Multiple sequence alignment - TraesCS1B01G400800

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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 TraesCS1B01G400800 chr1B 100.000 3772 0 0 569 4340 631222359 631218588 0.000000e+00 6966
1 TraesCS1B01G400800 chr1B 88.971 3509 350 26 845 4340 631203889 631200405 0.000000e+00 4301
2 TraesCS1B01G400800 chr1B 100.000 257 0 0 1 257 631222927 631222671 3.930000e-130 475
3 TraesCS1B01G400800 chr1D 91.486 3500 261 24 846 4335 459042384 459038912 0.000000e+00 4778
4 TraesCS1B01G400800 chr1D 85.214 3801 491 48 569 4339 459031886 459028127 0.000000e+00 3840
5 TraesCS1B01G400800 chr1D 83.529 255 15 11 1 254 459042815 459042587 3.400000e-51 213
6 TraesCS1B01G400800 chr1A 87.783 3315 364 30 874 4167 551463775 551460481 0.000000e+00 3840
7 TraesCS1B01G400800 chr1A 89.088 669 68 4 3674 4340 551443258 551442593 0.000000e+00 826
8 TraesCS1B01G400800 chr1A 89.020 255 21 5 1 254 551464491 551464243 4.220000e-80 309
9 TraesCS1B01G400800 chr3D 77.173 3417 664 80 981 4338 428245445 428248804 0.000000e+00 1882
10 TraesCS1B01G400800 chr3D 77.021 3390 676 68 998 4337 428251415 428254751 0.000000e+00 1849
11 TraesCS1B01G400800 chr3B 76.952 3406 682 71 981 4338 559880930 559884280 0.000000e+00 1845
12 TraesCS1B01G400800 chr3B 78.315 2006 386 29 998 2977 559886835 559888817 0.000000e+00 1249
13 TraesCS1B01G400800 chr3B 75.833 1320 283 33 3035 4337 559890712 559892012 4.730000e-179 638
14 TraesCS1B01G400800 chr3A 76.946 3392 682 68 998 4340 557413356 557410016 0.000000e+00 1840
15 TraesCS1B01G400800 chr3A 76.636 3407 685 72 992 4338 557419098 557415743 0.000000e+00 1779
16 TraesCS1B01G400800 chr6D 75.413 3388 683 100 1009 4340 469800207 469803500 0.000000e+00 1504
17 TraesCS1B01G400800 chrUn 74.904 3379 701 86 1015 4340 62079765 62076481 0.000000e+00 1406
18 TraesCS1B01G400800 chrUn 76.762 1717 313 43 1015 2703 331320436 331318778 0.000000e+00 881
19 TraesCS1B01G400800 chr7B 76.636 2598 510 69 1780 4340 746528366 746525829 0.000000e+00 1345
20 TraesCS1B01G400800 chr2D 76.613 2031 420 42 1520 3521 633210067 633212071 0.000000e+00 1068
21 TraesCS1B01G400800 chr2D 76.727 1998 411 41 1654 3617 633295418 633293441 0.000000e+00 1064
22 TraesCS1B01G400800 chr7A 76.000 725 144 20 2272 2975 736341960 736342675 8.930000e-92 348


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 TraesCS1B01G400800 chr1B 631218588 631222927 4339 True 3720.5 6966 100.000000 1 4340 2 chr1B.!!$R2 4339
1 TraesCS1B01G400800 chr1B 631200405 631203889 3484 True 4301.0 4301 88.971000 845 4340 1 chr1B.!!$R1 3495
2 TraesCS1B01G400800 chr1D 459028127 459031886 3759 True 3840.0 3840 85.214000 569 4339 1 chr1D.!!$R1 3770
3 TraesCS1B01G400800 chr1D 459038912 459042815 3903 True 2495.5 4778 87.507500 1 4335 2 chr1D.!!$R2 4334
4 TraesCS1B01G400800 chr1A 551460481 551464491 4010 True 2074.5 3840 88.401500 1 4167 2 chr1A.!!$R2 4166
5 TraesCS1B01G400800 chr1A 551442593 551443258 665 True 826.0 826 89.088000 3674 4340 1 chr1A.!!$R1 666
6 TraesCS1B01G400800 chr3D 428245445 428254751 9306 False 1865.5 1882 77.097000 981 4338 2 chr3D.!!$F1 3357
7 TraesCS1B01G400800 chr3B 559880930 559892012 11082 False 1244.0 1845 77.033333 981 4338 3 chr3B.!!$F1 3357
8 TraesCS1B01G400800 chr3A 557410016 557419098 9082 True 1809.5 1840 76.791000 992 4340 2 chr3A.!!$R1 3348
9 TraesCS1B01G400800 chr6D 469800207 469803500 3293 False 1504.0 1504 75.413000 1009 4340 1 chr6D.!!$F1 3331
10 TraesCS1B01G400800 chrUn 62076481 62079765 3284 True 1406.0 1406 74.904000 1015 4340 1 chrUn.!!$R1 3325
11 TraesCS1B01G400800 chrUn 331318778 331320436 1658 True 881.0 881 76.762000 1015 2703 1 chrUn.!!$R2 1688
12 TraesCS1B01G400800 chr7B 746525829 746528366 2537 True 1345.0 1345 76.636000 1780 4340 1 chr7B.!!$R1 2560
13 TraesCS1B01G400800 chr2D 633210067 633212071 2004 False 1068.0 1068 76.613000 1520 3521 1 chr2D.!!$F1 2001
14 TraesCS1B01G400800 chr2D 633293441 633295418 1977 True 1064.0 1064 76.727000 1654 3617 1 chr2D.!!$R1 1963
15 TraesCS1B01G400800 chr7A 736341960 736342675 715 False 348.0 348 76.000000 2272 2975 1 chr7A.!!$F1 703

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
211 214 0.033601 TGCCTTCACCACCTGTTTGT 60.034 50.000 0.00 0.0 0.00 2.83 F
748 755 0.555769 TTCCCCTCACTTTTGGCAGT 59.444 50.000 0.00 0.0 0.00 4.40 F
1176 1515 0.746063 CAGCTGACAAGGGCAACAAA 59.254 50.000 8.42 0.0 39.74 2.83 F
1356 1710 1.064906 CCTCTCCATGCTGTGTCCAAT 60.065 52.381 0.00 0.0 0.00 3.16 F
2053 8154 1.634973 TGGAGAACATGGAAGATGCCA 59.365 47.619 0.00 0.0 43.23 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1458 0.112995 ACTGTGGCATGATGGTGGTT 59.887 50.000 0.0 0.0 0.00 3.67 R
1718 7812 1.000521 ATGCACACCCACATCCTGG 60.001 57.895 0.0 0.0 40.26 4.45 R
3014 15038 0.038618 GTTTGGGATTTGTGGCGGAC 60.039 55.000 0.0 0.0 0.00 4.79 R
3299 23120 1.635663 CTTAAGTTGAGGCGGTGGCG 61.636 60.000 0.0 0.0 41.24 5.69 R
4020 23851 1.737008 GGACCTCTTGCGACGGAAC 60.737 63.158 0.0 0.0 0.00 3.62 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
32 33 3.208747 ACCTCGGATGTTTTCACTTGT 57.791 42.857 0.00 0.00 0.00 3.16
38 39 6.425721 CCTCGGATGTTTTCACTTGTTAGTTA 59.574 38.462 0.00 0.00 30.26 2.24
39 40 7.360101 CCTCGGATGTTTTCACTTGTTAGTTAG 60.360 40.741 0.00 0.00 30.26 2.34
40 41 6.987992 TCGGATGTTTTCACTTGTTAGTTAGT 59.012 34.615 0.00 0.00 30.26 2.24
41 42 7.496591 TCGGATGTTTTCACTTGTTAGTTAGTT 59.503 33.333 0.00 0.00 30.26 2.24
42 43 8.126700 CGGATGTTTTCACTTGTTAGTTAGTTT 58.873 33.333 0.00 0.00 30.26 2.66
43 44 9.797556 GGATGTTTTCACTTGTTAGTTAGTTTT 57.202 29.630 0.00 0.00 30.26 2.43
96 99 4.676924 GTCGGCACAAAAGAAGAATGAAAG 59.323 41.667 0.00 0.00 0.00 2.62
112 115 9.755804 AAGAATGAAAGGAAATCTGTCTTTTTC 57.244 29.630 0.00 0.00 30.08 2.29
119 122 4.024048 GGAAATCTGTCTTTTTCGCTGTGA 60.024 41.667 0.00 0.00 33.58 3.58
129 132 4.749245 TTTTCGCTGTGATCCTTTTCTC 57.251 40.909 0.00 0.00 0.00 2.87
137 140 5.060427 TGTGATCCTTTTCTCCCTTTCAA 57.940 39.130 0.00 0.00 0.00 2.69
138 141 5.644188 TGTGATCCTTTTCTCCCTTTCAAT 58.356 37.500 0.00 0.00 0.00 2.57
147 150 3.575805 TCTCCCTTTCAATGGTTTGCTT 58.424 40.909 0.00 0.00 32.61 3.91
172 175 9.806203 TTATTTATCTCGTCGTTCCAATTTCTA 57.194 29.630 0.00 0.00 0.00 2.10
211 214 0.033601 TGCCTTCACCACCTGTTTGT 60.034 50.000 0.00 0.00 0.00 2.83
227 230 0.687354 TTGTCCCTCCAGAAGCACTC 59.313 55.000 0.00 0.00 0.00 3.51
254 258 7.636150 ATTGTCGATTTCATTTCCTCAGATT 57.364 32.000 0.00 0.00 0.00 2.40
255 259 6.668541 TGTCGATTTCATTTCCTCAGATTC 57.331 37.500 0.00 0.00 0.00 2.52
598 602 8.198778 GGAATAAGTTTTTGTTCCTGTTTACCA 58.801 33.333 8.11 0.00 45.82 3.25
605 609 8.888716 GTTTTTGTTCCTGTTTACCATGATTTT 58.111 29.630 0.00 0.00 0.00 1.82
607 611 9.757227 TTTTGTTCCTGTTTACCATGATTTTAG 57.243 29.630 0.00 0.00 0.00 1.85
608 612 6.919721 TGTTCCTGTTTACCATGATTTTAGC 58.080 36.000 0.00 0.00 0.00 3.09
609 613 6.491745 TGTTCCTGTTTACCATGATTTTAGCA 59.508 34.615 0.00 0.00 0.00 3.49
610 614 6.757897 TCCTGTTTACCATGATTTTAGCAG 57.242 37.500 0.00 0.00 0.00 4.24
612 616 6.719370 TCCTGTTTACCATGATTTTAGCAGTT 59.281 34.615 0.00 0.00 0.00 3.16
614 618 8.519526 CCTGTTTACCATGATTTTAGCAGTTAA 58.480 33.333 0.00 0.00 0.00 2.01
625 629 8.335356 TGATTTTAGCAGTTAATATCAACTCGC 58.665 33.333 7.42 5.50 37.02 5.03
668 675 0.755686 CTCCTCCTGCATCCCACTAC 59.244 60.000 0.00 0.00 0.00 2.73
681 688 1.665137 CCACTACCCAAGTAACCCCT 58.335 55.000 0.00 0.00 35.76 4.79
682 689 1.558294 CCACTACCCAAGTAACCCCTC 59.442 57.143 0.00 0.00 35.76 4.30
684 691 1.152701 ACTACCCAAGTAACCCCTCCA 59.847 52.381 0.00 0.00 36.36 3.86
716 723 6.944234 AAAAGAAAAATCTGTCTTCGGAGT 57.056 33.333 0.00 0.00 32.90 3.85
717 724 6.944234 AAAGAAAAATCTGTCTTCGGAGTT 57.056 33.333 0.00 0.00 38.63 3.01
718 725 6.546972 AAGAAAAATCTGTCTTCGGAGTTC 57.453 37.500 0.00 0.00 36.44 3.01
719 726 5.859495 AGAAAAATCTGTCTTCGGAGTTCT 58.141 37.500 0.00 0.00 36.44 3.01
720 727 6.292150 AGAAAAATCTGTCTTCGGAGTTCTT 58.708 36.000 0.00 0.00 36.44 2.52
721 728 6.768381 AGAAAAATCTGTCTTCGGAGTTCTTT 59.232 34.615 0.00 0.00 36.44 2.52
722 729 6.944234 AAAATCTGTCTTCGGAGTTCTTTT 57.056 33.333 0.00 0.00 36.44 2.27
723 730 8.446599 AAAAATCTGTCTTCGGAGTTCTTTTA 57.553 30.769 0.00 0.00 36.44 1.52
724 731 7.422878 AAATCTGTCTTCGGAGTTCTTTTAC 57.577 36.000 0.00 0.00 32.79 2.01
725 732 4.879598 TCTGTCTTCGGAGTTCTTTTACC 58.120 43.478 0.00 0.00 0.00 2.85
726 733 4.587684 TCTGTCTTCGGAGTTCTTTTACCT 59.412 41.667 0.00 0.00 0.00 3.08
727 734 4.628074 TGTCTTCGGAGTTCTTTTACCTG 58.372 43.478 0.00 0.00 0.00 4.00
728 735 4.100498 TGTCTTCGGAGTTCTTTTACCTGT 59.900 41.667 0.00 0.00 0.00 4.00
729 736 5.055144 GTCTTCGGAGTTCTTTTACCTGTT 58.945 41.667 0.00 0.00 0.00 3.16
730 737 5.526479 GTCTTCGGAGTTCTTTTACCTGTTT 59.474 40.000 0.00 0.00 0.00 2.83
731 738 5.756833 TCTTCGGAGTTCTTTTACCTGTTTC 59.243 40.000 0.00 0.00 0.00 2.78
732 739 4.383173 TCGGAGTTCTTTTACCTGTTTCC 58.617 43.478 0.00 0.00 0.00 3.13
733 740 3.501062 CGGAGTTCTTTTACCTGTTTCCC 59.499 47.826 0.00 0.00 0.00 3.97
734 741 3.825014 GGAGTTCTTTTACCTGTTTCCCC 59.175 47.826 0.00 0.00 0.00 4.81
735 742 4.447325 GGAGTTCTTTTACCTGTTTCCCCT 60.447 45.833 0.00 0.00 0.00 4.79
736 743 4.726583 AGTTCTTTTACCTGTTTCCCCTC 58.273 43.478 0.00 0.00 0.00 4.30
737 744 4.167307 AGTTCTTTTACCTGTTTCCCCTCA 59.833 41.667 0.00 0.00 0.00 3.86
738 745 4.094830 TCTTTTACCTGTTTCCCCTCAC 57.905 45.455 0.00 0.00 0.00 3.51
739 746 3.720002 TCTTTTACCTGTTTCCCCTCACT 59.280 43.478 0.00 0.00 0.00 3.41
740 747 4.167307 TCTTTTACCTGTTTCCCCTCACTT 59.833 41.667 0.00 0.00 0.00 3.16
741 748 4.529716 TTTACCTGTTTCCCCTCACTTT 57.470 40.909 0.00 0.00 0.00 2.66
742 749 4.529716 TTACCTGTTTCCCCTCACTTTT 57.470 40.909 0.00 0.00 0.00 2.27
743 750 2.666317 ACCTGTTTCCCCTCACTTTTG 58.334 47.619 0.00 0.00 0.00 2.44
744 751 1.963515 CCTGTTTCCCCTCACTTTTGG 59.036 52.381 0.00 0.00 0.00 3.28
745 752 1.341209 CTGTTTCCCCTCACTTTTGGC 59.659 52.381 0.00 0.00 0.00 4.52
746 753 1.342474 TGTTTCCCCTCACTTTTGGCA 60.342 47.619 0.00 0.00 0.00 4.92
747 754 1.341209 GTTTCCCCTCACTTTTGGCAG 59.659 52.381 0.00 0.00 0.00 4.85
748 755 0.555769 TTCCCCTCACTTTTGGCAGT 59.444 50.000 0.00 0.00 0.00 4.40
749 756 0.555769 TCCCCTCACTTTTGGCAGTT 59.444 50.000 0.00 0.00 0.00 3.16
750 757 1.777878 TCCCCTCACTTTTGGCAGTTA 59.222 47.619 0.00 0.00 0.00 2.24
751 758 2.162681 CCCCTCACTTTTGGCAGTTAG 58.837 52.381 0.00 0.00 0.00 2.34
752 759 2.224769 CCCCTCACTTTTGGCAGTTAGA 60.225 50.000 0.00 0.00 0.00 2.10
753 760 3.486383 CCCTCACTTTTGGCAGTTAGAA 58.514 45.455 0.00 0.00 0.00 2.10
754 761 4.082125 CCCTCACTTTTGGCAGTTAGAAT 58.918 43.478 0.00 0.00 0.00 2.40
755 762 4.156739 CCCTCACTTTTGGCAGTTAGAATC 59.843 45.833 0.00 0.00 0.00 2.52
756 763 5.006386 CCTCACTTTTGGCAGTTAGAATCT 58.994 41.667 0.00 0.00 0.00 2.40
757 764 5.474876 CCTCACTTTTGGCAGTTAGAATCTT 59.525 40.000 0.00 0.00 0.00 2.40
758 765 6.348868 CCTCACTTTTGGCAGTTAGAATCTTC 60.349 42.308 0.00 0.00 0.00 2.87
759 766 5.473504 TCACTTTTGGCAGTTAGAATCTTCC 59.526 40.000 0.00 0.00 0.00 3.46
760 767 5.241506 CACTTTTGGCAGTTAGAATCTTCCA 59.758 40.000 0.00 0.00 0.00 3.53
761 768 5.833131 ACTTTTGGCAGTTAGAATCTTCCAA 59.167 36.000 0.00 0.00 36.69 3.53
762 769 6.323739 ACTTTTGGCAGTTAGAATCTTCCAAA 59.676 34.615 5.88 5.88 42.79 3.28
763 770 5.964958 TTGGCAGTTAGAATCTTCCAAAG 57.035 39.130 0.00 0.00 35.87 2.77
764 771 4.985538 TGGCAGTTAGAATCTTCCAAAGT 58.014 39.130 0.00 0.00 0.00 2.66
765 772 5.385198 TGGCAGTTAGAATCTTCCAAAGTT 58.615 37.500 0.00 0.00 0.00 2.66
766 773 5.833131 TGGCAGTTAGAATCTTCCAAAGTTT 59.167 36.000 0.00 0.00 0.00 2.66
767 774 6.016276 TGGCAGTTAGAATCTTCCAAAGTTTC 60.016 38.462 0.00 3.41 37.44 2.78
768 775 6.016276 GGCAGTTAGAATCTTCCAAAGTTTCA 60.016 38.462 11.18 0.00 38.88 2.69
769 776 7.309438 GGCAGTTAGAATCTTCCAAAGTTTCAT 60.309 37.037 11.18 2.65 38.88 2.57
770 777 7.752686 GCAGTTAGAATCTTCCAAAGTTTCATC 59.247 37.037 11.18 3.94 38.88 2.92
771 778 9.007901 CAGTTAGAATCTTCCAAAGTTTCATCT 57.992 33.333 11.18 5.47 38.88 2.90
777 784 9.495754 GAATCTTCCAAAGTTTCATCTATTTCG 57.504 33.333 5.89 0.00 37.24 3.46
778 785 7.979444 TCTTCCAAAGTTTCATCTATTTCGT 57.021 32.000 0.00 0.00 0.00 3.85
779 786 7.806690 TCTTCCAAAGTTTCATCTATTTCGTG 58.193 34.615 0.00 0.00 0.00 4.35
780 787 7.444183 TCTTCCAAAGTTTCATCTATTTCGTGT 59.556 33.333 0.00 0.00 0.00 4.49
781 788 7.129109 TCCAAAGTTTCATCTATTTCGTGTC 57.871 36.000 0.00 0.00 0.00 3.67
782 789 6.708502 TCCAAAGTTTCATCTATTTCGTGTCA 59.291 34.615 0.00 0.00 0.00 3.58
783 790 7.390440 TCCAAAGTTTCATCTATTTCGTGTCAT 59.610 33.333 0.00 0.00 0.00 3.06
784 791 8.023128 CCAAAGTTTCATCTATTTCGTGTCATT 58.977 33.333 0.00 0.00 0.00 2.57
787 794 8.771920 AGTTTCATCTATTTCGTGTCATTACA 57.228 30.769 0.00 0.00 0.00 2.41
803 810 7.101054 TGTCATTACACTACACCTTACAATCC 58.899 38.462 0.00 0.00 0.00 3.01
804 811 7.038587 TGTCATTACACTACACCTTACAATCCT 60.039 37.037 0.00 0.00 0.00 3.24
805 812 7.277981 GTCATTACACTACACCTTACAATCCTG 59.722 40.741 0.00 0.00 0.00 3.86
806 813 3.939066 ACACTACACCTTACAATCCTGC 58.061 45.455 0.00 0.00 0.00 4.85
807 814 3.583086 ACACTACACCTTACAATCCTGCT 59.417 43.478 0.00 0.00 0.00 4.24
808 815 4.775780 ACACTACACCTTACAATCCTGCTA 59.224 41.667 0.00 0.00 0.00 3.49
809 816 5.425539 ACACTACACCTTACAATCCTGCTAT 59.574 40.000 0.00 0.00 0.00 2.97
810 817 5.986135 CACTACACCTTACAATCCTGCTATC 59.014 44.000 0.00 0.00 0.00 2.08
811 818 5.900123 ACTACACCTTACAATCCTGCTATCT 59.100 40.000 0.00 0.00 0.00 1.98
812 819 5.028549 ACACCTTACAATCCTGCTATCTG 57.971 43.478 0.00 0.00 0.00 2.90
813 820 4.716784 ACACCTTACAATCCTGCTATCTGA 59.283 41.667 0.00 0.00 0.00 3.27
814 821 5.189736 ACACCTTACAATCCTGCTATCTGAA 59.810 40.000 0.00 0.00 0.00 3.02
815 822 6.115446 CACCTTACAATCCTGCTATCTGAAA 58.885 40.000 0.00 0.00 0.00 2.69
816 823 6.599244 CACCTTACAATCCTGCTATCTGAAAA 59.401 38.462 0.00 0.00 0.00 2.29
817 824 7.121168 CACCTTACAATCCTGCTATCTGAAAAA 59.879 37.037 0.00 0.00 0.00 1.94
818 825 7.836183 ACCTTACAATCCTGCTATCTGAAAAAT 59.164 33.333 0.00 0.00 0.00 1.82
819 826 8.348507 CCTTACAATCCTGCTATCTGAAAAATC 58.651 37.037 0.00 0.00 0.00 2.17
820 827 6.705863 ACAATCCTGCTATCTGAAAAATCC 57.294 37.500 0.00 0.00 0.00 3.01
821 828 5.595952 ACAATCCTGCTATCTGAAAAATCCC 59.404 40.000 0.00 0.00 0.00 3.85
822 829 4.860802 TCCTGCTATCTGAAAAATCCCA 57.139 40.909 0.00 0.00 0.00 4.37
823 830 5.191727 TCCTGCTATCTGAAAAATCCCAA 57.808 39.130 0.00 0.00 0.00 4.12
824 831 5.579047 TCCTGCTATCTGAAAAATCCCAAA 58.421 37.500 0.00 0.00 0.00 3.28
825 832 6.015918 TCCTGCTATCTGAAAAATCCCAAAA 58.984 36.000 0.00 0.00 0.00 2.44
826 833 6.496565 TCCTGCTATCTGAAAAATCCCAAAAA 59.503 34.615 0.00 0.00 0.00 1.94
827 834 6.815142 CCTGCTATCTGAAAAATCCCAAAAAG 59.185 38.462 0.00 0.00 0.00 2.27
828 835 6.165577 TGCTATCTGAAAAATCCCAAAAAGC 58.834 36.000 0.00 0.00 0.00 3.51
829 836 6.165577 GCTATCTGAAAAATCCCAAAAAGCA 58.834 36.000 0.00 0.00 0.00 3.91
830 837 6.650390 GCTATCTGAAAAATCCCAAAAAGCAA 59.350 34.615 0.00 0.00 0.00 3.91
831 838 7.173047 GCTATCTGAAAAATCCCAAAAAGCAAA 59.827 33.333 0.00 0.00 0.00 3.68
832 839 6.923928 TCTGAAAAATCCCAAAAAGCAAAG 57.076 33.333 0.00 0.00 0.00 2.77
833 840 6.648192 TCTGAAAAATCCCAAAAAGCAAAGA 58.352 32.000 0.00 0.00 0.00 2.52
834 841 7.108847 TCTGAAAAATCCCAAAAAGCAAAGAA 58.891 30.769 0.00 0.00 0.00 2.52
835 842 7.609532 TCTGAAAAATCCCAAAAAGCAAAGAAA 59.390 29.630 0.00 0.00 0.00 2.52
836 843 8.115490 TGAAAAATCCCAAAAAGCAAAGAAAA 57.885 26.923 0.00 0.00 0.00 2.29
837 844 8.579863 TGAAAAATCCCAAAAAGCAAAGAAAAA 58.420 25.926 0.00 0.00 0.00 1.94
838 845 9.585099 GAAAAATCCCAAAAAGCAAAGAAAAAT 57.415 25.926 0.00 0.00 0.00 1.82
867 874 2.829023 AGAAATCCGTCCCTGGAGTTA 58.171 47.619 0.00 0.00 45.62 2.24
871 878 3.560636 ATCCGTCCCTGGAGTTATTTG 57.439 47.619 0.00 0.00 42.45 2.32
880 1067 4.832823 CCCTGGAGTTATTTGACCTGTTTT 59.167 41.667 0.00 0.00 0.00 2.43
886 1073 6.208599 GGAGTTATTTGACCTGTTTTCCATCA 59.791 38.462 0.00 0.00 0.00 3.07
893 1080 5.139727 TGACCTGTTTTCCATCATTTGACT 58.860 37.500 0.00 0.00 0.00 3.41
904 1091 9.912634 TTTCCATCATTTGACTGTTAAAATCTC 57.087 29.630 1.72 0.00 0.00 2.75
911 1098 5.705609 TGACTGTTAAAATCTCCCAAAGC 57.294 39.130 0.00 0.00 0.00 3.51
951 1288 8.057011 TGTCTTATACACTACACCTAAGATCCA 58.943 37.037 0.00 0.00 32.70 3.41
1077 1416 1.002251 CTCCTCGCTGATACTTCGACC 60.002 57.143 0.00 0.00 0.00 4.79
1119 1458 1.338105 CGTGAGCTCCATGACCTTGAA 60.338 52.381 12.15 0.00 33.60 2.69
1174 1513 2.195567 GCAGCTGACAAGGGCAACA 61.196 57.895 20.43 0.00 39.74 3.33
1176 1515 0.746063 CAGCTGACAAGGGCAACAAA 59.254 50.000 8.42 0.00 39.74 2.83
1179 1518 1.408702 GCTGACAAGGGCAACAAAAGA 59.591 47.619 0.00 0.00 39.74 2.52
1193 1532 5.514279 CAACAAAAGAACTAAGCTGGACAG 58.486 41.667 0.00 0.00 0.00 3.51
1285 1624 1.237533 TGAGCGCAAATCAAAGAGCA 58.762 45.000 11.47 0.00 32.74 4.26
1318 1672 2.819595 CACCGCATTCCTCCACCG 60.820 66.667 0.00 0.00 0.00 4.94
1341 1695 3.456280 CAGCACTATTCTGAAGCCTCTC 58.544 50.000 0.00 0.00 33.54 3.20
1356 1710 1.064906 CCTCTCCATGCTGTGTCCAAT 60.065 52.381 0.00 0.00 0.00 3.16
1383 1738 3.074390 TGTCCAATCTGTCCTCCAACAAT 59.926 43.478 0.00 0.00 0.00 2.71
1534 7628 3.074390 TCTGGTCACATCAATTCCACCTT 59.926 43.478 0.00 0.00 0.00 3.50
1852 7946 5.765510 TCCAGTGCAAATTAAGGGACATAT 58.234 37.500 0.00 0.00 0.00 1.78
1915 8013 3.146066 TGGTTTGGAAAATCTGACGAGG 58.854 45.455 0.00 0.00 0.00 4.63
2053 8154 1.634973 TGGAGAACATGGAAGATGCCA 59.365 47.619 0.00 0.00 43.23 4.92
2093 8194 1.928868 AACCATGCCTTTTCTGGAGG 58.071 50.000 0.00 0.00 37.35 4.30
2371 8484 7.015680 AGGCTATATATATGACATGAGGGAGG 58.984 42.308 0.00 0.00 0.00 4.30
2438 8551 5.106078 ACGAGAACAGAAGAGTGGAAGATAC 60.106 44.000 0.00 0.00 0.00 2.24
2445 8558 6.214412 ACAGAAGAGTGGAAGATACTGGAAAT 59.786 38.462 0.00 0.00 0.00 2.17
2502 8615 9.527157 TTCTTTCAACCAATTGACCATAGATTA 57.473 29.630 7.12 0.00 44.66 1.75
2606 8725 3.356290 ACAAGGTGGCAGAAATACCATC 58.644 45.455 0.00 0.00 38.46 3.51
2644 8763 4.174411 TCTGTTCGTGTTGAGAGTATGG 57.826 45.455 0.00 0.00 0.00 2.74
2724 8846 6.879458 ACCCAGTTAAAGATGATGTAAGTGAC 59.121 38.462 0.00 0.00 32.28 3.67
2993 15017 4.640201 TGAAGGGCACAATGTTAATCTAGC 59.360 41.667 0.00 0.00 0.00 3.42
3003 15027 6.203530 ACAATGTTAATCTAGCACATGATCCG 59.796 38.462 0.00 0.00 31.37 4.18
3009 15033 2.623416 TCTAGCACATGATCCGTACAGG 59.377 50.000 0.00 0.00 42.97 4.00
3030 16894 2.034999 GGTCCGCCACAAATCCCA 59.965 61.111 0.00 0.00 34.09 4.37
3042 16906 4.244862 CACAAATCCCAAACATAGGCAAC 58.755 43.478 0.00 0.00 0.00 4.17
3063 22881 5.043737 ACCTAACTTTGCTCCAACAACTA 57.956 39.130 0.00 0.00 0.00 2.24
3204 23025 4.798593 GCTTTAGAGTTGAACCTACACCGT 60.799 45.833 0.00 0.00 0.00 4.83
3225 23046 8.500773 CACCGTAAAACTCATCTTAAAAGCTTA 58.499 33.333 0.00 0.00 0.00 3.09
3232 23053 8.807948 AACTCATCTTAAAAGCTTATGCCTTA 57.192 30.769 0.00 0.00 40.80 2.69
3250 23071 7.865530 TGCCTTAACTGGAGTTATATGGATA 57.134 36.000 13.45 0.00 39.89 2.59
3270 23091 7.217200 TGGATAACATAAATGTAGAGGACAGC 58.783 38.462 0.00 0.00 42.79 4.40
3272 23093 7.600752 GGATAACATAAATGTAGAGGACAGCTC 59.399 40.741 0.00 0.00 42.79 4.09
3299 23120 5.420739 ACTTAGAGATTCTGGAAGGTCTGAC 59.579 44.000 0.00 0.00 31.18 3.51
3339 23160 3.161866 GGGCCTCACAATCAAAGGTTAA 58.838 45.455 0.84 0.00 32.49 2.01
3409 23230 4.339530 AGAACTTGGAAACCTTTGAGCTTC 59.660 41.667 0.00 0.00 0.00 3.86
3481 23302 2.104572 TTGCTGCTCACTTCGCCTCT 62.105 55.000 0.00 0.00 0.00 3.69
3501 23322 4.415596 TCTGGAATGTGCCAAACCTAAAT 58.584 39.130 0.00 0.00 37.52 1.40
3622 23443 7.445121 TCAGTGGGAGAACATCATGAATATAC 58.555 38.462 0.00 0.00 0.00 1.47
3629 23450 8.725148 GGAGAACATCATGAATATACACCAATC 58.275 37.037 0.00 0.00 0.00 2.67
3644 23465 4.261801 CACCAATCGGTATCAAACCTTCT 58.738 43.478 0.00 0.00 46.94 2.85
3658 23479 5.466058 TCAAACCTTCTTTTGATAACGCGTA 59.534 36.000 14.46 0.72 39.94 4.42
3659 23480 5.927954 AACCTTCTTTTGATAACGCGTAA 57.072 34.783 14.46 0.00 0.00 3.18
3820 23651 7.333921 GGAATTTGTGATAGAGGATAGCATCAG 59.666 40.741 0.00 0.00 0.00 2.90
3907 23738 4.171878 TGGTTCCACCATCACAACTTAA 57.828 40.909 0.00 0.00 44.79 1.85
3916 23747 6.183360 CCACCATCACAACTTAACAGACTTTT 60.183 38.462 0.00 0.00 0.00 2.27
4020 23851 8.994429 AACTAAGATCATGACTTTGACTACAG 57.006 34.615 18.51 10.65 0.00 2.74
4056 23887 4.351111 AGGTCCTCCTACATTTGACAAAGT 59.649 41.667 6.77 7.36 43.12 2.66
4068 23899 5.906113 TTTGACAAAGTTAAGTTGGCTGA 57.094 34.783 0.00 0.00 34.88 4.26
4076 23907 7.448469 ACAAAGTTAAGTTGGCTGAATATCAGT 59.552 33.333 8.97 0.00 45.94 3.41
4210 24041 4.551388 CCATTATCTCTTACGAGGCTCAC 58.449 47.826 15.95 0.00 37.86 3.51
4238 24069 1.235724 GGTGTGTGGTTGGAGCTAAC 58.764 55.000 0.00 0.00 0.00 2.34
4277 24108 1.205655 CCGCACCTGAGAGATCTTGAA 59.794 52.381 0.00 0.00 0.00 2.69
4314 24145 1.820519 GCCTTGCATCCTTGTCAATCA 59.179 47.619 0.00 0.00 0.00 2.57
4324 24155 6.405508 GCATCCTTGTCAATCAGTCATTTGAT 60.406 38.462 0.00 0.00 39.42 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.755123 ACTAACAAGTGAAAACATCCGAGG 59.245 41.667 0.00 0.00 0.00 4.63
17 18 9.797556 AAAACTAACTAACAAGTGAAAACATCC 57.202 29.630 0.00 0.00 0.00 3.51
20 21 9.834628 CAGAAAACTAACTAACAAGTGAAAACA 57.165 29.630 0.00 0.00 0.00 2.83
38 39 8.140112 TCTAGAGGAAAATAGAGCAGAAAACT 57.860 34.615 0.00 0.00 0.00 2.66
39 40 8.956533 ATCTAGAGGAAAATAGAGCAGAAAAC 57.043 34.615 0.00 0.00 31.81 2.43
71 74 3.629855 TCATTCTTCTTTTGTGCCGACAA 59.370 39.130 0.00 0.00 40.45 3.18
96 99 4.024048 TCACAGCGAAAAAGACAGATTTCC 60.024 41.667 0.00 0.00 33.07 3.13
112 115 1.065854 AGGGAGAAAAGGATCACAGCG 60.066 52.381 0.00 0.00 0.00 5.18
119 122 5.015813 ACCATTGAAAGGGAGAAAAGGAT 57.984 39.130 0.00 0.00 33.23 3.24
129 132 8.260114 AGATAAATAAGCAAACCATTGAAAGGG 58.740 33.333 0.00 0.00 38.94 3.95
137 140 5.815740 ACGACGAGATAAATAAGCAAACCAT 59.184 36.000 0.00 0.00 0.00 3.55
138 141 5.172934 ACGACGAGATAAATAAGCAAACCA 58.827 37.500 0.00 0.00 0.00 3.67
147 150 9.241317 GTAGAAATTGGAACGACGAGATAAATA 57.759 33.333 0.00 0.00 0.00 1.40
172 175 2.624838 CAGCAGTGGATGAAAAACCTGT 59.375 45.455 0.00 0.00 30.05 4.00
211 214 0.710588 TAGGAGTGCTTCTGGAGGGA 59.289 55.000 0.00 0.00 0.00 4.20
227 230 6.763135 TCTGAGGAAATGAAATCGACAATAGG 59.237 38.462 0.00 0.00 0.00 2.57
576 580 8.294954 TCATGGTAAACAGGAACAAAAACTTA 57.705 30.769 0.00 0.00 36.87 2.24
585 589 6.919721 TGCTAAAATCATGGTAAACAGGAAC 58.080 36.000 0.00 0.00 43.90 3.62
605 609 4.928601 ACGCGAGTTGATATTAACTGCTA 58.071 39.130 16.87 0.00 46.40 3.49
606 610 3.782046 ACGCGAGTTGATATTAACTGCT 58.218 40.909 16.87 8.44 46.40 4.24
624 628 1.092348 GTGTTTATTGAGGGGGACGC 58.908 55.000 0.00 0.00 43.76 5.19
625 629 2.781681 AGTGTTTATTGAGGGGGACG 57.218 50.000 0.00 0.00 0.00 4.79
668 675 1.689412 GGTGGAGGGGTTACTTGGG 59.311 63.158 0.00 0.00 0.00 4.12
694 701 6.768381 AGAACTCCGAAGACAGATTTTTCTTT 59.232 34.615 0.00 0.00 32.04 2.52
695 702 6.292150 AGAACTCCGAAGACAGATTTTTCTT 58.708 36.000 0.00 0.00 34.68 2.52
697 704 6.546972 AAGAACTCCGAAGACAGATTTTTC 57.453 37.500 0.00 0.00 0.00 2.29
703 710 4.587684 AGGTAAAAGAACTCCGAAGACAGA 59.412 41.667 0.00 0.00 0.00 3.41
704 711 4.686554 CAGGTAAAAGAACTCCGAAGACAG 59.313 45.833 0.00 0.00 0.00 3.51
705 712 4.100498 ACAGGTAAAAGAACTCCGAAGACA 59.900 41.667 0.00 0.00 0.00 3.41
706 713 4.629092 ACAGGTAAAAGAACTCCGAAGAC 58.371 43.478 0.00 0.00 0.00 3.01
707 714 4.950205 ACAGGTAAAAGAACTCCGAAGA 57.050 40.909 0.00 0.00 0.00 2.87
708 715 5.049612 GGAAACAGGTAAAAGAACTCCGAAG 60.050 44.000 0.00 0.00 0.00 3.79
709 716 4.818005 GGAAACAGGTAAAAGAACTCCGAA 59.182 41.667 0.00 0.00 0.00 4.30
710 717 4.383173 GGAAACAGGTAAAAGAACTCCGA 58.617 43.478 0.00 0.00 0.00 4.55
711 718 3.501062 GGGAAACAGGTAAAAGAACTCCG 59.499 47.826 0.00 0.00 0.00 4.63
712 719 3.825014 GGGGAAACAGGTAAAAGAACTCC 59.175 47.826 0.00 0.00 0.00 3.85
713 720 4.726583 AGGGGAAACAGGTAAAAGAACTC 58.273 43.478 0.00 0.00 0.00 3.01
714 721 4.167307 TGAGGGGAAACAGGTAAAAGAACT 59.833 41.667 0.00 0.00 0.00 3.01
715 722 4.277672 GTGAGGGGAAACAGGTAAAAGAAC 59.722 45.833 0.00 0.00 0.00 3.01
716 723 4.167307 AGTGAGGGGAAACAGGTAAAAGAA 59.833 41.667 0.00 0.00 0.00 2.52
717 724 3.720002 AGTGAGGGGAAACAGGTAAAAGA 59.280 43.478 0.00 0.00 0.00 2.52
718 725 4.100279 AGTGAGGGGAAACAGGTAAAAG 57.900 45.455 0.00 0.00 0.00 2.27
719 726 4.529716 AAGTGAGGGGAAACAGGTAAAA 57.470 40.909 0.00 0.00 0.00 1.52
720 727 4.529716 AAAGTGAGGGGAAACAGGTAAA 57.470 40.909 0.00 0.00 0.00 2.01
721 728 4.211920 CAAAAGTGAGGGGAAACAGGTAA 58.788 43.478 0.00 0.00 0.00 2.85
722 729 3.435890 CCAAAAGTGAGGGGAAACAGGTA 60.436 47.826 0.00 0.00 0.00 3.08
723 730 2.666317 CAAAAGTGAGGGGAAACAGGT 58.334 47.619 0.00 0.00 0.00 4.00
724 731 1.963515 CCAAAAGTGAGGGGAAACAGG 59.036 52.381 0.00 0.00 0.00 4.00
725 732 1.341209 GCCAAAAGTGAGGGGAAACAG 59.659 52.381 0.00 0.00 0.00 3.16
726 733 1.342474 TGCCAAAAGTGAGGGGAAACA 60.342 47.619 0.00 0.00 0.00 2.83
727 734 1.341209 CTGCCAAAAGTGAGGGGAAAC 59.659 52.381 0.00 0.00 0.00 2.78
728 735 1.063266 ACTGCCAAAAGTGAGGGGAAA 60.063 47.619 0.00 0.00 0.00 3.13
729 736 0.555769 ACTGCCAAAAGTGAGGGGAA 59.444 50.000 0.00 0.00 0.00 3.97
730 737 0.555769 AACTGCCAAAAGTGAGGGGA 59.444 50.000 0.00 0.00 0.00 4.81
731 738 2.162681 CTAACTGCCAAAAGTGAGGGG 58.837 52.381 0.00 0.00 0.00 4.79
732 739 3.140325 TCTAACTGCCAAAAGTGAGGG 57.860 47.619 0.00 0.00 30.42 4.30
733 740 5.006386 AGATTCTAACTGCCAAAAGTGAGG 58.994 41.667 0.00 0.00 30.42 3.86
734 741 6.348868 GGAAGATTCTAACTGCCAAAAGTGAG 60.349 42.308 0.00 0.00 33.46 3.51
735 742 5.473504 GGAAGATTCTAACTGCCAAAAGTGA 59.526 40.000 0.00 0.00 33.46 3.41
736 743 5.241506 TGGAAGATTCTAACTGCCAAAAGTG 59.758 40.000 0.00 0.00 39.83 3.16
737 744 5.385198 TGGAAGATTCTAACTGCCAAAAGT 58.615 37.500 0.00 0.00 39.83 2.66
738 745 5.964958 TGGAAGATTCTAACTGCCAAAAG 57.035 39.130 0.00 0.00 39.83 2.27
742 749 4.985538 ACTTTGGAAGATTCTAACTGCCA 58.014 39.130 0.00 0.00 40.91 4.92
743 750 5.966742 AACTTTGGAAGATTCTAACTGCC 57.033 39.130 0.00 0.00 33.84 4.85
744 751 6.970484 TGAAACTTTGGAAGATTCTAACTGC 58.030 36.000 10.62 0.00 39.98 4.40
745 752 9.007901 AGATGAAACTTTGGAAGATTCTAACTG 57.992 33.333 10.62 0.00 39.98 3.16
751 758 9.495754 CGAAATAGATGAAACTTTGGAAGATTC 57.504 33.333 4.37 4.37 39.80 2.52
752 759 9.014297 ACGAAATAGATGAAACTTTGGAAGATT 57.986 29.630 0.00 0.00 0.00 2.40
753 760 8.454106 CACGAAATAGATGAAACTTTGGAAGAT 58.546 33.333 0.00 0.00 0.00 2.40
754 761 7.444183 ACACGAAATAGATGAAACTTTGGAAGA 59.556 33.333 0.00 0.00 0.00 2.87
755 762 7.584987 ACACGAAATAGATGAAACTTTGGAAG 58.415 34.615 0.00 0.00 0.00 3.46
756 763 7.227711 TGACACGAAATAGATGAAACTTTGGAA 59.772 33.333 0.00 0.00 0.00 3.53
757 764 6.708502 TGACACGAAATAGATGAAACTTTGGA 59.291 34.615 0.00 0.00 0.00 3.53
758 765 6.898041 TGACACGAAATAGATGAAACTTTGG 58.102 36.000 0.00 0.00 0.00 3.28
759 766 8.955061 AATGACACGAAATAGATGAAACTTTG 57.045 30.769 0.00 0.00 0.00 2.77
761 768 9.214957 TGTAATGACACGAAATAGATGAAACTT 57.785 29.630 0.00 0.00 0.00 2.66
762 769 8.656849 GTGTAATGACACGAAATAGATGAAACT 58.343 33.333 0.00 0.00 46.23 2.66
763 770 8.807397 GTGTAATGACACGAAATAGATGAAAC 57.193 34.615 0.00 0.00 46.23 2.78
778 785 7.038587 AGGATTGTAAGGTGTAGTGTAATGACA 60.039 37.037 0.00 0.00 0.00 3.58
779 786 7.277981 CAGGATTGTAAGGTGTAGTGTAATGAC 59.722 40.741 0.00 0.00 0.00 3.06
780 787 7.327975 CAGGATTGTAAGGTGTAGTGTAATGA 58.672 38.462 0.00 0.00 0.00 2.57
781 788 6.037172 GCAGGATTGTAAGGTGTAGTGTAATG 59.963 42.308 0.00 0.00 0.00 1.90
782 789 6.070194 AGCAGGATTGTAAGGTGTAGTGTAAT 60.070 38.462 0.00 0.00 0.00 1.89
783 790 5.247564 AGCAGGATTGTAAGGTGTAGTGTAA 59.752 40.000 0.00 0.00 0.00 2.41
784 791 4.775780 AGCAGGATTGTAAGGTGTAGTGTA 59.224 41.667 0.00 0.00 0.00 2.90
785 792 3.583086 AGCAGGATTGTAAGGTGTAGTGT 59.417 43.478 0.00 0.00 0.00 3.55
786 793 4.207891 AGCAGGATTGTAAGGTGTAGTG 57.792 45.455 0.00 0.00 0.00 2.74
787 794 5.900123 AGATAGCAGGATTGTAAGGTGTAGT 59.100 40.000 0.00 0.00 0.00 2.73
788 795 6.040955 TCAGATAGCAGGATTGTAAGGTGTAG 59.959 42.308 0.00 0.00 0.00 2.74
789 796 5.897250 TCAGATAGCAGGATTGTAAGGTGTA 59.103 40.000 0.00 0.00 0.00 2.90
790 797 4.716784 TCAGATAGCAGGATTGTAAGGTGT 59.283 41.667 0.00 0.00 0.00 4.16
791 798 5.282055 TCAGATAGCAGGATTGTAAGGTG 57.718 43.478 0.00 0.00 0.00 4.00
792 799 5.957771 TTCAGATAGCAGGATTGTAAGGT 57.042 39.130 0.00 0.00 0.00 3.50
793 800 7.630242 TTTTTCAGATAGCAGGATTGTAAGG 57.370 36.000 0.00 0.00 0.00 2.69
794 801 8.348507 GGATTTTTCAGATAGCAGGATTGTAAG 58.651 37.037 0.00 0.00 0.00 2.34
795 802 7.285401 GGGATTTTTCAGATAGCAGGATTGTAA 59.715 37.037 0.00 0.00 0.00 2.41
796 803 6.772716 GGGATTTTTCAGATAGCAGGATTGTA 59.227 38.462 0.00 0.00 0.00 2.41
797 804 5.595952 GGGATTTTTCAGATAGCAGGATTGT 59.404 40.000 0.00 0.00 0.00 2.71
798 805 5.595542 TGGGATTTTTCAGATAGCAGGATTG 59.404 40.000 0.00 0.00 0.00 2.67
799 806 5.769835 TGGGATTTTTCAGATAGCAGGATT 58.230 37.500 0.00 0.00 0.00 3.01
800 807 5.393068 TGGGATTTTTCAGATAGCAGGAT 57.607 39.130 0.00 0.00 0.00 3.24
801 808 4.860802 TGGGATTTTTCAGATAGCAGGA 57.139 40.909 0.00 0.00 0.00 3.86
802 809 5.920193 TTTGGGATTTTTCAGATAGCAGG 57.080 39.130 0.00 0.00 0.00 4.85
803 810 6.312180 GCTTTTTGGGATTTTTCAGATAGCAG 59.688 38.462 0.00 0.00 0.00 4.24
804 811 6.165577 GCTTTTTGGGATTTTTCAGATAGCA 58.834 36.000 0.00 0.00 0.00 3.49
805 812 6.165577 TGCTTTTTGGGATTTTTCAGATAGC 58.834 36.000 0.00 0.00 0.00 2.97
806 813 8.606040 TTTGCTTTTTGGGATTTTTCAGATAG 57.394 30.769 0.00 0.00 0.00 2.08
807 814 8.428063 TCTTTGCTTTTTGGGATTTTTCAGATA 58.572 29.630 0.00 0.00 0.00 1.98
808 815 7.281841 TCTTTGCTTTTTGGGATTTTTCAGAT 58.718 30.769 0.00 0.00 0.00 2.90
809 816 6.648192 TCTTTGCTTTTTGGGATTTTTCAGA 58.352 32.000 0.00 0.00 0.00 3.27
810 817 6.923928 TCTTTGCTTTTTGGGATTTTTCAG 57.076 33.333 0.00 0.00 0.00 3.02
811 818 7.693969 TTTCTTTGCTTTTTGGGATTTTTCA 57.306 28.000 0.00 0.00 0.00 2.69
812 819 8.978564 TTTTTCTTTGCTTTTTGGGATTTTTC 57.021 26.923 0.00 0.00 0.00 2.29
835 842 9.869757 CAGGGACGGATTTCTTTTATTTTATTT 57.130 29.630 0.00 0.00 0.00 1.40
836 843 8.474831 CCAGGGACGGATTTCTTTTATTTTATT 58.525 33.333 0.00 0.00 0.00 1.40
837 844 7.837187 TCCAGGGACGGATTTCTTTTATTTTAT 59.163 33.333 0.00 0.00 0.00 1.40
838 845 7.176490 TCCAGGGACGGATTTCTTTTATTTTA 58.824 34.615 0.00 0.00 0.00 1.52
839 846 6.014012 TCCAGGGACGGATTTCTTTTATTTT 58.986 36.000 0.00 0.00 0.00 1.82
840 847 5.576128 TCCAGGGACGGATTTCTTTTATTT 58.424 37.500 0.00 0.00 0.00 1.40
841 848 5.187621 TCCAGGGACGGATTTCTTTTATT 57.812 39.130 0.00 0.00 0.00 1.40
842 849 4.227527 ACTCCAGGGACGGATTTCTTTTAT 59.772 41.667 0.00 0.00 33.56 1.40
843 850 3.585732 ACTCCAGGGACGGATTTCTTTTA 59.414 43.478 0.00 0.00 33.56 1.52
844 851 2.375509 ACTCCAGGGACGGATTTCTTTT 59.624 45.455 0.00 0.00 33.56 2.27
845 852 1.985895 ACTCCAGGGACGGATTTCTTT 59.014 47.619 0.00 0.00 33.56 2.52
846 853 1.657804 ACTCCAGGGACGGATTTCTT 58.342 50.000 0.00 0.00 33.56 2.52
847 854 1.657804 AACTCCAGGGACGGATTTCT 58.342 50.000 0.00 0.00 33.56 2.52
848 855 3.840124 ATAACTCCAGGGACGGATTTC 57.160 47.619 0.00 0.00 33.56 2.17
858 865 5.048013 GGAAAACAGGTCAAATAACTCCAGG 60.048 44.000 0.00 0.00 0.00 4.45
867 874 6.930722 GTCAAATGATGGAAAACAGGTCAAAT 59.069 34.615 0.00 0.00 0.00 2.32
871 878 5.010012 ACAGTCAAATGATGGAAAACAGGTC 59.990 40.000 0.00 0.00 0.00 3.85
880 1067 7.122650 GGGAGATTTTAACAGTCAAATGATGGA 59.877 37.037 0.00 0.00 0.00 3.41
886 1073 7.015584 AGCTTTGGGAGATTTTAACAGTCAAAT 59.984 33.333 0.00 0.00 0.00 2.32
893 1080 5.393866 AGGAAGCTTTGGGAGATTTTAACA 58.606 37.500 0.00 0.00 33.28 2.41
904 1091 1.474077 CGAAATGGAGGAAGCTTTGGG 59.526 52.381 0.00 0.00 0.00 4.12
911 1098 6.338146 TGTATAAGACACGAAATGGAGGAAG 58.662 40.000 0.00 0.00 31.20 3.46
951 1288 5.999205 TTGGGCTGATTTTGACAATGTAT 57.001 34.783 0.00 0.00 0.00 2.29
1099 1438 0.247460 TCAAGGTCATGGAGCTCACG 59.753 55.000 17.19 2.80 39.62 4.35
1119 1458 0.112995 ACTGTGGCATGATGGTGGTT 59.887 50.000 0.00 0.00 0.00 3.67
1174 1513 5.006386 CCATCTGTCCAGCTTAGTTCTTTT 58.994 41.667 0.00 0.00 0.00 2.27
1176 1515 3.840666 TCCATCTGTCCAGCTTAGTTCTT 59.159 43.478 0.00 0.00 0.00 2.52
1179 1518 3.135530 GGATCCATCTGTCCAGCTTAGTT 59.864 47.826 6.95 0.00 34.57 2.24
1193 1532 3.955471 TGTTTGAGGTCTTGGATCCATC 58.045 45.455 17.06 10.40 0.00 3.51
1276 1615 1.561542 GGGATCCTTCCTGCTCTTTGA 59.438 52.381 12.58 0.00 42.20 2.69
1285 1624 1.575447 GGTGGCAAGGGATCCTTCCT 61.575 60.000 12.58 0.00 42.67 3.36
1318 1672 1.020437 GGCTTCAGAATAGTGCTGCC 58.980 55.000 0.00 0.00 33.45 4.85
1341 1695 0.677731 ACCGATTGGACACAGCATGG 60.678 55.000 5.81 0.00 38.85 3.66
1356 1710 1.275291 GAGGACAGATTGGACAACCGA 59.725 52.381 0.00 0.00 39.42 4.69
1383 1738 2.240493 GCTGGCGAATTAGCTTCCTA 57.760 50.000 10.49 0.00 36.99 2.94
1440 1795 7.254590 GCTGATAAGCAAAGAAGATCACGTAAT 60.255 37.037 0.00 0.00 34.41 1.89
1534 7628 5.929992 CCTTGTCACGACCTATTACTTTTGA 59.070 40.000 0.00 0.00 0.00 2.69
1718 7812 1.000521 ATGCACACCCACATCCTGG 60.001 57.895 0.00 0.00 40.26 4.45
1852 7946 4.276678 CAGGAATTTCTGTGAGTCTTGCAA 59.723 41.667 5.49 0.00 0.00 4.08
1915 8013 2.873797 GGAGTTGCTCCCATTCCAC 58.126 57.895 3.89 0.00 44.36 4.02
2053 8154 3.297134 TTGGAAGAGTGCCAAGAACTT 57.703 42.857 0.00 0.00 40.32 2.66
2093 8194 5.500931 CGCAAACTATGTTCTCCGATTTCTC 60.501 44.000 0.00 0.00 0.00 2.87
2371 8484 1.244019 GCCATCCACAGGTGAACCAC 61.244 60.000 1.62 0.00 38.89 4.16
2438 8551 4.458295 ACTCACTGAAGCAATCATTTCCAG 59.542 41.667 0.00 0.00 37.44 3.86
2445 8558 3.141398 GACCAACTCACTGAAGCAATCA 58.859 45.455 0.00 0.00 36.38 2.57
2502 8615 8.523658 AGATCATGCATAACATAGTATGTACGT 58.476 33.333 16.08 3.86 44.07 3.57
2606 8725 6.527023 ACGAACAGATAAATGTCGAACAGTAG 59.473 38.462 0.00 0.00 31.50 2.57
2607 8726 6.307077 CACGAACAGATAAATGTCGAACAGTA 59.693 38.462 0.00 0.00 31.50 2.74
2644 8763 5.691508 CAAATGCTTTGCTTATGCTGTAC 57.308 39.130 1.96 0.00 40.48 2.90
2724 8846 8.560576 AATTCCGCAATATCTGATTAAAAACG 57.439 30.769 0.00 0.00 0.00 3.60
2788 14806 2.642139 ATTGATTCTGGCAACTTGCG 57.358 45.000 7.67 0.00 46.21 4.85
3003 15027 1.600107 TGGCGGACCAATCCTGTAC 59.400 57.895 0.00 0.00 45.37 2.90
3014 15038 0.038618 GTTTGGGATTTGTGGCGGAC 60.039 55.000 0.00 0.00 0.00 4.79
3017 15041 2.159254 CCTATGTTTGGGATTTGTGGCG 60.159 50.000 0.00 0.00 0.00 5.69
3021 15045 3.260632 GGTTGCCTATGTTTGGGATTTGT 59.739 43.478 0.00 0.00 0.00 2.83
3030 16894 5.134202 GCAAAGTTAGGTTGCCTATGTTT 57.866 39.130 0.00 0.00 44.53 2.83
3042 16906 5.531287 ACTTAGTTGTTGGAGCAAAGTTAGG 59.469 40.000 0.00 0.00 0.00 2.69
3204 23025 9.243105 AGGCATAAGCTTTTAAGATGAGTTTTA 57.757 29.630 3.20 0.00 41.70 1.52
3225 23046 6.763715 TCCATATAACTCCAGTTAAGGCAT 57.236 37.500 3.31 0.00 42.93 4.40
3250 23071 6.109359 GTGAGCTGTCCTCTACATTTATGTT 58.891 40.000 0.00 0.00 41.35 2.71
3270 23091 5.186797 ACCTTCCAGAATCTCTAAGTGTGAG 59.813 44.000 1.83 0.00 0.00 3.51
3272 23093 5.186797 AGACCTTCCAGAATCTCTAAGTGTG 59.813 44.000 1.83 0.00 0.00 3.82
3299 23120 1.635663 CTTAAGTTGAGGCGGTGGCG 61.636 60.000 0.00 0.00 41.24 5.69
3339 23160 5.361857 CCAACCTGGATATTTTGCAGATCTT 59.638 40.000 0.00 0.00 46.09 2.40
3390 23211 4.926140 AAGAAGCTCAAAGGTTTCCAAG 57.074 40.909 0.00 0.00 35.86 3.61
3409 23230 5.393962 GCCTTCTAACACAGTGCAATTAAG 58.606 41.667 0.00 0.00 0.00 1.85
3481 23302 8.546083 AATATATTTAGGTTTGGCACATTCCA 57.454 30.769 0.00 0.00 39.30 3.53
3501 23322 7.989947 ACCTTCTGGAAGACAAGGTAATATA 57.010 36.000 11.44 0.00 46.03 0.86
3521 23342 8.646900 TGGCAATTGATAAACTTTTAAGACCTT 58.353 29.630 10.34 0.00 0.00 3.50
3644 23465 4.063689 TGAACCCTTACGCGTTATCAAAA 58.936 39.130 20.78 2.78 0.00 2.44
3658 23479 3.394606 ACTGAACCATGTACTGAACCCTT 59.605 43.478 0.00 0.00 0.00 3.95
3659 23480 2.979678 ACTGAACCATGTACTGAACCCT 59.020 45.455 0.00 0.00 0.00 4.34
3662 23483 7.667043 TTTGATACTGAACCATGTACTGAAC 57.333 36.000 0.00 0.00 0.00 3.18
3907 23738 4.889409 TGCATGAAGAAAGGAAAAGTCTGT 59.111 37.500 0.00 0.00 0.00 3.41
3916 23747 6.946340 TCTGTAATACTGCATGAAGAAAGGA 58.054 36.000 8.02 0.00 0.00 3.36
4020 23851 1.737008 GGACCTCTTGCGACGGAAC 60.737 63.158 0.00 0.00 0.00 3.62
4042 23873 7.067615 TCAGCCAACTTAACTTTGTCAAATGTA 59.932 33.333 0.00 0.00 0.00 2.29
4068 23899 5.171339 AGACACCAGCAAGAACTGATATT 57.829 39.130 0.00 0.00 40.25 1.28
4076 23907 2.170397 TGACTTGAGACACCAGCAAGAA 59.830 45.455 0.00 0.00 41.03 2.52
4210 24041 5.601662 CTCCAACCACACACCAGTATATAG 58.398 45.833 0.00 0.00 0.00 1.31
4238 24069 2.672478 CGGCAGACCACTACTGAAGAAG 60.672 54.545 0.00 0.00 37.54 2.85
4277 24108 2.639327 GCTTCCGCAGCCAACCATT 61.639 57.895 0.00 0.00 43.65 3.16
4314 24145 3.726557 TGCAAGGGAGATCAAATGACT 57.273 42.857 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.