Multiple sequence alignment - TraesCS2B01G385800

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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 TraesCS2B01G385800 chr2B 100.000 4507 0 0 1 4507 549195821 549191315 0.000000e+00 8323.0
1 TraesCS2B01G385800 chr2B 100.000 36 0 0 2092 2127 549193697 549193662 2.910000e-07 67.6
2 TraesCS2B01G385800 chr2B 100.000 36 0 0 2125 2160 549193730 549193695 2.910000e-07 67.6
3 TraesCS2B01G385800 chr2D 91.595 1630 74 36 1085 2675 470227802 470226197 0.000000e+00 2193.0
4 TraesCS2B01G385800 chr2D 92.871 1052 40 8 3481 4507 470224943 470223902 0.000000e+00 1495.0
5 TraesCS2B01G385800 chr2D 94.527 402 16 4 2669 3065 470226078 470225678 2.300000e-172 616.0
6 TraesCS2B01G385800 chr2D 88.840 457 15 8 3098 3525 470225388 470224939 3.090000e-146 529.0
7 TraesCS2B01G385800 chr2D 89.070 430 10 11 488 914 470228350 470227955 2.420000e-137 499.0
8 TraesCS2B01G385800 chr2D 87.626 396 37 7 1 393 470228746 470228360 2.470000e-122 449.0
9 TraesCS2B01G385800 chr2A 93.770 947 46 7 1573 2511 611957012 611956071 0.000000e+00 1410.0
10 TraesCS2B01G385800 chr2A 89.796 931 59 22 4 926 611965944 611965042 0.000000e+00 1160.0
11 TraesCS2B01G385800 chr2A 96.024 503 19 1 2563 3065 611956075 611955574 0.000000e+00 817.0
12 TraesCS2B01G385800 chr2A 83.749 843 77 20 3099 3892 611955277 611954446 0.000000e+00 743.0
13 TraesCS2B01G385800 chr2A 91.048 458 23 6 1123 1577 611957483 611957041 1.790000e-168 603.0
14 TraesCS2B01G385800 chr2A 92.798 361 18 4 3906 4266 611954334 611953982 2.400000e-142 516.0
15 TraesCS2B01G385800 chr2A 94.886 176 9 0 4217 4392 611953965 611953790 4.440000e-70 276.0


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 TraesCS2B01G385800 chr2B 549191315 549195821 4506 True 2819.4 8323 100.000000 1 4507 3 chr2B.!!$R1 4506
1 TraesCS2B01G385800 chr2D 470223902 470228746 4844 True 963.5 2193 90.754833 1 4507 6 chr2D.!!$R1 4506
2 TraesCS2B01G385800 chr2A 611965042 611965944 902 True 1160.0 1160 89.796000 4 926 1 chr2A.!!$R1 922
3 TraesCS2B01G385800 chr2A 611953790 611957483 3693 True 727.5 1410 92.045833 1123 4392 6 chr2A.!!$R2 3269


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
993 1006 0.031178 GTGTTTGCTGGTTCAGGCTG 59.969 55.0 8.58 8.58 31.21 4.85 F
1067 1087 0.093705 GCTTGTTTGAGTAGAGCGCG 59.906 55.0 0.00 0.00 0.00 6.86 F
1551 1618 1.176619 CCCCGTTTTCCAGTGGAACC 61.177 60.0 24.52 16.07 41.87 3.62 F
1751 1852 1.412079 AGGTTTTGCTGCACAATGGA 58.588 45.0 0.00 0.00 38.31 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2877 3114 1.604278 GCGATGTATCCTTTTCCAGCC 59.396 52.381 0.00 0.0 0.00 4.85 R
3066 3306 7.181125 ACTCTCAGTAATTCTTAAGATGGTGGT 59.819 37.037 5.89 0.0 0.00 4.16 R
3353 3888 1.051812 CTGGCAGGTCCCTATCGAAT 58.948 55.000 6.61 0.0 0.00 3.34 R
3737 4326 0.179018 GAACAGCAACAGTGGTCCCT 60.179 55.000 0.00 0.0 31.53 4.20 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
17 18 2.120940 TCACCCAAGGTCGGCCTA 59.879 61.111 10.18 0.00 46.33 3.93
18 19 1.306654 TCACCCAAGGTCGGCCTAT 60.307 57.895 10.18 0.00 46.33 2.57
26 27 3.244422 CCAAGGTCGGCCTATATTGCTTA 60.244 47.826 10.18 0.00 46.33 3.09
27 28 3.679824 AGGTCGGCCTATATTGCTTAC 57.320 47.619 6.89 0.00 44.90 2.34
34 35 3.746492 GGCCTATATTGCTTACTGGAACG 59.254 47.826 0.00 0.00 0.00 3.95
37 38 5.357257 CCTATATTGCTTACTGGAACGTGT 58.643 41.667 0.00 0.00 0.00 4.49
45 46 4.539870 CTTACTGGAACGTGTCGTCTTTA 58.460 43.478 0.00 0.00 39.99 1.85
62 63 3.944650 TCTTTAGTGCAGTTGACAGCAAA 59.055 39.130 0.00 0.00 40.04 3.68
63 64 3.969117 TTAGTGCAGTTGACAGCAAAG 57.031 42.857 0.00 0.00 40.04 2.77
70 72 4.037690 GCAGTTGACAGCAAAGTGTTAAG 58.962 43.478 0.00 0.00 35.42 1.85
72 74 5.266242 CAGTTGACAGCAAAGTGTTAAGAC 58.734 41.667 0.00 0.00 35.42 3.01
84 86 4.381411 AGTGTTAAGACCTGAGCTGAAAC 58.619 43.478 0.00 0.00 0.00 2.78
87 89 0.759346 AAGACCTGAGCTGAAACGGT 59.241 50.000 0.00 0.00 0.00 4.83
89 91 1.149148 GACCTGAGCTGAAACGGTTC 58.851 55.000 6.16 6.16 0.00 3.62
90 92 0.600255 ACCTGAGCTGAAACGGTTCG 60.600 55.000 8.98 4.72 36.46 3.95
93 95 1.204312 GAGCTGAAACGGTTCGTGC 59.796 57.895 19.15 19.15 39.99 5.34
95 97 0.032952 AGCTGAAACGGTTCGTGCTA 59.967 50.000 25.27 1.18 41.39 3.49
337 339 4.448210 GTGAACTGGGTAAGTGTTCTTGA 58.552 43.478 0.00 0.00 39.81 3.02
339 341 3.487120 ACTGGGTAAGTGTTCTTGACC 57.513 47.619 0.00 0.00 37.88 4.02
348 350 6.072673 GGTAAGTGTTCTTGACCGAATCAAAT 60.073 38.462 4.03 0.00 46.80 2.32
362 364 6.316390 ACCGAATCAAATGAACTCAGGATTAC 59.684 38.462 0.00 0.00 30.49 1.89
387 390 4.157289 AGCAGCATGAAAAATCTACCACAG 59.843 41.667 0.00 0.00 39.69 3.66
394 397 8.462016 GCATGAAAAATCTACCACAGAACTATT 58.538 33.333 0.00 0.00 36.67 1.73
445 448 2.773993 TGTCCCCGACAAGTATTTCC 57.226 50.000 0.00 0.00 39.78 3.13
447 450 0.538118 TCCCCGACAAGTATTTCCGG 59.462 55.000 0.00 0.00 39.85 5.14
449 452 1.140252 CCCCGACAAGTATTTCCGGAT 59.860 52.381 4.15 0.00 42.49 4.18
451 454 2.210116 CCGACAAGTATTTCCGGATGG 58.790 52.381 4.15 0.00 42.49 3.51
460 464 2.123597 TCCGGATGGAGGGGTACG 60.124 66.667 0.00 0.00 40.17 3.67
461 465 2.443390 CCGGATGGAGGGGTACGT 60.443 66.667 0.00 0.00 37.49 3.57
487 491 6.896883 TGATTCTTGAGAATGATGGATGAGT 58.103 36.000 10.77 0.00 44.14 3.41
488 492 6.766467 TGATTCTTGAGAATGATGGATGAGTG 59.234 38.462 10.77 0.00 44.14 3.51
489 493 5.688814 TCTTGAGAATGATGGATGAGTGT 57.311 39.130 0.00 0.00 0.00 3.55
490 494 5.425630 TCTTGAGAATGATGGATGAGTGTG 58.574 41.667 0.00 0.00 0.00 3.82
491 495 4.831674 TGAGAATGATGGATGAGTGTGT 57.168 40.909 0.00 0.00 0.00 3.72
492 496 4.510571 TGAGAATGATGGATGAGTGTGTG 58.489 43.478 0.00 0.00 0.00 3.82
729 737 0.409876 AGGCGGCCATCTCCTAGATA 59.590 55.000 23.09 0.00 32.12 1.98
730 738 0.820871 GGCGGCCATCTCCTAGATAG 59.179 60.000 15.62 0.00 32.12 2.08
731 739 1.617263 GGCGGCCATCTCCTAGATAGA 60.617 57.143 15.62 0.00 32.12 1.98
732 740 2.383855 GCGGCCATCTCCTAGATAGAT 58.616 52.381 2.24 0.00 32.12 1.98
733 741 2.100584 GCGGCCATCTCCTAGATAGATG 59.899 54.545 20.14 20.14 46.55 2.90
734 742 2.100584 CGGCCATCTCCTAGATAGATGC 59.899 54.545 21.05 17.31 45.94 3.91
735 743 2.433970 GGCCATCTCCTAGATAGATGCC 59.566 54.545 21.05 20.39 45.94 4.40
736 744 3.373830 GCCATCTCCTAGATAGATGCCT 58.626 50.000 21.05 0.00 45.94 4.75
755 763 2.715864 TTTTGCTTCGCTGCTGTCGC 62.716 55.000 0.00 0.00 0.00 5.19
762 770 4.271170 GCTGCTGTCGCGCGTATG 62.271 66.667 30.98 20.24 39.65 2.39
763 771 3.620428 CTGCTGTCGCGCGTATGG 61.620 66.667 30.98 18.38 39.65 2.74
764 772 4.429212 TGCTGTCGCGCGTATGGT 62.429 61.111 30.98 0.00 39.65 3.55
765 773 3.913573 GCTGTCGCGCGTATGGTG 61.914 66.667 30.98 15.36 0.00 4.17
766 774 2.506217 CTGTCGCGCGTATGGTGT 60.506 61.111 30.98 0.00 0.00 4.16
767 775 2.788176 CTGTCGCGCGTATGGTGTG 61.788 63.158 30.98 8.60 37.99 3.82
768 776 2.807895 GTCGCGCGTATGGTGTGT 60.808 61.111 30.98 0.00 37.86 3.72
769 777 2.807470 TCGCGCGTATGGTGTGTG 60.807 61.111 30.98 0.00 37.86 3.82
770 778 3.109547 CGCGCGTATGGTGTGTGT 61.110 61.111 24.19 0.00 32.04 3.72
771 779 2.474266 GCGCGTATGGTGTGTGTG 59.526 61.111 8.43 0.00 0.00 3.82
772 780 2.314647 GCGCGTATGGTGTGTGTGT 61.315 57.895 8.43 0.00 0.00 3.72
773 781 1.491127 CGCGTATGGTGTGTGTGTG 59.509 57.895 0.00 0.00 0.00 3.82
774 782 1.218875 CGCGTATGGTGTGTGTGTGT 61.219 55.000 0.00 0.00 0.00 3.72
775 783 0.234625 GCGTATGGTGTGTGTGTGTG 59.765 55.000 0.00 0.00 0.00 3.82
838 849 8.463607 TCGTGTGTTCATAACTTCATATAGACA 58.536 33.333 0.00 0.00 0.00 3.41
870 882 7.384660 TGCACAGTGATTAATTTGCCTAAAAAG 59.615 33.333 4.15 0.00 0.00 2.27
884 897 6.883744 TGCCTAAAAAGAAGATTGGTTTTGT 58.116 32.000 0.00 0.00 0.00 2.83
907 920 2.668457 CCATGTCTACAAGAACAGCGTC 59.332 50.000 0.00 0.00 0.00 5.19
921 934 1.999051 GCGTCAGCATTGTCGGTAG 59.001 57.895 0.00 0.00 44.35 3.18
922 935 1.999051 CGTCAGCATTGTCGGTAGC 59.001 57.895 0.00 0.00 33.23 3.58
923 936 0.735978 CGTCAGCATTGTCGGTAGCA 60.736 55.000 0.00 0.00 33.23 3.49
926 939 1.822371 TCAGCATTGTCGGTAGCAGTA 59.178 47.619 0.00 0.00 0.00 2.74
927 940 2.430694 TCAGCATTGTCGGTAGCAGTAT 59.569 45.455 0.00 0.00 0.00 2.12
928 941 3.634910 TCAGCATTGTCGGTAGCAGTATA 59.365 43.478 0.00 0.00 0.00 1.47
929 942 3.736252 CAGCATTGTCGGTAGCAGTATAC 59.264 47.826 0.00 0.00 0.00 1.47
930 943 2.724690 GCATTGTCGGTAGCAGTATACG 59.275 50.000 0.00 0.00 0.00 3.06
931 944 3.549423 GCATTGTCGGTAGCAGTATACGA 60.549 47.826 0.00 0.00 0.00 3.43
932 945 4.795268 CATTGTCGGTAGCAGTATACGAT 58.205 43.478 0.00 0.00 35.90 3.73
933 946 4.478843 TTGTCGGTAGCAGTATACGATC 57.521 45.455 0.00 0.00 35.90 3.69
934 947 2.477754 TGTCGGTAGCAGTATACGATCG 59.522 50.000 14.88 14.88 35.90 3.69
935 948 2.478134 GTCGGTAGCAGTATACGATCGT 59.522 50.000 25.94 25.94 35.90 3.73
936 949 2.477754 TCGGTAGCAGTATACGATCGTG 59.522 50.000 30.23 14.33 0.00 4.35
937 950 2.222678 CGGTAGCAGTATACGATCGTGT 59.777 50.000 30.23 25.67 0.00 4.49
938 951 3.429881 CGGTAGCAGTATACGATCGTGTA 59.570 47.826 30.23 24.53 0.00 2.90
939 952 4.665142 CGGTAGCAGTATACGATCGTGTAC 60.665 50.000 34.53 34.53 41.15 2.90
940 953 3.516681 AGCAGTATACGATCGTGTACG 57.483 47.619 34.53 30.07 44.05 3.67
941 954 2.868583 AGCAGTATACGATCGTGTACGT 59.131 45.455 34.53 25.31 44.05 3.57
942 955 3.310774 AGCAGTATACGATCGTGTACGTT 59.689 43.478 34.53 26.92 44.05 3.99
943 956 4.031028 GCAGTATACGATCGTGTACGTTT 58.969 43.478 34.53 22.57 44.05 3.60
944 957 4.496895 GCAGTATACGATCGTGTACGTTTT 59.503 41.667 34.53 22.29 44.05 2.43
945 958 5.551370 GCAGTATACGATCGTGTACGTTTTG 60.551 44.000 34.53 29.39 44.05 2.44
946 959 5.734035 CAGTATACGATCGTGTACGTTTTGA 59.266 40.000 34.53 14.31 44.05 2.69
947 960 5.961843 AGTATACGATCGTGTACGTTTTGAG 59.038 40.000 34.53 1.87 44.05 3.02
948 961 3.272439 ACGATCGTGTACGTTTTGAGA 57.728 42.857 22.06 0.00 39.75 3.27
949 962 3.631144 ACGATCGTGTACGTTTTGAGAA 58.369 40.909 22.06 0.00 39.75 2.87
950 963 3.667261 ACGATCGTGTACGTTTTGAGAAG 59.333 43.478 22.06 0.00 39.75 2.85
951 964 3.910170 CGATCGTGTACGTTTTGAGAAGA 59.090 43.478 7.03 0.00 40.80 2.87
952 965 4.201372 CGATCGTGTACGTTTTGAGAAGAC 60.201 45.833 7.03 0.00 40.80 3.01
953 966 3.038017 TCGTGTACGTTTTGAGAAGACG 58.962 45.455 0.00 0.00 42.13 4.18
954 967 2.408110 CGTGTACGTTTTGAGAAGACGC 60.408 50.000 0.00 0.00 40.22 5.19
955 968 1.782569 TGTACGTTTTGAGAAGACGCG 59.217 47.619 3.53 3.53 40.22 6.01
956 969 1.783140 GTACGTTTTGAGAAGACGCGT 59.217 47.619 13.85 13.85 40.22 6.01
957 970 2.124011 ACGTTTTGAGAAGACGCGTA 57.876 45.000 13.97 0.00 40.22 4.42
958 971 2.049228 ACGTTTTGAGAAGACGCGTAG 58.951 47.619 13.97 0.00 40.22 3.51
959 972 1.385743 CGTTTTGAGAAGACGCGTAGG 59.614 52.381 13.97 0.00 0.00 3.18
960 973 2.401351 GTTTTGAGAAGACGCGTAGGT 58.599 47.619 13.97 0.00 0.00 3.08
961 974 2.060326 TTTGAGAAGACGCGTAGGTG 57.940 50.000 13.97 0.00 0.00 4.00
962 975 0.956633 TTGAGAAGACGCGTAGGTGT 59.043 50.000 13.97 0.37 40.22 4.16
963 976 1.812235 TGAGAAGACGCGTAGGTGTA 58.188 50.000 13.97 0.00 36.92 2.90
964 977 2.153645 TGAGAAGACGCGTAGGTGTAA 58.846 47.619 13.97 0.00 36.92 2.41
965 978 2.161012 TGAGAAGACGCGTAGGTGTAAG 59.839 50.000 13.97 0.00 36.92 2.34
966 979 2.157738 AGAAGACGCGTAGGTGTAAGT 58.842 47.619 13.97 0.00 36.92 2.24
967 980 2.095364 AGAAGACGCGTAGGTGTAAGTG 60.095 50.000 13.97 0.00 36.92 3.16
968 981 1.242076 AGACGCGTAGGTGTAAGTGT 58.758 50.000 13.97 0.00 36.92 3.55
969 982 1.068748 AGACGCGTAGGTGTAAGTGTG 60.069 52.381 13.97 0.00 36.92 3.82
970 983 0.665369 ACGCGTAGGTGTAAGTGTGC 60.665 55.000 11.67 0.00 34.49 4.57
971 984 1.670971 CGCGTAGGTGTAAGTGTGCG 61.671 60.000 0.00 0.00 38.28 5.34
972 985 1.952266 GCGTAGGTGTAAGTGTGCGC 61.952 60.000 0.00 0.00 36.97 6.09
973 986 1.349259 CGTAGGTGTAAGTGTGCGCC 61.349 60.000 4.18 0.00 40.12 6.53
974 987 1.080366 TAGGTGTAAGTGTGCGCCG 60.080 57.895 4.18 0.00 44.16 6.46
975 988 1.808531 TAGGTGTAAGTGTGCGCCGT 61.809 55.000 4.18 0.00 44.16 5.68
978 991 1.521906 TGTAAGTGTGCGCCGTGTT 60.522 52.632 4.18 0.00 0.00 3.32
993 1006 0.031178 GTGTTTGCTGGTTCAGGCTG 59.969 55.000 8.58 8.58 31.21 4.85
1009 1024 1.336240 GGCTGGTTTTGATGTGCTCAC 60.336 52.381 0.00 0.00 32.17 3.51
1035 1050 2.549064 AAAAGTTTGAGGGCCATTGC 57.451 45.000 6.18 0.00 0.00 3.56
1036 1051 1.422531 AAAGTTTGAGGGCCATTGCA 58.577 45.000 6.18 0.00 40.13 4.08
1037 1052 0.681175 AAGTTTGAGGGCCATTGCAC 59.319 50.000 6.18 0.00 43.06 4.57
1042 1057 2.228545 TGAGGGCCATTGCACAATTA 57.771 45.000 6.18 0.00 46.13 1.40
1064 1079 4.068599 AGAAAGGCTTGTTTGAGTAGAGC 58.931 43.478 0.00 0.00 0.00 4.09
1067 1087 0.093705 GCTTGTTTGAGTAGAGCGCG 59.906 55.000 0.00 0.00 0.00 6.86
1079 1099 3.432051 GAGCGCGTACAGCCCATCT 62.432 63.158 8.43 0.00 44.76 2.90
1081 1101 1.661821 GCGCGTACAGCCCATCTAG 60.662 63.158 8.43 0.00 44.76 2.43
1091 1111 7.148623 GCGTACAGCCCATCTAGATAATAAAAC 60.149 40.741 4.54 0.00 40.81 2.43
1107 1141 3.473113 AAAACCAGGCCCATATCAACT 57.527 42.857 0.00 0.00 0.00 3.16
1111 1145 2.301346 CCAGGCCCATATCAACTCAAC 58.699 52.381 0.00 0.00 0.00 3.18
1118 1152 5.351458 GCCCATATCAACTCAACAAAATCC 58.649 41.667 0.00 0.00 0.00 3.01
1119 1153 5.682212 GCCCATATCAACTCAACAAAATCCC 60.682 44.000 0.00 0.00 0.00 3.85
1120 1154 5.163416 CCCATATCAACTCAACAAAATCCCC 60.163 44.000 0.00 0.00 0.00 4.81
1121 1155 5.658190 CCATATCAACTCAACAAAATCCCCT 59.342 40.000 0.00 0.00 0.00 4.79
1159 1223 3.499918 AGAAACTCGAGGCAATTTCACAG 59.500 43.478 21.42 0.00 34.22 3.66
1162 1226 2.808543 ACTCGAGGCAATTTCACAGTTC 59.191 45.455 18.41 0.00 0.00 3.01
1164 1228 2.154462 CGAGGCAATTTCACAGTTCCT 58.846 47.619 0.00 0.00 0.00 3.36
1221 1285 4.554036 GCCATGGCGGGAGAGGAC 62.554 72.222 23.48 0.00 34.06 3.85
1536 1603 1.228613 TAACCAAAAGGTGCCCCCG 60.229 57.895 0.00 0.00 38.74 5.73
1543 1610 2.591193 AAAGGTGCCCCCGTTTTCCA 62.591 55.000 0.00 0.00 38.74 3.53
1551 1618 1.176619 CCCCGTTTTCCAGTGGAACC 61.177 60.000 24.52 16.07 41.87 3.62
1647 1747 5.329399 TCAGTTGTAATGCCATTAGGGTTT 58.671 37.500 0.00 0.00 39.65 3.27
1672 1772 2.961062 GGCTTGTTCATGGCATCCTTAT 59.039 45.455 0.00 0.00 0.00 1.73
1673 1773 4.144297 GGCTTGTTCATGGCATCCTTATA 58.856 43.478 0.00 0.00 0.00 0.98
1676 1776 5.067674 GCTTGTTCATGGCATCCTTATACAA 59.932 40.000 0.00 1.76 0.00 2.41
1700 1800 9.400638 CAAGTTAAATTGCTAAATCACGGTTTA 57.599 29.630 2.29 0.00 0.00 2.01
1726 1827 5.065731 AGCAATATCTAAGCAGAACACAAGC 59.934 40.000 0.00 0.00 33.50 4.01
1729 1830 7.201644 GCAATATCTAAGCAGAACACAAGCTTA 60.202 37.037 0.00 0.00 45.91 3.09
1734 1835 5.886960 AAGCAGAACACAAGCTTAATAGG 57.113 39.130 0.00 0.00 45.91 2.57
1739 1840 6.363357 GCAGAACACAAGCTTAATAGGTTTTG 59.637 38.462 0.00 6.38 42.41 2.44
1746 1847 3.826157 AGCTTAATAGGTTTTGCTGCACA 59.174 39.130 0.00 0.00 0.00 4.57
1751 1852 1.412079 AGGTTTTGCTGCACAATGGA 58.588 45.000 0.00 0.00 38.31 3.41
1762 1863 3.952323 CTGCACAATGGATTGGAGATCTT 59.048 43.478 0.00 0.00 41.96 2.40
2028 2137 5.252969 TGTGATCCTTGAATGCTTATTGC 57.747 39.130 0.00 0.00 43.25 3.56
2060 2171 7.452501 TGATCCTTTTTCCACTCATGATTCTTT 59.547 33.333 0.00 0.00 0.00 2.52
2476 2587 3.576550 TGGCATTTAAAACCTGAGTTCCC 59.423 43.478 10.89 0.00 34.19 3.97
2493 2604 7.016296 TGAGTTCCCCTAGAAAATGGATTTTT 58.984 34.615 0.00 0.00 39.86 1.94
2784 3020 4.816786 AGCACAAAATTTTGATTGGCAC 57.183 36.364 32.20 14.92 40.55 5.01
2877 3114 6.092955 TGGTTACTACTTTGGTGTACAGAG 57.907 41.667 0.00 0.00 37.33 3.35
3024 3261 6.782494 AGGTTTGTCCTTTGTTCTTGGATAAT 59.218 34.615 0.00 0.00 45.67 1.28
3025 3262 7.290014 AGGTTTGTCCTTTGTTCTTGGATAATT 59.710 33.333 0.00 0.00 45.67 1.40
3026 3263 7.931407 GGTTTGTCCTTTGTTCTTGGATAATTT 59.069 33.333 0.00 0.00 32.51 1.82
3028 3265 9.898152 TTTGTCCTTTGTTCTTGGATAATTTTT 57.102 25.926 0.00 0.00 32.51 1.94
3069 3309 8.523915 AAATGATGCATTACTTAGAATGACCA 57.476 30.769 0.00 0.00 38.83 4.02
3070 3310 6.925610 TGATGCATTACTTAGAATGACCAC 57.074 37.500 0.00 0.00 38.83 4.16
3071 3311 5.822519 TGATGCATTACTTAGAATGACCACC 59.177 40.000 0.00 0.00 38.83 4.61
3072 3312 5.172687 TGCATTACTTAGAATGACCACCA 57.827 39.130 0.40 0.00 38.83 4.17
3073 3313 5.754782 TGCATTACTTAGAATGACCACCAT 58.245 37.500 0.40 0.00 38.83 3.55
3074 3314 5.822519 TGCATTACTTAGAATGACCACCATC 59.177 40.000 0.40 0.00 38.83 3.51
3075 3315 6.058183 GCATTACTTAGAATGACCACCATCT 58.942 40.000 0.40 0.00 38.83 2.90
3076 3316 6.543831 GCATTACTTAGAATGACCACCATCTT 59.456 38.462 0.40 0.00 38.83 2.40
3077 3317 7.715249 GCATTACTTAGAATGACCACCATCTTA 59.285 37.037 0.40 0.00 38.83 2.10
3078 3318 9.613428 CATTACTTAGAATGACCACCATCTTAA 57.387 33.333 0.00 0.00 38.83 1.85
3079 3319 9.838339 ATTACTTAGAATGACCACCATCTTAAG 57.162 33.333 0.00 0.00 37.25 1.85
3080 3320 7.496346 ACTTAGAATGACCACCATCTTAAGA 57.504 36.000 7.82 7.82 36.10 2.10
3081 3321 7.918076 ACTTAGAATGACCACCATCTTAAGAA 58.082 34.615 9.71 0.00 36.10 2.52
3082 3322 8.552296 ACTTAGAATGACCACCATCTTAAGAAT 58.448 33.333 9.71 0.00 36.10 2.40
3083 3323 9.401058 CTTAGAATGACCACCATCTTAAGAATT 57.599 33.333 9.71 1.92 35.40 2.17
3085 3325 8.738645 AGAATGACCACCATCTTAAGAATTAC 57.261 34.615 9.71 0.00 33.53 1.89
3086 3326 8.552296 AGAATGACCACCATCTTAAGAATTACT 58.448 33.333 9.71 0.00 33.53 2.24
3087 3327 8.511604 AATGACCACCATCTTAAGAATTACTG 57.488 34.615 9.71 2.62 33.53 2.74
3089 3329 7.331026 TGACCACCATCTTAAGAATTACTGAG 58.669 38.462 9.71 0.53 0.00 3.35
3091 3331 7.560368 ACCACCATCTTAAGAATTACTGAGAG 58.440 38.462 9.71 0.00 0.00 3.20
3092 3332 7.181125 ACCACCATCTTAAGAATTACTGAGAGT 59.819 37.037 9.71 0.00 0.00 3.24
3121 3626 3.359695 TTTGGTGTTAGATAGCCACCC 57.640 47.619 5.66 0.00 46.49 4.61
3269 3776 7.655328 CCACCTAATGATAACTCTCAGTCATTC 59.345 40.741 3.04 0.00 40.59 2.67
3277 3784 8.807118 TGATAACTCTCAGTCATTCTAACTTGT 58.193 33.333 0.00 0.00 0.00 3.16
3353 3888 4.639755 TGAAACAGATGCTGAAAACAGTCA 59.360 37.500 0.82 0.00 35.18 3.41
3359 3894 4.940046 AGATGCTGAAAACAGTCATTCGAT 59.060 37.500 0.00 0.00 0.00 3.59
3362 3897 4.631377 TGCTGAAAACAGTCATTCGATAGG 59.369 41.667 0.00 0.00 0.00 2.57
3449 3984 6.375455 TCAATTTTCCTTCACAGATAAGCCTC 59.625 38.462 0.00 0.00 0.00 4.70
3522 4093 3.285484 GAGTGATGATGACAGGGCAAAT 58.715 45.455 0.00 0.00 0.00 2.32
3584 4155 2.151502 TTTGAAGGTGAAACTGGGCA 57.848 45.000 0.00 0.00 36.74 5.36
3585 4156 2.151502 TTGAAGGTGAAACTGGGCAA 57.848 45.000 0.00 0.00 36.74 4.52
3589 4160 2.452600 AGGTGAAACTGGGCAAAGAA 57.547 45.000 0.00 0.00 36.74 2.52
3590 4161 2.962859 AGGTGAAACTGGGCAAAGAAT 58.037 42.857 0.00 0.00 36.74 2.40
3697 4286 2.769095 AGGAGGAGTAGCTGTTTCATCC 59.231 50.000 15.56 15.56 40.98 3.51
3721 4310 8.041919 TCCAGGATTAATTGTTCATGTACGTTA 58.958 33.333 0.00 0.00 0.00 3.18
3892 4488 4.142687 ACATGCGTAATTAACCAAGCACTC 60.143 41.667 0.00 0.00 37.44 3.51
3894 4490 2.096980 GCGTAATTAACCAAGCACTCCC 59.903 50.000 0.00 0.00 0.00 4.30
3903 4499 1.529244 AAGCACTCCCCAACACTGC 60.529 57.895 0.00 0.00 0.00 4.40
3934 4628 2.224475 CCATGAGGGAATCAGCACTAGG 60.224 54.545 0.00 0.00 42.53 3.02
3944 4638 2.108168 TCAGCACTAGGTAGGCGAAAT 58.892 47.619 0.00 0.00 0.00 2.17
3995 4689 3.721087 AATGCCCAAGCTAACAGTAGT 57.279 42.857 0.00 0.00 40.80 2.73
4039 4733 2.226437 GGTTAACCGTGACGACTACTCA 59.774 50.000 9.34 0.00 0.00 3.41
4075 4769 0.537143 AACCCAATCTGACGCTTGCA 60.537 50.000 0.00 0.00 0.00 4.08
4128 4822 2.094390 TGCTGTTAAGTAGTAGTGCCGG 60.094 50.000 0.00 0.00 0.00 6.13
4202 4896 2.769095 GAGGACAGGAGCCTAACAAGAT 59.231 50.000 0.00 0.00 35.44 2.40
4223 4975 0.107017 CAGGCAGGATTACACAGGGG 60.107 60.000 0.00 0.00 0.00 4.79
4357 5109 2.676748 AGGTCCTGCCAAAATTCAACA 58.323 42.857 0.00 0.00 40.61 3.33
4403 5169 0.109412 GGCTTCAACATGCACAGCTC 60.109 55.000 0.00 0.00 0.00 4.09
4409 5175 0.957395 AACATGCACAGCTCTTCCCG 60.957 55.000 0.00 0.00 0.00 5.14
4427 5193 5.897377 TCCCGTAGTAAACTAGTACCAAC 57.103 43.478 0.00 0.00 32.23 3.77
4469 5235 8.682710 GGCAATCTAACAAGTTTGGTATTATGA 58.317 33.333 0.00 0.00 28.54 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.863424 CGACACGTTCCAGTAAGCAATAT 59.137 43.478 0.00 0.00 0.00 1.28
18 19 3.247442 CGACACGTTCCAGTAAGCAATA 58.753 45.455 0.00 0.00 0.00 1.90
26 27 2.360165 ACTAAAGACGACACGTTCCAGT 59.640 45.455 0.00 0.00 41.37 4.00
27 28 2.724690 CACTAAAGACGACACGTTCCAG 59.275 50.000 0.00 0.00 41.37 3.86
34 35 3.060473 GTCAACTGCACTAAAGACGACAC 60.060 47.826 0.00 0.00 0.00 3.67
37 38 3.381045 CTGTCAACTGCACTAAAGACGA 58.619 45.455 0.00 0.00 0.00 4.20
62 63 4.381411 GTTTCAGCTCAGGTCTTAACACT 58.619 43.478 0.00 0.00 0.00 3.55
63 64 3.184581 CGTTTCAGCTCAGGTCTTAACAC 59.815 47.826 0.00 0.00 0.00 3.32
70 72 1.149148 GAACCGTTTCAGCTCAGGTC 58.851 55.000 0.00 0.00 33.50 3.85
72 74 0.600255 ACGAACCGTTTCAGCTCAGG 60.600 55.000 0.00 0.00 36.35 3.86
93 95 6.499172 TCTCGAAGTCAATTATCTGCAGTAG 58.501 40.000 14.67 0.00 0.00 2.57
95 97 5.330455 TCTCGAAGTCAATTATCTGCAGT 57.670 39.130 14.67 3.75 0.00 4.40
284 286 3.077556 TCCTTGGAGAGCGAGGCC 61.078 66.667 0.00 0.00 0.00 5.19
337 339 4.286297 TCCTGAGTTCATTTGATTCGGT 57.714 40.909 0.00 0.00 0.00 4.69
339 341 6.316140 TGGTAATCCTGAGTTCATTTGATTCG 59.684 38.462 0.00 0.00 34.23 3.34
348 350 2.355108 GCTGCTGGTAATCCTGAGTTCA 60.355 50.000 0.00 0.00 35.11 3.18
362 364 3.444742 TGGTAGATTTTTCATGCTGCTGG 59.555 43.478 0.00 0.00 0.00 4.85
406 409 7.996644 GGGGACATGAATAAAAATGTAGGAGTA 59.003 37.037 0.00 0.00 37.15 2.59
407 410 6.833933 GGGGACATGAATAAAAATGTAGGAGT 59.166 38.462 0.00 0.00 37.15 3.85
408 411 6.017109 CGGGGACATGAATAAAAATGTAGGAG 60.017 42.308 0.00 0.00 37.15 3.69
409 412 5.825679 CGGGGACATGAATAAAAATGTAGGA 59.174 40.000 0.00 0.00 37.15 2.94
410 413 5.825679 TCGGGGACATGAATAAAAATGTAGG 59.174 40.000 0.00 0.00 37.15 3.18
411 414 6.317642 TGTCGGGGACATGAATAAAAATGTAG 59.682 38.462 0.00 0.00 37.67 2.74
427 430 1.648504 CGGAAATACTTGTCGGGGAC 58.351 55.000 0.00 0.00 0.00 4.46
430 433 2.210116 CATCCGGAAATACTTGTCGGG 58.790 52.381 9.01 0.00 40.92 5.14
445 448 0.601558 CATACGTACCCCTCCATCCG 59.398 60.000 0.00 0.00 0.00 4.18
447 450 3.833070 AGAATCATACGTACCCCTCCATC 59.167 47.826 0.00 0.00 0.00 3.51
449 452 3.323774 AGAATCATACGTACCCCTCCA 57.676 47.619 0.00 0.00 0.00 3.86
451 454 4.583489 TCTCAAGAATCATACGTACCCCTC 59.417 45.833 0.00 0.00 0.00 4.30
460 464 8.843885 TCATCCATCATTCTCAAGAATCATAC 57.156 34.615 2.24 0.00 42.41 2.39
461 465 8.657712 ACTCATCCATCATTCTCAAGAATCATA 58.342 33.333 2.24 0.00 42.41 2.15
487 491 2.031012 CTTCCTCGCCTGCACACA 59.969 61.111 0.00 0.00 0.00 3.72
488 492 3.426568 GCTTCCTCGCCTGCACAC 61.427 66.667 0.00 0.00 0.00 3.82
489 493 3.939939 TGCTTCCTCGCCTGCACA 61.940 61.111 0.00 0.00 0.00 4.57
490 494 3.426568 GTGCTTCCTCGCCTGCAC 61.427 66.667 0.00 0.00 46.66 4.57
491 495 3.182590 AAGTGCTTCCTCGCCTGCA 62.183 57.895 0.00 0.00 0.00 4.41
492 496 2.359230 AAGTGCTTCCTCGCCTGC 60.359 61.111 0.00 0.00 0.00 4.85
755 763 1.218875 ACACACACACACCATACGCG 61.219 55.000 3.53 3.53 0.00 6.01
756 764 0.234625 CACACACACACACCATACGC 59.765 55.000 0.00 0.00 0.00 4.42
757 765 1.260297 CACACACACACACACCATACG 59.740 52.381 0.00 0.00 0.00 3.06
758 766 2.031560 CACACACACACACACACCATAC 59.968 50.000 0.00 0.00 0.00 2.39
759 767 2.284190 CACACACACACACACACCATA 58.716 47.619 0.00 0.00 0.00 2.74
760 768 1.093972 CACACACACACACACACCAT 58.906 50.000 0.00 0.00 0.00 3.55
761 769 0.250510 ACACACACACACACACACCA 60.251 50.000 0.00 0.00 0.00 4.17
762 770 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
763 771 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
764 772 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
765 773 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
766 774 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
767 775 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
768 776 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
769 777 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
770 778 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
771 779 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
772 780 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
773 781 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
774 782 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
775 783 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
838 849 2.189594 TTAATCACTGTGCAGCTGCT 57.810 45.000 36.61 16.43 42.66 4.24
884 897 3.244078 ACGCTGTTCTTGTAGACATGGAA 60.244 43.478 0.00 0.00 0.00 3.53
907 920 2.293677 TACTGCTACCGACAATGCTG 57.706 50.000 0.00 0.00 0.00 4.41
914 927 2.478134 ACGATCGTATACTGCTACCGAC 59.522 50.000 21.32 0.00 0.00 4.79
916 929 2.222678 ACACGATCGTATACTGCTACCG 59.777 50.000 22.26 6.35 0.00 4.02
919 932 4.051237 ACGTACACGATCGTATACTGCTA 58.949 43.478 28.28 7.64 43.02 3.49
921 934 3.244670 ACGTACACGATCGTATACTGC 57.755 47.619 28.28 8.52 43.02 4.40
922 935 5.734035 TCAAAACGTACACGATCGTATACTG 59.266 40.000 28.28 23.51 43.02 2.74
923 936 5.868257 TCAAAACGTACACGATCGTATACT 58.132 37.500 28.28 15.99 43.02 2.12
926 939 4.973396 TCTCAAAACGTACACGATCGTAT 58.027 39.130 22.26 13.37 43.02 3.06
927 940 4.403015 TCTCAAAACGTACACGATCGTA 57.597 40.909 22.26 2.95 43.02 3.43
928 941 3.272439 TCTCAAAACGTACACGATCGT 57.728 42.857 16.60 16.60 43.02 3.73
929 942 3.910170 TCTTCTCAAAACGTACACGATCG 59.090 43.478 14.88 14.88 43.02 3.69
930 943 4.201372 CGTCTTCTCAAAACGTACACGATC 60.201 45.833 9.04 0.00 43.02 3.69
931 944 3.667261 CGTCTTCTCAAAACGTACACGAT 59.333 43.478 9.04 0.00 43.02 3.73
932 945 3.038017 CGTCTTCTCAAAACGTACACGA 58.962 45.455 9.04 0.00 43.02 4.35
933 946 2.408110 GCGTCTTCTCAAAACGTACACG 60.408 50.000 0.00 0.00 46.33 4.49
934 947 2.408110 CGCGTCTTCTCAAAACGTACAC 60.408 50.000 0.00 0.00 38.60 2.90
935 948 1.782569 CGCGTCTTCTCAAAACGTACA 59.217 47.619 0.00 0.00 38.60 2.90
936 949 1.783140 ACGCGTCTTCTCAAAACGTAC 59.217 47.619 5.58 0.00 38.60 3.67
937 950 2.124011 ACGCGTCTTCTCAAAACGTA 57.876 45.000 5.58 0.00 38.60 3.57
938 951 2.049228 CTACGCGTCTTCTCAAAACGT 58.951 47.619 18.63 0.00 38.60 3.99
939 952 1.385743 CCTACGCGTCTTCTCAAAACG 59.614 52.381 18.63 0.00 39.33 3.60
940 953 2.155155 CACCTACGCGTCTTCTCAAAAC 59.845 50.000 18.63 0.00 0.00 2.43
941 954 2.223876 ACACCTACGCGTCTTCTCAAAA 60.224 45.455 18.63 0.00 0.00 2.44
942 955 1.338973 ACACCTACGCGTCTTCTCAAA 59.661 47.619 18.63 0.00 0.00 2.69
943 956 0.956633 ACACCTACGCGTCTTCTCAA 59.043 50.000 18.63 0.00 0.00 3.02
944 957 1.812235 TACACCTACGCGTCTTCTCA 58.188 50.000 18.63 0.00 0.00 3.27
945 958 2.161211 ACTTACACCTACGCGTCTTCTC 59.839 50.000 18.63 0.00 0.00 2.87
946 959 2.095364 CACTTACACCTACGCGTCTTCT 60.095 50.000 18.63 0.00 0.00 2.85
947 960 2.248487 CACTTACACCTACGCGTCTTC 58.752 52.381 18.63 0.00 0.00 2.87
948 961 1.610522 ACACTTACACCTACGCGTCTT 59.389 47.619 18.63 0.00 0.00 3.01
949 962 1.068748 CACACTTACACCTACGCGTCT 60.069 52.381 18.63 0.00 0.00 4.18
950 963 1.334054 CACACTTACACCTACGCGTC 58.666 55.000 18.63 0.00 0.00 5.19
951 964 0.665369 GCACACTTACACCTACGCGT 60.665 55.000 19.17 19.17 0.00 6.01
952 965 1.670971 CGCACACTTACACCTACGCG 61.671 60.000 3.53 3.53 35.14 6.01
953 966 1.952266 GCGCACACTTACACCTACGC 61.952 60.000 0.30 0.00 38.17 4.42
954 967 1.349259 GGCGCACACTTACACCTACG 61.349 60.000 10.83 0.00 0.00 3.51
955 968 1.349259 CGGCGCACACTTACACCTAC 61.349 60.000 10.83 0.00 0.00 3.18
956 969 1.080366 CGGCGCACACTTACACCTA 60.080 57.895 10.83 0.00 0.00 3.08
957 970 2.357034 CGGCGCACACTTACACCT 60.357 61.111 10.83 0.00 0.00 4.00
958 971 2.663852 ACGGCGCACACTTACACC 60.664 61.111 10.83 0.00 0.00 4.16
959 972 1.768112 AACACGGCGCACACTTACAC 61.768 55.000 10.83 0.00 0.00 2.90
960 973 1.090625 AAACACGGCGCACACTTACA 61.091 50.000 10.83 0.00 0.00 2.41
961 974 0.656205 CAAACACGGCGCACACTTAC 60.656 55.000 10.83 0.00 0.00 2.34
962 975 1.644372 CAAACACGGCGCACACTTA 59.356 52.632 10.83 0.00 0.00 2.24
963 976 2.407210 CAAACACGGCGCACACTT 59.593 55.556 10.83 0.00 0.00 3.16
964 977 4.250431 GCAAACACGGCGCACACT 62.250 61.111 10.83 0.00 0.00 3.55
965 978 4.250431 AGCAAACACGGCGCACAC 62.250 61.111 10.83 0.00 36.08 3.82
966 979 4.249020 CAGCAAACACGGCGCACA 62.249 61.111 10.83 0.00 36.08 4.57
967 980 4.980903 CCAGCAAACACGGCGCAC 62.981 66.667 10.83 0.00 36.08 5.34
969 982 4.264638 AACCAGCAAACACGGCGC 62.265 61.111 6.90 0.00 36.08 6.53
970 983 2.051345 GAACCAGCAAACACGGCG 60.051 61.111 4.80 4.80 36.08 6.46
971 984 1.008538 CTGAACCAGCAAACACGGC 60.009 57.895 0.00 0.00 0.00 5.68
972 985 1.654220 CCTGAACCAGCAAACACGG 59.346 57.895 0.00 0.00 0.00 4.94
973 986 1.008538 GCCTGAACCAGCAAACACG 60.009 57.895 0.00 0.00 0.00 4.49
974 987 0.031178 CAGCCTGAACCAGCAAACAC 59.969 55.000 0.00 0.00 0.00 3.32
975 988 1.108727 CCAGCCTGAACCAGCAAACA 61.109 55.000 0.00 0.00 0.00 2.83
978 991 0.396974 AAACCAGCCTGAACCAGCAA 60.397 50.000 0.00 0.00 0.00 3.91
985 998 1.340889 GCACATCAAAACCAGCCTGAA 59.659 47.619 0.00 0.00 0.00 3.02
1022 1037 1.350071 AATTGTGCAATGGCCCTCAA 58.650 45.000 0.00 0.00 40.13 3.02
1023 1038 2.101783 CTAATTGTGCAATGGCCCTCA 58.898 47.619 0.00 0.00 40.13 3.86
1024 1039 2.378038 TCTAATTGTGCAATGGCCCTC 58.622 47.619 0.00 0.00 40.13 4.30
1025 1040 2.530460 TCTAATTGTGCAATGGCCCT 57.470 45.000 0.00 0.00 40.13 5.19
1026 1041 3.524541 CTTTCTAATTGTGCAATGGCCC 58.475 45.455 0.00 0.00 40.13 5.80
1027 1042 3.524541 CCTTTCTAATTGTGCAATGGCC 58.475 45.455 0.00 0.00 40.13 5.36
1028 1043 2.931969 GCCTTTCTAATTGTGCAATGGC 59.068 45.455 0.00 2.64 41.68 4.40
1029 1044 4.460948 AGCCTTTCTAATTGTGCAATGG 57.539 40.909 0.00 0.00 0.00 3.16
1030 1045 5.232463 ACAAGCCTTTCTAATTGTGCAATG 58.768 37.500 0.00 0.00 34.71 2.82
1031 1046 5.473066 ACAAGCCTTTCTAATTGTGCAAT 57.527 34.783 0.00 0.00 34.71 3.56
1032 1047 4.935352 ACAAGCCTTTCTAATTGTGCAA 57.065 36.364 0.00 0.00 34.71 4.08
1033 1048 4.935352 AACAAGCCTTTCTAATTGTGCA 57.065 36.364 0.00 0.00 36.09 4.57
1034 1049 5.288804 TCAAACAAGCCTTTCTAATTGTGC 58.711 37.500 0.00 0.00 36.09 4.57
1035 1050 6.507023 ACTCAAACAAGCCTTTCTAATTGTG 58.493 36.000 0.00 0.00 36.09 3.33
1036 1051 6.715347 ACTCAAACAAGCCTTTCTAATTGT 57.285 33.333 0.00 0.00 37.47 2.71
1037 1052 8.099364 TCTACTCAAACAAGCCTTTCTAATTG 57.901 34.615 0.00 0.00 0.00 2.32
1042 1057 4.068599 GCTCTACTCAAACAAGCCTTTCT 58.931 43.478 0.00 0.00 0.00 2.52
1064 1079 0.598562 ATCTAGATGGGCTGTACGCG 59.401 55.000 3.53 3.53 40.44 6.01
1067 1087 8.154856 TGGTTTTATTATCTAGATGGGCTGTAC 58.845 37.037 15.79 5.50 0.00 2.90
1079 1099 8.225863 TGATATGGGCCTGGTTTTATTATCTA 57.774 34.615 4.53 0.00 0.00 1.98
1081 1101 7.451566 AGTTGATATGGGCCTGGTTTTATTATC 59.548 37.037 4.53 0.00 0.00 1.75
1091 1111 2.301346 GTTGAGTTGATATGGGCCTGG 58.699 52.381 4.53 0.00 0.00 4.45
1143 1207 2.151202 GGAACTGTGAAATTGCCTCGA 58.849 47.619 0.00 0.00 0.00 4.04
1145 1209 4.590850 AAAGGAACTGTGAAATTGCCTC 57.409 40.909 0.00 0.00 40.86 4.70
1159 1223 5.476091 TTCTTCTCTCTCTCCAAAGGAAC 57.524 43.478 0.00 0.00 0.00 3.62
1221 1285 2.363795 TACTCCGTCAGGGGCTGG 60.364 66.667 0.00 0.00 43.67 4.85
1365 1429 0.112412 TCTGTTTTCTCTTGGCCCCC 59.888 55.000 0.00 0.00 0.00 5.40
1366 1430 1.889170 CTTCTGTTTTCTCTTGGCCCC 59.111 52.381 0.00 0.00 0.00 5.80
1536 1603 3.660501 GGATTGGTTCCACTGGAAAAC 57.339 47.619 12.33 9.09 43.86 2.43
1551 1618 1.496429 AGGGCCTGGATTAGTGGATTG 59.504 52.381 4.50 0.00 0.00 2.67
1612 1712 7.611467 TGGCATTACAACTGATGAGAAAAGTAT 59.389 33.333 0.00 0.00 0.00 2.12
1613 1713 6.939730 TGGCATTACAACTGATGAGAAAAGTA 59.060 34.615 0.00 0.00 0.00 2.24
1620 1720 5.240183 CCCTAATGGCATTACAACTGATGAG 59.760 44.000 15.73 4.31 0.00 2.90
1647 1747 0.542467 ATGCCATGAACAAGCCCACA 60.542 50.000 0.00 0.00 0.00 4.17
1672 1772 8.101654 ACCGTGATTTAGCAATTTAACTTGTA 57.898 30.769 7.31 0.00 0.00 2.41
1673 1773 6.977213 ACCGTGATTTAGCAATTTAACTTGT 58.023 32.000 7.31 0.00 0.00 3.16
1700 1800 7.041508 GCTTGTGTTCTGCTTAGATATTGCTAT 60.042 37.037 0.00 0.00 0.00 2.97
1726 1827 5.577945 CCATTGTGCAGCAAAACCTATTAAG 59.422 40.000 0.00 0.00 40.91 1.85
1729 1830 3.577848 TCCATTGTGCAGCAAAACCTATT 59.422 39.130 0.00 0.00 40.91 1.73
1734 1835 2.481185 CCAATCCATTGTGCAGCAAAAC 59.519 45.455 0.00 0.00 40.91 2.43
1739 1840 1.466856 TCTCCAATCCATTGTGCAGC 58.533 50.000 0.00 0.00 36.06 5.25
1762 1863 7.160726 GGAATTTCACATTCCATTTCTTTGGA 58.839 34.615 8.47 0.00 45.21 3.53
1822 1928 7.192232 CAGAGGAAAGAAAACTATGCATTAGC 58.808 38.462 3.54 0.00 42.57 3.09
1842 1948 3.146104 TCCCTGAAAAGAAAGCAGAGG 57.854 47.619 0.00 0.00 0.00 3.69
1932 2041 3.667960 GCGTCATCATCCATAAAATCGGC 60.668 47.826 0.00 0.00 0.00 5.54
2028 2137 4.006319 GAGTGGAAAAAGGATCAGGAGTG 58.994 47.826 0.00 0.00 0.00 3.51
2213 2324 5.710099 CCTTAACAGGTGTGGTATTGTCATT 59.290 40.000 0.00 0.00 35.06 2.57
2239 2350 6.594159 TCTTTGTCTTCCTATTTTTAGCGGAG 59.406 38.462 0.00 0.00 0.00 4.63
2449 2560 8.040727 GGAACTCAGGTTTTAAATGCCATAAAT 58.959 33.333 10.67 0.00 35.58 1.40
2784 3020 4.878397 ACAGTGACAAGAAAAGAGGAACTG 59.122 41.667 0.00 0.00 41.55 3.16
2877 3114 1.604278 GCGATGTATCCTTTTCCAGCC 59.396 52.381 0.00 0.00 0.00 4.85
3056 3296 7.496346 TCTTAAGATGGTGGTCATTCTAAGT 57.504 36.000 0.00 0.00 35.97 2.24
3057 3297 8.970859 ATTCTTAAGATGGTGGTCATTCTAAG 57.029 34.615 5.89 0.00 35.97 2.18
3065 3305 7.556844 TCTCAGTAATTCTTAAGATGGTGGTC 58.443 38.462 5.89 0.00 0.00 4.02
3066 3306 7.181125 ACTCTCAGTAATTCTTAAGATGGTGGT 59.819 37.037 5.89 0.00 0.00 4.16
3067 3307 7.560368 ACTCTCAGTAATTCTTAAGATGGTGG 58.440 38.462 5.89 0.00 0.00 4.61
3119 3624 3.632145 AGTAGTGCAAGTTGACAAAAGGG 59.368 43.478 7.16 0.00 0.00 3.95
3121 3626 5.484173 TCAGTAGTGCAAGTTGACAAAAG 57.516 39.130 7.16 0.00 0.00 2.27
3277 3784 6.374333 GCTGTTGGAATCCATGTTCTAGTTAA 59.626 38.462 1.39 0.00 31.53 2.01
3353 3888 1.051812 CTGGCAGGTCCCTATCGAAT 58.948 55.000 6.61 0.00 0.00 3.34
3359 3894 3.672338 TAGCGCTGGCAGGTCCCTA 62.672 63.158 22.90 0.00 43.41 3.53
3362 3897 2.876368 ATTGTAGCGCTGGCAGGTCC 62.876 60.000 22.90 0.00 43.41 4.46
3449 3984 1.490693 CGATGGTGCGGAATTCCTCG 61.491 60.000 22.05 18.01 0.00 4.63
3491 4026 1.070445 CATCATCACTCCTCTGGCTCC 59.930 57.143 0.00 0.00 0.00 4.70
3538 4109 6.018180 CCATGCCGTCTTAATAGTTAGGTTTC 60.018 42.308 0.00 0.00 0.00 2.78
3584 4155 0.700564 TCCAGGCTCCAGCATTCTTT 59.299 50.000 0.03 0.00 44.36 2.52
3585 4156 0.255318 CTCCAGGCTCCAGCATTCTT 59.745 55.000 0.03 0.00 44.36 2.52
3652 4223 2.121948 AGGACCTTGATATGCAGCTCA 58.878 47.619 0.00 0.00 0.00 4.26
3721 4310 6.160105 AGTGGTCCCTAGTAGTACTACTCAAT 59.840 42.308 33.47 21.72 44.58 2.57
3736 4325 1.071699 GAACAGCAACAGTGGTCCCTA 59.928 52.381 0.00 0.00 31.53 3.53
3737 4326 0.179018 GAACAGCAACAGTGGTCCCT 60.179 55.000 0.00 0.00 31.53 4.20
3892 4488 3.130340 GGTATATTTGTGCAGTGTTGGGG 59.870 47.826 0.00 0.00 0.00 4.96
3894 4490 5.125257 TCATGGTATATTTGTGCAGTGTTGG 59.875 40.000 0.00 0.00 0.00 3.77
3903 4499 6.072286 GCTGATTCCCTCATGGTATATTTGTG 60.072 42.308 0.00 0.00 32.10 3.33
4039 4733 1.064979 GGTTGACCATCATACCCGGTT 60.065 52.381 0.00 0.00 35.64 4.44
4075 4769 2.102588 GGGTATGATGTCGCCTGTAGTT 59.897 50.000 0.00 0.00 0.00 2.24
4128 4822 3.557185 TCTGATGCGCTCATTTACATGTC 59.443 43.478 9.73 0.00 32.10 3.06
4202 4896 0.035152 CCTGTGTAATCCTGCCTGCA 60.035 55.000 0.00 0.00 0.00 4.41
4244 4996 1.180029 CTGGGAATTCTGCTGGGTTG 58.820 55.000 5.23 0.00 0.00 3.77
4300 5052 1.087771 GCAAGCAGAATGGCAATGGC 61.088 55.000 0.00 0.00 35.86 4.40
4403 5169 6.071952 TGTTGGTACTAGTTTACTACGGGAAG 60.072 42.308 0.00 0.00 0.00 3.46
4409 5175 9.662947 ATTGGAATGTTGGTACTAGTTTACTAC 57.337 33.333 0.00 0.01 0.00 2.73
4427 5193 4.344102 AGATTGCCCTTCATGATTGGAATG 59.656 41.667 13.71 1.76 0.00 2.67
4469 5235 5.305128 CCCACAACCTATTGCATCCATAAAT 59.695 40.000 0.00 0.00 39.66 1.40



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

AutoCloner maintained by Alex Coulton.