Multiple sequence alignment - TraesCS4B01G256500

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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 TraesCS4B01G256500 chr4B 100.000 8765 0 0 1 8765 522076876 522085640 0.000000e+00 16187
1 TraesCS4B01G256500 chr2A 99.620 5257 17 2 1433 6688 513661847 513656593 0.000000e+00 9594
2 TraesCS4B01G256500 chr2A 100.000 161 0 0 1432 1592 513656751 513656591 1.850000e-76 298
3 TraesCS4B01G256500 chr1A 99.544 5259 20 3 1434 6690 577781830 577776574 0.000000e+00 9575
4 TraesCS4B01G256500 chr1A 89.930 2870 205 30 1874 4720 364047801 364050609 0.000000e+00 3622
5 TraesCS4B01G256500 chr5D 90.752 5277 403 58 1433 6678 258841643 258836421 0.000000e+00 6962
6 TraesCS4B01G256500 chr5D 95.294 3230 105 17 1434 4651 298059502 298062696 0.000000e+00 5079
7 TraesCS4B01G256500 chr5D 97.078 1985 54 3 4702 6686 298062633 298064613 0.000000e+00 3341
8 TraesCS4B01G256500 chr7D 92.658 4195 260 21 2054 6233 595387596 595383435 0.000000e+00 5997
9 TraesCS4B01G256500 chr7D 93.968 630 29 5 1432 2055 595397497 595396871 0.000000e+00 944
10 TraesCS4B01G256500 chr3B 96.458 3360 90 9 1434 4768 96866220 96869575 0.000000e+00 5518
11 TraesCS4B01G256500 chr3B 97.568 2097 49 2 4592 6688 96869438 96871532 0.000000e+00 3589
12 TraesCS4B01G256500 chrUn 94.014 2957 130 10 1433 4371 16650962 16653889 0.000000e+00 4436
13 TraesCS4B01G256500 chrUn 94.548 642 27 4 1433 2068 16601556 16602195 0.000000e+00 985
14 TraesCS4B01G256500 chr1B 89.741 3324 247 66 1434 4720 179501042 179504308 0.000000e+00 4163
15 TraesCS4B01G256500 chr5A 91.528 2880 203 23 1862 4718 688367879 688365018 0.000000e+00 3928
16 TraesCS4B01G256500 chr2D 91.655 2864 165 28 1880 4725 13248638 13251445 0.000000e+00 3897
17 TraesCS4B01G256500 chr2D 95.791 1948 76 4 4741 6688 539316254 539318195 0.000000e+00 3138
18 TraesCS4B01G256500 chr2D 92.594 2012 133 10 4663 6672 13251327 13253324 0.000000e+00 2876
19 TraesCS4B01G256500 chr4D 91.114 2037 165 11 4648 6678 245245795 245247821 0.000000e+00 2745
20 TraesCS4B01G256500 chr4D 94.058 1481 53 10 6689 8144 425973640 425975110 0.000000e+00 2215
21 TraesCS4B01G256500 chr4D 89.906 1486 75 31 1 1433 425972181 425973644 0.000000e+00 1844
22 TraesCS4B01G256500 chr4D 93.293 820 55 0 2209 3028 245243279 245244098 0.000000e+00 1210
23 TraesCS4B01G256500 chr4D 89.971 339 15 8 8193 8512 425975121 425975459 3.780000e-113 420
24 TraesCS4B01G256500 chr3A 92.104 1887 138 8 4683 6569 717925833 717927708 0.000000e+00 2649
25 TraesCS4B01G256500 chr3A 89.229 1569 130 23 1515 3068 717922420 717923964 0.000000e+00 1925
26 TraesCS4B01G256500 chr3A 100.000 254 0 0 8512 8765 544193295 544193042 3.700000e-128 470
27 TraesCS4B01G256500 chr3A 100.000 253 0 0 8513 8765 634726061 634726313 1.330000e-127 468
28 TraesCS4B01G256500 chr3A 100.000 253 0 0 8513 8765 742312509 742312761 1.330000e-127 468
29 TraesCS4B01G256500 chr3A 81.667 240 26 8 8513 8749 707405129 707405353 5.400000e-42 183
30 TraesCS4B01G256500 chr3A 97.403 77 1 1 8512 8588 742299059 742299134 7.140000e-26 130
31 TraesCS4B01G256500 chr4A 88.830 1880 106 35 6689 8512 39052602 39050771 0.000000e+00 2213
32 TraesCS4B01G256500 chr4A 87.405 1445 97 39 36 1433 39054004 39052598 0.000000e+00 1581
33 TraesCS4B01G256500 chr6A 88.433 1781 196 5 4891 6667 88074191 88072417 0.000000e+00 2139
34 TraesCS4B01G256500 chr6A 91.592 1225 89 8 1880 3104 129321977 129323187 0.000000e+00 1679
35 TraesCS4B01G256500 chr6A 93.301 209 8 3 1434 1641 129321537 129321740 3.980000e-78 303
36 TraesCS4B01G256500 chr7B 99.611 257 1 0 8509 8765 605953010 605953266 3.700000e-128 470
37 TraesCS4B01G256500 chr7B 82.158 241 25 8 8512 8749 4136057 4136282 3.230000e-44 191


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 TraesCS4B01G256500 chr4B 522076876 522085640 8764 False 16187.0 16187 100.000000 1 8765 1 chr4B.!!$F1 8764
1 TraesCS4B01G256500 chr2A 513656591 513661847 5256 True 4946.0 9594 99.810000 1432 6688 2 chr2A.!!$R1 5256
2 TraesCS4B01G256500 chr1A 577776574 577781830 5256 True 9575.0 9575 99.544000 1434 6690 1 chr1A.!!$R1 5256
3 TraesCS4B01G256500 chr1A 364047801 364050609 2808 False 3622.0 3622 89.930000 1874 4720 1 chr1A.!!$F1 2846
4 TraesCS4B01G256500 chr5D 258836421 258841643 5222 True 6962.0 6962 90.752000 1433 6678 1 chr5D.!!$R1 5245
5 TraesCS4B01G256500 chr5D 298059502 298064613 5111 False 4210.0 5079 96.186000 1434 6686 2 chr5D.!!$F1 5252
6 TraesCS4B01G256500 chr7D 595383435 595387596 4161 True 5997.0 5997 92.658000 2054 6233 1 chr7D.!!$R1 4179
7 TraesCS4B01G256500 chr7D 595396871 595397497 626 True 944.0 944 93.968000 1432 2055 1 chr7D.!!$R2 623
8 TraesCS4B01G256500 chr3B 96866220 96871532 5312 False 4553.5 5518 97.013000 1434 6688 2 chr3B.!!$F1 5254
9 TraesCS4B01G256500 chrUn 16650962 16653889 2927 False 4436.0 4436 94.014000 1433 4371 1 chrUn.!!$F2 2938
10 TraesCS4B01G256500 chrUn 16601556 16602195 639 False 985.0 985 94.548000 1433 2068 1 chrUn.!!$F1 635
11 TraesCS4B01G256500 chr1B 179501042 179504308 3266 False 4163.0 4163 89.741000 1434 4720 1 chr1B.!!$F1 3286
12 TraesCS4B01G256500 chr5A 688365018 688367879 2861 True 3928.0 3928 91.528000 1862 4718 1 chr5A.!!$R1 2856
13 TraesCS4B01G256500 chr2D 13248638 13253324 4686 False 3386.5 3897 92.124500 1880 6672 2 chr2D.!!$F2 4792
14 TraesCS4B01G256500 chr2D 539316254 539318195 1941 False 3138.0 3138 95.791000 4741 6688 1 chr2D.!!$F1 1947
15 TraesCS4B01G256500 chr4D 245243279 245247821 4542 False 1977.5 2745 92.203500 2209 6678 2 chr4D.!!$F1 4469
16 TraesCS4B01G256500 chr4D 425972181 425975459 3278 False 1493.0 2215 91.311667 1 8512 3 chr4D.!!$F2 8511
17 TraesCS4B01G256500 chr3A 717922420 717927708 5288 False 2287.0 2649 90.666500 1515 6569 2 chr3A.!!$F5 5054
18 TraesCS4B01G256500 chr4A 39050771 39054004 3233 True 1897.0 2213 88.117500 36 8512 2 chr4A.!!$R1 8476
19 TraesCS4B01G256500 chr6A 88072417 88074191 1774 True 2139.0 2139 88.433000 4891 6667 1 chr6A.!!$R1 1776
20 TraesCS4B01G256500 chr6A 129321537 129323187 1650 False 991.0 1679 92.446500 1434 3104 2 chr6A.!!$F1 1670

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
931 998 0.384309 GCCTATCGTCGACATGACCA 59.616 55.000 17.16 0.0 45.23 4.02 F
1211 1293 0.034616 GCCTGCTGCCCTATCTGTAG 59.965 60.000 0.00 0.0 0.00 2.74 F
1230 1312 0.108615 GCTCTGTGCATCGTAGGTGT 60.109 55.000 0.00 0.0 42.31 4.16 F
1237 1319 1.001048 TGCATCGTAGGTGTATACGCC 60.001 52.381 25.20 25.2 46.28 5.68 F
4028 4602 0.322098 CCAACCACGGCACCATCTTA 60.322 55.000 0.00 0.0 0.00 2.10 F
6504 7381 1.378646 TCCAGTCTCTGCGTCGGAT 60.379 57.895 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2679 2922 4.016706 GGTGTGCCGTAGCCACCT 62.017 66.667 14.57 0.00 38.69 4.00 R
3674 4243 2.417586 TGCTTGACAAGAATGAGCATCG 59.582 45.455 19.51 0.00 38.33 3.84 R
4028 4602 2.027837 GGTGTATGGACAGGTTAACCGT 60.028 50.000 18.91 18.43 42.08 4.83 R
5624 6499 1.226407 CTCAGCGCGAAGACGATCA 60.226 57.895 12.10 0.00 42.66 2.92 R
7452 8357 0.782384 CGAACGGACGGAAGAAGTTG 59.218 55.000 0.00 0.00 0.00 3.16 R
8609 9576 0.032403 AAGCCACGTACACTTGCGTA 59.968 50.000 0.00 0.00 42.75 4.42 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
26 27 1.734477 CGTCGGCACAGGACAGAAG 60.734 63.158 0.00 0.00 34.04 2.85
39 40 4.711355 CAGGACAGAAGAGGAGAGAAAGAT 59.289 45.833 0.00 0.00 0.00 2.40
166 171 2.359975 GGCGAGTTGGGTTCAGGG 60.360 66.667 0.00 0.00 0.00 4.45
167 172 2.359975 GCGAGTTGGGTTCAGGGG 60.360 66.667 0.00 0.00 0.00 4.79
168 173 2.351276 CGAGTTGGGTTCAGGGGG 59.649 66.667 0.00 0.00 0.00 5.40
169 174 2.526046 CGAGTTGGGTTCAGGGGGT 61.526 63.158 0.00 0.00 0.00 4.95
170 175 1.196104 CGAGTTGGGTTCAGGGGGTA 61.196 60.000 0.00 0.00 0.00 3.69
201 208 1.659794 GTCGCAATGTTGGCCTTGT 59.340 52.632 3.32 0.00 0.00 3.16
207 214 2.513753 CAATGTTGGCCTTGTCCTACA 58.486 47.619 3.32 0.13 43.76 2.74
210 217 1.493022 TGTTGGCCTTGTCCTACAACT 59.507 47.619 3.32 0.00 41.32 3.16
234 241 5.874810 TGACTCAGAAAACCATATTCCTTCG 59.125 40.000 0.00 0.00 0.00 3.79
301 316 2.867368 TGTTAGTGTTGTAACGCCACTG 59.133 45.455 4.80 0.00 39.63 3.66
352 367 3.873883 GCGAGCCAGAGCATGCAC 61.874 66.667 21.98 14.59 43.56 4.57
354 369 2.036571 CGAGCCAGAGCATGCACAA 61.037 57.895 21.98 0.00 43.56 3.33
355 370 1.801332 GAGCCAGAGCATGCACAAG 59.199 57.895 21.98 10.14 43.56 3.16
381 399 2.698274 CAGGTGTAAAGGGGCAGTTTTT 59.302 45.455 0.00 0.00 0.00 1.94
409 430 5.523916 CCACTATCCAAAGACCTTAATGTCG 59.476 44.000 5.39 0.00 40.26 4.35
435 456 1.843734 TTTCACGGCGCCTTAAACGG 61.844 55.000 26.68 9.51 0.00 4.44
471 497 2.014857 CCAATCATGTGCTCCACTCTG 58.985 52.381 0.00 0.00 35.11 3.35
472 498 2.355412 CCAATCATGTGCTCCACTCTGA 60.355 50.000 0.00 1.31 35.11 3.27
473 499 2.937149 CAATCATGTGCTCCACTCTGAG 59.063 50.000 2.45 2.45 33.18 3.35
480 511 3.776616 CTCCACTCTGAGCCCATTC 57.223 57.895 4.19 0.00 0.00 2.67
483 514 1.988107 TCCACTCTGAGCCCATTCTTT 59.012 47.619 4.19 0.00 0.00 2.52
527 568 0.948678 CTCGGAAAACCAAAAGGCGA 59.051 50.000 0.00 0.00 0.00 5.54
653 694 6.147000 GTCTGCAGTTTTTCTTTTTGGTTCAA 59.853 34.615 14.67 0.00 0.00 2.69
657 698 6.147000 GCAGTTTTTCTTTTTGGTTCAACTCA 59.853 34.615 0.00 0.00 0.00 3.41
728 780 7.527457 CGAAATCCTCTTCGGTTTTTAATTCT 58.473 34.615 0.00 0.00 43.51 2.40
736 788 3.187637 TCGGTTTTTAATTCTGGTCTGCG 59.812 43.478 0.00 0.00 0.00 5.18
740 792 3.334583 TTTAATTCTGGTCTGCGAGCT 57.665 42.857 8.71 0.00 0.00 4.09
764 816 2.904434 GGAGGCGAAGGGATAGGAATTA 59.096 50.000 0.00 0.00 0.00 1.40
765 817 3.055747 GGAGGCGAAGGGATAGGAATTAG 60.056 52.174 0.00 0.00 0.00 1.73
766 818 2.907042 AGGCGAAGGGATAGGAATTAGG 59.093 50.000 0.00 0.00 0.00 2.69
767 819 2.027100 GGCGAAGGGATAGGAATTAGGG 60.027 54.545 0.00 0.00 0.00 3.53
768 820 2.904434 GCGAAGGGATAGGAATTAGGGA 59.096 50.000 0.00 0.00 0.00 4.20
776 833 6.068794 AGGGATAGGAATTAGGGAATTATGGC 60.069 42.308 0.00 0.00 35.33 4.40
779 836 3.074538 AGGAATTAGGGAATTATGGCGCT 59.925 43.478 7.64 0.00 35.33 5.92
811 868 7.525360 GCCAAGGATAGGAAAAGAATTCAAACA 60.525 37.037 8.44 0.00 0.00 2.83
895 956 2.358195 GCTTTCTCCTCTCCTCTCCTCT 60.358 54.545 0.00 0.00 0.00 3.69
906 967 0.998945 CTCTCCTCTCCTCCTCCCCT 60.999 65.000 0.00 0.00 0.00 4.79
908 969 2.015726 TCCTCTCCTCCTCCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
931 998 0.384309 GCCTATCGTCGACATGACCA 59.616 55.000 17.16 0.00 45.23 4.02
939 1006 1.132453 GTCGACATGACCACAGATCGA 59.868 52.381 11.55 0.00 42.04 3.59
957 1024 0.952984 GAGTGAAGCTGGCTGTGGAC 60.953 60.000 0.00 0.00 0.00 4.02
996 1078 1.402259 CGGATACAGTCGAGCTTGAGT 59.598 52.381 3.10 4.34 0.00 3.41
1104 1186 4.373116 GAGTGCGAGGTCGGCCAA 62.373 66.667 9.71 0.00 40.23 4.52
1185 1267 2.423446 CCGGCCTACCTCATGCTC 59.577 66.667 0.00 0.00 0.00 4.26
1206 1288 0.469917 TAAGTGCCTGCTGCCCTATC 59.530 55.000 0.00 0.00 40.16 2.08
1211 1293 0.034616 GCCTGCTGCCCTATCTGTAG 59.965 60.000 0.00 0.00 0.00 2.74
1225 1307 2.365582 TCTGTAGCTCTGTGCATCGTA 58.634 47.619 4.39 0.00 45.94 3.43
1226 1308 2.356069 TCTGTAGCTCTGTGCATCGTAG 59.644 50.000 4.39 0.00 45.94 3.51
1227 1309 1.405463 TGTAGCTCTGTGCATCGTAGG 59.595 52.381 4.39 0.00 45.94 3.18
1228 1310 1.405821 GTAGCTCTGTGCATCGTAGGT 59.594 52.381 4.39 0.00 45.94 3.08
1229 1311 0.174389 AGCTCTGTGCATCGTAGGTG 59.826 55.000 4.39 0.00 45.94 4.00
1230 1312 0.108615 GCTCTGTGCATCGTAGGTGT 60.109 55.000 0.00 0.00 42.31 4.16
1231 1313 1.134367 GCTCTGTGCATCGTAGGTGTA 59.866 52.381 0.00 0.00 42.31 2.90
1232 1314 2.223829 GCTCTGTGCATCGTAGGTGTAT 60.224 50.000 0.00 0.00 42.31 2.29
1233 1315 3.004419 GCTCTGTGCATCGTAGGTGTATA 59.996 47.826 0.00 0.00 42.31 1.47
1234 1316 4.537965 CTCTGTGCATCGTAGGTGTATAC 58.462 47.826 0.00 0.00 0.00 1.47
1236 1318 2.049228 GTGCATCGTAGGTGTATACGC 58.951 52.381 7.95 7.95 46.28 4.42
1237 1319 1.001048 TGCATCGTAGGTGTATACGCC 60.001 52.381 25.20 25.20 46.28 5.68
4028 4602 0.322098 CCAACCACGGCACCATCTTA 60.322 55.000 0.00 0.00 0.00 2.10
5624 6499 2.558795 TGCTCTTCTTCGACAGCTTACT 59.441 45.455 0.00 0.00 32.76 2.24
6504 7381 1.378646 TCCAGTCTCTGCGTCGGAT 60.379 57.895 0.00 0.00 0.00 4.18
6690 7572 6.716934 TCAATCCTCTAATCTCCTACACAC 57.283 41.667 0.00 0.00 0.00 3.82
6691 7573 5.299531 TCAATCCTCTAATCTCCTACACACG 59.700 44.000 0.00 0.00 0.00 4.49
6692 7574 3.552875 TCCTCTAATCTCCTACACACGG 58.447 50.000 0.00 0.00 0.00 4.94
6693 7575 2.623889 CCTCTAATCTCCTACACACGGG 59.376 54.545 0.00 0.00 0.00 5.28
6694 7576 3.552875 CTCTAATCTCCTACACACGGGA 58.447 50.000 0.00 0.00 0.00 5.14
6790 7672 8.327429 CACAGGTAAAACACAATTGAATTGAAC 58.673 33.333 23.37 10.82 42.83 3.18
6795 7677 9.900264 GTAAAACACAATTGAATTGAACTGAAC 57.100 29.630 23.37 10.89 42.83 3.18
6924 7829 1.992834 TTGCAGGAGGATGGGCGTA 60.993 57.895 0.00 0.00 0.00 4.42
6961 7866 1.599047 CATCTGGAGCGGTGGTTCT 59.401 57.895 0.00 0.00 0.00 3.01
6981 7886 2.737180 CTGATGGGCGCCGAGTAT 59.263 61.111 22.54 12.12 0.00 2.12
7049 7954 4.132441 CGGGCGGTGCGGTTACTA 62.132 66.667 0.00 0.00 0.00 1.82
7056 7961 2.137523 CGGTGCGGTTACTACAAGTTT 58.862 47.619 0.00 0.00 0.00 2.66
7134 8039 3.733960 GCGGCCGTTTTGTCCCTC 61.734 66.667 28.70 0.93 0.00 4.30
7167 8072 4.129737 GAGCAGCTGTACCGCCGA 62.130 66.667 16.64 0.00 0.00 5.54
7464 8369 0.250166 CCGTTCCCAACTTCTTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
7494 8399 4.424566 TGGTTCGCGTACGGCCTC 62.425 66.667 18.39 0.00 40.63 4.70
7683 8588 2.032860 GCATGAAGCGGCTAGGAGGA 62.033 60.000 1.35 0.00 0.00 3.71
7899 8814 4.137543 TCCTTTTTCTGGCAGAGAAGAAC 58.862 43.478 29.24 0.00 41.86 3.01
7911 8826 6.183360 TGGCAGAGAAGAACAGAAAAGAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
7912 8827 6.038714 GGCAGAGAAGAACAGAAAAGAAAAGA 59.961 38.462 0.00 0.00 0.00 2.52
7913 8828 7.415653 GGCAGAGAAGAACAGAAAAGAAAAGAA 60.416 37.037 0.00 0.00 0.00 2.52
7914 8829 7.970614 GCAGAGAAGAACAGAAAAGAAAAGAAA 59.029 33.333 0.00 0.00 0.00 2.52
7915 8830 9.846248 CAGAGAAGAACAGAAAAGAAAAGAAAA 57.154 29.630 0.00 0.00 0.00 2.29
8015 8939 3.443925 CGAGAGCCAGCCGTCTCA 61.444 66.667 8.94 0.00 39.43 3.27
8086 9018 1.786937 AGATGCTACTCACCCTGGAG 58.213 55.000 0.00 0.00 40.79 3.86
8166 9102 0.442310 CCGGCCATATTATTGCGACG 59.558 55.000 2.24 0.00 0.00 5.12
8167 9103 0.442310 CGGCCATATTATTGCGACGG 59.558 55.000 2.24 0.00 0.00 4.79
8189 9125 6.783708 GGCTAGATAGGCATATGAACTAGT 57.216 41.667 6.97 0.00 46.94 2.57
8190 9126 7.883391 GGCTAGATAGGCATATGAACTAGTA 57.117 40.000 6.97 3.92 46.94 1.82
8191 9127 7.936584 GGCTAGATAGGCATATGAACTAGTAG 58.063 42.308 6.97 12.53 46.94 2.57
8239 9178 1.548081 CCATCCAACTCAATGCACCA 58.452 50.000 0.00 0.00 0.00 4.17
8270 9209 1.460273 TATCTACGCGGCTCATGGCA 61.460 55.000 12.47 0.00 44.01 4.92
8393 9333 3.205536 GCCCAGCTTAGCTTCGCC 61.206 66.667 3.00 0.00 36.40 5.54
8411 9351 4.067016 CGTTCGTTTGACCGGCCG 62.067 66.667 21.04 21.04 0.00 6.13
8512 9479 0.457337 CGTACTGCGACCACCTAACC 60.457 60.000 0.00 0.00 44.77 2.85
8513 9480 0.604578 GTACTGCGACCACCTAACCA 59.395 55.000 0.00 0.00 0.00 3.67
8514 9481 0.892755 TACTGCGACCACCTAACCAG 59.107 55.000 0.00 0.00 0.00 4.00
8525 9492 1.200519 CCTAACCAGGGACGGATTCA 58.799 55.000 0.00 0.00 38.41 2.57
8526 9493 1.557832 CCTAACCAGGGACGGATTCAA 59.442 52.381 0.00 0.00 38.41 2.69
8527 9494 2.420129 CCTAACCAGGGACGGATTCAAG 60.420 54.545 0.00 0.00 38.41 3.02
8528 9495 0.328258 AACCAGGGACGGATTCAAGG 59.672 55.000 0.00 0.00 0.00 3.61
8529 9496 1.224592 CCAGGGACGGATTCAAGGG 59.775 63.158 0.00 0.00 0.00 3.95
8530 9497 1.224592 CAGGGACGGATTCAAGGGG 59.775 63.158 0.00 0.00 0.00 4.79
8531 9498 2.001269 AGGGACGGATTCAAGGGGG 61.001 63.158 0.00 0.00 0.00 5.40
8568 9535 2.108362 CCCCCTAACGATCGTGCC 59.892 66.667 23.51 0.00 0.00 5.01
8569 9536 2.279252 CCCCTAACGATCGTGCCG 60.279 66.667 23.51 12.68 0.00 5.69
8570 9537 2.960129 CCCTAACGATCGTGCCGC 60.960 66.667 23.51 0.00 0.00 6.53
8571 9538 2.202690 CCTAACGATCGTGCCGCA 60.203 61.111 23.51 4.16 0.00 5.69
8572 9539 2.514013 CCTAACGATCGTGCCGCAC 61.514 63.158 23.51 13.81 0.00 5.34
8573 9540 2.507547 TAACGATCGTGCCGCACC 60.508 61.111 23.51 3.14 0.00 5.01
8574 9541 2.884087 CTAACGATCGTGCCGCACCT 62.884 60.000 23.51 5.73 0.00 4.00
8575 9542 2.495366 TAACGATCGTGCCGCACCTT 62.495 55.000 23.51 4.93 0.00 3.50
8576 9543 2.202690 CGATCGTGCCGCACCTTA 60.203 61.111 17.81 4.22 0.00 2.69
8577 9544 1.807981 CGATCGTGCCGCACCTTAA 60.808 57.895 17.81 1.72 0.00 1.85
8578 9545 1.151777 CGATCGTGCCGCACCTTAAT 61.152 55.000 17.81 6.50 0.00 1.40
8579 9546 1.860676 GATCGTGCCGCACCTTAATA 58.139 50.000 17.81 0.00 0.00 0.98
8580 9547 1.792949 GATCGTGCCGCACCTTAATAG 59.207 52.381 17.81 2.08 0.00 1.73
8581 9548 0.808453 TCGTGCCGCACCTTAATAGC 60.808 55.000 17.81 0.00 0.00 2.97
8590 9557 4.458951 GCACCTTAATAGCGATCAGTTG 57.541 45.455 0.00 0.00 0.00 3.16
8591 9558 3.248602 GCACCTTAATAGCGATCAGTTGG 59.751 47.826 0.00 0.00 0.00 3.77
8592 9559 4.442706 CACCTTAATAGCGATCAGTTGGT 58.557 43.478 0.00 0.00 0.00 3.67
8593 9560 4.508124 CACCTTAATAGCGATCAGTTGGTC 59.492 45.833 0.00 0.00 0.00 4.02
8594 9561 3.736252 CCTTAATAGCGATCAGTTGGTCG 59.264 47.826 10.29 10.29 40.62 4.79
8602 9569 4.600012 CGATCAGTTGGTCGCTAATTTT 57.400 40.909 1.44 0.00 0.00 1.82
8603 9570 4.334443 CGATCAGTTGGTCGCTAATTTTG 58.666 43.478 1.44 0.00 0.00 2.44
8604 9571 4.142902 CGATCAGTTGGTCGCTAATTTTGT 60.143 41.667 1.44 0.00 0.00 2.83
8605 9572 5.616866 CGATCAGTTGGTCGCTAATTTTGTT 60.617 40.000 1.44 0.00 0.00 2.83
8606 9573 4.854399 TCAGTTGGTCGCTAATTTTGTTG 58.146 39.130 0.00 0.00 0.00 3.33
8607 9574 3.980775 CAGTTGGTCGCTAATTTTGTTGG 59.019 43.478 0.00 0.00 0.00 3.77
8608 9575 2.715737 TGGTCGCTAATTTTGTTGGC 57.284 45.000 0.00 0.00 0.00 4.52
8609 9576 2.235016 TGGTCGCTAATTTTGTTGGCT 58.765 42.857 0.00 0.00 0.00 4.75
8610 9577 3.413327 TGGTCGCTAATTTTGTTGGCTA 58.587 40.909 0.00 0.00 0.00 3.93
8611 9578 3.189702 TGGTCGCTAATTTTGTTGGCTAC 59.810 43.478 0.00 0.00 0.00 3.58
8612 9579 3.413558 GTCGCTAATTTTGTTGGCTACG 58.586 45.455 0.00 0.00 0.00 3.51
8613 9580 2.159626 TCGCTAATTTTGTTGGCTACGC 60.160 45.455 0.00 0.00 0.00 4.42
8614 9581 2.413502 CGCTAATTTTGTTGGCTACGCA 60.414 45.455 0.00 0.00 0.00 5.24
8615 9582 3.570559 GCTAATTTTGTTGGCTACGCAA 58.429 40.909 0.00 0.00 0.00 4.85
8628 9595 3.637714 CGCAAGTGTACGTGGCTT 58.362 55.556 0.00 0.00 0.00 4.35
8629 9596 1.204062 CGCAAGTGTACGTGGCTTG 59.796 57.895 18.09 18.09 41.61 4.01
8631 9598 2.616969 CAAGTGTACGTGGCTTGCT 58.383 52.632 12.99 0.00 34.16 3.91
8632 9599 0.944386 CAAGTGTACGTGGCTTGCTT 59.056 50.000 12.99 1.34 34.16 3.91
8633 9600 1.069906 CAAGTGTACGTGGCTTGCTTC 60.070 52.381 12.99 0.00 34.16 3.86
8634 9601 0.944311 AGTGTACGTGGCTTGCTTCG 60.944 55.000 0.00 7.90 0.00 3.79
8635 9602 2.314647 TGTACGTGGCTTGCTTCGC 61.315 57.895 0.00 0.00 0.00 4.70
8655 9622 1.966762 CCCCCTGTGTGATTTGTGC 59.033 57.895 0.00 0.00 0.00 4.57
8656 9623 0.540365 CCCCCTGTGTGATTTGTGCT 60.540 55.000 0.00 0.00 0.00 4.40
8657 9624 1.331214 CCCCTGTGTGATTTGTGCTT 58.669 50.000 0.00 0.00 0.00 3.91
8658 9625 1.270550 CCCCTGTGTGATTTGTGCTTC 59.729 52.381 0.00 0.00 0.00 3.86
8659 9626 1.270550 CCCTGTGTGATTTGTGCTTCC 59.729 52.381 0.00 0.00 0.00 3.46
8660 9627 1.270550 CCTGTGTGATTTGTGCTTCCC 59.729 52.381 0.00 0.00 0.00 3.97
8661 9628 1.955778 CTGTGTGATTTGTGCTTCCCA 59.044 47.619 0.00 0.00 0.00 4.37
8662 9629 2.559668 CTGTGTGATTTGTGCTTCCCAT 59.440 45.455 0.00 0.00 0.00 4.00
8663 9630 3.758023 CTGTGTGATTTGTGCTTCCCATA 59.242 43.478 0.00 0.00 0.00 2.74
8664 9631 3.758023 TGTGTGATTTGTGCTTCCCATAG 59.242 43.478 0.00 0.00 0.00 2.23
8665 9632 2.754552 TGTGATTTGTGCTTCCCATAGC 59.245 45.455 0.00 0.00 41.59 2.97
8666 9633 2.099756 GTGATTTGTGCTTCCCATAGCC 59.900 50.000 0.00 0.00 40.49 3.93
8667 9634 2.291475 TGATTTGTGCTTCCCATAGCCA 60.291 45.455 0.00 0.00 40.49 4.75
8668 9635 1.838112 TTTGTGCTTCCCATAGCCAG 58.162 50.000 0.00 0.00 40.49 4.85
8669 9636 0.680921 TTGTGCTTCCCATAGCCAGC 60.681 55.000 0.00 0.00 40.49 4.85
8670 9637 2.182842 GTGCTTCCCATAGCCAGCG 61.183 63.158 0.00 0.00 40.49 5.18
8671 9638 2.366393 TGCTTCCCATAGCCAGCGA 61.366 57.895 0.00 0.00 40.49 4.93
8672 9639 1.596477 GCTTCCCATAGCCAGCGAG 60.596 63.158 0.00 0.00 35.06 5.03
8673 9640 1.070445 CTTCCCATAGCCAGCGAGG 59.930 63.158 0.00 0.00 41.84 4.63
8674 9641 2.388890 CTTCCCATAGCCAGCGAGGG 62.389 65.000 9.85 9.85 40.98 4.30
8682 9649 3.479203 CCAGCGAGGGCCCATGTA 61.479 66.667 27.56 0.00 41.24 2.29
8683 9650 2.589540 CAGCGAGGGCCCATGTAA 59.410 61.111 27.56 0.00 41.24 2.41
8684 9651 1.149174 CAGCGAGGGCCCATGTAAT 59.851 57.895 27.56 0.00 41.24 1.89
8685 9652 1.149174 AGCGAGGGCCCATGTAATG 59.851 57.895 27.56 6.02 41.24 1.90
8701 9668 5.565592 TGTAATGGTGATCAGTTGATTGC 57.434 39.130 0.00 0.00 34.37 3.56
8702 9669 5.008980 TGTAATGGTGATCAGTTGATTGCA 58.991 37.500 0.00 0.00 34.37 4.08
8703 9670 4.713824 AATGGTGATCAGTTGATTGCAG 57.286 40.909 0.00 0.00 34.37 4.41
8704 9671 1.814394 TGGTGATCAGTTGATTGCAGC 59.186 47.619 0.00 1.85 34.37 5.25
8705 9672 1.133790 GGTGATCAGTTGATTGCAGCC 59.866 52.381 0.00 0.00 34.37 4.85
8706 9673 2.089980 GTGATCAGTTGATTGCAGCCT 58.910 47.619 0.00 0.00 34.37 4.58
8707 9674 3.273434 GTGATCAGTTGATTGCAGCCTA 58.727 45.455 0.00 0.00 34.37 3.93
8708 9675 3.691118 GTGATCAGTTGATTGCAGCCTAA 59.309 43.478 0.00 0.00 34.37 2.69
8709 9676 4.156556 GTGATCAGTTGATTGCAGCCTAAA 59.843 41.667 0.00 0.00 34.37 1.85
8710 9677 4.397103 TGATCAGTTGATTGCAGCCTAAAG 59.603 41.667 0.00 0.00 34.37 1.85
8711 9678 3.084039 TCAGTTGATTGCAGCCTAAAGG 58.916 45.455 0.00 0.00 38.53 3.11
8723 9690 1.780503 CCTAAAGGCCCAAATCCCAG 58.219 55.000 0.00 0.00 0.00 4.45
8724 9691 1.287739 CCTAAAGGCCCAAATCCCAGA 59.712 52.381 0.00 0.00 0.00 3.86
8725 9692 2.292192 CCTAAAGGCCCAAATCCCAGAA 60.292 50.000 0.00 0.00 0.00 3.02
8726 9693 2.414250 AAAGGCCCAAATCCCAGAAA 57.586 45.000 0.00 0.00 0.00 2.52
8727 9694 2.414250 AAGGCCCAAATCCCAGAAAA 57.586 45.000 0.00 0.00 0.00 2.29
8728 9695 2.414250 AGGCCCAAATCCCAGAAAAA 57.586 45.000 0.00 0.00 0.00 1.94
8729 9696 2.919881 AGGCCCAAATCCCAGAAAAAT 58.080 42.857 0.00 0.00 0.00 1.82
8730 9697 4.073425 AGGCCCAAATCCCAGAAAAATA 57.927 40.909 0.00 0.00 0.00 1.40
8731 9698 4.434195 AGGCCCAAATCCCAGAAAAATAA 58.566 39.130 0.00 0.00 0.00 1.40
8732 9699 4.849235 AGGCCCAAATCCCAGAAAAATAAA 59.151 37.500 0.00 0.00 0.00 1.40
8733 9700 5.311913 AGGCCCAAATCCCAGAAAAATAAAA 59.688 36.000 0.00 0.00 0.00 1.52
8734 9701 6.007076 GGCCCAAATCCCAGAAAAATAAAAA 58.993 36.000 0.00 0.00 0.00 1.94
8735 9702 6.150976 GGCCCAAATCCCAGAAAAATAAAAAG 59.849 38.462 0.00 0.00 0.00 2.27
8736 9703 6.150976 GCCCAAATCCCAGAAAAATAAAAAGG 59.849 38.462 0.00 0.00 0.00 3.11
8737 9704 7.457561 CCCAAATCCCAGAAAAATAAAAAGGA 58.542 34.615 0.00 0.00 0.00 3.36
8738 9705 7.941790 CCCAAATCCCAGAAAAATAAAAAGGAA 59.058 33.333 0.00 0.00 0.00 3.36
8739 9706 9.348476 CCAAATCCCAGAAAAATAAAAAGGAAA 57.652 29.630 0.00 0.00 0.00 3.13
8741 9708 9.913310 AAATCCCAGAAAAATAAAAAGGAAACA 57.087 25.926 0.00 0.00 0.00 2.83
8745 9712 8.935844 CCCAGAAAAATAAAAAGGAAACATAGC 58.064 33.333 0.00 0.00 0.00 2.97
8746 9713 8.935844 CCAGAAAAATAAAAAGGAAACATAGCC 58.064 33.333 0.00 0.00 0.00 3.93
8747 9714 8.935844 CAGAAAAATAAAAAGGAAACATAGCCC 58.064 33.333 0.00 0.00 0.00 5.19
8748 9715 8.655901 AGAAAAATAAAAAGGAAACATAGCCCA 58.344 29.630 0.00 0.00 0.00 5.36
8749 9716 9.448438 GAAAAATAAAAAGGAAACATAGCCCAT 57.552 29.630 0.00 0.00 0.00 4.00
8750 9717 9.448438 AAAAATAAAAAGGAAACATAGCCCATC 57.552 29.630 0.00 0.00 0.00 3.51
8751 9718 7.732222 AATAAAAAGGAAACATAGCCCATCA 57.268 32.000 0.00 0.00 0.00 3.07
8752 9719 7.919385 ATAAAAAGGAAACATAGCCCATCAT 57.081 32.000 0.00 0.00 0.00 2.45
8753 9720 5.603170 AAAAGGAAACATAGCCCATCATG 57.397 39.130 0.00 0.00 0.00 3.07
8754 9721 4.524802 AAGGAAACATAGCCCATCATGA 57.475 40.909 0.00 0.00 0.00 3.07
8755 9722 4.524802 AGGAAACATAGCCCATCATGAA 57.475 40.909 0.00 0.00 0.00 2.57
8756 9723 4.870636 AGGAAACATAGCCCATCATGAAA 58.129 39.130 0.00 0.00 0.00 2.69
8757 9724 4.891756 AGGAAACATAGCCCATCATGAAAG 59.108 41.667 0.00 0.00 0.00 2.62
8758 9725 4.500375 GGAAACATAGCCCATCATGAAAGC 60.500 45.833 0.00 2.94 0.00 3.51
8759 9726 2.224606 ACATAGCCCATCATGAAAGCG 58.775 47.619 0.00 0.00 0.00 4.68
8760 9727 2.158769 ACATAGCCCATCATGAAAGCGA 60.159 45.455 0.00 0.00 0.00 4.93
8761 9728 2.708216 TAGCCCATCATGAAAGCGAA 57.292 45.000 0.00 0.00 0.00 4.70
8762 9729 1.386533 AGCCCATCATGAAAGCGAAG 58.613 50.000 0.00 0.00 0.00 3.79
8763 9730 0.383231 GCCCATCATGAAAGCGAAGG 59.617 55.000 0.00 0.00 0.00 3.46
8764 9731 1.027357 CCCATCATGAAAGCGAAGGG 58.973 55.000 0.00 0.00 34.07 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.751542 TGTTTTATCGATTATCTTTCTCTCCTC 57.248 33.333 1.71 0.00 0.00 3.71
166 171 0.540133 GACCGATCTCTCCCCTACCC 60.540 65.000 0.00 0.00 0.00 3.69
167 172 0.890090 CGACCGATCTCTCCCCTACC 60.890 65.000 0.00 0.00 0.00 3.18
168 173 1.517210 GCGACCGATCTCTCCCCTAC 61.517 65.000 0.00 0.00 0.00 3.18
169 174 1.228184 GCGACCGATCTCTCCCCTA 60.228 63.158 0.00 0.00 0.00 3.53
170 175 2.519780 GCGACCGATCTCTCCCCT 60.520 66.667 0.00 0.00 0.00 4.79
201 208 4.407621 TGGTTTTCTGAGTCAGTTGTAGGA 59.592 41.667 19.53 0.00 32.61 2.94
207 214 6.784031 AGGAATATGGTTTTCTGAGTCAGTT 58.216 36.000 19.53 3.43 32.61 3.16
210 217 5.874810 CGAAGGAATATGGTTTTCTGAGTCA 59.125 40.000 0.00 0.00 0.00 3.41
234 241 2.583593 GTGAGCGCGAGTGGATCC 60.584 66.667 12.10 4.20 0.00 3.36
352 367 2.514803 CCCTTTACACCTGGTTCCTTG 58.485 52.381 0.00 0.00 0.00 3.61
354 369 1.073098 CCCCTTTACACCTGGTTCCT 58.927 55.000 0.00 0.00 0.00 3.36
355 370 0.611062 GCCCCTTTACACCTGGTTCC 60.611 60.000 0.00 0.00 0.00 3.62
381 399 1.082194 AGGTCTTTGGATAGTGGGGGA 59.918 52.381 0.00 0.00 0.00 4.81
409 430 1.084289 AGGCGCCGTGAAATTAAGAC 58.916 50.000 23.20 0.00 0.00 3.01
445 469 1.106285 GAGCACATGATTGGGGGTTC 58.894 55.000 0.00 0.00 0.00 3.62
510 551 0.039527 CCTCGCCTTTTGGTTTTCCG 60.040 55.000 0.00 0.00 44.36 4.30
539 580 1.423794 AAAAGAAGAGGCCCGACCCA 61.424 55.000 0.00 0.00 40.58 4.51
672 724 8.068380 CCTAAAGCTAAAATAATAACTCACGCC 58.932 37.037 0.00 0.00 0.00 5.68
740 792 2.443203 TATCCCTTCGCCTCCGCA 60.443 61.111 0.00 0.00 34.03 5.69
749 801 8.055790 CCATAATTCCCTAATTCCTATCCCTTC 58.944 40.741 0.00 0.00 36.67 3.46
764 816 1.151450 CCCAGCGCCATAATTCCCT 59.849 57.895 2.29 0.00 0.00 4.20
765 817 0.890996 CTCCCAGCGCCATAATTCCC 60.891 60.000 2.29 0.00 0.00 3.97
766 818 0.890996 CCTCCCAGCGCCATAATTCC 60.891 60.000 2.29 0.00 0.00 3.01
767 819 1.518903 GCCTCCCAGCGCCATAATTC 61.519 60.000 2.29 0.00 0.00 2.17
768 820 1.529244 GCCTCCCAGCGCCATAATT 60.529 57.895 2.29 0.00 0.00 1.40
776 833 2.388890 CTATCCTTGGCCTCCCAGCG 62.389 65.000 3.32 0.00 43.37 5.18
779 836 0.045623 TTCCTATCCTTGGCCTCCCA 59.954 55.000 3.32 0.00 40.06 4.37
906 967 4.193893 TCGACGATAGGCCGGGGA 62.194 66.667 2.18 0.00 46.50 4.81
908 969 2.561956 ATGTCGACGATAGGCCGGG 61.562 63.158 11.62 0.00 46.50 5.73
931 998 0.108424 GCCAGCTTCACTCGATCTGT 60.108 55.000 0.00 0.00 0.00 3.41
939 1006 1.072159 GTCCACAGCCAGCTTCACT 59.928 57.895 0.00 0.00 0.00 3.41
996 1078 0.106868 CCTCTGCATCTTCCATGGCA 60.107 55.000 6.96 0.00 34.66 4.92
1185 1267 3.127533 GGGCAGCAGGCACTTACG 61.128 66.667 4.75 0.00 44.81 3.18
1206 1288 2.542618 CCTACGATGCACAGAGCTACAG 60.543 54.545 0.00 0.00 45.94 2.74
1211 1293 0.108615 ACACCTACGATGCACAGAGC 60.109 55.000 0.00 0.00 45.96 4.09
1225 1307 2.443390 AGGCGGGCGTATACACCT 60.443 61.111 9.73 1.86 0.00 4.00
1226 1308 2.279918 CAGGCGGGCGTATACACC 60.280 66.667 0.93 0.93 0.00 4.16
1227 1309 2.965462 GCAGGCGGGCGTATACAC 60.965 66.667 3.32 0.00 0.00 2.90
1228 1310 3.151710 AGCAGGCGGGCGTATACA 61.152 61.111 3.32 0.00 39.27 2.29
1229 1311 2.661866 CAGCAGGCGGGCGTATAC 60.662 66.667 0.00 0.00 39.27 1.47
1230 1312 4.602259 GCAGCAGGCGGGCGTATA 62.602 66.667 0.00 0.00 39.27 1.47
1298 1391 1.863454 CACTACCAGCTGCAATCGATC 59.137 52.381 8.66 0.00 0.00 3.69
2679 2922 4.016706 GGTGTGCCGTAGCCACCT 62.017 66.667 14.57 0.00 38.69 4.00
3674 4243 2.417586 TGCTTGACAAGAATGAGCATCG 59.582 45.455 19.51 0.00 38.33 3.84
4028 4602 2.027837 GGTGTATGGACAGGTTAACCGT 60.028 50.000 18.91 18.43 42.08 4.83
5624 6499 1.226407 CTCAGCGCGAAGACGATCA 60.226 57.895 12.10 0.00 42.66 2.92
6691 7573 4.803908 CCGGGGCAGCTCTTTCCC 62.804 72.222 0.00 0.00 39.33 3.97
6981 7886 1.677637 TATCCGTGGCCATGTACGCA 61.678 55.000 23.39 1.28 38.87 5.24
7049 7954 2.877974 GACGGCGTGCGAAACTTGT 61.878 57.895 21.19 0.00 0.00 3.16
7167 8072 3.553437 CTCGACGTGGCTGAACCGT 62.553 63.158 0.00 0.00 43.94 4.83
7174 8079 2.569134 GAAGAGCTCGACGTGGCT 59.431 61.111 8.37 15.28 41.88 4.75
7449 8354 1.117142 ACGGACGGAAGAAGTTGGGA 61.117 55.000 0.00 0.00 0.00 4.37
7452 8357 0.782384 CGAACGGACGGAAGAAGTTG 59.218 55.000 0.00 0.00 0.00 3.16
7453 8358 0.942884 GCGAACGGACGGAAGAAGTT 60.943 55.000 5.76 0.00 0.00 2.66
7650 8555 0.837691 TCATGCACCACAGGTCCTCT 60.838 55.000 0.00 0.00 31.02 3.69
7677 8582 3.729489 TCGGACTCGCCTCCTCCT 61.729 66.667 0.00 0.00 36.13 3.69
7899 8814 5.175673 GCCCACGATTTTCTTTTCTTTTCTG 59.824 40.000 0.00 0.00 0.00 3.02
7911 8826 2.332654 ACAGCCGCCCACGATTTTC 61.333 57.895 0.00 0.00 43.93 2.29
7912 8827 2.282180 ACAGCCGCCCACGATTTT 60.282 55.556 0.00 0.00 43.93 1.82
7913 8828 3.055719 CACAGCCGCCCACGATTT 61.056 61.111 0.00 0.00 43.93 2.17
7914 8829 3.958147 CTCACAGCCGCCCACGATT 62.958 63.158 0.00 0.00 43.93 3.34
7915 8830 4.457496 CTCACAGCCGCCCACGAT 62.457 66.667 0.00 0.00 43.93 3.73
8086 9018 3.065371 CGAAAAACAGGGGAGATATGCAC 59.935 47.826 0.00 0.00 0.00 4.57
8087 9019 3.278574 CGAAAAACAGGGGAGATATGCA 58.721 45.455 0.00 0.00 0.00 3.96
8088 9020 3.279434 ACGAAAAACAGGGGAGATATGC 58.721 45.455 0.00 0.00 0.00 3.14
8089 9021 3.877508 GGACGAAAAACAGGGGAGATATG 59.122 47.826 0.00 0.00 0.00 1.78
8090 9022 3.118000 GGGACGAAAAACAGGGGAGATAT 60.118 47.826 0.00 0.00 0.00 1.63
8157 9093 1.201647 GCCTATCTAGCCGTCGCAATA 59.798 52.381 0.00 0.00 37.52 1.90
8166 9102 6.783708 ACTAGTTCATATGCCTATCTAGCC 57.216 41.667 0.00 0.00 0.00 3.93
8167 9103 8.514330 ACTACTAGTTCATATGCCTATCTAGC 57.486 38.462 0.00 0.00 0.00 3.42
8182 9118 9.953697 CCACTGATTACTTGATACTACTAGTTC 57.046 37.037 0.00 0.00 0.00 3.01
8183 9119 8.414778 GCCACTGATTACTTGATACTACTAGTT 58.585 37.037 0.00 0.00 0.00 2.24
8184 9120 7.560262 TGCCACTGATTACTTGATACTACTAGT 59.440 37.037 0.00 0.00 0.00 2.57
8185 9121 7.941919 TGCCACTGATTACTTGATACTACTAG 58.058 38.462 0.00 0.00 0.00 2.57
8186 9122 7.891498 TGCCACTGATTACTTGATACTACTA 57.109 36.000 0.00 0.00 0.00 1.82
8187 9123 6.791867 TGCCACTGATTACTTGATACTACT 57.208 37.500 0.00 0.00 0.00 2.57
8188 9124 6.073548 GCATGCCACTGATTACTTGATACTAC 60.074 42.308 6.36 0.00 0.00 2.73
8189 9125 5.991606 GCATGCCACTGATTACTTGATACTA 59.008 40.000 6.36 0.00 0.00 1.82
8190 9126 4.818546 GCATGCCACTGATTACTTGATACT 59.181 41.667 6.36 0.00 0.00 2.12
8191 9127 4.818546 AGCATGCCACTGATTACTTGATAC 59.181 41.667 15.66 0.00 0.00 2.24
8239 9178 1.749634 GCGTAGATACTCCACAGTGGT 59.250 52.381 19.65 3.57 39.03 4.16
8270 9209 3.359523 TACGGCGAGCGACACACT 61.360 61.111 16.62 0.00 0.00 3.55
8318 9257 1.436983 GCCCCATCAATTCGTCGTCC 61.437 60.000 0.00 0.00 0.00 4.79
8426 9366 2.914059 ACAGTGCAATATTCCCGGTAC 58.086 47.619 0.00 0.00 0.00 3.34
8427 9367 3.181463 GGTACAGTGCAATATTCCCGGTA 60.181 47.826 0.00 0.00 0.00 4.02
8428 9368 2.420967 GGTACAGTGCAATATTCCCGGT 60.421 50.000 0.00 0.00 0.00 5.28
8512 9479 1.224592 CCCCTTGAATCCGTCCCTG 59.775 63.158 0.00 0.00 0.00 4.45
8513 9480 2.001269 CCCCCTTGAATCCGTCCCT 61.001 63.158 0.00 0.00 0.00 4.20
8514 9481 2.595655 CCCCCTTGAATCCGTCCC 59.404 66.667 0.00 0.00 0.00 4.46
8551 9518 2.108362 GGCACGATCGTTAGGGGG 59.892 66.667 20.14 7.37 0.00 5.40
8564 9531 1.641677 CGCTATTAAGGTGCGGCAC 59.358 57.895 24.43 24.43 45.07 5.01
8565 9532 4.118480 CGCTATTAAGGTGCGGCA 57.882 55.556 0.00 0.00 45.07 5.69
8569 9536 3.248602 CCAACTGATCGCTATTAAGGTGC 59.751 47.826 0.00 0.00 0.00 5.01
8570 9537 4.442706 ACCAACTGATCGCTATTAAGGTG 58.557 43.478 0.00 0.00 0.00 4.00
8571 9538 4.694339 GACCAACTGATCGCTATTAAGGT 58.306 43.478 0.00 0.00 0.00 3.50
8572 9539 3.736252 CGACCAACTGATCGCTATTAAGG 59.264 47.826 0.00 0.00 0.00 2.69
8573 9540 4.956034 CGACCAACTGATCGCTATTAAG 57.044 45.455 0.00 0.00 0.00 1.85
8581 9548 4.142902 ACAAAATTAGCGACCAACTGATCG 60.143 41.667 0.00 0.00 41.32 3.69
8582 9549 5.296813 ACAAAATTAGCGACCAACTGATC 57.703 39.130 0.00 0.00 0.00 2.92
8583 9550 5.460646 CAACAAAATTAGCGACCAACTGAT 58.539 37.500 0.00 0.00 0.00 2.90
8584 9551 4.261405 CCAACAAAATTAGCGACCAACTGA 60.261 41.667 0.00 0.00 0.00 3.41
8585 9552 3.980775 CCAACAAAATTAGCGACCAACTG 59.019 43.478 0.00 0.00 0.00 3.16
8586 9553 3.552068 GCCAACAAAATTAGCGACCAACT 60.552 43.478 0.00 0.00 0.00 3.16
8587 9554 2.729360 GCCAACAAAATTAGCGACCAAC 59.271 45.455 0.00 0.00 0.00 3.77
8588 9555 2.625790 AGCCAACAAAATTAGCGACCAA 59.374 40.909 0.00 0.00 0.00 3.67
8589 9556 2.235016 AGCCAACAAAATTAGCGACCA 58.765 42.857 0.00 0.00 0.00 4.02
8590 9557 3.726782 CGTAGCCAACAAAATTAGCGACC 60.727 47.826 0.00 0.00 0.00 4.79
8591 9558 3.413558 CGTAGCCAACAAAATTAGCGAC 58.586 45.455 0.00 0.00 0.00 5.19
8592 9559 3.733024 CGTAGCCAACAAAATTAGCGA 57.267 42.857 0.00 0.00 0.00 4.93
8608 9575 0.388134 AGCCACGTACACTTGCGTAG 60.388 55.000 0.00 0.00 42.75 3.51
8609 9576 0.032403 AAGCCACGTACACTTGCGTA 59.968 50.000 0.00 0.00 42.75 4.42
8610 9577 1.227438 AAGCCACGTACACTTGCGT 60.227 52.632 0.00 0.00 45.85 5.24
8611 9578 1.204062 CAAGCCACGTACACTTGCG 59.796 57.895 10.33 0.00 34.90 4.85
8613 9580 0.944386 AAGCAAGCCACGTACACTTG 59.056 50.000 16.07 16.07 42.90 3.16
8614 9581 1.226746 GAAGCAAGCCACGTACACTT 58.773 50.000 0.00 0.00 0.00 3.16
8615 9582 0.944311 CGAAGCAAGCCACGTACACT 60.944 55.000 0.00 0.00 0.00 3.55
8616 9583 1.491563 CGAAGCAAGCCACGTACAC 59.508 57.895 0.00 0.00 0.00 2.90
8617 9584 3.945436 CGAAGCAAGCCACGTACA 58.055 55.556 0.00 0.00 0.00 2.90
8637 9604 0.540365 AGCACAAATCACACAGGGGG 60.540 55.000 0.00 0.00 0.00 5.40
8638 9605 1.270550 GAAGCACAAATCACACAGGGG 59.729 52.381 0.00 0.00 0.00 4.79
8639 9606 1.270550 GGAAGCACAAATCACACAGGG 59.729 52.381 0.00 0.00 0.00 4.45
8640 9607 1.270550 GGGAAGCACAAATCACACAGG 59.729 52.381 0.00 0.00 0.00 4.00
8641 9608 1.955778 TGGGAAGCACAAATCACACAG 59.044 47.619 0.00 0.00 0.00 3.66
8642 9609 2.064434 TGGGAAGCACAAATCACACA 57.936 45.000 0.00 0.00 0.00 3.72
8643 9610 3.428045 GCTATGGGAAGCACAAATCACAC 60.428 47.826 0.00 0.00 42.30 3.82
8644 9611 2.754552 GCTATGGGAAGCACAAATCACA 59.245 45.455 0.00 0.00 42.30 3.58
8645 9612 2.099756 GGCTATGGGAAGCACAAATCAC 59.900 50.000 0.00 0.00 44.64 3.06
8646 9613 2.291475 TGGCTATGGGAAGCACAAATCA 60.291 45.455 0.00 0.00 44.64 2.57
8647 9614 2.360165 CTGGCTATGGGAAGCACAAATC 59.640 50.000 0.00 0.00 44.64 2.17
8648 9615 2.381911 CTGGCTATGGGAAGCACAAAT 58.618 47.619 0.00 0.00 44.64 2.32
8649 9616 1.838112 CTGGCTATGGGAAGCACAAA 58.162 50.000 0.00 0.00 44.64 2.83
8650 9617 0.680921 GCTGGCTATGGGAAGCACAA 60.681 55.000 0.00 0.00 44.64 3.33
8651 9618 1.077501 GCTGGCTATGGGAAGCACA 60.078 57.895 0.00 0.00 44.64 4.57
8652 9619 2.182842 CGCTGGCTATGGGAAGCAC 61.183 63.158 0.00 0.00 44.64 4.40
8653 9620 2.190313 CGCTGGCTATGGGAAGCA 59.810 61.111 0.00 0.00 44.64 3.91
8654 9621 1.596477 CTCGCTGGCTATGGGAAGC 60.596 63.158 0.00 0.00 41.99 3.86
8655 9622 1.070445 CCTCGCTGGCTATGGGAAG 59.930 63.158 0.00 0.00 0.00 3.46
8656 9623 2.443394 CCCTCGCTGGCTATGGGAA 61.443 63.158 8.07 0.00 40.23 3.97
8657 9624 2.844362 CCCTCGCTGGCTATGGGA 60.844 66.667 8.07 0.00 40.23 4.37
8665 9632 2.343475 ATTACATGGGCCCTCGCTGG 62.343 60.000 25.70 8.31 34.44 4.85
8666 9633 1.149174 ATTACATGGGCCCTCGCTG 59.851 57.895 25.70 17.03 34.44 5.18
8667 9634 1.149174 CATTACATGGGCCCTCGCT 59.851 57.895 25.70 5.13 34.44 4.93
8668 9635 1.898574 CCATTACATGGGCCCTCGC 60.899 63.158 25.70 0.00 46.86 5.03
8669 9636 4.481195 CCATTACATGGGCCCTCG 57.519 61.111 25.70 16.65 46.86 4.63
8674 9641 7.860931 AATCAACTGATCACCATTACATGGGC 61.861 42.308 7.68 0.00 43.68 5.36
8675 9642 5.595542 AATCAACTGATCACCATTACATGGG 59.404 40.000 7.68 0.00 43.68 4.00
8676 9643 6.500910 CAATCAACTGATCACCATTACATGG 58.499 40.000 0.00 0.92 44.39 3.66
8677 9644 5.975344 GCAATCAACTGATCACCATTACATG 59.025 40.000 0.00 0.00 32.75 3.21
8678 9645 5.653330 TGCAATCAACTGATCACCATTACAT 59.347 36.000 0.00 0.00 32.75 2.29
8679 9646 5.008980 TGCAATCAACTGATCACCATTACA 58.991 37.500 0.00 0.00 32.75 2.41
8680 9647 5.565592 TGCAATCAACTGATCACCATTAC 57.434 39.130 0.00 0.00 32.75 1.89
8681 9648 4.096833 GCTGCAATCAACTGATCACCATTA 59.903 41.667 0.00 0.00 32.75 1.90
8682 9649 3.119245 GCTGCAATCAACTGATCACCATT 60.119 43.478 0.00 0.00 32.75 3.16
8683 9650 2.426024 GCTGCAATCAACTGATCACCAT 59.574 45.455 0.00 0.00 32.75 3.55
8684 9651 1.814394 GCTGCAATCAACTGATCACCA 59.186 47.619 0.00 0.00 32.75 4.17
8685 9652 1.133790 GGCTGCAATCAACTGATCACC 59.866 52.381 0.50 0.00 32.75 4.02
8686 9653 2.089980 AGGCTGCAATCAACTGATCAC 58.910 47.619 0.50 0.00 32.75 3.06
8687 9654 2.502142 AGGCTGCAATCAACTGATCA 57.498 45.000 0.50 0.00 32.75 2.92
8688 9655 4.201990 CCTTTAGGCTGCAATCAACTGATC 60.202 45.833 0.50 0.00 32.75 2.92
8689 9656 3.698040 CCTTTAGGCTGCAATCAACTGAT 59.302 43.478 0.50 0.00 36.07 2.90
8690 9657 3.084039 CCTTTAGGCTGCAATCAACTGA 58.916 45.455 0.50 0.00 0.00 3.41
8691 9658 3.498927 CCTTTAGGCTGCAATCAACTG 57.501 47.619 0.50 0.00 0.00 3.16
8704 9671 1.287739 TCTGGGATTTGGGCCTTTAGG 59.712 52.381 4.53 0.00 38.53 2.69
8705 9672 2.826674 TCTGGGATTTGGGCCTTTAG 57.173 50.000 4.53 0.00 0.00 1.85
8706 9673 3.551635 TTTCTGGGATTTGGGCCTTTA 57.448 42.857 4.53 0.00 0.00 1.85
8707 9674 2.414250 TTTCTGGGATTTGGGCCTTT 57.586 45.000 4.53 0.00 0.00 3.11
8708 9675 2.414250 TTTTCTGGGATTTGGGCCTT 57.586 45.000 4.53 0.00 0.00 4.35
8709 9676 2.414250 TTTTTCTGGGATTTGGGCCT 57.586 45.000 4.53 0.00 0.00 5.19
8710 9677 4.835284 TTATTTTTCTGGGATTTGGGCC 57.165 40.909 0.00 0.00 0.00 5.80
8711 9678 6.150976 CCTTTTTATTTTTCTGGGATTTGGGC 59.849 38.462 0.00 0.00 0.00 5.36
8712 9679 7.457561 TCCTTTTTATTTTTCTGGGATTTGGG 58.542 34.615 0.00 0.00 0.00 4.12
8713 9680 8.916628 TTCCTTTTTATTTTTCTGGGATTTGG 57.083 30.769 0.00 0.00 0.00 3.28
8715 9682 9.913310 TGTTTCCTTTTTATTTTTCTGGGATTT 57.087 25.926 0.00 0.00 0.00 2.17
8719 9686 8.935844 GCTATGTTTCCTTTTTATTTTTCTGGG 58.064 33.333 0.00 0.00 0.00 4.45
8720 9687 8.935844 GGCTATGTTTCCTTTTTATTTTTCTGG 58.064 33.333 0.00 0.00 0.00 3.86
8721 9688 8.935844 GGGCTATGTTTCCTTTTTATTTTTCTG 58.064 33.333 0.00 0.00 0.00 3.02
8722 9689 8.655901 TGGGCTATGTTTCCTTTTTATTTTTCT 58.344 29.630 0.00 0.00 0.00 2.52
8723 9690 8.840833 TGGGCTATGTTTCCTTTTTATTTTTC 57.159 30.769 0.00 0.00 0.00 2.29
8724 9691 9.448438 GATGGGCTATGTTTCCTTTTTATTTTT 57.552 29.630 0.00 0.00 0.00 1.94
8725 9692 8.601546 TGATGGGCTATGTTTCCTTTTTATTTT 58.398 29.630 0.00 0.00 0.00 1.82
8726 9693 8.144862 TGATGGGCTATGTTTCCTTTTTATTT 57.855 30.769 0.00 0.00 0.00 1.40
8727 9694 7.732222 TGATGGGCTATGTTTCCTTTTTATT 57.268 32.000 0.00 0.00 0.00 1.40
8728 9695 7.564660 TCATGATGGGCTATGTTTCCTTTTTAT 59.435 33.333 0.00 0.00 0.00 1.40
8729 9696 6.894654 TCATGATGGGCTATGTTTCCTTTTTA 59.105 34.615 0.00 0.00 0.00 1.52
8730 9697 5.721000 TCATGATGGGCTATGTTTCCTTTTT 59.279 36.000 0.00 0.00 0.00 1.94
8731 9698 5.271598 TCATGATGGGCTATGTTTCCTTTT 58.728 37.500 0.00 0.00 0.00 2.27
8732 9699 4.870636 TCATGATGGGCTATGTTTCCTTT 58.129 39.130 0.00 0.00 0.00 3.11
8733 9700 4.524802 TCATGATGGGCTATGTTTCCTT 57.475 40.909 0.00 0.00 0.00 3.36
8734 9701 4.524802 TTCATGATGGGCTATGTTTCCT 57.475 40.909 0.00 0.00 0.00 3.36
8735 9702 4.500375 GCTTTCATGATGGGCTATGTTTCC 60.500 45.833 0.00 0.00 0.00 3.13
8736 9703 4.614946 GCTTTCATGATGGGCTATGTTTC 58.385 43.478 0.00 0.00 0.00 2.78
8737 9704 3.067180 CGCTTTCATGATGGGCTATGTTT 59.933 43.478 0.00 0.00 0.00 2.83
8738 9705 2.620115 CGCTTTCATGATGGGCTATGTT 59.380 45.455 0.00 0.00 0.00 2.71
8739 9706 2.158769 TCGCTTTCATGATGGGCTATGT 60.159 45.455 0.00 0.00 0.00 2.29
8740 9707 2.497138 TCGCTTTCATGATGGGCTATG 58.503 47.619 0.00 0.00 0.00 2.23
8741 9708 2.936919 TCGCTTTCATGATGGGCTAT 57.063 45.000 0.00 0.00 0.00 2.97
8742 9709 2.564771 CTTCGCTTTCATGATGGGCTA 58.435 47.619 0.00 0.00 0.00 3.93
8743 9710 1.386533 CTTCGCTTTCATGATGGGCT 58.613 50.000 0.00 0.00 0.00 5.19
8744 9711 0.383231 CCTTCGCTTTCATGATGGGC 59.617 55.000 0.00 0.50 0.00 5.36
8745 9712 1.027357 CCCTTCGCTTTCATGATGGG 58.973 55.000 0.00 1.53 41.51 4.00


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

AutoCloner maintained by Alex Coulton.