Multiple sequence alignment - TraesCS3D01G049200

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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 TraesCS3D01G049200 chr3D 100.000 3182 0 0 1 3182 18876672 18879853 0.000000e+00 5877.0
1 TraesCS3D01G049200 chr3B 93.997 1999 67 22 81 2034 30491845 30493835 0.000000e+00 2977.0
2 TraesCS3D01G049200 chr3B 89.262 894 48 9 1146 2036 30462891 30463739 0.000000e+00 1075.0
3 TraesCS3D01G049200 chr3B 93.667 600 33 4 2584 3182 14473351 14472756 0.000000e+00 893.0
4 TraesCS3D01G049200 chr3B 82.479 1073 126 28 746 1787 29620474 29621515 0.000000e+00 883.0
5 TraesCS3D01G049200 chr3B 90.728 302 21 5 2143 2441 30493837 30494134 2.300000e-106 396.0
6 TraesCS3D01G049200 chr3B 93.590 156 10 0 952 1107 30462738 30462893 1.910000e-57 233.0
7 TraesCS3D01G049200 chr3B 88.043 184 19 1 2144 2324 30463736 30463919 6.910000e-52 215.0
8 TraesCS3D01G049200 chr3B 97.403 77 2 0 2408 2484 30494062 30494138 7.160000e-27 132.0
9 TraesCS3D01G049200 chr3B 98.113 53 1 0 2521 2573 30494141 30494193 3.380000e-15 93.5
10 TraesCS3D01G049200 chr3B 87.719 57 7 0 1 57 30486470 30486526 2.050000e-07 67.6
11 TraesCS3D01G049200 chr3B 100.000 34 0 0 2486 2519 30464101 30464068 2.650000e-06 63.9
12 TraesCS3D01G049200 chr3B 94.872 39 1 1 2440 2477 30464082 30464120 3.430000e-05 60.2
13 TraesCS3D01G049200 chr3B 97.143 35 1 0 199 233 71451126 71451092 3.430000e-05 60.2
14 TraesCS3D01G049200 chr3A 84.608 994 119 17 813 1788 26459253 26460230 0.000000e+00 957.0
15 TraesCS3D01G049200 chr3A 95.000 600 27 3 2584 3182 502935178 502935775 0.000000e+00 939.0
16 TraesCS3D01G049200 chr3A 93.489 599 39 0 2584 3182 738122039 738122637 0.000000e+00 891.0
17 TraesCS3D01G049200 chr3A 72.997 337 85 4 1101 1434 26413765 26414098 2.590000e-21 113.0
18 TraesCS3D01G049200 chr2B 95.167 600 26 3 2584 3182 742186806 742187403 0.000000e+00 944.0
19 TraesCS3D01G049200 chr2B 90.265 113 11 0 2031 2143 557987947 557988059 7.110000e-32 148.0
20 TraesCS3D01G049200 chr6B 93.667 600 34 4 2584 3182 102197518 102198114 0.000000e+00 894.0
21 TraesCS3D01G049200 chr6B 90.566 106 10 0 2038 2143 542370403 542370298 1.190000e-29 141.0
22 TraesCS3D01G049200 chr6B 85.714 126 15 2 2021 2143 377824082 377824207 2.580000e-26 130.0
23 TraesCS3D01G049200 chr6B 97.222 36 1 0 198 233 697681791 697681826 9.530000e-06 62.1
24 TraesCS3D01G049200 chr6B 97.143 35 1 0 199 233 18170175 18170209 3.430000e-05 60.2
25 TraesCS3D01G049200 chr2A 92.833 600 42 1 2584 3182 685202867 685203466 0.000000e+00 869.0
26 TraesCS3D01G049200 chr7A 92.654 599 43 1 2584 3182 690774990 690774393 0.000000e+00 861.0
27 TraesCS3D01G049200 chr7A 92.905 592 38 1 2591 3182 35706853 35706266 0.000000e+00 857.0
28 TraesCS3D01G049200 chr7A 91.472 598 50 1 2584 3181 33027420 33026824 0.000000e+00 821.0
29 TraesCS3D01G049200 chr4D 90.351 114 11 0 2030 2143 105237926 105237813 1.980000e-32 150.0
30 TraesCS3D01G049200 chrUn 91.509 106 9 0 2038 2143 30022466 30022361 2.560000e-31 147.0
31 TraesCS3D01G049200 chrUn 90.566 106 10 0 2038 2143 22143702 22143597 1.190000e-29 141.0
32 TraesCS3D01G049200 chr5B 90.566 106 10 0 2038 2143 425375008 425375113 1.190000e-29 141.0
33 TraesCS3D01G049200 chr4A 90.566 106 10 0 2038 2143 702148798 702148903 1.190000e-29 141.0
34 TraesCS3D01G049200 chr4A 97.059 34 1 0 200 233 31593372 31593339 1.230000e-04 58.4
35 TraesCS3D01G049200 chr2D 90.566 106 10 0 2038 2143 610294420 610294525 1.190000e-29 141.0
36 TraesCS3D01G049200 chr1B 97.143 35 1 0 199 233 17045660 17045626 3.430000e-05 60.2


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 TraesCS3D01G049200 chr3D 18876672 18879853 3181 False 5877.000 5877 100.00000 1 3182 1 chr3D.!!$F1 3181
1 TraesCS3D01G049200 chr3B 30491845 30494193 2348 False 899.625 2977 95.06025 81 2573 4 chr3B.!!$F4 2492
2 TraesCS3D01G049200 chr3B 14472756 14473351 595 True 893.000 893 93.66700 2584 3182 1 chr3B.!!$R1 598
3 TraesCS3D01G049200 chr3B 29620474 29621515 1041 False 883.000 883 82.47900 746 1787 1 chr3B.!!$F1 1041
4 TraesCS3D01G049200 chr3B 30462738 30464120 1382 False 395.800 1075 91.44175 952 2477 4 chr3B.!!$F3 1525
5 TraesCS3D01G049200 chr3A 26459253 26460230 977 False 957.000 957 84.60800 813 1788 1 chr3A.!!$F2 975
6 TraesCS3D01G049200 chr3A 502935178 502935775 597 False 939.000 939 95.00000 2584 3182 1 chr3A.!!$F3 598
7 TraesCS3D01G049200 chr3A 738122039 738122637 598 False 891.000 891 93.48900 2584 3182 1 chr3A.!!$F4 598
8 TraesCS3D01G049200 chr2B 742186806 742187403 597 False 944.000 944 95.16700 2584 3182 1 chr2B.!!$F2 598
9 TraesCS3D01G049200 chr6B 102197518 102198114 596 False 894.000 894 93.66700 2584 3182 1 chr6B.!!$F2 598
10 TraesCS3D01G049200 chr2A 685202867 685203466 599 False 869.000 869 92.83300 2584 3182 1 chr2A.!!$F1 598
11 TraesCS3D01G049200 chr7A 690774393 690774990 597 True 861.000 861 92.65400 2584 3182 1 chr7A.!!$R3 598
12 TraesCS3D01G049200 chr7A 35706266 35706853 587 True 857.000 857 92.90500 2591 3182 1 chr7A.!!$R2 591
13 TraesCS3D01G049200 chr7A 33026824 33027420 596 True 821.000 821 91.47200 2584 3181 1 chr7A.!!$R1 597

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
601 603 0.036294 GTTAGCAAGCGAGGAAGGGT 60.036 55.0 0.0 0.0 0.00 4.34 F
924 978 1.051812 ATTCTATCTCCCCACAGCCG 58.948 55.0 0.0 0.0 0.00 5.52 F
1296 1352 1.466856 ATGAGGAACGCAACATGCAT 58.533 45.0 0.0 0.0 44.24 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2115 0.108041 GTATTTCCGGACGGAGGCAA 60.108 55.0 13.64 6.20 46.06 4.52 R
2036 2117 0.177373 AAGTATTTCCGGACGGAGGC 59.823 55.0 13.64 5.83 46.06 4.70 R
3042 3233 0.179020 TTGCTCAGTGGGTTGGTCAG 60.179 55.0 0.00 0.00 0.00 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.839051 GCTCAACCAGTCAATTCCTTC 57.161 47.619 0.00 0.00 0.00 3.46
21 22 2.160417 GCTCAACCAGTCAATTCCTTCG 59.840 50.000 0.00 0.00 0.00 3.79
22 23 3.664107 CTCAACCAGTCAATTCCTTCGA 58.336 45.455 0.00 0.00 0.00 3.71
23 24 4.065088 CTCAACCAGTCAATTCCTTCGAA 58.935 43.478 0.00 0.00 0.00 3.71
24 25 3.813166 TCAACCAGTCAATTCCTTCGAAC 59.187 43.478 0.00 0.00 0.00 3.95
25 26 3.771577 ACCAGTCAATTCCTTCGAACT 57.228 42.857 0.00 0.00 0.00 3.01
26 27 3.665190 ACCAGTCAATTCCTTCGAACTC 58.335 45.455 0.00 0.00 0.00 3.01
27 28 3.071023 ACCAGTCAATTCCTTCGAACTCA 59.929 43.478 0.00 0.00 0.00 3.41
28 29 3.681897 CCAGTCAATTCCTTCGAACTCAG 59.318 47.826 0.00 0.00 0.00 3.35
29 30 3.681897 CAGTCAATTCCTTCGAACTCAGG 59.318 47.826 0.00 0.00 0.00 3.86
30 31 2.416893 GTCAATTCCTTCGAACTCAGGC 59.583 50.000 0.00 0.00 0.00 4.85
31 32 2.303022 TCAATTCCTTCGAACTCAGGCT 59.697 45.455 0.00 0.00 0.00 4.58
32 33 2.393271 ATTCCTTCGAACTCAGGCTG 57.607 50.000 8.58 8.58 0.00 4.85
33 34 1.048601 TTCCTTCGAACTCAGGCTGT 58.951 50.000 15.27 0.00 0.00 4.40
34 35 0.603569 TCCTTCGAACTCAGGCTGTC 59.396 55.000 15.27 3.85 0.00 3.51
35 36 0.605589 CCTTCGAACTCAGGCTGTCT 59.394 55.000 15.27 0.00 0.00 3.41
36 37 1.403514 CCTTCGAACTCAGGCTGTCTC 60.404 57.143 15.27 8.56 0.00 3.36
37 38 0.603569 TTCGAACTCAGGCTGTCTCC 59.396 55.000 15.27 2.30 0.00 3.71
38 39 1.216710 CGAACTCAGGCTGTCTCCC 59.783 63.158 15.27 0.89 0.00 4.30
39 40 1.536073 CGAACTCAGGCTGTCTCCCA 61.536 60.000 15.27 0.00 0.00 4.37
40 41 0.036858 GAACTCAGGCTGTCTCCCAC 60.037 60.000 15.27 0.00 0.00 4.61
41 42 1.484444 AACTCAGGCTGTCTCCCACC 61.484 60.000 15.27 0.00 0.00 4.61
42 43 1.611851 CTCAGGCTGTCTCCCACCT 60.612 63.158 15.27 0.00 0.00 4.00
43 44 1.610673 TCAGGCTGTCTCCCACCTC 60.611 63.158 15.27 0.00 0.00 3.85
44 45 2.284995 AGGCTGTCTCCCACCTCC 60.285 66.667 0.00 0.00 0.00 4.30
45 46 2.607750 GGCTGTCTCCCACCTCCA 60.608 66.667 0.00 0.00 0.00 3.86
46 47 1.997874 GGCTGTCTCCCACCTCCAT 60.998 63.158 0.00 0.00 0.00 3.41
47 48 1.524482 GCTGTCTCCCACCTCCATC 59.476 63.158 0.00 0.00 0.00 3.51
48 49 0.980231 GCTGTCTCCCACCTCCATCT 60.980 60.000 0.00 0.00 0.00 2.90
49 50 1.689575 GCTGTCTCCCACCTCCATCTA 60.690 57.143 0.00 0.00 0.00 1.98
50 51 2.969628 CTGTCTCCCACCTCCATCTAT 58.030 52.381 0.00 0.00 0.00 1.98
51 52 3.312890 CTGTCTCCCACCTCCATCTATT 58.687 50.000 0.00 0.00 0.00 1.73
52 53 3.713764 CTGTCTCCCACCTCCATCTATTT 59.286 47.826 0.00 0.00 0.00 1.40
53 54 4.111577 TGTCTCCCACCTCCATCTATTTT 58.888 43.478 0.00 0.00 0.00 1.82
54 55 4.540099 TGTCTCCCACCTCCATCTATTTTT 59.460 41.667 0.00 0.00 0.00 1.94
55 56 5.126779 GTCTCCCACCTCCATCTATTTTTC 58.873 45.833 0.00 0.00 0.00 2.29
56 57 5.039645 TCTCCCACCTCCATCTATTTTTCT 58.960 41.667 0.00 0.00 0.00 2.52
57 58 5.492524 TCTCCCACCTCCATCTATTTTTCTT 59.507 40.000 0.00 0.00 0.00 2.52
58 59 6.011628 TCTCCCACCTCCATCTATTTTTCTTT 60.012 38.462 0.00 0.00 0.00 2.52
59 60 6.561294 TCCCACCTCCATCTATTTTTCTTTT 58.439 36.000 0.00 0.00 0.00 2.27
60 61 6.437162 TCCCACCTCCATCTATTTTTCTTTTG 59.563 38.462 0.00 0.00 0.00 2.44
61 62 6.437162 CCCACCTCCATCTATTTTTCTTTTGA 59.563 38.462 0.00 0.00 0.00 2.69
62 63 7.039082 CCCACCTCCATCTATTTTTCTTTTGAA 60.039 37.037 0.00 0.00 36.52 2.69
63 64 8.367156 CCACCTCCATCTATTTTTCTTTTGAAA 58.633 33.333 0.00 0.00 45.65 2.69
76 77 7.769272 TTTCTTTTGAAAAATCATCGCTTGT 57.231 28.000 0.00 0.00 44.51 3.16
77 78 6.752335 TCTTTTGAAAAATCATCGCTTGTG 57.248 33.333 0.00 0.00 0.00 3.33
78 79 4.970472 TTTGAAAAATCATCGCTTGTGC 57.030 36.364 0.00 0.00 0.00 4.57
79 80 3.639716 TGAAAAATCATCGCTTGTGCA 57.360 38.095 0.00 0.00 39.64 4.57
95 96 4.824479 TGTGCAACCAGATCTATCTTCA 57.176 40.909 0.00 0.00 34.36 3.02
104 105 5.053145 CCAGATCTATCTTCAACCTTTCCG 58.947 45.833 0.00 0.00 34.22 4.30
128 129 1.684450 TCCACAACTAGCTTGTCGTCA 59.316 47.619 0.07 0.00 41.50 4.35
161 162 4.525912 AATGTCTTGCCTCCAAAATCAC 57.474 40.909 0.00 0.00 0.00 3.06
238 239 2.548295 GCCGACGGCCTTTTGTTGA 61.548 57.895 28.74 0.00 44.06 3.18
269 270 3.842820 CATAGGTGGAGATATGCTGACG 58.157 50.000 0.00 0.00 0.00 4.35
272 273 0.601311 GTGGAGATATGCTGACGGCC 60.601 60.000 3.22 0.00 40.92 6.13
415 416 1.118965 TGAGACGCAGGGACCTGAAA 61.119 55.000 22.03 0.00 46.30 2.69
421 422 3.081804 ACGCAGGGACCTGAAAAATAAG 58.918 45.455 22.03 4.71 46.30 1.73
454 456 1.221840 GCCCATCTTTCTCAGCGGA 59.778 57.895 0.00 0.00 0.00 5.54
512 514 8.055181 TGAGCTCCTGTATATTGATTTTTCCTT 58.945 33.333 12.15 0.00 0.00 3.36
515 517 9.120538 GCTCCTGTATATTGATTTTTCCTTGTA 57.879 33.333 0.00 0.00 0.00 2.41
601 603 0.036294 GTTAGCAAGCGAGGAAGGGT 60.036 55.000 0.00 0.00 0.00 4.34
640 642 7.448228 CACTTCTATCAACACATACAAGAACG 58.552 38.462 0.00 0.00 0.00 3.95
724 757 9.985730 ATTTCTTTTCTCATCATGTTTAAAGCA 57.014 25.926 0.00 0.00 0.00 3.91
725 758 9.814899 TTTCTTTTCTCATCATGTTTAAAGCAA 57.185 25.926 0.00 0.00 0.00 3.91
726 759 9.814899 TTCTTTTCTCATCATGTTTAAAGCAAA 57.185 25.926 0.00 0.00 0.00 3.68
731 764 7.092079 TCTCATCATGTTTAAAGCAAACCATG 58.908 34.615 7.54 7.54 45.05 3.66
890 944 6.763135 CACTCCCCCGTATATCATTCATTATG 59.237 42.308 0.00 0.00 35.45 1.90
924 978 1.051812 ATTCTATCTCCCCACAGCCG 58.948 55.000 0.00 0.00 0.00 5.52
998 1052 5.598417 ACCAATTCCAAGCCTTATATGTTCC 59.402 40.000 0.00 0.00 0.00 3.62
1004 1058 2.688507 AGCCTTATATGTTCCGATGCG 58.311 47.619 0.00 0.00 0.00 4.73
1176 1232 3.202706 GGGGCGGAAAGATCGTGC 61.203 66.667 0.00 0.00 0.00 5.34
1296 1352 1.466856 ATGAGGAACGCAACATGCAT 58.533 45.000 0.00 0.00 44.24 3.96
1521 1585 6.537301 ACAAGAGAAACACATTTGTTCGAGTA 59.463 34.615 0.00 0.00 45.69 2.59
1831 1904 5.188359 ACCCATGCTCTTAATTTGCTTTGAT 59.812 36.000 0.00 0.00 0.00 2.57
2012 2093 5.523188 CGACGACTAATTACTGACTAGAGGT 59.477 44.000 0.00 0.00 0.00 3.85
2035 2116 9.632638 AGGTACTCATGATTTGCATTAACTATT 57.367 29.630 0.00 0.00 34.15 1.73
2036 2117 9.669353 GGTACTCATGATTTGCATTAACTATTG 57.331 33.333 0.00 0.00 34.15 1.90
2037 2118 9.173939 GTACTCATGATTTGCATTAACTATTGC 57.826 33.333 0.00 0.00 39.33 3.56
2038 2119 7.205297 ACTCATGATTTGCATTAACTATTGCC 58.795 34.615 0.00 0.00 38.08 4.52
2039 2120 7.069085 ACTCATGATTTGCATTAACTATTGCCT 59.931 33.333 0.00 0.00 38.08 4.75
2040 2121 7.428020 TCATGATTTGCATTAACTATTGCCTC 58.572 34.615 0.00 0.00 38.08 4.70
2041 2122 6.147864 TGATTTGCATTAACTATTGCCTCC 57.852 37.500 0.00 0.00 38.08 4.30
2042 2123 4.630894 TTTGCATTAACTATTGCCTCCG 57.369 40.909 0.00 0.00 38.08 4.63
2043 2124 3.275617 TGCATTAACTATTGCCTCCGT 57.724 42.857 0.00 0.00 38.08 4.69
2044 2125 3.202906 TGCATTAACTATTGCCTCCGTC 58.797 45.455 0.00 0.00 38.08 4.79
2045 2126 2.548480 GCATTAACTATTGCCTCCGTCC 59.452 50.000 0.00 0.00 32.66 4.79
2046 2127 2.589798 TTAACTATTGCCTCCGTCCG 57.410 50.000 0.00 0.00 0.00 4.79
2047 2128 0.748450 TAACTATTGCCTCCGTCCGG 59.252 55.000 0.00 0.00 0.00 5.14
2048 2129 0.974010 AACTATTGCCTCCGTCCGGA 60.974 55.000 0.00 0.00 42.90 5.14
2049 2130 0.974010 ACTATTGCCTCCGTCCGGAA 60.974 55.000 5.23 0.00 44.66 4.30
2050 2131 0.177141 CTATTGCCTCCGTCCGGAAA 59.823 55.000 5.23 1.92 44.66 3.13
2051 2132 0.834612 TATTGCCTCCGTCCGGAAAT 59.165 50.000 5.23 9.21 44.66 2.17
2052 2133 0.834612 ATTGCCTCCGTCCGGAAATA 59.165 50.000 5.23 0.00 44.66 1.40
2053 2134 0.108041 TTGCCTCCGTCCGGAAATAC 60.108 55.000 5.23 0.00 44.66 1.89
2054 2135 0.974010 TGCCTCCGTCCGGAAATACT 60.974 55.000 5.23 0.00 44.66 2.12
2055 2136 0.177373 GCCTCCGTCCGGAAATACTT 59.823 55.000 5.23 0.00 44.66 2.24
2056 2137 1.935933 CCTCCGTCCGGAAATACTTG 58.064 55.000 5.23 0.00 44.66 3.16
2057 2138 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2058 2139 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2059 2140 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2060 2141 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2061 2142 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2062 2143 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
2063 2144 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
2064 2145 1.472728 CCGGAAATACTTGTCGGAGGG 60.473 57.143 0.00 0.00 42.94 4.30
2065 2146 1.206371 CGGAAATACTTGTCGGAGGGT 59.794 52.381 0.00 0.00 0.00 4.34
2066 2147 2.354403 CGGAAATACTTGTCGGAGGGTT 60.354 50.000 0.00 0.00 0.00 4.11
2067 2148 3.119029 CGGAAATACTTGTCGGAGGGTTA 60.119 47.826 0.00 0.00 0.00 2.85
2068 2149 4.439968 GGAAATACTTGTCGGAGGGTTAG 58.560 47.826 0.00 0.00 0.00 2.34
2069 2150 4.161001 GGAAATACTTGTCGGAGGGTTAGA 59.839 45.833 0.00 0.00 0.00 2.10
2070 2151 5.163332 GGAAATACTTGTCGGAGGGTTAGAT 60.163 44.000 0.00 0.00 0.00 1.98
2071 2152 4.939052 ATACTTGTCGGAGGGTTAGATG 57.061 45.455 0.00 0.00 0.00 2.90
2072 2153 2.537143 ACTTGTCGGAGGGTTAGATGT 58.463 47.619 0.00 0.00 0.00 3.06
2073 2154 3.705051 ACTTGTCGGAGGGTTAGATGTA 58.295 45.455 0.00 0.00 0.00 2.29
2074 2155 4.287552 ACTTGTCGGAGGGTTAGATGTAT 58.712 43.478 0.00 0.00 0.00 2.29
2075 2156 4.341520 ACTTGTCGGAGGGTTAGATGTATC 59.658 45.833 0.00 0.00 0.00 2.24
2076 2157 4.180377 TGTCGGAGGGTTAGATGTATCT 57.820 45.455 0.00 0.00 40.86 1.98
2077 2158 5.314718 TGTCGGAGGGTTAGATGTATCTA 57.685 43.478 0.00 0.00 38.32 1.98
2078 2159 5.888901 TGTCGGAGGGTTAGATGTATCTAT 58.111 41.667 2.65 0.00 39.02 1.98
2079 2160 7.024345 TGTCGGAGGGTTAGATGTATCTATA 57.976 40.000 2.65 0.00 39.02 1.31
2080 2161 6.883217 TGTCGGAGGGTTAGATGTATCTATAC 59.117 42.308 2.65 4.72 39.02 1.47
2081 2162 6.036953 GTCGGAGGGTTAGATGTATCTATACG 59.963 46.154 2.65 1.48 39.02 3.06
2082 2163 5.879223 CGGAGGGTTAGATGTATCTATACGT 59.121 44.000 2.65 0.00 39.02 3.57
2083 2164 7.044181 CGGAGGGTTAGATGTATCTATACGTA 58.956 42.308 0.00 0.00 39.02 3.57
2084 2165 7.550551 CGGAGGGTTAGATGTATCTATACGTAA 59.449 40.741 0.00 0.00 39.02 3.18
2085 2166 9.406113 GGAGGGTTAGATGTATCTATACGTAAT 57.594 37.037 0.00 0.00 39.02 1.89
2123 2204 8.827832 ACATCCATTTTTATCCATTTCTCTGA 57.172 30.769 0.00 0.00 0.00 3.27
2124 2205 8.689972 ACATCCATTTTTATCCATTTCTCTGAC 58.310 33.333 0.00 0.00 0.00 3.51
2125 2206 8.689061 CATCCATTTTTATCCATTTCTCTGACA 58.311 33.333 0.00 0.00 0.00 3.58
2126 2207 8.648698 TCCATTTTTATCCATTTCTCTGACAA 57.351 30.769 0.00 0.00 0.00 3.18
2127 2208 8.742777 TCCATTTTTATCCATTTCTCTGACAAG 58.257 33.333 0.00 0.00 0.00 3.16
2128 2209 8.526147 CCATTTTTATCCATTTCTCTGACAAGT 58.474 33.333 0.00 0.00 0.00 3.16
2135 2216 7.364522 TCCATTTCTCTGACAAGTATTTTCG 57.635 36.000 0.00 0.00 0.00 3.46
2136 2217 6.371548 TCCATTTCTCTGACAAGTATTTTCGG 59.628 38.462 0.00 0.00 0.00 4.30
2137 2218 6.371548 CCATTTCTCTGACAAGTATTTTCGGA 59.628 38.462 0.00 0.00 0.00 4.55
2138 2219 6.780706 TTTCTCTGACAAGTATTTTCGGAC 57.219 37.500 0.00 0.00 0.00 4.79
2139 2220 5.462530 TCTCTGACAAGTATTTTCGGACA 57.537 39.130 0.00 0.00 0.00 4.02
2140 2221 5.470368 TCTCTGACAAGTATTTTCGGACAG 58.530 41.667 0.00 0.00 0.00 3.51
2141 2222 5.243060 TCTCTGACAAGTATTTTCGGACAGA 59.757 40.000 0.00 0.00 0.00 3.41
2157 2238 9.967346 TTTCGGACAGAGTATTTATCTTATCAG 57.033 33.333 0.00 0.00 0.00 2.90
2288 2369 9.897349 CATGATATCGACATATCTGAAAATTCG 57.103 33.333 7.39 0.00 41.17 3.34
2303 2387 1.909700 ATTCGTGCACCCACTTGATT 58.090 45.000 12.15 0.00 39.86 2.57
2352 2436 2.040545 TCTTTCCTTGCCCCGTCAATTA 59.959 45.455 0.00 0.00 0.00 1.40
2372 2456 1.789523 GGATACTAGTGGAGTGCCCA 58.210 55.000 5.39 0.00 44.25 5.36
2381 2465 0.249120 TGGAGTGCCCATGTTAGACG 59.751 55.000 0.00 0.00 40.82 4.18
2382 2466 0.249398 GGAGTGCCCATGTTAGACGT 59.751 55.000 0.00 0.00 34.14 4.34
2383 2467 1.479323 GGAGTGCCCATGTTAGACGTA 59.521 52.381 0.00 0.00 34.14 3.57
2384 2468 2.537401 GAGTGCCCATGTTAGACGTAC 58.463 52.381 0.00 0.00 0.00 3.67
2385 2469 1.135199 AGTGCCCATGTTAGACGTACG 60.135 52.381 15.01 15.01 0.00 3.67
2386 2470 1.135315 GTGCCCATGTTAGACGTACGA 60.135 52.381 24.41 0.00 0.00 3.43
2387 2471 1.135315 TGCCCATGTTAGACGTACGAC 60.135 52.381 24.41 16.77 0.00 4.34
2388 2472 1.800286 GCCCATGTTAGACGTACGACC 60.800 57.143 24.41 13.05 0.00 4.79
2389 2473 1.473677 CCCATGTTAGACGTACGACCA 59.526 52.381 24.41 9.87 0.00 4.02
2390 2474 2.523015 CCATGTTAGACGTACGACCAC 58.477 52.381 24.41 15.48 0.00 4.16
2391 2475 2.523015 CATGTTAGACGTACGACCACC 58.477 52.381 24.41 6.72 0.00 4.61
2392 2476 0.516877 TGTTAGACGTACGACCACCG 59.483 55.000 24.41 0.00 45.44 4.94
2405 2489 4.676951 CACCGTTGCCCCCACCAT 62.677 66.667 0.00 0.00 0.00 3.55
2406 2490 2.936584 ACCGTTGCCCCCACCATA 60.937 61.111 0.00 0.00 0.00 2.74
2476 2663 8.899427 TTCATTCTTAGCCAGATTATTCTCTG 57.101 34.615 0.00 0.00 41.93 3.35
2484 2671 5.046014 AGCCAGATTATTCTCTGACAACACT 60.046 40.000 2.73 0.00 44.48 3.55
2486 2673 6.478344 GCCAGATTATTCTCTGACAACACTAG 59.522 42.308 2.73 0.00 44.48 2.57
2487 2674 7.631594 GCCAGATTATTCTCTGACAACACTAGA 60.632 40.741 0.00 0.00 44.48 2.43
2488 2675 8.253810 CCAGATTATTCTCTGACAACACTAGAA 58.746 37.037 0.00 0.00 44.48 2.10
2489 2676 9.814899 CAGATTATTCTCTGACAACACTAGAAT 57.185 33.333 0.00 0.00 44.48 2.40
2490 2677 9.814899 AGATTATTCTCTGACAACACTAGAATG 57.185 33.333 0.00 0.00 35.87 2.67
2491 2678 9.809096 GATTATTCTCTGACAACACTAGAATGA 57.191 33.333 0.00 0.00 35.87 2.57
2494 2681 7.895975 TTCTCTGACAACACTAGAATGAATG 57.104 36.000 0.00 0.00 0.00 2.67
2495 2682 6.401394 TCTCTGACAACACTAGAATGAATGG 58.599 40.000 0.00 0.00 0.00 3.16
2496 2683 4.937620 TCTGACAACACTAGAATGAATGGC 59.062 41.667 0.00 0.00 0.00 4.40
2497 2684 4.650734 TGACAACACTAGAATGAATGGCA 58.349 39.130 0.00 0.00 0.00 4.92
2498 2685 5.255687 TGACAACACTAGAATGAATGGCAT 58.744 37.500 0.00 0.00 39.43 4.40
2499 2686 6.413892 TGACAACACTAGAATGAATGGCATA 58.586 36.000 0.00 0.00 35.78 3.14
2500 2687 7.056006 TGACAACACTAGAATGAATGGCATAT 58.944 34.615 0.00 0.00 35.78 1.78
2501 2688 7.012610 TGACAACACTAGAATGAATGGCATATG 59.987 37.037 0.00 0.00 35.78 1.78
2502 2689 6.263842 ACAACACTAGAATGAATGGCATATGG 59.736 38.462 0.00 0.00 35.78 2.74
2503 2690 5.945310 ACACTAGAATGAATGGCATATGGT 58.055 37.500 0.00 0.00 35.78 3.55
2504 2691 5.766670 ACACTAGAATGAATGGCATATGGTG 59.233 40.000 0.00 0.00 39.30 4.17
2505 2692 5.182570 CACTAGAATGAATGGCATATGGTGG 59.817 44.000 0.00 0.00 35.78 4.61
2506 2693 3.503365 AGAATGAATGGCATATGGTGGG 58.497 45.455 0.00 0.00 35.78 4.61
2507 2694 2.314071 ATGAATGGCATATGGTGGGG 57.686 50.000 0.00 0.00 34.82 4.96
2508 2695 0.188096 TGAATGGCATATGGTGGGGG 59.812 55.000 0.00 0.00 0.00 5.40
2509 2696 1.152269 AATGGCATATGGTGGGGGC 60.152 57.895 0.00 0.00 0.00 5.80
2510 2697 1.959007 AATGGCATATGGTGGGGGCA 61.959 55.000 0.00 0.00 40.23 5.36
2511 2698 1.959007 ATGGCATATGGTGGGGGCAA 61.959 55.000 0.00 0.00 39.34 4.52
2512 2699 2.133641 GGCATATGGTGGGGGCAAC 61.134 63.158 4.56 0.00 0.00 4.17
2513 2700 2.489275 GCATATGGTGGGGGCAACG 61.489 63.158 4.56 0.00 37.60 4.10
2514 2701 1.827789 CATATGGTGGGGGCAACGG 60.828 63.158 0.00 0.00 37.60 4.44
2515 2702 2.313427 ATATGGTGGGGGCAACGGT 61.313 57.895 0.00 0.00 37.60 4.83
2516 2703 2.279037 ATATGGTGGGGGCAACGGTC 62.279 60.000 0.00 0.00 37.60 4.79
2519 2706 4.941309 GTGGGGGCAACGGTCGTT 62.941 66.667 2.65 2.65 39.13 3.85
2536 2723 2.557924 TCGTTGTACGTCTAACATGGGT 59.442 45.455 13.23 0.00 43.14 4.51
2573 2760 0.404040 ATTGACGGGGCAAGGAAAGA 59.596 50.000 0.00 0.00 0.00 2.52
2574 2761 0.536460 TTGACGGGGCAAGGAAAGAC 60.536 55.000 0.00 0.00 0.00 3.01
2575 2762 1.674651 GACGGGGCAAGGAAAGACC 60.675 63.158 0.00 0.00 39.35 3.85
2639 2826 6.761731 TTTGAATTAACAAAGCCATCAACG 57.238 33.333 0.00 0.00 35.29 4.10
2659 2847 2.683742 CGGGCCAGGAATTACAATCACT 60.684 50.000 4.39 0.00 0.00 3.41
2739 2927 1.538047 CAGCCTACAAGCACCACAAT 58.462 50.000 0.00 0.00 34.23 2.71
2829 3018 0.737367 CCGAAGCATGACAGCGAGAA 60.737 55.000 0.00 0.00 40.15 2.87
3067 3258 2.507484 CAACCCACTGAGCAAAGATCA 58.493 47.619 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.160417 CGAAGGAATTGACTGGTTGAGC 59.840 50.000 0.00 0.00 0.00 4.26
1 2 3.664107 TCGAAGGAATTGACTGGTTGAG 58.336 45.455 0.00 0.00 0.00 3.02
3 4 3.815401 AGTTCGAAGGAATTGACTGGTTG 59.185 43.478 0.00 0.00 34.05 3.77
4 5 4.065789 GAGTTCGAAGGAATTGACTGGTT 58.934 43.478 0.00 0.00 34.05 3.67
5 6 3.071023 TGAGTTCGAAGGAATTGACTGGT 59.929 43.478 0.00 0.00 34.05 4.00
6 7 3.664107 TGAGTTCGAAGGAATTGACTGG 58.336 45.455 0.00 0.00 34.05 4.00
7 8 3.681897 CCTGAGTTCGAAGGAATTGACTG 59.318 47.826 0.00 0.00 35.40 3.51
8 9 3.866449 GCCTGAGTTCGAAGGAATTGACT 60.866 47.826 5.02 0.00 35.40 3.41
9 10 2.416893 GCCTGAGTTCGAAGGAATTGAC 59.583 50.000 5.02 0.00 35.40 3.18
10 11 2.303022 AGCCTGAGTTCGAAGGAATTGA 59.697 45.455 5.02 0.00 35.40 2.57
11 12 2.417933 CAGCCTGAGTTCGAAGGAATTG 59.582 50.000 5.02 0.00 35.40 2.32
12 13 2.039084 ACAGCCTGAGTTCGAAGGAATT 59.961 45.455 5.02 0.00 35.40 2.17
13 14 1.625818 ACAGCCTGAGTTCGAAGGAAT 59.374 47.619 5.02 0.00 35.40 3.01
14 15 1.000955 GACAGCCTGAGTTCGAAGGAA 59.999 52.381 5.02 0.00 35.40 3.36
15 16 0.603569 GACAGCCTGAGTTCGAAGGA 59.396 55.000 5.02 0.00 35.40 3.36
16 17 0.605589 AGACAGCCTGAGTTCGAAGG 59.394 55.000 0.00 0.00 36.58 3.46
17 18 1.403514 GGAGACAGCCTGAGTTCGAAG 60.404 57.143 0.00 0.00 0.00 3.79
18 19 0.603569 GGAGACAGCCTGAGTTCGAA 59.396 55.000 0.00 0.00 0.00 3.71
19 20 1.251527 GGGAGACAGCCTGAGTTCGA 61.252 60.000 0.00 0.00 0.00 3.71
20 21 1.216710 GGGAGACAGCCTGAGTTCG 59.783 63.158 0.00 0.00 0.00 3.95
21 22 0.036858 GTGGGAGACAGCCTGAGTTC 60.037 60.000 0.00 0.00 0.00 3.01
22 23 1.484444 GGTGGGAGACAGCCTGAGTT 61.484 60.000 0.00 0.00 41.69 3.01
23 24 1.915769 GGTGGGAGACAGCCTGAGT 60.916 63.158 0.00 0.00 41.69 3.41
24 25 2.985456 GGTGGGAGACAGCCTGAG 59.015 66.667 0.00 0.00 41.69 3.35
30 31 2.461300 TAGATGGAGGTGGGAGACAG 57.539 55.000 0.00 0.00 0.00 3.51
31 32 3.421394 AATAGATGGAGGTGGGAGACA 57.579 47.619 0.00 0.00 0.00 3.41
32 33 4.779993 AAAATAGATGGAGGTGGGAGAC 57.220 45.455 0.00 0.00 0.00 3.36
33 34 5.039645 AGAAAAATAGATGGAGGTGGGAGA 58.960 41.667 0.00 0.00 0.00 3.71
34 35 5.379706 AGAAAAATAGATGGAGGTGGGAG 57.620 43.478 0.00 0.00 0.00 4.30
35 36 5.796502 AAGAAAAATAGATGGAGGTGGGA 57.203 39.130 0.00 0.00 0.00 4.37
36 37 6.437162 TCAAAAGAAAAATAGATGGAGGTGGG 59.563 38.462 0.00 0.00 0.00 4.61
37 38 7.466746 TCAAAAGAAAAATAGATGGAGGTGG 57.533 36.000 0.00 0.00 0.00 4.61
38 39 9.762933 TTTTCAAAAGAAAAATAGATGGAGGTG 57.237 29.630 1.26 0.00 31.90 4.00
50 51 8.663911 ACAAGCGATGATTTTTCAAAAGAAAAA 58.336 25.926 15.75 15.75 44.73 1.94
51 52 8.115520 CACAAGCGATGATTTTTCAAAAGAAAA 58.884 29.630 0.00 0.00 32.86 2.29
52 53 7.620215 CACAAGCGATGATTTTTCAAAAGAAA 58.380 30.769 0.00 0.00 0.00 2.52
53 54 6.292274 GCACAAGCGATGATTTTTCAAAAGAA 60.292 34.615 0.00 0.00 0.00 2.52
54 55 5.175491 GCACAAGCGATGATTTTTCAAAAGA 59.825 36.000 0.00 0.00 0.00 2.52
55 56 5.050904 TGCACAAGCGATGATTTTTCAAAAG 60.051 36.000 0.00 0.00 46.23 2.27
56 57 4.807834 TGCACAAGCGATGATTTTTCAAAA 59.192 33.333 0.00 0.00 46.23 2.44
57 58 4.366586 TGCACAAGCGATGATTTTTCAAA 58.633 34.783 0.00 0.00 46.23 2.69
58 59 3.974912 TGCACAAGCGATGATTTTTCAA 58.025 36.364 0.00 0.00 46.23 2.69
59 60 3.639716 TGCACAAGCGATGATTTTTCA 57.360 38.095 0.00 0.00 46.23 2.69
60 61 3.121778 GGTTGCACAAGCGATGATTTTTC 59.878 43.478 0.00 0.00 46.23 2.29
61 62 3.059166 GGTTGCACAAGCGATGATTTTT 58.941 40.909 0.00 0.00 46.23 1.94
62 63 2.035704 TGGTTGCACAAGCGATGATTTT 59.964 40.909 7.94 0.00 46.23 1.82
63 64 1.612950 TGGTTGCACAAGCGATGATTT 59.387 42.857 7.94 0.00 46.23 2.17
64 65 1.200716 CTGGTTGCACAAGCGATGATT 59.799 47.619 7.94 0.00 46.23 2.57
65 66 0.806868 CTGGTTGCACAAGCGATGAT 59.193 50.000 7.94 0.00 46.23 2.45
66 67 0.250252 TCTGGTTGCACAAGCGATGA 60.250 50.000 7.94 3.99 46.23 2.92
67 68 0.806868 ATCTGGTTGCACAAGCGATG 59.193 50.000 14.47 6.47 46.23 3.84
68 69 1.089920 GATCTGGTTGCACAAGCGAT 58.910 50.000 14.87 14.87 46.23 4.58
69 70 0.035317 AGATCTGGTTGCACAAGCGA 59.965 50.000 7.94 8.35 46.23 4.93
70 71 1.725641 TAGATCTGGTTGCACAAGCG 58.274 50.000 5.18 3.73 46.23 4.68
71 72 3.539604 AGATAGATCTGGTTGCACAAGC 58.460 45.455 5.18 5.64 37.19 4.01
72 73 5.181009 TGAAGATAGATCTGGTTGCACAAG 58.819 41.667 5.18 0.00 37.19 3.16
73 74 5.164620 TGAAGATAGATCTGGTTGCACAA 57.835 39.130 5.18 0.00 37.19 3.33
74 75 4.824479 TGAAGATAGATCTGGTTGCACA 57.176 40.909 5.18 0.00 37.19 4.57
75 76 4.333926 GGTTGAAGATAGATCTGGTTGCAC 59.666 45.833 5.18 0.00 37.19 4.57
76 77 4.225942 AGGTTGAAGATAGATCTGGTTGCA 59.774 41.667 5.18 0.00 37.19 4.08
77 78 4.775236 AGGTTGAAGATAGATCTGGTTGC 58.225 43.478 5.18 0.00 37.19 4.17
78 79 6.317391 GGAAAGGTTGAAGATAGATCTGGTTG 59.683 42.308 5.18 0.00 37.19 3.77
79 80 6.418946 GGAAAGGTTGAAGATAGATCTGGTT 58.581 40.000 5.18 0.00 37.19 3.67
95 96 1.746787 GTTGTGGACAACGGAAAGGTT 59.253 47.619 6.89 0.00 45.44 3.50
128 129 2.353406 GCAAGACATTTGGAGCAGCAAT 60.353 45.455 0.00 0.00 0.00 3.56
161 162 4.566545 TTCTGTGTGTTTAACAGGCATG 57.433 40.909 0.00 0.00 44.26 4.06
229 230 1.574428 CCGACGGCCTCAACAAAAG 59.426 57.895 0.00 0.00 0.00 2.27
242 243 1.244816 TATCTCCACCTATGCCGACG 58.755 55.000 0.00 0.00 0.00 5.12
253 254 0.601311 GGCCGTCAGCATATCTCCAC 60.601 60.000 0.00 0.00 46.50 4.02
265 266 3.068881 CCTTTCCTCAGGCCGTCA 58.931 61.111 0.00 0.00 0.00 4.35
272 273 2.125512 CCGACGGCCTTTCCTCAG 60.126 66.667 0.00 0.00 0.00 3.35
291 292 2.231478 CCGTCGGCATATTCTGAGGTAT 59.769 50.000 0.00 0.00 0.00 2.73
415 416 3.834610 CGAGTCCGTGAGTGTCTTATTT 58.165 45.455 0.00 0.00 0.00 1.40
421 422 2.126424 GGCGAGTCCGTGAGTGTC 60.126 66.667 0.00 0.00 38.24 3.67
454 456 9.807649 GGTATGAAACTCATAAAAATTCATGCT 57.192 29.630 12.34 0.00 40.64 3.79
466 468 6.100279 AGCTCATTCCAGGTATGAAACTCATA 59.900 38.462 9.86 0.00 38.26 2.15
468 470 4.225942 AGCTCATTCCAGGTATGAAACTCA 59.774 41.667 9.86 0.00 32.02 3.41
474 476 2.702478 CAGGAGCTCATTCCAGGTATGA 59.298 50.000 17.19 8.41 39.84 2.15
478 480 2.254152 TACAGGAGCTCATTCCAGGT 57.746 50.000 17.19 4.74 39.84 4.00
487 489 8.348507 CAAGGAAAAATCAATATACAGGAGCTC 58.651 37.037 4.71 4.71 0.00 4.09
601 603 7.410120 TGATAGAAGTGCTTCAGTCAATAGA 57.590 36.000 13.58 0.00 41.84 1.98
640 642 0.318699 GTGTTCAAAAAGGGAGGCGC 60.319 55.000 0.00 0.00 0.00 6.53
890 944 7.047271 GGAGATAGAATTCAGGGAGAATATGC 58.953 42.308 8.44 0.00 46.09 3.14
924 978 2.879002 TTGGAGATGAGCTGATCGTC 57.121 50.000 7.56 7.03 43.31 4.20
998 1052 1.948138 CAGCAGCTAGGACGCATCG 60.948 63.158 0.00 0.00 0.00 3.84
1296 1352 0.175760 GCTTGCCTAGGTCGATGACA 59.824 55.000 11.31 0.00 33.68 3.58
1521 1585 1.840635 GAACCATTGTAGAGCCCTCCT 59.159 52.381 0.00 0.00 0.00 3.69
1831 1904 9.693739 ATTACCATGGATAATTAGTTCAACACA 57.306 29.630 21.47 0.00 0.00 3.72
1851 1924 8.002459 AGGACTCCAAAAGAACTTAAATTACCA 58.998 33.333 0.00 0.00 0.00 3.25
2012 2093 8.352201 GGCAATAGTTAATGCAAATCATGAGTA 58.648 33.333 0.09 0.00 44.32 2.59
2034 2115 0.108041 GTATTTCCGGACGGAGGCAA 60.108 55.000 13.64 6.20 46.06 4.52
2035 2116 0.974010 AGTATTTCCGGACGGAGGCA 60.974 55.000 13.64 2.92 46.06 4.75
2036 2117 0.177373 AAGTATTTCCGGACGGAGGC 59.823 55.000 13.64 5.83 46.06 4.70
2037 2118 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2038 2119 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2039 2120 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2040 2121 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2041 2122 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
2042 2123 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
2043 2124 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
2044 2125 1.472728 CCCTCCGACAAGTATTTCCGG 60.473 57.143 0.00 0.00 41.36 5.14
2045 2126 1.206371 ACCCTCCGACAAGTATTTCCG 59.794 52.381 0.00 0.00 0.00 4.30
2046 2127 3.345508 AACCCTCCGACAAGTATTTCC 57.654 47.619 0.00 0.00 0.00 3.13
2047 2128 5.334724 TCTAACCCTCCGACAAGTATTTC 57.665 43.478 0.00 0.00 0.00 2.17
2048 2129 5.189145 ACATCTAACCCTCCGACAAGTATTT 59.811 40.000 0.00 0.00 0.00 1.40
2049 2130 4.715297 ACATCTAACCCTCCGACAAGTATT 59.285 41.667 0.00 0.00 0.00 1.89
2050 2131 4.287552 ACATCTAACCCTCCGACAAGTAT 58.712 43.478 0.00 0.00 0.00 2.12
2051 2132 3.705051 ACATCTAACCCTCCGACAAGTA 58.295 45.455 0.00 0.00 0.00 2.24
2052 2133 2.537143 ACATCTAACCCTCCGACAAGT 58.463 47.619 0.00 0.00 0.00 3.16
2053 2134 4.585162 AGATACATCTAACCCTCCGACAAG 59.415 45.833 0.00 0.00 34.85 3.16
2054 2135 4.543689 AGATACATCTAACCCTCCGACAA 58.456 43.478 0.00 0.00 34.85 3.18
2055 2136 4.180377 AGATACATCTAACCCTCCGACA 57.820 45.455 0.00 0.00 34.85 4.35
2056 2137 6.036953 CGTATAGATACATCTAACCCTCCGAC 59.963 46.154 3.16 0.00 42.20 4.79
2057 2138 6.111382 CGTATAGATACATCTAACCCTCCGA 58.889 44.000 3.16 0.00 42.20 4.55
2058 2139 5.879223 ACGTATAGATACATCTAACCCTCCG 59.121 44.000 3.16 3.27 42.20 4.63
2059 2140 8.798859 TTACGTATAGATACATCTAACCCTCC 57.201 38.462 0.00 0.00 42.20 4.30
2097 2178 9.919416 TCAGAGAAATGGATAAAAATGGATGTA 57.081 29.630 0.00 0.00 0.00 2.29
2098 2179 8.689972 GTCAGAGAAATGGATAAAAATGGATGT 58.310 33.333 0.00 0.00 0.00 3.06
2099 2180 8.689061 TGTCAGAGAAATGGATAAAAATGGATG 58.311 33.333 0.00 0.00 0.00 3.51
2100 2181 8.827832 TGTCAGAGAAATGGATAAAAATGGAT 57.172 30.769 0.00 0.00 0.00 3.41
2101 2182 8.648698 TTGTCAGAGAAATGGATAAAAATGGA 57.351 30.769 0.00 0.00 0.00 3.41
2102 2183 8.526147 ACTTGTCAGAGAAATGGATAAAAATGG 58.474 33.333 0.00 0.00 0.00 3.16
2109 2190 9.098355 CGAAAATACTTGTCAGAGAAATGGATA 57.902 33.333 0.00 0.00 0.00 2.59
2110 2191 7.066284 CCGAAAATACTTGTCAGAGAAATGGAT 59.934 37.037 0.00 0.00 0.00 3.41
2111 2192 6.371548 CCGAAAATACTTGTCAGAGAAATGGA 59.628 38.462 0.00 0.00 0.00 3.41
2112 2193 6.371548 TCCGAAAATACTTGTCAGAGAAATGG 59.628 38.462 0.00 0.00 0.00 3.16
2113 2194 7.095229 TGTCCGAAAATACTTGTCAGAGAAATG 60.095 37.037 0.00 0.00 0.00 2.32
2114 2195 6.934645 TGTCCGAAAATACTTGTCAGAGAAAT 59.065 34.615 0.00 0.00 0.00 2.17
2115 2196 6.285224 TGTCCGAAAATACTTGTCAGAGAAA 58.715 36.000 0.00 0.00 0.00 2.52
2116 2197 5.849510 TGTCCGAAAATACTTGTCAGAGAA 58.150 37.500 0.00 0.00 0.00 2.87
2117 2198 5.243060 TCTGTCCGAAAATACTTGTCAGAGA 59.757 40.000 0.00 0.00 0.00 3.10
2118 2199 5.470368 TCTGTCCGAAAATACTTGTCAGAG 58.530 41.667 0.00 0.00 0.00 3.35
2119 2200 5.010719 ACTCTGTCCGAAAATACTTGTCAGA 59.989 40.000 0.00 0.00 0.00 3.27
2120 2201 5.230942 ACTCTGTCCGAAAATACTTGTCAG 58.769 41.667 0.00 0.00 0.00 3.51
2121 2202 5.209818 ACTCTGTCCGAAAATACTTGTCA 57.790 39.130 0.00 0.00 0.00 3.58
2122 2203 7.829378 AATACTCTGTCCGAAAATACTTGTC 57.171 36.000 0.00 0.00 0.00 3.18
2123 2204 9.886132 ATAAATACTCTGTCCGAAAATACTTGT 57.114 29.630 0.00 0.00 0.00 3.16
2131 2212 9.967346 CTGATAAGATAAATACTCTGTCCGAAA 57.033 33.333 0.00 0.00 0.00 3.46
2132 2213 8.577296 CCTGATAAGATAAATACTCTGTCCGAA 58.423 37.037 0.00 0.00 0.00 4.30
2133 2214 7.942894 TCCTGATAAGATAAATACTCTGTCCGA 59.057 37.037 0.00 0.00 0.00 4.55
2134 2215 8.112016 TCCTGATAAGATAAATACTCTGTCCG 57.888 38.462 0.00 0.00 0.00 4.79
2153 2234 9.539194 AAGAATCTTTATTCCAAGTTTCCTGAT 57.461 29.630 0.00 0.00 42.20 2.90
2288 2369 1.290009 GCCAATCAAGTGGGTGCAC 59.710 57.895 8.80 8.80 39.26 4.57
2303 2387 4.640201 GGACAAAATTATGAGTAGCTGCCA 59.360 41.667 0.00 0.00 0.00 4.92
2352 2436 1.291033 TGGGCACTCCACTAGTATCCT 59.709 52.381 0.00 0.00 41.46 3.24
2367 2451 1.135315 GTCGTACGTCTAACATGGGCA 60.135 52.381 16.05 0.00 0.00 5.36
2368 2452 1.553308 GTCGTACGTCTAACATGGGC 58.447 55.000 16.05 0.00 0.00 5.36
2369 2453 1.473677 TGGTCGTACGTCTAACATGGG 59.526 52.381 16.05 0.00 0.00 4.00
2370 2454 2.523015 GTGGTCGTACGTCTAACATGG 58.477 52.381 16.05 0.00 0.00 3.66
2371 2455 2.523015 GGTGGTCGTACGTCTAACATG 58.477 52.381 16.05 0.00 0.00 3.21
2372 2456 1.131126 CGGTGGTCGTACGTCTAACAT 59.869 52.381 16.05 0.00 0.00 2.71
2373 2457 0.516877 CGGTGGTCGTACGTCTAACA 59.483 55.000 16.05 1.56 0.00 2.41
2374 2458 3.296516 CGGTGGTCGTACGTCTAAC 57.703 57.895 16.05 9.59 0.00 2.34
2388 2472 2.566111 ATATGGTGGGGGCAACGGTG 62.566 60.000 0.00 0.00 37.60 4.94
2389 2473 2.313427 ATATGGTGGGGGCAACGGT 61.313 57.895 0.00 0.00 37.60 4.83
2390 2474 1.827789 CATATGGTGGGGGCAACGG 60.828 63.158 0.00 0.00 37.60 4.44
2391 2475 2.489275 GCATATGGTGGGGGCAACG 61.489 63.158 4.56 0.00 37.60 4.10
2392 2476 2.133641 GGCATATGGTGGGGGCAAC 61.134 63.158 4.56 0.00 0.00 4.17
2393 2477 1.884456 AAGGCATATGGTGGGGGCAA 61.884 55.000 4.56 0.00 0.00 4.52
2394 2478 1.884456 AAAGGCATATGGTGGGGGCA 61.884 55.000 4.56 0.00 0.00 5.36
2395 2479 1.075301 AAAGGCATATGGTGGGGGC 60.075 57.895 4.56 0.00 0.00 5.80
2396 2480 0.261402 TGAAAGGCATATGGTGGGGG 59.739 55.000 4.56 0.00 0.00 5.40
2397 2481 2.386829 ATGAAAGGCATATGGTGGGG 57.613 50.000 4.56 0.00 34.82 4.96
2398 2482 3.569491 AGAATGAAAGGCATATGGTGGG 58.431 45.455 4.56 0.00 35.78 4.61
2399 2483 5.278660 GCTAAGAATGAAAGGCATATGGTGG 60.279 44.000 4.56 0.00 35.78 4.61
2400 2484 5.278660 GGCTAAGAATGAAAGGCATATGGTG 60.279 44.000 4.56 0.00 35.78 4.17
2401 2485 4.829492 GGCTAAGAATGAAAGGCATATGGT 59.171 41.667 4.56 0.00 35.78 3.55
2402 2486 4.828939 TGGCTAAGAATGAAAGGCATATGG 59.171 41.667 4.56 0.00 35.78 2.74
2403 2487 5.766670 TCTGGCTAAGAATGAAAGGCATATG 59.233 40.000 0.00 0.00 35.78 1.78
2404 2488 5.945310 TCTGGCTAAGAATGAAAGGCATAT 58.055 37.500 0.00 0.00 35.78 1.78
2405 2489 5.372343 TCTGGCTAAGAATGAAAGGCATA 57.628 39.130 0.00 0.00 35.78 3.14
2406 2490 4.240881 TCTGGCTAAGAATGAAAGGCAT 57.759 40.909 0.00 0.00 39.43 4.40
2476 2663 5.824904 ATGCCATTCATTCTAGTGTTGTC 57.175 39.130 0.00 0.00 29.16 3.18
2484 2671 4.508943 CCCCACCATATGCCATTCATTCTA 60.509 45.833 0.00 0.00 36.63 2.10
2486 2673 2.564062 CCCCACCATATGCCATTCATTC 59.436 50.000 0.00 0.00 36.63 2.67
2487 2674 2.612000 CCCCACCATATGCCATTCATT 58.388 47.619 0.00 0.00 36.63 2.57
2488 2675 1.203212 CCCCCACCATATGCCATTCAT 60.203 52.381 0.00 0.00 39.17 2.57
2489 2676 0.188096 CCCCCACCATATGCCATTCA 59.812 55.000 0.00 0.00 0.00 2.57
2490 2677 1.187567 GCCCCCACCATATGCCATTC 61.188 60.000 0.00 0.00 0.00 2.67
2491 2678 1.152269 GCCCCCACCATATGCCATT 60.152 57.895 0.00 0.00 0.00 3.16
2492 2679 1.959007 TTGCCCCCACCATATGCCAT 61.959 55.000 0.00 0.00 0.00 4.40
2493 2680 2.630510 TTGCCCCCACCATATGCCA 61.631 57.895 0.00 0.00 0.00 4.92
2494 2681 2.133641 GTTGCCCCCACCATATGCC 61.134 63.158 0.00 0.00 0.00 4.40
2495 2682 2.489275 CGTTGCCCCCACCATATGC 61.489 63.158 0.00 0.00 0.00 3.14
2496 2683 1.827789 CCGTTGCCCCCACCATATG 60.828 63.158 0.00 0.00 0.00 1.78
2497 2684 2.279037 GACCGTTGCCCCCACCATAT 62.279 60.000 0.00 0.00 0.00 1.78
2498 2685 2.936584 ACCGTTGCCCCCACCATA 60.937 61.111 0.00 0.00 0.00 2.74
2499 2686 4.360405 GACCGTTGCCCCCACCAT 62.360 66.667 0.00 0.00 0.00 3.55
2502 2689 4.941309 AACGACCGTTGCCCCCAC 62.941 66.667 7.02 0.00 36.91 4.61
2503 2690 4.939368 CAACGACCGTTGCCCCCA 62.939 66.667 20.06 0.00 46.92 4.96
2510 2697 2.032799 TGTTAGACGTACAACGACCGTT 59.967 45.455 6.44 1.53 46.05 4.44
2511 2698 1.601903 TGTTAGACGTACAACGACCGT 59.398 47.619 6.44 0.00 46.05 4.83
2512 2699 2.314561 TGTTAGACGTACAACGACCG 57.685 50.000 6.44 0.00 46.05 4.79
2513 2700 2.919229 CCATGTTAGACGTACAACGACC 59.081 50.000 6.44 0.00 46.05 4.79
2514 2701 2.919229 CCCATGTTAGACGTACAACGAC 59.081 50.000 6.44 0.00 46.05 4.34
2515 2702 2.557924 ACCCATGTTAGACGTACAACGA 59.442 45.455 6.44 0.00 46.05 3.85
2517 2704 5.064441 AGTACCCATGTTAGACGTACAAC 57.936 43.478 5.09 5.09 33.34 3.32
2518 2705 4.158394 GGAGTACCCATGTTAGACGTACAA 59.842 45.833 0.00 0.00 33.34 2.41
2519 2706 3.696051 GGAGTACCCATGTTAGACGTACA 59.304 47.826 0.00 0.00 33.34 2.90
2536 2723 6.334989 CGTCAATTGGTATACTTGTGGAGTA 58.665 40.000 5.42 0.00 44.62 2.59
2639 2826 2.952310 GAGTGATTGTAATTCCTGGCCC 59.048 50.000 0.00 0.00 0.00 5.80
2739 2927 8.123639 ACTGTAGTATCTTCTTGTGCTTTCTA 57.876 34.615 0.00 0.00 0.00 2.10
2829 3018 2.361119 GCGGGTTTTCCTCTTGAAGTTT 59.639 45.455 0.00 0.00 40.46 2.66
2894 3084 2.027385 GAGGGAAGGTTCAATGATGGC 58.973 52.381 0.00 0.00 0.00 4.40
2897 3087 3.192944 TGGAGAGGGAAGGTTCAATGAT 58.807 45.455 0.00 0.00 0.00 2.45
2974 3164 1.915141 AGGGTGAGTTGCTCCAATTG 58.085 50.000 0.00 0.00 31.65 2.32
2998 3188 7.658575 GTGCTCCAAAATATATACCGTTCCTTA 59.341 37.037 0.00 0.00 0.00 2.69
3039 3230 2.669569 CAGTGGGTTGGTCAGGCG 60.670 66.667 0.00 0.00 0.00 5.52
3042 3233 0.179020 TTGCTCAGTGGGTTGGTCAG 60.179 55.000 0.00 0.00 0.00 3.51
3067 3258 1.492993 GGTTGGGCTCTTCTCCTGGT 61.493 60.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.