Multiple sequence alignment - TraesCS7D01G067100

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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 TraesCS7D01G067100 chr7D 100.000 3041 0 0 1 3041 38078368 38075328 0.000000e+00 5616.0
1 TraesCS7D01G067100 chr7D 87.220 446 33 9 2608 3041 38196747 38197180 1.270000e-133 486.0
2 TraesCS7D01G067100 chr7D 97.030 101 3 0 2941 3041 38230351 38230451 1.450000e-38 171.0
3 TraesCS7D01G067100 chr4A 88.322 2295 136 51 787 3032 686529221 686531432 0.000000e+00 2632.0
4 TraesCS7D01G067100 chr4A 88.922 334 29 3 240 572 686528852 686529178 3.650000e-109 405.0
5 TraesCS7D01G067100 chr4A 81.851 281 34 11 2761 3041 642907271 642907008 1.420000e-53 220.0
6 TraesCS7D01G067100 chr7A 91.252 1646 83 28 803 2417 37361980 37360365 0.000000e+00 2185.0
7 TraesCS7D01G067100 chr7A 87.257 1130 79 30 1494 2622 37930395 37931460 0.000000e+00 1229.0
8 TraesCS7D01G067100 chr7A 89.260 419 28 10 64 474 37362867 37362458 2.700000e-140 508.0
9 TraesCS7D01G067100 chr7A 84.286 560 30 16 2496 3041 37360366 37359851 7.570000e-136 494.0
10 TraesCS7D01G067100 chr7A 96.216 185 6 1 585 769 733370408 733370591 4.930000e-78 302.0
11 TraesCS7D01G067100 chr7A 92.965 199 10 4 575 773 631446243 631446437 1.380000e-73 287.0
12 TraesCS7D01G067100 chr7A 81.657 169 17 8 2700 2859 37931553 37931716 8.850000e-26 128.0
13 TraesCS7D01G067100 chr7A 87.640 89 4 1 497 585 37362098 37362017 2.500000e-16 97.1
14 TraesCS7D01G067100 chr7A 97.778 45 1 0 2647 2691 37931461 37931505 9.040000e-11 78.7
15 TraesCS7D01G067100 chr3A 99.468 188 1 0 584 771 45126254 45126067 2.900000e-90 342.0
16 TraesCS7D01G067100 chr1B 99.465 187 1 0 584 770 141109676 141109862 1.040000e-89 340.0
17 TraesCS7D01G067100 chr1B 93.750 48 3 0 16 63 581232674 581232627 4.210000e-09 73.1
18 TraesCS7D01G067100 chr4B 97.838 185 3 1 586 770 642775252 642775435 4.890000e-83 318.0
19 TraesCS7D01G067100 chr3B 97.826 184 4 0 586 769 693340012 693340195 4.890000e-83 318.0
20 TraesCS7D01G067100 chr2B 97.790 181 3 1 586 766 555319686 555319865 8.190000e-81 311.0
21 TraesCS7D01G067100 chr2A 96.196 184 5 1 586 769 756217119 756216938 1.770000e-77 300.0
22 TraesCS7D01G067100 chr4D 95.213 188 4 1 584 771 102530061 102529879 2.970000e-75 292.0


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 TraesCS7D01G067100 chr7D 38075328 38078368 3040 True 5616.000000 5616 100.000000 1 3041 1 chr7D.!!$R1 3040
1 TraesCS7D01G067100 chr4A 686528852 686531432 2580 False 1518.500000 2632 88.622000 240 3032 2 chr4A.!!$F1 2792
2 TraesCS7D01G067100 chr7A 37359851 37362867 3016 True 821.025000 2185 88.109500 64 3041 4 chr7A.!!$R1 2977
3 TraesCS7D01G067100 chr7A 37930395 37931716 1321 False 478.566667 1229 88.897333 1494 2859 3 chr7A.!!$F3 1365

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
633 985 0.040958 GGCCGATGCATGAACGATTC 60.041 55.0 2.46 0.0 40.13 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2509 0.039618 GGAAACCAATGCTGGAGGGA 59.96 55.0 0.0 0.0 46.92 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
20 21 3.057969 CTACATGTTGAACCTGGAGCA 57.942 47.619 2.30 0.00 0.00 4.26
21 22 1.901591 ACATGTTGAACCTGGAGCAG 58.098 50.000 0.00 0.00 0.00 4.24
48 49 4.541648 CCTCGTCCCCCTCCGGAT 62.542 72.222 3.57 0.00 33.48 4.18
49 50 2.913060 CTCGTCCCCCTCCGGATC 60.913 72.222 3.57 0.00 33.48 3.36
50 51 4.534824 TCGTCCCCCTCCGGATCC 62.535 72.222 3.57 0.00 33.48 3.36
58 59 3.917760 CTCCGGATCCGCCACCTC 61.918 72.222 29.12 0.00 38.24 3.85
61 62 3.550431 CGGATCCGCCACCTCCAT 61.550 66.667 23.37 0.00 35.94 3.41
62 63 2.427753 GGATCCGCCACCTCCATC 59.572 66.667 0.00 0.00 36.34 3.51
70 71 1.188863 GCCACCTCCATCTGCATTTT 58.811 50.000 0.00 0.00 0.00 1.82
81 82 7.026631 TCCATCTGCATTTTAAGGTATTTCG 57.973 36.000 0.00 0.00 0.00 3.46
84 85 7.432252 CCATCTGCATTTTAAGGTATTTCGTTC 59.568 37.037 0.00 0.00 0.00 3.95
103 104 7.410800 TCGTTCTGAAATTTTACACACGTAT 57.589 32.000 0.00 0.00 0.00 3.06
104 105 8.518151 TCGTTCTGAAATTTTACACACGTATA 57.482 30.769 0.00 0.00 0.00 1.47
105 106 8.641155 TCGTTCTGAAATTTTACACACGTATAG 58.359 33.333 0.00 0.00 0.00 1.31
136 137 3.773860 TGTTCACGTGCACAATTCTTT 57.226 38.095 18.72 0.00 0.00 2.52
142 143 6.312399 TCACGTGCACAATTCTTTTTAGAT 57.688 33.333 18.64 0.00 0.00 1.98
175 176 2.629639 ATGGTTCGATTTTTGACGCC 57.370 45.000 0.00 0.00 0.00 5.68
194 197 1.547901 CCTCACTCCTTTTGTTCCCCC 60.548 57.143 0.00 0.00 0.00 5.40
230 233 6.017852 GGCAATATAGGAGTACTGTCTTTTGC 60.018 42.308 0.00 12.66 33.78 3.68
235 238 1.727335 GAGTACTGTCTTTTGCTCCGC 59.273 52.381 0.00 0.00 0.00 5.54
371 378 3.893813 AGAGGCAAATGCTTTCACTCTTT 59.106 39.130 5.25 0.00 41.70 2.52
382 389 5.065218 TGCTTTCACTCTTTTCACTGACTTC 59.935 40.000 0.00 0.00 0.00 3.01
396 403 3.068307 ACTGACTTCACTGCGAAACTAGT 59.932 43.478 0.00 0.00 31.71 2.57
437 444 4.448732 CAGTGCAAGCTTTATTTTTCCACC 59.551 41.667 0.00 0.00 0.00 4.61
474 481 6.955963 CGATTACACACTGCAATCTTTCTTAC 59.044 38.462 0.00 0.00 29.97 2.34
583 935 2.565834 CCCCACGTTCCTCTTCTTCTTA 59.434 50.000 0.00 0.00 0.00 2.10
584 936 3.007614 CCCCACGTTCCTCTTCTTCTTAA 59.992 47.826 0.00 0.00 0.00 1.85
585 937 4.246458 CCCACGTTCCTCTTCTTCTTAAG 58.754 47.826 0.00 0.00 0.00 1.85
586 938 4.021368 CCCACGTTCCTCTTCTTCTTAAGA 60.021 45.833 0.00 0.00 34.39 2.10
593 945 4.576106 CTCTTCTTCTTAAGAGCGTTGC 57.424 45.455 5.12 0.00 44.33 4.17
594 946 4.241681 CTCTTCTTCTTAAGAGCGTTGCT 58.758 43.478 5.12 0.00 44.33 3.91
595 947 5.386958 TCTTCTTCTTAAGAGCGTTGCTA 57.613 39.130 5.12 0.00 39.88 3.49
596 948 5.403246 TCTTCTTCTTAAGAGCGTTGCTAG 58.597 41.667 5.12 0.00 39.88 3.42
597 949 5.183331 TCTTCTTCTTAAGAGCGTTGCTAGA 59.817 40.000 5.12 0.38 39.88 2.43
598 950 4.734917 TCTTCTTAAGAGCGTTGCTAGAC 58.265 43.478 5.12 0.00 39.88 2.59
599 951 4.217767 TCTTCTTAAGAGCGTTGCTAGACA 59.782 41.667 5.12 0.00 39.88 3.41
600 952 4.098055 TCTTAAGAGCGTTGCTAGACAG 57.902 45.455 0.00 0.00 39.88 3.51
601 953 3.756963 TCTTAAGAGCGTTGCTAGACAGA 59.243 43.478 0.00 0.00 39.88 3.41
602 954 2.645730 AAGAGCGTTGCTAGACAGAG 57.354 50.000 0.00 0.00 39.88 3.35
603 955 0.814457 AGAGCGTTGCTAGACAGAGG 59.186 55.000 0.00 0.00 39.88 3.69
604 956 0.811915 GAGCGTTGCTAGACAGAGGA 59.188 55.000 0.00 0.00 39.88 3.71
605 957 1.407258 GAGCGTTGCTAGACAGAGGAT 59.593 52.381 0.00 0.00 39.88 3.24
606 958 1.135915 AGCGTTGCTAGACAGAGGATG 59.864 52.381 0.00 0.00 36.99 3.51
607 959 1.565305 CGTTGCTAGACAGAGGATGC 58.435 55.000 0.00 0.00 0.00 3.91
608 960 1.804372 CGTTGCTAGACAGAGGATGCC 60.804 57.143 0.00 0.00 0.00 4.40
609 961 1.484240 GTTGCTAGACAGAGGATGCCT 59.516 52.381 0.00 0.00 36.03 4.75
610 962 1.117994 TGCTAGACAGAGGATGCCTG 58.882 55.000 0.00 2.01 31.76 4.85
611 963 0.249826 GCTAGACAGAGGATGCCTGC 60.250 60.000 0.00 0.00 31.76 4.85
612 964 1.117994 CTAGACAGAGGATGCCTGCA 58.882 55.000 0.00 0.00 31.76 4.41
613 965 0.826715 TAGACAGAGGATGCCTGCAC 59.173 55.000 0.00 0.00 31.76 4.57
614 966 1.812922 GACAGAGGATGCCTGCACG 60.813 63.158 0.00 0.00 31.76 5.34
615 967 2.513204 CAGAGGATGCCTGCACGG 60.513 66.667 0.00 0.00 31.76 4.94
627 979 3.507924 GCACGGCCGATGCATGAA 61.508 61.111 33.23 0.00 42.88 2.57
628 980 2.404789 CACGGCCGATGCATGAAC 59.595 61.111 35.90 0.00 40.13 3.18
629 981 3.195002 ACGGCCGATGCATGAACG 61.195 61.111 35.90 6.01 40.13 3.95
630 982 2.889988 CGGCCGATGCATGAACGA 60.890 61.111 24.07 0.00 40.13 3.85
631 983 2.246739 CGGCCGATGCATGAACGAT 61.247 57.895 24.07 0.00 40.13 3.73
632 984 1.775039 CGGCCGATGCATGAACGATT 61.775 55.000 24.07 0.00 40.13 3.34
633 985 0.040958 GGCCGATGCATGAACGATTC 60.041 55.000 2.46 0.00 40.13 2.52
634 986 0.657312 GCCGATGCATGAACGATTCA 59.343 50.000 2.46 0.00 45.01 2.57
643 995 2.371910 TGAACGATTCATACGTGGCA 57.628 45.000 0.00 0.00 43.16 4.92
644 996 2.267426 TGAACGATTCATACGTGGCAG 58.733 47.619 0.00 0.00 43.16 4.85
645 997 1.004927 GAACGATTCATACGTGGCAGC 60.005 52.381 0.00 0.00 43.16 5.25
646 998 0.108377 ACGATTCATACGTGGCAGCA 60.108 50.000 0.00 0.00 42.37 4.41
647 999 0.301687 CGATTCATACGTGGCAGCAC 59.698 55.000 0.00 0.00 0.00 4.40
648 1000 0.657840 GATTCATACGTGGCAGCACC 59.342 55.000 0.00 0.00 39.84 5.01
662 1014 2.434884 CACCAGCAGCGACCGATT 60.435 61.111 0.00 0.00 0.00 3.34
663 1015 2.125512 ACCAGCAGCGACCGATTC 60.126 61.111 0.00 0.00 0.00 2.52
664 1016 2.185350 CCAGCAGCGACCGATTCT 59.815 61.111 0.00 0.00 0.00 2.40
665 1017 1.880340 CCAGCAGCGACCGATTCTC 60.880 63.158 0.00 0.00 0.00 2.87
666 1018 1.153765 CAGCAGCGACCGATTCTCA 60.154 57.895 0.00 0.00 0.00 3.27
667 1019 0.737367 CAGCAGCGACCGATTCTCAA 60.737 55.000 0.00 0.00 0.00 3.02
668 1020 0.176680 AGCAGCGACCGATTCTCAAT 59.823 50.000 0.00 0.00 0.00 2.57
669 1021 1.009829 GCAGCGACCGATTCTCAATT 58.990 50.000 0.00 0.00 0.00 2.32
670 1022 2.159099 AGCAGCGACCGATTCTCAATTA 60.159 45.455 0.00 0.00 0.00 1.40
671 1023 2.607635 GCAGCGACCGATTCTCAATTAA 59.392 45.455 0.00 0.00 0.00 1.40
672 1024 3.063452 GCAGCGACCGATTCTCAATTAAA 59.937 43.478 0.00 0.00 0.00 1.52
673 1025 4.436852 GCAGCGACCGATTCTCAATTAAAA 60.437 41.667 0.00 0.00 0.00 1.52
674 1026 5.627172 CAGCGACCGATTCTCAATTAAAAA 58.373 37.500 0.00 0.00 0.00 1.94
691 1043 0.961753 AAAAAGCACCAGCAGCTACC 59.038 50.000 0.00 0.00 42.53 3.18
692 1044 1.237285 AAAAGCACCAGCAGCTACCG 61.237 55.000 0.00 0.00 42.53 4.02
693 1045 2.397413 AAAGCACCAGCAGCTACCGT 62.397 55.000 0.00 0.00 42.53 4.83
694 1046 3.121030 GCACCAGCAGCTACCGTG 61.121 66.667 10.71 10.71 41.58 4.94
695 1047 3.121030 CACCAGCAGCTACCGTGC 61.121 66.667 0.00 0.00 41.54 5.34
696 1048 4.742201 ACCAGCAGCTACCGTGCG 62.742 66.667 0.00 0.00 46.06 5.34
697 1049 4.742201 CCAGCAGCTACCGTGCGT 62.742 66.667 0.00 0.00 46.06 5.24
698 1050 3.481903 CAGCAGCTACCGTGCGTG 61.482 66.667 0.00 0.00 46.06 5.34
699 1051 4.742201 AGCAGCTACCGTGCGTGG 62.742 66.667 0.00 0.00 46.06 4.94
700 1052 4.735132 GCAGCTACCGTGCGTGGA 62.735 66.667 0.37 0.00 38.13 4.02
701 1053 2.507102 CAGCTACCGTGCGTGGAG 60.507 66.667 0.37 0.00 38.13 3.86
702 1054 3.760035 AGCTACCGTGCGTGGAGG 61.760 66.667 0.37 0.00 38.13 4.30
703 1055 3.755628 GCTACCGTGCGTGGAGGA 61.756 66.667 0.37 0.00 0.00 3.71
704 1056 2.490217 CTACCGTGCGTGGAGGAG 59.510 66.667 0.37 0.00 0.00 3.69
705 1057 3.701604 CTACCGTGCGTGGAGGAGC 62.702 68.421 0.37 0.00 0.00 4.70
709 1061 4.767255 GTGCGTGGAGGAGCCCTG 62.767 72.222 0.00 0.00 31.76 4.45
711 1063 4.021925 GCGTGGAGGAGCCCTGTT 62.022 66.667 0.00 0.00 31.76 3.16
712 1064 2.046892 CGTGGAGGAGCCCTGTTG 60.047 66.667 0.00 0.00 31.76 3.33
713 1065 2.352805 GTGGAGGAGCCCTGTTGG 59.647 66.667 0.00 0.00 31.76 3.77
723 1075 4.250699 CCTGTTGGGGAGGGAGAA 57.749 61.111 0.00 0.00 0.00 2.87
724 1076 2.715295 CCTGTTGGGGAGGGAGAAT 58.285 57.895 0.00 0.00 0.00 2.40
725 1077 0.548510 CCTGTTGGGGAGGGAGAATC 59.451 60.000 0.00 0.00 0.00 2.52
726 1078 0.179000 CTGTTGGGGAGGGAGAATCG 59.821 60.000 0.00 0.00 34.37 3.34
727 1079 0.546747 TGTTGGGGAGGGAGAATCGT 60.547 55.000 0.00 0.00 34.37 3.73
728 1080 0.107654 GTTGGGGAGGGAGAATCGTG 60.108 60.000 0.00 0.00 34.37 4.35
729 1081 1.910580 TTGGGGAGGGAGAATCGTGC 61.911 60.000 0.00 0.00 34.37 5.34
730 1082 2.367202 GGGGAGGGAGAATCGTGCA 61.367 63.158 0.00 0.00 34.37 4.57
731 1083 1.602237 GGGAGGGAGAATCGTGCAA 59.398 57.895 0.00 0.00 34.37 4.08
732 1084 0.462759 GGGAGGGAGAATCGTGCAAG 60.463 60.000 0.00 0.00 34.37 4.01
733 1085 1.092345 GGAGGGAGAATCGTGCAAGC 61.092 60.000 0.00 0.00 34.37 4.01
734 1086 1.424493 GAGGGAGAATCGTGCAAGCG 61.424 60.000 0.00 0.00 34.37 4.68
735 1087 1.741770 GGGAGAATCGTGCAAGCGT 60.742 57.895 0.00 0.00 34.37 5.07
736 1088 1.696832 GGGAGAATCGTGCAAGCGTC 61.697 60.000 0.00 0.00 34.37 5.19
737 1089 1.341802 GAGAATCGTGCAAGCGTCG 59.658 57.895 0.00 0.00 0.00 5.12
738 1090 1.344942 GAGAATCGTGCAAGCGTCGT 61.345 55.000 0.00 0.00 0.00 4.34
739 1091 1.225475 GAATCGTGCAAGCGTCGTG 60.225 57.895 0.00 0.00 0.00 4.35
740 1092 3.295228 AATCGTGCAAGCGTCGTGC 62.295 57.895 9.89 9.89 46.98 5.34
744 1096 2.028337 TGCAAGCGTCGTGCACTA 59.972 55.556 16.19 0.00 46.76 2.74
745 1097 1.592939 TGCAAGCGTCGTGCACTAA 60.593 52.632 16.19 0.00 46.76 2.24
746 1098 1.827315 TGCAAGCGTCGTGCACTAAC 61.827 55.000 16.19 11.88 46.76 2.34
749 1101 2.732094 GCGTCGTGCACTAACCGT 60.732 61.111 16.19 0.00 45.45 4.83
750 1102 2.713894 GCGTCGTGCACTAACCGTC 61.714 63.158 16.19 0.00 45.45 4.79
751 1103 2.423031 CGTCGTGCACTAACCGTCG 61.423 63.158 16.19 7.08 0.00 5.12
752 1104 1.370900 GTCGTGCACTAACCGTCGT 60.371 57.895 16.19 0.00 0.00 4.34
753 1105 1.370778 TCGTGCACTAACCGTCGTG 60.371 57.895 16.19 0.00 0.00 4.35
754 1106 1.659335 CGTGCACTAACCGTCGTGT 60.659 57.895 16.19 0.00 33.78 4.49
755 1107 1.850640 GTGCACTAACCGTCGTGTG 59.149 57.895 10.32 0.00 33.78 3.82
756 1108 0.872881 GTGCACTAACCGTCGTGTGT 60.873 55.000 10.32 0.00 33.78 3.72
757 1109 0.667453 TGCACTAACCGTCGTGTGTA 59.333 50.000 0.00 0.00 33.78 2.90
758 1110 1.066757 TGCACTAACCGTCGTGTGTAA 59.933 47.619 0.00 0.00 33.78 2.41
759 1111 2.126467 GCACTAACCGTCGTGTGTAAA 58.874 47.619 0.00 0.00 33.78 2.01
760 1112 2.154389 GCACTAACCGTCGTGTGTAAAG 59.846 50.000 0.00 0.00 33.78 1.85
761 1113 2.154389 CACTAACCGTCGTGTGTAAAGC 59.846 50.000 0.00 0.00 0.00 3.51
762 1114 2.223782 ACTAACCGTCGTGTGTAAAGCA 60.224 45.455 0.00 0.00 0.00 3.91
763 1115 1.654317 AACCGTCGTGTGTAAAGCAA 58.346 45.000 0.00 0.00 0.00 3.91
764 1116 1.873698 ACCGTCGTGTGTAAAGCAAT 58.126 45.000 0.00 0.00 0.00 3.56
765 1117 2.215196 ACCGTCGTGTGTAAAGCAATT 58.785 42.857 0.00 0.00 0.00 2.32
766 1118 2.614983 ACCGTCGTGTGTAAAGCAATTT 59.385 40.909 0.00 0.00 0.00 1.82
767 1119 3.065648 ACCGTCGTGTGTAAAGCAATTTT 59.934 39.130 0.00 0.00 0.00 1.82
768 1120 3.420576 CCGTCGTGTGTAAAGCAATTTTG 59.579 43.478 0.00 0.00 0.00 2.44
769 1121 4.032355 CGTCGTGTGTAAAGCAATTTTGT 58.968 39.130 0.00 0.00 0.00 2.83
770 1122 4.144051 CGTCGTGTGTAAAGCAATTTTGTC 59.856 41.667 0.00 0.00 0.00 3.18
771 1123 5.270853 GTCGTGTGTAAAGCAATTTTGTCT 58.729 37.500 0.00 0.00 0.00 3.41
772 1124 5.741982 GTCGTGTGTAAAGCAATTTTGTCTT 59.258 36.000 0.00 0.00 0.00 3.01
773 1125 5.968848 TCGTGTGTAAAGCAATTTTGTCTTC 59.031 36.000 0.00 0.00 0.00 2.87
774 1126 5.971202 CGTGTGTAAAGCAATTTTGTCTTCT 59.029 36.000 0.00 0.00 0.00 2.85
775 1127 6.472163 CGTGTGTAAAGCAATTTTGTCTTCTT 59.528 34.615 0.00 0.00 0.00 2.52
782 1134 8.822652 AAAGCAATTTTGTCTTCTTAATCCAG 57.177 30.769 0.00 0.00 0.00 3.86
796 1172 5.926542 TCTTAATCCAGAGACAAACTGTTCG 59.073 40.000 0.00 0.00 34.04 3.95
807 1183 5.411669 AGACAAACTGTTCGAACTTGAAACT 59.588 36.000 26.31 19.69 0.00 2.66
870 1250 0.242286 CACTCCACTCCACACTCTCG 59.758 60.000 0.00 0.00 0.00 4.04
917 1298 2.391926 TTACACTCTCACCACCTCCA 57.608 50.000 0.00 0.00 0.00 3.86
963 1345 1.676014 CGGCCAAGAACCTCCAGTAAG 60.676 57.143 2.24 0.00 0.00 2.34
1036 1418 4.465446 TCCTGCCCCTCCTCCTCG 62.465 72.222 0.00 0.00 0.00 4.63
1161 1546 1.337817 CGTCCGACTTCGTCAAGCTG 61.338 60.000 0.00 0.00 37.74 4.24
1542 1927 4.662961 CTGGTGCTGACGTCGCCA 62.663 66.667 23.01 19.62 41.37 5.69
1860 2245 3.518998 ACCGAGATCGCCGACCTG 61.519 66.667 11.26 0.00 38.18 4.00
2103 2494 1.227764 ATCTCGCGCTACCGGTAGA 60.228 57.895 39.65 23.53 35.21 2.59
2133 2524 1.687612 CACTCCCTCCAGCATTGGT 59.312 57.895 0.00 0.00 45.26 3.67
2148 2539 0.690762 TTGGTTTCCTTCCTCGGGAG 59.309 55.000 0.00 0.00 34.06 4.30
2149 2540 0.473117 TGGTTTCCTTCCTCGGGAGT 60.473 55.000 0.00 0.00 34.06 3.85
2176 2570 4.408821 GGCCATGGGAGCGTGTCA 62.409 66.667 15.13 0.00 0.00 3.58
2291 2708 1.766069 GTGCGGACAATGTTTTGGAC 58.234 50.000 0.63 0.00 37.15 4.02
2292 2709 1.336755 GTGCGGACAATGTTTTGGACT 59.663 47.619 0.63 0.00 37.15 3.85
2333 2755 1.677633 CCATTTCCCCGCTCGGTTT 60.678 57.895 7.59 0.00 0.00 3.27
2404 2838 7.100458 AGAACATTGGGAGTACAATTATTGC 57.900 36.000 4.68 0.00 38.94 3.56
2417 2851 2.238847 TTATTGCAGACGAGGCCGCT 62.239 55.000 4.53 0.00 39.95 5.52
2418 2852 2.238847 TATTGCAGACGAGGCCGCTT 62.239 55.000 4.53 0.00 39.95 4.68
2419 2853 4.742201 TGCAGACGAGGCCGCTTC 62.742 66.667 4.71 4.71 39.95 3.86
2421 2855 4.116328 CAGACGAGGCCGCTTCGA 62.116 66.667 29.05 0.00 40.36 3.71
2422 2856 3.141488 AGACGAGGCCGCTTCGAT 61.141 61.111 29.05 15.18 40.36 3.59
2423 2857 2.655685 GACGAGGCCGCTTCGATC 60.656 66.667 29.05 18.42 40.36 3.69
2424 2858 3.127352 GACGAGGCCGCTTCGATCT 62.127 63.158 29.05 8.98 40.36 2.75
2425 2859 2.656651 CGAGGCCGCTTCGATCTG 60.657 66.667 19.28 0.00 40.36 2.90
2426 2860 2.964389 GAGGCCGCTTCGATCTGC 60.964 66.667 0.00 0.00 0.00 4.26
2427 2861 3.723235 GAGGCCGCTTCGATCTGCA 62.723 63.158 0.00 0.00 0.00 4.41
2428 2862 2.590007 GGCCGCTTCGATCTGCAT 60.590 61.111 0.00 0.00 0.00 3.96
2429 2863 2.630317 GCCGCTTCGATCTGCATG 59.370 61.111 0.00 0.00 0.00 4.06
2430 2864 1.884464 GCCGCTTCGATCTGCATGA 60.884 57.895 0.00 0.00 0.00 3.07
2431 2865 1.431488 GCCGCTTCGATCTGCATGAA 61.431 55.000 0.00 0.00 0.00 2.57
2432 2866 1.009078 CCGCTTCGATCTGCATGAAA 58.991 50.000 0.00 0.00 0.00 2.69
2433 2867 1.398041 CCGCTTCGATCTGCATGAAAA 59.602 47.619 0.00 0.00 0.00 2.29
2434 2868 2.032550 CCGCTTCGATCTGCATGAAAAT 59.967 45.455 0.00 0.00 0.00 1.82
2435 2869 3.286576 CGCTTCGATCTGCATGAAAATC 58.713 45.455 0.00 0.00 0.00 2.17
2436 2870 3.002042 CGCTTCGATCTGCATGAAAATCT 59.998 43.478 0.00 0.00 0.00 2.40
2437 2871 4.280461 GCTTCGATCTGCATGAAAATCTG 58.720 43.478 0.00 0.00 0.00 2.90
2438 2872 4.788840 GCTTCGATCTGCATGAAAATCTGG 60.789 45.833 0.00 0.00 0.00 3.86
2450 2884 6.595794 CATGAAAATCTGGTTGAACAAATGC 58.404 36.000 0.00 0.00 0.00 3.56
2462 2896 3.820467 TGAACAAATGCAGGGAAGTACAG 59.180 43.478 0.00 0.00 0.00 2.74
2470 2908 2.820037 GGAAGTACAGGGCTGCGC 60.820 66.667 8.86 8.86 0.00 6.09
2485 2923 4.802051 CGCCCATCCCAGGTGTGG 62.802 72.222 1.04 1.04 44.56 4.17
2719 3209 1.435105 CTTGGATCGAGCAGAGCGA 59.565 57.895 1.84 0.00 42.48 4.93
2720 3210 0.594540 CTTGGATCGAGCAGAGCGAG 60.595 60.000 1.84 0.00 41.49 5.03
2721 3211 2.354539 GGATCGAGCAGAGCGAGC 60.355 66.667 1.84 0.00 42.80 5.03
2723 3213 3.839642 GATCGAGCAGAGCGAGCCC 62.840 68.421 0.00 0.00 41.49 5.19
2736 3226 3.255397 AGCCCTGGAGCTGCTTGT 61.255 61.111 6.82 0.00 42.95 3.16
2779 3273 4.222114 GCACCGAATTATTGAGCTAATGC 58.778 43.478 0.00 0.00 40.05 3.56
2791 3287 0.665298 GCTAATGCTGGTAGCTTGGC 59.335 55.000 0.00 4.49 42.97 4.52
2831 3327 4.643387 ACAGTTGCCCGTCCTGCC 62.643 66.667 0.00 0.00 0.00 4.85
2850 3352 1.294780 CTCCCCGCCATGATAGCTC 59.705 63.158 0.00 0.00 0.00 4.09
2859 3361 1.469940 CCATGATAGCTCGGCCGTATC 60.470 57.143 27.15 23.63 0.00 2.24
2862 3364 0.882474 GATAGCTCGGCCGTATCAGT 59.118 55.000 27.15 8.26 0.00 3.41
2939 3442 9.924650 CTAACACCAAGTATCCTATGGTATTAC 57.075 37.037 0.00 0.00 45.45 1.89
2943 3456 5.046878 CCAAGTATCCTATGGTATTACGGCA 60.047 44.000 0.00 0.00 0.00 5.69
3032 3546 9.289303 GATACACAATGAATATTCAACCAACAC 57.711 33.333 21.50 7.27 41.13 3.32
3036 3550 7.168972 CACAATGAATATTCAACCAACACGTTT 59.831 33.333 21.50 5.17 41.13 3.60
3037 3551 8.353684 ACAATGAATATTCAACCAACACGTTTA 58.646 29.630 21.50 0.00 41.13 2.01
3038 3552 9.352784 CAATGAATATTCAACCAACACGTTTAT 57.647 29.630 21.50 0.00 41.13 1.40
3040 3554 9.997482 ATGAATATTCAACCAACACGTTTATAC 57.003 29.630 21.50 0.00 41.13 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.005554 CTGCTCCAGGTTCAACATGTAG 58.994 50.000 0.00 0.00 0.00 2.74
1 2 2.290260 CCTGCTCCAGGTTCAACATGTA 60.290 50.000 0.00 0.00 45.82 2.29
2 3 1.546323 CCTGCTCCAGGTTCAACATGT 60.546 52.381 0.81 0.00 45.82 3.21
3 4 1.171308 CCTGCTCCAGGTTCAACATG 58.829 55.000 0.00 0.00 45.82 3.21
4 5 3.658398 CCTGCTCCAGGTTCAACAT 57.342 52.632 3.09 0.00 45.82 2.71
41 42 3.917760 GAGGTGGCGGATCCGGAG 61.918 72.222 33.98 8.59 40.19 4.63
44 45 3.521529 GATGGAGGTGGCGGATCCG 62.522 68.421 30.03 30.03 43.09 4.18
45 46 2.143419 AGATGGAGGTGGCGGATCC 61.143 63.158 0.00 0.00 0.00 3.36
46 47 1.070445 CAGATGGAGGTGGCGGATC 59.930 63.158 0.00 0.00 0.00 3.36
47 48 3.112205 GCAGATGGAGGTGGCGGAT 62.112 63.158 0.00 0.00 0.00 4.18
48 49 3.785859 GCAGATGGAGGTGGCGGA 61.786 66.667 0.00 0.00 0.00 5.54
49 50 2.898920 AATGCAGATGGAGGTGGCGG 62.899 60.000 0.00 0.00 0.00 6.13
50 51 1.033746 AAATGCAGATGGAGGTGGCG 61.034 55.000 0.00 0.00 0.00 5.69
51 52 1.188863 AAAATGCAGATGGAGGTGGC 58.811 50.000 0.00 0.00 0.00 5.01
52 53 3.382546 CCTTAAAATGCAGATGGAGGTGG 59.617 47.826 0.00 0.00 0.00 4.61
53 54 4.019174 ACCTTAAAATGCAGATGGAGGTG 58.981 43.478 11.65 0.00 35.11 4.00
54 55 4.322057 ACCTTAAAATGCAGATGGAGGT 57.678 40.909 7.75 7.75 0.00 3.85
55 56 6.966534 AATACCTTAAAATGCAGATGGAGG 57.033 37.500 0.00 0.00 0.00 4.30
56 57 7.134815 CGAAATACCTTAAAATGCAGATGGAG 58.865 38.462 0.00 0.00 0.00 3.86
57 58 6.601613 ACGAAATACCTTAAAATGCAGATGGA 59.398 34.615 0.00 0.00 0.00 3.41
58 59 6.795399 ACGAAATACCTTAAAATGCAGATGG 58.205 36.000 0.00 0.00 0.00 3.51
59 60 8.184192 AGAACGAAATACCTTAAAATGCAGATG 58.816 33.333 0.00 0.00 0.00 2.90
60 61 8.184192 CAGAACGAAATACCTTAAAATGCAGAT 58.816 33.333 0.00 0.00 0.00 2.90
61 62 7.389330 TCAGAACGAAATACCTTAAAATGCAGA 59.611 33.333 0.00 0.00 0.00 4.26
62 63 7.526608 TCAGAACGAAATACCTTAAAATGCAG 58.473 34.615 0.00 0.00 0.00 4.41
148 149 7.306341 GCGTCAAAAATCGAACCATTTAGTTTT 60.306 33.333 0.00 0.00 0.00 2.43
149 150 6.143278 GCGTCAAAAATCGAACCATTTAGTTT 59.857 34.615 0.00 0.00 0.00 2.66
157 158 1.533731 GAGGCGTCAAAAATCGAACCA 59.466 47.619 0.52 0.00 0.00 3.67
158 159 1.533731 TGAGGCGTCAAAAATCGAACC 59.466 47.619 6.64 0.00 0.00 3.62
163 164 2.427506 AGGAGTGAGGCGTCAAAAATC 58.572 47.619 11.28 7.09 33.27 2.17
165 166 2.341846 AAGGAGTGAGGCGTCAAAAA 57.658 45.000 11.28 0.00 33.27 1.94
175 176 1.425448 AGGGGGAACAAAAGGAGTGAG 59.575 52.381 0.00 0.00 0.00 3.51
194 197 5.893824 ACTCCTATATTGCCCCAAGAAAAAG 59.106 40.000 0.00 0.00 0.00 2.27
230 233 3.376935 ATGTTGCCTCTCCGCGGAG 62.377 63.158 42.89 42.89 43.21 4.63
235 238 1.003355 ACCACATGTTGCCTCTCCG 60.003 57.895 0.00 0.00 0.00 4.63
382 389 1.199327 TCCGAGACTAGTTTCGCAGTG 59.801 52.381 25.87 14.70 36.09 3.66
437 444 2.591429 TAATCGGCGCATGGGCTG 60.591 61.111 31.90 31.90 40.73 4.85
450 457 8.034058 AGTAAGAAAGATTGCAGTGTGTAATC 57.966 34.615 9.06 9.06 45.72 1.75
474 481 9.217278 TCTACTACTACTTGACAACTTGAGTAG 57.783 37.037 11.81 11.81 44.40 2.57
523 873 8.615878 AATCTACTGTATCTACTGCTCACTAG 57.384 38.462 0.00 0.00 0.00 2.57
536 888 9.413048 GTGTTCCTGCTAATAATCTACTGTATC 57.587 37.037 0.00 0.00 0.00 2.24
537 889 8.368668 GGTGTTCCTGCTAATAATCTACTGTAT 58.631 37.037 0.00 0.00 0.00 2.29
538 890 7.201974 GGGTGTTCCTGCTAATAATCTACTGTA 60.202 40.741 0.00 0.00 0.00 2.74
539 891 6.408206 GGGTGTTCCTGCTAATAATCTACTGT 60.408 42.308 0.00 0.00 0.00 3.55
540 892 5.992217 GGGTGTTCCTGCTAATAATCTACTG 59.008 44.000 0.00 0.00 0.00 2.74
541 893 5.071923 GGGGTGTTCCTGCTAATAATCTACT 59.928 44.000 0.00 0.00 35.33 2.57
542 894 5.163237 TGGGGTGTTCCTGCTAATAATCTAC 60.163 44.000 0.00 0.00 35.33 2.59
573 925 4.258702 AGCAACGCTCTTAAGAAGAAGA 57.741 40.909 6.63 0.00 37.02 2.87
583 935 1.203523 CCTCTGTCTAGCAACGCTCTT 59.796 52.381 0.00 0.00 40.44 2.85
584 936 0.814457 CCTCTGTCTAGCAACGCTCT 59.186 55.000 0.00 0.00 40.44 4.09
585 937 0.811915 TCCTCTGTCTAGCAACGCTC 59.188 55.000 0.00 0.00 40.44 5.03
586 938 1.135915 CATCCTCTGTCTAGCAACGCT 59.864 52.381 0.00 0.00 43.41 5.07
587 939 1.565305 CATCCTCTGTCTAGCAACGC 58.435 55.000 0.00 0.00 0.00 4.84
588 940 1.565305 GCATCCTCTGTCTAGCAACG 58.435 55.000 0.00 0.00 0.00 4.10
589 941 1.484240 AGGCATCCTCTGTCTAGCAAC 59.516 52.381 0.00 0.00 38.30 4.17
590 942 1.483827 CAGGCATCCTCTGTCTAGCAA 59.516 52.381 0.00 0.00 37.87 3.91
591 943 1.117994 CAGGCATCCTCTGTCTAGCA 58.882 55.000 0.00 0.00 37.87 3.49
592 944 0.249826 GCAGGCATCCTCTGTCTAGC 60.250 60.000 0.00 0.00 37.87 3.42
593 945 1.117994 TGCAGGCATCCTCTGTCTAG 58.882 55.000 0.00 0.00 37.87 2.43
594 946 0.826715 GTGCAGGCATCCTCTGTCTA 59.173 55.000 0.00 0.00 37.87 2.59
595 947 1.601171 GTGCAGGCATCCTCTGTCT 59.399 57.895 0.00 0.00 41.73 3.41
596 948 1.812922 CGTGCAGGCATCCTCTGTC 60.813 63.158 0.00 0.00 34.89 3.51
597 949 2.267006 CGTGCAGGCATCCTCTGT 59.733 61.111 0.00 0.00 34.89 3.41
598 950 2.513204 CCGTGCAGGCATCCTCTG 60.513 66.667 0.00 0.00 35.49 3.35
610 962 3.507924 TTCATGCATCGGCCGTGC 61.508 61.111 32.27 32.27 42.81 5.34
611 963 2.404789 GTTCATGCATCGGCCGTG 59.595 61.111 27.15 22.51 40.13 4.94
612 964 2.923426 ATCGTTCATGCATCGGCCGT 62.923 55.000 27.15 10.00 40.13 5.68
613 965 1.775039 AATCGTTCATGCATCGGCCG 61.775 55.000 22.12 22.12 40.13 6.13
614 966 0.040958 GAATCGTTCATGCATCGGCC 60.041 55.000 0.00 0.00 40.13 6.13
615 967 0.657312 TGAATCGTTCATGCATCGGC 59.343 50.000 0.00 0.00 36.06 5.54
624 976 2.267426 CTGCCACGTATGAATCGTTCA 58.733 47.619 0.00 3.49 45.01 3.18
625 977 1.004927 GCTGCCACGTATGAATCGTTC 60.005 52.381 0.00 0.00 39.55 3.95
626 978 1.006832 GCTGCCACGTATGAATCGTT 58.993 50.000 0.00 0.00 39.55 3.85
627 979 0.108377 TGCTGCCACGTATGAATCGT 60.108 50.000 0.00 0.00 42.33 3.73
628 980 0.301687 GTGCTGCCACGTATGAATCG 59.698 55.000 0.00 0.00 31.34 3.34
629 981 0.657840 GGTGCTGCCACGTATGAATC 59.342 55.000 0.00 0.00 43.00 2.52
630 982 0.035534 TGGTGCTGCCACGTATGAAT 60.036 50.000 0.00 0.00 43.61 2.57
631 983 0.673333 CTGGTGCTGCCACGTATGAA 60.673 55.000 0.00 0.00 43.61 2.57
632 984 1.079197 CTGGTGCTGCCACGTATGA 60.079 57.895 0.00 0.00 43.61 2.15
633 985 2.753966 GCTGGTGCTGCCACGTATG 61.754 63.158 0.00 0.00 43.61 2.39
634 986 2.436646 GCTGGTGCTGCCACGTAT 60.437 61.111 0.00 0.00 43.61 3.06
635 987 3.881952 CTGCTGGTGCTGCCACGTA 62.882 63.158 0.00 0.00 43.61 3.57
645 997 2.434884 AATCGGTCGCTGCTGGTG 60.435 61.111 0.00 0.00 0.00 4.17
646 998 2.125512 GAATCGGTCGCTGCTGGT 60.126 61.111 0.00 0.00 0.00 4.00
647 999 1.880340 GAGAATCGGTCGCTGCTGG 60.880 63.158 0.00 0.00 0.00 4.85
648 1000 0.737367 TTGAGAATCGGTCGCTGCTG 60.737 55.000 0.00 0.00 38.61 4.41
649 1001 0.176680 ATTGAGAATCGGTCGCTGCT 59.823 50.000 0.00 0.00 38.61 4.24
650 1002 1.009829 AATTGAGAATCGGTCGCTGC 58.990 50.000 0.00 0.00 38.61 5.25
651 1003 4.857871 TTTAATTGAGAATCGGTCGCTG 57.142 40.909 0.00 0.00 38.61 5.18
652 1004 5.873179 TTTTTAATTGAGAATCGGTCGCT 57.127 34.783 0.00 0.00 38.61 4.93
672 1024 0.961753 GGTAGCTGCTGGTGCTTTTT 59.038 50.000 13.43 0.00 41.46 1.94
673 1025 1.237285 CGGTAGCTGCTGGTGCTTTT 61.237 55.000 13.43 0.00 41.46 2.27
674 1026 1.672356 CGGTAGCTGCTGGTGCTTT 60.672 57.895 13.43 0.00 41.46 3.51
675 1027 2.046892 CGGTAGCTGCTGGTGCTT 60.047 61.111 13.43 0.00 41.46 3.91
676 1028 3.314331 ACGGTAGCTGCTGGTGCT 61.314 61.111 15.55 5.30 43.79 4.40
677 1029 3.121030 CACGGTAGCTGCTGGTGC 61.121 66.667 15.55 3.82 40.20 5.01
678 1030 3.121030 GCACGGTAGCTGCTGGTG 61.121 66.667 15.55 17.25 0.00 4.17
679 1031 4.742201 CGCACGGTAGCTGCTGGT 62.742 66.667 15.55 4.70 32.03 4.00
680 1032 4.742201 ACGCACGGTAGCTGCTGG 62.742 66.667 15.55 5.28 32.03 4.85
681 1033 3.481903 CACGCACGGTAGCTGCTG 61.482 66.667 13.43 9.34 32.03 4.41
682 1034 4.742201 CCACGCACGGTAGCTGCT 62.742 66.667 7.57 7.57 32.03 4.24
683 1035 4.735132 TCCACGCACGGTAGCTGC 62.735 66.667 0.00 0.00 0.00 5.25
684 1036 2.507102 CTCCACGCACGGTAGCTG 60.507 66.667 0.00 0.00 0.00 4.24
685 1037 3.760035 CCTCCACGCACGGTAGCT 61.760 66.667 0.00 0.00 0.00 3.32
686 1038 3.701604 CTCCTCCACGCACGGTAGC 62.702 68.421 0.00 0.00 0.00 3.58
687 1039 2.490217 CTCCTCCACGCACGGTAG 59.510 66.667 0.00 0.00 0.00 3.18
688 1040 3.755628 GCTCCTCCACGCACGGTA 61.756 66.667 0.00 0.00 0.00 4.02
692 1044 4.767255 CAGGGCTCCTCCACGCAC 62.767 72.222 0.00 0.00 36.21 5.34
694 1046 4.021925 AACAGGGCTCCTCCACGC 62.022 66.667 0.00 0.00 36.21 5.34
695 1047 2.046892 CAACAGGGCTCCTCCACG 60.047 66.667 0.00 0.00 36.21 4.94
696 1048 2.352805 CCAACAGGGCTCCTCCAC 59.647 66.667 0.00 0.00 36.21 4.02
697 1049 2.935481 CCCAACAGGGCTCCTCCA 60.935 66.667 0.00 0.00 35.34 3.86
706 1058 0.548510 GATTCTCCCTCCCCAACAGG 59.451 60.000 0.00 0.00 0.00 4.00
707 1059 0.179000 CGATTCTCCCTCCCCAACAG 59.821 60.000 0.00 0.00 0.00 3.16
708 1060 0.546747 ACGATTCTCCCTCCCCAACA 60.547 55.000 0.00 0.00 0.00 3.33
709 1061 0.107654 CACGATTCTCCCTCCCCAAC 60.108 60.000 0.00 0.00 0.00 3.77
710 1062 1.910580 GCACGATTCTCCCTCCCCAA 61.911 60.000 0.00 0.00 0.00 4.12
711 1063 2.367202 GCACGATTCTCCCTCCCCA 61.367 63.158 0.00 0.00 0.00 4.96
712 1064 1.910580 TTGCACGATTCTCCCTCCCC 61.911 60.000 0.00 0.00 0.00 4.81
713 1065 0.462759 CTTGCACGATTCTCCCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
714 1066 1.092345 GCTTGCACGATTCTCCCTCC 61.092 60.000 0.00 0.00 0.00 4.30
715 1067 1.424493 CGCTTGCACGATTCTCCCTC 61.424 60.000 0.00 0.00 34.06 4.30
716 1068 1.448540 CGCTTGCACGATTCTCCCT 60.449 57.895 0.00 0.00 34.06 4.20
717 1069 1.696832 GACGCTTGCACGATTCTCCC 61.697 60.000 3.48 0.00 36.70 4.30
718 1070 1.710339 GACGCTTGCACGATTCTCC 59.290 57.895 3.48 0.00 36.70 3.71
719 1071 1.341802 CGACGCTTGCACGATTCTC 59.658 57.895 3.48 0.00 36.70 2.87
720 1072 1.372997 ACGACGCTTGCACGATTCT 60.373 52.632 3.48 0.00 36.70 2.40
721 1073 1.225475 CACGACGCTTGCACGATTC 60.225 57.895 3.48 0.00 36.70 2.52
722 1074 2.853210 CACGACGCTTGCACGATT 59.147 55.556 3.48 0.00 36.70 3.34
723 1075 3.777925 GCACGACGCTTGCACGAT 61.778 61.111 3.48 0.00 39.93 3.73
728 1080 1.154654 GTTAGTGCACGACGCTTGC 60.155 57.895 12.01 3.65 43.06 4.01
729 1081 1.491563 GGTTAGTGCACGACGCTTG 59.508 57.895 12.01 0.00 43.06 4.01
730 1082 2.019951 CGGTTAGTGCACGACGCTT 61.020 57.895 12.01 0.00 43.06 4.68
731 1083 2.430244 CGGTTAGTGCACGACGCT 60.430 61.111 12.01 0.00 43.06 5.07
732 1084 2.713894 GACGGTTAGTGCACGACGC 61.714 63.158 19.78 12.28 42.89 5.19
733 1085 2.423031 CGACGGTTAGTGCACGACG 61.423 63.158 12.01 16.25 39.01 5.12
734 1086 1.370900 ACGACGGTTAGTGCACGAC 60.371 57.895 12.01 14.04 0.00 4.34
735 1087 1.370778 CACGACGGTTAGTGCACGA 60.371 57.895 12.01 2.52 0.00 4.35
736 1088 1.659335 ACACGACGGTTAGTGCACG 60.659 57.895 12.01 0.95 41.72 5.34
737 1089 0.872881 ACACACGACGGTTAGTGCAC 60.873 55.000 9.40 9.40 41.72 4.57
738 1090 0.667453 TACACACGACGGTTAGTGCA 59.333 50.000 14.69 0.00 41.72 4.57
739 1091 1.769733 TTACACACGACGGTTAGTGC 58.230 50.000 14.69 0.00 41.72 4.40
740 1092 2.154389 GCTTTACACACGACGGTTAGTG 59.846 50.000 13.63 13.63 43.46 2.74
741 1093 2.223782 TGCTTTACACACGACGGTTAGT 60.224 45.455 0.00 0.00 0.00 2.24
742 1094 2.396601 TGCTTTACACACGACGGTTAG 58.603 47.619 0.00 0.00 0.00 2.34
743 1095 2.505628 TGCTTTACACACGACGGTTA 57.494 45.000 0.00 0.00 0.00 2.85
744 1096 1.654317 TTGCTTTACACACGACGGTT 58.346 45.000 0.00 0.00 0.00 4.44
745 1097 1.873698 ATTGCTTTACACACGACGGT 58.126 45.000 0.00 0.00 0.00 4.83
746 1098 2.961522 AATTGCTTTACACACGACGG 57.038 45.000 0.00 0.00 0.00 4.79
747 1099 4.032355 ACAAAATTGCTTTACACACGACG 58.968 39.130 0.00 0.00 0.00 5.12
748 1100 5.270853 AGACAAAATTGCTTTACACACGAC 58.729 37.500 0.00 0.00 0.00 4.34
749 1101 5.493133 AGACAAAATTGCTTTACACACGA 57.507 34.783 0.00 0.00 0.00 4.35
750 1102 5.971202 AGAAGACAAAATTGCTTTACACACG 59.029 36.000 0.00 0.00 0.00 4.49
751 1103 7.755582 AAGAAGACAAAATTGCTTTACACAC 57.244 32.000 0.00 0.00 0.00 3.82
754 1106 9.691362 GGATTAAGAAGACAAAATTGCTTTACA 57.309 29.630 0.00 0.00 0.00 2.41
755 1107 9.691362 TGGATTAAGAAGACAAAATTGCTTTAC 57.309 29.630 0.00 0.00 0.00 2.01
756 1108 9.912634 CTGGATTAAGAAGACAAAATTGCTTTA 57.087 29.630 0.00 0.00 0.00 1.85
757 1109 8.641541 TCTGGATTAAGAAGACAAAATTGCTTT 58.358 29.630 0.00 0.00 0.00 3.51
758 1110 8.181904 TCTGGATTAAGAAGACAAAATTGCTT 57.818 30.769 0.00 0.00 0.00 3.91
759 1111 7.667219 TCTCTGGATTAAGAAGACAAAATTGCT 59.333 33.333 0.00 0.00 0.00 3.91
760 1112 7.752686 GTCTCTGGATTAAGAAGACAAAATTGC 59.247 37.037 0.00 0.00 30.83 3.56
761 1113 8.786898 TGTCTCTGGATTAAGAAGACAAAATTG 58.213 33.333 1.28 0.00 34.40 2.32
762 1114 8.924511 TGTCTCTGGATTAAGAAGACAAAATT 57.075 30.769 1.28 0.00 34.40 1.82
763 1115 8.924511 TTGTCTCTGGATTAAGAAGACAAAAT 57.075 30.769 12.40 0.00 39.11 1.82
764 1116 8.621286 GTTTGTCTCTGGATTAAGAAGACAAAA 58.379 33.333 23.02 10.51 44.48 2.44
765 1117 7.993183 AGTTTGTCTCTGGATTAAGAAGACAAA 59.007 33.333 19.46 19.46 43.07 2.83
766 1118 7.442364 CAGTTTGTCTCTGGATTAAGAAGACAA 59.558 37.037 11.12 11.12 39.63 3.18
767 1119 6.931281 CAGTTTGTCTCTGGATTAAGAAGACA 59.069 38.462 0.00 0.00 34.96 3.41
768 1120 6.931840 ACAGTTTGTCTCTGGATTAAGAAGAC 59.068 38.462 0.00 0.00 37.25 3.01
769 1121 7.067496 ACAGTTTGTCTCTGGATTAAGAAGA 57.933 36.000 0.00 0.00 37.25 2.87
770 1122 7.359598 CGAACAGTTTGTCTCTGGATTAAGAAG 60.360 40.741 0.00 0.00 37.25 2.85
771 1123 6.423905 CGAACAGTTTGTCTCTGGATTAAGAA 59.576 38.462 0.00 0.00 37.25 2.52
772 1124 5.926542 CGAACAGTTTGTCTCTGGATTAAGA 59.073 40.000 0.00 0.00 37.25 2.10
773 1125 5.926542 TCGAACAGTTTGTCTCTGGATTAAG 59.073 40.000 0.15 0.00 37.25 1.85
774 1126 5.849510 TCGAACAGTTTGTCTCTGGATTAA 58.150 37.500 0.15 0.00 37.25 1.40
775 1127 5.462530 TCGAACAGTTTGTCTCTGGATTA 57.537 39.130 0.15 0.00 37.25 1.75
782 1134 5.464965 TTCAAGTTCGAACAGTTTGTCTC 57.535 39.130 28.78 0.00 0.00 3.36
796 1172 2.789339 GCGCTTTTGGAGTTTCAAGTTC 59.211 45.455 0.00 0.00 0.00 3.01
807 1183 2.086251 CTTGGCTTGGCGCTTTTGGA 62.086 55.000 7.64 0.00 39.13 3.53
870 1250 2.887783 TGGAGTGAGAGTGAGAGTGAAC 59.112 50.000 0.00 0.00 0.00 3.18
917 1298 5.013599 GGATGCTTTATAGAGAGTGGGGAAT 59.986 44.000 0.00 0.00 0.00 3.01
967 1349 2.253403 GAGGGGAATGTCGGGTGGTC 62.253 65.000 0.00 0.00 0.00 4.02
972 1354 1.144057 CTTCGAGGGGAATGTCGGG 59.856 63.158 0.00 0.00 36.81 5.14
973 1355 1.521681 GCTTCGAGGGGAATGTCGG 60.522 63.158 0.00 0.00 36.81 4.79
1018 1400 2.445654 GAGGAGGAGGGGCAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
1026 1408 4.824515 AGGGCGACGAGGAGGAGG 62.825 72.222 0.00 0.00 0.00 4.30
1027 1409 3.213402 GAGGGCGACGAGGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
1161 1546 2.595655 GGGCCCATGTGGTACTCC 59.404 66.667 19.95 0.00 36.04 3.85
1344 1729 3.701604 CTGGTCCGTGTAGAGCCGC 62.702 68.421 0.00 0.00 33.24 6.53
1431 1816 4.498520 ATCCGTGTCAGCGAGGCG 62.499 66.667 0.00 0.00 0.00 5.52
1542 1927 0.178958 AGTTCTCCACGTGGACCTCT 60.179 55.000 33.23 24.61 39.78 3.69
1581 1966 2.612221 CGGGAAGGTGAAGTAGTGGAAC 60.612 54.545 0.00 0.00 0.00 3.62
1791 2176 4.659172 TTGGCCAGCGGGTTGGAG 62.659 66.667 5.11 0.00 40.87 3.86
1836 2221 2.202892 GCGATCTCGGTGGGGAAC 60.203 66.667 1.34 0.00 40.23 3.62
1936 2322 2.388232 CGCCGTTGAGGTTGTAGGC 61.388 63.158 0.00 0.00 43.70 3.93
2089 2475 0.590195 ATACTTCTACCGGTAGCGCG 59.410 55.000 32.84 24.16 33.32 6.86
2096 2487 2.364647 GTGGGAGGAATACTTCTACCGG 59.635 54.545 0.00 0.00 30.21 5.28
2103 2494 2.629909 GGAGGGAGTGGGAGGAATACTT 60.630 54.545 0.00 0.00 0.00 2.24
2117 2508 1.467920 GAAACCAATGCTGGAGGGAG 58.532 55.000 0.00 0.00 46.92 4.30
2118 2509 0.039618 GGAAACCAATGCTGGAGGGA 59.960 55.000 0.00 0.00 46.92 4.20
2119 2510 0.040204 AGGAAACCAATGCTGGAGGG 59.960 55.000 0.00 0.00 46.92 4.30
2133 2524 0.981943 GGAACTCCCGAGGAAGGAAA 59.018 55.000 0.00 0.00 31.49 3.13
2176 2570 3.821748 TCGGCTCACTGACTCTATACAT 58.178 45.455 0.00 0.00 0.00 2.29
2291 2708 8.828644 TGGACAAAATGACATCAAATTTGAAAG 58.171 29.630 23.91 20.24 41.13 2.62
2292 2709 8.728337 TGGACAAAATGACATCAAATTTGAAA 57.272 26.923 23.91 11.02 41.13 2.69
2333 2755 9.982291 GTAGTAATGCTAATCAAATTTGAACGA 57.018 29.630 23.91 11.47 41.13 3.85
2404 2838 3.417275 ATCGAAGCGGCCTCGTCTG 62.417 63.158 19.27 3.95 38.89 3.51
2417 2851 4.264253 ACCAGATTTTCATGCAGATCGAA 58.736 39.130 0.00 0.00 0.00 3.71
2418 2852 3.877559 ACCAGATTTTCATGCAGATCGA 58.122 40.909 0.00 0.00 0.00 3.59
2419 2853 4.095334 TCAACCAGATTTTCATGCAGATCG 59.905 41.667 0.00 0.00 0.00 3.69
2420 2854 5.571784 TCAACCAGATTTTCATGCAGATC 57.428 39.130 0.00 0.00 0.00 2.75
2421 2855 5.244402 TGTTCAACCAGATTTTCATGCAGAT 59.756 36.000 0.00 0.00 0.00 2.90
2422 2856 4.583907 TGTTCAACCAGATTTTCATGCAGA 59.416 37.500 0.00 0.00 0.00 4.26
2423 2857 4.873817 TGTTCAACCAGATTTTCATGCAG 58.126 39.130 0.00 0.00 0.00 4.41
2424 2858 4.933505 TGTTCAACCAGATTTTCATGCA 57.066 36.364 0.00 0.00 0.00 3.96
2425 2859 6.595794 CATTTGTTCAACCAGATTTTCATGC 58.404 36.000 0.00 0.00 0.00 4.06
2426 2860 6.203145 TGCATTTGTTCAACCAGATTTTCATG 59.797 34.615 0.00 0.00 0.00 3.07
2427 2861 6.289834 TGCATTTGTTCAACCAGATTTTCAT 58.710 32.000 0.00 0.00 0.00 2.57
2428 2862 5.668471 TGCATTTGTTCAACCAGATTTTCA 58.332 33.333 0.00 0.00 0.00 2.69
2429 2863 5.178067 CCTGCATTTGTTCAACCAGATTTTC 59.822 40.000 0.00 0.00 0.00 2.29
2430 2864 5.058490 CCTGCATTTGTTCAACCAGATTTT 58.942 37.500 0.00 0.00 0.00 1.82
2431 2865 4.503643 CCCTGCATTTGTTCAACCAGATTT 60.504 41.667 0.00 0.00 0.00 2.17
2432 2866 3.007182 CCCTGCATTTGTTCAACCAGATT 59.993 43.478 0.00 0.00 0.00 2.40
2433 2867 2.564062 CCCTGCATTTGTTCAACCAGAT 59.436 45.455 0.00 0.00 0.00 2.90
2434 2868 1.962807 CCCTGCATTTGTTCAACCAGA 59.037 47.619 0.00 0.00 0.00 3.86
2435 2869 1.962807 TCCCTGCATTTGTTCAACCAG 59.037 47.619 0.00 0.00 0.00 4.00
2436 2870 2.079170 TCCCTGCATTTGTTCAACCA 57.921 45.000 0.00 0.00 0.00 3.67
2437 2871 2.365293 ACTTCCCTGCATTTGTTCAACC 59.635 45.455 0.00 0.00 0.00 3.77
2438 2872 3.733443 ACTTCCCTGCATTTGTTCAAC 57.267 42.857 0.00 0.00 0.00 3.18
2450 2884 1.078143 GCAGCCCTGTACTTCCCTG 60.078 63.158 0.00 0.00 0.00 4.45
2470 2908 3.759750 ATCCACACCTGGGATGGG 58.240 61.111 16.01 4.50 43.44 4.00
2485 2923 1.205179 TGTCATTGTGCAATGCCCATC 59.795 47.619 17.36 7.87 45.77 3.51
2486 2924 1.268066 TGTCATTGTGCAATGCCCAT 58.732 45.000 17.36 0.00 45.77 4.00
2487 2925 1.046204 TTGTCATTGTGCAATGCCCA 58.954 45.000 17.36 13.68 45.77 5.36
2488 2926 2.004017 CATTGTCATTGTGCAATGCCC 58.996 47.619 17.36 11.74 45.77 5.36
2492 2930 1.352114 GCGCATTGTCATTGTGCAAT 58.648 45.000 22.19 0.00 47.00 3.56
2719 3209 2.838467 AACAAGCAGCTCCAGGGCT 61.838 57.895 0.00 0.00 44.10 5.19
2720 3210 2.282745 AACAAGCAGCTCCAGGGC 60.283 61.111 0.00 0.00 0.00 5.19
2721 3211 2.633509 GCAACAAGCAGCTCCAGGG 61.634 63.158 0.00 0.00 44.79 4.45
2736 3226 1.116536 TACTGGTGACCACGGAGCAA 61.117 55.000 0.00 0.00 0.00 3.91
2779 3273 0.035317 TCACAGTGCCAAGCTACCAG 59.965 55.000 0.00 0.00 0.00 4.00
2781 3275 1.160137 CTTCACAGTGCCAAGCTACC 58.840 55.000 0.00 0.00 0.00 3.18
2790 3286 1.310933 CCATGGCTCCTTCACAGTGC 61.311 60.000 0.00 0.00 0.00 4.40
2791 3287 1.310933 GCCATGGCTCCTTCACAGTG 61.311 60.000 29.98 0.00 38.26 3.66
2831 3327 2.177594 GAGCTATCATGGCGGGGAGG 62.178 65.000 0.00 0.00 34.52 4.30
2850 3352 1.374252 GCCCATACTGATACGGCCG 60.374 63.158 26.86 26.86 33.30 6.13
2859 3361 1.673168 GAGAAAGCAGGCCCATACTG 58.327 55.000 0.00 0.00 38.95 2.74
2862 3364 1.271840 ACGGAGAAAGCAGGCCCATA 61.272 55.000 0.00 0.00 0.00 2.74
2939 3442 2.054687 AAATTGCATCGCATATGCCG 57.945 45.000 21.77 16.14 43.94 5.69
2943 3456 6.152932 AGAAGGAAAAATTGCATCGCATAT 57.847 33.333 0.00 0.00 38.76 1.78


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

AutoCloner maintained by Alex Coulton.