Multiple sequence alignment - TraesCS1A01G250000

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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 TraesCS1A01G250000 chr1A 100.000 3008 0 0 1 3008 441840989 441843996 0.000000e+00 5555.0
1 TraesCS1A01G250000 chr1A 94.778 383 18 2 2628 3008 328802074 328802456 2.000000e-166 595.0
2 TraesCS1A01G250000 chr1A 95.946 222 6 3 2787 3008 558706839 558707057 1.030000e-94 357.0
3 TraesCS1A01G250000 chr1A 95.349 215 8 2 2794 3008 75802634 75802422 1.030000e-89 340.0
4 TraesCS1A01G250000 chr1A 95.392 217 5 3 2794 3008 492618935 492618722 1.030000e-89 340.0
5 TraesCS1A01G250000 chr1A 93.119 218 12 2 2794 3008 492429113 492428896 1.740000e-82 316.0
6 TraesCS1A01G250000 chr1A 86.937 222 14 4 2342 2548 75803817 75803596 5.010000e-58 235.0
7 TraesCS1A01G250000 chr1A 85.586 222 17 2 2342 2548 492620119 492619898 5.050000e-53 219.0
8 TraesCS1A01G250000 chr1A 85.135 222 18 2 2342 2548 492430300 492430079 2.350000e-51 213.0
9 TraesCS1A01G250000 chr1A 84.685 222 19 2 2342 2548 558705671 558705892 1.090000e-49 207.0
10 TraesCS1A01G250000 chr1A 86.387 191 7 4 2628 2799 75803599 75803409 1.100000e-44 191.0
11 TraesCS1A01G250000 chr1A 85.864 191 7 6 2628 2799 492619901 492619712 5.120000e-43 185.0
12 TraesCS1A01G250000 chr1A 81.982 222 24 3 2342 2548 104829294 104829074 1.110000e-39 174.0
13 TraesCS1A01G250000 chr1A 84.817 191 9 6 2628 2799 492430082 492429893 1.110000e-39 174.0
14 TraesCS1A01G250000 chr1A 84.293 191 11 12 2628 2799 558705889 558706079 5.160000e-38 169.0
15 TraesCS1A01G250000 chr1A 85.088 114 14 3 2872 2983 463814643 463814531 2.450000e-21 113.0
16 TraesCS1A01G250000 chr1D 93.746 1775 58 19 579 2342 342169842 342171574 0.000000e+00 2614.0
17 TraesCS1A01G250000 chr1D 90.498 442 23 2 63 485 342169402 342169843 1.570000e-157 566.0
18 TraesCS1A01G250000 chr1D 85.333 75 8 2 2545 2616 142966611 142966685 1.160000e-09 75.0
19 TraesCS1A01G250000 chr1B 93.477 1625 71 13 579 2176 458081050 458082666 0.000000e+00 2381.0
20 TraesCS1A01G250000 chr1B 93.133 1631 86 18 579 2194 458129225 458130844 0.000000e+00 2368.0
21 TraesCS1A01G250000 chr1B 93.217 1607 79 14 579 2176 458262609 458264194 0.000000e+00 2337.0
22 TraesCS1A01G250000 chr1B 90.679 1223 85 7 856 2069 458172230 458173432 0.000000e+00 1600.0
23 TraesCS1A01G250000 chr1B 88.409 440 26 4 63 485 458080620 458081051 9.620000e-140 507.0
24 TraesCS1A01G250000 chr1B 91.129 124 11 0 63 186 458260930 458261053 5.160000e-38 169.0
25 TraesCS1A01G250000 chr1B 90.323 124 12 0 63 186 458126317 458126440 2.400000e-36 163.0
26 TraesCS1A01G250000 chr1B 89.286 112 11 1 473 583 132296913 132296802 4.040000e-29 139.0
27 TraesCS1A01G250000 chr1B 92.683 82 3 2 2545 2623 652640686 652640767 6.810000e-22 115.0
28 TraesCS1A01G250000 chr1B 85.227 88 8 2 2552 2634 256588809 256588722 5.340000e-13 86.1
29 TraesCS1A01G250000 chr5B 85.685 992 123 11 998 1978 585495922 585494939 0.000000e+00 1027.0
30 TraesCS1A01G250000 chr5B 83.562 73 8 3 2545 2616 175479988 175480057 6.960000e-07 65.8
31 TraesCS1A01G250000 chr5D 83.898 1093 144 17 912 1978 478001140 478000054 0.000000e+00 1014.0
32 TraesCS1A01G250000 chr5D 81.858 226 25 2 2338 2548 410380203 410380427 3.080000e-40 176.0
33 TraesCS1A01G250000 chr5D 92.079 101 8 0 483 583 266749453 266749353 3.130000e-30 143.0
34 TraesCS1A01G250000 chr5D 83.636 110 15 3 2872 2978 557802595 557802704 1.910000e-17 100.0
35 TraesCS1A01G250000 chr5D 82.418 91 13 2 2545 2634 319372090 319372178 3.220000e-10 76.8
36 TraesCS1A01G250000 chr5A 85.354 990 130 8 998 1978 597280073 597279090 0.000000e+00 1011.0
37 TraesCS1A01G250000 chr5A 85.155 869 114 6 998 1857 597265620 597264758 0.000000e+00 876.0
38 TraesCS1A01G250000 chr2D 82.225 962 139 16 1030 1972 637802130 637803078 0.000000e+00 800.0
39 TraesCS1A01G250000 chr2D 89.189 111 11 1 484 593 67559327 67559217 1.450000e-28 137.0
40 TraesCS1A01G250000 chr2A 84.639 664 91 6 1310 1972 761541929 761541276 0.000000e+00 651.0
41 TraesCS1A01G250000 chr2A 88.532 218 17 6 2794 3008 770507813 770507601 1.070000e-64 257.0
42 TraesCS1A01G250000 chr2A 79.279 222 18 7 2342 2548 601329403 601329195 2.430000e-26 130.0
43 TraesCS1A01G250000 chr2A 82.000 150 23 1 340 485 384331639 384331788 1.130000e-24 124.0
44 TraesCS1A01G250000 chr2A 79.739 153 21 8 340 485 568232084 568232233 5.310000e-18 102.0
45 TraesCS1A01G250000 chrUn 78.414 908 144 23 1116 2014 22860167 22861031 7.330000e-151 544.0
46 TraesCS1A01G250000 chr3B 81.132 424 30 20 2628 3005 20361487 20361068 8.150000e-76 294.0
47 TraesCS1A01G250000 chr3B 79.348 92 17 2 2545 2634 589147936 589147845 2.500000e-06 63.9
48 TraesCS1A01G250000 chr7D 89.778 225 14 7 2787 3008 193242028 193242246 2.280000e-71 279.0
49 TraesCS1A01G250000 chr7D 85.938 192 6 10 2628 2799 193240909 193241099 5.120000e-43 185.0
50 TraesCS1A01G250000 chr7D 81.614 223 25 7 2341 2548 511333304 511333525 1.430000e-38 171.0
51 TraesCS1A01G250000 chr7D 91.429 105 8 1 481 585 311884473 311884576 3.130000e-30 143.0
52 TraesCS1A01G250000 chr7D 78.667 150 28 1 340 485 562886410 562886261 2.470000e-16 97.1
53 TraesCS1A01G250000 chr4D 89.333 225 14 6 2787 3008 439748332 439748549 1.060000e-69 274.0
54 TraesCS1A01G250000 chr4D 82.143 224 24 2 2340 2548 20460029 20460251 8.570000e-41 178.0
55 TraesCS1A01G250000 chr4D 84.896 192 8 10 2628 2799 439747380 439747570 1.110000e-39 174.0
56 TraesCS1A01G250000 chr4D 86.316 95 8 4 2541 2630 191277059 191277153 6.860000e-17 99.0
57 TraesCS1A01G250000 chr3D 82.379 227 24 2 2337 2548 579365393 579365168 1.840000e-42 183.0
58 TraesCS1A01G250000 chr3D 82.648 219 22 4 2345 2548 46523820 46523603 2.380000e-41 180.0
59 TraesCS1A01G250000 chr3D 92.233 103 7 1 484 585 445342954 445343056 8.690000e-31 145.0
60 TraesCS1A01G250000 chr3D 91.429 105 7 2 482 585 84326673 84326570 3.130000e-30 143.0
61 TraesCS1A01G250000 chr3D 85.714 98 7 4 2539 2629 359514816 359514719 2.470000e-16 97.1
62 TraesCS1A01G250000 chr3D 93.651 63 4 0 2710 2772 11415572 11415634 8.880000e-16 95.3
63 TraesCS1A01G250000 chr3D 85.106 94 8 2 2544 2631 359514718 359514811 1.150000e-14 91.6
64 TraesCS1A01G250000 chr6B 84.456 193 9 5 2628 2799 14160611 14160803 1.430000e-38 171.0
65 TraesCS1A01G250000 chr6B 93.069 101 7 0 484 584 315650304 315650204 6.720000e-32 148.0
66 TraesCS1A01G250000 chr6B 93.902 82 4 1 2642 2722 715014665 715014746 4.070000e-24 122.0
67 TraesCS1A01G250000 chr6B 85.556 90 10 3 2541 2629 575327760 575327847 1.150000e-14 91.6
68 TraesCS1A01G250000 chr6B 76.087 184 29 9 2628 2797 439077418 439077600 6.910000e-12 82.4
69 TraesCS1A01G250000 chr4B 94.845 97 5 0 484 580 193527678 193527582 5.190000e-33 152.0
70 TraesCS1A01G250000 chr4B 86.139 101 9 5 2535 2631 517959088 517958989 1.480000e-18 104.0
71 TraesCS1A01G250000 chr4B 81.818 110 17 3 2872 2978 180053447 180053338 4.130000e-14 89.8
72 TraesCS1A01G250000 chr4A 90.090 111 9 2 477 585 710665510 710665620 3.130000e-30 143.0
73 TraesCS1A01G250000 chr4A 85.057 87 11 2 2545 2630 65459190 65459275 1.490000e-13 87.9
74 TraesCS1A01G250000 chr7B 91.667 96 7 1 2628 2722 33626726 33626821 6.770000e-27 132.0
75 TraesCS1A01G250000 chr7B 82.119 151 19 7 341 485 610486659 610486511 4.070000e-24 122.0
76 TraesCS1A01G250000 chr7A 81.333 150 24 1 340 485 708316970 708316821 5.270000e-23 119.0
77 TraesCS1A01G250000 chr7A 84.314 102 8 4 2545 2639 332418668 332418568 3.190000e-15 93.5
78 TraesCS1A01G250000 chr6A 80.000 150 26 1 340 485 405665733 405665882 1.140000e-19 108.0
79 TraesCS1A01G250000 chr6A 82.609 115 16 4 2872 2983 65535357 65535244 6.860000e-17 99.0
80 TraesCS1A01G250000 chr3A 80.000 150 26 1 340 485 468323487 468323636 1.140000e-19 108.0
81 TraesCS1A01G250000 chr3A 85.106 94 9 4 2541 2629 467874640 467874547 1.150000e-14 91.6
82 TraesCS1A01G250000 chr2B 82.609 92 12 4 2545 2632 79676179 79676088 8.940000e-11 78.7


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 TraesCS1A01G250000 chr1A 441840989 441843996 3007 False 5555.000000 5555 100.000000 1 3008 1 chr1A.!!$F2 3007
1 TraesCS1A01G250000 chr1A 75802422 75803817 1395 True 255.333333 340 89.557667 2342 3008 3 chr1A.!!$R3 666
2 TraesCS1A01G250000 chr1A 492618722 492620119 1397 True 248.000000 340 88.947333 2342 3008 3 chr1A.!!$R5 666
3 TraesCS1A01G250000 chr1A 558705671 558707057 1386 False 244.333333 357 88.308000 2342 3008 3 chr1A.!!$F3 666
4 TraesCS1A01G250000 chr1A 492428896 492430300 1404 True 234.333333 316 87.690333 2342 3008 3 chr1A.!!$R4 666
5 TraesCS1A01G250000 chr1D 342169402 342171574 2172 False 1590.000000 2614 92.122000 63 2342 2 chr1D.!!$F2 2279
6 TraesCS1A01G250000 chr1B 458172230 458173432 1202 False 1600.000000 1600 90.679000 856 2069 1 chr1B.!!$F1 1213
7 TraesCS1A01G250000 chr1B 458080620 458082666 2046 False 1444.000000 2381 90.943000 63 2176 2 chr1B.!!$F3 2113
8 TraesCS1A01G250000 chr1B 458126317 458130844 4527 False 1265.500000 2368 91.728000 63 2194 2 chr1B.!!$F4 2131
9 TraesCS1A01G250000 chr1B 458260930 458264194 3264 False 1253.000000 2337 92.173000 63 2176 2 chr1B.!!$F5 2113
10 TraesCS1A01G250000 chr5B 585494939 585495922 983 True 1027.000000 1027 85.685000 998 1978 1 chr5B.!!$R1 980
11 TraesCS1A01G250000 chr5D 478000054 478001140 1086 True 1014.000000 1014 83.898000 912 1978 1 chr5D.!!$R2 1066
12 TraesCS1A01G250000 chr5A 597279090 597280073 983 True 1011.000000 1011 85.354000 998 1978 1 chr5A.!!$R2 980
13 TraesCS1A01G250000 chr5A 597264758 597265620 862 True 876.000000 876 85.155000 998 1857 1 chr5A.!!$R1 859
14 TraesCS1A01G250000 chr2D 637802130 637803078 948 False 800.000000 800 82.225000 1030 1972 1 chr2D.!!$F1 942
15 TraesCS1A01G250000 chr2A 761541276 761541929 653 True 651.000000 651 84.639000 1310 1972 1 chr2A.!!$R2 662
16 TraesCS1A01G250000 chrUn 22860167 22861031 864 False 544.000000 544 78.414000 1116 2014 1 chrUn.!!$F1 898
17 TraesCS1A01G250000 chr7D 193240909 193242246 1337 False 232.000000 279 87.858000 2628 3008 2 chr7D.!!$F3 380
18 TraesCS1A01G250000 chr4D 439747380 439748549 1169 False 224.000000 274 87.114500 2628 3008 2 chr4D.!!$F3 380

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
38 39 0.034059 GCGTCCCTGCAGCTATGTAT 59.966 55.000 8.66 0.0 34.15 2.29 F
235 2736 1.208293 GGGAACTTCTGAGCCACCTAG 59.792 57.143 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 4494 0.460311 CGCTTGTAGAACCCGATCCT 59.540 55.0 0.0 0.0 0.00 3.24 R
2132 4742 0.457337 GCAGGCCGAAAGAAATGCTG 60.457 55.0 0.0 0.0 32.24 4.41 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 1.725164 GCCCTATATTAACACGCTCGC 59.275 52.381 0.00 0.00 0.00 5.03
21 22 1.983605 CCCTATATTAACACGCTCGCG 59.016 52.381 10.06 10.06 46.03 5.87
33 34 3.826754 CTCGCGTCCCTGCAGCTA 61.827 66.667 8.66 0.00 34.15 3.32
34 35 3.144120 CTCGCGTCCCTGCAGCTAT 62.144 63.158 8.66 0.00 34.15 2.97
35 36 2.963854 CGCGTCCCTGCAGCTATG 60.964 66.667 8.66 4.77 34.15 2.23
36 37 2.187946 GCGTCCCTGCAGCTATGT 59.812 61.111 8.66 0.00 34.15 2.29
37 38 1.441729 GCGTCCCTGCAGCTATGTA 59.558 57.895 8.66 0.00 34.15 2.29
38 39 0.034059 GCGTCCCTGCAGCTATGTAT 59.966 55.000 8.66 0.00 34.15 2.29
39 40 1.272490 GCGTCCCTGCAGCTATGTATA 59.728 52.381 8.66 0.00 34.15 1.47
40 41 2.927014 GCGTCCCTGCAGCTATGTATAC 60.927 54.545 8.66 0.00 34.15 1.47
41 42 2.668556 CGTCCCTGCAGCTATGTATACG 60.669 54.545 8.66 4.78 0.00 3.06
42 43 2.296471 GTCCCTGCAGCTATGTATACGT 59.704 50.000 8.66 2.56 0.00 3.57
43 44 2.963101 TCCCTGCAGCTATGTATACGTT 59.037 45.455 8.66 0.00 0.00 3.99
44 45 3.386726 TCCCTGCAGCTATGTATACGTTT 59.613 43.478 8.66 0.00 0.00 3.60
45 46 4.585581 TCCCTGCAGCTATGTATACGTTTA 59.414 41.667 8.66 0.00 0.00 2.01
46 47 5.069383 TCCCTGCAGCTATGTATACGTTTAA 59.931 40.000 8.66 0.00 0.00 1.52
47 48 5.405571 CCCTGCAGCTATGTATACGTTTAAG 59.594 44.000 8.66 0.00 0.00 1.85
48 49 5.983720 CCTGCAGCTATGTATACGTTTAAGT 59.016 40.000 8.66 0.00 0.00 2.24
49 50 6.144080 CCTGCAGCTATGTATACGTTTAAGTC 59.856 42.308 8.66 0.00 0.00 3.01
50 51 6.802608 TGCAGCTATGTATACGTTTAAGTCT 58.197 36.000 2.23 0.00 0.00 3.24
51 52 7.933396 TGCAGCTATGTATACGTTTAAGTCTA 58.067 34.615 2.23 0.00 0.00 2.59
52 53 8.074370 TGCAGCTATGTATACGTTTAAGTCTAG 58.926 37.037 2.23 0.00 0.00 2.43
53 54 8.074972 GCAGCTATGTATACGTTTAAGTCTAGT 58.925 37.037 2.23 0.00 0.00 2.57
54 55 9.947669 CAGCTATGTATACGTTTAAGTCTAGTT 57.052 33.333 2.23 0.00 0.00 2.24
235 2736 1.208293 GGGAACTTCTGAGCCACCTAG 59.792 57.143 0.00 0.00 0.00 3.02
286 2809 1.256812 ACAGGGCAGCATTGTTAACC 58.743 50.000 2.48 0.00 0.00 2.85
358 2884 1.280998 CCTCCCTCCGGCTCTTTTTAA 59.719 52.381 0.00 0.00 0.00 1.52
363 2889 3.610911 CCTCCGGCTCTTTTTAATCTGT 58.389 45.455 0.00 0.00 0.00 3.41
441 2967 7.933033 AGAAAAGCATCAACACAATACCAAATT 59.067 29.630 0.00 0.00 0.00 1.82
490 3016 8.974292 ATGTAGTTTCATGGTATATACTCCCT 57.026 34.615 12.54 2.95 0.00 4.20
491 3017 8.418597 TGTAGTTTCATGGTATATACTCCCTC 57.581 38.462 12.54 0.00 0.00 4.30
492 3018 6.936968 AGTTTCATGGTATATACTCCCTCC 57.063 41.667 12.54 0.00 0.00 4.30
493 3019 5.480772 AGTTTCATGGTATATACTCCCTCCG 59.519 44.000 12.54 0.00 0.00 4.63
494 3020 4.669866 TCATGGTATATACTCCCTCCGT 57.330 45.455 12.54 0.00 0.00 4.69
495 3021 4.597004 TCATGGTATATACTCCCTCCGTC 58.403 47.826 12.54 0.00 0.00 4.79
496 3022 4.291513 TCATGGTATATACTCCCTCCGTCT 59.708 45.833 12.54 0.00 0.00 4.18
497 3023 4.298103 TGGTATATACTCCCTCCGTCTC 57.702 50.000 12.54 0.00 0.00 3.36
498 3024 3.654321 TGGTATATACTCCCTCCGTCTCA 59.346 47.826 12.54 0.00 0.00 3.27
499 3025 4.105217 TGGTATATACTCCCTCCGTCTCAA 59.895 45.833 12.54 0.00 0.00 3.02
500 3026 5.075493 GGTATATACTCCCTCCGTCTCAAA 58.925 45.833 12.54 0.00 0.00 2.69
501 3027 5.537674 GGTATATACTCCCTCCGTCTCAAAA 59.462 44.000 12.54 0.00 0.00 2.44
502 3028 6.210984 GGTATATACTCCCTCCGTCTCAAAAT 59.789 42.308 12.54 0.00 0.00 1.82
503 3029 7.395489 GGTATATACTCCCTCCGTCTCAAAATA 59.605 40.741 12.54 0.00 0.00 1.40
504 3030 7.850935 ATATACTCCCTCCGTCTCAAAATAA 57.149 36.000 0.00 0.00 0.00 1.40
505 3031 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
506 3032 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
507 3033 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
508 3034 3.835978 TCCCTCCGTCTCAAAATAAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
509 3035 3.933332 CCCTCCGTCTCAAAATAAGTGAC 59.067 47.826 0.00 0.00 0.00 3.67
510 3036 4.322801 CCCTCCGTCTCAAAATAAGTGACT 60.323 45.833 0.00 0.00 0.00 3.41
511 3037 4.865365 CCTCCGTCTCAAAATAAGTGACTC 59.135 45.833 0.00 0.00 0.00 3.36
512 3038 5.462530 TCCGTCTCAAAATAAGTGACTCA 57.537 39.130 0.00 0.00 0.00 3.41
513 3039 5.849510 TCCGTCTCAAAATAAGTGACTCAA 58.150 37.500 0.00 0.00 0.00 3.02
514 3040 5.694910 TCCGTCTCAAAATAAGTGACTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
515 3041 5.696724 CCGTCTCAAAATAAGTGACTCAACT 59.303 40.000 0.00 0.00 0.00 3.16
516 3042 6.202954 CCGTCTCAAAATAAGTGACTCAACTT 59.797 38.462 0.00 0.00 42.89 2.66
517 3043 7.254795 CCGTCTCAAAATAAGTGACTCAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
518 3044 7.584123 CGTCTCAAAATAAGTGACTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
519 3045 8.398665 GTCTCAAAATAAGTGACTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
520 3046 9.607988 TCTCAAAATAAGTGACTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
521 3047 9.651718 CTCAAAATAAGTGACTCAACTTTGTAC 57.348 33.333 0.00 0.00 40.77 2.90
522 3048 9.391006 TCAAAATAAGTGACTCAACTTTGTACT 57.609 29.630 0.00 0.00 40.77 2.73
525 3051 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
526 3052 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
527 3053 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
528 3054 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
529 3055 7.723324 AGTGACTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
530 3056 7.868415 AGTGACTCAACTTTGTACTAGCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
531 3057 7.652507 GTGACTCAACTTTGTACTAGCTTTAGT 59.347 37.037 0.00 0.00 0.00 2.24
532 3058 8.853126 TGACTCAACTTTGTACTAGCTTTAGTA 58.147 33.333 0.00 0.00 0.00 1.82
571 3097 8.888579 ATATAGAGTCACTTATTTTGGAACGG 57.111 34.615 0.00 0.00 0.00 4.44
572 3098 5.223449 AGAGTCACTTATTTTGGAACGGA 57.777 39.130 0.00 0.00 0.00 4.69
573 3099 5.238583 AGAGTCACTTATTTTGGAACGGAG 58.761 41.667 0.00 0.00 0.00 4.63
574 3100 4.324267 AGTCACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
575 3101 4.041198 AGTCACTTATTTTGGAACGGAGGA 59.959 41.667 0.00 0.00 0.00 3.71
576 3102 4.758165 GTCACTTATTTTGGAACGGAGGAA 59.242 41.667 0.00 0.00 0.00 3.36
577 3103 5.001232 TCACTTATTTTGGAACGGAGGAAG 58.999 41.667 0.00 0.00 0.00 3.46
578 3104 4.760204 CACTTATTTTGGAACGGAGGAAGT 59.240 41.667 0.00 0.00 0.00 3.01
579 3105 5.935789 CACTTATTTTGGAACGGAGGAAGTA 59.064 40.000 0.00 0.00 0.00 2.24
591 3117 5.425630 ACGGAGGAAGTATATTTGGTGTTC 58.574 41.667 0.00 0.00 0.00 3.18
687 3224 4.623932 AAAGAACCAGAGCATACACTCA 57.376 40.909 0.00 0.00 39.26 3.41
855 3395 2.078226 ATGTTCGATGAACGTGGCG 58.922 52.632 3.74 0.00 44.55 5.69
857 3397 2.356433 TTCGATGAACGTGGCGCA 60.356 55.556 10.83 0.00 43.13 6.09
1935 4541 3.593794 GTCCTCGGCGTCGGCTAT 61.594 66.667 17.35 0.00 39.81 2.97
2019 4626 2.426752 CAGTGAAAAACGCCGGCG 60.427 61.111 44.88 44.88 46.03 6.46
2081 4691 4.398044 CCAGGAGTTCTCTTCTCTACTGTC 59.602 50.000 0.00 0.00 33.06 3.51
2085 4695 7.065803 CAGGAGTTCTCTTCTCTACTGTCTAAG 59.934 44.444 0.00 0.00 33.06 2.18
2090 4700 6.174760 TCTCTTCTCTACTGTCTAAGGTGAC 58.825 44.000 0.00 0.00 37.47 3.67
2226 4836 3.655777 ACCCTGGTTATGGAAAACTCTGA 59.344 43.478 0.00 0.00 0.00 3.27
2228 4838 4.506625 CCCTGGTTATGGAAAACTCTGACA 60.507 45.833 0.00 0.00 0.00 3.58
2238 4848 5.943416 TGGAAAACTCTGACAAGACTTTTGA 59.057 36.000 0.00 0.00 32.12 2.69
2257 4867 3.059884 TGAAGACGACATGAGAGCAAAC 58.940 45.455 0.00 0.00 0.00 2.93
2274 4884 0.795085 AACGAGACGAGACGAACGAT 59.205 50.000 0.14 0.00 34.70 3.73
2290 4900 2.045926 ATTCACGGGAGCTGGTGC 60.046 61.111 0.00 0.00 40.05 5.01
2291 4901 2.803155 GATTCACGGGAGCTGGTGCA 62.803 60.000 0.00 0.00 42.74 4.57
2292 4902 2.809861 ATTCACGGGAGCTGGTGCAG 62.810 60.000 0.00 0.00 42.74 4.41
2328 4938 2.887568 GATGGCCTCGCGACAGTG 60.888 66.667 3.71 0.00 0.00 3.66
2329 4939 3.649277 GATGGCCTCGCGACAGTGT 62.649 63.158 3.71 0.00 0.00 3.55
2351 4961 7.013464 AGTGTCGGAGTGAATAGAGGTAAATAG 59.987 40.741 0.00 0.00 0.00 1.73
2385 4995 6.088824 GCTTTAACTTGTCATGGATGTTCAG 58.911 40.000 0.00 0.00 0.00 3.02
2393 5003 5.620206 TGTCATGGATGTTCAGTTTAGTGT 58.380 37.500 0.00 0.00 0.00 3.55
2440 5065 2.725723 CACGAACGTGTAAATACGGTGT 59.274 45.455 17.44 0.00 45.22 4.16
2523 5148 0.258484 CATGATGTGGGGCCCAACTA 59.742 55.000 30.70 17.62 34.18 2.24
2530 5155 1.772453 GTGGGGCCCAACTATAGCTAA 59.228 52.381 30.70 0.00 34.18 3.09
2557 5182 8.672823 AAACATAATTATTACTCCTTCCGTCC 57.327 34.615 0.00 0.00 0.00 4.79
2558 5183 6.766429 ACATAATTATTACTCCTTCCGTCCC 58.234 40.000 0.00 0.00 0.00 4.46
2559 5184 6.328148 ACATAATTATTACTCCTTCCGTCCCA 59.672 38.462 0.00 0.00 0.00 4.37
2560 5185 5.703730 AATTATTACTCCTTCCGTCCCAA 57.296 39.130 0.00 0.00 0.00 4.12
2561 5186 5.703730 ATTATTACTCCTTCCGTCCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
2562 5187 5.502089 TTATTACTCCTTCCGTCCCAAAA 57.498 39.130 0.00 0.00 0.00 2.44
2563 5188 4.586306 ATTACTCCTTCCGTCCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
2564 5189 2.971901 ACTCCTTCCGTCCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
2565 5190 2.791655 ACTCCTTCCGTCCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
2566 5191 2.375509 ACTCCTTCCGTCCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
2567 5192 3.181433 ACTCCTTCCGTCCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
2568 5193 3.153919 TCCTTCCGTCCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
2569 5194 2.890945 CCTTCCGTCCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
2570 5195 3.057526 CCTTCCGTCCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
2571 5196 3.502123 TCCGTCCCAAAATTCTTGTCT 57.498 42.857 0.00 0.00 0.00 3.41
2572 5197 3.827722 TCCGTCCCAAAATTCTTGTCTT 58.172 40.909 0.00 0.00 0.00 3.01
2573 5198 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2574 5199 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2575 5200 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2576 5201 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2577 5202 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2578 5203 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2579 5204 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2580 5205 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2581 5206 8.923270 TCCCAAAATTCTTGTCTTAGATTTGTT 58.077 29.630 0.00 0.00 28.79 2.83
2582 5207 9.546428 CCCAAAATTCTTGTCTTAGATTTGTTT 57.454 29.630 0.00 0.00 28.79 2.83
2616 5241 9.354673 AGACAAATCTAAGACAAGAATTTTGGA 57.645 29.630 0.00 0.00 33.04 3.53
2617 5242 9.965824 GACAAATCTAAGACAAGAATTTTGGAA 57.034 29.630 0.00 0.00 33.04 3.53
2618 5243 9.750125 ACAAATCTAAGACAAGAATTTTGGAAC 57.250 29.630 0.00 0.00 33.04 3.62
2619 5244 9.196552 CAAATCTAAGACAAGAATTTTGGAACC 57.803 33.333 5.68 0.00 28.49 3.62
2620 5245 6.554334 TCTAAGACAAGAATTTTGGAACCG 57.446 37.500 5.68 0.00 0.00 4.44
2621 5246 6.292923 TCTAAGACAAGAATTTTGGAACCGA 58.707 36.000 0.00 0.00 0.00 4.69
2622 5247 5.438761 AAGACAAGAATTTTGGAACCGAG 57.561 39.130 0.00 0.00 0.00 4.63
2623 5248 4.714632 AGACAAGAATTTTGGAACCGAGA 58.285 39.130 0.00 0.00 0.00 4.04
2624 5249 4.757149 AGACAAGAATTTTGGAACCGAGAG 59.243 41.667 0.00 0.00 0.00 3.20
2625 5250 4.714632 ACAAGAATTTTGGAACCGAGAGA 58.285 39.130 0.00 0.00 0.00 3.10
2626 5251 5.130350 ACAAGAATTTTGGAACCGAGAGAA 58.870 37.500 0.00 0.00 0.00 2.87
2667 5292 3.584848 GACTCTATGACTAATGGGCCCAT 59.415 47.826 32.75 32.75 38.46 4.00
2723 5367 2.793278 AAAGTGCAACAAACCGGATC 57.207 45.000 9.46 0.00 41.43 3.36
2764 5408 6.231211 GCTAGCCACTATACCAAACATGTAT 58.769 40.000 2.29 0.00 33.63 2.29
2922 6525 3.561310 GGTAGCAGATTCGATTCATGCAA 59.439 43.478 22.12 0.00 39.34 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.144120 ATAGCTGCAGGGACGCGAG 62.144 63.158 15.93 0.00 33.35 5.03
17 18 3.147595 ATAGCTGCAGGGACGCGA 61.148 61.111 15.93 0.00 33.35 5.87
18 19 2.349969 TACATAGCTGCAGGGACGCG 62.350 60.000 17.12 3.53 33.35 6.01
19 20 0.034059 ATACATAGCTGCAGGGACGC 59.966 55.000 17.12 0.36 0.00 5.19
20 21 2.668556 CGTATACATAGCTGCAGGGACG 60.669 54.545 17.12 6.74 0.00 4.79
21 22 2.296471 ACGTATACATAGCTGCAGGGAC 59.704 50.000 17.12 0.00 0.00 4.46
22 23 2.594131 ACGTATACATAGCTGCAGGGA 58.406 47.619 17.12 0.00 0.00 4.20
23 24 3.386768 AACGTATACATAGCTGCAGGG 57.613 47.619 17.12 0.00 0.00 4.45
24 25 5.983720 ACTTAAACGTATACATAGCTGCAGG 59.016 40.000 17.12 0.31 0.00 4.85
25 26 6.918569 AGACTTAAACGTATACATAGCTGCAG 59.081 38.462 10.11 10.11 0.00 4.41
26 27 6.802608 AGACTTAAACGTATACATAGCTGCA 58.197 36.000 1.02 0.00 0.00 4.41
27 28 8.074972 ACTAGACTTAAACGTATACATAGCTGC 58.925 37.037 3.32 0.00 0.00 5.25
28 29 9.947669 AACTAGACTTAAACGTATACATAGCTG 57.052 33.333 3.32 0.00 0.00 4.24
44 45 9.555727 ACTGCAAATTGTAGAAAACTAGACTTA 57.444 29.630 17.61 0.00 34.09 2.24
45 46 8.451908 ACTGCAAATTGTAGAAAACTAGACTT 57.548 30.769 17.61 0.00 34.09 3.01
46 47 8.451908 AACTGCAAATTGTAGAAAACTAGACT 57.548 30.769 17.61 0.00 34.09 3.24
47 48 9.516314 AAAACTGCAAATTGTAGAAAACTAGAC 57.484 29.630 17.61 0.00 34.09 2.59
48 49 9.515020 CAAAACTGCAAATTGTAGAAAACTAGA 57.485 29.630 17.61 0.00 34.09 2.43
49 50 8.755018 CCAAAACTGCAAATTGTAGAAAACTAG 58.245 33.333 17.61 0.00 34.09 2.57
50 51 7.708752 CCCAAAACTGCAAATTGTAGAAAACTA 59.291 33.333 17.61 0.00 34.09 2.24
51 52 6.538381 CCCAAAACTGCAAATTGTAGAAAACT 59.462 34.615 17.61 0.00 34.09 2.66
52 53 6.536941 TCCCAAAACTGCAAATTGTAGAAAAC 59.463 34.615 17.61 0.00 34.09 2.43
53 54 6.644347 TCCCAAAACTGCAAATTGTAGAAAA 58.356 32.000 17.61 0.00 34.09 2.29
54 55 6.227298 TCCCAAAACTGCAAATTGTAGAAA 57.773 33.333 17.61 0.00 34.09 2.52
55 56 5.738783 GCTCCCAAAACTGCAAATTGTAGAA 60.739 40.000 17.61 0.00 34.09 2.10
56 57 4.261994 GCTCCCAAAACTGCAAATTGTAGA 60.262 41.667 17.61 0.00 34.09 2.59
57 58 3.989817 GCTCCCAAAACTGCAAATTGTAG 59.010 43.478 9.51 9.51 36.12 2.74
58 59 3.640967 AGCTCCCAAAACTGCAAATTGTA 59.359 39.130 0.00 0.00 0.00 2.41
59 60 2.435437 AGCTCCCAAAACTGCAAATTGT 59.565 40.909 0.00 0.00 0.00 2.71
60 61 2.803956 CAGCTCCCAAAACTGCAAATTG 59.196 45.455 0.00 0.00 0.00 2.32
61 62 2.699846 TCAGCTCCCAAAACTGCAAATT 59.300 40.909 0.00 0.00 0.00 1.82
219 2720 1.203187 TGTCCTAGGTGGCTCAGAAGT 60.203 52.381 9.08 0.00 35.26 3.01
235 2736 6.033966 GGATTTTTATTGAACCGATGTGTCC 58.966 40.000 0.00 0.00 0.00 4.02
286 2809 4.705519 CCGGTTGCCTGCAAAGCG 62.706 66.667 12.90 12.90 37.70 4.68
403 2929 8.559536 TGTTGATGCTTTTCTCTACAAGTTTAG 58.440 33.333 0.00 0.00 0.00 1.85
404 2930 8.342634 GTGTTGATGCTTTTCTCTACAAGTTTA 58.657 33.333 0.00 0.00 30.88 2.01
411 2937 7.094805 TGGTATTGTGTTGATGCTTTTCTCTAC 60.095 37.037 0.00 0.00 0.00 2.59
416 2942 7.656707 ATTTGGTATTGTGTTGATGCTTTTC 57.343 32.000 0.00 0.00 0.00 2.29
477 3003 4.298103 TGAGACGGAGGGAGTATATACC 57.702 50.000 9.32 1.51 0.00 2.73
485 3011 4.081642 TCACTTATTTTGAGACGGAGGGAG 60.082 45.833 0.00 0.00 0.00 4.30
486 3012 3.835978 TCACTTATTTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
487 3013 3.933332 GTCACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
488 3014 4.822026 AGTCACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 34.56 4.30
489 3015 5.470368 TGAGTCACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 34.56 4.63
490 3016 5.462530 TGAGTCACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 34.56 4.69
491 3017 5.696724 AGTTGAGTCACTTATTTTGAGACGG 59.303 40.000 0.00 0.00 34.56 4.79
492 3018 6.771188 AGTTGAGTCACTTATTTTGAGACG 57.229 37.500 0.00 0.00 34.56 4.18
493 3019 8.398665 ACAAAGTTGAGTCACTTATTTTGAGAC 58.601 33.333 14.62 0.00 35.87 3.36
494 3020 8.506168 ACAAAGTTGAGTCACTTATTTTGAGA 57.494 30.769 14.62 0.00 35.87 3.27
495 3021 9.651718 GTACAAAGTTGAGTCACTTATTTTGAG 57.348 33.333 14.62 0.00 35.87 3.02
496 3022 9.391006 AGTACAAAGTTGAGTCACTTATTTTGA 57.609 29.630 14.62 1.37 35.87 2.69
499 3025 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
500 3026 8.368668 AGCTAGTACAAAGTTGAGTCACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
501 3027 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
502 3028 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
503 3029 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
504 3030 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
505 3031 6.846325 AAAGCTAGTACAAAGTTGAGTCAC 57.154 37.500 0.00 0.00 0.00 3.67
506 3032 7.723324 ACTAAAGCTAGTACAAAGTTGAGTCA 58.277 34.615 0.00 0.00 36.56 3.41
545 3071 9.326413 CCGTTCCAAAATAAGTGACTCTATATT 57.674 33.333 0.00 0.00 0.00 1.28
546 3072 8.701895 TCCGTTCCAAAATAAGTGACTCTATAT 58.298 33.333 0.00 0.00 0.00 0.86
547 3073 8.070034 TCCGTTCCAAAATAAGTGACTCTATA 57.930 34.615 0.00 0.00 0.00 1.31
548 3074 6.942976 TCCGTTCCAAAATAAGTGACTCTAT 58.057 36.000 0.00 0.00 0.00 1.98
549 3075 6.349243 TCCGTTCCAAAATAAGTGACTCTA 57.651 37.500 0.00 0.00 0.00 2.43
550 3076 5.223449 TCCGTTCCAAAATAAGTGACTCT 57.777 39.130 0.00 0.00 0.00 3.24
551 3077 4.392138 CCTCCGTTCCAAAATAAGTGACTC 59.608 45.833 0.00 0.00 0.00 3.36
552 3078 4.041198 TCCTCCGTTCCAAAATAAGTGACT 59.959 41.667 0.00 0.00 0.00 3.41
553 3079 4.320870 TCCTCCGTTCCAAAATAAGTGAC 58.679 43.478 0.00 0.00 0.00 3.67
554 3080 4.627284 TCCTCCGTTCCAAAATAAGTGA 57.373 40.909 0.00 0.00 0.00 3.41
555 3081 4.760204 ACTTCCTCCGTTCCAAAATAAGTG 59.240 41.667 0.00 0.00 0.00 3.16
556 3082 4.981812 ACTTCCTCCGTTCCAAAATAAGT 58.018 39.130 0.00 0.00 0.00 2.24
557 3083 8.904099 ATATACTTCCTCCGTTCCAAAATAAG 57.096 34.615 0.00 0.00 0.00 1.73
558 3084 9.689501 AAATATACTTCCTCCGTTCCAAAATAA 57.310 29.630 0.00 0.00 0.00 1.40
559 3085 9.116067 CAAATATACTTCCTCCGTTCCAAAATA 57.884 33.333 0.00 0.00 0.00 1.40
560 3086 7.068226 CCAAATATACTTCCTCCGTTCCAAAAT 59.932 37.037 0.00 0.00 0.00 1.82
561 3087 6.376018 CCAAATATACTTCCTCCGTTCCAAAA 59.624 38.462 0.00 0.00 0.00 2.44
562 3088 5.883673 CCAAATATACTTCCTCCGTTCCAAA 59.116 40.000 0.00 0.00 0.00 3.28
563 3089 5.045432 ACCAAATATACTTCCTCCGTTCCAA 60.045 40.000 0.00 0.00 0.00 3.53
564 3090 4.472108 ACCAAATATACTTCCTCCGTTCCA 59.528 41.667 0.00 0.00 0.00 3.53
565 3091 4.814771 CACCAAATATACTTCCTCCGTTCC 59.185 45.833 0.00 0.00 0.00 3.62
566 3092 5.425630 ACACCAAATATACTTCCTCCGTTC 58.574 41.667 0.00 0.00 0.00 3.95
567 3093 5.431179 ACACCAAATATACTTCCTCCGTT 57.569 39.130 0.00 0.00 0.00 4.44
568 3094 5.189145 AGAACACCAAATATACTTCCTCCGT 59.811 40.000 0.00 0.00 0.00 4.69
569 3095 5.671493 AGAACACCAAATATACTTCCTCCG 58.329 41.667 0.00 0.00 0.00 4.63
570 3096 7.927092 GTCTAGAACACCAAATATACTTCCTCC 59.073 40.741 0.00 0.00 0.00 4.30
571 3097 7.648510 CGTCTAGAACACCAAATATACTTCCTC 59.351 40.741 0.00 0.00 0.00 3.71
572 3098 7.123847 ACGTCTAGAACACCAAATATACTTCCT 59.876 37.037 0.00 0.00 0.00 3.36
573 3099 7.263496 ACGTCTAGAACACCAAATATACTTCC 58.737 38.462 0.00 0.00 0.00 3.46
574 3100 8.699283 AACGTCTAGAACACCAAATATACTTC 57.301 34.615 0.00 0.00 0.00 3.01
685 3222 7.996644 TGGTGATCTATAGTGTACTGTGTATGA 59.003 37.037 0.00 0.00 0.00 2.15
687 3224 7.999545 ACTGGTGATCTATAGTGTACTGTGTAT 59.000 37.037 0.00 0.00 0.00 2.29
862 3402 0.737367 TGTGAGCTCGATCGGCTTTG 60.737 55.000 25.13 9.60 40.40 2.77
937 3480 3.449746 TTTATTGACCAGTTCTGGGGG 57.550 47.619 20.88 0.00 0.00 5.40
1888 4494 0.460311 CGCTTGTAGAACCCGATCCT 59.540 55.000 0.00 0.00 0.00 3.24
1935 4541 3.059982 CAGTCGAGGTTGCTCCCA 58.940 61.111 0.00 0.00 36.75 4.37
2019 4626 1.800586 CACATGCTGACACTGGTACAC 59.199 52.381 0.00 0.00 0.00 2.90
2081 4691 1.060713 CAACACGCTCGTCACCTTAG 58.939 55.000 0.00 0.00 0.00 2.18
2085 4695 3.712881 GGCAACACGCTCGTCACC 61.713 66.667 0.00 0.00 41.91 4.02
2123 4733 1.915614 AAGAAATGCTGGCTGACGCG 61.916 55.000 3.53 3.53 36.88 6.01
2132 4742 0.457337 GCAGGCCGAAAGAAATGCTG 60.457 55.000 0.00 0.00 32.24 4.41
2204 4814 3.655777 TCAGAGTTTTCCATAACCAGGGT 59.344 43.478 0.00 0.00 0.00 4.34
2226 4836 5.116180 TCATGTCGTCTTCAAAAGTCTTGT 58.884 37.500 0.00 0.00 0.00 3.16
2228 4838 5.601662 TCTCATGTCGTCTTCAAAAGTCTT 58.398 37.500 0.00 0.00 0.00 3.01
2238 4848 2.061773 CGTTTGCTCTCATGTCGTCTT 58.938 47.619 0.00 0.00 0.00 3.01
2257 4867 1.201888 TGAATCGTTCGTCTCGTCTCG 60.202 52.381 0.00 0.00 0.00 4.04
2274 4884 3.535629 CTGCACCAGCTCCCGTGAA 62.536 63.158 8.87 0.00 42.74 3.18
2324 4934 2.755655 ACCTCTATTCACTCCGACACTG 59.244 50.000 0.00 0.00 0.00 3.66
2328 4938 6.679843 CCTATTTACCTCTATTCACTCCGAC 58.320 44.000 0.00 0.00 0.00 4.79
2329 4939 5.243283 GCCTATTTACCTCTATTCACTCCGA 59.757 44.000 0.00 0.00 0.00 4.55
2351 4961 3.146847 ACAAGTTAAAGCACCACTAGCC 58.853 45.455 0.00 0.00 0.00 3.93
2393 5003 8.878769 GCCAAGTTTTAGAATTTCAAGTTCAAA 58.121 29.630 0.00 0.00 0.00 2.69
2440 5065 7.214381 CACTTTATGTCTACGGATGGGATTAA 58.786 38.462 0.00 0.00 0.00 1.40
2544 5169 3.585732 AGAATTTTGGGACGGAAGGAGTA 59.414 43.478 0.00 0.00 0.00 2.59
2545 5170 2.375509 AGAATTTTGGGACGGAAGGAGT 59.624 45.455 0.00 0.00 0.00 3.85
2546 5171 3.073274 AGAATTTTGGGACGGAAGGAG 57.927 47.619 0.00 0.00 0.00 3.69
2547 5172 3.153919 CAAGAATTTTGGGACGGAAGGA 58.846 45.455 0.00 0.00 0.00 3.36
2548 5173 2.890945 ACAAGAATTTTGGGACGGAAGG 59.109 45.455 0.00 0.00 0.00 3.46
2549 5174 3.821033 AGACAAGAATTTTGGGACGGAAG 59.179 43.478 0.00 0.00 0.00 3.46
2550 5175 3.827722 AGACAAGAATTTTGGGACGGAA 58.172 40.909 0.00 0.00 0.00 4.30
2551 5176 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2552 5177 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2553 5178 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2554 5179 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2555 5180 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2556 5181 9.546428 AAACAAATCTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.04 4.12
2590 5215 9.354673 TCCAAAATTCTTGTCTTAGATTTGTCT 57.645 29.630 0.00 0.00 28.79 3.41
2591 5216 9.965824 TTCCAAAATTCTTGTCTTAGATTTGTC 57.034 29.630 0.00 0.00 28.79 3.18
2592 5217 9.750125 GTTCCAAAATTCTTGTCTTAGATTTGT 57.250 29.630 0.00 0.00 28.79 2.83
2593 5218 9.196552 GGTTCCAAAATTCTTGTCTTAGATTTG 57.803 33.333 0.00 0.00 29.84 2.32
2594 5219 8.082242 CGGTTCCAAAATTCTTGTCTTAGATTT 58.918 33.333 0.00 0.00 0.00 2.17
2595 5220 7.447238 TCGGTTCCAAAATTCTTGTCTTAGATT 59.553 33.333 0.00 0.00 0.00 2.40
2596 5221 6.940298 TCGGTTCCAAAATTCTTGTCTTAGAT 59.060 34.615 0.00 0.00 0.00 1.98
2597 5222 6.292923 TCGGTTCCAAAATTCTTGTCTTAGA 58.707 36.000 0.00 0.00 0.00 2.10
2598 5223 6.426937 TCTCGGTTCCAAAATTCTTGTCTTAG 59.573 38.462 0.00 0.00 0.00 2.18
2599 5224 6.292923 TCTCGGTTCCAAAATTCTTGTCTTA 58.707 36.000 0.00 0.00 0.00 2.10
2600 5225 5.130350 TCTCGGTTCCAAAATTCTTGTCTT 58.870 37.500 0.00 0.00 0.00 3.01
2601 5226 4.714632 TCTCGGTTCCAAAATTCTTGTCT 58.285 39.130 0.00 0.00 0.00 3.41
2602 5227 4.755123 TCTCTCGGTTCCAAAATTCTTGTC 59.245 41.667 0.00 0.00 0.00 3.18
2603 5228 4.714632 TCTCTCGGTTCCAAAATTCTTGT 58.285 39.130 0.00 0.00 0.00 3.16
2604 5229 5.689383 TTCTCTCGGTTCCAAAATTCTTG 57.311 39.130 0.00 0.00 0.00 3.02
2605 5230 7.168905 AGTATTCTCTCGGTTCCAAAATTCTT 58.831 34.615 0.00 0.00 0.00 2.52
2606 5231 6.712276 AGTATTCTCTCGGTTCCAAAATTCT 58.288 36.000 0.00 0.00 0.00 2.40
2607 5232 6.986904 AGTATTCTCTCGGTTCCAAAATTC 57.013 37.500 0.00 0.00 0.00 2.17
2608 5233 6.940298 TCAAGTATTCTCTCGGTTCCAAAATT 59.060 34.615 0.00 0.00 0.00 1.82
2609 5234 6.472887 TCAAGTATTCTCTCGGTTCCAAAAT 58.527 36.000 0.00 0.00 0.00 1.82
2610 5235 5.860611 TCAAGTATTCTCTCGGTTCCAAAA 58.139 37.500 0.00 0.00 0.00 2.44
2611 5236 5.011738 ACTCAAGTATTCTCTCGGTTCCAAA 59.988 40.000 0.00 0.00 0.00 3.28
2612 5237 4.527038 ACTCAAGTATTCTCTCGGTTCCAA 59.473 41.667 0.00 0.00 0.00 3.53
2613 5238 4.087182 ACTCAAGTATTCTCTCGGTTCCA 58.913 43.478 0.00 0.00 0.00 3.53
2614 5239 4.722361 ACTCAAGTATTCTCTCGGTTCC 57.278 45.455 0.00 0.00 0.00 3.62
2615 5240 6.439675 AGTACTCAAGTATTCTCTCGGTTC 57.560 41.667 0.00 0.00 32.54 3.62
2616 5241 9.796180 ATATAGTACTCAAGTATTCTCTCGGTT 57.204 33.333 0.00 0.00 32.54 4.44
2658 5283 0.839946 GTACTGACAGATGGGCCCAT 59.160 55.000 38.12 38.12 39.69 4.00
2711 5337 0.179004 TGGCAGTGATCCGGTTTGTT 60.179 50.000 0.00 0.00 0.00 2.83
2723 5367 3.031964 GCGCAACTAGCTGGCAGTG 62.032 63.158 17.16 7.03 42.61 3.66


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

AutoCloner maintained by Alex Coulton.