Multiple sequence alignment - TraesCS6A01G143800

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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 TraesCS6A01G143800 chr6A 100.000 3313 0 0 1 3313 121234175 121237487 0.000000e+00 6119.0
1 TraesCS6A01G143800 chr4D 92.981 2536 74 43 788 3249 266762495 266759990 0.000000e+00 3602.0
2 TraesCS6A01G143800 chr4D 95.415 1265 30 13 2002 3249 249165674 249164421 0.000000e+00 1989.0
3 TraesCS6A01G143800 chr4D 89.302 215 22 1 593 806 266763050 266762836 5.450000e-68 268.0
4 TraesCS6A01G143800 chr1B 92.809 1933 116 16 537 2457 303011446 303013367 0.000000e+00 2778.0
5 TraesCS6A01G143800 chr1B 88.360 189 19 3 581 768 249269938 249270124 1.200000e-54 224.0
6 TraesCS6A01G143800 chr1B 85.646 209 26 4 694 900 232237260 232237054 2.000000e-52 217.0
7 TraesCS6A01G143800 chr2A 97.755 1381 28 3 1935 3313 380539195 380540574 0.000000e+00 2375.0
8 TraesCS6A01G143800 chr2A 96.335 1146 34 4 811 1951 380537874 380539016 0.000000e+00 1877.0
9 TraesCS6A01G143800 chr2A 95.673 832 30 6 2419 3249 425026130 425025304 0.000000e+00 1332.0
10 TraesCS6A01G143800 chr5B 94.996 1319 61 5 1141 2457 235764055 235762740 0.000000e+00 2065.0
11 TraesCS6A01G143800 chr5B 87.745 204 22 3 698 900 314809443 314809242 5.530000e-58 235.0
12 TraesCS6A01G143800 chr5B 89.231 65 5 2 1738 1800 304146752 304146816 2.740000e-11 80.5
13 TraesCS6A01G143800 chr5B 90.164 61 5 1 1738 1797 159180117 159180177 9.860000e-11 78.7
14 TraesCS6A01G143800 chr5D 97.222 1116 29 2 2198 3311 53010110 53008995 0.000000e+00 1888.0
15 TraesCS6A01G143800 chr7B 96.034 832 26 5 2419 3249 666894866 666894041 0.000000e+00 1347.0
16 TraesCS6A01G143800 chr7B 95.783 830 30 4 2421 3249 666855426 666854601 0.000000e+00 1334.0
17 TraesCS6A01G143800 chr7B 91.100 809 55 12 2004 2807 90425983 90426779 0.000000e+00 1079.0
18 TraesCS6A01G143800 chr7B 82.213 253 30 8 581 830 549075801 549075561 1.560000e-48 204.0
19 TraesCS6A01G143800 chr7B 87.209 172 21 1 730 900 43128192 43128021 9.380000e-46 195.0
20 TraesCS6A01G143800 chr1A 95.798 833 31 4 2419 3249 7984264 7983434 0.000000e+00 1341.0
21 TraesCS6A01G143800 chr1A 85.714 56 6 2 8 61 101268674 101268729 1.280000e-04 58.4
22 TraesCS6A01G143800 chrUn 95.678 833 32 4 2419 3249 268294215 268295045 0.000000e+00 1336.0
23 TraesCS6A01G143800 chr6B 92.780 651 25 9 2002 2631 462295657 462296306 0.000000e+00 922.0
24 TraesCS6A01G143800 chr3B 92.627 651 27 8 2002 2631 328471214 328471864 0.000000e+00 917.0
25 TraesCS6A01G143800 chr3B 86.617 269 32 3 1415 1681 456612030 456611764 8.990000e-76 294.0
26 TraesCS6A01G143800 chr4B 94.757 515 24 3 1945 2457 340780806 340781319 0.000000e+00 798.0
27 TraesCS6A01G143800 chr4B 85.263 95 12 2 1744 1836 338491830 338491736 2.720000e-16 97.1
28 TraesCS6A01G143800 chr4B 86.154 65 7 2 1738 1800 410968203 410968267 5.930000e-08 69.4
29 TraesCS6A01G143800 chr6D 89.206 491 28 9 40 509 100686013 100686499 1.020000e-164 590.0
30 TraesCS6A01G143800 chr6D 78.808 151 20 11 902 1047 231560128 231559985 1.270000e-14 91.6
31 TraesCS6A01G143800 chr3D 89.494 257 21 4 798 1054 464529705 464529455 1.480000e-83 320.0
32 TraesCS6A01G143800 chr3D 94.595 111 6 0 1065 1175 464529387 464529277 4.400000e-39 172.0
33 TraesCS6A01G143800 chr2B 87.747 253 25 5 579 830 546665475 546665228 1.160000e-74 291.0
34 TraesCS6A01G143800 chr2B 85.294 170 22 3 733 900 546665137 546664969 4.400000e-39 172.0
35 TraesCS6A01G143800 chr4A 81.301 123 20 3 1668 1788 479119272 479119151 2.720000e-16 97.1
36 TraesCS6A01G143800 chr4A 78.261 115 18 5 8 120 548309904 548309795 2.130000e-07 67.6


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 TraesCS6A01G143800 chr6A 121234175 121237487 3312 False 6119.0 6119 100.0000 1 3313 1 chr6A.!!$F1 3312
1 TraesCS6A01G143800 chr4D 249164421 249165674 1253 True 1989.0 1989 95.4150 2002 3249 1 chr4D.!!$R1 1247
2 TraesCS6A01G143800 chr4D 266759990 266763050 3060 True 1935.0 3602 91.1415 593 3249 2 chr4D.!!$R2 2656
3 TraesCS6A01G143800 chr1B 303011446 303013367 1921 False 2778.0 2778 92.8090 537 2457 1 chr1B.!!$F2 1920
4 TraesCS6A01G143800 chr2A 380537874 380540574 2700 False 2126.0 2375 97.0450 811 3313 2 chr2A.!!$F1 2502
5 TraesCS6A01G143800 chr2A 425025304 425026130 826 True 1332.0 1332 95.6730 2419 3249 1 chr2A.!!$R1 830
6 TraesCS6A01G143800 chr5B 235762740 235764055 1315 True 2065.0 2065 94.9960 1141 2457 1 chr5B.!!$R1 1316
7 TraesCS6A01G143800 chr5D 53008995 53010110 1115 True 1888.0 1888 97.2220 2198 3311 1 chr5D.!!$R1 1113
8 TraesCS6A01G143800 chr7B 666894041 666894866 825 True 1347.0 1347 96.0340 2419 3249 1 chr7B.!!$R4 830
9 TraesCS6A01G143800 chr7B 666854601 666855426 825 True 1334.0 1334 95.7830 2421 3249 1 chr7B.!!$R3 828
10 TraesCS6A01G143800 chr7B 90425983 90426779 796 False 1079.0 1079 91.1000 2004 2807 1 chr7B.!!$F1 803
11 TraesCS6A01G143800 chr1A 7983434 7984264 830 True 1341.0 1341 95.7980 2419 3249 1 chr1A.!!$R1 830
12 TraesCS6A01G143800 chrUn 268294215 268295045 830 False 1336.0 1336 95.6780 2419 3249 1 chrUn.!!$F1 830
13 TraesCS6A01G143800 chr6B 462295657 462296306 649 False 922.0 922 92.7800 2002 2631 1 chr6B.!!$F1 629
14 TraesCS6A01G143800 chr3B 328471214 328471864 650 False 917.0 917 92.6270 2002 2631 1 chr3B.!!$F1 629
15 TraesCS6A01G143800 chr4B 340780806 340781319 513 False 798.0 798 94.7570 1945 2457 1 chr4B.!!$F1 512
16 TraesCS6A01G143800 chr2B 546664969 546665475 506 True 231.5 291 86.5205 579 900 2 chr2B.!!$R1 321

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
285 286 0.037605 GTTCACCACGTCCCACTAGG 60.038 60.000 0.0 0.0 0.0 3.02 F
490 491 0.102120 CGCCTGAAGTGCCAAACAAA 59.898 50.000 0.0 0.0 0.0 2.83 F
681 691 1.210478 GCAGATCCTTCTTGCCACCTA 59.790 52.381 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2931 1.473677 CCGTCCACGACAATGTACCTA 59.526 52.381 0.0 0.0 43.02 3.08 R
2241 3049 9.926158 ATGTCAGATCAATAGATATGTTCTCAC 57.074 33.333 0.0 0.0 42.61 3.51 R
2750 3580 2.596452 CAACAGCAGACAGTACTACCG 58.404 52.381 0.0 0.0 0.00 4.02 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 9.579768 TTGAAAAAGTTCATCGATTTGAAAAGA 57.420 25.926 3.10 0.00 43.29 2.52
37 38 9.579768 TGAAAAAGTTCATCGATTTGAAAAGAA 57.420 25.926 3.10 0.00 38.88 2.52
41 42 9.748708 AAAGTTCATCGATTTGAAAAGAAATCA 57.251 25.926 3.10 0.00 40.83 2.57
42 43 9.918630 AAGTTCATCGATTTGAAAAGAAATCAT 57.081 25.926 3.10 0.00 40.83 2.45
43 44 9.565213 AGTTCATCGATTTGAAAAGAAATCATC 57.435 29.630 3.10 0.00 40.83 2.92
44 45 8.518660 GTTCATCGATTTGAAAAGAAATCATCG 58.481 33.333 3.10 0.00 40.83 3.84
45 46 7.751732 TCATCGATTTGAAAAGAAATCATCGT 58.248 30.769 0.00 0.00 40.83 3.73
46 47 8.878769 TCATCGATTTGAAAAGAAATCATCGTA 58.121 29.630 0.00 0.00 40.83 3.43
47 48 9.655769 CATCGATTTGAAAAGAAATCATCGTAT 57.344 29.630 0.00 0.00 40.83 3.06
78 79 8.970691 AAAAGATCGTTGACTTTGAATAATGG 57.029 30.769 0.00 0.00 36.62 3.16
79 80 7.687941 AAGATCGTTGACTTTGAATAATGGT 57.312 32.000 0.00 0.00 0.00 3.55
80 81 7.687941 AGATCGTTGACTTTGAATAATGGTT 57.312 32.000 0.00 0.00 0.00 3.67
81 82 7.752695 AGATCGTTGACTTTGAATAATGGTTC 58.247 34.615 0.00 0.00 0.00 3.62
82 83 6.869315 TCGTTGACTTTGAATAATGGTTCA 57.131 33.333 0.00 0.00 36.38 3.18
83 84 7.447374 TCGTTGACTTTGAATAATGGTTCAT 57.553 32.000 0.00 0.00 37.88 2.57
84 85 7.526608 TCGTTGACTTTGAATAATGGTTCATC 58.473 34.615 0.00 0.00 37.88 2.92
85 86 6.465781 CGTTGACTTTGAATAATGGTTCATCG 59.534 38.462 0.00 0.00 37.88 3.84
86 87 7.526608 GTTGACTTTGAATAATGGTTCATCGA 58.473 34.615 0.00 0.00 37.88 3.59
87 88 7.680442 TGACTTTGAATAATGGTTCATCGAA 57.320 32.000 0.00 0.00 37.88 3.71
88 89 8.279970 TGACTTTGAATAATGGTTCATCGAAT 57.720 30.769 0.00 0.00 37.88 3.34
89 90 8.739039 TGACTTTGAATAATGGTTCATCGAATT 58.261 29.630 0.00 0.00 37.88 2.17
90 91 9.573133 GACTTTGAATAATGGTTCATCGAATTT 57.427 29.630 0.00 0.00 37.88 1.82
91 92 9.357652 ACTTTGAATAATGGTTCATCGAATTTG 57.642 29.630 0.00 0.00 37.88 2.32
92 93 9.571810 CTTTGAATAATGGTTCATCGAATTTGA 57.428 29.630 0.00 0.00 37.88 2.69
93 94 9.920133 TTTGAATAATGGTTCATCGAATTTGAA 57.080 25.926 0.00 0.00 37.88 2.69
94 95 9.920133 TTGAATAATGGTTCATCGAATTTGAAA 57.080 25.926 0.00 0.00 37.88 2.69
95 96 9.920133 TGAATAATGGTTCATCGAATTTGAAAA 57.080 25.926 0.00 0.00 35.03 2.29
191 192 3.325293 TGTTTGCAAACAAGCCTTCAA 57.675 38.095 36.22 14.70 45.17 2.69
192 193 3.668447 TGTTTGCAAACAAGCCTTCAAA 58.332 36.364 36.22 14.00 45.17 2.69
193 194 3.434984 TGTTTGCAAACAAGCCTTCAAAC 59.565 39.130 36.22 11.78 45.17 2.93
194 195 3.608316 TTGCAAACAAGCCTTCAAACT 57.392 38.095 0.00 0.00 0.00 2.66
195 196 3.163630 TGCAAACAAGCCTTCAAACTC 57.836 42.857 0.00 0.00 0.00 3.01
196 197 2.119457 GCAAACAAGCCTTCAAACTCG 58.881 47.619 0.00 0.00 0.00 4.18
197 198 2.223479 GCAAACAAGCCTTCAAACTCGA 60.223 45.455 0.00 0.00 0.00 4.04
198 199 3.733684 GCAAACAAGCCTTCAAACTCGAA 60.734 43.478 0.00 0.00 0.00 3.71
199 200 4.420168 CAAACAAGCCTTCAAACTCGAAA 58.580 39.130 0.00 0.00 0.00 3.46
200 201 3.971032 ACAAGCCTTCAAACTCGAAAG 57.029 42.857 0.00 0.00 0.00 2.62
201 202 3.279434 ACAAGCCTTCAAACTCGAAAGT 58.721 40.909 0.00 0.00 37.32 2.66
202 203 4.448210 ACAAGCCTTCAAACTCGAAAGTA 58.552 39.130 0.00 0.00 33.48 2.24
203 204 4.511826 ACAAGCCTTCAAACTCGAAAGTAG 59.488 41.667 0.00 0.00 33.48 2.57
204 205 3.665190 AGCCTTCAAACTCGAAAGTAGG 58.335 45.455 0.00 0.00 33.48 3.18
205 206 3.323979 AGCCTTCAAACTCGAAAGTAGGA 59.676 43.478 0.00 0.00 31.60 2.94
206 207 4.062991 GCCTTCAAACTCGAAAGTAGGAA 58.937 43.478 0.00 0.00 31.60 3.36
207 208 4.514066 GCCTTCAAACTCGAAAGTAGGAAA 59.486 41.667 0.00 0.00 31.60 3.13
208 209 5.008316 GCCTTCAAACTCGAAAGTAGGAAAA 59.992 40.000 0.00 0.00 31.60 2.29
209 210 6.459161 GCCTTCAAACTCGAAAGTAGGAAAAA 60.459 38.462 0.00 0.00 31.60 1.94
274 275 8.926715 AAAGAAAGAAATTTGTAGTTCACCAC 57.073 30.769 0.00 0.00 30.96 4.16
275 276 6.725246 AGAAAGAAATTTGTAGTTCACCACG 58.275 36.000 0.00 0.00 30.96 4.94
276 277 6.317893 AGAAAGAAATTTGTAGTTCACCACGT 59.682 34.615 0.00 0.00 30.96 4.49
277 278 5.668558 AGAAATTTGTAGTTCACCACGTC 57.331 39.130 0.00 0.00 30.96 4.34
278 279 4.514066 AGAAATTTGTAGTTCACCACGTCC 59.486 41.667 0.00 0.00 30.96 4.79
279 280 2.243602 TTTGTAGTTCACCACGTCCC 57.756 50.000 0.00 0.00 0.00 4.46
280 281 1.121378 TTGTAGTTCACCACGTCCCA 58.879 50.000 0.00 0.00 0.00 4.37
281 282 0.390124 TGTAGTTCACCACGTCCCAC 59.610 55.000 0.00 0.00 0.00 4.61
282 283 0.677842 GTAGTTCACCACGTCCCACT 59.322 55.000 0.00 0.00 0.00 4.00
283 284 1.888512 GTAGTTCACCACGTCCCACTA 59.111 52.381 0.00 0.00 0.00 2.74
284 285 0.966920 AGTTCACCACGTCCCACTAG 59.033 55.000 0.00 0.00 0.00 2.57
285 286 0.037605 GTTCACCACGTCCCACTAGG 60.038 60.000 0.00 0.00 0.00 3.02
286 287 0.470456 TTCACCACGTCCCACTAGGT 60.470 55.000 0.00 0.00 36.75 3.08
287 288 1.292223 CACCACGTCCCACTAGGTG 59.708 63.158 4.77 4.77 43.14 4.00
296 297 2.047274 CACTAGGTGGCGTGGTGG 60.047 66.667 0.00 0.00 29.50 4.61
297 298 2.525877 ACTAGGTGGCGTGGTGGT 60.526 61.111 0.00 0.00 0.00 4.16
298 299 2.144738 ACTAGGTGGCGTGGTGGTT 61.145 57.895 0.00 0.00 0.00 3.67
299 300 0.832983 ACTAGGTGGCGTGGTGGTTA 60.833 55.000 0.00 0.00 0.00 2.85
300 301 0.539986 CTAGGTGGCGTGGTGGTTAT 59.460 55.000 0.00 0.00 0.00 1.89
301 302 1.758280 CTAGGTGGCGTGGTGGTTATA 59.242 52.381 0.00 0.00 0.00 0.98
302 303 1.209621 AGGTGGCGTGGTGGTTATAT 58.790 50.000 0.00 0.00 0.00 0.86
303 304 1.140252 AGGTGGCGTGGTGGTTATATC 59.860 52.381 0.00 0.00 0.00 1.63
304 305 1.214367 GTGGCGTGGTGGTTATATCG 58.786 55.000 0.00 0.00 0.00 2.92
305 306 0.105224 TGGCGTGGTGGTTATATCGG 59.895 55.000 0.00 0.00 0.00 4.18
306 307 0.601841 GGCGTGGTGGTTATATCGGG 60.602 60.000 0.00 0.00 0.00 5.14
307 308 0.105408 GCGTGGTGGTTATATCGGGT 59.895 55.000 0.00 0.00 0.00 5.28
308 309 1.473788 GCGTGGTGGTTATATCGGGTT 60.474 52.381 0.00 0.00 0.00 4.11
309 310 2.224018 GCGTGGTGGTTATATCGGGTTA 60.224 50.000 0.00 0.00 0.00 2.85
310 311 3.555586 GCGTGGTGGTTATATCGGGTTAT 60.556 47.826 0.00 0.00 0.00 1.89
311 312 4.240096 CGTGGTGGTTATATCGGGTTATC 58.760 47.826 0.00 0.00 0.00 1.75
312 313 4.021719 CGTGGTGGTTATATCGGGTTATCT 60.022 45.833 0.00 0.00 0.00 1.98
313 314 5.476614 GTGGTGGTTATATCGGGTTATCTC 58.523 45.833 0.00 0.00 0.00 2.75
314 315 4.219070 TGGTGGTTATATCGGGTTATCTCG 59.781 45.833 0.00 0.00 0.00 4.04
315 316 4.460382 GGTGGTTATATCGGGTTATCTCGA 59.540 45.833 0.00 0.00 39.79 4.04
316 317 5.397326 GTGGTTATATCGGGTTATCTCGAC 58.603 45.833 0.00 0.00 38.25 4.20
317 318 4.154737 TGGTTATATCGGGTTATCTCGACG 59.845 45.833 0.00 0.00 38.25 5.12
318 319 4.393062 GGTTATATCGGGTTATCTCGACGA 59.607 45.833 0.00 0.00 38.25 4.20
319 320 5.447010 GGTTATATCGGGTTATCTCGACGAG 60.447 48.000 18.91 18.91 38.25 4.18
320 321 0.592148 ATCGGGTTATCTCGACGAGC 59.408 55.000 20.11 5.85 38.25 5.03
321 322 1.368969 CGGGTTATCTCGACGAGCG 60.369 63.158 20.11 12.36 42.69 5.03
337 338 2.490217 CGAGGTCGCTGGTTCGAT 59.510 61.111 0.00 0.00 40.84 3.59
338 339 1.153823 CGAGGTCGCTGGTTCGATT 60.154 57.895 0.00 0.00 40.84 3.34
339 340 1.140407 CGAGGTCGCTGGTTCGATTC 61.140 60.000 0.00 0.00 40.84 2.52
340 341 0.108804 GAGGTCGCTGGTTCGATTCA 60.109 55.000 0.00 0.00 40.84 2.57
341 342 0.389948 AGGTCGCTGGTTCGATTCAC 60.390 55.000 0.00 0.00 40.84 3.18
342 343 0.669318 GGTCGCTGGTTCGATTCACA 60.669 55.000 0.00 0.00 40.84 3.58
343 344 1.144969 GTCGCTGGTTCGATTCACAA 58.855 50.000 0.00 0.00 40.84 3.33
344 345 1.529438 GTCGCTGGTTCGATTCACAAA 59.471 47.619 0.00 0.00 40.84 2.83
345 346 1.529438 TCGCTGGTTCGATTCACAAAC 59.471 47.619 0.00 0.00 33.02 2.93
346 347 1.262950 CGCTGGTTCGATTCACAAACA 59.737 47.619 0.00 0.00 0.00 2.83
347 348 2.662791 CGCTGGTTCGATTCACAAACAG 60.663 50.000 6.17 6.17 0.00 3.16
348 349 2.918131 GCTGGTTCGATTCACAAACAGC 60.918 50.000 15.82 15.82 0.00 4.40
349 350 2.549754 CTGGTTCGATTCACAAACAGCT 59.450 45.455 0.00 0.00 0.00 4.24
350 351 2.548057 TGGTTCGATTCACAAACAGCTC 59.452 45.455 0.00 0.00 0.00 4.09
351 352 2.411547 GGTTCGATTCACAAACAGCTCG 60.412 50.000 0.00 0.00 0.00 5.03
352 353 2.432206 TCGATTCACAAACAGCTCGA 57.568 45.000 0.00 0.00 33.23 4.04
353 354 2.959516 TCGATTCACAAACAGCTCGAT 58.040 42.857 0.00 0.00 30.94 3.59
354 355 4.104696 TCGATTCACAAACAGCTCGATA 57.895 40.909 0.00 0.00 30.94 2.92
355 356 4.682787 TCGATTCACAAACAGCTCGATAT 58.317 39.130 0.00 0.00 30.94 1.63
356 357 5.109210 TCGATTCACAAACAGCTCGATATT 58.891 37.500 0.00 0.00 30.94 1.28
357 358 5.580691 TCGATTCACAAACAGCTCGATATTT 59.419 36.000 0.00 0.00 30.94 1.40
358 359 6.092122 TCGATTCACAAACAGCTCGATATTTT 59.908 34.615 0.00 0.00 30.94 1.82
359 360 6.742718 CGATTCACAAACAGCTCGATATTTTT 59.257 34.615 0.00 0.00 0.00 1.94
360 361 7.045354 CGATTCACAAACAGCTCGATATTTTTC 60.045 37.037 0.00 0.00 0.00 2.29
361 362 6.801539 TCACAAACAGCTCGATATTTTTCT 57.198 33.333 0.00 0.00 0.00 2.52
362 363 7.899178 TCACAAACAGCTCGATATTTTTCTA 57.101 32.000 0.00 0.00 0.00 2.10
363 364 8.492673 TCACAAACAGCTCGATATTTTTCTAT 57.507 30.769 0.00 0.00 0.00 1.98
364 365 8.946085 TCACAAACAGCTCGATATTTTTCTATT 58.054 29.630 0.00 0.00 0.00 1.73
370 371 9.817809 ACAGCTCGATATTTTTCTATTAGAACA 57.182 29.630 5.62 0.00 33.26 3.18
372 373 9.817809 AGCTCGATATTTTTCTATTAGAACACA 57.182 29.630 5.62 0.00 33.26 3.72
397 398 3.658757 AAAACATGTTTGATGGGTCGG 57.341 42.857 23.93 0.00 32.36 4.79
398 399 0.887933 AACATGTTTGATGGGTCGGC 59.112 50.000 4.92 0.00 0.00 5.54
399 400 0.965363 ACATGTTTGATGGGTCGGCC 60.965 55.000 0.00 0.00 0.00 6.13
429 430 2.429069 GCTTCAAGCGCCCGTTTG 60.429 61.111 2.29 10.39 37.61 2.93
430 431 2.429069 CTTCAAGCGCCCGTTTGC 60.429 61.111 2.29 0.00 36.49 3.68
431 432 3.192954 CTTCAAGCGCCCGTTTGCA 62.193 57.895 2.29 1.47 36.49 4.08
432 433 2.676016 CTTCAAGCGCCCGTTTGCAA 62.676 55.000 2.29 0.00 36.49 4.08
433 434 2.279120 CAAGCGCCCGTTTGCAAA 60.279 55.556 8.05 8.05 30.30 3.68
434 435 1.880340 CAAGCGCCCGTTTGCAAAA 60.880 52.632 14.67 0.00 30.30 2.44
435 436 1.153549 AAGCGCCCGTTTGCAAAAA 60.154 47.368 14.67 0.00 0.00 1.94
436 437 1.425267 AAGCGCCCGTTTGCAAAAAC 61.425 50.000 14.67 1.81 0.00 2.43
437 438 2.167861 GCGCCCGTTTGCAAAAACA 61.168 52.632 14.67 0.00 33.08 2.83
438 439 1.633697 CGCCCGTTTGCAAAAACAC 59.366 52.632 14.67 0.57 33.08 3.32
439 440 0.804156 CGCCCGTTTGCAAAAACACT 60.804 50.000 14.67 0.00 33.08 3.55
440 441 1.534175 CGCCCGTTTGCAAAAACACTA 60.534 47.619 14.67 0.00 33.08 2.74
441 442 2.541556 GCCCGTTTGCAAAAACACTAA 58.458 42.857 14.67 0.00 33.08 2.24
442 443 3.127589 GCCCGTTTGCAAAAACACTAAT 58.872 40.909 14.67 0.00 33.08 1.73
443 444 4.299978 GCCCGTTTGCAAAAACACTAATA 58.700 39.130 14.67 0.00 33.08 0.98
444 445 4.745620 GCCCGTTTGCAAAAACACTAATAA 59.254 37.500 14.67 0.00 33.08 1.40
445 446 5.234543 GCCCGTTTGCAAAAACACTAATAAA 59.765 36.000 14.67 0.00 33.08 1.40
446 447 6.238130 GCCCGTTTGCAAAAACACTAATAAAA 60.238 34.615 14.67 0.00 33.08 1.52
447 448 7.341446 CCCGTTTGCAAAAACACTAATAAAAG 58.659 34.615 14.67 0.00 33.08 2.27
448 449 7.341446 CCGTTTGCAAAAACACTAATAAAAGG 58.659 34.615 14.67 0.00 33.08 3.11
449 450 7.341446 CGTTTGCAAAAACACTAATAAAAGGG 58.659 34.615 14.67 0.00 33.08 3.95
450 451 7.517575 CGTTTGCAAAAACACTAATAAAAGGGG 60.518 37.037 14.67 0.00 33.08 4.79
451 452 5.301555 TGCAAAAACACTAATAAAAGGGGC 58.698 37.500 0.00 0.00 0.00 5.80
452 453 4.387559 GCAAAAACACTAATAAAAGGGGCG 59.612 41.667 0.00 0.00 0.00 6.13
453 454 3.861276 AAACACTAATAAAAGGGGCGC 57.139 42.857 0.00 0.00 0.00 6.53
454 455 1.758936 ACACTAATAAAAGGGGCGCC 58.241 50.000 21.18 21.18 0.00 6.53
455 456 1.283905 ACACTAATAAAAGGGGCGCCT 59.716 47.619 28.56 18.22 0.00 5.52
456 457 2.506644 ACACTAATAAAAGGGGCGCCTA 59.493 45.455 28.56 11.01 0.00 3.93
457 458 3.139077 CACTAATAAAAGGGGCGCCTAG 58.861 50.000 28.56 19.02 0.00 3.02
458 459 2.775960 ACTAATAAAAGGGGCGCCTAGT 59.224 45.455 28.56 19.71 0.00 2.57
459 460 2.820728 AATAAAAGGGGCGCCTAGTT 57.179 45.000 28.56 21.06 0.00 2.24
460 461 2.343484 ATAAAAGGGGCGCCTAGTTC 57.657 50.000 28.56 9.02 0.00 3.01
461 462 1.282382 TAAAAGGGGCGCCTAGTTCT 58.718 50.000 28.56 13.16 0.00 3.01
462 463 1.282382 AAAAGGGGCGCCTAGTTCTA 58.718 50.000 28.56 0.00 0.00 2.10
463 464 1.282382 AAAGGGGCGCCTAGTTCTAA 58.718 50.000 28.56 0.00 0.00 2.10
464 465 1.282382 AAGGGGCGCCTAGTTCTAAA 58.718 50.000 28.56 0.00 0.00 1.85
465 466 1.282382 AGGGGCGCCTAGTTCTAAAA 58.718 50.000 28.56 0.00 0.00 1.52
466 467 1.631898 AGGGGCGCCTAGTTCTAAAAA 59.368 47.619 28.56 0.00 0.00 1.94
480 481 4.599036 AAAAAGGGCGCCTGAAGT 57.401 50.000 28.56 6.52 32.13 3.01
481 482 2.041153 AAAAAGGGCGCCTGAAGTG 58.959 52.632 28.56 0.00 32.13 3.16
487 488 2.050077 GCGCCTGAAGTGCCAAAC 60.050 61.111 0.00 0.00 46.76 2.93
488 489 2.844451 GCGCCTGAAGTGCCAAACA 61.844 57.895 0.00 0.00 46.76 2.83
489 490 1.732917 CGCCTGAAGTGCCAAACAA 59.267 52.632 0.00 0.00 0.00 2.83
490 491 0.102120 CGCCTGAAGTGCCAAACAAA 59.898 50.000 0.00 0.00 0.00 2.83
491 492 1.470632 CGCCTGAAGTGCCAAACAAAA 60.471 47.619 0.00 0.00 0.00 2.44
492 493 2.204237 GCCTGAAGTGCCAAACAAAAG 58.796 47.619 0.00 0.00 0.00 2.27
493 494 2.825205 CCTGAAGTGCCAAACAAAAGG 58.175 47.619 0.00 0.00 0.00 3.11
494 495 2.430332 CCTGAAGTGCCAAACAAAAGGA 59.570 45.455 0.00 0.00 0.00 3.36
495 496 3.447742 CTGAAGTGCCAAACAAAAGGAC 58.552 45.455 0.00 0.00 0.00 3.85
496 497 2.828520 TGAAGTGCCAAACAAAAGGACA 59.171 40.909 0.00 0.00 0.00 4.02
497 498 3.259374 TGAAGTGCCAAACAAAAGGACAA 59.741 39.130 0.00 0.00 0.00 3.18
498 499 4.081198 TGAAGTGCCAAACAAAAGGACAAT 60.081 37.500 0.00 0.00 0.00 2.71
499 500 4.486125 AGTGCCAAACAAAAGGACAATT 57.514 36.364 0.00 0.00 0.00 2.32
500 501 4.190772 AGTGCCAAACAAAAGGACAATTG 58.809 39.130 3.24 3.24 0.00 2.32
501 502 4.081198 AGTGCCAAACAAAAGGACAATTGA 60.081 37.500 13.59 0.00 0.00 2.57
502 503 4.815846 GTGCCAAACAAAAGGACAATTGAT 59.184 37.500 13.59 0.00 0.00 2.57
503 504 5.988561 GTGCCAAACAAAAGGACAATTGATA 59.011 36.000 13.59 0.00 0.00 2.15
504 505 6.650390 GTGCCAAACAAAAGGACAATTGATAT 59.350 34.615 13.59 0.00 0.00 1.63
505 506 7.816995 GTGCCAAACAAAAGGACAATTGATATA 59.183 33.333 13.59 0.00 0.00 0.86
506 507 8.538701 TGCCAAACAAAAGGACAATTGATATAT 58.461 29.630 13.59 0.00 0.00 0.86
645 655 2.433970 CCAGCCCCAAAAGAAGAAAACA 59.566 45.455 0.00 0.00 0.00 2.83
681 691 1.210478 GCAGATCCTTCTTGCCACCTA 59.790 52.381 0.00 0.00 0.00 3.08
718 728 2.363361 CCCGACCTCCTACCCACT 59.637 66.667 0.00 0.00 0.00 4.00
778 788 4.316823 TCCTCCCACCGTGCCTCT 62.317 66.667 0.00 0.00 0.00 3.69
1253 1850 4.794439 CGACTCATCGCCGGCACA 62.794 66.667 28.98 13.13 42.43 4.57
1621 2224 9.669887 CCAATCATTTGATAGGGAATTCAAAAA 57.330 29.630 7.93 0.00 43.04 1.94
1682 2286 3.519913 GGTTCAGGAAAGTAGACATCCCT 59.480 47.826 2.00 0.00 33.55 4.20
1713 2317 7.036220 ACACTCTTCTATATTTTCGGTCACAG 58.964 38.462 0.00 0.00 0.00 3.66
1965 2770 8.962679 TGACTATAGTTTCTTTTGGTTTGTTGT 58.037 29.630 6.88 0.00 0.00 3.32
2110 2918 3.813166 TGTTAGCAAGTTCAACTACCAGC 59.187 43.478 0.00 0.00 0.00 4.85
2123 2931 1.252904 TACCAGCCTACGCCGAGTTT 61.253 55.000 0.00 0.00 34.57 2.66
2664 3493 9.941664 CACATGGTATGACTATTCTGAAAAATC 57.058 33.333 0.00 0.00 0.00 2.17
2750 3580 7.762382 TCAAAGAAAAGGAGAGTTCAGAAAAC 58.238 34.615 0.00 0.00 0.00 2.43
2830 3660 1.827315 GCTACTTGTTGTGCGTGCGA 61.827 55.000 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.579768 TCTTTTCAAATCGATGAACTTTTTCAA 57.420 25.926 0.00 0.00 45.01 2.69
11 12 9.579768 TTCTTTTCAAATCGATGAACTTTTTCA 57.420 25.926 0.00 0.00 45.93 2.69
15 16 9.748708 TGATTTCTTTTCAAATCGATGAACTTT 57.251 25.926 0.00 0.00 43.19 2.66
16 17 9.918630 ATGATTTCTTTTCAAATCGATGAACTT 57.081 25.926 0.00 0.00 43.19 2.66
17 18 9.565213 GATGATTTCTTTTCAAATCGATGAACT 57.435 29.630 0.00 0.00 43.19 3.01
18 19 8.518660 CGATGATTTCTTTTCAAATCGATGAAC 58.481 33.333 0.00 0.00 43.19 3.18
19 20 8.236586 ACGATGATTTCTTTTCAAATCGATGAA 58.763 29.630 0.00 0.00 43.19 2.57
20 21 7.751732 ACGATGATTTCTTTTCAAATCGATGA 58.248 30.769 0.00 0.00 43.19 2.92
21 22 7.959718 ACGATGATTTCTTTTCAAATCGATG 57.040 32.000 0.00 0.00 43.19 3.84
52 53 9.410556 CCATTATTCAAAGTCAACGATCTTTTT 57.589 29.630 0.00 0.00 32.52 1.94
53 54 8.576442 ACCATTATTCAAAGTCAACGATCTTTT 58.424 29.630 0.00 0.00 32.52 2.27
54 55 8.110860 ACCATTATTCAAAGTCAACGATCTTT 57.889 30.769 0.00 0.00 34.74 2.52
55 56 7.687941 ACCATTATTCAAAGTCAACGATCTT 57.312 32.000 0.00 0.00 0.00 2.40
56 57 7.390440 TGAACCATTATTCAAAGTCAACGATCT 59.610 33.333 0.00 0.00 35.65 2.75
57 58 7.526608 TGAACCATTATTCAAAGTCAACGATC 58.473 34.615 0.00 0.00 35.65 3.69
58 59 7.447374 TGAACCATTATTCAAAGTCAACGAT 57.553 32.000 0.00 0.00 35.65 3.73
59 60 6.869315 TGAACCATTATTCAAAGTCAACGA 57.131 33.333 0.00 0.00 35.65 3.85
60 61 6.465781 CGATGAACCATTATTCAAAGTCAACG 59.534 38.462 0.00 0.00 41.78 4.10
61 62 7.526608 TCGATGAACCATTATTCAAAGTCAAC 58.473 34.615 0.00 0.00 41.78 3.18
62 63 7.680442 TCGATGAACCATTATTCAAAGTCAA 57.320 32.000 0.00 0.00 41.78 3.18
63 64 7.680442 TTCGATGAACCATTATTCAAAGTCA 57.320 32.000 0.00 0.00 41.78 3.41
64 65 9.573133 AAATTCGATGAACCATTATTCAAAGTC 57.427 29.630 0.00 0.00 41.78 3.01
65 66 9.357652 CAAATTCGATGAACCATTATTCAAAGT 57.642 29.630 0.00 0.00 41.78 2.66
66 67 9.571810 TCAAATTCGATGAACCATTATTCAAAG 57.428 29.630 0.00 0.00 41.78 2.77
67 68 9.920133 TTCAAATTCGATGAACCATTATTCAAA 57.080 25.926 0.00 0.00 41.78 2.69
68 69 9.920133 TTTCAAATTCGATGAACCATTATTCAA 57.080 25.926 0.00 0.00 41.78 2.69
69 70 9.920133 TTTTCAAATTCGATGAACCATTATTCA 57.080 25.926 0.00 0.00 42.62 2.57
159 160 6.551385 TGTTTGCAAACATGTGAACTTTTT 57.449 29.167 35.10 0.00 43.45 1.94
171 172 3.325293 TTGAAGGCTTGTTTGCAAACA 57.675 38.095 35.10 35.10 46.35 2.83
172 173 3.684305 AGTTTGAAGGCTTGTTTGCAAAC 59.316 39.130 30.95 30.95 43.05 2.93
173 174 3.932089 GAGTTTGAAGGCTTGTTTGCAAA 59.068 39.130 8.05 8.05 33.73 3.68
174 175 3.520569 GAGTTTGAAGGCTTGTTTGCAA 58.479 40.909 3.46 0.00 34.04 4.08
175 176 2.479389 CGAGTTTGAAGGCTTGTTTGCA 60.479 45.455 3.46 0.00 34.04 4.08
176 177 2.119457 CGAGTTTGAAGGCTTGTTTGC 58.881 47.619 3.46 0.00 0.00 3.68
177 178 3.691049 TCGAGTTTGAAGGCTTGTTTG 57.309 42.857 3.46 0.00 0.00 2.93
178 179 4.157840 ACTTTCGAGTTTGAAGGCTTGTTT 59.842 37.500 3.46 0.00 0.00 2.83
179 180 3.694566 ACTTTCGAGTTTGAAGGCTTGTT 59.305 39.130 3.46 0.00 0.00 2.83
180 181 3.279434 ACTTTCGAGTTTGAAGGCTTGT 58.721 40.909 3.46 0.00 0.00 3.16
181 182 3.971032 ACTTTCGAGTTTGAAGGCTTG 57.029 42.857 3.46 0.00 0.00 4.01
182 183 4.065789 CCTACTTTCGAGTTTGAAGGCTT 58.934 43.478 0.00 0.00 0.00 4.35
183 184 3.323979 TCCTACTTTCGAGTTTGAAGGCT 59.676 43.478 0.00 0.00 0.00 4.58
184 185 3.660865 TCCTACTTTCGAGTTTGAAGGC 58.339 45.455 0.00 0.00 0.00 4.35
185 186 6.613755 TTTTCCTACTTTCGAGTTTGAAGG 57.386 37.500 0.00 0.00 0.00 3.46
248 249 9.366216 GTGGTGAACTACAAATTTCTTTCTTTT 57.634 29.630 0.00 0.00 0.00 2.27
249 250 7.700656 CGTGGTGAACTACAAATTTCTTTCTTT 59.299 33.333 0.00 0.00 0.00 2.52
250 251 7.148137 ACGTGGTGAACTACAAATTTCTTTCTT 60.148 33.333 0.00 0.00 0.00 2.52
251 252 6.317893 ACGTGGTGAACTACAAATTTCTTTCT 59.682 34.615 0.00 0.00 0.00 2.52
252 253 6.492254 ACGTGGTGAACTACAAATTTCTTTC 58.508 36.000 0.00 0.00 0.00 2.62
253 254 6.445357 ACGTGGTGAACTACAAATTTCTTT 57.555 33.333 0.00 0.00 0.00 2.52
254 255 5.008316 GGACGTGGTGAACTACAAATTTCTT 59.992 40.000 0.00 0.00 0.00 2.52
255 256 4.514066 GGACGTGGTGAACTACAAATTTCT 59.486 41.667 0.00 0.00 0.00 2.52
256 257 4.319984 GGGACGTGGTGAACTACAAATTTC 60.320 45.833 0.00 0.00 0.00 2.17
257 258 3.566742 GGGACGTGGTGAACTACAAATTT 59.433 43.478 0.00 0.00 0.00 1.82
258 259 3.143728 GGGACGTGGTGAACTACAAATT 58.856 45.455 0.00 0.00 0.00 1.82
259 260 2.105134 TGGGACGTGGTGAACTACAAAT 59.895 45.455 0.00 0.00 0.00 2.32
260 261 1.485480 TGGGACGTGGTGAACTACAAA 59.515 47.619 0.00 0.00 0.00 2.83
261 262 1.121378 TGGGACGTGGTGAACTACAA 58.879 50.000 0.00 0.00 0.00 2.41
262 263 0.390124 GTGGGACGTGGTGAACTACA 59.610 55.000 0.00 0.00 0.00 2.74
263 264 0.677842 AGTGGGACGTGGTGAACTAC 59.322 55.000 0.00 0.00 0.00 2.73
264 265 2.165167 CTAGTGGGACGTGGTGAACTA 58.835 52.381 0.00 0.00 0.00 2.24
265 266 0.966920 CTAGTGGGACGTGGTGAACT 59.033 55.000 0.00 0.00 0.00 3.01
266 267 0.037605 CCTAGTGGGACGTGGTGAAC 60.038 60.000 0.00 0.00 37.23 3.18
267 268 0.470456 ACCTAGTGGGACGTGGTGAA 60.470 55.000 0.00 0.00 38.76 3.18
268 269 1.154454 ACCTAGTGGGACGTGGTGA 59.846 57.895 0.00 0.00 38.76 4.02
269 270 1.292223 CACCTAGTGGGACGTGGTG 59.708 63.158 0.00 0.00 38.89 4.17
270 271 3.787394 CACCTAGTGGGACGTGGT 58.213 61.111 0.00 0.00 38.76 4.16
279 280 2.047274 CCACCACGCCACCTAGTG 60.047 66.667 0.00 0.00 38.05 2.74
280 281 0.832983 TAACCACCACGCCACCTAGT 60.833 55.000 0.00 0.00 0.00 2.57
281 282 0.539986 ATAACCACCACGCCACCTAG 59.460 55.000 0.00 0.00 0.00 3.02
282 283 1.863325 TATAACCACCACGCCACCTA 58.137 50.000 0.00 0.00 0.00 3.08
283 284 1.140252 GATATAACCACCACGCCACCT 59.860 52.381 0.00 0.00 0.00 4.00
284 285 1.589803 GATATAACCACCACGCCACC 58.410 55.000 0.00 0.00 0.00 4.61
285 286 1.214367 CGATATAACCACCACGCCAC 58.786 55.000 0.00 0.00 0.00 5.01
286 287 0.105224 CCGATATAACCACCACGCCA 59.895 55.000 0.00 0.00 0.00 5.69
287 288 0.601841 CCCGATATAACCACCACGCC 60.602 60.000 0.00 0.00 0.00 5.68
288 289 0.105408 ACCCGATATAACCACCACGC 59.895 55.000 0.00 0.00 0.00 5.34
289 290 2.607631 AACCCGATATAACCACCACG 57.392 50.000 0.00 0.00 0.00 4.94
290 291 5.476614 GAGATAACCCGATATAACCACCAC 58.523 45.833 0.00 0.00 0.00 4.16
291 292 4.219070 CGAGATAACCCGATATAACCACCA 59.781 45.833 0.00 0.00 0.00 4.17
292 293 4.460382 TCGAGATAACCCGATATAACCACC 59.540 45.833 0.00 0.00 0.00 4.61
293 294 5.397326 GTCGAGATAACCCGATATAACCAC 58.603 45.833 0.00 0.00 37.14 4.16
294 295 4.154737 CGTCGAGATAACCCGATATAACCA 59.845 45.833 0.00 0.00 37.14 3.67
295 296 4.393062 TCGTCGAGATAACCCGATATAACC 59.607 45.833 0.00 0.00 37.14 2.85
296 297 5.536554 TCGTCGAGATAACCCGATATAAC 57.463 43.478 0.00 0.00 37.14 1.89
297 298 4.093998 GCTCGTCGAGATAACCCGATATAA 59.906 45.833 26.11 0.00 37.14 0.98
298 299 3.620374 GCTCGTCGAGATAACCCGATATA 59.380 47.826 26.11 0.00 37.14 0.86
299 300 2.419324 GCTCGTCGAGATAACCCGATAT 59.581 50.000 26.11 0.00 37.14 1.63
300 301 1.802960 GCTCGTCGAGATAACCCGATA 59.197 52.381 26.11 0.00 37.14 2.92
301 302 0.592148 GCTCGTCGAGATAACCCGAT 59.408 55.000 26.11 0.00 37.14 4.18
302 303 1.769098 CGCTCGTCGAGATAACCCGA 61.769 60.000 26.11 0.00 41.67 5.14
303 304 1.368969 CGCTCGTCGAGATAACCCG 60.369 63.158 26.11 14.06 41.67 5.28
304 305 2.020131 TCGCTCGTCGAGATAACCC 58.980 57.895 26.11 5.86 43.16 4.11
320 321 1.140407 GAATCGAACCAGCGACCTCG 61.140 60.000 0.00 0.00 43.79 4.63
321 322 0.108804 TGAATCGAACCAGCGACCTC 60.109 55.000 0.00 0.00 43.79 3.85
322 323 0.389948 GTGAATCGAACCAGCGACCT 60.390 55.000 0.00 0.00 43.79 3.85
323 324 0.669318 TGTGAATCGAACCAGCGACC 60.669 55.000 0.00 0.00 43.79 4.79
324 325 1.144969 TTGTGAATCGAACCAGCGAC 58.855 50.000 0.00 0.00 43.79 5.19
325 326 1.529438 GTTTGTGAATCGAACCAGCGA 59.471 47.619 0.00 0.00 45.22 4.93
326 327 1.262950 TGTTTGTGAATCGAACCAGCG 59.737 47.619 0.00 0.00 39.12 5.18
327 328 2.918131 GCTGTTTGTGAATCGAACCAGC 60.918 50.000 0.00 0.00 39.12 4.85
328 329 2.549754 AGCTGTTTGTGAATCGAACCAG 59.450 45.455 0.00 0.00 39.12 4.00
329 330 2.548057 GAGCTGTTTGTGAATCGAACCA 59.452 45.455 0.00 0.00 39.12 3.67
330 331 2.411547 CGAGCTGTTTGTGAATCGAACC 60.412 50.000 0.00 0.00 39.12 3.62
331 332 2.475111 TCGAGCTGTTTGTGAATCGAAC 59.525 45.455 0.00 0.00 40.01 3.95
332 333 2.749776 TCGAGCTGTTTGTGAATCGAA 58.250 42.857 0.00 0.00 36.37 3.71
333 334 2.432206 TCGAGCTGTTTGTGAATCGA 57.568 45.000 0.00 0.00 36.90 3.59
334 335 5.395325 AATATCGAGCTGTTTGTGAATCG 57.605 39.130 0.00 0.00 0.00 3.34
335 336 7.965107 AGAAAAATATCGAGCTGTTTGTGAATC 59.035 33.333 0.00 0.00 0.00 2.52
336 337 7.820648 AGAAAAATATCGAGCTGTTTGTGAAT 58.179 30.769 0.00 0.00 0.00 2.57
337 338 7.202016 AGAAAAATATCGAGCTGTTTGTGAA 57.798 32.000 0.00 0.00 0.00 3.18
338 339 6.801539 AGAAAAATATCGAGCTGTTTGTGA 57.198 33.333 0.00 0.00 0.00 3.58
344 345 9.817809 TGTTCTAATAGAAAAATATCGAGCTGT 57.182 29.630 4.04 0.00 35.75 4.40
346 347 9.817809 TGTGTTCTAATAGAAAAATATCGAGCT 57.182 29.630 4.04 0.00 35.75 4.09
376 377 3.801983 GCCGACCCATCAAACATGTTTTT 60.802 43.478 21.10 9.20 0.00 1.94
377 378 2.288763 GCCGACCCATCAAACATGTTTT 60.289 45.455 21.10 5.86 0.00 2.43
378 379 1.272212 GCCGACCCATCAAACATGTTT 59.728 47.619 18.13 18.13 0.00 2.83
379 380 0.887933 GCCGACCCATCAAACATGTT 59.112 50.000 4.92 4.92 0.00 2.71
380 381 0.965363 GGCCGACCCATCAAACATGT 60.965 55.000 0.00 0.00 0.00 3.21
381 382 1.809207 GGCCGACCCATCAAACATG 59.191 57.895 0.00 0.00 0.00 3.21
382 383 4.337013 GGCCGACCCATCAAACAT 57.663 55.556 0.00 0.00 0.00 2.71
412 413 2.429069 CAAACGGGCGCTTGAAGC 60.429 61.111 7.64 7.20 38.02 3.86
413 414 2.429069 GCAAACGGGCGCTTGAAG 60.429 61.111 7.64 0.00 0.00 3.02
414 415 2.284798 TTTGCAAACGGGCGCTTGAA 62.285 50.000 8.05 0.00 36.28 2.69
415 416 2.284798 TTTTGCAAACGGGCGCTTGA 62.285 50.000 12.39 0.00 36.28 3.02
416 417 1.424493 TTTTTGCAAACGGGCGCTTG 61.424 50.000 12.39 4.86 36.28 4.01
417 418 1.153549 TTTTTGCAAACGGGCGCTT 60.154 47.368 12.39 0.00 36.28 4.68
418 419 1.880796 GTTTTTGCAAACGGGCGCT 60.881 52.632 12.39 0.00 33.21 5.92
419 420 2.167861 TGTTTTTGCAAACGGGCGC 61.168 52.632 12.39 0.00 44.76 6.53
420 421 0.804156 AGTGTTTTTGCAAACGGGCG 60.804 50.000 12.39 0.00 44.76 6.13
421 422 2.211353 TAGTGTTTTTGCAAACGGGC 57.789 45.000 12.39 3.24 44.76 6.13
422 423 6.830114 TTTATTAGTGTTTTTGCAAACGGG 57.170 33.333 12.39 0.00 44.76 5.28
423 424 7.341446 CCTTTTATTAGTGTTTTTGCAAACGG 58.659 34.615 12.39 0.00 44.76 4.44
424 425 7.341446 CCCTTTTATTAGTGTTTTTGCAAACG 58.659 34.615 12.39 0.00 44.76 3.60
425 426 7.635423 CCCCTTTTATTAGTGTTTTTGCAAAC 58.365 34.615 12.39 2.38 42.49 2.93
426 427 6.261158 GCCCCTTTTATTAGTGTTTTTGCAAA 59.739 34.615 8.05 8.05 0.00 3.68
427 428 5.760743 GCCCCTTTTATTAGTGTTTTTGCAA 59.239 36.000 0.00 0.00 0.00 4.08
428 429 5.301555 GCCCCTTTTATTAGTGTTTTTGCA 58.698 37.500 0.00 0.00 0.00 4.08
429 430 4.387559 CGCCCCTTTTATTAGTGTTTTTGC 59.612 41.667 0.00 0.00 0.00 3.68
430 431 4.387559 GCGCCCCTTTTATTAGTGTTTTTG 59.612 41.667 0.00 0.00 0.00 2.44
431 432 4.561938 GGCGCCCCTTTTATTAGTGTTTTT 60.562 41.667 18.11 0.00 0.00 1.94
432 433 3.056393 GGCGCCCCTTTTATTAGTGTTTT 60.056 43.478 18.11 0.00 0.00 2.43
433 434 2.494471 GGCGCCCCTTTTATTAGTGTTT 59.506 45.455 18.11 0.00 0.00 2.83
434 435 2.097036 GGCGCCCCTTTTATTAGTGTT 58.903 47.619 18.11 0.00 0.00 3.32
435 436 1.283905 AGGCGCCCCTTTTATTAGTGT 59.716 47.619 26.15 0.00 38.74 3.55
436 437 2.052782 AGGCGCCCCTTTTATTAGTG 57.947 50.000 26.15 0.00 38.74 2.74
437 438 2.775960 ACTAGGCGCCCCTTTTATTAGT 59.224 45.455 26.15 18.44 42.87 2.24
438 439 3.487120 ACTAGGCGCCCCTTTTATTAG 57.513 47.619 26.15 17.74 42.87 1.73
439 440 3.457012 AGAACTAGGCGCCCCTTTTATTA 59.543 43.478 26.15 5.06 42.87 0.98
440 441 2.241430 AGAACTAGGCGCCCCTTTTATT 59.759 45.455 26.15 8.17 42.87 1.40
441 442 1.844497 AGAACTAGGCGCCCCTTTTAT 59.156 47.619 26.15 4.77 42.87 1.40
442 443 1.282382 AGAACTAGGCGCCCCTTTTA 58.718 50.000 26.15 7.60 42.87 1.52
443 444 1.282382 TAGAACTAGGCGCCCCTTTT 58.718 50.000 26.15 11.70 42.87 2.27
444 445 1.282382 TTAGAACTAGGCGCCCCTTT 58.718 50.000 26.15 13.80 42.87 3.11
445 446 1.282382 TTTAGAACTAGGCGCCCCTT 58.718 50.000 26.15 12.13 42.87 3.95
446 447 1.282382 TTTTAGAACTAGGCGCCCCT 58.718 50.000 26.15 14.92 45.61 4.79
447 448 2.118313 TTTTTAGAACTAGGCGCCCC 57.882 50.000 26.15 7.58 0.00 5.80
463 464 2.041153 CACTTCAGGCGCCCTTTTT 58.959 52.632 26.15 0.00 0.00 1.94
464 465 2.564721 GCACTTCAGGCGCCCTTTT 61.565 57.895 26.15 0.00 0.00 2.27
465 466 2.985847 GCACTTCAGGCGCCCTTT 60.986 61.111 26.15 0.18 0.00 3.11
469 470 3.294493 TTTGGCACTTCAGGCGCC 61.294 61.111 21.89 21.89 46.43 6.53
470 471 2.050077 GTTTGGCACTTCAGGCGC 60.050 61.111 0.00 0.00 36.77 6.53
471 472 0.102120 TTTGTTTGGCACTTCAGGCG 59.898 50.000 0.00 0.00 36.77 5.52
472 473 2.204237 CTTTTGTTTGGCACTTCAGGC 58.796 47.619 0.00 0.00 0.00 4.85
473 474 2.430332 TCCTTTTGTTTGGCACTTCAGG 59.570 45.455 0.00 0.00 0.00 3.86
474 475 3.119173 TGTCCTTTTGTTTGGCACTTCAG 60.119 43.478 0.00 0.00 0.00 3.02
475 476 2.828520 TGTCCTTTTGTTTGGCACTTCA 59.171 40.909 0.00 0.00 0.00 3.02
476 477 3.518634 TGTCCTTTTGTTTGGCACTTC 57.481 42.857 0.00 0.00 0.00 3.01
477 478 3.971245 TTGTCCTTTTGTTTGGCACTT 57.029 38.095 0.00 0.00 0.00 3.16
478 479 4.081198 TCAATTGTCCTTTTGTTTGGCACT 60.081 37.500 5.13 0.00 0.00 4.40
479 480 4.187694 TCAATTGTCCTTTTGTTTGGCAC 58.812 39.130 5.13 0.00 0.00 5.01
480 481 4.478206 TCAATTGTCCTTTTGTTTGGCA 57.522 36.364 5.13 0.00 0.00 4.92
481 482 8.947055 ATATATCAATTGTCCTTTTGTTTGGC 57.053 30.769 5.13 0.00 0.00 4.52
626 636 3.118408 GGTTGTTTTCTTCTTTTGGGGCT 60.118 43.478 0.00 0.00 0.00 5.19
645 655 3.090532 GCGGGGAGGATCAGGGTT 61.091 66.667 0.00 0.00 36.25 4.11
806 1202 4.056584 TCGAGGAGAAGGCCGGGA 62.057 66.667 2.18 0.00 0.00 5.14
834 1364 3.364964 ATGGGGAGAGGGTCGGGA 61.365 66.667 0.00 0.00 0.00 5.14
1259 1856 2.583441 CCACACGGGAGGAAGCAGA 61.583 63.158 0.00 0.00 40.01 4.26
1449 2052 3.450457 AGAAAACATGGCAAAGTTGGTCA 59.550 39.130 9.08 0.00 0.00 4.02
1621 2224 8.336801 TCACGTATGCTCATATATACTGTTCT 57.663 34.615 0.00 0.00 0.00 3.01
1713 2317 8.992835 ATTGAGCATTTTCTTCCTAATGTTTC 57.007 30.769 0.00 0.00 34.88 2.78
1965 2770 6.039829 TCTCTCGAATTTAGCTTGATCTGCTA 59.960 38.462 14.12 14.12 41.46 3.49
2110 2918 1.745087 TGTACCTAAACTCGGCGTAGG 59.255 52.381 16.93 16.93 40.32 3.18
2123 2931 1.473677 CCGTCCACGACAATGTACCTA 59.526 52.381 0.00 0.00 43.02 3.08
2241 3049 9.926158 ATGTCAGATCAATAGATATGTTCTCAC 57.074 33.333 0.00 0.00 42.61 3.51
2750 3580 2.596452 CAACAGCAGACAGTACTACCG 58.404 52.381 0.00 0.00 0.00 4.02
2830 3660 1.033746 ACAGCAGCAGCACACAAACT 61.034 50.000 3.17 0.00 45.49 2.66


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

AutoCloner maintained by Alex Coulton.