Multiple sequence alignment - TraesCS3A01G038000

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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 TraesCS3A01G038000 chr3A 100.000 4512 0 0 1 4512 20549680 20545169 0.000000e+00 8333.0
1 TraesCS3A01G038000 chr3A 80.018 1111 187 30 2415 3512 20557867 20556779 0.000000e+00 789.0
2 TraesCS3A01G038000 chr3A 96.573 321 11 0 4192 4512 20521756 20521436 2.390000e-147 532.0
3 TraesCS3A01G038000 chr3B 91.874 2449 115 42 1420 3848 23019840 23022224 0.000000e+00 3343.0
4 TraesCS3A01G038000 chr3B 92.239 1224 66 10 225 1430 23018553 23019765 0.000000e+00 1707.0
5 TraesCS3A01G038000 chr3B 80.331 1027 173 24 2415 3428 22916697 22917707 0.000000e+00 750.0
6 TraesCS3A01G038000 chr3B 88.462 442 35 3 4072 4498 23023140 23023580 1.860000e-143 520.0
7 TraesCS3A01G038000 chr3B 86.585 164 8 2 1 164 23017516 23017665 7.760000e-38 169.0
8 TraesCS3A01G038000 chr3D 92.318 1549 69 18 2270 3797 15966297 15964778 0.000000e+00 2156.0
9 TraesCS3A01G038000 chr3D 89.992 1219 67 17 220 1430 15968386 15967215 0.000000e+00 1524.0
10 TraesCS3A01G038000 chr3D 91.481 763 58 7 1420 2176 15967113 15966352 0.000000e+00 1042.0
11 TraesCS3A01G038000 chr3D 79.838 1111 189 30 2415 3512 15976736 15975648 0.000000e+00 778.0
12 TraesCS3A01G038000 chr3D 86.096 187 11 4 1 176 15969403 15969221 2.140000e-43 187.0
13 TraesCS3A01G038000 chr5D 78.398 986 195 14 2448 3422 498172940 498171962 3.830000e-175 625.0
14 TraesCS3A01G038000 chr5D 77.198 978 214 8 2451 3422 498290465 498289491 3.050000e-156 562.0
15 TraesCS3A01G038000 chr1B 88.475 295 24 4 2867 3152 683135772 683136065 9.290000e-92 348.0
16 TraesCS3A01G038000 chr1D 90.189 265 19 4 2914 3172 460610805 460611068 5.590000e-89 339.0
17 TraesCS3A01G038000 chr1D 86.829 205 12 5 3086 3278 489958049 489957848 9.830000e-52 215.0
18 TraesCS3A01G038000 chr1D 84.659 176 17 4 3164 3333 490256623 490256452 2.790000e-37 167.0
19 TraesCS3A01G038000 chr1D 87.805 123 11 2 3156 3278 489987665 489987547 1.690000e-29 141.0
20 TraesCS3A01G038000 chr1D 82.222 90 10 3 2329 2413 490256961 490256873 6.260000e-09 73.1


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 TraesCS3A01G038000 chr3A 20545169 20549680 4511 True 8333.00 8333 100.00000 1 4512 1 chr3A.!!$R2 4511
1 TraesCS3A01G038000 chr3A 20556779 20557867 1088 True 789.00 789 80.01800 2415 3512 1 chr3A.!!$R3 1097
2 TraesCS3A01G038000 chr3B 23017516 23023580 6064 False 1434.75 3343 89.79000 1 4498 4 chr3B.!!$F2 4497
3 TraesCS3A01G038000 chr3B 22916697 22917707 1010 False 750.00 750 80.33100 2415 3428 1 chr3B.!!$F1 1013
4 TraesCS3A01G038000 chr3D 15964778 15969403 4625 True 1227.25 2156 89.97175 1 3797 4 chr3D.!!$R2 3796
5 TraesCS3A01G038000 chr3D 15975648 15976736 1088 True 778.00 778 79.83800 2415 3512 1 chr3D.!!$R1 1097
6 TraesCS3A01G038000 chr5D 498171962 498172940 978 True 625.00 625 78.39800 2448 3422 1 chr5D.!!$R1 974
7 TraesCS3A01G038000 chr5D 498289491 498290465 974 True 562.00 562 77.19800 2451 3422 1 chr5D.!!$R2 971

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
329 1327 0.605319 CACATGTGTACGGGCTGGTT 60.605 55.0 18.03 0.0 0.00 3.67 F
330 1328 0.605319 ACATGTGTACGGGCTGGTTG 60.605 55.0 0.00 0.0 0.00 3.77 F
1459 2592 0.797249 GCGCTTGCAATGAAGCTCAG 60.797 55.0 0.00 0.0 45.26 3.35 F
2267 3407 0.521242 GCGCGCGACAGATTTTTGAT 60.521 50.0 37.18 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 2627 0.462581 GTCAGCTTCATGGCGATGGA 60.463 55.000 8.98 0.0 37.29 3.41 R
2082 3215 3.007920 CCTGAGGTGCCTGAGCCT 61.008 66.667 0.00 0.0 38.69 4.58 R
2338 3487 3.119849 GCAGCCAACACGTAGAAAATGAT 60.120 43.478 0.00 0.0 0.00 2.45 R
3623 4786 0.178891 ACTCATAGCCCCGATCCCAT 60.179 55.000 0.00 0.0 0.00 4.00 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
142 154 4.700213 CCGACTTTTACTCCAAATGGTGAT 59.300 41.667 8.41 0.00 36.34 3.06
155 167 3.827008 ATGGTGATACGCTCTGTTCAT 57.173 42.857 0.00 0.00 0.00 2.57
164 176 7.222805 GTGATACGCTCTGTTCATATTTCTTGA 59.777 37.037 0.00 0.00 0.00 3.02
165 177 7.763985 TGATACGCTCTGTTCATATTTCTTGAA 59.236 33.333 0.00 0.00 0.00 2.69
166 178 6.414408 ACGCTCTGTTCATATTTCTTGAAG 57.586 37.500 0.00 0.00 33.95 3.02
167 179 5.934625 ACGCTCTGTTCATATTTCTTGAAGT 59.065 36.000 0.00 0.00 33.95 3.01
169 181 7.602644 ACGCTCTGTTCATATTTCTTGAAGTAA 59.397 33.333 0.00 0.00 33.95 2.24
170 182 8.113062 CGCTCTGTTCATATTTCTTGAAGTAAG 58.887 37.037 0.00 0.00 33.95 2.34
171 183 9.155975 GCTCTGTTCATATTTCTTGAAGTAAGA 57.844 33.333 0.00 0.00 43.53 2.10
173 185 9.658799 TCTGTTCATATTTCTTGAAGTAAGAGG 57.341 33.333 0.00 0.00 45.66 3.69
174 186 9.658799 CTGTTCATATTTCTTGAAGTAAGAGGA 57.341 33.333 0.00 0.00 45.66 3.71
175 187 9.658799 TGTTCATATTTCTTGAAGTAAGAGGAG 57.341 33.333 0.00 0.00 45.66 3.69
176 188 9.877178 GTTCATATTTCTTGAAGTAAGAGGAGA 57.123 33.333 0.00 0.00 45.66 3.71
178 190 8.700051 TCATATTTCTTGAAGTAAGAGGAGAGG 58.300 37.037 0.00 0.00 45.66 3.69
179 191 8.700051 CATATTTCTTGAAGTAAGAGGAGAGGA 58.300 37.037 0.00 0.00 45.66 3.71
181 193 5.263872 TCTTGAAGTAAGAGGAGAGGAGT 57.736 43.478 0.00 0.00 40.43 3.85
184 196 7.415086 TCTTGAAGTAAGAGGAGAGGAGTTAT 58.585 38.462 0.00 0.00 40.43 1.89
185 197 7.340743 TCTTGAAGTAAGAGGAGAGGAGTTATG 59.659 40.741 0.00 0.00 40.43 1.90
186 198 6.494952 TGAAGTAAGAGGAGAGGAGTTATGT 58.505 40.000 0.00 0.00 0.00 2.29
187 199 6.954684 TGAAGTAAGAGGAGAGGAGTTATGTT 59.045 38.462 0.00 0.00 0.00 2.71
188 200 8.114102 TGAAGTAAGAGGAGAGGAGTTATGTTA 58.886 37.037 0.00 0.00 0.00 2.41
189 201 8.896722 AAGTAAGAGGAGAGGAGTTATGTTAA 57.103 34.615 0.00 0.00 0.00 2.01
190 202 8.896722 AGTAAGAGGAGAGGAGTTATGTTAAA 57.103 34.615 0.00 0.00 0.00 1.52
191 203 9.322769 AGTAAGAGGAGAGGAGTTATGTTAAAA 57.677 33.333 0.00 0.00 0.00 1.52
192 204 9.939802 GTAAGAGGAGAGGAGTTATGTTAAAAA 57.060 33.333 0.00 0.00 0.00 1.94
230 1227 6.719370 AGTCCTCTTGCTATAGGAGTATCTTG 59.281 42.308 7.93 0.00 42.57 3.02
233 1230 7.666388 TCCTCTTGCTATAGGAGTATCTTGTAC 59.334 40.741 1.04 0.00 36.97 2.90
287 1285 4.550577 TGTGTCAAAAGCACATGTGTAG 57.449 40.909 26.01 12.10 41.32 2.74
304 1302 5.502079 TGTGTAGTTCAAAAGAACTCCCAA 58.498 37.500 13.54 0.00 43.56 4.12
327 1325 2.398554 GCACATGTGTACGGGCTGG 61.399 63.158 26.01 0.00 0.00 4.85
328 1326 1.003839 CACATGTGTACGGGCTGGT 60.004 57.895 18.03 0.00 0.00 4.00
329 1327 0.605319 CACATGTGTACGGGCTGGTT 60.605 55.000 18.03 0.00 0.00 3.67
330 1328 0.605319 ACATGTGTACGGGCTGGTTG 60.605 55.000 0.00 0.00 0.00 3.77
331 1329 1.674322 ATGTGTACGGGCTGGTTGC 60.674 57.895 0.00 0.00 41.94 4.17
332 1330 2.032071 GTGTACGGGCTGGTTGCT 59.968 61.111 0.00 0.00 42.39 3.91
333 1331 1.294138 GTGTACGGGCTGGTTGCTA 59.706 57.895 0.00 0.00 42.39 3.49
335 1333 1.189524 TGTACGGGCTGGTTGCTACT 61.190 55.000 0.00 0.00 42.39 2.57
565 1565 7.885922 TGACCTAGATGATAGATCAACCTACTC 59.114 40.741 0.00 0.00 40.69 2.59
719 1719 2.484062 CCGAGATTGGCCATGGCAC 61.484 63.158 36.56 25.50 44.11 5.01
771 1771 2.282180 TTCGGCCACCTTTCTGCC 60.282 61.111 2.24 0.00 41.85 4.85
822 1822 5.947228 AACTGACAGACCAACATAACATG 57.053 39.130 10.08 0.00 0.00 3.21
831 1831 7.092891 ACAGACCAACATAACATGGATCTAGAA 60.093 37.037 0.00 0.00 39.12 2.10
834 1834 7.275920 ACCAACATAACATGGATCTAGAACTC 58.724 38.462 0.00 0.00 39.12 3.01
839 1839 2.292016 ACATGGATCTAGAACTCGCTCG 59.708 50.000 0.00 0.00 0.00 5.03
888 1888 3.051803 TCTCATCCCTCCTCACTTACCAT 60.052 47.826 0.00 0.00 0.00 3.55
896 1896 4.003648 CTCCTCACTTACCATCCAAACAC 58.996 47.826 0.00 0.00 0.00 3.32
919 1919 2.228925 TCATAGCAGCAGCAACAACAA 58.771 42.857 3.17 0.00 45.49 2.83
920 1920 2.030893 TCATAGCAGCAGCAACAACAAC 60.031 45.455 3.17 0.00 45.49 3.32
921 1921 1.387539 TAGCAGCAGCAACAACAACA 58.612 45.000 3.17 0.00 45.49 3.33
962 1966 4.489795 CGCTGCGCACACATCGAC 62.490 66.667 5.66 0.00 31.08 4.20
963 1967 4.489795 GCTGCGCACACATCGACG 62.490 66.667 5.66 0.00 0.00 5.12
974 1979 1.443702 CATCGACGCGTGGTTGAGA 60.444 57.895 20.70 6.53 42.31 3.27
987 1992 1.336980 GGTTGAGAGACGTTGTCCCTC 60.337 57.143 1.95 1.95 37.81 4.30
994 1999 2.431942 CGTTGTCCCTCCGGTTCG 60.432 66.667 0.00 0.00 0.00 3.95
1012 2017 1.349627 GTCGACATGGCATTCGCTG 59.650 57.895 19.99 5.54 38.60 5.18
1045 2054 5.654317 CATGTTGTCATGTCTATCTGCTC 57.346 43.478 0.00 0.00 44.37 4.26
1046 2055 5.358090 CATGTTGTCATGTCTATCTGCTCT 58.642 41.667 0.00 0.00 44.37 4.09
1100 2109 1.977293 GCCAAGGCCTAGTCTCCTGG 61.977 65.000 5.16 9.73 32.00 4.45
1113 2122 3.097614 GTCTCCTGGCTGGTCTAGTTTA 58.902 50.000 10.44 0.00 37.07 2.01
1185 2194 2.255406 TGGCATGGGCTTTATGTGTTT 58.745 42.857 0.00 0.00 40.87 2.83
1217 2239 5.644636 TGTTGGTATCGTCCCTGTAAATTTC 59.355 40.000 0.00 0.00 0.00 2.17
1239 2261 5.747565 TCAGTAGATTTTGTCGCAAACTTG 58.252 37.500 4.80 0.00 0.00 3.16
1241 2263 5.848036 CAGTAGATTTTGTCGCAAACTTGAG 59.152 40.000 4.80 0.00 0.00 3.02
1276 2298 0.895100 TTGCTGGACAAGATGTGGGC 60.895 55.000 0.00 0.00 33.24 5.36
1286 2308 1.289160 AGATGTGGGCTCCAAGCTAA 58.711 50.000 0.00 0.00 41.99 3.09
1299 2321 4.784177 TCCAAGCTAATCATGCATCTTCA 58.216 39.130 0.00 0.00 0.00 3.02
1317 2339 2.329614 ATCCGCCGGTTGTTTTCCG 61.330 57.895 1.63 0.00 46.49 4.30
1383 2405 6.816134 AGCTAGCGATCGATATGATATGAT 57.184 37.500 21.57 0.00 37.47 2.45
1386 2408 8.611757 AGCTAGCGATCGATATGATATGATATC 58.388 37.037 21.57 11.07 37.47 1.63
1414 2436 5.278266 CCCAACAAGAATCGTTACACATGTT 60.278 40.000 0.00 0.00 0.00 2.71
1418 2440 5.758296 ACAAGAATCGTTACACATGTTGTCT 59.242 36.000 0.00 0.00 39.91 3.41
1459 2592 0.797249 GCGCTTGCAATGAAGCTCAG 60.797 55.000 0.00 0.00 45.26 3.35
1491 2624 1.910772 AGCAGCACGGAGGAAGAGT 60.911 57.895 0.00 0.00 0.00 3.24
1494 2627 1.604023 AGCACGGAGGAAGAGTCGT 60.604 57.895 0.00 0.00 36.19 4.34
1604 2737 2.604686 TCCTGCTCGGAGTTGGCT 60.605 61.111 6.90 0.00 36.69 4.75
1791 2924 2.359230 GCCTATGCCGGGAGATGC 60.359 66.667 2.18 1.87 0.00 3.91
2082 3215 2.032634 GCCGTGGACAAGATCGCAA 61.033 57.895 0.00 0.00 0.00 4.85
2119 3252 2.593257 GAAGAAGACGGACAAGGTACG 58.407 52.381 0.00 0.00 46.43 3.67
2132 3265 2.678836 CAAGGTACGTGTGACCAAACAA 59.321 45.455 8.64 0.00 39.65 2.83
2133 3266 2.557317 AGGTACGTGTGACCAAACAAG 58.443 47.619 8.64 0.00 39.65 3.16
2136 3269 3.127376 GGTACGTGTGACCAAACAAGTTT 59.873 43.478 0.00 0.00 41.87 2.66
2139 3272 2.914214 CGTGTGACCAAACAAGTTTGTG 59.086 45.455 20.50 15.15 46.19 3.33
2140 3273 3.610585 CGTGTGACCAAACAAGTTTGTGT 60.611 43.478 20.50 17.55 46.19 3.72
2144 3283 7.422399 GTGTGACCAAACAAGTTTGTGTATAT 58.578 34.615 20.50 3.29 46.19 0.86
2145 3284 7.589954 GTGTGACCAAACAAGTTTGTGTATATC 59.410 37.037 20.50 10.63 46.19 1.63
2147 3286 8.132362 GTGACCAAACAAGTTTGTGTATATCAA 58.868 33.333 20.50 0.00 46.19 2.57
2206 3345 8.770438 TTGTTTTGAAACTTTTGAATGCTAGT 57.230 26.923 7.97 0.00 39.59 2.57
2207 3346 8.770438 TGTTTTGAAACTTTTGAATGCTAGTT 57.230 26.923 7.97 0.00 39.59 2.24
2208 3347 9.213799 TGTTTTGAAACTTTTGAATGCTAGTTT 57.786 25.926 7.97 0.00 41.93 2.66
2209 3348 9.476761 GTTTTGAAACTTTTGAATGCTAGTTTG 57.523 29.630 0.00 0.00 40.00 2.93
2210 3349 8.994429 TTTGAAACTTTTGAATGCTAGTTTGA 57.006 26.923 0.00 0.00 40.00 2.69
2211 3350 8.994429 TTGAAACTTTTGAATGCTAGTTTGAA 57.006 26.923 0.00 0.00 40.00 2.69
2212 3351 8.994429 TGAAACTTTTGAATGCTAGTTTGAAA 57.006 26.923 0.00 0.00 40.00 2.69
2213 3352 8.868916 TGAAACTTTTGAATGCTAGTTTGAAAC 58.131 29.630 0.00 0.00 40.00 2.78
2214 3353 9.087424 GAAACTTTTGAATGCTAGTTTGAAACT 57.913 29.630 15.57 15.57 45.40 2.66
2215 3354 9.435688 AAACTTTTGAATGCTAGTTTGAAACTT 57.564 25.926 16.49 0.00 42.81 2.66
2216 3355 9.435688 AACTTTTGAATGCTAGTTTGAAACTTT 57.564 25.926 16.49 4.14 42.81 2.66
2217 3356 8.872845 ACTTTTGAATGCTAGTTTGAAACTTTG 58.127 29.630 16.49 10.56 42.81 2.77
2218 3357 8.770438 TTTTGAATGCTAGTTTGAAACTTTGT 57.230 26.923 16.49 0.00 42.81 2.83
2219 3358 7.985634 TTGAATGCTAGTTTGAAACTTTGTC 57.014 32.000 16.49 7.70 42.81 3.18
2220 3359 7.094508 TGAATGCTAGTTTGAAACTTTGTCA 57.905 32.000 16.49 9.95 42.81 3.58
2221 3360 6.972328 TGAATGCTAGTTTGAAACTTTGTCAC 59.028 34.615 16.49 5.64 42.81 3.67
2222 3361 5.888691 TGCTAGTTTGAAACTTTGTCACA 57.111 34.783 16.49 3.54 42.81 3.58
2223 3362 5.879237 TGCTAGTTTGAAACTTTGTCACAG 58.121 37.500 16.49 6.64 42.81 3.66
2224 3363 5.163663 TGCTAGTTTGAAACTTTGTCACAGG 60.164 40.000 16.49 0.00 42.81 4.00
2225 3364 5.065988 GCTAGTTTGAAACTTTGTCACAGGA 59.934 40.000 16.49 0.00 42.81 3.86
2226 3365 5.975693 AGTTTGAAACTTTGTCACAGGAA 57.024 34.783 4.45 0.00 39.04 3.36
2227 3366 6.530019 AGTTTGAAACTTTGTCACAGGAAT 57.470 33.333 4.45 0.00 39.04 3.01
2265 3405 3.352536 GCGCGCGACAGATTTTTG 58.647 55.556 37.18 0.00 0.00 2.44
2266 3406 1.154488 GCGCGCGACAGATTTTTGA 60.154 52.632 37.18 0.00 0.00 2.69
2267 3407 0.521242 GCGCGCGACAGATTTTTGAT 60.521 50.000 37.18 0.00 0.00 2.57
2268 3408 1.174352 CGCGCGACAGATTTTTGATG 58.826 50.000 28.94 0.00 0.00 3.07
2318 3458 1.135024 CGCATGCAAAAACTATGGCCT 60.135 47.619 19.57 0.00 0.00 5.19
2319 3459 2.273557 GCATGCAAAAACTATGGCCTG 58.726 47.619 14.21 0.00 0.00 4.85
2322 3471 1.690893 TGCAAAAACTATGGCCTGCAA 59.309 42.857 9.37 0.00 36.89 4.08
2593 3746 2.166664 GGAGAACGAGCTCAAGTGGTAT 59.833 50.000 15.40 0.00 36.62 2.73
3518 4674 3.529533 GACATGAACCTCTGATGGTGAG 58.470 50.000 0.00 0.00 40.73 3.51
3537 4693 4.373116 CCACTCCACACCGACGGG 62.373 72.222 20.00 9.81 40.11 5.28
3557 4713 1.227943 TCCTTGCTCTTGCGTTGCT 60.228 52.632 0.00 0.00 43.34 3.91
3594 4757 2.804421 CGTGGACATGTACGTACGTA 57.196 50.000 23.60 23.60 35.70 3.57
3608 4771 2.724690 CGTACGTACTCCAGCATATTGC 59.275 50.000 22.55 0.00 45.46 3.56
3614 4777 4.321974 CGTACTCCAGCATATTGCCTATGA 60.322 45.833 7.40 0.00 46.52 2.15
3615 4778 4.283363 ACTCCAGCATATTGCCTATGAG 57.717 45.455 7.40 0.75 46.52 2.90
3619 4782 6.669591 ACTCCAGCATATTGCCTATGAGTATA 59.330 38.462 7.40 0.00 46.52 1.47
3621 4784 8.782137 TCCAGCATATTGCCTATGAGTATATA 57.218 34.615 7.40 0.00 46.52 0.86
3622 4785 9.384849 TCCAGCATATTGCCTATGAGTATATAT 57.615 33.333 7.40 0.00 46.52 0.86
3634 4797 7.561722 CCTATGAGTATATATATGGGATCGGGG 59.438 44.444 5.44 0.00 0.00 5.73
3635 4798 5.084519 TGAGTATATATATGGGATCGGGGC 58.915 45.833 5.44 0.00 0.00 5.80
3637 4800 6.046286 TGAGTATATATATGGGATCGGGGCTA 59.954 42.308 5.44 0.00 0.00 3.93
3715 4880 3.570926 TGATTCAGACTCACACGTACC 57.429 47.619 0.00 0.00 0.00 3.34
3777 4947 7.094592 TGCAGTAAATAAATGTGGATTTGTCGA 60.095 33.333 0.00 0.00 33.63 4.20
3797 4967 4.031028 CGATTTACCGTGTTACTCCTACG 58.969 47.826 0.00 0.00 37.55 3.51
3809 4979 3.870633 ACTCCTACGAGCAAGGTTAAG 57.129 47.619 0.00 0.00 40.03 1.85
3818 4988 3.609409 CGAGCAAGGTTAAGAACAAAGCC 60.609 47.826 0.00 0.00 0.00 4.35
3819 4989 2.628178 AGCAAGGTTAAGAACAAAGCCC 59.372 45.455 0.00 0.00 0.00 5.19
3857 5027 2.597510 GCCACGGCACCCTCTTTT 60.598 61.111 2.36 0.00 41.49 2.27
3858 5028 2.919494 GCCACGGCACCCTCTTTTG 61.919 63.158 2.36 0.00 41.49 2.44
3859 5029 1.528309 CCACGGCACCCTCTTTTGT 60.528 57.895 0.00 0.00 0.00 2.83
3860 5030 1.106944 CCACGGCACCCTCTTTTGTT 61.107 55.000 0.00 0.00 0.00 2.83
3861 5031 0.744281 CACGGCACCCTCTTTTGTTT 59.256 50.000 0.00 0.00 0.00 2.83
3862 5032 1.136110 CACGGCACCCTCTTTTGTTTT 59.864 47.619 0.00 0.00 0.00 2.43
3863 5033 1.136110 ACGGCACCCTCTTTTGTTTTG 59.864 47.619 0.00 0.00 0.00 2.44
3864 5034 1.136110 CGGCACCCTCTTTTGTTTTGT 59.864 47.619 0.00 0.00 0.00 2.83
3866 5036 2.935849 GGCACCCTCTTTTGTTTTGTTG 59.064 45.455 0.00 0.00 0.00 3.33
3867 5037 2.351418 GCACCCTCTTTTGTTTTGTTGC 59.649 45.455 0.00 0.00 0.00 4.17
3874 5579 5.096443 TCTTTTGTTTTGTTGCCCTCAAT 57.904 34.783 0.00 0.00 34.29 2.57
3885 5590 1.836802 TGCCCTCAATTAAATTGGCCC 59.163 47.619 0.00 0.00 40.61 5.80
3895 5600 7.563906 TCAATTAAATTGGCCCCTATTTCTTG 58.436 34.615 0.00 13.03 40.61 3.02
3898 5603 5.619132 AAATTGGCCCCTATTTCTTGATG 57.381 39.130 0.00 0.00 28.32 3.07
3902 5607 2.297701 GCCCCTATTTCTTGATGCGAA 58.702 47.619 0.00 0.00 0.00 4.70
3905 5610 4.557496 GCCCCTATTTCTTGATGCGAATTC 60.557 45.833 0.00 0.00 0.00 2.17
3907 5612 4.319766 CCCTATTTCTTGATGCGAATTCGG 60.320 45.833 27.78 11.16 40.23 4.30
3913 5618 4.661125 TCTTGATGCGAATTCGGAATTTG 58.339 39.130 25.86 21.35 44.19 2.32
3929 5634 0.306533 TTTGACGTTCTTTGGCTCGC 59.693 50.000 0.00 0.00 0.00 5.03
3940 5645 1.852942 TTGGCTCGCTCGATTCATAC 58.147 50.000 0.00 0.00 0.00 2.39
3947 5652 2.850060 TCGCTCGATTCATACGAACAAC 59.150 45.455 0.00 0.00 39.23 3.32
3948 5653 2.596862 CGCTCGATTCATACGAACAACA 59.403 45.455 0.00 0.00 39.23 3.33
3963 5668 4.452114 CGAACAACACAGATCCAATTCTGA 59.548 41.667 8.36 0.00 44.88 3.27
3965 5670 6.313658 CGAACAACACAGATCCAATTCTGATA 59.686 38.462 8.36 0.00 44.88 2.15
3968 5673 9.685276 AACAACACAGATCCAATTCTGATAATA 57.315 29.630 8.36 0.00 44.88 0.98
4004 5709 4.932146 ACGACTTTGGGAAAATGACTTTG 58.068 39.130 0.00 0.00 0.00 2.77
4007 5712 5.449862 CGACTTTGGGAAAATGACTTTGTCA 60.450 40.000 2.77 2.77 46.90 3.58
4008 5713 5.660460 ACTTTGGGAAAATGACTTTGTCAC 58.340 37.500 2.31 0.00 45.65 3.67
4009 5714 5.422012 ACTTTGGGAAAATGACTTTGTCACT 59.578 36.000 2.31 0.00 45.65 3.41
4010 5715 5.514274 TTGGGAAAATGACTTTGTCACTC 57.486 39.130 2.31 1.19 45.65 3.51
4011 5716 4.792068 TGGGAAAATGACTTTGTCACTCT 58.208 39.130 2.31 0.00 45.65 3.24
4012 5717 4.821805 TGGGAAAATGACTTTGTCACTCTC 59.178 41.667 2.31 1.83 45.65 3.20
4013 5718 4.216472 GGGAAAATGACTTTGTCACTCTCC 59.784 45.833 2.31 8.39 45.65 3.71
4014 5719 4.083802 GGAAAATGACTTTGTCACTCTCCG 60.084 45.833 2.31 0.00 45.65 4.63
4018 5723 3.653344 TGACTTTGTCACTCTCCGAATG 58.347 45.455 0.00 0.00 37.67 2.67
4021 5726 0.389817 TTGTCACTCTCCGAATGGCG 60.390 55.000 0.00 0.00 40.47 5.69
4024 5729 0.606096 TCACTCTCCGAATGGCGAAA 59.394 50.000 0.00 0.00 44.57 3.46
4026 5731 2.429250 TCACTCTCCGAATGGCGAAATA 59.571 45.455 0.00 0.00 44.57 1.40
4041 5746 2.489329 CGAAATATGGGGCATGGATGTC 59.511 50.000 0.00 0.00 0.00 3.06
4055 5760 2.659428 GGATGTCCTCCATTCTTTGGG 58.341 52.381 0.00 0.00 46.45 4.12
4056 5761 2.242196 GGATGTCCTCCATTCTTTGGGA 59.758 50.000 0.00 0.00 46.45 4.37
4057 5762 3.309121 GGATGTCCTCCATTCTTTGGGAA 60.309 47.826 0.00 0.00 46.45 3.97
4058 5763 3.893753 TGTCCTCCATTCTTTGGGAAA 57.106 42.857 0.00 0.00 46.45 3.13
4059 5764 4.191804 TGTCCTCCATTCTTTGGGAAAA 57.808 40.909 0.00 0.00 46.45 2.29
4060 5765 4.551671 TGTCCTCCATTCTTTGGGAAAAA 58.448 39.130 0.00 0.00 46.45 1.94
4114 5981 4.158394 CCATTGGTCAAACAGGTGATAAGG 59.842 45.833 0.00 0.00 0.00 2.69
4128 5995 5.242393 AGGTGATAAGGAAATACATGCATGC 59.758 40.000 26.53 11.82 0.00 4.06
4152 6019 6.624423 GCCTTATAAACCGGAAAAGAAGGAAC 60.624 42.308 23.05 9.56 35.27 3.62
4174 6041 4.462483 ACAGTAATTAAGTTGGTGCATGGG 59.538 41.667 0.00 0.00 0.00 4.00
4175 6042 4.462483 CAGTAATTAAGTTGGTGCATGGGT 59.538 41.667 0.00 0.00 0.00 4.51
4176 6043 3.959535 AATTAAGTTGGTGCATGGGTG 57.040 42.857 0.00 0.00 0.00 4.61
4199 6066 4.412207 CCTTTTAAATAGAGTTGGTGCGC 58.588 43.478 0.00 0.00 0.00 6.09
4210 6077 0.320334 TTGGTGCGCGAGAGATTCAA 60.320 50.000 12.10 0.60 0.00 2.69
4234 6116 3.665745 AACTTGGATCAAACATGCCAC 57.334 42.857 0.00 0.00 0.00 5.01
4244 6126 5.999205 TCAAACATGCCACAAGGAAATAT 57.001 34.783 0.00 0.00 36.89 1.28
4247 6129 4.724074 ACATGCCACAAGGAAATATGTG 57.276 40.909 0.00 0.00 45.06 3.21
4251 6133 3.119065 TGCCACAAGGAAATATGTGCATG 60.119 43.478 0.00 0.00 44.32 4.06
4262 6144 7.287466 AGGAAATATGTGCATGCCTTATAAACA 59.713 33.333 16.68 11.27 0.00 2.83
4263 6145 8.090214 GGAAATATGTGCATGCCTTATAAACAT 58.910 33.333 16.68 17.56 32.11 2.71
4325 6207 5.183713 CCTTTCAAATAGAGTTGGTGCATGA 59.816 40.000 0.00 0.00 0.00 3.07
4326 6208 5.885230 TTCAAATAGAGTTGGTGCATGAG 57.115 39.130 0.00 0.00 0.00 2.90
4343 6225 5.356190 TGCATGAGAGATTCAAGATCAAACC 59.644 40.000 0.00 0.00 39.77 3.27
4344 6226 5.589452 GCATGAGAGATTCAAGATCAAACCT 59.411 40.000 0.00 0.00 39.77 3.50
4345 6227 6.458478 GCATGAGAGATTCAAGATCAAACCTG 60.458 42.308 0.00 0.00 39.77 4.00
4386 6268 3.319198 GTGGAGCCGAGAACCCCA 61.319 66.667 0.00 0.00 0.00 4.96
4396 6278 2.228822 CCGAGAACCCCAAGTTTGATTG 59.771 50.000 0.00 0.00 39.40 2.67
4401 6283 2.397597 ACCCCAAGTTTGATTGTTGCT 58.602 42.857 0.00 0.00 0.00 3.91
4403 6285 2.289010 CCCCAAGTTTGATTGTTGCTCC 60.289 50.000 0.00 0.00 0.00 4.70
4459 6341 7.335127 ACATAGGAACATATGGGATTTAGCT 57.665 36.000 7.80 0.00 37.45 3.32
4473 6355 5.422145 GGATTTAGCTTTGCCATTTGATGT 58.578 37.500 0.00 0.00 0.00 3.06
4486 6368 4.630940 CCATTTGATGTGTTTGGTATTGGC 59.369 41.667 0.00 0.00 0.00 4.52
4491 6373 0.453782 GTGTTTGGTATTGGCGCGTC 60.454 55.000 2.29 2.29 0.00 5.19
4498 6380 1.399727 GGTATTGGCGCGTCATTATGC 60.400 52.381 16.97 9.84 0.00 3.14
4499 6381 1.262950 GTATTGGCGCGTCATTATGCA 59.737 47.619 16.97 0.00 37.49 3.96
4500 6382 0.953727 ATTGGCGCGTCATTATGCAT 59.046 45.000 16.97 3.79 37.49 3.96
4501 6383 0.029167 TTGGCGCGTCATTATGCATG 59.971 50.000 16.97 0.00 37.49 4.06
4502 6384 1.094650 TGGCGCGTCATTATGCATGT 61.095 50.000 10.57 0.00 37.49 3.21
4503 6385 0.658244 GGCGCGTCATTATGCATGTG 60.658 55.000 5.47 8.49 37.49 3.21
4504 6386 0.027979 GCGCGTCATTATGCATGTGT 59.972 50.000 10.16 0.00 37.49 3.72
4505 6387 1.917252 GCGCGTCATTATGCATGTGTC 60.917 52.381 10.16 5.38 37.49 3.67
4506 6388 1.654501 CGCGTCATTATGCATGTGTCG 60.655 52.381 20.46 20.46 37.49 4.35
4507 6389 1.592543 GCGTCATTATGCATGTGTCGA 59.407 47.619 25.32 8.99 37.58 4.20
4508 6390 2.347939 GCGTCATTATGCATGTGTCGAG 60.348 50.000 25.32 9.42 37.58 4.04
4509 6391 3.115554 CGTCATTATGCATGTGTCGAGA 58.884 45.455 20.27 4.45 34.06 4.04
4510 6392 3.060940 CGTCATTATGCATGTGTCGAGAC 60.061 47.826 20.27 5.61 34.06 3.36
4511 6393 3.060940 GTCATTATGCATGTGTCGAGACG 60.061 47.826 10.16 0.00 34.06 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.733988 CGAGCTAATGAAGAGCCGTACAA 60.734 47.826 0.00 0.00 41.06 2.41
18 22 3.019933 GGCCTACGAGCTAATGAAGAG 57.980 52.381 0.00 0.00 0.00 2.85
112 124 3.581755 TGGAGTAAAAGTCGGTCAATCG 58.418 45.455 0.00 0.00 0.00 3.34
116 128 4.069304 CCATTTGGAGTAAAAGTCGGTCA 58.931 43.478 0.00 0.00 37.39 4.02
117 129 4.070009 ACCATTTGGAGTAAAAGTCGGTC 58.930 43.478 3.01 0.00 38.94 4.79
118 130 3.818773 CACCATTTGGAGTAAAAGTCGGT 59.181 43.478 3.01 0.00 38.94 4.69
119 131 4.069304 TCACCATTTGGAGTAAAAGTCGG 58.931 43.478 3.01 0.00 38.94 4.79
142 154 7.097192 ACTTCAAGAAATATGAACAGAGCGTA 58.903 34.615 0.00 0.00 33.47 4.42
155 167 7.896496 ACTCCTCTCCTCTTACTTCAAGAAATA 59.104 37.037 0.00 0.00 42.76 1.40
164 176 8.896722 TTAACATAACTCCTCTCCTCTTACTT 57.103 34.615 0.00 0.00 0.00 2.24
165 177 8.896722 TTTAACATAACTCCTCTCCTCTTACT 57.103 34.615 0.00 0.00 0.00 2.24
166 178 9.939802 TTTTTAACATAACTCCTCTCCTCTTAC 57.060 33.333 0.00 0.00 0.00 2.34
218 230 4.868268 AGCCACTGTACAAGATACTCCTA 58.132 43.478 0.00 0.00 0.00 2.94
220 232 4.645588 ACTAGCCACTGTACAAGATACTCC 59.354 45.833 0.00 0.00 0.00 3.85
221 233 5.583495 CACTAGCCACTGTACAAGATACTC 58.417 45.833 0.00 0.00 0.00 2.59
230 1227 2.457366 AGTTGCACTAGCCACTGTAC 57.543 50.000 0.00 0.00 44.25 2.90
233 1230 2.611518 GTCTAGTTGCACTAGCCACTG 58.388 52.381 14.76 0.05 45.93 3.66
253 1250 7.007367 GTGCTTTTGACACATGATAATTGTACG 59.993 37.037 0.00 0.00 37.96 3.67
304 1302 1.000717 GCCCGTACACATGTGCTTTTT 60.001 47.619 25.68 8.44 0.00 1.94
310 1308 0.605319 AACCAGCCCGTACACATGTG 60.605 55.000 24.25 24.25 0.00 3.21
327 1325 3.186613 GTGCACAACTTAGGAGTAGCAAC 59.813 47.826 13.17 0.00 38.86 4.17
328 1326 3.181459 TGTGCACAACTTAGGAGTAGCAA 60.181 43.478 19.28 0.00 38.86 3.91
329 1327 2.367241 TGTGCACAACTTAGGAGTAGCA 59.633 45.455 19.28 0.00 36.55 3.49
330 1328 3.040147 TGTGCACAACTTAGGAGTAGC 57.960 47.619 19.28 0.00 34.21 3.58
332 1330 9.976511 GTATTATATGTGCACAACTTAGGAGTA 57.023 33.333 25.72 8.59 34.21 2.59
333 1331 7.652105 CGTATTATATGTGCACAACTTAGGAGT 59.348 37.037 25.72 6.31 37.87 3.85
335 1333 7.650504 GTCGTATTATATGTGCACAACTTAGGA 59.349 37.037 25.72 17.23 0.00 2.94
544 1544 6.494952 GGGGAGTAGGTTGATCTATCATCTA 58.505 44.000 0.00 0.00 36.56 1.98
545 1545 5.337788 GGGGAGTAGGTTGATCTATCATCT 58.662 45.833 0.00 0.00 36.56 2.90
546 1546 4.468153 GGGGGAGTAGGTTGATCTATCATC 59.532 50.000 0.00 0.00 36.56 2.92
547 1547 4.430441 GGGGGAGTAGGTTGATCTATCAT 58.570 47.826 0.00 0.00 36.56 2.45
548 1548 3.754172 CGGGGGAGTAGGTTGATCTATCA 60.754 52.174 0.00 0.00 34.44 2.15
549 1549 2.826725 CGGGGGAGTAGGTTGATCTATC 59.173 54.545 0.00 0.00 0.00 2.08
719 1719 4.242602 GGGAATGAAAGCTCCCCG 57.757 61.111 0.00 0.00 45.03 5.73
822 1822 0.039888 GGCGAGCGAGTTCTAGATCC 60.040 60.000 0.00 0.00 0.00 3.36
831 1831 2.755650 CAATTTATAGGGCGAGCGAGT 58.244 47.619 0.00 0.00 0.00 4.18
834 1834 0.517316 GGCAATTTATAGGGCGAGCG 59.483 55.000 0.00 0.00 0.00 5.03
839 1839 1.963515 CAGGGTGGCAATTTATAGGGC 59.036 52.381 0.00 0.00 0.00 5.19
888 1888 2.290832 TGCTGCTATGATGGTGTTTGGA 60.291 45.455 0.00 0.00 0.00 3.53
896 1896 1.385528 TGTTGCTGCTGCTATGATGG 58.614 50.000 17.00 0.00 40.48 3.51
919 1919 0.455972 GTGTGCGTTGTTGTTGCTGT 60.456 50.000 0.00 0.00 0.00 4.40
920 1920 1.462871 CGTGTGCGTTGTTGTTGCTG 61.463 55.000 0.00 0.00 0.00 4.41
921 1921 1.226267 CGTGTGCGTTGTTGTTGCT 60.226 52.632 0.00 0.00 0.00 3.91
962 1966 1.660575 AACGTCTCTCAACCACGCG 60.661 57.895 3.53 3.53 37.02 6.01
963 1967 0.874607 ACAACGTCTCTCAACCACGC 60.875 55.000 0.00 0.00 37.02 5.34
964 1968 1.129326 GACAACGTCTCTCAACCACG 58.871 55.000 0.00 0.00 39.48 4.94
987 1992 3.186047 GCCATGTCGACGAACCGG 61.186 66.667 11.62 0.00 0.00 5.28
994 1999 1.083806 TCAGCGAATGCCATGTCGAC 61.084 55.000 9.11 9.11 44.31 4.20
1088 2097 0.032615 AGACCAGCCAGGAGACTAGG 60.033 60.000 0.00 0.00 40.21 3.02
1100 2109 7.496529 TTGCAATCATATAAACTAGACCAGC 57.503 36.000 0.00 0.00 0.00 4.85
1113 2122 7.140705 CGTGAACATTGGTATTGCAATCATAT 58.859 34.615 16.86 2.96 0.00 1.78
1185 2194 1.527736 GACGATACCAACACGCAACAA 59.472 47.619 0.00 0.00 0.00 2.83
1217 2239 5.747565 TCAAGTTTGCGACAAAATCTACTG 58.252 37.500 6.59 2.60 0.00 2.74
1239 2261 2.097250 GCAAATTCACGCAAAACTGCTC 60.097 45.455 0.00 0.00 0.00 4.26
1241 2263 1.860326 AGCAAATTCACGCAAAACTGC 59.140 42.857 0.00 0.00 0.00 4.40
1276 2298 4.820173 TGAAGATGCATGATTAGCTTGGAG 59.180 41.667 2.46 0.00 0.00 3.86
1286 2308 1.531423 GGCGGATGAAGATGCATGAT 58.469 50.000 2.46 0.00 0.00 2.45
1299 2321 2.329614 CGGAAAACAACCGGCGGAT 61.330 57.895 35.78 20.37 45.65 4.18
1317 2339 7.094205 TGGCTTTAAAGAAGGAACTGATTGATC 60.094 37.037 19.48 0.00 40.86 2.92
1383 2405 4.771114 ACGATTCTTGTTGGGGATGATA 57.229 40.909 0.00 0.00 0.00 2.15
1386 2408 4.006989 TGTAACGATTCTTGTTGGGGATG 58.993 43.478 0.00 0.00 0.00 3.51
1414 2436 2.588596 CCTGCACACGCACAGACA 60.589 61.111 0.00 0.00 45.36 3.41
1418 2440 3.519973 CTCCTCCTGCACACGCACA 62.520 63.158 0.00 0.00 45.36 4.57
1437 2570 1.804326 GCTTCATTGCAAGCGCCAG 60.804 57.895 2.29 0.00 39.55 4.85
1491 2624 1.521457 GCTTCATGGCGATGGACGA 60.521 57.895 8.98 0.00 45.77 4.20
1494 2627 0.462581 GTCAGCTTCATGGCGATGGA 60.463 55.000 8.98 0.00 37.29 3.41
1613 2746 4.632974 GATGCCCAGCCGCCTAGG 62.633 72.222 3.67 3.67 44.97 3.02
2082 3215 3.007920 CCTGAGGTGCCTGAGCCT 61.008 66.667 0.00 0.00 38.69 4.58
2119 3252 3.908213 ACACAAACTTGTTTGGTCACAC 58.092 40.909 24.25 0.00 39.91 3.82
2180 3319 9.213799 ACTAGCATTCAAAAGTTTCAAAACAAA 57.786 25.926 8.23 0.00 41.30 2.83
2181 3320 8.770438 ACTAGCATTCAAAAGTTTCAAAACAA 57.230 26.923 8.23 0.00 41.30 2.83
2182 3321 8.770438 AACTAGCATTCAAAAGTTTCAAAACA 57.230 26.923 8.23 0.00 41.30 2.83
2183 3322 9.476761 CAAACTAGCATTCAAAAGTTTCAAAAC 57.523 29.630 0.00 0.00 39.50 2.43
2186 3325 8.994429 TTCAAACTAGCATTCAAAAGTTTCAA 57.006 26.923 0.00 0.00 39.50 2.69
2187 3326 8.868916 GTTTCAAACTAGCATTCAAAAGTTTCA 58.131 29.630 0.00 0.00 39.50 2.69
2188 3327 9.087424 AGTTTCAAACTAGCATTCAAAAGTTTC 57.913 29.630 0.00 0.00 39.50 2.78
2189 3328 9.435688 AAGTTTCAAACTAGCATTCAAAAGTTT 57.564 25.926 2.38 0.00 41.91 2.66
2190 3329 9.435688 AAAGTTTCAAACTAGCATTCAAAAGTT 57.564 25.926 2.38 0.00 41.91 2.66
2191 3330 8.872845 CAAAGTTTCAAACTAGCATTCAAAAGT 58.127 29.630 2.38 0.00 41.91 2.66
2192 3331 8.872845 ACAAAGTTTCAAACTAGCATTCAAAAG 58.127 29.630 2.38 0.00 41.91 2.27
2195 3334 7.487829 GTGACAAAGTTTCAAACTAGCATTCAA 59.512 33.333 2.38 0.00 41.91 2.69
2196 3335 6.972328 GTGACAAAGTTTCAAACTAGCATTCA 59.028 34.615 2.38 0.09 41.91 2.57
2197 3336 6.972328 TGTGACAAAGTTTCAAACTAGCATTC 59.028 34.615 2.38 0.00 41.91 2.67
2198 3337 6.862209 TGTGACAAAGTTTCAAACTAGCATT 58.138 32.000 2.38 0.00 41.91 3.56
2199 3338 6.449635 TGTGACAAAGTTTCAAACTAGCAT 57.550 33.333 2.38 0.00 41.91 3.79
2200 3339 5.163663 CCTGTGACAAAGTTTCAAACTAGCA 60.164 40.000 2.38 0.00 41.91 3.49
2201 3340 5.065988 TCCTGTGACAAAGTTTCAAACTAGC 59.934 40.000 2.38 0.00 41.91 3.42
2203 3342 7.639113 ATTCCTGTGACAAAGTTTCAAACTA 57.361 32.000 2.38 0.00 41.91 2.24
2204 3343 5.975693 TTCCTGTGACAAAGTTTCAAACT 57.024 34.783 0.00 0.00 45.46 2.66
2206 3345 8.690884 TCATTATTCCTGTGACAAAGTTTCAAA 58.309 29.630 0.00 0.00 0.00 2.69
2207 3346 8.134895 GTCATTATTCCTGTGACAAAGTTTCAA 58.865 33.333 0.00 0.00 41.35 2.69
2208 3347 7.284261 TGTCATTATTCCTGTGACAAAGTTTCA 59.716 33.333 5.07 0.00 46.45 2.69
2209 3348 7.648142 TGTCATTATTCCTGTGACAAAGTTTC 58.352 34.615 5.07 0.00 46.45 2.78
2210 3349 7.581213 TGTCATTATTCCTGTGACAAAGTTT 57.419 32.000 5.07 0.00 46.45 2.66
2217 3356 5.368145 TGCCTATGTCATTATTCCTGTGAC 58.632 41.667 0.00 0.00 41.90 3.67
2218 3357 5.628797 TGCCTATGTCATTATTCCTGTGA 57.371 39.130 0.00 0.00 0.00 3.58
2219 3358 5.589855 TGTTGCCTATGTCATTATTCCTGTG 59.410 40.000 0.00 0.00 0.00 3.66
2220 3359 5.754782 TGTTGCCTATGTCATTATTCCTGT 58.245 37.500 0.00 0.00 0.00 4.00
2221 3360 6.487668 TCATGTTGCCTATGTCATTATTCCTG 59.512 38.462 0.00 0.00 0.00 3.86
2222 3361 6.488006 GTCATGTTGCCTATGTCATTATTCCT 59.512 38.462 0.00 0.00 0.00 3.36
2223 3362 6.566564 CGTCATGTTGCCTATGTCATTATTCC 60.567 42.308 0.00 0.00 0.00 3.01
2224 3363 6.365839 CGTCATGTTGCCTATGTCATTATTC 58.634 40.000 0.00 0.00 0.00 1.75
2225 3364 5.277974 GCGTCATGTTGCCTATGTCATTATT 60.278 40.000 0.00 0.00 0.00 1.40
2226 3365 4.214119 GCGTCATGTTGCCTATGTCATTAT 59.786 41.667 0.00 0.00 0.00 1.28
2227 3366 3.559655 GCGTCATGTTGCCTATGTCATTA 59.440 43.478 0.00 0.00 0.00 1.90
2254 3394 8.219105 GCAATTCTGTTTCATCAAAAATCTGTC 58.781 33.333 0.00 0.00 0.00 3.51
2256 3396 8.078959 TGCAATTCTGTTTCATCAAAAATCTG 57.921 30.769 0.00 0.00 0.00 2.90
2257 3397 8.842358 ATGCAATTCTGTTTCATCAAAAATCT 57.158 26.923 0.00 0.00 0.00 2.40
2258 3398 9.325150 CAATGCAATTCTGTTTCATCAAAAATC 57.675 29.630 0.00 0.00 31.22 2.17
2260 3400 7.133513 GCAATGCAATTCTGTTTCATCAAAAA 58.866 30.769 0.00 0.00 31.22 1.94
2261 3401 6.260271 TGCAATGCAATTCTGTTTCATCAAAA 59.740 30.769 5.01 0.00 34.76 2.44
2262 3402 5.758784 TGCAATGCAATTCTGTTTCATCAAA 59.241 32.000 5.01 0.00 34.76 2.69
2263 3403 5.298347 TGCAATGCAATTCTGTTTCATCAA 58.702 33.333 5.01 0.00 34.76 2.57
2264 3404 4.884247 TGCAATGCAATTCTGTTTCATCA 58.116 34.783 5.01 0.00 34.76 3.07
2265 3405 6.312918 AGAATGCAATGCAATTCTGTTTCATC 59.687 34.615 22.50 6.36 43.62 2.92
2266 3406 6.170506 AGAATGCAATGCAATTCTGTTTCAT 58.829 32.000 22.50 6.78 43.62 2.57
2267 3407 5.543714 AGAATGCAATGCAATTCTGTTTCA 58.456 33.333 22.50 0.00 43.62 2.69
2268 3408 6.810182 AGTAGAATGCAATGCAATTCTGTTTC 59.190 34.615 27.21 19.00 43.62 2.78
2318 3458 5.693961 TGATTATCTAAATCCAGCCTTGCA 58.306 37.500 0.00 0.00 0.00 4.08
2319 3459 6.830873 ATGATTATCTAAATCCAGCCTTGC 57.169 37.500 0.00 0.00 0.00 4.01
2337 3486 4.615912 GCAGCCAACACGTAGAAAATGATT 60.616 41.667 0.00 0.00 0.00 2.57
2338 3487 3.119849 GCAGCCAACACGTAGAAAATGAT 60.120 43.478 0.00 0.00 0.00 2.45
2593 3746 3.166490 TTGCACCGCCTCCGTGTAA 62.166 57.895 0.00 0.00 0.00 2.41
3469 4625 3.319198 GGCTCGTCCCCCTTGTGA 61.319 66.667 0.00 0.00 0.00 3.58
3537 4693 1.576421 CAACGCAAGAGCAAGGACC 59.424 57.895 0.00 0.00 42.27 4.46
3540 4696 1.081641 CAGCAACGCAAGAGCAAGG 60.082 57.895 0.00 0.00 42.58 3.61
3557 4713 0.524414 CGTGTATCACCACCGACTCA 59.476 55.000 0.00 0.00 31.47 3.41
3594 4757 3.649981 ACTCATAGGCAATATGCTGGAGT 59.350 43.478 2.00 7.39 44.28 3.85
3608 4771 7.561722 CCCCGATCCCATATATATACTCATAGG 59.438 44.444 0.00 0.00 0.00 2.57
3614 4777 5.355670 AGCCCCGATCCCATATATATACT 57.644 43.478 0.00 0.00 0.00 2.12
3615 4778 6.895756 TCATAGCCCCGATCCCATATATATAC 59.104 42.308 0.00 0.00 0.00 1.47
3619 4782 4.163427 CTCATAGCCCCGATCCCATATAT 58.837 47.826 0.00 0.00 0.00 0.86
3621 4784 2.293184 ACTCATAGCCCCGATCCCATAT 60.293 50.000 0.00 0.00 0.00 1.78
3622 4785 1.078823 ACTCATAGCCCCGATCCCATA 59.921 52.381 0.00 0.00 0.00 2.74
3623 4786 0.178891 ACTCATAGCCCCGATCCCAT 60.179 55.000 0.00 0.00 0.00 4.00
3624 4787 0.485543 TACTCATAGCCCCGATCCCA 59.514 55.000 0.00 0.00 0.00 4.37
3635 4798 7.663905 CCCCACTATATAGCTAGCTACTCATAG 59.336 44.444 28.20 28.20 31.46 2.23
3637 4800 6.369629 CCCCACTATATAGCTAGCTACTCAT 58.630 44.000 26.41 19.99 0.00 2.90
3646 4809 2.829720 CAACGGCCCCACTATATAGCTA 59.170 50.000 9.78 0.00 0.00 3.32
3647 4810 1.623811 CAACGGCCCCACTATATAGCT 59.376 52.381 9.78 0.00 0.00 3.32
3648 4811 1.621814 TCAACGGCCCCACTATATAGC 59.378 52.381 9.78 0.00 0.00 2.97
3649 4812 3.162666 TCTCAACGGCCCCACTATATAG 58.837 50.000 8.27 8.27 0.00 1.31
3766 4936 3.666274 ACACGGTAAATCGACAAATCCA 58.334 40.909 0.00 0.00 0.00 3.41
3777 4947 4.439289 GCTCGTAGGAGTAACACGGTAAAT 60.439 45.833 13.65 0.00 42.53 1.40
3797 4967 3.305403 GGGCTTTGTTCTTAACCTTGCTC 60.305 47.826 0.00 0.00 0.00 4.26
3818 4988 0.973632 TGGTATATACCCAGCAGCGG 59.026 55.000 25.90 0.00 45.87 5.52
3819 4989 2.831685 TTGGTATATACCCAGCAGCG 57.168 50.000 25.90 0.00 45.87 5.18
3848 5018 2.093181 GGGCAACAAAACAAAAGAGGGT 60.093 45.455 0.00 0.00 39.74 4.34
3849 5019 2.170397 AGGGCAACAAAACAAAAGAGGG 59.830 45.455 0.00 0.00 39.74 4.30
3850 5020 3.118811 TGAGGGCAACAAAACAAAAGAGG 60.119 43.478 0.00 0.00 39.74 3.69
3851 5021 4.122143 TGAGGGCAACAAAACAAAAGAG 57.878 40.909 0.00 0.00 39.74 2.85
3852 5022 4.543590 TTGAGGGCAACAAAACAAAAGA 57.456 36.364 0.00 0.00 39.74 2.52
3853 5023 5.816449 AATTGAGGGCAACAAAACAAAAG 57.184 34.783 0.29 0.00 36.72 2.27
3854 5024 7.687941 TTTAATTGAGGGCAACAAAACAAAA 57.312 28.000 0.00 0.00 36.72 2.44
3855 5025 7.872113 ATTTAATTGAGGGCAACAAAACAAA 57.128 28.000 0.00 2.64 36.72 2.83
3856 5026 7.201767 CCAATTTAATTGAGGGCAACAAAACAA 60.202 33.333 18.13 0.00 42.83 2.83
3857 5027 6.261826 CCAATTTAATTGAGGGCAACAAAACA 59.738 34.615 18.13 0.00 42.83 2.83
3858 5028 6.667370 CCAATTTAATTGAGGGCAACAAAAC 58.333 36.000 18.13 0.00 42.83 2.43
3859 5029 5.240403 GCCAATTTAATTGAGGGCAACAAAA 59.760 36.000 18.13 0.00 42.83 2.44
3860 5030 4.759183 GCCAATTTAATTGAGGGCAACAAA 59.241 37.500 18.13 0.00 42.83 2.83
3861 5031 4.322567 GCCAATTTAATTGAGGGCAACAA 58.677 39.130 18.13 0.00 42.83 2.83
3862 5032 3.307339 GGCCAATTTAATTGAGGGCAACA 60.307 43.478 18.13 0.00 42.83 3.33
3863 5033 3.270027 GGCCAATTTAATTGAGGGCAAC 58.730 45.455 18.13 0.00 42.83 4.17
3864 5034 2.238395 GGGCCAATTTAATTGAGGGCAA 59.762 45.455 18.13 0.00 42.83 4.52
3866 5036 1.140852 GGGGCCAATTTAATTGAGGGC 59.859 52.381 18.13 14.08 42.83 5.19
3867 5037 2.763039 AGGGGCCAATTTAATTGAGGG 58.237 47.619 18.13 3.95 42.83 4.30
3874 5579 6.407979 GCATCAAGAAATAGGGGCCAATTTAA 60.408 38.462 14.05 4.03 0.00 1.52
3885 5590 4.511454 TCCGAATTCGCATCAAGAAATAGG 59.489 41.667 22.36 3.65 38.18 2.57
3895 5600 3.029074 CGTCAAATTCCGAATTCGCATC 58.971 45.455 22.36 4.00 38.18 3.91
3898 5603 2.520686 ACGTCAAATTCCGAATTCGC 57.479 45.000 22.36 5.12 38.18 4.70
3902 5607 4.794169 CCAAAGAACGTCAAATTCCGAAT 58.206 39.130 0.00 0.00 0.00 3.34
3905 5610 2.031157 AGCCAAAGAACGTCAAATTCCG 60.031 45.455 0.00 0.00 0.00 4.30
3907 5612 3.226347 CGAGCCAAAGAACGTCAAATTC 58.774 45.455 0.00 0.00 0.00 2.17
3913 5618 1.782181 GAGCGAGCCAAAGAACGTC 59.218 57.895 0.00 0.00 0.00 4.34
3929 5634 4.857037 TCTGTGTTGTTCGTATGAATCGAG 59.143 41.667 0.00 0.00 38.52 4.04
3940 5645 4.452114 TCAGAATTGGATCTGTGTTGTTCG 59.548 41.667 4.41 0.00 45.65 3.95
3965 5670 8.454106 CCAAAGTCGTCAAAATCAAGATCTATT 58.546 33.333 0.00 0.00 0.00 1.73
3968 5673 5.182001 CCCAAAGTCGTCAAAATCAAGATCT 59.818 40.000 0.00 0.00 0.00 2.75
3981 5686 4.830826 AAGTCATTTTCCCAAAGTCGTC 57.169 40.909 0.00 0.00 0.00 4.20
3983 5688 4.932146 ACAAAGTCATTTTCCCAAAGTCG 58.068 39.130 0.00 0.00 0.00 4.18
3984 5689 5.748630 GTGACAAAGTCATTTTCCCAAAGTC 59.251 40.000 2.90 0.00 44.63 3.01
4007 5712 3.393800 CATATTTCGCCATTCGGAGAGT 58.606 45.455 0.00 0.00 42.60 3.24
4008 5713 2.738846 CCATATTTCGCCATTCGGAGAG 59.261 50.000 0.00 0.00 42.60 3.20
4009 5714 2.549992 CCCATATTTCGCCATTCGGAGA 60.550 50.000 0.00 0.00 39.66 3.71
4010 5715 1.806542 CCCATATTTCGCCATTCGGAG 59.193 52.381 0.00 0.00 39.05 4.63
4011 5716 1.544537 CCCCATATTTCGCCATTCGGA 60.545 52.381 0.00 0.00 39.05 4.55
4012 5717 0.881118 CCCCATATTTCGCCATTCGG 59.119 55.000 0.00 0.00 39.05 4.30
4013 5718 0.240945 GCCCCATATTTCGCCATTCG 59.759 55.000 0.00 0.00 40.15 3.34
4014 5719 1.327303 TGCCCCATATTTCGCCATTC 58.673 50.000 0.00 0.00 0.00 2.67
4018 5723 0.539438 TCCATGCCCCATATTTCGCC 60.539 55.000 0.00 0.00 0.00 5.54
4021 5726 2.827921 GGACATCCATGCCCCATATTTC 59.172 50.000 0.00 0.00 35.64 2.17
4024 5729 1.637553 GAGGACATCCATGCCCCATAT 59.362 52.381 0.00 0.00 38.89 1.78
4026 5731 1.849116 GAGGACATCCATGCCCCAT 59.151 57.895 0.00 0.00 38.89 4.00
4058 5763 9.197306 AGTTATAGTCCACAGGAAAAACTTTTT 57.803 29.630 0.00 0.00 31.38 1.94
4059 5764 8.762481 AGTTATAGTCCACAGGAAAAACTTTT 57.238 30.769 0.00 0.00 31.38 2.27
4060 5765 8.762481 AAGTTATAGTCCACAGGAAAAACTTT 57.238 30.769 8.98 0.00 31.38 2.66
4091 5958 4.158394 CCTTATCACCTGTTTGACCAATGG 59.842 45.833 0.00 0.00 0.00 3.16
4104 5971 5.242393 GCATGCATGTATTTCCTTATCACCT 59.758 40.000 26.79 0.00 0.00 4.00
4114 5981 6.582295 CGGTTTATAAGGCATGCATGTATTTC 59.418 38.462 26.79 10.38 0.00 2.17
4128 5995 6.431852 TGTTCCTTCTTTTCCGGTTTATAAGG 59.568 38.462 16.50 16.50 34.79 2.69
4152 6019 4.462483 ACCCATGCACCAACTTAATTACTG 59.538 41.667 0.00 0.00 0.00 2.74
4174 6041 5.161358 GCACCAACTCTATTTAAAAGGCAC 58.839 41.667 0.00 0.00 0.00 5.01
4175 6042 4.083003 CGCACCAACTCTATTTAAAAGGCA 60.083 41.667 0.00 0.00 0.00 4.75
4176 6043 4.412207 CGCACCAACTCTATTTAAAAGGC 58.588 43.478 0.00 0.00 0.00 4.35
4178 6045 4.088648 CGCGCACCAACTCTATTTAAAAG 58.911 43.478 8.75 0.00 0.00 2.27
4181 6048 2.927477 CTCGCGCACCAACTCTATTTAA 59.073 45.455 8.75 0.00 0.00 1.52
4182 6049 2.164827 TCTCGCGCACCAACTCTATTTA 59.835 45.455 8.75 0.00 0.00 1.40
4199 6066 8.201554 TGATCCAAGTTTATTTGAATCTCTCG 57.798 34.615 0.00 0.00 0.00 4.04
4210 6077 6.165577 GTGGCATGTTTGATCCAAGTTTATT 58.834 36.000 0.00 0.00 0.00 1.40
4227 6109 3.119065 TGCACATATTTCCTTGTGGCATG 60.119 43.478 5.33 0.00 42.72 4.06
4229 6111 2.523245 TGCACATATTTCCTTGTGGCA 58.477 42.857 5.33 0.00 42.72 4.92
4234 6116 4.395959 AAGGCATGCACATATTTCCTTG 57.604 40.909 21.36 0.00 31.87 3.61
4244 6126 5.911378 TTCATGTTTATAAGGCATGCACA 57.089 34.783 21.36 13.51 39.64 4.57
4247 6129 7.975616 TCTTCTTTTCATGTTTATAAGGCATGC 59.024 33.333 9.90 9.90 39.64 4.06
4280 6162 1.204467 CGCCCATGCACCAACTAAATT 59.796 47.619 0.00 0.00 37.32 1.82
4325 6207 4.914983 TGCAGGTTTGATCTTGAATCTCT 58.085 39.130 0.00 0.00 0.00 3.10
4326 6208 5.413833 TCTTGCAGGTTTGATCTTGAATCTC 59.586 40.000 0.00 0.00 0.00 2.75
4343 6225 3.063180 GTCTCCATCGTCAATTCTTGCAG 59.937 47.826 0.00 0.00 0.00 4.41
4344 6226 3.002791 GTCTCCATCGTCAATTCTTGCA 58.997 45.455 0.00 0.00 0.00 4.08
4345 6227 2.029728 CGTCTCCATCGTCAATTCTTGC 59.970 50.000 0.00 0.00 0.00 4.01
4365 6247 2.432628 GTTCTCGGCTCCACCACG 60.433 66.667 0.00 0.00 39.03 4.94
4366 6248 2.047179 GGTTCTCGGCTCCACCAC 60.047 66.667 0.00 0.00 39.03 4.16
4386 6268 3.882888 TCTTCGGAGCAACAATCAAACTT 59.117 39.130 0.00 0.00 0.00 2.66
4401 6283 7.122204 TGAAAACATCAGTAGAGTATCTTCGGA 59.878 37.037 0.00 0.00 40.42 4.55
4428 6310 7.639113 TCCCATATGTTCCTATGTTTTTGAC 57.361 36.000 1.24 0.00 0.00 3.18
4435 6317 7.335127 AGCTAAATCCCATATGTTCCTATGT 57.665 36.000 1.24 0.00 0.00 2.29
4443 6325 4.545678 TGGCAAAGCTAAATCCCATATGT 58.454 39.130 1.24 0.00 0.00 2.29
4459 6341 4.148128 ACCAAACACATCAAATGGCAAA 57.852 36.364 0.00 0.00 34.45 3.68
4473 6355 0.885150 TGACGCGCCAATACCAAACA 60.885 50.000 5.73 0.00 0.00 2.83
4486 6368 1.654501 CGACACATGCATAATGACGCG 60.655 52.381 17.26 3.53 38.72 6.01
4491 6373 3.494309 CGTCTCGACACATGCATAATG 57.506 47.619 0.00 3.48 42.48 1.90


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

AutoCloner maintained by Alex Coulton.