Multiple sequence alignment - TraesCS5A01G226800

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 TraesCS5A01G226800 chr5A 100.000 4345 0 0 1 4345 442683367 442679023 0.000000e+00 8024.0
1 TraesCS5A01G226800 chr5A 91.229 1505 117 7 1792 3292 442506054 442504561 0.000000e+00 2034.0
2 TraesCS5A01G226800 chr5A 83.969 1048 147 16 1813 2846 442292346 442291306 0.000000e+00 985.0
3 TraesCS5A01G226800 chr5A 87.281 456 49 3 2842 3297 442291222 442290776 3.000000e-141 512.0
4 TraesCS5A01G226800 chr5A 88.675 415 47 0 3931 4345 477063013 477063427 1.390000e-139 507.0
5 TraesCS5A01G226800 chr5A 85.117 383 44 4 2038 2413 442539225 442538849 3.170000e-101 379.0
6 TraesCS5A01G226800 chr5A 84.950 299 17 17 991 1263 442509184 442508888 1.190000e-70 278.0
7 TraesCS5A01G226800 chr5D 95.594 2542 96 9 1753 4286 341532393 341529860 0.000000e+00 4060.0
8 TraesCS5A01G226800 chr5D 91.830 1530 105 11 1768 3292 341242757 341241243 0.000000e+00 2115.0
9 TraesCS5A01G226800 chr5D 88.562 1530 158 10 1779 3294 556722664 556721138 0.000000e+00 1840.0
10 TraesCS5A01G226800 chr5D 91.103 1034 48 15 214 1227 341533876 341532867 0.000000e+00 1360.0
11 TraesCS5A01G226800 chr5D 87.091 1131 126 10 2164 3294 560107204 560106094 0.000000e+00 1262.0
12 TraesCS5A01G226800 chr5D 83.973 1042 152 12 1812 2846 341076814 341075781 0.000000e+00 985.0
13 TraesCS5A01G226800 chr5D 83.417 796 112 16 1603 2385 341261664 341260876 0.000000e+00 721.0
14 TraesCS5A01G226800 chr5D 87.387 444 47 3 2842 3285 341075702 341075268 6.490000e-138 501.0
15 TraesCS5A01G226800 chr5D 81.352 488 51 24 801 1263 341246160 341245688 1.150000e-95 361.0
16 TraesCS5A01G226800 chr5D 88.532 218 24 1 928 1145 341311837 341311621 3.330000e-66 263.0
17 TraesCS5A01G226800 chr5D 91.935 186 13 2 960 1145 556723257 556723074 4.310000e-65 259.0
18 TraesCS5A01G226800 chr5D 91.257 183 15 1 981 1163 560108136 560107955 9.330000e-62 248.0
19 TraesCS5A01G226800 chr5D 83.721 258 24 11 1308 1555 341532817 341532568 1.220000e-55 228.0
20 TraesCS5A01G226800 chr5D 82.192 73 8 5 799 871 560108305 560108238 1.690000e-04 58.4
21 TraesCS5A01G226800 chr5B 96.375 1876 58 7 1754 3629 400999136 400997271 0.000000e+00 3079.0
22 TraesCS5A01G226800 chr5B 90.131 1530 110 16 1768 3292 400776651 400778144 0.000000e+00 1951.0
23 TraesCS5A01G226800 chr5B 84.895 1483 198 15 1812 3285 400564243 400562778 0.000000e+00 1474.0
24 TraesCS5A01G226800 chr5B 88.462 1248 78 36 18 1227 401000807 400999588 0.000000e+00 1447.0
25 TraesCS5A01G226800 chr5B 88.235 289 16 11 991 1263 400773230 400773516 3.240000e-86 329.0
26 TraesCS5A01G226800 chr5B 85.317 252 27 8 1308 1555 400999558 400999313 7.210000e-63 252.0
27 TraesCS5A01G226800 chr4A 88.383 1515 144 17 1811 3294 605086907 605085394 0.000000e+00 1794.0
28 TraesCS5A01G226800 chr4A 96.689 151 5 0 995 1145 605087319 605087169 7.210000e-63 252.0
29 TraesCS5A01G226800 chr4A 82.857 70 12 0 4009 4078 417575048 417575117 3.630000e-06 63.9
30 TraesCS5A01G226800 chr4A 71.228 285 68 11 4003 4280 635451356 635451633 4.690000e-05 60.2
31 TraesCS5A01G226800 chr3D 86.811 417 54 1 3930 4345 575031056 575030640 8.510000e-127 464.0
32 TraesCS5A01G226800 chr3D 84.521 407 63 0 3931 4337 386426478 386426884 1.880000e-108 403.0
33 TraesCS5A01G226800 chr3B 78.795 415 82 6 3934 4345 485212911 485212500 1.540000e-69 274.0
34 TraesCS5A01G226800 chr3A 83.710 221 32 4 3624 3842 589177084 589177302 5.700000e-49 206.0
35 TraesCS5A01G226800 chr6B 82.251 231 29 4 3623 3842 686554162 686554391 5.740000e-44 189.0
36 TraesCS5A01G226800 chr4B 81.624 234 31 4 3623 3845 479214925 479214693 2.670000e-42 183.0
37 TraesCS5A01G226800 chr2B 80.995 221 38 4 3623 3841 708671703 708671921 5.780000e-39 172.0
38 TraesCS5A01G226800 chr2A 80.851 235 31 9 3625 3847 642907275 642907507 5.780000e-39 172.0
39 TraesCS5A01G226800 chr6A 79.828 233 35 4 3623 3844 26424421 26424652 4.500000e-35 159.0
40 TraesCS5A01G226800 chr2D 72.772 404 93 13 3949 4344 94725098 94725492 2.120000e-23 121.0
41 TraesCS5A01G226800 chr6D 83.621 116 17 2 3623 3737 8154097 8153983 1.650000e-19 108.0
42 TraesCS5A01G226800 chr7B 72.222 342 85 9 3946 4282 65295169 65295505 3.580000e-16 97.1
43 TraesCS5A01G226800 chr1A 92.683 41 3 0 4235 4275 74317059 74317019 4.690000e-05 60.2


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 TraesCS5A01G226800 chr5A 442679023 442683367 4344 True 8024.000000 8024 100.000000 1 4345 1 chr5A.!!$R2 4344
1 TraesCS5A01G226800 chr5A 442504561 442509184 4623 True 1156.000000 2034 88.089500 991 3292 2 chr5A.!!$R4 2301
2 TraesCS5A01G226800 chr5A 442290776 442292346 1570 True 748.500000 985 85.625000 1813 3297 2 chr5A.!!$R3 1484
3 TraesCS5A01G226800 chr5D 341529860 341533876 4016 True 1882.666667 4060 90.139333 214 4286 3 chr5D.!!$R5 4072
4 TraesCS5A01G226800 chr5D 341241243 341246160 4917 True 1238.000000 2115 86.591000 801 3292 2 chr5D.!!$R4 2491
5 TraesCS5A01G226800 chr5D 556721138 556723257 2119 True 1049.500000 1840 90.248500 960 3294 2 chr5D.!!$R6 2334
6 TraesCS5A01G226800 chr5D 341075268 341076814 1546 True 743.000000 985 85.680000 1812 3285 2 chr5D.!!$R3 1473
7 TraesCS5A01G226800 chr5D 341260876 341261664 788 True 721.000000 721 83.417000 1603 2385 1 chr5D.!!$R1 782
8 TraesCS5A01G226800 chr5D 560106094 560108305 2211 True 522.800000 1262 86.846667 799 3294 3 chr5D.!!$R7 2495
9 TraesCS5A01G226800 chr5B 400997271 401000807 3536 True 1592.666667 3079 90.051333 18 3629 3 chr5B.!!$R2 3611
10 TraesCS5A01G226800 chr5B 400562778 400564243 1465 True 1474.000000 1474 84.895000 1812 3285 1 chr5B.!!$R1 1473
11 TraesCS5A01G226800 chr5B 400773230 400778144 4914 False 1140.000000 1951 89.183000 991 3292 2 chr5B.!!$F1 2301
12 TraesCS5A01G226800 chr4A 605085394 605087319 1925 True 1023.000000 1794 92.536000 995 3294 2 chr4A.!!$R1 2299


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
581 602 0.322726 TGGTGGTGGATGCTGTGATG 60.323 55.0 0.0 0.0 0.0 3.07 F
1557 2045 0.311165 TAAGCGCGAGTGCTAGATCC 59.689 55.0 12.1 0.0 46.6 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 2095 0.169230 CTTGTGTCTAGAGCGCGTCT 59.831 55.0 8.43 12.04 39.59 4.18 R
3480 7756 1.209621 AACACCACACCAGTACCACT 58.790 50.0 0.00 0.00 0.00 4.00 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
21 22 3.998913 TGGCCTTGATGTCACATAAGA 57.001 42.857 3.32 0.00 0.00 2.10
22 23 4.508551 TGGCCTTGATGTCACATAAGAT 57.491 40.909 3.32 0.00 0.00 2.40
23 24 4.201657 TGGCCTTGATGTCACATAAGATG 58.798 43.478 3.32 0.00 0.00 2.90
55 56 1.133790 GCATGGCTGGAATCTTGTGTC 59.866 52.381 0.00 0.00 0.00 3.67
62 63 2.493675 CTGGAATCTTGTGTCGAGGAGA 59.506 50.000 0.00 0.00 0.00 3.71
64 65 3.515502 TGGAATCTTGTGTCGAGGAGATT 59.484 43.478 10.50 10.50 40.50 2.40
66 67 4.382040 GGAATCTTGTGTCGAGGAGATTGA 60.382 45.833 13.85 0.00 38.56 2.57
67 68 5.350504 AATCTTGTGTCGAGGAGATTGAT 57.649 39.130 10.11 0.00 37.44 2.57
68 69 4.115401 TCTTGTGTCGAGGAGATTGATG 57.885 45.455 0.00 0.00 0.00 3.07
69 70 3.763897 TCTTGTGTCGAGGAGATTGATGA 59.236 43.478 0.00 0.00 0.00 2.92
70 71 4.403752 TCTTGTGTCGAGGAGATTGATGAT 59.596 41.667 0.00 0.00 0.00 2.45
71 72 4.050852 TGTGTCGAGGAGATTGATGATG 57.949 45.455 0.00 0.00 0.00 3.07
72 73 3.448660 TGTGTCGAGGAGATTGATGATGT 59.551 43.478 0.00 0.00 0.00 3.06
73 74 4.644685 TGTGTCGAGGAGATTGATGATGTA 59.355 41.667 0.00 0.00 0.00 2.29
74 75 5.302823 TGTGTCGAGGAGATTGATGATGTAT 59.697 40.000 0.00 0.00 0.00 2.29
75 76 6.490040 TGTGTCGAGGAGATTGATGATGTATA 59.510 38.462 0.00 0.00 0.00 1.47
78 79 9.413734 TGTCGAGGAGATTGATGATGTATATAT 57.586 33.333 0.00 0.00 0.00 0.86
97 98 3.795623 ATGACTGCATGGCTGAATTTC 57.204 42.857 0.00 0.00 32.31 2.17
99 100 3.159472 TGACTGCATGGCTGAATTTCTT 58.841 40.909 0.00 0.00 0.00 2.52
127 128 5.506982 CGCAGAGACTGACAATCTATGATCA 60.507 44.000 12.43 0.00 37.56 2.92
128 129 5.691305 GCAGAGACTGACAATCTATGATCAC 59.309 44.000 12.43 0.00 37.56 3.06
155 156 2.897326 TGAAATCTTGTGTCGAGGAGGA 59.103 45.455 0.00 0.00 0.00 3.71
159 160 2.739943 TCTTGTGTCGAGGAGGATGAT 58.260 47.619 0.00 0.00 0.00 2.45
160 161 2.428530 TCTTGTGTCGAGGAGGATGATG 59.571 50.000 0.00 0.00 0.00 3.07
169 170 2.902486 GAGGAGGATGATGATGTAGCCA 59.098 50.000 0.00 0.00 0.00 4.75
196 197 4.900054 GCTGAACTCTATTCCCTACCCTAA 59.100 45.833 0.00 0.00 0.00 2.69
199 202 6.374588 TGAACTCTATTCCCTACCCTAAGAG 58.625 44.000 0.00 0.00 36.06 2.85
201 204 4.738132 ACTCTATTCCCTACCCTAAGAGGT 59.262 45.833 0.00 0.00 44.37 3.85
204 207 2.862850 TCCCTACCCTAAGAGGTTCC 57.137 55.000 0.00 0.00 41.58 3.62
207 210 1.755380 CCTACCCTAAGAGGTTCCGTG 59.245 57.143 0.00 0.00 41.58 4.94
212 215 2.236395 CCCTAAGAGGTTCCGTGTGAAT 59.764 50.000 0.00 0.00 34.90 2.57
217 220 2.631062 AGAGGTTCCGTGTGAATGTGTA 59.369 45.455 0.00 0.00 34.90 2.90
321 333 6.465948 TGACAAGGCTGCATTATTGAAAAAT 58.534 32.000 0.00 0.00 0.00 1.82
400 414 7.961326 AATCACTTGGTAGCCTATTTTTCAT 57.039 32.000 0.00 0.00 0.00 2.57
473 487 5.925969 CCTAATTCATGCACTTTCCGTTTTT 59.074 36.000 0.00 0.00 0.00 1.94
549 570 2.723124 TGGAGCGAAATTCTTTTGGC 57.277 45.000 0.00 0.00 44.23 4.52
579 600 1.073025 GTGGTGGTGGATGCTGTGA 59.927 57.895 0.00 0.00 0.00 3.58
580 601 0.322816 GTGGTGGTGGATGCTGTGAT 60.323 55.000 0.00 0.00 0.00 3.06
581 602 0.322726 TGGTGGTGGATGCTGTGATG 60.323 55.000 0.00 0.00 0.00 3.07
582 603 0.322816 GGTGGTGGATGCTGTGATGT 60.323 55.000 0.00 0.00 0.00 3.06
583 604 0.806868 GTGGTGGATGCTGTGATGTG 59.193 55.000 0.00 0.00 0.00 3.21
598 619 2.629137 TGATGTGCAGCCACTCAATTTT 59.371 40.909 0.00 0.00 42.54 1.82
599 620 3.069872 TGATGTGCAGCCACTCAATTTTT 59.930 39.130 0.00 0.00 42.54 1.94
646 667 9.251440 TGTGGGACTCCTTACATATATATGTAC 57.749 37.037 27.71 18.09 45.78 2.90
755 777 2.586079 CCTTGATGGCGCGATCGT 60.586 61.111 24.51 1.40 38.14 3.73
926 965 5.278709 GCTTATGCTATGTGTAGAGAGAGCA 60.279 44.000 8.80 8.80 43.50 4.26
952 1000 2.380410 CGGCTGAACGTAGGCACAC 61.380 63.158 11.88 0.00 42.87 3.82
967 1017 1.545651 GCACACCCCTAGCTTGACTTT 60.546 52.381 0.00 0.00 0.00 2.66
974 1024 4.291249 ACCCCTAGCTTGACTTTAATTCCA 59.709 41.667 0.00 0.00 0.00 3.53
1229 1315 0.890996 GGCTGAGTCACTTGGGGTTG 60.891 60.000 0.00 0.00 0.00 3.77
1248 1339 0.949105 GGGTTGTACGAGTGTGGCTG 60.949 60.000 0.00 0.00 0.00 4.85
1252 1343 0.319555 TGTACGAGTGTGGCTGCTTC 60.320 55.000 0.00 0.00 0.00 3.86
1305 1777 4.893424 TTTTCTTTAGCATATCGTGGGC 57.107 40.909 0.00 0.00 0.00 5.36
1306 1778 3.552132 TTCTTTAGCATATCGTGGGCA 57.448 42.857 0.00 0.00 0.00 5.36
1307 1779 3.552132 TCTTTAGCATATCGTGGGCAA 57.448 42.857 0.00 0.00 0.00 4.52
1309 1781 3.876914 TCTTTAGCATATCGTGGGCAAAG 59.123 43.478 0.00 0.00 32.27 2.77
1310 1782 3.552132 TTAGCATATCGTGGGCAAAGA 57.448 42.857 0.00 0.00 0.00 2.52
1311 1783 2.645838 AGCATATCGTGGGCAAAGAT 57.354 45.000 0.00 0.00 0.00 2.40
1312 1784 2.224606 AGCATATCGTGGGCAAAGATG 58.775 47.619 0.09 0.00 0.00 2.90
1386 1862 5.432645 GAAGGAAGGAGAGTATTTTGAGGG 58.567 45.833 0.00 0.00 0.00 4.30
1398 1874 1.981256 TTTGAGGGAGCAAAGGACAC 58.019 50.000 0.00 0.00 33.16 3.67
1424 1907 2.413837 ACGCATGCTTTTAGACGACTT 58.586 42.857 17.13 0.00 0.00 3.01
1431 1914 2.076863 CTTTTAGACGACTTGCAGGGG 58.923 52.381 0.00 0.00 0.00 4.79
1432 1915 1.053424 TTTAGACGACTTGCAGGGGT 58.947 50.000 0.00 0.00 0.00 4.95
1463 1948 3.093278 GCAGTGCCAGTGCGATAC 58.907 61.111 9.05 0.00 41.78 2.24
1480 1965 5.705441 TGCGATACCTGAAACTTTGATTTCT 59.295 36.000 0.00 0.00 39.02 2.52
1481 1966 6.024049 GCGATACCTGAAACTTTGATTTCTG 58.976 40.000 0.00 0.00 39.02 3.02
1502 1990 5.415701 TCTGTCCCAAACTCTTCATAATTGC 59.584 40.000 0.00 0.00 0.00 3.56
1544 2032 8.443160 TGAACATCAAGCTATATATTTAAGCGC 58.557 33.333 0.00 0.00 41.19 5.92
1547 2035 6.871044 TCAAGCTATATATTTAAGCGCGAG 57.129 37.500 12.10 0.00 41.19 5.03
1548 2036 6.387465 TCAAGCTATATATTTAAGCGCGAGT 58.613 36.000 12.10 0.00 41.19 4.18
1549 2037 6.308041 TCAAGCTATATATTTAAGCGCGAGTG 59.692 38.462 12.10 0.00 41.19 3.51
1550 2038 4.563184 AGCTATATATTTAAGCGCGAGTGC 59.437 41.667 12.10 0.00 41.19 4.40
1553 2041 6.075310 GCTATATATTTAAGCGCGAGTGCTAG 60.075 42.308 12.10 3.59 46.60 3.42
1557 2045 0.311165 TAAGCGCGAGTGCTAGATCC 59.689 55.000 12.10 0.00 46.60 3.36
1578 2072 3.985279 CCAGCAATTGACATCACAAGTTG 59.015 43.478 10.34 0.00 33.22 3.16
1580 2074 5.045215 CAGCAATTGACATCACAAGTTGTT 58.955 37.500 10.34 0.00 33.22 2.83
1583 2077 6.864685 AGCAATTGACATCACAAGTTGTTATG 59.135 34.615 22.76 22.76 37.82 1.90
1584 2078 6.642131 GCAATTGACATCACAAGTTGTTATGT 59.358 34.615 27.73 27.73 44.93 2.29
1589 2083 6.258230 ACATCACAAGTTGTTATGTCCATG 57.742 37.500 23.87 12.15 40.09 3.66
1591 2085 6.939730 ACATCACAAGTTGTTATGTCCATGTA 59.060 34.615 23.87 0.00 40.09 2.29
1593 2087 7.433708 TCACAAGTTGTTATGTCCATGTAAG 57.566 36.000 5.57 0.00 0.00 2.34
1594 2088 6.995686 TCACAAGTTGTTATGTCCATGTAAGT 59.004 34.615 5.57 0.00 0.00 2.24
1595 2089 7.172532 TCACAAGTTGTTATGTCCATGTAAGTC 59.827 37.037 5.57 0.00 0.00 3.01
1596 2090 6.995686 ACAAGTTGTTATGTCCATGTAAGTCA 59.004 34.615 1.64 0.00 0.00 3.41
1598 2092 5.938125 AGTTGTTATGTCCATGTAAGTCACC 59.062 40.000 0.00 0.00 0.00 4.02
1599 2093 5.491323 TGTTATGTCCATGTAAGTCACCA 57.509 39.130 0.00 0.00 0.00 4.17
1600 2094 6.061022 TGTTATGTCCATGTAAGTCACCAT 57.939 37.500 0.00 0.00 0.00 3.55
1601 2095 7.189079 TGTTATGTCCATGTAAGTCACCATA 57.811 36.000 0.00 0.00 0.00 2.74
1605 2099 4.142249 TGTCCATGTAAGTCACCATAGACG 60.142 45.833 0.00 0.00 43.24 4.18
1610 2104 0.179134 AAGTCACCATAGACGCGCTC 60.179 55.000 5.73 2.87 43.24 5.03
1628 2632 1.269723 CTCTAGACACAAGGCACGACA 59.730 52.381 0.00 0.00 0.00 4.35
1695 4357 5.695818 CATAAACTAACGTGAAAACCCCAG 58.304 41.667 0.00 0.00 0.00 4.45
1738 4724 3.950397 TCCGACAAATGGTTTGAGCTAT 58.050 40.909 9.21 0.00 43.26 2.97
1751 4739 8.825667 TGGTTTGAGCTATAAAACAAATTTCC 57.174 30.769 16.58 7.56 37.89 3.13
1759 4780 9.929180 AGCTATAAAACAAATTTCCTTTCCTTC 57.071 29.630 0.00 0.00 32.27 3.46
1791 5800 2.724977 TGTCATTCCGTGTCTCACTC 57.275 50.000 0.00 0.00 31.34 3.51
1792 5801 2.239400 TGTCATTCCGTGTCTCACTCT 58.761 47.619 0.00 0.00 31.34 3.24
1793 5802 2.628178 TGTCATTCCGTGTCTCACTCTT 59.372 45.455 0.00 0.00 31.34 2.85
1794 5803 3.824443 TGTCATTCCGTGTCTCACTCTTA 59.176 43.478 0.00 0.00 31.34 2.10
1889 5898 3.884037 AAGAACTTGGTGACCCTGAAT 57.116 42.857 0.00 0.00 0.00 2.57
2123 6132 2.433664 GTCGGCATCGGTTTCGGT 60.434 61.111 0.00 0.00 36.95 4.69
2282 6461 0.527565 GCGGGCTGAACATGATGTTT 59.472 50.000 12.62 0.00 41.28 2.83
2288 6467 4.170292 GCTGAACATGATGTTTCAGCTT 57.830 40.909 31.81 8.78 46.08 3.74
2660 6839 0.904865 TCCTGACGGGCATCAACTCT 60.905 55.000 0.00 0.00 34.39 3.24
2682 6861 3.909258 CTGTTCTACGCGCCGGTGT 62.909 63.158 17.91 9.10 40.64 4.16
2984 7251 2.440796 CCGCTAGGGTGGACGGTA 60.441 66.667 6.02 0.00 45.39 4.02
3363 7639 8.734386 ACAAGTGAAGATCATTATCAAAGAACC 58.266 33.333 0.00 0.00 34.28 3.62
3364 7640 8.733458 CAAGTGAAGATCATTATCAAAGAACCA 58.267 33.333 0.00 0.00 34.28 3.67
3368 7644 6.910536 AGATCATTATCAAAGAACCACGAC 57.089 37.500 0.00 0.00 34.28 4.34
3479 7755 5.105187 AGGAGACGCACATGCACATATATAT 60.105 40.000 4.49 0.00 42.21 0.86
3480 7756 6.096846 AGGAGACGCACATGCACATATATATA 59.903 38.462 4.49 0.00 42.21 0.86
3489 7765 9.305925 CACATGCACATATATATAGTGGTACTG 57.694 37.037 18.66 5.55 33.98 2.74
3637 7913 7.867909 CGGATCACTAAGCATGTAATTTAGAGA 59.132 37.037 12.28 10.67 31.73 3.10
3658 7934 8.412608 AGAGATGACAAAAATGTATGTCTACG 57.587 34.615 7.35 0.00 44.86 3.51
3661 7937 8.820933 AGATGACAAAAATGTATGTCTACGATG 58.179 33.333 7.35 0.00 44.86 3.84
3733 8013 8.815565 TGATGAGATATATTGTCCTAGGAGAC 57.184 38.462 13.15 2.13 37.28 3.36
3737 8017 8.180165 TGAGATATATTGTCCTAGGAGACCATT 58.820 37.037 13.15 6.14 35.83 3.16
3825 8105 5.410355 ACGTGGCACTCCTAAAATAGTAA 57.590 39.130 16.72 0.00 0.00 2.24
3830 8110 7.493320 CGTGGCACTCCTAAAATAGTAACATTA 59.507 37.037 16.72 0.00 0.00 1.90
3916 8196 2.094649 AGACCCTTTTTCTCGCTCGTAG 60.095 50.000 0.00 0.00 0.00 3.51
3959 8239 4.647424 TTGTGTTGTGATTCAAGGGTTC 57.353 40.909 0.00 0.00 36.66 3.62
3971 8251 1.106944 AAGGGTTCTGTTTGGGCACG 61.107 55.000 0.00 0.00 0.00 5.34
3982 8262 3.322254 TGTTTGGGCACGGTTGATATTTT 59.678 39.130 0.00 0.00 0.00 1.82
4022 8302 6.962182 TGTCATCATCCTCATTCCTAAAGTT 58.038 36.000 0.00 0.00 0.00 2.66
4030 8310 4.514401 CTCATTCCTAAAGTTAAGGGCGT 58.486 43.478 0.00 0.00 34.66 5.68
4035 8315 2.353323 CTAAAGTTAAGGGCGTGGACC 58.647 52.381 0.00 0.00 0.00 4.46
4042 8322 1.617947 AAGGGCGTGGACCTGATCTC 61.618 60.000 0.00 0.00 42.44 2.75
4054 8334 4.442753 GGACCTGATCTCTCAATTCAGACC 60.443 50.000 0.90 1.46 39.36 3.85
4127 8411 1.606480 CGTCTCTCACCTGTTGCACAT 60.606 52.381 0.00 0.00 0.00 3.21
4136 8420 2.037251 ACCTGTTGCACATCGTACTCTT 59.963 45.455 0.00 0.00 0.00 2.85
4150 8434 6.600882 TCGTACTCTTTTCCCTTATCAGTT 57.399 37.500 0.00 0.00 0.00 3.16
4180 8464 0.918983 AAAGGGCGATTCATCCTGGA 59.081 50.000 0.00 0.00 0.00 3.86
4253 8537 5.985911 AGAAAAGCGGTAATCCTTAAGCTA 58.014 37.500 0.00 0.00 33.10 3.32
4282 8566 4.109050 GAGAAAGCTTATGACTCGGTCAG 58.891 47.826 0.00 1.63 46.04 3.51
4286 8570 2.826128 AGCTTATGACTCGGTCAGTTGA 59.174 45.455 11.50 0.00 46.04 3.18
4287 8571 3.258372 AGCTTATGACTCGGTCAGTTGAA 59.742 43.478 11.50 4.20 46.04 2.69
4288 8572 3.994392 GCTTATGACTCGGTCAGTTGAAA 59.006 43.478 11.50 2.56 46.04 2.69
4289 8573 4.092091 GCTTATGACTCGGTCAGTTGAAAG 59.908 45.833 11.50 10.09 46.04 2.62
4290 8574 3.753294 ATGACTCGGTCAGTTGAAAGT 57.247 42.857 11.50 0.00 46.04 2.66
4291 8575 3.536956 TGACTCGGTCAGTTGAAAGTT 57.463 42.857 3.02 0.00 37.67 2.66
4292 8576 3.869065 TGACTCGGTCAGTTGAAAGTTT 58.131 40.909 3.02 0.00 37.67 2.66
4293 8577 4.258543 TGACTCGGTCAGTTGAAAGTTTT 58.741 39.130 3.02 0.00 37.67 2.43
4294 8578 4.698304 TGACTCGGTCAGTTGAAAGTTTTT 59.302 37.500 3.02 0.00 37.67 1.94
4295 8579 5.875910 TGACTCGGTCAGTTGAAAGTTTTTA 59.124 36.000 3.02 0.00 37.67 1.52
4296 8580 6.115450 ACTCGGTCAGTTGAAAGTTTTTAC 57.885 37.500 0.00 0.00 26.56 2.01
4297 8581 5.644636 ACTCGGTCAGTTGAAAGTTTTTACA 59.355 36.000 0.00 0.00 26.56 2.41
4298 8582 6.114221 TCGGTCAGTTGAAAGTTTTTACAG 57.886 37.500 0.00 0.00 0.00 2.74
4299 8583 4.733405 CGGTCAGTTGAAAGTTTTTACAGC 59.267 41.667 0.00 0.00 0.00 4.40
4300 8584 5.646606 GGTCAGTTGAAAGTTTTTACAGCA 58.353 37.500 0.00 0.00 0.00 4.41
4301 8585 6.096695 GGTCAGTTGAAAGTTTTTACAGCAA 58.903 36.000 0.00 0.00 0.00 3.91
4302 8586 6.253512 GGTCAGTTGAAAGTTTTTACAGCAAG 59.746 38.462 0.00 0.00 0.00 4.01
4303 8587 6.806739 GTCAGTTGAAAGTTTTTACAGCAAGT 59.193 34.615 0.00 0.00 0.00 3.16
4304 8588 7.008357 GTCAGTTGAAAGTTTTTACAGCAAGTC 59.992 37.037 0.00 0.00 0.00 3.01
4305 8589 6.253512 CAGTTGAAAGTTTTTACAGCAAGTCC 59.746 38.462 0.00 0.00 0.00 3.85
4306 8590 6.152831 AGTTGAAAGTTTTTACAGCAAGTCCT 59.847 34.615 0.00 0.00 0.00 3.85
4307 8591 7.338449 AGTTGAAAGTTTTTACAGCAAGTCCTA 59.662 33.333 0.00 0.00 0.00 2.94
4308 8592 7.023197 TGAAAGTTTTTACAGCAAGTCCTAC 57.977 36.000 0.00 0.00 0.00 3.18
4309 8593 6.826741 TGAAAGTTTTTACAGCAAGTCCTACT 59.173 34.615 0.00 0.00 0.00 2.57
4310 8594 6.619801 AAGTTTTTACAGCAAGTCCTACTG 57.380 37.500 0.00 0.00 37.45 2.74
4311 8595 5.063880 AGTTTTTACAGCAAGTCCTACTGG 58.936 41.667 0.00 0.00 35.70 4.00
4312 8596 2.762535 TTACAGCAAGTCCTACTGGC 57.237 50.000 0.00 0.00 45.53 4.85
4317 8601 2.997485 GCAAGTCCTACTGGCAAAAG 57.003 50.000 1.49 0.00 44.56 2.27
4318 8602 1.541588 GCAAGTCCTACTGGCAAAAGG 59.458 52.381 8.21 8.21 44.56 3.11
4319 8603 1.541588 CAAGTCCTACTGGCAAAAGGC 59.458 52.381 9.42 5.78 43.74 4.35
4320 8604 1.068121 AGTCCTACTGGCAAAAGGCT 58.932 50.000 9.42 7.58 44.01 4.58
4321 8605 1.003696 AGTCCTACTGGCAAAAGGCTC 59.996 52.381 9.42 6.02 44.01 4.70
4322 8606 1.003696 GTCCTACTGGCAAAAGGCTCT 59.996 52.381 9.42 0.00 44.01 4.09
4323 8607 1.003580 TCCTACTGGCAAAAGGCTCTG 59.996 52.381 9.42 0.00 44.01 3.35
4324 8608 1.003580 CCTACTGGCAAAAGGCTCTGA 59.996 52.381 2.13 0.00 44.01 3.27
4325 8609 2.553028 CCTACTGGCAAAAGGCTCTGAA 60.553 50.000 2.13 0.00 44.01 3.02
4326 8610 1.613836 ACTGGCAAAAGGCTCTGAAG 58.386 50.000 0.97 0.88 44.01 3.02
4327 8611 0.886563 CTGGCAAAAGGCTCTGAAGG 59.113 55.000 0.97 0.00 44.01 3.46
4328 8612 0.478072 TGGCAAAAGGCTCTGAAGGA 59.522 50.000 0.97 0.00 44.01 3.36
4329 8613 1.172175 GGCAAAAGGCTCTGAAGGAG 58.828 55.000 0.97 0.00 44.01 3.69
4340 8624 4.751767 CTCTGAAGGAGCCTTTGTCTAT 57.248 45.455 2.85 0.00 36.26 1.98
4341 8625 5.860941 CTCTGAAGGAGCCTTTGTCTATA 57.139 43.478 2.85 0.00 36.26 1.31
4342 8626 5.841810 CTCTGAAGGAGCCTTTGTCTATAG 58.158 45.833 2.85 0.00 36.26 1.31
4343 8627 4.651503 TCTGAAGGAGCCTTTGTCTATAGG 59.348 45.833 2.85 0.00 36.26 2.57
4344 8628 3.711704 TGAAGGAGCCTTTGTCTATAGGG 59.288 47.826 2.85 0.00 36.26 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.508551 TCTTATGTGACATCAAGGCCAT 57.491 40.909 5.01 0.00 0.00 4.40
4 5 6.405065 CCCAAACATCTTATGTGACATCAAGG 60.405 42.308 0.00 0.00 44.07 3.61
5 6 6.151648 ACCCAAACATCTTATGTGACATCAAG 59.848 38.462 0.00 5.05 44.07 3.02
8 9 5.647658 TCACCCAAACATCTTATGTGACATC 59.352 40.000 0.00 0.00 44.07 3.06
9 10 5.569355 TCACCCAAACATCTTATGTGACAT 58.431 37.500 2.65 2.65 44.07 3.06
10 11 4.979335 TCACCCAAACATCTTATGTGACA 58.021 39.130 0.00 0.00 44.07 3.58
11 12 5.957842 TTCACCCAAACATCTTATGTGAC 57.042 39.130 0.00 0.00 44.07 3.67
12 13 5.105797 GCATTCACCCAAACATCTTATGTGA 60.106 40.000 0.00 0.00 44.07 3.58
13 14 5.104374 GCATTCACCCAAACATCTTATGTG 58.896 41.667 0.00 0.00 44.07 3.21
15 16 5.327616 TGCATTCACCCAAACATCTTATG 57.672 39.130 0.00 0.00 0.00 1.90
16 17 5.163385 CCATGCATTCACCCAAACATCTTAT 60.163 40.000 0.00 0.00 0.00 1.73
17 18 4.160065 CCATGCATTCACCCAAACATCTTA 59.840 41.667 0.00 0.00 0.00 2.10
18 19 3.055675 CCATGCATTCACCCAAACATCTT 60.056 43.478 0.00 0.00 0.00 2.40
19 20 2.498481 CCATGCATTCACCCAAACATCT 59.502 45.455 0.00 0.00 0.00 2.90
20 21 2.896168 CCATGCATTCACCCAAACATC 58.104 47.619 0.00 0.00 0.00 3.06
21 22 1.065998 GCCATGCATTCACCCAAACAT 60.066 47.619 0.00 0.00 0.00 2.71
22 23 0.321021 GCCATGCATTCACCCAAACA 59.679 50.000 0.00 0.00 0.00 2.83
23 24 0.609662 AGCCATGCATTCACCCAAAC 59.390 50.000 0.00 0.00 0.00 2.93
55 56 9.676195 GTCATATATACATCATCAATCTCCTCG 57.324 37.037 0.00 0.00 0.00 4.63
62 63 9.338622 CCATGCAGTCATATATACATCATCAAT 57.661 33.333 0.00 0.00 0.00 2.57
64 65 6.764560 GCCATGCAGTCATATATACATCATCA 59.235 38.462 0.00 0.00 0.00 3.07
66 67 6.766467 CAGCCATGCAGTCATATATACATCAT 59.234 38.462 0.00 0.00 0.00 2.45
67 68 6.070653 TCAGCCATGCAGTCATATATACATCA 60.071 38.462 0.00 0.00 0.00 3.07
68 69 6.343703 TCAGCCATGCAGTCATATATACATC 58.656 40.000 0.00 0.00 0.00 3.06
69 70 6.303903 TCAGCCATGCAGTCATATATACAT 57.696 37.500 0.00 0.00 0.00 2.29
70 71 5.743636 TCAGCCATGCAGTCATATATACA 57.256 39.130 0.00 0.00 0.00 2.29
71 72 7.621428 AATTCAGCCATGCAGTCATATATAC 57.379 36.000 0.00 0.00 0.00 1.47
72 73 8.105197 AGAAATTCAGCCATGCAGTCATATATA 58.895 33.333 0.00 0.00 0.00 0.86
73 74 6.946583 AGAAATTCAGCCATGCAGTCATATAT 59.053 34.615 0.00 0.00 0.00 0.86
74 75 6.301486 AGAAATTCAGCCATGCAGTCATATA 58.699 36.000 0.00 0.00 0.00 0.86
75 76 5.138276 AGAAATTCAGCCATGCAGTCATAT 58.862 37.500 0.00 0.00 0.00 1.78
78 79 2.799017 AGAAATTCAGCCATGCAGTCA 58.201 42.857 0.00 0.00 0.00 3.41
97 98 2.713895 TGTCAGTCTCTGCGAGAAAG 57.286 50.000 9.35 6.16 40.59 2.62
99 100 2.822561 AGATTGTCAGTCTCTGCGAGAA 59.177 45.455 9.35 0.00 40.59 2.87
114 115 5.300411 TCAGCCATGTGATCATAGATTGT 57.700 39.130 0.00 0.00 32.47 2.71
115 116 6.628919 TTTCAGCCATGTGATCATAGATTG 57.371 37.500 0.00 0.00 32.47 2.67
118 119 6.183810 AGATTTCAGCCATGTGATCATAGA 57.816 37.500 0.00 0.00 32.47 1.98
127 128 2.485426 CGACACAAGATTTCAGCCATGT 59.515 45.455 0.00 0.00 0.00 3.21
128 129 2.743664 TCGACACAAGATTTCAGCCATG 59.256 45.455 0.00 0.00 0.00 3.66
169 170 2.683768 AGGGAATAGAGTTCAGCGGAT 58.316 47.619 0.00 0.00 0.00 4.18
178 179 4.738132 ACCTCTTAGGGTAGGGAATAGAGT 59.262 45.833 0.00 0.00 40.58 3.24
196 197 1.416401 ACACATTCACACGGAACCTCT 59.584 47.619 0.00 0.00 38.60 3.69
199 202 2.676342 GGATACACATTCACACGGAACC 59.324 50.000 0.00 0.00 38.60 3.62
201 204 3.686916 TGGATACACATTCACACGGAA 57.313 42.857 0.00 0.00 46.17 4.30
247 250 7.971168 CCTCTATATATAGTTGTTTCAGAGCCG 59.029 40.741 17.44 0.00 0.00 5.52
358 370 9.533253 CAAGTGATTTTTGTCAACCTCTAAAAT 57.467 29.630 0.00 0.00 34.76 1.82
400 414 4.582240 TGACATGCCAAATGTTGACAAGTA 59.418 37.500 0.00 0.00 25.38 2.24
434 448 5.263599 TGAATTAGGATGCTGATTGGTTGT 58.736 37.500 9.01 0.00 0.00 3.32
473 487 3.055094 GCAAGACCATAACCAGGAGAGAA 60.055 47.826 0.00 0.00 0.00 2.87
549 570 1.374947 CCACCACCACCAGTACAGG 59.625 63.158 2.14 2.14 0.00 4.00
579 600 3.756933 AAAAATTGAGTGGCTGCACAT 57.243 38.095 0.50 0.00 0.00 3.21
598 619 1.284313 GGGCCCCCAATTTCATCAAA 58.716 50.000 12.23 0.00 35.81 2.69
599 620 0.975040 CGGGCCCCCAATTTCATCAA 60.975 55.000 18.66 0.00 35.37 2.57
755 777 4.847516 CTCGCGCCGGTCGATCAA 62.848 66.667 20.06 0.77 41.67 2.57
952 1000 4.855340 TGGAATTAAAGTCAAGCTAGGGG 58.145 43.478 0.00 0.00 0.00 4.79
967 1017 3.794399 TCTCCTCTCCTCTCCTGGAATTA 59.206 47.826 0.00 0.00 35.43 1.40
974 1024 1.522900 CTCCTCTCCTCTCCTCTCCT 58.477 60.000 0.00 0.00 0.00 3.69
1026 1080 1.544825 CCGCCCTCTCCTTCTTCACA 61.545 60.000 0.00 0.00 0.00 3.58
1202 1284 3.181471 CCAAGTGACTCAGCCGAGATTAT 60.181 47.826 3.36 0.00 42.34 1.28
1204 1286 1.066573 CCAAGTGACTCAGCCGAGATT 60.067 52.381 3.36 0.00 42.34 2.40
1229 1315 0.949105 CAGCCACACTCGTACAACCC 60.949 60.000 0.00 0.00 0.00 4.11
1292 1764 2.224606 CATCTTTGCCCACGATATGCT 58.775 47.619 0.00 0.00 0.00 3.79
1305 1777 5.065731 CCTCTAAGCAAGGTTAGCATCTTTG 59.934 44.000 12.81 0.00 31.10 2.77
1306 1778 5.189180 CCTCTAAGCAAGGTTAGCATCTTT 58.811 41.667 12.81 0.00 31.10 2.52
1307 1779 4.775236 CCTCTAAGCAAGGTTAGCATCTT 58.225 43.478 12.81 0.00 31.10 2.40
1309 1781 2.875317 GCCTCTAAGCAAGGTTAGCATC 59.125 50.000 12.81 2.66 36.21 3.91
1310 1782 2.422093 GGCCTCTAAGCAAGGTTAGCAT 60.422 50.000 12.81 0.00 36.21 3.79
1311 1783 1.065418 GGCCTCTAAGCAAGGTTAGCA 60.065 52.381 12.81 3.60 36.21 3.49
1312 1784 1.669604 GGCCTCTAAGCAAGGTTAGC 58.330 55.000 12.81 4.24 36.21 3.09
1314 1786 1.563924 TCGGCCTCTAAGCAAGGTTA 58.436 50.000 0.00 0.00 36.21 2.85
1363 1839 5.189934 TCCCTCAAAATACTCTCCTTCCTTC 59.810 44.000 0.00 0.00 0.00 3.46
1364 1840 5.101529 TCCCTCAAAATACTCTCCTTCCTT 58.898 41.667 0.00 0.00 0.00 3.36
1377 1853 2.893489 GTGTCCTTTGCTCCCTCAAAAT 59.107 45.455 0.00 0.00 35.75 1.82
1386 1862 1.261619 CGTTGTGAGTGTCCTTTGCTC 59.738 52.381 0.00 0.00 0.00 4.26
1398 1874 3.482786 GTCTAAAAGCATGCGTTGTGAG 58.517 45.455 19.65 15.95 0.00 3.51
1424 1907 0.321210 CGTGTTGTGATACCCCTGCA 60.321 55.000 0.00 0.00 0.00 4.41
1431 1914 1.136252 CACTGCAGCGTGTTGTGATAC 60.136 52.381 15.27 0.00 0.00 2.24
1432 1915 1.147473 CACTGCAGCGTGTTGTGATA 58.853 50.000 15.27 0.00 0.00 2.15
1459 1944 7.362142 GGGACAGAAATCAAAGTTTCAGGTATC 60.362 40.741 2.68 0.00 39.88 2.24
1461 1946 5.768164 GGGACAGAAATCAAAGTTTCAGGTA 59.232 40.000 2.68 0.00 39.88 3.08
1463 1948 4.584325 TGGGACAGAAATCAAAGTTTCAGG 59.416 41.667 2.68 0.00 39.88 3.86
1480 1965 5.076182 TGCAATTATGAAGAGTTTGGGACA 58.924 37.500 0.00 0.00 0.00 4.02
1481 1966 5.643379 TGCAATTATGAAGAGTTTGGGAC 57.357 39.130 0.00 0.00 0.00 4.46
1528 2016 4.563184 AGCACTCGCGCTTAAATATATAGC 59.437 41.667 5.56 0.00 45.49 2.97
1536 2024 2.460918 GATCTAGCACTCGCGCTTAAA 58.539 47.619 5.56 0.00 45.49 1.52
1539 2027 1.066587 GGATCTAGCACTCGCGCTT 59.933 57.895 5.56 0.00 45.49 4.68
1541 2029 1.659954 CTGGATCTAGCACTCGCGC 60.660 63.158 0.00 0.00 45.49 6.86
1549 2037 4.024218 GTGATGTCAATTGCTGGATCTAGC 60.024 45.833 23.11 23.11 43.95 3.42
1550 2038 5.121105 TGTGATGTCAATTGCTGGATCTAG 58.879 41.667 0.86 0.86 0.00 2.43
1551 2039 5.101648 TGTGATGTCAATTGCTGGATCTA 57.898 39.130 0.00 0.00 0.00 1.98
1553 2041 4.157289 ACTTGTGATGTCAATTGCTGGATC 59.843 41.667 0.00 0.35 0.00 3.36
1557 2045 4.613944 ACAACTTGTGATGTCAATTGCTG 58.386 39.130 0.00 0.00 0.00 4.41
1578 2072 7.497595 TCTATGGTGACTTACATGGACATAAC 58.502 38.462 0.00 0.00 30.94 1.89
1583 2077 4.360563 CGTCTATGGTGACTTACATGGAC 58.639 47.826 10.03 10.03 46.04 4.02
1584 2078 3.181479 GCGTCTATGGTGACTTACATGGA 60.181 47.826 0.00 0.00 35.00 3.41
1586 2080 2.789339 CGCGTCTATGGTGACTTACATG 59.211 50.000 0.00 0.00 35.00 3.21
1587 2081 2.798499 GCGCGTCTATGGTGACTTACAT 60.798 50.000 8.43 0.00 35.00 2.29
1589 2083 1.197910 GCGCGTCTATGGTGACTTAC 58.802 55.000 8.43 0.00 35.00 2.34
1591 2085 0.179134 GAGCGCGTCTATGGTGACTT 60.179 55.000 8.43 0.00 35.00 3.01
1593 2087 0.661552 TAGAGCGCGTCTATGGTGAC 59.338 55.000 8.43 0.00 36.64 3.67
1594 2088 0.945099 CTAGAGCGCGTCTATGGTGA 59.055 55.000 8.43 0.00 37.14 4.02
1595 2089 0.945099 TCTAGAGCGCGTCTATGGTG 59.055 55.000 8.43 2.69 37.14 4.17
1596 2090 0.945813 GTCTAGAGCGCGTCTATGGT 59.054 55.000 8.43 0.00 37.14 3.55
1598 2092 1.330829 TGTGTCTAGAGCGCGTCTATG 59.669 52.381 8.43 8.04 37.14 2.23
1599 2093 1.664873 TGTGTCTAGAGCGCGTCTAT 58.335 50.000 8.43 5.39 37.14 1.98
1600 2094 1.397343 CTTGTGTCTAGAGCGCGTCTA 59.603 52.381 8.43 12.55 36.64 2.59
1601 2095 0.169230 CTTGTGTCTAGAGCGCGTCT 59.831 55.000 8.43 12.04 39.59 4.18
1605 2099 1.079819 TGCCTTGTGTCTAGAGCGC 60.080 57.895 0.00 0.00 0.00 5.92
1610 2104 1.792949 GTTGTCGTGCCTTGTGTCTAG 59.207 52.381 0.00 0.00 0.00 2.43
1628 2632 6.149973 CACATGATCTCTTTACACCATGTGTT 59.850 38.462 19.29 0.00 45.08 3.32
1676 3958 1.951602 GCTGGGGTTTTCACGTTAGTT 59.048 47.619 0.00 0.00 0.00 2.24
1713 4610 3.081061 CTCAAACCATTTGTCGGATCCA 58.919 45.455 13.41 0.00 41.36 3.41
1719 4616 7.081349 TGTTTTATAGCTCAAACCATTTGTCG 58.919 34.615 11.58 0.00 41.36 4.35
1751 4739 7.874940 TGACATCAACACATTAAGAAGGAAAG 58.125 34.615 0.00 0.00 0.00 2.62
1759 4780 6.023435 CACGGAATGACATCAACACATTAAG 58.977 40.000 0.00 0.00 34.94 1.85
1791 5800 6.017934 ACTCCTGTTACAATATGCGCAATAAG 60.018 38.462 17.11 8.05 0.00 1.73
1792 5801 5.820423 ACTCCTGTTACAATATGCGCAATAA 59.180 36.000 17.11 2.95 0.00 1.40
1793 5802 5.236263 CACTCCTGTTACAATATGCGCAATA 59.764 40.000 17.11 8.17 0.00 1.90
1794 5803 4.035558 CACTCCTGTTACAATATGCGCAAT 59.964 41.667 17.11 6.72 0.00 3.56
1889 5898 4.037803 TGGTTGTCGTACTTGCAGTAGTTA 59.962 41.667 0.00 0.00 30.12 2.24
2123 6132 3.580895 TGTGAGCTTACCACACCTGATTA 59.419 43.478 6.13 0.00 39.36 1.75
2660 6839 1.357690 CGGCGCGTAGAACAGGATA 59.642 57.895 8.43 0.00 0.00 2.59
2984 7251 1.433879 CGGAAAGATCTCGCTCGGT 59.566 57.895 0.00 0.00 0.00 4.69
3358 7634 4.039973 TCCTATCAAAACAGTCGTGGTTCT 59.960 41.667 0.00 0.00 29.78 3.01
3363 7639 3.123621 GTGCTCCTATCAAAACAGTCGTG 59.876 47.826 0.00 0.00 0.00 4.35
3364 7640 3.244078 TGTGCTCCTATCAAAACAGTCGT 60.244 43.478 0.00 0.00 0.00 4.34
3368 7644 3.441222 TGCATGTGCTCCTATCAAAACAG 59.559 43.478 6.55 0.00 42.66 3.16
3479 7755 2.091098 ACACCACACCAGTACCACTA 57.909 50.000 0.00 0.00 0.00 2.74
3480 7756 1.209621 AACACCACACCAGTACCACT 58.790 50.000 0.00 0.00 0.00 4.00
3489 7765 2.301870 TGGAGATGACTAACACCACACC 59.698 50.000 0.00 0.00 0.00 4.16
3637 7913 8.716646 TCATCGTAGACATACATTTTTGTCAT 57.283 30.769 5.44 0.00 43.72 3.06
3710 7990 7.713518 TGGTCTCCTAGGACAATATATCTCAT 58.286 38.462 7.62 0.00 37.91 2.90
3714 7994 9.041354 AGAAATGGTCTCCTAGGACAATATATC 57.959 37.037 7.62 2.46 37.91 1.63
3716 7996 8.798975 AAGAAATGGTCTCCTAGGACAATATA 57.201 34.615 7.62 0.00 34.56 0.86
3727 8007 9.898152 CTTCTCTTATTTAAGAAATGGTCTCCT 57.102 33.333 1.97 0.00 41.37 3.69
3728 8008 9.892130 TCTTCTCTTATTTAAGAAATGGTCTCC 57.108 33.333 1.97 0.00 41.37 3.71
3787 8067 8.951787 AGTGCCACGTATAATAAATGTTAAGA 57.048 30.769 0.00 0.00 0.00 2.10
3792 8072 5.925509 AGGAGTGCCACGTATAATAAATGT 58.074 37.500 0.00 0.00 36.29 2.71
3800 8080 6.720112 ACTATTTTAGGAGTGCCACGTATA 57.280 37.500 0.00 0.00 36.29 1.47
3857 8137 4.351127 ACCGTGTCCTTTTAGAGGTCTAT 58.649 43.478 0.00 0.00 46.39 1.98
3877 8157 2.548480 GTCTGGCTGCGGATAAAATACC 59.452 50.000 0.00 0.00 0.00 2.73
3936 8216 5.363580 AGAACCCTTGAATCACAACACAAAT 59.636 36.000 0.00 0.00 34.56 2.32
3943 8223 4.099266 CCAAACAGAACCCTTGAATCACAA 59.901 41.667 0.00 0.00 36.97 3.33
3959 8239 1.529226 TATCAACCGTGCCCAAACAG 58.471 50.000 0.00 0.00 0.00 3.16
3971 8251 7.407337 CGTAGTTAAGCCTGAAAATATCAACC 58.593 38.462 0.00 0.00 37.67 3.77
3982 8262 1.890489 TGACAGCGTAGTTAAGCCTGA 59.110 47.619 0.00 0.00 0.00 3.86
4022 8302 0.325296 AGATCAGGTCCACGCCCTTA 60.325 55.000 0.00 0.00 0.00 2.69
4030 8310 4.161189 GTCTGAATTGAGAGATCAGGTCCA 59.839 45.833 0.00 0.00 40.71 4.02
4035 8315 6.424509 GCAATAGGTCTGAATTGAGAGATCAG 59.575 42.308 0.00 0.00 41.49 2.90
4042 8322 4.162040 AGGGCAATAGGTCTGAATTGAG 57.838 45.455 5.05 0.00 35.53 3.02
4054 8334 9.362151 TCCCAAAGTTATTAATAAGGGCAATAG 57.638 33.333 18.96 3.78 35.03 1.73
4083 8363 0.685097 GCATAGCCTATGACGGGGAA 59.315 55.000 15.88 0.00 38.45 3.97
4084 8364 1.192146 GGCATAGCCTATGACGGGGA 61.192 60.000 15.88 0.00 46.69 4.81
4103 8387 1.402194 GCAACAGGTGAGAGACGAGAG 60.402 57.143 0.00 0.00 0.00 3.20
4127 8411 6.600882 AACTGATAAGGGAAAAGAGTACGA 57.399 37.500 0.00 0.00 0.00 3.43
4136 8420 4.898861 ACAAAGGCAAACTGATAAGGGAAA 59.101 37.500 0.00 0.00 0.00 3.13
4180 8464 2.100252 TCGTGAAGACAAAGAACTCCGT 59.900 45.455 0.00 0.00 0.00 4.69
4192 8476 6.662414 TGTCATGGATAATTTCGTGAAGAC 57.338 37.500 0.00 0.00 0.00 3.01
4231 8515 6.018913 GTCTAGCTTAAGGATTACCGCTTTTC 60.019 42.308 4.29 0.00 38.21 2.29
4232 8516 5.816258 GTCTAGCTTAAGGATTACCGCTTTT 59.184 40.000 4.29 0.00 38.21 2.27
4238 8522 7.783042 TCTCAAAGTCTAGCTTAAGGATTACC 58.217 38.462 4.29 0.00 36.17 2.85
4253 8537 5.866633 CGAGTCATAAGCTTTCTCAAAGTCT 59.133 40.000 3.20 0.00 40.64 3.24
4282 8566 6.330278 AGGACTTGCTGTAAAAACTTTCAAC 58.670 36.000 0.00 0.00 0.00 3.18
4286 8570 6.039382 CCAGTAGGACTTGCTGTAAAAACTTT 59.961 38.462 2.15 0.00 36.89 2.66
4287 8571 5.531287 CCAGTAGGACTTGCTGTAAAAACTT 59.469 40.000 2.15 0.00 36.89 2.66
4288 8572 5.063880 CCAGTAGGACTTGCTGTAAAAACT 58.936 41.667 2.15 0.00 36.89 2.66
4289 8573 4.320275 GCCAGTAGGACTTGCTGTAAAAAC 60.320 45.833 2.15 0.00 34.40 2.43
4290 8574 3.818773 GCCAGTAGGACTTGCTGTAAAAA 59.181 43.478 2.15 0.00 34.40 1.94
4291 8575 3.181449 TGCCAGTAGGACTTGCTGTAAAA 60.181 43.478 2.15 0.00 37.71 1.52
4292 8576 2.370519 TGCCAGTAGGACTTGCTGTAAA 59.629 45.455 2.15 0.00 37.71 2.01
4293 8577 1.974957 TGCCAGTAGGACTTGCTGTAA 59.025 47.619 2.15 0.00 37.71 2.41
4294 8578 1.639722 TGCCAGTAGGACTTGCTGTA 58.360 50.000 2.15 0.00 37.71 2.74
4295 8579 0.764890 TTGCCAGTAGGACTTGCTGT 59.235 50.000 2.15 0.00 37.71 4.40
4296 8580 1.896220 TTTGCCAGTAGGACTTGCTG 58.104 50.000 4.55 0.00 37.71 4.41
4297 8581 2.508526 CTTTTGCCAGTAGGACTTGCT 58.491 47.619 4.55 0.00 37.71 3.91
4298 8582 1.541588 CCTTTTGCCAGTAGGACTTGC 59.458 52.381 0.00 0.00 37.39 4.01
4299 8583 1.541588 GCCTTTTGCCAGTAGGACTTG 59.458 52.381 0.00 0.00 36.89 3.16
4300 8584 1.425448 AGCCTTTTGCCAGTAGGACTT 59.575 47.619 0.00 0.00 42.71 3.01
4301 8585 1.003696 GAGCCTTTTGCCAGTAGGACT 59.996 52.381 0.00 0.00 42.71 3.85
4302 8586 1.003696 AGAGCCTTTTGCCAGTAGGAC 59.996 52.381 0.00 0.00 42.71 3.85
4303 8587 1.003580 CAGAGCCTTTTGCCAGTAGGA 59.996 52.381 0.00 0.00 42.71 2.94
4304 8588 1.003580 TCAGAGCCTTTTGCCAGTAGG 59.996 52.381 0.00 0.00 42.71 3.18
4305 8589 2.479566 TCAGAGCCTTTTGCCAGTAG 57.520 50.000 0.00 0.00 42.71 2.57
4306 8590 2.553028 CCTTCAGAGCCTTTTGCCAGTA 60.553 50.000 0.00 0.00 42.71 2.74
4307 8591 1.613836 CTTCAGAGCCTTTTGCCAGT 58.386 50.000 0.00 0.00 42.71 4.00
4308 8592 0.886563 CCTTCAGAGCCTTTTGCCAG 59.113 55.000 0.00 0.00 42.71 4.85
4309 8593 0.478072 TCCTTCAGAGCCTTTTGCCA 59.522 50.000 0.00 0.00 42.71 4.92
4310 8594 1.172175 CTCCTTCAGAGCCTTTTGCC 58.828 55.000 0.00 0.00 42.71 4.52
4319 8603 4.751767 ATAGACAAAGGCTCCTTCAGAG 57.248 45.455 1.05 0.00 46.29 3.35
4320 8604 4.651503 CCTATAGACAAAGGCTCCTTCAGA 59.348 45.833 0.00 0.00 34.84 3.27
4321 8605 4.202305 CCCTATAGACAAAGGCTCCTTCAG 60.202 50.000 0.00 1.09 34.84 3.02
4322 8606 3.711704 CCCTATAGACAAAGGCTCCTTCA 59.288 47.826 0.00 0.00 34.84 3.02
4323 8607 4.344359 CCCTATAGACAAAGGCTCCTTC 57.656 50.000 0.00 0.00 34.84 3.46



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

AutoCloner maintained by Alex Coulton.