Multiple sequence alignment - TraesCS3D01G173200

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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 TraesCS3D01G173200 chr3D 100.000 3774 0 0 1 3774 153847263 153851036 0.000000e+00 6970.0
1 TraesCS3D01G173200 chr3D 84.532 459 64 4 3317 3774 289697848 289697396 7.440000e-122 448.0
2 TraesCS3D01G173200 chr3A 93.906 2248 93 19 1 2223 172628774 172631002 0.000000e+00 3352.0
3 TraesCS3D01G173200 chr3A 94.595 740 22 4 2325 3046 172631033 172631772 0.000000e+00 1129.0
4 TraesCS3D01G173200 chr3A 96.319 163 6 0 3039 3201 172659087 172659249 6.210000e-68 268.0
5 TraesCS3D01G173200 chr3B 95.272 1671 43 15 596 2245 227419345 227417690 0.000000e+00 2615.0
6 TraesCS3D01G173200 chr3B 94.196 827 22 7 2325 3127 227417693 227416869 0.000000e+00 1238.0
7 TraesCS3D01G173200 chr3B 92.382 617 24 12 1 601 227425197 227424588 0.000000e+00 857.0
8 TraesCS3D01G173200 chr3B 100.000 76 0 0 3120 3195 227401382 227401307 1.410000e-29 141.0
9 TraesCS3D01G173200 chr5A 86.602 515 55 3 3255 3768 91523143 91523644 1.180000e-154 556.0
10 TraesCS3D01G173200 chr4D 75.930 511 84 28 3264 3763 306426395 306425913 3.790000e-55 226.0
11 TraesCS3D01G173200 chr6B 100.000 91 0 0 2238 2328 171735019 171735109 6.480000e-38 169.0
12 TraesCS3D01G173200 chr4A 97.959 98 1 1 2232 2328 661959778 661959875 6.480000e-38 169.0
13 TraesCS3D01G173200 chr4A 97.917 96 2 0 2238 2333 422945104 422945199 2.330000e-37 167.0
14 TraesCS3D01G173200 chr4A 95.192 104 4 1 2242 2344 603462348 603462451 3.020000e-36 163.0
15 TraesCS3D01G173200 chr7B 95.327 107 2 2 2226 2330 483787840 483787735 2.330000e-37 167.0
16 TraesCS3D01G173200 chr6D 98.925 93 1 0 2241 2333 380781869 380781777 2.330000e-37 167.0
17 TraesCS3D01G173200 chr1A 96.078 102 2 2 2235 2335 497890557 497890457 8.390000e-37 165.0
18 TraesCS3D01G173200 chr7D 94.393 107 5 1 2225 2330 136013295 136013401 3.020000e-36 163.0
19 TraesCS3D01G173200 chr1D 95.098 102 3 2 2239 2340 211632423 211632324 3.900000e-35 159.0
20 TraesCS3D01G173200 chr6A 90.566 53 5 0 1963 2015 569692348 569692400 1.880000e-08 71.3


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 TraesCS3D01G173200 chr3D 153847263 153851036 3773 False 6970.0 6970 100.0000 1 3774 1 chr3D.!!$F1 3773
1 TraesCS3D01G173200 chr3A 172628774 172631772 2998 False 2240.5 3352 94.2505 1 3046 2 chr3A.!!$F2 3045
2 TraesCS3D01G173200 chr3B 227416869 227419345 2476 True 1926.5 2615 94.7340 596 3127 2 chr3B.!!$R3 2531
3 TraesCS3D01G173200 chr3B 227424588 227425197 609 True 857.0 857 92.3820 1 601 1 chr3B.!!$R2 600
4 TraesCS3D01G173200 chr5A 91523143 91523644 501 False 556.0 556 86.6020 3255 3768 1 chr5A.!!$F1 513

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
873 896 0.105760 TCCCAGAGCTGAGAGATCCC 60.106 60.0 0.0 0.0 29.18 3.85 F
2099 2143 0.611062 TCCTCCCGTACTCACACCAG 60.611 60.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 2745 0.580104 CGGTGAACACGAACTTGACC 59.420 55.0 0.0 0.0 0.0 4.02 R
3146 3226 0.036164 CGGGGTGTTCTGTTGATGGA 59.964 55.0 0.0 0.0 0.0 3.41 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
63 64 1.970917 GCAGCTCCAAATCGTCCACG 61.971 60.000 0.00 0.00 41.45 4.94
169 170 4.704540 TCAGTTCGTAATCCATGGCAAAAT 59.295 37.500 6.96 0.00 0.00 1.82
185 186 3.338249 CAAAATGGACGAGATGGAGTGT 58.662 45.455 0.00 0.00 0.00 3.55
199 200 8.187480 CGAGATGGAGTGTCAATTATAGATAGG 58.813 40.741 0.00 0.00 0.00 2.57
200 201 8.372877 AGATGGAGTGTCAATTATAGATAGGG 57.627 38.462 0.00 0.00 0.00 3.53
201 202 6.360370 TGGAGTGTCAATTATAGATAGGGC 57.640 41.667 0.00 0.00 0.00 5.19
203 204 5.185249 GGAGTGTCAATTATAGATAGGGCGA 59.815 44.000 0.00 0.00 0.00 5.54
204 205 6.026947 AGTGTCAATTATAGATAGGGCGAC 57.973 41.667 0.00 0.00 0.00 5.19
217 228 2.811317 GCGACTGCCTCTTCCACG 60.811 66.667 0.00 0.00 33.98 4.94
219 230 2.435059 GACTGCCTCTTCCACGCC 60.435 66.667 0.00 0.00 0.00 5.68
220 231 2.925170 ACTGCCTCTTCCACGCCT 60.925 61.111 0.00 0.00 0.00 5.52
221 232 1.605058 GACTGCCTCTTCCACGCCTA 61.605 60.000 0.00 0.00 0.00 3.93
223 234 2.187163 GCCTCTTCCACGCCTACC 59.813 66.667 0.00 0.00 0.00 3.18
224 235 2.359967 GCCTCTTCCACGCCTACCT 61.360 63.158 0.00 0.00 0.00 3.08
225 236 1.041447 GCCTCTTCCACGCCTACCTA 61.041 60.000 0.00 0.00 0.00 3.08
226 237 1.033574 CCTCTTCCACGCCTACCTAG 58.966 60.000 0.00 0.00 0.00 3.02
227 238 0.386113 CTCTTCCACGCCTACCTAGC 59.614 60.000 0.00 0.00 0.00 3.42
228 239 1.041447 TCTTCCACGCCTACCTAGCC 61.041 60.000 0.00 0.00 0.00 3.93
250 261 0.179200 CCGACGCTGCCAAACAATAC 60.179 55.000 0.00 0.00 0.00 1.89
268 279 5.011943 ACAATACACCTACACTTTTCGGGTA 59.988 40.000 0.00 0.00 0.00 3.69
272 283 2.365293 ACCTACACTTTTCGGGTACGTT 59.635 45.455 0.00 0.00 41.85 3.99
301 317 2.601763 CGCCCTTAGTGATTGAACGTAC 59.398 50.000 0.00 0.00 0.00 3.67
302 318 2.601763 GCCCTTAGTGATTGAACGTACG 59.398 50.000 15.01 15.01 0.00 3.67
303 319 3.841643 CCCTTAGTGATTGAACGTACGT 58.158 45.455 16.72 16.72 0.00 3.57
304 320 4.240096 CCCTTAGTGATTGAACGTACGTT 58.760 43.478 32.17 32.17 41.54 3.99
307 326 6.293027 CCCTTAGTGATTGAACGTACGTTTTT 60.293 38.462 32.14 20.23 38.60 1.94
429 448 3.866327 GCTACTAGAAGGCAGCAAAGTAC 59.134 47.826 0.00 0.00 34.13 2.73
456 475 2.915604 CCATACTGGGGCCAAGAGATAT 59.084 50.000 16.85 0.00 32.67 1.63
563 586 6.612247 AACGAATTGACATTTGACAGTACA 57.388 33.333 0.00 0.00 0.00 2.90
649 672 5.347342 CACCAATCAAAAAGTAGTTGTGCA 58.653 37.500 0.00 0.00 0.00 4.57
678 701 2.496871 GCCATTCACATGATCCAACCAA 59.503 45.455 0.00 0.00 31.07 3.67
773 796 0.953727 GCCTGTGCTCACATTGTCAA 59.046 50.000 2.90 0.00 41.01 3.18
778 801 3.212685 TGTGCTCACATTGTCAACATGA 58.787 40.909 0.00 0.00 36.21 3.07
788 811 4.661993 TTGTCAACATGAGTACAATCGC 57.338 40.909 0.00 0.00 0.00 4.58
844 867 5.866335 TCCAAAACATATTTAGCGTTCGT 57.134 34.783 0.00 0.00 0.00 3.85
855 878 2.053282 AGCGTTCGTCTCTGTTTCTC 57.947 50.000 0.00 0.00 0.00 2.87
858 881 1.000607 CGTTCGTCTCTGTTTCTCCCA 60.001 52.381 0.00 0.00 0.00 4.37
859 882 2.678324 GTTCGTCTCTGTTTCTCCCAG 58.322 52.381 0.00 0.00 0.00 4.45
864 887 2.383368 CTCTGTTTCTCCCAGAGCTG 57.617 55.000 0.00 0.00 46.66 4.24
873 896 0.105760 TCCCAGAGCTGAGAGATCCC 60.106 60.000 0.00 0.00 29.18 3.85
877 900 2.492381 CCAGAGCTGAGAGATCCCCATA 60.492 54.545 0.00 0.00 29.18 2.74
878 901 2.562298 CAGAGCTGAGAGATCCCCATAC 59.438 54.545 0.00 0.00 29.18 2.39
879 902 1.543802 GAGCTGAGAGATCCCCATACG 59.456 57.143 0.00 0.00 0.00 3.06
1145 1171 3.136626 AGCCTGACAGGTAACAAGAGTTT 59.863 43.478 22.58 0.00 37.80 2.66
1147 1173 4.023963 GCCTGACAGGTAACAAGAGTTTTC 60.024 45.833 22.58 0.00 37.80 2.29
1153 1179 3.720002 AGGTAACAAGAGTTTTCCCCTCA 59.280 43.478 0.00 0.00 39.15 3.86
1336 1364 2.797278 GGACATCATCGGCTCCGGT 61.797 63.158 8.59 0.00 40.25 5.28
1860 1888 4.576053 TGCCCAACGAAATCTCAATCTATG 59.424 41.667 0.00 0.00 0.00 2.23
1897 1941 4.365899 ACATCATCATGCATGTGTGTTC 57.634 40.909 25.43 0.00 32.21 3.18
1914 1958 2.779951 TTCGCTGATCGGTGGTGTGG 62.780 60.000 15.01 0.00 39.05 4.17
2086 2130 1.419387 CATCCACCTCTCATTCCTCCC 59.581 57.143 0.00 0.00 0.00 4.30
2099 2143 0.611062 TCCTCCCGTACTCACACCAG 60.611 60.000 0.00 0.00 0.00 4.00
2241 2294 2.846950 ACCCCAACCTAGCTATCAACT 58.153 47.619 0.00 0.00 0.00 3.16
2243 2296 3.710165 ACCCCAACCTAGCTATCAACTAC 59.290 47.826 0.00 0.00 0.00 2.73
2244 2297 3.967987 CCCCAACCTAGCTATCAACTACT 59.032 47.826 0.00 0.00 0.00 2.57
2245 2298 4.039366 CCCCAACCTAGCTATCAACTACTC 59.961 50.000 0.00 0.00 0.00 2.59
2246 2299 4.039366 CCCAACCTAGCTATCAACTACTCC 59.961 50.000 0.00 0.00 0.00 3.85
2247 2300 4.039366 CCAACCTAGCTATCAACTACTCCC 59.961 50.000 0.00 0.00 0.00 4.30
2248 2301 4.817874 ACCTAGCTATCAACTACTCCCT 57.182 45.455 0.00 0.00 0.00 4.20
2249 2302 4.732065 ACCTAGCTATCAACTACTCCCTC 58.268 47.826 0.00 0.00 0.00 4.30
2250 2303 4.417518 ACCTAGCTATCAACTACTCCCTCT 59.582 45.833 0.00 0.00 0.00 3.69
2251 2304 4.764823 CCTAGCTATCAACTACTCCCTCTG 59.235 50.000 0.00 0.00 0.00 3.35
2252 2305 4.258457 AGCTATCAACTACTCCCTCTGT 57.742 45.455 0.00 0.00 0.00 3.41
2253 2306 5.390087 AGCTATCAACTACTCCCTCTGTA 57.610 43.478 0.00 0.00 0.00 2.74
2254 2307 5.767670 AGCTATCAACTACTCCCTCTGTAA 58.232 41.667 0.00 0.00 0.00 2.41
2255 2308 6.195700 AGCTATCAACTACTCCCTCTGTAAA 58.804 40.000 0.00 0.00 0.00 2.01
2256 2309 6.097129 AGCTATCAACTACTCCCTCTGTAAAC 59.903 42.308 0.00 0.00 0.00 2.01
2257 2310 6.097129 GCTATCAACTACTCCCTCTGTAAACT 59.903 42.308 0.00 0.00 0.00 2.66
2258 2311 7.284944 GCTATCAACTACTCCCTCTGTAAACTA 59.715 40.741 0.00 0.00 0.00 2.24
2259 2312 9.186837 CTATCAACTACTCCCTCTGTAAACTAA 57.813 37.037 0.00 0.00 0.00 2.24
2260 2313 8.611051 ATCAACTACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
2261 2314 9.710818 ATCAACTACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
2262 2315 9.710818 TCAACTACTCCCTCTGTAAACTAATAT 57.289 33.333 0.00 0.00 0.00 1.28
2268 2321 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2269 2322 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2270 2323 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2271 2324 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2272 2325 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2287 2340 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2288 2341 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2289 2342 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2290 2343 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
2291 2344 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
2292 2345 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
2293 2346 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
2299 2352 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
2300 2353 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
2301 2354 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
2302 2355 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
2303 2356 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
2317 2370 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2318 2371 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2319 2372 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2320 2373 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2321 2374 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2322 2375 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2323 2376 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2424 2485 2.509548 CCCAATGTACTCCCATCTTCCA 59.490 50.000 0.00 0.00 0.00 3.53
2495 2575 4.968719 TGGTCTGATAATGGACATGTACCT 59.031 41.667 5.38 0.00 34.49 3.08
2580 2660 3.749609 TGCTGACATCAGTTCATCTGTTG 59.250 43.478 10.50 0.00 45.45 3.33
2665 2745 1.448013 GTCTTTTCCGGCGGAGGAG 60.448 63.158 29.30 27.11 41.98 3.69
2883 2963 2.417978 TGCTGGGTTCTGCACAAAG 58.582 52.632 0.00 0.00 41.77 2.77
2932 3012 6.092944 CGCTACCAATGGTGTTGTATAAGAAA 59.907 38.462 16.41 0.00 36.19 2.52
3017 3097 3.182152 ACTGCTGGGTAGACATAGGTTT 58.818 45.455 0.00 0.00 0.00 3.27
3069 3149 4.161377 AGGAAACTTGATGACCTCTCTAGC 59.839 45.833 0.00 0.00 37.44 3.42
3124 3204 3.646611 TCCATGACAACTTTGTGCATG 57.353 42.857 18.15 18.15 42.43 4.06
3125 3205 2.957680 TCCATGACAACTTTGTGCATGT 59.042 40.909 20.72 0.00 42.43 3.21
3126 3206 3.054166 CCATGACAACTTTGTGCATGTG 58.946 45.455 20.72 14.06 42.43 3.21
3127 3207 2.206815 TGACAACTTTGTGCATGTGC 57.793 45.000 0.00 0.00 42.43 4.57
3139 3219 2.697431 GCATGTGCAAAACCTCGTAA 57.303 45.000 0.00 0.00 41.59 3.18
3140 3220 3.006659 GCATGTGCAAAACCTCGTAAA 57.993 42.857 0.00 0.00 41.59 2.01
3141 3221 2.979813 GCATGTGCAAAACCTCGTAAAG 59.020 45.455 0.00 0.00 41.59 1.85
3142 3222 4.156350 GCATGTGCAAAACCTCGTAAAGG 61.156 47.826 0.00 0.00 45.52 3.11
3143 3223 6.333079 GCATGTGCAAAACCTCGTAAAGGA 62.333 45.833 0.00 0.00 43.98 3.36
3153 3233 3.526931 CTCGTAAAGGAGCTCCATCAA 57.473 47.619 33.90 13.84 38.89 2.57
3154 3234 3.190874 CTCGTAAAGGAGCTCCATCAAC 58.809 50.000 33.90 22.69 38.89 3.18
3155 3235 2.565391 TCGTAAAGGAGCTCCATCAACA 59.435 45.455 33.90 11.23 38.89 3.33
3156 3236 2.932614 CGTAAAGGAGCTCCATCAACAG 59.067 50.000 33.90 14.76 38.89 3.16
3157 3237 3.368427 CGTAAAGGAGCTCCATCAACAGA 60.368 47.826 33.90 7.69 38.89 3.41
3158 3238 3.795688 AAAGGAGCTCCATCAACAGAA 57.204 42.857 33.90 0.00 38.89 3.02
3159 3239 2.777832 AGGAGCTCCATCAACAGAAC 57.222 50.000 33.90 2.68 38.89 3.01
3160 3240 1.980765 AGGAGCTCCATCAACAGAACA 59.019 47.619 33.90 0.00 38.89 3.18
3161 3241 2.079925 GGAGCTCCATCAACAGAACAC 58.920 52.381 28.43 0.00 35.64 3.32
3162 3242 2.079925 GAGCTCCATCAACAGAACACC 58.920 52.381 0.87 0.00 0.00 4.16
3163 3243 1.168714 GCTCCATCAACAGAACACCC 58.831 55.000 0.00 0.00 0.00 4.61
3164 3244 1.826385 CTCCATCAACAGAACACCCC 58.174 55.000 0.00 0.00 0.00 4.95
3165 3245 0.036164 TCCATCAACAGAACACCCCG 59.964 55.000 0.00 0.00 0.00 5.73
3166 3246 0.036164 CCATCAACAGAACACCCCGA 59.964 55.000 0.00 0.00 0.00 5.14
3167 3247 1.442769 CATCAACAGAACACCCCGAG 58.557 55.000 0.00 0.00 0.00 4.63
3168 3248 0.321653 ATCAACAGAACACCCCGAGC 60.322 55.000 0.00 0.00 0.00 5.03
3169 3249 1.966451 CAACAGAACACCCCGAGCC 60.966 63.158 0.00 0.00 0.00 4.70
3170 3250 2.147387 AACAGAACACCCCGAGCCT 61.147 57.895 0.00 0.00 0.00 4.58
3171 3251 2.113243 AACAGAACACCCCGAGCCTC 62.113 60.000 0.00 0.00 0.00 4.70
3172 3252 2.120718 AGAACACCCCGAGCCTCT 59.879 61.111 0.00 0.00 0.00 3.69
3173 3253 1.536662 AGAACACCCCGAGCCTCTT 60.537 57.895 0.00 0.00 0.00 2.85
3174 3254 1.079057 GAACACCCCGAGCCTCTTC 60.079 63.158 0.00 0.00 0.00 2.87
3175 3255 2.523453 GAACACCCCGAGCCTCTTCC 62.523 65.000 0.00 0.00 0.00 3.46
3176 3256 2.685380 CACCCCGAGCCTCTTCCT 60.685 66.667 0.00 0.00 0.00 3.36
3177 3257 2.364448 ACCCCGAGCCTCTTCCTC 60.364 66.667 0.00 0.00 0.00 3.71
3178 3258 2.364317 CCCCGAGCCTCTTCCTCA 60.364 66.667 0.00 0.00 0.00 3.86
3179 3259 1.990060 CCCCGAGCCTCTTCCTCAA 60.990 63.158 0.00 0.00 0.00 3.02
3180 3260 1.519719 CCCGAGCCTCTTCCTCAAG 59.480 63.158 0.00 0.00 0.00 3.02
3181 3261 1.153469 CCGAGCCTCTTCCTCAAGC 60.153 63.158 0.00 0.00 0.00 4.01
3182 3262 1.612395 CCGAGCCTCTTCCTCAAGCT 61.612 60.000 0.00 0.00 36.25 3.74
3183 3263 0.248843 CGAGCCTCTTCCTCAAGCTT 59.751 55.000 0.00 0.00 32.97 3.74
3184 3264 1.736612 GAGCCTCTTCCTCAAGCTTG 58.263 55.000 20.81 20.81 32.97 4.01
3185 3265 1.277557 GAGCCTCTTCCTCAAGCTTGA 59.722 52.381 26.87 26.87 32.97 3.02
3186 3266 1.914798 AGCCTCTTCCTCAAGCTTGAT 59.085 47.619 28.57 8.56 36.46 2.57
3187 3267 3.110705 AGCCTCTTCCTCAAGCTTGATA 58.889 45.455 28.57 17.25 36.46 2.15
3188 3268 3.715834 AGCCTCTTCCTCAAGCTTGATAT 59.284 43.478 28.57 5.34 36.46 1.63
3189 3269 4.064388 GCCTCTTCCTCAAGCTTGATATC 58.936 47.826 28.57 9.14 36.46 1.63
3190 3270 4.202346 GCCTCTTCCTCAAGCTTGATATCT 60.202 45.833 28.57 0.00 36.46 1.98
3191 3271 5.540911 CCTCTTCCTCAAGCTTGATATCTC 58.459 45.833 28.57 0.00 36.46 2.75
3192 3272 5.070180 CCTCTTCCTCAAGCTTGATATCTCA 59.930 44.000 28.57 10.98 36.46 3.27
3193 3273 6.407865 CCTCTTCCTCAAGCTTGATATCTCAA 60.408 42.308 28.57 13.62 39.07 3.02
3194 3274 6.950842 TCTTCCTCAAGCTTGATATCTCAAA 58.049 36.000 28.57 13.61 40.78 2.69
3195 3275 7.046652 TCTTCCTCAAGCTTGATATCTCAAAG 58.953 38.462 28.57 20.45 40.78 2.77
3196 3276 5.678583 TCCTCAAGCTTGATATCTCAAAGG 58.321 41.667 28.57 21.30 40.78 3.11
3197 3277 4.275443 CCTCAAGCTTGATATCTCAAAGGC 59.725 45.833 28.57 0.00 40.78 4.35
3198 3278 4.202441 TCAAGCTTGATATCTCAAAGGCC 58.798 43.478 25.16 0.00 40.78 5.19
3199 3279 4.080129 TCAAGCTTGATATCTCAAAGGCCT 60.080 41.667 25.16 0.00 40.78 5.19
3200 3280 4.516652 AGCTTGATATCTCAAAGGCCTT 57.483 40.909 13.78 13.78 40.78 4.35
3201 3281 4.205587 AGCTTGATATCTCAAAGGCCTTG 58.794 43.478 21.33 13.47 40.78 3.61
3202 3282 3.317430 GCTTGATATCTCAAAGGCCTTGG 59.683 47.826 21.33 17.73 40.78 3.61
3203 3283 3.582998 TGATATCTCAAAGGCCTTGGG 57.417 47.619 21.33 14.99 36.78 4.12
3204 3284 2.175499 TGATATCTCAAAGGCCTTGGGG 59.825 50.000 21.33 17.75 36.03 4.96
3214 3294 3.939564 CCTTGGGGCCACATTAGC 58.060 61.111 9.55 0.00 0.00 3.09
3215 3295 1.000233 CCTTGGGGCCACATTAGCA 60.000 57.895 9.55 0.00 0.00 3.49
3216 3296 0.614415 CCTTGGGGCCACATTAGCAA 60.614 55.000 9.55 0.00 0.00 3.91
3217 3297 1.488390 CTTGGGGCCACATTAGCAAT 58.512 50.000 9.55 0.00 0.00 3.56
3218 3298 2.665165 CTTGGGGCCACATTAGCAATA 58.335 47.619 9.55 0.00 0.00 1.90
3219 3299 3.233507 CTTGGGGCCACATTAGCAATAT 58.766 45.455 9.55 0.00 0.00 1.28
3220 3300 3.326946 TGGGGCCACATTAGCAATATT 57.673 42.857 1.54 0.00 0.00 1.28
3221 3301 3.652055 TGGGGCCACATTAGCAATATTT 58.348 40.909 1.54 0.00 0.00 1.40
3222 3302 3.387374 TGGGGCCACATTAGCAATATTTG 59.613 43.478 1.54 0.00 0.00 2.32
3233 3313 1.779221 CAATATTTGCCCTCCCAGCA 58.221 50.000 0.00 0.00 38.81 4.41
3234 3314 1.684983 CAATATTTGCCCTCCCAGCAG 59.315 52.381 0.00 0.00 42.17 4.24
3235 3315 0.186873 ATATTTGCCCTCCCAGCAGG 59.813 55.000 0.00 0.00 42.17 4.85
3236 3316 0.918799 TATTTGCCCTCCCAGCAGGA 60.919 55.000 0.00 0.00 44.91 3.86
3237 3317 1.803453 ATTTGCCCTCCCAGCAGGAA 61.803 55.000 0.00 0.00 46.94 3.36
3238 3318 2.017668 TTTGCCCTCCCAGCAGGAAA 62.018 55.000 0.00 0.00 46.94 3.13
3239 3319 2.044551 GCCCTCCCAGCAGGAAAG 60.045 66.667 0.00 0.00 46.94 2.62
3240 3320 2.679716 CCCTCCCAGCAGGAAAGG 59.320 66.667 0.00 3.05 46.94 3.11
3241 3321 2.679716 CCTCCCAGCAGGAAAGGG 59.320 66.667 0.00 0.00 46.94 3.95
3242 3322 1.925455 CCTCCCAGCAGGAAAGGGA 60.925 63.158 0.00 0.00 46.94 4.20
3244 3324 4.423231 CCCAGCAGGAAAGGGAAC 57.577 61.111 0.00 0.00 45.80 3.62
3245 3325 1.770324 CCCAGCAGGAAAGGGAACT 59.230 57.895 0.00 0.00 45.80 3.01
3246 3326 0.991920 CCCAGCAGGAAAGGGAACTA 59.008 55.000 0.00 0.00 45.80 2.24
3247 3327 1.566231 CCCAGCAGGAAAGGGAACTAT 59.434 52.381 0.00 0.00 45.80 2.12
3248 3328 2.422093 CCCAGCAGGAAAGGGAACTATC 60.422 54.545 0.00 0.00 45.80 2.08
3249 3329 2.555199 CAGCAGGAAAGGGAACTATCG 58.445 52.381 0.00 0.00 42.68 2.92
3250 3330 1.134371 AGCAGGAAAGGGAACTATCGC 60.134 52.381 0.00 0.00 42.68 4.58
3251 3331 1.406887 GCAGGAAAGGGAACTATCGCA 60.407 52.381 0.00 0.00 42.68 5.10
3252 3332 2.555199 CAGGAAAGGGAACTATCGCAG 58.445 52.381 0.00 0.00 42.68 5.18
3253 3333 2.093447 CAGGAAAGGGAACTATCGCAGT 60.093 50.000 0.00 0.00 42.68 4.40
3261 3341 0.978146 AACTATCGCAGTGCTCCCCT 60.978 55.000 14.33 0.00 37.63 4.79
3275 3355 3.151022 CCCTGCTCCTCCGTCTCC 61.151 72.222 0.00 0.00 0.00 3.71
3280 3360 3.522731 CTCCTCCGTCTCCGCCAG 61.523 72.222 0.00 0.00 0.00 4.85
3440 3520 3.699894 CTGCTGCCCGTGGTCTCT 61.700 66.667 0.00 0.00 0.00 3.10
3441 3521 3.947132 CTGCTGCCCGTGGTCTCTG 62.947 68.421 0.00 0.00 0.00 3.35
3450 3530 3.650950 TGGTCTCTGGCCTTGGCC 61.651 66.667 22.91 22.91 0.00 5.36
3455 3535 3.011517 TCTGGCCTTGGCCTCTCC 61.012 66.667 28.37 5.17 0.00 3.71
3543 3624 3.473647 CGATGGCCCAGGCTCTGA 61.474 66.667 8.89 0.00 41.60 3.27
3545 3626 1.228184 GATGGCCCAGGCTCTGATG 60.228 63.158 8.89 0.00 41.60 3.07
3549 3630 2.996395 CCCAGGCTCTGATGTGCT 59.004 61.111 4.00 0.00 32.44 4.40
3551 3632 1.298993 CCAGGCTCTGATGTGCTGT 59.701 57.895 4.00 0.00 32.44 4.40
3560 3641 1.002888 CTGATGTGCTGTGGAGGAAGT 59.997 52.381 0.00 0.00 0.00 3.01
3562 3643 0.036952 ATGTGCTGTGGAGGAAGTCG 60.037 55.000 0.00 0.00 0.00 4.18
3563 3644 1.374758 GTGCTGTGGAGGAAGTCGG 60.375 63.158 0.00 0.00 0.00 4.79
3608 3689 2.093216 CGCAGGAAGTTGGAGATGC 58.907 57.895 0.00 0.00 0.00 3.91
3655 3736 3.111939 CCTAGGTCGCACTCTCCG 58.888 66.667 0.00 0.00 0.00 4.63
3656 3737 2.482333 CCTAGGTCGCACTCTCCGG 61.482 68.421 0.00 0.00 0.00 5.14
3732 3813 1.198094 TGCTTTCGGGAGGGACATCA 61.198 55.000 0.00 0.00 0.00 3.07
3736 3817 3.849951 CGGGAGGGACATCACCGG 61.850 72.222 0.00 0.00 40.79 5.28
3738 3819 2.365105 GGAGGGACATCACCGGGA 60.365 66.667 6.32 0.00 0.00 5.14
3748 3829 2.507110 ATCACCGGGAAGACTGCACG 62.507 60.000 6.32 0.00 0.00 5.34
3768 3849 1.083489 TTTAAACCGCTCTGCATCCG 58.917 50.000 0.00 0.00 0.00 4.18
3769 3850 1.366111 TTAAACCGCTCTGCATCCGC 61.366 55.000 0.00 0.00 39.24 5.54
3770 3851 2.238847 TAAACCGCTCTGCATCCGCT 62.239 55.000 0.00 0.00 39.64 5.52
3771 3852 4.521062 ACCGCTCTGCATCCGCTC 62.521 66.667 0.00 0.00 39.64 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.808656 GGCTTCTTGCTCAGCCGC 61.809 66.667 0.00 0.00 46.19 6.53
169 170 1.627864 TTGACACTCCATCTCGTCCA 58.372 50.000 0.00 0.00 0.00 4.02
176 177 7.044798 GCCCTATCTATAATTGACACTCCATC 58.955 42.308 0.00 0.00 0.00 3.51
185 186 5.073311 GCAGTCGCCCTATCTATAATTGA 57.927 43.478 0.00 0.00 0.00 2.57
200 201 2.811317 CGTGGAAGAGGCAGTCGC 60.811 66.667 0.00 0.00 37.44 5.19
201 202 2.811317 GCGTGGAAGAGGCAGTCG 60.811 66.667 0.00 0.00 35.42 4.18
203 204 1.609501 TAGGCGTGGAAGAGGCAGT 60.610 57.895 0.00 0.00 37.18 4.40
204 205 1.153549 GTAGGCGTGGAAGAGGCAG 60.154 63.158 0.00 0.00 37.18 4.85
219 230 3.962421 CGTCGGCGGGCTAGGTAG 61.962 72.222 7.21 0.00 0.00 3.18
250 261 2.288395 ACGTACCCGAAAAGTGTAGGTG 60.288 50.000 0.00 0.00 33.69 4.00
268 279 0.977108 TAAGGGCGGTGGGATAACGT 60.977 55.000 0.00 0.00 0.00 3.99
272 283 0.031917 TCACTAAGGGCGGTGGGATA 60.032 55.000 0.00 0.00 34.57 2.59
301 317 0.040067 GCAGCTGGTCCTCAAAAACG 60.040 55.000 17.12 0.00 0.00 3.60
302 318 0.315251 GGCAGCTGGTCCTCAAAAAC 59.685 55.000 17.12 0.00 0.00 2.43
303 319 1.172180 CGGCAGCTGGTCCTCAAAAA 61.172 55.000 17.12 0.00 0.00 1.94
304 320 1.600636 CGGCAGCTGGTCCTCAAAA 60.601 57.895 17.12 0.00 0.00 2.44
307 326 3.695606 GTCGGCAGCTGGTCCTCA 61.696 66.667 17.12 0.00 0.00 3.86
334 353 1.884579 CAAACTTCAGTGAGCATGGCT 59.115 47.619 0.00 0.00 43.88 4.75
563 586 9.762381 TGTTTACCAGTTTATCCCATTCTATTT 57.238 29.630 0.00 0.00 0.00 1.40
601 624 2.049372 GCCAAATGCCTATCCCCAATT 58.951 47.619 0.00 0.00 0.00 2.32
773 796 3.052455 TGTTGGCGATTGTACTCATGT 57.948 42.857 0.00 0.00 0.00 3.21
778 801 3.417101 TGGATTTGTTGGCGATTGTACT 58.583 40.909 0.00 0.00 0.00 2.73
788 811 3.368739 GGAGGATGCTTTGGATTTGTTGG 60.369 47.826 0.00 0.00 0.00 3.77
855 878 1.120795 GGGGATCTCTCAGCTCTGGG 61.121 65.000 0.00 0.00 0.00 4.45
858 881 2.817463 CGTATGGGGATCTCTCAGCTCT 60.817 54.545 0.00 0.00 0.00 4.09
859 882 1.543802 CGTATGGGGATCTCTCAGCTC 59.456 57.143 0.00 0.00 0.00 4.09
864 887 0.882474 CCGTCGTATGGGGATCTCTC 59.118 60.000 0.00 0.00 0.00 3.20
873 896 0.999406 CAGAAGCAACCGTCGTATGG 59.001 55.000 0.00 0.00 0.00 2.74
877 900 1.772063 GCAACAGAAGCAACCGTCGT 61.772 55.000 0.00 0.00 0.00 4.34
878 901 1.082756 GCAACAGAAGCAACCGTCG 60.083 57.895 0.00 0.00 0.00 5.12
879 902 1.166531 AGGCAACAGAAGCAACCGTC 61.167 55.000 0.00 0.00 41.41 4.79
1145 1171 4.144297 CAAGAACTCATTTGTGAGGGGAA 58.856 43.478 9.92 0.00 40.08 3.97
1147 1173 2.821969 CCAAGAACTCATTTGTGAGGGG 59.178 50.000 9.92 0.78 40.08 4.79
1153 1179 8.547173 AGAGAAGATATCCAAGAACTCATTTGT 58.453 33.333 0.00 0.00 0.00 2.83
1336 1364 1.976474 GTACACCGTCCCGTACCCA 60.976 63.158 0.00 0.00 33.39 4.51
1729 1757 2.526873 AAGTCCGACACCCTGGCT 60.527 61.111 0.40 0.00 0.00 4.75
1897 1941 2.815211 CCACACCACCGATCAGCG 60.815 66.667 0.00 0.00 40.47 5.18
1914 1958 4.049186 TCGAAGTACTCTGAAGCAACAAC 58.951 43.478 0.00 0.00 0.00 3.32
2099 2143 9.430838 CGATCATTCAGATTTTAATTGAGTCAC 57.569 33.333 0.00 0.00 37.00 3.67
2243 2296 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2244 2297 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2245 2298 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2246 2299 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2261 2314 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2262 2315 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2263 2316 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2264 2317 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2265 2318 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2266 2319 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
2267 2320 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
2273 2326 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
2274 2327 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
2275 2328 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2276 2329 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2277 2330 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2291 2344 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2292 2345 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2293 2346 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2294 2347 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2295 2348 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2296 2349 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2297 2350 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2298 2351 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2299 2352 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2300 2353 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2301 2354 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
2302 2355 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
2304 2357 9.294614 CTAAGTACTCCCTCCGTAAACTAATAT 57.705 37.037 0.00 0.00 0.00 1.28
2305 2358 7.229506 GCTAAGTACTCCCTCCGTAAACTAATA 59.770 40.741 0.00 0.00 0.00 0.98
2306 2359 6.040278 GCTAAGTACTCCCTCCGTAAACTAAT 59.960 42.308 0.00 0.00 0.00 1.73
2307 2360 5.358160 GCTAAGTACTCCCTCCGTAAACTAA 59.642 44.000 0.00 0.00 0.00 2.24
2308 2361 4.884164 GCTAAGTACTCCCTCCGTAAACTA 59.116 45.833 0.00 0.00 0.00 2.24
2309 2362 3.698539 GCTAAGTACTCCCTCCGTAAACT 59.301 47.826 0.00 0.00 0.00 2.66
2310 2363 3.445096 TGCTAAGTACTCCCTCCGTAAAC 59.555 47.826 0.00 0.00 0.00 2.01
2311 2364 3.700538 TGCTAAGTACTCCCTCCGTAAA 58.299 45.455 0.00 0.00 0.00 2.01
2312 2365 3.370840 TGCTAAGTACTCCCTCCGTAA 57.629 47.619 0.00 0.00 0.00 3.18
2313 2366 3.370840 TTGCTAAGTACTCCCTCCGTA 57.629 47.619 0.00 0.00 0.00 4.02
2314 2367 2.226962 TTGCTAAGTACTCCCTCCGT 57.773 50.000 0.00 0.00 0.00 4.69
2315 2368 2.959707 AGATTGCTAAGTACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
2316 2369 3.707102 ACAGATTGCTAAGTACTCCCTCC 59.293 47.826 0.00 0.00 0.00 4.30
2317 2370 5.595133 AGTACAGATTGCTAAGTACTCCCTC 59.405 44.000 0.00 0.00 42.38 4.30
2318 2371 5.520751 AGTACAGATTGCTAAGTACTCCCT 58.479 41.667 0.00 0.00 42.38 4.20
2319 2372 5.855740 AGTACAGATTGCTAAGTACTCCC 57.144 43.478 0.00 0.00 42.38 4.30
2322 2375 4.948621 ACGGAGTACAGATTGCTAAGTACT 59.051 41.667 3.97 3.97 46.99 2.73
2323 2376 5.246145 ACGGAGTACAGATTGCTAAGTAC 57.754 43.478 0.00 0.00 41.94 2.73
2343 2396 5.235516 AGTTTTCTGATGGGTACAACTACG 58.764 41.667 0.00 0.00 0.00 3.51
2424 2485 4.274147 ACTAGTCCTCGTTGATCTGACAT 58.726 43.478 0.00 0.00 0.00 3.06
2580 2660 3.490933 GGTTTCCTTGACCTGAAAACAGC 60.491 47.826 0.00 0.00 37.94 4.40
2665 2745 0.580104 CGGTGAACACGAACTTGACC 59.420 55.000 0.00 0.00 0.00 4.02
2761 2841 1.134280 AGCCTGTACTATGCCAGCTTG 60.134 52.381 0.00 0.00 0.00 4.01
2847 2927 2.991190 AGCATGAATTTCGCAAAAGCAG 59.009 40.909 0.00 0.00 0.00 4.24
2883 2963 6.344702 CGTTTGCCGACAAAAATCTTCTAAAC 60.345 38.462 0.00 0.00 46.94 2.01
3017 3097 6.888105 TCATGATTCTTACTTGGATGCACTA 58.112 36.000 0.00 0.00 0.00 2.74
3124 3204 2.350484 GCTCCTTTACGAGGTTTTGCAC 60.350 50.000 0.00 0.00 46.39 4.57
3125 3205 1.877443 GCTCCTTTACGAGGTTTTGCA 59.123 47.619 0.00 0.00 46.39 4.08
3126 3206 2.152016 AGCTCCTTTACGAGGTTTTGC 58.848 47.619 0.00 0.00 46.39 3.68
3127 3207 2.742589 GGAGCTCCTTTACGAGGTTTTG 59.257 50.000 26.25 0.00 46.39 2.44
3128 3208 2.370849 TGGAGCTCCTTTACGAGGTTTT 59.629 45.455 32.28 0.00 46.39 2.43
3129 3209 1.975680 TGGAGCTCCTTTACGAGGTTT 59.024 47.619 32.28 0.00 46.39 3.27
3130 3210 1.640917 TGGAGCTCCTTTACGAGGTT 58.359 50.000 32.28 0.00 46.39 3.50
3131 3211 1.757699 GATGGAGCTCCTTTACGAGGT 59.242 52.381 32.28 7.91 46.39 3.85
3133 3213 3.190874 GTTGATGGAGCTCCTTTACGAG 58.809 50.000 32.28 0.00 36.82 4.18
3134 3214 2.565391 TGTTGATGGAGCTCCTTTACGA 59.435 45.455 32.28 17.08 36.82 3.43
3135 3215 2.932614 CTGTTGATGGAGCTCCTTTACG 59.067 50.000 32.28 17.95 36.82 3.18
3136 3216 4.207891 TCTGTTGATGGAGCTCCTTTAC 57.792 45.455 32.28 24.64 36.82 2.01
3137 3217 4.041567 TGTTCTGTTGATGGAGCTCCTTTA 59.958 41.667 32.28 20.61 36.82 1.85
3138 3218 3.181440 TGTTCTGTTGATGGAGCTCCTTT 60.181 43.478 32.28 20.25 36.82 3.11
3139 3219 2.373169 TGTTCTGTTGATGGAGCTCCTT 59.627 45.455 32.28 26.58 36.82 3.36
3140 3220 1.980765 TGTTCTGTTGATGGAGCTCCT 59.019 47.619 32.28 18.41 36.82 3.69
3141 3221 2.079925 GTGTTCTGTTGATGGAGCTCC 58.920 52.381 26.78 26.78 0.00 4.70
3142 3222 2.079925 GGTGTTCTGTTGATGGAGCTC 58.920 52.381 4.71 4.71 0.00 4.09
3143 3223 1.271597 GGGTGTTCTGTTGATGGAGCT 60.272 52.381 0.00 0.00 0.00 4.09
3144 3224 1.168714 GGGTGTTCTGTTGATGGAGC 58.831 55.000 0.00 0.00 0.00 4.70
3145 3225 1.826385 GGGGTGTTCTGTTGATGGAG 58.174 55.000 0.00 0.00 0.00 3.86
3146 3226 0.036164 CGGGGTGTTCTGTTGATGGA 59.964 55.000 0.00 0.00 0.00 3.41
3147 3227 0.036164 TCGGGGTGTTCTGTTGATGG 59.964 55.000 0.00 0.00 0.00 3.51
3148 3228 1.442769 CTCGGGGTGTTCTGTTGATG 58.557 55.000 0.00 0.00 0.00 3.07
3149 3229 0.321653 GCTCGGGGTGTTCTGTTGAT 60.322 55.000 0.00 0.00 0.00 2.57
3150 3230 1.070786 GCTCGGGGTGTTCTGTTGA 59.929 57.895 0.00 0.00 0.00 3.18
3151 3231 1.966451 GGCTCGGGGTGTTCTGTTG 60.966 63.158 0.00 0.00 0.00 3.33
3152 3232 2.113243 GAGGCTCGGGGTGTTCTGTT 62.113 60.000 0.00 0.00 0.00 3.16
3153 3233 2.526873 AGGCTCGGGGTGTTCTGT 60.527 61.111 0.00 0.00 0.00 3.41
3154 3234 1.831652 AAGAGGCTCGGGGTGTTCTG 61.832 60.000 9.22 0.00 0.00 3.02
3155 3235 1.536662 AAGAGGCTCGGGGTGTTCT 60.537 57.895 9.22 0.00 0.00 3.01
3156 3236 1.079057 GAAGAGGCTCGGGGTGTTC 60.079 63.158 9.22 2.49 0.00 3.18
3157 3237 2.593956 GGAAGAGGCTCGGGGTGTT 61.594 63.158 9.22 0.00 0.00 3.32
3158 3238 3.003763 GGAAGAGGCTCGGGGTGT 61.004 66.667 9.22 0.00 0.00 4.16
3159 3239 2.685380 AGGAAGAGGCTCGGGGTG 60.685 66.667 9.22 0.00 0.00 4.61
3160 3240 2.364448 GAGGAAGAGGCTCGGGGT 60.364 66.667 9.22 0.00 0.00 4.95
3161 3241 1.965754 CTTGAGGAAGAGGCTCGGGG 61.966 65.000 9.22 0.00 0.00 5.73
3162 3242 1.519719 CTTGAGGAAGAGGCTCGGG 59.480 63.158 9.22 0.00 0.00 5.14
3163 3243 1.153469 GCTTGAGGAAGAGGCTCGG 60.153 63.158 9.22 0.00 0.00 4.63
3164 3244 0.248843 AAGCTTGAGGAAGAGGCTCG 59.751 55.000 9.22 0.00 32.46 5.03
3165 3245 1.277557 TCAAGCTTGAGGAAGAGGCTC 59.722 52.381 25.16 6.34 32.50 4.70
3166 3246 1.356124 TCAAGCTTGAGGAAGAGGCT 58.644 50.000 25.16 0.00 32.50 4.58
3167 3247 2.416680 ATCAAGCTTGAGGAAGAGGC 57.583 50.000 31.14 0.00 41.08 4.70
3168 3248 5.070180 TGAGATATCAAGCTTGAGGAAGAGG 59.930 44.000 31.14 1.76 41.08 3.69
3169 3249 6.159299 TGAGATATCAAGCTTGAGGAAGAG 57.841 41.667 31.14 2.51 41.08 2.85
3170 3250 6.550938 TTGAGATATCAAGCTTGAGGAAGA 57.449 37.500 31.14 15.63 41.08 2.87
3171 3251 6.260493 CCTTTGAGATATCAAGCTTGAGGAAG 59.740 42.308 31.14 22.60 41.08 3.46
3172 3252 6.118170 CCTTTGAGATATCAAGCTTGAGGAA 58.882 40.000 31.14 20.26 41.08 3.36
3173 3253 5.678583 CCTTTGAGATATCAAGCTTGAGGA 58.321 41.667 31.14 22.48 41.08 3.71
3174 3254 4.275443 GCCTTTGAGATATCAAGCTTGAGG 59.725 45.833 31.14 23.43 41.08 3.86
3175 3255 4.275443 GGCCTTTGAGATATCAAGCTTGAG 59.725 45.833 31.14 16.06 41.08 3.02
3176 3256 4.080129 AGGCCTTTGAGATATCAAGCTTGA 60.080 41.667 30.23 30.23 42.14 3.02
3177 3257 4.205587 AGGCCTTTGAGATATCAAGCTTG 58.794 43.478 20.81 20.81 0.00 4.01
3178 3258 4.516652 AGGCCTTTGAGATATCAAGCTT 57.483 40.909 0.00 0.00 0.00 3.74
3179 3259 4.205587 CAAGGCCTTTGAGATATCAAGCT 58.794 43.478 17.61 0.00 39.21 3.74
3180 3260 3.317430 CCAAGGCCTTTGAGATATCAAGC 59.683 47.826 17.61 4.46 39.21 4.01
3181 3261 3.887716 CCCAAGGCCTTTGAGATATCAAG 59.112 47.826 17.61 0.00 39.21 3.02
3182 3262 3.373001 CCCCAAGGCCTTTGAGATATCAA 60.373 47.826 17.61 0.00 39.21 2.57
3183 3263 2.175499 CCCCAAGGCCTTTGAGATATCA 59.825 50.000 17.61 0.00 39.21 2.15
3184 3264 2.868899 CCCCAAGGCCTTTGAGATATC 58.131 52.381 17.61 0.00 39.21 1.63
3197 3277 0.614415 TTGCTAATGTGGCCCCAAGG 60.614 55.000 0.00 0.00 0.00 3.61
3198 3278 1.488390 ATTGCTAATGTGGCCCCAAG 58.512 50.000 0.00 0.00 0.00 3.61
3199 3279 2.836636 TATTGCTAATGTGGCCCCAA 57.163 45.000 0.00 0.00 0.00 4.12
3200 3280 3.326946 AATATTGCTAATGTGGCCCCA 57.673 42.857 0.00 0.00 0.00 4.96
3201 3281 3.993920 CAAATATTGCTAATGTGGCCCC 58.006 45.455 0.00 0.00 0.00 5.80
3214 3294 1.684983 CTGCTGGGAGGGCAAATATTG 59.315 52.381 0.00 0.00 39.30 1.90
3215 3295 1.412074 CCTGCTGGGAGGGCAAATATT 60.412 52.381 0.71 0.00 39.30 1.28
3216 3296 0.186873 CCTGCTGGGAGGGCAAATAT 59.813 55.000 0.71 0.00 39.30 1.28
3217 3297 0.918799 TCCTGCTGGGAGGGCAAATA 60.919 55.000 10.07 0.00 39.58 1.40
3218 3298 1.803453 TTCCTGCTGGGAGGGCAAAT 61.803 55.000 10.07 0.00 46.01 2.32
3219 3299 2.017668 TTTCCTGCTGGGAGGGCAAA 62.018 55.000 10.07 0.00 46.01 3.68
3220 3300 2.430704 CTTTCCTGCTGGGAGGGCAA 62.431 60.000 10.07 1.84 46.01 4.52
3221 3301 2.858476 TTTCCTGCTGGGAGGGCA 60.858 61.111 10.07 0.00 46.01 5.36
3222 3302 2.044551 CTTTCCTGCTGGGAGGGC 60.045 66.667 10.07 0.00 46.01 5.19
3223 3303 2.679716 CCTTTCCTGCTGGGAGGG 59.320 66.667 18.90 13.40 46.01 4.30
3224 3304 1.925455 TCCCTTTCCTGCTGGGAGG 60.925 63.158 19.41 19.41 46.01 4.30
3225 3305 3.826282 TCCCTTTCCTGCTGGGAG 58.174 61.111 10.07 8.17 46.01 4.30
3227 3307 0.991920 TAGTTCCCTTTCCTGCTGGG 59.008 55.000 10.07 0.00 42.20 4.45
3228 3308 2.743183 CGATAGTTCCCTTTCCTGCTGG 60.743 54.545 2.58 2.58 0.00 4.85
3229 3309 2.555199 CGATAGTTCCCTTTCCTGCTG 58.445 52.381 0.00 0.00 0.00 4.41
3230 3310 1.134371 GCGATAGTTCCCTTTCCTGCT 60.134 52.381 0.00 0.00 39.35 4.24
3231 3311 1.300481 GCGATAGTTCCCTTTCCTGC 58.700 55.000 0.00 0.00 39.35 4.85
3232 3312 2.093447 ACTGCGATAGTTCCCTTTCCTG 60.093 50.000 0.00 0.00 35.67 3.86
3233 3313 2.093447 CACTGCGATAGTTCCCTTTCCT 60.093 50.000 0.00 0.00 37.60 3.36
3234 3314 2.280628 CACTGCGATAGTTCCCTTTCC 58.719 52.381 0.00 0.00 37.60 3.13
3235 3315 1.666189 GCACTGCGATAGTTCCCTTTC 59.334 52.381 0.00 0.00 37.60 2.62
3236 3316 1.279271 AGCACTGCGATAGTTCCCTTT 59.721 47.619 0.00 0.00 37.60 3.11
3237 3317 0.905357 AGCACTGCGATAGTTCCCTT 59.095 50.000 0.00 0.00 37.60 3.95
3238 3318 0.461961 GAGCACTGCGATAGTTCCCT 59.538 55.000 0.00 0.00 37.60 4.20
3239 3319 0.530870 GGAGCACTGCGATAGTTCCC 60.531 60.000 0.00 0.00 37.60 3.97
3240 3320 0.530870 GGGAGCACTGCGATAGTTCC 60.531 60.000 0.00 0.00 37.60 3.62
3241 3321 0.530870 GGGGAGCACTGCGATAGTTC 60.531 60.000 0.00 0.00 37.60 3.01
3242 3322 0.978146 AGGGGAGCACTGCGATAGTT 60.978 55.000 0.00 0.00 37.60 2.24
3243 3323 1.381872 AGGGGAGCACTGCGATAGT 60.382 57.895 0.00 0.00 41.36 2.12
3244 3324 1.068753 CAGGGGAGCACTGCGATAG 59.931 63.158 0.00 0.00 0.00 2.08
3245 3325 3.220222 CAGGGGAGCACTGCGATA 58.780 61.111 0.00 0.00 0.00 2.92
3250 3330 3.007920 AGGAGCAGGGGAGCACTG 61.008 66.667 0.00 0.00 38.95 3.66
3251 3331 2.686835 GAGGAGCAGGGGAGCACT 60.687 66.667 0.00 0.00 36.85 4.40
3252 3332 3.791586 GGAGGAGCAGGGGAGCAC 61.792 72.222 0.00 0.00 36.85 4.40
3404 3484 1.225704 CCTGGATGAGACCAAGGCC 59.774 63.158 0.00 0.00 39.59 5.19
3409 3489 1.614525 AGCAGCCTGGATGAGACCA 60.615 57.895 17.53 0.00 38.33 4.02
3411 3491 1.818785 GCAGCAGCCTGGATGAGAC 60.819 63.158 17.53 0.00 39.54 3.36
3431 3511 2.046892 CCAAGGCCAGAGACCACG 60.047 66.667 5.01 0.00 0.00 4.94
3432 3512 2.360475 GCCAAGGCCAGAGACCAC 60.360 66.667 5.01 0.00 34.56 4.16
3525 3606 4.559063 CAGAGCCTGGGCCATCGG 62.559 72.222 6.72 7.15 43.17 4.18
3528 3609 2.005266 ACATCAGAGCCTGGGCCAT 61.005 57.895 6.72 0.00 43.17 4.40
3535 3616 1.196766 TCCACAGCACATCAGAGCCT 61.197 55.000 0.00 0.00 31.08 4.58
3539 3620 1.277273 CTTCCTCCACAGCACATCAGA 59.723 52.381 0.00 0.00 0.00 3.27
3543 3624 0.036952 CGACTTCCTCCACAGCACAT 60.037 55.000 0.00 0.00 0.00 3.21
3545 3626 1.374758 CCGACTTCCTCCACAGCAC 60.375 63.158 0.00 0.00 0.00 4.40
3549 3630 3.319198 GGCCCGACTTCCTCCACA 61.319 66.667 0.00 0.00 0.00 4.17
3633 3714 3.127352 GAGTGCGACCTAGGCCTCG 62.127 68.421 9.68 15.60 0.00 4.63
3647 3728 4.180946 CGAGGACGCCGGAGAGTG 62.181 72.222 13.83 0.00 0.00 3.51
3689 3770 1.464997 GAAACACAGCCCGAACAGATC 59.535 52.381 0.00 0.00 0.00 2.75
3692 3773 1.002468 CTTGAAACACAGCCCGAACAG 60.002 52.381 0.00 0.00 0.00 3.16
3701 3782 2.541588 CCCGAAAGCACTTGAAACACAG 60.542 50.000 0.00 0.00 0.00 3.66
3702 3783 1.403679 CCCGAAAGCACTTGAAACACA 59.596 47.619 0.00 0.00 0.00 3.72
3732 3813 2.319890 AAACGTGCAGTCTTCCCGGT 62.320 55.000 0.00 0.00 0.00 5.28
3736 3817 2.349155 CGGTTTAAACGTGCAGTCTTCC 60.349 50.000 12.07 0.00 0.00 3.46
3738 3819 1.003223 GCGGTTTAAACGTGCAGTCTT 60.003 47.619 22.13 0.00 33.06 3.01
3748 3829 1.202031 CGGATGCAGAGCGGTTTAAAC 60.202 52.381 9.98 9.98 0.00 2.01


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

AutoCloner maintained by Alex Coulton.