Multiple sequence alignment - TraesCS4D01G092700

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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 TraesCS4D01G092700 chr4D 100.000 7225 0 0 1 7225 67468081 67460857 0.000000e+00 13343.0
1 TraesCS4D01G092700 chr4A 94.763 3647 139 17 471 4092 516937500 516933881 0.000000e+00 5629.0
2 TraesCS4D01G092700 chr4A 89.517 2318 145 34 4955 7225 516933035 516930769 0.000000e+00 2844.0
3 TraesCS4D01G092700 chr4A 95.936 812 26 5 4091 4901 516933828 516933023 0.000000e+00 1310.0
4 TraesCS4D01G092700 chr4A 88.011 367 43 1 1 366 242879586 242879952 4.000000e-117 433.0
5 TraesCS4D01G092700 chr4A 87.978 366 44 0 1 366 516938567 516938202 4.000000e-117 433.0
6 TraesCS4D01G092700 chr4A 91.429 70 5 1 4888 4957 657204667 657204735 2.150000e-15 95.3
7 TraesCS4D01G092700 chr4B 92.360 2225 105 19 4955 7136 99966071 99963869 0.000000e+00 3107.0
8 TraesCS4D01G092700 chr4B 95.167 1883 66 13 1755 3617 99968749 99966872 0.000000e+00 2950.0
9 TraesCS4D01G092700 chr4B 96.760 1173 37 1 484 1655 99969915 99968743 0.000000e+00 1954.0
10 TraesCS4D01G092700 chr4B 96.129 465 15 3 4438 4901 99966521 99966059 0.000000e+00 756.0
11 TraesCS4D01G092700 chr4B 89.532 363 38 0 1 363 51123632 51123994 1.840000e-125 460.0
12 TraesCS4D01G092700 chr4B 93.289 149 6 2 3574 3722 99966869 99966725 4.390000e-52 217.0
13 TraesCS4D01G092700 chr4B 93.798 129 8 0 3718 3846 99966647 99966519 2.060000e-45 195.0
14 TraesCS4D01G092700 chr4B 97.196 107 3 0 1654 1760 414860746 414860852 1.600000e-41 182.0
15 TraesCS4D01G092700 chr4B 95.238 63 3 0 4895 4957 444048919 444048981 4.610000e-17 100.0
16 TraesCS4D01G092700 chr4B 92.647 68 3 1 3516 3581 209181544 209181477 5.970000e-16 97.1
17 TraesCS4D01G092700 chr3A 90.137 365 35 1 1 364 448712251 448711887 2.360000e-129 473.0
18 TraesCS4D01G092700 chr3A 97.196 107 3 0 1654 1760 477332042 477332148 1.600000e-41 182.0
19 TraesCS4D01G092700 chr3A 93.846 65 3 1 4893 4957 724319117 724319054 5.970000e-16 97.1
20 TraesCS4D01G092700 chr5D 89.286 364 39 0 1 364 312600808 312601171 2.380000e-124 457.0
21 TraesCS4D01G092700 chr2B 88.798 366 41 0 1 366 545174416 545174051 3.980000e-122 449.0
22 TraesCS4D01G092700 chr2B 88.187 364 42 1 1 364 55926476 55926114 4.000000e-117 433.0
23 TraesCS4D01G092700 chr2B 88.732 71 8 0 6140 6210 233270139 233270069 3.590000e-13 87.9
24 TraesCS4D01G092700 chr7D 87.978 366 44 0 1 366 88727285 88727650 4.000000e-117 433.0
25 TraesCS4D01G092700 chr7D 87.978 366 44 0 3 368 156785726 156786091 4.000000e-117 433.0
26 TraesCS4D01G092700 chr7D 93.043 115 6 2 1650 1763 392643225 392643338 4.480000e-37 167.0
27 TraesCS4D01G092700 chr7D 98.246 57 1 0 4902 4958 383900666 383900722 4.610000e-17 100.0
28 TraesCS4D01G092700 chr7D 92.647 68 3 1 3516 3581 44748070 44748003 5.970000e-16 97.1
29 TraesCS4D01G092700 chr6B 95.726 117 4 1 1653 1769 640973234 640973349 3.440000e-43 187.0
30 TraesCS4D01G092700 chr7B 96.330 109 4 0 1652 1760 683101575 683101467 5.760000e-41 180.0
31 TraesCS4D01G092700 chr7B 93.750 64 4 0 4894 4957 536117583 536117646 5.970000e-16 97.1
32 TraesCS4D01G092700 chr3D 95.413 109 5 0 1652 1760 536331030 536331138 2.680000e-39 174.0
33 TraesCS4D01G092700 chr3D 92.241 116 9 0 1651 1766 239351900 239352015 1.610000e-36 165.0
34 TraesCS4D01G092700 chr6A 92.373 118 5 2 1653 1769 570376963 570377077 1.610000e-36 165.0
35 TraesCS4D01G092700 chr3B 98.276 58 1 0 4900 4957 354006610 354006553 1.280000e-17 102.0
36 TraesCS4D01G092700 chr5A 98.246 57 1 0 4901 4957 463712164 463712220 4.610000e-17 100.0
37 TraesCS4D01G092700 chr5A 96.491 57 2 0 4901 4957 316516500 316516444 2.150000e-15 95.3
38 TraesCS4D01G092700 chrUn 91.549 71 4 1 3513 3581 45085042 45085112 5.970000e-16 97.1
39 TraesCS4D01G092700 chrUn 92.647 68 3 1 3516 3581 182460806 182460739 5.970000e-16 97.1
40 TraesCS4D01G092700 chrUn 91.549 71 4 1 3513 3581 231545689 231545759 5.970000e-16 97.1
41 TraesCS4D01G092700 chr6D 92.647 68 3 1 3516 3581 108505704 108505637 5.970000e-16 97.1
42 TraesCS4D01G092700 chr1A 91.549 71 4 1 3513 3581 355991563 355991633 5.970000e-16 97.1
43 TraesCS4D01G092700 chr2D 90.141 71 6 1 4886 4956 327962209 327962278 2.780000e-14 91.6
44 TraesCS4D01G092700 chr2D 91.667 60 5 0 6145 6204 176165468 176165409 4.640000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G092700 chr4D 67460857 67468081 7224 True 13343.000000 13343 100.000000 1 7225 1 chr4D.!!$R1 7224
1 TraesCS4D01G092700 chr4A 516930769 516938567 7798 True 2554.000000 5629 92.048500 1 7225 4 chr4A.!!$R1 7224
2 TraesCS4D01G092700 chr4B 99963869 99969915 6046 True 1529.833333 3107 94.583833 484 7136 6 chr4B.!!$R2 6652

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
429 534 0.378610 GCGGTGCTATTCAAAGCCTC 59.621 55.0 0.00 0.00 42.05 4.70 F
464 1028 0.470341 GGAGATGCTCTAACCCACCC 59.530 60.0 0.00 0.00 0.00 4.61 F
1077 1677 0.751643 AGAAGCCGGCCGCAATATTT 60.752 50.0 26.15 8.13 41.38 1.40 F
2025 2637 0.316204 ATGCTGTGCTTGTTGCCTTC 59.684 50.0 0.00 0.00 42.00 3.46 F
2756 3376 1.002366 CCGCTACACTGATGTCTTGC 58.998 55.0 0.00 0.00 40.48 4.01 F
4072 4834 0.902531 TCCTGGAGAATTGACCGTCC 59.097 55.0 0.00 0.00 0.00 4.79 F
4086 4848 0.107848 CCGTCCGCTCCAATAAACCT 60.108 55.0 0.00 0.00 0.00 3.50 F
4250 5067 0.613012 GTGCCTGCCCCTCAGATTTT 60.613 55.0 0.00 0.00 45.72 1.82 F
5460 6302 0.837691 TCCACATCCAGCACTCCACT 60.838 55.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 2449 0.390860 CCTGGTGGCCTAGAAGATCG 59.609 60.000 3.32 0.00 0.00 3.69 R
1850 2454 1.354368 CCTTTTCCTGGTGGCCTAGAA 59.646 52.381 3.32 0.00 0.00 2.10 R
2440 3060 3.306780 CCACGAGGTTAGAACTGAATGGT 60.307 47.826 0.00 0.00 0.00 3.55 R
3546 4170 1.001641 AGCACCAATCAGGCAGGAC 60.002 57.895 0.00 0.00 43.14 3.85 R
4086 4848 0.396139 AATACTCCCTACGACGGCCA 60.396 55.000 2.24 0.00 0.00 5.36 R
4895 5713 0.526211 CGGGCTGCCCTTTTTACTTC 59.474 55.000 33.39 5.18 42.67 3.01 R
4942 5760 0.693092 CTAATGGACCCTTCCCCGGA 60.693 60.000 0.73 0.00 42.01 5.14 R
5873 6720 1.269309 ACTCTACCGCAATCATCTCGC 60.269 52.381 0.00 0.00 0.00 5.03 R
6853 7721 0.519077 GGCCTTGAGTTTCAGAAGCG 59.481 55.000 0.00 0.00 0.00 4.68 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
56 57 5.474189 TCTTGCACAACATGATCATTGAGAA 59.526 36.000 14.50 0.29 0.00 2.87
61 62 5.121298 CACAACATGATCATTGAGAACGAGT 59.879 40.000 14.50 0.57 0.00 4.18
62 63 6.311200 CACAACATGATCATTGAGAACGAGTA 59.689 38.462 14.50 0.00 0.00 2.59
63 64 6.533012 ACAACATGATCATTGAGAACGAGTAG 59.467 38.462 14.50 0.00 0.00 2.57
70 71 5.254115 TCATTGAGAACGAGTAGGAAGAGA 58.746 41.667 0.00 0.00 0.00 3.10
81 82 4.337145 AGTAGGAAGAGACAGTGTTCGAT 58.663 43.478 0.00 0.00 28.71 3.59
83 84 6.123651 AGTAGGAAGAGACAGTGTTCGATAT 58.876 40.000 0.00 0.00 28.71 1.63
104 105 3.576078 TGAACCATATTACAGGCAGGG 57.424 47.619 0.00 0.00 0.00 4.45
107 108 2.487775 ACCATATTACAGGCAGGGTCA 58.512 47.619 0.00 0.00 0.00 4.02
109 110 3.073062 ACCATATTACAGGCAGGGTCATC 59.927 47.826 0.00 0.00 0.00 2.92
129 130 3.237746 TCTTGCCCAAATTGATCACCAA 58.762 40.909 0.00 0.00 39.41 3.67
136 137 3.128589 CCAAATTGATCACCAACTACCGG 59.871 47.826 0.00 0.00 37.63 5.28
156 157 1.410004 CATCATGGGCTGCATTCCTT 58.590 50.000 0.50 0.00 0.00 3.36
182 183 0.464735 CGTCAGGAGATCCGAGACCT 60.465 60.000 16.67 0.00 40.44 3.85
186 187 2.158740 TCAGGAGATCCGAGACCTACAG 60.159 54.545 0.00 0.00 42.08 2.74
200 201 3.340814 CCTACAGGTGCATCAAGAACT 57.659 47.619 0.00 0.00 0.00 3.01
209 210 2.885894 TGCATCAAGAACTGCAACATGA 59.114 40.909 0.00 0.00 44.87 3.07
228 229 2.636403 TGATCTGGTGGAGCATCTATGG 59.364 50.000 0.00 0.00 35.23 2.74
229 230 2.477104 TCTGGTGGAGCATCTATGGA 57.523 50.000 0.00 0.00 33.73 3.41
239 240 1.696336 GCATCTATGGAGGCTCAAGGA 59.304 52.381 17.69 8.25 44.64 3.36
243 244 3.387962 TCTATGGAGGCTCAAGGACAAT 58.612 45.455 17.69 0.80 0.00 2.71
255 256 3.197766 TCAAGGACAATGCCTAGTTCGAT 59.802 43.478 0.00 0.00 37.26 3.59
256 257 3.185246 AGGACAATGCCTAGTTCGATG 57.815 47.619 0.00 0.00 36.22 3.84
265 266 3.119291 GCCTAGTTCGATGTGTGATGAG 58.881 50.000 0.00 0.00 0.00 2.90
272 273 4.234530 TCGATGTGTGATGAGCTATGAG 57.765 45.455 0.00 0.00 0.00 2.90
281 282 8.668353 TGTGTGATGAGCTATGAGTTTTAATTC 58.332 33.333 0.00 0.00 0.00 2.17
282 283 8.668353 GTGTGATGAGCTATGAGTTTTAATTCA 58.332 33.333 0.00 0.00 0.00 2.57
306 307 5.201910 TGTTTGAATTACGAGTTTGCTTCG 58.798 37.500 0.00 0.00 0.00 3.79
312 313 5.607119 ATTACGAGTTTGCTTCGTTGAAT 57.393 34.783 5.58 0.00 40.70 2.57
318 319 7.577979 ACGAGTTTGCTTCGTTGAATTATTTA 58.422 30.769 0.00 0.00 36.67 1.40
319 320 8.071368 ACGAGTTTGCTTCGTTGAATTATTTAA 58.929 29.630 0.00 0.00 36.67 1.52
344 345 8.900511 ATTTGTATTGATTTCTGTGATGAACG 57.099 30.769 0.00 0.00 0.00 3.95
345 346 7.665561 TTGTATTGATTTCTGTGATGAACGA 57.334 32.000 0.00 0.00 0.00 3.85
402 507 1.447314 GAGTCTTACCGCCGGTTGG 60.447 63.158 16.82 8.06 37.09 3.77
403 508 2.435410 GTCTTACCGCCGGTTGGG 60.435 66.667 16.82 12.37 37.09 4.12
421 526 3.800440 GCGTTAAGCGGTGCTATTC 57.200 52.632 0.00 0.00 38.25 1.75
422 527 1.003851 GCGTTAAGCGGTGCTATTCA 58.996 50.000 0.00 0.00 38.25 2.57
429 534 0.378610 GCGGTGCTATTCAAAGCCTC 59.621 55.000 0.00 0.00 42.05 4.70
430 535 2.014068 GCGGTGCTATTCAAAGCCTCT 61.014 52.381 0.00 0.00 42.05 3.69
431 536 1.936547 CGGTGCTATTCAAAGCCTCTC 59.063 52.381 0.00 0.00 42.05 3.20
434 539 1.134401 TGCTATTCAAAGCCTCTCGGG 60.134 52.381 0.00 0.00 42.05 5.14
457 1021 2.159043 CGAAAGGCTGGAGATGCTCTAA 60.159 50.000 0.00 0.00 0.00 2.10
464 1028 0.470341 GGAGATGCTCTAACCCACCC 59.530 60.000 0.00 0.00 0.00 4.61
561 1160 2.436417 CCATCTTCTTCCCTGCGAAAA 58.564 47.619 0.00 0.00 0.00 2.29
611 1210 3.727258 CGCCATTCCCACCCTCCA 61.727 66.667 0.00 0.00 0.00 3.86
1052 1652 1.334149 GCTCAAGGTGCTCGACAAAAC 60.334 52.381 0.00 0.00 0.00 2.43
1077 1677 0.751643 AGAAGCCGGCCGCAATATTT 60.752 50.000 26.15 8.13 41.38 1.40
1194 1794 5.640218 TTTTCTTTGCTTTGCGAAATCAG 57.360 34.783 0.00 0.00 31.00 2.90
1253 1853 8.994429 TTTTTGCAAAAATAAGAAGAGTGACA 57.006 26.923 28.85 5.59 33.29 3.58
1258 1858 8.514594 TGCAAAAATAAGAAGAGTGACATTAGG 58.485 33.333 0.00 0.00 0.00 2.69
1311 1911 4.226846 AGTGAGTTGTGAATGATGGAGGAT 59.773 41.667 0.00 0.00 0.00 3.24
1345 1945 1.737199 AGTGGTTACCCTTAGTGCCA 58.263 50.000 0.00 0.00 33.97 4.92
1385 1985 1.466167 CTTCCAAGTGAAGCGTCATGG 59.534 52.381 14.10 14.10 43.79 3.66
1483 2083 8.462016 GCTACATTTTAACATGTGGATTCTCTT 58.538 33.333 18.92 0.00 37.74 2.85
1691 2291 8.428186 TGTTTTTATAAGACGTTTCAGACAGT 57.572 30.769 0.00 0.00 0.00 3.55
1701 2301 4.393680 ACGTTTCAGACAGTTTGCTTTGTA 59.606 37.500 0.00 0.00 0.00 2.41
1734 2334 4.750098 ACAGTGTCTGAATGTCTAAAACGG 59.250 41.667 3.70 0.00 35.18 4.44
1845 2449 8.816640 TTTGAGGAAAATAGCTCACATTTTTC 57.183 30.769 7.03 5.50 36.09 2.29
1847 2451 6.429692 TGAGGAAAATAGCTCACATTTTTCGA 59.570 34.615 7.03 0.00 38.40 3.71
1850 2454 7.337942 AGGAAAATAGCTCACATTTTTCGATCT 59.662 33.333 7.03 1.22 38.40 2.75
1904 2516 7.040686 GCTGGAGTTGGTGTTCTTTCTAATTTA 60.041 37.037 0.00 0.00 0.00 1.40
1987 2599 4.134563 TGTGAAACTTTAAGCTCCCTGAC 58.865 43.478 0.00 0.00 38.04 3.51
1991 2603 5.046878 TGAAACTTTAAGCTCCCTGACGATA 60.047 40.000 0.00 0.00 0.00 2.92
2016 2628 3.678289 TGTCATCTGTAATGCTGTGCTT 58.322 40.909 0.00 0.00 0.00 3.91
2025 2637 0.316204 ATGCTGTGCTTGTTGCCTTC 59.684 50.000 0.00 0.00 42.00 3.46
2036 2648 5.359576 TGCTTGTTGCCTTCGGATATTTTAT 59.640 36.000 0.00 0.00 42.00 1.40
2068 2681 3.287867 AGCTACCTGATGATGTTTGGG 57.712 47.619 0.00 0.00 0.00 4.12
2132 2745 7.556275 TCACATCCAAGTTATCCATTTTCTACC 59.444 37.037 0.00 0.00 0.00 3.18
2180 2793 3.244044 GCTCACTCTCTGTTTCCAAGTCT 60.244 47.826 0.00 0.00 0.00 3.24
2440 3060 7.068686 TGGGTATGGAAATTGTATCACGATA 57.931 36.000 0.00 0.00 0.00 2.92
2756 3376 1.002366 CCGCTACACTGATGTCTTGC 58.998 55.000 0.00 0.00 40.48 4.01
2961 3582 5.695851 AAGAAATAGCATATTTCCTGCCG 57.304 39.130 15.31 0.00 40.56 5.69
2990 3611 6.375455 TCTTTCTTTCTGATCCTAATTGGCAC 59.625 38.462 0.00 0.00 35.26 5.01
3062 3683 2.366533 TCTACTCAAGGTCCGCTAGTG 58.633 52.381 0.00 0.00 0.00 2.74
3077 3698 4.441415 CCGCTAGTGAATACATTCGAAGAC 59.559 45.833 4.44 0.00 39.62 3.01
3198 3819 5.389859 TGTTTCATTGAGTTGGCCTAATG 57.610 39.130 3.32 7.51 33.09 1.90
3305 3928 5.001237 TCGTTAAATCCTATCAACAGCGA 57.999 39.130 0.00 0.00 0.00 4.93
3371 3994 9.250624 AGCGTCACTAGAATCTATTTATTGAAC 57.749 33.333 0.00 0.00 0.00 3.18
3419 4042 3.971240 GCTTGCTTCTCTTCGTGAAAAAG 59.029 43.478 0.00 0.00 0.00 2.27
3494 4118 6.399639 AAGACTAGATTCTCTTTCGGATCC 57.600 41.667 0.00 0.00 0.00 3.36
3546 4170 7.024340 TCCAGTATTCTTAGCTTACTGTACG 57.976 40.000 17.23 6.42 40.66 3.67
3631 4301 3.055819 GCTGGATAGGACTGTGTTCTTCA 60.056 47.826 0.00 0.00 0.00 3.02
3831 4583 1.222387 CGTCCGGGATTAAAGGGCA 59.778 57.895 0.00 0.00 0.00 5.36
3846 4598 1.452108 GGCAGGCAGACCACCATAC 60.452 63.158 0.00 0.00 39.06 2.39
3850 4602 2.267642 GCAGACCACCATACGCCA 59.732 61.111 0.00 0.00 0.00 5.69
3851 4603 1.153168 GCAGACCACCATACGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
3852 4604 1.160329 GCAGACCACCATACGCCATC 61.160 60.000 0.00 0.00 0.00 3.51
3881 4633 7.475137 TTTGTTAGGCCATTGCTTTTATAGT 57.525 32.000 5.01 0.00 37.74 2.12
3885 4637 2.695147 GGCCATTGCTTTTATAGTGCCT 59.305 45.455 0.00 0.00 37.74 4.75
3887 4639 4.383010 GGCCATTGCTTTTATAGTGCCTTT 60.383 41.667 0.00 0.00 37.74 3.11
3919 4671 1.592669 CTATTGCTGGTCCCGCGAG 60.593 63.158 8.23 0.00 0.00 5.03
3987 4749 3.591695 TGCTATTGATTGGGGTATGCA 57.408 42.857 0.00 0.00 0.00 3.96
3998 4760 1.699634 GGGGTATGCAAGCAGGAGATA 59.300 52.381 0.00 0.00 0.00 1.98
3999 4761 2.289945 GGGGTATGCAAGCAGGAGATAG 60.290 54.545 0.00 0.00 0.00 2.08
4000 4762 2.634940 GGGTATGCAAGCAGGAGATAGA 59.365 50.000 0.00 0.00 0.00 1.98
4001 4763 3.071602 GGGTATGCAAGCAGGAGATAGAA 59.928 47.826 0.00 0.00 0.00 2.10
4002 4764 4.061596 GGTATGCAAGCAGGAGATAGAAC 58.938 47.826 0.00 0.00 0.00 3.01
4003 4765 3.920231 ATGCAAGCAGGAGATAGAACA 57.080 42.857 0.00 0.00 0.00 3.18
4004 4766 2.977914 TGCAAGCAGGAGATAGAACAC 58.022 47.619 0.00 0.00 0.00 3.32
4005 4767 2.302733 TGCAAGCAGGAGATAGAACACA 59.697 45.455 0.00 0.00 0.00 3.72
4006 4768 3.054875 TGCAAGCAGGAGATAGAACACAT 60.055 43.478 0.00 0.00 0.00 3.21
4007 4769 3.311871 GCAAGCAGGAGATAGAACACATG 59.688 47.826 0.00 0.00 0.00 3.21
4008 4770 3.191078 AGCAGGAGATAGAACACATGC 57.809 47.619 0.00 0.00 38.11 4.06
4009 4771 2.502947 AGCAGGAGATAGAACACATGCA 59.497 45.455 0.00 0.00 39.64 3.96
4010 4772 2.871022 GCAGGAGATAGAACACATGCAG 59.129 50.000 0.00 0.00 37.86 4.41
4011 4773 3.464907 CAGGAGATAGAACACATGCAGG 58.535 50.000 0.00 0.00 0.00 4.85
4012 4774 3.133542 CAGGAGATAGAACACATGCAGGA 59.866 47.826 4.84 0.00 0.00 3.86
4013 4775 3.387374 AGGAGATAGAACACATGCAGGAG 59.613 47.826 4.84 0.00 0.00 3.69
4014 4776 3.386078 GGAGATAGAACACATGCAGGAGA 59.614 47.826 4.84 0.00 0.00 3.71
4015 4777 4.040217 GGAGATAGAACACATGCAGGAGAT 59.960 45.833 4.84 0.00 0.00 2.75
4029 4791 2.166459 CAGGAGATTGAAGGACTACGCA 59.834 50.000 0.00 0.00 0.00 5.24
4037 4799 6.535508 AGATTGAAGGACTACGCAATTAAGAC 59.464 38.462 0.00 0.00 31.96 3.01
4043 4805 4.409570 GACTACGCAATTAAGACGACTGA 58.590 43.478 0.00 0.00 0.00 3.41
4046 4808 3.650139 ACGCAATTAAGACGACTGAGTT 58.350 40.909 0.00 0.00 0.00 3.01
4055 4817 2.494073 AGACGACTGAGTTCCTTGATCC 59.506 50.000 0.00 0.00 0.00 3.36
4072 4834 0.902531 TCCTGGAGAATTGACCGTCC 59.097 55.000 0.00 0.00 0.00 4.79
4084 4846 1.004595 GACCGTCCGCTCCAATAAAC 58.995 55.000 0.00 0.00 0.00 2.01
4086 4848 0.107848 CCGTCCGCTCCAATAAACCT 60.108 55.000 0.00 0.00 0.00 3.50
4113 4929 5.166398 CGTCGTAGGGAGTATTTGAAACTT 58.834 41.667 0.00 0.00 0.00 2.66
4127 4943 5.728351 TTGAAACTTAATTCGATAGGGCG 57.272 39.130 0.00 0.00 31.80 6.13
4142 4958 0.822164 GGGCGACACTGTACCTACAT 59.178 55.000 0.00 0.00 35.36 2.29
4221 5038 7.785028 ACTGGGTTTCTTTCCTTTTCTTAGAAT 59.215 33.333 0.00 0.00 0.00 2.40
4250 5067 0.613012 GTGCCTGCCCCTCAGATTTT 60.613 55.000 0.00 0.00 45.72 1.82
4416 5233 2.936498 AGGCCGTGATTTAGACATTTCG 59.064 45.455 0.00 0.00 0.00 3.46
4431 5248 5.937540 AGACATTTCGGTTCATACATTGACA 59.062 36.000 0.00 0.00 32.84 3.58
4520 5338 9.692749 TCTTAATCTTGTAGACACAGTTTGTAG 57.307 33.333 0.00 0.00 39.17 2.74
4721 5539 6.549912 AACGAGGTAAAGATGTGTAAAACC 57.450 37.500 0.00 0.00 0.00 3.27
4794 5612 9.788960 GTGAAGGACTATTTGTTCCATATTTTC 57.211 33.333 0.00 0.00 0.00 2.29
4865 5683 4.848562 AAGTTTTAGTACCTTTGCAGGC 57.151 40.909 0.00 0.00 45.56 4.85
4869 5687 3.780804 TTAGTACCTTTGCAGGCTTCA 57.219 42.857 0.00 0.00 45.56 3.02
4909 5727 6.834168 CTTCCATTAGAAGTAAAAAGGGCA 57.166 37.500 0.00 0.00 45.99 5.36
4910 5728 6.834168 TTCCATTAGAAGTAAAAAGGGCAG 57.166 37.500 0.00 0.00 0.00 4.85
4911 5729 4.705023 TCCATTAGAAGTAAAAAGGGCAGC 59.295 41.667 0.00 0.00 0.00 5.25
4912 5730 4.142160 CCATTAGAAGTAAAAAGGGCAGCC 60.142 45.833 1.26 1.26 0.00 4.85
4913 5731 1.924731 AGAAGTAAAAAGGGCAGCCC 58.075 50.000 24.90 24.90 45.90 5.19
4923 5741 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
4924 5742 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
4925 5743 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
4926 5744 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
4927 5745 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
4952 5770 4.778143 CGCAAGGTCCGGGGAAGG 62.778 72.222 0.00 0.00 0.00 3.46
4953 5771 4.426313 GCAAGGTCCGGGGAAGGG 62.426 72.222 0.00 0.00 0.00 3.95
5001 5819 3.091545 CACATGTGATGTAAAGGCCCTT 58.908 45.455 21.64 0.00 42.70 3.95
5014 5832 1.202770 AGGCCCTTGCGTATATTCCAC 60.203 52.381 0.00 0.00 38.85 4.02
5065 5891 4.751600 TCATTTAGGATGCTCATGCTTACG 59.248 41.667 9.11 0.00 40.14 3.18
5144 5979 1.742880 CCTGGTCGCAGTGTGATGG 60.743 63.158 10.07 8.99 0.00 3.51
5148 5983 1.091771 GGTCGCAGTGTGATGGATGG 61.092 60.000 10.07 0.00 0.00 3.51
5159 5994 4.580580 GTGTGATGGATGGATTACCCTTTC 59.419 45.833 0.00 0.00 35.38 2.62
5271 6113 4.439305 TTGCTACAAATGCTGAACATCC 57.561 40.909 0.00 0.00 38.34 3.51
5349 6191 1.202989 TGCCCCTTTGTGTATGCTTCA 60.203 47.619 0.00 0.00 0.00 3.02
5460 6302 0.837691 TCCACATCCAGCACTCCACT 60.838 55.000 0.00 0.00 0.00 4.00
5595 6437 9.165035 TCAAATTAATGGCATGATTCCTTTTTC 57.835 29.630 0.00 0.00 0.00 2.29
5596 6438 8.948145 CAAATTAATGGCATGATTCCTTTTTCA 58.052 29.630 0.00 0.00 0.00 2.69
5597 6439 8.496707 AATTAATGGCATGATTCCTTTTTCAC 57.503 30.769 0.00 0.00 0.00 3.18
5599 6441 2.566724 TGGCATGATTCCTTTTTCACCC 59.433 45.455 0.00 0.00 0.00 4.61
5600 6442 2.833943 GGCATGATTCCTTTTTCACCCT 59.166 45.455 0.00 0.00 0.00 4.34
5601 6443 3.261643 GGCATGATTCCTTTTTCACCCTT 59.738 43.478 0.00 0.00 0.00 3.95
5602 6444 4.248058 GCATGATTCCTTTTTCACCCTTG 58.752 43.478 0.00 0.00 0.00 3.61
5603 6445 4.248058 CATGATTCCTTTTTCACCCTTGC 58.752 43.478 0.00 0.00 0.00 4.01
5604 6446 2.295909 TGATTCCTTTTTCACCCTTGCG 59.704 45.455 0.00 0.00 0.00 4.85
5605 6447 1.036707 TTCCTTTTTCACCCTTGCGG 58.963 50.000 0.00 0.00 37.81 5.69
5606 6448 1.006220 CCTTTTTCACCCTTGCGGC 60.006 57.895 0.00 0.00 33.26 6.53
5644 6486 9.820725 TCAAATAATATTGCATTCCTTTTCTGG 57.179 29.630 0.00 0.00 0.00 3.86
5684 6526 2.027192 TGGGAGAACTGGTGCTTACATC 60.027 50.000 0.00 0.00 0.00 3.06
6084 6934 3.440173 GGATGCATATGGGATAAACCGTG 59.560 47.826 0.00 0.00 40.11 4.94
6089 6939 2.208132 ATGGGATAAACCGTGCAACA 57.792 45.000 0.00 0.00 40.11 3.33
6140 6990 9.440784 CAAACTCTCGTCTCTATAACTAACATC 57.559 37.037 0.00 0.00 0.00 3.06
6232 7082 0.874390 TCGAAGCGCTGAAGCATTTT 59.126 45.000 12.58 0.00 42.21 1.82
6290 7140 3.119101 ACCACCGTGATAATGTCAGACTC 60.119 47.826 0.00 0.00 37.56 3.36
6333 7190 8.984891 TCAAGAATTTGCAAACATATACTTGG 57.015 30.769 15.41 8.60 34.21 3.61
6336 7193 9.777297 AAGAATTTGCAAACATATACTTGGTTT 57.223 25.926 15.41 0.00 35.27 3.27
6402 7268 3.517901 CCTGTAGGGGTAATTGTGAGTCA 59.482 47.826 0.00 0.00 0.00 3.41
6407 7273 5.975988 AGGGGTAATTGTGAGTCATATGT 57.024 39.130 1.90 0.00 0.00 2.29
6448 7314 5.127845 TGACCATCTATCACCTTCTCACTTC 59.872 44.000 0.00 0.00 0.00 3.01
6485 7351 4.273480 GCTTAGCCGACATCATTGTTGTAT 59.727 41.667 0.00 0.00 35.79 2.29
6580 7446 3.804518 TTCACCAATTTGATCGTGTCG 57.195 42.857 0.00 0.00 0.00 4.35
6628 7496 0.464373 ACCCGCTATGCATTCACCTG 60.464 55.000 3.54 0.00 0.00 4.00
6630 7498 1.277739 CGCTATGCATTCACCTGCG 59.722 57.895 3.54 8.34 45.30 5.18
6745 7613 7.711846 ACAGATGTATGAACTCAGATGTCTAC 58.288 38.462 0.00 0.00 0.00 2.59
6853 7721 2.479566 TCTGTCCAGTTCTTGATGCC 57.520 50.000 0.00 0.00 0.00 4.40
6886 7754 3.949754 CTCAAGGCCAGAATCAAAGCATA 59.050 43.478 5.01 0.00 0.00 3.14
6889 7757 3.228453 AGGCCAGAATCAAAGCATATGG 58.772 45.455 5.01 0.00 0.00 2.74
6890 7758 3.022607 GCCAGAATCAAAGCATATGGC 57.977 47.619 4.56 0.00 44.27 4.40
6891 7759 2.288640 GCCAGAATCAAAGCATATGGCC 60.289 50.000 4.56 0.00 44.67 5.36
6955 7827 4.935352 TCCCTGTTTCATTCACCAAAAG 57.065 40.909 0.00 0.00 0.00 2.27
7026 7907 0.690192 TTCTTGCCCGTGGATTCTCA 59.310 50.000 0.00 0.00 0.00 3.27
7053 7934 1.690893 GACTATGGAGGCTGCATCTCA 59.309 52.381 25.38 7.29 33.18 3.27
7082 7963 1.511850 CTGCTCATGAACACACGGAA 58.488 50.000 0.00 0.00 0.00 4.30
7137 8018 3.624861 GCCACTGACCAAACATCTATGAG 59.375 47.826 0.00 0.00 0.00 2.90
7153 8034 8.216423 ACATCTATGAGCTCAGGATACAAAATT 58.784 33.333 24.91 8.49 41.41 1.82
7157 8038 4.766373 TGAGCTCAGGATACAAAATTGCAA 59.234 37.500 13.74 0.00 41.41 4.08
7185 8066 8.868522 TTCATCAAGGAAACAAGAACATATCT 57.131 30.769 0.00 0.00 41.32 1.98
7196 8077 4.500389 AGAACATATCTGGAGGGGAGAT 57.500 45.455 0.00 0.00 36.88 2.75
7199 8080 4.767000 ACATATCTGGAGGGGAGATGTA 57.233 45.455 2.74 0.00 41.75 2.29
7200 8081 5.093236 ACATATCTGGAGGGGAGATGTAA 57.907 43.478 2.74 0.00 41.75 2.41
7204 8085 7.739444 ACATATCTGGAGGGGAGATGTAAAATA 59.261 37.037 2.74 0.00 41.75 1.40
7209 8090 7.794683 TCTGGAGGGGAGATGTAAAATAATAGT 59.205 37.037 0.00 0.00 0.00 2.12
7214 8095 7.017651 AGGGGAGATGTAAAATAATAGTCCCTG 59.982 40.741 0.00 0.00 40.93 4.45
7223 8104 9.516314 GTAAAATAATAGTCCCTGTTTTCATGC 57.484 33.333 0.00 0.00 0.00 4.06
7224 8105 7.961326 AAATAATAGTCCCTGTTTTCATGCT 57.039 32.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.223845 TCATGTTGTGCAAGATGACACG 59.776 45.455 17.21 0.00 43.38 4.49
56 57 3.143211 ACACTGTCTCTTCCTACTCGT 57.857 47.619 0.00 0.00 0.00 4.18
61 62 6.602009 TCAATATCGAACACTGTCTCTTCCTA 59.398 38.462 0.00 0.00 0.00 2.94
62 63 5.419155 TCAATATCGAACACTGTCTCTTCCT 59.581 40.000 0.00 0.00 0.00 3.36
63 64 5.651530 TCAATATCGAACACTGTCTCTTCC 58.348 41.667 0.00 0.00 0.00 3.46
70 71 9.042008 GTAATATGGTTCAATATCGAACACTGT 57.958 33.333 8.73 0.00 45.82 3.55
81 82 5.133660 ACCCTGCCTGTAATATGGTTCAATA 59.866 40.000 0.00 0.00 0.00 1.90
83 84 3.268334 ACCCTGCCTGTAATATGGTTCAA 59.732 43.478 0.00 0.00 0.00 2.69
104 105 4.427312 GTGATCAATTTGGGCAAGATGAC 58.573 43.478 0.00 0.00 0.00 3.06
107 108 3.443052 TGGTGATCAATTTGGGCAAGAT 58.557 40.909 0.00 0.00 0.00 2.40
109 110 3.007182 AGTTGGTGATCAATTTGGGCAAG 59.993 43.478 0.00 0.00 37.73 4.01
118 119 1.280710 TGCCGGTAGTTGGTGATCAAT 59.719 47.619 1.90 0.00 37.73 2.57
129 130 2.072487 AGCCCATGATGCCGGTAGT 61.072 57.895 1.90 0.00 0.00 2.73
150 151 5.808366 TCTCCTGACGCATATTAAGGAAT 57.192 39.130 0.00 0.00 36.62 3.01
156 157 3.418047 TCGGATCTCCTGACGCATATTA 58.582 45.455 0.00 0.00 0.00 0.98
182 183 2.224499 TGCAGTTCTTGATGCACCTGTA 60.224 45.455 0.00 0.00 46.97 2.74
200 201 1.951895 GCTCCACCAGATCATGTTGCA 60.952 52.381 0.00 0.00 0.00 4.08
205 206 2.932855 AGATGCTCCACCAGATCATG 57.067 50.000 0.00 0.00 31.46 3.07
207 208 2.636403 CCATAGATGCTCCACCAGATCA 59.364 50.000 0.00 0.00 0.00 2.92
209 210 2.905085 CTCCATAGATGCTCCACCAGAT 59.095 50.000 0.00 0.00 0.00 2.90
222 223 2.550277 TGTCCTTGAGCCTCCATAGA 57.450 50.000 0.00 0.00 0.00 1.98
228 229 2.486796 GGCATTGTCCTTGAGCCTC 58.513 57.895 0.00 0.00 42.01 4.70
229 230 4.751431 GGCATTGTCCTTGAGCCT 57.249 55.556 0.00 0.00 42.01 4.58
239 240 3.002791 CACACATCGAACTAGGCATTGT 58.997 45.455 0.00 0.00 0.00 2.71
243 244 2.495669 TCATCACACATCGAACTAGGCA 59.504 45.455 0.00 0.00 0.00 4.75
255 256 8.565896 AATTAAAACTCATAGCTCATCACACA 57.434 30.769 0.00 0.00 0.00 3.72
256 257 8.668353 TGAATTAAAACTCATAGCTCATCACAC 58.332 33.333 0.00 0.00 0.00 3.82
281 282 6.183359 CGAAGCAAACTCGTAATTCAAACATG 60.183 38.462 0.00 0.00 0.00 3.21
282 283 5.851177 CGAAGCAAACTCGTAATTCAAACAT 59.149 36.000 0.00 0.00 0.00 2.71
294 295 6.911484 AAATAATTCAACGAAGCAAACTCG 57.089 33.333 0.00 0.00 0.00 4.18
318 319 9.345517 CGTTCATCACAGAAATCAATACAAATT 57.654 29.630 0.00 0.00 0.00 1.82
319 320 8.729756 TCGTTCATCACAGAAATCAATACAAAT 58.270 29.630 0.00 0.00 0.00 2.32
372 464 0.252103 TAAGACTCGGGTTCCCAGCT 60.252 55.000 8.70 0.00 0.00 4.24
383 475 1.804326 CAACCGGCGGTAAGACTCG 60.804 63.158 34.37 10.90 33.12 4.18
402 507 0.303796 GAATAGCACCGCTTAACGCC 59.696 55.000 0.00 0.00 40.44 5.68
403 508 1.003851 TGAATAGCACCGCTTAACGC 58.996 50.000 0.00 0.00 40.44 4.84
405 510 3.426323 GCTTTGAATAGCACCGCTTAAC 58.574 45.455 0.00 0.00 40.44 2.01
406 511 2.422127 GGCTTTGAATAGCACCGCTTAA 59.578 45.455 0.00 0.00 43.02 1.85
411 516 1.936547 GAGAGGCTTTGAATAGCACCG 59.063 52.381 0.00 0.00 43.02 4.94
436 541 2.687842 GAGCATCTCCAGCCTTTCG 58.312 57.895 0.00 0.00 0.00 3.46
457 1021 3.314331 CTGCTCGTCAGGGTGGGT 61.314 66.667 0.56 0.00 39.15 4.51
611 1210 2.127528 GGAAAGGGAGGGGGAGGT 59.872 66.667 0.00 0.00 0.00 3.85
1077 1677 1.549170 GGAAGGCCTCTAAAGTCGTCA 59.451 52.381 5.23 0.00 0.00 4.35
1286 1886 4.394300 CCTCCATCATTCACAACTCACTTC 59.606 45.833 0.00 0.00 0.00 3.01
1385 1985 3.274393 CTGTACAGCTATCGCCCAC 57.726 57.895 10.54 0.00 36.60 4.61
1411 2011 6.321181 TCCCTTAATCATAACCAGCACAATTC 59.679 38.462 0.00 0.00 0.00 2.17
1483 2083 1.547675 GGACTTCAATCCCAGTTGCCA 60.548 52.381 0.00 0.00 31.94 4.92
1691 2291 5.392767 TGTCCAAAACAGTACAAAGCAAA 57.607 34.783 0.00 0.00 32.81 3.68
1719 2319 9.005777 ACTTTTATAAGCCGTTTTAGACATTCA 57.994 29.630 0.00 0.00 34.60 2.57
1734 2334 9.819267 ATACTACCTCTGTTCACTTTTATAAGC 57.181 33.333 0.00 0.00 34.60 3.09
1845 2449 0.390860 CCTGGTGGCCTAGAAGATCG 59.609 60.000 3.32 0.00 0.00 3.69
1847 2451 2.270434 TTCCTGGTGGCCTAGAAGAT 57.730 50.000 3.32 0.00 0.00 2.40
1850 2454 1.354368 CCTTTTCCTGGTGGCCTAGAA 59.646 52.381 3.32 0.00 0.00 2.10
1915 2527 8.356657 ACAGCACTAGAGATGACAGATAAATAC 58.643 37.037 12.50 0.00 0.00 1.89
1916 2528 8.355913 CACAGCACTAGAGATGACAGATAAATA 58.644 37.037 12.50 0.00 0.00 1.40
1917 2529 7.147759 ACACAGCACTAGAGATGACAGATAAAT 60.148 37.037 12.50 0.00 0.00 1.40
1987 2599 6.644181 ACAGCATTACAGATGACAGAATATCG 59.356 38.462 0.00 0.00 0.00 2.92
1991 2603 4.334759 GCACAGCATTACAGATGACAGAAT 59.665 41.667 0.00 0.00 0.00 2.40
2025 2637 8.612619 AGCTTAAAGTGTCACATAAAATATCCG 58.387 33.333 5.62 0.00 0.00 4.18
2036 2648 4.948341 TCAGGTAGCTTAAAGTGTCACA 57.052 40.909 5.62 0.00 0.00 3.58
2440 3060 3.306780 CCACGAGGTTAGAACTGAATGGT 60.307 47.826 0.00 0.00 0.00 3.55
2756 3376 5.337554 CACAAGTTAATGATGCTCACATGG 58.662 41.667 0.00 0.00 36.35 3.66
2961 3582 9.631452 CCAATTAGGATCAGAAAGAAAGAAAAC 57.369 33.333 0.00 0.00 41.22 2.43
2990 3611 9.276590 TCATACTGCAGATTTTATATCCAACAG 57.723 33.333 23.35 0.00 0.00 3.16
3062 3683 5.938322 TGCCAAAAGTCTTCGAATGTATTC 58.062 37.500 0.00 0.00 0.00 1.75
3077 3698 3.822735 TCTCAAAGACCATCTGCCAAAAG 59.177 43.478 0.00 0.00 0.00 2.27
3198 3819 5.720261 AGACGAGAAACTGAAAACTGAAC 57.280 39.130 0.00 0.00 0.00 3.18
3301 3924 3.562343 TCTCATGTCCTACTAGTCGCT 57.438 47.619 0.00 0.00 0.00 4.93
3305 3928 7.482169 TTGAATGTTCTCATGTCCTACTAGT 57.518 36.000 0.00 0.00 34.19 2.57
3371 3994 3.175152 GACTGAGCAACTATCACGTCAG 58.825 50.000 0.00 0.00 37.91 3.51
3377 4000 2.354103 GCAGTGGACTGAGCAACTATCA 60.354 50.000 11.06 0.00 46.59 2.15
3419 4042 4.683320 GCTGATTCCAGTCAAAGAAAAAGC 59.317 41.667 0.00 0.00 42.35 3.51
3494 4118 1.270839 TGTTCTTCTCCTTTCAGGGCG 60.271 52.381 0.00 0.00 35.59 6.13
3546 4170 1.001641 AGCACCAATCAGGCAGGAC 60.002 57.895 0.00 0.00 43.14 3.85
3631 4301 9.902684 TTGATCAAAAATGGCCATTTACATATT 57.097 25.926 37.45 26.26 39.88 1.28
3761 4513 4.539870 GTGCATGCAACACATCCATATAC 58.460 43.478 24.58 0.03 36.64 1.47
3831 4583 2.584608 GCGTATGGTGGTCTGCCT 59.415 61.111 0.00 0.00 35.27 4.75
3846 4598 1.263217 GCCTAACAAATACGGATGGCG 59.737 52.381 0.00 0.00 0.00 5.69
3850 4602 3.317993 GCAATGGCCTAACAAATACGGAT 59.682 43.478 3.32 0.00 0.00 4.18
3851 4603 2.685897 GCAATGGCCTAACAAATACGGA 59.314 45.455 3.32 0.00 0.00 4.69
3852 4604 2.687935 AGCAATGGCCTAACAAATACGG 59.312 45.455 3.32 0.00 42.56 4.02
3862 4614 3.888930 GGCACTATAAAAGCAATGGCCTA 59.111 43.478 3.32 0.00 42.56 3.93
3919 4671 1.688772 AGCCTGCATGTCCAATCATC 58.311 50.000 0.00 0.00 0.00 2.92
3987 4749 3.054875 TGCATGTGTTCTATCTCCTGCTT 60.055 43.478 0.00 0.00 0.00 3.91
3998 4760 3.708403 TCAATCTCCTGCATGTGTTCT 57.292 42.857 0.00 0.00 0.00 3.01
3999 4761 3.128242 CCTTCAATCTCCTGCATGTGTTC 59.872 47.826 0.00 0.00 0.00 3.18
4000 4762 3.087031 CCTTCAATCTCCTGCATGTGTT 58.913 45.455 0.00 0.00 0.00 3.32
4001 4763 2.306805 TCCTTCAATCTCCTGCATGTGT 59.693 45.455 0.00 0.00 0.00 3.72
4002 4764 2.681848 GTCCTTCAATCTCCTGCATGTG 59.318 50.000 0.00 0.00 0.00 3.21
4003 4765 2.575279 AGTCCTTCAATCTCCTGCATGT 59.425 45.455 0.00 0.00 0.00 3.21
4004 4766 3.278668 AGTCCTTCAATCTCCTGCATG 57.721 47.619 0.00 0.00 0.00 4.06
4005 4767 3.181471 CGTAGTCCTTCAATCTCCTGCAT 60.181 47.826 0.00 0.00 0.00 3.96
4006 4768 2.166459 CGTAGTCCTTCAATCTCCTGCA 59.834 50.000 0.00 0.00 0.00 4.41
4007 4769 2.815478 CGTAGTCCTTCAATCTCCTGC 58.185 52.381 0.00 0.00 0.00 4.85
4008 4770 2.166459 TGCGTAGTCCTTCAATCTCCTG 59.834 50.000 0.00 0.00 0.00 3.86
4009 4771 2.457598 TGCGTAGTCCTTCAATCTCCT 58.542 47.619 0.00 0.00 0.00 3.69
4010 4772 2.961526 TGCGTAGTCCTTCAATCTCC 57.038 50.000 0.00 0.00 0.00 3.71
4011 4773 6.757010 TCTTAATTGCGTAGTCCTTCAATCTC 59.243 38.462 0.00 0.00 0.00 2.75
4012 4774 6.535508 GTCTTAATTGCGTAGTCCTTCAATCT 59.464 38.462 0.00 0.00 0.00 2.40
4013 4775 6.508088 CGTCTTAATTGCGTAGTCCTTCAATC 60.508 42.308 0.00 0.00 0.00 2.67
4014 4776 5.291128 CGTCTTAATTGCGTAGTCCTTCAAT 59.709 40.000 0.00 0.00 0.00 2.57
4015 4777 4.624024 CGTCTTAATTGCGTAGTCCTTCAA 59.376 41.667 0.00 0.00 0.00 2.69
4029 4791 6.097915 TCAAGGAACTCAGTCGTCTTAATT 57.902 37.500 0.00 0.00 38.49 1.40
4037 4799 2.417924 CCAGGATCAAGGAACTCAGTCG 60.418 54.545 0.00 0.00 38.49 4.18
4046 4808 3.200825 GGTCAATTCTCCAGGATCAAGGA 59.799 47.826 5.39 5.39 0.00 3.36
4055 4817 1.084370 GCGGACGGTCAATTCTCCAG 61.084 60.000 10.76 0.00 0.00 3.86
4072 4834 1.714899 CGGCCAGGTTTATTGGAGCG 61.715 60.000 2.24 0.00 37.96 5.03
4084 4846 2.898920 TACTCCCTACGACGGCCAGG 62.899 65.000 2.24 0.23 0.00 4.45
4086 4848 0.396139 AATACTCCCTACGACGGCCA 60.396 55.000 2.24 0.00 0.00 5.36
4113 4929 2.691526 ACAGTGTCGCCCTATCGAATTA 59.308 45.455 0.00 0.00 40.43 1.40
4162 4978 4.254492 GTTCTGAATTACACAGGAGACCC 58.746 47.826 0.00 0.00 36.22 4.46
4221 5038 1.228737 GGCAGGCACCCCTTGTTTA 60.229 57.895 0.00 0.00 40.33 2.01
4392 5209 2.672961 TGTCTAAATCACGGCCTCAG 57.327 50.000 0.00 0.00 0.00 3.35
4454 5271 5.163281 TGGTACCAAAGCCGAAAGTATTA 57.837 39.130 13.60 0.00 0.00 0.98
4721 5539 9.121517 CTTTATTTAGACACAGAAGCAACATTG 57.878 33.333 0.00 0.00 0.00 2.82
4794 5612 7.326454 AGAGCAATGGCATACAGTAGTATATG 58.674 38.462 0.00 0.00 44.61 1.78
4803 5621 3.441222 TGAACAAGAGCAATGGCATACAG 59.559 43.478 0.00 0.00 44.61 2.74
4815 5633 2.160219 TGCATCGTTGATGAACAAGAGC 59.840 45.455 10.81 0.00 42.09 4.09
4888 5706 4.705023 GCTGCCCTTTTTACTTCTAATGGA 59.295 41.667 0.00 0.00 0.00 3.41
4889 5707 4.142160 GGCTGCCCTTTTTACTTCTAATGG 60.142 45.833 7.66 0.00 0.00 3.16
4890 5708 4.142160 GGGCTGCCCTTTTTACTTCTAATG 60.142 45.833 30.42 0.00 41.34 1.90
4891 5709 4.023980 GGGCTGCCCTTTTTACTTCTAAT 58.976 43.478 30.42 0.00 41.34 1.73
4892 5710 3.427573 GGGCTGCCCTTTTTACTTCTAA 58.572 45.455 30.42 0.00 41.34 2.10
4893 5711 2.617021 CGGGCTGCCCTTTTTACTTCTA 60.617 50.000 33.39 0.00 42.67 2.10
4894 5712 1.886655 CGGGCTGCCCTTTTTACTTCT 60.887 52.381 33.39 0.00 42.67 2.85
4895 5713 0.526211 CGGGCTGCCCTTTTTACTTC 59.474 55.000 33.39 5.18 42.67 3.01
4896 5714 0.898326 CCGGGCTGCCCTTTTTACTT 60.898 55.000 33.39 0.00 42.67 2.24
4897 5715 1.304134 CCGGGCTGCCCTTTTTACT 60.304 57.895 33.39 0.00 42.67 2.24
4898 5716 1.605451 ACCGGGCTGCCCTTTTTAC 60.605 57.895 33.39 7.46 42.67 2.01
4899 5717 1.605165 CACCGGGCTGCCCTTTTTA 60.605 57.895 33.39 0.00 42.67 1.52
4900 5718 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
4906 5724 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
4907 5725 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
4908 5726 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
4909 5727 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
4910 5728 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
4911 5729 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
4935 5753 4.778143 CCTTCCCCGGACCTTGCG 62.778 72.222 0.73 0.00 0.00 4.85
4936 5754 4.426313 CCCTTCCCCGGACCTTGC 62.426 72.222 0.73 0.00 0.00 4.01
4937 5755 2.933834 ACCCTTCCCCGGACCTTG 60.934 66.667 0.73 0.00 0.00 3.61
4938 5756 2.609921 GACCCTTCCCCGGACCTT 60.610 66.667 0.73 0.00 0.00 3.50
4939 5757 4.735599 GGACCCTTCCCCGGACCT 62.736 72.222 0.73 0.00 35.57 3.85
4941 5759 0.984432 TAATGGACCCTTCCCCGGAC 60.984 60.000 0.73 0.00 42.01 4.79
4942 5760 0.693092 CTAATGGACCCTTCCCCGGA 60.693 60.000 0.73 0.00 42.01 5.14
4943 5761 0.693092 TCTAATGGACCCTTCCCCGG 60.693 60.000 0.00 0.00 42.01 5.73
4944 5762 1.141053 CTTCTAATGGACCCTTCCCCG 59.859 57.143 0.00 0.00 42.01 5.73
4945 5763 2.206223 ACTTCTAATGGACCCTTCCCC 58.794 52.381 0.00 0.00 42.01 4.81
4946 5764 3.181453 GCTACTTCTAATGGACCCTTCCC 60.181 52.174 0.00 0.00 42.01 3.97
4947 5765 3.712218 AGCTACTTCTAATGGACCCTTCC 59.288 47.826 0.00 0.00 43.19 3.46
4948 5766 5.104900 TCAAGCTACTTCTAATGGACCCTTC 60.105 44.000 0.00 0.00 0.00 3.46
4949 5767 4.783227 TCAAGCTACTTCTAATGGACCCTT 59.217 41.667 0.00 0.00 0.00 3.95
4950 5768 4.362677 TCAAGCTACTTCTAATGGACCCT 58.637 43.478 0.00 0.00 0.00 4.34
4951 5769 4.755266 TCAAGCTACTTCTAATGGACCC 57.245 45.455 0.00 0.00 0.00 4.46
4952 5770 5.735766 ACTTCAAGCTACTTCTAATGGACC 58.264 41.667 0.00 0.00 0.00 4.46
4953 5771 8.950208 ATTACTTCAAGCTACTTCTAATGGAC 57.050 34.615 0.00 0.00 0.00 4.02
5001 5819 6.761242 GCAATATATCTGGTGGAATATACGCA 59.239 38.462 0.00 0.00 0.00 5.24
5014 5832 4.553330 AAGTACCCGGCAATATATCTGG 57.447 45.455 0.00 0.00 0.00 3.86
5065 5891 5.967088 TGAAATCTTCACTACCACTAGAGC 58.033 41.667 0.00 0.00 34.08 4.09
5144 5979 2.952310 GTGCTGGAAAGGGTAATCCATC 59.048 50.000 0.00 0.00 44.41 3.51
5148 5983 4.489306 AGTAGTGCTGGAAAGGGTAATC 57.511 45.455 0.00 0.00 0.00 1.75
5256 6098 4.685169 AACTACGGATGTTCAGCATTTG 57.315 40.909 0.00 0.00 38.06 2.32
5349 6191 8.102484 ACAAGTAATATGGGTGAAAGAGGTAT 57.898 34.615 0.00 0.00 0.00 2.73
5527 6369 3.074538 ACAACTGGGTGCTCTTTAGGAAT 59.925 43.478 0.00 0.00 0.00 3.01
5605 6447 3.608316 TTATTTGAATGTGGGCAAGGC 57.392 42.857 0.00 0.00 0.00 4.35
5606 6448 6.203338 GCAATATTATTTGAATGTGGGCAAGG 59.797 38.462 0.00 0.00 0.00 3.61
5684 6526 8.183104 TCCTCTCTACTGTATTATGGATTGTG 57.817 38.462 0.00 0.00 0.00 3.33
5873 6720 1.269309 ACTCTACCGCAATCATCTCGC 60.269 52.381 0.00 0.00 0.00 5.03
6052 6899 4.105217 TCCCATATGCATCCAATTGAGTCT 59.895 41.667 0.19 0.00 0.00 3.24
6084 6934 6.806739 GGTTGATAAGGAATAGTTTGTGTTGC 59.193 38.462 0.00 0.00 0.00 4.17
6089 6939 7.942341 TGAGTTGGTTGATAAGGAATAGTTTGT 59.058 33.333 0.00 0.00 0.00 2.83
6140 6990 2.825861 ATTGTTCCTGCAAAGCCAAG 57.174 45.000 0.00 0.00 31.63 3.61
6232 7082 1.813753 GCATCAAGCTTACCGCCGA 60.814 57.895 0.00 0.00 41.15 5.54
6273 7123 9.335891 GAATATGTAGAGTCTGACATTATCACG 57.664 37.037 10.88 0.00 37.47 4.35
6308 7165 8.584157 ACCAAGTATATGTTTGCAAATTCTTGA 58.416 29.630 21.66 6.56 34.14 3.02
6332 7189 4.022416 TGTGAGGTTCATGTAATGCAAACC 60.022 41.667 6.16 6.16 46.20 3.27
6333 7190 5.119931 TGTGAGGTTCATGTAATGCAAAC 57.880 39.130 0.00 0.00 46.21 2.93
6336 7193 5.711506 AGAAATGTGAGGTTCATGTAATGCA 59.288 36.000 0.00 0.00 46.21 3.96
6339 7196 7.884877 TGAGAAGAAATGTGAGGTTCATGTAAT 59.115 33.333 0.00 0.00 0.00 1.89
6389 7255 6.292703 GGCCGTTACATATGACTCACAATTAC 60.293 42.308 10.38 0.00 0.00 1.89
6393 7259 3.196901 AGGCCGTTACATATGACTCACAA 59.803 43.478 10.38 0.00 0.00 3.33
6396 7262 3.028130 TCAGGCCGTTACATATGACTCA 58.972 45.455 10.38 0.00 0.00 3.41
6402 7268 3.825014 AGATACGTCAGGCCGTTACATAT 59.175 43.478 0.00 0.00 42.00 1.78
6407 7273 1.402968 GTCAGATACGTCAGGCCGTTA 59.597 52.381 0.00 0.00 42.00 3.18
6448 7314 4.394920 TCGGCTAAGCTTAACAAATTGAGG 59.605 41.667 7.74 0.00 0.00 3.86
6485 7351 4.976224 TCGAATTCCAGTCTTCGTGATA 57.024 40.909 0.00 0.00 43.49 2.15
6628 7496 0.588252 TTCAGCAAGAGAAGCAACGC 59.412 50.000 0.00 0.00 0.00 4.84
6630 7498 4.234530 ACAATTCAGCAAGAGAAGCAAC 57.765 40.909 0.00 0.00 0.00 4.17
6745 7613 1.083015 CGTCCGCGTCAAACTTTGG 60.083 57.895 4.92 0.00 0.00 3.28
6853 7721 0.519077 GGCCTTGAGTTTCAGAAGCG 59.481 55.000 0.00 0.00 0.00 4.68
6889 7757 2.812011 GGGACATACAAATATGGACGGC 59.188 50.000 0.00 0.00 42.32 5.68
6890 7758 3.064207 CGGGACATACAAATATGGACGG 58.936 50.000 0.00 0.00 42.32 4.79
6891 7759 3.985008 TCGGGACATACAAATATGGACG 58.015 45.455 0.00 1.64 42.32 4.79
6923 7791 4.422073 TGAAACAGGGATAGCCTACATG 57.578 45.455 0.00 0.00 0.00 3.21
6930 7802 3.620488 TGGTGAATGAAACAGGGATAGC 58.380 45.455 0.00 0.00 0.00 2.97
6955 7827 5.048434 GCTCACTGGATAAAAATGCTATCCC 60.048 44.000 6.51 0.00 42.91 3.85
7026 7907 2.520536 GCCTCCATAGTCCGCCCAT 61.521 63.158 0.00 0.00 0.00 4.00
7053 7934 3.117776 TGTTCATGAGCAGGCCTATTGAT 60.118 43.478 3.98 0.00 0.00 2.57
7082 7963 5.606348 TGGTTTTTCTGGTTGCAATAACT 57.394 34.783 0.59 0.00 0.00 2.24
7137 8018 6.973229 ATTTTGCAATTTTGTATCCTGAGC 57.027 33.333 0.00 0.00 0.00 4.26
7153 8034 6.580788 TCTTGTTTCCTTGATGAATTTTGCA 58.419 32.000 0.00 0.00 0.00 4.08
7185 8066 7.017254 GGACTATTATTTTACATCTCCCCTCCA 59.983 40.741 0.00 0.00 0.00 3.86
7199 8080 8.366359 AGCATGAAAACAGGGACTATTATTTT 57.634 30.769 0.00 0.00 36.02 1.82
7200 8081 7.961326 AGCATGAAAACAGGGACTATTATTT 57.039 32.000 0.00 0.00 36.02 1.40


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

AutoCloner maintained by Alex Coulton.