Multiple sequence alignment - TraesCS1D01G191100

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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 TraesCS1D01G191100 chr1D 100.000 2304 0 0 1 2304 263199944 263197641 0.000000e+00 4255
1 TraesCS1D01G191100 chr1D 100.000 180 0 0 2523 2702 263197422 263197243 1.550000e-87 333
2 TraesCS1D01G191100 chr1D 84.672 274 26 9 420 692 263199256 263198998 2.670000e-65 259
3 TraesCS1D01G191100 chr1D 84.672 274 26 9 689 947 263199525 263199253 2.670000e-65 259
4 TraesCS1D01G191100 chr1D 80.734 327 55 8 1003 1325 262341482 262341804 5.780000e-62 248
5 TraesCS1D01G191100 chr1D 75.478 314 71 5 1016 1326 262334597 262334907 6.030000e-32 148
6 TraesCS1D01G191100 chr1B 93.589 1201 40 11 765 1938 348906026 348904836 0.000000e+00 1757
7 TraesCS1D01G191100 chr1B 97.468 158 3 1 1936 2093 348904478 348904322 4.430000e-68 268
8 TraesCS1D01G191100 chr1B 80.317 315 54 8 1015 1325 349349469 349349159 5.820000e-57 231
9 TraesCS1D01G191100 chr1B 96.117 103 3 1 2081 2183 348903024 348902923 1.660000e-37 167
10 TraesCS1D01G191100 chr1B 94.681 94 4 1 502 594 348906026 348905933 7.800000e-31 145
11 TraesCS1D01G191100 chr1B 92.784 97 7 0 2523 2619 348902684 348902588 1.010000e-29 141
12 TraesCS1D01G191100 chr1B 93.478 92 6 0 428 519 348906196 348906105 1.300000e-28 137
13 TraesCS1D01G191100 chr1B 90.110 91 7 2 2188 2277 348902823 348902734 1.700000e-22 117
14 TraesCS1D01G191100 chr1B 91.667 84 6 1 2619 2702 348900621 348900539 6.110000e-22 115
15 TraesCS1D01G191100 chr1B 87.097 93 6 4 695 781 348906198 348906106 1.710000e-17 100
16 TraesCS1D01G191100 chr1A 90.182 1212 59 37 692 1847 337302108 337300901 0.000000e+00 1524
17 TraesCS1D01G191100 chr1A 87.586 725 46 13 8 688 337302543 337301819 0.000000e+00 800
18 TraesCS1D01G191100 chr1A 83.526 346 42 10 1843 2183 337300661 337300326 2.610000e-80 309
19 TraesCS1D01G191100 chr1A 80.892 314 54 6 1015 1325 337629803 337629493 2.690000e-60 243
20 TraesCS1D01G191100 chr1A 93.506 77 5 0 2201 2277 337300214 337300138 6.110000e-22 115


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 TraesCS1D01G191100 chr1D 263197243 263199944 2701 True 1276.500000 4255 92.336 1 2702 4 chr1D.!!$R1 2701
1 TraesCS1D01G191100 chr1B 348900539 348906198 5659 True 327.444444 1757 92.999 428 2702 9 chr1B.!!$R2 2274
2 TraesCS1D01G191100 chr1A 337300138 337302543 2405 True 687.000000 1524 88.700 8 2277 4 chr1A.!!$R2 2269

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
821 958 0.034198 TCGAACGTGCCCATCAAAGA 59.966 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 4412 0.109132 CCAGCATTTTTGGCCTCGTC 60.109 55.0 3.32 0.0 0.0 4.2 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
56 57 5.468072 AGTGATTGCTAGTTGAAAGTGACAG 59.532 40.000 0.00 0.00 0.00 3.51
70 71 6.821160 TGAAAGTGACAGTATGAAAGTTGTGA 59.179 34.615 0.00 0.00 39.69 3.58
73 74 7.251704 AGTGACAGTATGAAAGTTGTGAAAG 57.748 36.000 0.00 0.00 39.69 2.62
86 87 4.022589 AGTTGTGAAAGTCATGCAGAATGG 60.023 41.667 0.00 0.00 36.86 3.16
87 88 2.229543 TGTGAAAGTCATGCAGAATGGC 59.770 45.455 0.00 0.00 41.53 4.40
95 96 2.618241 TCATGCAGAATGGCGGTAATTC 59.382 45.455 0.00 0.00 36.86 2.17
107 108 3.069729 GGCGGTAATTCTCTAGGTGTGAT 59.930 47.826 0.00 0.00 0.00 3.06
117 118 5.073428 TCTCTAGGTGTGATGGTAGCTATG 58.927 45.833 0.00 0.00 0.00 2.23
124 125 4.976731 GTGTGATGGTAGCTATGTACGAAG 59.023 45.833 0.00 0.00 0.00 3.79
136 137 6.374894 AGCTATGTACGAAGAGTGTACTTTCT 59.625 38.462 5.07 0.00 42.09 2.52
145 146 4.360563 AGAGTGTACTTTCTTGTGTCGTG 58.639 43.478 0.00 0.00 0.00 4.35
160 168 4.336993 TGTGTCGTGGCTTGTAATTTTCTT 59.663 37.500 0.00 0.00 0.00 2.52
166 174 7.169140 GTCGTGGCTTGTAATTTTCTTTCATTT 59.831 33.333 0.00 0.00 0.00 2.32
191 201 3.373439 AGAAAAGCAAATAGAGCAGCTCG 59.627 43.478 16.99 3.32 36.07 5.03
217 227 2.499685 CGAGGTTTAGCGAGGGGG 59.500 66.667 0.00 0.00 0.00 5.40
222 232 0.837940 GGTTTAGCGAGGGGGATCTT 59.162 55.000 0.00 0.00 0.00 2.40
279 289 6.922247 ACTCTTGCTGATGATGTATCTTTG 57.078 37.500 0.00 0.00 36.71 2.77
280 290 5.821470 ACTCTTGCTGATGATGTATCTTTGG 59.179 40.000 0.00 0.00 36.71 3.28
284 294 4.571984 TGCTGATGATGTATCTTTGGTTCG 59.428 41.667 0.00 0.00 36.71 3.95
293 303 8.421002 TGATGTATCTTTGGTTCGAGATCAATA 58.579 33.333 0.00 0.00 34.60 1.90
356 367 4.168760 CGGAAAAGATAGGCAAAGCTTTG 58.831 43.478 30.70 30.70 41.03 2.77
377 388 2.285488 GCGAAGTATAGCTGCCACTTTC 59.715 50.000 11.62 3.40 32.79 2.62
380 392 2.482494 AGTATAGCTGCCACTTTCCCT 58.518 47.619 0.00 0.00 0.00 4.20
443 464 2.878406 TGGTTGCTGCTACTTTTCTCAC 59.122 45.455 13.54 0.00 0.00 3.51
455 476 4.399978 ACTTTTCTCACGACAAAACAACG 58.600 39.130 0.00 0.00 0.00 4.10
495 516 1.992233 TATCGTACCACGTCCGTGCC 61.992 60.000 14.06 3.78 44.16 5.01
609 746 2.224548 ACCTGCCAAACTCTTCCTGTAC 60.225 50.000 0.00 0.00 0.00 2.90
663 800 4.443457 GCTGGCTCTTATAATCAGACCACA 60.443 45.833 0.00 0.00 0.00 4.17
664 801 5.674525 CTGGCTCTTATAATCAGACCACAA 58.325 41.667 0.00 0.00 0.00 3.33
665 802 5.428253 TGGCTCTTATAATCAGACCACAAC 58.572 41.667 0.00 0.00 0.00 3.32
666 803 4.816925 GGCTCTTATAATCAGACCACAACC 59.183 45.833 0.00 0.00 0.00 3.77
667 804 4.816925 GCTCTTATAATCAGACCACAACCC 59.183 45.833 0.00 0.00 0.00 4.11
668 805 5.018539 TCTTATAATCAGACCACAACCCG 57.981 43.478 0.00 0.00 0.00 5.28
669 806 4.712829 TCTTATAATCAGACCACAACCCGA 59.287 41.667 0.00 0.00 0.00 5.14
670 807 3.543680 ATAATCAGACCACAACCCGAG 57.456 47.619 0.00 0.00 0.00 4.63
671 808 0.321653 AATCAGACCACAACCCGAGC 60.322 55.000 0.00 0.00 0.00 5.03
672 809 1.480212 ATCAGACCACAACCCGAGCA 61.480 55.000 0.00 0.00 0.00 4.26
673 810 1.003355 CAGACCACAACCCGAGCAT 60.003 57.895 0.00 0.00 0.00 3.79
674 811 0.606401 CAGACCACAACCCGAGCATT 60.606 55.000 0.00 0.00 0.00 3.56
675 812 0.321653 AGACCACAACCCGAGCATTC 60.322 55.000 0.00 0.00 0.00 2.67
676 813 0.321653 GACCACAACCCGAGCATTCT 60.322 55.000 0.00 0.00 0.00 2.40
677 814 0.606401 ACCACAACCCGAGCATTCTG 60.606 55.000 0.00 0.00 0.00 3.02
678 815 1.503542 CACAACCCGAGCATTCTGC 59.496 57.895 0.00 0.00 45.46 4.26
692 829 5.459110 GCATTCTGCAACCACATTTAATG 57.541 39.130 3.07 3.07 44.26 1.90
693 830 4.330620 GCATTCTGCAACCACATTTAATGG 59.669 41.667 9.88 0.00 44.26 3.16
694 831 6.083887 GCATTCTGCAACCACATTTAATGGT 61.084 40.000 9.88 0.00 43.72 3.55
695 832 8.041893 GCATTCTGCAACCACATTTAATGGTG 62.042 42.308 9.88 5.44 45.36 4.17
703 840 4.032703 CACATTTAATGGTGGCTGCTAC 57.967 45.455 7.70 7.70 33.60 3.58
704 841 3.696051 CACATTTAATGGTGGCTGCTACT 59.304 43.478 15.83 0.00 33.60 2.57
705 842 4.158394 CACATTTAATGGTGGCTGCTACTT 59.842 41.667 15.83 6.03 33.60 2.24
706 843 4.772100 ACATTTAATGGTGGCTGCTACTTT 59.228 37.500 15.83 11.89 33.60 2.66
707 844 5.245977 ACATTTAATGGTGGCTGCTACTTTT 59.754 36.000 15.83 11.58 33.60 2.27
708 845 5.385509 TTTAATGGTGGCTGCTACTTTTC 57.614 39.130 15.83 0.00 0.00 2.29
709 846 2.887151 ATGGTGGCTGCTACTTTTCT 57.113 45.000 15.83 0.00 0.00 2.52
710 847 2.185004 TGGTGGCTGCTACTTTTCTC 57.815 50.000 15.83 0.00 0.00 2.87
711 848 1.419762 TGGTGGCTGCTACTTTTCTCA 59.580 47.619 15.83 1.47 0.00 3.27
712 849 2.158682 TGGTGGCTGCTACTTTTCTCAA 60.159 45.455 15.83 0.00 0.00 3.02
713 850 2.485814 GGTGGCTGCTACTTTTCTCAAG 59.514 50.000 15.83 0.00 0.00 3.02
714 851 3.403038 GTGGCTGCTACTTTTCTCAAGA 58.597 45.455 9.05 0.00 0.00 3.02
715 852 3.187432 GTGGCTGCTACTTTTCTCAAGAC 59.813 47.826 9.05 0.00 0.00 3.01
716 853 3.181455 TGGCTGCTACTTTTCTCAAGACA 60.181 43.478 0.00 0.00 0.00 3.41
717 854 3.815401 GGCTGCTACTTTTCTCAAGACAA 59.185 43.478 0.00 0.00 0.00 3.18
718 855 4.275936 GGCTGCTACTTTTCTCAAGACAAA 59.724 41.667 0.00 0.00 0.00 2.83
719 856 5.447573 GCTGCTACTTTTCTCAAGACAAAG 58.552 41.667 0.00 10.48 33.03 2.77
720 857 5.008118 GCTGCTACTTTTCTCAAGACAAAGT 59.992 40.000 16.87 16.87 38.13 2.66
721 858 6.458888 GCTGCTACTTTTCTCAAGACAAAGTT 60.459 38.462 17.43 8.61 37.04 2.66
722 859 7.391148 TGCTACTTTTCTCAAGACAAAGTTT 57.609 32.000 17.43 0.00 37.04 2.66
723 860 7.250569 TGCTACTTTTCTCAAGACAAAGTTTG 58.749 34.615 14.13 14.13 37.04 2.93
724 861 7.120579 TGCTACTTTTCTCAAGACAAAGTTTGA 59.879 33.333 22.23 0.00 37.04 2.69
725 862 8.131731 GCTACTTTTCTCAAGACAAAGTTTGAT 58.868 33.333 22.23 7.38 37.04 2.57
728 865 9.710900 ACTTTTCTCAAGACAAAGTTTGATTTT 57.289 25.926 22.23 9.77 34.71 1.82
731 868 9.581099 TTTCTCAAGACAAAGTTTGATTTTACC 57.419 29.630 22.23 2.67 33.25 2.85
732 869 8.287439 TCTCAAGACAAAGTTTGATTTTACCA 57.713 30.769 22.23 0.00 33.25 3.25
733 870 8.912988 TCTCAAGACAAAGTTTGATTTTACCAT 58.087 29.630 22.23 0.00 33.25 3.55
734 871 9.185192 CTCAAGACAAAGTTTGATTTTACCATC 57.815 33.333 22.23 5.86 33.25 3.51
735 872 8.912988 TCAAGACAAAGTTTGATTTTACCATCT 58.087 29.630 22.23 8.01 0.00 2.90
736 873 8.971321 CAAGACAAAGTTTGATTTTACCATCTG 58.029 33.333 22.23 3.36 0.00 2.90
737 874 8.463930 AGACAAAGTTTGATTTTACCATCTGA 57.536 30.769 22.23 0.00 0.00 3.27
738 875 8.571336 AGACAAAGTTTGATTTTACCATCTGAG 58.429 33.333 22.23 0.00 0.00 3.35
739 876 8.237811 ACAAAGTTTGATTTTACCATCTGAGT 57.762 30.769 22.23 0.00 0.00 3.41
740 877 9.349713 ACAAAGTTTGATTTTACCATCTGAGTA 57.650 29.630 22.23 0.00 0.00 2.59
743 880 8.425577 AGTTTGATTTTACCATCTGAGTATCG 57.574 34.615 0.00 0.00 38.61 2.92
744 881 8.041323 AGTTTGATTTTACCATCTGAGTATCGT 58.959 33.333 0.00 0.00 38.61 3.73
745 882 9.309516 GTTTGATTTTACCATCTGAGTATCGTA 57.690 33.333 0.00 0.00 38.61 3.43
746 883 8.867112 TTGATTTTACCATCTGAGTATCGTAC 57.133 34.615 0.00 0.00 38.61 3.67
747 884 7.431249 TGATTTTACCATCTGAGTATCGTACC 58.569 38.462 0.00 0.00 38.61 3.34
748 885 6.778834 TTTTACCATCTGAGTATCGTACCA 57.221 37.500 0.00 0.00 38.61 3.25
749 886 5.762825 TTACCATCTGAGTATCGTACCAC 57.237 43.478 0.00 0.00 38.61 4.16
750 887 3.628008 ACCATCTGAGTATCGTACCACA 58.372 45.455 0.00 0.00 38.61 4.17
751 888 4.215908 ACCATCTGAGTATCGTACCACAT 58.784 43.478 0.00 0.00 38.61 3.21
752 889 4.278669 ACCATCTGAGTATCGTACCACATC 59.721 45.833 0.00 0.00 38.61 3.06
753 890 4.321304 CCATCTGAGTATCGTACCACATCC 60.321 50.000 0.00 0.00 38.61 3.51
754 891 2.876550 TCTGAGTATCGTACCACATCCG 59.123 50.000 0.00 0.00 38.61 4.18
755 892 2.617308 CTGAGTATCGTACCACATCCGT 59.383 50.000 0.00 0.00 38.61 4.69
756 893 2.356695 TGAGTATCGTACCACATCCGTG 59.643 50.000 0.00 0.00 39.86 4.94
757 894 1.066605 AGTATCGTACCACATCCGTGC 59.933 52.381 0.00 0.00 42.17 5.34
758 895 1.066605 GTATCGTACCACATCCGTGCT 59.933 52.381 0.00 0.00 42.17 4.40
759 896 0.179111 ATCGTACCACATCCGTGCTG 60.179 55.000 0.00 0.00 42.17 4.41
760 897 1.214325 CGTACCACATCCGTGCTGA 59.786 57.895 0.00 0.00 42.17 4.26
761 898 1.076533 CGTACCACATCCGTGCTGAC 61.077 60.000 0.00 0.00 42.17 3.51
762 899 1.076533 GTACCACATCCGTGCTGACG 61.077 60.000 0.00 0.00 45.67 4.35
772 909 3.664930 GTGCTGACGACATCAAAGC 57.335 52.632 0.00 0.00 36.69 3.51
773 910 0.166814 GTGCTGACGACATCAAAGCC 59.833 55.000 0.00 0.00 36.69 4.35
774 911 0.250252 TGCTGACGACATCAAAGCCA 60.250 50.000 0.00 0.00 36.69 4.75
775 912 0.166814 GCTGACGACATCAAAGCCAC 59.833 55.000 0.00 0.00 36.69 5.01
776 913 0.798776 CTGACGACATCAAAGCCACC 59.201 55.000 0.00 0.00 36.69 4.61
777 914 0.107643 TGACGACATCAAAGCCACCA 59.892 50.000 0.00 0.00 33.02 4.17
778 915 1.234821 GACGACATCAAAGCCACCAA 58.765 50.000 0.00 0.00 0.00 3.67
779 916 1.606668 GACGACATCAAAGCCACCAAA 59.393 47.619 0.00 0.00 0.00 3.28
780 917 1.336755 ACGACATCAAAGCCACCAAAC 59.663 47.619 0.00 0.00 0.00 2.93
781 918 1.335872 CGACATCAAAGCCACCAAACC 60.336 52.381 0.00 0.00 0.00 3.27
782 919 1.963515 GACATCAAAGCCACCAAACCT 59.036 47.619 0.00 0.00 0.00 3.50
783 920 1.963515 ACATCAAAGCCACCAAACCTC 59.036 47.619 0.00 0.00 0.00 3.85
784 921 1.962807 CATCAAAGCCACCAAACCTCA 59.037 47.619 0.00 0.00 0.00 3.86
785 922 2.151502 TCAAAGCCACCAAACCTCAA 57.848 45.000 0.00 0.00 0.00 3.02
786 923 1.754226 TCAAAGCCACCAAACCTCAAC 59.246 47.619 0.00 0.00 0.00 3.18
787 924 1.480137 CAAAGCCACCAAACCTCAACA 59.520 47.619 0.00 0.00 0.00 3.33
788 925 2.086610 AAGCCACCAAACCTCAACAT 57.913 45.000 0.00 0.00 0.00 2.71
789 926 2.086610 AGCCACCAAACCTCAACATT 57.913 45.000 0.00 0.00 0.00 2.71
790 927 2.397597 AGCCACCAAACCTCAACATTT 58.602 42.857 0.00 0.00 0.00 2.32
791 928 2.365293 AGCCACCAAACCTCAACATTTC 59.635 45.455 0.00 0.00 0.00 2.17
792 929 2.365293 GCCACCAAACCTCAACATTTCT 59.635 45.455 0.00 0.00 0.00 2.52
793 930 3.552890 GCCACCAAACCTCAACATTTCTC 60.553 47.826 0.00 0.00 0.00 2.87
794 931 3.891366 CCACCAAACCTCAACATTTCTCT 59.109 43.478 0.00 0.00 0.00 3.10
795 932 5.070001 CCACCAAACCTCAACATTTCTCTA 58.930 41.667 0.00 0.00 0.00 2.43
796 933 5.182001 CCACCAAACCTCAACATTTCTCTAG 59.818 44.000 0.00 0.00 0.00 2.43
797 934 5.765182 CACCAAACCTCAACATTTCTCTAGT 59.235 40.000 0.00 0.00 0.00 2.57
798 935 6.934645 CACCAAACCTCAACATTTCTCTAGTA 59.065 38.462 0.00 0.00 0.00 1.82
799 936 7.118390 CACCAAACCTCAACATTTCTCTAGTAG 59.882 40.741 0.00 0.00 0.00 2.57
800 937 6.092807 CCAAACCTCAACATTTCTCTAGTAGC 59.907 42.308 0.00 0.00 0.00 3.58
801 938 5.000012 ACCTCAACATTTCTCTAGTAGCG 58.000 43.478 0.00 0.00 0.00 4.26
802 939 4.463186 ACCTCAACATTTCTCTAGTAGCGT 59.537 41.667 0.00 0.00 0.00 5.07
803 940 5.038033 CCTCAACATTTCTCTAGTAGCGTC 58.962 45.833 0.00 0.00 0.00 5.19
804 941 4.659088 TCAACATTTCTCTAGTAGCGTCG 58.341 43.478 0.00 0.00 0.00 5.12
805 942 4.393990 TCAACATTTCTCTAGTAGCGTCGA 59.606 41.667 0.00 0.00 0.00 4.20
806 943 4.959596 ACATTTCTCTAGTAGCGTCGAA 57.040 40.909 0.00 0.00 0.00 3.71
807 944 4.660105 ACATTTCTCTAGTAGCGTCGAAC 58.340 43.478 0.00 0.00 0.00 3.95
808 945 3.380486 TTTCTCTAGTAGCGTCGAACG 57.620 47.619 0.00 0.00 45.88 3.95
809 946 2.001812 TCTCTAGTAGCGTCGAACGT 57.998 50.000 0.00 0.00 44.73 3.99
810 947 1.657594 TCTCTAGTAGCGTCGAACGTG 59.342 52.381 0.00 0.00 44.73 4.49
811 948 0.095935 TCTAGTAGCGTCGAACGTGC 59.904 55.000 0.00 0.00 44.73 5.34
812 949 0.860618 CTAGTAGCGTCGAACGTGCC 60.861 60.000 0.00 0.00 44.73 5.01
813 950 2.257286 TAGTAGCGTCGAACGTGCCC 62.257 60.000 0.00 3.41 44.73 5.36
814 951 3.672447 TAGCGTCGAACGTGCCCA 61.672 61.111 0.00 0.00 44.73 5.36
815 952 2.997075 TAGCGTCGAACGTGCCCAT 61.997 57.895 0.00 0.00 44.73 4.00
816 953 2.877360 TAGCGTCGAACGTGCCCATC 62.877 60.000 0.00 0.00 44.73 3.51
817 954 2.431771 CGTCGAACGTGCCCATCA 60.432 61.111 0.00 0.00 36.74 3.07
818 955 2.024868 CGTCGAACGTGCCCATCAA 61.025 57.895 0.00 0.00 36.74 2.57
819 956 1.561717 CGTCGAACGTGCCCATCAAA 61.562 55.000 0.00 0.00 36.74 2.69
820 957 0.165944 GTCGAACGTGCCCATCAAAG 59.834 55.000 0.00 0.00 0.00 2.77
821 958 0.034198 TCGAACGTGCCCATCAAAGA 59.966 50.000 0.00 0.00 0.00 2.52
822 959 0.165944 CGAACGTGCCCATCAAAGAC 59.834 55.000 0.00 0.00 0.00 3.01
823 960 0.165944 GAACGTGCCCATCAAAGACG 59.834 55.000 0.00 0.00 36.14 4.18
824 961 0.534203 AACGTGCCCATCAAAGACGT 60.534 50.000 0.00 0.00 44.67 4.34
825 962 0.949105 ACGTGCCCATCAAAGACGTC 60.949 55.000 7.70 7.70 38.87 4.34
826 963 1.787847 GTGCCCATCAAAGACGTCG 59.212 57.895 10.46 0.00 0.00 5.12
827 964 0.669318 GTGCCCATCAAAGACGTCGA 60.669 55.000 10.46 1.58 0.00 4.20
828 965 0.669318 TGCCCATCAAAGACGTCGAC 60.669 55.000 10.46 5.18 0.00 4.20
829 966 1.683790 GCCCATCAAAGACGTCGACG 61.684 60.000 34.58 34.58 46.33 5.12
841 978 2.756686 CGTCGACGTACCAATCAAAC 57.243 50.000 29.08 0.00 34.11 2.93
842 979 2.052891 CGTCGACGTACCAATCAAACA 58.947 47.619 29.08 0.00 34.11 2.83
843 980 2.090041 CGTCGACGTACCAATCAAACAG 59.910 50.000 29.08 0.00 34.11 3.16
844 981 2.063266 TCGACGTACCAATCAAACAGC 58.937 47.619 0.00 0.00 0.00 4.40
845 982 1.127951 CGACGTACCAATCAAACAGCC 59.872 52.381 0.00 0.00 0.00 4.85
846 983 2.147958 GACGTACCAATCAAACAGCCA 58.852 47.619 0.00 0.00 0.00 4.75
847 984 2.151202 ACGTACCAATCAAACAGCCAG 58.849 47.619 0.00 0.00 0.00 4.85
848 985 2.151202 CGTACCAATCAAACAGCCAGT 58.849 47.619 0.00 0.00 0.00 4.00
849 986 2.552315 CGTACCAATCAAACAGCCAGTT 59.448 45.455 0.00 0.00 43.89 3.16
859 996 3.868619 AACAGCCAGTTTACCTACCAA 57.131 42.857 0.00 0.00 37.03 3.67
860 997 4.382386 AACAGCCAGTTTACCTACCAAT 57.618 40.909 0.00 0.00 37.03 3.16
861 998 4.382386 ACAGCCAGTTTACCTACCAATT 57.618 40.909 0.00 0.00 0.00 2.32
862 999 4.332828 ACAGCCAGTTTACCTACCAATTC 58.667 43.478 0.00 0.00 0.00 2.17
863 1000 3.694566 CAGCCAGTTTACCTACCAATTCC 59.305 47.826 0.00 0.00 0.00 3.01
864 1001 3.021695 GCCAGTTTACCTACCAATTCCC 58.978 50.000 0.00 0.00 0.00 3.97
865 1002 3.562609 GCCAGTTTACCTACCAATTCCCA 60.563 47.826 0.00 0.00 0.00 4.37
866 1003 4.668636 CCAGTTTACCTACCAATTCCCAA 58.331 43.478 0.00 0.00 0.00 4.12
867 1004 5.269189 CCAGTTTACCTACCAATTCCCAAT 58.731 41.667 0.00 0.00 0.00 3.16
868 1005 5.359860 CCAGTTTACCTACCAATTCCCAATC 59.640 44.000 0.00 0.00 0.00 2.67
869 1006 6.187682 CAGTTTACCTACCAATTCCCAATCT 58.812 40.000 0.00 0.00 0.00 2.40
870 1007 6.318900 CAGTTTACCTACCAATTCCCAATCTC 59.681 42.308 0.00 0.00 0.00 2.75
888 1025 8.097662 CCCAATCTCTCTTCCTGTATATAAACC 58.902 40.741 0.00 0.00 0.00 3.27
891 1028 7.598759 TCTCTCTTCCTGTATATAAACCCAC 57.401 40.000 0.00 0.00 0.00 4.61
893 1030 5.895534 TCTCTTCCTGTATATAAACCCACGT 59.104 40.000 0.00 0.00 0.00 4.49
913 1050 1.070134 TGGGCTGGCTCGTATAATCAC 59.930 52.381 0.00 0.00 0.00 3.06
1375 1531 2.185608 GCAAGACGGAGGAGGAGC 59.814 66.667 0.00 0.00 0.00 4.70
1497 1653 2.007641 GTTCGTCGACGTCGTGCTT 61.008 57.895 34.40 0.00 40.80 3.91
1521 1677 3.718210 CTACCTCGGCTGGTTCGGC 62.718 68.421 4.45 0.00 41.22 5.54
1681 1837 4.680237 CCACCGTGCTCGCTTGGA 62.680 66.667 17.49 0.00 39.49 3.53
1708 1864 1.064060 GCAAAGCGAAGTGAACTGTGT 59.936 47.619 0.00 0.00 0.00 3.72
1709 1865 2.851008 GCAAAGCGAAGTGAACTGTGTC 60.851 50.000 0.00 0.00 0.00 3.67
1710 1866 2.604046 AAGCGAAGTGAACTGTGTCT 57.396 45.000 0.00 0.00 0.00 3.41
1711 1867 1.858091 AGCGAAGTGAACTGTGTCTG 58.142 50.000 0.00 0.00 0.00 3.51
1712 1868 1.137086 AGCGAAGTGAACTGTGTCTGT 59.863 47.619 0.00 0.00 0.00 3.41
1713 1869 1.258982 GCGAAGTGAACTGTGTCTGTG 59.741 52.381 0.00 0.00 0.00 3.66
1822 1996 1.751924 GTGTTGTACCAAGGGCAAACA 59.248 47.619 0.00 0.74 0.00 2.83
1901 2318 9.906660 TTTATTGATGCTTAAACAGAAAATCGT 57.093 25.926 0.00 0.00 0.00 3.73
2163 4260 3.890756 ACATGACAATGAAGCCAAACAGA 59.109 39.130 0.00 0.00 37.24 3.41
2189 4286 0.033503 TGATCTCTCGGCTACACCCA 60.034 55.000 0.00 0.00 33.26 4.51
2191 4288 1.384989 ATCTCTCGGCTACACCCACG 61.385 60.000 0.00 0.00 33.26 4.94
2192 4289 2.282674 TCTCGGCTACACCCACGT 60.283 61.111 0.00 0.00 33.26 4.49
2193 4290 1.874345 CTCTCGGCTACACCCACGTT 61.874 60.000 0.00 0.00 33.26 3.99
2194 4291 1.005394 CTCGGCTACACCCACGTTT 60.005 57.895 0.00 0.00 33.26 3.60
2195 4292 0.601841 CTCGGCTACACCCACGTTTT 60.602 55.000 0.00 0.00 33.26 2.43
2196 4293 0.881159 TCGGCTACACCCACGTTTTG 60.881 55.000 0.00 0.00 33.26 2.44
2197 4294 0.881159 CGGCTACACCCACGTTTTGA 60.881 55.000 0.00 0.00 33.26 2.69
2198 4295 1.530323 GGCTACACCCACGTTTTGAT 58.470 50.000 0.00 0.00 0.00 2.57
2218 4412 5.230182 TGATGTATATAGCGCTGAAACAGG 58.770 41.667 22.90 0.00 31.21 4.00
2221 4415 2.203800 TATAGCGCTGAAACAGGACG 57.796 50.000 22.90 0.00 31.21 4.79
2288 4503 5.395682 TGTTAACCATACTTCTAGCGTGT 57.604 39.130 2.48 0.00 0.00 4.49
2294 4509 4.387862 ACCATACTTCTAGCGTGTTTTTCG 59.612 41.667 0.00 0.00 0.00 3.46
2545 4760 1.339610 TGTTTTGCTCCAATTCCACCG 59.660 47.619 0.00 0.00 0.00 4.94
2561 4776 4.717629 CGCTGAACACGAGCCCGA 62.718 66.667 0.00 0.00 39.50 5.14
2607 4822 1.998530 CCCACCAAGAGCCCATGTA 59.001 57.895 0.00 0.00 0.00 2.29
2608 4823 0.394352 CCCACCAAGAGCCCATGTAC 60.394 60.000 0.00 0.00 0.00 2.90
2616 4831 1.135083 AGAGCCCATGTACGAACGAAG 60.135 52.381 0.14 0.00 0.00 3.79
2619 4834 0.999406 CCCATGTACGAACGAAGCAG 59.001 55.000 0.14 0.00 0.00 4.24
2620 4835 0.370273 CCATGTACGAACGAAGCAGC 59.630 55.000 0.14 0.00 0.00 5.25
2621 4836 1.067693 CATGTACGAACGAAGCAGCA 58.932 50.000 0.14 0.00 0.00 4.41
2622 4837 1.660607 CATGTACGAACGAAGCAGCAT 59.339 47.619 0.14 0.00 0.00 3.79
2623 4838 1.067693 TGTACGAACGAAGCAGCATG 58.932 50.000 0.14 0.00 40.87 4.06
2625 4840 1.927174 GTACGAACGAAGCAGCATGAT 59.073 47.619 0.00 0.00 39.69 2.45
2626 4841 1.002366 ACGAACGAAGCAGCATGATC 58.998 50.000 0.00 0.00 39.69 2.92
2628 4843 1.005242 CGAACGAAGCAGCATGATCTG 60.005 52.381 0.00 0.00 39.69 2.90
2629 4844 2.005451 GAACGAAGCAGCATGATCTGT 58.995 47.619 0.00 0.00 39.69 3.41
2636 6817 6.032094 CGAAGCAGCATGATCTGTTATTTTT 58.968 36.000 0.00 0.00 39.69 1.94
2675 6856 0.761802 GGGTCCTGATCTTAGCCCAG 59.238 60.000 9.91 0.00 36.25 4.45
2680 6861 0.879400 CTGATCTTAGCCCAGCAGCG 60.879 60.000 0.00 0.00 38.01 5.18
2682 6863 2.930385 GATCTTAGCCCAGCAGCGCA 62.930 60.000 11.47 0.00 38.01 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.032620 TCACTCTATCTCCCTTTCGCC 58.967 52.381 0.00 0.00 0.00 5.54
27 28 7.761704 TCACTTTCAACTAGCAATCACTCTATC 59.238 37.037 0.00 0.00 0.00 2.08
56 57 6.437928 TGCATGACTTTCACAACTTTCATAC 58.562 36.000 0.00 0.00 0.00 2.39
70 71 0.813184 CCGCCATTCTGCATGACTTT 59.187 50.000 0.00 0.00 34.31 2.66
73 74 1.378531 TTACCGCCATTCTGCATGAC 58.621 50.000 0.00 0.00 34.31 3.06
86 87 3.795623 TCACACCTAGAGAATTACCGC 57.204 47.619 0.00 0.00 0.00 5.68
87 88 4.099573 ACCATCACACCTAGAGAATTACCG 59.900 45.833 0.00 0.00 0.00 4.02
95 96 4.830046 ACATAGCTACCATCACACCTAGAG 59.170 45.833 0.00 0.00 0.00 2.43
107 108 4.267536 ACACTCTTCGTACATAGCTACCA 58.732 43.478 0.00 0.00 0.00 3.25
117 118 5.975939 ACACAAGAAAGTACACTCTTCGTAC 59.024 40.000 6.52 0.00 39.64 3.67
124 125 3.489785 CCACGACACAAGAAAGTACACTC 59.510 47.826 0.00 0.00 0.00 3.51
136 137 4.336993 AGAAAATTACAAGCCACGACACAA 59.663 37.500 0.00 0.00 0.00 3.33
160 168 9.013229 TGCTCTATTTGCTTTTCTAGAAATGAA 57.987 29.630 26.83 18.15 0.00 2.57
166 174 5.738909 AGCTGCTCTATTTGCTTTTCTAGA 58.261 37.500 0.00 0.00 30.96 2.43
172 182 2.704572 ACGAGCTGCTCTATTTGCTTT 58.295 42.857 25.59 0.00 35.76 3.51
191 201 3.762779 TCGCTAAACCTCGCTAAACTAC 58.237 45.455 0.00 0.00 0.00 2.73
203 213 0.837940 AAGATCCCCCTCGCTAAACC 59.162 55.000 0.00 0.00 0.00 3.27
217 227 2.027385 GGGTTCCTGCCATTGAAGATC 58.973 52.381 0.00 0.00 0.00 2.75
222 232 1.734420 TTGGGGGTTCCTGCCATTGA 61.734 55.000 0.00 0.00 36.20 2.57
279 289 4.272504 TGGCGATTTTATTGATCTCGAACC 59.727 41.667 2.80 0.00 0.00 3.62
280 290 5.403897 TGGCGATTTTATTGATCTCGAAC 57.596 39.130 2.80 0.00 0.00 3.95
284 294 6.320171 CCATCATGGCGATTTTATTGATCTC 58.680 40.000 0.00 0.00 29.21 2.75
326 337 3.323979 TGCCTATCTTTTCCGGGTATCTC 59.676 47.826 0.00 0.00 0.00 2.75
356 367 1.941325 AAGTGGCAGCTATACTTCGC 58.059 50.000 0.00 0.00 29.12 4.70
414 426 8.971073 AGAAAAGTAGCAGCAACCATTATTATT 58.029 29.630 0.00 0.00 0.00 1.40
421 442 3.503748 GTGAGAAAAGTAGCAGCAACCAT 59.496 43.478 0.00 0.00 0.00 3.55
426 447 2.223947 TGTCGTGAGAAAAGTAGCAGCA 60.224 45.455 0.00 0.00 45.01 4.41
443 464 5.443142 AAAATCAAACCGTTGTTTTGTCG 57.557 34.783 0.00 0.00 41.92 4.35
455 476 7.280205 ACGATACTCAGATGGTAAAATCAAACC 59.720 37.037 0.00 0.00 36.24 3.27
495 516 3.852471 TTGTTGACTTTGATGTCGTCG 57.148 42.857 0.00 0.00 39.64 5.12
668 805 7.609033 CCATTAAATGTGGTTGCAGAATGCTC 61.609 42.308 3.12 0.00 46.77 4.26
669 806 5.855441 CCATTAAATGTGGTTGCAGAATGCT 60.855 40.000 3.12 0.00 46.77 3.79
670 807 4.330620 CCATTAAATGTGGTTGCAGAATGC 59.669 41.667 0.00 0.00 46.81 3.56
681 818 1.826720 AGCAGCCACCATTAAATGTGG 59.173 47.619 17.98 17.98 42.55 4.17
682 819 3.696051 AGTAGCAGCCACCATTAAATGTG 59.304 43.478 0.00 1.74 0.00 3.21
683 820 3.968265 AGTAGCAGCCACCATTAAATGT 58.032 40.909 0.00 0.00 0.00 2.71
684 821 4.989279 AAGTAGCAGCCACCATTAAATG 57.011 40.909 0.00 0.00 0.00 2.32
685 822 5.716703 AGAAAAGTAGCAGCCACCATTAAAT 59.283 36.000 0.00 0.00 0.00 1.40
686 823 5.076873 AGAAAAGTAGCAGCCACCATTAAA 58.923 37.500 0.00 0.00 0.00 1.52
687 824 4.662278 AGAAAAGTAGCAGCCACCATTAA 58.338 39.130 0.00 0.00 0.00 1.40
688 825 4.261801 GAGAAAAGTAGCAGCCACCATTA 58.738 43.478 0.00 0.00 0.00 1.90
689 826 3.084786 GAGAAAAGTAGCAGCCACCATT 58.915 45.455 0.00 0.00 0.00 3.16
690 827 2.040278 TGAGAAAAGTAGCAGCCACCAT 59.960 45.455 0.00 0.00 0.00 3.55
691 828 1.419762 TGAGAAAAGTAGCAGCCACCA 59.580 47.619 0.00 0.00 0.00 4.17
692 829 2.185004 TGAGAAAAGTAGCAGCCACC 57.815 50.000 0.00 0.00 0.00 4.61
693 830 3.187432 GTCTTGAGAAAAGTAGCAGCCAC 59.813 47.826 0.00 0.00 0.00 5.01
694 831 3.181455 TGTCTTGAGAAAAGTAGCAGCCA 60.181 43.478 0.00 0.00 0.00 4.75
695 832 3.403038 TGTCTTGAGAAAAGTAGCAGCC 58.597 45.455 0.00 0.00 0.00 4.85
696 833 5.008118 ACTTTGTCTTGAGAAAAGTAGCAGC 59.992 40.000 14.18 0.00 41.19 5.25
697 834 6.610741 ACTTTGTCTTGAGAAAAGTAGCAG 57.389 37.500 14.18 1.13 41.19 4.24
698 835 7.120579 TCAAACTTTGTCTTGAGAAAAGTAGCA 59.879 33.333 15.24 6.04 41.93 3.49
699 836 7.472543 TCAAACTTTGTCTTGAGAAAAGTAGC 58.527 34.615 15.24 0.00 41.93 3.58
702 839 9.710900 AAAATCAAACTTTGTCTTGAGAAAAGT 57.289 25.926 1.44 11.83 44.01 2.66
705 842 9.581099 GGTAAAATCAAACTTTGTCTTGAGAAA 57.419 29.630 1.44 0.00 35.14 2.52
706 843 8.744652 TGGTAAAATCAAACTTTGTCTTGAGAA 58.255 29.630 1.44 0.00 35.14 2.87
707 844 8.287439 TGGTAAAATCAAACTTTGTCTTGAGA 57.713 30.769 1.44 0.00 35.14 3.27
708 845 9.185192 GATGGTAAAATCAAACTTTGTCTTGAG 57.815 33.333 1.44 0.00 35.14 3.02
709 846 8.912988 AGATGGTAAAATCAAACTTTGTCTTGA 58.087 29.630 1.44 0.00 36.08 3.02
710 847 8.971321 CAGATGGTAAAATCAAACTTTGTCTTG 58.029 33.333 1.44 0.00 0.00 3.02
711 848 8.912988 TCAGATGGTAAAATCAAACTTTGTCTT 58.087 29.630 1.44 0.00 0.00 3.01
712 849 8.463930 TCAGATGGTAAAATCAAACTTTGTCT 57.536 30.769 1.44 0.00 0.00 3.41
713 850 8.352942 ACTCAGATGGTAAAATCAAACTTTGTC 58.647 33.333 1.44 0.00 0.00 3.18
714 851 8.237811 ACTCAGATGGTAAAATCAAACTTTGT 57.762 30.769 1.44 0.00 0.00 2.83
717 854 8.883731 CGATACTCAGATGGTAAAATCAAACTT 58.116 33.333 0.00 0.00 0.00 2.66
718 855 8.041323 ACGATACTCAGATGGTAAAATCAAACT 58.959 33.333 0.00 0.00 0.00 2.66
719 856 8.197988 ACGATACTCAGATGGTAAAATCAAAC 57.802 34.615 0.00 0.00 0.00 2.93
720 857 9.309516 GTACGATACTCAGATGGTAAAATCAAA 57.690 33.333 0.00 0.00 0.00 2.69
721 858 7.924412 GGTACGATACTCAGATGGTAAAATCAA 59.076 37.037 0.00 0.00 0.00 2.57
722 859 7.068962 TGGTACGATACTCAGATGGTAAAATCA 59.931 37.037 0.00 0.00 0.00 2.57
723 860 7.381678 GTGGTACGATACTCAGATGGTAAAATC 59.618 40.741 0.00 0.00 0.00 2.17
724 861 7.147794 TGTGGTACGATACTCAGATGGTAAAAT 60.148 37.037 0.00 0.00 0.00 1.82
725 862 6.153170 TGTGGTACGATACTCAGATGGTAAAA 59.847 38.462 0.00 0.00 0.00 1.52
726 863 5.653330 TGTGGTACGATACTCAGATGGTAAA 59.347 40.000 0.00 0.00 0.00 2.01
727 864 5.195185 TGTGGTACGATACTCAGATGGTAA 58.805 41.667 0.00 0.00 0.00 2.85
728 865 4.784177 TGTGGTACGATACTCAGATGGTA 58.216 43.478 0.00 0.00 0.00 3.25
729 866 3.628008 TGTGGTACGATACTCAGATGGT 58.372 45.455 0.00 0.00 0.00 3.55
730 867 4.321304 GGATGTGGTACGATACTCAGATGG 60.321 50.000 0.00 0.00 0.00 3.51
731 868 4.613850 CGGATGTGGTACGATACTCAGATG 60.614 50.000 0.00 0.00 35.67 2.90
732 869 3.502595 CGGATGTGGTACGATACTCAGAT 59.497 47.826 0.00 0.00 35.67 2.90
733 870 2.876550 CGGATGTGGTACGATACTCAGA 59.123 50.000 0.00 0.00 35.67 3.27
734 871 2.617308 ACGGATGTGGTACGATACTCAG 59.383 50.000 0.00 0.00 37.67 3.35
735 872 2.356695 CACGGATGTGGTACGATACTCA 59.643 50.000 0.00 0.00 42.59 3.41
736 873 2.857489 GCACGGATGTGGTACGATACTC 60.857 54.545 0.00 0.00 46.51 2.59
737 874 1.066605 GCACGGATGTGGTACGATACT 59.933 52.381 0.00 0.00 46.51 2.12
738 875 1.484356 GCACGGATGTGGTACGATAC 58.516 55.000 0.00 0.00 46.51 2.24
739 876 3.951115 GCACGGATGTGGTACGATA 57.049 52.632 0.00 0.00 46.51 2.92
740 877 4.827481 GCACGGATGTGGTACGAT 57.173 55.556 0.00 0.00 46.51 3.73
746 883 2.094659 GTCGTCAGCACGGATGTGG 61.095 63.158 0.00 0.00 46.70 4.17
747 884 0.737367 ATGTCGTCAGCACGGATGTG 60.737 55.000 0.00 0.00 46.70 3.21
748 885 0.458543 GATGTCGTCAGCACGGATGT 60.459 55.000 0.00 0.00 46.70 3.06
749 886 0.458370 TGATGTCGTCAGCACGGATG 60.458 55.000 0.00 0.00 46.70 3.51
750 887 0.246360 TTGATGTCGTCAGCACGGAT 59.754 50.000 0.00 0.00 46.70 4.18
751 888 0.032815 TTTGATGTCGTCAGCACGGA 59.967 50.000 0.00 0.00 46.70 4.69
752 889 0.439985 CTTTGATGTCGTCAGCACGG 59.560 55.000 0.00 0.00 46.70 4.94
754 891 0.166814 GGCTTTGATGTCGTCAGCAC 59.833 55.000 0.00 0.00 39.76 4.40
755 892 0.250252 TGGCTTTGATGTCGTCAGCA 60.250 50.000 0.00 0.00 38.29 4.41
756 893 0.166814 GTGGCTTTGATGTCGTCAGC 59.833 55.000 0.00 0.00 38.29 4.26
757 894 0.798776 GGTGGCTTTGATGTCGTCAG 59.201 55.000 0.00 0.00 38.29 3.51
758 895 0.107643 TGGTGGCTTTGATGTCGTCA 59.892 50.000 0.00 0.00 34.25 4.35
759 896 1.234821 TTGGTGGCTTTGATGTCGTC 58.765 50.000 0.00 0.00 0.00 4.20
760 897 1.336755 GTTTGGTGGCTTTGATGTCGT 59.663 47.619 0.00 0.00 0.00 4.34
761 898 1.335872 GGTTTGGTGGCTTTGATGTCG 60.336 52.381 0.00 0.00 0.00 4.35
762 899 1.963515 AGGTTTGGTGGCTTTGATGTC 59.036 47.619 0.00 0.00 0.00 3.06
763 900 1.963515 GAGGTTTGGTGGCTTTGATGT 59.036 47.619 0.00 0.00 0.00 3.06
764 901 1.962807 TGAGGTTTGGTGGCTTTGATG 59.037 47.619 0.00 0.00 0.00 3.07
765 902 2.365293 GTTGAGGTTTGGTGGCTTTGAT 59.635 45.455 0.00 0.00 0.00 2.57
766 903 1.754226 GTTGAGGTTTGGTGGCTTTGA 59.246 47.619 0.00 0.00 0.00 2.69
767 904 1.480137 TGTTGAGGTTTGGTGGCTTTG 59.520 47.619 0.00 0.00 0.00 2.77
768 905 1.859302 TGTTGAGGTTTGGTGGCTTT 58.141 45.000 0.00 0.00 0.00 3.51
769 906 2.086610 ATGTTGAGGTTTGGTGGCTT 57.913 45.000 0.00 0.00 0.00 4.35
770 907 2.086610 AATGTTGAGGTTTGGTGGCT 57.913 45.000 0.00 0.00 0.00 4.75
771 908 2.365293 AGAAATGTTGAGGTTTGGTGGC 59.635 45.455 0.00 0.00 0.00 5.01
772 909 3.891366 AGAGAAATGTTGAGGTTTGGTGG 59.109 43.478 0.00 0.00 0.00 4.61
773 910 5.765182 ACTAGAGAAATGTTGAGGTTTGGTG 59.235 40.000 0.00 0.00 0.00 4.17
774 911 5.941788 ACTAGAGAAATGTTGAGGTTTGGT 58.058 37.500 0.00 0.00 0.00 3.67
775 912 6.092807 GCTACTAGAGAAATGTTGAGGTTTGG 59.907 42.308 0.00 0.00 0.00 3.28
776 913 6.183360 CGCTACTAGAGAAATGTTGAGGTTTG 60.183 42.308 0.00 0.00 0.00 2.93
777 914 5.869888 CGCTACTAGAGAAATGTTGAGGTTT 59.130 40.000 0.00 0.00 0.00 3.27
778 915 5.047235 ACGCTACTAGAGAAATGTTGAGGTT 60.047 40.000 0.00 0.00 0.00 3.50
779 916 4.463186 ACGCTACTAGAGAAATGTTGAGGT 59.537 41.667 0.00 0.00 0.00 3.85
780 917 5.000012 ACGCTACTAGAGAAATGTTGAGG 58.000 43.478 0.00 0.00 0.00 3.86
781 918 4.731000 CGACGCTACTAGAGAAATGTTGAG 59.269 45.833 0.00 0.00 0.00 3.02
782 919 4.393990 TCGACGCTACTAGAGAAATGTTGA 59.606 41.667 0.00 0.00 0.00 3.18
783 920 4.659088 TCGACGCTACTAGAGAAATGTTG 58.341 43.478 0.00 0.00 0.00 3.33
784 921 4.959596 TCGACGCTACTAGAGAAATGTT 57.040 40.909 0.00 0.00 0.00 2.71
785 922 4.660105 GTTCGACGCTACTAGAGAAATGT 58.340 43.478 0.00 0.00 0.00 2.71
786 923 3.719840 CGTTCGACGCTACTAGAGAAATG 59.280 47.826 0.00 0.00 33.65 2.32
787 924 3.937874 CGTTCGACGCTACTAGAGAAAT 58.062 45.455 0.00 0.00 33.65 2.17
788 925 3.380486 CGTTCGACGCTACTAGAGAAA 57.620 47.619 0.00 0.00 33.65 2.52
801 938 0.165944 CTTTGATGGGCACGTTCGAC 59.834 55.000 0.00 0.00 0.00 4.20
802 939 0.034198 TCTTTGATGGGCACGTTCGA 59.966 50.000 0.00 0.00 0.00 3.71
803 940 0.165944 GTCTTTGATGGGCACGTTCG 59.834 55.000 0.00 0.00 0.00 3.95
804 941 0.165944 CGTCTTTGATGGGCACGTTC 59.834 55.000 0.00 0.00 0.00 3.95
805 942 0.534203 ACGTCTTTGATGGGCACGTT 60.534 50.000 0.00 0.00 40.68 3.99
806 943 0.949105 GACGTCTTTGATGGGCACGT 60.949 55.000 8.70 0.00 45.92 4.49
807 944 1.787847 GACGTCTTTGATGGGCACG 59.212 57.895 8.70 0.00 36.54 5.34
808 945 0.669318 TCGACGTCTTTGATGGGCAC 60.669 55.000 14.70 0.00 0.00 5.01
809 946 0.669318 GTCGACGTCTTTGATGGGCA 60.669 55.000 14.70 0.00 0.00 5.36
810 947 1.683790 CGTCGACGTCTTTGATGGGC 61.684 60.000 29.08 0.00 34.11 5.36
811 948 2.359792 CGTCGACGTCTTTGATGGG 58.640 57.895 29.08 0.00 34.11 4.00
822 959 2.052891 TGTTTGATTGGTACGTCGACG 58.947 47.619 34.58 34.58 46.33 5.12
823 960 2.159881 GCTGTTTGATTGGTACGTCGAC 60.160 50.000 5.18 5.18 0.00 4.20
824 961 2.063266 GCTGTTTGATTGGTACGTCGA 58.937 47.619 0.00 0.00 0.00 4.20
825 962 1.127951 GGCTGTTTGATTGGTACGTCG 59.872 52.381 0.00 0.00 0.00 5.12
826 963 2.147958 TGGCTGTTTGATTGGTACGTC 58.852 47.619 0.00 0.00 0.00 4.34
827 964 2.151202 CTGGCTGTTTGATTGGTACGT 58.849 47.619 0.00 0.00 0.00 3.57
828 965 2.151202 ACTGGCTGTTTGATTGGTACG 58.849 47.619 0.00 0.00 0.00 3.67
829 966 4.584327 AAACTGGCTGTTTGATTGGTAC 57.416 40.909 19.82 0.00 46.08 3.34
839 976 3.868619 TTGGTAGGTAAACTGGCTGTT 57.131 42.857 3.70 3.70 41.29 3.16
840 977 4.332828 GAATTGGTAGGTAAACTGGCTGT 58.667 43.478 0.00 0.00 0.00 4.40
841 978 3.694566 GGAATTGGTAGGTAAACTGGCTG 59.305 47.826 0.00 0.00 0.00 4.85
842 979 3.308904 GGGAATTGGTAGGTAAACTGGCT 60.309 47.826 0.00 0.00 0.00 4.75
843 980 3.021695 GGGAATTGGTAGGTAAACTGGC 58.978 50.000 0.00 0.00 0.00 4.85
844 981 4.310022 TGGGAATTGGTAGGTAAACTGG 57.690 45.455 0.00 0.00 0.00 4.00
845 982 6.187682 AGATTGGGAATTGGTAGGTAAACTG 58.812 40.000 0.00 0.00 0.00 3.16
846 983 6.217693 AGAGATTGGGAATTGGTAGGTAAACT 59.782 38.462 0.00 0.00 0.00 2.66
847 984 6.424032 AGAGATTGGGAATTGGTAGGTAAAC 58.576 40.000 0.00 0.00 0.00 2.01
848 985 6.447084 AGAGAGATTGGGAATTGGTAGGTAAA 59.553 38.462 0.00 0.00 0.00 2.01
849 986 5.970640 AGAGAGATTGGGAATTGGTAGGTAA 59.029 40.000 0.00 0.00 0.00 2.85
850 987 5.538877 AGAGAGATTGGGAATTGGTAGGTA 58.461 41.667 0.00 0.00 0.00 3.08
851 988 4.375313 AGAGAGATTGGGAATTGGTAGGT 58.625 43.478 0.00 0.00 0.00 3.08
852 989 5.372373 GAAGAGAGATTGGGAATTGGTAGG 58.628 45.833 0.00 0.00 0.00 3.18
853 990 5.131809 AGGAAGAGAGATTGGGAATTGGTAG 59.868 44.000 0.00 0.00 0.00 3.18
854 991 5.039645 AGGAAGAGAGATTGGGAATTGGTA 58.960 41.667 0.00 0.00 0.00 3.25
855 992 3.854994 AGGAAGAGAGATTGGGAATTGGT 59.145 43.478 0.00 0.00 0.00 3.67
856 993 4.205587 CAGGAAGAGAGATTGGGAATTGG 58.794 47.826 0.00 0.00 0.00 3.16
857 994 4.853007 ACAGGAAGAGAGATTGGGAATTG 58.147 43.478 0.00 0.00 0.00 2.32
858 995 6.838401 ATACAGGAAGAGAGATTGGGAATT 57.162 37.500 0.00 0.00 0.00 2.17
859 996 9.621239 TTATATACAGGAAGAGAGATTGGGAAT 57.379 33.333 0.00 0.00 0.00 3.01
860 997 9.447279 TTTATATACAGGAAGAGAGATTGGGAA 57.553 33.333 0.00 0.00 0.00 3.97
861 998 8.871125 GTTTATATACAGGAAGAGAGATTGGGA 58.129 37.037 0.00 0.00 0.00 4.37
862 999 8.097662 GGTTTATATACAGGAAGAGAGATTGGG 58.902 40.741 0.00 0.00 0.00 4.12
863 1000 8.097662 GGGTTTATATACAGGAAGAGAGATTGG 58.902 40.741 0.00 0.00 0.00 3.16
864 1001 8.651389 TGGGTTTATATACAGGAAGAGAGATTG 58.349 37.037 0.00 0.00 0.00 2.67
865 1002 8.652290 GTGGGTTTATATACAGGAAGAGAGATT 58.348 37.037 0.00 0.00 0.00 2.40
866 1003 7.039644 CGTGGGTTTATATACAGGAAGAGAGAT 60.040 40.741 0.00 0.00 0.00 2.75
867 1004 6.264744 CGTGGGTTTATATACAGGAAGAGAGA 59.735 42.308 0.00 0.00 0.00 3.10
868 1005 6.040616 ACGTGGGTTTATATACAGGAAGAGAG 59.959 42.308 0.00 0.00 0.00 3.20
869 1006 5.895534 ACGTGGGTTTATATACAGGAAGAGA 59.104 40.000 0.00 0.00 0.00 3.10
870 1007 5.983720 CACGTGGGTTTATATACAGGAAGAG 59.016 44.000 7.95 0.00 0.00 2.85
891 1028 0.033504 ATTATACGAGCCAGCCCACG 59.966 55.000 0.00 0.00 0.00 4.94
893 1030 1.070134 GTGATTATACGAGCCAGCCCA 59.930 52.381 0.00 0.00 0.00 5.36
913 1050 0.606401 AGAATGCTCGGGTTGTGGTG 60.606 55.000 0.00 0.00 0.00 4.17
960 1116 2.668280 GGAGCAACGAACGGTGAGC 61.668 63.158 16.40 6.36 34.08 4.26
1688 1844 1.064060 ACACAGTTCACTTCGCTTTGC 59.936 47.619 0.00 0.00 0.00 3.68
1708 1864 1.591703 GATGTCACGGCCTCACAGA 59.408 57.895 0.00 0.00 0.00 3.41
1709 1865 1.807165 CGATGTCACGGCCTCACAG 60.807 63.158 0.00 0.00 0.00 3.66
1710 1866 2.261361 CGATGTCACGGCCTCACA 59.739 61.111 0.00 0.21 0.00 3.58
1711 1867 3.188786 GCGATGTCACGGCCTCAC 61.189 66.667 0.00 0.00 0.00 3.51
1822 1996 7.733402 ACAAACAGCAAAATTATTCAGCATT 57.267 28.000 4.80 0.00 0.00 3.56
2057 2846 0.462759 GAGAAAGTGATCTGCCCCGG 60.463 60.000 0.00 0.00 0.00 5.73
2163 4260 1.412079 AGCCGAGAGATCAGCAAGAT 58.588 50.000 0.00 0.00 40.48 2.40
2183 4280 5.526111 GCTATATACATCAAAACGTGGGTGT 59.474 40.000 6.33 6.33 33.14 4.16
2185 4282 4.748102 CGCTATATACATCAAAACGTGGGT 59.252 41.667 0.00 0.00 0.00 4.51
2186 4283 4.377022 GCGCTATATACATCAAAACGTGGG 60.377 45.833 0.00 0.00 0.00 4.61
2189 4286 5.286438 TCAGCGCTATATACATCAAAACGT 58.714 37.500 10.99 0.00 0.00 3.99
2191 4288 7.406553 TGTTTCAGCGCTATATACATCAAAAC 58.593 34.615 10.99 8.51 0.00 2.43
2192 4289 7.254761 CCTGTTTCAGCGCTATATACATCAAAA 60.255 37.037 10.99 0.00 0.00 2.44
2193 4290 6.202762 CCTGTTTCAGCGCTATATACATCAAA 59.797 38.462 10.99 0.00 0.00 2.69
2194 4291 5.696270 CCTGTTTCAGCGCTATATACATCAA 59.304 40.000 10.99 0.00 0.00 2.57
2195 4292 5.010617 TCCTGTTTCAGCGCTATATACATCA 59.989 40.000 10.99 0.96 0.00 3.07
2196 4293 5.346281 GTCCTGTTTCAGCGCTATATACATC 59.654 44.000 10.99 3.79 0.00 3.06
2197 4294 5.230942 GTCCTGTTTCAGCGCTATATACAT 58.769 41.667 10.99 0.00 0.00 2.29
2198 4295 4.617959 GTCCTGTTTCAGCGCTATATACA 58.382 43.478 10.99 11.96 0.00 2.29
2218 4412 0.109132 CCAGCATTTTTGGCCTCGTC 60.109 55.000 3.32 0.00 0.00 4.20
2221 4415 4.050852 CTATTCCAGCATTTTTGGCCTC 57.949 45.455 3.32 0.00 35.62 4.70
2532 4747 0.804989 GTTCAGCGGTGGAATTGGAG 59.195 55.000 15.67 0.00 0.00 3.86
2545 4760 3.112709 GTCGGGCTCGTGTTCAGC 61.113 66.667 5.57 0.00 37.69 4.26
2570 4785 1.448540 CTCAGATGTGGACGGGTGC 60.449 63.158 0.00 0.00 0.00 5.01
2607 4822 1.002366 GATCATGCTGCTTCGTTCGT 58.998 50.000 0.00 0.00 0.00 3.85
2608 4823 1.005242 CAGATCATGCTGCTTCGTTCG 60.005 52.381 0.00 0.00 0.00 3.95
2644 6825 0.620030 CAGGACCCATGTGGACATCA 59.380 55.000 0.00 0.00 37.39 3.07
2680 6861 3.554692 CGTTCGTCGCCCATCTGC 61.555 66.667 0.00 0.00 0.00 4.26
2682 6863 1.153823 CTTCGTTCGTCGCCCATCT 60.154 57.895 0.00 0.00 39.67 2.90


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

AutoCloner maintained by Alex Coulton.