Multiple sequence alignment - TraesCS6D01G313300

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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 TraesCS6D01G313300 chr6D 100.000 3478 0 0 1 3478 422189735 422193212 0.000000e+00 6423.0
1 TraesCS6D01G313300 chr6D 88.916 2066 131 51 680 2708 422205736 422203732 0.000000e+00 2457.0
2 TraesCS6D01G313300 chr6D 92.947 1347 80 9 1153 2494 409347221 409348557 0.000000e+00 1947.0
3 TraesCS6D01G313300 chr6D 87.943 423 26 6 260 660 422206346 422205927 3.140000e-130 475.0
4 TraesCS6D01G313300 chr6D 86.863 373 36 6 777 1149 409346574 409346933 4.180000e-109 405.0
5 TraesCS6D01G313300 chr6D 89.130 138 13 2 2491 2628 409348603 409348738 1.660000e-38 171.0
6 TraesCS6D01G313300 chr6B 90.408 2106 113 49 666 2737 636491310 636493360 0.000000e+00 2687.0
7 TraesCS6D01G313300 chr6B 90.645 2063 115 41 689 2721 636586182 636584168 0.000000e+00 2669.0
8 TraesCS6D01G313300 chr6B 91.156 1617 105 23 900 2490 614311632 614313236 0.000000e+00 2159.0
9 TraesCS6D01G313300 chr6B 91.044 1619 105 21 900 2490 614436943 614438549 0.000000e+00 2150.0
10 TraesCS6D01G313300 chr6B 90.999 1622 101 27 900 2490 614582000 614583607 0.000000e+00 2145.0
11 TraesCS6D01G313300 chr6B 94.294 333 17 1 329 661 636490820 636491150 3.100000e-140 508.0
12 TraesCS6D01G313300 chr6B 92.063 189 14 1 153 341 636490463 636490650 7.400000e-67 265.0
13 TraesCS6D01G313300 chr6B 83.696 184 22 7 2491 2672 614583657 614583834 2.150000e-37 167.0
14 TraesCS6D01G313300 chr6B 89.286 112 11 1 153 264 614434586 614434696 4.680000e-29 139.0
15 TraesCS6D01G313300 chr6B 87.850 107 12 1 347 452 614310956 614311062 1.310000e-24 124.0
16 TraesCS6D01G313300 chr6B 87.179 78 10 0 777 854 614311539 614311616 4.780000e-14 89.8
17 TraesCS6D01G313300 chr6B 87.179 78 10 0 777 854 614436850 614436927 4.780000e-14 89.8
18 TraesCS6D01G313300 chr6B 86.154 65 9 0 790 854 614581920 614581984 1.730000e-08 71.3
19 TraesCS6D01G313300 chr6B 97.436 39 1 0 3203 3241 472357955 472357917 2.240000e-07 67.6
20 TraesCS6D01G313300 chr6B 97.436 39 1 0 3203 3241 646686348 646686386 2.240000e-07 67.6
21 TraesCS6D01G313300 chr6A 93.221 1844 93 19 664 2495 564974516 564976339 0.000000e+00 2684.0
22 TraesCS6D01G313300 chr6A 92.144 1833 97 25 681 2487 564910999 564909188 0.000000e+00 2543.0
23 TraesCS6D01G313300 chr6A 93.820 1343 69 11 1153 2489 554824772 554826106 0.000000e+00 2008.0
24 TraesCS6D01G313300 chr6A 91.775 462 26 6 2491 2945 564976388 564976844 1.760000e-177 632.0
25 TraesCS6D01G313300 chr6A 88.462 442 26 9 153 585 564973826 564974251 8.610000e-141 510.0
26 TraesCS6D01G313300 chr6A 85.146 377 39 9 777 1151 554824112 554824473 1.520000e-98 370.0
27 TraesCS6D01G313300 chr6A 95.833 192 8 0 2998 3189 564976841 564977032 9.370000e-81 311.0
28 TraesCS6D01G313300 chr6A 90.222 225 14 5 3173 3395 564979542 564979760 1.580000e-73 287.0
29 TraesCS6D01G313300 chr6A 84.000 250 23 13 2491 2737 564909132 564908897 1.260000e-54 224.0
30 TraesCS6D01G313300 chr6A 84.071 226 23 10 2501 2725 564907831 564907618 4.550000e-49 206.0
31 TraesCS6D01G313300 chr6A 95.385 65 2 1 2522 2586 554826703 554826766 6.140000e-18 102.0
32 TraesCS6D01G313300 chrUn 89.831 59 5 1 3196 3253 371076458 371076400 1.340000e-09 75.0
33 TraesCS6D01G313300 chr4A 89.831 59 5 1 3196 3253 733438211 733438269 1.340000e-09 75.0
34 TraesCS6D01G313300 chr4A 97.436 39 1 0 3203 3241 675683862 675683900 2.240000e-07 67.6
35 TraesCS6D01G313300 chr3A 95.455 44 2 0 3198 3241 36311071 36311028 1.730000e-08 71.3
36 TraesCS6D01G313300 chr7B 97.436 39 1 0 3203 3241 6549333 6549295 2.240000e-07 67.6
37 TraesCS6D01G313300 chr1B 97.436 39 1 0 3203 3241 655665409 655665371 2.240000e-07 67.6


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 TraesCS6D01G313300 chr6D 422189735 422193212 3477 False 6423.000000 6423 100.000000 1 3478 1 chr6D.!!$F1 3477
1 TraesCS6D01G313300 chr6D 422203732 422206346 2614 True 1466.000000 2457 88.429500 260 2708 2 chr6D.!!$R1 2448
2 TraesCS6D01G313300 chr6D 409346574 409348738 2164 False 841.000000 1947 89.646667 777 2628 3 chr6D.!!$F2 1851
3 TraesCS6D01G313300 chr6B 636584168 636586182 2014 True 2669.000000 2669 90.645000 689 2721 1 chr6B.!!$R2 2032
4 TraesCS6D01G313300 chr6B 636490463 636493360 2897 False 1153.333333 2687 92.255000 153 2737 3 chr6B.!!$F5 2584
5 TraesCS6D01G313300 chr6B 614581920 614583834 1914 False 794.433333 2145 86.949667 790 2672 3 chr6B.!!$F4 1882
6 TraesCS6D01G313300 chr6B 614434586 614438549 3963 False 792.933333 2150 89.169667 153 2490 3 chr6B.!!$F3 2337
7 TraesCS6D01G313300 chr6B 614310956 614313236 2280 False 790.933333 2159 88.728333 347 2490 3 chr6B.!!$F2 2143
8 TraesCS6D01G313300 chr6A 564907618 564910999 3381 True 991.000000 2543 86.738333 681 2737 3 chr6A.!!$R1 2056
9 TraesCS6D01G313300 chr6A 564973826 564979760 5934 False 884.800000 2684 91.902600 153 3395 5 chr6A.!!$F2 3242
10 TraesCS6D01G313300 chr6A 554824112 554826766 2654 False 826.666667 2008 91.450333 777 2586 3 chr6A.!!$F1 1809

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 0.110419 GCAATGCTGCGTGACGTTTA 60.110 50.0 6.91 0.0 39.20 2.01 F
1919 4417 0.032813 CCACCAAGGGCATCCTCAAT 60.033 55.0 0.00 0.0 44.07 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 4501 0.106149 GGTTGTCCACGAAGGTCACT 59.894 55.0 0.00 0.00 35.09 3.41 R
3443 9181 0.036732 AAAGCACTCTTCGATGGCCA 59.963 50.0 8.56 8.56 0.00 5.36 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
26 27 9.787532 GCATTGTACATGTTCACATATTTTACT 57.212 29.630 2.30 0.00 34.26 2.24
47 48 2.252260 GCAATGCTGCGTGACGTT 59.748 55.556 6.91 0.00 39.20 3.99
48 49 1.370414 GCAATGCTGCGTGACGTTT 60.370 52.632 6.91 0.00 39.20 3.60
49 50 0.110419 GCAATGCTGCGTGACGTTTA 60.110 50.000 6.91 0.00 39.20 2.01
50 51 1.869503 CAATGCTGCGTGACGTTTAG 58.130 50.000 6.91 4.31 0.00 1.85
51 52 1.459209 CAATGCTGCGTGACGTTTAGA 59.541 47.619 6.91 0.00 0.00 2.10
52 53 1.068474 ATGCTGCGTGACGTTTAGAC 58.932 50.000 6.91 1.16 0.00 2.59
53 54 0.249114 TGCTGCGTGACGTTTAGACA 60.249 50.000 6.91 3.54 0.00 3.41
54 55 0.161024 GCTGCGTGACGTTTAGACAC 59.839 55.000 6.91 0.00 41.06 3.67
55 56 1.767289 CTGCGTGACGTTTAGACACT 58.233 50.000 6.91 0.00 42.02 3.55
56 57 2.919387 GCTGCGTGACGTTTAGACACTA 60.919 50.000 6.91 0.00 42.02 2.74
57 58 2.909244 CTGCGTGACGTTTAGACACTAG 59.091 50.000 6.91 0.00 42.02 2.57
58 59 2.549329 TGCGTGACGTTTAGACACTAGA 59.451 45.455 6.91 0.00 42.02 2.43
59 60 3.162068 GCGTGACGTTTAGACACTAGAG 58.838 50.000 6.91 0.00 42.02 2.43
60 61 3.120408 GCGTGACGTTTAGACACTAGAGA 60.120 47.826 6.91 0.00 42.02 3.10
61 62 4.639959 CGTGACGTTTAGACACTAGAGAG 58.360 47.826 0.00 0.00 42.02 3.20
62 63 4.405196 GTGACGTTTAGACACTAGAGAGC 58.595 47.826 0.00 0.00 41.21 4.09
63 64 4.070009 TGACGTTTAGACACTAGAGAGCA 58.930 43.478 0.00 0.00 0.00 4.26
64 65 4.700692 TGACGTTTAGACACTAGAGAGCAT 59.299 41.667 0.00 0.00 0.00 3.79
65 66 5.183331 TGACGTTTAGACACTAGAGAGCATT 59.817 40.000 0.00 0.00 0.00 3.56
66 67 5.403246 ACGTTTAGACACTAGAGAGCATTG 58.597 41.667 0.00 0.00 0.00 2.82
67 68 5.047943 ACGTTTAGACACTAGAGAGCATTGT 60.048 40.000 0.00 0.00 0.00 2.71
68 69 5.287274 CGTTTAGACACTAGAGAGCATTGTG 59.713 44.000 0.00 0.00 35.09 3.33
69 70 3.883830 AGACACTAGAGAGCATTGTGG 57.116 47.619 0.00 0.00 33.44 4.17
70 71 2.093764 AGACACTAGAGAGCATTGTGGC 60.094 50.000 0.00 0.00 36.96 5.01
71 72 1.625315 ACACTAGAGAGCATTGTGGCA 59.375 47.619 0.00 0.00 35.83 4.92
72 73 2.038952 ACACTAGAGAGCATTGTGGCAA 59.961 45.455 0.00 0.00 35.83 4.52
73 74 3.276857 CACTAGAGAGCATTGTGGCAAT 58.723 45.455 0.00 0.00 35.83 3.56
74 75 3.693085 CACTAGAGAGCATTGTGGCAATT 59.307 43.478 0.00 0.00 35.83 2.32
75 76 3.693085 ACTAGAGAGCATTGTGGCAATTG 59.307 43.478 0.00 0.00 35.83 2.32
76 77 1.822990 AGAGAGCATTGTGGCAATTGG 59.177 47.619 7.72 0.00 35.83 3.16
77 78 0.248289 AGAGCATTGTGGCAATTGGC 59.752 50.000 24.20 24.20 43.74 4.52
84 85 4.360643 TGGCAATTGGCATCTCCC 57.639 55.556 29.00 9.64 46.12 4.30
85 86 1.699137 TGGCAATTGGCATCTCCCT 59.301 52.632 29.00 0.00 46.12 4.20
86 87 0.396139 TGGCAATTGGCATCTCCCTC 60.396 55.000 29.00 0.00 46.12 4.30
87 88 2.816320 TGGCAATTGGCATCTCCCTCT 61.816 52.381 29.00 0.00 46.12 3.69
88 89 1.772836 GCAATTGGCATCTCCCTCTT 58.227 50.000 7.72 0.00 43.97 2.85
89 90 1.407979 GCAATTGGCATCTCCCTCTTG 59.592 52.381 7.72 0.00 43.97 3.02
90 91 2.947243 GCAATTGGCATCTCCCTCTTGA 60.947 50.000 7.72 0.00 43.97 3.02
91 92 3.359033 CAATTGGCATCTCCCTCTTGAA 58.641 45.455 0.00 0.00 0.00 2.69
92 93 3.744940 ATTGGCATCTCCCTCTTGAAA 57.255 42.857 0.00 0.00 0.00 2.69
93 94 2.795231 TGGCATCTCCCTCTTGAAAG 57.205 50.000 0.00 0.00 0.00 2.62
94 95 1.283029 TGGCATCTCCCTCTTGAAAGG 59.717 52.381 0.00 0.00 36.08 3.11
104 105 3.931578 CCTCTTGAAAGGGTACACTCTG 58.068 50.000 0.00 0.00 32.35 3.35
105 106 3.330267 CTCTTGAAAGGGTACACTCTGC 58.670 50.000 0.00 0.00 0.00 4.26
106 107 2.038557 TCTTGAAAGGGTACACTCTGCC 59.961 50.000 0.00 0.00 0.00 4.85
107 108 0.320374 TGAAAGGGTACACTCTGCCG 59.680 55.000 0.00 0.00 0.00 5.69
108 109 0.391263 GAAAGGGTACACTCTGCCGG 60.391 60.000 0.00 0.00 0.00 6.13
109 110 1.125711 AAAGGGTACACTCTGCCGGT 61.126 55.000 1.90 0.00 0.00 5.28
110 111 1.125711 AAGGGTACACTCTGCCGGTT 61.126 55.000 1.90 0.00 0.00 4.44
111 112 1.125711 AGGGTACACTCTGCCGGTTT 61.126 55.000 1.90 0.00 0.00 3.27
112 113 0.250597 GGGTACACTCTGCCGGTTTT 60.251 55.000 1.90 0.00 0.00 2.43
113 114 1.601166 GGTACACTCTGCCGGTTTTT 58.399 50.000 1.90 0.00 0.00 1.94
138 139 9.928236 TTTTGTTTTTGTTTTGATATAGCTTGC 57.072 25.926 0.00 0.00 0.00 4.01
139 140 7.650834 TGTTTTTGTTTTGATATAGCTTGCC 57.349 32.000 0.00 0.00 0.00 4.52
140 141 7.212976 TGTTTTTGTTTTGATATAGCTTGCCA 58.787 30.769 0.00 0.00 0.00 4.92
141 142 7.170658 TGTTTTTGTTTTGATATAGCTTGCCAC 59.829 33.333 0.00 0.00 0.00 5.01
142 143 6.588719 TTTGTTTTGATATAGCTTGCCACT 57.411 33.333 0.00 0.00 0.00 4.00
143 144 5.818136 TGTTTTGATATAGCTTGCCACTC 57.182 39.130 0.00 0.00 0.00 3.51
144 145 5.500234 TGTTTTGATATAGCTTGCCACTCT 58.500 37.500 0.00 0.00 0.00 3.24
145 146 5.945784 TGTTTTGATATAGCTTGCCACTCTT 59.054 36.000 0.00 0.00 0.00 2.85
146 147 6.127925 TGTTTTGATATAGCTTGCCACTCTTG 60.128 38.462 0.00 0.00 0.00 3.02
147 148 4.760530 TGATATAGCTTGCCACTCTTGT 57.239 40.909 0.00 0.00 0.00 3.16
148 149 4.697514 TGATATAGCTTGCCACTCTTGTC 58.302 43.478 0.00 0.00 0.00 3.18
149 150 4.162131 TGATATAGCTTGCCACTCTTGTCA 59.838 41.667 0.00 0.00 0.00 3.58
150 151 2.928801 TAGCTTGCCACTCTTGTCAA 57.071 45.000 0.00 0.00 0.00 3.18
151 152 1.602311 AGCTTGCCACTCTTGTCAAG 58.398 50.000 6.21 6.21 39.00 3.02
184 185 2.554032 AGTCAGTTCGATTTGCTTTGGG 59.446 45.455 0.00 0.00 0.00 4.12
187 188 0.603065 GTTCGATTTGCTTTGGGCCT 59.397 50.000 4.53 0.00 40.92 5.19
197 198 0.742990 CTTTGGGCCTCGCGATAACA 60.743 55.000 10.36 3.84 0.00 2.41
234 235 1.526686 CATGGCGCCTGCTTATCCA 60.527 57.895 29.70 3.35 42.25 3.41
243 244 1.094785 CTGCTTATCCAACCCAACGG 58.905 55.000 0.00 0.00 0.00 4.44
288 293 3.242316 GGTGAATAAAATGACGTCGAGGC 60.242 47.826 11.62 0.00 0.00 4.70
318 1861 0.961019 GCAACTGCATTGGGAAGTCA 59.039 50.000 9.81 0.00 41.59 3.41
331 1874 3.838317 TGGGAAGTCATCGGGGATATAAG 59.162 47.826 0.00 0.00 0.00 1.73
404 2129 1.328680 CCCTCACGAATTCAATGCTCG 59.671 52.381 6.22 0.00 38.53 5.03
531 2288 1.409427 AGTTTTATCCGCCTCGAGGAG 59.591 52.381 35.69 30.98 41.66 3.69
564 2321 4.461081 TCCACGTTATCCAGGAAATTTTGG 59.539 41.667 0.00 2.89 35.74 3.28
606 2363 6.975772 CGGATTTCTGTTTGTTAACCTGAAAA 59.024 34.615 14.56 3.21 38.24 2.29
607 2364 7.489757 CGGATTTCTGTTTGTTAACCTGAAAAA 59.510 33.333 14.56 2.91 38.24 1.94
612 2369 5.651530 TGTTTGTTAACCTGAAAAATGCGA 58.348 33.333 2.48 0.00 33.15 5.10
647 2428 1.152383 GCCCGCAGATCTTACGAACC 61.152 60.000 14.89 1.53 0.00 3.62
661 2447 1.626654 CGAACCGCTACAGCACTTGG 61.627 60.000 1.61 0.00 42.21 3.61
672 2743 6.183360 CGCTACAGCACTTGGATGTTTATTTA 60.183 38.462 1.61 0.00 45.58 1.40
677 2761 4.142026 GCACTTGGATGTTTATTTACCCCC 60.142 45.833 0.00 0.00 0.00 5.40
679 2763 5.660864 CACTTGGATGTTTATTTACCCCCAT 59.339 40.000 0.00 0.00 0.00 4.00
709 2793 4.688413 GTGTGAGTTCTGAGGAATTCTCAC 59.312 45.833 15.96 15.96 46.71 3.51
769 2889 1.957177 TCTGATACAAGGCTAGCTCCG 59.043 52.381 15.72 5.49 0.00 4.63
793 2926 1.961277 CGCCTTTTGAGCTCACCGT 60.961 57.895 18.03 0.00 0.00 4.83
794 2927 1.507141 CGCCTTTTGAGCTCACCGTT 61.507 55.000 18.03 0.00 0.00 4.44
884 3033 1.265095 ACATGTCTTGCAAGTTGCTCG 59.735 47.619 27.17 17.77 45.31 5.03
885 3034 1.532437 CATGTCTTGCAAGTTGCTCGA 59.468 47.619 27.17 19.59 45.31 4.04
886 3035 1.882912 TGTCTTGCAAGTTGCTCGAT 58.117 45.000 27.17 0.00 45.31 3.59
888 3037 1.800586 GTCTTGCAAGTTGCTCGATCA 59.199 47.619 27.17 4.26 45.31 2.92
889 3038 1.800586 TCTTGCAAGTTGCTCGATCAC 59.199 47.619 27.17 0.00 45.31 3.06
891 3040 1.291184 TGCAAGTTGCTCGATCACCG 61.291 55.000 27.17 0.00 45.31 4.94
1090 3244 5.045869 TCCGGTCAAATTCTCTTTCAGGTAT 60.046 40.000 0.00 0.00 0.00 2.73
1091 3245 5.648092 CCGGTCAAATTCTCTTTCAGGTATT 59.352 40.000 0.00 0.00 0.00 1.89
1122 3305 1.151668 CGGCAAGAACTGTCTTCAGG 58.848 55.000 0.47 0.00 42.45 3.86
1919 4417 0.032813 CCACCAAGGGCATCCTCAAT 60.033 55.000 0.00 0.00 44.07 2.57
2042 4540 4.980805 GACACCGGCTCCACGCAA 62.981 66.667 0.00 0.00 41.67 4.85
2135 4633 0.803768 GCATCGTGAGTCATCGTGCT 60.804 55.000 20.77 7.74 34.28 4.40
2144 4642 2.009774 AGTCATCGTGCTATTGCCAAC 58.990 47.619 0.00 0.00 38.71 3.77
2164 4664 7.229306 TGCCAACTCATCATATCTAAATTGTCC 59.771 37.037 0.00 0.00 0.00 4.02
2195 4709 3.944650 CCGTTCATATGAAACCATGACCA 59.055 43.478 19.55 0.00 35.58 4.02
2208 4722 5.200368 ACCATGACCAAACTGATGAAAAC 57.800 39.130 0.00 0.00 0.00 2.43
2212 4726 7.069331 ACCATGACCAAACTGATGAAAACTAAA 59.931 33.333 0.00 0.00 0.00 1.85
2354 4868 0.813184 CTGACGCCGACCTTTACCTA 59.187 55.000 0.00 0.00 0.00 3.08
2367 4881 2.336945 TTACCTAGCCGAGATCGACA 57.663 50.000 3.31 0.00 43.02 4.35
2384 4898 2.143122 GACAGCAAGGTCATCGTCAAA 58.857 47.619 0.00 0.00 37.73 2.69
2453 4967 3.788766 GTCGCGCACGGCAAAGAT 61.789 61.111 8.75 0.00 45.32 2.40
2499 5066 2.682856 GCAAAATTACCGGAGCTCATGA 59.317 45.455 17.19 0.00 0.00 3.07
2507 5074 0.873312 CGGAGCTCATGATGTCCACG 60.873 60.000 17.19 1.45 0.00 4.94
2622 5191 5.581085 GCTACTCATGGTTTACTCGATGTTT 59.419 40.000 0.00 0.00 0.00 2.83
2631 5200 5.048991 GGTTTACTCGATGTTTGTTGACCAT 60.049 40.000 0.00 0.00 0.00 3.55
2666 5235 4.357947 GCCAGTGACTCGTGCGGA 62.358 66.667 0.00 0.00 0.00 5.54
2751 5320 4.712476 AGGGCTCTACATAAGAAAGCATG 58.288 43.478 0.00 0.00 32.46 4.06
2811 5380 7.382759 GTCTGTAGCTTAGTTATACAATGCTCC 59.617 40.741 0.00 0.00 0.00 4.70
2829 5398 4.057432 GCTCCAGCTATCAGTTCTGAATC 58.943 47.826 6.60 0.12 38.21 2.52
2848 5417 3.413846 TCAACTTTGATCAGAGCTGCT 57.586 42.857 12.97 0.00 31.01 4.24
2857 5426 2.391616 TCAGAGCTGCTATGTGTTGG 57.608 50.000 22.14 0.00 0.00 3.77
2869 5438 6.182627 TGCTATGTGTTGGAGAAAATCTGAT 58.817 36.000 0.00 0.00 0.00 2.90
2927 5501 8.231304 ACGCTTTCTTTCATTCAAAATATGTG 57.769 30.769 0.00 0.00 0.00 3.21
2942 5516 6.935741 AAATATGTGCCGAGCAAAGTATAA 57.064 33.333 0.00 0.00 41.47 0.98
2943 5517 7.510549 AAATATGTGCCGAGCAAAGTATAAT 57.489 32.000 0.00 0.00 41.47 1.28
2944 5518 4.818534 ATGTGCCGAGCAAAGTATAATG 57.181 40.909 0.00 0.00 41.47 1.90
2945 5519 2.354510 TGTGCCGAGCAAAGTATAATGC 59.645 45.455 0.00 0.00 41.47 3.56
2946 5520 1.946768 TGCCGAGCAAAGTATAATGCC 59.053 47.619 0.00 0.00 43.57 4.40
2948 5522 1.069906 CCGAGCAAAGTATAATGCCGC 60.070 52.381 3.52 0.00 43.57 6.53
2950 5524 0.944386 AGCAAAGTATAATGCCGCGG 59.056 50.000 24.05 24.05 43.57 6.46
2951 5525 0.661020 GCAAAGTATAATGCCGCGGT 59.339 50.000 28.70 9.89 36.56 5.68
2953 5527 2.715268 CAAAGTATAATGCCGCGGTTG 58.285 47.619 28.70 15.67 0.00 3.77
2954 5528 0.661020 AAGTATAATGCCGCGGTTGC 59.339 50.000 28.70 13.41 37.91 4.17
2959 5533 2.751436 ATGCCGCGGTTGCATTCT 60.751 55.556 28.70 0.36 46.91 2.40
2960 5534 2.342650 ATGCCGCGGTTGCATTCTT 61.343 52.632 28.70 2.94 46.91 2.52
2963 5537 1.875963 CCGCGGTTGCATTCTTCTT 59.124 52.632 19.50 0.00 42.97 2.52
2964 5538 0.179189 CCGCGGTTGCATTCTTCTTC 60.179 55.000 19.50 0.00 42.97 2.87
2966 5540 0.179189 GCGGTTGCATTCTTCTTCGG 60.179 55.000 0.00 0.00 42.15 4.30
2967 5541 0.447801 CGGTTGCATTCTTCTTCGGG 59.552 55.000 0.00 0.00 0.00 5.14
2969 5543 0.179189 GTTGCATTCTTCTTCGGGCG 60.179 55.000 0.00 0.00 0.00 6.13
2970 5544 0.321210 TTGCATTCTTCTTCGGGCGA 60.321 50.000 0.00 0.00 0.00 5.54
2971 5545 0.740868 TGCATTCTTCTTCGGGCGAG 60.741 55.000 0.00 0.00 0.00 5.03
2973 5547 1.565305 CATTCTTCTTCGGGCGAGAG 58.435 55.000 0.00 0.00 0.00 3.20
2974 5548 1.135139 CATTCTTCTTCGGGCGAGAGA 59.865 52.381 0.00 0.00 0.00 3.10
2976 5550 0.811915 TCTTCTTCGGGCGAGAGAAG 59.188 55.000 13.11 13.11 43.70 2.85
2978 5552 2.483441 TCTTCGGGCGAGAGAAGAG 58.517 57.895 11.18 0.00 45.33 2.85
2980 5554 1.304217 TTCGGGCGAGAGAAGAGGT 60.304 57.895 0.00 0.00 0.00 3.85
2982 5556 2.896443 GGGCGAGAGAAGAGGTGG 59.104 66.667 0.00 0.00 0.00 4.61
2983 5557 1.985116 GGGCGAGAGAAGAGGTGGT 60.985 63.158 0.00 0.00 0.00 4.16
2985 5559 0.456628 GGCGAGAGAAGAGGTGGTAC 59.543 60.000 0.00 0.00 0.00 3.34
2986 5560 0.456628 GCGAGAGAAGAGGTGGTACC 59.543 60.000 4.43 4.43 38.99 3.34
2987 5561 1.835494 CGAGAGAAGAGGTGGTACCA 58.165 55.000 11.60 11.60 41.95 3.25
2988 5562 1.473278 CGAGAGAAGAGGTGGTACCAC 59.527 57.143 33.15 33.15 41.95 4.16
3174 6384 2.357517 GCGGTCTGTCAGTGGTGG 60.358 66.667 0.00 0.00 0.00 4.61
3181 6391 2.055689 CTGTCAGTGGTGGGAAGCCA 62.056 60.000 0.00 0.00 0.00 4.75
3254 8990 8.356000 ACAGAAGTAGTAGAAGCAAGAGTAAT 57.644 34.615 0.00 0.00 0.00 1.89
3255 8991 8.808092 ACAGAAGTAGTAGAAGCAAGAGTAATT 58.192 33.333 0.00 0.00 0.00 1.40
3305 9042 4.864726 AGGCTCCATATTTTCTCAAGCTT 58.135 39.130 0.00 0.00 0.00 3.74
3324 9061 3.797039 CTTCGGTCTAGCAATTGATCCA 58.203 45.455 10.34 0.00 0.00 3.41
3344 9082 5.580998 TCCAAGGAACTGACTAGAGTATGT 58.419 41.667 0.00 0.00 40.86 2.29
3355 9093 5.581479 TGACTAGAGTATGTCGAGAGAACAC 59.419 44.000 0.00 0.00 45.01 3.32
3356 9094 5.489249 ACTAGAGTATGTCGAGAGAACACA 58.511 41.667 0.00 0.00 45.01 3.72
3357 9095 4.955925 AGAGTATGTCGAGAGAACACAG 57.044 45.455 0.00 0.00 45.01 3.66
3364 9102 3.243873 TGTCGAGAGAACACAGCAGATTT 60.244 43.478 0.00 0.00 45.01 2.17
3366 9104 4.212214 GTCGAGAGAACACAGCAGATTTTT 59.788 41.667 0.00 0.00 45.01 1.94
3389 9127 5.981088 TTTCTTCTGAATTTGCAGCCATA 57.019 34.783 0.00 0.00 35.86 2.74
3390 9128 6.534475 TTTCTTCTGAATTTGCAGCCATAT 57.466 33.333 0.00 0.00 35.86 1.78
3391 9129 7.643569 TTTCTTCTGAATTTGCAGCCATATA 57.356 32.000 0.00 0.00 35.86 0.86
3395 9133 6.872628 TCTGAATTTGCAGCCATATAGAAG 57.127 37.500 0.00 0.00 35.86 2.85
3397 9135 6.830324 TCTGAATTTGCAGCCATATAGAAGTT 59.170 34.615 0.00 0.00 35.86 2.66
3399 9137 6.039717 TGAATTTGCAGCCATATAGAAGTTCC 59.960 38.462 0.00 0.00 0.00 3.62
3400 9138 4.502105 TTGCAGCCATATAGAAGTTCCA 57.498 40.909 0.00 0.00 0.00 3.53
3401 9139 4.502105 TGCAGCCATATAGAAGTTCCAA 57.498 40.909 0.00 0.00 0.00 3.53
3402 9140 4.454678 TGCAGCCATATAGAAGTTCCAAG 58.545 43.478 0.00 0.00 0.00 3.61
3403 9141 3.817647 GCAGCCATATAGAAGTTCCAAGG 59.182 47.826 0.00 0.00 0.00 3.61
3404 9142 4.687219 GCAGCCATATAGAAGTTCCAAGGT 60.687 45.833 0.00 0.00 0.00 3.50
3405 9143 5.059833 CAGCCATATAGAAGTTCCAAGGTC 58.940 45.833 0.00 0.00 0.00 3.85
3407 9145 5.059833 GCCATATAGAAGTTCCAAGGTCAG 58.940 45.833 0.00 0.00 0.00 3.51
3408 9146 5.059833 CCATATAGAAGTTCCAAGGTCAGC 58.940 45.833 0.00 0.00 0.00 4.26
3411 9149 0.877743 GAAGTTCCAAGGTCAGCAGC 59.122 55.000 0.00 0.00 0.00 5.25
3412 9150 0.538287 AAGTTCCAAGGTCAGCAGCC 60.538 55.000 0.00 0.00 0.00 4.85
3414 9152 0.823356 GTTCCAAGGTCAGCAGCCAA 60.823 55.000 0.00 0.00 0.00 4.52
3415 9153 0.106268 TTCCAAGGTCAGCAGCCAAA 60.106 50.000 0.00 0.00 0.00 3.28
3416 9154 0.112995 TCCAAGGTCAGCAGCCAAAT 59.887 50.000 0.00 0.00 0.00 2.32
3417 9155 0.245539 CCAAGGTCAGCAGCCAAATG 59.754 55.000 0.00 0.00 0.00 2.32
3427 9165 2.573340 GCCAAATGGAGGCGTTGG 59.427 61.111 2.98 0.00 43.15 3.77
3428 9166 1.976474 GCCAAATGGAGGCGTTGGA 60.976 57.895 2.98 0.00 43.82 3.53
3429 9167 1.937546 GCCAAATGGAGGCGTTGGAG 61.938 60.000 2.98 0.00 43.82 3.86
3431 9169 0.804989 CAAATGGAGGCGTTGGAGTC 59.195 55.000 0.00 0.00 0.00 3.36
3432 9170 0.322546 AAATGGAGGCGTTGGAGTCC 60.323 55.000 0.73 0.73 0.00 3.85
3433 9171 2.198304 AATGGAGGCGTTGGAGTCCC 62.198 60.000 6.74 0.00 0.00 4.46
3434 9172 3.003763 GGAGGCGTTGGAGTCCCT 61.004 66.667 6.74 0.00 0.00 4.20
3436 9174 1.079057 GAGGCGTTGGAGTCCCTTC 60.079 63.158 6.74 0.00 0.00 3.46
3437 9175 1.827399 GAGGCGTTGGAGTCCCTTCA 61.827 60.000 6.74 0.00 0.00 3.02
3439 9177 0.744771 GGCGTTGGAGTCCCTTCATC 60.745 60.000 6.74 0.00 0.00 2.92
3440 9178 0.250513 GCGTTGGAGTCCCTTCATCT 59.749 55.000 6.74 0.00 0.00 2.90
3442 9180 2.482142 GCGTTGGAGTCCCTTCATCTAG 60.482 54.545 6.74 0.00 0.00 2.43
3443 9181 2.761208 CGTTGGAGTCCCTTCATCTAGT 59.239 50.000 6.74 0.00 0.00 2.57
3444 9182 3.429547 CGTTGGAGTCCCTTCATCTAGTG 60.430 52.174 6.74 0.00 0.00 2.74
3445 9183 2.752030 TGGAGTCCCTTCATCTAGTGG 58.248 52.381 6.74 0.00 0.00 4.00
3446 9184 1.414550 GGAGTCCCTTCATCTAGTGGC 59.585 57.143 0.00 0.00 0.00 5.01
3447 9185 1.414550 GAGTCCCTTCATCTAGTGGCC 59.585 57.143 0.00 0.00 0.00 5.36
3449 9187 1.771255 GTCCCTTCATCTAGTGGCCAT 59.229 52.381 9.72 0.00 0.00 4.40
3450 9188 2.050144 TCCCTTCATCTAGTGGCCATC 58.950 52.381 9.72 2.38 0.00 3.51
3451 9189 1.270518 CCCTTCATCTAGTGGCCATCG 60.271 57.143 9.72 0.00 0.00 3.84
3453 9191 2.103094 CCTTCATCTAGTGGCCATCGAA 59.897 50.000 9.72 5.05 0.00 3.71
3454 9192 3.388308 CTTCATCTAGTGGCCATCGAAG 58.612 50.000 9.72 11.09 0.00 3.79
3456 9194 2.625314 TCATCTAGTGGCCATCGAAGAG 59.375 50.000 9.72 0.11 43.63 2.85
3458 9196 1.751351 TCTAGTGGCCATCGAAGAGTG 59.249 52.381 9.72 0.00 43.63 3.51
3459 9197 0.175760 TAGTGGCCATCGAAGAGTGC 59.824 55.000 9.72 0.00 43.63 4.40
3460 9198 1.078848 GTGGCCATCGAAGAGTGCT 60.079 57.895 9.72 0.00 43.63 4.40
3462 9200 0.036732 TGGCCATCGAAGAGTGCTTT 59.963 50.000 0.00 0.00 43.63 3.51
3463 9201 0.729690 GGCCATCGAAGAGTGCTTTC 59.270 55.000 0.00 0.00 43.63 2.62
3464 9202 1.442769 GCCATCGAAGAGTGCTTTCA 58.557 50.000 0.00 0.00 43.63 2.69
3465 9203 1.396301 GCCATCGAAGAGTGCTTTCAG 59.604 52.381 0.00 0.00 43.63 3.02
3466 9204 1.396301 CCATCGAAGAGTGCTTTCAGC 59.604 52.381 0.00 0.00 43.63 4.26
3467 9205 2.071540 CATCGAAGAGTGCTTTCAGCA 58.928 47.619 0.00 0.00 46.54 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.787532 AGTAAAATATGTGAACATGTACAATGC 57.212 29.630 5.58 0.00 37.15 3.56
13 14 8.506437 GCAGCATTGCTATAGTAAAATATGTGA 58.494 33.333 11.55 0.00 46.95 3.58
14 15 8.665175 GCAGCATTGCTATAGTAAAATATGTG 57.335 34.615 11.55 1.83 46.95 3.21
31 32 1.459209 TCTAAACGTCACGCAGCATTG 59.541 47.619 0.00 0.00 0.00 2.82
32 33 1.459592 GTCTAAACGTCACGCAGCATT 59.540 47.619 0.00 0.00 0.00 3.56
33 34 1.068474 GTCTAAACGTCACGCAGCAT 58.932 50.000 0.00 0.00 0.00 3.79
34 35 0.249114 TGTCTAAACGTCACGCAGCA 60.249 50.000 0.00 0.00 0.00 4.41
35 36 0.161024 GTGTCTAAACGTCACGCAGC 59.839 55.000 0.00 0.00 0.00 5.25
36 37 1.767289 AGTGTCTAAACGTCACGCAG 58.233 50.000 0.00 0.00 36.88 5.18
37 38 2.549329 TCTAGTGTCTAAACGTCACGCA 59.451 45.455 0.00 0.00 36.88 5.24
38 39 3.120408 TCTCTAGTGTCTAAACGTCACGC 60.120 47.826 0.00 0.00 36.88 5.34
39 40 4.639959 CTCTCTAGTGTCTAAACGTCACG 58.360 47.826 0.00 0.00 36.88 4.35
40 41 4.083431 TGCTCTCTAGTGTCTAAACGTCAC 60.083 45.833 0.00 0.00 32.76 3.67
41 42 4.070009 TGCTCTCTAGTGTCTAAACGTCA 58.930 43.478 0.00 0.00 0.00 4.35
42 43 4.681835 TGCTCTCTAGTGTCTAAACGTC 57.318 45.455 0.00 0.00 0.00 4.34
43 44 5.047943 ACAATGCTCTCTAGTGTCTAAACGT 60.048 40.000 0.00 0.00 0.00 3.99
44 45 5.287274 CACAATGCTCTCTAGTGTCTAAACG 59.713 44.000 0.00 0.00 0.00 3.60
45 46 5.578727 CCACAATGCTCTCTAGTGTCTAAAC 59.421 44.000 0.00 0.00 0.00 2.01
46 47 5.724328 CCACAATGCTCTCTAGTGTCTAAA 58.276 41.667 0.00 0.00 0.00 1.85
47 48 4.382040 GCCACAATGCTCTCTAGTGTCTAA 60.382 45.833 0.00 0.00 0.00 2.10
48 49 3.131223 GCCACAATGCTCTCTAGTGTCTA 59.869 47.826 0.00 0.00 0.00 2.59
49 50 2.093764 GCCACAATGCTCTCTAGTGTCT 60.094 50.000 0.00 0.00 0.00 3.41
50 51 2.275318 GCCACAATGCTCTCTAGTGTC 58.725 52.381 0.00 0.00 0.00 3.67
51 52 1.625315 TGCCACAATGCTCTCTAGTGT 59.375 47.619 0.00 0.00 0.00 3.55
52 53 2.391616 TGCCACAATGCTCTCTAGTG 57.608 50.000 0.00 0.00 0.00 2.74
53 54 3.641434 ATTGCCACAATGCTCTCTAGT 57.359 42.857 0.00 0.00 0.00 2.57
54 55 3.066342 CCAATTGCCACAATGCTCTCTAG 59.934 47.826 0.00 0.00 0.00 2.43
55 56 3.018856 CCAATTGCCACAATGCTCTCTA 58.981 45.455 0.00 0.00 0.00 2.43
56 57 1.822990 CCAATTGCCACAATGCTCTCT 59.177 47.619 0.00 0.00 0.00 3.10
57 58 1.738030 GCCAATTGCCACAATGCTCTC 60.738 52.381 0.00 0.00 0.00 3.20
58 59 0.248289 GCCAATTGCCACAATGCTCT 59.752 50.000 0.00 0.00 0.00 4.09
59 60 0.037139 TGCCAATTGCCACAATGCTC 60.037 50.000 0.00 0.00 40.16 4.26
60 61 0.616371 ATGCCAATTGCCACAATGCT 59.384 45.000 0.00 0.00 40.16 3.79
61 62 1.011333 GATGCCAATTGCCACAATGC 58.989 50.000 0.00 0.00 40.16 3.56
62 63 2.546778 GAGATGCCAATTGCCACAATG 58.453 47.619 0.00 0.00 40.16 2.82
63 64 1.483415 GGAGATGCCAATTGCCACAAT 59.517 47.619 0.00 0.00 40.16 2.71
64 65 0.896923 GGAGATGCCAATTGCCACAA 59.103 50.000 0.00 0.00 40.16 3.33
65 66 0.971959 GGGAGATGCCAATTGCCACA 60.972 55.000 0.00 0.00 40.16 4.17
66 67 0.685458 AGGGAGATGCCAATTGCCAC 60.685 55.000 0.00 0.00 40.16 5.01
67 68 0.396139 GAGGGAGATGCCAATTGCCA 60.396 55.000 0.00 0.00 40.16 4.92
68 69 0.106318 AGAGGGAGATGCCAATTGCC 60.106 55.000 0.00 0.00 40.16 4.52
69 70 1.407979 CAAGAGGGAGATGCCAATTGC 59.592 52.381 0.00 0.00 38.95 3.56
70 71 3.008835 TCAAGAGGGAGATGCCAATTG 57.991 47.619 0.00 0.00 38.95 2.32
71 72 3.744940 TTCAAGAGGGAGATGCCAATT 57.255 42.857 0.00 0.00 38.95 2.32
72 73 3.626729 CCTTTCAAGAGGGAGATGCCAAT 60.627 47.826 0.00 0.00 38.95 3.16
73 74 2.291153 CCTTTCAAGAGGGAGATGCCAA 60.291 50.000 0.00 0.00 38.95 4.52
74 75 1.283029 CCTTTCAAGAGGGAGATGCCA 59.717 52.381 0.00 0.00 38.95 4.92
75 76 2.049888 CCTTTCAAGAGGGAGATGCC 57.950 55.000 0.00 0.00 32.94 4.40
83 84 3.866449 GCAGAGTGTACCCTTTCAAGAGG 60.866 52.174 0.00 0.00 36.52 3.69
84 85 3.330267 GCAGAGTGTACCCTTTCAAGAG 58.670 50.000 0.00 0.00 0.00 2.85
85 86 2.038557 GGCAGAGTGTACCCTTTCAAGA 59.961 50.000 0.00 0.00 0.00 3.02
86 87 2.427506 GGCAGAGTGTACCCTTTCAAG 58.572 52.381 0.00 0.00 0.00 3.02
87 88 1.270625 CGGCAGAGTGTACCCTTTCAA 60.271 52.381 0.00 0.00 0.00 2.69
88 89 0.320374 CGGCAGAGTGTACCCTTTCA 59.680 55.000 0.00 0.00 0.00 2.69
89 90 0.391263 CCGGCAGAGTGTACCCTTTC 60.391 60.000 0.00 0.00 0.00 2.62
90 91 1.125711 ACCGGCAGAGTGTACCCTTT 61.126 55.000 0.00 0.00 0.00 3.11
91 92 1.125711 AACCGGCAGAGTGTACCCTT 61.126 55.000 0.00 0.00 0.00 3.95
92 93 1.125711 AAACCGGCAGAGTGTACCCT 61.126 55.000 0.00 0.00 0.00 4.34
93 94 0.250597 AAAACCGGCAGAGTGTACCC 60.251 55.000 0.00 0.00 0.00 3.69
94 95 1.601166 AAAAACCGGCAGAGTGTACC 58.399 50.000 0.00 0.00 0.00 3.34
112 113 9.928236 GCAAGCTATATCAAAACAAAAACAAAA 57.072 25.926 0.00 0.00 0.00 2.44
113 114 8.555361 GGCAAGCTATATCAAAACAAAAACAAA 58.445 29.630 0.00 0.00 0.00 2.83
114 115 7.712639 TGGCAAGCTATATCAAAACAAAAACAA 59.287 29.630 0.00 0.00 0.00 2.83
115 116 7.170658 GTGGCAAGCTATATCAAAACAAAAACA 59.829 33.333 0.00 0.00 0.00 2.83
116 117 7.384932 AGTGGCAAGCTATATCAAAACAAAAAC 59.615 33.333 0.00 0.00 0.00 2.43
117 118 7.441017 AGTGGCAAGCTATATCAAAACAAAAA 58.559 30.769 0.00 0.00 0.00 1.94
118 119 6.991938 AGTGGCAAGCTATATCAAAACAAAA 58.008 32.000 0.00 0.00 0.00 2.44
119 120 6.434028 AGAGTGGCAAGCTATATCAAAACAAA 59.566 34.615 0.00 0.00 0.00 2.83
120 121 5.945784 AGAGTGGCAAGCTATATCAAAACAA 59.054 36.000 0.00 0.00 0.00 2.83
121 122 5.500234 AGAGTGGCAAGCTATATCAAAACA 58.500 37.500 0.00 0.00 0.00 2.83
122 123 6.127897 ACAAGAGTGGCAAGCTATATCAAAAC 60.128 38.462 0.00 0.00 0.00 2.43
123 124 5.945784 ACAAGAGTGGCAAGCTATATCAAAA 59.054 36.000 0.00 0.00 0.00 2.44
124 125 5.500234 ACAAGAGTGGCAAGCTATATCAAA 58.500 37.500 0.00 0.00 0.00 2.69
125 126 5.102953 ACAAGAGTGGCAAGCTATATCAA 57.897 39.130 0.00 0.00 0.00 2.57
126 127 4.162131 TGACAAGAGTGGCAAGCTATATCA 59.838 41.667 0.00 0.00 40.96 2.15
127 128 4.697514 TGACAAGAGTGGCAAGCTATATC 58.302 43.478 0.00 0.00 40.96 1.63
128 129 4.760530 TGACAAGAGTGGCAAGCTATAT 57.239 40.909 0.00 0.00 40.96 0.86
136 137 2.418368 ACAACTTGACAAGAGTGGCA 57.582 45.000 21.95 0.00 42.77 4.92
137 138 2.945668 AGAACAACTTGACAAGAGTGGC 59.054 45.455 21.95 13.73 0.00 5.01
138 139 3.941483 ACAGAACAACTTGACAAGAGTGG 59.059 43.478 21.95 13.52 0.00 4.00
139 140 5.122239 TCAACAGAACAACTTGACAAGAGTG 59.878 40.000 21.95 18.91 0.00 3.51
140 141 5.245531 TCAACAGAACAACTTGACAAGAGT 58.754 37.500 21.95 15.54 0.00 3.24
141 142 5.352569 ACTCAACAGAACAACTTGACAAGAG 59.647 40.000 21.95 14.94 0.00 2.85
142 143 5.245531 ACTCAACAGAACAACTTGACAAGA 58.754 37.500 21.95 0.00 0.00 3.02
143 144 5.122239 TGACTCAACAGAACAACTTGACAAG 59.878 40.000 13.77 13.77 0.00 3.16
144 145 5.000591 TGACTCAACAGAACAACTTGACAA 58.999 37.500 0.00 0.00 0.00 3.18
145 146 4.574892 TGACTCAACAGAACAACTTGACA 58.425 39.130 0.00 0.00 0.00 3.58
146 147 4.631813 ACTGACTCAACAGAACAACTTGAC 59.368 41.667 0.00 0.00 40.63 3.18
147 148 4.832248 ACTGACTCAACAGAACAACTTGA 58.168 39.130 0.00 0.00 40.63 3.02
148 149 5.551760 AACTGACTCAACAGAACAACTTG 57.448 39.130 0.00 0.00 40.63 3.16
149 150 4.330074 CGAACTGACTCAACAGAACAACTT 59.670 41.667 0.00 0.00 40.63 2.66
150 151 3.865745 CGAACTGACTCAACAGAACAACT 59.134 43.478 0.00 0.00 40.63 3.16
151 152 3.863424 TCGAACTGACTCAACAGAACAAC 59.137 43.478 0.00 0.00 40.63 3.32
184 185 1.413382 CAGAGATGTTATCGCGAGGC 58.587 55.000 16.66 7.69 34.06 4.70
187 188 0.032130 GGCCAGAGATGTTATCGCGA 59.968 55.000 13.09 13.09 34.06 5.87
197 198 0.034616 GATAAGCGCTGGCCAGAGAT 59.965 55.000 37.11 30.37 41.24 2.75
318 1861 5.024803 TCCCTTCTTCTTATATCCCCGAT 57.975 43.478 0.00 0.00 0.00 4.18
331 1874 5.714806 TGTTCACCCATTTTATCCCTTCTTC 59.285 40.000 0.00 0.00 0.00 2.87
404 2129 1.005975 CCGAGCATTCATTCGTTCGAC 60.006 52.381 0.00 0.00 35.14 4.20
464 2217 2.833631 AACTTTCTGGTGAGTACCCG 57.166 50.000 0.00 0.00 46.96 5.28
485 2238 5.047164 ACATAAATCTGCCAGCATTGTTCAA 60.047 36.000 0.00 0.00 0.00 2.69
531 2288 0.810031 ATAACGTGGATGAGGTGCGC 60.810 55.000 0.00 0.00 0.00 6.09
564 2321 0.811281 CCGGGTCAGAAAATTCCTGC 59.189 55.000 0.00 0.00 0.00 4.85
606 2363 2.762745 ACTGACGGTTACTTTCGCATT 58.237 42.857 0.00 0.00 0.00 3.56
607 2364 2.450609 ACTGACGGTTACTTTCGCAT 57.549 45.000 0.00 0.00 0.00 4.73
612 2369 1.601166 GGGCAACTGACGGTTACTTT 58.399 50.000 0.00 0.00 36.23 2.66
647 2428 1.442769 AACATCCAAGTGCTGTAGCG 58.557 50.000 0.00 0.00 45.83 4.26
661 2447 5.820423 GCCAAAATGGGGGTAAATAAACATC 59.180 40.000 0.00 0.00 38.19 3.06
677 2761 2.290367 TCAGAACTCACACGCCAAAATG 59.710 45.455 0.00 0.00 0.00 2.32
679 2763 1.939934 CTCAGAACTCACACGCCAAAA 59.060 47.619 0.00 0.00 0.00 2.44
709 2793 1.009829 GCCAGTTATCCTGCTGAACG 58.990 55.000 0.00 0.00 40.06 3.95
752 2866 1.681793 TGACGGAGCTAGCCTTGTATC 59.318 52.381 12.13 0.38 0.00 2.24
763 2883 2.100879 AAAAGGCGAGTGACGGAGCT 62.101 55.000 0.00 0.00 42.83 4.09
769 2889 0.793250 GAGCTCAAAAGGCGAGTGAC 59.207 55.000 9.40 0.00 32.83 3.67
793 2926 1.676615 GGAGTTTGTTATCGGCCGGAA 60.677 52.381 27.83 17.38 0.00 4.30
794 2927 0.108041 GGAGTTTGTTATCGGCCGGA 60.108 55.000 27.83 12.89 0.00 5.14
884 3033 0.520404 GATGCATCATGCCGGTGATC 59.480 55.000 21.92 0.00 44.23 2.92
885 3034 0.892358 GGATGCATCATGCCGGTGAT 60.892 55.000 27.25 1.83 44.23 3.06
886 3035 1.526686 GGATGCATCATGCCGGTGA 60.527 57.895 27.25 0.00 44.23 4.02
888 3037 1.527611 CAGGATGCATCATGCCGGT 60.528 57.895 26.48 0.40 44.23 5.28
889 3038 3.351450 CAGGATGCATCATGCCGG 58.649 61.111 26.48 8.08 44.23 6.13
1075 3229 9.757227 CGAAGAAGATAATACCTGAAAGAGAAT 57.243 33.333 0.00 0.00 34.07 2.40
1090 3244 3.861276 TCTTGCCGACGAAGAAGATAA 57.139 42.857 0.00 0.00 0.00 1.75
1091 3245 3.192844 AGTTCTTGCCGACGAAGAAGATA 59.807 43.478 10.90 0.00 39.53 1.98
1097 3257 0.784778 GACAGTTCTTGCCGACGAAG 59.215 55.000 0.00 0.00 0.00 3.79
1122 3305 3.120923 CCAAAACAAAACATGATCGCAGC 60.121 43.478 0.00 0.00 0.00 5.25
1424 3922 1.958715 CGTGCGGTGGTTGATGACA 60.959 57.895 0.00 0.00 0.00 3.58
2003 4501 0.106149 GGTTGTCCACGAAGGTCACT 59.894 55.000 0.00 0.00 35.09 3.41
2042 4540 1.729267 AAGGGAAGGGCCACATGTGT 61.729 55.000 23.79 5.30 38.95 3.72
2173 4673 3.944650 TGGTCATGGTTTCATATGAACGG 59.055 43.478 17.76 6.23 42.52 4.44
2208 4722 8.689251 TCGTAGAACTGAAGAATCACATTTAG 57.311 34.615 0.00 0.00 0.00 1.85
2212 4726 6.867550 TGATCGTAGAACTGAAGAATCACAT 58.132 36.000 0.00 0.00 43.58 3.21
2354 4868 1.140589 CTTGCTGTCGATCTCGGCT 59.859 57.895 15.87 0.00 45.41 5.52
2367 4881 2.417719 GAGTTTGACGATGACCTTGCT 58.582 47.619 0.00 0.00 0.00 3.91
2384 4898 0.389391 CATCGTATCTTGGCCCGAGT 59.611 55.000 0.00 0.00 32.26 4.18
2453 4967 7.335924 GCTTATATTTTCTCCCATACGGCATAA 59.664 37.037 0.00 0.00 0.00 1.90
2499 5066 5.824904 ACTAAATCGTACTACGTGGACAT 57.175 39.130 5.70 0.00 43.14 3.06
2507 5074 6.258947 ACGGAGGAAGTACTAAATCGTACTAC 59.741 42.308 0.00 2.05 46.88 2.73
2531 5099 4.254492 GTCCCTCATCCTCACTTTTACAC 58.746 47.826 0.00 0.00 0.00 2.90
2622 5191 4.733230 GCGCTGCATAATTTATGGTCAACA 60.733 41.667 16.22 6.15 36.68 3.33
2631 5200 0.028770 GCCGTGCGCTGCATAATTTA 59.971 50.000 9.73 0.00 41.91 1.40
2666 5235 0.541296 AGCTTGGAGGTTGCATGCTT 60.541 50.000 20.33 1.54 44.40 3.91
2811 5380 6.981762 AAGTTGATTCAGAACTGATAGCTG 57.018 37.500 5.34 0.00 39.64 4.24
2829 5398 4.634883 ACATAGCAGCTCTGATCAAAGTTG 59.365 41.667 14.48 8.42 0.00 3.16
2897 5471 1.130561 GAATGAAAGAAAGCGTCGGGG 59.869 52.381 0.00 0.00 0.00 5.73
2905 5479 7.541783 TCGGCACATATTTTGAATGAAAGAAAG 59.458 33.333 0.00 0.00 0.00 2.62
2927 5501 1.069906 CGGCATTATACTTTGCTCGGC 60.070 52.381 0.00 0.00 38.88 5.54
2943 5517 2.976840 GAAGAATGCAACCGCGGCA 61.977 57.895 28.58 18.84 46.66 5.69
2944 5518 2.200170 AAGAAGAATGCAACCGCGGC 62.200 55.000 28.58 12.64 42.97 6.53
2945 5519 0.179189 GAAGAAGAATGCAACCGCGG 60.179 55.000 26.86 26.86 42.97 6.46
2946 5520 0.519175 CGAAGAAGAATGCAACCGCG 60.519 55.000 0.00 0.00 42.97 6.46
2948 5522 0.447801 CCCGAAGAAGAATGCAACCG 59.552 55.000 0.00 0.00 0.00 4.44
2950 5524 0.179189 CGCCCGAAGAAGAATGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
2951 5525 0.321210 TCGCCCGAAGAAGAATGCAA 60.321 50.000 0.00 0.00 0.00 4.08
2953 5527 0.460284 TCTCGCCCGAAGAAGAATGC 60.460 55.000 0.00 0.00 0.00 3.56
2954 5528 1.135139 TCTCTCGCCCGAAGAAGAATG 59.865 52.381 0.00 0.00 0.00 2.67
2958 5532 0.811915 TCTTCTCTCGCCCGAAGAAG 59.188 55.000 22.24 22.24 41.75 2.85
2959 5533 0.811915 CTCTTCTCTCGCCCGAAGAA 59.188 55.000 10.02 11.70 43.42 2.52
2960 5534 1.032657 CCTCTTCTCTCGCCCGAAGA 61.033 60.000 8.92 8.92 42.28 2.87
2963 5537 2.046864 CACCTCTTCTCTCGCCCGA 61.047 63.158 0.00 0.00 0.00 5.14
2964 5538 2.492090 CACCTCTTCTCTCGCCCG 59.508 66.667 0.00 0.00 0.00 6.13
2966 5540 0.456628 GTACCACCTCTTCTCTCGCC 59.543 60.000 0.00 0.00 0.00 5.54
2967 5541 0.456628 GGTACCACCTCTTCTCTCGC 59.543 60.000 7.15 0.00 34.73 5.03
2990 5564 4.015084 CAGCTTCAGTTCCATCCAAGAAT 58.985 43.478 0.00 0.00 0.00 2.40
2992 5566 2.373169 ACAGCTTCAGTTCCATCCAAGA 59.627 45.455 0.00 0.00 0.00 3.02
2994 5568 2.957402 ACAGCTTCAGTTCCATCCAA 57.043 45.000 0.00 0.00 0.00 3.53
2995 5569 2.106338 TGAACAGCTTCAGTTCCATCCA 59.894 45.455 11.64 0.00 43.57 3.41
2996 5570 2.783135 TGAACAGCTTCAGTTCCATCC 58.217 47.619 11.64 0.00 43.57 3.51
3174 6384 5.959618 AGTGTAGTACAAAATTGGCTTCC 57.040 39.130 4.11 0.00 0.00 3.46
3257 8993 8.477256 TCAGAATTGAGAGGAAAACAAAATTGT 58.523 29.630 0.00 0.00 44.72 2.71
3305 9042 3.432186 CCTTGGATCAATTGCTAGACCGA 60.432 47.826 0.00 0.00 0.00 4.69
3324 9061 5.498393 TCGACATACTCTAGTCAGTTCCTT 58.502 41.667 0.00 0.00 34.48 3.36
3344 9082 3.667497 AAATCTGCTGTGTTCTCTCGA 57.333 42.857 0.00 0.00 0.00 4.04
3366 9104 4.669206 TGGCTGCAAATTCAGAAGAAAA 57.331 36.364 0.50 0.00 37.29 2.29
3370 9108 6.872628 TCTATATGGCTGCAAATTCAGAAG 57.127 37.500 0.50 0.00 36.19 2.85
3371 9109 6.830324 ACTTCTATATGGCTGCAAATTCAGAA 59.170 34.615 0.50 6.26 36.19 3.02
3389 9127 3.620966 GCTGCTGACCTTGGAACTTCTAT 60.621 47.826 0.00 0.00 0.00 1.98
3390 9128 2.289694 GCTGCTGACCTTGGAACTTCTA 60.290 50.000 0.00 0.00 0.00 2.10
3391 9129 1.544314 GCTGCTGACCTTGGAACTTCT 60.544 52.381 0.00 0.00 0.00 2.85
3395 9133 0.823356 TTGGCTGCTGACCTTGGAAC 60.823 55.000 0.00 0.00 0.00 3.62
3397 9135 0.112995 ATTTGGCTGCTGACCTTGGA 59.887 50.000 0.00 0.00 0.00 3.53
3399 9137 0.245539 CCATTTGGCTGCTGACCTTG 59.754 55.000 0.00 0.00 0.00 3.61
3400 9138 0.112995 TCCATTTGGCTGCTGACCTT 59.887 50.000 0.00 0.00 34.44 3.50
3401 9139 0.323178 CTCCATTTGGCTGCTGACCT 60.323 55.000 0.00 0.00 34.44 3.85
3402 9140 1.318158 CCTCCATTTGGCTGCTGACC 61.318 60.000 0.00 0.00 34.44 4.02
3403 9141 1.941999 GCCTCCATTTGGCTGCTGAC 61.942 60.000 0.00 0.00 46.38 3.51
3404 9142 1.679977 GCCTCCATTTGGCTGCTGA 60.680 57.895 0.00 0.00 46.38 4.26
3405 9143 2.890371 GCCTCCATTTGGCTGCTG 59.110 61.111 0.00 0.00 46.38 4.41
3411 9149 0.609131 ACTCCAACGCCTCCATTTGG 60.609 55.000 0.00 0.00 41.12 3.28
3412 9150 0.804989 GACTCCAACGCCTCCATTTG 59.195 55.000 0.00 0.00 0.00 2.32
3414 9152 1.299976 GGACTCCAACGCCTCCATT 59.700 57.895 0.00 0.00 0.00 3.16
3415 9153 2.670148 GGGACTCCAACGCCTCCAT 61.670 63.158 0.00 0.00 0.00 3.41
3416 9154 3.319198 GGGACTCCAACGCCTCCA 61.319 66.667 0.00 0.00 0.00 3.86
3417 9155 2.523453 GAAGGGACTCCAACGCCTCC 62.523 65.000 0.00 0.00 38.49 4.30
3422 9160 2.761208 ACTAGATGAAGGGACTCCAACG 59.239 50.000 0.00 0.00 38.49 4.10
3423 9161 3.118592 CCACTAGATGAAGGGACTCCAAC 60.119 52.174 0.00 0.00 38.49 3.77
3424 9162 3.107601 CCACTAGATGAAGGGACTCCAA 58.892 50.000 0.00 0.00 38.49 3.53
3425 9163 2.752030 CCACTAGATGAAGGGACTCCA 58.248 52.381 0.00 0.00 38.49 3.86
3426 9164 1.414550 GCCACTAGATGAAGGGACTCC 59.585 57.143 0.00 0.00 38.49 3.85
3427 9165 1.414550 GGCCACTAGATGAAGGGACTC 59.585 57.143 0.00 0.00 38.49 3.36
3429 9167 1.204146 TGGCCACTAGATGAAGGGAC 58.796 55.000 0.00 0.00 0.00 4.46
3431 9169 1.270518 CGATGGCCACTAGATGAAGGG 60.271 57.143 8.16 0.00 0.00 3.95
3432 9170 1.688735 TCGATGGCCACTAGATGAAGG 59.311 52.381 8.16 0.00 0.00 3.46
3433 9171 3.068732 TCTTCGATGGCCACTAGATGAAG 59.931 47.826 8.16 14.91 34.40 3.02
3434 9172 3.031013 TCTTCGATGGCCACTAGATGAA 58.969 45.455 8.16 5.28 0.00 2.57
3436 9174 2.363680 ACTCTTCGATGGCCACTAGATG 59.636 50.000 8.16 10.37 0.00 2.90
3437 9175 2.363680 CACTCTTCGATGGCCACTAGAT 59.636 50.000 8.16 0.00 0.00 1.98
3439 9177 1.804372 GCACTCTTCGATGGCCACTAG 60.804 57.143 8.16 1.78 0.00 2.57
3440 9178 0.175760 GCACTCTTCGATGGCCACTA 59.824 55.000 8.16 0.00 0.00 2.74
3442 9180 0.674895 AAGCACTCTTCGATGGCCAC 60.675 55.000 8.16 0.47 0.00 5.01
3443 9181 0.036732 AAAGCACTCTTCGATGGCCA 59.963 50.000 8.56 8.56 0.00 5.36
3444 9182 0.729690 GAAAGCACTCTTCGATGGCC 59.270 55.000 0.00 0.00 0.00 5.36
3445 9183 1.396301 CTGAAAGCACTCTTCGATGGC 59.604 52.381 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.