Multiple sequence alignment - TraesCS5B01G386500

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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 TraesCS5B01G386500 chr5B 100.000 5240 0 0 1 5240 565902971 565897732 0.000000e+00 9677.0
1 TraesCS5B01G386500 chr5B 85.626 2254 219 56 1 2158 566120112 566122356 0.000000e+00 2270.0
2 TraesCS5B01G386500 chr5B 85.868 1118 134 12 143 1237 566043607 566044723 0.000000e+00 1168.0
3 TraesCS5B01G386500 chr5B 81.979 1354 209 19 3004 4342 566122806 566124139 0.000000e+00 1116.0
4 TraesCS5B01G386500 chr5B 88.969 834 66 12 1348 2158 566044825 566045655 0.000000e+00 1007.0
5 TraesCS5B01G386500 chr5B 84.751 341 43 7 2376 2708 566122431 566122770 3.020000e-87 333.0
6 TraesCS5B01G386500 chr5B 84.164 341 45 7 2376 2708 566054735 566055074 6.550000e-84 322.0
7 TraesCS5B01G386500 chr5B 95.858 169 7 0 2153 2321 575812973 575812805 1.860000e-69 274.0
8 TraesCS5B01G386500 chr5B 78.270 497 51 17 4791 5233 565880891 565880398 3.110000e-67 267.0
9 TraesCS5B01G386500 chr5D 92.912 2342 127 23 2357 4678 460240244 460237922 0.000000e+00 3369.0
10 TraesCS5B01G386500 chr5D 86.473 1035 110 18 132 1139 460430522 460431553 0.000000e+00 1109.0
11 TraesCS5B01G386500 chr5D 79.663 890 123 31 3445 4301 460447030 460447894 5.850000e-164 588.0
12 TraesCS5B01G386500 chr5D 88.750 480 32 7 1243 1701 460442124 460442602 7.620000e-158 568.0
13 TraesCS5B01G386500 chr5D 86.498 474 40 5 1695 2158 460443485 460443944 2.820000e-137 499.0
14 TraesCS5B01G386500 chr5D 84.889 450 59 7 3005 3447 460444404 460444851 3.720000e-121 446.0
15 TraesCS5B01G386500 chr5D 82.405 341 44 10 2384 2708 460444027 460444367 3.090000e-72 283.0
16 TraesCS5B01G386500 chr5D 84.163 221 26 7 4793 5013 460237677 460237466 6.880000e-49 206.0
17 TraesCS5B01G386500 chr5D 92.405 79 6 0 5122 5200 460227301 460227223 4.290000e-21 113.0
18 TraesCS5B01G386500 chr5A 90.589 1222 68 8 1 1201 580459038 580457843 0.000000e+00 1576.0
19 TraesCS5B01G386500 chr5A 89.719 1031 78 15 2320 3333 580456625 580455606 0.000000e+00 1291.0
20 TraesCS5B01G386500 chr5A 90.702 968 72 8 3831 4790 580452974 580452017 0.000000e+00 1273.0
21 TraesCS5B01G386500 chr5A 86.661 1132 124 11 132 1237 580556159 580557289 0.000000e+00 1229.0
22 TraesCS5B01G386500 chr5A 81.547 1306 183 36 3035 4301 580559589 580560875 0.000000e+00 1024.0
23 TraesCS5B01G386500 chr5A 91.223 638 37 7 1203 1823 580457682 580457047 0.000000e+00 850.0
24 TraesCS5B01G386500 chr5A 91.205 614 44 6 1554 2158 580558143 580558755 0.000000e+00 826.0
25 TraesCS5B01G386500 chr5A 92.146 522 35 1 3321 3836 580454300 580453779 0.000000e+00 732.0
26 TraesCS5B01G386500 chr5A 92.375 341 22 1 1822 2158 580456964 580456624 2.840000e-132 483.0
27 TraesCS5B01G386500 chr5A 78.200 500 41 26 4791 5233 580451983 580451495 1.870000e-64 257.0
28 TraesCS5B01G386500 chr5A 90.404 198 15 2 2376 2572 580558831 580559025 1.870000e-64 257.0
29 TraesCS5B01G386500 chr5A 89.412 85 7 2 4706 4790 480294217 480294299 7.180000e-19 106.0
30 TraesCS5B01G386500 chr5A 93.651 63 3 1 1501 1563 580557916 580557977 5.590000e-15 93.5
31 TraesCS5B01G386500 chr4A 95.402 174 7 1 2153 2325 362067907 362068080 5.170000e-70 276.0
32 TraesCS5B01G386500 chr3A 96.407 167 6 0 2157 2323 744921111 744920945 5.170000e-70 276.0
33 TraesCS5B01G386500 chr6D 95.858 169 6 1 2156 2324 13557730 13557563 6.690000e-69 272.0
34 TraesCS5B01G386500 chr2D 95.833 168 7 0 2157 2324 560959649 560959482 6.690000e-69 272.0
35 TraesCS5B01G386500 chr2B 94.828 174 9 0 2148 2321 719520678 719520505 6.690000e-69 272.0
36 TraesCS5B01G386500 chr2B 91.781 73 6 0 4702 4774 100027206 100027134 9.280000e-18 102.0
37 TraesCS5B01G386500 chr7D 93.370 181 10 2 2156 2334 213380410 213380230 3.110000e-67 267.0
38 TraesCS5B01G386500 chr7D 90.411 73 7 0 4702 4774 501886781 501886709 4.320000e-16 97.1
39 TraesCS5B01G386500 chr3B 91.237 194 15 2 2150 2342 62969924 62970116 4.020000e-66 263.0
40 TraesCS5B01G386500 chr6A 91.146 192 14 3 2131 2321 130354810 130354999 1.870000e-64 257.0
41 TraesCS5B01G386500 chr6A 90.411 73 7 0 4702 4774 15087607 15087535 4.320000e-16 97.1
42 TraesCS5B01G386500 chr6A 90.411 73 7 0 4702 4774 15298750 15298678 4.320000e-16 97.1
43 TraesCS5B01G386500 chr4B 81.605 299 43 7 2421 2708 448804447 448804744 2.440000e-58 237.0
44 TraesCS5B01G386500 chr7A 90.909 77 5 1 4710 4784 559195920 559195844 9.280000e-18 102.0
45 TraesCS5B01G386500 chr2A 88.372 86 7 2 4707 4790 557396102 557396018 3.340000e-17 100.0
46 TraesCS5B01G386500 chr6B 87.209 86 8 2 4707 4790 41027716 41027632 1.550000e-15 95.3


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 TraesCS5B01G386500 chr5B 565897732 565902971 5239 True 9677.000000 9677 100.000000 1 5240 1 chr5B.!!$R2 5239
1 TraesCS5B01G386500 chr5B 566120112 566124139 4027 False 1239.666667 2270 84.118667 1 4342 3 chr5B.!!$F3 4341
2 TraesCS5B01G386500 chr5B 566043607 566045655 2048 False 1087.500000 1168 87.418500 143 2158 2 chr5B.!!$F2 2015
3 TraesCS5B01G386500 chr5D 460237466 460240244 2778 True 1787.500000 3369 88.537500 2357 5013 2 chr5D.!!$R2 2656
4 TraesCS5B01G386500 chr5D 460430522 460431553 1031 False 1109.000000 1109 86.473000 132 1139 1 chr5D.!!$F1 1007
5 TraesCS5B01G386500 chr5D 460442124 460447894 5770 False 476.800000 588 84.441000 1243 4301 5 chr5D.!!$F2 3058
6 TraesCS5B01G386500 chr5A 580451495 580459038 7543 True 923.142857 1576 89.279143 1 5233 7 chr5A.!!$R1 5232
7 TraesCS5B01G386500 chr5A 580556159 580560875 4716 False 685.900000 1229 88.693600 132 4301 5 chr5A.!!$F2 4169

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
453 488 0.531532 CTGGGGATCACGAGCACATC 60.532 60.000 0.00 0.00 0.00 3.06 F
691 726 0.593773 CGCAACCCAAAACAAGGACG 60.594 55.000 0.00 0.00 0.00 4.79 F
1687 2502 0.034059 CGCACAGTGAGTCTCCCTTT 59.966 55.000 4.15 0.00 0.00 3.11 F
2168 3969 0.042131 TGACATCTACCCCCTCCGTT 59.958 55.000 0.00 0.00 0.00 4.44 F
3169 5382 0.387239 GTCGATTTGTTGTGGCTGGC 60.387 55.000 0.00 0.00 0.00 4.85 F
3859 10393 1.451028 GGCAAGCTGCTCGAGGATT 60.451 57.895 15.58 0.01 44.28 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 2502 0.472471 GGGATGGGAAATGGCGAGTA 59.528 55.000 0.00 0.00 0.00 2.59 R
2550 4376 0.736636 TGAGTATCAGTACCCACGCG 59.263 55.000 3.53 3.53 42.56 6.01 R
2567 4401 1.378531 GGTATTTGACAGCCGCATGA 58.621 50.000 0.00 0.00 0.00 3.07 R
3918 10457 2.128035 CTATTCCTTCCGATGCACGTC 58.872 52.381 0.00 0.00 40.78 4.34 R
4172 10741 0.107508 CCTGTCCACAATCCAGCGAT 60.108 55.000 0.00 0.00 0.00 4.58 R
5147 11915 0.179108 CTAGGCCAGTCCAACGTAGC 60.179 60.000 5.01 0.00 37.29 3.58 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
30 31 5.241285 TGCAGCAACAGTCTTATTGATTTCA 59.759 36.000 0.00 0.00 0.00 2.69
81 82 0.950836 TGCATTTTGACCGGTGTGAG 59.049 50.000 14.63 0.00 0.00 3.51
158 179 7.671398 AGCTTCCTCATTCAGAAAGGAATTTAA 59.329 33.333 14.37 0.00 43.38 1.52
240 268 2.482839 GGATGTCAGAGCTTGTAGAGGC 60.483 54.545 0.00 0.00 0.00 4.70
284 312 7.766278 CACTGAATCTAAGGTAATGTACTTGCT 59.234 37.037 0.00 0.00 0.00 3.91
322 350 1.067516 GCTCAAAAGCTTGCACTCCAA 59.932 47.619 0.00 0.00 45.55 3.53
344 375 3.256558 CTTGTGCATCTCATCGACTTCA 58.743 45.455 0.00 0.00 0.00 3.02
353 384 4.921547 TCTCATCGACTTCACTAATTCCG 58.078 43.478 0.00 0.00 0.00 4.30
355 386 4.669318 TCATCGACTTCACTAATTCCGTC 58.331 43.478 0.00 0.00 0.00 4.79
360 391 4.684703 CGACTTCACTAATTCCGTCTTTGT 59.315 41.667 0.00 0.00 0.00 2.83
370 401 4.451629 TTCCGTCTTTGTATCTCTGGTC 57.548 45.455 0.00 0.00 0.00 4.02
371 402 3.698289 TCCGTCTTTGTATCTCTGGTCT 58.302 45.455 0.00 0.00 0.00 3.85
430 465 3.764434 AGATCGTCTAGAGCTTGGTGAAA 59.236 43.478 0.00 0.00 44.27 2.69
444 479 1.886542 GGTGAAAACACTGGGGATCAC 59.113 52.381 0.00 0.00 37.14 3.06
452 487 1.267574 ACTGGGGATCACGAGCACAT 61.268 55.000 6.93 0.00 0.00 3.21
453 488 0.531532 CTGGGGATCACGAGCACATC 60.532 60.000 0.00 0.00 0.00 3.06
454 489 1.264045 TGGGGATCACGAGCACATCA 61.264 55.000 0.00 0.00 0.00 3.07
540 575 9.620259 AAGAAGGATAAGGATGTTTATTCAGTC 57.380 33.333 0.00 0.00 0.00 3.51
573 608 7.587037 TCTTTTGAATCAGTTGAGGACAATT 57.413 32.000 0.00 0.00 38.32 2.32
574 609 7.651808 TCTTTTGAATCAGTTGAGGACAATTC 58.348 34.615 0.00 0.00 38.32 2.17
585 620 6.154363 AGTTGAGGACAATTCAAAAGGACAAA 59.846 34.615 0.00 0.00 36.41 2.83
691 726 0.593773 CGCAACCCAAAACAAGGACG 60.594 55.000 0.00 0.00 0.00 4.79
735 770 2.157738 GAAGCTCTTGTGGCTCAACAT 58.842 47.619 0.00 0.00 39.30 2.71
831 866 6.315393 TCGGATTACTTGCTGTAAAGGATTTC 59.685 38.462 6.90 1.00 43.45 2.17
855 890 8.786826 TCGTTTGGAGTCAGTTCAATATAAAT 57.213 30.769 0.00 0.00 0.00 1.40
880 915 1.209019 AGGAGTTGCTGGACTATGCTG 59.791 52.381 0.00 0.00 0.00 4.41
1013 1069 6.811954 AGCTAAAGTAGATGAACTCCTTAGC 58.188 40.000 10.40 10.40 38.72 3.09
1036 1092 4.864806 CGAAGGAGAAAGATGACGAAATCA 59.135 41.667 0.00 0.00 43.13 2.57
1066 1122 1.656652 AAATCGCCAACCTGAGATCG 58.343 50.000 0.00 0.00 0.00 3.69
1079 1135 2.357323 CTGAGATCGCTAGTCTGAAGCA 59.643 50.000 0.00 0.00 40.08 3.91
1167 1223 5.947228 ATTTGTGTCGTGATCATGTCTTT 57.053 34.783 14.52 0.00 0.00 2.52
1272 1520 5.757850 AATTCACTTCTGTCAGTTTGGTC 57.242 39.130 0.00 0.00 0.00 4.02
1600 2415 3.586892 AGACTAGTAAAAAGCGCAGGAC 58.413 45.455 11.47 0.00 0.00 3.85
1687 2502 0.034059 CGCACAGTGAGTCTCCCTTT 59.966 55.000 4.15 0.00 0.00 3.11
1692 3396 2.820787 ACAGTGAGTCTCCCTTTACTCG 59.179 50.000 0.00 0.00 44.14 4.18
1748 3456 6.126796 TGCATCCCAGATCTACATTCTTGTTA 60.127 38.462 0.00 0.00 37.28 2.41
1798 3506 8.593945 TTTCATTGGTTAATCTCCTGCTAAAT 57.406 30.769 0.00 0.00 0.00 1.40
1806 3514 8.293157 GGTTAATCTCCTGCTAAATAATCTTGC 58.707 37.037 0.00 0.00 0.00 4.01
2002 3802 8.664211 ACTGATCCGAGAAACTTTATAAATCC 57.336 34.615 0.00 0.00 0.00 3.01
2039 3839 7.394359 GTGCTGGACAATAATGTATTATGGGAT 59.606 37.037 0.00 0.00 40.74 3.85
2069 3870 4.022464 ACACCATAACACGTTGTTGTTG 57.978 40.909 11.90 9.57 41.30 3.33
2162 3963 1.507140 TGTGGATGACATCTACCCCC 58.493 55.000 24.25 5.69 39.71 5.40
2163 3964 1.009552 TGTGGATGACATCTACCCCCT 59.990 52.381 24.25 0.00 39.71 4.79
2164 3965 1.694696 GTGGATGACATCTACCCCCTC 59.305 57.143 18.53 0.00 35.03 4.30
2165 3966 1.353091 GGATGACATCTACCCCCTCC 58.647 60.000 14.95 0.00 0.00 4.30
2166 3967 0.969894 GATGACATCTACCCCCTCCG 59.030 60.000 8.25 0.00 0.00 4.63
2167 3968 0.264955 ATGACATCTACCCCCTCCGT 59.735 55.000 0.00 0.00 0.00 4.69
2168 3969 0.042131 TGACATCTACCCCCTCCGTT 59.958 55.000 0.00 0.00 0.00 4.44
2169 3970 0.751452 GACATCTACCCCCTCCGTTC 59.249 60.000 0.00 0.00 0.00 3.95
2170 3971 0.690077 ACATCTACCCCCTCCGTTCC 60.690 60.000 0.00 0.00 0.00 3.62
2171 3972 0.398664 CATCTACCCCCTCCGTTCCT 60.399 60.000 0.00 0.00 0.00 3.36
2172 3973 1.133262 CATCTACCCCCTCCGTTCCTA 60.133 57.143 0.00 0.00 0.00 2.94
2173 3974 1.009997 TCTACCCCCTCCGTTCCTAA 58.990 55.000 0.00 0.00 0.00 2.69
2174 3975 1.362237 TCTACCCCCTCCGTTCCTAAA 59.638 52.381 0.00 0.00 0.00 1.85
2175 3976 2.022722 TCTACCCCCTCCGTTCCTAAAT 60.023 50.000 0.00 0.00 0.00 1.40
2176 3977 2.574074 ACCCCCTCCGTTCCTAAATA 57.426 50.000 0.00 0.00 0.00 1.40
2177 3978 3.070525 ACCCCCTCCGTTCCTAAATAT 57.929 47.619 0.00 0.00 0.00 1.28
2178 3979 3.400419 ACCCCCTCCGTTCCTAAATATT 58.600 45.455 0.00 0.00 0.00 1.28
2179 3980 3.789840 ACCCCCTCCGTTCCTAAATATTT 59.210 43.478 5.89 5.89 0.00 1.40
2180 3981 4.142038 CCCCCTCCGTTCCTAAATATTTG 58.858 47.826 11.05 1.40 0.00 2.32
2181 3982 4.385977 CCCCCTCCGTTCCTAAATATTTGT 60.386 45.833 11.05 0.00 0.00 2.83
2182 3983 4.820173 CCCCTCCGTTCCTAAATATTTGTC 59.180 45.833 11.05 0.00 0.00 3.18
2183 3984 5.397559 CCCCTCCGTTCCTAAATATTTGTCT 60.398 44.000 11.05 0.00 0.00 3.41
2184 3985 6.120220 CCCTCCGTTCCTAAATATTTGTCTT 58.880 40.000 11.05 0.00 0.00 3.01
2185 3986 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2186 3987 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2187 3988 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2188 3989 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2189 3990 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2190 3991 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2203 4004 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2204 4005 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2205 4006 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2206 4007 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2207 4008 8.204160 TCTTTCTAGAGATTTCAACAAGTGACA 58.796 33.333 0.00 0.00 35.39 3.58
2208 4009 8.731275 TTTCTAGAGATTTCAACAAGTGACAA 57.269 30.769 0.00 0.00 35.39 3.18
2209 4010 7.715265 TCTAGAGATTTCAACAAGTGACAAC 57.285 36.000 0.00 0.00 35.39 3.32
2210 4011 7.272244 TCTAGAGATTTCAACAAGTGACAACA 58.728 34.615 0.00 0.00 35.39 3.33
2211 4012 6.949352 AGAGATTTCAACAAGTGACAACAT 57.051 33.333 0.00 0.00 35.39 2.71
2212 4013 9.208022 CTAGAGATTTCAACAAGTGACAACATA 57.792 33.333 0.00 0.00 35.39 2.29
2213 4014 8.627208 AGAGATTTCAACAAGTGACAACATAT 57.373 30.769 0.00 0.00 35.39 1.78
2214 4015 8.509690 AGAGATTTCAACAAGTGACAACATATG 58.490 33.333 0.00 0.00 35.39 1.78
2215 4016 7.596494 AGATTTCAACAAGTGACAACATATGG 58.404 34.615 7.80 0.00 35.39 2.74
2216 4017 6.951062 TTTCAACAAGTGACAACATATGGA 57.049 33.333 7.80 0.00 35.39 3.41
2217 4018 6.558771 TTCAACAAGTGACAACATATGGAG 57.441 37.500 7.80 1.31 35.39 3.86
2218 4019 4.455533 TCAACAAGTGACAACATATGGAGC 59.544 41.667 7.80 0.00 0.00 4.70
2219 4020 4.019792 ACAAGTGACAACATATGGAGCA 57.980 40.909 7.80 0.00 0.00 4.26
2220 4021 4.397420 ACAAGTGACAACATATGGAGCAA 58.603 39.130 7.80 0.00 0.00 3.91
2221 4022 4.826733 ACAAGTGACAACATATGGAGCAAA 59.173 37.500 7.80 0.00 0.00 3.68
2222 4023 5.301551 ACAAGTGACAACATATGGAGCAAAA 59.698 36.000 7.80 0.00 0.00 2.44
2223 4024 6.015180 ACAAGTGACAACATATGGAGCAAAAT 60.015 34.615 7.80 0.00 0.00 1.82
2224 4025 5.957798 AGTGACAACATATGGAGCAAAATG 58.042 37.500 7.80 0.00 0.00 2.32
2225 4026 5.711506 AGTGACAACATATGGAGCAAAATGA 59.288 36.000 7.80 0.00 0.00 2.57
2226 4027 6.032094 GTGACAACATATGGAGCAAAATGAG 58.968 40.000 7.80 0.00 0.00 2.90
2227 4028 5.711506 TGACAACATATGGAGCAAAATGAGT 59.288 36.000 7.80 0.00 0.00 3.41
2228 4029 5.957798 ACAACATATGGAGCAAAATGAGTG 58.042 37.500 7.80 0.00 0.00 3.51
2229 4030 5.711506 ACAACATATGGAGCAAAATGAGTGA 59.288 36.000 7.80 0.00 0.00 3.41
2230 4031 6.209192 ACAACATATGGAGCAAAATGAGTGAA 59.791 34.615 7.80 0.00 0.00 3.18
2231 4032 7.093640 ACAACATATGGAGCAAAATGAGTGAAT 60.094 33.333 7.80 0.00 0.00 2.57
2232 4033 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
2233 4034 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
2234 4035 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
2235 4036 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
2236 4037 4.631377 TGGAGCAAAATGAGTGAATCTACG 59.369 41.667 0.00 0.00 0.00 3.51
2237 4038 4.494855 GGAGCAAAATGAGTGAATCTACGC 60.495 45.833 0.00 0.00 0.00 4.42
2238 4039 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
2239 4040 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
2240 4041 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
2241 4042 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
2242 4043 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
2243 4044 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
2244 4045 8.443160 CAAAATGAGTGAATCTACGCTCTAAAA 58.557 33.333 0.00 0.00 44.58 1.52
2245 4046 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
2246 4047 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
2247 4048 9.988815 AATGAGTGAATCTACGCTCTAAAATAT 57.011 29.630 0.00 0.00 44.58 1.28
2248 4049 8.803201 TGAGTGAATCTACGCTCTAAAATATG 57.197 34.615 0.00 0.00 44.58 1.78
2249 4050 8.414003 TGAGTGAATCTACGCTCTAAAATATGT 58.586 33.333 0.00 0.00 44.58 2.29
2250 4051 8.804688 AGTGAATCTACGCTCTAAAATATGTC 57.195 34.615 0.00 0.00 0.00 3.06
2251 4052 8.634444 AGTGAATCTACGCTCTAAAATATGTCT 58.366 33.333 0.00 0.00 0.00 3.41
2252 4053 9.894783 GTGAATCTACGCTCTAAAATATGTCTA 57.105 33.333 0.00 0.00 0.00 2.59
2276 4077 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
2312 4113 9.211485 TCTAAAAAGACAAGTATTTAGGAACGG 57.789 33.333 0.00 0.00 36.48 4.44
2313 4114 9.211485 CTAAAAAGACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 33.69 4.69
2314 4115 7.668525 AAAAGACAAGTATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2315 4116 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2316 4117 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2317 4118 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2318 4119 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2449 4274 2.706890 ACAACGTCTGGTTTTGTGACT 58.293 42.857 0.00 0.00 36.49 3.41
2477 4302 9.454585 AGCATCACATTTGAACATTATTAATCG 57.545 29.630 0.00 0.00 34.61 3.34
2491 4316 9.071276 ACATTATTAATCGCAGAAAATCCTGAT 57.929 29.630 0.00 0.00 43.58 2.90
2541 4367 2.027192 TGCACCTCTCTGAATTACCACC 60.027 50.000 0.00 0.00 0.00 4.61
2543 4369 3.866651 CACCTCTCTGAATTACCACCTG 58.133 50.000 0.00 0.00 0.00 4.00
2550 4376 3.263425 TCTGAATTACCACCTGTTCCTCC 59.737 47.826 0.00 0.00 0.00 4.30
2567 4401 0.394762 TCCGCGTGGGTACTGATACT 60.395 55.000 16.49 0.00 37.00 2.12
2573 4407 2.743938 GTGGGTACTGATACTCATGCG 58.256 52.381 0.00 0.00 43.79 4.73
2610 4780 2.772191 AGGGGTGCAGTGACCACA 60.772 61.111 14.12 0.00 42.55 4.17
2617 4787 3.605634 GGTGCAGTGACCACATACATAA 58.394 45.455 0.00 0.00 35.88 1.90
2618 4788 4.006989 GGTGCAGTGACCACATACATAAA 58.993 43.478 0.00 0.00 35.88 1.40
2619 4789 4.457603 GGTGCAGTGACCACATACATAAAA 59.542 41.667 0.00 0.00 35.88 1.52
2621 4791 6.029607 GTGCAGTGACCACATACATAAAATG 58.970 40.000 0.00 0.00 33.50 2.32
2622 4792 5.125257 TGCAGTGACCACATACATAAAATGG 59.875 40.000 0.00 0.00 36.46 3.16
2623 4793 5.356751 GCAGTGACCACATACATAAAATGGA 59.643 40.000 0.00 0.00 34.38 3.41
2624 4794 6.677920 GCAGTGACCACATACATAAAATGGAC 60.678 42.308 0.00 0.00 34.38 4.02
2625 4795 5.885912 AGTGACCACATACATAAAATGGACC 59.114 40.000 2.78 0.00 34.38 4.46
2626 4796 5.067283 GTGACCACATACATAAAATGGACCC 59.933 44.000 0.00 0.00 34.38 4.46
2627 4797 5.197451 GACCACATACATAAAATGGACCCA 58.803 41.667 0.00 0.00 34.38 4.51
2629 4799 6.019748 ACCACATACATAAAATGGACCCAAA 58.980 36.000 0.00 0.00 34.38 3.28
2630 4800 6.498651 ACCACATACATAAAATGGACCCAAAA 59.501 34.615 0.00 0.00 34.38 2.44
2632 4802 7.333174 CCACATACATAAAATGGACCCAAAAAC 59.667 37.037 0.00 0.00 31.69 2.43
2679 4866 1.774856 ACAAACCCTACACTTCAGGCT 59.225 47.619 0.00 0.00 0.00 4.58
2682 4869 2.921834 ACCCTACACTTCAGGCTAGA 57.078 50.000 0.00 0.00 0.00 2.43
2690 4877 6.322712 CCTACACTTCAGGCTAGAGTAGAAAT 59.677 42.308 18.01 0.00 38.36 2.17
2708 4895 8.816894 AGTAGAAATGTGAACTTCTTCCTGATA 58.183 33.333 0.00 0.00 33.89 2.15
2770 4957 9.440773 TCATAAAATATGTGGCTGATCTCATAC 57.559 33.333 0.00 0.00 0.00 2.39
2803 4990 9.621239 TCAGACCTTAGGAATTATTAGATGGAT 57.379 33.333 4.77 0.00 0.00 3.41
2892 5081 9.875708 ATTCTTGAGTAGTCTGTCCTTATCTAT 57.124 33.333 0.00 0.00 0.00 1.98
2893 5082 8.911918 TCTTGAGTAGTCTGTCCTTATCTATC 57.088 38.462 0.00 0.00 0.00 2.08
2894 5083 8.719596 TCTTGAGTAGTCTGTCCTTATCTATCT 58.280 37.037 0.00 0.00 0.00 1.98
2895 5084 9.349713 CTTGAGTAGTCTGTCCTTATCTATCTT 57.650 37.037 0.00 0.00 0.00 2.40
2896 5085 8.911918 TGAGTAGTCTGTCCTTATCTATCTTC 57.088 38.462 0.00 0.00 0.00 2.87
2897 5086 7.940137 TGAGTAGTCTGTCCTTATCTATCTTCC 59.060 40.741 0.00 0.00 0.00 3.46
2905 5094 9.699410 CTGTCCTTATCTATCTTCCATCTATCT 57.301 37.037 0.00 0.00 0.00 1.98
2932 5121 6.486253 TTGTGTGAGATACTTGATTGCTTC 57.514 37.500 0.00 0.00 0.00 3.86
2941 5130 7.899973 AGATACTTGATTGCTTCCAATTTTGT 58.100 30.769 0.00 0.00 41.60 2.83
2942 5131 7.816031 AGATACTTGATTGCTTCCAATTTTGTG 59.184 33.333 0.00 0.00 41.60 3.33
3091 5304 1.815003 AGTGTAAACGTCCCTAGTCGG 59.185 52.381 0.00 0.00 0.00 4.79
3096 5309 0.964358 AACGTCCCTAGTCGGTCTGG 60.964 60.000 0.00 0.00 0.00 3.86
3168 5381 0.950836 TGTCGATTTGTTGTGGCTGG 59.049 50.000 0.00 0.00 0.00 4.85
3169 5382 0.387239 GTCGATTTGTTGTGGCTGGC 60.387 55.000 0.00 0.00 0.00 4.85
3192 5405 4.202111 CGAGTGGATTTTGGTTCTTGGTTT 60.202 41.667 0.00 0.00 0.00 3.27
3229 5442 4.864704 ATTTGTGTTCGGTGGCTTTAAT 57.135 36.364 0.00 0.00 0.00 1.40
3254 5467 6.151144 TGGAAGCTCTTTGTCTAAAAATAGCC 59.849 38.462 0.00 0.00 39.05 3.93
3291 5506 6.151691 GCTTGTTCAACAGATGCAAATCTTA 58.848 36.000 0.00 0.00 0.00 2.10
3315 5530 2.749621 CAAGACCACAAATAGCAGGACC 59.250 50.000 0.00 0.00 0.00 4.46
3330 6861 3.368531 GCAGGACCTACACTCTTAAGGTG 60.369 52.174 17.45 17.45 43.69 4.00
3371 6902 2.092968 AGGATGTCGAGGCTAAAATGCA 60.093 45.455 0.00 0.00 34.04 3.96
3859 10393 1.451028 GGCAAGCTGCTCGAGGATT 60.451 57.895 15.58 0.01 44.28 3.01
3918 10457 3.648982 TGCGCGCTTCACCTTGTG 61.649 61.111 33.29 0.00 34.45 3.33
4310 10886 8.173775 CGAAGTCGAACTGTTAGAAGTCTATTA 58.826 37.037 4.90 0.00 43.02 0.98
4422 10998 3.260380 TGTTGGCTTTAATGGATGGTTGG 59.740 43.478 0.00 0.00 0.00 3.77
4509 11087 6.923508 TGCATGATACCTACTGTTTAAGATCG 59.076 38.462 0.00 0.00 0.00 3.69
4580 11160 5.180304 GCTAGCTCCTAAACTAAATGCATCC 59.820 44.000 7.70 0.00 0.00 3.51
4606 11186 4.202441 CAGGAGGTGCATACATTTTAGCT 58.798 43.478 0.00 0.00 0.00 3.32
4664 11245 8.219546 TCACATGTTTCAATACAAAGAAGTCA 57.780 30.769 0.00 0.00 0.00 3.41
4665 11246 8.681806 TCACATGTTTCAATACAAAGAAGTCAA 58.318 29.630 0.00 0.00 0.00 3.18
4702 11283 5.654209 GGGAACAGAAGAAGAATTAATGGCT 59.346 40.000 0.00 0.00 0.00 4.75
4772 11442 0.898320 CGGGTGAAGAGGTGATCTGT 59.102 55.000 0.00 0.00 38.67 3.41
4799 11510 5.183904 CGATTCTTTTGGTGGGAATTCTTCT 59.816 40.000 5.23 0.00 30.98 2.85
4812 11523 7.383300 GTGGGAATTCTTCTGTCTTGATTTTTG 59.617 37.037 5.23 0.00 0.00 2.44
4855 11566 5.629079 GCAAATGCTAAGGTTCTACTGTT 57.371 39.130 0.00 0.00 38.21 3.16
4881 11596 7.830940 TCTCAGTTTTGTTTACGTGACTTAA 57.169 32.000 0.00 0.00 0.00 1.85
4914 11652 1.501169 GCACAAATTGCCAGTTCCAC 58.499 50.000 0.00 0.00 46.63 4.02
5002 11740 5.316987 GCCATAACTAAGGGCATCTACAAT 58.683 41.667 0.00 0.00 46.92 2.71
5018 11756 1.247567 CAATTGGACCGCCTCAAACT 58.752 50.000 0.00 0.00 34.31 2.66
5019 11757 1.068333 CAATTGGACCGCCTCAAACTG 60.068 52.381 0.00 0.00 34.31 3.16
5020 11758 0.609131 ATTGGACCGCCTCAAACTGG 60.609 55.000 0.00 0.00 34.31 4.00
5021 11759 1.990160 TTGGACCGCCTCAAACTGGT 61.990 55.000 0.00 0.00 37.44 4.00
5022 11760 1.966451 GGACCGCCTCAAACTGGTG 60.966 63.158 0.00 0.00 34.12 4.17
5025 11763 3.655481 CGCCTCAAACTGGTGGAC 58.345 61.111 0.00 0.00 0.00 4.02
5026 11764 1.227823 CGCCTCAAACTGGTGGACA 60.228 57.895 0.00 0.00 0.00 4.02
5028 11766 0.668535 GCCTCAAACTGGTGGACAAC 59.331 55.000 0.00 0.00 0.00 3.32
5051 11804 4.275936 CCCAATCACTATCGGACATTTTCC 59.724 45.833 0.00 0.00 41.75 3.13
5056 11809 3.377172 CACTATCGGACATTTTCCCAACC 59.623 47.826 0.00 0.00 42.27 3.77
5057 11810 2.899303 ATCGGACATTTTCCCAACCT 57.101 45.000 0.00 0.00 42.27 3.50
5073 11826 0.692419 ACCTGACCCCTCATAGCCAG 60.692 60.000 0.00 0.00 0.00 4.85
5092 11859 2.654749 GCCTAAAGCACCCATCAAAC 57.345 50.000 0.00 0.00 42.97 2.93
5096 11863 1.799933 AAAGCACCCATCAAACCCAA 58.200 45.000 0.00 0.00 0.00 4.12
5102 11869 3.161067 CACCCATCAAACCCAACACATA 58.839 45.455 0.00 0.00 0.00 2.29
5104 11871 3.768757 ACCCATCAAACCCAACACATATG 59.231 43.478 0.00 0.00 0.00 1.78
5105 11872 3.132646 CCCATCAAACCCAACACATATGG 59.867 47.826 7.80 0.00 37.71 2.74
5111 11878 3.205815 CCAACACATATGGGGGTGG 57.794 57.895 16.42 16.42 39.31 4.61
5112 11879 0.628522 CCAACACATATGGGGGTGGA 59.371 55.000 22.61 0.00 39.31 4.02
5113 11880 1.684869 CCAACACATATGGGGGTGGAC 60.685 57.143 22.61 0.00 39.31 4.02
5115 11882 0.918983 ACACATATGGGGGTGGACAG 59.081 55.000 10.35 0.00 39.31 3.51
5116 11883 0.183492 CACATATGGGGGTGGACAGG 59.817 60.000 7.80 0.00 0.00 4.00
5117 11884 0.993509 ACATATGGGGGTGGACAGGG 60.994 60.000 7.80 0.00 0.00 4.45
5118 11885 0.697511 CATATGGGGGTGGACAGGGA 60.698 60.000 0.00 0.00 0.00 4.20
5125 11893 4.083862 GTGGACAGGGAGGCGGTC 62.084 72.222 0.00 0.00 0.00 4.79
5159 11927 4.430765 CGGCCGCTACGTTGGACT 62.431 66.667 14.67 0.00 0.00 3.85
5164 11932 2.663196 GCTACGTTGGACTGGCCT 59.337 61.111 3.32 0.00 37.63 5.19
5194 11962 3.243771 CCCAGTTCGACCTCACATATACC 60.244 52.174 0.00 0.00 0.00 2.73
5200 11968 4.649692 TCGACCTCACATATACCCTACTC 58.350 47.826 0.00 0.00 0.00 2.59
5216 11984 0.252197 ACTCCGGACCAAACCATAGC 59.748 55.000 0.00 0.00 0.00 2.97
5224 11992 1.985159 ACCAAACCATAGCCACTCTCA 59.015 47.619 0.00 0.00 0.00 3.27
5228 11996 4.323485 CCAAACCATAGCCACTCTCAACTA 60.323 45.833 0.00 0.00 0.00 2.24
5233 12001 2.614134 AGCCACTCTCAACTACTCCT 57.386 50.000 0.00 0.00 0.00 3.69
5234 12002 2.175202 AGCCACTCTCAACTACTCCTG 58.825 52.381 0.00 0.00 0.00 3.86
5235 12003 1.896465 GCCACTCTCAACTACTCCTGT 59.104 52.381 0.00 0.00 0.00 4.00
5236 12004 2.094442 GCCACTCTCAACTACTCCTGTC 60.094 54.545 0.00 0.00 0.00 3.51
5237 12005 2.494073 CCACTCTCAACTACTCCTGTCC 59.506 54.545 0.00 0.00 0.00 4.02
5238 12006 2.494073 CACTCTCAACTACTCCTGTCCC 59.506 54.545 0.00 0.00 0.00 4.46
5239 12007 1.746220 CTCTCAACTACTCCTGTCCCG 59.254 57.143 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 7.918562 AGCTAACACAAATTGAAATGTAACGTT 59.081 29.630 5.88 5.88 0.00 3.99
158 179 3.070018 GGCAGCGATATCAGTAGCAAAT 58.930 45.455 3.12 0.00 0.00 2.32
240 268 1.886542 GTGTTACCAAGGGCAAGAAGG 59.113 52.381 0.00 0.00 0.00 3.46
252 280 7.913789 ACATTACCTTAGATTCAGTGTTACCA 58.086 34.615 0.00 0.00 0.00 3.25
253 281 9.310716 GTACATTACCTTAGATTCAGTGTTACC 57.689 37.037 0.00 0.00 0.00 2.85
284 312 4.266714 TGAGCAATGCATCTGATTTCTCA 58.733 39.130 8.35 0.00 32.76 3.27
322 350 3.257393 GAAGTCGATGAGATGCACAAGT 58.743 45.455 0.00 0.00 0.00 3.16
344 375 6.154706 ACCAGAGATACAAAGACGGAATTAGT 59.845 38.462 0.00 0.00 0.00 2.24
353 384 4.159506 AGAGCAGACCAGAGATACAAAGAC 59.840 45.833 0.00 0.00 0.00 3.01
355 386 4.402155 AGAGAGCAGACCAGAGATACAAAG 59.598 45.833 0.00 0.00 0.00 2.77
360 391 6.132658 ACATTAAGAGAGCAGACCAGAGATA 58.867 40.000 0.00 0.00 0.00 1.98
370 401 8.113062 CAGTTTCGATTAACATTAAGAGAGCAG 58.887 37.037 3.01 0.00 0.00 4.24
371 402 7.817478 TCAGTTTCGATTAACATTAAGAGAGCA 59.183 33.333 3.01 0.00 0.00 4.26
430 465 1.296715 GCTCGTGATCCCCAGTGTT 59.703 57.895 0.00 0.00 0.00 3.32
444 479 3.093574 CAACGCTTTTATGATGTGCTCG 58.906 45.455 0.00 0.00 0.00 5.03
452 487 4.320202 GGTTTGCTCTCAACGCTTTTATGA 60.320 41.667 0.00 0.00 30.75 2.15
453 488 3.914364 GGTTTGCTCTCAACGCTTTTATG 59.086 43.478 0.00 0.00 30.75 1.90
454 489 3.821033 AGGTTTGCTCTCAACGCTTTTAT 59.179 39.130 0.00 0.00 30.75 1.40
540 575 8.861033 TCAACTGATTCAAAAGAACATCTTTG 57.139 30.769 6.14 0.00 45.19 2.77
558 593 5.299279 GTCCTTTTGAATTGTCCTCAACTGA 59.701 40.000 0.00 0.00 36.33 3.41
573 608 4.156922 TCAAAGAGCGTTTTGTCCTTTTGA 59.843 37.500 13.31 0.00 38.77 2.69
574 609 4.420168 TCAAAGAGCGTTTTGTCCTTTTG 58.580 39.130 13.31 0.00 38.77 2.44
585 620 4.636206 AGTTTCTTGTTCTCAAAGAGCGTT 59.364 37.500 0.00 0.00 32.87 4.84
671 706 0.249280 GTCCTTGTTTTGGGTTGCGG 60.249 55.000 0.00 0.00 0.00 5.69
691 726 2.996249 TGGAGTCTGCCAATCTCATC 57.004 50.000 0.00 0.00 34.31 2.92
713 748 2.368548 TGTTGAGCCACAAGAGCTTCTA 59.631 45.455 0.00 0.00 41.75 2.10
735 770 5.450818 AGGAACCCATTTCATGTAGCTTA 57.549 39.130 0.00 0.00 35.70 3.09
831 866 8.664798 TCATTTATATTGAACTGACTCCAAACG 58.335 33.333 0.00 0.00 0.00 3.60
880 915 5.278022 CCAGTTCCTTGTTCTTAAGAAGCAC 60.278 44.000 18.22 8.39 34.27 4.40
1011 1067 1.819288 TCGTCATCTTTCTCCTTCGCT 59.181 47.619 0.00 0.00 0.00 4.93
1013 1069 4.864806 TGATTTCGTCATCTTTCTCCTTCG 59.135 41.667 0.00 0.00 0.00 3.79
1036 1092 4.099419 AGGTTGGCGATTTTTGAGTTCTTT 59.901 37.500 0.00 0.00 0.00 2.52
1066 1122 2.478134 CACACTTGTGCTTCAGACTAGC 59.522 50.000 0.10 0.00 39.39 3.42
1079 1135 3.327757 TGATAAGGAAGAGGCACACTTGT 59.672 43.478 0.00 0.00 39.84 3.16
1368 1841 7.940178 TTACAGTGGCACATATAAGAATACG 57.060 36.000 21.41 0.00 44.52 3.06
1529 2168 5.608449 CTCTCCACAAGAGCATTATGATGA 58.392 41.667 0.85 0.00 44.95 2.92
1600 2415 6.709397 AGCTATATGCATTCCAATGATATCCG 59.291 38.462 3.54 0.00 45.94 4.18
1687 2502 0.472471 GGGATGGGAAATGGCGAGTA 59.528 55.000 0.00 0.00 0.00 2.59
1692 3396 1.114627 GAGTTGGGATGGGAAATGGC 58.885 55.000 0.00 0.00 0.00 4.40
1748 3456 8.602472 ATTCACTAGAACTTGAGGAGATTAGT 57.398 34.615 0.00 0.00 36.39 2.24
1798 3506 5.994250 AGATAAGAAGGCACTGCAAGATTA 58.006 37.500 2.82 0.00 40.86 1.75
1838 3630 3.181509 GCAGATGCAGAACATGAAGACAG 60.182 47.826 0.00 0.00 39.84 3.51
1925 3724 3.319137 TGCTAAGTGCTGAACAGGTAG 57.681 47.619 3.99 0.00 43.37 3.18
2002 3802 3.713858 TGTCCAGCACAAAATGTCAAG 57.286 42.857 0.00 0.00 29.30 3.02
2039 3839 6.038382 ACAACGTGTTATGGTGTAAAACATCA 59.962 34.615 0.00 0.00 44.26 3.07
2051 3851 3.668191 GCATCAACAACAACGTGTTATGG 59.332 43.478 0.00 0.00 38.77 2.74
2156 3957 2.574074 ATTTAGGAACGGAGGGGGTA 57.426 50.000 0.00 0.00 0.00 3.69
2157 3958 2.574074 TATTTAGGAACGGAGGGGGT 57.426 50.000 0.00 0.00 0.00 4.95
2158 3959 4.142038 CAAATATTTAGGAACGGAGGGGG 58.858 47.826 0.00 0.00 0.00 5.40
2159 3960 4.788679 ACAAATATTTAGGAACGGAGGGG 58.211 43.478 0.00 0.00 0.00 4.79
2160 3961 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2161 3962 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2162 3963 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2163 3964 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2164 3965 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2177 3978 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2178 3979 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2179 3980 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2180 3981 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2181 3982 8.204160 TGTCACTTGTTGAAATCTCTAGAAAGA 58.796 33.333 0.00 0.00 35.39 2.52
2182 3983 8.370493 TGTCACTTGTTGAAATCTCTAGAAAG 57.630 34.615 0.00 0.00 35.39 2.62
2183 3984 8.612619 GTTGTCACTTGTTGAAATCTCTAGAAA 58.387 33.333 0.00 0.00 35.39 2.52
2184 3985 7.768582 TGTTGTCACTTGTTGAAATCTCTAGAA 59.231 33.333 0.00 0.00 35.39 2.10
2185 3986 7.272244 TGTTGTCACTTGTTGAAATCTCTAGA 58.728 34.615 0.00 0.00 35.39 2.43
2186 3987 7.482654 TGTTGTCACTTGTTGAAATCTCTAG 57.517 36.000 0.00 0.00 35.39 2.43
2187 3988 9.725019 ATATGTTGTCACTTGTTGAAATCTCTA 57.275 29.630 0.00 0.00 35.39 2.43
2188 3989 6.949352 ATGTTGTCACTTGTTGAAATCTCT 57.051 33.333 0.00 0.00 35.39 3.10
2189 3990 7.752239 CCATATGTTGTCACTTGTTGAAATCTC 59.248 37.037 1.24 0.00 35.39 2.75
2190 3991 7.448161 TCCATATGTTGTCACTTGTTGAAATCT 59.552 33.333 1.24 0.00 35.39 2.40
2191 3992 7.592938 TCCATATGTTGTCACTTGTTGAAATC 58.407 34.615 1.24 0.00 35.39 2.17
2192 3993 7.523293 TCCATATGTTGTCACTTGTTGAAAT 57.477 32.000 1.24 0.00 35.39 2.17
2193 3994 6.514870 GCTCCATATGTTGTCACTTGTTGAAA 60.515 38.462 1.24 0.00 35.39 2.69
2194 3995 5.048782 GCTCCATATGTTGTCACTTGTTGAA 60.049 40.000 1.24 0.00 35.39 2.69
2195 3996 4.455533 GCTCCATATGTTGTCACTTGTTGA 59.544 41.667 1.24 0.00 0.00 3.18
2196 3997 4.216042 TGCTCCATATGTTGTCACTTGTTG 59.784 41.667 1.24 0.00 0.00 3.33
2197 3998 4.397420 TGCTCCATATGTTGTCACTTGTT 58.603 39.130 1.24 0.00 0.00 2.83
2198 3999 4.019792 TGCTCCATATGTTGTCACTTGT 57.980 40.909 1.24 0.00 0.00 3.16
2199 4000 5.375417 TTTGCTCCATATGTTGTCACTTG 57.625 39.130 1.24 0.00 0.00 3.16
2200 4001 6.209192 TCATTTTGCTCCATATGTTGTCACTT 59.791 34.615 1.24 0.00 0.00 3.16
2201 4002 5.711506 TCATTTTGCTCCATATGTTGTCACT 59.288 36.000 1.24 0.00 0.00 3.41
2202 4003 5.953183 TCATTTTGCTCCATATGTTGTCAC 58.047 37.500 1.24 0.00 0.00 3.67
2203 4004 5.711506 ACTCATTTTGCTCCATATGTTGTCA 59.288 36.000 1.24 0.00 0.00 3.58
2204 4005 6.032094 CACTCATTTTGCTCCATATGTTGTC 58.968 40.000 1.24 0.00 0.00 3.18
2205 4006 5.711506 TCACTCATTTTGCTCCATATGTTGT 59.288 36.000 1.24 0.00 0.00 3.32
2206 4007 6.198650 TCACTCATTTTGCTCCATATGTTG 57.801 37.500 1.24 0.00 0.00 3.33
2207 4008 6.839124 TTCACTCATTTTGCTCCATATGTT 57.161 33.333 1.24 0.00 0.00 2.71
2208 4009 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
2209 4010 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
2210 4011 7.172190 CGTAGATTCACTCATTTTGCTCCATAT 59.828 37.037 0.00 0.00 0.00 1.78
2211 4012 6.479990 CGTAGATTCACTCATTTTGCTCCATA 59.520 38.462 0.00 0.00 0.00 2.74
2212 4013 5.295292 CGTAGATTCACTCATTTTGCTCCAT 59.705 40.000 0.00 0.00 0.00 3.41
2213 4014 4.631377 CGTAGATTCACTCATTTTGCTCCA 59.369 41.667 0.00 0.00 0.00 3.86
2214 4015 4.494855 GCGTAGATTCACTCATTTTGCTCC 60.495 45.833 0.00 0.00 0.00 4.70
2215 4016 4.331168 AGCGTAGATTCACTCATTTTGCTC 59.669 41.667 0.00 0.00 0.00 4.26
2216 4017 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
2217 4018 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
2218 4019 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
2219 4020 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
2220 4021 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
2221 4022 9.988815 ATATTTTAGAGCGTAGATTCACTCATT 57.011 29.630 0.00 0.00 0.00 2.57
2222 4023 9.416794 CATATTTTAGAGCGTAGATTCACTCAT 57.583 33.333 0.00 0.00 0.00 2.90
2223 4024 8.414003 ACATATTTTAGAGCGTAGATTCACTCA 58.586 33.333 0.00 0.00 0.00 3.41
2224 4025 8.804688 ACATATTTTAGAGCGTAGATTCACTC 57.195 34.615 0.00 0.00 0.00 3.51
2225 4026 8.634444 AGACATATTTTAGAGCGTAGATTCACT 58.366 33.333 0.00 0.00 0.00 3.41
2226 4027 8.804688 AGACATATTTTAGAGCGTAGATTCAC 57.195 34.615 0.00 0.00 0.00 3.18
2286 4087 9.211485 CCGTTCCTAAATACTTGTCTTTTTAGA 57.789 33.333 0.00 0.00 34.90 2.10
2287 4088 9.211485 TCCGTTCCTAAATACTTGTCTTTTTAG 57.789 33.333 0.00 0.00 33.47 1.85
2288 4089 9.211485 CTCCGTTCCTAAATACTTGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2289 4090 7.174426 CCTCCGTTCCTAAATACTTGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2290 4091 6.653740 CCTCCGTTCCTAAATACTTGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2291 4092 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2292 4093 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2293 4094 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2294 4095 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2295 4096 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2296 4097 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2297 4098 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2298 4099 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2299 4100 5.136105 TCTACTCCCTCCGTTCCTAAATAC 58.864 45.833 0.00 0.00 0.00 1.89
2300 4101 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2301 4102 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2302 4103 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2303 4104 3.744940 TTCTACTCCCTCCGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
2304 4105 3.011032 ACTTTCTACTCCCTCCGTTCCTA 59.989 47.826 0.00 0.00 0.00 2.94
2305 4106 2.225318 ACTTTCTACTCCCTCCGTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
2306 4107 2.177734 ACTTTCTACTCCCTCCGTTCC 58.822 52.381 0.00 0.00 0.00 3.62
2307 4108 5.349809 CAATACTTTCTACTCCCTCCGTTC 58.650 45.833 0.00 0.00 0.00 3.95
2308 4109 4.161754 CCAATACTTTCTACTCCCTCCGTT 59.838 45.833 0.00 0.00 0.00 4.44
2309 4110 3.705072 CCAATACTTTCTACTCCCTCCGT 59.295 47.826 0.00 0.00 0.00 4.69
2310 4111 3.958798 TCCAATACTTTCTACTCCCTCCG 59.041 47.826 0.00 0.00 0.00 4.63
2311 4112 7.613551 TTATCCAATACTTTCTACTCCCTCC 57.386 40.000 0.00 0.00 0.00 4.30
2360 4164 6.017400 ACTTTGGTGCACTTGAAGATAATG 57.983 37.500 24.01 10.61 0.00 1.90
2431 4256 3.311596 GCTAAGTCACAAAACCAGACGTT 59.688 43.478 0.00 0.00 37.36 3.99
2477 4302 5.124645 AGATGACTCATCAGGATTTTCTGC 58.875 41.667 19.21 0.00 42.72 4.26
2491 4316 3.897505 TGACAGAGGAACAAGATGACTCA 59.102 43.478 0.00 0.00 0.00 3.41
2541 4367 2.642254 TACCCACGCGGAGGAACAG 61.642 63.158 21.81 7.79 34.64 3.16
2543 4369 2.125793 GTACCCACGCGGAGGAAC 60.126 66.667 21.81 14.39 34.64 3.62
2550 4376 0.736636 TGAGTATCAGTACCCACGCG 59.263 55.000 3.53 3.53 42.56 6.01
2567 4401 1.378531 GGTATTTGACAGCCGCATGA 58.621 50.000 0.00 0.00 0.00 3.07
2573 4407 2.156098 TCAAACCGGTATTTGACAGCC 58.844 47.619 16.10 0.00 42.32 4.85
2621 4791 8.779303 CCAAAGTATTTATTTGTTTTTGGGTCC 58.221 33.333 5.42 0.00 39.39 4.46
2625 4795 8.159344 TGCCCAAAGTATTTATTTGTTTTTGG 57.841 30.769 6.19 6.19 41.53 3.28
2632 4802 9.097257 CCACTTAATGCCCAAAGTATTTATTTG 57.903 33.333 0.00 0.00 35.03 2.32
2679 4866 8.307483 CAGGAAGAAGTTCACATTTCTACTCTA 58.693 37.037 5.50 0.00 33.49 2.43
2682 4869 7.067496 TCAGGAAGAAGTTCACATTTCTACT 57.933 36.000 5.50 0.00 33.49 2.57
2690 4877 8.049117 AGCAAATATATCAGGAAGAAGTTCACA 58.951 33.333 5.50 0.00 33.93 3.58
2719 4906 4.016666 TCACCCCTCCAAATTAATCCACAT 60.017 41.667 0.00 0.00 0.00 3.21
2770 4957 4.881019 ATTCCTAAGGTCTGATCCATCG 57.119 45.455 0.00 0.00 0.00 3.84
2803 4990 6.540914 ACAGAAGACGGACTATTTTGACAAAA 59.459 34.615 15.39 15.39 34.41 2.44
2804 4991 6.053005 ACAGAAGACGGACTATTTTGACAAA 58.947 36.000 0.00 0.00 0.00 2.83
2818 5005 7.747155 TCTTATAGATAGGAACAGAAGACGG 57.253 40.000 0.00 0.00 0.00 4.79
2854 5041 9.924650 AGACTACTCAAGAATAAAATACAACGT 57.075 29.630 0.00 0.00 0.00 3.99
2866 5053 9.875708 ATAGATAAGGACAGACTACTCAAGAAT 57.124 33.333 0.00 0.00 0.00 2.40
2867 5054 9.344772 GATAGATAAGGACAGACTACTCAAGAA 57.655 37.037 0.00 0.00 0.00 2.52
2879 5066 9.699410 AGATAGATGGAAGATAGATAAGGACAG 57.301 37.037 0.00 0.00 0.00 3.51
2891 5080 9.775854 CTCACACAAAATAGATAGATGGAAGAT 57.224 33.333 0.00 0.00 0.00 2.40
2892 5081 8.981659 TCTCACACAAAATAGATAGATGGAAGA 58.018 33.333 0.00 0.00 0.00 2.87
2893 5082 9.775854 ATCTCACACAAAATAGATAGATGGAAG 57.224 33.333 0.00 0.00 0.00 3.46
2905 5094 8.565896 AGCAATCAAGTATCTCACACAAAATA 57.434 30.769 0.00 0.00 0.00 1.40
2923 5112 4.809958 CACACACAAAATTGGAAGCAATCA 59.190 37.500 0.00 0.00 0.00 2.57
2932 5121 6.091986 AGCTAAAAACACACACACAAAATTGG 59.908 34.615 0.00 0.00 0.00 3.16
2941 5130 5.378292 TTGTGAAGCTAAAAACACACACA 57.622 34.783 0.00 0.00 41.78 3.72
2942 5131 6.885735 AATTGTGAAGCTAAAAACACACAC 57.114 33.333 0.00 0.00 41.78 3.82
3047 5260 4.929808 ACACATGGACTAAGAATGAACGAC 59.070 41.667 0.00 0.00 0.00 4.34
3091 5304 5.652994 AAGACATCTAGTTCAGACCAGAC 57.347 43.478 0.00 0.00 35.62 3.51
3096 5309 5.916661 TGGGTAAGACATCTAGTTCAGAC 57.083 43.478 0.00 0.00 35.62 3.51
3168 5381 2.351738 CCAAGAACCAAAATCCACTCGC 60.352 50.000 0.00 0.00 0.00 5.03
3169 5382 2.884639 ACCAAGAACCAAAATCCACTCG 59.115 45.455 0.00 0.00 0.00 4.18
3192 5405 9.566530 CGAACACAAATATCATCAAATTGGTAA 57.433 29.630 0.00 0.00 0.00 2.85
3206 5419 5.968528 TTAAAGCCACCGAACACAAATAT 57.031 34.783 0.00 0.00 0.00 1.28
3207 5420 5.336055 CCATTAAAGCCACCGAACACAAATA 60.336 40.000 0.00 0.00 0.00 1.40
3229 5442 6.151144 GGCTATTTTTAGACAAAGAGCTTCCA 59.849 38.462 11.39 0.00 46.02 3.53
3254 5467 4.418013 TGAACAAGCATACGAAACATGG 57.582 40.909 0.00 0.00 0.00 3.66
3291 5506 3.327757 TCCTGCTATTTGTGGTCTTGACT 59.672 43.478 0.61 0.00 0.00 3.41
3330 6861 7.708752 ACATCCTCGATCTTATTTGAACTCTTC 59.291 37.037 0.00 0.00 0.00 2.87
3371 6902 4.262938 CCTGCACATCTAGATGGTGATCAT 60.263 45.833 31.19 10.29 42.91 2.45
3918 10457 2.128035 CTATTCCTTCCGATGCACGTC 58.872 52.381 0.00 0.00 40.78 4.34
4172 10741 0.107508 CCTGTCCACAATCCAGCGAT 60.108 55.000 0.00 0.00 0.00 4.58
4176 10745 1.746615 CGCCCTGTCCACAATCCAG 60.747 63.158 0.00 0.00 0.00 3.86
4177 10746 2.350895 CGCCCTGTCCACAATCCA 59.649 61.111 0.00 0.00 0.00 3.41
4310 10886 5.013079 TGTGGGTGACTTCTGACAGAATTAT 59.987 40.000 18.04 7.33 33.13 1.28
4422 10998 0.598419 GTTCAGCCAACCAGCAAAGC 60.598 55.000 0.00 0.00 34.23 3.51
4509 11087 6.205658 GTCTAGATTGCCAATGAAATAGGGTC 59.794 42.308 0.00 0.00 0.00 4.46
4580 11160 0.548031 ATGTATGCACCTCCTGTGGG 59.452 55.000 0.00 0.00 45.55 4.61
4606 11186 9.429109 AGAAGAACAAAGGGGAAAAGTTTTATA 57.571 29.630 0.00 0.00 0.00 0.98
4640 11220 8.854979 TTGACTTCTTTGTATTGAAACATGTG 57.145 30.769 0.00 0.00 0.00 3.21
4683 11264 9.525409 CCAAAATAGCCATTAATTCTTCTTCTG 57.475 33.333 0.00 0.00 0.00 3.02
4772 11442 2.940994 TCCCACCAAAAGAATCGTGA 57.059 45.000 0.00 0.00 0.00 4.35
4799 11510 5.620206 TCAGCCTAGACAAAAATCAAGACA 58.380 37.500 0.00 0.00 0.00 3.41
4812 11523 3.127721 GCTCAAAAACCATCAGCCTAGAC 59.872 47.826 0.00 0.00 0.00 2.59
4855 11566 6.730960 AGTCACGTAAACAAAACTGAGAAA 57.269 33.333 0.00 0.00 0.00 2.52
4904 11642 0.451783 CAATTAGGCGTGGAACTGGC 59.548 55.000 0.00 0.00 36.50 4.85
4914 11652 5.749596 TCAATAATGACACCAATTAGGCG 57.250 39.130 0.00 0.00 43.14 5.52
4972 11710 4.274978 TGCCCTTAGTTATGGCTAAAACC 58.725 43.478 0.00 0.00 45.56 3.27
5002 11740 1.228124 CCAGTTTGAGGCGGTCCAA 60.228 57.895 0.00 0.00 33.74 3.53
5021 11759 2.093181 CCGATAGTGATTGGGTTGTCCA 60.093 50.000 0.00 0.00 45.43 4.02
5022 11760 2.169769 TCCGATAGTGATTGGGTTGTCC 59.830 50.000 0.00 0.00 37.24 4.02
5023 11761 3.195661 GTCCGATAGTGATTGGGTTGTC 58.804 50.000 0.00 0.00 37.24 3.18
5025 11763 3.260475 TGTCCGATAGTGATTGGGTTG 57.740 47.619 0.00 0.00 37.24 3.77
5026 11764 4.503714 AATGTCCGATAGTGATTGGGTT 57.496 40.909 0.00 0.00 37.24 4.11
5028 11766 4.275936 GGAAAATGTCCGATAGTGATTGGG 59.724 45.833 0.00 0.00 37.24 4.12
5029 11767 5.424121 GGAAAATGTCCGATAGTGATTGG 57.576 43.478 0.00 0.00 36.40 3.16
5051 11804 0.181350 GCTATGAGGGGTCAGGTTGG 59.819 60.000 0.00 0.00 0.00 3.77
5056 11809 1.449353 GCTGGCTATGAGGGGTCAG 59.551 63.158 0.00 0.00 38.11 3.51
5057 11810 2.072487 GGCTGGCTATGAGGGGTCA 61.072 63.158 0.00 0.00 0.00 4.02
5073 11826 1.204704 GGTTTGATGGGTGCTTTAGGC 59.795 52.381 0.00 0.00 42.22 3.93
5084 11851 4.389890 CCATATGTGTTGGGTTTGATGG 57.610 45.455 1.24 0.00 0.00 3.51
5096 11863 0.918983 CTGTCCACCCCCATATGTGT 59.081 55.000 1.24 0.00 0.00 3.72
5102 11869 2.286425 CTCCCTGTCCACCCCCAT 60.286 66.667 0.00 0.00 0.00 4.00
5111 11878 3.775654 CTGGACCGCCTCCCTGTC 61.776 72.222 0.00 0.00 38.49 3.51
5116 11883 4.864334 CATGCCTGGACCGCCTCC 62.864 72.222 0.00 0.00 39.97 4.30
5142 11910 4.430765 AGTCCAACGTAGCGGCCG 62.431 66.667 24.05 24.05 0.00 6.13
5145 11913 2.813908 GCCAGTCCAACGTAGCGG 60.814 66.667 0.00 0.00 0.00 5.52
5146 11914 1.940883 TAGGCCAGTCCAACGTAGCG 61.941 60.000 5.01 0.00 37.29 4.26
5147 11915 0.179108 CTAGGCCAGTCCAACGTAGC 60.179 60.000 5.01 0.00 37.29 3.58
5148 11916 0.460311 CCTAGGCCAGTCCAACGTAG 59.540 60.000 5.01 0.00 37.29 3.51
5149 11917 1.610554 GCCTAGGCCAGTCCAACGTA 61.611 60.000 24.19 0.00 37.29 3.57
5150 11918 2.955881 GCCTAGGCCAGTCCAACGT 61.956 63.158 24.19 0.00 37.29 3.99
5151 11919 1.327690 TAGCCTAGGCCAGTCCAACG 61.328 60.000 30.42 0.00 43.17 4.10
5152 11920 0.909623 TTAGCCTAGGCCAGTCCAAC 59.090 55.000 30.42 0.00 43.17 3.77
5153 11921 0.909623 GTTAGCCTAGGCCAGTCCAA 59.090 55.000 30.42 11.68 43.17 3.53
5154 11922 0.981277 GGTTAGCCTAGGCCAGTCCA 60.981 60.000 30.42 5.93 43.17 4.02
5155 11923 1.697082 GGGTTAGCCTAGGCCAGTCC 61.697 65.000 30.42 24.15 43.17 3.85
5159 11927 0.549169 AACTGGGTTAGCCTAGGCCA 60.549 55.000 30.42 15.20 46.41 5.36
5164 11932 1.188863 GGTCGAACTGGGTTAGCCTA 58.811 55.000 1.07 0.00 34.45 3.93
5194 11962 0.909623 ATGGTTTGGTCCGGAGTAGG 59.090 55.000 3.06 0.00 0.00 3.18
5200 11968 1.029947 GTGGCTATGGTTTGGTCCGG 61.030 60.000 0.00 0.00 0.00 5.14
5216 11984 2.494073 GGACAGGAGTAGTTGAGAGTGG 59.506 54.545 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.