Multiple sequence alignment - TraesCS3A01G358400

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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 TraesCS3A01G358400 chr3A 100.000 4523 0 0 1 4523 606577161 606572639 0.000000e+00 8353.0
1 TraesCS3A01G358400 chr3A 88.209 1340 123 11 2510 3825 606517243 606515915 0.000000e+00 1567.0
2 TraesCS3A01G358400 chr3A 99.264 679 5 0 3845 4523 683683154 683682476 0.000000e+00 1227.0
3 TraesCS3A01G358400 chr3A 87.247 792 79 12 982 1762 606519180 606518400 0.000000e+00 883.0
4 TraesCS3A01G358400 chr3A 82.526 784 107 15 886 1653 606446894 606446125 0.000000e+00 662.0
5 TraesCS3A01G358400 chr3A 86.990 392 41 4 145 534 606576639 606576256 2.500000e-117 433.0
6 TraesCS3A01G358400 chr3A 86.990 392 41 4 523 906 606577017 606576628 2.500000e-117 433.0
7 TraesCS3A01G358400 chr3A 92.958 71 5 0 1817 1887 606518132 606518062 2.230000e-18 104.0
8 TraesCS3A01G358400 chr3A 93.220 59 4 0 1763 1821 606518352 606518294 2.240000e-13 87.9
9 TraesCS3A01G358400 chr3D 92.162 2118 131 14 37 2138 463382773 463380675 0.000000e+00 2959.0
10 TraesCS3A01G358400 chr3D 89.158 1402 118 9 2468 3846 463228820 463227430 0.000000e+00 1716.0
11 TraesCS3A01G358400 chr3D 88.913 1380 118 10 2470 3826 463260230 463258863 0.000000e+00 1668.0
12 TraesCS3A01G358400 chr3D 90.302 1258 113 6 2592 3846 463379555 463378304 0.000000e+00 1639.0
13 TraesCS3A01G358400 chr3D 91.938 1104 60 9 680 1773 463262102 463261018 0.000000e+00 1519.0
14 TraesCS3A01G358400 chr3D 85.543 1003 111 18 902 1889 463230555 463229572 0.000000e+00 1018.0
15 TraesCS3A01G358400 chr3D 84.450 791 96 17 886 1664 463199352 463198577 0.000000e+00 754.0
16 TraesCS3A01G358400 chr3D 88.161 397 38 7 145 534 463382297 463381903 8.860000e-127 464.0
17 TraesCS3A01G358400 chr3D 93.493 292 19 0 2179 2470 283239397 283239106 6.950000e-118 435.0
18 TraesCS3A01G358400 chr3D 91.776 304 25 0 2167 2470 15618068 15617765 1.500000e-114 424.0
19 TraesCS3A01G358400 chr3D 87.187 359 34 4 523 873 463382665 463382311 9.120000e-107 398.0
20 TraesCS3A01G358400 chr3D 91.061 179 16 0 1991 2169 463229586 463229408 4.520000e-60 243.0
21 TraesCS3A01G358400 chr3D 91.061 179 16 0 1991 2169 463261001 463260823 4.520000e-60 243.0
22 TraesCS3A01G358400 chr3D 83.230 161 25 2 3851 4010 101542874 101543033 3.650000e-31 147.0
23 TraesCS3A01G358400 chr3D 84.906 106 16 0 532 637 463262208 463262103 1.720000e-19 108.0
24 TraesCS3A01G358400 chr3D 100.000 28 0 0 3 30 463398343 463398316 8.000000e-03 52.8
25 TraesCS3A01G358400 chr3B 87.044 1397 137 13 2468 3832 616646663 616645279 0.000000e+00 1537.0
26 TraesCS3A01G358400 chr3B 90.121 1154 97 8 3 1145 616685541 616684394 0.000000e+00 1483.0
27 TraesCS3A01G358400 chr3B 92.025 953 52 15 811 1762 616648016 616647087 0.000000e+00 1317.0
28 TraesCS3A01G358400 chr3B 91.786 767 53 6 3 763 616648775 616648013 0.000000e+00 1059.0
29 TraesCS3A01G358400 chr3B 83.081 792 93 17 891 1664 616427080 616426312 0.000000e+00 682.0
30 TraesCS3A01G358400 chr3B 87.855 387 44 2 145 528 616685025 616684639 6.900000e-123 451.0
31 TraesCS3A01G358400 chr3B 87.500 392 38 6 523 906 616648633 616648245 4.150000e-120 442.0
32 TraesCS3A01G358400 chr3B 85.969 392 41 9 523 906 616685399 616685014 1.510000e-109 407.0
33 TraesCS3A01G358400 chr3B 89.474 133 7 1 1763 1888 616647037 616646905 1.300000e-35 161.0
34 TraesCS3A01G358400 chr4A 99.122 683 6 0 3841 4523 594269067 594268385 0.000000e+00 1229.0
35 TraesCS3A01G358400 chr4A 94.286 35 1 1 21 54 142342407 142342373 8.000000e-03 52.8
36 TraesCS3A01G358400 chr6B 99.120 682 6 0 3842 4523 95567380 95568061 0.000000e+00 1227.0
37 TraesCS3A01G358400 chrUn 98.811 673 8 0 3851 4523 122297438 122298110 0.000000e+00 1199.0
38 TraesCS3A01G358400 chr5A 98.514 673 10 0 3851 4523 665602004 665602676 0.000000e+00 1188.0
39 TraesCS3A01G358400 chr5A 96.930 684 19 2 3842 4523 665134651 665133968 0.000000e+00 1146.0
40 TraesCS3A01G358400 chr5A 93.493 292 19 0 2179 2470 301231892 301231601 6.950000e-118 435.0
41 TraesCS3A01G358400 chr1D 94.143 683 38 2 3841 4521 235998131 235997449 0.000000e+00 1038.0
42 TraesCS3A01G358400 chr1D 93.836 292 18 0 2179 2470 218258741 218259032 1.490000e-119 440.0
43 TraesCS3A01G358400 chr1D 93.197 294 20 0 2177 2470 7423856 7424149 2.500000e-117 433.0
44 TraesCS3A01G358400 chr4D 89.134 681 49 13 3841 4521 403169676 403169021 0.000000e+00 824.0
45 TraesCS3A01G358400 chr2D 92.208 385 30 0 4137 4521 535017994 535018378 3.080000e-151 545.0
46 TraesCS3A01G358400 chr2B 92.508 307 21 2 2165 2470 691015613 691015918 5.370000e-119 438.0
47 TraesCS3A01G358400 chr5B 92.182 307 24 0 2164 2470 628675072 628675378 6.950000e-118 435.0
48 TraesCS3A01G358400 chr5B 91.857 307 25 0 2164 2470 625095523 625095829 3.230000e-116 429.0
49 TraesCS3A01G358400 chr5B 95.238 42 2 0 12 53 35555826 35555785 2.920000e-07 67.6
50 TraesCS3A01G358400 chr7D 91.776 304 25 0 2167 2470 635569559 635569256 1.500000e-114 424.0


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 TraesCS3A01G358400 chr3A 606572639 606577161 4522 True 3073.000000 8353 91.326667 1 4523 3 chr3A.!!$R4 4522
1 TraesCS3A01G358400 chr3A 683682476 683683154 678 True 1227.000000 1227 99.264000 3845 4523 1 chr3A.!!$R2 678
2 TraesCS3A01G358400 chr3A 606446125 606446894 769 True 662.000000 662 82.526000 886 1653 1 chr3A.!!$R1 767
3 TraesCS3A01G358400 chr3A 606515915 606519180 3265 True 660.475000 1567 90.408500 982 3825 4 chr3A.!!$R3 2843
4 TraesCS3A01G358400 chr3D 463378304 463382773 4469 True 1365.000000 2959 89.453000 37 3846 4 chr3D.!!$R7 3809
5 TraesCS3A01G358400 chr3D 463227430 463230555 3125 True 992.333333 1716 88.587333 902 3846 3 chr3D.!!$R5 2944
6 TraesCS3A01G358400 chr3D 463258863 463262208 3345 True 884.500000 1668 89.204500 532 3826 4 chr3D.!!$R6 3294
7 TraesCS3A01G358400 chr3D 463198577 463199352 775 True 754.000000 754 84.450000 886 1664 1 chr3D.!!$R3 778
8 TraesCS3A01G358400 chr3B 616645279 616648775 3496 True 903.200000 1537 89.565800 3 3832 5 chr3B.!!$R2 3829
9 TraesCS3A01G358400 chr3B 616684394 616685541 1147 True 780.333333 1483 87.981667 3 1145 3 chr3B.!!$R3 1142
10 TraesCS3A01G358400 chr3B 616426312 616427080 768 True 682.000000 682 83.081000 891 1664 1 chr3B.!!$R1 773
11 TraesCS3A01G358400 chr4A 594268385 594269067 682 True 1229.000000 1229 99.122000 3841 4523 1 chr4A.!!$R2 682
12 TraesCS3A01G358400 chr6B 95567380 95568061 681 False 1227.000000 1227 99.120000 3842 4523 1 chr6B.!!$F1 681
13 TraesCS3A01G358400 chrUn 122297438 122298110 672 False 1199.000000 1199 98.811000 3851 4523 1 chrUn.!!$F1 672
14 TraesCS3A01G358400 chr5A 665602004 665602676 672 False 1188.000000 1188 98.514000 3851 4523 1 chr5A.!!$F1 672
15 TraesCS3A01G358400 chr5A 665133968 665134651 683 True 1146.000000 1146 96.930000 3842 4523 1 chr5A.!!$R2 681
16 TraesCS3A01G358400 chr1D 235997449 235998131 682 True 1038.000000 1038 94.143000 3841 4521 1 chr1D.!!$R1 680
17 TraesCS3A01G358400 chr4D 403169021 403169676 655 True 824.000000 824 89.134000 3841 4521 1 chr4D.!!$R1 680

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
118 119 0.103208 GTGAGTCACTAGATGGGCGG 59.897 60.0 16.26 0.0 0.00 6.13 F
2005 2305 0.036765 TTTGGTACTAGCACCTGCCG 60.037 55.0 13.44 0.0 43.38 5.69 F
2178 2478 0.038166 CCGGCAATATACCTGGCCAT 59.962 55.0 5.51 0.0 46.75 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2317 0.443869 GTTGACACATAGTGCTGGCG 59.556 55.0 0.00 0.0 36.98 5.69 R
3240 4697 0.541392 CCTGGTAGTACATGGCAGCA 59.459 55.0 2.06 0.0 0.00 4.41 R
3810 5295 0.908910 TGACGCCCATGGTTAGATGT 59.091 50.0 11.73 0.0 0.00 3.06 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
70 71 4.697828 TGTCCTACATGATTGCGCTTTTAA 59.302 37.500 9.73 0.00 0.00 1.52
79 80 6.024552 TGATTGCGCTTTTAAAGGAGAAAT 57.975 33.333 9.73 6.94 0.00 2.17
118 119 0.103208 GTGAGTCACTAGATGGGCGG 59.897 60.000 16.26 0.00 0.00 6.13
126 127 2.428890 CACTAGATGGGCGGATAGATCC 59.571 54.545 0.00 0.00 43.65 3.36
166 167 3.302555 CATGCGCCTTTTATGTGCTATG 58.697 45.455 4.18 0.00 39.88 2.23
195 196 9.680315 TGGTGTAAAGTTAATTTTTCGTAATGG 57.320 29.630 0.94 0.00 32.01 3.16
231 232 7.607615 ACGTTACTATATGTGGGGTCTTATT 57.392 36.000 0.00 0.00 0.00 1.40
279 280 2.690497 ACATAGCTAGCACACGAGTCAT 59.310 45.455 18.83 0.00 0.00 3.06
289 290 1.159285 CACGAGTCATGCCACATTGT 58.841 50.000 0.00 0.00 0.00 2.71
387 390 1.765314 GCCCAGAGTCACCTGATGTAT 59.235 52.381 0.00 0.00 36.29 2.29
424 427 4.770362 TCTCCGCCCATCCCGTCA 62.770 66.667 0.00 0.00 0.00 4.35
425 428 3.550431 CTCCGCCCATCCCGTCAT 61.550 66.667 0.00 0.00 0.00 3.06
530 533 2.746375 CCCTTACCCTCCATGCGCT 61.746 63.158 9.73 0.00 0.00 5.92
542 549 4.095410 TCCATGCGCTTTTTATGTTCTG 57.905 40.909 9.73 0.00 0.00 3.02
553 560 9.009327 CGCTTTTTATGTTCTGTAATTGGTATG 57.991 33.333 0.00 0.00 0.00 2.39
655 664 0.321671 ACATAGCTGGCACACGAGTT 59.678 50.000 0.00 0.00 0.00 3.01
734 743 1.334384 GGGCCCACAAACAAACTGGT 61.334 55.000 19.95 0.00 0.00 4.00
750 759 1.961277 GGTCCACTTGTCACTGCCG 60.961 63.158 0.00 0.00 0.00 5.69
789 801 1.988107 TGACAATTTGAGCCCCTCTCT 59.012 47.619 2.79 0.00 42.38 3.10
802 814 1.383664 CTCTCTGGCCATCCCCTCA 60.384 63.158 5.51 0.00 0.00 3.86
805 817 4.559063 CTGGCCATCCCCTCAGCG 62.559 72.222 5.51 0.00 0.00 5.18
1024 1046 2.586635 GCGTTGACCACCACGACA 60.587 61.111 0.00 0.00 0.00 4.35
1058 1084 2.204244 GTCCCTTTCCCCTCCCCA 60.204 66.667 0.00 0.00 0.00 4.96
1167 1211 2.683933 CTGGAGGGGCTGTACCGT 60.684 66.667 0.00 0.00 40.62 4.83
1211 1255 3.161067 CCGAGGAGATACATCAGGTGAT 58.839 50.000 0.00 0.00 34.56 3.06
1242 1286 4.241555 GAGCACGGCCCCATCGAT 62.242 66.667 0.00 0.00 0.00 3.59
1398 1451 2.690881 CCCATCTCCCCGGTCCAA 60.691 66.667 0.00 0.00 0.00 3.53
1401 1454 1.522569 CATCTCCCCGGTCCAACTC 59.477 63.158 0.00 0.00 0.00 3.01
1429 1482 4.124351 CGGCGCCGAACACTCCTA 62.124 66.667 44.86 0.00 42.83 2.94
1499 1555 6.424176 TTCGACACGCCATTCAATTAAATA 57.576 33.333 0.00 0.00 0.00 1.40
1502 1558 6.258947 TCGACACGCCATTCAATTAAATATGA 59.741 34.615 0.00 0.00 0.00 2.15
1526 1582 1.471153 TGGCAATTGGCATGCAATACG 60.471 47.619 29.00 12.26 46.12 3.06
1529 1585 2.480073 GCAATTGGCATGCAATACGTCT 60.480 45.455 21.36 0.00 43.29 4.18
1530 1586 3.772932 CAATTGGCATGCAATACGTCTT 58.227 40.909 21.36 0.00 0.00 3.01
1531 1587 2.917701 TTGGCATGCAATACGTCTTG 57.082 45.000 21.36 9.17 0.00 3.02
1532 1588 2.106477 TGGCATGCAATACGTCTTGA 57.894 45.000 21.36 3.57 0.00 3.02
1554 1614 2.368439 TGATTAGCTTCCAAATGCGCT 58.632 42.857 9.73 0.00 36.56 5.92
1714 1789 3.712016 TCTGGGCAAATTACTAGCACA 57.288 42.857 0.00 0.00 39.77 4.57
1770 1895 7.239763 TCAGAAAGTGACATGATGGTAGTTA 57.760 36.000 0.00 0.00 0.00 2.24
1774 1899 5.599999 AGTGACATGATGGTAGTTAGGTC 57.400 43.478 0.00 0.00 0.00 3.85
1831 2129 5.928264 GCTTGGTTGTATTCTTTTTGCTCAT 59.072 36.000 0.00 0.00 0.00 2.90
1832 2130 7.090173 GCTTGGTTGTATTCTTTTTGCTCATA 58.910 34.615 0.00 0.00 0.00 2.15
1904 2202 2.046285 GCCATCCCACCCAAGTTCG 61.046 63.158 0.00 0.00 0.00 3.95
1911 2209 0.679505 CCACCCAAGTTCGAGTCTCA 59.320 55.000 0.00 0.00 0.00 3.27
1920 2218 2.362397 AGTTCGAGTCTCAGCTTTGACA 59.638 45.455 15.59 0.00 35.81 3.58
1924 2222 1.000163 GAGTCTCAGCTTTGACACGGA 60.000 52.381 15.59 0.00 35.81 4.69
1926 2224 1.728971 GTCTCAGCTTTGACACGGATG 59.271 52.381 10.10 0.00 33.75 3.51
1931 2229 1.421485 CTTTGACACGGATGCTCGC 59.579 57.895 0.00 0.00 0.00 5.03
1933 2231 4.794439 TGACACGGATGCTCGCGG 62.794 66.667 6.13 0.00 0.00 6.46
1939 2237 1.226859 CGGATGCTCGCGGAGTTTA 60.227 57.895 6.13 0.00 31.39 2.01
1942 2240 1.269831 GGATGCTCGCGGAGTTTATCT 60.270 52.381 6.13 0.00 31.39 1.98
1984 2284 3.555966 GTTATCCCCTGGATTGGTCTTG 58.444 50.000 0.15 0.00 39.79 3.02
1988 2288 2.178984 TCCCCTGGATTGGTCTTGTTTT 59.821 45.455 0.00 0.00 0.00 2.43
2005 2305 0.036765 TTTGGTACTAGCACCTGCCG 60.037 55.000 13.44 0.00 43.38 5.69
2006 2306 2.202892 GGTACTAGCACCTGCCGC 60.203 66.667 4.74 0.00 43.38 6.53
2017 2317 0.179108 ACCTGCCGCTTATCGTCTTC 60.179 55.000 0.00 0.00 36.19 2.87
2073 2373 0.186386 AGATCAGCCGGGTAGCTAGT 59.814 55.000 5.47 0.00 42.61 2.57
2086 2386 1.558233 AGCTAGTTGGCCGTAAGAGT 58.442 50.000 0.00 0.00 43.02 3.24
2129 2429 1.617018 AAGCAGTAGCCATCGCTCCA 61.617 55.000 0.00 0.00 43.95 3.86
2134 2434 1.090052 GTAGCCATCGCTCCACAACC 61.090 60.000 0.00 0.00 43.95 3.77
2141 2441 2.343758 GCTCCACAACCTCGCTCA 59.656 61.111 0.00 0.00 0.00 4.26
2147 2447 3.706055 ACAACCTCGCTCATGTTGT 57.294 47.368 1.68 1.68 45.59 3.32
2160 2460 2.047179 GTTGTGAGCCGGAGTCCC 60.047 66.667 5.05 0.00 0.00 4.46
2171 2471 3.929660 GGAGTCCCGGCAATATACC 57.070 57.895 0.00 0.00 0.00 2.73
2172 2472 1.349067 GGAGTCCCGGCAATATACCT 58.651 55.000 0.00 0.00 0.00 3.08
2173 2473 1.002087 GGAGTCCCGGCAATATACCTG 59.998 57.143 0.00 0.00 0.00 4.00
2175 2475 0.605589 GTCCCGGCAATATACCTGGC 60.606 60.000 0.00 1.19 31.92 4.85
2176 2476 1.303317 CCCGGCAATATACCTGGCC 60.303 63.158 0.00 0.00 42.98 5.36
2177 2477 1.454104 CCGGCAATATACCTGGCCA 59.546 57.895 4.71 4.71 46.75 5.36
2178 2478 0.038166 CCGGCAATATACCTGGCCAT 59.962 55.000 5.51 0.00 46.75 4.40
2193 2955 1.304952 CCATGGGTCGGGCCTTAAA 59.695 57.895 2.85 0.00 37.43 1.52
2195 2957 1.551452 CATGGGTCGGGCCTTAAAAA 58.449 50.000 0.84 0.00 37.43 1.94
2204 2966 2.672961 GGCCTTAAAAAGCCCATGAC 57.327 50.000 0.00 0.00 43.76 3.06
2205 2967 1.899142 GGCCTTAAAAAGCCCATGACA 59.101 47.619 0.00 0.00 43.76 3.58
2207 2969 2.825532 GCCTTAAAAAGCCCATGACAGA 59.174 45.455 0.00 0.00 0.00 3.41
2208 2970 3.258123 GCCTTAAAAAGCCCATGACAGAA 59.742 43.478 0.00 0.00 0.00 3.02
2209 2971 4.262420 GCCTTAAAAAGCCCATGACAGAAA 60.262 41.667 0.00 0.00 0.00 2.52
2210 2972 5.741673 GCCTTAAAAAGCCCATGACAGAAAA 60.742 40.000 0.00 0.00 0.00 2.29
2212 2974 6.462909 CCTTAAAAAGCCCATGACAGAAAACT 60.463 38.462 0.00 0.00 0.00 2.66
2214 2976 2.957402 AGCCCATGACAGAAAACTGA 57.043 45.000 0.00 0.00 0.00 3.41
2215 2977 2.787994 AGCCCATGACAGAAAACTGAG 58.212 47.619 0.00 0.00 0.00 3.35
2217 2979 1.815003 CCCATGACAGAAAACTGAGGC 59.185 52.381 0.00 0.00 0.00 4.70
2218 2980 1.815003 CCATGACAGAAAACTGAGGCC 59.185 52.381 0.00 0.00 0.00 5.19
2240 3002 3.034086 CCCTCCTAGGCCCTACCA 58.966 66.667 2.96 0.00 43.14 3.25
2242 3004 0.545548 CCCTCCTAGGCCCTACCATC 60.546 65.000 2.96 0.00 43.14 3.51
2243 3005 0.900647 CCTCCTAGGCCCTACCATCG 60.901 65.000 2.96 0.00 43.14 3.84
2245 3007 1.913762 CCTAGGCCCTACCATCGGG 60.914 68.421 0.00 0.00 44.89 5.14
2252 3014 0.763223 CCCTACCATCGGGCCTACTT 60.763 60.000 0.84 0.00 37.90 2.24
2253 3015 1.129058 CCTACCATCGGGCCTACTTT 58.871 55.000 0.84 0.00 37.90 2.66
2254 3016 1.489230 CCTACCATCGGGCCTACTTTT 59.511 52.381 0.84 0.00 37.90 2.27
2256 3018 3.135167 CCTACCATCGGGCCTACTTTTTA 59.865 47.826 0.84 0.00 37.90 1.52
2257 3019 3.724732 ACCATCGGGCCTACTTTTTAA 57.275 42.857 0.84 0.00 37.90 1.52
2258 3020 3.617284 ACCATCGGGCCTACTTTTTAAG 58.383 45.455 0.84 0.00 37.90 1.85
2259 3021 2.357952 CCATCGGGCCTACTTTTTAAGC 59.642 50.000 0.84 0.00 0.00 3.09
2260 3022 3.279434 CATCGGGCCTACTTTTTAAGCT 58.721 45.455 0.84 0.00 0.00 3.74
2261 3023 2.981898 TCGGGCCTACTTTTTAAGCTC 58.018 47.619 0.84 0.00 0.00 4.09
2262 3024 2.303600 TCGGGCCTACTTTTTAAGCTCA 59.696 45.455 0.84 0.00 0.00 4.26
2264 3026 3.127030 CGGGCCTACTTTTTAAGCTCAAG 59.873 47.826 0.84 0.00 0.00 3.02
2267 3029 3.119459 GCCTACTTTTTAAGCTCAAGCCC 60.119 47.826 0.00 0.00 43.38 5.19
2270 3032 2.297315 ACTTTTTAAGCTCAAGCCCAGC 59.703 45.455 0.00 0.00 43.38 4.85
2271 3033 1.256812 TTTTAAGCTCAAGCCCAGCC 58.743 50.000 0.00 0.00 43.38 4.85
2272 3034 0.611896 TTTAAGCTCAAGCCCAGCCC 60.612 55.000 0.00 0.00 43.38 5.19
2273 3035 1.788518 TTAAGCTCAAGCCCAGCCCA 61.789 55.000 0.00 0.00 43.38 5.36
2274 3036 1.574526 TAAGCTCAAGCCCAGCCCAT 61.575 55.000 0.00 0.00 43.38 4.00
2275 3037 2.832201 GCTCAAGCCCAGCCCATC 60.832 66.667 0.00 0.00 34.31 3.51
2276 3038 3.004951 CTCAAGCCCAGCCCATCT 58.995 61.111 0.00 0.00 0.00 2.90
2277 3039 1.453379 CTCAAGCCCAGCCCATCTG 60.453 63.158 0.00 0.00 42.49 2.90
2286 3048 2.947448 CAGCCCATCTGGTAAAAAGC 57.053 50.000 0.00 0.00 39.15 3.51
2287 3049 1.478105 CAGCCCATCTGGTAAAAAGCC 59.522 52.381 0.00 0.00 39.15 4.35
2288 3050 0.824109 GCCCATCTGGTAAAAAGCCC 59.176 55.000 0.00 0.00 36.04 5.19
2289 3051 1.619704 GCCCATCTGGTAAAAAGCCCT 60.620 52.381 0.00 0.00 36.04 5.19
2290 3052 2.102578 CCCATCTGGTAAAAAGCCCTG 58.897 52.381 0.00 0.00 0.00 4.45
2291 3053 2.291540 CCCATCTGGTAAAAAGCCCTGA 60.292 50.000 0.00 0.00 0.00 3.86
2292 3054 3.430453 CCATCTGGTAAAAAGCCCTGAA 58.570 45.455 0.00 0.00 0.00 3.02
2293 3055 3.831911 CCATCTGGTAAAAAGCCCTGAAA 59.168 43.478 0.00 0.00 0.00 2.69
2294 3056 4.283212 CCATCTGGTAAAAAGCCCTGAAAA 59.717 41.667 0.00 0.00 0.00 2.29
2295 3057 5.221621 CCATCTGGTAAAAAGCCCTGAAAAA 60.222 40.000 0.00 0.00 0.00 1.94
2296 3058 5.270893 TCTGGTAAAAAGCCCTGAAAAAC 57.729 39.130 0.00 0.00 0.00 2.43
2297 3059 4.100344 TCTGGTAAAAAGCCCTGAAAAACC 59.900 41.667 0.00 0.00 0.00 3.27
2298 3060 3.134985 TGGTAAAAAGCCCTGAAAAACCC 59.865 43.478 0.00 0.00 0.00 4.11
2299 3061 3.389983 GGTAAAAAGCCCTGAAAAACCCT 59.610 43.478 0.00 0.00 0.00 4.34
2300 3062 4.141574 GGTAAAAAGCCCTGAAAAACCCTT 60.142 41.667 0.00 0.00 0.00 3.95
2301 3063 5.070714 GGTAAAAAGCCCTGAAAAACCCTTA 59.929 40.000 0.00 0.00 0.00 2.69
2302 3064 4.955811 AAAAGCCCTGAAAAACCCTTAG 57.044 40.909 0.00 0.00 0.00 2.18
2303 3065 2.604912 AGCCCTGAAAAACCCTTAGG 57.395 50.000 0.00 0.00 40.04 2.69
2314 3076 2.134092 CCCTTAGGGCTTAGGGTCG 58.866 63.158 3.52 0.00 45.12 4.79
2315 3077 0.690077 CCCTTAGGGCTTAGGGTCGT 60.690 60.000 3.52 0.00 45.12 4.34
2316 3078 0.464452 CCTTAGGGCTTAGGGTCGTG 59.536 60.000 0.00 0.00 0.00 4.35
2317 3079 0.464452 CTTAGGGCTTAGGGTCGTGG 59.536 60.000 0.00 0.00 0.00 4.94
2318 3080 0.979187 TTAGGGCTTAGGGTCGTGGG 60.979 60.000 0.00 0.00 0.00 4.61
2319 3081 4.484872 GGGCTTAGGGTCGTGGGC 62.485 72.222 0.00 0.00 0.00 5.36
2320 3082 4.484872 GGCTTAGGGTCGTGGGCC 62.485 72.222 0.00 0.00 0.00 5.80
2321 3083 4.832608 GCTTAGGGTCGTGGGCCG 62.833 72.222 0.00 0.00 38.13 6.13
2322 3084 4.157120 CTTAGGGTCGTGGGCCGG 62.157 72.222 0.00 0.00 37.11 6.13
2333 3097 3.009714 GGGCCGGACCTCTTCCTT 61.010 66.667 23.07 0.00 43.25 3.36
2334 3098 1.688187 GGGCCGGACCTCTTCCTTA 60.688 63.158 23.07 0.00 43.25 2.69
2335 3099 1.269703 GGGCCGGACCTCTTCCTTAA 61.270 60.000 23.07 0.00 43.25 1.85
2336 3100 0.616891 GGCCGGACCTCTTCCTTAAA 59.383 55.000 5.05 0.00 43.25 1.52
2338 3102 2.356844 GGCCGGACCTCTTCCTTAAAAT 60.357 50.000 5.05 0.00 43.25 1.82
2339 3103 2.683362 GCCGGACCTCTTCCTTAAAATG 59.317 50.000 5.05 0.00 43.25 2.32
2340 3104 2.683362 CCGGACCTCTTCCTTAAAATGC 59.317 50.000 0.00 0.00 43.25 3.56
2341 3105 2.683362 CGGACCTCTTCCTTAAAATGCC 59.317 50.000 0.00 0.00 43.25 4.40
2343 3107 4.086457 GGACCTCTTCCTTAAAATGCCAA 58.914 43.478 0.00 0.00 41.95 4.52
2345 3109 5.891551 GGACCTCTTCCTTAAAATGCCAATA 59.108 40.000 0.00 0.00 41.95 1.90
2347 3111 7.352079 ACCTCTTCCTTAAAATGCCAATATG 57.648 36.000 0.00 0.00 0.00 1.78
2348 3112 6.183360 ACCTCTTCCTTAAAATGCCAATATGC 60.183 38.462 0.00 0.00 0.00 3.14
2351 3115 5.946942 TCCTTAAAATGCCAATATGCCAA 57.053 34.783 0.00 0.00 0.00 4.52
2354 3118 3.918294 AAAATGCCAATATGCCAAGCT 57.082 38.095 0.00 0.00 0.00 3.74
2355 3119 3.464111 AAATGCCAATATGCCAAGCTC 57.536 42.857 0.00 0.00 0.00 4.09
2356 3120 2.076207 ATGCCAATATGCCAAGCTCA 57.924 45.000 0.00 0.00 0.00 4.26
2358 3122 1.752498 TGCCAATATGCCAAGCTCAAG 59.248 47.619 0.00 0.00 0.00 3.02
2359 3123 1.537562 GCCAATATGCCAAGCTCAAGC 60.538 52.381 0.00 0.00 42.49 4.01
2360 3124 1.068127 CCAATATGCCAAGCTCAAGCC 59.932 52.381 0.00 0.00 43.38 4.35
2361 3125 1.068127 CAATATGCCAAGCTCAAGCCC 59.932 52.381 0.00 0.00 43.38 5.19
2362 3126 0.820891 ATATGCCAAGCTCAAGCCCG 60.821 55.000 0.00 0.00 43.38 6.13
2363 3127 2.196997 TATGCCAAGCTCAAGCCCGT 62.197 55.000 0.00 0.00 43.38 5.28
2364 3128 3.435186 GCCAAGCTCAAGCCCGTC 61.435 66.667 0.00 0.00 43.38 4.79
2365 3129 2.747855 CCAAGCTCAAGCCCGTCC 60.748 66.667 0.00 0.00 43.38 4.79
2366 3130 2.032528 CAAGCTCAAGCCCGTCCA 59.967 61.111 0.00 0.00 43.38 4.02
2368 3132 3.259633 AAGCTCAAGCCCGTCCAGG 62.260 63.158 0.00 0.00 43.38 4.45
2379 3143 3.402681 GTCCAGGCCCTGCAGCTA 61.403 66.667 8.66 0.00 0.00 3.32
2380 3144 3.085947 TCCAGGCCCTGCAGCTAG 61.086 66.667 8.66 0.00 0.00 3.42
2381 3145 4.186715 CCAGGCCCTGCAGCTAGG 62.187 72.222 8.66 5.57 37.59 3.02
2382 3146 4.871910 CAGGCCCTGCAGCTAGGC 62.872 72.222 20.64 20.64 46.37 3.93
2384 3148 4.560743 GGCCCTGCAGCTAGGCTC 62.561 72.222 25.58 15.37 46.31 4.70
2385 3149 3.790437 GCCCTGCAGCTAGGCTCA 61.790 66.667 21.28 0.00 43.62 4.26
2386 3150 2.993008 CCCTGCAGCTAGGCTCAA 59.007 61.111 8.66 0.00 36.40 3.02
2387 3151 1.300963 CCCTGCAGCTAGGCTCAAA 59.699 57.895 8.66 0.00 36.40 2.69
2388 3152 0.322816 CCCTGCAGCTAGGCTCAAAA 60.323 55.000 8.66 0.00 36.40 2.44
2389 3153 0.807496 CCTGCAGCTAGGCTCAAAAC 59.193 55.000 8.66 0.00 36.40 2.43
2390 3154 1.612726 CCTGCAGCTAGGCTCAAAACT 60.613 52.381 8.66 0.00 36.40 2.66
2391 3155 1.736681 CTGCAGCTAGGCTCAAAACTC 59.263 52.381 0.00 0.00 36.40 3.01
2392 3156 1.072173 TGCAGCTAGGCTCAAAACTCA 59.928 47.619 0.00 0.00 36.40 3.41
2393 3157 1.736681 GCAGCTAGGCTCAAAACTCAG 59.263 52.381 0.00 0.00 36.40 3.35
2394 3158 2.354259 CAGCTAGGCTCAAAACTCAGG 58.646 52.381 0.00 0.00 36.40 3.86
2395 3159 1.090728 GCTAGGCTCAAAACTCAGGC 58.909 55.000 0.00 0.00 35.42 4.85
2396 3160 1.743996 CTAGGCTCAAAACTCAGGCC 58.256 55.000 0.00 0.00 42.74 5.19
2397 3161 0.328258 TAGGCTCAAAACTCAGGCCC 59.672 55.000 0.00 0.00 43.36 5.80
2398 3162 1.228552 GGCTCAAAACTCAGGCCCA 60.229 57.895 0.00 0.00 37.12 5.36
2399 3163 0.827507 GGCTCAAAACTCAGGCCCAA 60.828 55.000 0.00 0.00 37.12 4.12
2400 3164 0.600057 GCTCAAAACTCAGGCCCAAG 59.400 55.000 0.00 0.00 0.00 3.61
2401 3165 0.600057 CTCAAAACTCAGGCCCAAGC 59.400 55.000 0.00 0.00 38.76 4.01
2446 3210 2.587522 GCCTAGGCCTTGGATTTTAGG 58.412 52.381 34.13 21.74 34.56 2.69
2447 3211 2.753168 GCCTAGGCCTTGGATTTTAGGG 60.753 54.545 34.13 7.14 34.56 3.53
2450 3214 2.115510 GCCTTGGATTTTAGGGCCG 58.884 57.895 0.00 0.00 37.12 6.13
2451 3215 1.391933 GCCTTGGATTTTAGGGCCGG 61.392 60.000 0.00 0.00 37.12 6.13
2452 3216 0.755327 CCTTGGATTTTAGGGCCGGG 60.755 60.000 2.18 0.00 0.00 5.73
2453 3217 1.380650 TTGGATTTTAGGGCCGGGC 60.381 57.895 22.00 22.00 0.00 6.13
2482 3246 2.436109 GGCAGTTGGGGAGAAGCA 59.564 61.111 0.00 0.00 0.00 3.91
2500 3264 6.008960 AGAAGCATTTTCCTTCTCATCTTGT 58.991 36.000 0.00 0.00 44.13 3.16
2506 3270 3.920231 TCCTTCTCATCTTGTCCATGG 57.080 47.619 4.97 4.97 0.00 3.66
2507 3271 3.184628 TCCTTCTCATCTTGTCCATGGT 58.815 45.455 12.58 0.00 0.00 3.55
2508 3272 3.588842 TCCTTCTCATCTTGTCCATGGTT 59.411 43.478 12.58 0.00 0.00 3.67
2519 3557 2.260154 CCATGGTTGTGTCGCTGCA 61.260 57.895 2.57 0.00 0.00 4.41
2541 3579 0.393537 GAGTGTCAATGGAGCAGGGG 60.394 60.000 0.00 0.00 0.00 4.79
2573 3611 6.020599 CGGAGTCATAGTCACAAGATTTAACG 60.021 42.308 0.00 0.00 0.00 3.18
2574 3612 6.812160 GGAGTCATAGTCACAAGATTTAACGT 59.188 38.462 0.00 0.00 0.00 3.99
2580 3618 3.972502 GTCACAAGATTTAACGTGTTGCC 59.027 43.478 0.00 0.00 31.00 4.52
2603 4052 3.366396 GGCTAGGCTATGTATCCTGCTA 58.634 50.000 9.46 0.00 34.02 3.49
2642 4091 5.103000 GCTCTTTTAATCGTCTCTGCACTA 58.897 41.667 0.00 0.00 0.00 2.74
2722 4171 1.139853 CAGGCCTAGCGAGAAATTCCT 59.860 52.381 3.98 0.00 0.00 3.36
2728 4177 2.338577 AGCGAGAAATTCCTCCCATG 57.661 50.000 0.00 0.00 0.00 3.66
2729 4178 0.665298 GCGAGAAATTCCTCCCATGC 59.335 55.000 0.00 0.00 0.00 4.06
2741 4190 1.833630 CTCCCATGCTGTAGGAAGACA 59.166 52.381 0.00 0.00 0.00 3.41
2742 4191 2.237143 CTCCCATGCTGTAGGAAGACAA 59.763 50.000 0.00 0.00 0.00 3.18
2743 4192 2.642311 TCCCATGCTGTAGGAAGACAAA 59.358 45.455 0.00 0.00 0.00 2.83
2775 4224 2.270858 TGTGGGCCTAATAGTGGAACA 58.729 47.619 4.53 0.00 41.43 3.18
2798 4247 1.305465 ATGCCAGCCAATCCAGCAA 60.305 52.632 0.00 0.00 36.95 3.91
2800 4249 2.277591 GCCAGCCAATCCAGCAACA 61.278 57.895 0.00 0.00 0.00 3.33
2890 4339 4.336433 TGCTCCTGTTTCTTTGAGTTTCAG 59.664 41.667 0.00 0.00 0.00 3.02
2892 4341 4.269183 TCCTGTTTCTTTGAGTTTCAGCA 58.731 39.130 0.00 0.00 0.00 4.41
2964 4413 4.800471 GCATAAGTTTATGTGCTTTCTGCC 59.200 41.667 12.14 0.00 41.92 4.85
2979 4428 1.211703 TCTGCCTCCCGATATTTTGCA 59.788 47.619 0.00 0.00 0.00 4.08
3020 4469 3.892588 GGGAAACACACAAAAGATACCCA 59.107 43.478 0.00 0.00 34.43 4.51
3033 4482 7.453126 ACAAAAGATACCCACAATCCAAACATA 59.547 33.333 0.00 0.00 0.00 2.29
3200 4657 3.390135 CGCCGATAATGTATCCAAGTGT 58.610 45.455 0.00 0.00 31.43 3.55
3294 4751 6.457663 CGAACAACTCCAACACTCAACAAATA 60.458 38.462 0.00 0.00 0.00 1.40
3304 4761 4.083855 ACACTCAACAAATATGTGTGCTCG 60.084 41.667 0.00 0.00 42.85 5.03
3334 4794 3.973516 CCGCCGGCAGCTACGATA 61.974 66.667 28.98 0.00 40.39 2.92
3336 4796 2.355956 GCCGGCAGCTACGATACC 60.356 66.667 24.80 0.00 38.99 2.73
3339 4799 2.741747 GGCAGCTACGATACCCCC 59.258 66.667 0.00 0.00 0.00 5.40
3345 4805 3.245948 CTACGATACCCCCGACGCG 62.246 68.421 3.53 3.53 0.00 6.01
3355 4815 3.740397 CCGACGCGTACTCCCACA 61.740 66.667 13.97 0.00 0.00 4.17
3538 4998 8.108999 TCAATCTATGAATTCTTTGGTGAAGGA 58.891 33.333 7.05 0.00 34.30 3.36
3655 5140 9.431690 TCATGGGATATTTATTTGGAATGTTGA 57.568 29.630 0.00 0.00 0.00 3.18
3719 5204 0.947960 TTGAAGCGTGCATCGGAAAA 59.052 45.000 10.02 0.00 40.26 2.29
3810 5295 8.609176 GGTTTTAGCTTGTTTCATCGTATCATA 58.391 33.333 0.00 0.00 0.00 2.15
3828 5313 2.902705 TACATCTAACCATGGGCGTC 57.097 50.000 18.09 0.00 0.00 5.19
3832 5317 2.799126 TCTAACCATGGGCGTCAAAT 57.201 45.000 18.09 0.00 0.00 2.32
3835 5320 1.102978 AACCATGGGCGTCAAATAGC 58.897 50.000 18.09 0.00 0.00 2.97
3843 5328 1.946768 GGCGTCAAATAGCTGCCAATA 59.053 47.619 0.00 0.00 45.06 1.90
3982 5467 4.884257 AAACGTTTCGCTTATGCAAATG 57.116 36.364 7.96 8.24 39.64 2.32
4081 5566 1.884579 GAGTAGTCCCGTTCACTGTCA 59.115 52.381 0.00 0.00 0.00 3.58
4165 5650 4.124351 GACGGTCGATGGTGGCGA 62.124 66.667 0.00 0.00 35.08 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.603021 TGTGCTCCCTCTGGATCTATC 58.397 52.381 0.00 0.00 40.80 2.08
126 127 1.673665 GCCAGTTGTGCTCCCTCTG 60.674 63.158 0.00 0.00 0.00 3.35
195 196 7.377928 CACATATAGTAACGTACAAGCTGGTAC 59.622 40.741 19.90 19.90 40.14 3.34
231 232 1.261885 CACCGCGTTTGTGTGATAACA 59.738 47.619 4.92 0.00 0.00 2.41
260 261 2.544694 GCATGACTCGTGTGCTAGCTAT 60.545 50.000 17.23 0.00 36.02 2.97
266 267 1.669115 GTGGCATGACTCGTGTGCT 60.669 57.895 0.00 0.00 38.83 4.40
289 290 6.995686 TCAGAACATAAGTTAAAGAAGCACCA 59.004 34.615 0.00 0.00 38.30 4.17
387 390 3.330701 AGAGGGGCTCAAATTGTCTTACA 59.669 43.478 0.00 0.00 32.06 2.41
421 424 0.165944 CGCGGTCAAAAGGTGATGAC 59.834 55.000 0.00 0.00 44.07 3.06
424 427 2.677003 CGCGCGGTCAAAAGGTGAT 61.677 57.895 24.84 0.00 38.90 3.06
425 428 3.342627 CGCGCGGTCAAAAGGTGA 61.343 61.111 24.84 0.00 0.00 4.02
492 495 1.071314 TTTGAAGGGGAGAAGGGGCA 61.071 55.000 0.00 0.00 0.00 5.36
567 574 7.723324 AGTAACGTACAAGCTGGTATCATTAT 58.277 34.615 3.76 0.00 0.00 1.28
655 664 0.964860 AAGCACCGCAATGTGGCATA 60.965 50.000 13.48 0.00 36.54 3.14
705 714 0.998928 TTGTGGGCCCATATGTCAGT 59.001 50.000 31.45 0.00 0.00 3.41
734 743 1.112916 TCTCGGCAGTGACAAGTGGA 61.113 55.000 0.00 0.00 0.00 4.02
750 759 4.421033 TCACGTACATCAAGTGACTCTC 57.579 45.455 0.00 0.00 40.20 3.20
805 817 4.700365 GCCACGCGGTCAAAAGGC 62.700 66.667 12.47 8.20 34.71 4.35
1242 1286 2.036733 CCAGTGGAAGACGTTCTTACCA 59.963 50.000 1.68 9.54 36.48 3.25
1304 1348 1.846541 GAAGTAGTCAGATCGCTGCC 58.153 55.000 0.00 0.00 42.01 4.85
1384 1437 1.689582 GGAGTTGGACCGGGGAGAT 60.690 63.158 6.32 0.00 0.00 2.75
1429 1482 2.027192 ACGTACCTTCTCCATTGCATGT 60.027 45.455 0.00 0.00 0.00 3.21
1499 1555 2.685897 GCATGCCAATTGCCAAAATCAT 59.314 40.909 6.36 0.00 40.16 2.45
1502 1558 2.201921 TGCATGCCAATTGCCAAAAT 57.798 40.000 16.68 0.00 39.39 1.82
1522 1578 6.582636 TGGAAGCTAATCAATCAAGACGTAT 58.417 36.000 0.00 0.00 0.00 3.06
1526 1582 6.474751 GCATTTGGAAGCTAATCAATCAAGAC 59.525 38.462 0.00 0.00 0.00 3.01
1529 1585 5.342433 CGCATTTGGAAGCTAATCAATCAA 58.658 37.500 0.00 0.00 0.00 2.57
1530 1586 4.734402 GCGCATTTGGAAGCTAATCAATCA 60.734 41.667 0.30 0.00 0.00 2.57
1531 1587 3.732721 GCGCATTTGGAAGCTAATCAATC 59.267 43.478 0.30 0.00 0.00 2.67
1532 1588 3.382546 AGCGCATTTGGAAGCTAATCAAT 59.617 39.130 11.47 0.00 38.29 2.57
1554 1614 2.073816 GCTAGGCTAAGAAACGCACAA 58.926 47.619 0.00 0.00 0.00 3.33
1714 1789 7.864882 CGACTATAGATGAGTCAACATTCATGT 59.135 37.037 6.78 0.00 42.97 3.21
1770 1895 3.011085 CATGCATGCATACGGACCT 57.989 52.632 31.73 6.60 34.91 3.85
1831 2129 1.976478 GCATCCGTGCGTGCACATTA 61.976 55.000 23.26 9.20 46.47 1.90
1832 2130 2.869646 CATCCGTGCGTGCACATT 59.130 55.556 23.26 5.74 46.47 2.71
1904 2202 1.000163 TCCGTGTCAAAGCTGAGACTC 60.000 52.381 16.84 13.12 42.35 3.36
1911 2209 1.016130 CGAGCATCCGTGTCAAAGCT 61.016 55.000 0.00 0.00 34.61 3.74
1920 2218 1.940883 TAAACTCCGCGAGCATCCGT 61.941 55.000 8.23 0.00 32.04 4.69
1924 2222 2.604046 AAGATAAACTCCGCGAGCAT 57.396 45.000 8.23 0.00 32.04 3.79
1926 2224 6.520792 TTTTATAAGATAAACTCCGCGAGC 57.479 37.500 8.23 0.00 32.04 5.03
1963 2261 3.053619 ACAAGACCAATCCAGGGGATAAC 60.054 47.826 0.00 0.00 42.27 1.89
1967 2265 1.455822 AACAAGACCAATCCAGGGGA 58.544 50.000 0.00 0.00 35.55 4.81
1971 2269 4.827284 AGTACCAAAACAAGACCAATCCAG 59.173 41.667 0.00 0.00 0.00 3.86
1975 2273 5.240844 GTGCTAGTACCAAAACAAGACCAAT 59.759 40.000 0.00 0.00 0.00 3.16
1978 2276 3.501062 GGTGCTAGTACCAAAACAAGACC 59.499 47.826 23.63 0.00 40.54 3.85
1984 2284 1.810755 GGCAGGTGCTAGTACCAAAAC 59.189 52.381 28.92 15.62 43.37 2.43
1988 2288 3.014085 GCGGCAGGTGCTAGTACCA 62.014 63.158 28.92 0.00 43.37 3.25
2005 2305 0.806102 TGCTGGCGAAGACGATAAGC 60.806 55.000 0.00 0.00 41.59 3.09
2006 2306 0.924090 GTGCTGGCGAAGACGATAAG 59.076 55.000 0.00 0.00 41.59 1.73
2017 2317 0.443869 GTTGACACATAGTGCTGGCG 59.556 55.000 0.00 0.00 36.98 5.69
2073 2373 1.972795 AGGTACAACTCTTACGGCCAA 59.027 47.619 2.24 0.00 0.00 4.52
2086 2386 5.596772 TGATCCAACATCTATCGAGGTACAA 59.403 40.000 0.00 0.00 32.12 2.41
2126 2426 0.396435 AACATGAGCGAGGTTGTGGA 59.604 50.000 0.00 0.00 0.00 4.02
2141 2441 1.296715 GGACTCCGGCTCACAACAT 59.703 57.895 0.00 0.00 0.00 2.71
2154 2454 1.002087 CCAGGTATATTGCCGGGACTC 59.998 57.143 2.18 0.00 42.80 3.36
2155 2455 1.056660 CCAGGTATATTGCCGGGACT 58.943 55.000 2.18 0.00 42.80 3.85
2166 2466 1.125093 CCGACCCATGGCCAGGTATA 61.125 60.000 16.33 0.00 36.17 1.47
2175 2475 0.323908 TTTTAAGGCCCGACCCATGG 60.324 55.000 4.14 4.14 40.58 3.66
2176 2476 1.476488 CTTTTTAAGGCCCGACCCATG 59.524 52.381 0.00 0.00 40.58 3.66
2177 2477 1.847328 CTTTTTAAGGCCCGACCCAT 58.153 50.000 0.00 0.00 40.58 4.00
2178 2478 0.896479 GCTTTTTAAGGCCCGACCCA 60.896 55.000 0.00 0.00 40.58 4.51
2189 2951 6.097554 TCAGTTTTCTGTCATGGGCTTTTTAA 59.902 34.615 0.00 0.00 46.98 1.52
2190 2952 5.596361 TCAGTTTTCTGTCATGGGCTTTTTA 59.404 36.000 0.00 0.00 46.98 1.52
2193 2955 3.565307 TCAGTTTTCTGTCATGGGCTTT 58.435 40.909 0.00 0.00 46.98 3.51
2195 2957 2.553904 CCTCAGTTTTCTGTCATGGGCT 60.554 50.000 0.00 0.00 46.98 5.19
2200 2962 1.425066 TGGGCCTCAGTTTTCTGTCAT 59.575 47.619 4.53 0.00 46.98 3.06
2201 2963 0.843309 TGGGCCTCAGTTTTCTGTCA 59.157 50.000 4.53 0.00 46.98 3.58
2202 2964 1.528129 CTGGGCCTCAGTTTTCTGTC 58.472 55.000 4.53 0.00 46.98 3.51
2204 2966 1.246737 GCCTGGGCCTCAGTTTTCTG 61.247 60.000 16.96 5.05 41.83 3.02
2205 2967 1.075659 GCCTGGGCCTCAGTTTTCT 59.924 57.895 16.96 0.00 41.83 2.52
2225 2987 0.900647 CCGATGGTAGGGCCTAGGAG 60.901 65.000 15.05 4.09 38.35 3.69
2226 2988 1.155390 CCGATGGTAGGGCCTAGGA 59.845 63.158 15.05 3.43 38.35 2.94
2227 2989 1.913762 CCCGATGGTAGGGCCTAGG 60.914 68.421 15.05 11.18 42.77 3.02
2228 2990 3.793060 CCCGATGGTAGGGCCTAG 58.207 66.667 15.05 1.15 42.77 3.02
2236 2998 4.773013 CTTAAAAAGTAGGCCCGATGGTA 58.227 43.478 0.00 0.00 0.00 3.25
2237 2999 3.617284 CTTAAAAAGTAGGCCCGATGGT 58.383 45.455 0.00 0.00 0.00 3.55
2238 3000 2.357952 GCTTAAAAAGTAGGCCCGATGG 59.642 50.000 0.00 0.00 0.00 3.51
2239 3001 3.279434 AGCTTAAAAAGTAGGCCCGATG 58.721 45.455 0.00 0.00 0.00 3.84
2240 3002 3.054655 TGAGCTTAAAAAGTAGGCCCGAT 60.055 43.478 0.00 0.00 0.00 4.18
2242 3004 2.706890 TGAGCTTAAAAAGTAGGCCCG 58.293 47.619 0.00 0.00 0.00 6.13
2243 3005 3.119459 GCTTGAGCTTAAAAAGTAGGCCC 60.119 47.826 0.00 0.00 38.21 5.80
2245 3007 3.119459 GGGCTTGAGCTTAAAAAGTAGGC 60.119 47.826 2.66 0.00 41.70 3.93
2246 3008 4.079253 TGGGCTTGAGCTTAAAAAGTAGG 58.921 43.478 2.66 0.00 41.70 3.18
2248 3010 3.506067 GCTGGGCTTGAGCTTAAAAAGTA 59.494 43.478 2.66 0.00 41.70 2.24
2249 3011 2.297315 GCTGGGCTTGAGCTTAAAAAGT 59.703 45.455 2.66 0.00 41.70 2.66
2252 3014 1.256812 GGCTGGGCTTGAGCTTAAAA 58.743 50.000 2.66 0.00 41.70 1.52
2253 3015 0.611896 GGGCTGGGCTTGAGCTTAAA 60.612 55.000 2.66 0.00 41.70 1.52
2254 3016 1.000896 GGGCTGGGCTTGAGCTTAA 60.001 57.895 2.66 0.00 41.70 1.85
2256 3018 2.850828 GATGGGCTGGGCTTGAGCTT 62.851 60.000 2.66 0.00 41.70 3.74
2257 3019 3.345028 ATGGGCTGGGCTTGAGCT 61.345 61.111 2.66 0.00 41.70 4.09
2258 3020 2.832201 GATGGGCTGGGCTTGAGC 60.832 66.667 0.00 0.00 41.14 4.26
2259 3021 1.453379 CAGATGGGCTGGGCTTGAG 60.453 63.158 0.00 0.00 41.07 3.02
2260 3022 2.679092 CAGATGGGCTGGGCTTGA 59.321 61.111 0.00 0.00 41.07 3.02
2267 3029 1.478105 GGCTTTTTACCAGATGGGCTG 59.522 52.381 3.48 0.00 44.49 4.85
2270 3032 2.102578 CAGGGCTTTTTACCAGATGGG 58.897 52.381 3.48 0.00 44.81 4.00
2271 3033 3.085952 TCAGGGCTTTTTACCAGATGG 57.914 47.619 0.00 0.00 42.17 3.51
2272 3034 5.467035 TTTTCAGGGCTTTTTACCAGATG 57.533 39.130 0.00 0.00 0.00 2.90
2273 3035 5.221641 GGTTTTTCAGGGCTTTTTACCAGAT 60.222 40.000 0.00 0.00 0.00 2.90
2274 3036 4.100344 GGTTTTTCAGGGCTTTTTACCAGA 59.900 41.667 0.00 0.00 0.00 3.86
2275 3037 4.377021 GGTTTTTCAGGGCTTTTTACCAG 58.623 43.478 0.00 0.00 0.00 4.00
2276 3038 3.134985 GGGTTTTTCAGGGCTTTTTACCA 59.865 43.478 0.00 0.00 0.00 3.25
2277 3039 3.389983 AGGGTTTTTCAGGGCTTTTTACC 59.610 43.478 0.00 0.00 0.00 2.85
2278 3040 4.682778 AGGGTTTTTCAGGGCTTTTTAC 57.317 40.909 0.00 0.00 0.00 2.01
2279 3041 5.305902 CCTAAGGGTTTTTCAGGGCTTTTTA 59.694 40.000 0.00 0.00 0.00 1.52
2280 3042 4.102524 CCTAAGGGTTTTTCAGGGCTTTTT 59.897 41.667 0.00 0.00 0.00 1.94
2281 3043 3.646162 CCTAAGGGTTTTTCAGGGCTTTT 59.354 43.478 0.00 0.00 0.00 2.27
2282 3044 3.239449 CCTAAGGGTTTTTCAGGGCTTT 58.761 45.455 0.00 0.00 0.00 3.51
2283 3045 2.492753 CCCTAAGGGTTTTTCAGGGCTT 60.493 50.000 0.00 0.00 39.62 4.35
2284 3046 1.077169 CCCTAAGGGTTTTTCAGGGCT 59.923 52.381 0.00 0.00 39.62 5.19
2285 3047 1.557099 CCCTAAGGGTTTTTCAGGGC 58.443 55.000 0.00 0.00 39.62 5.19
2286 3048 1.077169 AGCCCTAAGGGTTTTTCAGGG 59.923 52.381 0.00 0.37 46.51 4.45
2287 3049 2.604912 AGCCCTAAGGGTTTTTCAGG 57.395 50.000 0.00 0.00 46.51 3.86
2297 3059 0.464452 CACGACCCTAAGCCCTAAGG 59.536 60.000 0.00 0.00 0.00 2.69
2298 3060 0.464452 CCACGACCCTAAGCCCTAAG 59.536 60.000 0.00 0.00 0.00 2.18
2299 3061 0.979187 CCCACGACCCTAAGCCCTAA 60.979 60.000 0.00 0.00 0.00 2.69
2300 3062 1.382146 CCCACGACCCTAAGCCCTA 60.382 63.158 0.00 0.00 0.00 3.53
2301 3063 2.687566 CCCACGACCCTAAGCCCT 60.688 66.667 0.00 0.00 0.00 5.19
2302 3064 4.484872 GCCCACGACCCTAAGCCC 62.485 72.222 0.00 0.00 0.00 5.19
2303 3065 4.484872 GGCCCACGACCCTAAGCC 62.485 72.222 0.00 0.00 0.00 4.35
2313 3075 4.452733 GAAGAGGTCCGGCCCACG 62.453 72.222 3.37 0.00 43.80 4.94
2314 3076 4.097361 GGAAGAGGTCCGGCCCAC 62.097 72.222 3.37 0.00 36.40 4.61
2322 3084 5.921962 ATTGGCATTTTAAGGAAGAGGTC 57.078 39.130 0.00 0.00 0.00 3.85
2339 3103 1.537562 GCTTGAGCTTGGCATATTGGC 60.538 52.381 0.00 0.00 39.75 4.52
2340 3104 1.068127 GGCTTGAGCTTGGCATATTGG 59.932 52.381 2.66 0.00 41.70 3.16
2341 3105 1.068127 GGGCTTGAGCTTGGCATATTG 59.932 52.381 2.66 0.00 41.70 1.90
2343 3107 0.820891 CGGGCTTGAGCTTGGCATAT 60.821 55.000 2.66 0.00 41.70 1.78
2345 3109 2.753043 CGGGCTTGAGCTTGGCAT 60.753 61.111 2.66 0.00 41.70 4.40
2347 3111 3.435186 GACGGGCTTGAGCTTGGC 61.435 66.667 2.66 0.00 41.70 4.52
2348 3112 2.747855 GGACGGGCTTGAGCTTGG 60.748 66.667 2.66 0.00 41.70 3.61
2351 3115 3.710722 CCTGGACGGGCTTGAGCT 61.711 66.667 2.66 0.00 41.70 4.09
2362 3126 3.397613 CTAGCTGCAGGGCCTGGAC 62.398 68.421 33.43 23.73 31.21 4.02
2363 3127 3.085947 CTAGCTGCAGGGCCTGGA 61.086 66.667 33.43 30.27 31.21 3.86
2364 3128 4.186715 CCTAGCTGCAGGGCCTGG 62.187 72.222 33.43 19.54 31.47 4.45
2365 3129 4.871910 GCCTAGCTGCAGGGCCTG 62.872 72.222 29.44 29.44 39.96 4.85
2368 3132 2.826777 TTTGAGCCTAGCTGCAGGGC 62.827 60.000 21.09 21.09 45.57 5.19
2369 3133 0.322816 TTTTGAGCCTAGCTGCAGGG 60.323 55.000 17.12 9.60 39.88 4.45
2370 3134 0.807496 GTTTTGAGCCTAGCTGCAGG 59.193 55.000 17.12 8.05 39.88 4.85
2371 3135 1.736681 GAGTTTTGAGCCTAGCTGCAG 59.263 52.381 10.11 10.11 39.88 4.41
2372 3136 1.072173 TGAGTTTTGAGCCTAGCTGCA 59.928 47.619 1.02 0.00 39.88 4.41
2374 3138 2.354259 CCTGAGTTTTGAGCCTAGCTG 58.646 52.381 0.00 0.00 39.88 4.24
2375 3139 1.339535 GCCTGAGTTTTGAGCCTAGCT 60.340 52.381 0.00 0.00 43.88 3.32
2376 3140 1.090728 GCCTGAGTTTTGAGCCTAGC 58.909 55.000 0.00 0.00 0.00 3.42
2377 3141 1.680249 GGGCCTGAGTTTTGAGCCTAG 60.680 57.143 0.84 0.00 43.36 3.02
2378 3142 0.328258 GGGCCTGAGTTTTGAGCCTA 59.672 55.000 0.84 0.00 43.36 3.93
2379 3143 1.075659 GGGCCTGAGTTTTGAGCCT 59.924 57.895 0.84 0.00 43.36 4.58
2380 3144 0.827507 TTGGGCCTGAGTTTTGAGCC 60.828 55.000 4.53 0.00 43.09 4.70
2381 3145 0.600057 CTTGGGCCTGAGTTTTGAGC 59.400 55.000 4.53 0.00 0.00 4.26
2382 3146 0.600057 GCTTGGGCCTGAGTTTTGAG 59.400 55.000 4.53 0.00 0.00 3.02
2383 3147 2.732289 GCTTGGGCCTGAGTTTTGA 58.268 52.632 4.53 0.00 0.00 2.69
2426 3190 2.587522 CCTAAAATCCAAGGCCTAGGC 58.412 52.381 26.55 26.55 41.06 3.93
2427 3191 2.753168 GCCCTAAAATCCAAGGCCTAGG 60.753 54.545 5.16 6.28 37.66 3.02
2428 3192 2.587522 GCCCTAAAATCCAAGGCCTAG 58.412 52.381 5.16 0.00 37.66 3.02
2429 3193 2.748209 GCCCTAAAATCCAAGGCCTA 57.252 50.000 5.16 0.00 37.66 3.93
2430 3194 3.615597 GCCCTAAAATCCAAGGCCT 57.384 52.632 0.00 0.00 37.66 5.19
2432 3196 1.391933 CCGGCCCTAAAATCCAAGGC 61.392 60.000 0.00 0.00 43.09 4.35
2433 3197 0.755327 CCCGGCCCTAAAATCCAAGG 60.755 60.000 0.00 0.00 0.00 3.61
2434 3198 1.391933 GCCCGGCCCTAAAATCCAAG 61.392 60.000 0.00 0.00 0.00 3.61
2435 3199 1.380650 GCCCGGCCCTAAAATCCAA 60.381 57.895 0.00 0.00 0.00 3.53
2436 3200 2.277404 GCCCGGCCCTAAAATCCA 59.723 61.111 0.00 0.00 0.00 3.41
2437 3201 2.520982 GGCCCGGCCCTAAAATCC 60.521 66.667 18.83 0.00 44.06 3.01
2462 3226 4.344865 TTCTCCCCAACTGCCGGC 62.345 66.667 22.73 22.73 0.00 6.13
2463 3227 2.045926 CTTCTCCCCAACTGCCGG 60.046 66.667 0.00 0.00 0.00 6.13
2464 3228 2.747855 GCTTCTCCCCAACTGCCG 60.748 66.667 0.00 0.00 0.00 5.69
2465 3229 0.613012 AATGCTTCTCCCCAACTGCC 60.613 55.000 0.00 0.00 0.00 4.85
2466 3230 1.260544 AAATGCTTCTCCCCAACTGC 58.739 50.000 0.00 0.00 0.00 4.40
2482 3246 5.655532 CCATGGACAAGATGAGAAGGAAAAT 59.344 40.000 5.56 0.00 0.00 1.82
2500 3264 1.965930 GCAGCGACACAACCATGGA 60.966 57.895 21.47 0.00 0.00 3.41
2506 3270 1.391485 CACTCTATGCAGCGACACAAC 59.609 52.381 0.00 0.00 0.00 3.32
2507 3271 1.000843 ACACTCTATGCAGCGACACAA 59.999 47.619 0.00 0.00 0.00 3.33
2508 3272 0.603065 ACACTCTATGCAGCGACACA 59.397 50.000 0.00 0.00 0.00 3.72
2519 3557 2.437281 CCCTGCTCCATTGACACTCTAT 59.563 50.000 0.00 0.00 0.00 1.98
2541 3579 2.099427 GTGACTATGACTCCGAGGGTTC 59.901 54.545 0.00 0.00 0.00 3.62
2550 3588 7.328737 ACACGTTAAATCTTGTGACTATGACTC 59.671 37.037 0.00 0.00 36.25 3.36
2557 3595 4.261031 GGCAACACGTTAAATCTTGTGACT 60.261 41.667 0.00 0.00 36.25 3.41
2580 3618 1.478510 CAGGATACATAGCCTAGCCCG 59.521 57.143 0.00 0.00 40.79 6.13
2653 4102 3.142162 CAATCTGGGGCATGCGCA 61.142 61.111 32.47 14.96 41.24 6.09
2705 4154 1.541452 GGGAGGAATTTCTCGCTAGGC 60.541 57.143 20.78 0.78 41.62 3.93
2722 4171 1.951209 TGTCTTCCTACAGCATGGGA 58.049 50.000 0.00 0.00 43.62 4.37
2743 4192 9.267071 ACTATTAGGCCCACAAGAATTATTTTT 57.733 29.630 0.00 0.00 0.00 1.94
2748 4197 5.430417 TCCACTATTAGGCCCACAAGAATTA 59.570 40.000 0.00 0.00 0.00 1.40
2764 4213 1.472480 GGCATGCGTTGTTCCACTATT 59.528 47.619 12.44 0.00 0.00 1.73
2766 4215 0.250510 TGGCATGCGTTGTTCCACTA 60.251 50.000 12.44 0.00 0.00 2.74
2775 4224 2.713967 GGATTGGCTGGCATGCGTT 61.714 57.895 12.44 0.00 0.00 4.84
2857 4306 9.241919 TCAAAGAAACAGGAGCAATATAAATCA 57.758 29.630 0.00 0.00 0.00 2.57
2932 4381 8.980481 AGCACATAAACTTATGCTAAATACCT 57.020 30.769 8.98 0.00 43.30 3.08
2939 4388 6.785191 GCAGAAAGCACATAAACTTATGCTA 58.215 36.000 8.98 0.00 43.30 3.49
2964 4413 1.257936 CGTCGTGCAAAATATCGGGAG 59.742 52.381 0.00 0.00 0.00 4.30
2979 4428 2.418628 CCCATATTTTGCTCAACGTCGT 59.581 45.455 0.00 0.00 0.00 4.34
3020 4469 8.093927 CACAATTTTAGGGTATGTTTGGATTGT 58.906 33.333 0.00 0.00 35.19 2.71
3033 4482 7.463431 TGTCAGTATAACCACAATTTTAGGGT 58.537 34.615 0.00 0.00 34.43 4.34
3142 4599 2.933878 TAGGTTGCATTAGCCGCGGG 62.934 60.000 29.38 11.04 41.13 6.13
3200 4657 1.848400 CCATGCCCCATCATCTCCA 59.152 57.895 0.00 0.00 0.00 3.86
3240 4697 0.541392 CCTGGTAGTACATGGCAGCA 59.459 55.000 2.06 0.00 0.00 4.41
3294 4751 1.672356 GGGCAACTCGAGCACACAT 60.672 57.895 13.61 0.00 34.91 3.21
3332 4792 2.124151 AGTACGCGTCGGGGGTAT 60.124 61.111 18.63 0.00 44.64 2.73
3339 4799 2.202440 CTGTGGGAGTACGCGTCG 60.202 66.667 18.63 0.00 0.00 5.12
3345 4805 3.001406 ACGGGGCTGTGGGAGTAC 61.001 66.667 0.00 0.00 0.00 2.73
3514 4974 7.890127 TGTCCTTCACCAAAGAATTCATAGATT 59.110 33.333 8.44 0.00 37.12 2.40
3671 5156 9.767684 TTATGAAGCAATACACATTTTACTTCG 57.232 29.630 0.00 0.00 33.08 3.79
3745 5230 9.418045 GCACCTTGCAATAAAAAGATTTAACTA 57.582 29.630 0.00 0.00 44.26 2.24
3810 5295 0.908910 TGACGCCCATGGTTAGATGT 59.091 50.000 11.73 0.00 0.00 3.06
3828 5313 5.796424 AGGGAAATATTGGCAGCTATTTG 57.204 39.130 16.93 0.00 29.87 2.32
3832 5317 6.757173 TTAGTAGGGAAATATTGGCAGCTA 57.243 37.500 0.00 0.00 0.00 3.32
3835 5320 8.515414 GCTTTATTAGTAGGGAAATATTGGCAG 58.485 37.037 0.00 0.00 0.00 4.85
3843 5328 6.243216 TCCGTGCTTTATTAGTAGGGAAAT 57.757 37.500 2.51 0.00 46.26 2.17
3982 5467 8.514330 TGAATAATACCAAATTACAGGGTGTC 57.486 34.615 0.00 0.00 36.14 3.67
4165 5650 1.996292 CGTGAGGACAACGATGACAT 58.004 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.