Multiple sequence alignment - TraesCS2A01G452300

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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 TraesCS2A01G452300 chr2A 100.000 4033 0 0 1 4033 701491419 701487387 0.000000e+00 7448.0
1 TraesCS2A01G452300 chr2A 82.000 100 10 4 202 296 661863145 661863241 1.200000e-10 78.7
2 TraesCS2A01G452300 chr2A 100.000 29 0 0 202 230 136745700 136745672 2.000000e-03 54.7
3 TraesCS2A01G452300 chr2D 90.437 2405 124 47 1371 3711 561846864 561844502 0.000000e+00 3070.0
4 TraesCS2A01G452300 chr2D 90.639 876 71 6 342 1212 561847895 561847026 0.000000e+00 1153.0
5 TraesCS2A01G452300 chr2D 88.339 849 71 9 3201 4033 561842079 561841243 0.000000e+00 994.0
6 TraesCS2A01G452300 chr2D 95.522 201 9 0 1 201 561848088 561847888 5.030000e-84 322.0
7 TraesCS2A01G452300 chr2B 91.635 1841 88 32 1913 3712 670843126 670841311 0.000000e+00 2486.0
8 TraesCS2A01G452300 chr2B 88.797 848 69 11 3201 4033 670837614 670836778 0.000000e+00 1016.0
9 TraesCS2A01G452300 chr2B 90.924 606 48 4 608 1209 670844570 670843968 0.000000e+00 808.0
10 TraesCS2A01G452300 chr2B 86.557 424 31 11 1408 1830 670843532 670843134 1.030000e-120 444.0
11 TraesCS2A01G452300 chr2B 95.775 71 3 0 272 342 164618061 164617991 9.160000e-22 115.0
12 TraesCS2A01G452300 chr2B 95.714 70 3 0 272 341 512345113 512345182 3.290000e-21 113.0
13 TraesCS2A01G452300 chr6A 82.934 334 37 11 3383 3705 356978983 356978659 2.370000e-72 283.0
14 TraesCS2A01G452300 chr6B 82.477 331 36 13 3383 3702 347221472 347221791 1.850000e-68 270.0
15 TraesCS2A01G452300 chr6B 97.183 71 2 0 272 342 207309779 207309709 1.970000e-23 121.0
16 TraesCS2A01G452300 chr6B 93.151 73 5 0 272 344 75642131 75642059 1.530000e-19 108.0
17 TraesCS2A01G452300 chr6D 82.282 333 37 11 3383 3705 262779865 262779545 6.640000e-68 268.0
18 TraesCS2A01G452300 chr4B 95.833 72 3 0 272 343 613166397 613166326 2.550000e-22 117.0
19 TraesCS2A01G452300 chr7B 95.775 71 3 0 273 343 720475444 720475374 9.160000e-22 115.0
20 TraesCS2A01G452300 chr5B 95.714 70 3 0 272 341 513616251 513616182 3.290000e-21 113.0
21 TraesCS2A01G452300 chr5B 80.952 105 8 3 202 296 492081969 492082071 5.590000e-09 73.1
22 TraesCS2A01G452300 chr4A 93.333 75 4 1 268 342 728845989 728846062 4.260000e-20 110.0
23 TraesCS2A01G452300 chr1B 91.781 73 6 0 272 344 612930435 612930507 7.130000e-18 102.0
24 TraesCS2A01G452300 chr3B 95.238 63 3 0 203 265 23779543 23779481 2.560000e-17 100.0
25 TraesCS2A01G452300 chr4D 87.838 74 7 2 223 296 113170467 113170396 7.180000e-13 86.1
26 TraesCS2A01G452300 chr4D 82.105 95 10 3 202 296 439166184 439166097 1.550000e-09 75.0
27 TraesCS2A01G452300 chr4D 97.222 36 1 0 226 261 17753418 17753383 1.210000e-05 62.1
28 TraesCS2A01G452300 chr3D 95.918 49 2 0 225 273 67628488 67628536 3.340000e-11 80.5
29 TraesCS2A01G452300 chr5A 85.938 64 8 1 232 295 367334821 367334759 2.600000e-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 TraesCS2A01G452300 chr2A 701487387 701491419 4032 True 7448.00 7448 100.00000 1 4033 1 chr2A.!!$R2 4032
1 TraesCS2A01G452300 chr2D 561841243 561848088 6845 True 1384.75 3070 91.23425 1 4033 4 chr2D.!!$R1 4032
2 TraesCS2A01G452300 chr2B 670836778 670844570 7792 True 1188.50 2486 89.47825 608 4033 4 chr2B.!!$R2 3425

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
552 553 0.033228 GCGGAGAGGAGTGATGATGG 59.967 60.0 0.00 0.0 0.0 3.51 F
1235 1494 0.034059 CAGCTGTTTCGGTCAGTCCT 59.966 55.0 5.25 0.0 35.6 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1629 1.144716 TGCCAGACGCATGGAGATC 59.855 57.895 10.55 0.00 44.64 2.75 R
3051 3366 0.102300 AGCTTTGTTTGGCCACGAAC 59.898 50.000 3.88 9.52 40.70 3.95 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
59 60 4.756642 CCATAATGATGGCGAGTTGTGTAT 59.243 41.667 0.00 0.00 46.30 2.29
66 67 0.713883 GCGAGTTGTGTATGGTCACG 59.286 55.000 0.00 0.00 40.74 4.35
86 87 2.010582 GCAGGGCTCTGGTAGTCGAG 62.011 65.000 17.16 0.00 41.19 4.04
144 145 0.536724 TGTGTCATCATGGAGTCGGG 59.463 55.000 0.00 0.00 0.00 5.14
199 200 1.066573 AGCTGATTGGTGGTCTTCGAG 60.067 52.381 0.00 0.00 0.00 4.04
200 201 2.009042 GCTGATTGGTGGTCTTCGAGG 61.009 57.143 0.00 0.00 0.00 4.63
201 202 1.276421 CTGATTGGTGGTCTTCGAGGT 59.724 52.381 0.00 0.00 0.00 3.85
202 203 2.496070 CTGATTGGTGGTCTTCGAGGTA 59.504 50.000 0.00 0.00 0.00 3.08
203 204 2.496070 TGATTGGTGGTCTTCGAGGTAG 59.504 50.000 0.00 0.00 0.00 3.18
204 205 2.005370 TTGGTGGTCTTCGAGGTAGT 57.995 50.000 0.00 0.00 0.00 2.73
205 206 1.542492 TGGTGGTCTTCGAGGTAGTC 58.458 55.000 0.00 0.00 0.00 2.59
206 207 0.816373 GGTGGTCTTCGAGGTAGTCC 59.184 60.000 0.00 0.00 0.00 3.85
208 209 1.473278 GTGGTCTTCGAGGTAGTCCTG 59.527 57.143 0.00 0.00 45.24 3.86
209 210 1.104630 GGTCTTCGAGGTAGTCCTGG 58.895 60.000 0.00 0.00 45.24 4.45
210 211 0.456628 GTCTTCGAGGTAGTCCTGGC 59.543 60.000 0.00 0.00 45.24 4.85
211 212 0.683504 TCTTCGAGGTAGTCCTGGCC 60.684 60.000 0.00 0.00 45.24 5.36
212 213 0.970937 CTTCGAGGTAGTCCTGGCCA 60.971 60.000 4.71 4.71 45.24 5.36
213 214 0.325296 TTCGAGGTAGTCCTGGCCAT 60.325 55.000 5.51 0.00 45.24 4.40
214 215 1.043116 TCGAGGTAGTCCTGGCCATG 61.043 60.000 5.51 2.84 45.24 3.66
215 216 1.832912 GAGGTAGTCCTGGCCATGG 59.167 63.158 5.51 7.63 45.24 3.66
216 217 1.694169 AGGTAGTCCTGGCCATGGG 60.694 63.158 15.13 4.96 43.33 4.00
217 218 1.692749 GGTAGTCCTGGCCATGGGA 60.693 63.158 15.13 8.01 0.00 4.37
218 219 1.279025 GGTAGTCCTGGCCATGGGAA 61.279 60.000 15.05 0.00 33.01 3.97
219 220 0.181350 GTAGTCCTGGCCATGGGAAG 59.819 60.000 15.05 0.00 33.01 3.46
220 221 1.635817 TAGTCCTGGCCATGGGAAGC 61.636 60.000 15.05 4.61 33.01 3.86
221 222 2.614969 TCCTGGCCATGGGAAGCT 60.615 61.111 15.13 0.00 0.00 3.74
222 223 2.123982 CCTGGCCATGGGAAGCTC 60.124 66.667 15.13 0.00 0.00 4.09
223 224 2.515523 CTGGCCATGGGAAGCTCG 60.516 66.667 15.13 0.00 0.00 5.03
224 225 4.113815 TGGCCATGGGAAGCTCGG 62.114 66.667 15.13 0.00 0.00 4.63
227 228 4.883354 CCATGGGAAGCTCGGCCC 62.883 72.222 2.85 11.34 44.93 5.80
240 241 3.744719 GGCCCGGTCCGAAAAAGC 61.745 66.667 14.39 7.22 0.00 3.51
241 242 3.744719 GCCCGGTCCGAAAAAGCC 61.745 66.667 14.39 0.00 0.00 4.35
242 243 2.033602 CCCGGTCCGAAAAAGCCT 59.966 61.111 14.39 0.00 0.00 4.58
243 244 2.332654 CCCGGTCCGAAAAAGCCTG 61.333 63.158 14.39 0.00 0.00 4.85
244 245 1.302192 CCGGTCCGAAAAAGCCTGA 60.302 57.895 14.39 0.00 0.00 3.86
245 246 1.574702 CCGGTCCGAAAAAGCCTGAC 61.575 60.000 14.39 0.00 0.00 3.51
246 247 1.574702 CGGTCCGAAAAAGCCTGACC 61.575 60.000 4.91 0.00 41.64 4.02
247 248 1.241990 GGTCCGAAAAAGCCTGACCC 61.242 60.000 0.00 0.00 39.65 4.46
248 249 1.302192 TCCGAAAAAGCCTGACCCG 60.302 57.895 0.00 0.00 0.00 5.28
249 250 2.332654 CCGAAAAAGCCTGACCCGG 61.333 63.158 0.00 0.00 0.00 5.73
295 296 4.107029 GCCCGGGCCTAAGTTTTT 57.893 55.556 36.64 0.00 34.56 1.94
310 311 2.037871 TTTTTGTCTCGGGCTTGGC 58.962 52.632 0.00 0.00 0.00 4.52
311 312 0.467290 TTTTTGTCTCGGGCTTGGCT 60.467 50.000 0.00 0.00 0.00 4.75
312 313 0.398696 TTTTGTCTCGGGCTTGGCTA 59.601 50.000 0.00 0.00 0.00 3.93
313 314 0.036388 TTTGTCTCGGGCTTGGCTAG 60.036 55.000 0.00 0.00 0.00 3.42
314 315 1.899437 TTGTCTCGGGCTTGGCTAGG 61.899 60.000 0.00 0.00 0.00 3.02
337 338 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
338 339 2.598787 CCCGAGGTTTGGCCAGGTA 61.599 63.158 5.11 0.00 40.61 3.08
339 340 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
340 341 0.834612 CCGAGGTTTGGCCAGGTATA 59.165 55.000 5.11 0.00 40.61 1.47
341 342 1.474498 CCGAGGTTTGGCCAGGTATAC 60.474 57.143 5.11 0.40 40.61 1.47
342 343 1.485066 CGAGGTTTGGCCAGGTATACT 59.515 52.381 5.11 0.00 40.61 2.12
343 344 2.093128 CGAGGTTTGGCCAGGTATACTT 60.093 50.000 5.11 0.00 40.61 2.24
344 345 3.542648 GAGGTTTGGCCAGGTATACTTC 58.457 50.000 5.11 3.19 40.61 3.01
345 346 2.093128 AGGTTTGGCCAGGTATACTTCG 60.093 50.000 5.11 0.00 40.61 3.79
346 347 2.093341 GGTTTGGCCAGGTATACTTCGA 60.093 50.000 5.11 0.00 37.17 3.71
362 363 0.395862 TCGAGGAGGTCTAGCTTGGG 60.396 60.000 0.00 0.00 0.00 4.12
399 400 4.023792 GCATATTTCTTCCGCATGTGATCA 60.024 41.667 8.11 0.00 0.00 2.92
407 408 3.608796 TCCGCATGTGATCATCTTCAAA 58.391 40.909 8.11 0.00 31.15 2.69
417 418 9.676861 ATGTGATCATCTTCAAAGTCAGAATTA 57.323 29.630 0.00 0.00 0.00 1.40
432 433 3.804325 CAGAATTATCTCGTCGCCATTGT 59.196 43.478 0.00 0.00 32.03 2.71
443 444 1.901464 GCCATTGTTGGTGGTCCGT 60.901 57.895 0.00 0.00 45.57 4.69
470 471 3.010138 TGGCATAGCTCCTTGTAGGTTTT 59.990 43.478 0.00 0.00 36.53 2.43
471 472 3.378427 GGCATAGCTCCTTGTAGGTTTTG 59.622 47.826 0.00 0.00 36.53 2.44
480 481 0.382515 TGTAGGTTTTGTGCGGTTGC 59.617 50.000 0.00 0.00 43.20 4.17
482 483 0.665835 TAGGTTTTGTGCGGTTGCTG 59.334 50.000 0.00 0.00 43.34 4.41
524 525 4.009675 ACTTGTTTGCAGTGAACTCTGAA 58.990 39.130 7.86 0.00 37.61 3.02
550 551 2.037053 CGCGGAGAGGAGTGATGAT 58.963 57.895 0.00 0.00 0.00 2.45
552 553 0.033228 GCGGAGAGGAGTGATGATGG 59.967 60.000 0.00 0.00 0.00 3.51
554 555 1.068281 CGGAGAGGAGTGATGATGGTG 59.932 57.143 0.00 0.00 0.00 4.17
558 559 3.382278 AGAGGAGTGATGATGGTGATGT 58.618 45.455 0.00 0.00 0.00 3.06
567 568 3.490800 TGATGGTGATGTTTGCATTCG 57.509 42.857 0.00 0.00 35.07 3.34
572 573 2.228822 GGTGATGTTTGCATTCGACCTT 59.771 45.455 0.00 0.00 35.07 3.50
605 606 2.441375 TCTCTTCAACAATGTGGGTGGA 59.559 45.455 0.00 0.00 0.00 4.02
613 614 4.769345 ACAATGTGGGTGGATTTTGTTT 57.231 36.364 0.00 0.00 0.00 2.83
618 619 4.701765 TGTGGGTGGATTTTGTTTTGATG 58.298 39.130 0.00 0.00 0.00 3.07
633 634 1.596477 GATGCCCAGATCGACAGGC 60.596 63.158 9.30 9.30 45.96 4.85
737 743 6.096282 GCTACAAGACAAATATTTTAGCCCCA 59.904 38.462 13.05 0.00 0.00 4.96
738 744 6.926630 ACAAGACAAATATTTTAGCCCCAA 57.073 33.333 0.00 0.00 0.00 4.12
767 773 0.966179 AGTCTATCACGTGTGTGCCA 59.034 50.000 16.51 0.00 46.01 4.92
778 784 1.734465 GTGTGTGCCATAGTCAAGCTC 59.266 52.381 0.00 0.00 0.00 4.09
826 832 4.760047 GGACGGCGCATGACAGGT 62.760 66.667 10.83 0.00 0.00 4.00
844 850 1.614317 GGTTTGAGTGAGATGTGGGGG 60.614 57.143 0.00 0.00 0.00 5.40
847 853 1.222936 GAGTGAGATGTGGGGGCAG 59.777 63.158 0.00 0.00 0.00 4.85
857 863 2.088096 TGGGGGCAGGACTTCCAAA 61.088 57.895 0.00 0.00 38.89 3.28
875 881 4.037446 TCCAAACATGTAGACCAAAGTTGC 59.963 41.667 0.00 0.00 0.00 4.17
881 887 3.746940 TGTAGACCAAAGTTGCTTACCC 58.253 45.455 0.00 0.00 0.00 3.69
882 888 3.393278 TGTAGACCAAAGTTGCTTACCCT 59.607 43.478 0.00 0.00 0.00 4.34
914 920 4.684484 GGTCCTCCACCGTAGATAAAAT 57.316 45.455 0.00 0.00 34.56 1.82
948 956 3.735720 TCATGGTGGAAATGGATGTGA 57.264 42.857 0.00 0.00 0.00 3.58
994 1002 1.079127 AATTCGGCGACCTGGTCAG 60.079 57.895 25.42 18.30 32.09 3.51
1009 1017 5.420421 ACCTGGTCAGTATATATGCTGCTAG 59.580 44.000 22.06 20.97 39.87 3.42
1024 1032 2.365105 TAGGAAGCCAGGGGTCCG 60.365 66.667 0.00 0.00 0.00 4.79
1041 1049 1.863880 CGTCGCTCGTAGCACTCAC 60.864 63.158 7.47 0.00 42.58 3.51
1042 1050 1.502640 GTCGCTCGTAGCACTCACT 59.497 57.895 7.47 0.00 42.58 3.41
1043 1051 0.109689 GTCGCTCGTAGCACTCACTT 60.110 55.000 7.47 0.00 42.58 3.16
1044 1052 1.129998 GTCGCTCGTAGCACTCACTTA 59.870 52.381 7.47 0.00 42.58 2.24
1116 1125 2.360483 AGCAGATACAGACACCATCTCG 59.640 50.000 0.00 0.00 34.41 4.04
1122 1131 1.337260 ACAGACACCATCTCGTTCTGC 60.337 52.381 0.00 0.00 34.41 4.26
1165 1174 0.914644 TCAGGAAATCCAGCTCCAGG 59.085 55.000 1.67 0.00 38.89 4.45
1178 1187 1.414550 GCTCCAGGTCAGAGGTAATCC 59.585 57.143 0.00 0.00 0.00 3.01
1198 1207 0.809385 TCCTCTACTTGCGTTCCTCG 59.191 55.000 0.00 0.00 43.12 4.63
1212 1471 2.492019 TCCTCGAGCGTGATTATGTG 57.508 50.000 6.99 0.00 0.00 3.21
1214 1473 2.946990 TCCTCGAGCGTGATTATGTGTA 59.053 45.455 6.99 0.00 0.00 2.90
1215 1474 3.568430 TCCTCGAGCGTGATTATGTGTAT 59.432 43.478 6.99 0.00 0.00 2.29
1219 1478 3.120286 CGAGCGTGATTATGTGTATCAGC 59.880 47.826 0.00 0.00 32.96 4.26
1220 1479 4.302455 GAGCGTGATTATGTGTATCAGCT 58.698 43.478 0.00 0.00 38.26 4.24
1227 1486 5.523552 TGATTATGTGTATCAGCTGTTTCGG 59.476 40.000 14.67 0.00 0.00 4.30
1235 1494 0.034059 CAGCTGTTTCGGTCAGTCCT 59.966 55.000 5.25 0.00 35.60 3.85
1241 1500 1.002087 GTTTCGGTCAGTCCTGATGGT 59.998 52.381 0.00 0.00 42.18 3.55
1242 1501 0.608130 TTCGGTCAGTCCTGATGGTG 59.392 55.000 0.00 0.00 42.18 4.17
1243 1502 1.448540 CGGTCAGTCCTGATGGTGC 60.449 63.158 0.00 0.00 42.18 5.01
1244 1503 1.679311 GGTCAGTCCTGATGGTGCA 59.321 57.895 0.00 0.00 42.18 4.57
1245 1504 0.036732 GGTCAGTCCTGATGGTGCAA 59.963 55.000 0.00 0.00 42.18 4.08
1246 1505 1.545428 GGTCAGTCCTGATGGTGCAAA 60.545 52.381 0.00 0.00 42.18 3.68
1247 1506 1.537202 GTCAGTCCTGATGGTGCAAAC 59.463 52.381 0.00 0.00 42.18 2.93
1248 1507 1.142667 TCAGTCCTGATGGTGCAAACA 59.857 47.619 0.00 0.00 34.14 2.83
1249 1508 1.955778 CAGTCCTGATGGTGCAAACAA 59.044 47.619 0.00 0.00 34.23 2.83
1283 1558 0.240145 GTTTAACTGGCTGCGTTCCC 59.760 55.000 0.00 0.00 0.00 3.97
1289 1564 3.056328 GGCTGCGTTCCCAGTTCC 61.056 66.667 0.00 0.00 35.28 3.62
1291 1566 2.429930 CTGCGTTCCCAGTTCCCA 59.570 61.111 0.00 0.00 0.00 4.37
1293 1568 2.671963 GCGTTCCCAGTTCCCACC 60.672 66.667 0.00 0.00 0.00 4.61
1295 1570 2.033602 GTTCCCAGTTCCCACCGG 59.966 66.667 0.00 0.00 0.00 5.28
1297 1572 1.152074 TTCCCAGTTCCCACCGGTA 60.152 57.895 6.87 0.00 0.00 4.02
1301 1576 0.909623 CCAGTTCCCACCGGTAATCT 59.090 55.000 6.87 0.00 0.00 2.40
1303 1578 2.356135 CAGTTCCCACCGGTAATCTTG 58.644 52.381 6.87 0.00 0.00 3.02
1304 1579 1.280998 AGTTCCCACCGGTAATCTTGG 59.719 52.381 6.87 2.43 0.00 3.61
1305 1580 4.977393 CCCACCGGTAATCTTGGG 57.023 61.111 6.87 9.36 42.92 4.12
1308 1583 2.038387 CCACCGGTAATCTTGGGAAG 57.962 55.000 6.87 0.00 0.00 3.46
1309 1584 1.408266 CCACCGGTAATCTTGGGAAGG 60.408 57.143 6.87 0.00 0.00 3.46
1311 1586 0.814010 CCGGTAATCTTGGGAAGGCG 60.814 60.000 0.00 0.00 0.00 5.52
1313 1588 0.255033 GGTAATCTTGGGAAGGCGGT 59.745 55.000 0.00 0.00 0.00 5.68
1315 1590 2.092807 GGTAATCTTGGGAAGGCGGTAA 60.093 50.000 0.00 0.00 0.00 2.85
1316 1591 3.434596 GGTAATCTTGGGAAGGCGGTAAT 60.435 47.826 0.00 0.00 0.00 1.89
1317 1592 3.382083 AATCTTGGGAAGGCGGTAATT 57.618 42.857 0.00 0.00 0.00 1.40
1318 1593 2.413310 TCTTGGGAAGGCGGTAATTC 57.587 50.000 0.00 0.00 0.00 2.17
1319 1594 1.913419 TCTTGGGAAGGCGGTAATTCT 59.087 47.619 0.00 0.00 0.00 2.40
1321 1596 2.891191 TGGGAAGGCGGTAATTCTTT 57.109 45.000 0.00 0.00 0.00 2.52
1323 1598 2.224917 TGGGAAGGCGGTAATTCTTTGT 60.225 45.455 0.00 0.00 0.00 2.83
1325 1600 3.078837 GGAAGGCGGTAATTCTTTGTCA 58.921 45.455 0.00 0.00 0.00 3.58
1326 1601 3.504520 GGAAGGCGGTAATTCTTTGTCAA 59.495 43.478 0.00 0.00 0.00 3.18
1327 1602 4.022676 GGAAGGCGGTAATTCTTTGTCAAA 60.023 41.667 0.00 0.00 0.00 2.69
1328 1603 5.508320 GGAAGGCGGTAATTCTTTGTCAAAA 60.508 40.000 0.00 0.00 0.00 2.44
1329 1604 5.722021 AGGCGGTAATTCTTTGTCAAAAT 57.278 34.783 0.00 0.00 0.00 1.82
1331 1606 4.625311 GGCGGTAATTCTTTGTCAAAATGG 59.375 41.667 0.00 0.00 0.00 3.16
1332 1607 5.227152 GCGGTAATTCTTTGTCAAAATGGT 58.773 37.500 0.00 0.00 0.00 3.55
1333 1608 5.344933 GCGGTAATTCTTTGTCAAAATGGTC 59.655 40.000 0.00 0.00 0.00 4.02
1334 1609 5.567534 CGGTAATTCTTTGTCAAAATGGTCG 59.432 40.000 0.00 0.00 0.00 4.79
1335 1610 6.443792 GGTAATTCTTTGTCAAAATGGTCGT 58.556 36.000 0.00 0.00 0.00 4.34
1336 1611 6.581166 GGTAATTCTTTGTCAAAATGGTCGTC 59.419 38.462 0.00 0.00 0.00 4.20
1337 1612 5.766150 ATTCTTTGTCAAAATGGTCGTCA 57.234 34.783 0.00 0.00 0.00 4.35
1339 1614 5.107109 TCTTTGTCAAAATGGTCGTCATG 57.893 39.130 0.00 0.00 35.99 3.07
1340 1615 4.819088 TCTTTGTCAAAATGGTCGTCATGA 59.181 37.500 0.00 0.00 35.99 3.07
1342 1617 6.652900 TCTTTGTCAAAATGGTCGTCATGATA 59.347 34.615 0.00 0.00 35.99 2.15
1343 1618 5.794687 TGTCAAAATGGTCGTCATGATAC 57.205 39.130 0.00 0.20 35.99 2.24
1344 1619 4.328712 TGTCAAAATGGTCGTCATGATACG 59.671 41.667 0.00 0.00 44.19 3.06
1346 1621 3.536956 AAATGGTCGTCATGATACGGT 57.463 42.857 0.00 0.00 43.05 4.83
1347 1622 2.509052 ATGGTCGTCATGATACGGTG 57.491 50.000 0.00 0.00 43.05 4.94
1348 1623 0.179121 TGGTCGTCATGATACGGTGC 60.179 55.000 0.00 0.00 43.05 5.01
1349 1624 0.874607 GGTCGTCATGATACGGTGCC 60.875 60.000 0.00 0.07 43.05 5.01
1350 1625 0.874607 GTCGTCATGATACGGTGCCC 60.875 60.000 0.00 0.00 43.05 5.36
1362 1637 4.241555 GTGCCCGGCGATCTCCAT 62.242 66.667 9.30 0.00 0.00 3.41
1363 1638 4.240103 TGCCCGGCGATCTCCATG 62.240 66.667 9.30 0.00 0.00 3.66
1368 1643 2.419198 GGCGATCTCCATGCGTCT 59.581 61.111 0.00 0.00 0.00 4.18
1369 1644 1.953138 GGCGATCTCCATGCGTCTG 60.953 63.158 0.00 0.00 0.00 3.51
1387 1662 1.980772 GGCATGGCCTGTTCTTGCT 60.981 57.895 8.35 0.00 46.69 3.91
1403 1678 4.821589 CTCTGGTCGCGGCCCTTC 62.822 72.222 29.71 1.64 0.00 3.46
1405 1680 4.697756 CTGGTCGCGGCCCTTCAA 62.698 66.667 29.71 6.97 0.00 2.69
1421 1711 1.996292 TCAACTAGCTAGCAACGCAG 58.004 50.000 20.91 8.00 0.00 5.18
1471 1761 6.199937 ACAAGCATCCACATGTAATTTCTC 57.800 37.500 0.00 0.00 31.86 2.87
1503 1793 1.589803 AATATCCGCCGCCTAAACAC 58.410 50.000 0.00 0.00 0.00 3.32
1515 1805 2.500229 CCTAAACACTTCCGCCAAGAA 58.500 47.619 0.00 0.00 35.82 2.52
1540 1830 4.061357 AGCTATCGAAAAAGGAGCTACC 57.939 45.455 0.00 0.00 41.60 3.18
1553 1843 3.658709 GGAGCTACCTCATTACATCTGC 58.341 50.000 0.00 0.00 39.96 4.26
1554 1844 3.070159 GGAGCTACCTCATTACATCTGCA 59.930 47.826 0.00 0.00 39.96 4.41
1555 1845 4.305769 GAGCTACCTCATTACATCTGCAG 58.694 47.826 7.63 7.63 38.03 4.41
1556 1846 3.708631 AGCTACCTCATTACATCTGCAGT 59.291 43.478 14.67 0.00 0.00 4.40
1564 1854 1.713597 TACATCTGCAGTTCTGCACG 58.286 50.000 21.30 16.90 40.23 5.34
1567 1857 1.010935 ATCTGCAGTTCTGCACGTCG 61.011 55.000 21.30 12.93 40.23 5.12
1584 1874 2.535534 CGTCGTGCATGTAGCTTTCATG 60.536 50.000 20.20 20.20 45.94 3.07
1586 1876 2.416202 TCGTGCATGTAGCTTTCATGTG 59.584 45.455 23.10 16.61 45.94 3.21
1587 1877 2.476686 CGTGCATGTAGCTTTCATGTGG 60.477 50.000 23.10 13.89 45.94 4.17
1623 1915 4.096081 GGAGACAAGCAAATCATTGGAGAG 59.904 45.833 0.00 0.00 37.02 3.20
1677 1971 4.987285 CCGGTCATCTTATCTTCATGTGAG 59.013 45.833 0.00 0.00 0.00 3.51
1680 1974 6.577103 GGTCATCTTATCTTCATGTGAGTGA 58.423 40.000 0.00 0.00 0.00 3.41
1700 1994 8.612619 TGAGTGAATTCAGAAGTTGTTTCTTAC 58.387 33.333 8.80 0.00 43.68 2.34
1703 1997 9.226345 GTGAATTCAGAAGTTGTTTCTTACAAG 57.774 33.333 8.80 0.00 46.95 3.16
1704 1998 7.915397 TGAATTCAGAAGTTGTTTCTTACAAGC 59.085 33.333 3.38 0.00 46.95 4.01
1707 2001 7.151999 TCAGAAGTTGTTTCTTACAAGCAAA 57.848 32.000 0.00 0.00 46.95 3.68
1708 2002 7.771183 TCAGAAGTTGTTTCTTACAAGCAAAT 58.229 30.769 0.00 0.00 46.95 2.32
1710 2004 9.683069 CAGAAGTTGTTTCTTACAAGCAAATAT 57.317 29.630 0.00 0.00 46.95 1.28
1711 2005 9.899226 AGAAGTTGTTTCTTACAAGCAAATATC 57.101 29.630 0.00 0.00 46.95 1.63
1712 2006 9.899226 GAAGTTGTTTCTTACAAGCAAATATCT 57.101 29.630 0.00 0.00 46.95 1.98
1777 2076 0.621571 AGCCCTGGCCTACAATCAGA 60.622 55.000 3.32 0.00 43.17 3.27
1779 2078 2.019156 GCCCTGGCCTACAATCAGAAC 61.019 57.143 3.32 0.00 34.56 3.01
1810 2116 6.042143 TCAGTTTCTTCTGCAAAAATGAACC 58.958 36.000 8.77 0.00 36.77 3.62
1830 2136 1.812571 CGGGCTTTACTGATGCACTTT 59.187 47.619 0.00 0.00 29.96 2.66
1831 2137 2.414559 CGGGCTTTACTGATGCACTTTG 60.415 50.000 0.00 0.00 29.96 2.77
1832 2138 2.094545 GGGCTTTACTGATGCACTTTGG 60.095 50.000 0.00 0.00 0.00 3.28
1833 2139 2.094545 GGCTTTACTGATGCACTTTGGG 60.095 50.000 0.00 0.00 0.00 4.12
1853 2159 5.202004 TGGGAGTACTAAAGAGATCCACTC 58.798 45.833 0.00 0.00 45.22 3.51
1873 2179 6.204108 CCACTCACTAAAATTACGTCACCTTT 59.796 38.462 0.00 0.00 0.00 3.11
1916 2222 0.175760 TCCCGGAGCAAGAAGAATCG 59.824 55.000 0.73 0.00 0.00 3.34
2141 2456 2.420890 CTGCTCGCCATCCTCCTC 59.579 66.667 0.00 0.00 0.00 3.71
2216 2531 3.142393 CCCATCTACCTCGGGCTG 58.858 66.667 0.00 0.00 31.89 4.85
2378 2693 2.456119 GCTCATCGCCAACTCCGTG 61.456 63.158 0.00 0.00 0.00 4.94
2483 2798 2.110967 CACGCTGGGCTTCATCCTG 61.111 63.158 0.00 0.00 0.00 3.86
2492 2807 0.108424 GCTTCATCCTGACGCTGTCT 60.108 55.000 9.49 0.00 38.44 3.41
3038 3353 3.876589 TTTGCCCGCCTGAGACGTC 62.877 63.158 7.70 7.70 0.00 4.34
3042 3357 3.827898 CCGCCTGAGACGTCCCTC 61.828 72.222 13.01 4.77 0.00 4.30
3043 3358 4.180946 CGCCTGAGACGTCCCTCG 62.181 72.222 13.01 5.46 46.00 4.63
3052 3367 4.039357 CGTCCCTCGTGCTCGTGT 62.039 66.667 8.17 0.00 38.33 4.49
3053 3368 2.338984 GTCCCTCGTGCTCGTGTT 59.661 61.111 8.17 0.00 38.33 3.32
3054 3369 1.733399 GTCCCTCGTGCTCGTGTTC 60.733 63.158 8.17 0.00 38.33 3.18
3055 3370 2.805353 CCCTCGTGCTCGTGTTCG 60.805 66.667 8.17 0.00 38.33 3.95
3106 3425 3.954904 TGGTGTCCTAATAGCACTCTCTC 59.045 47.826 0.00 0.00 33.96 3.20
3110 3429 6.351456 GGTGTCCTAATAGCACTCTCTCTTTT 60.351 42.308 0.00 0.00 33.96 2.27
3111 3430 6.754675 GTGTCCTAATAGCACTCTCTCTTTTC 59.245 42.308 0.00 0.00 0.00 2.29
3114 3433 8.038351 GTCCTAATAGCACTCTCTCTTTTCTTT 58.962 37.037 0.00 0.00 0.00 2.52
3115 3434 8.598041 TCCTAATAGCACTCTCTCTTTTCTTTT 58.402 33.333 0.00 0.00 0.00 2.27
3182 3538 6.252995 TCAGGCCAAGTATTTTAGAAACCAT 58.747 36.000 5.01 0.00 0.00 3.55
3245 3601 1.745653 GCCACAGCAAATACCTTCTCC 59.254 52.381 0.00 0.00 39.53 3.71
3291 3649 4.101585 TCCTAGCGGAAAATGACATGAGAT 59.898 41.667 0.00 0.00 36.03 2.75
3292 3650 4.212847 CCTAGCGGAAAATGACATGAGATG 59.787 45.833 0.00 0.00 0.00 2.90
3301 3659 8.295288 GGAAAATGACATGAGATGGTATCAATC 58.705 37.037 0.00 0.00 33.60 2.67
3345 3707 7.770433 TCATTTGCTTGCAACTAGTATATCAGT 59.230 33.333 7.60 0.00 0.00 3.41
3427 8542 7.336931 AGAGCGAAATCCAGTTGTTTACATAAT 59.663 33.333 0.00 0.00 0.00 1.28
3428 8543 8.500753 AGCGAAATCCAGTTGTTTACATAATA 57.499 30.769 0.00 0.00 0.00 0.98
3429 8544 8.952278 AGCGAAATCCAGTTGTTTACATAATAA 58.048 29.630 0.00 0.00 0.00 1.40
3453 8568 5.314923 ACACATGCTTTGATTGTCATACC 57.685 39.130 0.00 0.00 0.00 2.73
3530 8648 6.825944 TGGGTTTGACGATCAAATTCATTA 57.174 33.333 13.63 0.70 46.55 1.90
3539 8657 7.220108 TGACGATCAAATTCATTAGTACAGTCG 59.780 37.037 0.00 0.00 0.00 4.18
3583 8701 4.470462 CTTTCCAAAGATCAGCAAACTCG 58.530 43.478 0.00 0.00 38.28 4.18
3586 8704 2.159787 CCAAAGATCAGCAAACTCGTCG 60.160 50.000 0.00 0.00 0.00 5.12
3592 8710 3.479269 GCAAACTCGTCGGGCTCG 61.479 66.667 0.00 0.00 37.82 5.03
3670 8788 1.302832 CTTGCCTGCCTTCTTCCGT 60.303 57.895 0.00 0.00 0.00 4.69
3806 8924 3.714144 TCTTTTTCCCCAGAACCACAAA 58.286 40.909 0.00 0.00 0.00 2.83
3827 8945 6.594159 ACAAAAAGATACCAACCAGACGATAG 59.406 38.462 0.00 0.00 46.19 2.08
3841 8959 6.071840 ACCAGACGATAGCACTAATCTATTCC 60.072 42.308 0.00 0.00 42.67 3.01
3857 8975 5.759059 TCTATTCCAGGTTTGCAGATCAAT 58.241 37.500 0.00 0.00 34.12 2.57
3940 9069 7.044181 TCTGAGAGAAACATAATGGATGACAC 58.956 38.462 0.00 0.00 39.06 3.67
3956 9085 2.620585 TGACACGCATTTGAATGTTCCA 59.379 40.909 5.68 0.00 38.65 3.53
3962 9091 4.244066 CGCATTTGAATGTTCCATTCCAA 58.756 39.130 12.92 9.43 38.65 3.53
4010 9140 5.787953 TTTCATGAAAAATGTGCTCCTCA 57.212 34.783 18.45 0.00 0.00 3.86
4011 9141 5.988310 TTCATGAAAAATGTGCTCCTCAT 57.012 34.783 5.45 0.00 0.00 2.90
4012 9142 7.465353 TTTCATGAAAAATGTGCTCCTCATA 57.535 32.000 18.45 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.172803 AATCAGACGCTACACCGGAC 59.827 55.000 9.46 0.00 0.00 4.79
17 18 1.130561 GGTTGCCAAATCAGACGCTAC 59.869 52.381 0.00 0.00 0.00 3.58
19 20 0.537143 TGGTTGCCAAATCAGACGCT 60.537 50.000 0.00 0.00 0.00 5.07
66 67 2.904131 GACTACCAGAGCCCTGCC 59.096 66.667 0.00 0.00 39.07 4.85
104 105 7.227156 ACACATTGAGACAAAGAGAAACCTAT 58.773 34.615 0.00 0.00 0.00 2.57
118 119 4.511527 ACTCCATGATGACACATTGAGAC 58.488 43.478 17.85 0.00 40.30 3.36
144 145 2.737830 GGCTCCATCGAGGTAGCC 59.262 66.667 18.05 18.05 46.34 3.93
199 200 1.279025 TTCCCATGGCCAGGACTACC 61.279 60.000 21.32 0.00 0.00 3.18
200 201 0.181350 CTTCCCATGGCCAGGACTAC 59.819 60.000 21.32 0.00 0.00 2.73
201 202 1.635817 GCTTCCCATGGCCAGGACTA 61.636 60.000 21.32 1.89 0.00 2.59
202 203 2.988839 GCTTCCCATGGCCAGGACT 61.989 63.158 21.32 0.00 0.00 3.85
203 204 2.440980 GCTTCCCATGGCCAGGAC 60.441 66.667 21.32 2.25 0.00 3.85
204 205 2.614969 AGCTTCCCATGGCCAGGA 60.615 61.111 21.32 15.01 0.00 3.86
205 206 2.123982 GAGCTTCCCATGGCCAGG 60.124 66.667 13.05 12.17 0.00 4.45
206 207 2.515523 CGAGCTTCCCATGGCCAG 60.516 66.667 13.05 5.05 0.00 4.85
207 208 4.113815 CCGAGCTTCCCATGGCCA 62.114 66.667 8.56 8.56 0.00 5.36
210 211 4.883354 GGGCCGAGCTTCCCATGG 62.883 72.222 4.14 4.14 42.18 3.66
223 224 3.744719 GCTTTTTCGGACCGGGCC 61.745 66.667 19.81 19.81 0.00 5.80
224 225 3.744719 GGCTTTTTCGGACCGGGC 61.745 66.667 15.25 0.21 0.00 6.13
225 226 2.033602 AGGCTTTTTCGGACCGGG 59.966 61.111 15.25 0.00 0.00 5.73
226 227 1.302192 TCAGGCTTTTTCGGACCGG 60.302 57.895 15.25 0.00 0.00 5.28
227 228 1.574702 GGTCAGGCTTTTTCGGACCG 61.575 60.000 7.84 7.84 39.06 4.79
228 229 1.241990 GGGTCAGGCTTTTTCGGACC 61.242 60.000 10.19 10.19 44.82 4.46
229 230 1.574702 CGGGTCAGGCTTTTTCGGAC 61.575 60.000 0.00 0.00 0.00 4.79
230 231 1.302192 CGGGTCAGGCTTTTTCGGA 60.302 57.895 0.00 0.00 0.00 4.55
231 232 2.332654 CCGGGTCAGGCTTTTTCGG 61.333 63.158 0.00 2.50 0.00 4.30
232 233 3.263941 CCGGGTCAGGCTTTTTCG 58.736 61.111 0.00 0.00 0.00 3.46
278 279 4.107029 AAAAACTTAGGCCCGGGC 57.893 55.556 38.57 38.57 41.06 6.13
292 293 0.467290 AGCCAAGCCCGAGACAAAAA 60.467 50.000 0.00 0.00 0.00 1.94
293 294 0.398696 TAGCCAAGCCCGAGACAAAA 59.601 50.000 0.00 0.00 0.00 2.44
294 295 0.036388 CTAGCCAAGCCCGAGACAAA 60.036 55.000 0.00 0.00 0.00 2.83
295 296 1.596934 CTAGCCAAGCCCGAGACAA 59.403 57.895 0.00 0.00 0.00 3.18
296 297 2.359169 CCTAGCCAAGCCCGAGACA 61.359 63.158 0.00 0.00 0.00 3.41
297 298 2.501610 CCTAGCCAAGCCCGAGAC 59.498 66.667 0.00 0.00 0.00 3.36
298 299 3.470888 GCCTAGCCAAGCCCGAGA 61.471 66.667 0.00 0.00 0.00 4.04
320 321 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
321 322 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
322 323 1.485066 AGTATACCTGGCCAAACCTCG 59.515 52.381 7.01 0.00 40.22 4.63
323 324 3.542648 GAAGTATACCTGGCCAAACCTC 58.457 50.000 7.01 0.00 40.22 3.85
324 325 2.093128 CGAAGTATACCTGGCCAAACCT 60.093 50.000 7.01 0.00 40.22 3.50
325 326 2.093341 TCGAAGTATACCTGGCCAAACC 60.093 50.000 7.01 0.00 39.84 3.27
326 327 3.195661 CTCGAAGTATACCTGGCCAAAC 58.804 50.000 7.01 0.00 0.00 2.93
327 328 2.169769 CCTCGAAGTATACCTGGCCAAA 59.830 50.000 7.01 0.00 0.00 3.28
328 329 1.760613 CCTCGAAGTATACCTGGCCAA 59.239 52.381 7.01 0.00 0.00 4.52
329 330 1.063492 TCCTCGAAGTATACCTGGCCA 60.063 52.381 4.71 4.71 0.00 5.36
330 331 1.614413 CTCCTCGAAGTATACCTGGCC 59.386 57.143 0.00 0.00 0.00 5.36
331 332 1.614413 CCTCCTCGAAGTATACCTGGC 59.386 57.143 0.00 0.00 0.00 4.85
332 333 2.885894 GACCTCCTCGAAGTATACCTGG 59.114 54.545 0.00 0.00 0.00 4.45
333 334 3.822940 AGACCTCCTCGAAGTATACCTG 58.177 50.000 0.00 0.00 0.00 4.00
334 335 4.505390 GCTAGACCTCCTCGAAGTATACCT 60.505 50.000 0.00 0.00 0.00 3.08
335 336 3.752747 GCTAGACCTCCTCGAAGTATACC 59.247 52.174 0.00 0.00 0.00 2.73
336 337 4.644498 AGCTAGACCTCCTCGAAGTATAC 58.356 47.826 0.00 0.00 0.00 1.47
337 338 4.978438 AGCTAGACCTCCTCGAAGTATA 57.022 45.455 0.00 0.00 0.00 1.47
338 339 3.868619 AGCTAGACCTCCTCGAAGTAT 57.131 47.619 0.00 0.00 0.00 2.12
339 340 3.280295 CAAGCTAGACCTCCTCGAAGTA 58.720 50.000 0.00 0.00 0.00 2.24
340 341 2.096248 CAAGCTAGACCTCCTCGAAGT 58.904 52.381 0.00 0.00 0.00 3.01
341 342 1.407258 CCAAGCTAGACCTCCTCGAAG 59.593 57.143 0.00 0.00 0.00 3.79
342 343 1.475403 CCAAGCTAGACCTCCTCGAA 58.525 55.000 0.00 0.00 0.00 3.71
343 344 0.395862 CCCAAGCTAGACCTCCTCGA 60.396 60.000 0.00 0.00 0.00 4.04
344 345 0.684805 ACCCAAGCTAGACCTCCTCG 60.685 60.000 0.00 0.00 0.00 4.63
345 346 1.116308 GACCCAAGCTAGACCTCCTC 58.884 60.000 0.00 0.00 0.00 3.71
346 347 0.684805 CGACCCAAGCTAGACCTCCT 60.685 60.000 0.00 0.00 0.00 3.69
387 388 3.376234 ACTTTGAAGATGATCACATGCGG 59.624 43.478 0.00 0.00 36.82 5.69
399 400 7.433719 CGACGAGATAATTCTGACTTTGAAGAT 59.566 37.037 0.00 0.00 30.30 2.40
407 408 2.688446 TGGCGACGAGATAATTCTGACT 59.312 45.455 0.00 0.00 30.30 3.41
417 418 2.767536 CCAACAATGGCGACGAGAT 58.232 52.632 0.00 0.00 40.58 2.75
432 433 1.668101 GCCAAACAACGGACCACCAA 61.668 55.000 0.00 0.00 35.59 3.67
443 444 2.875296 ACAAGGAGCTATGCCAAACAA 58.125 42.857 0.00 0.00 0.00 2.83
470 471 1.596752 CTACCACAGCAACCGCACA 60.597 57.895 0.00 0.00 42.27 4.57
471 472 2.325082 CCTACCACAGCAACCGCAC 61.325 63.158 0.00 0.00 42.27 5.34
480 481 2.890766 AACGGTGCCCCTACCACAG 61.891 63.158 0.00 0.00 40.89 3.66
482 483 2.193087 ATCAACGGTGCCCCTACCAC 62.193 60.000 0.00 0.00 40.89 4.16
502 503 3.609853 TCAGAGTTCACTGCAAACAAGT 58.390 40.909 2.79 0.00 37.75 3.16
535 536 2.392662 TCACCATCATCACTCCTCTCC 58.607 52.381 0.00 0.00 0.00 3.71
536 537 3.387374 ACATCACCATCATCACTCCTCTC 59.613 47.826 0.00 0.00 0.00 3.20
550 551 1.539388 GGTCGAATGCAAACATCACCA 59.461 47.619 0.00 0.00 34.62 4.17
552 553 3.058293 TGAAGGTCGAATGCAAACATCAC 60.058 43.478 0.00 0.00 34.62 3.06
554 555 3.829886 TGAAGGTCGAATGCAAACATC 57.170 42.857 0.00 0.00 34.62 3.06
572 573 2.303022 GTTGAAGAGAGGACCACCATGA 59.697 50.000 0.00 0.00 38.94 3.07
605 606 4.220382 TCGATCTGGGCATCAAAACAAAAT 59.780 37.500 0.00 0.00 0.00 1.82
613 614 0.178767 CCTGTCGATCTGGGCATCAA 59.821 55.000 0.00 0.00 0.00 2.57
618 619 4.899239 CCGCCTGTCGATCTGGGC 62.899 72.222 9.73 9.73 41.67 5.36
644 645 2.704725 AAACTGCTACAAATGCCGTG 57.295 45.000 0.00 0.00 0.00 4.94
645 646 3.726291 AAAAACTGCTACAAATGCCGT 57.274 38.095 0.00 0.00 0.00 5.68
646 647 5.512788 CAGATAAAAACTGCTACAAATGCCG 59.487 40.000 0.00 0.00 0.00 5.69
712 718 6.096282 TGGGGCTAAAATATTTGTCTTGTAGC 59.904 38.462 14.74 14.74 33.55 3.58
767 773 4.806247 GTGCATTAGTTCGAGCTTGACTAT 59.194 41.667 7.22 0.00 0.00 2.12
778 784 4.787563 GCATGATTGAGGTGCATTAGTTCG 60.788 45.833 0.00 0.00 38.68 3.95
826 832 0.038166 GCCCCCACATCTCACTCAAA 59.962 55.000 0.00 0.00 0.00 2.69
844 850 3.437049 GTCTACATGTTTGGAAGTCCTGC 59.563 47.826 2.30 0.00 36.82 4.85
847 853 4.015872 TGGTCTACATGTTTGGAAGTCC 57.984 45.455 2.30 2.68 0.00 3.85
857 863 4.760204 GGTAAGCAACTTTGGTCTACATGT 59.240 41.667 2.69 2.69 38.04 3.21
875 881 1.674322 CCCACGCCAACAGGGTAAG 60.674 63.158 0.00 0.00 40.21 2.34
881 887 3.901797 GAGGACCCCACGCCAACAG 62.902 68.421 0.00 0.00 0.00 3.16
882 888 3.948719 GAGGACCCCACGCCAACA 61.949 66.667 0.00 0.00 0.00 3.33
948 956 1.985473 TTGTTTGATGCCAGTGAGCT 58.015 45.000 0.00 0.00 0.00 4.09
983 991 4.738124 CAGCATATATACTGACCAGGTCG 58.262 47.826 15.24 11.84 35.90 4.79
1009 1017 4.097361 GACGGACCCCTGGCTTCC 62.097 72.222 2.43 2.43 0.00 3.46
1024 1032 0.109689 AAGTGAGTGCTACGAGCGAC 60.110 55.000 0.00 0.00 46.26 5.19
1041 1049 0.038159 CCTCGGCCCTCGCTAATAAG 60.038 60.000 0.00 0.00 39.05 1.73
1042 1050 1.469335 CCCTCGGCCCTCGCTAATAA 61.469 60.000 0.00 0.00 39.05 1.40
1043 1051 1.906824 CCCTCGGCCCTCGCTAATA 60.907 63.158 0.00 0.00 39.05 0.98
1044 1052 3.234730 CCCTCGGCCCTCGCTAAT 61.235 66.667 0.00 0.00 39.05 1.73
1122 1131 1.998315 CTCGACATGTTGCTCCAAGAG 59.002 52.381 8.34 0.00 0.00 2.85
1198 1207 4.149571 CAGCTGATACACATAATCACGCTC 59.850 45.833 8.42 0.00 36.54 5.03
1212 1471 2.924290 GACTGACCGAAACAGCTGATAC 59.076 50.000 23.35 9.55 38.74 2.24
1214 1473 1.338200 GGACTGACCGAAACAGCTGAT 60.338 52.381 23.35 5.41 38.74 2.90
1215 1474 0.033504 GGACTGACCGAAACAGCTGA 59.966 55.000 23.35 0.00 38.74 4.26
1219 1478 2.341257 CATCAGGACTGACCGAAACAG 58.659 52.381 3.82 0.00 43.11 3.16
1220 1479 1.001974 CCATCAGGACTGACCGAAACA 59.998 52.381 3.82 0.00 43.11 2.83
1227 1486 1.537202 GTTTGCACCATCAGGACTGAC 59.463 52.381 3.82 0.00 43.11 3.51
1245 1504 9.145865 AGTTAAACATCACGAAAACAAATTGTT 57.854 25.926 5.41 5.41 43.41 2.83
1246 1505 8.591312 CAGTTAAACATCACGAAAACAAATTGT 58.409 29.630 0.00 0.00 0.00 2.71
1247 1506 8.055402 CCAGTTAAACATCACGAAAACAAATTG 58.945 33.333 0.00 0.00 0.00 2.32
1248 1507 7.254286 GCCAGTTAAACATCACGAAAACAAATT 60.254 33.333 0.00 0.00 0.00 1.82
1249 1508 6.200097 GCCAGTTAAACATCACGAAAACAAAT 59.800 34.615 0.00 0.00 0.00 2.32
1259 1518 1.535462 ACGCAGCCAGTTAAACATCAC 59.465 47.619 0.00 0.00 0.00 3.06
1269 1528 3.120086 AACTGGGAACGCAGCCAGT 62.120 57.895 16.62 0.00 44.08 4.00
1283 1558 2.356135 CAAGATTACCGGTGGGAACTG 58.644 52.381 19.93 3.60 36.97 3.16
1289 1564 1.408266 CCTTCCCAAGATTACCGGTGG 60.408 57.143 19.93 8.66 0.00 4.61
1291 1566 0.255033 GCCTTCCCAAGATTACCGGT 59.745 55.000 13.98 13.98 0.00 5.28
1293 1568 0.814010 CCGCCTTCCCAAGATTACCG 60.814 60.000 0.00 0.00 0.00 4.02
1295 1570 2.994186 TACCGCCTTCCCAAGATTAC 57.006 50.000 0.00 0.00 0.00 1.89
1297 1572 3.053619 AGAATTACCGCCTTCCCAAGATT 60.054 43.478 0.00 0.00 0.00 2.40
1301 1576 2.823154 CAAAGAATTACCGCCTTCCCAA 59.177 45.455 0.00 0.00 0.00 4.12
1303 1578 2.422479 GACAAAGAATTACCGCCTTCCC 59.578 50.000 0.00 0.00 0.00 3.97
1304 1579 3.078837 TGACAAAGAATTACCGCCTTCC 58.921 45.455 0.00 0.00 0.00 3.46
1305 1580 4.759516 TTGACAAAGAATTACCGCCTTC 57.240 40.909 0.00 0.00 0.00 3.46
1306 1581 5.523438 TTTTGACAAAGAATTACCGCCTT 57.477 34.783 0.10 0.00 0.00 4.35
1307 1582 5.469479 CATTTTGACAAAGAATTACCGCCT 58.531 37.500 0.10 0.00 0.00 5.52
1308 1583 4.625311 CCATTTTGACAAAGAATTACCGCC 59.375 41.667 0.10 0.00 0.00 6.13
1309 1584 5.227152 ACCATTTTGACAAAGAATTACCGC 58.773 37.500 0.10 0.00 0.00 5.68
1311 1586 6.443792 ACGACCATTTTGACAAAGAATTACC 58.556 36.000 0.10 0.00 0.00 2.85
1313 1588 7.265647 TGACGACCATTTTGACAAAGAATTA 57.734 32.000 0.10 0.00 0.00 1.40
1315 1590 5.766150 TGACGACCATTTTGACAAAGAAT 57.234 34.783 0.10 0.00 0.00 2.40
1316 1591 5.298026 TCATGACGACCATTTTGACAAAGAA 59.702 36.000 0.10 0.00 31.94 2.52
1317 1592 4.819088 TCATGACGACCATTTTGACAAAGA 59.181 37.500 0.10 0.00 31.94 2.52
1318 1593 5.107109 TCATGACGACCATTTTGACAAAG 57.893 39.130 0.10 0.00 31.94 2.77
1319 1594 5.703978 ATCATGACGACCATTTTGACAAA 57.296 34.783 0.00 0.00 31.94 2.83
1321 1596 4.328712 CGTATCATGACGACCATTTTGACA 59.671 41.667 0.00 0.00 45.82 3.58
1323 1598 3.868661 CCGTATCATGACGACCATTTTGA 59.131 43.478 8.40 0.00 45.82 2.69
1325 1600 3.621268 CACCGTATCATGACGACCATTTT 59.379 43.478 8.40 0.00 45.82 1.82
1326 1601 3.194861 CACCGTATCATGACGACCATTT 58.805 45.455 8.40 0.00 45.82 2.32
1327 1602 2.821546 CACCGTATCATGACGACCATT 58.178 47.619 8.40 0.00 45.82 3.16
1328 1603 1.538204 GCACCGTATCATGACGACCAT 60.538 52.381 8.40 0.00 45.82 3.55
1329 1604 0.179121 GCACCGTATCATGACGACCA 60.179 55.000 8.40 0.00 45.82 4.02
1331 1606 0.874607 GGGCACCGTATCATGACGAC 60.875 60.000 8.40 4.24 45.82 4.34
1332 1607 1.440060 GGGCACCGTATCATGACGA 59.560 57.895 8.40 0.00 45.82 4.20
1333 1608 4.027755 GGGCACCGTATCATGACG 57.972 61.111 0.00 0.00 40.86 4.35
1346 1621 4.240103 CATGGAGATCGCCGGGCA 62.240 66.667 20.71 6.72 0.00 5.36
1349 1624 4.592192 ACGCATGGAGATCGCCGG 62.592 66.667 11.16 6.79 0.00 6.13
1350 1625 3.032609 GACGCATGGAGATCGCCG 61.033 66.667 11.16 1.22 0.00 6.46
1351 1626 1.953138 CAGACGCATGGAGATCGCC 60.953 63.158 8.81 8.81 0.00 5.54
1352 1627 1.953138 CCAGACGCATGGAGATCGC 60.953 63.158 0.10 0.00 43.57 4.58
1353 1628 1.953138 GCCAGACGCATGGAGATCG 60.953 63.158 10.55 0.00 43.57 3.69
1354 1629 1.144716 TGCCAGACGCATGGAGATC 59.855 57.895 10.55 0.00 44.64 2.75
1355 1630 3.312799 TGCCAGACGCATGGAGAT 58.687 55.556 10.55 0.00 44.64 2.75
1402 1677 1.272490 ACTGCGTTGCTAGCTAGTTGA 59.728 47.619 21.62 5.76 35.28 3.18
1403 1678 1.714794 ACTGCGTTGCTAGCTAGTTG 58.285 50.000 21.62 10.27 35.28 3.16
1405 1680 1.404315 GGAACTGCGTTGCTAGCTAGT 60.404 52.381 21.62 9.40 31.28 2.57
1421 1711 7.040961 TGCTAGTTGGTAAATTTACTGTGGAAC 60.041 37.037 23.89 17.79 34.16 3.62
1424 1714 6.811253 TGCTAGTTGGTAAATTTACTGTGG 57.189 37.500 23.89 11.53 34.16 4.17
1433 1723 5.105756 GGATGCTTGTTGCTAGTTGGTAAAT 60.106 40.000 0.00 0.00 43.37 1.40
1434 1724 4.217550 GGATGCTTGTTGCTAGTTGGTAAA 59.782 41.667 0.00 0.00 43.37 2.01
1457 1747 6.430925 TGAAGAAGGTGGAGAAATTACATGTG 59.569 38.462 9.11 0.00 0.00 3.21
1459 1749 7.452880 TTGAAGAAGGTGGAGAAATTACATG 57.547 36.000 0.00 0.00 0.00 3.21
1471 1761 3.066760 GGCGGATATTTTGAAGAAGGTGG 59.933 47.826 0.00 0.00 0.00 4.61
1515 1805 5.966742 AGCTCCTTTTTCGATAGCTTTTT 57.033 34.783 0.00 0.00 40.52 1.94
1520 1810 4.061357 AGGTAGCTCCTTTTTCGATAGC 57.939 45.455 0.00 0.00 45.67 2.97
1535 1825 4.065321 ACTGCAGATGTAATGAGGTAGC 57.935 45.455 23.35 0.00 0.00 3.58
1564 1854 2.416547 ACATGAAAGCTACATGCACGAC 59.583 45.455 24.30 0.00 45.95 4.34
1567 1857 2.489329 ACCACATGAAAGCTACATGCAC 59.511 45.455 24.30 0.00 45.95 4.57
1584 1874 6.183360 GCTTGTCTCCAATCAAATACTACCAC 60.183 42.308 0.00 0.00 0.00 4.16
1586 1876 5.880332 TGCTTGTCTCCAATCAAATACTACC 59.120 40.000 0.00 0.00 0.00 3.18
1587 1877 6.985188 TGCTTGTCTCCAATCAAATACTAC 57.015 37.500 0.00 0.00 0.00 2.73
1623 1915 4.947388 TGGGTGCTCTGTATTTATTTCCAC 59.053 41.667 0.00 0.00 0.00 4.02
1677 1971 9.226345 CTTGTAAGAAACAACTTCTGAATTCAC 57.774 33.333 3.38 0.00 44.00 3.18
1680 1974 7.771183 TGCTTGTAAGAAACAACTTCTGAATT 58.229 30.769 0.00 0.00 44.00 2.17
1700 1994 8.184192 CCAACTACTGGTTTAGATATTTGCTTG 58.816 37.037 0.00 0.00 40.78 4.01
1703 1997 7.859325 TCCAACTACTGGTTTAGATATTTGC 57.141 36.000 0.00 0.00 46.51 3.68
1704 1998 9.449719 AGTTCCAACTACTGGTTTAGATATTTG 57.550 33.333 0.00 0.00 46.51 2.32
1707 2001 8.047310 CCAAGTTCCAACTACTGGTTTAGATAT 58.953 37.037 2.97 0.00 46.51 1.63
1708 2002 7.236019 TCCAAGTTCCAACTACTGGTTTAGATA 59.764 37.037 9.16 0.00 46.51 1.98
1710 2004 5.367352 TCCAAGTTCCAACTACTGGTTTAGA 59.633 40.000 9.16 0.00 46.51 2.10
1711 2005 5.617252 TCCAAGTTCCAACTACTGGTTTAG 58.383 41.667 9.16 0.00 46.51 1.85
1712 2006 5.633655 TCCAAGTTCCAACTACTGGTTTA 57.366 39.130 9.16 0.00 46.51 2.01
1715 2009 4.398319 CATTCCAAGTTCCAACTACTGGT 58.602 43.478 9.16 0.00 46.51 4.00
1777 2076 4.943705 TGCAGAAGAAACTGAAACTGAGTT 59.056 37.500 0.00 0.00 39.94 3.01
1779 2078 5.490139 TTGCAGAAGAAACTGAAACTGAG 57.510 39.130 0.00 0.00 39.94 3.35
1810 2116 1.453155 AAGTGCATCAGTAAAGCCCG 58.547 50.000 0.00 0.00 0.00 6.13
1830 2136 5.202004 GAGTGGATCTCTTTAGTACTCCCA 58.798 45.833 0.00 0.00 39.86 4.37
1831 2137 5.068067 GTGAGTGGATCTCTTTAGTACTCCC 59.932 48.000 0.00 0.00 43.13 4.30
1832 2138 5.889289 AGTGAGTGGATCTCTTTAGTACTCC 59.111 44.000 0.00 0.00 43.13 3.85
1833 2139 8.508883 TTAGTGAGTGGATCTCTTTAGTACTC 57.491 38.462 0.00 0.00 43.13 2.59
1853 2159 7.636326 ACAGAAAAGGTGACGTAATTTTAGTG 58.364 34.615 0.00 0.00 0.00 2.74
1857 2163 5.591067 TGGACAGAAAAGGTGACGTAATTTT 59.409 36.000 0.00 0.00 0.00 1.82
1873 2179 5.542635 ACACTACCTTAATCAGTGGACAGAA 59.457 40.000 12.97 0.00 43.18 3.02
2057 2372 1.745087 CCGCCGGAGTTGTAGTAGTAA 59.255 52.381 5.05 0.00 0.00 2.24
2129 2444 2.123077 AGGAGGAGGAGGATGGCG 60.123 66.667 0.00 0.00 0.00 5.69
3038 3353 2.805353 CGAACACGAGCACGAGGG 60.805 66.667 11.40 1.82 42.66 4.30
3039 3354 2.050351 ACGAACACGAGCACGAGG 60.050 61.111 11.40 4.47 42.66 4.63
3040 3355 2.365068 CCACGAACACGAGCACGAG 61.365 63.158 11.40 4.74 42.66 4.18
3041 3356 2.354188 CCACGAACACGAGCACGA 60.354 61.111 11.40 0.00 42.66 4.35
3042 3357 4.059459 GCCACGAACACGAGCACG 62.059 66.667 0.76 0.76 45.75 5.34
3043 3358 3.712881 GGCCACGAACACGAGCAC 61.713 66.667 0.00 0.00 33.97 4.40
3044 3359 3.741830 TTGGCCACGAACACGAGCA 62.742 57.895 3.88 0.00 33.97 4.26
3045 3360 2.539338 TTTGGCCACGAACACGAGC 61.539 57.895 3.88 0.00 0.00 5.03
3046 3361 1.278637 GTTTGGCCACGAACACGAG 59.721 57.895 3.88 0.00 40.15 4.18
3047 3362 1.449778 TGTTTGGCCACGAACACGA 60.450 52.632 17.27 0.00 44.15 4.35
3048 3363 3.102985 TGTTTGGCCACGAACACG 58.897 55.556 17.27 0.00 44.15 4.49
3050 3365 0.179124 GCTTTGTTTGGCCACGAACA 60.179 50.000 17.27 17.27 46.61 3.18
3051 3366 0.102300 AGCTTTGTTTGGCCACGAAC 59.898 50.000 3.88 9.52 40.70 3.95
3052 3367 1.681538 TAGCTTTGTTTGGCCACGAA 58.318 45.000 3.88 0.00 0.00 3.85
3053 3368 1.681538 TTAGCTTTGTTTGGCCACGA 58.318 45.000 3.88 0.00 0.00 4.35
3054 3369 2.500509 TTTAGCTTTGTTTGGCCACG 57.499 45.000 3.88 0.00 0.00 4.94
3055 3370 5.755861 TGTAATTTTAGCTTTGTTTGGCCAC 59.244 36.000 3.88 0.00 0.00 5.01
3188 3544 9.847706 TGCATGTTATAATACATTGTTTTTCGT 57.152 25.926 0.00 0.00 36.64 3.85
3198 3554 5.304778 TCGTGCCTGCATGTTATAATACAT 58.695 37.500 10.87 0.00 39.27 2.29
3199 3555 4.698575 TCGTGCCTGCATGTTATAATACA 58.301 39.130 10.87 0.00 34.75 2.29
3271 3629 4.129380 CCATCTCATGTCATTTTCCGCTA 58.871 43.478 0.00 0.00 0.00 4.26
3291 3649 5.250200 AGCCTGTAAAAACGATTGATACCA 58.750 37.500 0.00 0.00 0.00 3.25
3292 3650 5.813080 AGCCTGTAAAAACGATTGATACC 57.187 39.130 0.00 0.00 0.00 2.73
3301 3659 3.347958 TGAGCAAAGCCTGTAAAAACG 57.652 42.857 0.00 0.00 0.00 3.60
3345 3707 2.828520 TGTTTCACCTTGTCTTTTGCCA 59.171 40.909 0.00 0.00 0.00 4.92
3427 8542 7.812191 GGTATGACAATCAAAGCATGTGTTTTA 59.188 33.333 0.00 0.00 0.00 1.52
3428 8543 6.646240 GGTATGACAATCAAAGCATGTGTTTT 59.354 34.615 0.00 0.00 0.00 2.43
3429 8544 6.158598 GGTATGACAATCAAAGCATGTGTTT 58.841 36.000 0.00 0.00 0.00 2.83
3453 8568 7.609760 TTTGCACTATTATGTGGTAGTTCTG 57.390 36.000 0.00 0.00 38.31 3.02
3539 8657 0.249114 GAAGACTAGCTAGTGCGGGC 60.249 60.000 30.70 15.51 45.42 6.13
3583 8701 3.644399 GAACACCCTCGAGCCCGAC 62.644 68.421 6.99 0.00 40.30 4.79
3586 8704 2.579738 GAGAACACCCTCGAGCCC 59.420 66.667 6.99 0.00 0.00 5.19
3592 8710 1.134965 CACGAGATGGAGAACACCCTC 60.135 57.143 0.00 0.00 0.00 4.30
3670 8788 1.447838 GATCCGCGCACTGGAGAAA 60.448 57.895 8.75 0.00 39.30 2.52
3806 8924 4.161565 TGCTATCGTCTGGTTGGTATCTTT 59.838 41.667 0.00 0.00 0.00 2.52
3827 8945 4.640201 TGCAAACCTGGAATAGATTAGTGC 59.360 41.667 0.00 0.00 0.00 4.40
3841 8959 4.976224 TCATGATTGATCTGCAAACCTG 57.024 40.909 0.00 0.00 40.48 4.00
3857 8975 8.141298 TGTTGGACCTAACTAACTAATCATGA 57.859 34.615 0.00 0.00 33.52 3.07
3956 9085 1.959985 TCGTGTTTGCACCATTGGAAT 59.040 42.857 10.37 0.00 42.39 3.01
3962 9091 2.090760 TGCATATCGTGTTTGCACCAT 58.909 42.857 0.00 0.00 41.18 3.55


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

AutoCloner maintained by Alex Coulton.