Multiple sequence alignment - TraesCS1A01G299500

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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 TraesCS1A01G299500 chr1A 100.000 6283 0 0 929 7211 494442747 494449029 0.000000e+00 11603.0
1 TraesCS1A01G299500 chr1A 100.000 590 0 0 1 590 494441819 494442408 0.000000e+00 1090.0
2 TraesCS1A01G299500 chr1A 86.047 86 12 0 1868 1953 567969924 567970009 7.700000e-15 93.5
3 TraesCS1A01G299500 chr1A 85.897 78 9 2 3249 3325 459309783 459309707 1.670000e-11 82.4
4 TraesCS1A01G299500 chr1D 93.821 3253 158 28 1952 5176 397073282 397076519 0.000000e+00 4854.0
5 TraesCS1A01G299500 chr1D 91.610 1764 84 28 5228 6954 397076516 397078252 0.000000e+00 2379.0
6 TraesCS1A01G299500 chr1D 90.632 950 56 12 931 1870 397072357 397073283 0.000000e+00 1230.0
7 TraesCS1A01G299500 chr1D 90.823 316 17 4 286 590 397072027 397072341 5.210000e-111 412.0
8 TraesCS1A01G299500 chr1D 91.575 273 16 3 25 297 397071738 397072003 3.180000e-98 370.0
9 TraesCS1A01G299500 chr1D 88.608 158 16 2 7046 7203 397078706 397078861 2.660000e-44 191.0
10 TraesCS1A01G299500 chr1D 81.132 106 20 0 6848 6953 25455433 25455538 1.290000e-12 86.1
11 TraesCS1A01G299500 chr1D 86.076 79 9 2 3249 3326 359840473 359840396 4.640000e-12 84.2
12 TraesCS1A01G299500 chr1D 85.185 81 12 0 6854 6934 433413269 433413349 4.640000e-12 84.2
13 TraesCS1A01G299500 chr1B 93.946 2362 108 25 1952 4290 532166067 532168416 0.000000e+00 3537.0
14 TraesCS1A01G299500 chr1B 95.306 980 37 6 5705 6676 532169914 532170892 0.000000e+00 1546.0
15 TraesCS1A01G299500 chr1B 95.380 909 34 5 4319 5223 532168412 532169316 0.000000e+00 1439.0
16 TraesCS1A01G299500 chr1B 93.706 715 34 5 934 1647 532165029 532165733 0.000000e+00 1061.0
17 TraesCS1A01G299500 chr1B 81.533 574 58 28 29 589 532164470 532165008 5.170000e-116 429.0
18 TraesCS1A01G299500 chr1B 86.721 369 19 12 5228 5594 532169405 532169745 4.080000e-102 383.0
19 TraesCS1A01G299500 chr1B 88.119 101 11 1 6854 6953 439850962 439851062 1.270000e-22 119.0
20 TraesCS1A01G299500 chr1B 86.076 79 9 2 3249 3326 481864828 481864751 4.640000e-12 84.2
21 TraesCS1A01G299500 chr1B 75.904 166 34 4 7046 7205 40370257 40370092 6.000000e-11 80.5
22 TraesCS1A01G299500 chr1B 79.612 103 14 4 6854 6953 359447143 359447045 4.670000e-07 67.6
23 TraesCS1A01G299500 chr2B 88.763 1148 85 21 4058 5177 612070811 612069680 0.000000e+00 1365.0
24 TraesCS1A01G299500 chr2B 88.763 1148 85 21 4058 5177 612077127 612075996 0.000000e+00 1365.0
25 TraesCS1A01G299500 chr2B 83.456 816 84 31 5670 6468 612069274 612068493 0.000000e+00 712.0
26 TraesCS1A01G299500 chr2B 83.456 816 84 31 5670 6468 612075590 612074809 0.000000e+00 712.0
27 TraesCS1A01G299500 chr2B 77.381 420 57 18 5229 5629 612069681 612069281 1.580000e-51 215.0
28 TraesCS1A01G299500 chr2B 77.381 420 57 18 5229 5629 612075997 612075597 1.580000e-51 215.0
29 TraesCS1A01G299500 chr2B 86.813 91 8 3 1869 1956 33942268 33942179 1.660000e-16 99.0
30 TraesCS1A01G299500 chr2B 94.231 52 2 1 5176 5227 532093828 532093878 2.160000e-10 78.7
31 TraesCS1A01G299500 chr2B 97.436 39 1 0 6476 6514 612068301 612068339 4.670000e-07 67.6
32 TraesCS1A01G299500 chr2B 97.436 39 1 0 6476 6514 612074617 612074655 4.670000e-07 67.6
33 TraesCS1A01G299500 chrUn 97.423 388 9 1 2834 3220 480370236 480369849 0.000000e+00 660.0
34 TraesCS1A01G299500 chrUn 88.889 63 6 1 5165 5227 110336261 110336322 7.760000e-10 76.8
35 TraesCS1A01G299500 chr5D 90.071 141 11 3 6674 6811 425429251 425429111 5.750000e-41 180.0
36 TraesCS1A01G299500 chr5D 87.333 150 16 3 6674 6820 289513914 289514063 1.240000e-37 169.0
37 TraesCS1A01G299500 chr5D 84.146 82 12 1 6854 6934 297970470 297970551 2.160000e-10 78.7
38 TraesCS1A01G299500 chr5D 83.333 84 10 3 7046 7125 108109186 108109269 2.790000e-09 75.0
39 TraesCS1A01G299500 chr3D 88.000 150 15 3 6674 6820 267491839 267491690 2.670000e-39 174.0
40 TraesCS1A01G299500 chr3D 78.313 249 46 4 6963 7205 571238294 571238540 3.480000e-33 154.0
41 TraesCS1A01G299500 chr3D 83.607 122 18 1 6952 7073 96129327 96129446 5.910000e-21 113.0
42 TraesCS1A01G299500 chr3D 84.536 97 12 2 1865 1960 565081503 565081597 7.700000e-15 93.5
43 TraesCS1A01G299500 chr3D 84.444 90 12 1 6963 7052 290790171 290790084 3.580000e-13 87.9
44 TraesCS1A01G299500 chr3D 88.710 62 5 1 5173 5232 545068019 545067958 2.790000e-09 75.0
45 TraesCS1A01G299500 chr7A 87.500 152 16 3 6674 6822 627249651 627249802 9.620000e-39 172.0
46 TraesCS1A01G299500 chr7A 83.516 91 12 3 1866 1956 501155584 501155497 1.670000e-11 82.4
47 TraesCS1A01G299500 chr7A 83.562 73 10 1 7135 7205 695003067 695002995 4.670000e-07 67.6
48 TraesCS1A01G299500 chr7A 84.211 57 9 0 7149 7205 694849609 694849553 1.000000e-03 56.5
49 TraesCS1A01G299500 chr4D 87.333 150 16 3 6674 6820 329936682 329936831 1.240000e-37 169.0
50 TraesCS1A01G299500 chr3B 87.333 150 16 3 6674 6820 243847815 243847964 1.240000e-37 169.0
51 TraesCS1A01G299500 chr3B 83.140 172 27 2 6990 7160 727262143 727261973 9.690000e-34 156.0
52 TraesCS1A01G299500 chr3B 87.324 71 7 1 7046 7116 334142217 334142285 6.000000e-11 80.5
53 TraesCS1A01G299500 chr3B 75.301 166 35 4 7046 7205 11238593 11238758 2.790000e-09 75.0
54 TraesCS1A01G299500 chr3A 87.333 150 16 3 6674 6820 277183756 277183905 1.240000e-37 169.0
55 TraesCS1A01G299500 chr3A 91.892 74 6 0 1880 1953 491189437 491189510 3.560000e-18 104.0
56 TraesCS1A01G299500 chr3A 91.525 59 3 1 5176 5232 117319967 117320025 6.000000e-11 80.5
57 TraesCS1A01G299500 chr3A 82.222 90 16 0 1865 1954 31846503 31846592 2.160000e-10 78.7
58 TraesCS1A01G299500 chr3A 91.525 59 2 2 5176 5232 603267353 603267296 2.160000e-10 78.7
59 TraesCS1A01G299500 chr3A 91.525 59 2 2 5176 5232 732054431 732054374 2.160000e-10 78.7
60 TraesCS1A01G299500 chr2D 87.333 150 16 3 6674 6820 359437617 359437766 1.240000e-37 169.0
61 TraesCS1A01G299500 chr2D 85.294 102 12 2 6854 6953 27583361 27583261 1.280000e-17 102.0
62 TraesCS1A01G299500 chr2D 97.436 39 1 0 6476 6514 520042885 520042923 4.670000e-07 67.6
63 TraesCS1A01G299500 chr7B 79.358 218 45 0 6987 7204 481282649 481282432 3.480000e-33 154.0
64 TraesCS1A01G299500 chr7B 84.615 91 10 1 1866 1956 450642199 450642113 3.580000e-13 87.9
65 TraesCS1A01G299500 chr7B 79.817 109 14 6 1858 1963 22060402 22060505 1.000000e-08 73.1
66 TraesCS1A01G299500 chr7D 82.524 103 13 3 6854 6953 18117842 18117942 1.290000e-12 86.1
67 TraesCS1A01G299500 chr7D 91.525 59 2 3 5176 5232 225203155 225203098 2.160000e-10 78.7
68 TraesCS1A01G299500 chr7D 94.118 51 2 1 5177 5227 104216886 104216935 7.760000e-10 76.8
69 TraesCS1A01G299500 chr6B 82.178 101 17 1 6854 6953 719336428 719336328 1.290000e-12 86.1
70 TraesCS1A01G299500 chr6B 82.955 88 14 1 1869 1956 29269957 29270043 2.160000e-10 78.7
71 TraesCS1A01G299500 chr4A 82.828 99 14 3 6854 6950 574846658 574846561 1.290000e-12 86.1
72 TraesCS1A01G299500 chr5A 82.105 95 15 1 7046 7140 139521062 139521154 6.000000e-11 80.5
73 TraesCS1A01G299500 chr6A 100.000 28 0 0 7046 7073 596509774 596509801 1.300000e-02 52.8


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 TraesCS1A01G299500 chr1A 494441819 494449029 7210 False 6346.500000 11603 100.000000 1 7211 2 chr1A.!!$F2 7210
1 TraesCS1A01G299500 chr1D 397071738 397078861 7123 False 1572.666667 4854 91.178167 25 7203 6 chr1D.!!$F3 7178
2 TraesCS1A01G299500 chr1B 532164470 532170892 6422 False 1399.166667 3537 91.098667 29 6676 6 chr1B.!!$F2 6647
3 TraesCS1A01G299500 chr2B 612068493 612077127 8634 True 764.000000 1365 83.200000 4058 6468 6 chr2B.!!$R2 2410

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
268 281 0.538057 TTGGAGCTTGGCAGAGTTGG 60.538 55.000 0.0 0.0 0.00 3.77 F
1310 1375 0.106894 CCCTTTCTCCCCTATCACGC 59.893 60.000 0.0 0.0 0.00 5.34 F
1311 1376 0.830648 CCTTTCTCCCCTATCACGCA 59.169 55.000 0.0 0.0 0.00 5.24 F
2772 2973 0.741326 CTCGGGAAGATCTGAAGCGA 59.259 55.000 0.0 0.0 0.00 4.93 F
3301 3503 1.199789 GGCGTTGTCTGCATTGATGAA 59.800 47.619 0.0 0.0 0.00 2.57 F
4394 4621 2.665165 TGTCCTGCATTGGAAACTGTT 58.335 42.857 0.0 0.0 37.93 3.16 F
5048 5282 1.261480 GTGAGCAGAGGGAGACTGAA 58.739 55.000 0.0 0.0 37.54 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2224 0.466739 TTATGCAGATGCTGGCCCAG 60.467 55.000 6.32 6.32 42.66 4.45 R
2444 2645 0.612732 CAGGGGCAGCATTTTCAGGA 60.613 55.000 0.00 0.00 0.00 3.86 R
3214 3416 1.202348 GGACACAGGCATTTGGTTAGC 59.798 52.381 0.00 0.00 0.00 3.09 R
4427 4656 0.470833 ATCCTATGGCAGGCGACTCT 60.471 55.000 0.00 0.00 45.10 3.24 R
4500 4731 1.032014 GCCTGGAAGAGCACAAAACA 58.968 50.000 0.00 0.00 34.07 2.83 R
5259 5577 1.483415 CCAAGAGGGGCCATTTCAATG 59.517 52.381 4.39 3.67 36.17 2.82 R
6869 13560 0.035152 TGCTAGGGATGGTGTTGCTG 60.035 55.000 0.00 0.00 0.00 4.41 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
22 23 4.058817 CGGTAGGATCAGTTAGAAATGCC 58.941 47.826 0.00 0.00 0.00 4.40
23 24 4.390264 GGTAGGATCAGTTAGAAATGCCC 58.610 47.826 0.00 0.00 0.00 5.36
91 101 2.035442 GTTGCGTCCTCTTCCCTGC 61.035 63.158 0.00 0.00 0.00 4.85
191 204 2.959275 GGTACGTCGCTCAATCCTG 58.041 57.895 0.00 0.00 0.00 3.86
212 225 2.186076 GGAGTCTCGCAATACAACTCG 58.814 52.381 0.00 0.00 37.76 4.18
213 226 1.584308 GAGTCTCGCAATACAACTCGC 59.416 52.381 0.00 0.00 0.00 5.03
214 227 1.202582 AGTCTCGCAATACAACTCGCT 59.797 47.619 0.00 0.00 0.00 4.93
215 228 1.584308 GTCTCGCAATACAACTCGCTC 59.416 52.381 0.00 0.00 0.00 5.03
259 272 4.659172 TGGCCGGTTGGAGCTTGG 62.659 66.667 1.90 0.00 37.49 3.61
268 281 0.538057 TTGGAGCTTGGCAGAGTTGG 60.538 55.000 0.00 0.00 0.00 3.77
324 372 2.625823 CCGAATGTGGCAAACGGCT 61.626 57.895 9.21 0.00 44.01 5.52
334 382 1.671054 CAAACGGCTGTCGATGGGT 60.671 57.895 9.35 0.00 42.43 4.51
363 411 2.709883 GCAAAATAGCAGCGGCCCA 61.710 57.895 4.82 0.00 42.56 5.36
379 427 2.350895 CAGATCCACGTGGCCCAA 59.649 61.111 30.25 13.34 34.44 4.12
523 582 4.473520 CGCCAACATCTCCCGCCT 62.474 66.667 0.00 0.00 0.00 5.52
973 1032 4.410400 CTCCCACCCCCGAAGCAC 62.410 72.222 0.00 0.00 0.00 4.40
1079 1138 1.153823 AAGACGTAAGCGCGCATCT 60.154 52.632 35.10 22.63 42.83 2.90
1080 1139 1.140407 AAGACGTAAGCGCGCATCTC 61.140 55.000 35.10 18.71 42.83 2.75
1081 1140 2.577785 GACGTAAGCGCGCATCTCC 61.578 63.158 35.10 14.63 42.83 3.71
1082 1141 3.330853 CGTAAGCGCGCATCTCCC 61.331 66.667 35.10 13.14 0.00 4.30
1083 1142 2.967615 GTAAGCGCGCATCTCCCC 60.968 66.667 35.10 9.49 0.00 4.81
1084 1143 3.154473 TAAGCGCGCATCTCCCCT 61.154 61.111 35.10 6.63 0.00 4.79
1085 1144 3.151958 TAAGCGCGCATCTCCCCTC 62.152 63.158 35.10 0.00 0.00 4.30
1141 1203 2.423577 GGCTCCTGTATGACGTTTTGT 58.576 47.619 0.00 0.00 0.00 2.83
1303 1368 2.689034 CGCCTCCCTTTCTCCCCT 60.689 66.667 0.00 0.00 0.00 4.79
1305 1370 0.764752 CGCCTCCCTTTCTCCCCTAT 60.765 60.000 0.00 0.00 0.00 2.57
1306 1371 1.060729 GCCTCCCTTTCTCCCCTATC 58.939 60.000 0.00 0.00 0.00 2.08
1307 1372 1.695989 GCCTCCCTTTCTCCCCTATCA 60.696 57.143 0.00 0.00 0.00 2.15
1308 1373 2.050918 CCTCCCTTTCTCCCCTATCAC 58.949 57.143 0.00 0.00 0.00 3.06
1309 1374 1.689273 CTCCCTTTCTCCCCTATCACG 59.311 57.143 0.00 0.00 0.00 4.35
1310 1375 0.106894 CCCTTTCTCCCCTATCACGC 59.893 60.000 0.00 0.00 0.00 5.34
1311 1376 0.830648 CCTTTCTCCCCTATCACGCA 59.169 55.000 0.00 0.00 0.00 5.24
1312 1377 1.473434 CCTTTCTCCCCTATCACGCAC 60.473 57.143 0.00 0.00 0.00 5.34
1341 1407 1.295423 CCTGGTCGATTCGGTGGTT 59.705 57.895 6.18 0.00 0.00 3.67
1347 1413 1.153309 CGATTCGGTGGTTACCCCC 60.153 63.158 0.00 0.00 44.53 5.40
1599 1665 0.999712 GAATCCCTTTCTCCCCACCA 59.000 55.000 0.00 0.00 0.00 4.17
1606 1672 3.205282 CCCTTTCTCCCCACCATAATCTT 59.795 47.826 0.00 0.00 0.00 2.40
1621 1687 5.681105 CCATAATCTTGTTTTATGCCGTTCG 59.319 40.000 0.00 0.00 36.27 3.95
1625 1691 3.315749 TCTTGTTTTATGCCGTTCGGTTT 59.684 39.130 12.81 3.62 0.00 3.27
1673 1853 7.497595 TGTATTAGTATTACACTGGCCAGAAG 58.502 38.462 39.19 29.66 38.24 2.85
1698 1878 5.587388 ATCTGAAAAGTTCCCGTCGTATA 57.413 39.130 0.00 0.00 0.00 1.47
1703 1883 5.415701 TGAAAAGTTCCCGTCGTATACTAGT 59.584 40.000 0.00 0.00 0.00 2.57
1718 1898 8.494347 TCGTATACTAGTATTTCTCTTTCTCGC 58.506 37.037 20.21 0.00 0.00 5.03
1734 1914 4.274602 TCTCGCGGAGAATAGATCTAGT 57.725 45.455 6.13 5.36 38.96 2.57
1806 1988 6.190954 CCAGTATTTGGTTTAAGGCAGTAC 57.809 41.667 0.00 0.00 42.41 2.73
1808 1990 4.939439 AGTATTTGGTTTAAGGCAGTACGG 59.061 41.667 0.00 0.00 0.00 4.02
1810 1992 3.706600 TTGGTTTAAGGCAGTACGGAT 57.293 42.857 0.00 0.00 0.00 4.18
1823 2005 4.271776 GCAGTACGGATATACCACCAAAAC 59.728 45.833 0.00 0.00 38.90 2.43
1825 2007 3.891422 ACGGATATACCACCAAAACGA 57.109 42.857 0.00 0.00 38.90 3.85
1827 2009 3.448301 ACGGATATACCACCAAAACGAGA 59.552 43.478 0.00 0.00 38.90 4.04
1830 2012 6.183360 ACGGATATACCACCAAAACGAGAATA 60.183 38.462 0.00 0.00 38.90 1.75
1887 2071 9.588096 AAACATCTACTCCCTTTTTATCAAAGT 57.412 29.630 0.00 0.00 0.00 2.66
1897 2081 9.457436 TCCCTTTTTATCAAAGTATAAGACACC 57.543 33.333 0.00 0.00 0.00 4.16
1898 2082 9.462606 CCCTTTTTATCAAAGTATAAGACACCT 57.537 33.333 0.00 0.00 0.00 4.00
1904 2088 6.569179 TCAAAGTATAAGACACCTTTTGGC 57.431 37.500 0.00 0.00 45.59 4.52
1905 2089 6.065374 TCAAAGTATAAGACACCTTTTGGCA 58.935 36.000 0.00 0.00 45.59 4.92
1906 2090 5.959618 AAGTATAAGACACCTTTTGGCAC 57.040 39.130 0.00 0.00 45.59 5.01
1907 2091 5.242795 AGTATAAGACACCTTTTGGCACT 57.757 39.130 0.00 0.00 45.59 4.40
1908 2092 6.368779 AGTATAAGACACCTTTTGGCACTA 57.631 37.500 0.00 0.00 45.59 2.74
1909 2093 6.958767 AGTATAAGACACCTTTTGGCACTAT 58.041 36.000 0.00 0.00 45.59 2.12
1910 2094 7.048512 AGTATAAGACACCTTTTGGCACTATC 58.951 38.462 0.00 0.00 45.59 2.08
1911 2095 2.699954 AGACACCTTTTGGCACTATCG 58.300 47.619 0.00 0.00 45.59 2.92
1912 2096 2.038557 AGACACCTTTTGGCACTATCGT 59.961 45.455 0.00 0.00 45.59 3.73
1913 2097 3.259876 AGACACCTTTTGGCACTATCGTA 59.740 43.478 0.00 0.00 45.59 3.43
1914 2098 3.596214 ACACCTTTTGGCACTATCGTAG 58.404 45.455 0.00 0.00 45.59 3.51
1915 2099 3.007614 ACACCTTTTGGCACTATCGTAGT 59.992 43.478 0.00 0.00 45.59 2.73
1951 2135 9.213777 TGTCTTATATTTTGATACAGAGGGAGT 57.786 33.333 0.00 0.00 0.00 3.85
1961 2145 5.189736 TGATACAGAGGGAGTAGTTTTGCAT 59.810 40.000 0.00 0.00 0.00 3.96
1971 2155 5.337578 AGTAGTTTTGCATTTGTGGTGTT 57.662 34.783 0.00 0.00 0.00 3.32
1987 2171 3.505680 TGGTGTTAGTGCAGCCAATTTAG 59.494 43.478 0.00 0.00 36.16 1.85
1990 2174 3.440173 TGTTAGTGCAGCCAATTTAGCTC 59.560 43.478 0.00 0.00 38.95 4.09
1991 2175 2.503895 AGTGCAGCCAATTTAGCTCT 57.496 45.000 0.00 0.00 38.95 4.09
1992 2176 2.800250 AGTGCAGCCAATTTAGCTCTT 58.200 42.857 0.00 0.00 38.95 2.85
1993 2177 2.490903 AGTGCAGCCAATTTAGCTCTTG 59.509 45.455 0.00 0.00 38.95 3.02
1997 2181 4.336433 TGCAGCCAATTTAGCTCTTGATAC 59.664 41.667 0.00 0.00 38.95 2.24
1998 2182 4.578105 GCAGCCAATTTAGCTCTTGATACT 59.422 41.667 0.00 0.00 38.95 2.12
2000 2184 5.587844 CAGCCAATTTAGCTCTTGATACTGT 59.412 40.000 0.00 0.00 38.95 3.55
2016 2207 6.185511 TGATACTGTGTGTAGCTAACTAGGT 58.814 40.000 0.00 0.00 38.29 3.08
2031 2227 3.375699 ACTAGGTATGTCCTTGTCCTGG 58.624 50.000 0.00 0.00 46.24 4.45
2042 2238 2.124403 GTCCTGGGCCAGCATCTG 60.124 66.667 28.51 14.08 0.00 2.90
2056 2252 4.476862 CAGCATCTGCATAATTCATGAGC 58.523 43.478 4.79 0.00 45.16 4.26
2108 2308 4.986054 TTTAGTGCCTTTTACTCCCTGA 57.014 40.909 0.00 0.00 0.00 3.86
2109 2309 4.553330 TTAGTGCCTTTTACTCCCTGAG 57.447 45.455 0.00 0.00 35.52 3.35
2125 2325 6.134535 TCCCTGAGGCTAATGTTCTTTTAA 57.865 37.500 0.00 0.00 0.00 1.52
2127 2327 6.603201 TCCCTGAGGCTAATGTTCTTTTAATG 59.397 38.462 0.00 0.00 0.00 1.90
2211 2411 1.453155 CCACTGCGGCTTTTATGTCT 58.547 50.000 0.00 0.00 0.00 3.41
2229 2429 3.513912 TGTCTCGTGAATACAGGGACATT 59.486 43.478 0.00 0.00 37.28 2.71
2332 2532 3.587061 TCAAGGAAGCCTCTTCCATGTTA 59.413 43.478 23.04 7.87 41.00 2.41
2335 2535 2.620585 GGAAGCCTCTTCCATGTTATGC 59.379 50.000 18.00 0.00 38.45 3.14
2444 2645 2.821969 GACATTGTCCATGCAAGAGGTT 59.178 45.455 5.44 0.00 36.14 3.50
2519 2720 7.551035 AGAAGATGATCTTGTAGATTGTTGC 57.449 36.000 13.18 0.00 36.73 4.17
2609 2810 5.221382 TGTTAGTGGTGTCTTCAGGTTAGTC 60.221 44.000 0.00 0.00 0.00 2.59
2627 2828 6.460399 GGTTAGTCTATCTACTGCCTTCACAG 60.460 46.154 0.00 0.00 43.59 3.66
2631 2832 5.126384 GTCTATCTACTGCCTTCACAGAAGT 59.874 44.000 6.08 0.00 40.25 3.01
2706 2907 3.452627 CCTACAGGACTGTCCTTATTGCT 59.547 47.826 26.37 9.58 46.91 3.91
2736 2937 3.558931 TCACTTCTGAACAAAGAGGCA 57.441 42.857 0.00 0.00 0.00 4.75
2742 2943 2.030893 TCTGAACAAAGAGGCAAATGCG 60.031 45.455 0.00 0.00 43.26 4.73
2772 2973 0.741326 CTCGGGAAGATCTGAAGCGA 59.259 55.000 0.00 0.00 0.00 4.93
2931 3132 3.583228 TGGAACTCACTTGAGAGGGTTA 58.417 45.455 13.27 0.00 44.74 2.85
2972 3173 5.840243 ATTGCTGCTGCTATATGTTTTCA 57.160 34.783 17.00 0.00 40.48 2.69
3088 3289 2.509548 AGCTGTTATGAACATAGCCCCA 59.490 45.455 6.29 0.00 41.26 4.96
3176 3377 2.464157 AGAGACTGGTAAGTTGCTGC 57.536 50.000 0.00 0.00 36.52 5.25
3193 3395 2.095567 GCTGCAGTTGTCCATACACTTG 60.096 50.000 16.64 0.00 34.61 3.16
3214 3416 6.771188 TTGTGTTTGGTTTTTGTACAAGTG 57.229 33.333 8.56 0.00 0.00 3.16
3301 3503 1.199789 GGCGTTGTCTGCATTGATGAA 59.800 47.619 0.00 0.00 0.00 2.57
3459 3661 9.499479 AATATATGGATCTGTAAGTTCTTGCAG 57.501 33.333 19.40 19.40 36.23 4.41
3460 3662 4.623932 TGGATCTGTAAGTTCTTGCAGT 57.376 40.909 22.61 14.08 36.30 4.40
3482 3684 6.418819 CAGTTTCTTTTCTGTGCTGTTAATGG 59.581 38.462 0.00 0.00 0.00 3.16
3531 3734 6.840527 TCTGATGATAATTTCTGGTGGCATA 58.159 36.000 0.00 0.00 0.00 3.14
3619 3822 9.146270 CGTTTTGATTTGCTTTTTATTGTTCTG 57.854 29.630 0.00 0.00 0.00 3.02
3740 3943 4.261741 CGGCAATGAGATTTATTTCAGGGG 60.262 45.833 0.00 0.00 0.00 4.79
3747 3950 6.925934 TGAGATTTATTTCAGGGGATTCCAT 58.074 36.000 4.80 0.00 38.24 3.41
3763 3966 5.279657 GGATTCCATTTCTTTCCAAGTGCTT 60.280 40.000 0.00 0.00 0.00 3.91
3768 3971 7.153985 TCCATTTCTTTCCAAGTGCTTAATTG 58.846 34.615 0.00 0.00 0.00 2.32
4131 4336 8.877808 TCTCTGATTACAATTATGCTGTGTAG 57.122 34.615 0.00 0.00 0.00 2.74
4154 4379 7.817418 AGAATACTACTTTCTGTTTTTGGCA 57.183 32.000 0.00 0.00 32.30 4.92
4160 4385 5.083533 ACTTTCTGTTTTTGGCATTGTCA 57.916 34.783 0.00 0.00 0.00 3.58
4216 4442 8.637196 TTTCATGTGTTAACATAATACACCCA 57.363 30.769 12.26 1.89 45.50 4.51
4313 4539 9.516314 GGTATTGTTCTATTTATCCTGCAAAAC 57.484 33.333 0.00 0.00 0.00 2.43
4320 4546 8.402798 TCTATTTATCCTGCAAAACACTTTGA 57.597 30.769 1.86 0.00 44.03 2.69
4394 4621 2.665165 TGTCCTGCATTGGAAACTGTT 58.335 42.857 0.00 0.00 37.93 3.16
4402 4631 5.587289 TGCATTGGAAACTGTTAAGTCAAC 58.413 37.500 0.00 0.00 34.77 3.18
4427 4656 7.615365 ACTGTGCCTTATATTTTGAAATCTGGA 59.385 33.333 0.00 0.00 0.00 3.86
4899 5131 1.419387 GAAGGATAGCAGGCACAGGAT 59.581 52.381 0.00 0.00 0.00 3.24
5048 5282 1.261480 GTGAGCAGAGGGAGACTGAA 58.739 55.000 0.00 0.00 37.54 3.02
5058 5292 5.125417 CAGAGGGAGACTGAAAAACAACAAA 59.875 40.000 0.00 0.00 37.54 2.83
5102 5336 2.375174 TGGTGATAATGTAGATGGGCCC 59.625 50.000 17.59 17.59 0.00 5.80
5184 5418 2.897969 TGTCAAGTGTTCTACTCCCTCC 59.102 50.000 0.00 0.00 39.18 4.30
5185 5419 2.897969 GTCAAGTGTTCTACTCCCTCCA 59.102 50.000 0.00 0.00 39.18 3.86
5284 5603 1.739608 AATGGCCCCTCTTGGTTGGT 61.740 55.000 0.00 0.00 0.00 3.67
5320 5639 9.740710 AAAATAGCCTGTCTCTATTTAACTGTT 57.259 29.630 8.00 0.00 42.59 3.16
5390 5726 9.813826 ATCCCCTTTATGTTAAATGGAGATAAG 57.186 33.333 3.70 0.00 0.00 1.73
5391 5727 9.009675 TCCCCTTTATGTTAAATGGAGATAAGA 57.990 33.333 3.70 0.00 0.00 2.10
5392 5728 9.289782 CCCCTTTATGTTAAATGGAGATAAGAG 57.710 37.037 3.70 0.00 0.00 2.85
5400 5736 3.699411 ATGGAGATAAGAGATGCTGCC 57.301 47.619 0.00 0.00 0.00 4.85
5409 5745 6.902416 AGATAAGAGATGCTGCCTATTAGGAT 59.098 38.462 14.16 0.00 37.67 3.24
5410 5746 5.839517 AAGAGATGCTGCCTATTAGGATT 57.160 39.130 14.16 0.00 37.67 3.01
5478 5815 5.246203 ACATGAACTCCACTTTACAGAGCTA 59.754 40.000 0.00 0.00 0.00 3.32
5598 5947 1.613437 GGTATGCCAAAACACTGCACT 59.387 47.619 0.00 0.00 37.92 4.40
5601 5950 0.459489 TGCCAAAACACTGCACTTCC 59.541 50.000 0.00 0.00 0.00 3.46
5632 12290 2.009774 ACATTTAGCTAGGCGTGCAAG 58.990 47.619 7.43 0.00 0.00 4.01
5642 12300 0.039256 GGCGTGCAAGCTCATGAAAA 60.039 50.000 23.72 0.00 37.29 2.29
5674 12332 6.316890 ACTGTTTTGCTGCAAATTGAAAAGAT 59.683 30.769 26.48 6.38 33.19 2.40
5821 12486 3.748568 GGATGTTTCTTCACAGAGGTCAC 59.251 47.826 0.00 0.00 0.00 3.67
5839 12504 4.261994 GGTCACTGCTTTGCCTGAAATTTA 60.262 41.667 0.00 0.00 0.00 1.40
5902 12567 6.467677 TGAATTGTTTTGTTTCCCTTGTGAA 58.532 32.000 0.00 0.00 0.00 3.18
6096 12773 4.846940 AGGGTTTTCTTCAGTGAGATACCT 59.153 41.667 15.66 8.17 34.06 3.08
6193 12870 4.194640 CAGGATAATGATAAGGGATGGCG 58.805 47.826 0.00 0.00 0.00 5.69
6278 12955 2.093973 TCCTGATCTGTTCTCCGCTTTC 60.094 50.000 0.00 0.00 0.00 2.62
6323 13000 0.242017 GAAACTCTGCATGTGTGGCC 59.758 55.000 0.00 0.00 0.00 5.36
6345 13022 3.610242 CGAGCTGTCTGTTGATGTACTTC 59.390 47.826 0.00 1.85 0.00 3.01
6346 13023 3.929610 GAGCTGTCTGTTGATGTACTTCC 59.070 47.826 6.32 0.00 0.00 3.46
6430 13113 6.188407 TGTCTGACCTAGTGCTATTTAGTCT 58.812 40.000 5.17 0.00 0.00 3.24
6446 13129 9.906660 CTATTTAGTCTCTGATTATGTCTGGTC 57.093 37.037 0.00 0.00 0.00 4.02
6590 13274 1.202510 TCGCTTGCTTGTTTGCCAAAT 60.203 42.857 0.00 0.00 31.20 2.32
6602 13287 2.529780 TGCCAAATTCTTGTTGCCTG 57.470 45.000 0.00 0.00 0.00 4.85
6715 13402 9.696917 GCCAAGTGGATATTAAAATTTCTATGG 57.303 33.333 0.18 0.00 37.39 2.74
6839 13530 2.151202 CTTGTCCTGGTACAAACGCAT 58.849 47.619 11.16 0.00 38.81 4.73
6842 13533 0.250510 TCCTGGTACAAACGCATGCA 60.251 50.000 19.57 0.00 38.70 3.96
6862 13553 0.605319 CCCACAACACACATAGGCGT 60.605 55.000 0.00 0.00 0.00 5.68
6896 13587 0.543277 CCATCCCTAGCACTGCAAGA 59.457 55.000 3.30 0.00 37.43 3.02
6909 13600 4.020617 CAAGAGCGGCCAGGGTGA 62.021 66.667 2.24 0.00 0.00 4.02
6910 13601 4.021925 AAGAGCGGCCAGGGTGAC 62.022 66.667 2.24 0.00 0.00 3.67
6934 13625 0.167908 TTGAACATGCCATCGCGAAC 59.832 50.000 15.24 6.54 38.08 3.95
6937 13628 0.810648 AACATGCCATCGCGAACAAT 59.189 45.000 15.24 1.55 38.08 2.71
6944 13635 1.538276 CATCGCGAACAATTGAAGCC 58.462 50.000 15.24 0.00 0.00 4.35
6953 13976 4.555313 CGAACAATTGAAGCCGCATATGAT 60.555 41.667 13.59 0.00 0.00 2.45
6959 13982 2.263077 GAAGCCGCATATGATACGAGG 58.737 52.381 6.97 0.56 0.00 4.63
6988 14011 1.673009 CGCCTTTTTCGCACCCCTA 60.673 57.895 0.00 0.00 0.00 3.53
7013 14036 3.760035 CCCGGTGTCGAGACCCAG 61.760 72.222 24.74 16.37 39.00 4.45
7015 14038 1.676635 CCGGTGTCGAGACCCAGTA 60.677 63.158 24.74 0.00 39.00 2.74
7018 14041 1.511768 GTGTCGAGACCCAGTAGGC 59.488 63.158 0.17 0.00 40.58 3.93
7023 14046 4.400251 AGACCCAGTAGGCCGGCT 62.400 66.667 28.56 15.07 40.58 5.52
7024 14047 4.162690 GACCCAGTAGGCCGGCTG 62.163 72.222 28.56 16.81 40.58 4.85
7028 14051 1.745489 CCAGTAGGCCGGCTGAAAC 60.745 63.158 28.56 18.36 34.87 2.78
7030 14053 0.535335 CAGTAGGCCGGCTGAAACTA 59.465 55.000 28.56 15.88 34.87 2.24
7049 14072 2.442272 CCTCCATCGACCCGTCCT 60.442 66.667 0.00 0.00 0.00 3.85
7118 14170 2.052690 GCTCGGTCCTGCTACCAGA 61.053 63.158 4.68 2.60 41.77 3.86
7120 14172 0.965866 CTCGGTCCTGCTACCAGACA 60.966 60.000 4.68 0.00 41.77 3.41
7125 14177 0.965866 TCCTGCTACCAGACACGAGG 60.966 60.000 0.00 0.00 41.77 4.63
7148 14200 3.963476 AGGTCAGTCCTGCTACTAGAT 57.037 47.619 0.00 0.00 46.19 1.98
7192 14244 2.680370 GGGAGATGGCCGACCCTTT 61.680 63.158 15.92 0.00 39.28 3.11
7195 14247 0.181350 GAGATGGCCGACCCTTTGAT 59.819 55.000 0.00 0.00 33.59 2.57
7203 14255 2.678336 GCCGACCCTTTGATGAAAGTAG 59.322 50.000 3.91 0.00 37.47 2.57
7204 14256 2.678336 CCGACCCTTTGATGAAAGTAGC 59.322 50.000 3.91 0.00 37.47 3.58
7205 14257 3.334691 CGACCCTTTGATGAAAGTAGCA 58.665 45.455 3.91 0.00 37.47 3.49
7206 14258 3.125316 CGACCCTTTGATGAAAGTAGCAC 59.875 47.826 3.91 0.00 37.47 4.40
7207 14259 4.072131 GACCCTTTGATGAAAGTAGCACA 58.928 43.478 3.91 0.00 37.47 4.57
7208 14260 3.821033 ACCCTTTGATGAAAGTAGCACAC 59.179 43.478 3.91 0.00 37.47 3.82
7209 14261 3.820467 CCCTTTGATGAAAGTAGCACACA 59.180 43.478 3.91 0.00 37.47 3.72
7210 14262 4.083110 CCCTTTGATGAAAGTAGCACACAG 60.083 45.833 3.91 0.00 37.47 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.058817 GGCATTTCTAACTGATCCTACCG 58.941 47.826 0.00 0.00 0.00 4.02
1 2 4.141482 TGGGCATTTCTAACTGATCCTACC 60.141 45.833 0.00 0.00 0.00 3.18
2 3 5.036117 TGGGCATTTCTAACTGATCCTAC 57.964 43.478 0.00 0.00 0.00 3.18
3 4 4.721776 ACTGGGCATTTCTAACTGATCCTA 59.278 41.667 0.00 0.00 0.00 2.94
4 5 3.525199 ACTGGGCATTTCTAACTGATCCT 59.475 43.478 0.00 0.00 0.00 3.24
5 6 3.891049 ACTGGGCATTTCTAACTGATCC 58.109 45.455 0.00 0.00 0.00 3.36
6 7 5.675538 AGTACTGGGCATTTCTAACTGATC 58.324 41.667 0.00 0.00 0.00 2.92
7 8 5.700402 AGTACTGGGCATTTCTAACTGAT 57.300 39.130 0.00 0.00 0.00 2.90
8 9 5.499004 AAGTACTGGGCATTTCTAACTGA 57.501 39.130 0.00 0.00 0.00 3.41
9 10 5.585047 GGTAAGTACTGGGCATTTCTAACTG 59.415 44.000 0.00 0.00 0.00 3.16
10 11 5.338953 GGGTAAGTACTGGGCATTTCTAACT 60.339 44.000 0.00 0.00 0.00 2.24
11 12 4.880120 GGGTAAGTACTGGGCATTTCTAAC 59.120 45.833 0.00 0.00 0.00 2.34
12 13 4.536888 TGGGTAAGTACTGGGCATTTCTAA 59.463 41.667 0.00 0.00 0.00 2.10
13 14 4.105577 TGGGTAAGTACTGGGCATTTCTA 58.894 43.478 0.00 0.00 0.00 2.10
14 15 2.916934 TGGGTAAGTACTGGGCATTTCT 59.083 45.455 0.00 0.00 0.00 2.52
15 16 3.279434 CTGGGTAAGTACTGGGCATTTC 58.721 50.000 0.00 0.00 0.00 2.17
16 17 2.025321 CCTGGGTAAGTACTGGGCATTT 60.025 50.000 0.00 0.00 0.00 2.32
17 18 1.564348 CCTGGGTAAGTACTGGGCATT 59.436 52.381 0.00 0.00 0.00 3.56
18 19 1.213296 CCTGGGTAAGTACTGGGCAT 58.787 55.000 0.00 0.00 0.00 4.40
19 20 0.178885 ACCTGGGTAAGTACTGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
20 21 0.989602 AACCTGGGTAAGTACTGGGC 59.010 55.000 0.00 0.00 0.00 5.36
21 22 5.446260 AATAAACCTGGGTAAGTACTGGG 57.554 43.478 0.00 0.00 0.00 4.45
22 23 6.150474 CACAAATAAACCTGGGTAAGTACTGG 59.850 42.308 0.00 0.00 0.00 4.00
23 24 6.150474 CCACAAATAAACCTGGGTAAGTACTG 59.850 42.308 0.00 0.00 0.00 2.74
78 85 2.182030 CGACGCAGGGAAGAGGAC 59.818 66.667 0.00 0.00 0.00 3.85
91 101 4.135153 CAGGGCTCTCCACCGACG 62.135 72.222 0.00 0.00 38.24 5.12
178 191 0.179097 GACTCCCAGGATTGAGCGAC 60.179 60.000 0.00 0.00 31.65 5.19
191 204 2.541556 GAGTTGTATTGCGAGACTCCC 58.458 52.381 0.00 0.00 32.58 4.30
273 286 1.522580 GCCTGGAAGAGTGGCGATC 60.523 63.158 0.00 0.00 37.11 3.69
274 287 2.586792 GCCTGGAAGAGTGGCGAT 59.413 61.111 0.00 0.00 37.11 4.58
275 288 3.706373 GGCCTGGAAGAGTGGCGA 61.706 66.667 0.00 0.00 46.97 5.54
277 290 4.021925 ACGGCCTGGAAGAGTGGC 62.022 66.667 0.00 0.00 45.42 5.01
283 296 1.966451 GAACACCACGGCCTGGAAG 60.966 63.158 23.24 17.42 43.95 3.46
298 346 3.590824 CCACATTCGGCCCAGAAC 58.409 61.111 0.00 0.00 32.39 3.01
343 391 1.226773 GGCCGCTGCTATTTTGCTG 60.227 57.895 0.00 0.00 37.74 4.41
363 411 2.185310 GACTTGGGCCACGTGGATCT 62.185 60.000 38.30 12.76 37.39 2.75
379 427 3.137459 CTCTCGCTCGCCAGGACT 61.137 66.667 0.00 0.00 0.00 3.85
387 435 2.942879 CGGATCCTCTCTCGCTCG 59.057 66.667 10.75 0.00 0.00 5.03
391 439 2.519541 TGGGCGGATCCTCTCTCG 60.520 66.667 10.75 0.00 34.39 4.04
523 582 2.266689 GCGTTTTAGGCGGGAGGA 59.733 61.111 0.00 0.00 0.00 3.71
551 610 0.563173 TGGGTTTGGATTTGGGGACA 59.437 50.000 0.00 0.00 39.83 4.02
928 987 2.015726 GGAGGGAGAGGGGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
929 988 2.612251 GGAGGGAGAGGGGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
930 989 3.036959 GGGAGGGAGAGGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
931 990 4.548513 CGGGAGGGAGAGGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
1172 1234 1.375908 CACGGCCTGCATGTACACT 60.376 57.895 0.00 0.00 0.00 3.55
1284 1346 2.687566 GGGAGAAAGGGAGGCGGA 60.688 66.667 0.00 0.00 0.00 5.54
1303 1368 1.153529 AAATCGGCGGTGCGTGATA 60.154 52.632 7.21 0.00 0.00 2.15
1305 1370 3.418913 CAAATCGGCGGTGCGTGA 61.419 61.111 7.21 0.00 0.00 4.35
1341 1407 2.158385 ACAGATGCAACAAAAGGGGGTA 60.158 45.455 0.00 0.00 0.00 3.69
1347 1413 3.820467 TCACCCTACAGATGCAACAAAAG 59.180 43.478 0.00 0.00 0.00 2.27
1599 1665 5.355910 ACCGAACGGCATAAAACAAGATTAT 59.644 36.000 13.32 0.00 39.32 1.28
1606 1672 4.215827 ACATAAACCGAACGGCATAAAACA 59.784 37.500 13.32 0.00 39.32 2.83
1673 1853 3.992427 ACGACGGGAACTTTTCAGATAAC 59.008 43.478 0.00 0.00 0.00 1.89
1698 1878 4.639310 TCCGCGAGAAAGAGAAATACTAGT 59.361 41.667 8.23 0.00 0.00 2.57
1703 1883 4.713824 TTCTCCGCGAGAAAGAGAAATA 57.286 40.909 18.39 1.33 44.37 1.40
1718 1898 7.324856 CGATTTCAACACTAGATCTATTCTCCG 59.675 40.741 2.11 0.00 35.79 4.63
1734 1914 1.606668 GGCTGTTCCACGATTTCAACA 59.393 47.619 0.00 0.00 34.01 3.33
1791 1973 5.221501 GGTATATCCGTACTGCCTTAAACCA 60.222 44.000 0.00 0.00 0.00 3.67
1805 1987 3.448301 TCTCGTTTTGGTGGTATATCCGT 59.552 43.478 0.00 0.00 39.52 4.69
1806 1988 4.049546 TCTCGTTTTGGTGGTATATCCG 57.950 45.455 0.00 0.00 39.52 4.18
1871 2055 9.457436 GGTGTCTTATACTTTGATAAAAAGGGA 57.543 33.333 3.15 0.00 0.00 4.20
1872 2056 9.462606 AGGTGTCTTATACTTTGATAAAAAGGG 57.537 33.333 3.15 0.00 0.00 3.95
1878 2062 8.736244 GCCAAAAGGTGTCTTATACTTTGATAA 58.264 33.333 0.00 0.00 33.79 1.75
1879 2063 7.885922 TGCCAAAAGGTGTCTTATACTTTGATA 59.114 33.333 0.00 0.00 33.79 2.15
1880 2064 6.719370 TGCCAAAAGGTGTCTTATACTTTGAT 59.281 34.615 0.00 0.00 33.79 2.57
1881 2065 6.016610 GTGCCAAAAGGTGTCTTATACTTTGA 60.017 38.462 0.00 0.00 33.79 2.69
1882 2066 6.016276 AGTGCCAAAAGGTGTCTTATACTTTG 60.016 38.462 0.00 0.00 33.79 2.77
1883 2067 6.068670 AGTGCCAAAAGGTGTCTTATACTTT 58.931 36.000 0.00 0.00 34.87 2.66
1884 2068 5.631119 AGTGCCAAAAGGTGTCTTATACTT 58.369 37.500 0.00 0.00 32.01 2.24
1885 2069 5.242795 AGTGCCAAAAGGTGTCTTATACT 57.757 39.130 0.00 0.00 32.01 2.12
1886 2070 6.018994 CGATAGTGCCAAAAGGTGTCTTATAC 60.019 42.308 0.00 0.00 32.01 1.47
1887 2071 6.046593 CGATAGTGCCAAAAGGTGTCTTATA 58.953 40.000 0.00 0.00 32.01 0.98
1888 2072 4.876107 CGATAGTGCCAAAAGGTGTCTTAT 59.124 41.667 0.00 0.00 32.01 1.73
1889 2073 4.250464 CGATAGTGCCAAAAGGTGTCTTA 58.750 43.478 0.00 0.00 32.01 2.10
1890 2074 3.074412 CGATAGTGCCAAAAGGTGTCTT 58.926 45.455 0.00 0.00 34.07 3.01
1891 2075 2.699954 CGATAGTGCCAAAAGGTGTCT 58.300 47.619 0.00 0.00 0.00 3.41
1925 2109 9.213777 ACTCCCTCTGTATCAAAATATAAGACA 57.786 33.333 0.00 0.00 0.00 3.41
1932 2116 9.667107 CAAAACTACTCCCTCTGTATCAAAATA 57.333 33.333 0.00 0.00 0.00 1.40
1933 2117 7.121315 GCAAAACTACTCCCTCTGTATCAAAAT 59.879 37.037 0.00 0.00 0.00 1.82
1934 2118 6.430000 GCAAAACTACTCCCTCTGTATCAAAA 59.570 38.462 0.00 0.00 0.00 2.44
1935 2119 5.938125 GCAAAACTACTCCCTCTGTATCAAA 59.062 40.000 0.00 0.00 0.00 2.69
1936 2120 5.012664 TGCAAAACTACTCCCTCTGTATCAA 59.987 40.000 0.00 0.00 0.00 2.57
1937 2121 4.530553 TGCAAAACTACTCCCTCTGTATCA 59.469 41.667 0.00 0.00 0.00 2.15
1938 2122 5.086104 TGCAAAACTACTCCCTCTGTATC 57.914 43.478 0.00 0.00 0.00 2.24
1939 2123 5.700402 ATGCAAAACTACTCCCTCTGTAT 57.300 39.130 0.00 0.00 0.00 2.29
1940 2124 5.499004 AATGCAAAACTACTCCCTCTGTA 57.501 39.130 0.00 0.00 0.00 2.74
1941 2125 4.373156 AATGCAAAACTACTCCCTCTGT 57.627 40.909 0.00 0.00 0.00 3.41
1942 2126 4.520492 ACAAATGCAAAACTACTCCCTCTG 59.480 41.667 0.00 0.00 0.00 3.35
1943 2127 4.520492 CACAAATGCAAAACTACTCCCTCT 59.480 41.667 0.00 0.00 0.00 3.69
1944 2128 4.321230 CCACAAATGCAAAACTACTCCCTC 60.321 45.833 0.00 0.00 0.00 4.30
1945 2129 3.573967 CCACAAATGCAAAACTACTCCCT 59.426 43.478 0.00 0.00 0.00 4.20
1946 2130 3.320826 ACCACAAATGCAAAACTACTCCC 59.679 43.478 0.00 0.00 0.00 4.30
1947 2131 4.202111 ACACCACAAATGCAAAACTACTCC 60.202 41.667 0.00 0.00 0.00 3.85
1948 2132 4.932146 ACACCACAAATGCAAAACTACTC 58.068 39.130 0.00 0.00 0.00 2.59
1949 2133 5.337578 AACACCACAAATGCAAAACTACT 57.662 34.783 0.00 0.00 0.00 2.57
1950 2134 6.198216 CACTAACACCACAAATGCAAAACTAC 59.802 38.462 0.00 0.00 0.00 2.73
1951 2135 6.269315 CACTAACACCACAAATGCAAAACTA 58.731 36.000 0.00 0.00 0.00 2.24
1952 2136 5.108517 CACTAACACCACAAATGCAAAACT 58.891 37.500 0.00 0.00 0.00 2.66
1961 2145 1.028905 GGCTGCACTAACACCACAAA 58.971 50.000 0.50 0.00 0.00 2.83
1971 2155 3.634397 AGAGCTAAATTGGCTGCACTA 57.366 42.857 8.98 0.00 40.40 2.74
1987 2171 4.116747 AGCTACACACAGTATCAAGAGC 57.883 45.455 0.00 0.00 30.93 4.09
1990 2174 7.148052 ACCTAGTTAGCTACACACAGTATCAAG 60.148 40.741 0.00 0.00 30.93 3.02
1991 2175 6.662234 ACCTAGTTAGCTACACACAGTATCAA 59.338 38.462 0.00 0.00 30.93 2.57
1992 2176 6.185511 ACCTAGTTAGCTACACACAGTATCA 58.814 40.000 0.00 0.00 30.93 2.15
1993 2177 6.696441 ACCTAGTTAGCTACACACAGTATC 57.304 41.667 0.00 0.00 30.93 2.24
1997 2181 6.452494 ACATACCTAGTTAGCTACACACAG 57.548 41.667 0.00 0.00 0.00 3.66
1998 2182 5.359009 GGACATACCTAGTTAGCTACACACA 59.641 44.000 0.00 0.00 35.41 3.72
2016 2207 0.548926 TGGCCCAGGACAAGGACATA 60.549 55.000 0.00 0.00 35.75 2.29
2028 2224 0.466739 TTATGCAGATGCTGGCCCAG 60.467 55.000 6.32 6.32 42.66 4.45
2031 2227 1.958579 TGAATTATGCAGATGCTGGCC 59.041 47.619 6.35 0.00 42.66 5.36
2090 2286 1.630878 CCTCAGGGAGTAAAAGGCACT 59.369 52.381 0.00 0.00 35.07 4.40
2091 2287 2.115343 CCTCAGGGAGTAAAAGGCAC 57.885 55.000 0.00 0.00 33.58 5.01
2093 2289 3.176728 GCCTCAGGGAGTAAAAGGC 57.823 57.895 0.00 0.00 45.11 4.35
2094 2290 4.080299 ACATTAGCCTCAGGGAGTAAAAGG 60.080 45.833 0.00 0.00 33.58 3.11
2095 2291 5.104259 ACATTAGCCTCAGGGAGTAAAAG 57.896 43.478 0.00 0.00 33.58 2.27
2097 2293 4.783227 AGAACATTAGCCTCAGGGAGTAAA 59.217 41.667 0.00 0.00 33.58 2.01
2099 2295 3.995636 AGAACATTAGCCTCAGGGAGTA 58.004 45.455 0.00 0.00 33.58 2.59
2100 2296 2.839228 AGAACATTAGCCTCAGGGAGT 58.161 47.619 0.00 0.00 33.58 3.85
2101 2297 3.922171 AAGAACATTAGCCTCAGGGAG 57.078 47.619 0.00 0.00 33.58 4.30
2148 2348 2.147387 AACCTTCGGCCTCACCAGT 61.147 57.895 0.00 0.00 39.03 4.00
2154 2354 2.289506 ACTCTTAACAACCTTCGGCCTC 60.290 50.000 0.00 0.00 0.00 4.70
2211 2411 5.362717 AGATGTAATGTCCCTGTATTCACGA 59.637 40.000 0.00 0.00 0.00 4.35
2305 2505 3.267812 TGGAAGAGGCTTCCTTGAATCAT 59.732 43.478 22.59 0.00 39.31 2.45
2332 2532 5.333299 TCAGATTTTAGCATTGCAAGCAT 57.667 34.783 18.74 7.18 0.00 3.79
2335 2535 6.312918 AGCAATTCAGATTTTAGCATTGCAAG 59.687 34.615 11.91 0.00 45.83 4.01
2444 2645 0.612732 CAGGGGCAGCATTTTCAGGA 60.613 55.000 0.00 0.00 0.00 3.86
2519 2720 1.961277 GACACGGTCACCTGGCTTG 60.961 63.158 0.00 0.00 32.09 4.01
2609 2810 5.126222 TGACTTCTGTGAAGGCAGTAGATAG 59.874 44.000 11.37 0.00 37.34 2.08
2736 2937 2.545952 CCGAGTATAGACAGGCGCATTT 60.546 50.000 10.83 0.00 0.00 2.32
2742 2943 2.584236 TCTTCCCGAGTATAGACAGGC 58.416 52.381 0.00 0.00 0.00 4.85
2799 3000 3.517296 TTCCCCAGCAAGTCAAATGTA 57.483 42.857 0.00 0.00 0.00 2.29
2943 3144 5.646793 ACATATAGCAGCAGCAATTATCTGG 59.353 40.000 3.17 0.00 45.49 3.86
2972 3173 7.722728 AGATACATGATGAGCATTACAACCAAT 59.277 33.333 0.00 0.00 34.15 3.16
3016 3217 4.042062 GGATCTCCCACCATCATCATGTTA 59.958 45.833 0.00 0.00 34.14 2.41
3088 3289 5.829924 CCTTCCAGTTGTTGATATAGCCAAT 59.170 40.000 0.00 0.00 0.00 3.16
3097 3298 2.176798 TGAACCCCTTCCAGTTGTTGAT 59.823 45.455 0.00 0.00 0.00 2.57
3176 3377 5.273170 CAAACACAAGTGTATGGACAACTG 58.727 41.667 6.24 0.00 44.13 3.16
3193 3395 4.926832 AGCACTTGTACAAAAACCAAACAC 59.073 37.500 10.03 0.00 0.00 3.32
3214 3416 1.202348 GGACACAGGCATTTGGTTAGC 59.798 52.381 0.00 0.00 0.00 3.09
3301 3503 8.781196 CGGTCTTGATCATTCATCTTATCAAAT 58.219 33.333 0.00 0.00 37.76 2.32
3403 3605 4.095483 GCTGCAGCAATTACACTACATCTT 59.905 41.667 33.36 0.00 41.59 2.40
3459 3661 5.175673 GCCATTAACAGCACAGAAAAGAAAC 59.824 40.000 0.00 0.00 0.00 2.78
3460 3662 5.163468 TGCCATTAACAGCACAGAAAAGAAA 60.163 36.000 0.00 0.00 33.08 2.52
3521 3724 3.742882 CGATCATACTGTTATGCCACCAG 59.257 47.826 0.00 0.00 35.86 4.00
3526 3729 5.984233 TTGAACGATCATACTGTTATGCC 57.016 39.130 0.00 0.00 35.86 4.40
3531 3734 6.876789 TGGTGTTATTGAACGATCATACTGTT 59.123 34.615 0.00 0.00 38.51 3.16
3619 3822 3.436015 CGATCTCAGCATCCATTTGATCC 59.564 47.826 0.00 0.00 0.00 3.36
3685 3888 5.125900 CACAAAATTACCTCCATCATCAGCA 59.874 40.000 0.00 0.00 0.00 4.41
3717 3920 4.261741 CCCCTGAAATAAATCTCATTGCCG 60.262 45.833 0.00 0.00 0.00 5.69
3719 3922 6.661304 ATCCCCTGAAATAAATCTCATTGC 57.339 37.500 0.00 0.00 0.00 3.56
3722 3925 6.925934 TGGAATCCCCTGAAATAAATCTCAT 58.074 36.000 0.00 0.00 35.38 2.90
4131 4336 8.915654 CAATGCCAAAAACAGAAAGTAGTATTC 58.084 33.333 0.00 0.00 0.00 1.75
4154 4379 5.476599 TGCAATGTTAAAGGCTACTGACAAT 59.523 36.000 0.00 0.00 0.00 2.71
4212 4438 7.406620 TTCCTTATCTTATGGAATGATGGGT 57.593 36.000 0.00 0.00 37.16 4.51
4262 4488 7.307989 CCCATTCTTACATGCTAAATCCTTACG 60.308 40.741 0.00 0.00 0.00 3.18
4320 4546 6.937436 AGAAATAAGTGAAAAACCGACACT 57.063 33.333 0.00 0.00 45.02 3.55
4402 4631 7.999679 TCCAGATTTCAAAATATAAGGCACAG 58.000 34.615 0.00 0.00 0.00 3.66
4427 4656 0.470833 ATCCTATGGCAGGCGACTCT 60.471 55.000 0.00 0.00 45.10 3.24
4500 4731 1.032014 GCCTGGAAGAGCACAAAACA 58.968 50.000 0.00 0.00 34.07 2.83
4625 4856 8.846211 GCCTATAAAAACATAAGTATGAGGCAA 58.154 33.333 15.09 0.00 40.54 4.52
5048 5282 5.931146 TGCATCTTGTTCAGTTTGTTGTTTT 59.069 32.000 0.00 0.00 0.00 2.43
5058 5292 1.242076 GCACCTGCATCTTGTTCAGT 58.758 50.000 0.00 0.00 41.59 3.41
5184 5418 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
5185 5419 7.839680 AAAGTTGAGACACTTATTTTGGGAT 57.160 32.000 0.00 0.00 35.87 3.85
5243 5561 9.492973 CCATTTCAATGTTAAAAAGGATGACTT 57.507 29.630 0.00 0.00 36.41 3.01
5259 5577 1.483415 CCAAGAGGGGCCATTTCAATG 59.517 52.381 4.39 3.67 36.17 2.82
5284 5603 4.289672 AGACAGGCTATTTTCTGGGAAAGA 59.710 41.667 0.00 0.00 35.47 2.52
5320 5639 9.219603 CTAACAAAATAACTCATTCTCAGGACA 57.780 33.333 0.00 0.00 0.00 4.02
5390 5726 6.890979 AAAAATCCTAATAGGCAGCATCTC 57.109 37.500 0.34 0.00 34.61 2.75
5417 5754 3.127376 TCTGATTGGATTGCATGTCAACG 59.873 43.478 4.96 0.00 37.53 4.10
5523 5864 8.621532 ATTGTTTACTGCTTCTGAGTATTCAA 57.378 30.769 0.00 0.00 31.69 2.69
5598 5947 7.936847 CCTAGCTAAATGTGTTATATGTGGGAA 59.063 37.037 0.00 0.00 0.00 3.97
5601 5950 6.128553 CGCCTAGCTAAATGTGTTATATGTGG 60.129 42.308 0.00 0.00 0.00 4.17
5642 12300 6.923928 ATTTGCAGCAAAACAGTAAATTGT 57.076 29.167 24.15 0.50 36.90 2.71
5821 12486 6.601741 TTTTGTAAATTTCAGGCAAAGCAG 57.398 33.333 0.00 0.00 31.87 4.24
5839 12504 8.791327 ATCAAACAAGAAGGTTCAAATTTTGT 57.209 26.923 8.89 0.00 0.00 2.83
5902 12567 5.047164 TGCTTCCATTCTGCACATTACAAAT 60.047 36.000 0.00 0.00 0.00 2.32
6034 12699 1.840635 AGGATGAACTCTACTTGGCCC 59.159 52.381 0.00 0.00 0.00 5.80
6096 12773 8.540388 ACCAGATCTAAAGAAGCAAAGTGTATA 58.460 33.333 0.00 0.00 0.00 1.47
6193 12870 5.469373 TGTGATTAGATGATGCGAACAAC 57.531 39.130 0.00 0.00 0.00 3.32
6278 12955 2.117865 AGCCTCTCCAGGAATTCAGAG 58.882 52.381 7.93 10.23 43.65 3.35
6323 13000 3.223423 AGTACATCAACAGACAGCTCG 57.777 47.619 0.00 0.00 0.00 5.03
6345 13022 8.970859 ACCTCACTGATAAAAATCAAGATAGG 57.029 34.615 0.00 0.00 0.00 2.57
6430 13113 4.443881 CCATGCAGACCAGACATAATCAGA 60.444 45.833 0.00 0.00 0.00 3.27
6464 13147 1.525941 GCCCGGTGCAACTAGTTTAA 58.474 50.000 5.07 0.00 40.77 1.52
6590 13274 4.261572 GCAAGATTACACAGGCAACAAGAA 60.262 41.667 0.00 0.00 41.41 2.52
6602 13287 1.026718 AGGCGCTGGCAAGATTACAC 61.027 55.000 7.64 0.00 42.47 2.90
6748 13437 9.799106 AAAGAATGGAGAAGAGAAAAATGTAGA 57.201 29.630 0.00 0.00 0.00 2.59
6754 13443 9.135189 TCATTCAAAGAATGGAGAAGAGAAAAA 57.865 29.630 16.97 0.00 0.00 1.94
6827 13518 4.859784 GGTGCATGCGTTTGTACC 57.140 55.556 14.09 10.09 43.62 3.34
6839 13530 1.603456 CTATGTGTGTTGTGGGTGCA 58.397 50.000 0.00 0.00 0.00 4.57
6842 13533 0.605319 CGCCTATGTGTGTTGTGGGT 60.605 55.000 0.00 0.00 0.00 4.51
6862 13553 1.855213 GATGGTGTTGCTGCGCTCAA 61.855 55.000 9.73 10.35 0.00 3.02
6869 13560 0.035152 TGCTAGGGATGGTGTTGCTG 60.035 55.000 0.00 0.00 0.00 4.41
6899 13590 3.971702 AAGGCTGTCACCCTGGCC 61.972 66.667 0.00 0.00 44.38 5.36
6900 13591 2.674380 CAAGGCTGTCACCCTGGC 60.674 66.667 0.00 0.00 37.77 4.85
6901 13592 0.890996 GTTCAAGGCTGTCACCCTGG 60.891 60.000 0.00 0.00 31.73 4.45
6902 13593 0.179020 TGTTCAAGGCTGTCACCCTG 60.179 55.000 0.00 0.00 31.73 4.45
6903 13594 0.773644 ATGTTCAAGGCTGTCACCCT 59.226 50.000 0.00 0.00 0.00 4.34
6904 13595 0.883833 CATGTTCAAGGCTGTCACCC 59.116 55.000 0.00 0.00 0.00 4.61
6905 13596 0.242017 GCATGTTCAAGGCTGTCACC 59.758 55.000 0.00 0.00 31.20 4.02
6906 13597 0.242017 GGCATGTTCAAGGCTGTCAC 59.758 55.000 0.00 0.00 35.38 3.67
6907 13598 0.178995 TGGCATGTTCAAGGCTGTCA 60.179 50.000 0.00 0.00 35.38 3.58
6908 13599 1.133790 GATGGCATGTTCAAGGCTGTC 59.866 52.381 3.81 0.00 35.38 3.51
6909 13600 1.180029 GATGGCATGTTCAAGGCTGT 58.820 50.000 3.81 0.00 35.38 4.40
6910 13601 0.099968 CGATGGCATGTTCAAGGCTG 59.900 55.000 3.81 0.00 35.38 4.85
6934 13625 4.152223 TCGTATCATATGCGGCTTCAATTG 59.848 41.667 0.00 0.00 38.93 2.32
6937 13628 3.317150 CTCGTATCATATGCGGCTTCAA 58.683 45.455 0.00 0.00 38.93 2.69
6944 13635 3.679980 CCTTTTCCCTCGTATCATATGCG 59.320 47.826 0.00 0.00 39.81 4.73
6953 13976 1.891722 GCGGGTCCTTTTCCCTCGTA 61.892 60.000 0.00 0.00 42.56 3.43
6999 14022 1.946475 GCCTACTGGGTCTCGACACC 61.946 65.000 0.42 0.42 37.43 4.16
7003 14026 2.439701 CGGCCTACTGGGTCTCGA 60.440 66.667 0.00 0.00 37.61 4.04
7013 14036 0.810426 GCTAGTTTCAGCCGGCCTAC 60.810 60.000 26.15 15.99 35.40 3.18
7015 14038 2.269241 GCTAGTTTCAGCCGGCCT 59.731 61.111 26.15 15.54 35.40 5.19
7023 14046 1.480954 GGTCGATGGAGGCTAGTTTCA 59.519 52.381 0.00 0.00 0.00 2.69
7024 14047 1.202545 GGGTCGATGGAGGCTAGTTTC 60.203 57.143 0.00 0.00 0.00 2.78
7028 14051 1.797211 GACGGGTCGATGGAGGCTAG 61.797 65.000 0.00 0.00 0.00 3.42
7030 14053 3.148279 GACGGGTCGATGGAGGCT 61.148 66.667 0.00 0.00 0.00 4.58
7060 14083 2.125912 ACCATGCTCGTCTCACGC 60.126 61.111 0.00 0.00 42.21 5.34
7063 14086 0.390340 GCAAGACCATGCTCGTCTCA 60.390 55.000 3.91 0.00 43.06 3.27
7079 14131 3.611674 TCTCGCACCCGACAGCAA 61.612 61.111 0.00 0.00 38.82 3.91
7082 14134 3.669036 CTCGTCTCGCACCCGACAG 62.669 68.421 0.00 0.00 38.82 3.51
7086 14138 4.838486 GAGCTCGTCTCGCACCCG 62.838 72.222 0.00 0.00 31.20 5.28
7104 14156 1.215647 CGTGTCTGGTAGCAGGACC 59.784 63.158 21.22 10.45 40.21 4.46
7118 14170 1.367840 GACTGACCTTGCCTCGTGT 59.632 57.895 0.00 0.00 0.00 4.49
7120 14172 3.060866 GGACTGACCTTGCCTCGT 58.939 61.111 0.00 0.00 35.41 4.18
7142 14194 0.810426 TCGCTCGTCTCGCATCTAGT 60.810 55.000 0.00 0.00 0.00 2.57
7147 14199 2.026734 CCATCGCTCGTCTCGCAT 59.973 61.111 0.00 0.00 0.00 4.73
7148 14200 3.131478 TCCATCGCTCGTCTCGCA 61.131 61.111 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.