Multiple sequence alignment - TraesCS2A01G143400

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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 TraesCS2A01G143400 chr2A 100.000 4208 0 0 1 4208 88298259 88294052 0.000000e+00 7771
1 TraesCS2A01G143400 chr2A 82.104 1369 154 49 614 1928 733797728 733796397 0.000000e+00 1086
2 TraesCS2A01G143400 chr2A 81.739 920 108 29 2374 3248 733795564 733794660 0.000000e+00 713
3 TraesCS2A01G143400 chr2B 92.288 1919 96 25 56 1949 141206416 141204525 0.000000e+00 2676
4 TraesCS2A01G143400 chr2B 87.611 1574 110 44 2032 3556 141204526 141202989 0.000000e+00 1748
5 TraesCS2A01G143400 chr2B 82.739 1373 143 48 614 1928 730083372 730082036 0.000000e+00 1136
6 TraesCS2A01G143400 chr2B 87.227 642 59 14 2625 3248 730080314 730079678 0.000000e+00 710
7 TraesCS2A01G143400 chr2B 91.473 258 18 3 3771 4027 141166386 141166132 6.690000e-93 351
8 TraesCS2A01G143400 chr2B 90.686 204 15 4 3555 3757 141202903 141202703 6.930000e-68 268
9 TraesCS2A01G143400 chr2B 93.023 172 6 3 4043 4208 141166148 141165977 3.250000e-61 246
10 TraesCS2A01G143400 chr2B 82.270 141 12 5 2374 2505 730081807 730081671 4.450000e-20 110
11 TraesCS2A01G143400 chr2D 92.702 1521 62 22 207 1693 87840394 87838889 0.000000e+00 2148
12 TraesCS2A01G143400 chr2D 88.178 1641 119 44 2037 3643 87836784 87835185 0.000000e+00 1886
13 TraesCS2A01G143400 chr2D 81.195 1138 122 45 614 1693 600164577 600163474 0.000000e+00 832
14 TraesCS2A01G143400 chr2D 85.171 762 83 16 2763 3518 600162048 600161311 0.000000e+00 754
15 TraesCS2A01G143400 chr2D 83.995 831 77 28 885 1693 600134205 600133409 0.000000e+00 747
16 TraesCS2A01G143400 chr2D 87.652 494 51 6 2757 3248 600131879 600131394 2.200000e-157 566
17 TraesCS2A01G143400 chr2D 92.640 394 25 3 3634 4027 87832032 87831643 7.900000e-157 564
18 TraesCS2A01G143400 chr2D 90.734 259 19 3 1693 1949 87837237 87836982 1.450000e-89 340
19 TraesCS2A01G143400 chr2D 93.678 174 10 1 1751 1924 600132759 600132587 4.170000e-65 259
20 TraesCS2A01G143400 chr2D 95.570 158 7 0 1767 1924 600162844 600162687 1.940000e-63 254
21 TraesCS2A01G143400 chr2D 93.919 148 4 1 4043 4185 87831659 87831512 7.080000e-53 219
22 TraesCS2A01G143400 chr2D 88.000 125 11 4 3852 3975 560153934 560154055 1.220000e-30 145
23 TraesCS2A01G143400 chr1D 89.565 115 10 1 3851 3965 445061656 445061768 1.220000e-30 145
24 TraesCS2A01G143400 chr1D 75.277 271 61 4 2939 3206 392948766 392948499 1.590000e-24 124
25 TraesCS2A01G143400 chr1A 88.696 115 11 1 3851 3965 540323952 540324064 5.670000e-29 139
26 TraesCS2A01G143400 chr6D 88.034 117 12 2 3850 3965 6756745 6756630 2.040000e-28 137
27 TraesCS2A01G143400 chr3D 86.719 128 12 4 3838 3965 380271992 380271870 2.040000e-28 137
28 TraesCS2A01G143400 chr5B 86.154 130 13 5 3850 3977 329149316 329149190 7.340000e-28 135
29 TraesCS2A01G143400 chr5A 86.885 122 12 2 3850 3970 19912110 19911992 2.640000e-27 134


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 TraesCS2A01G143400 chr2A 88294052 88298259 4207 True 7771.000000 7771 100.000000 1 4208 1 chr2A.!!$R1 4207
1 TraesCS2A01G143400 chr2A 733794660 733797728 3068 True 899.500000 1086 81.921500 614 3248 2 chr2A.!!$R2 2634
2 TraesCS2A01G143400 chr2B 141202703 141206416 3713 True 1564.000000 2676 90.195000 56 3757 3 chr2B.!!$R2 3701
3 TraesCS2A01G143400 chr2B 730079678 730083372 3694 True 652.000000 1136 84.078667 614 3248 3 chr2B.!!$R3 2634
4 TraesCS2A01G143400 chr2D 87831512 87840394 8882 True 1031.400000 2148 91.634600 207 4185 5 chr2D.!!$R1 3978
5 TraesCS2A01G143400 chr2D 600161311 600164577 3266 True 613.333333 832 87.312000 614 3518 3 chr2D.!!$R3 2904
6 TraesCS2A01G143400 chr2D 600131394 600134205 2811 True 524.000000 747 88.441667 885 3248 3 chr2D.!!$R2 2363

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
889 934 0.035915 GCTGTTCCTCACTTCCTCCC 60.036 60.0 0.00 0.0 0.0 4.30 F
1155 1245 0.105778 CGGCCTTCTTCTCCATCCTC 59.894 60.0 0.00 0.0 0.0 3.71 F
2062 4909 0.174389 TGCACATGCGTGTTGGTTTT 59.826 45.0 9.37 0.0 45.5 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 7611 1.073923 AGTGGGTGAAAACTAGCAGGG 59.926 52.381 0.0 0.0 0.00 4.45 R
3114 8006 2.437897 CCCCTGCTCTGCACCTTT 59.562 61.111 0.0 0.0 33.79 3.11 R
3690 11839 0.528684 GATCCTGTAGCTGCCGTGTC 60.529 60.000 0.0 0.0 0.00 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
23 24 6.596309 CCCTTAGAAAGCTTCTTTTTCCAT 57.404 37.500 0.00 0.00 41.14 3.41
24 25 6.625362 CCCTTAGAAAGCTTCTTTTTCCATC 58.375 40.000 0.00 0.00 41.14 3.51
25 26 6.317857 CCTTAGAAAGCTTCTTTTTCCATCG 58.682 40.000 0.00 0.00 41.14 3.84
26 27 6.149474 CCTTAGAAAGCTTCTTTTTCCATCGA 59.851 38.462 0.00 0.00 41.14 3.59
27 28 7.148171 CCTTAGAAAGCTTCTTTTTCCATCGAT 60.148 37.037 0.00 0.00 41.14 3.59
28 29 6.581171 AGAAAGCTTCTTTTTCCATCGATT 57.419 33.333 0.00 0.00 36.36 3.34
29 30 6.986250 AGAAAGCTTCTTTTTCCATCGATTT 58.014 32.000 0.00 0.00 36.36 2.17
30 31 7.436933 AGAAAGCTTCTTTTTCCATCGATTTT 58.563 30.769 0.00 0.00 36.36 1.82
31 32 7.928167 AGAAAGCTTCTTTTTCCATCGATTTTT 59.072 29.630 0.00 0.00 36.36 1.94
32 33 7.412137 AAGCTTCTTTTTCCATCGATTTTTG 57.588 32.000 0.00 0.00 0.00 2.44
33 34 5.928264 AGCTTCTTTTTCCATCGATTTTTGG 59.072 36.000 0.00 0.00 0.00 3.28
34 35 5.925969 GCTTCTTTTTCCATCGATTTTTGGA 59.074 36.000 1.24 1.24 40.24 3.53
40 41 5.385509 TTCCATCGATTTTTGGAACCTTC 57.614 39.130 13.05 0.00 44.92 3.46
41 42 4.662278 TCCATCGATTTTTGGAACCTTCT 58.338 39.130 2.94 0.00 39.05 2.85
42 43 5.811190 TCCATCGATTTTTGGAACCTTCTA 58.189 37.500 2.94 0.00 39.05 2.10
43 44 6.242396 TCCATCGATTTTTGGAACCTTCTAA 58.758 36.000 2.94 0.00 39.05 2.10
44 45 6.717540 TCCATCGATTTTTGGAACCTTCTAAA 59.282 34.615 2.94 0.00 39.05 1.85
45 46 7.396055 TCCATCGATTTTTGGAACCTTCTAAAT 59.604 33.333 2.94 0.00 39.05 1.40
46 47 7.702348 CCATCGATTTTTGGAACCTTCTAAATC 59.298 37.037 0.00 0.00 37.47 2.17
47 48 6.837992 TCGATTTTTGGAACCTTCTAAATCG 58.162 36.000 21.28 21.28 43.60 3.34
48 49 6.428771 TCGATTTTTGGAACCTTCTAAATCGT 59.571 34.615 23.39 8.26 43.27 3.73
49 50 6.523201 CGATTTTTGGAACCTTCTAAATCGTG 59.477 38.462 20.27 4.91 41.29 4.35
50 51 6.702716 TTTTTGGAACCTTCTAAATCGTGT 57.297 33.333 0.00 0.00 37.47 4.49
51 52 5.934935 TTTGGAACCTTCTAAATCGTGTC 57.065 39.130 0.00 0.00 33.53 3.67
52 53 3.934068 TGGAACCTTCTAAATCGTGTCC 58.066 45.455 0.00 0.00 0.00 4.02
53 54 3.268330 GGAACCTTCTAAATCGTGTCCC 58.732 50.000 0.00 0.00 0.00 4.46
54 55 3.055312 GGAACCTTCTAAATCGTGTCCCT 60.055 47.826 0.00 0.00 0.00 4.20
97 98 4.518970 ACAAAATTGATACAAGCTGGACGT 59.481 37.500 0.00 0.00 0.00 4.34
99 100 1.438651 TTGATACAAGCTGGACGTGC 58.561 50.000 0.00 0.00 0.00 5.34
103 104 2.077821 TACAAGCTGGACGTGCGACA 62.078 55.000 1.60 0.00 35.28 4.35
104 105 2.356313 AAGCTGGACGTGCGACAG 60.356 61.111 1.60 13.37 35.28 3.51
105 106 3.151958 AAGCTGGACGTGCGACAGT 62.152 57.895 1.60 6.61 34.79 3.55
120 121 2.159585 CGACAGTGCAATGCCGAAATTA 60.160 45.455 18.03 0.00 0.00 1.40
122 123 2.556189 ACAGTGCAATGCCGAAATTACA 59.444 40.909 15.18 0.00 0.00 2.41
126 127 3.925913 GTGCAATGCCGAAATTACAATGT 59.074 39.130 1.53 0.00 0.00 2.71
162 163 5.231991 CCAATAAATATTGCAACAAGGACGC 59.768 40.000 0.00 0.00 41.23 5.19
201 202 0.037326 CGTAGCAGGTTCAAGGCTGA 60.037 55.000 0.00 0.00 38.55 4.26
205 206 2.191400 AGCAGGTTCAAGGCTGATAGA 58.809 47.619 0.00 0.00 36.34 1.98
427 435 3.454375 CGAGGTAGAAACGCCATAATGT 58.546 45.455 0.00 0.00 0.00 2.71
473 481 1.553690 TTCTAGTGGGCTGGGCTGTC 61.554 60.000 0.00 0.00 0.00 3.51
529 538 2.483876 CGGCCCACACTCATATAACAG 58.516 52.381 0.00 0.00 0.00 3.16
659 679 3.899052 TCGTGAGTAATTTCCCCGATT 57.101 42.857 0.00 0.00 0.00 3.34
693 713 8.971073 CCCAAGTAAATCAGGAAAACAATCTAT 58.029 33.333 0.00 0.00 0.00 1.98
782 818 1.207593 GCATGTCGTCACCTTGTGC 59.792 57.895 0.00 0.00 32.98 4.57
809 845 0.106918 AGCCGTTTTCACCTCAACCA 60.107 50.000 0.00 0.00 0.00 3.67
862 907 0.836606 TCAATGGCGATTCCTGGCTA 59.163 50.000 0.00 0.00 35.26 3.93
889 934 0.035915 GCTGTTCCTCACTTCCTCCC 60.036 60.000 0.00 0.00 0.00 4.30
920 965 1.375523 CCCTGCAACCACCGTAGTC 60.376 63.158 0.00 0.00 0.00 2.59
921 966 1.375523 CCTGCAACCACCGTAGTCC 60.376 63.158 0.00 0.00 0.00 3.85
922 967 1.736645 CTGCAACCACCGTAGTCCG 60.737 63.158 0.00 0.00 0.00 4.79
923 968 2.341176 GCAACCACCGTAGTCCGT 59.659 61.111 0.00 0.00 33.66 4.69
924 969 1.177895 TGCAACCACCGTAGTCCGTA 61.178 55.000 0.00 0.00 33.66 4.02
925 970 0.457337 GCAACCACCGTAGTCCGTAG 60.457 60.000 0.00 0.00 33.66 3.51
926 971 0.457337 CAACCACCGTAGTCCGTAGC 60.457 60.000 0.00 0.00 33.66 3.58
927 972 0.610232 AACCACCGTAGTCCGTAGCT 60.610 55.000 0.00 0.00 33.66 3.32
928 973 0.253044 ACCACCGTAGTCCGTAGCTA 59.747 55.000 0.00 0.00 33.66 3.32
929 974 0.942962 CCACCGTAGTCCGTAGCTAG 59.057 60.000 0.00 0.00 33.66 3.42
947 996 1.517475 GCTCCGAAGCTCTTCCGTC 60.517 63.158 4.23 0.00 45.55 4.79
949 998 2.202623 CCGAAGCTCTTCCGTCCG 60.203 66.667 4.23 0.00 36.27 4.79
951 1000 1.080705 CGAAGCTCTTCCGTCCGTT 60.081 57.895 4.23 0.00 36.27 4.44
953 1002 1.069255 GAAGCTCTTCCGTCCGTTTC 58.931 55.000 0.00 0.00 33.64 2.78
956 1005 0.790814 GCTCTTCCGTCCGTTTCTTG 59.209 55.000 0.00 0.00 0.00 3.02
957 1006 1.429463 CTCTTCCGTCCGTTTCTTGG 58.571 55.000 0.00 0.00 0.00 3.61
958 1007 0.754472 TCTTCCGTCCGTTTCTTGGT 59.246 50.000 0.00 0.00 0.00 3.67
961 1010 0.316204 TCCGTCCGTTTCTTGGTCTC 59.684 55.000 0.00 0.00 0.00 3.36
962 1011 0.317479 CCGTCCGTTTCTTGGTCTCT 59.683 55.000 0.00 0.00 0.00 3.10
974 1025 2.103340 GTCTCTTCTCCCTCGCGC 59.897 66.667 0.00 0.00 0.00 6.86
1007 1097 0.745845 ACAGCCTAAGCCATGAAGCG 60.746 55.000 0.00 0.00 41.25 4.68
1009 1099 2.189499 GCCTAAGCCATGAAGCGGG 61.189 63.158 0.00 0.00 38.01 6.13
1155 1245 0.105778 CGGCCTTCTTCTCCATCCTC 59.894 60.000 0.00 0.00 0.00 3.71
1167 1257 2.447379 ATCCTCATCTGCGGGGCT 60.447 61.111 0.00 0.00 0.00 5.19
1512 1623 2.203451 AAACAGGCTGCTGCTGCT 60.203 55.556 26.79 13.03 40.48 4.24
1541 1661 2.101575 CGAGTTAGCGCGCCACTA 59.898 61.111 30.33 11.52 0.00 2.74
1542 1662 2.222217 CGAGTTAGCGCGCCACTAC 61.222 63.158 30.33 19.86 0.00 2.73
1550 1670 4.409218 GCGCCACTACCACGACGA 62.409 66.667 0.00 0.00 0.00 4.20
1888 4541 1.347707 AGCTTCCACCAGATGTTCGAA 59.652 47.619 0.00 0.00 0.00 3.71
1939 4592 0.324923 TATACACACCCGCACTCCCT 60.325 55.000 0.00 0.00 0.00 4.20
1943 4596 2.224159 ACACCCGCACTCCCTTCAT 61.224 57.895 0.00 0.00 0.00 2.57
1947 4600 1.564348 ACCCGCACTCCCTTCATTTAT 59.436 47.619 0.00 0.00 0.00 1.40
1948 4601 2.775384 ACCCGCACTCCCTTCATTTATA 59.225 45.455 0.00 0.00 0.00 0.98
1949 4602 3.139077 CCCGCACTCCCTTCATTTATAC 58.861 50.000 0.00 0.00 0.00 1.47
1950 4603 3.181454 CCCGCACTCCCTTCATTTATACT 60.181 47.826 0.00 0.00 0.00 2.12
1951 4604 4.058817 CCGCACTCCCTTCATTTATACTC 58.941 47.826 0.00 0.00 0.00 2.59
1952 4605 4.058817 CGCACTCCCTTCATTTATACTCC 58.941 47.826 0.00 0.00 0.00 3.85
1953 4606 4.390264 GCACTCCCTTCATTTATACTCCC 58.610 47.826 0.00 0.00 0.00 4.30
1954 4607 4.103311 GCACTCCCTTCATTTATACTCCCT 59.897 45.833 0.00 0.00 0.00 4.20
1955 4608 5.398012 GCACTCCCTTCATTTATACTCCCTT 60.398 44.000 0.00 0.00 0.00 3.95
1956 4609 6.292150 CACTCCCTTCATTTATACTCCCTTC 58.708 44.000 0.00 0.00 0.00 3.46
1957 4610 5.070580 ACTCCCTTCATTTATACTCCCTTCG 59.929 44.000 0.00 0.00 0.00 3.79
1958 4611 4.966805 TCCCTTCATTTATACTCCCTTCGT 59.033 41.667 0.00 0.00 0.00 3.85
1959 4612 5.070047 TCCCTTCATTTATACTCCCTTCGTC 59.930 44.000 0.00 0.00 0.00 4.20
1960 4613 5.070580 CCCTTCATTTATACTCCCTTCGTCT 59.929 44.000 0.00 0.00 0.00 4.18
1961 4614 6.217294 CCTTCATTTATACTCCCTTCGTCTC 58.783 44.000 0.00 0.00 0.00 3.36
1962 4615 6.183360 CCTTCATTTATACTCCCTTCGTCTCA 60.183 42.308 0.00 0.00 0.00 3.27
1963 4616 6.978674 TCATTTATACTCCCTTCGTCTCAT 57.021 37.500 0.00 0.00 0.00 2.90
1964 4617 8.473358 TTCATTTATACTCCCTTCGTCTCATA 57.527 34.615 0.00 0.00 0.00 2.15
1965 4618 8.473358 TCATTTATACTCCCTTCGTCTCATAA 57.527 34.615 0.00 0.00 0.00 1.90
1966 4619 9.090103 TCATTTATACTCCCTTCGTCTCATAAT 57.910 33.333 0.00 0.00 0.00 1.28
1972 4625 9.976776 ATACTCCCTTCGTCTCATAATATAGAA 57.023 33.333 0.00 0.00 0.00 2.10
1973 4626 8.113173 ACTCCCTTCGTCTCATAATATAGAAC 57.887 38.462 0.00 0.00 0.00 3.01
1974 4627 7.094720 ACTCCCTTCGTCTCATAATATAGAACG 60.095 40.741 0.00 0.00 0.00 3.95
1975 4628 6.713903 TCCCTTCGTCTCATAATATAGAACGT 59.286 38.462 0.00 0.00 0.00 3.99
1976 4629 7.230108 TCCCTTCGTCTCATAATATAGAACGTT 59.770 37.037 0.00 0.00 0.00 3.99
1977 4630 7.866393 CCCTTCGTCTCATAATATAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
1978 4631 9.245962 CCTTCGTCTCATAATATAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
1981 4634 8.950961 TCGTCTCATAATATAGAACGTTTTTCG 58.049 33.333 0.46 0.00 46.00 3.46
1982 4635 8.950961 CGTCTCATAATATAGAACGTTTTTCGA 58.049 33.333 0.46 0.00 42.86 3.71
1984 4637 9.791820 TCTCATAATATAGAACGTTTTTCGACA 57.208 29.630 0.46 0.00 42.86 4.35
1985 4638 9.831054 CTCATAATATAGAACGTTTTTCGACAC 57.169 33.333 0.46 0.00 42.86 3.67
1986 4639 9.577110 TCATAATATAGAACGTTTTTCGACACT 57.423 29.630 0.46 0.00 42.86 3.55
1989 4642 8.976986 AATATAGAACGTTTTTCGACACTAGT 57.023 30.769 0.46 0.00 42.86 2.57
1990 4643 6.686130 ATAGAACGTTTTTCGACACTAGTG 57.314 37.500 21.44 21.44 42.86 2.74
1992 4645 5.581605 AGAACGTTTTTCGACACTAGTGTA 58.418 37.500 27.98 11.50 45.05 2.90
1993 4646 5.684626 AGAACGTTTTTCGACACTAGTGTAG 59.315 40.000 27.98 26.46 45.05 2.74
1994 4647 4.925068 ACGTTTTTCGACACTAGTGTAGT 58.075 39.130 27.98 14.12 45.05 2.73
2024 4677 6.693315 AAAACATCTTACATTATGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
2025 4678 5.623956 AACATCTTACATTATGGGACGGA 57.376 39.130 0.00 0.00 0.00 4.69
2026 4679 5.215252 ACATCTTACATTATGGGACGGAG 57.785 43.478 0.00 0.00 0.00 4.63
2027 4680 4.040461 ACATCTTACATTATGGGACGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
2028 4681 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2029 4682 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2030 4683 2.118403 ACATTATGGGACGGAGGGAT 57.882 50.000 0.00 0.00 0.00 3.85
2056 4903 4.326766 GCCGTGCACATGCGTGTT 62.327 61.111 18.64 0.00 45.50 3.32
2062 4909 0.174389 TGCACATGCGTGTTGGTTTT 59.826 45.000 9.37 0.00 45.50 2.43
2141 4989 2.218530 CACACTATCACACACACACACG 59.781 50.000 0.00 0.00 0.00 4.49
2150 5018 1.328986 CACACACACACGCATACAACA 59.671 47.619 0.00 0.00 0.00 3.33
2173 5041 2.663826 AGTGAAGATCAGGTCGAAGC 57.336 50.000 0.00 0.00 0.00 3.86
2184 5053 1.211969 GTCGAAGCTGCGGAGTACA 59.788 57.895 15.70 0.00 0.00 2.90
2328 5830 1.080434 GACCAGTCACTCGTGGAGC 60.080 63.158 0.00 0.00 37.27 4.70
2329 5831 1.806461 GACCAGTCACTCGTGGAGCA 61.806 60.000 0.00 0.00 37.27 4.26
2330 5832 1.367471 CCAGTCACTCGTGGAGCAA 59.633 57.895 0.00 0.00 35.67 3.91
2332 5834 1.143305 CAGTCACTCGTGGAGCAAAG 58.857 55.000 0.00 0.00 32.04 2.77
2335 5837 1.000506 GTCACTCGTGGAGCAAAGGTA 59.999 52.381 0.00 0.00 32.04 3.08
2336 5838 1.000506 TCACTCGTGGAGCAAAGGTAC 59.999 52.381 0.00 0.00 32.04 3.34
2338 5840 1.272769 ACTCGTGGAGCAAAGGTACTC 59.727 52.381 0.00 0.00 31.47 2.59
2339 5841 1.546476 CTCGTGGAGCAAAGGTACTCT 59.454 52.381 0.00 0.00 38.49 3.24
2341 5843 2.490903 TCGTGGAGCAAAGGTACTCTAC 59.509 50.000 0.00 0.00 38.49 2.59
2342 5844 2.492484 CGTGGAGCAAAGGTACTCTACT 59.508 50.000 5.23 0.00 40.94 2.57
2343 5845 3.427773 CGTGGAGCAAAGGTACTCTACTC 60.428 52.174 5.23 0.00 40.94 2.59
2344 5846 3.764972 GTGGAGCAAAGGTACTCTACTCT 59.235 47.826 0.00 0.00 40.22 3.24
2345 5847 4.017808 TGGAGCAAAGGTACTCTACTCTC 58.982 47.826 0.00 0.00 38.49 3.20
2346 5848 4.263994 TGGAGCAAAGGTACTCTACTCTCT 60.264 45.833 0.00 0.00 38.49 3.10
2347 5849 4.337274 GGAGCAAAGGTACTCTACTCTCTC 59.663 50.000 0.00 0.00 38.49 3.20
2348 5850 5.187621 AGCAAAGGTACTCTACTCTCTCT 57.812 43.478 0.00 0.00 38.49 3.10
2349 5851 5.576128 AGCAAAGGTACTCTACTCTCTCTT 58.424 41.667 0.00 0.00 38.49 2.85
2350 5852 6.014012 AGCAAAGGTACTCTACTCTCTCTTT 58.986 40.000 0.00 0.00 38.49 2.52
2351 5853 6.495526 AGCAAAGGTACTCTACTCTCTCTTTT 59.504 38.462 0.00 0.00 38.49 2.27
2352 5854 7.015779 AGCAAAGGTACTCTACTCTCTCTTTTT 59.984 37.037 0.00 0.00 38.49 1.94
2512 7260 1.339610 TCAAAAGTGGAAACGCCCATG 59.660 47.619 0.00 0.00 43.65 3.66
2544 7292 2.481952 CTGGCTAGAACTTGTGCTTCAC 59.518 50.000 0.00 0.00 34.56 3.18
2646 7428 3.625853 TGTCTGGTAGTCATGAGAGAGG 58.374 50.000 0.00 0.00 0.00 3.69
2767 7611 5.048013 CCACTTTAACAACTCCAAGGAATCC 60.048 44.000 0.00 0.00 0.00 3.01
2800 7651 4.715534 TCACCCACTCATTTTAACCAGA 57.284 40.909 0.00 0.00 0.00 3.86
2831 7719 5.263968 TCCTCTCAAGACCACGATTAATC 57.736 43.478 5.30 5.30 0.00 1.75
2845 7733 6.373779 CACGATTAATCATTAGCACCATTCC 58.626 40.000 15.57 0.00 0.00 3.01
2846 7734 6.017192 CACGATTAATCATTAGCACCATTCCA 60.017 38.462 15.57 0.00 0.00 3.53
2849 7738 6.558771 TTAATCATTAGCACCATTCCATCG 57.441 37.500 0.00 0.00 0.00 3.84
2861 7750 4.597507 ACCATTCCATCGATAACCTGGTAT 59.402 41.667 16.09 4.66 34.13 2.73
2863 7752 5.513094 CCATTCCATCGATAACCTGGTATGT 60.513 44.000 15.96 0.00 36.59 2.29
2865 7754 3.576982 TCCATCGATAACCTGGTATGTCC 59.423 47.826 0.00 0.00 0.00 4.02
2878 7767 4.258543 TGGTATGTCCGAATTTTGTCCTC 58.741 43.478 0.00 0.00 39.52 3.71
2993 7885 2.434658 ATCGGCTTCGGCATATCGCA 62.435 55.000 0.00 0.00 45.17 5.10
3114 8006 0.613260 CCGAGGACTTCATGAACCCA 59.387 55.000 19.02 0.00 0.00 4.51
3163 8055 3.706594 ACTCGGTATCAATGTCTCCATGT 59.293 43.478 0.00 0.00 0.00 3.21
3248 8140 3.928727 ACAGTTTTGCTCCATGACATG 57.071 42.857 8.56 8.56 0.00 3.21
3249 8141 3.489355 ACAGTTTTGCTCCATGACATGA 58.511 40.909 17.24 2.55 0.00 3.07
3251 8143 3.504906 CAGTTTTGCTCCATGACATGAGT 59.495 43.478 17.24 0.00 0.00 3.41
3252 8144 3.755378 AGTTTTGCTCCATGACATGAGTC 59.245 43.478 17.24 5.57 45.19 3.36
3253 8145 2.408271 TTGCTCCATGACATGAGTCC 57.592 50.000 17.24 3.18 44.33 3.85
3254 8146 1.278537 TGCTCCATGACATGAGTCCA 58.721 50.000 17.24 5.62 44.33 4.02
3255 8147 1.208776 TGCTCCATGACATGAGTCCAG 59.791 52.381 17.24 5.66 44.33 3.86
3256 8148 1.474677 GCTCCATGACATGAGTCCAGG 60.475 57.143 17.24 0.00 44.33 4.45
3257 8149 2.113807 CTCCATGACATGAGTCCAGGA 58.886 52.381 17.24 2.78 44.33 3.86
3258 8150 2.704596 CTCCATGACATGAGTCCAGGAT 59.295 50.000 17.24 0.00 44.33 3.24
3259 8151 3.899980 CTCCATGACATGAGTCCAGGATA 59.100 47.826 17.24 0.00 44.33 2.59
3260 8152 4.496540 TCCATGACATGAGTCCAGGATAT 58.503 43.478 17.24 0.00 44.33 1.63
3261 8153 5.654370 TCCATGACATGAGTCCAGGATATA 58.346 41.667 17.24 0.00 44.33 0.86
3262 8154 6.266857 TCCATGACATGAGTCCAGGATATAT 58.733 40.000 17.24 0.00 44.33 0.86
3294 8186 4.111375 ACGTATATTGGATCATCGAGGC 57.889 45.455 0.00 0.00 0.00 4.70
3308 8203 2.876091 TCGAGGCTGAAACGATGTAAG 58.124 47.619 0.00 0.00 0.00 2.34
3330 8225 5.933617 AGCTTGGCACATATTCTTCATCTA 58.066 37.500 0.00 0.00 39.30 1.98
3371 8266 3.961408 ACCCAGTAGTGTAGGCATCTAAG 59.039 47.826 0.00 0.00 0.00 2.18
3372 8267 3.243907 CCCAGTAGTGTAGGCATCTAAGC 60.244 52.174 0.00 0.00 0.00 3.09
3376 8271 5.292101 CAGTAGTGTAGGCATCTAAGCAAAC 59.708 44.000 0.00 0.00 35.83 2.93
3386 8283 5.105756 GGCATCTAAGCAAACCAGTAATGTT 60.106 40.000 0.00 0.00 35.83 2.71
3486 8383 8.547894 CACCTTTGACAAGCCTTTTAAATAAAC 58.452 33.333 0.00 0.00 0.00 2.01
3488 8385 7.095816 CCTTTGACAAGCCTTTTAAATAAACCG 60.096 37.037 0.00 0.00 0.00 4.44
3489 8386 6.394025 TGACAAGCCTTTTAAATAAACCGT 57.606 33.333 0.00 0.00 0.00 4.83
3491 8388 6.697892 TGACAAGCCTTTTAAATAAACCGTTG 59.302 34.615 0.00 0.00 0.00 4.10
3492 8389 5.464057 ACAAGCCTTTTAAATAAACCGTTGC 59.536 36.000 0.00 0.00 0.00 4.17
3496 8395 6.708502 AGCCTTTTAAATAAACCGTTGCAAAT 59.291 30.769 0.00 0.00 0.00 2.32
3565 8551 5.359194 AGCCTAGCAAATAAACAGCTAGA 57.641 39.130 19.07 0.00 34.21 2.43
3646 11795 3.446161 CCTCACATGGACAATGCTTGAAT 59.554 43.478 0.00 0.00 40.22 2.57
3660 11809 3.075283 TGCTTGAATTCCACCTTCCCTAA 59.925 43.478 2.27 0.00 0.00 2.69
3668 11817 6.590656 ATTCCACCTTCCCTAATTGATGTA 57.409 37.500 0.00 0.00 0.00 2.29
3690 11839 1.328680 CCGAATCCACGATTTCTGCAG 59.671 52.381 7.63 7.63 31.89 4.41
3729 11878 0.692476 CCACCACTGAGATTGTCCCA 59.308 55.000 0.00 0.00 0.00 4.37
3745 11894 7.993183 AGATTGTCCCATACAGAAATTAACGAT 59.007 33.333 0.00 0.00 39.87 3.73
3759 11908 7.824289 AGAAATTAACGATCTCCAGACAATCAA 59.176 33.333 0.00 0.00 0.00 2.57
3769 11918 4.894784 TCCAGACAATCAAACTCCACTAC 58.105 43.478 0.00 0.00 0.00 2.73
3783 11932 5.892568 ACTCCACTACGACTTCATGAATAC 58.107 41.667 8.96 5.36 0.00 1.89
3807 11956 1.201429 AGAGGAAACCATGGCGAGGT 61.201 55.000 13.04 0.00 42.34 3.85
3831 11980 4.898829 TCTTTTGTCACAAGTGTCCATG 57.101 40.909 0.00 0.00 0.00 3.66
3835 11984 3.011566 TGTCACAAGTGTCCATGGTTT 57.988 42.857 12.58 0.00 0.00 3.27
3836 11985 3.360867 TGTCACAAGTGTCCATGGTTTT 58.639 40.909 12.58 0.00 0.00 2.43
3860 12009 6.659745 TTACATTAGCCGTGGACTACATAT 57.340 37.500 0.00 0.00 0.00 1.78
3874 12023 8.204836 GTGGACTACATATGGAGTAAAATGAGT 58.795 37.037 20.86 0.00 0.00 3.41
3983 12132 9.653516 CAGAGGGATATAGTACTATGATTCCAT 57.346 37.037 26.34 23.26 36.81 3.41
4025 12174 8.262227 AGAATTGGGTCGATTAACAAGTATACA 58.738 33.333 5.50 0.00 0.00 2.29
4026 12175 8.974060 AATTGGGTCGATTAACAAGTATACAT 57.026 30.769 5.50 0.00 0.00 2.29
4027 12176 8.974060 ATTGGGTCGATTAACAAGTATACATT 57.026 30.769 5.50 0.00 0.00 2.71
4028 12177 8.795842 TTGGGTCGATTAACAAGTATACATTT 57.204 30.769 5.50 0.00 0.00 2.32
4029 12178 8.428186 TGGGTCGATTAACAAGTATACATTTC 57.572 34.615 5.50 0.00 0.00 2.17
4030 12179 7.496591 TGGGTCGATTAACAAGTATACATTTCC 59.503 37.037 5.50 0.00 0.00 3.13
4031 12180 7.041576 GGGTCGATTAACAAGTATACATTTCCC 60.042 40.741 5.50 0.00 0.00 3.97
4032 12181 7.306983 GGTCGATTAACAAGTATACATTTCCCG 60.307 40.741 5.50 0.00 0.00 5.14
4033 12182 6.201425 TCGATTAACAAGTATACATTTCCCGC 59.799 38.462 5.50 0.00 0.00 6.13
4034 12183 6.018588 CGATTAACAAGTATACATTTCCCGCA 60.019 38.462 5.50 0.00 0.00 5.69
4035 12184 7.466185 CGATTAACAAGTATACATTTCCCGCAA 60.466 37.037 5.50 0.00 0.00 4.85
4036 12185 5.968528 AACAAGTATACATTTCCCGCAAA 57.031 34.783 5.50 0.00 0.00 3.68
4037 12186 5.968528 ACAAGTATACATTTCCCGCAAAA 57.031 34.783 5.50 0.00 0.00 2.44
4038 12187 6.334102 ACAAGTATACATTTCCCGCAAAAA 57.666 33.333 5.50 0.00 0.00 1.94
4095 12244 4.261572 GCATTGCAAGGTCAAAAGAGTGTA 60.262 41.667 13.30 0.00 0.00 2.90
4163 12317 2.423538 GCGTACCAATGCATTTCCTTCT 59.576 45.455 9.83 0.00 37.58 2.85
4185 12339 5.075067 TCTCATCTCTATCATCACCCCACTA 59.925 44.000 0.00 0.00 0.00 2.74
4186 12340 5.328565 TCATCTCTATCATCACCCCACTAG 58.671 45.833 0.00 0.00 0.00 2.57
4187 12341 5.075067 TCATCTCTATCATCACCCCACTAGA 59.925 44.000 0.00 0.00 0.00 2.43
4188 12342 5.403558 TCTCTATCATCACCCCACTAGAA 57.596 43.478 0.00 0.00 0.00 2.10
4189 12343 5.777449 TCTCTATCATCACCCCACTAGAAA 58.223 41.667 0.00 0.00 0.00 2.52
4190 12344 5.598830 TCTCTATCATCACCCCACTAGAAAC 59.401 44.000 0.00 0.00 0.00 2.78
4191 12345 3.933861 ATCATCACCCCACTAGAAACC 57.066 47.619 0.00 0.00 0.00 3.27
4192 12346 2.915869 TCATCACCCCACTAGAAACCT 58.084 47.619 0.00 0.00 0.00 3.50
4193 12347 2.571653 TCATCACCCCACTAGAAACCTG 59.428 50.000 0.00 0.00 0.00 4.00
4194 12348 0.690762 TCACCCCACTAGAAACCTGC 59.309 55.000 0.00 0.00 0.00 4.85
4195 12349 0.400213 CACCCCACTAGAAACCTGCA 59.600 55.000 0.00 0.00 0.00 4.41
4196 12350 1.145571 ACCCCACTAGAAACCTGCAA 58.854 50.000 0.00 0.00 0.00 4.08
4197 12351 1.710809 ACCCCACTAGAAACCTGCAAT 59.289 47.619 0.00 0.00 0.00 3.56
4198 12352 2.916934 ACCCCACTAGAAACCTGCAATA 59.083 45.455 0.00 0.00 0.00 1.90
4199 12353 3.054361 ACCCCACTAGAAACCTGCAATAG 60.054 47.826 0.00 0.00 0.00 1.73
4200 12354 3.054361 CCCCACTAGAAACCTGCAATAGT 60.054 47.826 0.00 0.00 0.00 2.12
4201 12355 4.163458 CCCCACTAGAAACCTGCAATAGTA 59.837 45.833 0.00 0.00 0.00 1.82
4202 12356 5.163195 CCCCACTAGAAACCTGCAATAGTAT 60.163 44.000 0.00 0.00 0.00 2.12
4203 12357 6.357367 CCCACTAGAAACCTGCAATAGTATT 58.643 40.000 0.00 0.00 0.00 1.89
4204 12358 6.483640 CCCACTAGAAACCTGCAATAGTATTC 59.516 42.308 0.00 0.00 0.00 1.75
4205 12359 7.047891 CCACTAGAAACCTGCAATAGTATTCA 58.952 38.462 0.00 0.00 0.00 2.57
4206 12360 7.716998 CCACTAGAAACCTGCAATAGTATTCAT 59.283 37.037 0.00 0.00 0.00 2.57
4207 12361 9.113838 CACTAGAAACCTGCAATAGTATTCATT 57.886 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.596309 ATGGAAAAAGAAGCTTTCTAAGGG 57.404 37.500 0.00 0.00 39.61 3.95
1 2 6.149474 TCGATGGAAAAAGAAGCTTTCTAAGG 59.851 38.462 0.00 0.00 39.61 2.69
2 3 7.133891 TCGATGGAAAAAGAAGCTTTCTAAG 57.866 36.000 0.00 0.00 39.61 2.18
3 4 7.687941 ATCGATGGAAAAAGAAGCTTTCTAA 57.312 32.000 0.00 0.00 39.61 2.10
4 5 7.687941 AATCGATGGAAAAAGAAGCTTTCTA 57.312 32.000 0.00 0.00 39.61 2.10
5 6 6.581171 AATCGATGGAAAAAGAAGCTTTCT 57.419 33.333 0.00 0.00 43.15 2.52
6 7 7.643528 AAAATCGATGGAAAAAGAAGCTTTC 57.356 32.000 0.00 0.00 32.96 2.62
7 8 7.041848 CCAAAAATCGATGGAAAAAGAAGCTTT 60.042 33.333 0.00 0.00 39.12 3.51
8 9 6.424812 CCAAAAATCGATGGAAAAAGAAGCTT 59.575 34.615 0.00 0.00 39.12 3.74
9 10 5.928264 CCAAAAATCGATGGAAAAAGAAGCT 59.072 36.000 0.00 0.00 39.12 3.74
10 11 5.925969 TCCAAAAATCGATGGAAAAAGAAGC 59.074 36.000 0.00 0.00 42.61 3.86
19 20 4.662278 AGAAGGTTCCAAAAATCGATGGA 58.338 39.130 0.00 0.00 43.84 3.41
20 21 6.509418 TTAGAAGGTTCCAAAAATCGATGG 57.491 37.500 0.00 0.00 38.09 3.51
21 22 7.429340 CGATTTAGAAGGTTCCAAAAATCGATG 59.571 37.037 23.95 0.00 45.40 3.84
22 23 7.120726 ACGATTTAGAAGGTTCCAAAAATCGAT 59.879 33.333 29.03 19.53 45.40 3.59
23 24 6.428771 ACGATTTAGAAGGTTCCAAAAATCGA 59.571 34.615 29.03 0.00 45.40 3.59
24 25 6.523201 CACGATTTAGAAGGTTCCAAAAATCG 59.477 38.462 25.13 25.13 46.39 3.34
25 26 7.368059 ACACGATTTAGAAGGTTCCAAAAATC 58.632 34.615 0.00 10.16 33.06 2.17
26 27 7.284919 ACACGATTTAGAAGGTTCCAAAAAT 57.715 32.000 0.00 0.00 0.00 1.82
27 28 6.238814 GGACACGATTTAGAAGGTTCCAAAAA 60.239 38.462 0.00 0.00 0.00 1.94
28 29 5.239963 GGACACGATTTAGAAGGTTCCAAAA 59.760 40.000 0.00 0.00 0.00 2.44
29 30 4.758165 GGACACGATTTAGAAGGTTCCAAA 59.242 41.667 0.00 0.00 0.00 3.28
30 31 4.320870 GGACACGATTTAGAAGGTTCCAA 58.679 43.478 0.00 0.00 0.00 3.53
31 32 3.307199 GGGACACGATTTAGAAGGTTCCA 60.307 47.826 0.00 0.00 0.00 3.53
32 33 3.055312 AGGGACACGATTTAGAAGGTTCC 60.055 47.826 0.00 0.00 0.00 3.62
33 34 4.203654 AGGGACACGATTTAGAAGGTTC 57.796 45.455 0.00 0.00 0.00 3.62
34 35 4.776308 ACTAGGGACACGATTTAGAAGGTT 59.224 41.667 0.00 0.00 0.00 3.50
35 36 4.351127 ACTAGGGACACGATTTAGAAGGT 58.649 43.478 0.00 0.00 0.00 3.50
36 37 5.340439 AACTAGGGACACGATTTAGAAGG 57.660 43.478 0.00 0.00 0.00 3.46
37 38 5.581085 CCAAACTAGGGACACGATTTAGAAG 59.419 44.000 0.00 0.00 0.00 2.85
38 39 5.246656 TCCAAACTAGGGACACGATTTAGAA 59.753 40.000 0.00 0.00 0.00 2.10
39 40 4.773674 TCCAAACTAGGGACACGATTTAGA 59.226 41.667 0.00 0.00 0.00 2.10
40 41 5.080969 TCCAAACTAGGGACACGATTTAG 57.919 43.478 0.00 0.00 0.00 1.85
50 51 1.180456 TCGTGCGTCCAAACTAGGGA 61.180 55.000 0.00 0.00 0.00 4.20
51 52 1.012486 GTCGTGCGTCCAAACTAGGG 61.012 60.000 0.00 0.00 0.00 3.53
52 53 1.342082 CGTCGTGCGTCCAAACTAGG 61.342 60.000 0.00 0.00 35.54 3.02
53 54 1.941476 GCGTCGTGCGTCCAAACTAG 61.941 60.000 0.00 0.00 43.66 2.57
54 55 2.017783 GCGTCGTGCGTCCAAACTA 61.018 57.895 0.00 0.00 43.66 2.24
72 73 6.128282 ACGTCCAGCTTGTATCAATTTTGTAG 60.128 38.462 0.00 0.00 0.00 2.74
74 75 4.518970 ACGTCCAGCTTGTATCAATTTTGT 59.481 37.500 0.00 0.00 0.00 2.83
97 98 3.725459 CGGCATTGCACTGTCGCA 61.725 61.111 18.18 1.65 37.44 5.10
99 100 0.168788 ATTTCGGCATTGCACTGTCG 59.831 50.000 23.28 23.28 45.28 4.35
103 104 3.932545 TTGTAATTTCGGCATTGCACT 57.067 38.095 11.39 0.00 29.54 4.40
104 105 3.925913 ACATTGTAATTTCGGCATTGCAC 59.074 39.130 11.39 0.00 29.54 4.57
105 106 4.185467 ACATTGTAATTTCGGCATTGCA 57.815 36.364 11.39 0.00 0.00 4.08
138 139 5.231991 GCGTCCTTGTTGCAATATTTATTGG 59.768 40.000 0.59 0.00 42.46 3.16
162 163 1.594862 GACTAGCCTTGTAGCATTGCG 59.405 52.381 2.38 0.00 34.23 4.85
188 189 3.950395 GCATTTCTATCAGCCTTGAACCT 59.050 43.478 0.00 0.00 36.78 3.50
240 241 7.093992 GGTATCCATATCTCTCTGTTGTAAGC 58.906 42.308 0.00 0.00 0.00 3.09
365 366 7.202526 TCAACACCATCTCAACAATTTTTCTC 58.797 34.615 0.00 0.00 0.00 2.87
366 367 7.111247 TCAACACCATCTCAACAATTTTTCT 57.889 32.000 0.00 0.00 0.00 2.52
427 435 0.618458 AGCGACCCTCTAAAATGGCA 59.382 50.000 0.00 0.00 0.00 4.92
473 481 4.109050 GGCTTTCTAGTCGTTCTGATGAG 58.891 47.826 0.00 0.00 0.00 2.90
659 679 5.991861 TCCTGATTTACTTGGGCGTTTATA 58.008 37.500 0.00 0.00 0.00 0.98
693 713 6.012337 TGGATGATGTGCTAATTAGGGAAA 57.988 37.500 14.28 0.00 0.00 3.13
782 818 0.868406 GTGAAAACGGCTGTCTCTGG 59.132 55.000 0.00 0.00 0.00 3.86
889 934 4.104102 TGGTTGCAGGGGGTTTATATAGAG 59.896 45.833 0.00 0.00 0.00 2.43
947 996 2.613223 GGGAGAAGAGACCAAGAAACGG 60.613 54.545 0.00 0.00 0.00 4.44
949 998 3.615351 CGAGGGAGAAGAGACCAAGAAAC 60.615 52.174 0.00 0.00 0.00 2.78
951 1000 2.171840 CGAGGGAGAAGAGACCAAGAA 58.828 52.381 0.00 0.00 0.00 2.52
953 1002 0.174617 GCGAGGGAGAAGAGACCAAG 59.825 60.000 0.00 0.00 0.00 3.61
956 1005 2.802106 CGCGAGGGAGAAGAGACC 59.198 66.667 0.00 0.00 0.00 3.85
957 1006 2.103340 GCGCGAGGGAGAAGAGAC 59.897 66.667 12.10 0.00 0.00 3.36
958 1007 3.141488 GGCGCGAGGGAGAAGAGA 61.141 66.667 12.10 0.00 0.00 3.10
961 1010 2.279784 GATGGCGCGAGGGAGAAG 60.280 66.667 12.10 0.00 0.00 2.85
962 1011 4.207281 CGATGGCGCGAGGGAGAA 62.207 66.667 12.10 0.00 0.00 2.87
974 1025 4.838152 CTGTCGGGTGGGCGATGG 62.838 72.222 0.00 0.00 0.00 3.51
985 1040 0.107703 TTCATGGCTTAGGCTGTCGG 60.108 55.000 7.43 0.00 38.73 4.79
1155 1245 2.033141 CCCATAGCCCCGCAGATG 59.967 66.667 0.00 0.00 0.00 2.90
1263 1353 3.325201 GAACCCCGTGGCGAGGATT 62.325 63.158 0.00 0.00 33.59 3.01
1540 1660 2.747460 CTCCCCGTCGTCGTGGTA 60.747 66.667 3.42 0.00 36.09 3.25
1888 4541 2.772924 CCACCAAGGCCCATTCCT 59.227 61.111 0.00 0.00 38.31 3.36
1939 4592 6.785337 TGAGACGAAGGGAGTATAAATGAA 57.215 37.500 0.00 0.00 0.00 2.57
1947 4600 9.228949 GTTCTATATTATGAGACGAAGGGAGTA 57.771 37.037 0.00 0.00 0.00 2.59
1948 4601 7.094720 CGTTCTATATTATGAGACGAAGGGAGT 60.095 40.741 0.00 0.00 0.00 3.85
1949 4602 7.094720 ACGTTCTATATTATGAGACGAAGGGAG 60.095 40.741 11.75 0.00 0.00 4.30
1950 4603 6.713903 ACGTTCTATATTATGAGACGAAGGGA 59.286 38.462 11.75 0.00 0.00 4.20
1951 4604 6.910995 ACGTTCTATATTATGAGACGAAGGG 58.089 40.000 11.75 0.00 0.00 3.95
1952 4605 8.798748 AAACGTTCTATATTATGAGACGAAGG 57.201 34.615 0.00 0.00 0.00 3.46
1955 4608 8.950961 CGAAAAACGTTCTATATTATGAGACGA 58.049 33.333 0.00 0.00 37.22 4.20
1956 4609 8.950961 TCGAAAAACGTTCTATATTATGAGACG 58.049 33.333 0.00 0.00 43.13 4.18
1958 4611 9.791820 TGTCGAAAAACGTTCTATATTATGAGA 57.208 29.630 0.00 0.00 43.13 3.27
1959 4612 9.831054 GTGTCGAAAAACGTTCTATATTATGAG 57.169 33.333 0.00 0.00 43.13 2.90
1960 4613 9.577110 AGTGTCGAAAAACGTTCTATATTATGA 57.423 29.630 0.00 0.00 43.13 2.15
1964 4617 8.857216 CACTAGTGTCGAAAAACGTTCTATATT 58.143 33.333 15.06 0.00 43.13 1.28
1965 4618 8.025445 ACACTAGTGTCGAAAAACGTTCTATAT 58.975 33.333 22.95 0.00 40.24 0.86
1966 4619 7.362662 ACACTAGTGTCGAAAAACGTTCTATA 58.637 34.615 22.95 0.00 40.24 1.31
1967 4620 6.211515 ACACTAGTGTCGAAAAACGTTCTAT 58.788 36.000 22.95 0.00 40.24 1.98
1968 4621 5.581605 ACACTAGTGTCGAAAAACGTTCTA 58.418 37.500 22.95 0.00 40.24 2.10
1969 4622 4.427312 ACACTAGTGTCGAAAAACGTTCT 58.573 39.130 22.95 0.00 40.24 3.01
1970 4623 4.766969 ACACTAGTGTCGAAAAACGTTC 57.233 40.909 22.95 0.00 40.24 3.95
1971 4624 5.343249 ACTACACTAGTGTCGAAAAACGTT 58.657 37.500 31.11 5.64 43.74 3.99
1972 4625 4.925068 ACTACACTAGTGTCGAAAAACGT 58.075 39.130 31.11 13.23 43.74 3.99
2000 4653 6.887545 TCCGTCCCATAATGTAAGATGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
2001 4654 6.419791 TCCGTCCCATAATGTAAGATGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
2002 4655 5.996644 TCCGTCCCATAATGTAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
2003 4656 5.454755 CCTCCGTCCCATAATGTAAGATGTT 60.455 44.000 0.00 0.00 0.00 2.71
2004 4657 4.040461 CCTCCGTCCCATAATGTAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
2005 4658 4.563580 CCCTCCGTCCCATAATGTAAGATG 60.564 50.000 0.00 0.00 0.00 2.90
2006 4659 3.583086 CCCTCCGTCCCATAATGTAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
2007 4660 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2008 4661 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2009 4662 3.049108 TCCCTCCGTCCCATAATGTAA 57.951 47.619 0.00 0.00 0.00 2.41
2010 4663 2.779429 TCCCTCCGTCCCATAATGTA 57.221 50.000 0.00 0.00 0.00 2.29
2011 4664 2.118403 ATCCCTCCGTCCCATAATGT 57.882 50.000 0.00 0.00 0.00 2.71
2012 4665 3.583086 ACTAATCCCTCCGTCCCATAATG 59.417 47.826 0.00 0.00 0.00 1.90
2013 4666 3.870559 ACTAATCCCTCCGTCCCATAAT 58.129 45.455 0.00 0.00 0.00 1.28
2014 4667 3.339713 ACTAATCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2015 4668 3.339713 AACTAATCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
2016 4669 2.191981 AACTAATCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
2017 4670 2.852714 TAACTAATCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
2018 4671 3.806157 GCAATAACTAATCCCTCCGTCCC 60.806 52.174 0.00 0.00 0.00 4.46
2019 4672 3.400255 GCAATAACTAATCCCTCCGTCC 58.600 50.000 0.00 0.00 0.00 4.79
2020 4673 3.400255 GGCAATAACTAATCCCTCCGTC 58.600 50.000 0.00 0.00 0.00 4.79
2021 4674 2.224209 CGGCAATAACTAATCCCTCCGT 60.224 50.000 0.00 0.00 0.00 4.69
2022 4675 2.224209 ACGGCAATAACTAATCCCTCCG 60.224 50.000 0.00 0.00 40.09 4.63
2023 4676 3.139077 CACGGCAATAACTAATCCCTCC 58.861 50.000 0.00 0.00 0.00 4.30
2024 4677 2.548480 GCACGGCAATAACTAATCCCTC 59.452 50.000 0.00 0.00 0.00 4.30
2025 4678 2.092646 TGCACGGCAATAACTAATCCCT 60.093 45.455 0.00 0.00 34.76 4.20
2026 4679 2.032924 GTGCACGGCAATAACTAATCCC 59.967 50.000 0.00 0.00 41.47 3.85
2027 4680 2.680841 TGTGCACGGCAATAACTAATCC 59.319 45.455 13.13 0.00 41.47 3.01
2028 4681 4.282068 CATGTGCACGGCAATAACTAATC 58.718 43.478 13.13 0.00 41.47 1.75
2029 4682 3.489059 GCATGTGCACGGCAATAACTAAT 60.489 43.478 23.55 0.70 41.47 1.73
2030 4683 2.159448 GCATGTGCACGGCAATAACTAA 60.159 45.455 23.55 0.00 41.47 2.24
2056 4903 5.009210 ACAAAGCTCGCAACTATAAAAACCA 59.991 36.000 0.00 0.00 0.00 3.67
2062 4909 4.311606 TGTGACAAAGCTCGCAACTATAA 58.688 39.130 0.00 0.00 0.00 0.98
2100 4947 5.567534 GTGTGTTTACATTGTAATTGGCGAG 59.432 40.000 9.95 0.00 39.39 5.03
2141 4989 5.419542 TGATCTTCACTAGGTGTTGTATGC 58.580 41.667 0.00 0.00 34.79 3.14
2150 5018 3.367646 TCGACCTGATCTTCACTAGGT 57.632 47.619 0.00 0.00 45.77 3.08
2173 5041 6.504398 TCTGATTATTAGTTGTACTCCGCAG 58.496 40.000 0.00 0.00 0.00 5.18
2350 5852 5.417580 AGAGTAGCACCTTTGTGTTCAAAAA 59.582 36.000 0.00 0.00 44.65 1.94
2351 5853 4.947388 AGAGTAGCACCTTTGTGTTCAAAA 59.053 37.500 0.00 0.00 44.65 2.44
2352 5854 4.523083 AGAGTAGCACCTTTGTGTTCAAA 58.477 39.130 0.00 0.00 44.65 2.69
2353 5855 4.150897 AGAGTAGCACCTTTGTGTTCAA 57.849 40.909 0.00 0.00 44.65 2.69
2354 5856 3.838244 AGAGTAGCACCTTTGTGTTCA 57.162 42.857 0.00 0.00 44.65 3.18
2355 5857 4.884247 AGTAGAGTAGCACCTTTGTGTTC 58.116 43.478 0.00 0.00 44.65 3.18
2356 5858 4.957684 AGTAGAGTAGCACCTTTGTGTT 57.042 40.909 0.00 0.00 44.65 3.32
2357 5859 4.344102 TCAAGTAGAGTAGCACCTTTGTGT 59.656 41.667 0.00 0.00 44.65 3.72
2358 5860 4.686554 GTCAAGTAGAGTAGCACCTTTGTG 59.313 45.833 0.00 0.00 45.65 3.33
2359 5861 4.589374 AGTCAAGTAGAGTAGCACCTTTGT 59.411 41.667 0.00 0.00 0.00 2.83
2415 5932 2.158957 TCATACATGGAAAGACTCGGCC 60.159 50.000 0.00 0.00 0.00 6.13
2416 5933 3.179443 TCATACATGGAAAGACTCGGC 57.821 47.619 0.00 0.00 0.00 5.54
2417 5934 4.759782 AGTTCATACATGGAAAGACTCGG 58.240 43.478 0.00 0.00 0.00 4.63
2512 7260 6.183360 ACAAGTTCTAGCCAGTGTTTGTTTAC 60.183 38.462 0.00 0.00 0.00 2.01
2544 7292 3.065371 GCATCGTAGAATTCCACCCTTTG 59.935 47.826 0.65 0.00 43.58 2.77
2551 7299 3.490933 CGGAAGAGCATCGTAGAATTCCA 60.491 47.826 0.65 0.00 43.58 3.53
2552 7300 3.053455 CGGAAGAGCATCGTAGAATTCC 58.947 50.000 0.65 0.00 43.58 3.01
2619 7372 9.898152 CTCTCTCATGACTACCAGACATATATA 57.102 37.037 0.00 0.00 29.94 0.86
2646 7428 3.866883 AGTGCTCTGCTCTACTTTCTC 57.133 47.619 0.00 0.00 30.33 2.87
2738 7536 4.237976 TGGAGTTGTTAAAGTGGGTCAA 57.762 40.909 0.00 0.00 0.00 3.18
2755 7554 1.419387 CTAGCAGGGGATTCCTTGGAG 59.581 57.143 3.97 0.00 45.47 3.86
2767 7611 1.073923 AGTGGGTGAAAACTAGCAGGG 59.926 52.381 0.00 0.00 0.00 4.45
2800 7651 7.792032 TCGTGGTCTTGAGAGGATATTATTTT 58.208 34.615 0.00 0.00 0.00 1.82
2814 7668 6.257849 GTGCTAATGATTAATCGTGGTCTTGA 59.742 38.462 10.93 0.00 0.00 3.02
2831 7719 5.106555 GGTTATCGATGGAATGGTGCTAATG 60.107 44.000 8.54 0.00 0.00 1.90
2845 7733 3.254903 TCGGACATACCAGGTTATCGATG 59.745 47.826 8.54 0.00 38.90 3.84
2846 7734 3.493334 TCGGACATACCAGGTTATCGAT 58.507 45.455 2.16 2.16 38.90 3.59
2849 7738 6.317893 ACAAAATTCGGACATACCAGGTTATC 59.682 38.462 0.00 0.00 38.90 1.75
2861 7750 7.461182 AAATAATGAGGACAAAATTCGGACA 57.539 32.000 0.00 0.00 0.00 4.02
2863 7752 8.243426 CAGAAAATAATGAGGACAAAATTCGGA 58.757 33.333 0.00 0.00 0.00 4.55
2865 7754 9.065871 GTCAGAAAATAATGAGGACAAAATTCG 57.934 33.333 0.00 0.00 0.00 3.34
2878 7767 6.140786 CCTGCATCATCGTCAGAAAATAATG 58.859 40.000 0.00 0.00 0.00 1.90
2993 7885 2.480845 GGCTGTTCTCGTTGTACACTT 58.519 47.619 0.00 0.00 0.00 3.16
3114 8006 2.437897 CCCCTGCTCTGCACCTTT 59.562 61.111 0.00 0.00 33.79 3.11
3163 8055 4.329545 GAGGCCTGCACCGACCAA 62.330 66.667 12.00 0.00 33.69 3.67
3270 8162 6.071560 AGCCTCGATGATCCAATATACGTAAA 60.072 38.462 0.00 0.00 0.00 2.01
3287 8179 3.448686 CTTACATCGTTTCAGCCTCGAT 58.551 45.455 0.00 0.00 43.52 3.59
3294 8186 2.483877 TGCCAAGCTTACATCGTTTCAG 59.516 45.455 0.00 0.00 0.00 3.02
3308 8203 5.049129 GGTAGATGAAGAATATGTGCCAAGC 60.049 44.000 0.00 0.00 0.00 4.01
3413 8310 3.874543 TGATAAGCACACACACTTTTCGT 59.125 39.130 0.00 0.00 29.60 3.85
3444 8341 6.757010 GTCAAAGGTGACGACATAATGTAGAT 59.243 38.462 0.00 0.00 44.58 1.98
3533 8432 0.680921 TTGCTAGGCTTGTGGATGGC 60.681 55.000 0.00 0.00 0.00 4.40
3534 8433 1.838112 TTTGCTAGGCTTGTGGATGG 58.162 50.000 0.00 0.00 0.00 3.51
3630 8617 3.196254 GGTGGAATTCAAGCATTGTCCAT 59.804 43.478 7.17 0.00 46.26 3.41
3646 11795 4.946160 ACATCAATTAGGGAAGGTGGAA 57.054 40.909 0.00 0.00 0.00 3.53
3660 11809 4.131649 TCGTGGATTCGGTTACATCAAT 57.868 40.909 0.00 0.00 0.00 2.57
3668 11817 1.737793 GCAGAAATCGTGGATTCGGTT 59.262 47.619 0.00 0.00 35.60 4.44
3690 11839 0.528684 GATCCTGTAGCTGCCGTGTC 60.529 60.000 0.00 0.00 0.00 3.67
3729 11878 7.782049 TGTCTGGAGATCGTTAATTTCTGTAT 58.218 34.615 0.00 0.00 0.00 2.29
3745 11894 3.648067 AGTGGAGTTTGATTGTCTGGAGA 59.352 43.478 0.00 0.00 0.00 3.71
3759 11908 4.866508 TTCATGAAGTCGTAGTGGAGTT 57.133 40.909 3.38 0.00 32.39 3.01
3769 11918 4.973051 CCTCTCTTCGTATTCATGAAGTCG 59.027 45.833 21.21 21.21 44.78 4.18
3783 11932 1.373570 GCCATGGTTTCCTCTCTTCG 58.626 55.000 14.67 0.00 0.00 3.79
3807 11956 4.522114 TGGACACTTGTGACAAAAGATGA 58.478 39.130 12.50 0.00 0.00 2.92
3835 11984 5.149973 TGTAGTCCACGGCTAATGTAAAA 57.850 39.130 0.00 0.00 0.00 1.52
3836 11985 4.804868 TGTAGTCCACGGCTAATGTAAA 57.195 40.909 0.00 0.00 0.00 2.01
3847 11996 7.207383 TCATTTTACTCCATATGTAGTCCACG 58.793 38.462 3.94 0.00 0.00 4.94
3860 12009 5.705441 GTGTGGATTCACTCATTTTACTCCA 59.295 40.000 5.55 0.00 43.94 3.86
3874 12023 6.484288 AGACATAATTTGGAGTGTGGATTCA 58.516 36.000 0.00 0.00 0.00 2.57
3958 12107 9.653516 CATGGAATCATAGTACTATATCCCTCT 57.346 37.037 24.67 14.50 31.33 3.69
3959 12108 9.647918 TCATGGAATCATAGTACTATATCCCTC 57.352 37.037 24.67 14.69 31.33 4.30
3983 12132 5.240891 CCAATTCTCTTTGTGCTAGAGTCA 58.759 41.667 0.00 0.00 40.04 3.41
3990 12139 2.154462 CGACCCAATTCTCTTTGTGCT 58.846 47.619 0.00 0.00 0.00 4.40
4044 12193 9.402320 TGCCAAATAAGCATCTATACTTGTTAA 57.598 29.630 0.00 0.00 34.69 2.01
4045 12194 8.972458 TGCCAAATAAGCATCTATACTTGTTA 57.028 30.769 0.00 0.00 34.69 2.41
4046 12195 7.880160 TGCCAAATAAGCATCTATACTTGTT 57.120 32.000 0.00 0.00 34.69 2.83
4047 12196 7.880160 TTGCCAAATAAGCATCTATACTTGT 57.120 32.000 0.00 0.00 40.59 3.16
4078 12227 5.276868 CGTGACTTACACTCTTTTGACCTTG 60.277 44.000 0.00 0.00 46.24 3.61
4095 12244 2.359900 GAGCATGGGATTTCGTGACTT 58.640 47.619 0.00 0.00 0.00 3.01
4163 12317 4.204792 AGTGGGGTGATGATAGAGATGA 57.795 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.