Multiple sequence alignment - TraesCS5B01G402600

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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 TraesCS5B01G402600 chr5B 100.000 3410 0 0 1 3410 579382049 579385458 0.000000e+00 6298.0
1 TraesCS5B01G402600 chr5B 91.382 557 16 7 1 556 579103487 579104012 0.000000e+00 734.0
2 TraesCS5B01G402600 chr5B 91.789 475 34 5 2937 3410 579080691 579081161 0.000000e+00 656.0
3 TraesCS5B01G402600 chr5B 87.393 468 48 8 2653 3109 579167569 579168036 8.380000e-146 527.0
4 TraesCS5B01G402600 chr5B 80.870 690 88 22 1979 2656 579150062 579150719 1.410000e-138 503.0
5 TraesCS5B01G402600 chr5B 79.499 678 84 27 1300 1942 579143215 579143872 6.760000e-117 431.0
6 TraesCS5B01G402600 chr5B 88.489 278 26 4 3135 3410 579168528 579168801 7.050000e-87 331.0
7 TraesCS5B01G402600 chr5B 82.888 374 44 12 30 394 579141207 579141569 5.490000e-83 318.0
8 TraesCS5B01G402600 chr5B 97.647 170 4 0 392 561 579366396 579366565 3.330000e-75 292.0
9 TraesCS5B01G402600 chr5B 73.566 889 164 47 1781 2656 579079420 579080250 1.210000e-69 274.0
10 TraesCS5B01G402600 chr5B 86.857 175 20 3 1331 1502 579078875 579079049 3.470000e-45 193.0
11 TraesCS5B01G402600 chr5B 87.500 160 6 7 2787 2935 579080371 579080527 4.520000e-39 172.0
12 TraesCS5B01G402600 chr5B 87.050 139 15 2 30 165 579179539 579179677 1.640000e-33 154.0
13 TraesCS5B01G402600 chr5B 86.861 137 16 2 780 915 579142768 579142903 5.890000e-33 152.0
14 TraesCS5B01G402600 chr5B 81.739 115 13 6 1513 1620 579079135 579079248 4.690000e-14 89.8
15 TraesCS5B01G402600 chr5B 86.885 61 8 0 30 90 579104980 579105040 6.110000e-08 69.4
16 TraesCS5B01G402600 chr5D 92.319 1341 59 11 1310 2645 472435174 472436475 0.000000e+00 1866.0
17 TraesCS5B01G402600 chr5D 86.184 152 13 5 777 922 472434693 472434842 1.270000e-34 158.0
18 TraesCS5B01G402600 chr5A 88.571 1365 79 22 1297 2656 591976552 591977844 0.000000e+00 1585.0
19 TraesCS5B01G402600 chr5A 94.196 224 12 1 3129 3352 591986719 591986941 1.170000e-89 340.0
20 TraesCS5B01G402600 chr5A 90.909 121 5 2 2796 2910 591977954 591978074 1.270000e-34 158.0
21 TraesCS5B01G402600 chr5A 100.000 55 0 0 2653 2707 591977901 591977955 6.020000e-18 102.0
22 TraesCS5B01G402600 chr6A 87.755 98 12 0 2025 2122 594959134 594959231 7.730000e-22 115.0
23 TraesCS5B01G402600 chr6D 86.735 98 13 0 2025 2122 448810596 448810693 3.600000e-20 110.0
24 TraesCS5B01G402600 chr6D 89.062 64 2 3 1227 1290 456108398 456108456 1.310000e-09 75.0
25 TraesCS5B01G402600 chr2B 95.349 43 2 0 1204 1246 143132100 143132142 6.110000e-08 69.4
26 TraesCS5B01G402600 chr2A 95.349 43 2 0 1204 1246 90217481 90217523 6.110000e-08 69.4


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 TraesCS5B01G402600 chr5B 579382049 579385458 3409 False 6298.000000 6298 100.000000 1 3410 1 chr5B.!!$F4 3409
1 TraesCS5B01G402600 chr5B 579150062 579150719 657 False 503.000000 503 80.870000 1979 2656 1 chr5B.!!$F1 677
2 TraesCS5B01G402600 chr5B 579167569 579168801 1232 False 429.000000 527 87.941000 2653 3410 2 chr5B.!!$F8 757
3 TraesCS5B01G402600 chr5B 579103487 579105040 1553 False 401.700000 734 89.133500 1 556 2 chr5B.!!$F6 555
4 TraesCS5B01G402600 chr5B 579141207 579143872 2665 False 300.333333 431 83.082667 30 1942 3 chr5B.!!$F7 1912
5 TraesCS5B01G402600 chr5B 579078875 579081161 2286 False 276.960000 656 84.290200 1331 3410 5 chr5B.!!$F5 2079
6 TraesCS5B01G402600 chr5D 472434693 472436475 1782 False 1012.000000 1866 89.251500 777 2645 2 chr5D.!!$F1 1868
7 TraesCS5B01G402600 chr5A 591976552 591978074 1522 False 615.000000 1585 93.160000 1297 2910 3 chr5A.!!$F2 1613

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
992 1890 0.037697 TTCCGGTGGTGTCGATCAAG 60.038 55.0 0.00 0.0 0.00 3.02 F
1209 2209 0.103208 GTAGGCACTGCGTATCAGCT 59.897 55.0 6.71 0.0 46.76 4.24 F
1211 2211 0.460987 AGGCACTGCGTATCAGCTTC 60.461 55.0 0.00 0.0 46.76 3.86 F
1321 2321 0.534873 TGCATGCGTAGGCTGACTTA 59.465 50.0 14.09 0.0 40.82 2.24 F
1975 3114 2.568509 CGGGTGGGTAACTTCTTAAGGA 59.431 50.0 1.85 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 3114 0.106015 AAGACCTTTGCAGCACCCTT 60.106 50.000 0.0 0.0 0.00 3.95 R
2188 3327 0.407528 TTCTTGCCAATAGGGTGCCA 59.592 50.000 0.0 0.0 39.65 4.92 R
2189 3328 0.817654 GTTCTTGCCAATAGGGTGCC 59.182 55.000 0.0 0.0 39.65 5.01 R
2190 3329 1.544724 TGTTCTTGCCAATAGGGTGC 58.455 50.000 0.0 0.0 39.65 5.01 R
3277 5134 2.086869 CATTGAGTTCGATGCCTTGGT 58.913 47.619 0.0 0.0 31.62 3.67 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
92 93 0.984230 CCTTTGAGGTGCTACAGGGA 59.016 55.000 0.00 0.00 0.00 4.20
147 152 5.937540 TGGACCTAGTTGATACAACATGTTG 59.062 40.000 32.03 32.03 45.58 3.33
175 180 6.367374 TTCACCCAAGATCAACTACACATA 57.633 37.500 0.00 0.00 0.00 2.29
205 210 7.132694 TGTAAATAGCACAAACACAGAGATG 57.867 36.000 0.00 0.00 0.00 2.90
226 232 3.629855 TGGAGAACTTTTGACGAATGCAA 59.370 39.130 0.00 0.00 0.00 4.08
228 234 4.222114 GAGAACTTTTGACGAATGCAAGG 58.778 43.478 0.00 0.00 0.00 3.61
394 404 4.236147 GAGTCGGTTTCTGGTTTCTAGTC 58.764 47.826 0.00 0.00 0.00 2.59
419 429 3.814842 TCAGGTACACTCTTCGACGTTAA 59.185 43.478 0.00 0.00 0.00 2.01
590 883 2.747460 CACGGGGGTGCATGTCTG 60.747 66.667 0.00 0.00 0.00 3.51
608 901 0.592637 TGCATGCCAACGTCAGAAAG 59.407 50.000 16.68 0.00 0.00 2.62
614 907 1.961793 CCAACGTCAGAAAGGAACCA 58.038 50.000 0.00 0.00 0.00 3.67
616 909 2.884639 CCAACGTCAGAAAGGAACCAAT 59.115 45.455 0.00 0.00 0.00 3.16
618 911 2.413837 ACGTCAGAAAGGAACCAATCG 58.586 47.619 0.00 0.00 0.00 3.34
619 912 2.036733 ACGTCAGAAAGGAACCAATCGA 59.963 45.455 0.00 0.00 0.00 3.59
620 913 3.262420 CGTCAGAAAGGAACCAATCGAT 58.738 45.455 0.00 0.00 0.00 3.59
621 914 3.307242 CGTCAGAAAGGAACCAATCGATC 59.693 47.826 0.00 0.00 0.00 3.69
622 915 3.307242 GTCAGAAAGGAACCAATCGATCG 59.693 47.826 9.36 9.36 0.00 3.69
623 916 3.194755 TCAGAAAGGAACCAATCGATCGA 59.805 43.478 21.86 21.86 0.00 3.59
624 917 3.307242 CAGAAAGGAACCAATCGATCGAC 59.693 47.826 22.06 6.26 0.00 4.20
625 918 1.922570 AAGGAACCAATCGATCGACG 58.077 50.000 22.06 14.50 44.09 5.12
646 939 1.648467 GAGCATTTGACTGGGCGTCC 61.648 60.000 0.00 0.00 42.13 4.79
647 940 1.675641 GCATTTGACTGGGCGTCCT 60.676 57.895 7.97 0.00 42.13 3.85
648 941 1.926511 GCATTTGACTGGGCGTCCTG 61.927 60.000 11.87 11.87 42.13 3.86
649 942 0.606401 CATTTGACTGGGCGTCCTGT 60.606 55.000 19.37 19.37 46.07 4.00
650 943 0.606401 ATTTGACTGGGCGTCCTGTG 60.606 55.000 24.27 8.03 43.90 3.66
651 944 1.978455 TTTGACTGGGCGTCCTGTGT 61.978 55.000 24.27 11.49 43.90 3.72
652 945 2.048127 GACTGGGCGTCCTGTGTC 60.048 66.667 24.27 16.36 43.90 3.67
653 946 3.916392 GACTGGGCGTCCTGTGTCG 62.916 68.421 24.27 0.00 43.90 4.35
654 947 3.991051 CTGGGCGTCCTGTGTCGT 61.991 66.667 7.97 0.00 0.00 4.34
655 948 2.598099 TGGGCGTCCTGTGTCGTA 60.598 61.111 7.97 0.00 0.00 3.43
656 949 2.181021 GGGCGTCCTGTGTCGTAG 59.819 66.667 0.00 0.00 0.00 3.51
659 952 0.179179 GGCGTCCTGTGTCGTAGTAC 60.179 60.000 0.00 0.00 0.00 2.73
664 957 2.736721 GTCCTGTGTCGTAGTACGTGTA 59.263 50.000 21.38 7.29 43.14 2.90
676 969 6.197282 TCGTAGTACGTGTATTCGAAGAGTAG 59.803 42.308 21.38 0.00 43.14 2.57
679 972 4.352600 ACGTGTATTCGAAGAGTAGGTG 57.647 45.455 3.35 0.00 38.43 4.00
681 974 3.427098 CGTGTATTCGAAGAGTAGGTGCA 60.427 47.826 3.35 0.00 38.43 4.57
682 975 3.858238 GTGTATTCGAAGAGTAGGTGCAC 59.142 47.826 8.80 8.80 38.43 4.57
683 976 3.508402 TGTATTCGAAGAGTAGGTGCACA 59.492 43.478 20.43 0.00 38.43 4.57
684 977 3.895232 ATTCGAAGAGTAGGTGCACAT 57.105 42.857 20.43 15.34 38.43 3.21
685 978 5.358725 TGTATTCGAAGAGTAGGTGCACATA 59.641 40.000 20.43 14.05 38.43 2.29
686 979 3.777465 TCGAAGAGTAGGTGCACATAC 57.223 47.619 29.29 29.29 33.71 2.39
687 980 3.086282 TCGAAGAGTAGGTGCACATACA 58.914 45.455 35.10 16.64 35.75 2.29
688 981 3.119602 TCGAAGAGTAGGTGCACATACAC 60.120 47.826 35.10 30.17 35.75 2.90
689 982 3.119459 CGAAGAGTAGGTGCACATACACT 60.119 47.826 35.10 31.61 40.52 3.55
690 983 4.425520 GAAGAGTAGGTGCACATACACTC 58.574 47.826 35.10 28.12 40.52 3.51
691 984 3.702792 AGAGTAGGTGCACATACACTCT 58.297 45.455 35.10 29.57 40.52 3.24
692 985 3.697045 AGAGTAGGTGCACATACACTCTC 59.303 47.826 35.10 25.47 38.64 3.20
693 986 3.431415 AGTAGGTGCACATACACTCTCA 58.569 45.455 35.10 3.31 40.52 3.27
694 987 4.026744 AGTAGGTGCACATACACTCTCAT 58.973 43.478 35.10 15.99 40.52 2.90
695 988 3.533606 AGGTGCACATACACTCTCATC 57.466 47.619 20.43 0.00 40.52 2.92
696 989 2.169352 AGGTGCACATACACTCTCATCC 59.831 50.000 20.43 0.00 40.52 3.51
697 990 2.555199 GTGCACATACACTCTCATCCC 58.445 52.381 13.17 0.00 37.58 3.85
698 991 2.093500 GTGCACATACACTCTCATCCCA 60.093 50.000 13.17 0.00 37.58 4.37
699 992 2.773661 TGCACATACACTCTCATCCCAT 59.226 45.455 0.00 0.00 0.00 4.00
700 993 3.136763 GCACATACACTCTCATCCCATG 58.863 50.000 0.00 0.00 0.00 3.66
701 994 3.136763 CACATACACTCTCATCCCATGC 58.863 50.000 0.00 0.00 0.00 4.06
702 995 2.773661 ACATACACTCTCATCCCATGCA 59.226 45.455 0.00 0.00 0.00 3.96
703 996 3.393609 ACATACACTCTCATCCCATGCAT 59.606 43.478 0.00 0.00 0.00 3.96
704 997 2.343484 ACACTCTCATCCCATGCATG 57.657 50.000 20.19 20.19 0.00 4.06
706 999 0.178998 ACTCTCATCCCATGCATGGC 60.179 55.000 36.08 0.00 46.70 4.40
707 1000 0.894184 CTCTCATCCCATGCATGGCC 60.894 60.000 36.08 0.00 46.70 5.36
708 1001 1.153061 CTCATCCCATGCATGGCCT 59.847 57.895 36.08 23.31 46.70 5.19
709 1002 0.402887 CTCATCCCATGCATGGCCTA 59.597 55.000 36.08 24.26 46.70 3.93
710 1003 1.005569 CTCATCCCATGCATGGCCTAT 59.994 52.381 36.08 25.24 46.70 2.57
711 1004 1.182667 CATCCCATGCATGGCCTATG 58.817 55.000 36.08 30.27 46.70 2.23
721 1014 2.079158 CATGGCCTATGCTTATCCACG 58.921 52.381 3.32 0.00 37.74 4.94
725 1018 1.139989 CCTATGCTTATCCACGCACG 58.860 55.000 0.00 0.00 39.21 5.34
726 1019 1.269569 CCTATGCTTATCCACGCACGA 60.270 52.381 0.00 0.00 39.21 4.35
735 1028 4.046998 CACGCACGACACGAGCAC 62.047 66.667 12.85 0.00 42.97 4.40
751 1044 1.609840 GCACGTGAGCGACTGAGTTC 61.610 60.000 22.23 0.00 42.00 3.01
753 1046 0.039978 ACGTGAGCGACTGAGTTCAG 60.040 55.000 7.57 7.57 44.41 3.02
765 1058 4.999751 CTGAGTTCAGTCAAGCTAAACC 57.000 45.455 0.91 0.00 39.09 3.27
767 1060 5.036117 TGAGTTCAGTCAAGCTAAACCTT 57.964 39.130 0.00 0.00 0.00 3.50
768 1061 5.057149 TGAGTTCAGTCAAGCTAAACCTTC 58.943 41.667 0.00 0.00 0.00 3.46
772 1141 4.642429 TCAGTCAAGCTAAACCTTCTTCC 58.358 43.478 0.00 0.00 0.00 3.46
773 1142 4.348168 TCAGTCAAGCTAAACCTTCTTCCT 59.652 41.667 0.00 0.00 0.00 3.36
774 1143 5.066593 CAGTCAAGCTAAACCTTCTTCCTT 58.933 41.667 0.00 0.00 0.00 3.36
775 1144 6.042781 TCAGTCAAGCTAAACCTTCTTCCTTA 59.957 38.462 0.00 0.00 0.00 2.69
778 1147 7.945109 AGTCAAGCTAAACCTTCTTCCTTAAAT 59.055 33.333 0.00 0.00 0.00 1.40
844 1732 6.295039 TGCAGCTACTTGTAAACTTGTAAC 57.705 37.500 0.00 0.00 0.00 2.50
849 1737 5.107337 GCTACTTGTAAACTTGTAACCGGAC 60.107 44.000 9.46 0.00 0.00 4.79
852 1740 6.218746 ACTTGTAAACTTGTAACCGGACTAG 58.781 40.000 9.46 5.75 0.00 2.57
897 1786 5.730010 GCTGCAAATTAAGCACAAGCAAAAA 60.730 36.000 0.00 0.00 45.49 1.94
923 1812 6.371809 CTGGAGCTCAGTACTTTCTACTAG 57.628 45.833 17.19 0.00 38.64 2.57
926 1815 7.049133 TGGAGCTCAGTACTTTCTACTAGTAG 58.951 42.308 21.87 21.87 34.56 2.57
948 1837 7.921745 AGTAGTATATCCGAAAGACAAAGAAGC 59.078 37.037 0.00 0.00 0.00 3.86
951 1849 2.404215 TCCGAAAGACAAAGAAGCTCG 58.596 47.619 0.00 0.00 0.00 5.03
952 1850 1.136224 CCGAAAGACAAAGAAGCTCGC 60.136 52.381 0.00 0.00 0.00 5.03
957 1855 0.711118 GACAAAGAAGCTCGCGACTC 59.289 55.000 3.71 1.89 0.00 3.36
960 1858 1.388431 CAAAGAAGCTCGCGACTCTTC 59.612 52.381 26.53 26.53 37.17 2.87
962 1860 0.170116 AGAAGCTCGCGACTCTTCAG 59.830 55.000 31.21 14.59 38.83 3.02
964 1862 0.814457 AAGCTCGCGACTCTTCAGAT 59.186 50.000 3.71 0.00 0.00 2.90
967 1865 0.653114 CTCGCGACTCTTCAGATCGA 59.347 55.000 3.71 0.00 38.10 3.59
986 1884 2.209064 ATCGAGTTCCGGTGGTGTCG 62.209 60.000 0.00 4.74 39.14 4.35
991 1889 0.320073 GTTCCGGTGGTGTCGATCAA 60.320 55.000 0.00 0.00 0.00 2.57
992 1890 0.037697 TTCCGGTGGTGTCGATCAAG 60.038 55.000 0.00 0.00 0.00 3.02
993 1891 2.100631 CCGGTGGTGTCGATCAAGC 61.101 63.158 0.00 0.00 0.00 4.01
994 1892 2.444624 CGGTGGTGTCGATCAAGCG 61.445 63.158 5.46 5.46 0.00 4.68
995 1893 2.740714 GGTGGTGTCGATCAAGCGC 61.741 63.158 0.00 0.00 0.00 5.92
996 1894 2.027073 GTGGTGTCGATCAAGCGCA 61.027 57.895 11.47 0.00 0.00 6.09
997 1895 2.027073 TGGTGTCGATCAAGCGCAC 61.027 57.895 11.47 0.00 37.48 5.34
998 1896 2.740714 GGTGTCGATCAAGCGCACC 61.741 63.158 11.47 14.83 44.51 5.01
999 1897 2.809174 TGTCGATCAAGCGCACCG 60.809 61.111 11.47 5.33 0.00 4.94
1001 1899 1.878522 GTCGATCAAGCGCACCGAT 60.879 57.895 11.47 8.18 0.00 4.18
1004 1988 2.514592 ATCAAGCGCACCGATGGG 60.515 61.111 11.47 0.00 41.65 4.00
1085 2081 9.599866 CAACAAGATTGACTGGTATGTTATCTA 57.400 33.333 0.00 0.00 31.64 1.98
1156 2156 4.439968 TCGAGTCTCGAGTATGTATGTGT 58.560 43.478 20.85 0.00 44.82 3.72
1181 2181 2.225068 GCCGCGCCAGTCATATATAT 57.775 50.000 0.00 0.00 0.00 0.86
1182 2182 3.364889 GCCGCGCCAGTCATATATATA 57.635 47.619 0.00 0.00 0.00 0.86
1184 2184 3.243434 GCCGCGCCAGTCATATATATACT 60.243 47.826 0.00 0.00 0.00 2.12
1188 2188 6.072673 CCGCGCCAGTCATATATATACTCATA 60.073 42.308 0.00 0.00 0.00 2.15
1189 2189 7.362142 CCGCGCCAGTCATATATATACTCATAT 60.362 40.741 0.00 0.00 0.00 1.78
1190 2190 7.483059 CGCGCCAGTCATATATATACTCATATG 59.517 40.741 0.00 0.00 36.75 1.78
1191 2191 8.300286 GCGCCAGTCATATATATACTCATATGT 58.700 37.037 0.00 0.00 36.76 2.29
1201 2201 2.515926 ACTCATATGTAGGCACTGCG 57.484 50.000 1.90 0.00 46.57 5.18
1202 2202 1.757118 ACTCATATGTAGGCACTGCGT 59.243 47.619 1.90 1.21 46.57 5.24
1203 2203 2.956333 ACTCATATGTAGGCACTGCGTA 59.044 45.455 1.90 0.00 46.57 4.42
1207 2207 2.515926 ATGTAGGCACTGCGTATCAG 57.484 50.000 6.71 0.00 46.57 2.90
1208 2208 0.179111 TGTAGGCACTGCGTATCAGC 60.179 55.000 6.71 0.00 46.57 4.26
1209 2209 0.103208 GTAGGCACTGCGTATCAGCT 59.897 55.000 6.71 0.00 46.76 4.24
1210 2210 0.824109 TAGGCACTGCGTATCAGCTT 59.176 50.000 0.00 0.00 46.76 3.74
1211 2211 0.460987 AGGCACTGCGTATCAGCTTC 60.461 55.000 0.00 0.00 46.76 3.86
1212 2212 0.740868 GGCACTGCGTATCAGCTTCA 60.741 55.000 0.00 0.00 46.76 3.02
1213 2213 0.649475 GCACTGCGTATCAGCTTCAG 59.351 55.000 0.00 0.00 46.76 3.02
1214 2214 2.001812 CACTGCGTATCAGCTTCAGT 57.998 50.000 0.00 0.00 46.76 3.41
1215 2215 1.923204 CACTGCGTATCAGCTTCAGTC 59.077 52.381 0.00 0.00 46.76 3.51
1216 2216 1.821753 ACTGCGTATCAGCTTCAGTCT 59.178 47.619 0.00 0.00 46.76 3.24
1217 2217 2.159310 ACTGCGTATCAGCTTCAGTCTC 60.159 50.000 0.00 0.00 46.76 3.36
1218 2218 2.095461 TGCGTATCAGCTTCAGTCTCT 58.905 47.619 0.00 0.00 38.13 3.10
1219 2219 2.493675 TGCGTATCAGCTTCAGTCTCTT 59.506 45.455 0.00 0.00 38.13 2.85
1220 2220 2.857152 GCGTATCAGCTTCAGTCTCTTG 59.143 50.000 0.00 0.00 0.00 3.02
1221 2221 3.674682 GCGTATCAGCTTCAGTCTCTTGT 60.675 47.826 0.00 0.00 0.00 3.16
1222 2222 4.489810 CGTATCAGCTTCAGTCTCTTGTT 58.510 43.478 0.00 0.00 0.00 2.83
1223 2223 4.926238 CGTATCAGCTTCAGTCTCTTGTTT 59.074 41.667 0.00 0.00 0.00 2.83
1224 2224 5.406780 CGTATCAGCTTCAGTCTCTTGTTTT 59.593 40.000 0.00 0.00 0.00 2.43
1225 2225 5.938438 ATCAGCTTCAGTCTCTTGTTTTC 57.062 39.130 0.00 0.00 0.00 2.29
1226 2226 4.769688 TCAGCTTCAGTCTCTTGTTTTCA 58.230 39.130 0.00 0.00 0.00 2.69
1227 2227 4.813161 TCAGCTTCAGTCTCTTGTTTTCAG 59.187 41.667 0.00 0.00 0.00 3.02
1228 2228 4.813161 CAGCTTCAGTCTCTTGTTTTCAGA 59.187 41.667 0.00 0.00 0.00 3.27
1229 2229 4.813697 AGCTTCAGTCTCTTGTTTTCAGAC 59.186 41.667 0.00 0.00 0.00 3.51
1230 2230 4.024472 GCTTCAGTCTCTTGTTTTCAGACC 60.024 45.833 0.00 0.00 0.00 3.85
1231 2231 5.359194 TTCAGTCTCTTGTTTTCAGACCT 57.641 39.130 0.00 0.00 0.00 3.85
1232 2232 5.359194 TCAGTCTCTTGTTTTCAGACCTT 57.641 39.130 0.00 0.00 0.00 3.50
1233 2233 5.745227 TCAGTCTCTTGTTTTCAGACCTTT 58.255 37.500 0.00 0.00 0.00 3.11
1234 2234 5.586243 TCAGTCTCTTGTTTTCAGACCTTTG 59.414 40.000 0.00 0.00 0.00 2.77
1235 2235 5.355350 CAGTCTCTTGTTTTCAGACCTTTGT 59.645 40.000 0.00 0.00 0.00 2.83
1236 2236 6.538742 CAGTCTCTTGTTTTCAGACCTTTGTA 59.461 38.462 0.00 0.00 0.00 2.41
1237 2237 7.227512 CAGTCTCTTGTTTTCAGACCTTTGTAT 59.772 37.037 0.00 0.00 0.00 2.29
1238 2238 7.775561 AGTCTCTTGTTTTCAGACCTTTGTATT 59.224 33.333 0.00 0.00 0.00 1.89
1239 2239 8.406297 GTCTCTTGTTTTCAGACCTTTGTATTT 58.594 33.333 0.00 0.00 0.00 1.40
1240 2240 8.621286 TCTCTTGTTTTCAGACCTTTGTATTTC 58.379 33.333 0.00 0.00 0.00 2.17
1241 2241 7.712797 TCTTGTTTTCAGACCTTTGTATTTCC 58.287 34.615 0.00 0.00 0.00 3.13
1242 2242 6.067263 TGTTTTCAGACCTTTGTATTTCCG 57.933 37.500 0.00 0.00 0.00 4.30
1243 2243 5.591067 TGTTTTCAGACCTTTGTATTTCCGT 59.409 36.000 0.00 0.00 0.00 4.69
1244 2244 6.095720 TGTTTTCAGACCTTTGTATTTCCGTT 59.904 34.615 0.00 0.00 0.00 4.44
1245 2245 7.282675 TGTTTTCAGACCTTTGTATTTCCGTTA 59.717 33.333 0.00 0.00 0.00 3.18
1246 2246 7.804843 TTTCAGACCTTTGTATTTCCGTTAA 57.195 32.000 0.00 0.00 0.00 2.01
1247 2247 7.429636 TTCAGACCTTTGTATTTCCGTTAAG 57.570 36.000 0.00 0.00 0.00 1.85
1248 2248 6.527423 TCAGACCTTTGTATTTCCGTTAAGT 58.473 36.000 0.00 0.00 0.00 2.24
1249 2249 6.425721 TCAGACCTTTGTATTTCCGTTAAGTG 59.574 38.462 0.00 0.00 0.00 3.16
1250 2250 6.425721 CAGACCTTTGTATTTCCGTTAAGTGA 59.574 38.462 0.00 0.00 0.00 3.41
1251 2251 7.119262 CAGACCTTTGTATTTCCGTTAAGTGAT 59.881 37.037 0.00 0.00 0.00 3.06
1252 2252 7.664318 AGACCTTTGTATTTCCGTTAAGTGATT 59.336 33.333 0.00 0.00 0.00 2.57
1253 2253 8.851541 ACCTTTGTATTTCCGTTAAGTGATTA 57.148 30.769 0.00 0.00 0.00 1.75
1254 2254 9.457436 ACCTTTGTATTTCCGTTAAGTGATTAT 57.543 29.630 0.00 0.00 0.00 1.28
1266 2266 8.349983 CCGTTAAGTGATTATTAATGGAAAGGG 58.650 37.037 9.98 0.00 45.90 3.95
1267 2267 8.349983 CGTTAAGTGATTATTAATGGAAAGGGG 58.650 37.037 0.00 0.00 0.00 4.79
1268 2268 9.416284 GTTAAGTGATTATTAATGGAAAGGGGA 57.584 33.333 0.00 0.00 0.00 4.81
1269 2269 9.998752 TTAAGTGATTATTAATGGAAAGGGGAA 57.001 29.630 0.00 0.00 0.00 3.97
1270 2270 8.909423 AAGTGATTATTAATGGAAAGGGGAAA 57.091 30.769 0.00 0.00 0.00 3.13
1271 2271 8.539117 AGTGATTATTAATGGAAAGGGGAAAG 57.461 34.615 0.00 0.00 0.00 2.62
1272 2272 7.069950 AGTGATTATTAATGGAAAGGGGAAAGC 59.930 37.037 0.00 0.00 0.00 3.51
1273 2273 6.326323 TGATTATTAATGGAAAGGGGAAAGCC 59.674 38.462 0.00 0.00 0.00 4.35
1282 2282 2.116556 GGGAAAGCCCGGTTGGAA 59.883 61.111 0.00 0.00 46.48 3.53
1283 2283 1.532078 GGGAAAGCCCGGTTGGAAA 60.532 57.895 0.00 0.00 46.48 3.13
1284 2284 1.116536 GGGAAAGCCCGGTTGGAAAA 61.117 55.000 0.00 0.00 46.48 2.29
1285 2285 0.753867 GGAAAGCCCGGTTGGAAAAA 59.246 50.000 0.00 0.00 37.49 1.94
1286 2286 1.270094 GGAAAGCCCGGTTGGAAAAAG 60.270 52.381 0.00 0.00 37.49 2.27
1287 2287 1.684450 GAAAGCCCGGTTGGAAAAAGA 59.316 47.619 0.00 0.00 37.49 2.52
1288 2288 1.783071 AAGCCCGGTTGGAAAAAGAA 58.217 45.000 0.00 0.00 37.49 2.52
1289 2289 1.783071 AGCCCGGTTGGAAAAAGAAA 58.217 45.000 0.00 0.00 37.49 2.52
1290 2290 2.112190 AGCCCGGTTGGAAAAAGAAAA 58.888 42.857 0.00 0.00 37.49 2.29
1291 2291 2.703536 AGCCCGGTTGGAAAAAGAAAAT 59.296 40.909 0.00 0.00 37.49 1.82
1292 2292 3.898741 AGCCCGGTTGGAAAAAGAAAATA 59.101 39.130 0.00 0.00 37.49 1.40
1293 2293 4.530553 AGCCCGGTTGGAAAAAGAAAATAT 59.469 37.500 0.00 0.00 37.49 1.28
1294 2294 4.629634 GCCCGGTTGGAAAAAGAAAATATG 59.370 41.667 0.00 0.00 37.49 1.78
1295 2295 4.629634 CCCGGTTGGAAAAAGAAAATATGC 59.370 41.667 0.00 0.00 37.49 3.14
1318 2318 1.448540 ACTGCATGCGTAGGCTGAC 60.449 57.895 22.06 0.00 40.82 3.51
1321 2321 0.534873 TGCATGCGTAGGCTGACTTA 59.465 50.000 14.09 0.00 40.82 2.24
1650 2777 4.996758 GGGAGTATTCGAGACTACTACCTC 59.003 50.000 19.04 3.15 43.16 3.85
1733 2860 2.894765 TGGTCGACCAACTTATGACTGA 59.105 45.455 34.60 6.57 44.35 3.41
1750 2877 4.339530 TGACTGATATGAGAAAGGAGGACG 59.660 45.833 0.00 0.00 0.00 4.79
1975 3114 2.568509 CGGGTGGGTAACTTCTTAAGGA 59.431 50.000 1.85 0.00 0.00 3.36
2188 3327 3.553437 CTCCGTGACGCGTTCTGGT 62.553 63.158 15.53 0.00 39.32 4.00
2189 3328 3.403057 CCGTGACGCGTTCTGGTG 61.403 66.667 15.53 0.17 39.32 4.17
2190 3329 3.403057 CGTGACGCGTTCTGGTGG 61.403 66.667 15.53 0.00 35.54 4.61
2196 3335 4.643387 GCGTTCTGGTGGCACCCT 62.643 66.667 32.61 0.00 37.50 4.34
2263 3402 1.149148 GTGGAAAAGCTGTCTCGACC 58.851 55.000 0.00 0.00 0.00 4.79
2265 3404 1.149148 GGAAAAGCTGTCTCGACCAC 58.851 55.000 0.00 0.00 0.00 4.16
2266 3405 0.784778 GAAAAGCTGTCTCGACCACG 59.215 55.000 0.00 0.00 41.26 4.94
2267 3406 0.387929 AAAAGCTGTCTCGACCACGA 59.612 50.000 0.00 0.00 46.56 4.35
2378 3520 5.539048 TCAAGCACAAACTACTTCTACCTC 58.461 41.667 0.00 0.00 0.00 3.85
2379 3521 5.069914 TCAAGCACAAACTACTTCTACCTCA 59.930 40.000 0.00 0.00 0.00 3.86
2380 3522 5.746990 AGCACAAACTACTTCTACCTCAT 57.253 39.130 0.00 0.00 0.00 2.90
2381 3523 5.725362 AGCACAAACTACTTCTACCTCATC 58.275 41.667 0.00 0.00 0.00 2.92
2382 3524 4.870991 GCACAAACTACTTCTACCTCATCC 59.129 45.833 0.00 0.00 0.00 3.51
2383 3525 5.103000 CACAAACTACTTCTACCTCATCCG 58.897 45.833 0.00 0.00 0.00 4.18
2384 3526 4.113354 CAAACTACTTCTACCTCATCCGC 58.887 47.826 0.00 0.00 0.00 5.54
2385 3527 3.014304 ACTACTTCTACCTCATCCGCA 57.986 47.619 0.00 0.00 0.00 5.69
2386 3528 2.688958 ACTACTTCTACCTCATCCGCAC 59.311 50.000 0.00 0.00 0.00 5.34
2387 3529 0.456221 ACTTCTACCTCATCCGCACG 59.544 55.000 0.00 0.00 0.00 5.34
2388 3530 0.249073 CTTCTACCTCATCCGCACGG 60.249 60.000 1.73 1.73 0.00 4.94
2389 3531 0.968901 TTCTACCTCATCCGCACGGT 60.969 55.000 9.23 0.00 36.47 4.83
2390 3532 1.065928 CTACCTCATCCGCACGGTC 59.934 63.158 9.23 0.00 36.47 4.79
2391 3533 1.379443 TACCTCATCCGCACGGTCT 60.379 57.895 9.23 0.00 36.47 3.85
2392 3534 1.381928 TACCTCATCCGCACGGTCTC 61.382 60.000 9.23 0.00 36.47 3.36
2393 3535 2.105128 CTCATCCGCACGGTCTCC 59.895 66.667 9.23 0.00 36.47 3.71
2394 3536 2.678580 TCATCCGCACGGTCTCCA 60.679 61.111 9.23 0.00 36.47 3.86
2395 3537 2.202797 CATCCGCACGGTCTCCAG 60.203 66.667 9.23 0.00 36.47 3.86
2435 3579 1.795286 GCTCCTTGTCGAAGTCAGTTG 59.205 52.381 0.00 0.00 0.00 3.16
2475 3623 6.075728 CGAATAAATGAAGTTCGTCGTCGTAT 60.076 38.462 1.33 0.00 39.70 3.06
2639 3791 4.164843 TCTGTTCTTGTAGCTTGGGTTT 57.835 40.909 0.00 0.00 0.00 3.27
2768 3984 9.959749 TTTTTGCTTTTCGTGATAATTTCTAGT 57.040 25.926 0.00 0.00 0.00 2.57
2779 3995 9.319143 CGTGATAATTTCTAGTGATCCTCTTTT 57.681 33.333 0.00 0.00 0.00 2.27
2957 4346 7.095910 TCCAACAAAATATTCACGCATTCAAT 58.904 30.769 0.00 0.00 0.00 2.57
3017 4406 3.430042 AATGGATCCATTCCCGATCAG 57.570 47.619 30.64 0.00 44.77 2.90
3070 4459 8.964476 ACAAAATATTCGAATCCACTACATCT 57.036 30.769 15.25 0.00 0.00 2.90
3137 4993 4.695455 CCTCCATACGGGCATAATTTACTG 59.305 45.833 0.00 0.00 36.21 2.74
3277 5134 1.508667 ATGGGCCATCTTCACCACCA 61.509 55.000 14.78 0.00 35.52 4.17
3290 5147 1.303236 CCACCACCAAGGCATCGAA 60.303 57.895 0.00 0.00 43.14 3.71
3328 5185 0.242017 GTCACACCATTGCAAGCCTC 59.758 55.000 4.94 0.00 0.00 4.70
3355 5213 3.319755 AGAAAATTTCACGCCATTGCAG 58.680 40.909 8.55 0.00 37.32 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 1.586154 TTTGCTTGCGCTTAGGAGGC 61.586 55.000 9.73 0.00 43.43 4.70
175 180 9.008965 TCTGTGTTTGTGCTATTTACATATGTT 57.991 29.630 14.77 0.00 0.00 2.71
205 210 3.896648 TGCATTCGTCAAAAGTTCTCC 57.103 42.857 0.00 0.00 0.00 3.71
226 232 0.759346 AAAGAGCAAGACACGACCCT 59.241 50.000 0.00 0.00 0.00 4.34
228 234 2.872858 AGAAAAAGAGCAAGACACGACC 59.127 45.455 0.00 0.00 0.00 4.79
266 272 3.144506 CATGCATGGTATCTTCCTGTCC 58.855 50.000 19.40 0.00 0.00 4.02
331 337 3.596214 GGGCTACATTGACGAGAGAAAA 58.404 45.455 0.00 0.00 0.00 2.29
337 343 1.883084 GCCGGGCTACATTGACGAG 60.883 63.158 12.87 0.00 0.00 4.18
339 345 2.173669 CAGCCGGGCTACATTGACG 61.174 63.158 23.37 2.36 36.40 4.35
394 404 2.412977 CGTCGAAGAGTGTACCTGACTG 60.413 54.545 0.00 0.00 36.95 3.51
429 719 8.738645 AATGAGTGGAAATAGTTATTGAGACC 57.261 34.615 0.00 0.00 0.00 3.85
504 795 2.037121 CCAGTCACCCAAAAACCCATTC 59.963 50.000 0.00 0.00 0.00 2.67
556 847 1.891919 TGTCCAGTTTGACGCCAGC 60.892 57.895 0.00 0.00 38.11 4.85
557 848 1.831389 CGTGTCCAGTTTGACGCCAG 61.831 60.000 0.00 0.00 41.59 4.85
558 849 1.885388 CGTGTCCAGTTTGACGCCA 60.885 57.895 0.00 0.00 41.59 5.69
559 850 2.604174 CCGTGTCCAGTTTGACGCC 61.604 63.158 0.00 0.00 41.59 5.68
560 851 2.604174 CCCGTGTCCAGTTTGACGC 61.604 63.158 0.00 0.00 41.29 5.19
562 853 1.599797 CCCCCGTGTCCAGTTTGAC 60.600 63.158 0.00 0.00 35.77 3.18
563 854 2.073716 ACCCCCGTGTCCAGTTTGA 61.074 57.895 0.00 0.00 0.00 2.69
564 855 1.896660 CACCCCCGTGTCCAGTTTG 60.897 63.158 0.00 0.00 35.10 2.93
565 856 2.513895 CACCCCCGTGTCCAGTTT 59.486 61.111 0.00 0.00 35.10 2.66
566 857 4.265056 GCACCCCCGTGTCCAGTT 62.265 66.667 0.00 0.00 42.39 3.16
568 859 4.033776 ATGCACCCCCGTGTCCAG 62.034 66.667 0.00 0.00 42.39 3.86
590 883 0.109597 CCTTTCTGACGTTGGCATGC 60.110 55.000 9.90 9.90 0.00 4.06
595 888 1.961793 TGGTTCCTTTCTGACGTTGG 58.038 50.000 0.00 0.00 0.00 3.77
608 901 1.808234 CGCGTCGATCGATTGGTTCC 61.808 60.000 22.50 5.29 42.86 3.62
614 907 0.595053 AATGCTCGCGTCGATCGATT 60.595 50.000 22.50 5.77 42.86 3.34
616 909 1.226575 AAATGCTCGCGTCGATCGA 60.227 52.632 15.15 15.15 42.86 3.59
618 911 0.043822 GTCAAATGCTCGCGTCGATC 60.044 55.000 5.77 0.00 34.61 3.69
619 912 0.458543 AGTCAAATGCTCGCGTCGAT 60.459 50.000 5.77 0.00 34.61 3.59
620 913 1.080772 AGTCAAATGCTCGCGTCGA 60.081 52.632 5.77 2.20 0.00 4.20
621 914 1.057822 CAGTCAAATGCTCGCGTCG 59.942 57.895 5.77 0.00 0.00 5.12
622 915 1.421485 CCAGTCAAATGCTCGCGTC 59.579 57.895 5.77 0.00 0.00 5.19
623 916 2.034879 CCCAGTCAAATGCTCGCGT 61.035 57.895 5.77 0.00 0.00 6.01
624 917 2.787249 CCCAGTCAAATGCTCGCG 59.213 61.111 0.00 0.00 0.00 5.87
625 918 2.486966 GCCCAGTCAAATGCTCGC 59.513 61.111 0.00 0.00 0.00 5.03
646 939 4.017919 CGAATACACGTACTACGACACAG 58.982 47.826 15.49 2.75 46.05 3.66
647 940 3.677596 TCGAATACACGTACTACGACACA 59.322 43.478 15.49 0.00 46.05 3.72
648 941 4.245025 TCGAATACACGTACTACGACAC 57.755 45.455 15.49 0.71 46.05 3.67
649 942 4.625311 TCTTCGAATACACGTACTACGACA 59.375 41.667 15.49 0.48 46.05 4.35
650 943 5.131168 TCTTCGAATACACGTACTACGAC 57.869 43.478 15.49 0.00 46.05 4.34
651 944 4.864806 ACTCTTCGAATACACGTACTACGA 59.135 41.667 15.49 0.00 46.05 3.43
653 946 6.256757 ACCTACTCTTCGAATACACGTACTAC 59.743 42.308 0.00 0.00 34.70 2.73
654 947 6.256539 CACCTACTCTTCGAATACACGTACTA 59.743 42.308 0.00 0.00 34.70 1.82
655 948 5.064452 CACCTACTCTTCGAATACACGTACT 59.936 44.000 0.00 0.00 34.70 2.73
656 949 5.261661 CACCTACTCTTCGAATACACGTAC 58.738 45.833 0.00 0.00 34.70 3.67
659 952 3.106672 GCACCTACTCTTCGAATACACG 58.893 50.000 0.00 0.00 0.00 4.49
664 957 3.895232 ATGTGCACCTACTCTTCGAAT 57.105 42.857 15.69 0.00 0.00 3.34
676 969 2.555199 GGATGAGAGTGTATGTGCACC 58.445 52.381 15.69 0.00 40.04 5.01
679 972 2.988010 TGGGATGAGAGTGTATGTGC 57.012 50.000 0.00 0.00 0.00 4.57
681 974 2.773661 TGCATGGGATGAGAGTGTATGT 59.226 45.455 0.00 0.00 0.00 2.29
682 975 3.480505 TGCATGGGATGAGAGTGTATG 57.519 47.619 0.00 0.00 0.00 2.39
683 976 3.244805 CCATGCATGGGATGAGAGTGTAT 60.245 47.826 34.31 0.00 44.31 2.29
684 977 2.105306 CCATGCATGGGATGAGAGTGTA 59.895 50.000 34.31 0.00 44.31 2.90
685 978 1.133884 CCATGCATGGGATGAGAGTGT 60.134 52.381 34.31 0.00 44.31 3.55
686 979 1.605753 CCATGCATGGGATGAGAGTG 58.394 55.000 34.31 7.78 44.31 3.51
701 994 2.079158 CGTGGATAAGCATAGGCCATG 58.921 52.381 5.01 8.21 42.56 3.66
702 995 1.611673 GCGTGGATAAGCATAGGCCAT 60.612 52.381 5.01 0.00 42.56 4.40
703 996 0.250295 GCGTGGATAAGCATAGGCCA 60.250 55.000 5.01 0.00 42.56 5.36
704 997 0.250295 TGCGTGGATAAGCATAGGCC 60.250 55.000 0.00 0.00 42.56 5.19
705 998 0.868406 GTGCGTGGATAAGCATAGGC 59.132 55.000 0.00 0.00 43.02 3.93
706 999 1.139989 CGTGCGTGGATAAGCATAGG 58.860 55.000 0.00 0.00 43.02 2.57
707 1000 1.787155 GTCGTGCGTGGATAAGCATAG 59.213 52.381 0.00 0.00 43.02 2.23
708 1001 1.135333 TGTCGTGCGTGGATAAGCATA 59.865 47.619 0.00 0.00 43.02 3.14
709 1002 0.108377 TGTCGTGCGTGGATAAGCAT 60.108 50.000 0.00 0.00 43.02 3.79
710 1003 1.011968 GTGTCGTGCGTGGATAAGCA 61.012 55.000 0.00 0.00 38.99 3.91
711 1004 1.708027 GTGTCGTGCGTGGATAAGC 59.292 57.895 0.00 0.00 0.00 3.09
712 1005 0.455464 TCGTGTCGTGCGTGGATAAG 60.455 55.000 0.00 0.00 0.00 1.73
713 1006 0.455464 CTCGTGTCGTGCGTGGATAA 60.455 55.000 0.00 0.00 0.00 1.75
714 1007 1.135939 CTCGTGTCGTGCGTGGATA 59.864 57.895 0.00 0.00 0.00 2.59
715 1008 2.126463 CTCGTGTCGTGCGTGGAT 60.126 61.111 0.00 0.00 0.00 3.41
716 1009 4.994201 GCTCGTGTCGTGCGTGGA 62.994 66.667 0.90 0.00 36.69 4.02
735 1028 2.718220 CTGAACTCAGTCGCTCACG 58.282 57.895 0.00 0.00 39.09 4.35
751 1044 4.646572 AGGAAGAAGGTTTAGCTTGACTG 58.353 43.478 0.00 0.00 0.00 3.51
753 1046 7.506328 TTTAAGGAAGAAGGTTTAGCTTGAC 57.494 36.000 0.00 0.00 0.00 3.18
764 1057 6.313164 GTCCACTCGTTATTTAAGGAAGAAGG 59.687 42.308 0.00 0.00 30.76 3.46
765 1058 7.097834 AGTCCACTCGTTATTTAAGGAAGAAG 58.902 38.462 0.00 0.00 30.76 2.85
767 1060 6.209986 TGAGTCCACTCGTTATTTAAGGAAGA 59.790 38.462 2.31 0.00 45.72 2.87
768 1061 6.395629 TGAGTCCACTCGTTATTTAAGGAAG 58.604 40.000 2.31 0.00 45.72 3.46
852 1740 8.288208 TGCAGCGAGAACTTACTTATATACTAC 58.712 37.037 0.00 0.00 0.00 2.73
923 1812 7.921745 AGCTTCTTTGTCTTTCGGATATACTAC 59.078 37.037 0.00 0.00 0.00 2.73
926 1815 6.074782 CGAGCTTCTTTGTCTTTCGGATATAC 60.075 42.308 0.00 0.00 0.00 1.47
931 1820 2.404215 CGAGCTTCTTTGTCTTTCGGA 58.596 47.619 0.00 0.00 0.00 4.55
932 1821 1.136224 GCGAGCTTCTTTGTCTTTCGG 60.136 52.381 0.00 0.00 0.00 4.30
933 1822 1.460913 CGCGAGCTTCTTTGTCTTTCG 60.461 52.381 0.00 0.00 0.00 3.46
934 1823 1.792949 TCGCGAGCTTCTTTGTCTTTC 59.207 47.619 3.71 0.00 0.00 2.62
935 1824 1.527311 GTCGCGAGCTTCTTTGTCTTT 59.473 47.619 10.24 0.00 0.00 2.52
940 1829 1.388431 GAAGAGTCGCGAGCTTCTTTG 59.612 52.381 29.87 0.00 36.12 2.77
944 1833 0.169230 TCTGAAGAGTCGCGAGCTTC 59.831 55.000 30.21 30.21 38.73 3.86
946 1835 0.380378 GATCTGAAGAGTCGCGAGCT 59.620 55.000 10.24 10.30 0.00 4.09
947 1836 0.927994 CGATCTGAAGAGTCGCGAGC 60.928 60.000 10.24 4.61 0.00 5.03
948 1837 0.653114 TCGATCTGAAGAGTCGCGAG 59.347 55.000 10.24 0.00 35.48 5.03
951 1849 1.261885 TCGATCGATCTGAAGAGTCGC 59.738 52.381 22.43 0.00 35.48 5.19
952 1850 2.542178 ACTCGATCGATCTGAAGAGTCG 59.458 50.000 19.78 8.30 41.71 4.18
957 1855 2.603412 CCGGAACTCGATCGATCTGAAG 60.603 54.545 23.11 17.75 42.43 3.02
960 1858 0.663688 ACCGGAACTCGATCGATCTG 59.336 55.000 19.78 18.17 42.43 2.90
962 1860 0.317938 CCACCGGAACTCGATCGATC 60.318 60.000 19.78 15.68 42.43 3.69
964 1862 1.676635 ACCACCGGAACTCGATCGA 60.677 57.895 18.32 18.32 42.43 3.59
967 1865 1.590147 GACACCACCGGAACTCGAT 59.410 57.895 9.46 0.00 42.43 3.59
986 1884 2.537560 CCCATCGGTGCGCTTGATC 61.538 63.158 9.73 0.00 0.00 2.92
991 1889 3.545124 TTGAACCCATCGGTGCGCT 62.545 57.895 9.73 0.00 43.71 5.92
992 1890 2.622011 TTTGAACCCATCGGTGCGC 61.622 57.895 0.00 0.00 43.71 6.09
993 1891 1.209127 GTTTGAACCCATCGGTGCG 59.791 57.895 0.00 0.00 43.71 5.34
994 1892 0.039527 GTGTTTGAACCCATCGGTGC 60.040 55.000 0.00 0.00 43.71 5.01
995 1893 0.596082 GGTGTTTGAACCCATCGGTG 59.404 55.000 0.00 0.00 43.71 4.94
997 1895 1.873165 CGGTGTTTGAACCCATCGG 59.127 57.895 0.00 0.00 36.84 4.18
998 1896 1.209127 GCGGTGTTTGAACCCATCG 59.791 57.895 0.00 0.00 36.84 3.84
999 1897 1.584495 GGCGGTGTTTGAACCCATC 59.416 57.895 0.00 0.00 36.84 3.51
1001 1899 2.902846 CGGCGGTGTTTGAACCCA 60.903 61.111 0.00 0.00 36.84 4.51
1004 1988 1.278637 CTGTCGGCGGTGTTTGAAC 59.721 57.895 7.21 0.00 0.00 3.18
1031 2015 0.036732 GATATGCTTCGGCCCATGGA 59.963 55.000 15.22 0.00 40.91 3.41
1033 2017 0.877071 GTGATATGCTTCGGCCCATG 59.123 55.000 0.00 0.00 40.91 3.66
1085 2081 4.575885 ACATAAATCGGGCTTGCGTATAT 58.424 39.130 0.00 0.00 0.00 0.86
1089 2085 2.319136 TACATAAATCGGGCTTGCGT 57.681 45.000 0.00 0.00 0.00 5.24
1181 2181 2.956333 ACGCAGTGCCTACATATGAGTA 59.044 45.455 10.38 0.00 42.51 2.59
1182 2182 1.757118 ACGCAGTGCCTACATATGAGT 59.243 47.619 10.38 0.00 42.51 3.41
1184 2184 3.572255 TGATACGCAGTGCCTACATATGA 59.428 43.478 10.38 0.00 45.73 2.15
1188 2188 1.539065 GCTGATACGCAGTGCCTACAT 60.539 52.381 10.11 0.00 46.62 2.29
1189 2189 0.179111 GCTGATACGCAGTGCCTACA 60.179 55.000 10.11 4.30 46.62 2.74
1190 2190 0.103208 AGCTGATACGCAGTGCCTAC 59.897 55.000 10.11 0.00 46.62 3.18
1191 2191 0.824109 AAGCTGATACGCAGTGCCTA 59.176 50.000 10.11 2.50 46.62 3.93
1192 2192 0.460987 GAAGCTGATACGCAGTGCCT 60.461 55.000 10.11 0.00 46.62 4.75
1193 2193 0.740868 TGAAGCTGATACGCAGTGCC 60.741 55.000 10.11 0.00 46.62 5.01
1194 2194 0.649475 CTGAAGCTGATACGCAGTGC 59.351 55.000 4.58 4.58 46.62 4.40
1196 2196 1.821753 AGACTGAAGCTGATACGCAGT 59.178 47.619 0.00 0.00 46.62 4.40
1198 2198 2.095461 AGAGACTGAAGCTGATACGCA 58.905 47.619 0.00 0.00 0.00 5.24
1199 2199 2.857152 CAAGAGACTGAAGCTGATACGC 59.143 50.000 0.00 0.00 0.00 4.42
1200 2200 4.103365 ACAAGAGACTGAAGCTGATACG 57.897 45.455 0.00 0.00 0.00 3.06
1201 2201 6.425114 TGAAAACAAGAGACTGAAGCTGATAC 59.575 38.462 0.00 0.00 0.00 2.24
1202 2202 6.524734 TGAAAACAAGAGACTGAAGCTGATA 58.475 36.000 0.00 0.00 0.00 2.15
1203 2203 5.371526 TGAAAACAAGAGACTGAAGCTGAT 58.628 37.500 0.00 0.00 0.00 2.90
1204 2204 4.769688 TGAAAACAAGAGACTGAAGCTGA 58.230 39.130 0.00 0.00 0.00 4.26
1205 2205 4.813161 TCTGAAAACAAGAGACTGAAGCTG 59.187 41.667 0.00 0.00 0.00 4.24
1206 2206 4.813697 GTCTGAAAACAAGAGACTGAAGCT 59.186 41.667 0.00 0.00 34.47 3.74
1207 2207 4.024472 GGTCTGAAAACAAGAGACTGAAGC 60.024 45.833 0.00 0.00 37.00 3.86
1208 2208 5.363939 AGGTCTGAAAACAAGAGACTGAAG 58.636 41.667 0.00 0.00 37.00 3.02
1209 2209 5.359194 AGGTCTGAAAACAAGAGACTGAA 57.641 39.130 0.00 0.00 37.00 3.02
1210 2210 5.359194 AAGGTCTGAAAACAAGAGACTGA 57.641 39.130 0.00 0.00 37.00 3.41
1211 2211 5.355350 ACAAAGGTCTGAAAACAAGAGACTG 59.645 40.000 0.00 0.00 37.00 3.51
1212 2212 5.501156 ACAAAGGTCTGAAAACAAGAGACT 58.499 37.500 0.00 0.00 37.00 3.24
1213 2213 5.819825 ACAAAGGTCTGAAAACAAGAGAC 57.180 39.130 0.00 0.00 36.22 3.36
1214 2214 8.519799 AAATACAAAGGTCTGAAAACAAGAGA 57.480 30.769 0.00 0.00 0.00 3.10
1215 2215 7.862873 GGAAATACAAAGGTCTGAAAACAAGAG 59.137 37.037 0.00 0.00 0.00 2.85
1216 2216 7.468084 CGGAAATACAAAGGTCTGAAAACAAGA 60.468 37.037 0.00 0.00 0.00 3.02
1217 2217 6.636850 CGGAAATACAAAGGTCTGAAAACAAG 59.363 38.462 0.00 0.00 0.00 3.16
1218 2218 6.095720 ACGGAAATACAAAGGTCTGAAAACAA 59.904 34.615 0.00 0.00 0.00 2.83
1219 2219 5.591067 ACGGAAATACAAAGGTCTGAAAACA 59.409 36.000 0.00 0.00 0.00 2.83
1220 2220 6.068473 ACGGAAATACAAAGGTCTGAAAAC 57.932 37.500 0.00 0.00 0.00 2.43
1221 2221 6.702716 AACGGAAATACAAAGGTCTGAAAA 57.297 33.333 0.00 0.00 0.00 2.29
1222 2222 7.499895 ACTTAACGGAAATACAAAGGTCTGAAA 59.500 33.333 0.00 0.00 0.00 2.69
1223 2223 6.993902 ACTTAACGGAAATACAAAGGTCTGAA 59.006 34.615 0.00 0.00 0.00 3.02
1224 2224 6.425721 CACTTAACGGAAATACAAAGGTCTGA 59.574 38.462 0.00 0.00 0.00 3.27
1225 2225 6.425721 TCACTTAACGGAAATACAAAGGTCTG 59.574 38.462 0.00 0.00 0.00 3.51
1226 2226 6.527423 TCACTTAACGGAAATACAAAGGTCT 58.473 36.000 0.00 0.00 0.00 3.85
1227 2227 6.790285 TCACTTAACGGAAATACAAAGGTC 57.210 37.500 0.00 0.00 0.00 3.85
1228 2228 7.754851 AATCACTTAACGGAAATACAAAGGT 57.245 32.000 0.00 0.00 0.00 3.50
1239 2239 9.116067 CCTTTCCATTAATAATCACTTAACGGA 57.884 33.333 0.00 0.00 30.80 4.69
1240 2240 8.349983 CCCTTTCCATTAATAATCACTTAACGG 58.650 37.037 0.00 0.00 0.00 4.44
1241 2241 8.349983 CCCCTTTCCATTAATAATCACTTAACG 58.650 37.037 0.00 0.00 0.00 3.18
1242 2242 9.416284 TCCCCTTTCCATTAATAATCACTTAAC 57.584 33.333 0.00 0.00 0.00 2.01
1243 2243 9.998752 TTCCCCTTTCCATTAATAATCACTTAA 57.001 29.630 0.00 0.00 0.00 1.85
1244 2244 9.998752 TTTCCCCTTTCCATTAATAATCACTTA 57.001 29.630 0.00 0.00 0.00 2.24
1245 2245 8.909423 TTTCCCCTTTCCATTAATAATCACTT 57.091 30.769 0.00 0.00 0.00 3.16
1246 2246 7.069950 GCTTTCCCCTTTCCATTAATAATCACT 59.930 37.037 0.00 0.00 0.00 3.41
1247 2247 7.210174 GCTTTCCCCTTTCCATTAATAATCAC 58.790 38.462 0.00 0.00 0.00 3.06
1248 2248 6.326323 GGCTTTCCCCTTTCCATTAATAATCA 59.674 38.462 0.00 0.00 0.00 2.57
1249 2249 6.759272 GGCTTTCCCCTTTCCATTAATAATC 58.241 40.000 0.00 0.00 0.00 1.75
1250 2250 6.747414 GGCTTTCCCCTTTCCATTAATAAT 57.253 37.500 0.00 0.00 0.00 1.28
1266 2266 0.753867 TTTTTCCAACCGGGCTTTCC 59.246 50.000 6.32 0.00 36.21 3.13
1267 2267 1.684450 TCTTTTTCCAACCGGGCTTTC 59.316 47.619 6.32 0.00 36.21 2.62
1268 2268 1.783071 TCTTTTTCCAACCGGGCTTT 58.217 45.000 6.32 0.00 36.21 3.51
1269 2269 1.783071 TTCTTTTTCCAACCGGGCTT 58.217 45.000 6.32 0.00 36.21 4.35
1270 2270 1.783071 TTTCTTTTTCCAACCGGGCT 58.217 45.000 6.32 0.00 36.21 5.19
1271 2271 2.605837 TTTTCTTTTTCCAACCGGGC 57.394 45.000 6.32 0.00 36.21 6.13
1272 2272 4.629634 GCATATTTTCTTTTTCCAACCGGG 59.370 41.667 6.32 0.00 38.37 5.73
1273 2273 5.233988 TGCATATTTTCTTTTTCCAACCGG 58.766 37.500 0.00 0.00 0.00 5.28
1274 2274 5.348451 CCTGCATATTTTCTTTTTCCAACCG 59.652 40.000 0.00 0.00 0.00 4.44
1275 2275 5.122239 GCCTGCATATTTTCTTTTTCCAACC 59.878 40.000 0.00 0.00 0.00 3.77
1276 2276 5.700373 TGCCTGCATATTTTCTTTTTCCAAC 59.300 36.000 0.00 0.00 0.00 3.77
1277 2277 5.700373 GTGCCTGCATATTTTCTTTTTCCAA 59.300 36.000 0.00 0.00 0.00 3.53
1278 2278 5.011943 AGTGCCTGCATATTTTCTTTTTCCA 59.988 36.000 0.00 0.00 0.00 3.53
1279 2279 5.349543 CAGTGCCTGCATATTTTCTTTTTCC 59.650 40.000 0.00 0.00 0.00 3.13
1280 2280 6.399204 CAGTGCCTGCATATTTTCTTTTTC 57.601 37.500 0.00 0.00 0.00 2.29
1321 2321 8.535335 GTCCCTGTGATATTGATACATACAGAT 58.465 37.037 0.00 0.00 36.96 2.90
1586 2690 2.278596 CGACATACCGTGGAGGCG 60.279 66.667 0.00 0.00 46.52 5.52
1587 2691 1.226888 GACGACATACCGTGGAGGC 60.227 63.158 0.00 0.00 46.52 4.70
1588 2692 1.063649 CGACGACATACCGTGGAGG 59.936 63.158 0.00 0.00 43.49 4.30
1650 2777 5.666969 TGTTGACCACTATTTTCAAGTCG 57.333 39.130 0.00 0.00 29.97 4.18
1733 2860 3.706594 TGCTTCGTCCTCCTTTCTCATAT 59.293 43.478 0.00 0.00 0.00 1.78
1750 2877 1.181098 TCTTGGCCTTGGCTTGCTTC 61.181 55.000 11.71 0.00 0.00 3.86
1865 3004 2.356227 GGTGGATTGAAGAGGAAGGTCC 60.356 54.545 0.00 0.00 36.58 4.46
1966 3105 1.423541 TGCAGCACCCTTCCTTAAGAA 59.576 47.619 3.36 0.00 34.37 2.52
1975 3114 0.106015 AAGACCTTTGCAGCACCCTT 60.106 50.000 0.00 0.00 0.00 3.95
2147 3286 2.438385 GAATGCCGCGAACGTTGTGT 62.438 55.000 8.23 0.00 37.70 3.72
2188 3327 0.407528 TTCTTGCCAATAGGGTGCCA 59.592 50.000 0.00 0.00 39.65 4.92
2189 3328 0.817654 GTTCTTGCCAATAGGGTGCC 59.182 55.000 0.00 0.00 39.65 5.01
2190 3329 1.544724 TGTTCTTGCCAATAGGGTGC 58.455 50.000 0.00 0.00 39.65 5.01
2195 3334 2.420022 CGGTCCTTGTTCTTGCCAATAG 59.580 50.000 0.00 0.00 0.00 1.73
2196 3335 2.432444 CGGTCCTTGTTCTTGCCAATA 58.568 47.619 0.00 0.00 0.00 1.90
2263 3402 3.250323 CGGATCGTGCAGCTCGTG 61.250 66.667 16.02 2.48 0.00 4.35
2266 3405 3.558411 GTGCGGATCGTGCAGCTC 61.558 66.667 11.11 0.00 44.21 4.09
2271 3410 4.796231 AGACCGTGCGGATCGTGC 62.796 66.667 18.16 1.85 38.96 5.34
2328 3467 2.982488 AGGGTAGCTATAATGCTTGGCT 59.018 45.455 0.00 0.00 43.74 4.75
2378 3520 2.202797 CTGGAGACCGTGCGGATG 60.203 66.667 18.16 0.00 38.96 3.51
2379 3521 4.148825 GCTGGAGACCGTGCGGAT 62.149 66.667 18.16 5.24 38.96 4.18
2382 3524 4.363990 ACTGCTGGAGACCGTGCG 62.364 66.667 2.24 0.00 0.00 5.34
2383 3525 2.740055 CACTGCTGGAGACCGTGC 60.740 66.667 2.24 0.00 0.00 5.34
2384 3526 2.740055 GCACTGCTGGAGACCGTG 60.740 66.667 2.24 0.00 0.00 4.94
2385 3527 4.008933 GGCACTGCTGGAGACCGT 62.009 66.667 2.24 0.00 0.00 4.83
2395 3537 3.503363 CAGCTAAGCCGGCACTGC 61.503 66.667 31.54 26.85 39.43 4.40
2475 3623 7.282675 TCCTGTGGTTTAATAACAAGAAAACGA 59.717 33.333 0.00 0.00 35.92 3.85
2608 3760 9.683069 CAAGCTACAAGAACAGATTTACAAATT 57.317 29.630 0.00 0.00 0.00 1.82
2781 3997 8.924303 ACTCAGTTTTGATGCTATATACCAGTA 58.076 33.333 0.00 0.00 31.68 2.74
2783 3999 8.668510 AACTCAGTTTTGATGCTATATACCAG 57.331 34.615 0.00 0.00 31.68 4.00
2785 4001 8.552034 GTGAACTCAGTTTTGATGCTATATACC 58.448 37.037 0.00 0.00 31.68 2.73
2844 4067 3.902218 TGGGATCAAGAATGGATCCAAC 58.098 45.455 20.67 15.80 44.91 3.77
2927 4154 6.914259 TGCGTGAATATTTTGTTGGATGTAA 58.086 32.000 0.00 0.00 0.00 2.41
2957 4346 8.052141 TGACCAATATGATGTTCTGGTTTGATA 58.948 33.333 0.00 0.00 40.48 2.15
3017 4406 9.953825 GATCGGTAATGTATGAATATTTTCGTC 57.046 33.333 0.00 0.00 34.39 4.20
3070 4459 5.219739 AGAGCTGGTCCTCCATCTTTATTA 58.780 41.667 2.76 0.00 43.43 0.98
3090 4480 7.775561 AGGGTAGAAATATTGTTTGGCTTAGAG 59.224 37.037 0.00 0.00 0.00 2.43
3277 5134 2.086869 CATTGAGTTCGATGCCTTGGT 58.913 47.619 0.00 0.00 31.62 3.67
3290 5147 3.193263 GACATGTCAGCGATCATTGAGT 58.807 45.455 21.07 0.00 0.00 3.41
3335 5192 2.412770 CCTGCAATGGCGTGAAATTTTC 59.587 45.455 2.05 2.05 45.35 2.29


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

AutoCloner maintained by Alex Coulton.