Multiple sequence alignment - TraesCS5A01G298900

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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 TraesCS5A01G298900 chr5A 100.000 5100 0 0 1 5100 506148110 506153209 0.000000e+00 9419.0
1 TraesCS5A01G298900 chr5A 86.255 924 115 10 3630 4551 507951989 507952902 0.000000e+00 992.0
2 TraesCS5A01G298900 chr5A 85.668 928 122 10 3626 4551 507092591 507093509 0.000000e+00 966.0
3 TraesCS5A01G298900 chr5A 88.082 730 64 15 2177 2897 508336356 508335641 0.000000e+00 845.0
4 TraesCS5A01G298900 chr5A 87.448 725 76 10 2179 2894 506654168 506654886 0.000000e+00 821.0
5 TraesCS5A01G298900 chr5D 93.200 4235 187 36 683 4878 401326079 401330251 0.000000e+00 6131.0
6 TraesCS5A01G298900 chr5D 94.171 3500 127 18 813 4283 400910342 400913793 0.000000e+00 5262.0
7 TraesCS5A01G298900 chr5D 93.371 2504 128 13 1809 4283 401090438 401092932 0.000000e+00 3670.0
8 TraesCS5A01G298900 chr5D 92.308 1183 24 14 535 1704 401033286 401034414 0.000000e+00 1618.0
9 TraesCS5A01G298900 chr5D 86.530 928 112 12 3626 4551 401408234 401409150 0.000000e+00 1009.0
10 TraesCS5A01G298900 chr5D 93.030 703 26 6 1 686 401323832 401324528 0.000000e+00 1005.0
11 TraesCS5A01G298900 chr5D 86.422 928 114 11 3626 4550 401409918 401410836 0.000000e+00 1005.0
12 TraesCS5A01G298900 chr5D 85.998 907 115 11 3626 4529 402016383 402017280 0.000000e+00 961.0
13 TraesCS5A01G298900 chr5D 85.022 928 128 11 3626 4551 402029329 402030247 0.000000e+00 933.0
14 TraesCS5A01G298900 chr5D 94.455 523 23 2 1 523 400909151 400909667 0.000000e+00 800.0
15 TraesCS5A01G298900 chr5D 93.881 523 26 2 1 523 401032629 401033145 0.000000e+00 784.0
16 TraesCS5A01G298900 chr5D 95.539 269 4 3 534 802 400909807 400910067 1.700000e-114 424.0
17 TraesCS5A01G298900 chr5D 89.790 333 13 8 4771 5100 401330253 401330567 1.710000e-109 407.0
18 TraesCS5A01G298900 chr5D 93.333 120 4 1 1697 1812 401034911 401035030 1.890000e-39 174.0
19 TraesCS5A01G298900 chr5B 87.905 1728 142 18 2160 3862 480801606 480803291 0.000000e+00 1971.0
20 TraesCS5A01G298900 chr5B 87.811 1731 146 19 2158 3862 480767194 480768885 0.000000e+00 1967.0
21 TraesCS5A01G298900 chr5B 86.936 1064 51 26 793 1813 480799731 480800749 0.000000e+00 1114.0
22 TraesCS5A01G298900 chr5B 86.548 1063 56 24 793 1813 480765323 480766340 0.000000e+00 1090.0
23 TraesCS5A01G298900 chr5B 89.889 722 62 8 2179 2892 481132963 481133681 0.000000e+00 918.0
24 TraesCS5A01G298900 chr5B 89.736 721 64 7 2179 2892 481065189 481065906 0.000000e+00 913.0
25 TraesCS5A01G298900 chr5B 93.410 607 30 4 1 603 480780068 480780668 0.000000e+00 891.0
26 TraesCS5A01G298900 chr5B 93.410 607 30 4 1 603 480798869 480799469 0.000000e+00 891.0
27 TraesCS5A01G298900 chr5B 93.410 607 30 4 1 603 480810977 480811577 0.000000e+00 891.0
28 TraesCS5A01G298900 chr5B 88.936 705 71 7 2192 2892 481071161 481071862 0.000000e+00 863.0
29 TraesCS5A01G298900 chr5B 92.809 598 33 5 1 594 480764325 480764916 0.000000e+00 857.0
30 TraesCS5A01G298900 chr5B 87.656 721 61 12 2179 2892 481119810 481120509 0.000000e+00 813.0
31 TraesCS5A01G298900 chr5B 90.528 549 47 3 3089 3636 481065903 481066447 0.000000e+00 721.0
32 TraesCS5A01G298900 chr5B 90.346 549 49 2 3089 3636 481083275 481083820 0.000000e+00 717.0
33 TraesCS5A01G298900 chr5B 90.346 549 48 3 3089 3636 481071859 481072403 0.000000e+00 715.0
34 TraesCS5A01G298900 chr5B 81.024 332 60 3 1813 2141 16369414 16369083 1.410000e-65 261.0
35 TraesCS5A01G298900 chr5B 90.374 187 6 5 600 780 480799571 480799751 8.540000e-58 235.0
36 TraesCS5A01G298900 chr5B 83.744 203 6 15 600 780 480765146 480765343 3.160000e-37 167.0
37 TraesCS5A01G298900 chrUn 86.936 1064 51 25 793 1813 298717719 298716701 0.000000e+00 1114.0
38 TraesCS5A01G298900 chrUn 88.493 869 82 6 2994 3862 349852538 349853388 0.000000e+00 1035.0
39 TraesCS5A01G298900 chrUn 93.575 607 29 4 1 603 298718580 298717980 0.000000e+00 896.0
40 TraesCS5A01G298900 chrUn 95.455 286 9 2 318 603 476557151 476556870 2.160000e-123 453.0
41 TraesCS5A01G298900 chr6B 84.211 323 48 3 1820 2141 10729290 10729610 1.380000e-80 311.0
42 TraesCS5A01G298900 chr7D 82.569 327 54 3 1813 2137 47221584 47221909 8.360000e-73 285.0
43 TraesCS5A01G298900 chr7D 82.090 335 50 10 1815 2144 13339894 13339565 1.400000e-70 278.0
44 TraesCS5A01G298900 chr7A 81.928 332 58 1 1812 2141 36332526 36332195 3.890000e-71 279.0
45 TraesCS5A01G298900 chr2A 81.571 331 56 5 1814 2141 18305564 18305892 8.420000e-68 268.0
46 TraesCS5A01G298900 chr1D 94.000 50 3 0 1721 1770 492613119 492613168 5.480000e-10 76.8
47 TraesCS5A01G298900 chr1A 94.000 50 3 0 1721 1770 591095977 591096026 5.480000e-10 76.8
48 TraesCS5A01G298900 chr7B 91.489 47 4 0 1724 1770 531604918 531604872 1.190000e-06 65.8
49 TraesCS5A01G298900 chr3D 97.297 37 1 0 1734 1770 502893365 502893401 4.260000e-06 63.9


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 TraesCS5A01G298900 chr5A 506148110 506153209 5099 False 9419.000000 9419 100.000000 1 5100 1 chr5A.!!$F1 5099
1 TraesCS5A01G298900 chr5A 507951989 507952902 913 False 992.000000 992 86.255000 3630 4551 1 chr5A.!!$F4 921
2 TraesCS5A01G298900 chr5A 507092591 507093509 918 False 966.000000 966 85.668000 3626 4551 1 chr5A.!!$F3 925
3 TraesCS5A01G298900 chr5A 508335641 508336356 715 True 845.000000 845 88.082000 2177 2897 1 chr5A.!!$R1 720
4 TraesCS5A01G298900 chr5A 506654168 506654886 718 False 821.000000 821 87.448000 2179 2894 1 chr5A.!!$F2 715
5 TraesCS5A01G298900 chr5D 401090438 401092932 2494 False 3670.000000 3670 93.371000 1809 4283 1 chr5D.!!$F1 2474
6 TraesCS5A01G298900 chr5D 401323832 401330567 6735 False 2514.333333 6131 92.006667 1 5100 3 chr5D.!!$F6 5099
7 TraesCS5A01G298900 chr5D 400909151 400913793 4642 False 2162.000000 5262 94.721667 1 4283 3 chr5D.!!$F4 4282
8 TraesCS5A01G298900 chr5D 401408234 401410836 2602 False 1007.000000 1009 86.476000 3626 4551 2 chr5D.!!$F7 925
9 TraesCS5A01G298900 chr5D 402016383 402017280 897 False 961.000000 961 85.998000 3626 4529 1 chr5D.!!$F2 903
10 TraesCS5A01G298900 chr5D 402029329 402030247 918 False 933.000000 933 85.022000 3626 4551 1 chr5D.!!$F3 925
11 TraesCS5A01G298900 chr5D 401032629 401035030 2401 False 858.666667 1618 93.174000 1 1812 3 chr5D.!!$F5 1811
12 TraesCS5A01G298900 chr5B 480798869 480803291 4422 False 1052.750000 1971 89.656250 1 3862 4 chr5B.!!$F7 3861
13 TraesCS5A01G298900 chr5B 480764325 480768885 4560 False 1020.250000 1967 87.728000 1 3862 4 chr5B.!!$F6 3861
14 TraesCS5A01G298900 chr5B 481132963 481133681 718 False 918.000000 918 89.889000 2179 2892 1 chr5B.!!$F5 713
15 TraesCS5A01G298900 chr5B 480780068 480780668 600 False 891.000000 891 93.410000 1 603 1 chr5B.!!$F1 602
16 TraesCS5A01G298900 chr5B 480810977 480811577 600 False 891.000000 891 93.410000 1 603 1 chr5B.!!$F2 602
17 TraesCS5A01G298900 chr5B 481065189 481066447 1258 False 817.000000 913 90.132000 2179 3636 2 chr5B.!!$F8 1457
18 TraesCS5A01G298900 chr5B 481119810 481120509 699 False 813.000000 813 87.656000 2179 2892 1 chr5B.!!$F4 713
19 TraesCS5A01G298900 chr5B 481071161 481072403 1242 False 789.000000 863 89.641000 2192 3636 2 chr5B.!!$F9 1444
20 TraesCS5A01G298900 chr5B 481083275 481083820 545 False 717.000000 717 90.346000 3089 3636 1 chr5B.!!$F3 547
21 TraesCS5A01G298900 chrUn 349852538 349853388 850 False 1035.000000 1035 88.493000 2994 3862 1 chrUn.!!$F1 868
22 TraesCS5A01G298900 chrUn 298716701 298718580 1879 True 1005.000000 1114 90.255500 1 1813 2 chrUn.!!$R2 1812

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
359 365 0.378257 ATAGAAATGCTTGCACGCGG 59.622 50.0 12.47 0.0 0.00 6.46 F
1231 3564 0.104855 ATCTCGCATGCACATACGGT 59.895 50.0 19.57 0.0 0.00 4.83 F
1232 3565 0.527600 TCTCGCATGCACATACGGTC 60.528 55.0 19.57 0.0 0.00 4.79 F
3022 6556 0.481128 TCCCATGCCATGCAGATCAT 59.519 50.0 0.00 0.0 43.65 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 3867 0.324943 AACCCGATGCAAGCTACAGT 59.675 50.000 0.0 0.0 0.0 3.55 R
2058 5460 1.205064 CGGCAAACTTCTGTCTGCG 59.795 57.895 0.0 0.0 35.6 5.18 R
3137 6671 2.028930 ACACTCCCGTTGTCATCTTCTC 60.029 50.000 0.0 0.0 0.0 2.87 R
4608 9870 0.034337 GTTGACCTTCCACACGCCTA 59.966 55.000 0.0 0.0 0.0 3.93 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
41 42 2.242708 AGGCGTAATCATTTAACCCCCA 59.757 45.455 0.00 0.00 0.00 4.96
153 154 0.392193 GTGCAGGAGGTGAGTGGATG 60.392 60.000 0.00 0.00 0.00 3.51
210 212 4.707934 TGGTAGATCTGATCGTGGTTTACA 59.292 41.667 11.73 2.38 0.00 2.41
297 299 0.983467 TGGGCTGCACTAGTCAATCA 59.017 50.000 2.50 0.00 30.64 2.57
359 365 0.378257 ATAGAAATGCTTGCACGCGG 59.622 50.000 12.47 0.00 0.00 6.46
360 366 2.252127 TAGAAATGCTTGCACGCGGC 62.252 55.000 12.47 12.14 45.13 6.53
361 367 3.615536 GAAATGCTTGCACGCGGCT 62.616 57.895 12.47 0.00 45.15 5.52
362 368 2.252127 GAAATGCTTGCACGCGGCTA 62.252 55.000 12.47 7.31 45.15 3.93
517 524 1.198759 ATACCCTCCGCAAGTGGTGT 61.199 55.000 0.00 0.00 32.66 4.16
811 2852 7.919313 TTTTGAGACAAACTAGTGTAGTACG 57.081 36.000 0.00 0.00 38.26 3.67
877 3182 0.813821 GCCCTGCCATTTCTGTCTTC 59.186 55.000 0.00 0.00 0.00 2.87
899 3204 1.001764 TTCGCCCTCTCCTCGTACA 60.002 57.895 0.00 0.00 0.00 2.90
900 3205 0.609957 TTCGCCCTCTCCTCGTACAA 60.610 55.000 0.00 0.00 0.00 2.41
1007 3340 2.093235 GGAGGGAGTTGAAGATGGTGAG 60.093 54.545 0.00 0.00 0.00 3.51
1014 3347 5.053978 AGTTGAAGATGGTGAGGAAGTTT 57.946 39.130 0.00 0.00 0.00 2.66
1231 3564 0.104855 ATCTCGCATGCACATACGGT 59.895 50.000 19.57 0.00 0.00 4.83
1232 3565 0.527600 TCTCGCATGCACATACGGTC 60.528 55.000 19.57 0.00 0.00 4.79
1233 3566 1.811217 CTCGCATGCACATACGGTCG 61.811 60.000 19.57 0.00 0.00 4.79
1234 3567 2.870341 CGCATGCACATACGGTCGG 61.870 63.158 19.57 0.00 0.00 4.79
1339 3678 4.572571 GTTGGTGGTGGTGCCGGA 62.573 66.667 5.05 0.00 41.21 5.14
1340 3679 4.263572 TTGGTGGTGGTGCCGGAG 62.264 66.667 5.05 0.00 41.21 4.63
1387 3726 3.712907 TAGGAAGCGTGGGGGCAC 61.713 66.667 0.00 0.00 34.64 5.01
1439 3778 4.505217 GCGTTGCTCATGCCGTCG 62.505 66.667 0.00 0.00 38.71 5.12
1523 3870 3.765349 GCTCGCTAGCTAGCTACTG 57.235 57.895 36.02 23.72 46.85 2.74
1618 3988 7.168219 TCAAAATTGATTCTGCACTACTACCT 58.832 34.615 0.00 0.00 31.01 3.08
2005 5407 3.507162 TCATCAGAACCTGGAAAAGCA 57.493 42.857 0.00 0.00 31.51 3.91
2058 5460 5.790495 CGAGTCCAATTTTCGATCAAACTTC 59.210 40.000 0.00 0.00 36.49 3.01
2616 6125 2.095212 CCCCTCTTTGTTTTAGCTTCGC 60.095 50.000 0.00 0.00 0.00 4.70
2714 6245 8.073768 ACCTTTTACACATCTAAACATTCGTTG 58.926 33.333 0.00 0.00 34.86 4.10
2791 6322 7.533426 CATGTTTTGCTAGGAGCCATATATTC 58.467 38.462 0.00 0.00 41.51 1.75
2818 6350 7.358023 CCAAAGTTATGTGTTAAATTGTCGTGC 60.358 37.037 0.00 0.00 29.09 5.34
2872 6406 6.430616 CCATTAGAAATGTGGCAAATTTTGGT 59.569 34.615 16.45 7.71 0.00 3.67
2969 6503 4.684485 CGATGAGTAAGGAAGGAATGGCTT 60.684 45.833 0.00 0.00 0.00 4.35
2983 6517 1.958205 GGCTTGATCTCCGGCGATG 60.958 63.158 12.63 0.00 0.00 3.84
3022 6556 0.481128 TCCCATGCCATGCAGATCAT 59.519 50.000 0.00 0.00 43.65 2.45
3137 6671 8.514594 TCTTCATGTTTAAACCTTATGCAGAAG 58.485 33.333 14.22 14.22 0.00 2.85
3153 6687 3.257393 CAGAAGAGAAGATGACAACGGG 58.743 50.000 0.00 0.00 0.00 5.28
3164 6701 4.431035 CAACGGGAGTGTTGTCGT 57.569 55.556 0.00 0.00 46.69 4.34
3165 6702 2.222592 CAACGGGAGTGTTGTCGTC 58.777 57.895 0.00 0.00 46.69 4.20
3167 6704 0.176219 AACGGGAGTGTTGTCGTCAA 59.824 50.000 0.00 0.00 46.69 3.18
3168 6705 0.391597 ACGGGAGTGTTGTCGTCAAT 59.608 50.000 0.00 0.00 44.82 2.57
3169 6706 0.790207 CGGGAGTGTTGTCGTCAATG 59.210 55.000 0.00 0.00 35.92 2.82
3175 6712 3.067106 AGTGTTGTCGTCAATGATGGAC 58.933 45.455 2.27 6.55 35.92 4.02
3273 6810 3.390639 AGCACTAGGAGGATGGAATTGAG 59.609 47.826 0.00 0.00 0.00 3.02
3344 6881 3.181826 CGCTGAACTGATGCGTTAAAA 57.818 42.857 0.00 0.00 44.00 1.52
3394 6931 3.632643 TGTCAATGCAGGAGCTTGATA 57.367 42.857 3.19 0.00 42.74 2.15
3399 6936 5.049543 GTCAATGCAGGAGCTTGATAAGATC 60.050 44.000 3.19 0.00 43.00 2.75
3404 6941 4.272991 GCAGGAGCTTGATAAGATCTGTTG 59.727 45.833 0.00 5.06 43.26 3.33
3436 6973 1.625818 GGATGGCCCCTAGATACACAG 59.374 57.143 0.00 0.00 0.00 3.66
3453 6990 4.404640 ACACAGTAGTACCTTCACTAGCA 58.595 43.478 0.00 0.00 31.73 3.49
3454 6991 4.459685 ACACAGTAGTACCTTCACTAGCAG 59.540 45.833 0.00 0.00 31.73 4.24
3455 6992 4.700692 CACAGTAGTACCTTCACTAGCAGA 59.299 45.833 0.00 0.00 31.73 4.26
3456 6993 5.358442 CACAGTAGTACCTTCACTAGCAGAT 59.642 44.000 0.00 0.00 31.73 2.90
3457 6994 5.358442 ACAGTAGTACCTTCACTAGCAGATG 59.642 44.000 0.00 0.00 31.73 2.90
3458 6995 4.890581 AGTAGTACCTTCACTAGCAGATGG 59.109 45.833 13.20 13.20 36.62 3.51
3459 6996 3.714144 AGTACCTTCACTAGCAGATGGT 58.286 45.455 20.25 20.25 43.48 3.55
3460 6997 4.868268 AGTACCTTCACTAGCAGATGGTA 58.132 43.478 18.81 18.81 41.87 3.25
3461 6998 5.459505 AGTACCTTCACTAGCAGATGGTAT 58.540 41.667 22.56 14.23 43.41 2.73
3462 6999 4.679373 ACCTTCACTAGCAGATGGTATG 57.321 45.455 16.93 0.00 40.52 2.39
3463 7000 4.033709 ACCTTCACTAGCAGATGGTATGT 58.966 43.478 16.93 0.00 40.52 2.29
3464 7001 4.141846 ACCTTCACTAGCAGATGGTATGTG 60.142 45.833 16.93 11.84 40.52 3.21
3465 7002 4.141846 CCTTCACTAGCAGATGGTATGTGT 60.142 45.833 15.03 1.27 33.33 3.72
3466 7003 5.069119 CCTTCACTAGCAGATGGTATGTGTA 59.931 44.000 15.03 9.22 33.33 2.90
3467 7004 6.406961 CCTTCACTAGCAGATGGTATGTGTAA 60.407 42.308 15.03 10.38 33.33 2.41
3468 7005 6.538945 TCACTAGCAGATGGTATGTGTAAA 57.461 37.500 15.03 2.31 33.33 2.01
3469 7006 7.124573 TCACTAGCAGATGGTATGTGTAAAT 57.875 36.000 15.03 0.00 33.33 1.40
3470 7007 8.245195 TCACTAGCAGATGGTATGTGTAAATA 57.755 34.615 15.03 1.85 33.33 1.40
3471 7008 8.141909 TCACTAGCAGATGGTATGTGTAAATAC 58.858 37.037 15.03 0.00 33.33 1.89
3510 7047 9.859427 CTCTATAATTTTCCAAATGAACAAGCA 57.141 29.630 0.00 0.00 31.05 3.91
3526 7063 2.957402 AGCATTGAGTTCTTGGACCA 57.043 45.000 0.00 0.00 0.00 4.02
3527 7064 3.446442 AGCATTGAGTTCTTGGACCAT 57.554 42.857 0.00 0.00 0.00 3.55
3528 7065 4.574674 AGCATTGAGTTCTTGGACCATA 57.425 40.909 0.00 0.00 0.00 2.74
3529 7066 5.121380 AGCATTGAGTTCTTGGACCATAT 57.879 39.130 0.00 0.00 0.00 1.78
3530 7067 6.252599 AGCATTGAGTTCTTGGACCATATA 57.747 37.500 0.00 0.00 0.00 0.86
3531 7068 6.294473 AGCATTGAGTTCTTGGACCATATAG 58.706 40.000 0.00 0.00 0.00 1.31
3532 7069 5.471456 GCATTGAGTTCTTGGACCATATAGG 59.529 44.000 0.00 0.00 45.67 2.57
3533 7070 4.689612 TGAGTTCTTGGACCATATAGGC 57.310 45.455 0.00 0.00 43.14 3.93
3534 7071 4.037222 TGAGTTCTTGGACCATATAGGCA 58.963 43.478 0.00 0.00 43.14 4.75
3535 7072 4.141711 TGAGTTCTTGGACCATATAGGCAC 60.142 45.833 0.00 0.00 43.14 5.01
3536 7073 3.780294 AGTTCTTGGACCATATAGGCACA 59.220 43.478 0.00 0.00 43.14 4.57
3537 7074 4.227300 AGTTCTTGGACCATATAGGCACAA 59.773 41.667 0.00 0.00 43.14 3.33
3538 7075 5.103940 AGTTCTTGGACCATATAGGCACAAT 60.104 40.000 0.00 0.00 43.14 2.71
3539 7076 6.101150 AGTTCTTGGACCATATAGGCACAATA 59.899 38.462 0.00 0.00 43.14 1.90
3540 7077 6.508030 TCTTGGACCATATAGGCACAATAA 57.492 37.500 0.00 0.00 43.14 1.40
3541 7078 7.090319 TCTTGGACCATATAGGCACAATAAT 57.910 36.000 0.00 0.00 43.14 1.28
3542 7079 8.213489 TCTTGGACCATATAGGCACAATAATA 57.787 34.615 0.00 0.00 43.14 0.98
3543 7080 8.664992 TCTTGGACCATATAGGCACAATAATAA 58.335 33.333 0.00 0.00 43.14 1.40
3544 7081 9.295825 CTTGGACCATATAGGCACAATAATAAA 57.704 33.333 0.00 0.00 43.14 1.40
3545 7082 8.862325 TGGACCATATAGGCACAATAATAAAG 57.138 34.615 0.00 0.00 43.14 1.85
3546 7083 8.664992 TGGACCATATAGGCACAATAATAAAGA 58.335 33.333 0.00 0.00 43.14 2.52
3547 7084 9.515226 GGACCATATAGGCACAATAATAAAGAA 57.485 33.333 0.00 0.00 43.14 2.52
3570 7107 8.619546 AGAATTTCATAGAAATAGCTCTTGTGC 58.380 33.333 5.50 0.00 0.00 4.57
3571 7108 6.683974 TTTCATAGAAATAGCTCTTGTGCC 57.316 37.500 0.00 0.00 0.00 5.01
3572 7109 5.357742 TCATAGAAATAGCTCTTGTGCCA 57.642 39.130 0.00 0.00 0.00 4.92
3573 7110 5.118990 TCATAGAAATAGCTCTTGTGCCAC 58.881 41.667 0.00 0.00 0.00 5.01
3574 7111 3.423539 AGAAATAGCTCTTGTGCCACA 57.576 42.857 0.00 0.00 0.00 4.17
3575 7112 3.960571 AGAAATAGCTCTTGTGCCACAT 58.039 40.909 0.00 0.00 0.00 3.21
3576 7113 5.102953 AGAAATAGCTCTTGTGCCACATA 57.897 39.130 0.00 0.00 0.00 2.29
3577 7114 4.878397 AGAAATAGCTCTTGTGCCACATAC 59.122 41.667 0.00 0.00 0.00 2.39
3578 7115 4.494091 AATAGCTCTTGTGCCACATACT 57.506 40.909 0.00 0.00 0.00 2.12
3579 7116 2.867109 AGCTCTTGTGCCACATACTT 57.133 45.000 0.00 0.00 0.00 2.24
3580 7117 3.146104 AGCTCTTGTGCCACATACTTT 57.854 42.857 0.00 0.00 0.00 2.66
3581 7118 3.077359 AGCTCTTGTGCCACATACTTTC 58.923 45.455 0.00 0.00 0.00 2.62
3582 7119 3.077359 GCTCTTGTGCCACATACTTTCT 58.923 45.455 0.00 0.00 0.00 2.52
3583 7120 3.120060 GCTCTTGTGCCACATACTTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
3584 7121 4.318332 CTCTTGTGCCACATACTTTCTGA 58.682 43.478 0.00 0.00 0.00 3.27
3585 7122 4.910195 TCTTGTGCCACATACTTTCTGAT 58.090 39.130 0.00 0.00 0.00 2.90
3586 7123 5.316167 TCTTGTGCCACATACTTTCTGATT 58.684 37.500 0.00 0.00 0.00 2.57
3587 7124 6.472016 TCTTGTGCCACATACTTTCTGATTA 58.528 36.000 0.00 0.00 0.00 1.75
3588 7125 6.939730 TCTTGTGCCACATACTTTCTGATTAA 59.060 34.615 0.00 0.00 0.00 1.40
3589 7126 6.494893 TGTGCCACATACTTTCTGATTAAC 57.505 37.500 0.00 0.00 0.00 2.01
3590 7127 5.121611 TGTGCCACATACTTTCTGATTAACG 59.878 40.000 0.00 0.00 0.00 3.18
3591 7128 5.121768 GTGCCACATACTTTCTGATTAACGT 59.878 40.000 0.00 0.00 0.00 3.99
3592 7129 5.703592 TGCCACATACTTTCTGATTAACGTT 59.296 36.000 5.88 5.88 0.00 3.99
3593 7130 6.205853 TGCCACATACTTTCTGATTAACGTTT 59.794 34.615 5.91 0.00 0.00 3.60
3594 7131 7.388224 TGCCACATACTTTCTGATTAACGTTTA 59.612 33.333 5.91 0.00 0.00 2.01
3595 7132 8.395633 GCCACATACTTTCTGATTAACGTTTAT 58.604 33.333 5.91 1.72 0.00 1.40
3607 7144 9.450807 CTGATTAACGTTTATTGAATCCAATCC 57.549 33.333 5.91 0.00 41.74 3.01
3608 7145 8.410141 TGATTAACGTTTATTGAATCCAATCCC 58.590 33.333 5.91 0.00 41.74 3.85
3609 7146 7.948034 TTAACGTTTATTGAATCCAATCCCT 57.052 32.000 5.91 0.00 41.74 4.20
3610 7147 9.635404 ATTAACGTTTATTGAATCCAATCCCTA 57.365 29.630 5.91 0.00 41.74 3.53
3611 7148 9.635404 TTAACGTTTATTGAATCCAATCCCTAT 57.365 29.630 5.91 0.00 41.74 2.57
3613 7150 8.848474 ACGTTTATTGAATCCAATCCCTATAG 57.152 34.615 0.00 0.00 41.74 1.31
3614 7151 7.390718 ACGTTTATTGAATCCAATCCCTATAGC 59.609 37.037 0.00 0.00 41.74 2.97
3615 7152 7.413000 CGTTTATTGAATCCAATCCCTATAGCG 60.413 40.741 0.00 0.00 41.74 4.26
3616 7153 3.334583 TGAATCCAATCCCTATAGCGC 57.665 47.619 0.00 0.00 0.00 5.92
3617 7154 2.637382 TGAATCCAATCCCTATAGCGCA 59.363 45.455 11.47 0.00 0.00 6.09
3618 7155 2.770164 ATCCAATCCCTATAGCGCAC 57.230 50.000 11.47 0.00 0.00 5.34
3619 7156 0.685097 TCCAATCCCTATAGCGCACC 59.315 55.000 11.47 0.00 0.00 5.01
3620 7157 0.670546 CCAATCCCTATAGCGCACCG 60.671 60.000 11.47 0.00 0.00 4.94
3621 7158 0.033504 CAATCCCTATAGCGCACCGT 59.966 55.000 11.47 0.00 0.00 4.83
3622 7159 0.756903 AATCCCTATAGCGCACCGTT 59.243 50.000 11.47 0.00 0.00 4.44
3623 7160 0.033504 ATCCCTATAGCGCACCGTTG 59.966 55.000 11.47 0.00 0.00 4.10
3624 7161 1.594293 CCCTATAGCGCACCGTTGG 60.594 63.158 11.47 3.55 0.00 3.77
3665 8899 5.934781 AGAGTTTTCAAGTGGTCAGATCTT 58.065 37.500 0.00 0.00 0.00 2.40
3685 8919 6.827586 TCTTTAAACCACTTGTCTGTGTTT 57.172 33.333 0.00 0.00 36.30 2.83
3691 8925 4.079253 ACCACTTGTCTGTGTTTTGTTCT 58.921 39.130 0.00 0.00 36.30 3.01
3966 9202 1.712350 CGTCGGTGAAGTACGTTTGAG 59.288 52.381 0.00 0.00 32.16 3.02
4062 9302 4.141413 TGCCAATATGATACTGGAGCTTGT 60.141 41.667 3.79 0.00 31.38 3.16
4063 9303 4.823989 GCCAATATGATACTGGAGCTTGTT 59.176 41.667 3.79 0.00 31.38 2.83
4185 9427 7.930513 AAGCAACTTAGCTATTTGTTGTTTC 57.069 32.000 23.40 14.05 45.89 2.78
4245 9489 6.603201 AGTTTGTACTATATTGCATTGTGGCT 59.397 34.615 0.00 0.00 31.21 4.75
4315 9563 9.913310 ATTTTACTGAATTTTTCCTTTTTGGGA 57.087 25.926 0.00 0.00 36.20 4.37
4390 9638 6.610741 TGGGTTGCATTTTCACAAAATTAC 57.389 33.333 0.00 0.00 38.97 1.89
4395 9643 6.915544 TGCATTTTCACAAAATTACAGCAA 57.084 29.167 0.00 0.00 38.97 3.91
4403 9651 6.634805 TCACAAAATTACAGCAACCTTTTCA 58.365 32.000 0.00 0.00 0.00 2.69
4476 9725 1.401539 GGTTTTGCGAGTGAGGCATTC 60.402 52.381 0.00 0.00 40.62 2.67
4488 9737 0.924823 AGGCATTCCTGGAGCTTGAT 59.075 50.000 7.73 0.00 42.34 2.57
4590 9848 1.519751 AAAACACGCTAATGCCGGCA 61.520 50.000 34.80 34.80 35.36 5.69
4591 9849 1.312371 AAACACGCTAATGCCGGCAT 61.312 50.000 36.10 36.10 38.46 4.40
4608 9870 4.082245 CCGGCATTCTAAAAACCACATTCT 60.082 41.667 0.00 0.00 0.00 2.40
4609 9871 5.124776 CCGGCATTCTAAAAACCACATTCTA 59.875 40.000 0.00 0.00 0.00 2.10
4639 9901 4.289934 TGGAAGGTCAACACCACCAATATA 59.710 41.667 7.38 0.00 46.68 0.86
4640 9902 5.222151 TGGAAGGTCAACACCACCAATATAA 60.222 40.000 7.38 0.00 46.68 0.98
4665 9927 9.862371 AACGCCATTGTTATAAAATACAAATGA 57.138 25.926 0.00 0.00 37.75 2.57
4680 9942 0.965363 AATGACATTGGTCCCCACGC 60.965 55.000 0.00 0.00 43.65 5.34
4699 9961 5.506649 CCACGCCATTGGTATTTTACATACC 60.507 44.000 4.26 0.85 43.27 2.73
4721 9983 0.391130 TGGCGTGGCACTATTCACTC 60.391 55.000 16.72 0.00 0.00 3.51
4722 9984 1.421410 GGCGTGGCACTATTCACTCG 61.421 60.000 16.72 0.00 0.00 4.18
4744 10006 2.682856 CGCCACAACTAATAGCAATGGT 59.317 45.455 6.27 0.00 0.00 3.55
4797 10059 7.661127 ACACAAGTAATAACAGCGTGATTTA 57.339 32.000 0.00 0.00 0.00 1.40
4847 10217 9.251792 GCAGTCAAATATTTATGCATTCATTCA 57.748 29.630 19.51 0.00 34.22 2.57
4903 10273 1.476891 GCCAAGATCCACGAGTCTACA 59.523 52.381 0.00 0.00 0.00 2.74
4922 10292 2.278989 CACCGTCGTGTCACCGTT 60.279 61.111 0.00 0.00 35.10 4.44
4923 10293 2.278989 ACCGTCGTGTCACCGTTG 60.279 61.111 0.00 0.00 0.00 4.10
4924 10294 3.698463 CCGTCGTGTCACCGTTGC 61.698 66.667 0.00 0.00 0.00 4.17
4925 10295 3.698463 CGTCGTGTCACCGTTGCC 61.698 66.667 0.00 0.00 0.00 4.52
4926 10296 2.586635 GTCGTGTCACCGTTGCCA 60.587 61.111 0.00 0.00 0.00 4.92
4927 10297 1.959226 GTCGTGTCACCGTTGCCAT 60.959 57.895 0.00 0.00 0.00 4.40
4928 10298 1.666553 TCGTGTCACCGTTGCCATC 60.667 57.895 0.00 0.00 0.00 3.51
4929 10299 2.860293 GTGTCACCGTTGCCATCG 59.140 61.111 0.00 0.00 0.00 3.84
4930 10300 1.959226 GTGTCACCGTTGCCATCGT 60.959 57.895 0.00 0.00 0.00 3.73
4931 10301 1.666553 TGTCACCGTTGCCATCGTC 60.667 57.895 0.00 0.00 0.00 4.20
4932 10302 1.666553 GTCACCGTTGCCATCGTCA 60.667 57.895 0.00 0.00 0.00 4.35
4943 10313 0.458370 CCATCGTCACTGTCATCGCA 60.458 55.000 0.00 0.00 0.00 5.10
4997 10370 1.204062 GTCGTCGTCGTCGTTACCA 59.796 57.895 11.41 0.00 38.33 3.25
5033 10406 3.776659 TTGTCGCCGCAAGTCGTCA 62.777 57.895 0.00 0.00 36.19 4.35
5036 10409 3.902063 CGCCGCAAGTCGTCATCG 61.902 66.667 0.00 0.00 36.19 3.84
5086 10459 1.602323 TTTGTCACCGCCACATCCC 60.602 57.895 0.00 0.00 0.00 3.85
5087 10460 3.561120 TTGTCACCGCCACATCCCC 62.561 63.158 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.738643 CGTTACCATCTTCGCCATGTCT 60.739 50.000 0.00 0.00 0.00 3.41
210 212 3.012518 GCCAAGCAATATGAGTGTCTGT 58.987 45.455 0.00 0.00 0.00 3.41
255 257 4.710324 ACAACAAGAATTAACTCCGTCCA 58.290 39.130 0.00 0.00 0.00 4.02
297 299 3.112263 TCCCCTACCACGATCAGATTTT 58.888 45.455 0.00 0.00 0.00 1.82
359 365 9.050601 AGTAATCATCAAATCAAACTAGCTAGC 57.949 33.333 20.91 6.62 0.00 3.42
361 367 9.249457 CGAGTAATCATCAAATCAAACTAGCTA 57.751 33.333 0.00 0.00 0.00 3.32
362 368 7.981789 TCGAGTAATCATCAAATCAAACTAGCT 59.018 33.333 0.00 0.00 0.00 3.32
530 552 2.678190 GCATCCTTGCTTCCTACTCGTT 60.678 50.000 0.00 0.00 45.77 3.85
725 2766 9.990360 GGACTAGGAATTTTTGGAAATTTGTAA 57.010 29.630 0.00 0.00 43.61 2.41
732 2773 4.453136 CGACGGACTAGGAATTTTTGGAAA 59.547 41.667 0.00 0.00 0.00 3.13
808 2849 5.050634 CGTGATTTCCACTTTGAAAGACGTA 60.051 40.000 12.53 0.00 43.53 3.57
809 2850 4.260620 CGTGATTTCCACTTTGAAAGACGT 60.261 41.667 12.53 0.00 43.53 4.34
810 2851 4.211389 CGTGATTTCCACTTTGAAAGACG 58.789 43.478 12.53 4.64 43.53 4.18
811 2852 3.975035 GCGTGATTTCCACTTTGAAAGAC 59.025 43.478 12.53 0.00 43.53 3.01
1007 3340 2.074576 GCGTCACTCCCTTAAACTTCC 58.925 52.381 0.00 0.00 0.00 3.46
1014 3347 4.124351 CGCGGCGTCACTCCCTTA 62.124 66.667 15.36 0.00 0.00 2.69
1231 3564 1.303074 CGATCGATCCCCTACCCGA 60.303 63.158 19.51 0.00 35.43 5.14
1232 3565 2.341101 CCGATCGATCCCCTACCCG 61.341 68.421 18.66 5.89 0.00 5.28
1233 3566 0.541296 TTCCGATCGATCCCCTACCC 60.541 60.000 18.66 0.00 0.00 3.69
1234 3567 0.889306 CTTCCGATCGATCCCCTACC 59.111 60.000 18.66 0.00 0.00 3.18
1339 3678 3.322466 CCACCCTCAACTCGGGCT 61.322 66.667 0.00 0.00 46.04 5.19
1342 3681 3.649277 CTCGCCACCCTCAACTCGG 62.649 68.421 0.00 0.00 0.00 4.63
1343 3682 2.125912 CTCGCCACCCTCAACTCG 60.126 66.667 0.00 0.00 0.00 4.18
1344 3683 2.435059 GCTCGCCACCCTCAACTC 60.435 66.667 0.00 0.00 0.00 3.01
1439 3778 3.195698 GATTCGTCCCCAGCGCAC 61.196 66.667 11.47 0.00 0.00 5.34
1518 3865 1.137086 ACCCGATGCAAGCTACAGTAG 59.863 52.381 2.85 2.85 0.00 2.57
1519 3866 1.191535 ACCCGATGCAAGCTACAGTA 58.808 50.000 0.00 0.00 0.00 2.74
1520 3867 0.324943 AACCCGATGCAAGCTACAGT 59.675 50.000 0.00 0.00 0.00 3.55
1521 3868 1.009829 GAACCCGATGCAAGCTACAG 58.990 55.000 0.00 0.00 0.00 2.74
1522 3869 0.613260 AGAACCCGATGCAAGCTACA 59.387 50.000 0.00 0.00 0.00 2.74
1523 3870 1.739067 AAGAACCCGATGCAAGCTAC 58.261 50.000 0.00 0.00 0.00 3.58
1618 3988 9.838339 GAAAGGGAAAAATCTATCACATCTAGA 57.162 33.333 0.00 0.00 0.00 2.43
1638 4008 3.499918 GGACGCATCAATCATAGAAAGGG 59.500 47.826 0.00 0.00 0.00 3.95
1771 4648 2.913617 CCCCTCAAAAGACTAGAACCCT 59.086 50.000 0.00 0.00 0.00 4.34
1882 5284 1.588082 GTGGGCCATGTCTTGCAAG 59.412 57.895 20.81 20.81 0.00 4.01
1883 5285 2.267351 CGTGGGCCATGTCTTGCAA 61.267 57.895 17.89 0.00 0.00 4.08
2005 5407 0.686224 AGCAACTCAGCAGAGCTCTT 59.314 50.000 15.27 0.00 46.09 2.85
2016 5418 3.056107 ACTCGGCAGTAATAAGCAACTCA 60.056 43.478 0.00 0.00 0.00 3.41
2058 5460 1.205064 CGGCAAACTTCTGTCTGCG 59.795 57.895 0.00 0.00 35.60 5.18
2451 5954 4.149571 CACGGAATCACGAATCTGATCATC 59.850 45.833 0.00 0.00 37.61 2.92
2616 6125 6.333416 TCTGTCTTGAAGTATGAATTCCTCG 58.667 40.000 2.27 0.00 0.00 4.63
2691 6221 8.155821 TCCAACGAATGTTTAGATGTGTAAAA 57.844 30.769 0.00 0.00 35.72 1.52
2708 6239 9.389755 TCTACAAATGATTATCAATCCAACGAA 57.610 29.630 0.00 0.00 37.09 3.85
2777 6308 5.669798 AACTTTGGGAATATATGGCTCCT 57.330 39.130 2.65 0.00 0.00 3.69
2791 6322 7.114247 CACGACAATTTAACACATAACTTTGGG 59.886 37.037 0.00 0.00 0.00 4.12
2818 6350 5.215252 TGTCCAGAGTTTAAAGTGAGGAG 57.785 43.478 11.49 0.00 0.00 3.69
2856 6388 6.173427 ACTTCTTACCAAAATTTGCCACAT 57.827 33.333 0.00 0.00 0.00 3.21
2894 6428 3.603857 CGCCCGCGATTTTAAACTATGAG 60.604 47.826 8.23 0.00 42.83 2.90
2921 6455 3.675775 GCCAAAATCTCTGCCGCAATTTA 60.676 43.478 2.67 0.00 0.00 1.40
2969 6503 4.284860 CGCCATCGCCGGAGATCA 62.285 66.667 18.68 0.00 0.00 2.92
3022 6556 6.038603 GCTATCACAAATCTGAAATGGCTACA 59.961 38.462 0.00 0.00 0.00 2.74
3137 6671 2.028930 ACACTCCCGTTGTCATCTTCTC 60.029 50.000 0.00 0.00 0.00 2.87
3153 6687 3.123621 GTCCATCATTGACGACAACACTC 59.876 47.826 1.63 0.00 38.90 3.51
3163 6700 7.649306 GGTTGCTTATATTTGTCCATCATTGAC 59.351 37.037 0.00 0.00 0.00 3.18
3164 6701 7.560991 AGGTTGCTTATATTTGTCCATCATTGA 59.439 33.333 0.00 0.00 0.00 2.57
3165 6702 7.719483 AGGTTGCTTATATTTGTCCATCATTG 58.281 34.615 0.00 0.00 0.00 2.82
3167 6704 7.175641 GCTAGGTTGCTTATATTTGTCCATCAT 59.824 37.037 0.00 0.00 0.00 2.45
3168 6705 6.486657 GCTAGGTTGCTTATATTTGTCCATCA 59.513 38.462 0.00 0.00 0.00 3.07
3169 6706 6.712547 AGCTAGGTTGCTTATATTTGTCCATC 59.287 38.462 0.00 0.00 40.93 3.51
3273 6810 2.394563 GCGAGTGCCTCCTTCAAGC 61.395 63.158 0.00 0.00 33.98 4.01
3394 6931 4.142534 CCAATCGCAATCACAACAGATCTT 60.143 41.667 0.00 0.00 0.00 2.40
3399 6936 3.431856 CATCCAATCGCAATCACAACAG 58.568 45.455 0.00 0.00 0.00 3.16
3404 6941 0.031178 GGCCATCCAATCGCAATCAC 59.969 55.000 0.00 0.00 0.00 3.06
3436 6973 4.645588 ACCATCTGCTAGTGAAGGTACTAC 59.354 45.833 11.27 0.00 38.49 2.73
3484 7021 9.859427 TGCTTGTTCATTTGGAAAATTATAGAG 57.141 29.630 0.00 0.00 37.23 2.43
3488 7025 9.504708 TCAATGCTTGTTCATTTGGAAAATTAT 57.495 25.926 0.00 0.00 37.23 1.28
3489 7026 8.899427 TCAATGCTTGTTCATTTGGAAAATTA 57.101 26.923 0.00 0.00 37.23 1.40
3490 7027 7.499895 ACTCAATGCTTGTTCATTTGGAAAATT 59.500 29.630 0.00 0.00 37.23 1.82
3491 7028 6.993902 ACTCAATGCTTGTTCATTTGGAAAAT 59.006 30.769 0.00 0.00 37.23 1.82
3492 7029 6.347696 ACTCAATGCTTGTTCATTTGGAAAA 58.652 32.000 0.00 0.00 37.23 2.29
3493 7030 5.916318 ACTCAATGCTTGTTCATTTGGAAA 58.084 33.333 0.00 0.00 37.23 3.13
3494 7031 5.534207 ACTCAATGCTTGTTCATTTGGAA 57.466 34.783 0.00 0.00 34.68 3.53
3495 7032 5.302568 AGAACTCAATGCTTGTTCATTTGGA 59.697 36.000 12.91 0.00 41.56 3.53
3496 7033 5.535333 AGAACTCAATGCTTGTTCATTTGG 58.465 37.500 12.91 0.00 41.56 3.28
3497 7034 6.073980 CCAAGAACTCAATGCTTGTTCATTTG 60.074 38.462 12.91 10.07 41.56 2.32
3498 7035 5.987347 CCAAGAACTCAATGCTTGTTCATTT 59.013 36.000 12.91 1.81 41.56 2.32
3499 7036 5.302568 TCCAAGAACTCAATGCTTGTTCATT 59.697 36.000 12.91 0.00 41.56 2.57
3500 7037 4.828939 TCCAAGAACTCAATGCTTGTTCAT 59.171 37.500 12.91 2.62 41.56 2.57
3501 7038 4.036734 GTCCAAGAACTCAATGCTTGTTCA 59.963 41.667 12.91 0.00 41.56 3.18
3502 7039 4.540824 GTCCAAGAACTCAATGCTTGTTC 58.459 43.478 0.00 0.00 37.82 3.18
3503 7040 3.319122 GGTCCAAGAACTCAATGCTTGTT 59.681 43.478 0.00 0.00 37.82 2.83
3504 7041 2.887152 GGTCCAAGAACTCAATGCTTGT 59.113 45.455 0.00 0.00 37.82 3.16
3505 7042 2.886523 TGGTCCAAGAACTCAATGCTTG 59.113 45.455 0.00 0.00 38.90 4.01
3506 7043 3.228188 TGGTCCAAGAACTCAATGCTT 57.772 42.857 0.00 0.00 0.00 3.91
3507 7044 2.957402 TGGTCCAAGAACTCAATGCT 57.043 45.000 0.00 0.00 0.00 3.79
3508 7045 5.471456 CCTATATGGTCCAAGAACTCAATGC 59.529 44.000 0.00 0.00 0.00 3.56
3509 7046 5.471456 GCCTATATGGTCCAAGAACTCAATG 59.529 44.000 0.00 0.00 38.35 2.82
3510 7047 5.132648 TGCCTATATGGTCCAAGAACTCAAT 59.867 40.000 0.00 0.00 38.35 2.57
3511 7048 4.473196 TGCCTATATGGTCCAAGAACTCAA 59.527 41.667 0.00 0.00 38.35 3.02
3512 7049 4.037222 TGCCTATATGGTCCAAGAACTCA 58.963 43.478 0.00 0.00 38.35 3.41
3513 7050 4.141711 TGTGCCTATATGGTCCAAGAACTC 60.142 45.833 0.00 0.00 38.35 3.01
3514 7051 3.780294 TGTGCCTATATGGTCCAAGAACT 59.220 43.478 0.00 0.00 38.35 3.01
3515 7052 4.150897 TGTGCCTATATGGTCCAAGAAC 57.849 45.455 0.00 0.00 38.35 3.01
3516 7053 4.853468 TTGTGCCTATATGGTCCAAGAA 57.147 40.909 0.00 0.00 38.35 2.52
3517 7054 6.508030 TTATTGTGCCTATATGGTCCAAGA 57.492 37.500 0.00 0.00 38.35 3.02
3518 7055 8.862325 TTATTATTGTGCCTATATGGTCCAAG 57.138 34.615 0.00 0.00 38.35 3.61
3519 7056 9.295825 CTTTATTATTGTGCCTATATGGTCCAA 57.704 33.333 0.00 0.00 38.35 3.53
3520 7057 8.664992 TCTTTATTATTGTGCCTATATGGTCCA 58.335 33.333 0.00 0.00 38.35 4.02
3521 7058 9.515226 TTCTTTATTATTGTGCCTATATGGTCC 57.485 33.333 0.00 0.00 38.35 4.46
3544 7081 8.619546 GCACAAGAGCTATTTCTATGAAATTCT 58.380 33.333 10.25 8.37 0.00 2.40
3545 7082 7.859875 GGCACAAGAGCTATTTCTATGAAATTC 59.140 37.037 10.25 3.77 34.17 2.17
3546 7083 7.340232 TGGCACAAGAGCTATTTCTATGAAATT 59.660 33.333 10.25 0.00 31.92 1.82
3547 7084 6.830324 TGGCACAAGAGCTATTTCTATGAAAT 59.170 34.615 9.93 9.93 31.92 2.17
3548 7085 6.094048 GTGGCACAAGAGCTATTTCTATGAAA 59.906 38.462 13.86 0.00 44.16 2.69
3549 7086 5.586243 GTGGCACAAGAGCTATTTCTATGAA 59.414 40.000 13.86 0.00 44.16 2.57
3550 7087 5.118990 GTGGCACAAGAGCTATTTCTATGA 58.881 41.667 13.86 0.00 44.16 2.15
3551 7088 4.877823 TGTGGCACAAGAGCTATTTCTATG 59.122 41.667 19.74 0.00 44.16 2.23
3552 7089 5.102953 TGTGGCACAAGAGCTATTTCTAT 57.897 39.130 19.74 0.00 44.16 1.98
3553 7090 4.551702 TGTGGCACAAGAGCTATTTCTA 57.448 40.909 19.74 0.00 44.16 2.10
3554 7091 3.423539 TGTGGCACAAGAGCTATTTCT 57.576 42.857 19.74 0.00 44.16 2.52
3555 7092 4.878397 AGTATGTGGCACAAGAGCTATTTC 59.122 41.667 25.95 3.26 44.16 2.17
3556 7093 4.848357 AGTATGTGGCACAAGAGCTATTT 58.152 39.130 25.95 7.13 44.16 1.40
3557 7094 4.494091 AGTATGTGGCACAAGAGCTATT 57.506 40.909 25.95 7.92 44.16 1.73
3558 7095 4.494091 AAGTATGTGGCACAAGAGCTAT 57.506 40.909 25.95 8.72 44.16 2.97
3559 7096 3.981071 AAGTATGTGGCACAAGAGCTA 57.019 42.857 25.95 9.19 44.16 3.32
3560 7097 2.867109 AAGTATGTGGCACAAGAGCT 57.133 45.000 25.95 16.18 44.16 4.09
3561 7098 3.077359 AGAAAGTATGTGGCACAAGAGC 58.923 45.455 25.95 14.23 44.16 4.09
3562 7099 4.318332 TCAGAAAGTATGTGGCACAAGAG 58.682 43.478 25.95 8.83 44.16 2.85
3563 7100 4.350368 TCAGAAAGTATGTGGCACAAGA 57.650 40.909 25.95 13.04 44.16 3.02
3564 7101 5.633830 AATCAGAAAGTATGTGGCACAAG 57.366 39.130 25.95 7.29 44.16 3.16
3565 7102 6.348132 CGTTAATCAGAAAGTATGTGGCACAA 60.348 38.462 25.95 11.25 44.16 3.33
3566 7103 5.121611 CGTTAATCAGAAAGTATGTGGCACA 59.878 40.000 24.36 24.36 0.00 4.57
3567 7104 5.121768 ACGTTAATCAGAAAGTATGTGGCAC 59.878 40.000 11.55 11.55 0.00 5.01
3568 7105 5.242434 ACGTTAATCAGAAAGTATGTGGCA 58.758 37.500 0.00 0.00 0.00 4.92
3569 7106 5.796350 ACGTTAATCAGAAAGTATGTGGC 57.204 39.130 0.00 0.00 0.00 5.01
3581 7118 9.450807 GGATTGGATTCAATAAACGTTAATCAG 57.549 33.333 17.87 3.12 43.08 2.90
3582 7119 8.410141 GGGATTGGATTCAATAAACGTTAATCA 58.590 33.333 17.87 4.06 43.08 2.57
3583 7120 8.630037 AGGGATTGGATTCAATAAACGTTAATC 58.370 33.333 0.00 6.71 43.08 1.75
3584 7121 8.533569 AGGGATTGGATTCAATAAACGTTAAT 57.466 30.769 0.00 0.00 43.08 1.40
3585 7122 7.948034 AGGGATTGGATTCAATAAACGTTAA 57.052 32.000 0.00 0.00 43.08 2.01
3587 7124 9.284968 CTATAGGGATTGGATTCAATAAACGTT 57.715 33.333 0.00 0.00 43.08 3.99
3588 7125 7.390718 GCTATAGGGATTGGATTCAATAAACGT 59.609 37.037 0.00 0.00 43.08 3.99
3589 7126 7.413000 CGCTATAGGGATTGGATTCAATAAACG 60.413 40.741 11.25 0.00 43.08 3.60
3590 7127 7.626452 GCGCTATAGGGATTGGATTCAATAAAC 60.626 40.741 20.21 0.00 43.08 2.01
3591 7128 6.374333 GCGCTATAGGGATTGGATTCAATAAA 59.626 38.462 20.21 0.00 43.08 1.40
3592 7129 5.880332 GCGCTATAGGGATTGGATTCAATAA 59.120 40.000 20.21 0.00 43.08 1.40
3593 7130 5.045942 TGCGCTATAGGGATTGGATTCAATA 60.046 40.000 20.21 0.00 43.08 1.90
3594 7131 4.263462 TGCGCTATAGGGATTGGATTCAAT 60.263 41.667 20.21 0.00 45.45 2.57
3595 7132 3.072330 TGCGCTATAGGGATTGGATTCAA 59.928 43.478 20.21 0.00 37.28 2.69
3596 7133 2.637382 TGCGCTATAGGGATTGGATTCA 59.363 45.455 20.21 3.52 0.00 2.57
3597 7134 3.003480 GTGCGCTATAGGGATTGGATTC 58.997 50.000 20.21 0.96 0.00 2.52
3598 7135 2.290323 GGTGCGCTATAGGGATTGGATT 60.290 50.000 20.21 0.00 0.00 3.01
3599 7136 1.279271 GGTGCGCTATAGGGATTGGAT 59.721 52.381 20.21 0.00 0.00 3.41
3600 7137 0.685097 GGTGCGCTATAGGGATTGGA 59.315 55.000 20.21 0.00 0.00 3.53
3601 7138 0.670546 CGGTGCGCTATAGGGATTGG 60.671 60.000 20.21 2.97 0.00 3.16
3602 7139 0.033504 ACGGTGCGCTATAGGGATTG 59.966 55.000 20.21 8.67 0.00 2.67
3603 7140 0.756903 AACGGTGCGCTATAGGGATT 59.243 50.000 20.21 3.52 0.00 3.01
3604 7141 0.033504 CAACGGTGCGCTATAGGGAT 59.966 55.000 20.21 0.00 0.00 3.85
3605 7142 1.440060 CAACGGTGCGCTATAGGGA 59.560 57.895 20.21 3.27 0.00 4.20
3606 7143 1.594293 CCAACGGTGCGCTATAGGG 60.594 63.158 9.73 12.30 0.00 3.53
3607 7144 0.386476 TACCAACGGTGCGCTATAGG 59.614 55.000 9.73 5.78 36.19 2.57
3608 7145 2.287970 TGATACCAACGGTGCGCTATAG 60.288 50.000 9.73 0.00 36.19 1.31
3609 7146 1.682323 TGATACCAACGGTGCGCTATA 59.318 47.619 9.73 0.00 36.19 1.31
3610 7147 0.462375 TGATACCAACGGTGCGCTAT 59.538 50.000 9.73 0.00 36.19 2.97
3611 7148 0.462375 ATGATACCAACGGTGCGCTA 59.538 50.000 9.73 0.00 36.19 4.26
3612 7149 1.089481 CATGATACCAACGGTGCGCT 61.089 55.000 9.73 0.00 36.19 5.92
3613 7150 1.351707 CATGATACCAACGGTGCGC 59.648 57.895 0.00 0.00 36.19 6.09
3614 7151 1.089481 AGCATGATACCAACGGTGCG 61.089 55.000 0.00 0.00 36.19 5.34
3615 7152 1.094785 AAGCATGATACCAACGGTGC 58.905 50.000 0.00 0.00 36.19 5.01
3616 7153 1.401552 CCAAGCATGATACCAACGGTG 59.598 52.381 0.00 0.00 36.19 4.94
3617 7154 1.681780 CCCAAGCATGATACCAACGGT 60.682 52.381 0.00 0.00 40.16 4.83
3618 7155 1.024271 CCCAAGCATGATACCAACGG 58.976 55.000 0.00 0.00 0.00 4.44
3619 7156 0.381801 GCCCAAGCATGATACCAACG 59.618 55.000 0.00 0.00 39.53 4.10
3620 7157 1.473258 TGCCCAAGCATGATACCAAC 58.527 50.000 0.00 0.00 46.52 3.77
3621 7158 3.996361 TGCCCAAGCATGATACCAA 57.004 47.368 0.00 0.00 46.52 3.67
3966 9202 3.004524 GCTCATCTCAAAATCAGGGCATC 59.995 47.826 0.00 0.00 0.00 3.91
3993 9229 0.323629 GGTCGGACAAGGATCACCAA 59.676 55.000 10.76 0.00 38.94 3.67
4062 9302 6.126409 TGTTCTTTTTCCTCTGCCTTCTTAA 58.874 36.000 0.00 0.00 0.00 1.85
4063 9303 5.690865 TGTTCTTTTTCCTCTGCCTTCTTA 58.309 37.500 0.00 0.00 0.00 2.10
4138 9380 9.801873 GCTTTATTTCACTCTTTGGCAATATTA 57.198 29.630 0.00 0.00 0.00 0.98
4185 9427 8.328146 ACAAATCATTAAGTCGTTCATACATCG 58.672 33.333 0.00 0.00 0.00 3.84
4245 9489 1.003476 ACATGGTCAGCACGCATGA 60.003 52.632 0.00 0.00 35.94 3.07
4295 9539 6.483307 GGTTCTCCCAAAAAGGAAAAATTCAG 59.517 38.462 0.00 0.00 41.22 3.02
4299 9543 7.872061 ATAGGTTCTCCCAAAAAGGAAAAAT 57.128 32.000 0.00 0.00 41.22 1.82
4315 9563 6.936335 CCCAAAAGCAAATTTGAATAGGTTCT 59.064 34.615 22.31 3.75 41.73 3.01
4567 9825 2.096819 CCGGCATTAGCGTGTTTTACAT 59.903 45.455 0.00 0.00 43.41 2.29
4575 9833 1.009675 GAATGCCGGCATTAGCGTG 60.010 57.895 45.55 0.00 45.50 5.34
4590 9848 5.944007 ACGCCTAGAATGTGGTTTTTAGAAT 59.056 36.000 0.00 0.00 0.00 2.40
4591 9849 5.180492 CACGCCTAGAATGTGGTTTTTAGAA 59.820 40.000 0.00 0.00 0.00 2.10
4593 9851 4.454504 ACACGCCTAGAATGTGGTTTTTAG 59.545 41.667 11.82 0.00 37.92 1.85
4608 9870 0.034337 GTTGACCTTCCACACGCCTA 59.966 55.000 0.00 0.00 0.00 3.93
4609 9871 1.227853 GTTGACCTTCCACACGCCT 60.228 57.895 0.00 0.00 0.00 5.52
4639 9901 9.862371 TCATTTGTATTTTATAACAATGGCGTT 57.138 25.926 0.00 0.00 35.64 4.84
4640 9902 9.296400 GTCATTTGTATTTTATAACAATGGCGT 57.704 29.630 0.00 0.00 35.64 5.68
4680 9942 5.009210 CCACCGGTATGTAAAATACCAATGG 59.991 44.000 6.87 14.22 43.16 3.16
4699 9961 2.435938 AATAGTGCCACGCCACCG 60.436 61.111 0.00 0.00 36.38 4.94
4721 9983 0.724549 TTGCTATTAGTTGTGGCGCG 59.275 50.000 0.00 0.00 0.00 6.86
4722 9984 2.541588 CCATTGCTATTAGTTGTGGCGC 60.542 50.000 0.00 0.00 0.00 6.53
4744 10006 2.439135 AGGTGTGCTATCCATGTGCATA 59.561 45.455 0.00 0.00 39.00 3.14
4885 10255 3.921021 GTGTTGTAGACTCGTGGATCTTG 59.079 47.826 0.00 0.00 0.00 3.02
4886 10256 3.056749 GGTGTTGTAGACTCGTGGATCTT 60.057 47.826 0.00 0.00 0.00 2.40
4916 10286 1.667830 AGTGACGATGGCAACGGTG 60.668 57.895 21.20 0.00 42.51 4.94
4917 10287 1.667830 CAGTGACGATGGCAACGGT 60.668 57.895 21.20 7.00 42.51 4.83
4918 10288 1.626654 GACAGTGACGATGGCAACGG 61.627 60.000 21.20 5.53 42.51 4.44
4919 10289 0.943835 TGACAGTGACGATGGCAACG 60.944 55.000 15.92 15.92 42.51 4.10
4920 10290 1.394917 GATGACAGTGACGATGGCAAC 59.605 52.381 0.00 0.00 39.65 4.17
4921 10291 1.725641 GATGACAGTGACGATGGCAA 58.274 50.000 0.00 0.00 39.65 4.52
4922 10292 0.458370 CGATGACAGTGACGATGGCA 60.458 55.000 0.00 0.00 40.74 4.92
4923 10293 1.756375 GCGATGACAGTGACGATGGC 61.756 60.000 0.00 0.00 0.00 4.40
4924 10294 0.458370 TGCGATGACAGTGACGATGG 60.458 55.000 0.00 0.00 0.00 3.51
4925 10295 1.257155 CATGCGATGACAGTGACGATG 59.743 52.381 0.00 0.97 0.00 3.84
4926 10296 1.134995 ACATGCGATGACAGTGACGAT 60.135 47.619 0.00 0.00 0.00 3.73
4927 10297 0.243636 ACATGCGATGACAGTGACGA 59.756 50.000 0.00 0.00 0.00 4.20
4928 10298 1.848608 CTACATGCGATGACAGTGACG 59.151 52.381 0.00 0.00 0.00 4.35
4929 10299 3.111838 CTCTACATGCGATGACAGTGAC 58.888 50.000 0.00 0.00 0.00 3.67
4930 10300 2.099756 CCTCTACATGCGATGACAGTGA 59.900 50.000 0.00 0.00 0.00 3.41
4931 10301 2.159184 ACCTCTACATGCGATGACAGTG 60.159 50.000 0.00 0.00 0.00 3.66
4932 10302 2.103373 ACCTCTACATGCGATGACAGT 58.897 47.619 0.00 0.00 0.00 3.55
4997 10370 0.690762 AATTGACACGGGGCTGTAGT 59.309 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.