Multiple sequence alignment - TraesCS3D01G110700

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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 TraesCS3D01G110700 chr3D 100.000 6951 0 0 1 6951 64369166 64376116 0.000000e+00 12837.0
1 TraesCS3D01G110700 chr3D 83.444 302 39 7 6654 6951 32703813 32703519 3.200000e-68 270.0
2 TraesCS3D01G110700 chr3A 97.445 4305 94 12 2219 6519 74782796 74787088 0.000000e+00 7326.0
3 TraesCS3D01G110700 chr3A 91.112 2149 84 42 76 2176 74780702 74782791 0.000000e+00 2811.0
4 TraesCS3D01G110700 chr3A 90.805 435 36 3 6517 6951 74788582 74789012 4.670000e-161 579.0
5 TraesCS3D01G110700 chr3A 88.073 218 20 4 6736 6951 718067168 718066955 3.220000e-63 254.0
6 TraesCS3D01G110700 chr3B 95.099 4081 108 26 2219 6263 106964013 106968037 0.000000e+00 6344.0
7 TraesCS3D01G110700 chr3B 88.530 1796 80 45 436 2176 106962214 106963938 0.000000e+00 2060.0
8 TraesCS3D01G110700 chr4D 82.692 312 39 11 6648 6951 461279651 461279955 5.350000e-66 263.0
9 TraesCS3D01G110700 chr4B 86.147 231 26 4 6723 6951 576406825 576407051 1.940000e-60 244.0
10 TraesCS3D01G110700 chr4B 91.026 78 7 0 5472 5549 653741829 653741752 9.540000e-19 106.0
11 TraesCS3D01G110700 chr6A 83.032 277 34 9 6680 6951 397429525 397429257 9.010000e-59 239.0
12 TraesCS3D01G110700 chr1D 80.097 206 31 9 6651 6852 425292207 425292008 2.020000e-30 145.0
13 TraesCS3D01G110700 chr5B 82.222 180 18 13 6779 6951 492130957 492130785 7.270000e-30 143.0
14 TraesCS3D01G110700 chr2B 83.333 66 8 3 6565 6629 608174643 608174580 2.710000e-04 58.4


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 TraesCS3D01G110700 chr3D 64369166 64376116 6950 False 12837 12837 100.000000 1 6951 1 chr3D.!!$F1 6950
1 TraesCS3D01G110700 chr3A 74780702 74789012 8310 False 3572 7326 93.120667 76 6951 3 chr3A.!!$F1 6875
2 TraesCS3D01G110700 chr3B 106962214 106968037 5823 False 4202 6344 91.814500 436 6263 2 chr3B.!!$F1 5827

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
49 50 0.028242 CTCGAGGGAGATCGACAACG 59.972 60.000 3.91 0.0 46.20 4.10 F
360 383 0.108019 GGGTTTACTAGCCCCCATCG 59.892 60.000 0.00 0.0 38.99 3.84 F
705 739 0.323629 AAAACGGGAGGCAGATCGAA 59.676 50.000 0.00 0.0 0.00 3.71 F
821 862 0.536687 GGCCCGTCCCCTTTTATAGC 60.537 60.000 0.00 0.0 0.00 2.97 F
1688 1772 0.877071 CTCGTTTGCTTGCATCACCT 59.123 50.000 0.00 0.0 0.00 4.00 F
1841 1925 1.087771 CCCGGTATTGTTGGAGTCGC 61.088 60.000 0.00 0.0 0.00 5.19 F
1975 2059 1.201414 GCGGATTTTGGGTAGGTTGTG 59.799 52.381 0.00 0.0 0.00 3.33 F
2600 2725 2.107378 TGTGGAACCATCACTAGCCAAA 59.893 45.455 0.00 0.0 36.21 3.28 F
4047 4196 1.311859 TTGTTGCCTTCTGTGCTGAG 58.688 50.000 0.00 0.0 0.00 3.35 F
4792 4948 2.351336 GACCTACGGTGCTGATCGGG 62.351 65.000 3.14 0.0 35.25 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1253 0.317020 GCGTCAGGCAAAACACAGAC 60.317 55.000 0.00 0.00 42.87 3.51 R
1797 1881 0.387202 CATACTGGGTGCGAGGAGAG 59.613 60.000 0.00 0.00 0.00 3.20 R
1841 1925 1.231958 TTTTAACGCGACCAGCTGGG 61.232 55.000 35.42 20.34 45.59 4.45 R
2192 2282 3.306472 TTGGTTTACCCTTGCTGAAGT 57.694 42.857 0.00 0.00 34.29 3.01 R
3678 3827 1.479323 GCCATCAAGGACAATGCACAT 59.521 47.619 0.00 0.00 41.22 3.21 R
4016 4165 8.081633 CACAGAAGGCAACAAACTGAAATATAA 58.918 33.333 0.00 0.00 36.96 0.98 R
4047 4196 5.964758 TCCCTGCAATCAACACATTTTATC 58.035 37.500 0.00 0.00 0.00 1.75 R
4215 4364 6.261603 TCAGATGTGTTCCAGATAATGCATTC 59.738 38.462 16.86 2.18 0.00 2.67 R
5491 5649 0.734889 CGCGGATTGCTCCAGAAATT 59.265 50.000 0.00 0.00 42.19 1.82 R
6684 8337 0.958876 GCCCAAACCGGACGAAATCT 60.959 55.000 9.46 0.00 36.56 2.40 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
20 21 3.430333 GAGACTCTTTGAGGATCCGAC 57.570 52.381 5.98 5.56 33.35 4.79
21 22 2.755655 GAGACTCTTTGAGGATCCGACA 59.244 50.000 5.98 8.34 33.35 4.35
22 23 3.370104 AGACTCTTTGAGGATCCGACAT 58.630 45.455 5.98 0.00 33.35 3.06
23 24 3.772025 AGACTCTTTGAGGATCCGACATT 59.228 43.478 5.98 0.00 33.35 2.71
24 25 4.116238 GACTCTTTGAGGATCCGACATTC 58.884 47.826 5.98 0.00 33.35 2.67
25 26 3.119291 CTCTTTGAGGATCCGACATTCG 58.881 50.000 5.98 3.40 40.07 3.34
26 27 6.471800 ACTCTTTGAGGATCCGACATTCGG 62.472 50.000 5.98 8.36 46.77 4.30
34 35 2.202610 CGACATTCGGCTGCTCGA 60.203 61.111 8.74 8.74 36.00 4.04
35 36 2.226896 CGACATTCGGCTGCTCGAG 61.227 63.158 8.45 8.45 40.42 4.04
36 37 1.880340 GACATTCGGCTGCTCGAGG 60.880 63.158 15.58 0.00 40.42 4.63
37 38 2.587194 CATTCGGCTGCTCGAGGG 60.587 66.667 15.58 6.33 40.42 4.30
38 39 2.759973 ATTCGGCTGCTCGAGGGA 60.760 61.111 15.58 0.00 40.42 4.20
39 40 2.790791 ATTCGGCTGCTCGAGGGAG 61.791 63.158 15.58 6.79 43.46 4.30
40 41 3.938637 TTCGGCTGCTCGAGGGAGA 62.939 63.158 15.58 0.00 43.27 3.71
41 42 3.222855 CGGCTGCTCGAGGGAGAT 61.223 66.667 15.58 0.00 43.27 2.75
42 43 2.733945 GGCTGCTCGAGGGAGATC 59.266 66.667 15.58 0.00 43.27 2.75
43 44 2.334653 GCTGCTCGAGGGAGATCG 59.665 66.667 15.58 0.00 43.27 3.69
45 46 1.652012 CTGCTCGAGGGAGATCGAC 59.348 63.158 15.58 0.00 46.20 4.20
46 47 1.077716 TGCTCGAGGGAGATCGACA 60.078 57.895 15.58 0.00 46.20 4.35
47 48 0.679960 TGCTCGAGGGAGATCGACAA 60.680 55.000 15.58 0.00 46.20 3.18
48 49 0.248702 GCTCGAGGGAGATCGACAAC 60.249 60.000 15.58 0.00 46.20 3.32
49 50 0.028242 CTCGAGGGAGATCGACAACG 59.972 60.000 3.91 0.00 46.20 4.10
59 60 2.552802 TCGACAACGAGGAGGAGAC 58.447 57.895 0.00 0.00 43.81 3.36
60 61 1.134901 CGACAACGAGGAGGAGACG 59.865 63.158 0.00 0.00 42.66 4.18
61 62 1.296755 CGACAACGAGGAGGAGACGA 61.297 60.000 0.00 0.00 42.66 4.20
62 63 0.168568 GACAACGAGGAGGAGACGAC 59.831 60.000 0.00 0.00 0.00 4.34
63 64 1.242665 ACAACGAGGAGGAGACGACC 61.243 60.000 0.00 0.00 0.00 4.79
64 65 0.961358 CAACGAGGAGGAGACGACCT 60.961 60.000 0.00 0.00 42.77 3.85
65 66 0.251253 AACGAGGAGGAGACGACCTT 60.251 55.000 0.00 0.00 40.85 3.50
66 67 0.961358 ACGAGGAGGAGACGACCTTG 60.961 60.000 0.00 0.00 43.73 3.61
67 68 1.658686 CGAGGAGGAGACGACCTTGG 61.659 65.000 0.00 0.00 40.85 3.61
68 69 0.612453 GAGGAGGAGACGACCTTGGT 60.612 60.000 0.00 0.00 40.85 3.67
69 70 0.612453 AGGAGGAGACGACCTTGGTC 60.612 60.000 9.62 9.62 40.73 4.02
70 71 0.898789 GGAGGAGACGACCTTGGTCA 60.899 60.000 18.51 0.00 40.73 4.02
71 72 0.244178 GAGGAGACGACCTTGGTCAC 59.756 60.000 18.51 11.84 40.73 3.67
72 73 1.080705 GGAGACGACCTTGGTCACG 60.081 63.158 18.51 9.51 36.87 4.35
73 74 1.733399 GAGACGACCTTGGTCACGC 60.733 63.158 18.51 10.24 36.87 5.34
74 75 3.103911 GACGACCTTGGTCACGCG 61.104 66.667 18.51 3.53 34.56 6.01
88 89 1.665169 TCACGCGCTAGTGACGTATAA 59.335 47.619 19.99 10.05 45.18 0.98
113 114 8.980143 ATCAAGTAAAATATTGGACAAAACGG 57.020 30.769 0.00 0.00 0.00 4.44
360 383 0.108019 GGGTTTACTAGCCCCCATCG 59.892 60.000 0.00 0.00 38.99 3.84
417 440 4.568152 ACAAACTGTTTATGCAGGTCAC 57.432 40.909 5.31 0.00 40.59 3.67
517 540 6.922980 CACATCTGTGTTTGCTCTAATTTG 57.077 37.500 2.09 0.00 40.96 2.32
588 611 4.590918 TCGGAAAGCCAACCAAATATACA 58.409 39.130 0.00 0.00 0.00 2.29
634 657 3.321968 ACATTTCTGGCTGGAAAAAGGTC 59.678 43.478 9.42 0.00 38.46 3.85
654 677 0.393673 TAATGACCCCCGTACGTCGA 60.394 55.000 15.21 0.00 42.86 4.20
662 694 2.202388 CGTACGTCGACGCCATGT 60.202 61.111 35.92 19.68 44.43 3.21
681 713 0.620410 TTCACCATCCATCGACCCCT 60.620 55.000 0.00 0.00 0.00 4.79
682 714 1.146930 CACCATCCATCGACCCCTG 59.853 63.158 0.00 0.00 0.00 4.45
703 737 1.287425 GTAAAACGGGAGGCAGATCG 58.713 55.000 0.00 0.00 0.00 3.69
704 738 1.134907 GTAAAACGGGAGGCAGATCGA 60.135 52.381 0.00 0.00 0.00 3.59
705 739 0.323629 AAAACGGGAGGCAGATCGAA 59.676 50.000 0.00 0.00 0.00 3.71
750 788 3.242511 GCGGCGAATTAAAGTATTTCCGT 60.243 43.478 12.98 0.00 40.09 4.69
753 791 3.958151 GCGAATTAAAGTATTTCCGTCGC 59.042 43.478 0.00 0.00 45.84 5.19
821 862 0.536687 GGCCCGTCCCCTTTTATAGC 60.537 60.000 0.00 0.00 0.00 2.97
871 912 4.096003 CGTCCCATCCCACGCCTT 62.096 66.667 0.00 0.00 0.00 4.35
881 922 4.785453 CACGCCTTCCCCAGCCTC 62.785 72.222 0.00 0.00 0.00 4.70
959 1000 2.852075 GACTCACCCACCCACCCA 60.852 66.667 0.00 0.00 0.00 4.51
960 1001 3.175710 ACTCACCCACCCACCCAC 61.176 66.667 0.00 0.00 0.00 4.61
961 1002 3.966543 CTCACCCACCCACCCACC 61.967 72.222 0.00 0.00 0.00 4.61
1059 1111 1.378250 CTCCCTGGTACGGACGTCT 60.378 63.158 16.46 0.00 36.31 4.18
1186 1251 6.864560 GAAGTAAGCTTCGTTTGTTTGTTT 57.135 33.333 0.00 0.00 41.27 2.83
1187 1252 7.273188 GAAGTAAGCTTCGTTTGTTTGTTTT 57.727 32.000 0.00 0.00 41.27 2.43
1188 1253 6.626199 AGTAAGCTTCGTTTGTTTGTTTTG 57.374 33.333 0.00 0.00 0.00 2.44
1189 1254 6.153756 AGTAAGCTTCGTTTGTTTGTTTTGT 58.846 32.000 0.00 0.00 0.00 2.83
1190 1255 5.509605 AAGCTTCGTTTGTTTGTTTTGTC 57.490 34.783 0.00 0.00 0.00 3.18
1548 1632 4.008933 GATCTGGGCGGGGATCGG 62.009 72.222 0.00 0.00 39.69 4.18
1605 1689 2.755103 GTGTTGCCTTGCCTAAGCTTAT 59.245 45.455 6.64 0.00 40.80 1.73
1606 1690 3.945285 GTGTTGCCTTGCCTAAGCTTATA 59.055 43.478 6.64 0.00 40.80 0.98
1607 1691 3.945285 TGTTGCCTTGCCTAAGCTTATAC 59.055 43.478 6.64 2.83 40.80 1.47
1652 1736 6.870971 TTTTAGAACTTTTGACGTGCCTAT 57.129 33.333 0.00 0.00 0.00 2.57
1688 1772 0.877071 CTCGTTTGCTTGCATCACCT 59.123 50.000 0.00 0.00 0.00 4.00
1841 1925 1.087771 CCCGGTATTGTTGGAGTCGC 61.088 60.000 0.00 0.00 0.00 5.19
1867 1951 3.917985 GCTGGTCGCGTTAAAATTTCAAT 59.082 39.130 5.77 0.00 0.00 2.57
1870 1954 6.451960 GCTGGTCGCGTTAAAATTTCAATTAC 60.452 38.462 5.77 0.00 0.00 1.89
1873 1957 7.958567 TGGTCGCGTTAAAATTTCAATTACTAG 59.041 33.333 5.77 0.00 0.00 2.57
1874 1958 7.959109 GGTCGCGTTAAAATTTCAATTACTAGT 59.041 33.333 5.77 0.00 0.00 2.57
1875 1959 9.956797 GTCGCGTTAAAATTTCAATTACTAGTA 57.043 29.630 5.77 0.00 0.00 1.82
1906 1990 8.865590 TTTTACATTTCCAGTTTCACTTTAGC 57.134 30.769 0.00 0.00 0.00 3.09
1914 1998 4.932200 CCAGTTTCACTTTAGCGAGAGAAT 59.068 41.667 0.00 0.00 0.00 2.40
1915 1999 6.071560 TCCAGTTTCACTTTAGCGAGAGAATA 60.072 38.462 0.00 0.00 0.00 1.75
1916 2000 6.758886 CCAGTTTCACTTTAGCGAGAGAATAT 59.241 38.462 0.00 0.00 0.00 1.28
1917 2001 7.278868 CCAGTTTCACTTTAGCGAGAGAATATT 59.721 37.037 0.00 0.00 0.00 1.28
1975 2059 1.201414 GCGGATTTTGGGTAGGTTGTG 59.799 52.381 0.00 0.00 0.00 3.33
2161 2251 7.661437 TGACTGCAAATTGATACTAAACTGACT 59.339 33.333 0.00 0.00 0.00 3.41
2162 2252 9.151471 GACTGCAAATTGATACTAAACTGACTA 57.849 33.333 0.00 0.00 0.00 2.59
2194 2284 9.253832 TGGTAAACCAATATTCATCATGAAACT 57.746 29.630 3.63 0.00 44.35 2.66
2198 2288 9.865321 AAACCAATATTCATCATGAAACTTCAG 57.135 29.630 3.63 0.00 40.12 3.02
2199 2289 7.486647 ACCAATATTCATCATGAAACTTCAGC 58.513 34.615 3.63 0.00 40.12 4.26
2200 2290 7.123098 ACCAATATTCATCATGAAACTTCAGCA 59.877 33.333 3.63 0.00 40.12 4.41
2201 2291 7.977293 CCAATATTCATCATGAAACTTCAGCAA 59.023 33.333 3.63 0.00 40.12 3.91
2202 2292 9.020813 CAATATTCATCATGAAACTTCAGCAAG 57.979 33.333 3.63 0.00 40.12 4.01
2203 2293 5.381174 TTCATCATGAAACTTCAGCAAGG 57.619 39.130 0.00 0.00 41.08 3.61
2204 2294 3.760151 TCATCATGAAACTTCAGCAAGGG 59.240 43.478 0.00 0.00 41.08 3.95
2205 2295 3.228188 TCATGAAACTTCAGCAAGGGT 57.772 42.857 0.00 0.00 41.08 4.34
2206 2296 4.365514 TCATGAAACTTCAGCAAGGGTA 57.634 40.909 0.00 0.00 41.08 3.69
2207 2297 4.724399 TCATGAAACTTCAGCAAGGGTAA 58.276 39.130 0.00 0.00 41.08 2.85
2209 2299 4.911514 TGAAACTTCAGCAAGGGTAAAC 57.088 40.909 0.00 0.00 33.37 2.01
2211 2301 3.306472 AACTTCAGCAAGGGTAAACCA 57.694 42.857 0.81 0.00 43.89 3.67
2213 2303 3.844640 ACTTCAGCAAGGGTAAACCAAT 58.155 40.909 0.81 0.00 43.89 3.16
2214 2304 4.993028 ACTTCAGCAAGGGTAAACCAATA 58.007 39.130 0.81 0.00 43.89 1.90
2216 2306 6.016555 ACTTCAGCAAGGGTAAACCAATATT 58.983 36.000 0.81 0.00 43.89 1.28
2217 2307 6.496911 ACTTCAGCAAGGGTAAACCAATATTT 59.503 34.615 0.81 0.00 43.89 1.40
2223 2345 5.022282 AGGGTAAACCAATATTTGCATGC 57.978 39.130 11.82 11.82 43.89 4.06
2313 2437 6.747280 CCAATTGACCACGAGAATTTGATAAC 59.253 38.462 7.12 0.00 0.00 1.89
2491 2616 3.002791 GAGAGATCCGCATCACAACAAA 58.997 45.455 0.00 0.00 0.00 2.83
2600 2725 2.107378 TGTGGAACCATCACTAGCCAAA 59.893 45.455 0.00 0.00 36.21 3.28
2633 2758 8.289618 TGTAAATCATTCTGGTCTTCTTTTTCG 58.710 33.333 0.00 0.00 0.00 3.46
2800 2925 9.371136 TGTTCTTGTAAGAAGATTAGCTATGTG 57.629 33.333 7.28 0.00 45.01 3.21
2801 2926 9.372369 GTTCTTGTAAGAAGATTAGCTATGTGT 57.628 33.333 7.28 0.00 45.01 3.72
2848 2973 4.032960 TCTGATAAAACCCACACTGCAT 57.967 40.909 0.00 0.00 0.00 3.96
3092 3218 3.387699 ACAAGTATGTTTGCCCAGCTTTT 59.612 39.130 0.00 0.00 35.91 2.27
3093 3219 4.141733 ACAAGTATGTTTGCCCAGCTTTTT 60.142 37.500 0.00 0.00 35.91 1.94
3094 3220 4.257267 AGTATGTTTGCCCAGCTTTTTC 57.743 40.909 0.00 0.00 0.00 2.29
3125 3251 8.464770 TCAAACTTGCAAGAATTATGTATTGC 57.535 30.769 32.50 1.96 46.36 3.56
3619 3768 3.374764 ACTGGAGAGGTATGCACATGTA 58.625 45.455 0.00 0.00 0.00 2.29
3633 3782 3.490526 GCACATGTACAAACTTTGCTTGG 59.509 43.478 0.00 0.00 0.00 3.61
3635 3784 4.977963 CACATGTACAAACTTTGCTTGGAG 59.022 41.667 0.00 0.00 0.00 3.86
3658 3807 9.032420 GGAGGAACTAAGACGTTATCAAAATAG 57.968 37.037 0.00 0.00 41.55 1.73
3660 3809 8.038944 AGGAACTAAGACGTTATCAAAATAGCA 58.961 33.333 0.00 0.00 36.02 3.49
3802 3951 5.804639 TCAGACACCTAGTAAATTGCATGT 58.195 37.500 0.00 0.00 0.00 3.21
3823 3972 9.531942 GCATGTTTATATGGTGATCATTTTGAA 57.468 29.630 0.00 0.00 37.30 2.69
3984 4133 3.247442 TCAGTTTTATCACGTGCTACCG 58.753 45.455 11.67 0.00 0.00 4.02
4016 4165 7.548097 TGTTCTTCAGTATCTCTAATTCGCTT 58.452 34.615 0.00 0.00 0.00 4.68
4047 4196 1.311859 TTGTTGCCTTCTGTGCTGAG 58.688 50.000 0.00 0.00 0.00 3.35
4792 4948 2.351336 GACCTACGGTGCTGATCGGG 62.351 65.000 3.14 0.00 35.25 5.14
5137 5293 6.093219 GCTATCCTGTACCATATGAAATGCAG 59.907 42.308 3.65 8.24 0.00 4.41
5157 5313 4.096081 GCAGCAGAGCTTAATGAAAGACAT 59.904 41.667 0.00 0.00 36.40 3.06
5408 5566 8.814038 ATGAAGTCCTGCTTAGTCAAAATAAT 57.186 30.769 0.00 0.00 37.59 1.28
5491 5649 2.243810 GGATTTGGCCTTGGTGTTGTA 58.756 47.619 3.32 0.00 0.00 2.41
5552 5710 1.209019 CTGCCTGTAAGTGCCTCTCAT 59.791 52.381 0.00 0.00 30.41 2.90
6083 6241 6.288294 ACATATATGCCGTGTCTGTTGTAAT 58.712 36.000 12.79 0.00 0.00 1.89
6296 6454 6.316390 GTGAAGGAGTTAACTAATGGATGGTG 59.684 42.308 8.42 0.00 0.00 4.17
6298 6456 6.388619 AGGAGTTAACTAATGGATGGTGTT 57.611 37.500 8.42 0.00 0.00 3.32
6304 6462 9.020731 AGTTAACTAATGGATGGTGTTAAAAGG 57.979 33.333 6.26 0.00 35.69 3.11
6315 6473 7.650504 GGATGGTGTTAAAAGGTTTAGTCAAAC 59.349 37.037 0.00 0.00 42.82 2.93
6388 6546 6.630840 GGTTTTGCATCAAAAACATTTTACCG 59.369 34.615 13.36 0.00 46.49 4.02
6478 6636 7.934855 ATCAATGGCTTGGATCTATTATCAC 57.065 36.000 0.00 0.00 32.95 3.06
6496 6654 2.038033 TCACGTGAAAAGGGGAGGTAAG 59.962 50.000 17.62 0.00 0.00 2.34
6505 6663 0.620700 GGGGAGGTAAGAGGGAGCAA 60.621 60.000 0.00 0.00 0.00 3.91
6506 6664 1.512735 GGGAGGTAAGAGGGAGCAAT 58.487 55.000 0.00 0.00 0.00 3.56
6507 6665 1.141858 GGGAGGTAAGAGGGAGCAATG 59.858 57.143 0.00 0.00 0.00 2.82
6508 6666 1.475930 GGAGGTAAGAGGGAGCAATGC 60.476 57.143 0.00 0.00 0.00 3.56
6509 6667 1.488393 GAGGTAAGAGGGAGCAATGCT 59.512 52.381 7.79 7.79 43.88 3.79
6513 6671 4.018415 AGGTAAGAGGGAGCAATGCTAAAA 60.018 41.667 8.12 0.00 39.88 1.52
6531 8184 8.586570 TGCTAAAATTTACCATTCAACAACTG 57.413 30.769 0.00 0.00 0.00 3.16
6537 8190 7.833285 ATTTACCATTCAACAACTGTAAGGT 57.167 32.000 0.00 0.00 39.30 3.50
6539 8192 7.972832 TTACCATTCAACAACTGTAAGGTAG 57.027 36.000 0.00 0.00 39.30 3.18
6572 8225 9.868277 CAACATCAAAAGTAATTATTAGGGCAA 57.132 29.630 0.00 0.00 0.00 4.52
6589 8242 0.606401 CAACTCCAATGCACGACCCT 60.606 55.000 0.00 0.00 0.00 4.34
6593 8246 2.026262 ACTCCAATGCACGACCCTAAAT 60.026 45.455 0.00 0.00 0.00 1.40
6595 8248 2.026729 TCCAATGCACGACCCTAAATGA 60.027 45.455 0.00 0.00 0.00 2.57
6620 8273 3.002965 GTCCGTTTTGTCTGGATTTCGTT 59.997 43.478 0.00 0.00 33.63 3.85
6622 8275 3.002862 CCGTTTTGTCTGGATTTCGTTCA 59.997 43.478 0.00 0.00 0.00 3.18
6625 8278 5.578776 GTTTTGTCTGGATTTCGTTCAGTT 58.421 37.500 0.00 0.00 0.00 3.16
6639 8292 2.045561 TCAGTTTGGCAGAAACGGAA 57.954 45.000 9.82 0.00 32.87 4.30
6641 8294 2.955660 TCAGTTTGGCAGAAACGGAAAT 59.044 40.909 9.82 0.00 32.87 2.17
6684 8337 0.102844 ACGGAAGTTCGTTTCGTCCA 59.897 50.000 0.00 0.00 46.40 4.02
6691 8344 2.729882 AGTTCGTTTCGTCCAGATTTCG 59.270 45.455 0.00 0.00 0.00 3.46
6692 8345 2.427232 TCGTTTCGTCCAGATTTCGT 57.573 45.000 0.00 0.00 0.00 3.85
6700 8353 1.463444 GTCCAGATTTCGTCCGGTTTG 59.537 52.381 0.00 0.00 0.00 2.93
6701 8354 0.802494 CCAGATTTCGTCCGGTTTGG 59.198 55.000 0.00 0.00 40.09 3.28
6711 8364 1.894756 CCGGTTTGGGCAGAAACGA 60.895 57.895 10.51 0.00 36.80 3.85
6720 8373 1.956043 GCAGAAACGAACATGCCCA 59.044 52.632 0.00 0.00 32.49 5.36
6723 8376 1.133025 CAGAAACGAACATGCCCATCC 59.867 52.381 0.00 0.00 0.00 3.51
6730 8383 3.142162 CATGCCCATCCGCTTGCA 61.142 61.111 0.00 0.00 38.23 4.08
6780 8433 1.226660 CGCCGCATCCCAAATTGTC 60.227 57.895 0.00 0.00 0.00 3.18
6781 8434 1.141665 GCCGCATCCCAAATTGTCC 59.858 57.895 0.00 0.00 0.00 4.02
6784 8437 0.179166 CGCATCCCAAATTGTCCGTG 60.179 55.000 0.00 0.00 0.00 4.94
6827 8480 6.929606 TGACCCAAAATAAACCCAAATAAACG 59.070 34.615 0.00 0.00 0.00 3.60
6840 8493 9.490379 AACCCAAATAAACGTTGCAAATAATTA 57.510 25.926 0.00 0.00 0.00 1.40
6841 8494 9.490379 ACCCAAATAAACGTTGCAAATAATTAA 57.510 25.926 0.00 0.00 0.00 1.40
6898 8551 4.392138 GTCCATAGTAGCCAAGTTCAACAC 59.608 45.833 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.755655 TGTCGGATCCTCAAAGAGTCTC 59.244 50.000 10.75 0.00 0.00 3.36
2 3 3.810310 ATGTCGGATCCTCAAAGAGTC 57.190 47.619 10.75 0.00 0.00 3.36
4 5 3.119291 CGAATGTCGGATCCTCAAAGAG 58.881 50.000 10.75 0.00 36.00 2.85
5 6 3.165058 CGAATGTCGGATCCTCAAAGA 57.835 47.619 10.75 0.00 36.00 2.52
17 18 2.202610 TCGAGCAGCCGAATGTCG 60.203 61.111 3.77 0.00 40.07 4.35
18 19 1.880340 CCTCGAGCAGCCGAATGTC 60.880 63.158 6.99 0.00 38.17 3.06
19 20 2.185350 CCTCGAGCAGCCGAATGT 59.815 61.111 6.99 0.00 38.17 2.71
20 21 2.587194 CCCTCGAGCAGCCGAATG 60.587 66.667 6.99 2.73 38.17 2.67
21 22 2.759973 TCCCTCGAGCAGCCGAAT 60.760 61.111 6.99 0.00 38.17 3.34
22 23 3.452786 CTCCCTCGAGCAGCCGAA 61.453 66.667 6.99 0.00 38.17 4.30
23 24 3.723097 ATCTCCCTCGAGCAGCCGA 62.723 63.158 6.99 5.94 35.94 5.54
24 25 3.206211 GATCTCCCTCGAGCAGCCG 62.206 68.421 6.99 0.00 35.94 5.52
25 26 2.733945 GATCTCCCTCGAGCAGCC 59.266 66.667 6.99 0.00 35.94 4.85
26 27 2.190170 TCGATCTCCCTCGAGCAGC 61.190 63.158 6.99 0.00 42.38 5.25
27 28 4.149346 TCGATCTCCCTCGAGCAG 57.851 61.111 6.99 5.04 42.38 4.24
31 32 0.392060 TCGTTGTCGATCTCCCTCGA 60.392 55.000 0.00 0.00 44.85 4.04
32 33 0.028242 CTCGTTGTCGATCTCCCTCG 59.972 60.000 0.00 0.00 45.21 4.63
33 34 0.382515 CCTCGTTGTCGATCTCCCTC 59.617 60.000 0.00 0.00 45.21 4.30
34 35 0.034380 TCCTCGTTGTCGATCTCCCT 60.034 55.000 0.00 0.00 45.21 4.20
35 36 0.382515 CTCCTCGTTGTCGATCTCCC 59.617 60.000 0.00 0.00 45.21 4.30
36 37 0.382515 CCTCCTCGTTGTCGATCTCC 59.617 60.000 0.00 0.00 45.21 3.71
37 38 1.332375 CTCCTCCTCGTTGTCGATCTC 59.668 57.143 0.00 0.00 45.21 2.75
38 39 1.065345 TCTCCTCCTCGTTGTCGATCT 60.065 52.381 0.00 0.00 45.21 2.75
39 40 1.064357 GTCTCCTCCTCGTTGTCGATC 59.936 57.143 0.00 0.00 45.21 3.69
40 41 1.096416 GTCTCCTCCTCGTTGTCGAT 58.904 55.000 0.00 0.00 45.21 3.59
41 42 1.296755 CGTCTCCTCCTCGTTGTCGA 61.297 60.000 0.00 0.00 44.12 4.20
42 43 1.134901 CGTCTCCTCCTCGTTGTCG 59.865 63.158 0.00 0.00 38.55 4.35
43 44 0.168568 GTCGTCTCCTCCTCGTTGTC 59.831 60.000 0.00 0.00 0.00 3.18
44 45 1.242665 GGTCGTCTCCTCCTCGTTGT 61.243 60.000 0.00 0.00 0.00 3.32
45 46 0.961358 AGGTCGTCTCCTCCTCGTTG 60.961 60.000 0.00 0.00 31.32 4.10
46 47 0.251253 AAGGTCGTCTCCTCCTCGTT 60.251 55.000 0.00 0.00 36.74 3.85
47 48 0.961358 CAAGGTCGTCTCCTCCTCGT 60.961 60.000 0.00 0.00 36.74 4.18
48 49 1.658686 CCAAGGTCGTCTCCTCCTCG 61.659 65.000 0.00 0.00 36.74 4.63
49 50 0.612453 ACCAAGGTCGTCTCCTCCTC 60.612 60.000 0.00 0.00 36.74 3.71
50 51 0.612453 GACCAAGGTCGTCTCCTCCT 60.612 60.000 3.08 0.00 36.74 3.69
51 52 1.891616 GACCAAGGTCGTCTCCTCC 59.108 63.158 3.08 0.00 36.74 4.30
60 61 1.805945 CTAGCGCGTGACCAAGGTC 60.806 63.158 12.30 12.30 44.77 3.85
61 62 2.261671 CTAGCGCGTGACCAAGGT 59.738 61.111 8.43 0.00 0.00 3.50
62 63 2.094659 CACTAGCGCGTGACCAAGG 61.095 63.158 8.43 0.00 37.06 3.61
63 64 1.080772 TCACTAGCGCGTGACCAAG 60.081 57.895 13.23 0.00 38.89 3.61
64 65 3.044280 TCACTAGCGCGTGACCAA 58.956 55.556 13.23 0.00 38.89 3.67
68 69 1.289276 TATACGTCACTAGCGCGTGA 58.711 50.000 13.23 13.23 41.33 4.35
69 70 2.095384 TTATACGTCACTAGCGCGTG 57.905 50.000 8.43 8.91 39.31 5.34
70 71 2.288729 TGATTATACGTCACTAGCGCGT 59.711 45.455 8.43 10.75 41.86 6.01
71 72 2.912366 TGATTATACGTCACTAGCGCG 58.088 47.619 0.00 0.00 0.00 6.86
72 73 4.288531 ACTTGATTATACGTCACTAGCGC 58.711 43.478 0.00 0.00 0.00 5.92
73 74 7.903452 TTTACTTGATTATACGTCACTAGCG 57.097 36.000 0.00 0.00 0.00 4.26
88 89 7.544217 GCCGTTTTGTCCAATATTTTACTTGAT 59.456 33.333 0.00 0.00 0.00 2.57
113 114 0.657840 AAAGTGTGAGCGAAGTGTGC 59.342 50.000 0.00 0.00 0.00 4.57
156 157 7.362662 CCATTTGTGTCACTTACATATATGGC 58.637 38.462 16.96 0.00 45.06 4.40
332 355 4.204799 GGGCTAGTAAACCCAAATAGTGG 58.795 47.826 3.45 0.00 46.22 4.00
341 364 0.108019 CGATGGGGGCTAGTAAACCC 59.892 60.000 0.00 0.00 46.24 4.11
342 365 0.835276 ACGATGGGGGCTAGTAAACC 59.165 55.000 0.00 0.00 0.00 3.27
343 366 4.347360 AATACGATGGGGGCTAGTAAAC 57.653 45.455 0.00 0.00 0.00 2.01
344 367 4.409574 TCAAATACGATGGGGGCTAGTAAA 59.590 41.667 0.00 0.00 0.00 2.01
345 368 3.968649 TCAAATACGATGGGGGCTAGTAA 59.031 43.478 0.00 0.00 0.00 2.24
346 369 3.576982 CTCAAATACGATGGGGGCTAGTA 59.423 47.826 0.00 0.00 0.00 1.82
347 370 2.368875 CTCAAATACGATGGGGGCTAGT 59.631 50.000 0.00 0.00 0.00 2.57
348 371 2.289694 CCTCAAATACGATGGGGGCTAG 60.290 54.545 0.00 0.00 34.60 3.42
349 372 1.697432 CCTCAAATACGATGGGGGCTA 59.303 52.381 0.00 0.00 34.60 3.93
350 373 0.474184 CCTCAAATACGATGGGGGCT 59.526 55.000 0.00 0.00 34.60 5.19
444 467 2.499289 CACTCTAATGCCTCTGTCCTGT 59.501 50.000 0.00 0.00 0.00 4.00
517 540 3.667960 GCGGAAACTGTCACATTCATGTC 60.668 47.826 0.00 0.00 39.39 3.06
550 573 5.461078 GCTTTCCGAAAATGATACGCTAGTA 59.539 40.000 0.00 0.00 37.24 1.82
551 574 4.270325 GCTTTCCGAAAATGATACGCTAGT 59.730 41.667 0.00 0.00 0.00 2.57
552 575 4.318831 GGCTTTCCGAAAATGATACGCTAG 60.319 45.833 0.00 0.00 0.00 3.42
634 657 0.029834 CGACGTACGGGGGTCATTAG 59.970 60.000 21.06 0.00 38.46 1.73
654 677 0.034186 ATGGATGGTGAACATGGCGT 60.034 50.000 0.00 0.00 40.72 5.68
657 680 1.942657 GTCGATGGATGGTGAACATGG 59.057 52.381 0.00 0.00 40.72 3.66
658 681 1.942657 GGTCGATGGATGGTGAACATG 59.057 52.381 0.00 0.00 40.72 3.21
659 682 1.134098 GGGTCGATGGATGGTGAACAT 60.134 52.381 0.00 0.00 44.18 2.71
662 694 0.620410 AGGGGTCGATGGATGGTGAA 60.620 55.000 0.00 0.00 0.00 3.18
681 713 0.759959 TCTGCCTCCCGTTTTACACA 59.240 50.000 0.00 0.00 0.00 3.72
682 714 2.007608 GATCTGCCTCCCGTTTTACAC 58.992 52.381 0.00 0.00 0.00 2.90
703 737 2.438385 TTTTCGCACGCCGCTTCTTC 62.438 55.000 0.00 0.00 39.08 2.87
704 738 1.852067 ATTTTCGCACGCCGCTTCTT 61.852 50.000 0.00 0.00 39.08 2.52
705 739 2.240612 GATTTTCGCACGCCGCTTCT 62.241 55.000 0.00 0.00 39.08 2.85
869 910 3.093172 GGAGGGAGGCTGGGGAAG 61.093 72.222 0.00 0.00 0.00 3.46
870 911 3.953652 TGGAGGGAGGCTGGGGAA 61.954 66.667 0.00 0.00 0.00 3.97
871 912 4.741239 GTGGAGGGAGGCTGGGGA 62.741 72.222 0.00 0.00 0.00 4.81
1182 1247 3.256879 TCAGGCAAAACACAGACAAAACA 59.743 39.130 0.00 0.00 0.00 2.83
1183 1248 3.612423 GTCAGGCAAAACACAGACAAAAC 59.388 43.478 0.00 0.00 0.00 2.43
1184 1249 3.671971 CGTCAGGCAAAACACAGACAAAA 60.672 43.478 0.00 0.00 0.00 2.44
1185 1250 2.159448 CGTCAGGCAAAACACAGACAAA 60.159 45.455 0.00 0.00 0.00 2.83
1186 1251 1.400142 CGTCAGGCAAAACACAGACAA 59.600 47.619 0.00 0.00 0.00 3.18
1187 1252 1.013596 CGTCAGGCAAAACACAGACA 58.986 50.000 0.00 0.00 0.00 3.41
1188 1253 0.317020 GCGTCAGGCAAAACACAGAC 60.317 55.000 0.00 0.00 42.87 3.51
1189 1254 2.021722 GCGTCAGGCAAAACACAGA 58.978 52.632 0.00 0.00 42.87 3.41
1190 1255 4.614673 GCGTCAGGCAAAACACAG 57.385 55.556 0.00 0.00 42.87 3.66
1245 1310 2.887568 CAGCTCGTGCATCCGTCC 60.888 66.667 12.58 0.00 42.74 4.79
1264 1329 3.465403 CCTCCTCCGCACCTCCAG 61.465 72.222 0.00 0.00 0.00 3.86
1548 1632 2.109425 ACTAGCGAACCCAAATGGAC 57.891 50.000 0.00 0.00 37.39 4.02
1632 1716 6.694447 ACTTATAGGCACGTCAAAAGTTCTA 58.306 36.000 0.00 0.00 0.00 2.10
1652 1736 2.745821 ACGAGACACGCATACTGACTTA 59.254 45.455 0.00 0.00 46.94 2.24
1688 1772 6.312399 ACTACGCATTTCAGATTTGTTTCA 57.688 33.333 0.00 0.00 0.00 2.69
1797 1881 0.387202 CATACTGGGTGCGAGGAGAG 59.613 60.000 0.00 0.00 0.00 3.20
1799 1883 1.443407 CCATACTGGGTGCGAGGAG 59.557 63.158 0.00 0.00 32.67 3.69
1841 1925 1.231958 TTTTAACGCGACCAGCTGGG 61.232 55.000 35.42 20.34 45.59 4.45
1975 2059 4.789095 TCGTTGTTTTGCTCAACTACTC 57.211 40.909 9.92 0.00 41.76 2.59
2161 2251 8.430431 TGATGAATATTGGTTTACCATACGGTA 58.570 33.333 1.81 0.00 46.71 4.02
2176 2266 8.920509 TTGCTGAAGTTTCATGATGAATATTG 57.079 30.769 8.90 0.00 36.11 1.90
2178 2268 7.201884 CCCTTGCTGAAGTTTCATGATGAATAT 60.202 37.037 8.90 0.00 36.11 1.28
2179 2269 6.095860 CCCTTGCTGAAGTTTCATGATGAATA 59.904 38.462 8.90 0.00 36.11 1.75
2180 2270 5.105473 CCCTTGCTGAAGTTTCATGATGAAT 60.105 40.000 8.90 0.00 36.11 2.57
2182 2272 3.760151 CCCTTGCTGAAGTTTCATGATGA 59.240 43.478 0.00 0.00 36.46 2.92
2184 2274 3.771216 ACCCTTGCTGAAGTTTCATGAT 58.229 40.909 0.00 0.00 36.46 2.45
2186 2276 5.222631 GTTTACCCTTGCTGAAGTTTCATG 58.777 41.667 0.00 0.00 36.46 3.07
2187 2277 4.280929 GGTTTACCCTTGCTGAAGTTTCAT 59.719 41.667 0.00 0.00 36.46 2.57
2188 2278 3.634910 GGTTTACCCTTGCTGAAGTTTCA 59.365 43.478 0.00 0.00 35.57 2.69
2189 2279 3.634910 TGGTTTACCCTTGCTGAAGTTTC 59.365 43.478 0.00 0.00 34.29 2.78
2190 2280 3.637769 TGGTTTACCCTTGCTGAAGTTT 58.362 40.909 0.00 0.00 34.29 2.66
2192 2282 3.306472 TTGGTTTACCCTTGCTGAAGT 57.694 42.857 0.00 0.00 34.29 3.01
2193 2283 6.530019 AATATTGGTTTACCCTTGCTGAAG 57.470 37.500 0.00 0.00 34.29 3.02
2194 2284 6.696411 CAAATATTGGTTTACCCTTGCTGAA 58.304 36.000 0.00 0.00 34.29 3.02
2196 2286 4.869861 GCAAATATTGGTTTACCCTTGCTG 59.130 41.667 0.00 0.00 34.29 4.41
2197 2287 4.530161 TGCAAATATTGGTTTACCCTTGCT 59.470 37.500 14.86 0.00 34.29 3.91
2198 2288 4.826556 TGCAAATATTGGTTTACCCTTGC 58.173 39.130 0.00 5.04 34.29 4.01
2199 2289 5.294060 GCATGCAAATATTGGTTTACCCTTG 59.706 40.000 14.21 0.00 34.29 3.61
2200 2290 5.046014 TGCATGCAAATATTGGTTTACCCTT 60.046 36.000 20.30 0.00 34.29 3.95
2201 2291 4.469227 TGCATGCAAATATTGGTTTACCCT 59.531 37.500 20.30 0.00 34.29 4.34
2202 2292 4.764172 TGCATGCAAATATTGGTTTACCC 58.236 39.130 20.30 0.00 34.29 3.69
2203 2293 6.923928 ATTGCATGCAAATATTGGTTTACC 57.076 33.333 34.84 0.00 39.55 2.85
2204 2294 9.063739 CAAAATTGCATGCAAATATTGGTTTAC 57.936 29.630 34.84 0.00 39.55 2.01
2205 2295 8.790718 ACAAAATTGCATGCAAATATTGGTTTA 58.209 25.926 34.50 17.39 39.55 2.01
2206 2296 7.659186 ACAAAATTGCATGCAAATATTGGTTT 58.341 26.923 34.50 26.96 39.55 3.27
2207 2297 7.216973 ACAAAATTGCATGCAAATATTGGTT 57.783 28.000 34.50 24.17 39.55 3.67
2216 2306 8.034215 AGCTAACTATAACAAAATTGCATGCAA 58.966 29.630 33.57 33.57 40.47 4.08
2217 2307 7.546358 AGCTAACTATAACAAAATTGCATGCA 58.454 30.769 18.46 18.46 0.00 3.96
2600 2725 8.814038 AAGACCAGAATGATTTACAGCTTATT 57.186 30.769 0.00 0.00 39.69 1.40
2633 2758 7.968405 CCTGCATACACATTAAGAAAACCTTAC 59.032 37.037 0.00 0.00 37.10 2.34
2774 2899 9.371136 CACATAGCTAATCTTCTTACAAGAACA 57.629 33.333 0.00 0.00 39.95 3.18
2800 2925 3.764885 ACAAGGAATTCGCTGCATTAC 57.235 42.857 0.00 0.00 0.00 1.89
2801 2926 3.755905 TCAACAAGGAATTCGCTGCATTA 59.244 39.130 0.00 0.00 0.00 1.90
2848 2973 4.334203 ACTGCAACAAATTGACTACGTTGA 59.666 37.500 3.44 0.00 39.39 3.18
3125 3251 4.941263 TCCAATCAGTCCCAAAGATAAACG 59.059 41.667 0.00 0.00 0.00 3.60
3133 3259 1.780309 ACACCTCCAATCAGTCCCAAA 59.220 47.619 0.00 0.00 0.00 3.28
3619 3768 3.365472 AGTTCCTCCAAGCAAAGTTTGT 58.635 40.909 16.70 1.59 0.00 2.83
3633 3782 8.541312 GCTATTTTGATAACGTCTTAGTTCCTC 58.459 37.037 0.00 0.00 35.70 3.71
3635 3784 8.193250 TGCTATTTTGATAACGTCTTAGTTCC 57.807 34.615 0.00 0.00 35.70 3.62
3640 3789 7.333423 AGTGCTTGCTATTTTGATAACGTCTTA 59.667 33.333 0.00 0.00 0.00 2.10
3658 3807 6.197842 GCACATATCAGATTTTAAGTGCTTGC 59.802 38.462 0.00 0.00 45.41 4.01
3678 3827 1.479323 GCCATCAAGGACAATGCACAT 59.521 47.619 0.00 0.00 41.22 3.21
4016 4165 8.081633 CACAGAAGGCAACAAACTGAAATATAA 58.918 33.333 0.00 0.00 36.96 0.98
4047 4196 5.964758 TCCCTGCAATCAACACATTTTATC 58.035 37.500 0.00 0.00 0.00 1.75
4215 4364 6.261603 TCAGATGTGTTCCAGATAATGCATTC 59.738 38.462 16.86 2.18 0.00 2.67
4792 4948 0.755686 CCCTGCCTACTCCAGATGTC 59.244 60.000 0.00 0.00 32.03 3.06
5137 5293 5.124457 TGGAATGTCTTTCATTAAGCTCTGC 59.876 40.000 0.00 0.00 45.49 4.26
5157 5313 8.635765 AGTATAAGAAGAAAGCAAACATGGAA 57.364 30.769 0.00 0.00 0.00 3.53
5408 5566 6.127054 CCCAGACAATCAGGTATGAAGAACTA 60.127 42.308 0.00 0.00 39.39 2.24
5491 5649 0.734889 CGCGGATTGCTCCAGAAATT 59.265 50.000 0.00 0.00 42.19 1.82
6083 6241 3.207265 TGCTTAACTTCTTCCACAGCA 57.793 42.857 0.00 0.00 33.46 4.41
6296 6454 6.375945 TCCCGTTTGACTAAACCTTTTAAC 57.624 37.500 0.00 0.00 42.50 2.01
6298 6456 7.585579 ATTTCCCGTTTGACTAAACCTTTTA 57.414 32.000 0.00 0.00 42.50 1.52
6388 6546 3.696898 TGTGTCACAAAAATTACACGGC 58.303 40.909 2.31 0.00 44.03 5.68
6458 6616 5.012046 TCACGTGATAATAGATCCAAGCCAT 59.988 40.000 15.76 0.00 0.00 4.40
6478 6636 2.354805 CCTCTTACCTCCCCTTTTCACG 60.355 54.545 0.00 0.00 0.00 4.35
6496 6654 5.127031 TGGTAAATTTTAGCATTGCTCCCTC 59.873 40.000 15.81 0.00 40.44 4.30
6505 6663 9.206870 CAGTTGTTGAATGGTAAATTTTAGCAT 57.793 29.630 22.09 22.09 37.26 3.79
6506 6664 8.200792 ACAGTTGTTGAATGGTAAATTTTAGCA 58.799 29.630 19.92 19.92 0.00 3.49
6507 6665 8.587952 ACAGTTGTTGAATGGTAAATTTTAGC 57.412 30.769 10.67 10.67 0.00 3.09
6513 6671 7.833285 ACCTTACAGTTGTTGAATGGTAAAT 57.167 32.000 0.00 0.00 0.00 1.40
6572 8225 0.981183 TTAGGGTCGTGCATTGGAGT 59.019 50.000 0.00 0.00 0.00 3.85
6589 8242 5.823570 TCCAGACAAAACGGACTTTCATTTA 59.176 36.000 0.00 0.00 0.00 1.40
6593 8246 3.269538 TCCAGACAAAACGGACTTTCA 57.730 42.857 0.00 0.00 0.00 2.69
6595 8248 4.261031 CGAAATCCAGACAAAACGGACTTT 60.261 41.667 0.00 0.00 0.00 2.66
6620 8273 2.045561 TTCCGTTTCTGCCAAACTGA 57.954 45.000 6.76 3.47 0.00 3.41
6622 8275 2.545742 GCATTTCCGTTTCTGCCAAACT 60.546 45.455 6.76 0.00 0.00 2.66
6625 8278 3.883997 GCATTTCCGTTTCTGCCAA 57.116 47.368 0.00 0.00 0.00 4.52
6639 8292 2.642700 GTGCGTTTGACGGGCATT 59.357 55.556 2.48 0.00 42.82 3.56
6641 8294 4.893601 TCGTGCGTTTGACGGGCA 62.894 61.111 2.48 0.00 42.82 5.36
6649 8302 2.825975 CGTTTGGGGTCGTGCGTTT 61.826 57.895 0.00 0.00 0.00 3.60
6673 8326 2.322161 GACGAAATCTGGACGAAACGA 58.678 47.619 0.00 0.00 0.00 3.85
6684 8337 0.958876 GCCCAAACCGGACGAAATCT 60.959 55.000 9.46 0.00 36.56 2.40
6691 8344 1.658114 GTTTCTGCCCAAACCGGAC 59.342 57.895 9.46 0.00 36.56 4.79
6692 8345 1.894756 CGTTTCTGCCCAAACCGGA 60.895 57.895 9.46 0.00 36.56 5.14
6700 8353 1.212751 GGCATGTTCGTTTCTGCCC 59.787 57.895 9.62 0.00 46.76 5.36
6701 8354 4.868195 GGCATGTTCGTTTCTGCC 57.132 55.556 0.00 6.18 46.54 4.85
6711 8364 2.713967 GCAAGCGGATGGGCATGTT 61.714 57.895 0.00 0.00 34.33 2.71
6720 8373 3.121030 GCACGACTGCAAGCGGAT 61.121 61.111 8.05 0.00 43.62 4.18
6759 8412 1.455587 AATTTGGGATGCGGCGGAT 60.456 52.632 15.43 15.43 0.00 4.18
6763 8416 1.141665 GGACAATTTGGGATGCGGC 59.858 57.895 0.78 0.00 0.00 6.53
6780 8433 6.362283 GTCAAAATTCAAGTCCAAATACACGG 59.638 38.462 0.00 0.00 0.00 4.94
6781 8434 6.362283 GGTCAAAATTCAAGTCCAAATACACG 59.638 38.462 0.00 0.00 0.00 4.49
6784 8437 6.754193 TGGGTCAAAATTCAAGTCCAAATAC 58.246 36.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.