Multiple sequence alignment - TraesCS4B01G335200

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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 TraesCS4B01G335200 chr4B 100.000 2354 0 0 1 2354 626070037 626067684 0.000000e+00 4348.0
1 TraesCS4B01G335200 chr4B 80.535 1197 164 35 1183 2343 639452143 639453306 0.000000e+00 856.0
2 TraesCS4B01G335200 chr4B 82.283 920 126 17 1257 2153 489294388 489293483 0.000000e+00 761.0
3 TraesCS4B01G335200 chr4B 100.000 384 0 0 2610 2993 626067428 626067045 0.000000e+00 710.0
4 TraesCS4B01G335200 chr4B 79.608 765 90 33 1166 1900 667343662 667344390 3.470000e-134 488.0
5 TraesCS4B01G335200 chr4B 97.786 271 6 0 1 271 245490302 245490572 4.520000e-128 468.0
6 TraesCS4B01G335200 chr4B 98.462 260 4 0 1 260 652250363 652250104 2.720000e-125 459.0
7 TraesCS4B01G335200 chr4B 80.916 262 21 21 1415 1648 667263235 667263495 2.370000e-41 180.0
8 TraesCS4B01G335200 chr4B 77.966 236 31 10 1431 1648 639294497 639294729 8.710000e-26 128.0
9 TraesCS4B01G335200 chr4B 95.745 47 2 0 1324 1370 667263180 667263226 3.200000e-10 76.8
10 TraesCS4B01G335200 chr4B 93.617 47 3 0 1324 1370 667277802 667277848 1.490000e-08 71.3
11 TraesCS4B01G335200 chr4B 87.302 63 2 1 1169 1225 667263079 667263141 1.930000e-07 67.6
12 TraesCS4B01G335200 chr4B 85.714 63 3 1 1169 1225 667289739 667289801 8.960000e-06 62.1
13 TraesCS4B01G335200 chr4B 100.000 31 0 0 1195 1225 667277733 667277763 1.160000e-04 58.4
14 TraesCS4B01G335200 chr4D 91.029 2118 144 10 260 2354 488667022 488664928 0.000000e+00 2817.0
15 TraesCS4B01G335200 chr4D 82.104 1017 137 22 1167 2153 397158338 397157337 0.000000e+00 828.0
16 TraesCS4B01G335200 chr4D 93.939 99 5 1 2671 2769 488664601 488664504 6.680000e-32 148.0
17 TraesCS4B01G335200 chr4D 100.000 33 0 0 2740 2772 397157092 397157060 8.960000e-06 62.1
18 TraesCS4B01G335200 chr5A 91.954 1392 95 7 967 2354 670426357 670424979 0.000000e+00 1934.0
19 TraesCS4B01G335200 chr5A 89.736 721 51 8 260 969 670427204 670426496 0.000000e+00 900.0
20 TraesCS4B01G335200 chr5A 79.918 1225 157 40 1167 2354 706678529 706677357 0.000000e+00 817.0
21 TraesCS4B01G335200 chr5A 89.059 393 25 4 2610 2989 670424932 670424545 3.490000e-129 472.0
22 TraesCS4B01G335200 chr4A 81.854 1014 142 21 1167 2153 54405912 54404914 0.000000e+00 815.0
23 TraesCS4B01G335200 chr4A 93.220 59 3 1 2740 2797 54404675 54404617 5.320000e-13 86.1
24 TraesCS4B01G335200 chrUn 79.975 799 96 33 1425 2204 30126436 30125683 5.680000e-147 531.0
25 TraesCS4B01G335200 chrUn 80.952 210 29 5 1167 1365 30126653 30126444 3.990000e-34 156.0
26 TraesCS4B01G335200 chr7B 99.231 260 2 0 1 260 513689368 513689627 1.260000e-128 470.0
27 TraesCS4B01G335200 chr7B 77.528 267 30 17 1 260 406940073 406940316 1.870000e-27 134.0
28 TraesCS4B01G335200 chr7A 99.231 260 2 0 1 260 236799809 236800068 1.260000e-128 470.0
29 TraesCS4B01G335200 chr7A 98.462 260 4 0 1 260 330929052 330929311 2.720000e-125 459.0
30 TraesCS4B01G335200 chr3B 99.231 260 2 0 1 260 760408243 760407984 1.260000e-128 470.0
31 TraesCS4B01G335200 chr3B 92.593 108 8 0 93 200 442086026 442086133 3.990000e-34 156.0
32 TraesCS4B01G335200 chr3B 90.909 99 7 2 1 97 687134052 687133954 6.730000e-27 132.0
33 TraesCS4B01G335200 chr2A 99.222 257 2 0 2 258 191903595 191903851 5.840000e-127 464.0
34 TraesCS4B01G335200 chr2B 92.105 114 9 0 93 206 770902448 770902335 8.590000e-36 161.0
35 TraesCS4B01G335200 chr2B 91.753 97 5 3 1 97 136839205 136839298 6.730000e-27 132.0
36 TraesCS4B01G335200 chr3A 95.833 72 3 0 199 270 459080663 459080734 1.890000e-22 117.0


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 TraesCS4B01G335200 chr4B 626067045 626070037 2992 True 2529.00 4348 100.000000 1 2993 2 chr4B.!!$R3 2992
1 TraesCS4B01G335200 chr4B 639452143 639453306 1163 False 856.00 856 80.535000 1183 2343 1 chr4B.!!$F3 1160
2 TraesCS4B01G335200 chr4B 489293483 489294388 905 True 761.00 761 82.283000 1257 2153 1 chr4B.!!$R1 896
3 TraesCS4B01G335200 chr4B 667343662 667344390 728 False 488.00 488 79.608000 1166 1900 1 chr4B.!!$F5 734
4 TraesCS4B01G335200 chr4D 488664504 488667022 2518 True 1482.50 2817 92.484000 260 2769 2 chr4D.!!$R2 2509
5 TraesCS4B01G335200 chr4D 397157060 397158338 1278 True 445.05 828 91.052000 1167 2772 2 chr4D.!!$R1 1605
6 TraesCS4B01G335200 chr5A 670424545 670427204 2659 True 1102.00 1934 90.249667 260 2989 3 chr5A.!!$R2 2729
7 TraesCS4B01G335200 chr5A 706677357 706678529 1172 True 817.00 817 79.918000 1167 2354 1 chr5A.!!$R1 1187
8 TraesCS4B01G335200 chr4A 54404617 54405912 1295 True 450.55 815 87.537000 1167 2797 2 chr4A.!!$R1 1630
9 TraesCS4B01G335200 chrUn 30125683 30126653 970 True 343.50 531 80.463500 1167 2204 2 chrUn.!!$R1 1037

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
776 798 0.037326 AATTCTGAAGCTCGCACGGA 60.037 50.000 0.00 0.0 0.00 4.69 F
1822 2077 1.078567 CAGCTGGAGGAGAAGGTGC 60.079 63.158 5.57 0.0 35.37 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2220 0.106819 GGATGCTGGCCTCAATGTCT 60.107 55.0 3.32 0.0 0.0 3.41 R
2888 3228 1.937191 TCTACTCCAGGACATGCACA 58.063 50.0 0.00 0.0 0.0 4.57 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
19 20 2.376808 GACCATCATCGGCTAGGATG 57.623 55.000 6.68 6.68 44.29 3.51
24 25 1.621992 TCATCGGCTAGGATGAGGAC 58.378 55.000 7.39 0.00 45.82 3.85
25 26 1.133482 TCATCGGCTAGGATGAGGACA 60.133 52.381 7.39 0.00 45.82 4.02
26 27 1.898472 CATCGGCTAGGATGAGGACAT 59.102 52.381 3.57 0.00 45.27 3.06
27 28 2.971901 TCGGCTAGGATGAGGACATA 57.028 50.000 0.00 0.00 36.82 2.29
28 29 3.238788 TCGGCTAGGATGAGGACATAA 57.761 47.619 0.00 0.00 36.82 1.90
29 30 3.572642 TCGGCTAGGATGAGGACATAAA 58.427 45.455 0.00 0.00 36.82 1.40
30 31 3.964688 TCGGCTAGGATGAGGACATAAAA 59.035 43.478 0.00 0.00 36.82 1.52
31 32 4.593206 TCGGCTAGGATGAGGACATAAAAT 59.407 41.667 0.00 0.00 36.82 1.82
32 33 4.692625 CGGCTAGGATGAGGACATAAAATG 59.307 45.833 0.00 0.00 36.82 2.32
33 34 5.511373 CGGCTAGGATGAGGACATAAAATGA 60.511 44.000 0.00 0.00 36.82 2.57
34 35 5.703130 GGCTAGGATGAGGACATAAAATGAC 59.297 44.000 0.00 0.00 36.82 3.06
35 36 6.291377 GCTAGGATGAGGACATAAAATGACA 58.709 40.000 0.00 0.00 36.82 3.58
36 37 6.767902 GCTAGGATGAGGACATAAAATGACAA 59.232 38.462 0.00 0.00 36.82 3.18
37 38 7.254932 GCTAGGATGAGGACATAAAATGACAAC 60.255 40.741 0.00 0.00 36.82 3.32
38 39 6.484288 AGGATGAGGACATAAAATGACAACA 58.516 36.000 0.00 0.00 36.82 3.33
39 40 7.121382 AGGATGAGGACATAAAATGACAACAT 58.879 34.615 0.00 0.00 36.82 2.71
40 41 7.067859 AGGATGAGGACATAAAATGACAACATG 59.932 37.037 0.00 0.00 36.82 3.21
41 42 6.513806 TGAGGACATAAAATGACAACATGG 57.486 37.500 0.00 0.00 36.79 3.66
42 43 6.009589 TGAGGACATAAAATGACAACATGGT 58.990 36.000 0.00 0.00 36.79 3.55
43 44 6.072008 TGAGGACATAAAATGACAACATGGTG 60.072 38.462 9.83 9.83 36.79 4.17
44 45 6.009589 AGGACATAAAATGACAACATGGTGA 58.990 36.000 19.90 0.00 36.79 4.02
45 46 6.151648 AGGACATAAAATGACAACATGGTGAG 59.848 38.462 19.90 0.00 36.79 3.51
46 47 5.713025 ACATAAAATGACAACATGGTGAGC 58.287 37.500 19.90 9.58 36.79 4.26
47 48 3.665745 AAAATGACAACATGGTGAGCC 57.334 42.857 19.90 6.68 36.79 4.70
58 59 2.719531 TGGTGAGCCACTGTGTTAAA 57.280 45.000 7.08 0.00 40.46 1.52
59 60 3.006112 TGGTGAGCCACTGTGTTAAAA 57.994 42.857 7.08 0.00 40.46 1.52
60 61 3.561143 TGGTGAGCCACTGTGTTAAAAT 58.439 40.909 7.08 0.00 40.46 1.82
61 62 4.720046 TGGTGAGCCACTGTGTTAAAATA 58.280 39.130 7.08 0.00 40.46 1.40
62 63 4.759693 TGGTGAGCCACTGTGTTAAAATAG 59.240 41.667 7.08 0.00 40.46 1.73
63 64 5.001232 GGTGAGCCACTGTGTTAAAATAGA 58.999 41.667 7.08 0.00 34.40 1.98
64 65 5.122396 GGTGAGCCACTGTGTTAAAATAGAG 59.878 44.000 7.08 0.00 34.40 2.43
65 66 5.701290 GTGAGCCACTGTGTTAAAATAGAGT 59.299 40.000 7.08 0.00 0.00 3.24
66 67 6.872020 GTGAGCCACTGTGTTAAAATAGAGTA 59.128 38.462 7.08 0.00 0.00 2.59
67 68 6.872020 TGAGCCACTGTGTTAAAATAGAGTAC 59.128 38.462 7.08 0.00 0.00 2.73
68 69 6.765403 AGCCACTGTGTTAAAATAGAGTACA 58.235 36.000 7.08 0.00 0.00 2.90
69 70 6.649557 AGCCACTGTGTTAAAATAGAGTACAC 59.350 38.462 7.08 0.00 39.52 2.90
70 71 6.649557 GCCACTGTGTTAAAATAGAGTACACT 59.350 38.462 7.08 0.00 39.73 3.55
71 72 7.148623 GCCACTGTGTTAAAATAGAGTACACTC 60.149 40.741 7.08 0.91 43.17 3.51
72 73 7.870954 CCACTGTGTTAAAATAGAGTACACTCA 59.129 37.037 11.75 0.00 45.21 3.41
73 74 9.424319 CACTGTGTTAAAATAGAGTACACTCAT 57.576 33.333 11.75 1.27 45.21 2.90
101 102 7.962995 TCAGGATATTATGTCATACTCCCTC 57.037 40.000 9.94 0.00 0.00 4.30
102 103 7.713518 TCAGGATATTATGTCATACTCCCTCT 58.286 38.462 9.94 0.00 0.00 3.69
103 104 7.617329 TCAGGATATTATGTCATACTCCCTCTG 59.383 40.741 9.94 6.74 0.00 3.35
104 105 7.398618 CAGGATATTATGTCATACTCCCTCTGT 59.601 40.741 9.94 0.00 0.00 3.41
105 106 7.958583 AGGATATTATGTCATACTCCCTCTGTT 59.041 37.037 9.94 0.00 0.00 3.16
106 107 8.254508 GGATATTATGTCATACTCCCTCTGTTC 58.745 40.741 0.00 0.00 0.00 3.18
107 108 5.871396 TTATGTCATACTCCCTCTGTTCC 57.129 43.478 0.00 0.00 0.00 3.62
108 109 2.100197 TGTCATACTCCCTCTGTTCCG 58.900 52.381 0.00 0.00 0.00 4.30
109 110 2.291346 TGTCATACTCCCTCTGTTCCGA 60.291 50.000 0.00 0.00 0.00 4.55
110 111 2.758979 GTCATACTCCCTCTGTTCCGAA 59.241 50.000 0.00 0.00 0.00 4.30
111 112 3.385111 GTCATACTCCCTCTGTTCCGAAT 59.615 47.826 0.00 0.00 0.00 3.34
112 113 4.030913 TCATACTCCCTCTGTTCCGAATT 58.969 43.478 0.00 0.00 0.00 2.17
113 114 5.068723 GTCATACTCCCTCTGTTCCGAATTA 59.931 44.000 0.00 0.00 0.00 1.40
114 115 3.889520 ACTCCCTCTGTTCCGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
115 116 3.442076 ACTCCCTCTGTTCCGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
116 117 3.447944 ACTCCCTCTGTTCCGAATTACTC 59.552 47.826 0.00 0.00 0.00 2.59
118 119 2.194271 CCTCTGTTCCGAATTACTCGC 58.806 52.381 0.00 0.00 46.71 5.03
119 120 2.194271 CTCTGTTCCGAATTACTCGCC 58.806 52.381 0.00 0.00 46.71 5.54
120 121 1.546923 TCTGTTCCGAATTACTCGCCA 59.453 47.619 0.00 0.00 46.71 5.69
121 122 1.659098 CTGTTCCGAATTACTCGCCAC 59.341 52.381 0.00 0.00 46.71 5.01
122 123 1.001068 TGTTCCGAATTACTCGCCACA 59.999 47.619 0.00 0.00 46.71 4.17
123 124 1.659098 GTTCCGAATTACTCGCCACAG 59.341 52.381 0.00 0.00 46.71 3.66
124 125 1.179152 TCCGAATTACTCGCCACAGA 58.821 50.000 0.00 0.00 46.71 3.41
125 126 1.546923 TCCGAATTACTCGCCACAGAA 59.453 47.619 0.00 0.00 46.71 3.02
126 127 2.028839 TCCGAATTACTCGCCACAGAAA 60.029 45.455 0.00 0.00 46.71 2.52
127 128 2.936498 CCGAATTACTCGCCACAGAAAT 59.064 45.455 0.00 0.00 46.71 2.17
128 129 4.116961 CCGAATTACTCGCCACAGAAATA 58.883 43.478 0.00 0.00 46.71 1.40
129 130 4.209288 CCGAATTACTCGCCACAGAAATAG 59.791 45.833 0.00 0.00 46.71 1.73
130 131 5.041287 CGAATTACTCGCCACAGAAATAGA 58.959 41.667 0.00 0.00 41.49 1.98
131 132 5.692204 CGAATTACTCGCCACAGAAATAGAT 59.308 40.000 0.00 0.00 41.49 1.98
132 133 6.346120 CGAATTACTCGCCACAGAAATAGATG 60.346 42.308 0.00 0.00 41.49 2.90
133 134 3.895232 ACTCGCCACAGAAATAGATGT 57.105 42.857 0.00 0.00 0.00 3.06
134 135 6.459670 TTACTCGCCACAGAAATAGATGTA 57.540 37.500 0.00 0.00 0.00 2.29
135 136 5.537300 ACTCGCCACAGAAATAGATGTAT 57.463 39.130 0.00 0.00 0.00 2.29
136 137 5.533482 ACTCGCCACAGAAATAGATGTATC 58.467 41.667 0.00 0.00 0.00 2.24
137 138 5.303078 ACTCGCCACAGAAATAGATGTATCT 59.697 40.000 0.00 0.00 40.86 1.98
138 139 6.490381 ACTCGCCACAGAAATAGATGTATCTA 59.510 38.462 4.22 4.22 43.00 1.98
139 140 7.014326 ACTCGCCACAGAAATAGATGTATCTAA 59.986 37.037 5.75 0.00 42.20 2.10
140 141 7.722363 TCGCCACAGAAATAGATGTATCTAAA 58.278 34.615 5.75 0.00 42.20 1.85
141 142 8.201464 TCGCCACAGAAATAGATGTATCTAAAA 58.799 33.333 5.75 0.00 42.20 1.52
142 143 8.276325 CGCCACAGAAATAGATGTATCTAAAAC 58.724 37.037 5.75 1.59 42.20 2.43
143 144 9.331282 GCCACAGAAATAGATGTATCTAAAACT 57.669 33.333 5.75 3.48 42.20 2.66
185 186 9.125026 ACATCCATTTCTATGACAAGTAATTCC 57.875 33.333 0.00 0.00 33.37 3.01
186 187 7.786178 TCCATTTCTATGACAAGTAATTCCG 57.214 36.000 0.00 0.00 33.37 4.30
187 188 7.561251 TCCATTTCTATGACAAGTAATTCCGA 58.439 34.615 0.00 0.00 33.37 4.55
188 189 8.044309 TCCATTTCTATGACAAGTAATTCCGAA 58.956 33.333 0.00 0.00 33.37 4.30
189 190 8.122952 CCATTTCTATGACAAGTAATTCCGAAC 58.877 37.037 0.00 0.00 33.37 3.95
190 191 6.880822 TTCTATGACAAGTAATTCCGAACG 57.119 37.500 0.00 0.00 0.00 3.95
191 192 5.345702 TCTATGACAAGTAATTCCGAACGG 58.654 41.667 6.94 6.94 0.00 4.44
192 193 3.663995 TGACAAGTAATTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
193 194 3.581755 TGACAAGTAATTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
194 195 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
195 196 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
196 197 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
197 198 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
198 199 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
199 200 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
200 201 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
201 202 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
202 203 0.038744 TCCGAACGGAGGGAGTACTT 59.961 55.000 12.04 0.00 39.76 2.24
203 204 1.281867 TCCGAACGGAGGGAGTACTTA 59.718 52.381 12.04 0.00 39.76 2.24
204 205 2.092212 TCCGAACGGAGGGAGTACTTAT 60.092 50.000 12.04 0.00 39.76 1.73
205 206 2.692041 CCGAACGGAGGGAGTACTTATT 59.308 50.000 7.53 0.00 37.50 1.40
206 207 3.131755 CCGAACGGAGGGAGTACTTATTT 59.868 47.826 7.53 0.00 37.50 1.40
207 208 4.382362 CCGAACGGAGGGAGTACTTATTTT 60.382 45.833 7.53 0.00 37.50 1.82
208 209 4.565564 CGAACGGAGGGAGTACTTATTTTG 59.434 45.833 0.00 0.00 0.00 2.44
209 210 5.485620 GAACGGAGGGAGTACTTATTTTGT 58.514 41.667 0.00 0.00 0.00 2.83
210 211 5.494390 ACGGAGGGAGTACTTATTTTGTT 57.506 39.130 0.00 0.00 0.00 2.83
211 212 6.610075 ACGGAGGGAGTACTTATTTTGTTA 57.390 37.500 0.00 0.00 0.00 2.41
212 213 6.637657 ACGGAGGGAGTACTTATTTTGTTAG 58.362 40.000 0.00 0.00 0.00 2.34
213 214 5.522824 CGGAGGGAGTACTTATTTTGTTAGC 59.477 44.000 0.00 0.00 0.00 3.09
214 215 5.821470 GGAGGGAGTACTTATTTTGTTAGCC 59.179 44.000 0.00 0.00 0.00 3.93
215 216 6.382919 AGGGAGTACTTATTTTGTTAGCCA 57.617 37.500 0.00 0.00 0.00 4.75
216 217 6.970191 AGGGAGTACTTATTTTGTTAGCCAT 58.030 36.000 0.00 0.00 0.00 4.40
217 218 8.097791 AGGGAGTACTTATTTTGTTAGCCATA 57.902 34.615 0.00 0.00 0.00 2.74
218 219 8.554011 AGGGAGTACTTATTTTGTTAGCCATAA 58.446 33.333 0.00 0.00 0.00 1.90
219 220 9.350951 GGGAGTACTTATTTTGTTAGCCATAAT 57.649 33.333 0.00 0.00 0.00 1.28
239 240 2.570442 TTTTTGTCTCCCGTTGCAAC 57.430 45.000 19.89 19.89 0.00 4.17
249 250 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
250 251 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
251 252 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
252 253 1.590610 TTGCAACGCACGGGCATATT 61.591 50.000 11.77 0.00 38.71 1.28
253 254 1.138671 GCAACGCACGGGCATATTT 59.861 52.632 11.77 0.00 41.24 1.40
254 255 1.139226 GCAACGCACGGGCATATTTG 61.139 55.000 11.77 8.22 41.24 2.32
285 286 1.803366 AAAGCTTGCAGGCTCAGCAC 61.803 55.000 24.80 0.00 42.54 4.40
290 291 1.457823 TTGCAGGCTCAGCACAAAGG 61.458 55.000 0.00 0.00 42.54 3.11
300 301 2.986306 GCACAAAGGATGCAGCGCT 61.986 57.895 2.64 2.64 42.88 5.92
307 308 3.407424 AAGGATGCAGCGCTATAATCA 57.593 42.857 10.99 3.62 0.00 2.57
379 380 5.914033 TGCATACTAGTGGAGTTCATAACC 58.086 41.667 5.39 0.00 39.81 2.85
389 390 6.182507 TGGAGTTCATAACCACTGTACTTT 57.817 37.500 0.00 0.00 0.00 2.66
404 405 2.364972 ACTTTCCCTCCAACACCAAG 57.635 50.000 0.00 0.00 0.00 3.61
475 476 1.953686 CATTCGACACCCCAACAACTT 59.046 47.619 0.00 0.00 0.00 2.66
519 520 2.915659 AGACCTCGTCCGGCAACA 60.916 61.111 0.00 0.00 32.18 3.33
555 556 8.710239 TGCACACTAGTTTTCTATATATCCCAA 58.290 33.333 0.00 0.00 0.00 4.12
618 619 3.282745 GAGGAGGTGCGCGACAGAA 62.283 63.158 12.10 0.00 0.00 3.02
630 631 2.034001 CGCGACAGAACGAGTTTCTTTT 60.034 45.455 0.00 0.00 42.37 2.27
631 632 3.543460 CGCGACAGAACGAGTTTCTTTTT 60.543 43.478 0.00 0.00 42.37 1.94
633 634 4.493545 GCGACAGAACGAGTTTCTTTTTGA 60.494 41.667 0.00 0.00 42.37 2.69
635 636 5.448162 CGACAGAACGAGTTTCTTTTTGAAC 59.552 40.000 0.00 0.00 42.37 3.18
636 637 6.496338 ACAGAACGAGTTTCTTTTTGAACT 57.504 33.333 0.00 0.00 42.37 3.01
637 638 6.314784 ACAGAACGAGTTTCTTTTTGAACTG 58.685 36.000 0.00 0.00 42.37 3.16
674 694 6.150641 CGGATCTCTCGGGTGTATTAAAGATA 59.849 42.308 0.00 0.00 0.00 1.98
675 695 7.540299 GGATCTCTCGGGTGTATTAAAGATAG 58.460 42.308 0.00 0.00 0.00 2.08
677 697 6.607970 TCTCTCGGGTGTATTAAAGATAGGA 58.392 40.000 0.00 0.00 0.00 2.94
678 698 6.489361 TCTCTCGGGTGTATTAAAGATAGGAC 59.511 42.308 0.00 0.00 0.00 3.85
698 719 2.361757 ACGCAGGAGATCTTCAGAGATG 59.638 50.000 3.21 0.00 42.66 2.90
703 724 3.207321 AGGAGATCTTCAGAGATGGGAGT 59.793 47.826 3.21 0.00 42.66 3.85
759 780 7.013750 GGAGAGAAAAGGTGTTGAGAAAGAAAT 59.986 37.037 0.00 0.00 0.00 2.17
776 798 0.037326 AATTCTGAAGCTCGCACGGA 60.037 50.000 0.00 0.00 0.00 4.69
852 883 1.677217 GCCTCTGTAAGCAAGACAGGG 60.677 57.143 11.39 8.67 43.83 4.45
888 919 3.557595 AGAAGAGAACACAAGAAACGCAG 59.442 43.478 0.00 0.00 0.00 5.18
929 963 3.071479 TGTGTTCGCCAGAAATTCTACC 58.929 45.455 0.00 0.00 38.23 3.18
931 965 3.751698 GTGTTCGCCAGAAATTCTACCTT 59.248 43.478 0.00 0.00 38.23 3.50
943 977 9.454859 CAGAAATTCTACCTTTCTAGATTGGTT 57.545 33.333 18.44 4.02 40.16 3.67
952 986 6.044404 ACCTTTCTAGATTGGTTTTCCTCTGA 59.956 38.462 10.37 0.00 41.38 3.27
1043 1218 1.922570 CTTACGCAGACGGTAAGCAT 58.077 50.000 5.34 0.00 46.04 3.79
1058 1233 5.345202 CGGTAAGCATATTAATCTGGTCGTC 59.655 44.000 6.06 1.50 0.00 4.20
1106 1281 1.730064 GTTCAGATGCGGCGAGTTAAA 59.270 47.619 12.98 0.00 0.00 1.52
1118 1293 5.362711 CGGCGAGTTAAATTTTCTTTTTGC 58.637 37.500 0.00 0.46 0.00 3.68
1142 1317 4.319118 GGATAAGATGCTGCGAGTTAAAGC 60.319 45.833 0.00 0.00 37.46 3.51
1156 1331 6.091441 GCGAGTTAAAGCTAGCTATGCATAAT 59.909 38.462 19.70 0.00 34.88 1.28
1157 1332 7.360438 GCGAGTTAAAGCTAGCTATGCATAATT 60.360 37.037 19.70 8.47 34.88 1.40
1220 1400 3.243907 GGAGCTAGCTTACATGTACCAGG 60.244 52.174 20.42 0.00 0.00 4.45
1386 1590 3.680525 CTCGTCGTCATTGCCGAG 58.319 61.111 0.00 0.00 40.54 4.63
1463 1670 2.484417 CCATCATCCAACTTCCTCTCCG 60.484 54.545 0.00 0.00 0.00 4.63
1508 1730 4.087892 GCTTCTCCGGCTGGCAGA 62.088 66.667 20.86 8.17 34.14 4.26
1527 1749 1.213926 GAGCAATGGAGTCCAAGGGAT 59.786 52.381 17.71 7.28 36.95 3.85
1676 1931 1.299541 AAAGGTGCGTGACAAGACAG 58.700 50.000 0.00 0.00 0.00 3.51
1702 1957 3.567164 GGCTCCATTTATGTGATCACCAG 59.433 47.826 22.85 6.39 0.00 4.00
1703 1958 4.454678 GCTCCATTTATGTGATCACCAGA 58.545 43.478 22.85 5.05 0.00 3.86
1740 1995 2.755103 GGCTGCAGCTTAAATAGTTGGT 59.245 45.455 35.82 0.00 41.70 3.67
1776 2031 4.293662 TCAGACTGACAAGCTCTCTCTA 57.706 45.455 0.00 0.00 0.00 2.43
1822 2077 1.078567 CAGCTGGAGGAGAAGGTGC 60.079 63.158 5.57 0.00 35.37 5.01
1830 2085 1.995626 GGAGAAGGTGCAGGCCCTA 60.996 63.158 0.00 0.00 0.00 3.53
1882 2143 2.431454 TGGTGTTCGATAGCAAATGCA 58.569 42.857 8.28 0.00 45.16 3.96
1952 2220 4.051167 TCCGGGTACTCGAGCCCA 62.051 66.667 18.83 6.51 45.07 5.36
1988 2256 2.967397 CGAGGGAACACGGCACTA 59.033 61.111 0.00 0.00 40.94 2.74
2037 2305 0.543277 GGTGCTGGTGATGATCCTGA 59.457 55.000 0.00 0.00 0.00 3.86
2063 2331 0.391130 TCGAAAATCAGGGCCTGTCG 60.391 55.000 31.60 29.87 32.61 4.35
2170 2444 9.282569 TGCTCATATATACATTGTGCAAATGTA 57.717 29.630 24.01 24.01 44.35 2.29
2274 2556 2.828661 TTCTCCAGATCGAAGAGGGA 57.171 50.000 9.04 0.00 43.63 4.20
2278 2560 2.360801 CTCCAGATCGAAGAGGGAGTTC 59.639 54.545 14.26 0.00 43.66 3.01
2349 2631 4.096681 TCAGCTGGAAGTAGAATGGAAGA 58.903 43.478 15.13 0.00 35.30 2.87
2630 2912 0.182775 ACAAAAACAGGAGCTCCGGT 59.817 50.000 30.15 30.15 46.34 5.28
2652 2941 6.313164 CGGTCTTCTAGGAAAACCATCTTTAC 59.687 42.308 4.07 0.00 0.00 2.01
2697 3037 8.655651 TTTATGTTTTCTTTTTCCGAGCAAAT 57.344 26.923 0.00 0.00 0.00 2.32
2728 3068 4.082787 CCGCTGCCTTTTCATTAAGAGAAA 60.083 41.667 0.00 2.68 33.48 2.52
2785 3125 3.636300 AGATCTCTTCCTCTGATTCCGTG 59.364 47.826 0.00 0.00 0.00 4.94
2786 3126 2.808919 TCTCTTCCTCTGATTCCGTGT 58.191 47.619 0.00 0.00 0.00 4.49
2787 3127 2.755655 TCTCTTCCTCTGATTCCGTGTC 59.244 50.000 0.00 0.00 0.00 3.67
2788 3128 2.757868 CTCTTCCTCTGATTCCGTGTCT 59.242 50.000 0.00 0.00 0.00 3.41
2791 3131 4.158025 TCTTCCTCTGATTCCGTGTCTAAC 59.842 45.833 0.00 0.00 0.00 2.34
2828 3168 4.910195 AGAATGCTCCACATACAAGAACA 58.090 39.130 0.00 0.00 38.34 3.18
2829 3169 4.697352 AGAATGCTCCACATACAAGAACAC 59.303 41.667 0.00 0.00 38.34 3.32
2833 3173 4.019771 TGCTCCACATACAAGAACACCATA 60.020 41.667 0.00 0.00 0.00 2.74
2840 3180 6.914215 CACATACAAGAACACCATATGAATGC 59.086 38.462 3.65 0.00 0.00 3.56
2848 3188 6.648310 AGAACACCATATGAATGCTCTAATCG 59.352 38.462 3.65 0.00 0.00 3.34
2888 3228 7.630242 TGAATGTTCTGAAACTTCTTGTCTT 57.370 32.000 11.94 0.00 36.30 3.01
2947 3287 3.782523 AGATTCTGCCTAAATCCACCTGA 59.217 43.478 0.00 0.00 34.34 3.86
2959 3299 8.310382 CCTAAATCCACCTGAATACAGAGATAG 58.690 40.741 0.00 0.00 46.03 2.08
2960 3300 5.736951 ATCCACCTGAATACAGAGATAGC 57.263 43.478 0.00 0.00 46.03 2.97
2969 3309 7.201758 CCTGAATACAGAGATAGCAAATTGCAA 60.202 37.037 20.82 0.00 45.46 4.08
2986 3326 2.877168 TGCAAATTTTGGTGGAATGTGC 59.123 40.909 10.96 5.30 44.37 4.57
2989 3329 3.405823 AATTTTGGTGGAATGTGCCTG 57.594 42.857 0.00 0.00 0.00 4.85
2990 3330 1.786937 TTTTGGTGGAATGTGCCTGT 58.213 45.000 0.00 0.00 0.00 4.00
2991 3331 1.786937 TTTGGTGGAATGTGCCTGTT 58.213 45.000 0.00 0.00 0.00 3.16
2992 3332 1.039068 TTGGTGGAATGTGCCTGTTG 58.961 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.895798 TCATCCTAGCCGATGATGGTC 59.104 52.381 7.39 0.00 42.89 4.02
1 2 1.898472 CTCATCCTAGCCGATGATGGT 59.102 52.381 10.87 0.00 45.76 3.55
2 3 1.206610 CCTCATCCTAGCCGATGATGG 59.793 57.143 10.87 10.52 45.76 3.51
3 4 2.094286 GTCCTCATCCTAGCCGATGATG 60.094 54.545 10.87 9.07 45.76 3.07
4 5 2.175202 GTCCTCATCCTAGCCGATGAT 58.825 52.381 10.87 0.00 45.76 2.45
5 6 1.133482 TGTCCTCATCCTAGCCGATGA 60.133 52.381 10.23 10.23 44.98 2.92
6 7 1.332195 TGTCCTCATCCTAGCCGATG 58.668 55.000 3.31 3.31 40.92 3.84
7 8 2.317371 ATGTCCTCATCCTAGCCGAT 57.683 50.000 0.00 0.00 0.00 4.18
8 9 2.971901 TATGTCCTCATCCTAGCCGA 57.028 50.000 0.00 0.00 35.70 5.54
9 10 4.336889 TTTTATGTCCTCATCCTAGCCG 57.663 45.455 0.00 0.00 35.70 5.52
10 11 5.703130 GTCATTTTATGTCCTCATCCTAGCC 59.297 44.000 0.00 0.00 35.70 3.93
11 12 6.291377 TGTCATTTTATGTCCTCATCCTAGC 58.709 40.000 0.00 0.00 35.70 3.42
12 13 7.770433 TGTTGTCATTTTATGTCCTCATCCTAG 59.230 37.037 0.00 0.00 35.70 3.02
13 14 7.629157 TGTTGTCATTTTATGTCCTCATCCTA 58.371 34.615 0.00 0.00 35.70 2.94
14 15 6.484288 TGTTGTCATTTTATGTCCTCATCCT 58.516 36.000 0.00 0.00 35.70 3.24
15 16 6.757897 TGTTGTCATTTTATGTCCTCATCC 57.242 37.500 0.00 0.00 35.70 3.51
16 17 7.148018 ACCATGTTGTCATTTTATGTCCTCATC 60.148 37.037 0.00 0.00 32.46 2.92
17 18 6.664816 ACCATGTTGTCATTTTATGTCCTCAT 59.335 34.615 0.00 0.00 33.76 2.90
18 19 6.009589 ACCATGTTGTCATTTTATGTCCTCA 58.990 36.000 0.00 0.00 31.15 3.86
19 20 6.150976 TCACCATGTTGTCATTTTATGTCCTC 59.849 38.462 0.00 0.00 31.15 3.71
20 21 6.009589 TCACCATGTTGTCATTTTATGTCCT 58.990 36.000 0.00 0.00 31.15 3.85
21 22 6.266168 TCACCATGTTGTCATTTTATGTCC 57.734 37.500 0.00 0.00 31.15 4.02
22 23 5.801947 GCTCACCATGTTGTCATTTTATGTC 59.198 40.000 0.00 0.00 31.15 3.06
23 24 5.336690 GGCTCACCATGTTGTCATTTTATGT 60.337 40.000 0.00 0.00 35.26 2.29
24 25 5.104374 GGCTCACCATGTTGTCATTTTATG 58.896 41.667 0.00 0.00 35.26 1.90
25 26 4.771577 TGGCTCACCATGTTGTCATTTTAT 59.228 37.500 0.00 0.00 42.67 1.40
26 27 4.148079 TGGCTCACCATGTTGTCATTTTA 58.852 39.130 0.00 0.00 42.67 1.52
27 28 2.964464 TGGCTCACCATGTTGTCATTTT 59.036 40.909 0.00 0.00 42.67 1.82
28 29 2.596346 TGGCTCACCATGTTGTCATTT 58.404 42.857 0.00 0.00 42.67 2.32
29 30 2.291209 TGGCTCACCATGTTGTCATT 57.709 45.000 0.00 0.00 42.67 2.57
39 40 2.719531 TTTAACACAGTGGCTCACCA 57.280 45.000 5.31 0.00 46.51 4.17
40 41 5.001232 TCTATTTTAACACAGTGGCTCACC 58.999 41.667 5.31 0.00 34.49 4.02
41 42 5.701290 ACTCTATTTTAACACAGTGGCTCAC 59.299 40.000 5.31 0.00 34.10 3.51
42 43 5.865085 ACTCTATTTTAACACAGTGGCTCA 58.135 37.500 5.31 0.00 0.00 4.26
43 44 6.872020 TGTACTCTATTTTAACACAGTGGCTC 59.128 38.462 5.31 0.00 0.00 4.70
44 45 6.649557 GTGTACTCTATTTTAACACAGTGGCT 59.350 38.462 5.31 0.00 40.08 4.75
45 46 6.649557 AGTGTACTCTATTTTAACACAGTGGC 59.350 38.462 5.31 0.00 42.21 5.01
46 47 7.870954 TGAGTGTACTCTATTTTAACACAGTGG 59.129 37.037 12.75 0.00 42.21 4.00
47 48 8.812147 TGAGTGTACTCTATTTTAACACAGTG 57.188 34.615 12.75 0.00 42.21 3.66
75 76 9.647918 GAGGGAGTATGACATAATATCCTGATA 57.352 37.037 16.95 0.00 0.00 2.15
76 77 8.350648 AGAGGGAGTATGACATAATATCCTGAT 58.649 37.037 16.95 7.27 0.00 2.90
77 78 7.617329 CAGAGGGAGTATGACATAATATCCTGA 59.383 40.741 16.95 0.00 0.00 3.86
78 79 7.398618 ACAGAGGGAGTATGACATAATATCCTG 59.601 40.741 16.95 13.31 0.00 3.86
79 80 7.483018 ACAGAGGGAGTATGACATAATATCCT 58.517 38.462 13.72 13.72 0.00 3.24
80 81 7.726033 ACAGAGGGAGTATGACATAATATCC 57.274 40.000 11.60 11.60 0.00 2.59
81 82 8.254508 GGAACAGAGGGAGTATGACATAATATC 58.745 40.741 0.00 0.00 0.00 1.63
82 83 7.093727 CGGAACAGAGGGAGTATGACATAATAT 60.094 40.741 0.00 0.00 0.00 1.28
83 84 6.208797 CGGAACAGAGGGAGTATGACATAATA 59.791 42.308 0.00 0.00 0.00 0.98
84 85 5.011125 CGGAACAGAGGGAGTATGACATAAT 59.989 44.000 0.00 0.00 0.00 1.28
85 86 4.341235 CGGAACAGAGGGAGTATGACATAA 59.659 45.833 0.00 0.00 0.00 1.90
86 87 3.889538 CGGAACAGAGGGAGTATGACATA 59.110 47.826 0.00 0.00 0.00 2.29
87 88 2.695666 CGGAACAGAGGGAGTATGACAT 59.304 50.000 0.00 0.00 0.00 3.06
88 89 2.100197 CGGAACAGAGGGAGTATGACA 58.900 52.381 0.00 0.00 0.00 3.58
89 90 2.376109 TCGGAACAGAGGGAGTATGAC 58.624 52.381 0.00 0.00 0.00 3.06
90 91 2.820728 TCGGAACAGAGGGAGTATGA 57.179 50.000 0.00 0.00 0.00 2.15
91 92 4.408182 AATTCGGAACAGAGGGAGTATG 57.592 45.455 0.00 0.00 0.00 2.39
92 93 5.209659 AGTAATTCGGAACAGAGGGAGTAT 58.790 41.667 0.00 0.00 0.00 2.12
93 94 4.607239 AGTAATTCGGAACAGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
94 95 3.442076 AGTAATTCGGAACAGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
95 96 3.489398 CGAGTAATTCGGAACAGAGGGAG 60.489 52.174 0.00 0.00 45.54 4.30
96 97 2.426024 CGAGTAATTCGGAACAGAGGGA 59.574 50.000 0.00 0.00 45.54 4.20
97 98 2.810650 CGAGTAATTCGGAACAGAGGG 58.189 52.381 0.00 0.00 45.54 4.30
108 109 6.480320 ACATCTATTTCTGTGGCGAGTAATTC 59.520 38.462 0.00 0.00 0.00 2.17
109 110 6.349300 ACATCTATTTCTGTGGCGAGTAATT 58.651 36.000 0.00 0.00 0.00 1.40
110 111 5.918608 ACATCTATTTCTGTGGCGAGTAAT 58.081 37.500 0.00 0.00 0.00 1.89
111 112 5.339008 ACATCTATTTCTGTGGCGAGTAA 57.661 39.130 0.00 0.00 0.00 2.24
112 113 6.490381 AGATACATCTATTTCTGTGGCGAGTA 59.510 38.462 0.00 0.00 34.85 2.59
113 114 3.895232 ACATCTATTTCTGTGGCGAGT 57.105 42.857 0.00 0.00 0.00 4.18
114 115 5.777802 AGATACATCTATTTCTGTGGCGAG 58.222 41.667 0.00 0.00 34.85 5.03
115 116 5.791336 AGATACATCTATTTCTGTGGCGA 57.209 39.130 0.00 0.00 34.85 5.54
116 117 7.946655 TTTAGATACATCTATTTCTGTGGCG 57.053 36.000 0.00 0.00 39.02 5.69
117 118 9.331282 AGTTTTAGATACATCTATTTCTGTGGC 57.669 33.333 0.00 0.00 39.02 5.01
159 160 9.125026 GGAATTACTTGTCATAGAAATGGATGT 57.875 33.333 0.00 0.00 33.61 3.06
160 161 8.285394 CGGAATTACTTGTCATAGAAATGGATG 58.715 37.037 0.00 0.00 33.61 3.51
161 162 8.210946 TCGGAATTACTTGTCATAGAAATGGAT 58.789 33.333 0.00 0.00 33.61 3.41
162 163 7.561251 TCGGAATTACTTGTCATAGAAATGGA 58.439 34.615 0.00 0.00 33.61 3.41
163 164 7.786178 TCGGAATTACTTGTCATAGAAATGG 57.214 36.000 0.00 0.00 33.61 3.16
164 165 7.846107 CGTTCGGAATTACTTGTCATAGAAATG 59.154 37.037 0.00 0.00 0.00 2.32
165 166 7.011109 CCGTTCGGAATTACTTGTCATAGAAAT 59.989 37.037 5.19 0.00 0.00 2.17
166 167 6.311935 CCGTTCGGAATTACTTGTCATAGAAA 59.688 38.462 5.19 0.00 0.00 2.52
167 168 5.808540 CCGTTCGGAATTACTTGTCATAGAA 59.191 40.000 5.19 0.00 0.00 2.10
168 169 5.125900 TCCGTTCGGAATTACTTGTCATAGA 59.874 40.000 11.66 0.00 0.00 1.98
169 170 5.345702 TCCGTTCGGAATTACTTGTCATAG 58.654 41.667 11.66 0.00 0.00 2.23
170 171 5.327616 TCCGTTCGGAATTACTTGTCATA 57.672 39.130 11.66 0.00 0.00 2.15
171 172 4.181578 CTCCGTTCGGAATTACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
172 173 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
173 174 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
174 175 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
175 176 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
176 177 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
177 178 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
178 179 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
179 180 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
180 181 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
181 182 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
182 183 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
183 184 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
184 185 1.755179 TAAGTACTCCCTCCGTTCGG 58.245 55.000 4.74 4.74 0.00 4.30
185 186 4.382345 AAATAAGTACTCCCTCCGTTCG 57.618 45.455 0.00 0.00 0.00 3.95
186 187 5.485620 ACAAAATAAGTACTCCCTCCGTTC 58.514 41.667 0.00 0.00 0.00 3.95
187 188 5.494390 ACAAAATAAGTACTCCCTCCGTT 57.506 39.130 0.00 0.00 0.00 4.44
188 189 5.494390 AACAAAATAAGTACTCCCTCCGT 57.506 39.130 0.00 0.00 0.00 4.69
189 190 5.522824 GCTAACAAAATAAGTACTCCCTCCG 59.477 44.000 0.00 0.00 0.00 4.63
190 191 5.821470 GGCTAACAAAATAAGTACTCCCTCC 59.179 44.000 0.00 0.00 0.00 4.30
191 192 6.412214 TGGCTAACAAAATAAGTACTCCCTC 58.588 40.000 0.00 0.00 0.00 4.30
192 193 6.382919 TGGCTAACAAAATAAGTACTCCCT 57.617 37.500 0.00 0.00 0.00 4.20
193 194 8.741603 TTATGGCTAACAAAATAAGTACTCCC 57.258 34.615 0.00 0.00 0.00 4.30
220 221 2.570442 GTTGCAACGGGAGACAAAAA 57.430 45.000 14.90 0.00 0.00 1.94
232 233 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
233 234 1.590610 AATATGCCCGTGCGTTGCAA 61.591 50.000 0.00 0.00 41.47 4.08
234 235 1.590610 AAATATGCCCGTGCGTTGCA 61.591 50.000 8.11 8.11 41.78 4.08
235 236 1.138671 AAATATGCCCGTGCGTTGC 59.861 52.632 0.00 0.00 41.78 4.17
236 237 2.942545 CAAATATGCCCGTGCGTTG 58.057 52.632 0.00 0.00 41.78 4.10
248 249 9.736023 GCAAGCTTTATGTTAACTAGCAAATAT 57.264 29.630 18.06 2.13 34.37 1.28
249 250 8.735315 TGCAAGCTTTATGTTAACTAGCAAATA 58.265 29.630 18.06 2.50 34.37 1.40
250 251 7.601856 TGCAAGCTTTATGTTAACTAGCAAAT 58.398 30.769 18.06 3.28 34.37 2.32
251 252 6.976088 TGCAAGCTTTATGTTAACTAGCAAA 58.024 32.000 18.06 8.71 34.37 3.68
252 253 6.349280 CCTGCAAGCTTTATGTTAACTAGCAA 60.349 38.462 18.06 3.81 34.37 3.91
253 254 5.123820 CCTGCAAGCTTTATGTTAACTAGCA 59.876 40.000 18.06 0.00 34.37 3.49
254 255 5.573146 CCTGCAAGCTTTATGTTAACTAGC 58.427 41.667 7.22 10.12 0.00 3.42
255 256 5.355350 AGCCTGCAAGCTTTATGTTAACTAG 59.645 40.000 3.30 0.00 41.41 2.57
256 257 5.253330 AGCCTGCAAGCTTTATGTTAACTA 58.747 37.500 3.30 0.00 41.41 2.24
257 258 4.082125 AGCCTGCAAGCTTTATGTTAACT 58.918 39.130 3.30 0.00 41.41 2.24
258 259 4.082787 TGAGCCTGCAAGCTTTATGTTAAC 60.083 41.667 11.94 0.00 45.15 2.01
264 265 1.101331 GCTGAGCCTGCAAGCTTTAT 58.899 50.000 11.94 0.00 45.15 1.40
285 286 3.499537 TGATTATAGCGCTGCATCCTTTG 59.500 43.478 22.90 0.00 0.00 2.77
290 291 3.181513 CCATGTGATTATAGCGCTGCATC 60.182 47.826 22.90 17.93 0.00 3.91
300 301 7.684317 TGTTTAGGAGACCCATGTGATTATA 57.316 36.000 0.00 0.00 33.88 0.98
307 308 3.517901 TCGATTGTTTAGGAGACCCATGT 59.482 43.478 0.00 0.00 33.88 3.21
379 380 3.139077 GTGTTGGAGGGAAAGTACAGTG 58.861 50.000 0.00 0.00 0.00 3.66
389 390 1.440618 TAAGCTTGGTGTTGGAGGGA 58.559 50.000 9.86 0.00 0.00 4.20
404 405 6.278363 TCTAGTGTACATTTTCCGGATAAGC 58.722 40.000 4.15 0.00 0.00 3.09
465 466 0.248866 GACGGTTGCAAGTTGTTGGG 60.249 55.000 0.00 0.00 33.87 4.12
475 476 3.947841 GCAAGTGCGACGGTTGCA 61.948 61.111 18.87 18.87 44.87 4.08
494 495 0.314302 CGGACGAGGTCTGTTTCACT 59.686 55.000 0.00 0.00 34.54 3.41
500 501 2.915659 TTGCCGGACGAGGTCTGT 60.916 61.111 5.05 0.00 37.24 3.41
555 556 0.620556 AGGTCCGATGAAAGTGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
618 619 6.094881 TGAATCCAGTTCAAAAAGAAACTCGT 59.905 34.615 0.00 0.00 43.64 4.18
630 631 3.260632 TCCGTGATCTGAATCCAGTTCAA 59.739 43.478 7.51 0.00 45.45 2.69
631 632 2.831526 TCCGTGATCTGAATCCAGTTCA 59.168 45.455 0.00 0.00 43.23 3.18
633 634 3.708631 AGATCCGTGATCTGAATCCAGTT 59.291 43.478 13.53 0.00 46.21 3.16
674 694 1.110442 CTGAAGATCTCCTGCGTCCT 58.890 55.000 0.00 0.00 0.00 3.85
675 695 1.066908 CTCTGAAGATCTCCTGCGTCC 59.933 57.143 0.00 0.00 0.00 4.79
677 697 2.136298 TCTCTGAAGATCTCCTGCGT 57.864 50.000 0.00 0.00 0.00 5.24
678 698 2.288334 CCATCTCTGAAGATCTCCTGCG 60.288 54.545 0.00 0.00 40.38 5.18
698 719 2.109126 GCCTGACATCGCAACTCCC 61.109 63.158 0.00 0.00 0.00 4.30
703 724 0.671472 CTGAGTGCCTGACATCGCAA 60.671 55.000 0.00 0.00 36.60 4.85
759 780 1.080501 CTCCGTGCGAGCTTCAGAA 60.081 57.895 0.00 0.00 0.00 3.02
776 798 0.107410 TTGGTTTCACAGTCCGCACT 60.107 50.000 0.00 0.00 0.00 4.40
787 811 3.357203 TGTACTTGCAGGTTTGGTTTCA 58.643 40.909 6.84 0.00 0.00 2.69
852 883 6.201997 GTGTTCTCTTCTTTCTTGACTTCCTC 59.798 42.308 0.00 0.00 0.00 3.71
888 919 3.515901 ACATACCTGAAACCTCTGTCCTC 59.484 47.826 0.00 0.00 0.00 3.71
929 963 6.093357 GCTCAGAGGAAAACCAATCTAGAAAG 59.907 42.308 0.00 0.00 0.00 2.62
931 965 5.249393 AGCTCAGAGGAAAACCAATCTAGAA 59.751 40.000 0.00 0.00 0.00 2.10
943 977 4.284490 AGACACATACAAGCTCAGAGGAAA 59.716 41.667 0.00 0.00 0.00 3.13
952 986 7.201679 GCTTGATGATTAAGACACATACAAGCT 60.202 37.037 21.13 0.00 42.64 3.74
992 1167 2.551459 GGTTGCTCCATCATATCACTGC 59.449 50.000 0.00 0.00 35.97 4.40
1043 1218 8.354426 TGATTACGATTGACGACCAGATTAATA 58.646 33.333 0.00 0.00 45.77 0.98
1058 1233 9.083080 TGTAGATGTTACAAGTGATTACGATTG 57.917 33.333 0.00 0.00 0.00 2.67
1097 1272 5.174216 TCCGCAAAAAGAAAATTTAACTCGC 59.826 36.000 0.00 0.00 0.00 5.03
1106 1281 6.532657 CAGCATCTTATCCGCAAAAAGAAAAT 59.467 34.615 0.00 0.00 33.26 1.82
1118 1293 1.858091 AACTCGCAGCATCTTATCCG 58.142 50.000 0.00 0.00 0.00 4.18
1142 1317 8.781196 AGATGTCACAAAATTATGCATAGCTAG 58.219 33.333 6.50 0.72 0.00 3.42
1156 1331 5.638657 GCCATTGCAATAAGATGTCACAAAA 59.361 36.000 12.53 0.00 37.47 2.44
1157 1332 5.170021 GCCATTGCAATAAGATGTCACAAA 58.830 37.500 12.53 0.00 37.47 2.83
1220 1400 0.910338 GGTACTGGACCCCCTTCTTC 59.090 60.000 0.00 0.00 43.25 2.87
1254 1452 2.257676 GCTCTGCAAACTGCTGCC 59.742 61.111 0.00 0.00 45.31 4.85
1386 1590 0.531974 TGCCGATCCGAATGGTAAGC 60.532 55.000 0.00 0.00 36.30 3.09
1491 1698 4.087892 TCTGCCAGCCGGAGAAGC 62.088 66.667 5.05 1.72 0.00 3.86
1508 1730 1.064166 CATCCCTTGGACTCCATTGCT 60.064 52.381 0.00 0.00 32.98 3.91
1513 1735 0.548031 GCATCATCCCTTGGACTCCA 59.452 55.000 0.00 0.00 32.98 3.86
1651 1885 1.745232 TGTCACGCACCTTTTTGAGT 58.255 45.000 0.00 0.00 0.00 3.41
1676 1931 3.633525 TGATCACATAAATGGAGCCAAGC 59.366 43.478 0.00 0.00 0.00 4.01
1684 1939 4.336433 GGTGTCTGGTGATCACATAAATGG 59.664 45.833 26.47 8.45 34.27 3.16
1702 1957 1.296715 CCTGCAGGTACCTGGTGTC 59.703 63.158 36.91 23.28 43.77 3.67
1703 1958 2.895424 GCCTGCAGGTACCTGGTGT 61.895 63.158 36.91 4.24 43.77 4.16
1740 1995 7.281841 TGTCAGTCTGAATAATATGGCAATGA 58.718 34.615 3.51 0.00 0.00 2.57
1776 2031 0.335361 AGTCGATGGTACTCCCCAGT 59.665 55.000 0.00 0.00 38.07 4.00
1822 2077 2.191641 GCCTTGCTCTAGGGCCTG 59.808 66.667 18.53 6.47 45.39 4.85
1882 2143 1.138266 CGTTGTCGGGAGGGATATGTT 59.862 52.381 0.00 0.00 0.00 2.71
1932 2200 2.439883 GCTCGAGTACCCGGACCT 60.440 66.667 15.13 0.00 0.00 3.85
1952 2220 0.106819 GGATGCTGGCCTCAATGTCT 60.107 55.000 3.32 0.00 0.00 3.41
1988 2256 5.095145 TCTTCTTGCAGCAGATATTCAGT 57.905 39.130 0.00 0.00 0.00 3.41
2037 2305 0.108138 CCCTGATTTTCGAGCTCGGT 60.108 55.000 33.98 18.40 40.29 4.69
2063 2331 6.260050 ACGGTATGATGTTGGTGTTTATGATC 59.740 38.462 0.00 0.00 0.00 2.92
2095 2363 1.028868 GGTGATGTTGAGGCAGGAGC 61.029 60.000 0.00 0.00 41.10 4.70
2170 2444 8.345565 CAGTTTATTCTCTTGCAAGTTGTTACT 58.654 33.333 25.19 16.65 35.68 2.24
2248 2526 5.065704 TCTTCGATCTGGAGAAAAGTGAG 57.934 43.478 0.00 0.00 0.00 3.51
2613 2895 0.765510 AGACCGGAGCTCCTGTTTTT 59.234 50.000 28.05 15.49 33.44 1.94
2624 2906 2.565834 TGGTTTTCCTAGAAGACCGGAG 59.434 50.000 9.46 0.00 41.38 4.63
2630 2912 9.503399 GAAAGTAAAGATGGTTTTCCTAGAAGA 57.497 33.333 0.00 0.00 41.38 2.87
2652 2941 8.137437 ACATAAATGGTTGACAAACTCAGAAAG 58.863 33.333 4.57 0.00 36.48 2.62
2801 3141 4.558226 TGTATGTGGAGCATTCTTGTCT 57.442 40.909 0.00 0.00 38.94 3.41
2811 3151 2.778299 TGGTGTTCTTGTATGTGGAGC 58.222 47.619 0.00 0.00 0.00 4.70
2812 3152 6.348498 TCATATGGTGTTCTTGTATGTGGAG 58.652 40.000 2.13 0.00 0.00 3.86
2828 3168 7.933577 TCTTTTCGATTAGAGCATTCATATGGT 59.066 33.333 2.13 0.00 44.77 3.55
2829 3169 8.315391 TCTTTTCGATTAGAGCATTCATATGG 57.685 34.615 2.13 0.00 32.15 2.74
2833 3173 8.186821 CCTTTTCTTTTCGATTAGAGCATTCAT 58.813 33.333 0.00 0.00 0.00 2.57
2840 3180 9.587772 TCATCTACCTTTTCTTTTCGATTAGAG 57.412 33.333 0.00 0.00 0.00 2.43
2848 3188 9.617975 CAGAACATTCATCTACCTTTTCTTTTC 57.382 33.333 0.00 0.00 0.00 2.29
2888 3228 1.937191 TCTACTCCAGGACATGCACA 58.063 50.000 0.00 0.00 0.00 4.57
2947 3287 9.880157 AAATTTGCAATTTGCTATCTCTGTATT 57.120 25.926 21.19 6.83 45.31 1.89
2959 3299 4.564940 TCCACCAAAATTTGCAATTTGC 57.435 36.364 16.63 14.49 45.29 3.68
2960 3300 6.418226 CACATTCCACCAAAATTTGCAATTTG 59.582 34.615 15.54 15.54 36.52 2.32
2969 3309 2.705127 ACAGGCACATTCCACCAAAATT 59.295 40.909 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.