Multiple sequence alignment - TraesCS5D01G139300

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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 TraesCS5D01G139300 chr5D 100.000 4806 0 0 1 4806 221878462 221883267 0.000000e+00 8876.0
1 TraesCS5D01G139300 chr5D 91.026 78 7 0 4722 4799 400411576 400411653 6.580000e-19 106.0
2 TraesCS5D01G139300 chr5D 85.567 97 14 0 79 175 133312185 133312281 8.510000e-18 102.0
3 TraesCS5D01G139300 chr5B 93.275 2855 125 33 172 2980 244410652 244413485 0.000000e+00 4146.0
4 TraesCS5D01G139300 chr5B 93.911 427 12 6 3696 4112 244414287 244414709 2.440000e-177 632.0
5 TraesCS5D01G139300 chr5B 97.403 308 8 0 3078 3385 244413528 244413835 4.260000e-145 525.0
6 TraesCS5D01G139300 chr5B 96.220 291 6 2 3413 3698 244413894 244414184 5.630000e-129 472.0
7 TraesCS5D01G139300 chr5A 94.726 2332 74 23 1809 4112 301572712 301570402 0.000000e+00 3579.0
8 TraesCS5D01G139300 chr5A 94.853 1671 54 22 172 1826 301574379 301572725 0.000000e+00 2580.0
9 TraesCS5D01G139300 chr5A 82.609 92 15 1 84 175 104244189 104244279 3.990000e-11 80.5
10 TraesCS5D01G139300 chr5A 100.000 31 0 0 1964 1994 48342685 48342655 1.870000e-04 58.4
11 TraesCS5D01G139300 chr2D 93.678 696 43 1 4112 4806 590943300 590942605 0.000000e+00 1040.0
12 TraesCS5D01G139300 chr2D 92.120 698 48 4 4112 4806 470139376 470138683 0.000000e+00 977.0
13 TraesCS5D01G139300 chr2D 82.474 97 17 0 79 175 322542159 322542063 8.570000e-13 86.1
14 TraesCS5D01G139300 chr6A 92.645 707 50 2 4102 4806 33181687 33180981 0.000000e+00 1016.0
15 TraesCS5D01G139300 chr6A 84.571 175 26 1 1 174 594739917 594740091 6.390000e-39 172.0
16 TraesCS5D01G139300 chr6A 87.500 64 4 3 1914 1975 562929063 562929124 2.400000e-08 71.3
17 TraesCS5D01G139300 chr2A 92.098 696 54 1 4112 4806 10005291 10005986 0.000000e+00 979.0
18 TraesCS5D01G139300 chr2A 97.368 38 1 0 1924 1961 565154334 565154297 1.120000e-06 65.8
19 TraesCS5D01G139300 chr3A 91.691 698 48 7 4112 4806 136520353 136521043 0.000000e+00 959.0
20 TraesCS5D01G139300 chr3A 91.511 695 54 3 4113 4806 656959666 656958976 0.000000e+00 952.0
21 TraesCS5D01G139300 chr3A 80.198 101 20 0 77 177 23148071 23147971 5.160000e-10 76.8
22 TraesCS5D01G139300 chr3A 96.875 32 1 0 1963 1994 433331747 433331716 2.000000e-03 54.7
23 TraesCS5D01G139300 chr3B 91.416 699 51 7 4113 4806 532904014 532903320 0.000000e+00 950.0
24 TraesCS5D01G139300 chr3B 91.837 49 3 1 1917 1965 534275764 534275811 3.100000e-07 67.6
25 TraesCS5D01G139300 chr6B 90.824 643 54 3 4114 4753 647894190 647894830 0.000000e+00 856.0
26 TraesCS5D01G139300 chr6B 97.619 42 1 0 1924 1965 491623873 491623832 6.670000e-09 73.1
27 TraesCS5D01G139300 chr1D 88.506 696 68 8 4113 4801 194182943 194182253 0.000000e+00 832.0
28 TraesCS5D01G139300 chr1D 100.000 28 0 0 1963 1990 468568823 468568796 9.000000e-03 52.8
29 TraesCS5D01G139300 chr4B 74.574 704 131 33 4112 4801 291896593 291895924 1.030000e-66 265.0
30 TraesCS5D01G139300 chr7D 92.453 106 8 0 70 175 351729222 351729117 8.330000e-33 152.0
31 TraesCS5D01G139300 chr4D 97.826 46 1 0 1920 1965 497887283 497887328 3.990000e-11 80.5
32 TraesCS5D01G139300 chr7A 81.522 92 16 1 84 175 721746798 721746888 1.860000e-09 75.0
33 TraesCS5D01G139300 chrUn 89.583 48 5 0 1918 1965 1419338 1419291 1.440000e-05 62.1
34 TraesCS5D01G139300 chrUn 89.583 48 5 0 1918 1965 1431970 1431923 1.440000e-05 62.1
35 TraesCS5D01G139300 chr1A 100.000 28 0 0 1963 1990 561382629 561382602 9.000000e-03 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 TraesCS5D01G139300 chr5D 221878462 221883267 4805 False 8876.00 8876 100.00000 1 4806 1 chr5D.!!$F2 4805
1 TraesCS5D01G139300 chr5B 244410652 244414709 4057 False 1443.75 4146 95.20225 172 4112 4 chr5B.!!$F1 3940
2 TraesCS5D01G139300 chr5A 301570402 301574379 3977 True 3079.50 3579 94.78950 172 4112 2 chr5A.!!$R2 3940
3 TraesCS5D01G139300 chr2D 590942605 590943300 695 True 1040.00 1040 93.67800 4112 4806 1 chr2D.!!$R3 694
4 TraesCS5D01G139300 chr2D 470138683 470139376 693 True 977.00 977 92.12000 4112 4806 1 chr2D.!!$R2 694
5 TraesCS5D01G139300 chr6A 33180981 33181687 706 True 1016.00 1016 92.64500 4102 4806 1 chr6A.!!$R1 704
6 TraesCS5D01G139300 chr2A 10005291 10005986 695 False 979.00 979 92.09800 4112 4806 1 chr2A.!!$F1 694
7 TraesCS5D01G139300 chr3A 136520353 136521043 690 False 959.00 959 91.69100 4112 4806 1 chr3A.!!$F1 694
8 TraesCS5D01G139300 chr3A 656958976 656959666 690 True 952.00 952 91.51100 4113 4806 1 chr3A.!!$R3 693
9 TraesCS5D01G139300 chr3B 532903320 532904014 694 True 950.00 950 91.41600 4113 4806 1 chr3B.!!$R1 693
10 TraesCS5D01G139300 chr6B 647894190 647894830 640 False 856.00 856 90.82400 4114 4753 1 chr6B.!!$F1 639
11 TraesCS5D01G139300 chr1D 194182253 194182943 690 True 832.00 832 88.50600 4113 4801 1 chr1D.!!$R1 688
12 TraesCS5D01G139300 chr4B 291895924 291896593 669 True 265.00 265 74.57400 4112 4801 1 chr4B.!!$R1 689

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
61 62 0.036164 CAGTCCACCAAACGGATCCA 59.964 55.0 13.41 0.0 34.32 3.41 F
147 148 0.036765 ATTTGCGTCGCCCTCTACAA 60.037 50.0 15.88 0.0 0.00 2.41 F
151 152 0.179108 GCGTCGCCCTCTACAATCTT 60.179 55.0 5.75 0.0 0.00 2.40 F
951 988 0.242017 GGCCACAATCAGCAACTGAC 59.758 55.0 0.00 0.0 43.63 3.51 F
1882 1972 0.306228 CTCGTGATCGCGACAGAGAT 59.694 55.0 26.46 0.0 39.62 2.75 F
2054 2146 0.394216 TCACGGATCTTGGGGCAATG 60.394 55.0 0.00 0.0 0.00 2.82 F
2280 2374 0.598158 GTCAACGTCGTGCCACCTTA 60.598 55.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1370 0.103390 TCAACTGTCCGTTTCGCTCA 59.897 50.000 0.00 0.00 32.27 4.26 R
1996 2088 0.449786 TGTGTATTCCAAATGCGGCG 59.550 50.000 0.51 0.51 0.00 6.46 R
2178 2272 2.810650 ACATAGCAATCGACGTCTTCC 58.189 47.619 14.70 0.00 0.00 3.46 R
2280 2374 0.467290 AATGGACACCACGCCTTTGT 60.467 50.000 0.00 0.00 35.80 2.83 R
3358 3471 0.323451 AACCTCCCCGCTGGAAATTC 60.323 55.000 0.00 0.00 44.57 2.17 R
3448 3598 0.909610 TGATTCCCCAGAAGAGCGGT 60.910 55.000 0.00 0.00 34.86 5.68 R
4255 4535 0.033796 ACACCTTCATCATGGGGCTG 60.034 55.000 0.00 0.42 0.00 4.85 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 3.982058 CAGTAAGAGTCGCGATTTATCCC 59.018 47.826 14.06 0.00 0.00 3.85
23 24 2.135664 AAGAGTCGCGATTTATCCCG 57.864 50.000 14.06 0.00 0.00 5.14
24 25 0.314302 AGAGTCGCGATTTATCCCGG 59.686 55.000 14.06 0.00 0.00 5.73
25 26 0.666577 GAGTCGCGATTTATCCCGGG 60.667 60.000 16.85 16.85 39.59 5.73
26 27 1.068585 GTCGCGATTTATCCCGGGT 59.931 57.895 22.86 10.79 39.32 5.28
27 28 0.314935 GTCGCGATTTATCCCGGGTA 59.685 55.000 22.86 9.65 39.32 3.69
28 29 0.599558 TCGCGATTTATCCCGGGTAG 59.400 55.000 22.86 1.47 39.32 3.18
29 30 0.389426 CGCGATTTATCCCGGGTAGG 60.389 60.000 22.86 5.26 40.63 3.18
30 31 0.971386 GCGATTTATCCCGGGTAGGA 59.029 55.000 22.86 0.00 45.00 2.94
32 33 2.418334 GCGATTTATCCCGGGTAGGATC 60.418 54.545 22.86 17.93 43.48 3.36
33 34 2.829720 CGATTTATCCCGGGTAGGATCA 59.170 50.000 22.86 0.00 43.48 2.92
34 35 3.451178 CGATTTATCCCGGGTAGGATCAT 59.549 47.826 22.86 7.15 43.48 2.45
35 36 4.441634 CGATTTATCCCGGGTAGGATCATC 60.442 50.000 22.86 12.57 43.48 2.92
36 37 3.847042 TTATCCCGGGTAGGATCATCT 57.153 47.619 22.86 0.00 43.48 2.90
37 38 2.723530 ATCCCGGGTAGGATCATCTT 57.276 50.000 22.86 0.00 43.48 2.40
38 39 2.489528 TCCCGGGTAGGATCATCTTT 57.510 50.000 22.86 0.00 45.00 2.52
39 40 2.771688 TCCCGGGTAGGATCATCTTTT 58.228 47.619 22.86 0.00 45.00 2.27
40 41 2.704065 TCCCGGGTAGGATCATCTTTTC 59.296 50.000 22.86 0.00 45.00 2.29
41 42 2.224548 CCCGGGTAGGATCATCTTTTCC 60.225 54.545 14.18 0.00 45.00 3.13
42 43 2.224548 CCGGGTAGGATCATCTTTTCCC 60.225 54.545 0.00 1.19 45.00 3.97
43 44 2.438021 CGGGTAGGATCATCTTTTCCCA 59.562 50.000 9.36 0.00 33.92 4.37
44 45 3.495100 CGGGTAGGATCATCTTTTCCCAG 60.495 52.174 9.36 1.36 33.92 4.45
45 46 3.459969 GGGTAGGATCATCTTTTCCCAGT 59.540 47.826 0.00 0.00 34.39 4.00
46 47 4.445019 GGGTAGGATCATCTTTTCCCAGTC 60.445 50.000 0.00 0.00 34.39 3.51
47 48 3.941704 AGGATCATCTTTTCCCAGTCC 57.058 47.619 0.00 0.00 32.05 3.85
48 49 3.192944 AGGATCATCTTTTCCCAGTCCA 58.807 45.455 0.00 0.00 32.05 4.02
49 50 3.054065 AGGATCATCTTTTCCCAGTCCAC 60.054 47.826 0.00 0.00 32.05 4.02
50 51 2.879103 TCATCTTTTCCCAGTCCACC 57.121 50.000 0.00 0.00 0.00 4.61
51 52 2.061848 TCATCTTTTCCCAGTCCACCA 58.938 47.619 0.00 0.00 0.00 4.17
52 53 2.445145 TCATCTTTTCCCAGTCCACCAA 59.555 45.455 0.00 0.00 0.00 3.67
53 54 3.117322 TCATCTTTTCCCAGTCCACCAAA 60.117 43.478 0.00 0.00 0.00 3.28
54 55 2.661718 TCTTTTCCCAGTCCACCAAAC 58.338 47.619 0.00 0.00 0.00 2.93
55 56 1.336755 CTTTTCCCAGTCCACCAAACG 59.663 52.381 0.00 0.00 0.00 3.60
56 57 0.466555 TTTCCCAGTCCACCAAACGG 60.467 55.000 0.00 0.00 0.00 4.44
57 58 1.346479 TTCCCAGTCCACCAAACGGA 61.346 55.000 0.00 0.00 0.00 4.69
58 59 1.131303 TCCCAGTCCACCAAACGGAT 61.131 55.000 0.00 0.00 34.32 4.18
59 60 0.676782 CCCAGTCCACCAAACGGATC 60.677 60.000 0.00 0.00 34.32 3.36
60 61 0.676782 CCAGTCCACCAAACGGATCC 60.677 60.000 0.00 0.00 34.32 3.36
61 62 0.036164 CAGTCCACCAAACGGATCCA 59.964 55.000 13.41 0.00 34.32 3.41
62 63 0.324943 AGTCCACCAAACGGATCCAG 59.675 55.000 13.41 7.30 34.32 3.86
63 64 0.676782 GTCCACCAAACGGATCCAGG 60.677 60.000 13.41 10.08 34.32 4.45
64 65 0.838554 TCCACCAAACGGATCCAGGA 60.839 55.000 13.41 4.03 0.00 3.86
65 66 0.255890 CCACCAAACGGATCCAGGAT 59.744 55.000 13.41 0.00 0.00 3.24
66 67 1.382522 CACCAAACGGATCCAGGATG 58.617 55.000 13.41 4.77 0.00 3.51
67 68 0.991920 ACCAAACGGATCCAGGATGT 59.008 50.000 13.41 0.00 0.00 3.06
68 69 2.093181 CACCAAACGGATCCAGGATGTA 60.093 50.000 13.41 0.00 0.00 2.29
69 70 2.574369 ACCAAACGGATCCAGGATGTAA 59.426 45.455 13.41 0.00 0.00 2.41
70 71 3.009695 ACCAAACGGATCCAGGATGTAAA 59.990 43.478 13.41 0.00 0.00 2.01
71 72 4.207165 CCAAACGGATCCAGGATGTAAAT 58.793 43.478 13.41 0.00 0.00 1.40
72 73 4.644685 CCAAACGGATCCAGGATGTAAATT 59.355 41.667 13.41 0.00 0.00 1.82
73 74 5.450412 CCAAACGGATCCAGGATGTAAATTG 60.450 44.000 13.41 5.74 0.00 2.32
74 75 4.771114 ACGGATCCAGGATGTAAATTGA 57.229 40.909 13.41 0.00 0.00 2.57
75 76 5.310409 ACGGATCCAGGATGTAAATTGAT 57.690 39.130 13.41 0.00 0.00 2.57
76 77 5.308825 ACGGATCCAGGATGTAAATTGATC 58.691 41.667 13.41 0.00 0.00 2.92
77 78 4.389992 CGGATCCAGGATGTAAATTGATCG 59.610 45.833 13.41 0.00 30.33 3.69
78 79 4.697352 GGATCCAGGATGTAAATTGATCGG 59.303 45.833 6.70 0.00 30.33 4.18
79 80 4.085357 TCCAGGATGTAAATTGATCGGG 57.915 45.455 0.00 0.00 0.00 5.14
80 81 3.714280 TCCAGGATGTAAATTGATCGGGA 59.286 43.478 0.00 0.00 0.00 5.14
81 82 4.350816 TCCAGGATGTAAATTGATCGGGAT 59.649 41.667 0.00 0.00 0.00 3.85
82 83 4.697352 CCAGGATGTAAATTGATCGGGATC 59.303 45.833 1.69 1.69 38.29 3.36
83 84 4.389992 CAGGATGTAAATTGATCGGGATCG 59.610 45.833 4.36 0.00 40.63 3.69
94 95 1.605753 TCGGGATCGATGAGTACAGG 58.394 55.000 0.54 0.00 40.88 4.00
95 96 0.598562 CGGGATCGATGAGTACAGGG 59.401 60.000 0.54 0.00 39.00 4.45
96 97 1.705873 GGGATCGATGAGTACAGGGT 58.294 55.000 0.54 0.00 0.00 4.34
97 98 2.812983 CGGGATCGATGAGTACAGGGTA 60.813 54.545 0.54 0.00 39.00 3.69
98 99 3.432378 GGGATCGATGAGTACAGGGTAT 58.568 50.000 0.54 0.00 0.00 2.73
99 100 3.193691 GGGATCGATGAGTACAGGGTATG 59.806 52.174 0.54 0.00 0.00 2.39
100 101 3.193691 GGATCGATGAGTACAGGGTATGG 59.806 52.174 0.54 0.00 0.00 2.74
101 102 3.588210 TCGATGAGTACAGGGTATGGA 57.412 47.619 0.00 0.00 0.00 3.41
102 103 3.220110 TCGATGAGTACAGGGTATGGAC 58.780 50.000 0.00 0.00 43.91 4.02
108 109 3.821421 GTACAGGGTATGGACTTCAGG 57.179 52.381 0.00 0.00 39.95 3.86
109 110 1.584724 ACAGGGTATGGACTTCAGGG 58.415 55.000 0.00 0.00 0.00 4.45
110 111 1.080498 ACAGGGTATGGACTTCAGGGA 59.920 52.381 0.00 0.00 0.00 4.20
111 112 2.293856 ACAGGGTATGGACTTCAGGGAT 60.294 50.000 0.00 0.00 0.00 3.85
112 113 2.780010 CAGGGTATGGACTTCAGGGATT 59.220 50.000 0.00 0.00 0.00 3.01
113 114 3.203040 CAGGGTATGGACTTCAGGGATTT 59.797 47.826 0.00 0.00 0.00 2.17
114 115 3.203040 AGGGTATGGACTTCAGGGATTTG 59.797 47.826 0.00 0.00 0.00 2.32
115 116 3.202151 GGGTATGGACTTCAGGGATTTGA 59.798 47.826 0.00 0.00 0.00 2.69
116 117 4.325030 GGGTATGGACTTCAGGGATTTGAA 60.325 45.833 0.00 0.00 35.83 2.69
122 123 2.359900 CTTCAGGGATTTGAAGGTCGG 58.640 52.381 7.66 0.00 46.55 4.79
123 124 0.618458 TCAGGGATTTGAAGGTCGGG 59.382 55.000 0.00 0.00 0.00 5.14
124 125 0.394352 CAGGGATTTGAAGGTCGGGG 60.394 60.000 0.00 0.00 0.00 5.73
125 126 0.845102 AGGGATTTGAAGGTCGGGGT 60.845 55.000 0.00 0.00 0.00 4.95
126 127 0.039180 GGGATTTGAAGGTCGGGGTT 59.961 55.000 0.00 0.00 0.00 4.11
127 128 1.460504 GGATTTGAAGGTCGGGGTTC 58.539 55.000 0.00 0.00 0.00 3.62
128 129 1.271707 GGATTTGAAGGTCGGGGTTCA 60.272 52.381 0.00 0.00 0.00 3.18
129 130 2.620627 GGATTTGAAGGTCGGGGTTCAT 60.621 50.000 0.00 0.00 32.79 2.57
130 131 2.668144 TTTGAAGGTCGGGGTTCATT 57.332 45.000 0.00 0.00 32.79 2.57
131 132 2.668144 TTGAAGGTCGGGGTTCATTT 57.332 45.000 0.00 0.00 32.79 2.32
132 133 1.904287 TGAAGGTCGGGGTTCATTTG 58.096 50.000 0.00 0.00 0.00 2.32
133 134 0.526211 GAAGGTCGGGGTTCATTTGC 59.474 55.000 0.00 0.00 0.00 3.68
134 135 1.241315 AAGGTCGGGGTTCATTTGCG 61.241 55.000 0.00 0.00 0.00 4.85
135 136 1.969589 GGTCGGGGTTCATTTGCGT 60.970 57.895 0.00 0.00 0.00 5.24
136 137 1.500396 GTCGGGGTTCATTTGCGTC 59.500 57.895 0.00 0.00 0.00 5.19
137 138 2.030401 TCGGGGTTCATTTGCGTCG 61.030 57.895 0.00 0.00 0.00 5.12
138 139 2.178273 GGGGTTCATTTGCGTCGC 59.822 61.111 11.10 11.10 0.00 5.19
139 140 2.178273 GGGTTCATTTGCGTCGCC 59.822 61.111 15.88 0.00 0.00 5.54
140 141 2.178273 GGTTCATTTGCGTCGCCC 59.822 61.111 15.88 2.42 0.00 6.13
141 142 2.332654 GGTTCATTTGCGTCGCCCT 61.333 57.895 15.88 0.00 0.00 5.19
142 143 1.134694 GTTCATTTGCGTCGCCCTC 59.865 57.895 15.88 0.00 0.00 4.30
143 144 1.003839 TTCATTTGCGTCGCCCTCT 60.004 52.632 15.88 0.00 0.00 3.69
144 145 0.248012 TTCATTTGCGTCGCCCTCTA 59.752 50.000 15.88 0.00 0.00 2.43
145 146 0.459585 TCATTTGCGTCGCCCTCTAC 60.460 55.000 15.88 0.00 0.00 2.59
146 147 0.739462 CATTTGCGTCGCCCTCTACA 60.739 55.000 15.88 0.00 0.00 2.74
147 148 0.036765 ATTTGCGTCGCCCTCTACAA 60.037 50.000 15.88 0.00 0.00 2.41
148 149 0.036765 TTTGCGTCGCCCTCTACAAT 60.037 50.000 15.88 0.00 0.00 2.71
149 150 0.459585 TTGCGTCGCCCTCTACAATC 60.460 55.000 15.88 0.00 0.00 2.67
150 151 1.320344 TGCGTCGCCCTCTACAATCT 61.320 55.000 15.88 0.00 0.00 2.40
151 152 0.179108 GCGTCGCCCTCTACAATCTT 60.179 55.000 5.75 0.00 0.00 2.40
152 153 1.066605 GCGTCGCCCTCTACAATCTTA 59.933 52.381 5.75 0.00 0.00 2.10
153 154 2.480759 GCGTCGCCCTCTACAATCTTAA 60.481 50.000 5.75 0.00 0.00 1.85
154 155 3.372954 CGTCGCCCTCTACAATCTTAAG 58.627 50.000 0.00 0.00 0.00 1.85
155 156 3.718815 GTCGCCCTCTACAATCTTAAGG 58.281 50.000 1.85 0.00 0.00 2.69
156 157 3.132467 GTCGCCCTCTACAATCTTAAGGT 59.868 47.826 1.85 0.00 0.00 3.50
157 158 3.773119 TCGCCCTCTACAATCTTAAGGTT 59.227 43.478 1.85 0.00 0.00 3.50
158 159 4.120589 CGCCCTCTACAATCTTAAGGTTC 58.879 47.826 0.00 0.00 0.00 3.62
159 160 4.382685 CGCCCTCTACAATCTTAAGGTTCA 60.383 45.833 0.00 0.00 0.00 3.18
160 161 5.497474 GCCCTCTACAATCTTAAGGTTCAA 58.503 41.667 0.00 0.00 0.00 2.69
161 162 5.944007 GCCCTCTACAATCTTAAGGTTCAAA 59.056 40.000 0.00 0.00 0.00 2.69
162 163 6.433093 GCCCTCTACAATCTTAAGGTTCAAAA 59.567 38.462 0.00 0.00 0.00 2.44
163 164 7.122799 GCCCTCTACAATCTTAAGGTTCAAAAT 59.877 37.037 0.00 0.00 0.00 1.82
164 165 9.681062 CCCTCTACAATCTTAAGGTTCAAAATA 57.319 33.333 0.00 0.00 0.00 1.40
174 175 9.490379 TCTTAAGGTTCAAAATAGACTTCACTC 57.510 33.333 1.85 0.00 0.00 3.51
191 192 0.818296 CTCTCGATTTGAGGGTCGGT 59.182 55.000 1.00 0.00 45.32 4.69
280 281 3.788766 CGCGACGGAAGCAAAGGG 61.789 66.667 0.00 0.00 34.19 3.95
337 339 2.511600 CGGCTTCATCCGTCACCC 60.512 66.667 0.00 0.00 44.18 4.61
391 410 2.910479 ACACGCTGACACTCCGGA 60.910 61.111 2.93 2.93 0.00 5.14
425 454 2.924185 CAGATAATGCTCGCCAGGG 58.076 57.895 0.00 0.00 0.00 4.45
467 496 4.598894 CTCCTCGATGCGGGCTGG 62.599 72.222 0.00 0.00 0.00 4.85
758 792 0.821711 CAAAAGGAAGTCCGGCCACA 60.822 55.000 2.24 0.00 42.08 4.17
802 838 4.771590 ACACAAGGAAAGATACGTACGA 57.228 40.909 24.41 6.04 0.00 3.43
951 988 0.242017 GGCCACAATCAGCAACTGAC 59.758 55.000 0.00 0.00 43.63 3.51
989 1027 3.012934 AGCTAGGTGTGGTTTGTTTGT 57.987 42.857 0.00 0.00 0.00 2.83
998 1036 2.929398 GTGGTTTGTTTGTTTGAGCCAG 59.071 45.455 0.00 0.00 0.00 4.85
1197 1235 1.557269 CCAACCAGTCCCTCCTCCTG 61.557 65.000 0.00 0.00 0.00 3.86
1213 1251 3.694566 CCTCCTGCCAAGGTAATAACAAC 59.305 47.826 0.00 0.00 44.82 3.32
1290 1329 0.952497 CGCAGGATCCATGGATTCGG 60.952 60.000 27.93 26.16 35.34 4.30
1329 1370 9.955102 TCTCTGCATGCATATAGATCTTTTATT 57.045 29.630 22.97 0.00 0.00 1.40
1343 1384 4.059511 TCTTTTATTGAGCGAAACGGACA 58.940 39.130 0.00 0.00 0.00 4.02
1352 1397 1.399727 GCGAAACGGACAGTTGATTGG 60.400 52.381 0.00 0.00 43.37 3.16
1355 1400 3.424829 CGAAACGGACAGTTGATTGGATG 60.425 47.826 0.00 0.00 43.37 3.51
1384 1429 4.345859 TGTTCCGCTCTTCCTTAGAAAA 57.654 40.909 0.00 0.00 30.91 2.29
1431 1476 6.458232 TCTCTAGTTAGTGATGAAGCTTCC 57.542 41.667 23.42 9.74 0.00 3.46
1683 1742 1.498865 CCATATGGGACGCGTCTTGC 61.499 60.000 35.50 20.77 40.01 4.01
1709 1768 9.454585 CTGTGATATCAATAATCGCACAATTTT 57.545 29.630 7.07 0.00 33.65 1.82
1820 1879 0.404426 AGCCACCAACCTAGTTTCCC 59.596 55.000 0.00 0.00 0.00 3.97
1858 1948 5.081032 AGTATATCTCACTGGCCTAGTTCC 58.919 45.833 3.32 0.00 37.60 3.62
1882 1972 0.306228 CTCGTGATCGCGACAGAGAT 59.694 55.000 26.46 0.00 39.62 2.75
1935 2026 2.632987 AAATTATTCCCTCCGTCCCG 57.367 50.000 0.00 0.00 0.00 5.14
1937 2028 2.386829 ATTATTCCCTCCGTCCCGTA 57.613 50.000 0.00 0.00 0.00 4.02
1942 2033 3.524095 TTCCCTCCGTCCCGTAATATA 57.476 47.619 0.00 0.00 0.00 0.86
1996 2088 6.987403 ATAGGATGAAGGGAGTAGTTTCTC 57.013 41.667 0.00 0.00 0.00 2.87
2002 2094 1.214589 GGAGTAGTTTCTCGCCGCA 59.785 57.895 0.00 0.00 35.52 5.69
2054 2146 0.394216 TCACGGATCTTGGGGCAATG 60.394 55.000 0.00 0.00 0.00 2.82
2267 2361 4.614673 GCAACTTGCAGGTCAACG 57.385 55.556 8.97 0.00 44.26 4.10
2280 2374 0.598158 GTCAACGTCGTGCCACCTTA 60.598 55.000 0.00 0.00 0.00 2.69
2475 2570 7.041167 CGAGCTTATGGATGAATAAACCATCAA 60.041 37.037 0.00 0.00 42.44 2.57
2478 2573 7.470424 GCTTATGGATGAATAAACCATCAAGCA 60.470 37.037 20.50 3.74 42.17 3.91
2501 2596 3.065233 GTGACAGTGACAACATTTGAGCA 59.935 43.478 0.00 0.00 0.00 4.26
2592 2688 9.535878 GAGTATTTGTTTTGGTTATTGGTTGAA 57.464 29.630 0.00 0.00 0.00 2.69
2717 2816 2.362077 GCAGAAGAAACAAAGGGAAGCA 59.638 45.455 0.00 0.00 0.00 3.91
2718 2817 3.181476 GCAGAAGAAACAAAGGGAAGCAA 60.181 43.478 0.00 0.00 0.00 3.91
2788 2887 2.688666 TAGGGCCTGGCTGTCCTG 60.689 66.667 18.53 0.00 0.00 3.86
2860 2959 7.324388 TCCAAGGAATTTCTACACCTTTCTA 57.676 36.000 0.00 0.00 40.21 2.10
2886 2995 5.716094 ACAAGTTTTGGTGTTCTTTGTACC 58.284 37.500 0.00 0.00 34.12 3.34
2950 3059 4.335400 TGTGCTTGTGATGAGTTAGACA 57.665 40.909 0.00 0.00 0.00 3.41
2957 3066 8.695456 TGCTTGTGATGAGTTAGACAATCTATA 58.305 33.333 0.00 0.00 0.00 1.31
3057 3170 4.700700 TCACTGAGAATGGAGCATGTATG 58.299 43.478 0.00 0.00 0.00 2.39
3339 3452 3.187699 CTCCCTCCTCGTCGCATCG 62.188 68.421 0.00 0.00 0.00 3.84
3358 3471 2.097629 TCGGTAAGCTCGATCAAGTCTG 59.902 50.000 0.00 0.00 0.00 3.51
3417 3567 5.355596 TCTTGCTAATTTTGTTGGTGTTGG 58.644 37.500 0.00 0.00 0.00 3.77
3418 3568 4.744795 TGCTAATTTTGTTGGTGTTGGT 57.255 36.364 0.00 0.00 0.00 3.67
3419 3569 5.091261 TGCTAATTTTGTTGGTGTTGGTT 57.909 34.783 0.00 0.00 0.00 3.67
3420 3570 5.491982 TGCTAATTTTGTTGGTGTTGGTTT 58.508 33.333 0.00 0.00 0.00 3.27
3421 3571 5.352569 TGCTAATTTTGTTGGTGTTGGTTTG 59.647 36.000 0.00 0.00 0.00 2.93
3613 3763 2.744202 CGAGAATCCCAAGAACAAGGTG 59.256 50.000 0.00 0.00 0.00 4.00
3625 3775 4.643387 AAGGTGACCGCTGTGCCC 62.643 66.667 0.00 0.00 0.00 5.36
3719 3978 8.034313 TGTAGCTTGGAAGGAATAATAGTCAT 57.966 34.615 0.00 0.00 0.00 3.06
3902 4177 1.678269 GCGCGTGTGCTACTCTCTTG 61.678 60.000 8.43 0.00 39.65 3.02
3973 4248 1.198637 AGCTGTTCAAATTCTCGCAGC 59.801 47.619 13.61 13.61 46.60 5.25
4006 4281 1.523758 GCCGTCTTCAGTTGGATGTT 58.476 50.000 0.00 0.00 0.00 2.71
4040 4319 7.394816 TGTAGTAGCAAATAAGCTTTCTTCCT 58.605 34.615 3.20 0.00 43.70 3.36
4152 4431 4.598894 CCTCCGGCCTCTGCATCG 62.599 72.222 0.00 0.00 40.13 3.84
4255 4535 1.912371 GCAACGCTGTTGCTACTCCC 61.912 60.000 27.53 7.70 41.87 4.30
4257 4537 0.320771 AACGCTGTTGCTACTCCCAG 60.321 55.000 0.00 0.00 36.97 4.45
4262 4542 2.204074 TTGCTACTCCCAGCCCCA 60.204 61.111 0.00 0.00 41.04 4.96
4500 4786 1.064906 CCTCTCTGCCATCAACACCAT 60.065 52.381 0.00 0.00 0.00 3.55
4748 5039 0.332972 GGTTTCCCCTGAAGCATCCT 59.667 55.000 0.00 0.00 33.74 3.24
4766 5057 1.674441 CCTGAGCATGATGACGCAAAT 59.326 47.619 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.982058 GGGATAAATCGCGACTCTTACTG 59.018 47.826 12.93 0.00 0.00 2.74
11 12 0.971386 TCCTACCCGGGATAAATCGC 59.029 55.000 32.02 0.00 36.51 4.58
12 13 2.829720 TGATCCTACCCGGGATAAATCG 59.170 50.000 32.02 6.81 45.18 3.34
13 14 4.717280 AGATGATCCTACCCGGGATAAATC 59.283 45.833 32.02 22.84 45.18 2.17
14 15 4.699994 AGATGATCCTACCCGGGATAAAT 58.300 43.478 32.02 15.26 45.18 1.40
15 16 4.141990 AGATGATCCTACCCGGGATAAA 57.858 45.455 32.02 10.45 45.18 1.40
16 17 3.847042 AGATGATCCTACCCGGGATAA 57.153 47.619 32.02 11.42 45.18 1.75
17 18 3.847042 AAGATGATCCTACCCGGGATA 57.153 47.619 32.02 15.02 45.18 2.59
19 20 2.489528 AAAGATGATCCTACCCGGGA 57.510 50.000 32.02 10.31 39.95 5.14
20 21 2.224548 GGAAAAGATGATCCTACCCGGG 60.225 54.545 22.25 22.25 32.75 5.73
21 22 2.224548 GGGAAAAGATGATCCTACCCGG 60.225 54.545 0.00 0.00 35.95 5.73
22 23 2.438021 TGGGAAAAGATGATCCTACCCG 59.562 50.000 0.00 0.00 38.96 5.28
23 24 3.459969 ACTGGGAAAAGATGATCCTACCC 59.540 47.826 0.00 0.00 35.95 3.69
24 25 4.445019 GGACTGGGAAAAGATGATCCTACC 60.445 50.000 0.00 0.00 35.95 3.18
25 26 4.164221 TGGACTGGGAAAAGATGATCCTAC 59.836 45.833 0.00 0.00 35.95 3.18
26 27 4.164221 GTGGACTGGGAAAAGATGATCCTA 59.836 45.833 0.00 0.00 35.95 2.94
27 28 3.054065 GTGGACTGGGAAAAGATGATCCT 60.054 47.826 0.00 0.00 35.95 3.24
28 29 3.282885 GTGGACTGGGAAAAGATGATCC 58.717 50.000 0.00 0.00 34.85 3.36
29 30 3.282885 GGTGGACTGGGAAAAGATGATC 58.717 50.000 0.00 0.00 0.00 2.92
30 31 2.649312 TGGTGGACTGGGAAAAGATGAT 59.351 45.455 0.00 0.00 0.00 2.45
31 32 2.061848 TGGTGGACTGGGAAAAGATGA 58.938 47.619 0.00 0.00 0.00 2.92
32 33 2.584835 TGGTGGACTGGGAAAAGATG 57.415 50.000 0.00 0.00 0.00 2.90
33 34 3.230976 GTTTGGTGGACTGGGAAAAGAT 58.769 45.455 0.00 0.00 0.00 2.40
34 35 2.661718 GTTTGGTGGACTGGGAAAAGA 58.338 47.619 0.00 0.00 0.00 2.52
35 36 1.336755 CGTTTGGTGGACTGGGAAAAG 59.663 52.381 0.00 0.00 0.00 2.27
36 37 1.394618 CGTTTGGTGGACTGGGAAAA 58.605 50.000 0.00 0.00 0.00 2.29
37 38 0.466555 CCGTTTGGTGGACTGGGAAA 60.467 55.000 0.00 0.00 0.00 3.13
38 39 1.149627 CCGTTTGGTGGACTGGGAA 59.850 57.895 0.00 0.00 0.00 3.97
39 40 1.131303 ATCCGTTTGGTGGACTGGGA 61.131 55.000 0.00 0.00 38.60 4.37
40 41 0.676782 GATCCGTTTGGTGGACTGGG 60.677 60.000 0.00 0.00 38.60 4.45
41 42 0.676782 GGATCCGTTTGGTGGACTGG 60.677 60.000 0.00 0.00 38.60 4.00
42 43 0.036164 TGGATCCGTTTGGTGGACTG 59.964 55.000 7.39 0.00 38.60 3.51
43 44 0.324943 CTGGATCCGTTTGGTGGACT 59.675 55.000 7.39 0.00 38.60 3.85
44 45 0.676782 CCTGGATCCGTTTGGTGGAC 60.677 60.000 7.39 0.00 38.60 4.02
45 46 0.838554 TCCTGGATCCGTTTGGTGGA 60.839 55.000 7.39 3.21 40.46 4.02
46 47 0.255890 ATCCTGGATCCGTTTGGTGG 59.744 55.000 7.39 0.84 36.30 4.61
47 48 1.340017 ACATCCTGGATCCGTTTGGTG 60.340 52.381 6.13 4.40 36.30 4.17
48 49 0.991920 ACATCCTGGATCCGTTTGGT 59.008 50.000 6.13 0.00 36.30 3.67
49 50 3.275617 TTACATCCTGGATCCGTTTGG 57.724 47.619 6.13 6.90 0.00 3.28
50 51 5.356751 TCAATTTACATCCTGGATCCGTTTG 59.643 40.000 6.13 7.69 0.00 2.93
51 52 5.505780 TCAATTTACATCCTGGATCCGTTT 58.494 37.500 6.13 0.00 0.00 3.60
52 53 5.110814 TCAATTTACATCCTGGATCCGTT 57.889 39.130 6.13 0.00 0.00 4.44
53 54 4.771114 TCAATTTACATCCTGGATCCGT 57.229 40.909 6.13 5.56 0.00 4.69
54 55 4.389992 CGATCAATTTACATCCTGGATCCG 59.610 45.833 6.13 0.00 0.00 4.18
55 56 4.697352 CCGATCAATTTACATCCTGGATCC 59.303 45.833 6.13 4.20 0.00 3.36
56 57 4.697352 CCCGATCAATTTACATCCTGGATC 59.303 45.833 6.13 0.00 0.00 3.36
57 58 4.350816 TCCCGATCAATTTACATCCTGGAT 59.649 41.667 2.57 2.57 0.00 3.41
58 59 3.714280 TCCCGATCAATTTACATCCTGGA 59.286 43.478 0.00 0.00 0.00 3.86
59 60 4.085357 TCCCGATCAATTTACATCCTGG 57.915 45.455 0.00 0.00 0.00 4.45
60 61 4.389992 CGATCCCGATCAATTTACATCCTG 59.610 45.833 5.59 0.00 37.69 3.86
61 62 4.283467 TCGATCCCGATCAATTTACATCCT 59.717 41.667 5.59 0.00 40.30 3.24
62 63 4.566004 TCGATCCCGATCAATTTACATCC 58.434 43.478 5.59 0.00 40.30 3.51
76 77 0.598562 CCCTGTACTCATCGATCCCG 59.401 60.000 0.00 0.00 37.07 5.14
77 78 1.705873 ACCCTGTACTCATCGATCCC 58.294 55.000 0.00 0.00 0.00 3.85
78 79 3.193691 CCATACCCTGTACTCATCGATCC 59.806 52.174 0.00 0.00 0.00 3.36
79 80 4.079970 TCCATACCCTGTACTCATCGATC 58.920 47.826 0.00 0.00 0.00 3.69
80 81 3.827302 GTCCATACCCTGTACTCATCGAT 59.173 47.826 0.00 0.00 0.00 3.59
81 82 3.117625 AGTCCATACCCTGTACTCATCGA 60.118 47.826 0.00 0.00 0.00 3.59
82 83 3.223435 AGTCCATACCCTGTACTCATCG 58.777 50.000 0.00 0.00 0.00 3.84
83 84 4.649674 TGAAGTCCATACCCTGTACTCATC 59.350 45.833 0.00 0.00 0.00 2.92
84 85 4.620723 TGAAGTCCATACCCTGTACTCAT 58.379 43.478 0.00 0.00 0.00 2.90
85 86 4.023980 CTGAAGTCCATACCCTGTACTCA 58.976 47.826 0.00 0.00 0.00 3.41
86 87 3.385111 CCTGAAGTCCATACCCTGTACTC 59.615 52.174 0.00 0.00 0.00 2.59
87 88 3.375699 CCTGAAGTCCATACCCTGTACT 58.624 50.000 0.00 0.00 0.00 2.73
88 89 2.434702 CCCTGAAGTCCATACCCTGTAC 59.565 54.545 0.00 0.00 0.00 2.90
89 90 2.316677 TCCCTGAAGTCCATACCCTGTA 59.683 50.000 0.00 0.00 0.00 2.74
90 91 1.080498 TCCCTGAAGTCCATACCCTGT 59.920 52.381 0.00 0.00 0.00 4.00
91 92 1.879575 TCCCTGAAGTCCATACCCTG 58.120 55.000 0.00 0.00 0.00 4.45
92 93 2.897823 ATCCCTGAAGTCCATACCCT 57.102 50.000 0.00 0.00 0.00 4.34
93 94 3.202151 TCAAATCCCTGAAGTCCATACCC 59.798 47.826 0.00 0.00 0.00 3.69
94 95 4.503714 TCAAATCCCTGAAGTCCATACC 57.496 45.455 0.00 0.00 0.00 2.73
103 104 1.004277 CCCGACCTTCAAATCCCTGAA 59.996 52.381 0.00 0.00 34.22 3.02
104 105 0.618458 CCCGACCTTCAAATCCCTGA 59.382 55.000 0.00 0.00 0.00 3.86
105 106 0.394352 CCCCGACCTTCAAATCCCTG 60.394 60.000 0.00 0.00 0.00 4.45
106 107 0.845102 ACCCCGACCTTCAAATCCCT 60.845 55.000 0.00 0.00 0.00 4.20
107 108 0.039180 AACCCCGACCTTCAAATCCC 59.961 55.000 0.00 0.00 0.00 3.85
108 109 1.271707 TGAACCCCGACCTTCAAATCC 60.272 52.381 0.00 0.00 0.00 3.01
109 110 2.194201 TGAACCCCGACCTTCAAATC 57.806 50.000 0.00 0.00 0.00 2.17
110 111 2.899303 ATGAACCCCGACCTTCAAAT 57.101 45.000 0.00 0.00 30.32 2.32
111 112 2.625790 CAAATGAACCCCGACCTTCAAA 59.374 45.455 0.00 0.00 30.32 2.69
112 113 2.235016 CAAATGAACCCCGACCTTCAA 58.765 47.619 0.00 0.00 30.32 2.69
113 114 1.904287 CAAATGAACCCCGACCTTCA 58.096 50.000 0.00 0.00 0.00 3.02
114 115 0.526211 GCAAATGAACCCCGACCTTC 59.474 55.000 0.00 0.00 0.00 3.46
115 116 1.241315 CGCAAATGAACCCCGACCTT 61.241 55.000 0.00 0.00 0.00 3.50
116 117 1.674322 CGCAAATGAACCCCGACCT 60.674 57.895 0.00 0.00 0.00 3.85
117 118 1.918868 GACGCAAATGAACCCCGACC 61.919 60.000 0.00 0.00 0.00 4.79
118 119 1.500396 GACGCAAATGAACCCCGAC 59.500 57.895 0.00 0.00 0.00 4.79
119 120 2.030401 CGACGCAAATGAACCCCGA 61.030 57.895 0.00 0.00 0.00 5.14
120 121 2.478746 CGACGCAAATGAACCCCG 59.521 61.111 0.00 0.00 0.00 5.73
121 122 2.178273 GCGACGCAAATGAACCCC 59.822 61.111 16.42 0.00 0.00 4.95
122 123 2.178273 GGCGACGCAAATGAACCC 59.822 61.111 23.09 0.00 0.00 4.11
123 124 2.178273 GGGCGACGCAAATGAACC 59.822 61.111 23.09 7.76 0.00 3.62
124 125 1.134694 GAGGGCGACGCAAATGAAC 59.865 57.895 23.09 1.43 0.00 3.18
125 126 0.248012 TAGAGGGCGACGCAAATGAA 59.752 50.000 23.09 0.00 0.00 2.57
126 127 0.459585 GTAGAGGGCGACGCAAATGA 60.460 55.000 23.09 0.06 0.00 2.57
127 128 0.739462 TGTAGAGGGCGACGCAAATG 60.739 55.000 23.09 0.00 0.00 2.32
128 129 0.036765 TTGTAGAGGGCGACGCAAAT 60.037 50.000 23.09 6.25 0.00 2.32
129 130 0.036765 ATTGTAGAGGGCGACGCAAA 60.037 50.000 23.09 4.26 0.00 3.68
130 131 0.459585 GATTGTAGAGGGCGACGCAA 60.460 55.000 23.09 5.52 0.00 4.85
131 132 1.141019 GATTGTAGAGGGCGACGCA 59.859 57.895 23.09 0.00 0.00 5.24
132 133 0.179108 AAGATTGTAGAGGGCGACGC 60.179 55.000 12.43 12.43 0.00 5.19
133 134 3.372954 CTTAAGATTGTAGAGGGCGACG 58.627 50.000 0.00 0.00 0.00 5.12
134 135 3.132467 ACCTTAAGATTGTAGAGGGCGAC 59.868 47.826 3.36 0.00 0.00 5.19
135 136 3.371965 ACCTTAAGATTGTAGAGGGCGA 58.628 45.455 3.36 0.00 0.00 5.54
136 137 3.821421 ACCTTAAGATTGTAGAGGGCG 57.179 47.619 3.36 0.00 0.00 6.13
137 138 5.099042 TGAACCTTAAGATTGTAGAGGGC 57.901 43.478 3.36 0.00 0.00 5.19
138 139 7.996098 TTTTGAACCTTAAGATTGTAGAGGG 57.004 36.000 3.36 0.00 0.00 4.30
148 149 9.490379 GAGTGAAGTCTATTTTGAACCTTAAGA 57.510 33.333 3.36 0.00 0.00 2.10
149 150 9.495572 AGAGTGAAGTCTATTTTGAACCTTAAG 57.504 33.333 0.00 0.00 0.00 1.85
150 151 9.490379 GAGAGTGAAGTCTATTTTGAACCTTAA 57.510 33.333 0.00 0.00 0.00 1.85
151 152 7.813148 CGAGAGTGAAGTCTATTTTGAACCTTA 59.187 37.037 0.00 0.00 0.00 2.69
152 153 6.647067 CGAGAGTGAAGTCTATTTTGAACCTT 59.353 38.462 0.00 0.00 0.00 3.50
153 154 6.015350 TCGAGAGTGAAGTCTATTTTGAACCT 60.015 38.462 0.00 0.00 0.00 3.50
154 155 6.157211 TCGAGAGTGAAGTCTATTTTGAACC 58.843 40.000 0.00 0.00 0.00 3.62
155 156 7.820044 ATCGAGAGTGAAGTCTATTTTGAAC 57.180 36.000 0.00 0.00 0.00 3.18
156 157 8.712363 CAAATCGAGAGTGAAGTCTATTTTGAA 58.288 33.333 0.00 0.00 29.55 2.69
157 158 8.088365 TCAAATCGAGAGTGAAGTCTATTTTGA 58.912 33.333 11.68 11.68 32.20 2.69
158 159 8.244494 TCAAATCGAGAGTGAAGTCTATTTTG 57.756 34.615 0.00 8.93 0.00 2.44
159 160 7.547370 CCTCAAATCGAGAGTGAAGTCTATTTT 59.453 37.037 0.00 0.00 45.45 1.82
160 161 7.038659 CCTCAAATCGAGAGTGAAGTCTATTT 58.961 38.462 0.00 0.00 45.45 1.40
161 162 6.406400 CCCTCAAATCGAGAGTGAAGTCTATT 60.406 42.308 0.00 0.00 45.45 1.73
162 163 5.068460 CCCTCAAATCGAGAGTGAAGTCTAT 59.932 44.000 0.00 0.00 45.45 1.98
163 164 4.399618 CCCTCAAATCGAGAGTGAAGTCTA 59.600 45.833 0.00 0.00 45.45 2.59
164 165 3.194542 CCCTCAAATCGAGAGTGAAGTCT 59.805 47.826 0.00 0.00 45.45 3.24
165 166 3.056465 ACCCTCAAATCGAGAGTGAAGTC 60.056 47.826 0.00 0.00 45.45 3.01
166 167 2.900546 ACCCTCAAATCGAGAGTGAAGT 59.099 45.455 0.00 0.00 45.45 3.01
167 168 3.516615 GACCCTCAAATCGAGAGTGAAG 58.483 50.000 0.00 0.00 45.45 3.02
168 169 2.094700 CGACCCTCAAATCGAGAGTGAA 60.095 50.000 0.00 0.00 45.45 3.18
169 170 1.472878 CGACCCTCAAATCGAGAGTGA 59.527 52.381 0.00 0.00 45.45 3.41
170 171 1.469940 CCGACCCTCAAATCGAGAGTG 60.470 57.143 0.00 0.00 45.45 3.51
171 172 0.818296 CCGACCCTCAAATCGAGAGT 59.182 55.000 0.00 0.00 45.45 3.24
172 173 0.818296 ACCGACCCTCAAATCGAGAG 59.182 55.000 0.00 0.00 45.45 3.20
173 174 0.530744 CACCGACCCTCAAATCGAGA 59.469 55.000 0.00 0.00 45.45 4.04
174 175 0.246635 ACACCGACCCTCAAATCGAG 59.753 55.000 0.00 0.00 40.86 4.04
191 192 4.036977 GGAAACGCACCTCGAACA 57.963 55.556 0.00 0.00 41.67 3.18
214 215 3.383601 GCGCGTGGTTTTCGTTGC 61.384 61.111 8.43 0.00 0.00 4.17
302 304 4.854924 TGCGCGGGTGGATGGATG 62.855 66.667 8.83 0.00 0.00 3.51
303 305 4.856801 GTGCGCGGGTGGATGGAT 62.857 66.667 8.83 0.00 0.00 3.41
380 399 0.608035 GGCCAAAATCCGGAGTGTCA 60.608 55.000 11.34 0.00 0.00 3.58
381 400 1.644786 CGGCCAAAATCCGGAGTGTC 61.645 60.000 11.34 0.00 42.99 3.67
382 401 1.674322 CGGCCAAAATCCGGAGTGT 60.674 57.895 11.34 0.00 42.99 3.55
383 402 1.369091 CTCGGCCAAAATCCGGAGTG 61.369 60.000 11.34 7.98 46.43 3.51
384 403 1.078426 CTCGGCCAAAATCCGGAGT 60.078 57.895 11.34 3.58 46.43 3.85
565 599 5.737063 GCAGATTTTCCTGAAGCAAAGTTGA 60.737 40.000 0.00 0.00 36.29 3.18
631 665 1.135286 CGTGTCTTACCGTCTAACCCC 60.135 57.143 0.00 0.00 0.00 4.95
802 838 3.983420 CACCTGGGGCCCACACAT 61.983 66.667 24.76 3.94 0.00 3.21
891 928 0.036294 GGACGGGTGAAAGGGAGAAG 60.036 60.000 0.00 0.00 0.00 2.85
892 929 0.765135 TGGACGGGTGAAAGGGAGAA 60.765 55.000 0.00 0.00 0.00 2.87
893 930 0.765135 TTGGACGGGTGAAAGGGAGA 60.765 55.000 0.00 0.00 0.00 3.71
951 988 5.715753 CCTAGCTAGGTAAGGTATTACAGGG 59.284 48.000 28.90 0.57 42.66 4.45
998 1036 1.875963 CTGAACACCGCCAACATCC 59.124 57.895 0.00 0.00 0.00 3.51
1197 1235 3.365565 CGGTGTGTTGTTATTACCTTGGC 60.366 47.826 0.00 0.00 0.00 4.52
1306 1345 9.989869 CTCAATAAAAGATCTATATGCATGCAG 57.010 33.333 26.69 12.45 0.00 4.41
1329 1370 0.103390 TCAACTGTCCGTTTCGCTCA 59.897 50.000 0.00 0.00 32.27 4.26
1343 1384 4.335416 ACAAACGATCCATCCAATCAACT 58.665 39.130 0.00 0.00 0.00 3.16
1352 1397 1.327764 GAGCGGAACAAACGATCCATC 59.672 52.381 0.00 0.00 40.51 3.51
1355 1400 1.393883 GAAGAGCGGAACAAACGATCC 59.606 52.381 0.00 0.00 46.81 3.36
1431 1476 1.556911 ACCAGCTAACCTCACCATCAG 59.443 52.381 0.00 0.00 0.00 2.90
1536 1582 0.946221 CATCTAGGCGGGCGCTAAAG 60.946 60.000 7.64 0.00 41.60 1.85
1683 1742 9.454585 AAAATTGTGCGATTATTGATATCACAG 57.545 29.630 4.48 0.00 34.02 3.66
1709 1768 2.698797 CCGCCCTTCTAATAAGGACAGA 59.301 50.000 5.35 0.00 39.81 3.41
1797 1856 2.040342 AACTAGGTTGGTGGCTAGGT 57.960 50.000 0.00 0.00 0.00 3.08
1820 1879 9.119329 GTGAGATATACTACAAGCGATAAACTG 57.881 37.037 0.00 0.00 0.00 3.16
1882 1972 7.518211 CGAGCAATATGTTCATCAACGGATAAA 60.518 37.037 0.00 0.00 34.95 1.40
1975 2067 3.702045 CGAGAAACTACTCCCTTCATCCT 59.298 47.826 0.00 0.00 33.83 3.24
1981 2073 0.531200 CGGCGAGAAACTACTCCCTT 59.469 55.000 0.00 0.00 33.83 3.95
1996 2088 0.449786 TGTGTATTCCAAATGCGGCG 59.550 50.000 0.51 0.51 0.00 6.46
2178 2272 2.810650 ACATAGCAATCGACGTCTTCC 58.189 47.619 14.70 0.00 0.00 3.46
2267 2361 0.872388 CCTTTGTAAGGTGGCACGAC 59.128 55.000 12.17 10.02 43.95 4.34
2280 2374 0.467290 AATGGACACCACGCCTTTGT 60.467 50.000 0.00 0.00 35.80 2.83
2437 2532 2.046283 TAAGCTCGTCACGTCAACAG 57.954 50.000 0.00 0.00 0.00 3.16
2475 2570 2.627515 ATGTTGTCACTGTCACTGCT 57.372 45.000 0.00 0.00 0.00 4.24
2478 2573 3.313526 GCTCAAATGTTGTCACTGTCACT 59.686 43.478 0.00 0.00 0.00 3.41
2501 2596 5.270893 AGCACCCGTTAAATTCAAGTTTT 57.729 34.783 0.00 0.00 0.00 2.43
2592 2688 0.542232 ACTACTGCTCCCTCAACGGT 60.542 55.000 0.00 0.00 0.00 4.83
2717 2816 1.910580 CGTATGGGCCACAGGGTCTT 61.911 60.000 9.28 0.00 39.39 3.01
2718 2817 2.367202 CGTATGGGCCACAGGGTCT 61.367 63.158 9.28 0.00 39.39 3.85
2860 2959 7.171848 GGTACAAAGAACACCAAAACTTGTTTT 59.828 33.333 5.74 5.74 32.32 2.43
2886 2995 5.856126 TTAGGTAAAGCATCAACGACTTG 57.144 39.130 0.00 0.00 0.00 3.16
3032 3145 2.756840 TGCTCCATTCTCAGTGAGTG 57.243 50.000 19.53 11.41 32.91 3.51
3270 3383 4.767255 CTGCCGGTGAGCTGGGAC 62.767 72.222 1.90 0.00 41.51 4.46
3339 3452 3.784701 TCAGACTTGATCGAGCTTACC 57.215 47.619 10.09 0.00 0.00 2.85
3358 3471 0.323451 AACCTCCCCGCTGGAAATTC 60.323 55.000 0.00 0.00 44.57 2.17
3448 3598 0.909610 TGATTCCCCAGAAGAGCGGT 60.910 55.000 0.00 0.00 34.86 5.68
3625 3775 2.158986 ACAGATTTCCTCCTCATCTGCG 60.159 50.000 8.06 0.00 45.38 5.18
3719 3978 2.443255 AGCCCAAGTCTTCTTTTCCTCA 59.557 45.455 0.00 0.00 0.00 3.86
3902 4177 5.163953 CCGAACAGTTCACATAAGATCACAC 60.164 44.000 13.82 0.00 0.00 3.82
3973 4248 2.890474 CGGCCGGTCTTGAATCCG 60.890 66.667 20.10 0.62 45.42 4.18
4152 4431 1.731433 ATGGCTGCATGCATCGTTCC 61.731 55.000 22.97 16.66 45.15 3.62
4255 4535 0.033796 ACACCTTCATCATGGGGCTG 60.034 55.000 0.00 0.42 0.00 4.85
4257 4537 1.669999 GCACACCTTCATCATGGGGC 61.670 60.000 0.00 0.00 0.00 5.80
4262 4542 2.425143 ATTCGGCACACCTTCATCAT 57.575 45.000 0.00 0.00 0.00 2.45
4418 4703 2.095461 CGAGAGAAGATGGAGGTGACA 58.905 52.381 0.00 0.00 0.00 3.58
4496 4782 0.107993 CTGTCTGGCGTCATGATGGT 60.108 55.000 16.59 0.00 0.00 3.55
4500 4786 0.390340 GAAGCTGTCTGGCGTCATGA 60.390 55.000 0.00 0.00 39.72 3.07
4605 4893 2.034812 GGAGGAGCGGTGTTACATCTAG 59.965 54.545 0.00 0.00 0.00 2.43
4748 5039 2.732912 GCAATTTGCGTCATCATGCTCA 60.733 45.455 5.49 0.00 35.31 4.26
4766 5057 0.882484 TTGAGGCATCGTCGTTGCAA 60.882 50.000 25.10 11.68 41.95 4.08


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

AutoCloner maintained by Alex Coulton.