Multiple sequence alignment - TraesCS6A01G146000

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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 TraesCS6A01G146000 chr6A 100.000 3118 0 0 1 3118 124310503 124313620 0.000000e+00 5758
1 TraesCS6A01G146000 chr6A 83.076 1359 172 31 828 2173 1062162 1063475 0.000000e+00 1182
2 TraesCS6A01G146000 chr6A 90.305 361 32 2 2760 3118 124426449 124426808 1.310000e-128 470
3 TraesCS6A01G146000 chr6A 90.305 361 32 2 2760 3118 124914239 124913880 1.310000e-128 470
4 TraesCS6A01G146000 chr6A 83.708 356 27 10 2309 2635 124426065 124426418 1.090000e-79 307
5 TraesCS6A01G146000 chr6D 92.874 2175 98 21 49 2185 103034315 103036470 0.000000e+00 3105
6 TraesCS6A01G146000 chr6D 97.784 361 8 0 2758 3118 103036808 103037168 9.500000e-175 623
7 TraesCS6A01G146000 chr6D 93.878 245 8 3 2309 2547 103036473 103036716 2.290000e-96 363
8 TraesCS6A01G146000 chr6D 91.057 123 11 0 2621 2743 103085330 103085452 1.920000e-37 167
9 TraesCS6A01G146000 chr6B 91.085 1088 61 17 281 1350 188695352 188696421 0.000000e+00 1439
10 TraesCS6A01G146000 chr6B 95.427 831 30 4 1350 2176 188696457 188697283 0.000000e+00 1317
11 TraesCS6A01G146000 chr6B 88.321 822 88 4 1352 2173 5101613 5102426 0.000000e+00 979
12 TraesCS6A01G146000 chr6B 80.408 490 80 10 828 1305 5101111 5101596 2.960000e-95 359
13 TraesCS6A01G146000 chr7D 89.617 366 29 4 2758 3118 169538931 169538570 1.020000e-124 457
14 TraesCS6A01G146000 chr7D 87.936 373 31 3 2758 3118 169428100 169427730 7.990000e-116 427
15 TraesCS6A01G146000 chr7D 85.154 357 21 9 2306 2635 169428481 169428130 1.390000e-88 337
16 TraesCS6A01G146000 chr7D 86.364 110 9 3 2309 2412 169482965 169482856 7.070000e-22 115
17 TraesCS6A01G146000 chrUn 88.830 376 24 3 2758 3118 82710747 82710375 2.210000e-121 446
18 TraesCS6A01G146000 chrUn 88.643 361 39 1 2760 3118 293554964 293555324 3.690000e-119 438
19 TraesCS6A01G146000 chrUn 88.643 361 39 1 2760 3118 314487726 314488086 3.690000e-119 438
20 TraesCS6A01G146000 chrUn 89.205 352 36 1 2769 3118 325381999 325381648 3.690000e-119 438
21 TraesCS6A01G146000 chrUn 91.870 123 10 0 2621 2743 218481588 218481710 4.130000e-39 172
22 TraesCS6A01G146000 chr7A 89.205 352 36 1 2769 3118 171944347 171943996 3.690000e-119 438
23 TraesCS6A01G146000 chr7A 93.130 131 9 0 2181 2311 732956111 732956241 3.170000e-45 193
24 TraesCS6A01G146000 chr7A 96.262 107 4 0 2633 2739 619573567 619573673 3.200000e-40 176
25 TraesCS6A01G146000 chr4B 77.827 672 123 16 1470 2119 6061083 6061750 2.920000e-105 392
26 TraesCS6A01G146000 chr4B 92.248 129 10 0 2183 2311 170678373 170678501 1.910000e-42 183
27 TraesCS6A01G146000 chr5D 95.312 128 6 0 2184 2311 106454597 106454724 1.470000e-48 204
28 TraesCS6A01G146000 chr2B 92.593 135 10 0 2177 2311 90047872 90047738 8.820000e-46 195
29 TraesCS6A01G146000 chr1D 92.366 131 10 0 2181 2311 138635326 138635456 1.480000e-43 187
30 TraesCS6A01G146000 chr7B 92.308 130 8 2 2183 2311 141249962 141249834 1.910000e-42 183
31 TraesCS6A01G146000 chr7B 85.366 123 13 4 2309 2426 134632139 134632017 4.220000e-24 122
32 TraesCS6A01G146000 chr1B 92.248 129 10 0 2183 2311 459326058 459326186 1.910000e-42 183
33 TraesCS6A01G146000 chr1B 91.729 133 9 2 2180 2311 637547581 637547712 1.910000e-42 183
34 TraesCS6A01G146000 chr1B 94.595 111 6 0 2630 2740 632206488 632206598 4.130000e-39 172
35 TraesCS6A01G146000 chr5A 91.603 131 11 0 2181 2311 239650251 239650381 6.870000e-42 182
36 TraesCS6A01G146000 chr5A 96.296 108 4 0 2633 2740 343457869 343457976 8.890000e-41 178
37 TraesCS6A01G146000 chr1A 95.614 114 4 1 2633 2745 202083501 202083388 6.870000e-42 182
38 TraesCS6A01G146000 chr1A 94.737 114 5 1 2633 2745 366270939 366271052 3.200000e-40 176
39 TraesCS6A01G146000 chr3A 96.296 108 4 0 2633 2740 233523253 233523146 8.890000e-41 178
40 TraesCS6A01G146000 chr3A 96.262 107 4 0 2633 2739 48364412 48364518 3.200000e-40 176


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 TraesCS6A01G146000 chr6A 124310503 124313620 3117 False 5758.000000 5758 100.000000 1 3118 1 chr6A.!!$F2 3117
1 TraesCS6A01G146000 chr6A 1062162 1063475 1313 False 1182.000000 1182 83.076000 828 2173 1 chr6A.!!$F1 1345
2 TraesCS6A01G146000 chr6A 124426065 124426808 743 False 388.500000 470 87.006500 2309 3118 2 chr6A.!!$F3 809
3 TraesCS6A01G146000 chr6D 103034315 103037168 2853 False 1363.666667 3105 94.845333 49 3118 3 chr6D.!!$F2 3069
4 TraesCS6A01G146000 chr6B 188695352 188697283 1931 False 1378.000000 1439 93.256000 281 2176 2 chr6B.!!$F2 1895
5 TraesCS6A01G146000 chr6B 5101111 5102426 1315 False 669.000000 979 84.364500 828 2173 2 chr6B.!!$F1 1345
6 TraesCS6A01G146000 chr7D 169427730 169428481 751 True 382.000000 427 86.545000 2306 3118 2 chr7D.!!$R3 812
7 TraesCS6A01G146000 chr4B 6061083 6061750 667 False 392.000000 392 77.827000 1470 2119 1 chr4B.!!$F1 649

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
19 20 0.104671 ATGTGCACAACAAACCAGCC 59.895 50.0 25.72 0.0 43.61 4.85 F
21 22 0.528249 GTGCACAACAAACCAGCCAG 60.528 55.0 13.17 0.0 0.00 4.85 F
202 203 0.531974 GCCTATTCATTCACGGGCGA 60.532 55.0 0.00 0.0 0.00 5.54 F
680 693 1.166531 AACAAGTTGGAGTGAGCGGC 61.167 55.0 7.96 0.0 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1047 0.723981 GCTTGTTCATCGTCTCTGCC 59.276 55.000 0.00 0.0 0.00 4.85 R
1245 1287 0.734889 CAATGATGAAGCCGTGGGAC 59.265 55.000 0.00 0.0 0.00 4.46 R
1844 1950 1.141881 CCTGCACTCGCGGTAGAAT 59.858 57.895 6.13 0.0 43.56 2.40 R
2437 2557 0.310854 CCAGCCCAAGACACGAAAAC 59.689 55.000 0.00 0.0 0.00 2.43 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
18 19 3.665544 ATGTGCACAACAAACCAGC 57.334 47.368 25.72 0.00 43.61 4.85
19 20 0.104671 ATGTGCACAACAAACCAGCC 59.895 50.000 25.72 0.00 43.61 4.85
20 21 1.253593 TGTGCACAACAAACCAGCCA 61.254 50.000 19.28 0.00 35.24 4.75
21 22 0.528249 GTGCACAACAAACCAGCCAG 60.528 55.000 13.17 0.00 0.00 4.85
22 23 1.592400 GCACAACAAACCAGCCAGC 60.592 57.895 0.00 0.00 0.00 4.85
23 24 1.067916 CACAACAAACCAGCCAGCC 59.932 57.895 0.00 0.00 0.00 4.85
24 25 1.381056 ACAACAAACCAGCCAGCCA 60.381 52.632 0.00 0.00 0.00 4.75
25 26 1.067916 CAACAAACCAGCCAGCCAC 59.932 57.895 0.00 0.00 0.00 5.01
26 27 2.489275 AACAAACCAGCCAGCCACG 61.489 57.895 0.00 0.00 0.00 4.94
27 28 3.673484 CAAACCAGCCAGCCACGG 61.673 66.667 0.00 0.00 0.00 4.94
28 29 3.884774 AAACCAGCCAGCCACGGA 61.885 61.111 0.00 0.00 0.00 4.69
29 30 4.643387 AACCAGCCAGCCACGGAC 62.643 66.667 0.00 0.00 0.00 4.79
31 32 4.415150 CCAGCCAGCCACGGACAT 62.415 66.667 0.00 0.00 0.00 3.06
32 33 2.821366 CAGCCAGCCACGGACATC 60.821 66.667 0.00 0.00 0.00 3.06
33 34 4.457496 AGCCAGCCACGGACATCG 62.457 66.667 0.00 0.00 45.88 3.84
89 90 0.544357 AAGGAGTGACCGGGACATGA 60.544 55.000 6.32 0.00 44.74 3.07
121 122 7.801547 AACACATAAAAATCTCGAGCAATTG 57.198 32.000 7.81 0.00 0.00 2.32
122 123 6.913170 ACACATAAAAATCTCGAGCAATTGT 58.087 32.000 7.81 0.00 0.00 2.71
143 144 9.965824 AATTGTAACTGGTTTAACTTCATTCTG 57.034 29.630 0.00 0.00 0.00 3.02
148 149 8.691661 AACTGGTTTAACTTCATTCTGTACAT 57.308 30.769 0.00 0.00 0.00 2.29
150 151 7.936847 ACTGGTTTAACTTCATTCTGTACATCA 59.063 33.333 0.00 0.00 0.00 3.07
161 162 3.695816 TCTGTACATCATTCGAAGCTCG 58.304 45.455 3.35 0.00 42.10 5.03
172 173 4.485024 TTCGAAGCTCGGATGTACTATC 57.515 45.455 0.00 0.00 40.88 2.08
173 174 3.473625 TCGAAGCTCGGATGTACTATCA 58.526 45.455 5.87 0.00 40.88 2.15
174 175 4.072839 TCGAAGCTCGGATGTACTATCAT 58.927 43.478 5.87 0.00 40.88 2.45
175 176 4.083271 TCGAAGCTCGGATGTACTATCATG 60.083 45.833 5.87 0.00 40.88 3.07
176 177 4.320567 CGAAGCTCGGATGTACTATCATGT 60.321 45.833 0.00 0.00 36.00 3.21
177 178 5.106673 CGAAGCTCGGATGTACTATCATGTA 60.107 44.000 0.00 0.00 36.00 2.29
202 203 0.531974 GCCTATTCATTCACGGGCGA 60.532 55.000 0.00 0.00 0.00 5.54
217 218 4.494811 CGAGGCTGAACGCACATA 57.505 55.556 0.00 0.00 41.67 2.29
239 248 2.939103 CCTCGGTTGCTCTATTTTCAGG 59.061 50.000 0.00 0.00 0.00 3.86
250 260 7.596494 TGCTCTATTTTCAGGAAAAATGTCAG 58.404 34.615 10.86 5.14 45.15 3.51
265 275 6.869421 AAATGTCAGAAACAAAACAACGAG 57.131 33.333 0.00 0.00 42.37 4.18
268 278 4.162812 GTCAGAAACAAAACAACGAGCAA 58.837 39.130 0.00 0.00 0.00 3.91
275 285 3.056465 ACAAAACAACGAGCAAAAAGGGA 60.056 39.130 0.00 0.00 0.00 4.20
278 288 3.878160 ACAACGAGCAAAAAGGGAAAA 57.122 38.095 0.00 0.00 0.00 2.29
379 389 3.914312 ACTGTGAGTTAACATCGTGGAG 58.086 45.455 8.61 0.00 0.00 3.86
391 401 1.878522 CGTGGAGAAGCGAATCGGG 60.879 63.158 4.35 0.00 0.00 5.14
398 408 1.480954 AGAAGCGAATCGGGTACACAT 59.519 47.619 4.35 0.00 0.00 3.21
543 556 7.591426 CAGAATTACTGCTGAAAACAAAGTACC 59.409 37.037 0.00 0.00 39.86 3.34
569 582 6.215845 ACAAAATCTTGTTGCACAATCCTAC 58.784 36.000 0.00 0.00 43.45 3.18
570 583 6.040842 ACAAAATCTTGTTGCACAATCCTACT 59.959 34.615 0.00 0.00 43.45 2.57
571 584 7.230510 ACAAAATCTTGTTGCACAATCCTACTA 59.769 33.333 0.00 0.00 43.45 1.82
587 600 5.603596 TCCTACTACTTCTTAGCTCTCTCG 58.396 45.833 0.00 0.00 0.00 4.04
612 625 5.919707 CAGAGTTCTCATGATATCGAACCAG 59.080 44.000 17.38 7.90 37.15 4.00
678 691 4.749245 AATTAACAAGTTGGAGTGAGCG 57.251 40.909 7.96 0.00 0.00 5.03
680 693 1.166531 AACAAGTTGGAGTGAGCGGC 61.167 55.000 7.96 0.00 0.00 6.53
699 712 1.997311 CCAGCCCACTCCCATGAGA 60.997 63.158 0.00 0.00 41.42 3.27
764 779 4.040339 GGGGGACAGTTCAATGAACAAATT 59.960 41.667 25.63 8.41 44.11 1.82
882 899 3.685058 GAAGTGCTTTTAGGCTAATGCG 58.315 45.455 20.20 9.64 40.82 4.73
883 900 2.711542 AGTGCTTTTAGGCTAATGCGT 58.288 42.857 20.20 11.96 40.82 5.24
884 901 3.081804 AGTGCTTTTAGGCTAATGCGTT 58.918 40.909 20.20 12.29 40.82 4.84
933 957 5.337788 TCCTATAAATTTGCCACCTTGGTT 58.662 37.500 0.00 0.00 40.46 3.67
980 1004 4.428615 AAGCTCTCGTTAAGACAGAGAC 57.571 45.455 8.74 2.42 36.25 3.36
1011 1047 1.812922 GTGAGAGATGGCAGCACCG 60.813 63.158 5.19 0.00 43.94 4.94
1053 1095 2.347490 GCCGAGGTTCTCAAGGCA 59.653 61.111 8.34 0.00 46.48 4.75
1054 1096 2.035442 GCCGAGGTTCTCAAGGCAC 61.035 63.158 8.34 0.00 46.48 5.01
1119 1161 2.189499 GGTGGATGAGAATGCGGCC 61.189 63.158 0.00 0.00 0.00 6.13
1182 1224 3.073101 GGAACCTACCCCGTCGCT 61.073 66.667 0.00 0.00 0.00 4.93
1302 1349 4.041740 TCGCTACCATCTTCACATGTAC 57.958 45.455 0.00 0.00 0.00 2.90
1303 1350 3.445805 TCGCTACCATCTTCACATGTACA 59.554 43.478 0.00 0.00 0.00 2.90
1304 1351 3.798878 CGCTACCATCTTCACATGTACAG 59.201 47.826 0.00 0.00 0.00 2.74
1305 1352 4.678044 CGCTACCATCTTCACATGTACAGT 60.678 45.833 0.00 0.00 0.00 3.55
1306 1353 5.449999 CGCTACCATCTTCACATGTACAGTA 60.450 44.000 0.00 0.00 0.00 2.74
1387 1474 7.395772 TCTCAGAAGATGATCTGTTGTAACTCT 59.604 37.037 0.00 0.00 45.65 3.24
1388 1475 7.318893 TCAGAAGATGATCTGTTGTAACTCTG 58.681 38.462 9.21 9.21 45.65 3.35
1389 1476 7.039434 TCAGAAGATGATCTGTTGTAACTCTGT 60.039 37.037 13.23 0.00 45.65 3.41
1390 1477 8.246871 CAGAAGATGATCTGTTGTAACTCTGTA 58.753 37.037 0.00 0.00 41.54 2.74
1397 1488 8.749354 TGATCTGTTGTAACTCTGTATGTATGT 58.251 33.333 0.00 0.00 0.00 2.29
1399 1490 8.757164 TCTGTTGTAACTCTGTATGTATGTTG 57.243 34.615 0.00 0.00 0.00 3.33
1430 1521 6.371548 TGGTGATCAACTAACTAATTCTGCAC 59.628 38.462 12.94 0.00 0.00 4.57
1725 1822 1.225704 CAGCCCAAGATCCTCACCC 59.774 63.158 0.00 0.00 0.00 4.61
1921 2027 2.509336 GGACATGCTGGACGACGG 60.509 66.667 0.00 0.00 0.00 4.79
2032 2145 1.601419 CTGAATGCTGCCCTTGGTGG 61.601 60.000 0.00 0.00 0.00 4.61
2148 2262 1.467920 GCTCATGCCAAAGTTAGCCT 58.532 50.000 0.00 0.00 0.00 4.58
2181 2295 5.493809 TGGCCCACTAAATAAAGTACAGAC 58.506 41.667 0.00 0.00 0.00 3.51
2185 2299 6.982724 GCCCACTAAATAAAGTACAGACGTAT 59.017 38.462 0.00 0.00 0.00 3.06
2187 2301 9.028185 CCCACTAAATAAAGTACAGACGTATTC 57.972 37.037 0.00 0.00 0.00 1.75
2188 2302 9.028185 CCACTAAATAAAGTACAGACGTATTCC 57.972 37.037 0.00 0.00 0.00 3.01
2189 2303 9.028185 CACTAAATAAAGTACAGACGTATTCCC 57.972 37.037 0.00 0.00 0.00 3.97
2190 2304 8.975295 ACTAAATAAAGTACAGACGTATTCCCT 58.025 33.333 0.00 0.00 0.00 4.20
2191 2305 9.460906 CTAAATAAAGTACAGACGTATTCCCTC 57.539 37.037 0.00 0.00 0.00 4.30
2192 2306 4.732672 AAAGTACAGACGTATTCCCTCC 57.267 45.455 0.00 0.00 0.00 4.30
2193 2307 2.295885 AGTACAGACGTATTCCCTCCG 58.704 52.381 0.00 0.00 0.00 4.63
2194 2308 2.019984 GTACAGACGTATTCCCTCCGT 58.980 52.381 0.00 0.00 37.56 4.69
2195 2309 1.553706 ACAGACGTATTCCCTCCGTT 58.446 50.000 0.00 0.00 34.51 4.44
2196 2310 1.475682 ACAGACGTATTCCCTCCGTTC 59.524 52.381 0.00 0.00 34.51 3.95
2197 2311 1.109609 AGACGTATTCCCTCCGTTCC 58.890 55.000 0.00 0.00 34.51 3.62
2198 2312 0.819582 GACGTATTCCCTCCGTTCCA 59.180 55.000 0.00 0.00 34.51 3.53
2199 2313 1.205417 GACGTATTCCCTCCGTTCCAA 59.795 52.381 0.00 0.00 34.51 3.53
2200 2314 1.624813 ACGTATTCCCTCCGTTCCAAA 59.375 47.619 0.00 0.00 0.00 3.28
2201 2315 2.038820 ACGTATTCCCTCCGTTCCAAAA 59.961 45.455 0.00 0.00 0.00 2.44
2202 2316 3.275999 CGTATTCCCTCCGTTCCAAAAT 58.724 45.455 0.00 0.00 0.00 1.82
2203 2317 4.080975 ACGTATTCCCTCCGTTCCAAAATA 60.081 41.667 0.00 0.00 0.00 1.40
2204 2318 4.271776 CGTATTCCCTCCGTTCCAAAATAC 59.728 45.833 0.00 0.00 0.00 1.89
2205 2319 4.586306 ATTCCCTCCGTTCCAAAATACT 57.414 40.909 0.00 0.00 0.00 2.12
2206 2320 4.376225 TTCCCTCCGTTCCAAAATACTT 57.624 40.909 0.00 0.00 0.00 2.24
2207 2321 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
2208 2322 3.328343 TCCCTCCGTTCCAAAATACTTGA 59.672 43.478 0.00 0.00 0.00 3.02
2209 2323 4.018779 TCCCTCCGTTCCAAAATACTTGAT 60.019 41.667 0.00 0.00 0.00 2.57
2210 2324 4.705023 CCCTCCGTTCCAAAATACTTGATT 59.295 41.667 0.00 0.00 0.00 2.57
2211 2325 5.185056 CCCTCCGTTCCAAAATACTTGATTT 59.815 40.000 0.00 0.00 39.56 2.17
2212 2326 6.322491 CCTCCGTTCCAAAATACTTGATTTC 58.678 40.000 0.00 0.00 36.71 2.17
2213 2327 6.262193 TCCGTTCCAAAATACTTGATTTCC 57.738 37.500 0.00 0.00 36.71 3.13
2214 2328 5.770663 TCCGTTCCAAAATACTTGATTTCCA 59.229 36.000 0.00 0.00 36.71 3.53
2215 2329 6.435904 TCCGTTCCAAAATACTTGATTTCCAT 59.564 34.615 0.00 0.00 36.71 3.41
2216 2330 7.039363 TCCGTTCCAAAATACTTGATTTCCATT 60.039 33.333 0.00 0.00 36.71 3.16
2217 2331 7.602265 CCGTTCCAAAATACTTGATTTCCATTT 59.398 33.333 0.00 0.00 36.71 2.32
2218 2332 8.434661 CGTTCCAAAATACTTGATTTCCATTTG 58.565 33.333 0.00 0.00 36.71 2.32
2219 2333 9.271828 GTTCCAAAATACTTGATTTCCATTTGT 57.728 29.630 0.00 0.00 36.71 2.83
2220 2334 9.844257 TTCCAAAATACTTGATTTCCATTTGTT 57.156 25.926 0.00 0.00 36.71 2.83
2221 2335 9.487790 TCCAAAATACTTGATTTCCATTTGTTC 57.512 29.630 0.00 0.00 36.71 3.18
2222 2336 9.270640 CCAAAATACTTGATTTCCATTTGTTCA 57.729 29.630 0.00 0.00 36.71 3.18
2236 2350 9.921637 TTCCATTTGTTCAAAAATAGATGTACC 57.078 29.630 2.11 0.00 0.00 3.34
2237 2351 9.308000 TCCATTTGTTCAAAAATAGATGTACCT 57.692 29.630 2.11 0.00 0.00 3.08
2294 2408 9.467258 ACTTTGACAAATGAAAGACATGTATTG 57.533 29.630 6.46 0.00 39.39 1.90
2295 2409 9.467258 CTTTGACAAATGAAAGACATGTATTGT 57.533 29.630 6.46 0.00 38.99 2.71
2296 2410 8.800231 TTGACAAATGAAAGACATGTATTGTG 57.200 30.769 6.46 3.52 37.49 3.33
2297 2411 8.164058 TGACAAATGAAAGACATGTATTGTGA 57.836 30.769 6.46 0.00 37.49 3.58
2298 2412 8.628280 TGACAAATGAAAGACATGTATTGTGAA 58.372 29.630 6.46 0.00 37.49 3.18
2299 2413 9.462174 GACAAATGAAAGACATGTATTGTGAAA 57.538 29.630 6.46 0.00 37.49 2.69
2300 2414 9.248291 ACAAATGAAAGACATGTATTGTGAAAC 57.752 29.630 6.46 0.00 39.18 2.78
2301 2415 8.702438 CAAATGAAAGACATGTATTGTGAAACC 58.298 33.333 6.46 0.00 39.18 3.27
2302 2416 5.996219 TGAAAGACATGTATTGTGAAACCG 58.004 37.500 6.46 0.00 39.18 4.44
2303 2417 5.760743 TGAAAGACATGTATTGTGAAACCGA 59.239 36.000 6.46 0.00 39.18 4.69
2304 2418 5.862924 AAGACATGTATTGTGAAACCGAG 57.137 39.130 4.61 0.00 39.18 4.63
2305 2419 4.253685 AGACATGTATTGTGAAACCGAGG 58.746 43.478 0.00 0.00 39.18 4.63
2306 2420 3.343617 ACATGTATTGTGAAACCGAGGG 58.656 45.455 0.00 0.00 37.11 4.30
2307 2421 3.008594 ACATGTATTGTGAAACCGAGGGA 59.991 43.478 0.00 0.00 37.11 4.20
2419 2539 7.013846 GCTCTGTTTCCAGATGTATACTACTCT 59.986 40.741 4.17 1.36 46.38 3.24
2501 2621 2.826488 ACTAGGTGCAGTTCTGATCCT 58.174 47.619 15.68 15.68 0.00 3.24
2639 2788 4.047166 TCATGTGGATGGATTTACTCCCT 58.953 43.478 0.00 0.00 44.23 4.20
2640 2789 4.103153 TCATGTGGATGGATTTACTCCCTC 59.897 45.833 0.00 0.00 44.23 4.30
2642 2791 2.841442 GGATGGATTTACTCCCTCCG 57.159 55.000 0.00 0.00 45.51 4.63
2643 2792 2.047830 GGATGGATTTACTCCCTCCGT 58.952 52.381 0.00 0.00 45.51 4.69
2644 2793 2.438392 GGATGGATTTACTCCCTCCGTT 59.562 50.000 0.00 0.00 45.51 4.44
2645 2794 3.494573 GGATGGATTTACTCCCTCCGTTC 60.495 52.174 0.00 0.00 45.51 3.95
2646 2795 1.835531 TGGATTTACTCCCTCCGTTCC 59.164 52.381 0.00 0.00 44.23 3.62
2647 2796 1.202498 GGATTTACTCCCTCCGTTCCG 60.202 57.143 0.00 0.00 38.19 4.30
2648 2797 1.753073 GATTTACTCCCTCCGTTCCGA 59.247 52.381 0.00 0.00 0.00 4.55
2649 2798 1.631405 TTTACTCCCTCCGTTCCGAA 58.369 50.000 0.00 0.00 0.00 4.30
2650 2799 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
2651 2800 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2652 2801 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2653 2802 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2654 2803 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2655 2804 1.753073 TCCCTCCGTTCCGAATTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2657 2806 1.133790 CCTCCGTTCCGAATTACTCGT 59.866 52.381 0.00 0.00 46.65 4.18
2658 2807 2.448219 CTCCGTTCCGAATTACTCGTC 58.552 52.381 0.00 0.00 46.65 4.20
2659 2808 1.811965 TCCGTTCCGAATTACTCGTCA 59.188 47.619 0.00 0.00 46.65 4.35
2660 2809 2.424601 TCCGTTCCGAATTACTCGTCAT 59.575 45.455 0.00 0.00 46.65 3.06
2664 2813 5.268544 CGTTCCGAATTACTCGTCATAGAA 58.731 41.667 0.00 0.00 46.65 2.10
2666 2815 6.417044 CGTTCCGAATTACTCGTCATAGAAAT 59.583 38.462 0.00 0.00 46.65 2.17
2670 2819 9.011095 TCCGAATTACTCGTCATAGAAATAGAT 57.989 33.333 0.00 0.00 46.65 1.98
2672 2821 9.613957 CGAATTACTCGTCATAGAAATAGATGT 57.386 33.333 0.00 0.00 42.89 3.06
2711 2860 8.718102 TTAGTTCTAGATACATCCACTTTTGC 57.282 34.615 0.00 0.00 0.00 3.68
2712 2861 5.812642 AGTTCTAGATACATCCACTTTTGCG 59.187 40.000 0.00 0.00 0.00 4.85
2713 2862 5.592104 TCTAGATACATCCACTTTTGCGA 57.408 39.130 0.00 0.00 0.00 5.10
2714 2863 5.348986 TCTAGATACATCCACTTTTGCGAC 58.651 41.667 0.00 0.00 0.00 5.19
2715 2864 2.930040 AGATACATCCACTTTTGCGACG 59.070 45.455 0.00 0.00 0.00 5.12
2716 2865 2.442212 TACATCCACTTTTGCGACGA 57.558 45.000 0.00 0.00 0.00 4.20
2717 2866 1.148310 ACATCCACTTTTGCGACGAG 58.852 50.000 0.00 0.00 0.00 4.18
2718 2867 1.148310 CATCCACTTTTGCGACGAGT 58.852 50.000 0.00 0.00 0.00 4.18
2719 2868 2.288579 ACATCCACTTTTGCGACGAGTA 60.289 45.455 0.00 0.00 0.00 2.59
2720 2869 2.512485 TCCACTTTTGCGACGAGTAA 57.488 45.000 0.00 0.00 0.00 2.24
2721 2870 3.034721 TCCACTTTTGCGACGAGTAAT 57.965 42.857 0.00 0.00 0.00 1.89
2722 2871 3.395639 TCCACTTTTGCGACGAGTAATT 58.604 40.909 0.00 0.00 0.00 1.40
2723 2872 3.810941 TCCACTTTTGCGACGAGTAATTT 59.189 39.130 0.00 0.00 0.00 1.82
2724 2873 3.906008 CCACTTTTGCGACGAGTAATTTG 59.094 43.478 0.00 0.00 0.00 2.32
2725 2874 3.906008 CACTTTTGCGACGAGTAATTTGG 59.094 43.478 0.00 0.00 0.00 3.28
2726 2875 3.810941 ACTTTTGCGACGAGTAATTTGGA 59.189 39.130 0.00 0.00 0.00 3.53
2727 2876 4.273969 ACTTTTGCGACGAGTAATTTGGAA 59.726 37.500 0.00 0.00 0.00 3.53
2728 2877 3.799137 TTGCGACGAGTAATTTGGAAC 57.201 42.857 0.00 0.00 0.00 3.62
2729 2878 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2730 2879 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
2731 2880 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2732 2881 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2733 2882 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2734 2883 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2735 2884 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2736 2885 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2737 2886 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2738 2887 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2739 2888 4.720273 AGTAATTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
2740 2889 5.901276 AGTAATTTGGAACGGAGGGAGTATA 59.099 40.000 0.00 0.00 0.00 1.47
2741 2890 5.906772 AATTTGGAACGGAGGGAGTATAT 57.093 39.130 0.00 0.00 0.00 0.86
2742 2891 5.906772 ATTTGGAACGGAGGGAGTATATT 57.093 39.130 0.00 0.00 0.00 1.28
2743 2892 4.950205 TTGGAACGGAGGGAGTATATTC 57.050 45.455 0.00 0.00 0.00 1.75
2744 2893 3.918566 TGGAACGGAGGGAGTATATTCA 58.081 45.455 0.00 0.00 0.00 2.57
2745 2894 4.291792 TGGAACGGAGGGAGTATATTCAA 58.708 43.478 0.00 0.00 0.00 2.69
2746 2895 4.344102 TGGAACGGAGGGAGTATATTCAAG 59.656 45.833 0.00 0.00 0.00 3.02
2747 2896 4.262506 GGAACGGAGGGAGTATATTCAAGG 60.263 50.000 0.00 0.00 0.00 3.61
2748 2897 3.240302 ACGGAGGGAGTATATTCAAGGG 58.760 50.000 0.00 0.00 0.00 3.95
2749 2898 3.116862 ACGGAGGGAGTATATTCAAGGGA 60.117 47.826 0.00 0.00 0.00 4.20
2750 2899 3.901844 CGGAGGGAGTATATTCAAGGGAA 59.098 47.826 0.00 0.00 37.45 3.97
2751 2900 4.347000 CGGAGGGAGTATATTCAAGGGAAA 59.653 45.833 0.00 0.00 36.43 3.13
2752 2901 5.511545 CGGAGGGAGTATATTCAAGGGAAAG 60.512 48.000 0.00 0.00 36.43 2.62
2753 2902 5.221945 GGAGGGAGTATATTCAAGGGAAAGG 60.222 48.000 0.00 0.00 36.43 3.11
2754 2903 4.665483 AGGGAGTATATTCAAGGGAAAGGG 59.335 45.833 0.00 0.00 36.43 3.95
2755 2904 4.202577 GGGAGTATATTCAAGGGAAAGGGG 60.203 50.000 0.00 0.00 36.43 4.79
2756 2905 4.202577 GGAGTATATTCAAGGGAAAGGGGG 60.203 50.000 0.00 0.00 36.43 5.40
2757 2906 4.652628 AGTATATTCAAGGGAAAGGGGGA 58.347 43.478 0.00 0.00 36.43 4.81
2758 2907 5.243566 AGTATATTCAAGGGAAAGGGGGAT 58.756 41.667 0.00 0.00 36.43 3.85
2824 2973 3.004734 ACAACACCATTTTCTGTAGCTGC 59.995 43.478 0.00 0.00 0.00 5.25
2853 3002 2.594962 CCACGACGCACCACAGTTC 61.595 63.158 0.00 0.00 0.00 3.01
2855 3004 3.403057 CGACGCACCACAGTTCGG 61.403 66.667 0.00 0.00 36.92 4.30
3023 3184 9.715121 AGTGATCATATGAAAAATTGCTTTGTT 57.285 25.926 9.99 0.00 0.00 2.83
3028 3189 8.149647 TCATATGAAAAATTGCTTTGTTGGAGT 58.850 29.630 1.98 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104671 GGCTGGTTTGTTGTGCACAT 59.895 50.000 22.39 0.00 34.43 3.21
1 2 1.253593 TGGCTGGTTTGTTGTGCACA 61.254 50.000 17.42 17.42 0.00 4.57
2 3 0.528249 CTGGCTGGTTTGTTGTGCAC 60.528 55.000 10.75 10.75 0.00 4.57
5 6 1.067916 GGCTGGCTGGTTTGTTGTG 59.932 57.895 0.00 0.00 0.00 3.33
6 7 1.381056 TGGCTGGCTGGTTTGTTGT 60.381 52.632 2.00 0.00 0.00 3.32
7 8 1.067916 GTGGCTGGCTGGTTTGTTG 59.932 57.895 2.00 0.00 0.00 3.33
8 9 2.489275 CGTGGCTGGCTGGTTTGTT 61.489 57.895 2.00 0.00 0.00 2.83
9 10 2.906897 CGTGGCTGGCTGGTTTGT 60.907 61.111 2.00 0.00 0.00 2.83
10 11 3.673484 CCGTGGCTGGCTGGTTTG 61.673 66.667 2.00 0.00 0.00 2.93
11 12 3.884774 TCCGTGGCTGGCTGGTTT 61.885 61.111 2.00 0.00 0.00 3.27
12 13 4.643387 GTCCGTGGCTGGCTGGTT 62.643 66.667 2.00 0.00 0.00 3.67
14 15 4.415150 ATGTCCGTGGCTGGCTGG 62.415 66.667 2.00 4.76 0.00 4.85
15 16 2.821366 GATGTCCGTGGCTGGCTG 60.821 66.667 2.00 0.00 0.00 4.85
16 17 4.457496 CGATGTCCGTGGCTGGCT 62.457 66.667 2.00 0.00 0.00 4.75
26 27 0.804544 TCGATTTGTCGGCGATGTCC 60.805 55.000 14.79 0.00 0.00 4.02
27 28 1.209128 ATCGATTTGTCGGCGATGTC 58.791 50.000 14.79 8.21 42.48 3.06
28 29 3.362581 ATCGATTTGTCGGCGATGT 57.637 47.368 14.79 0.00 42.48 3.06
30 31 1.067060 TCTCATCGATTTGTCGGCGAT 59.933 47.619 14.79 0.00 44.65 4.58
31 32 0.454196 TCTCATCGATTTGTCGGCGA 59.546 50.000 4.99 4.99 38.51 5.54
32 33 1.277326 TTCTCATCGATTTGTCGGCG 58.723 50.000 0.00 0.00 0.00 6.46
33 34 3.602491 CGAATTCTCATCGATTTGTCGGC 60.602 47.826 3.52 0.00 42.76 5.54
34 35 3.796717 TCGAATTCTCATCGATTTGTCGG 59.203 43.478 3.52 0.00 43.76 4.79
42 43 5.568685 AGACTCTTTCGAATTCTCATCGA 57.431 39.130 0.00 0.00 46.64 3.59
43 44 5.574830 ACAAGACTCTTTCGAATTCTCATCG 59.425 40.000 0.00 0.00 41.53 3.84
44 45 6.959671 ACAAGACTCTTTCGAATTCTCATC 57.040 37.500 0.00 0.00 0.00 2.92
45 46 6.931281 TCAACAAGACTCTTTCGAATTCTCAT 59.069 34.615 0.00 0.00 0.00 2.90
46 47 6.280643 TCAACAAGACTCTTTCGAATTCTCA 58.719 36.000 0.00 0.00 0.00 3.27
47 48 6.771188 TCAACAAGACTCTTTCGAATTCTC 57.229 37.500 0.00 0.00 0.00 2.87
109 110 3.678056 ACCAGTTACAATTGCTCGAGA 57.322 42.857 18.75 0.00 0.00 4.04
113 114 7.422399 TGAAGTTAAACCAGTTACAATTGCTC 58.578 34.615 5.05 0.00 0.00 4.26
121 122 9.048446 TGTACAGAATGAAGTTAAACCAGTTAC 57.952 33.333 0.00 0.00 39.69 2.50
122 123 9.787435 ATGTACAGAATGAAGTTAAACCAGTTA 57.213 29.630 0.33 0.00 39.69 2.24
143 144 3.079960 TCCGAGCTTCGAATGATGTAC 57.920 47.619 0.00 0.00 43.74 2.90
148 149 2.688446 AGTACATCCGAGCTTCGAATGA 59.312 45.455 10.67 0.40 36.71 2.57
150 151 4.519350 TGATAGTACATCCGAGCTTCGAAT 59.481 41.667 0.00 0.00 43.74 3.34
161 162 6.381420 AGGCCATACTACATGATAGTACATCC 59.619 42.308 5.01 13.58 33.41 3.51
168 169 9.539825 GAATGAATAGGCCATACTACATGATAG 57.460 37.037 5.01 0.00 0.00 2.08
169 170 9.045745 TGAATGAATAGGCCATACTACATGATA 57.954 33.333 5.01 0.00 0.00 2.15
172 173 6.091305 CGTGAATGAATAGGCCATACTACATG 59.909 42.308 5.01 0.00 0.00 3.21
173 174 6.166279 CGTGAATGAATAGGCCATACTACAT 58.834 40.000 5.01 0.00 0.00 2.29
174 175 5.510690 CCGTGAATGAATAGGCCATACTACA 60.511 44.000 5.01 0.00 0.00 2.74
175 176 4.929808 CCGTGAATGAATAGGCCATACTAC 59.070 45.833 5.01 0.00 0.00 2.73
176 177 4.020573 CCCGTGAATGAATAGGCCATACTA 60.021 45.833 5.01 0.00 0.00 1.82
177 178 3.244561 CCCGTGAATGAATAGGCCATACT 60.245 47.826 5.01 0.00 0.00 2.12
217 218 3.600388 CTGAAAATAGAGCAACCGAGGT 58.400 45.455 0.00 0.00 0.00 3.85
239 248 7.725142 TCGTTGTTTTGTTTCTGACATTTTTC 58.275 30.769 0.00 0.00 38.26 2.29
250 260 5.312838 CCTTTTTGCTCGTTGTTTTGTTTC 58.687 37.500 0.00 0.00 0.00 2.78
265 275 4.400529 TCTGTTCCTTTTCCCTTTTTGC 57.599 40.909 0.00 0.00 0.00 3.68
268 278 7.730332 AGTAATCATCTGTTCCTTTTCCCTTTT 59.270 33.333 0.00 0.00 0.00 2.27
275 285 6.006449 AGTGCAGTAATCATCTGTTCCTTTT 58.994 36.000 0.00 0.00 35.60 2.27
278 288 4.833478 AGTGCAGTAATCATCTGTTCCT 57.167 40.909 0.00 0.00 35.60 3.36
310 320 2.621338 CTGTTAGCATCACGGACATGT 58.379 47.619 0.00 0.00 0.00 3.21
311 321 1.935873 CCTGTTAGCATCACGGACATG 59.064 52.381 0.00 0.00 0.00 3.21
379 389 1.859080 GATGTGTACCCGATTCGCTTC 59.141 52.381 0.00 0.00 0.00 3.86
398 408 5.165676 ACGCGTACAAGAATTTCATAGTGA 58.834 37.500 11.67 0.00 0.00 3.41
475 488 3.823873 ACTATTAGGTCAGATCTGCTCCG 59.176 47.826 18.36 11.09 32.57 4.63
492 505 9.314133 TGTCCAGAGAACATATATGCTACTATT 57.686 33.333 12.79 0.00 0.00 1.73
493 506 8.885693 TGTCCAGAGAACATATATGCTACTAT 57.114 34.615 12.79 4.51 0.00 2.12
494 507 8.164070 TCTGTCCAGAGAACATATATGCTACTA 58.836 37.037 12.79 0.00 32.82 1.82
495 508 7.007116 TCTGTCCAGAGAACATATATGCTACT 58.993 38.462 12.79 9.21 32.82 2.57
569 582 3.874543 TCTGCGAGAGAGCTAAGAAGTAG 59.125 47.826 0.00 0.00 38.13 2.57
570 583 3.874543 CTCTGCGAGAGAGCTAAGAAGTA 59.125 47.826 7.22 0.00 45.07 2.24
571 584 2.682856 CTCTGCGAGAGAGCTAAGAAGT 59.317 50.000 7.22 0.00 45.07 3.01
587 600 4.683781 GGTTCGATATCATGAGAACTCTGC 59.316 45.833 19.25 5.24 41.72 4.26
605 618 2.065993 TTTCGCTTCTCTCTGGTTCG 57.934 50.000 0.00 0.00 0.00 3.95
612 625 6.481954 TTTCCTGTAAATTTCGCTTCTCTC 57.518 37.500 0.00 0.00 0.00 3.20
667 680 4.020617 CTGGGCCGCTCACTCCAA 62.021 66.667 0.00 0.00 0.00 3.53
680 693 3.016971 TCATGGGAGTGGGCTGGG 61.017 66.667 0.00 0.00 0.00 4.45
686 699 3.794737 CATGGTCTCATGGGAGTGG 57.205 57.895 0.00 0.00 45.19 4.00
699 712 4.019860 GCACAGTATAGATGGGATCATGGT 60.020 45.833 0.00 0.00 32.98 3.55
764 779 8.981659 TGAATAAGACTGATTCCATCTAACTGA 58.018 33.333 9.69 0.00 33.18 3.41
874 891 2.933906 TGTGGCTACTTAACGCATTAGC 59.066 45.455 0.64 0.00 36.92 3.09
882 899 7.248437 GTGGATGTTAATTGTGGCTACTTAAC 58.752 38.462 14.41 14.41 35.58 2.01
883 900 6.376018 GGTGGATGTTAATTGTGGCTACTTAA 59.624 38.462 0.64 0.00 0.00 1.85
884 901 5.883673 GGTGGATGTTAATTGTGGCTACTTA 59.116 40.000 0.64 0.00 0.00 2.24
933 957 3.181482 GGTTGCGATGATGAGAAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
980 1004 1.345741 TCTCTCACTCAAGCCACCAAG 59.654 52.381 0.00 0.00 0.00 3.61
1011 1047 0.723981 GCTTGTTCATCGTCTCTGCC 59.276 55.000 0.00 0.00 0.00 4.85
1086 1128 1.874019 CACCTGAATCGCCTCGACG 60.874 63.158 0.00 0.00 39.18 5.12
1128 1170 4.195334 ATCAGCACCGGGATGGGC 62.195 66.667 6.32 0.76 44.64 5.36
1131 1173 1.592669 GACGATCAGCACCGGGATG 60.593 63.158 6.32 3.83 0.00 3.51
1245 1287 0.734889 CAATGATGAAGCCGTGGGAC 59.265 55.000 0.00 0.00 0.00 4.46
1306 1353 8.408601 GCATCATTGTTGAGGTAATTTCTGTAT 58.591 33.333 0.00 0.00 36.07 2.29
1387 1474 3.755905 CACCACAAGCCAACATACATACA 59.244 43.478 0.00 0.00 0.00 2.29
1388 1475 4.006989 TCACCACAAGCCAACATACATAC 58.993 43.478 0.00 0.00 0.00 2.39
1389 1476 4.293662 TCACCACAAGCCAACATACATA 57.706 40.909 0.00 0.00 0.00 2.29
1390 1477 3.153369 TCACCACAAGCCAACATACAT 57.847 42.857 0.00 0.00 0.00 2.29
1397 1488 2.363306 AGTTGATCACCACAAGCCAA 57.637 45.000 0.00 0.00 0.00 4.52
1399 1490 3.412386 AGTTAGTTGATCACCACAAGCC 58.588 45.455 0.00 0.00 0.00 4.35
1430 1521 3.004629 TGCTGAACTGCACTACAAAATGG 59.995 43.478 2.46 0.00 38.12 3.16
1725 1822 2.896443 GAAGGAGGAGGGCTCGTG 59.104 66.667 0.00 0.00 0.00 4.35
1844 1950 1.141881 CCTGCACTCGCGGTAGAAT 59.858 57.895 6.13 0.00 43.56 2.40
1921 2027 2.361104 TGATGAACTTGGGGGCGC 60.361 61.111 0.00 0.00 0.00 6.53
2032 2145 3.475575 GCCTCAAGATCTCCATCTTTCC 58.524 50.000 0.00 0.00 45.68 3.13
2161 2275 8.937634 AATACGTCTGTACTTTATTTAGTGGG 57.062 34.615 0.00 0.00 32.26 4.61
2181 2295 2.389962 TTTGGAACGGAGGGAATACG 57.610 50.000 0.00 0.00 42.79 3.06
2185 2299 4.076394 CAAGTATTTTGGAACGGAGGGAA 58.924 43.478 0.00 0.00 0.00 3.97
2187 2301 3.681593 TCAAGTATTTTGGAACGGAGGG 58.318 45.455 0.00 0.00 0.00 4.30
2188 2302 5.897377 AATCAAGTATTTTGGAACGGAGG 57.103 39.130 0.00 0.00 0.00 4.30
2189 2303 6.072175 TGGAAATCAAGTATTTTGGAACGGAG 60.072 38.462 0.00 0.00 37.93 4.63
2190 2304 5.770663 TGGAAATCAAGTATTTTGGAACGGA 59.229 36.000 0.00 0.00 37.93 4.69
2191 2305 6.019779 TGGAAATCAAGTATTTTGGAACGG 57.980 37.500 0.00 0.00 37.93 4.44
2192 2306 8.434661 CAAATGGAAATCAAGTATTTTGGAACG 58.565 33.333 0.00 0.00 37.93 3.95
2193 2307 9.271828 ACAAATGGAAATCAAGTATTTTGGAAC 57.728 29.630 0.00 0.00 37.93 3.62
2194 2308 9.844257 AACAAATGGAAATCAAGTATTTTGGAA 57.156 25.926 0.00 0.00 37.93 3.53
2195 2309 9.487790 GAACAAATGGAAATCAAGTATTTTGGA 57.512 29.630 0.00 0.00 37.93 3.53
2196 2310 9.270640 TGAACAAATGGAAATCAAGTATTTTGG 57.729 29.630 0.00 0.00 37.93 3.28
2210 2324 9.921637 GGTACATCTATTTTTGAACAAATGGAA 57.078 29.630 0.00 0.00 37.24 3.53
2211 2325 9.308000 AGGTACATCTATTTTTGAACAAATGGA 57.692 29.630 0.00 0.00 37.84 3.41
2268 2382 9.467258 CAATACATGTCTTTCATTTGTCAAAGT 57.533 29.630 0.00 0.00 34.09 2.66
2269 2383 9.467258 ACAATACATGTCTTTCATTTGTCAAAG 57.533 29.630 0.00 0.00 37.96 2.77
2270 2384 9.247126 CACAATACATGTCTTTCATTTGTCAAA 57.753 29.630 0.00 0.00 41.46 2.69
2271 2385 8.628280 TCACAATACATGTCTTTCATTTGTCAA 58.372 29.630 0.00 0.00 41.46 3.18
2272 2386 8.164058 TCACAATACATGTCTTTCATTTGTCA 57.836 30.769 0.00 0.00 41.46 3.58
2273 2387 9.462174 TTTCACAATACATGTCTTTCATTTGTC 57.538 29.630 0.00 0.00 41.46 3.18
2274 2388 9.248291 GTTTCACAATACATGTCTTTCATTTGT 57.752 29.630 0.00 0.02 41.46 2.83
2275 2389 8.702438 GGTTTCACAATACATGTCTTTCATTTG 58.298 33.333 0.00 0.00 41.46 2.32
2276 2390 7.594758 CGGTTTCACAATACATGTCTTTCATTT 59.405 33.333 0.00 0.00 41.46 2.32
2277 2391 7.040755 TCGGTTTCACAATACATGTCTTTCATT 60.041 33.333 0.00 0.00 41.46 2.57
2278 2392 6.429692 TCGGTTTCACAATACATGTCTTTCAT 59.570 34.615 0.00 0.00 41.46 2.57
2279 2393 5.760743 TCGGTTTCACAATACATGTCTTTCA 59.239 36.000 0.00 0.00 41.46 2.69
2280 2394 6.236017 TCGGTTTCACAATACATGTCTTTC 57.764 37.500 0.00 0.00 41.46 2.62
2281 2395 5.181245 CCTCGGTTTCACAATACATGTCTTT 59.819 40.000 0.00 0.00 41.46 2.52
2282 2396 4.695455 CCTCGGTTTCACAATACATGTCTT 59.305 41.667 0.00 0.00 41.46 3.01
2283 2397 4.253685 CCTCGGTTTCACAATACATGTCT 58.746 43.478 0.00 0.00 41.46 3.41
2284 2398 3.374058 CCCTCGGTTTCACAATACATGTC 59.626 47.826 0.00 0.00 41.46 3.06
2285 2399 3.008594 TCCCTCGGTTTCACAATACATGT 59.991 43.478 2.69 2.69 45.34 3.21
2286 2400 3.605634 TCCCTCGGTTTCACAATACATG 58.394 45.455 0.00 0.00 0.00 3.21
2287 2401 3.263425 ACTCCCTCGGTTTCACAATACAT 59.737 43.478 0.00 0.00 0.00 2.29
2288 2402 2.635915 ACTCCCTCGGTTTCACAATACA 59.364 45.455 0.00 0.00 0.00 2.29
2289 2403 3.329929 ACTCCCTCGGTTTCACAATAC 57.670 47.619 0.00 0.00 0.00 1.89
2290 2404 3.196254 GGTACTCCCTCGGTTTCACAATA 59.804 47.826 0.00 0.00 0.00 1.90
2291 2405 2.027469 GGTACTCCCTCGGTTTCACAAT 60.027 50.000 0.00 0.00 0.00 2.71
2292 2406 1.345415 GGTACTCCCTCGGTTTCACAA 59.655 52.381 0.00 0.00 0.00 3.33
2293 2407 0.971386 GGTACTCCCTCGGTTTCACA 59.029 55.000 0.00 0.00 0.00 3.58
2294 2408 1.264295 AGGTACTCCCTCGGTTTCAC 58.736 55.000 0.00 0.00 40.71 3.18
2295 2409 3.780307 AGGTACTCCCTCGGTTTCA 57.220 52.632 0.00 0.00 40.71 2.69
2369 2489 1.073763 AGTACCATTGCAGGCTCACAA 59.926 47.619 2.24 2.24 0.00 3.33
2419 2539 8.286800 CACGAAAACCAAGATTTATACTCACAA 58.713 33.333 0.00 0.00 0.00 3.33
2429 2549 4.202111 CCCAAGACACGAAAACCAAGATTT 60.202 41.667 0.00 0.00 0.00 2.17
2437 2557 0.310854 CCAGCCCAAGACACGAAAAC 59.689 55.000 0.00 0.00 0.00 2.43
2685 2834 9.162764 GCAAAAGTGGATGTATCTAGAACTAAA 57.837 33.333 0.00 0.00 0.00 1.85
2687 2836 6.978659 CGCAAAAGTGGATGTATCTAGAACTA 59.021 38.462 0.00 0.00 0.00 2.24
2688 2837 5.812642 CGCAAAAGTGGATGTATCTAGAACT 59.187 40.000 0.00 0.00 0.00 3.01
2689 2838 5.810587 TCGCAAAAGTGGATGTATCTAGAAC 59.189 40.000 0.00 0.00 0.00 3.01
2690 2839 5.810587 GTCGCAAAAGTGGATGTATCTAGAA 59.189 40.000 0.00 0.00 0.00 2.10
2691 2840 5.348986 GTCGCAAAAGTGGATGTATCTAGA 58.651 41.667 0.00 0.00 0.00 2.43
2692 2841 4.207224 CGTCGCAAAAGTGGATGTATCTAG 59.793 45.833 0.00 0.00 0.00 2.43
2693 2842 4.109766 CGTCGCAAAAGTGGATGTATCTA 58.890 43.478 0.00 0.00 0.00 1.98
2694 2843 2.930040 CGTCGCAAAAGTGGATGTATCT 59.070 45.455 0.00 0.00 0.00 1.98
2695 2844 2.927477 TCGTCGCAAAAGTGGATGTATC 59.073 45.455 0.00 0.00 0.00 2.24
2696 2845 2.930040 CTCGTCGCAAAAGTGGATGTAT 59.070 45.455 0.00 0.00 0.00 2.29
2697 2846 2.288579 ACTCGTCGCAAAAGTGGATGTA 60.289 45.455 0.00 0.00 0.00 2.29
2698 2847 1.148310 CTCGTCGCAAAAGTGGATGT 58.852 50.000 0.00 0.00 0.00 3.06
2699 2848 1.148310 ACTCGTCGCAAAAGTGGATG 58.852 50.000 0.00 0.00 0.00 3.51
2700 2849 2.736144 TACTCGTCGCAAAAGTGGAT 57.264 45.000 0.00 0.00 0.00 3.41
2701 2850 2.512485 TTACTCGTCGCAAAAGTGGA 57.488 45.000 0.00 0.00 0.00 4.02
2702 2851 3.806316 AATTACTCGTCGCAAAAGTGG 57.194 42.857 0.00 0.00 0.00 4.00
2703 2852 3.906008 CCAAATTACTCGTCGCAAAAGTG 59.094 43.478 0.00 0.00 0.00 3.16
2704 2853 3.810941 TCCAAATTACTCGTCGCAAAAGT 59.189 39.130 0.00 0.00 0.00 2.66
2705 2854 4.398549 TCCAAATTACTCGTCGCAAAAG 57.601 40.909 0.00 0.00 0.00 2.27
2706 2855 4.529446 GTTCCAAATTACTCGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
2707 2856 3.363182 CGTTCCAAATTACTCGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
2708 2857 2.156117 CGTTCCAAATTACTCGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
2709 2858 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2710 2859 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2711 2860 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2712 2861 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2713 2862 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2714 2863 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2715 2864 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2716 2865 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2717 2866 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2718 2867 7.071447 TGAATATACTCCCTCCGTTCCAAATTA 59.929 37.037 0.00 0.00 0.00 1.40
2719 2868 5.906772 ATATACTCCCTCCGTTCCAAATT 57.093 39.130 0.00 0.00 0.00 1.82
2720 2869 5.368523 TGAATATACTCCCTCCGTTCCAAAT 59.631 40.000 0.00 0.00 0.00 2.32
2721 2870 4.717778 TGAATATACTCCCTCCGTTCCAAA 59.282 41.667 0.00 0.00 0.00 3.28
2722 2871 4.291792 TGAATATACTCCCTCCGTTCCAA 58.708 43.478 0.00 0.00 0.00 3.53
2723 2872 3.918566 TGAATATACTCCCTCCGTTCCA 58.081 45.455 0.00 0.00 0.00 3.53
2724 2873 4.262506 CCTTGAATATACTCCCTCCGTTCC 60.263 50.000 0.00 0.00 0.00 3.62
2725 2874 4.262506 CCCTTGAATATACTCCCTCCGTTC 60.263 50.000 0.00 0.00 0.00 3.95
2726 2875 3.646637 CCCTTGAATATACTCCCTCCGTT 59.353 47.826 0.00 0.00 0.00 4.44
2727 2876 3.116862 TCCCTTGAATATACTCCCTCCGT 60.117 47.826 0.00 0.00 0.00 4.69
2728 2877 3.507411 TCCCTTGAATATACTCCCTCCG 58.493 50.000 0.00 0.00 0.00 4.63
2729 2878 5.221945 CCTTTCCCTTGAATATACTCCCTCC 60.222 48.000 0.00 0.00 0.00 4.30
2730 2879 5.221945 CCCTTTCCCTTGAATATACTCCCTC 60.222 48.000 0.00 0.00 0.00 4.30
2731 2880 4.665483 CCCTTTCCCTTGAATATACTCCCT 59.335 45.833 0.00 0.00 0.00 4.20
2732 2881 4.202577 CCCCTTTCCCTTGAATATACTCCC 60.203 50.000 0.00 0.00 0.00 4.30
2733 2882 4.202577 CCCCCTTTCCCTTGAATATACTCC 60.203 50.000 0.00 0.00 0.00 3.85
2734 2883 4.663592 TCCCCCTTTCCCTTGAATATACTC 59.336 45.833 0.00 0.00 0.00 2.59
2735 2884 4.652628 TCCCCCTTTCCCTTGAATATACT 58.347 43.478 0.00 0.00 0.00 2.12
2736 2885 5.600669 ATCCCCCTTTCCCTTGAATATAC 57.399 43.478 0.00 0.00 0.00 1.47
2737 2886 5.679139 TCAATCCCCCTTTCCCTTGAATATA 59.321 40.000 0.00 0.00 0.00 0.86
2738 2887 4.485775 TCAATCCCCCTTTCCCTTGAATAT 59.514 41.667 0.00 0.00 0.00 1.28
2739 2888 3.861695 TCAATCCCCCTTTCCCTTGAATA 59.138 43.478 0.00 0.00 0.00 1.75
2740 2889 2.659521 TCAATCCCCCTTTCCCTTGAAT 59.340 45.455 0.00 0.00 0.00 2.57
2741 2890 2.077803 TCAATCCCCCTTTCCCTTGAA 58.922 47.619 0.00 0.00 0.00 2.69
2742 2891 1.766951 TCAATCCCCCTTTCCCTTGA 58.233 50.000 0.00 0.00 0.00 3.02
2743 2892 2.854736 ATCAATCCCCCTTTCCCTTG 57.145 50.000 0.00 0.00 0.00 3.61
2744 2893 3.206464 TGTATCAATCCCCCTTTCCCTT 58.794 45.455 0.00 0.00 0.00 3.95
2745 2894 2.871796 TGTATCAATCCCCCTTTCCCT 58.128 47.619 0.00 0.00 0.00 4.20
2746 2895 3.680777 TTGTATCAATCCCCCTTTCCC 57.319 47.619 0.00 0.00 0.00 3.97
2747 2896 5.660864 TGATTTTGTATCAATCCCCCTTTCC 59.339 40.000 0.00 0.00 30.64 3.13
2748 2897 6.183360 CCTGATTTTGTATCAATCCCCCTTTC 60.183 42.308 0.00 0.00 30.64 2.62
2749 2898 5.662657 CCTGATTTTGTATCAATCCCCCTTT 59.337 40.000 0.00 0.00 30.64 3.11
2750 2899 5.211201 CCTGATTTTGTATCAATCCCCCTT 58.789 41.667 0.00 0.00 30.64 3.95
2751 2900 4.808042 CCTGATTTTGTATCAATCCCCCT 58.192 43.478 0.00 0.00 30.64 4.79
2752 2901 3.321968 GCCTGATTTTGTATCAATCCCCC 59.678 47.826 0.00 0.00 30.64 5.40
2753 2902 4.218312 AGCCTGATTTTGTATCAATCCCC 58.782 43.478 0.00 0.00 30.64 4.81
2754 2903 5.241728 GGTAGCCTGATTTTGTATCAATCCC 59.758 44.000 0.00 0.00 30.64 3.85
2755 2904 5.241728 GGGTAGCCTGATTTTGTATCAATCC 59.758 44.000 2.95 0.00 30.64 3.01
2756 2905 6.064717 AGGGTAGCCTGATTTTGTATCAATC 58.935 40.000 14.01 0.00 0.00 2.67
2757 2906 6.018433 AGGGTAGCCTGATTTTGTATCAAT 57.982 37.500 14.01 0.00 0.00 2.57
2758 2907 5.450818 AGGGTAGCCTGATTTTGTATCAA 57.549 39.130 14.01 0.00 0.00 2.57
2853 3002 1.466167 CCTGAGCAACTGATGAAACCG 59.534 52.381 0.00 0.00 0.00 4.44
2855 3004 1.200948 GGCCTGAGCAACTGATGAAAC 59.799 52.381 0.00 0.00 42.56 2.78
3023 3184 1.762370 TCAGCAGTCTTGTCAACTCCA 59.238 47.619 0.00 0.00 0.00 3.86
3028 3189 3.969287 ATAGCTCAGCAGTCTTGTCAA 57.031 42.857 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.