Multiple sequence alignment - TraesCS7D01G410700

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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 TraesCS7D01G410700 chr7D 100.000 2384 0 0 1 2384 529771570 529773953 0.000000e+00 4403.0
1 TraesCS7D01G410700 chr7D 90.720 1541 88 24 850 2384 529682217 529680726 0.000000e+00 2002.0
2 TraesCS7D01G410700 chr7D 80.370 270 29 8 537 804 529682477 529682230 1.460000e-42 183.0
3 TraesCS7D01G410700 chr7B 93.696 920 38 10 1480 2384 567636604 567635690 0.000000e+00 1360.0
4 TraesCS7D01G410700 chr7B 93.567 886 47 6 1500 2384 567883712 567884588 0.000000e+00 1312.0
5 TraesCS7D01G410700 chr7B 91.088 965 63 10 518 1479 567882324 567883268 0.000000e+00 1284.0
6 TraesCS7D01G410700 chr7B 97.260 365 10 0 1021 1385 567637087 567636723 9.360000e-174 619.0
7 TraesCS7D01G410700 chr7B 87.205 508 38 15 539 1027 567639316 567638817 9.630000e-154 553.0
8 TraesCS7D01G410700 chr7B 86.747 83 10 1 182 263 567882242 567882324 9.070000e-15 91.6
9 TraesCS7D01G410700 chr7A 89.630 974 50 25 522 1483 609335373 609336307 0.000000e+00 1192.0
10 TraesCS7D01G410700 chr7A 93.590 780 42 1 1610 2381 609338908 609339687 0.000000e+00 1157.0
11 TraesCS7D01G410700 chr7A 93.843 536 26 3 850 1385 609172780 609172252 0.000000e+00 800.0
12 TraesCS7D01G410700 chr7A 94.131 443 26 0 1942 2384 609134305 609133863 0.000000e+00 675.0
13 TraesCS7D01G410700 chr7A 95.673 208 9 0 1706 1913 609134511 609134304 3.800000e-88 335.0
14 TraesCS7D01G410700 chr7A 88.031 259 29 2 259 516 663489945 663489688 2.980000e-79 305.0
15 TraesCS7D01G410700 chr7A 84.211 285 25 14 537 807 609173067 609172789 2.350000e-65 259.0
16 TraesCS7D01G410700 chr7A 91.228 57 4 1 2 58 670831811 670831756 2.540000e-10 76.8
17 TraesCS7D01G410700 chr5B 88.722 266 26 4 262 524 276947044 276947308 2.960000e-84 322.0
18 TraesCS7D01G410700 chr5B 87.843 255 26 5 273 524 347589584 347589332 6.440000e-76 294.0
19 TraesCS7D01G410700 chr5B 93.103 58 3 1 2 58 393583205 393583148 1.520000e-12 84.2
20 TraesCS7D01G410700 chr4A 88.123 261 26 5 260 517 483944629 483944887 2.980000e-79 305.0
21 TraesCS7D01G410700 chr5A 87.692 260 29 3 259 516 352869604 352869862 1.390000e-77 300.0
22 TraesCS7D01G410700 chr3B 87.938 257 28 3 262 516 648742524 648742269 1.390000e-77 300.0
23 TraesCS7D01G410700 chr4B 87.500 256 31 1 262 516 170675961 170675706 6.440000e-76 294.0
24 TraesCS7D01G410700 chr4B 78.049 164 26 6 1247 1404 654751736 654751577 7.020000e-16 95.3
25 TraesCS7D01G410700 chr4B 94.915 59 1 1 2 58 453508618 453508676 9.070000e-15 91.6
26 TraesCS7D01G410700 chr4B 77.439 164 27 6 1247 1404 654761975 654761816 3.260000e-14 89.8
27 TraesCS7D01G410700 chr4B 77.439 164 27 6 1247 1404 654774181 654774022 3.260000e-14 89.8
28 TraesCS7D01G410700 chr4B 76.829 164 28 6 1247 1404 654699241 654699082 1.520000e-12 84.2
29 TraesCS7D01G410700 chr6B 86.923 260 30 4 260 518 469709376 469709632 3.000000e-74 289.0
30 TraesCS7D01G410700 chr6B 98.246 57 1 0 2 58 151173154 151173210 1.510000e-17 100.0
31 TraesCS7D01G410700 chr5D 87.109 256 32 1 262 516 64191504 64191249 3.000000e-74 289.0
32 TraesCS7D01G410700 chr3A 96.491 57 2 0 2 58 723341999 723342055 7.020000e-16 95.3
33 TraesCS7D01G410700 chr3D 93.220 59 3 1 2 59 9465183 9465241 4.220000e-13 86.1
34 TraesCS7D01G410700 chr3D 93.103 58 3 1 2 58 46125484 46125427 1.520000e-12 84.2


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 TraesCS7D01G410700 chr7D 529771570 529773953 2383 False 4403.000000 4403 100.000000 1 2384 1 chr7D.!!$F1 2383
1 TraesCS7D01G410700 chr7D 529680726 529682477 1751 True 1092.500000 2002 85.545000 537 2384 2 chr7D.!!$R1 1847
2 TraesCS7D01G410700 chr7B 567882242 567884588 2346 False 895.866667 1312 90.467333 182 2384 3 chr7B.!!$F1 2202
3 TraesCS7D01G410700 chr7B 567635690 567639316 3626 True 844.000000 1360 92.720333 539 2384 3 chr7B.!!$R1 1845
4 TraesCS7D01G410700 chr7A 609335373 609339687 4314 False 1174.500000 1192 91.610000 522 2381 2 chr7A.!!$F1 1859
5 TraesCS7D01G410700 chr7A 609172252 609173067 815 True 529.500000 800 89.027000 537 1385 2 chr7A.!!$R4 848
6 TraesCS7D01G410700 chr7A 609133863 609134511 648 True 505.000000 675 94.902000 1706 2384 2 chr7A.!!$R3 678

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
105 106 0.038526 GACGAGACAAGCGGGAGAAA 60.039 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 3169 0.683412 CTGATGCCTCGATGGATGGA 59.317 55.0 0.0 0.0 38.35 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.753713 CGAGACTCTCTGTAATGTGTTTG 57.246 43.478 4.52 0.00 0.00 2.93
23 24 4.090642 CGAGACTCTCTGTAATGTGTTTGC 59.909 45.833 4.52 0.00 0.00 3.68
24 25 4.960938 AGACTCTCTGTAATGTGTTTGCA 58.039 39.130 0.00 0.00 0.00 4.08
25 26 5.555017 AGACTCTCTGTAATGTGTTTGCAT 58.445 37.500 0.00 0.00 29.03 3.96
26 27 5.410746 AGACTCTCTGTAATGTGTTTGCATG 59.589 40.000 0.00 0.00 29.03 4.06
27 28 5.308014 ACTCTCTGTAATGTGTTTGCATGA 58.692 37.500 0.00 0.00 29.03 3.07
28 29 5.942236 ACTCTCTGTAATGTGTTTGCATGAT 59.058 36.000 0.00 0.00 29.03 2.45
29 30 6.432162 ACTCTCTGTAATGTGTTTGCATGATT 59.568 34.615 0.00 0.00 29.03 2.57
30 31 7.607607 ACTCTCTGTAATGTGTTTGCATGATTA 59.392 33.333 0.00 0.00 29.03 1.75
31 32 8.334263 TCTCTGTAATGTGTTTGCATGATTAA 57.666 30.769 0.00 0.00 29.03 1.40
32 33 8.959548 TCTCTGTAATGTGTTTGCATGATTAAT 58.040 29.630 0.00 0.00 29.03 1.40
38 39 7.775397 ATGTGTTTGCATGATTAATAAAGGC 57.225 32.000 0.00 0.00 0.00 4.35
39 40 6.105333 TGTGTTTGCATGATTAATAAAGGCC 58.895 36.000 0.00 0.00 0.00 5.19
40 41 5.231991 GTGTTTGCATGATTAATAAAGGCCG 59.768 40.000 0.00 0.00 0.00 6.13
41 42 5.126222 TGTTTGCATGATTAATAAAGGCCGA 59.874 36.000 0.00 0.00 0.00 5.54
42 43 4.829064 TGCATGATTAATAAAGGCCGAC 57.171 40.909 0.00 0.00 0.00 4.79
43 44 3.249799 TGCATGATTAATAAAGGCCGACG 59.750 43.478 0.00 0.00 0.00 5.12
44 45 3.250040 GCATGATTAATAAAGGCCGACGT 59.750 43.478 0.00 0.00 0.00 4.34
45 46 4.261031 GCATGATTAATAAAGGCCGACGTT 60.261 41.667 0.00 0.00 0.00 3.99
46 47 5.440685 CATGATTAATAAAGGCCGACGTTC 58.559 41.667 0.00 0.00 0.00 3.95
47 48 4.761975 TGATTAATAAAGGCCGACGTTCT 58.238 39.130 0.00 0.00 0.00 3.01
48 49 4.807304 TGATTAATAAAGGCCGACGTTCTC 59.193 41.667 0.00 0.00 0.00 2.87
49 50 4.460948 TTAATAAAGGCCGACGTTCTCT 57.539 40.909 0.00 0.00 0.00 3.10
50 51 2.580966 ATAAAGGCCGACGTTCTCTC 57.419 50.000 0.00 0.00 0.00 3.20
51 52 1.250328 TAAAGGCCGACGTTCTCTCA 58.750 50.000 0.00 0.00 0.00 3.27
52 53 0.391597 AAAGGCCGACGTTCTCTCAA 59.608 50.000 0.00 0.00 0.00 3.02
53 54 0.391597 AAGGCCGACGTTCTCTCAAA 59.608 50.000 0.00 0.00 0.00 2.69
54 55 0.391597 AGGCCGACGTTCTCTCAAAA 59.608 50.000 0.00 0.00 0.00 2.44
55 56 1.202604 AGGCCGACGTTCTCTCAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
76 77 5.461032 AAAAGTCAACAGAAACCACAACA 57.539 34.783 0.00 0.00 0.00 3.33
77 78 4.434713 AAGTCAACAGAAACCACAACAC 57.565 40.909 0.00 0.00 0.00 3.32
78 79 3.417101 AGTCAACAGAAACCACAACACA 58.583 40.909 0.00 0.00 0.00 3.72
79 80 3.440173 AGTCAACAGAAACCACAACACAG 59.560 43.478 0.00 0.00 0.00 3.66
80 81 2.752354 TCAACAGAAACCACAACACAGG 59.248 45.455 0.00 0.00 0.00 4.00
81 82 1.102978 ACAGAAACCACAACACAGGC 58.897 50.000 0.00 0.00 0.00 4.85
82 83 0.385390 CAGAAACCACAACACAGGCC 59.615 55.000 0.00 0.00 0.00 5.19
83 84 0.755327 AGAAACCACAACACAGGCCC 60.755 55.000 0.00 0.00 0.00 5.80
84 85 2.070654 GAAACCACAACACAGGCCCG 62.071 60.000 0.00 0.00 0.00 6.13
85 86 2.847366 AAACCACAACACAGGCCCGT 62.847 55.000 0.00 0.00 0.00 5.28
86 87 3.286751 CCACAACACAGGCCCGTG 61.287 66.667 17.83 17.83 42.81 4.94
87 88 2.203139 CACAACACAGGCCCGTGA 60.203 61.111 25.94 0.00 39.34 4.35
88 89 2.203153 ACAACACAGGCCCGTGAC 60.203 61.111 25.94 0.00 39.34 3.67
89 90 3.345808 CAACACAGGCCCGTGACG 61.346 66.667 25.94 11.66 39.34 4.35
90 91 3.542676 AACACAGGCCCGTGACGA 61.543 61.111 25.94 0.00 39.34 4.20
91 92 3.515316 AACACAGGCCCGTGACGAG 62.515 63.158 25.94 0.00 39.34 4.18
92 93 3.680786 CACAGGCCCGTGACGAGA 61.681 66.667 14.31 0.00 39.34 4.04
93 94 3.681835 ACAGGCCCGTGACGAGAC 61.682 66.667 6.54 0.00 0.00 3.36
94 95 3.680786 CAGGCCCGTGACGAGACA 61.681 66.667 6.54 0.00 0.00 3.41
95 96 2.915659 AGGCCCGTGACGAGACAA 60.916 61.111 6.54 0.00 0.00 3.18
96 97 2.432628 GGCCCGTGACGAGACAAG 60.433 66.667 6.54 0.00 0.00 3.16
97 98 3.112709 GCCCGTGACGAGACAAGC 61.113 66.667 6.54 0.00 0.00 4.01
98 99 2.805353 CCCGTGACGAGACAAGCG 60.805 66.667 6.54 0.00 0.00 4.68
99 100 2.805353 CCGTGACGAGACAAGCGG 60.805 66.667 6.54 0.00 0.00 5.52
100 101 2.805353 CGTGACGAGACAAGCGGG 60.805 66.667 0.00 0.00 0.00 6.13
101 102 2.649034 GTGACGAGACAAGCGGGA 59.351 61.111 0.00 0.00 0.00 5.14
102 103 1.444553 GTGACGAGACAAGCGGGAG 60.445 63.158 0.00 0.00 0.00 4.30
103 104 1.602605 TGACGAGACAAGCGGGAGA 60.603 57.895 0.00 0.00 0.00 3.71
104 105 1.176619 TGACGAGACAAGCGGGAGAA 61.177 55.000 0.00 0.00 0.00 2.87
105 106 0.038526 GACGAGACAAGCGGGAGAAA 60.039 55.000 0.00 0.00 0.00 2.52
106 107 0.319641 ACGAGACAAGCGGGAGAAAC 60.320 55.000 0.00 0.00 0.00 2.78
107 108 0.319555 CGAGACAAGCGGGAGAAACA 60.320 55.000 0.00 0.00 0.00 2.83
108 109 1.673033 CGAGACAAGCGGGAGAAACAT 60.673 52.381 0.00 0.00 0.00 2.71
109 110 2.427506 GAGACAAGCGGGAGAAACATT 58.572 47.619 0.00 0.00 0.00 2.71
110 111 2.154462 AGACAAGCGGGAGAAACATTG 58.846 47.619 0.00 0.00 0.00 2.82
111 112 0.598065 ACAAGCGGGAGAAACATTGC 59.402 50.000 0.00 0.00 0.00 3.56
112 113 0.597568 CAAGCGGGAGAAACATTGCA 59.402 50.000 0.00 0.00 0.00 4.08
113 114 0.598065 AAGCGGGAGAAACATTGCAC 59.402 50.000 0.00 0.00 0.00 4.57
114 115 1.154225 GCGGGAGAAACATTGCACG 60.154 57.895 0.00 0.00 0.00 5.34
115 116 1.573829 GCGGGAGAAACATTGCACGA 61.574 55.000 0.00 0.00 0.00 4.35
116 117 0.871722 CGGGAGAAACATTGCACGAA 59.128 50.000 0.00 0.00 0.00 3.85
117 118 1.265635 CGGGAGAAACATTGCACGAAA 59.734 47.619 0.00 0.00 0.00 3.46
118 119 2.287308 CGGGAGAAACATTGCACGAAAA 60.287 45.455 0.00 0.00 0.00 2.29
119 120 3.611530 CGGGAGAAACATTGCACGAAAAT 60.612 43.478 0.00 0.00 0.00 1.82
120 121 4.306600 GGGAGAAACATTGCACGAAAATT 58.693 39.130 0.00 0.00 0.00 1.82
121 122 4.150451 GGGAGAAACATTGCACGAAAATTG 59.850 41.667 0.00 0.00 0.00 2.32
122 123 4.744631 GGAGAAACATTGCACGAAAATTGT 59.255 37.500 0.00 0.00 0.00 2.71
123 124 5.918011 GGAGAAACATTGCACGAAAATTGTA 59.082 36.000 0.00 0.00 0.00 2.41
124 125 6.088085 GGAGAAACATTGCACGAAAATTGTAG 59.912 38.462 0.00 0.00 0.00 2.74
125 126 5.402270 AGAAACATTGCACGAAAATTGTAGC 59.598 36.000 0.00 0.00 0.00 3.58
126 127 4.235939 ACATTGCACGAAAATTGTAGCA 57.764 36.364 0.00 0.00 0.00 3.49
127 128 4.808558 ACATTGCACGAAAATTGTAGCAT 58.191 34.783 0.00 0.00 0.00 3.79
128 129 4.858692 ACATTGCACGAAAATTGTAGCATC 59.141 37.500 0.00 0.00 0.00 3.91
129 130 4.764679 TTGCACGAAAATTGTAGCATCT 57.235 36.364 0.00 0.00 0.00 2.90
130 131 4.764679 TGCACGAAAATTGTAGCATCTT 57.235 36.364 0.00 0.00 0.00 2.40
131 132 5.119931 TGCACGAAAATTGTAGCATCTTT 57.880 34.783 0.00 0.00 0.00 2.52
132 133 6.247727 TGCACGAAAATTGTAGCATCTTTA 57.752 33.333 0.00 0.00 0.00 1.85
133 134 6.673106 TGCACGAAAATTGTAGCATCTTTAA 58.327 32.000 0.00 0.00 0.00 1.52
134 135 7.312154 TGCACGAAAATTGTAGCATCTTTAAT 58.688 30.769 0.00 0.00 0.00 1.40
135 136 7.812191 TGCACGAAAATTGTAGCATCTTTAATT 59.188 29.630 0.00 0.00 0.00 1.40
136 137 8.103924 GCACGAAAATTGTAGCATCTTTAATTG 58.896 33.333 0.00 0.00 0.00 2.32
137 138 9.128107 CACGAAAATTGTAGCATCTTTAATTGT 57.872 29.630 0.00 0.00 0.00 2.71
138 139 9.341899 ACGAAAATTGTAGCATCTTTAATTGTC 57.658 29.630 0.00 0.00 0.00 3.18
139 140 9.559958 CGAAAATTGTAGCATCTTTAATTGTCT 57.440 29.630 0.00 0.00 0.00 3.41
143 144 9.630098 AATTGTAGCATCTTTAATTGTCTTGTG 57.370 29.630 0.00 0.00 0.00 3.33
144 145 7.744087 TGTAGCATCTTTAATTGTCTTGTGT 57.256 32.000 0.00 0.00 0.00 3.72
145 146 7.584108 TGTAGCATCTTTAATTGTCTTGTGTG 58.416 34.615 0.00 0.00 0.00 3.82
146 147 6.882610 AGCATCTTTAATTGTCTTGTGTGA 57.117 33.333 0.00 0.00 0.00 3.58
147 148 6.906659 AGCATCTTTAATTGTCTTGTGTGAG 58.093 36.000 0.00 0.00 0.00 3.51
148 149 6.712095 AGCATCTTTAATTGTCTTGTGTGAGA 59.288 34.615 0.00 0.00 0.00 3.27
149 150 6.798959 GCATCTTTAATTGTCTTGTGTGAGAC 59.201 38.462 0.00 0.00 44.97 3.36
150 151 7.308229 GCATCTTTAATTGTCTTGTGTGAGACT 60.308 37.037 6.59 0.00 44.99 3.24
151 152 8.562892 CATCTTTAATTGTCTTGTGTGAGACTT 58.437 33.333 6.59 0.00 44.99 3.01
152 153 9.778741 ATCTTTAATTGTCTTGTGTGAGACTTA 57.221 29.630 6.59 0.00 44.99 2.24
153 154 9.607988 TCTTTAATTGTCTTGTGTGAGACTTAA 57.392 29.630 6.59 2.28 44.99 1.85
157 158 8.450578 AATTGTCTTGTGTGAGACTTAAATGA 57.549 30.769 6.59 0.00 44.99 2.57
158 159 7.482654 TTGTCTTGTGTGAGACTTAAATGAG 57.517 36.000 6.59 0.00 44.99 2.90
159 160 6.816136 TGTCTTGTGTGAGACTTAAATGAGA 58.184 36.000 6.59 0.00 44.99 3.27
160 161 6.701841 TGTCTTGTGTGAGACTTAAATGAGAC 59.298 38.462 6.59 0.00 44.99 3.36
161 162 6.701841 GTCTTGTGTGAGACTTAAATGAGACA 59.298 38.462 0.00 0.00 42.18 3.41
162 163 7.386299 GTCTTGTGTGAGACTTAAATGAGACAT 59.614 37.037 0.00 0.00 42.18 3.06
163 164 8.585018 TCTTGTGTGAGACTTAAATGAGACATA 58.415 33.333 0.00 0.00 0.00 2.29
164 165 8.763049 TTGTGTGAGACTTAAATGAGACATAG 57.237 34.615 0.00 0.00 0.00 2.23
165 166 6.813649 TGTGTGAGACTTAAATGAGACATAGC 59.186 38.462 0.00 0.00 0.00 2.97
166 167 7.038659 GTGTGAGACTTAAATGAGACATAGCT 58.961 38.462 0.00 0.00 0.00 3.32
167 168 8.191446 GTGTGAGACTTAAATGAGACATAGCTA 58.809 37.037 0.00 0.00 0.00 3.32
168 169 8.749354 TGTGAGACTTAAATGAGACATAGCTAA 58.251 33.333 0.00 0.00 0.00 3.09
169 170 9.587772 GTGAGACTTAAATGAGACATAGCTAAA 57.412 33.333 0.00 0.00 0.00 1.85
180 181 8.932434 TGAGACATAGCTAAATCTCATCTACT 57.068 34.615 25.51 4.36 41.99 2.57
184 185 6.717540 ACATAGCTAAATCTCATCTACTCCGT 59.282 38.462 0.00 0.00 0.00 4.69
205 206 8.454570 TCCGTTAATGAATAAAGGATTAACCC 57.545 34.615 0.00 0.00 44.18 4.11
206 207 8.276477 TCCGTTAATGAATAAAGGATTAACCCT 58.724 33.333 0.00 0.00 44.18 4.34
287 289 8.100508 ACTTCCTACATTTCTTTTTAGTCTGC 57.899 34.615 0.00 0.00 0.00 4.26
288 290 7.719633 ACTTCCTACATTTCTTTTTAGTCTGCA 59.280 33.333 0.00 0.00 0.00 4.41
289 291 8.635765 TTCCTACATTTCTTTTTAGTCTGCAT 57.364 30.769 0.00 0.00 0.00 3.96
290 292 9.733556 TTCCTACATTTCTTTTTAGTCTGCATA 57.266 29.630 0.00 0.00 0.00 3.14
291 293 9.905713 TCCTACATTTCTTTTTAGTCTGCATAT 57.094 29.630 0.00 0.00 0.00 1.78
302 304 9.997482 TTTTTAGTCTGCATATAAAATTCGGTC 57.003 29.630 10.07 0.00 30.75 4.79
303 305 8.725405 TTTAGTCTGCATATAAAATTCGGTCA 57.275 30.769 0.00 0.00 0.00 4.02
304 306 8.725405 TTAGTCTGCATATAAAATTCGGTCAA 57.275 30.769 0.00 0.00 0.00 3.18
305 307 7.624360 AGTCTGCATATAAAATTCGGTCAAA 57.376 32.000 0.00 0.00 0.00 2.69
306 308 8.050778 AGTCTGCATATAAAATTCGGTCAAAA 57.949 30.769 0.00 0.00 0.00 2.44
307 309 8.686334 AGTCTGCATATAAAATTCGGTCAAAAT 58.314 29.630 0.00 0.00 0.00 1.82
308 310 8.958043 GTCTGCATATAAAATTCGGTCAAAATC 58.042 33.333 0.00 0.00 0.00 2.17
309 311 8.681806 TCTGCATATAAAATTCGGTCAAAATCA 58.318 29.630 0.00 0.00 0.00 2.57
310 312 9.299963 CTGCATATAAAATTCGGTCAAAATCAA 57.700 29.630 0.00 0.00 0.00 2.57
311 313 9.645059 TGCATATAAAATTCGGTCAAAATCAAA 57.355 25.926 0.00 0.00 0.00 2.69
317 319 5.861222 ATTCGGTCAAAATCAAATTTGGC 57.139 34.783 17.90 0.00 42.68 4.52
318 320 4.327982 TCGGTCAAAATCAAATTTGGCA 57.672 36.364 17.90 0.00 44.64 4.92
319 321 4.697514 TCGGTCAAAATCAAATTTGGCAA 58.302 34.783 17.90 0.00 44.64 4.52
320 322 5.118990 TCGGTCAAAATCAAATTTGGCAAA 58.881 33.333 16.01 16.01 44.64 3.68
321 323 5.236047 TCGGTCAAAATCAAATTTGGCAAAG 59.764 36.000 18.61 5.12 44.64 2.77
322 324 5.007528 CGGTCAAAATCAAATTTGGCAAAGT 59.992 36.000 18.61 13.28 44.64 2.66
323 325 6.458070 CGGTCAAAATCAAATTTGGCAAAGTT 60.458 34.615 18.86 18.86 44.64 2.66
324 326 7.257003 GGTCAAAATCAAATTTGGCAAAGTTT 58.743 30.769 21.58 15.92 44.64 2.66
325 327 7.220491 GGTCAAAATCAAATTTGGCAAAGTTTG 59.780 33.333 21.58 23.95 44.64 2.93
331 333 7.532682 TCAAATTTGGCAAAGTTTGACTAAC 57.467 32.000 27.50 2.54 43.22 2.34
387 389 8.735692 TGAAATCAATAGTGTTAGATGCATCA 57.264 30.769 27.81 11.65 0.00 3.07
388 390 8.833493 TGAAATCAATAGTGTTAGATGCATCAG 58.167 33.333 27.81 5.22 0.00 2.90
389 391 7.741027 AATCAATAGTGTTAGATGCATCAGG 57.259 36.000 27.81 3.27 0.00 3.86
390 392 6.484364 TCAATAGTGTTAGATGCATCAGGA 57.516 37.500 27.81 10.43 0.00 3.86
391 393 6.888105 TCAATAGTGTTAGATGCATCAGGAA 58.112 36.000 27.81 15.61 0.00 3.36
392 394 7.337938 TCAATAGTGTTAGATGCATCAGGAAA 58.662 34.615 27.81 13.39 0.00 3.13
393 395 7.994911 TCAATAGTGTTAGATGCATCAGGAAAT 59.005 33.333 27.81 12.49 0.00 2.17
394 396 8.627403 CAATAGTGTTAGATGCATCAGGAAATT 58.373 33.333 27.81 14.49 0.00 1.82
395 397 9.851686 AATAGTGTTAGATGCATCAGGAAATTA 57.148 29.630 27.81 12.10 0.00 1.40
396 398 9.851686 ATAGTGTTAGATGCATCAGGAAATTAA 57.148 29.630 27.81 12.89 0.00 1.40
397 399 8.757982 AGTGTTAGATGCATCAGGAAATTAAT 57.242 30.769 27.81 6.25 0.00 1.40
398 400 9.193806 AGTGTTAGATGCATCAGGAAATTAATT 57.806 29.630 27.81 5.73 0.00 1.40
399 401 9.807649 GTGTTAGATGCATCAGGAAATTAATTT 57.192 29.630 27.81 13.24 0.00 1.82
403 405 8.937634 AGATGCATCAGGAAATTAATTTTCAC 57.062 30.769 27.81 11.12 44.67 3.18
404 406 8.533657 AGATGCATCAGGAAATTAATTTTCACA 58.466 29.630 27.81 10.33 44.67 3.58
405 407 7.887996 TGCATCAGGAAATTAATTTTCACAC 57.112 32.000 19.24 5.26 44.67 3.82
406 408 6.873076 TGCATCAGGAAATTAATTTTCACACC 59.127 34.615 19.24 13.00 44.67 4.16
407 409 6.873076 GCATCAGGAAATTAATTTTCACACCA 59.127 34.615 19.24 1.33 44.67 4.17
408 410 7.550196 GCATCAGGAAATTAATTTTCACACCAT 59.450 33.333 19.24 0.09 44.67 3.55
424 426 9.899661 TTTCACACCATATAGCTTTAGTATTGT 57.100 29.630 0.00 0.00 0.00 2.71
425 427 8.887036 TCACACCATATAGCTTTAGTATTGTG 57.113 34.615 0.00 1.93 31.48 3.33
426 428 7.931407 TCACACCATATAGCTTTAGTATTGTGG 59.069 37.037 0.00 0.00 30.19 4.17
427 429 7.931407 CACACCATATAGCTTTAGTATTGTGGA 59.069 37.037 0.00 0.00 30.19 4.02
428 430 8.660435 ACACCATATAGCTTTAGTATTGTGGAT 58.340 33.333 0.00 0.00 30.19 3.41
429 431 8.939929 CACCATATAGCTTTAGTATTGTGGATG 58.060 37.037 0.00 0.00 0.00 3.51
430 432 8.660435 ACCATATAGCTTTAGTATTGTGGATGT 58.340 33.333 0.00 0.00 0.00 3.06
431 433 9.507329 CCATATAGCTTTAGTATTGTGGATGTT 57.493 33.333 0.00 0.00 0.00 2.71
437 439 9.632638 AGCTTTAGTATTGTGGATGTTGATATT 57.367 29.630 0.00 0.00 0.00 1.28
482 484 8.434733 AAACTCTACAAAGTTTGACTTAGACC 57.565 34.615 22.23 0.00 45.38 3.85
483 485 7.120923 ACTCTACAAAGTTTGACTTAGACCA 57.879 36.000 22.23 0.00 37.47 4.02
484 486 7.562135 ACTCTACAAAGTTTGACTTAGACCAA 58.438 34.615 22.23 0.00 37.47 3.67
485 487 8.044908 ACTCTACAAAGTTTGACTTAGACCAAA 58.955 33.333 22.23 0.00 37.47 3.28
486 488 8.974060 TCTACAAAGTTTGACTTAGACCAAAT 57.026 30.769 22.23 0.00 37.47 2.32
487 489 9.403583 TCTACAAAGTTTGACTTAGACCAAATT 57.596 29.630 22.23 0.00 37.47 1.82
498 500 9.679661 TGACTTAGACCAAATTTTATATGCAGA 57.320 29.630 0.00 0.00 0.00 4.26
499 501 9.937175 GACTTAGACCAAATTTTATATGCAGAC 57.063 33.333 0.00 0.00 0.00 3.51
500 502 9.686683 ACTTAGACCAAATTTTATATGCAGACT 57.313 29.630 0.00 0.00 0.00 3.24
515 517 6.566197 ATGCAGACTAAAAAGAAACAGAGG 57.434 37.500 0.00 0.00 0.00 3.69
516 518 5.680619 TGCAGACTAAAAAGAAACAGAGGA 58.319 37.500 0.00 0.00 0.00 3.71
517 519 6.119536 TGCAGACTAAAAAGAAACAGAGGAA 58.880 36.000 0.00 0.00 0.00 3.36
695 704 2.794631 GCCGGCCGATTACAAGAATTTG 60.795 50.000 30.73 5.15 40.24 2.32
793 814 3.985279 CACTTCAGTGTGCAAATCATTGG 59.015 43.478 0.00 0.00 40.96 3.16
838 859 1.544724 TCCAGAAAAAGGCCAATCGG 58.455 50.000 5.01 3.91 0.00 4.18
887 909 0.950836 CGGCCACACAGTTTTGATCA 59.049 50.000 2.24 0.00 0.00 2.92
910 932 6.726299 TCACCTATAAATACCCTCCAGATCAG 59.274 42.308 0.00 0.00 0.00 2.90
929 951 4.281657 TCAGTGCCATATACTCACTCACT 58.718 43.478 0.00 0.00 38.85 3.41
995 1036 0.888619 CCCACTCACGAACTAGAGCA 59.111 55.000 0.00 0.00 35.28 4.26
1366 3143 2.575461 GATGCAAGGTGCCCAAGC 59.425 61.111 0.00 0.00 44.23 4.01
1386 3163 4.838152 TTCCGCTGCGCCTGATCC 62.838 66.667 18.00 0.00 0.00 3.36
1390 3167 2.976903 GCTGCGCCTGATCCATCC 60.977 66.667 4.18 0.00 0.00 3.51
1391 3168 2.507452 CTGCGCCTGATCCATCCA 59.493 61.111 4.18 0.00 0.00 3.41
1392 3169 1.072678 CTGCGCCTGATCCATCCAT 59.927 57.895 4.18 0.00 0.00 3.41
1393 3170 0.954449 CTGCGCCTGATCCATCCATC 60.954 60.000 4.18 0.00 0.00 3.51
1394 3171 1.673665 GCGCCTGATCCATCCATCC 60.674 63.158 0.00 0.00 0.00 3.51
1395 3172 1.756665 CGCCTGATCCATCCATCCA 59.243 57.895 0.00 0.00 0.00 3.41
1396 3173 0.327259 CGCCTGATCCATCCATCCAT 59.673 55.000 0.00 0.00 0.00 3.41
1397 3174 1.678123 CGCCTGATCCATCCATCCATC 60.678 57.143 0.00 0.00 0.00 3.51
1398 3175 1.340795 GCCTGATCCATCCATCCATCC 60.341 57.143 0.00 0.00 0.00 3.51
1402 3179 2.237893 TGATCCATCCATCCATCCATCG 59.762 50.000 0.00 0.00 0.00 3.84
1455 3260 1.008194 GTGCGTGTACGTGTCAGGA 60.008 57.895 15.61 0.00 42.22 3.86
1497 3346 2.436417 TCTGTAATTCCCAGCTTGTGC 58.564 47.619 0.00 0.00 40.05 4.57
1498 3347 2.161855 CTGTAATTCCCAGCTTGTGCA 58.838 47.619 0.00 0.00 42.74 4.57
1511 3758 2.791567 CTTGTGCACGTTGTAAAAGCA 58.208 42.857 13.13 0.00 0.00 3.91
1523 3776 5.108405 CGTTGTAAAAGCAACATTTTCCTCG 60.108 40.000 9.20 0.00 46.47 4.63
1532 3786 8.831715 AAGCAACATTTTCCTCGAATAAAAAT 57.168 26.923 8.22 7.24 33.94 1.82
1569 4706 5.904941 ACGTATATTTTATGGTCACGGTCA 58.095 37.500 0.00 0.00 32.52 4.02
1591 4737 4.328440 CAGTTTATTCGCAGTCTCTGGAAG 59.672 45.833 0.00 0.00 29.46 3.46
1592 4738 2.586258 TATTCGCAGTCTCTGGAAGC 57.414 50.000 0.00 0.00 29.46 3.86
1594 4740 0.610174 TTCGCAGTCTCTGGAAGCAT 59.390 50.000 0.00 0.00 31.21 3.79
1669 6378 4.459089 GACCTGCGGAGGGTGCTC 62.459 72.222 27.88 11.76 44.84 4.26
1677 6386 1.216710 GGAGGGTGCTCTCTTCGTG 59.783 63.158 0.00 0.00 34.39 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.090642 GCAAACACATTACAGAGAGTCTCG 59.909 45.833 14.47 11.65 35.36 4.04
1 2 4.991056 TGCAAACACATTACAGAGAGTCTC 59.009 41.667 12.54 12.54 0.00 3.36
2 3 4.960938 TGCAAACACATTACAGAGAGTCT 58.039 39.130 0.00 0.00 0.00 3.24
3 4 5.409520 TCATGCAAACACATTACAGAGAGTC 59.590 40.000 0.00 0.00 0.00 3.36
5 6 5.868043 TCATGCAAACACATTACAGAGAG 57.132 39.130 0.00 0.00 0.00 3.20
13 14 7.280652 GGCCTTTATTAATCATGCAAACACATT 59.719 33.333 0.00 0.00 0.00 2.71
14 15 6.762661 GGCCTTTATTAATCATGCAAACACAT 59.237 34.615 0.00 0.00 0.00 3.21
15 16 6.105333 GGCCTTTATTAATCATGCAAACACA 58.895 36.000 0.00 0.00 0.00 3.72
18 19 5.458779 GTCGGCCTTTATTAATCATGCAAAC 59.541 40.000 0.00 0.00 0.00 2.93
19 20 5.587289 GTCGGCCTTTATTAATCATGCAAA 58.413 37.500 0.00 0.00 0.00 3.68
20 21 4.260990 CGTCGGCCTTTATTAATCATGCAA 60.261 41.667 0.00 0.00 0.00 4.08
21 22 3.249799 CGTCGGCCTTTATTAATCATGCA 59.750 43.478 0.00 0.00 0.00 3.96
22 23 3.250040 ACGTCGGCCTTTATTAATCATGC 59.750 43.478 0.00 0.00 0.00 4.06
23 24 5.236478 AGAACGTCGGCCTTTATTAATCATG 59.764 40.000 0.00 0.00 0.00 3.07
24 25 5.365619 AGAACGTCGGCCTTTATTAATCAT 58.634 37.500 0.00 0.00 0.00 2.45
25 26 4.761975 AGAACGTCGGCCTTTATTAATCA 58.238 39.130 0.00 0.00 0.00 2.57
26 27 5.048507 AGAGAACGTCGGCCTTTATTAATC 58.951 41.667 0.00 0.00 0.00 1.75
27 28 5.019785 AGAGAACGTCGGCCTTTATTAAT 57.980 39.130 0.00 0.00 0.00 1.40
28 29 4.082081 TGAGAGAACGTCGGCCTTTATTAA 60.082 41.667 0.00 0.00 0.00 1.40
29 30 3.444742 TGAGAGAACGTCGGCCTTTATTA 59.555 43.478 0.00 0.00 0.00 0.98
30 31 2.232941 TGAGAGAACGTCGGCCTTTATT 59.767 45.455 0.00 0.00 0.00 1.40
31 32 1.822990 TGAGAGAACGTCGGCCTTTAT 59.177 47.619 0.00 0.00 0.00 1.40
32 33 1.250328 TGAGAGAACGTCGGCCTTTA 58.750 50.000 0.00 0.00 0.00 1.85
33 34 0.391597 TTGAGAGAACGTCGGCCTTT 59.608 50.000 0.00 0.00 0.00 3.11
34 35 0.391597 TTTGAGAGAACGTCGGCCTT 59.608 50.000 0.00 0.00 0.00 4.35
35 36 0.391597 TTTTGAGAGAACGTCGGCCT 59.608 50.000 0.00 0.00 0.00 5.19
36 37 1.223187 TTTTTGAGAGAACGTCGGCC 58.777 50.000 0.00 0.00 0.00 6.13
53 54 5.694458 GTGTTGTGGTTTCTGTTGACTTTTT 59.306 36.000 0.00 0.00 0.00 1.94
54 55 5.221342 TGTGTTGTGGTTTCTGTTGACTTTT 60.221 36.000 0.00 0.00 0.00 2.27
55 56 4.279671 TGTGTTGTGGTTTCTGTTGACTTT 59.720 37.500 0.00 0.00 0.00 2.66
56 57 3.823873 TGTGTTGTGGTTTCTGTTGACTT 59.176 39.130 0.00 0.00 0.00 3.01
57 58 3.417101 TGTGTTGTGGTTTCTGTTGACT 58.583 40.909 0.00 0.00 0.00 3.41
58 59 3.427503 CCTGTGTTGTGGTTTCTGTTGAC 60.428 47.826 0.00 0.00 0.00 3.18
59 60 2.752354 CCTGTGTTGTGGTTTCTGTTGA 59.248 45.455 0.00 0.00 0.00 3.18
60 61 2.735126 GCCTGTGTTGTGGTTTCTGTTG 60.735 50.000 0.00 0.00 0.00 3.33
61 62 1.476488 GCCTGTGTTGTGGTTTCTGTT 59.524 47.619 0.00 0.00 0.00 3.16
62 63 1.102978 GCCTGTGTTGTGGTTTCTGT 58.897 50.000 0.00 0.00 0.00 3.41
63 64 0.385390 GGCCTGTGTTGTGGTTTCTG 59.615 55.000 0.00 0.00 0.00 3.02
64 65 0.755327 GGGCCTGTGTTGTGGTTTCT 60.755 55.000 0.84 0.00 0.00 2.52
65 66 1.739667 GGGCCTGTGTTGTGGTTTC 59.260 57.895 0.84 0.00 0.00 2.78
66 67 2.124693 CGGGCCTGTGTTGTGGTTT 61.125 57.895 2.29 0.00 0.00 3.27
67 68 2.518349 CGGGCCTGTGTTGTGGTT 60.518 61.111 2.29 0.00 0.00 3.67
68 69 3.804329 ACGGGCCTGTGTTGTGGT 61.804 61.111 18.90 0.00 0.00 4.16
69 70 3.286751 CACGGGCCTGTGTTGTGG 61.287 66.667 32.99 9.81 35.12 4.17
70 71 2.203139 TCACGGGCCTGTGTTGTG 60.203 61.111 37.57 17.67 40.74 3.33
71 72 2.203153 GTCACGGGCCTGTGTTGT 60.203 61.111 37.57 5.08 40.74 3.32
72 73 3.345808 CGTCACGGGCCTGTGTTG 61.346 66.667 37.57 28.03 40.74 3.33
73 74 3.515316 CTCGTCACGGGCCTGTGTT 62.515 63.158 37.57 5.92 40.74 3.32
74 75 3.991051 CTCGTCACGGGCCTGTGT 61.991 66.667 37.57 16.43 40.74 3.72
75 76 3.680786 TCTCGTCACGGGCCTGTG 61.681 66.667 35.06 35.06 41.28 3.66
76 77 3.681835 GTCTCGTCACGGGCCTGT 61.682 66.667 12.85 12.85 0.00 4.00
77 78 3.220999 TTGTCTCGTCACGGGCCTG 62.221 63.158 11.02 11.02 0.00 4.85
78 79 2.915659 TTGTCTCGTCACGGGCCT 60.916 61.111 0.84 0.00 0.00 5.19
79 80 2.432628 CTTGTCTCGTCACGGGCC 60.433 66.667 0.00 0.00 0.00 5.80
80 81 3.112709 GCTTGTCTCGTCACGGGC 61.113 66.667 0.00 0.00 0.00 6.13
81 82 2.805353 CGCTTGTCTCGTCACGGG 60.805 66.667 0.00 0.00 0.00 5.28
82 83 2.805353 CCGCTTGTCTCGTCACGG 60.805 66.667 0.00 0.00 0.00 4.94
83 84 2.805353 CCCGCTTGTCTCGTCACG 60.805 66.667 0.00 0.00 0.00 4.35
84 85 1.444553 CTCCCGCTTGTCTCGTCAC 60.445 63.158 0.00 0.00 0.00 3.67
85 86 1.176619 TTCTCCCGCTTGTCTCGTCA 61.177 55.000 0.00 0.00 0.00 4.35
86 87 0.038526 TTTCTCCCGCTTGTCTCGTC 60.039 55.000 0.00 0.00 0.00 4.20
87 88 0.319641 GTTTCTCCCGCTTGTCTCGT 60.320 55.000 0.00 0.00 0.00 4.18
88 89 0.319555 TGTTTCTCCCGCTTGTCTCG 60.320 55.000 0.00 0.00 0.00 4.04
89 90 2.100605 ATGTTTCTCCCGCTTGTCTC 57.899 50.000 0.00 0.00 0.00 3.36
90 91 2.154462 CAATGTTTCTCCCGCTTGTCT 58.846 47.619 0.00 0.00 0.00 3.41
91 92 1.401539 GCAATGTTTCTCCCGCTTGTC 60.402 52.381 0.00 0.00 0.00 3.18
92 93 0.598065 GCAATGTTTCTCCCGCTTGT 59.402 50.000 0.00 0.00 0.00 3.16
93 94 0.597568 TGCAATGTTTCTCCCGCTTG 59.402 50.000 0.00 0.00 0.00 4.01
94 95 0.598065 GTGCAATGTTTCTCCCGCTT 59.402 50.000 0.00 0.00 0.00 4.68
95 96 1.577328 CGTGCAATGTTTCTCCCGCT 61.577 55.000 0.00 0.00 0.00 5.52
96 97 1.154225 CGTGCAATGTTTCTCCCGC 60.154 57.895 0.00 0.00 0.00 6.13
97 98 0.871722 TTCGTGCAATGTTTCTCCCG 59.128 50.000 0.00 0.00 0.00 5.14
98 99 3.363341 TTTTCGTGCAATGTTTCTCCC 57.637 42.857 0.00 0.00 0.00 4.30
99 100 4.744631 ACAATTTTCGTGCAATGTTTCTCC 59.255 37.500 0.00 0.00 0.00 3.71
100 101 5.888412 ACAATTTTCGTGCAATGTTTCTC 57.112 34.783 0.00 0.00 0.00 2.87
101 102 5.402270 GCTACAATTTTCGTGCAATGTTTCT 59.598 36.000 0.00 0.00 0.00 2.52
102 103 5.174761 TGCTACAATTTTCGTGCAATGTTTC 59.825 36.000 0.00 0.00 0.00 2.78
103 104 5.046529 TGCTACAATTTTCGTGCAATGTTT 58.953 33.333 0.00 0.00 0.00 2.83
104 105 4.615949 TGCTACAATTTTCGTGCAATGTT 58.384 34.783 0.00 0.00 0.00 2.71
105 106 4.235939 TGCTACAATTTTCGTGCAATGT 57.764 36.364 0.00 0.00 0.00 2.71
106 107 5.097529 AGATGCTACAATTTTCGTGCAATG 58.902 37.500 0.00 0.00 34.07 2.82
107 108 5.314923 AGATGCTACAATTTTCGTGCAAT 57.685 34.783 0.00 0.00 34.07 3.56
108 109 4.764679 AGATGCTACAATTTTCGTGCAA 57.235 36.364 0.00 0.00 34.07 4.08
109 110 4.764679 AAGATGCTACAATTTTCGTGCA 57.235 36.364 0.00 0.00 34.88 4.57
110 111 7.740519 ATTAAAGATGCTACAATTTTCGTGC 57.259 32.000 0.00 0.00 0.00 5.34
111 112 9.128107 ACAATTAAAGATGCTACAATTTTCGTG 57.872 29.630 0.00 0.00 0.00 4.35
112 113 9.341899 GACAATTAAAGATGCTACAATTTTCGT 57.658 29.630 0.00 0.00 0.00 3.85
113 114 9.559958 AGACAATTAAAGATGCTACAATTTTCG 57.440 29.630 0.00 0.00 0.00 3.46
117 118 9.630098 CACAAGACAATTAAAGATGCTACAATT 57.370 29.630 0.00 0.00 0.00 2.32
118 119 8.796475 ACACAAGACAATTAAAGATGCTACAAT 58.204 29.630 0.00 0.00 0.00 2.71
119 120 8.075574 CACACAAGACAATTAAAGATGCTACAA 58.924 33.333 0.00 0.00 0.00 2.41
120 121 7.443879 TCACACAAGACAATTAAAGATGCTACA 59.556 33.333 0.00 0.00 0.00 2.74
121 122 7.806690 TCACACAAGACAATTAAAGATGCTAC 58.193 34.615 0.00 0.00 0.00 3.58
122 123 7.877612 TCTCACACAAGACAATTAAAGATGCTA 59.122 33.333 0.00 0.00 0.00 3.49
123 124 6.712095 TCTCACACAAGACAATTAAAGATGCT 59.288 34.615 0.00 0.00 0.00 3.79
124 125 6.798959 GTCTCACACAAGACAATTAAAGATGC 59.201 38.462 0.00 0.00 44.20 3.91
125 126 8.092521 AGTCTCACACAAGACAATTAAAGATG 57.907 34.615 6.79 0.00 46.65 2.90
126 127 8.682936 AAGTCTCACACAAGACAATTAAAGAT 57.317 30.769 6.79 0.00 46.65 2.40
127 128 9.607988 TTAAGTCTCACACAAGACAATTAAAGA 57.392 29.630 6.79 0.00 46.65 2.52
131 132 9.554395 TCATTTAAGTCTCACACAAGACAATTA 57.446 29.630 6.79 0.00 46.65 1.40
132 133 8.450578 TCATTTAAGTCTCACACAAGACAATT 57.549 30.769 6.79 0.00 46.65 2.32
133 134 7.933577 TCTCATTTAAGTCTCACACAAGACAAT 59.066 33.333 6.79 0.00 46.65 2.71
134 135 7.224753 GTCTCATTTAAGTCTCACACAAGACAA 59.775 37.037 6.79 0.00 46.65 3.18
135 136 6.701841 GTCTCATTTAAGTCTCACACAAGACA 59.298 38.462 6.79 0.00 46.65 3.41
136 137 6.701841 TGTCTCATTTAAGTCTCACACAAGAC 59.298 38.462 0.00 0.00 44.96 3.01
137 138 6.816136 TGTCTCATTTAAGTCTCACACAAGA 58.184 36.000 0.00 0.00 0.00 3.02
138 139 7.664082 ATGTCTCATTTAAGTCTCACACAAG 57.336 36.000 0.00 0.00 0.00 3.16
139 140 7.331934 GCTATGTCTCATTTAAGTCTCACACAA 59.668 37.037 0.00 0.00 0.00 3.33
140 141 6.813649 GCTATGTCTCATTTAAGTCTCACACA 59.186 38.462 0.00 0.00 0.00 3.72
141 142 7.038659 AGCTATGTCTCATTTAAGTCTCACAC 58.961 38.462 0.00 0.00 0.00 3.82
142 143 7.175347 AGCTATGTCTCATTTAAGTCTCACA 57.825 36.000 0.00 0.00 0.00 3.58
143 144 9.587772 TTTAGCTATGTCTCATTTAAGTCTCAC 57.412 33.333 0.00 0.00 0.00 3.51
156 157 8.458843 GGAGTAGATGAGATTTAGCTATGTCTC 58.541 40.741 20.75 20.75 38.03 3.36
157 158 7.120579 CGGAGTAGATGAGATTTAGCTATGTCT 59.879 40.741 7.83 7.83 0.00 3.41
158 159 7.094549 ACGGAGTAGATGAGATTTAGCTATGTC 60.095 40.741 0.00 0.00 41.94 3.06
159 160 6.717540 ACGGAGTAGATGAGATTTAGCTATGT 59.282 38.462 0.00 0.00 41.94 2.29
160 161 7.151999 ACGGAGTAGATGAGATTTAGCTATG 57.848 40.000 0.00 0.00 41.94 2.23
161 162 7.768807 AACGGAGTAGATGAGATTTAGCTAT 57.231 36.000 0.00 0.00 45.00 2.97
162 163 8.687292 TTAACGGAGTAGATGAGATTTAGCTA 57.313 34.615 0.00 0.00 45.00 3.32
163 164 7.584122 TTAACGGAGTAGATGAGATTTAGCT 57.416 36.000 0.00 0.00 45.00 3.32
164 165 8.082852 TCATTAACGGAGTAGATGAGATTTAGC 58.917 37.037 0.00 0.00 45.00 3.09
165 166 9.967346 TTCATTAACGGAGTAGATGAGATTTAG 57.033 33.333 0.00 0.00 45.00 1.85
170 171 9.967346 CTTTATTCATTAACGGAGTAGATGAGA 57.033 33.333 0.00 0.00 45.00 3.27
171 172 9.197694 CCTTTATTCATTAACGGAGTAGATGAG 57.802 37.037 0.00 0.00 45.00 2.90
172 173 8.920174 TCCTTTATTCATTAACGGAGTAGATGA 58.080 33.333 0.00 0.00 45.00 2.92
173 174 9.712305 ATCCTTTATTCATTAACGGAGTAGATG 57.288 33.333 0.00 0.00 45.00 2.90
179 180 8.565416 GGGTTAATCCTTTATTCATTAACGGAG 58.435 37.037 0.00 0.00 40.45 4.63
180 181 8.276477 AGGGTTAATCCTTTATTCATTAACGGA 58.724 33.333 0.00 0.00 41.15 4.69
212 213 8.550710 ACACCAACGCTATACTTACATTTTTA 57.449 30.769 0.00 0.00 0.00 1.52
263 265 8.099364 TGCAGACTAAAAAGAAATGTAGGAAG 57.901 34.615 0.00 0.00 0.00 3.46
264 266 8.635765 ATGCAGACTAAAAAGAAATGTAGGAA 57.364 30.769 0.00 0.00 0.00 3.36
265 267 9.905713 ATATGCAGACTAAAAAGAAATGTAGGA 57.094 29.630 0.00 0.00 0.00 2.94
276 278 9.997482 GACCGAATTTTATATGCAGACTAAAAA 57.003 29.630 12.21 7.43 30.60 1.94
277 279 9.168451 TGACCGAATTTTATATGCAGACTAAAA 57.832 29.630 11.15 11.15 0.00 1.52
278 280 8.725405 TGACCGAATTTTATATGCAGACTAAA 57.275 30.769 0.00 0.00 0.00 1.85
279 281 8.725405 TTGACCGAATTTTATATGCAGACTAA 57.275 30.769 0.00 0.00 0.00 2.24
280 282 8.725405 TTTGACCGAATTTTATATGCAGACTA 57.275 30.769 0.00 0.00 0.00 2.59
281 283 7.624360 TTTGACCGAATTTTATATGCAGACT 57.376 32.000 0.00 0.00 0.00 3.24
282 284 8.856490 ATTTTGACCGAATTTTATATGCAGAC 57.144 30.769 0.00 0.00 0.00 3.51
283 285 8.681806 TGATTTTGACCGAATTTTATATGCAGA 58.318 29.630 0.00 0.00 0.00 4.26
284 286 8.854979 TGATTTTGACCGAATTTTATATGCAG 57.145 30.769 0.00 0.00 0.00 4.41
285 287 9.645059 TTTGATTTTGACCGAATTTTATATGCA 57.355 25.926 0.00 0.00 0.00 3.96
291 293 8.286097 GCCAAATTTGATTTTGACCGAATTTTA 58.714 29.630 19.86 0.00 38.58 1.52
292 294 7.138081 GCCAAATTTGATTTTGACCGAATTTT 58.862 30.769 19.86 0.00 38.58 1.82
293 295 6.261826 TGCCAAATTTGATTTTGACCGAATTT 59.738 30.769 19.86 0.00 38.58 1.82
294 296 5.762218 TGCCAAATTTGATTTTGACCGAATT 59.238 32.000 19.86 0.00 38.58 2.17
295 297 5.303971 TGCCAAATTTGATTTTGACCGAAT 58.696 33.333 19.86 0.00 38.58 3.34
296 298 4.697514 TGCCAAATTTGATTTTGACCGAA 58.302 34.783 19.86 0.00 38.58 4.30
297 299 4.327982 TGCCAAATTTGATTTTGACCGA 57.672 36.364 19.86 0.00 38.58 4.69
298 300 5.007528 ACTTTGCCAAATTTGATTTTGACCG 59.992 36.000 19.86 0.58 38.58 4.79
299 301 6.375945 ACTTTGCCAAATTTGATTTTGACC 57.624 33.333 19.86 0.00 38.58 4.02
300 302 7.967303 TCAAACTTTGCCAAATTTGATTTTGAC 59.033 29.630 19.86 1.04 38.58 3.18
301 303 7.967303 GTCAAACTTTGCCAAATTTGATTTTGA 59.033 29.630 19.86 16.23 41.64 2.69
302 304 7.969508 AGTCAAACTTTGCCAAATTTGATTTTG 59.030 29.630 19.86 14.50 41.64 2.44
303 305 8.054152 AGTCAAACTTTGCCAAATTTGATTTT 57.946 26.923 19.86 3.80 41.64 1.82
304 306 7.628769 AGTCAAACTTTGCCAAATTTGATTT 57.371 28.000 19.86 13.86 41.64 2.17
305 307 8.611757 GTTAGTCAAACTTTGCCAAATTTGATT 58.388 29.630 19.86 19.03 41.64 2.57
306 308 7.986889 AGTTAGTCAAACTTTGCCAAATTTGAT 59.013 29.630 19.86 15.02 46.61 2.57
307 309 7.327214 AGTTAGTCAAACTTTGCCAAATTTGA 58.673 30.769 19.86 16.66 46.61 2.69
308 310 7.538303 AGTTAGTCAAACTTTGCCAAATTTG 57.462 32.000 11.40 11.40 46.61 2.32
361 363 9.346005 TGATGCATCTAACACTATTGATTTCAT 57.654 29.630 26.32 0.00 0.00 2.57
362 364 8.735692 TGATGCATCTAACACTATTGATTTCA 57.264 30.769 26.32 0.00 0.00 2.69
363 365 8.288208 CCTGATGCATCTAACACTATTGATTTC 58.712 37.037 26.32 0.00 0.00 2.17
364 366 7.994911 TCCTGATGCATCTAACACTATTGATTT 59.005 33.333 26.32 0.00 0.00 2.17
365 367 7.512130 TCCTGATGCATCTAACACTATTGATT 58.488 34.615 26.32 0.00 0.00 2.57
366 368 7.071069 TCCTGATGCATCTAACACTATTGAT 57.929 36.000 26.32 0.00 0.00 2.57
367 369 6.484364 TCCTGATGCATCTAACACTATTGA 57.516 37.500 26.32 1.69 0.00 2.57
368 370 7.558161 TTTCCTGATGCATCTAACACTATTG 57.442 36.000 26.32 4.24 0.00 1.90
369 371 8.757982 AATTTCCTGATGCATCTAACACTATT 57.242 30.769 26.32 13.88 0.00 1.73
370 372 9.851686 TTAATTTCCTGATGCATCTAACACTAT 57.148 29.630 26.32 9.99 0.00 2.12
371 373 9.851686 ATTAATTTCCTGATGCATCTAACACTA 57.148 29.630 26.32 4.41 0.00 2.74
372 374 8.757982 ATTAATTTCCTGATGCATCTAACACT 57.242 30.769 26.32 9.08 0.00 3.55
373 375 9.807649 AAATTAATTTCCTGATGCATCTAACAC 57.192 29.630 26.32 0.82 0.00 3.32
378 380 8.533657 TGTGAAAATTAATTTCCTGATGCATCT 58.466 29.630 26.32 7.85 45.67 2.90
379 381 8.598075 GTGTGAAAATTAATTTCCTGATGCATC 58.402 33.333 20.14 20.14 45.67 3.91
380 382 7.550196 GGTGTGAAAATTAATTTCCTGATGCAT 59.450 33.333 13.68 0.00 45.67 3.96
381 383 6.873076 GGTGTGAAAATTAATTTCCTGATGCA 59.127 34.615 13.68 0.00 45.67 3.96
382 384 6.873076 TGGTGTGAAAATTAATTTCCTGATGC 59.127 34.615 13.68 2.63 45.67 3.91
398 400 9.899661 ACAATACTAAAGCTATATGGTGTGAAA 57.100 29.630 0.00 0.00 0.00 2.69
399 401 9.325198 CACAATACTAAAGCTATATGGTGTGAA 57.675 33.333 7.95 0.00 34.78 3.18
400 402 7.931407 CCACAATACTAAAGCTATATGGTGTGA 59.069 37.037 12.97 0.00 34.78 3.58
401 403 7.931407 TCCACAATACTAAAGCTATATGGTGTG 59.069 37.037 11.13 9.25 31.00 3.82
402 404 8.029782 TCCACAATACTAAAGCTATATGGTGT 57.970 34.615 11.13 0.00 31.00 4.16
403 405 8.939929 CATCCACAATACTAAAGCTATATGGTG 58.060 37.037 0.00 0.00 32.24 4.17
404 406 8.660435 ACATCCACAATACTAAAGCTATATGGT 58.340 33.333 0.00 0.00 0.00 3.55
405 407 9.507329 AACATCCACAATACTAAAGCTATATGG 57.493 33.333 0.00 0.00 0.00 2.74
411 413 9.632638 AATATCAACATCCACAATACTAAAGCT 57.367 29.630 0.00 0.00 0.00 3.74
458 460 7.562135 TGGTCTAAGTCAAACTTTGTAGAGTT 58.438 34.615 1.44 0.00 39.51 3.01
459 461 7.120923 TGGTCTAAGTCAAACTTTGTAGAGT 57.879 36.000 1.44 0.00 39.51 3.24
460 462 8.433421 TTTGGTCTAAGTCAAACTTTGTAGAG 57.567 34.615 1.44 0.00 39.51 2.43
461 463 8.974060 ATTTGGTCTAAGTCAAACTTTGTAGA 57.026 30.769 1.44 0.00 39.51 2.59
472 474 9.679661 TCTGCATATAAAATTTGGTCTAAGTCA 57.320 29.630 0.00 0.00 0.00 3.41
473 475 9.937175 GTCTGCATATAAAATTTGGTCTAAGTC 57.063 33.333 0.00 0.00 0.00 3.01
474 476 9.686683 AGTCTGCATATAAAATTTGGTCTAAGT 57.313 29.630 0.00 0.00 0.00 2.24
489 491 9.383519 CCTCTGTTTCTTTTTAGTCTGCATATA 57.616 33.333 0.00 0.00 0.00 0.86
490 492 8.103305 TCCTCTGTTTCTTTTTAGTCTGCATAT 58.897 33.333 0.00 0.00 0.00 1.78
491 493 7.450074 TCCTCTGTTTCTTTTTAGTCTGCATA 58.550 34.615 0.00 0.00 0.00 3.14
492 494 6.299141 TCCTCTGTTTCTTTTTAGTCTGCAT 58.701 36.000 0.00 0.00 0.00 3.96
493 495 5.680619 TCCTCTGTTTCTTTTTAGTCTGCA 58.319 37.500 0.00 0.00 0.00 4.41
494 496 6.619801 TTCCTCTGTTTCTTTTTAGTCTGC 57.380 37.500 0.00 0.00 0.00 4.26
695 704 4.317291 GTCGATTTGTGAAATTGCGTGTAC 59.683 41.667 0.00 0.00 33.19 2.90
793 814 0.878086 GCTAGCTCAGGGCAATCGAC 60.878 60.000 7.70 0.00 44.79 4.20
819 840 1.203001 ACCGATTGGCCTTTTTCTGGA 60.203 47.619 3.32 0.00 39.70 3.86
838 859 4.837896 TGGTCATCGATCTGATACTGAC 57.162 45.455 13.92 13.92 34.83 3.51
887 909 6.498651 CACTGATCTGGAGGGTATTTATAGGT 59.501 42.308 4.49 0.00 0.00 3.08
910 932 4.142160 TGACAGTGAGTGAGTATATGGCAC 60.142 45.833 0.00 0.00 0.00 5.01
929 951 4.981806 AGTTTGCTTTAGCTTTGTGACA 57.018 36.364 0.00 0.00 42.66 3.58
995 1036 2.362760 TGGATGCCGCCATTGCTT 60.363 55.556 0.00 0.00 31.66 3.91
1386 3163 1.678123 GCCTCGATGGATGGATGGATG 60.678 57.143 5.24 0.00 38.35 3.51
1390 3167 1.002773 TGATGCCTCGATGGATGGATG 59.997 52.381 0.00 0.00 38.35 3.51
1391 3168 1.278413 CTGATGCCTCGATGGATGGAT 59.722 52.381 0.00 0.00 38.35 3.41
1392 3169 0.683412 CTGATGCCTCGATGGATGGA 59.317 55.000 0.00 0.00 38.35 3.41
1393 3170 0.954449 GCTGATGCCTCGATGGATGG 60.954 60.000 0.00 0.00 38.35 3.51
1394 3171 2.541288 GCTGATGCCTCGATGGATG 58.459 57.895 0.00 0.00 38.35 3.51
1431 3208 1.130411 CACGTACACGCACATGCAG 59.870 57.895 4.49 0.00 44.43 4.41
1455 3260 4.966965 TGTTGATAACCAAAACACACGT 57.033 36.364 0.00 0.00 36.36 4.49
1511 3758 9.410556 CAGTGATTTTTATTCGAGGAAAATGTT 57.589 29.630 15.58 3.65 34.22 2.71
1555 4692 4.865925 CGAATAAACTGACCGTGACCATAA 59.134 41.667 0.00 0.00 0.00 1.90
1569 4706 4.499183 CTTCCAGAGACTGCGAATAAACT 58.501 43.478 0.00 0.00 0.00 2.66
1592 4738 5.343058 GCCTATAATTAAACGTGCATGCATG 59.657 40.000 33.18 33.18 38.78 4.06
1594 4740 4.261405 GGCCTATAATTAAACGTGCATGCA 60.261 41.667 18.46 18.46 0.00 3.96
1656 6365 2.604686 AAGAGAGCACCCTCCGCA 60.605 61.111 0.00 0.00 38.96 5.69
1666 6375 4.070552 ACCGGCCACGAAGAGAGC 62.071 66.667 0.00 0.00 44.60 4.09
1667 6376 2.125912 CACCGGCCACGAAGAGAG 60.126 66.667 0.00 0.00 44.60 3.20
1669 6378 2.125912 CTCACCGGCCACGAAGAG 60.126 66.667 0.00 0.00 44.60 2.85


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

AutoCloner maintained by Alex Coulton.