Multiple sequence alignment - TraesCS6B01G391900

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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 TraesCS6B01G391900 chr6B 100.000 1668 0 0 1 1668 666828183 666826516 0.000000e+00 3081.0
1 TraesCS6B01G391900 chr6B 83.379 1101 165 15 424 1518 63423911 63422823 0.000000e+00 1003.0
2 TraesCS6B01G391900 chr6B 100.000 519 0 0 2052 2570 666826132 666825614 0.000000e+00 959.0
3 TraesCS6B01G391900 chr6B 89.689 514 53 0 2053 2566 65235818 65235305 0.000000e+00 656.0
4 TraesCS6B01G391900 chr6B 95.745 47 2 0 1622 1668 629912409 629912455 2.740000e-10 76.8
5 TraesCS6B01G391900 chr6B 95.745 47 0 2 1622 1668 601997227 601997183 9.860000e-10 75.0
6 TraesCS6B01G391900 chr6B 87.302 63 5 3 1607 1668 28112574 28112514 4.590000e-08 69.4
7 TraesCS6B01G391900 chr7B 96.059 1218 43 5 409 1625 34220949 34222162 0.000000e+00 1978.0
8 TraesCS6B01G391900 chr7B 78.825 1157 215 22 421 1565 571591144 571592282 0.000000e+00 752.0
9 TraesCS6B01G391900 chr7B 85.714 112 16 0 416 527 34231632 34231521 4.490000e-23 119.0
10 TraesCS6B01G391900 chr1B 94.968 1093 54 1 536 1627 551220118 551219026 0.000000e+00 1712.0
11 TraesCS6B01G391900 chr1B 89.980 509 50 1 2062 2570 279247958 279247451 0.000000e+00 656.0
12 TraesCS6B01G391900 chr1B 85.345 116 13 4 411 524 551186327 551186440 1.620000e-22 117.0
13 TraesCS6B01G391900 chr1B 92.453 53 2 2 1616 1667 386991962 386991911 9.860000e-10 75.0
14 TraesCS6B01G391900 chr6D 83.485 1102 151 22 424 1518 469087430 469086353 0.000000e+00 998.0
15 TraesCS6B01G391900 chr6D 89.557 316 28 3 5 319 441536657 441536346 1.850000e-106 396.0
16 TraesCS6B01G391900 chr4B 83.288 1101 166 17 424 1518 67559232 67558144 0.000000e+00 998.0
17 TraesCS6B01G391900 chr4B 89.595 519 52 2 2053 2570 396835774 396835257 0.000000e+00 658.0
18 TraesCS6B01G391900 chr4B 89.474 513 54 0 2053 2565 25334888 25335400 0.000000e+00 649.0
19 TraesCS6B01G391900 chr4B 95.652 46 1 1 1623 1668 80414812 80414768 3.550000e-09 73.1
20 TraesCS6B01G391900 chr3D 83.212 1102 152 23 424 1518 496843181 496842106 0.000000e+00 979.0
21 TraesCS6B01G391900 chr7D 96.957 460 13 1 1169 1627 2487318 2486859 0.000000e+00 771.0
22 TraesCS6B01G391900 chr7D 83.486 109 16 1 418 524 2479378 2479486 1.630000e-17 100.0
23 TraesCS6B01G391900 chr6A 78.893 1156 215 22 421 1565 584918310 584919447 0.000000e+00 756.0
24 TraesCS6B01G391900 chr4A 78.769 1154 215 22 424 1565 690106653 690105518 0.000000e+00 747.0
25 TraesCS6B01G391900 chr5B 89.961 518 50 2 2053 2570 284480499 284481014 0.000000e+00 667.0
26 TraesCS6B01G391900 chr5B 89.768 518 53 0 2053 2570 289924961 289924444 0.000000e+00 664.0
27 TraesCS6B01G391900 chr5B 93.878 49 2 1 1620 1668 497941657 497941704 3.550000e-09 73.1
28 TraesCS6B01G391900 chr3B 89.320 515 55 0 2056 2570 67465807 67465293 0.000000e+00 647.0
29 TraesCS6B01G391900 chr3B 89.189 518 56 0 2053 2570 718762087 718761570 0.000000e+00 647.0
30 TraesCS6B01G391900 chr3B 90.909 55 5 0 1614 1668 434235662 434235716 9.860000e-10 75.0
31 TraesCS6B01G391900 chr2B 89.189 518 55 1 2053 2570 687647671 687648187 0.000000e+00 645.0
32 TraesCS6B01G391900 chr2B 94.000 50 2 1 1620 1668 111175296 111175345 9.860000e-10 75.0
33 TraesCS6B01G391900 chr1A 97.778 45 1 0 1624 1668 148153772 148153728 7.620000e-11 78.7


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 TraesCS6B01G391900 chr6B 666825614 666828183 2569 True 2020 3081 100.000 1 2570 2 chr6B.!!$R5 2569
1 TraesCS6B01G391900 chr6B 63422823 63423911 1088 True 1003 1003 83.379 424 1518 1 chr6B.!!$R2 1094
2 TraesCS6B01G391900 chr6B 65235305 65235818 513 True 656 656 89.689 2053 2566 1 chr6B.!!$R3 513
3 TraesCS6B01G391900 chr7B 34220949 34222162 1213 False 1978 1978 96.059 409 1625 1 chr7B.!!$F1 1216
4 TraesCS6B01G391900 chr7B 571591144 571592282 1138 False 752 752 78.825 421 1565 1 chr7B.!!$F2 1144
5 TraesCS6B01G391900 chr1B 551219026 551220118 1092 True 1712 1712 94.968 536 1627 1 chr1B.!!$R3 1091
6 TraesCS6B01G391900 chr1B 279247451 279247958 507 True 656 656 89.980 2062 2570 1 chr1B.!!$R1 508
7 TraesCS6B01G391900 chr6D 469086353 469087430 1077 True 998 998 83.485 424 1518 1 chr6D.!!$R2 1094
8 TraesCS6B01G391900 chr4B 67558144 67559232 1088 True 998 998 83.288 424 1518 1 chr4B.!!$R1 1094
9 TraesCS6B01G391900 chr4B 396835257 396835774 517 True 658 658 89.595 2053 2570 1 chr4B.!!$R3 517
10 TraesCS6B01G391900 chr4B 25334888 25335400 512 False 649 649 89.474 2053 2565 1 chr4B.!!$F1 512
11 TraesCS6B01G391900 chr3D 496842106 496843181 1075 True 979 979 83.212 424 1518 1 chr3D.!!$R1 1094
12 TraesCS6B01G391900 chr6A 584918310 584919447 1137 False 756 756 78.893 421 1565 1 chr6A.!!$F1 1144
13 TraesCS6B01G391900 chr4A 690105518 690106653 1135 True 747 747 78.769 424 1565 1 chr4A.!!$R1 1141
14 TraesCS6B01G391900 chr5B 284480499 284481014 515 False 667 667 89.961 2053 2570 1 chr5B.!!$F1 517
15 TraesCS6B01G391900 chr5B 289924444 289924961 517 True 664 664 89.768 2053 2570 1 chr5B.!!$R1 517
16 TraesCS6B01G391900 chr3B 67465293 67465807 514 True 647 647 89.320 2056 2570 1 chr3B.!!$R1 514
17 TraesCS6B01G391900 chr3B 718761570 718762087 517 True 647 647 89.189 2053 2570 1 chr3B.!!$R2 517
18 TraesCS6B01G391900 chr2B 687647671 687648187 516 False 645 645 89.189 2053 2570 1 chr2B.!!$F2 517

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
328 329 0.033781 CCCACAATGGTGTTGCCTTG 59.966 55.0 0.0 0.0 43.71 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2074 1.289066 CCGTGTCGAAGAGCTTGGA 59.711 57.895 0.0 0.0 36.95 3.53 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
24 25 6.391227 AATGTTTCTTCACAAGTCCGATTT 57.609 33.333 0.00 0.00 0.00 2.17
25 26 5.418310 TGTTTCTTCACAAGTCCGATTTC 57.582 39.130 0.00 0.00 0.00 2.17
26 27 4.878971 TGTTTCTTCACAAGTCCGATTTCA 59.121 37.500 0.00 0.00 0.00 2.69
27 28 5.355630 TGTTTCTTCACAAGTCCGATTTCAA 59.644 36.000 0.00 0.00 0.00 2.69
28 29 6.039270 TGTTTCTTCACAAGTCCGATTTCAAT 59.961 34.615 0.00 0.00 0.00 2.57
29 30 5.862924 TCTTCACAAGTCCGATTTCAATC 57.137 39.130 0.00 0.00 0.00 2.67
30 31 5.304778 TCTTCACAAGTCCGATTTCAATCA 58.695 37.500 0.62 0.00 35.11 2.57
31 32 5.762711 TCTTCACAAGTCCGATTTCAATCAA 59.237 36.000 0.62 0.00 35.11 2.57
32 33 6.262049 TCTTCACAAGTCCGATTTCAATCAAA 59.738 34.615 0.62 0.00 35.11 2.69
33 34 6.000891 TCACAAGTCCGATTTCAATCAAAG 57.999 37.500 0.62 0.00 35.11 2.77
34 35 5.762711 TCACAAGTCCGATTTCAATCAAAGA 59.237 36.000 0.62 0.00 35.11 2.52
35 36 6.262049 TCACAAGTCCGATTTCAATCAAAGAA 59.738 34.615 0.62 0.00 35.11 2.52
36 37 6.917477 CACAAGTCCGATTTCAATCAAAGAAA 59.083 34.615 0.62 0.00 39.11 2.52
37 38 7.434897 CACAAGTCCGATTTCAATCAAAGAAAA 59.565 33.333 0.62 0.00 38.36 2.29
38 39 7.978975 ACAAGTCCGATTTCAATCAAAGAAAAA 59.021 29.630 0.62 0.00 38.36 1.94
61 62 6.436843 AAAAACATGGTTCCATATCGAGTC 57.563 37.500 0.00 0.00 0.00 3.36
62 63 5.359194 AAACATGGTTCCATATCGAGTCT 57.641 39.130 3.88 0.00 0.00 3.24
63 64 6.479972 AAACATGGTTCCATATCGAGTCTA 57.520 37.500 3.88 0.00 0.00 2.59
64 65 5.713792 ACATGGTTCCATATCGAGTCTAG 57.286 43.478 3.88 0.00 0.00 2.43
65 66 5.386060 ACATGGTTCCATATCGAGTCTAGA 58.614 41.667 3.88 0.00 0.00 2.43
66 67 5.833667 ACATGGTTCCATATCGAGTCTAGAA 59.166 40.000 3.88 0.00 0.00 2.10
67 68 6.495181 ACATGGTTCCATATCGAGTCTAGAAT 59.505 38.462 3.88 0.00 0.00 2.40
68 69 6.978674 TGGTTCCATATCGAGTCTAGAATT 57.021 37.500 0.00 0.00 0.00 2.17
69 70 7.361457 TGGTTCCATATCGAGTCTAGAATTT 57.639 36.000 0.00 0.00 0.00 1.82
70 71 7.210174 TGGTTCCATATCGAGTCTAGAATTTG 58.790 38.462 0.00 0.00 0.00 2.32
71 72 6.647067 GGTTCCATATCGAGTCTAGAATTTGG 59.353 42.308 0.00 0.00 0.00 3.28
72 73 7.434492 GTTCCATATCGAGTCTAGAATTTGGA 58.566 38.462 9.16 9.16 0.00 3.53
73 74 7.782897 TCCATATCGAGTCTAGAATTTGGAT 57.217 36.000 9.16 8.20 0.00 3.41
74 75 7.831753 TCCATATCGAGTCTAGAATTTGGATC 58.168 38.462 9.16 0.00 0.00 3.36
75 76 7.451566 TCCATATCGAGTCTAGAATTTGGATCA 59.548 37.037 9.16 0.00 0.00 2.92
76 77 7.543868 CCATATCGAGTCTAGAATTTGGATCAC 59.456 40.741 0.00 0.00 0.00 3.06
77 78 5.914898 TCGAGTCTAGAATTTGGATCACA 57.085 39.130 0.00 0.00 0.00 3.58
78 79 6.280855 TCGAGTCTAGAATTTGGATCACAA 57.719 37.500 0.00 0.00 37.28 3.33
79 80 6.878317 TCGAGTCTAGAATTTGGATCACAAT 58.122 36.000 0.00 0.00 39.21 2.71
80 81 8.007405 TCGAGTCTAGAATTTGGATCACAATA 57.993 34.615 0.00 0.00 39.21 1.90
81 82 8.138074 TCGAGTCTAGAATTTGGATCACAATAG 58.862 37.037 0.00 0.00 39.21 1.73
82 83 7.383572 CGAGTCTAGAATTTGGATCACAATAGG 59.616 40.741 0.00 0.00 39.21 2.57
83 84 8.095452 AGTCTAGAATTTGGATCACAATAGGT 57.905 34.615 0.00 0.00 39.21 3.08
89 90 4.352009 TTTGGATCACAATAGGTGCCAAT 58.648 39.130 0.00 0.00 44.15 3.16
90 91 4.776837 TTTGGATCACAATAGGTGCCAATT 59.223 37.500 0.00 0.00 44.15 2.32
91 92 5.248020 TTTGGATCACAATAGGTGCCAATTT 59.752 36.000 0.00 0.00 44.15 1.82
92 93 6.239829 TTTGGATCACAATAGGTGCCAATTTT 60.240 34.615 0.00 0.00 44.15 1.82
93 94 7.038729 TTTGGATCACAATAGGTGCCAATTTTA 60.039 33.333 0.00 0.00 44.15 1.52
135 136 9.529325 GTAGATTTGGCTTTTTATATTTCCACC 57.471 33.333 0.00 0.00 0.00 4.61
136 137 8.379428 AGATTTGGCTTTTTATATTTCCACCT 57.621 30.769 0.00 0.00 0.00 4.00
137 138 8.825774 AGATTTGGCTTTTTATATTTCCACCTT 58.174 29.630 0.00 0.00 0.00 3.50
138 139 9.098355 GATTTGGCTTTTTATATTTCCACCTTC 57.902 33.333 0.00 0.00 0.00 3.46
139 140 7.546250 TTGGCTTTTTATATTTCCACCTTCA 57.454 32.000 0.00 0.00 0.00 3.02
140 141 7.169158 TGGCTTTTTATATTTCCACCTTCAG 57.831 36.000 0.00 0.00 0.00 3.02
141 142 6.154363 TGGCTTTTTATATTTCCACCTTCAGG 59.846 38.462 0.00 0.00 42.17 3.86
142 143 6.042777 GCTTTTTATATTTCCACCTTCAGGC 58.957 40.000 0.00 0.00 39.32 4.85
143 144 6.127338 GCTTTTTATATTTCCACCTTCAGGCT 60.127 38.462 0.00 0.00 39.32 4.58
144 145 7.579531 GCTTTTTATATTTCCACCTTCAGGCTT 60.580 37.037 0.00 0.00 39.32 4.35
145 146 6.773976 TTTATATTTCCACCTTCAGGCTTG 57.226 37.500 0.00 0.00 39.32 4.01
146 147 2.683211 ATTTCCACCTTCAGGCTTGT 57.317 45.000 0.00 0.00 39.32 3.16
147 148 2.452600 TTTCCACCTTCAGGCTTGTT 57.547 45.000 0.00 0.00 39.32 2.83
148 149 3.586470 TTTCCACCTTCAGGCTTGTTA 57.414 42.857 0.00 0.00 39.32 2.41
149 150 3.586470 TTCCACCTTCAGGCTTGTTAA 57.414 42.857 0.00 0.00 39.32 2.01
150 151 3.806949 TCCACCTTCAGGCTTGTTAAT 57.193 42.857 0.00 0.00 39.32 1.40
151 152 4.112634 TCCACCTTCAGGCTTGTTAATT 57.887 40.909 0.00 0.00 39.32 1.40
152 153 4.479158 TCCACCTTCAGGCTTGTTAATTT 58.521 39.130 0.00 0.00 39.32 1.82
153 154 4.280677 TCCACCTTCAGGCTTGTTAATTTG 59.719 41.667 0.00 0.00 39.32 2.32
154 155 4.039124 CCACCTTCAGGCTTGTTAATTTGT 59.961 41.667 0.00 0.00 39.32 2.83
155 156 5.242838 CCACCTTCAGGCTTGTTAATTTGTA 59.757 40.000 0.00 0.00 39.32 2.41
156 157 6.239176 CCACCTTCAGGCTTGTTAATTTGTAA 60.239 38.462 0.00 0.00 39.32 2.41
157 158 7.206687 CACCTTCAGGCTTGTTAATTTGTAAA 58.793 34.615 0.00 0.00 39.32 2.01
158 159 7.169140 CACCTTCAGGCTTGTTAATTTGTAAAC 59.831 37.037 0.00 0.00 39.32 2.01
159 160 7.069455 ACCTTCAGGCTTGTTAATTTGTAAACT 59.931 33.333 0.00 0.00 39.32 2.66
160 161 7.595130 CCTTCAGGCTTGTTAATTTGTAAACTC 59.405 37.037 0.00 0.00 0.00 3.01
161 162 7.817418 TCAGGCTTGTTAATTTGTAAACTCT 57.183 32.000 0.00 0.00 0.00 3.24
162 163 7.871853 TCAGGCTTGTTAATTTGTAAACTCTC 58.128 34.615 0.00 0.00 0.00 3.20
163 164 7.719633 TCAGGCTTGTTAATTTGTAAACTCTCT 59.280 33.333 0.00 0.00 0.00 3.10
164 165 8.352942 CAGGCTTGTTAATTTGTAAACTCTCTT 58.647 33.333 0.00 0.00 0.00 2.85
165 166 9.569122 AGGCTTGTTAATTTGTAAACTCTCTTA 57.431 29.630 0.00 0.00 0.00 2.10
181 182 8.579850 AACTCTCTTAATTAATGAATGTGCCA 57.420 30.769 0.00 0.00 0.00 4.92
182 183 8.579850 ACTCTCTTAATTAATGAATGTGCCAA 57.420 30.769 0.00 0.00 0.00 4.52
183 184 8.680903 ACTCTCTTAATTAATGAATGTGCCAAG 58.319 33.333 0.00 0.00 0.00 3.61
184 185 8.806429 TCTCTTAATTAATGAATGTGCCAAGA 57.194 30.769 0.00 0.00 0.00 3.02
185 186 9.241919 TCTCTTAATTAATGAATGTGCCAAGAA 57.758 29.630 0.00 0.00 0.00 2.52
186 187 9.512435 CTCTTAATTAATGAATGTGCCAAGAAG 57.488 33.333 0.00 0.00 0.00 2.85
187 188 9.241919 TCTTAATTAATGAATGTGCCAAGAAGA 57.758 29.630 0.00 0.00 0.00 2.87
188 189 9.859427 CTTAATTAATGAATGTGCCAAGAAGAA 57.141 29.630 0.00 0.00 0.00 2.52
189 190 9.638239 TTAATTAATGAATGTGCCAAGAAGAAC 57.362 29.630 0.00 0.00 0.00 3.01
190 191 6.899393 TTAATGAATGTGCCAAGAAGAACT 57.101 33.333 0.00 0.00 0.00 3.01
191 192 4.778534 ATGAATGTGCCAAGAAGAACTG 57.221 40.909 0.00 0.00 0.00 3.16
192 193 2.294233 TGAATGTGCCAAGAAGAACTGC 59.706 45.455 0.00 0.00 0.00 4.40
193 194 2.283145 ATGTGCCAAGAAGAACTGCT 57.717 45.000 0.00 0.00 0.00 4.24
194 195 1.597742 TGTGCCAAGAAGAACTGCTC 58.402 50.000 0.00 0.00 0.00 4.26
195 196 0.877743 GTGCCAAGAAGAACTGCTCC 59.122 55.000 0.00 0.00 0.00 4.70
196 197 0.250901 TGCCAAGAAGAACTGCTCCC 60.251 55.000 0.00 0.00 0.00 4.30
197 198 0.037447 GCCAAGAAGAACTGCTCCCT 59.963 55.000 0.00 0.00 0.00 4.20
198 199 1.279271 GCCAAGAAGAACTGCTCCCTA 59.721 52.381 0.00 0.00 0.00 3.53
199 200 2.290323 GCCAAGAAGAACTGCTCCCTAA 60.290 50.000 0.00 0.00 0.00 2.69
200 201 3.339141 CCAAGAAGAACTGCTCCCTAAC 58.661 50.000 0.00 0.00 0.00 2.34
201 202 3.244561 CCAAGAAGAACTGCTCCCTAACA 60.245 47.826 0.00 0.00 0.00 2.41
202 203 4.389374 CAAGAAGAACTGCTCCCTAACAA 58.611 43.478 0.00 0.00 0.00 2.83
203 204 4.706842 AGAAGAACTGCTCCCTAACAAA 57.293 40.909 0.00 0.00 0.00 2.83
204 205 5.048846 AGAAGAACTGCTCCCTAACAAAA 57.951 39.130 0.00 0.00 0.00 2.44
205 206 5.445964 AGAAGAACTGCTCCCTAACAAAAA 58.554 37.500 0.00 0.00 0.00 1.94
206 207 6.071320 AGAAGAACTGCTCCCTAACAAAAAT 58.929 36.000 0.00 0.00 0.00 1.82
207 208 5.712152 AGAACTGCTCCCTAACAAAAATG 57.288 39.130 0.00 0.00 0.00 2.32
208 209 5.140454 AGAACTGCTCCCTAACAAAAATGT 58.860 37.500 0.00 0.00 0.00 2.71
209 210 6.303839 AGAACTGCTCCCTAACAAAAATGTA 58.696 36.000 0.00 0.00 0.00 2.29
210 211 6.431234 AGAACTGCTCCCTAACAAAAATGTAG 59.569 38.462 0.00 0.00 0.00 2.74
211 212 5.010282 ACTGCTCCCTAACAAAAATGTAGG 58.990 41.667 0.00 0.00 0.00 3.18
212 213 4.993028 TGCTCCCTAACAAAAATGTAGGT 58.007 39.130 0.00 0.00 0.00 3.08
213 214 4.764823 TGCTCCCTAACAAAAATGTAGGTG 59.235 41.667 0.00 0.00 0.00 4.00
214 215 5.007682 GCTCCCTAACAAAAATGTAGGTGA 58.992 41.667 0.00 0.00 0.00 4.02
215 216 5.652452 GCTCCCTAACAAAAATGTAGGTGAT 59.348 40.000 0.00 0.00 0.00 3.06
216 217 6.404734 GCTCCCTAACAAAAATGTAGGTGATG 60.405 42.308 0.00 0.00 0.00 3.07
217 218 6.785076 TCCCTAACAAAAATGTAGGTGATGA 58.215 36.000 0.00 0.00 0.00 2.92
218 219 7.410174 TCCCTAACAAAAATGTAGGTGATGAT 58.590 34.615 0.00 0.00 0.00 2.45
219 220 7.339212 TCCCTAACAAAAATGTAGGTGATGATG 59.661 37.037 0.00 0.00 0.00 3.07
220 221 7.339212 CCCTAACAAAAATGTAGGTGATGATGA 59.661 37.037 0.00 0.00 0.00 2.92
221 222 8.739039 CCTAACAAAAATGTAGGTGATGATGAA 58.261 33.333 0.00 0.00 0.00 2.57
222 223 9.559958 CTAACAAAAATGTAGGTGATGATGAAC 57.440 33.333 0.00 0.00 0.00 3.18
223 224 6.611381 ACAAAAATGTAGGTGATGATGAACG 58.389 36.000 0.00 0.00 0.00 3.95
224 225 4.882671 AAATGTAGGTGATGATGAACGC 57.117 40.909 0.00 0.00 0.00 4.84
225 226 3.541996 ATGTAGGTGATGATGAACGCA 57.458 42.857 0.00 0.00 0.00 5.24
226 227 3.541996 TGTAGGTGATGATGAACGCAT 57.458 42.857 0.00 0.00 37.47 4.73
227 228 4.664150 TGTAGGTGATGATGAACGCATA 57.336 40.909 0.00 0.00 34.11 3.14
228 229 5.017294 TGTAGGTGATGATGAACGCATAA 57.983 39.130 0.00 0.00 34.11 1.90
229 230 5.423886 TGTAGGTGATGATGAACGCATAAA 58.576 37.500 0.00 0.00 34.11 1.40
230 231 5.877564 TGTAGGTGATGATGAACGCATAAAA 59.122 36.000 0.00 0.00 34.11 1.52
231 232 5.490139 AGGTGATGATGAACGCATAAAAG 57.510 39.130 0.00 0.00 34.11 2.27
232 233 5.185454 AGGTGATGATGAACGCATAAAAGA 58.815 37.500 0.00 0.00 34.11 2.52
233 234 5.824624 AGGTGATGATGAACGCATAAAAGAT 59.175 36.000 0.00 0.00 34.11 2.40
234 235 5.911280 GGTGATGATGAACGCATAAAAGATG 59.089 40.000 0.00 0.00 34.11 2.90
235 236 6.238456 GGTGATGATGAACGCATAAAAGATGA 60.238 38.462 0.00 0.00 34.11 2.92
236 237 7.358066 GTGATGATGAACGCATAAAAGATGAT 58.642 34.615 0.00 0.00 34.11 2.45
237 238 7.859377 GTGATGATGAACGCATAAAAGATGATT 59.141 33.333 0.00 0.00 34.11 2.57
238 239 7.858879 TGATGATGAACGCATAAAAGATGATTG 59.141 33.333 0.00 0.00 34.11 2.67
239 240 7.087409 TGATGAACGCATAAAAGATGATTGT 57.913 32.000 0.00 0.00 34.11 2.71
240 241 8.207521 TGATGAACGCATAAAAGATGATTGTA 57.792 30.769 0.00 0.00 34.11 2.41
241 242 8.839343 TGATGAACGCATAAAAGATGATTGTAT 58.161 29.630 0.00 0.00 34.11 2.29
242 243 9.322776 GATGAACGCATAAAAGATGATTGTATC 57.677 33.333 0.00 0.00 34.11 2.24
243 244 7.639039 TGAACGCATAAAAGATGATTGTATCC 58.361 34.615 0.00 0.00 0.00 2.59
244 245 7.498900 TGAACGCATAAAAGATGATTGTATCCT 59.501 33.333 0.00 0.00 0.00 3.24
245 246 7.194607 ACGCATAAAAGATGATTGTATCCTG 57.805 36.000 0.00 0.00 0.00 3.86
246 247 6.767902 ACGCATAAAAGATGATTGTATCCTGT 59.232 34.615 0.00 0.00 0.00 4.00
247 248 7.073883 CGCATAAAAGATGATTGTATCCTGTG 58.926 38.462 0.00 0.00 0.00 3.66
248 249 7.254898 CGCATAAAAGATGATTGTATCCTGTGT 60.255 37.037 0.00 0.00 0.00 3.72
249 250 8.408601 GCATAAAAGATGATTGTATCCTGTGTT 58.591 33.333 0.00 0.00 0.00 3.32
250 251 9.726232 CATAAAAGATGATTGTATCCTGTGTTG 57.274 33.333 0.00 0.00 0.00 3.33
251 252 7.765695 AAAAGATGATTGTATCCTGTGTTGT 57.234 32.000 0.00 0.00 0.00 3.32
252 253 6.992063 AAGATGATTGTATCCTGTGTTGTC 57.008 37.500 0.00 0.00 0.00 3.18
253 254 5.431765 AGATGATTGTATCCTGTGTTGTCC 58.568 41.667 0.00 0.00 0.00 4.02
254 255 4.908601 TGATTGTATCCTGTGTTGTCCT 57.091 40.909 0.00 0.00 0.00 3.85
255 256 6.384015 AGATGATTGTATCCTGTGTTGTCCTA 59.616 38.462 0.00 0.00 0.00 2.94
256 257 6.367374 TGATTGTATCCTGTGTTGTCCTAA 57.633 37.500 0.00 0.00 0.00 2.69
257 258 6.170506 TGATTGTATCCTGTGTTGTCCTAAC 58.829 40.000 0.00 0.00 0.00 2.34
258 259 5.818678 TTGTATCCTGTGTTGTCCTAACT 57.181 39.130 0.00 0.00 0.00 2.24
259 260 5.818678 TGTATCCTGTGTTGTCCTAACTT 57.181 39.130 0.00 0.00 0.00 2.66
260 261 6.182507 TGTATCCTGTGTTGTCCTAACTTT 57.817 37.500 0.00 0.00 0.00 2.66
261 262 6.597562 TGTATCCTGTGTTGTCCTAACTTTT 58.402 36.000 0.00 0.00 0.00 2.27
262 263 7.057894 TGTATCCTGTGTTGTCCTAACTTTTT 58.942 34.615 0.00 0.00 0.00 1.94
287 288 9.650539 TTTGAAAATCAGTCTTGTCAAATTTGA 57.349 25.926 16.91 16.91 31.82 2.69
288 289 9.820725 TTGAAAATCAGTCTTGTCAAATTTGAT 57.179 25.926 23.05 4.08 39.73 2.57
289 290 9.820725 TGAAAATCAGTCTTGTCAAATTTGATT 57.179 25.926 23.05 9.20 39.73 2.57
292 293 9.820725 AAATCAGTCTTGTCAAATTTGATTTCA 57.179 25.926 23.05 13.97 38.63 2.69
293 294 9.472361 AATCAGTCTTGTCAAATTTGATTTCAG 57.528 29.630 23.05 15.57 39.73 3.02
294 295 7.999679 TCAGTCTTGTCAAATTTGATTTCAGT 58.000 30.769 23.05 8.90 39.73 3.41
295 296 8.131100 TCAGTCTTGTCAAATTTGATTTCAGTC 58.869 33.333 23.05 13.47 39.73 3.51
296 297 7.112565 CAGTCTTGTCAAATTTGATTTCAGTCG 59.887 37.037 23.05 9.51 39.73 4.18
297 298 7.012327 AGTCTTGTCAAATTTGATTTCAGTCGA 59.988 33.333 23.05 11.26 39.73 4.20
298 299 7.322222 GTCTTGTCAAATTTGATTTCAGTCGAG 59.678 37.037 23.05 16.10 39.73 4.04
299 300 6.859420 TGTCAAATTTGATTTCAGTCGAGA 57.141 33.333 23.05 0.00 39.73 4.04
300 301 7.258022 TGTCAAATTTGATTTCAGTCGAGAA 57.742 32.000 23.05 0.00 39.73 2.87
301 302 7.702386 TGTCAAATTTGATTTCAGTCGAGAAA 58.298 30.769 23.05 2.70 41.31 2.52
302 303 8.187480 TGTCAAATTTGATTTCAGTCGAGAAAA 58.813 29.630 23.05 0.00 40.54 2.29
303 304 9.019764 GTCAAATTTGATTTCAGTCGAGAAAAA 57.980 29.630 23.05 0.00 40.54 1.94
320 321 2.618442 AAAAGCAACCCACAATGGTG 57.382 45.000 0.00 0.00 44.85 4.17
321 322 1.494960 AAAGCAACCCACAATGGTGT 58.505 45.000 0.00 0.00 43.71 4.16
322 323 1.494960 AAGCAACCCACAATGGTGTT 58.505 45.000 0.00 0.00 43.71 3.32
323 324 0.752054 AGCAACCCACAATGGTGTTG 59.248 50.000 17.77 17.77 44.37 3.33
324 325 3.287482 CAACCCACAATGGTGTTGC 57.713 52.632 12.98 0.00 43.71 4.17
325 326 0.249826 CAACCCACAATGGTGTTGCC 60.250 55.000 12.98 0.00 43.71 4.52
326 327 0.398381 AACCCACAATGGTGTTGCCT 60.398 50.000 0.00 0.00 43.71 4.75
327 328 0.398381 ACCCACAATGGTGTTGCCTT 60.398 50.000 0.00 0.00 43.71 4.35
328 329 0.033781 CCCACAATGGTGTTGCCTTG 59.966 55.000 0.00 0.00 43.71 3.61
329 330 0.752054 CCACAATGGTGTTGCCTTGT 59.248 50.000 0.00 0.00 43.71 3.16
330 331 1.269726 CCACAATGGTGTTGCCTTGTC 60.270 52.381 0.00 0.00 43.71 3.18
331 332 1.682854 CACAATGGTGTTGCCTTGTCT 59.317 47.619 0.00 0.00 40.24 3.41
332 333 2.884012 CACAATGGTGTTGCCTTGTCTA 59.116 45.455 0.00 0.00 40.24 2.59
333 334 3.507233 CACAATGGTGTTGCCTTGTCTAT 59.493 43.478 0.00 0.00 40.24 1.98
334 335 4.022068 CACAATGGTGTTGCCTTGTCTATT 60.022 41.667 0.00 0.00 40.24 1.73
335 336 4.588528 ACAATGGTGTTGCCTTGTCTATTT 59.411 37.500 0.00 0.00 35.30 1.40
336 337 5.070313 ACAATGGTGTTGCCTTGTCTATTTT 59.930 36.000 0.00 0.00 35.30 1.82
337 338 5.806654 ATGGTGTTGCCTTGTCTATTTTT 57.193 34.783 0.00 0.00 38.35 1.94
338 339 6.909550 ATGGTGTTGCCTTGTCTATTTTTA 57.090 33.333 0.00 0.00 38.35 1.52
339 340 6.716934 TGGTGTTGCCTTGTCTATTTTTAA 57.283 33.333 0.00 0.00 38.35 1.52
340 341 7.113658 TGGTGTTGCCTTGTCTATTTTTAAA 57.886 32.000 0.00 0.00 38.35 1.52
341 342 7.556844 TGGTGTTGCCTTGTCTATTTTTAAAA 58.443 30.769 0.00 0.00 38.35 1.52
342 343 7.708752 TGGTGTTGCCTTGTCTATTTTTAAAAG 59.291 33.333 0.14 0.00 38.35 2.27
343 344 7.923878 GGTGTTGCCTTGTCTATTTTTAAAAGA 59.076 33.333 0.14 0.00 0.00 2.52
344 345 8.968242 GTGTTGCCTTGTCTATTTTTAAAAGAG 58.032 33.333 5.79 5.79 0.00 2.85
345 346 8.908903 TGTTGCCTTGTCTATTTTTAAAAGAGA 58.091 29.630 10.26 10.26 0.00 3.10
346 347 9.181805 GTTGCCTTGTCTATTTTTAAAAGAGAC 57.818 33.333 27.95 27.95 36.36 3.36
347 348 8.691661 TGCCTTGTCTATTTTTAAAAGAGACT 57.308 30.769 31.55 6.31 36.58 3.24
348 349 8.784043 TGCCTTGTCTATTTTTAAAAGAGACTC 58.216 33.333 31.55 22.06 36.58 3.36
349 350 9.004717 GCCTTGTCTATTTTTAAAAGAGACTCT 57.995 33.333 31.55 0.00 36.58 3.24
365 366 9.525409 AAAGAGACTCTTCACAAATTTGATTTG 57.475 29.630 24.64 12.46 44.17 2.32
366 367 8.906867 AAGAGACTCTTCACAAATTTGATTTGA 58.093 29.630 24.64 14.55 41.29 2.69
382 383 8.864069 TTTGATTTGAGTCGAATTAAAAAGCA 57.136 26.923 16.73 5.40 0.00 3.91
383 384 8.864069 TTGATTTGAGTCGAATTAAAAAGCAA 57.136 26.923 6.90 10.50 32.43 3.91
384 385 8.280909 TGATTTGAGTCGAATTAAAAAGCAAC 57.719 30.769 6.90 0.00 0.00 4.17
385 386 7.918033 TGATTTGAGTCGAATTAAAAAGCAACA 59.082 29.630 6.90 0.00 0.00 3.33
386 387 7.444558 TTTGAGTCGAATTAAAAAGCAACAC 57.555 32.000 0.00 0.00 0.00 3.32
387 388 6.125327 TGAGTCGAATTAAAAAGCAACACA 57.875 33.333 0.00 0.00 0.00 3.72
388 389 5.968848 TGAGTCGAATTAAAAAGCAACACAC 59.031 36.000 0.00 0.00 0.00 3.82
389 390 5.885881 AGTCGAATTAAAAAGCAACACACA 58.114 33.333 0.00 0.00 0.00 3.72
390 391 5.971202 AGTCGAATTAAAAAGCAACACACAG 59.029 36.000 0.00 0.00 0.00 3.66
391 392 5.741982 GTCGAATTAAAAAGCAACACACAGT 59.258 36.000 0.00 0.00 0.00 3.55
392 393 5.741510 TCGAATTAAAAAGCAACACACAGTG 59.258 36.000 0.00 0.00 39.75 3.66
393 394 5.051774 CGAATTAAAAAGCAACACACAGTGG 60.052 40.000 5.31 0.00 37.94 4.00
394 395 4.792521 TTAAAAAGCAACACACAGTGGT 57.207 36.364 5.31 0.00 37.94 4.16
408 409 5.437289 CACAGTGGTGTTGTCATGTATTT 57.563 39.130 0.00 0.00 40.24 1.40
409 410 5.830912 CACAGTGGTGTTGTCATGTATTTT 58.169 37.500 0.00 0.00 40.24 1.82
410 411 6.272318 CACAGTGGTGTTGTCATGTATTTTT 58.728 36.000 0.00 0.00 40.24 1.94
492 493 5.494724 CTGAACTCTGATTCCCTGAAATCA 58.505 41.667 0.00 0.00 42.01 2.57
631 633 1.213094 CGTAGGGCGCTCATAAACCG 61.213 60.000 11.40 0.00 0.00 4.44
675 677 0.681887 TGTCTCTCCCCGAACGCATA 60.682 55.000 0.00 0.00 0.00 3.14
745 763 0.179000 GGTGGTTGATCGCTGGAGAT 59.821 55.000 0.00 0.00 0.00 2.75
766 784 0.465097 CAAGAAGATCATGGCGGCCT 60.465 55.000 21.46 0.00 0.00 5.19
904 925 9.174166 GGGCTTTTAGTTTGTGAGATAATTCTA 57.826 33.333 0.00 0.00 30.30 2.10
1006 1028 4.996758 CGGTTTGTGCTATCATCATGGATA 59.003 41.667 0.00 0.00 0.00 2.59
1147 1169 4.817318 TTGCCAGAAGTGAAAGGTTTTT 57.183 36.364 0.00 0.00 0.00 1.94
1468 1490 7.194112 TGTGTAAATCCATCATCCTTGACTA 57.806 36.000 0.00 0.00 33.85 2.59
1472 1494 8.206867 TGTAAATCCATCATCCTTGACTAGAAG 58.793 37.037 0.00 0.00 33.85 2.85
1581 1604 4.140663 AGGCTAACATAGAGGTACAGGGAT 60.141 45.833 0.00 0.00 0.00 3.85
1603 1626 6.541641 GGATAGAGTTCTCAATTGCATGTTCT 59.458 38.462 0.00 4.02 0.00 3.01
1627 1650 6.067217 AGAAGATTACATTACTGGCACCTT 57.933 37.500 0.00 0.00 0.00 3.50
1628 1651 5.882557 AGAAGATTACATTACTGGCACCTTG 59.117 40.000 0.00 0.00 0.00 3.61
1629 1652 5.179452 AGATTACATTACTGGCACCTTGT 57.821 39.130 0.00 0.00 0.00 3.16
1630 1653 5.186198 AGATTACATTACTGGCACCTTGTC 58.814 41.667 0.00 0.00 0.00 3.18
1631 1654 1.808411 ACATTACTGGCACCTTGTCG 58.192 50.000 0.00 0.00 0.00 4.35
1632 1655 1.086696 CATTACTGGCACCTTGTCGG 58.913 55.000 0.00 0.00 33.80 4.79
1633 1656 0.035439 ATTACTGGCACCTTGTCGGG 60.035 55.000 0.00 0.00 31.31 5.14
1634 1657 2.119484 TTACTGGCACCTTGTCGGGG 62.119 60.000 0.00 0.00 40.11 5.73
1635 1658 4.722700 CTGGCACCTTGTCGGGGG 62.723 72.222 0.00 0.00 36.36 5.40
1652 1675 4.506255 GGATGAACCCCGGGCAGG 62.506 72.222 17.73 3.81 40.63 4.85
1662 1685 4.038080 CGGGCAGGCAACGGAAAC 62.038 66.667 0.00 0.00 46.39 2.78
1663 1686 3.680786 GGGCAGGCAACGGAAACC 61.681 66.667 0.00 0.00 46.39 3.27
2159 2182 2.606519 AAGCCAGCTCCACCCGTA 60.607 61.111 0.00 0.00 0.00 4.02
2191 2214 1.680522 ATCTAGCCACGGGTCAGCTG 61.681 60.000 7.63 7.63 37.45 4.24
2249 2272 0.893270 CCACCGATGACCAAGGCAAA 60.893 55.000 0.00 0.00 0.00 3.68
2264 2287 1.680651 CAAAAGTGCCCCGCCCATA 60.681 57.895 0.00 0.00 0.00 2.74
2306 2329 3.127425 GCAATAGTGCCCCTAACCTAG 57.873 52.381 3.16 0.00 45.68 3.02
2388 2411 1.004440 GACCTCACAGAGTGCCACC 60.004 63.158 0.00 0.00 32.98 4.61
2454 2477 0.982852 CACAGTCCCCCTAGGCATGA 60.983 60.000 2.05 0.00 34.51 3.07
2530 2553 2.291043 GGTCCCTGGACACCGACAT 61.291 63.158 17.64 0.00 46.20 3.06
2566 2589 7.390996 ACCGATTTGTAACATTACCATTGTACA 59.609 33.333 0.00 0.00 32.72 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.039270 TGAAATCGGACTTGTGAAGAAACATT 59.961 34.615 0.00 0.00 0.00 2.71
2 3 5.530915 TGAAATCGGACTTGTGAAGAAACAT 59.469 36.000 0.00 0.00 0.00 2.71
4 5 5.418310 TGAAATCGGACTTGTGAAGAAAC 57.582 39.130 0.00 0.00 0.00 2.78
5 6 6.262049 TGATTGAAATCGGACTTGTGAAGAAA 59.738 34.615 0.00 0.00 38.26 2.52
6 7 5.762711 TGATTGAAATCGGACTTGTGAAGAA 59.237 36.000 0.00 0.00 38.26 2.52
7 8 5.304778 TGATTGAAATCGGACTTGTGAAGA 58.695 37.500 0.00 0.00 38.26 2.87
8 9 5.611796 TGATTGAAATCGGACTTGTGAAG 57.388 39.130 0.00 0.00 38.26 3.02
9 10 6.262049 TCTTTGATTGAAATCGGACTTGTGAA 59.738 34.615 0.00 0.00 38.26 3.18
10 11 5.762711 TCTTTGATTGAAATCGGACTTGTGA 59.237 36.000 0.00 0.00 38.26 3.58
11 12 6.000891 TCTTTGATTGAAATCGGACTTGTG 57.999 37.500 0.00 0.00 38.26 3.33
12 13 6.633500 TTCTTTGATTGAAATCGGACTTGT 57.367 33.333 0.00 0.00 38.26 3.16
13 14 7.928908 TTTTCTTTGATTGAAATCGGACTTG 57.071 32.000 0.00 0.00 38.26 3.16
38 39 6.180472 AGACTCGATATGGAACCATGTTTTT 58.820 36.000 15.59 0.00 37.82 1.94
39 40 5.745227 AGACTCGATATGGAACCATGTTTT 58.255 37.500 15.59 0.00 37.82 2.43
40 41 5.359194 AGACTCGATATGGAACCATGTTT 57.641 39.130 15.59 1.76 37.82 2.83
41 42 5.833667 TCTAGACTCGATATGGAACCATGTT 59.166 40.000 15.59 4.07 37.82 2.71
42 43 5.386060 TCTAGACTCGATATGGAACCATGT 58.614 41.667 15.59 9.51 37.82 3.21
43 44 5.966742 TCTAGACTCGATATGGAACCATG 57.033 43.478 15.59 2.17 37.82 3.66
44 45 7.546250 AATTCTAGACTCGATATGGAACCAT 57.454 36.000 11.20 11.20 40.19 3.55
45 46 6.978674 AATTCTAGACTCGATATGGAACCA 57.021 37.500 0.00 0.00 0.00 3.67
46 47 6.647067 CCAAATTCTAGACTCGATATGGAACC 59.353 42.308 0.00 0.00 0.00 3.62
47 48 7.434492 TCCAAATTCTAGACTCGATATGGAAC 58.566 38.462 0.00 0.00 30.77 3.62
48 49 7.597288 TCCAAATTCTAGACTCGATATGGAA 57.403 36.000 0.00 0.00 30.77 3.53
49 50 7.451566 TGATCCAAATTCTAGACTCGATATGGA 59.548 37.037 0.00 0.71 37.61 3.41
50 51 7.543868 GTGATCCAAATTCTAGACTCGATATGG 59.456 40.741 0.00 0.00 0.00 2.74
51 52 8.084684 TGTGATCCAAATTCTAGACTCGATATG 58.915 37.037 0.00 0.00 0.00 1.78
52 53 8.183104 TGTGATCCAAATTCTAGACTCGATAT 57.817 34.615 0.00 0.00 0.00 1.63
53 54 7.582667 TGTGATCCAAATTCTAGACTCGATA 57.417 36.000 0.00 0.00 0.00 2.92
54 55 6.471233 TGTGATCCAAATTCTAGACTCGAT 57.529 37.500 0.00 0.00 0.00 3.59
55 56 5.914898 TGTGATCCAAATTCTAGACTCGA 57.085 39.130 0.00 0.00 0.00 4.04
56 57 7.383572 CCTATTGTGATCCAAATTCTAGACTCG 59.616 40.741 0.00 0.00 36.44 4.18
57 58 8.207545 ACCTATTGTGATCCAAATTCTAGACTC 58.792 37.037 0.00 0.00 36.44 3.36
58 59 8.095452 ACCTATTGTGATCCAAATTCTAGACT 57.905 34.615 0.00 0.00 36.44 3.24
109 110 9.529325 GGTGGAAATATAAAAAGCCAAATCTAC 57.471 33.333 0.00 0.00 0.00 2.59
110 111 9.487442 AGGTGGAAATATAAAAAGCCAAATCTA 57.513 29.630 0.00 0.00 0.00 1.98
111 112 8.379428 AGGTGGAAATATAAAAAGCCAAATCT 57.621 30.769 0.00 0.00 0.00 2.40
112 113 9.098355 GAAGGTGGAAATATAAAAAGCCAAATC 57.902 33.333 0.00 0.00 0.00 2.17
113 114 8.601546 TGAAGGTGGAAATATAAAAAGCCAAAT 58.398 29.630 0.00 0.00 0.00 2.32
114 115 7.967908 TGAAGGTGGAAATATAAAAAGCCAAA 58.032 30.769 0.00 0.00 0.00 3.28
115 116 7.310361 CCTGAAGGTGGAAATATAAAAAGCCAA 60.310 37.037 0.00 0.00 0.00 4.52
116 117 6.154363 CCTGAAGGTGGAAATATAAAAAGCCA 59.846 38.462 0.00 0.00 0.00 4.75
117 118 6.573434 CCTGAAGGTGGAAATATAAAAAGCC 58.427 40.000 0.00 0.00 0.00 4.35
118 119 6.042777 GCCTGAAGGTGGAAATATAAAAAGC 58.957 40.000 0.00 0.00 37.57 3.51
119 120 7.410120 AGCCTGAAGGTGGAAATATAAAAAG 57.590 36.000 0.00 0.00 37.57 2.27
120 121 7.234577 ACAAGCCTGAAGGTGGAAATATAAAAA 59.765 33.333 0.00 0.00 37.57 1.94
121 122 6.723977 ACAAGCCTGAAGGTGGAAATATAAAA 59.276 34.615 0.00 0.00 37.57 1.52
122 123 6.252995 ACAAGCCTGAAGGTGGAAATATAAA 58.747 36.000 0.00 0.00 37.57 1.40
123 124 5.826643 ACAAGCCTGAAGGTGGAAATATAA 58.173 37.500 0.00 0.00 37.57 0.98
124 125 5.450818 ACAAGCCTGAAGGTGGAAATATA 57.549 39.130 0.00 0.00 37.57 0.86
125 126 4.322057 ACAAGCCTGAAGGTGGAAATAT 57.678 40.909 0.00 0.00 37.57 1.28
126 127 3.806949 ACAAGCCTGAAGGTGGAAATA 57.193 42.857 0.00 0.00 37.57 1.40
127 128 2.683211 ACAAGCCTGAAGGTGGAAAT 57.317 45.000 0.00 0.00 37.57 2.17
128 129 2.452600 AACAAGCCTGAAGGTGGAAA 57.547 45.000 0.00 0.00 37.57 3.13
129 130 3.586470 TTAACAAGCCTGAAGGTGGAA 57.414 42.857 0.00 0.00 37.57 3.53
130 131 3.806949 ATTAACAAGCCTGAAGGTGGA 57.193 42.857 0.00 0.00 37.57 4.02
131 132 4.039124 ACAAATTAACAAGCCTGAAGGTGG 59.961 41.667 0.00 0.00 37.57 4.61
132 133 5.200368 ACAAATTAACAAGCCTGAAGGTG 57.800 39.130 0.00 0.00 37.57 4.00
133 134 6.969993 TTACAAATTAACAAGCCTGAAGGT 57.030 33.333 0.00 0.00 37.57 3.50
134 135 7.433680 AGTTTACAAATTAACAAGCCTGAAGG 58.566 34.615 0.00 0.00 38.53 3.46
135 136 8.352942 AGAGTTTACAAATTAACAAGCCTGAAG 58.647 33.333 0.00 0.00 0.00 3.02
136 137 8.232913 AGAGTTTACAAATTAACAAGCCTGAA 57.767 30.769 0.00 0.00 0.00 3.02
137 138 7.719633 AGAGAGTTTACAAATTAACAAGCCTGA 59.280 33.333 0.00 0.00 0.00 3.86
138 139 7.875971 AGAGAGTTTACAAATTAACAAGCCTG 58.124 34.615 0.00 0.00 0.00 4.85
139 140 8.465273 AAGAGAGTTTACAAATTAACAAGCCT 57.535 30.769 0.00 0.00 0.00 4.58
155 156 9.023962 TGGCACATTCATTAATTAAGAGAGTTT 57.976 29.630 3.94 0.00 0.00 2.66
156 157 8.579850 TGGCACATTCATTAATTAAGAGAGTT 57.420 30.769 3.94 0.00 0.00 3.01
157 158 8.579850 TTGGCACATTCATTAATTAAGAGAGT 57.420 30.769 3.94 0.00 39.30 3.24
158 159 8.896744 TCTTGGCACATTCATTAATTAAGAGAG 58.103 33.333 3.94 0.00 39.30 3.20
159 160 8.806429 TCTTGGCACATTCATTAATTAAGAGA 57.194 30.769 3.94 1.95 39.30 3.10
160 161 9.512435 CTTCTTGGCACATTCATTAATTAAGAG 57.488 33.333 3.94 0.00 39.30 2.85
161 162 9.241919 TCTTCTTGGCACATTCATTAATTAAGA 57.758 29.630 3.94 0.00 39.30 2.10
162 163 9.859427 TTCTTCTTGGCACATTCATTAATTAAG 57.141 29.630 3.94 0.00 39.30 1.85
163 164 9.638239 GTTCTTCTTGGCACATTCATTAATTAA 57.362 29.630 0.00 0.00 39.30 1.40
164 165 9.023962 AGTTCTTCTTGGCACATTCATTAATTA 57.976 29.630 0.00 0.00 39.30 1.40
165 166 7.816031 CAGTTCTTCTTGGCACATTCATTAATT 59.184 33.333 0.00 0.00 39.30 1.40
166 167 7.318141 CAGTTCTTCTTGGCACATTCATTAAT 58.682 34.615 0.00 0.00 39.30 1.40
167 168 6.680810 CAGTTCTTCTTGGCACATTCATTAA 58.319 36.000 0.00 0.00 39.30 1.40
168 169 5.335897 GCAGTTCTTCTTGGCACATTCATTA 60.336 40.000 0.00 0.00 39.30 1.90
169 170 4.560108 GCAGTTCTTCTTGGCACATTCATT 60.560 41.667 0.00 0.00 39.30 2.57
170 171 3.057033 GCAGTTCTTCTTGGCACATTCAT 60.057 43.478 0.00 0.00 39.30 2.57
171 172 2.294233 GCAGTTCTTCTTGGCACATTCA 59.706 45.455 0.00 0.00 39.30 2.57
172 173 2.555757 AGCAGTTCTTCTTGGCACATTC 59.444 45.455 0.00 0.00 39.30 2.67
173 174 2.555757 GAGCAGTTCTTCTTGGCACATT 59.444 45.455 0.00 0.00 39.30 2.71
174 175 2.157738 GAGCAGTTCTTCTTGGCACAT 58.842 47.619 0.00 0.00 39.30 3.21
175 176 1.597742 GAGCAGTTCTTCTTGGCACA 58.402 50.000 0.00 0.00 0.00 4.57
176 177 0.877743 GGAGCAGTTCTTCTTGGCAC 59.122 55.000 0.00 0.00 0.00 5.01
177 178 0.250901 GGGAGCAGTTCTTCTTGGCA 60.251 55.000 0.00 0.00 0.00 4.92
178 179 0.037447 AGGGAGCAGTTCTTCTTGGC 59.963 55.000 0.00 0.00 0.00 4.52
179 180 3.244561 TGTTAGGGAGCAGTTCTTCTTGG 60.245 47.826 0.00 0.00 0.00 3.61
180 181 4.008074 TGTTAGGGAGCAGTTCTTCTTG 57.992 45.455 0.00 0.00 0.00 3.02
181 182 4.706842 TTGTTAGGGAGCAGTTCTTCTT 57.293 40.909 0.00 0.00 0.00 2.52
182 183 4.706842 TTTGTTAGGGAGCAGTTCTTCT 57.293 40.909 0.00 0.00 0.00 2.85
183 184 5.767816 TTTTTGTTAGGGAGCAGTTCTTC 57.232 39.130 0.00 0.00 0.00 2.87
184 185 5.598417 ACATTTTTGTTAGGGAGCAGTTCTT 59.402 36.000 0.00 0.00 0.00 2.52
185 186 5.140454 ACATTTTTGTTAGGGAGCAGTTCT 58.860 37.500 0.00 0.00 0.00 3.01
186 187 5.453567 ACATTTTTGTTAGGGAGCAGTTC 57.546 39.130 0.00 0.00 0.00 3.01
187 188 5.476945 CCTACATTTTTGTTAGGGAGCAGTT 59.523 40.000 0.00 0.00 0.00 3.16
188 189 5.010282 CCTACATTTTTGTTAGGGAGCAGT 58.990 41.667 0.00 0.00 0.00 4.40
189 190 5.010282 ACCTACATTTTTGTTAGGGAGCAG 58.990 41.667 0.00 0.00 32.43 4.24
190 191 4.764823 CACCTACATTTTTGTTAGGGAGCA 59.235 41.667 0.00 0.00 32.43 4.26
191 192 5.007682 TCACCTACATTTTTGTTAGGGAGC 58.992 41.667 0.00 0.00 32.43 4.70
192 193 6.884295 TCATCACCTACATTTTTGTTAGGGAG 59.116 38.462 0.00 0.00 32.43 4.30
193 194 6.785076 TCATCACCTACATTTTTGTTAGGGA 58.215 36.000 0.00 0.00 32.43 4.20
194 195 7.339212 TCATCATCACCTACATTTTTGTTAGGG 59.661 37.037 0.00 0.00 32.43 3.53
195 196 8.279970 TCATCATCACCTACATTTTTGTTAGG 57.720 34.615 0.00 0.00 0.00 2.69
196 197 9.559958 GTTCATCATCACCTACATTTTTGTTAG 57.440 33.333 0.00 0.00 0.00 2.34
197 198 8.233868 CGTTCATCATCACCTACATTTTTGTTA 58.766 33.333 0.00 0.00 0.00 2.41
198 199 7.083858 CGTTCATCATCACCTACATTTTTGTT 58.916 34.615 0.00 0.00 0.00 2.83
199 200 6.611381 CGTTCATCATCACCTACATTTTTGT 58.389 36.000 0.00 0.00 0.00 2.83
200 201 5.512788 GCGTTCATCATCACCTACATTTTTG 59.487 40.000 0.00 0.00 0.00 2.44
201 202 5.182950 TGCGTTCATCATCACCTACATTTTT 59.817 36.000 0.00 0.00 0.00 1.94
202 203 4.699735 TGCGTTCATCATCACCTACATTTT 59.300 37.500 0.00 0.00 0.00 1.82
203 204 4.260985 TGCGTTCATCATCACCTACATTT 58.739 39.130 0.00 0.00 0.00 2.32
204 205 3.872696 TGCGTTCATCATCACCTACATT 58.127 40.909 0.00 0.00 0.00 2.71
205 206 3.541996 TGCGTTCATCATCACCTACAT 57.458 42.857 0.00 0.00 0.00 2.29
206 207 3.541996 ATGCGTTCATCATCACCTACA 57.458 42.857 0.00 0.00 0.00 2.74
207 208 5.984233 TTTATGCGTTCATCATCACCTAC 57.016 39.130 0.00 0.00 34.22 3.18
208 209 6.345298 TCTTTTATGCGTTCATCATCACCTA 58.655 36.000 0.00 0.00 34.22 3.08
209 210 5.185454 TCTTTTATGCGTTCATCATCACCT 58.815 37.500 0.00 0.00 34.22 4.00
210 211 5.484173 TCTTTTATGCGTTCATCATCACC 57.516 39.130 0.00 0.00 34.22 4.02
211 212 6.718388 TCATCTTTTATGCGTTCATCATCAC 58.282 36.000 0.00 0.00 34.22 3.06
212 213 6.923928 TCATCTTTTATGCGTTCATCATCA 57.076 33.333 0.00 0.00 34.22 3.07
213 214 7.859377 ACAATCATCTTTTATGCGTTCATCATC 59.141 33.333 0.00 0.00 34.22 2.92
214 215 7.709947 ACAATCATCTTTTATGCGTTCATCAT 58.290 30.769 0.00 0.00 34.22 2.45
215 216 7.087409 ACAATCATCTTTTATGCGTTCATCA 57.913 32.000 0.00 0.00 34.22 3.07
216 217 9.322776 GATACAATCATCTTTTATGCGTTCATC 57.677 33.333 0.00 0.00 34.22 2.92
217 218 8.292448 GGATACAATCATCTTTTATGCGTTCAT 58.708 33.333 0.00 0.00 36.73 2.57
218 219 7.498900 AGGATACAATCATCTTTTATGCGTTCA 59.501 33.333 0.00 0.00 41.41 3.18
219 220 7.800380 CAGGATACAATCATCTTTTATGCGTTC 59.200 37.037 0.00 0.00 41.41 3.95
220 221 7.283127 ACAGGATACAATCATCTTTTATGCGTT 59.717 33.333 0.00 0.00 41.41 4.84
221 222 6.767902 ACAGGATACAATCATCTTTTATGCGT 59.232 34.615 0.00 0.00 41.41 5.24
222 223 7.073883 CACAGGATACAATCATCTTTTATGCG 58.926 38.462 0.00 0.00 41.41 4.73
223 224 7.934457 ACACAGGATACAATCATCTTTTATGC 58.066 34.615 0.00 0.00 41.41 3.14
224 225 9.726232 CAACACAGGATACAATCATCTTTTATG 57.274 33.333 0.00 0.00 41.41 1.90
225 226 9.466497 ACAACACAGGATACAATCATCTTTTAT 57.534 29.630 0.00 0.00 41.41 1.40
226 227 8.862325 ACAACACAGGATACAATCATCTTTTA 57.138 30.769 0.00 0.00 41.41 1.52
227 228 7.094205 GGACAACACAGGATACAATCATCTTTT 60.094 37.037 0.00 0.00 41.41 2.27
228 229 6.375455 GGACAACACAGGATACAATCATCTTT 59.625 38.462 0.00 0.00 41.41 2.52
229 230 5.882557 GGACAACACAGGATACAATCATCTT 59.117 40.000 0.00 0.00 41.41 2.40
230 231 5.190528 AGGACAACACAGGATACAATCATCT 59.809 40.000 0.00 0.00 41.41 2.90
231 232 5.431765 AGGACAACACAGGATACAATCATC 58.568 41.667 0.00 0.00 41.41 2.92
232 233 5.441718 AGGACAACACAGGATACAATCAT 57.558 39.130 0.00 0.00 41.41 2.45
233 234 4.908601 AGGACAACACAGGATACAATCA 57.091 40.909 0.00 0.00 41.41 2.57
234 235 6.407202 AGTTAGGACAACACAGGATACAATC 58.593 40.000 0.00 0.00 41.41 2.67
235 236 6.374417 AGTTAGGACAACACAGGATACAAT 57.626 37.500 0.00 0.00 41.41 2.71
236 237 5.818678 AGTTAGGACAACACAGGATACAA 57.181 39.130 0.00 0.00 41.41 2.41
237 238 5.818678 AAGTTAGGACAACACAGGATACA 57.181 39.130 0.00 0.00 41.41 2.29
238 239 7.506328 AAAAAGTTAGGACAACACAGGATAC 57.494 36.000 0.00 0.00 0.00 2.24
261 262 9.650539 TCAAATTTGACAAGACTGATTTTCAAA 57.349 25.926 16.91 11.23 37.37 2.69
262 263 9.820725 ATCAAATTTGACAAGACTGATTTTCAA 57.179 25.926 22.71 0.00 40.49 2.69
263 264 9.820725 AATCAAATTTGACAAGACTGATTTTCA 57.179 25.926 22.71 0.00 40.49 2.69
266 267 9.820725 TGAAATCAAATTTGACAAGACTGATTT 57.179 25.926 22.71 21.34 41.99 2.17
267 268 9.472361 CTGAAATCAAATTTGACAAGACTGATT 57.528 29.630 22.71 7.46 40.49 2.57
268 269 8.636213 ACTGAAATCAAATTTGACAAGACTGAT 58.364 29.630 22.71 1.19 40.49 2.90
269 270 7.999679 ACTGAAATCAAATTTGACAAGACTGA 58.000 30.769 22.71 0.00 40.49 3.41
270 271 7.112565 CGACTGAAATCAAATTTGACAAGACTG 59.887 37.037 22.71 16.34 40.49 3.51
271 272 7.012327 TCGACTGAAATCAAATTTGACAAGACT 59.988 33.333 22.71 3.45 40.49 3.24
272 273 7.132213 TCGACTGAAATCAAATTTGACAAGAC 58.868 34.615 22.71 15.15 40.49 3.01
273 274 7.226523 TCTCGACTGAAATCAAATTTGACAAGA 59.773 33.333 22.71 12.44 40.49 3.02
274 275 7.355017 TCTCGACTGAAATCAAATTTGACAAG 58.645 34.615 22.71 17.88 40.49 3.16
275 276 7.258022 TCTCGACTGAAATCAAATTTGACAA 57.742 32.000 22.71 8.13 40.49 3.18
276 277 6.859420 TCTCGACTGAAATCAAATTTGACA 57.141 33.333 22.71 14.96 40.49 3.58
277 278 8.560576 TTTTCTCGACTGAAATCAAATTTGAC 57.439 30.769 22.71 11.19 40.49 3.18
300 301 2.916640 CACCATTGTGGGTTGCTTTTT 58.083 42.857 0.52 0.00 43.37 1.94
301 302 2.618442 CACCATTGTGGGTTGCTTTT 57.382 45.000 0.52 0.00 43.37 2.27
312 313 2.071778 AGACAAGGCAACACCATTGT 57.928 45.000 0.00 0.00 43.14 2.71
313 314 4.789012 AATAGACAAGGCAACACCATTG 57.211 40.909 0.00 0.00 43.14 2.82
314 315 5.806654 AAAATAGACAAGGCAACACCATT 57.193 34.783 0.00 0.00 43.14 3.16
315 316 5.806654 AAAAATAGACAAGGCAACACCAT 57.193 34.783 0.00 0.00 43.14 3.55
316 317 6.716934 TTAAAAATAGACAAGGCAACACCA 57.283 33.333 0.00 0.00 43.14 4.17
317 318 7.923878 TCTTTTAAAAATAGACAAGGCAACACC 59.076 33.333 1.66 0.00 41.41 4.16
318 319 8.865590 TCTTTTAAAAATAGACAAGGCAACAC 57.134 30.769 1.66 0.00 41.41 3.32
319 320 8.908903 TCTCTTTTAAAAATAGACAAGGCAACA 58.091 29.630 1.66 0.00 41.41 3.33
320 321 9.181805 GTCTCTTTTAAAAATAGACAAGGCAAC 57.818 33.333 24.65 7.67 37.20 4.17
321 322 9.131791 AGTCTCTTTTAAAAATAGACAAGGCAA 57.868 29.630 27.98 4.08 39.20 4.52
322 323 8.691661 AGTCTCTTTTAAAAATAGACAAGGCA 57.308 30.769 27.98 4.58 39.20 4.75
323 324 9.004717 AGAGTCTCTTTTAAAAATAGACAAGGC 57.995 33.333 27.98 19.52 39.20 4.35
339 340 9.525409 CAAATCAAATTTGTGAAGAGTCTCTTT 57.475 29.630 16.26 0.70 43.47 2.52
356 357 9.474920 TGCTTTTTAATTCGACTCAAATCAAAT 57.525 25.926 0.00 0.00 0.00 2.32
357 358 8.864069 TGCTTTTTAATTCGACTCAAATCAAA 57.136 26.923 0.00 0.00 0.00 2.69
358 359 8.751335 GTTGCTTTTTAATTCGACTCAAATCAA 58.249 29.630 0.00 0.00 0.00 2.57
359 360 7.918033 TGTTGCTTTTTAATTCGACTCAAATCA 59.082 29.630 0.00 0.00 0.00 2.57
360 361 8.207906 GTGTTGCTTTTTAATTCGACTCAAATC 58.792 33.333 0.00 0.00 0.00 2.17
361 362 7.704472 TGTGTTGCTTTTTAATTCGACTCAAAT 59.296 29.630 0.00 0.00 0.00 2.32
362 363 7.008810 GTGTGTTGCTTTTTAATTCGACTCAAA 59.991 33.333 0.00 0.00 0.00 2.69
363 364 6.470877 GTGTGTTGCTTTTTAATTCGACTCAA 59.529 34.615 0.00 0.00 0.00 3.02
364 365 5.968848 GTGTGTTGCTTTTTAATTCGACTCA 59.031 36.000 0.00 0.00 0.00 3.41
365 366 5.968848 TGTGTGTTGCTTTTTAATTCGACTC 59.031 36.000 0.00 0.00 0.00 3.36
366 367 5.885881 TGTGTGTTGCTTTTTAATTCGACT 58.114 33.333 0.00 0.00 0.00 4.18
367 368 5.741982 ACTGTGTGTTGCTTTTTAATTCGAC 59.258 36.000 0.00 0.00 0.00 4.20
368 369 5.741510 CACTGTGTGTTGCTTTTTAATTCGA 59.258 36.000 0.00 0.00 0.00 3.71
369 370 5.051774 CCACTGTGTGTTGCTTTTTAATTCG 60.052 40.000 7.08 0.00 0.00 3.34
370 371 5.810074 ACCACTGTGTGTTGCTTTTTAATTC 59.190 36.000 7.08 0.00 0.00 2.17
371 372 5.580297 CACCACTGTGTGTTGCTTTTTAATT 59.420 36.000 7.08 0.00 37.72 1.40
372 373 5.108517 CACCACTGTGTGTTGCTTTTTAAT 58.891 37.500 7.08 0.00 37.72 1.40
373 374 4.489810 CACCACTGTGTGTTGCTTTTTAA 58.510 39.130 7.08 0.00 37.72 1.52
374 375 4.103365 CACCACTGTGTGTTGCTTTTTA 57.897 40.909 7.08 0.00 37.72 1.52
375 376 2.958213 CACCACTGTGTGTTGCTTTTT 58.042 42.857 7.08 0.00 37.72 1.94
376 377 2.652941 CACCACTGTGTGTTGCTTTT 57.347 45.000 7.08 0.00 37.72 2.27
387 388 6.463995 AAAAATACATGACAACACCACTGT 57.536 33.333 0.00 0.00 0.00 3.55
436 437 6.745116 TCAGACTTTGAGTACGAATTCAAGA 58.255 36.000 6.22 0.00 33.45 3.02
492 493 3.037549 GGATTGGAGAGGACAGAGTGAT 58.962 50.000 0.00 0.00 0.00 3.06
631 633 2.109126 GGAGATGGGTTCGTGCTGC 61.109 63.158 0.00 0.00 0.00 5.25
675 677 0.029267 AGGAGATGGGGCTGAAGGAT 60.029 55.000 0.00 0.00 0.00 3.24
745 763 1.378882 GCCGCCATGATCTTCTTGCA 61.379 55.000 0.00 0.00 0.00 4.08
766 784 2.158813 GGGGATTACCAGCGATTTCTGA 60.159 50.000 0.00 0.00 42.91 3.27
904 925 5.163683 CCGAAGTGAATGCAAGATCAAATCT 60.164 40.000 0.00 0.00 42.61 2.40
1006 1028 1.992667 CACATTCAGTATGTCACGCGT 59.007 47.619 5.58 5.58 45.71 6.01
1147 1169 5.787953 TTGAAAGGAACATGATCAGCAAA 57.212 34.783 0.00 0.00 0.00 3.68
1411 1433 5.220624 GCACATCTTCTTCTGCAGTTATGAG 60.221 44.000 14.67 7.03 0.00 2.90
1468 1490 4.141711 TGGTACAAGCAAGTTCTCACTTCT 60.142 41.667 0.00 0.00 36.75 2.85
1581 1604 7.840931 TCTAGAACATGCAATTGAGAACTCTA 58.159 34.615 10.34 7.99 0.00 2.43
1603 1626 6.808321 AGGTGCCAGTAATGTAATCTTCTA 57.192 37.500 0.00 0.00 0.00 2.10
1635 1658 4.506255 CCTGCCCGGGGTTCATCC 62.506 72.222 25.28 3.41 0.00 3.51
1645 1668 4.038080 GTTTCCGTTGCCTGCCCG 62.038 66.667 0.00 0.00 0.00 6.13
1646 1669 3.680786 GGTTTCCGTTGCCTGCCC 61.681 66.667 0.00 0.00 0.00 5.36
1647 1670 4.038080 CGGTTTCCGTTGCCTGCC 62.038 66.667 0.00 0.00 42.73 4.85
1648 1671 4.038080 CCGGTTTCCGTTGCCTGC 62.038 66.667 7.40 0.00 46.80 4.85
1649 1672 1.674322 ATCCGGTTTCCGTTGCCTG 60.674 57.895 0.00 0.00 46.80 4.85
1650 1673 2.754375 ATCCGGTTTCCGTTGCCT 59.246 55.556 0.00 0.00 46.80 4.75
2051 2074 1.289066 CCGTGTCGAAGAGCTTGGA 59.711 57.895 0.00 0.00 36.95 3.53
2066 2089 2.354305 GTCGACGTGTCTTGCCGT 60.354 61.111 0.00 0.00 40.54 5.68
2175 2198 4.082523 GCAGCTGACCCGTGGCTA 62.083 66.667 20.43 0.00 34.71 3.93
2249 2272 4.123545 GGTATGGGCGGGGCACTT 62.124 66.667 0.00 0.00 30.56 3.16
2300 2323 2.660064 CCTGGTCAGCGGCTAGGTT 61.660 63.158 0.26 0.00 31.03 3.50
2375 2398 0.944311 GTGTACGGTGGCACTCTGTG 60.944 60.000 18.45 5.32 41.84 3.66
2388 2411 1.058438 CCGAGTCGAGTCGTGTACG 59.942 63.158 33.69 18.74 38.32 3.67
2454 2477 4.760220 CCCTAGGTGTGGGCCCCT 62.760 72.222 22.27 11.86 37.99 4.79
2478 2501 2.192175 GGGGGCCTATGGTTCGTG 59.808 66.667 0.84 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.