Multiple sequence alignment - TraesCS7A01G018400

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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 TraesCS7A01G018400 chr7A 100.000 3669 0 0 1 3669 7775376 7771708 0.000000e+00 6776.0
1 TraesCS7A01G018400 chr7A 92.163 906 64 6 2770 3669 47014230 47015134 0.000000e+00 1273.0
2 TraesCS7A01G018400 chr7A 84.375 224 29 5 412 630 7880787 7880565 7.980000e-52 215.0
3 TraesCS7A01G018400 chr4A 87.385 1958 116 60 819 2727 733606168 733604293 0.000000e+00 2126.0
4 TraesCS7A01G018400 chr4A 91.773 1021 55 16 1749 2752 733389096 733390104 0.000000e+00 1393.0
5 TraesCS7A01G018400 chr4A 90.746 389 12 11 1155 1543 733388732 733389096 7.080000e-137 497.0
6 TraesCS7A01G018400 chr4A 79.487 351 53 15 287 627 733061160 733061501 7.920000e-57 231.0
7 TraesCS7A01G018400 chr4A 79.202 351 54 15 287 627 733120974 733121315 3.690000e-55 226.0
8 TraesCS7A01G018400 chr4A 79.202 351 54 15 287 627 733243476 733243817 3.690000e-55 226.0
9 TraesCS7A01G018400 chr4A 91.111 90 7 1 974 1063 733356091 733356179 1.790000e-23 121.0
10 TraesCS7A01G018400 chr7D 95.700 1000 32 5 1734 2727 6793902 6792908 0.000000e+00 1598.0
11 TraesCS7A01G018400 chr7D 94.778 900 45 2 2770 3669 451043915 451044812 0.000000e+00 1400.0
12 TraesCS7A01G018400 chr7D 91.706 856 37 7 804 1646 6794845 6794011 0.000000e+00 1157.0
13 TraesCS7A01G018400 chr7D 84.180 866 69 26 239 1059 6817787 6816945 0.000000e+00 778.0
14 TraesCS7A01G018400 chr7D 87.273 220 24 3 412 630 6797626 6797410 7.870000e-62 248.0
15 TraesCS7A01G018400 chr3D 94.883 899 44 2 2771 3669 125801137 125802033 0.000000e+00 1404.0
16 TraesCS7A01G018400 chr3D 87.500 48 5 1 683 729 447974931 447974884 2.000000e-03 54.7
17 TraesCS7A01G018400 chr1A 94.013 902 50 4 2770 3669 32465719 32466618 0.000000e+00 1363.0
18 TraesCS7A01G018400 chr1A 93.005 386 26 1 2770 3155 497184695 497185079 2.470000e-156 562.0
19 TraesCS7A01G018400 chr1A 80.473 169 32 1 2480 2648 32995855 32996022 1.070000e-25 128.0
20 TraesCS7A01G018400 chr1A 100.000 34 0 0 686 719 586510582 586510615 3.060000e-06 63.9
21 TraesCS7A01G018400 chr2A 91.504 871 68 4 2800 3669 694900416 694901281 0.000000e+00 1194.0
22 TraesCS7A01G018400 chr2A 91.754 764 60 3 2770 3532 632542806 632543567 0.000000e+00 1059.0
23 TraesCS7A01G018400 chr6D 91.928 830 36 5 2770 3598 202257122 202256323 0.000000e+00 1133.0
24 TraesCS7A01G018400 chr6D 100.000 39 0 0 718 756 350562182 350562220 5.080000e-09 73.1
25 TraesCS7A01G018400 chr2D 91.711 760 54 6 2770 3527 275248990 275248238 0.000000e+00 1046.0
26 TraesCS7A01G018400 chr2D 93.182 44 1 2 716 759 634570617 634570658 3.060000e-06 63.9
27 TraesCS7A01G018400 chr4D 95.229 524 23 2 3146 3669 506095933 506096454 0.000000e+00 828.0
28 TraesCS7A01G018400 chr4D 82.609 92 3 2 683 761 30415639 30415730 6.570000e-08 69.4
29 TraesCS7A01G018400 chr5D 76.040 505 102 15 2152 2648 390452155 390451662 1.020000e-60 244.0
30 TraesCS7A01G018400 chr5D 90.741 54 5 0 703 756 112241372 112241319 5.080000e-09 73.1
31 TraesCS7A01G018400 chr5D 91.304 46 4 0 716 761 371845108 371845153 3.060000e-06 63.9
32 TraesCS7A01G018400 chr5B 75.591 508 106 13 2152 2648 470520654 470520154 6.130000e-58 235.0
33 TraesCS7A01G018400 chr1B 89.286 84 7 1 683 766 67023420 67023339 1.800000e-18 104.0
34 TraesCS7A01G018400 chr1B 93.023 43 2 1 678 720 114603219 114603260 1.100000e-05 62.1
35 TraesCS7A01G018400 chr6A 97.561 41 1 0 716 756 609274764 609274804 1.830000e-08 71.3
36 TraesCS7A01G018400 chr3B 87.302 63 6 1 699 761 438330682 438330742 1.830000e-08 71.3
37 TraesCS7A01G018400 chr3B 90.909 44 2 2 687 729 24750290 24750332 1.420000e-04 58.4
38 TraesCS7A01G018400 chr7B 97.297 37 1 0 684 720 164978053 164978089 3.060000e-06 63.9
39 TraesCS7A01G018400 chr2B 93.182 44 1 2 716 759 61099355 61099396 3.060000e-06 63.9
40 TraesCS7A01G018400 chr4B 94.872 39 1 1 682 720 567009342 567009305 3.960000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G018400 chr7A 7771708 7775376 3668 True 6776 6776 100.000000 1 3669 1 chr7A.!!$R1 3668
1 TraesCS7A01G018400 chr7A 47014230 47015134 904 False 1273 1273 92.163000 2770 3669 1 chr7A.!!$F1 899
2 TraesCS7A01G018400 chr4A 733604293 733606168 1875 True 2126 2126 87.385000 819 2727 1 chr4A.!!$R1 1908
3 TraesCS7A01G018400 chr4A 733388732 733390104 1372 False 945 1393 91.259500 1155 2752 2 chr4A.!!$F5 1597
4 TraesCS7A01G018400 chr7D 451043915 451044812 897 False 1400 1400 94.778000 2770 3669 1 chr7D.!!$F1 899
5 TraesCS7A01G018400 chr7D 6792908 6797626 4718 True 1001 1598 91.559667 412 2727 3 chr7D.!!$R2 2315
6 TraesCS7A01G018400 chr7D 6816945 6817787 842 True 778 778 84.180000 239 1059 1 chr7D.!!$R1 820
7 TraesCS7A01G018400 chr3D 125801137 125802033 896 False 1404 1404 94.883000 2771 3669 1 chr3D.!!$F1 898
8 TraesCS7A01G018400 chr1A 32465719 32466618 899 False 1363 1363 94.013000 2770 3669 1 chr1A.!!$F1 899
9 TraesCS7A01G018400 chr2A 694900416 694901281 865 False 1194 1194 91.504000 2800 3669 1 chr2A.!!$F2 869
10 TraesCS7A01G018400 chr2A 632542806 632543567 761 False 1059 1059 91.754000 2770 3532 1 chr2A.!!$F1 762
11 TraesCS7A01G018400 chr6D 202256323 202257122 799 True 1133 1133 91.928000 2770 3598 1 chr6D.!!$R1 828
12 TraesCS7A01G018400 chr2D 275248238 275248990 752 True 1046 1046 91.711000 2770 3527 1 chr2D.!!$R1 757
13 TraesCS7A01G018400 chr4D 506095933 506096454 521 False 828 828 95.229000 3146 3669 1 chr4D.!!$F2 523
14 TraesCS7A01G018400 chr5B 470520154 470520654 500 True 235 235 75.591000 2152 2648 1 chr5B.!!$R1 496

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
973 3432 1.060409 GCGCCACAACAAACAAACAAG 59.94 47.619 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 5286 0.179067 AAAGTTTGACTCGCCGGTCA 60.179 50.0 1.9 4.62 43.41 4.02 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 5.627499 TTAGCTCACAAATAAGGTTGCTG 57.373 39.130 0.00 0.00 31.08 4.41
23 24 3.490348 AGCTCACAAATAAGGTTGCTGT 58.510 40.909 0.00 0.00 31.29 4.40
24 25 4.651778 AGCTCACAAATAAGGTTGCTGTA 58.348 39.130 0.00 0.00 31.29 2.74
25 26 5.070001 AGCTCACAAATAAGGTTGCTGTAA 58.930 37.500 0.00 0.00 31.29 2.41
26 27 5.048713 AGCTCACAAATAAGGTTGCTGTAAC 60.049 40.000 0.00 0.00 38.60 2.50
36 37 3.813529 GTTGCTGTAACCTGTCACATC 57.186 47.619 0.00 0.00 33.01 3.06
37 38 3.138304 GTTGCTGTAACCTGTCACATCA 58.862 45.455 0.00 0.00 33.01 3.07
38 39 3.483808 TGCTGTAACCTGTCACATCAA 57.516 42.857 0.00 0.00 0.00 2.57
39 40 3.814625 TGCTGTAACCTGTCACATCAAA 58.185 40.909 0.00 0.00 0.00 2.69
40 41 4.397420 TGCTGTAACCTGTCACATCAAAT 58.603 39.130 0.00 0.00 0.00 2.32
41 42 5.555966 TGCTGTAACCTGTCACATCAAATA 58.444 37.500 0.00 0.00 0.00 1.40
42 43 5.411361 TGCTGTAACCTGTCACATCAAATAC 59.589 40.000 0.00 0.00 0.00 1.89
43 44 5.643777 GCTGTAACCTGTCACATCAAATACT 59.356 40.000 0.00 0.00 0.00 2.12
44 45 6.183360 GCTGTAACCTGTCACATCAAATACTC 60.183 42.308 0.00 0.00 0.00 2.59
45 46 7.004555 TGTAACCTGTCACATCAAATACTCT 57.995 36.000 0.00 0.00 0.00 3.24
46 47 7.097192 TGTAACCTGTCACATCAAATACTCTC 58.903 38.462 0.00 0.00 0.00 3.20
47 48 5.745312 ACCTGTCACATCAAATACTCTCA 57.255 39.130 0.00 0.00 0.00 3.27
48 49 6.305272 ACCTGTCACATCAAATACTCTCAT 57.695 37.500 0.00 0.00 0.00 2.90
49 50 6.344500 ACCTGTCACATCAAATACTCTCATC 58.656 40.000 0.00 0.00 0.00 2.92
50 51 6.155910 ACCTGTCACATCAAATACTCTCATCT 59.844 38.462 0.00 0.00 0.00 2.90
51 52 6.700960 CCTGTCACATCAAATACTCTCATCTC 59.299 42.308 0.00 0.00 0.00 2.75
52 53 7.174107 TGTCACATCAAATACTCTCATCTCA 57.826 36.000 0.00 0.00 0.00 3.27
53 54 7.263496 TGTCACATCAAATACTCTCATCTCAG 58.737 38.462 0.00 0.00 0.00 3.35
54 55 6.700960 GTCACATCAAATACTCTCATCTCAGG 59.299 42.308 0.00 0.00 0.00 3.86
55 56 6.608808 TCACATCAAATACTCTCATCTCAGGA 59.391 38.462 0.00 0.00 0.00 3.86
56 57 6.700960 CACATCAAATACTCTCATCTCAGGAC 59.299 42.308 0.00 0.00 0.00 3.85
57 58 5.860941 TCAAATACTCTCATCTCAGGACC 57.139 43.478 0.00 0.00 0.00 4.46
58 59 5.272402 TCAAATACTCTCATCTCAGGACCA 58.728 41.667 0.00 0.00 0.00 4.02
59 60 5.901853 TCAAATACTCTCATCTCAGGACCAT 59.098 40.000 0.00 0.00 0.00 3.55
60 61 6.041409 TCAAATACTCTCATCTCAGGACCATC 59.959 42.308 0.00 0.00 0.00 3.51
61 62 3.686227 ACTCTCATCTCAGGACCATCT 57.314 47.619 0.00 0.00 0.00 2.90
62 63 3.565307 ACTCTCATCTCAGGACCATCTC 58.435 50.000 0.00 0.00 0.00 2.75
63 64 3.205056 ACTCTCATCTCAGGACCATCTCT 59.795 47.826 0.00 0.00 0.00 3.10
64 65 4.415179 ACTCTCATCTCAGGACCATCTCTA 59.585 45.833 0.00 0.00 0.00 2.43
65 66 5.103728 ACTCTCATCTCAGGACCATCTCTAA 60.104 44.000 0.00 0.00 0.00 2.10
66 67 5.770919 TCTCATCTCAGGACCATCTCTAAA 58.229 41.667 0.00 0.00 0.00 1.85
67 68 6.197903 TCTCATCTCAGGACCATCTCTAAAA 58.802 40.000 0.00 0.00 0.00 1.52
68 69 6.669591 TCTCATCTCAGGACCATCTCTAAAAA 59.330 38.462 0.00 0.00 0.00 1.94
69 70 7.346698 TCTCATCTCAGGACCATCTCTAAAAAT 59.653 37.037 0.00 0.00 0.00 1.82
70 71 7.278135 TCATCTCAGGACCATCTCTAAAAATG 58.722 38.462 0.00 0.00 0.00 2.32
71 72 6.627087 TCTCAGGACCATCTCTAAAAATGT 57.373 37.500 0.00 0.00 0.00 2.71
72 73 7.733773 TCTCAGGACCATCTCTAAAAATGTA 57.266 36.000 0.00 0.00 0.00 2.29
73 74 7.556844 TCTCAGGACCATCTCTAAAAATGTAC 58.443 38.462 0.00 0.00 0.00 2.90
74 75 7.400339 TCTCAGGACCATCTCTAAAAATGTACT 59.600 37.037 0.00 0.00 0.00 2.73
75 76 8.603898 TCAGGACCATCTCTAAAAATGTACTA 57.396 34.615 0.00 0.00 0.00 1.82
76 77 8.696374 TCAGGACCATCTCTAAAAATGTACTAG 58.304 37.037 0.00 0.00 0.00 2.57
77 78 7.928706 CAGGACCATCTCTAAAAATGTACTAGG 59.071 40.741 0.00 0.00 0.00 3.02
78 79 7.844779 AGGACCATCTCTAAAAATGTACTAGGA 59.155 37.037 0.00 0.00 0.00 2.94
79 80 7.927092 GGACCATCTCTAAAAATGTACTAGGAC 59.073 40.741 0.00 0.00 0.00 3.85
80 81 7.793036 ACCATCTCTAAAAATGTACTAGGACC 58.207 38.462 1.66 0.00 0.00 4.46
81 82 7.402071 ACCATCTCTAAAAATGTACTAGGACCA 59.598 37.037 1.66 0.00 0.00 4.02
82 83 8.432805 CCATCTCTAAAAATGTACTAGGACCAT 58.567 37.037 1.66 0.00 0.00 3.55
85 86 8.639761 TCTCTAAAAATGTACTAGGACCATAGC 58.360 37.037 1.66 0.00 0.00 2.97
86 87 8.548880 TCTAAAAATGTACTAGGACCATAGCT 57.451 34.615 1.66 0.00 0.00 3.32
87 88 9.650714 TCTAAAAATGTACTAGGACCATAGCTA 57.349 33.333 1.66 0.00 0.00 3.32
88 89 9.915629 CTAAAAATGTACTAGGACCATAGCTAG 57.084 37.037 1.66 0.00 0.00 3.42
89 90 6.919775 AAATGTACTAGGACCATAGCTAGG 57.080 41.667 1.66 0.00 0.00 3.02
90 91 5.602291 ATGTACTAGGACCATAGCTAGGT 57.398 43.478 12.88 12.88 43.46 3.08
91 92 6.715350 ATGTACTAGGACCATAGCTAGGTA 57.285 41.667 12.97 3.73 40.09 3.08
92 93 5.874093 TGTACTAGGACCATAGCTAGGTAC 58.126 45.833 13.80 13.80 40.09 3.34
97 98 3.306613 GGACCATAGCTAGGTACTTGGT 58.693 50.000 21.66 21.66 44.84 3.67
98 99 3.069729 GGACCATAGCTAGGTACTTGGTG 59.930 52.174 24.97 11.07 42.47 4.17
99 100 3.705072 GACCATAGCTAGGTACTTGGTGT 59.295 47.826 24.97 7.84 42.47 4.16
100 101 3.451178 ACCATAGCTAGGTACTTGGTGTG 59.549 47.826 21.11 7.68 45.96 3.82
101 102 4.060038 CATAGCTAGGTACTTGGTGTGG 57.940 50.000 3.24 0.00 43.78 4.17
102 103 2.025636 AGCTAGGTACTTGGTGTGGT 57.974 50.000 0.00 0.00 40.81 4.16
103 104 2.335933 AGCTAGGTACTTGGTGTGGTT 58.664 47.619 0.00 0.00 40.81 3.67
104 105 2.709397 AGCTAGGTACTTGGTGTGGTTT 59.291 45.455 0.00 0.00 40.81 3.27
105 106 3.905591 AGCTAGGTACTTGGTGTGGTTTA 59.094 43.478 0.00 0.00 40.81 2.01
106 107 4.534897 AGCTAGGTACTTGGTGTGGTTTAT 59.465 41.667 0.00 0.00 40.81 1.40
107 108 4.874396 GCTAGGTACTTGGTGTGGTTTATC 59.126 45.833 0.00 0.00 41.75 1.75
108 109 4.986054 AGGTACTTGGTGTGGTTTATCA 57.014 40.909 0.00 0.00 27.25 2.15
109 110 5.514500 AGGTACTTGGTGTGGTTTATCAT 57.486 39.130 0.00 0.00 27.25 2.45
110 111 5.253330 AGGTACTTGGTGTGGTTTATCATG 58.747 41.667 0.00 0.00 27.25 3.07
111 112 4.398044 GGTACTTGGTGTGGTTTATCATGG 59.602 45.833 0.00 0.00 0.00 3.66
112 113 4.112634 ACTTGGTGTGGTTTATCATGGT 57.887 40.909 0.00 0.00 0.00 3.55
113 114 5.249780 ACTTGGTGTGGTTTATCATGGTA 57.750 39.130 0.00 0.00 0.00 3.25
114 115 5.007682 ACTTGGTGTGGTTTATCATGGTAC 58.992 41.667 0.00 0.00 0.00 3.34
139 140 6.978343 TGGTACAAGGAGATAATTTCGTTG 57.022 37.500 8.71 8.71 42.83 4.10
140 141 5.353123 TGGTACAAGGAGATAATTTCGTTGC 59.647 40.000 9.76 0.00 41.61 4.17
141 142 4.965119 ACAAGGAGATAATTTCGTTGCC 57.035 40.909 9.76 0.00 41.61 4.52
142 143 4.331968 ACAAGGAGATAATTTCGTTGCCA 58.668 39.130 9.76 0.00 41.61 4.92
143 144 4.764823 ACAAGGAGATAATTTCGTTGCCAA 59.235 37.500 9.76 0.00 41.61 4.52
144 145 5.106157 ACAAGGAGATAATTTCGTTGCCAAG 60.106 40.000 9.76 0.00 41.61 3.61
145 146 4.843728 AGGAGATAATTTCGTTGCCAAGA 58.156 39.130 0.00 0.00 0.00 3.02
146 147 5.253330 AGGAGATAATTTCGTTGCCAAGAA 58.747 37.500 0.00 0.00 0.00 2.52
147 148 5.710099 AGGAGATAATTTCGTTGCCAAGAAA 59.290 36.000 1.58 1.58 40.14 2.52
148 149 6.208599 AGGAGATAATTTCGTTGCCAAGAAAA 59.791 34.615 3.17 0.00 39.42 2.29
149 150 6.866248 GGAGATAATTTCGTTGCCAAGAAAAA 59.134 34.615 3.17 0.00 39.42 1.94
184 185 5.261209 TCAAGTTCTGAAACAATTGGTGG 57.739 39.130 10.83 0.00 37.88 4.61
185 186 4.952957 TCAAGTTCTGAAACAATTGGTGGA 59.047 37.500 10.83 0.24 37.88 4.02
186 187 5.420421 TCAAGTTCTGAAACAATTGGTGGAA 59.580 36.000 10.83 6.56 37.88 3.53
187 188 5.930837 AGTTCTGAAACAATTGGTGGAAA 57.069 34.783 10.83 0.00 37.88 3.13
188 189 6.293004 AGTTCTGAAACAATTGGTGGAAAA 57.707 33.333 10.83 0.00 37.88 2.29
189 190 6.106003 AGTTCTGAAACAATTGGTGGAAAAC 58.894 36.000 10.83 7.11 37.88 2.43
190 191 5.930837 TCTGAAACAATTGGTGGAAAACT 57.069 34.783 10.83 0.00 0.00 2.66
191 192 5.901552 TCTGAAACAATTGGTGGAAAACTC 58.098 37.500 10.83 0.00 0.00 3.01
192 193 5.420421 TCTGAAACAATTGGTGGAAAACTCA 59.580 36.000 10.83 0.97 0.00 3.41
193 194 6.042638 TGAAACAATTGGTGGAAAACTCAA 57.957 33.333 10.83 0.00 0.00 3.02
194 195 6.648192 TGAAACAATTGGTGGAAAACTCAAT 58.352 32.000 10.83 0.00 33.62 2.57
195 196 7.108847 TGAAACAATTGGTGGAAAACTCAATT 58.891 30.769 10.83 0.00 38.82 2.32
196 197 7.609532 TGAAACAATTGGTGGAAAACTCAATTT 59.390 29.630 10.83 0.00 37.46 1.82
197 198 6.923928 ACAATTGGTGGAAAACTCAATTTG 57.076 33.333 10.83 0.00 37.46 2.32
198 199 6.648192 ACAATTGGTGGAAAACTCAATTTGA 58.352 32.000 10.83 0.00 37.46 2.69
199 200 7.281841 ACAATTGGTGGAAAACTCAATTTGAT 58.718 30.769 10.83 0.00 37.46 2.57
200 201 8.428063 ACAATTGGTGGAAAACTCAATTTGATA 58.572 29.630 10.83 0.00 37.46 2.15
201 202 9.270640 CAATTGGTGGAAAACTCAATTTGATAA 57.729 29.630 0.00 0.00 37.46 1.75
202 203 9.844257 AATTGGTGGAAAACTCAATTTGATAAA 57.156 25.926 0.00 0.00 36.81 1.40
203 204 9.844257 ATTGGTGGAAAACTCAATTTGATAAAA 57.156 25.926 0.00 0.00 30.20 1.52
204 205 9.844257 TTGGTGGAAAACTCAATTTGATAAAAT 57.156 25.926 0.00 0.00 0.00 1.82
304 306 5.460748 GGAAAAGGTTGACATACAAAAACGG 59.539 40.000 0.00 0.00 40.36 4.44
306 308 5.432885 AAGGTTGACATACAAAAACGGAG 57.567 39.130 0.00 0.00 40.36 4.63
307 309 4.710324 AGGTTGACATACAAAAACGGAGA 58.290 39.130 0.00 0.00 40.36 3.71
310 312 4.345859 TGACATACAAAAACGGAGACCT 57.654 40.909 0.00 0.00 0.00 3.85
318 320 1.348064 AAACGGAGACCTGATCCACA 58.652 50.000 0.00 0.00 36.57 4.17
320 322 1.142748 CGGAGACCTGATCCACAGC 59.857 63.158 0.00 0.00 44.52 4.40
324 326 2.356535 GGAGACCTGATCCACAGCAATT 60.357 50.000 0.00 0.00 44.52 2.32
344 346 6.128472 GCAATTTGAGTCACCATCAATTTTCC 60.128 38.462 0.00 0.00 36.60 3.13
348 350 7.773489 TTGAGTCACCATCAATTTTCCAATA 57.227 32.000 0.00 0.00 31.86 1.90
349 351 7.156876 TGAGTCACCATCAATTTTCCAATAC 57.843 36.000 0.00 0.00 0.00 1.89
359 361 7.610580 TCAATTTTCCAATACCAACCTTCTT 57.389 32.000 0.00 0.00 0.00 2.52
360 362 7.666623 TCAATTTTCCAATACCAACCTTCTTC 58.333 34.615 0.00 0.00 0.00 2.87
390 392 7.783090 AGATTAACTACATGATTGTCTGCTG 57.217 36.000 0.00 0.00 37.28 4.41
398 400 5.190677 ACATGATTGTCTGCTGATTGATGA 58.809 37.500 0.00 0.00 0.00 2.92
399 401 5.828328 ACATGATTGTCTGCTGATTGATGAT 59.172 36.000 0.00 0.00 0.00 2.45
400 402 5.751243 TGATTGTCTGCTGATTGATGATG 57.249 39.130 0.00 0.00 0.00 3.07
402 404 5.527582 TGATTGTCTGCTGATTGATGATGAG 59.472 40.000 0.00 0.00 0.00 2.90
405 407 3.808726 GTCTGCTGATTGATGATGAGACC 59.191 47.826 0.00 0.00 0.00 3.85
406 408 3.710165 TCTGCTGATTGATGATGAGACCT 59.290 43.478 0.00 0.00 0.00 3.85
410 412 4.202233 GCTGATTGATGATGAGACCTCTGA 60.202 45.833 0.00 0.00 0.00 3.27
422 440 6.624352 TGAGACCTCTGAATTTTTCTGTTG 57.376 37.500 0.00 0.00 0.00 3.33
510 529 5.181009 TCATAAGCTCTGATGACAGGTTTG 58.819 41.667 0.00 0.00 43.60 2.93
523 542 7.819415 TGATGACAGGTTTGAGTATAGAACAAG 59.181 37.037 0.00 0.00 0.00 3.16
714 3147 8.687292 TCTCTCCGTAAACTAATATAAGAGCA 57.313 34.615 0.00 0.00 0.00 4.26
813 3260 5.926542 AGTAACAACATGCTGTACTAGTGTG 59.073 40.000 5.39 0.00 0.00 3.82
863 3313 4.753610 TCAGATGCAGAACAAGAAGACAAG 59.246 41.667 0.00 0.00 0.00 3.16
880 3330 2.485426 ACAAGAATGTCGCCATCACTTG 59.515 45.455 18.05 18.05 43.30 3.16
894 3344 5.807011 GCCATCACTTGTCCAATGTTATTTC 59.193 40.000 0.00 0.00 0.00 2.17
898 3348 3.192633 ACTTGTCCAATGTTATTTCGGCC 59.807 43.478 0.00 0.00 0.00 6.13
968 3427 2.103143 CCGCGCCACAACAAACAA 59.897 55.556 0.00 0.00 0.00 2.83
973 3432 1.060409 GCGCCACAACAAACAAACAAG 59.940 47.619 0.00 0.00 0.00 3.16
1368 3834 1.930204 TGGAGGACTAGGAGTGATCCA 59.070 52.381 0.00 5.63 37.20 3.41
1627 4093 1.908793 ATCGGATCAGGTAGGCCCG 60.909 63.158 0.00 0.00 41.36 6.13
1654 4127 7.482169 AGACCCTTCTTTTCTTTTGTTTTCT 57.518 32.000 0.00 0.00 0.00 2.52
1655 4128 7.907389 AGACCCTTCTTTTCTTTTGTTTTCTT 58.093 30.769 0.00 0.00 0.00 2.52
1656 4129 8.035394 AGACCCTTCTTTTCTTTTGTTTTCTTC 58.965 33.333 0.00 0.00 0.00 2.87
1657 4130 7.907389 ACCCTTCTTTTCTTTTGTTTTCTTCT 58.093 30.769 0.00 0.00 0.00 2.85
1658 4131 9.031537 ACCCTTCTTTTCTTTTGTTTTCTTCTA 57.968 29.630 0.00 0.00 0.00 2.10
1696 4169 0.458669 GAGCAAATCCATGGCCACTG 59.541 55.000 8.16 7.97 0.00 3.66
1702 4175 0.254178 ATCCATGGCCACTGTCACTC 59.746 55.000 8.16 0.00 0.00 3.51
1703 4176 0.837691 TCCATGGCCACTGTCACTCT 60.838 55.000 8.16 0.00 0.00 3.24
1705 4178 0.035881 CATGGCCACTGTCACTCTGT 59.964 55.000 8.16 0.00 0.00 3.41
1707 4180 0.679505 TGGCCACTGTCACTCTGTAC 59.320 55.000 0.00 0.00 0.00 2.90
1708 4181 0.969894 GGCCACTGTCACTCTGTACT 59.030 55.000 0.00 0.00 0.00 2.73
1709 4182 1.337260 GGCCACTGTCACTCTGTACTG 60.337 57.143 0.00 0.00 0.00 2.74
1710 4183 1.341531 GCCACTGTCACTCTGTACTGT 59.658 52.381 0.00 0.00 0.00 3.55
1711 4184 2.224066 GCCACTGTCACTCTGTACTGTT 60.224 50.000 0.00 0.00 0.00 3.16
1712 4185 3.005472 GCCACTGTCACTCTGTACTGTTA 59.995 47.826 0.00 0.00 0.00 2.41
1713 4186 4.547532 CCACTGTCACTCTGTACTGTTAC 58.452 47.826 0.00 0.00 0.00 2.50
1714 4187 4.037565 CCACTGTCACTCTGTACTGTTACA 59.962 45.833 0.00 0.00 36.72 2.41
2095 4619 4.847444 GAGCCCAAGAGCGCCTCC 62.847 72.222 2.29 0.00 38.01 4.30
2687 5221 5.930135 TCTAGTCAGTGGCTTTCTTTCTTT 58.070 37.500 0.72 0.00 0.00 2.52
2688 5222 5.992217 TCTAGTCAGTGGCTTTCTTTCTTTC 59.008 40.000 0.72 0.00 0.00 2.62
2689 5223 4.786425 AGTCAGTGGCTTTCTTTCTTTCT 58.214 39.130 0.00 0.00 0.00 2.52
2690 5224 5.196695 AGTCAGTGGCTTTCTTTCTTTCTT 58.803 37.500 0.00 0.00 0.00 2.52
2695 5229 5.008118 AGTGGCTTTCTTTCTTTCTTCTTCG 59.992 40.000 0.00 0.00 0.00 3.79
2701 5235 2.550830 TTCTTTCTTCTTCGCCTGCT 57.449 45.000 0.00 0.00 0.00 4.24
2759 5293 7.933728 TTTAACTCTTTTATTTTTGACCGGC 57.066 32.000 0.00 0.00 0.00 6.13
2760 5294 4.155310 ACTCTTTTATTTTTGACCGGCG 57.845 40.909 0.00 0.00 0.00 6.46
2761 5295 3.816523 ACTCTTTTATTTTTGACCGGCGA 59.183 39.130 9.30 0.00 0.00 5.54
2762 5296 4.083484 ACTCTTTTATTTTTGACCGGCGAG 60.083 41.667 9.30 0.06 0.00 5.03
2763 5297 3.816523 TCTTTTATTTTTGACCGGCGAGT 59.183 39.130 9.30 4.21 0.00 4.18
2764 5298 3.817148 TTTATTTTTGACCGGCGAGTC 57.183 42.857 9.30 14.89 37.28 3.36
2765 5299 2.459060 TATTTTTGACCGGCGAGTCA 57.541 45.000 21.66 21.66 44.89 3.41
2797 5331 7.953005 TTTTAGGAAATGACATCATGGCTAA 57.047 32.000 0.00 0.00 36.56 3.09
2830 5364 8.722480 TCATCTCAAATAACGACAAATCATCT 57.278 30.769 0.00 0.00 0.00 2.90
2881 5416 3.148963 TCCGTCCACACACACCGT 61.149 61.111 0.00 0.00 0.00 4.83
2960 5495 5.221880 GCACAATGCTCAAAACTAACATGA 58.778 37.500 0.00 0.00 40.96 3.07
3024 5560 4.335594 GGGTCGCTATTGAATTAACTGCTT 59.664 41.667 0.00 0.00 0.00 3.91
3082 5618 7.806690 TCTGTGTGAAATAGCAGTTTATGAAC 58.193 34.615 0.00 0.00 35.97 3.18
3086 5622 6.714810 TGTGAAATAGCAGTTTATGAACACCT 59.285 34.615 2.93 1.24 38.26 4.00
3117 5653 2.669391 GCAAATTGCAGACCCTTCTTCG 60.669 50.000 13.73 0.00 44.26 3.79
3184 5720 2.776536 AGGAGACCTCAGCTGCAATAAT 59.223 45.455 9.47 0.00 0.00 1.28
3210 5746 3.494573 GCCAGCATCATCTCTCAAGATCA 60.495 47.826 0.00 0.00 40.38 2.92
3280 5818 1.185618 AGCTTGACTGTACCCTGCGA 61.186 55.000 0.00 0.00 0.00 5.10
3301 5839 4.443739 CGATGGTTTAGCCCACATTACCTA 60.444 45.833 0.00 0.00 37.31 3.08
3378 5966 7.936496 TGTATTGATAAGGCAGAACATTCAA 57.064 32.000 0.00 0.00 0.00 2.69
3407 5995 6.894339 TGTATCTTTTTCTCCTTTTCCACC 57.106 37.500 0.00 0.00 0.00 4.61
3414 6002 2.418669 TCTCCTTTTCCACCCTGTCTT 58.581 47.619 0.00 0.00 0.00 3.01
3535 6123 0.613853 TAGTACAGCTGAACCGGCCT 60.614 55.000 23.35 7.16 36.20 5.19
3561 6150 6.377327 TCAACATTCAGAGTTCTTTCAACC 57.623 37.500 0.00 0.00 0.00 3.77
3635 6227 4.989279 ATAAAGCATGCCGAATGTCTTT 57.011 36.364 15.66 8.25 41.42 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.490348 ACAGCAACCTTATTTGTGAGCT 58.510 40.909 0.00 0.00 0.00 4.09
16 17 3.138304 TGATGTGACAGGTTACAGCAAC 58.862 45.455 12.02 1.34 41.39 4.17
17 18 3.483808 TGATGTGACAGGTTACAGCAA 57.516 42.857 12.02 0.00 41.39 3.91
18 19 3.483808 TTGATGTGACAGGTTACAGCA 57.516 42.857 10.63 10.63 42.35 4.41
19 20 5.643777 AGTATTTGATGTGACAGGTTACAGC 59.356 40.000 5.74 5.74 36.25 4.40
20 21 7.099764 AGAGTATTTGATGTGACAGGTTACAG 58.900 38.462 3.44 0.00 32.53 2.74
21 22 7.004555 AGAGTATTTGATGTGACAGGTTACA 57.995 36.000 0.00 0.00 33.56 2.41
22 23 7.097192 TGAGAGTATTTGATGTGACAGGTTAC 58.903 38.462 0.00 0.00 0.00 2.50
23 24 7.239763 TGAGAGTATTTGATGTGACAGGTTA 57.760 36.000 0.00 0.00 0.00 2.85
24 25 6.114187 TGAGAGTATTTGATGTGACAGGTT 57.886 37.500 0.00 0.00 0.00 3.50
25 26 5.745312 TGAGAGTATTTGATGTGACAGGT 57.255 39.130 0.00 0.00 0.00 4.00
26 27 6.580788 AGATGAGAGTATTTGATGTGACAGG 58.419 40.000 0.00 0.00 0.00 4.00
27 28 7.263496 TGAGATGAGAGTATTTGATGTGACAG 58.737 38.462 0.00 0.00 0.00 3.51
28 29 7.174107 TGAGATGAGAGTATTTGATGTGACA 57.826 36.000 0.00 0.00 0.00 3.58
29 30 6.700960 CCTGAGATGAGAGTATTTGATGTGAC 59.299 42.308 0.00 0.00 0.00 3.67
30 31 6.608808 TCCTGAGATGAGAGTATTTGATGTGA 59.391 38.462 0.00 0.00 0.00 3.58
31 32 6.700960 GTCCTGAGATGAGAGTATTTGATGTG 59.299 42.308 0.00 0.00 0.00 3.21
32 33 6.183360 GGTCCTGAGATGAGAGTATTTGATGT 60.183 42.308 0.00 0.00 0.00 3.06
33 34 6.183360 TGGTCCTGAGATGAGAGTATTTGATG 60.183 42.308 0.00 0.00 0.00 3.07
34 35 5.901853 TGGTCCTGAGATGAGAGTATTTGAT 59.098 40.000 0.00 0.00 0.00 2.57
35 36 5.272402 TGGTCCTGAGATGAGAGTATTTGA 58.728 41.667 0.00 0.00 0.00 2.69
36 37 5.604758 TGGTCCTGAGATGAGAGTATTTG 57.395 43.478 0.00 0.00 0.00 2.32
37 38 6.142498 AGATGGTCCTGAGATGAGAGTATTT 58.858 40.000 0.00 0.00 0.00 1.40
38 39 5.714863 AGATGGTCCTGAGATGAGAGTATT 58.285 41.667 0.00 0.00 0.00 1.89
39 40 5.074929 AGAGATGGTCCTGAGATGAGAGTAT 59.925 44.000 0.00 0.00 0.00 2.12
40 41 4.415179 AGAGATGGTCCTGAGATGAGAGTA 59.585 45.833 0.00 0.00 0.00 2.59
41 42 3.205056 AGAGATGGTCCTGAGATGAGAGT 59.795 47.826 0.00 0.00 0.00 3.24
42 43 3.836146 AGAGATGGTCCTGAGATGAGAG 58.164 50.000 0.00 0.00 0.00 3.20
43 44 3.969466 AGAGATGGTCCTGAGATGAGA 57.031 47.619 0.00 0.00 0.00 3.27
44 45 6.477053 TTTTAGAGATGGTCCTGAGATGAG 57.523 41.667 0.00 0.00 0.00 2.90
45 46 6.874278 TTTTTAGAGATGGTCCTGAGATGA 57.126 37.500 0.00 0.00 0.00 2.92
46 47 7.052873 ACATTTTTAGAGATGGTCCTGAGATG 58.947 38.462 0.00 0.00 0.00 2.90
47 48 7.205515 ACATTTTTAGAGATGGTCCTGAGAT 57.794 36.000 0.00 0.00 0.00 2.75
48 49 6.627087 ACATTTTTAGAGATGGTCCTGAGA 57.373 37.500 0.00 0.00 0.00 3.27
49 50 7.560368 AGTACATTTTTAGAGATGGTCCTGAG 58.440 38.462 0.00 0.00 0.00 3.35
50 51 7.496346 AGTACATTTTTAGAGATGGTCCTGA 57.504 36.000 0.00 0.00 0.00 3.86
51 52 7.928706 CCTAGTACATTTTTAGAGATGGTCCTG 59.071 40.741 0.00 0.00 0.00 3.86
52 53 7.844779 TCCTAGTACATTTTTAGAGATGGTCCT 59.155 37.037 0.00 0.00 0.00 3.85
53 54 7.927092 GTCCTAGTACATTTTTAGAGATGGTCC 59.073 40.741 0.00 0.00 0.00 4.46
54 55 7.927092 GGTCCTAGTACATTTTTAGAGATGGTC 59.073 40.741 0.00 0.00 0.00 4.02
55 56 7.402071 TGGTCCTAGTACATTTTTAGAGATGGT 59.598 37.037 0.00 0.00 0.00 3.55
56 57 7.792032 TGGTCCTAGTACATTTTTAGAGATGG 58.208 38.462 0.00 0.00 0.00 3.51
59 60 8.639761 GCTATGGTCCTAGTACATTTTTAGAGA 58.360 37.037 0.00 0.00 0.00 3.10
60 61 8.643324 AGCTATGGTCCTAGTACATTTTTAGAG 58.357 37.037 0.00 0.00 0.00 2.43
61 62 8.548880 AGCTATGGTCCTAGTACATTTTTAGA 57.451 34.615 0.00 0.00 0.00 2.10
62 63 9.915629 CTAGCTATGGTCCTAGTACATTTTTAG 57.084 37.037 0.00 0.00 0.00 1.85
63 64 8.867097 CCTAGCTATGGTCCTAGTACATTTTTA 58.133 37.037 0.00 0.00 31.29 1.52
64 65 7.347485 ACCTAGCTATGGTCCTAGTACATTTTT 59.653 37.037 8.55 0.00 31.03 1.94
65 66 6.844917 ACCTAGCTATGGTCCTAGTACATTTT 59.155 38.462 8.55 0.00 31.03 1.82
66 67 6.382925 ACCTAGCTATGGTCCTAGTACATTT 58.617 40.000 8.55 0.00 31.03 2.32
67 68 5.966684 ACCTAGCTATGGTCCTAGTACATT 58.033 41.667 8.55 0.00 31.03 2.71
68 69 5.602291 ACCTAGCTATGGTCCTAGTACAT 57.398 43.478 8.55 0.00 31.03 2.29
69 70 5.610132 AGTACCTAGCTATGGTCCTAGTACA 59.390 44.000 15.48 0.00 38.88 2.90
70 71 6.125589 AGTACCTAGCTATGGTCCTAGTAC 57.874 45.833 15.48 9.22 38.88 2.73
71 72 6.466904 CCAAGTACCTAGCTATGGTCCTAGTA 60.467 46.154 15.48 0.00 38.88 1.82
72 73 5.386924 CAAGTACCTAGCTATGGTCCTAGT 58.613 45.833 15.48 2.93 38.88 2.57
73 74 4.767928 CCAAGTACCTAGCTATGGTCCTAG 59.232 50.000 15.48 7.53 38.88 3.02
74 75 4.169461 ACCAAGTACCTAGCTATGGTCCTA 59.831 45.833 15.48 0.35 36.47 2.94
75 76 3.052033 ACCAAGTACCTAGCTATGGTCCT 60.052 47.826 15.48 9.11 36.47 3.85
76 77 3.069729 CACCAAGTACCTAGCTATGGTCC 59.930 52.174 15.48 7.29 39.05 4.46
77 78 3.705072 ACACCAAGTACCTAGCTATGGTC 59.295 47.826 15.48 9.49 39.05 4.02
78 79 3.451178 CACACCAAGTACCTAGCTATGGT 59.549 47.826 16.07 16.07 41.65 3.55
79 80 3.181465 CCACACCAAGTACCTAGCTATGG 60.181 52.174 7.17 7.17 0.00 2.74
80 81 3.451178 ACCACACCAAGTACCTAGCTATG 59.549 47.826 0.00 0.00 0.00 2.23
81 82 3.721021 ACCACACCAAGTACCTAGCTAT 58.279 45.455 0.00 0.00 0.00 2.97
82 83 3.179902 ACCACACCAAGTACCTAGCTA 57.820 47.619 0.00 0.00 0.00 3.32
83 84 2.025636 ACCACACCAAGTACCTAGCT 57.974 50.000 0.00 0.00 0.00 3.32
84 85 2.853235 AACCACACCAAGTACCTAGC 57.147 50.000 0.00 0.00 0.00 3.42
85 86 6.045072 TGATAAACCACACCAAGTACCTAG 57.955 41.667 0.00 0.00 0.00 3.02
86 87 6.411376 CATGATAAACCACACCAAGTACCTA 58.589 40.000 0.00 0.00 0.00 3.08
87 88 4.986054 TGATAAACCACACCAAGTACCT 57.014 40.909 0.00 0.00 0.00 3.08
88 89 4.398044 CCATGATAAACCACACCAAGTACC 59.602 45.833 0.00 0.00 0.00 3.34
89 90 5.007682 ACCATGATAAACCACACCAAGTAC 58.992 41.667 0.00 0.00 0.00 2.73
90 91 5.249780 ACCATGATAAACCACACCAAGTA 57.750 39.130 0.00 0.00 0.00 2.24
91 92 4.112634 ACCATGATAAACCACACCAAGT 57.887 40.909 0.00 0.00 0.00 3.16
92 93 5.007034 TGTACCATGATAAACCACACCAAG 58.993 41.667 0.00 0.00 0.00 3.61
93 94 4.986783 TGTACCATGATAAACCACACCAA 58.013 39.130 0.00 0.00 0.00 3.67
94 95 4.642466 TGTACCATGATAAACCACACCA 57.358 40.909 0.00 0.00 0.00 4.17
95 96 4.338118 CCATGTACCATGATAAACCACACC 59.662 45.833 5.80 0.00 0.00 4.16
96 97 4.947388 ACCATGTACCATGATAAACCACAC 59.053 41.667 5.80 0.00 0.00 3.82
97 98 5.186256 ACCATGTACCATGATAAACCACA 57.814 39.130 5.80 0.00 0.00 4.17
98 99 6.116806 TGTACCATGTACCATGATAAACCAC 58.883 40.000 5.80 0.00 0.00 4.16
99 100 6.314899 TGTACCATGTACCATGATAAACCA 57.685 37.500 5.80 0.00 0.00 3.67
100 101 6.262273 CCTTGTACCATGTACCATGATAAACC 59.738 42.308 5.80 0.00 0.00 3.27
101 102 7.051623 TCCTTGTACCATGTACCATGATAAAC 58.948 38.462 5.80 0.20 0.00 2.01
102 103 7.126573 TCTCCTTGTACCATGTACCATGATAAA 59.873 37.037 5.80 0.00 0.00 1.40
103 104 6.613679 TCTCCTTGTACCATGTACCATGATAA 59.386 38.462 5.80 0.00 0.00 1.75
104 105 6.140377 TCTCCTTGTACCATGTACCATGATA 58.860 40.000 5.80 0.00 0.00 2.15
105 106 4.968719 TCTCCTTGTACCATGTACCATGAT 59.031 41.667 5.80 0.00 0.00 2.45
106 107 4.358214 TCTCCTTGTACCATGTACCATGA 58.642 43.478 5.80 0.00 0.00 3.07
107 108 4.753516 TCTCCTTGTACCATGTACCATG 57.246 45.455 2.22 0.00 0.00 3.66
108 109 7.633018 ATTATCTCCTTGTACCATGTACCAT 57.367 36.000 2.22 0.00 0.00 3.55
109 110 7.446106 AATTATCTCCTTGTACCATGTACCA 57.554 36.000 2.22 0.00 0.00 3.25
110 111 7.170998 CGAAATTATCTCCTTGTACCATGTACC 59.829 40.741 2.22 0.00 0.00 3.34
111 112 7.709613 ACGAAATTATCTCCTTGTACCATGTAC 59.290 37.037 0.00 0.00 0.00 2.90
112 113 7.788026 ACGAAATTATCTCCTTGTACCATGTA 58.212 34.615 0.00 0.00 0.00 2.29
113 114 6.650120 ACGAAATTATCTCCTTGTACCATGT 58.350 36.000 0.00 0.00 0.00 3.21
114 115 7.409697 CAACGAAATTATCTCCTTGTACCATG 58.590 38.462 0.00 0.00 0.00 3.66
115 116 6.038271 GCAACGAAATTATCTCCTTGTACCAT 59.962 38.462 0.00 0.00 0.00 3.55
116 117 5.353123 GCAACGAAATTATCTCCTTGTACCA 59.647 40.000 0.00 0.00 0.00 3.25
117 118 5.220796 GGCAACGAAATTATCTCCTTGTACC 60.221 44.000 0.00 0.00 0.00 3.34
118 119 5.353123 TGGCAACGAAATTATCTCCTTGTAC 59.647 40.000 0.00 0.00 42.51 2.90
119 120 5.492895 TGGCAACGAAATTATCTCCTTGTA 58.507 37.500 0.00 0.00 42.51 2.41
120 121 4.331968 TGGCAACGAAATTATCTCCTTGT 58.668 39.130 0.00 0.00 42.51 3.16
121 122 4.963276 TGGCAACGAAATTATCTCCTTG 57.037 40.909 0.00 0.00 42.51 3.61
122 123 5.253330 TCTTGGCAACGAAATTATCTCCTT 58.747 37.500 0.00 0.00 42.51 3.36
123 124 4.843728 TCTTGGCAACGAAATTATCTCCT 58.156 39.130 0.00 0.00 42.51 3.69
124 125 5.560966 TTCTTGGCAACGAAATTATCTCC 57.439 39.130 0.00 0.00 42.51 3.71
125 126 7.867445 TTTTTCTTGGCAACGAAATTATCTC 57.133 32.000 18.71 0.00 42.51 2.75
161 162 5.420421 TCCACCAATTGTTTCAGAACTTGAA 59.580 36.000 4.43 0.00 43.92 2.69
162 163 4.952957 TCCACCAATTGTTTCAGAACTTGA 59.047 37.500 4.43 0.00 36.70 3.02
163 164 5.261209 TCCACCAATTGTTTCAGAACTTG 57.739 39.130 4.43 0.00 36.70 3.16
164 165 5.930837 TTCCACCAATTGTTTCAGAACTT 57.069 34.783 4.43 0.00 36.70 2.66
165 166 5.930837 TTTCCACCAATTGTTTCAGAACT 57.069 34.783 4.43 0.00 36.70 3.01
166 167 6.106003 AGTTTTCCACCAATTGTTTCAGAAC 58.894 36.000 4.43 3.27 36.29 3.01
167 168 6.071108 TGAGTTTTCCACCAATTGTTTCAGAA 60.071 34.615 4.43 0.00 0.00 3.02
168 169 5.420421 TGAGTTTTCCACCAATTGTTTCAGA 59.580 36.000 4.43 0.00 0.00 3.27
169 170 5.659463 TGAGTTTTCCACCAATTGTTTCAG 58.341 37.500 4.43 0.00 0.00 3.02
170 171 5.667539 TGAGTTTTCCACCAATTGTTTCA 57.332 34.783 4.43 0.00 0.00 2.69
171 172 7.552458 AATTGAGTTTTCCACCAATTGTTTC 57.448 32.000 4.43 0.00 36.08 2.78
172 173 7.609532 TCAAATTGAGTTTTCCACCAATTGTTT 59.390 29.630 4.43 0.00 36.84 2.83
173 174 7.108847 TCAAATTGAGTTTTCCACCAATTGTT 58.891 30.769 4.43 0.00 36.84 2.83
174 175 6.648192 TCAAATTGAGTTTTCCACCAATTGT 58.352 32.000 4.43 0.00 36.84 2.71
175 176 7.733402 ATCAAATTGAGTTTTCCACCAATTG 57.267 32.000 1.10 0.00 36.84 2.32
176 177 9.844257 TTTATCAAATTGAGTTTTCCACCAATT 57.156 25.926 1.10 0.00 37.63 2.32
177 178 9.844257 TTTTATCAAATTGAGTTTTCCACCAAT 57.156 25.926 1.10 0.00 31.32 3.16
178 179 9.844257 ATTTTATCAAATTGAGTTTTCCACCAA 57.156 25.926 1.10 0.00 0.00 3.67
223 224 9.878667 TGTCTATACATAATTCCGAGACAAAAA 57.121 29.630 0.00 0.00 38.99 1.94
231 232 9.268268 GGTCAAAATGTCTATACATAATTCCGA 57.732 33.333 0.00 0.00 45.79 4.55
232 233 9.273016 AGGTCAAAATGTCTATACATAATTCCG 57.727 33.333 0.00 0.00 45.79 4.30
245 246 9.313118 GTGAAATAAAACAAGGTCAAAATGTCT 57.687 29.630 0.00 0.00 0.00 3.41
246 247 9.313118 AGTGAAATAAAACAAGGTCAAAATGTC 57.687 29.630 0.00 0.00 0.00 3.06
247 248 9.313118 GAGTGAAATAAAACAAGGTCAAAATGT 57.687 29.630 0.00 0.00 0.00 2.71
254 255 8.807581 CAACTTTGAGTGAAATAAAACAAGGTC 58.192 33.333 0.00 0.00 30.00 3.85
256 257 7.978975 TCCAACTTTGAGTGAAATAAAACAAGG 59.021 33.333 0.00 0.00 0.00 3.61
270 271 4.770010 TGTCAACCTTTTCCAACTTTGAGT 59.230 37.500 0.00 0.00 0.00 3.41
304 306 2.706339 ATTGCTGTGGATCAGGTCTC 57.294 50.000 0.00 0.00 43.78 3.36
306 308 3.084039 TCAAATTGCTGTGGATCAGGTC 58.916 45.455 0.00 0.00 43.78 3.85
307 309 3.087031 CTCAAATTGCTGTGGATCAGGT 58.913 45.455 0.00 0.00 43.78 4.00
310 312 3.503363 GTGACTCAAATTGCTGTGGATCA 59.497 43.478 0.00 0.00 0.00 2.92
318 320 5.733620 AATTGATGGTGACTCAAATTGCT 57.266 34.783 0.00 0.00 36.30 3.91
320 322 6.930164 TGGAAAATTGATGGTGACTCAAATTG 59.070 34.615 0.00 0.00 36.30 2.32
324 326 6.669125 ATTGGAAAATTGATGGTGACTCAA 57.331 33.333 0.00 0.00 37.06 3.02
344 346 8.970859 ATCTATCAAGAAGAAGGTTGGTATTG 57.029 34.615 0.00 0.00 34.73 1.90
348 350 8.606830 AGTTAATCTATCAAGAAGAAGGTTGGT 58.393 33.333 0.00 0.00 34.73 3.67
376 378 5.751243 TCATCAATCAGCAGACAATCATG 57.249 39.130 0.00 0.00 0.00 3.07
378 380 5.433526 TCATCATCAATCAGCAGACAATCA 58.566 37.500 0.00 0.00 0.00 2.57
390 392 7.804843 AAATTCAGAGGTCTCATCATCAATC 57.195 36.000 0.55 0.00 0.00 2.67
398 400 7.000472 TCAACAGAAAAATTCAGAGGTCTCAT 59.000 34.615 0.55 0.00 0.00 2.90
399 401 6.356556 TCAACAGAAAAATTCAGAGGTCTCA 58.643 36.000 0.55 0.00 0.00 3.27
400 402 6.867662 TCAACAGAAAAATTCAGAGGTCTC 57.132 37.500 0.00 0.00 0.00 3.36
402 404 7.206981 TGATCAACAGAAAAATTCAGAGGTC 57.793 36.000 0.00 0.00 0.00 3.85
405 407 7.485277 GCAGATGATCAACAGAAAAATTCAGAG 59.515 37.037 0.00 0.00 0.00 3.35
406 408 7.040271 TGCAGATGATCAACAGAAAAATTCAGA 60.040 33.333 0.00 0.00 0.00 3.27
410 412 7.548075 GGAATGCAGATGATCAACAGAAAAATT 59.452 33.333 0.00 0.00 0.00 1.82
422 440 4.590918 AGATCCATGGAATGCAGATGATC 58.409 43.478 20.67 7.56 44.97 2.92
491 510 3.072184 ACTCAAACCTGTCATCAGAGCTT 59.928 43.478 0.00 0.00 43.76 3.74
510 529 2.869192 GCAGGCTGCTTGTTCTATACTC 59.131 50.000 31.37 0.00 40.96 2.59
523 542 0.171903 CCAAATGTAGTGCAGGCTGC 59.828 55.000 31.91 31.91 45.29 5.25
535 554 3.557686 GCATTTTCCTTGGCTCCAAATGT 60.558 43.478 2.69 0.00 37.23 2.71
570 589 3.785859 TCTCTGTGGCCGGCATCC 61.786 66.667 30.85 15.60 0.00 3.51
630 650 7.910584 AGGAATATCAATTGAAAAGCTTGGTT 58.089 30.769 13.09 0.00 0.00 3.67
669 709 9.660180 GGAGAGAGTACTATCTTGTTTCAAAAT 57.340 33.333 20.50 0.00 35.08 1.82
670 710 7.813148 CGGAGAGAGTACTATCTTGTTTCAAAA 59.187 37.037 20.50 0.00 35.08 2.44
671 711 7.039923 ACGGAGAGAGTACTATCTTGTTTCAAA 60.040 37.037 20.50 0.00 35.08 2.69
797 3244 3.002791 CCAACCACACTAGTACAGCATG 58.997 50.000 0.00 0.00 46.00 4.06
798 3245 2.637872 ACCAACCACACTAGTACAGCAT 59.362 45.455 0.00 0.00 0.00 3.79
813 3260 2.922740 TGGTGTCTTCTGTACCAACC 57.077 50.000 0.00 0.00 41.25 3.77
880 3330 1.741145 ACGGCCGAAATAACATTGGAC 59.259 47.619 35.90 0.00 0.00 4.02
898 3348 1.666872 GAGGTCGACCCAACCAACG 60.667 63.158 30.82 0.00 39.39 4.10
911 3361 0.729816 GTGTTCTCGCTCGTGAGGTC 60.730 60.000 7.56 2.78 36.61 3.85
968 3427 3.012518 CGATCCAAATCCTCTGCTTGTT 58.987 45.455 0.00 0.00 0.00 2.83
973 3432 1.937391 CGCGATCCAAATCCTCTGC 59.063 57.895 0.00 0.00 0.00 4.26
1368 3834 2.354704 CCTGACCAACACATACACGGAT 60.355 50.000 0.00 0.00 0.00 4.18
1647 4120 9.621629 TGTTTCTGTTAAGGATAGAAGAAAACA 57.378 29.630 0.00 0.00 36.91 2.83
1649 4122 9.847224 ACTGTTTCTGTTAAGGATAGAAGAAAA 57.153 29.630 0.00 0.00 36.91 2.29
1650 4123 9.847224 AACTGTTTCTGTTAAGGATAGAAGAAA 57.153 29.630 0.00 0.00 36.91 2.52
1651 4124 9.273016 CAACTGTTTCTGTTAAGGATAGAAGAA 57.727 33.333 0.00 0.00 36.91 2.52
1652 4125 8.647796 TCAACTGTTTCTGTTAAGGATAGAAGA 58.352 33.333 0.00 0.00 36.91 2.87
1653 4126 8.833231 TCAACTGTTTCTGTTAAGGATAGAAG 57.167 34.615 0.00 0.00 36.91 2.85
1654 4127 7.387948 GCTCAACTGTTTCTGTTAAGGATAGAA 59.612 37.037 0.00 0.00 34.17 2.10
1655 4128 6.874134 GCTCAACTGTTTCTGTTAAGGATAGA 59.126 38.462 0.00 0.00 0.00 1.98
1656 4129 6.650807 TGCTCAACTGTTTCTGTTAAGGATAG 59.349 38.462 0.00 0.00 0.00 2.08
1657 4130 6.530120 TGCTCAACTGTTTCTGTTAAGGATA 58.470 36.000 0.00 0.00 0.00 2.59
1658 4131 5.376625 TGCTCAACTGTTTCTGTTAAGGAT 58.623 37.500 0.00 0.00 0.00 3.24
1659 4132 4.776349 TGCTCAACTGTTTCTGTTAAGGA 58.224 39.130 0.00 0.00 0.00 3.36
1660 4133 5.499139 TTGCTCAACTGTTTCTGTTAAGG 57.501 39.130 0.00 0.00 0.00 2.69
1703 4176 7.822334 CCAATCATCCTAAACTGTAACAGTACA 59.178 37.037 0.00 0.00 44.62 2.90
1705 4178 7.822334 CACCAATCATCCTAAACTGTAACAGTA 59.178 37.037 0.00 0.00 44.62 2.74
1707 4180 6.655003 ACACCAATCATCCTAAACTGTAACAG 59.345 38.462 0.00 0.00 37.52 3.16
1708 4181 6.539173 ACACCAATCATCCTAAACTGTAACA 58.461 36.000 0.00 0.00 0.00 2.41
1709 4182 8.556213 TTACACCAATCATCCTAAACTGTAAC 57.444 34.615 0.00 0.00 0.00 2.50
1710 4183 9.747898 AATTACACCAATCATCCTAAACTGTAA 57.252 29.630 0.00 0.00 0.00 2.41
1711 4184 9.173021 CAATTACACCAATCATCCTAAACTGTA 57.827 33.333 0.00 0.00 0.00 2.74
1712 4185 7.122650 CCAATTACACCAATCATCCTAAACTGT 59.877 37.037 0.00 0.00 0.00 3.55
1713 4186 7.339212 TCCAATTACACCAATCATCCTAAACTG 59.661 37.037 0.00 0.00 0.00 3.16
1714 4187 7.410174 TCCAATTACACCAATCATCCTAAACT 58.590 34.615 0.00 0.00 0.00 2.66
1715 4188 7.639113 TCCAATTACACCAATCATCCTAAAC 57.361 36.000 0.00 0.00 0.00 2.01
2308 4842 1.596477 GATCAGCGCCATGGTCTCC 60.596 63.158 14.67 0.00 0.00 3.71
2575 5109 3.445518 GATGCCGACGAGGATGCCA 62.446 63.158 0.00 0.00 45.00 4.92
2687 5221 1.840737 ACTCTAGCAGGCGAAGAAGA 58.159 50.000 0.00 0.00 0.00 2.87
2688 5222 2.946329 TCTACTCTAGCAGGCGAAGAAG 59.054 50.000 0.00 0.00 0.00 2.85
2689 5223 3.000684 TCTACTCTAGCAGGCGAAGAA 57.999 47.619 0.00 0.00 0.00 2.52
2690 5224 2.711978 TCTACTCTAGCAGGCGAAGA 57.288 50.000 0.00 0.63 0.00 2.87
2716 5250 1.813513 AAACACTCCAGATTGCCTCG 58.186 50.000 0.00 0.00 0.00 4.63
2752 5286 0.179067 AAAGTTTGACTCGCCGGTCA 60.179 50.000 1.90 4.62 43.41 4.02
2753 5287 0.942252 AAAAGTTTGACTCGCCGGTC 59.058 50.000 1.90 0.00 36.81 4.79
2754 5288 1.385528 AAAAAGTTTGACTCGCCGGT 58.614 45.000 1.90 0.00 0.00 5.28
2830 5364 9.280174 CCATCTTTTATCCGTAGCCTTATTTTA 57.720 33.333 0.00 0.00 0.00 1.52
2881 5416 2.250273 AGAAGGGCTAGGGTTGATCCTA 59.750 50.000 0.00 0.00 38.30 2.94
2960 5495 8.149647 TGCTTTGAGATTTGTGATAATTTTGGT 58.850 29.630 0.00 0.00 0.00 3.67
2971 5506 8.975410 TCTTAATGATTGCTTTGAGATTTGTG 57.025 30.769 0.00 0.00 0.00 3.33
3000 5535 3.877508 GCAGTTAATTCAATAGCGACCCT 59.122 43.478 0.00 0.00 0.00 4.34
3024 5560 8.331740 AGAATTGGTCAAGGAGATTAATCAAGA 58.668 33.333 17.56 5.02 0.00 3.02
3082 5618 4.918037 GCAATTTGCAGATTCTCTAGGTG 58.082 43.478 16.35 0.00 44.26 4.00
3100 5636 2.678190 GCTACGAAGAAGGGTCTGCAAT 60.678 50.000 0.00 0.00 33.05 3.56
3133 5669 8.194104 TGGGTAAAACAATTGATGCATATACAC 58.806 33.333 13.59 6.95 0.00 2.90
3184 5720 2.242043 TGAGAGATGATGCTGGCGATA 58.758 47.619 0.00 0.00 0.00 2.92
3210 5746 2.648059 GAGTACTGCTTCCATTGGCAT 58.352 47.619 0.00 0.00 37.83 4.40
3280 5818 5.372661 AGATAGGTAATGTGGGCTAAACCAT 59.627 40.000 0.00 0.00 43.59 3.55
3301 5839 2.154462 CTGTTCAACTTCCGGCAAGAT 58.846 47.619 17.18 5.82 35.82 2.40
3378 5966 8.797438 GGAAAAGGAGAAAAAGATACATGAACT 58.203 33.333 0.00 0.00 0.00 3.01
3384 5972 5.773176 GGGTGGAAAAGGAGAAAAAGATACA 59.227 40.000 0.00 0.00 0.00 2.29
3393 5981 2.418669 AGACAGGGTGGAAAAGGAGAA 58.581 47.619 0.00 0.00 0.00 2.87
3403 5991 0.771127 TGGGAAAGAAGACAGGGTGG 59.229 55.000 0.00 0.00 0.00 4.61
3407 5995 2.887151 ATGGTGGGAAAGAAGACAGG 57.113 50.000 0.00 0.00 0.00 4.00
3414 6002 2.638325 TGGTTCCTATGGTGGGAAAGA 58.362 47.619 0.00 0.00 43.39 2.52
3535 6123 8.567948 GGTTGAAAGAACTCTGAATGTTGATAA 58.432 33.333 0.00 0.00 0.00 1.75
3561 6150 7.503902 TGGGAAAATTTGGGTTTATTGGAAAAG 59.496 33.333 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.