Multiple sequence alignment - TraesCS1B01G255800

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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 TraesCS1B01G255800 chr1B 100.000 4244 0 0 955 5198 450612736 450608493 0.000000e+00 7838
1 TraesCS1B01G255800 chr1B 100.000 786 0 0 1 786 450613690 450612905 0.000000e+00 1452
2 TraesCS1B01G255800 chr1A 95.492 4059 121 21 1025 5059 432637942 432633922 0.000000e+00 6425
3 TraesCS1B01G255800 chr1A 91.753 194 13 3 189 381 432638759 432638568 3.090000e-67 267
4 TraesCS1B01G255800 chr1A 88.950 181 9 4 467 647 432638526 432638357 4.080000e-51 213
5 TraesCS1B01G255800 chr1D 96.284 2395 65 6 956 3341 335077457 335075078 0.000000e+00 3908
6 TraesCS1B01G255800 chr1D 94.756 1888 64 13 3341 5198 335074837 335072955 0.000000e+00 2905
7 TraesCS1B01G255800 chr1D 88.677 839 68 14 2553 3376 465414487 465413661 0.000000e+00 998
8 TraesCS1B01G255800 chr1D 85.691 615 38 20 173 786 335078077 335077512 2.070000e-168 603
9 TraesCS1B01G255800 chr1D 83.518 631 60 19 2988 3609 468786821 468787416 2.740000e-152 549
10 TraesCS1B01G255800 chr1D 83.967 605 52 20 3015 3609 468789214 468789783 5.920000e-149 538
11 TraesCS1B01G255800 chr1D 83.609 604 54 19 3015 3609 468788426 468788993 4.610000e-145 525
12 TraesCS1B01G255800 chr1D 83.333 606 53 22 3015 3609 468787637 468788205 2.780000e-142 516
13 TraesCS1B01G255800 chr1D 87.624 202 24 1 2605 2805 468786135 468786336 3.130000e-57 233
14 TraesCS1B01G255800 chr1D 88.050 159 18 1 3452 3609 28014149 28014307 2.470000e-43 187
15 TraesCS1B01G255800 chr1D 93.277 119 8 0 3491 3609 468789846 468789964 5.350000e-40 176
16 TraesCS1B01G255800 chr1D 93.277 119 8 0 3491 3609 468790027 468790145 5.350000e-40 176
17 TraesCS1B01G255800 chr7A 88.262 1082 95 19 2553 3609 686308848 686309922 0.000000e+00 1266
18 TraesCS1B01G255800 chr7D 83.987 612 54 18 3007 3609 618432858 618432282 9.840000e-152 547
19 TraesCS1B01G255800 chr7D 90.980 255 21 2 2553 2805 618433623 618433369 4.980000e-90 342
20 TraesCS1B01G255800 chr6A 83.467 623 58 20 2988 3600 536230674 536231261 5.920000e-149 538
21 TraesCS1B01G255800 chr6A 90.041 241 23 1 2566 2805 536229929 536230169 1.410000e-80 311
22 TraesCS1B01G255800 chr2A 92.126 254 19 1 2553 2805 762849452 762849705 1.780000e-94 357
23 TraesCS1B01G255800 chr5B 93.431 137 9 0 2553 2689 509690176 509690312 2.450000e-48 204
24 TraesCS1B01G255800 chr5B 92.029 138 10 1 2553 2689 509824052 509823915 5.310000e-45 193


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 TraesCS1B01G255800 chr1B 450608493 450613690 5197 True 4645.000000 7838 100.000000 1 5198 2 chr1B.!!$R1 5197
1 TraesCS1B01G255800 chr1A 432633922 432638759 4837 True 2301.666667 6425 92.065000 189 5059 3 chr1A.!!$R1 4870
2 TraesCS1B01G255800 chr1D 335072955 335078077 5122 True 2472.000000 3908 92.243667 173 5198 3 chr1D.!!$R2 5025
3 TraesCS1B01G255800 chr1D 465413661 465414487 826 True 998.000000 998 88.677000 2553 3376 1 chr1D.!!$R1 823
4 TraesCS1B01G255800 chr1D 468786135 468790145 4010 False 387.571429 549 86.943571 2605 3609 7 chr1D.!!$F2 1004
5 TraesCS1B01G255800 chr7A 686308848 686309922 1074 False 1266.000000 1266 88.262000 2553 3609 1 chr7A.!!$F1 1056
6 TraesCS1B01G255800 chr7D 618432282 618433623 1341 True 444.500000 547 87.483500 2553 3609 2 chr7D.!!$R1 1056
7 TraesCS1B01G255800 chr6A 536229929 536231261 1332 False 424.500000 538 86.754000 2566 3600 2 chr6A.!!$F1 1034

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
114 115 0.036294 CCTCCCGTTTCCCTCTTCAC 60.036 60.000 0.00 0.00 0.00 3.18 F
156 157 0.179032 TCGCCATGGTTTGTCACTGT 60.179 50.000 14.67 0.00 0.00 3.55 F
465 468 0.248949 GTACGCAACGATCTCCCTCC 60.249 60.000 0.00 0.00 0.00 4.30 F
470 473 0.397816 CAACGATCTCCCTCCCTCCT 60.398 60.000 0.00 0.00 0.00 3.69 F
1662 1721 0.399454 AGATGCCGGGGAATGATCTG 59.601 55.000 2.18 0.00 0.00 2.90 F
1848 1907 1.080705 GCACGAGGCGTTCTACACT 60.081 57.895 0.00 0.00 38.32 3.55 F
2160 2219 1.208776 GGTGGGTACGTGGCTTTCTAT 59.791 52.381 0.00 0.00 0.00 1.98 F
2710 2774 1.723542 CTTGCTGTTGAACGCTGCG 60.724 57.895 21.91 21.91 34.23 5.18 F
3891 7378 0.463654 TCTGTGGCAGCGAACTGTTT 60.464 50.000 0.00 0.00 46.30 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1907 1.219124 GCGGCCACTGAAGATCTCA 59.781 57.895 2.24 0.0 0.00 3.27 R
1917 1976 3.613299 GCGGCTTTCTAGTGAAGTAGAAC 59.387 47.826 7.04 0.0 38.49 3.01 R
2160 2219 3.054948 CCTTCCGGTAAATAGTTGGTGGA 60.055 47.826 0.00 0.0 0.00 4.02 R
2238 2297 9.159364 CACTCATTCAAGAATTTGATCAGTCTA 57.841 33.333 0.00 0.0 42.60 2.59 R
2858 2932 0.697658 TGGTGGCATTGGATCTGACA 59.302 50.000 0.00 0.0 0.00 3.58 R
3064 3580 1.268066 ACAATTGGTGCCATCATGCA 58.732 45.000 10.83 0.0 39.37 3.96 R
3891 7378 1.202830 ACAAACTGTCGGGGCACATAA 60.203 47.619 0.00 0.0 0.00 1.90 R
4167 7654 1.648568 TCCATCAGAAGAGGGTCTCCT 59.351 52.381 0.00 0.0 45.75 3.69 R
5039 8546 2.831685 TCATACACGGCTCAAACACT 57.168 45.000 0.00 0.0 0.00 3.55 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 2.872370 GTTGCACTTTCAGCCATGATC 58.128 47.619 0.00 0.00 34.73 2.92
21 22 1.089112 TGCACTTTCAGCCATGATCG 58.911 50.000 0.00 0.00 34.73 3.69
22 23 1.338960 TGCACTTTCAGCCATGATCGA 60.339 47.619 0.00 0.00 34.73 3.59
23 24 1.739466 GCACTTTCAGCCATGATCGAA 59.261 47.619 0.00 0.00 34.73 3.71
24 25 2.223203 GCACTTTCAGCCATGATCGAAG 60.223 50.000 0.00 0.00 34.73 3.79
25 26 3.264947 CACTTTCAGCCATGATCGAAGA 58.735 45.455 0.00 0.00 45.75 2.87
26 27 3.875727 CACTTTCAGCCATGATCGAAGAT 59.124 43.478 0.00 0.00 45.12 2.40
27 28 4.334759 CACTTTCAGCCATGATCGAAGATT 59.665 41.667 0.00 0.00 45.12 2.40
28 29 5.525012 CACTTTCAGCCATGATCGAAGATTA 59.475 40.000 0.00 0.00 45.12 1.75
29 30 6.037500 CACTTTCAGCCATGATCGAAGATTAA 59.962 38.462 0.00 0.00 45.12 1.40
30 31 6.769822 ACTTTCAGCCATGATCGAAGATTAAT 59.230 34.615 0.00 0.00 45.12 1.40
31 32 7.933577 ACTTTCAGCCATGATCGAAGATTAATA 59.066 33.333 0.00 0.00 45.12 0.98
32 33 7.895975 TTCAGCCATGATCGAAGATTAATAG 57.104 36.000 0.00 0.00 45.12 1.73
33 34 7.232118 TCAGCCATGATCGAAGATTAATAGA 57.768 36.000 0.00 0.00 45.12 1.98
34 35 7.845037 TCAGCCATGATCGAAGATTAATAGAT 58.155 34.615 0.00 0.00 45.12 1.98
35 36 8.316946 TCAGCCATGATCGAAGATTAATAGATT 58.683 33.333 0.00 0.00 45.12 2.40
36 37 9.591792 CAGCCATGATCGAAGATTAATAGATTA 57.408 33.333 0.00 0.00 45.12 1.75
37 38 9.814899 AGCCATGATCGAAGATTAATAGATTAG 57.185 33.333 0.00 0.00 45.12 1.73
38 39 9.809096 GCCATGATCGAAGATTAATAGATTAGA 57.191 33.333 0.00 0.00 45.12 2.10
83 84 8.458843 AGATGTGAAGTTCATTAAATAAACCCG 58.541 33.333 9.18 0.00 0.00 5.28
84 85 7.747155 TGTGAAGTTCATTAAATAAACCCGA 57.253 32.000 9.18 0.00 0.00 5.14
85 86 8.167605 TGTGAAGTTCATTAAATAAACCCGAA 57.832 30.769 9.18 0.00 0.00 4.30
86 87 8.293867 TGTGAAGTTCATTAAATAAACCCGAAG 58.706 33.333 9.18 0.00 0.00 3.79
87 88 8.508875 GTGAAGTTCATTAAATAAACCCGAAGA 58.491 33.333 9.18 0.00 0.00 2.87
88 89 8.726988 TGAAGTTCATTAAATAAACCCGAAGAG 58.273 33.333 0.08 0.00 0.00 2.85
89 90 7.625828 AGTTCATTAAATAAACCCGAAGAGG 57.374 36.000 0.00 0.00 40.63 3.69
90 91 6.095021 AGTTCATTAAATAAACCCGAAGAGGC 59.905 38.462 0.00 0.00 39.21 4.70
91 92 4.885325 TCATTAAATAAACCCGAAGAGGCC 59.115 41.667 0.00 0.00 39.21 5.19
92 93 2.139323 AAATAAACCCGAAGAGGCCC 57.861 50.000 0.00 0.00 39.21 5.80
93 94 1.296002 AATAAACCCGAAGAGGCCCT 58.704 50.000 0.00 0.00 39.21 5.19
94 95 0.837940 ATAAACCCGAAGAGGCCCTC 59.162 55.000 1.26 1.26 39.21 4.30
95 96 1.269703 TAAACCCGAAGAGGCCCTCC 61.270 60.000 7.26 0.00 39.21 4.30
104 105 4.677151 AGGCCCTCCCTCCCGTTT 62.677 66.667 0.00 0.00 41.21 3.60
105 106 4.111053 GGCCCTCCCTCCCGTTTC 62.111 72.222 0.00 0.00 0.00 2.78
106 107 4.111053 GCCCTCCCTCCCGTTTCC 62.111 72.222 0.00 0.00 0.00 3.13
107 108 3.408853 CCCTCCCTCCCGTTTCCC 61.409 72.222 0.00 0.00 0.00 3.97
108 109 2.285442 CCTCCCTCCCGTTTCCCT 60.285 66.667 0.00 0.00 0.00 4.20
109 110 2.368011 CCTCCCTCCCGTTTCCCTC 61.368 68.421 0.00 0.00 0.00 4.30
110 111 1.306226 CTCCCTCCCGTTTCCCTCT 60.306 63.158 0.00 0.00 0.00 3.69
111 112 0.910088 CTCCCTCCCGTTTCCCTCTT 60.910 60.000 0.00 0.00 0.00 2.85
112 113 0.908180 TCCCTCCCGTTTCCCTCTTC 60.908 60.000 0.00 0.00 0.00 2.87
113 114 1.198759 CCCTCCCGTTTCCCTCTTCA 61.199 60.000 0.00 0.00 0.00 3.02
114 115 0.036294 CCTCCCGTTTCCCTCTTCAC 60.036 60.000 0.00 0.00 0.00 3.18
115 116 0.036294 CTCCCGTTTCCCTCTTCACC 60.036 60.000 0.00 0.00 0.00 4.02
116 117 0.473117 TCCCGTTTCCCTCTTCACCT 60.473 55.000 0.00 0.00 0.00 4.00
117 118 0.400594 CCCGTTTCCCTCTTCACCTT 59.599 55.000 0.00 0.00 0.00 3.50
118 119 1.626825 CCCGTTTCCCTCTTCACCTTA 59.373 52.381 0.00 0.00 0.00 2.69
119 120 2.354805 CCCGTTTCCCTCTTCACCTTAG 60.355 54.545 0.00 0.00 0.00 2.18
120 121 2.565834 CCGTTTCCCTCTTCACCTTAGA 59.434 50.000 0.00 0.00 0.00 2.10
121 122 3.586892 CGTTTCCCTCTTCACCTTAGAC 58.413 50.000 0.00 0.00 0.00 2.59
122 123 3.258622 CGTTTCCCTCTTCACCTTAGACT 59.741 47.826 0.00 0.00 0.00 3.24
123 124 4.461781 CGTTTCCCTCTTCACCTTAGACTA 59.538 45.833 0.00 0.00 0.00 2.59
124 125 5.393243 CGTTTCCCTCTTCACCTTAGACTAG 60.393 48.000 0.00 0.00 0.00 2.57
125 126 5.531753 TTCCCTCTTCACCTTAGACTAGA 57.468 43.478 0.00 0.00 0.00 2.43
126 127 5.118729 TCCCTCTTCACCTTAGACTAGAG 57.881 47.826 0.00 0.00 0.00 2.43
127 128 4.540906 TCCCTCTTCACCTTAGACTAGAGT 59.459 45.833 0.00 0.00 0.00 3.24
128 129 4.885325 CCCTCTTCACCTTAGACTAGAGTC 59.115 50.000 0.00 1.17 45.08 3.36
129 130 4.885325 CCTCTTCACCTTAGACTAGAGTCC 59.115 50.000 6.05 0.00 45.85 3.85
130 131 4.857679 TCTTCACCTTAGACTAGAGTCCC 58.142 47.826 6.05 0.00 45.85 4.46
131 132 4.291513 TCTTCACCTTAGACTAGAGTCCCA 59.708 45.833 6.05 0.00 45.85 4.37
132 133 4.883021 TCACCTTAGACTAGAGTCCCAT 57.117 45.455 6.05 0.00 45.85 4.00
133 134 4.794334 TCACCTTAGACTAGAGTCCCATC 58.206 47.826 6.05 0.00 45.85 3.51
134 135 4.479056 TCACCTTAGACTAGAGTCCCATCT 59.521 45.833 6.05 0.00 45.85 2.90
135 136 5.670818 TCACCTTAGACTAGAGTCCCATCTA 59.329 44.000 6.05 0.00 45.85 1.98
136 137 6.159928 TCACCTTAGACTAGAGTCCCATCTAA 59.840 42.308 6.05 0.00 45.85 2.10
137 138 7.007723 CACCTTAGACTAGAGTCCCATCTAAT 58.992 42.308 6.05 0.00 45.85 1.73
138 139 7.175990 CACCTTAGACTAGAGTCCCATCTAATC 59.824 44.444 6.05 0.00 45.85 1.75
139 140 6.373216 CCTTAGACTAGAGTCCCATCTAATCG 59.627 46.154 6.05 0.00 45.85 3.34
140 141 4.076394 AGACTAGAGTCCCATCTAATCGC 58.924 47.826 6.05 0.00 45.85 4.58
141 142 3.158676 ACTAGAGTCCCATCTAATCGCC 58.841 50.000 0.00 0.00 31.51 5.54
142 143 2.088104 AGAGTCCCATCTAATCGCCA 57.912 50.000 0.00 0.00 0.00 5.69
143 144 2.614259 AGAGTCCCATCTAATCGCCAT 58.386 47.619 0.00 0.00 0.00 4.40
144 145 2.301296 AGAGTCCCATCTAATCGCCATG 59.699 50.000 0.00 0.00 0.00 3.66
145 146 1.349026 AGTCCCATCTAATCGCCATGG 59.651 52.381 7.63 7.63 37.42 3.66
146 147 1.072331 GTCCCATCTAATCGCCATGGT 59.928 52.381 14.67 0.00 36.12 3.55
147 148 1.774254 TCCCATCTAATCGCCATGGTT 59.226 47.619 14.67 2.11 36.12 3.67
148 149 2.174639 TCCCATCTAATCGCCATGGTTT 59.825 45.455 14.67 7.71 36.12 3.27
149 150 2.294233 CCCATCTAATCGCCATGGTTTG 59.706 50.000 14.67 3.93 36.12 2.93
150 151 2.951642 CCATCTAATCGCCATGGTTTGT 59.048 45.455 14.67 0.00 33.57 2.83
151 152 3.003689 CCATCTAATCGCCATGGTTTGTC 59.996 47.826 14.67 0.00 33.57 3.18
152 153 3.342377 TCTAATCGCCATGGTTTGTCA 57.658 42.857 14.67 0.00 0.00 3.58
153 154 3.006940 TCTAATCGCCATGGTTTGTCAC 58.993 45.455 14.67 0.00 0.00 3.67
154 155 1.909700 AATCGCCATGGTTTGTCACT 58.090 45.000 14.67 0.00 0.00 3.41
155 156 1.167851 ATCGCCATGGTTTGTCACTG 58.832 50.000 14.67 0.00 0.00 3.66
156 157 0.179032 TCGCCATGGTTTGTCACTGT 60.179 50.000 14.67 0.00 0.00 3.55
157 158 1.070914 TCGCCATGGTTTGTCACTGTA 59.929 47.619 14.67 0.00 0.00 2.74
158 159 1.464608 CGCCATGGTTTGTCACTGTAG 59.535 52.381 14.67 0.00 0.00 2.74
159 160 2.504367 GCCATGGTTTGTCACTGTAGT 58.496 47.619 14.67 0.00 0.00 2.73
160 161 2.884639 GCCATGGTTTGTCACTGTAGTT 59.115 45.455 14.67 0.00 0.00 2.24
161 162 3.304659 GCCATGGTTTGTCACTGTAGTTG 60.305 47.826 14.67 0.00 0.00 3.16
162 163 4.133820 CCATGGTTTGTCACTGTAGTTGA 58.866 43.478 2.57 0.00 0.00 3.18
163 164 4.761739 CCATGGTTTGTCACTGTAGTTGAT 59.238 41.667 2.57 0.00 0.00 2.57
164 165 5.241506 CCATGGTTTGTCACTGTAGTTGATT 59.758 40.000 2.57 0.00 0.00 2.57
165 166 6.429692 CCATGGTTTGTCACTGTAGTTGATTA 59.570 38.462 2.57 0.00 0.00 1.75
166 167 7.121168 CCATGGTTTGTCACTGTAGTTGATTAT 59.879 37.037 2.57 0.00 0.00 1.28
167 168 9.161629 CATGGTTTGTCACTGTAGTTGATTATA 57.838 33.333 0.00 0.00 0.00 0.98
168 169 8.771920 TGGTTTGTCACTGTAGTTGATTATAG 57.228 34.615 0.00 0.00 0.00 1.31
169 170 7.333423 TGGTTTGTCACTGTAGTTGATTATAGC 59.667 37.037 0.00 0.00 0.00 2.97
170 171 7.201617 GGTTTGTCACTGTAGTTGATTATAGCC 60.202 40.741 0.00 0.00 0.00 3.93
171 172 5.914033 TGTCACTGTAGTTGATTATAGCCC 58.086 41.667 0.00 0.00 0.00 5.19
245 247 3.309296 TCCCCAACATCCAGATCTACTC 58.691 50.000 0.00 0.00 0.00 2.59
251 253 4.484026 ACATCCAGATCTACTCCCATCT 57.516 45.455 0.00 0.00 0.00 2.90
300 302 0.519792 CATGTGCGACTCATGCAACG 60.520 55.000 0.00 0.00 45.23 4.10
346 348 1.227380 GATGCGGATCGTTCCAGCT 60.227 57.895 21.48 12.33 42.74 4.24
458 461 4.925786 CGCAAGTACGCAACGATC 57.074 55.556 0.00 0.00 0.00 3.69
459 462 2.359792 CGCAAGTACGCAACGATCT 58.640 52.632 0.00 0.00 0.00 2.75
460 463 0.294887 CGCAAGTACGCAACGATCTC 59.705 55.000 0.00 0.00 0.00 2.75
461 464 0.645868 GCAAGTACGCAACGATCTCC 59.354 55.000 0.00 0.00 0.00 3.71
462 465 1.278238 CAAGTACGCAACGATCTCCC 58.722 55.000 0.00 0.00 0.00 4.30
463 466 1.135083 CAAGTACGCAACGATCTCCCT 60.135 52.381 0.00 0.00 0.00 4.20
464 467 0.739561 AGTACGCAACGATCTCCCTC 59.260 55.000 0.00 0.00 0.00 4.30
465 468 0.248949 GTACGCAACGATCTCCCTCC 60.249 60.000 0.00 0.00 0.00 4.30
470 473 0.397816 CAACGATCTCCCTCCCTCCT 60.398 60.000 0.00 0.00 0.00 3.69
498 509 4.025401 CCGTTTCCACGCTGGTGC 62.025 66.667 4.33 0.00 45.72 5.01
557 570 4.148825 CTTCTCCCCCACCGCGAG 62.149 72.222 8.23 0.00 0.00 5.03
640 653 0.603569 AGTAAGCCACACTCCACTCG 59.396 55.000 0.00 0.00 0.00 4.18
1134 1184 1.597854 CGACTTCAGCAACTGGGCA 60.598 57.895 0.00 0.00 35.83 5.36
1135 1185 0.957395 CGACTTCAGCAACTGGGCAT 60.957 55.000 0.00 0.00 35.83 4.40
1137 1187 0.957395 ACTTCAGCAACTGGGCATCG 60.957 55.000 0.00 0.00 35.83 3.84
1140 1190 2.110967 CAGCAACTGGGCATCGGAG 61.111 63.158 0.00 0.00 35.83 4.63
1253 1303 4.504916 CTGCCTCGACCGCTCCAG 62.505 72.222 1.75 0.00 0.00 3.86
1560 1619 2.180159 TTGACTTCCTGCCCTACGCC 62.180 60.000 0.00 0.00 36.24 5.68
1662 1721 0.399454 AGATGCCGGGGAATGATCTG 59.601 55.000 2.18 0.00 0.00 2.90
1686 1745 4.260948 GGGAAGCATTTCGATGTTGATCTC 60.261 45.833 0.00 0.00 33.98 2.75
1848 1907 1.080705 GCACGAGGCGTTCTACACT 60.081 57.895 0.00 0.00 38.32 3.55
1917 1976 2.896854 CCGGATGTGGATGCCGTG 60.897 66.667 0.00 0.00 43.35 4.94
2160 2219 1.208776 GGTGGGTACGTGGCTTTCTAT 59.791 52.381 0.00 0.00 0.00 1.98
2238 2297 2.756760 GGATCTGCATGTGAATGTTGGT 59.243 45.455 0.00 0.00 0.00 3.67
2710 2774 1.723542 CTTGCTGTTGAACGCTGCG 60.724 57.895 21.91 21.91 34.23 5.18
2721 2786 2.812609 CGCTGCGCTCTGTCACAT 60.813 61.111 9.88 0.00 0.00 3.21
2810 2876 8.052141 TCCAAAACATGATCACCACTTGATATA 58.948 33.333 0.00 0.00 45.67 0.86
2909 2983 9.733556 TCTGAACCATTTAATCTAAAACAGCTA 57.266 29.630 0.00 0.00 0.00 3.32
3176 6055 4.540359 TTCCTTTTCCATTCTTGGCATG 57.460 40.909 0.00 0.00 43.29 4.06
3187 6066 5.335127 CATTCTTGGCATGTGTTAGCTTAC 58.665 41.667 0.00 0.00 0.00 2.34
3239 6122 4.937620 TCTGGTTACTAAAGCTCAATGCAG 59.062 41.667 0.00 0.00 45.94 4.41
3303 6187 6.592870 ACTACTGGGCATAAAAGATAACCTC 58.407 40.000 0.00 0.00 0.00 3.85
3311 6195 5.560953 GCATAAAAGATAACCTCACCGATGC 60.561 44.000 0.00 0.00 0.00 3.91
3331 6215 4.786507 TGCGCTTTATATCATTGTGATGC 58.213 39.130 9.73 0.00 37.70 3.91
3653 7140 4.766891 TCCATCCACATCCTTTTGTTTCTC 59.233 41.667 0.00 0.00 0.00 2.87
3654 7141 4.082026 CCATCCACATCCTTTTGTTTCTCC 60.082 45.833 0.00 0.00 0.00 3.71
3870 7357 3.304257 GCATGGGCGAAGATAAGATTGTG 60.304 47.826 0.00 0.00 0.00 3.33
3891 7378 0.463654 TCTGTGGCAGCGAACTGTTT 60.464 50.000 0.00 0.00 46.30 2.83
4020 7507 4.809673 ACTCGCCTCAAAATTTTGATTCC 58.190 39.130 28.86 19.42 45.26 3.01
4167 7654 3.201266 AGGTAATCCGGCTTATGTCCAAA 59.799 43.478 0.29 0.00 39.05 3.28
4385 7872 2.359975 GGGGTTCAGCTTGGTCCG 60.360 66.667 0.00 0.00 0.00 4.79
4636 8131 7.822161 TTGTGTTTGTCTAGTACTACTACCA 57.178 36.000 0.00 0.00 0.00 3.25
4846 8341 9.498176 GGTTCTGACTTTAGTATTCACCTAAAA 57.502 33.333 0.00 0.00 34.82 1.52
4945 8450 4.436242 TGAAATCGACGTCTCTAGCTTT 57.564 40.909 14.70 1.95 0.00 3.51
5023 8530 6.106673 ACATATACACAAACTGGACTAGCAC 58.893 40.000 0.00 0.00 0.00 4.40
5054 8561 1.535462 GCATAAGTGTTTGAGCCGTGT 59.465 47.619 0.00 0.00 0.00 4.49
5061 8568 4.827692 AGTGTTTGAGCCGTGTATGATAA 58.172 39.130 0.00 0.00 0.00 1.75
5062 8569 4.870426 AGTGTTTGAGCCGTGTATGATAAG 59.130 41.667 0.00 0.00 0.00 1.73
5063 8570 4.630069 GTGTTTGAGCCGTGTATGATAAGT 59.370 41.667 0.00 0.00 0.00 2.24
5064 8571 4.868171 TGTTTGAGCCGTGTATGATAAGTC 59.132 41.667 0.00 0.00 0.00 3.01
5068 8578 4.081917 TGAGCCGTGTATGATAAGTCAACA 60.082 41.667 0.00 0.00 38.01 3.33
5103 8613 6.713276 TCTTCATTGTTTCGGTAAATAGGGA 58.287 36.000 0.00 0.00 0.00 4.20
5127 8637 6.566197 ACTTGATGTCTCTTTGAATTCACC 57.434 37.500 7.89 0.00 0.00 4.02
5140 8650 4.522114 TGAATTCACCAGAGTTTGTGTGA 58.478 39.130 3.38 0.00 36.12 3.58
5142 8652 5.066375 TGAATTCACCAGAGTTTGTGTGAAG 59.934 40.000 3.38 0.00 43.60 3.02
5143 8653 2.288666 TCACCAGAGTTTGTGTGAAGC 58.711 47.619 3.51 0.00 35.46 3.86
5144 8654 2.092968 TCACCAGAGTTTGTGTGAAGCT 60.093 45.455 3.51 0.00 35.46 3.74
5145 8655 2.684881 CACCAGAGTTTGTGTGAAGCTT 59.315 45.455 0.00 0.00 32.80 3.74
5146 8656 3.876914 CACCAGAGTTTGTGTGAAGCTTA 59.123 43.478 0.00 0.00 32.80 3.09
5148 8658 4.947388 ACCAGAGTTTGTGTGAAGCTTAAA 59.053 37.500 0.00 0.00 0.00 1.52
5149 8659 5.417580 ACCAGAGTTTGTGTGAAGCTTAAAA 59.582 36.000 0.00 0.00 0.00 1.52
5150 8660 6.096846 ACCAGAGTTTGTGTGAAGCTTAAAAT 59.903 34.615 0.00 0.00 0.00 1.82
5151 8661 6.638468 CCAGAGTTTGTGTGAAGCTTAAAATC 59.362 38.462 0.00 4.96 0.00 2.17
5152 8662 7.195646 CAGAGTTTGTGTGAAGCTTAAAATCA 58.804 34.615 16.85 2.02 30.42 2.57
5155 8665 9.677567 GAGTTTGTGTGAAGCTTAAAATCATTA 57.322 29.630 12.02 0.00 0.00 1.90
5156 8666 9.463443 AGTTTGTGTGAAGCTTAAAATCATTAC 57.537 29.630 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.730090 CGATCATGGCTGAAAGTGCAAC 60.730 50.000 0.00 0.00 34.37 4.17
1 2 1.469703 CGATCATGGCTGAAAGTGCAA 59.530 47.619 0.00 0.00 34.37 4.08
2 3 1.089112 CGATCATGGCTGAAAGTGCA 58.911 50.000 0.00 0.00 34.37 4.57
3 4 1.372582 TCGATCATGGCTGAAAGTGC 58.627 50.000 0.00 0.00 34.37 4.40
4 5 3.264947 TCTTCGATCATGGCTGAAAGTG 58.735 45.455 0.00 0.00 34.37 3.16
5 6 3.616956 TCTTCGATCATGGCTGAAAGT 57.383 42.857 0.00 0.00 34.37 2.66
6 7 6.609237 TTAATCTTCGATCATGGCTGAAAG 57.391 37.500 0.00 0.00 34.37 2.62
7 8 8.150296 TCTATTAATCTTCGATCATGGCTGAAA 58.850 33.333 0.00 0.00 34.37 2.69
8 9 7.670364 TCTATTAATCTTCGATCATGGCTGAA 58.330 34.615 0.00 0.00 34.37 3.02
9 10 7.232118 TCTATTAATCTTCGATCATGGCTGA 57.768 36.000 0.00 0.00 35.41 4.26
10 11 8.489990 AATCTATTAATCTTCGATCATGGCTG 57.510 34.615 0.00 0.00 0.00 4.85
11 12 9.814899 CTAATCTATTAATCTTCGATCATGGCT 57.185 33.333 0.00 0.00 0.00 4.75
12 13 9.809096 TCTAATCTATTAATCTTCGATCATGGC 57.191 33.333 0.00 0.00 0.00 4.40
57 58 8.458843 CGGGTTTATTTAATGAACTTCACATCT 58.541 33.333 11.41 0.00 0.00 2.90
58 59 8.455682 TCGGGTTTATTTAATGAACTTCACATC 58.544 33.333 11.41 0.00 0.00 3.06
59 60 8.343168 TCGGGTTTATTTAATGAACTTCACAT 57.657 30.769 11.41 0.00 0.00 3.21
60 61 7.747155 TCGGGTTTATTTAATGAACTTCACA 57.253 32.000 11.41 0.00 0.00 3.58
61 62 8.508875 TCTTCGGGTTTATTTAATGAACTTCAC 58.491 33.333 11.41 0.00 0.00 3.18
62 63 8.624367 TCTTCGGGTTTATTTAATGAACTTCA 57.376 30.769 11.41 0.00 0.00 3.02
63 64 8.182227 CCTCTTCGGGTTTATTTAATGAACTTC 58.818 37.037 11.41 5.07 0.00 3.01
64 65 7.362660 GCCTCTTCGGGTTTATTTAATGAACTT 60.363 37.037 11.41 0.00 0.00 2.66
65 66 6.095021 GCCTCTTCGGGTTTATTTAATGAACT 59.905 38.462 11.41 0.00 0.00 3.01
66 67 6.263344 GCCTCTTCGGGTTTATTTAATGAAC 58.737 40.000 4.31 4.31 0.00 3.18
67 68 5.358725 GGCCTCTTCGGGTTTATTTAATGAA 59.641 40.000 0.00 0.00 0.00 2.57
68 69 4.885325 GGCCTCTTCGGGTTTATTTAATGA 59.115 41.667 0.00 0.00 0.00 2.57
69 70 4.037565 GGGCCTCTTCGGGTTTATTTAATG 59.962 45.833 0.84 0.00 0.00 1.90
70 71 4.079385 AGGGCCTCTTCGGGTTTATTTAAT 60.079 41.667 0.00 0.00 0.00 1.40
71 72 3.267551 AGGGCCTCTTCGGGTTTATTTAA 59.732 43.478 0.00 0.00 0.00 1.52
72 73 2.848071 AGGGCCTCTTCGGGTTTATTTA 59.152 45.455 0.00 0.00 0.00 1.40
73 74 1.639108 AGGGCCTCTTCGGGTTTATTT 59.361 47.619 0.00 0.00 0.00 1.40
74 75 1.212195 GAGGGCCTCTTCGGGTTTATT 59.788 52.381 26.44 0.00 0.00 1.40
75 76 0.837940 GAGGGCCTCTTCGGGTTTAT 59.162 55.000 26.44 0.00 0.00 1.40
76 77 1.269703 GGAGGGCCTCTTCGGGTTTA 61.270 60.000 31.39 0.00 0.00 2.01
77 78 2.603652 GGAGGGCCTCTTCGGGTTT 61.604 63.158 31.39 0.00 0.00 3.27
78 79 3.009714 GGAGGGCCTCTTCGGGTT 61.010 66.667 31.39 0.00 0.00 4.11
80 81 4.806339 AGGGAGGGCCTCTTCGGG 62.806 72.222 31.39 0.00 0.00 5.14
81 82 3.157949 GAGGGAGGGCCTCTTCGG 61.158 72.222 31.39 0.00 0.00 4.30
82 83 3.157949 GGAGGGAGGGCCTCTTCG 61.158 72.222 31.39 0.00 34.95 3.79
83 84 2.770475 GGGAGGGAGGGCCTCTTC 60.770 72.222 31.39 26.19 34.95 2.87
84 85 4.806339 CGGGAGGGAGGGCCTCTT 62.806 72.222 31.39 20.49 34.95 2.85
87 88 4.677151 AAACGGGAGGGAGGGCCT 62.677 66.667 5.25 5.25 0.00 5.19
88 89 4.111053 GAAACGGGAGGGAGGGCC 62.111 72.222 0.00 0.00 0.00 5.80
89 90 4.111053 GGAAACGGGAGGGAGGGC 62.111 72.222 0.00 0.00 0.00 5.19
90 91 3.408853 GGGAAACGGGAGGGAGGG 61.409 72.222 0.00 0.00 0.00 4.30
91 92 2.285442 AGGGAAACGGGAGGGAGG 60.285 66.667 0.00 0.00 0.00 4.30
92 93 0.910088 AAGAGGGAAACGGGAGGGAG 60.910 60.000 0.00 0.00 0.00 4.30
93 94 0.908180 GAAGAGGGAAACGGGAGGGA 60.908 60.000 0.00 0.00 0.00 4.20
94 95 1.198759 TGAAGAGGGAAACGGGAGGG 61.199 60.000 0.00 0.00 0.00 4.30
95 96 0.036294 GTGAAGAGGGAAACGGGAGG 60.036 60.000 0.00 0.00 0.00 4.30
96 97 0.036294 GGTGAAGAGGGAAACGGGAG 60.036 60.000 0.00 0.00 0.00 4.30
97 98 0.473117 AGGTGAAGAGGGAAACGGGA 60.473 55.000 0.00 0.00 0.00 5.14
98 99 0.400594 AAGGTGAAGAGGGAAACGGG 59.599 55.000 0.00 0.00 0.00 5.28
99 100 2.565834 TCTAAGGTGAAGAGGGAAACGG 59.434 50.000 0.00 0.00 0.00 4.44
100 101 3.258622 AGTCTAAGGTGAAGAGGGAAACG 59.741 47.826 0.00 0.00 0.00 3.60
101 102 4.893829 AGTCTAAGGTGAAGAGGGAAAC 57.106 45.455 0.00 0.00 0.00 2.78
102 103 5.900437 TCTAGTCTAAGGTGAAGAGGGAAA 58.100 41.667 0.00 0.00 0.00 3.13
103 104 5.015391 ACTCTAGTCTAAGGTGAAGAGGGAA 59.985 44.000 0.00 0.00 35.80 3.97
104 105 4.540906 ACTCTAGTCTAAGGTGAAGAGGGA 59.459 45.833 0.00 0.00 35.80 4.20
105 106 4.862371 ACTCTAGTCTAAGGTGAAGAGGG 58.138 47.826 0.00 0.00 35.80 4.30
106 107 4.885325 GGACTCTAGTCTAAGGTGAAGAGG 59.115 50.000 9.84 0.00 44.20 3.69
107 108 4.885325 GGGACTCTAGTCTAAGGTGAAGAG 59.115 50.000 9.84 0.00 44.20 2.85
108 109 4.291513 TGGGACTCTAGTCTAAGGTGAAGA 59.708 45.833 9.84 0.00 44.20 2.87
109 110 4.601084 TGGGACTCTAGTCTAAGGTGAAG 58.399 47.826 9.84 0.00 44.20 3.02
110 111 4.669866 TGGGACTCTAGTCTAAGGTGAA 57.330 45.455 9.84 0.00 44.20 3.18
111 112 4.479056 AGATGGGACTCTAGTCTAAGGTGA 59.521 45.833 9.84 0.00 44.20 4.02
112 113 4.798882 AGATGGGACTCTAGTCTAAGGTG 58.201 47.826 9.84 0.00 44.20 4.00
113 114 6.593759 TTAGATGGGACTCTAGTCTAAGGT 57.406 41.667 9.84 0.00 44.20 3.50
114 115 6.373216 CGATTAGATGGGACTCTAGTCTAAGG 59.627 46.154 9.84 0.00 44.20 2.69
115 116 6.128117 GCGATTAGATGGGACTCTAGTCTAAG 60.128 46.154 9.84 0.00 44.20 2.18
116 117 5.706369 GCGATTAGATGGGACTCTAGTCTAA 59.294 44.000 9.84 1.55 44.20 2.10
117 118 5.247084 GCGATTAGATGGGACTCTAGTCTA 58.753 45.833 9.84 0.89 44.20 2.59
118 119 4.076394 GCGATTAGATGGGACTCTAGTCT 58.924 47.826 9.84 0.00 44.20 3.24
119 120 3.191791 GGCGATTAGATGGGACTCTAGTC 59.808 52.174 1.30 1.30 44.04 2.59
120 121 3.158676 GGCGATTAGATGGGACTCTAGT 58.841 50.000 0.00 0.00 0.00 2.57
121 122 3.157881 TGGCGATTAGATGGGACTCTAG 58.842 50.000 0.00 0.00 0.00 2.43
122 123 3.238788 TGGCGATTAGATGGGACTCTA 57.761 47.619 0.00 0.00 0.00 2.43
123 124 2.088104 TGGCGATTAGATGGGACTCT 57.912 50.000 0.00 0.00 0.00 3.24
124 125 2.613977 CCATGGCGATTAGATGGGACTC 60.614 54.545 0.00 0.00 34.14 3.36
125 126 1.349026 CCATGGCGATTAGATGGGACT 59.651 52.381 0.00 0.00 34.14 3.85
126 127 1.072331 ACCATGGCGATTAGATGGGAC 59.928 52.381 13.04 0.00 40.96 4.46
127 128 1.434188 ACCATGGCGATTAGATGGGA 58.566 50.000 13.04 0.00 40.96 4.37
128 129 2.276732 AACCATGGCGATTAGATGGG 57.723 50.000 13.04 0.00 40.96 4.00
129 130 2.951642 ACAAACCATGGCGATTAGATGG 59.048 45.455 13.04 0.00 42.17 3.51
130 131 3.627123 TGACAAACCATGGCGATTAGATG 59.373 43.478 13.04 2.08 41.43 2.90
131 132 3.627577 GTGACAAACCATGGCGATTAGAT 59.372 43.478 13.04 0.00 41.43 1.98
132 133 3.006940 GTGACAAACCATGGCGATTAGA 58.993 45.455 13.04 0.00 41.43 2.10
133 134 3.009723 AGTGACAAACCATGGCGATTAG 58.990 45.455 13.04 0.00 41.43 1.73
134 135 2.746904 CAGTGACAAACCATGGCGATTA 59.253 45.455 13.04 0.00 41.43 1.75
135 136 1.541147 CAGTGACAAACCATGGCGATT 59.459 47.619 13.04 1.43 41.43 3.34
136 137 1.167851 CAGTGACAAACCATGGCGAT 58.832 50.000 13.04 0.00 41.43 4.58
137 138 0.179032 ACAGTGACAAACCATGGCGA 60.179 50.000 13.04 0.00 41.43 5.54
138 139 1.464608 CTACAGTGACAAACCATGGCG 59.535 52.381 13.04 2.89 41.43 5.69
139 140 2.504367 ACTACAGTGACAAACCATGGC 58.496 47.619 13.04 0.00 37.68 4.40
140 141 4.133820 TCAACTACAGTGACAAACCATGG 58.866 43.478 11.19 11.19 0.00 3.66
141 142 5.947228 ATCAACTACAGTGACAAACCATG 57.053 39.130 0.00 0.00 0.00 3.66
142 143 9.383519 CTATAATCAACTACAGTGACAAACCAT 57.616 33.333 0.00 0.00 0.00 3.55
143 144 7.333423 GCTATAATCAACTACAGTGACAAACCA 59.667 37.037 0.00 0.00 0.00 3.67
144 145 7.201617 GGCTATAATCAACTACAGTGACAAACC 60.202 40.741 0.00 0.00 0.00 3.27
145 146 7.201617 GGGCTATAATCAACTACAGTGACAAAC 60.202 40.741 0.00 0.00 0.00 2.93
146 147 6.821665 GGGCTATAATCAACTACAGTGACAAA 59.178 38.462 0.00 0.00 0.00 2.83
147 148 6.156256 AGGGCTATAATCAACTACAGTGACAA 59.844 38.462 0.00 0.00 0.00 3.18
148 149 5.661312 AGGGCTATAATCAACTACAGTGACA 59.339 40.000 0.00 0.00 0.00 3.58
149 150 6.163135 AGGGCTATAATCAACTACAGTGAC 57.837 41.667 0.00 0.00 0.00 3.67
150 151 7.907841 TTAGGGCTATAATCAACTACAGTGA 57.092 36.000 0.00 0.00 0.00 3.41
151 152 8.958119 TTTTAGGGCTATAATCAACTACAGTG 57.042 34.615 0.00 0.00 0.00 3.66
179 180 2.303022 GGGCCTATAATCAGCTAGTGCA 59.697 50.000 0.84 0.00 42.74 4.57
181 182 4.223700 TGATGGGCCTATAATCAGCTAGTG 59.776 45.833 0.00 0.00 0.00 2.74
183 184 5.426504 CTTGATGGGCCTATAATCAGCTAG 58.573 45.833 0.00 0.00 32.23 3.42
187 188 4.298103 AGCTTGATGGGCCTATAATCAG 57.702 45.455 0.00 0.00 32.23 2.90
245 247 4.514401 GGTGGTTTGTACTCTAAGATGGG 58.486 47.826 0.00 0.00 0.00 4.00
251 253 4.634199 CGAAAGGGTGGTTTGTACTCTAA 58.366 43.478 0.00 0.00 0.00 2.10
290 292 2.009051 TGTTAGATGGCGTTGCATGAG 58.991 47.619 0.00 0.00 0.00 2.90
291 293 2.106477 TGTTAGATGGCGTTGCATGA 57.894 45.000 0.00 0.00 0.00 3.07
300 302 7.869429 CCATTCATTAAGGAATTGTTAGATGGC 59.131 37.037 12.46 0.00 35.37 4.40
302 304 9.740239 CACCATTCATTAAGGAATTGTTAGATG 57.260 33.333 14.73 3.54 35.37 2.90
395 398 9.511272 CCCACCACTTTAGTTTATTAGTAGTTT 57.489 33.333 0.00 0.00 0.00 2.66
396 399 8.105197 CCCCACCACTTTAGTTTATTAGTAGTT 58.895 37.037 0.00 0.00 0.00 2.24
397 400 7.458806 TCCCCACCACTTTAGTTTATTAGTAGT 59.541 37.037 0.00 0.00 0.00 2.73
398 401 7.854337 TCCCCACCACTTTAGTTTATTAGTAG 58.146 38.462 0.00 0.00 0.00 2.57
399 402 7.679453 TCTCCCCACCACTTTAGTTTATTAGTA 59.321 37.037 0.00 0.00 0.00 1.82
400 403 6.502863 TCTCCCCACCACTTTAGTTTATTAGT 59.497 38.462 0.00 0.00 0.00 2.24
401 404 6.954232 TCTCCCCACCACTTTAGTTTATTAG 58.046 40.000 0.00 0.00 0.00 1.73
402 405 6.956102 TCTCCCCACCACTTTAGTTTATTA 57.044 37.500 0.00 0.00 0.00 0.98
403 406 5.853572 TCTCCCCACCACTTTAGTTTATT 57.146 39.130 0.00 0.00 0.00 1.40
446 449 0.248949 GGAGGGAGATCGTTGCGTAC 60.249 60.000 0.00 0.00 0.00 3.67
447 450 1.389609 GGGAGGGAGATCGTTGCGTA 61.390 60.000 0.00 0.00 0.00 4.42
449 452 2.107141 GGGAGGGAGATCGTTGCG 59.893 66.667 0.00 0.00 0.00 4.85
450 453 1.443828 GAGGGAGGGAGATCGTTGC 59.556 63.158 0.00 0.00 0.00 4.17
451 454 0.397816 AGGAGGGAGGGAGATCGTTG 60.398 60.000 0.00 0.00 0.00 4.10
452 455 0.340208 AAGGAGGGAGGGAGATCGTT 59.660 55.000 0.00 0.00 0.00 3.85
453 456 0.105913 GAAGGAGGGAGGGAGATCGT 60.106 60.000 0.00 0.00 0.00 3.73
454 457 0.830023 GGAAGGAGGGAGGGAGATCG 60.830 65.000 0.00 0.00 0.00 3.69
455 458 0.472925 GGGAAGGAGGGAGGGAGATC 60.473 65.000 0.00 0.00 0.00 2.75
456 459 0.938926 AGGGAAGGAGGGAGGGAGAT 60.939 60.000 0.00 0.00 0.00 2.75
457 460 1.550374 AGGGAAGGAGGGAGGGAGA 60.550 63.158 0.00 0.00 0.00 3.71
458 461 1.074850 GAGGGAAGGAGGGAGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
459 462 2.647949 GGAGGGAAGGAGGGAGGGA 61.648 68.421 0.00 0.00 0.00 4.20
460 463 2.040359 GGAGGGAAGGAGGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
461 464 2.040359 GGGAGGGAAGGAGGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
462 465 1.074850 GAGGGAGGGAAGGAGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
463 466 2.647949 GGAGGGAGGGAAGGAGGGA 61.648 68.421 0.00 0.00 0.00 4.20
464 467 2.040359 GGAGGGAGGGAAGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
465 468 2.040359 GGGAGGGAGGGAAGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
470 473 1.921857 GGAAACGGGAGGGAGGGAA 60.922 63.158 0.00 0.00 0.00 3.97
513 524 1.002274 GAGAGAGAAGGGGAGGGCA 59.998 63.158 0.00 0.00 0.00 5.36
521 534 2.015227 GCGGCCAGAGAGAGAGAAGG 62.015 65.000 2.24 0.00 0.00 3.46
522 535 1.037030 AGCGGCCAGAGAGAGAGAAG 61.037 60.000 2.24 0.00 0.00 2.85
523 536 0.613292 AAGCGGCCAGAGAGAGAGAA 60.613 55.000 2.24 0.00 0.00 2.87
555 568 3.726631 CTCGTGGTCGCTCTCGCTC 62.727 68.421 0.00 0.00 36.96 5.03
556 569 3.805307 CTCGTGGTCGCTCTCGCT 61.805 66.667 0.00 0.00 36.96 4.93
558 571 3.726631 GAGCTCGTGGTCGCTCTCG 62.727 68.421 0.00 0.00 46.87 4.04
559 572 2.101380 GAGCTCGTGGTCGCTCTC 59.899 66.667 0.00 0.00 46.87 3.20
981 994 4.777854 TCGGGCTGCCTCTGCCTA 62.778 66.667 19.68 0.00 45.73 3.93
988 1001 3.859414 GAGCATCTCGGGCTGCCT 61.859 66.667 19.68 0.00 42.78 4.75
997 1010 1.439644 GGTCCTGGACGAGCATCTC 59.560 63.158 19.98 0.38 32.65 2.75
998 1011 2.418910 CGGTCCTGGACGAGCATCT 61.419 63.158 19.98 0.00 32.65 2.90
1140 1190 1.220477 GAGGAGCTTGGAGGAGTGC 59.780 63.158 0.00 0.00 0.00 4.40
1230 1280 4.200283 CGGTCGAGGCAGAGGAGC 62.200 72.222 0.00 0.00 0.00 4.70
1276 1326 2.687566 CGGGTAGGGGAGCTTGGT 60.688 66.667 0.00 0.00 0.00 3.67
1542 1601 2.656069 GGCGTAGGGCAGGAAGTCA 61.656 63.158 3.83 0.00 46.16 3.41
1560 1619 2.432628 GTCTTGCGGACGTGGGAG 60.433 66.667 0.00 0.00 35.07 4.30
1645 1704 1.457604 CCAGATCATTCCCCGGCAT 59.542 57.895 0.00 0.00 0.00 4.40
1662 1721 2.091541 TCAACATCGAAATGCTTCCCC 58.908 47.619 0.00 0.00 36.26 4.81
1848 1907 1.219124 GCGGCCACTGAAGATCTCA 59.781 57.895 2.24 0.00 0.00 3.27
1917 1976 3.613299 GCGGCTTTCTAGTGAAGTAGAAC 59.387 47.826 7.04 0.00 38.49 3.01
2160 2219 3.054948 CCTTCCGGTAAATAGTTGGTGGA 60.055 47.826 0.00 0.00 0.00 4.02
2238 2297 9.159364 CACTCATTCAAGAATTTGATCAGTCTA 57.841 33.333 0.00 0.00 42.60 2.59
2664 2723 3.744238 TTGCTATGCTCGGCAAGTATA 57.256 42.857 2.68 0.00 43.62 1.47
2710 2774 3.005554 ACTTGTATGCATGTGACAGAGC 58.994 45.455 10.16 5.93 32.65 4.09
2721 2786 5.411361 GGTAACAATCACTCACTTGTATGCA 59.589 40.000 0.00 0.00 34.61 3.96
2858 2932 0.697658 TGGTGGCATTGGATCTGACA 59.302 50.000 0.00 0.00 0.00 3.58
2909 2983 8.071177 AGGTTCAACACGGTAATATAGTTAGT 57.929 34.615 0.00 0.00 0.00 2.24
2917 2991 4.497300 GCACTAGGTTCAACACGGTAATA 58.503 43.478 0.00 0.00 0.00 0.98
2923 2997 1.588674 TTGGCACTAGGTTCAACACG 58.411 50.000 0.00 0.00 0.00 4.49
2994 3509 9.545105 TGAGCAAAAATGTGTTTATTCTCAAAT 57.455 25.926 0.00 0.00 0.00 2.32
3064 3580 1.268066 ACAATTGGTGCCATCATGCA 58.732 45.000 10.83 0.00 39.37 3.96
3066 3582 2.417239 GCAAACAATTGGTGCCATCATG 59.583 45.455 20.15 5.15 37.02 3.07
3067 3583 2.038689 TGCAAACAATTGGTGCCATCAT 59.961 40.909 25.02 0.00 37.48 2.45
3239 6122 6.696441 AATTGGAGATGATCTCTTTTCTGC 57.304 37.500 20.73 4.31 42.95 4.26
3303 6187 4.083855 ACAATGATATAAAGCGCATCGGTG 60.084 41.667 11.47 7.88 37.73 4.94
3311 6195 5.993891 ACAGCATCACAATGATATAAAGCG 58.006 37.500 0.00 0.00 34.28 4.68
3419 6544 3.245284 CAGAATTCGCATAAGGTGGTACG 59.755 47.826 0.00 0.00 0.00 3.67
3653 7140 4.193865 TGATTGACAGCACATACATGAGG 58.806 43.478 0.00 0.00 0.00 3.86
3654 7141 5.806366 TTGATTGACAGCACATACATGAG 57.194 39.130 0.00 0.00 0.00 2.90
3870 7357 1.571460 CAGTTCGCTGCCACAGAAC 59.429 57.895 9.27 9.27 43.13 3.01
3891 7378 1.202830 ACAAACTGTCGGGGCACATAA 60.203 47.619 0.00 0.00 0.00 1.90
4020 7507 2.815647 GTTCCGGCCAGAGCTTCG 60.816 66.667 2.24 0.00 39.73 3.79
4167 7654 1.648568 TCCATCAGAAGAGGGTCTCCT 59.351 52.381 0.00 0.00 45.75 3.69
4636 8131 6.491062 CAGATATTCTCTGTCTCAGTCCAGAT 59.509 42.308 0.00 0.00 45.42 2.90
4765 8260 8.996271 AGTGAATACTACCTTTAAACTTTTCCG 58.004 33.333 0.00 0.00 34.74 4.30
4779 8274 8.507524 AAATAGAGGCAAAAGTGAATACTACC 57.492 34.615 0.00 0.00 35.69 3.18
4807 8302 6.715347 AAGTCAGAACCTTTGCTAAACAAT 57.285 33.333 0.00 0.00 38.31 2.71
4869 8364 5.104941 ACGGATCTCTGTCATTCATGGTTTA 60.105 40.000 0.00 0.00 0.00 2.01
4873 8371 3.129109 CACGGATCTCTGTCATTCATGG 58.871 50.000 0.00 0.00 32.07 3.66
4910 8415 6.425721 ACGTCGATTTCAAAGAACCTTGATAA 59.574 34.615 0.00 0.00 35.31 1.75
4914 8419 4.211374 AGACGTCGATTTCAAAGAACCTTG 59.789 41.667 10.46 0.00 0.00 3.61
4945 8450 6.350110 GCTGGAATATCAAGTTGCAAAAGGTA 60.350 38.462 0.00 0.00 0.00 3.08
5023 8530 6.264832 TCAAACACTTATGCACAACTTTCAG 58.735 36.000 0.00 0.00 0.00 3.02
5035 8542 4.629634 TCATACACGGCTCAAACACTTATG 59.370 41.667 0.00 0.00 0.00 1.90
5037 8544 4.260139 TCATACACGGCTCAAACACTTA 57.740 40.909 0.00 0.00 0.00 2.24
5039 8546 2.831685 TCATACACGGCTCAAACACT 57.168 45.000 0.00 0.00 0.00 3.55
5045 8552 4.081917 TGTTGACTTATCATACACGGCTCA 60.082 41.667 0.00 0.00 33.85 4.26
5094 8604 8.602424 TCAAAGAGACATCAAGTTCCCTATTTA 58.398 33.333 0.00 0.00 0.00 1.40
5103 8613 6.547141 TGGTGAATTCAAAGAGACATCAAGTT 59.453 34.615 10.35 0.00 0.00 2.66
5127 8637 7.195646 TGATTTTAAGCTTCACACAAACTCTG 58.804 34.615 0.00 0.00 0.00 3.35
5148 8658 9.844790 CATCAAGTGTGTAATTGTGTAATGATT 57.155 29.630 0.00 0.00 33.80 2.57
5149 8659 9.013229 ACATCAAGTGTGTAATTGTGTAATGAT 57.987 29.630 0.00 0.00 40.28 2.45
5150 8660 8.389779 ACATCAAGTGTGTAATTGTGTAATGA 57.610 30.769 0.00 0.00 40.28 2.57
5172 8696 6.037098 GTCTACTTCAATACGAGCTTCACAT 58.963 40.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.