Multiple sequence alignment - TraesCS4A01G266000

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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 TraesCS4A01G266000 chr4A 100.000 3014 0 0 1 3014 578177188 578174175 0.000000e+00 5529
1 TraesCS4A01G266000 chr4A 93.390 2133 109 11 1 2123 578006029 578008139 0.000000e+00 3129
2 TraesCS4A01G266000 chr4A 89.961 1036 93 8 982 2016 578233566 578234591 0.000000e+00 1327
3 TraesCS4A01G266000 chr4A 98.551 207 3 0 2193 2399 578174740 578174534 1.710000e-97 366
4 TraesCS4A01G266000 chr4A 98.551 207 3 0 2449 2655 578174996 578174790 1.710000e-97 366
5 TraesCS4A01G266000 chr4A 81.337 359 40 11 121 474 578104756 578104420 1.780000e-67 267
6 TraesCS4A01G266000 chr4A 85.841 113 14 2 5 116 578104925 578104814 5.280000e-23 119
7 TraesCS4A01G266000 chr4B 91.900 2210 127 26 7 2179 37298432 37296238 0.000000e+00 3042
8 TraesCS4A01G266000 chr4B 89.768 1036 95 7 982 2016 37174481 37173456 0.000000e+00 1315
9 TraesCS4A01G266000 chr4B 78.657 834 143 20 1137 1963 36013811 36013006 3.440000e-144 521
10 TraesCS4A01G266000 chr4D 92.279 2176 110 21 1 2150 25364989 25362846 0.000000e+00 3035
11 TraesCS4A01G266000 chr4D 90.887 1240 97 9 926 2161 25321329 25320102 0.000000e+00 1650
12 TraesCS4A01G266000 chr4D 89.672 1036 96 8 982 2016 25194510 25193485 0.000000e+00 1310
13 TraesCS4A01G266000 chr4D 78.513 861 148 24 1134 1986 25159691 25160522 5.720000e-147 531
14 TraesCS4A01G266000 chr4D 85.893 319 27 5 625 927 25338833 25338517 1.040000e-84 324
15 TraesCS4A01G266000 chr3B 89.969 1595 112 19 578 2128 39544729 39546319 0.000000e+00 2015
16 TraesCS4A01G266000 chr3B 89.773 440 32 6 2582 3014 800827953 800827520 4.390000e-153 551
17 TraesCS4A01G266000 chr3B 93.113 363 16 4 2657 3014 756249383 756249025 9.570000e-145 523
18 TraesCS4A01G266000 chr3B 93.113 363 15 5 2657 3014 770343681 770344038 9.570000e-145 523
19 TraesCS4A01G266000 chr3B 94.444 90 3 1 2581 2668 756249498 756249409 1.460000e-28 137
20 TraesCS4A01G266000 chr3B 97.368 76 2 0 2323 2398 770343564 770343639 2.440000e-26 130
21 TraesCS4A01G266000 chr3B 97.297 74 2 0 2325 2398 756249498 756249425 3.150000e-25 126
22 TraesCS4A01G266000 chr5A 93.939 363 13 5 2657 3012 564741045 564741405 9.510000e-150 540
23 TraesCS4A01G266000 chr5A 95.364 151 7 0 2434 2584 564743637 564743787 1.080000e-59 241
24 TraesCS4A01G266000 chr5A 93.478 92 4 1 2579 2668 564740928 564741019 5.240000e-28 135
25 TraesCS4A01G266000 chr5A 97.015 67 2 0 2155 2221 564737243 564737177 2.460000e-21 113
26 TraesCS4A01G266000 chr6B 92.632 380 15 6 2642 3014 692803995 692804368 4.420000e-148 534
27 TraesCS4A01G266000 chr6B 91.842 380 18 7 2642 3014 696371631 696371258 4.450000e-143 518
28 TraesCS4A01G266000 chr6B 96.026 151 5 1 2159 2308 49697389 49697239 8.350000e-61 244
29 TraesCS4A01G266000 chr6B 94.702 151 8 0 2433 2583 696371906 696371756 5.020000e-58 235
30 TraesCS4A01G266000 chr6B 83.396 265 13 10 2435 2668 692803722 692803986 1.820000e-52 217
31 TraesCS4A01G266000 chr6B 81.702 235 14 9 2193 2398 692803736 692803970 5.170000e-38 169
32 TraesCS4A01G266000 chr6B 94.565 92 3 1 2579 2668 49696784 49696693 1.130000e-29 141
33 TraesCS4A01G266000 chr6B 94.565 92 3 1 2579 2668 696371731 696371640 1.130000e-29 141
34 TraesCS4A01G266000 chr6B 97.368 76 2 0 2323 2398 49696784 49696709 2.440000e-26 130
35 TraesCS4A01G266000 chr6B 97.368 76 2 0 2323 2398 696371731 696371656 2.440000e-26 130
36 TraesCS4A01G266000 chr1A 93.664 363 13 5 2657 3014 589455711 589456068 4.420000e-148 534
37 TraesCS4A01G266000 chr1A 93.548 93 2 3 2579 2668 514555944 514556035 5.240000e-28 135
38 TraesCS4A01G266000 chr1A 97.368 76 1 1 2323 2398 514555944 514556018 8.770000e-26 128
39 TraesCS4A01G266000 chr5B 92.368 380 17 6 2642 3014 684052867 684053241 5.720000e-147 531
40 TraesCS4A01G266000 chr5B 94.702 151 8 0 2433 2583 684052591 684052741 5.020000e-58 235
41 TraesCS4A01G266000 chr2D 92.021 376 19 7 2642 3014 10034846 10035213 4.450000e-143 518
42 TraesCS4A01G266000 chr2D 93.642 173 11 0 2159 2331 609943677 609943505 2.980000e-65 259
43 TraesCS4A01G266000 chr2D 94.156 154 9 0 2431 2584 551838995 551839148 5.020000e-58 235
44 TraesCS4A01G266000 chr2D 95.652 69 2 1 2154 2221 551838899 551838967 3.180000e-20 110
45 TraesCS4A01G266000 chr2A 88.806 402 34 7 2620 3014 8710744 8711141 1.620000e-132 483
46 TraesCS4A01G266000 chr2A 95.364 151 7 0 2434 2584 22156195 22156345 1.080000e-59 241
47 TraesCS4A01G266000 chr2A 93.571 140 8 1 2190 2328 22156206 22156345 1.100000e-49 207
48 TraesCS4A01G266000 chr2A 97.368 76 2 0 2323 2398 707295727 707295652 2.440000e-26 130
49 TraesCS4A01G266000 chr6A 92.982 171 12 0 2158 2328 37779182 37779352 1.790000e-62 250
50 TraesCS4A01G266000 chr6A 95.652 92 2 1 2579 2668 537816446 537816537 2.420000e-31 147
51 TraesCS4A01G266000 chr6A 98.684 76 1 0 2323 2398 537816446 537816521 5.240000e-28 135
52 TraesCS4A01G266000 chr7B 95.484 155 7 0 2433 2587 707282240 707282086 6.450000e-62 248
53 TraesCS4A01G266000 chr7B 93.525 139 9 0 2193 2331 707282224 707282086 1.100000e-49 207
54 TraesCS4A01G266000 chr7B 94.286 70 4 0 2152 2221 606793330 606793261 1.140000e-19 108
55 TraesCS4A01G266000 chr3A 94.839 155 8 0 2433 2587 25183122 25182968 3.000000e-60 243
56 TraesCS4A01G266000 chr3A 91.765 170 14 0 2159 2328 93319854 93320023 1.400000e-58 237
57 TraesCS4A01G266000 chr3A 93.007 143 9 1 2190 2331 25183110 25182968 1.100000e-49 207
58 TraesCS4A01G266000 chr3A 94.521 73 2 1 2149 2221 693572480 693572550 8.830000e-21 111
59 TraesCS4A01G266000 chr2B 95.364 151 7 0 2433 2583 49653960 49654110 1.080000e-59 241
60 TraesCS4A01G266000 chr7D 94.737 152 8 0 2433 2584 613216616 613216767 1.400000e-58 237
61 TraesCS4A01G266000 chr7D 89.610 154 15 1 2178 2331 105373844 105373692 8.530000e-46 195


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 TraesCS4A01G266000 chr4A 578174175 578177188 3013 True 2087.000000 5529 99.034000 1 3014 3 chr4A.!!$R2 3013
1 TraesCS4A01G266000 chr4A 578006029 578008139 2110 False 3129.000000 3129 93.390000 1 2123 1 chr4A.!!$F1 2122
2 TraesCS4A01G266000 chr4A 578233566 578234591 1025 False 1327.000000 1327 89.961000 982 2016 1 chr4A.!!$F2 1034
3 TraesCS4A01G266000 chr4B 37296238 37298432 2194 True 3042.000000 3042 91.900000 7 2179 1 chr4B.!!$R3 2172
4 TraesCS4A01G266000 chr4B 37173456 37174481 1025 True 1315.000000 1315 89.768000 982 2016 1 chr4B.!!$R2 1034
5 TraesCS4A01G266000 chr4B 36013006 36013811 805 True 521.000000 521 78.657000 1137 1963 1 chr4B.!!$R1 826
6 TraesCS4A01G266000 chr4D 25362846 25364989 2143 True 3035.000000 3035 92.279000 1 2150 1 chr4D.!!$R4 2149
7 TraesCS4A01G266000 chr4D 25320102 25321329 1227 True 1650.000000 1650 90.887000 926 2161 1 chr4D.!!$R2 1235
8 TraesCS4A01G266000 chr4D 25193485 25194510 1025 True 1310.000000 1310 89.672000 982 2016 1 chr4D.!!$R1 1034
9 TraesCS4A01G266000 chr4D 25159691 25160522 831 False 531.000000 531 78.513000 1134 1986 1 chr4D.!!$F1 852
10 TraesCS4A01G266000 chr3B 39544729 39546319 1590 False 2015.000000 2015 89.969000 578 2128 1 chr3B.!!$F1 1550
11 TraesCS4A01G266000 chr5A 564740928 564743787 2859 False 305.333333 540 94.260333 2434 3012 3 chr5A.!!$F1 578
12 TraesCS4A01G266000 chr6B 692803722 692804368 646 False 306.666667 534 85.910000 2193 3014 3 chr6B.!!$F1 821
13 TraesCS4A01G266000 chr6B 696371258 696371906 648 True 256.000000 518 94.619250 2323 3014 4 chr6B.!!$R2 691
14 TraesCS4A01G266000 chr5B 684052591 684053241 650 False 383.000000 531 93.535000 2433 3014 2 chr5B.!!$F1 581

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
351 371 1.809869 CTGGAGAATGACGAGGCGA 59.19 57.895 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 2330 0.038526 CGGCCTTACTATGCCTACGG 60.039 60.0 0.0 0.0 45.71 4.02 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
136 137 8.243426 TGAGATACTTATGTTGGTGAAATTTGC 58.757 33.333 0.00 0.00 0.00 3.68
162 163 5.130292 TCTTAACTCGGTTAGTGGACTTG 57.870 43.478 0.00 0.00 38.88 3.16
187 188 7.920151 TGAATTATGTTTGGAACTTTGTGACAG 59.080 33.333 0.00 0.00 0.00 3.51
188 189 6.767524 TTATGTTTGGAACTTTGTGACAGT 57.232 33.333 0.00 0.00 0.00 3.55
189 190 5.659440 ATGTTTGGAACTTTGTGACAGTT 57.341 34.783 0.00 0.00 37.18 3.16
190 191 4.804108 TGTTTGGAACTTTGTGACAGTTG 58.196 39.130 0.00 0.00 34.49 3.16
191 192 4.520874 TGTTTGGAACTTTGTGACAGTTGA 59.479 37.500 0.00 0.00 34.49 3.18
192 193 4.695217 TTGGAACTTTGTGACAGTTGAC 57.305 40.909 0.00 0.00 34.49 3.18
193 194 3.680490 TGGAACTTTGTGACAGTTGACA 58.320 40.909 0.00 0.00 34.49 3.58
227 228 6.475727 AGACGTACATTATGTTGATGTAGTGC 59.524 38.462 2.23 0.00 39.81 4.40
294 297 7.624360 AACAATGTATTGATAACACGGTCAT 57.376 32.000 11.29 0.00 40.14 3.06
319 339 5.600669 AAATAAAAGGAGAAGGTGGAGGT 57.399 39.130 0.00 0.00 0.00 3.85
320 340 2.959465 AAAAGGAGAAGGTGGAGGTG 57.041 50.000 0.00 0.00 0.00 4.00
321 341 1.821088 AAAGGAGAAGGTGGAGGTGT 58.179 50.000 0.00 0.00 0.00 4.16
351 371 1.809869 CTGGAGAATGACGAGGCGA 59.190 57.895 0.00 0.00 0.00 5.54
382 403 3.882888 GCAATTGCAGTTAGGGTATAGCA 59.117 43.478 25.36 0.00 41.59 3.49
418 440 8.803397 AAGATTGATCTCAAGAATGTGAATGA 57.197 30.769 0.00 0.00 39.47 2.57
428 450 9.159364 CTCAAGAATGTGAATGAAGATCTAACA 57.841 33.333 0.00 0.00 0.00 2.41
439 462 4.651503 TGAAGATCTAACAGCTAGGGGAAG 59.348 45.833 0.00 0.00 0.00 3.46
553 578 4.844349 ACAAGTGTATCTTACCAGCCAT 57.156 40.909 0.00 0.00 34.66 4.40
689 717 4.081917 AGCAATGTTTTACGGGGGTATTTG 60.082 41.667 0.00 0.00 0.00 2.32
720 748 6.705863 AGCTTTGGCATAAATCTCCTTAAG 57.294 37.500 0.00 0.00 41.70 1.85
857 920 3.076621 CTCAGCACAGTCAGCCAAATTA 58.923 45.455 0.00 0.00 0.00 1.40
951 1040 7.809665 TCATCAATTTCATCATACTATTGCCG 58.190 34.615 0.00 0.00 0.00 5.69
1043 1138 2.669569 GCCGCAGCTTCACCTCAA 60.670 61.111 0.00 0.00 35.50 3.02
1156 1251 0.173708 GTTCCGCCTGATCGACTTCT 59.826 55.000 0.00 0.00 0.00 2.85
1159 1254 0.030908 CCGCCTGATCGACTTCTACC 59.969 60.000 0.00 0.00 0.00 3.18
1602 1700 4.555709 TCCCGCGCCGGCAAATAT 62.556 61.111 28.98 0.00 46.86 1.28
1753 1852 3.522731 CCGTCCTGGAGCTCCTCG 61.523 72.222 32.28 26.59 42.00 4.63
2017 2125 0.179137 CGAGCAGCGGTGTTGATAGA 60.179 55.000 17.07 0.00 36.03 1.98
2059 2177 3.245797 ACTGTCACATTCTCGAATCGTG 58.754 45.455 1.52 0.00 34.34 4.35
2113 2234 3.944087 AGTGGACCATACTTTGAGCTTC 58.056 45.455 0.00 0.00 0.00 3.86
2128 2249 1.139947 CTTCGAAGGGTCTCGCTCC 59.860 63.158 17.70 0.00 38.73 4.70
2158 2279 4.624125 GCATCTCCAGCCCATACCTTATAC 60.624 50.000 0.00 0.00 0.00 1.47
2159 2280 4.207698 TCTCCAGCCCATACCTTATACA 57.792 45.455 0.00 0.00 0.00 2.29
2160 2281 3.901844 TCTCCAGCCCATACCTTATACAC 59.098 47.826 0.00 0.00 0.00 2.90
2161 2282 3.904339 CTCCAGCCCATACCTTATACACT 59.096 47.826 0.00 0.00 0.00 3.55
2162 2283 5.082633 TCCAGCCCATACCTTATACACTA 57.917 43.478 0.00 0.00 0.00 2.74
2163 2284 4.836736 TCCAGCCCATACCTTATACACTAC 59.163 45.833 0.00 0.00 0.00 2.73
2164 2285 4.020485 CCAGCCCATACCTTATACACTACC 60.020 50.000 0.00 0.00 0.00 3.18
2165 2286 3.830755 AGCCCATACCTTATACACTACCG 59.169 47.826 0.00 0.00 0.00 4.02
2166 2287 3.056322 GCCCATACCTTATACACTACCGG 60.056 52.174 0.00 0.00 0.00 5.28
2167 2288 4.410099 CCCATACCTTATACACTACCGGA 58.590 47.826 9.46 0.00 0.00 5.14
2168 2289 4.834496 CCCATACCTTATACACTACCGGAA 59.166 45.833 9.46 0.00 0.00 4.30
2172 2293 8.031277 CCATACCTTATACACTACCGGAATAAC 58.969 40.741 9.46 0.00 0.00 1.89
2173 2294 6.410942 ACCTTATACACTACCGGAATAACC 57.589 41.667 9.46 0.00 0.00 2.85
2174 2295 6.138967 ACCTTATACACTACCGGAATAACCT 58.861 40.000 9.46 0.00 36.31 3.50
2175 2296 6.612863 ACCTTATACACTACCGGAATAACCTT 59.387 38.462 9.46 0.00 36.31 3.50
2181 2302 6.461640 ACACTACCGGAATAACCTTATATGC 58.538 40.000 9.46 0.00 36.31 3.14
2182 2303 5.873164 CACTACCGGAATAACCTTATATGCC 59.127 44.000 9.46 0.00 36.31 4.40
2183 2304 5.783875 ACTACCGGAATAACCTTATATGCCT 59.216 40.000 9.46 0.00 36.31 4.75
2184 2305 6.955851 ACTACCGGAATAACCTTATATGCCTA 59.044 38.462 9.46 0.00 36.31 3.93
2185 2306 6.046290 ACCGGAATAACCTTATATGCCTAC 57.954 41.667 9.46 0.00 36.31 3.18
2186 2307 5.107133 CCGGAATAACCTTATATGCCTACG 58.893 45.833 0.00 0.00 36.31 3.51
2187 2308 5.107133 CGGAATAACCTTATATGCCTACGG 58.893 45.833 0.00 0.00 36.31 4.02
2188 2309 4.874396 GGAATAACCTTATATGCCTACGGC 59.126 45.833 0.00 0.00 41.73 5.68
2189 2310 6.144057 GGAATAACCTTATATGCCTACGGCC 61.144 48.000 1.94 0.00 41.11 6.13
2190 2311 8.264233 GGAATAACCTTATATGCCTACGGCCT 62.264 46.154 0.00 0.00 41.11 5.19
2191 2312 9.638739 GGAATAACCTTATATGCCTACGGCCTT 62.639 44.444 0.00 0.00 41.11 4.35
2199 2320 2.011540 GCCTACGGCCTTATCTATGC 57.988 55.000 0.00 0.00 44.06 3.14
2200 2321 1.405661 GCCTACGGCCTTATCTATGCC 60.406 57.143 0.00 0.00 44.06 4.40
2205 2326 2.086054 GGCCTTATCTATGCCGACAG 57.914 55.000 0.00 0.00 35.08 3.51
2206 2327 1.433534 GCCTTATCTATGCCGACAGC 58.566 55.000 0.00 0.00 44.14 4.40
2207 2328 1.001406 GCCTTATCTATGCCGACAGCT 59.999 52.381 0.00 0.00 44.23 4.24
2208 2329 2.681706 CCTTATCTATGCCGACAGCTG 58.318 52.381 13.48 13.48 44.23 4.24
2209 2330 2.064762 CTTATCTATGCCGACAGCTGC 58.935 52.381 15.27 5.81 44.23 5.25
2210 2331 0.318441 TATCTATGCCGACAGCTGCC 59.682 55.000 15.27 0.16 44.23 4.85
2211 2332 2.705934 ATCTATGCCGACAGCTGCCG 62.706 60.000 16.16 16.16 44.23 5.69
2212 2333 3.723235 CTATGCCGACAGCTGCCGT 62.723 63.158 21.14 5.47 44.23 5.68
2213 2334 2.349969 CTATGCCGACAGCTGCCGTA 62.350 60.000 21.14 10.17 44.23 4.02
2214 2335 2.349969 TATGCCGACAGCTGCCGTAG 62.350 60.000 21.14 7.96 44.23 3.51
2231 2352 4.338327 GGCATAGTAAGGCCGTCG 57.662 61.111 0.00 0.00 43.74 5.12
2232 2353 1.300697 GGCATAGTAAGGCCGTCGG 60.301 63.158 6.99 6.99 43.74 4.79
2247 2368 4.750952 CCGTCGGCATATATCGATCTAT 57.249 45.455 0.00 0.00 37.73 1.98
2248 2369 4.467735 CCGTCGGCATATATCGATCTATG 58.532 47.826 20.76 20.76 37.73 2.23
2249 2370 3.908978 CGTCGGCATATATCGATCTATGC 59.091 47.826 32.20 32.20 46.08 3.14
2255 2376 5.394802 GCATATATCGATCTATGCCTACGG 58.605 45.833 30.95 9.81 42.76 4.02
2280 2401 4.373348 CCGTAGGCATAGTTAGGCTATC 57.627 50.000 0.00 0.00 46.14 2.08
2281 2402 3.181499 CCGTAGGCATAGTTAGGCTATCG 60.181 52.174 0.00 0.00 46.14 2.92
2282 2403 3.181499 CGTAGGCATAGTTAGGCTATCGG 60.181 52.174 0.00 0.00 44.47 4.18
2283 2404 1.550976 AGGCATAGTTAGGCTATCGGC 59.449 52.381 0.00 2.11 40.43 5.54
2284 2405 1.275291 GGCATAGTTAGGCTATCGGCA 59.725 52.381 14.38 0.55 44.01 5.69
2285 2406 2.093447 GGCATAGTTAGGCTATCGGCAT 60.093 50.000 14.38 0.00 44.01 4.40
2286 2407 3.132289 GGCATAGTTAGGCTATCGGCATA 59.868 47.826 14.38 0.00 44.01 3.14
2287 2408 4.363999 GCATAGTTAGGCTATCGGCATAG 58.636 47.826 0.00 0.00 44.01 2.23
2288 2409 4.098044 GCATAGTTAGGCTATCGGCATAGA 59.902 45.833 0.00 0.00 44.01 1.98
2289 2410 5.734786 GCATAGTTAGGCTATCGGCATAGAG 60.735 48.000 0.00 0.00 44.01 2.43
2290 2411 3.093057 AGTTAGGCTATCGGCATAGAGG 58.907 50.000 0.00 0.00 44.01 3.69
2291 2412 2.826725 GTTAGGCTATCGGCATAGAGGT 59.173 50.000 0.00 0.00 44.01 3.85
2292 2413 1.261480 AGGCTATCGGCATAGAGGTG 58.739 55.000 7.77 0.00 44.01 4.00
2293 2414 0.247736 GGCTATCGGCATAGAGGTGG 59.752 60.000 7.77 0.00 44.01 4.61
2294 2415 0.390472 GCTATCGGCATAGAGGTGGC 60.390 60.000 7.77 0.00 41.35 5.01
2295 2416 0.247736 CTATCGGCATAGAGGTGGCC 59.752 60.000 0.00 0.00 44.27 5.36
2296 2417 1.192146 TATCGGCATAGAGGTGGCCC 61.192 60.000 0.00 0.00 44.90 5.80
2297 2418 2.972589 ATCGGCATAGAGGTGGCCCT 62.973 60.000 0.00 0.00 44.90 5.19
2313 2434 4.087892 CTCGTGGCCAGGGGACAG 62.088 72.222 21.06 8.49 43.97 3.51
2314 2435 4.631740 TCGTGGCCAGGGGACAGA 62.632 66.667 24.54 1.67 43.97 3.41
2315 2436 4.394712 CGTGGCCAGGGGACAGAC 62.395 72.222 17.92 0.00 43.97 3.51
2316 2437 4.394712 GTGGCCAGGGGACAGACG 62.395 72.222 5.11 0.00 43.97 4.18
2355 2476 6.662414 CCGTCGGCATAAATATCATATGTT 57.338 37.500 0.00 0.00 34.06 2.71
2356 2477 7.072177 CCGTCGGCATAAATATCATATGTTT 57.928 36.000 0.00 0.00 34.06 2.83
2357 2478 7.526608 CCGTCGGCATAAATATCATATGTTTT 58.473 34.615 0.00 4.77 34.06 2.43
2358 2479 8.020819 CCGTCGGCATAAATATCATATGTTTTT 58.979 33.333 0.00 4.44 34.06 1.94
2377 2498 3.343941 TTTTATTAGGAGCTGCCACGT 57.656 42.857 0.00 0.00 40.02 4.49
2378 2499 2.309528 TTATTAGGAGCTGCCACGTG 57.690 50.000 9.08 9.08 40.02 4.49
2379 2500 0.464036 TATTAGGAGCTGCCACGTGG 59.536 55.000 30.66 30.66 40.02 4.94
2389 2510 4.115279 CCACGTGGCAGAGCTATG 57.885 61.111 24.02 3.34 32.30 2.23
2390 2511 2.176273 CCACGTGGCAGAGCTATGC 61.176 63.158 24.98 24.98 45.74 3.14
2391 2512 1.153489 CACGTGGCAGAGCTATGCT 60.153 57.895 30.51 10.16 45.75 3.79
2392 2513 1.153489 ACGTGGCAGAGCTATGCTG 60.153 57.895 30.51 22.24 45.75 4.41
2393 2514 1.142531 CGTGGCAGAGCTATGCTGA 59.857 57.895 30.51 16.25 45.75 4.26
2394 2515 1.150567 CGTGGCAGAGCTATGCTGAC 61.151 60.000 30.51 24.37 45.75 3.51
2395 2516 1.142531 TGGCAGAGCTATGCTGACG 59.857 57.895 30.51 0.00 44.47 4.35
2396 2517 1.593750 GGCAGAGCTATGCTGACGG 60.594 63.158 30.51 0.00 45.75 4.79
2397 2518 2.243264 GCAGAGCTATGCTGACGGC 61.243 63.158 25.63 0.00 43.07 5.68
2398 2519 1.440893 CAGAGCTATGCTGACGGCT 59.559 57.895 7.96 0.00 39.88 5.52
2426 2547 4.251760 GATGGAGCTATGCCGACG 57.748 61.111 0.00 0.00 0.00 5.12
2427 2548 1.373497 GATGGAGCTATGCCGACGG 60.373 63.158 10.29 10.29 0.00 4.79
2428 2549 2.088674 GATGGAGCTATGCCGACGGT 62.089 60.000 16.73 0.00 0.00 4.83
2429 2550 2.027751 GGAGCTATGCCGACGGTC 59.972 66.667 16.73 8.54 0.00 4.79
2430 2551 2.491022 GGAGCTATGCCGACGGTCT 61.491 63.158 16.73 5.65 0.00 3.85
2431 2552 1.170919 GGAGCTATGCCGACGGTCTA 61.171 60.000 16.73 6.57 0.00 2.59
2432 2553 0.040246 GAGCTATGCCGACGGTCTAC 60.040 60.000 16.73 0.00 0.00 2.59
2433 2554 1.007618 GCTATGCCGACGGTCTACC 60.008 63.158 16.73 0.00 0.00 3.18
2444 2565 2.412605 GGTCTACCGTCGGCATAGT 58.587 57.895 12.28 0.00 0.00 2.12
2445 2566 0.743097 GGTCTACCGTCGGCATAGTT 59.257 55.000 12.28 0.00 0.00 2.24
2446 2567 1.268948 GGTCTACCGTCGGCATAGTTC 60.269 57.143 12.28 5.08 0.00 3.01
2447 2568 1.027357 TCTACCGTCGGCATAGTTCC 58.973 55.000 12.28 0.00 0.00 3.62
2448 2569 0.742505 CTACCGTCGGCATAGTTCCA 59.257 55.000 12.28 0.00 0.00 3.53
2449 2570 1.340248 CTACCGTCGGCATAGTTCCAT 59.660 52.381 12.28 0.00 0.00 3.41
2450 2571 0.104304 ACCGTCGGCATAGTTCCATC 59.896 55.000 12.28 0.00 0.00 3.51
2451 2572 0.389391 CCGTCGGCATAGTTCCATCT 59.611 55.000 0.00 0.00 0.00 2.90
2452 2573 1.611977 CCGTCGGCATAGTTCCATCTA 59.388 52.381 0.00 0.00 0.00 1.98
2453 2574 2.231478 CCGTCGGCATAGTTCCATCTAT 59.769 50.000 0.00 0.00 0.00 1.98
2454 2575 3.245797 CGTCGGCATAGTTCCATCTATG 58.754 50.000 8.72 8.72 45.70 2.23
2461 2582 4.748892 CATAGTTCCATCTATGCCTACGG 58.251 47.826 0.00 0.00 40.14 4.02
2487 2608 4.338327 GGCATAGTAAGGCCGTCG 57.662 61.111 0.00 0.00 43.74 5.12
2488 2609 1.300697 GGCATAGTAAGGCCGTCGG 60.301 63.158 6.99 6.99 43.74 4.79
2503 2624 4.750952 CCGTCGGCATATATCGATCTAT 57.249 45.455 0.00 0.00 37.73 1.98
2504 2625 4.467735 CCGTCGGCATATATCGATCTATG 58.532 47.826 20.76 20.76 37.73 2.23
2505 2626 3.908978 CGTCGGCATATATCGATCTATGC 59.091 47.826 32.20 32.20 46.08 3.14
2511 2632 5.394802 GCATATATCGATCTATGCCTACGG 58.605 45.833 30.95 9.81 42.76 4.02
2536 2657 4.373348 CCGTAGGCATAGTTAGGCTATC 57.627 50.000 0.00 0.00 46.14 2.08
2537 2658 3.181499 CCGTAGGCATAGTTAGGCTATCG 60.181 52.174 0.00 0.00 46.14 2.92
2538 2659 3.181499 CGTAGGCATAGTTAGGCTATCGG 60.181 52.174 0.00 0.00 44.47 4.18
2539 2660 1.550976 AGGCATAGTTAGGCTATCGGC 59.449 52.381 0.00 2.11 40.43 5.54
2540 2661 1.275291 GGCATAGTTAGGCTATCGGCA 59.725 52.381 14.38 0.55 44.01 5.69
2541 2662 2.093447 GGCATAGTTAGGCTATCGGCAT 60.093 50.000 14.38 0.00 44.01 4.40
2542 2663 3.132289 GGCATAGTTAGGCTATCGGCATA 59.868 47.826 14.38 0.00 44.01 3.14
2543 2664 4.363999 GCATAGTTAGGCTATCGGCATAG 58.636 47.826 0.00 0.00 44.01 2.23
2544 2665 4.098044 GCATAGTTAGGCTATCGGCATAGA 59.902 45.833 0.00 0.00 44.01 1.98
2545 2666 5.734786 GCATAGTTAGGCTATCGGCATAGAG 60.735 48.000 0.00 0.00 44.01 2.43
2546 2667 3.093057 AGTTAGGCTATCGGCATAGAGG 58.907 50.000 0.00 0.00 44.01 3.69
2547 2668 2.826725 GTTAGGCTATCGGCATAGAGGT 59.173 50.000 0.00 0.00 44.01 3.85
2548 2669 1.261480 AGGCTATCGGCATAGAGGTG 58.739 55.000 7.77 0.00 44.01 4.00
2549 2670 0.247736 GGCTATCGGCATAGAGGTGG 59.752 60.000 7.77 0.00 44.01 4.61
2550 2671 0.390472 GCTATCGGCATAGAGGTGGC 60.390 60.000 7.77 0.00 41.35 5.01
2551 2672 0.247736 CTATCGGCATAGAGGTGGCC 59.752 60.000 0.00 0.00 44.27 5.36
2552 2673 1.192146 TATCGGCATAGAGGTGGCCC 61.192 60.000 0.00 0.00 44.90 5.80
2553 2674 2.972589 ATCGGCATAGAGGTGGCCCT 62.973 60.000 0.00 0.00 44.90 5.19
2569 2690 4.087892 CTCGTGGCCAGGGGACAG 62.088 72.222 21.06 8.49 43.97 3.51
2570 2691 4.631740 TCGTGGCCAGGGGACAGA 62.632 66.667 24.54 1.67 43.97 3.41
2571 2692 4.394712 CGTGGCCAGGGGACAGAC 62.395 72.222 17.92 0.00 43.97 3.51
2572 2693 4.394712 GTGGCCAGGGGACAGACG 62.395 72.222 5.11 0.00 43.97 4.18
2647 2769 1.153489 CACGTGGCAGAGCTATGCT 60.153 57.895 30.51 10.16 45.75 3.79
2654 2776 1.440893 CAGAGCTATGCTGACGGCT 59.559 57.895 7.96 0.00 39.88 5.52
2849 3016 9.496873 CACAAATTATATATCGACTTGGGGTAA 57.503 33.333 0.00 0.00 0.00 2.85
2915 3084 6.330278 TGAGTATGTTAGAAATGTGACCTCG 58.670 40.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 6.883744 AGTTAAGAAAGGCAAATTTCACCAA 58.116 32.000 9.00 0.65 40.86 3.67
136 137 4.928020 GTCCACTAACCGAGTTAAGAAAGG 59.072 45.833 0.00 0.00 35.64 3.11
162 163 7.920682 ACTGTCACAAAGTTCCAAACATAATTC 59.079 33.333 0.00 0.00 0.00 2.17
187 188 6.174451 TGTACGTCTATCTACAGTGTCAAC 57.826 41.667 0.00 0.00 0.00 3.18
188 189 6.997239 ATGTACGTCTATCTACAGTGTCAA 57.003 37.500 0.00 0.00 0.00 3.18
189 190 6.997239 AATGTACGTCTATCTACAGTGTCA 57.003 37.500 0.00 0.00 0.00 3.58
190 191 8.557864 ACATAATGTACGTCTATCTACAGTGTC 58.442 37.037 0.00 0.00 0.00 3.67
191 192 8.447924 ACATAATGTACGTCTATCTACAGTGT 57.552 34.615 0.00 0.00 0.00 3.55
192 193 9.170584 CAACATAATGTACGTCTATCTACAGTG 57.829 37.037 0.00 0.00 0.00 3.66
193 194 9.117183 TCAACATAATGTACGTCTATCTACAGT 57.883 33.333 0.00 0.00 0.00 3.55
285 288 6.001460 TCTCCTTTTATTTTCATGACCGTGT 58.999 36.000 0.00 0.00 0.00 4.49
289 292 7.315890 CACCTTCTCCTTTTATTTTCATGACC 58.684 38.462 0.00 0.00 0.00 4.02
294 297 6.010219 CCTCCACCTTCTCCTTTTATTTTCA 58.990 40.000 0.00 0.00 0.00 2.69
351 371 0.606401 ACTGCAATTGCCGCTACTGT 60.606 50.000 26.94 11.26 41.18 3.55
382 403 6.154203 TGAGATCAATCTTCACTTCGCTAT 57.846 37.500 0.00 0.00 37.25 2.97
418 440 4.651962 GTCTTCCCCTAGCTGTTAGATCTT 59.348 45.833 0.00 0.00 0.00 2.40
428 450 1.742308 TGGTTTGTCTTCCCCTAGCT 58.258 50.000 0.00 0.00 0.00 3.32
576 601 2.773993 TACACCGGTTTCCTCCATTC 57.226 50.000 2.97 0.00 0.00 2.67
678 706 2.375146 CTTTCCTTCCAAATACCCCCG 58.625 52.381 0.00 0.00 0.00 5.73
689 717 4.535526 TTTATGCCAAAGCTTTCCTTCC 57.464 40.909 9.23 0.00 40.80 3.46
825 888 4.453478 TGACTGTGCTGAGATTTTGATGTC 59.547 41.667 0.00 0.00 0.00 3.06
1503 1601 2.815211 GCAGGCTTGATGTCGCGA 60.815 61.111 3.71 3.71 0.00 5.87
1990 2090 0.729116 CACCGCTGCTCGATCAATTT 59.271 50.000 0.00 0.00 41.67 1.82
1993 2093 1.005037 AACACCGCTGCTCGATCAA 60.005 52.632 0.00 0.00 41.67 2.57
2128 2249 1.446791 GGCTGGAGATGCTCTCAGG 59.553 63.158 13.06 7.46 45.12 3.86
2142 2263 4.321750 CGGTAGTGTATAAGGTATGGGCTG 60.322 50.000 0.00 0.00 0.00 4.85
2147 2268 8.031277 GGTTATTCCGGTAGTGTATAAGGTATG 58.969 40.741 0.00 0.00 0.00 2.39
2150 2271 6.138967 AGGTTATTCCGGTAGTGTATAAGGT 58.861 40.000 0.00 0.00 41.99 3.50
2158 2279 5.873164 GGCATATAAGGTTATTCCGGTAGTG 59.127 44.000 0.00 0.00 41.99 2.74
2159 2280 5.783875 AGGCATATAAGGTTATTCCGGTAGT 59.216 40.000 0.00 0.00 41.99 2.73
2160 2281 6.295719 AGGCATATAAGGTTATTCCGGTAG 57.704 41.667 0.00 0.00 41.99 3.18
2161 2282 6.127647 CGTAGGCATATAAGGTTATTCCGGTA 60.128 42.308 0.00 0.00 41.99 4.02
2162 2283 5.337009 CGTAGGCATATAAGGTTATTCCGGT 60.337 44.000 0.00 0.00 41.99 5.28
2163 2284 5.107133 CGTAGGCATATAAGGTTATTCCGG 58.893 45.833 0.00 0.00 41.99 5.14
2164 2285 5.107133 CCGTAGGCATATAAGGTTATTCCG 58.893 45.833 0.00 0.00 46.14 4.30
2186 2307 1.941668 GCTGTCGGCATAGATAAGGCC 60.942 57.143 0.00 0.00 44.27 5.19
2187 2308 1.001406 AGCTGTCGGCATAGATAAGGC 59.999 52.381 6.39 0.00 44.79 4.35
2188 2309 2.681706 CAGCTGTCGGCATAGATAAGG 58.318 52.381 5.25 0.00 44.79 2.69
2189 2310 2.064762 GCAGCTGTCGGCATAGATAAG 58.935 52.381 16.64 0.00 44.79 1.73
2190 2311 1.270305 GGCAGCTGTCGGCATAGATAA 60.270 52.381 16.64 0.00 44.79 1.75
2191 2312 0.318441 GGCAGCTGTCGGCATAGATA 59.682 55.000 16.64 0.00 44.79 1.98
2192 2313 1.070445 GGCAGCTGTCGGCATAGAT 59.930 57.895 16.64 0.00 44.79 1.98
2193 2314 2.501128 GGCAGCTGTCGGCATAGA 59.499 61.111 16.64 0.00 44.79 1.98
2194 2315 2.963854 CGGCAGCTGTCGGCATAG 60.964 66.667 32.36 3.20 44.79 2.23
2209 2330 0.038526 CGGCCTTACTATGCCTACGG 60.039 60.000 0.00 0.00 45.71 4.02
2210 2331 0.672342 ACGGCCTTACTATGCCTACG 59.328 55.000 0.00 0.00 45.71 3.51
2211 2332 1.335689 CGACGGCCTTACTATGCCTAC 60.336 57.143 0.00 0.00 45.71 3.18
2212 2333 0.956633 CGACGGCCTTACTATGCCTA 59.043 55.000 0.00 0.00 45.71 3.93
2213 2334 1.740285 CGACGGCCTTACTATGCCT 59.260 57.895 0.00 0.00 45.71 4.75
2214 2335 1.300697 CCGACGGCCTTACTATGCC 60.301 63.158 0.00 0.00 44.41 4.40
2215 2336 1.954651 GCCGACGGCCTTACTATGC 60.955 63.158 28.74 0.00 44.06 3.14
2216 2337 4.338327 GCCGACGGCCTTACTATG 57.662 61.111 28.74 0.00 44.06 2.23
2226 2347 4.467735 CATAGATCGATATATGCCGACGG 58.532 47.826 23.01 10.29 37.64 4.79
2227 2348 3.908978 GCATAGATCGATATATGCCGACG 59.091 47.826 37.54 17.20 46.67 5.12
2256 2377 5.887941 ATAGCCTAACTATGCCTACGGCTG 61.888 50.000 9.93 0.00 45.23 4.85
2257 2378 3.818294 ATAGCCTAACTATGCCTACGGCT 60.818 47.826 6.43 0.00 46.98 5.52
2258 2379 2.496470 ATAGCCTAACTATGCCTACGGC 59.504 50.000 0.00 0.00 40.23 5.68
2259 2380 3.181499 CGATAGCCTAACTATGCCTACGG 60.181 52.174 0.00 0.00 41.87 4.02
2260 2381 3.181499 CCGATAGCCTAACTATGCCTACG 60.181 52.174 0.00 0.00 41.87 3.51
2261 2382 3.429135 GCCGATAGCCTAACTATGCCTAC 60.429 52.174 0.00 0.00 41.87 3.18
2262 2383 2.758979 GCCGATAGCCTAACTATGCCTA 59.241 50.000 0.00 0.00 41.87 3.93
2263 2384 1.550976 GCCGATAGCCTAACTATGCCT 59.449 52.381 0.00 0.00 41.87 4.75
2264 2385 1.275291 TGCCGATAGCCTAACTATGCC 59.725 52.381 0.00 0.00 41.87 4.40
2265 2386 2.743636 TGCCGATAGCCTAACTATGC 57.256 50.000 0.00 0.00 41.87 3.14
2266 2387 5.221145 CCTCTATGCCGATAGCCTAACTATG 60.221 48.000 0.00 0.00 41.87 2.23
2267 2388 4.890581 CCTCTATGCCGATAGCCTAACTAT 59.109 45.833 0.00 0.00 44.62 2.12
2268 2389 4.263816 ACCTCTATGCCGATAGCCTAACTA 60.264 45.833 0.00 0.00 42.71 2.24
2269 2390 3.093057 CCTCTATGCCGATAGCCTAACT 58.907 50.000 0.00 0.00 42.71 2.24
2270 2391 2.826725 ACCTCTATGCCGATAGCCTAAC 59.173 50.000 0.00 0.00 42.71 2.34
2271 2392 2.826128 CACCTCTATGCCGATAGCCTAA 59.174 50.000 0.00 0.00 42.71 2.69
2272 2393 2.447443 CACCTCTATGCCGATAGCCTA 58.553 52.381 0.00 0.00 42.71 3.93
2273 2394 1.261480 CACCTCTATGCCGATAGCCT 58.739 55.000 0.00 0.00 42.71 4.58
2274 2395 0.247736 CCACCTCTATGCCGATAGCC 59.752 60.000 0.00 0.00 42.71 3.93
2275 2396 0.390472 GCCACCTCTATGCCGATAGC 60.390 60.000 0.00 0.00 44.14 2.97
2276 2397 0.247736 GGCCACCTCTATGCCGATAG 59.752 60.000 0.00 0.00 35.08 2.08
2277 2398 1.192146 GGGCCACCTCTATGCCGATA 61.192 60.000 4.39 0.00 46.31 2.92
2278 2399 2.520536 GGGCCACCTCTATGCCGAT 61.521 63.158 4.39 0.00 46.31 4.18
2279 2400 3.161450 GGGCCACCTCTATGCCGA 61.161 66.667 4.39 0.00 46.31 5.54
2280 2401 3.164269 AGGGCCACCTCTATGCCG 61.164 66.667 6.18 0.00 46.95 5.69
2296 2417 4.087892 CTGTCCCCTGGCCACGAG 62.088 72.222 0.00 0.00 0.00 4.18
2297 2418 4.631740 TCTGTCCCCTGGCCACGA 62.632 66.667 0.00 0.00 0.00 4.35
2298 2419 4.394712 GTCTGTCCCCTGGCCACG 62.395 72.222 0.00 0.00 0.00 4.94
2299 2420 4.394712 CGTCTGTCCCCTGGCCAC 62.395 72.222 0.00 0.00 0.00 5.01
2332 2453 6.662414 AACATATGATATTTATGCCGACGG 57.338 37.500 10.29 10.29 31.54 4.79
2333 2454 8.948853 AAAAACATATGATATTTATGCCGACG 57.051 30.769 10.38 0.00 31.54 5.12
2356 2477 3.438781 CACGTGGCAGCTCCTAATAAAAA 59.561 43.478 7.95 0.00 35.26 1.94
2357 2478 3.006940 CACGTGGCAGCTCCTAATAAAA 58.993 45.455 7.95 0.00 35.26 1.52
2358 2479 2.627945 CACGTGGCAGCTCCTAATAAA 58.372 47.619 7.95 0.00 35.26 1.40
2359 2480 1.134521 CCACGTGGCAGCTCCTAATAA 60.135 52.381 24.02 0.00 35.26 1.40
2360 2481 0.464036 CCACGTGGCAGCTCCTAATA 59.536 55.000 24.02 0.00 35.26 0.98
2361 2482 1.221840 CCACGTGGCAGCTCCTAAT 59.778 57.895 24.02 0.00 35.26 1.73
2362 2483 2.662596 CCACGTGGCAGCTCCTAA 59.337 61.111 24.02 0.00 35.26 2.69
2372 2493 2.176273 GCATAGCTCTGCCACGTGG 61.176 63.158 30.66 30.66 36.10 4.94
2373 2494 1.153489 AGCATAGCTCTGCCACGTG 60.153 57.895 19.47 9.08 43.33 4.49
2374 2495 1.153489 CAGCATAGCTCTGCCACGT 60.153 57.895 19.47 0.00 43.33 4.49
2375 2496 1.142531 TCAGCATAGCTCTGCCACG 59.857 57.895 19.47 9.48 43.33 4.94
2376 2497 1.150567 CGTCAGCATAGCTCTGCCAC 61.151 60.000 19.47 15.11 43.33 5.01
2377 2498 1.142531 CGTCAGCATAGCTCTGCCA 59.857 57.895 19.47 4.94 43.33 4.92
2378 2499 1.593750 CCGTCAGCATAGCTCTGCC 60.594 63.158 19.47 4.79 43.33 4.85
2379 2500 2.243264 GCCGTCAGCATAGCTCTGC 61.243 63.158 15.84 15.84 42.97 4.26
2380 2501 4.024698 GCCGTCAGCATAGCTCTG 57.975 61.111 0.00 0.00 42.97 3.35
2409 2530 1.373497 CCGTCGGCATAGCTCCATC 60.373 63.158 0.00 0.00 0.00 3.51
2410 2531 2.088674 GACCGTCGGCATAGCTCCAT 62.089 60.000 12.28 0.00 0.00 3.41
2411 2532 2.758327 ACCGTCGGCATAGCTCCA 60.758 61.111 12.28 0.00 0.00 3.86
2412 2533 1.170919 TAGACCGTCGGCATAGCTCC 61.171 60.000 12.28 0.00 0.00 4.70
2413 2534 0.040246 GTAGACCGTCGGCATAGCTC 60.040 60.000 12.28 0.00 0.00 4.09
2414 2535 1.453762 GGTAGACCGTCGGCATAGCT 61.454 60.000 12.28 3.91 0.00 3.32
2415 2536 1.007618 GGTAGACCGTCGGCATAGC 60.008 63.158 12.28 10.32 0.00 2.97
2426 2547 0.743097 AACTATGCCGACGGTAGACC 59.257 55.000 16.73 0.00 0.00 3.85
2427 2548 1.268948 GGAACTATGCCGACGGTAGAC 60.269 57.143 16.73 9.54 0.00 2.59
2428 2549 1.027357 GGAACTATGCCGACGGTAGA 58.973 55.000 16.73 7.55 0.00 2.59
2429 2550 0.742505 TGGAACTATGCCGACGGTAG 59.257 55.000 16.73 12.52 0.00 3.18
2430 2551 1.338973 GATGGAACTATGCCGACGGTA 59.661 52.381 16.73 12.27 0.00 4.02
2431 2552 0.104304 GATGGAACTATGCCGACGGT 59.896 55.000 16.73 0.00 0.00 4.83
2432 2553 0.389391 AGATGGAACTATGCCGACGG 59.611 55.000 10.29 10.29 0.00 4.79
2433 2554 3.245797 CATAGATGGAACTATGCCGACG 58.754 50.000 0.00 0.00 41.70 5.12
2439 2560 4.748892 CCGTAGGCATAGATGGAACTATG 58.251 47.826 0.00 0.00 46.14 2.23
2465 2586 0.038526 CGGCCTTACTATGCCTACGG 60.039 60.000 0.00 0.00 45.71 4.02
2466 2587 0.672342 ACGGCCTTACTATGCCTACG 59.328 55.000 0.00 0.00 45.71 3.51
2467 2588 1.335689 CGACGGCCTTACTATGCCTAC 60.336 57.143 0.00 0.00 45.71 3.18
2468 2589 0.956633 CGACGGCCTTACTATGCCTA 59.043 55.000 0.00 0.00 45.71 3.93
2469 2590 1.740285 CGACGGCCTTACTATGCCT 59.260 57.895 0.00 0.00 45.71 4.75
2470 2591 1.300697 CCGACGGCCTTACTATGCC 60.301 63.158 0.00 0.00 44.41 4.40
2471 2592 1.954651 GCCGACGGCCTTACTATGC 60.955 63.158 28.74 0.00 44.06 3.14
2472 2593 4.338327 GCCGACGGCCTTACTATG 57.662 61.111 28.74 0.00 44.06 2.23
2482 2603 4.467735 CATAGATCGATATATGCCGACGG 58.532 47.826 23.01 10.29 37.64 4.79
2483 2604 3.908978 GCATAGATCGATATATGCCGACG 59.091 47.826 37.54 17.20 46.67 5.12
2512 2633 5.887941 ATAGCCTAACTATGCCTACGGCTG 61.888 50.000 9.93 0.00 45.23 4.85
2513 2634 3.818294 ATAGCCTAACTATGCCTACGGCT 60.818 47.826 6.43 0.00 46.98 5.52
2514 2635 2.496470 ATAGCCTAACTATGCCTACGGC 59.504 50.000 0.00 0.00 40.23 5.68
2515 2636 3.181499 CGATAGCCTAACTATGCCTACGG 60.181 52.174 0.00 0.00 41.87 4.02
2516 2637 3.181499 CCGATAGCCTAACTATGCCTACG 60.181 52.174 0.00 0.00 41.87 3.51
2517 2638 3.429135 GCCGATAGCCTAACTATGCCTAC 60.429 52.174 0.00 0.00 41.87 3.18
2518 2639 2.758979 GCCGATAGCCTAACTATGCCTA 59.241 50.000 0.00 0.00 41.87 3.93
2519 2640 1.550976 GCCGATAGCCTAACTATGCCT 59.449 52.381 0.00 0.00 41.87 4.75
2520 2641 1.275291 TGCCGATAGCCTAACTATGCC 59.725 52.381 0.00 0.00 41.87 4.40
2521 2642 2.743636 TGCCGATAGCCTAACTATGC 57.256 50.000 0.00 0.00 41.87 3.14
2522 2643 5.221145 CCTCTATGCCGATAGCCTAACTATG 60.221 48.000 0.00 0.00 41.87 2.23
2523 2644 4.890581 CCTCTATGCCGATAGCCTAACTAT 59.109 45.833 0.00 0.00 44.62 2.12
2524 2645 4.263816 ACCTCTATGCCGATAGCCTAACTA 60.264 45.833 0.00 0.00 42.71 2.24
2525 2646 3.093057 CCTCTATGCCGATAGCCTAACT 58.907 50.000 0.00 0.00 42.71 2.24
2526 2647 2.826725 ACCTCTATGCCGATAGCCTAAC 59.173 50.000 0.00 0.00 42.71 2.34
2527 2648 2.826128 CACCTCTATGCCGATAGCCTAA 59.174 50.000 0.00 0.00 42.71 2.69
2528 2649 2.447443 CACCTCTATGCCGATAGCCTA 58.553 52.381 0.00 0.00 42.71 3.93
2529 2650 1.261480 CACCTCTATGCCGATAGCCT 58.739 55.000 0.00 0.00 42.71 4.58
2530 2651 0.247736 CCACCTCTATGCCGATAGCC 59.752 60.000 0.00 0.00 42.71 3.93
2531 2652 0.390472 GCCACCTCTATGCCGATAGC 60.390 60.000 0.00 0.00 44.14 2.97
2532 2653 0.247736 GGCCACCTCTATGCCGATAG 59.752 60.000 0.00 0.00 35.08 2.08
2533 2654 1.192146 GGGCCACCTCTATGCCGATA 61.192 60.000 4.39 0.00 46.31 2.92
2534 2655 2.520536 GGGCCACCTCTATGCCGAT 61.521 63.158 4.39 0.00 46.31 4.18
2535 2656 3.161450 GGGCCACCTCTATGCCGA 61.161 66.667 4.39 0.00 46.31 5.54
2536 2657 3.164269 AGGGCCACCTCTATGCCG 61.164 66.667 6.18 0.00 46.95 5.69
2552 2673 4.087892 CTGTCCCCTGGCCACGAG 62.088 72.222 0.00 0.00 0.00 4.18
2553 2674 4.631740 TCTGTCCCCTGGCCACGA 62.632 66.667 0.00 0.00 0.00 4.35
2554 2675 4.394712 GTCTGTCCCCTGGCCACG 62.395 72.222 0.00 0.00 0.00 4.94
2555 2676 4.394712 CGTCTGTCCCCTGGCCAC 62.395 72.222 0.00 0.00 0.00 5.01
2834 3001 6.246919 TGGAAAATTTTACCCCAAGTCGATA 58.753 36.000 10.68 0.00 0.00 2.92
2915 3084 8.904099 ATAAGGACCTATATGCAAAAGTACAC 57.096 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.