Multiple sequence alignment - TraesCS3D01G097600

Loading Multiple Alignment...

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 TraesCS3D01G097600 chr3D 100.000 4678 0 0 1 4678 49637366 49642043 0.000000e+00 8639.0
1 TraesCS3D01G097600 chr3D 80.172 464 70 13 1386 1837 335214263 335214716 1.260000e-85 327.0
2 TraesCS3D01G097600 chr3A 95.660 2189 67 14 2083 4256 63066969 63069144 0.000000e+00 3491.0
3 TraesCS3D01G097600 chr3A 92.385 1983 92 27 82 2027 63065011 63066971 0.000000e+00 2771.0
4 TraesCS3D01G097600 chr3A 91.277 321 23 5 4245 4561 63071346 63071665 2.590000e-117 433.0
5 TraesCS3D01G097600 chr3A 88.000 175 7 9 4493 4657 63071622 63071792 1.330000e-45 195.0
6 TraesCS3D01G097600 chr3A 92.105 76 4 2 2011 2085 727071253 727071327 6.400000e-19 106.0
7 TraesCS3D01G097600 chr3B 92.397 1986 83 21 82 2027 79119427 79121384 0.000000e+00 2769.0
8 TraesCS3D01G097600 chr3B 96.862 1179 31 4 2681 3859 79121942 79123114 0.000000e+00 1967.0
9 TraesCS3D01G097600 chr3B 96.649 567 16 2 2083 2648 79121382 79121946 0.000000e+00 939.0
10 TraesCS3D01G097600 chr3B 91.538 520 23 6 3903 4415 79123379 79123884 0.000000e+00 697.0
11 TraesCS3D01G097600 chr3B 100.000 32 0 0 2333 2364 73587675 73587706 5.060000e-05 60.2
12 TraesCS3D01G097600 chr1D 81.319 455 73 8 1386 1837 468031860 468032305 4.450000e-95 359.0
13 TraesCS3D01G097600 chr1D 78.878 303 48 13 2154 2448 109974658 109974364 1.720000e-44 191.0
14 TraesCS3D01G097600 chr1D 85.802 162 22 1 995 1156 109975939 109975779 2.240000e-38 171.0
15 TraesCS3D01G097600 chr4A 80.088 452 78 10 1387 1835 638240065 638239623 4.510000e-85 326.0
16 TraesCS3D01G097600 chr4A 100.000 32 0 0 2333 2364 735595592 735595623 5.060000e-05 60.2
17 TraesCS3D01G097600 chr5B 80.088 452 77 11 1387 1835 407321073 407320632 1.620000e-84 324.0
18 TraesCS3D01G097600 chr1A 79.914 463 73 11 1386 1837 163096403 163096856 5.840000e-84 322.0
19 TraesCS3D01G097600 chr1A 78.641 309 53 10 2145 2448 113859899 113859599 4.780000e-45 193.0
20 TraesCS3D01G097600 chr1A 88.811 143 16 0 995 1137 113861155 113861013 4.810000e-40 176.0
21 TraesCS3D01G097600 chr1A 98.387 62 1 0 2024 2085 11205815 11205754 4.950000e-20 110.0
22 TraesCS3D01G097600 chr1A 100.000 32 0 0 2333 2364 69993920 69993951 5.060000e-05 60.2
23 TraesCS3D01G097600 chr5D 80.088 452 71 11 1395 1837 69676738 69677179 7.550000e-83 318.0
24 TraesCS3D01G097600 chr5D 94.118 68 3 1 2019 2085 446233626 446233693 8.280000e-18 102.0
25 TraesCS3D01G097600 chr2A 79.355 465 68 15 1386 1837 448553731 448553282 7.610000e-78 302.0
26 TraesCS3D01G097600 chr1B 78.526 312 51 13 2145 2448 166593295 166592992 1.720000e-44 191.0
27 TraesCS3D01G097600 chr1B 86.250 160 19 3 995 1154 166594594 166594438 2.240000e-38 171.0
28 TraesCS3D01G097600 chr1B 91.667 72 6 0 2018 2089 15280832 15280761 2.980000e-17 100.0
29 TraesCS3D01G097600 chr2B 96.923 65 1 1 2022 2085 49220925 49220989 1.780000e-19 108.0
30 TraesCS3D01G097600 chr7A 96.875 64 1 1 2024 2086 47699117 47699180 6.400000e-19 106.0
31 TraesCS3D01G097600 chr7A 94.286 70 1 3 2021 2089 263729997 263730064 2.300000e-18 104.0
32 TraesCS3D01G097600 chr7A 95.455 66 2 1 2021 2085 621854665 621854730 2.300000e-18 104.0
33 TraesCS3D01G097600 chr4B 96.875 64 1 1 2025 2087 340684679 340684616 6.400000e-19 106.0
34 TraesCS3D01G097600 chrUn 100.000 32 0 0 2333 2364 8833377 8833408 5.060000e-05 60.2
35 TraesCS3D01G097600 chr4D 100.000 32 0 0 2333 2364 73444234 73444265 5.060000e-05 60.2
36 TraesCS3D01G097600 chr5A 100.000 31 0 0 2333 2363 706493266 706493236 1.820000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G097600 chr3D 49637366 49642043 4677 False 8639.0 8639 100.0000 1 4678 1 chr3D.!!$F1 4677
1 TraesCS3D01G097600 chr3A 63065011 63071792 6781 False 1722.5 3491 91.8305 82 4657 4 chr3A.!!$F2 4575
2 TraesCS3D01G097600 chr3B 79119427 79123884 4457 False 1593.0 2769 94.3615 82 4415 4 chr3B.!!$F2 4333

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
167 174 0.106708 TCCTCCATCCGTGCTTATGC 59.893 55.0 0.00 0.00 40.20 3.14 F
1729 1776 0.248458 AGCACAAACCTTTTGACGCG 60.248 50.0 3.53 3.53 0.00 6.01 F
3168 3230 0.178767 TCGGCTATGTCTTGCTGCAT 59.821 50.0 1.84 0.00 35.69 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2135 0.170561 ACTCACGCGACATGTACTCC 59.829 55.000 15.93 0.0 0.00 3.85 R
3530 3592 2.019337 TCATGCAGATGACATGCGC 58.981 52.632 0.00 0.0 46.87 6.09 R
4657 7199 0.248377 GTACCGTACAAGCGAGCGAT 60.248 55.000 3.69 0.0 0.00 4.58 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
25 26 2.032528 CGTGAGCACCACCCACAT 59.967 61.111 4.06 0.00 42.76 3.21
26 27 2.034879 CGTGAGCACCACCCACATC 61.035 63.158 4.06 0.00 42.76 3.06
27 28 1.376466 GTGAGCACCACCCACATCT 59.624 57.895 0.00 0.00 39.86 2.90
28 29 0.674895 GTGAGCACCACCCACATCTC 60.675 60.000 0.00 0.00 39.86 2.75
29 30 1.448540 GAGCACCACCCACATCTCG 60.449 63.158 0.00 0.00 0.00 4.04
30 31 1.888436 GAGCACCACCCACATCTCGA 61.888 60.000 0.00 0.00 0.00 4.04
31 32 1.741770 GCACCACCCACATCTCGAC 60.742 63.158 0.00 0.00 0.00 4.20
32 33 1.079127 CACCACCCACATCTCGACC 60.079 63.158 0.00 0.00 0.00 4.79
33 34 1.535444 ACCACCCACATCTCGACCA 60.535 57.895 0.00 0.00 0.00 4.02
34 35 1.125093 ACCACCCACATCTCGACCAA 61.125 55.000 0.00 0.00 0.00 3.67
35 36 0.673644 CCACCCACATCTCGACCAAC 60.674 60.000 0.00 0.00 0.00 3.77
36 37 0.673644 CACCCACATCTCGACCAACC 60.674 60.000 0.00 0.00 0.00 3.77
37 38 0.836400 ACCCACATCTCGACCAACCT 60.836 55.000 0.00 0.00 0.00 3.50
38 39 1.191535 CCCACATCTCGACCAACCTA 58.808 55.000 0.00 0.00 0.00 3.08
39 40 1.762957 CCCACATCTCGACCAACCTAT 59.237 52.381 0.00 0.00 0.00 2.57
40 41 2.483714 CCCACATCTCGACCAACCTATG 60.484 54.545 0.00 0.00 0.00 2.23
41 42 2.168521 CCACATCTCGACCAACCTATGT 59.831 50.000 0.00 0.00 0.00 2.29
42 43 3.369471 CCACATCTCGACCAACCTATGTT 60.369 47.826 0.00 0.00 34.14 2.71
43 44 4.253685 CACATCTCGACCAACCTATGTTT 58.746 43.478 0.00 0.00 30.42 2.83
44 45 4.330074 CACATCTCGACCAACCTATGTTTC 59.670 45.833 0.00 0.00 30.42 2.78
45 46 4.020573 ACATCTCGACCAACCTATGTTTCA 60.021 41.667 0.00 0.00 30.42 2.69
46 47 4.610605 TCTCGACCAACCTATGTTTCAA 57.389 40.909 0.00 0.00 30.42 2.69
47 48 4.566004 TCTCGACCAACCTATGTTTCAAG 58.434 43.478 0.00 0.00 30.42 3.02
48 49 4.039973 TCTCGACCAACCTATGTTTCAAGT 59.960 41.667 0.00 0.00 30.42 3.16
49 50 4.312443 TCGACCAACCTATGTTTCAAGTC 58.688 43.478 0.00 0.00 30.42 3.01
50 51 3.435671 CGACCAACCTATGTTTCAAGTCC 59.564 47.826 0.00 0.00 30.42 3.85
51 52 3.756963 GACCAACCTATGTTTCAAGTCCC 59.243 47.826 0.00 0.00 30.42 4.46
52 53 2.747446 CCAACCTATGTTTCAAGTCCCG 59.253 50.000 0.00 0.00 30.42 5.14
53 54 2.747446 CAACCTATGTTTCAAGTCCCGG 59.253 50.000 0.00 0.00 30.42 5.73
54 55 2.262637 ACCTATGTTTCAAGTCCCGGA 58.737 47.619 0.73 0.00 0.00 5.14
55 56 2.640826 ACCTATGTTTCAAGTCCCGGAA 59.359 45.455 0.73 0.00 0.00 4.30
56 57 3.073356 ACCTATGTTTCAAGTCCCGGAAA 59.927 43.478 0.73 0.00 0.00 3.13
57 58 4.076394 CCTATGTTTCAAGTCCCGGAAAA 58.924 43.478 0.73 0.00 35.03 2.29
58 59 4.521256 CCTATGTTTCAAGTCCCGGAAAAA 59.479 41.667 0.73 0.00 35.03 1.94
59 60 3.786516 TGTTTCAAGTCCCGGAAAAAC 57.213 42.857 0.73 4.80 35.03 2.43
60 61 2.427812 TGTTTCAAGTCCCGGAAAAACC 59.572 45.455 0.73 0.00 35.03 3.27
61 62 2.427812 GTTTCAAGTCCCGGAAAAACCA 59.572 45.455 0.73 0.00 38.90 3.67
62 63 2.668144 TCAAGTCCCGGAAAAACCAT 57.332 45.000 0.73 0.00 38.90 3.55
63 64 2.952116 TCAAGTCCCGGAAAAACCATT 58.048 42.857 0.73 0.00 38.90 3.16
64 65 4.101645 TCAAGTCCCGGAAAAACCATTA 57.898 40.909 0.73 0.00 38.90 1.90
65 66 3.822167 TCAAGTCCCGGAAAAACCATTAC 59.178 43.478 0.73 0.00 38.90 1.89
66 67 2.799017 AGTCCCGGAAAAACCATTACC 58.201 47.619 0.73 0.00 38.90 2.85
67 68 1.820519 GTCCCGGAAAAACCATTACCC 59.179 52.381 0.73 0.00 38.90 3.69
68 69 1.428139 TCCCGGAAAAACCATTACCCA 59.572 47.619 0.73 0.00 38.90 4.51
69 70 1.546923 CCCGGAAAAACCATTACCCAC 59.453 52.381 0.73 0.00 38.90 4.61
70 71 2.240279 CCGGAAAAACCATTACCCACA 58.760 47.619 0.00 0.00 38.90 4.17
71 72 2.829120 CCGGAAAAACCATTACCCACAT 59.171 45.455 0.00 0.00 38.90 3.21
72 73 3.119280 CCGGAAAAACCATTACCCACATC 60.119 47.826 0.00 0.00 38.90 3.06
73 74 3.761752 CGGAAAAACCATTACCCACATCT 59.238 43.478 0.00 0.00 38.90 2.90
74 75 4.142469 CGGAAAAACCATTACCCACATCTC 60.142 45.833 0.00 0.00 38.90 2.75
75 76 4.142469 GGAAAAACCATTACCCACATCTCG 60.142 45.833 0.00 0.00 38.79 4.04
76 77 3.992943 AAACCATTACCCACATCTCGA 57.007 42.857 0.00 0.00 0.00 4.04
77 78 2.981859 ACCATTACCCACATCTCGAC 57.018 50.000 0.00 0.00 0.00 4.20
78 79 1.485066 ACCATTACCCACATCTCGACC 59.515 52.381 0.00 0.00 0.00 4.79
79 80 1.484653 CCATTACCCACATCTCGACCA 59.515 52.381 0.00 0.00 0.00 4.02
80 81 2.093181 CCATTACCCACATCTCGACCAA 60.093 50.000 0.00 0.00 0.00 3.67
90 91 4.023980 ACATCTCGACCAACCTCTTATCA 58.976 43.478 0.00 0.00 0.00 2.15
131 138 2.357593 ATCCATCCCCACCAATCCGC 62.358 60.000 0.00 0.00 0.00 5.54
133 140 2.696125 ATCCCCACCAATCCGCCT 60.696 61.111 0.00 0.00 0.00 5.52
152 159 0.340208 TCCCTTCCCCTCTTCTCCTC 59.660 60.000 0.00 0.00 0.00 3.71
155 162 1.344906 CCTTCCCCTCTTCTCCTCCAT 60.345 57.143 0.00 0.00 0.00 3.41
167 174 0.106708 TCCTCCATCCGTGCTTATGC 59.893 55.000 0.00 0.00 40.20 3.14
183 190 4.733542 GCCGCACCCTAAGCCCAA 62.734 66.667 0.00 0.00 0.00 4.12
201 208 4.500545 GCCCAACATTTACACATTCACACA 60.501 41.667 0.00 0.00 0.00 3.72
250 258 9.748708 ATACATAAACATTCATAAACACCATGC 57.251 29.630 0.00 0.00 0.00 4.06
278 286 7.225145 TGCTCAAAGTTGAATGAATTGGAAAAG 59.775 33.333 0.00 0.00 36.64 2.27
457 470 5.814705 CACCTACTGCGTACTACTACTACTT 59.185 44.000 0.00 0.00 0.00 2.24
479 492 1.834188 AATCAAACATGTCCCCGGAC 58.166 50.000 0.73 6.95 44.77 4.79
490 503 2.124320 CCCGGACCAAATCGCCAT 60.124 61.111 0.73 0.00 0.00 4.40
491 504 1.752694 CCCGGACCAAATCGCCATT 60.753 57.895 0.73 0.00 0.00 3.16
518 531 2.355197 CTGCGGTGGTTGATAATCACA 58.645 47.619 7.20 0.00 33.45 3.58
629 642 2.420827 CGGTTAGCAGGAGAGAGAGAGA 60.421 54.545 0.00 0.00 0.00 3.10
630 643 3.214328 GGTTAGCAGGAGAGAGAGAGAG 58.786 54.545 0.00 0.00 0.00 3.20
631 644 3.118038 GGTTAGCAGGAGAGAGAGAGAGA 60.118 52.174 0.00 0.00 0.00 3.10
632 645 4.130118 GTTAGCAGGAGAGAGAGAGAGAG 58.870 52.174 0.00 0.00 0.00 3.20
633 646 1.492176 AGCAGGAGAGAGAGAGAGAGG 59.508 57.143 0.00 0.00 0.00 3.69
634 647 1.490490 GCAGGAGAGAGAGAGAGAGGA 59.510 57.143 0.00 0.00 0.00 3.71
739 752 3.581687 GATCAGATCCCTCGCCGCC 62.582 68.421 0.00 0.00 0.00 6.13
802 815 2.426522 CTCCGAGCACTTGGATTTTCA 58.573 47.619 7.10 0.00 42.06 2.69
803 816 2.813754 CTCCGAGCACTTGGATTTTCAA 59.186 45.455 7.10 0.00 42.06 2.69
804 817 2.552315 TCCGAGCACTTGGATTTTCAAC 59.448 45.455 2.24 0.00 38.21 3.18
805 818 2.293122 CCGAGCACTTGGATTTTCAACA 59.707 45.455 0.00 0.00 36.15 3.33
825 838 1.999634 AAGAGGTTGGTGGTGCTGCT 62.000 55.000 0.00 0.00 0.00 4.24
826 839 2.203394 AGGTTGGTGGTGCTGCTG 60.203 61.111 0.00 0.00 0.00 4.41
827 840 3.982241 GGTTGGTGGTGCTGCTGC 61.982 66.667 8.89 8.89 40.20 5.25
970 992 1.521450 GCTGCTGCTTCTTGCTTCCA 61.521 55.000 8.53 0.00 43.37 3.53
980 1002 0.873054 CTTGCTTCCAGTGCTCTGTG 59.127 55.000 14.31 6.50 39.82 3.66
1178 1201 2.757077 CCCCGCTCCTTGTCCTTT 59.243 61.111 0.00 0.00 0.00 3.11
1271 1313 4.082523 TCGTGGGCAGTGGCTAGC 62.083 66.667 17.16 6.04 40.87 3.42
1311 1353 6.413818 CGTGAGAATTTTGTTTACTGTGAACC 59.586 38.462 12.19 0.00 0.00 3.62
1352 1394 2.159179 TGTCTCGATGAGGGGAATCA 57.841 50.000 0.00 0.00 0.00 2.57
1456 1498 9.713740 CTCAACTTGAATGAATTACAGCTATTC 57.286 33.333 1.40 1.40 33.58 1.75
1464 1507 8.970859 AATGAATTACAGCTATTCTGCTTAGT 57.029 30.769 8.73 0.00 46.76 2.24
1534 1577 6.055588 AGCTTACATAGTGCCAAACGATATT 58.944 36.000 0.00 0.00 0.00 1.28
1539 1582 6.785191 ACATAGTGCCAAACGATATTTTGAG 58.215 36.000 2.09 0.00 38.54 3.02
1661 1708 1.818642 GTTGACAAGCTGGCATCTCT 58.181 50.000 0.00 0.00 33.90 3.10
1678 1725 4.687901 TCTCTTGGTGACATTCTGTTCA 57.312 40.909 0.00 0.00 42.32 3.18
1681 1728 4.380531 TCTTGGTGACATTCTGTTCACTC 58.619 43.478 2.04 0.00 42.32 3.51
1729 1776 0.248458 AGCACAAACCTTTTGACGCG 60.248 50.000 3.53 3.53 0.00 6.01
1822 1869 5.153950 ACTCTGTTGGTTTCTATCAGGTC 57.846 43.478 0.00 0.00 0.00 3.85
1825 1872 4.593206 TCTGTTGGTTTCTATCAGGTCAGT 59.407 41.667 0.00 0.00 0.00 3.41
1826 1873 5.071788 TCTGTTGGTTTCTATCAGGTCAGTT 59.928 40.000 0.00 0.00 0.00 3.16
1827 1874 5.063204 TGTTGGTTTCTATCAGGTCAGTTG 58.937 41.667 0.00 0.00 0.00 3.16
1833 1890 5.808366 TTCTATCAGGTCAGTTGTGTTCT 57.192 39.130 0.00 0.00 0.00 3.01
1838 1895 2.024414 AGGTCAGTTGTGTTCTTTGCC 58.976 47.619 0.00 0.00 0.00 4.52
2025 2082 8.887393 AGGAGAAGGGTTTCAGTTAAGTTATTA 58.113 33.333 0.00 0.00 35.70 0.98
2026 2083 8.944029 GGAGAAGGGTTTCAGTTAAGTTATTAC 58.056 37.037 0.00 0.00 35.70 1.89
2027 2084 9.722184 GAGAAGGGTTTCAGTTAAGTTATTACT 57.278 33.333 0.00 0.00 35.70 2.24
2028 2085 9.722184 AGAAGGGTTTCAGTTAAGTTATTACTC 57.278 33.333 0.00 0.00 35.70 2.59
2029 2086 8.859236 AAGGGTTTCAGTTAAGTTATTACTCC 57.141 34.615 0.00 0.00 31.99 3.85
2030 2087 7.400439 AGGGTTTCAGTTAAGTTATTACTCCC 58.600 38.462 0.00 0.00 31.99 4.30
2031 2088 7.239143 AGGGTTTCAGTTAAGTTATTACTCCCT 59.761 37.037 6.15 6.15 31.99 4.20
2032 2089 7.551974 GGGTTTCAGTTAAGTTATTACTCCCTC 59.448 40.741 0.00 0.00 31.99 4.30
2033 2090 7.551974 GGTTTCAGTTAAGTTATTACTCCCTCC 59.448 40.741 0.00 0.00 31.99 4.30
2034 2091 6.461110 TCAGTTAAGTTATTACTCCCTCCG 57.539 41.667 0.00 0.00 31.99 4.63
2035 2092 5.954150 TCAGTTAAGTTATTACTCCCTCCGT 59.046 40.000 0.00 0.00 31.99 4.69
2036 2093 6.438425 TCAGTTAAGTTATTACTCCCTCCGTT 59.562 38.462 0.00 0.00 31.99 4.44
2037 2094 6.755607 CAGTTAAGTTATTACTCCCTCCGTTC 59.244 42.308 0.00 0.00 31.99 3.95
2038 2095 4.750021 AAGTTATTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 31.99 3.62
2039 2096 3.716431 AGTTATTACTCCCTCCGTTCCA 58.284 45.455 0.00 0.00 0.00 3.53
2040 2097 4.098894 AGTTATTACTCCCTCCGTTCCAA 58.901 43.478 0.00 0.00 0.00 3.53
2041 2098 4.533311 AGTTATTACTCCCTCCGTTCCAAA 59.467 41.667 0.00 0.00 0.00 3.28
2042 2099 5.191124 AGTTATTACTCCCTCCGTTCCAAAT 59.809 40.000 0.00 0.00 0.00 2.32
2043 2100 4.586306 ATTACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
2044 2101 5.703730 ATTACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
2045 2102 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2046 2103 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2047 2104 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2048 2105 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2049 2106 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2050 2107 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2051 2108 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2052 2109 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2053 2110 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2054 2111 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2055 2112 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2056 2113 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2057 2114 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2058 2115 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2059 2116 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2060 2117 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2061 2118 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2062 2119 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2063 2120 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2064 2121 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2065 2122 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2066 2123 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2067 2124 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2068 2125 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2069 2126 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2070 2127 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2071 2128 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2072 2129 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2082 2139 3.502123 TCAAATTTGAACGGAGGGAGT 57.498 42.857 18.45 0.00 33.55 3.85
2297 2359 9.862371 TCTGACTGATTTTCTATCTTTACTGTC 57.138 33.333 0.00 0.00 0.00 3.51
2565 2627 9.366216 TGTAGTTTGTCAGTATTAGCTAATGTG 57.634 33.333 25.99 21.60 0.00 3.21
2621 2683 5.163652 ACTGTGTTTTCTTAACAGCCACTTC 60.164 40.000 2.09 0.00 44.14 3.01
2646 2708 7.929785 TCGTTTCTACTTTCCTGTTGAACTTAT 59.070 33.333 0.00 0.00 33.08 1.73
2679 2741 6.490721 ACTGTAGATTTTCTATCCTACTCGGG 59.509 42.308 0.00 0.00 34.26 5.14
2883 2945 0.546122 TTGGTCCATTCCTCGATGGG 59.454 55.000 3.03 0.00 45.42 4.00
3002 3064 4.572389 ACGGCTTCATGTGATTCATAGTTC 59.428 41.667 0.00 0.00 34.67 3.01
3168 3230 0.178767 TCGGCTATGTCTTGCTGCAT 59.821 50.000 1.84 0.00 35.69 3.96
3342 3404 5.742926 GCTTTGAGCTCTTGATATTTTCTGC 59.257 40.000 16.19 0.00 38.45 4.26
3371 3433 0.967380 TCCTGATCTGCTGAGCGACA 60.967 55.000 0.00 0.00 0.00 4.35
3444 3506 8.282256 AGTCCACTTTATAAGCCCTATCAATTT 58.718 33.333 0.00 0.00 0.00 1.82
3530 3592 8.958175 TGCTACAATTTTCTTGTTATTTACCG 57.042 30.769 0.00 0.00 34.11 4.02
3548 3610 1.768112 CGCGCATGTCATCTGCATGA 61.768 55.000 8.75 0.00 44.60 3.07
3563 3625 2.158623 TGCATGACAGGTGAAAGAAGGT 60.159 45.455 0.00 0.00 0.00 3.50
3683 3745 4.166011 GCACGGGCATGAACGCTC 62.166 66.667 3.77 0.00 40.72 5.03
3869 3931 3.434882 CCTTGTTCCATTTTTGGGCCTTT 60.435 43.478 4.53 0.00 0.00 3.11
4031 4314 1.345422 TGGGCAGGGGATCTCTTGTAT 60.345 52.381 6.57 0.00 0.00 2.29
4101 4393 4.384846 CGCAAGACTCAACACGTAGTTTAT 59.615 41.667 0.00 0.00 38.61 1.40
4132 4424 1.948104 TGTACAAGTGTCCACTGCAC 58.052 50.000 0.00 0.82 41.58 4.57
4161 4453 2.620585 GGTGAGCTTTTGAGCTTTCAGT 59.379 45.455 2.06 0.00 46.36 3.41
4190 4484 8.768019 TGTGATATAAGATGCATTTTTCTCTCG 58.232 33.333 7.89 0.00 0.00 4.04
4323 6830 5.104374 GCCAATTTTGTTCGATCATGATGT 58.896 37.500 14.30 0.00 0.00 3.06
4495 7003 5.611374 TCTTCTCTCTCACAAAACCGAAAT 58.389 37.500 0.00 0.00 0.00 2.17
4498 7006 5.123227 TCTCTCTCACAAAACCGAAATGTT 58.877 37.500 0.00 0.00 0.00 2.71
4502 7010 6.018262 TCTCTCACAAAACCGAAATGTTAGTG 60.018 38.462 0.00 0.00 36.50 2.74
4544 7052 9.914923 CAAAATGTTAGGTTTTCTTTTTAGTGC 57.085 29.630 0.00 0.00 0.00 4.40
4549 7089 9.181061 TGTTAGGTTTTCTTTTTAGTGCTAACT 57.819 29.630 0.00 0.00 40.67 2.24
4587 7127 3.902881 AAAACTTGGCACATGAACCAA 57.097 38.095 18.73 18.73 43.59 3.67
4659 7201 3.120796 TGATGCAGGCCCATCAATC 57.879 52.632 18.98 8.05 46.18 2.67
4660 7202 0.820482 TGATGCAGGCCCATCAATCG 60.820 55.000 18.98 0.00 46.18 3.34
4661 7203 2.138656 GATGCAGGCCCATCAATCGC 62.139 60.000 15.00 0.17 40.96 4.58
4662 7204 2.517875 GCAGGCCCATCAATCGCT 60.518 61.111 0.00 0.00 0.00 4.93
4663 7205 2.550101 GCAGGCCCATCAATCGCTC 61.550 63.158 0.00 0.00 0.00 5.03
4664 7206 2.109799 AGGCCCATCAATCGCTCG 59.890 61.111 0.00 0.00 0.00 5.03
4665 7207 3.654020 GGCCCATCAATCGCTCGC 61.654 66.667 0.00 0.00 0.00 5.03
4666 7208 2.590007 GCCCATCAATCGCTCGCT 60.590 61.111 0.00 0.00 0.00 4.93
4667 7209 2.182842 GCCCATCAATCGCTCGCTT 61.183 57.895 0.00 0.00 0.00 4.68
4668 7210 1.645455 CCCATCAATCGCTCGCTTG 59.355 57.895 0.02 0.02 0.00 4.01
4669 7211 1.091771 CCCATCAATCGCTCGCTTGT 61.092 55.000 5.88 0.00 0.00 3.16
4670 7212 1.570813 CCATCAATCGCTCGCTTGTA 58.429 50.000 5.88 0.00 0.00 2.41
4671 7213 1.258982 CCATCAATCGCTCGCTTGTAC 59.741 52.381 5.88 0.00 0.00 2.90
4672 7214 1.071894 CATCAATCGCTCGCTTGTACG 60.072 52.381 5.88 0.00 0.00 3.67
4673 7215 0.800683 TCAATCGCTCGCTTGTACGG 60.801 55.000 5.88 0.00 0.00 4.02
4674 7216 1.076533 CAATCGCTCGCTTGTACGGT 61.077 55.000 0.00 0.00 0.00 4.83
4675 7217 0.452987 AATCGCTCGCTTGTACGGTA 59.547 50.000 0.00 0.00 0.00 4.02
4676 7218 0.248377 ATCGCTCGCTTGTACGGTAC 60.248 55.000 11.33 11.33 0.00 3.34
4677 7219 1.870901 CGCTCGCTTGTACGGTACC 60.871 63.158 15.26 0.16 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.679311 GAGATGTGGGTGGTGCTCA 59.321 57.895 0.00 0.00 0.00 4.26
11 12 1.448540 CGAGATGTGGGTGGTGCTC 60.449 63.158 0.00 0.00 0.00 4.26
12 13 1.913262 TCGAGATGTGGGTGGTGCT 60.913 57.895 0.00 0.00 0.00 4.40
13 14 1.741770 GTCGAGATGTGGGTGGTGC 60.742 63.158 0.00 0.00 0.00 5.01
14 15 1.079127 GGTCGAGATGTGGGTGGTG 60.079 63.158 0.00 0.00 0.00 4.17
15 16 1.125093 TTGGTCGAGATGTGGGTGGT 61.125 55.000 0.00 0.00 0.00 4.16
16 17 0.673644 GTTGGTCGAGATGTGGGTGG 60.674 60.000 0.00 0.00 0.00 4.61
17 18 0.673644 GGTTGGTCGAGATGTGGGTG 60.674 60.000 0.00 0.00 0.00 4.61
18 19 0.836400 AGGTTGGTCGAGATGTGGGT 60.836 55.000 0.00 0.00 0.00 4.51
19 20 1.191535 TAGGTTGGTCGAGATGTGGG 58.808 55.000 0.00 0.00 0.00 4.61
20 21 2.168521 ACATAGGTTGGTCGAGATGTGG 59.831 50.000 0.00 0.00 0.00 4.17
21 22 3.526931 ACATAGGTTGGTCGAGATGTG 57.473 47.619 0.00 0.00 0.00 3.21
22 23 4.020573 TGAAACATAGGTTGGTCGAGATGT 60.021 41.667 0.00 0.00 37.30 3.06
23 24 4.503910 TGAAACATAGGTTGGTCGAGATG 58.496 43.478 0.00 0.00 37.30 2.90
24 25 4.819105 TGAAACATAGGTTGGTCGAGAT 57.181 40.909 0.00 0.00 37.30 2.75
25 26 4.039973 ACTTGAAACATAGGTTGGTCGAGA 59.960 41.667 13.58 0.00 37.30 4.04
26 27 4.315803 ACTTGAAACATAGGTTGGTCGAG 58.684 43.478 7.39 7.39 37.30 4.04
27 28 4.312443 GACTTGAAACATAGGTTGGTCGA 58.688 43.478 0.00 0.00 37.30 4.20
28 29 3.435671 GGACTTGAAACATAGGTTGGTCG 59.564 47.826 0.00 0.00 37.30 4.79
29 30 3.756963 GGGACTTGAAACATAGGTTGGTC 59.243 47.826 0.00 1.09 37.30 4.02
30 31 3.763057 GGGACTTGAAACATAGGTTGGT 58.237 45.455 0.00 0.00 37.30 3.67
31 32 2.747446 CGGGACTTGAAACATAGGTTGG 59.253 50.000 0.00 0.00 37.30 3.77
32 33 2.747446 CCGGGACTTGAAACATAGGTTG 59.253 50.000 0.00 0.00 37.30 3.77
33 34 2.640826 TCCGGGACTTGAAACATAGGTT 59.359 45.455 0.00 0.00 39.43 3.50
34 35 2.262637 TCCGGGACTTGAAACATAGGT 58.737 47.619 0.00 0.00 0.00 3.08
35 36 3.343941 TTCCGGGACTTGAAACATAGG 57.656 47.619 0.00 0.00 0.00 2.57
36 37 5.458015 GTTTTTCCGGGACTTGAAACATAG 58.542 41.667 0.00 0.00 30.64 2.23
37 38 4.278919 GGTTTTTCCGGGACTTGAAACATA 59.721 41.667 18.30 0.00 30.64 2.29
38 39 3.069016 GGTTTTTCCGGGACTTGAAACAT 59.931 43.478 18.30 0.00 30.64 2.71
39 40 2.427812 GGTTTTTCCGGGACTTGAAACA 59.572 45.455 18.30 0.00 30.64 2.83
40 41 2.427812 TGGTTTTTCCGGGACTTGAAAC 59.572 45.455 0.00 0.00 39.52 2.78
41 42 2.736347 TGGTTTTTCCGGGACTTGAAA 58.264 42.857 0.00 0.00 39.52 2.69
42 43 2.438800 TGGTTTTTCCGGGACTTGAA 57.561 45.000 0.00 0.00 39.52 2.69
43 44 2.668144 ATGGTTTTTCCGGGACTTGA 57.332 45.000 0.00 0.00 39.52 3.02
44 45 3.057104 GGTAATGGTTTTTCCGGGACTTG 60.057 47.826 0.00 0.00 39.52 3.16
45 46 3.159472 GGTAATGGTTTTTCCGGGACTT 58.841 45.455 0.00 0.00 39.52 3.01
46 47 2.555892 GGGTAATGGTTTTTCCGGGACT 60.556 50.000 0.00 0.00 39.52 3.85
47 48 1.820519 GGGTAATGGTTTTTCCGGGAC 59.179 52.381 0.00 0.00 39.52 4.46
48 49 1.428139 TGGGTAATGGTTTTTCCGGGA 59.572 47.619 0.00 0.00 39.52 5.14
49 50 1.546923 GTGGGTAATGGTTTTTCCGGG 59.453 52.381 0.00 0.00 39.52 5.73
50 51 2.240279 TGTGGGTAATGGTTTTTCCGG 58.760 47.619 0.00 0.00 39.52 5.14
51 52 3.761752 AGATGTGGGTAATGGTTTTTCCG 59.238 43.478 0.00 0.00 39.52 4.30
52 53 4.142469 CGAGATGTGGGTAATGGTTTTTCC 60.142 45.833 0.00 0.00 0.00 3.13
53 54 4.698304 TCGAGATGTGGGTAATGGTTTTTC 59.302 41.667 0.00 0.00 0.00 2.29
54 55 4.457949 GTCGAGATGTGGGTAATGGTTTTT 59.542 41.667 0.00 0.00 0.00 1.94
55 56 4.007659 GTCGAGATGTGGGTAATGGTTTT 58.992 43.478 0.00 0.00 0.00 2.43
56 57 3.606687 GTCGAGATGTGGGTAATGGTTT 58.393 45.455 0.00 0.00 0.00 3.27
57 58 2.093128 GGTCGAGATGTGGGTAATGGTT 60.093 50.000 0.00 0.00 0.00 3.67
58 59 1.485066 GGTCGAGATGTGGGTAATGGT 59.515 52.381 0.00 0.00 0.00 3.55
59 60 1.484653 TGGTCGAGATGTGGGTAATGG 59.515 52.381 0.00 0.00 0.00 3.16
60 61 2.936498 GTTGGTCGAGATGTGGGTAATG 59.064 50.000 0.00 0.00 0.00 1.90
61 62 2.093128 GGTTGGTCGAGATGTGGGTAAT 60.093 50.000 0.00 0.00 0.00 1.89
62 63 1.276989 GGTTGGTCGAGATGTGGGTAA 59.723 52.381 0.00 0.00 0.00 2.85
63 64 0.899720 GGTTGGTCGAGATGTGGGTA 59.100 55.000 0.00 0.00 0.00 3.69
64 65 0.836400 AGGTTGGTCGAGATGTGGGT 60.836 55.000 0.00 0.00 0.00 4.51
65 66 0.108138 GAGGTTGGTCGAGATGTGGG 60.108 60.000 0.00 0.00 0.00 4.61
66 67 0.898320 AGAGGTTGGTCGAGATGTGG 59.102 55.000 0.00 0.00 0.00 4.17
67 68 2.751166 AAGAGGTTGGTCGAGATGTG 57.249 50.000 0.00 0.00 0.00 3.21
68 69 4.023980 TGATAAGAGGTTGGTCGAGATGT 58.976 43.478 0.00 0.00 0.00 3.06
69 70 4.655762 TGATAAGAGGTTGGTCGAGATG 57.344 45.455 0.00 0.00 0.00 2.90
70 71 5.605534 CAATGATAAGAGGTTGGTCGAGAT 58.394 41.667 0.00 0.00 0.00 2.75
71 72 4.680708 GCAATGATAAGAGGTTGGTCGAGA 60.681 45.833 0.00 0.00 0.00 4.04
72 73 3.557595 GCAATGATAAGAGGTTGGTCGAG 59.442 47.826 0.00 0.00 0.00 4.04
73 74 3.197766 AGCAATGATAAGAGGTTGGTCGA 59.802 43.478 0.00 0.00 0.00 4.20
74 75 3.535561 AGCAATGATAAGAGGTTGGTCG 58.464 45.455 0.00 0.00 0.00 4.79
75 76 5.297029 GGTTAGCAATGATAAGAGGTTGGTC 59.703 44.000 0.00 0.00 34.54 4.02
76 77 5.193679 GGTTAGCAATGATAAGAGGTTGGT 58.806 41.667 0.00 0.00 36.42 3.67
77 78 4.580580 GGGTTAGCAATGATAAGAGGTTGG 59.419 45.833 0.00 0.00 0.00 3.77
78 79 4.580580 GGGGTTAGCAATGATAAGAGGTTG 59.419 45.833 0.00 0.00 0.00 3.77
79 80 4.229582 TGGGGTTAGCAATGATAAGAGGTT 59.770 41.667 0.00 0.00 0.00 3.50
80 81 3.785887 TGGGGTTAGCAATGATAAGAGGT 59.214 43.478 0.00 0.00 0.00 3.85
90 91 1.559682 ACGATGACTGGGGTTAGCAAT 59.440 47.619 0.00 0.00 0.00 3.56
131 138 0.692756 GGAGAAGAGGGGAAGGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
133 140 0.340208 GAGGAGAAGAGGGGAAGGGA 59.660 60.000 0.00 0.00 0.00 4.20
152 159 2.896801 GCGGCATAAGCACGGATGG 61.897 63.158 0.00 0.00 44.61 3.51
167 174 2.750237 GTTGGGCTTAGGGTGCGG 60.750 66.667 0.00 0.00 0.00 5.69
183 190 7.759489 ACCTAATGTGTGAATGTGTAAATGT 57.241 32.000 0.00 0.00 0.00 2.71
237 245 2.093890 TGAGCAGGCATGGTGTTTATG 58.906 47.619 8.23 0.00 37.25 1.90
250 258 4.927425 CCAATTCATTCAACTTTGAGCAGG 59.073 41.667 0.00 0.00 38.61 4.85
278 286 1.109323 AGGTGGTGCAAAAGTGAGCC 61.109 55.000 0.00 0.00 0.00 4.70
457 470 2.841266 TCCGGGGACATGTTTGATTAGA 59.159 45.455 0.00 0.00 0.00 2.10
479 492 1.675720 GGGGGTGAATGGCGATTTGG 61.676 60.000 0.00 0.00 0.00 3.28
506 519 4.080863 AGGGACCTGAGTGTGATTATCAAC 60.081 45.833 0.00 0.00 0.00 3.18
518 531 2.681778 CTCGCCAGGGACCTGAGT 60.682 66.667 19.65 0.00 46.30 3.41
629 642 1.304952 CACCCGTCCTCTCTCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
630 643 1.755008 CCACCCGTCCTCTCTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
631 644 2.218115 CTCCACCCGTCCTCTCTCCT 62.218 65.000 0.00 0.00 0.00 3.69
632 645 1.755008 CTCCACCCGTCCTCTCTCC 60.755 68.421 0.00 0.00 0.00 3.71
633 646 1.755008 CCTCCACCCGTCCTCTCTC 60.755 68.421 0.00 0.00 0.00 3.20
634 647 2.360980 CCTCCACCCGTCCTCTCT 59.639 66.667 0.00 0.00 0.00 3.10
739 752 3.237741 GGAGATCTGAGGGGGCGG 61.238 72.222 0.00 0.00 0.00 6.13
802 815 1.111277 GCACCACCAACCTCTTTGTT 58.889 50.000 0.00 0.00 32.71 2.83
803 816 0.258774 AGCACCACCAACCTCTTTGT 59.741 50.000 0.00 0.00 32.71 2.83
804 817 0.670162 CAGCACCACCAACCTCTTTG 59.330 55.000 0.00 0.00 34.63 2.77
805 818 1.109323 GCAGCACCACCAACCTCTTT 61.109 55.000 0.00 0.00 0.00 2.52
825 838 3.604667 CAAAGCAACCGGGCAGCA 61.605 61.111 6.32 0.00 35.83 4.41
826 839 3.294493 TCAAAGCAACCGGGCAGC 61.294 61.111 6.32 6.67 35.83 5.25
827 840 2.644992 GTCAAAGCAACCGGGCAG 59.355 61.111 6.32 0.00 35.83 4.85
927 940 4.373116 GCTTCCAGACGCGGACCA 62.373 66.667 12.47 0.00 33.75 4.02
970 992 2.345244 CCTTCGCCACAGAGCACT 59.655 61.111 0.00 0.00 0.00 4.40
1011 1033 1.492133 CCAGCTGGAACTTCTCCCCA 61.492 60.000 29.88 0.00 44.69 4.96
1271 1313 0.391130 TCACGAGCCCAAGATTTCCG 60.391 55.000 0.00 0.00 0.00 4.30
1352 1394 2.203596 AGGAACTCCACCGACGGT 60.204 61.111 15.37 15.37 38.89 4.83
1456 1498 1.802960 CCAGCAAGTCACACTAAGCAG 59.197 52.381 0.00 0.00 33.47 4.24
1464 1507 4.096833 GCATATTCATTCCAGCAAGTCACA 59.903 41.667 0.00 0.00 0.00 3.58
1534 1577 6.248569 ACCACTACTCTTTTCTTCCTCAAA 57.751 37.500 0.00 0.00 0.00 2.69
1539 1582 6.468543 AGATGAACCACTACTCTTTTCTTCC 58.531 40.000 0.00 0.00 0.00 3.46
1678 1725 2.440517 TGCATAATGCCACATGGAGT 57.559 45.000 0.87 0.00 44.23 3.85
1681 1728 3.649073 CTTCATGCATAATGCCACATGG 58.351 45.455 0.00 0.00 44.23 3.66
1729 1776 1.221021 GAACCCCATGACGGTCCTC 59.779 63.158 5.55 0.00 31.48 3.71
1822 1869 2.023673 TGGAGGCAAAGAACACAACTG 58.976 47.619 0.00 0.00 0.00 3.16
1825 1872 2.023673 CAGTGGAGGCAAAGAACACAA 58.976 47.619 0.00 0.00 34.65 3.33
1826 1873 1.064758 ACAGTGGAGGCAAAGAACACA 60.065 47.619 0.00 0.00 34.65 3.72
1827 1874 1.334869 CACAGTGGAGGCAAAGAACAC 59.665 52.381 0.00 0.00 0.00 3.32
1833 1890 2.600164 TGGCACAGTGGAGGCAAA 59.400 55.556 10.90 0.00 37.24 3.68
1917 1974 7.171848 ACACTAATTTTATGCACACTCAACGTA 59.828 33.333 0.00 0.00 0.00 3.57
1984 2041 4.499183 CTTCTCCTAAGATGTCGTTTGCT 58.501 43.478 0.00 0.00 0.00 3.91
2025 2082 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2026 2083 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2027 2084 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2028 2085 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2029 2086 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2030 2087 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2031 2088 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2032 2089 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2033 2090 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2034 2091 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2035 2092 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2036 2093 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2037 2094 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2038 2095 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2039 2096 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2040 2097 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2041 2098 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2042 2099 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2043 2100 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2044 2101 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2045 2102 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2046 2103 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2047 2104 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2048 2105 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2061 2118 3.827722 ACTCCCTCCGTTCAAATTTGAA 58.172 40.909 26.01 26.01 44.31 2.69
2062 2119 3.502123 ACTCCCTCCGTTCAAATTTGA 57.498 42.857 16.91 16.91 34.92 2.69
2063 2120 4.069304 TGTACTCCCTCCGTTCAAATTTG 58.931 43.478 12.15 12.15 0.00 2.32
2064 2121 4.360951 TGTACTCCCTCCGTTCAAATTT 57.639 40.909 0.00 0.00 0.00 1.82
2065 2122 4.261801 CATGTACTCCCTCCGTTCAAATT 58.738 43.478 0.00 0.00 0.00 1.82
2066 2123 3.263425 ACATGTACTCCCTCCGTTCAAAT 59.737 43.478 0.00 0.00 0.00 2.32
2067 2124 2.635915 ACATGTACTCCCTCCGTTCAAA 59.364 45.455 0.00 0.00 0.00 2.69
2068 2125 2.232941 GACATGTACTCCCTCCGTTCAA 59.767 50.000 0.00 0.00 0.00 2.69
2069 2126 1.822990 GACATGTACTCCCTCCGTTCA 59.177 52.381 0.00 0.00 0.00 3.18
2070 2127 1.202268 CGACATGTACTCCCTCCGTTC 60.202 57.143 0.00 0.00 0.00 3.95
2071 2128 0.815734 CGACATGTACTCCCTCCGTT 59.184 55.000 0.00 0.00 0.00 4.44
2072 2129 1.664321 GCGACATGTACTCCCTCCGT 61.664 60.000 0.00 0.00 0.00 4.69
2073 2130 1.065928 GCGACATGTACTCCCTCCG 59.934 63.158 0.00 0.00 0.00 4.63
2074 2131 1.065928 CGCGACATGTACTCCCTCC 59.934 63.158 0.00 0.00 0.00 4.30
2075 2132 0.525668 CACGCGACATGTACTCCCTC 60.526 60.000 15.93 0.00 0.00 4.30
2076 2133 0.963856 TCACGCGACATGTACTCCCT 60.964 55.000 15.93 0.00 0.00 4.20
2077 2134 0.525668 CTCACGCGACATGTACTCCC 60.526 60.000 15.93 0.00 0.00 4.30
2078 2135 0.170561 ACTCACGCGACATGTACTCC 59.829 55.000 15.93 0.00 0.00 3.85
2079 2136 1.260206 CACTCACGCGACATGTACTC 58.740 55.000 15.93 0.00 0.00 2.59
2080 2137 0.732880 GCACTCACGCGACATGTACT 60.733 55.000 15.93 0.00 0.00 2.73
2081 2138 1.702299 GCACTCACGCGACATGTAC 59.298 57.895 15.93 0.00 0.00 2.90
2082 2139 4.162640 GCACTCACGCGACATGTA 57.837 55.556 15.93 0.00 0.00 2.29
2297 2359 4.427394 GCTGGATGTAGCGACTGG 57.573 61.111 0.00 0.00 33.46 4.00
2564 2626 6.655003 GGGAGTCACTTCTGTTCATTATTTCA 59.345 38.462 0.00 0.00 0.00 2.69
2565 2627 6.881602 AGGGAGTCACTTCTGTTCATTATTTC 59.118 38.462 0.00 0.00 0.00 2.17
2576 2638 2.175202 AGCTGTAGGGAGTCACTTCTG 58.825 52.381 0.00 0.16 0.00 3.02
2621 2683 5.986004 AGTTCAACAGGAAAGTAGAAACG 57.014 39.130 0.00 0.00 37.23 3.60
2883 2945 8.321005 GCAAAGACATTTTTGTTAGTCAGAAAC 58.679 33.333 0.00 0.00 39.62 2.78
3002 3064 6.414408 AGAACTGCAGAAATGATAAGAACG 57.586 37.500 23.35 0.00 0.00 3.95
3168 3230 3.973206 TTTCTCCAGCTAAACGGATCA 57.027 42.857 0.00 0.00 0.00 2.92
3342 3404 4.643334 TCAGCAGATCAGGATTCCAAAATG 59.357 41.667 5.29 0.00 0.00 2.32
3371 3433 6.712547 GTGGCTTATGCTTACTCCTTAATCAT 59.287 38.462 0.13 0.00 39.59 2.45
3444 3506 8.562052 CAGCTACATATGAAGCACATCAAATTA 58.438 33.333 10.38 0.00 41.32 1.40
3446 3508 6.016527 CCAGCTACATATGAAGCACATCAAAT 60.017 38.462 10.38 0.00 41.32 2.32
3530 3592 2.019337 TCATGCAGATGACATGCGC 58.981 52.632 0.00 0.00 46.87 6.09
3548 3610 4.103153 TCTGATTCACCTTCTTTCACCTGT 59.897 41.667 0.00 0.00 0.00 4.00
3563 3625 2.027285 TGCGATCAAAGGGTCTGATTCA 60.027 45.455 0.00 0.00 33.63 2.57
3683 3745 3.003173 TTCAGAGGTCGGGGCAGG 61.003 66.667 0.00 0.00 0.00 4.85
3949 4232 2.564062 CTGCCATTTGGAGTCATTTGGT 59.436 45.455 0.00 0.00 37.39 3.67
4008 4291 3.883549 GAGATCCCCTGCCCAGCC 61.884 72.222 0.00 0.00 0.00 4.85
4113 4405 1.804746 CGTGCAGTGGACACTTGTACA 60.805 52.381 15.55 0.00 40.20 2.90
4132 4424 2.414481 CTCAAAAGCTCACCACAGATCG 59.586 50.000 0.00 0.00 0.00 3.69
4190 4484 0.825010 CTGGCATATGGGACCCAAGC 60.825 60.000 19.58 20.82 36.95 4.01
4353 6860 8.766476 CCACCATCTATTATCATAGGACAAGAT 58.234 37.037 0.00 0.00 34.12 2.40
4358 6865 7.496346 TTCCCACCATCTATTATCATAGGAC 57.504 40.000 0.00 0.00 34.12 3.85
4364 6871 5.912149 AAGCTTCCCACCATCTATTATCA 57.088 39.130 0.00 0.00 0.00 2.15
4453 6961 9.030452 AGAGAAGAAACAAGATGTCAGTAGTAT 57.970 33.333 0.00 0.00 0.00 2.12
4454 6962 8.410673 AGAGAAGAAACAAGATGTCAGTAGTA 57.589 34.615 0.00 0.00 0.00 1.82
4455 6963 7.232534 AGAGAGAAGAAACAAGATGTCAGTAGT 59.767 37.037 0.00 0.00 0.00 2.73
4476 6984 5.424121 AACATTTCGGTTTTGTGAGAGAG 57.576 39.130 0.00 0.00 0.00 3.20
4508 7016 5.864198 ACCTAACATTTTGGTTACCCCTA 57.136 39.130 0.00 0.00 32.29 3.53
4518 7026 9.914923 GCACTAAAAAGAAAACCTAACATTTTG 57.085 29.630 0.00 0.00 29.44 2.44
4569 7109 3.494749 CCATTTGGTTCATGTGCCAAGTT 60.495 43.478 18.04 10.88 44.43 2.66
4571 7111 2.613474 CCCATTTGGTTCATGTGCCAAG 60.613 50.000 18.04 11.12 44.43 3.61
4572 7112 1.347050 CCCATTTGGTTCATGTGCCAA 59.653 47.619 15.97 15.97 42.38 4.52
4574 7114 0.391528 GCCCATTTGGTTCATGTGCC 60.392 55.000 0.00 0.00 36.04 5.01
4576 7116 1.205417 GAGGCCCATTTGGTTCATGTG 59.795 52.381 0.00 0.00 36.04 3.21
4651 7193 1.258982 GTACAAGCGAGCGATTGATGG 59.741 52.381 24.90 1.46 43.35 3.51
4657 7199 0.248377 GTACCGTACAAGCGAGCGAT 60.248 55.000 3.69 0.00 0.00 4.58
4658 7200 1.135315 GTACCGTACAAGCGAGCGA 59.865 57.895 3.69 0.00 0.00 4.93
4659 7201 1.870901 GGTACCGTACAAGCGAGCG 60.871 63.158 10.81 0.00 0.00 5.03
4660 7202 4.083746 GGTACCGTACAAGCGAGC 57.916 61.111 10.81 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.