Multiple sequence alignment - TraesCS7B01G113000

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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 TraesCS7B01G113000 chr7B 100.000 3476 0 0 1 3476 130748403 130744928 0.000000e+00 6420.0
1 TraesCS7B01G113000 chr7B 86.523 512 46 10 1162 1672 394403791 394404280 3.050000e-150 542.0
2 TraesCS7B01G113000 chr7B 78.049 164 34 2 166 328 167012496 167012658 6.140000e-18 102.0
3 TraesCS7B01G113000 chr7B 100.000 28 0 0 166 193 186973782 186973809 6.000000e-03 52.8
4 TraesCS7B01G113000 chr7D 94.988 2534 89 17 508 3023 166514888 166512375 0.000000e+00 3941.0
5 TraesCS7B01G113000 chr7D 90.313 351 19 4 3138 3476 166510545 166510198 2.460000e-121 446.0
6 TraesCS7B01G113000 chr7D 78.182 220 35 9 87 300 412655961 412655749 1.010000e-25 128.0
7 TraesCS7B01G113000 chr7A 93.528 2534 108 19 653 3155 167905104 167902596 0.000000e+00 3720.0
8 TraesCS7B01G113000 chr7A 88.454 511 58 1 1162 1672 448101467 448101976 1.770000e-172 616.0
9 TraesCS7B01G113000 chr7A 91.030 301 12 4 3167 3452 167902271 167901971 3.250000e-105 392.0
10 TraesCS7B01G113000 chr7A 97.500 80 2 0 580 659 167905260 167905181 1.680000e-28 137.0
11 TraesCS7B01G113000 chr6D 84.053 1367 185 22 1124 2478 383228088 383226743 0.000000e+00 1286.0
12 TraesCS7B01G113000 chr6D 71.857 1066 259 33 1350 2393 429010528 429011574 5.720000e-68 268.0
13 TraesCS7B01G113000 chr6D 77.872 235 45 3 112 344 86658600 86658829 4.680000e-29 139.0
14 TraesCS7B01G113000 chr6D 100.000 31 0 0 15 45 159518063 159518033 1.350000e-04 58.4
15 TraesCS7B01G113000 chr6A 82.892 1473 208 32 1031 2485 525031061 525029615 0.000000e+00 1284.0
16 TraesCS7B01G113000 chr6A 71.684 1063 264 30 1350 2392 574242402 574243447 9.570000e-66 261.0
17 TraesCS7B01G113000 chr6A 91.919 99 8 0 1133 1231 608403357 608403455 4.680000e-29 139.0
18 TraesCS7B01G113000 chr6B 82.517 1470 219 28 1031 2485 573415046 573413600 0.000000e+00 1256.0
19 TraesCS7B01G113000 chr1B 82.556 1330 191 23 1156 2475 645142627 645141329 0.000000e+00 1133.0
20 TraesCS7B01G113000 chr1A 82.057 1332 197 24 1156 2475 559707901 559706600 0.000000e+00 1098.0
21 TraesCS7B01G113000 chr1D 81.811 1325 206 19 1158 2475 467439116 467437820 0.000000e+00 1079.0
22 TraesCS7B01G113000 chr4A 80.299 1137 209 12 1350 2477 600366384 600367514 0.000000e+00 845.0
23 TraesCS7B01G113000 chr4A 79.248 771 125 26 1723 2471 62538734 62539491 4.000000e-139 505.0
24 TraesCS7B01G113000 chr3D 75.236 1058 237 17 1350 2393 553233076 553232030 2.430000e-131 479.0
25 TraesCS7B01G113000 chr3D 93.103 58 4 0 1229 1286 6467704 6467647 6.180000e-13 86.1
26 TraesCS7B01G113000 chr3A 84.277 159 24 1 1132 1290 13814004 13814161 1.670000e-33 154.0
27 TraesCS7B01G113000 chr5D 79.808 208 33 7 121 325 417607121 417607322 3.620000e-30 143.0


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 TraesCS7B01G113000 chr7B 130744928 130748403 3475 True 6420.000000 6420 100.000000 1 3476 1 chr7B.!!$R1 3475
1 TraesCS7B01G113000 chr7D 166510198 166514888 4690 True 2193.500000 3941 92.650500 508 3476 2 chr7D.!!$R2 2968
2 TraesCS7B01G113000 chr7A 167901971 167905260 3289 True 1416.333333 3720 94.019333 580 3452 3 chr7A.!!$R1 2872
3 TraesCS7B01G113000 chr7A 448101467 448101976 509 False 616.000000 616 88.454000 1162 1672 1 chr7A.!!$F1 510
4 TraesCS7B01G113000 chr6D 383226743 383228088 1345 True 1286.000000 1286 84.053000 1124 2478 1 chr6D.!!$R2 1354
5 TraesCS7B01G113000 chr6D 429010528 429011574 1046 False 268.000000 268 71.857000 1350 2393 1 chr6D.!!$F2 1043
6 TraesCS7B01G113000 chr6A 525029615 525031061 1446 True 1284.000000 1284 82.892000 1031 2485 1 chr6A.!!$R1 1454
7 TraesCS7B01G113000 chr6A 574242402 574243447 1045 False 261.000000 261 71.684000 1350 2392 1 chr6A.!!$F1 1042
8 TraesCS7B01G113000 chr6B 573413600 573415046 1446 True 1256.000000 1256 82.517000 1031 2485 1 chr6B.!!$R1 1454
9 TraesCS7B01G113000 chr1B 645141329 645142627 1298 True 1133.000000 1133 82.556000 1156 2475 1 chr1B.!!$R1 1319
10 TraesCS7B01G113000 chr1A 559706600 559707901 1301 True 1098.000000 1098 82.057000 1156 2475 1 chr1A.!!$R1 1319
11 TraesCS7B01G113000 chr1D 467437820 467439116 1296 True 1079.000000 1079 81.811000 1158 2475 1 chr1D.!!$R1 1317
12 TraesCS7B01G113000 chr4A 600366384 600367514 1130 False 845.000000 845 80.299000 1350 2477 1 chr4A.!!$F2 1127
13 TraesCS7B01G113000 chr4A 62538734 62539491 757 False 505.000000 505 79.248000 1723 2471 1 chr4A.!!$F1 748
14 TraesCS7B01G113000 chr3D 553232030 553233076 1046 True 479.000000 479 75.236000 1350 2393 1 chr3D.!!$R2 1043

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
472 473 0.179000 CTGCTGAGAGGGCGGTTATT 59.821 55.0 0.0 0.0 0.0 1.40 F
473 474 0.618458 TGCTGAGAGGGCGGTTATTT 59.382 50.0 0.0 0.0 0.0 1.40 F
717 801 0.784778 GAAACGACGAAGCTGTCCTG 59.215 55.0 0.0 0.0 35.4 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1641 1.202758 ACGACAAGGAAGTCAATGGCA 60.203 47.619 0.00 0.0 38.43 4.92 R
2058 2172 1.291184 TGAATGACAGCGCGAACAGG 61.291 55.000 12.10 0.0 0.00 4.00 R
2583 2734 0.833287 AAGCACACACCAGACTGACT 59.167 50.000 3.32 0.0 0.00 3.41 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
17 18 3.996614 AAATCGCCGTCCTTTGGG 58.003 55.556 0.00 0.00 0.00 4.12
18 19 1.074248 AAATCGCCGTCCTTTGGGT 59.926 52.632 0.00 0.00 0.00 4.51
19 20 0.958876 AAATCGCCGTCCTTTGGGTC 60.959 55.000 0.00 0.00 0.00 4.46
20 21 3.659089 ATCGCCGTCCTTTGGGTCG 62.659 63.158 0.00 0.00 42.22 4.79
43 44 3.017048 CCATTGGGGTTGCTCTAATCA 57.983 47.619 0.00 0.00 0.00 2.57
44 45 3.364549 CCATTGGGGTTGCTCTAATCAA 58.635 45.455 0.00 0.00 0.00 2.57
45 46 3.962718 CCATTGGGGTTGCTCTAATCAAT 59.037 43.478 0.00 0.00 0.00 2.57
46 47 4.406649 CCATTGGGGTTGCTCTAATCAATT 59.593 41.667 0.00 0.00 0.00 2.32
47 48 5.104817 CCATTGGGGTTGCTCTAATCAATTT 60.105 40.000 0.00 0.00 0.00 1.82
48 49 5.404466 TTGGGGTTGCTCTAATCAATTTG 57.596 39.130 0.00 0.00 0.00 2.32
49 50 3.195396 TGGGGTTGCTCTAATCAATTTGC 59.805 43.478 0.00 0.00 0.00 3.68
50 51 3.448660 GGGGTTGCTCTAATCAATTTGCT 59.551 43.478 0.00 0.00 0.00 3.91
51 52 4.440663 GGGGTTGCTCTAATCAATTTGCTC 60.441 45.833 0.00 0.00 0.00 4.26
52 53 4.400567 GGGTTGCTCTAATCAATTTGCTCT 59.599 41.667 0.00 0.00 0.00 4.09
53 54 5.449725 GGGTTGCTCTAATCAATTTGCTCTC 60.450 44.000 0.00 0.00 0.00 3.20
54 55 5.449725 GGTTGCTCTAATCAATTTGCTCTCC 60.450 44.000 0.00 0.00 0.00 3.71
55 56 5.108187 TGCTCTAATCAATTTGCTCTCCT 57.892 39.130 0.00 0.00 0.00 3.69
56 57 4.880120 TGCTCTAATCAATTTGCTCTCCTG 59.120 41.667 0.00 0.00 0.00 3.86
57 58 4.880696 GCTCTAATCAATTTGCTCTCCTGT 59.119 41.667 0.00 0.00 0.00 4.00
58 59 6.051717 GCTCTAATCAATTTGCTCTCCTGTA 58.948 40.000 0.00 0.00 0.00 2.74
59 60 6.018343 GCTCTAATCAATTTGCTCTCCTGTAC 60.018 42.308 0.00 0.00 0.00 2.90
60 61 7.187824 TCTAATCAATTTGCTCTCCTGTACT 57.812 36.000 0.00 0.00 0.00 2.73
61 62 7.624549 TCTAATCAATTTGCTCTCCTGTACTT 58.375 34.615 0.00 0.00 0.00 2.24
62 63 6.749923 AATCAATTTGCTCTCCTGTACTTC 57.250 37.500 0.00 0.00 0.00 3.01
63 64 5.489792 TCAATTTGCTCTCCTGTACTTCT 57.510 39.130 0.00 0.00 0.00 2.85
64 65 6.605471 TCAATTTGCTCTCCTGTACTTCTA 57.395 37.500 0.00 0.00 0.00 2.10
65 66 7.004555 TCAATTTGCTCTCCTGTACTTCTAA 57.995 36.000 0.00 0.00 0.00 2.10
66 67 7.099764 TCAATTTGCTCTCCTGTACTTCTAAG 58.900 38.462 0.00 0.00 0.00 2.18
67 68 5.407407 TTTGCTCTCCTGTACTTCTAAGG 57.593 43.478 0.00 0.00 0.00 2.69
68 69 4.317530 TGCTCTCCTGTACTTCTAAGGA 57.682 45.455 0.00 0.00 37.78 3.36
69 70 4.673968 TGCTCTCCTGTACTTCTAAGGAA 58.326 43.478 0.99 0.00 39.59 3.36
70 71 5.084519 TGCTCTCCTGTACTTCTAAGGAAA 58.915 41.667 0.99 0.00 39.59 3.13
71 72 5.542635 TGCTCTCCTGTACTTCTAAGGAAAA 59.457 40.000 0.99 0.00 39.59 2.29
72 73 6.042781 TGCTCTCCTGTACTTCTAAGGAAAAA 59.957 38.462 0.99 0.00 39.59 1.94
106 107 8.446599 AAACAAGGTACTCCATTATAAATCCG 57.553 34.615 0.00 0.00 38.49 4.18
107 108 7.369551 ACAAGGTACTCCATTATAAATCCGA 57.630 36.000 0.00 0.00 38.49 4.55
108 109 7.215085 ACAAGGTACTCCATTATAAATCCGAC 58.785 38.462 0.00 0.00 38.49 4.79
109 110 6.989155 AGGTACTCCATTATAAATCCGACA 57.011 37.500 0.00 0.00 35.89 4.35
110 111 7.369551 AGGTACTCCATTATAAATCCGACAA 57.630 36.000 0.00 0.00 35.89 3.18
111 112 7.974504 AGGTACTCCATTATAAATCCGACAAT 58.025 34.615 0.00 0.00 35.89 2.71
112 113 8.437575 AGGTACTCCATTATAAATCCGACAATT 58.562 33.333 0.00 0.00 35.89 2.32
113 114 9.063615 GGTACTCCATTATAAATCCGACAATTT 57.936 33.333 0.00 0.00 33.54 1.82
178 179 9.883142 TGTTTTTCATTTAAGGATGACAAGTTT 57.117 25.926 0.00 0.00 35.86 2.66
184 185 9.567776 TCATTTAAGGATGACAAGTTTAGTTGA 57.432 29.630 4.40 0.00 31.35 3.18
185 186 9.612620 CATTTAAGGATGACAAGTTTAGTTGAC 57.387 33.333 4.40 0.00 0.00 3.18
186 187 5.924475 AAGGATGACAAGTTTAGTTGACG 57.076 39.130 4.40 0.00 0.00 4.35
187 188 5.209818 AGGATGACAAGTTTAGTTGACGA 57.790 39.130 4.40 0.00 0.00 4.20
188 189 5.230942 AGGATGACAAGTTTAGTTGACGAG 58.769 41.667 4.40 0.00 0.00 4.18
189 190 4.143094 GGATGACAAGTTTAGTTGACGAGC 60.143 45.833 4.40 0.00 0.00 5.03
190 191 3.787785 TGACAAGTTTAGTTGACGAGCA 58.212 40.909 4.40 0.00 0.00 4.26
191 192 4.377021 TGACAAGTTTAGTTGACGAGCAT 58.623 39.130 4.40 0.00 0.00 3.79
192 193 4.211164 TGACAAGTTTAGTTGACGAGCATG 59.789 41.667 4.40 0.00 0.00 4.06
193 194 4.377021 ACAAGTTTAGTTGACGAGCATGA 58.623 39.130 0.00 0.00 0.00 3.07
194 195 4.997395 ACAAGTTTAGTTGACGAGCATGAT 59.003 37.500 0.00 0.00 0.00 2.45
195 196 6.163476 ACAAGTTTAGTTGACGAGCATGATA 58.837 36.000 0.00 0.00 0.00 2.15
196 197 6.649141 ACAAGTTTAGTTGACGAGCATGATAA 59.351 34.615 0.00 0.00 0.00 1.75
197 198 7.172532 ACAAGTTTAGTTGACGAGCATGATAAA 59.827 33.333 0.00 0.00 0.00 1.40
198 199 7.849804 AGTTTAGTTGACGAGCATGATAAAT 57.150 32.000 0.00 0.00 0.00 1.40
199 200 8.942338 AGTTTAGTTGACGAGCATGATAAATA 57.058 30.769 0.00 0.00 0.00 1.40
200 201 9.547753 AGTTTAGTTGACGAGCATGATAAATAT 57.452 29.630 0.00 0.00 0.00 1.28
201 202 9.586150 GTTTAGTTGACGAGCATGATAAATATG 57.414 33.333 0.00 0.00 0.00 1.78
202 203 8.887036 TTAGTTGACGAGCATGATAAATATGT 57.113 30.769 0.00 0.00 0.00 2.29
203 204 7.413475 AGTTGACGAGCATGATAAATATGTC 57.587 36.000 0.00 0.00 0.00 3.06
204 205 7.212976 AGTTGACGAGCATGATAAATATGTCT 58.787 34.615 0.00 0.00 0.00 3.41
205 206 7.712639 AGTTGACGAGCATGATAAATATGTCTT 59.287 33.333 0.00 0.00 0.00 3.01
206 207 8.978539 GTTGACGAGCATGATAAATATGTCTTA 58.021 33.333 0.00 0.00 0.00 2.10
207 208 8.520835 TGACGAGCATGATAAATATGTCTTAC 57.479 34.615 0.00 0.00 0.00 2.34
208 209 8.360390 TGACGAGCATGATAAATATGTCTTACT 58.640 33.333 0.00 0.00 0.00 2.24
209 210 9.197694 GACGAGCATGATAAATATGTCTTACTT 57.802 33.333 0.00 0.00 0.00 2.24
210 211 9.547753 ACGAGCATGATAAATATGTCTTACTTT 57.452 29.630 0.00 0.00 0.00 2.66
235 236 5.676532 TTTTTGTTAGAAAATCGCCGAGA 57.323 34.783 0.00 0.00 0.00 4.04
236 237 5.873179 TTTTGTTAGAAAATCGCCGAGAT 57.127 34.783 0.00 0.00 42.43 2.75
248 249 6.920569 AATCGCCGAGATTACAAACTAAAT 57.079 33.333 0.00 0.00 46.99 1.40
249 250 6.920569 ATCGCCGAGATTACAAACTAAATT 57.079 33.333 0.00 0.00 35.73 1.82
250 251 6.730960 TCGCCGAGATTACAAACTAAATTT 57.269 33.333 0.00 0.00 0.00 1.82
251 252 7.830940 TCGCCGAGATTACAAACTAAATTTA 57.169 32.000 0.00 0.00 0.00 1.40
252 253 8.428186 TCGCCGAGATTACAAACTAAATTTAT 57.572 30.769 0.00 0.00 0.00 1.40
253 254 8.545420 TCGCCGAGATTACAAACTAAATTTATC 58.455 33.333 0.00 0.00 0.00 1.75
254 255 8.332464 CGCCGAGATTACAAACTAAATTTATCA 58.668 33.333 0.00 0.00 0.00 2.15
263 264 8.841444 ACAAACTAAATTTATCATCATCACGC 57.159 30.769 0.00 0.00 0.00 5.34
264 265 8.677300 ACAAACTAAATTTATCATCATCACGCT 58.323 29.630 0.00 0.00 0.00 5.07
277 278 7.751732 TCATCATCACGCTAATATAAATTGCC 58.248 34.615 0.00 0.00 0.00 4.52
278 279 7.390162 TCATCATCACGCTAATATAAATTGCCA 59.610 33.333 0.00 0.00 0.00 4.92
279 280 6.898041 TCATCACGCTAATATAAATTGCCAC 58.102 36.000 0.00 0.00 0.00 5.01
280 281 6.484977 TCATCACGCTAATATAAATTGCCACA 59.515 34.615 0.00 0.00 0.00 4.17
281 282 6.685527 TCACGCTAATATAAATTGCCACAA 57.314 33.333 0.00 0.00 0.00 3.33
282 283 7.089770 TCACGCTAATATAAATTGCCACAAA 57.910 32.000 0.00 0.00 0.00 2.83
283 284 7.539436 TCACGCTAATATAAATTGCCACAAAA 58.461 30.769 0.00 0.00 0.00 2.44
284 285 8.029522 TCACGCTAATATAAATTGCCACAAAAA 58.970 29.630 0.00 0.00 0.00 1.94
307 308 9.558396 AAAAAGTCAGATTTGCCATTCATAAAA 57.442 25.926 0.00 0.00 0.00 1.52
308 309 9.558396 AAAAGTCAGATTTGCCATTCATAAAAA 57.442 25.926 0.00 0.00 0.00 1.94
309 310 9.729281 AAAGTCAGATTTGCCATTCATAAAAAT 57.271 25.926 0.00 0.00 0.00 1.82
310 311 8.937634 AGTCAGATTTGCCATTCATAAAAATC 57.062 30.769 0.00 0.00 37.46 2.17
311 312 7.983484 AGTCAGATTTGCCATTCATAAAAATCC 59.017 33.333 0.00 0.00 37.76 3.01
312 313 6.979817 TCAGATTTGCCATTCATAAAAATCCG 59.020 34.615 0.00 0.00 37.76 4.18
313 314 6.979817 CAGATTTGCCATTCATAAAAATCCGA 59.020 34.615 0.00 0.00 37.76 4.55
314 315 7.654520 CAGATTTGCCATTCATAAAAATCCGAT 59.345 33.333 0.00 0.00 37.76 4.18
315 316 7.654520 AGATTTGCCATTCATAAAAATCCGATG 59.345 33.333 0.00 0.00 37.76 3.84
316 317 5.850557 TGCCATTCATAAAAATCCGATGT 57.149 34.783 0.00 0.00 0.00 3.06
317 318 6.219417 TGCCATTCATAAAAATCCGATGTT 57.781 33.333 0.00 0.00 0.00 2.71
318 319 7.340122 TGCCATTCATAAAAATCCGATGTTA 57.660 32.000 0.00 0.00 0.00 2.41
319 320 7.424803 TGCCATTCATAAAAATCCGATGTTAG 58.575 34.615 0.00 0.00 0.00 2.34
320 321 7.284261 TGCCATTCATAAAAATCCGATGTTAGA 59.716 33.333 0.00 0.00 0.00 2.10
321 322 8.299570 GCCATTCATAAAAATCCGATGTTAGAT 58.700 33.333 0.00 0.00 0.00 1.98
330 331 8.911247 AAAATCCGATGTTAGATTTTTAGTGC 57.089 30.769 5.18 0.00 45.74 4.40
331 332 7.865706 AATCCGATGTTAGATTTTTAGTGCT 57.134 32.000 0.00 0.00 28.19 4.40
332 333 7.865706 ATCCGATGTTAGATTTTTAGTGCTT 57.134 32.000 0.00 0.00 0.00 3.91
333 334 7.303634 TCCGATGTTAGATTTTTAGTGCTTC 57.696 36.000 0.00 0.00 0.00 3.86
334 335 7.103641 TCCGATGTTAGATTTTTAGTGCTTCT 58.896 34.615 0.00 0.00 0.00 2.85
335 336 7.064609 TCCGATGTTAGATTTTTAGTGCTTCTG 59.935 37.037 0.00 0.00 0.00 3.02
336 337 7.064609 CCGATGTTAGATTTTTAGTGCTTCTGA 59.935 37.037 0.00 0.00 0.00 3.27
337 338 8.443160 CGATGTTAGATTTTTAGTGCTTCTGAA 58.557 33.333 0.00 0.00 0.00 3.02
340 341 9.950680 TGTTAGATTTTTAGTGCTTCTGAAAAG 57.049 29.630 13.68 0.00 42.15 2.27
350 351 9.561069 TTAGTGCTTCTGAAAAGAAATTCTACT 57.439 29.630 0.00 0.00 0.00 2.57
351 352 8.457238 AGTGCTTCTGAAAAGAAATTCTACTT 57.543 30.769 0.00 0.00 0.00 2.24
352 353 8.348507 AGTGCTTCTGAAAAGAAATTCTACTTG 58.651 33.333 0.00 0.00 0.00 3.16
353 354 8.131731 GTGCTTCTGAAAAGAAATTCTACTTGT 58.868 33.333 0.00 0.00 0.00 3.16
354 355 8.686334 TGCTTCTGAAAAGAAATTCTACTTGTT 58.314 29.630 0.00 0.00 0.00 2.83
355 356 9.175060 GCTTCTGAAAAGAAATTCTACTTGTTC 57.825 33.333 0.00 0.00 0.00 3.18
367 368 8.521170 AATTCTACTTGTTCTATTTAAGGGGC 57.479 34.615 0.00 0.00 0.00 5.80
368 369 5.997843 TCTACTTGTTCTATTTAAGGGGCC 58.002 41.667 0.00 0.00 0.00 5.80
369 370 4.668138 ACTTGTTCTATTTAAGGGGCCA 57.332 40.909 4.39 0.00 0.00 5.36
370 371 4.341487 ACTTGTTCTATTTAAGGGGCCAC 58.659 43.478 4.39 0.00 0.00 5.01
371 372 3.375647 TGTTCTATTTAAGGGGCCACC 57.624 47.619 0.00 0.57 40.67 4.61
372 373 2.650322 TGTTCTATTTAAGGGGCCACCA 59.350 45.455 0.00 0.00 43.89 4.17
373 374 3.076182 TGTTCTATTTAAGGGGCCACCAA 59.924 43.478 0.00 0.00 43.89 3.67
374 375 4.264623 TGTTCTATTTAAGGGGCCACCAAT 60.265 41.667 0.00 0.00 43.89 3.16
375 376 3.909732 TCTATTTAAGGGGCCACCAATG 58.090 45.455 0.00 0.00 43.89 2.82
396 397 4.728772 TGGGACATTTGTCTGAATCAACT 58.271 39.130 10.32 0.00 44.20 3.16
397 398 5.139727 TGGGACATTTGTCTGAATCAACTT 58.860 37.500 10.32 0.00 44.20 2.66
398 399 6.303054 TGGGACATTTGTCTGAATCAACTTA 58.697 36.000 10.32 0.00 44.20 2.24
399 400 6.947733 TGGGACATTTGTCTGAATCAACTTAT 59.052 34.615 10.32 0.00 44.20 1.73
400 401 8.106462 TGGGACATTTGTCTGAATCAACTTATA 58.894 33.333 10.32 0.00 44.20 0.98
401 402 8.616076 GGGACATTTGTCTGAATCAACTTATAG 58.384 37.037 10.32 0.00 44.20 1.31
402 403 8.616076 GGACATTTGTCTGAATCAACTTATAGG 58.384 37.037 10.32 0.00 44.20 2.57
403 404 8.511604 ACATTTGTCTGAATCAACTTATAGGG 57.488 34.615 0.00 0.00 0.00 3.53
404 405 7.557719 ACATTTGTCTGAATCAACTTATAGGGG 59.442 37.037 0.00 0.00 0.00 4.79
405 406 5.630415 TGTCTGAATCAACTTATAGGGGG 57.370 43.478 0.00 0.00 0.00 5.40
425 426 6.665992 GGGGGAAAAATCTCTACTTGTTTT 57.334 37.500 0.00 0.00 0.00 2.43
426 427 7.770366 GGGGGAAAAATCTCTACTTGTTTTA 57.230 36.000 0.00 0.00 0.00 1.52
427 428 8.362464 GGGGGAAAAATCTCTACTTGTTTTAT 57.638 34.615 0.00 0.00 0.00 1.40
428 429 9.470399 GGGGGAAAAATCTCTACTTGTTTTATA 57.530 33.333 0.00 0.00 0.00 0.98
457 458 3.567478 AGTTGAAGAACTTGTCCTGCT 57.433 42.857 0.00 0.00 39.56 4.24
458 459 3.209410 AGTTGAAGAACTTGTCCTGCTG 58.791 45.455 0.00 0.00 39.56 4.41
459 460 3.118261 AGTTGAAGAACTTGTCCTGCTGA 60.118 43.478 0.00 0.00 39.56 4.26
460 461 3.117491 TGAAGAACTTGTCCTGCTGAG 57.883 47.619 0.00 0.00 0.00 3.35
461 462 2.700371 TGAAGAACTTGTCCTGCTGAGA 59.300 45.455 0.00 0.00 0.00 3.27
462 463 3.244009 TGAAGAACTTGTCCTGCTGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
463 464 1.622811 AGAACTTGTCCTGCTGAGAGG 59.377 52.381 0.00 0.00 0.00 3.69
464 465 0.689623 AACTTGTCCTGCTGAGAGGG 59.310 55.000 0.00 0.00 33.41 4.30
465 466 1.078567 CTTGTCCTGCTGAGAGGGC 60.079 63.158 0.00 0.00 38.32 5.19
466 467 2.849120 CTTGTCCTGCTGAGAGGGCG 62.849 65.000 0.00 0.00 41.03 6.13
467 468 4.154347 GTCCTGCTGAGAGGGCGG 62.154 72.222 0.00 0.00 33.41 6.13
468 469 4.704103 TCCTGCTGAGAGGGCGGT 62.704 66.667 0.00 0.00 34.56 5.68
469 470 3.710722 CCTGCTGAGAGGGCGGTT 61.711 66.667 0.00 0.00 34.56 4.44
470 471 2.359169 CCTGCTGAGAGGGCGGTTA 61.359 63.158 0.00 0.00 34.56 2.85
471 472 1.690219 CCTGCTGAGAGGGCGGTTAT 61.690 60.000 0.00 0.00 34.56 1.89
472 473 0.179000 CTGCTGAGAGGGCGGTTATT 59.821 55.000 0.00 0.00 0.00 1.40
473 474 0.618458 TGCTGAGAGGGCGGTTATTT 59.382 50.000 0.00 0.00 0.00 1.40
474 475 1.834896 TGCTGAGAGGGCGGTTATTTA 59.165 47.619 0.00 0.00 0.00 1.40
475 476 2.237643 TGCTGAGAGGGCGGTTATTTAA 59.762 45.455 0.00 0.00 0.00 1.52
476 477 3.275999 GCTGAGAGGGCGGTTATTTAAA 58.724 45.455 0.00 0.00 0.00 1.52
477 478 3.883489 GCTGAGAGGGCGGTTATTTAAAT 59.117 43.478 5.89 5.89 0.00 1.40
478 479 5.061179 GCTGAGAGGGCGGTTATTTAAATA 58.939 41.667 3.71 3.71 0.00 1.40
479 480 5.529800 GCTGAGAGGGCGGTTATTTAAATAA 59.470 40.000 15.19 15.19 0.00 1.40
480 481 6.038936 GCTGAGAGGGCGGTTATTTAAATAAA 59.961 38.462 19.67 4.58 33.05 1.40
481 482 7.255486 GCTGAGAGGGCGGTTATTTAAATAAAT 60.255 37.037 19.67 4.05 39.14 1.40
482 483 7.936584 TGAGAGGGCGGTTATTTAAATAAATG 58.063 34.615 19.67 15.82 36.62 2.32
483 484 6.745116 AGAGGGCGGTTATTTAAATAAATGC 58.255 36.000 24.16 24.16 36.62 3.56
484 485 5.849510 AGGGCGGTTATTTAAATAAATGCC 58.150 37.500 32.51 32.51 44.49 4.40
485 486 5.364157 AGGGCGGTTATTTAAATAAATGCCA 59.636 36.000 36.05 14.85 45.66 4.92
486 487 6.049790 GGGCGGTTATTTAAATAAATGCCAA 58.950 36.000 36.05 15.58 45.66 4.52
487 488 6.201997 GGGCGGTTATTTAAATAAATGCCAAG 59.798 38.462 36.05 20.32 45.66 3.61
488 489 6.981559 GGCGGTTATTTAAATAAATGCCAAGA 59.018 34.615 33.76 11.04 44.54 3.02
489 490 7.169140 GGCGGTTATTTAAATAAATGCCAAGAG 59.831 37.037 33.76 18.00 44.54 2.85
490 491 7.169140 GCGGTTATTTAAATAAATGCCAAGAGG 59.831 37.037 22.87 11.01 36.62 3.69
491 492 7.651704 CGGTTATTTAAATAAATGCCAAGAGGG 59.348 37.037 19.67 3.30 36.62 4.30
492 493 7.441157 GGTTATTTAAATAAATGCCAAGAGGGC 59.559 37.037 19.67 0.00 46.19 5.19
501 502 3.948735 CCAAGAGGGCGGTTCTAAA 57.051 52.632 0.00 0.00 0.00 1.85
502 503 2.194201 CCAAGAGGGCGGTTCTAAAA 57.806 50.000 0.00 0.00 0.00 1.52
503 504 2.510613 CCAAGAGGGCGGTTCTAAAAA 58.489 47.619 0.00 0.00 0.00 1.94
531 532 1.075374 ACTTGCCCTGCTGTATTTCCA 59.925 47.619 0.00 0.00 0.00 3.53
534 535 2.603021 TGCCCTGCTGTATTTCCAAAA 58.397 42.857 0.00 0.00 0.00 2.44
535 536 2.562298 TGCCCTGCTGTATTTCCAAAAG 59.438 45.455 0.00 0.00 0.00 2.27
536 537 2.825532 GCCCTGCTGTATTTCCAAAAGA 59.174 45.455 0.00 0.00 0.00 2.52
537 538 3.258123 GCCCTGCTGTATTTCCAAAAGAA 59.742 43.478 0.00 0.00 0.00 2.52
538 539 4.081476 GCCCTGCTGTATTTCCAAAAGAAT 60.081 41.667 0.00 0.00 33.44 2.40
539 540 5.413499 CCCTGCTGTATTTCCAAAAGAATG 58.587 41.667 0.00 0.00 33.44 2.67
540 541 5.413499 CCTGCTGTATTTCCAAAAGAATGG 58.587 41.667 0.00 0.00 42.12 3.16
559 560 9.617523 AAGAATGGAAAAATGATCTGTTTGTTT 57.382 25.926 0.00 0.00 0.00 2.83
572 573 9.605955 TGATCTGTTTGTTTTATTTACATGTCG 57.394 29.630 0.00 0.00 0.00 4.35
616 617 3.306364 CCATGTTCCCCGAGATCTATCAC 60.306 52.174 0.00 0.00 0.00 3.06
684 768 2.879103 AGTGACACTAAACATGGGGG 57.121 50.000 6.24 0.00 0.00 5.40
717 801 0.784778 GAAACGACGAAGCTGTCCTG 59.215 55.000 0.00 0.00 35.40 3.86
728 812 1.908793 CTGTCCTGTCACCGAGGGT 60.909 63.158 0.00 0.00 35.62 4.34
840 924 2.479837 CTGTGCTCGTAAAGACCAACA 58.520 47.619 0.00 0.00 0.00 3.33
914 998 2.037251 CCTTCTCCCGAACTCAACTCAA 59.963 50.000 0.00 0.00 0.00 3.02
921 1005 2.550978 CGAACTCAACTCAACACCAGT 58.449 47.619 0.00 0.00 0.00 4.00
1024 1114 2.997315 CCTCGTCACCCCAGCTCA 60.997 66.667 0.00 0.00 0.00 4.26
1498 1603 1.298713 CTCGTCATCTTCTCCGCCG 60.299 63.158 0.00 0.00 0.00 6.46
1551 1656 1.683011 CCCGATGCCATTGACTTCCTT 60.683 52.381 0.00 0.00 0.00 3.36
1779 1884 1.337074 CCCAACTACTACGTCGGCAAA 60.337 52.381 0.00 0.00 0.00 3.68
2073 2187 2.049156 CTCCTGTTCGCGCTGTCA 60.049 61.111 5.56 0.10 0.00 3.58
2527 2668 2.887783 TGTCTCTCTCTGTCGCTTTCTT 59.112 45.455 0.00 0.00 0.00 2.52
2532 2673 3.057174 TCTCTCTGTCGCTTTCTTTCTCC 60.057 47.826 0.00 0.00 0.00 3.71
2579 2730 2.659428 GCCCCATGCATTTCTTCTACT 58.341 47.619 0.00 0.00 40.77 2.57
2580 2731 3.820557 GCCCCATGCATTTCTTCTACTA 58.179 45.455 0.00 0.00 40.77 1.82
2581 2732 4.401925 GCCCCATGCATTTCTTCTACTAT 58.598 43.478 0.00 0.00 40.77 2.12
2583 2734 5.624159 CCCCATGCATTTCTTCTACTATCA 58.376 41.667 0.00 0.00 0.00 2.15
2600 2751 0.104855 TCAGTCAGTCTGGTGTGTGC 59.895 55.000 0.00 0.00 43.76 4.57
3023 3180 6.584942 TGTACTGCTACGAGTTTGACAATAAG 59.415 38.462 0.00 0.00 0.00 1.73
3125 5051 9.862371 ATTTACTAGCTGCACATATACTACATC 57.138 33.333 1.02 0.00 0.00 3.06
3126 5052 6.901081 ACTAGCTGCACATATACTACATCA 57.099 37.500 1.02 0.00 0.00 3.07
3128 5054 5.798125 AGCTGCACATATACTACATCACT 57.202 39.130 1.02 0.00 0.00 3.41
3129 5055 5.536260 AGCTGCACATATACTACATCACTG 58.464 41.667 1.02 0.00 0.00 3.66
3130 5056 4.151335 GCTGCACATATACTACATCACTGC 59.849 45.833 0.00 0.00 0.00 4.40
3131 5057 5.275067 TGCACATATACTACATCACTGCA 57.725 39.130 0.00 0.00 0.00 4.41
3132 5058 5.857268 TGCACATATACTACATCACTGCAT 58.143 37.500 0.00 0.00 0.00 3.96
3133 5059 5.697633 TGCACATATACTACATCACTGCATG 59.302 40.000 0.00 0.00 0.00 4.06
3134 5060 5.928264 GCACATATACTACATCACTGCATGA 59.072 40.000 0.00 0.00 43.13 3.07
3136 5062 7.201504 GCACATATACTACATCACTGCATGATC 60.202 40.741 0.00 0.00 45.52 2.92
3223 5462 2.556287 GTGCGCTTCCAAACTCCG 59.444 61.111 9.73 0.00 0.00 4.63
3238 5488 2.283809 CCGACCCATCCCTCTCCT 59.716 66.667 0.00 0.00 0.00 3.69
3247 5497 0.178909 ATCCCTCTCCTGCGATGGAT 60.179 55.000 0.00 0.00 34.74 3.41
3248 5498 0.482887 TCCCTCTCCTGCGATGGATA 59.517 55.000 0.00 0.00 35.30 2.59
3317 5567 2.683933 GAAGAGTGGGAGGGCGGA 60.684 66.667 0.00 0.00 0.00 5.54
3436 5690 2.191128 ATCTTGCCAGTTTCGCTCTT 57.809 45.000 0.00 0.00 0.00 2.85
3444 5698 3.134458 CCAGTTTCGCTCTTGTTCTTCT 58.866 45.455 0.00 0.00 0.00 2.85
3452 5706 2.135933 CTCTTGTTCTTCTTCGCCGTT 58.864 47.619 0.00 0.00 0.00 4.44
3453 5707 2.132762 TCTTGTTCTTCTTCGCCGTTC 58.867 47.619 0.00 0.00 0.00 3.95
3454 5708 0.856641 TTGTTCTTCTTCGCCGTTCG 59.143 50.000 0.00 0.00 40.15 3.95
3455 5709 1.130009 GTTCTTCTTCGCCGTTCGC 59.870 57.895 0.00 0.00 38.27 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.958876 GACCCAAAGGACGGCGATTT 60.959 55.000 16.62 8.82 36.73 2.17
1 2 1.376812 GACCCAAAGGACGGCGATT 60.377 57.895 16.62 1.89 36.73 3.34
2 3 2.267961 GACCCAAAGGACGGCGAT 59.732 61.111 16.62 0.00 36.73 4.58
3 4 4.367023 CGACCCAAAGGACGGCGA 62.367 66.667 16.62 0.00 45.86 5.54
23 24 3.017048 TGATTAGAGCAACCCCAATGG 57.983 47.619 0.00 0.00 41.37 3.16
24 25 5.603170 AATTGATTAGAGCAACCCCAATG 57.397 39.130 0.00 0.00 0.00 2.82
25 26 5.627503 GCAAATTGATTAGAGCAACCCCAAT 60.628 40.000 0.00 0.00 0.00 3.16
26 27 4.322650 GCAAATTGATTAGAGCAACCCCAA 60.323 41.667 0.00 0.00 0.00 4.12
27 28 3.195396 GCAAATTGATTAGAGCAACCCCA 59.805 43.478 0.00 0.00 0.00 4.96
28 29 3.448660 AGCAAATTGATTAGAGCAACCCC 59.551 43.478 0.00 0.00 0.00 4.95
29 30 4.400567 AGAGCAAATTGATTAGAGCAACCC 59.599 41.667 0.00 0.00 0.00 4.11
30 31 5.449725 GGAGAGCAAATTGATTAGAGCAACC 60.450 44.000 0.00 0.00 0.00 3.77
31 32 5.356470 AGGAGAGCAAATTGATTAGAGCAAC 59.644 40.000 0.00 0.00 0.00 4.17
32 33 5.356190 CAGGAGAGCAAATTGATTAGAGCAA 59.644 40.000 0.00 0.00 0.00 3.91
33 34 4.880120 CAGGAGAGCAAATTGATTAGAGCA 59.120 41.667 0.00 0.00 0.00 4.26
34 35 4.880696 ACAGGAGAGCAAATTGATTAGAGC 59.119 41.667 0.00 0.00 0.00 4.09
35 36 7.271511 AGTACAGGAGAGCAAATTGATTAGAG 58.728 38.462 0.00 0.00 0.00 2.43
36 37 7.187824 AGTACAGGAGAGCAAATTGATTAGA 57.812 36.000 0.00 0.00 0.00 2.10
37 38 7.768120 AGAAGTACAGGAGAGCAAATTGATTAG 59.232 37.037 0.00 0.00 0.00 1.73
38 39 7.624549 AGAAGTACAGGAGAGCAAATTGATTA 58.375 34.615 0.00 0.00 0.00 1.75
39 40 6.479884 AGAAGTACAGGAGAGCAAATTGATT 58.520 36.000 0.00 0.00 0.00 2.57
40 41 6.059787 AGAAGTACAGGAGAGCAAATTGAT 57.940 37.500 0.00 0.00 0.00 2.57
41 42 5.489792 AGAAGTACAGGAGAGCAAATTGA 57.510 39.130 0.00 0.00 0.00 2.57
42 43 6.314896 CCTTAGAAGTACAGGAGAGCAAATTG 59.685 42.308 0.00 0.00 0.00 2.32
43 44 6.213600 TCCTTAGAAGTACAGGAGAGCAAATT 59.786 38.462 0.00 0.00 32.61 1.82
44 45 5.721960 TCCTTAGAAGTACAGGAGAGCAAAT 59.278 40.000 0.00 0.00 32.61 2.32
45 46 5.084519 TCCTTAGAAGTACAGGAGAGCAAA 58.915 41.667 0.00 0.00 32.61 3.68
46 47 4.673968 TCCTTAGAAGTACAGGAGAGCAA 58.326 43.478 0.00 0.00 32.61 3.91
47 48 4.317530 TCCTTAGAAGTACAGGAGAGCA 57.682 45.455 0.00 0.00 32.61 4.26
48 49 5.662674 TTTCCTTAGAAGTACAGGAGAGC 57.337 43.478 0.00 0.00 38.00 4.09
80 81 8.899771 CGGATTTATAATGGAGTACCTTGTTTT 58.100 33.333 0.00 0.00 37.04 2.43
81 82 8.269317 TCGGATTTATAATGGAGTACCTTGTTT 58.731 33.333 0.00 0.00 37.04 2.83
82 83 7.713942 GTCGGATTTATAATGGAGTACCTTGTT 59.286 37.037 0.00 0.00 37.04 2.83
83 84 7.147620 TGTCGGATTTATAATGGAGTACCTTGT 60.148 37.037 0.00 0.00 37.04 3.16
84 85 7.214381 TGTCGGATTTATAATGGAGTACCTTG 58.786 38.462 0.00 0.00 37.04 3.61
85 86 7.369551 TGTCGGATTTATAATGGAGTACCTT 57.630 36.000 0.00 0.00 37.04 3.50
86 87 6.989155 TGTCGGATTTATAATGGAGTACCT 57.011 37.500 0.00 0.00 37.04 3.08
87 88 8.617290 AATTGTCGGATTTATAATGGAGTACC 57.383 34.615 0.00 0.00 0.00 3.34
152 153 9.883142 AAACTTGTCATCCTTAAATGAAAAACA 57.117 25.926 0.00 0.00 37.41 2.83
158 159 9.567776 TCAACTAAACTTGTCATCCTTAAATGA 57.432 29.630 0.00 0.00 33.30 2.57
159 160 9.612620 GTCAACTAAACTTGTCATCCTTAAATG 57.387 33.333 0.00 0.00 0.00 2.32
160 161 8.504005 CGTCAACTAAACTTGTCATCCTTAAAT 58.496 33.333 0.00 0.00 0.00 1.40
161 162 7.711772 TCGTCAACTAAACTTGTCATCCTTAAA 59.288 33.333 0.00 0.00 0.00 1.52
162 163 7.211573 TCGTCAACTAAACTTGTCATCCTTAA 58.788 34.615 0.00 0.00 0.00 1.85
163 164 6.751157 TCGTCAACTAAACTTGTCATCCTTA 58.249 36.000 0.00 0.00 0.00 2.69
164 165 5.607477 TCGTCAACTAAACTTGTCATCCTT 58.393 37.500 0.00 0.00 0.00 3.36
165 166 5.209818 TCGTCAACTAAACTTGTCATCCT 57.790 39.130 0.00 0.00 0.00 3.24
166 167 4.143094 GCTCGTCAACTAAACTTGTCATCC 60.143 45.833 0.00 0.00 0.00 3.51
167 168 4.447724 TGCTCGTCAACTAAACTTGTCATC 59.552 41.667 0.00 0.00 0.00 2.92
168 169 4.377021 TGCTCGTCAACTAAACTTGTCAT 58.623 39.130 0.00 0.00 0.00 3.06
169 170 3.787785 TGCTCGTCAACTAAACTTGTCA 58.212 40.909 0.00 0.00 0.00 3.58
170 171 4.447724 TCATGCTCGTCAACTAAACTTGTC 59.552 41.667 0.00 0.00 0.00 3.18
171 172 4.377021 TCATGCTCGTCAACTAAACTTGT 58.623 39.130 0.00 0.00 0.00 3.16
172 173 4.990543 TCATGCTCGTCAACTAAACTTG 57.009 40.909 0.00 0.00 0.00 3.16
173 174 7.667043 TTTATCATGCTCGTCAACTAAACTT 57.333 32.000 0.00 0.00 0.00 2.66
174 175 7.849804 ATTTATCATGCTCGTCAACTAAACT 57.150 32.000 0.00 0.00 0.00 2.66
175 176 9.586150 CATATTTATCATGCTCGTCAACTAAAC 57.414 33.333 0.00 0.00 0.00 2.01
176 177 9.325198 ACATATTTATCATGCTCGTCAACTAAA 57.675 29.630 0.00 0.00 0.00 1.85
177 178 8.887036 ACATATTTATCATGCTCGTCAACTAA 57.113 30.769 0.00 0.00 0.00 2.24
178 179 8.360390 AGACATATTTATCATGCTCGTCAACTA 58.640 33.333 0.00 0.00 0.00 2.24
179 180 7.212976 AGACATATTTATCATGCTCGTCAACT 58.787 34.615 0.00 0.00 0.00 3.16
180 181 7.413475 AGACATATTTATCATGCTCGTCAAC 57.587 36.000 0.00 0.00 0.00 3.18
181 182 8.978539 GTAAGACATATTTATCATGCTCGTCAA 58.021 33.333 0.00 0.00 0.00 3.18
182 183 8.360390 AGTAAGACATATTTATCATGCTCGTCA 58.640 33.333 0.00 0.00 0.00 4.35
183 184 8.749841 AGTAAGACATATTTATCATGCTCGTC 57.250 34.615 0.00 0.00 0.00 4.20
184 185 9.547753 AAAGTAAGACATATTTATCATGCTCGT 57.452 29.630 0.00 0.00 0.00 4.18
213 214 5.676532 TCTCGGCGATTTTCTAACAAAAA 57.323 34.783 11.27 0.00 32.99 1.94
214 215 5.873179 ATCTCGGCGATTTTCTAACAAAA 57.127 34.783 11.27 0.00 0.00 2.44
215 216 5.873179 AATCTCGGCGATTTTCTAACAAA 57.127 34.783 11.27 0.00 39.28 2.83
216 217 5.870433 TGTAATCTCGGCGATTTTCTAACAA 59.130 36.000 11.27 0.00 42.26 2.83
217 218 5.412640 TGTAATCTCGGCGATTTTCTAACA 58.587 37.500 11.27 6.26 42.26 2.41
218 219 5.961395 TGTAATCTCGGCGATTTTCTAAC 57.039 39.130 11.27 3.58 42.26 2.34
219 220 6.592607 AGTTTGTAATCTCGGCGATTTTCTAA 59.407 34.615 11.27 6.15 42.26 2.10
220 221 6.103997 AGTTTGTAATCTCGGCGATTTTCTA 58.896 36.000 11.27 0.00 42.26 2.10
221 222 4.935808 AGTTTGTAATCTCGGCGATTTTCT 59.064 37.500 11.27 0.00 42.26 2.52
222 223 5.217895 AGTTTGTAATCTCGGCGATTTTC 57.782 39.130 11.27 6.24 42.26 2.29
223 224 6.730960 TTAGTTTGTAATCTCGGCGATTTT 57.269 33.333 11.27 9.87 42.26 1.82
224 225 6.730960 TTTAGTTTGTAATCTCGGCGATTT 57.269 33.333 11.27 10.26 42.26 2.17
225 226 6.920569 ATTTAGTTTGTAATCTCGGCGATT 57.079 33.333 11.27 5.36 44.35 3.34
226 227 6.920569 AATTTAGTTTGTAATCTCGGCGAT 57.079 33.333 11.27 0.00 0.00 4.58
227 228 6.730960 AAATTTAGTTTGTAATCTCGGCGA 57.269 33.333 10.14 10.14 0.00 5.54
228 229 8.332464 TGATAAATTTAGTTTGTAATCTCGGCG 58.668 33.333 0.00 0.00 0.00 6.46
237 238 9.929722 GCGTGATGATGATAAATTTAGTTTGTA 57.070 29.630 3.94 0.00 0.00 2.41
238 239 8.677300 AGCGTGATGATGATAAATTTAGTTTGT 58.323 29.630 3.94 0.00 0.00 2.83
251 252 8.400947 GGCAATTTATATTAGCGTGATGATGAT 58.599 33.333 0.00 0.00 0.00 2.45
252 253 7.390162 TGGCAATTTATATTAGCGTGATGATGA 59.610 33.333 0.00 0.00 0.00 2.92
253 254 7.482743 GTGGCAATTTATATTAGCGTGATGATG 59.517 37.037 0.00 0.00 0.00 3.07
254 255 7.174772 TGTGGCAATTTATATTAGCGTGATGAT 59.825 33.333 0.00 0.00 0.00 2.45
255 256 6.484977 TGTGGCAATTTATATTAGCGTGATGA 59.515 34.615 0.00 0.00 0.00 2.92
256 257 6.667370 TGTGGCAATTTATATTAGCGTGATG 58.333 36.000 0.00 0.00 0.00 3.07
257 258 6.875948 TGTGGCAATTTATATTAGCGTGAT 57.124 33.333 0.00 0.00 0.00 3.06
258 259 6.685527 TTGTGGCAATTTATATTAGCGTGA 57.314 33.333 0.00 0.00 0.00 4.35
259 260 7.748031 TTTTGTGGCAATTTATATTAGCGTG 57.252 32.000 0.00 0.00 0.00 5.34
281 282 9.558396 TTTTATGAATGGCAAATCTGACTTTTT 57.442 25.926 0.00 0.00 28.28 1.94
282 283 9.558396 TTTTTATGAATGGCAAATCTGACTTTT 57.442 25.926 0.00 0.00 28.28 2.27
283 284 9.729281 ATTTTTATGAATGGCAAATCTGACTTT 57.271 25.926 0.00 0.00 30.75 2.66
284 285 9.374838 GATTTTTATGAATGGCAAATCTGACTT 57.625 29.630 0.00 0.00 33.08 3.01
285 286 7.983484 GGATTTTTATGAATGGCAAATCTGACT 59.017 33.333 0.00 0.00 35.21 3.41
286 287 7.043192 CGGATTTTTATGAATGGCAAATCTGAC 60.043 37.037 7.12 0.00 40.46 3.51
287 288 6.979817 CGGATTTTTATGAATGGCAAATCTGA 59.020 34.615 7.12 0.00 40.46 3.27
288 289 6.979817 TCGGATTTTTATGAATGGCAAATCTG 59.020 34.615 0.00 0.00 39.82 2.90
289 290 7.111247 TCGGATTTTTATGAATGGCAAATCT 57.889 32.000 0.00 0.00 35.21 2.40
290 291 7.439056 ACATCGGATTTTTATGAATGGCAAATC 59.561 33.333 0.00 0.00 34.44 2.17
291 292 7.274447 ACATCGGATTTTTATGAATGGCAAAT 58.726 30.769 0.00 0.00 0.00 2.32
292 293 6.638610 ACATCGGATTTTTATGAATGGCAAA 58.361 32.000 0.00 0.00 0.00 3.68
293 294 6.219417 ACATCGGATTTTTATGAATGGCAA 57.781 33.333 0.00 0.00 0.00 4.52
294 295 5.850557 ACATCGGATTTTTATGAATGGCA 57.149 34.783 0.00 0.00 0.00 4.92
295 296 7.648142 TCTAACATCGGATTTTTATGAATGGC 58.352 34.615 0.00 0.00 0.00 4.40
306 307 8.281212 AGCACTAAAAATCTAACATCGGATTT 57.719 30.769 0.00 0.00 41.92 2.17
307 308 7.865706 AGCACTAAAAATCTAACATCGGATT 57.134 32.000 0.00 0.00 34.14 3.01
308 309 7.770897 AGAAGCACTAAAAATCTAACATCGGAT 59.229 33.333 0.00 0.00 0.00 4.18
309 310 7.064609 CAGAAGCACTAAAAATCTAACATCGGA 59.935 37.037 0.00 0.00 0.00 4.55
310 311 7.064609 TCAGAAGCACTAAAAATCTAACATCGG 59.935 37.037 0.00 0.00 0.00 4.18
311 312 7.963981 TCAGAAGCACTAAAAATCTAACATCG 58.036 34.615 0.00 0.00 0.00 3.84
314 315 9.950680 CTTTTCAGAAGCACTAAAAATCTAACA 57.049 29.630 0.00 0.00 0.00 2.41
324 325 9.561069 AGTAGAATTTCTTTTCAGAAGCACTAA 57.439 29.630 3.86 0.00 40.28 2.24
325 326 9.561069 AAGTAGAATTTCTTTTCAGAAGCACTA 57.439 29.630 3.86 0.00 40.28 2.74
326 327 8.348507 CAAGTAGAATTTCTTTTCAGAAGCACT 58.651 33.333 3.86 0.00 40.28 4.40
327 328 8.131731 ACAAGTAGAATTTCTTTTCAGAAGCAC 58.868 33.333 3.86 0.00 40.28 4.40
328 329 8.225603 ACAAGTAGAATTTCTTTTCAGAAGCA 57.774 30.769 3.86 0.00 40.28 3.91
329 330 9.175060 GAACAAGTAGAATTTCTTTTCAGAAGC 57.825 33.333 3.86 0.00 40.28 3.86
341 342 8.967918 GCCCCTTAAATAGAACAAGTAGAATTT 58.032 33.333 0.00 0.00 0.00 1.82
342 343 7.560262 GGCCCCTTAAATAGAACAAGTAGAATT 59.440 37.037 0.00 0.00 0.00 2.17
343 344 7.061054 GGCCCCTTAAATAGAACAAGTAGAAT 58.939 38.462 0.00 0.00 0.00 2.40
344 345 6.012333 TGGCCCCTTAAATAGAACAAGTAGAA 60.012 38.462 0.00 0.00 0.00 2.10
345 346 5.489637 TGGCCCCTTAAATAGAACAAGTAGA 59.510 40.000 0.00 0.00 0.00 2.59
346 347 5.589050 GTGGCCCCTTAAATAGAACAAGTAG 59.411 44.000 0.00 0.00 0.00 2.57
347 348 5.503002 GTGGCCCCTTAAATAGAACAAGTA 58.497 41.667 0.00 0.00 0.00 2.24
348 349 4.341487 GTGGCCCCTTAAATAGAACAAGT 58.659 43.478 0.00 0.00 0.00 3.16
349 350 3.699538 GGTGGCCCCTTAAATAGAACAAG 59.300 47.826 0.00 0.00 0.00 3.16
350 351 3.076182 TGGTGGCCCCTTAAATAGAACAA 59.924 43.478 0.00 0.00 0.00 2.83
351 352 2.650322 TGGTGGCCCCTTAAATAGAACA 59.350 45.455 0.00 0.00 0.00 3.18
352 353 3.375647 TGGTGGCCCCTTAAATAGAAC 57.624 47.619 0.00 0.00 0.00 3.01
353 354 4.285863 CATTGGTGGCCCCTTAAATAGAA 58.714 43.478 0.00 0.00 0.00 2.10
354 355 3.373658 CCATTGGTGGCCCCTTAAATAGA 60.374 47.826 0.00 0.00 39.01 1.98
355 356 2.965147 CCATTGGTGGCCCCTTAAATAG 59.035 50.000 0.00 0.00 39.01 1.73
356 357 2.359781 CCCATTGGTGGCCCCTTAAATA 60.360 50.000 0.00 0.00 44.62 1.40
357 358 1.624949 CCCATTGGTGGCCCCTTAAAT 60.625 52.381 0.00 0.00 44.62 1.40
358 359 0.252467 CCCATTGGTGGCCCCTTAAA 60.252 55.000 0.00 0.00 44.62 1.52
359 360 1.149782 TCCCATTGGTGGCCCCTTAA 61.150 55.000 0.00 0.00 44.62 1.85
360 361 1.545173 TCCCATTGGTGGCCCCTTA 60.545 57.895 0.00 0.00 44.62 2.69
361 362 2.868566 TCCCATTGGTGGCCCCTT 60.869 61.111 0.00 0.00 44.62 3.95
362 363 3.672503 GTCCCATTGGTGGCCCCT 61.673 66.667 0.00 0.00 44.62 4.79
363 364 2.820899 AATGTCCCATTGGTGGCCCC 62.821 60.000 0.00 0.85 44.62 5.80
364 365 0.909133 AAATGTCCCATTGGTGGCCC 60.909 55.000 0.00 0.00 44.62 5.80
365 366 0.249955 CAAATGTCCCATTGGTGGCC 59.750 55.000 0.00 0.00 44.62 5.36
366 367 0.975887 ACAAATGTCCCATTGGTGGC 59.024 50.000 1.20 0.00 44.62 5.01
367 368 2.231964 CAGACAAATGTCCCATTGGTGG 59.768 50.000 9.84 0.00 45.85 4.61
368 369 3.156293 TCAGACAAATGTCCCATTGGTG 58.844 45.455 9.84 0.87 45.85 4.17
369 370 3.524095 TCAGACAAATGTCCCATTGGT 57.476 42.857 9.84 0.00 45.85 3.67
370 371 4.463539 TGATTCAGACAAATGTCCCATTGG 59.536 41.667 9.84 0.00 45.85 3.16
371 372 5.648178 TGATTCAGACAAATGTCCCATTG 57.352 39.130 9.84 2.54 45.85 2.82
372 373 5.776716 AGTTGATTCAGACAAATGTCCCATT 59.223 36.000 9.84 0.00 45.85 3.16
373 374 5.327732 AGTTGATTCAGACAAATGTCCCAT 58.672 37.500 9.84 0.40 45.85 4.00
374 375 4.728772 AGTTGATTCAGACAAATGTCCCA 58.271 39.130 9.84 0.00 45.85 4.37
375 376 5.712152 AAGTTGATTCAGACAAATGTCCC 57.288 39.130 9.84 0.00 45.85 4.46
376 377 8.616076 CCTATAAGTTGATTCAGACAAATGTCC 58.384 37.037 9.84 0.00 45.85 4.02
377 378 8.616076 CCCTATAAGTTGATTCAGACAAATGTC 58.384 37.037 5.40 5.40 45.08 3.06
378 379 7.557719 CCCCTATAAGTTGATTCAGACAAATGT 59.442 37.037 0.00 0.00 0.00 2.71
379 380 7.013655 CCCCCTATAAGTTGATTCAGACAAATG 59.986 40.741 0.00 0.00 0.00 2.32
380 381 7.062957 CCCCCTATAAGTTGATTCAGACAAAT 58.937 38.462 0.00 0.00 0.00 2.32
381 382 6.423182 CCCCCTATAAGTTGATTCAGACAAA 58.577 40.000 0.00 0.00 0.00 2.83
382 383 6.001449 CCCCCTATAAGTTGATTCAGACAA 57.999 41.667 0.00 0.00 0.00 3.18
383 384 5.630415 CCCCCTATAAGTTGATTCAGACA 57.370 43.478 0.00 0.00 0.00 3.41
402 403 6.665992 AAAACAAGTAGAGATTTTTCCCCC 57.334 37.500 0.00 0.00 0.00 5.40
437 438 3.118261 TCAGCAGGACAAGTTCTTCAACT 60.118 43.478 0.00 0.00 45.43 3.16
438 439 3.206150 TCAGCAGGACAAGTTCTTCAAC 58.794 45.455 0.00 0.00 0.00 3.18
439 440 3.134623 TCTCAGCAGGACAAGTTCTTCAA 59.865 43.478 0.00 0.00 0.00 2.69
440 441 2.700371 TCTCAGCAGGACAAGTTCTTCA 59.300 45.455 0.00 0.00 0.00 3.02
441 442 3.324993 CTCTCAGCAGGACAAGTTCTTC 58.675 50.000 0.00 0.00 0.00 2.87
442 443 2.038295 CCTCTCAGCAGGACAAGTTCTT 59.962 50.000 0.00 0.00 35.20 2.52
443 444 1.622811 CCTCTCAGCAGGACAAGTTCT 59.377 52.381 0.00 0.00 35.20 3.01
444 445 1.338579 CCCTCTCAGCAGGACAAGTTC 60.339 57.143 0.00 0.00 35.20 3.01
445 446 0.689623 CCCTCTCAGCAGGACAAGTT 59.310 55.000 0.00 0.00 35.20 2.66
446 447 1.835927 GCCCTCTCAGCAGGACAAGT 61.836 60.000 0.00 0.00 35.20 3.16
447 448 1.078567 GCCCTCTCAGCAGGACAAG 60.079 63.158 0.00 0.00 35.20 3.16
448 449 2.947532 CGCCCTCTCAGCAGGACAA 61.948 63.158 0.00 0.00 35.20 3.18
449 450 3.385384 CGCCCTCTCAGCAGGACA 61.385 66.667 0.00 0.00 35.20 4.02
450 451 4.154347 CCGCCCTCTCAGCAGGAC 62.154 72.222 0.00 0.00 35.20 3.85
451 452 2.798445 TAACCGCCCTCTCAGCAGGA 62.798 60.000 0.00 0.00 35.20 3.86
452 453 1.690219 ATAACCGCCCTCTCAGCAGG 61.690 60.000 0.00 0.00 0.00 4.85
453 454 0.179000 AATAACCGCCCTCTCAGCAG 59.821 55.000 0.00 0.00 0.00 4.24
454 455 0.618458 AAATAACCGCCCTCTCAGCA 59.382 50.000 0.00 0.00 0.00 4.41
455 456 2.614829 TAAATAACCGCCCTCTCAGC 57.385 50.000 0.00 0.00 0.00 4.26
456 457 7.562454 TTTATTTAAATAACCGCCCTCTCAG 57.438 36.000 18.16 0.00 31.03 3.35
457 458 7.469456 GCATTTATTTAAATAACCGCCCTCTCA 60.469 37.037 18.16 2.87 34.36 3.27
458 459 6.861572 GCATTTATTTAAATAACCGCCCTCTC 59.138 38.462 18.16 0.64 34.36 3.20
459 460 6.239204 GGCATTTATTTAAATAACCGCCCTCT 60.239 38.462 29.48 8.13 39.86 3.69
460 461 5.924254 GGCATTTATTTAAATAACCGCCCTC 59.076 40.000 29.48 16.57 39.86 4.30
461 462 5.364157 TGGCATTTATTTAAATAACCGCCCT 59.636 36.000 32.62 12.77 42.37 5.19
462 463 5.602628 TGGCATTTATTTAAATAACCGCCC 58.397 37.500 32.62 23.71 42.37 6.13
463 464 6.981559 TCTTGGCATTTATTTAAATAACCGCC 59.018 34.615 31.11 31.11 42.84 6.13
464 465 7.169140 CCTCTTGGCATTTATTTAAATAACCGC 59.831 37.037 18.16 20.29 35.46 5.68
465 466 7.651704 CCCTCTTGGCATTTATTTAAATAACCG 59.348 37.037 18.16 13.47 35.46 4.44
466 467 8.887036 CCCTCTTGGCATTTATTTAAATAACC 57.113 34.615 18.16 16.22 34.36 2.85
483 484 2.194201 TTTTAGAACCGCCCTCTTGG 57.806 50.000 0.00 0.00 37.09 3.61
504 505 2.110578 ACAGCAGGGCAAGTTCTTTTT 58.889 42.857 0.00 0.00 0.00 1.94
505 506 1.780503 ACAGCAGGGCAAGTTCTTTT 58.219 45.000 0.00 0.00 0.00 2.27
506 507 2.656947 TACAGCAGGGCAAGTTCTTT 57.343 45.000 0.00 0.00 0.00 2.52
531 532 9.617523 ACAAACAGATCATTTTTCCATTCTTTT 57.382 25.926 0.00 0.00 0.00 2.27
534 535 9.617523 AAAACAAACAGATCATTTTTCCATTCT 57.382 25.926 0.00 0.00 0.00 2.40
559 560 6.636705 AGTAAGAGCACCGACATGTAAATAA 58.363 36.000 0.00 0.00 0.00 1.40
561 562 5.086104 AGTAAGAGCACCGACATGTAAAT 57.914 39.130 0.00 0.00 0.00 1.40
566 567 3.182967 GAGAAGTAAGAGCACCGACATG 58.817 50.000 0.00 0.00 0.00 3.21
570 571 1.819288 CTGGAGAAGTAAGAGCACCGA 59.181 52.381 0.00 0.00 0.00 4.69
572 573 1.406205 GGCTGGAGAAGTAAGAGCACC 60.406 57.143 0.00 0.00 0.00 5.01
616 617 4.524714 ACCAGACCACTAATCATAGATCGG 59.475 45.833 0.00 0.00 33.15 4.18
677 761 4.534141 GCATTTGCGGCCCCCATG 62.534 66.667 0.00 0.00 0.00 3.66
684 768 0.093365 CGTTTCAATGCATTTGCGGC 59.907 50.000 9.83 0.00 45.83 6.53
733 817 2.025037 TGCTAATCCAGGACCATGCTTT 60.025 45.455 0.00 0.00 0.00 3.51
735 819 1.216064 TGCTAATCCAGGACCATGCT 58.784 50.000 0.00 0.00 0.00 3.79
914 998 0.524862 GTGTACCGATCGACTGGTGT 59.475 55.000 18.66 7.20 39.30 4.16
921 1005 4.874282 CGCGCGTGTACCGATCGA 62.874 66.667 24.19 0.00 39.56 3.59
1326 1425 3.568578 GAGGCCCCCTCGATGAAT 58.431 61.111 0.00 0.00 41.08 2.57
1536 1641 1.202758 ACGACAAGGAAGTCAATGGCA 60.203 47.619 0.00 0.00 38.43 4.92
1551 1656 1.300931 GAGGCTGCAGTTGACGACA 60.301 57.895 16.64 0.00 0.00 4.35
2058 2172 1.291184 TGAATGACAGCGCGAACAGG 61.291 55.000 12.10 0.00 0.00 4.00
2172 2289 4.194720 AGCTCGTCGATCACCGCC 62.195 66.667 0.00 0.00 38.37 6.13
2325 2442 1.883084 GATCATCCACACGCGGTCC 60.883 63.158 12.47 0.00 0.00 4.46
2379 2496 2.507944 GGCTCGATGCACTCCCAT 59.492 61.111 8.71 0.00 45.15 4.00
2527 2668 7.482169 AGTTGTCTACAGATACAATGGAGAA 57.518 36.000 0.00 0.00 39.34 2.87
2583 2734 0.833287 AAGCACACACCAGACTGACT 59.167 50.000 3.32 0.00 0.00 3.41
2600 2751 3.154589 GGTTTAGCACCGAGGGAAG 57.845 57.895 0.00 0.00 35.12 3.46
2731 2886 2.159627 CAGATCCGGCATATTTAACGCC 59.840 50.000 0.00 0.00 42.64 5.68
2733 2888 4.150627 CAGACAGATCCGGCATATTTAACG 59.849 45.833 0.00 0.00 0.00 3.18
2800 2955 0.970427 ATTAAGCCCTTTGTGCCGGG 60.970 55.000 2.18 0.00 43.60 5.73
3031 3188 7.668492 GGAGATGGTAGTAAACTATTTCCGAT 58.332 38.462 0.00 0.00 39.52 4.18
3032 3189 7.047460 GGAGATGGTAGTAAACTATTTCCGA 57.953 40.000 0.00 0.00 39.52 4.55
3124 5050 3.195610 AGGTAAACTCGATCATGCAGTGA 59.804 43.478 0.00 0.00 42.06 3.41
3125 5051 3.525537 AGGTAAACTCGATCATGCAGTG 58.474 45.455 0.00 0.00 0.00 3.66
3126 5052 3.895232 AGGTAAACTCGATCATGCAGT 57.105 42.857 0.00 0.00 0.00 4.40
3128 5054 3.616821 CGAAAGGTAAACTCGATCATGCA 59.383 43.478 0.00 0.00 34.52 3.96
3129 5055 4.183539 CGAAAGGTAAACTCGATCATGC 57.816 45.455 0.00 0.00 34.52 4.06
3156 5082 2.388232 CGCTCGTACCCAAGGCAAC 61.388 63.158 0.00 0.00 0.00 4.17
3164 5403 2.711924 CCTCGTACGCTCGTACCC 59.288 66.667 22.05 4.02 45.80 3.69
3165 5404 2.711924 CCCTCGTACGCTCGTACC 59.288 66.667 22.05 8.74 45.80 3.34
3223 5462 2.801631 CGCAGGAGAGGGATGGGTC 61.802 68.421 0.00 0.00 0.00 4.46
3247 5497 2.790433 GCCAGGCCCATAAATTCGATA 58.210 47.619 0.00 0.00 0.00 2.92
3248 5498 1.620822 GCCAGGCCCATAAATTCGAT 58.379 50.000 0.00 0.00 0.00 3.59
3317 5567 1.280710 TCCTCCATGCCACATTTACGT 59.719 47.619 0.00 0.00 0.00 3.57
3436 5690 1.554042 GCGAACGGCGAAGAAGAACA 61.554 55.000 16.62 0.00 44.57 3.18


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

AutoCloner maintained by Alex Coulton.