Multiple sequence alignment - TraesCS2A01G216100

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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 TraesCS2A01G216100 chr2A 100.000 7657 0 0 1 7657 203010782 203003126 0.000000e+00 14140.0
1 TraesCS2A01G216100 chr2A 89.944 179 14 2 2912 3087 203007714 203007537 2.150000e-55 228.0
2 TraesCS2A01G216100 chr2A 89.944 179 14 2 3069 3246 203007871 203007696 2.150000e-55 228.0
3 TraesCS2A01G216100 chr2B 95.105 3085 85 19 4144 7197 245010907 245007858 0.000000e+00 4800.0
4 TraesCS2A01G216100 chr2B 92.467 1646 68 15 675 2282 245015516 245013889 0.000000e+00 2302.0
5 TraesCS2A01G216100 chr2B 95.013 1143 40 2 3040 4165 245012229 245011087 0.000000e+00 1779.0
6 TraesCS2A01G216100 chr2B 92.844 545 29 7 2552 3087 245012565 245012022 0.000000e+00 782.0
7 TraesCS2A01G216100 chr2B 98.221 281 5 0 2280 2560 245013766 245013486 6.900000e-135 492.0
8 TraesCS2A01G216100 chr2B 91.144 271 7 4 7375 7639 245007367 245007108 1.220000e-92 351.0
9 TraesCS2A01G216100 chr2B 90.230 174 15 2 1 172 359178271 359178098 7.730000e-55 226.0
10 TraesCS2A01G216100 chr2D 91.104 2979 177 30 1 2930 188892397 188889458 0.000000e+00 3952.0
11 TraesCS2A01G216100 chr2D 92.840 1690 94 12 5509 7197 188885014 188883351 0.000000e+00 2425.0
12 TraesCS2A01G216100 chr2D 92.672 1119 56 13 3897 5005 188888286 188887184 0.000000e+00 1589.0
13 TraesCS2A01G216100 chr2D 88.765 899 58 24 3040 3900 188889281 188888388 0.000000e+00 1061.0
14 TraesCS2A01G216100 chr2D 88.942 416 31 3 5060 5461 188886770 188887184 4.130000e-137 499.0
15 TraesCS2A01G216100 chr2D 90.821 207 13 3 2886 3087 188889282 188889077 9.790000e-69 272.0
16 TraesCS2A01G216100 chr2D 90.909 176 13 3 1 174 207874966 207875140 4.620000e-57 233.0
17 TraesCS2A01G216100 chr4B 77.778 612 104 22 5673 6269 465736804 465737398 1.580000e-91 348.0
18 TraesCS2A01G216100 chr4B 85.542 83 11 1 5462 5543 242748562 242748644 1.370000e-12 86.1
19 TraesCS2A01G216100 chr4D 78.506 549 95 19 5730 6269 379149829 379150363 9.520000e-89 339.0
20 TraesCS2A01G216100 chr4A 83.791 364 45 7 5676 6026 85903944 85903582 4.430000e-87 333.0
21 TraesCS2A01G216100 chr6B 90.230 174 15 2 1 172 225844840 225844667 7.730000e-55 226.0
22 TraesCS2A01G216100 chr3D 89.831 177 16 2 1 175 59935870 59935694 7.730000e-55 226.0
23 TraesCS2A01G216100 chr3D 90.173 173 16 1 1 172 254642018 254642190 2.780000e-54 224.0
24 TraesCS2A01G216100 chr3D 90.173 173 16 1 1 172 263382426 263382254 2.780000e-54 224.0
25 TraesCS2A01G216100 chr3D 89.714 175 17 1 1 174 375323160 375323334 1.000000e-53 222.0
26 TraesCS2A01G216100 chr3D 92.982 57 3 1 5085 5140 127917453 127917509 1.770000e-11 82.4
27 TraesCS2A01G216100 chr3D 83.133 83 13 1 5057 5139 59307875 59307956 2.960000e-09 75.0
28 TraesCS2A01G216100 chr5B 89.773 176 17 1 1 175 355844734 355844559 2.780000e-54 224.0
29 TraesCS2A01G216100 chr5D 92.308 52 2 2 5089 5139 463043234 463043284 1.070000e-08 73.1
30 TraesCS2A01G216100 chr7D 90.385 52 5 0 5089 5140 139193478 139193427 1.380000e-07 69.4
31 TraesCS2A01G216100 chr6D 88.889 45 5 0 5095 5139 470768135 470768179 1.000000e-03 56.5


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 TraesCS2A01G216100 chr2A 203003126 203010782 7656 True 4865.333333 14140 93.296000 1 7657 3 chr2A.!!$R1 7656
1 TraesCS2A01G216100 chr2B 245007108 245015516 8408 True 1751.000000 4800 94.132333 675 7639 6 chr2B.!!$R2 6964
2 TraesCS2A01G216100 chr2D 188883351 188892397 9046 True 1859.800000 3952 91.240400 1 7197 5 chr2D.!!$R1 7196
3 TraesCS2A01G216100 chr4B 465736804 465737398 594 False 348.000000 348 77.778000 5673 6269 1 chr4B.!!$F2 596
4 TraesCS2A01G216100 chr4D 379149829 379150363 534 False 339.000000 339 78.506000 5730 6269 1 chr4D.!!$F1 539

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
422 424 0.313987 CACCGGGGTTTTCTTCAAGC 59.686 55.000 6.32 0.0 0.00 4.01 F
623 632 0.529773 TCTCTCTCTCTCTCTCGCGC 60.530 60.000 0.00 0.0 0.00 6.86 F
829 846 0.603707 CAGTGTCATCCAACGGCTGT 60.604 55.000 0.00 0.0 0.00 4.40 F
830 847 0.603707 AGTGTCATCCAACGGCTGTG 60.604 55.000 0.00 0.0 0.00 3.66 F
1334 1380 0.866061 CTGGCGTCTCGGACATTACG 60.866 60.000 5.15 0.0 38.34 3.18 F
1339 1385 1.731424 CGTCTCGGACATTACGCAACT 60.731 52.381 5.15 0.0 32.09 3.16 F
1583 1630 1.893801 TGGCATTGTTCATGTGATGCA 59.106 42.857 19.07 0.0 44.99 3.96 F
1867 1914 1.992557 TCCTGGCAAACTCTATGGGTT 59.007 47.619 0.00 0.0 0.00 4.11 F
2381 2554 3.117888 TCTCCAGTCTTGGTTCTTGCTTT 60.118 43.478 0.00 0.0 45.26 3.51 F
3518 4847 0.176449 GCCAATGTGAATTGCTCCCC 59.824 55.000 0.00 0.0 0.00 4.81 F
4848 6564 0.256752 TGCTGCATTGGCTGGATACT 59.743 50.000 0.00 0.0 41.91 2.12 F
5563 8981 0.974383 TCTTCTGAAACGGAGGGACC 59.026 55.000 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1268 0.251916 TGGTAATCCCGCAAGACCAG 59.748 55.000 0.00 0.0 34.69 4.00 R
1827 1874 2.697761 GCGGTCTGGCGTGAGACTA 61.698 63.158 13.50 0.0 41.90 2.59 R
2713 3819 3.360340 AGCTGCTGTTCGCTTGCC 61.360 61.111 0.00 0.0 38.76 4.52 R
2843 3949 8.081633 TGTTTGCTGTACTTTAATCCTCAATTG 58.918 33.333 0.00 0.0 0.00 2.32 R
3016 4123 3.213506 GCATAGACACATGGTAATGGCA 58.786 45.455 0.00 0.0 38.19 4.92 R
3018 4125 6.712095 AGTTATGCATAGACACATGGTAATGG 59.288 38.462 6.50 0.0 38.19 3.16 R
3413 4742 4.020543 AGTTTGGTACAGAAGGCAAACAA 58.979 39.130 18.89 0.0 42.39 2.83 R
3518 4847 7.692908 AGTTAACACATTTTGAATGGAAACG 57.307 32.000 8.61 0.0 0.00 3.60 R
3958 5436 2.695666 AGTCGCTACTGCAGATGGTAAT 59.304 45.455 23.35 0.0 39.64 1.89 R
5385 7102 1.404843 TTGTACTTTGTGCCAACCCC 58.595 50.000 0.00 0.0 0.00 4.95 R
6331 9762 1.004745 CTTGCCAGGGTCCACTACATT 59.995 52.381 0.00 0.0 0.00 2.71 R
7023 10456 0.169009 GAGGCTTGCACGAAATCCAC 59.831 55.000 0.00 0.0 0.00 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.635487 TGCCAATCCTTGTCCTTAGCT 59.365 47.619 0.00 0.00 0.00 3.32
59 60 2.312390 GAGGGGTCCACATCTCTAGTC 58.688 57.143 0.00 0.00 0.00 2.59
64 65 3.034635 GGTCCACATCTCTAGTCCATGT 58.965 50.000 0.00 0.00 0.00 3.21
69 70 4.343239 CCACATCTCTAGTCCATGTCATGA 59.657 45.833 14.67 0.00 0.00 3.07
78 79 8.021898 TCTAGTCCATGTCATGACAATCATTA 57.978 34.615 31.00 18.74 45.41 1.90
84 85 8.751242 TCCATGTCATGACAATCATTAAACATT 58.249 29.630 31.00 8.22 45.41 2.71
154 156 7.782897 TGTTATGAATTACCAAAACCATCCA 57.217 32.000 0.00 0.00 0.00 3.41
155 157 8.195165 TGTTATGAATTACCAAAACCATCCAA 57.805 30.769 0.00 0.00 0.00 3.53
158 160 4.530161 TGAATTACCAAAACCATCCAAGGG 59.470 41.667 0.00 0.00 0.00 3.95
179 181 5.467735 AGGGTTAGTTACACTTTTAACGCAG 59.532 40.000 11.21 0.00 37.10 5.18
184 186 9.276397 GTTAGTTACACTTTTAACGCAGAAAAA 57.724 29.630 0.00 0.00 37.10 1.94
187 189 9.659830 AGTTACACTTTTAACGCAGAAAAATAG 57.340 29.630 0.00 0.00 37.10 1.73
245 247 9.934190 CATGAAAATTTTCTAAAACCAACAAGG 57.066 29.630 26.73 4.97 39.66 3.61
256 258 0.875059 CCAACAAGGAACCTTCTCGC 59.125 55.000 2.84 0.00 41.22 5.03
274 276 0.462759 GCTCCTGCTATTGGCGAAGT 60.463 55.000 0.00 0.00 45.43 3.01
278 280 0.376152 CTGCTATTGGCGAAGTGCTG 59.624 55.000 9.16 5.78 45.43 4.41
298 300 2.025699 TGGTGGTTCCTAATAGGTTGGC 60.026 50.000 6.17 0.00 36.53 4.52
303 305 1.218844 TCCTAATAGGTTGGCCCACC 58.781 55.000 18.48 18.48 36.53 4.61
307 309 2.713828 AATAGGTTGGCCCACCTTTT 57.286 45.000 32.01 26.26 45.76 2.27
311 313 1.045911 GGTTGGCCCACCTTTTGACA 61.046 55.000 18.84 0.00 36.63 3.58
335 337 6.967767 CACTATTAAGCGATCTAAGGGATACG 59.032 42.308 0.00 0.00 34.33 3.06
337 339 3.644884 AAGCGATCTAAGGGATACGTG 57.355 47.619 0.00 0.00 34.33 4.49
361 363 1.069204 CTAGCGCACATACATCCACCT 59.931 52.381 11.47 0.00 0.00 4.00
362 364 0.462581 AGCGCACATACATCCACCTG 60.463 55.000 11.47 0.00 0.00 4.00
365 367 1.019673 GCACATACATCCACCTGCTG 58.980 55.000 0.00 0.00 0.00 4.41
376 378 3.165657 ACCTGCTGGTGGTAGAAGT 57.834 52.632 15.36 0.00 46.51 3.01
415 417 0.675837 GGCTAGACACCGGGGTTTTC 60.676 60.000 12.70 0.00 0.00 2.29
418 420 2.696506 CTAGACACCGGGGTTTTCTTC 58.303 52.381 12.70 0.00 0.00 2.87
422 424 0.313987 CACCGGGGTTTTCTTCAAGC 59.686 55.000 6.32 0.00 0.00 4.01
453 455 2.695147 AGCTCAAACAAACTGGAAAGGG 59.305 45.455 0.00 0.00 0.00 3.95
457 459 4.605183 TCAAACAAACTGGAAAGGGAGAA 58.395 39.130 0.00 0.00 0.00 2.87
470 472 1.635487 AGGGAGAATGCTTAGCCACAA 59.365 47.619 0.29 0.00 0.00 3.33
471 473 1.745653 GGGAGAATGCTTAGCCACAAC 59.254 52.381 0.29 0.00 0.00 3.32
484 486 4.060038 AGCCACAACCGACTGATAATAG 57.940 45.455 0.00 0.00 0.00 1.73
485 487 2.544267 GCCACAACCGACTGATAATAGC 59.456 50.000 0.00 0.00 0.00 2.97
526 535 1.007038 GGCACGTCACGTCCTTGTA 60.007 57.895 0.00 0.00 38.32 2.41
546 555 2.362889 CCCCACACATGGCTTCCC 60.363 66.667 0.00 0.00 45.76 3.97
557 566 1.153147 GGCTTCCCCATCGACCTTC 60.153 63.158 0.00 0.00 0.00 3.46
558 567 1.627297 GGCTTCCCCATCGACCTTCT 61.627 60.000 0.00 0.00 0.00 2.85
561 570 1.834263 CTTCCCCATCGACCTTCTCTT 59.166 52.381 0.00 0.00 0.00 2.85
604 613 5.435291 CATCTCTTCCTTCCAGCATAAACT 58.565 41.667 0.00 0.00 0.00 2.66
617 626 5.009010 CCAGCATAAACTCTCTCTCTCTCTC 59.991 48.000 0.00 0.00 0.00 3.20
619 628 6.017605 CAGCATAAACTCTCTCTCTCTCTCTC 60.018 46.154 0.00 0.00 0.00 3.20
620 629 5.050091 GCATAAACTCTCTCTCTCTCTCTCG 60.050 48.000 0.00 0.00 0.00 4.04
621 630 2.604046 ACTCTCTCTCTCTCTCTCGC 57.396 55.000 0.00 0.00 0.00 5.03
622 631 1.202417 ACTCTCTCTCTCTCTCTCGCG 60.202 57.143 0.00 0.00 0.00 5.87
623 632 0.529773 TCTCTCTCTCTCTCTCGCGC 60.530 60.000 0.00 0.00 0.00 6.86
624 633 1.821241 CTCTCTCTCTCTCTCGCGCG 61.821 65.000 26.76 26.76 0.00 6.86
625 634 3.506312 CTCTCTCTCTCTCGCGCGC 62.506 68.421 27.95 23.91 0.00 6.86
626 635 4.936248 CTCTCTCTCTCGCGCGCG 62.936 72.222 44.84 44.84 41.35 6.86
672 681 7.913789 ACCATTGTTAAGGTTATGACTGACTA 58.086 34.615 0.00 0.00 33.39 2.59
829 846 0.603707 CAGTGTCATCCAACGGCTGT 60.604 55.000 0.00 0.00 0.00 4.40
830 847 0.603707 AGTGTCATCCAACGGCTGTG 60.604 55.000 0.00 0.00 0.00 3.66
890 933 6.789268 TCTATCCCATCACAAAAAGAAAGGA 58.211 36.000 0.00 0.00 0.00 3.36
1140 1183 2.161609 CGGTTTGATTCTTTCTTCCCCG 59.838 50.000 0.00 0.00 0.00 5.73
1168 1211 4.054780 TCTCCGTCTTCCATTATTTCCG 57.945 45.455 0.00 0.00 0.00 4.30
1213 1256 5.631992 TCGCATCTAGAGATATACGCTTTG 58.368 41.667 0.00 0.00 32.63 2.77
1225 1268 1.165270 ACGCTTTGCTAACATGGGAC 58.835 50.000 0.00 0.00 0.00 4.46
1242 1285 1.653151 GACTGGTCTTGCGGGATTAC 58.347 55.000 0.00 0.00 0.00 1.89
1271 1314 1.196012 GCTAGGGTCAGGTAGCTGTT 58.804 55.000 20.76 8.58 38.92 3.16
1305 1348 2.093764 CAGTTCTCTAGTGAGGGCTTGG 60.094 54.545 0.00 0.00 40.58 3.61
1333 1379 1.146358 GCTGGCGTCTCGGACATTAC 61.146 60.000 5.15 0.00 32.09 1.89
1334 1380 0.866061 CTGGCGTCTCGGACATTACG 60.866 60.000 5.15 0.00 38.34 3.18
1339 1385 1.731424 CGTCTCGGACATTACGCAACT 60.731 52.381 5.15 0.00 32.09 3.16
1376 1422 8.853345 CATGTTCACAAAGTTTACATATTGAGC 58.147 33.333 2.23 0.00 0.00 4.26
1430 1476 5.583854 CCTGCATTATTCTATGGATTCGGAG 59.416 44.000 0.00 0.00 0.00 4.63
1524 1571 6.266103 ACCATGGAATAGTTGCAAATCATAGG 59.734 38.462 21.47 7.70 33.68 2.57
1547 1594 5.359576 GGCATGAATTATGTTGAGTAACCCA 59.640 40.000 0.00 0.00 39.08 4.51
1554 1601 6.995511 TTATGTTGAGTAACCCAAGCATAC 57.004 37.500 0.00 0.00 35.92 2.39
1583 1630 1.893801 TGGCATTGTTCATGTGATGCA 59.106 42.857 19.07 0.00 44.99 3.96
1642 1689 4.141869 GCGGGAGAGTTGTAAAAGGGTATA 60.142 45.833 0.00 0.00 0.00 1.47
1643 1690 5.454329 GCGGGAGAGTTGTAAAAGGGTATAT 60.454 44.000 0.00 0.00 0.00 0.86
1644 1691 6.589135 CGGGAGAGTTGTAAAAGGGTATATT 58.411 40.000 0.00 0.00 0.00 1.28
1645 1692 7.052248 CGGGAGAGTTGTAAAAGGGTATATTT 58.948 38.462 0.00 0.00 0.00 1.40
1646 1693 7.226128 CGGGAGAGTTGTAAAAGGGTATATTTC 59.774 40.741 0.00 0.00 0.00 2.17
1647 1694 8.050930 GGGAGAGTTGTAAAAGGGTATATTTCA 58.949 37.037 0.00 0.00 0.00 2.69
1648 1695 9.628500 GGAGAGTTGTAAAAGGGTATATTTCAT 57.372 33.333 0.00 0.00 0.00 2.57
1767 1814 5.990668 ACCTTGTGAAAGATACTCCATACC 58.009 41.667 0.00 0.00 0.00 2.73
1827 1874 6.202570 CGAATCCAACCACATTTGTTCAATTT 59.797 34.615 0.00 0.00 0.00 1.82
1867 1914 1.992557 TCCTGGCAAACTCTATGGGTT 59.007 47.619 0.00 0.00 0.00 4.11
1919 1966 5.358090 CAGAGCACTGTGATGTTAGATGAT 58.642 41.667 12.86 0.00 39.11 2.45
2121 2169 7.859325 TTCTAACTACAATAGCAATCCCAAC 57.141 36.000 0.00 0.00 0.00 3.77
2137 2185 3.202151 TCCCAACACTCCACTTTCTCTTT 59.798 43.478 0.00 0.00 0.00 2.52
2141 2189 5.368989 CAACACTCCACTTTCTCTTTAGGT 58.631 41.667 0.00 0.00 0.00 3.08
2381 2554 3.117888 TCTCCAGTCTTGGTTCTTGCTTT 60.118 43.478 0.00 0.00 45.26 3.51
2417 2590 7.114811 GTGCACACAAGAAACTTTATAACATGG 59.885 37.037 13.17 0.00 0.00 3.66
2627 3733 3.323691 AGAAGTTTATGTTTGTTGCCCCC 59.676 43.478 0.00 0.00 0.00 5.40
2843 3949 4.688879 TGTATTCGTGAATGGTTCTGACAC 59.311 41.667 5.37 0.00 32.50 3.67
2853 3959 4.371624 TGGTTCTGACACAATTGAGGAT 57.628 40.909 13.59 0.00 0.00 3.24
2909 4016 7.201644 CCGTAATTTATGTCTTGAGTTCATGCT 60.202 37.037 0.00 0.00 0.00 3.79
2914 4021 8.791327 TTTATGTCTTGAGTTCATGCTATTCA 57.209 30.769 0.00 0.00 0.00 2.57
2916 4023 7.876936 ATGTCTTGAGTTCATGCTATTCAAT 57.123 32.000 6.21 0.00 0.00 2.57
2917 4024 7.692460 TGTCTTGAGTTCATGCTATTCAATT 57.308 32.000 6.21 0.00 0.00 2.32
2918 4025 8.114331 TGTCTTGAGTTCATGCTATTCAATTT 57.886 30.769 6.21 0.00 0.00 1.82
2919 4026 8.579006 TGTCTTGAGTTCATGCTATTCAATTTT 58.421 29.630 6.21 0.00 0.00 1.82
2922 4029 9.294030 CTTGAGTTCATGCTATTCAATTTTACC 57.706 33.333 6.21 0.00 0.00 2.85
2923 4030 8.347004 TGAGTTCATGCTATTCAATTTTACCA 57.653 30.769 0.00 0.00 0.00 3.25
2924 4031 8.461222 TGAGTTCATGCTATTCAATTTTACCAG 58.539 33.333 0.00 0.00 0.00 4.00
2925 4032 8.579850 AGTTCATGCTATTCAATTTTACCAGA 57.420 30.769 0.00 0.00 0.00 3.86
2926 4033 9.023962 AGTTCATGCTATTCAATTTTACCAGAA 57.976 29.630 0.00 0.00 0.00 3.02
2927 4034 9.076596 GTTCATGCTATTCAATTTTACCAGAAC 57.923 33.333 0.00 0.00 0.00 3.01
2928 4035 8.579850 TCATGCTATTCAATTTTACCAGAACT 57.420 30.769 0.00 0.00 0.00 3.01
2929 4036 9.679661 TCATGCTATTCAATTTTACCAGAACTA 57.320 29.630 0.00 0.00 0.00 2.24
2933 4040 9.237846 GCTATTCAATTTTACCAGAACTATTGC 57.762 33.333 0.00 0.00 0.00 3.56
2935 4042 8.986477 ATTCAATTTTACCAGAACTATTGCAC 57.014 30.769 0.00 0.00 0.00 4.57
2936 4043 7.517614 TCAATTTTACCAGAACTATTGCACA 57.482 32.000 0.00 0.00 0.00 4.57
2937 4044 7.946207 TCAATTTTACCAGAACTATTGCACAA 58.054 30.769 0.00 0.00 0.00 3.33
2938 4045 8.417106 TCAATTTTACCAGAACTATTGCACAAA 58.583 29.630 0.00 0.00 0.00 2.83
2939 4046 9.206870 CAATTTTACCAGAACTATTGCACAAAT 57.793 29.630 0.00 0.00 0.00 2.32
2946 4053 9.189156 ACCAGAACTATTGCACAAATATAATGT 57.811 29.630 0.00 0.00 30.26 2.71
2954 4061 8.978874 ATTGCACAAATATAATGTAGTCAGGA 57.021 30.769 0.00 0.00 0.00 3.86
2955 4062 8.978874 TTGCACAAATATAATGTAGTCAGGAT 57.021 30.769 0.00 0.00 0.00 3.24
2956 4063 8.978874 TGCACAAATATAATGTAGTCAGGATT 57.021 30.769 0.00 0.00 0.00 3.01
2957 4064 9.407380 TGCACAAATATAATGTAGTCAGGATTT 57.593 29.630 0.00 0.00 0.00 2.17
2967 4074 8.871686 AATGTAGTCAGGATTTTGTTGTTTTC 57.128 30.769 0.00 0.00 0.00 2.29
2968 4075 7.639113 TGTAGTCAGGATTTTGTTGTTTTCT 57.361 32.000 0.00 0.00 0.00 2.52
2969 4076 7.479980 TGTAGTCAGGATTTTGTTGTTTTCTG 58.520 34.615 0.00 0.00 0.00 3.02
2970 4077 5.351458 AGTCAGGATTTTGTTGTTTTCTGC 58.649 37.500 0.00 0.00 0.00 4.26
2971 4078 5.127682 AGTCAGGATTTTGTTGTTTTCTGCT 59.872 36.000 0.00 0.00 0.00 4.24
2972 4079 6.321181 AGTCAGGATTTTGTTGTTTTCTGCTA 59.679 34.615 0.00 0.00 0.00 3.49
2973 4080 6.978080 GTCAGGATTTTGTTGTTTTCTGCTAA 59.022 34.615 0.00 0.00 0.00 3.09
2974 4081 6.978080 TCAGGATTTTGTTGTTTTCTGCTAAC 59.022 34.615 0.00 0.00 0.00 2.34
2975 4082 6.756074 CAGGATTTTGTTGTTTTCTGCTAACA 59.244 34.615 0.00 0.00 33.92 2.41
2976 4083 6.756542 AGGATTTTGTTGTTTTCTGCTAACAC 59.243 34.615 0.00 0.00 35.39 3.32
2977 4084 6.019075 GGATTTTGTTGTTTTCTGCTAACACC 60.019 38.462 0.00 0.00 35.39 4.16
2978 4085 5.652994 TTTGTTGTTTTCTGCTAACACCT 57.347 34.783 0.00 0.00 35.39 4.00
2979 4086 5.652994 TTGTTGTTTTCTGCTAACACCTT 57.347 34.783 0.00 0.00 35.39 3.50
2980 4087 5.652994 TGTTGTTTTCTGCTAACACCTTT 57.347 34.783 0.00 0.00 35.39 3.11
2981 4088 6.031751 TGTTGTTTTCTGCTAACACCTTTT 57.968 33.333 0.00 0.00 35.39 2.27
2982 4089 7.159322 TGTTGTTTTCTGCTAACACCTTTTA 57.841 32.000 0.00 0.00 35.39 1.52
2983 4090 7.254852 TGTTGTTTTCTGCTAACACCTTTTAG 58.745 34.615 0.00 0.00 35.39 1.85
2996 4103 7.683437 AACACCTTTTAGCTGTAACTAATCC 57.317 36.000 0.00 0.00 32.35 3.01
2997 4104 6.775708 ACACCTTTTAGCTGTAACTAATCCA 58.224 36.000 0.00 0.00 32.35 3.41
2998 4105 7.402862 ACACCTTTTAGCTGTAACTAATCCAT 58.597 34.615 0.00 0.00 32.35 3.41
2999 4106 7.553044 ACACCTTTTAGCTGTAACTAATCCATC 59.447 37.037 0.00 0.00 32.35 3.51
3000 4107 6.761714 ACCTTTTAGCTGTAACTAATCCATCG 59.238 38.462 0.00 0.00 32.35 3.84
3001 4108 6.761714 CCTTTTAGCTGTAACTAATCCATCGT 59.238 38.462 0.00 0.00 32.35 3.73
3002 4109 7.924412 CCTTTTAGCTGTAACTAATCCATCGTA 59.076 37.037 0.00 0.00 32.35 3.43
3003 4110 9.477484 CTTTTAGCTGTAACTAATCCATCGTAT 57.523 33.333 0.00 0.00 32.35 3.06
3007 4114 8.988064 AGCTGTAACTAATCCATCGTATAATG 57.012 34.615 0.00 0.00 0.00 1.90
3008 4115 8.035394 AGCTGTAACTAATCCATCGTATAATGG 58.965 37.037 0.00 0.00 46.44 3.16
3009 4116 7.201530 GCTGTAACTAATCCATCGTATAATGGC 60.202 40.741 0.00 0.00 44.98 4.40
3010 4117 7.672240 TGTAACTAATCCATCGTATAATGGCA 58.328 34.615 0.00 0.00 44.98 4.92
3011 4118 8.318412 TGTAACTAATCCATCGTATAATGGCAT 58.682 33.333 0.00 0.00 44.98 4.40
3012 4119 9.811995 GTAACTAATCCATCGTATAATGGCATA 57.188 33.333 0.00 0.00 44.98 3.14
3014 4121 9.905713 AACTAATCCATCGTATAATGGCATATT 57.094 29.630 0.00 0.00 44.98 1.28
3015 4122 9.547753 ACTAATCCATCGTATAATGGCATATTC 57.452 33.333 0.00 0.00 44.98 1.75
3016 4123 9.770097 CTAATCCATCGTATAATGGCATATTCT 57.230 33.333 0.00 0.00 44.98 2.40
3017 4124 8.442632 AATCCATCGTATAATGGCATATTCTG 57.557 34.615 0.00 0.00 44.98 3.02
3030 4137 4.801891 GCATATTCTGCCATTACCATGTG 58.198 43.478 0.00 0.00 45.66 3.21
3031 4138 4.279169 GCATATTCTGCCATTACCATGTGT 59.721 41.667 0.00 0.00 45.66 3.72
3032 4139 5.563475 GCATATTCTGCCATTACCATGTGTC 60.563 44.000 0.00 0.00 45.66 3.67
3033 4140 3.719268 TTCTGCCATTACCATGTGTCT 57.281 42.857 0.00 0.00 0.00 3.41
3034 4141 4.835284 TTCTGCCATTACCATGTGTCTA 57.165 40.909 0.00 0.00 0.00 2.59
3035 4142 5.372343 TTCTGCCATTACCATGTGTCTAT 57.628 39.130 0.00 0.00 0.00 1.98
3036 4143 4.707105 TCTGCCATTACCATGTGTCTATG 58.293 43.478 0.00 0.00 0.00 2.23
3037 4144 3.213506 TGCCATTACCATGTGTCTATGC 58.786 45.455 0.00 0.00 0.00 3.14
3038 4145 3.213506 GCCATTACCATGTGTCTATGCA 58.786 45.455 0.00 0.00 0.00 3.96
3039 4146 3.822735 GCCATTACCATGTGTCTATGCAT 59.177 43.478 3.79 3.79 0.00 3.96
3040 4147 5.003160 GCCATTACCATGTGTCTATGCATA 58.997 41.667 6.20 6.20 0.00 3.14
3041 4148 5.473162 GCCATTACCATGTGTCTATGCATAA 59.527 40.000 8.00 0.00 0.00 1.90
3042 4149 6.568462 GCCATTACCATGTGTCTATGCATAAC 60.568 42.308 8.00 9.45 0.00 1.89
3043 4150 6.712095 CCATTACCATGTGTCTATGCATAACT 59.288 38.462 8.00 0.00 0.00 2.24
3044 4151 7.229306 CCATTACCATGTGTCTATGCATAACTT 59.771 37.037 8.00 0.00 0.00 2.66
3045 4152 9.271828 CATTACCATGTGTCTATGCATAACTTA 57.728 33.333 8.00 3.88 0.00 2.24
3047 4154 7.734924 ACCATGTGTCTATGCATAACTTATG 57.265 36.000 8.00 14.35 39.18 1.90
3370 4699 6.147164 TCAGCTAGAATGAAAAGGTAAACGTG 59.853 38.462 0.00 0.00 0.00 4.49
3518 4847 0.176449 GCCAATGTGAATTGCTCCCC 59.824 55.000 0.00 0.00 0.00 4.81
3533 4862 2.233676 GCTCCCCGTTTCCATTCAAAAT 59.766 45.455 0.00 0.00 0.00 1.82
3541 4870 6.074034 CCCGTTTCCATTCAAAATGTGTTAAC 60.074 38.462 0.00 0.00 0.00 2.01
3807 5164 5.306394 GTTTGTTAGCTAGTTCTGTTCCCT 58.694 41.667 0.00 0.00 0.00 4.20
3958 5436 1.371467 ACCATGTCATTGTCCCCTCA 58.629 50.000 0.00 0.00 0.00 3.86
3975 5453 3.397482 CCTCATTACCATCTGCAGTAGC 58.603 50.000 14.67 0.00 42.57 3.58
4178 5858 6.484643 GGAGTTGCTCAAATGCTATGAGAATA 59.515 38.462 15.21 1.88 45.74 1.75
4305 5985 5.861251 GTGATATCAGATAACAAGCTCCTCG 59.139 44.000 5.42 0.00 0.00 4.63
4481 6162 4.910458 AGGGCTGAGTACTGTGTATTTT 57.090 40.909 0.00 0.00 0.00 1.82
4667 6383 1.799933 TGCCACCTTGGGTCATTTTT 58.200 45.000 0.00 0.00 38.19 1.94
4708 6424 2.505819 GCCACCTTTATCCTCAGGAGAA 59.494 50.000 0.00 0.00 34.05 2.87
4848 6564 0.256752 TGCTGCATTGGCTGGATACT 59.743 50.000 0.00 0.00 41.91 2.12
4912 6628 9.092876 TGTATTTTGTGTTTTTCTGATTGAACC 57.907 29.630 0.00 0.00 33.88 3.62
4933 6649 2.566952 AAGATGCCAAATAGCGCAAC 57.433 45.000 11.47 0.00 38.75 4.17
5037 6753 8.951787 AATATGAAAATGTGTTTCATGATGGG 57.048 30.769 19.59 0.00 45.55 4.00
5043 6759 7.722949 AAATGTGTTTCATGATGGGTCTAAT 57.277 32.000 0.00 0.00 36.81 1.73
5099 6815 5.913137 ACATGGACAACTTTGACTTTTGA 57.087 34.783 0.00 0.00 0.00 2.69
5148 6864 6.841229 TGAAACAGAGGGAGTATCAGATACAT 59.159 38.462 20.62 7.59 38.21 2.29
5220 6936 4.729868 ACCTGCTAAACAAAATCTCCACT 58.270 39.130 0.00 0.00 0.00 4.00
5222 6938 4.520492 CCTGCTAAACAAAATCTCCACTGT 59.480 41.667 0.00 0.00 0.00 3.55
5311 7028 3.763360 CTCCCAAGATATGCCAACAACAA 59.237 43.478 0.00 0.00 0.00 2.83
5385 7102 6.194463 CGTCAAGTATATCAACCAAGCAATG 58.806 40.000 0.00 0.00 0.00 2.82
5413 7130 3.068873 GGCACAAAGTACAAACCAATGGA 59.931 43.478 6.16 0.00 0.00 3.41
5561 8979 1.712056 TGTCTTCTGAAACGGAGGGA 58.288 50.000 0.00 0.00 0.00 4.20
5562 8980 1.343465 TGTCTTCTGAAACGGAGGGAC 59.657 52.381 0.00 0.00 0.00 4.46
5563 8981 0.974383 TCTTCTGAAACGGAGGGACC 59.026 55.000 0.00 0.00 0.00 4.46
5644 9063 5.348451 GGTTATTGTTGTTGCTTTATGCCTG 59.652 40.000 0.00 0.00 42.00 4.85
6063 9493 3.853671 GTGTTCTTTGATTATGCGGCTTG 59.146 43.478 0.00 0.00 0.00 4.01
6290 9721 6.835819 TTCCTTCTAAAATCAGTCTCGAGA 57.164 37.500 12.08 12.08 0.00 4.04
6655 10086 6.582636 TGTTAGAATCTTACCTACCAGCATG 58.417 40.000 0.00 0.00 0.00 4.06
6656 10087 6.382859 TGTTAGAATCTTACCTACCAGCATGA 59.617 38.462 0.00 0.00 39.69 3.07
6680 10111 0.445436 GCAAGAGACAACATCAGCCG 59.555 55.000 0.00 0.00 0.00 5.52
6734 10165 0.624206 TCCCATCTCCAATGGCCTGA 60.624 55.000 3.32 0.00 37.85 3.86
6739 10170 3.147629 CATCTCCAATGGCCTGAATCTC 58.852 50.000 3.32 0.00 0.00 2.75
6753 10184 5.827797 GCCTGAATCTCATGTTAAATACCCA 59.172 40.000 0.00 0.00 0.00 4.51
6827 10258 3.454082 GGAGGAAGATGAACCATCAGAGT 59.546 47.826 9.30 0.00 42.72 3.24
6853 10284 7.465960 TGCTGACCATCTCTAGTATCTTAGAT 58.534 38.462 0.00 0.00 0.00 1.98
6864 10295 9.398538 CTCTAGTATCTTAGATATGGTGTACCC 57.601 40.741 5.15 0.00 34.29 3.69
6897 10328 5.463061 CCTTGATGTTGTTGCTTTGTTTAGG 59.537 40.000 0.00 0.00 0.00 2.69
6903 10334 6.223852 TGTTGTTGCTTTGTTTAGGTGAAAA 58.776 32.000 0.00 0.00 0.00 2.29
6919 10350 2.424705 AAAAGCGTGCAGGCACATGG 62.425 55.000 30.90 8.98 46.47 3.66
6926 10357 1.942657 GTGCAGGCACATGGTATACAG 59.057 52.381 18.84 0.00 45.53 2.74
7023 10456 3.119884 TCAGGCAGTTTTAATGATGCACG 60.120 43.478 0.00 0.00 40.46 5.34
7066 10499 8.481492 TCCAATGATGTCCAAATAGCAATAAT 57.519 30.769 0.00 0.00 0.00 1.28
7067 10500 9.585369 TCCAATGATGTCCAAATAGCAATAATA 57.415 29.630 0.00 0.00 0.00 0.98
7068 10501 9.630098 CCAATGATGTCCAAATAGCAATAATAC 57.370 33.333 0.00 0.00 0.00 1.89
7159 10592 4.240096 GTGCATGTTTCTTTAGCATTGCT 58.760 39.130 16.63 16.63 43.41 3.91
7160 10593 5.048154 TGTGCATGTTTCTTTAGCATTGCTA 60.048 36.000 14.33 14.33 40.44 3.49
7197 10630 4.338879 AGCCTAGAGACGGTAAAAGTACA 58.661 43.478 0.00 0.00 31.21 2.90
7199 10632 4.397417 GCCTAGAGACGGTAAAAGTACAGA 59.603 45.833 0.00 0.00 31.21 3.41
7221 10685 6.258727 CAGATCAATAGTCAAACTACGGCATT 59.741 38.462 0.00 0.00 32.84 3.56
7223 10687 8.150945 AGATCAATAGTCAAACTACGGCATTAT 58.849 33.333 0.00 0.00 32.84 1.28
7226 10690 9.602568 TCAATAGTCAAACTACGGCATTATTTA 57.397 29.630 0.00 0.00 32.84 1.40
7263 10729 4.436451 GGGAACTACGGCAATAAACGAAAG 60.436 45.833 0.00 0.00 0.00 2.62
7283 10749 4.510167 AGTATTTCCTCCACTGGAATGG 57.490 45.455 0.00 0.00 44.55 3.16
7286 10752 1.198094 TTCCTCCACTGGAATGGCGA 61.198 55.000 0.00 0.00 40.80 5.54
7295 10761 4.497300 CACTGGAATGGCGATCAATTTTT 58.503 39.130 0.00 0.00 0.00 1.94
7316 10782 7.872163 TTTTTGGAATGACGATCAATTTGAG 57.128 32.000 5.21 0.00 0.00 3.02
7317 10783 6.573664 TTTGGAATGACGATCAATTTGAGT 57.426 33.333 5.21 0.00 0.00 3.41
7318 10784 6.573664 TTGGAATGACGATCAATTTGAGTT 57.426 33.333 5.21 0.00 0.00 3.01
7319 10785 6.182039 TGGAATGACGATCAATTTGAGTTC 57.818 37.500 5.21 2.21 0.00 3.01
7320 10786 5.939883 TGGAATGACGATCAATTTGAGTTCT 59.060 36.000 5.21 0.00 0.00 3.01
7321 10787 7.102993 TGGAATGACGATCAATTTGAGTTCTA 58.897 34.615 5.21 0.00 0.00 2.10
7322 10788 7.770433 TGGAATGACGATCAATTTGAGTTCTAT 59.230 33.333 5.21 0.00 0.00 1.98
7323 10789 9.261180 GGAATGACGATCAATTTGAGTTCTATA 57.739 33.333 5.21 0.00 0.00 1.31
7325 10791 9.823647 AATGACGATCAATTTGAGTTCTATACT 57.176 29.630 5.21 0.00 40.71 2.12
7326 10792 8.634475 TGACGATCAATTTGAGTTCTATACTG 57.366 34.615 5.21 0.00 37.17 2.74
7327 10793 8.251026 TGACGATCAATTTGAGTTCTATACTGT 58.749 33.333 5.21 0.00 37.17 3.55
7328 10794 9.088512 GACGATCAATTTGAGTTCTATACTGTT 57.911 33.333 5.21 0.00 37.17 3.16
7329 10795 9.436957 ACGATCAATTTGAGTTCTATACTGTTT 57.563 29.630 5.21 0.00 37.17 2.83
7330 10796 9.907576 CGATCAATTTGAGTTCTATACTGTTTC 57.092 33.333 5.21 0.00 37.17 2.78
7361 10827 8.644318 AAATTTGAGTTCTATACTATTCGCGT 57.356 30.769 5.77 0.00 37.17 6.01
7368 10834 5.372547 TCTATACTATTCGCGTGATGCTT 57.627 39.130 5.77 0.00 43.27 3.91
7370 10836 6.905578 TCTATACTATTCGCGTGATGCTTAA 58.094 36.000 5.77 0.00 43.27 1.85
7373 10839 1.635844 ATTCGCGTGATGCTTAACGA 58.364 45.000 13.44 0.00 42.32 3.85
7377 10843 1.006832 GCGTGATGCTTAACGATGGT 58.993 50.000 13.44 0.00 42.32 3.55
7378 10844 1.004927 GCGTGATGCTTAACGATGGTC 60.005 52.381 13.44 0.00 42.32 4.02
7379 10845 1.593006 CGTGATGCTTAACGATGGTCC 59.407 52.381 3.38 0.00 42.32 4.46
7380 10846 2.738643 CGTGATGCTTAACGATGGTCCT 60.739 50.000 3.38 0.00 42.32 3.85
7381 10847 3.270877 GTGATGCTTAACGATGGTCCTT 58.729 45.455 0.00 0.00 0.00 3.36
7382 10848 3.689649 GTGATGCTTAACGATGGTCCTTT 59.310 43.478 0.00 0.00 0.00 3.11
7384 10850 1.810151 TGCTTAACGATGGTCCTTTGC 59.190 47.619 0.00 0.00 0.00 3.68
7385 10851 1.810151 GCTTAACGATGGTCCTTTGCA 59.190 47.619 0.00 0.00 0.00 4.08
7390 11179 1.384191 GATGGTCCTTTGCACCCCT 59.616 57.895 0.00 0.00 32.24 4.79
7426 11215 4.021102 AGGGGAAACGATAATATGCCTG 57.979 45.455 0.00 0.00 0.00 4.85
7436 11225 2.355010 AATATGCCTGCCTGGAGAAC 57.645 50.000 0.00 0.00 38.35 3.01
7474 11263 0.322816 TTCTTGCCCTGTGATGCTCC 60.323 55.000 0.00 0.00 0.00 4.70
7495 11284 2.063266 CGTTTGTGCGGTGTATAGTGT 58.937 47.619 0.00 0.00 0.00 3.55
7577 11372 4.165036 CGCGAGATGAGATTCTAATCTGG 58.835 47.826 16.95 16.13 45.39 3.86
7590 11385 6.971250 GATTCTAATCTGGCCATCTGTGGAAT 60.971 42.308 5.51 11.19 38.84 3.01
7591 11386 8.915087 GATTCTAATCTGGCCATCTGTGGAATG 61.915 44.444 5.51 0.00 38.84 2.67
7639 11434 2.908817 GGACCACGACGTGATTGTT 58.091 52.632 28.83 7.56 35.23 2.83
7640 11435 0.788391 GGACCACGACGTGATTGTTC 59.212 55.000 28.83 13.39 35.23 3.18
7641 11436 0.788391 GACCACGACGTGATTGTTCC 59.212 55.000 28.83 4.44 35.23 3.62
7642 11437 0.601841 ACCACGACGTGATTGTTCCC 60.602 55.000 28.83 0.00 35.23 3.97
7643 11438 0.320421 CCACGACGTGATTGTTCCCT 60.320 55.000 28.83 0.00 35.23 4.20
7644 11439 1.508632 CACGACGTGATTGTTCCCTT 58.491 50.000 23.39 0.00 35.23 3.95
7645 11440 1.194547 CACGACGTGATTGTTCCCTTG 59.805 52.381 23.39 0.00 35.23 3.61
7646 11441 0.796312 CGACGTGATTGTTCCCTTGG 59.204 55.000 0.00 0.00 0.00 3.61
7647 11442 0.521735 GACGTGATTGTTCCCTTGGC 59.478 55.000 0.00 0.00 0.00 4.52
7648 11443 0.110486 ACGTGATTGTTCCCTTGGCT 59.890 50.000 0.00 0.00 0.00 4.75
7649 11444 0.523072 CGTGATTGTTCCCTTGGCTG 59.477 55.000 0.00 0.00 0.00 4.85
7650 11445 1.881925 CGTGATTGTTCCCTTGGCTGA 60.882 52.381 0.00 0.00 0.00 4.26
7651 11446 2.238521 GTGATTGTTCCCTTGGCTGAA 58.761 47.619 0.00 0.00 0.00 3.02
7652 11447 2.627699 GTGATTGTTCCCTTGGCTGAAA 59.372 45.455 0.00 0.00 0.00 2.69
7653 11448 2.627699 TGATTGTTCCCTTGGCTGAAAC 59.372 45.455 0.00 0.00 0.00 2.78
7654 11449 1.408969 TTGTTCCCTTGGCTGAAACC 58.591 50.000 0.00 0.00 0.00 3.27
7655 11450 0.260230 TGTTCCCTTGGCTGAAACCA 59.740 50.000 0.00 0.00 38.16 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.507622 CCCCTCAAAAAGCTAAGGACAAG 59.492 47.826 0.00 0.00 0.00 3.16
34 35 2.716424 AGAGATGTGGACCCCTCAAAAA 59.284 45.455 0.00 0.00 30.64 1.94
59 60 8.936070 AATGTTTAATGATTGTCATGACATGG 57.064 30.769 28.32 0.00 41.52 3.66
128 130 8.091449 TGGATGGTTTTGGTAATTCATAACAAC 58.909 33.333 0.00 0.00 40.88 3.32
147 149 4.296621 GTGTAACTAACCCTTGGATGGT 57.703 45.455 0.00 0.00 37.85 3.55
165 167 9.575783 TTTTCTATTTTTCTGCGTTAAAAGTGT 57.424 25.926 0.00 0.00 0.00 3.55
219 221 9.934190 CCTTGTTGGTTTTAGAAAATTTTCATG 57.066 29.630 28.00 9.67 39.61 3.07
226 228 7.432148 AGGTTCCTTGTTGGTTTTAGAAAAT 57.568 32.000 0.00 0.00 37.07 1.82
227 229 6.860790 AGGTTCCTTGTTGGTTTTAGAAAA 57.139 33.333 0.00 0.00 37.07 2.29
245 247 4.193653 GCAGGAGCGAGAAGGTTC 57.806 61.111 0.00 0.00 0.00 3.62
256 258 1.293924 CACTTCGCCAATAGCAGGAG 58.706 55.000 0.00 0.00 44.04 3.69
274 276 2.557869 ACCTATTAGGAACCACCAGCA 58.442 47.619 16.80 0.00 37.67 4.41
278 280 2.651455 GCCAACCTATTAGGAACCACC 58.349 52.381 16.80 0.00 37.67 4.61
298 300 4.142687 CGCTTAATAGTGTCAAAAGGTGGG 60.143 45.833 0.00 0.00 0.00 4.61
303 305 8.543774 CCTTAGATCGCTTAATAGTGTCAAAAG 58.456 37.037 0.00 0.00 33.54 2.27
307 309 5.831525 TCCCTTAGATCGCTTAATAGTGTCA 59.168 40.000 0.00 0.00 33.54 3.58
311 313 6.658391 ACGTATCCCTTAGATCGCTTAATAGT 59.342 38.462 0.00 0.00 36.33 2.12
335 337 1.990799 TGTATGTGCGCTAGTGACAC 58.009 50.000 9.73 18.18 34.86 3.67
337 339 2.128035 GGATGTATGTGCGCTAGTGAC 58.872 52.381 9.73 0.00 0.00 3.67
361 363 1.278127 GGCTTACTTCTACCACCAGCA 59.722 52.381 0.00 0.00 0.00 4.41
362 364 1.739371 CGGCTTACTTCTACCACCAGC 60.739 57.143 0.00 0.00 0.00 4.85
365 367 2.889852 CTTCGGCTTACTTCTACCACC 58.110 52.381 0.00 0.00 0.00 4.61
395 397 2.133359 AAAACCCCGGTGTCTAGCCC 62.133 60.000 0.00 0.00 0.00 5.19
415 417 3.501062 TGAGCTTTCACATCAGCTTGAAG 59.499 43.478 0.00 0.00 46.72 3.02
418 420 3.909776 TTGAGCTTTCACATCAGCTTG 57.090 42.857 0.00 0.00 46.72 4.01
422 424 5.457799 CAGTTTGTTTGAGCTTTCACATCAG 59.542 40.000 0.00 0.00 0.00 2.90
453 455 1.398390 CGGTTGTGGCTAAGCATTCTC 59.602 52.381 0.00 0.00 0.00 2.87
457 459 0.324943 AGTCGGTTGTGGCTAAGCAT 59.675 50.000 0.00 0.00 0.00 3.79
470 472 0.039437 CCGCGCTATTATCAGTCGGT 60.039 55.000 5.56 0.00 32.71 4.69
471 473 0.732880 CCCGCGCTATTATCAGTCGG 60.733 60.000 5.56 0.00 35.21 4.79
511 513 0.595095 GGTCTACAAGGACGTGACGT 59.405 55.000 11.70 11.70 45.10 4.34
514 523 0.178955 TGGGGTCTACAAGGACGTGA 60.179 55.000 0.00 0.00 37.12 4.35
526 535 1.380302 GAAGCCATGTGTGGGGTCT 59.620 57.895 0.00 0.00 46.14 3.85
546 555 4.081087 TCCCTTTTAAGAGAAGGTCGATGG 60.081 45.833 4.17 0.00 41.70 3.51
557 566 5.316327 GGATGTTGCTTCCCTTTTAAGAG 57.684 43.478 0.00 0.00 0.00 2.85
581 590 5.435291 AGTTTATGCTGGAAGGAAGAGATG 58.565 41.667 0.00 0.00 38.32 2.90
604 613 0.529773 GCGCGAGAGAGAGAGAGAGA 60.530 60.000 12.10 0.00 0.00 3.10
624 633 2.862000 GGTTTCGTAAACGCGCGC 60.862 61.111 32.58 23.91 42.29 6.86
625 634 2.566262 CGGTTTCGTAAACGCGCG 60.566 61.111 30.96 30.96 42.29 6.86
839 856 1.736645 CAGTTGGGCACTACGGTCG 60.737 63.158 0.00 0.00 32.76 4.79
842 859 1.600023 TTTTCAGTTGGGCACTACGG 58.400 50.000 0.00 0.00 32.76 4.02
1079 1122 2.375345 GGATCTGCCTTCGGGGGAA 61.375 63.158 0.00 0.00 34.18 3.97
1101 1144 2.347490 GGAACGAAGAGGCTGGCA 59.653 61.111 3.38 0.00 0.00 4.92
1140 1183 0.903454 TGGAAGACGGAGAAGGGGAC 60.903 60.000 0.00 0.00 0.00 4.46
1168 1211 3.669536 AGAAAGCTGAGAGTGGTTAAGC 58.330 45.455 0.00 0.00 0.00 3.09
1213 1256 2.359900 CAAGACCAGTCCCATGTTAGC 58.640 52.381 0.00 0.00 0.00 3.09
1225 1268 0.251916 TGGTAATCCCGCAAGACCAG 59.748 55.000 0.00 0.00 34.69 4.00
1271 1314 0.396974 AGAACTGCCCAGCCAAAACA 60.397 50.000 0.00 0.00 0.00 2.83
1305 1348 3.057736 TCCGAGACGCCAGCTTATATAAC 60.058 47.826 0.00 0.00 0.00 1.89
1417 1463 5.541845 TCATAAAGCACTCCGAATCCATAG 58.458 41.667 0.00 0.00 0.00 2.23
1483 1530 4.538490 TCCATGGTACCCTCTGTATGTTTT 59.462 41.667 12.58 0.00 0.00 2.43
1507 1554 6.964807 TTCATGCCTATGATTTGCAACTAT 57.035 33.333 0.00 0.00 42.60 2.12
1524 1571 6.449635 TGGGTTACTCAACATAATTCATGC 57.550 37.500 0.00 0.00 38.29 4.06
1547 1594 2.794103 TGCCAGAACATGTGTATGCTT 58.206 42.857 0.00 0.00 37.85 3.91
1554 1601 3.646611 TGAACAATGCCAGAACATGTG 57.353 42.857 0.00 0.00 0.00 3.21
1583 1630 4.134563 AGAACCAGTTGTGCGATTAGTTT 58.865 39.130 0.00 0.00 0.00 2.66
1657 1704 5.877012 GCAGAACAGAGTTCATTTCCTATGA 59.123 40.000 11.92 0.00 0.00 2.15
1692 1739 8.621532 TTTCATCATATGGTTCATAGTTAGCC 57.378 34.615 2.13 0.00 29.42 3.93
1767 1814 7.933577 TCCATCTTTATGTACCATCTAAGCAAG 59.066 37.037 0.00 0.00 0.00 4.01
1827 1874 2.697761 GCGGTCTGGCGTGAGACTA 61.698 63.158 13.50 0.00 41.90 2.59
1867 1914 5.827797 AGGCTTTGTCACAGATAAACAGAAA 59.172 36.000 0.00 0.00 0.00 2.52
2121 2169 3.748568 GCACCTAAAGAGAAAGTGGAGTG 59.251 47.826 0.00 0.00 0.00 3.51
2137 2185 5.296151 CAAAGATGGAATAGAGGCACCTA 57.704 43.478 0.00 0.00 0.00 3.08
2381 2554 4.817318 TCTTGTGTGCACATGTAGGATA 57.183 40.909 24.69 2.62 41.52 2.59
2627 3733 5.339990 ACATGAAAGGAAACAACTCAAACG 58.660 37.500 0.00 0.00 0.00 3.60
2713 3819 3.360340 AGCTGCTGTTCGCTTGCC 61.360 61.111 0.00 0.00 38.76 4.52
2843 3949 8.081633 TGTTTGCTGTACTTTAATCCTCAATTG 58.918 33.333 0.00 0.00 0.00 2.32
2912 4019 7.517614 TGTGCAATAGTTCTGGTAAAATTGA 57.482 32.000 0.00 0.00 0.00 2.57
2920 4027 9.189156 ACATTATATTTGTGCAATAGTTCTGGT 57.811 29.630 0.00 0.00 30.48 4.00
2929 4036 8.978874 TCCTGACTACATTATATTTGTGCAAT 57.021 30.769 0.00 0.00 0.00 3.56
2930 4037 8.978874 ATCCTGACTACATTATATTTGTGCAA 57.021 30.769 0.00 0.00 0.00 4.08
2931 4038 8.978874 AATCCTGACTACATTATATTTGTGCA 57.021 30.769 2.20 0.00 0.00 4.57
2941 4048 9.959749 GAAAACAACAAAATCCTGACTACATTA 57.040 29.630 0.00 0.00 0.00 1.90
2942 4049 8.695456 AGAAAACAACAAAATCCTGACTACATT 58.305 29.630 0.00 0.00 0.00 2.71
2943 4050 8.137437 CAGAAAACAACAAAATCCTGACTACAT 58.863 33.333 0.00 0.00 0.00 2.29
2944 4051 7.479980 CAGAAAACAACAAAATCCTGACTACA 58.520 34.615 0.00 0.00 0.00 2.74
2945 4052 6.417930 GCAGAAAACAACAAAATCCTGACTAC 59.582 38.462 0.00 0.00 0.00 2.73
2946 4053 6.321181 AGCAGAAAACAACAAAATCCTGACTA 59.679 34.615 0.00 0.00 0.00 2.59
2947 4054 5.127682 AGCAGAAAACAACAAAATCCTGACT 59.872 36.000 0.00 0.00 0.00 3.41
2948 4055 5.351458 AGCAGAAAACAACAAAATCCTGAC 58.649 37.500 0.00 0.00 0.00 3.51
2949 4056 5.596836 AGCAGAAAACAACAAAATCCTGA 57.403 34.783 0.00 0.00 0.00 3.86
2950 4057 6.756074 TGTTAGCAGAAAACAACAAAATCCTG 59.244 34.615 0.00 0.00 34.04 3.86
2951 4058 6.756542 GTGTTAGCAGAAAACAACAAAATCCT 59.243 34.615 0.00 0.00 38.50 3.24
2952 4059 6.019075 GGTGTTAGCAGAAAACAACAAAATCC 60.019 38.462 0.00 0.00 42.78 3.01
2953 4060 6.756542 AGGTGTTAGCAGAAAACAACAAAATC 59.243 34.615 6.75 0.00 45.11 2.17
2954 4061 6.639563 AGGTGTTAGCAGAAAACAACAAAAT 58.360 32.000 6.75 0.00 45.11 1.82
2955 4062 6.031751 AGGTGTTAGCAGAAAACAACAAAA 57.968 33.333 6.75 0.00 45.11 2.44
2956 4063 5.652994 AGGTGTTAGCAGAAAACAACAAA 57.347 34.783 6.75 0.00 45.11 2.83
2957 4064 5.652994 AAGGTGTTAGCAGAAAACAACAA 57.347 34.783 6.75 0.00 45.11 2.83
2958 4065 5.652994 AAAGGTGTTAGCAGAAAACAACA 57.347 34.783 6.75 0.00 45.11 3.33
2959 4066 7.679659 CTAAAAGGTGTTAGCAGAAAACAAC 57.320 36.000 0.00 0.00 43.43 3.32
2975 4082 6.761714 CGATGGATTAGTTACAGCTAAAAGGT 59.238 38.462 0.00 0.00 34.98 3.50
2976 4083 6.761714 ACGATGGATTAGTTACAGCTAAAAGG 59.238 38.462 0.00 0.00 34.98 3.11
2977 4084 7.772332 ACGATGGATTAGTTACAGCTAAAAG 57.228 36.000 0.00 0.00 34.98 2.27
2982 4089 8.988064 CATTATACGATGGATTAGTTACAGCT 57.012 34.615 0.00 0.00 0.00 4.24
3009 4116 5.766670 AGACACATGGTAATGGCAGAATATG 59.233 40.000 0.00 0.00 38.19 1.78
3010 4117 5.945310 AGACACATGGTAATGGCAGAATAT 58.055 37.500 0.00 0.00 38.19 1.28
3011 4118 5.372343 AGACACATGGTAATGGCAGAATA 57.628 39.130 0.00 0.00 38.19 1.75
3012 4119 4.240881 AGACACATGGTAATGGCAGAAT 57.759 40.909 0.00 0.00 38.19 2.40
3013 4120 3.719268 AGACACATGGTAATGGCAGAA 57.281 42.857 0.00 0.00 38.19 3.02
3014 4121 4.707105 CATAGACACATGGTAATGGCAGA 58.293 43.478 0.00 0.00 38.19 4.26
3015 4122 3.251729 GCATAGACACATGGTAATGGCAG 59.748 47.826 0.00 0.00 38.19 4.85
3016 4123 3.213506 GCATAGACACATGGTAATGGCA 58.786 45.455 0.00 0.00 38.19 4.92
3017 4124 3.213506 TGCATAGACACATGGTAATGGC 58.786 45.455 0.00 0.00 38.19 4.40
3018 4125 6.712095 AGTTATGCATAGACACATGGTAATGG 59.288 38.462 6.50 0.00 38.19 3.16
3019 4126 7.734924 AGTTATGCATAGACACATGGTAATG 57.265 36.000 6.50 1.99 39.89 1.90
3021 4128 9.271828 CATAAGTTATGCATAGACACATGGTAA 57.728 33.333 9.88 0.00 0.00 2.85
3022 4129 8.831715 CATAAGTTATGCATAGACACATGGTA 57.168 34.615 9.88 0.00 0.00 3.25
3023 4130 7.734924 CATAAGTTATGCATAGACACATGGT 57.265 36.000 9.88 0.00 0.00 3.55
3067 4174 9.691362 GCAATAGTTCTTCTGGTAAAATTGAAA 57.309 29.630 0.00 0.00 0.00 2.69
3232 4561 9.294030 CTATTCTTAATGATTCTTGTGGCAAAC 57.706 33.333 0.00 0.00 0.00 2.93
3370 4699 7.965655 GCCTTCTAATTTTGCTTCTAGAGTTTC 59.034 37.037 0.00 0.00 0.00 2.78
3413 4742 4.020543 AGTTTGGTACAGAAGGCAAACAA 58.979 39.130 18.89 0.00 42.39 2.83
3518 4847 7.692908 AGTTAACACATTTTGAATGGAAACG 57.307 32.000 8.61 0.00 0.00 3.60
3905 5383 7.851228 TCCTATATTCCACAGCCAATACATAG 58.149 38.462 0.00 0.00 0.00 2.23
3911 5389 6.018433 AGTTTCCTATATTCCACAGCCAAT 57.982 37.500 0.00 0.00 0.00 3.16
3958 5436 2.695666 AGTCGCTACTGCAGATGGTAAT 59.304 45.455 23.35 0.00 39.64 1.89
3975 5453 5.519927 TGTATGCACAACTGATCATTAGTCG 59.480 40.000 0.00 0.00 0.00 4.18
4178 5858 7.201644 CCTTTTCAGTATATGCAACATCGTTCT 60.202 37.037 0.00 0.00 0.00 3.01
4386 6067 7.378966 TCCAGAGTTTCAGATAAACTGTAGTG 58.621 38.462 7.80 1.44 45.86 2.74
4387 6068 7.540474 TCCAGAGTTTCAGATAAACTGTAGT 57.460 36.000 7.80 0.00 45.86 2.73
4388 6069 9.092876 GATTCCAGAGTTTCAGATAAACTGTAG 57.907 37.037 7.80 0.00 45.86 2.74
4389 6070 8.816894 AGATTCCAGAGTTTCAGATAAACTGTA 58.183 33.333 7.80 0.00 45.86 2.74
4390 6071 7.684529 AGATTCCAGAGTTTCAGATAAACTGT 58.315 34.615 7.80 1.46 45.86 3.55
4391 6072 8.449397 CAAGATTCCAGAGTTTCAGATAAACTG 58.551 37.037 7.80 0.00 46.97 3.16
4392 6073 8.160106 ACAAGATTCCAGAGTTTCAGATAAACT 58.840 33.333 2.92 2.92 42.62 2.66
4481 6162 7.420214 GGTGATTAATATTGTTGAGGGGAGAGA 60.420 40.741 0.00 0.00 0.00 3.10
4598 6280 9.074576 ACGAAATAGGAAAAAGGAAACAACTAT 57.925 29.630 0.00 0.00 0.00 2.12
4667 6383 6.542370 GGTGGCAGTCTTCTATAAGCAATAAA 59.458 38.462 0.00 0.00 32.36 1.40
4890 6606 9.364989 CTTAGGTTCAATCAGAAAAACACAAAA 57.635 29.630 0.00 0.00 38.13 2.44
4912 6628 3.313526 AGTTGCGCTATTTGGCATCTTAG 59.686 43.478 9.73 0.00 39.21 2.18
5025 6741 5.647658 TGTGTCATTAGACCCATCATGAAAC 59.352 40.000 0.00 0.00 44.33 2.78
5311 7028 6.998673 ACTAAGTGCTCTTTCATAACCAACTT 59.001 34.615 6.31 0.00 35.36 2.66
5385 7102 1.404843 TTGTACTTTGTGCCAACCCC 58.595 50.000 0.00 0.00 0.00 4.95
5386 7103 2.482316 GGTTTGTACTTTGTGCCAACCC 60.482 50.000 9.47 0.00 37.75 4.11
5399 7116 6.919721 TGCTATTTCTTCCATTGGTTTGTAC 58.080 36.000 1.86 0.00 0.00 2.90
5413 7130 5.882000 TGCTGACACATGTATGCTATTTCTT 59.118 36.000 0.00 0.00 0.00 2.52
5520 8938 5.879223 ACAAGGTGCATCAATTTTGTGAAAA 59.121 32.000 0.00 0.00 34.41 2.29
5561 8979 3.390311 ACAAAACTTCTTACTCCCTCGGT 59.610 43.478 0.00 0.00 0.00 4.69
5562 8980 4.004196 ACAAAACTTCTTACTCCCTCGG 57.996 45.455 0.00 0.00 0.00 4.63
5563 8981 7.668525 AAATACAAAACTTCTTACTCCCTCG 57.331 36.000 0.00 0.00 0.00 4.63
5611 9029 5.951747 AGCAACAACAATAACCCTGTGATAT 59.048 36.000 0.00 0.00 0.00 1.63
5644 9063 2.860735 CGTAAACTACAGAGGCATGCTC 59.139 50.000 18.92 12.89 0.00 4.26
6331 9762 1.004745 CTTGCCAGGGTCCACTACATT 59.995 52.381 0.00 0.00 0.00 2.71
6655 10086 3.603532 TGATGTTGTCTCTTGCATCCTC 58.396 45.455 0.00 0.00 37.51 3.71
6656 10087 3.607741 CTGATGTTGTCTCTTGCATCCT 58.392 45.455 0.00 0.00 37.51 3.24
6734 10165 6.936900 CGAGGATGGGTATTTAACATGAGATT 59.063 38.462 0.00 0.00 0.00 2.40
6739 10170 4.968259 TCCGAGGATGGGTATTTAACATG 58.032 43.478 0.00 0.00 34.48 3.21
6753 10184 6.049955 TCACAACTTCTTTAATCCGAGGAT 57.950 37.500 0.00 0.00 36.23 3.24
6827 10258 7.290813 TCTAAGATACTAGAGATGGTCAGCAA 58.709 38.462 0.00 0.00 0.00 3.91
6853 10284 1.557832 GTCCTTGCAGGGTACACCATA 59.442 52.381 15.41 0.00 43.89 2.74
6864 10295 2.233271 ACAACATCAAGGTCCTTGCAG 58.767 47.619 24.66 20.27 40.84 4.41
6897 10328 1.658409 GTGCCTGCACGCTTTTCAC 60.658 57.895 6.50 0.00 37.19 3.18
6919 10350 4.689612 TCAGGAAAGATGGGCTGTATAC 57.310 45.455 0.00 0.00 0.00 1.47
6926 10357 1.316651 GAGCATCAGGAAAGATGGGC 58.683 55.000 6.13 0.00 44.33 5.36
7023 10456 0.169009 GAGGCTTGCACGAAATCCAC 59.831 55.000 0.00 0.00 0.00 4.02
7066 10499 7.989170 TGAGAGTCGTAATGTAACCAGATAGTA 59.011 37.037 0.00 0.00 0.00 1.82
7067 10500 6.827251 TGAGAGTCGTAATGTAACCAGATAGT 59.173 38.462 0.00 0.00 0.00 2.12
7068 10501 7.260558 TGAGAGTCGTAATGTAACCAGATAG 57.739 40.000 0.00 0.00 0.00 2.08
7160 10593 7.711339 CGTCTCTAGGCTTTAACTGGATTTTAT 59.289 37.037 0.00 0.00 0.00 1.40
7167 10600 2.496470 ACCGTCTCTAGGCTTTAACTGG 59.504 50.000 0.00 0.00 0.00 4.00
7197 10630 5.339008 TGCCGTAGTTTGACTATTGATCT 57.661 39.130 0.00 0.00 32.65 2.75
7199 10632 8.677148 AATAATGCCGTAGTTTGACTATTGAT 57.323 30.769 0.00 0.00 32.65 2.57
7242 10706 5.273523 ACTTTCGTTTATTGCCGTAGTTC 57.726 39.130 0.00 0.00 0.00 3.01
7254 10718 5.935789 CCAGTGGAGGAAATACTTTCGTTTA 59.064 40.000 1.68 0.00 40.57 2.01
7295 10761 6.430925 AGAACTCAAATTGATCGTCATTCCAA 59.569 34.615 0.00 0.00 0.00 3.53
7296 10762 5.939883 AGAACTCAAATTGATCGTCATTCCA 59.060 36.000 0.00 0.00 0.00 3.53
7297 10763 6.428385 AGAACTCAAATTGATCGTCATTCC 57.572 37.500 0.00 0.00 0.00 3.01
7299 10765 9.823647 AGTATAGAACTCAAATTGATCGTCATT 57.176 29.630 0.00 0.00 30.33 2.57
7300 10766 9.254133 CAGTATAGAACTCAAATTGATCGTCAT 57.746 33.333 0.00 0.00 35.76 3.06
7301 10767 8.251026 ACAGTATAGAACTCAAATTGATCGTCA 58.749 33.333 0.00 0.00 35.76 4.35
7302 10768 8.635877 ACAGTATAGAACTCAAATTGATCGTC 57.364 34.615 0.00 0.00 35.76 4.20
7303 10769 9.436957 AAACAGTATAGAACTCAAATTGATCGT 57.563 29.630 0.00 0.00 35.76 3.73
7304 10770 9.907576 GAAACAGTATAGAACTCAAATTGATCG 57.092 33.333 0.00 0.00 35.76 3.69
7334 10800 9.916397 CGCGAATAGTATAGAACTCAAATTTTT 57.084 29.630 0.00 0.00 39.80 1.94
7335 10801 9.095065 ACGCGAATAGTATAGAACTCAAATTTT 57.905 29.630 15.93 0.00 39.80 1.82
7336 10802 8.540492 CACGCGAATAGTATAGAACTCAAATTT 58.460 33.333 15.93 0.00 39.80 1.82
7337 10803 7.919091 TCACGCGAATAGTATAGAACTCAAATT 59.081 33.333 15.93 0.00 39.80 1.82
7338 10804 7.423199 TCACGCGAATAGTATAGAACTCAAAT 58.577 34.615 15.93 0.00 39.80 2.32
7339 10805 6.788243 TCACGCGAATAGTATAGAACTCAAA 58.212 36.000 15.93 0.00 39.80 2.69
7340 10806 6.367686 TCACGCGAATAGTATAGAACTCAA 57.632 37.500 15.93 0.00 39.80 3.02
7361 10827 3.627395 AAGGACCATCGTTAAGCATCA 57.373 42.857 0.00 0.00 0.00 3.07
7368 10834 1.612199 GGGTGCAAAGGACCATCGTTA 60.612 52.381 9.89 0.00 34.89 3.18
7370 10836 1.303317 GGGTGCAAAGGACCATCGT 60.303 57.895 9.89 0.00 34.89 3.73
7373 10839 0.190815 AAAGGGGTGCAAAGGACCAT 59.809 50.000 9.89 0.00 34.89 3.55
7377 10843 2.199652 CGCAAAGGGGTGCAAAGGA 61.200 57.895 0.00 0.00 45.19 3.36
7378 10844 2.339712 CGCAAAGGGGTGCAAAGG 59.660 61.111 0.00 0.00 45.19 3.11
7379 10845 2.339712 CCGCAAAGGGGTGCAAAG 59.660 61.111 0.00 0.00 45.19 2.77
7390 11179 1.395826 CCCCTTTTGACACCCGCAAA 61.396 55.000 0.00 0.00 33.76 3.68
7426 11215 0.526524 CGTGATCTCGTTCTCCAGGC 60.527 60.000 8.97 0.00 0.00 4.85
7495 11284 2.043992 ACTAGTGGTTGCTGTGGTGTA 58.956 47.619 0.00 0.00 0.00 2.90
7577 11372 2.482490 GCATTTCCATTCCACAGATGGC 60.482 50.000 0.00 0.00 46.80 4.40
7590 11385 1.021920 TCGATTTCGGCGCATTTCCA 61.022 50.000 10.83 0.00 40.29 3.53
7591 11386 0.307760 ATCGATTTCGGCGCATTTCC 59.692 50.000 10.83 0.00 40.29 3.13
7592 11387 1.663494 GATCGATTTCGGCGCATTTC 58.337 50.000 10.83 0.00 40.29 2.17
7593 11388 0.042188 CGATCGATTTCGGCGCATTT 60.042 50.000 10.26 0.00 40.29 2.32
7594 11389 1.151777 ACGATCGATTTCGGCGCATT 61.152 50.000 24.34 0.00 43.33 3.56


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

AutoCloner maintained by Alex Coulton.