Multiple sequence alignment - TraesCS3D01G492000

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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 TraesCS3D01G492000 chr3D 100.000 3985 0 0 1 3985 585877527 585881511 0.000000e+00 7360.0
1 TraesCS3D01G492000 chr3D 91.892 111 9 0 2186 2296 585909152 585909262 5.330000e-34 156.0
2 TraesCS3D01G492000 chr1D 97.400 1692 35 5 2296 3985 467450491 467452175 0.000000e+00 2872.0
3 TraesCS3D01G492000 chr7D 97.396 1690 35 4 2300 3985 602782440 602780756 0.000000e+00 2868.0
4 TraesCS3D01G492000 chr7D 77.596 183 35 4 1043 1220 629557488 629557669 5.450000e-19 106.0
5 TraesCS3D01G492000 chr2B 96.505 1688 52 5 2299 3985 773931550 773929869 0.000000e+00 2784.0
6 TraesCS3D01G492000 chr7A 96.443 1687 53 3 2300 3985 5448952 5450632 0.000000e+00 2776.0
7 TraesCS3D01G492000 chr7A 75.956 183 38 4 1043 1220 725609236 725609417 5.490000e-14 89.8
8 TraesCS3D01G492000 chr3B 96.152 1689 56 5 2300 3985 792246189 792247871 0.000000e+00 2750.0
9 TraesCS3D01G492000 chr3B 95.972 1688 59 5 2300 3985 792159928 792161608 0.000000e+00 2732.0
10 TraesCS3D01G492000 chr3B 92.445 953 50 6 1 937 782169559 782170505 0.000000e+00 1341.0
11 TraesCS3D01G492000 chr3B 92.235 953 52 6 1 937 782252060 782253006 0.000000e+00 1330.0
12 TraesCS3D01G492000 chr3B 92.130 953 52 7 1 937 782210658 782211603 0.000000e+00 1323.0
13 TraesCS3D01G492000 chr3B 92.130 953 52 7 1 937 782293884 782294829 0.000000e+00 1323.0
14 TraesCS3D01G492000 chr3B 85.839 572 76 1 1179 1750 782216208 782216774 1.580000e-168 603.0
15 TraesCS3D01G492000 chr3B 85.839 572 76 3 1179 1750 782257615 782258181 1.580000e-168 603.0
16 TraesCS3D01G492000 chr3B 85.664 572 77 3 1179 1750 782299428 782299994 7.370000e-167 597.0
17 TraesCS3D01G492000 chr3B 83.754 634 74 10 1115 1738 782423396 782424010 1.240000e-159 573.0
18 TraesCS3D01G492000 chr3B 93.277 357 24 0 1944 2300 782478049 782478405 9.810000e-146 527.0
19 TraesCS3D01G492000 chr3B 92.150 293 23 0 2001 2293 782178486 782178778 7.970000e-112 414.0
20 TraesCS3D01G492000 chr3B 91.809 293 24 0 2001 2293 782261574 782261866 3.710000e-110 409.0
21 TraesCS3D01G492000 chr3B 91.468 293 25 0 2001 2293 782220167 782220459 1.720000e-108 403.0
22 TraesCS3D01G492000 chr3B 91.468 293 25 0 2001 2293 782303387 782303679 1.720000e-108 403.0
23 TraesCS3D01G492000 chr3B 96.067 178 7 0 1007 1184 782211614 782211791 1.400000e-74 291.0
24 TraesCS3D01G492000 chr3B 95.506 178 8 0 1007 1184 782170516 782170693 6.520000e-73 285.0
25 TraesCS3D01G492000 chr3B 95.506 178 8 0 1007 1184 782253017 782253194 6.520000e-73 285.0
26 TraesCS3D01G492000 chr3B 95.858 169 7 0 1007 1175 782294840 782295008 1.410000e-69 274.0
27 TraesCS3D01G492000 chr3B 90.323 186 15 1 1815 2000 782258182 782258364 1.430000e-59 241.0
28 TraesCS3D01G492000 chr3B 90.857 175 16 0 1826 2000 782216783 782216957 6.660000e-58 235.0
29 TraesCS3D01G492000 chr3B 88.710 186 18 1 1815 2000 782299995 782300177 1.440000e-54 224.0
30 TraesCS3D01G492000 chr4A 95.946 1702 52 9 2288 3985 552843240 552841552 0.000000e+00 2745.0
31 TraesCS3D01G492000 chr6B 96.028 1687 58 5 2300 3985 452035213 452036891 0.000000e+00 2736.0
32 TraesCS3D01G492000 chr6B 94.517 1696 80 9 2293 3985 51116940 51115255 0.000000e+00 2604.0
33 TraesCS3D01G492000 chr7B 79.355 155 27 3 1043 1192 732475661 732475507 1.960000e-18 104.0


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 TraesCS3D01G492000 chr3D 585877527 585881511 3984 False 7360.000000 7360 100.000000 1 3985 1 chr3D.!!$F1 3984
1 TraesCS3D01G492000 chr1D 467450491 467452175 1684 False 2872.000000 2872 97.400000 2296 3985 1 chr1D.!!$F1 1689
2 TraesCS3D01G492000 chr7D 602780756 602782440 1684 True 2868.000000 2868 97.396000 2300 3985 1 chr7D.!!$R1 1685
3 TraesCS3D01G492000 chr2B 773929869 773931550 1681 True 2784.000000 2784 96.505000 2299 3985 1 chr2B.!!$R1 1686
4 TraesCS3D01G492000 chr7A 5448952 5450632 1680 False 2776.000000 2776 96.443000 2300 3985 1 chr7A.!!$F1 1685
5 TraesCS3D01G492000 chr3B 792246189 792247871 1682 False 2750.000000 2750 96.152000 2300 3985 1 chr3B.!!$F5 1685
6 TraesCS3D01G492000 chr3B 792159928 792161608 1680 False 2732.000000 2732 95.972000 2300 3985 1 chr3B.!!$F4 1685
7 TraesCS3D01G492000 chr3B 782169559 782170693 1134 False 813.000000 1341 93.975500 1 1184 2 chr3B.!!$F6 1183
8 TraesCS3D01G492000 chr3B 782252060 782253194 1134 False 807.500000 1330 93.870500 1 1184 2 chr3B.!!$F9 1183
9 TraesCS3D01G492000 chr3B 782210658 782211791 1133 False 807.000000 1323 94.098500 1 1184 2 chr3B.!!$F7 1183
10 TraesCS3D01G492000 chr3B 782293884 782295008 1124 False 798.500000 1323 93.994000 1 1175 2 chr3B.!!$F11 1174
11 TraesCS3D01G492000 chr3B 782423396 782424010 614 False 573.000000 573 83.754000 1115 1738 1 chr3B.!!$F2 623
12 TraesCS3D01G492000 chr3B 782257615 782261866 4251 False 417.666667 603 89.323667 1179 2293 3 chr3B.!!$F10 1114
13 TraesCS3D01G492000 chr3B 782216208 782220459 4251 False 413.666667 603 89.388000 1179 2293 3 chr3B.!!$F8 1114
14 TraesCS3D01G492000 chr3B 782299428 782303679 4251 False 408.000000 597 88.614000 1179 2293 3 chr3B.!!$F12 1114
15 TraesCS3D01G492000 chr4A 552841552 552843240 1688 True 2745.000000 2745 95.946000 2288 3985 1 chr4A.!!$R1 1697
16 TraesCS3D01G492000 chr6B 452035213 452036891 1678 False 2736.000000 2736 96.028000 2300 3985 1 chr6B.!!$F1 1685
17 TraesCS3D01G492000 chr6B 51115255 51116940 1685 True 2604.000000 2604 94.517000 2293 3985 1 chr6B.!!$R1 1692

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
983 1000 0.029300 TATTAGCACGTCCGCGGTAC 59.971 55.0 27.15 20.07 43.45 3.34 F
1777 1804 0.104304 GGACATACGGGCAGAACGAT 59.896 55.0 0.00 0.00 34.93 3.73 F
2059 5296 0.036294 GTACAGACTGGGACCTTGCC 60.036 60.0 7.51 0.00 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 5270 0.178903 TCCCAGTCTGTACCCTTGCT 60.179 55.0 0.00 0.0 0.0 3.91 R
2749 5989 0.824109 GCAATTCCCCAAGGCCTTAC 59.176 55.0 20.00 0.0 0.0 2.34 R
3872 7121 0.394762 ATGATGCATGGAGTGGCGTT 60.395 50.0 2.46 0.0 0.0 4.84 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
34 35 4.043200 GTTGGCCGGACTTGCAGC 62.043 66.667 9.82 0.00 0.00 5.25
57 58 1.440938 CTGGAAAACCCGTCGTGCAA 61.441 55.000 0.00 0.00 37.93 4.08
59 60 1.161563 GGAAAACCCGTCGTGCAAGA 61.162 55.000 0.00 0.00 0.00 3.02
63 64 0.661020 AACCCGTCGTGCAAGAAAAG 59.339 50.000 3.20 0.00 0.00 2.27
68 69 2.155155 CCGTCGTGCAAGAAAAGTAGAC 59.845 50.000 3.20 0.00 0.00 2.59
94 95 3.782042 GCTAACGAGCTTCACCGG 58.218 61.111 0.00 0.00 45.98 5.28
95 96 2.453638 GCTAACGAGCTTCACCGGC 61.454 63.158 0.00 0.00 45.98 6.13
142 151 1.249407 GAAGGTGGAGTCGACTCACT 58.751 55.000 38.52 30.19 44.60 3.41
146 155 1.072678 TGGAGTCGACTCACTCGGT 59.927 57.895 38.52 8.66 43.43 4.69
152 161 2.022129 CGACTCACTCGGTGTTGGC 61.022 63.158 4.33 1.45 38.87 4.52
216 225 1.079197 CACGCATCACCTACTGGCA 60.079 57.895 0.00 0.00 36.63 4.92
252 261 0.251077 ACGAACGAGGAGGTAGTGGT 60.251 55.000 0.14 0.00 0.00 4.16
267 276 2.361610 GGTGGGCATGGTCACAGG 60.362 66.667 0.00 0.00 35.74 4.00
274 283 0.546122 GCATGGTCACAGGGGACATA 59.454 55.000 3.82 0.00 39.59 2.29
319 328 0.250295 TCTTCGAGCCCACACAAAGG 60.250 55.000 0.00 0.00 0.00 3.11
395 404 2.676471 AACAACCATGAGGCCGGC 60.676 61.111 21.18 21.18 39.06 6.13
450 459 1.536943 GGACTCCGGCAAGTCAGAGT 61.537 60.000 21.23 6.74 46.15 3.24
501 510 0.318441 TGTCTTGCTCTTCCTCACCG 59.682 55.000 0.00 0.00 0.00 4.94
535 544 0.442310 CAGGGCGTTGTACATGTTCG 59.558 55.000 2.30 5.90 0.00 3.95
673 682 8.085720 TGAAAATTGTCCAGTTTGCATAAATG 57.914 30.769 0.00 0.00 0.00 2.32
734 751 3.632604 CCCATATCAGTGTCTACGTGTCT 59.367 47.826 0.00 0.00 0.00 3.41
737 754 1.314730 TCAGTGTCTACGTGTCTGCA 58.685 50.000 0.00 0.00 0.00 4.41
752 769 1.001293 TCTGCAGACACATCCAGACAC 59.999 52.381 13.74 0.00 30.00 3.67
779 796 4.750098 GGTGAACGGATACTATGTCCATTG 59.250 45.833 0.00 0.00 35.41 2.82
789 806 7.569111 GGATACTATGTCCATTGTAGGGGATAT 59.431 40.741 7.45 0.00 38.40 1.63
790 807 9.656323 GATACTATGTCCATTGTAGGGGATATA 57.344 37.037 7.45 0.00 36.55 0.86
795 812 7.597288 TGTCCATTGTAGGGGATATATATCG 57.403 40.000 15.06 0.38 35.25 2.92
848 865 0.598065 ATCAGAAAACGTGCTTGGGC 59.402 50.000 0.00 0.00 39.26 5.36
858 875 0.391793 GTGCTTGGGCTAGACAGGAC 60.392 60.000 0.00 0.00 39.59 3.85
873 890 7.013846 GCTAGACAGGACAACTATAATCAGACT 59.986 40.741 0.00 0.00 0.00 3.24
874 891 7.106439 AGACAGGACAACTATAATCAGACTG 57.894 40.000 0.00 0.00 0.00 3.51
906 923 2.039348 TCCCGGTAGAAGTTGGAAAAGG 59.961 50.000 0.00 0.00 0.00 3.11
937 954 4.651778 TGGAACTGAATCTGAAATTCGGT 58.348 39.130 6.45 6.45 46.29 4.69
938 955 4.695455 TGGAACTGAATCTGAAATTCGGTC 59.305 41.667 11.52 6.10 44.30 4.79
939 956 4.095036 GGAACTGAATCTGAAATTCGGTCC 59.905 45.833 11.52 10.30 44.30 4.46
940 957 3.262420 ACTGAATCTGAAATTCGGTCCG 58.738 45.455 4.39 4.39 42.19 4.79
941 958 3.056107 ACTGAATCTGAAATTCGGTCCGA 60.056 43.478 10.71 10.71 42.19 4.55
942 959 3.259064 TGAATCTGAAATTCGGTCCGAC 58.741 45.455 15.07 2.72 34.89 4.79
943 960 3.259064 GAATCTGAAATTCGGTCCGACA 58.741 45.455 15.07 7.83 34.89 4.35
944 961 3.543680 ATCTGAAATTCGGTCCGACAT 57.456 42.857 15.07 8.23 34.89 3.06
945 962 2.616960 TCTGAAATTCGGTCCGACATG 58.383 47.619 15.07 3.54 34.89 3.21
946 963 1.062587 CTGAAATTCGGTCCGACATGC 59.937 52.381 15.07 4.93 34.89 4.06
947 964 1.083489 GAAATTCGGTCCGACATGCA 58.917 50.000 15.07 0.00 34.89 3.96
948 965 1.466950 GAAATTCGGTCCGACATGCAA 59.533 47.619 15.07 0.00 34.89 4.08
949 966 1.529226 AATTCGGTCCGACATGCAAA 58.471 45.000 15.07 0.00 34.89 3.68
950 967 1.750193 ATTCGGTCCGACATGCAAAT 58.250 45.000 15.07 0.00 34.89 2.32
951 968 2.388310 TTCGGTCCGACATGCAAATA 57.612 45.000 15.07 0.00 34.89 1.40
952 969 2.613026 TCGGTCCGACATGCAAATAT 57.387 45.000 10.71 0.00 0.00 1.28
953 970 3.737032 TCGGTCCGACATGCAAATATA 57.263 42.857 10.71 0.00 0.00 0.86
954 971 4.265904 TCGGTCCGACATGCAAATATAT 57.734 40.909 10.71 0.00 0.00 0.86
955 972 4.637276 TCGGTCCGACATGCAAATATATT 58.363 39.130 10.71 0.00 0.00 1.28
956 973 4.688879 TCGGTCCGACATGCAAATATATTC 59.311 41.667 10.71 0.00 0.00 1.75
957 974 4.450757 CGGTCCGACATGCAAATATATTCA 59.549 41.667 4.91 0.00 0.00 2.57
958 975 5.049749 CGGTCCGACATGCAAATATATTCAA 60.050 40.000 4.91 0.00 0.00 2.69
959 976 6.512578 CGGTCCGACATGCAAATATATTCAAA 60.513 38.462 4.91 0.00 0.00 2.69
960 977 6.857964 GGTCCGACATGCAAATATATTCAAAG 59.142 38.462 0.00 0.00 0.00 2.77
961 978 6.360681 GTCCGACATGCAAATATATTCAAAGC 59.639 38.462 0.00 2.38 0.00 3.51
962 979 6.262944 TCCGACATGCAAATATATTCAAAGCT 59.737 34.615 0.00 0.00 0.00 3.74
963 980 7.443879 TCCGACATGCAAATATATTCAAAGCTA 59.556 33.333 0.00 0.00 0.00 3.32
964 981 8.239314 CCGACATGCAAATATATTCAAAGCTAT 58.761 33.333 0.00 0.00 0.00 2.97
980 997 1.614385 CTATATTAGCACGTCCGCGG 58.386 55.000 22.12 22.12 43.45 6.46
981 998 0.953727 TATATTAGCACGTCCGCGGT 59.046 50.000 27.15 7.03 43.45 5.68
982 999 0.953727 ATATTAGCACGTCCGCGGTA 59.046 50.000 27.15 9.34 43.45 4.02
983 1000 0.029300 TATTAGCACGTCCGCGGTAC 59.971 55.000 27.15 20.07 43.45 3.34
984 1001 2.618312 ATTAGCACGTCCGCGGTACC 62.618 60.000 27.15 13.40 43.45 3.34
986 1003 2.867793 TAGCACGTCCGCGGTACCTA 62.868 60.000 27.15 15.85 43.45 3.08
987 1004 2.406401 CACGTCCGCGGTACCTAG 59.594 66.667 27.15 13.17 43.45 3.02
988 1005 2.045926 ACGTCCGCGGTACCTAGT 60.046 61.111 27.15 13.81 43.45 2.57
989 1006 1.089481 CACGTCCGCGGTACCTAGTA 61.089 60.000 27.15 0.00 43.45 1.82
990 1007 0.811616 ACGTCCGCGGTACCTAGTAG 60.812 60.000 27.15 10.17 43.45 2.57
991 1008 0.811616 CGTCCGCGGTACCTAGTAGT 60.812 60.000 27.15 0.00 0.00 2.73
992 1009 1.538204 CGTCCGCGGTACCTAGTAGTA 60.538 57.143 27.15 0.00 0.00 1.82
993 1010 1.867865 GTCCGCGGTACCTAGTAGTAC 59.132 57.143 27.15 7.29 41.60 2.73
994 1011 1.484653 TCCGCGGTACCTAGTAGTACA 59.515 52.381 27.15 0.00 43.66 2.90
995 1012 2.093181 TCCGCGGTACCTAGTAGTACAA 60.093 50.000 27.15 0.00 43.66 2.41
996 1013 2.032178 CCGCGGTACCTAGTAGTACAAC 59.968 54.545 19.50 2.74 43.66 3.32
997 1014 2.677836 CGCGGTACCTAGTAGTACAACA 59.322 50.000 10.90 0.00 43.66 3.33
998 1015 3.313526 CGCGGTACCTAGTAGTACAACAT 59.686 47.826 10.90 0.00 43.66 2.71
999 1016 4.553547 CGCGGTACCTAGTAGTACAACATC 60.554 50.000 10.90 0.00 43.66 3.06
1000 1017 4.336433 GCGGTACCTAGTAGTACAACATCA 59.664 45.833 10.90 0.00 43.66 3.07
1001 1018 5.505324 GCGGTACCTAGTAGTACAACATCAG 60.505 48.000 10.90 0.00 43.66 2.90
1002 1019 5.819379 CGGTACCTAGTAGTACAACATCAGA 59.181 44.000 10.90 0.00 43.66 3.27
1003 1020 6.485984 CGGTACCTAGTAGTACAACATCAGAT 59.514 42.308 10.90 0.00 43.66 2.90
1004 1021 7.013083 CGGTACCTAGTAGTACAACATCAGATT 59.987 40.741 10.90 0.00 43.66 2.40
1005 1022 8.351461 GGTACCTAGTAGTACAACATCAGATTC 58.649 40.741 4.06 0.00 43.66 2.52
1009 1026 8.283992 CCTAGTAGTACAACATCAGATTCGTAG 58.716 40.741 2.52 0.00 0.00 3.51
1013 1030 7.860918 AGTACAACATCAGATTCGTAGTAGA 57.139 36.000 0.00 0.00 0.00 2.59
1025 1042 5.806366 TTCGTAGTAGAACACATCGATGA 57.194 39.130 31.33 5.19 35.57 2.92
1307 1328 3.420214 GACTCGCCGCCCGTATTCA 62.420 63.158 0.00 0.00 38.35 2.57
1320 1341 1.066605 CGTATTCATCCCGGTTCGACT 59.933 52.381 0.00 0.00 0.00 4.18
1392 1413 2.398554 GGCTTCTCAATGGCGCGAA 61.399 57.895 12.10 0.00 0.00 4.70
1462 1483 0.827507 ACAACCATGGCCCTGTCAAC 60.828 55.000 13.04 0.00 0.00 3.18
1529 1550 2.500509 GCTAGTATGCGAGCTGAACT 57.499 50.000 8.61 0.33 39.73 3.01
1532 1553 0.460987 AGTATGCGAGCTGAACTGCC 60.461 55.000 0.00 0.00 0.00 4.85
1535 1556 2.817396 GCGAGCTGAACTGCCTCC 60.817 66.667 0.00 0.00 0.00 4.30
1574 1595 0.664466 CAGCGAAGACTGTTGCTCGA 60.664 55.000 10.14 0.00 34.99 4.04
1577 1598 1.337817 CGAAGACTGTTGCTCGACGG 61.338 60.000 0.00 0.00 0.00 4.79
1581 1602 2.805353 CTGTTGCTCGACGGACGG 60.805 66.667 0.00 0.00 42.82 4.79
1584 1605 3.289062 TTGCTCGACGGACGGACA 61.289 61.111 0.00 0.00 42.82 4.02
1585 1606 3.547249 TTGCTCGACGGACGGACAC 62.547 63.158 0.00 0.00 42.82 3.67
1624 1645 2.414161 GGCGCCAAACTACTCAACATTC 60.414 50.000 24.80 0.00 0.00 2.67
1633 1654 5.568620 ACTACTCAACATTCTTCAGGGTT 57.431 39.130 0.00 0.00 0.00 4.11
1634 1655 5.552178 ACTACTCAACATTCTTCAGGGTTC 58.448 41.667 0.00 0.00 0.00 3.62
1642 1663 0.329261 TCTTCAGGGTTCTGGCCATG 59.671 55.000 5.51 0.00 41.25 3.66
1670 1691 1.478137 CTGCGACAACGGCTATCTAC 58.522 55.000 0.00 0.00 40.15 2.59
1675 1696 2.194271 GACAACGGCTATCTACACTGC 58.806 52.381 0.00 0.00 0.00 4.40
1764 1791 3.792736 GCACGGCCCCTGGACATA 61.793 66.667 0.00 0.00 0.00 2.29
1765 1792 2.189521 CACGGCCCCTGGACATAC 59.810 66.667 0.00 0.00 0.00 2.39
1766 1793 3.467226 ACGGCCCCTGGACATACG 61.467 66.667 0.00 0.00 0.00 3.06
1767 1794 4.235762 CGGCCCCTGGACATACGG 62.236 72.222 0.00 0.00 0.00 4.02
1768 1795 3.873812 GGCCCCTGGACATACGGG 61.874 72.222 0.00 0.00 38.70 5.28
1770 1797 3.087253 CCCCTGGACATACGGGCA 61.087 66.667 0.00 0.00 36.62 5.36
1771 1798 2.505982 CCCTGGACATACGGGCAG 59.494 66.667 0.00 0.00 35.47 4.85
1772 1799 2.063979 CCCTGGACATACGGGCAGA 61.064 63.158 0.00 0.00 35.47 4.26
1773 1800 1.622607 CCCTGGACATACGGGCAGAA 61.623 60.000 0.00 0.00 35.47 3.02
1774 1801 0.462047 CCTGGACATACGGGCAGAAC 60.462 60.000 0.00 0.00 0.00 3.01
1775 1802 0.806102 CTGGACATACGGGCAGAACG 60.806 60.000 0.00 0.00 37.36 3.95
1776 1803 1.252215 TGGACATACGGGCAGAACGA 61.252 55.000 0.00 0.00 34.93 3.85
1777 1804 0.104304 GGACATACGGGCAGAACGAT 59.896 55.000 0.00 0.00 34.93 3.73
1778 1805 1.209128 GACATACGGGCAGAACGATG 58.791 55.000 0.00 0.00 34.93 3.84
1779 1806 0.810031 ACATACGGGCAGAACGATGC 60.810 55.000 0.00 0.00 45.74 3.91
1786 1813 3.853330 CAGAACGATGCCGCCGTG 61.853 66.667 0.00 0.00 40.44 4.94
1814 1841 2.360852 GCATGGTGCACTGGCTCT 60.361 61.111 17.98 0.00 44.26 4.09
1815 1842 2.697761 GCATGGTGCACTGGCTCTG 61.698 63.158 17.98 6.64 44.26 3.35
1816 1843 1.303074 CATGGTGCACTGGCTCTGT 60.303 57.895 17.98 0.00 41.91 3.41
1817 1844 1.303074 ATGGTGCACTGGCTCTGTG 60.303 57.895 17.98 7.52 41.91 3.66
1818 1845 1.771783 ATGGTGCACTGGCTCTGTGA 61.772 55.000 17.98 0.00 41.91 3.58
1819 1846 1.963338 GGTGCACTGGCTCTGTGAC 60.963 63.158 17.98 9.54 41.91 3.67
1823 1850 1.662608 CACTGGCTCTGTGACGACT 59.337 57.895 0.00 0.00 35.76 4.18
1824 1851 0.665670 CACTGGCTCTGTGACGACTG 60.666 60.000 0.00 0.00 35.76 3.51
1827 1854 1.080434 GGCTCTGTGACGACTGGTC 60.080 63.158 0.00 0.00 46.27 4.02
1932 1959 4.515404 GCTACCGGCGATCAAACT 57.485 55.556 9.30 0.00 0.00 2.66
1939 1966 0.443869 CGGCGATCAAACTCACCTTG 59.556 55.000 0.00 0.00 0.00 3.61
1961 1988 5.396485 TGGAATATTTTCATATGGCTGGCT 58.604 37.500 2.13 0.00 33.23 4.75
1964 1991 6.015180 GGAATATTTTCATATGGCTGGCTTCA 60.015 38.462 2.13 0.00 33.23 3.02
1986 2013 0.876342 GGGGCGCTCTCGTTATTCTG 60.876 60.000 7.48 0.00 38.14 3.02
1991 2018 1.849219 CGCTCTCGTTATTCTGTCTGC 59.151 52.381 0.00 0.00 0.00 4.26
1995 2022 4.237724 CTCTCGTTATTCTGTCTGCACAA 58.762 43.478 0.00 0.00 29.82 3.33
2008 5245 1.538950 CTGCACAAGGAAGAAGAAGGC 59.461 52.381 0.00 0.00 0.00 4.35
2012 5249 1.352687 ACAAGGAAGAAGAAGGCCTCC 59.647 52.381 5.23 0.00 0.00 4.30
2033 5270 1.681538 GCTAGAGATCTGGACACGGA 58.318 55.000 0.00 0.00 36.20 4.69
2035 5272 1.606668 CTAGAGATCTGGACACGGAGC 59.393 57.143 0.00 0.00 38.67 4.70
2042 5279 1.534476 TGGACACGGAGCAAGGGTA 60.534 57.895 0.00 0.00 0.00 3.69
2051 5288 0.250513 GAGCAAGGGTACAGACTGGG 59.749 60.000 7.51 0.00 0.00 4.45
2059 5296 0.036294 GTACAGACTGGGACCTTGCC 60.036 60.000 7.51 0.00 0.00 4.52
2071 5308 2.046892 CTTGCCAGGGTGGTCGAG 60.047 66.667 0.00 0.00 40.46 4.04
2083 5320 2.179517 GTCGAGCTGAGACCACGG 59.820 66.667 7.51 0.00 32.78 4.94
2106 5343 5.396884 GGATTGAGGGAGTGCTATACTTGTT 60.397 44.000 0.00 0.00 40.53 2.83
2124 5361 1.882623 GTTGCCTGGAGAAAAGAGTGG 59.117 52.381 0.00 0.00 0.00 4.00
2128 5365 1.528129 CTGGAGAAAAGAGTGGCACC 58.472 55.000 15.27 5.99 0.00 5.01
2144 5381 1.800805 CACCTTGCTCATCAACTCGT 58.199 50.000 0.00 0.00 0.00 4.18
2147 5384 2.299013 ACCTTGCTCATCAACTCGTACA 59.701 45.455 0.00 0.00 0.00 2.90
2148 5385 3.244078 ACCTTGCTCATCAACTCGTACAA 60.244 43.478 0.00 0.00 0.00 2.41
2182 5419 0.459585 TTGCTTATCTCGACACCGGC 60.460 55.000 0.00 0.00 36.24 6.13
2202 5439 3.305064 GGCGCAGTGGAGAAAATAACAAA 60.305 43.478 10.83 0.00 0.00 2.83
2216 5453 8.977505 AGAAAATAACAAACGAATTTCATGGTG 58.022 29.630 0.00 0.00 31.06 4.17
2221 5458 4.338118 ACAAACGAATTTCATGGTGTGACT 59.662 37.500 0.00 0.00 36.32 3.41
2256 5493 3.243359 TCCCATGGAAATAGATTGGCC 57.757 47.619 15.22 0.00 0.00 5.36
2263 5500 3.694072 TGGAAATAGATTGGCCGTCTTTG 59.306 43.478 14.84 0.00 0.00 2.77
2286 5523 1.194781 ATGTCTCGGCTTGGTGGACT 61.195 55.000 0.00 0.00 0.00 3.85
2296 5533 3.877508 GGCTTGGTGGACTGTGATAATAC 59.122 47.826 0.00 0.00 0.00 1.89
2297 5534 4.384208 GGCTTGGTGGACTGTGATAATACT 60.384 45.833 0.00 0.00 0.00 2.12
2350 5587 1.609555 TGCCGGTCCAAACATTTGTAC 59.390 47.619 1.90 0.00 36.45 2.90
2449 5687 5.537300 AGGCATAGAAGATACGACAACAT 57.463 39.130 0.00 0.00 0.00 2.71
2452 5690 5.523916 GGCATAGAAGATACGACAACATGTT 59.476 40.000 4.92 4.92 0.00 2.71
2537 5777 3.966154 AGGCATAGAAGATACGACAACG 58.034 45.455 0.00 0.00 45.75 4.10
2687 5927 4.837085 AGCATGCCAAGAACTGCT 57.163 50.000 15.66 0.00 40.02 4.24
2745 5985 7.238486 TGCAGTTCCCAATAACATAAAACAT 57.762 32.000 0.00 0.00 0.00 2.71
2746 5986 8.354711 TGCAGTTCCCAATAACATAAAACATA 57.645 30.769 0.00 0.00 0.00 2.29
2747 5987 8.807118 TGCAGTTCCCAATAACATAAAACATAA 58.193 29.630 0.00 0.00 0.00 1.90
2748 5988 9.301153 GCAGTTCCCAATAACATAAAACATAAG 57.699 33.333 0.00 0.00 0.00 1.73
2749 5989 9.801873 CAGTTCCCAATAACATAAAACATAAGG 57.198 33.333 0.00 0.00 0.00 2.69
2807 6047 3.053095 ACAGCATGGGAAAGGAATCAGAT 60.053 43.478 0.00 0.00 43.62 2.90
2903 6145 5.105797 TGTTTAGGATGTGCCAAGCATTTAG 60.106 40.000 0.00 0.00 41.91 1.85
3088 6333 7.228108 TCAGGCAATTTCAAGATATCATGACTC 59.772 37.037 10.08 0.00 0.00 3.36
3174 6419 6.727824 ATATATTCATGGCGTAGTTTCAGC 57.272 37.500 0.00 0.00 0.00 4.26
3335 6583 5.105310 TGCTTCTACCTGAATCTCAAGGTAC 60.105 44.000 0.00 0.00 32.70 3.34
3393 6641 6.127980 ACAATGACATGCTCTCTGATTTCAAG 60.128 38.462 0.00 0.00 0.00 3.02
3526 6774 5.774498 TCAAGTCTGAGATATGCACGTAT 57.226 39.130 0.00 0.00 0.00 3.06
3578 6826 9.251440 ACCAGAACTAACTACAATACATAGTCA 57.749 33.333 0.00 0.00 31.51 3.41
3872 7121 1.843851 GATGGAGATGGTTGGTACCCA 59.156 52.381 10.07 0.00 44.35 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.321298 ACGACGGGTTTTCCAGATGG 60.321 55.000 0.00 0.00 42.91 3.51
37 38 1.595929 GCACGACGGGTTTTCCAGA 60.596 57.895 0.00 0.00 42.91 3.86
57 58 2.351544 GCGGTCTGACGTCTACTTTTCT 60.352 50.000 17.92 0.00 35.98 2.52
59 60 1.612463 AGCGGTCTGACGTCTACTTTT 59.388 47.619 17.92 2.61 35.98 2.27
63 64 1.528603 CGTTAGCGGTCTGACGTCTAC 60.529 57.143 17.92 14.33 44.26 2.59
102 111 2.287915 CGCCATAATAGTGTGGAAGTGC 59.712 50.000 10.41 0.00 38.27 4.40
142 151 2.280524 CTGGAACGCCAACACCGA 60.281 61.111 0.00 0.00 45.41 4.69
146 155 2.429930 CCCTCTGGAACGCCAACA 59.570 61.111 0.00 0.00 45.41 3.33
169 178 2.926200 CGAGATTGTAGTGCTGGTTCTG 59.074 50.000 0.00 0.00 0.00 3.02
216 225 4.642429 GTTCGTCATAGATTTGCCCCTAT 58.358 43.478 0.00 0.00 0.00 2.57
252 261 3.660571 CCCCTGTGACCATGCCCA 61.661 66.667 0.00 0.00 0.00 5.36
267 276 2.169769 TGGTCGATGAAGGTTATGTCCC 59.830 50.000 0.00 0.00 0.00 4.46
274 283 1.135083 CGCTACTGGTCGATGAAGGTT 60.135 52.381 0.00 0.00 0.00 3.50
304 313 1.227823 TGACCTTTGTGTGGGCTCG 60.228 57.895 0.00 0.00 32.71 5.03
307 316 3.030652 CGTGACCTTTGTGTGGGC 58.969 61.111 0.00 0.00 0.00 5.36
395 404 2.363680 AGCTCACAGATCGAAGTATGGG 59.636 50.000 0.00 0.00 0.00 4.00
450 459 2.682494 GTGGCTCCCGTGTCCCTA 60.682 66.667 0.00 0.00 0.00 3.53
472 481 1.198713 GAGCAAGACATGGGAGGAGA 58.801 55.000 0.00 0.00 0.00 3.71
501 510 0.605589 CCCTGTTCTTCCCCACGTTC 60.606 60.000 0.00 0.00 0.00 3.95
618 627 6.573434 ACTTGGACCAAATTCAAGAAAGTTC 58.427 36.000 8.59 0.00 39.97 3.01
634 643 6.202762 GGACAATTTTCATTTCAACTTGGACC 59.797 38.462 0.00 0.00 0.00 4.46
673 682 1.269723 GGCTAAGAACAAACAGGGTGC 59.730 52.381 0.00 0.00 0.00 5.01
674 683 2.293399 GTGGCTAAGAACAAACAGGGTG 59.707 50.000 0.00 0.00 0.00 4.61
675 684 2.583143 GTGGCTAAGAACAAACAGGGT 58.417 47.619 0.00 0.00 0.00 4.34
680 689 4.281525 TCAAACGTGGCTAAGAACAAAC 57.718 40.909 0.00 0.00 0.00 2.93
734 751 0.758123 TGTGTCTGGATGTGTCTGCA 59.242 50.000 0.00 0.00 0.00 4.41
737 754 1.205655 CCGATGTGTCTGGATGTGTCT 59.794 52.381 0.00 0.00 0.00 3.41
752 769 4.227538 GACATAGTATCCGTTCACCGATG 58.772 47.826 0.00 0.00 39.56 3.84
779 796 4.040095 GGCCCAACGATATATATCCCCTAC 59.960 50.000 15.61 3.32 0.00 3.18
789 806 0.396435 CAGCCAGGCCCAACGATATA 59.604 55.000 8.22 0.00 0.00 0.86
790 807 1.149174 CAGCCAGGCCCAACGATAT 59.851 57.895 8.22 0.00 0.00 1.63
791 808 2.589540 CAGCCAGGCCCAACGATA 59.410 61.111 8.22 0.00 0.00 2.92
812 829 9.353999 GTTTTCTGATTAATATTTGACACCACC 57.646 33.333 0.00 0.00 0.00 4.61
848 865 8.349245 CAGTCTGATTATAGTTGTCCTGTCTAG 58.651 40.741 0.00 0.00 0.00 2.43
858 875 7.251281 TCGTCTTCACAGTCTGATTATAGTTG 58.749 38.462 6.91 0.00 0.00 3.16
873 890 0.250858 TACCGGGACTCGTCTTCACA 60.251 55.000 6.32 0.00 37.11 3.58
874 891 0.450983 CTACCGGGACTCGTCTTCAC 59.549 60.000 6.32 0.00 37.11 3.18
906 923 3.064545 CAGATTCAGTTCCAAATCGGCTC 59.935 47.826 0.00 0.00 37.06 4.70
937 954 6.262944 AGCTTTGAATATATTTGCATGTCGGA 59.737 34.615 0.00 0.00 0.00 4.55
938 955 6.441274 AGCTTTGAATATATTTGCATGTCGG 58.559 36.000 0.00 0.00 0.00 4.79
958 975 5.990317 CCGCGGACGTGCTAATATAGCTT 62.990 52.174 24.07 0.00 43.78 3.74
959 976 4.581301 CCGCGGACGTGCTAATATAGCT 62.581 54.545 24.07 0.00 43.78 3.32
960 977 2.316807 CCGCGGACGTGCTAATATAGC 61.317 57.143 24.07 2.45 43.73 2.97
961 978 1.068748 ACCGCGGACGTGCTAATATAG 60.069 52.381 35.90 0.00 37.70 1.31
962 979 0.953727 ACCGCGGACGTGCTAATATA 59.046 50.000 35.90 0.00 37.70 0.86
963 980 0.953727 TACCGCGGACGTGCTAATAT 59.046 50.000 35.90 6.98 37.70 1.28
964 981 0.029300 GTACCGCGGACGTGCTAATA 59.971 55.000 35.90 7.27 37.70 0.98
965 982 1.226773 GTACCGCGGACGTGCTAAT 60.227 57.895 35.90 8.50 37.70 1.73
966 983 2.179018 GTACCGCGGACGTGCTAA 59.821 61.111 35.90 3.04 37.70 3.09
967 984 2.867793 TAGGTACCGCGGACGTGCTA 62.868 60.000 35.90 17.57 37.70 3.49
969 986 3.746409 CTAGGTACCGCGGACGTGC 62.746 68.421 35.90 13.62 37.70 5.34
970 987 1.089481 TACTAGGTACCGCGGACGTG 61.089 60.000 35.90 20.24 37.70 4.49
971 988 0.811616 CTACTAGGTACCGCGGACGT 60.812 60.000 35.90 26.31 37.70 4.34
972 989 0.811616 ACTACTAGGTACCGCGGACG 60.812 60.000 35.90 14.65 39.67 4.79
973 990 1.867865 GTACTACTAGGTACCGCGGAC 59.132 57.143 35.90 24.28 36.88 4.79
974 991 1.484653 TGTACTACTAGGTACCGCGGA 59.515 52.381 35.90 13.31 40.72 5.54
975 992 1.953559 TGTACTACTAGGTACCGCGG 58.046 55.000 26.86 26.86 40.72 6.46
976 993 2.677836 TGTTGTACTACTAGGTACCGCG 59.322 50.000 6.18 0.00 40.72 6.46
977 994 4.336433 TGATGTTGTACTACTAGGTACCGC 59.664 45.833 6.18 1.98 40.72 5.68
978 995 5.819379 TCTGATGTTGTACTACTAGGTACCG 59.181 44.000 6.18 0.00 40.72 4.02
979 996 7.820578 ATCTGATGTTGTACTACTAGGTACC 57.179 40.000 2.73 2.73 40.72 3.34
980 997 8.068977 CGAATCTGATGTTGTACTACTAGGTAC 58.931 40.741 8.88 0.00 41.51 3.34
981 998 7.772292 ACGAATCTGATGTTGTACTACTAGGTA 59.228 37.037 8.88 0.00 0.00 3.08
982 999 6.602406 ACGAATCTGATGTTGTACTACTAGGT 59.398 38.462 8.88 0.00 0.00 3.08
983 1000 7.028926 ACGAATCTGATGTTGTACTACTAGG 57.971 40.000 8.88 0.00 0.00 3.02
984 1001 8.828644 ACTACGAATCTGATGTTGTACTACTAG 58.171 37.037 8.88 5.17 0.00 2.57
985 1002 8.728337 ACTACGAATCTGATGTTGTACTACTA 57.272 34.615 8.88 0.00 0.00 1.82
986 1003 7.627298 ACTACGAATCTGATGTTGTACTACT 57.373 36.000 8.88 0.00 0.00 2.57
987 1004 8.824781 TCTACTACGAATCTGATGTTGTACTAC 58.175 37.037 0.05 0.05 0.00 2.73
988 1005 8.953368 TCTACTACGAATCTGATGTTGTACTA 57.047 34.615 0.00 0.00 0.00 1.82
989 1006 7.860918 TCTACTACGAATCTGATGTTGTACT 57.139 36.000 0.00 0.00 0.00 2.73
990 1007 7.966753 TGTTCTACTACGAATCTGATGTTGTAC 59.033 37.037 0.00 0.00 0.00 2.90
991 1008 7.966753 GTGTTCTACTACGAATCTGATGTTGTA 59.033 37.037 0.00 0.00 0.00 2.41
992 1009 6.807230 GTGTTCTACTACGAATCTGATGTTGT 59.193 38.462 0.00 0.00 0.00 3.32
993 1010 6.806739 TGTGTTCTACTACGAATCTGATGTTG 59.193 38.462 0.00 0.00 0.00 3.33
994 1011 6.920817 TGTGTTCTACTACGAATCTGATGTT 58.079 36.000 0.00 0.00 0.00 2.71
995 1012 6.510879 TGTGTTCTACTACGAATCTGATGT 57.489 37.500 0.00 0.00 0.00 3.06
996 1013 6.358294 CGATGTGTTCTACTACGAATCTGATG 59.642 42.308 0.00 0.00 33.19 3.07
997 1014 6.260271 TCGATGTGTTCTACTACGAATCTGAT 59.740 38.462 0.00 0.00 35.79 2.90
998 1015 5.583457 TCGATGTGTTCTACTACGAATCTGA 59.417 40.000 0.00 0.00 35.79 3.27
999 1016 5.807344 TCGATGTGTTCTACTACGAATCTG 58.193 41.667 0.00 0.00 35.79 2.90
1000 1017 6.260271 TCATCGATGTGTTCTACTACGAATCT 59.740 38.462 24.09 0.00 39.39 2.40
1001 1018 6.427974 TCATCGATGTGTTCTACTACGAATC 58.572 40.000 24.09 0.00 39.39 2.52
1002 1019 6.373186 TCATCGATGTGTTCTACTACGAAT 57.627 37.500 24.09 0.00 39.39 3.34
1003 1020 5.806366 TCATCGATGTGTTCTACTACGAA 57.194 39.130 24.09 0.00 39.39 3.85
1004 1021 5.277828 CCATCATCGATGTGTTCTACTACGA 60.278 44.000 24.09 1.20 38.28 3.43
1005 1022 4.912187 CCATCATCGATGTGTTCTACTACG 59.088 45.833 24.09 3.78 38.28 3.51
1009 1026 4.322080 TCCCATCATCGATGTGTTCTAC 57.678 45.455 24.09 0.00 38.28 2.59
1013 1030 3.133691 CGATTCCCATCATCGATGTGTT 58.866 45.455 24.09 8.63 45.30 3.32
1025 1042 2.822399 GGCCGTCTCGATTCCCAT 59.178 61.111 0.00 0.00 0.00 4.00
1096 1113 4.389576 CAGCGAAACAGCGTGGCC 62.390 66.667 0.00 0.00 43.00 5.36
1307 1328 2.707849 CCGACAGTCGAACCGGGAT 61.708 63.158 24.88 0.00 43.74 3.85
1346 1367 2.747855 GCGTGGGCTGAGAAAGGG 60.748 66.667 0.00 0.00 35.83 3.95
1445 1466 1.228862 GGTTGACAGGGCCATGGTT 60.229 57.895 23.35 0.05 0.00 3.67
1492 1513 3.730761 GGTGGAAGCACAGCGCAG 61.731 66.667 11.47 3.33 46.13 5.18
1497 1518 0.530744 TACTAGCGGTGGAAGCACAG 59.469 55.000 4.52 0.00 37.01 3.66
1547 1568 3.305398 ACAGTCTTCGCTGGTTAGAAG 57.695 47.619 0.00 0.00 43.70 2.85
1624 1645 0.682209 CCATGGCCAGAACCCTGAAG 60.682 60.000 13.05 0.00 43.02 3.02
1652 1673 0.812549 TGTAGATAGCCGTTGTCGCA 59.187 50.000 0.00 0.00 35.54 5.10
1675 1696 0.882042 ACGAGAACCTGTGCAAGCTG 60.882 55.000 0.00 0.00 0.00 4.24
1750 1777 4.235762 CCGTATGTCCAGGGGCCG 62.236 72.222 0.00 0.00 0.00 6.13
1753 1780 3.087253 TGCCCGTATGTCCAGGGG 61.087 66.667 1.65 0.00 45.18 4.79
1755 1782 0.462047 GTTCTGCCCGTATGTCCAGG 60.462 60.000 0.00 0.00 0.00 4.45
1756 1783 0.806102 CGTTCTGCCCGTATGTCCAG 60.806 60.000 0.00 0.00 0.00 3.86
1757 1784 1.216977 CGTTCTGCCCGTATGTCCA 59.783 57.895 0.00 0.00 0.00 4.02
1758 1785 0.104304 ATCGTTCTGCCCGTATGTCC 59.896 55.000 0.00 0.00 0.00 4.02
1759 1786 1.209128 CATCGTTCTGCCCGTATGTC 58.791 55.000 0.00 0.00 0.00 3.06
1760 1787 0.810031 GCATCGTTCTGCCCGTATGT 60.810 55.000 0.00 0.00 36.10 2.29
1761 1788 1.934463 GCATCGTTCTGCCCGTATG 59.066 57.895 0.00 0.00 36.10 2.39
1762 1789 4.438346 GCATCGTTCTGCCCGTAT 57.562 55.556 0.00 0.00 36.10 3.06
1769 1796 3.853330 CACGGCGGCATCGTTCTG 61.853 66.667 13.24 0.00 38.94 3.02
1792 1819 3.740397 CAGTGCACCATGCCACCG 61.740 66.667 14.63 0.00 44.23 4.94
1793 1820 3.376078 CCAGTGCACCATGCCACC 61.376 66.667 14.63 0.00 44.23 4.61
1794 1821 4.060038 GCCAGTGCACCATGCCAC 62.060 66.667 14.63 0.00 44.23 5.01
1795 1822 4.289101 AGCCAGTGCACCATGCCA 62.289 61.111 14.63 0.00 44.23 4.92
1796 1823 3.446570 GAGCCAGTGCACCATGCC 61.447 66.667 14.63 0.00 44.23 4.40
1797 1824 2.360852 AGAGCCAGTGCACCATGC 60.361 61.111 14.63 13.84 45.29 4.06
1798 1825 1.303074 ACAGAGCCAGTGCACCATG 60.303 57.895 14.63 6.13 41.13 3.66
1799 1826 1.303074 CACAGAGCCAGTGCACCAT 60.303 57.895 14.63 0.00 41.13 3.55
1800 1827 2.111669 CACAGAGCCAGTGCACCA 59.888 61.111 14.63 0.00 41.13 4.17
1801 1828 1.963338 GTCACAGAGCCAGTGCACC 60.963 63.158 14.63 0.00 41.13 5.01
1802 1829 2.313172 CGTCACAGAGCCAGTGCAC 61.313 63.158 9.40 9.40 41.13 4.57
1803 1830 2.029518 CGTCACAGAGCCAGTGCA 59.970 61.111 0.00 0.00 41.13 4.57
1804 1831 2.024319 GTCGTCACAGAGCCAGTGC 61.024 63.158 0.00 0.00 36.93 4.40
1805 1832 0.665670 CAGTCGTCACAGAGCCAGTG 60.666 60.000 0.00 0.00 38.32 3.66
1806 1833 1.662608 CAGTCGTCACAGAGCCAGT 59.337 57.895 0.00 0.00 0.00 4.00
1807 1834 1.080230 CCAGTCGTCACAGAGCCAG 60.080 63.158 0.00 0.00 0.00 4.85
1808 1835 1.806461 GACCAGTCGTCACAGAGCCA 61.806 60.000 0.00 0.00 41.54 4.75
1809 1836 1.080434 GACCAGTCGTCACAGAGCC 60.080 63.158 0.00 0.00 41.54 4.70
1810 1837 1.442857 CGACCAGTCGTCACAGAGC 60.443 63.158 11.94 0.00 46.99 4.09
1811 1838 4.849336 CGACCAGTCGTCACAGAG 57.151 61.111 11.94 0.00 46.99 3.35
1823 1850 2.562738 AGTCATTGATGTCTGACGACCA 59.437 45.455 2.98 0.00 45.08 4.02
1824 1851 3.238108 AGTCATTGATGTCTGACGACC 57.762 47.619 2.98 0.00 45.08 4.79
1838 1865 8.743085 ATTGTGACATAGCTTATCAAGTCATT 57.257 30.769 0.00 0.00 38.16 2.57
1845 1872 6.293027 CGCATCAATTGTGACATAGCTTATCA 60.293 38.462 5.13 0.00 38.12 2.15
1848 1875 4.260743 GCGCATCAATTGTGACATAGCTTA 60.261 41.667 0.30 0.00 38.12 3.09
1856 1883 1.129879 CTGCGCGCATCAATTGTGAC 61.130 55.000 36.48 0.00 38.12 3.67
1932 1959 7.014518 CAGCCATATGAAAATATTCCAAGGTGA 59.985 37.037 3.65 0.00 34.49 4.02
1939 1966 5.990120 AGCCAGCCATATGAAAATATTCC 57.010 39.130 3.65 0.00 34.49 3.01
1961 1988 4.735132 CGAGAGCGCCCCGTTGAA 62.735 66.667 2.29 0.00 0.00 2.69
1964 1991 2.234913 AATAACGAGAGCGCCCCGTT 62.235 55.000 26.60 26.60 46.41 4.44
1986 2013 2.810852 CCTTCTTCTTCCTTGTGCAGAC 59.189 50.000 0.00 0.00 0.00 3.51
1991 2018 2.431454 GAGGCCTTCTTCTTCCTTGTG 58.569 52.381 6.77 0.00 0.00 3.33
1995 2022 1.268283 CCGGAGGCCTTCTTCTTCCT 61.268 60.000 6.77 0.00 46.14 3.36
2012 5249 0.309302 CGTGTCCAGATCTCTAGCCG 59.691 60.000 0.00 0.00 0.00 5.52
2033 5270 0.178903 TCCCAGTCTGTACCCTTGCT 60.179 55.000 0.00 0.00 0.00 3.91
2035 5272 0.613777 GGTCCCAGTCTGTACCCTTG 59.386 60.000 9.52 0.00 0.00 3.61
2042 5279 1.770110 TGGCAAGGTCCCAGTCTGT 60.770 57.895 0.00 0.00 0.00 3.41
2051 5288 2.034221 GACCACCCTGGCAAGGTC 59.966 66.667 4.38 8.43 42.67 3.85
2059 5296 1.979155 TCTCAGCTCGACCACCCTG 60.979 63.158 0.00 0.00 0.00 4.45
2071 5308 0.460987 CCTCAATCCGTGGTCTCAGC 60.461 60.000 0.00 0.00 0.00 4.26
2079 5316 0.824109 TAGCACTCCCTCAATCCGTG 59.176 55.000 0.00 0.00 0.00 4.94
2083 5320 5.283457 ACAAGTATAGCACTCCCTCAATC 57.717 43.478 0.00 0.00 36.04 2.67
2106 5343 0.250901 GCCACTCTTTTCTCCAGGCA 60.251 55.000 0.00 0.00 40.29 4.75
2124 5361 0.445436 CGAGTTGATGAGCAAGGTGC 59.555 55.000 0.00 0.00 45.46 5.01
2128 5365 3.369147 CCTTGTACGAGTTGATGAGCAAG 59.631 47.826 9.32 0.00 37.12 4.01
2144 5381 4.225042 AGCAACATACATGTCCTCCTTGTA 59.775 41.667 0.00 0.00 40.80 2.41
2147 5384 4.307032 AAGCAACATACATGTCCTCCTT 57.693 40.909 0.00 0.00 40.80 3.36
2148 5385 5.367937 AGATAAGCAACATACATGTCCTCCT 59.632 40.000 0.00 0.00 40.80 3.69
2182 5419 3.906008 CGTTTGTTATTTTCTCCACTGCG 59.094 43.478 0.00 0.00 0.00 5.18
2202 5439 3.678072 CGTAGTCACACCATGAAATTCGT 59.322 43.478 0.00 0.00 39.72 3.85
2216 5453 2.586258 ACAGCATCATCCGTAGTCAC 57.414 50.000 0.00 0.00 0.00 3.67
2221 5458 1.199615 TGGGAACAGCATCATCCGTA 58.800 50.000 0.00 0.00 33.90 4.02
2256 5493 1.126846 GCCGAGACATGAACAAAGACG 59.873 52.381 0.00 0.00 0.00 4.18
2263 5500 0.798776 CACCAAGCCGAGACATGAAC 59.201 55.000 0.00 0.00 0.00 3.18
2286 5523 9.175312 GATCCCGATCTAGTTAGTATTATCACA 57.825 37.037 0.00 0.00 35.04 3.58
2296 5533 1.466024 GCGCGATCCCGATCTAGTTAG 60.466 57.143 12.10 0.00 38.22 2.34
2297 5534 0.520404 GCGCGATCCCGATCTAGTTA 59.480 55.000 12.10 0.00 38.22 2.24
2328 5565 0.673437 CAAATGTTTGGACCGGCACT 59.327 50.000 0.00 0.00 34.59 4.40
2350 5587 8.126871 TGTTAAGTAGCTTCTTATTATGTGCG 57.873 34.615 12.91 0.00 31.28 5.34
2452 5690 8.572185 TGCATAGTTGTAAATTGTCTTTAAGCA 58.428 29.630 0.00 0.00 0.00 3.91
2687 5927 2.708861 AGTGTTTAGGATCCCACACACA 59.291 45.455 28.47 15.41 41.73 3.72
2748 5988 1.485124 CAATTCCCCAAGGCCTTACC 58.515 55.000 20.00 0.00 39.61 2.85
2749 5989 0.824109 GCAATTCCCCAAGGCCTTAC 59.176 55.000 20.00 0.00 0.00 2.34
2807 6047 5.888691 TGCTTTTATCCGCAACTGATTTA 57.111 34.783 0.00 0.00 32.40 1.40
2917 6161 4.744137 TGTTTGCAACAAAATCCTGATTCG 59.256 37.500 0.00 0.00 38.72 3.34
3088 6333 6.774354 AGCTTTGTTTTAATCACAGCAATG 57.226 33.333 14.14 3.80 39.94 2.82
3335 6583 3.120546 CGTTAATCTTGGCTGTCACTGTG 60.121 47.826 0.17 0.17 0.00 3.66
3578 6826 8.463930 TGGTATTTTCTCACTTTTGATTCACT 57.536 30.769 0.00 0.00 0.00 3.41
3872 7121 0.394762 ATGATGCATGGAGTGGCGTT 60.395 50.000 2.46 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.