Multiple sequence alignment - TraesCS5B01G184200

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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 TraesCS5B01G184200 chr5B 100.000 2744 0 0 1 2744 334878729 334875986 0.000000e+00 5068.0
1 TraesCS5B01G184200 chr5B 97.426 544 9 2 217 760 576892676 576892138 0.000000e+00 922.0
2 TraesCS5B01G184200 chr5D 93.739 1661 87 6 783 2428 293377627 293375969 0.000000e+00 2475.0
3 TraesCS5B01G184200 chr5D 90.526 285 12 1 2426 2695 293376009 293375725 2.010000e-96 363.0
4 TraesCS5B01G184200 chr5D 100.000 30 0 0 2714 2743 293375075 293375046 3.820000e-04 56.5
5 TraesCS5B01G184200 chr5D 100.000 29 0 0 2696 2724 293375511 293375483 1.000000e-03 54.7
6 TraesCS5B01G184200 chr5A 93.225 1594 77 8 846 2424 386184575 386182998 0.000000e+00 2316.0
7 TraesCS5B01G184200 chr5A 86.607 336 19 8 2426 2743 386183034 386182707 5.620000e-92 348.0
8 TraesCS5B01G184200 chr5A 100.000 28 0 0 12 39 669563314 669563341 5.000000e-03 52.8
9 TraesCS5B01G184200 chr1B 98.172 547 9 1 217 762 604021709 604021163 0.000000e+00 953.0
10 TraesCS5B01G184200 chr7B 97.982 545 11 0 217 761 595685883 595685339 0.000000e+00 946.0
11 TraesCS5B01G184200 chr7B 90.741 54 5 0 1216 1269 674572398 674572345 3.790000e-09 73.1
12 TraesCS5B01G184200 chr2B 97.978 544 11 0 217 760 412066636 412067179 0.000000e+00 944.0
13 TraesCS5B01G184200 chr4A 93.738 543 33 1 217 759 722015396 722014855 0.000000e+00 813.0
14 TraesCS5B01G184200 chr4A 81.274 518 95 2 242 759 659091380 659091895 4.230000e-113 418.0
15 TraesCS5B01G184200 chr3D 86.924 543 69 2 217 759 100413224 100413764 2.340000e-170 608.0
16 TraesCS5B01G184200 chr3D 82.101 514 90 2 245 758 61753549 61753038 3.240000e-119 438.0
17 TraesCS5B01G184200 chr3D 100.000 29 0 0 12 40 175495492 175495520 1.000000e-03 54.7
18 TraesCS5B01G184200 chr7D 83.230 483 71 8 1711 2186 596467472 596466993 4.200000e-118 435.0
19 TraesCS5B01G184200 chr1A 81.323 514 94 2 245 758 155699059 155698548 1.520000e-112 416.0
20 TraesCS5B01G184200 chr7A 88.448 277 29 3 1711 1986 689677340 689677066 5.660000e-87 331.0
21 TraesCS5B01G184200 chr4D 79.422 277 42 12 2026 2300 451445837 451445574 6.040000e-42 182.0


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 TraesCS5B01G184200 chr5B 334875986 334878729 2743 True 5068.0 5068 100.00000 1 2744 1 chr5B.!!$R1 2743
1 TraesCS5B01G184200 chr5B 576892138 576892676 538 True 922.0 922 97.42600 217 760 1 chr5B.!!$R2 543
2 TraesCS5B01G184200 chr5D 293375046 293377627 2581 True 737.3 2475 96.06625 783 2743 4 chr5D.!!$R1 1960
3 TraesCS5B01G184200 chr5A 386182707 386184575 1868 True 1332.0 2316 89.91600 846 2743 2 chr5A.!!$R1 1897
4 TraesCS5B01G184200 chr1B 604021163 604021709 546 True 953.0 953 98.17200 217 762 1 chr1B.!!$R1 545
5 TraesCS5B01G184200 chr7B 595685339 595685883 544 True 946.0 946 97.98200 217 761 1 chr7B.!!$R1 544
6 TraesCS5B01G184200 chr2B 412066636 412067179 543 False 944.0 944 97.97800 217 760 1 chr2B.!!$F1 543
7 TraesCS5B01G184200 chr4A 722014855 722015396 541 True 813.0 813 93.73800 217 759 1 chr4A.!!$R1 542
8 TraesCS5B01G184200 chr4A 659091380 659091895 515 False 418.0 418 81.27400 242 759 1 chr4A.!!$F1 517
9 TraesCS5B01G184200 chr3D 100413224 100413764 540 False 608.0 608 86.92400 217 759 1 chr3D.!!$F1 542
10 TraesCS5B01G184200 chr3D 61753038 61753549 511 True 438.0 438 82.10100 245 758 1 chr3D.!!$R1 513
11 TraesCS5B01G184200 chr1A 155698548 155699059 511 True 416.0 416 81.32300 245 758 1 chr1A.!!$R1 513

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
131 132 0.035739 TTAAAGGGTCGACACAGCCC 59.964 55.0 22.01 10.52 42.64 5.19 F
1156 1171 0.040058 TTACCTACAGTCGAGCCCCA 59.960 55.0 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1366 0.387929 TCGACCACACAGTTCACCTC 59.612 55.0 0.00 0.0 0.00 3.85 R
2510 2529 0.104855 CAGAGTAATGCTAGGCGCCA 59.895 55.0 31.54 14.0 38.05 5.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.693532 TGTTGACTGCATCCGGAC 57.306 55.556 6.12 0.00 0.00 4.79
18 19 1.751563 TGTTGACTGCATCCGGACA 59.248 52.632 6.12 0.00 0.00 4.02
19 20 0.320683 TGTTGACTGCATCCGGACAG 60.321 55.000 18.05 18.05 39.86 3.51
20 21 1.375908 TTGACTGCATCCGGACAGC 60.376 57.895 20.71 20.71 37.42 4.40
21 22 1.830587 TTGACTGCATCCGGACAGCT 61.831 55.000 25.71 11.24 37.42 4.24
22 23 1.520342 GACTGCATCCGGACAGCTC 60.520 63.158 25.71 15.35 37.42 4.09
23 24 2.584418 CTGCATCCGGACAGCTCG 60.584 66.667 25.71 15.70 0.00 5.03
25 26 4.148825 GCATCCGGACAGCTCGGT 62.149 66.667 20.35 0.00 46.82 4.69
26 27 2.579201 CATCCGGACAGCTCGGTT 59.421 61.111 6.12 1.49 46.82 4.44
27 28 1.519455 CATCCGGACAGCTCGGTTC 60.519 63.158 6.12 0.00 46.82 3.62
28 29 3.064987 ATCCGGACAGCTCGGTTCG 62.065 63.158 6.12 5.14 46.82 3.95
30 31 3.744719 CGGACAGCTCGGTTCGGA 61.745 66.667 0.00 0.00 36.13 4.55
31 32 2.126031 GGACAGCTCGGTTCGGAC 60.126 66.667 0.00 0.00 0.00 4.79
32 33 2.504244 GACAGCTCGGTTCGGACG 60.504 66.667 0.00 0.00 0.00 4.79
33 34 4.719369 ACAGCTCGGTTCGGACGC 62.719 66.667 0.00 0.00 0.00 5.19
34 35 4.421479 CAGCTCGGTTCGGACGCT 62.421 66.667 0.00 0.00 0.00 5.07
35 36 3.681835 AGCTCGGTTCGGACGCTT 61.682 61.111 0.00 0.00 0.00 4.68
36 37 3.479269 GCTCGGTTCGGACGCTTG 61.479 66.667 0.00 0.00 0.00 4.01
37 38 3.479269 CTCGGTTCGGACGCTTGC 61.479 66.667 0.00 0.00 0.00 4.01
50 51 4.379243 CTTGCGGCCGAGTCCACT 62.379 66.667 33.48 0.00 0.00 4.00
51 52 3.883744 CTTGCGGCCGAGTCCACTT 62.884 63.158 33.48 0.00 0.00 3.16
52 53 3.469863 TTGCGGCCGAGTCCACTTT 62.470 57.895 33.48 0.00 0.00 2.66
53 54 3.423154 GCGGCCGAGTCCACTTTG 61.423 66.667 33.48 0.00 0.00 2.77
54 55 2.742372 CGGCCGAGTCCACTTTGG 60.742 66.667 24.07 0.00 39.43 3.28
55 56 2.747686 GGCCGAGTCCACTTTGGA 59.252 61.111 0.00 0.00 45.98 3.53
69 70 6.010219 TCCACTTTGGAGGATTTCTTTTAGG 58.990 40.000 0.00 0.00 42.67 2.69
70 71 5.185828 CCACTTTGGAGGATTTCTTTTAGGG 59.814 44.000 0.00 0.00 40.96 3.53
71 72 5.185828 CACTTTGGAGGATTTCTTTTAGGGG 59.814 44.000 0.00 0.00 0.00 4.79
72 73 4.331159 TTGGAGGATTTCTTTTAGGGGG 57.669 45.455 0.00 0.00 0.00 5.40
86 87 2.359011 GGGGGCCGGTTTGAAGAT 59.641 61.111 1.90 0.00 0.00 2.40
87 88 1.304962 GGGGGCCGGTTTGAAGATT 60.305 57.895 1.90 0.00 0.00 2.40
88 89 0.902984 GGGGGCCGGTTTGAAGATTT 60.903 55.000 1.90 0.00 0.00 2.17
89 90 0.973632 GGGGCCGGTTTGAAGATTTT 59.026 50.000 1.90 0.00 0.00 1.82
90 91 1.346395 GGGGCCGGTTTGAAGATTTTT 59.654 47.619 1.90 0.00 0.00 1.94
129 130 5.616488 TTTTATTAAAGGGTCGACACAGC 57.384 39.130 22.01 0.06 0.00 4.40
130 131 2.109425 ATTAAAGGGTCGACACAGCC 57.891 50.000 22.01 10.64 0.00 4.85
131 132 0.035739 TTAAAGGGTCGACACAGCCC 59.964 55.000 22.01 10.52 42.64 5.19
132 133 2.162338 TAAAGGGTCGACACAGCCCG 62.162 60.000 22.01 0.00 46.69 6.13
134 135 4.736896 GGGTCGACACAGCCCGTC 62.737 72.222 18.91 0.00 32.16 4.79
135 136 4.736896 GGTCGACACAGCCCGTCC 62.737 72.222 18.91 0.00 0.00 4.79
136 137 4.736896 GTCGACACAGCCCGTCCC 62.737 72.222 11.55 0.00 0.00 4.46
138 139 4.082523 CGACACAGCCCGTCCCAT 62.083 66.667 0.00 0.00 0.00 4.00
139 140 2.436646 GACACAGCCCGTCCCATG 60.437 66.667 0.00 0.00 0.00 3.66
140 141 4.722700 ACACAGCCCGTCCCATGC 62.723 66.667 0.00 0.00 0.00 4.06
146 147 4.489771 CCCGTCCCATGCCAGTCC 62.490 72.222 0.00 0.00 0.00 3.85
147 148 4.489771 CCGTCCCATGCCAGTCCC 62.490 72.222 0.00 0.00 0.00 4.46
148 149 3.402681 CGTCCCATGCCAGTCCCT 61.403 66.667 0.00 0.00 0.00 4.20
149 150 2.971598 CGTCCCATGCCAGTCCCTT 61.972 63.158 0.00 0.00 0.00 3.95
150 151 1.384191 GTCCCATGCCAGTCCCTTT 59.616 57.895 0.00 0.00 0.00 3.11
151 152 0.251787 GTCCCATGCCAGTCCCTTTT 60.252 55.000 0.00 0.00 0.00 2.27
152 153 1.005450 GTCCCATGCCAGTCCCTTTTA 59.995 52.381 0.00 0.00 0.00 1.52
153 154 1.005450 TCCCATGCCAGTCCCTTTTAC 59.995 52.381 0.00 0.00 0.00 2.01
154 155 1.094785 CCATGCCAGTCCCTTTTACG 58.905 55.000 0.00 0.00 0.00 3.18
155 156 1.094785 CATGCCAGTCCCTTTTACGG 58.905 55.000 0.00 0.00 0.00 4.02
156 157 0.696501 ATGCCAGTCCCTTTTACGGT 59.303 50.000 0.00 0.00 0.00 4.83
157 158 0.035739 TGCCAGTCCCTTTTACGGTC 59.964 55.000 0.00 0.00 0.00 4.79
158 159 1.017701 GCCAGTCCCTTTTACGGTCG 61.018 60.000 0.00 0.00 0.00 4.79
159 160 0.390735 CCAGTCCCTTTTACGGTCGG 60.391 60.000 0.00 0.00 0.00 4.79
160 161 0.390735 CAGTCCCTTTTACGGTCGGG 60.391 60.000 0.00 0.00 38.07 5.14
161 162 1.742880 GTCCCTTTTACGGTCGGGC 60.743 63.158 0.00 0.00 36.61 6.13
162 163 1.914764 TCCCTTTTACGGTCGGGCT 60.915 57.895 0.00 0.00 36.61 5.19
163 164 1.743995 CCCTTTTACGGTCGGGCTG 60.744 63.158 0.00 0.00 0.00 4.85
164 165 1.743995 CCTTTTACGGTCGGGCTGG 60.744 63.158 0.00 0.00 0.00 4.85
165 166 1.004200 CTTTTACGGTCGGGCTGGT 60.004 57.895 0.00 0.00 0.00 4.00
166 167 1.296056 CTTTTACGGTCGGGCTGGTG 61.296 60.000 0.00 0.00 0.00 4.17
167 168 3.887335 TTTACGGTCGGGCTGGTGC 62.887 63.158 0.00 0.00 38.76 5.01
187 188 3.884774 GGCCGGCCCATATGGACA 61.885 66.667 36.64 0.00 45.87 4.02
188 189 2.281761 GCCGGCCCATATGGACAG 60.282 66.667 24.00 12.44 45.87 3.51
189 190 2.431683 CCGGCCCATATGGACAGG 59.568 66.667 24.00 18.02 45.87 4.00
190 191 2.452064 CCGGCCCATATGGACAGGT 61.452 63.158 24.00 0.00 45.87 4.00
191 192 1.071471 CGGCCCATATGGACAGGTC 59.929 63.158 24.00 6.79 45.87 3.85
192 193 1.410850 CGGCCCATATGGACAGGTCT 61.411 60.000 24.00 0.00 45.87 3.85
193 194 0.109342 GGCCCATATGGACAGGTCTG 59.891 60.000 24.00 4.68 44.36 3.51
194 195 0.536006 GCCCATATGGACAGGTCTGC 60.536 60.000 24.00 11.22 37.39 4.26
195 196 1.135094 CCCATATGGACAGGTCTGCT 58.865 55.000 24.00 0.00 37.39 4.24
196 197 1.071385 CCCATATGGACAGGTCTGCTC 59.929 57.143 24.00 0.00 37.39 4.26
197 198 1.764723 CCATATGGACAGGTCTGCTCA 59.235 52.381 17.49 0.00 37.39 4.26
198 199 2.171237 CCATATGGACAGGTCTGCTCAA 59.829 50.000 17.49 0.00 37.39 3.02
199 200 3.201290 CATATGGACAGGTCTGCTCAAC 58.799 50.000 0.00 0.00 0.00 3.18
200 201 1.059098 ATGGACAGGTCTGCTCAACA 58.941 50.000 0.00 0.00 0.00 3.33
201 202 0.106708 TGGACAGGTCTGCTCAACAC 59.893 55.000 0.00 0.00 0.00 3.32
202 203 0.946221 GGACAGGTCTGCTCAACACG 60.946 60.000 0.00 0.00 0.00 4.49
203 204 1.560860 GACAGGTCTGCTCAACACGC 61.561 60.000 0.00 0.00 0.00 5.34
204 205 1.595109 CAGGTCTGCTCAACACGCA 60.595 57.895 0.00 0.00 35.80 5.24
208 209 2.974148 CTGCTCAACACGCAGCCA 60.974 61.111 0.00 0.00 46.98 4.75
209 210 3.245948 CTGCTCAACACGCAGCCAC 62.246 63.158 0.00 0.00 46.98 5.01
210 211 4.374702 GCTCAACACGCAGCCACG 62.375 66.667 0.00 0.00 39.50 4.94
212 213 2.943345 CTCAACACGCAGCCACGTC 61.943 63.158 0.00 0.00 46.34 4.34
213 214 4.012895 CAACACGCAGCCACGTCC 62.013 66.667 0.00 0.00 46.34 4.79
214 215 4.539083 AACACGCAGCCACGTCCA 62.539 61.111 0.00 0.00 46.34 4.02
460 461 0.908910 TGCTTTGGCCGAGGATCTTA 59.091 50.000 6.22 0.00 37.74 2.10
774 775 3.412061 AAAAACCGCAACGCTCGA 58.588 50.000 0.00 0.00 0.00 4.04
775 776 1.278637 AAAAACCGCAACGCTCGAG 59.721 52.632 8.45 8.45 0.00 4.04
776 777 1.433837 AAAAACCGCAACGCTCGAGT 61.434 50.000 15.13 0.00 0.00 4.18
777 778 0.598158 AAAACCGCAACGCTCGAGTA 60.598 50.000 15.13 0.00 0.00 2.59
778 779 1.280206 AAACCGCAACGCTCGAGTAC 61.280 55.000 15.13 0.00 0.00 2.73
779 780 2.879462 CCGCAACGCTCGAGTACC 60.879 66.667 15.13 0.00 0.00 3.34
780 781 2.126618 CGCAACGCTCGAGTACCA 60.127 61.111 15.13 0.00 0.00 3.25
781 782 2.434134 CGCAACGCTCGAGTACCAC 61.434 63.158 15.13 0.60 0.00 4.16
819 820 1.932604 GCACTCCACACTCTCAGTTCG 60.933 57.143 0.00 0.00 0.00 3.95
831 832 2.116772 AGTTCGTCTCCCCGGTCA 59.883 61.111 0.00 0.00 0.00 4.02
833 834 2.993264 TTCGTCTCCCCGGTCACC 60.993 66.667 0.00 0.00 0.00 4.02
901 902 2.432444 CCTGCGAAGGTCCATGTAAAA 58.568 47.619 0.00 0.00 0.00 1.52
943 950 0.588252 GATTTGCATATCGCTGCCGT 59.412 50.000 1.19 0.00 41.58 5.68
974 981 1.542547 CGGTTCCCCCATTAGAATCGG 60.543 57.143 0.00 0.00 41.70 4.18
975 982 1.202891 GGTTCCCCCATTAGAATCGGG 60.203 57.143 0.00 0.00 36.66 5.14
1077 1086 1.310933 GGGTAAGACTCTCGTCGCCA 61.311 60.000 0.00 0.00 44.93 5.69
1084 1093 0.180642 ACTCTCGTCGCCAGAGGATA 59.819 55.000 13.68 0.00 41.66 2.59
1156 1171 0.040058 TTACCTACAGTCGAGCCCCA 59.960 55.000 0.00 0.00 0.00 4.96
1162 1177 0.400213 ACAGTCGAGCCCCAAAATCA 59.600 50.000 0.00 0.00 0.00 2.57
1271 1286 3.099170 AGCGCCTTCCATGGGGAT 61.099 61.111 13.02 0.00 44.48 3.85
1308 1323 2.429494 GGCAGCTCTATCCCTGGC 59.571 66.667 0.00 0.00 45.37 4.85
1311 1326 1.051812 GCAGCTCTATCCCTGGCTTA 58.948 55.000 0.00 0.00 32.30 3.09
1318 1333 4.805609 GCTCTATCCCTGGCTTAATTGGAG 60.806 50.000 0.00 0.00 0.00 3.86
1322 1337 2.102578 CCCTGGCTTAATTGGAGGTTG 58.897 52.381 0.00 0.00 0.00 3.77
1350 1365 6.368805 TCTGATAGCAAGGAGAGATGAAGTA 58.631 40.000 0.00 0.00 0.00 2.24
1351 1366 6.489700 TCTGATAGCAAGGAGAGATGAAGTAG 59.510 42.308 0.00 0.00 0.00 2.57
1355 1370 3.704061 GCAAGGAGAGATGAAGTAGAGGT 59.296 47.826 0.00 0.00 0.00 3.85
1414 1429 2.146342 CTGTGGACATCAACTGGACAC 58.854 52.381 0.00 0.00 36.62 3.67
1506 1521 4.559862 AGATCTCACCGATGTTTCCTTT 57.440 40.909 0.00 0.00 30.84 3.11
1549 1564 4.868195 CACATCGTCTCGTGCTCA 57.132 55.556 0.00 0.00 0.00 4.26
1609 1624 1.558294 TGATGGCTGAGAGCAAGATGT 59.442 47.619 0.00 0.00 44.75 3.06
1683 1698 9.242477 CTCCATTACATATATCATAGTTCGCTG 57.758 37.037 0.00 0.00 0.00 5.18
1701 1716 2.707849 GCCTGATGCTGGCAAGGTG 61.708 63.158 12.94 0.00 45.75 4.00
2061 2077 7.868415 CACACAAGAAAGCTAGAGTAAACTAGT 59.132 37.037 0.00 0.00 41.10 2.57
2095 2111 6.209192 GGCATGATAATGGAATGGTGATACAA 59.791 38.462 0.00 0.00 0.00 2.41
2141 2157 4.819630 TGTTATATTGGCATTCCCTTCGTC 59.180 41.667 0.00 0.00 0.00 4.20
2143 2159 0.748005 ATTGGCATTCCCTTCGTCGG 60.748 55.000 0.00 0.00 0.00 4.79
2194 2210 4.208873 CAGTAGAGTACTCCTAACGTAGCG 59.791 50.000 19.38 2.25 36.76 4.26
2244 2260 4.569943 TCTAGAGAAGACATGCCAACAAC 58.430 43.478 0.00 0.00 0.00 3.32
2255 2271 0.811281 GCCAACAACTGTATCCCAGC 59.189 55.000 0.00 0.00 45.68 4.85
2371 2387 2.806945 TTGGCGGAATTTCTCTGGAT 57.193 45.000 0.00 0.00 0.00 3.41
2387 2403 3.129287 TCTGGATACGACCTTTTACGTCC 59.871 47.826 0.00 0.00 42.61 4.79
2388 2404 2.824936 TGGATACGACCTTTTACGTCCA 59.175 45.455 0.00 0.00 42.61 4.02
2389 2405 3.257873 TGGATACGACCTTTTACGTCCAA 59.742 43.478 0.00 0.00 42.61 3.53
2390 2406 3.614176 GGATACGACCTTTTACGTCCAAC 59.386 47.826 0.00 0.00 42.61 3.77
2391 2407 1.869774 ACGACCTTTTACGTCCAACC 58.130 50.000 0.00 0.00 38.34 3.77
2392 2408 1.413812 ACGACCTTTTACGTCCAACCT 59.586 47.619 0.00 0.00 38.34 3.50
2393 2409 2.064014 CGACCTTTTACGTCCAACCTC 58.936 52.381 0.00 0.00 0.00 3.85
2394 2410 2.546373 CGACCTTTTACGTCCAACCTCA 60.546 50.000 0.00 0.00 0.00 3.86
2395 2411 2.804527 GACCTTTTACGTCCAACCTCAC 59.195 50.000 0.00 0.00 0.00 3.51
2396 2412 2.436911 ACCTTTTACGTCCAACCTCACT 59.563 45.455 0.00 0.00 0.00 3.41
2397 2413 2.806244 CCTTTTACGTCCAACCTCACTG 59.194 50.000 0.00 0.00 0.00 3.66
2398 2414 3.463944 CTTTTACGTCCAACCTCACTGT 58.536 45.455 0.00 0.00 0.00 3.55
2399 2415 2.519377 TTACGTCCAACCTCACTGTG 57.481 50.000 0.17 0.17 0.00 3.66
2400 2416 1.694844 TACGTCCAACCTCACTGTGA 58.305 50.000 10.50 10.50 0.00 3.58
2401 2417 1.048601 ACGTCCAACCTCACTGTGAT 58.951 50.000 11.45 0.00 0.00 3.06
2402 2418 1.000955 ACGTCCAACCTCACTGTGATC 59.999 52.381 11.45 0.00 0.00 2.92
2403 2419 1.673033 CGTCCAACCTCACTGTGATCC 60.673 57.143 11.45 0.00 0.00 3.36
2404 2420 0.984230 TCCAACCTCACTGTGATCCC 59.016 55.000 11.45 0.00 0.00 3.85
2405 2421 0.391661 CCAACCTCACTGTGATCCCG 60.392 60.000 11.45 0.00 0.00 5.14
2406 2422 0.321671 CAACCTCACTGTGATCCCGT 59.678 55.000 11.45 2.87 0.00 5.28
2407 2423 0.321671 AACCTCACTGTGATCCCGTG 59.678 55.000 11.45 0.00 0.00 4.94
2408 2424 0.832135 ACCTCACTGTGATCCCGTGT 60.832 55.000 11.45 0.00 0.00 4.49
2409 2425 0.108615 CCTCACTGTGATCCCGTGTC 60.109 60.000 11.45 0.00 0.00 3.67
2410 2426 0.891373 CTCACTGTGATCCCGTGTCT 59.109 55.000 11.45 0.00 0.00 3.41
2411 2427 0.888619 TCACTGTGATCCCGTGTCTC 59.111 55.000 6.36 0.00 0.00 3.36
2412 2428 0.603065 CACTGTGATCCCGTGTCTCA 59.397 55.000 0.32 0.00 0.00 3.27
2413 2429 1.205655 CACTGTGATCCCGTGTCTCAT 59.794 52.381 0.32 0.00 0.00 2.90
2414 2430 1.902508 ACTGTGATCCCGTGTCTCATT 59.097 47.619 0.00 0.00 0.00 2.57
2415 2431 2.303022 ACTGTGATCCCGTGTCTCATTT 59.697 45.455 0.00 0.00 0.00 2.32
2416 2432 3.244561 ACTGTGATCCCGTGTCTCATTTT 60.245 43.478 0.00 0.00 0.00 1.82
2417 2433 3.073678 TGTGATCCCGTGTCTCATTTTG 58.926 45.455 0.00 0.00 0.00 2.44
2418 2434 3.074412 GTGATCCCGTGTCTCATTTTGT 58.926 45.455 0.00 0.00 0.00 2.83
2419 2435 4.250464 GTGATCCCGTGTCTCATTTTGTA 58.750 43.478 0.00 0.00 0.00 2.41
2420 2436 4.693566 GTGATCCCGTGTCTCATTTTGTAA 59.306 41.667 0.00 0.00 0.00 2.41
2421 2437 4.935205 TGATCCCGTGTCTCATTTTGTAAG 59.065 41.667 0.00 0.00 0.00 2.34
2422 2438 4.345859 TCCCGTGTCTCATTTTGTAAGT 57.654 40.909 0.00 0.00 0.00 2.24
2423 2439 5.471556 TCCCGTGTCTCATTTTGTAAGTA 57.528 39.130 0.00 0.00 0.00 2.24
2424 2440 5.856156 TCCCGTGTCTCATTTTGTAAGTAA 58.144 37.500 0.00 0.00 0.00 2.24
2493 2512 4.164981 TCCATGGTGGTTAACTAGTGTCT 58.835 43.478 12.58 0.00 39.03 3.41
2494 2513 4.222145 TCCATGGTGGTTAACTAGTGTCTC 59.778 45.833 12.58 0.00 39.03 3.36
2539 2558 5.071788 CCTAGCATTACTCTGTTATTGGGGA 59.928 44.000 0.00 0.00 0.00 4.81
2612 2646 1.161843 GCAGCGGTTAAGTTTGGCTA 58.838 50.000 0.00 0.00 31.72 3.93
2743 3408 7.288852 CCTTCCTCCAATATTCTCACTTCTCTA 59.711 40.741 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320683 CTGTCCGGATGCAGTCAACA 60.321 55.000 7.81 0.00 0.00 3.33
1 2 1.639298 GCTGTCCGGATGCAGTCAAC 61.639 60.000 22.23 2.71 35.33 3.18
2 3 1.375908 GCTGTCCGGATGCAGTCAA 60.376 57.895 22.23 0.00 35.33 3.18
3 4 2.230994 GAGCTGTCCGGATGCAGTCA 62.231 60.000 26.66 11.64 35.33 3.41
5 6 2.581354 GAGCTGTCCGGATGCAGT 59.419 61.111 26.66 13.44 35.33 4.40
6 7 2.584418 CGAGCTGTCCGGATGCAG 60.584 66.667 26.66 21.78 35.93 4.41
13 14 3.744719 TCCGAACCGAGCTGTCCG 61.745 66.667 0.00 0.00 0.00 4.79
14 15 2.126031 GTCCGAACCGAGCTGTCC 60.126 66.667 0.00 0.00 0.00 4.02
15 16 2.504244 CGTCCGAACCGAGCTGTC 60.504 66.667 0.00 0.00 0.00 3.51
16 17 4.719369 GCGTCCGAACCGAGCTGT 62.719 66.667 0.00 0.00 0.00 4.40
17 18 3.916392 AAGCGTCCGAACCGAGCTG 62.916 63.158 0.00 0.00 38.28 4.24
18 19 3.681835 AAGCGTCCGAACCGAGCT 61.682 61.111 0.00 0.00 40.20 4.09
19 20 3.479269 CAAGCGTCCGAACCGAGC 61.479 66.667 0.00 0.00 0.00 5.03
20 21 3.479269 GCAAGCGTCCGAACCGAG 61.479 66.667 0.00 0.00 0.00 4.63
33 34 3.883744 AAGTGGACTCGGCCGCAAG 62.884 63.158 23.51 17.03 40.91 4.01
34 35 3.469863 AAAGTGGACTCGGCCGCAA 62.470 57.895 23.51 2.44 40.91 4.85
35 36 3.936203 AAAGTGGACTCGGCCGCA 61.936 61.111 23.51 10.15 40.91 5.69
36 37 3.423154 CAAAGTGGACTCGGCCGC 61.423 66.667 23.51 6.96 38.73 6.53
37 38 2.742372 CCAAAGTGGACTCGGCCG 60.742 66.667 22.12 22.12 40.96 6.13
38 39 1.376037 CTCCAAAGTGGACTCGGCC 60.376 63.158 0.00 0.00 42.67 6.13
39 40 1.376037 CCTCCAAAGTGGACTCGGC 60.376 63.158 0.00 0.00 42.67 5.54
40 41 0.905357 ATCCTCCAAAGTGGACTCGG 59.095 55.000 0.00 0.00 42.67 4.63
41 42 2.770164 AATCCTCCAAAGTGGACTCG 57.230 50.000 0.00 0.00 42.67 4.18
42 43 4.293662 AGAAATCCTCCAAAGTGGACTC 57.706 45.455 0.00 0.00 42.67 3.36
43 44 4.731313 AAGAAATCCTCCAAAGTGGACT 57.269 40.909 0.00 0.00 42.67 3.85
44 45 5.791336 AAAAGAAATCCTCCAAAGTGGAC 57.209 39.130 0.00 0.00 42.67 4.02
45 46 6.010219 CCTAAAAGAAATCCTCCAAAGTGGA 58.990 40.000 0.00 0.00 45.98 4.02
46 47 5.185828 CCCTAAAAGAAATCCTCCAAAGTGG 59.814 44.000 0.00 0.00 39.43 4.00
47 48 5.185828 CCCCTAAAAGAAATCCTCCAAAGTG 59.814 44.000 0.00 0.00 0.00 3.16
48 49 5.333581 CCCCTAAAAGAAATCCTCCAAAGT 58.666 41.667 0.00 0.00 0.00 2.66
49 50 4.711846 CCCCCTAAAAGAAATCCTCCAAAG 59.288 45.833 0.00 0.00 0.00 2.77
50 51 4.683643 CCCCCTAAAAGAAATCCTCCAAA 58.316 43.478 0.00 0.00 0.00 3.28
51 52 4.331159 CCCCCTAAAAGAAATCCTCCAA 57.669 45.455 0.00 0.00 0.00 3.53
69 70 0.902984 AAATCTTCAAACCGGCCCCC 60.903 55.000 0.00 0.00 0.00 5.40
70 71 0.973632 AAAATCTTCAAACCGGCCCC 59.026 50.000 0.00 0.00 0.00 5.80
71 72 2.831685 AAAAATCTTCAAACCGGCCC 57.168 45.000 0.00 0.00 0.00 5.80
106 107 5.391629 GGCTGTGTCGACCCTTTAATAAAAG 60.392 44.000 14.12 0.00 41.57 2.27
107 108 4.456566 GGCTGTGTCGACCCTTTAATAAAA 59.543 41.667 14.12 0.00 0.00 1.52
108 109 4.004982 GGCTGTGTCGACCCTTTAATAAA 58.995 43.478 14.12 0.00 0.00 1.40
109 110 3.602483 GGCTGTGTCGACCCTTTAATAA 58.398 45.455 14.12 0.00 0.00 1.40
110 111 2.093341 GGGCTGTGTCGACCCTTTAATA 60.093 50.000 14.12 0.00 40.75 0.98
111 112 1.339727 GGGCTGTGTCGACCCTTTAAT 60.340 52.381 14.12 0.00 40.75 1.40
112 113 0.035739 GGGCTGTGTCGACCCTTTAA 59.964 55.000 14.12 0.00 40.75 1.52
113 114 1.675219 GGGCTGTGTCGACCCTTTA 59.325 57.895 14.12 0.00 40.75 1.85
114 115 2.430367 GGGCTGTGTCGACCCTTT 59.570 61.111 14.12 0.00 40.75 3.11
115 116 4.003788 CGGGCTGTGTCGACCCTT 62.004 66.667 14.12 0.00 41.86 3.95
117 118 4.736896 GACGGGCTGTGTCGACCC 62.737 72.222 14.12 5.44 40.51 4.46
118 119 4.736896 GGACGGGCTGTGTCGACC 62.737 72.222 14.12 5.06 37.22 4.79
119 120 4.736896 GGGACGGGCTGTGTCGAC 62.737 72.222 9.11 9.11 37.22 4.20
121 122 4.082523 ATGGGACGGGCTGTGTCG 62.083 66.667 2.25 0.00 37.22 4.35
122 123 2.436646 CATGGGACGGGCTGTGTC 60.437 66.667 2.25 0.00 35.60 3.67
123 124 4.722700 GCATGGGACGGGCTGTGT 62.723 66.667 2.25 0.00 0.00 3.72
129 130 4.489771 GGACTGGCATGGGACGGG 62.490 72.222 0.00 0.00 30.11 5.28
130 131 4.489771 GGGACTGGCATGGGACGG 62.490 72.222 0.00 0.00 0.00 4.79
131 132 2.484287 AAAGGGACTGGCATGGGACG 62.484 60.000 0.00 0.00 40.86 4.79
132 133 0.251787 AAAAGGGACTGGCATGGGAC 60.252 55.000 0.00 0.00 40.86 4.46
133 134 1.005450 GTAAAAGGGACTGGCATGGGA 59.995 52.381 0.00 0.00 40.86 4.37
134 135 1.474330 GTAAAAGGGACTGGCATGGG 58.526 55.000 0.00 0.00 40.86 4.00
135 136 1.094785 CGTAAAAGGGACTGGCATGG 58.905 55.000 0.00 0.00 40.86 3.66
136 137 1.094785 CCGTAAAAGGGACTGGCATG 58.905 55.000 0.00 0.00 40.86 4.06
137 138 0.696501 ACCGTAAAAGGGACTGGCAT 59.303 50.000 0.00 0.00 40.86 4.40
138 139 0.035739 GACCGTAAAAGGGACTGGCA 59.964 55.000 0.00 0.00 40.86 4.92
139 140 1.017701 CGACCGTAAAAGGGACTGGC 61.018 60.000 0.00 0.00 40.86 4.85
140 141 0.390735 CCGACCGTAAAAGGGACTGG 60.391 60.000 0.00 0.00 40.86 4.00
141 142 0.390735 CCCGACCGTAAAAGGGACTG 60.391 60.000 0.00 0.00 46.64 3.51
142 143 1.977685 CCCGACCGTAAAAGGGACT 59.022 57.895 0.00 0.00 46.64 3.85
143 144 1.742880 GCCCGACCGTAAAAGGGAC 60.743 63.158 3.19 0.00 46.64 4.46
144 145 1.914764 AGCCCGACCGTAAAAGGGA 60.915 57.895 3.19 0.00 46.64 4.20
145 146 1.743995 CAGCCCGACCGTAAAAGGG 60.744 63.158 0.00 0.00 46.44 3.95
146 147 1.743995 CCAGCCCGACCGTAAAAGG 60.744 63.158 0.00 0.00 37.30 3.11
147 148 1.004200 ACCAGCCCGACCGTAAAAG 60.004 57.895 0.00 0.00 0.00 2.27
148 149 1.301874 CACCAGCCCGACCGTAAAA 60.302 57.895 0.00 0.00 0.00 1.52
149 150 2.344500 CACCAGCCCGACCGTAAA 59.656 61.111 0.00 0.00 0.00 2.01
150 151 4.382320 GCACCAGCCCGACCGTAA 62.382 66.667 0.00 0.00 33.58 3.18
170 171 3.850098 CTGTCCATATGGGCCGGCC 62.850 68.421 38.57 38.57 39.61 6.13
171 172 2.281761 CTGTCCATATGGGCCGGC 60.282 66.667 23.51 21.18 39.61 6.13
172 173 2.431683 CCTGTCCATATGGGCCGG 59.568 66.667 23.51 22.11 39.61 6.13
173 174 1.071471 GACCTGTCCATATGGGCCG 59.929 63.158 23.51 16.99 39.61 6.13
174 175 0.109342 CAGACCTGTCCATATGGGCC 59.891 60.000 23.51 13.71 39.61 5.80
175 176 0.536006 GCAGACCTGTCCATATGGGC 60.536 60.000 19.94 19.94 41.09 5.36
176 177 1.071385 GAGCAGACCTGTCCATATGGG 59.929 57.143 21.78 8.00 35.41 4.00
177 178 1.764723 TGAGCAGACCTGTCCATATGG 59.235 52.381 16.25 16.25 0.00 2.74
178 179 3.201290 GTTGAGCAGACCTGTCCATATG 58.799 50.000 0.00 0.00 0.00 1.78
179 180 2.840038 TGTTGAGCAGACCTGTCCATAT 59.160 45.455 0.00 0.00 0.00 1.78
180 181 2.028112 GTGTTGAGCAGACCTGTCCATA 60.028 50.000 0.00 0.00 0.00 2.74
181 182 1.059098 TGTTGAGCAGACCTGTCCAT 58.941 50.000 0.00 0.00 0.00 3.41
182 183 0.106708 GTGTTGAGCAGACCTGTCCA 59.893 55.000 0.00 0.00 0.00 4.02
183 184 0.946221 CGTGTTGAGCAGACCTGTCC 60.946 60.000 0.00 0.00 0.00 4.02
184 185 1.560860 GCGTGTTGAGCAGACCTGTC 61.561 60.000 0.00 0.00 34.19 3.51
185 186 1.595382 GCGTGTTGAGCAGACCTGT 60.595 57.895 0.00 0.00 34.19 4.00
186 187 1.595109 TGCGTGTTGAGCAGACCTG 60.595 57.895 0.00 0.00 40.01 4.00
187 188 2.821685 TGCGTGTTGAGCAGACCT 59.178 55.556 0.00 0.00 40.01 3.85
192 193 3.279116 GTGGCTGCGTGTTGAGCA 61.279 61.111 0.00 0.00 42.99 4.26
193 194 4.374702 CGTGGCTGCGTGTTGAGC 62.375 66.667 0.00 0.00 34.23 4.26
194 195 2.943345 GACGTGGCTGCGTGTTGAG 61.943 63.158 11.83 0.00 45.79 3.02
195 196 2.964925 GACGTGGCTGCGTGTTGA 60.965 61.111 11.83 0.00 45.79 3.18
196 197 4.012895 GGACGTGGCTGCGTGTTG 62.013 66.667 11.83 0.00 45.79 3.33
197 198 4.539083 TGGACGTGGCTGCGTGTT 62.539 61.111 11.83 0.00 45.79 3.32
203 204 3.716006 CTTGCGTGGACGTGGCTG 61.716 66.667 0.00 0.00 42.22 4.85
206 207 2.048597 TAGCTTGCGTGGACGTGG 60.049 61.111 0.00 0.00 42.22 4.94
207 208 2.380410 GGTAGCTTGCGTGGACGTG 61.380 63.158 0.00 0.00 42.22 4.49
208 209 2.048503 GGTAGCTTGCGTGGACGT 60.049 61.111 0.00 0.00 42.22 4.34
209 210 2.813908 GGGTAGCTTGCGTGGACG 60.814 66.667 0.00 0.00 43.27 4.79
210 211 2.436115 GGGGTAGCTTGCGTGGAC 60.436 66.667 0.00 0.00 0.00 4.02
211 212 3.712907 GGGGGTAGCTTGCGTGGA 61.713 66.667 0.00 0.00 0.00 4.02
460 461 3.127548 GCGATGATCAGGTTGTTCAACAT 59.872 43.478 15.89 7.43 30.83 2.71
644 645 2.646175 CCCGCACCGAGAGAAAGGA 61.646 63.158 0.00 0.00 0.00 3.36
645 646 2.125512 CCCGCACCGAGAGAAAGG 60.126 66.667 0.00 0.00 0.00 3.11
762 763 2.879462 GGTACTCGAGCGTTGCGG 60.879 66.667 13.61 0.00 0.00 5.69
763 764 2.126618 TGGTACTCGAGCGTTGCG 60.127 61.111 13.61 0.00 0.00 4.85
764 765 2.092882 GGTGGTACTCGAGCGTTGC 61.093 63.158 13.61 0.08 0.00 4.17
765 766 0.732880 CTGGTGGTACTCGAGCGTTG 60.733 60.000 13.61 0.00 0.00 4.10
766 767 1.177256 ACTGGTGGTACTCGAGCGTT 61.177 55.000 13.61 0.00 30.95 4.84
767 768 1.584380 GACTGGTGGTACTCGAGCGT 61.584 60.000 13.61 0.00 30.95 5.07
768 769 1.136984 GACTGGTGGTACTCGAGCG 59.863 63.158 13.61 0.00 30.95 5.03
769 770 1.511768 GGACTGGTGGTACTCGAGC 59.488 63.158 13.61 0.00 30.95 5.03
770 771 0.611062 TGGGACTGGTGGTACTCGAG 60.611 60.000 11.84 11.84 33.97 4.04
771 772 0.178955 TTGGGACTGGTGGTACTCGA 60.179 55.000 0.00 0.00 0.00 4.04
772 773 0.037605 GTTGGGACTGGTGGTACTCG 60.038 60.000 0.00 0.00 0.00 4.18
773 774 0.323957 GGTTGGGACTGGTGGTACTC 59.676 60.000 0.00 0.00 0.00 2.59
774 775 1.131928 GGGTTGGGACTGGTGGTACT 61.132 60.000 0.00 0.00 0.00 2.73
775 776 1.131928 AGGGTTGGGACTGGTGGTAC 61.132 60.000 0.00 0.00 0.00 3.34
776 777 0.492730 TAGGGTTGGGACTGGTGGTA 59.507 55.000 0.00 0.00 0.00 3.25
777 778 0.840722 CTAGGGTTGGGACTGGTGGT 60.841 60.000 0.00 0.00 0.00 4.16
778 779 1.991230 CTAGGGTTGGGACTGGTGG 59.009 63.158 0.00 0.00 0.00 4.61
779 780 1.299976 GCTAGGGTTGGGACTGGTG 59.700 63.158 0.00 0.00 0.00 4.17
780 781 1.923909 GGCTAGGGTTGGGACTGGT 60.924 63.158 0.00 0.00 0.00 4.00
781 782 2.998949 GGCTAGGGTTGGGACTGG 59.001 66.667 0.00 0.00 0.00 4.00
819 820 2.901042 GATGGTGACCGGGGAGAC 59.099 66.667 6.32 0.00 0.00 3.36
831 832 2.670148 GGAAGAGGGGTGCGATGGT 61.670 63.158 0.00 0.00 0.00 3.55
833 834 1.153289 CAGGAAGAGGGGTGCGATG 60.153 63.158 0.00 0.00 0.00 3.84
890 891 1.005347 CGTCGGCGATTTTACATGGAC 60.005 52.381 14.79 0.00 41.33 4.02
974 981 1.521681 CCTCGGATTTGACCTCGCC 60.522 63.158 0.00 0.00 0.00 5.54
975 982 1.521681 CCCTCGGATTTGACCTCGC 60.522 63.158 0.00 0.00 0.00 5.03
1077 1086 5.277876 CGCGTTTACATCACTAGTATCCTCT 60.278 44.000 0.00 0.00 0.00 3.69
1084 1093 2.094906 TGCTCGCGTTTACATCACTAGT 60.095 45.455 5.77 0.00 0.00 2.57
1090 1099 1.343821 CGGTGCTCGCGTTTACATC 59.656 57.895 5.77 0.00 0.00 3.06
1156 1171 5.587844 GCACTGTGATGAGGACTATGATTTT 59.412 40.000 12.86 0.00 0.00 1.82
1162 1177 1.410517 CCGCACTGTGATGAGGACTAT 59.589 52.381 12.86 0.00 41.76 2.12
1308 1323 5.902613 TCAGAATGCAACCTCCAATTAAG 57.097 39.130 0.00 0.00 34.76 1.85
1311 1326 4.340381 GCTATCAGAATGCAACCTCCAATT 59.660 41.667 0.00 0.00 34.76 2.32
1318 1333 3.282021 TCCTTGCTATCAGAATGCAACC 58.718 45.455 8.76 0.00 41.06 3.77
1322 1337 4.333913 TCTCTCCTTGCTATCAGAATGC 57.666 45.455 0.00 0.00 34.76 3.56
1350 1365 0.389391 CGACCACACAGTTCACCTCT 59.611 55.000 0.00 0.00 0.00 3.69
1351 1366 0.387929 TCGACCACACAGTTCACCTC 59.612 55.000 0.00 0.00 0.00 3.85
1355 1370 1.206132 AGTTGTCGACCACACAGTTCA 59.794 47.619 20.56 0.00 33.41 3.18
1414 1429 2.005451 CTTCAGCGATGAAGTTGGAGG 58.995 52.381 30.30 8.55 40.13 4.30
1506 1521 2.989639 CTCTCCCCGCCAACATGA 59.010 61.111 0.00 0.00 0.00 3.07
1539 1554 0.393944 ATCGGGTAGTGAGCACGAGA 60.394 55.000 0.00 0.00 36.97 4.04
1548 1563 1.065928 GACTGGCGATCGGGTAGTG 59.934 63.158 18.30 0.00 0.00 2.74
1549 1564 0.683504 AAGACTGGCGATCGGGTAGT 60.684 55.000 18.30 0.00 0.00 2.73
1609 1624 5.801380 CATGTCATGGATGGTGATAGATGA 58.199 41.667 4.78 0.00 0.00 2.92
1641 1656 3.726557 TGGAGCATTGATCTGAAGGTT 57.273 42.857 1.44 0.00 0.00 3.50
1701 1716 1.428912 TGCCATGGGGGAAGAATATCC 59.571 52.381 15.13 0.00 40.01 2.59
2061 2077 9.631257 CCATTCCATTATCATGCCTAATATACA 57.369 33.333 0.00 0.00 0.00 2.29
2141 2157 2.906354 ACTAAGCACAAAGGATAGCCG 58.094 47.619 0.00 0.00 39.96 5.52
2143 2159 8.664211 AAATAGTACTAAGCACAAAGGATAGC 57.336 34.615 6.70 0.00 0.00 2.97
2194 2210 2.213499 CGGTAACCTGAAGCCATGATC 58.787 52.381 0.00 0.00 0.00 2.92
2255 2271 4.034858 CAGGCACATAAGAACAGCATACAG 59.965 45.833 0.00 0.00 0.00 2.74
2270 2286 5.832539 AGGCTAGATATAAACAGGCACAT 57.167 39.130 0.00 0.00 36.12 3.21
2301 2317 0.740149 TCAACTTGCCACTGTTGCTG 59.260 50.000 5.42 1.42 42.11 4.41
2371 2387 2.627699 AGGTTGGACGTAAAAGGTCGTA 59.372 45.455 0.00 0.00 40.39 3.43
2387 2403 0.321671 ACGGGATCACAGTGAGGTTG 59.678 55.000 9.64 2.05 0.00 3.77
2388 2404 0.321671 CACGGGATCACAGTGAGGTT 59.678 55.000 9.64 0.00 38.06 3.50
2389 2405 0.832135 ACACGGGATCACAGTGAGGT 60.832 55.000 21.40 1.77 39.04 3.85
2390 2406 0.108615 GACACGGGATCACAGTGAGG 60.109 60.000 21.40 1.15 39.04 3.86
2391 2407 0.891373 AGACACGGGATCACAGTGAG 59.109 55.000 21.40 0.00 39.04 3.51
2392 2408 0.888619 GAGACACGGGATCACAGTGA 59.111 55.000 21.40 5.50 39.04 3.41
2393 2409 0.603065 TGAGACACGGGATCACAGTG 59.397 55.000 15.39 15.39 41.28 3.66
2394 2410 1.561643 ATGAGACACGGGATCACAGT 58.438 50.000 0.00 0.00 0.00 3.55
2395 2411 2.680312 AATGAGACACGGGATCACAG 57.320 50.000 0.00 0.00 0.00 3.66
2396 2412 3.073678 CAAAATGAGACACGGGATCACA 58.926 45.455 0.00 0.00 0.00 3.58
2397 2413 3.074412 ACAAAATGAGACACGGGATCAC 58.926 45.455 0.00 0.00 0.00 3.06
2398 2414 3.417069 ACAAAATGAGACACGGGATCA 57.583 42.857 0.00 0.00 0.00 2.92
2399 2415 4.935808 ACTTACAAAATGAGACACGGGATC 59.064 41.667 0.00 0.00 0.00 3.36
2400 2416 4.906618 ACTTACAAAATGAGACACGGGAT 58.093 39.130 0.00 0.00 0.00 3.85
2401 2417 4.345859 ACTTACAAAATGAGACACGGGA 57.654 40.909 0.00 0.00 0.00 5.14
2402 2418 5.467399 TGTTACTTACAAAATGAGACACGGG 59.533 40.000 0.00 0.00 32.64 5.28
2403 2419 6.533819 TGTTACTTACAAAATGAGACACGG 57.466 37.500 0.00 0.00 32.64 4.94
2415 2431 5.979993 TCACAGTGAGGTTGTTACTTACAA 58.020 37.500 0.00 0.00 44.31 2.41
2416 2432 5.601583 TCACAGTGAGGTTGTTACTTACA 57.398 39.130 0.00 0.00 34.12 2.41
2417 2433 5.638234 GGATCACAGTGAGGTTGTTACTTAC 59.362 44.000 9.64 0.00 0.00 2.34
2418 2434 5.542635 AGGATCACAGTGAGGTTGTTACTTA 59.457 40.000 9.64 0.00 0.00 2.24
2419 2435 4.348168 AGGATCACAGTGAGGTTGTTACTT 59.652 41.667 9.64 0.00 0.00 2.24
2420 2436 3.904339 AGGATCACAGTGAGGTTGTTACT 59.096 43.478 9.64 0.00 0.00 2.24
2421 2437 3.997021 CAGGATCACAGTGAGGTTGTTAC 59.003 47.826 9.64 0.00 0.00 2.50
2422 2438 3.646162 ACAGGATCACAGTGAGGTTGTTA 59.354 43.478 9.64 0.00 0.00 2.41
2423 2439 2.439507 ACAGGATCACAGTGAGGTTGTT 59.560 45.455 9.64 0.00 0.00 2.83
2424 2440 2.050144 ACAGGATCACAGTGAGGTTGT 58.950 47.619 9.64 9.63 0.00 3.32
2456 2472 5.185454 CACCATGGATCAAGTTGCTACTTA 58.815 41.667 21.47 3.44 42.67 2.24
2466 2482 5.586243 CACTAGTTAACCACCATGGATCAAG 59.414 44.000 21.47 4.22 40.96 3.02
2472 2488 4.504858 GAGACACTAGTTAACCACCATGG 58.495 47.826 11.19 11.19 45.02 3.66
2510 2529 0.104855 CAGAGTAATGCTAGGCGCCA 59.895 55.000 31.54 14.00 38.05 5.69
2522 2541 5.514136 CCACTTGTCCCCAATAACAGAGTAA 60.514 44.000 0.00 0.00 0.00 2.24
2529 2548 2.823747 GTTCCCACTTGTCCCCAATAAC 59.176 50.000 0.00 0.00 0.00 1.89
2539 2558 5.067283 GTCATTGTAAACTGTTCCCACTTGT 59.933 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.