Multiple sequence alignment - TraesCS4A01G093900

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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 TraesCS4A01G093900 chr4A 100.000 4160 0 0 1 4160 101752292 101748133 0.000000e+00 7683.0
1 TraesCS4A01G093900 chr4A 100.000 545 0 0 4582 5126 101747711 101747167 0.000000e+00 1007.0
2 TraesCS4A01G093900 chr4A 92.899 169 8 3 1812 1980 150653310 150653474 5.130000e-60 243.0
3 TraesCS4A01G093900 chr4D 97.684 1986 43 2 2175 4159 363677581 363679564 0.000000e+00 3410.0
4 TraesCS4A01G093900 chr4D 92.927 2036 83 16 1 2010 363675583 363677583 0.000000e+00 2905.0
5 TraesCS4A01G093900 chr4D 92.791 541 20 5 4598 5126 363679654 363680187 0.000000e+00 765.0
6 TraesCS4A01G093900 chr4D 95.930 172 7 0 2012 2183 75782053 75782224 3.910000e-71 279.0
7 TraesCS4A01G093900 chr4D 90.055 181 12 4 1806 1985 465125481 465125306 3.990000e-56 230.0
8 TraesCS4A01G093900 chr4B 93.244 2013 108 17 2157 4159 449123659 449125653 0.000000e+00 2939.0
9 TraesCS4A01G093900 chr4B 90.395 1749 82 26 350 2038 449121875 449123597 0.000000e+00 2220.0
10 TraesCS4A01G093900 chr4B 93.889 360 14 1 2 361 449104110 449104461 2.100000e-148 536.0
11 TraesCS4A01G093900 chr4B 93.169 366 16 2 1 365 449101480 449101837 3.510000e-146 529.0
12 TraesCS4A01G093900 chr4B 93.030 330 18 4 4802 5126 449127401 449127730 1.290000e-130 477.0
13 TraesCS4A01G093900 chr4B 94.419 215 7 2 4597 4807 449125742 449125955 4.950000e-85 326.0
14 TraesCS4A01G093900 chr4B 77.387 199 31 11 1 194 49113018 49113207 7.020000e-19 106.0
15 TraesCS4A01G093900 chr5A 84.906 371 45 11 1807 2176 229516147 229515787 1.050000e-96 364.0
16 TraesCS4A01G093900 chr5A 95.455 176 5 3 2004 2179 670399152 670399324 1.410000e-70 278.0
17 TraesCS4A01G093900 chr5D 98.802 167 2 0 2012 2178 330702306 330702472 1.080000e-76 298.0
18 TraesCS4A01G093900 chr5D 91.908 173 9 4 1815 1987 103636660 103636827 2.390000e-58 237.0
19 TraesCS4A01G093900 chr6D 97.633 169 3 1 2008 2176 473079339 473079506 6.490000e-74 289.0
20 TraesCS4A01G093900 chr2D 97.059 170 4 1 2012 2181 543178827 543178659 8.400000e-73 285.0
21 TraesCS4A01G093900 chr2D 93.956 182 10 1 2012 2192 560959485 560959666 1.820000e-69 274.0
22 TraesCS4A01G093900 chr2A 95.906 171 7 0 2008 2178 746757158 746756988 1.410000e-70 278.0
23 TraesCS4A01G093900 chr2B 91.327 196 11 4 1983 2177 464433113 464432923 3.940000e-66 263.0
24 TraesCS4A01G093900 chr6B 91.765 170 14 0 1815 1984 199740969 199740800 2.390000e-58 237.0
25 TraesCS4A01G093900 chr3D 89.305 187 14 5 1814 2000 87925999 87926179 3.990000e-56 230.0
26 TraesCS4A01G093900 chrUn 88.649 185 14 5 1796 1978 80232852 80232673 8.640000e-53 219.0
27 TraesCS4A01G093900 chrUn 76.963 191 40 4 14 203 75994389 75994202 7.020000e-19 106.0
28 TraesCS4A01G093900 chrUn 76.963 191 40 4 14 203 231198092 231197905 7.020000e-19 106.0
29 TraesCS4A01G093900 chr6A 78.641 206 36 7 1 204 39459100 39459299 4.170000e-26 130.0
30 TraesCS4A01G093900 chr6A 77.778 171 26 9 1 168 213394621 213394782 1.520000e-15 95.3
31 TraesCS4A01G093900 chr3A 77.670 206 40 6 1 204 21333315 21333114 2.510000e-23 121.0
32 TraesCS4A01G093900 chr7D 77.295 207 40 6 1 204 623708794 623708592 1.170000e-21 115.0


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 TraesCS4A01G093900 chr4A 101747167 101752292 5125 True 4345.0 7683 100.000000 1 5126 2 chr4A.!!$R1 5125
1 TraesCS4A01G093900 chr4D 363675583 363680187 4604 False 2360.0 3410 94.467333 1 5126 3 chr4D.!!$F2 5125
2 TraesCS4A01G093900 chr4B 449121875 449127730 5855 False 1490.5 2939 92.772000 350 5126 4 chr4B.!!$F3 4776
3 TraesCS4A01G093900 chr4B 449101480 449104461 2981 False 532.5 536 93.529000 1 365 2 chr4B.!!$F2 364

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
911 1183 0.035458 CCGAGCCTCTGACTTTTGGT 59.965 55.000 0.00 0.00 0.0 3.67 F
1007 1280 0.095935 GCTGTTACTGTCATGCGCTG 59.904 55.000 9.73 4.58 0.0 5.18 F
2130 2552 0.973632 TTGCTCCGTATGTGGTCACT 59.026 50.000 2.66 0.00 0.0 3.41 F
2131 2553 0.973632 TGCTCCGTATGTGGTCACTT 59.026 50.000 2.66 0.00 0.0 3.16 F
2132 2554 1.337728 TGCTCCGTATGTGGTCACTTG 60.338 52.381 2.66 0.00 0.0 3.16 F
2133 2555 1.337823 GCTCCGTATGTGGTCACTTGT 60.338 52.381 2.66 0.00 0.0 3.16 F
3523 4060 1.380302 CTAAGGGGCCACACAAGCT 59.620 57.895 8.31 0.00 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2583 0.464452 CCATGTACTCCCTCCGTTCC 59.536 60.000 0.00 0.0 0.00 3.62 R
2162 2584 1.192428 ACCATGTACTCCCTCCGTTC 58.808 55.000 0.00 0.0 0.00 3.95 R
3928 4465 0.034059 CGCTGTGAAGTGGAAGGAGT 59.966 55.000 0.00 0.0 0.00 3.85 R
4041 4578 0.179225 GTATCGCGCCAAACACACAG 60.179 55.000 0.00 0.0 0.00 3.66 R
4068 4605 1.078918 CTGTTCATCGGGCTGCAGA 60.079 57.895 20.43 0.0 0.00 4.26 R
4110 4647 1.760405 AAGGCTATAATCCCTGGGGG 58.240 55.000 14.00 0.0 46.11 5.40 R
5064 7640 0.108615 GTGTGAGGTGGACGGAGATG 60.109 60.000 0.00 0.0 0.00 2.90 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
101 102 9.740239 TTTATATGACTACTACGGTGACATTTC 57.260 33.333 0.00 0.00 0.00 2.17
186 187 3.440173 TCCGAGCACCTGATTTTGATTTC 59.560 43.478 0.00 0.00 0.00 2.17
468 471 0.179111 TCTATCCGTTGCTCAAGCCG 60.179 55.000 0.00 0.00 41.18 5.52
470 473 1.895020 TATCCGTTGCTCAAGCCGGT 61.895 55.000 15.99 8.75 43.29 5.28
613 659 2.193248 CATCTTCTTCCCCGCCCC 59.807 66.667 0.00 0.00 0.00 5.80
725 984 2.679934 TTCGCGCCTCGTCTCGTAA 61.680 57.895 0.00 0.00 39.67 3.18
728 987 2.004489 GCGCCTCGTCTCGTAATCG 61.004 63.158 0.00 0.00 38.55 3.34
762 1021 0.826715 AGCTTGCTCGATTAGAGGCA 59.173 50.000 0.00 0.00 46.91 4.75
793 1052 0.317160 TCGAACGATGCAGTCTGGTT 59.683 50.000 1.14 0.00 0.00 3.67
794 1053 0.439985 CGAACGATGCAGTCTGGTTG 59.560 55.000 1.14 0.00 0.00 3.77
796 1055 1.195448 GAACGATGCAGTCTGGTTGTG 59.805 52.381 1.14 0.00 0.00 3.33
849 1121 3.519930 GGGGTCTCGAGCCTCGAC 61.520 72.222 13.77 4.97 44.82 4.20
869 1141 1.081892 GCGTGAGTCACATTGCATCT 58.918 50.000 22.66 0.00 33.40 2.90
877 1149 1.303561 ACATTGCATCTGTGGGCGT 60.304 52.632 1.90 0.00 0.00 5.68
893 1165 2.186826 CGTCGAATTGGATGCCCCC 61.187 63.158 0.00 0.00 0.00 5.40
895 1167 2.191908 CGAATTGGATGCCCCCGA 59.808 61.111 0.00 0.00 0.00 5.14
910 1182 0.674895 CCCGAGCCTCTGACTTTTGG 60.675 60.000 0.00 0.00 0.00 3.28
911 1183 0.035458 CCGAGCCTCTGACTTTTGGT 59.965 55.000 0.00 0.00 0.00 3.67
921 1193 2.285083 TGACTTTTGGTCCACAACGAG 58.715 47.619 0.00 0.00 43.89 4.18
943 1215 3.934579 GTGAATCAATCCCCAAATGCAAC 59.065 43.478 0.00 0.00 0.00 4.17
960 1232 1.432023 AACGGGGAAATGGAGTGGGT 61.432 55.000 0.00 0.00 0.00 4.51
971 1243 1.010793 TGGAGTGGGTGGGAGGATAAT 59.989 52.381 0.00 0.00 0.00 1.28
1007 1280 0.095935 GCTGTTACTGTCATGCGCTG 59.904 55.000 9.73 4.58 0.00 5.18
1011 1284 1.067693 TTACTGTCATGCGCTGTTCG 58.932 50.000 9.73 0.00 42.12 3.95
1040 1313 3.018423 ACTCCATCATTTAAGGGCCAC 57.982 47.619 6.18 0.00 0.00 5.01
1042 1315 3.217626 CTCCATCATTTAAGGGCCACTC 58.782 50.000 6.18 0.00 0.00 3.51
1281 1654 4.156008 CAGATGCTGGTTTACCCTAACAAC 59.844 45.833 0.00 0.00 34.29 3.32
1480 1853 5.836821 TGTGCATGTTTTGTGGTTTAGTA 57.163 34.783 0.00 0.00 0.00 1.82
1494 1867 7.676947 TGTGGTTTAGTACTTGATAGAAAGCT 58.323 34.615 0.00 0.00 0.00 3.74
1543 1916 6.403200 GCAACACGTGAAAATACATCACCTAT 60.403 38.462 25.01 0.00 43.34 2.57
1647 2020 4.163078 AGAATGGTATCTCCTGTGTCCTTG 59.837 45.833 0.00 0.00 37.07 3.61
1648 2021 2.902608 TGGTATCTCCTGTGTCCTTGT 58.097 47.619 0.00 0.00 37.07 3.16
1649 2022 3.248024 TGGTATCTCCTGTGTCCTTGTT 58.752 45.455 0.00 0.00 37.07 2.83
1650 2023 3.007940 TGGTATCTCCTGTGTCCTTGTTG 59.992 47.826 0.00 0.00 37.07 3.33
1651 2024 2.867109 ATCTCCTGTGTCCTTGTTGG 57.133 50.000 0.00 0.00 37.10 3.77
1678 2066 3.243367 TGAGGCGTTGGAAATTTCAACTG 60.243 43.478 19.49 15.77 41.47 3.16
1809 2228 4.320567 CGAGCAGAAACTGAGAAGTACTGA 60.321 45.833 0.00 0.00 32.44 3.41
2007 2429 5.831103 ACTTGTATTCACCCCTTTGATGAT 58.169 37.500 0.00 0.00 0.00 2.45
2008 2430 6.969043 ACTTGTATTCACCCCTTTGATGATA 58.031 36.000 0.00 0.00 0.00 2.15
2009 2431 6.828785 ACTTGTATTCACCCCTTTGATGATAC 59.171 38.462 0.00 0.00 0.00 2.24
2010 2432 5.364778 TGTATTCACCCCTTTGATGATACG 58.635 41.667 0.00 0.00 0.00 3.06
2011 2433 3.992943 TTCACCCCTTTGATGATACGT 57.007 42.857 0.00 0.00 0.00 3.57
2012 2434 5.623956 ATTCACCCCTTTGATGATACGTA 57.376 39.130 0.00 0.00 0.00 3.57
2013 2435 4.395959 TCACCCCTTTGATGATACGTAC 57.604 45.455 0.00 0.00 0.00 3.67
2014 2436 4.028131 TCACCCCTTTGATGATACGTACT 58.972 43.478 0.00 0.00 0.00 2.73
2015 2437 4.468510 TCACCCCTTTGATGATACGTACTT 59.531 41.667 0.00 0.00 0.00 2.24
2016 2438 4.809426 CACCCCTTTGATGATACGTACTTC 59.191 45.833 0.00 0.00 0.00 3.01
2017 2439 4.141779 ACCCCTTTGATGATACGTACTTCC 60.142 45.833 0.00 0.00 0.00 3.46
2018 2440 4.101119 CCCCTTTGATGATACGTACTTCCT 59.899 45.833 0.00 0.00 0.00 3.36
2019 2441 5.290386 CCCTTTGATGATACGTACTTCCTC 58.710 45.833 0.00 0.00 0.00 3.71
2020 2442 5.290386 CCTTTGATGATACGTACTTCCTCC 58.710 45.833 0.00 0.00 0.00 4.30
2021 2443 4.563337 TTGATGATACGTACTTCCTCCG 57.437 45.455 0.00 0.00 0.00 4.63
2022 2444 3.548770 TGATGATACGTACTTCCTCCGT 58.451 45.455 0.00 0.00 38.53 4.69
2023 2445 3.949754 TGATGATACGTACTTCCTCCGTT 59.050 43.478 0.00 0.00 36.12 4.44
2024 2446 4.036027 TGATGATACGTACTTCCTCCGTTC 59.964 45.833 0.00 0.00 36.12 3.95
2025 2447 2.684881 TGATACGTACTTCCTCCGTTCC 59.315 50.000 0.00 0.00 36.12 3.62
2026 2448 2.496899 TACGTACTTCCTCCGTTCCT 57.503 50.000 0.00 0.00 36.12 3.36
2027 2449 2.496899 ACGTACTTCCTCCGTTCCTA 57.503 50.000 0.00 0.00 0.00 2.94
2028 2450 2.795329 ACGTACTTCCTCCGTTCCTAA 58.205 47.619 0.00 0.00 0.00 2.69
2029 2451 3.157087 ACGTACTTCCTCCGTTCCTAAA 58.843 45.455 0.00 0.00 0.00 1.85
2030 2452 3.766051 ACGTACTTCCTCCGTTCCTAAAT 59.234 43.478 0.00 0.00 0.00 1.40
2031 2453 4.949856 ACGTACTTCCTCCGTTCCTAAATA 59.050 41.667 0.00 0.00 0.00 1.40
2032 2454 5.595952 ACGTACTTCCTCCGTTCCTAAATAT 59.404 40.000 0.00 0.00 0.00 1.28
2033 2455 6.097412 ACGTACTTCCTCCGTTCCTAAATATT 59.903 38.462 0.00 0.00 0.00 1.28
2034 2456 6.982724 CGTACTTCCTCCGTTCCTAAATATTT 59.017 38.462 5.89 5.89 0.00 1.40
2035 2457 7.042925 CGTACTTCCTCCGTTCCTAAATATTTG 60.043 40.741 11.05 1.40 0.00 2.32
2036 2458 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
2037 2459 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
2038 2460 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
2039 2461 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
2040 2462 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
2041 2463 7.551617 TCCTCCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
2042 2464 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2043 2465 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2044 2466 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2045 2467 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2064 2486 9.567776 TTTCTAGACATTTCAAATGAACTACCA 57.432 29.630 17.30 5.05 33.13 3.25
2065 2487 8.547967 TCTAGACATTTCAAATGAACTACCAC 57.452 34.615 17.30 0.00 33.13 4.16
2066 2488 8.154203 TCTAGACATTTCAAATGAACTACCACA 58.846 33.333 17.30 0.66 33.13 4.17
2067 2489 7.765695 AGACATTTCAAATGAACTACCACAT 57.234 32.000 17.30 0.00 33.13 3.21
2068 2490 8.862325 AGACATTTCAAATGAACTACCACATA 57.138 30.769 17.30 0.00 33.13 2.29
2069 2491 8.730680 AGACATTTCAAATGAACTACCACATAC 58.269 33.333 17.30 0.00 33.13 2.39
2070 2492 7.526608 ACATTTCAAATGAACTACCACATACG 58.473 34.615 17.30 0.00 33.13 3.06
2071 2493 6.489127 TTTCAAATGAACTACCACATACGG 57.511 37.500 0.00 0.00 33.13 4.02
2072 2494 5.408880 TCAAATGAACTACCACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
2073 2495 5.984725 TCAAATGAACTACCACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
2074 2496 5.815222 TCAAATGAACTACCACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
2076 2498 6.474140 AATGAACTACCACATACGGATGTA 57.526 37.500 14.23 0.00 44.82 2.29
2077 2499 6.665992 ATGAACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
2116 2538 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2117 2539 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2118 2540 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2119 2541 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2120 2542 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2121 2543 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2122 2544 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2123 2545 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2124 2546 3.684305 TCACTCATTTTGCTCCGTATGTG 59.316 43.478 0.00 0.00 0.00 3.21
2125 2547 3.009723 ACTCATTTTGCTCCGTATGTGG 58.990 45.455 0.00 0.00 0.00 4.17
2126 2548 3.009723 CTCATTTTGCTCCGTATGTGGT 58.990 45.455 0.00 0.00 0.00 4.16
2127 2549 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
2128 2550 2.552599 TTTTGCTCCGTATGTGGTCA 57.447 45.000 0.00 0.00 0.00 4.02
2129 2551 1.803334 TTTGCTCCGTATGTGGTCAC 58.197 50.000 0.00 0.00 0.00 3.67
2130 2552 0.973632 TTGCTCCGTATGTGGTCACT 59.026 50.000 2.66 0.00 0.00 3.41
2131 2553 0.973632 TGCTCCGTATGTGGTCACTT 59.026 50.000 2.66 0.00 0.00 3.16
2132 2554 1.337728 TGCTCCGTATGTGGTCACTTG 60.338 52.381 2.66 0.00 0.00 3.16
2133 2555 1.337823 GCTCCGTATGTGGTCACTTGT 60.338 52.381 2.66 0.00 0.00 3.16
2134 2556 2.870435 GCTCCGTATGTGGTCACTTGTT 60.870 50.000 2.66 0.00 0.00 2.83
2135 2557 2.736721 CTCCGTATGTGGTCACTTGTTG 59.263 50.000 2.66 0.00 0.00 3.33
2136 2558 2.365941 TCCGTATGTGGTCACTTGTTGA 59.634 45.455 2.66 0.00 0.00 3.18
2137 2559 3.135225 CCGTATGTGGTCACTTGTTGAA 58.865 45.455 2.66 0.00 35.39 2.69
2138 2560 3.562141 CCGTATGTGGTCACTTGTTGAAA 59.438 43.478 2.66 0.00 35.39 2.69
2139 2561 4.215399 CCGTATGTGGTCACTTGTTGAAAT 59.785 41.667 2.66 0.00 35.39 2.17
2140 2562 5.382303 CGTATGTGGTCACTTGTTGAAATC 58.618 41.667 2.66 0.00 35.39 2.17
2141 2563 5.179368 CGTATGTGGTCACTTGTTGAAATCT 59.821 40.000 2.66 0.00 35.39 2.40
2142 2564 5.695851 ATGTGGTCACTTGTTGAAATCTC 57.304 39.130 2.66 0.00 35.39 2.75
2143 2565 4.780815 TGTGGTCACTTGTTGAAATCTCT 58.219 39.130 2.66 0.00 35.39 3.10
2144 2566 5.924356 TGTGGTCACTTGTTGAAATCTCTA 58.076 37.500 2.66 0.00 35.39 2.43
2145 2567 5.991606 TGTGGTCACTTGTTGAAATCTCTAG 59.008 40.000 2.66 0.00 35.39 2.43
2146 2568 6.183360 TGTGGTCACTTGTTGAAATCTCTAGA 60.183 38.462 2.66 0.00 35.39 2.43
2147 2569 6.706270 GTGGTCACTTGTTGAAATCTCTAGAA 59.294 38.462 0.00 0.00 35.39 2.10
2148 2570 7.226720 GTGGTCACTTGTTGAAATCTCTAGAAA 59.773 37.037 0.00 0.00 35.39 2.52
2149 2571 7.442364 TGGTCACTTGTTGAAATCTCTAGAAAG 59.558 37.037 0.00 0.00 35.39 2.62
2150 2572 7.657761 GGTCACTTGTTGAAATCTCTAGAAAGA 59.342 37.037 0.00 0.00 35.39 2.52
2151 2573 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2152 2574 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
2153 2575 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
2154 2576 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2167 2589 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2168 2590 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2169 2591 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2170 2592 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2171 2593 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2172 2594 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2173 2595 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2213 2740 6.966534 AAATTGAGCATAGAAATAGTGGGG 57.033 37.500 0.00 0.00 0.00 4.96
2552 3087 5.510430 GTGAAGAGGGAGAAAAATGGGTAT 58.490 41.667 0.00 0.00 0.00 2.73
2657 3192 7.556733 TTATGTTTACTGTCACCTCGTTTTT 57.443 32.000 0.00 0.00 0.00 1.94
2836 3372 2.223340 GCATTCATACAAAGCTGGTCCG 60.223 50.000 0.00 0.00 0.00 4.79
2947 3483 6.147164 CGGTAGCGTATTCATGAATGGTAATT 59.853 38.462 27.59 12.39 32.50 1.40
3177 3714 5.882040 TGTAATGTTCATGGAGTAAACCCA 58.118 37.500 0.00 0.00 38.19 4.51
3209 3746 4.389382 TGAAATTGGCAAATTGAAGCATCG 59.611 37.500 5.05 0.00 36.11 3.84
3426 3963 2.885894 GGACGTTAGAGTCTATCCTGGG 59.114 54.545 10.04 0.00 40.76 4.45
3523 4060 1.380302 CTAAGGGGCCACACAAGCT 59.620 57.895 8.31 0.00 0.00 3.74
3822 4359 3.817084 CCATGAAAGCACTGTCAGAAGAA 59.183 43.478 6.91 0.00 0.00 2.52
3929 4466 4.999939 CACGCCCGCCAAGCAAAC 63.000 66.667 0.00 0.00 0.00 2.93
3996 4533 3.072915 TGAAGAAGAACATGGAAGAGGCA 59.927 43.478 0.00 0.00 0.00 4.75
4041 4578 4.056125 GGGTTTGAAGCTGCCCGC 62.056 66.667 0.00 0.00 39.57 6.13
4068 4605 2.202703 GGCGCGATACCGAACAGT 60.203 61.111 12.10 0.00 38.22 3.55
4143 4680 2.054453 GCCTTTCCACCTCCATGCC 61.054 63.158 0.00 0.00 0.00 4.40
4148 4685 3.443045 CCACCTCCATGCCGTTGC 61.443 66.667 0.00 0.00 38.26 4.17
4155 4692 3.195002 CATGCCGTTGCCGTCGAT 61.195 61.111 0.00 0.00 36.33 3.59
4159 4696 3.005898 CCGTTGCCGTCGATCATG 58.994 61.111 0.00 0.00 0.00 3.07
4791 5642 9.368921 CATGTATGTATGCTTTGTAACATAACG 57.631 33.333 0.00 0.00 36.77 3.18
4855 7420 4.340894 TTCGCAACAATTCTATGTGCTC 57.659 40.909 0.00 0.00 32.81 4.26
4926 7494 2.685897 GTTCCTGTGTGCCACTTGTTAA 59.314 45.455 0.00 0.00 35.11 2.01
5021 7597 1.282875 GTCGTGTTTGCTTCCTGGC 59.717 57.895 0.00 0.00 0.00 4.85
5064 7640 2.925306 GCATCATCCGTCCGGTATACAC 60.925 54.545 0.00 0.00 36.47 2.90
5104 7680 3.560068 ACGATTCCGACCAAATTCATAGC 59.440 43.478 0.00 0.00 39.50 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.595173 TGATGTAGTGGAAATGTCACCG 58.405 45.455 0.00 0.00 35.87 4.94
101 102 7.630242 AAAATCCACAGTAATGATGTAGTGG 57.370 36.000 0.00 0.00 45.92 4.00
204 205 5.715434 ATCGGCAAGTTTAAGGCTTTAAA 57.285 34.783 4.45 9.49 36.63 1.52
205 206 5.941647 AGTATCGGCAAGTTTAAGGCTTTAA 59.058 36.000 4.45 0.00 0.00 1.52
206 207 5.493809 AGTATCGGCAAGTTTAAGGCTTTA 58.506 37.500 4.45 0.00 0.00 1.85
207 208 4.332828 AGTATCGGCAAGTTTAAGGCTTT 58.667 39.130 4.45 0.00 0.00 3.51
208 209 3.951663 AGTATCGGCAAGTTTAAGGCTT 58.048 40.909 4.58 4.58 0.00 4.35
209 210 3.629142 AGTATCGGCAAGTTTAAGGCT 57.371 42.857 0.00 0.00 0.00 4.58
210 211 3.687698 TGAAGTATCGGCAAGTTTAAGGC 59.312 43.478 0.00 0.00 0.00 4.35
211 212 4.693566 TGTGAAGTATCGGCAAGTTTAAGG 59.306 41.667 0.00 0.00 0.00 2.69
273 274 5.567138 ATTATCCAAAGCGAAGACAAAGG 57.433 39.130 0.00 0.00 0.00 3.11
318 319 2.355132 CACTCTTTGATCATCCTGCAGC 59.645 50.000 8.66 0.00 0.00 5.25
468 471 0.036388 TCCGGATTCTCAGTGCAACC 60.036 55.000 0.00 0.00 37.80 3.77
470 473 0.036388 GGTCCGGATTCTCAGTGCAA 60.036 55.000 7.81 0.00 0.00 4.08
534 545 2.023414 AACACCGCTGTTCCTGTCGA 62.023 55.000 0.00 0.00 35.57 4.20
553 564 1.307517 GGGGACTGTGGGGGTATCA 60.308 63.158 0.00 0.00 0.00 2.15
722 981 1.488527 CGAGCCCTAACTGCGATTAC 58.511 55.000 0.00 0.00 0.00 1.89
725 984 2.107141 GCGAGCCCTAACTGCGAT 59.893 61.111 0.00 0.00 0.00 4.58
728 987 3.198489 GCTGCGAGCCCTAACTGC 61.198 66.667 0.00 0.00 34.48 4.40
762 1021 3.365868 GCATCGTTCGATCTGAGCTCTAT 60.366 47.826 16.19 8.57 0.00 1.98
793 1052 1.134367 GGAGATCCGACGATGAACACA 59.866 52.381 0.00 0.00 0.00 3.72
794 1053 1.536284 GGGAGATCCGACGATGAACAC 60.536 57.143 0.00 0.00 36.71 3.32
796 1055 0.032267 GGGGAGATCCGACGATGAAC 59.968 60.000 0.00 0.00 36.71 3.18
844 1116 0.729478 AATGTGACTCACGCGTCGAG 60.729 55.000 26.39 26.39 37.14 4.04
848 1120 0.950555 ATGCAATGTGACTCACGCGT 60.951 50.000 5.58 5.58 37.14 6.01
849 1121 0.247419 GATGCAATGTGACTCACGCG 60.247 55.000 3.53 3.53 37.14 6.01
869 1141 1.024046 CATCCAATTCGACGCCCACA 61.024 55.000 0.00 0.00 0.00 4.17
877 1149 2.191908 CGGGGGCATCCAATTCGA 59.808 61.111 0.00 0.00 37.22 3.71
893 1165 1.433534 GACCAAAAGTCAGAGGCTCG 58.566 55.000 9.22 4.43 45.55 5.03
910 1182 3.125316 GGATTGATTCACTCGTTGTGGAC 59.875 47.826 10.35 4.80 46.20 4.02
911 1183 3.334691 GGATTGATTCACTCGTTGTGGA 58.665 45.455 10.35 3.68 46.20 4.02
921 1193 3.891422 TGCATTTGGGGATTGATTCAC 57.109 42.857 0.00 0.00 0.00 3.18
943 1215 1.378514 CACCCACTCCATTTCCCCG 60.379 63.158 0.00 0.00 0.00 5.73
960 1232 1.012049 AGTTCCCCCATTATCCTCCCA 59.988 52.381 0.00 0.00 0.00 4.37
971 1243 0.846427 AGCAGAATCCAGTTCCCCCA 60.846 55.000 0.00 0.00 37.56 4.96
1040 1313 0.882927 TTTCCAAGGAACACGGCGAG 60.883 55.000 16.62 8.85 33.41 5.03
1042 1315 0.596082 AATTTCCAAGGAACACGGCG 59.404 50.000 4.80 4.80 33.41 6.46
1048 1321 2.867647 GCCACTGCAATTTCCAAGGAAC 60.868 50.000 0.00 0.00 37.47 3.62
1123 1396 1.014352 GCCGTGGTGAATATGGTGAC 58.986 55.000 0.00 0.00 0.00 3.67
1281 1654 0.457035 CCGGCCCACTGAATTTCATG 59.543 55.000 0.00 1.48 0.00 3.07
1349 1722 6.515272 AATTTATGTTGAATCTCGGCAACT 57.485 33.333 0.00 0.00 43.52 3.16
1480 1853 6.127786 GGCTTCATTTGAGCTTTCTATCAAGT 60.128 38.462 0.00 0.00 36.81 3.16
1494 1867 5.565455 AAAAATTGGGAGGCTTCATTTGA 57.435 34.783 0.00 0.00 0.00 2.69
1543 1916 3.897239 CATAGATAGGGCCAAACACCAA 58.103 45.455 6.18 0.00 0.00 3.67
1647 2020 1.066430 TCCAACGCCTCAGTATCCAAC 60.066 52.381 0.00 0.00 0.00 3.77
1648 2021 1.271856 TCCAACGCCTCAGTATCCAA 58.728 50.000 0.00 0.00 0.00 3.53
1649 2022 1.271856 TTCCAACGCCTCAGTATCCA 58.728 50.000 0.00 0.00 0.00 3.41
1650 2023 2.396590 TTTCCAACGCCTCAGTATCC 57.603 50.000 0.00 0.00 0.00 2.59
1651 2024 4.394920 TGAAATTTCCAACGCCTCAGTATC 59.605 41.667 15.48 0.00 0.00 2.24
1656 2029 2.955660 AGTTGAAATTTCCAACGCCTCA 59.044 40.909 15.48 0.00 46.10 3.86
1809 2228 7.628501 ATTTAGGAACGGAGGGAGTATTATT 57.371 36.000 0.00 0.00 0.00 1.40
2007 2429 2.496899 AGGAACGGAGGAAGTACGTA 57.503 50.000 0.00 0.00 40.31 3.57
2008 2430 2.496899 TAGGAACGGAGGAAGTACGT 57.503 50.000 0.00 0.00 43.43 3.57
2009 2431 3.855689 TTTAGGAACGGAGGAAGTACG 57.144 47.619 0.00 0.00 0.00 3.67
2010 2432 7.767659 ACAAATATTTAGGAACGGAGGAAGTAC 59.232 37.037 0.00 0.00 0.00 2.73
2011 2433 7.854337 ACAAATATTTAGGAACGGAGGAAGTA 58.146 34.615 0.00 0.00 0.00 2.24
2012 2434 6.718294 ACAAATATTTAGGAACGGAGGAAGT 58.282 36.000 0.00 0.00 0.00 3.01
2013 2435 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
2014 2436 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
2015 2437 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
2016 2438 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2017 2439 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2018 2440 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2019 2441 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2038 2460 9.567776 TGGTAGTTCATTTGAAATGTCTAGAAA 57.432 29.630 16.62 1.15 35.58 2.52
2039 2461 8.999431 GTGGTAGTTCATTTGAAATGTCTAGAA 58.001 33.333 16.62 1.82 35.58 2.10
2040 2462 8.154203 TGTGGTAGTTCATTTGAAATGTCTAGA 58.846 33.333 16.62 8.31 35.58 2.43
2041 2463 8.322906 TGTGGTAGTTCATTTGAAATGTCTAG 57.677 34.615 16.62 0.00 35.58 2.43
2042 2464 8.862325 ATGTGGTAGTTCATTTGAAATGTCTA 57.138 30.769 16.62 15.91 35.58 2.59
2043 2465 7.765695 ATGTGGTAGTTCATTTGAAATGTCT 57.234 32.000 16.62 16.73 35.58 3.41
2044 2466 7.692291 CGTATGTGGTAGTTCATTTGAAATGTC 59.308 37.037 16.62 11.39 35.58 3.06
2045 2467 7.361713 CCGTATGTGGTAGTTCATTTGAAATGT 60.362 37.037 16.62 1.69 35.58 2.71
2046 2468 6.966632 CCGTATGTGGTAGTTCATTTGAAATG 59.033 38.462 11.54 11.54 35.58 2.32
2047 2469 6.882140 TCCGTATGTGGTAGTTCATTTGAAAT 59.118 34.615 0.00 0.00 35.58 2.17
2048 2470 6.231951 TCCGTATGTGGTAGTTCATTTGAAA 58.768 36.000 0.00 0.00 35.58 2.69
2049 2471 5.795972 TCCGTATGTGGTAGTTCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
2050 2472 5.408880 TCCGTATGTGGTAGTTCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
2051 2473 5.584649 ACATCCGTATGTGGTAGTTCATTTG 59.415 40.000 0.00 0.00 44.79 2.32
2052 2474 5.741011 ACATCCGTATGTGGTAGTTCATTT 58.259 37.500 0.00 0.00 44.79 2.32
2053 2475 5.353394 ACATCCGTATGTGGTAGTTCATT 57.647 39.130 0.00 0.00 44.79 2.57
2054 2476 6.455647 CATACATCCGTATGTGGTAGTTCAT 58.544 40.000 3.56 0.00 46.70 2.57
2055 2477 5.838529 CATACATCCGTATGTGGTAGTTCA 58.161 41.667 3.56 0.00 46.70 3.18
2094 2516 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2095 2517 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2096 2518 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2097 2519 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2098 2520 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2099 2521 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2100 2522 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2101 2523 4.154015 CACATACGGAGCAAAATGAGTGAA 59.846 41.667 0.00 0.00 0.00 3.18
2102 2524 3.684305 CACATACGGAGCAAAATGAGTGA 59.316 43.478 0.00 0.00 0.00 3.41
2103 2525 3.181507 CCACATACGGAGCAAAATGAGTG 60.182 47.826 0.00 0.00 0.00 3.51
2104 2526 3.009723 CCACATACGGAGCAAAATGAGT 58.990 45.455 0.00 0.00 0.00 3.41
2105 2527 3.009723 ACCACATACGGAGCAAAATGAG 58.990 45.455 0.00 0.00 0.00 2.90
2106 2528 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
2107 2529 2.746904 TGACCACATACGGAGCAAAATG 59.253 45.455 0.00 0.00 0.00 2.32
2108 2530 2.747446 GTGACCACATACGGAGCAAAAT 59.253 45.455 0.00 0.00 0.00 1.82
2109 2531 2.147958 GTGACCACATACGGAGCAAAA 58.852 47.619 0.00 0.00 0.00 2.44
2110 2532 1.346395 AGTGACCACATACGGAGCAAA 59.654 47.619 2.78 0.00 0.00 3.68
2111 2533 0.973632 AGTGACCACATACGGAGCAA 59.026 50.000 2.78 0.00 0.00 3.91
2112 2534 0.973632 AAGTGACCACATACGGAGCA 59.026 50.000 2.78 0.00 0.00 4.26
2113 2535 1.337823 ACAAGTGACCACATACGGAGC 60.338 52.381 2.78 0.00 0.00 4.70
2114 2536 2.736721 CAACAAGTGACCACATACGGAG 59.263 50.000 2.78 0.00 0.00 4.63
2115 2537 2.365941 TCAACAAGTGACCACATACGGA 59.634 45.455 2.78 0.00 0.00 4.69
2116 2538 2.761559 TCAACAAGTGACCACATACGG 58.238 47.619 2.78 0.00 0.00 4.02
2117 2539 4.804608 TTTCAACAAGTGACCACATACG 57.195 40.909 2.78 0.00 35.39 3.06
2118 2540 6.428159 AGAGATTTCAACAAGTGACCACATAC 59.572 38.462 2.78 0.00 35.39 2.39
2119 2541 6.533730 AGAGATTTCAACAAGTGACCACATA 58.466 36.000 2.78 0.00 35.39 2.29
2120 2542 5.380043 AGAGATTTCAACAAGTGACCACAT 58.620 37.500 2.78 0.00 35.39 3.21
2121 2543 4.780815 AGAGATTTCAACAAGTGACCACA 58.219 39.130 2.78 0.00 35.39 4.17
2122 2544 6.223852 TCTAGAGATTTCAACAAGTGACCAC 58.776 40.000 0.00 0.00 35.39 4.16
2123 2545 6.419484 TCTAGAGATTTCAACAAGTGACCA 57.581 37.500 0.00 0.00 35.39 4.02
2124 2546 7.657761 TCTTTCTAGAGATTTCAACAAGTGACC 59.342 37.037 0.00 0.00 35.39 4.02
2125 2547 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2126 2548 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2127 2549 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2128 2550 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2141 2563 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2142 2564 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2143 2565 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2144 2566 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2145 2567 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2146 2568 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2147 2569 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2148 2570 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2149 2571 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2150 2572 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2151 2573 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2152 2574 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2153 2575 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
2154 2576 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2155 2577 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2156 2578 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2157 2579 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2158 2580 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2159 2581 2.662866 CATGTACTCCCTCCGTTCCTA 58.337 52.381 0.00 0.00 0.00 2.94
2160 2582 1.486211 CATGTACTCCCTCCGTTCCT 58.514 55.000 0.00 0.00 0.00 3.36
2161 2583 0.464452 CCATGTACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
2162 2584 1.192428 ACCATGTACTCCCTCCGTTC 58.808 55.000 0.00 0.00 0.00 3.95
2163 2585 2.537633 TACCATGTACTCCCTCCGTT 57.462 50.000 0.00 0.00 0.00 4.44
2164 2586 2.537633 TTACCATGTACTCCCTCCGT 57.462 50.000 0.00 0.00 0.00 4.69
2165 2587 2.483188 GCTTTACCATGTACTCCCTCCG 60.483 54.545 0.00 0.00 0.00 4.63
2166 2588 2.504175 TGCTTTACCATGTACTCCCTCC 59.496 50.000 0.00 0.00 0.00 4.30
2167 2589 3.197983 ACTGCTTTACCATGTACTCCCTC 59.802 47.826 0.00 0.00 0.00 4.30
2168 2590 3.182152 ACTGCTTTACCATGTACTCCCT 58.818 45.455 0.00 0.00 0.00 4.20
2169 2591 3.629142 ACTGCTTTACCATGTACTCCC 57.371 47.619 0.00 0.00 0.00 4.30
2170 2592 7.335924 TCAATTTACTGCTTTACCATGTACTCC 59.664 37.037 0.00 0.00 0.00 3.85
2171 2593 8.263940 TCAATTTACTGCTTTACCATGTACTC 57.736 34.615 0.00 0.00 0.00 2.59
2172 2594 7.148239 GCTCAATTTACTGCTTTACCATGTACT 60.148 37.037 0.00 0.00 0.00 2.73
2173 2595 6.967199 GCTCAATTTACTGCTTTACCATGTAC 59.033 38.462 0.00 0.00 0.00 2.90
2213 2740 5.816955 AAGTCATTAGATAGCTTCCCTCC 57.183 43.478 0.00 0.00 0.00 4.30
3209 3746 5.824904 TTGCTCTCTTTGAGATATTTGCC 57.175 39.130 0.00 0.00 45.39 4.52
3393 3930 5.855045 ACTCTAACGTCCAGATTGAGTTTT 58.145 37.500 0.00 0.00 30.33 2.43
3426 3963 1.980951 TTGAATCTGCATGGTCGCGC 61.981 55.000 0.00 0.00 33.35 6.86
3523 4060 2.398588 ACTAGCCCAAGCAGCTACATA 58.601 47.619 0.00 0.00 43.56 2.29
3535 4072 2.384828 TGAATAGCTCGAACTAGCCCA 58.615 47.619 1.57 0.00 43.86 5.36
3537 4074 5.742446 CAAAATGAATAGCTCGAACTAGCC 58.258 41.667 1.57 0.00 43.86 3.93
3822 4359 0.987294 CCTCTGTCAGTGGGATTGGT 59.013 55.000 12.40 0.00 0.00 3.67
3928 4465 0.034059 CGCTGTGAAGTGGAAGGAGT 59.966 55.000 0.00 0.00 0.00 3.85
3929 4466 0.034059 ACGCTGTGAAGTGGAAGGAG 59.966 55.000 0.00 0.00 0.00 3.69
4041 4578 0.179225 GTATCGCGCCAAACACACAG 60.179 55.000 0.00 0.00 0.00 3.66
4068 4605 1.078918 CTGTTCATCGGGCTGCAGA 60.079 57.895 20.43 0.00 0.00 4.26
4110 4647 1.760405 AAGGCTATAATCCCTGGGGG 58.240 55.000 14.00 0.00 46.11 5.40
4581 5118 4.226761 CTGCCAAAAGTCAAACGGTAATC 58.773 43.478 0.00 0.00 0.00 1.75
4582 5119 3.005367 CCTGCCAAAAGTCAAACGGTAAT 59.995 43.478 0.00 0.00 0.00 1.89
4583 5120 2.359531 CCTGCCAAAAGTCAAACGGTAA 59.640 45.455 0.00 0.00 0.00 2.85
4584 5121 1.950909 CCTGCCAAAAGTCAAACGGTA 59.049 47.619 0.00 0.00 0.00 4.02
4585 5122 0.744281 CCTGCCAAAAGTCAAACGGT 59.256 50.000 0.00 0.00 0.00 4.83
4586 5123 0.597377 GCCTGCCAAAAGTCAAACGG 60.597 55.000 0.00 0.00 0.00 4.44
4587 5124 0.597377 GGCCTGCCAAAAGTCAAACG 60.597 55.000 2.58 0.00 35.81 3.60
4588 5125 0.249868 GGGCCTGCCAAAAGTCAAAC 60.250 55.000 10.86 0.00 37.98 2.93
4589 5126 0.398381 AGGGCCTGCCAAAAGTCAAA 60.398 50.000 4.50 0.00 37.98 2.69
4590 5127 0.398381 AAGGGCCTGCCAAAAGTCAA 60.398 50.000 6.92 0.00 37.98 3.18
4591 5128 1.114722 CAAGGGCCTGCCAAAAGTCA 61.115 55.000 6.92 0.00 37.98 3.41
4592 5129 1.667722 CAAGGGCCTGCCAAAAGTC 59.332 57.895 6.92 0.00 37.98 3.01
4593 5130 2.510551 GCAAGGGCCTGCCAAAAGT 61.511 57.895 6.92 0.00 36.25 2.66
4594 5131 1.761500 AAGCAAGGGCCTGCCAAAAG 61.761 55.000 19.86 0.00 43.73 2.27
4595 5132 1.344191 AAAGCAAGGGCCTGCCAAAA 61.344 50.000 19.86 0.00 43.73 2.44
4600 5137 2.387476 AAAGCAAAGCAAGGGCCTGC 62.387 55.000 6.92 13.55 45.18 4.85
4716 5257 1.664016 CGAGCGCTTCAACTTTGCAAT 60.664 47.619 13.26 0.00 0.00 3.56
4791 5642 1.301401 TGGAGTAGTTGCCACGCAC 60.301 57.895 0.00 0.00 38.71 5.34
4855 7420 1.453379 CAGATGGGCCAAGAGCAGG 60.453 63.158 11.89 0.00 46.50 4.85
4926 7494 2.031870 GACCAAAAGCACTCCAGGTTT 58.968 47.619 0.00 0.00 40.59 3.27
5021 7597 2.361610 AGCGGGGGTCAATTGCTG 60.362 61.111 0.00 0.00 33.99 4.41
5064 7640 0.108615 GTGTGAGGTGGACGGAGATG 60.109 60.000 0.00 0.00 0.00 2.90
5104 7680 2.776312 AGTGCGTGTATATGTCTCGG 57.224 50.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.