Multiple sequence alignment - TraesCS5D01G490500

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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 TraesCS5D01G490500 chr5D 100.000 2513 0 0 1 2513 525155944 525153432 0.000000e+00 4641.0
1 TraesCS5D01G490500 chr5D 93.544 666 30 7 920 1573 525086527 525085863 0.000000e+00 979.0
2 TraesCS5D01G490500 chr5D 95.802 405 9 1 1 397 489755680 489755276 0.000000e+00 647.0
3 TraesCS5D01G490500 chr5D 85.538 650 55 18 928 1552 525119497 525118862 0.000000e+00 643.0
4 TraesCS5D01G490500 chr5D 93.571 420 12 3 1 406 125658089 125657671 1.650000e-171 612.0
5 TraesCS5D01G490500 chr5D 93.580 405 18 1 1 397 284885284 284884880 4.630000e-167 597.0
6 TraesCS5D01G490500 chr5D 91.509 424 9 2 1 397 423749361 423748938 2.180000e-155 558.0
7 TraesCS5D01G490500 chr5D 91.038 424 11 8 1 397 474542956 474542533 4.730000e-152 547.0
8 TraesCS5D01G490500 chr5D 89.425 435 16 13 1 405 78754991 78754557 2.860000e-144 521.0
9 TraesCS5D01G490500 chr5D 80.712 534 69 23 1000 1513 525321861 525322380 3.920000e-103 385.0
10 TraesCS5D01G490500 chr5D 92.748 262 10 1 677 929 424910089 424910350 1.100000e-98 370.0
11 TraesCS5D01G490500 chr5D 92.278 259 11 1 677 926 382946555 382946813 2.380000e-95 359.0
12 TraesCS5D01G490500 chr5D 92.278 259 11 1 677 926 486229277 486229019 2.380000e-95 359.0
13 TraesCS5D01G490500 chr5D 96.552 203 7 0 398 600 525120122 525119920 1.110000e-88 337.0
14 TraesCS5D01G490500 chr5D 78.821 543 82 21 996 1517 23863564 23864094 4.010000e-88 335.0
15 TraesCS5D01G490500 chr5D 79.104 536 71 26 998 1517 525253722 525254232 5.180000e-87 331.0
16 TraesCS5D01G490500 chr5D 85.782 211 11 3 1724 1934 525085486 525085295 3.280000e-49 206.0
17 TraesCS5D01G490500 chr5D 88.496 113 7 3 1651 1762 525089739 525089632 5.640000e-27 132.0
18 TraesCS5D01G490500 chr5D 92.958 71 5 0 1587 1657 525085820 525085750 1.230000e-18 104.0
19 TraesCS5D01G490500 chr5D 88.372 86 4 3 1566 1650 525118804 525118724 5.720000e-17 99.0
20 TraesCS5D01G490500 chr5A 85.108 1014 77 25 929 1880 651518061 651517060 0.000000e+00 968.0
21 TraesCS5D01G490500 chr5A 88.112 143 8 4 2371 2513 651515958 651515825 7.190000e-36 161.0
22 TraesCS5D01G490500 chr5A 83.766 154 8 8 2222 2374 651516138 651516001 2.030000e-26 130.0
23 TraesCS5D01G490500 chr5A 89.623 106 5 4 1567 1671 651522411 651522311 2.030000e-26 130.0
24 TraesCS5D01G490500 chr5B 89.023 665 48 6 928 1573 659471808 659471150 0.000000e+00 800.0
25 TraesCS5D01G490500 chr5B 84.802 658 74 13 928 1574 659475805 659475163 2.730000e-179 638.0
26 TraesCS5D01G490500 chr5B 84.411 603 61 14 928 1515 659463256 659462672 1.690000e-156 562.0
27 TraesCS5D01G490500 chr5B 80.855 538 74 20 995 1513 659743608 659744135 1.810000e-106 396.0
28 TraesCS5D01G490500 chr5B 80.725 524 72 16 997 1513 659704427 659704928 5.070000e-102 381.0
29 TraesCS5D01G490500 chr5B 80.110 543 71 22 996 1513 659739526 659740056 1.100000e-98 370.0
30 TraesCS5D01G490500 chr5B 94.606 241 5 2 1572 1804 659471116 659470876 1.420000e-97 366.0
31 TraesCS5D01G490500 chr5B 88.259 247 19 2 1844 2081 659470886 659470641 1.140000e-73 287.0
32 TraesCS5D01G490500 chr5B 85.034 147 9 5 2371 2513 659470424 659470287 1.210000e-28 137.0
33 TraesCS5D01G490500 chr5B 91.667 60 5 0 398 457 659464225 659464166 1.600000e-12 84.2
34 TraesCS5D01G490500 chr3D 95.500 400 14 2 1 397 152703295 152702897 9.800000e-179 636.0
35 TraesCS5D01G490500 chr3D 94.862 253 10 1 677 926 7183435 7183687 2.340000e-105 392.0
36 TraesCS5D01G490500 chr2D 95.098 408 12 1 1 400 102620183 102619776 9.800000e-179 636.0
37 TraesCS5D01G490500 chr2D 92.664 259 10 1 677 926 462486848 462487106 5.110000e-97 364.0
38 TraesCS5D01G490500 chr2A 93.431 411 19 4 1 403 139971820 139972230 9.940000e-169 603.0
39 TraesCS5D01G490500 chr7D 92.381 420 10 2 1 398 508795467 508795048 1.680000e-161 579.0
40 TraesCS5D01G490500 chr7D 89.647 425 13 5 1 398 41466807 41467227 1.720000e-141 512.0
41 TraesCS5D01G490500 chr7D 93.050 259 9 3 677 926 29578030 29578288 1.100000e-98 370.0
42 TraesCS5D01G490500 chr7D 92.748 262 10 1 677 929 599464486 599464747 1.100000e-98 370.0
43 TraesCS5D01G490500 chr1D 91.686 421 8 2 1 394 481961219 481961639 2.180000e-155 558.0
44 TraesCS5D01G490500 chr1D 96.000 250 10 0 677 926 45136177 45136426 8.370000e-110 407.0
45 TraesCS5D01G490500 chrUn 93.023 258 8 2 679 926 28303697 28303440 3.950000e-98 368.0


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 TraesCS5D01G490500 chr5D 525153432 525155944 2512 True 4641.000000 4641 100.0000 1 2513 1 chr5D.!!$R8 2512
1 TraesCS5D01G490500 chr5D 525321861 525322380 519 False 385.000000 385 80.7120 1000 1513 1 chr5D.!!$F5 513
2 TraesCS5D01G490500 chr5D 525118724 525120122 1398 True 359.666667 643 90.1540 398 1650 3 chr5D.!!$R10 1252
3 TraesCS5D01G490500 chr5D 525085295 525089739 4444 True 355.250000 979 90.1950 920 1934 4 chr5D.!!$R9 1014
4 TraesCS5D01G490500 chr5D 23863564 23864094 530 False 335.000000 335 78.8210 996 1517 1 chr5D.!!$F1 521
5 TraesCS5D01G490500 chr5D 525253722 525254232 510 False 331.000000 331 79.1040 998 1517 1 chr5D.!!$F4 519
6 TraesCS5D01G490500 chr5A 651515825 651518061 2236 True 419.666667 968 85.6620 929 2513 3 chr5A.!!$R2 1584
7 TraesCS5D01G490500 chr5B 659470287 659475805 5518 True 445.600000 800 88.3448 928 2513 5 chr5B.!!$R2 1585
8 TraesCS5D01G490500 chr5B 659739526 659744135 4609 False 383.000000 396 80.4825 995 1513 2 chr5B.!!$F2 518
9 TraesCS5D01G490500 chr5B 659704427 659704928 501 False 381.000000 381 80.7250 997 1513 1 chr5B.!!$F1 516
10 TraesCS5D01G490500 chr5B 659462672 659464225 1553 True 323.100000 562 88.0390 398 1515 2 chr5B.!!$R1 1117

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
175 176 0.035739 GGGGCTCTGTTTTGTACCGA 59.964 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 5553 0.247736 GAGGGATCGAGCACAGTGTT 59.752 55.0 5.38 0.0 0.0 3.32 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
19 20 2.124693 CGACCAGCTCCTCCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
20 21 2.043450 ACCAGCTCCTCCTCCTCG 60.043 66.667 0.00 0.00 0.00 4.63
23 24 2.441901 AGCTCCTCCTCCTCGCTG 60.442 66.667 0.00 0.00 0.00 5.18
24 25 4.219999 GCTCCTCCTCCTCGCTGC 62.220 72.222 0.00 0.00 0.00 5.25
28 29 2.489275 CCTCCTCCTCGCTGCTCTC 61.489 68.421 0.00 0.00 0.00 3.20
29 30 2.441164 TCCTCCTCGCTGCTCTCC 60.441 66.667 0.00 0.00 0.00 3.71
31 32 2.489275 CCTCCTCGCTGCTCTCCTC 61.489 68.421 0.00 0.00 0.00 3.71
33 34 1.447317 CTCCTCGCTGCTCTCCTCTC 61.447 65.000 0.00 0.00 0.00 3.20
39 40 0.760189 GCTGCTCTCCTCTCCATCCT 60.760 60.000 0.00 0.00 0.00 3.24
40 41 1.792115 CTGCTCTCCTCTCCATCCTT 58.208 55.000 0.00 0.00 0.00 3.36
44 45 2.038659 CTCTCCTCTCCATCCTTCCAC 58.961 57.143 0.00 0.00 0.00 4.02
45 46 0.749649 CTCCTCTCCATCCTTCCACG 59.250 60.000 0.00 0.00 0.00 4.94
50 51 2.511600 CCATCCTTCCACGACGGC 60.512 66.667 0.00 0.00 33.14 5.68
51 52 2.264480 CATCCTTCCACGACGGCA 59.736 61.111 0.00 0.00 33.14 5.69
52 53 1.153369 CATCCTTCCACGACGGCAT 60.153 57.895 0.00 0.00 33.14 4.40
57 58 0.108615 CTTCCACGACGGCATCTTCT 60.109 55.000 0.00 0.00 33.14 2.85
66 67 2.280186 GCATCTTCTACGGCGGGG 60.280 66.667 13.24 3.07 0.00 5.73
73 74 3.846430 CTACGGCGGGGAGGGAAC 61.846 72.222 13.24 0.00 0.00 3.62
113 114 3.086600 GGGGACAGGGCAGAGGAG 61.087 72.222 0.00 0.00 0.00 3.69
115 116 2.664081 GGGACAGGGCAGAGGAGTG 61.664 68.421 0.00 0.00 0.00 3.51
116 117 1.610673 GGACAGGGCAGAGGAGTGA 60.611 63.158 0.00 0.00 0.00 3.41
117 118 1.612395 GGACAGGGCAGAGGAGTGAG 61.612 65.000 0.00 0.00 0.00 3.51
118 119 0.613292 GACAGGGCAGAGGAGTGAGA 60.613 60.000 0.00 0.00 0.00 3.27
119 120 0.614415 ACAGGGCAGAGGAGTGAGAG 60.614 60.000 0.00 0.00 0.00 3.20
121 122 0.614415 AGGGCAGAGGAGTGAGAGTG 60.614 60.000 0.00 0.00 0.00 3.51
122 123 0.613292 GGGCAGAGGAGTGAGAGTGA 60.613 60.000 0.00 0.00 0.00 3.41
126 127 0.326595 AGAGGAGTGAGAGTGAGCGA 59.673 55.000 0.00 0.00 0.00 4.93
128 129 0.037590 AGGAGTGAGAGTGAGCGAGT 59.962 55.000 0.00 0.00 0.00 4.18
136 137 1.228583 AGTGAGCGAGTGGAGTGGA 60.229 57.895 0.00 0.00 0.00 4.02
140 141 1.528292 GAGCGAGTGGAGTGGAGTGT 61.528 60.000 0.00 0.00 0.00 3.55
141 142 1.373497 GCGAGTGGAGTGGAGTGTG 60.373 63.158 0.00 0.00 0.00 3.82
143 144 0.242286 CGAGTGGAGTGGAGTGTGAG 59.758 60.000 0.00 0.00 0.00 3.51
144 145 0.037790 GAGTGGAGTGGAGTGTGAGC 60.038 60.000 0.00 0.00 0.00 4.26
146 147 2.262915 GGAGTGGAGTGTGAGCGG 59.737 66.667 0.00 0.00 0.00 5.52
148 149 3.226429 GAGTGGAGTGTGAGCGGCA 62.226 63.158 1.45 0.00 0.00 5.69
149 150 2.740055 GTGGAGTGTGAGCGGCAG 60.740 66.667 1.45 0.00 0.00 4.85
152 153 3.695606 GAGTGTGAGCGGCAGGGA 61.696 66.667 1.45 0.00 0.00 4.20
155 156 4.007644 TGTGAGCGGCAGGGAGTG 62.008 66.667 1.45 0.00 0.00 3.51
165 166 3.947041 AGGGAGTGGGGGCTCTGT 61.947 66.667 0.00 0.00 35.89 3.41
166 167 2.936032 GGGAGTGGGGGCTCTGTT 60.936 66.667 0.00 0.00 35.89 3.16
168 169 1.460699 GGAGTGGGGGCTCTGTTTT 59.539 57.895 0.00 0.00 35.89 2.43
169 170 0.895559 GGAGTGGGGGCTCTGTTTTG 60.896 60.000 0.00 0.00 35.89 2.44
170 171 0.178990 GAGTGGGGGCTCTGTTTTGT 60.179 55.000 0.00 0.00 32.99 2.83
171 172 1.073284 GAGTGGGGGCTCTGTTTTGTA 59.927 52.381 0.00 0.00 32.99 2.41
172 173 1.202891 AGTGGGGGCTCTGTTTTGTAC 60.203 52.381 0.00 0.00 0.00 2.90
174 175 0.958876 GGGGGCTCTGTTTTGTACCG 60.959 60.000 0.00 0.00 0.00 4.02
175 176 0.035739 GGGGCTCTGTTTTGTACCGA 59.964 55.000 0.00 0.00 0.00 4.69
176 177 1.154197 GGGCTCTGTTTTGTACCGAC 58.846 55.000 0.00 0.00 0.00 4.79
182 183 0.470766 TGTTTTGTACCGACAGCCCT 59.529 50.000 0.00 0.00 36.76 5.19
183 184 1.693062 TGTTTTGTACCGACAGCCCTA 59.307 47.619 0.00 0.00 36.76 3.53
189 190 2.183555 CCGACAGCCCTAACGGTC 59.816 66.667 0.00 0.00 40.42 4.79
192 193 1.153881 GACAGCCCTAACGGTCGTC 60.154 63.158 0.00 0.00 0.00 4.20
194 195 1.290955 CAGCCCTAACGGTCGTCAA 59.709 57.895 0.00 0.00 0.00 3.18
195 196 1.012486 CAGCCCTAACGGTCGTCAAC 61.012 60.000 0.00 0.00 0.00 3.18
198 199 1.667151 CCTAACGGTCGTCAACCCA 59.333 57.895 0.00 0.00 46.27 4.51
199 200 0.668401 CCTAACGGTCGTCAACCCAC 60.668 60.000 0.00 0.00 46.27 4.61
203 204 2.737376 GGTCGTCAACCCACTCGC 60.737 66.667 0.00 0.00 42.85 5.03
206 207 4.657824 CGTCAACCCACTCGCCGT 62.658 66.667 0.00 0.00 0.00 5.68
255 256 2.436109 GGCCAGCCCTGTCAGAAA 59.564 61.111 0.00 0.00 0.00 2.52
261 262 0.687354 AGCCCTGTCAGAAATCGTGT 59.313 50.000 0.00 0.00 0.00 4.49
262 263 1.072331 AGCCCTGTCAGAAATCGTGTT 59.928 47.619 0.00 0.00 0.00 3.32
264 265 3.071479 GCCCTGTCAGAAATCGTGTTAA 58.929 45.455 0.00 0.00 0.00 2.01
266 267 4.315803 CCCTGTCAGAAATCGTGTTAACT 58.684 43.478 7.22 0.00 0.00 2.24
274 275 1.231221 ATCGTGTTAACTGCGGCAAA 58.769 45.000 18.02 0.00 0.00 3.68
276 277 0.659123 CGTGTTAACTGCGGCAAACC 60.659 55.000 12.12 4.70 0.00 3.27
287 288 3.978460 GGCAAACCGGTCATTTGTT 57.022 47.368 8.04 0.00 38.93 2.83
289 290 2.556257 GGCAAACCGGTCATTTGTTTT 58.444 42.857 8.04 0.00 38.93 2.43
291 292 4.120589 GGCAAACCGGTCATTTGTTTTTA 58.879 39.130 8.04 0.00 38.93 1.52
292 293 4.752604 GGCAAACCGGTCATTTGTTTTTAT 59.247 37.500 8.04 0.00 38.93 1.40
294 295 6.132724 GCAAACCGGTCATTTGTTTTTATTG 58.867 36.000 8.04 4.87 38.93 1.90
295 296 6.018669 GCAAACCGGTCATTTGTTTTTATTGA 60.019 34.615 8.04 0.00 38.93 2.57
297 298 6.642707 ACCGGTCATTTGTTTTTATTGAGA 57.357 33.333 0.00 0.00 0.00 3.27
298 299 7.045126 ACCGGTCATTTGTTTTTATTGAGAA 57.955 32.000 0.00 0.00 0.00 2.87
300 301 7.982354 ACCGGTCATTTGTTTTTATTGAGAAAA 59.018 29.630 0.00 0.00 0.00 2.29
301 302 8.987890 CCGGTCATTTGTTTTTATTGAGAAAAT 58.012 29.630 0.00 0.00 0.00 1.82
320 321 8.528044 AGAAAATTTACAAGTAAAGTGGTGGA 57.472 30.769 10.70 0.00 38.30 4.02
321 322 9.143155 AGAAAATTTACAAGTAAAGTGGTGGAT 57.857 29.630 10.70 0.00 38.30 3.41
322 323 9.758651 GAAAATTTACAAGTAAAGTGGTGGATT 57.241 29.630 10.70 0.00 38.30 3.01
326 327 8.934507 TTTACAAGTAAAGTGGTGGATTTTTG 57.065 30.769 1.46 0.00 31.95 2.44
329 330 4.810345 AGTAAAGTGGTGGATTTTTGGGA 58.190 39.130 0.00 0.00 0.00 4.37
332 333 0.038618 GTGGTGGATTTTTGGGACGC 60.039 55.000 0.00 0.00 0.00 5.19
337 338 1.807742 TGGATTTTTGGGACGCGTTAG 59.192 47.619 15.53 0.00 0.00 2.34
342 343 3.546002 TTTTGGGACGCGTTAGAAATG 57.454 42.857 15.53 0.00 0.00 2.32
343 344 2.172851 TTGGGACGCGTTAGAAATGT 57.827 45.000 15.53 0.00 0.00 2.71
344 345 1.434555 TGGGACGCGTTAGAAATGTG 58.565 50.000 15.53 0.00 0.00 3.21
345 346 0.725117 GGGACGCGTTAGAAATGTGG 59.275 55.000 15.53 0.00 32.27 4.17
352 353 2.094752 GCGTTAGAAATGTGGTGCCAAT 60.095 45.455 0.00 0.00 0.00 3.16
353 354 3.613910 GCGTTAGAAATGTGGTGCCAATT 60.614 43.478 0.00 0.00 0.00 2.32
354 355 3.919804 CGTTAGAAATGTGGTGCCAATTG 59.080 43.478 0.00 0.00 0.00 2.32
355 356 4.244862 GTTAGAAATGTGGTGCCAATTGG 58.755 43.478 20.81 20.81 38.53 3.16
360 361 0.542467 TGTGGTGCCAATTGGATGCT 60.542 50.000 29.02 0.00 37.39 3.79
361 362 0.609662 GTGGTGCCAATTGGATGCTT 59.390 50.000 29.02 0.00 37.39 3.91
363 364 0.896923 GGTGCCAATTGGATGCTTCA 59.103 50.000 29.02 12.23 37.39 3.02
368 369 2.737679 GCCAATTGGATGCTTCAGCTTC 60.738 50.000 29.02 6.21 42.42 3.86
373 374 3.861276 TGGATGCTTCAGCTTCAAATG 57.139 42.857 14.67 0.00 44.21 2.32
374 375 3.159472 TGGATGCTTCAGCTTCAAATGT 58.841 40.909 14.67 0.00 44.21 2.71
375 376 3.057104 TGGATGCTTCAGCTTCAAATGTG 60.057 43.478 14.67 0.00 44.21 3.21
377 378 2.309613 TGCTTCAGCTTCAAATGTGGT 58.690 42.857 0.00 0.00 42.66 4.16
378 379 2.034939 TGCTTCAGCTTCAAATGTGGTG 59.965 45.455 0.00 0.00 42.66 4.17
381 382 2.665165 TCAGCTTCAAATGTGGTGGTT 58.335 42.857 0.00 0.00 0.00 3.67
382 383 3.030291 TCAGCTTCAAATGTGGTGGTTT 58.970 40.909 0.00 0.00 0.00 3.27
383 384 3.450457 TCAGCTTCAAATGTGGTGGTTTT 59.550 39.130 0.00 0.00 0.00 2.43
602 603 4.614306 GCGCTATGCATGCAAATATCTGAA 60.614 41.667 26.68 0.00 45.45 3.02
603 604 4.849926 CGCTATGCATGCAAATATCTGAAC 59.150 41.667 26.68 4.47 0.00 3.18
607 608 6.570672 ATGCATGCAAATATCTGAACCTAG 57.429 37.500 26.68 0.00 0.00 3.02
608 609 4.276678 TGCATGCAAATATCTGAACCTAGC 59.723 41.667 20.30 0.00 0.00 3.42
611 612 3.879295 TGCAAATATCTGAACCTAGCTGC 59.121 43.478 0.00 0.00 0.00 5.25
617 618 1.977854 TCTGAACCTAGCTGCTTTGGA 59.022 47.619 22.37 0.00 0.00 3.53
618 619 2.079925 CTGAACCTAGCTGCTTTGGAC 58.920 52.381 22.37 16.52 0.00 4.02
619 620 1.699634 TGAACCTAGCTGCTTTGGACT 59.300 47.619 22.37 12.06 0.00 3.85
623 624 2.093235 ACCTAGCTGCTTTGGACTGATC 60.093 50.000 22.37 0.00 0.00 2.92
631 632 3.126831 GCTTTGGACTGATCAGATACCG 58.873 50.000 29.27 15.30 0.00 4.02
678 679 3.249799 CGCAAAACCATGAACTACTCACA 59.750 43.478 0.00 0.00 36.69 3.58
681 682 5.221048 GCAAAACCATGAACTACTCACAGTT 60.221 40.000 0.00 0.00 41.44 3.16
683 684 6.619801 AAACCATGAACTACTCACAGTTTC 57.380 37.500 0.00 0.00 37.78 2.78
689 690 7.819415 CCATGAACTACTCACAGTTTCAAGATA 59.181 37.037 0.00 0.00 38.86 1.98
691 692 9.778741 ATGAACTACTCACAGTTTCAAGATAAA 57.221 29.630 0.00 0.00 38.86 1.40
699 700 8.731275 TCACAGTTTCAAGATAAAAAGAGTGA 57.269 30.769 0.00 0.00 31.96 3.41
700 701 8.830580 TCACAGTTTCAAGATAAAAAGAGTGAG 58.169 33.333 0.00 0.00 31.36 3.51
702 703 9.396022 ACAGTTTCAAGATAAAAAGAGTGAGAA 57.604 29.630 0.00 0.00 0.00 2.87
716 717 4.696402 AGAGTGAGAAAGGTAGTAGTCGTG 59.304 45.833 0.00 0.00 0.00 4.35
727 728 2.567985 AGTAGTCGTGGGTTGGTTTTG 58.432 47.619 0.00 0.00 0.00 2.44
728 729 1.605232 GTAGTCGTGGGTTGGTTTTGG 59.395 52.381 0.00 0.00 0.00 3.28
729 730 1.066752 GTCGTGGGTTGGTTTTGGC 59.933 57.895 0.00 0.00 0.00 4.52
732 733 1.445518 GTGGGTTGGTTTTGGCCTG 59.554 57.895 3.32 0.00 0.00 4.85
734 735 2.140138 GGGTTGGTTTTGGCCTGCT 61.140 57.895 3.32 0.00 0.00 4.24
735 736 1.069596 GGTTGGTTTTGGCCTGCTG 59.930 57.895 3.32 0.00 0.00 4.41
737 738 2.139484 TTGGTTTTGGCCTGCTGGG 61.139 57.895 12.06 1.66 38.36 4.45
746 747 2.987547 CCTGCTGGGCTGTGGTTG 60.988 66.667 0.71 0.00 0.00 3.77
753 754 2.037121 GCTGGGCTGTGGTTGTTTAAAT 59.963 45.455 0.00 0.00 0.00 1.40
756 757 5.104259 TGGGCTGTGGTTGTTTAAATTTT 57.896 34.783 0.00 0.00 0.00 1.82
758 759 4.260990 GGGCTGTGGTTGTTTAAATTTTGC 60.261 41.667 0.00 0.00 0.00 3.68
759 760 4.333926 GGCTGTGGTTGTTTAAATTTTGCA 59.666 37.500 0.00 0.00 0.00 4.08
760 761 5.008514 GGCTGTGGTTGTTTAAATTTTGCAT 59.991 36.000 0.00 0.00 0.00 3.96
762 763 6.369059 TGTGGTTGTTTAAATTTTGCATGG 57.631 33.333 0.00 0.00 0.00 3.66
765 766 6.259829 GTGGTTGTTTAAATTTTGCATGGTCT 59.740 34.615 0.00 0.00 0.00 3.85
766 767 6.259608 TGGTTGTTTAAATTTTGCATGGTCTG 59.740 34.615 0.00 0.00 0.00 3.51
815 816 2.925578 ATAACGTGTGTAGCGTGCTA 57.074 45.000 0.00 0.00 42.10 3.49
819 820 3.220507 ACGTGTGTAGCGTGCTAATTA 57.779 42.857 2.62 0.00 41.33 1.40
820 821 2.919229 ACGTGTGTAGCGTGCTAATTAC 59.081 45.455 2.62 4.52 41.33 1.89
841 842 1.590792 AATTAGCGTCGTAGCGGCC 60.591 57.895 0.00 0.00 43.00 6.13
850 851 0.528249 TCGTAGCGGCCGATTTTACC 60.528 55.000 33.48 9.31 0.00 2.85
854 855 1.249407 AGCGGCCGATTTTACCAAAA 58.751 45.000 33.48 0.00 34.41 2.44
855 856 1.068125 AGCGGCCGATTTTACCAAAAC 60.068 47.619 33.48 5.79 32.37 2.43
857 858 1.069091 CGGCCGATTTTACCAAAACGT 60.069 47.619 24.07 0.00 32.37 3.99
859 860 3.725600 CGGCCGATTTTACCAAAACGTAG 60.726 47.826 24.07 0.00 32.37 3.51
861 862 3.409949 CCGATTTTACCAAAACGTAGCG 58.590 45.455 0.00 0.00 32.37 4.26
865 866 4.713854 TTTTACCAAAACGTAGCGTCTC 57.286 40.909 0.00 0.00 39.99 3.36
867 868 0.320160 ACCAAAACGTAGCGTCTCCC 60.320 55.000 0.00 0.00 39.99 4.30
868 869 0.037605 CCAAAACGTAGCGTCTCCCT 60.038 55.000 0.00 0.00 39.99 4.20
870 871 2.140717 CAAAACGTAGCGTCTCCCTTT 58.859 47.619 0.00 0.00 39.99 3.11
871 872 2.075979 AAACGTAGCGTCTCCCTTTC 57.924 50.000 0.00 0.00 39.99 2.62
872 873 0.109412 AACGTAGCGTCTCCCTTTCG 60.109 55.000 0.00 0.00 39.99 3.46
873 874 0.957395 ACGTAGCGTCTCCCTTTCGA 60.957 55.000 0.00 0.00 33.69 3.71
878 879 3.099267 AGCGTCTCCCTTTCGAATATG 57.901 47.619 0.00 0.00 0.00 1.78
879 880 1.527311 GCGTCTCCCTTTCGAATATGC 59.473 52.381 0.00 0.00 0.00 3.14
882 883 4.810790 CGTCTCCCTTTCGAATATGCTAT 58.189 43.478 0.00 0.00 0.00 2.97
885 886 6.308282 CGTCTCCCTTTCGAATATGCTATAAC 59.692 42.308 0.00 0.00 0.00 1.89
889 890 4.201589 CCTTTCGAATATGCTATAACCGCG 60.202 45.833 0.00 0.00 0.00 6.46
890 891 2.256174 TCGAATATGCTATAACCGCGC 58.744 47.619 0.00 0.00 0.00 6.86
892 893 3.127376 TCGAATATGCTATAACCGCGCTA 59.873 43.478 5.56 0.00 0.00 4.26
896 897 6.344780 CGAATATGCTATAACCGCGCTATAAC 60.345 42.308 5.56 0.37 0.00 1.89
905 906 1.527736 CCGCGCTATAACGGCAAAATA 59.472 47.619 5.56 0.00 43.44 1.40
911 912 2.468532 ATAACGGCAAAATAGCGTGC 57.531 45.000 0.00 0.00 40.14 5.34
912 913 1.444836 TAACGGCAAAATAGCGTGCT 58.555 45.000 0.00 0.00 40.70 4.40
913 914 1.444836 AACGGCAAAATAGCGTGCTA 58.555 45.000 3.73 3.73 40.70 3.49
1344 4469 4.415150 CACATCTGCGGGCTGGGT 62.415 66.667 0.00 0.00 0.00 4.51
1348 4473 2.905996 ATCTGCGGGCTGGGTTTCA 61.906 57.895 0.00 0.00 0.00 2.69
1447 4575 3.126879 CGCTGCTGCCGGATCAAA 61.127 61.111 5.05 0.00 35.36 2.69
1454 4582 0.322456 CTGCCGGATCAAAAGGTGGA 60.322 55.000 5.05 0.00 0.00 4.02
1802 5308 3.733988 CGGCATTGACTGACTACGTACAT 60.734 47.826 0.00 0.00 0.00 2.29
1804 5310 5.529791 GGCATTGACTGACTACGTACATAT 58.470 41.667 0.00 0.00 0.00 1.78
1805 5311 6.567132 CGGCATTGACTGACTACGTACATATA 60.567 42.308 0.00 0.00 0.00 0.86
1806 5312 6.581542 GGCATTGACTGACTACGTACATATAC 59.418 42.308 0.00 0.00 0.00 1.47
1997 5512 4.010667 ACGGTAAGCATTTGACCAACTA 57.989 40.909 0.00 0.00 32.39 2.24
2012 5527 4.701956 CCAACTAATGGCAACTTACAGG 57.298 45.455 0.00 0.00 43.80 4.00
2017 5532 2.969821 ATGGCAACTTACAGGTTCCA 57.030 45.000 0.00 0.00 34.02 3.53
2020 5535 2.890311 TGGCAACTTACAGGTTCCATTG 59.110 45.455 0.00 0.00 37.61 2.82
2021 5536 2.352715 GGCAACTTACAGGTTCCATTGC 60.353 50.000 0.00 0.00 40.11 3.56
2025 5540 3.679389 ACTTACAGGTTCCATTGCAGAG 58.321 45.455 0.00 0.00 0.00 3.35
2038 5553 0.401356 TGCAGAGATTGGCAAGTGGA 59.599 50.000 5.96 0.00 37.03 4.02
2076 5591 4.439968 CCTCCCTTTTCATTCCTACGTAC 58.560 47.826 0.00 0.00 0.00 3.67
2092 5711 3.928211 ACGTACGTACATACACGATGAC 58.072 45.455 21.41 0.00 44.69 3.06
2134 5769 4.552278 CGTAGTCGTGCTCTGCAA 57.448 55.556 0.00 0.00 41.47 4.08
2162 5797 1.530013 GGGAAGCTGCATGCACAACT 61.530 55.000 18.46 11.79 45.94 3.16
2163 5798 1.167851 GGAAGCTGCATGCACAACTA 58.832 50.000 18.46 0.00 45.94 2.24
2164 5799 1.131883 GGAAGCTGCATGCACAACTAG 59.868 52.381 18.46 7.18 45.94 2.57
2165 5800 0.524862 AAGCTGCATGCACAACTAGC 59.475 50.000 18.46 17.59 45.94 3.42
2167 5802 1.805254 CTGCATGCACAACTAGCCC 59.195 57.895 18.46 0.00 0.00 5.19
2168 5803 1.985447 CTGCATGCACAACTAGCCCG 61.985 60.000 18.46 0.00 0.00 6.13
2169 5804 2.764314 GCATGCACAACTAGCCCGG 61.764 63.158 14.21 0.00 0.00 5.73
2170 5805 2.438434 ATGCACAACTAGCCCGGC 60.438 61.111 0.00 0.00 0.00 6.13
2191 5826 2.895372 CCGGCCGCCACAATACTC 60.895 66.667 22.85 0.00 0.00 2.59
2192 5827 2.186903 CGGCCGCCACAATACTCT 59.813 61.111 14.67 0.00 0.00 3.24
2193 5828 1.883084 CGGCCGCCACAATACTCTC 60.883 63.158 14.67 0.00 0.00 3.20
2194 5829 1.883084 GGCCGCCACAATACTCTCG 60.883 63.158 3.91 0.00 0.00 4.04
2195 5830 1.141019 GCCGCCACAATACTCTCGA 59.859 57.895 0.00 0.00 0.00 4.04
2196 5831 1.146358 GCCGCCACAATACTCTCGAC 61.146 60.000 0.00 0.00 0.00 4.20
2197 5832 0.866061 CCGCCACAATACTCTCGACG 60.866 60.000 0.00 0.00 0.00 5.12
2198 5833 1.472276 CGCCACAATACTCTCGACGC 61.472 60.000 0.00 0.00 0.00 5.19
2199 5834 0.179134 GCCACAATACTCTCGACGCT 60.179 55.000 0.00 0.00 0.00 5.07
2201 5836 1.457738 CACAATACTCTCGACGCTCG 58.542 55.000 0.00 1.67 42.10 5.03
2209 5844 4.452753 TCGACGCTCGATTGACAC 57.547 55.556 6.09 0.00 44.82 3.67
2210 5845 1.511254 TCGACGCTCGATTGACACG 60.511 57.895 6.09 0.10 44.82 4.49
2216 5851 2.959372 TCGATTGACACGAGCGGT 59.041 55.556 0.00 0.00 34.85 5.68
2217 5852 2.173433 TCGATTGACACGAGCGGTA 58.827 52.632 0.00 0.00 34.85 4.02
2220 6305 1.731424 CGATTGACACGAGCGGTAGTT 60.731 52.381 0.00 0.00 0.00 2.24
2235 6320 2.286025 GGTAGTTGCGTCAAAGAACGTT 59.714 45.455 0.00 0.00 44.38 3.99
2242 6327 2.342948 GCGTCAAAGAACGTTTTGCAAA 59.657 40.909 8.05 8.05 44.38 3.68
2252 6337 6.992766 AGAACGTTTTGCAAAAGAGAAAATG 58.007 32.000 24.46 9.83 33.61 2.32
2260 6345 4.508861 TGCAAAAGAGAAAATGAAAGCAGC 59.491 37.500 0.00 0.00 0.00 5.25
2308 6393 3.936661 CATGAATGCAAGATGACGTCAG 58.063 45.455 24.41 11.20 0.00 3.51
2309 6394 1.733912 TGAATGCAAGATGACGTCAGC 59.266 47.619 25.68 25.68 0.00 4.26
2310 6395 1.733912 GAATGCAAGATGACGTCAGCA 59.266 47.619 32.88 29.25 41.97 4.41
2311 6396 1.081892 ATGCAAGATGACGTCAGCAC 58.918 50.000 32.88 22.12 41.05 4.40
2330 6415 3.246226 GCACGGATCTGTGTACATCATTC 59.754 47.826 30.44 11.07 41.94 2.67
2335 6420 2.797491 TCTGTGTACATCATTCTCGCG 58.203 47.619 0.00 0.00 0.00 5.87
2338 6423 1.518929 GTGTACATCATTCTCGCGCTC 59.481 52.381 5.56 0.00 0.00 5.03
2363 6449 0.883833 GCCACTGATTTGTGTCCCAG 59.116 55.000 0.00 0.00 36.30 4.45
2390 6522 0.234884 CAGGTTCGGACAAGTTTCGC 59.765 55.000 0.00 0.00 0.00 4.70
2399 6531 0.311790 ACAAGTTTCGCTGTGCATGG 59.688 50.000 0.00 0.00 0.00 3.66
2406 6538 0.608856 TCGCTGTGCATGGTCCAATT 60.609 50.000 0.00 0.00 0.00 2.32
2420 6552 7.039504 GCATGGTCCAATTATTACAGGAATGAT 60.040 37.037 0.00 0.00 0.00 2.45
2425 6561 8.562892 GTCCAATTATTACAGGAATGATGTCTG 58.437 37.037 0.00 0.00 32.02 3.51
2437 6573 7.440556 CAGGAATGATGTCTGTATCCAAACTAG 59.559 40.741 0.00 0.00 0.00 2.57
2438 6574 7.126421 AGGAATGATGTCTGTATCCAAACTAGT 59.874 37.037 0.00 0.00 0.00 2.57
2439 6575 8.421784 GGAATGATGTCTGTATCCAAACTAGTA 58.578 37.037 0.00 0.00 0.00 1.82
2440 6576 9.250624 GAATGATGTCTGTATCCAAACTAGTAC 57.749 37.037 0.00 0.00 0.00 2.73
2441 6577 7.956328 TGATGTCTGTATCCAAACTAGTACT 57.044 36.000 0.00 0.00 0.00 2.73
2442 6578 7.772166 TGATGTCTGTATCCAAACTAGTACTG 58.228 38.462 5.39 0.00 0.00 2.74
2443 6579 7.396339 TGATGTCTGTATCCAAACTAGTACTGT 59.604 37.037 5.39 0.00 0.00 3.55
2444 6580 8.818622 ATGTCTGTATCCAAACTAGTACTGTA 57.181 34.615 5.39 0.00 0.00 2.74
2445 6581 8.277490 TGTCTGTATCCAAACTAGTACTGTAG 57.723 38.462 5.39 0.00 0.00 2.74
2476 6612 1.603678 GGACAGTTGACGCGGTTAAGA 60.604 52.381 12.47 0.00 0.00 2.10
2477 6613 2.129607 GACAGTTGACGCGGTTAAGAA 58.870 47.619 12.47 0.00 0.00 2.52
2478 6614 2.132762 ACAGTTGACGCGGTTAAGAAG 58.867 47.619 12.47 0.00 0.00 2.85
2499 6635 0.238817 TTGTCATTGGCCGCGTAAAC 59.761 50.000 4.92 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.151022 GGAGGAGGAGCTGGTCGG 61.151 72.222 0.00 0.00 0.00 4.79
1 2 2.043450 AGGAGGAGGAGCTGGTCG 60.043 66.667 0.00 0.00 0.00 4.79
3 4 2.043450 CGAGGAGGAGGAGCTGGT 60.043 66.667 0.00 0.00 0.00 4.00
8 9 2.441901 AGCAGCGAGGAGGAGGAG 60.442 66.667 0.00 0.00 0.00 3.69
9 10 2.441164 GAGCAGCGAGGAGGAGGA 60.441 66.667 0.00 0.00 0.00 3.71
19 20 1.363443 GATGGAGAGGAGAGCAGCG 59.637 63.158 0.00 0.00 0.00 5.18
20 21 0.760189 AGGATGGAGAGGAGAGCAGC 60.760 60.000 0.00 0.00 0.00 5.25
23 24 1.047801 GGAAGGATGGAGAGGAGAGC 58.952 60.000 0.00 0.00 0.00 4.09
24 25 2.038659 GTGGAAGGATGGAGAGGAGAG 58.961 57.143 0.00 0.00 0.00 3.20
28 29 0.461961 GTCGTGGAAGGATGGAGAGG 59.538 60.000 0.00 0.00 31.14 3.69
29 30 0.101399 CGTCGTGGAAGGATGGAGAG 59.899 60.000 0.00 0.00 34.26 3.20
31 32 4.814900 CGTCGTGGAAGGATGGAG 57.185 61.111 0.00 0.00 34.26 3.86
39 40 1.135199 GTAGAAGATGCCGTCGTGGAA 60.135 52.381 0.51 0.00 42.00 3.53
40 41 0.454600 GTAGAAGATGCCGTCGTGGA 59.545 55.000 0.51 0.00 42.00 4.02
44 45 1.944676 GCCGTAGAAGATGCCGTCG 60.945 63.158 0.00 0.00 0.00 5.12
45 46 1.944676 CGCCGTAGAAGATGCCGTC 60.945 63.158 0.00 0.00 0.00 4.79
50 51 1.364171 CTCCCCGCCGTAGAAGATG 59.636 63.158 0.00 0.00 0.00 2.90
51 52 1.833049 CCTCCCCGCCGTAGAAGAT 60.833 63.158 0.00 0.00 0.00 2.40
52 53 2.441532 CCTCCCCGCCGTAGAAGA 60.442 66.667 0.00 0.00 0.00 2.87
66 67 4.452733 CGGAGGCACGGTTCCCTC 62.453 72.222 13.61 13.61 45.52 4.30
88 89 4.722700 CCCTGTCCCCTGTTGCCG 62.723 72.222 0.00 0.00 0.00 5.69
93 94 2.608988 CTCTGCCCTGTCCCCTGT 60.609 66.667 0.00 0.00 0.00 4.00
98 99 1.610673 TCACTCCTCTGCCCTGTCC 60.611 63.158 0.00 0.00 0.00 4.02
102 103 0.614415 CACTCTCACTCCTCTGCCCT 60.614 60.000 0.00 0.00 0.00 5.19
106 107 0.451383 CGCTCACTCTCACTCCTCTG 59.549 60.000 0.00 0.00 0.00 3.35
113 114 0.170116 CTCCACTCGCTCACTCTCAC 59.830 60.000 0.00 0.00 0.00 3.51
115 116 0.170116 CACTCCACTCGCTCACTCTC 59.830 60.000 0.00 0.00 0.00 3.20
116 117 1.247419 CCACTCCACTCGCTCACTCT 61.247 60.000 0.00 0.00 0.00 3.24
117 118 1.214062 CCACTCCACTCGCTCACTC 59.786 63.158 0.00 0.00 0.00 3.51
118 119 1.228583 TCCACTCCACTCGCTCACT 60.229 57.895 0.00 0.00 0.00 3.41
119 120 1.214062 CTCCACTCCACTCGCTCAC 59.786 63.158 0.00 0.00 0.00 3.51
121 122 1.214062 CACTCCACTCCACTCGCTC 59.786 63.158 0.00 0.00 0.00 5.03
122 123 1.531840 ACACTCCACTCCACTCGCT 60.532 57.895 0.00 0.00 0.00 4.93
126 127 1.810606 CGCTCACACTCCACTCCACT 61.811 60.000 0.00 0.00 0.00 4.00
128 129 2.574018 CCGCTCACACTCCACTCCA 61.574 63.158 0.00 0.00 0.00 3.86
136 137 3.699894 CTCCCTGCCGCTCACACT 61.700 66.667 0.00 0.00 0.00 3.55
148 149 3.507143 AACAGAGCCCCCACTCCCT 62.507 63.158 0.00 0.00 37.39 4.20
149 150 2.081585 AAAACAGAGCCCCCACTCCC 62.082 60.000 0.00 0.00 37.39 4.30
152 153 1.145571 TACAAAACAGAGCCCCCACT 58.854 50.000 0.00 0.00 0.00 4.00
155 156 0.958876 CGGTACAAAACAGAGCCCCC 60.959 60.000 0.00 0.00 0.00 5.40
158 159 1.798813 CTGTCGGTACAAAACAGAGCC 59.201 52.381 13.38 0.00 34.49 4.70
160 161 1.798813 GGCTGTCGGTACAAAACAGAG 59.201 52.381 19.70 2.53 34.49 3.35
161 162 1.541670 GGGCTGTCGGTACAAAACAGA 60.542 52.381 19.70 0.00 34.49 3.41
165 166 2.769893 GTTAGGGCTGTCGGTACAAAA 58.230 47.619 0.00 0.00 34.49 2.44
166 167 1.337074 CGTTAGGGCTGTCGGTACAAA 60.337 52.381 0.00 0.00 34.49 2.83
168 169 1.597797 CCGTTAGGGCTGTCGGTACA 61.598 60.000 0.00 0.00 38.45 2.90
169 170 1.140375 CCGTTAGGGCTGTCGGTAC 59.860 63.158 0.00 0.00 38.45 3.34
170 171 3.607163 CCGTTAGGGCTGTCGGTA 58.393 61.111 0.00 0.00 38.45 4.02
172 173 2.183555 GACCGTTAGGGCTGTCGG 59.816 66.667 0.00 0.00 44.23 4.79
174 175 1.153881 GACGACCGTTAGGGCTGTC 60.154 63.158 0.00 1.50 45.93 3.51
175 176 1.466025 TTGACGACCGTTAGGGCTGT 61.466 55.000 0.00 0.00 45.93 4.40
176 177 1.012486 GTTGACGACCGTTAGGGCTG 61.012 60.000 0.00 0.00 45.93 4.85
188 189 4.351938 CGGCGAGTGGGTTGACGA 62.352 66.667 0.00 0.00 45.14 4.20
192 193 2.738521 CAGACGGCGAGTGGGTTG 60.739 66.667 16.62 0.00 0.00 3.77
245 246 4.377431 GCAGTTAACACGATTTCTGACAGG 60.377 45.833 8.61 0.00 0.00 4.00
247 248 3.183574 CGCAGTTAACACGATTTCTGACA 59.816 43.478 13.89 0.00 0.00 3.58
249 250 2.734606 CCGCAGTTAACACGATTTCTGA 59.265 45.455 19.04 0.00 0.00 3.27
251 252 1.463444 GCCGCAGTTAACACGATTTCT 59.537 47.619 19.04 0.00 0.00 2.52
255 256 1.069500 GTTTGCCGCAGTTAACACGAT 60.069 47.619 19.04 0.00 0.00 3.73
274 275 6.642707 TCTCAATAAAAACAAATGACCGGT 57.357 33.333 6.92 6.92 0.00 5.28
292 293 9.796120 CACCACTTTACTTGTAAATTTTCTCAA 57.204 29.630 0.00 0.00 0.00 3.02
294 295 8.626526 TCCACCACTTTACTTGTAAATTTTCTC 58.373 33.333 0.00 0.00 0.00 2.87
295 296 8.528044 TCCACCACTTTACTTGTAAATTTTCT 57.472 30.769 0.00 0.00 0.00 2.52
300 301 9.541143 CAAAAATCCACCACTTTACTTGTAAAT 57.459 29.630 6.44 0.00 0.00 1.40
301 302 7.982354 CCAAAAATCCACCACTTTACTTGTAAA 59.018 33.333 5.92 5.92 0.00 2.01
303 304 6.041069 CCCAAAAATCCACCACTTTACTTGTA 59.959 38.462 0.00 0.00 0.00 2.41
306 307 5.069914 GTCCCAAAAATCCACCACTTTACTT 59.930 40.000 0.00 0.00 0.00 2.24
312 313 1.616159 CGTCCCAAAAATCCACCACT 58.384 50.000 0.00 0.00 0.00 4.00
313 314 0.038618 GCGTCCCAAAAATCCACCAC 60.039 55.000 0.00 0.00 0.00 4.16
315 316 1.211709 CGCGTCCCAAAAATCCACC 59.788 57.895 0.00 0.00 0.00 4.61
317 318 1.807742 CTAACGCGTCCCAAAAATCCA 59.192 47.619 14.44 0.00 0.00 3.41
320 321 4.022676 ACATTTCTAACGCGTCCCAAAAAT 60.023 37.500 14.44 11.68 0.00 1.82
321 322 3.315749 ACATTTCTAACGCGTCCCAAAAA 59.684 39.130 14.44 9.80 0.00 1.94
322 323 2.879646 ACATTTCTAACGCGTCCCAAAA 59.120 40.909 14.44 11.65 0.00 2.44
323 324 2.224549 CACATTTCTAACGCGTCCCAAA 59.775 45.455 14.44 12.00 0.00 3.28
325 326 1.434555 CACATTTCTAACGCGTCCCA 58.565 50.000 14.44 0.00 0.00 4.37
326 327 0.725117 CCACATTTCTAACGCGTCCC 59.275 55.000 14.44 0.00 0.00 4.46
329 330 0.515564 GCACCACATTTCTAACGCGT 59.484 50.000 5.58 5.58 0.00 6.01
332 333 3.848272 ATTGGCACCACATTTCTAACG 57.152 42.857 0.00 0.00 0.00 3.18
337 338 3.264104 CATCCAATTGGCACCACATTTC 58.736 45.455 20.33 0.00 34.44 2.17
342 343 0.609662 AAGCATCCAATTGGCACCAC 59.390 50.000 20.33 7.11 34.44 4.16
343 344 0.896923 GAAGCATCCAATTGGCACCA 59.103 50.000 20.33 2.46 34.44 4.17
344 345 0.896923 TGAAGCATCCAATTGGCACC 59.103 50.000 20.33 9.51 34.44 5.01
345 346 1.738030 GCTGAAGCATCCAATTGGCAC 60.738 52.381 20.33 11.00 41.59 5.01
352 353 3.575256 ACATTTGAAGCTGAAGCATCCAA 59.425 39.130 4.90 0.88 45.16 3.53
353 354 3.057104 CACATTTGAAGCTGAAGCATCCA 60.057 43.478 4.90 0.00 45.16 3.41
354 355 3.508762 CACATTTGAAGCTGAAGCATCC 58.491 45.455 4.90 0.00 45.16 3.51
355 356 3.057033 ACCACATTTGAAGCTGAAGCATC 60.057 43.478 4.90 2.65 45.16 3.91
360 361 2.665165 ACCACCACATTTGAAGCTGAA 58.335 42.857 0.00 0.00 0.00 3.02
361 362 2.363306 ACCACCACATTTGAAGCTGA 57.637 45.000 0.00 0.00 0.00 4.26
363 364 4.486125 AAAAACCACCACATTTGAAGCT 57.514 36.364 0.00 0.00 0.00 3.74
381 382 7.706179 CCAAGAACTAAGACTGAATTGCAAAAA 59.294 33.333 1.71 0.00 0.00 1.94
382 383 7.068103 TCCAAGAACTAAGACTGAATTGCAAAA 59.932 33.333 1.71 0.00 0.00 2.44
383 384 6.545666 TCCAAGAACTAAGACTGAATTGCAAA 59.454 34.615 1.71 0.00 0.00 3.68
385 386 5.620206 TCCAAGAACTAAGACTGAATTGCA 58.380 37.500 0.00 0.00 0.00 4.08
391 392 4.323028 CCAGCATCCAAGAACTAAGACTGA 60.323 45.833 0.00 0.00 0.00 3.41
394 395 3.935828 GTCCAGCATCCAAGAACTAAGAC 59.064 47.826 0.00 0.00 0.00 3.01
395 396 3.840666 AGTCCAGCATCCAAGAACTAAGA 59.159 43.478 0.00 0.00 0.00 2.10
595 596 3.774766 TCCAAAGCAGCTAGGTTCAGATA 59.225 43.478 12.36 0.00 36.83 1.98
597 598 1.977854 TCCAAAGCAGCTAGGTTCAGA 59.022 47.619 12.36 0.00 36.83 3.27
598 599 2.079925 GTCCAAAGCAGCTAGGTTCAG 58.920 52.381 12.36 0.00 36.83 3.02
602 603 1.352083 TCAGTCCAAAGCAGCTAGGT 58.648 50.000 12.36 0.00 0.00 3.08
603 604 2.093288 TGATCAGTCCAAAGCAGCTAGG 60.093 50.000 0.00 0.60 0.00 3.02
607 608 2.105006 TCTGATCAGTCCAAAGCAGC 57.895 50.000 21.92 0.00 0.00 5.25
608 609 4.125703 GGTATCTGATCAGTCCAAAGCAG 58.874 47.826 21.92 0.00 0.00 4.24
611 612 4.098654 ACTCGGTATCTGATCAGTCCAAAG 59.901 45.833 21.92 20.11 0.00 2.77
617 618 5.407407 AAAACACTCGGTATCTGATCAGT 57.593 39.130 21.92 12.01 0.00 3.41
618 619 7.036220 ACTAAAAACACTCGGTATCTGATCAG 58.964 38.462 17.07 17.07 0.00 2.90
619 620 6.931838 ACTAAAAACACTCGGTATCTGATCA 58.068 36.000 0.00 0.00 0.00 2.92
623 624 7.411588 GCTGTAACTAAAAACACTCGGTATCTG 60.412 40.741 0.00 0.00 0.00 2.90
631 632 6.373186 ACTTGGCTGTAACTAAAAACACTC 57.627 37.500 0.00 0.00 0.00 3.51
681 682 8.980481 ACCTTTCTCACTCTTTTTATCTTGAA 57.020 30.769 0.00 0.00 0.00 2.69
683 684 9.495572 ACTACCTTTCTCACTCTTTTTATCTTG 57.504 33.333 0.00 0.00 0.00 3.02
689 690 7.146648 CGACTACTACCTTTCTCACTCTTTTT 58.853 38.462 0.00 0.00 0.00 1.94
691 692 5.769162 ACGACTACTACCTTTCTCACTCTTT 59.231 40.000 0.00 0.00 0.00 2.52
693 694 4.696402 CACGACTACTACCTTTCTCACTCT 59.304 45.833 0.00 0.00 0.00 3.24
699 700 3.166560 ACCCACGACTACTACCTTTCT 57.833 47.619 0.00 0.00 0.00 2.52
700 701 3.582780 CAACCCACGACTACTACCTTTC 58.417 50.000 0.00 0.00 0.00 2.62
702 703 1.897802 CCAACCCACGACTACTACCTT 59.102 52.381 0.00 0.00 0.00 3.50
703 704 1.203100 ACCAACCCACGACTACTACCT 60.203 52.381 0.00 0.00 0.00 3.08
704 705 1.260544 ACCAACCCACGACTACTACC 58.739 55.000 0.00 0.00 0.00 3.18
707 708 2.567985 CAAAACCAACCCACGACTACT 58.432 47.619 0.00 0.00 0.00 2.57
710 711 1.388837 GCCAAAACCAACCCACGACT 61.389 55.000 0.00 0.00 0.00 4.18
712 713 2.128507 GGCCAAAACCAACCCACGA 61.129 57.895 0.00 0.00 0.00 4.35
716 717 2.140138 AGCAGGCCAAAACCAACCC 61.140 57.895 5.01 0.00 0.00 4.11
729 730 2.987547 CAACCACAGCCCAGCAGG 60.988 66.667 0.00 0.00 39.47 4.85
732 733 1.036707 TTAAACAACCACAGCCCAGC 58.963 50.000 0.00 0.00 0.00 4.85
734 735 4.762289 AAATTTAAACAACCACAGCCCA 57.238 36.364 0.00 0.00 0.00 5.36
735 736 4.260990 GCAAAATTTAAACAACCACAGCCC 60.261 41.667 0.00 0.00 0.00 5.19
737 738 5.476752 TGCAAAATTTAAACAACCACAGC 57.523 34.783 0.00 0.00 0.00 4.40
738 739 6.038050 ACCATGCAAAATTTAAACAACCACAG 59.962 34.615 0.00 0.00 0.00 3.66
758 759 2.570169 CGTTTTAACGTGCAGACCATG 58.430 47.619 6.84 0.00 46.63 3.66
759 760 2.961522 CGTTTTAACGTGCAGACCAT 57.038 45.000 6.84 0.00 46.63 3.55
770 771 4.598697 CGTTGTAGCGTTACACGTTTTAAC 59.401 41.667 11.98 5.01 44.73 2.01
772 773 3.794028 ACGTTGTAGCGTTACACGTTTTA 59.206 39.130 23.30 5.10 44.73 1.52
773 774 2.602660 ACGTTGTAGCGTTACACGTTTT 59.397 40.909 23.30 10.17 44.73 2.43
774 775 2.192624 ACGTTGTAGCGTTACACGTTT 58.807 42.857 23.30 10.66 44.73 3.60
776 777 3.549997 ACGTTGTAGCGTTACACGT 57.450 47.368 23.30 23.30 44.73 4.49
796 797 2.925578 TAGCACGCTACACACGTTAT 57.074 45.000 0.00 0.00 42.96 1.89
797 798 2.702898 TTAGCACGCTACACACGTTA 57.297 45.000 0.00 0.00 42.96 3.18
798 799 2.074547 ATTAGCACGCTACACACGTT 57.925 45.000 0.00 0.00 42.96 3.99
831 832 0.528249 GGTAAAATCGGCCGCTACGA 60.528 55.000 23.51 2.08 45.19 3.43
834 835 2.110901 TTTGGTAAAATCGGCCGCTA 57.889 45.000 23.51 4.04 0.00 4.26
835 836 1.068125 GTTTTGGTAAAATCGGCCGCT 60.068 47.619 23.51 8.48 32.22 5.52
836 837 1.342555 GTTTTGGTAAAATCGGCCGC 58.657 50.000 23.51 4.66 32.22 6.53
841 842 4.056452 ACGCTACGTTTTGGTAAAATCG 57.944 40.909 0.00 0.00 41.87 3.34
850 851 1.792006 AAGGGAGACGCTACGTTTTG 58.208 50.000 0.00 0.00 41.37 2.44
854 855 0.957395 TCGAAAGGGAGACGCTACGT 60.957 55.000 0.00 0.00 45.10 3.57
855 856 0.169672 TTCGAAAGGGAGACGCTACG 59.830 55.000 0.00 0.00 0.00 3.51
857 858 3.552273 GCATATTCGAAAGGGAGACGCTA 60.552 47.826 0.00 0.00 0.00 4.26
859 860 1.527311 GCATATTCGAAAGGGAGACGC 59.473 52.381 0.00 0.00 0.00 5.19
861 862 6.590677 GGTTATAGCATATTCGAAAGGGAGAC 59.409 42.308 0.00 0.00 0.00 3.36
865 866 4.092968 GCGGTTATAGCATATTCGAAAGGG 59.907 45.833 0.00 0.00 34.19 3.95
867 868 4.721226 GCGCGGTTATAGCATATTCGAAAG 60.721 45.833 8.83 0.00 34.19 2.62
868 869 3.122278 GCGCGGTTATAGCATATTCGAAA 59.878 43.478 8.83 0.00 34.19 3.46
870 871 2.094906 AGCGCGGTTATAGCATATTCGA 60.095 45.455 4.23 0.00 34.19 3.71
871 872 2.259618 AGCGCGGTTATAGCATATTCG 58.740 47.619 4.23 0.00 34.19 3.34
872 873 6.344780 CGTTATAGCGCGGTTATAGCATATTC 60.345 42.308 19.09 3.14 34.19 1.75
873 874 5.457799 CGTTATAGCGCGGTTATAGCATATT 59.542 40.000 19.09 0.00 34.19 1.28
878 879 1.916000 CCGTTATAGCGCGGTTATAGC 59.084 52.381 19.09 12.72 42.73 2.97
889 890 3.541711 CACGCTATTTTGCCGTTATAGC 58.458 45.455 0.00 0.00 41.97 2.97
890 891 3.247648 AGCACGCTATTTTGCCGTTATAG 59.752 43.478 0.00 0.00 39.75 1.31
892 893 2.014128 AGCACGCTATTTTGCCGTTAT 58.986 42.857 0.00 0.00 39.75 1.89
896 897 2.755836 AATAGCACGCTATTTTGCCG 57.244 45.000 16.70 0.00 44.18 5.69
917 918 4.208460 GTCGTGTGAGAGAATCAACGAAAA 59.792 41.667 13.03 0.00 44.83 2.29
919 920 3.243267 TGTCGTGTGAGAGAATCAACGAA 60.243 43.478 13.03 5.74 44.83 3.85
920 921 2.292292 TGTCGTGTGAGAGAATCAACGA 59.708 45.455 0.00 9.55 43.07 3.85
922 923 2.410053 GCTGTCGTGTGAGAGAATCAAC 59.590 50.000 0.00 0.00 40.43 3.18
925 926 2.354109 TGCTGTCGTGTGAGAGAATC 57.646 50.000 0.00 0.00 37.70 2.52
956 4027 1.153628 CCGTCCTTGGTAGGCTTCG 60.154 63.158 0.00 0.00 41.69 3.79
1344 4469 0.960364 GCGCCTGTCCCATCTTGAAA 60.960 55.000 0.00 0.00 0.00 2.69
1348 4473 2.586792 GAGCGCCTGTCCCATCTT 59.413 61.111 2.29 0.00 0.00 2.40
1447 4575 3.655211 CTGCTGCCCCTCCACCTT 61.655 66.667 0.00 0.00 0.00 3.50
1688 4913 4.899239 CGCAGGAGCCGGATGGTC 62.899 72.222 5.05 0.00 40.86 4.02
1716 4983 5.048713 GGCCGGGAAGTTTCATTCAATATAG 60.049 44.000 2.18 0.00 0.00 1.31
1891 5397 3.036084 CTCCACGCGTGCGAAACT 61.036 61.111 33.17 0.00 42.83 2.66
1918 5424 3.763897 CCACCTTAATTAGTGCTTGCCTT 59.236 43.478 0.41 0.00 32.48 4.35
1997 5512 3.237268 TGGAACCTGTAAGTTGCCATT 57.763 42.857 0.00 0.00 37.28 3.16
2005 5520 3.942829 TCTCTGCAATGGAACCTGTAAG 58.057 45.455 0.00 0.00 0.00 2.34
2008 5523 3.087031 CAATCTCTGCAATGGAACCTGT 58.913 45.455 0.00 0.00 0.00 4.00
2012 5527 1.820519 TGCCAATCTCTGCAATGGAAC 59.179 47.619 6.39 0.00 34.82 3.62
2017 5532 1.822990 CCACTTGCCAATCTCTGCAAT 59.177 47.619 0.00 0.00 45.57 3.56
2020 5535 1.200948 GTTCCACTTGCCAATCTCTGC 59.799 52.381 0.00 0.00 0.00 4.26
2021 5536 2.227388 GTGTTCCACTTGCCAATCTCTG 59.773 50.000 0.00 0.00 0.00 3.35
2025 5540 1.956477 ACAGTGTTCCACTTGCCAATC 59.044 47.619 0.00 0.00 42.59 2.67
2038 5553 0.247736 GAGGGATCGAGCACAGTGTT 59.752 55.000 5.38 0.00 0.00 3.32
2042 5557 1.333636 AAGGGAGGGATCGAGCACAG 61.334 60.000 5.38 0.00 0.00 3.66
2076 5591 3.165890 ACGTTGTCATCGTGTATGTACG 58.834 45.455 8.12 0.00 44.98 3.67
2087 5706 1.186030 CGTACCGCTACGTTGTCATC 58.814 55.000 0.00 0.00 40.83 2.92
2142 5777 2.277591 TTGTGCATGCAGCTTCCCC 61.278 57.895 23.41 8.03 45.94 4.81
2153 5788 2.438434 GCCGGGCTAGTTGTGCAT 60.438 61.111 12.87 0.00 0.00 3.96
2175 5810 1.883084 GAGAGTATTGTGGCGGCCG 60.883 63.158 24.05 24.05 0.00 6.13
2176 5811 1.883084 CGAGAGTATTGTGGCGGCC 60.883 63.158 13.32 13.32 0.00 6.13
2177 5812 1.141019 TCGAGAGTATTGTGGCGGC 59.859 57.895 0.00 0.00 0.00 6.53
2178 5813 0.866061 CGTCGAGAGTATTGTGGCGG 60.866 60.000 0.00 0.00 0.00 6.13
2179 5814 1.472276 GCGTCGAGAGTATTGTGGCG 61.472 60.000 0.00 0.00 0.00 5.69
2180 5815 0.179134 AGCGTCGAGAGTATTGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
2181 5816 1.828832 GAGCGTCGAGAGTATTGTGG 58.171 55.000 0.00 0.00 0.00 4.17
2182 5817 1.062148 TCGAGCGTCGAGAGTATTGTG 59.938 52.381 0.00 0.00 44.82 3.33
2183 5818 1.366679 TCGAGCGTCGAGAGTATTGT 58.633 50.000 0.00 0.00 44.82 2.71
2193 5828 1.456678 CTCGTGTCAATCGAGCGTCG 61.457 60.000 2.59 1.67 45.77 5.12
2194 5829 2.270091 CTCGTGTCAATCGAGCGTC 58.730 57.895 2.59 0.00 45.77 5.19
2195 5830 4.459973 CTCGTGTCAATCGAGCGT 57.540 55.556 2.59 0.00 45.77 5.07
2199 5834 0.098200 CTACCGCTCGTGTCAATCGA 59.902 55.000 0.00 0.00 35.96 3.59
2201 5836 1.654105 CAACTACCGCTCGTGTCAATC 59.346 52.381 0.00 0.00 0.00 2.67
2202 5837 1.710013 CAACTACCGCTCGTGTCAAT 58.290 50.000 0.00 0.00 0.00 2.57
2204 5839 1.372499 GCAACTACCGCTCGTGTCA 60.372 57.895 0.00 0.00 0.00 3.58
2205 5840 2.434134 CGCAACTACCGCTCGTGTC 61.434 63.158 0.00 0.00 0.00 3.67
2206 5841 2.430244 CGCAACTACCGCTCGTGT 60.430 61.111 0.00 0.00 0.00 4.49
2207 5842 2.430244 ACGCAACTACCGCTCGTG 60.430 61.111 0.00 0.00 31.74 4.35
2208 5843 2.126580 GACGCAACTACCGCTCGT 60.127 61.111 0.00 0.00 35.98 4.18
2209 5844 1.279527 TTTGACGCAACTACCGCTCG 61.280 55.000 0.00 0.00 0.00 5.03
2210 5845 0.438830 CTTTGACGCAACTACCGCTC 59.561 55.000 0.00 0.00 0.00 5.03
2212 5847 0.863144 TTCTTTGACGCAACTACCGC 59.137 50.000 0.00 0.00 0.00 5.68
2213 5848 1.136721 CGTTCTTTGACGCAACTACCG 60.137 52.381 0.00 0.00 36.12 4.02
2214 5849 1.862827 ACGTTCTTTGACGCAACTACC 59.137 47.619 0.00 0.00 46.47 3.18
2215 5850 3.580794 AACGTTCTTTGACGCAACTAC 57.419 42.857 0.00 0.00 46.47 2.73
2216 5851 4.336101 CAAAACGTTCTTTGACGCAACTA 58.664 39.130 0.00 0.00 46.47 2.24
2217 5852 3.168193 CAAAACGTTCTTTGACGCAACT 58.832 40.909 0.00 0.00 46.47 3.16
2220 6305 1.135660 TGCAAAACGTTCTTTGACGCA 60.136 42.857 15.21 7.71 46.47 5.24
2235 6320 6.457257 GCTGCTTTCATTTTCTCTTTTGCAAA 60.457 34.615 8.05 8.05 0.00 3.68
2242 6327 5.335504 GCTAGTGCTGCTTTCATTTTCTCTT 60.336 40.000 0.00 0.00 36.03 2.85
2260 6345 2.422479 TGCAACGTACTCCTAGCTAGTG 59.578 50.000 19.31 13.53 0.00 2.74
2267 6352 2.821546 GCATGATGCAACGTACTCCTA 58.178 47.619 13.36 0.00 44.26 2.94
2268 6353 1.656652 GCATGATGCAACGTACTCCT 58.343 50.000 13.36 0.00 44.26 3.69
2307 6392 1.824852 TGATGTACACAGATCCGTGCT 59.175 47.619 9.04 0.00 40.73 4.40
2308 6393 2.293677 TGATGTACACAGATCCGTGC 57.706 50.000 9.04 0.00 40.73 5.34
2309 6394 4.686972 AGAATGATGTACACAGATCCGTG 58.313 43.478 7.55 7.55 42.81 4.94
2310 6395 4.498177 CGAGAATGATGTACACAGATCCGT 60.498 45.833 0.00 0.00 0.00 4.69
2311 6396 3.977579 CGAGAATGATGTACACAGATCCG 59.022 47.826 0.00 4.78 0.00 4.18
2312 6397 3.738282 GCGAGAATGATGTACACAGATCC 59.262 47.826 0.00 0.00 0.00 3.36
2313 6398 3.423536 CGCGAGAATGATGTACACAGATC 59.576 47.826 0.00 2.44 0.00 2.75
2314 6399 3.375642 CGCGAGAATGATGTACACAGAT 58.624 45.455 0.00 0.00 0.00 2.90
2315 6400 2.797491 CGCGAGAATGATGTACACAGA 58.203 47.619 0.00 0.00 0.00 3.41
2338 6423 4.817063 CAAATCAGTGGCGGCGCG 62.817 66.667 26.95 12.29 0.00 6.86
2363 6449 2.110213 TCCGAACCTGTGCACACC 59.890 61.111 17.42 4.63 0.00 4.16
2390 6522 5.221106 CCTGTAATAATTGGACCATGCACAG 60.221 44.000 0.00 3.90 0.00 3.66
2399 6531 8.562892 CAGACATCATTCCTGTAATAATTGGAC 58.437 37.037 0.00 0.00 0.00 4.02
2406 6538 8.491045 TGGATACAGACATCATTCCTGTAATA 57.509 34.615 0.00 0.00 46.17 0.98
2425 6561 5.597594 AGGCCTACAGTACTAGTTTGGATAC 59.402 44.000 1.29 0.00 0.00 2.24
2437 6573 1.751924 CCAGACTCAGGCCTACAGTAC 59.248 57.143 15.12 9.78 0.00 2.73
2438 6574 1.639108 TCCAGACTCAGGCCTACAGTA 59.361 52.381 15.12 0.00 0.00 2.74
2439 6575 0.409876 TCCAGACTCAGGCCTACAGT 59.590 55.000 15.08 15.08 0.00 3.55
2440 6576 0.820871 GTCCAGACTCAGGCCTACAG 59.179 60.000 3.98 7.22 0.00 2.74
2441 6577 0.114364 TGTCCAGACTCAGGCCTACA 59.886 55.000 3.98 0.00 0.00 2.74
2442 6578 0.820871 CTGTCCAGACTCAGGCCTAC 59.179 60.000 3.98 0.00 0.00 3.18
2443 6579 0.409876 ACTGTCCAGACTCAGGCCTA 59.590 55.000 3.98 0.00 36.17 3.93
2444 6580 0.472734 AACTGTCCAGACTCAGGCCT 60.473 55.000 0.00 0.00 36.17 5.19
2445 6581 0.321122 CAACTGTCCAGACTCAGGCC 60.321 60.000 0.00 0.00 36.17 5.19
2476 6612 2.964978 GCGGCCAATGACAAGCTT 59.035 55.556 2.24 0.00 0.00 3.74
2477 6613 2.796483 TACGCGGCCAATGACAAGCT 62.796 55.000 12.47 0.00 0.00 3.74
2478 6614 1.917782 TTACGCGGCCAATGACAAGC 61.918 55.000 12.47 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.