Multiple sequence alignment - TraesCS7A01G504100

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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 TraesCS7A01G504100 chr7A 100.000 3897 0 0 1 3897 692524384 692520488 0.000000e+00 7197.0
1 TraesCS7A01G504100 chr7A 87.318 686 86 1 2326 3010 692615694 692615009 0.000000e+00 784.0
2 TraesCS7A01G504100 chr7A 85.061 743 97 7 2326 3054 692613514 692614256 0.000000e+00 745.0
3 TraesCS7A01G504100 chr7A 87.539 321 30 4 2011 2325 692616054 692615738 2.860000e-96 363.0
4 TraesCS7A01G504100 chr7A 86.275 306 39 3 936 1239 692617231 692616927 2.900000e-86 329.0
5 TraesCS7A01G504100 chr7A 89.189 222 20 2 1281 1499 692762395 692762615 1.380000e-69 274.0
6 TraesCS7A01G504100 chr7A 91.371 197 17 0 1296 1492 692616817 692616621 1.780000e-68 270.0
7 TraesCS7A01G504100 chr7A 92.147 191 13 1 2095 2283 692613248 692613438 6.420000e-68 268.0
8 TraesCS7A01G504100 chr7A 87.838 222 26 1 1631 1851 692612955 692613176 3.860000e-65 259.0
9 TraesCS7A01G504100 chr7A 89.941 169 17 0 2103 2271 692769980 692770148 6.560000e-53 219.0
10 TraesCS7A01G504100 chr7A 81.481 297 24 12 1216 1498 692612621 692612900 8.480000e-52 215.0
11 TraesCS7A01G504100 chr7A 90.909 143 13 0 1701 1843 692616259 692616117 3.970000e-45 193.0
12 TraesCS7A01G504100 chr7A 80.663 181 24 8 1 173 692624058 692623881 3.160000e-26 130.0
13 TraesCS7A01G504100 chr7A 75.646 271 37 12 532 800 692618092 692617849 1.480000e-19 108.0
14 TraesCS7A01G504100 chr7D 96.734 1194 30 6 1985 3175 600702709 600701522 0.000000e+00 1980.0
15 TraesCS7A01G504100 chr7D 85.909 1611 97 73 354 1903 600704269 600702728 0.000000e+00 1598.0
16 TraesCS7A01G504100 chr7D 84.930 710 93 7 2326 3021 600755570 600756279 0.000000e+00 706.0
17 TraesCS7A01G504100 chr7D 82.108 816 111 26 2077 2869 600874698 600875501 0.000000e+00 665.0
18 TraesCS7A01G504100 chr7D 86.466 532 50 11 943 1457 600748422 600748948 7.310000e-157 564.0
19 TraesCS7A01G504100 chr7D 90.204 245 20 3 1281 1525 600873904 600874144 2.260000e-82 316.0
20 TraesCS7A01G504100 chr7D 93.651 189 12 0 2095 2283 600754025 600754213 2.290000e-72 283.0
21 TraesCS7A01G504100 chr7D 86.207 232 31 1 1631 1861 600753729 600753960 2.320000e-62 250.0
22 TraesCS7A01G504100 chr7D 85.207 169 23 2 2103 2270 17760414 17760247 5.180000e-39 172.0
23 TraesCS7A01G504100 chr7B 92.609 1150 76 6 2033 3175 679930088 679928941 0.000000e+00 1644.0
24 TraesCS7A01G504100 chr7B 86.610 1531 96 49 354 1835 679931623 679930153 0.000000e+00 1591.0
25 TraesCS7A01G504100 chr7B 88.338 686 79 1 2326 3010 679998371 679997686 0.000000e+00 822.0
26 TraesCS7A01G504100 chr7B 82.396 818 108 26 2076 2870 680096620 680097424 0.000000e+00 680.0
27 TraesCS7A01G504100 chr7B 83.688 423 43 15 1099 1519 680095618 680096016 3.680000e-100 375.0
28 TraesCS7A01G504100 chr7B 88.929 280 21 5 991 1266 679986839 679987112 1.730000e-88 337.0
29 TraesCS7A01G504100 chr7B 87.692 260 28 3 1584 1843 680004263 680004008 2.280000e-77 300.0
30 TraesCS7A01G504100 chr7B 90.625 224 21 0 1276 1499 679987240 679987463 8.190000e-77 298.0
31 TraesCS7A01G504100 chr7B 91.204 216 15 2 2110 2325 679998626 679998415 1.370000e-74 291.0
32 TraesCS7A01G504100 chr7B 92.632 190 13 1 2095 2283 679987819 679988008 4.960000e-69 272.0
33 TraesCS7A01G504100 chr7B 87.317 205 26 0 1631 1835 679987526 679987730 6.510000e-58 235.0
34 TraesCS7A01G504100 chr7B 83.500 200 18 11 12 202 680006215 680006022 5.180000e-39 172.0
35 TraesCS7A01G504100 chr2A 95.862 725 23 5 3174 3897 32542844 32542126 0.000000e+00 1166.0
36 TraesCS7A01G504100 chr6A 94.890 724 30 4 3174 3897 572016066 572016782 0.000000e+00 1125.0
37 TraesCS7A01G504100 chr5A 94.613 724 31 6 3176 3897 436818960 436819677 0.000000e+00 1114.0
38 TraesCS7A01G504100 chr3B 93.923 724 34 7 3174 3897 171321575 171320862 0.000000e+00 1085.0
39 TraesCS7A01G504100 chr3B 95.960 99 4 0 1111 1209 17988404 17988502 1.120000e-35 161.0
40 TraesCS7A01G504100 chr3B 97.701 87 0 1 3798 3882 705510123 705510209 8.720000e-32 148.0
41 TraesCS7A01G504100 chr3B 96.970 33 0 1 1945 1976 814550995 814551027 2.000000e-03 54.7
42 TraesCS7A01G504100 chr3A 93.777 691 36 5 3207 3897 720689264 720688581 0.000000e+00 1031.0
43 TraesCS7A01G504100 chr3A 94.888 626 28 3 3176 3800 263764734 263765356 0.000000e+00 976.0
44 TraesCS7A01G504100 chr2B 95.638 619 25 2 3182 3800 570474975 570474359 0.000000e+00 992.0
45 TraesCS7A01G504100 chr2B 98.750 80 1 0 3803 3882 34992798 34992719 4.060000e-30 143.0
46 TraesCS7A01G504100 chr5D 95.048 626 26 4 3176 3800 481095871 481095250 0.000000e+00 979.0
47 TraesCS7A01G504100 chr6B 94.880 625 26 4 3176 3800 644643257 644643875 0.000000e+00 972.0
48 TraesCS7A01G504100 chr6B 96.552 87 1 1 3798 3882 405125217 405125303 4.060000e-30 143.0
49 TraesCS7A01G504100 chr4A 82.081 519 88 5 2355 2869 715639159 715638642 4.620000e-119 438.0
50 TraesCS7A01G504100 chr4A 90.400 125 10 2 1098 1222 11678303 11678181 3.120000e-36 163.0
51 TraesCS7A01G504100 chr4A 92.500 40 3 0 1934 1973 8929795 8929834 1.510000e-04 58.4
52 TraesCS7A01G504100 chr4D 81.679 393 50 17 1098 1484 456047126 456047502 1.360000e-79 307.0
53 TraesCS7A01G504100 chr4B 81.330 391 55 13 1098 1484 570138574 570138950 6.330000e-78 302.0
54 TraesCS7A01G504100 chr4B 98.750 80 1 0 3803 3882 197450717 197450638 4.060000e-30 143.0


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 TraesCS7A01G504100 chr7A 692520488 692524384 3896 True 7197.000000 7197 100.000000 1 3897 1 chr7A.!!$R1 3896
1 TraesCS7A01G504100 chr7A 692612621 692614256 1635 False 371.750000 745 86.631750 1216 3054 4 chr7A.!!$F3 1838
2 TraesCS7A01G504100 chr7A 692615009 692618092 3083 True 341.166667 784 86.509667 532 3010 6 chr7A.!!$R3 2478
3 TraesCS7A01G504100 chr7D 600701522 600704269 2747 True 1789.000000 1980 91.321500 354 3175 2 chr7D.!!$R2 2821
4 TraesCS7A01G504100 chr7D 600748422 600748948 526 False 564.000000 564 86.466000 943 1457 1 chr7D.!!$F1 514
5 TraesCS7A01G504100 chr7D 600873904 600875501 1597 False 490.500000 665 86.156000 1281 2869 2 chr7D.!!$F3 1588
6 TraesCS7A01G504100 chr7D 600753729 600756279 2550 False 413.000000 706 88.262667 1631 3021 3 chr7D.!!$F2 1390
7 TraesCS7A01G504100 chr7B 679928941 679931623 2682 True 1617.500000 1644 89.609500 354 3175 2 chr7B.!!$R1 2821
8 TraesCS7A01G504100 chr7B 679997686 679998626 940 True 556.500000 822 89.771000 2110 3010 2 chr7B.!!$R2 900
9 TraesCS7A01G504100 chr7B 680095618 680097424 1806 False 527.500000 680 83.042000 1099 2870 2 chr7B.!!$F2 1771
10 TraesCS7A01G504100 chr7B 679986839 679988008 1169 False 285.500000 337 89.875750 991 2283 4 chr7B.!!$F1 1292
11 TraesCS7A01G504100 chr7B 680004008 680006215 2207 True 236.000000 300 85.596000 12 1843 2 chr7B.!!$R3 1831
12 TraesCS7A01G504100 chr2A 32542126 32542844 718 True 1166.000000 1166 95.862000 3174 3897 1 chr2A.!!$R1 723
13 TraesCS7A01G504100 chr6A 572016066 572016782 716 False 1125.000000 1125 94.890000 3174 3897 1 chr6A.!!$F1 723
14 TraesCS7A01G504100 chr5A 436818960 436819677 717 False 1114.000000 1114 94.613000 3176 3897 1 chr5A.!!$F1 721
15 TraesCS7A01G504100 chr3B 171320862 171321575 713 True 1085.000000 1085 93.923000 3174 3897 1 chr3B.!!$R1 723
16 TraesCS7A01G504100 chr3A 720688581 720689264 683 True 1031.000000 1031 93.777000 3207 3897 1 chr3A.!!$R1 690
17 TraesCS7A01G504100 chr3A 263764734 263765356 622 False 976.000000 976 94.888000 3176 3800 1 chr3A.!!$F1 624
18 TraesCS7A01G504100 chr2B 570474359 570474975 616 True 992.000000 992 95.638000 3182 3800 1 chr2B.!!$R2 618
19 TraesCS7A01G504100 chr5D 481095250 481095871 621 True 979.000000 979 95.048000 3176 3800 1 chr5D.!!$R1 624
20 TraesCS7A01G504100 chr6B 644643257 644643875 618 False 972.000000 972 94.880000 3176 3800 1 chr6B.!!$F2 624
21 TraesCS7A01G504100 chr4A 715638642 715639159 517 True 438.000000 438 82.081000 2355 2869 1 chr4A.!!$R2 514

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
916 1527 0.035152 TGCAACAGCCACCAGATAGG 60.035 55.0 0.0 0.0 45.67 2.57 F
1890 3330 0.594796 CCGCTTGTTTTGCTGGTCAC 60.595 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 3552 0.257039 GACATCCCTCATGGCCTGTT 59.743 55.0 3.32 0.0 33.74 3.16 R
3711 6543 0.615331 CCCACAGCCACACTCTACAT 59.385 55.0 0.00 0.0 0.00 2.29 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
27 28 0.478072 ATGACTTGTTGGGGAGCACA 59.522 50.000 0.00 0.00 0.00 4.57
31 32 0.179020 CTTGTTGGGGAGCACAGTGA 60.179 55.000 4.15 0.00 0.00 3.41
34 35 1.702401 TGTTGGGGAGCACAGTGATTA 59.298 47.619 4.15 0.00 0.00 1.75
40 41 4.411869 TGGGGAGCACAGTGATTATTATGA 59.588 41.667 4.15 0.00 0.00 2.15
60 61 4.894784 TGATTGGAGTTAAGTGGACTCAC 58.105 43.478 6.59 0.00 44.15 3.51
83 84 4.501915 CCCACATGAAGCAAATCTTGTTGT 60.502 41.667 0.00 0.00 36.04 3.32
92 93 4.338964 AGCAAATCTTGTTGTCATGTGTCA 59.661 37.500 0.00 0.00 0.00 3.58
93 94 4.442073 GCAAATCTTGTTGTCATGTGTCAC 59.558 41.667 0.00 0.00 0.00 3.67
98 99 2.622436 TGTTGTCATGTGTCACGAACA 58.378 42.857 0.00 0.00 34.78 3.18
99 100 2.607180 TGTTGTCATGTGTCACGAACAG 59.393 45.455 0.00 0.00 38.97 3.16
100 101 2.595124 TGTCATGTGTCACGAACAGT 57.405 45.000 0.00 0.00 38.97 3.55
103 104 2.863740 GTCATGTGTCACGAACAGTTGA 59.136 45.455 0.00 0.00 38.97 3.18
104 105 3.308595 GTCATGTGTCACGAACAGTTGAA 59.691 43.478 0.00 0.00 38.97 2.69
105 106 3.308595 TCATGTGTCACGAACAGTTGAAC 59.691 43.478 0.00 0.00 38.97 3.18
106 107 2.689646 TGTGTCACGAACAGTTGAACA 58.310 42.857 0.00 0.00 38.97 3.18
107 108 2.413796 TGTGTCACGAACAGTTGAACAC 59.586 45.455 0.00 0.70 38.97 3.32
110 111 3.063316 TGTCACGAACAGTTGAACACATG 59.937 43.478 0.00 0.00 32.81 3.21
111 112 3.308595 GTCACGAACAGTTGAACACATGA 59.691 43.478 0.00 0.00 0.00 3.07
112 113 4.024893 GTCACGAACAGTTGAACACATGAT 60.025 41.667 0.00 0.00 0.00 2.45
159 164 3.072330 TGTGCCTCATCTTACAACTCCAA 59.928 43.478 0.00 0.00 0.00 3.53
173 178 9.965824 CTTACAACTCCAATTACAAAGTTCATT 57.034 29.630 0.00 0.00 29.78 2.57
195 200 2.158986 AGTGCAGTGGACTATGAGATGC 60.159 50.000 16.55 0.00 0.00 3.91
196 201 2.113807 TGCAGTGGACTATGAGATGCT 58.886 47.619 0.00 0.00 33.47 3.79
197 202 2.102084 TGCAGTGGACTATGAGATGCTC 59.898 50.000 0.00 0.00 33.47 4.26
198 203 2.102084 GCAGTGGACTATGAGATGCTCA 59.898 50.000 0.00 0.00 44.99 4.26
199 204 3.715495 CAGTGGACTATGAGATGCTCAC 58.285 50.000 0.00 0.00 43.63 3.51
200 205 3.131755 CAGTGGACTATGAGATGCTCACA 59.868 47.826 0.00 0.00 43.63 3.58
201 206 3.966006 AGTGGACTATGAGATGCTCACAT 59.034 43.478 0.00 0.00 43.63 3.21
202 207 4.056740 GTGGACTATGAGATGCTCACATG 58.943 47.826 0.00 0.00 43.63 3.21
203 208 3.065655 GGACTATGAGATGCTCACATGC 58.934 50.000 0.00 0.00 43.63 4.06
204 209 3.493873 GGACTATGAGATGCTCACATGCA 60.494 47.826 0.00 0.00 43.63 3.96
205 210 4.124970 GACTATGAGATGCTCACATGCAA 58.875 43.478 0.00 0.00 43.63 4.08
206 211 3.875727 ACTATGAGATGCTCACATGCAAC 59.124 43.478 0.00 0.00 43.63 4.17
207 212 2.188062 TGAGATGCTCACATGCAACA 57.812 45.000 0.00 0.00 46.61 3.33
208 213 2.506444 TGAGATGCTCACATGCAACAA 58.494 42.857 0.00 0.00 46.61 2.83
209 214 3.086282 TGAGATGCTCACATGCAACAAT 58.914 40.909 0.00 0.00 46.61 2.71
210 215 3.508402 TGAGATGCTCACATGCAACAATT 59.492 39.130 0.00 0.00 46.61 2.32
211 216 4.021807 TGAGATGCTCACATGCAACAATTT 60.022 37.500 0.00 0.00 46.61 1.82
212 217 4.890088 AGATGCTCACATGCAACAATTTT 58.110 34.783 0.00 0.00 46.61 1.82
213 218 5.302360 AGATGCTCACATGCAACAATTTTT 58.698 33.333 0.00 0.00 46.61 1.94
232 237 3.542712 TTTTTGCGAGAACTCAGATGC 57.457 42.857 2.78 0.00 0.00 3.91
233 238 2.168326 TTTGCGAGAACTCAGATGCA 57.832 45.000 0.00 0.00 0.00 3.96
234 239 2.168326 TTGCGAGAACTCAGATGCAA 57.832 45.000 9.50 9.50 39.73 4.08
235 240 1.432514 TGCGAGAACTCAGATGCAAC 58.567 50.000 0.00 0.00 0.00 4.17
236 241 1.270252 TGCGAGAACTCAGATGCAACA 60.270 47.619 0.00 0.00 0.00 3.33
237 242 2.005451 GCGAGAACTCAGATGCAACAT 58.995 47.619 0.00 0.00 0.00 2.71
238 243 3.190079 GCGAGAACTCAGATGCAACATA 58.810 45.455 0.00 0.00 0.00 2.29
239 244 3.806521 GCGAGAACTCAGATGCAACATAT 59.193 43.478 0.00 0.00 0.00 1.78
240 245 4.984785 GCGAGAACTCAGATGCAACATATA 59.015 41.667 0.00 0.00 0.00 0.86
241 246 5.463392 GCGAGAACTCAGATGCAACATATAA 59.537 40.000 0.00 0.00 0.00 0.98
242 247 6.146837 GCGAGAACTCAGATGCAACATATAAT 59.853 38.462 0.00 0.00 0.00 1.28
243 248 7.329471 GCGAGAACTCAGATGCAACATATAATA 59.671 37.037 0.00 0.00 0.00 0.98
244 249 9.363763 CGAGAACTCAGATGCAACATATAATAT 57.636 33.333 0.00 0.00 0.00 1.28
291 296 4.334443 GCATAAAAGATGCTACACACACG 58.666 43.478 2.29 0.00 41.52 4.49
292 297 4.727734 GCATAAAAGATGCTACACACACGG 60.728 45.833 2.29 0.00 41.52 4.94
293 298 2.831685 AAAGATGCTACACACACGGA 57.168 45.000 0.00 0.00 0.00 4.69
294 299 3.334583 AAAGATGCTACACACACGGAT 57.665 42.857 0.00 0.00 0.00 4.18
295 300 3.334583 AAGATGCTACACACACGGATT 57.665 42.857 0.00 0.00 0.00 3.01
296 301 3.334583 AGATGCTACACACACGGATTT 57.665 42.857 0.00 0.00 0.00 2.17
298 303 4.827692 AGATGCTACACACACGGATTTTA 58.172 39.130 0.00 0.00 0.00 1.52
299 304 4.870426 AGATGCTACACACACGGATTTTAG 59.130 41.667 0.00 0.00 0.00 1.85
300 305 3.997762 TGCTACACACACGGATTTTAGT 58.002 40.909 0.00 0.00 0.00 2.24
301 306 4.382291 TGCTACACACACGGATTTTAGTT 58.618 39.130 0.00 0.00 0.00 2.24
302 307 4.817464 TGCTACACACACGGATTTTAGTTT 59.183 37.500 0.00 0.00 0.00 2.66
303 308 5.990386 TGCTACACACACGGATTTTAGTTTA 59.010 36.000 0.00 0.00 0.00 2.01
304 309 6.651643 TGCTACACACACGGATTTTAGTTTAT 59.348 34.615 0.00 0.00 0.00 1.40
306 311 8.112449 GCTACACACACGGATTTTAGTTTATAC 58.888 37.037 0.00 0.00 0.00 1.47
313 318 8.092687 ACACGGATTTTAGTTTATACACAGACT 58.907 33.333 0.00 0.00 0.00 3.24
314 319 9.577110 CACGGATTTTAGTTTATACACAGACTA 57.423 33.333 0.00 0.00 0.00 2.59
323 328 8.809468 AGTTTATACACAGACTATCTCTCACA 57.191 34.615 0.00 0.00 0.00 3.58
324 329 9.244292 AGTTTATACACAGACTATCTCTCACAA 57.756 33.333 0.00 0.00 0.00 3.33
325 330 9.856488 GTTTATACACAGACTATCTCTCACAAA 57.144 33.333 0.00 0.00 0.00 2.83
327 332 9.856488 TTATACACAGACTATCTCTCACAAAAC 57.144 33.333 0.00 0.00 0.00 2.43
328 333 5.223382 ACACAGACTATCTCTCACAAAACG 58.777 41.667 0.00 0.00 0.00 3.60
329 334 4.090642 CACAGACTATCTCTCACAAAACGC 59.909 45.833 0.00 0.00 0.00 4.84
330 335 4.237724 CAGACTATCTCTCACAAAACGCA 58.762 43.478 0.00 0.00 0.00 5.24
331 336 4.325741 CAGACTATCTCTCACAAAACGCAG 59.674 45.833 0.00 0.00 0.00 5.18
332 337 4.218635 AGACTATCTCTCACAAAACGCAGA 59.781 41.667 0.00 0.00 0.00 4.26
333 338 4.883083 ACTATCTCTCACAAAACGCAGAA 58.117 39.130 0.00 0.00 0.00 3.02
334 339 5.297547 ACTATCTCTCACAAAACGCAGAAA 58.702 37.500 0.00 0.00 0.00 2.52
335 340 5.934625 ACTATCTCTCACAAAACGCAGAAAT 59.065 36.000 0.00 0.00 0.00 2.17
336 341 7.097192 ACTATCTCTCACAAAACGCAGAAATA 58.903 34.615 0.00 0.00 0.00 1.40
337 342 6.992063 ATCTCTCACAAAACGCAGAAATAT 57.008 33.333 0.00 0.00 0.00 1.28
338 343 6.408858 TCTCTCACAAAACGCAGAAATATC 57.591 37.500 0.00 0.00 0.00 1.63
339 344 6.166279 TCTCTCACAAAACGCAGAAATATCT 58.834 36.000 0.00 0.00 35.88 1.98
340 345 6.311445 TCTCTCACAAAACGCAGAAATATCTC 59.689 38.462 0.00 0.00 32.03 2.75
341 346 5.931724 TCTCACAAAACGCAGAAATATCTCA 59.068 36.000 0.00 0.00 32.03 3.27
342 347 6.091305 TCTCACAAAACGCAGAAATATCTCAG 59.909 38.462 0.00 0.00 32.03 3.35
343 348 5.931724 TCACAAAACGCAGAAATATCTCAGA 59.068 36.000 0.00 0.00 32.03 3.27
344 349 6.426633 TCACAAAACGCAGAAATATCTCAGAA 59.573 34.615 0.00 0.00 32.03 3.02
345 350 7.119699 TCACAAAACGCAGAAATATCTCAGAAT 59.880 33.333 0.00 0.00 32.03 2.40
346 351 7.752239 CACAAAACGCAGAAATATCTCAGAATT 59.248 33.333 0.00 0.00 32.03 2.17
347 352 8.299570 ACAAAACGCAGAAATATCTCAGAATTT 58.700 29.630 0.00 0.00 32.03 1.82
348 353 9.132521 CAAAACGCAGAAATATCTCAGAATTTT 57.867 29.630 0.00 0.00 32.03 1.82
349 354 8.679288 AAACGCAGAAATATCTCAGAATTTTG 57.321 30.769 0.00 0.00 32.03 2.44
350 355 6.789262 ACGCAGAAATATCTCAGAATTTTGG 58.211 36.000 0.00 0.00 32.03 3.28
351 356 5.684626 CGCAGAAATATCTCAGAATTTTGGC 59.315 40.000 0.00 0.00 32.03 4.52
352 357 5.981915 GCAGAAATATCTCAGAATTTTGGCC 59.018 40.000 0.00 0.00 32.03 5.36
365 372 6.095860 CAGAATTTTGGCCATCTCACTGAATA 59.904 38.462 6.09 0.00 0.00 1.75
375 382 7.137426 GCCATCTCACTGAATATTGCTTTAAG 58.863 38.462 0.00 0.00 0.00 1.85
405 413 7.061752 ACAAAACTATCTCTCACAATTACGC 57.938 36.000 0.00 0.00 0.00 4.42
406 414 6.649141 ACAAAACTATCTCTCACAATTACGCA 59.351 34.615 0.00 0.00 0.00 5.24
408 416 5.836821 ACTATCTCTCACAATTACGCAGA 57.163 39.130 0.00 0.00 0.00 4.26
429 437 5.684184 CAGAAATATCATCAAACACGCATGG 59.316 40.000 0.00 0.00 0.00 3.66
430 438 5.357878 AGAAATATCATCAAACACGCATGGT 59.642 36.000 0.00 0.00 0.00 3.55
431 439 4.818534 ATATCATCAAACACGCATGGTC 57.181 40.909 0.00 0.00 0.00 4.02
432 440 1.889545 TCATCAAACACGCATGGTCA 58.110 45.000 0.00 0.00 0.00 4.02
433 441 2.225467 TCATCAAACACGCATGGTCAA 58.775 42.857 0.00 0.00 0.00 3.18
434 442 2.226200 TCATCAAACACGCATGGTCAAG 59.774 45.455 0.00 0.00 0.00 3.02
447 466 0.609406 GGTCAAGCTTGGGGGAGAAC 60.609 60.000 25.73 14.21 0.00 3.01
449 468 1.675641 CAAGCTTGGGGGAGAACCG 60.676 63.158 19.14 0.00 41.60 4.44
451 470 3.327404 GCTTGGGGGAGAACCGGA 61.327 66.667 9.46 0.00 41.60 5.14
452 471 2.680370 GCTTGGGGGAGAACCGGAT 61.680 63.158 9.46 0.00 41.60 4.18
453 472 1.342672 GCTTGGGGGAGAACCGGATA 61.343 60.000 9.46 0.00 41.60 2.59
454 473 1.209621 CTTGGGGGAGAACCGGATAA 58.790 55.000 9.46 0.00 41.60 1.75
455 474 1.562475 CTTGGGGGAGAACCGGATAAA 59.438 52.381 9.46 0.00 41.60 1.40
456 475 0.913924 TGGGGGAGAACCGGATAAAC 59.086 55.000 9.46 0.00 41.60 2.01
457 476 1.210538 GGGGGAGAACCGGATAAACT 58.789 55.000 9.46 0.00 41.60 2.66
458 477 1.140452 GGGGGAGAACCGGATAAACTC 59.860 57.143 9.46 8.87 41.60 3.01
459 478 2.117051 GGGGAGAACCGGATAAACTCT 58.883 52.381 9.46 0.00 41.60 3.24
460 479 2.158943 GGGGAGAACCGGATAAACTCTG 60.159 54.545 9.46 0.00 41.60 3.35
492 511 1.406219 CGCGCTCATCCGATATTCCG 61.406 60.000 5.56 0.00 0.00 4.30
527 554 2.439701 TGGAGTACCGGCGAGGAG 60.440 66.667 9.30 0.00 45.00 3.69
613 640 2.611800 TGGCAGGCAGGACAGGAT 60.612 61.111 0.00 0.00 0.00 3.24
615 642 1.452833 GGCAGGCAGGACAGGATTC 60.453 63.158 0.00 0.00 0.00 2.52
617 644 1.817099 CAGGCAGGACAGGATTCGC 60.817 63.158 0.00 0.00 0.00 4.70
624 651 1.073923 AGGACAGGATTCGCAAAAGGT 59.926 47.619 0.00 0.00 0.00 3.50
625 652 1.886542 GGACAGGATTCGCAAAAGGTT 59.113 47.619 0.00 0.00 0.00 3.50
629 656 2.295909 CAGGATTCGCAAAAGGTTGGAA 59.704 45.455 0.00 0.00 35.10 3.53
655 682 0.949105 GAAACTGGACCGCGACACAT 60.949 55.000 8.23 0.00 0.00 3.21
661 688 3.181469 ACTGGACCGCGACACATTATAAT 60.181 43.478 8.23 0.00 0.00 1.28
662 689 3.799366 TGGACCGCGACACATTATAATT 58.201 40.909 8.23 0.00 0.00 1.40
663 690 3.805422 TGGACCGCGACACATTATAATTC 59.195 43.478 8.23 0.00 0.00 2.17
664 691 4.056050 GGACCGCGACACATTATAATTCT 58.944 43.478 8.23 0.00 0.00 2.40
665 692 5.221283 TGGACCGCGACACATTATAATTCTA 60.221 40.000 8.23 0.00 0.00 2.10
684 713 4.084888 CCGCCGCTCGTGTTTTCC 62.085 66.667 0.00 0.00 36.19 3.13
859 1438 3.950794 GACCGGTGAGCGCATCCAA 62.951 63.158 14.63 0.00 0.00 3.53
886 1497 6.382869 ACCATTTAAAGCTACTGCATCATC 57.617 37.500 0.00 0.00 42.74 2.92
916 1527 0.035152 TGCAACAGCCACCAGATAGG 60.035 55.000 0.00 0.00 45.67 2.57
924 1535 2.540265 CCACCAGATAGGCAGCTAAG 57.460 55.000 0.00 0.00 43.14 2.18
925 1536 1.071385 CCACCAGATAGGCAGCTAAGG 59.929 57.143 0.00 0.00 43.14 2.69
926 1537 0.761802 ACCAGATAGGCAGCTAAGGC 59.238 55.000 0.00 0.00 43.14 4.35
975 1587 1.153086 CAAGGGATCTCGGGCCTTG 60.153 63.158 11.73 11.73 33.27 3.61
1228 1880 8.161425 TCCAGGTGACTAGCTAATTAAGTTTTT 58.839 33.333 0.00 0.00 40.21 1.94
1232 1887 9.774742 GGTGACTAGCTAATTAAGTTTTTCATG 57.225 33.333 0.00 0.00 0.00 3.07
1277 2057 2.742372 ACTTGCACGCATCCGTCC 60.742 61.111 0.00 0.00 46.39 4.79
1351 2140 1.131883 CGGATTACTTCGACGTGGTCT 59.868 52.381 4.57 0.00 0.00 3.85
1501 2532 4.825634 CCGTCTGGTGAGGATTACATAGTA 59.174 45.833 0.00 0.00 0.00 1.82
1503 2534 5.531659 CGTCTGGTGAGGATTACATAGTAGT 59.468 44.000 0.00 0.00 0.00 2.73
1727 3156 2.640302 GGAGCTGCTCGGAGACACA 61.640 63.158 22.25 0.00 0.00 3.72
1885 3325 1.001487 TGTCATCCGCTTGTTTTGCTG 60.001 47.619 0.00 0.00 0.00 4.41
1890 3330 0.594796 CCGCTTGTTTTGCTGGTCAC 60.595 55.000 0.00 0.00 0.00 3.67
1903 3343 6.662414 TTGCTGGTCACTATTTTTCGATAG 57.338 37.500 0.00 0.00 36.04 2.08
1919 3359 9.915629 TTTTTCGATAGCTAATATTCTCTCTCC 57.084 33.333 0.00 0.00 0.00 3.71
1920 3360 8.637196 TTTCGATAGCTAATATTCTCTCTCCA 57.363 34.615 0.00 0.00 0.00 3.86
1922 3362 8.445275 TCGATAGCTAATATTCTCTCTCCATC 57.555 38.462 0.00 0.00 0.00 3.51
1923 3363 7.500892 TCGATAGCTAATATTCTCTCTCCATCC 59.499 40.741 0.00 0.00 0.00 3.51
1924 3364 7.284261 CGATAGCTAATATTCTCTCTCCATCCA 59.716 40.741 0.00 0.00 0.00 3.41
1925 3365 8.907829 ATAGCTAATATTCTCTCTCCATCCAA 57.092 34.615 0.00 0.00 0.00 3.53
1926 3366 7.623999 AGCTAATATTCTCTCTCCATCCAAA 57.376 36.000 0.00 0.00 0.00 3.28
1927 3367 8.038862 AGCTAATATTCTCTCTCCATCCAAAA 57.961 34.615 0.00 0.00 0.00 2.44
1928 3368 8.497745 AGCTAATATTCTCTCTCCATCCAAAAA 58.502 33.333 0.00 0.00 0.00 1.94
1929 3369 9.294614 GCTAATATTCTCTCTCCATCCAAAAAT 57.705 33.333 0.00 0.00 0.00 1.82
1934 3374 7.928307 TTCTCTCTCCATCCAAAAATAAGTG 57.072 36.000 0.00 0.00 0.00 3.16
1935 3375 6.418101 TCTCTCTCCATCCAAAAATAAGTGG 58.582 40.000 0.00 0.00 36.13 4.00
1936 3376 4.949856 TCTCTCCATCCAAAAATAAGTGGC 59.050 41.667 0.00 0.00 34.68 5.01
1937 3377 3.694072 TCTCCATCCAAAAATAAGTGGCG 59.306 43.478 0.00 0.00 34.68 5.69
1938 3378 3.426615 TCCATCCAAAAATAAGTGGCGT 58.573 40.909 0.00 0.00 34.68 5.68
1939 3379 3.829601 TCCATCCAAAAATAAGTGGCGTT 59.170 39.130 0.00 0.00 34.68 4.84
1942 3382 5.410067 CATCCAAAAATAAGTGGCGTTGAT 58.590 37.500 0.00 0.00 34.68 2.57
1944 3384 4.764823 TCCAAAAATAAGTGGCGTTGATCT 59.235 37.500 0.00 0.00 34.68 2.75
1948 3388 7.065324 CCAAAAATAAGTGGCGTTGATCTAGTA 59.935 37.037 0.00 0.00 0.00 1.82
1949 3389 8.447833 CAAAAATAAGTGGCGTTGATCTAGTAA 58.552 33.333 0.00 0.00 0.00 2.24
1951 3391 8.556213 AAATAAGTGGCGTTGATCTAGTAAAA 57.444 30.769 0.00 0.00 0.00 1.52
1954 3394 5.548406 AGTGGCGTTGATCTAGTAAAACTT 58.452 37.500 0.00 0.00 0.00 2.66
1959 3399 7.095523 TGGCGTTGATCTAGTAAAACTTTGTAC 60.096 37.037 0.00 0.00 0.00 2.90
2051 3491 2.543777 TGCAGTGACAGGAGGTTTAC 57.456 50.000 0.00 0.00 0.00 2.01
2331 5118 2.355108 GGAGCTTGCTAACATCCTCACA 60.355 50.000 0.00 0.00 0.00 3.58
2341 5128 6.714810 TGCTAACATCCTCACAAACTTACATT 59.285 34.615 0.00 0.00 0.00 2.71
2855 5657 4.695993 TTGCCCGCATGCTGTCGA 62.696 61.111 17.13 0.00 0.00 4.20
3073 5891 9.594478 GGAAAAGGAAACAGAATTTTACTCAAA 57.406 29.630 0.00 0.00 27.34 2.69
3160 5981 9.962783 CGCTCTACTGTAATTTTATACTACCTT 57.037 33.333 0.00 0.00 0.00 3.50
3263 6085 2.766828 AGCCTGGCGGAATATATAGGAC 59.233 50.000 13.96 0.00 0.00 3.85
3288 6112 9.672673 ACTTGACACTGAGTATAGCAAAATATT 57.327 29.630 0.00 0.00 0.00 1.28
3679 6511 3.256136 AGGGAAACTACACGAGTGAGAAG 59.744 47.826 10.50 6.81 38.87 2.85
3711 6543 4.578516 CCTGGTGTGTCTATGTTTGTGAAA 59.421 41.667 0.00 0.00 0.00 2.69
3779 6611 2.423538 CAGTTTTCACCGATTGGGATCC 59.576 50.000 1.92 1.92 40.75 3.36
3848 6680 7.282585 TCACATAGCTCTAGGCATGTTTAATT 58.717 34.615 0.00 0.00 44.79 1.40
3882 6714 1.194121 ATTTTCTGCAGGTTGGGGGC 61.194 55.000 15.13 0.00 0.00 5.80
3883 6715 4.659172 TTCTGCAGGTTGGGGGCG 62.659 66.667 15.13 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.646492 GCTCCCCAACAAGTCATAATTCAT 59.354 41.667 0.00 0.00 0.00 2.57
3 4 4.016444 TGCTCCCCAACAAGTCATAATTC 58.984 43.478 0.00 0.00 0.00 2.17
4 5 3.763897 GTGCTCCCCAACAAGTCATAATT 59.236 43.478 0.00 0.00 0.00 1.40
5 6 3.245229 TGTGCTCCCCAACAAGTCATAAT 60.245 43.478 0.00 0.00 0.00 1.28
7 8 1.702401 TGTGCTCCCCAACAAGTCATA 59.298 47.619 0.00 0.00 0.00 2.15
9 10 0.179020 CTGTGCTCCCCAACAAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
10 11 0.179018 ACTGTGCTCCCCAACAAGTC 60.179 55.000 0.00 0.00 0.00 3.01
11 12 0.466189 CACTGTGCTCCCCAACAAGT 60.466 55.000 0.00 0.00 0.00 3.16
12 13 0.179020 TCACTGTGCTCCCCAACAAG 60.179 55.000 2.12 0.00 0.00 3.16
13 14 0.478072 ATCACTGTGCTCCCCAACAA 59.522 50.000 2.12 0.00 0.00 2.83
14 15 0.478072 AATCACTGTGCTCCCCAACA 59.522 50.000 2.12 0.00 0.00 3.33
15 16 2.489938 TAATCACTGTGCTCCCCAAC 57.510 50.000 2.12 0.00 0.00 3.77
16 17 3.737559 AATAATCACTGTGCTCCCCAA 57.262 42.857 2.12 0.00 0.00 4.12
17 18 4.411869 TCATAATAATCACTGTGCTCCCCA 59.588 41.667 2.12 0.00 0.00 4.96
34 35 7.770897 GTGAGTCCACTTAACTCCAATCATAAT 59.229 37.037 1.17 0.00 42.03 1.28
40 41 3.009143 GGGTGAGTCCACTTAACTCCAAT 59.991 47.826 1.17 0.00 42.03 3.16
56 57 3.087031 AGATTTGCTTCATGTGGGTGAG 58.913 45.455 0.00 0.00 0.00 3.51
60 61 3.947910 ACAAGATTTGCTTCATGTGGG 57.052 42.857 0.00 0.00 33.60 4.61
83 84 3.172229 TCAACTGTTCGTGACACATGA 57.828 42.857 6.37 0.00 33.82 3.07
92 93 4.126437 TGATCATGTGTTCAACTGTTCGT 58.874 39.130 0.00 0.00 0.00 3.85
93 94 4.730600 TGATCATGTGTTCAACTGTTCG 57.269 40.909 0.00 0.00 0.00 3.95
98 99 7.919091 GCATAATGATTGATCATGTGTTCAACT 59.081 33.333 7.21 0.73 46.22 3.16
99 100 7.096763 CGCATAATGATTGATCATGTGTTCAAC 60.097 37.037 7.21 4.85 46.22 3.18
100 101 6.913673 CGCATAATGATTGATCATGTGTTCAA 59.086 34.615 7.21 8.47 46.22 2.69
103 104 5.532032 TCCGCATAATGATTGATCATGTGTT 59.468 36.000 7.21 0.00 46.22 3.32
104 105 5.065235 TCCGCATAATGATTGATCATGTGT 58.935 37.500 7.21 0.00 46.22 3.72
105 106 5.616488 TCCGCATAATGATTGATCATGTG 57.384 39.130 7.21 10.10 46.22 3.21
106 107 7.468220 GCATATCCGCATAATGATTGATCATGT 60.468 37.037 7.21 0.00 46.22 3.21
107 108 6.856426 GCATATCCGCATAATGATTGATCATG 59.144 38.462 7.21 0.00 46.22 3.07
110 111 6.367686 TGCATATCCGCATAATGATTGATC 57.632 37.500 0.00 0.00 36.86 2.92
145 146 9.349713 TGAACTTTGTAATTGGAGTTGTAAGAT 57.650 29.630 0.00 0.00 32.85 2.40
146 147 8.740123 TGAACTTTGTAATTGGAGTTGTAAGA 57.260 30.769 0.00 0.00 32.85 2.10
147 148 9.965824 AATGAACTTTGTAATTGGAGTTGTAAG 57.034 29.630 0.00 0.00 32.85 2.34
150 151 9.131791 ACTAATGAACTTTGTAATTGGAGTTGT 57.868 29.630 0.00 0.00 32.85 3.32
151 152 9.398170 CACTAATGAACTTTGTAATTGGAGTTG 57.602 33.333 0.00 0.00 32.85 3.16
152 153 8.082242 GCACTAATGAACTTTGTAATTGGAGTT 58.918 33.333 0.00 0.00 35.22 3.01
153 154 7.230510 TGCACTAATGAACTTTGTAATTGGAGT 59.769 33.333 0.00 0.00 0.00 3.85
154 155 7.592938 TGCACTAATGAACTTTGTAATTGGAG 58.407 34.615 0.00 0.00 0.00 3.86
159 164 6.714810 TCCACTGCACTAATGAACTTTGTAAT 59.285 34.615 0.00 0.00 0.00 1.89
173 178 3.068732 GCATCTCATAGTCCACTGCACTA 59.931 47.826 0.00 0.00 0.00 2.74
174 179 2.158986 GCATCTCATAGTCCACTGCACT 60.159 50.000 0.00 0.00 0.00 4.40
212 217 2.877786 TGCATCTGAGTTCTCGCAAAAA 59.122 40.909 0.00 0.00 0.00 1.94
213 218 2.493035 TGCATCTGAGTTCTCGCAAAA 58.507 42.857 0.00 0.00 0.00 2.44
214 219 2.168326 TGCATCTGAGTTCTCGCAAA 57.832 45.000 0.00 0.00 0.00 3.68
215 220 1.800586 GTTGCATCTGAGTTCTCGCAA 59.199 47.619 8.12 8.12 37.05 4.85
216 221 1.270252 TGTTGCATCTGAGTTCTCGCA 60.270 47.619 0.00 0.00 0.00 5.10
217 222 1.432514 TGTTGCATCTGAGTTCTCGC 58.567 50.000 0.00 0.00 0.00 5.03
218 223 7.649370 ATTATATGTTGCATCTGAGTTCTCG 57.351 36.000 0.00 0.00 0.00 4.04
234 239 9.624373 ACGACGAAGGGAGTATATATTATATGT 57.376 33.333 0.00 0.00 0.00 2.29
244 249 9.265901 GCTATATTATACGACGAAGGGAGTATA 57.734 37.037 0.00 0.00 32.71 1.47
245 250 7.772292 TGCTATATTATACGACGAAGGGAGTAT 59.228 37.037 0.00 0.00 34.58 2.12
246 251 7.105588 TGCTATATTATACGACGAAGGGAGTA 58.894 38.462 0.00 0.00 0.00 2.59
247 252 5.942236 TGCTATATTATACGACGAAGGGAGT 59.058 40.000 0.00 0.00 0.00 3.85
248 253 6.432607 TGCTATATTATACGACGAAGGGAG 57.567 41.667 0.00 0.00 0.00 4.30
249 254 8.510243 TTATGCTATATTATACGACGAAGGGA 57.490 34.615 0.00 0.00 0.00 4.20
250 255 9.577110 TTTTATGCTATATTATACGACGAAGGG 57.423 33.333 0.00 0.00 0.00 3.95
269 274 4.334443 CGTGTGTGTAGCATCTTTTATGC 58.666 43.478 1.74 1.74 44.85 3.14
278 283 4.575885 ACTAAAATCCGTGTGTGTAGCAT 58.424 39.130 0.00 0.00 0.00 3.79
285 290 7.874016 TCTGTGTATAAACTAAAATCCGTGTGT 59.126 33.333 0.00 0.00 0.00 3.72
287 292 8.092687 AGTCTGTGTATAAACTAAAATCCGTGT 58.907 33.333 0.00 0.00 0.00 4.49
288 293 8.475331 AGTCTGTGTATAAACTAAAATCCGTG 57.525 34.615 0.00 0.00 0.00 4.94
298 303 8.809468 TGTGAGAGATAGTCTGTGTATAAACT 57.191 34.615 0.00 0.00 34.71 2.66
299 304 9.856488 TTTGTGAGAGATAGTCTGTGTATAAAC 57.144 33.333 0.00 0.00 34.71 2.01
301 306 9.856488 GTTTTGTGAGAGATAGTCTGTGTATAA 57.144 33.333 0.00 0.00 34.71 0.98
302 307 8.182227 CGTTTTGTGAGAGATAGTCTGTGTATA 58.818 37.037 0.00 0.00 34.71 1.47
303 308 7.030165 CGTTTTGTGAGAGATAGTCTGTGTAT 58.970 38.462 0.00 0.00 34.71 2.29
304 309 6.379386 CGTTTTGTGAGAGATAGTCTGTGTA 58.621 40.000 0.00 0.00 34.71 2.90
306 311 4.090642 GCGTTTTGTGAGAGATAGTCTGTG 59.909 45.833 0.00 0.00 34.71 3.66
313 318 7.981789 AGATATTTCTGCGTTTTGTGAGAGATA 59.018 33.333 0.00 0.00 0.00 1.98
314 319 6.820656 AGATATTTCTGCGTTTTGTGAGAGAT 59.179 34.615 0.00 0.00 0.00 2.75
315 320 6.166279 AGATATTTCTGCGTTTTGTGAGAGA 58.834 36.000 0.00 0.00 0.00 3.10
316 321 6.091305 TGAGATATTTCTGCGTTTTGTGAGAG 59.909 38.462 0.00 0.00 30.30 3.20
317 322 5.931724 TGAGATATTTCTGCGTTTTGTGAGA 59.068 36.000 0.00 0.00 30.30 3.27
318 323 6.091305 TCTGAGATATTTCTGCGTTTTGTGAG 59.909 38.462 0.00 0.00 30.30 3.51
319 324 5.931724 TCTGAGATATTTCTGCGTTTTGTGA 59.068 36.000 0.00 0.00 30.30 3.58
320 325 6.169419 TCTGAGATATTTCTGCGTTTTGTG 57.831 37.500 0.00 0.00 30.30 3.33
321 326 6.801539 TTCTGAGATATTTCTGCGTTTTGT 57.198 33.333 0.00 0.00 30.30 2.83
322 327 8.679288 AAATTCTGAGATATTTCTGCGTTTTG 57.321 30.769 0.00 0.00 30.30 2.44
323 328 9.132521 CAAAATTCTGAGATATTTCTGCGTTTT 57.867 29.630 0.00 3.32 30.30 2.43
324 329 7.756722 CCAAAATTCTGAGATATTTCTGCGTTT 59.243 33.333 0.00 0.00 30.30 3.60
325 330 7.253422 CCAAAATTCTGAGATATTTCTGCGTT 58.747 34.615 0.00 0.00 30.30 4.84
326 331 6.678900 GCCAAAATTCTGAGATATTTCTGCGT 60.679 38.462 0.00 0.00 30.30 5.24
327 332 5.684626 GCCAAAATTCTGAGATATTTCTGCG 59.315 40.000 0.00 0.00 30.30 5.18
328 333 5.981915 GGCCAAAATTCTGAGATATTTCTGC 59.018 40.000 0.00 8.14 30.30 4.26
329 334 7.104043 TGGCCAAAATTCTGAGATATTTCTG 57.896 36.000 0.61 0.00 30.30 3.02
330 335 7.783596 AGATGGCCAAAATTCTGAGATATTTCT 59.216 33.333 10.96 0.00 33.88 2.52
331 336 7.949434 AGATGGCCAAAATTCTGAGATATTTC 58.051 34.615 10.96 0.00 0.00 2.17
332 337 7.562454 TGAGATGGCCAAAATTCTGAGATATTT 59.438 33.333 10.96 0.00 0.00 1.40
333 338 7.014038 GTGAGATGGCCAAAATTCTGAGATATT 59.986 37.037 10.96 0.00 0.00 1.28
334 339 6.489361 GTGAGATGGCCAAAATTCTGAGATAT 59.511 38.462 10.96 0.00 0.00 1.63
335 340 5.824624 GTGAGATGGCCAAAATTCTGAGATA 59.175 40.000 10.96 0.00 0.00 1.98
336 341 4.643784 GTGAGATGGCCAAAATTCTGAGAT 59.356 41.667 10.96 0.00 0.00 2.75
337 342 4.012374 GTGAGATGGCCAAAATTCTGAGA 58.988 43.478 10.96 0.00 0.00 3.27
338 343 4.015084 AGTGAGATGGCCAAAATTCTGAG 58.985 43.478 10.96 0.00 0.00 3.35
339 344 3.760151 CAGTGAGATGGCCAAAATTCTGA 59.240 43.478 10.96 0.00 0.00 3.27
340 345 3.760151 TCAGTGAGATGGCCAAAATTCTG 59.240 43.478 10.96 16.02 0.00 3.02
341 346 4.038271 TCAGTGAGATGGCCAAAATTCT 57.962 40.909 10.96 8.20 0.00 2.40
342 347 4.789012 TTCAGTGAGATGGCCAAAATTC 57.211 40.909 10.96 1.72 0.00 2.17
343 348 7.270047 CAATATTCAGTGAGATGGCCAAAATT 58.730 34.615 10.96 0.00 0.00 1.82
344 349 6.684613 GCAATATTCAGTGAGATGGCCAAAAT 60.685 38.462 10.96 0.00 0.00 1.82
345 350 5.394443 GCAATATTCAGTGAGATGGCCAAAA 60.394 40.000 10.96 0.00 0.00 2.44
346 351 4.098349 GCAATATTCAGTGAGATGGCCAAA 59.902 41.667 10.96 0.00 0.00 3.28
347 352 3.633525 GCAATATTCAGTGAGATGGCCAA 59.366 43.478 10.96 0.00 0.00 4.52
348 353 3.117776 AGCAATATTCAGTGAGATGGCCA 60.118 43.478 8.56 8.56 0.00 5.36
349 354 3.484407 AGCAATATTCAGTGAGATGGCC 58.516 45.455 11.17 0.00 0.00 5.36
350 355 5.511234 AAAGCAATATTCAGTGAGATGGC 57.489 39.130 7.95 7.95 0.00 4.40
351 356 8.442632 TCTTAAAGCAATATTCAGTGAGATGG 57.557 34.615 0.00 0.00 0.00 3.51
381 389 6.649141 TGCGTAATTGTGAGAGATAGTTTTGT 59.351 34.615 0.00 0.00 0.00 2.83
405 413 5.684184 CCATGCGTGTTTGATGATATTTCTG 59.316 40.000 4.96 0.00 0.00 3.02
406 414 5.357878 ACCATGCGTGTTTGATGATATTTCT 59.642 36.000 4.96 0.00 0.00 2.52
408 416 5.125257 TGACCATGCGTGTTTGATGATATTT 59.875 36.000 4.96 0.00 0.00 1.40
429 437 0.609406 GGTTCTCCCCCAAGCTTGAC 60.609 60.000 28.05 15.02 0.00 3.18
430 438 1.767692 GGTTCTCCCCCAAGCTTGA 59.232 57.895 28.05 6.71 0.00 3.02
431 439 1.675641 CGGTTCTCCCCCAAGCTTG 60.676 63.158 19.93 19.93 0.00 4.01
432 440 2.757077 CGGTTCTCCCCCAAGCTT 59.243 61.111 0.00 0.00 0.00 3.74
433 441 3.330720 CCGGTTCTCCCCCAAGCT 61.331 66.667 0.00 0.00 0.00 3.74
434 442 1.342672 TATCCGGTTCTCCCCCAAGC 61.343 60.000 0.00 0.00 0.00 4.01
447 466 4.116961 TCGTATTTGCAGAGTTTATCCGG 58.883 43.478 0.00 0.00 0.00 5.14
449 468 4.318121 CGCTCGTATTTGCAGAGTTTATCC 60.318 45.833 2.31 0.00 34.69 2.59
451 470 3.001330 GCGCTCGTATTTGCAGAGTTTAT 59.999 43.478 0.00 0.00 34.69 1.40
452 471 2.347452 GCGCTCGTATTTGCAGAGTTTA 59.653 45.455 0.00 0.00 34.69 2.01
453 472 1.128692 GCGCTCGTATTTGCAGAGTTT 59.871 47.619 0.00 0.00 34.69 2.66
454 473 0.721718 GCGCTCGTATTTGCAGAGTT 59.278 50.000 0.00 0.00 34.69 3.01
455 474 1.413767 CGCGCTCGTATTTGCAGAGT 61.414 55.000 5.56 0.00 34.69 3.24
456 475 1.270968 CGCGCTCGTATTTGCAGAG 59.729 57.895 5.56 0.00 35.28 3.35
457 476 2.798501 GCGCGCTCGTATTTGCAGA 61.799 57.895 26.67 0.00 38.14 4.26
458 477 2.350091 GCGCGCTCGTATTTGCAG 60.350 61.111 26.67 0.00 38.14 4.41
459 478 4.203542 CGCGCGCTCGTATTTGCA 62.204 61.111 30.48 0.00 38.14 4.08
509 532 2.753043 TCCTCGCCGGTACTCCAC 60.753 66.667 1.90 0.00 0.00 4.02
511 534 1.318158 TTTCTCCTCGCCGGTACTCC 61.318 60.000 1.90 0.00 0.00 3.85
520 547 1.588861 GACACGCTATTTTCTCCTCGC 59.411 52.381 0.00 0.00 0.00 5.03
566 593 7.201652 GCTTTCTTCAGTCTTTGTGTTTACTCT 60.202 37.037 0.00 0.00 0.00 3.24
613 640 4.664150 ATCTTTTCCAACCTTTTGCGAA 57.336 36.364 0.00 0.00 0.00 4.70
615 642 4.367450 TCAATCTTTTCCAACCTTTTGCG 58.633 39.130 0.00 0.00 0.00 4.85
617 644 7.201635 CCAGTTTCAATCTTTTCCAACCTTTTG 60.202 37.037 0.00 0.00 0.00 2.44
624 651 4.037446 CGGTCCAGTTTCAATCTTTTCCAA 59.963 41.667 0.00 0.00 0.00 3.53
625 652 3.568007 CGGTCCAGTTTCAATCTTTTCCA 59.432 43.478 0.00 0.00 0.00 3.53
629 656 1.535462 CGCGGTCCAGTTTCAATCTTT 59.465 47.619 0.00 0.00 0.00 2.52
705 742 2.171940 GAAAGCTCAGTGCACGCG 59.828 61.111 12.01 3.53 45.94 6.01
714 751 4.408821 ATGGCCGCGGAAAGCTCA 62.409 61.111 33.48 16.08 45.59 4.26
774 818 4.389374 AGAAGTTGAAATCAAGGAGCGAA 58.611 39.130 0.00 0.00 36.39 4.70
847 1426 1.971167 GGTTGGTTGGATGCGCTCA 60.971 57.895 9.73 1.22 0.00 4.26
851 1430 3.584406 TTAAATGGTTGGTTGGATGCG 57.416 42.857 0.00 0.00 0.00 4.73
852 1431 3.684305 GCTTTAAATGGTTGGTTGGATGC 59.316 43.478 0.00 0.00 0.00 3.91
855 1434 5.242838 CAGTAGCTTTAAATGGTTGGTTGGA 59.757 40.000 0.00 0.00 0.00 3.53
859 1438 4.148838 TGCAGTAGCTTTAAATGGTTGGT 58.851 39.130 0.00 0.00 42.74 3.67
916 1527 1.149401 CCCCTTAGGCCTTAGCTGC 59.851 63.158 12.58 0.00 39.73 5.25
920 1531 0.470341 GCTGTCCCCTTAGGCCTTAG 59.530 60.000 12.58 12.23 34.51 2.18
921 1532 0.986550 GGCTGTCCCCTTAGGCCTTA 60.987 60.000 12.58 0.00 39.68 2.69
922 1533 2.309504 GGCTGTCCCCTTAGGCCTT 61.310 63.158 12.58 0.00 39.68 4.35
923 1534 2.692741 GGCTGTCCCCTTAGGCCT 60.693 66.667 11.78 11.78 39.68 5.19
924 1535 2.150014 TTTGGCTGTCCCCTTAGGCC 62.150 60.000 0.00 0.00 42.73 5.19
925 1536 0.251608 TTTTGGCTGTCCCCTTAGGC 60.252 55.000 0.00 0.00 39.67 3.93
926 1537 1.545841 GTTTTGGCTGTCCCCTTAGG 58.454 55.000 0.00 0.00 0.00 2.69
975 1587 0.802607 CGCTCTAGTTCCGAACTGGC 60.803 60.000 21.78 19.46 42.84 4.85
986 1598 1.522569 GGCATGGTTCCGCTCTAGT 59.477 57.895 0.00 0.00 0.00 2.57
1083 1699 4.802051 GGGCTGGCAGGCGATGAA 62.802 66.667 31.29 0.00 42.43 2.57
1228 1880 9.234827 CAGGATATGATTGCCTAAATTACATGA 57.765 33.333 0.00 0.00 0.00 3.07
1232 1887 7.693969 AGCAGGATATGATTGCCTAAATTAC 57.306 36.000 0.00 0.00 38.58 1.89
1277 2057 0.607620 ACCCCCAACAATTCATTGCG 59.392 50.000 0.00 0.00 41.38 4.85
1611 3040 7.452880 TGCTGCTCAAAAGATTTTACATACT 57.547 32.000 0.00 0.00 0.00 2.12
1903 3343 8.682936 TTTTTGGATGGAGAGAGAATATTAGC 57.317 34.615 0.00 0.00 0.00 3.09
1911 3351 6.418101 CCACTTATTTTTGGATGGAGAGAGA 58.582 40.000 0.00 0.00 34.46 3.10
1912 3352 5.067023 GCCACTTATTTTTGGATGGAGAGAG 59.933 44.000 0.00 0.00 34.46 3.20
1913 3353 4.949856 GCCACTTATTTTTGGATGGAGAGA 59.050 41.667 0.00 0.00 34.46 3.10
1914 3354 4.201950 CGCCACTTATTTTTGGATGGAGAG 60.202 45.833 0.00 0.00 34.46 3.20
1915 3355 3.694072 CGCCACTTATTTTTGGATGGAGA 59.306 43.478 0.00 0.00 34.46 3.71
1917 3357 3.426615 ACGCCACTTATTTTTGGATGGA 58.573 40.909 0.00 0.00 34.46 3.41
1919 3359 4.804108 TCAACGCCACTTATTTTTGGATG 58.196 39.130 0.00 0.00 34.46 3.51
1920 3360 5.418840 AGATCAACGCCACTTATTTTTGGAT 59.581 36.000 0.00 0.00 34.46 3.41
1922 3362 5.059404 AGATCAACGCCACTTATTTTTGG 57.941 39.130 0.00 0.00 35.81 3.28
1923 3363 6.842163 ACTAGATCAACGCCACTTATTTTTG 58.158 36.000 0.00 0.00 0.00 2.44
1924 3364 8.556213 TTACTAGATCAACGCCACTTATTTTT 57.444 30.769 0.00 0.00 0.00 1.94
1925 3365 8.556213 TTTACTAGATCAACGCCACTTATTTT 57.444 30.769 0.00 0.00 0.00 1.82
1926 3366 8.448615 GTTTTACTAGATCAACGCCACTTATTT 58.551 33.333 0.00 0.00 0.00 1.40
1927 3367 7.822822 AGTTTTACTAGATCAACGCCACTTATT 59.177 33.333 0.00 0.00 0.00 1.40
1928 3368 7.328737 AGTTTTACTAGATCAACGCCACTTAT 58.671 34.615 0.00 0.00 0.00 1.73
1929 3369 6.694447 AGTTTTACTAGATCAACGCCACTTA 58.306 36.000 0.00 0.00 0.00 2.24
1930 3370 5.548406 AGTTTTACTAGATCAACGCCACTT 58.452 37.500 0.00 0.00 0.00 3.16
1931 3371 5.148651 AGTTTTACTAGATCAACGCCACT 57.851 39.130 0.00 0.00 0.00 4.00
1932 3372 5.857822 AAGTTTTACTAGATCAACGCCAC 57.142 39.130 0.00 0.00 0.00 5.01
1933 3373 5.761234 ACAAAGTTTTACTAGATCAACGCCA 59.239 36.000 0.00 0.00 0.00 5.69
1934 3374 6.237313 ACAAAGTTTTACTAGATCAACGCC 57.763 37.500 0.00 0.00 0.00 5.68
1935 3375 8.015409 AGTACAAAGTTTTACTAGATCAACGC 57.985 34.615 0.00 0.00 0.00 4.84
1992 3432 9.790297 ACAATCATATATACTACTCCCTCCATT 57.210 33.333 0.00 0.00 0.00 3.16
1994 3434 8.177456 ACACAATCATATATACTACTCCCTCCA 58.823 37.037 0.00 0.00 0.00 3.86
2029 3469 0.326264 AACCTCCTGTCACTGCATCC 59.674 55.000 0.00 0.00 0.00 3.51
2051 3491 4.063998 AGCTTTGCTTTTGAAAGAAGGG 57.936 40.909 7.63 0.00 33.89 3.95
2101 3552 0.257039 GACATCCCTCATGGCCTGTT 59.743 55.000 3.32 0.00 33.74 3.16
2331 5118 3.366273 CGCATGCACCTCAATGTAAGTTT 60.366 43.478 19.57 0.00 0.00 2.66
2473 5260 3.971245 AACTTCTCTTCGATCTTGGCT 57.029 42.857 0.00 0.00 0.00 4.75
2872 5680 4.278310 ACACAAGTTTGTAGGCCTCTTTT 58.722 39.130 9.68 0.00 39.91 2.27
2875 5683 4.273148 CTACACAAGTTTGTAGGCCTCT 57.727 45.455 9.68 0.00 43.63 3.69
3073 5891 5.359009 CACATTGGCCATGACTATTTCTTCT 59.641 40.000 6.09 0.00 36.24 2.85
3508 6338 1.409064 CATCAGGAAGCGGCTACACTA 59.591 52.381 1.35 0.00 0.00 2.74
3514 6344 2.437359 GCACATCAGGAAGCGGCT 60.437 61.111 0.00 0.00 0.00 5.52
3605 6435 1.568504 AATCTGGGACGAGGCTACAA 58.431 50.000 0.00 0.00 0.00 2.41
3606 6436 1.568504 AAATCTGGGACGAGGCTACA 58.431 50.000 0.00 0.00 0.00 2.74
3607 6437 2.280628 CAAAATCTGGGACGAGGCTAC 58.719 52.381 0.00 0.00 0.00 3.58
3700 6532 5.278463 GCCACACTCTACATTTCACAAACAT 60.278 40.000 0.00 0.00 0.00 2.71
3711 6543 0.615331 CCCACAGCCACACTCTACAT 59.385 55.000 0.00 0.00 0.00 2.29
3822 6654 4.970860 AACATGCCTAGAGCTATGTGAT 57.029 40.909 15.09 5.47 40.23 3.06
3848 6680 4.522789 GCAGAAAATGTTTGAAGACCCCTA 59.477 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.