Multiple sequence alignment - TraesCS7D01G217400

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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 TraesCS7D01G217400 chr7D 100.000 3834 0 0 1 3834 178011533 178007700 0.000000e+00 7081.0
1 TraesCS7D01G217400 chr7D 83.333 432 65 6 1486 1912 629824293 629824722 3.590000e-105 392.0
2 TraesCS7D01G217400 chr7B 90.307 2961 173 49 12 2930 144079419 144076531 0.000000e+00 3773.0
3 TraesCS7D01G217400 chr7B 92.661 436 20 7 3405 3834 144075319 144074890 5.440000e-173 617.0
4 TraesCS7D01G217400 chr7B 82.569 436 67 7 1483 1912 732644807 732645239 3.620000e-100 375.0
5 TraesCS7D01G217400 chr7B 93.714 175 6 2 3202 3371 144075492 144075318 1.370000e-64 257.0
6 TraesCS7D01G217400 chr7B 80.952 315 45 11 99 404 715819417 715819109 6.400000e-58 235.0
7 TraesCS7D01G217400 chr7B 95.276 127 4 1 2921 3047 144075650 144075526 2.340000e-47 200.0
8 TraesCS7D01G217400 chr7B 90.551 127 12 0 3087 3213 567885579 567885453 6.590000e-38 169.0
9 TraesCS7D01G217400 chr7A 93.850 2504 105 28 399 2868 182020749 182018261 0.000000e+00 3725.0
10 TraesCS7D01G217400 chr7A 87.834 674 35 19 3202 3834 182017957 182017290 0.000000e+00 747.0
11 TraesCS7D01G217400 chr7A 82.069 435 71 6 1483 1912 725912686 725913118 7.830000e-97 364.0
12 TraesCS7D01G217400 chr7A 94.273 227 8 2 2866 3089 182018179 182017955 3.670000e-90 342.0
13 TraesCS7D01G217400 chr5D 82.160 426 69 6 1492 1912 433061703 433062126 3.640000e-95 359.0
14 TraesCS7D01G217400 chr5B 81.755 433 70 8 1486 1912 526643246 526643675 1.690000e-93 353.0
15 TraesCS7D01G217400 chr5B 81.250 304 48 8 108 403 650178730 650178428 1.780000e-58 237.0
16 TraesCS7D01G217400 chr5A 80.787 432 76 6 1486 1912 547719979 547720408 7.940000e-87 331.0
17 TraesCS7D01G217400 chr5A 82.524 309 39 11 106 403 280979974 280979670 1.370000e-64 257.0
18 TraesCS7D01G217400 chr6A 86.381 257 32 3 107 361 80803378 80803123 1.050000e-70 278.0
19 TraesCS7D01G217400 chr6A 82.051 312 45 8 103 404 46548850 46549160 4.920000e-64 255.0
20 TraesCS7D01G217400 chr2D 82.680 306 38 11 107 401 130782485 130782786 1.370000e-64 257.0
21 TraesCS7D01G217400 chr2D 91.200 125 10 1 3088 3212 95519542 95519665 6.590000e-38 169.0
22 TraesCS7D01G217400 chr2D 97.500 40 1 0 2093 2132 57328662 57328623 6.870000e-08 69.4
23 TraesCS7D01G217400 chr2D 97.436 39 1 0 2094 2132 57270679 57270641 2.470000e-07 67.6
24 TraesCS7D01G217400 chr1A 81.250 304 48 5 107 403 502803493 502803192 1.780000e-58 237.0
25 TraesCS7D01G217400 chr1D 81.046 306 49 7 105 403 481338204 481338507 6.400000e-58 235.0
26 TraesCS7D01G217400 chr1D 90.226 133 11 2 3088 3218 209564264 209564132 5.090000e-39 172.0
27 TraesCS7D01G217400 chr3D 95.763 118 5 0 3087 3204 613777480 613777597 1.410000e-44 191.0
28 TraesCS7D01G217400 chr3D 92.623 122 9 0 3084 3205 2403042 2403163 3.940000e-40 176.0
29 TraesCS7D01G217400 chr4A 92.000 125 10 0 3087 3211 153242612 153242488 3.940000e-40 176.0
30 TraesCS7D01G217400 chr4A 90.625 128 11 1 3086 3212 544199319 544199446 6.590000e-38 169.0
31 TraesCS7D01G217400 chr2B 90.769 130 11 1 3078 3206 723434360 723434231 5.090000e-39 172.0
32 TraesCS7D01G217400 chr4B 91.870 123 8 1 3084 3204 73268629 73268751 1.830000e-38 171.0
33 TraesCS7D01G217400 chr6D 95.122 41 2 0 2092 2132 316488840 316488800 8.890000e-07 65.8


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 TraesCS7D01G217400 chr7D 178007700 178011533 3833 True 7081.000000 7081 100.000000 1 3834 1 chr7D.!!$R1 3833
1 TraesCS7D01G217400 chr7B 144074890 144079419 4529 True 1211.750000 3773 92.989500 12 3834 4 chr7B.!!$R3 3822
2 TraesCS7D01G217400 chr7A 182017290 182020749 3459 True 1604.666667 3725 91.985667 399 3834 3 chr7A.!!$R1 3435

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
216 219 0.457681 GCACCTTCGAGAGACTGAGC 60.458 60.0 0.0 0.0 41.84 4.26 F
1077 1099 0.043334 TGGAGGAAGGGAGGAAGGAG 59.957 60.0 0.0 0.0 0.00 3.69 F
2237 2275 0.687920 TGCATTGGGACGTTGGACTA 59.312 50.0 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2253 0.671251 TCCAACGTCCCAATGCAAAC 59.329 50.0 0.00 0.0 0.00 2.93 R
2382 2441 0.678048 GGCTCCATCAAAACGCTCCT 60.678 55.0 0.00 0.0 0.00 3.69 R
3090 4136 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.0 13.64 0.0 46.06 4.20 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
77 78 9.717942 AGTTTACAAAAATAATTATGGCTTGCA 57.282 25.926 0.00 0.00 0.00 4.08
84 85 9.768662 AAAAATAATTATGGCTTGCAGATAAGG 57.231 29.630 0.00 0.00 0.00 2.69
94 95 1.065199 TGCAGATAAGGGAGTTGGCAG 60.065 52.381 0.00 0.00 0.00 4.85
106 107 2.554032 GAGTTGGCAGTGCTTAATGTGT 59.446 45.455 16.11 0.00 0.00 3.72
140 142 4.576053 ACAATATAGATGCAAAGCGCTCAA 59.424 37.500 12.06 0.00 43.06 3.02
148 150 2.675844 TGCAAAGCGCTCAAATATACGT 59.324 40.909 12.06 0.00 43.06 3.57
150 152 3.485216 GCAAAGCGCTCAAATATACGTGT 60.485 43.478 12.06 0.00 37.77 4.49
156 158 5.628193 AGCGCTCAAATATACGTGTATACAC 59.372 40.000 23.53 23.53 43.15 2.90
158 160 6.143438 GCGCTCAAATATACGTGTATACACTT 59.857 38.462 28.53 23.34 44.34 3.16
166 168 6.884280 ATACGTGTATACACTTACCCCTAC 57.116 41.667 28.53 3.95 44.34 3.18
170 172 5.163663 CGTGTATACACTTACCCCTACGAAA 60.164 44.000 28.53 0.00 44.34 3.46
176 178 2.289257 ACTTACCCCTACGAAAGCACAC 60.289 50.000 0.00 0.00 0.00 3.82
179 181 1.289109 CCCCTACGAAAGCACACACG 61.289 60.000 0.00 0.00 0.00 4.49
182 184 0.790207 CTACGAAAGCACACACGCAT 59.210 50.000 0.00 0.00 0.00 4.73
215 218 1.132262 GAGCACCTTCGAGAGACTGAG 59.868 57.143 0.00 0.00 41.84 3.35
216 219 0.457681 GCACCTTCGAGAGACTGAGC 60.458 60.000 0.00 0.00 41.84 4.26
231 234 2.899900 ACTGAGCCGGCATATCATCTTA 59.100 45.455 31.54 0.00 0.00 2.10
240 243 7.831193 AGCCGGCATATCATCTTAAGATTTTAT 59.169 33.333 31.54 11.93 31.21 1.40
241 244 7.912250 GCCGGCATATCATCTTAAGATTTTATG 59.088 37.037 24.80 24.49 33.85 1.90
250 253 7.987458 TCATCTTAAGATTTTATGAAGTCGCCT 59.013 33.333 15.49 0.00 31.21 5.52
254 257 9.314321 CTTAAGATTTTATGAAGTCGCCTTAGA 57.686 33.333 0.00 0.00 0.00 2.10
257 260 2.486951 TATGAAGTCGCCTTAGACGC 57.513 50.000 0.00 0.00 45.26 5.19
260 263 0.525882 GAAGTCGCCTTAGACGCCTC 60.526 60.000 0.00 0.00 45.26 4.70
261 264 1.248785 AAGTCGCCTTAGACGCCTCA 61.249 55.000 0.00 0.00 45.26 3.86
264 267 0.666913 TCGCCTTAGACGCCTCATAC 59.333 55.000 0.00 0.00 0.00 2.39
272 275 2.331805 CGCCTCATACTCGACGGG 59.668 66.667 0.00 0.00 0.00 5.28
291 294 3.672767 GGAACGTCTCTTCCCACTAAA 57.327 47.619 0.00 0.00 34.59 1.85
293 296 3.243975 GGAACGTCTCTTCCCACTAAACA 60.244 47.826 0.00 0.00 34.59 2.83
296 299 3.323979 ACGTCTCTTCCCACTAAACACAT 59.676 43.478 0.00 0.00 0.00 3.21
300 303 5.749109 GTCTCTTCCCACTAAACACATATCG 59.251 44.000 0.00 0.00 0.00 2.92
301 304 5.421056 TCTCTTCCCACTAAACACATATCGT 59.579 40.000 0.00 0.00 0.00 3.73
309 312 7.117454 CCACTAAACACATATCGTCGAAAATC 58.883 38.462 0.00 0.00 0.00 2.17
312 315 8.192774 ACTAAACACATATCGTCGAAAATCCTA 58.807 33.333 0.00 0.00 0.00 2.94
348 351 1.742761 AATGCGACCATCAGGACTTG 58.257 50.000 0.00 0.00 38.69 3.16
351 354 1.079503 GCGACCATCAGGACTTGAAC 58.920 55.000 0.00 0.00 39.77 3.18
353 356 1.676014 CGACCATCAGGACTTGAACCC 60.676 57.143 0.00 0.00 39.77 4.11
382 386 6.126409 GGGATAACATTGTCCATCTAACCAA 58.874 40.000 9.34 0.00 39.93 3.67
387 391 5.332743 ACATTGTCCATCTAACCAACCAAT 58.667 37.500 0.00 0.00 0.00 3.16
392 396 6.726379 TGTCCATCTAACCAACCAATCATAA 58.274 36.000 0.00 0.00 0.00 1.90
396 401 8.694540 TCCATCTAACCAACCAATCATAAATTG 58.305 33.333 0.00 0.00 0.00 2.32
470 475 2.357952 GGCCGTCAGTCAAAAAGAAACT 59.642 45.455 0.00 0.00 0.00 2.66
472 477 4.524749 GCCGTCAGTCAAAAAGAAACTAC 58.475 43.478 0.00 0.00 0.00 2.73
712 719 3.500558 TGTGCTTCTTCTCATCTCTCG 57.499 47.619 0.00 0.00 0.00 4.04
746 753 1.783067 CGTGTCGTGTGAAATGCATCG 60.783 52.381 0.00 0.00 0.00 3.84
775 789 8.588472 CATAGTACACCTTCTGGAATATCATCA 58.412 37.037 0.00 0.00 37.04 3.07
1077 1099 0.043334 TGGAGGAAGGGAGGAAGGAG 59.957 60.000 0.00 0.00 0.00 3.69
1224 1246 7.258022 TCTCTCTTCGATCTTCATAGAGTTG 57.742 40.000 7.67 3.81 35.13 3.16
1243 1265 2.126228 CTTTGCATGCCCGCACAG 60.126 61.111 16.68 0.00 42.87 3.66
1324 1346 5.757850 AATGGCAAATTCGTAGAGGAATC 57.242 39.130 0.00 0.00 38.43 2.52
1373 1395 1.311859 CCTAATGGCATGTCGCATGT 58.688 50.000 17.22 4.57 45.17 3.21
1398 1420 3.257393 CATGAACAGTGACTGCTAGGAC 58.743 50.000 13.37 0.00 34.37 3.85
1399 1421 1.269723 TGAACAGTGACTGCTAGGACG 59.730 52.381 13.37 0.00 34.37 4.79
1427 1449 7.287466 CCATGATGTAGAATAGATAGGGAGGAG 59.713 44.444 0.00 0.00 0.00 3.69
1469 1492 9.859427 AAGTTAATTGTGTGTGGATTATTGATG 57.141 29.630 0.00 0.00 0.00 3.07
1470 1493 9.241919 AGTTAATTGTGTGTGGATTATTGATGA 57.758 29.630 0.00 0.00 0.00 2.92
1473 1496 8.936070 AATTGTGTGTGGATTATTGATGATTG 57.064 30.769 0.00 0.00 0.00 2.67
1475 1498 7.885009 TGTGTGTGGATTATTGATGATTGAT 57.115 32.000 0.00 0.00 0.00 2.57
1477 1500 8.192110 TGTGTGTGGATTATTGATGATTGATTG 58.808 33.333 0.00 0.00 0.00 2.67
1478 1501 8.192774 GTGTGTGGATTATTGATGATTGATTGT 58.807 33.333 0.00 0.00 0.00 2.71
1479 1502 9.406113 TGTGTGGATTATTGATGATTGATTGTA 57.594 29.630 0.00 0.00 0.00 2.41
1888 1916 2.158959 GTTCGTCATCTCCGGCGTG 61.159 63.158 6.01 0.00 0.00 5.34
2072 2101 8.086522 AGCTGGGTACGTACATAATTATACTTG 58.913 37.037 26.02 5.11 0.00 3.16
2118 2149 3.319122 AGATGCAGACGCTCATACATACA 59.681 43.478 0.00 0.00 39.64 2.29
2119 2150 3.733443 TGCAGACGCTCATACATACAT 57.267 42.857 0.00 0.00 39.64 2.29
2120 2151 4.846779 TGCAGACGCTCATACATACATA 57.153 40.909 0.00 0.00 39.64 2.29
2121 2152 4.546570 TGCAGACGCTCATACATACATAC 58.453 43.478 0.00 0.00 39.64 2.39
2122 2153 4.037446 TGCAGACGCTCATACATACATACA 59.963 41.667 0.00 0.00 39.64 2.29
2123 2154 5.164233 GCAGACGCTCATACATACATACAT 58.836 41.667 0.00 0.00 34.30 2.29
2181 2219 5.399858 ACTATATTACAGCCGCATAAGTCG 58.600 41.667 0.00 0.00 0.00 4.18
2184 2222 2.882927 TACAGCCGCATAAGTCGATT 57.117 45.000 0.00 0.00 0.00 3.34
2215 2253 4.237724 TCGTAGTCAGCAGAACAAGAATG 58.762 43.478 0.00 0.00 0.00 2.67
2237 2275 0.687920 TGCATTGGGACGTTGGACTA 59.312 50.000 0.00 0.00 0.00 2.59
2239 2277 2.156098 GCATTGGGACGTTGGACTAAA 58.844 47.619 0.00 0.00 0.00 1.85
2245 2283 3.195661 GGGACGTTGGACTAAAGCTATG 58.804 50.000 0.00 0.00 0.00 2.23
2282 2326 9.436957 CAGAAAGATTAACTGAAAAGCCTAGTA 57.563 33.333 0.00 0.00 34.07 1.82
2308 2352 8.651391 TCGTGTTTCAGTCAAAAAGATAGTAA 57.349 30.769 0.00 0.00 0.00 2.24
2353 2412 7.565789 GCGTGTTTCATCAGTCAAAAAGAAATC 60.566 37.037 0.00 0.00 0.00 2.17
2359 2418 8.400184 TCATCAGTCAAAAAGAAATCAGATGT 57.600 30.769 0.00 0.00 33.02 3.06
2380 2439 0.813210 GCTGTCCTGGCATCTGCTAC 60.813 60.000 1.70 0.00 41.70 3.58
2381 2440 0.829333 CTGTCCTGGCATCTGCTACT 59.171 55.000 1.70 0.00 41.70 2.57
2382 2441 2.034878 CTGTCCTGGCATCTGCTACTA 58.965 52.381 1.70 0.00 41.70 1.82
2598 2663 6.035843 TGTTTGTGAGCTTCTTGTTGAATTC 58.964 36.000 0.00 0.00 33.71 2.17
3041 4087 2.052237 GTGGCGCGAGTGTTTGTG 60.052 61.111 12.10 0.00 0.00 3.33
3089 4135 4.753233 TGCATGCATGGTTTTAATGGTAC 58.247 39.130 27.34 6.96 0.00 3.34
3090 4136 4.465660 TGCATGCATGGTTTTAATGGTACT 59.534 37.500 27.34 0.00 0.00 2.73
3091 4137 5.043248 GCATGCATGGTTTTAATGGTACTC 58.957 41.667 27.34 1.60 0.00 2.59
3092 4138 5.591099 CATGCATGGTTTTAATGGTACTCC 58.409 41.667 19.40 0.00 0.00 3.85
3093 4139 4.020543 TGCATGGTTTTAATGGTACTCCC 58.979 43.478 0.00 0.00 0.00 4.30
3094 4140 4.264172 TGCATGGTTTTAATGGTACTCCCT 60.264 41.667 0.00 0.00 0.00 4.20
3095 4141 4.338400 GCATGGTTTTAATGGTACTCCCTC 59.662 45.833 0.00 0.00 0.00 4.30
3096 4142 4.579647 TGGTTTTAATGGTACTCCCTCC 57.420 45.455 0.00 0.00 0.00 4.30
3097 4143 3.054948 TGGTTTTAATGGTACTCCCTCCG 60.055 47.826 0.00 0.00 0.00 4.63
3098 4144 3.054875 GGTTTTAATGGTACTCCCTCCGT 60.055 47.826 0.00 0.00 0.00 4.69
3099 4145 4.186926 GTTTTAATGGTACTCCCTCCGTC 58.813 47.826 0.00 0.00 0.00 4.79
3100 4146 2.077687 TAATGGTACTCCCTCCGTCC 57.922 55.000 0.00 0.00 0.00 4.79
3101 4147 1.041447 AATGGTACTCCCTCCGTCCG 61.041 60.000 0.00 0.00 0.00 4.79
3102 4148 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
3103 4149 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
3104 4150 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3105 4151 0.754587 GTACTCCCTCCGTCCGGAAT 60.755 60.000 5.23 0.00 44.66 3.01
3106 4152 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
3107 4153 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
3108 4154 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
3109 4155 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
3110 4156 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
3111 4157 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3112 4158 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3113 4159 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3114 4160 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3115 4161 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
3116 4162 1.717194 GTCCGGAATTACTTGTCGCA 58.283 50.000 5.23 0.00 0.00 5.10
3117 4163 1.659098 GTCCGGAATTACTTGTCGCAG 59.341 52.381 5.23 0.00 0.00 5.18
3118 4164 1.546923 TCCGGAATTACTTGTCGCAGA 59.453 47.619 0.00 0.00 0.00 4.26
3119 4165 2.028839 TCCGGAATTACTTGTCGCAGAA 60.029 45.455 0.00 0.00 39.69 3.02
3120 4166 2.739913 CCGGAATTACTTGTCGCAGAAA 59.260 45.455 0.00 0.00 39.69 2.52
3121 4167 3.374058 CCGGAATTACTTGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
3122 4168 4.334443 CGGAATTACTTGTCGCAGAAATG 58.666 43.478 0.00 0.00 39.69 2.32
3123 4169 4.092821 CGGAATTACTTGTCGCAGAAATGA 59.907 41.667 0.00 0.00 39.69 2.57
3124 4170 5.390461 CGGAATTACTTGTCGCAGAAATGAA 60.390 40.000 0.00 0.00 39.69 2.57
3125 4171 6.555315 GGAATTACTTGTCGCAGAAATGAAT 58.445 36.000 0.00 0.00 39.69 2.57
3126 4172 7.029563 GGAATTACTTGTCGCAGAAATGAATT 58.970 34.615 0.00 0.00 39.69 2.17
3127 4173 8.181573 GGAATTACTTGTCGCAGAAATGAATTA 58.818 33.333 0.00 0.00 39.69 1.40
3128 4174 9.554724 GAATTACTTGTCGCAGAAATGAATTAA 57.445 29.630 0.00 0.00 39.69 1.40
3129 4175 9.906660 AATTACTTGTCGCAGAAATGAATTAAA 57.093 25.926 0.00 0.00 39.69 1.52
3130 4176 9.906660 ATTACTTGTCGCAGAAATGAATTAAAA 57.093 25.926 0.00 0.00 39.69 1.52
3131 4177 9.906660 TTACTTGTCGCAGAAATGAATTAAAAT 57.093 25.926 0.00 0.00 39.69 1.82
3132 4178 8.231304 ACTTGTCGCAGAAATGAATTAAAATG 57.769 30.769 0.00 0.00 39.69 2.32
3133 4179 7.329226 ACTTGTCGCAGAAATGAATTAAAATGG 59.671 33.333 0.00 0.00 39.69 3.16
3134 4180 6.918626 TGTCGCAGAAATGAATTAAAATGGA 58.081 32.000 0.00 0.00 39.69 3.41
3135 4181 7.546358 TGTCGCAGAAATGAATTAAAATGGAT 58.454 30.769 0.00 0.00 39.69 3.41
3136 4182 7.488792 TGTCGCAGAAATGAATTAAAATGGATG 59.511 33.333 0.00 0.00 39.69 3.51
3137 4183 7.489113 GTCGCAGAAATGAATTAAAATGGATGT 59.511 33.333 0.00 0.00 39.69 3.06
3138 4184 8.681806 TCGCAGAAATGAATTAAAATGGATGTA 58.318 29.630 0.00 0.00 0.00 2.29
3139 4185 9.467258 CGCAGAAATGAATTAAAATGGATGTAT 57.533 29.630 0.00 0.00 0.00 2.29
3177 4223 6.978343 TGTCTAGGTACATTCATTTTTCCG 57.022 37.500 0.00 0.00 0.00 4.30
3178 4224 6.703319 TGTCTAGGTACATTCATTTTTCCGA 58.297 36.000 0.00 0.00 0.00 4.55
3179 4225 6.592607 TGTCTAGGTACATTCATTTTTCCGAC 59.407 38.462 0.00 0.00 0.00 4.79
3180 4226 6.592607 GTCTAGGTACATTCATTTTTCCGACA 59.407 38.462 0.00 0.00 0.00 4.35
3181 4227 7.118680 GTCTAGGTACATTCATTTTTCCGACAA 59.881 37.037 0.00 0.00 0.00 3.18
3182 4228 6.254281 AGGTACATTCATTTTTCCGACAAG 57.746 37.500 0.00 0.00 0.00 3.16
3183 4229 5.768164 AGGTACATTCATTTTTCCGACAAGT 59.232 36.000 0.00 0.00 0.00 3.16
3184 4230 6.938030 AGGTACATTCATTTTTCCGACAAGTA 59.062 34.615 0.00 0.00 0.00 2.24
3185 4231 7.610305 AGGTACATTCATTTTTCCGACAAGTAT 59.390 33.333 0.00 0.00 0.00 2.12
3186 4232 8.241367 GGTACATTCATTTTTCCGACAAGTATT 58.759 33.333 0.00 0.00 0.00 1.89
3187 4233 9.620660 GTACATTCATTTTTCCGACAAGTATTT 57.379 29.630 0.00 0.00 0.00 1.40
3188 4234 8.742554 ACATTCATTTTTCCGACAAGTATTTC 57.257 30.769 0.00 0.00 0.00 2.17
3189 4235 7.812669 ACATTCATTTTTCCGACAAGTATTTCC 59.187 33.333 0.00 0.00 0.00 3.13
3190 4236 5.933790 TCATTTTTCCGACAAGTATTTCCG 58.066 37.500 0.00 0.00 0.00 4.30
3191 4237 4.752661 TTTTTCCGACAAGTATTTCCGG 57.247 40.909 0.00 0.00 41.36 5.14
3192 4238 3.681593 TTTCCGACAAGTATTTCCGGA 57.318 42.857 0.00 0.00 46.18 5.14
3193 4239 2.660189 TCCGACAAGTATTTCCGGAC 57.340 50.000 1.83 0.00 43.47 4.79
3194 4240 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
3195 4241 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3196 4242 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3197 4243 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3198 4244 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3199 4245 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3200 4246 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3201 4247 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3202 4248 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3203 4249 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3204 4250 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
3381 4450 0.992072 ATGACACAATCGTTCGCTCG 59.008 50.000 0.00 0.00 0.00 5.03
3399 4468 0.038526 CGTTTGACGCTACCTGAGGT 60.039 55.000 10.00 10.00 35.55 3.85
3400 4469 1.429463 GTTTGACGCTACCTGAGGTG 58.571 55.000 15.83 5.54 36.19 4.00
3402 4471 0.888619 TTGACGCTACCTGAGGTGAG 59.111 55.000 15.83 8.70 36.19 3.51
3403 4472 0.965866 TGACGCTACCTGAGGTGAGG 60.966 60.000 15.83 5.23 36.19 3.86
3405 4474 0.251653 ACGCTACCTGAGGTGAGGAA 60.252 55.000 15.83 0.00 36.19 3.36
3406 4475 0.895530 CGCTACCTGAGGTGAGGAAA 59.104 55.000 15.83 0.00 36.19 3.13
3407 4476 1.404315 CGCTACCTGAGGTGAGGAAAC 60.404 57.143 15.83 0.00 36.19 2.78
3509 4589 3.818961 AGACATGCGTGACAAATTCTG 57.181 42.857 14.17 0.00 0.00 3.02
3709 4796 2.129555 AATCAGCACAAGGGGACGCT 62.130 55.000 0.00 0.00 34.29 5.07
3710 4797 1.264749 ATCAGCACAAGGGGACGCTA 61.265 55.000 0.00 0.00 32.29 4.26
3711 4798 1.448540 CAGCACAAGGGGACGCTAG 60.449 63.158 0.00 0.00 32.29 3.42
3712 4799 2.820037 GCACAAGGGGACGCTAGC 60.820 66.667 4.06 4.06 0.00 3.42
3716 4803 1.224592 CAAGGGGACGCTAGCCAAT 59.775 57.895 9.66 0.00 0.00 3.16
3722 4809 1.070134 GGGACGCTAGCCAATATGTCA 59.930 52.381 9.66 0.00 0.00 3.58
3723 4810 2.484770 GGGACGCTAGCCAATATGTCAA 60.485 50.000 9.66 0.00 0.00 3.18
3728 4815 4.457603 ACGCTAGCCAATATGTCAAAACAA 59.542 37.500 9.66 0.00 39.30 2.83
3743 4830 8.472683 TGTCAAAACAAACAAGAAACATAAGG 57.527 30.769 0.00 0.00 30.70 2.69
3813 4900 6.594788 TTTTGGCATAGATTTCTTCAAGCT 57.405 33.333 0.00 0.00 34.66 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 2.019984 GCCAACTCCCTTATCTGCAAG 58.980 52.381 0.00 0.00 0.00 4.01
77 78 1.065126 GCACTGCCAACTCCCTTATCT 60.065 52.381 0.00 0.00 0.00 1.98
83 84 1.474077 CATTAAGCACTGCCAACTCCC 59.526 52.381 0.00 0.00 0.00 4.30
84 85 2.095059 CACATTAAGCACTGCCAACTCC 60.095 50.000 0.00 0.00 0.00 3.85
115 117 4.214980 GCGCTTTGCATCTATATTGTGT 57.785 40.909 0.00 0.00 45.45 3.72
133 135 5.829681 GTGTATACACGTATATTTGAGCGC 58.170 41.667 19.71 0.00 37.10 5.92
148 150 5.163519 GCTTTCGTAGGGGTAAGTGTATACA 60.164 44.000 0.08 0.08 0.00 2.29
150 152 4.955450 TGCTTTCGTAGGGGTAAGTGTATA 59.045 41.667 0.00 0.00 0.00 1.47
156 158 2.289195 TGTGTGCTTTCGTAGGGGTAAG 60.289 50.000 0.00 0.00 0.00 2.34
158 160 1.001181 GTGTGTGCTTTCGTAGGGGTA 59.999 52.381 0.00 0.00 0.00 3.69
166 168 1.267532 GGATATGCGTGTGTGCTTTCG 60.268 52.381 0.00 0.00 35.36 3.46
170 172 1.202533 GGTAGGATATGCGTGTGTGCT 60.203 52.381 0.00 0.00 35.36 4.40
176 178 3.429547 GCTCATAGGGTAGGATATGCGTG 60.430 52.174 0.00 0.00 30.89 5.34
179 181 3.118592 GGTGCTCATAGGGTAGGATATGC 60.119 52.174 0.00 0.00 30.89 3.14
182 184 4.417437 GAAGGTGCTCATAGGGTAGGATA 58.583 47.826 0.00 0.00 0.00 2.59
215 218 5.886960 AAATCTTAAGATGATATGCCGGC 57.113 39.130 22.73 22.73 34.49 6.13
216 219 9.166173 TCATAAAATCTTAAGATGATATGCCGG 57.834 33.333 27.11 15.43 35.76 6.13
247 250 1.335142 CGAGTATGAGGCGTCTAAGGC 60.335 57.143 8.06 0.00 0.00 4.35
250 253 1.596260 CGTCGAGTATGAGGCGTCTAA 59.404 52.381 8.06 0.00 0.00 2.10
254 257 2.478890 CCCGTCGAGTATGAGGCGT 61.479 63.158 0.00 0.00 33.10 5.68
257 260 0.029035 CGTTCCCGTCGAGTATGAGG 59.971 60.000 0.00 0.00 0.00 3.86
272 275 3.739810 GTGTTTAGTGGGAAGAGACGTTC 59.260 47.826 0.00 0.00 0.00 3.95
281 284 4.158209 TCGACGATATGTGTTTAGTGGGAA 59.842 41.667 0.00 0.00 0.00 3.97
282 285 3.695556 TCGACGATATGTGTTTAGTGGGA 59.304 43.478 0.00 0.00 0.00 4.37
283 286 4.036567 TCGACGATATGTGTTTAGTGGG 57.963 45.455 0.00 0.00 0.00 4.61
289 292 7.837202 TTAGGATTTTCGACGATATGTGTTT 57.163 32.000 0.00 0.00 0.00 2.83
291 294 7.837202 TTTTAGGATTTTCGACGATATGTGT 57.163 32.000 0.00 0.00 0.00 3.72
322 325 3.901222 TCCTGATGGTCGCATTTATCCTA 59.099 43.478 0.00 0.00 34.23 2.94
325 328 3.733337 AGTCCTGATGGTCGCATTTATC 58.267 45.455 0.00 0.00 34.23 1.75
353 356 3.364460 TGGACAATGTTATCCCACCAG 57.636 47.619 0.00 0.00 33.69 4.00
357 360 5.192722 TGGTTAGATGGACAATGTTATCCCA 59.807 40.000 7.61 1.76 33.69 4.37
360 363 6.601613 TGGTTGGTTAGATGGACAATGTTATC 59.398 38.462 0.00 0.00 0.00 1.75
364 368 4.380843 TGGTTGGTTAGATGGACAATGT 57.619 40.909 0.00 0.00 0.00 2.71
387 391 3.126858 GCACTGAGCGAACCAATTTATGA 59.873 43.478 0.00 0.00 0.00 2.15
470 475 2.430694 CCACATCCAAGGATCTCGTGTA 59.569 50.000 13.69 0.00 31.62 2.90
472 477 1.945387 CCACATCCAAGGATCTCGTG 58.055 55.000 9.80 9.80 31.62 4.35
746 753 4.737855 TTCCAGAAGGTGTACTATGCTC 57.262 45.455 0.00 0.00 35.89 4.26
753 760 6.480320 GTGTGATGATATTCCAGAAGGTGTAC 59.520 42.308 0.00 0.00 35.89 2.90
775 789 4.783055 TGGTTGGTGTAATGTTACAGTGT 58.217 39.130 0.00 0.00 43.67 3.55
1023 1045 1.410517 TGAGATCCTCCATTCGTCTGC 59.589 52.381 0.00 0.00 0.00 4.26
1077 1099 1.147153 GCAGCCCTGGTCATAGTCC 59.853 63.158 0.00 0.00 0.00 3.85
1243 1265 6.205658 GCATTATCCCTCAATTACCAGAAGTC 59.794 42.308 0.00 0.00 0.00 3.01
1324 1346 1.321474 ATGGCTTGGTGTGACAACAG 58.679 50.000 2.60 0.00 36.84 3.16
1373 1395 0.950555 GCAGTCACTGTTCATGGCGA 60.951 55.000 6.68 0.00 33.43 5.54
1398 1420 6.603599 TCCCTATCTATTCTACATCATGGACG 59.396 42.308 0.00 0.00 0.00 4.79
1399 1421 7.069331 CCTCCCTATCTATTCTACATCATGGAC 59.931 44.444 0.00 0.00 0.00 4.02
1427 1449 6.747659 ATTAACTTTCACGCAACAACATTC 57.252 33.333 0.00 0.00 0.00 2.67
1469 1492 7.412346 GGCGATGATCTACACATACAATCAATC 60.412 40.741 0.00 0.00 30.76 2.67
1470 1493 6.369890 GGCGATGATCTACACATACAATCAAT 59.630 38.462 0.00 0.00 30.76 2.57
1471 1494 5.696270 GGCGATGATCTACACATACAATCAA 59.304 40.000 0.00 0.00 30.76 2.57
1473 1496 4.324669 CGGCGATGATCTACACATACAATC 59.675 45.833 0.00 0.00 0.00 2.67
1475 1498 3.316868 TCGGCGATGATCTACACATACAA 59.683 43.478 4.99 0.00 0.00 2.41
1477 1500 3.188667 TCTCGGCGATGATCTACACATAC 59.811 47.826 11.27 0.00 0.00 2.39
1478 1501 3.408634 TCTCGGCGATGATCTACACATA 58.591 45.455 11.27 0.00 0.00 2.29
1479 1502 2.230660 TCTCGGCGATGATCTACACAT 58.769 47.619 11.27 0.00 0.00 3.21
1480 1503 1.675552 TCTCGGCGATGATCTACACA 58.324 50.000 11.27 0.00 0.00 3.72
1547 1575 0.823356 TGCCCCTTGCTCTTGTTGAC 60.823 55.000 0.00 0.00 42.00 3.18
1648 1676 3.524648 GACGGCCGGGTTGAAGTGA 62.525 63.158 31.76 0.00 0.00 3.41
1789 1817 4.329545 GTGCCGGGGAAGTGCTCA 62.330 66.667 2.18 0.00 0.00 4.26
1888 1916 1.668151 GGCTCTGTTGTCGGTGGAC 60.668 63.158 0.00 0.00 43.71 4.02
1936 1964 3.722555 ATCATACGCGAGTTTGTTGTG 57.277 42.857 15.93 0.00 46.40 3.33
2089 2118 3.969899 TGAGCGTCTGCATCTGTATTAG 58.030 45.455 0.00 0.00 46.23 1.73
2118 2149 4.094294 GGACGTGCAAATGTGTGTATGTAT 59.906 41.667 0.63 0.00 34.04 2.29
2119 2150 3.433957 GGACGTGCAAATGTGTGTATGTA 59.566 43.478 0.63 0.00 34.04 2.29
2120 2151 2.225491 GGACGTGCAAATGTGTGTATGT 59.775 45.455 0.63 0.00 36.24 2.29
2121 2152 2.225255 TGGACGTGCAAATGTGTGTATG 59.775 45.455 7.52 0.00 0.00 2.39
2122 2153 2.499197 TGGACGTGCAAATGTGTGTAT 58.501 42.857 7.52 0.00 0.00 2.29
2123 2154 1.954927 TGGACGTGCAAATGTGTGTA 58.045 45.000 7.52 0.00 0.00 2.90
2150 2181 4.929808 GCGGCTGTAATATAGTATGTGCTT 59.070 41.667 0.00 0.00 0.00 3.91
2181 2219 8.186178 TCTGCTGACTACGAAAATTCTAAATC 57.814 34.615 0.00 0.00 0.00 2.17
2184 2222 6.926826 TGTTCTGCTGACTACGAAAATTCTAA 59.073 34.615 0.00 0.00 0.00 2.10
2215 2253 0.671251 TCCAACGTCCCAATGCAAAC 59.329 50.000 0.00 0.00 0.00 2.93
2237 2275 4.973168 TCTGACTGAAACACCATAGCTTT 58.027 39.130 0.00 0.00 0.00 3.51
2239 2277 4.623932 TTCTGACTGAAACACCATAGCT 57.376 40.909 0.00 0.00 0.00 3.32
2245 2283 7.226720 TCAGTTAATCTTTCTGACTGAAACACC 59.773 37.037 3.59 0.00 42.49 4.16
2275 2319 4.106029 TGACTGAAACACGATACTAGGC 57.894 45.455 0.00 0.00 0.00 3.93
2282 2326 7.730364 ACTATCTTTTTGACTGAAACACGAT 57.270 32.000 0.00 0.00 0.00 3.73
2308 2352 6.946229 CACGCTACTAGTGTTTTCAGTTAT 57.054 37.500 5.39 0.00 36.71 1.89
2327 2373 4.597079 TCTTTTTGACTGATGAAACACGC 58.403 39.130 0.00 0.00 0.00 5.34
2353 2412 1.748122 GCCAGGACAGCCACATCTG 60.748 63.158 0.00 0.00 39.86 2.90
2359 2418 2.672908 CAGATGCCAGGACAGCCA 59.327 61.111 0.00 0.00 36.29 4.75
2380 2439 1.936547 GCTCCATCAAAACGCTCCTAG 59.063 52.381 0.00 0.00 0.00 3.02
2381 2440 1.406887 GGCTCCATCAAAACGCTCCTA 60.407 52.381 0.00 0.00 0.00 2.94
2382 2441 0.678048 GGCTCCATCAAAACGCTCCT 60.678 55.000 0.00 0.00 0.00 3.69
2558 2617 9.899226 GCTCACAAACATTTTCTTCTTAGTATT 57.101 29.630 0.00 0.00 0.00 1.89
2559 2618 9.289782 AGCTCACAAACATTTTCTTCTTAGTAT 57.710 29.630 0.00 0.00 0.00 2.12
2561 2620 7.573968 AGCTCACAAACATTTTCTTCTTAGT 57.426 32.000 0.00 0.00 0.00 2.24
2562 2621 8.348507 AGAAGCTCACAAACATTTTCTTCTTAG 58.651 33.333 0.00 0.00 36.58 2.18
2563 2622 8.225603 AGAAGCTCACAAACATTTTCTTCTTA 57.774 30.769 0.00 0.00 36.58 2.10
2564 2623 7.105241 AGAAGCTCACAAACATTTTCTTCTT 57.895 32.000 0.00 0.00 36.58 2.52
2598 2663 2.912025 ACACCGGCCTGCCAAAAG 60.912 61.111 0.00 0.00 35.37 2.27
2881 3034 0.750249 ATATGGCCACGATGACGACA 59.250 50.000 8.16 0.00 42.66 4.35
3070 4116 4.649218 GGGAGTACCATTAAAACCATGCAT 59.351 41.667 0.00 0.00 39.85 3.96
3078 4124 3.198417 GGACGGAGGGAGTACCATTAAAA 59.802 47.826 0.00 0.00 43.89 1.52
3079 4125 2.767960 GGACGGAGGGAGTACCATTAAA 59.232 50.000 0.00 0.00 43.89 1.52
3089 4135 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3090 4136 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
3091 4137 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3092 4138 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3093 4139 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3094 4140 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3095 4141 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3096 4142 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
3097 4143 1.659098 CTGCGACAAGTAATTCCGGAC 59.341 52.381 1.83 0.00 0.00 4.79
3098 4144 1.546923 TCTGCGACAAGTAATTCCGGA 59.453 47.619 0.00 0.00 0.00 5.14
3099 4145 2.004583 TCTGCGACAAGTAATTCCGG 57.995 50.000 0.00 0.00 0.00 5.14
3100 4146 4.092821 TCATTTCTGCGACAAGTAATTCCG 59.907 41.667 0.00 0.00 0.00 4.30
3101 4147 5.545658 TCATTTCTGCGACAAGTAATTCC 57.454 39.130 0.00 0.00 0.00 3.01
3102 4148 9.554724 TTAATTCATTTCTGCGACAAGTAATTC 57.445 29.630 0.00 0.00 0.00 2.17
3103 4149 9.906660 TTTAATTCATTTCTGCGACAAGTAATT 57.093 25.926 0.00 0.00 0.00 1.40
3104 4150 9.906660 TTTTAATTCATTTCTGCGACAAGTAAT 57.093 25.926 0.00 0.00 0.00 1.89
3105 4151 9.906660 ATTTTAATTCATTTCTGCGACAAGTAA 57.093 25.926 0.00 0.00 0.00 2.24
3106 4152 9.340695 CATTTTAATTCATTTCTGCGACAAGTA 57.659 29.630 0.00 0.00 0.00 2.24
3107 4153 7.329226 CCATTTTAATTCATTTCTGCGACAAGT 59.671 33.333 0.00 0.00 0.00 3.16
3108 4154 7.541783 TCCATTTTAATTCATTTCTGCGACAAG 59.458 33.333 0.00 0.00 0.00 3.16
3109 4155 7.374272 TCCATTTTAATTCATTTCTGCGACAA 58.626 30.769 0.00 0.00 0.00 3.18
3110 4156 6.918626 TCCATTTTAATTCATTTCTGCGACA 58.081 32.000 0.00 0.00 0.00 4.35
3111 4157 7.489113 ACATCCATTTTAATTCATTTCTGCGAC 59.511 33.333 0.00 0.00 0.00 5.19
3112 4158 7.546358 ACATCCATTTTAATTCATTTCTGCGA 58.454 30.769 0.00 0.00 0.00 5.10
3113 4159 7.760131 ACATCCATTTTAATTCATTTCTGCG 57.240 32.000 0.00 0.00 0.00 5.18
3151 4197 9.273016 CGGAAAAATGAATGTACCTAGACATAT 57.727 33.333 0.00 0.00 39.16 1.78
3152 4198 8.479689 TCGGAAAAATGAATGTACCTAGACATA 58.520 33.333 0.00 0.00 39.16 2.29
3153 4199 7.280205 GTCGGAAAAATGAATGTACCTAGACAT 59.720 37.037 0.00 0.00 41.92 3.06
3154 4200 6.592607 GTCGGAAAAATGAATGTACCTAGACA 59.407 38.462 0.00 0.00 0.00 3.41
3155 4201 6.592607 TGTCGGAAAAATGAATGTACCTAGAC 59.407 38.462 0.00 0.00 0.00 2.59
3156 4202 6.703319 TGTCGGAAAAATGAATGTACCTAGA 58.297 36.000 0.00 0.00 0.00 2.43
3157 4203 6.978343 TGTCGGAAAAATGAATGTACCTAG 57.022 37.500 0.00 0.00 0.00 3.02
3158 4204 6.938030 ACTTGTCGGAAAAATGAATGTACCTA 59.062 34.615 0.00 0.00 0.00 3.08
3159 4205 5.768164 ACTTGTCGGAAAAATGAATGTACCT 59.232 36.000 0.00 0.00 0.00 3.08
3160 4206 6.009115 ACTTGTCGGAAAAATGAATGTACC 57.991 37.500 0.00 0.00 0.00 3.34
3161 4207 9.620660 AAATACTTGTCGGAAAAATGAATGTAC 57.379 29.630 0.00 0.00 0.00 2.90
3162 4208 9.834628 GAAATACTTGTCGGAAAAATGAATGTA 57.165 29.630 0.00 0.00 0.00 2.29
3163 4209 7.812669 GGAAATACTTGTCGGAAAAATGAATGT 59.187 33.333 0.00 0.00 0.00 2.71
3164 4210 7.008266 CGGAAATACTTGTCGGAAAAATGAATG 59.992 37.037 0.00 0.00 0.00 2.67
3165 4211 7.027161 CGGAAATACTTGTCGGAAAAATGAAT 58.973 34.615 0.00 0.00 0.00 2.57
3166 4212 6.375377 CGGAAATACTTGTCGGAAAAATGAA 58.625 36.000 0.00 0.00 0.00 2.57
3167 4213 5.106475 CCGGAAATACTTGTCGGAAAAATGA 60.106 40.000 0.00 0.00 42.94 2.57
3168 4214 5.092781 CCGGAAATACTTGTCGGAAAAATG 58.907 41.667 0.00 0.00 42.94 2.32
3169 4215 5.005094 TCCGGAAATACTTGTCGGAAAAAT 58.995 37.500 0.00 0.00 45.40 1.82
3170 4216 4.387598 TCCGGAAATACTTGTCGGAAAAA 58.612 39.130 0.00 0.00 45.40 1.94
3171 4217 4.005487 TCCGGAAATACTTGTCGGAAAA 57.995 40.909 0.00 0.00 45.40 2.29
3172 4218 3.681593 TCCGGAAATACTTGTCGGAAA 57.318 42.857 0.00 0.00 45.40 3.13
3174 4220 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
3175 4221 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
3176 4222 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3177 4223 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3178 4224 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3179 4225 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3180 4226 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3181 4227 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3182 4228 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3183 4229 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3184 4230 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3185 4231 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3186 4232 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3187 4233 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
3188 4234 0.534652 CTAGTACTCCCTCCGTCCGG 60.535 65.000 0.00 0.00 0.00 5.14
3189 4235 1.165284 GCTAGTACTCCCTCCGTCCG 61.165 65.000 0.00 0.00 0.00 4.79
3190 4236 0.183252 AGCTAGTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
3191 4237 2.055684 AAGCTAGTACTCCCTCCGTC 57.944 55.000 0.00 0.00 0.00 4.79
3192 4238 3.659183 TTAAGCTAGTACTCCCTCCGT 57.341 47.619 0.00 0.00 0.00 4.69
3193 4239 6.645790 TTAATTAAGCTAGTACTCCCTCCG 57.354 41.667 0.00 0.00 0.00 4.63
3194 4240 7.577236 CGGATTAATTAAGCTAGTACTCCCTCC 60.577 44.444 12.84 4.86 0.00 4.30
3195 4241 7.039853 ACGGATTAATTAAGCTAGTACTCCCTC 60.040 40.741 12.84 0.00 0.00 4.30
3196 4242 6.781507 ACGGATTAATTAAGCTAGTACTCCCT 59.218 38.462 12.84 0.00 0.00 4.20
3197 4243 6.867293 CACGGATTAATTAAGCTAGTACTCCC 59.133 42.308 12.84 0.00 0.00 4.30
3198 4244 6.365518 GCACGGATTAATTAAGCTAGTACTCC 59.634 42.308 12.84 6.75 0.00 3.85
3199 4245 6.921857 TGCACGGATTAATTAAGCTAGTACTC 59.078 38.462 12.84 7.27 0.00 2.59
3200 4246 6.812998 TGCACGGATTAATTAAGCTAGTACT 58.187 36.000 12.84 0.00 0.00 2.73
3201 4247 6.700520 ACTGCACGGATTAATTAAGCTAGTAC 59.299 38.462 12.84 8.92 0.00 2.73
3202 4248 6.812998 ACTGCACGGATTAATTAAGCTAGTA 58.187 36.000 12.84 3.09 0.00 1.82
3203 4249 5.671493 ACTGCACGGATTAATTAAGCTAGT 58.329 37.500 12.84 10.42 0.00 2.57
3204 4250 6.037172 ACAACTGCACGGATTAATTAAGCTAG 59.963 38.462 12.84 9.86 0.00 3.42
3381 4450 1.000506 TCACCTCAGGTAGCGTCAAAC 59.999 52.381 0.00 0.00 32.11 2.93
3509 4589 4.038282 TGGAGAATTGCCATGTTGCATATC 59.962 41.667 0.00 0.67 41.70 1.63
3709 4796 7.946207 TCTTGTTTGTTTTGACATATTGGCTA 58.054 30.769 0.00 0.00 0.00 3.93
3710 4797 6.815089 TCTTGTTTGTTTTGACATATTGGCT 58.185 32.000 0.00 0.00 0.00 4.75
3711 4798 7.475771 TTCTTGTTTGTTTTGACATATTGGC 57.524 32.000 0.00 0.00 0.00 4.52
3712 4799 8.877779 TGTTTCTTGTTTGTTTTGACATATTGG 58.122 29.630 0.00 0.00 0.00 3.16
3722 4809 8.091449 TGACACCTTATGTTTCTTGTTTGTTTT 58.909 29.630 0.00 0.00 43.56 2.43
3723 4810 7.607250 TGACACCTTATGTTTCTTGTTTGTTT 58.393 30.769 0.00 0.00 43.56 2.83
3728 4815 6.306987 AGGATGACACCTTATGTTTCTTGTT 58.693 36.000 0.00 0.00 43.56 2.83
3743 4830 5.983540 AGAAGAATTGGAGTAGGATGACAC 58.016 41.667 0.00 0.00 0.00 3.67
3813 4900 3.914426 GGTGGCTCTAATCAAGAAGGA 57.086 47.619 0.00 0.00 32.46 3.36


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

AutoCloner maintained by Alex Coulton.