00 2.69
56 57 5.505181 AGAGAAAGTCCCTAGCAAATCAA 57.495 39.130 0.00 0.00 0.00 2.57
57 58 6.620877 TTAGAGAAAGTCCCTAGCAAATCA 57.379 37.500 0.00 0.00 0.00 2.57
58 59 6.708502 GGATTAGAGAAAGTCCCTAGCAAATC 59.291 42.308 0.00 0.00 0.00 2.17
59 60 6.409810 GGGATTAGAGAAAGTCCCTAGCAAAT 60.410 42.308 2.09 0.00 45.57 2.32
60 61 5.104485 GGGATTAGAGAAAGTCCCTAGCAAA 60.104 44.000 2.09 0.00 45.57 3.68
61 62 4.409247 GGGATTAGAGAAAGTCCCTAGCAA 59.591 45.833 2.09 0.00 45.57 3.91
62 63 3.967987 GGGATTAGAGAAAGTCCCTAGCA 59.032 47.826 2.09 0.00 45.57 3.49
63 64 4.610605 GGGATTAGAGAAAGTCCCTAGC 57.389 50.000 2.09 0.00 45.57 3.42
68 69 4.906618 TGTGTTGGGATTAGAGAAAGTCC 58.093 43.478 0.00 0.00 0.00 3.85
69 70 6.877611 TTTGTGTTGGGATTAGAGAAAGTC 57.122 37.500 0.00 0.00 0.00 3.01
70 71 7.654022 TTTTTGTGTTGGGATTAGAGAAAGT 57.346 32.000 0.00 0.00 0.00 2.66
91 92 4.323180 GGTGTTTGGTTTCAGGGACTTTTT 60.323 41.667 0.00 0.00 34.60 1.94
92 93 3.196901 GGTGTTTGGTTTCAGGGACTTTT 59.803 43.478 0.00 0.00 34.60 2.27
93 94 2.764010 GGTGTTTGGTTTCAGGGACTTT 59.236 45.455 0.00 0.00 34.60 2.66
94 95 2.384828 GGTGTTTGGTTTCAGGGACTT 58.615 47.619 0.00 0.00 34.60 3.01
95 96 1.411074 GGGTGTTTGGTTTCAGGGACT 60.411 52.381 0.00 0.00 43.88 3.85
96 97 1.037493 GGGTGTTTGGTTTCAGGGAC 58.963 55.000 0.00 0.00 0.00 4.46
97 98 0.105913 GGGGTGTTTGGTTTCAGGGA 60.106 55.000 0.00 0.00 0.00 4.20
98 99 1.118965 GGGGGTGTTTGGTTTCAGGG 61.119 60.000 0.00 0.00 0.00 4.45
99 100 0.105709 AGGGGGTGTTTGGTTTCAGG 60.106 55.000 0.00 0.00 0.00 3.86
100 101 2.668144 TAGGGGGTGTTTGGTTTCAG 57.332 50.000 0.00 0.00 0.00 3.02
101 102 2.245287 ACTTAGGGGGTGTTTGGTTTCA 59.755 45.455 0.00 0.00 0.00 2.69
102 103 2.889045 GACTTAGGGGGTGTTTGGTTTC 59.111 50.000 0.00 0.00 0.00 2.78
103 104 2.245287 TGACTTAGGGGGTGTTTGGTTT 59.755 45.455 0.00 0.00 0.00 3.27
104 105 1.854280 TGACTTAGGGGGTGTTTGGTT 59.146 47.619 0.00 0.00 0.00 3.67
105 106 1.525175 TGACTTAGGGGGTGTTTGGT 58.475 50.000 0.00 0.00 0.00 3.67
106 107 2.514803 CTTGACTTAGGGGGTGTTTGG 58.485 52.381 0.00 0.00 0.00 3.28
107 108 1.886542 GCTTGACTTAGGGGGTGTTTG 59.113 52.381 0.00 0.00 0.00 2.93
108 109 1.544759 CGCTTGACTTAGGGGGTGTTT 60.545 52.381 0.00 0.00 0.00 2.83
109 110 0.036306 CGCTTGACTTAGGGGGTGTT 59.964 55.000 0.00 0.00 0.00 3.32
110 111 1.677552 CGCTTGACTTAGGGGGTGT 59.322 57.895 0.00 0.00 0.00 4.16
111 112 1.078426 CCGCTTGACTTAGGGGGTG 60.078 63.158 0.00 0.00 42.78 4.61
112 113 3.400188 CCGCTTGACTTAGGGGGT 58.600 61.111 0.00 0.00 42.78 4.95
115 116 3.340727 CGTACCGCTTGACTTAGGG 57.659 57.895 0.00 0.00 0.00 3.53
135 136 2.463589 TTAGGAACTGGCGCCCACTG 62.464 60.000 26.77 13.99 41.52 3.66
136 137 1.774894 TTTAGGAACTGGCGCCCACT 61.775 55.000 26.77 16.54 41.52 4.00
137 138 1.302993 TTTAGGAACTGGCGCCCAC 60.303 57.895 26.77 12.24 41.52 4.61
138 139 1.302993 GTTTAGGAACTGGCGCCCA 60.303 57.895 26.77 11.42 41.52 5.36
139 140 2.044555 GGTTTAGGAACTGGCGCCC 61.045 63.158 26.77 8.13 41.52 6.13
140 141 2.396157 CGGTTTAGGAACTGGCGCC 61.396 63.158 22.73 22.73 41.52 6.53
141 142 3.174788 CGGTTTAGGAACTGGCGC 58.825 61.111 0.00 0.00 41.52 6.53
145 146 1.024579 ATGCGCCGGTTTAGGAACTG 61.025 55.000 4.18 0.00 41.52 3.16
146 147 0.538118 TATGCGCCGGTTTAGGAACT 59.462 50.000 4.18 0.00 46.37 3.01
147 148 1.371595 TTATGCGCCGGTTTAGGAAC 58.628 50.000 4.18 0.00 34.96 3.62
148 149 2.011222 CTTTATGCGCCGGTTTAGGAA 58.989 47.619 4.18 0.00 0.00 3.36
149 150 1.065998 ACTTTATGCGCCGGTTTAGGA 60.066 47.619 4.18 0.00 0.00 2.94
150 151 1.063469 CACTTTATGCGCCGGTTTAGG 59.937 52.381 4.18 0.00 0.00 2.69
151 152 1.531058 GCACTTTATGCGCCGGTTTAG 60.531 52.381 4.18 0.00 46.55 1.85
152 153 0.448593 GCACTTTATGCGCCGGTTTA 59.551 50.000 4.18 0.00 46.55 2.01
153 154 1.211709 GCACTTTATGCGCCGGTTT 59.788 52.632 4.18 0.00 46.55 3.27
154 155 2.874751 GCACTTTATGCGCCGGTT 59.125 55.556 4.18 0.00 46.55 4.44
162 163 3.270877 AGCTCCTAAACGGCACTTTATG 58.729 45.455 0.00 0.00 0.00 1.90
163 164 3.197983 AGAGCTCCTAAACGGCACTTTAT 59.802 43.478 10.93 0.00 0.00 1.40
164 165 2.565834 AGAGCTCCTAAACGGCACTTTA 59.434 45.455 10.93 0.00 0.00 1.85
165 166 1.348036 AGAGCTCCTAAACGGCACTTT 59.652 47.619 10.93 0.00 0.00 2.66
166 167 0.977395 AGAGCTCCTAAACGGCACTT 59.023 50.000 10.93 0.00 0.00 3.16
167 168 0.977395 AAGAGCTCCTAAACGGCACT 59.023 50.000 10.93 0.00 0.00 4.40
168 169 1.079503 CAAGAGCTCCTAAACGGCAC 58.920 55.000 10.93 0.00 0.00 5.01
169 170 0.673644 GCAAGAGCTCCTAAACGGCA 60.674 55.000 10.93 0.00 37.91 5.69
170 171 2.090693 GCAAGAGCTCCTAAACGGC 58.909 57.895 10.93 0.06 37.91 5.68
197 198 1.077265 AATGTCTGGGCCCTGTTGG 59.923 57.895 25.70 8.09 37.09 3.77
198 199 1.880819 GCAATGTCTGGGCCCTGTTG 61.881 60.000 25.70 22.21 0.00 3.33
199 200 1.607467 GCAATGTCTGGGCCCTGTT 60.607 57.895 25.70 10.36 0.00 3.16
200 201 2.036256 GCAATGTCTGGGCCCTGT 59.964 61.111 25.70 3.51 0.00 4.00
201 202 1.751927 GAGCAATGTCTGGGCCCTG 60.752 63.158 25.70 23.93 0.00 4.45
202 203 2.679716 GAGCAATGTCTGGGCCCT 59.320 61.111 25.70 0.00 0.00 5.19
203 204 2.825836 CGAGCAATGTCTGGGCCC 60.826 66.667 17.59 17.59 0.00 5.80
204 205 1.244019 AAACGAGCAATGTCTGGGCC 61.244 55.000 0.00 0.00 0.00 5.80
205 206 0.598065 AAAACGAGCAATGTCTGGGC 59.402 50.000 0.00 0.00 0.00 5.36
206 207 2.095567 CAGAAAACGAGCAATGTCTGGG 60.096 50.000 0.00 0.00 31.02 4.45
207 208 2.807967 TCAGAAAACGAGCAATGTCTGG 59.192 45.455 0.00 0.00 34.57 3.86
208 209 4.675190 ATCAGAAAACGAGCAATGTCTG 57.325 40.909 0.00 0.00 35.01 3.51
209 210 4.999950 AGAATCAGAAAACGAGCAATGTCT 59.000 37.500 0.00 0.00 0.00 3.41
210 211 5.288543 AGAATCAGAAAACGAGCAATGTC 57.711 39.130 0.00 0.00 0.00 3.06
211 212 4.154918 GGAGAATCAGAAAACGAGCAATGT 59.845 41.667 0.00 0.00 36.25 2.71
212 213 4.437930 GGGAGAATCAGAAAACGAGCAATG 60.438 45.833 0.00 0.00 36.25 2.82
332 333 1.375523 GACGGCGACAACCTTGGAT 60.376 57.895 16.62 0.00 0.00 3.41
577 585 9.823098 CAATTTCTCAACAATTGACAACAAAAA 57.177 25.926 13.59 4.38 42.10 1.94
639 658 9.265901 GTAATGCAATAGAGAGATGCTTTCTAA 57.734 33.333 0.00 0.00 40.66 2.10
643 662 7.387397 GCTAGTAATGCAATAGAGAGATGCTTT 59.613 37.037 0.00 0.00 40.66 3.51
678 697 7.503566 AGAATGCTTGCCAGTAATACAATACAT 59.496 33.333 0.00 0.00 0.00 2.29
754 891 2.906389 TGTCCCTACAGCAACAGAGAAT 59.094 45.455 0.00 0.00 0.00 2.40
813 950 7.330946 CACACGAACATCAACTTAAGGAGATTA 59.669 37.037 7.53 0.00 0.00 1.75
861 998 0.657840 GCTGCATTACTAACCCTGCG 59.342 55.000 0.00 0.00 37.44 5.18
947 1092 2.745515 AACCGAGGTCTTGAGTTAGC 57.254 50.000 0.00 0.00 0.00 3.09
987 1132 5.760253 GCCTAGAAGCATGAACAGCTAATAA 59.240 40.000 0.00 0.00 42.53 1.40
988 1133 5.300752 GCCTAGAAGCATGAACAGCTAATA 58.699 41.667 0.00 0.00 42.53 0.98
989 1134 4.133078 GCCTAGAAGCATGAACAGCTAAT 58.867 43.478 0.00 0.00 42.53 1.73
1045 1190 2.719354 GCAAACCGAACGGCAAGT 59.281 55.556 13.32 0.00 39.32 3.16
1055 1200 1.178534 AGTTGTCCATGGGCAAACCG 61.179 55.000 32.54 0.00 44.64 4.44
1092 1237 2.174210 ACGGTACCAGAGTAGATGGCTA 59.826 50.000 13.54 0.00 41.87 3.93
1187 1332 1.821136 CCCCTTGCTTTGTTGATCTCC 59.179 52.381 0.00 0.00 0.00 3.71
1250 1395 4.263905 CCTTGCCATTATATGCCTTCCCTA 60.264 45.833 0.00 0.00 0.00 3.53
1331 1476 6.294473 AGCATACCATGATTTCCTAACTGAG 58.706 40.000 0.00 0.00 0.00 3.35
1355 1500 5.508200 AACGAACTGCACTTTTCCATTAA 57.492 34.783 0.00 0.00 0.00 1.40
1500 1645 3.526931 TCCGCACTTATTCCTCTCTTG 57.473 47.619 0.00 0.00 0.00 3.02
1502 1647 7.122715 AGATATATCCGCACTTATTCCTCTCT 58.877 38.462 9.18 0.00 0.00 3.10
1665 1810 0.861837 CGTTCTCCAGCTGACAACAC 59.138 55.000 17.39 4.17 0.00 3.32
1683 1828 3.181501 TGTTCTGAAAAACCTGACAAGCG 60.182 43.478 0.00 0.00 0.00 4.68
1713 1858 4.772434 CTGTCCACGACACAGTATTTTTG 58.228 43.478 0.00 0.00 37.67 2.44
1740 1885 2.722094 TCCTGCGCATAACCAGAAATT 58.278 42.857 12.24 0.00 0.00 1.82
1809 1954 0.399833 TGTCATTAGGCCTGCACACA 59.600 50.000 17.99 10.43 0.00 3.72
1935 2080 5.723492 TTGATATCAGTGCATTTGAGACG 57.277 39.130 5.39 0.00 0.00 4.18
2011 2156 1.145738 AGAAACCAGGTCCTTGCACAT 59.854 47.619 0.00 0.00 0.00 3.21
2076 2221 7.647907 TTCTTTTAGTAAGCTTAGACAACGG 57.352 36.000 6.38 0.00 0.00 4.44
2078 2223 9.827411 CCATTTCTTTTAGTAAGCTTAGACAAC 57.173 33.333 6.38 0.00 0.00 3.32
2115 2260 5.736951 AGGAGATTACATCAGGCACTATC 57.263 43.478 0.00 0.00 36.02 2.08
2211 2356 4.168101 ACTCTGGTTCTATTCCAAGTCCA 58.832 43.478 0.00 0.00 34.35 4.02
2358 2503 5.581126 GAATGTTTCCATGCATCCTACAA 57.419 39.130 0.00 0.00 0.00 2.41
2433 2578 1.936547 GCTAGCTGTACATGAGTTGCC 59.063 52.381 7.70 0.00 0.00 4.52
2559 2704 5.640357 TGTGAAAGTATAAACCTTACTGCCG 59.360 40.000 0.00 0.00 30.46 5.69
2651 2796 6.914215 CAGCACATCATGTTTGTATTCCATAC 59.086 38.462 0.00 0.00 36.29 2.39
2720 2865 6.655003 CCCAATACTTTACTCAGAGCTCAAAA 59.345 38.462 17.77 7.18 0.00 2.44
2733 2878 7.114529 CGACGTTATCATCTCCCAATACTTTAC 59.885 40.741 0.00 0.00 0.00 2.01
2754 2899 4.678622 TCATATACAAATGACTGCGACGT 58.321 39.130 0.00 0.00 30.92 4.34
2757 2904 7.209475 TGATCTTCATATACAAATGACTGCGA 58.791 34.615 0.00 0.00 35.63 5.10
2797 2948 4.070716 AGGTGAGAGTCATGCTTTTTCTG 58.929 43.478 0.00 0.00 0.00 3.02
2884 3035 0.595095 GTGGGAAAACTCTGCTGCTG 59.405 55.000 0.00 0.00 0.00 4.41
2890 3041 1.202651 ACGTCAGGTGGGAAAACTCTG 60.203 52.381 0.00 0.00 0.00 3.35
2973 3124 6.697892 GCAGCCTAGTCTAATTAACAGTGTAG 59.302 42.308 0.00 0.00 0.00 2.74
2980 3131 6.807789 ACTAGTGCAGCCTAGTCTAATTAAC 58.192 40.000 14.55 0.00 43.17 2.01
2981 3132 8.529424 TTACTAGTGCAGCCTAGTCTAATTAA 57.471 34.615 20.61 10.32 43.17 1.40
3011 3162 0.596082 AAGTTCCCAAATGGTTCGCG 59.404 50.000 0.00 0.00 34.77 5.87
3198 3356 0.765510 AGGCCGATTAGGGGATTGAC 59.234 55.000 0.00 0.00 41.48 3.18
3200 3358 1.421646 AGAAGGCCGATTAGGGGATTG 59.578 52.381 0.00 0.00 41.48 2.67
3211 3369 5.871396 AGAGACAATTATTAGAAGGCCGA 57.129 39.130 0.00 0.00 0.00 5.54
3214 3372 8.338986 GCAACTAAGAGACAATTATTAGAAGGC 58.661 37.037 0.00 0.00 0.00 4.35
3228 3386 4.757149 ACCACAAGAATGCAACTAAGAGAC 59.243 41.667 0.00 0.00 0.00 3.36
3267 3718 4.885325 TCTTCCACAAACCACTAAAAGGAC 59.115 41.667 0.00 0.00 0.00 3.85
3323 3774 5.582689 AACATAGGTGGAAAGCAATAAGC 57.417 39.130 0.00 0.00 46.19 3.09
3441 3892 2.276740 CAGGATGGAACCCTGGGC 59.723 66.667 14.08 0.00 45.66 5.36
3457 3908 4.201980 CGAACACACCTATAAGATCGACCA 60.202 45.833 0.00 0.00 0.00 4.02
3462 3913 6.200475 GCTTAACCGAACACACCTATAAGATC 59.800 42.308 0.00 0.00 0.00 2.75
3490 3941 0.179084 AGATGGGTACAATCCACGCG 60.179 55.000 3.53 3.53 37.08 6.01
3575 4108 9.687717 CTTTACACAAAATGCAACTGTTAAAAG 57.312 29.630 0.00 3.56 0.00 2.27
3577 4110 7.331934 TGCTTTACACAAAATGCAACTGTTAAA 59.668 29.630 0.00 2.91 32.16 1.52
3578 4111 6.813649 TGCTTTACACAAAATGCAACTGTTAA 59.186 30.769 0.00 0.00 32.16 2.01
3587 4120 6.918022 AGAAAGTACTGCTTTACACAAAATGC 59.082 34.615 0.00 0.00 46.54 3.56
3642 4175 3.242413 CGCGACTCTTATTGGGTTTGATG 60.242 47.826 0.00 0.00 0.00 3.07
3645 4178 2.073816 ACGCGACTCTTATTGGGTTTG 58.926 47.619 15.93 0.00 0.00 2.93
3646 4179 2.073816 CACGCGACTCTTATTGGGTTT 58.926 47.619 15.93 0.00 0.00 3.27
3647 4180 1.274167 TCACGCGACTCTTATTGGGTT 59.726 47.619 15.93 0.00 0.00 4.11
3648 4181 0.892755 TCACGCGACTCTTATTGGGT 59.107 50.000 15.93 0.00 0.00 4.51
3649 4182 2.004583 TTCACGCGACTCTTATTGGG 57.995 50.000 15.93 0.00 0.00 4.12
3650 4183 2.285220 CCATTCACGCGACTCTTATTGG 59.715 50.000 15.93 4.72 0.00 3.16
3651 4184 2.285834 GCCATTCACGCGACTCTTATTG 60.286 50.000 15.93 0.00 0.00 1.90
3652 4185 1.933853 GCCATTCACGCGACTCTTATT 59.066 47.619 15.93 0.00 0.00 1.40
3653 4186 1.571919 GCCATTCACGCGACTCTTAT 58.428 50.000 15.93 0.00 0.00 1.73
3654 4187 3.044809 GCCATTCACGCGACTCTTA 57.955 52.632 15.93 0.00 0.00 2.10
3655 4188 3.876300 GCCATTCACGCGACTCTT 58.124 55.556 15.93 0.00 0.00 2.85
3663 4196 4.214383 CAGCGAGCGCCATTCACG 62.214 66.667 11.66 1.90 43.17 4.35
3664 4197 3.869272 CCAGCGAGCGCCATTCAC 61.869 66.667 11.66 0.00 43.17 3.18
3672 4205 4.147449 TGGATCACCCAGCGAGCG 62.147 66.667 0.00 0.00 40.82 5.03
3679 4212 0.322098 AAAATCGCGTGGATCACCCA 60.322 50.000 5.77 0.00 44.25 4.51
3680 4213 1.329599 GTAAAATCGCGTGGATCACCC 59.670 52.381 5.77 0.00 33.02 4.61
3681 4214 2.030457 CAGTAAAATCGCGTGGATCACC 59.970 50.000 5.77 0.00 33.02 4.02
3682 4215 2.671396 ACAGTAAAATCGCGTGGATCAC 59.329 45.455 5.77 0.00 33.02 3.06
3683 4216 2.670905 CACAGTAAAATCGCGTGGATCA 59.329 45.455 5.77 0.00 33.02 2.92
3684 4217 2.536928 GCACAGTAAAATCGCGTGGATC 60.537 50.000 5.77 0.00 33.02 3.36
3685 4218 1.396996 GCACAGTAAAATCGCGTGGAT 59.603 47.619 5.77 0.00 36.78 3.41
3686 4219 0.793861 GCACAGTAAAATCGCGTGGA 59.206 50.000 5.77 0.00 0.00 4.02
3687 4220 0.179200 GGCACAGTAAAATCGCGTGG 60.179 55.000 5.77 0.00 0.00 4.94
3688 4221 0.518355 CGGCACAGTAAAATCGCGTG 60.518 55.000 5.77 0.00 0.00 5.34
3689 4222 0.668096 TCGGCACAGTAAAATCGCGT 60.668 50.000 5.77 0.00 0.00 6.01
3690 4223 0.650512 ATCGGCACAGTAAAATCGCG 59.349 50.000 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.