Multiple sequence alignment - TraesCS1D01G307400

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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 TraesCS1D01G307400 chr1D 100.000 4053 0 0 1 4053 403727547 403723495 0.000000e+00 7485
1 TraesCS1D01G307400 chr1D 92.701 137 10 0 54 190 411276769 411276905 8.890000e-47 198
2 TraesCS1D01G307400 chr1A 87.661 2488 146 77 182 2550 499446249 499443804 0.000000e+00 2745
3 TraesCS1D01G307400 chr1A 94.668 844 29 5 2436 3270 499443803 499442967 0.000000e+00 1295
4 TraesCS1D01G307400 chr1A 86.875 800 55 22 3268 4051 499442905 499442140 0.000000e+00 850
5 TraesCS1D01G307400 chr1A 84.417 892 85 31 891 1731 584982887 584981999 0.000000e+00 828
6 TraesCS1D01G307400 chr1B 85.412 1467 119 49 336 1722 543090040 543088589 0.000000e+00 1435
7 TraesCS1D01G307400 chr1B 90.418 814 43 13 2502 3283 543086577 543085767 0.000000e+00 1038
8 TraesCS1D01G307400 chr1B 90.000 750 40 14 3329 4053 543085762 543085023 0.000000e+00 937
9 TraesCS1D01G307400 chr1B 88.830 761 64 11 1717 2464 543087329 543086577 0.000000e+00 915
10 TraesCS1D01G307400 chr1B 93.333 135 9 0 56 190 252161795 252161661 2.470000e-47 200
11 TraesCS1D01G307400 chr1B 93.333 135 9 0 56 190 642955625 642955759 2.470000e-47 200
12 TraesCS1D01G307400 chr1B 82.018 228 28 8 437 652 543177828 543177602 8.950000e-42 182
13 TraesCS1D01G307400 chr6D 88.465 1205 90 27 1236 2415 454304794 454303614 0.000000e+00 1410
14 TraesCS1D01G307400 chr2D 88.337 1209 94 24 1236 2415 312028954 312030144 0.000000e+00 1408
15 TraesCS1D01G307400 chr3D 88.007 1209 97 24 1236 2415 67534304 67535493 0.000000e+00 1386
16 TraesCS1D01G307400 chr3D 92.806 139 6 3 54 190 466963087 466963223 8.890000e-47 198
17 TraesCS1D01G307400 chr7A 87.906 893 83 11 1531 2415 333610272 333609397 0.000000e+00 1027
18 TraesCS1D01G307400 chr7A 83.507 576 80 10 918 1480 633798894 633799467 1.290000e-144 523
19 TraesCS1D01G307400 chr6A 84.804 895 78 30 891 1732 33174454 33173565 0.000000e+00 846
20 TraesCS1D01G307400 chr4A 82.646 582 68 16 918 1483 623983260 623982696 6.090000e-133 484
21 TraesCS1D01G307400 chr4A 91.667 180 11 2 1636 1811 623982616 623982437 3.130000e-61 246
22 TraesCS1D01G307400 chr4D 93.431 137 9 0 54 190 416431720 416431856 1.910000e-48 204
23 TraesCS1D01G307400 chr4D 90.476 147 12 2 56 201 465765779 465765924 4.130000e-45 193
24 TraesCS1D01G307400 chr6B 93.333 135 9 0 56 190 688594719 688594585 2.470000e-47 200
25 TraesCS1D01G307400 chr6B 89.172 157 12 4 56 211 163822761 163822913 1.490000e-44 191
26 TraesCS1D01G307400 chr5B 93.333 135 9 0 56 190 320385772 320385638 2.470000e-47 200


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 TraesCS1D01G307400 chr1D 403723495 403727547 4052 True 7485.00 7485 100.000000 1 4053 1 chr1D.!!$R1 4052
1 TraesCS1D01G307400 chr1A 499442140 499446249 4109 True 1630.00 2745 89.734667 182 4051 3 chr1A.!!$R2 3869
2 TraesCS1D01G307400 chr1A 584981999 584982887 888 True 828.00 828 84.417000 891 1731 1 chr1A.!!$R1 840
3 TraesCS1D01G307400 chr1B 543085023 543090040 5017 True 1081.25 1435 88.665000 336 4053 4 chr1B.!!$R3 3717
4 TraesCS1D01G307400 chr6D 454303614 454304794 1180 True 1410.00 1410 88.465000 1236 2415 1 chr6D.!!$R1 1179
5 TraesCS1D01G307400 chr2D 312028954 312030144 1190 False 1408.00 1408 88.337000 1236 2415 1 chr2D.!!$F1 1179
6 TraesCS1D01G307400 chr3D 67534304 67535493 1189 False 1386.00 1386 88.007000 1236 2415 1 chr3D.!!$F1 1179
7 TraesCS1D01G307400 chr7A 333609397 333610272 875 True 1027.00 1027 87.906000 1531 2415 1 chr7A.!!$R1 884
8 TraesCS1D01G307400 chr7A 633798894 633799467 573 False 523.00 523 83.507000 918 1480 1 chr7A.!!$F1 562
9 TraesCS1D01G307400 chr6A 33173565 33174454 889 True 846.00 846 84.804000 891 1732 1 chr6A.!!$R1 841
10 TraesCS1D01G307400 chr4A 623982437 623983260 823 True 365.00 484 87.156500 918 1811 2 chr4A.!!$R1 893

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
25 26 0.036483 TCTAGCGGAATTGCACAGCA 60.036 50.0 0.00 0.00 37.31 4.41 F
280 282 0.173708 GGACGCAACTACCTCCTCTG 59.826 60.0 0.00 0.00 0.00 3.35 F
281 283 0.173708 GACGCAACTACCTCCTCTGG 59.826 60.0 0.00 0.00 0.00 3.86 F
422 431 0.179001 AGTTTGTTTGAGGGGGTCGG 60.179 55.0 0.00 0.00 0.00 4.79 F
619 655 0.299300 CTCACTACGACGAGCGAGAG 59.701 60.0 0.00 8.03 44.57 3.20 F
2127 3593 0.666913 CAGCTGTGCTTGGATATGCC 59.333 55.0 5.25 0.00 36.40 4.40 F
2696 4283 0.314302 GCTGAAGCATCATCCATGGC 59.686 55.0 6.96 0.00 41.59 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1283 0.530288 GAGCGGGGCAAAAGCAAATA 59.470 50.000 0.00 0.00 0.00 1.40 R
2150 3616 0.790814 GTTGTACAAGAGCGAGCACC 59.209 55.000 8.98 0.00 0.00 5.01 R
2256 3732 2.023673 TCGGCTGCCCAAGAAATATTG 58.976 47.619 14.12 0.00 0.00 1.90 R
2371 3851 2.025887 ACTAAATCTGGAAGGGCCACAG 60.026 50.000 6.18 11.48 43.33 3.66 R
2468 3953 4.656112 ACTCTAGTGGCTGCACCTATAAAT 59.344 41.667 0.50 0.00 40.22 1.40 R
2965 4580 0.115152 TCCCAGAACTCTCTGCTCCA 59.885 55.000 0.00 0.00 46.76 3.86 R
3696 5405 2.420372 GCTCGGTTCCTGAATTTTCTCC 59.580 50.000 0.00 0.00 0.00 3.71 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
20 21 3.165058 CAGTAGTCTAGCGGAATTGCA 57.835 47.619 0.00 0.00 37.31 4.08
21 22 2.860735 CAGTAGTCTAGCGGAATTGCAC 59.139 50.000 0.00 0.00 37.31 4.57
22 23 2.496070 AGTAGTCTAGCGGAATTGCACA 59.504 45.455 0.00 0.00 37.31 4.57
23 24 2.015736 AGTCTAGCGGAATTGCACAG 57.984 50.000 0.00 0.00 37.31 3.66
24 25 0.375106 GTCTAGCGGAATTGCACAGC 59.625 55.000 0.00 0.00 37.31 4.40
25 26 0.036483 TCTAGCGGAATTGCACAGCA 60.036 50.000 0.00 0.00 37.31 4.41
34 35 2.845019 TTGCACAGCAAGAGATCCG 58.155 52.632 0.00 0.00 43.99 4.18
35 36 1.300971 TTGCACAGCAAGAGATCCGC 61.301 55.000 0.00 0.00 43.99 5.54
36 37 1.742880 GCACAGCAAGAGATCCGCA 60.743 57.895 0.00 0.00 0.00 5.69
37 38 1.094073 GCACAGCAAGAGATCCGCAT 61.094 55.000 0.00 0.00 0.00 4.73
38 39 0.935898 CACAGCAAGAGATCCGCATC 59.064 55.000 0.00 0.00 0.00 3.91
39 40 0.829333 ACAGCAAGAGATCCGCATCT 59.171 50.000 0.00 0.00 42.59 2.90
40 41 1.209019 ACAGCAAGAGATCCGCATCTT 59.791 47.619 0.00 0.00 39.71 2.40
41 42 2.286872 CAGCAAGAGATCCGCATCTTT 58.713 47.619 0.00 0.00 39.71 2.52
42 43 2.681848 CAGCAAGAGATCCGCATCTTTT 59.318 45.455 0.00 0.00 39.71 2.27
43 44 3.873361 CAGCAAGAGATCCGCATCTTTTA 59.127 43.478 0.00 0.00 39.71 1.52
44 45 4.514441 CAGCAAGAGATCCGCATCTTTTAT 59.486 41.667 0.00 0.00 39.71 1.40
45 46 5.008415 CAGCAAGAGATCCGCATCTTTTATT 59.992 40.000 0.00 0.00 39.71 1.40
46 47 6.203530 CAGCAAGAGATCCGCATCTTTTATTA 59.796 38.462 0.00 0.00 39.71 0.98
47 48 6.939163 AGCAAGAGATCCGCATCTTTTATTAT 59.061 34.615 0.00 0.00 39.71 1.28
48 49 7.020010 GCAAGAGATCCGCATCTTTTATTATG 58.980 38.462 0.00 0.00 39.71 1.90
49 50 6.734104 AGAGATCCGCATCTTTTATTATGC 57.266 37.500 0.00 0.00 39.71 3.14
50 51 6.471146 AGAGATCCGCATCTTTTATTATGCT 58.529 36.000 0.00 0.00 45.03 3.79
51 52 6.370994 AGAGATCCGCATCTTTTATTATGCTG 59.629 38.462 0.00 0.00 45.03 4.41
52 53 4.488126 TCCGCATCTTTTATTATGCTGC 57.512 40.909 5.83 0.00 45.03 5.25
53 54 4.136796 TCCGCATCTTTTATTATGCTGCT 58.863 39.130 0.00 0.00 45.03 4.24
54 55 5.304778 TCCGCATCTTTTATTATGCTGCTA 58.695 37.500 0.00 0.00 45.03 3.49
55 56 5.762711 TCCGCATCTTTTATTATGCTGCTAA 59.237 36.000 0.00 0.00 45.03 3.09
56 57 6.430925 TCCGCATCTTTTATTATGCTGCTAAT 59.569 34.615 0.00 5.53 45.03 1.73
57 58 7.606073 TCCGCATCTTTTATTATGCTGCTAATA 59.394 33.333 0.00 4.61 45.03 0.98
58 59 8.236586 CCGCATCTTTTATTATGCTGCTAATAA 58.763 33.333 14.61 14.61 45.03 1.40
59 60 9.611284 CGCATCTTTTATTATGCTGCTAATAAA 57.389 29.630 20.52 20.52 45.03 1.40
90 91 9.683069 ATTTTCATCATATGCCTATTTCGTTTC 57.317 29.630 0.00 0.00 0.00 2.78
91 92 7.800155 TTCATCATATGCCTATTTCGTTTCA 57.200 32.000 0.00 0.00 0.00 2.69
92 93 7.189693 TCATCATATGCCTATTTCGTTTCAC 57.810 36.000 0.00 0.00 0.00 3.18
93 94 6.765512 TCATCATATGCCTATTTCGTTTCACA 59.234 34.615 0.00 0.00 0.00 3.58
94 95 6.993786 TCATATGCCTATTTCGTTTCACAA 57.006 33.333 0.00 0.00 0.00 3.33
95 96 7.384439 TCATATGCCTATTTCGTTTCACAAA 57.616 32.000 0.00 0.00 0.00 2.83
96 97 7.247728 TCATATGCCTATTTCGTTTCACAAAC 58.752 34.615 0.00 0.00 38.02 2.93
97 98 4.902443 TGCCTATTTCGTTTCACAAACA 57.098 36.364 0.40 0.00 41.44 2.83
98 99 5.446143 TGCCTATTTCGTTTCACAAACAT 57.554 34.783 0.40 0.00 41.44 2.71
99 100 5.457140 TGCCTATTTCGTTTCACAAACATC 58.543 37.500 0.40 0.00 41.44 3.06
100 101 4.553429 GCCTATTTCGTTTCACAAACATCG 59.447 41.667 0.40 0.00 41.44 3.84
101 102 5.615984 GCCTATTTCGTTTCACAAACATCGA 60.616 40.000 0.00 0.00 41.44 3.59
102 103 6.542852 CCTATTTCGTTTCACAAACATCGAT 58.457 36.000 0.00 0.00 41.44 3.59
103 104 7.675403 GCCTATTTCGTTTCACAAACATCGATA 60.675 37.037 0.00 0.00 41.44 2.92
104 105 8.335356 CCTATTTCGTTTCACAAACATCGATAT 58.665 33.333 0.00 0.00 41.44 1.63
112 113 9.885743 GTTTCACAAACATCGATATATTTTTGC 57.114 29.630 0.00 0.00 41.04 3.68
113 114 9.631452 TTTCACAAACATCGATATATTTTTGCA 57.369 25.926 0.00 0.00 0.00 4.08
114 115 8.613613 TCACAAACATCGATATATTTTTGCAC 57.386 30.769 0.00 0.00 0.00 4.57
115 116 8.239998 TCACAAACATCGATATATTTTTGCACA 58.760 29.630 0.00 0.00 0.00 4.57
116 117 8.858186 CACAAACATCGATATATTTTTGCACAA 58.142 29.630 0.00 0.00 0.00 3.33
117 118 9.416794 ACAAACATCGATATATTTTTGCACAAA 57.583 25.926 0.00 0.00 0.00 2.83
118 119 9.674208 CAAACATCGATATATTTTTGCACAAAC 57.326 29.630 0.00 0.00 0.00 2.93
119 120 9.638239 AAACATCGATATATTTTTGCACAAACT 57.362 25.926 0.00 0.00 0.00 2.66
120 121 8.841444 ACATCGATATATTTTTGCACAAACTC 57.159 30.769 0.00 0.00 0.00 3.01
121 122 7.639850 ACATCGATATATTTTTGCACAAACTCG 59.360 33.333 0.00 7.44 0.00 4.18
122 123 6.482835 TCGATATATTTTTGCACAAACTCGG 58.517 36.000 15.38 1.49 0.00 4.63
123 124 6.092944 TCGATATATTTTTGCACAAACTCGGT 59.907 34.615 15.38 0.00 0.00 4.69
124 125 6.410914 CGATATATTTTTGCACAAACTCGGTC 59.589 38.462 0.00 0.00 0.00 4.79
125 126 3.791973 ATTTTTGCACAAACTCGGTCA 57.208 38.095 0.00 0.00 0.00 4.02
126 127 3.577649 TTTTTGCACAAACTCGGTCAA 57.422 38.095 0.00 0.00 0.00 3.18
127 128 3.577649 TTTTGCACAAACTCGGTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
128 129 2.553079 TTGCACAAACTCGGTCAAAC 57.447 45.000 0.00 0.00 0.00 2.93
129 130 0.375454 TGCACAAACTCGGTCAAACG 59.625 50.000 0.00 0.00 0.00 3.60
130 131 0.375803 GCACAAACTCGGTCAAACGT 59.624 50.000 0.00 0.00 34.94 3.99
131 132 1.202098 GCACAAACTCGGTCAAACGTT 60.202 47.619 0.00 0.00 34.94 3.99
132 133 2.030701 GCACAAACTCGGTCAAACGTTA 59.969 45.455 0.00 0.00 34.94 3.18
133 134 3.303526 GCACAAACTCGGTCAAACGTTAT 60.304 43.478 0.00 0.00 34.94 1.89
134 135 4.208355 CACAAACTCGGTCAAACGTTATG 58.792 43.478 0.00 2.59 34.94 1.90
135 136 4.025563 CACAAACTCGGTCAAACGTTATGA 60.026 41.667 0.00 5.15 34.94 2.15
136 137 4.753107 ACAAACTCGGTCAAACGTTATGAT 59.247 37.500 0.00 0.00 34.94 2.45
137 138 5.927689 ACAAACTCGGTCAAACGTTATGATA 59.072 36.000 0.00 0.00 34.94 2.15
138 139 6.090358 ACAAACTCGGTCAAACGTTATGATAG 59.910 38.462 0.00 9.22 34.94 2.08
139 140 5.320549 ACTCGGTCAAACGTTATGATAGT 57.679 39.130 0.00 9.75 34.94 2.12
140 141 5.717119 ACTCGGTCAAACGTTATGATAGTT 58.283 37.500 0.00 0.00 34.94 2.24
141 142 6.161381 ACTCGGTCAAACGTTATGATAGTTT 58.839 36.000 0.00 0.00 38.46 2.66
148 149 6.980051 AAACGTTATGATAGTTTGACCCTC 57.020 37.500 0.00 0.00 36.81 4.30
149 150 5.019785 ACGTTATGATAGTTTGACCCTCC 57.980 43.478 0.00 0.00 0.00 4.30
150 151 4.468510 ACGTTATGATAGTTTGACCCTCCA 59.531 41.667 0.00 0.00 0.00 3.86
151 152 5.046159 ACGTTATGATAGTTTGACCCTCCAA 60.046 40.000 0.00 0.00 0.00 3.53
152 153 5.293569 CGTTATGATAGTTTGACCCTCCAAC 59.706 44.000 0.00 0.00 0.00 3.77
153 154 4.927267 ATGATAGTTTGACCCTCCAACA 57.073 40.909 0.00 0.00 0.00 3.33
154 155 4.715534 TGATAGTTTGACCCTCCAACAA 57.284 40.909 0.00 0.00 0.00 2.83
155 156 5.055265 TGATAGTTTGACCCTCCAACAAA 57.945 39.130 0.00 0.00 0.00 2.83
156 157 5.070001 TGATAGTTTGACCCTCCAACAAAG 58.930 41.667 0.00 0.00 34.86 2.77
157 158 3.382083 AGTTTGACCCTCCAACAAAGT 57.618 42.857 0.00 0.00 34.86 2.66
158 159 3.708451 AGTTTGACCCTCCAACAAAGTT 58.292 40.909 0.00 0.00 34.79 2.66
159 160 3.447229 AGTTTGACCCTCCAACAAAGTTG 59.553 43.478 3.00 3.00 34.79 3.16
160 161 2.065899 TGACCCTCCAACAAAGTTGG 57.934 50.000 20.09 20.09 40.87 3.77
161 162 1.566703 TGACCCTCCAACAAAGTTGGA 59.433 47.619 25.17 25.17 45.61 3.53
162 163 2.024846 TGACCCTCCAACAAAGTTGGAA 60.025 45.455 26.25 12.88 46.85 3.53
163 164 2.623416 GACCCTCCAACAAAGTTGGAAG 59.377 50.000 26.25 21.51 46.85 3.46
164 165 2.024369 ACCCTCCAACAAAGTTGGAAGT 60.024 45.455 26.25 22.95 46.85 3.01
165 166 3.203487 ACCCTCCAACAAAGTTGGAAGTA 59.797 43.478 26.25 9.67 46.85 2.24
166 167 3.568430 CCCTCCAACAAAGTTGGAAGTAC 59.432 47.826 26.25 0.00 46.85 2.73
167 168 4.204012 CCTCCAACAAAGTTGGAAGTACA 58.796 43.478 26.25 8.75 46.85 2.90
168 169 4.036380 CCTCCAACAAAGTTGGAAGTACAC 59.964 45.833 26.25 0.00 46.85 2.90
169 170 4.850680 TCCAACAAAGTTGGAAGTACACT 58.149 39.130 24.83 0.00 44.90 3.55
170 171 4.879545 TCCAACAAAGTTGGAAGTACACTC 59.120 41.667 24.83 0.00 44.90 3.51
171 172 4.881850 CCAACAAAGTTGGAAGTACACTCT 59.118 41.667 21.24 0.00 42.06 3.24
172 173 5.357032 CCAACAAAGTTGGAAGTACACTCTT 59.643 40.000 21.24 0.00 42.06 2.85
173 174 6.127730 CCAACAAAGTTGGAAGTACACTCTTT 60.128 38.462 21.24 0.00 42.06 2.52
174 175 7.066525 CCAACAAAGTTGGAAGTACACTCTTTA 59.933 37.037 21.24 0.00 42.06 1.85
175 176 8.455682 CAACAAAGTTGGAAGTACACTCTTTAA 58.544 33.333 2.05 0.00 0.00 1.52
176 177 8.570068 ACAAAGTTGGAAGTACACTCTTTAAA 57.430 30.769 0.00 0.00 0.00 1.52
177 178 8.674607 ACAAAGTTGGAAGTACACTCTTTAAAG 58.325 33.333 9.04 9.04 0.00 1.85
178 179 8.889717 CAAAGTTGGAAGTACACTCTTTAAAGA 58.110 33.333 16.85 16.85 0.00 2.52
179 180 9.457436 AAAGTTGGAAGTACACTCTTTAAAGAA 57.543 29.630 18.25 1.42 34.03 2.52
180 181 8.434733 AGTTGGAAGTACACTCTTTAAAGAAC 57.565 34.615 18.25 13.23 34.03 3.01
181 182 7.224167 AGTTGGAAGTACACTCTTTAAAGAACG 59.776 37.037 18.25 13.97 34.03 3.95
182 183 5.987347 TGGAAGTACACTCTTTAAAGAACGG 59.013 40.000 18.25 12.59 34.03 4.44
183 184 6.183360 TGGAAGTACACTCTTTAAAGAACGGA 60.183 38.462 18.25 6.84 34.03 4.69
184 185 6.365518 GGAAGTACACTCTTTAAAGAACGGAG 59.634 42.308 18.25 9.21 34.03 4.63
185 186 5.780984 AGTACACTCTTTAAAGAACGGAGG 58.219 41.667 18.25 8.55 34.03 4.30
186 187 4.950205 ACACTCTTTAAAGAACGGAGGA 57.050 40.909 18.25 0.00 34.03 3.71
187 188 5.286267 ACACTCTTTAAAGAACGGAGGAA 57.714 39.130 18.25 0.00 34.03 3.36
188 189 5.298347 ACACTCTTTAAAGAACGGAGGAAG 58.702 41.667 18.25 6.57 34.03 3.46
189 190 5.163332 ACACTCTTTAAAGAACGGAGGAAGT 60.163 40.000 18.25 7.16 34.03 3.01
190 191 5.177696 CACTCTTTAAAGAACGGAGGAAGTG 59.822 44.000 18.25 14.43 34.03 3.16
270 272 1.736645 CGGAATCGTGGACGCAACT 60.737 57.895 0.00 0.00 39.60 3.16
280 282 0.173708 GGACGCAACTACCTCCTCTG 59.826 60.000 0.00 0.00 0.00 3.35
281 283 0.173708 GACGCAACTACCTCCTCTGG 59.826 60.000 0.00 0.00 0.00 3.86
282 284 0.251653 ACGCAACTACCTCCTCTGGA 60.252 55.000 0.00 0.00 0.00 3.86
284 286 1.482593 CGCAACTACCTCCTCTGGATT 59.517 52.381 0.00 0.00 0.00 3.01
285 287 2.093447 CGCAACTACCTCCTCTGGATTT 60.093 50.000 0.00 0.00 0.00 2.17
286 288 3.132289 CGCAACTACCTCCTCTGGATTTA 59.868 47.826 0.00 0.00 0.00 1.40
287 289 4.382685 CGCAACTACCTCCTCTGGATTTAA 60.383 45.833 0.00 0.00 0.00 1.52
288 290 5.497474 GCAACTACCTCCTCTGGATTTAAA 58.503 41.667 0.00 0.00 0.00 1.52
289 291 6.122964 GCAACTACCTCCTCTGGATTTAAAT 58.877 40.000 0.00 0.00 0.00 1.40
290 292 6.603599 GCAACTACCTCCTCTGGATTTAAATT 59.396 38.462 1.43 0.00 0.00 1.82
291 293 7.122799 GCAACTACCTCCTCTGGATTTAAATTT 59.877 37.037 1.43 0.00 0.00 1.82
292 294 8.678199 CAACTACCTCCTCTGGATTTAAATTTC 58.322 37.037 1.43 0.00 0.00 2.17
293 295 7.347252 ACTACCTCCTCTGGATTTAAATTTCC 58.653 38.462 1.43 1.45 0.00 3.13
294 296 6.152638 ACCTCCTCTGGATTTAAATTTCCA 57.847 37.500 9.63 9.63 39.70 3.53
397 406 1.013596 TTGTGCACCACTTCTTGACG 58.986 50.000 15.69 0.00 35.11 4.35
422 431 0.179001 AGTTTGTTTGAGGGGGTCGG 60.179 55.000 0.00 0.00 0.00 4.79
534 550 1.734707 GCCACAGCATCATCAACTTGC 60.735 52.381 0.00 0.00 39.53 4.01
538 554 1.063616 CAGCATCATCAACTTGCCTCG 59.936 52.381 0.00 0.00 37.07 4.63
594 628 3.612681 CACACAGGGTCGACGGGT 61.613 66.667 9.92 4.49 0.00 5.28
601 635 1.676967 GGGTCGACGGGTCACTACT 60.677 63.158 9.92 0.00 0.00 2.57
612 648 2.341257 GGTCACTACTCACTACGACGA 58.659 52.381 0.00 0.00 0.00 4.20
619 655 0.299300 CTCACTACGACGAGCGAGAG 59.701 60.000 0.00 8.03 44.57 3.20
779 846 2.257371 TCGCCGAGACAAACTCCG 59.743 61.111 0.00 0.00 42.18 4.63
867 939 1.743252 CCTTCTCTCTTGCGTGGGC 60.743 63.158 0.00 0.00 40.52 5.36
1062 1165 3.787001 GACCTCCGGGGAAGCCTG 61.787 72.222 0.37 0.00 38.76 4.85
1073 1176 3.378399 GAAGCCTGGAGGAGGTCGC 62.378 68.421 0.00 0.00 44.97 5.19
1174 1283 1.736681 GAATGCTTTCTCGCTTGCTCT 59.263 47.619 5.13 0.00 0.00 4.09
1483 1600 4.988716 TCCCCTCCACGCGACACT 62.989 66.667 15.93 0.00 0.00 3.55
1494 1637 2.476051 CGACACTGGAATGCGTGC 59.524 61.111 0.00 0.00 34.58 5.34
1732 1889 0.982852 TACTCATGTGCCTCCCCTGG 60.983 60.000 0.00 0.00 0.00 4.45
1770 3199 3.313526 AGGATGTGCATGATTTTAGCGTC 59.686 43.478 0.00 0.00 0.00 5.19
1903 3354 2.215196 TCACTTCCTGCAACCGTTTAC 58.785 47.619 0.00 0.00 0.00 2.01
2034 3500 1.603455 ACATGTTGGCCCCTTGACG 60.603 57.895 0.00 0.00 0.00 4.35
2127 3593 0.666913 CAGCTGTGCTTGGATATGCC 59.333 55.000 5.25 0.00 36.40 4.40
2150 3616 1.135689 GCATGTAAGTTTGTCTGCCCG 60.136 52.381 0.00 0.00 0.00 6.13
2271 3747 8.133024 AGATACAAAACAATATTTCTTGGGCA 57.867 30.769 6.10 0.00 0.00 5.36
2280 3758 0.887933 TTTCTTGGGCAGCCGATTTC 59.112 50.000 5.00 0.00 0.00 2.17
2371 3851 7.920151 TGCATTAGTTTGGAATACAATATGCAC 59.080 33.333 11.25 0.00 40.67 4.57
2401 3885 4.938226 CCTTCCAGATTTAGTGGTTCTCAC 59.062 45.833 0.00 0.00 46.39 3.51
2429 3914 6.611613 TCAAGCCTACATTATGATAGGAGG 57.388 41.667 18.35 9.71 40.53 4.30
2530 4116 5.176774 GCTTACCTTGTTAATTTTGTGTGGC 59.823 40.000 0.00 0.00 0.00 5.01
2696 4283 0.314302 GCTGAAGCATCATCCATGGC 59.686 55.000 6.96 0.00 41.59 4.40
2703 4290 1.752498 GCATCATCCATGGCTTCAACA 59.248 47.619 6.96 0.00 32.37 3.33
2852 4439 4.104086 ACAGTCTTGTATTCCATCTCCCA 58.896 43.478 0.00 0.00 35.25 4.37
2863 4478 1.207089 CCATCTCCCAGTTTGTCGCTA 59.793 52.381 0.00 0.00 0.00 4.26
2917 4532 0.882042 AAGACTGCTTGCTGTCCACG 60.882 55.000 22.67 0.00 34.02 4.94
2965 4580 3.604582 GGAGCAGCTCTTGAACTACATT 58.395 45.455 21.99 0.00 0.00 2.71
3079 4695 2.230266 TCGGTGATCATCGTGAGTTTGA 59.770 45.455 26.55 3.08 36.14 2.69
3080 4696 2.600420 CGGTGATCATCGTGAGTTTGAG 59.400 50.000 20.30 0.00 0.00 3.02
3107 4729 7.040409 TCGCATATGCTGTAGATATATGGTAGG 60.040 40.741 24.56 3.45 36.03 3.18
3157 4779 1.879380 TCTTTTGTGTGATTCCGCCTG 59.121 47.619 0.00 0.00 0.00 4.85
3166 4788 2.914777 GATTCCGCCTGCTCTCGCTT 62.915 60.000 0.00 0.00 36.97 4.68
3275 4963 8.734386 CATAAAAGCCTCTCCCATGTATATTTC 58.266 37.037 0.00 0.00 0.00 2.17
3290 4978 6.414732 TGTATATTTCTGAGGTTTCTGGGTG 58.585 40.000 0.00 0.00 0.00 4.61
3360 5053 5.634118 AGGTCATTGGACTCTGAAATTCAA 58.366 37.500 0.00 0.00 43.77 2.69
3364 5057 5.413833 TCATTGGACTCTGAAATTCAAGAGC 59.586 40.000 16.66 11.75 30.22 4.09
3376 5069 3.963428 TTCAAGAGCCAAGACCTACTC 57.037 47.619 0.00 0.00 0.00 2.59
3384 5077 2.623502 GCCAAGACCTACTCTGGACCTA 60.624 54.545 0.00 0.00 32.50 3.08
3395 5088 7.071321 ACCTACTCTGGACCTATTATTTGGAAG 59.929 40.741 0.00 0.00 0.00 3.46
3437 5133 4.227300 ACCCAGCATTACTCCAAACTCATA 59.773 41.667 0.00 0.00 0.00 2.15
3441 5137 6.769822 CCAGCATTACTCCAAACTCATAATCT 59.230 38.462 0.00 0.00 0.00 2.40
3472 5169 7.741027 CTATTTGAGCATGGATATCACAAGT 57.259 36.000 4.83 1.51 0.00 3.16
3474 5171 3.721035 TGAGCATGGATATCACAAGTCG 58.279 45.455 4.83 0.00 0.00 4.18
3520 5220 4.877823 TGCAGCCATCTAACTAACTTCATG 59.122 41.667 0.00 0.00 0.00 3.07
3536 5236 6.259550 ACTTCATGACTGGTTTAAGCATTC 57.740 37.500 7.42 7.42 0.00 2.67
3537 5237 5.769662 ACTTCATGACTGGTTTAAGCATTCA 59.230 36.000 16.97 16.97 39.11 2.57
3543 5243 9.669353 CATGACTGGTTTAAGCATTCATATTAC 57.331 33.333 22.82 0.00 41.81 1.89
3594 5296 9.117145 CATTATGTTGTCATGTGAACAACTTAC 57.883 33.333 22.26 5.08 42.78 2.34
3601 5303 6.259167 TGTCATGTGAACAACTTACTAACACC 59.741 38.462 0.00 0.00 0.00 4.16
3607 5309 4.942761 ACAACTTACTAACACCGGAGAA 57.057 40.909 9.46 0.00 0.00 2.87
3691 5393 7.384932 CCAATTAAAGAACCAACCTGATGTTTC 59.615 37.037 0.00 0.00 34.00 2.78
3696 5405 3.045601 ACCAACCTGATGTTTCGAGAG 57.954 47.619 0.00 0.00 34.00 3.20
3708 5417 6.369890 TGATGTTTCGAGAGGAGAAAATTCAG 59.630 38.462 0.00 0.00 39.03 3.02
3740 5449 3.181439 TGTTACCATCATGAACACCACCA 60.181 43.478 0.00 0.00 0.00 4.17
3926 5643 1.170290 ACAACGCGGGAAAGGGAAAG 61.170 55.000 12.47 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.860735 GTGCAATTCCGCTAGACTACTG 59.139 50.000 0.00 0.00 0.00 2.74
1 2 2.496070 TGTGCAATTCCGCTAGACTACT 59.504 45.455 0.00 0.00 0.00 2.57
2 3 2.860735 CTGTGCAATTCCGCTAGACTAC 59.139 50.000 0.00 0.00 0.00 2.73
3 4 2.738643 GCTGTGCAATTCCGCTAGACTA 60.739 50.000 0.00 0.00 0.00 2.59
4 5 2.009042 GCTGTGCAATTCCGCTAGACT 61.009 52.381 0.00 0.00 0.00 3.24
5 6 0.375106 GCTGTGCAATTCCGCTAGAC 59.625 55.000 0.00 0.00 0.00 2.59
6 7 0.036483 TGCTGTGCAATTCCGCTAGA 60.036 50.000 0.00 0.00 34.76 2.43
7 8 0.804364 TTGCTGTGCAATTCCGCTAG 59.196 50.000 0.45 0.00 43.99 3.42
8 9 2.939781 TTGCTGTGCAATTCCGCTA 58.060 47.368 0.45 0.00 43.99 4.26
9 10 3.762293 TTGCTGTGCAATTCCGCT 58.238 50.000 0.45 0.00 43.99 5.52
16 17 1.300971 GCGGATCTCTTGCTGTGCAA 61.301 55.000 4.87 4.87 46.80 4.08
17 18 1.742880 GCGGATCTCTTGCTGTGCA 60.743 57.895 0.00 0.00 36.47 4.57
18 19 1.094073 ATGCGGATCTCTTGCTGTGC 61.094 55.000 0.00 0.00 0.00 4.57
19 20 0.935898 GATGCGGATCTCTTGCTGTG 59.064 55.000 9.99 0.00 0.00 3.66
20 21 0.829333 AGATGCGGATCTCTTGCTGT 59.171 50.000 14.37 0.00 33.20 4.40
21 22 1.950828 AAGATGCGGATCTCTTGCTG 58.049 50.000 20.43 0.00 38.03 4.41
22 23 2.706339 AAAGATGCGGATCTCTTGCT 57.294 45.000 20.43 0.59 38.03 3.91
23 24 5.429957 AATAAAAGATGCGGATCTCTTGC 57.570 39.130 20.43 0.00 38.03 4.01
24 25 7.020010 GCATAATAAAAGATGCGGATCTCTTG 58.980 38.462 20.43 10.55 38.03 3.02
25 26 7.138692 GCATAATAAAAGATGCGGATCTCTT 57.861 36.000 20.43 15.22 38.03 2.85
26 27 6.734104 GCATAATAAAAGATGCGGATCTCT 57.266 37.500 20.43 12.62 38.03 3.10
64 65 9.683069 GAAACGAAATAGGCATATGATGAAAAT 57.317 29.630 6.97 0.00 0.00 1.82
65 66 8.681806 TGAAACGAAATAGGCATATGATGAAAA 58.318 29.630 6.97 0.00 0.00 2.29
66 67 8.128582 GTGAAACGAAATAGGCATATGATGAAA 58.871 33.333 6.97 0.00 0.00 2.69
67 68 7.281999 TGTGAAACGAAATAGGCATATGATGAA 59.718 33.333 6.97 0.00 42.39 2.57
68 69 6.765512 TGTGAAACGAAATAGGCATATGATGA 59.234 34.615 6.97 0.00 42.39 2.92
69 70 6.958255 TGTGAAACGAAATAGGCATATGATG 58.042 36.000 6.97 0.00 42.39 3.07
70 71 7.566760 TTGTGAAACGAAATAGGCATATGAT 57.433 32.000 6.97 0.00 42.39 2.45
71 72 6.993786 TTGTGAAACGAAATAGGCATATGA 57.006 33.333 6.97 0.00 42.39 2.15
72 73 7.026562 TGTTTGTGAAACGAAATAGGCATATG 58.973 34.615 0.00 0.00 42.99 1.78
73 74 7.151999 TGTTTGTGAAACGAAATAGGCATAT 57.848 32.000 0.00 0.00 42.99 1.78
74 75 6.561737 TGTTTGTGAAACGAAATAGGCATA 57.438 33.333 0.00 0.00 42.99 3.14
75 76 5.446143 TGTTTGTGAAACGAAATAGGCAT 57.554 34.783 0.00 0.00 42.99 4.40
76 77 4.902443 TGTTTGTGAAACGAAATAGGCA 57.098 36.364 0.00 0.00 42.99 4.75
77 78 4.553429 CGATGTTTGTGAAACGAAATAGGC 59.447 41.667 0.00 0.00 42.99 3.93
78 79 5.922546 TCGATGTTTGTGAAACGAAATAGG 58.077 37.500 0.00 0.00 42.99 2.57
86 87 9.885743 GCAAAAATATATCGATGTTTGTGAAAC 57.114 29.630 18.98 0.00 34.74 2.78
87 88 9.631452 TGCAAAAATATATCGATGTTTGTGAAA 57.369 25.926 18.98 9.16 34.74 2.69
88 89 9.071221 GTGCAAAAATATATCGATGTTTGTGAA 57.929 29.630 18.98 10.99 34.74 3.18
89 90 8.239998 TGTGCAAAAATATATCGATGTTTGTGA 58.760 29.630 18.98 8.03 34.74 3.58
90 91 8.392124 TGTGCAAAAATATATCGATGTTTGTG 57.608 30.769 8.54 12.16 35.50 3.33
91 92 8.978564 TTGTGCAAAAATATATCGATGTTTGT 57.021 26.923 8.54 0.00 0.00 2.83
92 93 9.674208 GTTTGTGCAAAAATATATCGATGTTTG 57.326 29.630 8.54 11.04 31.33 2.93
93 94 9.638239 AGTTTGTGCAAAAATATATCGATGTTT 57.362 25.926 8.54 3.93 31.33 2.83
94 95 9.289303 GAGTTTGTGCAAAAATATATCGATGTT 57.711 29.630 8.54 0.00 31.33 2.71
95 96 7.639850 CGAGTTTGTGCAAAAATATATCGATGT 59.360 33.333 17.34 3.54 31.33 3.06
96 97 7.112009 CCGAGTTTGTGCAAAAATATATCGATG 59.888 37.037 21.09 9.25 31.33 3.84
97 98 7.132213 CCGAGTTTGTGCAAAAATATATCGAT 58.868 34.615 21.09 2.16 31.33 3.59
98 99 6.092944 ACCGAGTTTGTGCAAAAATATATCGA 59.907 34.615 21.09 0.00 31.33 3.59
99 100 6.255215 ACCGAGTTTGTGCAAAAATATATCG 58.745 36.000 5.11 12.38 31.33 2.92
100 101 7.247728 TGACCGAGTTTGTGCAAAAATATATC 58.752 34.615 5.11 1.66 31.33 1.63
101 102 7.151999 TGACCGAGTTTGTGCAAAAATATAT 57.848 32.000 5.11 0.00 31.33 0.86
102 103 6.561737 TGACCGAGTTTGTGCAAAAATATA 57.438 33.333 5.11 0.00 31.33 0.86
103 104 5.446143 TGACCGAGTTTGTGCAAAAATAT 57.554 34.783 5.11 0.00 31.33 1.28
104 105 4.902443 TGACCGAGTTTGTGCAAAAATA 57.098 36.364 5.11 0.00 31.33 1.40
105 106 3.791973 TGACCGAGTTTGTGCAAAAAT 57.208 38.095 5.11 0.00 31.33 1.82
106 107 3.577649 TTGACCGAGTTTGTGCAAAAA 57.422 38.095 0.00 0.00 31.33 1.94
107 108 3.246619 GTTTGACCGAGTTTGTGCAAAA 58.753 40.909 0.00 0.00 31.33 2.44
108 109 2.729467 CGTTTGACCGAGTTTGTGCAAA 60.729 45.455 0.00 0.00 0.00 3.68
109 110 1.202087 CGTTTGACCGAGTTTGTGCAA 60.202 47.619 0.00 0.00 0.00 4.08
110 111 0.375454 CGTTTGACCGAGTTTGTGCA 59.625 50.000 0.00 0.00 0.00 4.57
111 112 0.375803 ACGTTTGACCGAGTTTGTGC 59.624 50.000 0.00 0.00 0.00 4.57
112 113 2.817538 AACGTTTGACCGAGTTTGTG 57.182 45.000 0.00 0.00 0.00 3.33
113 114 4.121317 TCATAACGTTTGACCGAGTTTGT 58.879 39.130 5.91 0.00 0.00 2.83
114 115 4.718858 TCATAACGTTTGACCGAGTTTG 57.281 40.909 5.91 0.00 0.00 2.93
115 116 6.161381 ACTATCATAACGTTTGACCGAGTTT 58.839 36.000 5.91 0.00 0.00 2.66
116 117 5.717119 ACTATCATAACGTTTGACCGAGTT 58.283 37.500 5.91 0.00 0.00 3.01
117 118 5.320549 ACTATCATAACGTTTGACCGAGT 57.679 39.130 5.91 11.07 0.00 4.18
118 119 6.309494 TCAAACTATCATAACGTTTGACCGAG 59.691 38.462 5.91 10.53 46.60 4.63
119 120 6.157904 TCAAACTATCATAACGTTTGACCGA 58.842 36.000 5.91 0.00 46.60 4.69
120 121 6.397831 TCAAACTATCATAACGTTTGACCG 57.602 37.500 5.91 7.50 46.60 4.79
124 125 6.183360 GGAGGGTCAAACTATCATAACGTTTG 60.183 42.308 5.91 5.11 45.29 2.93
125 126 5.878669 GGAGGGTCAAACTATCATAACGTTT 59.121 40.000 5.91 0.00 0.00 3.60
126 127 5.046159 TGGAGGGTCAAACTATCATAACGTT 60.046 40.000 5.88 5.88 0.00 3.99
127 128 4.468510 TGGAGGGTCAAACTATCATAACGT 59.531 41.667 0.00 0.00 0.00 3.99
128 129 5.018539 TGGAGGGTCAAACTATCATAACG 57.981 43.478 0.00 0.00 0.00 3.18
129 130 6.177610 TGTTGGAGGGTCAAACTATCATAAC 58.822 40.000 0.00 0.00 0.00 1.89
130 131 6.381498 TGTTGGAGGGTCAAACTATCATAA 57.619 37.500 0.00 0.00 0.00 1.90
131 132 6.381498 TTGTTGGAGGGTCAAACTATCATA 57.619 37.500 0.00 0.00 0.00 2.15
132 133 4.927267 TGTTGGAGGGTCAAACTATCAT 57.073 40.909 0.00 0.00 0.00 2.45
133 134 4.715534 TTGTTGGAGGGTCAAACTATCA 57.284 40.909 0.00 0.00 0.00 2.15
134 135 5.070685 ACTTTGTTGGAGGGTCAAACTATC 58.929 41.667 0.00 0.00 0.00 2.08
135 136 5.061721 ACTTTGTTGGAGGGTCAAACTAT 57.938 39.130 0.00 0.00 0.00 2.12
136 137 4.513406 ACTTTGTTGGAGGGTCAAACTA 57.487 40.909 0.00 0.00 0.00 2.24
137 138 3.382083 ACTTTGTTGGAGGGTCAAACT 57.618 42.857 0.00 0.00 0.00 2.66
138 139 3.430236 CCAACTTTGTTGGAGGGTCAAAC 60.430 47.826 21.06 0.00 42.06 2.93
139 140 2.763448 CCAACTTTGTTGGAGGGTCAAA 59.237 45.455 21.06 0.00 42.06 2.69
140 141 2.024846 TCCAACTTTGTTGGAGGGTCAA 60.025 45.455 23.38 4.76 43.17 3.18
141 142 1.566703 TCCAACTTTGTTGGAGGGTCA 59.433 47.619 23.38 5.39 43.17 4.02
142 143 2.358322 TCCAACTTTGTTGGAGGGTC 57.642 50.000 23.38 0.00 43.17 4.46
147 148 4.850680 AGTGTACTTCCAACTTTGTTGGA 58.149 39.130 23.38 23.38 46.08 3.53
148 149 4.881850 AGAGTGTACTTCCAACTTTGTTGG 59.118 41.667 19.97 19.97 40.87 3.77
149 150 6.436843 AAGAGTGTACTTCCAACTTTGTTG 57.563 37.500 3.69 3.69 0.00 3.33
150 151 8.570068 TTAAAGAGTGTACTTCCAACTTTGTT 57.430 30.769 0.00 0.00 31.02 2.83
151 152 8.570068 TTTAAAGAGTGTACTTCCAACTTTGT 57.430 30.769 0.00 0.00 31.02 2.83
152 153 8.889717 TCTTTAAAGAGTGTACTTCCAACTTTG 58.110 33.333 13.99 0.00 31.02 2.77
153 154 9.457436 TTCTTTAAAGAGTGTACTTCCAACTTT 57.543 29.630 17.05 0.00 36.22 2.66
154 155 8.890718 GTTCTTTAAAGAGTGTACTTCCAACTT 58.109 33.333 17.05 0.00 36.22 2.66
155 156 7.224167 CGTTCTTTAAAGAGTGTACTTCCAACT 59.776 37.037 17.05 0.00 36.22 3.16
156 157 7.342942 CGTTCTTTAAAGAGTGTACTTCCAAC 58.657 38.462 17.05 7.83 36.22 3.77
157 158 6.480981 CCGTTCTTTAAAGAGTGTACTTCCAA 59.519 38.462 17.05 0.00 36.22 3.53
158 159 5.987347 CCGTTCTTTAAAGAGTGTACTTCCA 59.013 40.000 17.05 0.00 36.22 3.53
159 160 6.218746 TCCGTTCTTTAAAGAGTGTACTTCC 58.781 40.000 17.05 0.00 36.22 3.46
160 161 6.365518 CCTCCGTTCTTTAAAGAGTGTACTTC 59.634 42.308 17.05 3.05 36.22 3.01
161 162 6.041296 TCCTCCGTTCTTTAAAGAGTGTACTT 59.959 38.462 17.05 0.00 36.22 2.24
162 163 5.537674 TCCTCCGTTCTTTAAAGAGTGTACT 59.462 40.000 17.05 0.00 36.22 2.73
163 164 5.776744 TCCTCCGTTCTTTAAAGAGTGTAC 58.223 41.667 17.05 11.81 36.22 2.90
164 165 6.041296 ACTTCCTCCGTTCTTTAAAGAGTGTA 59.959 38.462 17.05 0.75 36.22 2.90
165 166 4.950205 TCCTCCGTTCTTTAAAGAGTGT 57.050 40.909 17.05 0.00 36.22 3.55
166 167 5.177696 CACTTCCTCCGTTCTTTAAAGAGTG 59.822 44.000 17.05 13.92 36.22 3.51
167 168 5.298347 CACTTCCTCCGTTCTTTAAAGAGT 58.702 41.667 17.05 6.58 36.22 3.24
168 169 4.152580 GCACTTCCTCCGTTCTTTAAAGAG 59.847 45.833 17.05 7.62 36.22 2.85
169 170 4.062991 GCACTTCCTCCGTTCTTTAAAGA 58.937 43.478 13.99 13.99 0.00 2.52
170 171 3.813166 TGCACTTCCTCCGTTCTTTAAAG 59.187 43.478 9.04 9.04 0.00 1.85
171 172 3.811083 TGCACTTCCTCCGTTCTTTAAA 58.189 40.909 0.00 0.00 0.00 1.52
172 173 3.181458 ACTGCACTTCCTCCGTTCTTTAA 60.181 43.478 0.00 0.00 0.00 1.52
173 174 2.367567 ACTGCACTTCCTCCGTTCTTTA 59.632 45.455 0.00 0.00 0.00 1.85
174 175 1.141053 ACTGCACTTCCTCCGTTCTTT 59.859 47.619 0.00 0.00 0.00 2.52
175 176 0.759346 ACTGCACTTCCTCCGTTCTT 59.241 50.000 0.00 0.00 0.00 2.52
176 177 0.034059 CACTGCACTTCCTCCGTTCT 59.966 55.000 0.00 0.00 0.00 3.01
177 178 0.951040 CCACTGCACTTCCTCCGTTC 60.951 60.000 0.00 0.00 0.00 3.95
178 179 1.071471 CCACTGCACTTCCTCCGTT 59.929 57.895 0.00 0.00 0.00 4.44
179 180 0.830444 TACCACTGCACTTCCTCCGT 60.830 55.000 0.00 0.00 0.00 4.69
180 181 0.108615 CTACCACTGCACTTCCTCCG 60.109 60.000 0.00 0.00 0.00 4.63
181 182 1.267121 TCTACCACTGCACTTCCTCC 58.733 55.000 0.00 0.00 0.00 4.30
182 183 3.526534 GAATCTACCACTGCACTTCCTC 58.473 50.000 0.00 0.00 0.00 3.71
183 184 2.093973 CGAATCTACCACTGCACTTCCT 60.094 50.000 0.00 0.00 0.00 3.36
184 185 2.271800 CGAATCTACCACTGCACTTCC 58.728 52.381 0.00 0.00 0.00 3.46
185 186 2.668457 CACGAATCTACCACTGCACTTC 59.332 50.000 0.00 0.00 0.00 3.01
186 187 2.037251 ACACGAATCTACCACTGCACTT 59.963 45.455 0.00 0.00 0.00 3.16
187 188 1.618837 ACACGAATCTACCACTGCACT 59.381 47.619 0.00 0.00 0.00 4.40
188 189 1.993370 GACACGAATCTACCACTGCAC 59.007 52.381 0.00 0.00 0.00 4.57
189 190 1.616374 TGACACGAATCTACCACTGCA 59.384 47.619 0.00 0.00 0.00 4.41
190 191 1.993370 GTGACACGAATCTACCACTGC 59.007 52.381 0.00 0.00 0.00 4.40
229 231 0.097674 CAAGCCAGCAATAGCACGTC 59.902 55.000 0.00 0.00 45.49 4.34
270 272 7.278724 TGGAAATTTAAATCCAGAGGAGGTA 57.721 36.000 6.46 0.00 40.74 3.08
280 282 7.561356 TCTCCTTCTGGATGGAAATTTAAATCC 59.439 37.037 18.56 18.56 42.29 3.01
281 283 8.525290 TCTCCTTCTGGATGGAAATTTAAATC 57.475 34.615 0.10 0.00 42.29 2.17
282 284 8.899887 TTCTCCTTCTGGATGGAAATTTAAAT 57.100 30.769 0.00 0.00 42.29 1.40
284 286 7.728083 TGTTTCTCCTTCTGGATGGAAATTTAA 59.272 33.333 6.66 0.00 42.29 1.52
285 287 7.237982 TGTTTCTCCTTCTGGATGGAAATTTA 58.762 34.615 6.66 0.00 42.29 1.40
286 288 6.077322 TGTTTCTCCTTCTGGATGGAAATTT 58.923 36.000 6.66 0.00 42.29 1.82
287 289 5.644188 TGTTTCTCCTTCTGGATGGAAATT 58.356 37.500 6.66 0.00 42.29 1.82
288 290 5.261040 TGTTTCTCCTTCTGGATGGAAAT 57.739 39.130 6.66 0.00 42.29 2.17
289 291 4.722526 TGTTTCTCCTTCTGGATGGAAA 57.277 40.909 6.66 0.00 42.29 3.13
290 292 4.722526 TTGTTTCTCCTTCTGGATGGAA 57.277 40.909 6.66 0.00 42.29 3.53
291 293 4.722526 TTTGTTTCTCCTTCTGGATGGA 57.277 40.909 5.34 5.34 42.29 3.41
292 294 5.302823 AGTTTTTGTTTCTCCTTCTGGATGG 59.697 40.000 0.00 0.00 42.29 3.51
293 295 6.264067 AGAGTTTTTGTTTCTCCTTCTGGATG 59.736 38.462 0.00 0.00 42.29 3.51
294 296 6.368805 AGAGTTTTTGTTTCTCCTTCTGGAT 58.631 36.000 0.00 0.00 42.29 3.41
305 307 6.052360 AGGAGAGACAGAGAGTTTTTGTTTC 58.948 40.000 0.00 0.00 0.00 2.78
397 406 1.547901 CCCCTCAAACAAACTCTCCCC 60.548 57.143 0.00 0.00 0.00 4.81
422 431 3.061848 CACCGGCAACATCACCCC 61.062 66.667 0.00 0.00 0.00 4.95
572 606 4.961511 TCGACCCTGTGTGCGTGC 62.962 66.667 0.00 0.00 0.00 5.34
580 614 2.416107 TAGTGACCCGTCGACCCTGT 62.416 60.000 10.58 4.38 0.00 4.00
594 628 1.998315 GCTCGTCGTAGTGAGTAGTGA 59.002 52.381 0.00 0.00 34.60 3.41
601 635 0.108945 TCTCTCGCTCGTCGTAGTGA 60.109 55.000 7.43 7.43 39.67 3.41
612 648 0.179124 GTGCCGATTTCTCTCTCGCT 60.179 55.000 0.00 0.00 33.63 4.93
619 655 1.787847 CACCACGTGCCGATTTCTC 59.212 57.895 10.91 0.00 0.00 2.87
718 754 3.979497 GTGGGTGGGGGAAGGTGG 61.979 72.222 0.00 0.00 0.00 4.61
1162 1269 2.680312 AGCAAATAGAGCAAGCGAGA 57.320 45.000 0.00 0.00 0.00 4.04
1174 1283 0.530288 GAGCGGGGCAAAAGCAAATA 59.470 50.000 0.00 0.00 0.00 1.40
1209 1318 1.676529 CAGAATCAGGCCATGCTCAAG 59.323 52.381 5.01 0.00 0.00 3.02
1483 1600 3.364441 GCCACAGCACGCATTCCA 61.364 61.111 0.00 0.00 39.53 3.53
1494 1637 3.289834 AAACGCAGGCAGCCACAG 61.290 61.111 15.80 6.35 41.38 3.66
1845 3284 7.321271 CGACTGTGTTTTTAATTAGCTCTTGTG 59.679 37.037 0.00 0.00 0.00 3.33
1903 3354 5.459768 TGAAAATGTGGTGTCATTTCATCG 58.540 37.500 5.36 0.00 44.10 3.84
1947 3398 1.373570 GAAGTGCCCCATTCTCTTCG 58.626 55.000 0.00 0.00 0.00 3.79
1971 3422 4.970662 ATGTGTTCCATTTCCATTCTCG 57.029 40.909 0.00 0.00 0.00 4.04
2127 3593 1.869503 CAGACAAACTTACATGCGCG 58.130 50.000 0.00 0.00 0.00 6.86
2150 3616 0.790814 GTTGTACAAGAGCGAGCACC 59.209 55.000 8.98 0.00 0.00 5.01
2247 3723 7.010460 GCTGCCCAAGAAATATTGTTTTGTATC 59.990 37.037 0.00 0.00 0.00 2.24
2256 3732 2.023673 TCGGCTGCCCAAGAAATATTG 58.976 47.619 14.12 0.00 0.00 1.90
2271 3747 8.506168 TTCAAAACTATATCAAGAAATCGGCT 57.494 30.769 0.00 0.00 0.00 5.52
2368 3848 2.490270 ATCTGGAAGGGCCACAGTGC 62.490 60.000 18.33 2.66 43.33 4.40
2371 3851 2.025887 ACTAAATCTGGAAGGGCCACAG 60.026 50.000 6.18 11.48 43.33 3.66
2401 3885 6.980978 CCTATCATAATGTAGGCTTGATACCG 59.019 42.308 0.00 0.00 31.79 4.02
2429 3914 4.734695 GCAAATGCAGGCAGATAACTTACC 60.735 45.833 0.00 0.00 41.59 2.85
2466 3951 6.498651 ACTCTAGTGGCTGCACCTATAAATAT 59.501 38.462 0.50 0.00 40.22 1.28
2467 3952 5.839063 ACTCTAGTGGCTGCACCTATAAATA 59.161 40.000 0.50 0.00 40.22 1.40
2468 3953 4.656112 ACTCTAGTGGCTGCACCTATAAAT 59.344 41.667 0.50 0.00 40.22 1.40
2530 4116 7.630924 ACTTGTGATTCTAACTCTTTTGAACG 58.369 34.615 0.00 0.00 30.66 3.95
2557 4144 7.722285 TGCCTACAGGAAATTAACAAAGTAAGT 59.278 33.333 0.00 0.00 37.39 2.24
2696 4283 2.476619 ACGCTTCGATGTTCTGTTGAAG 59.523 45.455 0.00 0.00 39.20 3.02
2720 4307 2.526304 TAGTTTTGAGTCAGCGCTGT 57.474 45.000 34.70 18.99 0.00 4.40
2818 4405 3.914312 ACAAGACTGTATGGAGAACACG 58.086 45.455 0.00 0.00 32.54 4.49
2917 4532 4.770010 TCCTAACCACCCATCATTGAAAAC 59.230 41.667 0.00 0.00 0.00 2.43
2965 4580 0.115152 TCCCAGAACTCTCTGCTCCA 59.885 55.000 0.00 0.00 46.76 3.86
3006 4621 8.958060 TGACTGTATAATCCTAATAAGCTCCT 57.042 34.615 0.00 0.00 0.00 3.69
3166 4788 1.664588 GCGCATACAAAAACTCGGCAA 60.665 47.619 0.30 0.00 0.00 4.52
3275 4963 1.339151 GGTAGCACCCAGAAACCTCAG 60.339 57.143 0.00 0.00 30.04 3.35
3290 4978 2.760385 ACAGCCTCGGAGGGTAGC 60.760 66.667 26.95 11.76 45.88 3.58
3329 5022 9.753674 TTTCAGAGTCCAATGACCTTTTATATT 57.246 29.630 0.00 0.00 42.81 1.28
3334 5027 6.550854 TGAATTTCAGAGTCCAATGACCTTTT 59.449 34.615 0.00 0.00 42.81 2.27
3339 5032 6.622462 GCTCTTGAATTTCAGAGTCCAATGAC 60.622 42.308 18.63 0.00 42.09 3.06
3360 5053 1.359474 TCCAGAGTAGGTCTTGGCTCT 59.641 52.381 0.00 0.00 38.69 4.09
3364 5057 2.239681 AGGTCCAGAGTAGGTCTTGG 57.760 55.000 0.00 0.00 30.64 3.61
3376 5069 4.792068 TGCCTTCCAAATAATAGGTCCAG 58.208 43.478 0.00 0.00 0.00 3.86
3384 5077 2.762327 CACTGCCTGCCTTCCAAATAAT 59.238 45.455 0.00 0.00 0.00 1.28
3395 5088 0.250295 TGTTCTGTACACTGCCTGCC 60.250 55.000 0.00 0.00 0.00 4.85
3485 5185 2.728690 TGGCTGCAATGATGTTTCAC 57.271 45.000 0.50 0.00 33.85 3.18
3520 5220 9.884465 GATGTAATATGAATGCTTAAACCAGTC 57.116 33.333 0.00 0.00 0.00 3.51
3557 5257 8.853126 ACATGACAACATAATGCTGCTTTATAT 58.147 29.630 17.21 6.81 35.09 0.86
3565 5267 5.701855 TGTTCACATGACAACATAATGCTG 58.298 37.500 0.00 0.00 35.09 4.41
3571 5273 9.549078 TTAGTAAGTTGTTCACATGACAACATA 57.451 29.630 23.28 16.21 44.22 2.29
3631 5333 2.813042 GCGTCAGAGCAGTGCCTC 60.813 66.667 12.58 8.91 37.05 4.70
3632 5334 3.619767 TGCGTCAGAGCAGTGCCT 61.620 61.111 12.58 5.85 42.92 4.75
3691 5393 3.935828 GGTTCCTGAATTTTCTCCTCTCG 59.064 47.826 0.00 0.00 0.00 4.04
3696 5405 2.420372 GCTCGGTTCCTGAATTTTCTCC 59.580 50.000 0.00 0.00 0.00 3.71
3740 5449 3.744530 CGACTCTTTTCTTTGGTCCCTGT 60.745 47.826 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.