Multiple sequence alignment - TraesCS7B01G253500

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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 TraesCS7B01G253500 chr7B 100.000 3893 0 0 1 3893 467447534 467443642 0.000000e+00 7190.0
1 TraesCS7B01G253500 chr7B 92.798 722 45 5 3177 3893 428928607 428929326 0.000000e+00 1038.0
2 TraesCS7B01G253500 chr7A 90.030 1986 139 38 1214 3172 546631587 546633540 0.000000e+00 2516.0
3 TraesCS7B01G253500 chr7A 94.167 120 7 0 680 799 514778224 514778105 2.390000e-42 183.0
4 TraesCS7B01G253500 chr7D 97.226 1442 34 4 1745 3180 449460242 449458801 0.000000e+00 2436.0
5 TraesCS7B01G253500 chr7D 91.969 772 31 16 866 1615 449461138 449460376 0.000000e+00 1053.0
6 TraesCS7B01G253500 chr7D 92.083 480 31 6 1 475 449462221 449461744 0.000000e+00 669.0
7 TraesCS7B01G253500 chr7D 95.413 109 5 0 482 590 449461461 449461353 1.440000e-39 174.0
8 TraesCS7B01G253500 chr7D 100.000 60 0 0 603 662 579041783 579041842 1.140000e-20 111.0
9 TraesCS7B01G253500 chr2B 93.767 722 41 2 3175 3893 571813479 571814199 0.000000e+00 1081.0
10 TraesCS7B01G253500 chr2B 90.984 732 50 9 3173 3893 175651935 175651209 0.000000e+00 972.0
11 TraesCS7B01G253500 chr2B 93.496 123 7 1 679 801 30160586 30160465 8.590000e-42 182.0
12 TraesCS7B01G253500 chr1B 93.251 726 44 3 3172 3893 453697420 453698144 0.000000e+00 1064.0
13 TraesCS7B01G253500 chr1B 90.997 722 48 9 3175 3893 363453233 363453940 0.000000e+00 957.0
14 TraesCS7B01G253500 chr1B 94.915 118 6 0 676 793 592409195 592409312 6.640000e-43 185.0
15 TraesCS7B01G253500 chr1B 94.118 119 6 1 680 798 65429016 65428899 3.090000e-41 180.0
16 TraesCS7B01G253500 chr1B 94.118 51 1 2 826 875 685176719 685176768 4.170000e-10 76.8
17 TraesCS7B01G253500 chr4B 93.084 723 45 3 3175 3893 47031306 47030585 0.000000e+00 1053.0
18 TraesCS7B01G253500 chr4B 91.609 727 54 5 3172 3893 29195240 29195964 0.000000e+00 998.0
19 TraesCS7B01G253500 chr4B 96.552 116 4 0 680 795 575776800 575776915 3.970000e-45 193.0
20 TraesCS7B01G253500 chr5B 90.041 723 65 5 3175 3893 536430485 536431204 0.000000e+00 929.0
21 TraesCS7B01G253500 chr5B 95.763 118 5 0 676 793 557534277 557534394 1.430000e-44 191.0
22 TraesCS7B01G253500 chr1D 88.587 736 63 14 3170 3893 426441540 426440814 0.000000e+00 874.0
23 TraesCS7B01G253500 chr1D 98.413 63 1 0 603 665 185743713 185743651 1.140000e-20 111.0
24 TraesCS7B01G253500 chr1D 100.000 60 0 0 603 662 204063289 204063348 1.140000e-20 111.0
25 TraesCS7B01G253500 chr2A 95.652 115 5 0 680 794 60769394 60769508 6.640000e-43 185.0
26 TraesCS7B01G253500 chr3B 94.118 119 7 0 676 794 240342898 240343016 8.590000e-42 182.0
27 TraesCS7B01G253500 chr1A 92.683 123 9 0 676 798 49126773 49126651 1.110000e-40 178.0
28 TraesCS7B01G253500 chr6A 94.253 87 4 1 791 876 155857392 155857478 8.780000e-27 132.0
29 TraesCS7B01G253500 chr5D 95.946 74 3 0 794 867 80018342 80018269 1.900000e-23 121.0
30 TraesCS7B01G253500 chr5D 100.000 60 0 0 603 662 301054449 301054508 1.140000e-20 111.0
31 TraesCS7B01G253500 chr6B 94.595 74 4 0 794 867 606985543 606985616 8.840000e-22 115.0
32 TraesCS7B01G253500 chrUn 98.413 63 1 0 603 665 281713797 281713735 1.140000e-20 111.0
33 TraesCS7B01G253500 chrUn 100.000 60 0 0 603 662 378556588 378556647 1.140000e-20 111.0
34 TraesCS7B01G253500 chrUn 100.000 60 0 0 603 662 424118945 424119004 1.140000e-20 111.0
35 TraesCS7B01G253500 chrUn 98.413 63 1 0 603 665 430366081 430366019 1.140000e-20 111.0
36 TraesCS7B01G253500 chr2D 100.000 60 0 0 603 662 200926346 200926405 1.140000e-20 111.0
37 TraesCS7B01G253500 chr4A 92.208 77 6 0 791 867 350172333 350172409 4.110000e-20 110.0


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 TraesCS7B01G253500 chr7B 467443642 467447534 3892 True 7190 7190 100.00000 1 3893 1 chr7B.!!$R1 3892
1 TraesCS7B01G253500 chr7B 428928607 428929326 719 False 1038 1038 92.79800 3177 3893 1 chr7B.!!$F1 716
2 TraesCS7B01G253500 chr7A 546631587 546633540 1953 False 2516 2516 90.03000 1214 3172 1 chr7A.!!$F1 1958
3 TraesCS7B01G253500 chr7D 449458801 449462221 3420 True 1083 2436 94.17275 1 3180 4 chr7D.!!$R1 3179
4 TraesCS7B01G253500 chr2B 571813479 571814199 720 False 1081 1081 93.76700 3175 3893 1 chr2B.!!$F1 718
5 TraesCS7B01G253500 chr2B 175651209 175651935 726 True 972 972 90.98400 3173 3893 1 chr2B.!!$R2 720
6 TraesCS7B01G253500 chr1B 453697420 453698144 724 False 1064 1064 93.25100 3172 3893 1 chr1B.!!$F2 721
7 TraesCS7B01G253500 chr1B 363453233 363453940 707 False 957 957 90.99700 3175 3893 1 chr1B.!!$F1 718
8 TraesCS7B01G253500 chr4B 47030585 47031306 721 True 1053 1053 93.08400 3175 3893 1 chr4B.!!$R1 718
9 TraesCS7B01G253500 chr4B 29195240 29195964 724 False 998 998 91.60900 3172 3893 1 chr4B.!!$F1 721
10 TraesCS7B01G253500 chr5B 536430485 536431204 719 False 929 929 90.04100 3175 3893 1 chr5B.!!$F1 718
11 TraesCS7B01G253500 chr1D 426440814 426441540 726 True 874 874 88.58700 3170 3893 1 chr1D.!!$R2 723

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
855 1149 0.033504 GGGTCTGTCGCTCAGTTGAA 59.966 55.0 7.18 0.0 43.97 2.69 F
2051 2425 0.254178 AATCTGCAGTGGATTCGGCT 59.746 50.0 14.67 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 2937 0.317770 TTTTCAGCCTTTTCTGCGCG 60.318 50.000 0.00 0.0 34.19 6.86 R
3133 3511 1.372997 CGGTGTCCGGTCAACTGAG 60.373 63.158 14.83 0.0 44.15 3.35 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
26 28 7.712264 TCACAAACATTTTTGAATCATGGAC 57.288 32.000 11.21 0.00 44.38 4.02
310 316 6.679327 TTTAAAACATTTTTGGAAACCGGG 57.321 33.333 6.32 0.00 0.00 5.73
315 321 2.162264 TTTTTGGAAACCGGGGAACT 57.838 45.000 6.32 0.00 0.00 3.01
409 415 9.762933 TTAGAATCTTTTTGAAATCCCAAACAG 57.237 29.630 0.00 0.00 35.95 3.16
413 419 7.841915 TCTTTTTGAAATCCCAAACAGTTTC 57.158 32.000 0.00 0.00 36.06 2.78
418 424 7.595819 TTGAAATCCCAAACAGTTTCTACAT 57.404 32.000 0.00 0.00 33.06 2.29
420 426 8.698973 TGAAATCCCAAACAGTTTCTACATAA 57.301 30.769 0.00 0.00 33.06 1.90
539 821 2.364632 TGGTCTTTGTTGGTGTCACTG 58.635 47.619 2.35 0.00 0.00 3.66
606 900 8.352752 GCTTTGTTGCCAATTAGGATTATTAC 57.647 34.615 0.00 0.00 41.22 1.89
607 901 7.978975 GCTTTGTTGCCAATTAGGATTATTACA 59.021 33.333 0.00 0.00 41.22 2.41
609 903 8.815565 TTGTTGCCAATTAGGATTATTACAGA 57.184 30.769 0.00 0.00 41.22 3.41
610 904 8.995027 TGTTGCCAATTAGGATTATTACAGAT 57.005 30.769 0.00 0.00 41.22 2.90
611 905 8.849168 TGTTGCCAATTAGGATTATTACAGATG 58.151 33.333 0.00 0.00 41.22 2.90
612 906 8.299570 GTTGCCAATTAGGATTATTACAGATGG 58.700 37.037 0.00 0.00 41.22 3.51
613 907 7.754624 TGCCAATTAGGATTATTACAGATGGA 58.245 34.615 0.00 0.00 41.22 3.41
614 908 7.665559 TGCCAATTAGGATTATTACAGATGGAC 59.334 37.037 0.00 0.00 41.22 4.02
616 910 9.573166 CCAATTAGGATTATTACAGATGGACAA 57.427 33.333 0.00 0.00 41.22 3.18
643 937 6.959639 TGTTTGGAAACAGAGCTCTTTTAT 57.040 33.333 15.27 5.32 43.45 1.40
644 938 6.970484 TGTTTGGAAACAGAGCTCTTTTATC 58.030 36.000 15.27 13.44 43.45 1.75
645 939 5.862924 TTGGAAACAGAGCTCTTTTATCG 57.137 39.130 15.27 4.00 44.54 2.92
646 940 3.684788 TGGAAACAGAGCTCTTTTATCGC 59.315 43.478 15.27 5.00 35.01 4.58
649 943 1.476891 ACAGAGCTCTTTTATCGCGGA 59.523 47.619 15.27 0.00 0.00 5.54
651 945 3.126831 CAGAGCTCTTTTATCGCGGAAT 58.873 45.455 15.27 0.00 0.00 3.01
653 947 4.745125 CAGAGCTCTTTTATCGCGGAATTA 59.255 41.667 15.27 0.00 0.00 1.40
654 948 4.985409 AGAGCTCTTTTATCGCGGAATTAG 59.015 41.667 11.45 0.00 0.00 1.73
656 950 4.745620 AGCTCTTTTATCGCGGAATTAGAC 59.254 41.667 6.13 0.63 0.00 2.59
657 951 4.084485 GCTCTTTTATCGCGGAATTAGACC 60.084 45.833 6.13 0.00 0.00 3.85
658 952 5.013568 TCTTTTATCGCGGAATTAGACCA 57.986 39.130 6.13 0.00 0.00 4.02
659 953 5.047847 TCTTTTATCGCGGAATTAGACCAG 58.952 41.667 6.13 0.00 0.00 4.00
660 954 2.433868 TATCGCGGAATTAGACCAGC 57.566 50.000 6.13 0.00 0.00 4.85
661 955 0.753262 ATCGCGGAATTAGACCAGCT 59.247 50.000 6.13 0.00 0.00 4.24
662 956 0.535335 TCGCGGAATTAGACCAGCTT 59.465 50.000 6.13 0.00 0.00 3.74
663 957 1.066430 TCGCGGAATTAGACCAGCTTT 60.066 47.619 6.13 0.00 0.00 3.51
664 958 1.737793 CGCGGAATTAGACCAGCTTTT 59.262 47.619 0.00 0.00 0.00 2.27
665 959 2.161609 CGCGGAATTAGACCAGCTTTTT 59.838 45.455 0.00 0.00 0.00 1.94
685 979 4.875544 TTTTTAGCATCAGTACATCGCC 57.124 40.909 0.00 0.00 0.00 5.54
686 980 2.134201 TTAGCATCAGTACATCGCCG 57.866 50.000 0.00 0.00 0.00 6.46
687 981 1.314730 TAGCATCAGTACATCGCCGA 58.685 50.000 0.00 0.00 0.00 5.54
688 982 0.459899 AGCATCAGTACATCGCCGAA 59.540 50.000 0.00 0.00 0.00 4.30
689 983 1.134818 AGCATCAGTACATCGCCGAAA 60.135 47.619 0.00 0.00 0.00 3.46
690 984 1.663643 GCATCAGTACATCGCCGAAAA 59.336 47.619 0.00 0.00 0.00 2.29
691 985 2.287915 GCATCAGTACATCGCCGAAAAT 59.712 45.455 0.00 0.00 0.00 1.82
692 986 3.604772 GCATCAGTACATCGCCGAAAATC 60.605 47.826 0.00 0.00 0.00 2.17
693 987 2.546778 TCAGTACATCGCCGAAAATCC 58.453 47.619 0.00 0.00 0.00 3.01
694 988 2.167693 TCAGTACATCGCCGAAAATCCT 59.832 45.455 0.00 0.00 0.00 3.24
695 989 2.285220 CAGTACATCGCCGAAAATCCTG 59.715 50.000 0.00 0.00 0.00 3.86
696 990 2.167693 AGTACATCGCCGAAAATCCTGA 59.832 45.455 0.00 0.00 0.00 3.86
697 991 2.107950 ACATCGCCGAAAATCCTGAA 57.892 45.000 0.00 0.00 0.00 3.02
700 994 4.196193 ACATCGCCGAAAATCCTGAAATA 58.804 39.130 0.00 0.00 0.00 1.40
704 998 5.816919 TCGCCGAAAATCCTGAAATAAATC 58.183 37.500 0.00 0.00 0.00 2.17
705 999 4.976116 CGCCGAAAATCCTGAAATAAATCC 59.024 41.667 0.00 0.00 0.00 3.01
706 1000 5.449862 CGCCGAAAATCCTGAAATAAATCCA 60.450 40.000 0.00 0.00 0.00 3.41
707 1001 5.979517 GCCGAAAATCCTGAAATAAATCCAG 59.020 40.000 0.00 0.00 0.00 3.86
709 1003 7.630513 GCCGAAAATCCTGAAATAAATCCAGAA 60.631 37.037 0.00 0.00 0.00 3.02
719 1013 9.734620 CTGAAATAAATCCAGAAATAATGCGAA 57.265 29.630 0.00 0.00 0.00 4.70
722 1016 8.856490 AATAAATCCAGAAATAATGCGAACAC 57.144 30.769 0.00 0.00 0.00 3.32
723 1017 4.900635 ATCCAGAAATAATGCGAACACC 57.099 40.909 0.00 0.00 0.00 4.16
725 1019 3.689161 TCCAGAAATAATGCGAACACCAG 59.311 43.478 0.00 0.00 0.00 4.00
729 1023 4.949856 AGAAATAATGCGAACACCAGGATT 59.050 37.500 0.00 0.00 33.17 3.01
732 1026 2.198827 ATGCGAACACCAGGATTTGA 57.801 45.000 0.00 0.00 0.00 2.69
733 1027 1.974265 TGCGAACACCAGGATTTGAA 58.026 45.000 0.00 0.00 0.00 2.69
734 1028 1.606668 TGCGAACACCAGGATTTGAAC 59.393 47.619 0.00 0.00 0.00 3.18
735 1029 1.068541 GCGAACACCAGGATTTGAACC 60.069 52.381 0.00 0.00 0.00 3.62
736 1030 1.539827 CGAACACCAGGATTTGAACCC 59.460 52.381 0.00 0.00 0.00 4.11
743 1037 1.888512 CAGGATTTGAACCCTGGTGTG 59.111 52.381 0.00 0.00 44.68 3.82
744 1038 1.499007 AGGATTTGAACCCTGGTGTGT 59.501 47.619 0.00 0.00 0.00 3.72
746 1040 2.035832 GGATTTGAACCCTGGTGTGTTG 59.964 50.000 0.00 0.00 0.00 3.33
747 1041 2.516227 TTTGAACCCTGGTGTGTTGA 57.484 45.000 0.00 0.00 0.00 3.18
748 1042 2.516227 TTGAACCCTGGTGTGTTGAA 57.484 45.000 0.00 0.00 0.00 2.69
750 1044 1.562008 TGAACCCTGGTGTGTTGAAGA 59.438 47.619 0.00 0.00 0.00 2.87
753 1047 3.418684 ACCCTGGTGTGTTGAAGATAC 57.581 47.619 0.00 0.00 0.00 2.24
754 1048 2.039879 ACCCTGGTGTGTTGAAGATACC 59.960 50.000 1.17 1.17 0.00 2.73
755 1049 2.039746 CCCTGGTGTGTTGAAGATACCA 59.960 50.000 10.36 10.36 38.98 3.25
756 1050 3.074412 CCTGGTGTGTTGAAGATACCAC 58.926 50.000 6.85 0.00 36.56 4.16
757 1051 3.244561 CCTGGTGTGTTGAAGATACCACT 60.245 47.826 6.85 0.00 36.56 4.00
758 1052 3.738982 TGGTGTGTTGAAGATACCACTG 58.261 45.455 6.85 0.00 36.56 3.66
760 1054 3.746492 GGTGTGTTGAAGATACCACTGTC 59.254 47.826 3.37 0.00 0.00 3.51
761 1055 3.746492 GTGTGTTGAAGATACCACTGTCC 59.254 47.826 0.00 0.00 0.00 4.02
762 1056 3.389656 TGTGTTGAAGATACCACTGTCCA 59.610 43.478 0.00 0.00 0.00 4.02
763 1057 3.746492 GTGTTGAAGATACCACTGTCCAC 59.254 47.826 0.00 0.00 0.00 4.02
764 1058 3.244422 TGTTGAAGATACCACTGTCCACC 60.244 47.826 0.00 0.00 0.00 4.61
765 1059 2.902608 TGAAGATACCACTGTCCACCT 58.097 47.619 0.00 0.00 0.00 4.00
767 1061 4.422057 TGAAGATACCACTGTCCACCTAA 58.578 43.478 0.00 0.00 0.00 2.69
768 1062 4.222145 TGAAGATACCACTGTCCACCTAAC 59.778 45.833 0.00 0.00 0.00 2.34
769 1063 3.105283 AGATACCACTGTCCACCTAACC 58.895 50.000 0.00 0.00 0.00 2.85
771 1065 1.742308 ACCACTGTCCACCTAACCAT 58.258 50.000 0.00 0.00 0.00 3.55
772 1066 1.628846 ACCACTGTCCACCTAACCATC 59.371 52.381 0.00 0.00 0.00 3.51
773 1067 1.909302 CCACTGTCCACCTAACCATCT 59.091 52.381 0.00 0.00 0.00 2.90
775 1069 2.567169 CACTGTCCACCTAACCATCTCA 59.433 50.000 0.00 0.00 0.00 3.27
776 1070 3.007940 CACTGTCCACCTAACCATCTCAA 59.992 47.826 0.00 0.00 0.00 3.02
778 1072 2.304761 TGTCCACCTAACCATCTCAACC 59.695 50.000 0.00 0.00 0.00 3.77
780 1074 2.304761 TCCACCTAACCATCTCAACCAC 59.695 50.000 0.00 0.00 0.00 4.16
781 1075 2.039746 CCACCTAACCATCTCAACCACA 59.960 50.000 0.00 0.00 0.00 4.17
783 1077 2.305927 ACCTAACCATCTCAACCACAGG 59.694 50.000 0.00 0.00 0.00 4.00
793 1087 3.412722 AACCACAGGTTGATTCGCA 57.587 47.368 0.00 0.00 45.07 5.10
794 1088 1.686355 AACCACAGGTTGATTCGCAA 58.314 45.000 0.00 0.00 45.07 4.85
795 1089 1.909700 ACCACAGGTTGATTCGCAAT 58.090 45.000 0.00 0.00 39.03 3.56
796 1090 2.238521 ACCACAGGTTGATTCGCAATT 58.761 42.857 0.00 0.00 39.03 2.32
797 1091 3.417101 ACCACAGGTTGATTCGCAATTA 58.583 40.909 0.00 0.00 39.03 1.40
798 1092 3.440173 ACCACAGGTTGATTCGCAATTAG 59.560 43.478 0.00 0.00 39.03 1.73
799 1093 3.689161 CCACAGGTTGATTCGCAATTAGA 59.311 43.478 0.00 0.00 39.03 2.10
800 1094 4.437390 CCACAGGTTGATTCGCAATTAGAC 60.437 45.833 0.00 0.00 39.03 2.59
801 1095 4.393062 CACAGGTTGATTCGCAATTAGACT 59.607 41.667 0.00 0.00 39.03 3.24
802 1096 5.580691 CACAGGTTGATTCGCAATTAGACTA 59.419 40.000 0.00 0.00 39.03 2.59
803 1097 5.812642 ACAGGTTGATTCGCAATTAGACTAG 59.187 40.000 0.00 0.00 39.03 2.57
804 1098 4.811557 AGGTTGATTCGCAATTAGACTAGC 59.188 41.667 0.00 0.00 39.03 3.42
805 1099 4.811557 GGTTGATTCGCAATTAGACTAGCT 59.188 41.667 0.00 0.00 39.03 3.32
806 1100 5.983720 GGTTGATTCGCAATTAGACTAGCTA 59.016 40.000 0.00 0.00 39.03 3.32
807 1101 6.647067 GGTTGATTCGCAATTAGACTAGCTAT 59.353 38.462 0.00 0.00 39.03 2.97
809 1103 9.193133 GTTGATTCGCAATTAGACTAGCTATTA 57.807 33.333 0.00 0.00 39.03 0.98
810 1104 9.758651 TTGATTCGCAATTAGACTAGCTATTAA 57.241 29.630 0.00 0.00 0.00 1.40
811 1105 9.193133 TGATTCGCAATTAGACTAGCTATTAAC 57.807 33.333 0.00 0.00 0.00 2.01
812 1106 7.618964 TTCGCAATTAGACTAGCTATTAACG 57.381 36.000 0.00 0.00 0.00 3.18
815 1109 7.166970 TCGCAATTAGACTAGCTATTAACGTTG 59.833 37.037 11.99 0.00 0.00 4.10
816 1110 7.564988 GCAATTAGACTAGCTATTAACGTTGG 58.435 38.462 11.99 0.00 0.00 3.77
817 1111 7.564988 CAATTAGACTAGCTATTAACGTTGGC 58.435 38.462 11.99 9.85 0.00 4.52
818 1112 6.461110 TTAGACTAGCTATTAACGTTGGCT 57.539 37.500 11.99 16.16 37.08 4.75
823 1117 6.221659 ACTAGCTATTAACGTTGGCTTATCC 58.778 40.000 11.99 0.00 34.88 2.59
842 1136 4.778415 CCAGTCGCGTCGGGTCTG 62.778 72.222 23.09 23.09 0.00 3.51
843 1137 4.039357 CAGTCGCGTCGGGTCTGT 62.039 66.667 22.19 0.37 0.00 3.41
844 1138 3.735029 AGTCGCGTCGGGTCTGTC 61.735 66.667 5.77 0.00 0.00 3.51
849 1143 3.733960 CGTCGGGTCTGTCGCTCA 61.734 66.667 0.00 0.00 0.00 4.26
850 1144 2.179517 GTCGGGTCTGTCGCTCAG 59.820 66.667 1.88 1.88 44.85 3.35
851 1145 2.282251 TCGGGTCTGTCGCTCAGT 60.282 61.111 7.18 0.00 43.97 3.41
852 1146 1.901948 TCGGGTCTGTCGCTCAGTT 60.902 57.895 7.18 0.00 43.97 3.16
853 1147 1.734477 CGGGTCTGTCGCTCAGTTG 60.734 63.158 7.18 0.00 43.97 3.16
854 1148 1.666011 GGGTCTGTCGCTCAGTTGA 59.334 57.895 7.18 0.00 43.97 3.18
855 1149 0.033504 GGGTCTGTCGCTCAGTTGAA 59.966 55.000 7.18 0.00 43.97 2.69
856 1150 1.540363 GGGTCTGTCGCTCAGTTGAAA 60.540 52.381 7.18 0.00 43.97 2.69
857 1151 1.795286 GGTCTGTCGCTCAGTTGAAAG 59.205 52.381 7.18 0.00 43.97 2.62
858 1152 1.193426 GTCTGTCGCTCAGTTGAAAGC 59.807 52.381 7.18 0.00 43.97 3.51
859 1153 1.069204 TCTGTCGCTCAGTTGAAAGCT 59.931 47.619 7.18 0.00 43.97 3.74
860 1154 2.296190 TCTGTCGCTCAGTTGAAAGCTA 59.704 45.455 0.00 0.00 43.97 3.32
861 1155 3.056536 TCTGTCGCTCAGTTGAAAGCTAT 60.057 43.478 0.00 0.00 43.97 2.97
862 1156 2.995939 TGTCGCTCAGTTGAAAGCTATG 59.004 45.455 0.00 0.00 36.35 2.23
863 1157 3.254060 GTCGCTCAGTTGAAAGCTATGA 58.746 45.455 0.00 0.00 36.35 2.15
864 1158 3.679980 GTCGCTCAGTTGAAAGCTATGAA 59.320 43.478 0.00 0.00 36.35 2.57
906 1200 4.451900 ACCTCCGGACATTCAATGTATTC 58.548 43.478 2.04 0.00 45.03 1.75
950 1244 3.947910 AGTAAAGTGCGTGTTAGCCTA 57.052 42.857 0.00 0.00 36.02 3.93
951 1245 4.261578 AGTAAAGTGCGTGTTAGCCTAA 57.738 40.909 0.00 0.00 36.02 2.69
952 1246 4.634199 AGTAAAGTGCGTGTTAGCCTAAA 58.366 39.130 0.00 0.00 36.02 1.85
988 1282 0.741915 CGCTTGTACCTCTCCTCCTC 59.258 60.000 0.00 0.00 0.00 3.71
1069 1363 2.572104 GCCCTCTCCTTCTTCCACTTAA 59.428 50.000 0.00 0.00 0.00 1.85
1080 1374 9.594478 TCCTTCTTCCACTTAATTTTGTTTTTC 57.406 29.630 0.00 0.00 0.00 2.29
1104 1399 5.188751 CAGAATCTCCTTCTCCCACTTACTT 59.811 44.000 0.00 0.00 42.48 2.24
1105 1400 5.788014 AGAATCTCCTTCTCCCACTTACTTT 59.212 40.000 0.00 0.00 40.26 2.66
1106 1401 6.273495 AGAATCTCCTTCTCCCACTTACTTTT 59.727 38.462 0.00 0.00 40.26 2.27
1107 1402 5.228945 TCTCCTTCTCCCACTTACTTTTG 57.771 43.478 0.00 0.00 0.00 2.44
1108 1403 4.658901 TCTCCTTCTCCCACTTACTTTTGT 59.341 41.667 0.00 0.00 0.00 2.83
1109 1404 5.132144 TCTCCTTCTCCCACTTACTTTTGTT 59.868 40.000 0.00 0.00 0.00 2.83
1143 1438 4.856801 AGCGCTACAATGGCCCCG 62.857 66.667 8.99 0.00 0.00 5.73
1160 1455 1.949631 CGAGGGCCGAAACGCTATC 60.950 63.158 0.00 0.00 41.76 2.08
1186 1481 1.659098 CACGAAAGAATACGCTGGTCC 59.341 52.381 0.00 0.00 0.00 4.46
1187 1482 1.274167 ACGAAAGAATACGCTGGTCCA 59.726 47.619 0.00 0.00 0.00 4.02
1188 1483 1.927174 CGAAAGAATACGCTGGTCCAG 59.073 52.381 15.15 15.15 34.12 3.86
1197 1492 3.076092 CTGGTCCAGCTCAGCCTT 58.924 61.111 5.79 0.00 0.00 4.35
1208 1503 2.504585 AGCTCAGCCTTCTCATCATCAA 59.495 45.455 0.00 0.00 0.00 2.57
1262 1589 2.037144 GGAGAGGGTTAGAATACGGCA 58.963 52.381 0.00 0.00 0.00 5.69
1281 1608 2.477863 GCAAAATATCCGCAACGAGCTT 60.478 45.455 0.00 0.00 42.61 3.74
1551 1878 4.224370 CAGGCTTAGGTTGGGAGTAGTTAA 59.776 45.833 0.00 0.00 0.00 2.01
1599 1928 1.812571 ACACCTGTCGGAAATTGATGC 59.187 47.619 0.00 0.00 0.00 3.91
1601 1930 0.378257 CCTGTCGGAAATTGATGCGG 59.622 55.000 0.00 0.00 34.66 5.69
1621 1958 3.057174 CGGCCTTGTTTATGTAAAAGCCA 60.057 43.478 0.00 0.00 0.00 4.75
1632 1969 1.681264 GTAAAAGCCAAGCTGTGTGGT 59.319 47.619 4.86 0.00 39.62 4.16
1635 1972 2.292828 AAGCCAAGCTGTGTGGTTAT 57.707 45.000 4.86 0.00 39.62 1.89
1650 1987 5.180492 GTGTGGTTATCCTTGTTCATCGAAA 59.820 40.000 0.00 0.00 34.23 3.46
1663 2000 0.984230 ATCGAAAGGGAGCCTTGTGA 59.016 50.000 0.00 0.00 43.92 3.58
1664 2001 0.984230 TCGAAAGGGAGCCTTGTGAT 59.016 50.000 0.00 0.00 43.92 3.06
1675 2014 4.400251 GGAGCCTTGTGATGATTGATGAAA 59.600 41.667 0.00 0.00 0.00 2.69
1680 2019 6.694411 GCCTTGTGATGATTGATGAAATGTAC 59.306 38.462 0.00 0.00 0.00 2.90
1681 2020 7.415989 GCCTTGTGATGATTGATGAAATGTACT 60.416 37.037 0.00 0.00 0.00 2.73
1682 2021 7.913821 CCTTGTGATGATTGATGAAATGTACTG 59.086 37.037 0.00 0.00 0.00 2.74
1683 2022 7.926674 TGTGATGATTGATGAAATGTACTGT 57.073 32.000 0.00 0.00 0.00 3.55
1684 2023 9.447157 TTGTGATGATTGATGAAATGTACTGTA 57.553 29.630 0.00 0.00 0.00 2.74
1685 2024 9.617523 TGTGATGATTGATGAAATGTACTGTAT 57.382 29.630 0.00 0.00 0.00 2.29
1727 2066 8.804912 TTGGGGGATTTGAATGAAAATAATTG 57.195 30.769 0.00 0.00 29.89 2.32
1739 2078 9.925268 GAATGAAAATAATTGTCATGGCATTTC 57.075 29.630 10.51 12.36 32.38 2.17
1740 2079 7.522901 TGAAAATAATTGTCATGGCATTTCG 57.477 32.000 10.51 0.00 0.00 3.46
1741 2080 5.971895 AAATAATTGTCATGGCATTTCGC 57.028 34.783 10.51 0.00 41.28 4.70
1742 2081 4.652421 ATAATTGTCATGGCATTTCGCA 57.348 36.364 10.51 0.00 45.17 5.10
1743 2082 3.316071 AATTGTCATGGCATTTCGCAA 57.684 38.095 0.00 1.29 45.17 4.85
1744 2083 3.530265 ATTGTCATGGCATTTCGCAAT 57.470 38.095 0.00 3.69 45.17 3.56
2017 2391 1.889545 GCAGAAGCCATGGGAGATAC 58.110 55.000 15.13 0.00 33.58 2.24
2047 2421 3.003482 GCTGATGAATCTGCAGTGGATTC 59.997 47.826 14.67 15.73 46.81 2.52
2050 2424 0.659957 GAATCTGCAGTGGATTCGGC 59.340 55.000 14.67 0.00 39.39 5.54
2051 2425 0.254178 AATCTGCAGTGGATTCGGCT 59.746 50.000 14.67 0.00 0.00 5.52
2057 2431 1.306141 AGTGGATTCGGCTCCAGGA 60.306 57.895 7.07 0.00 45.87 3.86
2090 2464 4.672587 TGGTAATGATGAGGTAGCAGAC 57.327 45.455 0.00 0.00 0.00 3.51
2324 2700 9.426837 CTTGAATTGATTTCCTTGCAGATAAAA 57.573 29.630 0.00 0.00 33.04 1.52
2465 2841 8.314751 CCTGAAACTAAAGAAATAGAGACCTCA 58.685 37.037 0.00 0.00 0.00 3.86
2630 3006 5.365314 AGTTTACTTCAAATCCAAAAGGCCA 59.635 36.000 5.01 0.00 0.00 5.36
2893 3270 2.423892 TCTGAGACGATGGCTAGTTGAC 59.576 50.000 0.00 0.00 0.00 3.18
3049 3427 2.446435 GGCCAATGTGACAGGTACAAT 58.554 47.619 0.00 0.00 0.00 2.71
3133 3511 0.038892 CAGTGGCAGTTGGTTCATGC 60.039 55.000 0.00 0.00 39.25 4.06
3241 3620 2.566724 TGGGGTAAAACGGACGAATAGT 59.433 45.455 0.00 0.00 0.00 2.12
3445 3834 3.351885 ACCCTCTCTCTCCCGCCT 61.352 66.667 0.00 0.00 0.00 5.52
3500 3889 4.899239 CTCCTCACCGCGCATCCC 62.899 72.222 8.75 0.00 0.00 3.85
3578 3985 2.094904 CCATAGTTTTGGCCGTCGG 58.905 57.895 6.99 6.99 0.00 4.79
3771 4182 2.726633 CGCAAGGTGTTCGACATTTTT 58.273 42.857 0.00 0.00 0.00 1.94
3790 4201 3.885976 TTCCCACAAAGGTATGGACAA 57.114 42.857 0.00 0.00 38.34 3.18
3812 4223 3.165875 TGGAGACGAGTTCTTCTTCCAT 58.834 45.455 0.00 0.00 33.22 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 9.649024 AAACGTTCTTAAAAATGATTGCAAATG 57.351 25.926 1.71 0.00 0.00 2.32
291 297 2.772515 TCCCCGGTTTCCAAAAATGTTT 59.227 40.909 0.00 0.00 0.00 2.83
389 395 7.619965 AGAAACTGTTTGGGATTTCAAAAAGA 58.380 30.769 11.03 0.00 41.93 2.52
430 436 4.344102 GCCCCTGTTTTTCTTTCCTTTAGT 59.656 41.667 0.00 0.00 0.00 2.24
475 481 1.091771 CATCATCGTCCCTGTGTGGC 61.092 60.000 0.00 0.00 0.00 5.01
477 483 0.536724 TCCATCATCGTCCCTGTGTG 59.463 55.000 0.00 0.00 0.00 3.82
478 484 1.500474 ATCCATCATCGTCCCTGTGT 58.500 50.000 0.00 0.00 0.00 3.72
480 486 1.839994 ACAATCCATCATCGTCCCTGT 59.160 47.619 0.00 0.00 0.00 4.00
488 770 7.064371 CGAAGATCCAAGATACAATCCATCATC 59.936 40.741 0.00 0.00 0.00 2.92
489 771 6.877855 CGAAGATCCAAGATACAATCCATCAT 59.122 38.462 0.00 0.00 0.00 2.45
539 821 0.733223 GCTTCGAGAGTTGTCGGGTC 60.733 60.000 0.00 0.00 40.49 4.46
607 901 5.598005 TGTTTCCAAACAGATTTGTCCATCT 59.402 36.000 0.55 0.00 43.45 2.90
609 903 5.867903 TGTTTCCAAACAGATTTGTCCAT 57.132 34.783 0.55 0.00 43.45 3.41
620 914 6.293407 CGATAAAAGAGCTCTGTTTCCAAACA 60.293 38.462 24.05 4.99 45.88 2.83
621 915 6.080406 CGATAAAAGAGCTCTGTTTCCAAAC 58.920 40.000 24.05 4.58 39.33 2.93
622 916 5.334879 GCGATAAAAGAGCTCTGTTTCCAAA 60.335 40.000 24.05 6.49 0.00 3.28
623 917 4.154195 GCGATAAAAGAGCTCTGTTTCCAA 59.846 41.667 24.05 6.88 0.00 3.53
624 918 3.684788 GCGATAAAAGAGCTCTGTTTCCA 59.315 43.478 24.05 7.26 0.00 3.53
625 919 3.242123 CGCGATAAAAGAGCTCTGTTTCC 60.242 47.826 24.05 14.51 0.00 3.13
627 921 2.673368 CCGCGATAAAAGAGCTCTGTTT 59.327 45.455 24.05 21.73 0.00 2.83
628 922 2.094182 TCCGCGATAAAAGAGCTCTGTT 60.094 45.455 22.60 22.60 0.00 3.16
629 923 1.476891 TCCGCGATAAAAGAGCTCTGT 59.523 47.619 19.06 9.37 0.00 3.41
630 924 2.209838 TCCGCGATAAAAGAGCTCTG 57.790 50.000 19.06 4.39 0.00 3.35
631 925 2.961526 TTCCGCGATAAAAGAGCTCT 57.038 45.000 11.45 11.45 0.00 4.09
632 926 4.982916 TCTAATTCCGCGATAAAAGAGCTC 59.017 41.667 8.23 5.27 0.00 4.09
633 927 4.745620 GTCTAATTCCGCGATAAAAGAGCT 59.254 41.667 8.23 0.00 0.00 4.09
634 928 4.084485 GGTCTAATTCCGCGATAAAAGAGC 60.084 45.833 8.23 13.83 0.00 4.09
635 929 5.047847 TGGTCTAATTCCGCGATAAAAGAG 58.952 41.667 8.23 1.24 0.00 2.85
636 930 5.013568 TGGTCTAATTCCGCGATAAAAGA 57.986 39.130 8.23 6.59 0.00 2.52
638 932 3.558418 GCTGGTCTAATTCCGCGATAAAA 59.442 43.478 8.23 0.00 0.00 1.52
640 934 2.364324 AGCTGGTCTAATTCCGCGATAA 59.636 45.455 8.23 1.02 32.79 1.75
641 935 1.961394 AGCTGGTCTAATTCCGCGATA 59.039 47.619 8.23 0.00 32.79 2.92
643 937 0.535335 AAGCTGGTCTAATTCCGCGA 59.465 50.000 8.23 0.00 32.79 5.87
644 938 1.369625 AAAGCTGGTCTAATTCCGCG 58.630 50.000 0.00 0.00 32.79 6.46
645 939 3.850122 AAAAAGCTGGTCTAATTCCGC 57.150 42.857 0.00 0.00 0.00 5.54
664 958 3.308595 CGGCGATGTACTGATGCTAAAAA 59.691 43.478 0.00 0.00 0.00 1.94
665 959 2.863740 CGGCGATGTACTGATGCTAAAA 59.136 45.455 0.00 0.00 0.00 1.52
666 960 2.100087 TCGGCGATGTACTGATGCTAAA 59.900 45.455 4.99 0.00 0.00 1.85
667 961 1.679153 TCGGCGATGTACTGATGCTAA 59.321 47.619 4.99 0.00 0.00 3.09
668 962 1.314730 TCGGCGATGTACTGATGCTA 58.685 50.000 4.99 0.00 0.00 3.49
669 963 0.459899 TTCGGCGATGTACTGATGCT 59.540 50.000 11.76 0.00 0.00 3.79
670 964 1.286501 TTTCGGCGATGTACTGATGC 58.713 50.000 11.76 0.00 0.00 3.91
671 965 3.059597 GGATTTTCGGCGATGTACTGATG 60.060 47.826 11.76 0.00 0.00 3.07
672 966 3.131396 GGATTTTCGGCGATGTACTGAT 58.869 45.455 11.76 0.00 0.00 2.90
673 967 2.167693 AGGATTTTCGGCGATGTACTGA 59.832 45.455 11.76 0.00 0.00 3.41
674 968 2.285220 CAGGATTTTCGGCGATGTACTG 59.715 50.000 11.76 12.21 0.00 2.74
675 969 2.167693 TCAGGATTTTCGGCGATGTACT 59.832 45.455 11.76 2.70 0.00 2.73
676 970 2.546778 TCAGGATTTTCGGCGATGTAC 58.453 47.619 11.76 0.00 0.00 2.90
677 971 2.971660 TCAGGATTTTCGGCGATGTA 57.028 45.000 11.76 0.00 0.00 2.29
678 972 2.107950 TTCAGGATTTTCGGCGATGT 57.892 45.000 11.76 0.00 0.00 3.06
679 973 3.698029 ATTTCAGGATTTTCGGCGATG 57.302 42.857 11.76 4.79 0.00 3.84
680 974 5.828299 TTTATTTCAGGATTTTCGGCGAT 57.172 34.783 11.76 0.00 0.00 4.58
681 975 5.220970 GGATTTATTTCAGGATTTTCGGCGA 60.221 40.000 4.99 4.99 0.00 5.54
682 976 4.976116 GGATTTATTTCAGGATTTTCGGCG 59.024 41.667 0.00 0.00 0.00 6.46
683 977 5.901552 TGGATTTATTTCAGGATTTTCGGC 58.098 37.500 0.00 0.00 0.00 5.54
684 978 7.333528 TCTGGATTTATTTCAGGATTTTCGG 57.666 36.000 0.00 0.00 0.00 4.30
685 979 9.807649 ATTTCTGGATTTATTTCAGGATTTTCG 57.192 29.630 0.00 0.00 0.00 3.46
691 985 8.352201 CGCATTATTTCTGGATTTATTTCAGGA 58.648 33.333 0.00 0.00 0.00 3.86
692 986 8.352201 TCGCATTATTTCTGGATTTATTTCAGG 58.648 33.333 0.00 0.00 0.00 3.86
693 987 9.734620 TTCGCATTATTTCTGGATTTATTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
694 988 9.515020 GTTCGCATTATTTCTGGATTTATTTCA 57.485 29.630 0.00 0.00 0.00 2.69
695 989 9.515020 TGTTCGCATTATTTCTGGATTTATTTC 57.485 29.630 0.00 0.00 0.00 2.17
696 990 9.301153 GTGTTCGCATTATTTCTGGATTTATTT 57.699 29.630 0.00 0.00 0.00 1.40
697 991 7.920682 GGTGTTCGCATTATTTCTGGATTTATT 59.079 33.333 0.00 0.00 0.00 1.40
700 994 5.184864 TGGTGTTCGCATTATTTCTGGATTT 59.815 36.000 0.00 0.00 0.00 2.17
704 998 3.181497 CCTGGTGTTCGCATTATTTCTGG 60.181 47.826 0.00 0.00 0.00 3.86
705 999 3.689161 TCCTGGTGTTCGCATTATTTCTG 59.311 43.478 0.00 0.00 0.00 3.02
706 1000 3.950397 TCCTGGTGTTCGCATTATTTCT 58.050 40.909 0.00 0.00 0.00 2.52
707 1001 4.900635 ATCCTGGTGTTCGCATTATTTC 57.099 40.909 0.00 0.00 0.00 2.17
709 1003 4.704540 TCAAATCCTGGTGTTCGCATTATT 59.295 37.500 0.00 0.00 0.00 1.40
716 1010 1.539827 GGGTTCAAATCCTGGTGTTCG 59.460 52.381 0.00 0.00 0.00 3.95
725 1019 1.995376 ACACACCAGGGTTCAAATCC 58.005 50.000 0.00 0.00 0.00 3.01
729 1023 2.025793 TCTTCAACACACCAGGGTTCAA 60.026 45.455 0.00 0.00 0.00 2.69
732 1026 3.497942 GGTATCTTCAACACACCAGGGTT 60.498 47.826 0.00 0.00 0.00 4.11
733 1027 2.039879 GGTATCTTCAACACACCAGGGT 59.960 50.000 0.00 0.00 0.00 4.34
734 1028 2.039746 TGGTATCTTCAACACACCAGGG 59.960 50.000 0.00 0.00 34.40 4.45
735 1029 3.074412 GTGGTATCTTCAACACACCAGG 58.926 50.000 0.00 0.00 39.85 4.45
736 1030 3.748048 CAGTGGTATCTTCAACACACCAG 59.252 47.826 0.00 0.00 39.85 4.00
738 1032 3.740115 ACAGTGGTATCTTCAACACACC 58.260 45.455 0.00 0.00 36.35 4.16
739 1033 3.746492 GGACAGTGGTATCTTCAACACAC 59.254 47.826 0.00 0.00 36.35 3.82
741 1035 3.746492 GTGGACAGTGGTATCTTCAACAC 59.254 47.826 0.00 0.00 0.00 3.32
743 1037 3.008049 AGGTGGACAGTGGTATCTTCAAC 59.992 47.826 0.00 0.00 0.00 3.18
744 1038 3.248024 AGGTGGACAGTGGTATCTTCAA 58.752 45.455 0.00 0.00 0.00 2.69
746 1040 4.382793 GGTTAGGTGGACAGTGGTATCTTC 60.383 50.000 0.00 0.00 0.00 2.87
747 1041 3.518303 GGTTAGGTGGACAGTGGTATCTT 59.482 47.826 0.00 0.00 0.00 2.40
748 1042 3.105283 GGTTAGGTGGACAGTGGTATCT 58.895 50.000 0.00 0.00 0.00 1.98
750 1044 2.910544 TGGTTAGGTGGACAGTGGTAT 58.089 47.619 0.00 0.00 0.00 2.73
753 1047 1.909302 AGATGGTTAGGTGGACAGTGG 59.091 52.381 0.00 0.00 0.00 4.00
754 1048 2.567169 TGAGATGGTTAGGTGGACAGTG 59.433 50.000 0.00 0.00 0.00 3.66
755 1049 2.902608 TGAGATGGTTAGGTGGACAGT 58.097 47.619 0.00 0.00 0.00 3.55
756 1050 3.600388 GTTGAGATGGTTAGGTGGACAG 58.400 50.000 0.00 0.00 0.00 3.51
757 1051 2.304761 GGTTGAGATGGTTAGGTGGACA 59.695 50.000 0.00 0.00 0.00 4.02
758 1052 2.304761 TGGTTGAGATGGTTAGGTGGAC 59.695 50.000 0.00 0.00 0.00 4.02
760 1054 2.039746 TGTGGTTGAGATGGTTAGGTGG 59.960 50.000 0.00 0.00 0.00 4.61
761 1055 3.338249 CTGTGGTTGAGATGGTTAGGTG 58.662 50.000 0.00 0.00 0.00 4.00
762 1056 2.305927 CCTGTGGTTGAGATGGTTAGGT 59.694 50.000 0.00 0.00 0.00 3.08
763 1057 2.305927 ACCTGTGGTTGAGATGGTTAGG 59.694 50.000 0.00 0.00 27.29 2.69
764 1058 3.703001 ACCTGTGGTTGAGATGGTTAG 57.297 47.619 0.00 0.00 27.29 2.34
776 1070 1.909700 ATTGCGAATCAACCTGTGGT 58.090 45.000 0.00 0.00 37.53 4.16
778 1072 4.393062 AGTCTAATTGCGAATCAACCTGTG 59.607 41.667 0.00 0.00 37.53 3.66
780 1074 5.277058 GCTAGTCTAATTGCGAATCAACCTG 60.277 44.000 0.00 0.00 37.53 4.00
781 1075 4.811557 GCTAGTCTAATTGCGAATCAACCT 59.188 41.667 0.00 0.00 37.53 3.50
783 1077 5.975410 AGCTAGTCTAATTGCGAATCAAC 57.025 39.130 0.00 0.00 37.53 3.18
785 1079 9.193133 GTTAATAGCTAGTCTAATTGCGAATCA 57.807 33.333 0.00 0.00 0.00 2.57
786 1080 8.366666 CGTTAATAGCTAGTCTAATTGCGAATC 58.633 37.037 0.00 0.00 0.00 2.52
787 1081 7.866393 ACGTTAATAGCTAGTCTAATTGCGAAT 59.134 33.333 0.00 0.00 0.00 3.34
788 1082 7.198390 ACGTTAATAGCTAGTCTAATTGCGAA 58.802 34.615 0.00 0.00 0.00 4.70
789 1083 6.732154 ACGTTAATAGCTAGTCTAATTGCGA 58.268 36.000 0.00 0.00 0.00 5.10
790 1084 6.988109 ACGTTAATAGCTAGTCTAATTGCG 57.012 37.500 0.00 0.12 0.00 4.85
791 1085 7.564988 CCAACGTTAATAGCTAGTCTAATTGC 58.435 38.462 0.00 0.00 0.00 3.56
792 1086 7.438459 AGCCAACGTTAATAGCTAGTCTAATTG 59.562 37.037 0.00 0.00 30.46 2.32
793 1087 7.498443 AGCCAACGTTAATAGCTAGTCTAATT 58.502 34.615 0.00 0.00 30.46 1.40
794 1088 7.052142 AGCCAACGTTAATAGCTAGTCTAAT 57.948 36.000 0.00 0.00 30.46 1.73
795 1089 6.461110 AGCCAACGTTAATAGCTAGTCTAA 57.539 37.500 0.00 0.00 30.46 2.10
796 1090 6.461110 AAGCCAACGTTAATAGCTAGTCTA 57.539 37.500 12.78 0.00 32.39 2.59
797 1091 5.340439 AAGCCAACGTTAATAGCTAGTCT 57.660 39.130 12.78 0.00 32.39 3.24
798 1092 6.365518 GGATAAGCCAACGTTAATAGCTAGTC 59.634 42.308 12.78 12.72 36.34 2.59
799 1093 6.221659 GGATAAGCCAACGTTAATAGCTAGT 58.778 40.000 12.78 0.00 36.34 2.57
800 1094 5.345202 CGGATAAGCCAACGTTAATAGCTAG 59.655 44.000 12.78 0.00 35.94 3.42
801 1095 5.224888 CGGATAAGCCAACGTTAATAGCTA 58.775 41.667 12.78 0.00 35.94 3.32
802 1096 4.056050 CGGATAAGCCAACGTTAATAGCT 58.944 43.478 0.00 4.41 35.94 3.32
803 1097 3.363673 GCGGATAAGCCAACGTTAATAGC 60.364 47.826 0.00 1.83 35.94 2.97
804 1098 4.385244 GCGGATAAGCCAACGTTAATAG 57.615 45.455 0.00 0.00 35.94 1.73
826 1120 3.948086 GACAGACCCGACGCGACTG 62.948 68.421 15.93 13.81 35.14 3.51
827 1121 3.735029 GACAGACCCGACGCGACT 61.735 66.667 15.93 0.00 0.00 4.18
832 1126 3.733960 TGAGCGACAGACCCGACG 61.734 66.667 0.00 0.00 0.00 5.12
841 1135 2.812358 TAGCTTTCAACTGAGCGACA 57.188 45.000 0.00 0.00 43.53 4.35
842 1136 3.254060 TCATAGCTTTCAACTGAGCGAC 58.746 45.455 0.00 0.00 43.53 5.19
843 1137 3.592898 TCATAGCTTTCAACTGAGCGA 57.407 42.857 0.00 0.00 43.53 4.93
844 1138 4.398247 GTTTCATAGCTTTCAACTGAGCG 58.602 43.478 0.00 0.00 43.53 5.03
845 1139 4.216257 TGGTTTCATAGCTTTCAACTGAGC 59.784 41.667 0.00 0.00 39.17 4.26
846 1140 5.947228 TGGTTTCATAGCTTTCAACTGAG 57.053 39.130 0.00 0.00 0.00 3.35
847 1141 6.240894 AGATGGTTTCATAGCTTTCAACTGA 58.759 36.000 0.00 0.00 32.98 3.41
848 1142 6.506500 AGATGGTTTCATAGCTTTCAACTG 57.493 37.500 0.00 0.00 32.98 3.16
849 1143 7.373493 CAAAGATGGTTTCATAGCTTTCAACT 58.627 34.615 0.00 0.00 30.05 3.16
850 1144 6.587608 CCAAAGATGGTTTCATAGCTTTCAAC 59.412 38.462 0.00 0.00 42.18 3.18
851 1145 6.690530 CCAAAGATGGTTTCATAGCTTTCAA 58.309 36.000 0.00 0.00 42.18 2.69
852 1146 6.271488 CCAAAGATGGTTTCATAGCTTTCA 57.729 37.500 0.00 0.00 42.18 2.69
959 1253 5.279056 GGAGAGGTACAAGCGCTTATTAGAT 60.279 44.000 24.55 7.50 0.00 1.98
970 1264 1.116308 GGAGGAGGAGAGGTACAAGC 58.884 60.000 0.00 0.00 0.00 4.01
975 1269 2.232622 CGGAGGAGGAGGAGAGGTA 58.767 63.158 0.00 0.00 0.00 3.08
1005 1299 3.537689 GCAATGTATTCGCGATATCGACG 60.538 47.826 28.63 26.81 43.02 5.12
1104 1399 1.104577 GTGGCTCCACCCGAAACAAA 61.105 55.000 7.82 0.00 40.79 2.83
1105 1400 1.527380 GTGGCTCCACCCGAAACAA 60.527 57.895 7.82 0.00 40.79 2.83
1106 1401 2.112297 GTGGCTCCACCCGAAACA 59.888 61.111 7.82 0.00 40.79 2.83
1107 1402 2.112297 TGTGGCTCCACCCGAAAC 59.888 61.111 15.76 0.00 45.63 2.78
1108 1403 2.112297 GTGTGGCTCCACCCGAAA 59.888 61.111 15.76 0.00 45.63 3.46
1109 1404 3.164977 TGTGTGGCTCCACCCGAA 61.165 61.111 15.76 0.00 45.63 4.30
1143 1438 0.876342 CAGATAGCGTTTCGGCCCTC 60.876 60.000 0.00 0.00 0.00 4.30
1160 1455 1.006832 CGTATTCTTTCGTGGGCCAG 58.993 55.000 6.40 0.73 0.00 4.85
1186 1481 2.158943 TGATGATGAGAAGGCTGAGCTG 60.159 50.000 3.72 0.00 0.00 4.24
1187 1482 2.117051 TGATGATGAGAAGGCTGAGCT 58.883 47.619 3.72 0.00 0.00 4.09
1188 1483 2.613133 GTTGATGATGAGAAGGCTGAGC 59.387 50.000 0.00 0.00 0.00 4.26
1189 1484 3.870274 TGTTGATGATGAGAAGGCTGAG 58.130 45.455 0.00 0.00 0.00 3.35
1190 1485 3.370209 CCTGTTGATGATGAGAAGGCTGA 60.370 47.826 0.00 0.00 0.00 4.26
1191 1486 2.943690 CCTGTTGATGATGAGAAGGCTG 59.056 50.000 0.00 0.00 0.00 4.85
1192 1487 2.092538 CCCTGTTGATGATGAGAAGGCT 60.093 50.000 0.00 0.00 0.00 4.58
1193 1488 2.295885 CCCTGTTGATGATGAGAAGGC 58.704 52.381 0.00 0.00 0.00 4.35
1194 1489 2.295885 GCCCTGTTGATGATGAGAAGG 58.704 52.381 0.00 0.00 0.00 3.46
1195 1490 2.092538 AGGCCCTGTTGATGATGAGAAG 60.093 50.000 0.00 0.00 0.00 2.85
1196 1491 1.918262 AGGCCCTGTTGATGATGAGAA 59.082 47.619 0.00 0.00 0.00 2.87
1197 1492 1.211212 CAGGCCCTGTTGATGATGAGA 59.789 52.381 1.39 0.00 0.00 3.27
1281 1608 2.024868 CGTCGTCGCCATTTCCACA 61.025 57.895 0.00 0.00 0.00 4.17
1551 1878 5.491982 CCACCTAAATTGCTCTCAAGTACT 58.508 41.667 0.00 0.00 35.37 2.73
1599 1928 3.057174 TGGCTTTTACATAAACAAGGCCG 60.057 43.478 0.00 0.00 31.43 6.13
1601 1930 4.388773 GCTTGGCTTTTACATAAACAAGGC 59.611 41.667 11.89 8.20 32.21 4.35
1621 1958 3.508845 ACAAGGATAACCACACAGCTT 57.491 42.857 0.00 0.00 38.94 3.74
1632 1969 5.428253 CTCCCTTTCGATGAACAAGGATAA 58.572 41.667 13.33 0.10 32.50 1.75
1635 1972 2.615493 GCTCCCTTTCGATGAACAAGGA 60.615 50.000 13.33 0.58 32.50 3.36
1650 1987 1.918262 TCAATCATCACAAGGCTCCCT 59.082 47.619 0.00 0.00 33.87 4.20
1681 2020 9.166222 CCCCAATGCTAGGGTTATATATATACA 57.834 37.037 1.73 0.00 45.28 2.29
1682 2021 8.603304 CCCCCAATGCTAGGGTTATATATATAC 58.397 40.741 1.73 0.00 45.28 1.47
1683 2022 8.533329 TCCCCCAATGCTAGGGTTATATATATA 58.467 37.037 0.00 0.00 45.28 0.86
1684 2023 7.386497 TCCCCCAATGCTAGGGTTATATATAT 58.614 38.462 0.00 0.00 45.28 0.86
1685 2024 6.768914 TCCCCCAATGCTAGGGTTATATATA 58.231 40.000 7.71 0.00 45.28 0.86
1686 2025 5.619926 TCCCCCAATGCTAGGGTTATATAT 58.380 41.667 7.71 0.00 45.28 0.86
1687 2026 5.044317 TCCCCCAATGCTAGGGTTATATA 57.956 43.478 7.71 0.00 45.28 0.86
1688 2027 3.894587 TCCCCCAATGCTAGGGTTATAT 58.105 45.455 7.71 0.00 45.28 0.86
1693 2032 1.062962 CAAATCCCCCAATGCTAGGGT 60.063 52.381 7.71 0.00 45.28 4.34
1697 2036 4.262891 TCATTCAAATCCCCCAATGCTA 57.737 40.909 0.00 0.00 0.00 3.49
1701 2040 9.411189 CAATTATTTTCATTCAAATCCCCCAAT 57.589 29.630 0.00 0.00 0.00 3.16
1727 2066 5.971895 ATAAAATTGCGAAATGCCATGAC 57.028 34.783 0.00 0.00 45.60 3.06
1739 2078 9.515020 AGTTTATGGTCACATAATAAAATTGCG 57.485 29.630 1.49 0.00 46.01 4.85
1818 2183 1.215647 CTGCTACCACCACCTCGTC 59.784 63.158 0.00 0.00 0.00 4.20
2017 2391 1.791204 CAGATTCATCAGCGACATCGG 59.209 52.381 3.08 0.00 40.23 4.18
2050 2424 2.350522 CAACAACTTCGGATCCTGGAG 58.649 52.381 10.75 10.04 0.00 3.86
2051 2425 1.003118 CCAACAACTTCGGATCCTGGA 59.997 52.381 10.75 0.00 0.00 3.86
2057 2431 5.496556 TCATCATTACCAACAACTTCGGAT 58.503 37.500 0.00 0.00 0.00 4.18
2090 2464 1.301677 GCTCTGGCTTTTCGACTGGG 61.302 60.000 0.00 0.00 35.22 4.45
2217 2592 5.353394 AAGTAAGAGAATGGTGCCGATTA 57.647 39.130 0.00 0.00 0.00 1.75
2324 2700 1.553706 CAAGCTCCCCTGCAAGATTT 58.446 50.000 0.00 0.00 34.07 2.17
2465 2841 2.540383 TCAACCTCATCAGCTACTGGT 58.460 47.619 0.00 0.00 31.51 4.00
2561 2937 0.317770 TTTTCAGCCTTTTCTGCGCG 60.318 50.000 0.00 0.00 34.19 6.86
2893 3270 9.155975 ACTATAACACAAGCTTATCTGAAGTTG 57.844 33.333 0.00 0.00 0.00 3.16
3049 3427 1.991813 TGGGATGATGACAGTTGGGAA 59.008 47.619 0.00 0.00 0.00 3.97
3133 3511 1.372997 CGGTGTCCGGTCAACTGAG 60.373 63.158 14.83 0.00 44.15 3.35
3151 3529 7.226918 GCCTTAGTCCTTACCATAAGTCAAATC 59.773 40.741 0.00 0.00 0.00 2.17
3157 3535 4.368067 TGGCCTTAGTCCTTACCATAAGT 58.632 43.478 3.32 0.00 0.00 2.24
3578 3985 2.046217 GGCCAAACCTCCTCCGAC 60.046 66.667 0.00 0.00 34.51 4.79
3771 4182 3.563261 CCATTGTCCATACCTTTGTGGGA 60.563 47.826 0.00 0.00 41.11 4.37
3790 4201 3.165875 TGGAAGAAGAACTCGTCTCCAT 58.834 45.455 8.58 0.00 34.56 3.41
3812 4223 3.399330 GTCCGATGAACAAAGGAAGTGA 58.601 45.455 0.00 0.00 34.17 3.41


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

AutoCloner maintained by Alex Coulton.