Multiple sequence alignment - TraesCS4B01G350600

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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 TraesCS4B01G350600 chr4B 100.000 5929 0 0 1 5929 643313903 643307975 0.000000e+00 10949.0
1 TraesCS4B01G350600 chr4D 92.011 5282 214 84 21 5216 500026480 500021321 0.000000e+00 7225.0
2 TraesCS4B01G350600 chr5A 90.169 5157 240 106 138 5219 680845868 680840904 0.000000e+00 6468.0
3 TraesCS4B01G350600 chr5A 93.525 695 44 1 5236 5929 451146727 451147421 0.000000e+00 1033.0
4 TraesCS4B01G350600 chr5A 93.617 94 5 1 21 113 680845953 680845860 8.010000e-29 139.0
5 TraesCS4B01G350600 chr5A 94.737 38 2 0 2788 2825 502072220 502072257 6.420000e-05 60.2
6 TraesCS4B01G350600 chr1B 94.364 692 35 4 5240 5929 627789455 627790144 0.000000e+00 1059.0
7 TraesCS4B01G350600 chr5B 94.211 691 38 2 5240 5929 43839135 43839824 0.000000e+00 1053.0
8 TraesCS4B01G350600 chr5B 93.353 692 43 3 5240 5929 522016119 522016809 0.000000e+00 1020.0
9 TraesCS4B01G350600 chr5B 83.333 102 17 0 2741 2842 535700244 535700345 1.760000e-15 95.3
10 TraesCS4B01G350600 chr5B 94.737 38 2 0 2788 2825 476170498 476170535 6.420000e-05 60.2
11 TraesCS4B01G350600 chr3A 94.084 693 38 3 5239 5929 709420315 709419624 0.000000e+00 1050.0
12 TraesCS4B01G350600 chr6B 93.922 691 38 3 5240 5929 115540653 115541340 0.000000e+00 1040.0
13 TraesCS4B01G350600 chr2A 93.343 691 44 2 5240 5929 656358919 656359608 0.000000e+00 1020.0
14 TraesCS4B01G350600 chr2A 92.785 693 47 3 5238 5929 640263013 640262323 0.000000e+00 1000.0
15 TraesCS4B01G350600 chr2A 83.721 86 12 2 2744 2828 763313718 763313634 4.930000e-11 80.5
16 TraesCS4B01G350600 chr7B 93.033 689 44 4 5244 5929 610626327 610627014 0.000000e+00 1003.0
17 TraesCS4B01G350600 chr1D 76.378 254 49 10 2578 2824 270231109 270231358 6.240000e-25 126.0
18 TraesCS4B01G350600 chr2B 78.000 150 25 7 2683 2828 794866991 794866846 2.940000e-13 87.9
19 TraesCS4B01G350600 chr5D 94.737 38 2 0 2788 2825 396370474 396370511 6.420000e-05 60.2


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 TraesCS4B01G350600 chr4B 643307975 643313903 5928 True 10949.0 10949 100.000 1 5929 1 chr4B.!!$R1 5928
1 TraesCS4B01G350600 chr4D 500021321 500026480 5159 True 7225.0 7225 92.011 21 5216 1 chr4D.!!$R1 5195
2 TraesCS4B01G350600 chr5A 680840904 680845953 5049 True 3303.5 6468 91.893 21 5219 2 chr5A.!!$R1 5198
3 TraesCS4B01G350600 chr5A 451146727 451147421 694 False 1033.0 1033 93.525 5236 5929 1 chr5A.!!$F1 693
4 TraesCS4B01G350600 chr1B 627789455 627790144 689 False 1059.0 1059 94.364 5240 5929 1 chr1B.!!$F1 689
5 TraesCS4B01G350600 chr5B 43839135 43839824 689 False 1053.0 1053 94.211 5240 5929 1 chr5B.!!$F1 689
6 TraesCS4B01G350600 chr5B 522016119 522016809 690 False 1020.0 1020 93.353 5240 5929 1 chr5B.!!$F3 689
7 TraesCS4B01G350600 chr3A 709419624 709420315 691 True 1050.0 1050 94.084 5239 5929 1 chr3A.!!$R1 690
8 TraesCS4B01G350600 chr6B 115540653 115541340 687 False 1040.0 1040 93.922 5240 5929 1 chr6B.!!$F1 689
9 TraesCS4B01G350600 chr2A 656358919 656359608 689 False 1020.0 1020 93.343 5240 5929 1 chr2A.!!$F1 689
10 TraesCS4B01G350600 chr2A 640262323 640263013 690 True 1000.0 1000 92.785 5238 5929 1 chr2A.!!$R1 691
11 TraesCS4B01G350600 chr7B 610626327 610627014 687 False 1003.0 1003 93.033 5244 5929 1 chr7B.!!$F1 685

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
903 931 0.035056 TTAGCTTTGGAGAGCCCTGC 60.035 55.0 0.0 0.0 43.74 4.85 F
1821 1863 0.105401 TACCGTCCCCATGCATCCTA 60.105 55.0 0.0 0.0 0.00 2.94 F
3544 3649 0.178846 TGGAGGTGGAGGATTTCCCA 60.179 55.0 0.0 0.0 46.19 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2224 0.030638 ACCAGTTTCACGCAATGCAC 59.969 50.0 5.91 0.00 0.00 4.57 R
3550 3655 0.103390 TTTTCGTGTCGAGGCTGACA 59.897 50.0 13.41 13.41 46.15 3.58 R
5479 5667 1.045407 TGGTAGCGCGGGATATCTTT 58.955 50.0 8.83 0.00 0.00 2.52 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
107 108 1.074951 AAAGCGAAGTTGGGAGGGG 59.925 57.895 0.00 0.00 0.00 4.79
112 113 2.204306 AAGTTGGGAGGGGGAGGG 60.204 66.667 0.00 0.00 0.00 4.30
142 143 2.506881 CATGGAAAAAGCGCGGGC 60.507 61.111 17.92 17.92 40.37 6.13
185 186 2.275418 CCTCCCCCATTCCAACGG 59.725 66.667 0.00 0.00 0.00 4.44
187 188 2.533232 TCCCCCATTCCAACGGGT 60.533 61.111 0.00 0.00 41.30 5.28
210 211 1.063567 TGACTAGGCCTCTCCTTCTCC 60.064 57.143 9.68 0.00 44.75 3.71
330 344 2.128507 AGCCAGGCCGTAGCTAGAC 61.129 63.158 14.57 0.00 39.73 2.59
340 354 1.249407 GTAGCTAGACGGCTAGGCAT 58.751 55.000 26.46 0.00 44.17 4.40
341 355 1.068194 GTAGCTAGACGGCTAGGCATG 60.068 57.143 26.46 1.95 44.17 4.06
342 356 1.666234 GCTAGACGGCTAGGCATGC 60.666 63.158 26.46 9.90 43.54 4.06
343 357 1.742146 CTAGACGGCTAGGCATGCA 59.258 57.895 18.22 0.00 40.37 3.96
344 358 0.319383 CTAGACGGCTAGGCATGCAG 60.319 60.000 18.22 10.51 40.37 4.41
345 359 1.748329 TAGACGGCTAGGCATGCAGG 61.748 60.000 21.36 9.62 0.00 4.85
346 360 4.864334 ACGGCTAGGCATGCAGGC 62.864 66.667 21.36 16.47 44.61 4.85
375 389 2.653115 GGCCAGCCAAAGACAAGC 59.347 61.111 3.12 0.00 35.81 4.01
391 405 2.771943 ACAAGCGGAGAAGATTGGGATA 59.228 45.455 0.22 0.00 41.34 2.59
392 406 3.392616 ACAAGCGGAGAAGATTGGGATAT 59.607 43.478 0.22 0.00 41.34 1.63
393 407 4.141390 ACAAGCGGAGAAGATTGGGATATT 60.141 41.667 0.22 0.00 41.34 1.28
394 408 4.713792 AGCGGAGAAGATTGGGATATTT 57.286 40.909 0.00 0.00 0.00 1.40
395 409 4.646572 AGCGGAGAAGATTGGGATATTTC 58.353 43.478 0.00 0.00 0.00 2.17
401 415 7.308830 CGGAGAAGATTGGGATATTTCATTTCC 60.309 40.741 0.00 0.00 0.00 3.13
431 445 0.526954 CAAAAGCCATGCATCCGAGC 60.527 55.000 0.00 0.00 0.00 5.03
432 446 1.996786 AAAAGCCATGCATCCGAGCG 61.997 55.000 0.00 0.00 37.31 5.03
433 447 2.874648 AAAGCCATGCATCCGAGCGA 62.875 55.000 0.00 0.00 37.31 4.93
434 448 3.344215 GCCATGCATCCGAGCGAG 61.344 66.667 0.00 0.00 37.31 5.03
475 489 1.304464 GCAAAGGACCCAAGGGAGG 60.304 63.158 13.15 0.00 38.96 4.30
504 526 0.907230 AGGGACAGGGAGAGCTTGTC 60.907 60.000 6.90 6.90 40.29 3.18
507 529 1.338579 GGACAGGGAGAGCTTGTCAAG 60.339 57.143 15.47 8.31 42.24 3.02
535 560 0.789383 GAATCCGAGCGTTGTTTGCG 60.789 55.000 0.00 0.00 37.44 4.85
558 583 3.325870 GCAAAATAACCCCACAAGCTTC 58.674 45.455 0.00 0.00 0.00 3.86
609 634 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
610 635 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
611 636 2.612251 CTCCCTCCCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
614 639 2.612251 CCTCCCTCCCTCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
630 655 1.289530 TCTCCCTTCTTCCTCCTCTCC 59.710 57.143 0.00 0.00 0.00 3.71
680 706 3.024356 TCGGCCTCCTCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
683 709 2.123033 GCCTCCTCTCCTCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
688 714 2.612251 CTCTCCTCCTCCCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
708 734 1.894466 CTCCTCCTCATGCATCGATCT 59.106 52.381 0.00 0.00 0.00 2.75
709 735 1.891811 TCCTCCTCATGCATCGATCTC 59.108 52.381 0.00 0.00 0.00 2.75
713 739 4.009002 CTCCTCATGCATCGATCTCTCTA 58.991 47.826 0.00 0.00 0.00 2.43
714 740 3.755905 TCCTCATGCATCGATCTCTCTAC 59.244 47.826 0.00 0.00 0.00 2.59
715 741 3.758023 CCTCATGCATCGATCTCTCTACT 59.242 47.826 0.00 0.00 0.00 2.57
716 742 4.379708 CCTCATGCATCGATCTCTCTACTG 60.380 50.000 0.00 0.00 0.00 2.74
717 743 3.057666 TCATGCATCGATCTCTCTACTGC 60.058 47.826 0.00 0.00 0.00 4.40
718 744 2.580962 TGCATCGATCTCTCTACTGCT 58.419 47.619 0.00 0.00 0.00 4.24
728 754 4.786425 TCTCTCTACTGCTTGCTCATCTA 58.214 43.478 0.00 0.00 0.00 1.98
754 780 6.569179 TTGGTTGGTTTCTACTTTCTATGC 57.431 37.500 0.00 0.00 0.00 3.14
782 808 2.278854 CTCATGTGTGTGTGTGTGTCA 58.721 47.619 0.00 0.00 0.00 3.58
783 809 2.874086 CTCATGTGTGTGTGTGTGTCAT 59.126 45.455 0.00 0.00 0.00 3.06
784 810 3.277715 TCATGTGTGTGTGTGTGTCATT 58.722 40.909 0.00 0.00 0.00 2.57
785 811 3.065095 TCATGTGTGTGTGTGTGTCATTG 59.935 43.478 0.00 0.00 0.00 2.82
786 812 1.742268 TGTGTGTGTGTGTGTCATTGG 59.258 47.619 0.00 0.00 0.00 3.16
787 813 2.013400 GTGTGTGTGTGTGTCATTGGA 58.987 47.619 0.00 0.00 0.00 3.53
788 814 2.421775 GTGTGTGTGTGTGTCATTGGAA 59.578 45.455 0.00 0.00 0.00 3.53
832 860 1.835121 CCGACGACGATTCATTGCTA 58.165 50.000 9.28 0.00 42.66 3.49
835 863 2.464865 GACGACGATTCATTGCTAGCT 58.535 47.619 17.23 0.00 0.00 3.32
836 864 3.629058 GACGACGATTCATTGCTAGCTA 58.371 45.455 17.23 9.14 0.00 3.32
856 884 1.500474 TATAGCTGGCTGGCTGTTCT 58.500 50.000 13.94 2.41 43.01 3.01
899 927 2.478539 CGCATTTTAGCTTTGGAGAGCC 60.479 50.000 0.00 0.00 43.74 4.70
900 928 2.159184 GCATTTTAGCTTTGGAGAGCCC 60.159 50.000 0.00 0.00 43.74 5.19
901 929 3.359950 CATTTTAGCTTTGGAGAGCCCT 58.640 45.455 0.00 0.00 43.74 5.19
902 930 2.496899 TTTAGCTTTGGAGAGCCCTG 57.503 50.000 0.00 0.00 43.74 4.45
903 931 0.035056 TTAGCTTTGGAGAGCCCTGC 60.035 55.000 0.00 0.00 43.74 4.85
904 932 1.915078 TAGCTTTGGAGAGCCCTGCC 61.915 60.000 0.00 0.00 43.74 4.85
905 933 3.085223 CTTTGGAGAGCCCTGCCT 58.915 61.111 0.00 0.00 35.38 4.75
906 934 1.378250 CTTTGGAGAGCCCTGCCTG 60.378 63.158 0.00 0.00 35.38 4.85
982 1010 1.683629 GCTCTCGGAGGAAGAGGAAGA 60.684 57.143 4.96 0.00 36.45 2.87
983 1011 2.729194 CTCTCGGAGGAAGAGGAAGAA 58.271 52.381 4.96 0.00 36.45 2.52
984 1012 2.687935 CTCTCGGAGGAAGAGGAAGAAG 59.312 54.545 4.96 0.00 36.45 2.85
985 1013 2.041891 TCTCGGAGGAAGAGGAAGAAGT 59.958 50.000 4.96 0.00 36.45 3.01
986 1014 2.829120 CTCGGAGGAAGAGGAAGAAGTT 59.171 50.000 0.00 0.00 32.38 2.66
987 1015 4.017808 CTCGGAGGAAGAGGAAGAAGTTA 58.982 47.826 0.00 0.00 32.38 2.24
988 1016 4.413760 TCGGAGGAAGAGGAAGAAGTTAA 58.586 43.478 0.00 0.00 0.00 2.01
989 1017 5.024118 TCGGAGGAAGAGGAAGAAGTTAAT 58.976 41.667 0.00 0.00 0.00 1.40
990 1018 6.192773 TCGGAGGAAGAGGAAGAAGTTAATA 58.807 40.000 0.00 0.00 0.00 0.98
1177 1206 1.604278 GTGCGTGCTTTCTTCTTCCTT 59.396 47.619 0.00 0.00 0.00 3.36
1178 1207 1.873591 TGCGTGCTTTCTTCTTCCTTC 59.126 47.619 0.00 0.00 0.00 3.46
1179 1208 1.197949 GCGTGCTTTCTTCTTCCTTCC 59.802 52.381 0.00 0.00 0.00 3.46
1180 1209 2.772287 CGTGCTTTCTTCTTCCTTCCT 58.228 47.619 0.00 0.00 0.00 3.36
1181 1210 3.864921 GCGTGCTTTCTTCTTCCTTCCTA 60.865 47.826 0.00 0.00 0.00 2.94
1183 1212 4.938226 CGTGCTTTCTTCTTCCTTCCTAAT 59.062 41.667 0.00 0.00 0.00 1.73
1185 1214 6.256757 CGTGCTTTCTTCTTCCTTCCTAATAG 59.743 42.308 0.00 0.00 0.00 1.73
1186 1215 7.331791 GTGCTTTCTTCTTCCTTCCTAATAGA 58.668 38.462 0.00 0.00 0.00 1.98
1187 1216 7.824779 GTGCTTTCTTCTTCCTTCCTAATAGAA 59.175 37.037 0.00 0.00 0.00 2.10
1188 1217 8.383175 TGCTTTCTTCTTCCTTCCTAATAGAAA 58.617 33.333 0.00 0.00 0.00 2.52
1196 1225 9.982651 TCTTCCTTCCTAATAGAAATATGTTCG 57.017 33.333 0.00 0.00 0.00 3.95
1197 1226 9.765795 CTTCCTTCCTAATAGAAATATGTTCGT 57.234 33.333 0.00 0.00 0.00 3.85
1203 1232 9.431887 TCCTAATAGAAATATGTTCGTATTGGC 57.568 33.333 0.00 0.00 0.00 4.52
1204 1233 9.214957 CCTAATAGAAATATGTTCGTATTGGCA 57.785 33.333 0.00 0.00 0.00 4.92
1206 1235 8.677148 AATAGAAATATGTTCGTATTGGCACT 57.323 30.769 0.00 0.00 0.00 4.40
1237 1270 6.652900 GCTCCTGATTAGAGTATTTCAATCCC 59.347 42.308 0.00 0.00 33.69 3.85
1251 1284 0.251073 AATCCCAAACCCTACGTCCG 59.749 55.000 0.00 0.00 0.00 4.79
1309 1342 4.024670 AGGTCCTCGTAGCTAATTTCACT 58.975 43.478 0.00 0.00 0.00 3.41
1311 1344 5.067544 AGGTCCTCGTAGCTAATTTCACTAC 59.932 44.000 0.00 0.00 34.29 2.73
1327 1360 7.781548 TTTCACTACCAACTTCAGTAGAAAC 57.218 36.000 4.30 0.00 38.60 2.78
1331 1364 7.494625 TCACTACCAACTTCAGTAGAAACTTTG 59.505 37.037 4.30 0.00 38.60 2.77
1346 1380 6.901300 AGAAACTTTGGGGATAAGGAGATAC 58.099 40.000 0.00 0.00 0.00 2.24
1363 1397 2.335316 TACAAGCGTTCCAAACTGGT 57.665 45.000 0.00 0.00 39.03 4.00
1373 1407 6.711645 AGCGTTCCAAACTGGTAGTTAATTAA 59.288 34.615 0.00 0.00 37.47 1.40
1406 1440 5.745312 TCTCTTTTGGACAGAAGATAGCA 57.255 39.130 5.85 0.00 32.16 3.49
1437 1471 9.583765 GAATTACTCTGTTATAAGTCTTCCGTT 57.416 33.333 0.00 0.00 0.00 4.44
1464 1498 3.591196 TTATGGGATTTTGCACTGCAC 57.409 42.857 2.26 0.00 38.71 4.57
1524 1558 7.233348 ACACCACTCTGATATTTGTTTTGGATT 59.767 33.333 0.00 0.00 0.00 3.01
1525 1559 7.756722 CACCACTCTGATATTTGTTTTGGATTC 59.243 37.037 0.00 0.00 0.00 2.52
1604 1638 2.494870 AGAAATGCCAGTGCCAATTCTC 59.505 45.455 0.00 0.00 36.33 2.87
1619 1653 7.226720 GTGCCAATTCTCGAGGAAAGAATAATA 59.773 37.037 13.56 0.00 41.47 0.98
1620 1654 7.939039 TGCCAATTCTCGAGGAAAGAATAATAT 59.061 33.333 13.56 0.00 41.47 1.28
1621 1655 8.447053 GCCAATTCTCGAGGAAAGAATAATATC 58.553 37.037 13.56 0.00 41.47 1.63
1622 1656 9.494271 CCAATTCTCGAGGAAAGAATAATATCA 57.506 33.333 13.56 0.00 41.47 2.15
1664 1698 7.896811 TGAGCACTTCATCGTCCTATTATATT 58.103 34.615 0.00 0.00 0.00 1.28
1665 1699 7.814587 TGAGCACTTCATCGTCCTATTATATTG 59.185 37.037 0.00 0.00 0.00 1.90
1666 1700 7.896811 AGCACTTCATCGTCCTATTATATTGA 58.103 34.615 0.00 0.00 0.00 2.57
1752 1794 7.180051 TGCCTTTGTAGAATATTTGGTTTCCAT 59.820 33.333 0.00 0.00 31.53 3.41
1818 1860 0.814010 GTGTACCGTCCCCATGCATC 60.814 60.000 0.00 0.00 0.00 3.91
1819 1861 1.227853 GTACCGTCCCCATGCATCC 60.228 63.158 0.00 0.00 0.00 3.51
1820 1862 1.383943 TACCGTCCCCATGCATCCT 60.384 57.895 0.00 0.00 0.00 3.24
1821 1863 0.105401 TACCGTCCCCATGCATCCTA 60.105 55.000 0.00 0.00 0.00 2.94
1822 1864 1.372683 CCGTCCCCATGCATCCTAG 59.627 63.158 0.00 0.00 0.00 3.02
2049 2093 6.038714 GGAAAGAAATCCTTTATCACAGCGAT 59.961 38.462 0.00 0.00 44.63 4.58
2113 2157 5.050091 TCACGCAGAGATTTGAAGAAAAGAC 60.050 40.000 0.00 0.00 0.00 3.01
2155 2199 3.676646 GCAATTTGCTTTCGAGCTTGATT 59.323 39.130 14.11 0.00 40.96 2.57
2174 2218 6.418057 TGATTGTTTGCTAAAAATCACCCT 57.582 33.333 18.77 0.00 0.00 4.34
2180 2224 3.084039 TGCTAAAAATCACCCTGCTGAG 58.916 45.455 0.00 0.00 0.00 3.35
2270 2342 4.346709 TCTTTGGTGAGTGACAATACCAGA 59.653 41.667 5.91 2.14 43.44 3.86
2274 2346 5.630121 TGGTGAGTGACAATACCAGAAAAT 58.370 37.500 2.21 0.00 38.23 1.82
2275 2347 6.774673 TGGTGAGTGACAATACCAGAAAATA 58.225 36.000 2.21 0.00 38.23 1.40
2276 2348 7.227873 TGGTGAGTGACAATACCAGAAAATAA 58.772 34.615 2.21 0.00 38.23 1.40
2277 2349 7.721842 TGGTGAGTGACAATACCAGAAAATAAA 59.278 33.333 2.21 0.00 38.23 1.40
2278 2350 8.739972 GGTGAGTGACAATACCAGAAAATAAAT 58.260 33.333 0.00 0.00 33.42 1.40
2377 2449 2.283145 AGTTGCACAGCTTCCAAGAT 57.717 45.000 0.00 0.00 0.00 2.40
2382 2454 4.226427 TGCACAGCTTCCAAGATAAGAT 57.774 40.909 0.00 0.00 0.00 2.40
2383 2455 5.357742 TGCACAGCTTCCAAGATAAGATA 57.642 39.130 0.00 0.00 0.00 1.98
2384 2456 5.744171 TGCACAGCTTCCAAGATAAGATAA 58.256 37.500 0.00 0.00 0.00 1.75
2385 2457 6.359804 TGCACAGCTTCCAAGATAAGATAAT 58.640 36.000 0.00 0.00 0.00 1.28
2428 2500 7.414436 TGTCTAGTTTTTCTTTTGAACGATGG 58.586 34.615 0.00 0.00 38.30 3.51
2438 2510 1.776662 TGAACGATGGTAGGCTAGCT 58.223 50.000 22.88 9.85 0.00 3.32
2439 2511 2.940158 TGAACGATGGTAGGCTAGCTA 58.060 47.619 22.88 11.00 0.00 3.32
2457 2529 8.679100 GGCTAGCTATATATAATGGTCGATAGG 58.321 40.741 15.72 0.00 0.00 2.57
2469 2544 2.365582 GTCGATAGGCACATTTGGGTT 58.634 47.619 0.00 0.00 43.13 4.11
2470 2545 2.097466 GTCGATAGGCACATTTGGGTTG 59.903 50.000 0.00 0.00 43.13 3.77
2471 2546 2.091541 CGATAGGCACATTTGGGTTGT 58.908 47.619 0.00 0.00 0.00 3.32
2472 2547 2.159393 CGATAGGCACATTTGGGTTGTG 60.159 50.000 0.00 0.00 45.74 3.33
2518 2598 6.330178 AGGTACACCTACTCATAGAAGACT 57.670 41.667 0.00 0.00 46.48 3.24
2724 2804 2.969443 AAGACCGCAAAGTGAATTCG 57.031 45.000 0.04 0.00 0.00 3.34
2775 2855 1.462731 TTGTGTACTACCGTGGCCGT 61.463 55.000 0.00 0.00 0.00 5.68
2864 2945 1.718396 GACAACGGCTTACAGGTACC 58.282 55.000 2.73 2.73 0.00 3.34
2929 3013 8.731275 AATCATGACGTAATCATTTGAGGTTA 57.269 30.769 0.00 0.00 46.54 2.85
2930 3014 8.731275 ATCATGACGTAATCATTTGAGGTTAA 57.269 30.769 0.00 0.00 46.54 2.01
2931 3015 8.731275 TCATGACGTAATCATTTGAGGTTAAT 57.269 30.769 0.00 0.00 46.54 1.40
2932 3016 9.173021 TCATGACGTAATCATTTGAGGTTAATT 57.827 29.630 0.00 0.00 46.54 1.40
2944 3028 7.716799 TTTGAGGTTAATTCCACATATTGCT 57.283 32.000 0.00 0.00 0.00 3.91
3009 3114 3.493129 TGTGTCGGATTTTCAAGAAGACG 59.507 43.478 0.00 0.00 0.00 4.18
3222 3327 1.347707 GGGTTCGGGATGCAGATGATA 59.652 52.381 0.00 0.00 0.00 2.15
3385 3490 9.982651 ATTACAGATGTATACAGAAATAACGCT 57.017 29.630 11.91 0.00 0.00 5.07
3538 3643 1.925888 GCCATTGGAGGTGGAGGAT 59.074 57.895 6.95 0.00 39.12 3.24
3544 3649 0.178846 TGGAGGTGGAGGATTTCCCA 60.179 55.000 0.00 0.00 46.19 4.37
3550 3655 1.285280 TGGAGGATTTCCCACACGAT 58.715 50.000 0.00 0.00 46.19 3.73
3568 3673 1.737201 TGTCAGCCTCGACACGAAA 59.263 52.632 0.00 0.00 40.94 3.46
3637 3742 4.007644 CTGTCAGTGGCCTCGGCA 62.008 66.667 10.51 4.02 44.11 5.69
3667 3772 1.153086 GATCAATGGCTCCGGCAGT 60.153 57.895 0.00 0.00 42.43 4.40
3734 3842 0.108804 CGGCCACTACATGAACGAGT 60.109 55.000 2.24 0.00 31.42 4.18
3832 3940 2.070861 GTCAATGACGAGGCGTGAC 58.929 57.895 0.00 0.00 41.37 3.67
4122 4254 5.642063 CCGCAGAGAATTCAGGTACTTAAAA 59.358 40.000 8.44 0.00 34.60 1.52
4142 4274 9.369904 CTTAAAATTTTGGCTGTAACATATGCT 57.630 29.630 13.76 0.00 0.00 3.79
4156 4306 5.252586 ACATATGCTCTCCATTGGCTTAT 57.747 39.130 1.58 0.00 35.34 1.73
4292 4442 0.536006 CCCCCATCTTCTCGCAATCC 60.536 60.000 0.00 0.00 0.00 3.01
4327 4477 1.062587 CGCTCTTGCTATTGGTTTCGG 59.937 52.381 0.00 0.00 36.97 4.30
4367 4517 2.741211 GACCCCAACGCGTCCTTC 60.741 66.667 14.44 0.96 0.00 3.46
4446 4596 1.808411 GAAGACATTCTTCCACCGCA 58.192 50.000 4.81 0.00 45.34 5.69
4454 4604 4.467084 TTCCACCGCATCGAGCCC 62.467 66.667 0.00 0.00 41.38 5.19
4550 4706 0.788391 CCGTCACGTCCAAAGTTAGC 59.212 55.000 0.00 0.00 0.00 3.09
4706 4865 1.403679 CAGATCGTGTCACTCCTCCTC 59.596 57.143 0.65 0.00 0.00 3.71
4747 4906 1.851658 GAGCGAGAAGAAGAGATGGC 58.148 55.000 0.00 0.00 0.00 4.40
4748 4907 0.102120 AGCGAGAAGAAGAGATGGCG 59.898 55.000 0.00 0.00 0.00 5.69
4759 4930 0.531753 GAGATGGCGAGGAAGAAGGC 60.532 60.000 0.00 0.00 0.00 4.35
4947 5121 0.249155 AAAGGTCGCACGTCTTTCGA 60.249 50.000 0.00 0.00 42.86 3.71
4955 5129 1.057847 GCACGTCTTTCGATTCGACTG 59.942 52.381 8.55 4.80 42.86 3.51
4965 5141 3.270877 TCGATTCGACTGTCTCTGATCA 58.729 45.455 4.29 0.00 0.00 2.92
4966 5142 3.879892 TCGATTCGACTGTCTCTGATCAT 59.120 43.478 4.29 0.00 0.00 2.45
4967 5143 3.973767 CGATTCGACTGTCTCTGATCATG 59.026 47.826 6.21 0.00 0.00 3.07
4968 5144 4.260948 CGATTCGACTGTCTCTGATCATGA 60.261 45.833 6.21 0.00 0.00 3.07
5016 5195 7.859325 TTGTTTGTTTCTTCTACTGTAAGCT 57.141 32.000 0.00 0.00 37.60 3.74
5017 5196 7.478520 TGTTTGTTTCTTCTACTGTAAGCTC 57.521 36.000 0.00 0.00 37.60 4.09
5018 5197 6.200286 TGTTTGTTTCTTCTACTGTAAGCTCG 59.800 38.462 0.00 0.00 37.60 5.03
5019 5198 5.700722 TGTTTCTTCTACTGTAAGCTCGA 57.299 39.130 0.00 0.00 37.60 4.04
5059 5238 2.105134 TCTGTTGATTAACCGGGTGTGT 59.895 45.455 0.00 0.00 35.92 3.72
5060 5239 2.222886 TGTTGATTAACCGGGTGTGTG 58.777 47.619 0.00 0.00 35.92 3.82
5075 5254 1.456892 TGTGACTGGAGGGTGTCGT 60.457 57.895 0.00 0.00 36.10 4.34
5079 5258 2.258591 CTGGAGGGTGTCGTCACG 59.741 66.667 6.71 0.00 44.68 4.35
5085 5264 0.949105 AGGGTGTCGTCACGATTTGC 60.949 55.000 1.61 0.00 44.68 3.68
5225 5412 7.712264 TTTTCCTGCAAAATTGTATTCAGTG 57.288 32.000 0.00 0.00 0.00 3.66
5226 5413 6.403866 TTCCTGCAAAATTGTATTCAGTGT 57.596 33.333 0.00 0.00 0.00 3.55
5227 5414 6.403866 TCCTGCAAAATTGTATTCAGTGTT 57.596 33.333 0.00 0.00 0.00 3.32
5228 5415 6.815089 TCCTGCAAAATTGTATTCAGTGTTT 58.185 32.000 0.00 0.00 0.00 2.83
5229 5416 7.271511 TCCTGCAAAATTGTATTCAGTGTTTT 58.728 30.769 0.00 0.00 0.00 2.43
5230 5417 7.768120 TCCTGCAAAATTGTATTCAGTGTTTTT 59.232 29.630 0.00 0.00 0.00 1.94
5278 5465 2.844362 CCCCGGCCTCTGCATCTA 60.844 66.667 0.00 0.00 40.13 1.98
5282 5469 0.179000 CCGGCCTCTGCATCTAAACT 59.821 55.000 0.00 0.00 40.13 2.66
5347 5534 6.378710 AGGTCTTAAAGTCTGAAAGCAAAC 57.621 37.500 0.00 0.00 0.00 2.93
5413 5601 2.131067 CCCAAAAGCCACAACCGGT 61.131 57.895 0.00 0.00 0.00 5.28
5479 5667 3.088259 CCGCCATCCAAATCGGTTA 57.912 52.632 0.00 0.00 37.33 2.85
5683 5874 1.136305 ACAACGCGCATACTCCTACAT 59.864 47.619 5.73 0.00 0.00 2.29
5873 6064 3.492337 AGCTACACCTAGTAGATCCTGC 58.508 50.000 6.47 0.00 45.93 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.181525 CTTTTTCCATGCCCGGCG 59.818 61.111 4.58 0.00 0.00 6.46
142 143 0.822164 AGGTTGGTACTCGATTCCCG 59.178 55.000 0.00 0.00 40.25 5.14
174 175 1.303236 TCAGCACCCGTTGGAATGG 60.303 57.895 0.00 0.00 34.81 3.16
185 186 1.681486 GGAGAGGCCTAGTCAGCACC 61.681 65.000 4.42 0.00 0.00 5.01
187 188 4.364318 GGAGAGGCCTAGTCAGCA 57.636 61.111 4.42 0.00 0.00 4.41
310 320 3.798954 CTAGCTACGGCCTGGCTGC 62.799 68.421 27.03 19.87 37.28 5.25
311 321 2.127869 TCTAGCTACGGCCTGGCTG 61.128 63.158 25.62 25.62 37.28 4.85
312 322 2.128507 GTCTAGCTACGGCCTGGCT 61.129 63.158 19.68 15.30 40.47 4.75
321 331 1.068194 CATGCCTAGCCGTCTAGCTAC 60.068 57.143 0.00 0.00 42.70 3.58
325 335 0.319383 CTGCATGCCTAGCCGTCTAG 60.319 60.000 16.68 0.00 41.52 2.43
375 389 7.308830 GGAAATGAAATATCCCAATCTTCTCCG 60.309 40.741 0.00 0.00 0.00 4.63
391 405 7.493499 TTTGTGTATGGGATGGAAATGAAAT 57.507 32.000 0.00 0.00 0.00 2.17
392 406 6.924913 TTTGTGTATGGGATGGAAATGAAA 57.075 33.333 0.00 0.00 0.00 2.69
393 407 6.574073 GCTTTTGTGTATGGGATGGAAATGAA 60.574 38.462 0.00 0.00 0.00 2.57
394 408 5.105392 GCTTTTGTGTATGGGATGGAAATGA 60.105 40.000 0.00 0.00 0.00 2.57
395 409 5.111293 GCTTTTGTGTATGGGATGGAAATG 58.889 41.667 0.00 0.00 0.00 2.32
401 415 3.738899 GCATGGCTTTTGTGTATGGGATG 60.739 47.826 0.00 0.00 0.00 3.51
432 446 2.180131 CTTTGTGCTGCGTCAGGCTC 62.180 60.000 8.57 3.87 44.05 4.70
433 447 2.203195 TTTGTGCTGCGTCAGGCT 60.203 55.556 8.57 0.00 44.05 4.58
434 448 2.253452 CTTTGTGCTGCGTCAGGC 59.747 61.111 8.57 0.00 43.96 4.85
475 489 1.261238 CCCTGTCCCTGTCTCTGTCC 61.261 65.000 0.00 0.00 0.00 4.02
477 491 0.252012 CTCCCTGTCCCTGTCTCTGT 60.252 60.000 0.00 0.00 0.00 3.41
478 492 0.040351 TCTCCCTGTCCCTGTCTCTG 59.960 60.000 0.00 0.00 0.00 3.35
504 526 2.803451 CTCGGATTCTTCTCGTCCTTG 58.197 52.381 0.00 0.00 0.00 3.61
507 529 0.592754 CGCTCGGATTCTTCTCGTCC 60.593 60.000 0.00 0.00 0.00 4.79
535 560 1.708822 CTTGTGGGGTTATTTTGCGC 58.291 50.000 0.00 0.00 0.00 6.09
537 562 3.325870 GAAGCTTGTGGGGTTATTTTGC 58.674 45.455 2.10 0.00 0.00 3.68
576 601 3.744155 GGAAAGGGGCAGAGGGGG 61.744 72.222 0.00 0.00 0.00 5.40
609 634 2.666317 GAGAGGAGGAAGAAGGGAGAG 58.334 57.143 0.00 0.00 0.00 3.20
610 635 1.289530 GGAGAGGAGGAAGAAGGGAGA 59.710 57.143 0.00 0.00 0.00 3.71
611 636 1.691163 GGGAGAGGAGGAAGAAGGGAG 60.691 61.905 0.00 0.00 0.00 4.30
614 639 0.692756 GGGGGAGAGGAGGAAGAAGG 60.693 65.000 0.00 0.00 0.00 3.46
680 706 1.630333 ATGAGGAGGAGGAGGGGGA 60.630 63.158 0.00 0.00 0.00 4.81
683 709 0.767446 ATGCATGAGGAGGAGGAGGG 60.767 60.000 0.00 0.00 0.00 4.30
688 714 1.894466 AGATCGATGCATGAGGAGGAG 59.106 52.381 2.46 0.00 0.00 3.69
708 734 5.921962 TTTAGATGAGCAAGCAGTAGAGA 57.078 39.130 0.00 0.00 0.00 3.10
709 735 6.018098 CCAATTTAGATGAGCAAGCAGTAGAG 60.018 42.308 0.00 0.00 0.00 2.43
713 739 4.338879 ACCAATTTAGATGAGCAAGCAGT 58.661 39.130 0.00 0.00 0.00 4.40
714 740 4.978083 ACCAATTTAGATGAGCAAGCAG 57.022 40.909 0.00 0.00 0.00 4.24
715 741 4.082081 CCAACCAATTTAGATGAGCAAGCA 60.082 41.667 0.00 0.00 0.00 3.91
716 742 4.082026 ACCAACCAATTTAGATGAGCAAGC 60.082 41.667 0.00 0.00 0.00 4.01
717 743 5.649782 ACCAACCAATTTAGATGAGCAAG 57.350 39.130 0.00 0.00 0.00 4.01
718 744 6.267471 AGAAACCAACCAATTTAGATGAGCAA 59.733 34.615 0.00 0.00 0.00 3.91
728 754 8.088365 GCATAGAAAGTAGAAACCAACCAATTT 58.912 33.333 0.00 0.00 0.00 1.82
782 808 4.404073 TGTACAAAACCTGCAAGTTCCAAT 59.596 37.500 0.14 0.00 0.00 3.16
783 809 3.764434 TGTACAAAACCTGCAAGTTCCAA 59.236 39.130 0.14 0.00 0.00 3.53
784 810 3.357203 TGTACAAAACCTGCAAGTTCCA 58.643 40.909 0.14 0.00 0.00 3.53
785 811 4.584327 ATGTACAAAACCTGCAAGTTCC 57.416 40.909 0.14 0.00 0.00 3.62
786 812 5.810074 ACAAATGTACAAAACCTGCAAGTTC 59.190 36.000 0.14 0.00 0.00 3.01
787 813 5.729510 ACAAATGTACAAAACCTGCAAGTT 58.270 33.333 0.00 0.00 0.00 2.66
788 814 5.337578 ACAAATGTACAAAACCTGCAAGT 57.662 34.783 0.00 0.00 0.00 3.16
835 863 3.242867 AGAACAGCCAGCCAGCTATATA 58.757 45.455 0.00 0.00 42.61 0.86
836 864 2.053244 AGAACAGCCAGCCAGCTATAT 58.947 47.619 0.00 0.00 42.61 0.86
856 884 4.033776 GCCACACCAGCCCTGCTA 62.034 66.667 0.00 0.00 36.40 3.49
982 1010 5.506317 GCGCCATGAATCTGCTTATTAACTT 60.506 40.000 0.00 0.00 0.00 2.66
983 1011 4.023707 GCGCCATGAATCTGCTTATTAACT 60.024 41.667 0.00 0.00 0.00 2.24
984 1012 4.222114 GCGCCATGAATCTGCTTATTAAC 58.778 43.478 0.00 0.00 0.00 2.01
985 1013 3.253188 GGCGCCATGAATCTGCTTATTAA 59.747 43.478 24.80 0.00 0.00 1.40
986 1014 2.813754 GGCGCCATGAATCTGCTTATTA 59.186 45.455 24.80 0.00 0.00 0.98
987 1015 1.610522 GGCGCCATGAATCTGCTTATT 59.389 47.619 24.80 0.00 0.00 1.40
988 1016 1.242076 GGCGCCATGAATCTGCTTAT 58.758 50.000 24.80 0.00 0.00 1.73
989 1017 1.159713 CGGCGCCATGAATCTGCTTA 61.160 55.000 28.98 0.00 0.00 3.09
990 1018 2.475466 CGGCGCCATGAATCTGCTT 61.475 57.895 28.98 0.00 0.00 3.91
1041 1069 3.936585 GATGAGCTCCTCGTCAGTC 57.063 57.895 12.15 0.00 43.66 3.51
1177 1206 9.431887 GCCAATACGAACATATTTCTATTAGGA 57.568 33.333 0.00 0.00 0.00 2.94
1178 1207 9.214957 TGCCAATACGAACATATTTCTATTAGG 57.785 33.333 0.00 0.00 0.00 2.69
1180 1209 9.772973 AGTGCCAATACGAACATATTTCTATTA 57.227 29.630 0.00 0.00 0.00 0.98
1181 1210 8.677148 AGTGCCAATACGAACATATTTCTATT 57.323 30.769 0.00 0.00 0.00 1.73
1183 1212 7.384115 GCTAGTGCCAATACGAACATATTTCTA 59.616 37.037 0.00 0.00 0.00 2.10
1185 1214 6.202954 AGCTAGTGCCAATACGAACATATTTC 59.797 38.462 0.00 0.00 40.80 2.17
1186 1215 6.055588 AGCTAGTGCCAATACGAACATATTT 58.944 36.000 0.00 0.00 40.80 1.40
1187 1216 5.611374 AGCTAGTGCCAATACGAACATATT 58.389 37.500 0.00 0.00 40.80 1.28
1188 1217 5.215252 AGCTAGTGCCAATACGAACATAT 57.785 39.130 0.00 0.00 40.80 1.78
1190 1219 3.543680 AGCTAGTGCCAATACGAACAT 57.456 42.857 0.00 0.00 40.80 2.71
1192 1221 2.795470 GCTAGCTAGTGCCAATACGAAC 59.205 50.000 21.62 0.00 40.80 3.95
1194 1223 2.293677 GAGCTAGCTAGTGCCAATACGA 59.706 50.000 19.38 0.00 40.80 3.43
1195 1224 2.608261 GGAGCTAGCTAGTGCCAATACG 60.608 54.545 19.38 0.00 40.80 3.06
1196 1225 2.630580 AGGAGCTAGCTAGTGCCAATAC 59.369 50.000 25.84 0.19 40.80 1.89
1197 1226 2.630098 CAGGAGCTAGCTAGTGCCAATA 59.370 50.000 25.84 0.00 40.80 1.90
1201 1230 1.337118 ATCAGGAGCTAGCTAGTGCC 58.663 55.000 19.38 20.75 40.80 5.01
1202 1231 3.823873 TCTAATCAGGAGCTAGCTAGTGC 59.176 47.826 19.38 13.41 40.05 4.40
1203 1232 5.070001 ACTCTAATCAGGAGCTAGCTAGTG 58.930 45.833 19.38 17.61 34.46 2.74
1204 1233 5.319043 ACTCTAATCAGGAGCTAGCTAGT 57.681 43.478 19.38 11.20 34.46 2.57
1205 1234 7.938140 AATACTCTAATCAGGAGCTAGCTAG 57.062 40.000 19.38 16.84 34.46 3.42
1206 1235 7.945109 TGAAATACTCTAATCAGGAGCTAGCTA 59.055 37.037 19.38 1.43 34.46 3.32
1237 1270 2.331194 CTTACACGGACGTAGGGTTTG 58.669 52.381 3.66 0.00 0.00 2.93
1251 1284 5.449177 GGGAATTAACTGCTGATGCTTACAC 60.449 44.000 0.00 0.00 40.48 2.90
1309 1342 6.059484 CCCAAAGTTTCTACTGAAGTTGGTA 58.941 40.000 0.00 0.00 37.98 3.25
1311 1344 4.278419 CCCCAAAGTTTCTACTGAAGTTGG 59.722 45.833 0.00 0.00 38.62 3.77
1327 1360 5.066593 GCTTGTATCTCCTTATCCCCAAAG 58.933 45.833 0.00 0.00 0.00 2.77
1331 1364 2.633481 ACGCTTGTATCTCCTTATCCCC 59.367 50.000 0.00 0.00 0.00 4.81
1346 1380 2.218603 ACTACCAGTTTGGAACGCTTG 58.781 47.619 1.40 0.00 40.96 4.01
1379 1413 9.167311 GCTATCTTCTGTCCAAAAGAGAATTTA 57.833 33.333 0.00 0.00 36.73 1.40
1380 1414 7.667219 TGCTATCTTCTGTCCAAAAGAGAATTT 59.333 33.333 0.00 0.00 36.73 1.82
1385 1419 5.486526 ACTGCTATCTTCTGTCCAAAAGAG 58.513 41.667 0.00 0.00 35.13 2.85
1392 1426 6.749923 AATTCAAACTGCTATCTTCTGTCC 57.250 37.500 0.00 0.00 0.00 4.02
1437 1471 6.985645 GCAGTGCAAAATCCCATAATTAATCA 59.014 34.615 11.09 0.00 0.00 2.57
1524 1558 4.651778 CTTAATGTCTTCACAACAGGGGA 58.348 43.478 0.00 0.00 35.64 4.81
1525 1559 3.191371 GCTTAATGTCTTCACAACAGGGG 59.809 47.826 0.00 0.00 35.64 4.79
1604 1638 8.552034 GGAACTTGTGATATTATTCTTTCCTCG 58.448 37.037 0.00 0.00 0.00 4.63
1664 1698 7.149202 ACAAGGGCCAGTTAATATTAGATCA 57.851 36.000 6.18 0.00 0.00 2.92
1665 1699 7.719633 TGAACAAGGGCCAGTTAATATTAGATC 59.280 37.037 13.40 0.15 0.00 2.75
1666 1700 7.582719 TGAACAAGGGCCAGTTAATATTAGAT 58.417 34.615 13.40 0.00 0.00 1.98
1729 1769 8.748412 TGGATGGAAACCAAATATTCTACAAAG 58.252 33.333 0.00 0.00 34.98 2.77
1787 1829 7.240897 TGGGGACGGTACACTAAACTATATAT 58.759 38.462 0.00 0.00 0.00 0.86
1788 1830 6.609876 TGGGGACGGTACACTAAACTATATA 58.390 40.000 0.00 0.00 0.00 0.86
1822 1864 0.951040 ACACAAACAGAGCGCTAGGC 60.951 55.000 11.50 0.00 44.05 3.93
1958 2002 6.780522 TGGCCTTTACACTTAGGAGAATTTTT 59.219 34.615 3.32 0.00 33.13 1.94
2155 2199 3.640967 AGCAGGGTGATTTTTAGCAAACA 59.359 39.130 0.00 0.00 0.00 2.83
2180 2224 0.030638 ACCAGTTTCACGCAATGCAC 59.969 50.000 5.91 0.00 0.00 4.57
2233 2278 5.123227 TCACCAAAGAAGAACAGACGAATT 58.877 37.500 0.00 0.00 0.00 2.17
2237 2282 3.246226 CACTCACCAAAGAAGAACAGACG 59.754 47.826 0.00 0.00 0.00 4.18
2240 2285 4.191544 TGTCACTCACCAAAGAAGAACAG 58.808 43.478 0.00 0.00 0.00 3.16
2277 2349 8.718734 GGTCATCTTTAAACTCACGTTCTTAAT 58.281 33.333 0.00 0.00 31.66 1.40
2278 2350 7.929785 AGGTCATCTTTAAACTCACGTTCTTAA 59.070 33.333 0.00 0.00 31.66 1.85
2279 2351 7.439381 AGGTCATCTTTAAACTCACGTTCTTA 58.561 34.615 0.00 0.00 31.66 2.10
2280 2352 6.289064 AGGTCATCTTTAAACTCACGTTCTT 58.711 36.000 0.00 0.00 31.66 2.52
2281 2353 5.855045 AGGTCATCTTTAAACTCACGTTCT 58.145 37.500 0.00 0.00 31.66 3.01
2282 2354 7.384387 ACTTAGGTCATCTTTAAACTCACGTTC 59.616 37.037 0.00 0.00 31.66 3.95
2283 2355 7.215085 ACTTAGGTCATCTTTAAACTCACGTT 58.785 34.615 0.00 0.00 34.03 3.99
2284 2356 6.756221 ACTTAGGTCATCTTTAAACTCACGT 58.244 36.000 0.00 0.00 0.00 4.49
2285 2357 6.866770 TGACTTAGGTCATCTTTAAACTCACG 59.133 38.462 3.11 0.00 46.19 4.35
2428 2500 8.618702 TCGACCATTATATATAGCTAGCCTAC 57.381 38.462 12.13 0.00 0.00 3.18
2439 2511 9.330063 CAAATGTGCCTATCGACCATTATATAT 57.670 33.333 0.00 0.00 0.00 0.86
2466 2541 5.818136 TGATTAGAGCTAATTGCACAACC 57.182 39.130 4.40 0.00 45.94 3.77
2467 2542 6.183360 ACCATGATTAGAGCTAATTGCACAAC 60.183 38.462 4.40 0.00 45.94 3.32
2469 2544 5.439721 ACCATGATTAGAGCTAATTGCACA 58.560 37.500 4.40 0.00 45.94 4.57
2470 2545 6.382869 AACCATGATTAGAGCTAATTGCAC 57.617 37.500 4.40 0.00 45.94 4.57
2471 2546 7.229306 CCTTAACCATGATTAGAGCTAATTGCA 59.771 37.037 4.40 0.35 45.94 4.08
2472 2547 7.229506 ACCTTAACCATGATTAGAGCTAATTGC 59.770 37.037 4.40 0.00 43.29 3.56
2550 2630 2.839228 AGGTAAGGGAGAAGTCATGCT 58.161 47.619 0.00 0.00 0.00 3.79
2724 2804 1.227999 TACCAACTGCACGCTTCTGC 61.228 55.000 0.00 0.00 37.70 4.26
2864 2945 6.777213 AGAACTGTAGTAGGGAGTAATGTG 57.223 41.667 0.00 0.00 0.00 3.21
2929 3013 7.112122 TGTTAGTCTGAGCAATATGTGGAATT 58.888 34.615 0.00 0.00 0.00 2.17
2930 3014 6.653020 TGTTAGTCTGAGCAATATGTGGAAT 58.347 36.000 0.00 0.00 0.00 3.01
2931 3015 6.048732 TGTTAGTCTGAGCAATATGTGGAA 57.951 37.500 0.00 0.00 0.00 3.53
2932 3016 5.675684 TGTTAGTCTGAGCAATATGTGGA 57.324 39.130 0.00 0.00 0.00 4.02
2944 3028 6.767524 ACAAAACCATGTTTGTTAGTCTGA 57.232 33.333 8.26 0.00 46.97 3.27
3060 3165 4.803426 GTCCACTGAGGCGGCTCG 62.803 72.222 30.84 26.15 37.29 5.03
3065 3170 3.057547 CTCGGAGTCCACTGAGGCG 62.058 68.421 10.49 0.00 38.99 5.52
3102 3207 1.270839 CCTCTTCCATCACACGGTGTT 60.271 52.381 11.82 0.00 34.79 3.32
3198 3303 3.995506 CTGCATCCCGAACCCACCC 62.996 68.421 0.00 0.00 0.00 4.61
3385 3490 7.828508 TTACTACCTGAAGTCTGAAACAGTA 57.171 36.000 0.00 0.00 32.61 2.74
3459 3564 0.740868 AACATCCACCTGCATCGACG 60.741 55.000 0.00 0.00 0.00 5.12
3509 3614 2.676121 CAATGGCGGCAGGGTCAA 60.676 61.111 19.29 0.00 0.00 3.18
3512 3617 4.431131 CTCCAATGGCGGCAGGGT 62.431 66.667 25.30 9.19 0.00 4.34
3538 3643 0.605319 GGCTGACATCGTGTGGGAAA 60.605 55.000 0.00 0.00 0.00 3.13
3544 3649 1.213013 GTCGAGGCTGACATCGTGT 59.787 57.895 0.00 0.00 39.86 4.49
3550 3655 0.103390 TTTTCGTGTCGAGGCTGACA 59.897 50.000 13.41 13.41 46.15 3.58
3568 3673 1.264749 TGCTCTGGAGTATGCCGGTT 61.265 55.000 1.90 0.00 35.72 4.44
3601 3706 2.907892 AGGAACTCCTGGAGAATGTCA 58.092 47.619 29.71 0.00 46.55 3.58
3625 3730 2.685017 TGAGATGCCGAGGCCACT 60.685 61.111 12.05 10.43 41.09 4.00
3637 3742 2.224572 GCCATTGATCAGCTCCTGAGAT 60.225 50.000 0.00 0.00 44.08 2.75
3667 3772 2.899900 CCACATATCAGGGTAGCTGCTA 59.100 50.000 5.02 5.02 0.00 3.49
3734 3842 2.420372 CGAGATCAACGAGAGAGGACAA 59.580 50.000 6.49 0.00 0.00 3.18
3822 3930 3.164011 GTTCGTCGTCACGCCTCG 61.164 66.667 0.00 0.00 46.28 4.63
4122 4254 5.300286 GGAGAGCATATGTTACAGCCAAAAT 59.700 40.000 4.29 0.00 0.00 1.82
4156 4306 3.759086 CACCTCTGTGTACAAGAGCTAGA 59.241 47.826 20.64 9.04 37.72 2.43
4169 4319 1.669115 CGTGAAGGCCACCTCTGTG 60.669 63.158 5.01 0.00 42.76 3.66
4170 4320 2.743718 CGTGAAGGCCACCTCTGT 59.256 61.111 5.01 0.00 42.76 3.41
4178 4328 1.305219 TTAGTGCATGCGTGAAGGCC 61.305 55.000 14.09 0.00 0.00 5.19
4292 4442 2.811317 GCGAAGTCGTCAGGCTGG 60.811 66.667 15.73 0.00 42.22 4.85
4367 4517 3.690745 ACCTTCCCGTACAGGTCG 58.309 61.111 0.00 0.00 39.37 4.79
4446 4596 2.435693 CCTTCTTCGGGGGCTCGAT 61.436 63.158 4.59 0.00 39.03 3.59
4454 4604 3.145228 GAAGCTGACCTTCTTCGGG 57.855 57.895 0.00 0.00 45.27 5.14
4550 4706 2.290093 GCTACTGCTACTACCACTACCG 59.710 54.545 0.00 0.00 36.03 4.02
4665 4824 2.378858 GCAGCTCACTCACTGTCGC 61.379 63.158 0.00 0.00 36.26 5.19
4706 4865 3.599285 TACGGCTTCCTTGGGTGCG 62.599 63.158 0.00 0.00 0.00 5.34
4747 4906 1.811679 GGCTTCGCCTTCTTCCTCG 60.812 63.158 0.00 0.00 46.69 4.63
4748 4907 4.210307 GGCTTCGCCTTCTTCCTC 57.790 61.111 0.00 0.00 46.69 3.71
4947 5121 5.588958 TTCATGATCAGAGACAGTCGAAT 57.411 39.130 0.09 0.00 0.00 3.34
4955 5129 9.979578 AATAAGTAGTCATTCATGATCAGAGAC 57.020 33.333 0.09 4.80 39.30 3.36
5016 5195 2.771639 AAGCGCCGCTACTGATCGA 61.772 57.895 14.02 0.00 38.25 3.59
5017 5196 2.278857 AAGCGCCGCTACTGATCG 60.279 61.111 14.02 0.00 38.25 3.69
5018 5197 2.875786 GCAAGCGCCGCTACTGATC 61.876 63.158 14.02 0.00 38.25 2.92
5019 5198 2.892425 GCAAGCGCCGCTACTGAT 60.892 61.111 14.02 0.00 38.25 2.90
5059 5238 1.152631 TGACGACACCCTCCAGTCA 60.153 57.895 0.00 0.00 39.21 3.41
5060 5239 1.289380 GTGACGACACCCTCCAGTC 59.711 63.158 6.77 0.00 40.74 3.51
5075 5254 3.182538 ACGTACGTGCAAATCGTGA 57.817 47.368 22.14 0.00 41.62 4.35
5202 5389 6.815089 ACACTGAATACAATTTTGCAGGAAA 58.185 32.000 0.00 0.00 0.00 3.13
5237 5424 5.941058 GTGTCCCCCTTTTTGAAAAGAAAAA 59.059 36.000 15.79 0.00 46.39 1.94
5242 5429 3.469008 GGTGTCCCCCTTTTTGAAAAG 57.531 47.619 8.83 8.83 43.82 2.27
5347 5534 2.421424 GTGTGAGCTGGCCATTTTCTAG 59.579 50.000 5.51 0.00 0.00 2.43
5413 5601 8.189119 AGTTTTCCTATCTTTTGTTATGCCAA 57.811 30.769 0.00 0.00 0.00 4.52
5479 5667 1.045407 TGGTAGCGCGGGATATCTTT 58.955 50.000 8.83 0.00 0.00 2.52
5545 5733 2.391926 TGTGGTCCTTACTCACTCCA 57.608 50.000 0.00 0.00 31.73 3.86
5631 5822 7.118101 GCAATTTGAAACTGCAGGAATGATTTA 59.882 33.333 19.93 0.00 36.09 1.40
5683 5874 3.006430 TCCGAAACAGCTAGACACATTCA 59.994 43.478 0.00 0.00 0.00 2.57
5758 5949 5.580297 CCGTGCAAATTGCCTTTAACATTAT 59.420 36.000 15.98 0.00 44.23 1.28
5873 6064 3.508744 ATTTGATTAAGCGCAACTGGG 57.491 42.857 11.47 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.