Multiple sequence alignment - TraesCS4B01G282800

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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 TraesCS4B01G282800 chr4B 100.000 5777 0 0 1 5777 566228219 566233995 0.000000e+00 10669.0
1 TraesCS4B01G282800 chr4D 88.992 2698 152 55 3133 5777 453044226 453046831 0.000000e+00 3203.0
2 TraesCS4B01G282800 chr4D 88.928 1418 69 29 729 2113 453042861 453044223 0.000000e+00 1668.0
3 TraesCS4B01G282800 chr4D 89.880 751 43 13 1 726 453042082 453042824 0.000000e+00 935.0
4 TraesCS4B01G282800 chr4D 91.525 59 5 0 3569 3627 481170970 481171028 1.330000e-11 82.4
5 TraesCS4B01G282800 chr4A 87.943 1949 151 54 1 1905 14178193 14176285 0.000000e+00 2220.0
6 TraesCS4B01G282800 chr4A 91.917 1534 75 21 3623 5126 14175712 14174198 0.000000e+00 2100.0
7 TraesCS4B01G282800 chr4A 88.675 415 46 1 3136 3549 14176123 14175709 6.680000e-139 505.0
8 TraesCS4B01G282800 chr4A 81.314 487 26 21 5285 5744 14170085 14169637 9.280000e-88 335.0
9 TraesCS4B01G282800 chr4A 83.459 133 16 5 3145 3276 14175695 14175568 1.020000e-22 119.0
10 TraesCS4B01G282800 chr4A 100.000 28 0 0 581 608 613117424 613117451 1.000000e-02 52.8
11 TraesCS4B01G282800 chr2B 96.981 1027 27 3 2112 3136 128344657 128345681 0.000000e+00 1722.0
12 TraesCS4B01G282800 chr2B 96.004 1026 40 1 2112 3136 744313655 744314680 0.000000e+00 1666.0
13 TraesCS4B01G282800 chr2B 95.988 1022 39 2 2112 3132 733616575 733615555 0.000000e+00 1659.0
14 TraesCS4B01G282800 chr2B 95.793 1022 41 2 2112 3132 733606804 733605784 0.000000e+00 1648.0
15 TraesCS4B01G282800 chr2B 80.000 105 17 3 1674 1777 12845973 12845872 2.230000e-09 75.0
16 TraesCS4B01G282800 chr7B 96.199 1026 38 1 2112 3136 94757224 94758249 0.000000e+00 1677.0
17 TraesCS4B01G282800 chr7B 96.004 1026 40 1 2112 3136 733259383 733258358 0.000000e+00 1666.0
18 TraesCS4B01G282800 chr7B 82.096 229 36 3 4601 4825 741485568 741485341 2.120000e-44 191.0
19 TraesCS4B01G282800 chr7B 83.333 150 23 2 4567 4715 741638305 741638453 2.810000e-28 137.0
20 TraesCS4B01G282800 chr7B 100.000 28 0 0 581 608 724693193 724693166 1.000000e-02 52.8
21 TraesCS4B01G282800 chr5B 96.296 1026 31 5 2112 3136 548457371 548456352 0.000000e+00 1677.0
22 TraesCS4B01G282800 chr1B 95.809 1026 38 4 2112 3136 571495811 571496832 0.000000e+00 1652.0
23 TraesCS4B01G282800 chr1B 94.915 59 3 0 3569 3627 618697636 618697578 6.160000e-15 93.5
24 TraesCS4B01G282800 chr1A 95.424 1027 45 2 2112 3137 19087038 19088063 0.000000e+00 1635.0
25 TraesCS4B01G282800 chr1A 93.103 58 4 0 3569 3626 473033817 473033760 1.030000e-12 86.1
26 TraesCS4B01G282800 chr7D 86.861 137 16 2 4641 4776 634749688 634749823 1.000000e-32 152.0
27 TraesCS4B01G282800 chr7D 84.404 109 12 4 4586 4692 583551862 583551757 1.020000e-17 102.0
28 TraesCS4B01G282800 chr7D 86.022 93 6 6 3542 3627 121937438 121937346 6.160000e-15 93.5
29 TraesCS4B01G282800 chr7D 93.103 58 4 0 3569 3626 151326501 151326444 1.030000e-12 86.1
30 TraesCS4B01G282800 chr7D 93.103 58 4 0 3569 3626 446245062 446245005 1.030000e-12 86.1
31 TraesCS4B01G282800 chr7D 95.455 44 2 0 4149 4192 634756589 634756632 2.890000e-08 71.3
32 TraesCS4B01G282800 chr7D 100.000 28 0 0 581 608 114620421 114620394 1.000000e-02 52.8
33 TraesCS4B01G282800 chr7A 84.314 153 22 1 4563 4715 731673572 731673722 1.300000e-31 148.0
34 TraesCS4B01G282800 chr7A 84.459 148 19 4 4584 4729 731503796 731503941 6.030000e-30 143.0
35 TraesCS4B01G282800 chr7A 76.703 279 44 11 3934 4194 731575172 731575447 1.010000e-27 135.0
36 TraesCS4B01G282800 chr7A 82.051 156 23 5 4540 4692 675028021 675027868 1.690000e-25 128.0
37 TraesCS4B01G282800 chr7A 78.453 181 33 5 4516 4692 675025005 675024827 4.730000e-21 113.0
38 TraesCS4B01G282800 chr5A 93.220 59 4 0 3569 3627 662339329 662339271 2.870000e-13 87.9
39 TraesCS4B01G282800 chr5A 93.103 58 4 0 3569 3626 360079112 360079169 1.030000e-12 86.1
40 TraesCS4B01G282800 chr5A 100.000 28 0 0 581 608 29407206 29407179 1.000000e-02 52.8
41 TraesCS4B01G282800 chr3D 100.000 30 0 0 473 502 365177187 365177158 8.090000e-04 56.5
42 TraesCS4B01G282800 chr3D 100.000 28 0 0 581 608 139339332 139339305 1.000000e-02 52.8
43 TraesCS4B01G282800 chr3A 100.000 28 0 0 581 608 121781160 121781187 1.000000e-02 52.8
44 TraesCS4B01G282800 chr3A 100.000 28 0 0 581 608 187900096 187900069 1.000000e-02 52.8


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 TraesCS4B01G282800 chr4B 566228219 566233995 5776 False 10669.000000 10669 100.000000 1 5777 1 chr4B.!!$F1 5776
1 TraesCS4B01G282800 chr4D 453042082 453046831 4749 False 1935.333333 3203 89.266667 1 5777 3 chr4D.!!$F2 5776
2 TraesCS4B01G282800 chr4A 14174198 14178193 3995 True 1236.000000 2220 87.998500 1 5126 4 chr4A.!!$R2 5125
3 TraesCS4B01G282800 chr2B 128344657 128345681 1024 False 1722.000000 1722 96.981000 2112 3136 1 chr2B.!!$F1 1024
4 TraesCS4B01G282800 chr2B 744313655 744314680 1025 False 1666.000000 1666 96.004000 2112 3136 1 chr2B.!!$F2 1024
5 TraesCS4B01G282800 chr2B 733615555 733616575 1020 True 1659.000000 1659 95.988000 2112 3132 1 chr2B.!!$R3 1020
6 TraesCS4B01G282800 chr2B 733605784 733606804 1020 True 1648.000000 1648 95.793000 2112 3132 1 chr2B.!!$R2 1020
7 TraesCS4B01G282800 chr7B 94757224 94758249 1025 False 1677.000000 1677 96.199000 2112 3136 1 chr7B.!!$F1 1024
8 TraesCS4B01G282800 chr7B 733258358 733259383 1025 True 1666.000000 1666 96.004000 2112 3136 1 chr7B.!!$R2 1024
9 TraesCS4B01G282800 chr5B 548456352 548457371 1019 True 1677.000000 1677 96.296000 2112 3136 1 chr5B.!!$R1 1024
10 TraesCS4B01G282800 chr1B 571495811 571496832 1021 False 1652.000000 1652 95.809000 2112 3136 1 chr1B.!!$F1 1024
11 TraesCS4B01G282800 chr1A 19087038 19088063 1025 False 1635.000000 1635 95.424000 2112 3137 1 chr1A.!!$F1 1025

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
925 1000 0.100861 GTTGTCGTTCCCGCCAAAAA 59.899 50.0 0.00 0.0 33.30 1.94 F
992 1067 0.491371 AGATCCATCTCCTCCCCTCC 59.509 60.0 0.00 0.0 29.30 4.30 F
1778 1882 0.178992 TGAGAAAGTTGGGGCCAGTG 60.179 55.0 4.39 0.0 0.00 3.66 F
3181 3299 0.108945 GCTCCTTGCCATTCACTTGC 60.109 55.0 0.00 0.0 35.15 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1862 0.555769 ACTGGCCCCAACTTTCTCAA 59.444 50.0 0.00 0.00 0.00 3.02 R
2231 2347 0.841289 AACCTCGAACTCCCAACCAA 59.159 50.0 0.00 0.00 0.00 3.67 R
3386 3505 0.388659 GTGAATTTGTGGTGGCAGCA 59.611 50.0 16.56 16.56 0.00 4.41 R
5077 5238 0.178995 TGTCTCAGGGTTGCAATGCA 60.179 50.0 2.72 2.72 36.47 3.96 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
32 33 3.614616 CACACATCCTCGAAAGTCTTAGC 59.385 47.826 0.00 0.00 0.00 3.09
115 117 2.902523 GGAACCTTCTAGCCGGTTTAG 58.097 52.381 14.28 6.04 43.23 1.85
157 170 5.959618 TTCCGATTTTCTTCCTTCTTTCC 57.040 39.130 0.00 0.00 0.00 3.13
173 186 9.434275 TCCTTCTTTCCTTTTATTTTCCTTTCT 57.566 29.630 0.00 0.00 0.00 2.52
390 409 3.275143 TCAACCTTTCTTGACTTCGCAA 58.725 40.909 0.00 0.00 0.00 4.85
406 425 7.918033 TGACTTCGCAAAACTTTTTCATATTCA 59.082 29.630 0.00 0.00 0.00 2.57
439 458 9.861138 TTTAATTCGCAAAATTTTTGTGATCAG 57.139 25.926 28.91 12.87 38.53 2.90
547 577 6.084277 GGACTTTTTCATATTCACGGACAAC 58.916 40.000 0.00 0.00 0.00 3.32
753 822 3.554692 GCGACACGAATGAGCCGG 61.555 66.667 0.00 0.00 0.00 6.13
809 883 3.356529 CCCATAGGCAATATCCAGACC 57.643 52.381 0.00 0.00 0.00 3.85
810 884 2.644299 CCCATAGGCAATATCCAGACCA 59.356 50.000 0.00 0.00 0.00 4.02
811 885 3.560025 CCCATAGGCAATATCCAGACCAC 60.560 52.174 0.00 0.00 0.00 4.16
812 886 3.560025 CCATAGGCAATATCCAGACCACC 60.560 52.174 0.00 0.00 0.00 4.61
813 887 0.469917 AGGCAATATCCAGACCACCG 59.530 55.000 0.00 0.00 0.00 4.94
814 888 0.535102 GGCAATATCCAGACCACCGG 60.535 60.000 0.00 0.00 0.00 5.28
815 889 0.468226 GCAATATCCAGACCACCGGA 59.532 55.000 9.46 0.00 35.27 5.14
816 890 1.541233 GCAATATCCAGACCACCGGAG 60.541 57.143 9.46 0.00 33.97 4.63
817 891 0.759346 AATATCCAGACCACCGGAGC 59.241 55.000 9.46 0.00 33.97 4.70
818 892 0.105453 ATATCCAGACCACCGGAGCT 60.105 55.000 9.46 0.00 33.97 4.09
819 893 0.755698 TATCCAGACCACCGGAGCTC 60.756 60.000 9.46 4.71 33.97 4.09
820 894 2.805313 ATCCAGACCACCGGAGCTCA 62.805 60.000 17.19 0.00 33.97 4.26
821 895 2.575993 CAGACCACCGGAGCTCAG 59.424 66.667 17.19 12.02 0.00 3.35
822 896 1.979155 CAGACCACCGGAGCTCAGA 60.979 63.158 17.19 0.00 0.00 3.27
828 902 0.318441 CACCGGAGCTCAGAAACAGA 59.682 55.000 17.19 0.00 0.00 3.41
884 959 2.508526 CCAGAAACAGAAACAGAGGGG 58.491 52.381 0.00 0.00 0.00 4.79
888 963 4.644685 CAGAAACAGAAACAGAGGGGAAAA 59.355 41.667 0.00 0.00 0.00 2.29
925 1000 0.100861 GTTGTCGTTCCCGCCAAAAA 59.899 50.000 0.00 0.00 33.30 1.94
943 1018 5.064579 CCAAAAAGGAAGCAACAAATCGTTT 59.935 36.000 0.00 0.00 41.22 3.60
992 1067 0.491371 AGATCCATCTCCTCCCCTCC 59.509 60.000 0.00 0.00 29.30 4.30
1241 1325 4.440880 CAGGATGGTGCTAAGAAGAAGAG 58.559 47.826 0.00 0.00 0.00 2.85
1242 1326 3.454082 AGGATGGTGCTAAGAAGAAGAGG 59.546 47.826 0.00 0.00 0.00 3.69
1243 1327 3.452627 GGATGGTGCTAAGAAGAAGAGGA 59.547 47.826 0.00 0.00 0.00 3.71
1251 1335 4.953579 GCTAAGAAGAAGAGGAAGGAGAGA 59.046 45.833 0.00 0.00 0.00 3.10
1278 1362 4.473520 CCCAAGCTCACGCCGGAT 62.474 66.667 5.05 0.00 36.60 4.18
1391 1475 0.877649 CTGCCGATCAACTCCATCCG 60.878 60.000 0.00 0.00 0.00 4.18
1418 1502 6.012508 TGGACAATGAATACCTCCTTTCTCTT 60.013 38.462 0.00 0.00 0.00 2.85
1510 1595 5.230726 GCCGATGCTTTCATTTCTTGTTATG 59.769 40.000 0.00 0.00 31.96 1.90
1517 1602 7.495279 TGCTTTCATTTCTTGTTATGCACTTTT 59.505 29.630 0.00 0.00 0.00 2.27
1551 1636 3.728864 GCATACGTGCCATCAAAAGTCAG 60.729 47.826 0.00 0.00 45.76 3.51
1552 1637 0.593128 ACGTGCCATCAAAAGTCAGC 59.407 50.000 0.00 0.00 0.00 4.26
1555 1640 1.610522 GTGCCATCAAAAGTCAGCACT 59.389 47.619 5.73 0.00 45.40 4.40
1556 1641 1.881973 TGCCATCAAAAGTCAGCACTC 59.118 47.619 0.00 0.00 29.93 3.51
1567 1653 5.854010 AAGTCAGCACTCCGAATAGATAA 57.146 39.130 0.00 0.00 29.93 1.75
1573 1659 7.327275 GTCAGCACTCCGAATAGATAATTGTAG 59.673 40.741 0.00 0.00 0.00 2.74
1584 1670 9.155975 GAATAGATAATTGTAGCCTATGTGTGG 57.844 37.037 0.00 0.00 0.00 4.17
1587 1673 4.301072 AATTGTAGCCTATGTGTGGTGT 57.699 40.909 0.00 0.00 0.00 4.16
1589 1675 4.893829 TTGTAGCCTATGTGTGGTGTAA 57.106 40.909 0.00 0.00 0.00 2.41
1590 1676 5.429681 TTGTAGCCTATGTGTGGTGTAAT 57.570 39.130 0.00 0.00 0.00 1.89
1591 1677 6.547930 TTGTAGCCTATGTGTGGTGTAATA 57.452 37.500 0.00 0.00 0.00 0.98
1592 1678 6.740944 TGTAGCCTATGTGTGGTGTAATAT 57.259 37.500 0.00 0.00 0.00 1.28
1594 1680 7.892609 TGTAGCCTATGTGTGGTGTAATATAG 58.107 38.462 0.00 0.00 0.00 1.31
1607 1711 4.051237 TGTAATATAGCTTGCTCACTGCG 58.949 43.478 0.00 0.00 46.63 5.18
1624 1728 2.346803 TGCGCACTTGTCCTTATTCTC 58.653 47.619 5.66 0.00 0.00 2.87
1639 1743 1.860641 TTCTCATCTCCGTTGGCCTA 58.139 50.000 3.32 0.00 0.00 3.93
1659 1763 7.104290 GGCCTACTAAATGACTTACTGTCTTT 58.896 38.462 0.00 0.00 45.54 2.52
1758 1862 1.334059 CGATCAGTTTGTGCGCAAAGT 60.334 47.619 24.99 24.47 46.01 2.66
1778 1882 0.178992 TGAGAAAGTTGGGGCCAGTG 60.179 55.000 4.39 0.00 0.00 3.66
1825 1930 3.920197 TCCTTTCAGGGTTTCCTTCCATA 59.080 43.478 0.00 0.00 42.67 2.74
1862 1967 8.600449 AAATTGAGTAGTCTTCAGAGAAGTTG 57.400 34.615 6.65 0.00 32.66 3.16
1880 1985 0.850100 TGCAGGGTTTCCTTTCAGGA 59.150 50.000 0.00 0.00 44.10 3.86
1905 2010 2.403252 TTAGCTCTGCAGGGTTAAGC 57.597 50.000 17.96 16.28 0.00 3.09
1946 2056 2.303175 TGGCTTTGTAAAGTCACCACC 58.697 47.619 7.51 0.00 44.93 4.61
1957 2067 7.225011 TGTAAAGTCACCACCAACATATGTTA 58.775 34.615 20.39 0.81 36.32 2.41
1958 2068 7.885922 TGTAAAGTCACCACCAACATATGTTAT 59.114 33.333 20.39 9.47 36.32 1.89
1959 2069 7.391148 AAAGTCACCACCAACATATGTTATC 57.609 36.000 20.39 5.81 36.32 1.75
1960 2070 6.313519 AGTCACCACCAACATATGTTATCT 57.686 37.500 20.39 3.66 36.32 1.98
1961 2071 6.721318 AGTCACCACCAACATATGTTATCTT 58.279 36.000 20.39 3.06 36.32 2.40
1962 2072 7.857456 AGTCACCACCAACATATGTTATCTTA 58.143 34.615 20.39 1.63 36.32 2.10
1963 2073 7.769044 AGTCACCACCAACATATGTTATCTTAC 59.231 37.037 20.39 12.40 36.32 2.34
1964 2074 7.769044 GTCACCACCAACATATGTTATCTTACT 59.231 37.037 20.39 0.00 36.32 2.24
1965 2075 8.983789 TCACCACCAACATATGTTATCTTACTA 58.016 33.333 20.39 1.62 36.32 1.82
1966 2076 9.778741 CACCACCAACATATGTTATCTTACTAT 57.221 33.333 20.39 0.00 36.32 2.12
1967 2077 9.778741 ACCACCAACATATGTTATCTTACTATG 57.221 33.333 20.39 5.43 36.32 2.23
1968 2078 9.219603 CCACCAACATATGTTATCTTACTATGG 57.780 37.037 20.39 15.76 36.32 2.74
1969 2079 8.721478 CACCAACATATGTTATCTTACTATGGC 58.279 37.037 20.39 0.00 36.32 4.40
1970 2080 7.883311 ACCAACATATGTTATCTTACTATGGCC 59.117 37.037 20.39 0.00 36.32 5.36
1971 2081 8.103305 CCAACATATGTTATCTTACTATGGCCT 58.897 37.037 20.39 0.00 36.32 5.19
1972 2082 9.507329 CAACATATGTTATCTTACTATGGCCTT 57.493 33.333 20.39 0.00 36.32 4.35
1974 2084 9.726438 ACATATGTTATCTTACTATGGCCTTTC 57.274 33.333 3.32 0.00 0.00 2.62
1975 2085 9.950496 CATATGTTATCTTACTATGGCCTTTCT 57.050 33.333 3.32 0.00 0.00 2.52
2022 2137 9.241317 CATGATGGCTTTGTAAATCTCAATAAC 57.759 33.333 0.00 0.00 0.00 1.89
2120 2236 5.927115 GTGAACATAAAAAGAGTCTCCTCGT 59.073 40.000 0.00 0.00 42.86 4.18
2231 2347 4.070552 GCTGTCCTTCGGCTCGGT 62.071 66.667 0.00 0.00 44.39 4.69
2258 2374 2.298163 GGGAGTTCGAGGTTGTGAGTTA 59.702 50.000 0.00 0.00 0.00 2.24
2363 2479 0.498685 AGGTTCCCCTCCTCCTCTTT 59.501 55.000 0.00 0.00 35.62 2.52
2546 2663 4.617520 TTGCGGCTGCTCCAACGA 62.618 61.111 20.27 0.00 43.34 3.85
2627 2745 3.555795 CCTTTGAGCTGTTCTGTCTAGCA 60.556 47.826 0.00 0.00 39.84 3.49
2853 2971 1.001764 CCTGTGGAAGATGGCTGCA 60.002 57.895 0.50 0.00 0.00 4.41
3059 3177 8.983702 TGTTTGTAATACTTTGTAAGGTCCTT 57.016 30.769 9.62 9.62 0.00 3.36
3092 3210 2.128771 AAAGTGGCCGTATGCATCTT 57.871 45.000 0.19 0.00 43.89 2.40
3181 3299 0.108945 GCTCCTTGCCATTCACTTGC 60.109 55.000 0.00 0.00 35.15 4.01
3192 3310 5.419788 TGCCATTCACTTGCTCAGAAAATAT 59.580 36.000 0.00 0.00 0.00 1.28
3221 3339 6.064060 TCTCATCAATCTGTTGGTTCTTGTT 58.936 36.000 0.00 0.00 35.99 2.83
3272 3390 9.570488 GAATATGTGTAGAATTACCGTATCCTC 57.430 37.037 0.00 0.00 0.00 3.71
3277 3395 5.468072 TGTAGAATTACCGTATCCTCGAGAC 59.532 44.000 15.71 3.00 0.00 3.36
3278 3396 3.497640 AGAATTACCGTATCCTCGAGACG 59.502 47.826 15.71 15.83 45.15 4.18
3290 3408 3.510360 TCCTCGAGACGATTCTTCCTTTT 59.490 43.478 15.71 0.00 34.61 2.27
3341 3460 0.809241 GAGCAGTCTTCCGAGCATGG 60.809 60.000 0.00 0.00 0.00 3.66
3344 3463 0.803768 CAGTCTTCCGAGCATGGTCG 60.804 60.000 34.22 34.22 39.77 4.79
3363 3482 6.406370 TGGTCGACTGAACTGATTTGATTAT 58.594 36.000 16.46 0.00 31.14 1.28
3386 3505 4.844655 TCTCCTTCAGGGTTAAGTTAAGCT 59.155 41.667 20.88 7.60 36.47 3.74
3435 3554 2.411583 TCACTATGGGATGATGGCTGT 58.588 47.619 0.00 0.00 0.00 4.40
3495 3614 2.722094 ACGATAGGCAATGCAAAAGGA 58.278 42.857 7.79 0.00 43.77 3.36
3556 3676 3.245122 GGACATGAAAAAGTACTCCCCCA 60.245 47.826 0.00 0.00 0.00 4.96
3604 3730 6.359480 ACTTTGTACTAAAGCTGTGACAAC 57.641 37.500 14.06 0.00 0.00 3.32
3645 3771 7.359514 GGGAGTACAACAATACGTCTGTAAAAC 60.360 40.741 0.00 0.00 33.44 2.43
3744 3870 6.072673 CGCAAGATTATGTTTAGGGGGAATAC 60.073 42.308 0.00 0.00 43.02 1.89
3767 3893 6.285990 ACGTGTAGATTTAACTTGTCCTTGT 58.714 36.000 0.00 0.00 0.00 3.16
3847 3990 3.562973 GTGCTTCCATCATGTCAATCGAT 59.437 43.478 0.00 0.00 0.00 3.59
3854 3997 5.882000 TCCATCATGTCAATCGATCTTGTTT 59.118 36.000 0.00 0.00 0.00 2.83
3913 4056 8.497745 TCCTTCCTTATCTTAGAGATGCATTTT 58.502 33.333 0.00 0.00 35.37 1.82
3944 4087 3.829311 AAGGGTTGCCAGAGGGGGA 62.829 63.158 0.00 0.00 37.04 4.81
3970 4113 0.321671 ACACTACTGCATCAACCGCT 59.678 50.000 0.00 0.00 0.00 5.52
4339 4491 2.600731 CTGTTGTCAGCTCTAAGGACG 58.399 52.381 0.00 0.00 34.79 4.79
4344 4496 2.099263 TGTCAGCTCTAAGGACGCATAC 59.901 50.000 0.00 0.00 34.32 2.39
4463 4615 2.492012 CTGAAGCCATGCCTAGACATC 58.508 52.381 0.00 0.00 0.00 3.06
4497 4650 9.199982 CTGTACTCTAGTTACTCTAGTATGAGC 57.800 40.741 9.10 0.42 44.59 4.26
4587 4740 2.032681 GGAGGCGCTGAACAACCT 59.967 61.111 7.64 0.00 34.43 3.50
4696 4849 3.272334 CGCGCATGGAGGCTAACC 61.272 66.667 8.75 0.00 0.00 2.85
4787 4940 0.179029 ACCACCTAAAAGCGTGCAGT 60.179 50.000 0.00 0.00 0.00 4.40
4833 4986 5.611796 TGTTAAGCTGTGTAAGAAGCATG 57.388 39.130 0.00 0.00 42.06 4.06
4834 4987 5.304778 TGTTAAGCTGTGTAAGAAGCATGA 58.695 37.500 0.00 0.00 42.06 3.07
4848 5001 0.238289 GCATGAGTGGTGTGTTTCCG 59.762 55.000 0.00 0.00 0.00 4.30
4850 5003 0.472471 ATGAGTGGTGTGTTTCCGGT 59.528 50.000 0.00 0.00 0.00 5.28
4935 5088 2.290323 GGTGTGGAAGCTGGTAATCTGT 60.290 50.000 0.00 0.00 0.00 3.41
4957 5110 2.727123 TGCCAGAAGAGTTGGTGAAA 57.273 45.000 0.00 0.00 38.02 2.69
4958 5111 3.011566 TGCCAGAAGAGTTGGTGAAAA 57.988 42.857 0.00 0.00 38.02 2.29
4960 5113 2.034685 GCCAGAAGAGTTGGTGAAAACC 59.965 50.000 0.00 0.00 38.02 3.27
4998 5151 1.302192 GGCGGTGGACAAGCTACAA 60.302 57.895 0.00 0.00 0.00 2.41
5003 5156 2.223377 CGGTGGACAAGCTACAAAAGAC 59.777 50.000 0.00 0.00 0.00 3.01
5034 5190 4.024048 CCAAACATGTAGCTGTTTTCTCGT 60.024 41.667 0.00 0.00 44.76 4.18
5075 5236 1.473965 CGCATCTGTTATGGCTCCTGT 60.474 52.381 0.00 0.00 0.00 4.00
5076 5237 2.648059 GCATCTGTTATGGCTCCTGTT 58.352 47.619 0.00 0.00 0.00 3.16
5077 5238 3.019564 GCATCTGTTATGGCTCCTGTTT 58.980 45.455 0.00 0.00 0.00 2.83
5078 5239 3.181493 GCATCTGTTATGGCTCCTGTTTG 60.181 47.826 0.00 0.00 0.00 2.93
5079 5240 2.436417 TCTGTTATGGCTCCTGTTTGC 58.564 47.619 0.00 0.00 0.00 3.68
5097 5258 0.242017 GCATTGCAACCCTGAGACAC 59.758 55.000 0.00 0.00 0.00 3.67
5108 5269 1.287730 CTGAGACACGCAGCAGGAAC 61.288 60.000 0.00 0.00 0.00 3.62
5149 5313 9.642343 TTACTTTATATGAGACCTGAAGCTCTA 57.358 33.333 0.00 0.00 32.44 2.43
5158 5322 5.486526 AGACCTGAAGCTCTAAATGTTGAG 58.513 41.667 0.00 0.00 0.00 3.02
5173 5337 6.906157 AATGTTGAGTGAGAATTGGATTGT 57.094 33.333 0.00 0.00 0.00 2.71
5181 5345 6.624423 AGTGAGAATTGGATTGTTTGTATGC 58.376 36.000 0.00 0.00 0.00 3.14
5183 5347 6.529125 GTGAGAATTGGATTGTTTGTATGCAG 59.471 38.462 0.00 0.00 0.00 4.41
5184 5348 5.969423 AGAATTGGATTGTTTGTATGCAGG 58.031 37.500 0.00 0.00 0.00 4.85
5185 5349 5.481473 AGAATTGGATTGTTTGTATGCAGGT 59.519 36.000 0.00 0.00 0.00 4.00
5186 5350 5.743636 ATTGGATTGTTTGTATGCAGGTT 57.256 34.783 0.00 0.00 0.00 3.50
5187 5351 4.782019 TGGATTGTTTGTATGCAGGTTC 57.218 40.909 0.00 0.00 0.00 3.62
5188 5352 3.190327 TGGATTGTTTGTATGCAGGTTCG 59.810 43.478 0.00 0.00 0.00 3.95
5189 5353 3.190535 GGATTGTTTGTATGCAGGTTCGT 59.809 43.478 0.00 0.00 0.00 3.85
5190 5354 4.393680 GGATTGTTTGTATGCAGGTTCGTA 59.606 41.667 0.00 0.00 0.00 3.43
5191 5355 5.065988 GGATTGTTTGTATGCAGGTTCGTAT 59.934 40.000 0.00 0.00 0.00 3.06
5192 5356 4.937696 TGTTTGTATGCAGGTTCGTATG 57.062 40.909 0.00 0.00 0.00 2.39
5193 5357 3.687212 TGTTTGTATGCAGGTTCGTATGG 59.313 43.478 0.00 0.00 0.00 2.74
5194 5358 3.897141 TTGTATGCAGGTTCGTATGGA 57.103 42.857 0.00 0.00 0.00 3.41
5195 5359 3.897141 TGTATGCAGGTTCGTATGGAA 57.103 42.857 0.00 0.00 0.00 3.53
5227 5391 4.761739 GTCCATCATGAAGAACCTTTGTGA 59.238 41.667 0.00 0.00 0.00 3.58
5228 5392 5.241506 GTCCATCATGAAGAACCTTTGTGAA 59.758 40.000 0.00 0.00 0.00 3.18
5247 5411 0.111253 ATACATTAGCCCTGCCCTGC 59.889 55.000 0.00 0.00 0.00 4.85
5279 5443 1.482748 CCTGCTTTTGGGGCCAACAT 61.483 55.000 4.39 0.00 35.46 2.71
5283 5447 1.881591 CTTTTGGGGCCAACATGTTG 58.118 50.000 28.18 28.18 40.13 3.33
5335 5510 3.477530 ACTGAACCTGAGTAAAGGCAAC 58.522 45.455 0.00 0.00 41.46 4.17
5353 5528 3.305539 GCAACTTGAAATCATCAGTGCCA 60.306 43.478 0.00 0.00 39.77 4.92
5358 5533 2.686405 TGAAATCATCAGTGCCATGAGC 59.314 45.455 0.00 0.00 33.74 4.26
5363 5538 3.954200 TCATCAGTGCCATGAGCTTTAA 58.046 40.909 0.00 0.00 44.23 1.52
5404 5579 8.371699 CCCCAAAAATGGACTTTACATTCTTAA 58.628 33.333 0.00 0.00 37.55 1.85
5405 5580 9.942850 CCCAAAAATGGACTTTACATTCTTAAT 57.057 29.630 0.00 0.00 37.55 1.40
5408 5583 9.435688 AAAAATGGACTTTACATTCTTAATGGC 57.564 29.630 4.78 0.00 43.21 4.40
5409 5584 6.715347 ATGGACTTTACATTCTTAATGGCC 57.285 37.500 0.00 0.00 43.21 5.36
5411 5586 6.252995 TGGACTTTACATTCTTAATGGCCTT 58.747 36.000 3.32 0.00 43.21 4.35
5412 5587 6.152661 TGGACTTTACATTCTTAATGGCCTTG 59.847 38.462 3.32 0.00 43.21 3.61
5413 5588 6.377146 GGACTTTACATTCTTAATGGCCTTGA 59.623 38.462 3.32 0.00 43.21 3.02
5414 5589 7.093945 GGACTTTACATTCTTAATGGCCTTGAA 60.094 37.037 3.32 0.00 43.21 2.69
5415 5590 7.830739 ACTTTACATTCTTAATGGCCTTGAAG 58.169 34.615 9.16 9.16 43.21 3.02
5416 5591 4.725790 ACATTCTTAATGGCCTTGAAGC 57.274 40.909 10.41 0.00 43.21 3.86
5417 5592 4.088634 ACATTCTTAATGGCCTTGAAGCA 58.911 39.130 10.41 0.93 43.21 3.91
5418 5593 4.713321 ACATTCTTAATGGCCTTGAAGCAT 59.287 37.500 10.41 3.28 43.21 3.79
5421 5596 6.395426 TTCTTAATGGCCTTGAAGCATATG 57.605 37.500 10.41 0.00 0.00 1.78
5422 5597 4.828939 TCTTAATGGCCTTGAAGCATATGG 59.171 41.667 10.41 0.00 0.00 2.74
5423 5598 1.335145 ATGGCCTTGAAGCATATGGC 58.665 50.000 3.32 0.00 45.30 4.40
5425 5600 2.811307 GCCTTGAAGCATATGGCCA 58.189 52.632 8.56 8.56 46.50 5.36
5426 5601 1.335145 GCCTTGAAGCATATGGCCAT 58.665 50.000 24.45 24.45 46.50 4.40
5427 5602 1.000506 GCCTTGAAGCATATGGCCATG 59.999 52.381 29.04 15.61 46.50 3.66
5469 5659 2.280797 GACCAACCGAGCAGCACA 60.281 61.111 0.00 0.00 0.00 4.57
5470 5660 2.591715 ACCAACCGAGCAGCACAC 60.592 61.111 0.00 0.00 0.00 3.82
5524 5714 3.625853 TCCAATTTCCGTTATCATGGCA 58.374 40.909 0.00 0.00 0.00 4.92
5527 5717 4.202141 CCAATTTCCGTTATCATGGCATGT 60.202 41.667 25.62 15.77 0.00 3.21
5529 5719 2.998316 TCCGTTATCATGGCATGTCA 57.002 45.000 25.62 0.60 0.00 3.58
5530 5720 3.274095 TCCGTTATCATGGCATGTCAA 57.726 42.857 25.62 17.45 0.00 3.18
5531 5721 3.819368 TCCGTTATCATGGCATGTCAAT 58.181 40.909 25.62 15.10 0.00 2.57
5532 5722 3.565063 TCCGTTATCATGGCATGTCAATG 59.435 43.478 25.62 22.09 36.82 2.82
5533 5723 3.304861 CCGTTATCATGGCATGTCAATGG 60.305 47.826 25.62 25.80 34.09 3.16
5552 5742 2.123726 ATGGCGGGCTCCAAATCC 60.124 61.111 2.38 0.00 39.96 3.01
5561 5751 2.575532 GGCTCCAAATCCATCGAATCA 58.424 47.619 0.00 0.00 0.00 2.57
5584 5774 2.236146 ACTCACCAGGAATCATTGCGTA 59.764 45.455 0.00 0.00 0.00 4.42
5607 5799 1.249407 CCCTCATCGTCCTAGGTAGC 58.751 60.000 9.08 0.00 0.00 3.58
5608 5800 1.478837 CCCTCATCGTCCTAGGTAGCA 60.479 57.143 9.08 0.00 0.00 3.49
5609 5801 1.883275 CCTCATCGTCCTAGGTAGCAG 59.117 57.143 9.08 0.00 0.00 4.24
5610 5802 2.577700 CTCATCGTCCTAGGTAGCAGT 58.422 52.381 9.08 0.00 0.00 4.40
5611 5803 3.496337 CCTCATCGTCCTAGGTAGCAGTA 60.496 52.174 9.08 0.00 0.00 2.74
5612 5804 3.741249 TCATCGTCCTAGGTAGCAGTAG 58.259 50.000 9.08 0.00 0.00 2.57
5616 5808 2.657143 GTCCTAGGTAGCAGTAGCACT 58.343 52.381 9.08 0.00 45.49 4.40
5638 5830 0.036164 TATGCCAAGTTGCCGACTGT 59.964 50.000 0.00 0.00 39.00 3.55
5653 5845 0.593128 ACTGTCTGCAATTTGGTCGC 59.407 50.000 0.00 0.00 0.00 5.19
5654 5846 0.109597 CTGTCTGCAATTTGGTCGCC 60.110 55.000 0.00 0.00 0.00 5.54
5664 5856 1.104577 TTTGGTCGCCTGTGGAAACC 61.105 55.000 0.00 0.00 31.95 3.27
5665 5857 2.112297 GGTCGCCTGTGGAAACCA 59.888 61.111 0.00 0.00 31.73 3.67
5667 5859 1.305930 GGTCGCCTGTGGAAACCATC 61.306 60.000 0.00 0.00 35.28 3.51
5668 5860 0.321653 GTCGCCTGTGGAAACCATCT 60.322 55.000 0.00 0.00 35.28 2.90
5689 5881 3.508840 CCAAATCGAGCCGGCCAC 61.509 66.667 26.15 17.23 0.00 5.01
5690 5882 2.436646 CAAATCGAGCCGGCCACT 60.437 61.111 26.15 3.93 0.00 4.00
5691 5883 1.153449 CAAATCGAGCCGGCCACTA 60.153 57.895 26.15 10.54 0.00 2.74
5692 5884 1.144057 AAATCGAGCCGGCCACTAG 59.856 57.895 26.15 10.46 0.00 2.57
5693 5885 2.311688 AAATCGAGCCGGCCACTAGG 62.312 60.000 26.15 6.22 38.23 3.02
5737 5929 0.884704 TCGAAGCTGAAAGTGCCACC 60.885 55.000 0.00 0.00 35.30 4.61
5752 5944 2.126385 ACCGCGTGCATTGCATTG 60.126 55.556 15.49 11.65 41.91 2.82
5753 5945 3.547313 CCGCGTGCATTGCATTGC 61.547 61.111 23.33 23.33 41.91 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.369471 CCCATTGCTAAGACTTTCGAGGA 60.369 47.826 0.00 0.00 0.00 3.71
114 116 4.937201 AAAAATCGACCAAAAGCTTCCT 57.063 36.364 0.00 0.00 0.00 3.36
137 140 5.966742 AAGGAAAGAAGGAAGAAAATCGG 57.033 39.130 0.00 0.00 0.00 4.18
138 141 9.914131 AATAAAAGGAAAGAAGGAAGAAAATCG 57.086 29.630 0.00 0.00 0.00 3.34
305 321 8.375465 GCGAATTGGAAAATTCATGAAGTAAAG 58.625 33.333 14.54 1.08 38.70 1.85
727 796 2.095617 TCATTCGTGTCGCTCGTTTAGA 60.096 45.455 2.34 0.00 0.00 2.10
753 822 4.154195 ACGGATTATTGCACACTTTCAGTC 59.846 41.667 0.00 0.00 0.00 3.51
801 875 2.039624 AGCTCCGGTGGTCTGGAT 59.960 61.111 0.00 0.00 46.68 3.41
802 876 2.680352 GAGCTCCGGTGGTCTGGA 60.680 66.667 24.51 0.00 45.86 3.86
803 877 2.997315 TGAGCTCCGGTGGTCTGG 60.997 66.667 29.52 3.83 41.27 3.86
804 878 1.536073 TTCTGAGCTCCGGTGGTCTG 61.536 60.000 29.52 28.17 35.68 3.51
805 879 0.832135 TTTCTGAGCTCCGGTGGTCT 60.832 55.000 29.52 9.92 35.68 3.85
806 880 0.670854 GTTTCTGAGCTCCGGTGGTC 60.671 60.000 24.91 24.91 35.28 4.02
807 881 1.371558 GTTTCTGAGCTCCGGTGGT 59.628 57.895 12.15 8.15 0.00 4.16
808 882 0.671781 CTGTTTCTGAGCTCCGGTGG 60.672 60.000 12.15 0.00 0.00 4.61
809 883 0.318441 TCTGTTTCTGAGCTCCGGTG 59.682 55.000 12.15 0.00 0.00 4.94
810 884 0.605589 CTCTGTTTCTGAGCTCCGGT 59.394 55.000 12.15 0.00 0.00 5.28
811 885 0.108424 CCTCTGTTTCTGAGCTCCGG 60.108 60.000 12.15 0.00 0.00 5.14
812 886 0.108424 CCCTCTGTTTCTGAGCTCCG 60.108 60.000 12.15 4.74 0.00 4.63
813 887 1.270907 TCCCTCTGTTTCTGAGCTCC 58.729 55.000 12.15 0.00 0.00 4.70
814 888 3.409026 TTTCCCTCTGTTTCTGAGCTC 57.591 47.619 6.82 6.82 0.00 4.09
815 889 3.328931 TCATTTCCCTCTGTTTCTGAGCT 59.671 43.478 0.00 0.00 0.00 4.09
816 890 3.679389 TCATTTCCCTCTGTTTCTGAGC 58.321 45.455 0.00 0.00 0.00 4.26
817 891 4.639310 CCATCATTTCCCTCTGTTTCTGAG 59.361 45.833 0.00 0.00 0.00 3.35
818 892 4.592942 CCATCATTTCCCTCTGTTTCTGA 58.407 43.478 0.00 0.00 0.00 3.27
819 893 3.129988 GCCATCATTTCCCTCTGTTTCTG 59.870 47.826 0.00 0.00 0.00 3.02
820 894 3.359950 GCCATCATTTCCCTCTGTTTCT 58.640 45.455 0.00 0.00 0.00 2.52
821 895 2.428530 GGCCATCATTTCCCTCTGTTTC 59.571 50.000 0.00 0.00 0.00 2.78
822 896 2.460669 GGCCATCATTTCCCTCTGTTT 58.539 47.619 0.00 0.00 0.00 2.83
828 902 0.935942 TCATGGGCCATCATTTCCCT 59.064 50.000 18.16 0.00 40.69 4.20
884 959 1.215382 GGTTGGCGCCATCCTTTTC 59.785 57.895 38.23 19.04 34.04 2.29
888 963 4.740822 GTGGGTTGGCGCCATCCT 62.741 66.667 41.20 0.00 36.37 3.24
925 1000 3.243737 GGGAAAACGATTTGTTGCTTCCT 60.244 43.478 15.32 0.00 42.96 3.36
943 1018 0.837272 GAATCGGAGTGGATGGGGAA 59.163 55.000 0.00 0.00 0.00 3.97
1077 1152 1.208165 GGTTGGTGGAGGAGGATGGT 61.208 60.000 0.00 0.00 0.00 3.55
1241 1325 2.103340 GCGTCGCTCTCTCCTTCC 59.897 66.667 10.68 0.00 0.00 3.46
1242 1326 2.277628 CGCGTCGCTCTCTCCTTC 60.278 66.667 16.36 0.00 0.00 3.46
1243 1327 3.816524 CCGCGTCGCTCTCTCCTT 61.817 66.667 16.36 0.00 0.00 3.36
1353 1437 1.758440 GCAGGCATACCTCGGATCCA 61.758 60.000 13.41 0.00 46.34 3.41
1373 1457 1.143838 CGGATGGAGTTGATCGGCA 59.856 57.895 0.00 0.00 0.00 5.69
1391 1475 3.933861 AGGAGGTATTCATTGTCCACC 57.066 47.619 0.00 0.00 0.00 4.61
1418 1502 7.623630 TGATCATCTAATTGAACTGGAACTGA 58.376 34.615 0.00 0.00 0.00 3.41
1510 1595 8.173130 ACGTATGCAGTAAATTACTAAAAGTGC 58.827 33.333 5.23 5.70 37.23 4.40
1534 1619 0.592637 TGCTGACTTTTGATGGCACG 59.407 50.000 0.00 0.00 0.00 5.34
1551 1636 5.348997 GGCTACAATTATCTATTCGGAGTGC 59.651 44.000 0.00 0.00 0.00 4.40
1552 1637 6.692486 AGGCTACAATTATCTATTCGGAGTG 58.308 40.000 0.00 0.00 0.00 3.51
1555 1640 8.251026 CACATAGGCTACAATTATCTATTCGGA 58.749 37.037 0.00 0.00 0.00 4.55
1556 1641 8.035394 ACACATAGGCTACAATTATCTATTCGG 58.965 37.037 0.00 0.00 0.00 4.30
1567 1653 5.429681 TTACACCACACATAGGCTACAAT 57.570 39.130 0.00 0.00 0.00 2.71
1573 1659 5.794894 AGCTATATTACACCACACATAGGC 58.205 41.667 0.00 0.00 0.00 3.93
1584 1670 4.084849 CGCAGTGAGCAAGCTATATTACAC 60.085 45.833 0.00 0.00 46.13 2.90
1587 1673 3.059884 GCGCAGTGAGCAAGCTATATTA 58.940 45.455 14.47 0.00 46.13 0.98
1589 1675 1.202568 TGCGCAGTGAGCAAGCTATAT 60.203 47.619 19.79 0.00 46.13 0.86
1590 1676 0.175531 TGCGCAGTGAGCAAGCTATA 59.824 50.000 19.79 0.00 46.13 1.31
1591 1677 1.078918 TGCGCAGTGAGCAAGCTAT 60.079 52.632 19.79 0.00 46.13 2.97
1592 1678 2.029288 GTGCGCAGTGAGCAAGCTA 61.029 57.895 23.56 0.00 46.97 3.32
1594 1680 2.901292 AAGTGCGCAGTGAGCAAGC 61.901 57.895 23.56 12.02 46.97 4.01
1607 1711 4.813697 GGAGATGAGAATAAGGACAAGTGC 59.186 45.833 0.00 0.00 0.00 4.40
1624 1728 3.536956 TTTAGTAGGCCAACGGAGATG 57.463 47.619 5.01 0.00 0.00 2.90
1758 1862 0.555769 ACTGGCCCCAACTTTCTCAA 59.444 50.000 0.00 0.00 0.00 3.02
1778 1882 2.864378 AAGCTTACCCTAACGCGGCC 62.864 60.000 12.47 0.00 0.00 6.13
1880 1985 6.039829 GCTTAACCCTGCAGAGCTAATAAAAT 59.960 38.462 17.39 0.00 0.00 1.82
1905 2010 1.351017 TCTCCTGCCAAAGTAAGGTGG 59.649 52.381 0.00 0.00 38.00 4.61
1946 2056 9.507329 AAGGCCATAGTAAGATAACATATGTTG 57.493 33.333 27.62 10.04 38.90 3.33
1980 2090 6.552350 AGCCATCATGCCATAGTAAGATTTTT 59.448 34.615 0.00 0.00 0.00 1.94
1981 2091 6.073314 AGCCATCATGCCATAGTAAGATTTT 58.927 36.000 0.00 0.00 0.00 1.82
1982 2092 5.638133 AGCCATCATGCCATAGTAAGATTT 58.362 37.500 0.00 0.00 0.00 2.17
1983 2093 5.252586 AGCCATCATGCCATAGTAAGATT 57.747 39.130 0.00 0.00 0.00 2.40
2022 2137 9.395707 GTCATAGAAATATACTACACCAAGTCG 57.604 37.037 0.00 0.00 0.00 4.18
2042 2158 2.820059 TCTATTGCCTGCCGTCATAG 57.180 50.000 0.00 0.00 0.00 2.23
2231 2347 0.841289 AACCTCGAACTCCCAACCAA 59.159 50.000 0.00 0.00 0.00 3.67
2627 2745 3.024547 ACGGCATGTACTGATACAGAGT 58.975 45.455 5.76 0.00 44.51 3.24
3059 3177 9.787435 ATACGGCCACTTTATTAATTATTCTCA 57.213 29.630 2.24 0.00 0.00 3.27
3092 3210 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
3181 3299 7.563888 TTGATGAGAAGGCATATTTTCTGAG 57.436 36.000 0.00 0.00 33.97 3.35
3192 3310 3.245016 ACCAACAGATTGATGAGAAGGCA 60.245 43.478 0.00 0.00 38.15 4.75
3221 3339 6.493115 CCCCATAAACATAATCTTATGCCACA 59.507 38.462 9.34 0.00 43.30 4.17
3272 3390 2.673368 CCCAAAAGGAAGAATCGTCTCG 59.327 50.000 0.00 0.00 38.24 4.04
3277 3395 3.826729 AGGAAACCCAAAAGGAAGAATCG 59.173 43.478 0.00 0.00 39.89 3.34
3278 3396 5.279506 GGAAGGAAACCCAAAAGGAAGAATC 60.280 44.000 0.00 0.00 39.89 2.52
3290 3408 0.482446 ACAGCATGGAAGGAAACCCA 59.518 50.000 0.00 0.00 43.62 4.51
3341 3460 7.043059 GGAGATAATCAAATCAGTTCAGTCGAC 60.043 40.741 7.70 7.70 0.00 4.20
3344 3463 8.729805 AAGGAGATAATCAAATCAGTTCAGTC 57.270 34.615 0.00 0.00 0.00 3.51
3363 3482 4.844655 AGCTTAACTTAACCCTGAAGGAGA 59.155 41.667 0.00 0.00 39.89 3.71
3386 3505 0.388659 GTGAATTTGTGGTGGCAGCA 59.611 50.000 16.56 16.56 0.00 4.41
3456 3575 8.587111 CCTATCGTCATGAAAATATACGTCATG 58.413 37.037 0.00 13.33 46.56 3.07
3457 3576 7.275779 GCCTATCGTCATGAAAATATACGTCAT 59.724 37.037 0.00 0.00 35.21 3.06
3461 3580 6.944557 TGCCTATCGTCATGAAAATATACG 57.055 37.500 0.00 0.00 34.99 3.06
3495 3614 1.534717 AATGTGCTGCAGGCCCTTT 60.535 52.632 17.12 1.31 40.92 3.11
3556 3676 9.338622 GTTGTACTAAAGCTGGTAATATGGATT 57.661 33.333 0.00 0.00 0.00 3.01
3598 3724 6.072649 TCCCTCCGATACATATTAGTTGTCA 58.927 40.000 0.00 0.00 0.00 3.58
3599 3725 6.208994 ACTCCCTCCGATACATATTAGTTGTC 59.791 42.308 0.00 0.00 0.00 3.18
3604 3730 7.176165 TGTTGTACTCCCTCCGATACATATTAG 59.824 40.741 0.00 0.00 0.00 1.73
3615 3741 2.165030 ACGTATTGTTGTACTCCCTCCG 59.835 50.000 0.00 0.00 0.00 4.63
3744 3870 6.590357 CACAAGGACAAGTTAAATCTACACG 58.410 40.000 0.00 0.00 0.00 4.49
3767 3893 9.361315 CAATCAATTGAAATCTGTGAAATAGCA 57.639 29.630 13.09 0.00 40.14 3.49
3810 3945 4.468153 TGGAAGCACCCAAAAACTAAAAGT 59.532 37.500 0.00 0.00 38.00 2.66
3847 3990 5.255397 ACATATGTCCAGGGAAAACAAGA 57.745 39.130 1.41 0.00 0.00 3.02
3854 3997 5.071788 GTGAGGAATACATATGTCCAGGGAA 59.928 44.000 12.68 0.00 33.57 3.97
3913 4056 2.632512 GCAACCCTTTCCTTCAATTCCA 59.367 45.455 0.00 0.00 0.00 3.53
3944 4087 4.100189 GGTTGATGCAGTAGTGTAGGATCT 59.900 45.833 0.00 0.00 0.00 2.75
3970 4113 4.956700 CCTCTGGTATGACTTCTTCCACTA 59.043 45.833 0.00 0.00 0.00 2.74
4111 4254 2.034939 TGCAACAGAGTGAGCAATTTGG 59.965 45.455 0.00 0.00 31.56 3.28
4339 4491 5.347635 TGAATCACACAGAACTTACGTATGC 59.652 40.000 8.29 0.00 0.00 3.14
4344 4496 4.330074 GGGATGAATCACACAGAACTTACG 59.670 45.833 0.00 0.00 0.00 3.18
4353 4505 3.202595 TCATGGATGGGATGAATCACACA 59.797 43.478 0.00 0.00 44.07 3.72
4398 4550 7.543756 TCTGCTACTAACAGTTTTTGCTTTTT 58.456 30.769 0.00 0.00 36.50 1.94
4419 4571 2.693069 ACTGACACTAACAGCATCTGC 58.307 47.619 0.00 0.00 38.74 4.26
4463 4615 7.051623 AGAGTAACTAGAGTACAGAGTCCATG 58.948 42.308 0.00 0.00 0.00 3.66
4493 4646 4.393680 ACTTTTTAATCCGCATAACGCTCA 59.606 37.500 0.00 0.00 41.76 4.26
4497 4650 5.171337 GCATCACTTTTTAATCCGCATAACG 59.829 40.000 0.00 0.00 43.15 3.18
4587 4740 1.834856 CTGCCTCTCTTGGAGCCACA 61.835 60.000 0.00 0.00 40.57 4.17
4787 4940 2.270352 AGGCGGAGTGATTCAAAACA 57.730 45.000 0.00 0.00 0.00 2.83
4833 4986 2.140717 CTTACCGGAAACACACCACTC 58.859 52.381 9.46 0.00 0.00 3.51
4834 4987 1.202722 CCTTACCGGAAACACACCACT 60.203 52.381 9.46 0.00 33.16 4.00
4848 5001 0.331616 ACACCATCTTGGCCCTTACC 59.668 55.000 0.00 0.00 42.67 2.85
4850 5003 1.339631 CGAACACCATCTTGGCCCTTA 60.340 52.381 0.00 0.00 42.67 2.69
4892 5045 5.239087 ACCGGCGAAAGTAAAATGTTTTCTA 59.761 36.000 9.30 0.00 0.00 2.10
4909 5062 4.680237 CAGCTTCCACACCGGCGA 62.680 66.667 9.30 0.00 33.14 5.54
4935 5088 3.011566 TCACCAACTCTTCTGGCAAAA 57.988 42.857 0.00 0.00 37.48 2.44
4957 5110 1.942657 CAGCACAGCAATATAGCGGTT 59.057 47.619 0.00 0.00 40.93 4.44
4958 5111 1.586422 CAGCACAGCAATATAGCGGT 58.414 50.000 0.00 0.00 43.65 5.68
4960 5113 1.262417 CACCAGCACAGCAATATAGCG 59.738 52.381 0.00 0.00 40.15 4.26
4998 5151 4.779696 ACATGTTTGGCCAAAATGTCTTT 58.220 34.783 31.66 20.21 32.23 2.52
5003 5156 3.680937 CAGCTACATGTTTGGCCAAAATG 59.319 43.478 31.92 31.21 31.33 2.32
5076 5237 0.961019 GTCTCAGGGTTGCAATGCAA 59.039 50.000 17.55 17.55 46.80 4.08
5077 5238 0.178995 TGTCTCAGGGTTGCAATGCA 60.179 50.000 2.72 2.72 36.47 3.96
5078 5239 0.242017 GTGTCTCAGGGTTGCAATGC 59.758 55.000 0.59 0.00 0.00 3.56
5079 5240 0.518636 CGTGTCTCAGGGTTGCAATG 59.481 55.000 0.59 0.00 0.00 2.82
5097 5258 2.032549 GCATACATAAGTTCCTGCTGCG 60.033 50.000 0.00 0.00 0.00 5.18
5138 5302 5.240891 TCACTCAACATTTAGAGCTTCAGG 58.759 41.667 0.00 0.00 35.28 3.86
5149 5313 7.294017 ACAATCCAATTCTCACTCAACATTT 57.706 32.000 0.00 0.00 0.00 2.32
5158 5322 6.389091 TGCATACAAACAATCCAATTCTCAC 58.611 36.000 0.00 0.00 0.00 3.51
5173 5337 4.209307 TCCATACGAACCTGCATACAAA 57.791 40.909 0.00 0.00 0.00 2.83
5185 5349 1.338294 ACACGCATGGTTCCATACGAA 60.338 47.619 25.10 0.00 36.87 3.85
5186 5350 0.248012 ACACGCATGGTTCCATACGA 59.752 50.000 25.10 0.00 36.87 3.43
5187 5351 0.650512 GACACGCATGGTTCCATACG 59.349 55.000 19.04 19.04 38.66 3.06
5188 5352 1.014352 GGACACGCATGGTTCCATAC 58.986 55.000 3.88 0.00 0.00 2.39
5189 5353 0.615850 TGGACACGCATGGTTCCATA 59.384 50.000 3.88 0.00 33.64 2.74
5190 5354 0.034186 ATGGACACGCATGGTTCCAT 60.034 50.000 16.24 16.24 39.55 3.41
5191 5355 0.676466 GATGGACACGCATGGTTCCA 60.676 55.000 14.36 14.36 38.94 3.53
5192 5356 0.676466 TGATGGACACGCATGGTTCC 60.676 55.000 0.00 2.55 0.00 3.62
5193 5357 1.064505 CATGATGGACACGCATGGTTC 59.935 52.381 0.00 0.00 36.61 3.62
5194 5358 1.097232 CATGATGGACACGCATGGTT 58.903 50.000 0.00 0.00 36.61 3.67
5195 5359 0.252761 TCATGATGGACACGCATGGT 59.747 50.000 13.57 0.00 39.76 3.55
5196 5360 1.332686 CTTCATGATGGACACGCATGG 59.667 52.381 13.57 0.00 39.76 3.66
5201 5365 2.977914 AGGTTCTTCATGATGGACACG 58.022 47.619 18.92 0.00 0.00 4.49
5227 5391 1.479389 GCAGGGCAGGGCTAATGTATT 60.479 52.381 0.00 0.00 0.00 1.89
5228 5392 0.111253 GCAGGGCAGGGCTAATGTAT 59.889 55.000 0.00 0.00 0.00 2.29
5247 5411 4.142600 CCAAAAGCAGGATAGTTTCTTCGG 60.143 45.833 0.00 0.00 0.00 4.30
5252 5416 2.166459 GCCCCAAAAGCAGGATAGTTTC 59.834 50.000 0.00 0.00 0.00 2.78
5295 5463 1.623811 GTTCTGGTGGCTCCTGTTCTA 59.376 52.381 7.19 0.00 36.66 2.10
5335 5510 4.733815 GCTCATGGCACTGATGATTTCAAG 60.734 45.833 0.00 0.00 41.35 3.02
5346 5521 4.157289 AGAATGTTAAAGCTCATGGCACTG 59.843 41.667 8.58 0.00 44.79 3.66
5353 5528 8.478066 GGGGAATTTAAGAATGTTAAAGCTCAT 58.522 33.333 1.96 0.00 0.00 2.90
5404 5579 1.335145 GCCATATGCTTCAAGGCCAT 58.665 50.000 5.01 0.00 39.42 4.40
5405 5580 2.811307 GCCATATGCTTCAAGGCCA 58.189 52.632 5.01 0.00 39.42 5.36
5407 5582 1.000506 CATGGCCATATGCTTCAAGGC 59.999 52.381 20.30 0.00 44.48 4.35
5416 5591 0.524414 CATCCGTGCATGGCCATATG 59.476 55.000 20.30 13.64 0.00 1.78
5417 5592 0.609957 CCATCCGTGCATGGCCATAT 60.610 55.000 20.30 3.94 37.12 1.78
5418 5593 1.228215 CCATCCGTGCATGGCCATA 60.228 57.895 20.30 0.00 37.12 2.74
5421 5596 1.829533 ATTCCATCCGTGCATGGCC 60.830 57.895 20.86 0.00 42.97 5.36
5422 5597 1.361271 CATTCCATCCGTGCATGGC 59.639 57.895 20.86 0.00 42.97 4.40
5423 5598 2.035421 CCATTCCATCCGTGCATGG 58.965 57.895 19.62 19.62 44.45 3.66
5424 5599 1.361271 GCCATTCCATCCGTGCATG 59.639 57.895 0.00 0.00 0.00 4.06
5425 5600 1.829533 GGCCATTCCATCCGTGCAT 60.830 57.895 0.00 0.00 34.01 3.96
5426 5601 2.440065 GGCCATTCCATCCGTGCA 60.440 61.111 0.00 0.00 34.01 4.57
5427 5602 0.465460 TAAGGCCATTCCATCCGTGC 60.465 55.000 5.01 0.00 37.29 5.34
5428 5603 2.154462 GATAAGGCCATTCCATCCGTG 58.846 52.381 5.01 0.00 37.29 4.94
5469 5659 1.684983 TCCTTTTCGTCCAACTCGAGT 59.315 47.619 13.58 13.58 38.52 4.18
5470 5660 2.059541 GTCCTTTTCGTCCAACTCGAG 58.940 52.381 11.84 11.84 38.52 4.04
5524 5714 2.129146 CCCGCCATGCCATTGACAT 61.129 57.895 0.00 0.00 0.00 3.06
5527 5717 4.445710 AGCCCGCCATGCCATTGA 62.446 61.111 0.00 0.00 0.00 2.57
5533 5723 3.142820 GATTTGGAGCCCGCCATGC 62.143 63.158 0.00 0.00 37.86 4.06
5534 5724 2.492773 GGATTTGGAGCCCGCCATG 61.493 63.158 0.00 0.00 37.86 3.66
5552 5742 3.599343 TCCTGGTGAGTTTGATTCGATG 58.401 45.455 0.00 0.00 0.00 3.84
5561 5751 2.489329 CGCAATGATTCCTGGTGAGTTT 59.511 45.455 0.00 0.00 0.00 2.66
5584 5774 1.051812 CCTAGGACGATGAGGGCATT 58.948 55.000 1.05 0.00 34.11 3.56
5607 5799 4.392921 ACTTGGCATAGTAGTGCTACTG 57.607 45.455 18.97 7.86 45.25 2.74
5608 5800 7.874358 GGCAACTTGGCATAGTAGTGCTACT 62.874 48.000 15.18 15.18 44.24 2.57
5609 5801 3.309954 GCAACTTGGCATAGTAGTGCTAC 59.690 47.826 14.04 1.33 44.45 3.58
5610 5802 3.531538 GCAACTTGGCATAGTAGTGCTA 58.468 45.455 14.04 0.00 44.45 3.49
5611 5803 2.359900 GCAACTTGGCATAGTAGTGCT 58.640 47.619 14.04 0.00 44.45 4.40
5612 5804 1.401905 GGCAACTTGGCATAGTAGTGC 59.598 52.381 10.37 13.42 43.14 4.40
5616 5808 1.553248 AGTCGGCAACTTGGCATAGTA 59.447 47.619 15.09 0.00 43.94 1.82
5638 5830 0.537143 ACAGGCGACCAAATTGCAGA 60.537 50.000 0.00 0.00 39.86 4.26
5653 5845 2.162681 GGTCAAGATGGTTTCCACAGG 58.837 52.381 0.00 0.00 35.80 4.00
5654 5846 2.862541 TGGTCAAGATGGTTTCCACAG 58.137 47.619 0.00 0.00 35.80 3.66
5664 5856 1.328680 CGGCTCGATTTGGTCAAGATG 59.671 52.381 0.00 0.00 0.00 2.90
5665 5857 1.656652 CGGCTCGATTTGGTCAAGAT 58.343 50.000 0.00 0.00 0.00 2.40
5667 5859 1.982073 GCCGGCTCGATTTGGTCAAG 61.982 60.000 22.15 0.00 0.00 3.02
5668 5860 2.038269 GCCGGCTCGATTTGGTCAA 61.038 57.895 22.15 0.00 0.00 3.18
5694 5886 4.263572 TATCCGGGGCGCCATTGG 62.264 66.667 30.85 25.29 0.00 3.16
5695 5887 2.669569 CTATCCGGGGCGCCATTG 60.670 66.667 30.85 16.88 0.00 2.82
5696 5888 4.643387 GCTATCCGGGGCGCCATT 62.643 66.667 30.85 9.92 0.00 3.16
5703 5895 1.168407 TTCGACGTAGCTATCCGGGG 61.168 60.000 0.00 0.00 0.00 5.73
5752 5944 1.661112 GTACGAAGCAAGTCTGGATGC 59.339 52.381 0.00 0.00 42.87 3.91
5753 5945 2.668457 GTGTACGAAGCAAGTCTGGATG 59.332 50.000 0.00 0.00 0.00 3.51
5754 5946 2.299013 TGTGTACGAAGCAAGTCTGGAT 59.701 45.455 0.00 0.00 0.00 3.41
5755 5947 1.684450 TGTGTACGAAGCAAGTCTGGA 59.316 47.619 0.00 0.00 0.00 3.86
5756 5948 2.148916 TGTGTACGAAGCAAGTCTGG 57.851 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.