Multiple sequence alignment - TraesCS4D01G055900

Loading Multiple Alignment...

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 TraesCS4D01G055900 chr4D 100.000 6334 0 0 1 6334 30961651 30955318 0.000000e+00 11697
1 TraesCS4D01G055900 chr4B 93.263 3711 177 36 393 4064 44189540 44185864 0.000000e+00 5400
2 TraesCS4D01G055900 chr4B 93.747 1855 85 15 4282 6121 44185712 44183874 0.000000e+00 2754
3 TraesCS4D01G055900 chr4B 83.000 300 29 12 2 301 44190162 44189885 1.050000e-62 252
4 TraesCS4D01G055900 chr4A 93.631 3093 105 40 257 3309 571776557 571779597 0.000000e+00 4536
5 TraesCS4D01G055900 chr4A 94.315 2779 96 36 3373 6108 571779993 571782752 0.000000e+00 4200
6 TraesCS4D01G055900 chr4A 89.848 197 11 5 1 197 571776365 571776552 1.760000e-60 244


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 TraesCS4D01G055900 chr4D 30955318 30961651 6333 True 11697.000000 11697 100.000000 1 6334 1 chr4D.!!$R1 6333
1 TraesCS4D01G055900 chr4B 44183874 44190162 6288 True 2802.000000 5400 90.003333 2 6121 3 chr4B.!!$R1 6119
2 TraesCS4D01G055900 chr4A 571776365 571782752 6387 False 2993.333333 4536 92.598000 1 6108 3 chr4A.!!$F1 6107

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
373 400 0.106217 AACCTCACCAAACCCACCTG 60.106 55.000 0.00 0.00 0.00 4.00 F
1819 2147 0.317269 CAAGCTGTCAAGTGTTGCCG 60.317 55.000 0.00 0.00 0.00 5.69 F
2220 2551 0.179086 CCGCAAGTTTGGCAAAGGTT 60.179 50.000 13.94 7.28 0.00 3.50 F
3103 3440 2.489329 CCATCATGTGTCCCAACAGAAC 59.511 50.000 0.00 0.00 35.64 3.01 F
4248 4946 4.076394 GGCAACTTAACATGGGTCAAGTA 58.924 43.478 0.00 0.00 31.20 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2224 0.179045 GTCCACGCCCAGCATAGAAT 60.179 55.000 0.0 0.0 0.00 2.40 R
3089 3426 1.134220 TCACCAGTTCTGTTGGGACAC 60.134 52.381 0.0 0.0 39.29 3.67 R
3776 4450 2.158667 TGGTGACTTTCCCCTTCTTGAC 60.159 50.000 0.0 0.0 0.00 3.18 R
4351 5053 1.345741 CCAAGAGTGGCAAGAGTGAGA 59.654 52.381 0.0 0.0 38.35 3.27 R
5503 6211 0.112218 CACCTCACATTCCAACCCCA 59.888 55.000 0.0 0.0 0.00 4.96 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
32 33 3.064324 GCGCCACCTTTGCATCCT 61.064 61.111 0.00 0.00 0.00 3.24
139 147 3.579302 CACCCCACCCTGCCTCAA 61.579 66.667 0.00 0.00 0.00 3.02
141 149 4.366684 CCCCACCCTGCCTCAACC 62.367 72.222 0.00 0.00 0.00 3.77
143 151 3.260100 CCACCCTGCCTCAACCCT 61.260 66.667 0.00 0.00 0.00 4.34
144 152 2.352805 CACCCTGCCTCAACCCTC 59.647 66.667 0.00 0.00 0.00 4.30
145 153 2.121963 ACCCTGCCTCAACCCTCA 60.122 61.111 0.00 0.00 0.00 3.86
146 154 1.542375 ACCCTGCCTCAACCCTCAT 60.542 57.895 0.00 0.00 0.00 2.90
147 155 1.077212 CCCTGCCTCAACCCTCATG 60.077 63.158 0.00 0.00 0.00 3.07
148 156 1.751927 CCTGCCTCAACCCTCATGC 60.752 63.158 0.00 0.00 0.00 4.06
149 157 2.046023 TGCCTCAACCCTCATGCG 60.046 61.111 0.00 0.00 0.00 4.73
150 158 3.512516 GCCTCAACCCTCATGCGC 61.513 66.667 0.00 0.00 0.00 6.09
151 159 2.825836 CCTCAACCCTCATGCGCC 60.826 66.667 4.18 0.00 0.00 6.53
152 160 3.197790 CTCAACCCTCATGCGCCG 61.198 66.667 4.18 0.00 0.00 6.46
153 161 3.958147 CTCAACCCTCATGCGCCGT 62.958 63.158 4.18 0.00 0.00 5.68
154 162 3.803082 CAACCCTCATGCGCCGTG 61.803 66.667 4.18 3.88 0.00 4.94
197 205 4.181010 AATCAGAGCGCCGCCCAT 62.181 61.111 4.98 0.00 0.00 4.00
198 206 4.923942 ATCAGAGCGCCGCCCATG 62.924 66.667 4.98 1.91 0.00 3.66
286 306 0.250295 TGCTTGACCGGGAACTGAAG 60.250 55.000 6.32 0.00 36.31 3.02
373 400 0.106217 AACCTCACCAAACCCACCTG 60.106 55.000 0.00 0.00 0.00 4.00
374 401 0.991355 ACCTCACCAAACCCACCTGA 60.991 55.000 0.00 0.00 0.00 3.86
375 402 0.537371 CCTCACCAAACCCACCTGAC 60.537 60.000 0.00 0.00 0.00 3.51
376 403 0.537371 CTCACCAAACCCACCTGACC 60.537 60.000 0.00 0.00 0.00 4.02
377 404 1.530655 CACCAAACCCACCTGACCC 60.531 63.158 0.00 0.00 0.00 4.46
488 770 5.715434 AGCATTAAACGCCTTCCTTAAAA 57.285 34.783 0.00 0.00 0.00 1.52
567 849 1.139853 GCCACATCTCCCTCCTGTTAG 59.860 57.143 0.00 0.00 0.00 2.34
665 961 3.611674 GGGGTGCGTGGGGTTTTG 61.612 66.667 0.00 0.00 0.00 2.44
670 966 3.680786 GCGTGGGGTTTTGGGCTC 61.681 66.667 0.00 0.00 0.00 4.70
942 1255 1.043116 TGCCGCTGCAGTAGTATCCT 61.043 55.000 16.64 0.00 44.23 3.24
953 1266 0.952497 TAGTATCCTAGCGTCGCGGG 60.952 60.000 20.85 20.85 0.00 6.13
1006 1319 1.207791 GGAGGAGGTGGTGATGATGT 58.792 55.000 0.00 0.00 0.00 3.06
1007 1320 2.398588 GGAGGAGGTGGTGATGATGTA 58.601 52.381 0.00 0.00 0.00 2.29
1769 2097 1.227853 AGCTGTTCAACCGGGTGAC 60.228 57.895 25.10 17.87 0.00 3.67
1819 2147 0.317269 CAAGCTGTCAAGTGTTGCCG 60.317 55.000 0.00 0.00 0.00 5.69
1820 2148 1.447317 AAGCTGTCAAGTGTTGCCGG 61.447 55.000 0.00 0.00 0.00 6.13
1821 2149 2.186826 GCTGTCAAGTGTTGCCGGT 61.187 57.895 1.90 0.00 0.00 5.28
1957 2285 3.663176 CACCAACGCCACAGCCTG 61.663 66.667 0.00 0.00 34.57 4.85
1958 2286 3.872603 ACCAACGCCACAGCCTGA 61.873 61.111 0.00 0.00 34.57 3.86
2028 2359 7.477864 TGAAGTATATATTGATTGGGGCCATT 58.522 34.615 4.39 0.00 0.00 3.16
2083 2414 2.606795 GCCGTTGTGTATTGCATTGTGT 60.607 45.455 0.00 0.00 0.00 3.72
2118 2449 3.197927 AGGAGTGATCAGAGGGAAAGT 57.802 47.619 0.00 0.00 0.00 2.66
2220 2551 0.179086 CCGCAAGTTTGGCAAAGGTT 60.179 50.000 13.94 7.28 0.00 3.50
2469 2800 6.189859 TGGTCATTGCTTTGATAAAGAGGAT 58.810 36.000 5.54 0.00 41.02 3.24
2741 3073 4.501400 CCCCCATTCCAAATTAATCGAAGC 60.501 45.833 0.00 0.00 0.00 3.86
2982 3319 7.213678 TCAACGTGATGATTATACTGGCATTA 58.786 34.615 0.00 0.00 0.00 1.90
3103 3440 2.489329 CCATCATGTGTCCCAACAGAAC 59.511 50.000 0.00 0.00 35.64 3.01
3309 3646 6.868864 GTCGTGTAGTGGCATCTCATTATTAT 59.131 38.462 0.00 0.00 0.00 1.28
3310 3647 7.385205 GTCGTGTAGTGGCATCTCATTATTATT 59.615 37.037 0.00 0.00 0.00 1.40
3311 3648 7.931407 TCGTGTAGTGGCATCTCATTATTATTT 59.069 33.333 0.00 0.00 0.00 1.40
3314 3651 9.219603 TGTAGTGGCATCTCATTATTATTTAGC 57.780 33.333 0.00 0.00 0.00 3.09
3317 3654 9.964354 AGTGGCATCTCATTATTATTTAGCATA 57.036 29.630 0.00 0.00 0.00 3.14
3344 3681 4.342665 ACATTTTTAGGCGTTTTCCTTCCA 59.657 37.500 0.00 0.00 37.66 3.53
3590 4261 8.225603 ACAAAATGATAGGCAATTCTACGATT 57.774 30.769 0.00 0.00 0.00 3.34
3647 4319 7.801716 AATATCAACCTGTTACGCACAATAT 57.198 32.000 0.00 0.00 33.87 1.28
3776 4450 4.094294 TGGAAGTTTGAGTGAAGTTTGTCG 59.906 41.667 0.00 0.00 0.00 4.35
3978 4656 6.596497 CACCATACTAGGTCCGTTACAAAATT 59.404 38.462 0.00 0.00 40.77 1.82
4061 4758 4.202192 TGACTCGAGCTCTCATTATTGCAT 60.202 41.667 13.61 0.00 0.00 3.96
4248 4946 4.076394 GGCAACTTAACATGGGTCAAGTA 58.924 43.478 0.00 0.00 31.20 2.24
4317 5019 7.263100 TGAGCATTGTAGTAATTATTGCAGG 57.737 36.000 0.00 0.00 0.00 4.85
4326 5028 9.839817 TGTAGTAATTATTGCAGGCAATTACTA 57.160 29.630 26.19 26.19 46.21 1.82
4350 5052 9.202273 CTAGATGCCACTTCTATAGATTTTGTC 57.798 37.037 2.58 0.00 0.00 3.18
4351 5053 7.800092 AGATGCCACTTCTATAGATTTTGTCT 58.200 34.615 2.58 0.00 41.11 3.41
4354 5056 7.268586 TGCCACTTCTATAGATTTTGTCTCTC 58.731 38.462 2.58 0.00 38.42 3.20
4355 5057 7.093333 TGCCACTTCTATAGATTTTGTCTCTCA 60.093 37.037 2.58 0.00 38.42 3.27
4356 5058 7.223777 GCCACTTCTATAGATTTTGTCTCTCAC 59.776 40.741 2.58 0.00 38.42 3.51
4357 5059 8.474025 CCACTTCTATAGATTTTGTCTCTCACT 58.526 37.037 2.58 0.00 38.42 3.41
4358 5060 9.515020 CACTTCTATAGATTTTGTCTCTCACTC 57.485 37.037 2.58 0.00 38.42 3.51
4359 5061 9.474313 ACTTCTATAGATTTTGTCTCTCACTCT 57.526 33.333 2.58 0.00 38.42 3.24
4362 5064 8.194104 TCTATAGATTTTGTCTCTCACTCTTGC 58.806 37.037 0.00 0.00 38.42 4.01
4399 5101 8.932610 ACTCACTGAGGATGTATTAGATCAAAT 58.067 33.333 10.86 0.00 33.35 2.32
4562 5264 3.750501 AAATTAAATCCCCTCCGGTGT 57.249 42.857 0.00 0.00 0.00 4.16
4660 5363 5.172934 TCATTGATTTGAAGCATTTCAGCC 58.827 37.500 0.00 0.00 43.76 4.85
4664 5367 4.281435 TGATTTGAAGCATTTCAGCCTTGA 59.719 37.500 0.00 0.00 43.76 3.02
5006 5714 2.543653 GGCAATTGTCGCAAAGTCTTGT 60.544 45.455 7.40 0.00 34.79 3.16
5093 5801 8.049721 CCCTTGAAAGTGGTAAGAGAAGATAAT 58.950 37.037 0.00 0.00 0.00 1.28
5216 5924 8.408601 CCTTCAAGGGATGATAACATGTTTAAG 58.591 37.037 17.78 0.00 38.03 1.85
5240 5948 4.272018 CGGTCAGAGACAATCAAATCATCC 59.728 45.833 0.00 0.00 33.68 3.51
5243 5951 3.003068 CAGAGACAATCAAATCATCCGGC 59.997 47.826 0.00 0.00 0.00 6.13
5371 6079 3.005367 TCTTTTTGCGATCCTTTGGGTTC 59.995 43.478 0.00 0.00 0.00 3.62
5484 6192 0.815213 TTCGCAAGCAGCAGACTGTT 60.815 50.000 3.99 0.00 46.30 3.16
5525 6233 1.073923 GGGTTGGAATGTGAGGTGAGT 59.926 52.381 0.00 0.00 0.00 3.41
5527 6235 1.537202 GTTGGAATGTGAGGTGAGTGC 59.463 52.381 0.00 0.00 0.00 4.40
5686 6399 6.623486 TCCTGCTGTAATTGATTGTTTCATG 58.377 36.000 0.00 0.00 33.34 3.07
5841 6568 2.278332 AGACCTGAGAAAAGGCCAAC 57.722 50.000 5.01 0.00 41.46 3.77
5850 6577 2.036346 AGAAAAGGCCAACTTGTGATGC 59.964 45.455 5.01 0.00 39.96 3.91
5885 6612 2.041701 AGGCCAAAACTGCAAATGTCT 58.958 42.857 5.01 0.00 0.00 3.41
5895 6622 3.117794 CTGCAAATGTCTGTTTGTGGTG 58.882 45.455 0.00 0.00 40.38 4.17
5939 6666 1.382522 AGCGGGATTGCTGTAATGTG 58.617 50.000 0.00 0.00 45.28 3.21
6096 6826 8.900511 TTTCTCTTCTGCATTTTCAAATATCG 57.099 30.769 0.00 0.00 0.00 2.92
6108 6838 4.316205 TCAAATATCGTCCATACTGCGT 57.684 40.909 0.00 0.00 0.00 5.24
6114 6844 1.078426 GTCCATACTGCGTGGGCTT 60.078 57.895 0.00 0.00 38.32 4.35
6126 6856 4.496336 GGGCTTGGGCTCAGCGAT 62.496 66.667 0.00 0.00 39.12 4.58
6127 6857 3.207669 GGCTTGGGCTCAGCGATG 61.208 66.667 0.00 0.00 38.73 3.84
6128 6858 2.124983 GCTTGGGCTCAGCGATGA 60.125 61.111 2.19 2.19 35.22 2.92
6129 6859 1.746615 GCTTGGGCTCAGCGATGAA 60.747 57.895 4.32 0.00 35.22 2.57
6130 6860 1.712977 GCTTGGGCTCAGCGATGAAG 61.713 60.000 4.32 0.00 35.22 3.02
6131 6861 0.392193 CTTGGGCTCAGCGATGAAGT 60.392 55.000 4.32 0.00 0.00 3.01
6132 6862 0.901827 TTGGGCTCAGCGATGAAGTA 59.098 50.000 4.32 0.00 0.00 2.24
6133 6863 0.901827 TGGGCTCAGCGATGAAGTAA 59.098 50.000 4.32 0.00 0.00 2.24
6134 6864 1.486310 TGGGCTCAGCGATGAAGTAAT 59.514 47.619 4.32 0.00 0.00 1.89
6135 6865 1.869767 GGGCTCAGCGATGAAGTAATG 59.130 52.381 4.32 0.00 0.00 1.90
6136 6866 2.555199 GGCTCAGCGATGAAGTAATGT 58.445 47.619 4.32 0.00 0.00 2.71
6137 6867 3.492656 GGGCTCAGCGATGAAGTAATGTA 60.493 47.826 4.32 0.00 0.00 2.29
6138 6868 3.491267 GGCTCAGCGATGAAGTAATGTAC 59.509 47.826 4.32 0.00 0.00 2.90
6139 6869 4.112634 GCTCAGCGATGAAGTAATGTACA 58.887 43.478 4.32 0.00 0.00 2.90
6140 6870 4.026475 GCTCAGCGATGAAGTAATGTACAC 60.026 45.833 4.32 0.00 0.00 2.90
6141 6871 5.324784 TCAGCGATGAAGTAATGTACACT 57.675 39.130 0.00 0.00 0.00 3.55
6142 6872 5.102313 TCAGCGATGAAGTAATGTACACTG 58.898 41.667 0.00 0.00 0.00 3.66
6143 6873 4.864806 CAGCGATGAAGTAATGTACACTGT 59.135 41.667 0.00 0.00 0.00 3.55
6144 6874 4.864806 AGCGATGAAGTAATGTACACTGTG 59.135 41.667 6.19 6.19 0.00 3.66
6145 6875 4.862574 GCGATGAAGTAATGTACACTGTGA 59.137 41.667 15.86 0.00 0.00 3.58
6146 6876 5.004821 GCGATGAAGTAATGTACACTGTGAG 59.995 44.000 15.86 0.00 0.00 3.51
6147 6877 6.322491 CGATGAAGTAATGTACACTGTGAGA 58.678 40.000 15.86 0.00 0.00 3.27
6148 6878 6.806739 CGATGAAGTAATGTACACTGTGAGAA 59.193 38.462 15.86 0.00 0.00 2.87
6149 6879 7.201359 CGATGAAGTAATGTACACTGTGAGAAC 60.201 40.741 15.86 9.84 0.00 3.01
6150 6880 6.811954 TGAAGTAATGTACACTGTGAGAACA 58.188 36.000 15.86 14.85 0.00 3.18
6151 6881 6.700081 TGAAGTAATGTACACTGTGAGAACAC 59.300 38.462 15.86 5.14 46.09 3.32
6164 6894 5.136250 GTGAGAACACATGAATCGCTTAG 57.864 43.478 0.00 0.00 45.32 2.18
6165 6895 4.627467 GTGAGAACACATGAATCGCTTAGT 59.373 41.667 0.00 0.00 45.32 2.24
6166 6896 5.805486 GTGAGAACACATGAATCGCTTAGTA 59.195 40.000 0.00 0.00 45.32 1.82
6167 6897 5.805486 TGAGAACACATGAATCGCTTAGTAC 59.195 40.000 0.00 0.00 0.00 2.73
6168 6898 5.109903 AGAACACATGAATCGCTTAGTACC 58.890 41.667 0.00 0.00 0.00 3.34
6169 6899 4.465632 ACACATGAATCGCTTAGTACCA 57.534 40.909 0.00 0.00 0.00 3.25
6170 6900 4.181578 ACACATGAATCGCTTAGTACCAC 58.818 43.478 0.00 0.00 0.00 4.16
6171 6901 4.180817 CACATGAATCGCTTAGTACCACA 58.819 43.478 0.00 0.00 0.00 4.17
6172 6902 4.629634 CACATGAATCGCTTAGTACCACAA 59.370 41.667 0.00 0.00 0.00 3.33
6173 6903 5.294306 CACATGAATCGCTTAGTACCACAAT 59.706 40.000 0.00 0.00 0.00 2.71
6174 6904 5.294306 ACATGAATCGCTTAGTACCACAATG 59.706 40.000 0.00 0.00 0.00 2.82
6175 6905 3.621268 TGAATCGCTTAGTACCACAATGC 59.379 43.478 0.00 0.00 0.00 3.56
6176 6906 2.018542 TCGCTTAGTACCACAATGCC 57.981 50.000 0.00 0.00 0.00 4.40
6177 6907 1.276705 TCGCTTAGTACCACAATGCCA 59.723 47.619 0.00 0.00 0.00 4.92
6178 6908 2.080693 CGCTTAGTACCACAATGCCAA 58.919 47.619 0.00 0.00 0.00 4.52
6179 6909 2.682856 CGCTTAGTACCACAATGCCAAT 59.317 45.455 0.00 0.00 0.00 3.16
6180 6910 3.242739 CGCTTAGTACCACAATGCCAATC 60.243 47.826 0.00 0.00 0.00 2.67
6181 6911 3.694072 GCTTAGTACCACAATGCCAATCA 59.306 43.478 0.00 0.00 0.00 2.57
6182 6912 4.157656 GCTTAGTACCACAATGCCAATCAA 59.842 41.667 0.00 0.00 0.00 2.57
6183 6913 5.637006 TTAGTACCACAATGCCAATCAAC 57.363 39.130 0.00 0.00 0.00 3.18
6184 6914 2.825532 AGTACCACAATGCCAATCAACC 59.174 45.455 0.00 0.00 0.00 3.77
6185 6915 2.014010 ACCACAATGCCAATCAACCT 57.986 45.000 0.00 0.00 0.00 3.50
6186 6916 3.168035 ACCACAATGCCAATCAACCTA 57.832 42.857 0.00 0.00 0.00 3.08
6187 6917 3.505386 ACCACAATGCCAATCAACCTAA 58.495 40.909 0.00 0.00 0.00 2.69
6188 6918 3.900601 ACCACAATGCCAATCAACCTAAA 59.099 39.130 0.00 0.00 0.00 1.85
6189 6919 4.531732 ACCACAATGCCAATCAACCTAAAT 59.468 37.500 0.00 0.00 0.00 1.40
6190 6920 5.012975 ACCACAATGCCAATCAACCTAAATT 59.987 36.000 0.00 0.00 0.00 1.82
6191 6921 5.939296 CCACAATGCCAATCAACCTAAATTT 59.061 36.000 0.00 0.00 0.00 1.82
6192 6922 6.430616 CCACAATGCCAATCAACCTAAATTTT 59.569 34.615 0.00 0.00 0.00 1.82
6193 6923 7.605691 CCACAATGCCAATCAACCTAAATTTTA 59.394 33.333 0.00 0.00 0.00 1.52
6194 6924 8.997323 CACAATGCCAATCAACCTAAATTTTAA 58.003 29.630 0.00 0.00 0.00 1.52
6195 6925 9.566432 ACAATGCCAATCAACCTAAATTTTAAA 57.434 25.926 0.00 0.00 0.00 1.52
6198 6928 8.964476 TGCCAATCAACCTAAATTTTAAAACA 57.036 26.923 1.97 0.00 0.00 2.83
6199 6929 9.050601 TGCCAATCAACCTAAATTTTAAAACAG 57.949 29.630 1.97 1.37 0.00 3.16
6200 6930 9.051679 GCCAATCAACCTAAATTTTAAAACAGT 57.948 29.630 1.97 0.00 0.00 3.55
6215 6945 9.621629 TTTTAAAACAGTTGAAGATAGGAGACA 57.378 29.630 0.00 0.00 0.00 3.41
6216 6946 9.793259 TTTAAAACAGTTGAAGATAGGAGACAT 57.207 29.630 0.00 0.00 0.00 3.06
6217 6947 7.678947 AAAACAGTTGAAGATAGGAGACATG 57.321 36.000 0.00 0.00 0.00 3.21
6218 6948 6.365970 AACAGTTGAAGATAGGAGACATGT 57.634 37.500 0.00 0.00 0.00 3.21
6219 6949 6.365970 ACAGTTGAAGATAGGAGACATGTT 57.634 37.500 0.00 0.00 0.00 2.71
6220 6950 6.402222 ACAGTTGAAGATAGGAGACATGTTC 58.598 40.000 0.00 0.00 0.00 3.18
6221 6951 6.014242 ACAGTTGAAGATAGGAGACATGTTCA 60.014 38.462 0.00 0.00 34.82 3.18
6222 6952 7.046652 CAGTTGAAGATAGGAGACATGTTCAT 58.953 38.462 0.00 0.10 36.09 2.57
6223 6953 8.200120 CAGTTGAAGATAGGAGACATGTTCATA 58.800 37.037 0.00 2.49 36.09 2.15
6224 6954 8.762645 AGTTGAAGATAGGAGACATGTTCATAA 58.237 33.333 0.00 0.00 36.09 1.90
6225 6955 9.383519 GTTGAAGATAGGAGACATGTTCATAAA 57.616 33.333 0.00 0.00 36.09 1.40
6226 6956 9.958180 TTGAAGATAGGAGACATGTTCATAAAA 57.042 29.630 0.00 0.00 36.09 1.52
6227 6957 9.383519 TGAAGATAGGAGACATGTTCATAAAAC 57.616 33.333 0.00 0.05 32.52 2.43
6228 6958 9.383519 GAAGATAGGAGACATGTTCATAAAACA 57.616 33.333 0.00 0.00 34.31 2.83
6229 6959 8.954950 AGATAGGAGACATGTTCATAAAACAG 57.045 34.615 0.00 0.00 33.18 3.16
6230 6960 8.543774 AGATAGGAGACATGTTCATAAAACAGT 58.456 33.333 0.00 0.00 33.18 3.55
6231 6961 9.167311 GATAGGAGACATGTTCATAAAACAGTT 57.833 33.333 0.00 0.00 33.18 3.16
6232 6962 7.206981 AGGAGACATGTTCATAAAACAGTTG 57.793 36.000 0.00 0.00 33.18 3.16
6233 6963 6.998074 AGGAGACATGTTCATAAAACAGTTGA 59.002 34.615 0.00 0.00 33.18 3.18
6234 6964 7.502226 AGGAGACATGTTCATAAAACAGTTGAA 59.498 33.333 0.00 0.00 33.18 2.69
6235 6965 7.805071 GGAGACATGTTCATAAAACAGTTGAAG 59.195 37.037 0.00 0.00 33.18 3.02
6236 6966 8.450578 AGACATGTTCATAAAACAGTTGAAGA 57.549 30.769 0.00 0.00 33.18 2.87
6237 6967 9.071276 AGACATGTTCATAAAACAGTTGAAGAT 57.929 29.630 0.00 0.00 34.72 2.40
6240 6970 8.908678 CATGTTCATAAAACAGTTGAAGATGTG 58.091 33.333 11.93 0.00 42.04 3.21
6241 6971 8.219546 TGTTCATAAAACAGTTGAAGATGTGA 57.780 30.769 0.00 0.00 30.50 3.58
6242 6972 8.344831 TGTTCATAAAACAGTTGAAGATGTGAG 58.655 33.333 0.00 0.00 30.50 3.51
6243 6973 8.559536 GTTCATAAAACAGTTGAAGATGTGAGA 58.440 33.333 0.00 0.00 30.50 3.27
6244 6974 8.853077 TCATAAAACAGTTGAAGATGTGAGAT 57.147 30.769 0.00 0.00 0.00 2.75
6245 6975 9.942850 TCATAAAACAGTTGAAGATGTGAGATA 57.057 29.630 0.00 0.00 0.00 1.98
6248 6978 8.627208 AAAACAGTTGAAGATGTGAGATATGT 57.373 30.769 0.00 0.00 0.00 2.29
6249 6979 8.627208 AAACAGTTGAAGATGTGAGATATGTT 57.373 30.769 0.00 0.00 0.00 2.71
6250 6980 7.840342 ACAGTTGAAGATGTGAGATATGTTC 57.160 36.000 0.00 0.00 0.00 3.18
6251 6981 7.619050 ACAGTTGAAGATGTGAGATATGTTCT 58.381 34.615 0.00 0.00 37.41 3.01
6252 6982 8.099537 ACAGTTGAAGATGTGAGATATGTTCTT 58.900 33.333 0.00 0.00 33.74 2.52
6253 6983 9.591792 CAGTTGAAGATGTGAGATATGTTCTTA 57.408 33.333 0.00 0.00 33.74 2.10
6282 7012 9.703892 AAGAACAAAGATATATCTTCAGATCGG 57.296 33.333 24.75 12.54 45.83 4.18
6283 7013 8.310382 AGAACAAAGATATATCTTCAGATCGGG 58.690 37.037 24.75 11.47 45.83 5.14
6284 7014 6.940739 ACAAAGATATATCTTCAGATCGGGG 58.059 40.000 24.75 10.66 45.83 5.73
6285 7015 6.498651 ACAAAGATATATCTTCAGATCGGGGT 59.501 38.462 24.75 11.14 45.83 4.95
6286 7016 6.783708 AAGATATATCTTCAGATCGGGGTC 57.216 41.667 20.20 0.00 43.27 4.46
6287 7017 5.205056 AGATATATCTTCAGATCGGGGTCC 58.795 45.833 9.57 0.00 36.05 4.46
6288 7018 2.767644 TATCTTCAGATCGGGGTCCA 57.232 50.000 0.00 0.00 36.05 4.02
6289 7019 2.109229 ATCTTCAGATCGGGGTCCAT 57.891 50.000 0.00 0.00 0.00 3.41
6290 7020 2.767644 TCTTCAGATCGGGGTCCATA 57.232 50.000 0.00 0.00 0.00 2.74
6291 7021 2.598565 TCTTCAGATCGGGGTCCATAG 58.401 52.381 0.00 0.00 0.00 2.23
6292 7022 1.620819 CTTCAGATCGGGGTCCATAGG 59.379 57.143 0.00 0.00 0.00 2.57
6293 7023 0.857675 TCAGATCGGGGTCCATAGGA 59.142 55.000 0.00 0.00 0.00 2.94
6294 7024 1.203063 TCAGATCGGGGTCCATAGGAG 60.203 57.143 0.00 0.00 29.39 3.69
6295 7025 0.115349 AGATCGGGGTCCATAGGAGG 59.885 60.000 0.00 0.00 29.39 4.30
6296 7026 0.114560 GATCGGGGTCCATAGGAGGA 59.885 60.000 0.00 0.00 34.64 3.71
6297 7027 0.793617 ATCGGGGTCCATAGGAGGAT 59.206 55.000 0.00 0.00 40.42 3.24
6298 7028 0.114560 TCGGGGTCCATAGGAGGATC 59.885 60.000 0.00 0.00 40.42 3.36
6299 7029 0.115349 CGGGGTCCATAGGAGGATCT 59.885 60.000 0.00 0.00 40.42 2.75
6300 7030 1.650528 GGGGTCCATAGGAGGATCTG 58.349 60.000 0.00 0.00 40.42 2.90
6301 7031 0.980423 GGGTCCATAGGAGGATCTGC 59.020 60.000 0.00 0.00 40.42 4.26
6302 7032 0.605589 GGTCCATAGGAGGATCTGCG 59.394 60.000 0.00 0.00 40.42 5.18
6303 7033 0.037790 GTCCATAGGAGGATCTGCGC 60.038 60.000 0.00 0.00 40.42 6.09
6304 7034 0.178950 TCCATAGGAGGATCTGCGCT 60.179 55.000 9.73 0.00 33.73 5.92
6305 7035 0.246086 CCATAGGAGGATCTGCGCTC 59.754 60.000 9.73 0.00 33.73 5.03
6306 7036 0.964700 CATAGGAGGATCTGCGCTCA 59.035 55.000 9.73 0.00 33.73 4.26
6307 7037 1.549620 CATAGGAGGATCTGCGCTCAT 59.450 52.381 9.73 0.00 33.73 2.90
6308 7038 0.964700 TAGGAGGATCTGCGCTCATG 59.035 55.000 9.73 0.00 33.73 3.07
6309 7039 1.960250 GGAGGATCTGCGCTCATGC 60.960 63.158 9.73 5.70 33.73 4.06
6310 7040 1.227468 GAGGATCTGCGCTCATGCA 60.227 57.895 9.73 0.00 43.95 3.96
6319 7049 3.200593 GCTCATGCAGTGGCGGAG 61.201 66.667 0.00 0.00 45.35 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 156 4.742201 CTCCTGTCCACCACGGCG 62.742 72.222 4.80 4.80 33.14 6.46
149 157 2.391724 TTTCTCCTGTCCACCACGGC 62.392 60.000 0.00 0.00 33.14 5.68
150 158 0.602905 GTTTCTCCTGTCCACCACGG 60.603 60.000 0.00 0.00 0.00 4.94
151 159 0.105964 TGTTTCTCCTGTCCACCACG 59.894 55.000 0.00 0.00 0.00 4.94
152 160 2.341846 TTGTTTCTCCTGTCCACCAC 57.658 50.000 0.00 0.00 0.00 4.16
153 161 3.020984 GTTTTGTTTCTCCTGTCCACCA 58.979 45.455 0.00 0.00 0.00 4.17
154 162 3.020984 TGTTTTGTTTCTCCTGTCCACC 58.979 45.455 0.00 0.00 0.00 4.61
155 163 4.338118 TGATGTTTTGTTTCTCCTGTCCAC 59.662 41.667 0.00 0.00 0.00 4.02
253 273 3.655810 AAGCAAGCGAGCGAGGGAG 62.656 63.158 0.00 0.00 40.15 4.30
254 274 3.695606 AAGCAAGCGAGCGAGGGA 61.696 61.111 0.00 0.00 40.15 4.20
255 275 3.494336 CAAGCAAGCGAGCGAGGG 61.494 66.667 0.00 0.00 40.15 4.30
256 276 2.433145 TCAAGCAAGCGAGCGAGG 60.433 61.111 0.00 0.00 40.15 4.63
257 277 2.734673 GGTCAAGCAAGCGAGCGAG 61.735 63.158 0.00 0.00 40.15 5.03
258 278 2.738521 GGTCAAGCAAGCGAGCGA 60.739 61.111 0.00 0.00 40.15 4.93
259 279 4.139420 CGGTCAAGCAAGCGAGCG 62.139 66.667 7.04 7.04 45.25 5.03
260 280 3.793144 CCGGTCAAGCAAGCGAGC 61.793 66.667 0.00 0.00 42.48 5.03
261 281 3.121030 CCCGGTCAAGCAAGCGAG 61.121 66.667 0.00 0.00 42.48 5.03
286 306 0.234884 CGACTGGTTTCGGTTTCAGC 59.765 55.000 0.00 0.00 35.26 4.26
354 381 0.106217 CAGGTGGGTTTGGTGAGGTT 60.106 55.000 0.00 0.00 0.00 3.50
398 425 1.447317 CTGTTGCCTTGCCACGTCTT 61.447 55.000 0.00 0.00 0.00 3.01
488 770 0.399376 GTGGGGAGGGGTTTTGGTTT 60.399 55.000 0.00 0.00 0.00 3.27
547 829 1.139853 CTAACAGGAGGGAGATGTGGC 59.860 57.143 0.00 0.00 0.00 5.01
548 830 2.432510 GACTAACAGGAGGGAGATGTGG 59.567 54.545 0.00 0.00 0.00 4.17
549 831 3.370104 AGACTAACAGGAGGGAGATGTG 58.630 50.000 0.00 0.00 0.00 3.21
550 832 3.628769 GGAGACTAACAGGAGGGAGATGT 60.629 52.174 0.00 0.00 0.00 3.06
567 849 1.000612 AGACGGGGAAGAGGGAGAC 59.999 63.158 0.00 0.00 0.00 3.36
648 944 3.611674 CAAAACCCCACGCACCCC 61.612 66.667 0.00 0.00 0.00 4.95
652 948 4.531426 AGCCCAAAACCCCACGCA 62.531 61.111 0.00 0.00 0.00 5.24
658 954 2.112815 CGATCCGAGCCCAAAACCC 61.113 63.158 0.00 0.00 0.00 4.11
984 1297 3.083997 ATCACCACCTCCTCCCGC 61.084 66.667 0.00 0.00 0.00 6.13
985 1298 1.050988 ATCATCACCACCTCCTCCCG 61.051 60.000 0.00 0.00 0.00 5.14
986 1299 0.471617 CATCATCACCACCTCCTCCC 59.528 60.000 0.00 0.00 0.00 4.30
991 1304 2.540515 CGTGTACATCATCACCACCTC 58.459 52.381 0.00 0.00 0.00 3.85
992 1305 1.405526 GCGTGTACATCATCACCACCT 60.406 52.381 0.00 0.00 0.00 4.00
1450 1778 3.741476 GTTGCTGAGCCCCGCAAG 61.741 66.667 0.23 0.00 45.68 4.01
1543 1871 2.620886 CGGAGAGGTTGAGAGTCCCTAA 60.621 54.545 0.00 0.00 0.00 2.69
1736 2064 1.534235 AGCTGACGGAAGGTGTCCT 60.534 57.895 0.00 0.00 45.36 3.85
1769 2097 2.867109 ATTCCCAGAGATATTGGCCG 57.133 50.000 0.00 0.00 34.26 6.13
1819 2147 1.073923 AGAGGACACATTTCCACCACC 59.926 52.381 0.00 0.00 38.25 4.61
1820 2148 2.154462 CAGAGGACACATTTCCACCAC 58.846 52.381 0.00 0.00 38.25 4.16
1821 2149 2.038952 CTCAGAGGACACATTTCCACCA 59.961 50.000 0.00 0.00 38.25 4.17
1896 2224 0.179045 GTCCACGCCCAGCATAGAAT 60.179 55.000 0.00 0.00 0.00 2.40
1969 2297 3.417069 TCCATTCTTCTTTTCAGGCGA 57.583 42.857 0.00 0.00 0.00 5.54
2083 2414 2.024273 CACTCCTACCCCTCCTAGAACA 60.024 54.545 0.00 0.00 0.00 3.18
2220 2551 5.015515 TGGTCATAAGCAAATGAATCACCA 58.984 37.500 2.87 4.57 37.61 4.17
2412 2743 2.105766 AGCCTTTCATGCAATCCCTTC 58.894 47.619 0.00 0.00 0.00 3.46
2469 2800 6.360370 AACCTATACACAAGAAGCTTCTCA 57.640 37.500 28.58 12.29 36.28 3.27
2741 3073 5.059833 AGTTTGACTTGGACAAAGCTAGAG 58.940 41.667 0.00 0.00 39.76 2.43
2772 3105 8.783093 CACATTTTCACATAGACTTGGTAAGAA 58.217 33.333 0.00 0.00 0.00 2.52
2776 3109 6.237901 AGCACATTTTCACATAGACTTGGTA 58.762 36.000 0.00 0.00 0.00 3.25
2839 3172 8.860088 AGTTTTAGCATTGTCCTAAATTTGACT 58.140 29.630 0.00 0.00 35.42 3.41
2909 3245 7.596749 AGATAAAAGATCACAAACCTGTACG 57.403 36.000 0.00 0.00 33.22 3.67
2982 3319 1.187567 GGAATGTTGGGCCAGCACTT 61.188 55.000 25.99 19.09 0.00 3.16
3085 3422 2.487086 CCAGTTCTGTTGGGACACATGA 60.487 50.000 0.00 0.00 39.29 3.07
3089 3426 1.134220 TCACCAGTTCTGTTGGGACAC 60.134 52.381 0.00 0.00 39.29 3.67
3103 3440 3.449018 AGTGTATTCCTAGCTGTCACCAG 59.551 47.826 0.00 0.00 41.91 4.00
3139 3476 4.823989 AGCAATATCCAGTCCATTAAGTGC 59.176 41.667 0.00 0.00 0.00 4.40
3191 3528 2.198304 ATTCGGGCAAGGGACAGGAC 62.198 60.000 0.00 0.00 0.00 3.85
3198 3535 3.669251 TTTTTGTTATTCGGGCAAGGG 57.331 42.857 0.00 0.00 0.00 3.95
3263 3600 5.640732 GACAGCGAAAATTATGTCCAACAT 58.359 37.500 0.00 0.00 42.35 2.71
3313 3650 8.325282 GGAAAACGCCTAAAAATGTTAATATGC 58.675 33.333 0.00 0.00 0.00 3.14
3314 3651 9.581099 AGGAAAACGCCTAAAAATGTTAATATG 57.419 29.630 0.00 0.00 36.22 1.78
3317 3654 7.601130 GGAAGGAAAACGCCTAAAAATGTTAAT 59.399 33.333 0.00 0.00 37.26 1.40
3321 3658 4.342665 TGGAAGGAAAACGCCTAAAAATGT 59.657 37.500 0.00 0.00 37.26 2.71
3324 3661 6.651975 TTATGGAAGGAAAACGCCTAAAAA 57.348 33.333 0.00 0.00 37.26 1.94
3325 3662 6.651975 TTTATGGAAGGAAAACGCCTAAAA 57.348 33.333 0.00 0.00 37.26 1.52
3326 3663 6.651975 TTTTATGGAAGGAAAACGCCTAAA 57.348 33.333 0.00 0.00 37.26 1.85
3327 3664 6.040616 TGTTTTTATGGAAGGAAAACGCCTAA 59.959 34.615 0.00 0.00 42.94 2.69
3328 3665 5.535406 TGTTTTTATGGAAGGAAAACGCCTA 59.465 36.000 0.00 0.00 42.94 3.93
3329 3666 4.342665 TGTTTTTATGGAAGGAAAACGCCT 59.657 37.500 0.00 0.00 42.94 5.52
3330 3667 4.623002 TGTTTTTATGGAAGGAAAACGCC 58.377 39.130 0.00 0.00 42.94 5.68
3331 3668 6.591313 TTTGTTTTTATGGAAGGAAAACGC 57.409 33.333 0.00 0.00 42.94 4.84
3332 3669 8.279800 GGAATTTGTTTTTATGGAAGGAAAACG 58.720 33.333 0.00 0.00 42.94 3.60
3457 4126 9.520204 CACAAACAAGAAAATGACTGAAGTAAT 57.480 29.630 0.00 0.00 0.00 1.89
3464 4133 7.420002 TGATCTCACAAACAAGAAAATGACTG 58.580 34.615 0.00 0.00 0.00 3.51
3468 4137 9.850628 ATGTATGATCTCACAAACAAGAAAATG 57.149 29.630 4.41 0.00 0.00 2.32
3586 4257 6.032094 CCTGGTGAAATGAATGAGAAAATCG 58.968 40.000 0.00 0.00 0.00 3.34
3590 4261 5.832595 TGTTCCTGGTGAAATGAATGAGAAA 59.167 36.000 0.00 0.00 33.94 2.52
3636 4308 6.331369 TCTCTCATGATCATATTGTGCGTA 57.669 37.500 8.15 0.00 0.00 4.42
3647 4319 7.594351 ACAGCTAGTATTTCTCTCATGATCA 57.406 36.000 0.00 0.00 0.00 2.92
3776 4450 2.158667 TGGTGACTTTCCCCTTCTTGAC 60.159 50.000 0.00 0.00 0.00 3.18
3978 4656 4.272489 AGCATAATTTACAGGCTTGAGCA 58.728 39.130 1.40 0.00 44.36 4.26
4061 4758 5.135383 GGGACATGATCAATTGAAGATGGA 58.865 41.667 23.70 5.05 0.00 3.41
4317 5019 8.307483 TCTATAGAAGTGGCATCTAGTAATTGC 58.693 37.037 0.00 0.00 33.17 3.56
4326 5028 7.800092 AGACAAAATCTATAGAAGTGGCATCT 58.200 34.615 6.52 2.09 35.15 2.90
4339 5041 6.112058 GGCAAGAGTGAGAGACAAAATCTAT 58.888 40.000 0.00 0.00 38.00 1.98
4348 5050 1.892474 AGAGTGGCAAGAGTGAGAGAC 59.108 52.381 0.00 0.00 0.00 3.36
4350 5052 2.612471 CCAAGAGTGGCAAGAGTGAGAG 60.612 54.545 0.00 0.00 38.35 3.20
4351 5053 1.345741 CCAAGAGTGGCAAGAGTGAGA 59.654 52.381 0.00 0.00 38.35 3.27
4371 5073 5.521906 TCTAATACATCCTCAGTGAGTGC 57.478 43.478 18.74 0.00 0.00 4.40
4476 5178 6.919721 TGGTGACAACTGAAAAATATTAGGC 58.080 36.000 0.00 0.00 37.44 3.93
4562 5264 7.330900 TCCCAGAAAACAATACAACGTTAAA 57.669 32.000 0.00 0.00 0.00 1.52
4660 5363 9.646427 GCCTAAACTAGAGGATATATTGTCAAG 57.354 37.037 0.00 0.00 35.99 3.02
4664 5367 7.023120 TGGGCCTAAACTAGAGGATATATTGT 58.977 38.462 4.53 0.00 35.99 2.71
5006 5714 4.927425 CGTTTCGAAGACCTAGGATTCAAA 59.073 41.667 17.98 16.45 34.32 2.69
5216 5924 3.002791 TGATTTGATTGTCTCTGACCGC 58.997 45.455 0.00 0.00 0.00 5.68
5240 5948 4.776322 TCACCATTGCTCCCGCCG 62.776 66.667 0.00 0.00 34.43 6.46
5243 5951 1.605710 GAATGATCACCATTGCTCCCG 59.394 52.381 0.00 0.00 45.00 5.14
5348 6056 3.165071 ACCCAAAGGATCGCAAAAAGAT 58.835 40.909 0.00 0.00 36.73 2.40
5503 6211 0.112218 CACCTCACATTCCAACCCCA 59.888 55.000 0.00 0.00 0.00 4.96
5525 6233 1.411246 GTATACACCGACCTCCATGCA 59.589 52.381 0.00 0.00 0.00 3.96
5527 6235 1.343465 GGGTATACACCGACCTCCATG 59.657 57.143 5.01 0.00 46.86 3.66
5686 6399 6.092748 ACGAACATTTTTGCTATGATCAACC 58.907 36.000 0.00 0.00 0.00 3.77
5789 6511 0.868406 GCACGGTGTTTTCTCTCCAG 59.132 55.000 10.24 0.00 0.00 3.86
5841 6568 1.202533 CCGGTAGGTAGGCATCACAAG 60.203 57.143 0.00 0.00 0.00 3.16
5850 6577 0.179702 GGCCTTTTCCGGTAGGTAGG 59.820 60.000 17.28 12.05 39.05 3.18
5885 6612 2.122167 GGCCGGAACACCACAAACA 61.122 57.895 5.05 0.00 0.00 2.83
6047 6777 1.413118 AAAGGTTCTTTGCCCAGTGG 58.587 50.000 0.63 0.63 0.00 4.00
6072 6802 8.044060 ACGATATTTGAAAATGCAGAAGAGAA 57.956 30.769 0.00 0.00 0.00 2.87
6073 6803 7.201644 GGACGATATTTGAAAATGCAGAAGAGA 60.202 37.037 0.00 0.00 0.00 3.10
6074 6804 6.909357 GGACGATATTTGAAAATGCAGAAGAG 59.091 38.462 0.00 0.00 0.00 2.85
6075 6805 6.374053 TGGACGATATTTGAAAATGCAGAAGA 59.626 34.615 0.00 0.00 0.00 2.87
6076 6806 6.554419 TGGACGATATTTGAAAATGCAGAAG 58.446 36.000 0.00 0.00 0.00 2.85
6077 6807 6.507958 TGGACGATATTTGAAAATGCAGAA 57.492 33.333 0.00 0.00 0.00 3.02
6078 6808 6.698008 ATGGACGATATTTGAAAATGCAGA 57.302 33.333 0.00 0.00 0.00 4.26
6096 6826 1.078426 AAGCCCACGCAGTATGGAC 60.078 57.895 0.00 0.00 41.61 4.02
6114 6844 0.901827 TTACTTCATCGCTGAGCCCA 59.098 50.000 0.00 0.00 31.68 5.36
6121 6851 4.864806 CACAGTGTACATTACTTCATCGCT 59.135 41.667 0.00 0.00 0.00 4.93
6122 6852 4.862574 TCACAGTGTACATTACTTCATCGC 59.137 41.667 0.00 0.00 0.00 4.58
6123 6853 6.322491 TCTCACAGTGTACATTACTTCATCG 58.678 40.000 0.00 0.00 0.00 3.84
6124 6854 7.598869 TGTTCTCACAGTGTACATTACTTCATC 59.401 37.037 0.00 0.00 0.00 2.92
6125 6855 7.385205 GTGTTCTCACAGTGTACATTACTTCAT 59.615 37.037 0.00 0.00 43.37 2.57
6126 6856 6.700081 GTGTTCTCACAGTGTACATTACTTCA 59.300 38.462 0.00 0.00 43.37 3.02
6127 6857 7.106663 GTGTTCTCACAGTGTACATTACTTC 57.893 40.000 0.00 0.00 43.37 3.01
6142 6872 4.627467 ACTAAGCGATTCATGTGTTCTCAC 59.373 41.667 0.00 0.00 44.08 3.51
6143 6873 4.820897 ACTAAGCGATTCATGTGTTCTCA 58.179 39.130 0.00 0.00 0.00 3.27
6144 6874 5.232414 GGTACTAAGCGATTCATGTGTTCTC 59.768 44.000 0.00 0.00 0.00 2.87
6145 6875 5.109903 GGTACTAAGCGATTCATGTGTTCT 58.890 41.667 0.00 0.00 0.00 3.01
6146 6876 4.868171 TGGTACTAAGCGATTCATGTGTTC 59.132 41.667 0.00 0.00 0.00 3.18
6147 6877 4.630069 GTGGTACTAAGCGATTCATGTGTT 59.370 41.667 0.00 0.00 0.00 3.32
6148 6878 4.181578 GTGGTACTAAGCGATTCATGTGT 58.818 43.478 0.00 0.00 0.00 3.72
6149 6879 4.180817 TGTGGTACTAAGCGATTCATGTG 58.819 43.478 0.00 0.00 0.00 3.21
6150 6880 4.465632 TGTGGTACTAAGCGATTCATGT 57.534 40.909 0.00 0.00 0.00 3.21
6151 6881 5.741425 CATTGTGGTACTAAGCGATTCATG 58.259 41.667 0.00 0.00 0.00 3.07
6152 6882 4.273480 GCATTGTGGTACTAAGCGATTCAT 59.727 41.667 0.00 0.00 0.00 2.57
6153 6883 3.621268 GCATTGTGGTACTAAGCGATTCA 59.379 43.478 0.00 0.00 0.00 2.57
6154 6884 3.002348 GGCATTGTGGTACTAAGCGATTC 59.998 47.826 0.00 0.00 0.00 2.52
6155 6885 2.943033 GGCATTGTGGTACTAAGCGATT 59.057 45.455 0.00 0.00 0.00 3.34
6156 6886 2.093181 TGGCATTGTGGTACTAAGCGAT 60.093 45.455 0.00 0.00 0.00 4.58
6157 6887 1.276705 TGGCATTGTGGTACTAAGCGA 59.723 47.619 0.00 0.00 0.00 4.93
6158 6888 1.732941 TGGCATTGTGGTACTAAGCG 58.267 50.000 0.00 0.00 0.00 4.68
6159 6889 3.694072 TGATTGGCATTGTGGTACTAAGC 59.306 43.478 0.00 0.00 0.00 3.09
6160 6890 5.393027 GGTTGATTGGCATTGTGGTACTAAG 60.393 44.000 0.00 0.00 0.00 2.18
6161 6891 4.461081 GGTTGATTGGCATTGTGGTACTAA 59.539 41.667 0.00 0.00 0.00 2.24
6162 6892 4.013728 GGTTGATTGGCATTGTGGTACTA 58.986 43.478 0.00 0.00 0.00 1.82
6163 6893 2.825532 GGTTGATTGGCATTGTGGTACT 59.174 45.455 0.00 0.00 0.00 2.73
6164 6894 2.825532 AGGTTGATTGGCATTGTGGTAC 59.174 45.455 0.00 0.00 0.00 3.34
6165 6895 3.168035 AGGTTGATTGGCATTGTGGTA 57.832 42.857 0.00 0.00 0.00 3.25
6166 6896 2.014010 AGGTTGATTGGCATTGTGGT 57.986 45.000 0.00 0.00 0.00 4.16
6167 6897 4.533919 TTTAGGTTGATTGGCATTGTGG 57.466 40.909 0.00 0.00 0.00 4.17
6168 6898 7.437793 AAAATTTAGGTTGATTGGCATTGTG 57.562 32.000 0.00 0.00 0.00 3.33
6169 6899 9.566432 TTTAAAATTTAGGTTGATTGGCATTGT 57.434 25.926 0.00 0.00 0.00 2.71
6172 6902 9.566432 TGTTTTAAAATTTAGGTTGATTGGCAT 57.434 25.926 3.52 0.00 0.00 4.40
6173 6903 8.964476 TGTTTTAAAATTTAGGTTGATTGGCA 57.036 26.923 3.52 0.00 0.00 4.92
6174 6904 9.051679 ACTGTTTTAAAATTTAGGTTGATTGGC 57.948 29.630 3.52 0.00 0.00 4.52
6189 6919 9.621629 TGTCTCCTATCTTCAACTGTTTTAAAA 57.378 29.630 0.00 0.00 0.00 1.52
6190 6920 9.793259 ATGTCTCCTATCTTCAACTGTTTTAAA 57.207 29.630 0.00 0.00 0.00 1.52
6191 6921 9.219603 CATGTCTCCTATCTTCAACTGTTTTAA 57.780 33.333 0.00 0.00 0.00 1.52
6192 6922 8.375506 ACATGTCTCCTATCTTCAACTGTTTTA 58.624 33.333 0.00 0.00 0.00 1.52
6193 6923 7.227156 ACATGTCTCCTATCTTCAACTGTTTT 58.773 34.615 0.00 0.00 0.00 2.43
6194 6924 6.773638 ACATGTCTCCTATCTTCAACTGTTT 58.226 36.000 0.00 0.00 0.00 2.83
6195 6925 6.365970 ACATGTCTCCTATCTTCAACTGTT 57.634 37.500 0.00 0.00 0.00 3.16
6196 6926 6.014242 TGAACATGTCTCCTATCTTCAACTGT 60.014 38.462 0.00 0.00 0.00 3.55
6197 6927 6.401394 TGAACATGTCTCCTATCTTCAACTG 58.599 40.000 0.00 0.00 0.00 3.16
6198 6928 6.611613 TGAACATGTCTCCTATCTTCAACT 57.388 37.500 0.00 0.00 0.00 3.16
6199 6929 8.948631 TTATGAACATGTCTCCTATCTTCAAC 57.051 34.615 0.00 0.00 0.00 3.18
6200 6930 9.958180 TTTTATGAACATGTCTCCTATCTTCAA 57.042 29.630 0.00 0.00 0.00 2.69
6201 6931 9.383519 GTTTTATGAACATGTCTCCTATCTTCA 57.616 33.333 0.00 0.00 0.00 3.02
6202 6932 9.383519 TGTTTTATGAACATGTCTCCTATCTTC 57.616 33.333 0.00 0.00 0.00 2.87
6203 6933 9.388506 CTGTTTTATGAACATGTCTCCTATCTT 57.611 33.333 0.00 0.00 0.00 2.40
6204 6934 8.543774 ACTGTTTTATGAACATGTCTCCTATCT 58.456 33.333 0.00 0.00 0.00 1.98
6205 6935 8.723942 ACTGTTTTATGAACATGTCTCCTATC 57.276 34.615 0.00 0.00 0.00 2.08
6206 6936 8.950210 CAACTGTTTTATGAACATGTCTCCTAT 58.050 33.333 0.00 0.00 0.00 2.57
6207 6937 8.154203 TCAACTGTTTTATGAACATGTCTCCTA 58.846 33.333 0.00 0.00 0.00 2.94
6208 6938 6.998074 TCAACTGTTTTATGAACATGTCTCCT 59.002 34.615 0.00 0.00 0.00 3.69
6209 6939 7.202016 TCAACTGTTTTATGAACATGTCTCC 57.798 36.000 0.00 0.00 0.00 3.71
6210 6940 8.559536 TCTTCAACTGTTTTATGAACATGTCTC 58.440 33.333 0.00 0.00 0.00 3.36
6211 6941 8.450578 TCTTCAACTGTTTTATGAACATGTCT 57.549 30.769 0.00 0.00 0.00 3.41
6212 6942 9.121517 CATCTTCAACTGTTTTATGAACATGTC 57.878 33.333 0.00 0.00 29.99 3.06
6213 6943 8.632679 ACATCTTCAACTGTTTTATGAACATGT 58.367 29.630 7.56 7.56 37.65 3.21
6214 6944 8.908678 CACATCTTCAACTGTTTTATGAACATG 58.091 33.333 6.64 6.64 36.30 3.21
6215 6945 8.849168 TCACATCTTCAACTGTTTTATGAACAT 58.151 29.630 0.00 0.00 0.00 2.71
6216 6946 8.219546 TCACATCTTCAACTGTTTTATGAACA 57.780 30.769 0.00 0.00 0.00 3.18
6217 6947 8.559536 TCTCACATCTTCAACTGTTTTATGAAC 58.440 33.333 0.00 0.00 0.00 3.18
6218 6948 8.675705 TCTCACATCTTCAACTGTTTTATGAA 57.324 30.769 0.00 0.00 0.00 2.57
6219 6949 8.853077 ATCTCACATCTTCAACTGTTTTATGA 57.147 30.769 0.00 0.00 0.00 2.15
6222 6952 9.725019 ACATATCTCACATCTTCAACTGTTTTA 57.275 29.630 0.00 0.00 0.00 1.52
6223 6953 8.627208 ACATATCTCACATCTTCAACTGTTTT 57.373 30.769 0.00 0.00 0.00 2.43
6224 6954 8.627208 AACATATCTCACATCTTCAACTGTTT 57.373 30.769 0.00 0.00 0.00 2.83
6225 6955 8.099537 AGAACATATCTCACATCTTCAACTGTT 58.900 33.333 0.00 0.00 30.46 3.16
6226 6956 7.619050 AGAACATATCTCACATCTTCAACTGT 58.381 34.615 0.00 0.00 30.46 3.55
6227 6957 8.489990 AAGAACATATCTCACATCTTCAACTG 57.510 34.615 0.00 0.00 37.42 3.16
6256 6986 9.703892 CCGATCTGAAGATATATCTTTGTTCTT 57.296 33.333 25.21 11.28 46.47 2.52
6257 6987 8.310382 CCCGATCTGAAGATATATCTTTGTTCT 58.690 37.037 25.21 12.01 46.47 3.01
6258 6988 7.547370 CCCCGATCTGAAGATATATCTTTGTTC 59.453 40.741 25.21 21.09 46.47 3.18
6259 6989 7.016661 ACCCCGATCTGAAGATATATCTTTGTT 59.983 37.037 25.21 16.65 46.47 2.83
6260 6990 6.498651 ACCCCGATCTGAAGATATATCTTTGT 59.501 38.462 25.21 13.59 46.47 2.83
6261 6991 6.940739 ACCCCGATCTGAAGATATATCTTTG 58.059 40.000 25.21 20.40 46.47 2.77
6262 6992 6.155393 GGACCCCGATCTGAAGATATATCTTT 59.845 42.308 25.21 12.25 46.47 2.52
6264 6994 5.205056 GGACCCCGATCTGAAGATATATCT 58.795 45.833 9.57 9.57 39.22 1.98
6265 6995 4.956700 TGGACCCCGATCTGAAGATATATC 59.043 45.833 4.42 4.42 34.37 1.63
6266 6996 4.947883 TGGACCCCGATCTGAAGATATAT 58.052 43.478 0.00 0.00 34.37 0.86
6267 6997 4.397919 TGGACCCCGATCTGAAGATATA 57.602 45.455 0.00 0.00 34.37 0.86
6268 6998 3.260269 TGGACCCCGATCTGAAGATAT 57.740 47.619 0.00 0.00 34.37 1.63
6269 6999 2.767644 TGGACCCCGATCTGAAGATA 57.232 50.000 0.00 0.00 34.37 1.98
6270 7000 2.109229 ATGGACCCCGATCTGAAGAT 57.891 50.000 0.00 0.00 37.51 2.40
6271 7001 2.598565 CTATGGACCCCGATCTGAAGA 58.401 52.381 0.00 0.00 0.00 2.87
6272 7002 1.620819 CCTATGGACCCCGATCTGAAG 59.379 57.143 0.00 0.00 0.00 3.02
6273 7003 1.219469 TCCTATGGACCCCGATCTGAA 59.781 52.381 0.00 0.00 0.00 3.02
6274 7004 0.857675 TCCTATGGACCCCGATCTGA 59.142 55.000 0.00 0.00 0.00 3.27
6275 7005 1.261480 CTCCTATGGACCCCGATCTG 58.739 60.000 0.00 0.00 0.00 2.90
6276 7006 0.115349 CCTCCTATGGACCCCGATCT 59.885 60.000 0.00 0.00 0.00 2.75
6277 7007 0.114560 TCCTCCTATGGACCCCGATC 59.885 60.000 0.00 0.00 0.00 3.69
6278 7008 0.793617 ATCCTCCTATGGACCCCGAT 59.206 55.000 0.00 0.00 39.17 4.18
6279 7009 0.114560 GATCCTCCTATGGACCCCGA 59.885 60.000 0.00 0.00 39.17 5.14
6280 7010 0.115349 AGATCCTCCTATGGACCCCG 59.885 60.000 0.00 0.00 39.17 5.73
6281 7011 1.650528 CAGATCCTCCTATGGACCCC 58.349 60.000 0.00 0.00 39.17 4.95
6282 7012 0.980423 GCAGATCCTCCTATGGACCC 59.020 60.000 0.00 0.00 39.17 4.46
6283 7013 0.605589 CGCAGATCCTCCTATGGACC 59.394 60.000 0.00 0.00 39.17 4.46
6284 7014 0.037790 GCGCAGATCCTCCTATGGAC 60.038 60.000 0.30 0.00 39.17 4.02
6285 7015 0.178950 AGCGCAGATCCTCCTATGGA 60.179 55.000 11.47 0.00 40.82 3.41
6286 7016 0.246086 GAGCGCAGATCCTCCTATGG 59.754 60.000 11.47 0.00 36.66 2.74
6287 7017 0.964700 TGAGCGCAGATCCTCCTATG 59.035 55.000 11.47 0.00 45.64 2.23
6288 7018 1.549620 CATGAGCGCAGATCCTCCTAT 59.450 52.381 11.47 0.00 45.64 2.57
6289 7019 0.964700 CATGAGCGCAGATCCTCCTA 59.035 55.000 11.47 0.00 45.64 2.94
6290 7020 1.747145 CATGAGCGCAGATCCTCCT 59.253 57.895 11.47 0.00 45.64 3.69
6291 7021 1.960250 GCATGAGCGCAGATCCTCC 60.960 63.158 11.47 0.00 45.64 4.30
6292 7022 1.227468 TGCATGAGCGCAGATCCTC 60.227 57.895 11.47 0.00 45.64 3.71
6293 7023 2.905681 TGCATGAGCGCAGATCCT 59.094 55.556 11.47 0.00 45.64 3.24
6302 7032 3.200593 CTCCGCCACTGCATGAGC 61.201 66.667 0.00 0.00 42.57 4.26
6303 7033 3.200593 GCTCCGCCACTGCATGAG 61.201 66.667 0.00 0.00 38.44 2.90


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

AutoCloner maintained by Alex Coulton.