Multiple sequence alignment - TraesCS6D01G259600

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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 TraesCS6D01G259600 chr6D 100.000 3415 0 0 936 4350 365849487 365846073 0.000000e+00 6307.0
1 TraesCS6D01G259600 chr6D 100.000 3287 0 0 4673 7959 365845750 365842464 0.000000e+00 6071.0
2 TraesCS6D01G259600 chr6D 100.000 466 0 0 1 466 365850422 365849957 0.000000e+00 861.0
3 TraesCS6D01G259600 chr6D 89.326 356 36 2 3187 3542 158356429 158356782 5.670000e-121 446.0
4 TraesCS6D01G259600 chr6D 89.326 356 36 2 3187 3542 267533165 267532812 5.670000e-121 446.0
5 TraesCS6D01G259600 chr6B 95.876 3395 118 12 939 4316 551980369 551976980 0.000000e+00 5474.0
6 TraesCS6D01G259600 chr6B 95.366 3129 83 26 4743 7864 551976861 551973788 0.000000e+00 4918.0
7 TraesCS6D01G259600 chr6B 94.972 179 5 2 289 466 551980872 551980697 2.190000e-70 278.0
8 TraesCS6D01G259600 chr6B 93.056 72 5 0 7835 7906 551973769 551973698 1.090000e-18 106.0
9 TraesCS6D01G259600 chr6A 96.415 3180 85 14 936 4106 506645427 506642268 0.000000e+00 5214.0
10 TraesCS6D01G259600 chr6A 95.731 2881 75 20 4907 7777 506642278 506639436 0.000000e+00 4595.0
11 TraesCS6D01G259600 chr6A 96.067 178 4 1 289 466 506645662 506645488 3.630000e-73 287.0
12 TraesCS6D01G259600 chr6A 91.220 205 18 0 1 205 506646027 506645823 6.080000e-71 279.0
13 TraesCS6D01G259600 chr6A 94.118 51 3 0 7863 7913 506639087 506639037 2.380000e-10 78.7
14 TraesCS6D01G259600 chr3B 90.625 352 30 3 3186 3537 71401512 71401860 1.560000e-126 464.0
15 TraesCS6D01G259600 chr3B 90.278 360 28 6 3187 3542 694031267 694031623 1.560000e-126 464.0
16 TraesCS6D01G259600 chr2D 90.423 355 30 4 3187 3541 380416879 380416529 1.560000e-126 464.0
17 TraesCS6D01G259600 chr2D 97.917 48 1 0 7912 7959 423376248 423376295 5.120000e-12 84.2
18 TraesCS6D01G259600 chr4A 89.694 359 30 5 3187 3541 119071854 119071499 1.220000e-122 451.0
19 TraesCS6D01G259600 chr4A 88.430 121 13 1 3021 3141 441757702 441757583 2.310000e-30 145.0
20 TraesCS6D01G259600 chr5D 89.385 358 35 3 3187 3543 360542210 360541855 1.580000e-121 448.0
21 TraesCS6D01G259600 chr5D 86.818 220 25 4 5873 6090 479457133 479456916 7.980000e-60 243.0
22 TraesCS6D01G259600 chr5B 85.845 219 29 2 5873 6090 587125089 587124872 1.730000e-56 231.0
23 TraesCS6D01G259600 chr5B 97.917 48 1 0 7912 7959 30401979 30402026 5.120000e-12 84.2
24 TraesCS6D01G259600 chr5B 97.917 48 1 0 7912 7959 217593469 217593516 5.120000e-12 84.2
25 TraesCS6D01G259600 chr5B 97.917 48 1 0 7912 7959 217609589 217609636 5.120000e-12 84.2
26 TraesCS6D01G259600 chr3D 90.816 98 9 0 3036 3133 73896358 73896455 1.800000e-26 132.0
27 TraesCS6D01G259600 chr3D 86.667 105 14 0 3032 3136 604669509 604669405 5.050000e-22 117.0
28 TraesCS6D01G259600 chr7D 85.714 119 16 1 3018 3135 432494896 432494778 3.020000e-24 124.0
29 TraesCS6D01G259600 chr4D 89.474 95 8 2 3039 3132 259497352 259497259 1.400000e-22 119.0
30 TraesCS6D01G259600 chr1D 84.821 112 16 1 3021 3132 24714572 24714462 2.350000e-20 111.0
31 TraesCS6D01G259600 chr1D 97.917 48 1 0 7912 7959 37516268 37516221 5.120000e-12 84.2
32 TraesCS6D01G259600 chrUn 82.645 121 19 2 3026 3145 269322175 269322056 1.090000e-18 106.0
33 TraesCS6D01G259600 chrUn 97.917 48 1 0 7912 7959 111116217 111116170 5.120000e-12 84.2
34 TraesCS6D01G259600 chr1B 97.917 48 1 0 7912 7959 152828844 152828891 5.120000e-12 84.2
35 TraesCS6D01G259600 chr2A 92.857 56 2 2 7906 7959 240479167 240479112 6.620000e-11 80.5
36 TraesCS6D01G259600 chr2B 95.833 48 2 0 7912 7959 46600265 46600218 2.380000e-10 78.7


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 TraesCS6D01G259600 chr6D 365842464 365850422 7958 True 4413.00 6307 100.0000 1 7959 3 chr6D.!!$R2 7958
1 TraesCS6D01G259600 chr6B 551973698 551980872 7174 True 2694.00 5474 94.8175 289 7906 4 chr6B.!!$R1 7617
2 TraesCS6D01G259600 chr6A 506639037 506646027 6990 True 2090.74 5214 94.7102 1 7913 5 chr6A.!!$R1 7912

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
360 441 0.401738 AATCACTGACAGGGTGGTGG 59.598 55.0 4.24 0.0 35.61 4.61 F
1744 1838 0.320247 GAGGCCATGAGCAGGTATCG 60.320 60.0 5.01 0.0 46.50 2.92 F
1866 1960 0.692476 TCCTCCACATGTTCCACCAG 59.308 55.0 0.00 0.0 0.00 4.00 F
3265 3365 0.737019 GCGATGGTTTGGGCATGTTG 60.737 55.0 0.00 0.0 0.00 3.33 F
4319 4427 0.178767 CATCGTCAGCTTCATCCCCA 59.821 55.0 0.00 0.0 0.00 4.96 F
4322 4430 0.179089 CGTCAGCTTCATCCCCAGAG 60.179 60.0 0.00 0.0 0.00 3.35 F
4323 4431 0.179936 GTCAGCTTCATCCCCAGAGG 59.820 60.0 0.00 0.0 0.00 3.69 F
4925 5124 0.250467 TGTTGCTTCCAGAGTGAGGC 60.250 55.0 0.00 0.0 37.81 4.70 F
5150 5349 0.102481 TTTATCGGGCTCAGTCGCTC 59.898 55.0 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1926 1.194772 GGAGGAACTTCAACGCTTTCG 59.805 52.381 0.00 0.00 41.55 3.46 R
3743 3844 1.069513 CTCACGGTTTGTACCACCAGA 59.930 52.381 11.01 7.41 45.31 3.86 R
3938 4039 7.630924 CGACAGAACAAGAAGTCAGTATTTTT 58.369 34.615 0.00 0.00 0.00 1.94 R
5147 5346 0.035630 ACACCAATCCAGCTCTGAGC 60.036 55.000 21.72 21.72 42.84 4.26 R
5148 5347 2.234661 TGTACACCAATCCAGCTCTGAG 59.765 50.000 0.00 0.00 0.00 3.35 R
5149 5348 2.256306 TGTACACCAATCCAGCTCTGA 58.744 47.619 0.00 0.00 0.00 3.27 R
5150 5349 2.768253 TGTACACCAATCCAGCTCTG 57.232 50.000 0.00 0.00 0.00 3.35 R
6036 6237 3.283751 CGCCTGTTAATTCCCATTGGTA 58.716 45.455 1.20 0.00 0.00 3.25 R
7079 7280 2.864946 CAGAAAGCCTGTCATCAGATCG 59.135 50.000 0.00 0.00 43.76 3.69 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
66 67 2.681778 AGCAGGGACGAGGACCAG 60.682 66.667 0.00 0.00 0.00 4.00
78 79 1.889829 GAGGACCAGAGGGACATATCG 59.110 57.143 0.00 0.00 38.05 2.92
88 89 5.123186 CAGAGGGACATATCGAGACTATCAC 59.877 48.000 0.00 0.00 0.00 3.06
89 90 4.986783 AGGGACATATCGAGACTATCACA 58.013 43.478 0.00 0.00 0.00 3.58
95 96 5.241949 ACATATCGAGACTATCACAGGAACC 59.758 44.000 0.00 0.00 0.00 3.62
101 102 1.139058 ACTATCACAGGAACCATCGCC 59.861 52.381 0.00 0.00 0.00 5.54
122 123 2.376808 ATGAGAACAAGAGCAGTCGG 57.623 50.000 0.00 0.00 0.00 4.79
145 146 4.783242 CGACAACGATCAAACTTGGAAAT 58.217 39.130 0.00 0.00 42.66 2.17
151 152 5.491982 ACGATCAAACTTGGAAATCTAGCT 58.508 37.500 0.00 0.00 0.00 3.32
154 155 6.259608 CGATCAAACTTGGAAATCTAGCTGAT 59.740 38.462 0.00 0.00 36.89 2.90
161 162 2.421952 GGAAATCTAGCTGATGCACCCA 60.422 50.000 0.00 0.00 42.74 4.51
169 170 1.666888 GCTGATGCACCCAAGTTTTCG 60.667 52.381 0.00 0.00 39.41 3.46
173 174 3.632604 TGATGCACCCAAGTTTTCGTTAA 59.367 39.130 0.00 0.00 0.00 2.01
213 254 3.292460 CCCACTTGTTGTCCTTAACCAA 58.708 45.455 0.00 0.00 0.00 3.67
226 267 4.119862 CCTTAACCAATCGTCGTCATCAT 58.880 43.478 0.00 0.00 0.00 2.45
227 268 4.209288 CCTTAACCAATCGTCGTCATCATC 59.791 45.833 0.00 0.00 0.00 2.92
228 269 2.959507 ACCAATCGTCGTCATCATCA 57.040 45.000 0.00 0.00 0.00 3.07
230 271 2.427095 ACCAATCGTCGTCATCATCAGA 59.573 45.455 0.00 0.00 0.00 3.27
231 272 3.048501 CCAATCGTCGTCATCATCAGAG 58.951 50.000 0.00 0.00 0.00 3.35
232 273 3.243201 CCAATCGTCGTCATCATCAGAGA 60.243 47.826 0.00 0.00 0.00 3.10
250 291 6.595682 TCAGAGAGTTTTGATGGACTTTTCT 58.404 36.000 0.00 0.00 0.00 2.52
273 314 9.528018 TTCTCCATCTTGATGTTTTTACAAAAC 57.472 29.630 9.41 5.33 0.00 2.43
274 315 8.141268 TCTCCATCTTGATGTTTTTACAAAACC 58.859 33.333 9.12 0.00 0.00 3.27
275 316 8.017418 TCCATCTTGATGTTTTTACAAAACCT 57.983 30.769 9.12 0.49 0.00 3.50
277 318 9.191995 CCATCTTGATGTTTTTACAAAACCTAC 57.808 33.333 9.12 2.86 0.00 3.18
280 321 9.403583 TCTTGATGTTTTTACAAAACCTACTCT 57.596 29.630 9.12 0.00 0.00 3.24
281 322 9.665264 CTTGATGTTTTTACAAAACCTACTCTC 57.335 33.333 9.12 0.04 0.00 3.20
282 323 8.161699 TGATGTTTTTACAAAACCTACTCTCC 57.838 34.615 9.12 0.00 0.00 3.71
283 324 7.996644 TGATGTTTTTACAAAACCTACTCTCCT 59.003 33.333 9.12 0.00 0.00 3.69
284 325 8.762481 ATGTTTTTACAAAACCTACTCTCCTT 57.238 30.769 9.12 0.00 0.00 3.36
285 326 8.584063 TGTTTTTACAAAACCTACTCTCCTTT 57.416 30.769 9.12 0.00 0.00 3.11
286 327 9.027202 TGTTTTTACAAAACCTACTCTCCTTTT 57.973 29.630 9.12 0.00 0.00 2.27
287 328 9.865321 GTTTTTACAAAACCTACTCTCCTTTTT 57.135 29.630 1.31 0.00 0.00 1.94
358 439 0.693049 GGAATCACTGACAGGGTGGT 59.307 55.000 4.24 0.00 35.61 4.16
359 440 1.611673 GGAATCACTGACAGGGTGGTG 60.612 57.143 4.24 0.00 35.61 4.17
360 441 0.401738 AATCACTGACAGGGTGGTGG 59.598 55.000 4.24 0.00 35.61 4.61
1323 1408 4.808238 GGCGAGGACGACGACGAC 62.808 72.222 15.32 7.84 42.66 4.34
1325 1410 3.473166 CGAGGACGACGACGACGA 61.473 66.667 25.15 0.00 41.06 4.20
1326 1411 2.796425 CGAGGACGACGACGACGAT 61.796 63.158 25.15 10.97 41.06 3.73
1661 1755 4.921515 TCGAACCACATTTTCTCGTCTAAG 59.078 41.667 0.00 0.00 0.00 2.18
1744 1838 0.320247 GAGGCCATGAGCAGGTATCG 60.320 60.000 5.01 0.00 46.50 2.92
1818 1912 3.058155 CGAATCCCGATACTACAGAGTGG 60.058 52.174 0.00 0.00 41.76 4.00
1866 1960 0.692476 TCCTCCACATGTTCCACCAG 59.308 55.000 0.00 0.00 0.00 4.00
1908 2002 5.730550 AGTAGCTCACCGATGATAACAAAA 58.269 37.500 0.00 0.00 33.22 2.44
1909 2003 6.170506 AGTAGCTCACCGATGATAACAAAAA 58.829 36.000 0.00 0.00 33.22 1.94
1978 2072 5.469373 TGTAAATGCTGCAGTATCTTTCG 57.531 39.130 18.12 0.00 0.00 3.46
2001 2095 8.731275 TCGGTTGAACATTGATAGTTATTCAT 57.269 30.769 0.00 0.00 0.00 2.57
2081 2175 3.634910 GACTTTCAGGCCACCAAAGTAAA 59.365 43.478 20.66 3.66 39.84 2.01
2082 2176 3.636764 ACTTTCAGGCCACCAAAGTAAAG 59.363 43.478 19.73 12.23 38.34 1.85
2083 2177 1.616159 TCAGGCCACCAAAGTAAAGC 58.384 50.000 5.01 0.00 0.00 3.51
2086 2181 2.029918 CAGGCCACCAAAGTAAAGCTTC 60.030 50.000 5.01 0.00 36.17 3.86
2091 2186 4.745125 GCCACCAAAGTAAAGCTTCTTTTC 59.255 41.667 9.75 0.00 36.17 2.29
2110 2207 6.428465 TCTTTTCCAGCGATACATGTTAAACA 59.572 34.615 2.30 0.00 0.00 2.83
2563 2662 3.057586 TCCCTCCCTTCTGGTTTGTTAA 58.942 45.455 0.00 0.00 34.77 2.01
2846 2945 8.755696 TGCCATTAGAAAATACAACATTTGAC 57.244 30.769 0.00 0.00 0.00 3.18
2863 2962 9.974980 AACATTTGACGTTTCTAATGGTTATTT 57.025 25.926 13.21 0.23 40.64 1.40
3032 3132 4.090819 GGAGGGAGTAGATGATACTTCCC 58.909 52.174 8.47 10.24 42.91 3.97
3059 3159 6.545666 TGTCCCATATTAATTGACGCTCAAAT 59.454 34.615 0.00 0.48 40.12 2.32
3091 3191 7.987268 TCTAGCACTGAAATACGTTTAGATG 57.013 36.000 0.00 0.00 0.00 2.90
3265 3365 0.737019 GCGATGGTTTGGGCATGTTG 60.737 55.000 0.00 0.00 0.00 3.33
3377 3477 2.024273 TGGGAGGAGTCCGTAAAGAGAT 60.024 50.000 2.76 0.00 45.05 2.75
3382 3482 4.208746 AGGAGTCCGTAAAGAGATACCTG 58.791 47.826 2.76 0.00 0.00 4.00
3499 3599 3.649023 TGTGGGTTTCAACTCTAGCCTAA 59.351 43.478 0.00 0.00 0.00 2.69
3539 3639 4.636249 TGAAAGGCTTTGTTGTTGTTGTT 58.364 34.783 18.79 0.00 0.00 2.83
3540 3640 4.450419 TGAAAGGCTTTGTTGTTGTTGTTG 59.550 37.500 18.79 0.00 0.00 3.33
3541 3641 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3581 3682 8.079809 GTCAGTTTTCGGATGGAATAAAAGAAA 58.920 33.333 0.00 0.00 33.85 2.52
3734 3835 6.128445 CCAGCTTAAAATATCGATACCTGCTG 60.128 42.308 23.03 23.03 41.52 4.41
3743 3844 2.764010 TCGATACCTGCTGTACCACAAT 59.236 45.455 0.00 0.00 30.62 2.71
4149 4257 3.134804 ACCGTAGAGGCAATTGCTATCTT 59.865 43.478 30.28 19.77 46.52 2.40
4251 4359 4.783242 CACACAGGTAAAAATCCGAACAG 58.217 43.478 0.00 0.00 0.00 3.16
4266 4374 3.063997 CCGAACAGTATCAACCATGAAGC 59.936 47.826 0.00 0.00 39.49 3.86
4267 4375 3.935203 CGAACAGTATCAACCATGAAGCT 59.065 43.478 0.00 0.00 39.49 3.74
4271 4379 4.256110 CAGTATCAACCATGAAGCTGTCA 58.744 43.478 0.00 0.00 39.49 3.58
4299 4407 2.630098 CAGTGTTGAGGACCTCTCTTCA 59.370 50.000 22.14 12.35 42.86 3.02
4304 4412 2.095461 TGAGGACCTCTCTTCACATCG 58.905 52.381 22.14 0.00 42.86 3.84
4308 4416 2.159310 GGACCTCTCTTCACATCGTCAG 60.159 54.545 0.00 0.00 0.00 3.51
4309 4417 1.203523 ACCTCTCTTCACATCGTCAGC 59.796 52.381 0.00 0.00 0.00 4.26
4310 4418 1.476085 CCTCTCTTCACATCGTCAGCT 59.524 52.381 0.00 0.00 0.00 4.24
4311 4419 2.094286 CCTCTCTTCACATCGTCAGCTT 60.094 50.000 0.00 0.00 0.00 3.74
4312 4420 3.178267 CTCTCTTCACATCGTCAGCTTC 58.822 50.000 0.00 0.00 0.00 3.86
4313 4421 2.558359 TCTCTTCACATCGTCAGCTTCA 59.442 45.455 0.00 0.00 0.00 3.02
4314 4422 3.194329 TCTCTTCACATCGTCAGCTTCAT 59.806 43.478 0.00 0.00 0.00 2.57
4315 4423 3.515630 TCTTCACATCGTCAGCTTCATC 58.484 45.455 0.00 0.00 0.00 2.92
4316 4424 2.299993 TCACATCGTCAGCTTCATCC 57.700 50.000 0.00 0.00 0.00 3.51
4317 4425 1.134699 TCACATCGTCAGCTTCATCCC 60.135 52.381 0.00 0.00 0.00 3.85
4318 4426 0.179000 ACATCGTCAGCTTCATCCCC 59.821 55.000 0.00 0.00 0.00 4.81
4319 4427 0.178767 CATCGTCAGCTTCATCCCCA 59.821 55.000 0.00 0.00 0.00 4.96
4320 4428 0.467384 ATCGTCAGCTTCATCCCCAG 59.533 55.000 0.00 0.00 0.00 4.45
4321 4429 0.614697 TCGTCAGCTTCATCCCCAGA 60.615 55.000 0.00 0.00 0.00 3.86
4322 4430 0.179089 CGTCAGCTTCATCCCCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
4323 4431 0.179936 GTCAGCTTCATCCCCAGAGG 59.820 60.000 0.00 0.00 0.00 3.69
4324 4432 1.153005 CAGCTTCATCCCCAGAGGC 60.153 63.158 0.00 0.00 38.26 4.70
4325 4433 1.617536 AGCTTCATCCCCAGAGGCA 60.618 57.895 0.00 0.00 40.19 4.75
4326 4434 0.992431 AGCTTCATCCCCAGAGGCAT 60.992 55.000 0.00 0.00 40.19 4.40
4327 4435 0.822532 GCTTCATCCCCAGAGGCATG 60.823 60.000 0.00 0.00 37.93 4.06
4328 4436 0.822532 CTTCATCCCCAGAGGCATGC 60.823 60.000 9.90 9.90 34.51 4.06
4329 4437 2.203451 CATCCCCAGAGGCATGCC 60.203 66.667 30.12 30.12 34.51 4.40
4340 4448 1.210538 AGGCATGCCTCAGATCTTCA 58.789 50.000 34.07 0.00 44.43 3.02
4341 4449 1.562942 AGGCATGCCTCAGATCTTCAA 59.437 47.619 34.07 0.00 44.43 2.69
4342 4450 1.674962 GGCATGCCTCAGATCTTCAAC 59.325 52.381 29.98 0.00 0.00 3.18
4343 4451 1.674962 GCATGCCTCAGATCTTCAACC 59.325 52.381 6.36 0.00 0.00 3.77
4344 4452 2.942752 GCATGCCTCAGATCTTCAACCA 60.943 50.000 6.36 0.00 0.00 3.67
4345 4453 3.552875 CATGCCTCAGATCTTCAACCAT 58.447 45.455 0.00 0.00 0.00 3.55
4346 4454 3.272574 TGCCTCAGATCTTCAACCATC 57.727 47.619 0.00 0.00 0.00 3.51
4347 4455 2.573009 TGCCTCAGATCTTCAACCATCA 59.427 45.455 0.00 0.00 0.00 3.07
4348 4456 3.204526 GCCTCAGATCTTCAACCATCAG 58.795 50.000 0.00 0.00 0.00 2.90
4349 4457 3.370315 GCCTCAGATCTTCAACCATCAGT 60.370 47.826 0.00 0.00 0.00 3.41
4694 4802 4.397481 AAAACATACTACCGGTAGAGCC 57.603 45.455 41.26 0.00 36.97 4.70
4705 4813 2.563471 GGTAGAGCCGTGTCTTGTAG 57.437 55.000 0.00 0.00 0.00 2.74
4710 4818 0.320771 AGCCGTGTCTTGTAGCCTTG 60.321 55.000 0.00 0.00 0.00 3.61
4720 4828 4.094146 GTCTTGTAGCCTTGCATCTTCTTC 59.906 45.833 0.00 0.00 0.00 2.87
4754 4953 3.776969 TCTCCACCTCATTAACTCAGCAT 59.223 43.478 0.00 0.00 0.00 3.79
4810 5009 1.676967 CTCAACTTCCAGCAGGCCC 60.677 63.158 0.00 0.00 33.74 5.80
4829 5028 3.181367 GCACAGGGCAGTCAATCG 58.819 61.111 0.00 0.00 43.97 3.34
4833 5032 2.434884 AGGGCAGTCAATCGCACG 60.435 61.111 0.00 0.00 36.38 5.34
4876 5075 2.236395 GGTATATATGAAGGTGCCCGCT 59.764 50.000 0.00 0.00 0.00 5.52
4921 5120 2.497138 TGATGTGTTGCTTCCAGAGTG 58.503 47.619 0.00 0.00 0.00 3.51
4922 5121 2.104622 TGATGTGTTGCTTCCAGAGTGA 59.895 45.455 0.00 0.00 0.00 3.41
4923 5122 2.245159 TGTGTTGCTTCCAGAGTGAG 57.755 50.000 0.00 0.00 0.00 3.51
4924 5123 1.202687 TGTGTTGCTTCCAGAGTGAGG 60.203 52.381 0.00 0.00 0.00 3.86
4925 5124 0.250467 TGTTGCTTCCAGAGTGAGGC 60.250 55.000 0.00 0.00 37.81 4.70
4926 5125 0.250467 GTTGCTTCCAGAGTGAGGCA 60.250 55.000 0.00 0.00 44.44 4.75
5121 5320 9.223099 CAAAGGAATTCTTGCTTTCCATAAATT 57.777 29.630 5.23 0.00 46.45 1.82
5145 5344 7.696992 TTTTAAAAGATTTATCGGGCTCAGT 57.303 32.000 0.00 0.00 0.00 3.41
5146 5345 6.920569 TTAAAAGATTTATCGGGCTCAGTC 57.079 37.500 0.00 0.00 0.00 3.51
5147 5346 2.802787 AGATTTATCGGGCTCAGTCG 57.197 50.000 0.00 0.00 0.00 4.18
5148 5347 1.140816 GATTTATCGGGCTCAGTCGC 58.859 55.000 0.00 0.00 0.00 5.19
5149 5348 0.753262 ATTTATCGGGCTCAGTCGCT 59.247 50.000 0.00 0.00 0.00 4.93
5150 5349 0.102481 TTTATCGGGCTCAGTCGCTC 59.898 55.000 0.00 0.00 0.00 5.03
5151 5350 1.035385 TTATCGGGCTCAGTCGCTCA 61.035 55.000 0.00 0.00 0.00 4.26
5152 5351 1.448119 TATCGGGCTCAGTCGCTCAG 61.448 60.000 0.00 0.00 0.00 3.35
5205 5404 9.103048 CAGTCGAAATTAACACAGTTTTATGTC 57.897 33.333 0.00 0.00 0.00 3.06
5431 5630 9.631257 AATGACATGTATGGAGATCACATTTTA 57.369 29.630 0.00 0.00 30.59 1.52
5462 5661 8.801715 AAATAATATCTTGGCATTTACTTGCG 57.198 30.769 0.00 0.00 43.71 4.85
5470 5669 3.181501 TGGCATTTACTTGCGCATACTTC 60.182 43.478 12.75 0.00 43.71 3.01
5474 5673 4.514545 TTTACTTGCGCATACTTCGATG 57.485 40.909 12.75 0.00 0.00 3.84
5488 5687 7.968405 GCATACTTCGATGTTCCTACAATTTTT 59.032 33.333 9.44 0.00 37.91 1.94
5587 5786 2.440409 AGGCTTTGGTATGCTTCACAG 58.560 47.619 0.00 0.00 0.00 3.66
6036 6237 8.851541 AACATCCAAATTTTGTTTATGCTGAT 57.148 26.923 8.26 0.00 29.60 2.90
6057 6258 2.099405 ACCAATGGGAATTAACAGGCG 58.901 47.619 3.55 0.00 38.05 5.52
6062 6263 1.173913 GGGAATTAACAGGCGTGCTT 58.826 50.000 6.26 3.15 0.00 3.91
6066 6267 1.904287 ATTAACAGGCGTGCTTTCCA 58.096 45.000 6.26 0.00 0.00 3.53
6189 6390 5.957798 TGAATTTGTCAGAAGAATCCATGC 58.042 37.500 0.00 0.00 0.00 4.06
6368 6569 5.284861 AGGTGGTGCACGAATATTACATA 57.715 39.130 11.45 0.00 34.83 2.29
6393 6594 8.467402 AAAGTGTCTTGATAGTCTGAAATACG 57.533 34.615 0.00 0.00 0.00 3.06
6394 6595 7.392494 AGTGTCTTGATAGTCTGAAATACGA 57.608 36.000 0.00 0.00 0.00 3.43
6395 6596 7.476667 AGTGTCTTGATAGTCTGAAATACGAG 58.523 38.462 0.00 0.00 0.00 4.18
6396 6597 7.121463 AGTGTCTTGATAGTCTGAAATACGAGT 59.879 37.037 0.00 0.00 0.00 4.18
6397 6598 8.396390 GTGTCTTGATAGTCTGAAATACGAGTA 58.604 37.037 0.00 0.00 0.00 2.59
6398 6599 9.121658 TGTCTTGATAGTCTGAAATACGAGTAT 57.878 33.333 0.00 0.00 0.00 2.12
6399 6600 9.601971 GTCTTGATAGTCTGAAATACGAGTATC 57.398 37.037 0.00 0.00 40.50 2.24
6459 6660 3.922240 CCATTTGGATTTGAGCTGAAACG 59.078 43.478 0.00 0.00 37.39 3.60
6971 7172 3.255888 GGACATGTAGATACGCATCCTGA 59.744 47.826 0.00 0.00 0.00 3.86
7079 7280 2.750948 TCAACGCTGAAACTCAGTACC 58.249 47.619 5.61 0.00 45.94 3.34
7460 7664 5.106712 CGATTCCCTCATTTTTCGAGTTGAA 60.107 40.000 0.00 0.00 33.85 2.69
7534 7743 1.269012 TCCGGTACTTTCAACCCGAT 58.731 50.000 0.00 0.00 43.01 4.18
7578 7787 5.181056 CACATTTCACATGTTAGGTGCACTA 59.819 40.000 17.98 4.35 36.22 2.74
7637 7846 8.041323 GTCTAATGTTGAGAGGTTGAGGAAATA 58.959 37.037 0.00 0.00 0.00 1.40
7646 7855 9.046846 TGAGAGGTTGAGGAAATAAGAAATCTA 57.953 33.333 0.00 0.00 0.00 1.98
7709 7918 8.689972 AGGGAAATGCACATTCTAAAAGAATAG 58.310 33.333 12.37 0.67 42.67 1.73
7746 7957 7.581011 AGTTTTTGCGGATTGACATATTTTC 57.419 32.000 0.00 0.00 0.00 2.29
7772 7983 2.777459 AATGATACTCCCTCCGTCCT 57.223 50.000 0.00 0.00 0.00 3.85
7774 7985 4.405756 AATGATACTCCCTCCGTCCTAT 57.594 45.455 0.00 0.00 0.00 2.57
7775 7986 5.531753 AATGATACTCCCTCCGTCCTATA 57.468 43.478 0.00 0.00 0.00 1.31
7776 7987 5.735733 ATGATACTCCCTCCGTCCTATAT 57.264 43.478 0.00 0.00 0.00 0.86
7777 7988 5.531753 TGATACTCCCTCCGTCCTATATT 57.468 43.478 0.00 0.00 0.00 1.28
7778 7989 5.507637 TGATACTCCCTCCGTCCTATATTC 58.492 45.833 0.00 0.00 0.00 1.75
7779 7990 3.172471 ACTCCCTCCGTCCTATATTCC 57.828 52.381 0.00 0.00 0.00 3.01
7780 7991 2.449730 ACTCCCTCCGTCCTATATTCCA 59.550 50.000 0.00 0.00 0.00 3.53
7781 7992 3.077695 ACTCCCTCCGTCCTATATTCCAT 59.922 47.826 0.00 0.00 0.00 3.41
7782 7993 4.294168 ACTCCCTCCGTCCTATATTCCATA 59.706 45.833 0.00 0.00 0.00 2.74
7783 7994 5.222484 ACTCCCTCCGTCCTATATTCCATAA 60.222 44.000 0.00 0.00 0.00 1.90
7784 7995 5.850278 TCCCTCCGTCCTATATTCCATAAT 58.150 41.667 0.00 0.00 0.00 1.28
7785 7996 6.988725 TCCCTCCGTCCTATATTCCATAATA 58.011 40.000 0.00 0.00 32.20 0.98
7786 7997 7.601942 TCCCTCCGTCCTATATTCCATAATAT 58.398 38.462 0.00 0.00 40.59 1.28
7787 7998 8.739552 TCCCTCCGTCCTATATTCCATAATATA 58.260 37.037 0.00 0.00 38.81 0.86
7838 8076 3.039252 ACCCTATCTACAGAGCTGCTT 57.961 47.619 2.53 0.00 0.00 3.91
7880 8413 0.115152 CTTTCCAAAGAGGGGCCCTT 59.885 55.000 29.49 16.34 38.28 3.95
7881 8414 1.357761 CTTTCCAAAGAGGGGCCCTTA 59.642 52.381 29.49 5.54 38.28 2.69
7883 8416 1.222567 TCCAAAGAGGGGCCCTTATC 58.777 55.000 29.49 15.02 38.24 1.75
7924 8457 5.695851 AGGCACTTTTTGTCTCAACATAG 57.304 39.130 0.00 0.00 33.64 2.23
7925 8458 4.022849 AGGCACTTTTTGTCTCAACATAGC 60.023 41.667 0.00 0.00 33.64 2.97
7926 8459 4.229876 GCACTTTTTGTCTCAACATAGCC 58.770 43.478 0.00 0.00 34.73 3.93
7927 8460 4.466828 CACTTTTTGTCTCAACATAGCCG 58.533 43.478 0.00 0.00 34.73 5.52
7928 8461 3.502211 ACTTTTTGTCTCAACATAGCCGG 59.498 43.478 0.00 0.00 34.73 6.13
7929 8462 2.851263 TTTGTCTCAACATAGCCGGT 57.149 45.000 1.90 0.00 34.73 5.28
7930 8463 2.380084 TTGTCTCAACATAGCCGGTC 57.620 50.000 1.90 0.00 34.73 4.79
7931 8464 0.535335 TGTCTCAACATAGCCGGTCC 59.465 55.000 1.90 0.00 0.00 4.46
7932 8465 0.179081 GTCTCAACATAGCCGGTCCC 60.179 60.000 1.90 0.00 0.00 4.46
7933 8466 0.616395 TCTCAACATAGCCGGTCCCA 60.616 55.000 1.90 0.00 0.00 4.37
7934 8467 0.251916 CTCAACATAGCCGGTCCCAA 59.748 55.000 1.90 0.00 0.00 4.12
7935 8468 0.251916 TCAACATAGCCGGTCCCAAG 59.748 55.000 1.90 0.00 0.00 3.61
7936 8469 1.077716 AACATAGCCGGTCCCAAGC 60.078 57.895 1.90 0.00 0.00 4.01
7937 8470 2.203209 CATAGCCGGTCCCAAGCC 60.203 66.667 1.90 0.00 0.00 4.35
7938 8471 3.489513 ATAGCCGGTCCCAAGCCC 61.490 66.667 1.90 0.00 0.00 5.19
7943 8476 3.158648 CGGTCCCAAGCCCGGATA 61.159 66.667 0.73 0.00 40.54 2.59
7944 8477 2.737881 CGGTCCCAAGCCCGGATAA 61.738 63.158 0.73 0.00 40.54 1.75
7945 8478 1.610873 GGTCCCAAGCCCGGATAAA 59.389 57.895 0.73 0.00 0.00 1.40
7946 8479 0.465642 GGTCCCAAGCCCGGATAAAG 60.466 60.000 0.73 0.00 0.00 1.85
7947 8480 0.465642 GTCCCAAGCCCGGATAAAGG 60.466 60.000 0.73 0.00 0.00 3.11
7948 8481 0.622154 TCCCAAGCCCGGATAAAGGA 60.622 55.000 0.73 0.00 0.00 3.36
7949 8482 0.179018 CCCAAGCCCGGATAAAGGAG 60.179 60.000 0.73 0.00 0.00 3.69
7950 8483 0.179018 CCAAGCCCGGATAAAGGAGG 60.179 60.000 0.73 0.00 0.00 4.30
7951 8484 0.837272 CAAGCCCGGATAAAGGAGGA 59.163 55.000 0.73 0.00 0.00 3.71
7952 8485 1.132500 AAGCCCGGATAAAGGAGGAG 58.868 55.000 0.73 0.00 0.00 3.69
7953 8486 0.764752 AGCCCGGATAAAGGAGGAGG 60.765 60.000 0.73 0.00 0.00 4.30
7954 8487 0.763223 GCCCGGATAAAGGAGGAGGA 60.763 60.000 0.73 0.00 0.00 3.71
7955 8488 2.031495 CCCGGATAAAGGAGGAGGAT 57.969 55.000 0.73 0.00 0.00 3.24
7956 8489 2.339769 CCCGGATAAAGGAGGAGGATT 58.660 52.381 0.73 0.00 0.00 3.01
7957 8490 2.039084 CCCGGATAAAGGAGGAGGATTG 59.961 54.545 0.73 0.00 0.00 2.67
7958 8491 2.706190 CCGGATAAAGGAGGAGGATTGT 59.294 50.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.202463 CCCTGCTCGTAGTCTCCAATG 60.202 57.143 0.00 0.00 0.00 2.82
37 38 0.039180 TCCCTGCTCGTAGTCTCCAA 59.961 55.000 0.00 0.00 0.00 3.53
66 67 5.004448 TGTGATAGTCTCGATATGTCCCTC 58.996 45.833 0.00 0.00 0.00 4.30
78 79 3.797184 GCGATGGTTCCTGTGATAGTCTC 60.797 52.174 0.00 0.00 0.00 3.36
88 89 1.019673 CTCATTGGCGATGGTTCCTG 58.980 55.000 14.66 0.00 36.37 3.86
89 90 0.911769 TCTCATTGGCGATGGTTCCT 59.088 50.000 14.66 0.00 36.37 3.36
95 96 2.223203 GCTCTTGTTCTCATTGGCGATG 60.223 50.000 8.51 8.51 37.08 3.84
101 102 2.414481 CCGACTGCTCTTGTTCTCATTG 59.586 50.000 0.00 0.00 0.00 2.82
122 123 1.529438 TCCAAGTTTGATCGTTGTCGC 59.471 47.619 0.00 0.00 36.96 5.19
127 128 5.940470 AGCTAGATTTCCAAGTTTGATCGTT 59.060 36.000 0.00 0.00 0.00 3.85
128 129 5.352569 CAGCTAGATTTCCAAGTTTGATCGT 59.647 40.000 0.00 0.00 0.00 3.73
145 146 1.279496 ACTTGGGTGCATCAGCTAGA 58.721 50.000 0.00 0.00 42.74 2.43
151 152 1.686355 ACGAAAACTTGGGTGCATCA 58.314 45.000 0.00 0.00 0.00 3.07
154 155 2.359531 CCTTAACGAAAACTTGGGTGCA 59.640 45.455 0.00 0.00 0.00 4.57
161 162 7.442364 GTCCTTAAGGTACCTTAACGAAAACTT 59.558 37.037 33.80 10.70 41.78 2.66
169 170 6.644347 GGTAAGGTCCTTAAGGTACCTTAAC 58.356 44.000 36.34 35.72 46.72 2.01
173 174 3.079534 TGGGTAAGGTCCTTAAGGTACCT 59.920 47.826 27.12 27.12 43.10 3.08
192 193 2.938838 TGGTTAAGGACAACAAGTGGG 58.061 47.619 0.00 0.00 0.00 4.61
213 254 3.210227 ACTCTCTGATGATGACGACGAT 58.790 45.455 0.00 0.00 0.00 3.73
226 267 6.595682 AGAAAAGTCCATCAAAACTCTCTGA 58.404 36.000 0.00 0.00 0.00 3.27
227 268 6.072783 GGAGAAAAGTCCATCAAAACTCTCTG 60.073 42.308 0.00 0.00 36.51 3.35
228 269 6.000840 GGAGAAAAGTCCATCAAAACTCTCT 58.999 40.000 0.00 0.00 36.51 3.10
230 271 5.694995 TGGAGAAAAGTCCATCAAAACTCT 58.305 37.500 0.00 0.00 41.99 3.24
250 291 8.017418 AGGTTTTGTAAAAACATCAAGATGGA 57.983 30.769 14.04 0.00 42.91 3.41
303 384 4.022329 CCCATTACTGTTTTGGAAGTCACC 60.022 45.833 9.53 0.00 31.94 4.02
388 470 2.114616 GGGAGCCAGATTCTTCTCTCA 58.885 52.381 10.72 0.00 28.79 3.27
395 477 2.427245 CGGACGGGAGCCAGATTCT 61.427 63.158 0.00 0.00 0.00 2.40
1318 1403 3.003793 TCCTCATCATCTTCATCGTCGTC 59.996 47.826 0.00 0.00 0.00 4.20
1319 1404 2.952310 TCCTCATCATCTTCATCGTCGT 59.048 45.455 0.00 0.00 0.00 4.34
1320 1405 3.632855 TCCTCATCATCTTCATCGTCG 57.367 47.619 0.00 0.00 0.00 5.12
1321 1406 5.131594 TCATCCTCATCATCTTCATCGTC 57.868 43.478 0.00 0.00 0.00 4.20
1322 1407 5.245526 TCATCATCCTCATCATCTTCATCGT 59.754 40.000 0.00 0.00 0.00 3.73
1323 1408 5.721232 TCATCATCCTCATCATCTTCATCG 58.279 41.667 0.00 0.00 0.00 3.84
1324 1409 7.279090 GTCATCATCATCCTCATCATCTTCATC 59.721 40.741 0.00 0.00 0.00 2.92
1325 1410 7.106890 GTCATCATCATCCTCATCATCTTCAT 58.893 38.462 0.00 0.00 0.00 2.57
1326 1411 6.465084 GTCATCATCATCCTCATCATCTTCA 58.535 40.000 0.00 0.00 0.00 3.02
1744 1838 7.062605 CAGTTGTGCAATGTAAAGGAAATCATC 59.937 37.037 0.00 0.00 0.00 2.92
1832 1926 1.194772 GGAGGAACTTCAACGCTTTCG 59.805 52.381 0.00 0.00 41.55 3.46
1866 1960 6.195165 GCTACTTGCTAGTTATTGCATTCAC 58.805 40.000 6.03 0.00 39.07 3.18
1908 2002 5.640732 CACAAAAGCGCAGTATCCTTAATT 58.359 37.500 11.47 0.00 0.00 1.40
1909 2003 4.438744 GCACAAAAGCGCAGTATCCTTAAT 60.439 41.667 11.47 0.00 0.00 1.40
1922 2016 1.267806 AGTGGATTCTGCACAAAAGCG 59.732 47.619 1.65 0.00 41.46 4.68
1978 2072 9.722056 GTCATGAATAACTATCAATGTTCAACC 57.278 33.333 0.00 0.00 0.00 3.77
2081 2175 3.334583 TGTATCGCTGGAAAAGAAGCT 57.665 42.857 0.00 0.00 37.27 3.74
2082 2176 3.375299 ACATGTATCGCTGGAAAAGAAGC 59.625 43.478 0.00 0.00 36.03 3.86
2083 2177 5.551760 AACATGTATCGCTGGAAAAGAAG 57.448 39.130 0.00 0.00 0.00 2.85
2086 2181 6.607689 TGTTTAACATGTATCGCTGGAAAAG 58.392 36.000 0.00 0.00 0.00 2.27
2091 2186 5.545658 ACTTGTTTAACATGTATCGCTGG 57.454 39.130 13.73 0.00 35.13 4.85
2490 2589 9.971922 ACAGTTTCTATGAAATGAAAAAGAAGG 57.028 29.630 0.00 0.00 34.52 3.46
2590 2689 8.189119 TCCTAAAGCAATGAACCTTACAAAAT 57.811 30.769 0.00 0.00 0.00 1.82
2601 2700 6.775629 AGTTTACCTGTTCCTAAAGCAATGAA 59.224 34.615 0.00 0.00 0.00 2.57
2864 2963 8.942338 ACACAACACGAGTTATATATCACAAT 57.058 30.769 0.00 0.00 35.85 2.71
2886 2986 7.121168 TCCCTAGATTGACAATTTGATCAACAC 59.879 37.037 7.89 7.61 37.64 3.32
2887 2987 7.174413 TCCCTAGATTGACAATTTGATCAACA 58.826 34.615 7.89 0.00 37.64 3.33
3032 3132 7.406398 TTGAGCGTCAATTAATATGGGACAGG 61.406 42.308 0.00 0.00 34.12 4.00
3059 3159 6.040504 ACGTATTTCAGTGCTAGATACATCCA 59.959 38.462 0.00 0.00 0.00 3.41
3377 3477 4.654262 GGTGATATTCCAGTCCTTCAGGTA 59.346 45.833 0.00 0.00 36.34 3.08
3382 3482 5.745227 TCTTTGGTGATATTCCAGTCCTTC 58.255 41.667 1.83 0.00 36.28 3.46
3539 3639 3.356639 GACGAGGCGGCATCTCACA 62.357 63.158 13.08 0.00 33.63 3.58
3540 3640 2.583593 GACGAGGCGGCATCTCAC 60.584 66.667 13.08 0.42 33.63 3.51
3541 3641 3.068064 TGACGAGGCGGCATCTCA 61.068 61.111 13.08 11.89 41.22 3.27
3605 3706 9.887629 AAATGCATGAACATAACATGGAAATAA 57.112 25.926 0.00 0.00 45.72 1.40
3623 3724 5.351233 ACAACAAATGAAGCAAATGCATG 57.649 34.783 0.00 0.00 45.16 4.06
3743 3844 1.069513 CTCACGGTTTGTACCACCAGA 59.930 52.381 11.01 7.41 45.31 3.86
3938 4039 7.630924 CGACAGAACAAGAAGTCAGTATTTTT 58.369 34.615 0.00 0.00 0.00 1.94
4044 4149 3.909776 ATGCACTGAACTTGACATGTG 57.090 42.857 1.15 0.00 0.00 3.21
4251 4359 4.002982 TGTGACAGCTTCATGGTTGATAC 58.997 43.478 0.00 0.00 36.32 2.24
4266 4374 3.310774 CCTCAACACTGAACTTGTGACAG 59.689 47.826 0.00 0.00 38.65 3.51
4267 4375 3.055458 TCCTCAACACTGAACTTGTGACA 60.055 43.478 0.00 0.00 38.65 3.58
4271 4379 2.505819 AGGTCCTCAACACTGAACTTGT 59.494 45.455 0.00 0.00 0.00 3.16
4299 4407 0.179000 GGGGATGAAGCTGACGATGT 59.821 55.000 0.00 0.00 0.00 3.06
4304 4412 0.179936 CCTCTGGGGATGAAGCTGAC 59.820 60.000 0.00 0.00 37.23 3.51
4308 4416 1.535685 ATGCCTCTGGGGATGAAGC 59.464 57.895 0.00 0.00 42.21 3.86
4313 4421 2.369291 AGGCATGCCTCTGGGGAT 60.369 61.111 34.07 9.48 44.43 3.85
4322 4430 1.674962 GTTGAAGATCTGAGGCATGCC 59.325 52.381 30.12 30.12 0.00 4.40
4323 4431 1.674962 GGTTGAAGATCTGAGGCATGC 59.325 52.381 9.90 9.90 0.00 4.06
4324 4432 2.995283 TGGTTGAAGATCTGAGGCATG 58.005 47.619 0.00 0.00 0.00 4.06
4325 4433 3.201487 TGATGGTTGAAGATCTGAGGCAT 59.799 43.478 0.00 0.00 0.00 4.40
4326 4434 2.573009 TGATGGTTGAAGATCTGAGGCA 59.427 45.455 0.00 0.00 0.00 4.75
4327 4435 3.204526 CTGATGGTTGAAGATCTGAGGC 58.795 50.000 0.00 0.00 0.00 4.70
4328 4436 4.484537 ACTGATGGTTGAAGATCTGAGG 57.515 45.455 0.00 0.00 0.00 3.86
4672 4780 4.763073 GGCTCTACCGGTAGTATGTTTTT 58.237 43.478 34.80 0.00 34.84 1.94
4673 4781 4.397481 GGCTCTACCGGTAGTATGTTTT 57.603 45.455 34.80 0.00 34.84 2.43
4686 4794 1.469423 GCTACAAGACACGGCTCTACC 60.469 57.143 0.00 0.00 0.00 3.18
4687 4795 1.469423 GGCTACAAGACACGGCTCTAC 60.469 57.143 0.00 0.00 0.00 2.59
4688 4796 0.815734 GGCTACAAGACACGGCTCTA 59.184 55.000 0.00 0.00 0.00 2.43
4689 4797 0.900647 AGGCTACAAGACACGGCTCT 60.901 55.000 0.00 0.00 0.00 4.09
4690 4798 0.037232 AAGGCTACAAGACACGGCTC 60.037 55.000 0.00 0.00 0.00 4.70
4691 4799 0.320771 CAAGGCTACAAGACACGGCT 60.321 55.000 0.00 0.00 0.00 5.52
4692 4800 1.912371 GCAAGGCTACAAGACACGGC 61.912 60.000 0.00 0.00 0.00 5.68
4693 4801 0.602638 TGCAAGGCTACAAGACACGG 60.603 55.000 0.00 0.00 0.00 4.94
4694 4802 1.394917 GATGCAAGGCTACAAGACACG 59.605 52.381 0.00 0.00 0.00 4.49
4695 4803 2.704572 AGATGCAAGGCTACAAGACAC 58.295 47.619 0.00 0.00 0.00 3.67
4696 4804 3.008375 AGAAGATGCAAGGCTACAAGACA 59.992 43.478 0.00 0.00 0.00 3.41
4697 4805 3.604582 AGAAGATGCAAGGCTACAAGAC 58.395 45.455 0.00 0.00 0.00 3.01
4698 4806 3.988976 AGAAGATGCAAGGCTACAAGA 57.011 42.857 0.00 0.00 0.00 3.02
4699 4807 4.260170 AGAAGAAGATGCAAGGCTACAAG 58.740 43.478 0.00 0.00 0.00 3.16
4700 4808 4.292186 AGAAGAAGATGCAAGGCTACAA 57.708 40.909 0.00 0.00 0.00 2.41
4701 4809 3.988976 AGAAGAAGATGCAAGGCTACA 57.011 42.857 0.00 0.00 0.00 2.74
4702 4810 5.178797 TGTTAGAAGAAGATGCAAGGCTAC 58.821 41.667 0.00 0.00 0.00 3.58
4703 4811 5.420725 TGTTAGAAGAAGATGCAAGGCTA 57.579 39.130 0.00 0.00 0.00 3.93
4704 4812 4.292186 TGTTAGAAGAAGATGCAAGGCT 57.708 40.909 0.00 0.00 0.00 4.58
4705 4813 4.637534 TGATGTTAGAAGAAGATGCAAGGC 59.362 41.667 0.00 0.00 0.00 4.35
4710 4818 8.127954 GGAGAAAATGATGTTAGAAGAAGATGC 58.872 37.037 0.00 0.00 0.00 3.91
4720 4828 7.636150 AATGAGGTGGAGAAAATGATGTTAG 57.364 36.000 0.00 0.00 0.00 2.34
4782 4981 4.141620 TGCTGGAAGTTGAGAGAAGAACTT 60.142 41.667 0.00 0.00 43.50 2.66
4785 4984 3.244353 CCTGCTGGAAGTTGAGAGAAGAA 60.244 47.826 2.92 0.00 35.30 2.52
4788 4987 1.271054 GCCTGCTGGAAGTTGAGAGAA 60.271 52.381 14.77 0.00 35.30 2.87
4810 5009 1.642037 CGATTGACTGCCCTGTGCTG 61.642 60.000 0.00 0.00 43.93 4.41
4843 5042 9.279233 ACCTTCATATATACCAGGCATATGTAA 57.721 33.333 4.29 3.30 35.23 2.41
4921 5120 1.552792 AGTTCTGTTAGCCTCTGCCTC 59.447 52.381 0.00 0.00 38.69 4.70
4922 5121 1.552792 GAGTTCTGTTAGCCTCTGCCT 59.447 52.381 0.00 0.00 38.69 4.75
4923 5122 1.737363 CGAGTTCTGTTAGCCTCTGCC 60.737 57.143 0.00 0.00 38.69 4.85
4924 5123 1.202582 TCGAGTTCTGTTAGCCTCTGC 59.797 52.381 0.00 0.00 37.95 4.26
4925 5124 3.577649 TTCGAGTTCTGTTAGCCTCTG 57.422 47.619 0.00 0.00 0.00 3.35
4926 5125 3.321111 TGTTTCGAGTTCTGTTAGCCTCT 59.679 43.478 0.00 0.00 0.00 3.69
5067 5266 4.451096 TCAGAATTTGGTTGTCGCTTACTC 59.549 41.667 0.00 0.00 0.00 2.59
5121 5320 7.413657 CGACTGAGCCCGATAAATCTTTTAAAA 60.414 37.037 0.00 0.00 0.00 1.52
5147 5346 0.035630 ACACCAATCCAGCTCTGAGC 60.036 55.000 21.72 21.72 42.84 4.26
5148 5347 2.234661 TGTACACCAATCCAGCTCTGAG 59.765 50.000 0.00 0.00 0.00 3.35
5149 5348 2.256306 TGTACACCAATCCAGCTCTGA 58.744 47.619 0.00 0.00 0.00 3.27
5150 5349 2.768253 TGTACACCAATCCAGCTCTG 57.232 50.000 0.00 0.00 0.00 3.35
5151 5350 6.942163 ATATATGTACACCAATCCAGCTCT 57.058 37.500 0.00 0.00 0.00 4.09
5152 5351 7.661437 TGAAATATATGTACACCAATCCAGCTC 59.339 37.037 0.00 0.00 0.00 4.09
5205 5404 8.341173 GCAGTCATTGAAATAGTTCCTATCTTG 58.659 37.037 0.00 0.00 32.28 3.02
5450 5649 3.029074 CGAAGTATGCGCAAGTAAATGC 58.971 45.455 17.11 0.00 42.94 3.56
5462 5661 6.604735 AATTGTAGGAACATCGAAGTATGC 57.395 37.500 0.00 0.00 34.97 3.14
5856 6056 6.087555 CACTTTAAAACGAACCATGTATGTGC 59.912 38.462 0.00 0.00 0.00 4.57
5896 6096 5.067674 AGCAAATGCACTTCTTCACAGTAAA 59.932 36.000 8.28 0.00 45.16 2.01
6036 6237 3.283751 CGCCTGTTAATTCCCATTGGTA 58.716 45.455 1.20 0.00 0.00 3.25
6057 6258 3.460103 CCATGCCATATTTGGAAAGCAC 58.540 45.455 6.35 0.00 46.92 4.40
6062 6263 3.306613 TCATGCCATGCCATATTTGGAA 58.693 40.909 6.35 0.00 46.92 3.53
6066 6267 6.268158 TGTCTATTTCATGCCATGCCATATTT 59.732 34.615 0.00 0.00 0.00 1.40
6083 6284 4.993705 TCAGGGGTCAAGTTGTCTATTT 57.006 40.909 2.11 0.00 0.00 1.40
6170 6371 5.988310 AATGCATGGATTCTTCTGACAAA 57.012 34.783 6.63 0.00 0.00 2.83
6368 6569 8.304596 TCGTATTTCAGACTATCAAGACACTTT 58.695 33.333 0.00 0.00 0.00 2.66
6392 6593 9.959775 GACTCTTAAGAAATTGTTTGATACTCG 57.040 33.333 6.63 0.00 0.00 4.18
6393 6594 9.959775 CGACTCTTAAGAAATTGTTTGATACTC 57.040 33.333 6.63 0.00 0.00 2.59
6394 6595 9.490379 ACGACTCTTAAGAAATTGTTTGATACT 57.510 29.630 6.63 0.00 0.00 2.12
6397 6598 9.665264 GAAACGACTCTTAAGAAATTGTTTGAT 57.335 29.630 25.65 12.28 31.84 2.57
6398 6599 8.889717 AGAAACGACTCTTAAGAAATTGTTTGA 58.110 29.630 25.65 0.00 31.84 2.69
6399 6600 9.159470 GAGAAACGACTCTTAAGAAATTGTTTG 57.841 33.333 25.65 13.01 31.84 2.93
6459 6660 5.768317 TGAAAGCAGTAACAAAATGTAGCC 58.232 37.500 0.00 0.00 0.00 3.93
6595 6796 7.406799 AGCTATTTTTGTTTATGTTGCACAC 57.593 32.000 0.00 0.00 0.00 3.82
6615 6816 6.233434 AGACTCAATTTCATGTGACAAGCTA 58.767 36.000 0.00 0.00 0.00 3.32
6971 7172 6.750148 AGTAGTCGAAGAAAACTGAAGTGAT 58.250 36.000 0.00 0.00 39.69 3.06
7079 7280 2.864946 CAGAAAGCCTGTCATCAGATCG 59.135 50.000 0.00 0.00 43.76 3.69
7460 7664 7.831193 ACCAAGAAGATTAATGAACAGTGCTAT 59.169 33.333 0.00 0.00 0.00 2.97
7530 7739 3.832490 TCTACCTGGAATACCATCATCGG 59.168 47.826 0.00 0.00 45.87 4.18
7534 7743 3.388024 GTGCTCTACCTGGAATACCATCA 59.612 47.826 0.00 0.00 45.87 3.07
7578 7787 1.687563 AACGCTTTTGGTTGCTACCT 58.312 45.000 18.31 0.00 45.27 3.08
7709 7918 3.305964 GCAAAAACTTTTAGTCCGAGGC 58.694 45.455 0.00 0.00 0.00 4.70
7746 7957 4.101119 ACGGAGGGAGTATCATTTTACCAG 59.899 45.833 0.00 0.00 36.25 4.00
7757 7968 4.294168 TGGAATATAGGACGGAGGGAGTAT 59.706 45.833 0.00 0.00 0.00 2.12
7795 8006 9.322773 GGGTACAAGTAGGATAATTTTGTACTC 57.677 37.037 19.08 14.83 46.56 2.59
7796 8007 9.054580 AGGGTACAAGTAGGATAATTTTGTACT 57.945 33.333 19.08 5.71 46.56 2.73
7804 8015 9.756571 CTGTAGATAGGGTACAAGTAGGATAAT 57.243 37.037 0.00 0.00 30.04 1.28
7805 8016 8.952602 TCTGTAGATAGGGTACAAGTAGGATAA 58.047 37.037 0.00 0.00 30.04 1.75
7880 8413 2.474410 TATGAGCGAGAGAGCCGATA 57.526 50.000 0.00 0.00 38.01 2.92
7881 8414 1.832883 ATATGAGCGAGAGAGCCGAT 58.167 50.000 0.00 0.00 38.01 4.18
7883 8416 2.159448 CCTTATATGAGCGAGAGAGCCG 60.159 54.545 0.00 0.00 38.01 5.52
7913 8446 0.179081 GGGACCGGCTATGTTGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
7914 8447 0.616395 TGGGACCGGCTATGTTGAGA 60.616 55.000 0.00 0.00 0.00 3.27
7915 8448 0.251916 TTGGGACCGGCTATGTTGAG 59.748 55.000 0.00 0.00 0.00 3.02
7916 8449 0.251916 CTTGGGACCGGCTATGTTGA 59.748 55.000 0.00 0.00 0.00 3.18
7917 8450 1.376609 GCTTGGGACCGGCTATGTTG 61.377 60.000 0.00 0.00 0.00 3.33
7918 8451 1.077716 GCTTGGGACCGGCTATGTT 60.078 57.895 0.00 0.00 0.00 2.71
7919 8452 2.590092 GCTTGGGACCGGCTATGT 59.410 61.111 0.00 0.00 0.00 2.29
7920 8453 2.203209 GGCTTGGGACCGGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
7921 8454 3.489513 GGGCTTGGGACCGGCTAT 61.490 66.667 0.00 0.00 0.00 2.97
7927 8460 0.465642 CTTTATCCGGGCTTGGGACC 60.466 60.000 0.00 0.00 36.14 4.46
7928 8461 0.465642 CCTTTATCCGGGCTTGGGAC 60.466 60.000 0.00 0.00 36.14 4.46
7929 8462 0.622154 TCCTTTATCCGGGCTTGGGA 60.622 55.000 0.00 1.62 38.10 4.37
7930 8463 0.179018 CTCCTTTATCCGGGCTTGGG 60.179 60.000 0.00 0.00 0.00 4.12
7931 8464 0.179018 CCTCCTTTATCCGGGCTTGG 60.179 60.000 0.00 0.00 0.00 3.61
7932 8465 0.837272 TCCTCCTTTATCCGGGCTTG 59.163 55.000 0.00 0.00 0.00 4.01
7933 8466 1.132500 CTCCTCCTTTATCCGGGCTT 58.868 55.000 0.00 0.00 0.00 4.35
7934 8467 0.764752 CCTCCTCCTTTATCCGGGCT 60.765 60.000 0.00 0.00 0.00 5.19
7935 8468 0.763223 TCCTCCTCCTTTATCCGGGC 60.763 60.000 0.00 0.00 0.00 6.13
7936 8469 2.031495 ATCCTCCTCCTTTATCCGGG 57.969 55.000 0.00 0.00 0.00 5.73
7937 8470 2.706190 ACAATCCTCCTCCTTTATCCGG 59.294 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.