Multiple sequence alignment - TraesCS6A01G138100

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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 TraesCS6A01G138100 chr6A 100.000 4811 0 0 869 5679 109382793 109387603 0.000000e+00 8885.0
1 TraesCS6A01G138100 chr6A 100.000 622 0 0 1 622 109381925 109382546 0.000000e+00 1149.0
2 TraesCS6A01G138100 chr6A 86.747 83 7 4 1 81 29751384 29751304 7.840000e-14 89.8
3 TraesCS6A01G138100 chr6A 88.000 75 9 0 1 75 294394790 294394716 7.840000e-14 89.8
4 TraesCS6A01G138100 chr6A 82.653 98 11 6 5147 5240 397535851 397535946 1.310000e-11 82.4
5 TraesCS6A01G138100 chr6B 93.327 3222 114 34 869 4031 173573381 173576560 0.000000e+00 4665.0
6 TraesCS6A01G138100 chr6B 93.321 1093 48 13 4063 5143 173577028 173578107 0.000000e+00 1591.0
7 TraesCS6A01G138100 chr6B 93.645 535 20 6 98 622 173572728 173573258 0.000000e+00 787.0
8 TraesCS6A01G138100 chr6B 79.581 382 51 17 5165 5527 541166243 541166616 1.220000e-61 248.0
9 TraesCS6A01G138100 chr6B 84.884 86 9 4 5147 5230 432482117 432482034 3.650000e-12 84.2
10 TraesCS6A01G138100 chr6D 92.908 2087 85 24 3068 5121 91043663 91045719 0.000000e+00 2976.0
11 TraesCS6A01G138100 chr6D 94.005 1935 80 18 869 2792 91041565 91043474 0.000000e+00 2898.0
12 TraesCS6A01G138100 chr6D 96.422 559 11 5 72 622 91040885 91041442 0.000000e+00 913.0
13 TraesCS6A01G138100 chr3A 82.847 548 73 9 5148 5677 550501871 550501327 6.660000e-129 472.0
14 TraesCS6A01G138100 chr3A 79.667 541 88 19 5149 5677 466239121 466238591 2.500000e-98 370.0
15 TraesCS6A01G138100 chr3A 88.889 72 8 0 1 72 360847809 360847880 7.840000e-14 89.8
16 TraesCS6A01G138100 chr4D 81.056 549 81 8 5147 5679 339546951 339547492 3.170000e-112 416.0
17 TraesCS6A01G138100 chr4D 94.643 56 3 0 5146 5201 47495214 47495269 2.820000e-13 87.9
18 TraesCS6A01G138100 chr7B 79.566 553 87 16 5145 5679 244419489 244418945 6.950000e-99 372.0
19 TraesCS6A01G138100 chr7B 88.312 77 6 3 1 75 568389595 568389520 7.840000e-14 89.8
20 TraesCS6A01G138100 chr7D 79.566 553 85 16 5145 5679 264071377 264070835 2.500000e-98 370.0
21 TraesCS6A01G138100 chr7A 78.431 561 86 19 5145 5679 287548714 287548163 3.280000e-87 333.0
22 TraesCS6A01G138100 chr7A 82.270 141 19 5 4528 4665 653543392 653543255 3.590000e-22 117.0
23 TraesCS6A01G138100 chr7A 79.032 124 25 1 5517 5640 285107150 285107028 3.650000e-12 84.2
24 TraesCS6A01G138100 chr3D 78.080 552 90 20 5146 5679 337312542 337312004 2.550000e-83 320.0
25 TraesCS6A01G138100 chr1D 87.072 263 25 5 2790 3047 49419967 49419709 7.200000e-74 289.0
26 TraesCS6A01G138100 chr1B 88.889 234 22 2 2791 3024 69541333 69541104 9.310000e-73 285.0
27 TraesCS6A01G138100 chr1B 89.474 76 7 1 1 75 649315634 649315559 1.680000e-15 95.3
28 TraesCS6A01G138100 chr5D 84.291 261 31 8 2790 3047 113741357 113741610 4.390000e-61 246.0
29 TraesCS6A01G138100 chr2A 85.417 240 28 4 2808 3047 493408402 493408634 5.680000e-60 243.0
30 TraesCS6A01G138100 chr2A 87.059 85 6 5 1 83 16301517 16301436 2.180000e-14 91.6
31 TraesCS6A01G138100 chr4B 77.130 446 76 22 5147 5579 182668924 182669356 9.510000e-58 235.0
32 TraesCS6A01G138100 chr4B 96.429 56 2 0 5146 5201 69314002 69314057 6.060000e-15 93.5
33 TraesCS6A01G138100 chr4B 86.364 88 8 4 5147 5234 82349632 82349549 6.060000e-15 93.5
34 TraesCS6A01G138100 chr2B 78.049 369 76 5 5311 5677 28455369 28455004 1.590000e-55 228.0
35 TraesCS6A01G138100 chr2B 87.356 87 11 0 5147 5233 272427487 272427573 3.620000e-17 100.0
36 TraesCS6A01G138100 chr2B 87.500 80 9 1 1 79 443151753 443151832 2.180000e-14 91.6
37 TraesCS6A01G138100 chr2B 87.500 80 6 4 9 86 162014445 162014522 7.840000e-14 89.8
38 TraesCS6A01G138100 chr3B 82.331 266 36 8 5253 5513 342889489 342889748 2.660000e-53 220.0
39 TraesCS6A01G138100 chr3B 78.873 284 42 8 5148 5414 704704080 704703798 5.850000e-40 176.0
40 TraesCS6A01G138100 chr2D 76.620 355 79 4 5324 5677 469035212 469034861 5.810000e-45 193.0
41 TraesCS6A01G138100 chr2D 78.652 267 43 12 2787 3047 179426795 179426537 1.270000e-36 165.0
42 TraesCS6A01G138100 chrUn 76.515 264 50 10 2789 3047 24270133 24269877 3.570000e-27 134.0
43 TraesCS6A01G138100 chrUn 83.117 77 11 2 5146 5220 463610014 463609938 1.020000e-07 69.4
44 TraesCS6A01G138100 chr1A 76.426 263 50 9 2790 3047 285563697 285563442 1.280000e-26 132.0
45 TraesCS6A01G138100 chr1A 76.245 261 54 7 2790 3047 331542326 331542581 1.280000e-26 132.0
46 TraesCS6A01G138100 chr5B 89.333 75 7 1 1 74 259424603 259424529 6.060000e-15 93.5


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 TraesCS6A01G138100 chr6A 109381925 109387603 5678 False 5017.000000 8885 100.000 1 5679 2 chr6A.!!$F2 5678
1 TraesCS6A01G138100 chr6B 173572728 173578107 5379 False 2347.666667 4665 93.431 98 5143 3 chr6B.!!$F2 5045
2 TraesCS6A01G138100 chr6D 91040885 91045719 4834 False 2262.333333 2976 94.445 72 5121 3 chr6D.!!$F1 5049
3 TraesCS6A01G138100 chr3A 550501327 550501871 544 True 472.000000 472 82.847 5148 5677 1 chr3A.!!$R2 529
4 TraesCS6A01G138100 chr3A 466238591 466239121 530 True 370.000000 370 79.667 5149 5677 1 chr3A.!!$R1 528
5 TraesCS6A01G138100 chr4D 339546951 339547492 541 False 416.000000 416 81.056 5147 5679 1 chr4D.!!$F2 532
6 TraesCS6A01G138100 chr7B 244418945 244419489 544 True 372.000000 372 79.566 5145 5679 1 chr7B.!!$R1 534
7 TraesCS6A01G138100 chr7D 264070835 264071377 542 True 370.000000 370 79.566 5145 5679 1 chr7D.!!$R1 534
8 TraesCS6A01G138100 chr7A 287548163 287548714 551 True 333.000000 333 78.431 5145 5679 1 chr7A.!!$R2 534
9 TraesCS6A01G138100 chr3D 337312004 337312542 538 True 320.000000 320 78.080 5146 5679 1 chr3D.!!$R1 533

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
203 205 0.036010 CGGTTGAGCCTTCCACATCT 60.036 55.000 0.00 0.00 34.25 2.90 F
254 261 0.538057 CTGCAAGCAAGTGGAGGGAA 60.538 55.000 0.00 0.00 33.61 3.97 F
482 494 0.579156 GATTCGATTCGACTGGCTGC 59.421 55.000 8.55 0.00 34.89 5.25 F
1278 1340 0.681733 TTAGAGATCGGATGGCTGGC 59.318 55.000 0.00 0.00 0.00 4.85 F
1394 1457 0.753262 ACTCTGGTCACGCAAAGTCT 59.247 50.000 0.00 0.00 0.00 3.24 F
2447 2517 1.444553 CCTCGAGGTTGCTGACGAC 60.445 63.158 24.04 0.00 0.00 4.34 F
3891 4151 0.383949 GTGCGTGAAAAAGGCCTTGA 59.616 50.000 21.33 0.11 38.97 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1147 0.034089 AATTGAAGAAGCGGGAGGGG 60.034 55.000 0.00 0.00 0.00 4.79 R
1276 1338 0.181350 CTTGACACCCCCTATCTGCC 59.819 60.000 0.00 0.00 0.00 4.85 R
1688 1757 0.229753 CGGTCGAATAGCATCGCAAC 59.770 55.000 0.00 0.00 42.44 4.17 R
2585 2655 0.107703 ATGCACCATACCTGTGACCG 60.108 55.000 0.00 0.00 35.74 4.79 R
3024 3102 1.296145 CTTCACAATGTAGCGCGCG 60.296 57.895 28.44 28.44 0.00 6.86 R
4151 4852 0.108520 GACCGGTAGCATGTCGGAAA 60.109 55.000 7.34 0.00 45.96 3.13 R
4896 5608 0.317938 GCGACAGCTCGTATACCCTG 60.318 60.000 9.89 9.89 42.33 4.45 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
53 54 7.547697 TTTTTAGGATTTGAAGGTTTAGGGG 57.452 36.000 0.00 0.00 0.00 4.79
54 55 5.871324 TTAGGATTTGAAGGTTTAGGGGT 57.129 39.130 0.00 0.00 0.00 4.95
55 56 6.973700 TTAGGATTTGAAGGTTTAGGGGTA 57.026 37.500 0.00 0.00 0.00 3.69
56 57 5.188988 AGGATTTGAAGGTTTAGGGGTAC 57.811 43.478 0.00 0.00 0.00 3.34
57 58 4.856182 AGGATTTGAAGGTTTAGGGGTACT 59.144 41.667 0.00 0.00 0.00 2.73
58 59 6.034003 AGGATTTGAAGGTTTAGGGGTACTA 58.966 40.000 0.00 0.00 0.00 1.82
59 60 6.069789 AGGATTTGAAGGTTTAGGGGTACTAC 60.070 42.308 0.00 0.00 0.00 2.73
60 61 6.069789 GGATTTGAAGGTTTAGGGGTACTACT 60.070 42.308 0.00 0.00 0.00 2.57
61 62 7.126268 GGATTTGAAGGTTTAGGGGTACTACTA 59.874 40.741 0.00 0.00 0.00 1.82
62 63 7.486407 TTTGAAGGTTTAGGGGTACTACTAG 57.514 40.000 0.00 0.00 0.00 2.57
63 64 6.157862 TGAAGGTTTAGGGGTACTACTAGT 57.842 41.667 0.00 0.00 0.00 2.57
64 65 7.284014 TGAAGGTTTAGGGGTACTACTAGTA 57.716 40.000 1.89 1.89 0.00 1.82
65 66 7.708624 TGAAGGTTTAGGGGTACTACTAGTAA 58.291 38.462 3.76 0.00 31.62 2.24
66 67 8.346828 TGAAGGTTTAGGGGTACTACTAGTAAT 58.653 37.037 3.76 0.00 31.62 1.89
67 68 8.544687 AAGGTTTAGGGGTACTACTAGTAATG 57.455 38.462 3.76 0.00 31.62 1.90
68 69 6.552725 AGGTTTAGGGGTACTACTAGTAATGC 59.447 42.308 3.76 0.00 31.62 3.56
69 70 6.552725 GGTTTAGGGGTACTACTAGTAATGCT 59.447 42.308 3.76 0.00 31.62 3.79
70 71 7.255766 GGTTTAGGGGTACTACTAGTAATGCTC 60.256 44.444 3.76 0.00 31.62 4.26
78 79 7.718753 GGTACTACTAGTAATGCTCTTAGACCA 59.281 40.741 3.76 0.00 31.62 4.02
203 205 0.036010 CGGTTGAGCCTTCCACATCT 60.036 55.000 0.00 0.00 34.25 2.90
227 234 3.264052 CCCACCCCACCATCACCA 61.264 66.667 0.00 0.00 0.00 4.17
228 235 2.035626 CCACCCCACCATCACCAC 59.964 66.667 0.00 0.00 0.00 4.16
229 236 2.035626 CACCCCACCATCACCACC 59.964 66.667 0.00 0.00 0.00 4.61
254 261 0.538057 CTGCAAGCAAGTGGAGGGAA 60.538 55.000 0.00 0.00 33.61 3.97
482 494 0.579156 GATTCGATTCGACTGGCTGC 59.421 55.000 8.55 0.00 34.89 5.25
913 935 3.382803 CTTCCTGCTCCCTCCTGCG 62.383 68.421 0.00 0.00 0.00 5.18
958 980 1.208844 TGAGGAGAGGAGGAGACGGT 61.209 60.000 0.00 0.00 0.00 4.83
965 987 2.276116 GGAGGAGACGGTGCTGTCA 61.276 63.158 12.96 0.00 41.41 3.58
972 994 4.662961 CGGTGCTGTCAGTGGCGA 62.663 66.667 0.93 0.00 0.00 5.54
1111 1136 1.213182 TCACCAACAGGTAAACCAGCA 59.787 47.619 1.26 0.00 38.89 4.41
1122 1147 0.835971 AAACCAGCACCCCCAATTCC 60.836 55.000 0.00 0.00 0.00 3.01
1149 1174 3.127721 CCCGCTTCTTCAATTTCTCTTCC 59.872 47.826 0.00 0.00 0.00 3.46
1197 1246 1.433064 CTCAGCTCAGCTCCGAGAC 59.567 63.158 8.08 0.00 36.40 3.36
1223 1284 2.184322 GTTCAGCTGGATCCGCGA 59.816 61.111 15.13 16.07 0.00 5.87
1275 1337 3.509575 GTGAGATTAGAGATCGGATGGCT 59.490 47.826 0.00 0.00 0.00 4.75
1276 1338 3.509184 TGAGATTAGAGATCGGATGGCTG 59.491 47.826 0.00 0.00 0.00 4.85
1277 1339 2.830923 AGATTAGAGATCGGATGGCTGG 59.169 50.000 0.00 0.00 0.00 4.85
1278 1340 0.681733 TTAGAGATCGGATGGCTGGC 59.318 55.000 0.00 0.00 0.00 4.85
1288 1350 2.134630 GATGGCTGGCAGATAGGGGG 62.135 65.000 20.86 0.00 0.00 5.40
1291 1353 2.378634 GCTGGCAGATAGGGGGTGT 61.379 63.158 20.86 0.00 0.00 4.16
1309 1371 1.032114 GTCAAGGCTCGATTTGGGGG 61.032 60.000 0.00 0.00 0.00 5.40
1363 1425 1.340017 CCCCGCCATCGAATAATCCAT 60.340 52.381 0.00 0.00 38.10 3.41
1394 1457 0.753262 ACTCTGGTCACGCAAAGTCT 59.247 50.000 0.00 0.00 0.00 3.24
1497 1560 4.503910 GGCAATTTTCCCTTACCACAATC 58.496 43.478 0.00 0.00 0.00 2.67
1552 1616 8.780846 ATCTCGATATAATTGTAGAGACGAGT 57.219 34.615 19.12 11.15 42.96 4.18
1658 1723 1.538512 TGAACGTCTACCTCTGTTCGG 59.461 52.381 0.00 0.00 42.71 4.30
1667 1732 2.530701 ACCTCTGTTCGGTCTCTTGAT 58.469 47.619 0.00 0.00 0.00 2.57
1668 1733 2.232452 ACCTCTGTTCGGTCTCTTGATG 59.768 50.000 0.00 0.00 0.00 3.07
1669 1734 2.493675 CCTCTGTTCGGTCTCTTGATGA 59.506 50.000 0.00 0.00 0.00 2.92
1688 1757 5.874810 TGATGAATTGGACTAGTCTTTTCCG 59.125 40.000 21.88 0.00 31.38 4.30
1740 1809 4.142403 GGAAATGATTCTTGTGCATTCGGA 60.142 41.667 0.00 0.00 35.79 4.55
1805 1874 3.340034 TCCATTACCGAATCAAAGCGTT 58.660 40.909 0.00 0.00 0.00 4.84
1868 1937 4.347360 AAAGGTACTGGTGGTGTACTTC 57.653 45.455 0.00 0.00 40.86 3.01
1882 1951 5.130477 TGGTGTACTTCTCCCTCCATTAATC 59.870 44.000 0.00 0.00 0.00 1.75
1911 1980 7.975058 TGTCAAGTATTCCATAATTGCACATTG 59.025 33.333 0.00 0.00 39.79 2.82
1990 2059 7.594386 TGCTGTGTGATGTGTATTGTAAATTTG 59.406 33.333 0.00 0.00 0.00 2.32
2009 2078 5.804692 TTTGTTATATTGTACCACCTGCG 57.195 39.130 0.00 0.00 0.00 5.18
2015 2084 2.863132 TTGTACCACCTGCGGTAATT 57.137 45.000 0.00 0.00 43.14 1.40
2070 2139 6.582672 GCTAGGTTCAAGAACTGCAAAAATAC 59.417 38.462 12.22 0.00 40.94 1.89
2088 2157 9.180678 CAAAAATACAAAGATGTGTTACCAGAC 57.819 33.333 0.00 0.00 39.62 3.51
2130 2199 4.389890 ACAGTACGTACCAAGTTTGTCA 57.610 40.909 21.80 0.00 0.00 3.58
2445 2515 2.811317 GCCTCGAGGTTGCTGACG 60.811 66.667 31.43 4.23 37.57 4.35
2446 2516 2.962569 CCTCGAGGTTGCTGACGA 59.037 61.111 24.04 0.00 0.00 4.20
2447 2517 1.444553 CCTCGAGGTTGCTGACGAC 60.445 63.158 24.04 0.00 0.00 4.34
2585 2655 4.036380 GGGGTCATAATTCGGTTTGTCATC 59.964 45.833 0.00 0.00 0.00 2.92
2599 2669 1.480545 TGTCATCGGTCACAGGTATGG 59.519 52.381 0.00 0.00 0.00 2.74
2712 2782 7.949903 AACGTGTCATAAATTGTACACAGTA 57.050 32.000 0.00 0.00 41.79 2.74
2728 2801 6.178239 ACACAGTAACTCTTTTGTCACAAC 57.822 37.500 0.00 0.00 0.00 3.32
2923 3001 2.878406 ACCACTGCATACAACACAAGAC 59.122 45.455 0.00 0.00 0.00 3.01
2930 3008 4.881273 TGCATACAACACAAGACAGACTTT 59.119 37.500 0.00 0.00 36.61 2.66
2934 3012 7.095229 GCATACAACACAAGACAGACTTTCATA 60.095 37.037 0.00 0.00 36.61 2.15
3069 3147 7.442666 GGAGTATGATTTAGGAGTGGTTTCATC 59.557 40.741 0.00 0.00 0.00 2.92
3098 3347 9.826574 ACTTTTGAGTTTAGTAATATCCGCATA 57.173 29.630 0.00 0.00 0.00 3.14
3136 3385 5.711698 TGAGGGGTCCTTTTATTTGTTCTT 58.288 37.500 0.00 0.00 31.76 2.52
3176 3429 8.610035 GGCTGTAGAATAATGGTTGTTAAGTAC 58.390 37.037 0.00 0.00 0.00 2.73
3203 3456 8.889717 TGTAGTCTCAGTTTTCCACTTTAAAAG 58.110 33.333 0.00 0.00 30.92 2.27
3236 3489 6.817140 AGAGTTTGGACAAGGTATTTATCGAC 59.183 38.462 0.00 0.00 0.00 4.20
3258 3511 8.415553 TCGACGGAGAGGATATTGTTAAAATAA 58.584 33.333 0.00 0.00 0.00 1.40
3305 3558 9.915629 GTTAAGTCATGCATAGCTTATAGTAGT 57.084 33.333 17.44 0.00 0.00 2.73
3308 3561 9.521841 AAGTCATGCATAGCTTATAGTAGTAGA 57.478 33.333 11.73 0.00 0.00 2.59
3309 3562 8.952278 AGTCATGCATAGCTTATAGTAGTAGAC 58.048 37.037 0.00 0.00 0.00 2.59
3504 3761 2.412847 GGAGTGACGCTGTTATTGTTGC 60.413 50.000 0.00 0.00 0.00 4.17
3724 3981 2.134789 ATGCCCTTTACAGCTCCAAG 57.865 50.000 0.00 0.00 0.00 3.61
3751 4010 1.128692 GGCTAAATGAGTGTGTGCGTC 59.871 52.381 0.00 0.00 0.00 5.19
3765 4024 2.289631 TGTGCGTCCATCTGTCATTTCT 60.290 45.455 0.00 0.00 0.00 2.52
3769 4028 3.307242 GCGTCCATCTGTCATTTCTGTAC 59.693 47.826 0.00 0.00 0.00 2.90
3853 4113 6.622427 ACCACCCTAACTAGGATAATATGC 57.378 41.667 4.23 0.00 46.63 3.14
3860 4120 7.202011 CCCTAACTAGGATAATATGCGGCTATT 60.202 40.741 4.23 5.83 46.63 1.73
3891 4151 0.383949 GTGCGTGAAAAAGGCCTTGA 59.616 50.000 21.33 0.11 38.97 3.02
3892 4152 0.383949 TGCGTGAAAAAGGCCTTGAC 59.616 50.000 21.33 13.81 38.97 3.18
3893 4153 0.383949 GCGTGAAAAAGGCCTTGACA 59.616 50.000 21.33 16.30 33.42 3.58
3895 4155 2.922335 GCGTGAAAAAGGCCTTGACATC 60.922 50.000 21.33 14.99 33.42 3.06
3896 4156 2.351738 CGTGAAAAAGGCCTTGACATCC 60.352 50.000 21.33 5.03 0.00 3.51
3897 4157 1.885887 TGAAAAAGGCCTTGACATCCG 59.114 47.619 21.33 0.00 0.00 4.18
3898 4158 2.159382 GAAAAAGGCCTTGACATCCGA 58.841 47.619 21.33 0.00 0.00 4.55
3899 4159 2.514458 AAAAGGCCTTGACATCCGAT 57.486 45.000 21.33 0.00 0.00 4.18
3900 4160 2.044123 AAAGGCCTTGACATCCGATC 57.956 50.000 21.33 0.00 0.00 3.69
3903 4168 1.561542 AGGCCTTGACATCCGATCTTT 59.438 47.619 0.00 0.00 0.00 2.52
3909 4174 5.731686 GCCTTGACATCCGATCTTTCATTTC 60.732 44.000 0.00 0.00 0.00 2.17
3968 4233 4.019321 TGGAAGCCAAGAGTATATATGGGC 60.019 45.833 0.00 0.00 40.18 5.36
4008 4273 7.493367 CCCTGTCCTATCTGAAAAGTAAGTAG 58.507 42.308 0.00 0.00 0.00 2.57
4054 4739 5.725551 TGGATCTCTCCTTCTCTTAGAGT 57.274 43.478 9.25 0.00 42.59 3.24
4064 4765 5.602978 TCCTTCTCTTAGAGTTCAAAGGTGT 59.397 40.000 20.04 0.00 34.00 4.16
4077 4778 6.828785 AGTTCAAAGGTGTTAAGATCTGTTGT 59.171 34.615 0.00 0.00 0.00 3.32
4127 4828 2.054232 ATGAGCCTGAGCATTGGAAG 57.946 50.000 0.00 0.00 43.56 3.46
4136 4837 0.605319 AGCATTGGAAGTTCGGCGAA 60.605 50.000 19.83 19.83 0.00 4.70
4151 4852 3.133362 TCGGCGAACCAGGAAATAAGTAT 59.867 43.478 7.35 0.00 34.57 2.12
4211 4912 8.704668 TCAAAAGATCTAGCAACCTACATATCA 58.295 33.333 0.00 0.00 0.00 2.15
4252 4953 6.805713 TCATAAGTTCTCATGTAATCTCGCA 58.194 36.000 0.00 0.00 0.00 5.10
4257 4958 4.046938 TCTCATGTAATCTCGCACTTCC 57.953 45.455 0.00 0.00 0.00 3.46
4263 4964 4.832248 TGTAATCTCGCACTTCCATCTTT 58.168 39.130 0.00 0.00 0.00 2.52
4265 4966 6.403049 TGTAATCTCGCACTTCCATCTTTTA 58.597 36.000 0.00 0.00 0.00 1.52
4285 4992 7.669722 TCTTTTATGGTTCTGGTGAAAGCTAAT 59.330 33.333 0.00 0.00 33.52 1.73
4289 4996 6.084326 TGGTTCTGGTGAAAGCTAATTTTC 57.916 37.500 0.00 0.00 37.53 2.29
4300 5007 6.707161 TGAAAGCTAATTTTCTTGCTGCAAAT 59.293 30.769 16.74 3.99 37.81 2.32
4304 5011 6.148315 AGCTAATTTTCTTGCTGCAAATTTCC 59.852 34.615 16.74 7.49 34.37 3.13
4305 5012 6.073112 GCTAATTTTCTTGCTGCAAATTTCCA 60.073 34.615 16.74 0.00 34.37 3.53
4311 5018 6.783892 TCTTGCTGCAAATTTCCATTTAAC 57.216 33.333 16.74 0.00 30.90 2.01
4326 5033 1.534336 TTAACGCCAGGCACGTCCTA 61.534 55.000 13.30 0.00 45.52 2.94
4439 5146 0.038744 CCACCTGGTGAGCTTCCATT 59.961 55.000 27.94 1.09 35.23 3.16
4445 5152 1.559682 TGGTGAGCTTCCATTACTCCC 59.440 52.381 7.38 0.00 0.00 4.30
4449 5156 2.846206 TGAGCTTCCATTACTCCCATGT 59.154 45.455 0.00 0.00 0.00 3.21
4466 5176 9.004231 ACTCCCATGTCTTATAACTCCTTAATT 57.996 33.333 0.00 0.00 0.00 1.40
4681 5392 3.695830 TGGAATTCCACTTTCTAGCGT 57.304 42.857 23.63 0.00 42.01 5.07
4701 5412 0.320508 GGTCGGAACCCTGACTGAAC 60.321 60.000 0.00 0.00 45.72 3.18
4723 5434 3.099141 CAGAAGAAGCTCTCCTCTCCTT 58.901 50.000 0.00 0.00 0.00 3.36
4724 5435 3.131046 CAGAAGAAGCTCTCCTCTCCTTC 59.869 52.174 0.00 0.00 35.19 3.46
4725 5436 2.917713 AGAAGCTCTCCTCTCCTTCA 57.082 50.000 0.00 0.00 36.91 3.02
5093 5810 6.153510 GGCTCACTCTAAATGAAAGGGAAAAT 59.846 38.462 0.00 0.00 0.00 1.82
5117 5834 3.071874 TGATCTGCCGTTCCAAAGATT 57.928 42.857 0.00 0.00 29.59 2.40
5124 5841 5.067936 TCTGCCGTTCCAAAGATTTTGTAAA 59.932 36.000 1.40 0.00 0.00 2.01
5126 5843 6.982852 TGCCGTTCCAAAGATTTTGTAAATA 58.017 32.000 1.40 0.00 0.00 1.40
5143 5860 6.493978 TGTAAATATGTGATGTGATTTGCCG 58.506 36.000 0.00 0.00 0.00 5.69
5200 5919 2.656947 AAGCAAACCACTAGAGCCAA 57.343 45.000 0.00 0.00 0.00 4.52
5207 5926 4.917906 AACCACTAGAGCCAAAAGATCT 57.082 40.909 0.00 0.00 45.27 2.75
5235 5954 0.955919 TTCACACCGCACACACACAA 60.956 50.000 0.00 0.00 0.00 3.33
5237 5956 0.523125 CACACCGCACACACACAAAG 60.523 55.000 0.00 0.00 0.00 2.77
5238 5957 0.958382 ACACCGCACACACACAAAGT 60.958 50.000 0.00 0.00 0.00 2.66
5240 5959 1.011333 ACCGCACACACACAAAGTAC 58.989 50.000 0.00 0.00 0.00 2.73
5241 5960 0.042535 CCGCACACACACAAAGTACG 60.043 55.000 0.00 0.00 0.00 3.67
5250 5987 1.893801 ACACAAAGTACGAGAGAGGGG 59.106 52.381 0.00 0.00 0.00 4.79
5251 5988 0.896226 ACAAAGTACGAGAGAGGGGC 59.104 55.000 0.00 0.00 0.00 5.80
5273 6010 0.517316 GCTAAGGGCACAACTCAACG 59.483 55.000 0.00 0.00 41.35 4.10
5274 6011 1.156736 CTAAGGGCACAACTCAACGG 58.843 55.000 0.00 0.00 0.00 4.44
5280 6017 1.528309 CACAACTCAACGGGCCCTT 60.528 57.895 22.43 7.92 0.00 3.95
5281 6018 1.528309 ACAACTCAACGGGCCCTTG 60.528 57.895 22.43 21.87 0.00 3.61
5287 6032 2.224917 ACTCAACGGGCCCTTGATAAAA 60.225 45.455 26.88 12.12 0.00 1.52
5292 6037 1.813786 CGGGCCCTTGATAAAACGAAA 59.186 47.619 22.43 0.00 0.00 3.46
5293 6038 2.229302 CGGGCCCTTGATAAAACGAAAA 59.771 45.455 22.43 0.00 0.00 2.29
5294 6039 3.672241 CGGGCCCTTGATAAAACGAAAAG 60.672 47.826 22.43 0.00 0.00 2.27
5445 6190 1.453928 GGCTAAGAGGCCGCCAAAT 60.454 57.895 13.15 0.00 42.82 2.32
5461 6206 3.431207 GCCAAATCTGCAAATAGCCACAT 60.431 43.478 0.00 0.00 44.83 3.21
5471 6216 7.760794 TCTGCAAATAGCCACATATTTTGAAAG 59.239 33.333 0.00 0.00 44.83 2.62
5476 6221 2.673610 GCCACATATTTTGAAAGCCGCA 60.674 45.455 0.00 0.00 0.00 5.69
5503 6248 0.583438 CACGTTGAAGAGGCACACAG 59.417 55.000 0.00 0.00 0.00 3.66
5514 6259 1.074405 AGGCACACAGTGGATCACAAT 59.926 47.619 5.31 0.00 36.74 2.71
5530 6275 7.340743 TGGATCACAATTTTATTACGGACCATT 59.659 33.333 0.00 0.00 0.00 3.16
5544 6289 1.880027 GACCATTCAAAGCGTCCAAGT 59.120 47.619 0.00 0.00 0.00 3.16
5563 6308 3.538387 AGTTAGAACCCCAATACCCAGT 58.462 45.455 0.00 0.00 0.00 4.00
5567 6312 0.326927 AACCCCAATACCCAGTCACG 59.673 55.000 0.00 0.00 0.00 4.35
5595 6341 1.376037 GGAAACGCTGTGGAGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
5635 6381 0.673437 CGGGGAAGTTGTTGTTGCAT 59.327 50.000 0.00 0.00 0.00 3.96
5642 6394 4.496673 GGAAGTTGTTGTTGCATCAACGTA 60.497 41.667 27.10 18.48 46.13 3.57
5673 6425 0.183971 TCCCGGAAGCAACTCCAAAA 59.816 50.000 0.73 0.00 34.91 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.077095 ACCCCTAAACCTTCAAATCCTAAAAA 58.923 34.615 0.00 0.00 0.00 1.94
30 31 6.626238 ACCCCTAAACCTTCAAATCCTAAAA 58.374 36.000 0.00 0.00 0.00 1.52
31 32 6.222227 ACCCCTAAACCTTCAAATCCTAAA 57.778 37.500 0.00 0.00 0.00 1.85
32 33 5.871324 ACCCCTAAACCTTCAAATCCTAA 57.129 39.130 0.00 0.00 0.00 2.69
33 34 6.034003 AGTACCCCTAAACCTTCAAATCCTA 58.966 40.000 0.00 0.00 0.00 2.94
34 35 4.856182 AGTACCCCTAAACCTTCAAATCCT 59.144 41.667 0.00 0.00 0.00 3.24
35 36 5.188988 AGTACCCCTAAACCTTCAAATCC 57.811 43.478 0.00 0.00 0.00 3.01
36 37 6.955364 AGTAGTACCCCTAAACCTTCAAATC 58.045 40.000 0.00 0.00 0.00 2.17
37 38 6.964876 AGTAGTACCCCTAAACCTTCAAAT 57.035 37.500 0.00 0.00 0.00 2.32
38 39 7.018769 ACTAGTAGTACCCCTAAACCTTCAAA 58.981 38.462 0.00 0.00 0.00 2.69
39 40 6.565036 ACTAGTAGTACCCCTAAACCTTCAA 58.435 40.000 0.00 0.00 0.00 2.69
40 41 6.157862 ACTAGTAGTACCCCTAAACCTTCA 57.842 41.667 0.00 0.00 0.00 3.02
41 42 8.637099 CATTACTAGTAGTACCCCTAAACCTTC 58.363 40.741 9.62 0.00 28.93 3.46
42 43 7.070447 GCATTACTAGTAGTACCCCTAAACCTT 59.930 40.741 9.62 0.00 28.93 3.50
43 44 6.552725 GCATTACTAGTAGTACCCCTAAACCT 59.447 42.308 9.62 0.00 28.93 3.50
44 45 6.552725 AGCATTACTAGTAGTACCCCTAAACC 59.447 42.308 9.62 0.00 28.93 3.27
45 46 7.505248 AGAGCATTACTAGTAGTACCCCTAAAC 59.495 40.741 9.62 0.00 28.93 2.01
46 47 7.589993 AGAGCATTACTAGTAGTACCCCTAAA 58.410 38.462 9.62 0.00 28.93 1.85
47 48 7.159201 AGAGCATTACTAGTAGTACCCCTAA 57.841 40.000 9.62 0.00 28.93 2.69
48 49 6.776887 AGAGCATTACTAGTAGTACCCCTA 57.223 41.667 9.62 0.00 28.93 3.53
49 50 5.666474 AGAGCATTACTAGTAGTACCCCT 57.334 43.478 9.62 6.11 28.93 4.79
50 51 7.174772 GTCTAAGAGCATTACTAGTAGTACCCC 59.825 44.444 9.62 1.59 28.93 4.95
51 52 7.174772 GGTCTAAGAGCATTACTAGTAGTACCC 59.825 44.444 9.62 1.92 28.93 3.69
52 53 7.718753 TGGTCTAAGAGCATTACTAGTAGTACC 59.281 40.741 9.62 6.53 35.04 3.34
53 54 8.674263 TGGTCTAAGAGCATTACTAGTAGTAC 57.326 38.462 9.62 0.00 35.04 2.73
54 55 8.492782 ACTGGTCTAAGAGCATTACTAGTAGTA 58.507 37.037 5.90 5.90 39.36 1.82
55 56 7.348033 ACTGGTCTAAGAGCATTACTAGTAGT 58.652 38.462 8.14 8.14 39.36 2.73
56 57 7.811117 ACTGGTCTAAGAGCATTACTAGTAG 57.189 40.000 2.23 0.00 39.36 2.57
57 58 7.440556 CGTACTGGTCTAAGAGCATTACTAGTA 59.559 40.741 2.91 0.00 41.04 1.82
58 59 6.260493 CGTACTGGTCTAAGAGCATTACTAGT 59.740 42.308 0.00 0.00 41.04 2.57
59 60 6.482641 TCGTACTGGTCTAAGAGCATTACTAG 59.517 42.308 2.91 5.99 41.04 2.57
60 61 6.351711 TCGTACTGGTCTAAGAGCATTACTA 58.648 40.000 2.91 0.00 41.04 1.82
61 62 5.191426 TCGTACTGGTCTAAGAGCATTACT 58.809 41.667 2.91 0.00 41.04 2.24
62 63 5.496133 TCGTACTGGTCTAAGAGCATTAC 57.504 43.478 0.00 0.00 40.36 1.89
63 64 6.519679 TTTCGTACTGGTCTAAGAGCATTA 57.480 37.500 0.00 0.00 39.36 1.90
64 65 5.401531 TTTCGTACTGGTCTAAGAGCATT 57.598 39.130 0.00 0.00 39.36 3.56
65 66 5.169295 GTTTTCGTACTGGTCTAAGAGCAT 58.831 41.667 0.00 0.00 39.36 3.79
66 67 4.553323 GTTTTCGTACTGGTCTAAGAGCA 58.447 43.478 0.00 0.00 37.74 4.26
67 68 3.607209 CGTTTTCGTACTGGTCTAAGAGC 59.393 47.826 0.00 0.00 38.65 4.09
68 69 3.607209 GCGTTTTCGTACTGGTCTAAGAG 59.393 47.826 0.00 0.00 46.03 2.85
69 70 3.568538 GCGTTTTCGTACTGGTCTAAGA 58.431 45.455 0.00 0.00 46.03 2.10
70 71 2.340577 CGCGTTTTCGTACTGGTCTAAG 59.659 50.000 0.00 0.00 46.03 2.18
78 79 2.156310 GGTCAAATCGCGTTTTCGTACT 59.844 45.455 12.03 0.00 46.03 2.73
203 205 4.995058 GGTGGGGTGGGGTGAGGA 62.995 72.222 0.00 0.00 0.00 3.71
227 234 4.269523 TTGCTTGCAGCGGAGGGT 62.270 61.111 0.00 0.00 46.26 4.34
228 235 3.437795 CTTGCTTGCAGCGGAGGG 61.438 66.667 0.00 0.00 46.26 4.30
229 236 2.670934 ACTTGCTTGCAGCGGAGG 60.671 61.111 12.41 3.04 46.26 4.30
254 261 2.358860 CTGCTGCTGCTGCTGAGT 60.359 61.111 27.67 0.00 40.01 3.41
320 331 1.807165 CGGCGCGGATAGATGGATG 60.807 63.158 9.72 0.00 0.00 3.51
482 494 0.312729 GTGGTGGCGGGTAAAACAAG 59.687 55.000 0.00 0.00 0.00 3.16
913 935 0.886490 CACCTTCTCCCACAGTGCAC 60.886 60.000 9.40 9.40 0.00 4.57
958 980 3.558099 CTCGTCGCCACTGACAGCA 62.558 63.158 1.25 0.00 38.84 4.41
1023 1048 1.450312 CTTGGACACGCCTCCATCC 60.450 63.158 2.59 0.00 40.18 3.51
1111 1136 2.620464 GGAGGGGGAATTGGGGGT 60.620 66.667 0.00 0.00 0.00 4.95
1122 1147 0.034089 AATTGAAGAAGCGGGAGGGG 60.034 55.000 0.00 0.00 0.00 4.79
1149 1174 0.540454 TGAGCTGAGCTGGGAATCTG 59.460 55.000 13.71 0.00 39.88 2.90
1197 1246 1.098869 TCCAGCTGAACTCGAGCTAG 58.901 55.000 17.39 9.48 45.24 3.42
1223 1284 3.753434 CAGAGGCTGGCGAGACGT 61.753 66.667 0.00 0.00 29.20 4.34
1275 1337 0.548926 TTGACACCCCCTATCTGCCA 60.549 55.000 0.00 0.00 0.00 4.92
1276 1338 0.181350 CTTGACACCCCCTATCTGCC 59.819 60.000 0.00 0.00 0.00 4.85
1277 1339 0.181350 CCTTGACACCCCCTATCTGC 59.819 60.000 0.00 0.00 0.00 4.26
1278 1340 0.181350 GCCTTGACACCCCCTATCTG 59.819 60.000 0.00 0.00 0.00 2.90
1288 1350 0.804989 CCCAAATCGAGCCTTGACAC 59.195 55.000 6.32 0.00 0.00 3.67
1291 1353 1.302949 CCCCCAAATCGAGCCTTGA 59.697 57.895 6.32 0.00 0.00 3.02
1331 1393 2.115291 GGCGGGGCAGAATGAAGAC 61.115 63.158 0.00 0.00 39.69 3.01
1363 1425 2.171659 TGACCAGAGTAGCCAAAACACA 59.828 45.455 0.00 0.00 0.00 3.72
1394 1457 2.336945 ATTCGGCAGCATCAGAATCA 57.663 45.000 0.00 0.00 0.00 2.57
1505 1569 2.107750 CGCAGGATCATCCGCACT 59.892 61.111 17.22 0.00 42.75 4.40
1552 1616 8.540388 GGAGGATACATCACCTAGCAATAATAA 58.460 37.037 0.00 0.00 36.57 1.40
1658 1723 6.872920 AGACTAGTCCAATTCATCAAGAGAC 58.127 40.000 19.38 0.00 0.00 3.36
1667 1732 5.223449 ACGGAAAAGACTAGTCCAATTCA 57.777 39.130 19.38 0.00 0.00 2.57
1668 1733 5.617087 GCAACGGAAAAGACTAGTCCAATTC 60.617 44.000 19.38 18.51 0.00 2.17
1669 1734 4.215613 GCAACGGAAAAGACTAGTCCAATT 59.784 41.667 19.38 11.63 0.00 2.32
1688 1757 0.229753 CGGTCGAATAGCATCGCAAC 59.770 55.000 0.00 0.00 42.44 4.17
1740 1809 3.972133 TCCACATTCTGGATCAAGCAAT 58.028 40.909 0.00 0.00 44.99 3.56
1788 1857 2.739913 CCTCAACGCTTTGATTCGGTAA 59.260 45.455 6.04 0.00 41.05 2.85
1805 1874 2.260822 ACTAGAGCTTTGCCTTCCTCA 58.739 47.619 0.00 0.00 0.00 3.86
1868 1937 5.130145 ACTTGACAGAGATTAATGGAGGGAG 59.870 44.000 0.00 0.00 0.00 4.30
1882 1951 7.066163 TGTGCAATTATGGAATACTTGACAGAG 59.934 37.037 0.00 0.00 40.64 3.35
1911 1980 6.148315 TGCAGCTGCTGTACAATATGAATATC 59.852 38.462 36.61 8.40 42.66 1.63
2015 2084 9.783081 ACATGATAATCAAACTATGTATCAGCA 57.217 29.630 0.00 0.00 0.00 4.41
2070 2139 5.063204 TCTTGGTCTGGTAACACATCTTTG 58.937 41.667 0.00 0.00 46.17 2.77
2088 2157 7.440198 ACTGTACATCATGATGAGTATCTTGG 58.560 38.462 36.37 18.87 41.20 3.61
2130 2199 7.472334 AAGGAACAAATATGTGCTCAAGAAT 57.528 32.000 0.00 0.00 40.46 2.40
2180 2250 2.158623 TGCCAGTCAGTCAGAACCATTT 60.159 45.455 0.00 0.00 0.00 2.32
2445 2515 8.669243 AGCAAGTTAGCTATAAAGTTGAATGTC 58.331 33.333 16.17 2.18 44.50 3.06
2446 2516 8.567285 AGCAAGTTAGCTATAAAGTTGAATGT 57.433 30.769 16.17 0.00 44.50 2.71
2447 2517 9.495754 GAAGCAAGTTAGCTATAAAGTTGAATG 57.504 33.333 16.17 0.00 45.89 2.67
2585 2655 0.107703 ATGCACCATACCTGTGACCG 60.108 55.000 0.00 0.00 35.74 4.79
2740 2816 8.673626 AAAATGACAAAAGATATACAACTGCG 57.326 30.769 0.00 0.00 0.00 5.18
2993 3071 8.464770 TTTTCTCAAAGTCAAACATCACAAAG 57.535 30.769 0.00 0.00 0.00 2.77
3024 3102 1.296145 CTTCACAATGTAGCGCGCG 60.296 57.895 28.44 28.44 0.00 6.86
3069 3147 7.908601 GCGGATATTACTAAACTCAAAAGTTGG 59.091 37.037 0.00 0.00 45.07 3.77
3098 3347 1.558756 CCCTCAAGCCTCAAGATCAGT 59.441 52.381 0.00 0.00 0.00 3.41
3136 3385 2.645838 ACAGCCTTCTCTTGCAGAAA 57.354 45.000 0.00 0.00 40.83 2.52
3176 3429 8.433421 TTTAAAGTGGAAAACTGAGACTACAG 57.567 34.615 0.00 0.00 39.81 2.74
3203 3456 1.967319 TGTCCAAACTCTGAAGCCAC 58.033 50.000 0.00 0.00 0.00 5.01
3205 3458 1.882623 CCTTGTCCAAACTCTGAAGCC 59.117 52.381 0.00 0.00 0.00 4.35
3305 3558 7.646526 CCATAAACGTACATTCATTCTCGTCTA 59.353 37.037 0.00 0.00 0.00 2.59
3306 3559 6.475727 CCATAAACGTACATTCATTCTCGTCT 59.524 38.462 0.00 0.00 0.00 4.18
3307 3560 6.637365 CCATAAACGTACATTCATTCTCGTC 58.363 40.000 0.00 0.00 0.00 4.20
3308 3561 5.006358 GCCATAAACGTACATTCATTCTCGT 59.994 40.000 0.00 0.00 0.00 4.18
3309 3562 5.006261 TGCCATAAACGTACATTCATTCTCG 59.994 40.000 0.00 0.00 0.00 4.04
3504 3761 3.094572 AGCATTTCAGTCCAAATGAGGG 58.905 45.455 9.57 0.00 43.70 4.30
3724 3981 3.279434 CACACTCATTTAGCCCCTAACC 58.721 50.000 0.00 0.00 0.00 2.85
3751 4010 6.402983 GCTTTGAGTACAGAAATGACAGATGG 60.403 42.308 0.00 0.00 0.00 3.51
3853 4113 3.181397 CACAGGAATGCAAAAATAGCCG 58.819 45.455 0.00 0.00 0.00 5.52
3860 4120 1.028130 TCACGCACAGGAATGCAAAA 58.972 45.000 0.00 0.00 46.47 2.44
3877 4137 1.885887 CGGATGTCAAGGCCTTTTTCA 59.114 47.619 17.61 15.27 0.00 2.69
3891 4151 3.629398 GCTGGAAATGAAAGATCGGATGT 59.371 43.478 0.00 0.00 0.00 3.06
3892 4152 3.628942 TGCTGGAAATGAAAGATCGGATG 59.371 43.478 0.00 0.00 0.00 3.51
3893 4153 3.889815 TGCTGGAAATGAAAGATCGGAT 58.110 40.909 0.00 0.00 0.00 4.18
3895 4155 3.728864 CGTTGCTGGAAATGAAAGATCGG 60.729 47.826 0.00 0.00 0.00 4.18
3896 4156 3.419915 CGTTGCTGGAAATGAAAGATCG 58.580 45.455 0.00 0.00 0.00 3.69
3897 4157 3.119708 AGCGTTGCTGGAAATGAAAGATC 60.120 43.478 0.00 0.00 37.57 2.75
3898 4158 2.821969 AGCGTTGCTGGAAATGAAAGAT 59.178 40.909 0.00 0.00 37.57 2.40
3899 4159 2.229792 AGCGTTGCTGGAAATGAAAGA 58.770 42.857 0.00 0.00 37.57 2.52
3900 4160 2.712057 AGCGTTGCTGGAAATGAAAG 57.288 45.000 0.00 0.00 37.57 2.62
3903 4168 0.597568 CCAAGCGTTGCTGGAAATGA 59.402 50.000 0.00 0.00 39.62 2.57
3909 4174 0.957395 ATCTGTCCAAGCGTTGCTGG 60.957 55.000 0.00 0.00 39.62 4.85
3968 4233 0.744874 CAGGGCCAGATTTCATGCAG 59.255 55.000 6.18 0.00 0.00 4.41
4051 4736 7.012421 ACAACAGATCTTAACACCTTTGAACTC 59.988 37.037 0.00 0.00 0.00 3.01
4054 4739 7.054124 AGACAACAGATCTTAACACCTTTGAA 58.946 34.615 0.00 0.00 0.00 2.69
4085 4786 2.044793 ATCTCACACCCCTGGAGAAA 57.955 50.000 0.00 0.00 40.71 2.52
4086 4787 2.044492 AGTATCTCACACCCCTGGAGAA 59.956 50.000 0.00 0.00 40.71 2.87
4127 4828 1.729284 TATTTCCTGGTTCGCCGAAC 58.271 50.000 21.20 21.20 41.32 3.95
4151 4852 0.108520 GACCGGTAGCATGTCGGAAA 60.109 55.000 7.34 0.00 45.96 3.13
4226 4927 7.928167 TGCGAGATTACATGAGAACTTATGATT 59.072 33.333 12.31 0.00 31.82 2.57
4243 4944 6.483307 CCATAAAAGATGGAAGTGCGAGATTA 59.517 38.462 0.00 0.00 41.64 1.75
4248 4949 3.950397 ACCATAAAAGATGGAAGTGCGA 58.050 40.909 10.52 0.00 41.64 5.10
4252 4953 5.711976 CACCAGAACCATAAAAGATGGAAGT 59.288 40.000 10.52 0.00 41.64 3.01
4257 4958 6.071728 AGCTTTCACCAGAACCATAAAAGATG 60.072 38.462 0.00 0.00 32.39 2.90
4263 4964 7.775053 AAATTAGCTTTCACCAGAACCATAA 57.225 32.000 0.00 0.00 32.39 1.90
4265 4966 6.494835 AGAAAATTAGCTTTCACCAGAACCAT 59.505 34.615 0.00 0.00 37.70 3.55
4285 4992 6.696441 AAATGGAAATTTGCAGCAAGAAAA 57.304 29.167 17.67 0.00 30.13 2.29
4289 4996 5.610975 CGTTAAATGGAAATTTGCAGCAAG 58.389 37.500 17.67 3.91 30.13 4.01
4300 5007 1.271102 GTGCCTGGCGTTAAATGGAAA 59.729 47.619 14.98 0.00 0.00 3.13
4304 5011 0.179200 GACGTGCCTGGCGTTAAATG 60.179 55.000 14.98 3.86 43.04 2.32
4305 5012 1.303091 GGACGTGCCTGGCGTTAAAT 61.303 55.000 14.98 0.00 43.04 1.40
4392 5099 0.811915 AACAGAGTCTCCGGTCATCG 59.188 55.000 0.00 0.00 38.88 3.84
4439 5146 9.670442 ATTAAGGAGTTATAAGACATGGGAGTA 57.330 33.333 0.00 0.00 0.00 2.59
4445 5152 9.326413 ACGGAAATTAAGGAGTTATAAGACATG 57.674 33.333 0.00 0.00 0.00 3.21
4449 5156 8.533657 TGTCACGGAAATTAAGGAGTTATAAGA 58.466 33.333 0.00 0.00 0.00 2.10
4651 5362 0.326595 TGGAATTCCACAGCGCCTTA 59.673 50.000 23.63 0.00 42.01 2.69
4701 5412 1.756538 GGAGAGGAGAGCTTCTTCTGG 59.243 57.143 12.83 0.00 41.86 3.86
4765 5477 7.432148 ACCTACAGGATGAATTACATACACA 57.568 36.000 1.29 0.00 42.01 3.72
4875 5587 2.781595 TTCGCCTTCACCTTCGCCTC 62.782 60.000 0.00 0.00 0.00 4.70
4876 5588 2.788191 CTTCGCCTTCACCTTCGCCT 62.788 60.000 0.00 0.00 0.00 5.52
4877 5589 2.358247 TTCGCCTTCACCTTCGCC 60.358 61.111 0.00 0.00 0.00 5.54
4878 5590 3.028366 GCTTCGCCTTCACCTTCGC 62.028 63.158 0.00 0.00 0.00 4.70
4879 5591 1.630244 CTGCTTCGCCTTCACCTTCG 61.630 60.000 0.00 0.00 0.00 3.79
4880 5592 1.301677 CCTGCTTCGCCTTCACCTTC 61.302 60.000 0.00 0.00 0.00 3.46
4896 5608 0.317938 GCGACAGCTCGTATACCCTG 60.318 60.000 9.89 9.89 42.33 4.45
4904 5616 4.742201 AATGCGGCGACAGCTCGT 62.742 61.111 12.98 0.00 42.33 4.18
5048 5764 3.004734 GCCTCAGCTGTTACAAACACAAT 59.995 43.478 14.67 0.00 36.25 2.71
5093 5810 2.488204 TTGGAACGGCAGATCATGAA 57.512 45.000 0.00 0.00 0.00 2.57
5117 5834 7.487509 CGGCAAATCACATCACATATTTACAAA 59.512 33.333 0.00 0.00 0.00 2.83
5124 5841 3.216800 AGCGGCAAATCACATCACATAT 58.783 40.909 1.45 0.00 0.00 1.78
5126 5843 1.466856 AGCGGCAAATCACATCACAT 58.533 45.000 1.45 0.00 0.00 3.21
5143 5860 3.734231 GTGAAAGCCTTTTTCGGTAAAGC 59.266 43.478 0.00 0.00 34.51 3.51
5194 5911 6.375455 TGAACCTTTATGAGATCTTTTGGCTC 59.625 38.462 0.00 0.00 0.00 4.70
5200 5919 5.643777 CGGTGTGAACCTTTATGAGATCTTT 59.356 40.000 0.00 0.00 0.00 2.52
5207 5926 2.147958 GTGCGGTGTGAACCTTTATGA 58.852 47.619 0.00 0.00 0.00 2.15
5235 5954 0.684805 CAGGCCCCTCTCTCGTACTT 60.685 60.000 0.00 0.00 0.00 2.24
5237 5956 2.787567 GCAGGCCCCTCTCTCGTAC 61.788 68.421 0.00 0.00 0.00 3.67
5238 5957 1.642513 TAGCAGGCCCCTCTCTCGTA 61.643 60.000 0.00 0.00 0.00 3.43
5240 5959 1.743321 CTTAGCAGGCCCCTCTCTCG 61.743 65.000 0.00 0.00 0.00 4.04
5241 5960 1.406860 CCTTAGCAGGCCCCTCTCTC 61.407 65.000 0.00 0.00 31.53 3.20
5273 6010 3.508402 TCTTTTCGTTTTATCAAGGGCCC 59.492 43.478 16.46 16.46 0.00 5.80
5274 6011 4.776795 TCTTTTCGTTTTATCAAGGGCC 57.223 40.909 0.00 0.00 0.00 5.80
5280 6017 4.276431 ACCGCCTTTCTTTTCGTTTTATCA 59.724 37.500 0.00 0.00 0.00 2.15
5281 6018 4.615541 CACCGCCTTTCTTTTCGTTTTATC 59.384 41.667 0.00 0.00 0.00 1.75
5287 6032 1.792118 GCCACCGCCTTTCTTTTCGT 61.792 55.000 0.00 0.00 0.00 3.85
5292 6037 1.302832 CTGAGCCACCGCCTTTCTT 60.303 57.895 0.00 0.00 34.57 2.52
5293 6038 2.348998 CTGAGCCACCGCCTTTCT 59.651 61.111 0.00 0.00 34.57 2.52
5294 6039 2.747855 CCTGAGCCACCGCCTTTC 60.748 66.667 0.00 0.00 34.57 2.62
5371 6116 0.744281 TAGATCTTCGCGTGATGGCA 59.256 50.000 18.51 0.00 0.00 4.92
5445 6190 6.772360 TCAAAATATGTGGCTATTTGCAGA 57.228 33.333 0.00 0.00 45.15 4.26
5461 6206 4.201910 GCTACTGATGCGGCTTTCAAAATA 60.202 41.667 0.00 0.00 0.00 1.40
5471 6216 2.100631 AACGTGCTACTGATGCGGC 61.101 57.895 0.00 0.00 0.00 6.53
5476 6221 2.675317 GCCTCTTCAACGTGCTACTGAT 60.675 50.000 0.00 0.00 0.00 2.90
5503 6248 6.094325 TGGTCCGTAATAAAATTGTGATCCAC 59.906 38.462 0.00 0.00 34.56 4.02
5514 6259 5.181622 ACGCTTTGAATGGTCCGTAATAAAA 59.818 36.000 0.00 0.00 0.00 1.52
5530 6275 3.135994 GGTTCTAACTTGGACGCTTTGA 58.864 45.455 0.00 0.00 0.00 2.69
5544 6289 3.264964 GTGACTGGGTATTGGGGTTCTAA 59.735 47.826 0.00 0.00 0.00 2.10
5580 6325 2.925170 AGCCCTCTCCACAGCGTT 60.925 61.111 0.00 0.00 0.00 4.84
5595 6341 1.432270 CCTCTTCGCGGAAATCCAGC 61.432 60.000 6.13 3.58 35.14 4.85
5635 6381 1.108727 AGGTGGTCGGTGTACGTTGA 61.109 55.000 0.00 0.00 44.69 3.18


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

AutoCloner maintained by Alex Coulton.