Multiple sequence alignment - TraesCS2A01G146600

Loading Multiple Alignment...

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 TraesCS2A01G146600 chr2A 100.000 4084 0 0 1 4084 92319358 92315275 0.000000e+00 7542
1 TraesCS2A01G146600 chr2B 93.284 3082 115 43 759 3795 146442787 146439753 0.000000e+00 4460
2 TraesCS2A01G146600 chr2B 95.937 443 9 6 295 731 146443193 146442754 0.000000e+00 710
3 TraesCS2A01G146600 chr2B 88.214 280 29 3 3799 4077 146439834 146439558 8.460000e-87 331
4 TraesCS2A01G146600 chr2B 94.472 199 11 0 1 199 146443414 146443216 1.430000e-79 307
5 TraesCS2A01G146600 chr2D 92.690 2011 85 27 1809 3795 94318468 94316496 0.000000e+00 2843
6 TraesCS2A01G146600 chr2D 89.499 1057 39 32 749 1776 94319752 94318739 0.000000e+00 1271
7 TraesCS2A01G146600 chr2D 93.952 463 6 12 295 751 94320149 94319703 0.000000e+00 680
8 TraesCS2A01G146600 chr2D 87.031 293 29 6 3799 4084 94316576 94316286 5.090000e-84 322
9 TraesCS2A01G146600 chr2D 92.891 211 11 4 1 210 94320368 94320161 1.840000e-78 303
10 TraesCS2A01G146600 chr5B 85.965 285 34 4 36 315 671705217 671704934 2.390000e-77 300
11 TraesCS2A01G146600 chr5B 86.634 202 24 2 1096 1294 416851135 416850934 1.910000e-53 220
12 TraesCS2A01G146600 chr5A 87.624 202 22 2 1096 1294 453877115 453876914 8.830000e-57 231
13 TraesCS2A01G146600 chr5D 86.634 202 24 2 1096 1294 352219245 352219446 1.910000e-53 220
14 TraesCS2A01G146600 chr5D 83.598 189 31 0 1105 1293 558247758 558247570 1.170000e-40 178
15 TraesCS2A01G146600 chr4A 84.656 189 29 0 1105 1293 610490449 610490261 5.390000e-44 189
16 TraesCS2A01G146600 chr1D 83.957 187 28 2 1105 1290 439022280 439022465 1.170000e-40 178
17 TraesCS2A01G146600 chr1B 83.957 187 28 2 1105 1290 595176892 595177077 1.170000e-40 178


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 TraesCS2A01G146600 chr2A 92315275 92319358 4083 True 7542.0 7542 100.00000 1 4084 1 chr2A.!!$R1 4083
1 TraesCS2A01G146600 chr2B 146439558 146443414 3856 True 1452.0 4460 92.97675 1 4077 4 chr2B.!!$R1 4076
2 TraesCS2A01G146600 chr2D 94316286 94320368 4082 True 1083.8 2843 91.21260 1 4084 5 chr2D.!!$R1 4083

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
464 471 0.178992 CCTTCCAGCACCACCTTTGA 60.179 55.0 0.0 0.0 0.0 2.69 F
1417 1463 0.249398 TCTTCCTCCGGTTTGCTAGC 59.751 55.0 8.1 8.1 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1467 0.680601 TACACGCCATGGACGACCTA 60.681 55.0 27.68 14.19 37.04 3.08 R
3300 3620 1.148310 GCAAGCAGCAAACTACTCGA 58.852 50.0 0.00 0.00 44.79 4.04 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
88 90 3.743396 CCTTGCACTGTTTGACTAGTCTC 59.257 47.826 23.01 13.66 0.00 3.36
94 96 5.368989 CACTGTTTGACTAGTCTCCCTTTT 58.631 41.667 23.01 0.56 0.00 2.27
163 165 1.202604 TGACGTGGGTCTGAGAAAACC 60.203 52.381 0.00 0.00 43.79 3.27
186 188 1.336517 CCTTGACCATTTGCACTGCAG 60.337 52.381 13.48 13.48 40.61 4.41
204 206 3.044235 CAGTTTTGGAGGAAAATGCCC 57.956 47.619 0.00 0.00 35.96 5.36
210 212 0.688749 GGAGGAAAATGCCCCATGCT 60.689 55.000 0.00 0.00 42.00 3.79
211 213 1.197812 GAGGAAAATGCCCCATGCTT 58.802 50.000 0.00 0.00 42.00 3.91
212 214 1.556451 GAGGAAAATGCCCCATGCTTT 59.444 47.619 0.00 0.00 42.00 3.51
213 215 2.765699 GAGGAAAATGCCCCATGCTTTA 59.234 45.455 0.00 0.00 42.00 1.85
214 216 2.767960 AGGAAAATGCCCCATGCTTTAG 59.232 45.455 0.00 0.00 42.00 1.85
215 217 2.501316 GGAAAATGCCCCATGCTTTAGT 59.499 45.455 0.00 0.00 42.00 2.24
216 218 3.704061 GGAAAATGCCCCATGCTTTAGTA 59.296 43.478 0.00 0.00 42.00 1.82
236 238 8.773404 TTAGTAGCATACAAGTTTTTCTCTCC 57.227 34.615 0.00 0.00 46.26 3.71
237 239 6.174049 AGTAGCATACAAGTTTTTCTCTCCC 58.826 40.000 0.00 0.00 46.26 4.30
238 240 4.985538 AGCATACAAGTTTTTCTCTCCCA 58.014 39.130 0.00 0.00 0.00 4.37
239 241 5.385198 AGCATACAAGTTTTTCTCTCCCAA 58.615 37.500 0.00 0.00 0.00 4.12
240 242 5.474876 AGCATACAAGTTTTTCTCTCCCAAG 59.525 40.000 0.00 0.00 0.00 3.61
241 243 5.473504 GCATACAAGTTTTTCTCTCCCAAGA 59.526 40.000 0.00 0.00 0.00 3.02
242 244 6.016276 GCATACAAGTTTTTCTCTCCCAAGAA 60.016 38.462 0.00 0.00 33.50 2.52
243 245 7.470009 GCATACAAGTTTTTCTCTCCCAAGAAA 60.470 37.037 0.00 0.00 42.12 2.52
244 246 8.579863 CATACAAGTTTTTCTCTCCCAAGAAAT 58.420 33.333 0.35 0.00 43.02 2.17
245 247 7.423844 ACAAGTTTTTCTCTCCCAAGAAATT 57.576 32.000 0.35 0.00 43.02 1.82
246 248 8.533569 ACAAGTTTTTCTCTCCCAAGAAATTA 57.466 30.769 0.35 0.00 43.02 1.40
247 249 8.633561 ACAAGTTTTTCTCTCCCAAGAAATTAG 58.366 33.333 0.35 0.00 43.02 1.73
248 250 8.633561 CAAGTTTTTCTCTCCCAAGAAATTAGT 58.366 33.333 0.35 0.00 43.02 2.24
249 251 9.862149 AAGTTTTTCTCTCCCAAGAAATTAGTA 57.138 29.630 0.35 0.00 43.02 1.82
250 252 9.508642 AGTTTTTCTCTCCCAAGAAATTAGTAG 57.491 33.333 0.35 0.00 43.02 2.57
251 253 7.923414 TTTTCTCTCCCAAGAAATTAGTAGC 57.077 36.000 0.35 0.00 43.02 3.58
252 254 6.620877 TTCTCTCCCAAGAAATTAGTAGCA 57.379 37.500 0.00 0.00 32.42 3.49
253 255 6.620877 TCTCTCCCAAGAAATTAGTAGCAA 57.379 37.500 0.00 0.00 0.00 3.91
254 256 7.016153 TCTCTCCCAAGAAATTAGTAGCAAA 57.984 36.000 0.00 0.00 0.00 3.68
255 257 7.458397 TCTCTCCCAAGAAATTAGTAGCAAAA 58.542 34.615 0.00 0.00 0.00 2.44
256 258 8.109634 TCTCTCCCAAGAAATTAGTAGCAAAAT 58.890 33.333 0.00 0.00 0.00 1.82
257 259 9.396022 CTCTCCCAAGAAATTAGTAGCAAAATA 57.604 33.333 0.00 0.00 0.00 1.40
258 260 9.920946 TCTCCCAAGAAATTAGTAGCAAAATAT 57.079 29.630 0.00 0.00 0.00 1.28
259 261 9.956720 CTCCCAAGAAATTAGTAGCAAAATATG 57.043 33.333 0.00 0.00 0.00 1.78
260 262 9.474313 TCCCAAGAAATTAGTAGCAAAATATGT 57.526 29.630 0.00 0.00 0.00 2.29
288 290 9.981460 TCATAGCTATACATAAATCTGGAGAGA 57.019 33.333 5.77 0.00 0.00 3.10
293 295 9.801873 GCTATACATAAATCTGGAGAGATCTTC 57.198 37.037 0.00 0.00 38.03 2.87
367 373 3.872696 TGCACATTGACCAGTACTATGG 58.127 45.455 0.00 0.00 46.47 2.74
462 469 0.555769 TTCCTTCCAGCACCACCTTT 59.444 50.000 0.00 0.00 0.00 3.11
464 471 0.178992 CCTTCCAGCACCACCTTTGA 60.179 55.000 0.00 0.00 0.00 2.69
465 472 1.691196 CTTCCAGCACCACCTTTGAA 58.309 50.000 0.00 0.00 0.00 2.69
710 736 2.616330 GGGGCGTGTCATGTGTGTG 61.616 63.158 0.00 0.00 0.00 3.82
711 737 1.891919 GGGCGTGTCATGTGTGTGT 60.892 57.895 0.00 0.00 0.00 3.72
712 738 1.279539 GGCGTGTCATGTGTGTGTG 59.720 57.895 0.00 0.00 0.00 3.82
713 739 1.436195 GGCGTGTCATGTGTGTGTGT 61.436 55.000 0.00 0.00 0.00 3.72
714 740 0.316114 GCGTGTCATGTGTGTGTGTG 60.316 55.000 0.00 0.00 0.00 3.82
715 741 1.006086 CGTGTCATGTGTGTGTGTGT 58.994 50.000 0.00 0.00 0.00 3.72
716 742 1.267483 CGTGTCATGTGTGTGTGTGTG 60.267 52.381 0.00 0.00 0.00 3.82
717 743 1.737236 GTGTCATGTGTGTGTGTGTGT 59.263 47.619 0.00 0.00 0.00 3.72
718 744 1.736681 TGTCATGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
719 745 1.737236 GTCATGTGTGTGTGTGTGTGT 59.263 47.619 0.00 0.00 0.00 3.72
720 746 1.736681 TCATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
721 747 1.468127 CATGTGTGTGTGTGTGTGTGT 59.532 47.619 0.00 0.00 0.00 3.72
722 748 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
723 749 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
724 750 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
725 751 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
726 752 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
727 753 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
728 754 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
729 755 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
730 756 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
731 757 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
732 758 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
733 759 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
734 760 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
735 761 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
736 762 1.393539 GTGTGTGTGTGTGTGTGTCTC 59.606 52.381 0.00 0.00 0.00 3.36
737 763 1.275010 TGTGTGTGTGTGTGTGTCTCT 59.725 47.619 0.00 0.00 0.00 3.10
738 764 1.660607 GTGTGTGTGTGTGTGTCTCTG 59.339 52.381 0.00 0.00 0.00 3.35
739 765 1.275010 TGTGTGTGTGTGTGTCTCTGT 59.725 47.619 0.00 0.00 0.00 3.41
740 766 1.660607 GTGTGTGTGTGTGTCTCTGTG 59.339 52.381 0.00 0.00 0.00 3.66
741 767 1.275010 TGTGTGTGTGTGTCTCTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
742 768 1.660607 GTGTGTGTGTGTCTCTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
743 769 1.275010 TGTGTGTGTGTCTCTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
744 770 1.660607 GTGTGTGTGTCTCTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
745 771 1.275010 TGTGTGTGTCTCTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
746 772 1.660607 GTGTGTGTCTCTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
747 773 1.275010 TGTGTGTCTCTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
748 774 1.660607 GTGTGTCTCTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
749 775 1.275010 TGTGTCTCTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
750 776 1.660607 GTGTCTCTGTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
751 777 1.275010 TGTCTCTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
752 778 1.927174 GTCTCTGTGTGTGTGTGTGTC 59.073 52.381 0.00 0.00 0.00 3.67
753 779 1.824852 TCTCTGTGTGTGTGTGTGTCT 59.175 47.619 0.00 0.00 0.00 3.41
754 780 1.929169 CTCTGTGTGTGTGTGTGTCTG 59.071 52.381 0.00 0.00 0.00 3.51
755 781 1.275010 TCTGTGTGTGTGTGTGTCTGT 59.725 47.619 0.00 0.00 0.00 3.41
756 782 1.394572 CTGTGTGTGTGTGTGTCTGTG 59.605 52.381 0.00 0.00 0.00 3.66
757 783 1.270571 TGTGTGTGTGTGTGTCTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
758 784 1.128507 GTGTGTGTGTGTGTCTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
759 785 1.270571 TGTGTGTGTGTGTCTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
760 786 1.128507 GTGTGTGTGTGTCTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
761 787 1.270571 TGTGTGTGTGTCTGTGTGTGT 60.271 47.619 0.00 0.00 0.00 3.72
762 788 1.393539 GTGTGTGTGTCTGTGTGTGTC 59.606 52.381 0.00 0.00 0.00 3.67
763 789 1.275010 TGTGTGTGTCTGTGTGTGTCT 59.725 47.619 0.00 0.00 0.00 3.41
764 790 1.660607 GTGTGTGTCTGTGTGTGTCTG 59.339 52.381 0.00 0.00 0.00 3.51
765 791 1.275010 TGTGTGTCTGTGTGTGTCTGT 59.725 47.619 0.00 0.00 0.00 3.41
766 792 1.660607 GTGTGTCTGTGTGTGTCTGTG 59.339 52.381 0.00 0.00 0.00 3.66
767 793 1.275010 TGTGTCTGTGTGTGTCTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
768 794 1.660607 GTGTCTGTGTGTGTCTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
769 795 1.275010 TGTCTGTGTGTGTCTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
770 796 1.660607 GTCTGTGTGTGTCTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
771 797 1.275010 TCTGTGTGTGTCTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
778 804 1.128507 GTGTCTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
780 806 1.128507 GTCTGTGTGTGTGTGTGTGTG 59.871 52.381 0.00 0.00 0.00 3.82
782 808 1.128507 CTGTGTGTGTGTGTGTGTGTC 59.871 52.381 0.00 0.00 0.00 3.67
827 853 5.714806 AGACTGGAGATATAGCTAAAGAGGC 59.285 44.000 0.00 0.00 0.00 4.70
874 903 1.687996 CCCTCACTCTCCCTCTCTTCC 60.688 61.905 0.00 0.00 0.00 3.46
875 904 1.006519 CCTCACTCTCCCTCTCTTCCA 59.993 57.143 0.00 0.00 0.00 3.53
876 905 2.378038 CTCACTCTCCCTCTCTTCCAG 58.622 57.143 0.00 0.00 0.00 3.86
877 906 1.713647 TCACTCTCCCTCTCTTCCAGT 59.286 52.381 0.00 0.00 0.00 4.00
878 907 2.099405 CACTCTCCCTCTCTTCCAGTC 58.901 57.143 0.00 0.00 0.00 3.51
932 961 1.205893 CTCCTTCTTCTTCTCCACCCG 59.794 57.143 0.00 0.00 0.00 5.28
992 1025 1.146707 GGGGTGTACGTGTGGTTGT 59.853 57.895 0.00 0.00 0.00 3.32
995 1028 1.214367 GGTGTACGTGTGGTTGTGAG 58.786 55.000 0.00 0.00 0.00 3.51
1273 1309 1.412710 ACAACTTCTCCAGCTTCGTCA 59.587 47.619 0.00 0.00 0.00 4.35
1315 1354 4.486125 TGTTACTCATTATCTGCTGCCA 57.514 40.909 0.00 0.00 0.00 4.92
1317 1356 4.191544 GTTACTCATTATCTGCTGCCACA 58.808 43.478 0.00 0.00 0.00 4.17
1318 1357 2.636830 ACTCATTATCTGCTGCCACAC 58.363 47.619 0.00 0.00 0.00 3.82
1323 1362 0.396060 TATCTGCTGCCACACACACA 59.604 50.000 0.00 0.00 0.00 3.72
1324 1363 0.887836 ATCTGCTGCCACACACACAG 60.888 55.000 0.00 0.00 34.48 3.66
1325 1364 1.524393 CTGCTGCCACACACACAGA 60.524 57.895 0.00 0.00 33.10 3.41
1365 1407 2.009051 CGCATGCATGTTTAGTCCAGA 58.991 47.619 26.79 0.00 0.00 3.86
1369 1411 4.676196 GCATGCATGTTTAGTCCAGAAAGG 60.676 45.833 26.79 0.00 39.47 3.11
1392 1434 4.504097 GCTGCTCTTTGTTCGATTTGTTTT 59.496 37.500 0.00 0.00 0.00 2.43
1417 1463 0.249398 TCTTCCTCCGGTTTGCTAGC 59.751 55.000 8.10 8.10 0.00 3.42
1420 1466 1.789523 TCCTCCGGTTTGCTAGCTAT 58.210 50.000 17.23 0.00 0.00 2.97
1421 1467 2.116238 TCCTCCGGTTTGCTAGCTATT 58.884 47.619 17.23 0.00 0.00 1.73
1422 1468 3.302161 TCCTCCGGTTTGCTAGCTATTA 58.698 45.455 17.23 0.00 0.00 0.98
1425 1471 3.036091 TCCGGTTTGCTAGCTATTAGGT 58.964 45.455 17.23 0.46 0.00 3.08
1436 1488 1.935300 GCTATTAGGTCGTCCATGGCG 60.935 57.143 18.73 18.73 35.89 5.69
1469 1521 5.951148 TGTGGGATGTGTTCATGTTCATTAT 59.049 36.000 0.00 0.00 34.06 1.28
1470 1522 7.066887 GTGTGGGATGTGTTCATGTTCATTATA 59.933 37.037 0.00 0.00 34.06 0.98
1649 1715 3.463329 AGGGCTGTATATGGGTGTGATTT 59.537 43.478 0.00 0.00 0.00 2.17
1693 1759 1.039856 TTCCTTGCTTCCTGGTTTGC 58.960 50.000 0.00 0.00 0.00 3.68
1760 1827 1.748493 TCACCCACACTGTTCTTTTGC 59.252 47.619 0.00 0.00 0.00 3.68
1825 2131 5.827756 CCCCCTCCATTTCTTACTACTTTT 58.172 41.667 0.00 0.00 0.00 2.27
1837 2143 6.725246 TCTTACTACTTTTGTCTTGCTTTGC 58.275 36.000 0.00 0.00 0.00 3.68
1868 2174 1.269448 TGCAAGCTGGACGATTTTTCC 59.731 47.619 0.00 0.00 0.00 3.13
1978 2284 8.257306 TGGTTTCTTCTTTTAAAGCATGAGTTT 58.743 29.630 0.00 0.00 37.96 2.66
2200 2508 7.515586 TGTAGAGCTATGCCCTACGTATATAT 58.484 38.462 0.00 0.00 36.47 0.86
2201 2509 8.654094 TGTAGAGCTATGCCCTACGTATATATA 58.346 37.037 0.00 0.00 36.47 0.86
2202 2510 9.669887 GTAGAGCTATGCCCTACGTATATATAT 57.330 37.037 0.00 0.00 0.00 0.86
2204 2512 9.669887 AGAGCTATGCCCTACGTATATATATAC 57.330 37.037 19.12 19.12 36.15 1.47
2249 2557 4.772624 ACCACACTACATGACATGACTACT 59.227 41.667 22.19 1.59 0.00 2.57
2250 2558 5.949952 ACCACACTACATGACATGACTACTA 59.050 40.000 22.19 2.73 0.00 1.82
2251 2559 6.607600 ACCACACTACATGACATGACTACTAT 59.392 38.462 22.19 0.10 0.00 2.12
2252 2560 7.778382 ACCACACTACATGACATGACTACTATA 59.222 37.037 22.19 1.33 0.00 1.31
2453 2765 0.620556 ACAGATGGGAGTTCGCCAAT 59.379 50.000 0.00 0.00 0.00 3.16
2591 2903 2.281484 GGCAACACCTTCTCGCCA 60.281 61.111 0.00 0.00 42.50 5.69
2651 2966 0.250124 CGGTGTACCAGCACTTCCAA 60.250 55.000 1.50 0.00 39.21 3.53
3090 3405 1.954362 AAGCGAGGTCTAGGCTGCTG 61.954 60.000 9.43 0.00 37.06 4.41
3223 3539 1.883084 CGGGTGCTGGTCGATTAGC 60.883 63.158 14.70 14.70 40.29 3.09
3224 3540 1.522569 GGGTGCTGGTCGATTAGCT 59.477 57.895 20.03 0.00 40.52 3.32
3300 3620 3.385111 GGAACGTAGGATCAATCAGGTCT 59.615 47.826 0.00 0.00 0.00 3.85
3399 3721 0.250252 GAGGGCCTGCTATCTTGCTC 60.250 60.000 12.95 0.00 0.00 4.26
3459 3787 6.418057 AGTGTTCTCTTCTTTCTCTCATGT 57.582 37.500 0.00 0.00 0.00 3.21
3460 3788 6.454795 AGTGTTCTCTTCTTTCTCTCATGTC 58.545 40.000 0.00 0.00 0.00 3.06
3461 3789 6.041409 AGTGTTCTCTTCTTTCTCTCATGTCA 59.959 38.462 0.00 0.00 0.00 3.58
3462 3790 6.873076 GTGTTCTCTTCTTTCTCTCATGTCAT 59.127 38.462 0.00 0.00 0.00 3.06
3592 3934 5.236911 CACCACATGAAAAACAAAGGAATGG 59.763 40.000 0.00 0.00 0.00 3.16
3598 3940 5.540911 TGAAAAACAAAGGAATGGCAGATC 58.459 37.500 0.00 0.00 0.00 2.75
3602 3944 4.038271 ACAAAGGAATGGCAGATCTGAA 57.962 40.909 27.04 13.65 0.00 3.02
3616 3958 5.579511 GCAGATCTGAATTGGTGGAAATTTG 59.420 40.000 27.04 0.00 29.89 2.32
3617 3959 5.579511 CAGATCTGAATTGGTGGAAATTTGC 59.420 40.000 18.34 2.22 29.89 3.68
3621 3963 1.739750 ATTGGTGGAAATTTGCCCCA 58.260 45.000 9.78 9.78 0.00 4.96
3669 4011 6.590234 ATGACTTTTTGGTAAGGATTCCAC 57.410 37.500 5.29 0.00 33.12 4.02
3675 4017 2.196595 TGGTAAGGATTCCACTCCTGG 58.803 52.381 5.29 0.00 45.15 4.45
3676 4018 2.225779 TGGTAAGGATTCCACTCCTGGA 60.226 50.000 5.29 0.00 45.15 3.86
3684 4026 1.857965 TCCACTCCTGGAGTCTGATG 58.142 55.000 26.11 14.46 42.15 3.07
3686 4028 1.480137 CCACTCCTGGAGTCTGATGAC 59.520 57.143 26.11 0.00 41.37 3.06
3687 4029 2.174360 CACTCCTGGAGTCTGATGACA 58.826 52.381 26.11 0.00 41.37 3.58
3688 4030 2.166050 CACTCCTGGAGTCTGATGACAG 59.834 54.545 26.11 8.39 41.37 3.51
3689 4031 2.225242 ACTCCTGGAGTCTGATGACAGT 60.225 50.000 23.49 0.00 45.20 3.55
3690 4032 3.010696 ACTCCTGGAGTCTGATGACAGTA 59.989 47.826 23.49 0.00 45.20 2.74
3691 4033 4.214310 CTCCTGGAGTCTGATGACAGTAT 58.786 47.826 15.76 0.00 45.20 2.12
3692 4034 3.956848 TCCTGGAGTCTGATGACAGTATG 59.043 47.826 0.00 0.00 45.20 2.39
3702 4044 1.623163 TGACAGTATGACACACGGGA 58.377 50.000 0.00 0.00 39.69 5.14
3714 4056 6.392625 TGACACACGGGAATAATTTTGAAA 57.607 33.333 0.00 0.00 0.00 2.69
3716 4058 5.227152 ACACACGGGAATAATTTTGAAAGC 58.773 37.500 0.00 0.00 0.00 3.51
3728 4070 4.942761 TTTTGAAAGCTGCAAATCCTCT 57.057 36.364 13.74 0.00 35.41 3.69
3729 4071 4.510038 TTTGAAAGCTGCAAATCCTCTC 57.490 40.909 10.08 0.00 30.87 3.20
3748 4090 7.761409 TCCTCTCAAAATTATGTGAAATTCCG 58.239 34.615 0.00 0.00 0.00 4.30
3768 4110 2.293122 CGTTGAATCAAAGAAGCCCACA 59.707 45.455 2.77 0.00 0.00 4.17
3770 4112 3.507162 TGAATCAAAGAAGCCCACAGA 57.493 42.857 0.00 0.00 0.00 3.41
3771 4113 3.415212 TGAATCAAAGAAGCCCACAGAG 58.585 45.455 0.00 0.00 0.00 3.35
3772 4114 3.181440 TGAATCAAAGAAGCCCACAGAGT 60.181 43.478 0.00 0.00 0.00 3.24
3773 4115 2.260844 TCAAAGAAGCCCACAGAGTG 57.739 50.000 0.00 0.00 0.00 3.51
3774 4116 1.490490 TCAAAGAAGCCCACAGAGTGT 59.510 47.619 0.00 0.00 0.00 3.55
3775 4117 1.876156 CAAAGAAGCCCACAGAGTGTC 59.124 52.381 0.00 0.00 0.00 3.67
3776 4118 1.131638 AAGAAGCCCACAGAGTGTCA 58.868 50.000 0.00 0.00 0.00 3.58
3777 4119 0.683973 AGAAGCCCACAGAGTGTCAG 59.316 55.000 0.00 0.00 0.00 3.51
3778 4120 0.952984 GAAGCCCACAGAGTGTCAGC 60.953 60.000 0.00 0.00 0.00 4.26
3779 4121 2.721971 AAGCCCACAGAGTGTCAGCG 62.722 60.000 0.00 0.00 30.94 5.18
3780 4122 2.737180 CCCACAGAGTGTCAGCGT 59.263 61.111 0.00 0.00 0.00 5.07
3781 4123 1.964448 CCCACAGAGTGTCAGCGTA 59.036 57.895 0.00 0.00 0.00 4.42
3782 4124 0.388649 CCCACAGAGTGTCAGCGTAC 60.389 60.000 0.00 0.00 0.00 3.67
3783 4125 0.729478 CCACAGAGTGTCAGCGTACG 60.729 60.000 11.84 11.84 0.00 3.67
3784 4126 0.237498 CACAGAGTGTCAGCGTACGA 59.763 55.000 21.65 0.00 0.00 3.43
3785 4127 0.517755 ACAGAGTGTCAGCGTACGAG 59.482 55.000 21.65 10.77 0.00 4.18
3786 4128 0.794981 CAGAGTGTCAGCGTACGAGC 60.795 60.000 21.65 1.24 37.41 5.03
3787 4129 1.514443 GAGTGTCAGCGTACGAGCC 60.514 63.158 21.65 0.54 38.01 4.70
3788 4130 1.924320 GAGTGTCAGCGTACGAGCCT 61.924 60.000 21.65 3.39 38.01 4.58
3789 4131 0.675837 AGTGTCAGCGTACGAGCCTA 60.676 55.000 21.65 0.00 38.01 3.93
3790 4132 0.522915 GTGTCAGCGTACGAGCCTAC 60.523 60.000 21.65 9.35 38.01 3.18
3791 4133 0.956902 TGTCAGCGTACGAGCCTACA 60.957 55.000 21.65 11.85 38.01 2.74
3792 4134 0.169672 GTCAGCGTACGAGCCTACAA 59.830 55.000 21.65 0.00 38.01 2.41
3793 4135 1.100510 TCAGCGTACGAGCCTACAAT 58.899 50.000 21.65 0.00 38.01 2.71
3794 4136 1.475280 TCAGCGTACGAGCCTACAATT 59.525 47.619 21.65 0.00 38.01 2.32
3795 4137 1.852895 CAGCGTACGAGCCTACAATTC 59.147 52.381 21.65 0.00 38.01 2.17
3796 4138 1.475280 AGCGTACGAGCCTACAATTCA 59.525 47.619 21.65 0.00 38.01 2.57
3797 4139 2.100916 AGCGTACGAGCCTACAATTCAT 59.899 45.455 21.65 0.00 38.01 2.57
3798 4140 3.317149 AGCGTACGAGCCTACAATTCATA 59.683 43.478 21.65 0.00 38.01 2.15
3799 4141 3.669122 GCGTACGAGCCTACAATTCATAG 59.331 47.826 21.65 0.00 0.00 2.23
3800 4142 4.227538 CGTACGAGCCTACAATTCATAGG 58.772 47.826 10.44 7.66 42.01 2.57
3801 4143 4.023450 CGTACGAGCCTACAATTCATAGGA 60.023 45.833 10.44 0.00 41.70 2.94
3802 4144 5.335740 CGTACGAGCCTACAATTCATAGGAT 60.336 44.000 10.44 9.08 41.17 3.24
3803 4145 4.887748 ACGAGCCTACAATTCATAGGATG 58.112 43.478 14.20 7.19 38.56 3.51
3804 4146 3.681897 CGAGCCTACAATTCATAGGATGC 59.318 47.826 14.20 2.16 38.56 3.91
3805 4147 4.645535 GAGCCTACAATTCATAGGATGCA 58.354 43.478 14.20 0.00 38.56 3.96
3806 4148 5.052693 AGCCTACAATTCATAGGATGCAA 57.947 39.130 14.20 0.00 41.70 4.08
3807 4149 5.448654 AGCCTACAATTCATAGGATGCAAA 58.551 37.500 14.20 0.00 41.70 3.68
3808 4150 6.073314 AGCCTACAATTCATAGGATGCAAAT 58.927 36.000 14.20 0.00 41.70 2.32
3809 4151 6.208204 AGCCTACAATTCATAGGATGCAAATC 59.792 38.462 14.20 0.00 41.70 2.17
3810 4152 6.571150 GCCTACAATTCATAGGATGCAAATCC 60.571 42.308 14.20 0.00 41.70 3.01
3825 4167 9.252962 GGATGCAAATCCTCTAAAAATTATGTG 57.747 33.333 0.00 0.00 37.73 3.21
3834 4176 9.768215 TCCTCTAAAAATTATGTGAAATTCCCT 57.232 29.630 0.00 0.00 0.00 4.20
3844 4186 9.880157 ATTATGTGAAATTCCCTTGAATCAAAG 57.120 29.630 0.00 0.00 40.34 2.77
3845 4187 6.975196 TGTGAAATTCCCTTGAATCAAAGA 57.025 33.333 0.00 0.00 40.34 2.52
3846 4188 7.358770 TGTGAAATTCCCTTGAATCAAAGAA 57.641 32.000 9.59 9.59 40.34 2.52
3847 4189 7.436118 TGTGAAATTCCCTTGAATCAAAGAAG 58.564 34.615 11.92 0.00 40.34 2.85
3848 4190 6.367149 GTGAAATTCCCTTGAATCAAAGAAGC 59.633 38.462 11.92 6.55 40.34 3.86
3849 4191 5.411831 AATTCCCTTGAATCAAAGAAGCC 57.588 39.130 11.92 0.00 40.34 4.35
3850 4192 2.807676 TCCCTTGAATCAAAGAAGCCC 58.192 47.619 0.00 0.00 0.00 5.19
3851 4193 2.109834 TCCCTTGAATCAAAGAAGCCCA 59.890 45.455 0.00 0.00 0.00 5.36
3852 4194 3.102204 CCCTTGAATCAAAGAAGCCCAT 58.898 45.455 0.00 0.00 0.00 4.00
3853 4195 3.118884 CCCTTGAATCAAAGAAGCCCATG 60.119 47.826 0.00 0.00 0.00 3.66
3854 4196 3.512724 CCTTGAATCAAAGAAGCCCATGT 59.487 43.478 0.00 0.00 0.00 3.21
3885 4227 6.363577 ACATACGAGCCTACAATTTTCATG 57.636 37.500 0.00 0.00 0.00 3.07
3886 4228 3.764885 ACGAGCCTACAATTTTCATGC 57.235 42.857 0.00 0.00 0.00 4.06
3893 4235 1.923356 ACAATTTTCATGCGAGGGGT 58.077 45.000 0.00 0.00 0.00 4.95
3902 4244 1.140852 CATGCGAGGGGTGGAGATAAA 59.859 52.381 0.00 0.00 0.00 1.40
3918 4260 8.027189 GTGGAGATAAACCTAATTTGGACAAAC 58.973 37.037 13.16 1.85 32.51 2.93
3934 4282 4.137543 GACAAACAGAAGACAACCCTCAT 58.862 43.478 0.00 0.00 0.00 2.90
3939 4287 7.123547 ACAAACAGAAGACAACCCTCATAAAAA 59.876 33.333 0.00 0.00 0.00 1.94
3987 4335 0.593128 AGCGCAGTTTGATGGACAAC 59.407 50.000 11.47 0.00 38.29 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 90 1.710816 TGGCCAAGGTGTAAAAAGGG 58.289 50.000 0.61 0.00 0.00 3.95
94 96 1.677300 CGCCATGGCCAAGGTGTAA 60.677 57.895 30.79 0.00 37.98 2.41
141 143 0.033504 TTTCTCAGACCCACGTCAGC 59.966 55.000 0.00 0.00 41.87 4.26
142 144 2.135933 GTTTTCTCAGACCCACGTCAG 58.864 52.381 0.00 0.00 41.87 3.51
146 148 2.076863 GATGGTTTTCTCAGACCCACG 58.923 52.381 0.00 0.00 34.99 4.94
163 165 2.673043 GCAGTGCAAATGGTCAAGGATG 60.673 50.000 11.09 0.00 28.90 3.51
186 188 1.696884 TGGGGCATTTTCCTCCAAAAC 59.303 47.619 0.00 0.00 36.78 2.43
210 212 9.216117 GGAGAGAAAAACTTGTATGCTACTAAA 57.784 33.333 0.00 0.00 0.00 1.85
211 213 7.822822 GGGAGAGAAAAACTTGTATGCTACTAA 59.177 37.037 0.00 0.00 0.00 2.24
212 214 7.038587 TGGGAGAGAAAAACTTGTATGCTACTA 60.039 37.037 0.00 0.00 0.00 1.82
213 215 6.174049 GGGAGAGAAAAACTTGTATGCTACT 58.826 40.000 0.00 0.00 0.00 2.57
214 216 5.938125 TGGGAGAGAAAAACTTGTATGCTAC 59.062 40.000 0.00 0.00 0.00 3.58
215 217 6.121776 TGGGAGAGAAAAACTTGTATGCTA 57.878 37.500 0.00 0.00 0.00 3.49
216 218 4.985538 TGGGAGAGAAAAACTTGTATGCT 58.014 39.130 0.00 0.00 0.00 3.79
227 229 7.458397 TGCTACTAATTTCTTGGGAGAGAAAA 58.542 34.615 4.40 0.00 45.68 2.29
228 230 7.016153 TGCTACTAATTTCTTGGGAGAGAAA 57.984 36.000 2.91 2.91 46.36 2.52
229 231 6.620877 TGCTACTAATTTCTTGGGAGAGAA 57.379 37.500 0.00 0.00 34.00 2.87
230 232 6.620877 TTGCTACTAATTTCTTGGGAGAGA 57.379 37.500 0.00 0.00 32.44 3.10
231 233 7.687941 TTTTGCTACTAATTTCTTGGGAGAG 57.312 36.000 0.00 0.00 32.44 3.20
232 234 9.920946 ATATTTTGCTACTAATTTCTTGGGAGA 57.079 29.630 0.00 0.00 0.00 3.71
233 235 9.956720 CATATTTTGCTACTAATTTCTTGGGAG 57.043 33.333 0.00 0.00 0.00 4.30
234 236 9.474313 ACATATTTTGCTACTAATTTCTTGGGA 57.526 29.630 0.00 0.00 0.00 4.37
262 264 9.981460 TCTCTCCAGATTTATGTATAGCTATGA 57.019 33.333 16.77 3.16 0.00 2.15
266 268 9.545928 AAGATCTCTCCAGATTTATGTATAGCT 57.454 33.333 0.00 0.00 39.71 3.32
267 269 9.801873 GAAGATCTCTCCAGATTTATGTATAGC 57.198 37.037 0.00 0.00 39.71 2.97
270 272 8.313292 GCAGAAGATCTCTCCAGATTTATGTAT 58.687 37.037 0.00 0.00 39.71 2.29
271 273 7.508636 AGCAGAAGATCTCTCCAGATTTATGTA 59.491 37.037 0.00 0.00 39.71 2.29
272 274 6.327104 AGCAGAAGATCTCTCCAGATTTATGT 59.673 38.462 0.00 0.00 39.71 2.29
273 275 6.647481 CAGCAGAAGATCTCTCCAGATTTATG 59.353 42.308 0.00 0.00 39.71 1.90
274 276 6.554228 TCAGCAGAAGATCTCTCCAGATTTAT 59.446 38.462 0.00 0.00 39.71 1.40
275 277 5.896106 TCAGCAGAAGATCTCTCCAGATTTA 59.104 40.000 0.00 0.00 39.71 1.40
276 278 4.715792 TCAGCAGAAGATCTCTCCAGATTT 59.284 41.667 0.00 0.00 39.71 2.17
277 279 4.288398 TCAGCAGAAGATCTCTCCAGATT 58.712 43.478 0.00 0.00 39.71 2.40
278 280 3.893200 CTCAGCAGAAGATCTCTCCAGAT 59.107 47.826 0.00 0.00 42.59 2.90
279 281 3.053768 TCTCAGCAGAAGATCTCTCCAGA 60.054 47.826 0.00 0.00 29.07 3.86
280 282 3.289836 TCTCAGCAGAAGATCTCTCCAG 58.710 50.000 0.00 0.00 29.07 3.86
281 283 3.378861 TCTCAGCAGAAGATCTCTCCA 57.621 47.619 0.00 0.00 29.07 3.86
282 284 4.022589 CAGATCTCAGCAGAAGATCTCTCC 60.023 50.000 17.66 0.00 44.68 3.71
283 285 4.823442 TCAGATCTCAGCAGAAGATCTCTC 59.177 45.833 17.66 0.00 44.68 3.20
284 286 4.795469 TCAGATCTCAGCAGAAGATCTCT 58.205 43.478 17.66 2.72 44.68 3.10
285 287 5.163530 TGTTCAGATCTCAGCAGAAGATCTC 60.164 44.000 17.66 10.69 44.68 2.75
286 288 4.710865 TGTTCAGATCTCAGCAGAAGATCT 59.289 41.667 15.75 15.75 46.64 2.75
287 289 5.008619 TGTTCAGATCTCAGCAGAAGATC 57.991 43.478 12.57 12.57 38.85 2.75
288 290 5.364446 AGATGTTCAGATCTCAGCAGAAGAT 59.636 40.000 0.00 0.00 30.24 2.40
289 291 4.710865 AGATGTTCAGATCTCAGCAGAAGA 59.289 41.667 0.00 0.00 30.24 2.87
290 292 4.806775 CAGATGTTCAGATCTCAGCAGAAG 59.193 45.833 0.00 0.00 29.72 2.85
293 295 4.388378 TCAGATGTTCAGATCTCAGCAG 57.612 45.455 0.00 0.00 29.72 4.24
367 373 4.331168 CAGTCCTAATGTGCTTAGTTGAGC 59.669 45.833 0.00 0.00 43.00 4.26
408 414 4.083003 GGGTCGATGTTGCAACTGAATTAA 60.083 41.667 28.61 8.52 0.00 1.40
462 469 3.623060 GTGCTTCAGAGTGTTCAAGTTCA 59.377 43.478 0.00 0.00 0.00 3.18
464 471 3.609853 TGTGCTTCAGAGTGTTCAAGTT 58.390 40.909 0.00 0.00 0.00 2.66
465 472 3.266510 TGTGCTTCAGAGTGTTCAAGT 57.733 42.857 0.00 0.00 0.00 3.16
710 736 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
711 737 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
712 738 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
713 739 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
714 740 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
715 741 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
716 742 1.393539 GAGACACACACACACACACAC 59.606 52.381 0.00 0.00 0.00 3.82
717 743 1.275010 AGAGACACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
718 744 1.660607 CAGAGACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
719 745 1.275010 ACAGAGACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
720 746 1.660607 CACAGAGACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
721 747 1.275010 ACACAGAGACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
722 748 1.660607 CACACAGAGACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
723 749 1.275010 ACACACAGAGACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
724 750 1.660607 CACACACAGAGACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
725 751 1.275010 ACACACACAGAGACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
726 752 1.660607 CACACACACAGAGACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
727 753 1.275010 ACACACACACAGAGACACACA 59.725 47.619 0.00 0.00 0.00 3.72
728 754 1.660607 CACACACACACAGAGACACAC 59.339 52.381 0.00 0.00 0.00 3.82
729 755 1.275010 ACACACACACACAGAGACACA 59.725 47.619 0.00 0.00 0.00 3.72
730 756 1.660607 CACACACACACACAGAGACAC 59.339 52.381 0.00 0.00 0.00 3.67
731 757 1.275010 ACACACACACACACAGAGACA 59.725 47.619 0.00 0.00 0.00 3.41
732 758 1.927174 GACACACACACACACAGAGAC 59.073 52.381 0.00 0.00 0.00 3.36
733 759 1.824852 AGACACACACACACACAGAGA 59.175 47.619 0.00 0.00 0.00 3.10
734 760 1.929169 CAGACACACACACACACAGAG 59.071 52.381 0.00 0.00 0.00 3.35
735 761 1.275010 ACAGACACACACACACACAGA 59.725 47.619 0.00 0.00 0.00 3.41
736 762 1.394572 CACAGACACACACACACACAG 59.605 52.381 0.00 0.00 0.00 3.66
737 763 1.270571 ACACAGACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
738 764 1.128507 CACACAGACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
739 765 1.270571 ACACACAGACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
740 766 1.128507 CACACACAGACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
741 767 1.270571 ACACACACAGACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
742 768 1.393539 GACACACACAGACACACACAC 59.606 52.381 0.00 0.00 0.00 3.82
743 769 1.275010 AGACACACACAGACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
744 770 1.660607 CAGACACACACAGACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
745 771 1.275010 ACAGACACACACAGACACACA 59.725 47.619 0.00 0.00 0.00 3.72
746 772 1.660607 CACAGACACACACAGACACAC 59.339 52.381 0.00 0.00 0.00 3.82
747 773 1.275010 ACACAGACACACACAGACACA 59.725 47.619 0.00 0.00 0.00 3.72
748 774 1.660607 CACACAGACACACACAGACAC 59.339 52.381 0.00 0.00 0.00 3.67
749 775 1.275010 ACACACAGACACACACAGACA 59.725 47.619 0.00 0.00 0.00 3.41
750 776 1.660607 CACACACAGACACACACAGAC 59.339 52.381 0.00 0.00 0.00 3.51
751 777 1.275010 ACACACACAGACACACACAGA 59.725 47.619 0.00 0.00 0.00 3.41
752 778 1.394572 CACACACACAGACACACACAG 59.605 52.381 0.00 0.00 0.00 3.66
753 779 1.270571 ACACACACACAGACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
754 780 1.128507 CACACACACACAGACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
755 781 1.270571 ACACACACACACAGACACACA 60.271 47.619 0.00 0.00 0.00 3.72
756 782 1.128507 CACACACACACACAGACACAC 59.871 52.381 0.00 0.00 0.00 3.82
757 783 1.270571 ACACACACACACACAGACACA 60.271 47.619 0.00 0.00 0.00 3.72
758 784 1.128507 CACACACACACACACAGACAC 59.871 52.381 0.00 0.00 0.00 3.67
759 785 1.270571 ACACACACACACACACAGACA 60.271 47.619 0.00 0.00 0.00 3.41
760 786 1.128507 CACACACACACACACACAGAC 59.871 52.381 0.00 0.00 0.00 3.51
761 787 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
762 788 1.128507 GACACACACACACACACACAG 59.871 52.381 0.00 0.00 0.00 3.66
763 789 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
764 790 1.128507 CAGACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
765 791 1.270571 ACAGACACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
766 792 1.128507 CACAGACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
767 793 1.270571 ACACAGACACACACACACACA 60.271 47.619 0.00 0.00 0.00 3.72
768 794 1.128507 CACACAGACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
769 795 1.001406 TCACACAGACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
770 796 1.660607 CTCACACAGACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
771 797 1.275010 ACTCACACAGACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
778 804 0.030773 TCTCGCACTCACACAGACAC 59.969 55.000 0.00 0.00 0.00 3.67
780 806 0.030773 TGTCTCGCACTCACACAGAC 59.969 55.000 0.00 0.00 35.11 3.51
782 808 0.031314 ACTGTCTCGCACTCACACAG 59.969 55.000 0.00 0.00 40.33 3.66
827 853 1.466558 GAGGAAGAAAGAAAGGCTGCG 59.533 52.381 0.00 0.00 0.00 5.18
874 903 0.980231 CCCAGGGAGGAGGAAGACTG 60.980 65.000 0.00 0.00 41.22 3.51
875 904 1.394151 CCCAGGGAGGAGGAAGACT 59.606 63.158 0.00 0.00 41.22 3.24
876 905 2.371259 GCCCAGGGAGGAGGAAGAC 61.371 68.421 10.89 0.00 41.22 3.01
877 906 2.041265 GCCCAGGGAGGAGGAAGA 59.959 66.667 10.89 0.00 41.22 2.87
878 907 0.326618 TAAGCCCAGGGAGGAGGAAG 60.327 60.000 10.89 0.00 41.22 3.46
932 961 1.079750 GGACTCGGTCACTCAAGGC 60.080 63.158 6.41 0.00 33.68 4.35
992 1025 1.803453 AAGGAAAGCCATGGCCCTCA 61.803 55.000 33.14 0.00 43.17 3.86
995 1028 1.610379 ACAAGGAAAGCCATGGCCC 60.610 57.895 33.14 25.84 43.17 5.80
1273 1309 0.987294 ACATAGGTGTTGAGCTGCCT 59.013 50.000 0.00 0.00 34.01 4.75
1343 1385 1.468127 TGGACTAAACATGCATGCGTG 59.532 47.619 33.18 33.18 38.78 5.34
1365 1407 1.967319 TCGAACAAAGAGCAGCCTTT 58.033 45.000 3.70 3.70 36.87 3.11
1369 1411 3.273919 ACAAATCGAACAAAGAGCAGC 57.726 42.857 0.00 0.00 0.00 5.25
1417 1463 1.340248 ACGCCATGGACGACCTAATAG 59.660 52.381 27.68 3.81 37.04 1.73
1420 1466 1.216977 CACGCCATGGACGACCTAA 59.783 57.895 27.68 0.00 37.04 2.69
1421 1467 0.680601 TACACGCCATGGACGACCTA 60.681 55.000 27.68 14.19 37.04 3.08
1422 1468 1.327690 ATACACGCCATGGACGACCT 61.328 55.000 27.68 14.94 37.04 3.85
1425 1471 1.684450 ACATATACACGCCATGGACGA 59.316 47.619 27.68 11.69 0.00 4.20
1436 1488 5.182487 TGAACACATCCCACACATATACAC 58.818 41.667 0.00 0.00 0.00 2.90
1469 1521 9.503399 AAAATACCAAACCAAACAAAACTTGTA 57.497 25.926 0.00 0.00 44.59 2.41
1649 1715 8.862325 ACTAATAATCTTGTTGGAATGTCACA 57.138 30.769 0.00 0.00 0.00 3.58
1700 1766 3.735240 CAGCTTGATCTATTCGACAGCTC 59.265 47.826 0.00 0.00 0.00 4.09
1805 1872 8.507249 CAAGACAAAAGTAGTAAGAAATGGAGG 58.493 37.037 0.00 0.00 0.00 4.30
1825 2131 0.890542 ATCGCCAGCAAAGCAAGACA 60.891 50.000 0.00 0.00 0.00 3.41
1837 2143 1.268896 CCAGCTTGCATAAATCGCCAG 60.269 52.381 0.00 0.00 0.00 4.85
1868 2174 6.893958 AACTGATGAACTAACTGATTAGCG 57.106 37.500 0.00 0.00 41.48 4.26
1914 2220 2.005971 AAACGGTCCTCGCTTATCAC 57.994 50.000 0.00 0.00 43.89 3.06
1978 2284 3.732212 CATATGGCAAGTGCAGCTAGTA 58.268 45.455 5.52 0.00 44.36 1.82
2285 2593 1.345741 AGGGAGATACATGACATGGCG 59.654 52.381 19.39 0.00 33.60 5.69
2386 2698 1.300853 AAACCGCAATGCCAAGTGC 60.301 52.632 0.00 0.00 43.88 4.40
2453 2765 1.625818 GCTCCCTTCCTGAAGAACTCA 59.374 52.381 8.46 0.00 40.79 3.41
3047 3362 2.607668 GATCATGGGCGACGACGTCA 62.608 60.000 26.26 9.10 46.58 4.35
3119 3434 6.559157 TCCTCTCTCCTCTCTATGTACATACA 59.441 42.308 11.62 0.94 40.98 2.29
3120 3435 7.011499 TCCTCTCTCCTCTCTATGTACATAC 57.989 44.000 11.62 0.00 0.00 2.39
3121 3436 6.790461 ACTCCTCTCTCCTCTCTATGTACATA 59.210 42.308 14.75 14.75 0.00 2.29
3122 3437 5.610982 ACTCCTCTCTCCTCTCTATGTACAT 59.389 44.000 13.93 13.93 0.00 2.29
3223 3539 7.724287 TCATTGATCCTAACTCATCTCTCAAG 58.276 38.462 0.00 0.00 0.00 3.02
3224 3540 7.201983 CCTCATTGATCCTAACTCATCTCTCAA 60.202 40.741 0.00 0.00 0.00 3.02
3300 3620 1.148310 GCAAGCAGCAAACTACTCGA 58.852 50.000 0.00 0.00 44.79 4.04
3459 3787 5.074115 ACTTTTTCCATTCCCGTGTTATGA 58.926 37.500 0.00 0.00 0.00 2.15
3460 3788 5.385509 ACTTTTTCCATTCCCGTGTTATG 57.614 39.130 0.00 0.00 0.00 1.90
3461 3789 6.478129 TCTACTTTTTCCATTCCCGTGTTAT 58.522 36.000 0.00 0.00 0.00 1.89
3462 3790 5.867330 TCTACTTTTTCCATTCCCGTGTTA 58.133 37.500 0.00 0.00 0.00 2.41
3592 3934 4.996788 ATTTCCACCAATTCAGATCTGC 57.003 40.909 18.36 0.00 0.00 4.26
3598 3940 3.337358 GGGCAAATTTCCACCAATTCAG 58.663 45.455 8.36 0.00 0.00 3.02
3602 3944 1.739750 TGGGGCAAATTTCCACCAAT 58.260 45.000 0.00 0.00 0.00 3.16
3616 3958 4.525100 TCCTTTACACACTATTTTTGGGGC 59.475 41.667 0.00 0.00 0.00 5.80
3617 3959 6.658188 TTCCTTTACACACTATTTTTGGGG 57.342 37.500 0.00 0.00 0.00 4.96
3647 3989 5.701224 AGTGGAATCCTTACCAAAAAGTCA 58.299 37.500 0.00 0.00 37.94 3.41
3650 3992 5.644977 GGAGTGGAATCCTTACCAAAAAG 57.355 43.478 0.00 0.00 37.94 2.27
3669 4011 2.455557 ACTGTCATCAGACTCCAGGAG 58.544 52.381 15.72 15.72 45.20 3.69
3675 4017 5.098893 GTGTGTCATACTGTCATCAGACTC 58.901 45.833 2.17 0.00 45.20 3.36
3676 4018 4.379918 CGTGTGTCATACTGTCATCAGACT 60.380 45.833 2.17 0.00 45.20 3.24
3677 4019 3.854240 CGTGTGTCATACTGTCATCAGAC 59.146 47.826 2.17 0.00 43.76 3.51
3678 4020 3.119495 CCGTGTGTCATACTGTCATCAGA 60.119 47.826 2.17 0.00 43.76 3.27
3679 4021 3.182182 CCGTGTGTCATACTGTCATCAG 58.818 50.000 0.00 0.00 46.18 2.90
3680 4022 2.094234 CCCGTGTGTCATACTGTCATCA 60.094 50.000 0.00 0.00 0.00 3.07
3681 4023 2.165641 TCCCGTGTGTCATACTGTCATC 59.834 50.000 0.00 0.00 0.00 2.92
3682 4024 2.176045 TCCCGTGTGTCATACTGTCAT 58.824 47.619 0.00 0.00 0.00 3.06
3683 4025 1.623163 TCCCGTGTGTCATACTGTCA 58.377 50.000 0.00 0.00 0.00 3.58
3684 4026 2.736144 TTCCCGTGTGTCATACTGTC 57.264 50.000 0.00 0.00 0.00 3.51
3686 4028 6.677781 AAATTATTCCCGTGTGTCATACTG 57.322 37.500 0.00 0.00 0.00 2.74
3687 4029 6.882140 TCAAAATTATTCCCGTGTGTCATACT 59.118 34.615 0.00 0.00 0.00 2.12
3688 4030 7.079182 TCAAAATTATTCCCGTGTGTCATAC 57.921 36.000 0.00 0.00 0.00 2.39
3689 4031 7.689446 TTCAAAATTATTCCCGTGTGTCATA 57.311 32.000 0.00 0.00 0.00 2.15
3690 4032 6.582677 TTCAAAATTATTCCCGTGTGTCAT 57.417 33.333 0.00 0.00 0.00 3.06
3691 4033 6.392625 TTTCAAAATTATTCCCGTGTGTCA 57.607 33.333 0.00 0.00 0.00 3.58
3692 4034 5.344933 GCTTTCAAAATTATTCCCGTGTGTC 59.655 40.000 0.00 0.00 0.00 3.67
3702 4044 8.098912 AGAGGATTTGCAGCTTTCAAAATTATT 58.901 29.630 13.09 0.00 37.04 1.40
3714 4056 6.154021 ACATAATTTTGAGAGGATTTGCAGCT 59.846 34.615 2.69 0.00 0.00 4.24
3716 4058 7.541162 TCACATAATTTTGAGAGGATTTGCAG 58.459 34.615 2.69 0.00 0.00 4.41
3728 4070 9.703892 ATTCAACGGAATTTCACATAATTTTGA 57.296 25.926 2.69 0.00 40.87 2.69
3729 4071 9.956797 GATTCAACGGAATTTCACATAATTTTG 57.043 29.630 0.00 0.00 43.69 2.44
3748 4090 3.569701 TCTGTGGGCTTCTTTGATTCAAC 59.430 43.478 0.00 0.00 0.00 3.18
3768 4110 1.502640 GCTCGTACGCTGACACTCT 59.497 57.895 11.24 0.00 0.00 3.24
3770 4112 0.675837 TAGGCTCGTACGCTGACACT 60.676 55.000 11.24 5.30 0.00 3.55
3771 4113 0.522915 GTAGGCTCGTACGCTGACAC 60.523 60.000 11.24 5.74 0.00 3.67
3772 4114 0.956902 TGTAGGCTCGTACGCTGACA 60.957 55.000 11.24 7.25 0.00 3.58
3773 4115 0.169672 TTGTAGGCTCGTACGCTGAC 59.830 55.000 11.24 8.16 0.00 3.51
3774 4116 1.100510 ATTGTAGGCTCGTACGCTGA 58.899 50.000 11.24 0.00 0.00 4.26
3775 4117 1.852895 GAATTGTAGGCTCGTACGCTG 59.147 52.381 11.24 7.07 0.00 5.18
3776 4118 1.475280 TGAATTGTAGGCTCGTACGCT 59.525 47.619 11.24 4.66 0.00 5.07
3777 4119 1.917273 TGAATTGTAGGCTCGTACGC 58.083 50.000 11.24 0.00 0.00 4.42
3778 4120 4.023450 TCCTATGAATTGTAGGCTCGTACG 60.023 45.833 9.53 9.53 38.86 3.67
3779 4121 5.449107 TCCTATGAATTGTAGGCTCGTAC 57.551 43.478 0.00 0.00 38.86 3.67
3780 4122 5.566826 GCATCCTATGAATTGTAGGCTCGTA 60.567 44.000 0.00 0.00 38.86 3.43
3781 4123 4.800914 GCATCCTATGAATTGTAGGCTCGT 60.801 45.833 0.00 0.00 38.86 4.18
3782 4124 3.681897 GCATCCTATGAATTGTAGGCTCG 59.318 47.826 0.00 2.41 38.86 5.03
3783 4125 4.645535 TGCATCCTATGAATTGTAGGCTC 58.354 43.478 0.00 0.00 38.86 4.70
3784 4126 4.712051 TGCATCCTATGAATTGTAGGCT 57.288 40.909 8.14 0.00 38.86 4.58
3785 4127 5.772825 TTTGCATCCTATGAATTGTAGGC 57.227 39.130 8.14 0.00 38.86 3.93
3786 4128 6.917533 GGATTTGCATCCTATGAATTGTAGG 58.082 40.000 0.00 7.04 45.41 3.18
3808 4150 9.768215 AGGGAATTTCACATAATTTTTAGAGGA 57.232 29.630 0.73 0.00 0.00 3.71
3818 4160 9.880157 CTTTGATTCAAGGGAATTTCACATAAT 57.120 29.630 0.73 0.00 43.69 1.28
3819 4161 9.087871 TCTTTGATTCAAGGGAATTTCACATAA 57.912 29.630 8.47 0.00 43.69 1.90
3820 4162 8.648698 TCTTTGATTCAAGGGAATTTCACATA 57.351 30.769 8.47 0.00 43.69 2.29
3821 4163 7.543359 TCTTTGATTCAAGGGAATTTCACAT 57.457 32.000 8.47 0.00 43.69 3.21
3822 4164 6.975196 TCTTTGATTCAAGGGAATTTCACA 57.025 33.333 8.47 0.00 43.69 3.58
3823 4165 6.367149 GCTTCTTTGATTCAAGGGAATTTCAC 59.633 38.462 8.47 0.00 43.69 3.18
3824 4166 6.458210 GCTTCTTTGATTCAAGGGAATTTCA 58.542 36.000 8.47 0.00 43.69 2.69
3825 4167 5.871524 GGCTTCTTTGATTCAAGGGAATTTC 59.128 40.000 8.47 6.01 43.69 2.17
3826 4168 5.280164 GGGCTTCTTTGATTCAAGGGAATTT 60.280 40.000 8.47 0.00 43.69 1.82
3827 4169 4.223700 GGGCTTCTTTGATTCAAGGGAATT 59.776 41.667 8.47 0.00 43.69 2.17
3828 4170 3.771479 GGGCTTCTTTGATTCAAGGGAAT 59.229 43.478 8.47 0.00 46.27 3.01
3829 4171 3.165071 GGGCTTCTTTGATTCAAGGGAA 58.835 45.455 8.47 11.05 37.45 3.97
3830 4172 2.109834 TGGGCTTCTTTGATTCAAGGGA 59.890 45.455 8.47 0.00 0.00 4.20
3831 4173 2.528564 TGGGCTTCTTTGATTCAAGGG 58.471 47.619 8.47 2.67 0.00 3.95
3832 4174 3.512724 ACATGGGCTTCTTTGATTCAAGG 59.487 43.478 2.25 2.25 0.00 3.61
3833 4175 4.796038 ACATGGGCTTCTTTGATTCAAG 57.204 40.909 0.00 0.00 0.00 3.02
3834 4176 5.183713 CACTACATGGGCTTCTTTGATTCAA 59.816 40.000 0.00 0.00 0.00 2.69
3835 4177 4.701651 CACTACATGGGCTTCTTTGATTCA 59.298 41.667 0.00 0.00 0.00 2.57
3836 4178 4.702131 ACACTACATGGGCTTCTTTGATTC 59.298 41.667 0.00 0.00 0.00 2.52
3837 4179 4.666512 ACACTACATGGGCTTCTTTGATT 58.333 39.130 0.00 0.00 0.00 2.57
3838 4180 4.263462 TGACACTACATGGGCTTCTTTGAT 60.263 41.667 0.00 0.00 0.00 2.57
3839 4181 3.072330 TGACACTACATGGGCTTCTTTGA 59.928 43.478 0.00 0.00 0.00 2.69
3840 4182 3.411446 TGACACTACATGGGCTTCTTTG 58.589 45.455 0.00 0.00 0.00 2.77
3841 4183 3.788227 TGACACTACATGGGCTTCTTT 57.212 42.857 0.00 0.00 0.00 2.52
3842 4184 3.181445 TGTTGACACTACATGGGCTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3843 4185 2.371841 TGTTGACACTACATGGGCTTCT 59.628 45.455 0.00 0.00 0.00 2.85
3844 4186 2.778299 TGTTGACACTACATGGGCTTC 58.222 47.619 0.00 0.00 0.00 3.86
3845 4187 2.949177 TGTTGACACTACATGGGCTT 57.051 45.000 0.00 0.00 0.00 4.35
3846 4188 3.678806 CGTATGTTGACACTACATGGGCT 60.679 47.826 0.00 0.00 36.89 5.19
3847 4189 2.607635 CGTATGTTGACACTACATGGGC 59.392 50.000 0.00 0.00 36.89 5.36
3848 4190 4.112634 CTCGTATGTTGACACTACATGGG 58.887 47.826 0.00 0.00 36.89 4.00
3849 4191 3.551890 GCTCGTATGTTGACACTACATGG 59.448 47.826 0.00 0.00 36.89 3.66
3850 4192 3.551890 GGCTCGTATGTTGACACTACATG 59.448 47.826 3.47 0.00 36.89 3.21
3851 4193 3.447586 AGGCTCGTATGTTGACACTACAT 59.552 43.478 0.00 0.00 39.44 2.29
3852 4194 2.823747 AGGCTCGTATGTTGACACTACA 59.176 45.455 0.00 0.00 0.00 2.74
3853 4195 3.505464 AGGCTCGTATGTTGACACTAC 57.495 47.619 0.00 0.00 0.00 2.73
3854 4196 4.011698 TGTAGGCTCGTATGTTGACACTA 58.988 43.478 0.00 0.00 0.00 2.74
3885 4227 0.179054 GGTTTATCTCCACCCCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
3886 4228 1.497161 AGGTTTATCTCCACCCCTCG 58.503 55.000 0.00 0.00 32.92 4.63
3893 4235 7.726291 TGTTTGTCCAAATTAGGTTTATCTCCA 59.274 33.333 0.00 0.00 32.36 3.86
3902 4244 6.126409 TGTCTTCTGTTTGTCCAAATTAGGT 58.874 36.000 0.00 0.00 32.36 3.08
3939 4287 9.790389 CCAATACATGCATGCAAAATTTTAAAT 57.210 25.926 26.68 0.00 0.00 1.40
3954 4302 0.107752 TGCGCTCTCCAATACATGCA 60.108 50.000 9.73 0.00 0.00 3.96
3987 4335 6.824305 ATTCCTTAATCTCACACAACAAGG 57.176 37.500 0.00 0.00 33.81 3.61


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

AutoCloner maintained by Alex Coulton.