Multiple sequence alignment - TraesCS1B01G465200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G465200 chr1B 100.000 3706 0 0 1 3706 676117383 676121088 0.000000e+00 6844.0
1 TraesCS1B01G465200 chr1B 89.177 1312 113 18 1604 2888 676150219 676148910 0.000000e+00 1609.0
2 TraesCS1B01G465200 chr1B 86.166 759 46 19 292 1016 676161767 676161034 0.000000e+00 765.0
3 TraesCS1B01G465200 chr1B 87.120 559 44 16 3145 3697 676148756 676148220 3.160000e-170 608.0
4 TraesCS1B01G465200 chr1B 83.059 608 76 14 1014 1607 676151235 676150641 9.120000e-146 527.0
5 TraesCS1B01G465200 chr1B 72.133 1116 268 34 1613 2693 676469350 676468243 7.780000e-77 298.0
6 TraesCS1B01G465200 chr1B 76.221 307 71 2 1854 2160 676391184 676390880 1.070000e-35 161.0
7 TraesCS1B01G465200 chr1B 92.079 101 7 1 3047 3147 676148886 676148787 1.390000e-29 141.0
8 TraesCS1B01G465200 chr1B 94.030 67 2 2 143 208 74119993 74119928 2.360000e-17 100.0
9 TraesCS1B01G465200 chr1A 95.478 1548 55 8 1604 3143 583115968 583117508 0.000000e+00 2457.0
10 TraesCS1B01G465200 chr1A 90.132 1439 65 28 207 1607 583113751 583115150 0.000000e+00 1799.0
11 TraesCS1B01G465200 chr1A 89.816 1198 100 15 1715 2895 583130792 583129600 0.000000e+00 1517.0
12 TraesCS1B01G465200 chr1A 87.489 1175 86 24 292 1420 583132669 583131510 0.000000e+00 1299.0
13 TraesCS1B01G465200 chr1A 93.134 568 19 3 3139 3706 583122876 583123423 0.000000e+00 815.0
14 TraesCS1B01G465200 chr1A 86.727 550 56 12 3141 3687 583129492 583128957 2.460000e-166 595.0
15 TraesCS1B01G465200 chr1A 83.654 104 14 3 207 309 583137388 583137287 1.100000e-15 95.3
16 TraesCS1B01G465200 chr1A 91.304 69 5 1 1604 1671 583130954 583130886 3.940000e-15 93.5
17 TraesCS1B01G465200 chr5B 80.502 1554 241 34 1604 3106 585006138 585007680 0.000000e+00 1134.0
18 TraesCS1B01G465200 chr5B 88.312 77 6 2 3078 3153 585007526 585007600 5.100000e-14 89.8
19 TraesCS1B01G465200 chr5A 81.053 1367 206 27 1604 2927 596566218 596567574 0.000000e+00 1040.0
20 TraesCS1B01G465200 chr5A 88.462 78 7 1 3076 3153 596567625 596567700 3.940000e-15 93.5
21 TraesCS1B01G465200 chr5D 81.053 1367 198 28 1604 2927 477379017 477380365 0.000000e+00 1033.0
22 TraesCS1B01G465200 chr5D 78.947 722 106 24 862 1572 477377860 477378546 2.030000e-122 449.0
23 TraesCS1B01G465200 chr5D 89.744 78 6 1 3076 3153 477380416 477380491 8.470000e-17 99.0
24 TraesCS1B01G465200 chr1D 87.215 571 34 11 258 794 485573899 485573334 6.800000e-172 614.0
25 TraesCS1B01G465200 chr1D 71.937 702 156 32 1879 2547 485818838 485818145 2.290000e-37 167.0
26 TraesCS1B01G465200 chr2A 86.429 420 45 7 3161 3578 93885080 93884671 2.030000e-122 449.0
27 TraesCS1B01G465200 chr2A 84.926 272 32 6 2659 2927 93885622 93885357 2.190000e-67 267.0
28 TraesCS1B01G465200 chr2A 75.776 161 32 7 52 209 18304647 18304803 1.430000e-09 75.0
29 TraesCS1B01G465200 chr7B 96.209 211 8 0 1 211 112114892 112114682 2.740000e-91 346.0
30 TraesCS1B01G465200 chr2B 95.673 208 9 0 1 208 22663496 22663289 5.930000e-88 335.0
31 TraesCS1B01G465200 chr2B 80.508 354 47 15 3352 3702 712911748 712912082 6.140000e-63 252.0
32 TraesCS1B01G465200 chr2B 95.161 62 1 2 157 218 70860115 70860056 3.050000e-16 97.1
33 TraesCS1B01G465200 chr4A 95.169 207 10 0 1 207 696167025 696166819 9.920000e-86 327.0
34 TraesCS1B01G465200 chr4A 84.043 188 24 4 2574 2760 46639313 46639131 3.800000e-40 176.0
35 TraesCS1B01G465200 chr4A 73.320 491 100 21 3171 3643 46625480 46625003 6.410000e-33 152.0
36 TraesCS1B01G465200 chr4D 76.978 278 45 9 3205 3474 418225218 418225484 1.390000e-29 141.0
37 TraesCS1B01G465200 chr3D 86.735 98 11 2 112 208 47798372 47798468 1.410000e-19 108.0
38 TraesCS1B01G465200 chr3B 98.077 52 1 0 157 208 345085460 345085409 1.420000e-14 91.6
39 TraesCS1B01G465200 chr4B 91.045 67 4 2 143 208 580501537 580501472 5.100000e-14 89.8
40 TraesCS1B01G465200 chr4B 86.364 66 7 2 429 493 670390316 670390380 1.850000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G465200 chr1B 676117383 676121088 3705 False 6844.000 6844 100.00000 1 3706 1 chr1B.!!$F1 3705
1 TraesCS1B01G465200 chr1B 676161034 676161767 733 True 765.000 765 86.16600 292 1016 1 chr1B.!!$R2 724
2 TraesCS1B01G465200 chr1B 676148220 676151235 3015 True 721.250 1609 87.85875 1014 3697 4 chr1B.!!$R5 2683
3 TraesCS1B01G465200 chr1B 676468243 676469350 1107 True 298.000 298 72.13300 1613 2693 1 chr1B.!!$R4 1080
4 TraesCS1B01G465200 chr1A 583113751 583117508 3757 False 2128.000 2457 92.80500 207 3143 2 chr1A.!!$F2 2936
5 TraesCS1B01G465200 chr1A 583128957 583132669 3712 True 876.125 1517 88.83400 292 3687 4 chr1A.!!$R2 3395
6 TraesCS1B01G465200 chr1A 583122876 583123423 547 False 815.000 815 93.13400 3139 3706 1 chr1A.!!$F1 567
7 TraesCS1B01G465200 chr5B 585006138 585007680 1542 False 611.900 1134 84.40700 1604 3153 2 chr5B.!!$F1 1549
8 TraesCS1B01G465200 chr5A 596566218 596567700 1482 False 566.750 1040 84.75750 1604 3153 2 chr5A.!!$F1 1549
9 TraesCS1B01G465200 chr5D 477377860 477380491 2631 False 527.000 1033 83.24800 862 3153 3 chr5D.!!$F1 2291
10 TraesCS1B01G465200 chr1D 485573334 485573899 565 True 614.000 614 87.21500 258 794 1 chr1D.!!$R1 536
11 TraesCS1B01G465200 chr2A 93884671 93885622 951 True 358.000 449 85.67750 2659 3578 2 chr2A.!!$R1 919

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
162 163 0.035598 TCCGACGGCTGAAAATCCAA 59.964 50.0 9.66 0.0 0.00 3.53 F
166 167 0.039527 ACGGCTGAAAATCCAAACGC 60.040 50.0 0.00 0.0 0.00 4.84 F
167 168 0.039617 CGGCTGAAAATCCAAACGCA 60.040 50.0 0.00 0.0 0.00 5.24 F
174 175 0.250553 AAATCCAAACGCACGGGAGA 60.251 50.0 0.00 0.0 33.47 3.71 F
175 176 0.673644 AATCCAAACGCACGGGAGAG 60.674 55.0 0.00 0.0 33.47 3.20 F
183 184 1.021390 CGCACGGGAGAGCTTCATTT 61.021 55.0 0.00 0.0 44.57 2.32 F
322 325 1.048601 CTACACACACCCTCACACCT 58.951 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1327 0.878086 GAATCTGAGCTACCAGGCGC 60.878 60.000 0.00 0.0 37.29 6.53 R
2113 3100 1.534729 ACCTTGTGAAGAAATCGGGC 58.465 50.000 0.00 0.0 0.00 6.13 R
2262 3285 7.325660 AGCCACTTCAGATAAAATGTGTATG 57.674 36.000 0.00 0.0 0.00 2.39 R
2263 3286 7.394359 ACAAGCCACTTCAGATAAAATGTGTAT 59.606 33.333 0.00 0.0 0.00 2.29 R
2297 3320 8.910666 CAGAGCAATAAAGATAGTGTCGATAAG 58.089 37.037 0.00 0.0 29.96 1.73 R
2414 3437 8.795786 TTTTGAGTGAACACAAATACATAAGC 57.204 30.769 6.84 0.0 36.58 3.09 R
2756 3800 5.248380 AGATTCAGTCAGGCTAAAAAGGT 57.752 39.130 0.00 0.0 0.00 3.50 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 2.301346 GTGGGGCATGAGATTTACAGG 58.699 52.381 0.00 0.00 0.00 4.00
21 22 1.322442 GGGGCATGAGATTTACAGGC 58.678 55.000 0.00 0.00 42.94 4.85
22 23 0.947244 GGGCATGAGATTTACAGGCG 59.053 55.000 0.00 0.00 44.27 5.52
23 24 0.947244 GGCATGAGATTTACAGGCGG 59.053 55.000 0.00 0.00 44.27 6.13
24 25 1.668419 GCATGAGATTTACAGGCGGT 58.332 50.000 0.00 0.00 35.53 5.68
25 26 1.331756 GCATGAGATTTACAGGCGGTG 59.668 52.381 0.00 0.00 35.53 4.94
26 27 1.942657 CATGAGATTTACAGGCGGTGG 59.057 52.381 0.00 0.00 0.00 4.61
27 28 0.392461 TGAGATTTACAGGCGGTGGC 60.392 55.000 0.00 0.00 38.90 5.01
28 29 0.392461 GAGATTTACAGGCGGTGGCA 60.392 55.000 0.00 0.00 42.47 4.92
29 30 0.676782 AGATTTACAGGCGGTGGCAC 60.677 55.000 9.70 9.70 42.47 5.01
30 31 1.654023 GATTTACAGGCGGTGGCACC 61.654 60.000 26.95 26.95 42.47 5.01
31 32 2.419011 ATTTACAGGCGGTGGCACCA 62.419 55.000 34.11 14.26 38.47 4.17
32 33 3.835790 TTACAGGCGGTGGCACCAC 62.836 63.158 34.11 25.82 45.49 4.16
40 41 3.918544 GTGGCACCACACAACAGT 58.081 55.556 14.97 0.00 45.53 3.55
41 42 1.433064 GTGGCACCACACAACAGTG 59.567 57.895 14.97 0.00 45.53 3.66
42 43 1.001517 TGGCACCACACAACAGTGT 60.002 52.632 0.00 0.00 46.90 3.55
43 44 0.610509 TGGCACCACACAACAGTGTT 60.611 50.000 1.64 1.64 43.66 3.32
44 45 0.530288 GGCACCACACAACAGTGTTT 59.470 50.000 5.57 0.00 43.66 2.83
45 46 1.067213 GGCACCACACAACAGTGTTTT 60.067 47.619 5.57 0.00 43.66 2.43
46 47 1.991965 GCACCACACAACAGTGTTTTG 59.008 47.619 18.38 18.38 43.66 2.44
47 48 2.609244 GCACCACACAACAGTGTTTTGT 60.609 45.455 19.62 19.62 43.66 2.83
48 49 3.648009 CACCACACAACAGTGTTTTGTT 58.352 40.909 22.10 8.96 43.66 2.83
49 50 3.672867 CACCACACAACAGTGTTTTGTTC 59.327 43.478 22.10 0.00 43.66 3.18
50 51 2.914214 CCACACAACAGTGTTTTGTTCG 59.086 45.455 22.10 13.43 43.66 3.95
51 52 3.365465 CCACACAACAGTGTTTTGTTCGA 60.365 43.478 22.10 0.00 43.66 3.71
52 53 4.411327 CACACAACAGTGTTTTGTTCGAT 58.589 39.130 22.10 1.29 43.66 3.59
53 54 4.495472 CACACAACAGTGTTTTGTTCGATC 59.505 41.667 22.10 0.00 43.66 3.69
54 55 4.035017 CACAACAGTGTTTTGTTCGATCC 58.965 43.478 13.00 0.00 39.17 3.36
55 56 3.242608 ACAACAGTGTTTTGTTCGATCCG 60.243 43.478 5.57 0.00 39.17 4.18
56 57 2.828877 ACAGTGTTTTGTTCGATCCGA 58.171 42.857 0.00 0.00 0.00 4.55
57 58 2.542595 ACAGTGTTTTGTTCGATCCGAC 59.457 45.455 0.00 0.00 34.89 4.79
58 59 1.790623 AGTGTTTTGTTCGATCCGACG 59.209 47.619 0.00 0.00 34.89 5.12
59 60 1.136446 GTGTTTTGTTCGATCCGACGG 60.136 52.381 7.84 7.84 34.89 4.79
60 61 0.441145 GTTTTGTTCGATCCGACGGG 59.559 55.000 15.25 0.00 34.89 5.28
61 62 1.293267 TTTTGTTCGATCCGACGGGC 61.293 55.000 15.25 5.81 34.89 6.13
62 63 2.437518 TTTGTTCGATCCGACGGGCA 62.438 55.000 15.25 0.00 34.89 5.36
63 64 2.582498 GTTCGATCCGACGGGCAG 60.582 66.667 15.25 5.57 34.89 4.85
64 65 3.833645 TTCGATCCGACGGGCAGG 61.834 66.667 15.25 1.38 34.89 4.85
65 66 4.807631 TCGATCCGACGGGCAGGA 62.808 66.667 15.25 3.93 41.30 3.86
68 69 3.606662 ATCCGACGGGCAGGATCG 61.607 66.667 15.25 0.00 43.27 3.69
69 70 4.807631 TCCGACGGGCAGGATCGA 62.808 66.667 15.25 0.00 38.10 3.59
70 71 3.606662 CCGACGGGCAGGATCGAT 61.607 66.667 5.81 0.00 38.10 3.59
71 72 2.355126 CGACGGGCAGGATCGATG 60.355 66.667 0.54 0.00 38.10 3.84
72 73 2.815308 GACGGGCAGGATCGATGT 59.185 61.111 0.54 0.00 0.00 3.06
73 74 1.792118 CGACGGGCAGGATCGATGTA 61.792 60.000 0.54 0.00 38.10 2.29
74 75 0.039074 GACGGGCAGGATCGATGTAG 60.039 60.000 0.54 0.00 0.00 2.74
75 76 0.467474 ACGGGCAGGATCGATGTAGA 60.467 55.000 0.54 0.00 0.00 2.59
76 77 0.039074 CGGGCAGGATCGATGTAGAC 60.039 60.000 0.54 0.00 0.00 2.59
77 78 0.039074 GGGCAGGATCGATGTAGACG 60.039 60.000 0.54 0.00 0.00 4.18
78 79 0.952280 GGCAGGATCGATGTAGACGA 59.048 55.000 0.54 0.00 43.65 4.20
79 80 1.337071 GGCAGGATCGATGTAGACGAA 59.663 52.381 0.54 0.00 42.80 3.85
80 81 2.605823 GGCAGGATCGATGTAGACGAAG 60.606 54.545 0.54 0.00 42.80 3.79
81 82 2.290916 GCAGGATCGATGTAGACGAAGA 59.709 50.000 0.54 0.00 42.80 2.87
82 83 3.057876 GCAGGATCGATGTAGACGAAGAT 60.058 47.826 0.54 0.00 42.80 2.40
83 84 4.717991 CAGGATCGATGTAGACGAAGATC 58.282 47.826 0.54 0.00 42.80 2.75
84 85 4.086199 GGATCGATGTAGACGAAGATCC 57.914 50.000 0.54 6.54 44.64 3.36
85 86 3.425094 GGATCGATGTAGACGAAGATCCG 60.425 52.174 0.54 0.00 42.86 4.18
86 87 2.830104 TCGATGTAGACGAAGATCCGA 58.170 47.619 0.00 0.00 36.84 4.55
87 88 2.543012 TCGATGTAGACGAAGATCCGAC 59.457 50.000 0.00 0.00 36.84 4.79
88 89 2.659558 CGATGTAGACGAAGATCCGACG 60.660 54.545 0.00 0.79 0.00 5.12
89 90 1.012086 TGTAGACGAAGATCCGACGG 58.988 55.000 7.84 7.84 0.00 4.79
90 91 0.316854 GTAGACGAAGATCCGACGGC 60.317 60.000 9.66 0.00 35.11 5.68
91 92 1.442526 TAGACGAAGATCCGACGGCC 61.443 60.000 9.66 3.31 35.51 6.13
92 93 3.060020 GACGAAGATCCGACGGCCA 62.060 63.158 9.66 0.00 0.00 5.36
93 94 2.278857 CGAAGATCCGACGGCCAG 60.279 66.667 9.66 0.00 0.00 4.85
94 95 2.107141 GAAGATCCGACGGCCAGG 59.893 66.667 9.66 2.49 0.00 4.45
95 96 2.363795 AAGATCCGACGGCCAGGA 60.364 61.111 9.66 13.18 41.30 3.86
98 99 3.606662 ATCCGACGGCCAGGATCG 61.607 66.667 16.20 12.32 43.27 3.69
101 102 4.933064 CGACGGCCAGGATCGCTC 62.933 72.222 2.24 0.00 0.00 5.03
102 103 3.532155 GACGGCCAGGATCGCTCT 61.532 66.667 2.24 0.00 0.00 4.09
103 104 3.781770 GACGGCCAGGATCGCTCTG 62.782 68.421 2.24 0.00 0.00 3.35
107 108 3.473647 CCAGGATCGCTCTGGGCA 61.474 66.667 0.00 0.00 45.95 5.36
108 109 2.586245 CAGGATCGCTCTGGGCAA 59.414 61.111 0.00 0.00 41.91 4.52
109 110 1.078214 CAGGATCGCTCTGGGCAAA 60.078 57.895 0.00 0.00 41.91 3.68
110 111 0.677731 CAGGATCGCTCTGGGCAAAA 60.678 55.000 0.00 0.00 41.91 2.44
111 112 0.038166 AGGATCGCTCTGGGCAAAAA 59.962 50.000 0.00 0.00 41.91 1.94
112 113 1.106285 GGATCGCTCTGGGCAAAAAT 58.894 50.000 0.00 0.00 41.91 1.82
113 114 1.066152 GGATCGCTCTGGGCAAAAATC 59.934 52.381 0.00 0.00 41.91 2.17
114 115 1.066152 GATCGCTCTGGGCAAAAATCC 59.934 52.381 0.00 0.00 41.91 3.01
115 116 1.137404 CGCTCTGGGCAAAAATCCG 59.863 57.895 0.00 0.00 41.91 4.18
116 117 1.305219 CGCTCTGGGCAAAAATCCGA 61.305 55.000 0.00 0.00 41.91 4.55
117 118 0.171231 GCTCTGGGCAAAAATCCGAC 59.829 55.000 0.00 0.00 41.35 4.79
118 119 0.447801 CTCTGGGCAAAAATCCGACG 59.552 55.000 0.00 0.00 0.00 5.12
119 120 0.958382 TCTGGGCAAAAATCCGACGG 60.958 55.000 7.84 7.84 0.00 4.79
120 121 2.180769 GGGCAAAAATCCGACGGC 59.819 61.111 9.66 0.00 0.00 5.68
121 122 2.180769 GGCAAAAATCCGACGGCC 59.819 61.111 9.66 0.47 0.00 6.13
122 123 2.180769 GCAAAAATCCGACGGCCC 59.819 61.111 9.66 0.00 0.00 5.80
123 124 2.882132 CAAAAATCCGACGGCCCC 59.118 61.111 9.66 0.00 0.00 5.80
124 125 2.748647 AAAAATCCGACGGCCCCG 60.749 61.111 9.66 4.96 46.03 5.73
125 126 3.256824 AAAAATCCGACGGCCCCGA 62.257 57.895 14.44 0.00 42.83 5.14
126 127 2.546114 AAAAATCCGACGGCCCCGAT 62.546 55.000 14.44 0.00 42.83 4.18
127 128 2.935627 AAAATCCGACGGCCCCGATC 62.936 60.000 14.44 6.49 42.83 3.69
132 133 4.162690 GACGGCCCCGATCAGCTT 62.163 66.667 14.44 0.00 42.83 3.74
133 134 4.473520 ACGGCCCCGATCAGCTTG 62.474 66.667 14.44 0.00 42.83 4.01
135 136 3.797353 GGCCCCGATCAGCTTGGA 61.797 66.667 0.00 0.00 0.00 3.53
136 137 2.272146 GCCCCGATCAGCTTGGAA 59.728 61.111 0.00 0.00 0.00 3.53
137 138 1.821332 GCCCCGATCAGCTTGGAAG 60.821 63.158 0.00 0.00 0.00 3.46
138 139 1.153086 CCCCGATCAGCTTGGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
139 140 1.821332 CCCGATCAGCTTGGAAGGC 60.821 63.158 0.00 0.00 0.00 4.35
140 141 1.222936 CCGATCAGCTTGGAAGGCT 59.777 57.895 0.00 0.00 41.07 4.58
141 142 0.465705 CCGATCAGCTTGGAAGGCTA 59.534 55.000 0.00 0.00 38.03 3.93
142 143 1.134401 CCGATCAGCTTGGAAGGCTAA 60.134 52.381 0.00 0.00 38.03 3.09
143 144 2.486191 CCGATCAGCTTGGAAGGCTAAT 60.486 50.000 0.00 0.00 38.03 1.73
144 145 2.805099 CGATCAGCTTGGAAGGCTAATC 59.195 50.000 0.00 0.00 38.03 1.75
145 146 2.717639 TCAGCTTGGAAGGCTAATCC 57.282 50.000 0.00 0.00 38.03 3.01
146 147 1.134401 TCAGCTTGGAAGGCTAATCCG 60.134 52.381 0.96 0.00 39.98 4.18
147 148 1.134401 CAGCTTGGAAGGCTAATCCGA 60.134 52.381 0.96 0.00 39.98 4.55
148 149 1.134371 AGCTTGGAAGGCTAATCCGAC 60.134 52.381 0.96 0.00 39.98 4.79
149 150 1.571919 CTTGGAAGGCTAATCCGACG 58.428 55.000 0.96 0.00 39.98 5.12
150 151 0.177141 TTGGAAGGCTAATCCGACGG 59.823 55.000 7.84 7.84 39.98 4.79
151 152 1.594564 GGAAGGCTAATCCGACGGC 60.595 63.158 9.66 0.00 40.77 5.68
152 153 1.442148 GAAGGCTAATCCGACGGCT 59.558 57.895 9.66 0.00 40.77 5.52
153 154 0.876342 GAAGGCTAATCCGACGGCTG 60.876 60.000 9.66 0.00 40.77 4.85
154 155 1.327690 AAGGCTAATCCGACGGCTGA 61.328 55.000 9.66 0.00 40.77 4.26
155 156 1.143183 GGCTAATCCGACGGCTGAA 59.857 57.895 9.66 0.00 0.00 3.02
156 157 0.461339 GGCTAATCCGACGGCTGAAA 60.461 55.000 9.66 0.00 0.00 2.69
157 158 1.365699 GCTAATCCGACGGCTGAAAA 58.634 50.000 9.66 0.00 0.00 2.29
158 159 1.940613 GCTAATCCGACGGCTGAAAAT 59.059 47.619 9.66 0.00 0.00 1.82
159 160 2.032808 GCTAATCCGACGGCTGAAAATC 60.033 50.000 9.66 0.00 0.00 2.17
160 161 1.379527 AATCCGACGGCTGAAAATCC 58.620 50.000 9.66 0.00 0.00 3.01
161 162 0.251916 ATCCGACGGCTGAAAATCCA 59.748 50.000 9.66 0.00 0.00 3.41
162 163 0.035598 TCCGACGGCTGAAAATCCAA 59.964 50.000 9.66 0.00 0.00 3.53
163 164 0.878416 CCGACGGCTGAAAATCCAAA 59.122 50.000 0.00 0.00 0.00 3.28
164 165 1.401018 CCGACGGCTGAAAATCCAAAC 60.401 52.381 0.00 0.00 0.00 2.93
165 166 1.724654 CGACGGCTGAAAATCCAAACG 60.725 52.381 0.00 0.00 0.00 3.60
166 167 0.039527 ACGGCTGAAAATCCAAACGC 60.040 50.000 0.00 0.00 0.00 4.84
167 168 0.039617 CGGCTGAAAATCCAAACGCA 60.040 50.000 0.00 0.00 0.00 5.24
168 169 1.418373 GGCTGAAAATCCAAACGCAC 58.582 50.000 0.00 0.00 0.00 5.34
169 170 1.052287 GCTGAAAATCCAAACGCACG 58.948 50.000 0.00 0.00 0.00 5.34
170 171 1.685302 CTGAAAATCCAAACGCACGG 58.315 50.000 0.00 0.00 0.00 4.94
171 172 0.312416 TGAAAATCCAAACGCACGGG 59.688 50.000 0.00 0.00 0.00 5.28
172 173 0.594110 GAAAATCCAAACGCACGGGA 59.406 50.000 0.00 0.00 34.70 5.14
173 174 0.596082 AAAATCCAAACGCACGGGAG 59.404 50.000 0.00 0.00 33.47 4.30
174 175 0.250553 AAATCCAAACGCACGGGAGA 60.251 50.000 0.00 0.00 33.47 3.71
175 176 0.673644 AATCCAAACGCACGGGAGAG 60.674 55.000 0.00 0.00 33.47 3.20
176 177 3.423154 CCAAACGCACGGGAGAGC 61.423 66.667 0.00 0.00 43.27 4.09
177 178 2.357517 CAAACGCACGGGAGAGCT 60.358 61.111 0.00 0.00 44.57 4.09
178 179 1.961277 CAAACGCACGGGAGAGCTT 60.961 57.895 0.00 0.00 44.57 3.74
179 180 1.668151 AAACGCACGGGAGAGCTTC 60.668 57.895 0.00 0.00 44.57 3.86
180 181 2.377628 AAACGCACGGGAGAGCTTCA 62.378 55.000 0.00 0.00 44.57 3.02
181 182 2.172483 AACGCACGGGAGAGCTTCAT 62.172 55.000 0.00 0.00 44.57 2.57
182 183 1.448540 CGCACGGGAGAGCTTCATT 60.449 57.895 0.00 0.00 44.57 2.57
183 184 1.021390 CGCACGGGAGAGCTTCATTT 61.021 55.000 0.00 0.00 44.57 2.32
184 185 1.168714 GCACGGGAGAGCTTCATTTT 58.831 50.000 0.00 0.00 43.37 1.82
185 186 1.135575 GCACGGGAGAGCTTCATTTTG 60.136 52.381 0.00 0.00 43.37 2.44
186 187 1.470098 CACGGGAGAGCTTCATTTTGG 59.530 52.381 0.00 0.00 0.00 3.28
187 188 1.073923 ACGGGAGAGCTTCATTTTGGT 59.926 47.619 0.00 0.00 0.00 3.67
188 189 1.740025 CGGGAGAGCTTCATTTTGGTC 59.260 52.381 0.00 0.00 0.00 4.02
189 190 2.616510 CGGGAGAGCTTCATTTTGGTCT 60.617 50.000 0.00 0.00 42.72 3.85
190 191 2.751806 GGGAGAGCTTCATTTTGGTCTG 59.248 50.000 0.00 0.00 40.53 3.51
191 192 2.751806 GGAGAGCTTCATTTTGGTCTGG 59.248 50.000 0.00 0.00 40.53 3.86
192 193 3.560025 GGAGAGCTTCATTTTGGTCTGGA 60.560 47.826 0.00 0.00 40.53 3.86
193 194 3.416156 AGAGCTTCATTTTGGTCTGGAC 58.584 45.455 0.00 0.00 39.23 4.02
194 195 3.073650 AGAGCTTCATTTTGGTCTGGACT 59.926 43.478 0.00 0.00 39.23 3.85
195 196 3.416156 AGCTTCATTTTGGTCTGGACTC 58.584 45.455 0.67 0.00 0.00 3.36
196 197 3.073650 AGCTTCATTTTGGTCTGGACTCT 59.926 43.478 0.67 0.00 0.00 3.24
197 198 4.287067 AGCTTCATTTTGGTCTGGACTCTA 59.713 41.667 0.67 0.00 0.00 2.43
198 199 5.003804 GCTTCATTTTGGTCTGGACTCTAA 58.996 41.667 0.67 0.00 0.00 2.10
199 200 5.106515 GCTTCATTTTGGTCTGGACTCTAAC 60.107 44.000 0.67 0.00 0.00 2.34
200 201 5.560722 TCATTTTGGTCTGGACTCTAACA 57.439 39.130 0.67 0.00 0.00 2.41
201 202 5.935945 TCATTTTGGTCTGGACTCTAACAA 58.064 37.500 0.67 0.00 0.00 2.83
202 203 5.997746 TCATTTTGGTCTGGACTCTAACAAG 59.002 40.000 0.67 0.00 0.00 3.16
203 204 4.351874 TTTGGTCTGGACTCTAACAAGG 57.648 45.455 0.67 0.00 0.00 3.61
204 205 2.257207 TGGTCTGGACTCTAACAAGGG 58.743 52.381 0.67 0.00 0.00 3.95
205 206 1.555533 GGTCTGGACTCTAACAAGGGG 59.444 57.143 0.67 0.00 0.00 4.79
311 314 2.524640 TCCACCGGCCTACACACA 60.525 61.111 0.00 0.00 0.00 3.72
312 315 2.358247 CCACCGGCCTACACACAC 60.358 66.667 0.00 0.00 0.00 3.82
322 325 1.048601 CTACACACACCCTCACACCT 58.951 55.000 0.00 0.00 0.00 4.00
404 408 3.138798 GAGACGGCGCTCCTACCA 61.139 66.667 6.90 0.00 0.00 3.25
412 416 4.208686 GCTCCTACCAGCGGTCGG 62.209 72.222 10.67 10.67 39.56 4.79
413 417 2.439701 CTCCTACCAGCGGTCGGA 60.440 66.667 16.27 16.27 43.86 4.55
431 435 2.751436 CCCGGGTACGAGGACGAA 60.751 66.667 14.18 0.00 44.60 3.85
432 436 2.768492 CCCGGGTACGAGGACGAAG 61.768 68.421 14.18 0.00 44.60 3.79
434 438 1.427020 CGGGTACGAGGACGAAGAC 59.573 63.158 0.00 0.00 44.60 3.01
630 680 5.048643 CCGTTTCATATTGTTGGTGTGGTAA 60.049 40.000 0.00 0.00 0.00 2.85
656 706 4.090354 GGTATACGCGCGCTTAATTCATTA 59.910 41.667 32.58 11.05 0.00 1.90
669 719 9.657121 CGCTTAATTCATTATCTCTCTTTTTCC 57.343 33.333 0.00 0.00 0.00 3.13
678 728 8.887717 CATTATCTCTCTTTTTCCAATCTCGTT 58.112 33.333 0.00 0.00 0.00 3.85
698 748 6.223852 TCGTTTAGATTCATCCTGATTAGCC 58.776 40.000 0.00 0.00 0.00 3.93
721 771 8.678199 AGCCTAGATTTCAGTAGCAAAAATTAC 58.322 33.333 0.00 0.00 0.00 1.89
722 772 7.915923 GCCTAGATTTCAGTAGCAAAAATTACC 59.084 37.037 0.00 0.00 0.00 2.85
733 783 6.199937 AGCAAAAATTACCACTAGATGCTG 57.800 37.500 0.00 0.00 39.87 4.41
737 787 7.370383 CAAAAATTACCACTAGATGCTGTGTT 58.630 34.615 0.00 0.00 32.76 3.32
801 851 6.994496 TGAAAATATCCCTCTCTGCAATGTAG 59.006 38.462 0.00 0.00 0.00 2.74
802 852 6.506538 AAATATCCCTCTCTGCAATGTAGT 57.493 37.500 0.00 0.00 0.00 2.73
803 853 7.618019 AAATATCCCTCTCTGCAATGTAGTA 57.382 36.000 0.00 0.00 0.00 1.82
826 884 8.038944 AGTAATACGTTCCTGTCATATTGTTGT 58.961 33.333 0.00 0.00 0.00 3.32
829 887 4.819630 ACGTTCCTGTCATATTGTTGTTGT 59.180 37.500 0.00 0.00 0.00 3.32
830 888 5.146460 CGTTCCTGTCATATTGTTGTTGTG 58.854 41.667 0.00 0.00 0.00 3.33
831 889 5.460646 GTTCCTGTCATATTGTTGTTGTGG 58.539 41.667 0.00 0.00 0.00 4.17
832 890 4.979335 TCCTGTCATATTGTTGTTGTGGA 58.021 39.130 0.00 0.00 0.00 4.02
1131 1192 3.423154 CTCGCCACCGACTTTGCC 61.423 66.667 0.00 0.00 38.82 4.52
1327 1394 1.999648 TGAGGCATTGCAAGTCCTTT 58.000 45.000 19.52 3.20 0.00 3.11
1369 1436 7.410174 AGTTTCCTTGGTGGTATGATTATTGA 58.590 34.615 0.00 0.00 37.07 2.57
1463 1541 8.571336 GGGATTCTGTGGTTGATTAGATTATTG 58.429 37.037 0.00 0.00 0.00 1.90
1537 1630 7.710896 AGAATTTAGCTAATCTTGCCAATGTC 58.289 34.615 7.08 0.00 0.00 3.06
1607 1708 7.603024 GCTCTAGTTAAAAGTGTACCATCTTGT 59.397 37.037 0.00 0.00 0.00 3.16
1608 1709 8.827177 TCTAGTTAAAAGTGTACCATCTTGTG 57.173 34.615 0.00 0.00 0.00 3.33
1610 1711 9.701098 CTAGTTAAAAGTGTACCATCTTGTGTA 57.299 33.333 0.00 0.00 0.00 2.90
1611 1712 8.603242 AGTTAAAAGTGTACCATCTTGTGTAG 57.397 34.615 0.00 0.00 0.00 2.74
1876 2851 7.923888 TGCAATTTTCTATAGAAGTCTGCATC 58.076 34.615 26.94 12.41 37.93 3.91
2038 3013 4.006319 GTCTCAGAGGTTCAAATTCCTGG 58.994 47.826 0.00 0.00 33.83 4.45
2113 3100 3.013276 TGAATCTACGCCGCAGATTAG 57.987 47.619 12.31 0.00 41.66 1.73
2262 3285 4.205792 CGACCGTAATGTTTCCGAACTATC 59.794 45.833 0.00 0.00 36.70 2.08
2263 3286 5.075858 ACCGTAATGTTTCCGAACTATCA 57.924 39.130 0.00 0.00 36.70 2.15
2297 3320 4.067896 TCTGAAGTGGCTTGTTGATCTTC 58.932 43.478 0.00 0.00 34.02 2.87
2889 3944 3.750371 ACAGTAGTTTTGGCATGTGCTA 58.250 40.909 4.84 0.00 41.70 3.49
2901 3956 2.033049 GCATGTGCTATCTTTGCTCCTG 59.967 50.000 0.00 0.00 38.21 3.86
2951 4031 8.206867 TCTTTCACAGGGAATTATCATCTACTG 58.793 37.037 0.00 0.00 34.91 2.74
2992 4072 1.382522 AGCGACAATACCTTGGCATG 58.617 50.000 0.00 0.00 40.74 4.06
2993 4073 0.248621 GCGACAATACCTTGGCATGC 60.249 55.000 9.90 9.90 40.74 4.06
2997 4077 2.094675 ACAATACCTTGGCATGCTGAC 58.905 47.619 18.92 0.95 36.64 3.51
2999 4079 2.691526 CAATACCTTGGCATGCTGACAT 59.308 45.455 18.92 3.62 33.90 3.06
3007 4087 1.931172 GGCATGCTGACATTTTGATGC 59.069 47.619 18.92 0.00 32.87 3.91
3008 4088 1.931172 GCATGCTGACATTTTGATGCC 59.069 47.619 11.37 0.00 32.87 4.40
3013 4093 2.229543 GCTGACATTTTGATGCCTGTGA 59.770 45.455 0.00 0.00 0.00 3.58
3024 4104 3.503800 ATGCCTGTGATAGTGCATCAT 57.496 42.857 0.00 0.00 45.37 2.45
3093 4173 2.550830 TTTGGGTCTCTTCTCACTGC 57.449 50.000 0.00 0.00 0.00 4.40
3234 4535 8.854117 GCATATTTGGATCCTCAAACTTCTATT 58.146 33.333 14.23 0.00 39.13 1.73
3241 4542 8.772250 TGGATCCTCAAACTTCTATTAGTGAAT 58.228 33.333 14.23 0.00 0.00 2.57
3242 4543 9.620259 GGATCCTCAAACTTCTATTAGTGAATT 57.380 33.333 3.84 0.00 0.00 2.17
3278 4588 6.601332 TGAGATCCAAGTAAGGTTTTTCTGT 58.399 36.000 0.00 0.00 0.00 3.41
3483 4799 9.993454 TTGTTTTACCAATCAATCAATCAATCA 57.007 25.926 0.00 0.00 0.00 2.57
3500 4817 5.531634 TCAATCAAAGTTCTGTGCAAATCC 58.468 37.500 0.00 0.00 0.00 3.01
3507 4824 1.675310 CTGTGCAAATCCGGAGCCA 60.675 57.895 11.34 7.62 0.00 4.75
3687 5005 1.243342 TTGCTGTTTGCCATCCCTCG 61.243 55.000 0.00 0.00 42.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.301346 CCTGTAAATCTCATGCCCCAC 58.699 52.381 0.00 0.00 0.00 4.61
1 2 1.410083 GCCTGTAAATCTCATGCCCCA 60.410 52.381 0.00 0.00 0.00 4.96
2 3 1.322442 GCCTGTAAATCTCATGCCCC 58.678 55.000 0.00 0.00 0.00 5.80
3 4 0.947244 CGCCTGTAAATCTCATGCCC 59.053 55.000 0.00 0.00 0.00 5.36
4 5 0.947244 CCGCCTGTAAATCTCATGCC 59.053 55.000 0.00 0.00 0.00 4.40
5 6 1.331756 CACCGCCTGTAAATCTCATGC 59.668 52.381 0.00 0.00 0.00 4.06
7 8 1.747206 GCCACCGCCTGTAAATCTCAT 60.747 52.381 0.00 0.00 0.00 2.90
8 9 0.392461 GCCACCGCCTGTAAATCTCA 60.392 55.000 0.00 0.00 0.00 3.27
9 10 0.392461 TGCCACCGCCTGTAAATCTC 60.392 55.000 0.00 0.00 0.00 2.75
10 11 0.676782 GTGCCACCGCCTGTAAATCT 60.677 55.000 0.00 0.00 0.00 2.40
11 12 1.654023 GGTGCCACCGCCTGTAAATC 61.654 60.000 0.00 0.00 38.62 2.17
12 13 1.677633 GGTGCCACCGCCTGTAAAT 60.678 57.895 0.00 0.00 38.62 1.40
13 14 2.281900 GGTGCCACCGCCTGTAAA 60.282 61.111 0.00 0.00 38.62 2.01
14 15 3.561241 TGGTGCCACCGCCTGTAA 61.561 61.111 9.78 0.00 42.58 2.41
15 16 4.323477 GTGGTGCCACCGCCTGTA 62.323 66.667 16.73 0.00 42.80 2.74
21 22 2.826287 TGTTGTGTGGTGCCACCG 60.826 61.111 17.65 0.00 45.63 4.94
22 23 1.752694 ACTGTTGTGTGGTGCCACC 60.753 57.895 17.65 7.01 45.63 4.61
23 24 1.433064 CACTGTTGTGTGGTGCCAC 59.567 57.895 14.04 14.04 46.33 5.01
24 25 3.917058 CACTGTTGTGTGGTGCCA 58.083 55.556 0.00 0.00 39.24 4.92
32 33 7.416901 TCGGATCGAACAAAACACTGTTGTG 62.417 44.000 10.15 10.15 39.63 3.33
33 34 3.242608 CGGATCGAACAAAACACTGTTGT 60.243 43.478 0.00 0.00 39.63 3.32
34 35 3.001838 TCGGATCGAACAAAACACTGTTG 59.998 43.478 0.00 0.00 39.63 3.33
35 36 3.001939 GTCGGATCGAACAAAACACTGTT 59.998 43.478 0.00 0.00 42.23 3.16
36 37 2.542595 GTCGGATCGAACAAAACACTGT 59.457 45.455 0.00 0.00 37.72 3.55
37 38 2.409752 CGTCGGATCGAACAAAACACTG 60.410 50.000 0.00 0.00 37.72 3.66
38 39 1.790623 CGTCGGATCGAACAAAACACT 59.209 47.619 0.00 0.00 37.72 3.55
39 40 1.136446 CCGTCGGATCGAACAAAACAC 60.136 52.381 4.91 0.00 37.72 3.32
40 41 1.141645 CCGTCGGATCGAACAAAACA 58.858 50.000 4.91 0.00 37.72 2.83
41 42 0.441145 CCCGTCGGATCGAACAAAAC 59.559 55.000 14.39 0.00 37.72 2.43
42 43 1.293267 GCCCGTCGGATCGAACAAAA 61.293 55.000 14.39 0.00 37.72 2.44
43 44 1.738830 GCCCGTCGGATCGAACAAA 60.739 57.895 14.39 0.00 37.72 2.83
44 45 2.125832 GCCCGTCGGATCGAACAA 60.126 61.111 14.39 0.00 37.72 2.83
45 46 3.350909 CTGCCCGTCGGATCGAACA 62.351 63.158 14.39 0.08 37.72 3.18
46 47 2.582498 CTGCCCGTCGGATCGAAC 60.582 66.667 14.39 0.00 37.72 3.95
47 48 3.833645 CCTGCCCGTCGGATCGAA 61.834 66.667 14.39 0.00 37.72 3.71
48 49 4.807631 TCCTGCCCGTCGGATCGA 62.808 66.667 14.39 0.00 0.00 3.59
49 50 3.559657 GATCCTGCCCGTCGGATCG 62.560 68.421 14.39 0.00 44.32 3.69
50 51 2.340443 GATCCTGCCCGTCGGATC 59.660 66.667 14.39 3.29 46.22 3.36
51 52 3.606662 CGATCCTGCCCGTCGGAT 61.607 66.667 14.39 0.00 42.55 4.18
52 53 4.807631 TCGATCCTGCCCGTCGGA 62.808 66.667 14.39 0.00 36.14 4.55
53 54 3.606662 ATCGATCCTGCCCGTCGG 61.607 66.667 3.60 3.60 36.14 4.79
54 55 1.792118 TACATCGATCCTGCCCGTCG 61.792 60.000 0.00 0.00 36.75 5.12
55 56 0.039074 CTACATCGATCCTGCCCGTC 60.039 60.000 0.00 0.00 0.00 4.79
56 57 0.467474 TCTACATCGATCCTGCCCGT 60.467 55.000 0.00 0.00 0.00 5.28
57 58 0.039074 GTCTACATCGATCCTGCCCG 60.039 60.000 0.00 0.00 0.00 6.13
58 59 0.039074 CGTCTACATCGATCCTGCCC 60.039 60.000 0.00 0.00 0.00 5.36
59 60 0.952280 TCGTCTACATCGATCCTGCC 59.048 55.000 0.00 0.00 32.30 4.85
60 61 2.290916 TCTTCGTCTACATCGATCCTGC 59.709 50.000 0.00 0.00 37.18 4.85
61 62 4.378978 GGATCTTCGTCTACATCGATCCTG 60.379 50.000 0.00 0.00 42.15 3.86
62 63 3.754323 GGATCTTCGTCTACATCGATCCT 59.246 47.826 0.00 0.00 42.15 3.24
63 64 3.425094 CGGATCTTCGTCTACATCGATCC 60.425 52.174 0.00 0.00 42.05 3.36
64 65 3.432592 TCGGATCTTCGTCTACATCGATC 59.567 47.826 0.00 0.00 37.18 3.69
65 66 3.186817 GTCGGATCTTCGTCTACATCGAT 59.813 47.826 0.00 0.00 37.18 3.59
66 67 2.543012 GTCGGATCTTCGTCTACATCGA 59.457 50.000 0.00 0.00 35.50 3.59
67 68 2.659558 CGTCGGATCTTCGTCTACATCG 60.660 54.545 0.00 0.00 0.00 3.84
68 69 2.349627 CCGTCGGATCTTCGTCTACATC 60.350 54.545 4.91 0.00 0.00 3.06
69 70 1.602851 CCGTCGGATCTTCGTCTACAT 59.397 52.381 4.91 0.00 0.00 2.29
70 71 1.012086 CCGTCGGATCTTCGTCTACA 58.988 55.000 4.91 0.00 0.00 2.74
71 72 0.316854 GCCGTCGGATCTTCGTCTAC 60.317 60.000 17.49 0.00 0.00 2.59
72 73 1.442526 GGCCGTCGGATCTTCGTCTA 61.443 60.000 17.49 0.00 0.00 2.59
73 74 2.772691 GGCCGTCGGATCTTCGTCT 61.773 63.158 17.49 0.00 0.00 4.18
74 75 2.278661 GGCCGTCGGATCTTCGTC 60.279 66.667 17.49 0.00 0.00 4.20
75 76 3.064987 CTGGCCGTCGGATCTTCGT 62.065 63.158 17.49 0.00 0.00 3.85
76 77 2.278857 CTGGCCGTCGGATCTTCG 60.279 66.667 17.49 0.00 0.00 3.79
77 78 1.749334 ATCCTGGCCGTCGGATCTTC 61.749 60.000 17.49 0.00 35.08 2.87
78 79 1.762460 ATCCTGGCCGTCGGATCTT 60.762 57.895 17.49 0.00 35.08 2.40
79 80 2.123251 ATCCTGGCCGTCGGATCT 60.123 61.111 17.49 0.00 35.08 2.75
80 81 2.340443 GATCCTGGCCGTCGGATC 59.660 66.667 24.24 24.24 46.22 3.36
81 82 3.606662 CGATCCTGGCCGTCGGAT 61.607 66.667 17.49 17.95 42.55 4.18
84 85 4.933064 GAGCGATCCTGGCCGTCG 62.933 72.222 13.27 13.27 38.34 5.12
85 86 3.532155 AGAGCGATCCTGGCCGTC 61.532 66.667 0.00 0.00 0.00 4.79
86 87 3.842923 CAGAGCGATCCTGGCCGT 61.843 66.667 0.00 0.00 0.00 5.68
87 88 4.598894 CCAGAGCGATCCTGGCCG 62.599 72.222 0.00 4.35 43.93 6.13
98 99 0.171231 GTCGGATTTTTGCCCAGAGC 59.829 55.000 0.00 0.00 44.14 4.09
99 100 0.447801 CGTCGGATTTTTGCCCAGAG 59.552 55.000 0.00 0.00 0.00 3.35
100 101 0.958382 CCGTCGGATTTTTGCCCAGA 60.958 55.000 4.91 0.00 0.00 3.86
101 102 1.506262 CCGTCGGATTTTTGCCCAG 59.494 57.895 4.91 0.00 0.00 4.45
102 103 2.631580 GCCGTCGGATTTTTGCCCA 61.632 57.895 17.49 0.00 0.00 5.36
103 104 2.180769 GCCGTCGGATTTTTGCCC 59.819 61.111 17.49 0.00 0.00 5.36
104 105 2.180769 GGCCGTCGGATTTTTGCC 59.819 61.111 17.49 2.66 0.00 4.52
105 106 2.180769 GGGCCGTCGGATTTTTGC 59.819 61.111 17.49 0.00 0.00 3.68
106 107 2.882132 GGGGCCGTCGGATTTTTG 59.118 61.111 17.49 0.00 0.00 2.44
107 108 2.546114 ATCGGGGCCGTCGGATTTTT 62.546 55.000 17.49 0.00 40.74 1.94
108 109 2.935627 GATCGGGGCCGTCGGATTTT 62.936 60.000 17.49 0.00 40.74 1.82
109 110 3.456105 GATCGGGGCCGTCGGATTT 62.456 63.158 17.49 0.00 40.74 2.17
110 111 3.925090 GATCGGGGCCGTCGGATT 61.925 66.667 17.49 3.34 40.74 3.01
115 116 4.162690 AAGCTGATCGGGGCCGTC 62.163 66.667 3.14 0.00 40.74 4.79
116 117 4.473520 CAAGCTGATCGGGGCCGT 62.474 66.667 3.14 0.00 40.74 5.68
118 119 3.344137 TTCCAAGCTGATCGGGGCC 62.344 63.158 3.14 0.00 0.00 5.80
119 120 1.821332 CTTCCAAGCTGATCGGGGC 60.821 63.158 3.14 0.22 0.00 5.80
120 121 1.153086 CCTTCCAAGCTGATCGGGG 60.153 63.158 3.14 0.00 0.00 5.73
121 122 1.821332 GCCTTCCAAGCTGATCGGG 60.821 63.158 3.14 0.00 0.00 5.14
122 123 0.465705 TAGCCTTCCAAGCTGATCGG 59.534 55.000 0.00 0.00 41.71 4.18
123 124 2.315925 TTAGCCTTCCAAGCTGATCG 57.684 50.000 0.00 0.00 41.71 3.69
124 125 3.145286 GGATTAGCCTTCCAAGCTGATC 58.855 50.000 8.54 8.54 46.91 2.92
125 126 2.486191 CGGATTAGCCTTCCAAGCTGAT 60.486 50.000 0.00 0.00 41.71 2.90
126 127 1.134401 CGGATTAGCCTTCCAAGCTGA 60.134 52.381 0.00 0.00 41.71 4.26
127 128 1.134401 TCGGATTAGCCTTCCAAGCTG 60.134 52.381 0.00 0.00 41.71 4.24
128 129 1.134371 GTCGGATTAGCCTTCCAAGCT 60.134 52.381 0.00 0.00 44.49 3.74
129 130 1.300481 GTCGGATTAGCCTTCCAAGC 58.700 55.000 0.00 0.00 32.45 4.01
130 131 1.571919 CGTCGGATTAGCCTTCCAAG 58.428 55.000 0.00 0.00 32.45 3.61
131 132 0.177141 CCGTCGGATTAGCCTTCCAA 59.823 55.000 4.91 0.00 32.45 3.53
132 133 1.820581 CCGTCGGATTAGCCTTCCA 59.179 57.895 4.91 0.00 32.45 3.53
133 134 1.594564 GCCGTCGGATTAGCCTTCC 60.595 63.158 17.49 0.00 0.00 3.46
134 135 0.876342 CAGCCGTCGGATTAGCCTTC 60.876 60.000 17.49 0.00 0.00 3.46
135 136 1.144057 CAGCCGTCGGATTAGCCTT 59.856 57.895 17.49 0.00 0.00 4.35
136 137 1.327690 TTCAGCCGTCGGATTAGCCT 61.328 55.000 17.49 0.00 0.00 4.58
137 138 0.461339 TTTCAGCCGTCGGATTAGCC 60.461 55.000 17.49 0.00 0.00 3.93
138 139 1.365699 TTTTCAGCCGTCGGATTAGC 58.634 50.000 17.49 0.00 0.00 3.09
139 140 2.544267 GGATTTTCAGCCGTCGGATTAG 59.456 50.000 17.49 0.00 0.00 1.73
140 141 2.093394 TGGATTTTCAGCCGTCGGATTA 60.093 45.455 17.49 0.00 0.00 1.75
141 142 1.339631 TGGATTTTCAGCCGTCGGATT 60.340 47.619 17.49 0.00 0.00 3.01
142 143 0.251916 TGGATTTTCAGCCGTCGGAT 59.748 50.000 17.49 5.54 0.00 4.18
143 144 0.035598 TTGGATTTTCAGCCGTCGGA 59.964 50.000 17.49 0.00 0.00 4.55
144 145 0.878416 TTTGGATTTTCAGCCGTCGG 59.122 50.000 6.99 6.99 0.00 4.79
145 146 1.724654 CGTTTGGATTTTCAGCCGTCG 60.725 52.381 0.00 0.00 0.00 5.12
146 147 1.963747 CGTTTGGATTTTCAGCCGTC 58.036 50.000 0.00 0.00 0.00 4.79
147 148 0.039527 GCGTTTGGATTTTCAGCCGT 60.040 50.000 0.00 0.00 0.00 5.68
148 149 0.039617 TGCGTTTGGATTTTCAGCCG 60.040 50.000 0.00 0.00 0.00 5.52
149 150 1.418373 GTGCGTTTGGATTTTCAGCC 58.582 50.000 0.00 0.00 0.00 4.85
150 151 1.052287 CGTGCGTTTGGATTTTCAGC 58.948 50.000 0.00 0.00 0.00 4.26
151 152 1.665735 CCCGTGCGTTTGGATTTTCAG 60.666 52.381 0.00 0.00 0.00 3.02
152 153 0.312416 CCCGTGCGTTTGGATTTTCA 59.688 50.000 0.00 0.00 0.00 2.69
153 154 0.594110 TCCCGTGCGTTTGGATTTTC 59.406 50.000 0.00 0.00 0.00 2.29
154 155 0.596082 CTCCCGTGCGTTTGGATTTT 59.404 50.000 0.00 0.00 0.00 1.82
155 156 0.250553 TCTCCCGTGCGTTTGGATTT 60.251 50.000 0.00 0.00 0.00 2.17
156 157 0.673644 CTCTCCCGTGCGTTTGGATT 60.674 55.000 0.00 0.00 0.00 3.01
157 158 1.079127 CTCTCCCGTGCGTTTGGAT 60.079 57.895 0.00 0.00 0.00 3.41
158 159 2.342279 CTCTCCCGTGCGTTTGGA 59.658 61.111 0.00 0.00 0.00 3.53
159 160 3.423154 GCTCTCCCGTGCGTTTGG 61.423 66.667 0.00 0.00 0.00 3.28
160 161 1.901650 GAAGCTCTCCCGTGCGTTTG 61.902 60.000 0.00 0.00 34.94 2.93
161 162 1.668151 GAAGCTCTCCCGTGCGTTT 60.668 57.895 0.00 0.00 34.94 3.60
162 163 2.048127 GAAGCTCTCCCGTGCGTT 60.048 61.111 0.00 0.00 34.94 4.84
163 164 2.172483 AATGAAGCTCTCCCGTGCGT 62.172 55.000 0.00 0.00 34.94 5.24
164 165 1.021390 AAATGAAGCTCTCCCGTGCG 61.021 55.000 0.00 0.00 34.94 5.34
165 166 1.135575 CAAAATGAAGCTCTCCCGTGC 60.136 52.381 0.00 0.00 0.00 5.34
166 167 1.470098 CCAAAATGAAGCTCTCCCGTG 59.530 52.381 0.00 0.00 0.00 4.94
167 168 1.073923 ACCAAAATGAAGCTCTCCCGT 59.926 47.619 0.00 0.00 0.00 5.28
168 169 1.740025 GACCAAAATGAAGCTCTCCCG 59.260 52.381 0.00 0.00 0.00 5.14
169 170 2.751806 CAGACCAAAATGAAGCTCTCCC 59.248 50.000 0.00 0.00 0.00 4.30
170 171 2.751806 CCAGACCAAAATGAAGCTCTCC 59.248 50.000 0.00 0.00 0.00 3.71
171 172 3.438434 GTCCAGACCAAAATGAAGCTCTC 59.562 47.826 0.00 0.00 0.00 3.20
172 173 3.073650 AGTCCAGACCAAAATGAAGCTCT 59.926 43.478 0.00 0.00 0.00 4.09
173 174 3.416156 AGTCCAGACCAAAATGAAGCTC 58.584 45.455 0.00 0.00 0.00 4.09
174 175 3.073650 AGAGTCCAGACCAAAATGAAGCT 59.926 43.478 0.00 0.00 0.00 3.74
175 176 3.416156 AGAGTCCAGACCAAAATGAAGC 58.584 45.455 0.00 0.00 0.00 3.86
176 177 5.997746 TGTTAGAGTCCAGACCAAAATGAAG 59.002 40.000 0.00 0.00 0.00 3.02
177 178 5.935945 TGTTAGAGTCCAGACCAAAATGAA 58.064 37.500 0.00 0.00 0.00 2.57
178 179 5.560722 TGTTAGAGTCCAGACCAAAATGA 57.439 39.130 0.00 0.00 0.00 2.57
179 180 5.182001 CCTTGTTAGAGTCCAGACCAAAATG 59.818 44.000 0.00 0.00 0.00 2.32
180 181 5.316987 CCTTGTTAGAGTCCAGACCAAAAT 58.683 41.667 0.00 0.00 0.00 1.82
181 182 4.445735 CCCTTGTTAGAGTCCAGACCAAAA 60.446 45.833 0.00 0.00 0.00 2.44
182 183 3.072476 CCCTTGTTAGAGTCCAGACCAAA 59.928 47.826 0.00 0.00 0.00 3.28
183 184 2.637872 CCCTTGTTAGAGTCCAGACCAA 59.362 50.000 0.00 0.00 0.00 3.67
184 185 2.257207 CCCTTGTTAGAGTCCAGACCA 58.743 52.381 0.00 0.00 0.00 4.02
185 186 1.555533 CCCCTTGTTAGAGTCCAGACC 59.444 57.143 0.00 0.00 0.00 3.85
186 187 2.537143 TCCCCTTGTTAGAGTCCAGAC 58.463 52.381 0.00 0.00 0.00 3.51
187 188 3.491766 ATCCCCTTGTTAGAGTCCAGA 57.508 47.619 0.00 0.00 0.00 3.86
188 189 3.878778 CAATCCCCTTGTTAGAGTCCAG 58.121 50.000 0.00 0.00 0.00 3.86
189 190 2.026262 GCAATCCCCTTGTTAGAGTCCA 60.026 50.000 0.00 0.00 37.18 4.02
190 191 2.026262 TGCAATCCCCTTGTTAGAGTCC 60.026 50.000 0.00 0.00 37.18 3.85
191 192 3.350219 TGCAATCCCCTTGTTAGAGTC 57.650 47.619 0.00 0.00 37.18 3.36
192 193 5.132648 TCATATGCAATCCCCTTGTTAGAGT 59.867 40.000 0.00 0.00 37.18 3.24
193 194 5.471456 GTCATATGCAATCCCCTTGTTAGAG 59.529 44.000 0.00 0.00 37.18 2.43
194 195 5.132648 AGTCATATGCAATCCCCTTGTTAGA 59.867 40.000 0.00 0.00 37.18 2.10
195 196 5.380043 AGTCATATGCAATCCCCTTGTTAG 58.620 41.667 0.00 0.00 37.18 2.34
196 197 5.387113 AGTCATATGCAATCCCCTTGTTA 57.613 39.130 0.00 0.00 37.18 2.41
197 198 4.255510 AGTCATATGCAATCCCCTTGTT 57.744 40.909 0.00 0.00 37.18 2.83
198 199 3.959495 AGTCATATGCAATCCCCTTGT 57.041 42.857 0.00 0.00 37.18 3.16
199 200 4.978099 ACTAGTCATATGCAATCCCCTTG 58.022 43.478 0.00 0.00 37.94 3.61
200 201 6.763715 TTACTAGTCATATGCAATCCCCTT 57.236 37.500 0.00 0.00 0.00 3.95
201 202 6.501805 TCATTACTAGTCATATGCAATCCCCT 59.498 38.462 0.00 0.00 0.00 4.79
202 203 6.711277 TCATTACTAGTCATATGCAATCCCC 58.289 40.000 0.00 0.00 0.00 4.81
203 204 8.621532 TTTCATTACTAGTCATATGCAATCCC 57.378 34.615 0.00 0.00 0.00 3.85
232 233 9.567848 CTGAATCTACTTGACTAGAGTTTTCTC 57.432 37.037 0.00 0.00 46.50 2.87
239 240 4.336993 ACGGCTGAATCTACTTGACTAGAG 59.663 45.833 0.00 0.00 0.00 2.43
311 314 2.923035 CGGTGGAGGTGTGAGGGT 60.923 66.667 0.00 0.00 0.00 4.34
312 315 4.394712 GCGGTGGAGGTGTGAGGG 62.395 72.222 0.00 0.00 0.00 4.30
322 325 1.534476 TTCTGTGTAGGGCGGTGGA 60.534 57.895 0.00 0.00 0.00 4.02
409 413 4.802051 CCTCGTACCCGGGTCCGA 62.802 72.222 35.23 35.23 42.83 4.55
412 416 3.512516 CGTCCTCGTACCCGGGTC 61.513 72.222 34.27 20.73 30.56 4.46
413 417 3.567579 TTCGTCCTCGTACCCGGGT 62.568 63.158 32.66 32.66 38.33 5.28
420 424 0.247460 TCCTCGTCTTCGTCCTCGTA 59.753 55.000 0.00 0.00 38.33 3.43
425 429 0.677414 ACTCCTCCTCGTCTTCGTCC 60.677 60.000 0.00 0.00 38.33 4.79
427 431 1.587933 GCACTCCTCCTCGTCTTCGT 61.588 60.000 0.00 0.00 38.33 3.85
431 435 2.752238 CGGCACTCCTCCTCGTCT 60.752 66.667 0.00 0.00 0.00 4.18
432 436 4.500116 GCGGCACTCCTCCTCGTC 62.500 72.222 0.00 0.00 0.00 4.20
434 438 3.781770 GATGCGGCACTCCTCCTCG 62.782 68.421 4.03 0.00 0.00 4.63
630 680 0.101040 TTAAGCGCGCGTATACCACT 59.899 50.000 32.35 15.06 0.00 4.00
656 706 8.314751 TCTAAACGAGATTGGAAAAAGAGAGAT 58.685 33.333 0.00 0.00 0.00 2.75
698 748 9.774742 GTGGTAATTTTTGCTACTGAAATCTAG 57.225 33.333 0.00 0.00 0.00 2.43
721 771 5.178061 TCACATAAACACAGCATCTAGTGG 58.822 41.667 0.00 0.00 39.99 4.00
722 772 6.712549 CATCACATAAACACAGCATCTAGTG 58.287 40.000 0.00 0.00 41.40 2.74
733 783 3.305094 GCAATGCAGCATCACATAAACAC 59.695 43.478 8.77 0.00 0.00 3.32
737 787 2.100989 TGGCAATGCAGCATCACATAA 58.899 42.857 8.77 0.00 35.83 1.90
801 851 8.193250 ACAACAATATGACAGGAACGTATTAC 57.807 34.615 0.00 0.00 31.12 1.89
802 852 8.661257 CAACAACAATATGACAGGAACGTATTA 58.339 33.333 0.00 0.00 31.12 0.98
803 853 7.174253 ACAACAACAATATGACAGGAACGTATT 59.826 33.333 0.00 0.00 32.03 1.89
826 884 2.105649 TCAGCACTACCACAATCCACAA 59.894 45.455 0.00 0.00 0.00 3.33
829 887 3.719268 ATTCAGCACTACCACAATCCA 57.281 42.857 0.00 0.00 0.00 3.41
830 888 3.378427 GGAATTCAGCACTACCACAATCC 59.622 47.826 7.93 0.00 0.00 3.01
831 889 4.265073 AGGAATTCAGCACTACCACAATC 58.735 43.478 7.93 0.00 0.00 2.67
832 890 4.307032 AGGAATTCAGCACTACCACAAT 57.693 40.909 7.93 0.00 0.00 2.71
1113 1174 2.665185 GCAAAGTCGGTGGCGAGT 60.665 61.111 0.00 0.00 0.00 4.18
1266 1327 0.878086 GAATCTGAGCTACCAGGCGC 60.878 60.000 0.00 0.00 37.29 6.53
1327 1394 5.705441 AGGAAACTTCAACAGCAAATATCGA 59.295 36.000 0.00 0.00 37.44 3.59
1369 1436 6.936900 CGGACATAGGATATTGGTTGAGAAAT 59.063 38.462 0.00 0.00 0.00 2.17
1463 1541 5.461407 GCTTTACTACGGTATTGGAAGCTAC 59.539 44.000 15.00 0.00 36.19 3.58
1476 1563 5.738370 GCATTAACAGATGCTTTACTACGG 58.262 41.667 2.79 0.00 46.85 4.02
1537 1630 8.099364 ACTGTAAATACACAATCAGGACAAAG 57.901 34.615 0.00 0.00 31.93 2.77
1607 1708 6.104146 TGTCAACTATTAACACCTGCTACA 57.896 37.500 0.00 0.00 0.00 2.74
1608 1709 6.037172 CCATGTCAACTATTAACACCTGCTAC 59.963 42.308 0.00 0.00 0.00 3.58
1610 1711 4.943705 CCATGTCAACTATTAACACCTGCT 59.056 41.667 0.00 0.00 0.00 4.24
1611 1712 4.438744 GCCATGTCAACTATTAACACCTGC 60.439 45.833 0.00 0.00 0.00 4.85
1690 2612 4.439700 GCCAACATTGAGACATGATCTTGG 60.440 45.833 12.76 8.12 38.00 3.61
1876 2851 7.704578 TTACGATCCCTCTGAAGAATATAGG 57.295 40.000 0.00 0.00 0.00 2.57
2038 3013 3.427863 GCAGAAGCAAAAGATGAAGCAAC 59.572 43.478 0.00 0.00 41.58 4.17
2113 3100 1.534729 ACCTTGTGAAGAAATCGGGC 58.465 50.000 0.00 0.00 0.00 6.13
2262 3285 7.325660 AGCCACTTCAGATAAAATGTGTATG 57.674 36.000 0.00 0.00 0.00 2.39
2263 3286 7.394359 ACAAGCCACTTCAGATAAAATGTGTAT 59.606 33.333 0.00 0.00 0.00 2.29
2297 3320 8.910666 CAGAGCAATAAAGATAGTGTCGATAAG 58.089 37.037 0.00 0.00 29.96 1.73
2414 3437 8.795786 TTTTGAGTGAACACAAATACATAAGC 57.204 30.769 6.84 0.00 36.58 3.09
2756 3800 5.248380 AGATTCAGTCAGGCTAAAAAGGT 57.752 39.130 0.00 0.00 0.00 3.50
2813 3866 3.061006 CAGTGAACAGCGAAACAAAATGC 60.061 43.478 0.00 0.00 0.00 3.56
2889 3944 3.777106 TCAACAGACAGGAGCAAAGAT 57.223 42.857 0.00 0.00 0.00 2.40
2901 3956 0.606673 GACTGCCCCCTTCAACAGAC 60.607 60.000 0.00 0.00 34.25 3.51
2951 4031 2.028658 TGACACTGAGCAGAGATCCAAC 60.029 50.000 4.21 0.00 0.00 3.77
2992 4072 2.229543 TCACAGGCATCAAAATGTCAGC 59.770 45.455 0.00 0.00 40.10 4.26
2993 4073 4.713824 ATCACAGGCATCAAAATGTCAG 57.286 40.909 0.00 0.00 40.10 3.51
2997 4077 4.142337 TGCACTATCACAGGCATCAAAATG 60.142 41.667 0.00 0.00 35.87 2.32
2999 4079 3.419943 TGCACTATCACAGGCATCAAAA 58.580 40.909 0.00 0.00 0.00 2.44
3093 4173 4.876107 AGGTGTCATCGCTTAATAAACTGG 59.124 41.667 0.00 0.00 0.00 4.00
3165 4457 2.841442 AGCCTACTTGAACCACACTC 57.159 50.000 0.00 0.00 0.00 3.51
3237 4538 8.539117 TGGATCTCAGTATCTCACTTAATTCA 57.461 34.615 0.00 0.00 34.26 2.57
3241 4542 7.962995 ACTTGGATCTCAGTATCTCACTTAA 57.037 36.000 0.00 0.00 34.26 1.85
3242 4543 9.126151 CTTACTTGGATCTCAGTATCTCACTTA 57.874 37.037 5.66 0.00 34.26 2.24
3278 4588 2.489971 CCTTACAAAAGCCACGTCAGA 58.510 47.619 0.00 0.00 0.00 3.27
3348 4658 5.479724 TGGAAGACCAATGATGCAACAAATA 59.520 36.000 0.00 0.00 43.91 1.40
3349 4659 4.283978 TGGAAGACCAATGATGCAACAAAT 59.716 37.500 0.00 0.00 43.91 2.32
3379 4689 6.309712 TGCTTCTTTTCAGAGTTCAGAATG 57.690 37.500 0.00 0.00 37.54 2.67
3478 4794 4.383649 CGGATTTGCACAGAACTTTGATTG 59.616 41.667 0.00 0.00 0.00 2.67
3479 4795 4.549458 CGGATTTGCACAGAACTTTGATT 58.451 39.130 0.00 0.00 0.00 2.57
3480 4796 3.057315 CCGGATTTGCACAGAACTTTGAT 60.057 43.478 0.00 0.00 0.00 2.57
3481 4797 2.293122 CCGGATTTGCACAGAACTTTGA 59.707 45.455 0.00 0.00 0.00 2.69
3482 4798 2.293122 TCCGGATTTGCACAGAACTTTG 59.707 45.455 0.00 0.00 0.00 2.77
3483 4799 2.554032 CTCCGGATTTGCACAGAACTTT 59.446 45.455 3.57 0.00 0.00 2.66
3507 4824 0.249405 CACAAAGTTGCACGGCCAAT 60.249 50.000 2.24 0.00 0.00 3.16
3533 4850 5.123227 GCATTGTGCAAGAGGGTAAGTATA 58.877 41.667 0.00 0.00 44.26 1.47
3534 4851 3.947834 GCATTGTGCAAGAGGGTAAGTAT 59.052 43.478 0.00 0.00 44.26 2.12
3535 4852 3.343617 GCATTGTGCAAGAGGGTAAGTA 58.656 45.455 0.00 0.00 44.26 2.24
3536 4853 2.162681 GCATTGTGCAAGAGGGTAAGT 58.837 47.619 0.00 0.00 44.26 2.24


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

AutoCloner maintained by Alex Coulton.