Multiple sequence alignment - TraesCS5D01G313600

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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 TraesCS5D01G313600 chr5D 100.000 2840 0 0 1 2840 408743470 408740631 0.000000e+00 5245.0
1 TraesCS5D01G313600 chr5D 93.076 1112 50 14 869 1966 408659912 408658814 0.000000e+00 1602.0
2 TraesCS5D01G313600 chr5D 78.757 885 117 42 971 1827 408770120 408769279 6.970000e-146 527.0
3 TraesCS5D01G313600 chr5D 76.613 868 126 38 1007 1843 408649702 408648881 9.470000e-110 407.0
4 TraesCS5D01G313600 chr5D 97.191 178 4 1 691 868 539072824 539072648 1.650000e-77 300.0
5 TraesCS5D01G313600 chr5D 89.767 215 15 6 487 695 408660117 408659904 4.660000e-68 268.0
6 TraesCS5D01G313600 chr5B 94.789 1209 55 4 869 2071 490359609 490358403 0.000000e+00 1877.0
7 TraesCS5D01G313600 chr5B 89.086 1237 73 27 884 2074 490298430 490297210 0.000000e+00 1480.0
8 TraesCS5D01G313600 chr5B 85.652 690 60 20 10 695 490360255 490359601 0.000000e+00 689.0
9 TraesCS5D01G313600 chr5B 80.855 585 88 15 1274 1840 490611800 490611222 3.360000e-119 438.0
10 TraesCS5D01G313600 chr5B 78.937 508 77 11 1354 1843 490232667 490232172 4.570000e-83 318.0
11 TraesCS5D01G313600 chr5B 82.410 307 54 0 7 313 512940522 512940828 4.660000e-68 268.0
12 TraesCS5D01G313600 chr5B 92.913 127 8 1 569 695 490299317 490299192 1.740000e-42 183.0
13 TraesCS5D01G313600 chr5B 90.385 52 5 0 486 537 490299836 490299785 5.080000e-08 69.4
14 TraesCS5D01G313600 chr5B 90.385 52 5 0 486 537 490312183 490312132 5.080000e-08 69.4
15 TraesCS5D01G313600 chr5A 92.007 1226 69 16 869 2071 515496214 515494995 0.000000e+00 1694.0
16 TraesCS5D01G313600 chr5A 91.193 1215 90 9 869 2071 516814754 516815963 0.000000e+00 1635.0
17 TraesCS5D01G313600 chr5A 90.962 1206 91 13 875 2071 516664861 516663665 0.000000e+00 1607.0
18 TraesCS5D01G313600 chr5A 77.941 884 122 34 971 1825 519693966 519693127 4.250000e-133 484.0
19 TraesCS5D01G313600 chr5A 96.053 152 6 0 539 690 516665017 516664866 6.080000e-62 248.0
20 TraesCS5D01G313600 chr5A 93.284 134 9 0 557 690 516814624 516814757 6.210000e-47 198.0
21 TraesCS5D01G313600 chr5A 90.132 152 14 1 545 695 515496357 515496206 2.230000e-46 196.0
22 TraesCS5D01G313600 chr5A 92.647 136 10 0 429 564 515497179 515497044 2.230000e-46 196.0
23 TraesCS5D01G313600 chr1B 78.921 797 121 30 2071 2839 204720821 204721598 5.460000e-137 497.0
24 TraesCS5D01G313600 chr1B 78.294 797 117 38 2071 2836 193144646 193145417 1.990000e-126 462.0
25 TraesCS5D01G313600 chr1B 80.455 527 70 22 2318 2840 1823089 1822592 3.460000e-99 372.0
26 TraesCS5D01G313600 chr1B 81.994 311 53 3 6 314 431405248 431405557 7.800000e-66 261.0
27 TraesCS5D01G313600 chr7D 82.699 578 76 11 2274 2839 621056961 621057526 2.540000e-135 492.0
28 TraesCS5D01G313600 chr6D 82.064 591 82 14 2262 2839 448117998 448117419 1.530000e-132 483.0
29 TraesCS5D01G313600 chr6D 84.345 313 49 0 1 313 337846915 337847227 9.880000e-80 307.0
30 TraesCS5D01G313600 chr6D 97.727 176 4 0 693 868 470664465 470664640 1.280000e-78 303.0
31 TraesCS5D01G313600 chr6D 85.294 204 30 0 2071 2274 352916723 352916520 7.970000e-51 211.0
32 TraesCS5D01G313600 chr3D 82.261 575 78 13 2279 2839 583869651 583869087 2.560000e-130 475.0
33 TraesCS5D01G313600 chr3D 83.960 399 48 9 2274 2670 577399133 577399517 4.470000e-98 368.0
34 TraesCS5D01G313600 chr3D 96.089 179 7 0 692 870 587946658 587946836 2.770000e-75 292.0
35 TraesCS5D01G313600 chr3D 86.029 136 15 1 2071 2206 598085631 598085500 2.950000e-30 143.0
36 TraesCS5D01G313600 chr6B 80.210 571 89 17 2274 2840 211884531 211883981 9.470000e-110 407.0
37 TraesCS5D01G313600 chr1D 78.647 665 102 24 2192 2835 428203964 428204609 3.410000e-109 405.0
38 TraesCS5D01G313600 chr1D 78.846 624 89 26 2192 2793 428205864 428206466 5.740000e-102 381.0
39 TraesCS5D01G313600 chr1D 97.740 177 4 0 695 871 427704536 427704712 3.550000e-79 305.0
40 TraesCS5D01G313600 chr1D 96.629 178 6 0 691 868 110906660 110906837 2.140000e-76 296.0
41 TraesCS5D01G313600 chr1D 82.109 313 52 3 2 312 311755410 311755720 6.030000e-67 265.0
42 TraesCS5D01G313600 chr4D 97.740 177 4 0 695 871 3846754 3846930 3.550000e-79 305.0
43 TraesCS5D01G313600 chr4D 97.701 174 3 1 696 869 472411889 472412061 5.950000e-77 298.0
44 TraesCS5D01G313600 chr4D 82.581 310 53 1 7 316 80952160 80951852 3.610000e-69 272.0
45 TraesCS5D01G313600 chr2D 97.701 174 4 0 696 869 62026284 62026111 1.650000e-77 300.0
46 TraesCS5D01G313600 chr2D 82.736 307 47 5 10 313 617956659 617956356 4.660000e-68 268.0
47 TraesCS5D01G313600 chr2D 82.085 307 55 0 7 313 520511460 520511766 2.170000e-66 263.0
48 TraesCS5D01G313600 chrUn 97.688 173 4 0 696 868 102837101 102836929 5.950000e-77 298.0
49 TraesCS5D01G313600 chr1A 78.714 451 88 5 1396 1841 2075211 2075658 7.690000e-76 294.0
50 TraesCS5D01G313600 chr1A 76.042 576 100 26 1271 1841 547004632 547005174 6.030000e-67 265.0
51 TraesCS5D01G313600 chr1A 81.962 316 51 5 1 313 285955817 285956129 2.170000e-66 263.0
52 TraesCS5D01G313600 chr6A 81.270 315 55 4 10 324 28668705 28668395 4.700000e-63 252.0
53 TraesCS5D01G313600 chr4B 87.766 188 23 0 2071 2258 7194785 7194972 1.320000e-53 220.0
54 TraesCS5D01G313600 chr4B 87.234 188 24 0 2071 2258 7241446 7241633 6.160000e-52 215.0
55 TraesCS5D01G313600 chr2A 77.528 356 61 13 2487 2840 22598504 22598166 2.230000e-46 196.0


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 TraesCS5D01G313600 chr5D 408740631 408743470 2839 True 5245.000000 5245 100.000000 1 2840 1 chr5D.!!$R2 2839
1 TraesCS5D01G313600 chr5D 408658814 408660117 1303 True 935.000000 1602 91.421500 487 1966 2 chr5D.!!$R5 1479
2 TraesCS5D01G313600 chr5D 408769279 408770120 841 True 527.000000 527 78.757000 971 1827 1 chr5D.!!$R3 856
3 TraesCS5D01G313600 chr5D 408648881 408649702 821 True 407.000000 407 76.613000 1007 1843 1 chr5D.!!$R1 836
4 TraesCS5D01G313600 chr5B 490358403 490360255 1852 True 1283.000000 1877 90.220500 10 2071 2 chr5B.!!$R5 2061
5 TraesCS5D01G313600 chr5B 490297210 490299836 2626 True 577.466667 1480 90.794667 486 2074 3 chr5B.!!$R4 1588
6 TraesCS5D01G313600 chr5B 490611222 490611800 578 True 438.000000 438 80.855000 1274 1840 1 chr5B.!!$R3 566
7 TraesCS5D01G313600 chr5A 516663665 516665017 1352 True 927.500000 1607 93.507500 539 2071 2 chr5A.!!$R3 1532
8 TraesCS5D01G313600 chr5A 516814624 516815963 1339 False 916.500000 1635 92.238500 557 2071 2 chr5A.!!$F1 1514
9 TraesCS5D01G313600 chr5A 515494995 515497179 2184 True 695.333333 1694 91.595333 429 2071 3 chr5A.!!$R2 1642
10 TraesCS5D01G313600 chr5A 519693127 519693966 839 True 484.000000 484 77.941000 971 1825 1 chr5A.!!$R1 854
11 TraesCS5D01G313600 chr1B 204720821 204721598 777 False 497.000000 497 78.921000 2071 2839 1 chr1B.!!$F2 768
12 TraesCS5D01G313600 chr1B 193144646 193145417 771 False 462.000000 462 78.294000 2071 2836 1 chr1B.!!$F1 765
13 TraesCS5D01G313600 chr7D 621056961 621057526 565 False 492.000000 492 82.699000 2274 2839 1 chr7D.!!$F1 565
14 TraesCS5D01G313600 chr6D 448117419 448117998 579 True 483.000000 483 82.064000 2262 2839 1 chr6D.!!$R2 577
15 TraesCS5D01G313600 chr3D 583869087 583869651 564 True 475.000000 475 82.261000 2279 2839 1 chr3D.!!$R1 560
16 TraesCS5D01G313600 chr6B 211883981 211884531 550 True 407.000000 407 80.210000 2274 2840 1 chr6B.!!$R1 566
17 TraesCS5D01G313600 chr1D 428203964 428206466 2502 False 393.000000 405 78.746500 2192 2835 2 chr1D.!!$F4 643
18 TraesCS5D01G313600 chr1A 547004632 547005174 542 False 265.000000 265 76.042000 1271 1841 1 chr1A.!!$F3 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
293 294 0.03438 AGGTGGTCTCGGAATCTCGA 60.034 55.0 0.0 0.0 37.6 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 3892 0.248621 GCGCCAGATTTACCATGCAC 60.249 55.0 0.0 0.0 0.0 4.57 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
36 37 1.568606 GGAGCTCCGACGTAAATTCC 58.431 55.000 19.06 0.00 0.00 3.01
45 46 2.844804 CGACGTAAATTCCTGTCGTCTC 59.155 50.000 14.52 0.00 46.56 3.36
49 50 3.612860 CGTAAATTCCTGTCGTCTCCTTG 59.387 47.826 0.00 0.00 0.00 3.61
52 53 1.827399 TTCCTGTCGTCTCCTTGGGC 61.827 60.000 0.00 0.00 0.00 5.36
59 60 3.003173 TCTCCTTGGGCCGGTGAG 61.003 66.667 1.90 4.27 0.00 3.51
63 64 2.598787 CCTTGGGCCGGTGAGGTTA 61.599 63.158 1.90 0.00 43.70 2.85
77 78 3.056035 GTGAGGTTAGGGTTTCTCGTCAT 60.056 47.826 0.00 0.00 0.00 3.06
82 83 0.321653 AGGGTTTCTCGTCATGTGGC 60.322 55.000 0.00 0.00 0.00 5.01
85 86 0.163788 GTTTCTCGTCATGTGGCGTG 59.836 55.000 6.91 4.85 44.53 5.34
94 95 1.454847 ATGTGGCGTGGTTTGGTGT 60.455 52.632 0.00 0.00 0.00 4.16
97 98 1.152860 TGGCGTGGTTTGGTGTCAT 60.153 52.632 0.00 0.00 0.00 3.06
107 108 1.608055 TTGGTGTCATGTGCTTCAGG 58.392 50.000 0.00 0.00 0.00 3.86
113 114 3.620374 GTGTCATGTGCTTCAGGTCTATG 59.380 47.826 0.00 0.00 0.00 2.23
125 126 2.749621 CAGGTCTATGCAAGGGTTCAAC 59.250 50.000 0.00 0.00 0.00 3.18
146 147 2.626780 CGACGACTGTGGCTCCAGA 61.627 63.158 10.95 0.00 36.30 3.86
161 162 0.895530 CCAGAGCGTTGGTCCTTAGA 59.104 55.000 1.74 0.00 33.38 2.10
166 167 1.019805 GCGTTGGTCCTTAGAGGCAC 61.020 60.000 0.00 0.00 34.61 5.01
185 186 1.355381 ACATGCATGAAGACTTCCCCA 59.645 47.619 32.75 7.26 0.00 4.96
194 195 0.898320 AGACTTCCCCACTGTCATCG 59.102 55.000 0.00 0.00 33.56 3.84
198 199 1.001974 CTTCCCCACTGTCATCGACAA 59.998 52.381 0.00 0.00 42.26 3.18
202 203 1.270839 CCCACTGTCATCGACAAGGTT 60.271 52.381 11.90 0.00 42.26 3.50
214 215 4.035102 AAGGTTGAGCCGGCTCCC 62.035 66.667 44.85 38.55 42.09 4.30
218 219 2.045045 TTGAGCCGGCTCCCATTG 60.045 61.111 44.85 0.00 42.09 2.82
221 222 3.764160 GAGCCGGCTCCCATTGAGG 62.764 68.421 40.99 0.00 41.73 3.86
230 231 0.982852 TCCCATTGAGGAGTGGCGAT 60.983 55.000 0.00 0.00 41.22 4.58
262 263 2.960170 GGCTTGTTCTGGCAGCAG 59.040 61.111 10.34 4.14 0.00 4.24
263 264 1.900498 GGCTTGTTCTGGCAGCAGT 60.900 57.895 10.34 0.00 0.00 4.40
264 265 0.606401 GGCTTGTTCTGGCAGCAGTA 60.606 55.000 10.34 0.00 0.00 2.74
265 266 0.801251 GCTTGTTCTGGCAGCAGTAG 59.199 55.000 10.34 5.94 0.00 2.57
266 267 1.879796 GCTTGTTCTGGCAGCAGTAGT 60.880 52.381 10.34 0.00 0.00 2.73
267 268 1.802960 CTTGTTCTGGCAGCAGTAGTG 59.197 52.381 10.34 0.00 0.00 2.74
270 271 0.321671 TTCTGGCAGCAGTAGTGGTC 59.678 55.000 10.34 0.00 29.64 4.02
271 272 1.446792 CTGGCAGCAGTAGTGGTCG 60.447 63.158 0.00 0.00 29.64 4.79
272 273 2.159819 CTGGCAGCAGTAGTGGTCGT 62.160 60.000 0.00 0.00 29.64 4.34
273 274 1.004918 GGCAGCAGTAGTGGTCGTT 60.005 57.895 0.00 0.00 29.64 3.85
274 275 0.245539 GGCAGCAGTAGTGGTCGTTA 59.754 55.000 0.00 0.00 29.64 3.18
275 276 1.630148 GCAGCAGTAGTGGTCGTTAG 58.370 55.000 0.00 0.00 29.64 2.34
276 277 1.736032 GCAGCAGTAGTGGTCGTTAGG 60.736 57.143 0.00 0.00 29.64 2.69
277 278 1.544691 CAGCAGTAGTGGTCGTTAGGT 59.455 52.381 0.00 0.00 29.64 3.08
278 279 1.544691 AGCAGTAGTGGTCGTTAGGTG 59.455 52.381 0.00 0.00 0.00 4.00
279 280 1.403780 GCAGTAGTGGTCGTTAGGTGG 60.404 57.143 0.00 0.00 0.00 4.61
281 282 2.094854 CAGTAGTGGTCGTTAGGTGGTC 60.095 54.545 0.00 0.00 0.00 4.02
282 283 2.165998 GTAGTGGTCGTTAGGTGGTCT 58.834 52.381 0.00 0.00 0.00 3.85
283 284 1.254954 AGTGGTCGTTAGGTGGTCTC 58.745 55.000 0.00 0.00 0.00 3.36
284 285 0.109412 GTGGTCGTTAGGTGGTCTCG 60.109 60.000 0.00 0.00 0.00 4.04
285 286 1.246056 TGGTCGTTAGGTGGTCTCGG 61.246 60.000 0.00 0.00 0.00 4.63
286 287 0.962356 GGTCGTTAGGTGGTCTCGGA 60.962 60.000 0.00 0.00 0.00 4.55
287 288 0.883833 GTCGTTAGGTGGTCTCGGAA 59.116 55.000 0.00 0.00 0.00 4.30
288 289 1.475682 GTCGTTAGGTGGTCTCGGAAT 59.524 52.381 0.00 0.00 0.00 3.01
289 290 1.747355 TCGTTAGGTGGTCTCGGAATC 59.253 52.381 0.00 0.00 0.00 2.52
290 291 1.749634 CGTTAGGTGGTCTCGGAATCT 59.250 52.381 0.00 0.00 0.00 2.40
291 292 2.223525 CGTTAGGTGGTCTCGGAATCTC 60.224 54.545 0.00 0.00 0.00 2.75
292 293 1.676746 TAGGTGGTCTCGGAATCTCG 58.323 55.000 0.00 0.00 0.00 4.04
293 294 0.034380 AGGTGGTCTCGGAATCTCGA 60.034 55.000 0.00 0.00 37.60 4.04
294 295 1.033574 GGTGGTCTCGGAATCTCGAT 58.966 55.000 0.00 0.00 38.55 3.59
295 296 1.269309 GGTGGTCTCGGAATCTCGATG 60.269 57.143 0.00 0.00 38.55 3.84
296 297 0.385751 TGGTCTCGGAATCTCGATGC 59.614 55.000 0.00 0.00 38.55 3.91
297 298 0.385751 GGTCTCGGAATCTCGATGCA 59.614 55.000 0.00 0.00 38.55 3.96
298 299 1.202417 GGTCTCGGAATCTCGATGCAA 60.202 52.381 0.00 0.00 38.55 4.08
299 300 2.123342 GTCTCGGAATCTCGATGCAAG 58.877 52.381 0.00 0.00 38.55 4.01
300 301 1.751351 TCTCGGAATCTCGATGCAAGT 59.249 47.619 0.00 0.00 38.55 3.16
301 302 2.166459 TCTCGGAATCTCGATGCAAGTT 59.834 45.455 0.00 0.00 38.55 2.66
302 303 2.932614 CTCGGAATCTCGATGCAAGTTT 59.067 45.455 0.00 0.00 38.55 2.66
303 304 3.334691 TCGGAATCTCGATGCAAGTTTT 58.665 40.909 0.00 0.00 33.92 2.43
304 305 4.500127 TCGGAATCTCGATGCAAGTTTTA 58.500 39.130 0.00 0.00 33.92 1.52
305 306 5.116180 TCGGAATCTCGATGCAAGTTTTAT 58.884 37.500 0.00 0.00 33.92 1.40
306 307 5.584649 TCGGAATCTCGATGCAAGTTTTATT 59.415 36.000 0.00 0.00 33.92 1.40
307 308 6.759356 TCGGAATCTCGATGCAAGTTTTATTA 59.241 34.615 0.00 0.00 33.92 0.98
308 309 7.441157 TCGGAATCTCGATGCAAGTTTTATTAT 59.559 33.333 0.00 0.00 33.92 1.28
309 310 7.531871 CGGAATCTCGATGCAAGTTTTATTATG 59.468 37.037 0.00 0.00 0.00 1.90
333 334 6.544564 TGTTTCGGTGAACTTTTAGATCCTTT 59.455 34.615 0.00 0.00 0.00 3.11
382 383 1.339610 CCAAAAGGTCATTTCGGCACA 59.660 47.619 0.00 0.00 0.00 4.57
537 538 7.042456 TCGTTTCTTCTCTCTTTTTCTCACATG 60.042 37.037 0.00 0.00 0.00 3.21
546 1263 7.279615 TCTCTTTTTCTCACATGGTGACTAAA 58.720 34.615 0.00 0.00 37.67 1.85
604 1748 8.599624 AATTGTCATCTATTGGTTCCTTCAAT 57.400 30.769 0.00 0.00 38.29 2.57
608 1752 7.939039 TGTCATCTATTGGTTCCTTCAATATCC 59.061 37.037 0.00 0.00 36.75 2.59
690 1834 5.187967 AGAGACCATTTCCGTGAGATAAACT 59.812 40.000 0.00 0.00 0.00 2.66
691 1835 5.805728 AGACCATTTCCGTGAGATAAACTT 58.194 37.500 0.00 0.00 0.00 2.66
692 1836 6.942976 AGACCATTTCCGTGAGATAAACTTA 58.057 36.000 0.00 0.00 0.00 2.24
693 1837 7.565680 AGACCATTTCCGTGAGATAAACTTAT 58.434 34.615 0.00 0.00 0.00 1.73
694 1838 8.701895 AGACCATTTCCGTGAGATAAACTTATA 58.298 33.333 0.00 0.00 0.00 0.98
695 1839 8.888579 ACCATTTCCGTGAGATAAACTTATAG 57.111 34.615 0.00 0.00 0.00 1.31
696 1840 7.931948 ACCATTTCCGTGAGATAAACTTATAGG 59.068 37.037 0.00 0.00 0.00 2.57
697 1841 7.387948 CCATTTCCGTGAGATAAACTTATAGGG 59.612 40.741 0.00 0.00 0.00 3.53
698 1842 7.664552 TTTCCGTGAGATAAACTTATAGGGA 57.335 36.000 0.00 0.00 0.00 4.20
699 1843 6.896021 TCCGTGAGATAAACTTATAGGGAG 57.104 41.667 0.00 0.00 0.00 4.30
700 1844 6.371278 TCCGTGAGATAAACTTATAGGGAGT 58.629 40.000 0.00 0.00 0.00 3.85
701 1845 6.264744 TCCGTGAGATAAACTTATAGGGAGTG 59.735 42.308 0.00 0.00 0.00 3.51
702 1846 5.921408 CGTGAGATAAACTTATAGGGAGTGC 59.079 44.000 0.00 0.00 0.00 4.40
703 1847 6.224584 GTGAGATAAACTTATAGGGAGTGCC 58.775 44.000 0.00 0.00 0.00 5.01
704 1848 6.042208 GTGAGATAAACTTATAGGGAGTGCCT 59.958 42.308 8.78 8.78 0.00 4.75
705 1849 7.232941 GTGAGATAAACTTATAGGGAGTGCCTA 59.767 40.741 13.42 13.42 0.00 3.93
706 1850 7.451877 TGAGATAAACTTATAGGGAGTGCCTAG 59.548 40.741 16.26 6.97 0.00 3.02
707 1851 7.536625 AGATAAACTTATAGGGAGTGCCTAGA 58.463 38.462 16.26 8.85 0.00 2.43
708 1852 8.011290 AGATAAACTTATAGGGAGTGCCTAGAA 58.989 37.037 15.94 15.94 0.00 2.10
709 1853 5.873146 AACTTATAGGGAGTGCCTAGAAC 57.127 43.478 16.26 0.00 0.00 3.01
710 1854 5.145513 ACTTATAGGGAGTGCCTAGAACT 57.854 43.478 16.26 4.20 0.00 3.01
711 1855 5.141910 ACTTATAGGGAGTGCCTAGAACTC 58.858 45.833 16.26 14.10 42.79 3.01
712 1856 3.689872 ATAGGGAGTGCCTAGAACTCA 57.310 47.619 16.26 7.02 44.86 3.41
713 1857 2.559381 AGGGAGTGCCTAGAACTCAT 57.441 50.000 20.54 10.40 44.86 2.90
714 1858 2.839228 AGGGAGTGCCTAGAACTCATT 58.161 47.619 20.54 9.88 44.86 2.57
715 1859 3.185455 AGGGAGTGCCTAGAACTCATTT 58.815 45.455 20.54 8.10 44.86 2.32
716 1860 4.362677 AGGGAGTGCCTAGAACTCATTTA 58.637 43.478 20.54 0.00 44.86 1.40
717 1861 4.407296 AGGGAGTGCCTAGAACTCATTTAG 59.593 45.833 20.54 0.00 44.86 1.85
718 1862 4.406003 GGGAGTGCCTAGAACTCATTTAGA 59.594 45.833 20.54 0.00 44.86 2.10
719 1863 5.071115 GGGAGTGCCTAGAACTCATTTAGAT 59.929 44.000 20.54 0.00 44.86 1.98
720 1864 5.988561 GGAGTGCCTAGAACTCATTTAGATG 59.011 44.000 20.54 0.00 44.86 2.90
721 1865 6.183360 GGAGTGCCTAGAACTCATTTAGATGA 60.183 42.308 20.54 0.00 44.86 2.92
744 1888 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
745 1889 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
746 1890 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
747 1891 9.347240 AGATATAATTTGGTCTCATTCACCTTG 57.653 33.333 0.00 0.00 34.66 3.61
748 1892 9.342308 GATATAATTTGGTCTCATTCACCTTGA 57.658 33.333 0.00 0.00 34.66 3.02
749 1893 9.699410 ATATAATTTGGTCTCATTCACCTTGAA 57.301 29.630 0.00 0.00 41.09 2.69
750 1894 6.729690 AATTTGGTCTCATTCACCTTGAAA 57.270 33.333 0.00 0.00 40.12 2.69
751 1895 6.729690 ATTTGGTCTCATTCACCTTGAAAA 57.270 33.333 0.00 0.00 40.12 2.29
752 1896 5.514274 TTGGTCTCATTCACCTTGAAAAC 57.486 39.130 0.00 0.00 40.12 2.43
753 1897 4.531854 TGGTCTCATTCACCTTGAAAACA 58.468 39.130 0.00 0.00 40.12 2.83
754 1898 4.952957 TGGTCTCATTCACCTTGAAAACAA 59.047 37.500 0.00 0.00 40.12 2.83
755 1899 5.420421 TGGTCTCATTCACCTTGAAAACAAA 59.580 36.000 0.00 0.00 40.12 2.83
756 1900 6.071108 TGGTCTCATTCACCTTGAAAACAAAA 60.071 34.615 0.00 0.00 40.12 2.44
757 1901 6.816140 GGTCTCATTCACCTTGAAAACAAAAA 59.184 34.615 0.00 0.00 40.12 1.94
758 1902 7.201522 GGTCTCATTCACCTTGAAAACAAAAAC 60.202 37.037 0.00 0.00 40.12 2.43
759 1903 7.330700 GTCTCATTCACCTTGAAAACAAAAACA 59.669 33.333 0.00 0.00 40.12 2.83
760 1904 7.545265 TCTCATTCACCTTGAAAACAAAAACAG 59.455 33.333 0.00 0.00 40.12 3.16
761 1905 6.593382 TCATTCACCTTGAAAACAAAAACAGG 59.407 34.615 0.00 0.00 40.12 4.00
762 1906 5.476091 TCACCTTGAAAACAAAAACAGGT 57.524 34.783 0.00 0.00 0.00 4.00
763 1907 6.591750 TCACCTTGAAAACAAAAACAGGTA 57.408 33.333 0.00 0.00 0.00 3.08
764 1908 6.391537 TCACCTTGAAAACAAAAACAGGTAC 58.608 36.000 0.00 0.00 0.00 3.34
765 1909 6.015350 TCACCTTGAAAACAAAAACAGGTACA 60.015 34.615 0.00 0.00 0.00 2.90
766 1910 6.647067 CACCTTGAAAACAAAAACAGGTACAA 59.353 34.615 0.00 0.00 0.00 2.41
767 1911 6.647481 ACCTTGAAAACAAAAACAGGTACAAC 59.353 34.615 0.00 0.00 0.00 3.32
768 1912 6.091577 CCTTGAAAACAAAAACAGGTACAACC 59.908 38.462 0.00 0.00 38.99 3.77
779 1923 1.706443 GGTACAACCTACGTCAGCAC 58.294 55.000 0.00 0.00 34.73 4.40
780 1924 1.000060 GGTACAACCTACGTCAGCACA 60.000 52.381 0.00 0.00 34.73 4.57
781 1925 2.056577 GTACAACCTACGTCAGCACAC 58.943 52.381 0.00 0.00 0.00 3.82
782 1926 0.462375 ACAACCTACGTCAGCACACA 59.538 50.000 0.00 0.00 0.00 3.72
783 1927 0.859232 CAACCTACGTCAGCACACAC 59.141 55.000 0.00 0.00 0.00 3.82
784 1928 0.596600 AACCTACGTCAGCACACACG 60.597 55.000 0.00 0.00 41.90 4.49
785 1929 2.372690 CCTACGTCAGCACACACGC 61.373 63.158 0.00 0.00 39.73 5.34
786 1930 1.660264 CTACGTCAGCACACACGCA 60.660 57.895 0.00 0.00 39.73 5.24
787 1931 1.006688 TACGTCAGCACACACGCAT 60.007 52.632 0.00 0.00 39.73 4.73
788 1932 1.006825 TACGTCAGCACACACGCATC 61.007 55.000 0.00 0.00 39.73 3.91
789 1933 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
790 1934 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
791 1935 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
792 1936 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
793 1937 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
794 1938 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
795 1939 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
796 1940 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
797 1941 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
798 1942 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
799 1943 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
800 1944 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
801 1945 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
802 1946 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
803 1947 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
804 1948 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
805 1949 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
806 1950 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
807 1951 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
808 1952 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
809 1953 6.404403 GCATCTTATAGCATCACATCCAATGG 60.404 42.308 0.00 0.00 33.60 3.16
810 1954 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40
811 1955 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
812 1956 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
813 1957 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
814 1958 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
815 1959 4.989277 AGCATCACATCCAATGGCTATAA 58.011 39.130 0.00 0.00 33.60 0.98
816 1960 5.387788 AGCATCACATCCAATGGCTATAAA 58.612 37.500 0.00 0.00 33.60 1.40
817 1961 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
818 1962 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
819 1963 6.016024 GCATCACATCCAATGGCTATAAAAGA 60.016 38.462 0.00 0.00 33.60 2.52
820 1964 7.309621 GCATCACATCCAATGGCTATAAAAGAT 60.310 37.037 0.00 0.00 33.60 2.40
821 1965 7.514784 TCACATCCAATGGCTATAAAAGATG 57.485 36.000 0.00 8.84 36.73 2.90
822 1966 7.289310 TCACATCCAATGGCTATAAAAGATGA 58.711 34.615 14.33 1.03 35.13 2.92
823 1967 7.779326 TCACATCCAATGGCTATAAAAGATGAA 59.221 33.333 14.33 4.30 35.13 2.57
824 1968 8.582437 CACATCCAATGGCTATAAAAGATGAAT 58.418 33.333 14.33 0.00 35.13 2.57
825 1969 8.582437 ACATCCAATGGCTATAAAAGATGAATG 58.418 33.333 14.33 0.00 35.13 2.67
826 1970 8.799367 CATCCAATGGCTATAAAAGATGAATGA 58.201 33.333 0.00 0.00 33.35 2.57
827 1971 8.400184 TCCAATGGCTATAAAAGATGAATGAG 57.600 34.615 0.00 0.00 0.00 2.90
828 1972 8.219868 TCCAATGGCTATAAAAGATGAATGAGA 58.780 33.333 0.00 0.00 0.00 3.27
829 1973 8.295288 CCAATGGCTATAAAAGATGAATGAGAC 58.705 37.037 0.00 0.00 0.00 3.36
830 1974 7.992754 ATGGCTATAAAAGATGAATGAGACC 57.007 36.000 0.00 0.00 0.00 3.85
831 1975 6.899089 TGGCTATAAAAGATGAATGAGACCA 58.101 36.000 0.00 0.00 0.00 4.02
832 1976 7.345691 TGGCTATAAAAGATGAATGAGACCAA 58.654 34.615 0.00 0.00 0.00 3.67
833 1977 7.833682 TGGCTATAAAAGATGAATGAGACCAAA 59.166 33.333 0.00 0.00 0.00 3.28
834 1978 8.131731 GGCTATAAAAGATGAATGAGACCAAAC 58.868 37.037 0.00 0.00 0.00 2.93
835 1979 8.897752 GCTATAAAAGATGAATGAGACCAAACT 58.102 33.333 0.00 0.00 0.00 2.66
870 2014 8.539770 CTAGATGAGTTCTAGCAAAACTGAAA 57.460 34.615 0.32 0.00 45.63 2.69
871 2015 7.195839 AGATGAGTTCTAGCAAAACTGAAAC 57.804 36.000 0.32 0.00 37.10 2.78
872 2016 6.995091 AGATGAGTTCTAGCAAAACTGAAACT 59.005 34.615 0.32 0.00 37.10 2.66
924 2823 3.500680 CACCGGTATAAATACATGGCCAC 59.499 47.826 8.16 0.00 35.15 5.01
928 2827 4.141287 GGTATAAATACATGGCCACAGCA 58.859 43.478 8.16 0.00 36.41 4.41
1449 3373 3.269347 GACGCCGCCGCATACATT 61.269 61.111 0.00 0.00 38.22 2.71
1878 3838 1.948145 CCCTACGTTATCTCGTGAGCT 59.052 52.381 0.00 0.00 43.93 4.09
1917 3892 1.205820 TCGCGTACGATAGATGCCG 59.794 57.895 21.65 10.39 45.12 5.69
2090 4102 1.346395 ACTAGTCATCAACCCGTGCAA 59.654 47.619 0.00 0.00 0.00 4.08
2092 4104 0.108585 AGTCATCAACCCGTGCAACT 59.891 50.000 0.00 0.00 31.75 3.16
2093 4105 0.951558 GTCATCAACCCGTGCAACTT 59.048 50.000 0.00 0.00 31.75 2.66
2110 4122 1.078759 CTTCACGGGCTAGCGACTTG 61.079 60.000 9.00 8.30 0.00 3.16
2114 4126 1.517257 CGGGCTAGCGACTTGAGTG 60.517 63.158 9.00 0.00 0.00 3.51
2121 4133 3.365364 GCTAGCGACTTGAGTGCAAAAAT 60.365 43.478 0.00 0.00 32.73 1.82
2133 4145 7.672983 TGAGTGCAAAAATTTGGTGTTTAAA 57.327 28.000 7.89 0.00 38.57 1.52
2138 4150 9.774742 GTGCAAAAATTTGGTGTTTAAAATACA 57.225 25.926 7.89 0.00 38.57 2.29
2220 4232 6.100668 TCGATATCACGGTCACATTGTTTAA 58.899 36.000 3.12 0.00 0.00 1.52
2221 4233 6.759356 TCGATATCACGGTCACATTGTTTAAT 59.241 34.615 3.12 0.00 0.00 1.40
2239 4251 8.523523 TGTTTAATCTTTCAATCAATGCACAG 57.476 30.769 0.00 0.00 0.00 3.66
2246 4258 4.642445 TCAATCAATGCACAGCCATAAG 57.358 40.909 0.00 0.00 0.00 1.73
2247 4259 3.120792 CAATCAATGCACAGCCATAAGC 58.879 45.455 0.00 0.00 44.25 3.09
2266 4278 7.927629 CCATAAGCAGTGGCAATGTATAAATTT 59.072 33.333 16.96 0.00 44.61 1.82
2272 4312 7.920151 GCAGTGGCAATGTATAAATTTGATGTA 59.080 33.333 16.96 0.00 40.72 2.29
2461 4503 6.819284 TCAATTTGAGATAATTGGGATTGGC 58.181 36.000 8.67 0.00 42.84 4.52
2464 4506 6.469782 TTTGAGATAATTGGGATTGGCTTC 57.530 37.500 0.00 0.00 0.00 3.86
2481 4524 2.285488 GCTTCTGCTGAGCGGTAATTAC 59.715 50.000 13.72 7.09 36.18 1.89
2566 4612 9.555727 AAGTATTATAAATGGTTGCGAGTGTAT 57.444 29.630 0.00 0.00 0.00 2.29
2634 4680 8.675705 TGAGAAGTGTTGATTCTTTATTGACA 57.324 30.769 0.00 0.00 37.14 3.58
2724 4781 6.677781 TGCATACCTAAAATTGCTCACTAC 57.322 37.500 0.00 0.00 36.10 2.73
2735 4792 8.409358 AAAATTGCTCACTACCATTTACTCTT 57.591 30.769 0.00 0.00 0.00 2.85
2736 4793 9.515226 AAAATTGCTCACTACCATTTACTCTTA 57.485 29.630 0.00 0.00 0.00 2.10
2762 4821 2.038387 ACTGCAACTTGGTCGACTTT 57.962 45.000 16.46 1.08 0.00 2.66
2776 4835 7.033530 TGGTCGACTTTGAAATAACATTTGT 57.966 32.000 16.46 0.00 0.00 2.83
2777 4836 7.136119 TGGTCGACTTTGAAATAACATTTGTC 58.864 34.615 16.46 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.933332 CCAAGGAGACGACAGGAATTTAC 59.067 47.826 0.00 0.00 0.00 2.01
31 32 1.279271 CCCAAGGAGACGACAGGAATT 59.721 52.381 0.00 0.00 0.00 2.17
32 33 0.905357 CCCAAGGAGACGACAGGAAT 59.095 55.000 0.00 0.00 0.00 3.01
33 34 1.827399 GCCCAAGGAGACGACAGGAA 61.827 60.000 0.00 0.00 0.00 3.36
34 35 2.283529 GCCCAAGGAGACGACAGGA 61.284 63.158 0.00 0.00 0.00 3.86
35 36 2.266055 GCCCAAGGAGACGACAGG 59.734 66.667 0.00 0.00 0.00 4.00
36 37 2.266055 GGCCCAAGGAGACGACAG 59.734 66.667 0.00 0.00 0.00 3.51
41 42 3.316573 CTCACCGGCCCAAGGAGAC 62.317 68.421 0.00 0.00 0.00 3.36
45 46 2.536997 CTAACCTCACCGGCCCAAGG 62.537 65.000 0.00 5.86 35.61 3.61
49 50 3.793888 CCCTAACCTCACCGGCCC 61.794 72.222 0.00 0.00 35.61 5.80
52 53 0.981943 AGAAACCCTAACCTCACCGG 59.018 55.000 0.00 0.00 39.35 5.28
59 60 3.000727 CACATGACGAGAAACCCTAACC 58.999 50.000 0.00 0.00 0.00 2.85
63 64 0.321653 GCCACATGACGAGAAACCCT 60.322 55.000 0.00 0.00 0.00 4.34
77 78 2.044848 ACACCAAACCACGCCACA 60.045 55.556 0.00 0.00 0.00 4.17
82 83 0.317770 GCACATGACACCAAACCACG 60.318 55.000 0.00 0.00 0.00 4.94
85 86 1.680735 TGAAGCACATGACACCAAACC 59.319 47.619 0.00 0.00 0.00 3.27
94 95 2.236893 TGCATAGACCTGAAGCACATGA 59.763 45.455 0.00 0.00 0.00 3.07
97 98 2.616256 CCTTGCATAGACCTGAAGCACA 60.616 50.000 0.00 0.00 34.56 4.57
107 108 1.737793 CCGTTGAACCCTTGCATAGAC 59.262 52.381 0.00 0.00 0.00 2.59
113 114 2.975799 TCGCCGTTGAACCCTTGC 60.976 61.111 0.00 0.00 0.00 4.01
146 147 1.192146 TGCCTCTAAGGACCAACGCT 61.192 55.000 0.00 0.00 37.67 5.07
150 151 1.340017 GCATGTGCCTCTAAGGACCAA 60.340 52.381 0.00 0.00 37.67 3.67
161 162 2.089980 GAAGTCTTCATGCATGTGCCT 58.910 47.619 25.43 12.46 41.18 4.75
166 167 1.747355 GTGGGGAAGTCTTCATGCATG 59.253 52.381 21.07 21.07 0.00 4.06
185 186 2.868044 GCTCAACCTTGTCGATGACAGT 60.868 50.000 0.00 0.00 43.69 3.55
194 195 2.032681 AGCCGGCTCAACCTTGTC 59.967 61.111 27.08 0.00 35.61 3.18
214 215 2.477825 CACTATCGCCACTCCTCAATG 58.522 52.381 0.00 0.00 0.00 2.82
218 219 1.068250 GCCACTATCGCCACTCCTC 59.932 63.158 0.00 0.00 0.00 3.71
221 222 2.962253 GCGCCACTATCGCCACTC 60.962 66.667 0.00 0.00 46.18 3.51
243 244 4.410743 GCTGCCAGAACAAGCCGC 62.411 66.667 0.00 0.00 32.09 6.53
247 248 1.802960 CACTACTGCTGCCAGAACAAG 59.197 52.381 0.00 0.00 41.77 3.16
258 259 1.544691 CACCTAACGACCACTACTGCT 59.455 52.381 0.00 0.00 0.00 4.24
262 263 2.163211 GAGACCACCTAACGACCACTAC 59.837 54.545 0.00 0.00 0.00 2.73
263 264 2.440409 GAGACCACCTAACGACCACTA 58.560 52.381 0.00 0.00 0.00 2.74
264 265 1.254954 GAGACCACCTAACGACCACT 58.745 55.000 0.00 0.00 0.00 4.00
265 266 0.109412 CGAGACCACCTAACGACCAC 60.109 60.000 0.00 0.00 0.00 4.16
266 267 1.246056 CCGAGACCACCTAACGACCA 61.246 60.000 0.00 0.00 0.00 4.02
267 268 0.962356 TCCGAGACCACCTAACGACC 60.962 60.000 0.00 0.00 0.00 4.79
270 271 1.749634 AGATTCCGAGACCACCTAACG 59.250 52.381 0.00 0.00 0.00 3.18
271 272 2.223525 CGAGATTCCGAGACCACCTAAC 60.224 54.545 0.00 0.00 0.00 2.34
272 273 2.022195 CGAGATTCCGAGACCACCTAA 58.978 52.381 0.00 0.00 0.00 2.69
273 274 1.211212 TCGAGATTCCGAGACCACCTA 59.789 52.381 0.00 0.00 34.19 3.08
274 275 0.034380 TCGAGATTCCGAGACCACCT 60.034 55.000 0.00 0.00 34.19 4.00
275 276 1.033574 ATCGAGATTCCGAGACCACC 58.966 55.000 0.00 0.00 42.21 4.61
276 277 1.866063 GCATCGAGATTCCGAGACCAC 60.866 57.143 0.00 0.00 42.21 4.16
277 278 0.385751 GCATCGAGATTCCGAGACCA 59.614 55.000 0.00 0.00 42.21 4.02
278 279 0.385751 TGCATCGAGATTCCGAGACC 59.614 55.000 0.00 0.00 42.21 3.85
279 280 2.123342 CTTGCATCGAGATTCCGAGAC 58.877 52.381 0.00 0.00 42.21 3.36
281 282 2.215907 ACTTGCATCGAGATTCCGAG 57.784 50.000 0.00 0.00 42.21 4.63
282 283 2.672961 AACTTGCATCGAGATTCCGA 57.327 45.000 0.00 0.00 43.16 4.55
283 284 3.747099 AAAACTTGCATCGAGATTCCG 57.253 42.857 0.00 0.00 0.00 4.30
284 285 8.345565 ACATAATAAAACTTGCATCGAGATTCC 58.654 33.333 0.00 0.00 0.00 3.01
285 286 9.722056 AACATAATAAAACTTGCATCGAGATTC 57.278 29.630 0.00 0.00 0.00 2.52
287 288 9.722056 GAAACATAATAAAACTTGCATCGAGAT 57.278 29.630 0.00 0.00 0.00 2.75
288 289 7.902917 CGAAACATAATAAAACTTGCATCGAGA 59.097 33.333 0.00 0.00 0.00 4.04
289 290 7.164171 CCGAAACATAATAAAACTTGCATCGAG 59.836 37.037 0.00 0.00 0.00 4.04
290 291 6.964370 CCGAAACATAATAAAACTTGCATCGA 59.036 34.615 0.00 0.00 0.00 3.59
291 292 6.745450 ACCGAAACATAATAAAACTTGCATCG 59.255 34.615 0.00 0.00 0.00 3.84
292 293 7.753132 TCACCGAAACATAATAAAACTTGCATC 59.247 33.333 0.00 0.00 0.00 3.91
293 294 7.598278 TCACCGAAACATAATAAAACTTGCAT 58.402 30.769 0.00 0.00 0.00 3.96
294 295 6.971602 TCACCGAAACATAATAAAACTTGCA 58.028 32.000 0.00 0.00 0.00 4.08
295 296 7.593644 AGTTCACCGAAACATAATAAAACTTGC 59.406 33.333 0.00 0.00 0.00 4.01
296 297 9.458374 AAGTTCACCGAAACATAATAAAACTTG 57.542 29.630 0.00 0.00 33.39 3.16
304 305 8.674607 GGATCTAAAAGTTCACCGAAACATAAT 58.325 33.333 0.00 0.00 0.00 1.28
305 306 7.881232 AGGATCTAAAAGTTCACCGAAACATAA 59.119 33.333 0.00 0.00 0.00 1.90
306 307 7.391620 AGGATCTAAAAGTTCACCGAAACATA 58.608 34.615 0.00 0.00 0.00 2.29
307 308 6.238648 AGGATCTAAAAGTTCACCGAAACAT 58.761 36.000 0.00 0.00 0.00 2.71
308 309 5.617252 AGGATCTAAAAGTTCACCGAAACA 58.383 37.500 0.00 0.00 0.00 2.83
309 310 6.555812 AAGGATCTAAAAGTTCACCGAAAC 57.444 37.500 0.00 0.00 0.00 2.78
359 360 0.894835 CCGAAATGACCTTTTGGGGG 59.105 55.000 2.30 0.00 42.63 5.40
360 361 0.246360 GCCGAAATGACCTTTTGGGG 59.754 55.000 10.51 0.06 45.38 4.96
425 426 7.232737 TGGATAGTCACTTACTCACAAGAAAGA 59.767 37.037 0.00 0.00 39.80 2.52
537 538 7.602644 TGTGAAGTCACTAATCATTTAGTCACC 59.397 37.037 12.43 0.00 44.94 4.02
546 1263 5.555017 AGCAGTTGTGAAGTCACTAATCAT 58.445 37.500 12.43 0.00 46.55 2.45
559 1276 5.677319 ATTAGGTTAGCTAGCAGTTGTGA 57.323 39.130 18.83 0.00 0.00 3.58
608 1752 4.894896 GTATGGGCCCGGGCTTGG 62.895 72.222 42.70 8.03 41.60 3.61
690 1834 5.138758 TGAGTTCTAGGCACTCCCTATAA 57.861 43.478 16.20 0.00 45.11 0.98
691 1835 4.808767 TGAGTTCTAGGCACTCCCTATA 57.191 45.455 16.20 0.39 45.11 1.31
692 1836 3.689872 TGAGTTCTAGGCACTCCCTAT 57.310 47.619 16.20 0.00 45.11 2.57
693 1837 3.689872 ATGAGTTCTAGGCACTCCCTA 57.310 47.619 16.20 3.46 44.08 3.53
694 1838 9.047928 CATCTAAATGAGTTCTAGGCACTCCCT 62.048 44.444 16.20 5.46 40.12 4.20
695 1839 3.636153 AAATGAGTTCTAGGCACTCCC 57.364 47.619 16.20 0.00 40.12 4.30
696 1840 5.599999 TCTAAATGAGTTCTAGGCACTCC 57.400 43.478 16.20 4.17 40.12 3.85
697 1841 6.810911 TCATCTAAATGAGTTCTAGGCACTC 58.189 40.000 13.40 13.40 37.09 3.51
698 1842 6.798427 TCATCTAAATGAGTTCTAGGCACT 57.202 37.500 0.00 0.00 38.74 4.40
720 1864 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
721 1865 9.347240 CAAGGTGAATGAGACCAAATTATATCT 57.653 33.333 0.00 0.00 35.76 1.98
722 1866 9.342308 TCAAGGTGAATGAGACCAAATTATATC 57.658 33.333 0.00 0.00 35.76 1.63
723 1867 9.699410 TTCAAGGTGAATGAGACCAAATTATAT 57.301 29.630 0.00 0.00 35.76 0.86
724 1868 9.527157 TTTCAAGGTGAATGAGACCAAATTATA 57.473 29.630 0.00 0.00 36.11 0.98
725 1869 8.421249 TTTCAAGGTGAATGAGACCAAATTAT 57.579 30.769 0.00 0.00 36.11 1.28
726 1870 7.831691 TTTCAAGGTGAATGAGACCAAATTA 57.168 32.000 0.00 0.00 36.11 1.40
727 1871 6.729690 TTTCAAGGTGAATGAGACCAAATT 57.270 33.333 0.00 0.00 36.11 1.82
728 1872 6.098124 TGTTTTCAAGGTGAATGAGACCAAAT 59.902 34.615 0.00 0.00 36.11 2.32
729 1873 5.420421 TGTTTTCAAGGTGAATGAGACCAAA 59.580 36.000 0.00 0.00 36.11 3.28
730 1874 4.952957 TGTTTTCAAGGTGAATGAGACCAA 59.047 37.500 0.00 0.00 36.11 3.67
731 1875 4.531854 TGTTTTCAAGGTGAATGAGACCA 58.468 39.130 0.00 0.00 36.11 4.02
732 1876 5.514274 TTGTTTTCAAGGTGAATGAGACC 57.486 39.130 0.00 0.00 36.11 3.85
733 1877 7.330700 TGTTTTTGTTTTCAAGGTGAATGAGAC 59.669 33.333 0.00 0.00 41.09 3.36
734 1878 7.382110 TGTTTTTGTTTTCAAGGTGAATGAGA 58.618 30.769 0.00 0.00 41.09 3.27
735 1879 7.201548 CCTGTTTTTGTTTTCAAGGTGAATGAG 60.202 37.037 0.00 0.00 41.09 2.90
736 1880 6.593382 CCTGTTTTTGTTTTCAAGGTGAATGA 59.407 34.615 0.00 0.00 41.09 2.57
737 1881 6.371271 ACCTGTTTTTGTTTTCAAGGTGAATG 59.629 34.615 0.00 0.00 41.09 2.67
738 1882 6.472016 ACCTGTTTTTGTTTTCAAGGTGAAT 58.528 32.000 0.00 0.00 41.09 2.57
739 1883 5.859495 ACCTGTTTTTGTTTTCAAGGTGAA 58.141 33.333 0.00 0.00 41.09 3.18
740 1884 5.476091 ACCTGTTTTTGTTTTCAAGGTGA 57.524 34.783 0.00 0.00 41.09 4.02
741 1885 6.159988 TGTACCTGTTTTTGTTTTCAAGGTG 58.840 36.000 0.00 0.00 41.09 4.00
742 1886 6.347859 TGTACCTGTTTTTGTTTTCAAGGT 57.652 33.333 0.00 0.00 41.09 3.50
743 1887 6.091577 GGTTGTACCTGTTTTTGTTTTCAAGG 59.908 38.462 0.00 0.00 36.86 3.61
744 1888 7.056002 GGTTGTACCTGTTTTTGTTTTCAAG 57.944 36.000 0.00 0.00 36.86 3.02
760 1904 1.000060 TGTGCTGACGTAGGTTGTACC 60.000 52.381 0.00 0.00 38.99 3.34
761 1905 2.056577 GTGTGCTGACGTAGGTTGTAC 58.943 52.381 0.00 0.00 0.00 2.90
762 1906 1.682323 TGTGTGCTGACGTAGGTTGTA 59.318 47.619 0.00 0.00 0.00 2.41
763 1907 0.462375 TGTGTGCTGACGTAGGTTGT 59.538 50.000 0.00 0.00 0.00 3.32
764 1908 0.859232 GTGTGTGCTGACGTAGGTTG 59.141 55.000 0.00 0.00 0.00 3.77
765 1909 0.596600 CGTGTGTGCTGACGTAGGTT 60.597 55.000 0.00 0.00 0.00 3.50
766 1910 1.007734 CGTGTGTGCTGACGTAGGT 60.008 57.895 0.00 0.00 0.00 3.08
767 1911 2.372690 GCGTGTGTGCTGACGTAGG 61.373 63.158 0.00 0.00 37.89 3.18
768 1912 1.008875 ATGCGTGTGTGCTGACGTAG 61.009 55.000 0.00 0.00 37.89 3.51
769 1913 1.006688 ATGCGTGTGTGCTGACGTA 60.007 52.632 0.00 0.00 37.89 3.57
770 1914 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
771 1915 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
772 1916 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
773 1917 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
774 1918 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
775 1919 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
776 1920 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
777 1921 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
778 1922 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
779 1923 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
780 1924 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
781 1925 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
782 1926 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
783 1927 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
784 1928 6.404403 CCATTGGATGTGATGCTATAAGATGC 60.404 42.308 0.00 0.00 0.00 3.91
785 1929 6.404403 GCCATTGGATGTGATGCTATAAGATG 60.404 42.308 6.95 0.00 0.00 2.90
786 1930 5.651139 GCCATTGGATGTGATGCTATAAGAT 59.349 40.000 6.95 0.00 0.00 2.40
787 1931 5.005740 GCCATTGGATGTGATGCTATAAGA 58.994 41.667 6.95 0.00 0.00 2.10
788 1932 5.008331 AGCCATTGGATGTGATGCTATAAG 58.992 41.667 6.95 0.00 0.00 1.73
789 1933 4.989277 AGCCATTGGATGTGATGCTATAA 58.011 39.130 6.95 0.00 0.00 0.98
790 1934 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
791 1935 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
792 1936 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
793 1937 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
794 1938 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
795 1939 7.514784 TCTTTTATAGCCATTGGATGTGATG 57.485 36.000 6.95 0.00 0.00 3.07
796 1940 7.946219 TCATCTTTTATAGCCATTGGATGTGAT 59.054 33.333 6.95 0.00 33.39 3.06
797 1941 7.289310 TCATCTTTTATAGCCATTGGATGTGA 58.711 34.615 6.95 0.00 33.39 3.58
798 1942 7.514784 TCATCTTTTATAGCCATTGGATGTG 57.485 36.000 6.95 0.00 33.39 3.21
799 1943 8.582437 CATTCATCTTTTATAGCCATTGGATGT 58.418 33.333 6.95 0.10 33.39 3.06
800 1944 8.799367 TCATTCATCTTTTATAGCCATTGGATG 58.201 33.333 6.95 0.00 0.00 3.51
801 1945 8.945195 TCATTCATCTTTTATAGCCATTGGAT 57.055 30.769 6.95 1.78 0.00 3.41
802 1946 8.219868 TCTCATTCATCTTTTATAGCCATTGGA 58.780 33.333 6.95 0.00 0.00 3.53
803 1947 8.295288 GTCTCATTCATCTTTTATAGCCATTGG 58.705 37.037 0.00 0.00 0.00 3.16
804 1948 8.295288 GGTCTCATTCATCTTTTATAGCCATTG 58.705 37.037 0.00 0.00 0.00 2.82
805 1949 8.000709 TGGTCTCATTCATCTTTTATAGCCATT 58.999 33.333 0.00 0.00 0.00 3.16
806 1950 7.520798 TGGTCTCATTCATCTTTTATAGCCAT 58.479 34.615 0.00 0.00 0.00 4.40
807 1951 6.899089 TGGTCTCATTCATCTTTTATAGCCA 58.101 36.000 0.00 0.00 0.00 4.75
808 1952 7.807977 TTGGTCTCATTCATCTTTTATAGCC 57.192 36.000 0.00 0.00 0.00 3.93
809 1953 8.897752 AGTTTGGTCTCATTCATCTTTTATAGC 58.102 33.333 0.00 0.00 0.00 2.97
846 1990 8.150945 AGTTTCAGTTTTGCTAGAACTCATCTA 58.849 33.333 0.00 0.00 39.71 1.98
847 1991 6.995091 AGTTTCAGTTTTGCTAGAACTCATCT 59.005 34.615 0.00 0.00 42.48 2.90
848 1992 7.195839 AGTTTCAGTTTTGCTAGAACTCATC 57.804 36.000 0.00 0.00 35.26 2.92
849 1993 7.573968 AAGTTTCAGTTTTGCTAGAACTCAT 57.426 32.000 0.00 0.00 35.26 2.90
850 1994 8.677148 ATAAGTTTCAGTTTTGCTAGAACTCA 57.323 30.769 0.00 0.00 35.26 3.41
853 1997 9.278734 GCATATAAGTTTCAGTTTTGCTAGAAC 57.721 33.333 0.00 0.00 0.00 3.01
854 1998 8.175069 CGCATATAAGTTTCAGTTTTGCTAGAA 58.825 33.333 0.00 0.00 0.00 2.10
855 1999 7.547722 TCGCATATAAGTTTCAGTTTTGCTAGA 59.452 33.333 0.00 0.00 0.00 2.43
856 2000 7.684670 TCGCATATAAGTTTCAGTTTTGCTAG 58.315 34.615 0.00 0.00 0.00 3.42
857 2001 7.201609 CCTCGCATATAAGTTTCAGTTTTGCTA 60.202 37.037 0.00 0.00 0.00 3.49
858 2002 6.403636 CCTCGCATATAAGTTTCAGTTTTGCT 60.404 38.462 0.00 0.00 0.00 3.91
859 2003 5.739161 CCTCGCATATAAGTTTCAGTTTTGC 59.261 40.000 0.00 0.00 0.00 3.68
860 2004 6.842163 ACCTCGCATATAAGTTTCAGTTTTG 58.158 36.000 0.00 0.00 0.00 2.44
861 2005 6.879458 AGACCTCGCATATAAGTTTCAGTTTT 59.121 34.615 0.00 0.00 0.00 2.43
862 2006 6.407202 AGACCTCGCATATAAGTTTCAGTTT 58.593 36.000 0.00 0.00 0.00 2.66
863 2007 5.978814 AGACCTCGCATATAAGTTTCAGTT 58.021 37.500 0.00 0.00 0.00 3.16
864 2008 5.127194 TGAGACCTCGCATATAAGTTTCAGT 59.873 40.000 0.00 0.00 0.00 3.41
865 2009 5.592054 TGAGACCTCGCATATAAGTTTCAG 58.408 41.667 0.00 0.00 0.00 3.02
866 2010 5.592104 TGAGACCTCGCATATAAGTTTCA 57.408 39.130 0.00 0.00 0.00 2.69
867 2011 5.234543 GGTTGAGACCTCGCATATAAGTTTC 59.765 44.000 0.00 0.00 42.99 2.78
868 2012 5.116882 GGTTGAGACCTCGCATATAAGTTT 58.883 41.667 0.00 0.00 42.99 2.66
869 2013 4.694339 GGTTGAGACCTCGCATATAAGTT 58.306 43.478 0.00 0.00 42.99 2.66
870 2014 3.243434 CGGTTGAGACCTCGCATATAAGT 60.243 47.826 0.00 0.00 44.20 2.24
871 2015 3.309388 CGGTTGAGACCTCGCATATAAG 58.691 50.000 0.00 0.00 44.20 1.73
872 2016 2.545113 GCGGTTGAGACCTCGCATATAA 60.545 50.000 0.00 0.00 46.33 0.98
924 2823 1.620819 ACCTGTAGTTCCACTCTGCTG 59.379 52.381 0.00 0.00 0.00 4.41
928 2827 2.444421 CGGTACCTGTAGTTCCACTCT 58.556 52.381 10.90 0.00 35.70 3.24
1878 3838 3.154710 AGAGTTGTCTCGTGATGTACCA 58.845 45.455 0.00 0.00 44.65 3.25
1917 3892 0.248621 GCGCCAGATTTACCATGCAC 60.249 55.000 0.00 0.00 0.00 4.57
2077 4089 0.951558 GTGAAGTTGCACGGGTTGAT 59.048 50.000 0.00 0.00 0.00 2.57
2090 4102 1.533469 AAGTCGCTAGCCCGTGAAGT 61.533 55.000 9.66 0.00 0.00 3.01
2092 4104 1.080093 CAAGTCGCTAGCCCGTGAA 60.080 57.895 9.66 0.00 0.00 3.18
2093 4105 1.934220 CTCAAGTCGCTAGCCCGTGA 61.934 60.000 9.66 12.48 0.00 4.35
2189 4201 5.097529 TGTGACCGTGATATCGAAAAGTAC 58.902 41.667 0.00 0.00 0.00 2.73
2198 4210 8.142994 AGATTAAACAATGTGACCGTGATATC 57.857 34.615 0.00 0.00 0.00 1.63
2220 4232 3.512329 TGGCTGTGCATTGATTGAAAGAT 59.488 39.130 0.00 0.00 0.00 2.40
2221 4233 2.892215 TGGCTGTGCATTGATTGAAAGA 59.108 40.909 0.00 0.00 0.00 2.52
2246 4258 6.757947 ACATCAAATTTATACATTGCCACTGC 59.242 34.615 0.00 0.00 38.26 4.40
2247 4259 9.970395 ATACATCAAATTTATACATTGCCACTG 57.030 29.630 0.00 0.00 0.00 3.66
2461 4503 3.521560 TGTAATTACCGCTCAGCAGAAG 58.478 45.455 13.01 0.00 0.00 2.85
2464 4506 4.678509 TTTTGTAATTACCGCTCAGCAG 57.321 40.909 13.01 0.00 0.00 4.24
2498 4541 8.385898 AGTACTGACATAAACAATTCCGAAAA 57.614 30.769 0.00 0.00 0.00 2.29
2508 4551 8.204160 CCATGGATAAGAGTACTGACATAAACA 58.796 37.037 5.56 0.00 0.00 2.83
2514 4557 3.388024 GCCCATGGATAAGAGTACTGACA 59.612 47.826 15.22 0.00 0.00 3.58
2682 4739 8.575589 GGTATGCAAATGTATGACATCCATTTA 58.424 33.333 16.02 5.37 37.97 1.40
2735 4792 7.101054 AGTCGACCAAGTTGCAGTATAAAATA 58.899 34.615 13.01 0.00 0.00 1.40
2736 4793 5.938125 AGTCGACCAAGTTGCAGTATAAAAT 59.062 36.000 13.01 0.00 0.00 1.82
2743 4802 1.670811 CAAAGTCGACCAAGTTGCAGT 59.329 47.619 13.01 0.00 0.00 4.40
2762 4821 5.640147 AGGGACTGGACAAATGTTATTTCA 58.360 37.500 0.00 0.00 37.18 2.69
2776 4835 6.552008 AAATTGTTATTTCTCAGGGACTGGA 58.448 36.000 0.00 0.00 42.67 3.86
2777 4836 6.840780 AAATTGTTATTTCTCAGGGACTGG 57.159 37.500 0.00 0.00 42.67 4.00


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

AutoCloner maintained by Alex Coulton.