Multiple sequence alignment - TraesCS1A01G419800

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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 TraesCS1A01G419800 chr1A 100.000 6092 0 0 1 6092 576537495 576531404 0.000000e+00 11250.0
1 TraesCS1A01G419800 chr1A 89.600 1000 79 13 4205 5197 155076247 155077228 0.000000e+00 1247.0
2 TraesCS1A01G419800 chr1A 89.211 760 61 10 2884 3627 155070518 155071272 0.000000e+00 929.0
3 TraesCS1A01G419800 chr1A 86.795 727 68 10 1460 2179 155069228 155069933 0.000000e+00 785.0
4 TraesCS1A01G419800 chr1A 92.166 434 32 2 2415 2847 155070088 155070520 4.040000e-171 612.0
5 TraesCS1A01G419800 chr1A 87.342 553 39 18 1018 1552 155068694 155069233 6.750000e-169 604.0
6 TraesCS1A01G419800 chr1A 93.204 309 21 0 3623 3931 155073066 155073374 7.200000e-124 455.0
7 TraesCS1A01G419800 chr1A 94.891 274 13 1 3924 4196 155074907 155075180 1.570000e-115 427.0
8 TraesCS1A01G419800 chr1A 90.323 62 6 0 5198 5259 155077250 155077311 1.410000e-11 82.4
9 TraesCS1A01G419800 chr1D 94.374 3448 128 24 795 4207 479923565 479926981 0.000000e+00 5232.0
10 TraesCS1A01G419800 chr1D 94.222 1748 69 19 4205 5936 479927718 479929449 0.000000e+00 2639.0
11 TraesCS1A01G419800 chr1D 91.880 1330 84 12 2884 4196 137637580 137636258 0.000000e+00 1836.0
12 TraesCS1A01G419800 chr1D 88.271 1151 89 25 4205 5330 137635626 137634497 0.000000e+00 1336.0
13 TraesCS1A01G419800 chr1D 85.814 1283 101 29 933 2179 137644479 137643242 0.000000e+00 1286.0
14 TraesCS1A01G419800 chr1D 85.117 383 34 8 343 725 479918417 479918776 2.680000e-98 370.0
15 TraesCS1A01G419800 chr1D 96.907 194 6 0 2657 2850 137637768 137637575 5.890000e-85 326.0
16 TraesCS1A01G419800 chr1D 95.312 64 3 0 2258 2321 137643151 137643088 1.080000e-17 102.0
17 TraesCS1A01G419800 chr1B 94.626 2884 104 25 2415 5259 668141278 668144149 0.000000e+00 4420.0
18 TraesCS1A01G419800 chr1B 89.834 1328 113 10 2884 4196 209995408 209994088 0.000000e+00 1685.0
19 TraesCS1A01G419800 chr1B 95.000 1060 49 2 953 2012 668140165 668141220 0.000000e+00 1661.0
20 TraesCS1A01G419800 chr1B 89.829 1288 109 10 2884 4154 209652751 209651469 0.000000e+00 1633.0
21 TraesCS1A01G419800 chr1B 86.308 1154 107 28 4205 5330 209643733 209642603 0.000000e+00 1208.0
22 TraesCS1A01G419800 chr1B 84.174 1011 105 20 1204 2182 209996971 209995984 0.000000e+00 929.0
23 TraesCS1A01G419800 chr1B 84.761 794 92 16 1398 2182 209654100 209653327 0.000000e+00 769.0
24 TraesCS1A01G419800 chr1B 85.997 757 61 19 51 774 668138038 668138782 0.000000e+00 769.0
25 TraesCS1A01G419800 chr1B 91.048 458 27 6 5645 6092 668144784 668145237 1.880000e-169 606.0
26 TraesCS1A01G419800 chr1B 90.183 438 38 3 2415 2851 209653178 209652745 3.190000e-157 566.0
27 TraesCS1A01G419800 chr1B 88.584 438 45 3 2415 2851 209995835 209995402 1.500000e-145 527.0
28 TraesCS1A01G419800 chr1B 88.067 419 28 11 5258 5658 668144273 668144687 1.540000e-130 477.0
29 TraesCS1A01G419800 chr1B 82.723 382 39 19 1018 1387 209654772 209654406 1.270000e-81 315.0
30 TraesCS1A01G419800 chr1B 81.935 310 50 5 1682 1987 58374181 58373874 2.180000e-64 257.0
31 TraesCS1A01G419800 chr1B 91.837 98 6 2 830 927 668140071 668140166 1.070000e-27 135.0
32 TraesCS1A01G419800 chr1B 96.875 64 2 0 2258 2321 209653235 209653172 2.320000e-19 108.0
33 TraesCS1A01G419800 chr1B 100.000 44 0 0 799 842 668140011 668140054 1.410000e-11 82.4
34 TraesCS1A01G419800 chr2A 86.053 337 39 6 5609 5940 698277433 698277766 7.510000e-94 355.0
35 TraesCS1A01G419800 chr2A 91.892 37 3 0 5584 5620 764339058 764339022 1.100000e-02 52.8
36 TraesCS1A01G419800 chr7A 84.589 292 41 4 1711 2001 63743664 63743952 2.780000e-73 287.0
37 TraesCS1A01G419800 chr7A 100.000 32 0 0 2319 2350 2741865 2741896 6.590000e-05 60.2
38 TraesCS1A01G419800 chr7A 100.000 32 0 0 2319 2350 2762635 2762666 6.590000e-05 60.2
39 TraesCS1A01G419800 chr4D 85.333 150 13 7 3377 3525 20120619 20120760 4.920000e-31 147.0
40 TraesCS1A01G419800 chr6D 81.657 169 21 3 3329 3495 79673182 79673342 1.380000e-26 132.0
41 TraesCS1A01G419800 chr2D 100.000 29 0 0 5585 5613 635309372 635309344 3.000000e-03 54.7
42 TraesCS1A01G419800 chr2B 100.000 29 0 0 5585 5613 779639202 779639174 3.000000e-03 54.7


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 TraesCS1A01G419800 chr1A 576531404 576537495 6091 True 11250.000000 11250 100.000000 1 6092 1 chr1A.!!$R1 6091
1 TraesCS1A01G419800 chr1A 155068694 155077311 8617 False 642.675000 1247 90.441500 1018 5259 8 chr1A.!!$F1 4241
2 TraesCS1A01G419800 chr1D 479923565 479929449 5884 False 3935.500000 5232 94.298000 795 5936 2 chr1D.!!$F2 5141
3 TraesCS1A01G419800 chr1D 137634497 137637768 3271 True 1166.000000 1836 92.352667 2657 5330 3 chr1D.!!$R1 2673
4 TraesCS1A01G419800 chr1D 137643088 137644479 1391 True 694.000000 1286 90.563000 933 2321 2 chr1D.!!$R2 1388
5 TraesCS1A01G419800 chr1B 209642603 209643733 1130 True 1208.000000 1208 86.308000 4205 5330 1 chr1B.!!$R2 1125
6 TraesCS1A01G419800 chr1B 668138038 668145237 7199 False 1164.342857 4420 92.367857 51 6092 7 chr1B.!!$F1 6041
7 TraesCS1A01G419800 chr1B 209994088 209996971 2883 True 1047.000000 1685 87.530667 1204 4196 3 chr1B.!!$R4 2992
8 TraesCS1A01G419800 chr1B 209651469 209654772 3303 True 678.200000 1633 88.874200 1018 4154 5 chr1B.!!$R3 3136

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
272 299 0.040067 CCCGCAACTTCACTTCTTGC 60.040 55.000 0.00 0.00 37.52 4.01 F
282 309 0.170561 CACTTCTTGCAGCTGATGGC 59.829 55.000 20.43 1.45 42.19 4.40 F
537 570 0.178891 ATGACCGGCTCCCCTATCAT 60.179 55.000 0.00 0.00 31.87 2.45 F
645 678 0.527565 CACCCTTTTCCGAGCCATTG 59.472 55.000 0.00 0.00 0.00 2.82 F
2093 3794 1.101635 CCTGGCATGCTCATGAGGTG 61.102 60.000 23.89 0.02 41.20 4.00 F
2878 4648 0.251916 TAATTGACCTGCCCCTCACG 59.748 55.000 0.00 0.00 0.00 4.35 F
2883 4653 2.311688 GACCTGCCCCTCACGGTATG 62.312 65.000 0.00 0.00 0.00 2.39 F
4496 11451 1.421268 AGCAATGGTTCAGGAGACACA 59.579 47.619 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 3723 0.108585 TGGGTGCAGAAGTCCAAGAC 59.891 55.000 0.00 0.00 0.00 3.01 R
2252 4015 1.201647 CTTTCCTGTGCAATCAGCCTG 59.798 52.381 0.00 0.00 44.83 4.85 R
2399 4168 6.683974 TGGTATTTACTACTCCGTAGTGTC 57.316 41.667 14.99 3.46 46.99 3.67 R
2579 4349 2.301296 CCATGGTCAGACACTTCACTCT 59.699 50.000 2.57 0.00 0.00 3.24 R
3717 7330 3.003378 AGAGCGTAAAAAGTCAGCCAAAC 59.997 43.478 0.00 0.00 0.00 2.93 R
4496 11451 1.226262 AAGTGCCCCGTTGACACTT 59.774 52.632 1.94 1.94 46.86 3.16 R
4667 11625 1.761198 TCATCATCTCCAGCCACAGAG 59.239 52.381 0.00 0.00 0.00 3.35 R
5895 13141 1.876156 GGAGCAGAACAACACTTCCAG 59.124 52.381 0.00 0.00 0.00 3.86 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
17 18 4.319133 CCTTGTGCATAACCGGCT 57.681 55.556 0.00 0.00 0.00 5.52
18 19 1.802636 CCTTGTGCATAACCGGCTG 59.197 57.895 0.00 0.00 0.00 4.85
19 20 1.656818 CCTTGTGCATAACCGGCTGG 61.657 60.000 11.02 11.02 42.84 4.85
20 21 2.270297 CTTGTGCATAACCGGCTGGC 62.270 60.000 12.89 0.23 39.70 4.85
21 22 3.876198 GTGCATAACCGGCTGGCG 61.876 66.667 17.39 17.39 39.70 5.69
22 23 4.089239 TGCATAACCGGCTGGCGA 62.089 61.111 25.90 5.47 39.70 5.54
23 24 2.822255 GCATAACCGGCTGGCGAA 60.822 61.111 25.90 10.31 39.70 4.70
24 25 2.823829 GCATAACCGGCTGGCGAAG 61.824 63.158 25.90 11.72 39.70 3.79
25 26 1.153449 CATAACCGGCTGGCGAAGA 60.153 57.895 25.90 9.37 39.70 2.87
26 27 1.144057 ATAACCGGCTGGCGAAGAG 59.856 57.895 25.90 10.57 39.70 2.85
27 28 2.311688 ATAACCGGCTGGCGAAGAGG 62.312 60.000 25.90 10.18 39.70 3.69
38 39 1.798813 GGCGAAGAGGCAAATATACGG 59.201 52.381 0.00 0.00 45.92 4.02
39 40 1.194772 GCGAAGAGGCAAATATACGGC 59.805 52.381 0.00 0.00 0.00 5.68
40 41 2.479837 CGAAGAGGCAAATATACGGCA 58.520 47.619 0.00 0.00 0.00 5.69
41 42 2.869801 CGAAGAGGCAAATATACGGCAA 59.130 45.455 0.00 0.00 0.00 4.52
42 43 3.059597 CGAAGAGGCAAATATACGGCAAG 60.060 47.826 0.00 0.00 0.00 4.01
43 44 3.560636 AGAGGCAAATATACGGCAAGT 57.439 42.857 0.00 0.00 0.00 3.16
44 45 3.886123 AGAGGCAAATATACGGCAAGTT 58.114 40.909 0.00 0.00 0.00 2.66
45 46 3.877508 AGAGGCAAATATACGGCAAGTTC 59.122 43.478 0.00 0.00 0.00 3.01
46 47 3.616219 AGGCAAATATACGGCAAGTTCA 58.384 40.909 0.00 0.00 0.00 3.18
47 48 3.377172 AGGCAAATATACGGCAAGTTCAC 59.623 43.478 0.00 0.00 0.00 3.18
48 49 3.350912 GCAAATATACGGCAAGTTCACG 58.649 45.455 0.00 0.00 0.00 4.35
49 50 3.787476 GCAAATATACGGCAAGTTCACGG 60.787 47.826 1.41 0.00 0.00 4.94
97 98 0.395312 GGAGGACCCAAACTTCGTCA 59.605 55.000 0.00 0.00 34.14 4.35
127 128 2.202932 CGCTCTACAAGGCCGCAT 60.203 61.111 0.00 0.00 0.00 4.73
141 142 1.361668 CCGCATGTAGCACTCACACC 61.362 60.000 0.00 0.00 46.13 4.16
149 150 3.046087 CACTCACACCGGCTGCAG 61.046 66.667 10.11 10.11 0.00 4.41
150 151 3.550431 ACTCACACCGGCTGCAGT 61.550 61.111 16.64 2.55 0.00 4.40
180 181 4.292178 GAGGAGGATGCGGAGGCG 62.292 72.222 0.00 0.00 44.10 5.52
210 211 2.525422 CATGCGATCATGGACGAGG 58.475 57.895 14.43 1.98 44.84 4.63
211 212 0.947660 CATGCGATCATGGACGAGGG 60.948 60.000 14.43 1.71 44.84 4.30
212 213 2.663188 GCGATCATGGACGAGGGC 60.663 66.667 14.43 0.00 0.00 5.19
230 231 2.598045 CGTCTCCGCATCATTCTGG 58.402 57.895 0.00 0.00 0.00 3.86
238 240 4.488136 ATCATTCTGGCGCCCGCA 62.488 61.111 26.77 8.75 44.11 5.69
269 296 1.048601 TCTCCCGCAACTTCACTTCT 58.951 50.000 0.00 0.00 0.00 2.85
272 299 0.040067 CCCGCAACTTCACTTCTTGC 60.040 55.000 0.00 0.00 37.52 4.01
273 300 0.662619 CCGCAACTTCACTTCTTGCA 59.337 50.000 0.00 0.00 40.31 4.08
275 302 1.763634 GCAACTTCACTTCTTGCAGC 58.236 50.000 0.00 0.00 40.09 5.25
276 303 1.336125 GCAACTTCACTTCTTGCAGCT 59.664 47.619 0.00 0.00 40.09 4.24
277 304 2.857489 GCAACTTCACTTCTTGCAGCTG 60.857 50.000 10.11 10.11 40.09 4.24
278 305 2.615447 CAACTTCACTTCTTGCAGCTGA 59.385 45.455 20.43 0.00 0.00 4.26
280 307 2.812591 ACTTCACTTCTTGCAGCTGATG 59.187 45.455 20.43 6.29 0.00 3.07
282 309 0.170561 CACTTCTTGCAGCTGATGGC 59.829 55.000 20.43 1.45 42.19 4.40
283 310 0.964358 ACTTCTTGCAGCTGATGGCC 60.964 55.000 20.43 0.00 43.05 5.36
284 311 1.989966 CTTCTTGCAGCTGATGGCCG 61.990 60.000 20.43 0.00 43.05 6.13
286 313 1.450134 CTTGCAGCTGATGGCCGTA 60.450 57.895 20.43 0.00 43.05 4.02
299 331 1.523938 GCCGTAGCATGGGGAAGAC 60.524 63.158 0.00 0.00 39.53 3.01
301 333 0.251916 CCGTAGCATGGGGAAGACAA 59.748 55.000 0.00 0.00 0.00 3.18
334 366 2.675423 CCCCTCCACAGTCGACGA 60.675 66.667 10.46 0.00 0.00 4.20
401 434 7.281999 TCGGCTATTGTTTGATGAAATATGTCA 59.718 33.333 0.00 0.00 0.00 3.58
448 481 8.071122 GATTTGAATGAAAATCGTTTGGTTCA 57.929 30.769 0.00 0.00 36.95 3.18
456 489 6.983307 TGAAAATCGTTTGGTTCACATGAAAT 59.017 30.769 0.00 0.00 35.58 2.17
459 492 6.768029 ATCGTTTGGTTCACATGAAATTTG 57.232 33.333 0.00 0.00 35.58 2.32
462 495 5.051106 CGTTTGGTTCACATGAAATTTGTCC 60.051 40.000 0.00 0.00 35.58 4.02
464 497 4.942852 TGGTTCACATGAAATTTGTCCAC 58.057 39.130 0.00 0.00 35.58 4.02
512 545 5.046878 TGTGTCTAACCGTTTGATGGATAGT 60.047 40.000 0.00 0.00 33.04 2.12
537 570 0.178891 ATGACCGGCTCCCCTATCAT 60.179 55.000 0.00 0.00 31.87 2.45
545 578 1.541233 GCTCCCCTATCATTGTCCACG 60.541 57.143 0.00 0.00 0.00 4.94
551 584 2.430694 CCTATCATTGTCCACGGACTCA 59.569 50.000 16.88 4.64 44.80 3.41
557 590 2.209690 TGTCCACGGACTCATCTACA 57.790 50.000 16.88 0.00 44.80 2.74
558 591 2.521126 TGTCCACGGACTCATCTACAA 58.479 47.619 16.88 0.00 44.80 2.41
575 608 5.276270 TCTACAAACGAATAGTATGTCCGC 58.724 41.667 0.00 0.00 0.00 5.54
580 613 5.464965 AACGAATAGTATGTCCGCTTTTG 57.535 39.130 0.00 0.00 0.00 2.44
606 639 0.548510 AGCTTTGGAGATGCCCTACC 59.451 55.000 0.00 0.00 34.97 3.18
612 645 1.922447 TGGAGATGCCCTACCACAATT 59.078 47.619 0.00 0.00 34.97 2.32
637 670 1.067635 CAATCTTGCCACCCTTTTCCG 60.068 52.381 0.00 0.00 0.00 4.30
640 673 1.866853 CTTGCCACCCTTTTCCGAGC 61.867 60.000 0.00 0.00 0.00 5.03
644 677 0.611896 CCACCCTTTTCCGAGCCATT 60.612 55.000 0.00 0.00 0.00 3.16
645 678 0.527565 CACCCTTTTCCGAGCCATTG 59.472 55.000 0.00 0.00 0.00 2.82
694 727 1.786937 ATGTTGCCAAAAGTGTGGGA 58.213 45.000 0.00 0.00 39.26 4.37
760 793 8.077386 GGTGAATACCAAAATCTGACGTAAAAA 58.923 33.333 0.00 0.00 46.71 1.94
844 2109 5.864418 TCCGTACAAGGCTATATTTGAGT 57.136 39.130 0.00 0.00 0.00 3.41
938 2203 4.941263 TCTTCAATCCCGTATCCAAAGTTG 59.059 41.667 0.00 0.00 0.00 3.16
1110 2375 1.454847 CCTCTACAGCGCCCTCTCT 60.455 63.158 2.29 0.00 0.00 3.10
1157 2422 3.578968 AAAGCCCCACCGGTAAGCC 62.579 63.158 6.87 0.00 0.00 4.35
1393 2687 3.981308 CGGGATTTCACACCGCTT 58.019 55.556 0.00 0.00 41.23 4.68
1491 3161 1.950216 GGAGAAATCCGAGGGAATTGC 59.050 52.381 0.00 0.00 34.34 3.56
1759 3447 2.282462 GTGTGCTTGGGGTCCAGG 60.282 66.667 0.00 0.00 33.81 4.45
1795 3483 1.149101 ACAAGGGTGAGTGGGTCATT 58.851 50.000 0.00 0.00 37.56 2.57
1800 3488 1.534729 GGTGAGTGGGTCATTTGGTC 58.465 55.000 0.00 0.00 37.56 4.02
1820 3508 7.730364 TGGTCATCTTTGTTCTTCTAGTTTC 57.270 36.000 0.00 0.00 0.00 2.78
1965 3659 8.502387 GCAAAATTAAGGCATGTTTCAATTACA 58.498 29.630 0.00 0.00 0.00 2.41
1994 3688 5.710513 TGATTTACAATGCTCAGCTGTTT 57.289 34.783 14.67 0.99 0.00 2.83
2002 3696 4.756084 ATGCTCAGCTGTTTTGTTAGAC 57.244 40.909 14.67 0.00 0.00 2.59
2003 3697 3.540617 TGCTCAGCTGTTTTGTTAGACA 58.459 40.909 14.67 2.00 0.00 3.41
2004 3698 3.312421 TGCTCAGCTGTTTTGTTAGACAC 59.688 43.478 14.67 0.00 0.00 3.67
2005 3699 3.561725 GCTCAGCTGTTTTGTTAGACACT 59.438 43.478 14.67 0.00 0.00 3.55
2006 3700 4.035675 GCTCAGCTGTTTTGTTAGACACTT 59.964 41.667 14.67 0.00 0.00 3.16
2007 3701 5.734855 TCAGCTGTTTTGTTAGACACTTC 57.265 39.130 14.67 0.00 0.00 3.01
2008 3702 5.428253 TCAGCTGTTTTGTTAGACACTTCT 58.572 37.500 14.67 0.00 35.66 2.85
2009 3703 5.523916 TCAGCTGTTTTGTTAGACACTTCTC 59.476 40.000 14.67 0.00 32.75 2.87
2010 3704 5.525378 CAGCTGTTTTGTTAGACACTTCTCT 59.475 40.000 5.25 0.00 32.75 3.10
2011 3705 6.037610 CAGCTGTTTTGTTAGACACTTCTCTT 59.962 38.462 5.25 0.00 32.75 2.85
2012 3706 6.599638 AGCTGTTTTGTTAGACACTTCTCTTT 59.400 34.615 0.00 0.00 32.75 2.52
2013 3707 6.688813 GCTGTTTTGTTAGACACTTCTCTTTG 59.311 38.462 0.00 0.00 32.75 2.77
2014 3708 7.626452 GCTGTTTTGTTAGACACTTCTCTTTGT 60.626 37.037 0.00 0.00 32.75 2.83
2015 3709 8.106247 TGTTTTGTTAGACACTTCTCTTTGTT 57.894 30.769 0.00 0.00 32.75 2.83
2016 3710 9.221933 TGTTTTGTTAGACACTTCTCTTTGTTA 57.778 29.630 0.00 0.00 32.75 2.41
2017 3711 9.704098 GTTTTGTTAGACACTTCTCTTTGTTAG 57.296 33.333 0.00 0.00 32.75 2.34
2018 3712 9.661563 TTTTGTTAGACACTTCTCTTTGTTAGA 57.338 29.630 0.00 0.00 32.75 2.10
2019 3713 9.832445 TTTGTTAGACACTTCTCTTTGTTAGAT 57.168 29.630 0.00 0.00 32.75 1.98
2093 3794 1.101635 CCTGGCATGCTCATGAGGTG 61.102 60.000 23.89 0.02 41.20 4.00
2115 3816 3.610821 GCGATTAATATTGTTTCCCGGCC 60.611 47.826 0.00 0.00 0.00 6.13
2130 3831 2.021457 CCGGCCGTAATTTCTTCCAAT 58.979 47.619 26.12 0.00 0.00 3.16
2252 4015 7.384932 CCATCTTTTGTCTTTTATTTCCCACAC 59.615 37.037 0.00 0.00 0.00 3.82
2345 4111 9.221933 ACTACCTCTGTCTCATAATATAAGACG 57.778 37.037 0.00 0.00 41.84 4.18
2346 4112 9.221933 CTACCTCTGTCTCATAATATAAGACGT 57.778 37.037 0.00 0.00 41.84 4.34
2579 4349 4.333649 CAGAAGTCTGCAGAAACAGTTCAA 59.666 41.667 20.19 0.00 38.84 2.69
2694 4464 2.183046 GTCCGCTCAGCTGACCTC 59.817 66.667 13.74 4.06 36.93 3.85
2875 4645 2.487986 CCTCATAATTGACCTGCCCCTC 60.488 54.545 0.00 0.00 0.00 4.30
2878 4648 0.251916 TAATTGACCTGCCCCTCACG 59.748 55.000 0.00 0.00 0.00 4.35
2883 4653 2.311688 GACCTGCCCCTCACGGTATG 62.312 65.000 0.00 0.00 0.00 2.39
2884 4654 2.505982 CTGCCCCTCACGGTATGG 59.494 66.667 0.00 0.00 0.00 2.74
2948 4725 6.019896 GTTGGAAACTTCACGATGTTTTTG 57.980 37.500 11.10 0.00 45.32 2.44
2949 4726 5.317733 TGGAAACTTCACGATGTTTTTGT 57.682 34.783 11.10 0.00 38.34 2.83
2950 4727 5.715070 TGGAAACTTCACGATGTTTTTGTT 58.285 33.333 11.10 0.00 38.34 2.83
2951 4728 5.802956 TGGAAACTTCACGATGTTTTTGTTC 59.197 36.000 11.10 1.06 38.34 3.18
2952 4729 5.802956 GGAAACTTCACGATGTTTTTGTTCA 59.197 36.000 11.10 0.00 38.34 3.18
3133 4940 4.457603 ACTTTGCTCAGTTGTGTTGTTGTA 59.542 37.500 0.00 0.00 0.00 2.41
3155 4966 9.461312 TTGTAGCAGACAACAGGATAATAAAAT 57.539 29.630 0.38 0.00 43.30 1.82
3557 5371 7.119262 ACAAGGTGAAATATTTCTTCCACTACG 59.881 37.037 27.74 18.88 38.02 3.51
3592 5406 8.304596 CAGTCTTGTTGTGTCTAGAACCTATAA 58.695 37.037 0.00 0.00 29.49 0.98
3717 7330 4.265073 AGCAGTATAACAAGCTTTCAGGG 58.735 43.478 0.00 0.00 32.52 4.45
3750 7363 6.979465 ACTTTTTACGCTCTCTACTGTACTT 58.021 36.000 0.00 0.00 0.00 2.24
4197 9351 5.125739 TCGAGTCATTTCTCCTTTACTCTCC 59.874 44.000 0.00 0.00 32.96 3.71
4496 11451 1.421268 AGCAATGGTTCAGGAGACACA 59.579 47.619 0.00 0.00 0.00 3.72
4656 11611 6.645003 GGAGACAATAAAACACATTGGAAACC 59.355 38.462 0.00 0.00 37.64 3.27
4802 11760 1.885233 TGCATGAAAGCCGTGAATCAA 59.115 42.857 0.00 0.00 33.60 2.57
4946 11909 1.862827 GTTGGTTGACTCGCGTTACTT 59.137 47.619 5.77 0.00 0.00 2.24
4953 11916 1.127817 CTCGCGTTACTTGCACACG 59.872 57.895 5.77 0.00 36.98 4.49
4992 11955 0.039165 CTTGCCCCGTTGAAAAGCTC 60.039 55.000 0.00 0.00 0.00 4.09
5049 12012 6.318900 GTCAAAACTATGGGGAAGTTCATAGG 59.681 42.308 5.01 0.00 44.13 2.57
5069 12032 4.747810 AGGTTGTTGCTTCAGTTTTTCAG 58.252 39.130 0.00 0.00 0.00 3.02
5072 12035 5.062183 GGTTGTTGCTTCAGTTTTTCAGAAC 59.938 40.000 0.00 0.00 0.00 3.01
5076 12039 5.596836 TGCTTCAGTTTTTCAGAACCAAT 57.403 34.783 0.00 0.00 0.00 3.16
5135 12103 7.116075 ACATTTAATGAAGCCAAGCATGTAT 57.884 32.000 12.28 0.00 0.00 2.29
5136 12104 6.982141 ACATTTAATGAAGCCAAGCATGTATG 59.018 34.615 12.28 0.00 0.00 2.39
5137 12105 6.528537 TTTAATGAAGCCAAGCATGTATGT 57.471 33.333 0.00 0.00 0.00 2.29
5138 12106 6.528537 TTAATGAAGCCAAGCATGTATGTT 57.471 33.333 0.00 0.00 0.00 2.71
5139 12107 5.410355 AATGAAGCCAAGCATGTATGTTT 57.590 34.783 0.00 0.00 0.00 2.83
5140 12108 4.870123 TGAAGCCAAGCATGTATGTTTT 57.130 36.364 0.00 0.00 0.00 2.43
5141 12109 5.973899 TGAAGCCAAGCATGTATGTTTTA 57.026 34.783 0.00 0.00 0.00 1.52
5160 12128 6.589523 TGTTTTACACGTAGGTTTGCGTATAT 59.410 34.615 0.00 0.00 43.92 0.86
5305 12428 3.496331 CTGTTATTTTCCCACACCCAGT 58.504 45.455 0.00 0.00 0.00 4.00
5335 12458 2.817839 GCACCACACCCCAGTTCTTATT 60.818 50.000 0.00 0.00 0.00 1.40
5336 12459 3.081804 CACCACACCCCAGTTCTTATTC 58.918 50.000 0.00 0.00 0.00 1.75
5337 12460 2.714250 ACCACACCCCAGTTCTTATTCA 59.286 45.455 0.00 0.00 0.00 2.57
5338 12461 3.139397 ACCACACCCCAGTTCTTATTCAA 59.861 43.478 0.00 0.00 0.00 2.69
5339 12462 3.506067 CCACACCCCAGTTCTTATTCAAC 59.494 47.826 0.00 0.00 0.00 3.18
5341 12464 4.582656 CACACCCCAGTTCTTATTCAACAA 59.417 41.667 0.00 0.00 0.00 2.83
5344 12473 6.183360 ACACCCCAGTTCTTATTCAACAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
5346 12475 5.538433 CCCCAGTTCTTATTCAACAAAAGGA 59.462 40.000 0.00 0.00 0.00 3.36
5359 12488 8.885494 TTCAACAAAAGGAAAACATGATAAGG 57.115 30.769 0.00 0.00 0.00 2.69
5364 12493 5.649782 AAGGAAAACATGATAAGGTGCTG 57.350 39.130 0.00 0.00 0.00 4.41
5494 12625 2.629617 CCCCAGATTTTCTTGTTGCAGT 59.370 45.455 0.00 0.00 0.00 4.40
5541 12673 4.112634 TGGTATTTTTCTGGAGGTGCTT 57.887 40.909 0.00 0.00 0.00 3.91
5546 12678 6.015772 GGTATTTTTCTGGAGGTGCTTTGTAA 60.016 38.462 0.00 0.00 0.00 2.41
5557 12689 6.294010 GGAGGTGCTTTGTAACCTTTTCTTAG 60.294 42.308 0.00 0.00 46.97 2.18
5558 12690 6.127101 AGGTGCTTTGTAACCTTTTCTTAGT 58.873 36.000 0.00 0.00 44.63 2.24
5821 13067 9.384764 GGAGAAAAACAGTAAGATATAGCTTGT 57.615 33.333 13.46 0.69 0.00 3.16
5895 13141 3.621558 AGTACAATAGGGGCTGAAAAGC 58.378 45.455 0.00 0.00 0.00 3.51
5929 13175 6.472016 TGTTCTGCTCCAAGATGTACAATAA 58.528 36.000 0.00 0.00 0.00 1.40
6043 13295 8.450578 AAAAATATTCGTGGAGATATGAGCAA 57.549 30.769 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.656818 CCAGCCGGTTATGCACAAGG 61.657 60.000 1.90 0.00 0.00 3.61
1 2 1.802636 CCAGCCGGTTATGCACAAG 59.197 57.895 1.90 0.00 0.00 3.16
2 3 2.339556 GCCAGCCGGTTATGCACAA 61.340 57.895 1.90 0.00 33.28 3.33
3 4 2.749839 GCCAGCCGGTTATGCACA 60.750 61.111 1.90 0.00 33.28 4.57
4 5 3.876198 CGCCAGCCGGTTATGCAC 61.876 66.667 1.90 0.00 33.28 4.57
5 6 3.613877 TTCGCCAGCCGGTTATGCA 62.614 57.895 1.90 0.00 37.59 3.96
6 7 2.822255 TTCGCCAGCCGGTTATGC 60.822 61.111 1.90 2.18 37.59 3.14
7 8 1.153449 TCTTCGCCAGCCGGTTATG 60.153 57.895 1.90 0.00 37.59 1.90
8 9 1.144057 CTCTTCGCCAGCCGGTTAT 59.856 57.895 1.90 0.00 37.59 1.89
9 10 2.577059 CTCTTCGCCAGCCGGTTA 59.423 61.111 1.90 0.00 37.59 2.85
10 11 4.394712 CCTCTTCGCCAGCCGGTT 62.395 66.667 1.90 0.00 37.59 4.44
14 15 0.748005 TATTTGCCTCTTCGCCAGCC 60.748 55.000 0.00 0.00 0.00 4.85
15 16 1.312815 ATATTTGCCTCTTCGCCAGC 58.687 50.000 0.00 0.00 0.00 4.85
16 17 2.476619 CGTATATTTGCCTCTTCGCCAG 59.523 50.000 0.00 0.00 0.00 4.85
17 18 2.479837 CGTATATTTGCCTCTTCGCCA 58.520 47.619 0.00 0.00 0.00 5.69
18 19 1.798813 CCGTATATTTGCCTCTTCGCC 59.201 52.381 0.00 0.00 0.00 5.54
19 20 1.194772 GCCGTATATTTGCCTCTTCGC 59.805 52.381 0.00 0.00 0.00 4.70
20 21 2.479837 TGCCGTATATTTGCCTCTTCG 58.520 47.619 0.00 0.00 0.00 3.79
21 22 3.877508 ACTTGCCGTATATTTGCCTCTTC 59.122 43.478 0.00 0.00 0.00 2.87
22 23 3.886123 ACTTGCCGTATATTTGCCTCTT 58.114 40.909 0.00 0.00 0.00 2.85
23 24 3.560636 ACTTGCCGTATATTTGCCTCT 57.439 42.857 0.00 0.00 0.00 3.69
24 25 3.625764 TGAACTTGCCGTATATTTGCCTC 59.374 43.478 0.00 0.00 0.00 4.70
25 26 3.377172 GTGAACTTGCCGTATATTTGCCT 59.623 43.478 0.00 0.00 0.00 4.75
26 27 3.691498 GTGAACTTGCCGTATATTTGCC 58.309 45.455 0.00 0.00 0.00 4.52
27 28 3.350912 CGTGAACTTGCCGTATATTTGC 58.649 45.455 0.00 0.00 0.00 3.68
28 29 3.242608 CCCGTGAACTTGCCGTATATTTG 60.243 47.826 0.00 0.00 0.00 2.32
29 30 2.940410 CCCGTGAACTTGCCGTATATTT 59.060 45.455 0.00 0.00 0.00 1.40
30 31 2.557317 CCCGTGAACTTGCCGTATATT 58.443 47.619 0.00 0.00 0.00 1.28
31 32 1.808891 GCCCGTGAACTTGCCGTATAT 60.809 52.381 0.00 0.00 0.00 0.86
32 33 0.460635 GCCCGTGAACTTGCCGTATA 60.461 55.000 0.00 0.00 0.00 1.47
33 34 1.743995 GCCCGTGAACTTGCCGTAT 60.744 57.895 0.00 0.00 0.00 3.06
34 35 2.357760 GCCCGTGAACTTGCCGTA 60.358 61.111 0.00 0.00 0.00 4.02
37 38 3.423154 CTCGCCCGTGAACTTGCC 61.423 66.667 0.00 0.00 0.00 4.52
38 39 3.423154 CCTCGCCCGTGAACTTGC 61.423 66.667 0.00 0.00 0.00 4.01
39 40 1.738099 CTCCTCGCCCGTGAACTTG 60.738 63.158 0.00 0.00 0.00 3.16
40 41 2.657237 CTCCTCGCCCGTGAACTT 59.343 61.111 0.00 0.00 0.00 2.66
41 42 3.382832 CCTCCTCGCCCGTGAACT 61.383 66.667 0.00 0.00 0.00 3.01
127 128 2.207229 AGCCGGTGTGAGTGCTACA 61.207 57.895 1.90 0.00 30.97 2.74
161 162 3.610669 CCTCCGCATCCTCCTCCG 61.611 72.222 0.00 0.00 0.00 4.63
193 194 1.368950 CCCTCGTCCATGATCGCAT 59.631 57.895 0.00 0.00 34.29 4.73
194 195 2.814604 CCCTCGTCCATGATCGCA 59.185 61.111 0.00 0.00 0.00 5.10
221 222 3.779850 ATGCGGGCGCCAGAATGAT 62.780 57.895 31.49 12.40 41.09 2.45
238 240 1.517832 CGGGAGAAGAGCGAACCAT 59.482 57.895 0.00 0.00 0.00 3.55
249 251 1.416401 AGAAGTGAAGTTGCGGGAGAA 59.584 47.619 0.00 0.00 0.00 2.87
273 300 1.227764 CATGCTACGGCCATCAGCT 60.228 57.895 18.09 4.68 43.05 4.24
275 302 1.598962 CCCATGCTACGGCCATCAG 60.599 63.158 2.24 0.00 37.74 2.90
276 303 2.510411 CCCATGCTACGGCCATCA 59.490 61.111 2.24 0.00 37.74 3.07
277 304 2.281761 CCCCATGCTACGGCCATC 60.282 66.667 2.24 0.00 37.74 3.51
278 305 2.343475 CTTCCCCATGCTACGGCCAT 62.343 60.000 2.24 0.00 37.74 4.40
280 307 2.203209 CTTCCCCATGCTACGGCC 60.203 66.667 0.00 0.00 37.74 6.13
282 309 0.251916 TTGTCTTCCCCATGCTACGG 59.748 55.000 0.00 0.00 0.00 4.02
283 310 2.107950 TTTGTCTTCCCCATGCTACG 57.892 50.000 0.00 0.00 0.00 3.51
284 311 2.161609 CGTTTTGTCTTCCCCATGCTAC 59.838 50.000 0.00 0.00 0.00 3.58
286 313 1.247567 CGTTTTGTCTTCCCCATGCT 58.752 50.000 0.00 0.00 0.00 3.79
317 349 2.214181 CTTCGTCGACTGTGGAGGGG 62.214 65.000 14.70 0.00 0.00 4.79
334 366 7.612677 ACATACAAAAACCTAGTCGAGATCTT 58.387 34.615 0.00 0.00 0.00 2.40
401 434 4.582656 TCGGACCAAAGTCATGTCATTTTT 59.417 37.500 0.00 0.00 45.48 1.94
444 477 6.756074 TCAAAGTGGACAAATTTCATGTGAAC 59.244 34.615 0.00 0.00 33.13 3.18
447 480 7.718272 AATCAAAGTGGACAAATTTCATGTG 57.282 32.000 0.00 0.00 0.00 3.21
448 481 9.829507 TTTAATCAAAGTGGACAAATTTCATGT 57.170 25.926 0.00 0.00 0.00 3.21
483 516 5.049060 CCATCAAACGGTTAGACACATTTCA 60.049 40.000 0.00 0.00 0.00 2.69
484 517 5.180492 TCCATCAAACGGTTAGACACATTTC 59.820 40.000 0.00 0.00 0.00 2.17
487 520 4.280436 TCCATCAAACGGTTAGACACAT 57.720 40.909 0.00 0.00 0.00 3.21
488 521 3.755112 TCCATCAAACGGTTAGACACA 57.245 42.857 0.00 0.00 0.00 3.72
489 522 5.416947 ACTATCCATCAAACGGTTAGACAC 58.583 41.667 0.00 0.00 32.40 3.67
490 523 5.670792 ACTATCCATCAAACGGTTAGACA 57.329 39.130 0.00 0.00 32.40 3.41
491 524 6.980051 AAACTATCCATCAAACGGTTAGAC 57.020 37.500 0.00 0.00 32.40 2.59
492 525 6.373216 CCAAAACTATCCATCAAACGGTTAGA 59.627 38.462 0.00 0.00 32.40 2.10
493 526 6.373216 TCCAAAACTATCCATCAAACGGTTAG 59.627 38.462 0.00 0.00 33.68 2.34
494 527 6.239396 TCCAAAACTATCCATCAAACGGTTA 58.761 36.000 0.00 0.00 0.00 2.85
496 529 4.658063 TCCAAAACTATCCATCAAACGGT 58.342 39.130 0.00 0.00 0.00 4.83
497 530 5.356751 TCATCCAAAACTATCCATCAAACGG 59.643 40.000 0.00 0.00 0.00 4.44
498 531 6.258160 GTCATCCAAAACTATCCATCAAACG 58.742 40.000 0.00 0.00 0.00 3.60
512 545 1.001393 GGGAGCCGGTCATCCAAAA 60.001 57.895 19.84 0.00 37.33 2.44
537 570 2.521126 TGTAGATGAGTCCGTGGACAA 58.479 47.619 20.51 9.10 46.76 3.18
545 578 8.136165 ACATACTATTCGTTTGTAGATGAGTCC 58.864 37.037 0.00 0.00 36.27 3.85
551 584 5.919141 GCGGACATACTATTCGTTTGTAGAT 59.081 40.000 0.00 0.00 37.82 1.98
557 590 5.163794 CCAAAAGCGGACATACTATTCGTTT 60.164 40.000 0.00 0.00 0.00 3.60
558 591 4.331717 CCAAAAGCGGACATACTATTCGTT 59.668 41.667 0.00 0.00 0.00 3.85
575 608 2.036346 CTCCAAAGCTGTTCCCCAAAAG 59.964 50.000 0.00 0.00 0.00 2.27
580 613 1.467920 CATCTCCAAAGCTGTTCCCC 58.532 55.000 0.00 0.00 0.00 4.81
584 617 0.407139 AGGGCATCTCCAAAGCTGTT 59.593 50.000 0.00 0.00 36.21 3.16
588 621 0.255890 TGGTAGGGCATCTCCAAAGC 59.744 55.000 0.00 0.00 36.21 3.51
637 670 1.105759 GCCCCTCATGTCAATGGCTC 61.106 60.000 0.00 0.00 34.30 4.70
640 673 2.107031 TCTATGCCCCTCATGTCAATGG 59.893 50.000 0.00 0.00 36.63 3.16
644 677 3.497103 CAATCTATGCCCCTCATGTCA 57.503 47.619 0.00 0.00 36.63 3.58
694 727 1.708341 AGCCTCATGTTTGGTTTGCT 58.292 45.000 0.00 0.00 0.00 3.91
844 2109 1.675801 CTGAAGAGCAGGCTGTGGA 59.324 57.895 17.16 0.00 41.07 4.02
893 2158 8.697507 AAGACAACCAGAATACTCAAATTTCT 57.302 30.769 0.00 0.00 0.00 2.52
1131 2396 2.436824 GTGGGGCTTTCGAGGAGC 60.437 66.667 12.85 12.85 39.41 4.70
1491 3161 4.831307 CCTCGCCGTCGTTCTCCG 62.831 72.222 0.00 0.00 36.96 4.63
1585 3255 1.302511 GCTACCACCACCACCACAG 60.303 63.158 0.00 0.00 0.00 3.66
1795 3483 7.042051 CGAAACTAGAAGAACAAAGATGACCAA 60.042 37.037 0.00 0.00 0.00 3.67
1800 3488 5.122396 CCCCGAAACTAGAAGAACAAAGATG 59.878 44.000 0.00 0.00 0.00 2.90
1820 3508 0.322997 TAAACACAATCCCAGCCCCG 60.323 55.000 0.00 0.00 0.00 5.73
1965 3659 7.491372 CAGCTGAGCATTGTAAATCAAATTGAT 59.509 33.333 8.42 2.07 39.09 2.57
1978 3672 3.806625 AACAAAACAGCTGAGCATTGT 57.193 38.095 23.35 20.10 0.00 2.71
2008 3702 9.871238 GTCCAAGACAATACTATCTAACAAAGA 57.129 33.333 0.00 0.00 33.73 2.52
2009 3703 9.877178 AGTCCAAGACAATACTATCTAACAAAG 57.123 33.333 0.00 0.00 34.60 2.77
2011 3705 9.871238 GAAGTCCAAGACAATACTATCTAACAA 57.129 33.333 0.00 0.00 34.60 2.83
2012 3706 9.256228 AGAAGTCCAAGACAATACTATCTAACA 57.744 33.333 0.00 0.00 34.60 2.41
2013 3707 9.522804 CAGAAGTCCAAGACAATACTATCTAAC 57.477 37.037 0.00 0.00 34.60 2.34
2014 3708 8.198109 GCAGAAGTCCAAGACAATACTATCTAA 58.802 37.037 0.00 0.00 34.60 2.10
2015 3709 7.342026 TGCAGAAGTCCAAGACAATACTATCTA 59.658 37.037 0.00 0.00 34.60 1.98
2016 3710 6.155221 TGCAGAAGTCCAAGACAATACTATCT 59.845 38.462 0.00 0.00 34.60 1.98
2017 3711 6.256757 GTGCAGAAGTCCAAGACAATACTATC 59.743 42.308 0.00 0.00 34.60 2.08
2018 3712 6.109359 GTGCAGAAGTCCAAGACAATACTAT 58.891 40.000 0.00 0.00 34.60 2.12
2019 3713 5.479306 GTGCAGAAGTCCAAGACAATACTA 58.521 41.667 0.00 0.00 34.60 1.82
2020 3714 4.319177 GTGCAGAAGTCCAAGACAATACT 58.681 43.478 0.00 0.00 34.60 2.12
2021 3715 3.437049 GGTGCAGAAGTCCAAGACAATAC 59.563 47.826 0.00 0.00 34.60 1.89
2026 3723 0.108585 TGGGTGCAGAAGTCCAAGAC 59.891 55.000 0.00 0.00 0.00 3.01
2093 3794 3.561503 GCCGGGAAACAATATTAATCGC 58.438 45.455 2.18 0.00 0.00 4.58
2115 3816 7.584123 CAGCTCGAAATATTGGAAGAAATTACG 59.416 37.037 0.00 0.00 0.00 3.18
2130 3831 6.183360 ACAAAACCAAAGTTCAGCTCGAAATA 60.183 34.615 0.96 0.00 34.19 1.40
2252 4015 1.201647 CTTTCCTGTGCAATCAGCCTG 59.798 52.381 0.00 0.00 44.83 4.85
2399 4168 6.683974 TGGTATTTACTACTCCGTAGTGTC 57.316 41.667 14.99 3.46 46.99 3.67
2579 4349 2.301296 CCATGGTCAGACACTTCACTCT 59.699 50.000 2.57 0.00 0.00 3.24
2655 4425 3.511699 CATGTCACGTGCACTGTAGTAT 58.488 45.455 16.19 6.65 0.00 2.12
2662 4432 1.301716 GGACCATGTCACGTGCACT 60.302 57.895 16.19 0.00 33.68 4.40
2694 4464 5.893897 AAGACTGGTAAGGAAGTACTACG 57.106 43.478 0.00 0.00 0.00 3.51
2875 4645 2.004583 AACATCGTCACCATACCGTG 57.995 50.000 0.00 0.00 34.93 4.94
2878 4648 4.759516 ACAAAAACATCGTCACCATACC 57.240 40.909 0.00 0.00 0.00 2.73
2883 4653 4.035208 ACTCAGAACAAAAACATCGTCACC 59.965 41.667 0.00 0.00 0.00 4.02
2884 4654 5.156804 ACTCAGAACAAAAACATCGTCAC 57.843 39.130 0.00 0.00 0.00 3.67
2936 4713 9.825972 ACTAATTCTATGAACAAAAACATCGTG 57.174 29.630 0.00 0.00 0.00 4.35
2944 4721 9.778741 ACAGTCAGACTAATTCTATGAACAAAA 57.221 29.630 1.67 0.00 31.12 2.44
2947 4724 9.020731 TGTACAGTCAGACTAATTCTATGAACA 57.979 33.333 1.67 0.00 31.12 3.18
2948 4725 9.509855 CTGTACAGTCAGACTAATTCTATGAAC 57.490 37.037 15.06 0.00 37.61 3.18
2949 4726 9.244292 ACTGTACAGTCAGACTAATTCTATGAA 57.756 33.333 22.95 0.00 36.92 2.57
2950 4727 8.809468 ACTGTACAGTCAGACTAATTCTATGA 57.191 34.615 22.95 0.00 36.92 2.15
2951 4728 9.295214 CAACTGTACAGTCAGACTAATTCTATG 57.705 37.037 28.04 13.54 41.58 2.23
2952 4729 9.026121 ACAACTGTACAGTCAGACTAATTCTAT 57.974 33.333 28.04 5.15 41.58 1.98
2998 4803 4.614555 TTATCGAATGTGCAAAGCGAAT 57.385 36.364 8.47 1.93 34.46 3.34
3034 4839 6.495872 ACCTACTTACAACACCTCTATGTTCA 59.504 38.462 0.00 0.00 40.89 3.18
3076 4883 6.248569 ACCAGAAAACTCTCTTTGGTTAGA 57.751 37.500 0.00 0.00 0.00 2.10
3133 4940 8.579850 TCAATTTTATTATCCTGTTGTCTGCT 57.420 30.769 0.00 0.00 0.00 4.24
3219 5031 3.281727 ACTGGAAGCAAACAGTCTCAA 57.718 42.857 1.91 0.00 44.08 3.02
3557 5371 5.066505 AGACACAACAAGACTGAATGGAAAC 59.933 40.000 0.00 0.00 0.00 2.78
3717 7330 3.003378 AGAGCGTAAAAAGTCAGCCAAAC 59.997 43.478 0.00 0.00 0.00 2.93
3750 7363 9.063615 CAACTATGATTCTTCCATCATCATTGA 57.936 33.333 8.99 0.00 42.01 2.57
4197 9351 6.933426 CACAAAAATAACGTGCAAACATTG 57.067 33.333 0.00 0.00 0.00 2.82
4481 11436 1.837439 ACACTTGTGTCTCCTGAACCA 59.163 47.619 0.00 0.00 0.00 3.67
4496 11451 1.226262 AAGTGCCCCGTTGACACTT 59.774 52.632 1.94 1.94 46.86 3.16
4661 11616 1.897225 CTCCAGCCACAGAGGAGGTG 61.897 65.000 0.00 0.00 44.10 4.00
4667 11625 1.761198 TCATCATCTCCAGCCACAGAG 59.239 52.381 0.00 0.00 0.00 3.35
4802 11760 2.168521 ACACAGCAGCTTACCGATACAT 59.831 45.455 0.00 0.00 0.00 2.29
4846 11804 7.446931 TGTTCATCATTTAACAACTAGAGCCAA 59.553 33.333 0.00 0.00 32.86 4.52
4946 11909 1.668793 CTGCCTGATGACGTGTGCA 60.669 57.895 0.00 0.00 0.00 4.57
4953 11916 0.329596 AGAAACCCCTGCCTGATGAC 59.670 55.000 0.00 0.00 0.00 3.06
4992 11955 0.035056 GTGTCTTGATCCACTGGGGG 60.035 60.000 0.00 0.00 37.22 5.40
5049 12012 5.062183 GGTTCTGAAAAACTGAAGCAACAAC 59.938 40.000 0.00 0.00 46.51 3.32
5085 12048 7.660112 AGCAACAACATCTAACATTTCAATGA 58.340 30.769 6.53 0.00 39.67 2.57
5135 12103 2.935201 ACGCAAACCTACGTGTAAAACA 59.065 40.909 0.00 0.00 41.76 2.83
5136 12104 3.590720 ACGCAAACCTACGTGTAAAAC 57.409 42.857 0.00 0.00 41.76 2.43
5137 12105 6.589523 ACATATACGCAAACCTACGTGTAAAA 59.410 34.615 0.00 0.00 43.44 1.52
5138 12106 6.034790 CACATATACGCAAACCTACGTGTAAA 59.965 38.462 0.00 0.00 43.44 2.01
5139 12107 5.515982 CACATATACGCAAACCTACGTGTAA 59.484 40.000 0.00 0.00 43.44 2.41
5140 12108 5.036090 CACATATACGCAAACCTACGTGTA 58.964 41.667 0.00 0.00 43.44 2.90
5141 12109 3.861113 CACATATACGCAAACCTACGTGT 59.139 43.478 0.00 0.00 43.44 4.49
5160 12128 3.560481 CAGCCAAACAAAAATGCATCACA 59.440 39.130 0.00 0.00 0.00 3.58
5305 12428 2.741092 GTGTGGTGCTCCTCGGAA 59.259 61.111 6.34 0.00 34.23 4.30
5335 12458 7.925483 CACCTTATCATGTTTTCCTTTTGTTGA 59.075 33.333 0.00 0.00 0.00 3.18
5336 12459 7.307337 GCACCTTATCATGTTTTCCTTTTGTTG 60.307 37.037 0.00 0.00 0.00 3.33
5337 12460 6.705825 GCACCTTATCATGTTTTCCTTTTGTT 59.294 34.615 0.00 0.00 0.00 2.83
5338 12461 6.041979 AGCACCTTATCATGTTTTCCTTTTGT 59.958 34.615 0.00 0.00 0.00 2.83
5339 12462 6.366877 CAGCACCTTATCATGTTTTCCTTTTG 59.633 38.462 0.00 0.00 0.00 2.44
5341 12464 5.047092 CCAGCACCTTATCATGTTTTCCTTT 60.047 40.000 0.00 0.00 0.00 3.11
5344 12473 3.429410 GCCAGCACCTTATCATGTTTTCC 60.429 47.826 0.00 0.00 0.00 3.13
5346 12475 2.497273 GGCCAGCACCTTATCATGTTTT 59.503 45.455 0.00 0.00 0.00 2.43
5425 12556 2.908688 AAAAACATGGCCCAAGTGAC 57.091 45.000 0.00 0.00 0.00 3.67
5494 12625 8.450578 ACAAATCTGAGTATTTCAACAACTCA 57.549 30.769 4.51 4.51 45.48 3.41
5557 12689 6.551736 CACACCTGCCATACAAATAACTTAC 58.448 40.000 0.00 0.00 0.00 2.34
5558 12690 5.124776 GCACACCTGCCATACAAATAACTTA 59.875 40.000 0.00 0.00 37.45 2.24
5727 12973 4.942761 ATGTGGCAAAGAAATGACAACT 57.057 36.364 0.00 0.00 40.79 3.16
5821 13067 3.884693 TGCTCTCAAAGTGCAATTTCTCA 59.115 39.130 9.56 1.00 41.15 3.27
5895 13141 1.876156 GGAGCAGAACAACACTTCCAG 59.124 52.381 0.00 0.00 0.00 3.86
5996 13247 7.856145 TTTTCAACATAAACTTTGCATGGTT 57.144 28.000 0.00 0.00 0.00 3.67
6049 13301 6.470557 AAGCATTTTGGAACATCGATTTTG 57.529 33.333 0.60 0.00 39.30 2.44
6052 13304 7.156876 TCTAAAGCATTTTGGAACATCGATT 57.843 32.000 0.00 0.00 40.09 3.34
6053 13305 6.757897 TCTAAAGCATTTTGGAACATCGAT 57.242 33.333 0.00 0.00 40.09 3.59
6054 13306 6.567687 TTCTAAAGCATTTTGGAACATCGA 57.432 33.333 0.00 0.00 38.40 3.59


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

AutoCloner maintained by Alex Coulton.