Multiple sequence alignment - TraesCS1A01G327300

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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 TraesCS1A01G327300 chr1A 100.000 4516 0 0 1 4516 516852696 516848181 0.000000e+00 8340.0
1 TraesCS1A01G327300 chr1A 82.609 713 97 19 1477 2184 516788655 516787965 5.000000e-169 604.0
2 TraesCS1A01G327300 chr1A 81.337 643 88 19 2262 2886 516787836 516787208 1.130000e-135 494.0
3 TraesCS1A01G327300 chr1A 78.374 615 96 20 2935 3532 516786931 516786337 9.230000e-97 364.0
4 TraesCS1A01G327300 chr1A 98.601 143 2 0 1 143 71442154 71442296 2.090000e-63 254.0
5 TraesCS1A01G327300 chr1A 97.500 40 1 0 144 183 511241876 511241837 8.110000e-08 69.4
6 TraesCS1A01G327300 chr1D 96.489 3361 66 21 481 3802 420567783 420564436 0.000000e+00 5505.0
7 TraesCS1A01G327300 chr1D 81.918 730 107 17 1460 2184 420556169 420555460 1.080000e-165 593.0
8 TraesCS1A01G327300 chr1D 89.639 415 27 7 4079 4492 420564191 420563792 8.660000e-142 514.0
9 TraesCS1A01G327300 chr1D 83.051 531 65 14 2375 2886 420555224 420554700 4.120000e-125 459.0
10 TraesCS1A01G327300 chr1D 90.123 324 16 11 181 489 420568317 420567995 1.510000e-109 407.0
11 TraesCS1A01G327300 chr1D 91.176 238 9 6 3787 4020 420564420 420564191 3.390000e-81 313.0
12 TraesCS1A01G327300 chr1B 93.635 1414 45 22 2314 3699 568644329 568642933 0.000000e+00 2071.0
13 TraesCS1A01G327300 chr1B 93.106 1262 61 14 948 2200 568645624 568644380 0.000000e+00 1825.0
14 TraesCS1A01G327300 chr1B 82.667 675 90 19 1492 2163 568570844 568570194 1.410000e-159 573.0
15 TraesCS1A01G327300 chr1B 80.401 648 89 24 2264 2886 568570043 568569409 4.120000e-125 459.0
16 TraesCS1A01G327300 chr1B 79.058 616 92 20 2934 3532 568569163 568568568 5.480000e-104 388.0
17 TraesCS1A01G327300 chr1B 86.243 189 19 5 3773 3959 568642830 568642647 9.910000e-47 198.0
18 TraesCS1A01G327300 chr7B 91.284 218 12 3 181 397 741338389 741338178 1.590000e-74 291.0
19 TraesCS1A01G327300 chr7B 98.611 144 2 0 1 144 640169949 640170092 5.800000e-64 255.0
20 TraesCS1A01G327300 chr7B 79.949 389 17 11 399 737 741338140 741337763 3.510000e-56 230.0
21 TraesCS1A01G327300 chr7B 100.000 37 0 0 144 180 694256563 694256599 8.110000e-08 69.4
22 TraesCS1A01G327300 chr2D 76.603 577 80 23 1605 2175 642350936 642351463 2.680000e-67 267.0
23 TraesCS1A01G327300 chr3A 99.301 143 1 0 1 143 47619545 47619403 4.480000e-65 259.0
24 TraesCS1A01G327300 chr3A 98.601 143 2 0 1 143 741355849 741355991 2.090000e-63 254.0
25 TraesCS1A01G327300 chr3A 78.899 109 23 0 2549 2657 566326001 566325893 1.740000e-09 75.0
26 TraesCS1A01G327300 chr7A 98.611 144 2 0 1 144 724959570 724959713 5.800000e-64 255.0
27 TraesCS1A01G327300 chr7A 98.601 143 2 0 1 143 9174526 9174668 2.090000e-63 254.0
28 TraesCS1A01G327300 chr5B 98.611 144 2 0 1 144 501103198 501103055 5.800000e-64 255.0
29 TraesCS1A01G327300 chr5B 100.000 38 0 0 144 181 251344637 251344600 2.250000e-08 71.3
30 TraesCS1A01G327300 chr4A 98.601 143 2 0 1 143 589321533 589321391 2.090000e-63 254.0
31 TraesCS1A01G327300 chr6A 96.711 152 4 1 1 151 560435493 560435644 7.500000e-63 252.0
32 TraesCS1A01G327300 chr6D 85.714 175 7 3 563 728 63299817 63299982 7.770000e-38 169.0
33 TraesCS1A01G327300 chr6D 85.143 175 8 3 563 728 63063159 63062994 3.610000e-36 163.0
34 TraesCS1A01G327300 chr6D 88.136 59 7 0 507 565 63063232 63063174 2.250000e-08 71.3
35 TraesCS1A01G327300 chr6D 88.136 59 7 0 507 565 63299744 63299802 2.250000e-08 71.3
36 TraesCS1A01G327300 chr5D 90.625 96 9 0 1243 1338 428546057 428546152 1.320000e-25 128.0
37 TraesCS1A01G327300 chr3D 91.954 87 7 0 1243 1329 307676397 307676483 6.130000e-24 122.0
38 TraesCS1A01G327300 chr3D 78.333 120 22 3 2539 2654 422649308 422649427 1.740000e-09 75.0
39 TraesCS1A01G327300 chr5A 88.889 72 8 0 1243 1314 500833160 500833231 6.220000e-14 89.8
40 TraesCS1A01G327300 chr5A 97.297 37 1 0 144 180 470044035 470044071 3.770000e-06 63.9
41 TraesCS1A01G327300 chr3B 79.245 106 22 0 2549 2654 550731709 550731814 1.740000e-09 75.0
42 TraesCS1A01G327300 chrUn 97.561 41 0 1 144 184 32174670 32174709 8.110000e-08 69.4
43 TraesCS1A01G327300 chr7D 100.000 37 0 0 144 180 53359674 53359710 8.110000e-08 69.4
44 TraesCS1A01G327300 chr7D 95.122 41 2 0 144 184 8885927 8885967 1.050000e-06 65.8
45 TraesCS1A01G327300 chr2B 100.000 36 0 0 144 179 423341807 423341842 2.920000e-07 67.6
46 TraesCS1A01G327300 chr6B 100.000 35 0 0 146 180 623367287 623367321 1.050000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G327300 chr1A 516848181 516852696 4515 True 8340.000000 8340 100.000000 1 4516 1 chr1A.!!$R2 4515
1 TraesCS1A01G327300 chr1A 516786337 516788655 2318 True 487.333333 604 80.773333 1477 3532 3 chr1A.!!$R3 2055
2 TraesCS1A01G327300 chr1D 420563792 420568317 4525 True 1684.750000 5505 91.856750 181 4492 4 chr1D.!!$R2 4311
3 TraesCS1A01G327300 chr1D 420554700 420556169 1469 True 526.000000 593 82.484500 1460 2886 2 chr1D.!!$R1 1426
4 TraesCS1A01G327300 chr1B 568642647 568645624 2977 True 1364.666667 2071 90.994667 948 3959 3 chr1B.!!$R2 3011
5 TraesCS1A01G327300 chr1B 568568568 568570844 2276 True 473.333333 573 80.708667 1492 3532 3 chr1B.!!$R1 2040
6 TraesCS1A01G327300 chr7B 741337763 741338389 626 True 260.500000 291 85.616500 181 737 2 chr7B.!!$R1 556
7 TraesCS1A01G327300 chr2D 642350936 642351463 527 False 267.000000 267 76.603000 1605 2175 1 chr2D.!!$F1 570

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
82 83 0.108567 TGTCGGCATAGCGCAAAGTA 60.109 50.0 11.47 0.0 45.17 2.24 F
140 141 0.177373 GTAGGGCCAGTTTCCGGTAG 59.823 60.0 6.18 0.0 0.00 3.18 F
141 142 0.252375 TAGGGCCAGTTTCCGGTAGT 60.252 55.0 6.18 0.0 0.00 2.73 F
1330 1643 0.439985 CATGTTCGTCGGACTGCAAG 59.560 55.0 5.05 0.0 42.29 4.01 F
1331 1644 0.670546 ATGTTCGTCGGACTGCAAGG 60.671 55.0 5.05 0.0 39.30 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2388 0.182061 ATGCCTGTGCCTGATCGAAT 59.818 50.000 0.00 0.0 36.33 3.34 R
2152 2497 3.008485 AGGAGGAGCGAGAAAACAAAGAT 59.992 43.478 0.00 0.0 0.00 2.40 R
2177 2522 5.297776 GGAGTAGGTAGTAACACGAATAGCA 59.702 44.000 0.00 0.0 0.00 3.49 R
3153 3823 4.101585 TCAGCGATGGGATAAGTTTCAGAT 59.898 41.667 0.00 0.0 0.00 2.90 R
3537 4225 6.963049 AATTCTACTACAACGTAGCAAAGG 57.037 37.500 1.08 0.0 37.40 3.11 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 2.107141 GCCGTCGGCTTAGCTCAT 59.893 61.111 28.98 0.00 46.69 2.90
21 22 2.240500 GCCGTCGGCTTAGCTCATG 61.241 63.158 28.98 0.00 46.69 3.07
22 23 1.592669 CCGTCGGCTTAGCTCATGG 60.593 63.158 3.59 2.03 0.00 3.66
23 24 1.141881 CGTCGGCTTAGCTCATGGT 59.858 57.895 3.59 0.00 0.00 3.55
24 25 0.384309 CGTCGGCTTAGCTCATGGTA 59.616 55.000 3.59 0.00 0.00 3.25
25 26 1.600663 CGTCGGCTTAGCTCATGGTAG 60.601 57.143 3.59 0.00 0.00 3.18
26 27 0.389391 TCGGCTTAGCTCATGGTAGC 59.611 55.000 3.59 0.00 43.11 3.58
27 28 0.601311 CGGCTTAGCTCATGGTAGCC 60.601 60.000 3.59 8.17 43.86 3.93
28 29 0.250510 GGCTTAGCTCATGGTAGCCC 60.251 60.000 3.59 0.00 43.86 5.19
29 30 0.601311 GCTTAGCTCATGGTAGCCCG 60.601 60.000 0.00 0.00 43.86 6.13
30 31 1.040646 CTTAGCTCATGGTAGCCCGA 58.959 55.000 2.91 0.00 43.86 5.14
31 32 0.750850 TTAGCTCATGGTAGCCCGAC 59.249 55.000 2.91 0.00 43.86 4.79
32 33 1.452953 TAGCTCATGGTAGCCCGACG 61.453 60.000 2.91 0.00 43.86 5.12
33 34 2.417516 CTCATGGTAGCCCGACGG 59.582 66.667 6.99 6.99 0.00 4.79
43 44 2.279252 CCCGACGGCCAAGATACG 60.279 66.667 8.86 0.00 0.00 3.06
44 45 2.960129 CCGACGGCCAAGATACGC 60.960 66.667 2.24 0.00 0.00 4.42
45 46 2.960129 CGACGGCCAAGATACGCC 60.960 66.667 2.24 0.00 42.05 5.68
50 51 2.960129 GCCAAGATACGCCGACGG 60.960 66.667 10.29 10.29 46.04 4.79
51 52 2.960129 CCAAGATACGCCGACGGC 60.960 66.667 29.10 29.10 46.75 5.68
68 69 2.738521 CCAAGACGTGGCTGTCGG 60.739 66.667 0.00 2.74 41.72 4.79
69 70 3.414700 CAAGACGTGGCTGTCGGC 61.415 66.667 0.00 0.00 43.70 5.54
70 71 3.923864 AAGACGTGGCTGTCGGCA 61.924 61.111 5.89 0.00 43.70 5.69
78 79 3.195002 GCTGTCGGCATAGCGCAA 61.195 61.111 11.47 0.00 45.17 4.85
79 80 2.749865 GCTGTCGGCATAGCGCAAA 61.750 57.895 11.47 0.00 45.17 3.68
80 81 1.349627 CTGTCGGCATAGCGCAAAG 59.650 57.895 11.47 0.00 45.17 2.77
81 82 1.361668 CTGTCGGCATAGCGCAAAGT 61.362 55.000 11.47 0.00 45.17 2.66
82 83 0.108567 TGTCGGCATAGCGCAAAGTA 60.109 50.000 11.47 0.00 45.17 2.24
83 84 0.577269 GTCGGCATAGCGCAAAGTAG 59.423 55.000 11.47 0.00 45.17 2.57
84 85 0.529773 TCGGCATAGCGCAAAGTAGG 60.530 55.000 11.47 0.00 45.17 3.18
85 86 1.649267 GGCATAGCGCAAAGTAGGC 59.351 57.895 11.47 6.30 45.17 3.93
86 87 1.649267 GCATAGCGCAAAGTAGGCC 59.351 57.895 11.47 0.00 41.79 5.19
87 88 1.934463 CATAGCGCAAAGTAGGCCG 59.066 57.895 11.47 0.00 0.00 6.13
88 89 0.529773 CATAGCGCAAAGTAGGCCGA 60.530 55.000 11.47 0.00 0.00 5.54
89 90 0.529992 ATAGCGCAAAGTAGGCCGAC 60.530 55.000 11.47 8.12 0.00 4.79
90 91 2.877360 TAGCGCAAAGTAGGCCGACG 62.877 60.000 11.47 0.00 0.00 5.12
91 92 3.186047 CGCAAAGTAGGCCGACGG 61.186 66.667 10.29 10.29 0.00 4.79
113 114 1.226660 CCGTCGGCATTGATTTGGC 60.227 57.895 0.00 0.00 38.71 4.52
114 115 1.226660 CGTCGGCATTGATTTGGCC 60.227 57.895 0.00 0.00 44.27 5.36
117 118 4.812814 GGCATTGATTTGGCCGTC 57.187 55.556 0.00 0.00 38.04 4.79
118 119 1.226660 GGCATTGATTTGGCCGTCG 60.227 57.895 0.00 0.00 38.04 5.12
119 120 1.226660 GCATTGATTTGGCCGTCGG 60.227 57.895 6.99 6.99 0.00 4.79
120 121 1.433064 CATTGATTTGGCCGTCGGG 59.567 57.895 14.38 0.00 0.00 5.14
121 122 1.752694 ATTGATTTGGCCGTCGGGG 60.753 57.895 14.38 0.00 39.58 5.73
122 123 2.493273 ATTGATTTGGCCGTCGGGGT 62.493 55.000 14.38 0.00 38.44 4.95
123 124 1.839148 TTGATTTGGCCGTCGGGGTA 61.839 55.000 14.38 0.00 38.44 3.69
124 125 1.523032 GATTTGGCCGTCGGGGTAG 60.523 63.158 14.38 0.00 38.44 3.18
125 126 2.935627 GATTTGGCCGTCGGGGTAGG 62.936 65.000 14.38 0.00 38.44 3.18
132 133 3.007323 GTCGGGGTAGGGCCAGTT 61.007 66.667 6.18 0.00 39.65 3.16
133 134 2.204029 TCGGGGTAGGGCCAGTTT 60.204 61.111 6.18 0.00 39.65 2.66
134 135 2.271173 CGGGGTAGGGCCAGTTTC 59.729 66.667 6.18 0.00 39.65 2.78
135 136 2.681591 GGGGTAGGGCCAGTTTCC 59.318 66.667 6.18 0.00 39.65 3.13
136 137 2.271173 GGGTAGGGCCAGTTTCCG 59.729 66.667 6.18 0.00 39.65 4.30
137 138 2.271173 GGTAGGGCCAGTTTCCGG 59.729 66.667 6.18 0.00 37.17 5.14
138 139 2.599757 GGTAGGGCCAGTTTCCGGT 61.600 63.158 6.18 0.00 37.17 5.28
139 140 1.266867 GGTAGGGCCAGTTTCCGGTA 61.267 60.000 6.18 0.00 37.17 4.02
140 141 0.177373 GTAGGGCCAGTTTCCGGTAG 59.823 60.000 6.18 0.00 0.00 3.18
141 142 0.252375 TAGGGCCAGTTTCCGGTAGT 60.252 55.000 6.18 0.00 0.00 2.73
142 143 1.376812 GGGCCAGTTTCCGGTAGTG 60.377 63.158 4.39 4.23 0.00 2.74
143 144 1.376812 GGCCAGTTTCCGGTAGTGG 60.377 63.158 21.59 21.59 38.81 4.00
144 145 4.296265 CCAGTTTCCGGTAGTGGC 57.704 61.111 16.61 0.00 29.86 5.01
145 146 1.373435 CCAGTTTCCGGTAGTGGCA 59.627 57.895 16.61 0.00 29.86 4.92
146 147 0.673644 CCAGTTTCCGGTAGTGGCAG 60.674 60.000 16.61 0.00 29.86 4.85
147 148 1.003718 AGTTTCCGGTAGTGGCAGC 60.004 57.895 0.00 0.00 0.00 5.25
148 149 2.047655 TTTCCGGTAGTGGCAGCG 60.048 61.111 0.00 0.00 39.07 5.18
149 150 4.752879 TTCCGGTAGTGGCAGCGC 62.753 66.667 0.00 0.00 38.07 5.92
152 153 3.490759 CGGTAGTGGCAGCGCAAG 61.491 66.667 11.47 2.01 43.44 4.01
153 154 2.358737 GGTAGTGGCAGCGCAAGT 60.359 61.111 11.47 0.00 41.68 3.16
154 155 1.966451 GGTAGTGGCAGCGCAAGTT 60.966 57.895 11.47 0.00 41.68 2.66
155 156 1.497722 GTAGTGGCAGCGCAAGTTC 59.502 57.895 11.47 0.00 41.68 3.01
156 157 0.951040 GTAGTGGCAGCGCAAGTTCT 60.951 55.000 11.47 4.87 41.68 3.01
157 158 0.670546 TAGTGGCAGCGCAAGTTCTC 60.671 55.000 11.47 0.34 41.68 2.87
158 159 3.043713 TGGCAGCGCAAGTTCTCG 61.044 61.111 11.47 0.00 41.68 4.04
159 160 3.793144 GGCAGCGCAAGTTCTCGG 61.793 66.667 11.47 0.00 41.68 4.63
160 161 2.738521 GCAGCGCAAGTTCTCGGA 60.739 61.111 11.47 0.00 41.68 4.55
161 162 3.016474 GCAGCGCAAGTTCTCGGAC 62.016 63.158 11.47 0.00 41.68 4.79
162 163 2.048127 AGCGCAAGTTCTCGGACC 60.048 61.111 11.47 0.00 41.68 4.46
163 164 3.479269 GCGCAAGTTCTCGGACCG 61.479 66.667 7.84 7.84 41.68 4.79
164 165 3.479269 CGCAAGTTCTCGGACCGC 61.479 66.667 9.66 0.00 0.00 5.68
165 166 3.119096 GCAAGTTCTCGGACCGCC 61.119 66.667 9.66 0.00 0.00 6.13
166 167 2.342279 CAAGTTCTCGGACCGCCA 59.658 61.111 9.66 0.00 0.00 5.69
167 168 1.738099 CAAGTTCTCGGACCGCCAG 60.738 63.158 9.66 2.10 0.00 4.85
168 169 2.207924 AAGTTCTCGGACCGCCAGT 61.208 57.895 9.66 0.00 0.00 4.00
169 170 2.432628 GTTCTCGGACCGCCAGTG 60.433 66.667 9.66 0.00 0.00 3.66
170 171 4.373116 TTCTCGGACCGCCAGTGC 62.373 66.667 9.66 0.00 0.00 4.40
175 176 2.676471 GGACCGCCAGTGCCATTT 60.676 61.111 0.00 0.00 0.00 2.32
176 177 1.377987 GGACCGCCAGTGCCATTTA 60.378 57.895 0.00 0.00 0.00 1.40
177 178 1.654023 GGACCGCCAGTGCCATTTAC 61.654 60.000 0.00 0.00 0.00 2.01
178 179 0.676782 GACCGCCAGTGCCATTTACT 60.677 55.000 0.00 0.00 0.00 2.24
179 180 0.676782 ACCGCCAGTGCCATTTACTC 60.677 55.000 0.00 0.00 0.00 2.59
205 206 3.863142 ACAGCATGGCTTCAAAATCTC 57.137 42.857 0.00 0.00 43.62 2.75
215 216 4.201861 GGCTTCAAAATCTCGAACAGGATC 60.202 45.833 0.00 0.00 0.00 3.36
348 350 2.107141 GCGTGCTCCTCGCCTAAT 59.893 61.111 0.00 0.00 46.61 1.73
349 351 1.951631 GCGTGCTCCTCGCCTAATC 60.952 63.158 0.00 0.00 46.61 1.75
350 352 1.658717 CGTGCTCCTCGCCTAATCG 60.659 63.158 0.00 0.00 38.05 3.34
351 353 1.734137 GTGCTCCTCGCCTAATCGA 59.266 57.895 0.00 0.00 38.05 3.59
360 362 2.792947 GCCTAATCGAGGGGTGCGA 61.793 63.158 0.00 0.00 46.81 5.10
361 363 1.820581 CCTAATCGAGGGGTGCGAA 59.179 57.895 0.00 0.00 42.39 4.70
398 401 4.129737 CGGCGGTGTCGTCCTCAT 62.130 66.667 0.00 0.00 37.80 2.90
399 402 2.509336 GGCGGTGTCGTCCTCATG 60.509 66.667 0.00 0.00 38.89 3.07
400 403 2.509336 GCGGTGTCGTCCTCATGG 60.509 66.667 0.00 0.00 38.89 3.66
401 404 2.184322 CGGTGTCGTCCTCATGGG 59.816 66.667 0.00 0.00 0.00 4.00
403 406 2.662596 GTGTCGTCCTCATGGGCA 59.337 61.111 0.00 0.00 37.98 5.36
404 407 1.741770 GTGTCGTCCTCATGGGCAC 60.742 63.158 0.00 0.00 37.98 5.01
406 409 1.221840 GTCGTCCTCATGGGCACAT 59.778 57.895 0.00 0.00 37.98 3.21
407 410 0.464036 GTCGTCCTCATGGGCACATA 59.536 55.000 0.00 0.00 37.98 2.29
408 411 1.070758 GTCGTCCTCATGGGCACATAT 59.929 52.381 0.00 0.00 37.98 1.78
410 413 1.879372 CGTCCTCATGGGCACATATGG 60.879 57.143 0.00 7.13 37.98 2.74
412 415 0.773014 CCTCATGGGCACATATGGGA 59.227 55.000 9.80 0.00 34.99 4.37
836 1149 5.719173 AGACAGAGAAGAGATTCTTTTCGG 58.281 41.667 10.36 7.57 41.06 4.30
839 1152 6.525629 ACAGAGAAGAGATTCTTTTCGGAAA 58.474 36.000 13.49 0.00 41.06 3.13
842 1155 4.691216 AGAAGAGATTCTTTTCGGAAACCG 59.309 41.667 1.96 3.66 41.98 4.44
843 1156 3.751698 AAGAGATTCTTTTCGGAAACCGG 59.248 43.478 0.00 0.00 39.65 5.28
946 1259 2.255881 CCGTTTCACCACGAACCCC 61.256 63.158 0.00 0.00 43.15 4.95
969 1282 2.033194 CAACCCTTCCTTCGGCGAC 61.033 63.158 10.16 0.00 0.00 5.19
1330 1643 0.439985 CATGTTCGTCGGACTGCAAG 59.560 55.000 5.05 0.00 42.29 4.01
1331 1644 0.670546 ATGTTCGTCGGACTGCAAGG 60.671 55.000 5.05 0.00 39.30 3.61
1332 1645 1.300697 GTTCGTCGGACTGCAAGGT 60.301 57.895 6.57 0.00 39.30 3.50
1333 1646 1.006571 TTCGTCGGACTGCAAGGTC 60.007 57.895 6.57 0.00 39.30 3.85
1435 1748 7.572523 TTCAATCTCCTTATGTAATTGCTGG 57.427 36.000 0.00 0.00 0.00 4.85
1487 1800 2.024414 TGATGACCGACGATCACTGAT 58.976 47.619 0.00 0.00 0.00 2.90
1490 1803 3.416119 TGACCGACGATCACTGATTAC 57.584 47.619 0.00 0.00 0.00 1.89
1914 2256 4.267349 AGCAACGGTATTTACACTGTCT 57.733 40.909 0.00 0.00 37.02 3.41
1939 2283 7.906327 TCATATAGTCCTGCACAGCATTATTA 58.094 34.615 0.00 0.00 38.13 0.98
2043 2388 2.437449 AGCATTGGTCAGGCTGCA 59.563 55.556 10.34 0.00 36.34 4.41
2152 2497 2.855963 GCACTGAGCGCGTAAGTATTTA 59.144 45.455 8.43 0.00 41.68 1.40
2177 2522 1.416401 TGTTTTCTCGCTCCTCCTTGT 59.584 47.619 0.00 0.00 0.00 3.16
2219 2564 7.179269 CCTACTCCCTCTGTAATATAAGAGCT 58.821 42.308 0.00 0.00 38.91 4.09
3111 3781 4.743955 GCAGGTGAGTTGGTCTAAGAGTTT 60.744 45.833 0.00 0.00 0.00 2.66
3153 3823 4.672542 GCAAAAATACTGCAAGAGCGATCA 60.673 41.667 2.38 0.00 46.23 2.92
3537 4225 0.965439 TTGCAAATGTAGGTGGTGCC 59.035 50.000 0.00 0.00 34.25 5.01
3539 4227 0.611896 GCAAATGTAGGTGGTGCCCT 60.612 55.000 0.00 0.00 38.26 5.19
3679 4386 7.320443 TGACTTTGTTATCTGGATTACATGC 57.680 36.000 3.77 0.00 31.51 4.06
3760 4467 5.032863 CCTGCTGCATTTTTAGAGATTTCG 58.967 41.667 1.31 0.00 0.00 3.46
3802 4550 6.526526 TGAGCCAAATTGTTAGTGTGTACTA 58.473 36.000 0.00 0.00 38.36 1.82
3806 4589 7.817962 AGCCAAATTGTTAGTGTGTACTAGTAG 59.182 37.037 1.87 0.00 40.33 2.57
3870 4653 6.533723 TCAAGATGTTACACCTTTACTATGCG 59.466 38.462 0.00 0.00 0.00 4.73
3887 4670 7.715265 ACTATGCGGAGTTGATATGTTTTAG 57.285 36.000 0.00 0.00 0.00 1.85
3888 4671 7.272978 ACTATGCGGAGTTGATATGTTTTAGT 58.727 34.615 0.00 0.00 0.00 2.24
3889 4672 8.418662 ACTATGCGGAGTTGATATGTTTTAGTA 58.581 33.333 0.00 0.00 0.00 1.82
3930 4713 5.751586 ACACCATTATTTGATCCTTACCGT 58.248 37.500 0.00 0.00 0.00 4.83
3959 4742 4.528596 ACTGCTAGCCTATCGTAATGGAAT 59.471 41.667 13.29 0.00 0.00 3.01
3968 4751 6.641314 GCCTATCGTAATGGAATCGGTATATG 59.359 42.308 0.00 0.00 0.00 1.78
3970 4753 5.988310 TCGTAATGGAATCGGTATATGGT 57.012 39.130 0.00 0.00 0.00 3.55
4011 4794 8.358148 TCTCTCGTTTTAGAGACTTGTTTACAT 58.642 33.333 0.00 0.00 45.54 2.29
4021 4804 8.410673 AGAGACTTGTTTACATTACAGAGAGA 57.589 34.615 0.00 0.00 0.00 3.10
4022 4805 8.519526 AGAGACTTGTTTACATTACAGAGAGAG 58.480 37.037 0.00 0.00 0.00 3.20
4023 4806 8.184304 AGACTTGTTTACATTACAGAGAGAGT 57.816 34.615 0.00 0.00 0.00 3.24
4024 4807 9.298250 AGACTTGTTTACATTACAGAGAGAGTA 57.702 33.333 0.00 0.00 0.00 2.59
4025 4808 9.344309 GACTTGTTTACATTACAGAGAGAGTAC 57.656 37.037 0.00 0.00 0.00 2.73
4026 4809 8.857098 ACTTGTTTACATTACAGAGAGAGTACA 58.143 33.333 0.00 0.00 0.00 2.90
4027 4810 9.862371 CTTGTTTACATTACAGAGAGAGTACAT 57.138 33.333 0.00 0.00 0.00 2.29
4050 4833 9.326413 ACATATTATGTACAAGACAAGTAAGGC 57.674 33.333 7.55 0.00 42.78 4.35
4051 4834 6.903883 ATTATGTACAAGACAAGTAAGGCG 57.096 37.500 0.00 0.00 42.78 5.52
4052 4835 3.738830 TGTACAAGACAAGTAAGGCGT 57.261 42.857 0.00 0.00 34.15 5.68
4053 4836 3.645884 TGTACAAGACAAGTAAGGCGTC 58.354 45.455 0.00 0.00 34.15 5.19
4054 4837 2.902705 ACAAGACAAGTAAGGCGTCA 57.097 45.000 0.00 0.00 31.92 4.35
4055 4838 3.188159 ACAAGACAAGTAAGGCGTCAA 57.812 42.857 0.00 0.00 31.92 3.18
4056 4839 3.740115 ACAAGACAAGTAAGGCGTCAAT 58.260 40.909 0.00 0.00 31.92 2.57
4057 4840 3.498397 ACAAGACAAGTAAGGCGTCAATG 59.502 43.478 0.00 0.00 31.92 2.82
4058 4841 2.699954 AGACAAGTAAGGCGTCAATGG 58.300 47.619 0.00 0.00 31.92 3.16
4059 4842 2.038557 AGACAAGTAAGGCGTCAATGGT 59.961 45.455 0.00 0.00 31.92 3.55
4060 4843 2.812011 GACAAGTAAGGCGTCAATGGTT 59.188 45.455 0.00 0.00 0.00 3.67
4061 4844 3.998341 GACAAGTAAGGCGTCAATGGTTA 59.002 43.478 0.00 0.00 0.00 2.85
4062 4845 3.749609 ACAAGTAAGGCGTCAATGGTTAC 59.250 43.478 0.00 0.00 0.00 2.50
4063 4846 3.975168 AGTAAGGCGTCAATGGTTACT 57.025 42.857 0.00 0.00 0.00 2.24
4064 4847 5.172934 CAAGTAAGGCGTCAATGGTTACTA 58.827 41.667 0.00 0.00 33.75 1.82
4065 4848 5.410355 AGTAAGGCGTCAATGGTTACTAA 57.590 39.130 0.00 0.00 33.24 2.24
4066 4849 5.985911 AGTAAGGCGTCAATGGTTACTAAT 58.014 37.500 0.00 0.00 33.24 1.73
4067 4850 7.116075 AGTAAGGCGTCAATGGTTACTAATA 57.884 36.000 0.00 0.00 33.24 0.98
4068 4851 7.732996 AGTAAGGCGTCAATGGTTACTAATAT 58.267 34.615 0.00 0.00 33.24 1.28
4069 4852 8.863086 AGTAAGGCGTCAATGGTTACTAATATA 58.137 33.333 0.00 0.00 33.24 0.86
4070 4853 9.649167 GTAAGGCGTCAATGGTTACTAATATAT 57.351 33.333 0.00 0.00 0.00 0.86
4112 4895 6.699575 ATATCTTCCCCAATCTTTTTGACG 57.300 37.500 0.00 0.00 0.00 4.35
4147 4930 7.471721 TGCATAGAACTTGTATTATTGTGCAC 58.528 34.615 10.75 10.75 33.36 4.57
4211 4994 7.771183 TCATTAAAAGAACACATGAATAGCCC 58.229 34.615 0.00 0.00 0.00 5.19
4241 5024 6.919721 TGTACAATATATCATGTGCGCTAGA 58.080 36.000 9.73 1.08 35.27 2.43
4242 5025 7.375053 TGTACAATATATCATGTGCGCTAGAA 58.625 34.615 9.73 0.00 35.27 2.10
4259 5042 4.496507 GCTAGAAAATGAGAATTGGGCGTC 60.497 45.833 0.00 0.00 0.00 5.19
4262 5045 1.463674 AATGAGAATTGGGCGTCCAC 58.536 50.000 9.15 0.00 43.94 4.02
4264 5047 2.046314 AGAATTGGGCGTCCACCG 60.046 61.111 9.15 0.00 43.94 4.94
4295 5079 2.124570 AGCATGCTAAGTGCCCGG 60.125 61.111 21.21 0.00 43.50 5.73
4315 5099 3.972276 CCCGCCAACCCGTGTTTG 61.972 66.667 0.00 0.00 30.42 2.93
4364 5148 4.327680 GTGCTCACCTTTCTCCTTACAAT 58.672 43.478 0.00 0.00 0.00 2.71
4365 5149 4.393371 GTGCTCACCTTTCTCCTTACAATC 59.607 45.833 0.00 0.00 0.00 2.67
4367 5151 4.633565 GCTCACCTTTCTCCTTACAATCAG 59.366 45.833 0.00 0.00 0.00 2.90
4368 5152 5.165961 TCACCTTTCTCCTTACAATCAGG 57.834 43.478 0.00 0.00 0.00 3.86
4373 5157 2.492025 TCTCCTTACAATCAGGGCCAT 58.508 47.619 6.18 0.00 31.50 4.40
4391 5175 1.492176 CATTGAGGGGCTAGACATGGT 59.508 52.381 0.00 0.00 0.00 3.55
4393 5177 1.043116 TGAGGGGCTAGACATGGTCG 61.043 60.000 0.00 0.00 37.67 4.79
4401 5185 2.353803 GCTAGACATGGTCGGTCAAGTT 60.354 50.000 0.00 0.00 37.67 2.66
4404 5188 2.028930 AGACATGGTCGGTCAAGTTCTC 60.029 50.000 0.00 0.00 37.67 2.87
4431 5215 8.389586 TGTATGCGCTATAGATAAATAACACG 57.610 34.615 9.73 0.00 0.00 4.49
4435 5219 6.525628 TGCGCTATAGATAAATAACACGCTAC 59.474 38.462 9.73 0.00 42.77 3.58
4454 5238 5.502382 CGCTACTTGCTACCAATGTATTGTG 60.502 44.000 4.12 0.00 40.11 3.33
4462 5246 5.874810 GCTACCAATGTATTGTGTTGAGAGA 59.125 40.000 4.12 0.00 36.06 3.10
4501 5285 8.519492 TTGCTAACAATGTATTCTTCTTTTGC 57.481 30.769 0.00 0.00 0.00 3.68
4502 5286 6.801377 TGCTAACAATGTATTCTTCTTTTGCG 59.199 34.615 0.00 0.00 0.00 4.85
4503 5287 6.251376 GCTAACAATGTATTCTTCTTTTGCGG 59.749 38.462 0.00 0.00 0.00 5.69
4504 5288 5.059404 ACAATGTATTCTTCTTTTGCGGG 57.941 39.130 0.00 0.00 0.00 6.13
4505 5289 4.082245 ACAATGTATTCTTCTTTTGCGGGG 60.082 41.667 0.00 0.00 0.00 5.73
4506 5290 3.149005 TGTATTCTTCTTTTGCGGGGT 57.851 42.857 0.00 0.00 0.00 4.95
4507 5291 4.289238 TGTATTCTTCTTTTGCGGGGTA 57.711 40.909 0.00 0.00 0.00 3.69
4508 5292 4.653868 TGTATTCTTCTTTTGCGGGGTAA 58.346 39.130 0.00 0.00 0.00 2.85
4509 5293 4.456566 TGTATTCTTCTTTTGCGGGGTAAC 59.543 41.667 0.00 0.00 0.00 2.50
4510 5294 2.642154 TCTTCTTTTGCGGGGTAACA 57.358 45.000 0.00 0.00 39.74 2.41
4511 5295 2.933573 TCTTCTTTTGCGGGGTAACAA 58.066 42.857 0.00 0.00 39.74 2.83
4512 5296 3.492337 TCTTCTTTTGCGGGGTAACAAT 58.508 40.909 0.00 0.00 39.74 2.71
4513 5297 3.254657 TCTTCTTTTGCGGGGTAACAATG 59.745 43.478 0.00 0.00 39.74 2.82
4514 5298 2.588620 TCTTTTGCGGGGTAACAATGT 58.411 42.857 0.00 0.00 39.74 2.71
4515 5299 2.294791 TCTTTTGCGGGGTAACAATGTG 59.705 45.455 0.00 0.00 39.74 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.592669 CCATGAGCTAAGCCGACGG 60.593 63.158 10.29 10.29 0.00 4.79
5 6 0.384309 TACCATGAGCTAAGCCGACG 59.616 55.000 0.00 0.00 0.00 5.12
6 7 1.870167 GCTACCATGAGCTAAGCCGAC 60.870 57.143 0.00 0.00 39.50 4.79
7 8 0.389391 GCTACCATGAGCTAAGCCGA 59.611 55.000 0.00 0.00 39.50 5.54
8 9 0.601311 GGCTACCATGAGCTAAGCCG 60.601 60.000 6.38 0.00 42.98 5.52
9 10 3.314083 GGCTACCATGAGCTAAGCC 57.686 57.895 6.38 7.07 45.37 4.35
10 11 0.601311 CGGGCTACCATGAGCTAAGC 60.601 60.000 6.38 2.13 42.43 3.09
11 12 1.040646 TCGGGCTACCATGAGCTAAG 58.959 55.000 6.38 0.00 42.43 2.18
12 13 0.750850 GTCGGGCTACCATGAGCTAA 59.249 55.000 6.38 0.00 42.43 3.09
13 14 1.452953 CGTCGGGCTACCATGAGCTA 61.453 60.000 6.38 0.00 42.43 3.32
14 15 2.786495 CGTCGGGCTACCATGAGCT 61.786 63.158 6.38 0.00 42.43 4.09
15 16 2.279517 CGTCGGGCTACCATGAGC 60.280 66.667 0.00 0.00 42.05 4.26
16 17 2.417516 CCGTCGGGCTACCATGAG 59.582 66.667 2.34 0.00 36.13 2.90
26 27 2.279252 CGTATCTTGGCCGTCGGG 60.279 66.667 14.38 0.00 0.00 5.14
27 28 2.960129 GCGTATCTTGGCCGTCGG 60.960 66.667 6.99 6.99 0.00 4.79
28 29 2.960129 GGCGTATCTTGGCCGTCG 60.960 66.667 0.00 0.00 39.93 5.12
32 33 2.960129 CGTCGGCGTATCTTGGCC 60.960 66.667 6.85 0.00 45.95 5.36
33 34 2.960129 CCGTCGGCGTATCTTGGC 60.960 66.667 9.28 0.00 36.15 4.52
34 35 2.960129 GCCGTCGGCGTATCTTGG 60.960 66.667 22.50 2.17 39.62 3.61
52 53 3.414700 GCCGACAGCCACGTCTTG 61.415 66.667 0.00 0.00 33.54 3.02
53 54 1.884075 TATGCCGACAGCCACGTCTT 61.884 55.000 0.00 0.00 42.71 3.01
54 55 2.284798 CTATGCCGACAGCCACGTCT 62.285 60.000 0.00 0.00 42.71 4.18
55 56 1.878522 CTATGCCGACAGCCACGTC 60.879 63.158 0.00 0.00 42.71 4.34
56 57 2.184322 CTATGCCGACAGCCACGT 59.816 61.111 0.00 0.00 42.71 4.49
57 58 3.264897 GCTATGCCGACAGCCACG 61.265 66.667 0.00 0.00 42.71 4.94
58 59 3.264897 CGCTATGCCGACAGCCAC 61.265 66.667 0.00 0.00 42.71 5.01
61 62 2.637715 CTTTGCGCTATGCCGACAGC 62.638 60.000 9.73 0.00 45.60 4.40
62 63 1.349627 CTTTGCGCTATGCCGACAG 59.650 57.895 9.73 0.00 45.60 3.51
63 64 0.108567 TACTTTGCGCTATGCCGACA 60.109 50.000 9.73 0.00 45.60 4.35
64 65 0.577269 CTACTTTGCGCTATGCCGAC 59.423 55.000 9.73 0.00 45.60 4.79
65 66 0.529773 CCTACTTTGCGCTATGCCGA 60.530 55.000 9.73 0.00 45.60 5.54
66 67 1.934463 CCTACTTTGCGCTATGCCG 59.066 57.895 9.73 0.00 45.60 5.69
67 68 1.649267 GCCTACTTTGCGCTATGCC 59.351 57.895 9.73 0.00 45.60 4.40
68 69 1.649267 GGCCTACTTTGCGCTATGC 59.351 57.895 9.73 0.68 46.70 3.14
69 70 0.529773 TCGGCCTACTTTGCGCTATG 60.530 55.000 9.73 6.01 0.00 2.23
70 71 0.529992 GTCGGCCTACTTTGCGCTAT 60.530 55.000 9.73 0.00 0.00 2.97
71 72 1.153706 GTCGGCCTACTTTGCGCTA 60.154 57.895 9.73 0.00 0.00 4.26
72 73 2.434359 GTCGGCCTACTTTGCGCT 60.434 61.111 9.73 0.00 0.00 5.92
73 74 3.849953 CGTCGGCCTACTTTGCGC 61.850 66.667 0.00 0.00 0.00 6.09
74 75 3.186047 CCGTCGGCCTACTTTGCG 61.186 66.667 5.79 0.00 0.00 4.85
75 76 3.497031 GCCGTCGGCCTACTTTGC 61.497 66.667 26.23 2.05 44.06 3.68
95 96 1.226660 GCCAAATCAATGCCGACGG 60.227 57.895 10.29 10.29 0.00 4.79
96 97 1.226660 GGCCAAATCAATGCCGACG 60.227 57.895 0.00 0.00 35.08 5.12
97 98 4.812814 GGCCAAATCAATGCCGAC 57.187 55.556 0.00 0.00 35.08 4.79
100 101 1.226660 CGACGGCCAAATCAATGCC 60.227 57.895 2.24 0.00 41.85 4.40
101 102 1.226660 CCGACGGCCAAATCAATGC 60.227 57.895 2.24 0.00 0.00 3.56
102 103 1.433064 CCCGACGGCCAAATCAATG 59.567 57.895 8.86 0.00 0.00 2.82
103 104 1.752694 CCCCGACGGCCAAATCAAT 60.753 57.895 8.86 0.00 0.00 2.57
104 105 1.839148 TACCCCGACGGCCAAATCAA 61.839 55.000 8.86 0.00 33.26 2.57
105 106 2.246761 CTACCCCGACGGCCAAATCA 62.247 60.000 8.86 0.00 33.26 2.57
106 107 1.523032 CTACCCCGACGGCCAAATC 60.523 63.158 8.86 0.00 33.26 2.17
107 108 2.587889 CTACCCCGACGGCCAAAT 59.412 61.111 8.86 0.00 33.26 2.32
108 109 3.708544 CCTACCCCGACGGCCAAA 61.709 66.667 8.86 0.00 33.26 3.28
115 116 2.532465 GAAACTGGCCCTACCCCGAC 62.532 65.000 0.00 0.00 37.83 4.79
116 117 2.204029 AAACTGGCCCTACCCCGA 60.204 61.111 0.00 0.00 37.83 5.14
117 118 2.271173 GAAACTGGCCCTACCCCG 59.729 66.667 0.00 0.00 37.83 5.73
118 119 2.681591 GGAAACTGGCCCTACCCC 59.318 66.667 0.00 0.00 37.83 4.95
119 120 2.271173 CGGAAACTGGCCCTACCC 59.729 66.667 0.00 0.00 37.83 3.69
120 121 1.266867 TACCGGAAACTGGCCCTACC 61.267 60.000 9.46 0.00 39.84 3.18
121 122 0.177373 CTACCGGAAACTGGCCCTAC 59.823 60.000 9.46 0.00 0.00 3.18
122 123 0.252375 ACTACCGGAAACTGGCCCTA 60.252 55.000 9.46 0.00 0.00 3.53
123 124 1.538135 ACTACCGGAAACTGGCCCT 60.538 57.895 9.46 0.00 0.00 5.19
124 125 1.376812 CACTACCGGAAACTGGCCC 60.377 63.158 9.46 0.00 0.00 5.80
125 126 1.376812 CCACTACCGGAAACTGGCC 60.377 63.158 9.46 0.00 0.00 5.36
126 127 2.038837 GCCACTACCGGAAACTGGC 61.039 63.158 9.46 14.80 40.68 4.85
127 128 0.673644 CTGCCACTACCGGAAACTGG 60.674 60.000 9.46 8.20 0.00 4.00
128 129 1.298859 GCTGCCACTACCGGAAACTG 61.299 60.000 9.46 0.00 0.00 3.16
129 130 1.003718 GCTGCCACTACCGGAAACT 60.004 57.895 9.46 0.00 0.00 2.66
130 131 2.388232 CGCTGCCACTACCGGAAAC 61.388 63.158 9.46 0.00 0.00 2.78
131 132 2.047655 CGCTGCCACTACCGGAAA 60.048 61.111 9.46 0.00 0.00 3.13
132 133 4.752879 GCGCTGCCACTACCGGAA 62.753 66.667 9.46 0.00 0.00 4.30
135 136 3.490759 CTTGCGCTGCCACTACCG 61.491 66.667 9.73 0.00 0.00 4.02
136 137 1.912371 GAACTTGCGCTGCCACTACC 61.912 60.000 9.73 0.00 0.00 3.18
137 138 0.951040 AGAACTTGCGCTGCCACTAC 60.951 55.000 9.73 0.00 0.00 2.73
138 139 0.670546 GAGAACTTGCGCTGCCACTA 60.671 55.000 9.73 0.00 0.00 2.74
139 140 1.963338 GAGAACTTGCGCTGCCACT 60.963 57.895 9.73 2.56 0.00 4.00
140 141 2.558313 GAGAACTTGCGCTGCCAC 59.442 61.111 9.73 0.00 0.00 5.01
141 142 3.043713 CGAGAACTTGCGCTGCCA 61.044 61.111 9.73 0.00 0.00 4.92
142 143 3.793144 CCGAGAACTTGCGCTGCC 61.793 66.667 9.73 0.00 0.00 4.85
143 144 2.738521 TCCGAGAACTTGCGCTGC 60.739 61.111 9.73 0.00 0.00 5.25
144 145 2.383527 GGTCCGAGAACTTGCGCTG 61.384 63.158 9.73 3.92 0.00 5.18
145 146 2.048127 GGTCCGAGAACTTGCGCT 60.048 61.111 9.73 0.00 0.00 5.92
146 147 3.479269 CGGTCCGAGAACTTGCGC 61.479 66.667 4.91 0.00 0.00 6.09
147 148 3.479269 GCGGTCCGAGAACTTGCG 61.479 66.667 17.49 0.00 0.00 4.85
148 149 3.119096 GGCGGTCCGAGAACTTGC 61.119 66.667 17.49 0.00 0.00 4.01
149 150 1.738099 CTGGCGGTCCGAGAACTTG 60.738 63.158 17.49 0.00 34.14 3.16
150 151 2.207924 ACTGGCGGTCCGAGAACTT 61.208 57.895 17.49 0.00 34.14 2.66
151 152 2.600769 ACTGGCGGTCCGAGAACT 60.601 61.111 17.49 0.00 34.14 3.01
152 153 2.432628 CACTGGCGGTCCGAGAAC 60.433 66.667 17.49 1.92 34.14 3.01
153 154 4.373116 GCACTGGCGGTCCGAGAA 62.373 66.667 17.49 0.00 34.14 2.87
158 159 1.377987 TAAATGGCACTGGCGGTCC 60.378 57.895 0.00 1.78 42.47 4.46
159 160 0.676782 AGTAAATGGCACTGGCGGTC 60.677 55.000 0.00 0.00 42.47 4.79
160 161 0.676782 GAGTAAATGGCACTGGCGGT 60.677 55.000 0.00 0.00 42.47 5.68
161 162 1.705337 CGAGTAAATGGCACTGGCGG 61.705 60.000 0.00 0.00 42.47 6.13
162 163 1.019278 ACGAGTAAATGGCACTGGCG 61.019 55.000 0.00 0.00 42.47 5.69
163 164 1.135689 CAACGAGTAAATGGCACTGGC 60.136 52.381 0.00 0.00 40.13 4.85
164 165 2.422597 TCAACGAGTAAATGGCACTGG 58.577 47.619 0.00 0.00 0.00 4.00
165 166 3.249799 TGTTCAACGAGTAAATGGCACTG 59.750 43.478 0.00 0.00 0.00 3.66
166 167 3.472652 TGTTCAACGAGTAAATGGCACT 58.527 40.909 0.00 0.00 0.00 4.40
167 168 3.810373 CTGTTCAACGAGTAAATGGCAC 58.190 45.455 0.00 0.00 0.00 5.01
168 169 2.225491 GCTGTTCAACGAGTAAATGGCA 59.775 45.455 0.00 0.00 0.00 4.92
169 170 2.225491 TGCTGTTCAACGAGTAAATGGC 59.775 45.455 0.00 0.00 0.00 4.40
170 171 4.406069 CATGCTGTTCAACGAGTAAATGG 58.594 43.478 0.00 0.00 0.00 3.16
171 172 4.406069 CCATGCTGTTCAACGAGTAAATG 58.594 43.478 0.00 0.00 0.00 2.32
172 173 3.119849 GCCATGCTGTTCAACGAGTAAAT 60.120 43.478 0.00 0.00 0.00 1.40
173 174 2.225491 GCCATGCTGTTCAACGAGTAAA 59.775 45.455 0.00 0.00 0.00 2.01
174 175 1.804151 GCCATGCTGTTCAACGAGTAA 59.196 47.619 0.00 0.00 0.00 2.24
175 176 1.001974 AGCCATGCTGTTCAACGAGTA 59.998 47.619 0.00 0.00 37.57 2.59
176 177 0.250467 AGCCATGCTGTTCAACGAGT 60.250 50.000 0.00 0.00 37.57 4.18
177 178 0.877071 AAGCCATGCTGTTCAACGAG 59.123 50.000 0.00 0.00 39.62 4.18
178 179 0.874390 GAAGCCATGCTGTTCAACGA 59.126 50.000 0.00 0.00 39.62 3.85
179 180 0.592637 TGAAGCCATGCTGTTCAACG 59.407 50.000 0.00 0.00 39.62 4.10
205 206 4.655762 TTGGAGATGTAGATCCTGTTCG 57.344 45.455 0.00 0.00 36.50 3.95
215 216 5.665459 AGGTCGAGAAAATTGGAGATGTAG 58.335 41.667 0.00 0.00 0.00 2.74
348 350 4.812476 CGCATTCGCACCCCTCGA 62.812 66.667 0.00 0.00 38.40 4.04
349 351 4.812476 TCGCATTCGCACCCCTCG 62.812 66.667 0.00 0.00 38.40 4.63
350 352 2.203070 ATCGCATTCGCACCCCTC 60.203 61.111 0.00 0.00 38.40 4.30
351 353 2.514592 CATCGCATTCGCACCCCT 60.515 61.111 0.00 0.00 38.40 4.79
352 354 3.585990 CCATCGCATTCGCACCCC 61.586 66.667 0.00 0.00 38.40 4.95
353 355 2.824041 ACCATCGCATTCGCACCC 60.824 61.111 0.00 0.00 38.40 4.61
354 356 2.404789 CACCATCGCATTCGCACC 59.595 61.111 0.00 0.00 38.40 5.01
355 357 2.277501 GCACCATCGCATTCGCAC 60.278 61.111 0.00 0.00 38.40 5.34
356 358 3.863543 CGCACCATCGCATTCGCA 61.864 61.111 0.00 0.00 38.40 5.10
358 360 3.195002 ACCGCACCATCGCATTCG 61.195 61.111 0.00 0.00 0.00 3.34
360 362 3.133464 CCACCGCACCATCGCATT 61.133 61.111 0.00 0.00 0.00 3.56
361 363 4.408821 ACCACCGCACCATCGCAT 62.409 61.111 0.00 0.00 0.00 4.73
398 401 0.923729 AACCCTCCCATATGTGCCCA 60.924 55.000 1.24 0.00 0.00 5.36
399 402 0.178990 GAACCCTCCCATATGTGCCC 60.179 60.000 1.24 0.00 0.00 5.36
400 403 0.550914 TGAACCCTCCCATATGTGCC 59.449 55.000 1.24 0.00 0.00 5.01
401 404 2.233271 CATGAACCCTCCCATATGTGC 58.767 52.381 1.24 0.00 0.00 4.57
403 406 1.782752 CCCATGAACCCTCCCATATGT 59.217 52.381 1.24 0.00 0.00 2.29
404 407 2.065007 TCCCATGAACCCTCCCATATG 58.935 52.381 0.00 0.00 0.00 1.78
406 409 2.531177 ATCCCATGAACCCTCCCATA 57.469 50.000 0.00 0.00 0.00 2.74
407 410 2.089408 TCTATCCCATGAACCCTCCCAT 60.089 50.000 0.00 0.00 0.00 4.00
408 411 1.296832 TCTATCCCATGAACCCTCCCA 59.703 52.381 0.00 0.00 0.00 4.37
410 413 1.344763 CGTCTATCCCATGAACCCTCC 59.655 57.143 0.00 0.00 0.00 4.30
412 415 1.424638 CCGTCTATCCCATGAACCCT 58.575 55.000 0.00 0.00 0.00 4.34
816 1129 6.128418 GGTTTCCGAAAAGAATCTCTTCTCTG 60.128 42.308 0.00 0.00 40.93 3.35
946 1259 2.641197 CGAAGGAAGGGTTGGGTTG 58.359 57.895 0.00 0.00 0.00 3.77
969 1282 2.790791 CCCGTGCCCTAGCTCTCTG 61.791 68.421 0.00 0.00 40.80 3.35
1427 1740 8.998377 GTAAATTTGTAATCCAAACCAGCAATT 58.002 29.630 0.00 0.00 45.43 2.32
1456 1769 5.278604 TCGTCGGTCATCAGTGTTATTATG 58.721 41.667 0.00 0.00 0.00 1.90
1473 1786 5.461526 ACATATGTAATCAGTGATCGTCGG 58.538 41.667 6.56 0.00 0.00 4.79
1487 1800 4.398988 CCAGAGCCTGCAAAACATATGTAA 59.601 41.667 9.21 0.00 0.00 2.41
1490 1803 2.100252 CCCAGAGCCTGCAAAACATATG 59.900 50.000 0.00 0.00 0.00 1.78
1607 1935 1.201855 GCGTTCTGCTTCAACTGATCG 60.202 52.381 0.00 0.00 41.73 3.69
1740 2076 4.766373 TCTGATTCCATGTAGCTGCAAAAA 59.234 37.500 9.07 4.02 0.00 1.94
1914 2256 4.694760 AATGCTGTGCAGGACTATATGA 57.305 40.909 1.11 0.00 43.65 2.15
1939 2283 9.579932 AGTGAAAAATCTCAAAACTAGAGGAAT 57.420 29.630 0.00 0.00 33.92 3.01
2043 2388 0.182061 ATGCCTGTGCCTGATCGAAT 59.818 50.000 0.00 0.00 36.33 3.34
2152 2497 3.008485 AGGAGGAGCGAGAAAACAAAGAT 59.992 43.478 0.00 0.00 0.00 2.40
2177 2522 5.297776 GGAGTAGGTAGTAACACGAATAGCA 59.702 44.000 0.00 0.00 0.00 3.49
2699 3133 5.313623 CGAAAACCATCGTTAGCTAAACTG 58.686 41.667 7.99 6.03 38.01 3.16
3153 3823 4.101585 TCAGCGATGGGATAAGTTTCAGAT 59.898 41.667 0.00 0.00 0.00 2.90
3537 4225 6.963049 AATTCTACTACAACGTAGCAAAGG 57.037 37.500 1.08 0.00 37.40 3.11
3539 4227 8.086522 AGAGAAATTCTACTACAACGTAGCAAA 58.913 33.333 0.00 0.00 37.40 3.68
3676 4383 1.137675 TCATACTCTGCAGAAGCGCAT 59.862 47.619 18.85 0.00 46.23 4.73
3679 4386 2.995939 TGTTTCATACTCTGCAGAAGCG 59.004 45.455 18.85 8.94 46.23 4.68
3760 4467 6.051717 TGGCTCAGCAGACTTATTTCTTATC 58.948 40.000 0.00 0.00 0.00 1.75
3870 4653 9.391006 TGATTGGTACTAAAACATATCAACTCC 57.609 33.333 0.00 0.00 0.00 3.85
3887 4670 8.458573 TGGTGTATATTCCATTTGATTGGTAC 57.541 34.615 0.00 0.00 38.01 3.34
3930 4713 2.279741 CGATAGGCTAGCAGTGCAAAA 58.720 47.619 19.20 0.94 0.00 2.44
3968 4751 7.948278 ACGAGAGAGTAATAATTAATGCACC 57.052 36.000 0.00 0.00 0.00 5.01
3989 4772 9.531942 TGTAATGTAAACAAGTCTCTAAAACGA 57.468 29.630 0.00 0.00 0.00 3.85
3990 4773 9.793245 CTGTAATGTAAACAAGTCTCTAAAACG 57.207 33.333 0.00 0.00 0.00 3.60
4024 4807 9.326413 GCCTTACTTGTCTTGTACATAATATGT 57.674 33.333 10.98 10.98 46.92 2.29
4025 4808 8.487970 CGCCTTACTTGTCTTGTACATAATATG 58.512 37.037 0.00 0.00 38.10 1.78
4026 4809 8.202137 ACGCCTTACTTGTCTTGTACATAATAT 58.798 33.333 0.00 0.00 38.10 1.28
4027 4810 7.549839 ACGCCTTACTTGTCTTGTACATAATA 58.450 34.615 0.00 0.00 38.10 0.98
4028 4811 6.403878 ACGCCTTACTTGTCTTGTACATAAT 58.596 36.000 0.00 0.00 38.10 1.28
4029 4812 5.786311 ACGCCTTACTTGTCTTGTACATAA 58.214 37.500 0.00 0.00 38.10 1.90
4030 4813 5.047872 TGACGCCTTACTTGTCTTGTACATA 60.048 40.000 0.00 0.00 38.10 2.29
4031 4814 4.243270 GACGCCTTACTTGTCTTGTACAT 58.757 43.478 0.00 0.00 38.10 2.29
4032 4815 3.068448 TGACGCCTTACTTGTCTTGTACA 59.932 43.478 0.00 0.00 35.88 2.90
4033 4816 3.645884 TGACGCCTTACTTGTCTTGTAC 58.354 45.455 0.00 0.00 33.81 2.90
4034 4817 4.325028 TTGACGCCTTACTTGTCTTGTA 57.675 40.909 0.00 0.00 33.81 2.41
4035 4818 2.902705 TGACGCCTTACTTGTCTTGT 57.097 45.000 0.00 0.00 33.81 3.16
4036 4819 3.120199 CCATTGACGCCTTACTTGTCTTG 60.120 47.826 0.00 0.00 33.81 3.02
4037 4820 3.074412 CCATTGACGCCTTACTTGTCTT 58.926 45.455 0.00 0.00 33.81 3.01
4038 4821 2.038557 ACCATTGACGCCTTACTTGTCT 59.961 45.455 0.00 0.00 33.81 3.41
4039 4822 2.423577 ACCATTGACGCCTTACTTGTC 58.576 47.619 0.00 0.00 0.00 3.18
4040 4823 2.561478 ACCATTGACGCCTTACTTGT 57.439 45.000 0.00 0.00 0.00 3.16
4041 4824 4.000988 AGTAACCATTGACGCCTTACTTG 58.999 43.478 0.00 0.00 0.00 3.16
4042 4825 4.281898 AGTAACCATTGACGCCTTACTT 57.718 40.909 0.00 0.00 0.00 2.24
4043 4826 3.975168 AGTAACCATTGACGCCTTACT 57.025 42.857 0.00 0.00 0.00 2.24
4044 4827 7.958053 ATATTAGTAACCATTGACGCCTTAC 57.042 36.000 0.00 0.00 0.00 2.34
4074 4857 9.170890 TGGGGAAGATATTAAAGATATGTGAGT 57.829 33.333 0.00 0.00 0.00 3.41
4147 4930 2.385013 TCTCCCACATCATTCACACG 57.615 50.000 0.00 0.00 0.00 4.49
4188 4971 6.377146 ACGGGCTATTCATGTGTTCTTTTAAT 59.623 34.615 0.00 0.00 0.00 1.40
4193 4976 3.350219 ACGGGCTATTCATGTGTTCTT 57.650 42.857 0.00 0.00 0.00 2.52
4209 4992 8.175069 GCACATGATATATTGTACAATAACGGG 58.825 37.037 27.45 17.96 36.90 5.28
4211 4994 7.422462 GCGCACATGATATATTGTACAATAACG 59.578 37.037 27.45 19.38 36.90 3.18
4241 5024 2.231235 GTGGACGCCCAATTCTCATTTT 59.769 45.455 0.00 0.00 45.59 1.82
4242 5025 1.818674 GTGGACGCCCAATTCTCATTT 59.181 47.619 0.00 0.00 45.59 2.32
4259 5042 1.609555 CTCTAGCTAGCTAACCGGTGG 59.390 57.143 24.20 11.56 0.00 4.61
4262 5045 1.319541 TGCTCTAGCTAGCTAACCGG 58.680 55.000 24.20 13.28 43.19 5.28
4264 5047 2.298729 AGCATGCTCTAGCTAGCTAACC 59.701 50.000 24.20 15.30 45.03 2.85
4342 5126 3.402628 TGTAAGGAGAAAGGTGAGCAC 57.597 47.619 0.00 0.00 0.00 4.40
4343 5127 4.041567 TGATTGTAAGGAGAAAGGTGAGCA 59.958 41.667 0.00 0.00 0.00 4.26
4344 5128 4.579869 TGATTGTAAGGAGAAAGGTGAGC 58.420 43.478 0.00 0.00 0.00 4.26
4345 5129 5.181748 CCTGATTGTAAGGAGAAAGGTGAG 58.818 45.833 0.00 0.00 36.91 3.51
4346 5130 4.019321 CCCTGATTGTAAGGAGAAAGGTGA 60.019 45.833 0.00 0.00 36.91 4.02
4347 5131 4.265073 CCCTGATTGTAAGGAGAAAGGTG 58.735 47.826 0.00 0.00 36.91 4.00
4348 5132 3.308473 GCCCTGATTGTAAGGAGAAAGGT 60.308 47.826 0.00 0.00 36.91 3.50
4349 5133 3.282885 GCCCTGATTGTAAGGAGAAAGG 58.717 50.000 0.00 0.00 36.91 3.11
4350 5134 3.282885 GGCCCTGATTGTAAGGAGAAAG 58.717 50.000 0.00 0.00 36.91 2.62
4351 5135 2.647299 TGGCCCTGATTGTAAGGAGAAA 59.353 45.455 0.00 0.00 36.91 2.52
4364 5148 3.743017 GCCCCTCAATGGCCCTGA 61.743 66.667 0.00 1.74 43.33 3.86
4373 5157 1.204146 GACCATGTCTAGCCCCTCAA 58.796 55.000 0.00 0.00 0.00 3.02
4409 5193 6.100004 AGCGTGTTATTTATCTATAGCGCAT 58.900 36.000 11.47 3.63 42.93 4.73
4431 5215 5.354234 ACACAATACATTGGTAGCAAGTAGC 59.646 40.000 13.51 0.00 41.96 3.58
4435 5219 6.149308 TCTCAACACAATACATTGGTAGCAAG 59.851 38.462 13.51 7.84 41.96 4.01
4454 5238 9.846248 AGCAATTAACATGTTATTTCTCTCAAC 57.154 29.630 18.69 5.50 0.00 3.18
4492 5276 3.005367 ACATTGTTACCCCGCAAAAGAAG 59.995 43.478 0.00 0.00 0.00 2.85
4493 5277 2.959707 ACATTGTTACCCCGCAAAAGAA 59.040 40.909 0.00 0.00 0.00 2.52
4494 5278 2.294791 CACATTGTTACCCCGCAAAAGA 59.705 45.455 0.00 0.00 0.00 2.52
4495 5279 2.671596 CACATTGTTACCCCGCAAAAG 58.328 47.619 0.00 0.00 0.00 2.27
4496 5280 2.802787 CACATTGTTACCCCGCAAAA 57.197 45.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.