Multiple sequence alignment - TraesCS7D01G304700

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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 TraesCS7D01G304700 chr7D 100.000 1720 0 0 430 2149 386560056 386561775 0.000000e+00 3177.0
1 TraesCS7D01G304700 chr7D 100.000 1447 0 0 2499 3945 386562125 386563571 0.000000e+00 2673.0
2 TraesCS7D01G304700 chr7D 88.564 411 30 7 1743 2149 23499648 23500045 2.130000e-132 483.0
3 TraesCS7D01G304700 chr7D 100.000 155 0 0 1 155 386559627 386559781 1.790000e-73 287.0
4 TraesCS7D01G304700 chr7D 94.545 165 6 3 853 1016 23499229 23499391 6.540000e-63 252.0
5 TraesCS7D01G304700 chr7D 88.889 126 10 3 855 977 542854239 542854115 6.830000e-33 152.0
6 TraesCS7D01G304700 chr7B 92.929 891 28 9 3083 3945 380855658 380856541 0.000000e+00 1264.0
7 TraesCS7D01G304700 chr7B 93.548 775 33 6 3184 3941 380863356 380864130 0.000000e+00 1138.0
8 TraesCS7D01G304700 chr7B 82.857 385 28 8 859 1221 567634575 567634207 1.060000e-80 311.0
9 TraesCS7D01G304700 chr7B 86.147 231 26 5 2618 2844 380730767 380730995 1.100000e-60 244.0
10 TraesCS7D01G304700 chr7B 79.558 362 53 12 486 829 380862434 380862792 5.090000e-59 239.0
11 TraesCS7D01G304700 chr7B 95.000 40 1 1 2994 3032 380863165 380863204 1.180000e-05 62.1
12 TraesCS7D01G304700 chr7A 92.683 779 35 9 3180 3942 435864694 435865466 0.000000e+00 1103.0
13 TraesCS7D01G304700 chr7A 92.602 757 40 5 3197 3942 435826887 435827638 0.000000e+00 1074.0
14 TraesCS7D01G304700 chr7A 87.217 618 46 18 2596 3202 435821873 435822468 0.000000e+00 673.0
15 TraesCS7D01G304700 chr7A 90.215 419 36 5 441 856 435821264 435821680 3.470000e-150 542.0
16 TraesCS7D01G304700 chr7A 95.122 41 1 1 1350 1390 138911131 138911170 3.290000e-06 63.9
17 TraesCS7D01G304700 chr6A 89.130 828 55 18 1350 2149 7192555 7193375 0.000000e+00 998.0
18 TraesCS7D01G304700 chr6A 90.533 169 10 2 1752 1916 299720375 299720541 6.640000e-53 219.0
19 TraesCS7D01G304700 chr3A 90.496 705 41 12 1013 1694 745636367 745637068 0.000000e+00 907.0
20 TraesCS7D01G304700 chr3B 89.024 738 48 15 1013 1720 828547209 828547943 0.000000e+00 883.0
21 TraesCS7D01G304700 chr3B 91.358 162 13 1 1762 1922 6978018 6978179 1.850000e-53 220.0
22 TraesCS7D01G304700 chr3B 86.538 52 5 2 2767 2817 760475923 760475873 5.510000e-04 56.5
23 TraesCS7D01G304700 chr3D 88.712 753 44 18 1013 1736 610930237 610930977 0.000000e+00 881.0
24 TraesCS7D01G304700 chr3D 87.162 148 17 2 855 1000 405820886 405820739 2.440000e-37 167.0
25 TraesCS7D01G304700 chr3D 97.826 46 1 0 1995 2040 559127666 559127621 3.270000e-11 80.5
26 TraesCS7D01G304700 chr3D 97.368 38 1 0 2789 2826 574784826 574784863 9.150000e-07 65.8
27 TraesCS7D01G304700 chr4D 89.474 247 25 1 1762 2007 490406330 490406576 1.060000e-80 311.0
28 TraesCS7D01G304700 chr6B 82.262 389 31 13 858 1224 84925179 84924807 6.410000e-78 302.0
29 TraesCS7D01G304700 chr6B 86.245 269 27 7 1885 2149 695074133 695073871 2.320000e-72 283.0
30 TraesCS7D01G304700 chr6B 81.330 391 34 9 853 1221 708381384 708381757 8.350000e-72 281.0
31 TraesCS7D01G304700 chr6B 86.667 255 25 6 1894 2146 695085031 695084784 1.400000e-69 274.0
32 TraesCS7D01G304700 chr6B 80.720 389 37 10 855 1221 652624343 652624715 6.500000e-68 268.0
33 TraesCS7D01G304700 chr6B 91.011 178 12 1 1743 1916 695074359 695074182 1.830000e-58 237.0
34 TraesCS7D01G304700 chr6B 88.202 178 17 4 1743 1916 695085269 695085092 3.990000e-50 209.0
35 TraesCS7D01G304700 chr4B 87.226 274 24 8 1878 2146 212505638 212505905 6.410000e-78 302.0
36 TraesCS7D01G304700 chr4B 82.716 324 34 14 1836 2147 415766133 415766446 6.500000e-68 268.0
37 TraesCS7D01G304700 chr4B 91.237 194 16 1 1815 2007 591925798 591925991 3.020000e-66 263.0
38 TraesCS7D01G304700 chr4B 89.820 167 14 3 855 1019 212504996 212505161 1.110000e-50 211.0
39 TraesCS7D01G304700 chr4B 85.000 100 13 2 2499 2597 591926137 591926235 2.510000e-17 100.0
40 TraesCS7D01G304700 chr5A 88.664 247 20 4 1762 2007 671983174 671983413 1.070000e-75 294.0
41 TraesCS7D01G304700 chr2B 86.290 248 17 6 1350 1592 779221241 779221476 1.820000e-63 254.0
42 TraesCS7D01G304700 chr2B 97.297 37 1 0 2789 2825 546838330 546838366 3.290000e-06 63.9
43 TraesCS7D01G304700 chr2D 87.500 200 9 6 853 1051 440615654 440615838 2.390000e-52 217.0
44 TraesCS7D01G304700 chr2D 89.431 123 9 2 855 976 624649299 624649180 6.830000e-33 152.0
45 TraesCS7D01G304700 chr2D 87.850 107 10 3 911 1016 619213861 619213757 5.350000e-24 122.0
46 TraesCS7D01G304700 chr2D 97.297 37 1 0 2789 2825 468756367 468756403 3.290000e-06 63.9
47 TraesCS7D01G304700 chr2A 90.789 152 12 2 855 1005 81169567 81169717 6.680000e-48 202.0
48 TraesCS7D01G304700 chr2A 88.462 52 4 2 2773 2823 277141371 277141421 1.180000e-05 62.1
49 TraesCS7D01G304700 chr1D 84.314 204 17 5 853 1055 290413621 290413432 6.730000e-43 185.0
50 TraesCS7D01G304700 chr1D 92.784 97 7 0 1743 1839 10893267 10893171 1.480000e-29 141.0
51 TraesCS7D01G304700 chr5D 87.013 154 15 4 855 1007 473517061 473516912 6.780000e-38 169.0
52 TraesCS7D01G304700 chr1A 88.095 126 12 1 853 975 12375235 12375110 3.180000e-31 147.0
53 TraesCS7D01G304700 chr6D 90.741 54 4 1 2772 2825 27087794 27087846 1.970000e-08 71.3
54 TraesCS7D01G304700 chr5B 88.462 52 4 2 2773 2823 538034060 538034110 1.180000e-05 62.1


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 TraesCS7D01G304700 chr7D 386559627 386563571 3944 False 2045.666667 3177 100.000000 1 3945 3 chr7D.!!$F2 3944
1 TraesCS7D01G304700 chr7D 23499229 23500045 816 False 367.500000 483 91.554500 853 2149 2 chr7D.!!$F1 1296
2 TraesCS7D01G304700 chr7B 380855658 380856541 883 False 1264.000000 1264 92.929000 3083 3945 1 chr7B.!!$F2 862
3 TraesCS7D01G304700 chr7B 380862434 380864130 1696 False 479.700000 1138 89.368667 486 3941 3 chr7B.!!$F3 3455
4 TraesCS7D01G304700 chr7A 435864694 435865466 772 False 1103.000000 1103 92.683000 3180 3942 1 chr7A.!!$F3 762
5 TraesCS7D01G304700 chr7A 435826887 435827638 751 False 1074.000000 1074 92.602000 3197 3942 1 chr7A.!!$F2 745
6 TraesCS7D01G304700 chr7A 435821264 435822468 1204 False 607.500000 673 88.716000 441 3202 2 chr7A.!!$F4 2761
7 TraesCS7D01G304700 chr6A 7192555 7193375 820 False 998.000000 998 89.130000 1350 2149 1 chr6A.!!$F1 799
8 TraesCS7D01G304700 chr3A 745636367 745637068 701 False 907.000000 907 90.496000 1013 1694 1 chr3A.!!$F1 681
9 TraesCS7D01G304700 chr3B 828547209 828547943 734 False 883.000000 883 89.024000 1013 1720 1 chr3B.!!$F2 707
10 TraesCS7D01G304700 chr3D 610930237 610930977 740 False 881.000000 881 88.712000 1013 1736 1 chr3D.!!$F2 723
11 TraesCS7D01G304700 chr4B 212504996 212505905 909 False 256.500000 302 88.523000 855 2146 2 chr4B.!!$F2 1291

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
749 764 0.033504 GCTTTGTGAGGTCACCGAGA 59.966 55.0 7.64 0.0 45.88 4.04 F
1187 1373 0.031449 GGAGCGGGAGAAGAAGATCG 59.969 60.0 0.00 0.0 0.00 3.69 F
2556 2908 0.040067 GCAAAACGAGCCTGTTGGAG 60.040 55.0 0.00 0.0 34.57 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2889 0.040067 CTCCAACAGGCTCGTTTTGC 60.040 55.0 0.00 0.00 0.00 3.68 R
2799 3160 0.039527 CGAAAAAGGCTTTCACCCCG 60.040 55.0 13.76 8.65 0.00 5.73 R
3824 4238 2.445565 TCGCAGAGTATCATCATGGC 57.554 50.0 0.00 0.00 37.82 4.40 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
17 18 3.731136 GGCTTTGTCGTCAGTGCA 58.269 55.556 9.94 0.00 0.00 4.57
18 19 1.279840 GGCTTTGTCGTCAGTGCAC 59.720 57.895 9.40 9.40 0.00 4.57
19 20 1.160329 GGCTTTGTCGTCAGTGCACT 61.160 55.000 15.25 15.25 0.00 4.40
20 21 0.233332 GCTTTGTCGTCAGTGCACTC 59.767 55.000 18.64 5.86 0.00 3.51
21 22 1.570813 CTTTGTCGTCAGTGCACTCA 58.429 50.000 18.64 8.91 0.00 3.41
22 23 2.138320 CTTTGTCGTCAGTGCACTCAT 58.862 47.619 18.64 0.00 0.00 2.90
23 24 2.238942 TTGTCGTCAGTGCACTCATT 57.761 45.000 18.64 0.00 0.00 2.57
24 25 2.238942 TGTCGTCAGTGCACTCATTT 57.761 45.000 18.64 0.00 0.00 2.32
25 26 2.135139 TGTCGTCAGTGCACTCATTTC 58.865 47.619 18.64 8.54 0.00 2.17
26 27 1.125021 GTCGTCAGTGCACTCATTTCG 59.875 52.381 18.64 16.19 0.00 3.46
27 28 1.139989 CGTCAGTGCACTCATTTCGT 58.860 50.000 18.64 0.00 0.00 3.85
28 29 1.125021 CGTCAGTGCACTCATTTCGTC 59.875 52.381 18.64 1.50 0.00 4.20
29 30 1.461127 GTCAGTGCACTCATTTCGTCC 59.539 52.381 18.64 0.00 0.00 4.79
30 31 0.798776 CAGTGCACTCATTTCGTCCC 59.201 55.000 18.64 0.00 0.00 4.46
31 32 0.687354 AGTGCACTCATTTCGTCCCT 59.313 50.000 15.25 0.00 0.00 4.20
32 33 1.899814 AGTGCACTCATTTCGTCCCTA 59.100 47.619 15.25 0.00 0.00 3.53
33 34 2.501723 AGTGCACTCATTTCGTCCCTAT 59.498 45.455 15.25 0.00 0.00 2.57
34 35 2.866762 GTGCACTCATTTCGTCCCTATC 59.133 50.000 10.32 0.00 0.00 2.08
35 36 2.499693 TGCACTCATTTCGTCCCTATCA 59.500 45.455 0.00 0.00 0.00 2.15
36 37 3.134623 TGCACTCATTTCGTCCCTATCAT 59.865 43.478 0.00 0.00 0.00 2.45
37 38 3.496130 GCACTCATTTCGTCCCTATCATG 59.504 47.826 0.00 0.00 0.00 3.07
38 39 4.697514 CACTCATTTCGTCCCTATCATGT 58.302 43.478 0.00 0.00 0.00 3.21
39 40 4.509230 CACTCATTTCGTCCCTATCATGTG 59.491 45.833 0.00 0.00 0.00 3.21
40 41 4.162320 ACTCATTTCGTCCCTATCATGTGT 59.838 41.667 0.00 0.00 0.00 3.72
41 42 4.441792 TCATTTCGTCCCTATCATGTGTG 58.558 43.478 0.00 0.00 0.00 3.82
42 43 4.161377 TCATTTCGTCCCTATCATGTGTGA 59.839 41.667 0.00 0.00 39.04 3.58
43 44 4.753516 TTTCGTCCCTATCATGTGTGAT 57.246 40.909 0.00 0.00 46.54 3.06
44 45 4.753516 TTCGTCCCTATCATGTGTGATT 57.246 40.909 0.00 0.00 42.37 2.57
45 46 4.058721 TCGTCCCTATCATGTGTGATTG 57.941 45.455 0.00 0.00 42.37 2.67
52 53 3.744940 ATCATGTGTGATTGGGAAGGT 57.255 42.857 0.00 0.00 42.37 3.50
53 54 3.524095 TCATGTGTGATTGGGAAGGTT 57.476 42.857 0.00 0.00 0.00 3.50
54 55 3.843422 TCATGTGTGATTGGGAAGGTTT 58.157 40.909 0.00 0.00 0.00 3.27
55 56 4.991776 TCATGTGTGATTGGGAAGGTTTA 58.008 39.130 0.00 0.00 0.00 2.01
56 57 5.389520 TCATGTGTGATTGGGAAGGTTTAA 58.610 37.500 0.00 0.00 0.00 1.52
57 58 6.015918 TCATGTGTGATTGGGAAGGTTTAAT 58.984 36.000 0.00 0.00 0.00 1.40
58 59 7.178573 TCATGTGTGATTGGGAAGGTTTAATA 58.821 34.615 0.00 0.00 0.00 0.98
59 60 7.339212 TCATGTGTGATTGGGAAGGTTTAATAG 59.661 37.037 0.00 0.00 0.00 1.73
60 61 5.417580 TGTGTGATTGGGAAGGTTTAATAGC 59.582 40.000 0.00 0.00 0.00 2.97
61 62 4.953579 TGTGATTGGGAAGGTTTAATAGCC 59.046 41.667 0.00 0.00 0.00 3.93
62 63 5.201243 GTGATTGGGAAGGTTTAATAGCCT 58.799 41.667 0.00 0.00 36.51 4.58
63 64 5.299531 GTGATTGGGAAGGTTTAATAGCCTC 59.700 44.000 0.00 0.00 33.24 4.70
64 65 3.945640 TGGGAAGGTTTAATAGCCTCC 57.054 47.619 0.00 0.00 33.24 4.30
65 66 3.470868 TGGGAAGGTTTAATAGCCTCCT 58.529 45.455 0.00 0.00 33.24 3.69
66 67 3.856206 TGGGAAGGTTTAATAGCCTCCTT 59.144 43.478 0.00 0.00 40.59 3.36
67 68 4.207955 GGGAAGGTTTAATAGCCTCCTTG 58.792 47.826 0.00 0.00 38.42 3.61
68 69 4.325109 GGGAAGGTTTAATAGCCTCCTTGT 60.325 45.833 0.00 0.00 38.42 3.16
69 70 5.104235 GGGAAGGTTTAATAGCCTCCTTGTA 60.104 44.000 0.00 0.00 38.42 2.41
70 71 6.410504 GGGAAGGTTTAATAGCCTCCTTGTAT 60.411 42.308 0.00 0.00 38.42 2.29
71 72 7.202158 GGGAAGGTTTAATAGCCTCCTTGTATA 60.202 40.741 0.00 0.00 38.42 1.47
72 73 7.660617 GGAAGGTTTAATAGCCTCCTTGTATAC 59.339 40.741 0.00 0.00 38.42 1.47
73 74 7.932683 AGGTTTAATAGCCTCCTTGTATACT 57.067 36.000 4.17 0.00 0.00 2.12
74 75 9.443365 AAGGTTTAATAGCCTCCTTGTATACTA 57.557 33.333 4.17 0.00 37.17 1.82
75 76 9.091220 AGGTTTAATAGCCTCCTTGTATACTAG 57.909 37.037 7.29 7.29 0.00 2.57
76 77 7.818446 GGTTTAATAGCCTCCTTGTATACTAGC 59.182 40.741 8.62 0.00 0.00 3.42
77 78 5.646577 AATAGCCTCCTTGTATACTAGCG 57.353 43.478 8.62 3.37 0.00 4.26
78 79 2.946785 AGCCTCCTTGTATACTAGCGT 58.053 47.619 8.62 0.00 0.00 5.07
79 80 4.096190 AGCCTCCTTGTATACTAGCGTA 57.904 45.455 8.62 0.00 0.00 4.42
80 81 4.467769 AGCCTCCTTGTATACTAGCGTAA 58.532 43.478 8.62 0.00 0.00 3.18
81 82 5.078256 AGCCTCCTTGTATACTAGCGTAAT 58.922 41.667 8.62 0.00 0.00 1.89
82 83 5.047943 AGCCTCCTTGTATACTAGCGTAATG 60.048 44.000 8.62 0.00 0.00 1.90
83 84 5.710984 CCTCCTTGTATACTAGCGTAATGG 58.289 45.833 8.62 0.00 0.00 3.16
84 85 5.130292 TCCTTGTATACTAGCGTAATGGC 57.870 43.478 8.62 0.00 0.00 4.40
85 86 4.021719 TCCTTGTATACTAGCGTAATGGCC 60.022 45.833 8.62 0.00 0.00 5.36
86 87 4.262292 CCTTGTATACTAGCGTAATGGCCA 60.262 45.833 8.56 8.56 0.00 5.36
87 88 4.514781 TGTATACTAGCGTAATGGCCAG 57.485 45.455 13.05 0.00 0.00 4.85
88 89 3.893200 TGTATACTAGCGTAATGGCCAGT 59.107 43.478 13.05 12.48 38.43 4.00
89 90 4.342951 TGTATACTAGCGTAATGGCCAGTT 59.657 41.667 12.70 8.36 36.33 3.16
90 91 2.024176 ACTAGCGTAATGGCCAGTTG 57.976 50.000 12.70 5.80 30.58 3.16
91 92 1.299541 CTAGCGTAATGGCCAGTTGG 58.700 55.000 12.70 4.72 38.53 3.77
92 93 0.107410 TAGCGTAATGGCCAGTTGGG 60.107 55.000 12.70 1.80 40.85 4.12
93 94 2.414785 GCGTAATGGCCAGTTGGGG 61.415 63.158 12.70 0.00 37.04 4.96
94 95 1.301623 CGTAATGGCCAGTTGGGGA 59.698 57.895 12.70 0.00 37.04 4.81
95 96 0.748005 CGTAATGGCCAGTTGGGGAG 60.748 60.000 12.70 0.00 37.04 4.30
96 97 1.037579 GTAATGGCCAGTTGGGGAGC 61.038 60.000 12.70 0.00 37.04 4.70
97 98 1.214305 TAATGGCCAGTTGGGGAGCT 61.214 55.000 12.70 0.00 37.04 4.09
98 99 2.097978 AATGGCCAGTTGGGGAGCTT 62.098 55.000 13.05 0.00 37.04 3.74
99 100 2.677875 GGCCAGTTGGGGAGCTTG 60.678 66.667 0.00 0.00 37.04 4.01
100 101 2.436109 GCCAGTTGGGGAGCTTGA 59.564 61.111 0.00 0.00 37.04 3.02
101 102 1.676967 GCCAGTTGGGGAGCTTGAG 60.677 63.158 0.00 0.00 37.04 3.02
102 103 1.676967 CCAGTTGGGGAGCTTGAGC 60.677 63.158 0.00 0.00 42.49 4.26
103 104 1.676967 CAGTTGGGGAGCTTGAGCC 60.677 63.158 0.00 0.00 43.38 4.70
104 105 2.156098 AGTTGGGGAGCTTGAGCCA 61.156 57.895 0.00 0.00 43.38 4.75
105 106 1.228552 GTTGGGGAGCTTGAGCCAA 60.229 57.895 0.00 0.00 43.38 4.52
106 107 0.827507 GTTGGGGAGCTTGAGCCAAA 60.828 55.000 0.00 0.00 43.38 3.28
107 108 0.105760 TTGGGGAGCTTGAGCCAAAA 60.106 50.000 0.00 0.00 43.38 2.44
108 109 0.114954 TGGGGAGCTTGAGCCAAAAT 59.885 50.000 0.00 0.00 43.38 1.82
109 110 0.820226 GGGGAGCTTGAGCCAAAATC 59.180 55.000 0.00 0.00 43.38 2.17
110 111 0.453390 GGGAGCTTGAGCCAAAATCG 59.547 55.000 0.00 0.00 43.38 3.34
111 112 1.168714 GGAGCTTGAGCCAAAATCGT 58.831 50.000 0.00 0.00 43.38 3.73
112 113 1.541588 GGAGCTTGAGCCAAAATCGTT 59.458 47.619 0.00 0.00 43.38 3.85
113 114 2.589014 GAGCTTGAGCCAAAATCGTTG 58.411 47.619 0.00 0.00 43.38 4.10
114 115 1.270550 AGCTTGAGCCAAAATCGTTGG 59.729 47.619 0.00 0.56 43.38 3.77
115 116 1.669795 GCTTGAGCCAAAATCGTTGGG 60.670 52.381 7.20 0.00 39.90 4.12
116 117 0.965439 TTGAGCCAAAATCGTTGGGG 59.035 50.000 7.20 0.00 39.90 4.96
117 118 0.897863 TGAGCCAAAATCGTTGGGGG 60.898 55.000 7.20 0.00 39.90 5.40
150 151 7.543947 CACAATCACTATGTGCTGATCTTAA 57.456 36.000 0.00 0.00 41.42 1.85
151 152 8.151141 CACAATCACTATGTGCTGATCTTAAT 57.849 34.615 0.00 0.00 41.42 1.40
152 153 8.068380 CACAATCACTATGTGCTGATCTTAATG 58.932 37.037 0.00 0.00 41.42 1.90
153 154 7.228108 ACAATCACTATGTGCTGATCTTAATGG 59.772 37.037 0.00 0.00 32.98 3.16
154 155 6.484364 TCACTATGTGCTGATCTTAATGGA 57.516 37.500 0.00 0.00 32.98 3.41
451 452 0.611618 TGGCATTCCATTTCGGCTGT 60.612 50.000 0.00 0.00 37.47 4.40
453 454 1.098050 GCATTCCATTTCGGCTGTCT 58.902 50.000 0.00 0.00 33.14 3.41
456 457 3.614870 GCATTCCATTTCGGCTGTCTTTT 60.615 43.478 0.00 0.00 33.14 2.27
481 482 1.676635 GTGAAGGCAGCAGCATGGA 60.677 57.895 2.65 0.00 44.61 3.41
482 483 1.035932 GTGAAGGCAGCAGCATGGAT 61.036 55.000 2.65 0.00 44.61 3.41
593 594 4.284490 ACAAGGTCTCTCTATCAAAGCACA 59.716 41.667 0.00 0.00 0.00 4.57
620 621 0.591170 AAATTGGCACGACGGAACTG 59.409 50.000 0.00 0.00 0.00 3.16
656 659 4.998671 TCAAGTTGCCACTCAAAATTCA 57.001 36.364 0.00 0.00 36.26 2.57
662 676 4.305989 TGCCACTCAAAATTCAGACAAC 57.694 40.909 0.00 0.00 0.00 3.32
683 697 1.187087 GATCTGTGGTCGTCTTCCCT 58.813 55.000 0.00 0.00 0.00 4.20
744 759 0.531974 TGTCCGCTTTGTGAGGTCAC 60.532 55.000 2.99 2.99 46.59 3.67
749 764 0.033504 GCTTTGTGAGGTCACCGAGA 59.966 55.000 7.64 0.00 45.88 4.04
791 806 4.386652 TCACTTACGTTACCGCTCAATTTC 59.613 41.667 0.00 0.00 37.70 2.17
793 808 4.387862 ACTTACGTTACCGCTCAATTTCTG 59.612 41.667 0.00 0.00 37.70 3.02
794 809 2.762745 ACGTTACCGCTCAATTTCTGT 58.237 42.857 0.00 0.00 37.70 3.41
811 828 4.095410 TCTGTGTGCTGTTTTTGTGAAG 57.905 40.909 0.00 0.00 0.00 3.02
816 833 2.845967 GTGCTGTTTTTGTGAAGTCGTG 59.154 45.455 0.00 0.00 0.00 4.35
822 839 5.067273 TGTTTTTGTGAAGTCGTGGGATAT 58.933 37.500 0.00 0.00 0.00 1.63
824 841 6.370442 TGTTTTTGTGAAGTCGTGGGATATAG 59.630 38.462 0.00 0.00 0.00 1.31
825 842 5.925506 TTTGTGAAGTCGTGGGATATAGA 57.074 39.130 0.00 0.00 0.00 1.98
928 1050 1.908065 CTGCCGGCGAAAAATTAAGG 58.092 50.000 23.90 0.00 0.00 2.69
938 1060 3.169908 GAAAAATTAAGGCTGGGGGTGA 58.830 45.455 0.00 0.00 0.00 4.02
961 1083 0.916086 AATATCCACTCGTTGCCCCA 59.084 50.000 0.00 0.00 0.00 4.96
984 1106 2.668632 CACGTACCCAGCCACCAT 59.331 61.111 0.00 0.00 0.00 3.55
1037 1212 1.065928 CCTACTCGGTGGCGATGAC 59.934 63.158 0.00 0.00 0.00 3.06
1068 1254 2.049063 GCTGCTGAACTCGTCGGT 60.049 61.111 0.00 0.00 34.76 4.69
1165 1351 2.044946 GCCCTTGTCGAGGCCAAT 60.045 61.111 5.01 0.00 44.85 3.16
1166 1352 1.223487 GCCCTTGTCGAGGCCAATA 59.777 57.895 5.01 0.00 44.85 1.90
1187 1373 0.031449 GGAGCGGGAGAAGAAGATCG 59.969 60.000 0.00 0.00 0.00 3.69
1274 1466 2.524044 TGGACGACCAGGAGGACA 59.476 61.111 1.37 0.00 41.77 4.02
1328 1520 2.060980 AGCATCGAGGTGGAGGACC 61.061 63.158 0.00 0.00 46.58 4.46
1390 1582 2.521465 CACAGCAAGCCCAACCCA 60.521 61.111 0.00 0.00 0.00 4.51
1399 1591 4.028490 CCCAACCCAGCCACGCTA 62.028 66.667 0.00 0.00 36.40 4.26
1444 1642 3.406200 AGCTGCATCTCCCGGCTT 61.406 61.111 1.02 0.00 41.98 4.35
1452 1650 4.052229 CTCCCGGCTTGTCGTCGT 62.052 66.667 0.00 0.00 39.61 4.34
1465 1663 2.963371 GTCGTCGACTCCAAGGCT 59.037 61.111 18.09 0.00 0.00 4.58
1620 1840 2.025155 GTCCCTGTCTAGCAAGATCGA 58.975 52.381 0.00 0.00 33.30 3.59
1624 1844 1.064803 CTGTCTAGCAAGATCGAGCGT 59.935 52.381 0.00 0.00 33.30 5.07
1993 2342 1.527844 GATGGATGAGGGCTGGTGC 60.528 63.158 0.00 0.00 38.76 5.01
2045 2394 3.196685 CGGGAGAAAGAGGAGATTCTTGT 59.803 47.826 0.00 0.00 37.48 3.16
2114 2466 4.373156 AGGAGAGAGAGATTAGAGGCTC 57.627 50.000 6.34 6.34 0.00 4.70
2116 2468 3.496160 GGAGAGAGAGATTAGAGGCTCGT 60.496 52.174 9.22 0.00 36.29 4.18
2518 2870 4.743975 TTGCATGCGCCGGTCGTA 62.744 61.111 14.09 14.25 41.07 3.43
2521 2873 2.508439 CATGCGCCGGTCGTAGTT 60.508 61.111 17.38 0.00 41.07 2.24
2522 2874 2.098233 CATGCGCCGGTCGTAGTTT 61.098 57.895 17.38 0.00 41.07 2.66
2523 2875 1.375013 ATGCGCCGGTCGTAGTTTT 60.375 52.632 17.38 0.00 41.07 2.43
2524 2876 1.356527 ATGCGCCGGTCGTAGTTTTC 61.357 55.000 17.38 2.54 41.07 2.29
2525 2877 3.063052 GCGCCGGTCGTAGTTTTCG 62.063 63.158 17.38 3.59 41.07 3.46
2526 2878 1.730547 CGCCGGTCGTAGTTTTCGT 60.731 57.895 1.90 0.00 0.00 3.85
2527 2879 1.277495 CGCCGGTCGTAGTTTTCGTT 61.277 55.000 1.90 0.00 0.00 3.85
2528 2880 1.696988 GCCGGTCGTAGTTTTCGTTA 58.303 50.000 1.90 0.00 0.00 3.18
2529 2881 2.058057 GCCGGTCGTAGTTTTCGTTAA 58.942 47.619 1.90 0.00 0.00 2.01
2530 2882 2.474735 GCCGGTCGTAGTTTTCGTTAAA 59.525 45.455 1.90 0.00 0.00 1.52
2531 2883 3.123453 GCCGGTCGTAGTTTTCGTTAAAT 59.877 43.478 1.90 0.00 0.00 1.40
2532 2884 4.722066 GCCGGTCGTAGTTTTCGTTAAATC 60.722 45.833 1.90 0.00 0.00 2.17
2533 2885 4.201618 CCGGTCGTAGTTTTCGTTAAATCC 60.202 45.833 0.00 0.00 0.00 3.01
2534 2886 4.489206 CGGTCGTAGTTTTCGTTAAATCCG 60.489 45.833 0.00 0.00 0.00 4.18
2535 2887 4.201618 GGTCGTAGTTTTCGTTAAATCCGG 60.202 45.833 0.00 0.00 0.00 5.14
2536 2888 3.367630 TCGTAGTTTTCGTTAAATCCGGC 59.632 43.478 0.00 0.00 0.00 6.13
2537 2889 2.886587 AGTTTTCGTTAAATCCGGCG 57.113 45.000 0.00 0.00 0.00 6.46
2538 2890 1.135888 AGTTTTCGTTAAATCCGGCGC 60.136 47.619 0.00 0.00 0.00 6.53
2539 2891 0.873054 TTTTCGTTAAATCCGGCGCA 59.127 45.000 10.83 0.00 0.00 6.09
2540 2892 0.873054 TTTCGTTAAATCCGGCGCAA 59.127 45.000 10.83 0.00 0.00 4.85
2541 2893 0.873054 TTCGTTAAATCCGGCGCAAA 59.127 45.000 10.83 0.00 0.00 3.68
2542 2894 0.873054 TCGTTAAATCCGGCGCAAAA 59.127 45.000 10.83 0.00 0.00 2.44
2543 2895 0.979098 CGTTAAATCCGGCGCAAAAC 59.021 50.000 10.83 1.32 0.00 2.43
2554 2906 4.633980 GCAAAACGAGCCTGTTGG 57.366 55.556 0.00 0.00 31.10 3.77
2555 2907 2.029743 GCAAAACGAGCCTGTTGGA 58.970 52.632 0.00 0.00 34.57 3.53
2556 2908 0.040067 GCAAAACGAGCCTGTTGGAG 60.040 55.000 0.00 0.00 34.57 3.86
2557 2909 1.308998 CAAAACGAGCCTGTTGGAGT 58.691 50.000 0.00 0.00 34.57 3.85
2558 2910 1.002468 CAAAACGAGCCTGTTGGAGTG 60.002 52.381 0.00 0.00 34.57 3.51
2559 2911 1.166531 AAACGAGCCTGTTGGAGTGC 61.167 55.000 0.00 0.00 34.57 4.40
2560 2912 3.114616 CGAGCCTGTTGGAGTGCG 61.115 66.667 0.00 0.00 34.57 5.34
2561 2913 2.343758 GAGCCTGTTGGAGTGCGA 59.656 61.111 0.00 0.00 34.57 5.10
2562 2914 2.029844 GAGCCTGTTGGAGTGCGAC 61.030 63.158 0.00 0.00 34.57 5.19
2563 2915 2.031163 GCCTGTTGGAGTGCGACT 59.969 61.111 3.45 0.00 34.57 4.18
2564 2916 2.320587 GCCTGTTGGAGTGCGACTG 61.321 63.158 3.45 2.85 34.57 3.51
2565 2917 1.669115 CCTGTTGGAGTGCGACTGG 60.669 63.158 12.58 12.58 34.57 4.00
2566 2918 1.669115 CTGTTGGAGTGCGACTGGG 60.669 63.158 3.45 0.00 0.00 4.45
2567 2919 2.099652 CTGTTGGAGTGCGACTGGGA 62.100 60.000 3.45 0.00 0.00 4.37
2568 2920 1.668151 GTTGGAGTGCGACTGGGAC 60.668 63.158 0.00 0.00 37.22 4.46
2569 2921 2.137528 TTGGAGTGCGACTGGGACA 61.138 57.895 0.00 0.00 39.86 4.02
2570 2922 2.048127 GGAGTGCGACTGGGACAC 60.048 66.667 0.00 0.00 39.86 3.67
2571 2923 2.430921 GAGTGCGACTGGGACACG 60.431 66.667 0.00 0.00 39.86 4.49
2572 2924 3.208884 GAGTGCGACTGGGACACGT 62.209 63.158 0.00 0.00 39.86 4.49
2573 2925 2.279918 GTGCGACTGGGACACGTT 60.280 61.111 0.00 0.00 36.89 3.99
2574 2926 1.885850 GTGCGACTGGGACACGTTT 60.886 57.895 0.00 0.00 36.89 3.60
2575 2927 1.153329 TGCGACTGGGACACGTTTT 60.153 52.632 0.00 0.00 0.00 2.43
2576 2928 0.745128 TGCGACTGGGACACGTTTTT 60.745 50.000 0.00 0.00 0.00 1.94
2577 2929 1.219646 GCGACTGGGACACGTTTTTA 58.780 50.000 0.00 0.00 0.00 1.52
2578 2930 1.598601 GCGACTGGGACACGTTTTTAA 59.401 47.619 0.00 0.00 0.00 1.52
2579 2931 2.600556 GCGACTGGGACACGTTTTTAAC 60.601 50.000 0.00 0.00 0.00 2.01
2619 2979 4.437239 AGTCACCATCGATGATTTCACTC 58.563 43.478 26.86 8.27 0.00 3.51
2637 2997 6.581388 TCACTCCTCAATTTTGGGATCTAT 57.419 37.500 0.00 0.00 30.63 1.98
2705 3066 4.345837 CCATGGGCCTATTGTTTTGATGAT 59.654 41.667 2.85 0.00 0.00 2.45
2711 3072 4.590222 GCCTATTGTTTTGATGATCCCCAT 59.410 41.667 0.00 0.00 38.43 4.00
2722 3083 6.935741 TGATGATCCCCATAACTTTAAACG 57.064 37.500 0.00 0.00 35.17 3.60
2723 3084 6.419791 TGATGATCCCCATAACTTTAAACGT 58.580 36.000 0.00 0.00 35.17 3.99
2724 3085 6.887545 TGATGATCCCCATAACTTTAAACGTT 59.112 34.615 0.00 0.00 35.17 3.99
2754 3115 7.546778 TTTCCTTTTATTTTGACTGTTTGGC 57.453 32.000 0.00 0.00 0.00 4.52
2758 3119 2.818130 ATTTTGACTGTTTGGCGCAT 57.182 40.000 10.83 0.00 0.00 4.73
2791 3152 4.887071 TGTTTGGTGGTCTATTGCCATATC 59.113 41.667 0.00 0.00 38.40 1.63
2799 3160 7.281100 GGTGGTCTATTGCCATATCTATAAAGC 59.719 40.741 0.00 0.00 38.40 3.51
2802 3163 6.480320 GTCTATTGCCATATCTATAAAGCGGG 59.520 42.308 0.00 0.00 0.00 6.13
2827 3189 6.183360 GGTGAAAGCCTTTTTCGATAATAGCT 60.183 38.462 6.95 6.95 0.00 3.32
2830 3192 5.036117 AGCCTTTTTCGATAATAGCTCCA 57.964 39.130 0.00 0.00 0.00 3.86
2831 3193 5.625150 AGCCTTTTTCGATAATAGCTCCAT 58.375 37.500 0.00 0.00 0.00 3.41
2835 3197 8.515414 GCCTTTTTCGATAATAGCTCCATAATT 58.485 33.333 0.00 0.00 0.00 1.40
2866 3236 7.205515 AGGGTCTGTAATGATTTCAAGAGAT 57.794 36.000 0.00 0.00 0.00 2.75
2882 3252 0.749649 AGATACTTCTGGGCGCTCAG 59.250 55.000 31.77 31.77 36.17 3.35
2903 3273 1.075482 CCTCCAAAGCAGGCCAGAA 59.925 57.895 5.01 0.00 0.00 3.02
2916 3286 4.925646 GCAGGCCAGAAAGTTAAATCTTTG 59.074 41.667 5.01 0.00 37.70 2.77
2919 3289 6.642540 CAGGCCAGAAAGTTAAATCTTTGAAC 59.357 38.462 5.01 0.00 37.70 3.18
2976 3346 8.352942 AGCTCTTTTATGGGCGAATTAATAAAG 58.647 33.333 0.00 0.00 0.00 1.85
2983 3353 6.677781 TGGGCGAATTAATAAAGTTCTCTG 57.322 37.500 0.00 0.00 0.00 3.35
3048 3420 6.138761 GGCATGAATTATGACAACTCGAATC 58.861 40.000 0.00 0.00 44.72 2.52
3217 3618 1.471684 GAGAAGCATCAAACCAGCCAG 59.528 52.381 0.00 0.00 0.00 4.85
3332 3733 1.743321 CTCTCCCTCGGCATCTCACC 61.743 65.000 0.00 0.00 0.00 4.02
3342 3743 0.678048 GCATCTCACCACCTTGGACC 60.678 60.000 0.00 0.00 40.96 4.46
3754 4159 3.699038 AGTAGCTCTAGCACTTGAGAAGG 59.301 47.826 12.40 0.00 45.16 3.46
3824 4238 1.942657 CTCTGGACTGGTTGTGTTGTG 59.057 52.381 0.00 0.00 0.00 3.33
3825 4239 0.381801 CTGGACTGGTTGTGTTGTGC 59.618 55.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.160329 AGTGCACTGACGACAAAGCC 61.160 55.000 20.97 0.00 0.00 4.35
1 2 0.233332 GAGTGCACTGACGACAAAGC 59.767 55.000 27.27 0.95 0.00 3.51
2 3 1.570813 TGAGTGCACTGACGACAAAG 58.429 50.000 27.27 0.00 0.00 2.77
3 4 2.238942 ATGAGTGCACTGACGACAAA 57.761 45.000 27.27 0.00 0.00 2.83
4 5 2.238942 AATGAGTGCACTGACGACAA 57.761 45.000 27.27 0.76 0.00 3.18
5 6 2.135139 GAAATGAGTGCACTGACGACA 58.865 47.619 27.27 16.11 0.00 4.35
6 7 1.125021 CGAAATGAGTGCACTGACGAC 59.875 52.381 27.27 10.06 0.00 4.34
7 8 1.269569 ACGAAATGAGTGCACTGACGA 60.270 47.619 27.27 5.45 0.00 4.20
8 9 1.125021 GACGAAATGAGTGCACTGACG 59.875 52.381 27.27 18.30 0.00 4.35
9 10 1.461127 GGACGAAATGAGTGCACTGAC 59.539 52.381 27.27 11.73 0.00 3.51
10 11 1.608025 GGGACGAAATGAGTGCACTGA 60.608 52.381 27.27 18.28 0.00 3.41
11 12 0.798776 GGGACGAAATGAGTGCACTG 59.201 55.000 27.27 11.33 0.00 3.66
12 13 0.687354 AGGGACGAAATGAGTGCACT 59.313 50.000 21.88 21.88 0.00 4.40
13 14 2.380084 TAGGGACGAAATGAGTGCAC 57.620 50.000 9.40 9.40 0.00 4.57
14 15 2.499693 TGATAGGGACGAAATGAGTGCA 59.500 45.455 0.00 0.00 0.00 4.57
15 16 3.179443 TGATAGGGACGAAATGAGTGC 57.821 47.619 0.00 0.00 0.00 4.40
16 17 4.509230 CACATGATAGGGACGAAATGAGTG 59.491 45.833 0.00 0.00 0.00 3.51
17 18 4.162320 ACACATGATAGGGACGAAATGAGT 59.838 41.667 0.00 0.00 0.00 3.41
18 19 4.509230 CACACATGATAGGGACGAAATGAG 59.491 45.833 0.00 0.00 0.00 2.90
19 20 4.161377 TCACACATGATAGGGACGAAATGA 59.839 41.667 0.00 0.00 0.00 2.57
20 21 4.441792 TCACACATGATAGGGACGAAATG 58.558 43.478 0.00 0.00 0.00 2.32
21 22 4.753516 TCACACATGATAGGGACGAAAT 57.246 40.909 0.00 0.00 0.00 2.17
22 23 4.753516 ATCACACATGATAGGGACGAAA 57.246 40.909 0.00 0.00 44.11 3.46
23 24 4.441792 CAATCACACATGATAGGGACGAA 58.558 43.478 0.00 0.00 45.26 3.85
24 25 3.181466 CCAATCACACATGATAGGGACGA 60.181 47.826 0.00 0.00 45.26 4.20
25 26 3.133691 CCAATCACACATGATAGGGACG 58.866 50.000 0.00 0.00 45.26 4.79
26 27 3.136443 TCCCAATCACACATGATAGGGAC 59.864 47.826 0.00 0.00 45.26 4.46
27 28 3.392730 TCCCAATCACACATGATAGGGA 58.607 45.455 0.00 3.29 45.26 4.20
28 29 3.862877 TCCCAATCACACATGATAGGG 57.137 47.619 0.00 0.75 45.26 3.53
29 30 4.139786 CCTTCCCAATCACACATGATAGG 58.860 47.826 0.00 0.00 45.26 2.57
30 31 4.785301 ACCTTCCCAATCACACATGATAG 58.215 43.478 0.00 0.00 45.26 2.08
31 32 4.860802 ACCTTCCCAATCACACATGATA 57.139 40.909 0.00 0.00 45.26 2.15
33 34 3.524095 AACCTTCCCAATCACACATGA 57.476 42.857 0.00 0.00 39.83 3.07
34 35 5.720371 TTAAACCTTCCCAATCACACATG 57.280 39.130 0.00 0.00 0.00 3.21
35 36 6.096846 GCTATTAAACCTTCCCAATCACACAT 59.903 38.462 0.00 0.00 0.00 3.21
36 37 5.417580 GCTATTAAACCTTCCCAATCACACA 59.582 40.000 0.00 0.00 0.00 3.72
37 38 5.163550 GGCTATTAAACCTTCCCAATCACAC 60.164 44.000 0.00 0.00 0.00 3.82
38 39 4.953579 GGCTATTAAACCTTCCCAATCACA 59.046 41.667 0.00 0.00 0.00 3.58
39 40 5.201243 AGGCTATTAAACCTTCCCAATCAC 58.799 41.667 0.00 0.00 29.74 3.06
40 41 5.445964 GAGGCTATTAAACCTTCCCAATCA 58.554 41.667 0.00 0.00 36.05 2.57
41 42 4.827835 GGAGGCTATTAAACCTTCCCAATC 59.172 45.833 0.00 0.00 36.05 2.67
42 43 4.482398 AGGAGGCTATTAAACCTTCCCAAT 59.518 41.667 0.00 0.00 36.05 3.16
43 44 3.856206 AGGAGGCTATTAAACCTTCCCAA 59.144 43.478 0.00 0.00 36.05 4.12
44 45 3.470868 AGGAGGCTATTAAACCTTCCCA 58.529 45.455 0.00 0.00 36.05 4.37
45 46 4.207955 CAAGGAGGCTATTAAACCTTCCC 58.792 47.826 0.23 0.00 38.65 3.97
46 47 4.856509 ACAAGGAGGCTATTAAACCTTCC 58.143 43.478 0.23 1.55 38.65 3.46
47 48 8.430431 AGTATACAAGGAGGCTATTAAACCTTC 58.570 37.037 5.50 0.00 38.65 3.46
48 49 8.333226 AGTATACAAGGAGGCTATTAAACCTT 57.667 34.615 5.50 0.00 40.91 3.50
49 50 7.932683 AGTATACAAGGAGGCTATTAAACCT 57.067 36.000 5.50 0.00 39.65 3.50
50 51 7.818446 GCTAGTATACAAGGAGGCTATTAAACC 59.182 40.741 5.50 0.00 0.00 3.27
51 52 7.541437 CGCTAGTATACAAGGAGGCTATTAAAC 59.459 40.741 5.50 0.00 0.00 2.01
52 53 7.232127 ACGCTAGTATACAAGGAGGCTATTAAA 59.768 37.037 5.50 0.00 0.00 1.52
53 54 6.718454 ACGCTAGTATACAAGGAGGCTATTAA 59.282 38.462 5.50 0.00 0.00 1.40
54 55 6.243900 ACGCTAGTATACAAGGAGGCTATTA 58.756 40.000 5.50 0.00 0.00 0.98
55 56 5.078256 ACGCTAGTATACAAGGAGGCTATT 58.922 41.667 5.50 0.00 0.00 1.73
56 57 4.664392 ACGCTAGTATACAAGGAGGCTAT 58.336 43.478 5.50 0.00 0.00 2.97
57 58 4.096190 ACGCTAGTATACAAGGAGGCTA 57.904 45.455 5.50 0.00 0.00 3.93
58 59 2.946785 ACGCTAGTATACAAGGAGGCT 58.053 47.619 5.50 0.00 0.00 4.58
59 60 4.843220 TTACGCTAGTATACAAGGAGGC 57.157 45.455 5.50 0.00 32.12 4.70
60 61 5.710984 CCATTACGCTAGTATACAAGGAGG 58.289 45.833 5.50 0.00 32.12 4.30
61 62 5.162075 GCCATTACGCTAGTATACAAGGAG 58.838 45.833 5.50 0.00 32.12 3.69
62 63 4.021719 GGCCATTACGCTAGTATACAAGGA 60.022 45.833 5.50 0.00 32.12 3.36
63 64 4.243270 GGCCATTACGCTAGTATACAAGG 58.757 47.826 5.50 0.00 32.12 3.61
64 65 4.878439 TGGCCATTACGCTAGTATACAAG 58.122 43.478 0.00 0.00 32.12 3.16
65 66 4.878439 CTGGCCATTACGCTAGTATACAA 58.122 43.478 5.51 0.00 33.02 2.41
66 67 4.514781 CTGGCCATTACGCTAGTATACA 57.485 45.455 5.51 0.00 33.02 2.29
72 73 1.299541 CCAACTGGCCATTACGCTAG 58.700 55.000 5.51 0.00 42.62 3.42
73 74 0.107410 CCCAACTGGCCATTACGCTA 60.107 55.000 5.51 0.00 0.00 4.26
74 75 1.378514 CCCAACTGGCCATTACGCT 60.379 57.895 5.51 0.00 0.00 5.07
75 76 2.414785 CCCCAACTGGCCATTACGC 61.415 63.158 5.51 0.00 0.00 4.42
76 77 0.748005 CTCCCCAACTGGCCATTACG 60.748 60.000 5.51 0.00 0.00 3.18
77 78 1.037579 GCTCCCCAACTGGCCATTAC 61.038 60.000 5.51 0.00 0.00 1.89
78 79 1.214305 AGCTCCCCAACTGGCCATTA 61.214 55.000 5.51 0.00 0.00 1.90
79 80 2.037847 GCTCCCCAACTGGCCATT 59.962 61.111 5.51 0.00 0.00 3.16
80 81 2.551413 AAGCTCCCCAACTGGCCAT 61.551 57.895 5.51 0.00 0.00 4.40
81 82 3.185203 AAGCTCCCCAACTGGCCA 61.185 61.111 4.71 4.71 0.00 5.36
82 83 2.677875 CAAGCTCCCCAACTGGCC 60.678 66.667 0.00 0.00 0.00 5.36
83 84 1.676967 CTCAAGCTCCCCAACTGGC 60.677 63.158 0.00 0.00 0.00 4.85
84 85 1.676967 GCTCAAGCTCCCCAACTGG 60.677 63.158 0.00 0.00 38.21 4.00
85 86 1.676967 GGCTCAAGCTCCCCAACTG 60.677 63.158 1.46 0.00 41.70 3.16
86 87 1.719063 TTGGCTCAAGCTCCCCAACT 61.719 55.000 1.46 0.00 41.70 3.16
87 88 0.827507 TTTGGCTCAAGCTCCCCAAC 60.828 55.000 1.46 0.00 41.70 3.77
88 89 0.105760 TTTTGGCTCAAGCTCCCCAA 60.106 50.000 1.46 0.00 41.70 4.12
89 90 0.114954 ATTTTGGCTCAAGCTCCCCA 59.885 50.000 1.46 0.00 41.70 4.96
90 91 0.820226 GATTTTGGCTCAAGCTCCCC 59.180 55.000 1.46 0.00 41.70 4.81
91 92 0.453390 CGATTTTGGCTCAAGCTCCC 59.547 55.000 1.46 0.00 41.70 4.30
92 93 1.168714 ACGATTTTGGCTCAAGCTCC 58.831 50.000 1.46 0.00 41.70 4.70
93 94 2.589014 CAACGATTTTGGCTCAAGCTC 58.411 47.619 1.46 0.00 41.70 4.09
94 95 1.270550 CCAACGATTTTGGCTCAAGCT 59.729 47.619 1.46 0.00 41.70 3.74
95 96 1.669795 CCCAACGATTTTGGCTCAAGC 60.670 52.381 0.00 0.00 38.23 4.01
96 97 1.067635 CCCCAACGATTTTGGCTCAAG 60.068 52.381 0.00 0.00 38.23 3.02
97 98 0.965439 CCCCAACGATTTTGGCTCAA 59.035 50.000 0.00 0.00 38.23 3.02
98 99 0.897863 CCCCCAACGATTTTGGCTCA 60.898 55.000 0.00 0.00 38.23 4.26
99 100 1.890174 CCCCCAACGATTTTGGCTC 59.110 57.895 0.00 0.00 38.23 4.70
100 101 4.111967 CCCCCAACGATTTTGGCT 57.888 55.556 0.00 0.00 38.23 4.75
120 121 2.643551 CACATAGTGATTGTGTCCCCC 58.356 52.381 0.00 0.00 39.66 5.40
121 122 2.017049 GCACATAGTGATTGTGTCCCC 58.983 52.381 0.58 0.00 44.96 4.81
122 123 2.679837 CAGCACATAGTGATTGTGTCCC 59.320 50.000 0.58 0.00 44.96 4.46
123 124 3.599343 TCAGCACATAGTGATTGTGTCC 58.401 45.455 0.58 0.00 44.96 4.02
124 125 5.114780 AGATCAGCACATAGTGATTGTGTC 58.885 41.667 0.58 3.00 44.96 3.67
125 126 5.095145 AGATCAGCACATAGTGATTGTGT 57.905 39.130 0.58 0.00 44.96 3.72
126 127 7.543947 TTAAGATCAGCACATAGTGATTGTG 57.456 36.000 0.58 0.00 45.74 3.33
127 128 7.228108 CCATTAAGATCAGCACATAGTGATTGT 59.772 37.037 0.58 0.00 35.23 2.71
128 129 7.443272 TCCATTAAGATCAGCACATAGTGATTG 59.557 37.037 0.58 0.00 35.23 2.67
129 130 7.512130 TCCATTAAGATCAGCACATAGTGATT 58.488 34.615 0.58 0.00 35.23 2.57
130 131 7.071069 TCCATTAAGATCAGCACATAGTGAT 57.929 36.000 0.58 0.00 35.23 3.06
131 132 6.484364 TCCATTAAGATCAGCACATAGTGA 57.516 37.500 0.58 0.00 35.23 3.41
433 434 0.101219 GACAGCCGAAATGGAATGCC 59.899 55.000 0.00 0.00 42.00 4.40
434 435 1.098050 AGACAGCCGAAATGGAATGC 58.902 50.000 0.00 0.00 42.00 3.56
435 436 3.855689 AAAGACAGCCGAAATGGAATG 57.144 42.857 0.00 0.00 42.00 2.67
436 437 3.056607 CCAAAAGACAGCCGAAATGGAAT 60.057 43.478 0.00 0.00 42.00 3.01
437 438 2.295909 CCAAAAGACAGCCGAAATGGAA 59.704 45.455 0.00 0.00 42.00 3.53
438 439 1.885887 CCAAAAGACAGCCGAAATGGA 59.114 47.619 0.00 0.00 42.00 3.41
439 440 1.067635 CCCAAAAGACAGCCGAAATGG 60.068 52.381 0.00 0.00 42.50 3.16
451 452 1.228429 CCTTCACCGGCCCAAAAGA 60.228 57.895 0.00 0.00 0.00 2.52
453 454 2.915137 GCCTTCACCGGCCCAAAA 60.915 61.111 0.00 0.00 44.41 2.44
475 476 0.672342 GACATCAAGCCCATCCATGC 59.328 55.000 0.00 0.00 0.00 4.06
481 482 1.064906 CAGGTCAGACATCAAGCCCAT 60.065 52.381 2.17 0.00 0.00 4.00
482 483 0.325933 CAGGTCAGACATCAAGCCCA 59.674 55.000 2.17 0.00 0.00 5.36
593 594 0.537143 TCGTGCCAATTTCAGCCACT 60.537 50.000 0.00 0.00 0.00 4.00
620 621 2.755650 ACTTGATCGACCACACTTGTC 58.244 47.619 0.00 0.00 0.00 3.18
656 659 1.964223 ACGACCACAGATCAGTTGTCT 59.036 47.619 16.91 5.28 33.39 3.41
662 676 1.134965 GGGAAGACGACCACAGATCAG 60.135 57.143 0.00 0.00 0.00 2.90
667 681 0.818296 CCTAGGGAAGACGACCACAG 59.182 60.000 0.00 0.00 0.00 3.66
744 759 6.677781 ACAATATGTGGTTATTGTTCTCGG 57.322 37.500 4.45 0.00 45.85 4.63
791 806 3.836949 ACTTCACAAAAACAGCACACAG 58.163 40.909 0.00 0.00 0.00 3.66
793 808 2.845967 CGACTTCACAAAAACAGCACAC 59.154 45.455 0.00 0.00 0.00 3.82
794 809 2.486203 ACGACTTCACAAAAACAGCACA 59.514 40.909 0.00 0.00 0.00 4.57
811 828 3.626670 CGATACCCTCTATATCCCACGAC 59.373 52.174 0.00 0.00 0.00 4.34
816 833 3.633418 AGCACGATACCCTCTATATCCC 58.367 50.000 0.00 0.00 0.00 3.85
822 839 4.789807 AGAAGTTAGCACGATACCCTCTA 58.210 43.478 0.00 0.00 0.00 2.43
824 841 4.113354 CAAGAAGTTAGCACGATACCCTC 58.887 47.826 0.00 0.00 0.00 4.30
825 842 3.118738 CCAAGAAGTTAGCACGATACCCT 60.119 47.826 0.00 0.00 0.00 4.34
961 1083 4.675029 GCTGGGTACGTGCGTGGT 62.675 66.667 7.55 0.00 0.00 4.16
1153 1339 1.686325 GCTCCCTATTGGCCTCGACA 61.686 60.000 3.32 0.00 0.00 4.35
1165 1351 0.629596 TCTTCTTCTCCCGCTCCCTA 59.370 55.000 0.00 0.00 0.00 3.53
1166 1352 0.031616 ATCTTCTTCTCCCGCTCCCT 60.032 55.000 0.00 0.00 0.00 4.20
1187 1373 1.809684 GAGTACTTGGTGCCCTTGAC 58.190 55.000 0.00 0.00 0.00 3.18
1255 1447 2.675423 TCCTCCTGGTCGTCCACG 60.675 66.667 0.00 0.00 39.03 4.94
1274 1466 0.322277 CAGATGCTGCACACCTCCTT 60.322 55.000 3.57 0.00 0.00 3.36
1452 1650 1.898154 GCCTTAGCCTTGGAGTCGA 59.102 57.895 0.00 0.00 0.00 4.20
1525 1744 2.043852 GACCTCCTCCGGCTCAGA 60.044 66.667 0.00 0.00 0.00 3.27
1538 1757 2.675772 GGACCTCGTCCGTGACCT 60.676 66.667 0.00 0.00 43.14 3.85
1572 1791 1.878656 CGACGAGAGGCCCTTGAAGT 61.879 60.000 13.69 1.22 33.32 3.01
1804 2065 4.803426 CTCCTCACCGCCGCTGAC 62.803 72.222 0.00 0.00 0.00 3.51
1875 2136 4.924187 CCTCTCCCGCCGGATCCT 62.924 72.222 5.05 0.00 37.60 3.24
1885 2146 4.467107 ACCCGAGCTCCCTCTCCC 62.467 72.222 8.47 0.00 35.90 4.30
1976 2324 2.280404 CTGCACCAGCCCTCATCCAT 62.280 60.000 0.00 0.00 41.13 3.41
1977 2325 2.934932 TGCACCAGCCCTCATCCA 60.935 61.111 0.00 0.00 41.13 3.41
1993 2342 2.581354 CCCTTCTCCTCCACGCTG 59.419 66.667 0.00 0.00 0.00 5.18
2023 2372 3.196685 ACAAGAATCTCCTCTTTCTCCCG 59.803 47.826 0.00 0.00 33.25 5.14
2065 2414 2.227089 CTGACTAGGCCCACCACGTC 62.227 65.000 0.00 0.00 39.06 4.34
2114 2466 1.875963 CTGCAAAAGGCCCACTACG 59.124 57.895 0.00 0.00 43.89 3.51
2116 2468 1.606313 GGCTGCAAAAGGCCCACTA 60.606 57.895 0.00 0.00 45.73 2.74
2501 2853 4.743975 TACGACCGGCGCATGCAA 62.744 61.111 19.57 0.00 46.04 4.08
2504 2856 1.632046 AAAACTACGACCGGCGCATG 61.632 55.000 10.83 0.76 46.04 4.06
2505 2857 1.356527 GAAAACTACGACCGGCGCAT 61.357 55.000 10.83 0.00 46.04 4.73
2506 2858 2.023223 GAAAACTACGACCGGCGCA 61.023 57.895 10.83 4.81 46.04 6.09
2507 2859 2.774126 GAAAACTACGACCGGCGC 59.226 61.111 16.48 0.00 46.04 6.53
2509 2861 1.696988 TAACGAAAACTACGACCGGC 58.303 50.000 0.00 0.00 34.70 6.13
2510 2862 4.201618 GGATTTAACGAAAACTACGACCGG 60.202 45.833 0.00 0.00 34.70 5.28
2511 2863 4.489206 CGGATTTAACGAAAACTACGACCG 60.489 45.833 0.00 0.00 34.70 4.79
2512 2864 4.201618 CCGGATTTAACGAAAACTACGACC 60.202 45.833 0.00 0.00 34.70 4.79
2513 2865 4.722066 GCCGGATTTAACGAAAACTACGAC 60.722 45.833 5.05 0.00 34.70 4.34
2514 2866 3.367630 GCCGGATTTAACGAAAACTACGA 59.632 43.478 5.05 0.00 34.70 3.43
2515 2867 3.662863 GCCGGATTTAACGAAAACTACG 58.337 45.455 5.05 0.00 0.00 3.51
2516 2868 3.662863 CGCCGGATTTAACGAAAACTAC 58.337 45.455 5.05 0.00 0.00 2.73
2517 2869 2.094099 GCGCCGGATTTAACGAAAACTA 59.906 45.455 5.05 0.00 0.00 2.24
2518 2870 1.135888 GCGCCGGATTTAACGAAAACT 60.136 47.619 5.05 0.00 0.00 2.66
2519 2871 1.253116 GCGCCGGATTTAACGAAAAC 58.747 50.000 5.05 0.00 0.00 2.43
2520 2872 0.873054 TGCGCCGGATTTAACGAAAA 59.127 45.000 5.05 0.00 0.00 2.29
2521 2873 0.873054 TTGCGCCGGATTTAACGAAA 59.127 45.000 5.05 0.00 0.00 3.46
2522 2874 0.873054 TTTGCGCCGGATTTAACGAA 59.127 45.000 5.05 0.00 0.00 3.85
2523 2875 0.873054 TTTTGCGCCGGATTTAACGA 59.127 45.000 5.05 0.00 0.00 3.85
2524 2876 0.979098 GTTTTGCGCCGGATTTAACG 59.021 50.000 5.05 0.00 0.00 3.18
2525 2877 0.979098 CGTTTTGCGCCGGATTTAAC 59.021 50.000 5.05 0.94 0.00 2.01
2526 2878 0.873054 TCGTTTTGCGCCGGATTTAA 59.127 45.000 5.05 0.00 41.07 1.52
2527 2879 0.444651 CTCGTTTTGCGCCGGATTTA 59.555 50.000 5.05 0.00 41.07 1.40
2528 2880 1.209127 CTCGTTTTGCGCCGGATTT 59.791 52.632 5.05 0.00 41.07 2.17
2529 2881 2.867472 CTCGTTTTGCGCCGGATT 59.133 55.556 5.05 0.00 41.07 3.01
2530 2882 3.799755 GCTCGTTTTGCGCCGGAT 61.800 61.111 5.05 0.00 41.07 4.18
2534 2886 3.194272 AACAGGCTCGTTTTGCGCC 62.194 57.895 4.18 0.00 44.09 6.53
2535 2887 2.010817 CAACAGGCTCGTTTTGCGC 61.011 57.895 0.00 0.00 41.07 6.09
2536 2888 1.370414 CCAACAGGCTCGTTTTGCG 60.370 57.895 0.00 0.00 43.01 4.85
2537 2889 0.040067 CTCCAACAGGCTCGTTTTGC 60.040 55.000 0.00 0.00 0.00 3.68
2538 2890 1.002468 CACTCCAACAGGCTCGTTTTG 60.002 52.381 0.00 0.00 0.00 2.44
2539 2891 1.308998 CACTCCAACAGGCTCGTTTT 58.691 50.000 0.00 0.00 0.00 2.43
2540 2892 1.166531 GCACTCCAACAGGCTCGTTT 61.167 55.000 0.00 0.00 0.00 3.60
2541 2893 1.598130 GCACTCCAACAGGCTCGTT 60.598 57.895 0.00 0.00 0.00 3.85
2542 2894 2.031163 GCACTCCAACAGGCTCGT 59.969 61.111 0.00 0.00 0.00 4.18
2543 2895 3.114616 CGCACTCCAACAGGCTCG 61.115 66.667 0.00 0.00 0.00 5.03
2544 2896 2.029844 GTCGCACTCCAACAGGCTC 61.030 63.158 0.00 0.00 0.00 4.70
2545 2897 2.031163 GTCGCACTCCAACAGGCT 59.969 61.111 0.00 0.00 0.00 4.58
2546 2898 2.031163 AGTCGCACTCCAACAGGC 59.969 61.111 0.00 0.00 0.00 4.85
2547 2899 1.669115 CCAGTCGCACTCCAACAGG 60.669 63.158 0.00 0.00 0.00 4.00
2548 2900 1.669115 CCCAGTCGCACTCCAACAG 60.669 63.158 0.00 0.00 0.00 3.16
2549 2901 2.137528 TCCCAGTCGCACTCCAACA 61.138 57.895 0.00 0.00 0.00 3.33
2550 2902 1.668151 GTCCCAGTCGCACTCCAAC 60.668 63.158 0.00 0.00 0.00 3.77
2551 2903 2.137528 TGTCCCAGTCGCACTCCAA 61.138 57.895 0.00 0.00 0.00 3.53
2552 2904 2.523168 TGTCCCAGTCGCACTCCA 60.523 61.111 0.00 0.00 0.00 3.86
2553 2905 2.048127 GTGTCCCAGTCGCACTCC 60.048 66.667 0.00 0.00 0.00 3.85
2554 2906 2.430921 CGTGTCCCAGTCGCACTC 60.431 66.667 0.00 0.00 0.00 3.51
2555 2907 2.306255 AAACGTGTCCCAGTCGCACT 62.306 55.000 0.00 0.00 0.00 4.40
2556 2908 1.433837 AAAACGTGTCCCAGTCGCAC 61.434 55.000 0.00 0.00 0.00 5.34
2557 2909 0.745128 AAAAACGTGTCCCAGTCGCA 60.745 50.000 0.00 0.00 0.00 5.10
2558 2910 1.219646 TAAAAACGTGTCCCAGTCGC 58.780 50.000 0.00 0.00 0.00 5.19
2559 2911 3.243226 GTTAAAAACGTGTCCCAGTCG 57.757 47.619 0.00 0.00 0.00 4.18
2591 2943 6.430925 TGAAATCATCGATGGTGACTCTTTTT 59.569 34.615 24.61 6.62 0.00 1.94
2592 2944 5.939883 TGAAATCATCGATGGTGACTCTTTT 59.060 36.000 24.61 7.37 0.00 2.27
2593 2945 5.352569 GTGAAATCATCGATGGTGACTCTTT 59.647 40.000 24.61 8.11 0.00 2.52
2594 2946 4.872691 GTGAAATCATCGATGGTGACTCTT 59.127 41.667 24.61 8.86 0.00 2.85
2601 2961 3.452264 TGAGGAGTGAAATCATCGATGGT 59.548 43.478 24.61 16.18 32.74 3.55
2619 2979 6.017605 CGACAAGATAGATCCCAAAATTGAGG 60.018 42.308 0.00 0.00 0.00 3.86
2637 2997 2.258591 GCGAGTGAGGCGACAAGA 59.741 61.111 0.00 0.00 0.00 3.02
2758 3119 5.372343 AGACCACCAAACATATGCATAGA 57.628 39.130 12.79 0.00 0.00 1.98
2766 3127 4.308526 TGGCAATAGACCACCAAACATA 57.691 40.909 0.00 0.00 30.29 2.29
2791 3152 1.947456 GGCTTTCACCCCGCTTTATAG 59.053 52.381 0.00 0.00 0.00 1.31
2799 3160 0.039527 CGAAAAAGGCTTTCACCCCG 60.040 55.000 13.76 8.65 0.00 5.73
2802 3163 5.971792 GCTATTATCGAAAAAGGCTTTCACC 59.028 40.000 13.76 4.71 0.00 4.02
2839 3201 8.602424 TCTCTTGAAATCATTACAGACCCTAAA 58.398 33.333 0.00 0.00 0.00 1.85
2842 3204 6.627087 TCTCTTGAAATCATTACAGACCCT 57.373 37.500 0.00 0.00 0.00 4.34
2843 3205 8.207545 AGTATCTCTTGAAATCATTACAGACCC 58.792 37.037 0.00 0.00 0.00 4.46
2859 3227 1.137872 AGCGCCCAGAAGTATCTCTTG 59.862 52.381 2.29 0.00 36.40 3.02
2860 3228 1.410882 GAGCGCCCAGAAGTATCTCTT 59.589 52.381 2.29 0.00 39.32 2.85
2866 3236 2.359169 CCCTGAGCGCCCAGAAGTA 61.359 63.158 21.71 0.00 36.29 2.24
2887 3257 0.185901 ACTTTCTGGCCTGCTTTGGA 59.814 50.000 3.32 0.00 0.00 3.53
2945 3315 6.715347 ATTCGCCCATAAAAGAGCTTTATT 57.285 33.333 0.00 0.00 38.00 1.40
2948 3318 6.524101 TTAATTCGCCCATAAAAGAGCTTT 57.476 33.333 0.00 0.00 0.00 3.51
2951 3321 8.135529 ACTTTATTAATTCGCCCATAAAAGAGC 58.864 33.333 8.01 0.00 0.00 4.09
2957 3327 8.836413 CAGAGAACTTTATTAATTCGCCCATAA 58.164 33.333 0.00 0.00 0.00 1.90
2958 3328 7.444183 CCAGAGAACTTTATTAATTCGCCCATA 59.556 37.037 0.00 0.00 0.00 2.74
3181 3576 4.167268 GCTTCTCTACTAGTGAACAACGG 58.833 47.826 5.39 0.00 0.00 4.44
3189 3584 5.724328 TGGTTTGATGCTTCTCTACTAGTG 58.276 41.667 5.39 0.00 0.00 2.74
3332 3733 1.959226 CAACGTCCGGTCCAAGGTG 60.959 63.158 0.00 0.00 0.00 4.00
3342 3743 0.316204 AAGGTACAGGTCAACGTCCG 59.684 55.000 0.00 0.00 0.00 4.79
3527 3928 2.890371 CTCCGGTTCCAGTACCCG 59.110 66.667 0.00 0.97 41.37 5.28
3677 4078 3.793144 GCTCTCCTTGTTGCCGCG 61.793 66.667 0.00 0.00 0.00 6.46
3824 4238 2.445565 TCGCAGAGTATCATCATGGC 57.554 50.000 0.00 0.00 37.82 4.40
3825 4239 8.571336 TGTATATATCGCAGAGTATCATCATGG 58.429 37.037 0.00 0.00 43.63 3.66


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

AutoCloner maintained by Alex Coulton.