Multiple sequence alignment - TraesCS2D01G071800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G071800 chr2D 100.000 6783 0 0 952 7734 30341769 30334987 0.000000e+00 12526.0
1 TraesCS2D01G071800 chr2D 100.000 631 0 0 1 631 30342720 30342090 0.000000e+00 1166.0
2 TraesCS2D01G071800 chr2B 93.877 5945 252 42 952 6821 48796993 48802900 0.000000e+00 8859.0
3 TraesCS2D01G071800 chr2B 94.571 921 42 4 6818 7734 48803022 48803938 0.000000e+00 1417.0
4 TraesCS2D01G071800 chr2B 84.932 584 68 12 7161 7734 48817219 48816646 2.420000e-159 573.0
5 TraesCS2D01G071800 chr2B 81.798 445 59 9 1 433 48795863 48796297 3.430000e-93 353.0
6 TraesCS2D01G071800 chr2B 92.135 89 7 0 543 631 48796782 48796870 8.150000e-25 126.0
7 TraesCS2D01G071800 chr2A 94.402 4698 206 26 952 5632 32272573 32267916 0.000000e+00 7166.0
8 TraesCS2D01G071800 chr2A 92.707 2139 87 21 5605 7734 32267913 32265835 0.000000e+00 3022.0
9 TraesCS2D01G071800 chr2A 86.852 540 59 8 7163 7698 32230613 32231144 1.860000e-165 593.0
10 TraesCS2D01G071800 chr2A 77.516 467 74 14 3631 4089 739856706 739856263 1.290000e-62 252.0
11 TraesCS2D01G071800 chr2A 91.620 179 7 1 453 631 32272851 32272681 2.790000e-59 241.0
12 TraesCS2D01G071800 chr3D 85.320 579 68 8 7166 7734 35044952 35044381 4.020000e-162 582.0
13 TraesCS2D01G071800 chr3B 85.147 579 69 8 7166 7734 58008102 58007531 1.870000e-160 577.0
14 TraesCS2D01G071800 chr3A 81.746 378 54 11 3717 4091 702597277 702596912 1.260000e-77 302.0
15 TraesCS2D01G071800 chr7B 74.170 542 102 26 7156 7693 37421219 37420712 2.850000e-44 191.0
16 TraesCS2D01G071800 chr7D 74.170 542 98 29 7158 7693 88142467 88142972 3.690000e-43 187.0
17 TraesCS2D01G071800 chr7A 73.346 544 106 28 7156 7693 89809077 89809587 1.730000e-36 165.0
18 TraesCS2D01G071800 chr6B 76.667 210 37 11 3249 3449 373890708 373890502 1.060000e-18 106.0
19 TraesCS2D01G071800 chr1B 76.667 210 37 11 3249 3449 554223812 554223606 1.060000e-18 106.0
20 TraesCS2D01G071800 chr4D 76.687 163 31 7 147 306 27148165 27148323 4.970000e-12 84.2
21 TraesCS2D01G071800 chr5D 75.000 176 32 11 157 327 348275759 348275927 3.870000e-08 71.3
22 TraesCS2D01G071800 chr6D 84.722 72 8 3 3381 3449 121229133 121229062 1.390000e-07 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G071800 chr2D 30334987 30342720 7733 True 6846.000000 12526 100.000000 1 7734 2 chr2D.!!$R1 7733
1 TraesCS2D01G071800 chr2B 48795863 48803938 8075 False 2688.750000 8859 90.595250 1 7734 4 chr2B.!!$F1 7733
2 TraesCS2D01G071800 chr2B 48816646 48817219 573 True 573.000000 573 84.932000 7161 7734 1 chr2B.!!$R1 573
3 TraesCS2D01G071800 chr2A 32265835 32272851 7016 True 3476.333333 7166 92.909667 453 7734 3 chr2A.!!$R2 7281
4 TraesCS2D01G071800 chr2A 32230613 32231144 531 False 593.000000 593 86.852000 7163 7698 1 chr2A.!!$F1 535
5 TraesCS2D01G071800 chr3D 35044381 35044952 571 True 582.000000 582 85.320000 7166 7734 1 chr3D.!!$R1 568
6 TraesCS2D01G071800 chr3B 58007531 58008102 571 True 577.000000 577 85.147000 7166 7734 1 chr3B.!!$R1 568

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
606 1049 0.321210 CCCCGCCAAAAACCATTTCC 60.321 55.000 0.00 0.00 0.00 3.13 F
1400 1867 0.318441 CGTGTCAAGGAGGAGAAGCA 59.682 55.000 0.00 0.00 0.00 3.91 F
1402 1869 0.979665 TGTCAAGGAGGAGAAGCAGG 59.020 55.000 0.00 0.00 0.00 4.85 F
2223 2723 1.790755 TCGTGTTTCCGACAATGGAG 58.209 50.000 0.00 0.00 40.65 3.86 F
2951 3454 1.758936 CTGATGAGCAGGCCATTTCA 58.241 50.000 5.01 5.43 41.07 2.69 F
3646 4150 1.404748 CTGTGCATGTTTGGTGACACA 59.595 47.619 8.08 0.00 42.67 3.72 F
4682 5196 1.336240 GCAGGTGTGTTTTCAGCCATC 60.336 52.381 0.00 0.00 36.62 3.51 F
5710 6258 0.250989 CGGTTCCTTAAAGGGGCACA 60.251 55.000 0.00 0.00 35.59 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2525 0.804364 GTTCGCAATGCACCATGAGA 59.196 50.000 5.91 0.00 0.00 3.27 R
2401 2901 2.154462 CAAGGATGAGTTGTCGCCTTT 58.846 47.619 0.00 0.00 37.76 3.11 R
2951 3454 4.677673 AATTTTGTTCAAGGCAGCTTCT 57.322 36.364 0.00 0.00 0.00 2.85 R
3620 4124 1.321474 CCAAACATGCACAGACAGGT 58.679 50.000 0.00 0.00 35.80 4.00 R
4521 5035 1.055849 TCCTGTGAAAGGCACTGCTA 58.944 50.000 0.00 0.00 46.92 3.49 R
4953 5468 1.118838 CTTCTGCCACCTAGAGGGAG 58.881 60.000 13.99 13.99 45.03 4.30 R
5981 6529 0.878523 TCCAGTTGTTCTTGGCGTCG 60.879 55.000 0.00 0.00 0.00 5.12 R
6787 7354 0.038166 TTACCAAGGGCCTGAAGCTG 59.962 55.000 6.92 0.00 43.05 4.24 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
28 29 6.846283 GCAATACAATATAAGTGTGACGAAGC 59.154 38.462 0.00 0.00 0.00 3.86
45 46 3.181489 CGAAGCCGTGAATAACTCTACCT 60.181 47.826 0.00 0.00 0.00 3.08
49 50 3.069729 GCCGTGAATAACTCTACCTCCAT 59.930 47.826 0.00 0.00 0.00 3.41
77 78 6.210185 ACGTAGTTGACTAGGATTTGTAACCT 59.790 38.462 15.47 0.00 37.78 3.50
78 79 6.530534 CGTAGTTGACTAGGATTTGTAACCTG 59.469 42.308 5.20 0.00 36.68 4.00
89 90 0.546747 TGTAACCTGAGGGACCCCAG 60.547 60.000 17.76 17.76 38.92 4.45
101 102 8.242325 CCTGAGGGACCCCAGTATATTATATAT 58.758 40.741 21.10 0.00 38.92 0.86
111 112 8.175431 CCCAGTATATTATATATACCGGGGTCT 58.825 40.741 20.82 0.00 41.32 3.85
117 118 0.788383 ATATACCGGGGTCTGGGCTA 59.212 55.000 6.32 0.00 0.00 3.93
125 126 1.550409 GGGGTCTGGGCTAGTCGATAT 60.550 57.143 0.00 0.00 0.00 1.63
135 136 7.834681 TCTGGGCTAGTCGATATAACATCTTAT 59.165 37.037 0.00 0.00 0.00 1.73
137 138 9.642343 TGGGCTAGTCGATATAACATCTTATAT 57.358 33.333 0.00 0.00 37.98 0.86
174 175 6.882140 CCCTTGGTTCATACATGTACTTTGTA 59.118 38.462 7.96 10.38 34.29 2.41
180 181 6.614694 TCATACATGTACTTTGTACACCCT 57.385 37.500 7.96 2.11 32.70 4.34
181 182 7.011499 TCATACATGTACTTTGTACACCCTT 57.989 36.000 7.96 1.62 32.70 3.95
185 186 6.103997 ACATGTACTTTGTACACCCTTATCG 58.896 40.000 11.99 0.00 0.00 2.92
186 187 4.497300 TGTACTTTGTACACCCTTATCGC 58.503 43.478 6.48 0.00 0.00 4.58
188 189 4.216411 ACTTTGTACACCCTTATCGCAT 57.784 40.909 0.00 0.00 0.00 4.73
206 207 4.380839 GCATTATACACATGCGAGAGTG 57.619 45.455 0.00 0.00 37.88 3.51
207 208 3.185188 GCATTATACACATGCGAGAGTGG 59.815 47.826 0.00 0.00 37.88 4.00
208 209 3.452755 TTATACACATGCGAGAGTGGG 57.547 47.619 0.00 0.00 39.99 4.61
224 225 3.800826 GGGGCATTACCTCAATCGT 57.199 52.632 0.00 0.00 39.64 3.73
247 248 2.574824 AGGGCACGAACCTAGGTAAATT 59.425 45.455 16.67 0.00 36.32 1.82
249 250 3.128068 GGGCACGAACCTAGGTAAATTTG 59.872 47.826 16.67 5.90 0.00 2.32
250 251 3.754850 GGCACGAACCTAGGTAAATTTGT 59.245 43.478 16.67 6.62 0.00 2.83
261 262 7.447545 ACCTAGGTAAATTTGTCTCCTTGTTTC 59.552 37.037 14.41 0.00 0.00 2.78
265 266 5.791336 AAATTTGTCTCCTTGTTTCCCTC 57.209 39.130 0.00 0.00 0.00 4.30
267 268 3.771577 TTGTCTCCTTGTTTCCCTCTC 57.228 47.619 0.00 0.00 0.00 3.20
268 269 2.977808 TGTCTCCTTGTTTCCCTCTCT 58.022 47.619 0.00 0.00 0.00 3.10
269 270 2.634940 TGTCTCCTTGTTTCCCTCTCTG 59.365 50.000 0.00 0.00 0.00 3.35
270 271 2.027653 GTCTCCTTGTTTCCCTCTCTGG 60.028 54.545 0.00 0.00 0.00 3.86
271 272 0.693049 TCCTTGTTTCCCTCTCTGGC 59.307 55.000 0.00 0.00 0.00 4.85
272 273 0.322906 CCTTGTTTCCCTCTCTGGCC 60.323 60.000 0.00 0.00 0.00 5.36
283 284 3.357203 CCTCTCTGGCCTAATCGCTATA 58.643 50.000 3.32 0.00 0.00 1.31
287 288 0.892755 TGGCCTAATCGCTATACCGG 59.107 55.000 3.32 0.00 0.00 5.28
288 289 1.180029 GGCCTAATCGCTATACCGGA 58.820 55.000 9.46 0.00 0.00 5.14
296 297 0.595095 CGCTATACCGGACACCCTAC 59.405 60.000 9.46 0.00 0.00 3.18
309 310 3.460995 CCTACCGAGGGATCTGCC 58.539 66.667 0.00 0.00 39.48 4.85
310 311 1.457643 CCTACCGAGGGATCTGCCA 60.458 63.158 0.00 0.00 39.48 4.92
338 339 1.811266 CCGACACCAGGCATCTTCG 60.811 63.158 0.00 0.00 0.00 3.79
354 355 4.238761 TCTTCGAGGTCAGTTACACAAG 57.761 45.455 0.00 0.00 0.00 3.16
371 383 1.614903 CAAGCTCAAAGGCACATCCAA 59.385 47.619 0.00 0.00 37.29 3.53
372 384 1.542492 AGCTCAAAGGCACATCCAAG 58.458 50.000 0.00 0.00 37.29 3.61
381 393 1.732259 GGCACATCCAAGACGTGTTAG 59.268 52.381 0.00 0.00 33.13 2.34
382 394 1.128692 GCACATCCAAGACGTGTTAGC 59.871 52.381 0.00 0.00 33.13 3.09
400 412 7.412020 CGTGTTAGCCTTCACTTAGATTCTTTC 60.412 40.741 0.00 0.00 33.07 2.62
432 444 7.619964 TTTTTAGAGGCGGGTCTTTATTTAG 57.380 36.000 0.00 0.00 0.00 1.85
433 445 5.945144 TTAGAGGCGGGTCTTTATTTAGT 57.055 39.130 0.00 0.00 0.00 2.24
434 446 4.838904 AGAGGCGGGTCTTTATTTAGTT 57.161 40.909 0.00 0.00 0.00 2.24
435 447 5.175388 AGAGGCGGGTCTTTATTTAGTTT 57.825 39.130 0.00 0.00 0.00 2.66
436 448 5.567430 AGAGGCGGGTCTTTATTTAGTTTT 58.433 37.500 0.00 0.00 0.00 2.43
437 449 6.008331 AGAGGCGGGTCTTTATTTAGTTTTT 58.992 36.000 0.00 0.00 0.00 1.94
527 970 3.611674 CACGTGGCCCCCAAAACC 61.612 66.667 7.95 0.00 34.18 3.27
558 1001 0.605319 TCACCTCACCGCCACAATTC 60.605 55.000 0.00 0.00 0.00 2.17
606 1049 0.321210 CCCCGCCAAAAACCATTTCC 60.321 55.000 0.00 0.00 0.00 3.13
984 1427 1.301716 CAATACCATCCCCGCCGAG 60.302 63.158 0.00 0.00 0.00 4.63
1277 1744 4.135153 CGACGCTACAGCTGCCCT 62.135 66.667 15.27 0.00 39.32 5.19
1300 1767 1.945354 GCCGACGATCAGGGTGAAGA 61.945 60.000 0.00 0.00 0.00 2.87
1308 1775 2.120718 AGGGTGAAGACCGAGGCT 59.879 61.111 0.00 0.00 44.23 4.58
1329 1796 2.027625 CGACGTGCCCAAGAAGGAC 61.028 63.158 0.00 0.00 41.22 3.85
1333 1800 2.852075 TGCCCAAGAAGGACCGGT 60.852 61.111 6.92 6.92 41.22 5.28
1336 1803 1.296715 CCCAAGAAGGACCGGTCTG 59.703 63.158 32.52 22.02 41.22 3.51
1394 1861 4.373116 GCGCCGTGTCAAGGAGGA 62.373 66.667 9.22 0.00 0.00 3.71
1395 1862 2.125912 CGCCGTGTCAAGGAGGAG 60.126 66.667 9.22 0.00 0.00 3.69
1396 1863 2.636412 CGCCGTGTCAAGGAGGAGA 61.636 63.158 9.22 0.00 0.00 3.71
1397 1864 1.671742 GCCGTGTCAAGGAGGAGAA 59.328 57.895 9.22 0.00 0.00 2.87
1398 1865 0.390472 GCCGTGTCAAGGAGGAGAAG 60.390 60.000 9.22 0.00 0.00 2.85
1399 1866 0.390472 CCGTGTCAAGGAGGAGAAGC 60.390 60.000 0.00 0.00 0.00 3.86
1400 1867 0.318441 CGTGTCAAGGAGGAGAAGCA 59.682 55.000 0.00 0.00 0.00 3.91
1401 1868 1.671261 CGTGTCAAGGAGGAGAAGCAG 60.671 57.143 0.00 0.00 0.00 4.24
1402 1869 0.979665 TGTCAAGGAGGAGAAGCAGG 59.020 55.000 0.00 0.00 0.00 4.85
1813 2304 4.194720 CGGAGCTCGGGGACTTCG 62.195 72.222 13.25 1.94 34.75 3.79
1836 2327 3.069778 GAGCCCGACTGGTTCCTT 58.930 61.111 0.00 0.00 38.37 3.36
2034 2525 1.830477 GGAGAGGTGAACTGCTCTCAT 59.170 52.381 14.67 0.00 42.80 2.90
2035 2526 2.159114 GGAGAGGTGAACTGCTCTCATC 60.159 54.545 14.67 0.47 42.80 2.92
2041 2541 3.196463 GTGAACTGCTCTCATCTCATGG 58.804 50.000 0.00 0.00 0.00 3.66
2068 2568 4.621068 TGCGAACTCATGATTGGAATTC 57.379 40.909 0.00 0.00 0.00 2.17
2074 2574 7.308169 GCGAACTCATGATTGGAATTCATATCA 60.308 37.037 18.40 18.40 32.09 2.15
2084 2584 7.407393 TTGGAATTCATATCATTCTGTGCAA 57.593 32.000 7.93 0.00 32.13 4.08
2088 2588 9.970395 GGAATTCATATCATTCTGTGCAAAATA 57.030 29.630 7.93 0.00 32.13 1.40
2103 2603 7.546358 TGTGCAAAATAATCTTAATCCTGTGG 58.454 34.615 0.00 0.00 0.00 4.17
2127 2627 6.753744 GGAACTTTTGATGGTTATTGCAGATC 59.246 38.462 0.00 0.00 0.00 2.75
2187 2687 2.952310 GCTGGTGAACTCTTCCAAAGTT 59.048 45.455 0.00 0.00 39.61 2.66
2223 2723 1.790755 TCGTGTTTCCGACAATGGAG 58.209 50.000 0.00 0.00 40.65 3.86
2287 2787 5.756833 TGACTGATGATGATACAATGTGCTC 59.243 40.000 0.00 0.00 0.00 4.26
2360 2860 4.162131 TGCAAGTCTGACCAATGCTAGATA 59.838 41.667 22.77 7.59 37.86 1.98
2401 2901 3.342377 TTCACAAGTCAGTGTTCACCA 57.658 42.857 0.00 0.00 40.37 4.17
2524 3024 7.055667 TCTATCAAGGTATAACTGAAGCCAG 57.944 40.000 0.00 0.00 45.76 4.85
2544 3046 6.884295 AGCCAGTTTATTCAACTATGCAGTTA 59.116 34.615 0.00 0.00 44.60 2.24
2567 3069 3.765381 TGTGGTGTTCATGATGAATGGT 58.235 40.909 11.46 0.00 38.79 3.55
2698 3201 8.158132 TGTTACTGTCCCAAATTATTCAGTGTA 58.842 33.333 6.52 0.00 36.89 2.90
2736 3239 4.301072 AGCAAAGCAAGTATACCCTGAA 57.699 40.909 0.00 0.00 0.00 3.02
2783 3286 3.243704 GCTGTTCCACATTTGTAAGCCAA 60.244 43.478 0.00 0.00 0.00 4.52
2800 3303 5.649782 AGCCAATTTGGTTTCTGTATCTG 57.350 39.130 16.62 0.00 40.46 2.90
2816 3319 5.595885 TGTATCTGTCTTTGATGCTAGCTC 58.404 41.667 17.23 11.33 0.00 4.09
2821 3324 6.643388 TCTGTCTTTGATGCTAGCTCATTAA 58.357 36.000 17.23 2.18 0.00 1.40
2951 3454 1.758936 CTGATGAGCAGGCCATTTCA 58.241 50.000 5.01 5.43 41.07 2.69
3042 3545 7.587629 CATTTCTGTTTCACTCTTGCTCATAA 58.412 34.615 0.00 0.00 0.00 1.90
3071 3574 7.573710 TCTATTTGCATGGGAACTAATGTACT 58.426 34.615 0.00 0.00 0.00 2.73
3072 3575 8.710239 TCTATTTGCATGGGAACTAATGTACTA 58.290 33.333 0.00 0.00 0.00 1.82
3197 3700 3.568853 CAGAATTGGAGAAGGGATGCATC 59.431 47.826 18.81 18.81 0.00 3.91
3272 3775 2.230992 TGCTGACAAGTGTGTGCTTTTT 59.769 40.909 0.00 0.00 38.41 1.94
3454 3957 6.318900 GGGTAAGTCTTTTATGATGGTTCCTG 59.681 42.308 0.00 0.00 0.00 3.86
3512 4015 6.696411 TGTAAGGTTTATCATTTTGCCTTGG 58.304 36.000 0.00 0.00 37.01 3.61
3554 4057 8.895932 ATTGATTTGCTAATACTGTTTCGAAC 57.104 30.769 0.00 0.00 0.00 3.95
3555 4058 7.428282 TGATTTGCTAATACTGTTTCGAACA 57.572 32.000 0.00 0.00 39.52 3.18
3556 4059 8.039603 TGATTTGCTAATACTGTTTCGAACAT 57.960 30.769 0.00 0.00 41.26 2.71
3557 4060 7.962373 TGATTTGCTAATACTGTTTCGAACATG 59.038 33.333 0.00 0.00 41.26 3.21
3559 4062 6.795098 TGCTAATACTGTTTCGAACATGTT 57.205 33.333 11.78 11.78 41.26 2.71
3560 4063 6.598525 TGCTAATACTGTTTCGAACATGTTG 58.401 36.000 17.58 8.66 41.26 3.33
3616 4120 3.228188 TGCCTTTGTTGAGGATTCTGT 57.772 42.857 0.00 0.00 39.25 3.41
3617 4121 2.886523 TGCCTTTGTTGAGGATTCTGTG 59.113 45.455 0.00 0.00 39.25 3.66
3620 4124 4.037923 GCCTTTGTTGAGGATTCTGTGAAA 59.962 41.667 0.00 0.00 39.25 2.69
3626 4130 4.008074 TGAGGATTCTGTGAAACCTGTC 57.992 45.455 12.70 2.50 34.36 3.51
3646 4150 1.404748 CTGTGCATGTTTGGTGACACA 59.595 47.619 8.08 0.00 42.67 3.72
3648 4152 2.429971 TGTGCATGTTTGGTGACACAAT 59.570 40.909 8.08 0.00 42.67 2.71
3669 4173 6.260936 ACAATGCTTACCACACTGATATTAGC 59.739 38.462 0.00 0.00 0.00 3.09
3691 4195 7.425224 AGCTGATAGACTTTAAGCCTAAGAA 57.575 36.000 0.00 0.00 34.35 2.52
3755 4259 3.322828 ACAATGCTTTCATTTGCCTCACT 59.677 39.130 0.00 0.00 40.74 3.41
3771 4275 5.838521 TGCCTCACTGGATCATAGTTATGTA 59.161 40.000 0.00 0.00 38.35 2.29
4209 4720 5.873712 TGCATGTTCAATCAACTTGTTTGTT 59.126 32.000 10.88 0.00 40.65 2.83
4211 4722 6.035866 GCATGTTCAATCAACTTGTTTGTTCA 59.964 34.615 10.88 11.02 40.65 3.18
4477 4991 9.920946 AGATAATAGCTTTTCTTGGGAAACATA 57.079 29.630 0.00 0.00 40.63 2.29
4479 4993 6.775594 ATAGCTTTTCTTGGGAAACATACC 57.224 37.500 0.00 0.00 40.63 2.73
4483 4997 5.475564 GCTTTTCTTGGGAAACATACCTGTA 59.524 40.000 0.00 0.00 40.63 2.74
4490 5004 7.893302 TCTTGGGAAACATACCTGTATCATTTT 59.107 33.333 0.00 0.00 33.36 1.82
4496 5010 9.503427 GAAACATACCTGTATCATTTTGCTAAC 57.497 33.333 0.00 0.00 33.36 2.34
4497 5011 8.807948 AACATACCTGTATCATTTTGCTAACT 57.192 30.769 0.00 0.00 33.36 2.24
4682 5196 1.336240 GCAGGTGTGTTTTCAGCCATC 60.336 52.381 0.00 0.00 36.62 3.51
4736 5250 8.821686 TTGGATGTGATAATTCCAAGTATTGT 57.178 30.769 0.00 0.00 46.99 2.71
4737 5251 8.821686 TGGATGTGATAATTCCAAGTATTGTT 57.178 30.769 0.00 0.00 46.99 2.83
4953 5468 5.159209 CCTGATTCACAAGCTGTTTTGATC 58.841 41.667 0.00 0.00 0.00 2.92
5287 5802 1.325943 GAAGCGCTTTTCAGGAGATCG 59.674 52.381 25.84 0.00 0.00 3.69
5312 5827 9.182933 CGAAGGTATATGCTTCTAAGAGTTTAC 57.817 37.037 0.00 0.00 0.00 2.01
5499 6014 8.190784 GGCAATGTTCTTAACAACTATGCTAAT 58.809 33.333 16.92 0.00 45.86 1.73
5570 6085 4.130118 CTGGTCATCAGGTTAGCCATTAC 58.870 47.826 0.00 0.00 39.76 1.89
5571 6086 3.780294 TGGTCATCAGGTTAGCCATTACT 59.220 43.478 0.00 0.00 37.19 2.24
5587 6102 3.955771 TTACTCGCAACAAAACCACTC 57.044 42.857 0.00 0.00 0.00 3.51
5602 6117 3.005554 ACCACTCTCTTGCATTTCATCG 58.994 45.455 0.00 0.00 0.00 3.84
5603 6118 2.223203 CCACTCTCTTGCATTTCATCGC 60.223 50.000 0.00 0.00 0.00 4.58
5618 6166 7.646314 CATTTCATCGCCTCATCTTCTAATTT 58.354 34.615 0.00 0.00 0.00 1.82
5710 6258 0.250989 CGGTTCCTTAAAGGGGCACA 60.251 55.000 0.00 0.00 35.59 4.57
5742 6290 3.138128 GCCGTGCCATTGTACCCC 61.138 66.667 0.00 0.00 0.00 4.95
5981 6529 2.202623 CAGTGCCGCTACGAGGTC 60.203 66.667 0.00 0.00 0.00 3.85
6104 6652 6.238869 GCCAGTTCACTTCTTTCTTTGATCTT 60.239 38.462 0.00 0.00 0.00 2.40
6313 6869 6.097270 TGCTGATCTTTTATCCCTGGAAATTG 59.903 38.462 0.00 0.00 0.00 2.32
6325 6881 4.019174 CCTGGAAATTGATTAGGTGCTGT 58.981 43.478 0.00 0.00 0.00 4.40
6417 6977 1.697432 CCACCTTACCCTCTGTGTCAA 59.303 52.381 0.00 0.00 0.00 3.18
6424 6984 2.902608 ACCCTCTGTGTCAATCCAGTA 58.097 47.619 0.00 0.00 0.00 2.74
6463 7024 5.643379 TTTGCTTGGTGATACATTTCCTC 57.357 39.130 0.00 0.00 0.00 3.71
6467 7028 3.281727 TGGTGATACATTTCCTCTGGC 57.718 47.619 0.00 0.00 0.00 4.85
6474 7035 1.822990 ACATTTCCTCTGGCAGCAATG 59.177 47.619 10.34 16.03 31.64 2.82
6480 7041 1.460504 CTCTGGCAGCAATGTGTGAT 58.539 50.000 10.34 0.00 0.00 3.06
6499 7062 7.174253 TGTGTGATAATAACCAAGTTCTGTTCC 59.826 37.037 0.00 0.00 0.00 3.62
6507 7070 1.521423 CAAGTTCTGTTCCGTGTCGAC 59.479 52.381 9.11 9.11 0.00 4.20
6589 7152 3.036429 GCAGAAGAGGGCGGTCCAT 62.036 63.158 0.00 0.00 38.24 3.41
6787 7354 8.578151 AGGATTTTGTATAGTAGCAGTAGTAGC 58.422 37.037 0.00 0.00 0.00 3.58
6806 7378 0.038166 CAGCTTCAGGCCCTTGGTAA 59.962 55.000 0.00 0.00 43.05 2.85
6816 7388 5.012768 TCAGGCCCTTGGTAATAGTTATAGC 59.987 44.000 0.00 0.00 0.00 2.97
6922 7619 1.072331 GTTCATGTGTCCCCAGTCACT 59.928 52.381 0.00 0.00 33.75 3.41
6952 7651 6.049149 GCAGCTGTATATTTTGTCTAGTGGA 58.951 40.000 16.64 0.00 0.00 4.02
6991 7690 7.336931 CGAAGGAGAAATCTTGGGAAGAATTTA 59.663 37.037 0.00 0.00 41.63 1.40
7031 7731 6.814043 TGATCCTCTGTTCAATCATAGAGTG 58.186 40.000 0.00 0.00 35.93 3.51
7052 7752 9.820725 AGAGTGAAAAATTCATCATTTGTGAAA 57.179 25.926 0.00 0.00 42.47 2.69
7054 7754 8.553696 AGTGAAAAATTCATCATTTGTGAAAGC 58.446 29.630 0.00 0.00 42.47 3.51
7055 7755 7.799914 GTGAAAAATTCATCATTTGTGAAAGCC 59.200 33.333 0.00 0.00 42.47 4.35
7101 7801 4.357918 ACAACTTCCACTATCACAGCTT 57.642 40.909 0.00 0.00 0.00 3.74
7180 7880 1.745264 GGCGAGCTCAGCTAGGAAT 59.255 57.895 23.23 0.00 39.88 3.01
7183 7883 0.599728 CGAGCTCAGCTAGGAATGCC 60.600 60.000 15.40 0.00 39.88 4.40
7185 7885 1.140652 GAGCTCAGCTAGGAATGCCTT 59.859 52.381 9.40 0.00 45.98 4.35
7475 8190 4.284860 CGCGCCGGATCATCCTCA 62.285 66.667 5.05 0.00 33.30 3.86
7476 8191 2.356793 GCGCCGGATCATCCTCAG 60.357 66.667 5.05 0.00 33.30 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.254455 GCTTCGTCACACTTATATTGTATTGCT 60.254 37.037 0.00 0.00 0.00 3.91
5 6 6.200286 CGGCTTCGTCACACTTATATTGTATT 59.800 38.462 0.00 0.00 0.00 1.89
12 13 2.488937 TCACGGCTTCGTCACACTTATA 59.511 45.455 0.00 0.00 46.38 0.98
19 20 2.334838 AGTTATTCACGGCTTCGTCAC 58.665 47.619 0.00 0.00 46.38 3.67
28 29 4.556898 CGATGGAGGTAGAGTTATTCACGG 60.557 50.000 0.00 0.00 0.00 4.94
33 34 4.205587 ACGTCGATGGAGGTAGAGTTATT 58.794 43.478 9.90 0.00 39.36 1.40
36 37 2.125773 ACGTCGATGGAGGTAGAGTT 57.874 50.000 9.90 0.00 39.36 3.01
45 46 2.941064 CCTAGTCAACTACGTCGATGGA 59.059 50.000 9.90 0.00 0.00 3.41
49 50 4.456911 ACAAATCCTAGTCAACTACGTCGA 59.543 41.667 0.00 0.00 0.00 4.20
58 59 5.045869 CCCTCAGGTTACAAATCCTAGTCAA 60.046 44.000 0.00 0.00 32.26 3.18
59 60 4.469945 CCCTCAGGTTACAAATCCTAGTCA 59.530 45.833 0.00 0.00 32.26 3.41
60 61 4.715297 TCCCTCAGGTTACAAATCCTAGTC 59.285 45.833 0.00 0.00 32.26 2.59
66 67 2.356844 GGGGTCCCTCAGGTTACAAATC 60.357 54.545 8.15 0.00 0.00 2.17
78 79 9.544579 GGTATATATAATATACTGGGGTCCCTC 57.455 40.741 8.15 0.00 36.94 4.30
89 90 7.093596 GCCCAGACCCCGGTATATATAATATAC 60.094 44.444 0.00 8.07 0.00 1.47
101 102 2.281091 CTAGCCCAGACCCCGGTA 59.719 66.667 0.00 0.00 0.00 4.02
111 112 7.956328 ATAAGATGTTATATCGACTAGCCCA 57.044 36.000 0.00 0.00 0.00 5.36
137 138 8.553153 TGTATGAACCAAGGGATTGTTCTATTA 58.447 33.333 0.00 0.00 0.00 0.98
140 141 6.381498 TGTATGAACCAAGGGATTGTTCTA 57.619 37.500 0.00 0.00 0.00 2.10
142 143 5.418840 ACATGTATGAACCAAGGGATTGTTC 59.581 40.000 0.00 0.00 0.00 3.18
143 144 5.332743 ACATGTATGAACCAAGGGATTGTT 58.667 37.500 0.00 0.00 0.00 2.83
174 175 5.284861 TGTGTATAATGCGATAAGGGTGT 57.715 39.130 0.00 0.00 0.00 4.16
185 186 3.185188 CCACTCTCGCATGTGTATAATGC 59.815 47.826 6.09 0.00 45.62 3.56
186 187 3.742882 CCCACTCTCGCATGTGTATAATG 59.257 47.826 6.09 0.40 32.76 1.90
188 189 2.102420 CCCCACTCTCGCATGTGTATAA 59.898 50.000 6.09 0.00 32.76 0.98
200 201 1.204146 TGAGGTAATGCCCCACTCTC 58.796 55.000 0.00 0.00 38.26 3.20
201 202 1.668826 TTGAGGTAATGCCCCACTCT 58.331 50.000 0.00 0.00 38.26 3.24
202 203 2.576615 GATTGAGGTAATGCCCCACTC 58.423 52.381 0.00 0.00 38.26 3.51
203 204 1.134098 CGATTGAGGTAATGCCCCACT 60.134 52.381 0.00 0.00 38.26 4.00
204 205 1.308998 CGATTGAGGTAATGCCCCAC 58.691 55.000 0.00 0.00 38.26 4.61
205 206 0.916086 ACGATTGAGGTAATGCCCCA 59.084 50.000 0.00 0.00 38.26 4.96
206 207 1.134220 TCACGATTGAGGTAATGCCCC 60.134 52.381 0.00 0.00 38.26 5.80
207 208 2.213499 CTCACGATTGAGGTAATGCCC 58.787 52.381 0.00 0.00 45.06 5.36
224 225 0.040058 TACCTAGGTTCGTGCCCTCA 59.960 55.000 22.11 0.00 33.35 3.86
229 230 4.694037 AGACAAATTTACCTAGGTTCGTGC 59.306 41.667 22.11 8.03 0.00 5.34
231 232 5.247792 AGGAGACAAATTTACCTAGGTTCGT 59.752 40.000 22.11 6.78 0.00 3.85
239 240 5.538813 GGGAAACAAGGAGACAAATTTACCT 59.461 40.000 0.00 0.00 31.26 3.08
247 248 3.071602 CAGAGAGGGAAACAAGGAGACAA 59.928 47.826 0.00 0.00 0.00 3.18
249 250 2.027653 CCAGAGAGGGAAACAAGGAGAC 60.028 54.545 0.00 0.00 0.00 3.36
250 251 2.260822 CCAGAGAGGGAAACAAGGAGA 58.739 52.381 0.00 0.00 0.00 3.71
261 262 1.118356 AGCGATTAGGCCAGAGAGGG 61.118 60.000 5.01 0.00 38.09 4.30
265 266 2.159366 CGGTATAGCGATTAGGCCAGAG 60.159 54.545 19.22 0.00 0.00 3.35
267 268 1.135083 CCGGTATAGCGATTAGGCCAG 60.135 57.143 25.01 1.66 0.00 4.85
268 269 0.892755 CCGGTATAGCGATTAGGCCA 59.107 55.000 25.01 0.00 0.00 5.36
269 270 1.135170 GTCCGGTATAGCGATTAGGCC 60.135 57.143 25.01 0.00 0.00 5.19
270 271 1.542915 TGTCCGGTATAGCGATTAGGC 59.457 52.381 25.01 10.56 0.00 3.93
271 272 2.094854 GGTGTCCGGTATAGCGATTAGG 60.095 54.545 25.01 8.42 0.00 2.69
272 273 2.094854 GGGTGTCCGGTATAGCGATTAG 60.095 54.545 25.01 8.78 0.00 1.73
283 284 2.362120 CTCGGTAGGGTGTCCGGT 60.362 66.667 0.00 0.00 45.79 5.28
296 297 1.670590 GATCTGGCAGATCCCTCGG 59.329 63.158 36.53 2.22 44.08 4.63
309 310 2.099921 CCTGGTGTCGGAACTAGATCTG 59.900 54.545 5.18 2.44 30.63 2.90
310 311 2.379972 CCTGGTGTCGGAACTAGATCT 58.620 52.381 0.00 0.00 30.63 2.75
318 319 0.036388 GAAGATGCCTGGTGTCGGAA 60.036 55.000 0.00 0.00 0.00 4.30
338 339 3.386768 TGAGCTTGTGTAACTGACCTC 57.613 47.619 0.00 0.00 38.04 3.85
354 355 1.200948 GTCTTGGATGTGCCTTTGAGC 59.799 52.381 0.00 0.00 37.63 4.26
371 383 3.825014 TCTAAGTGAAGGCTAACACGTCT 59.175 43.478 13.87 8.46 41.22 4.18
372 384 4.170292 TCTAAGTGAAGGCTAACACGTC 57.830 45.455 13.87 0.00 41.22 4.34
381 393 6.402222 TCTCTGAAAGAATCTAAGTGAAGGC 58.598 40.000 0.00 0.00 46.34 4.35
436 448 1.133606 AGACCTTTGCCTCGGGAAAAA 60.134 47.619 4.21 0.00 35.16 1.94
437 449 0.476771 AGACCTTTGCCTCGGGAAAA 59.523 50.000 4.21 0.00 35.16 2.29
438 450 0.476771 AAGACCTTTGCCTCGGGAAA 59.523 50.000 2.62 2.62 34.42 3.13
439 451 0.476771 AAAGACCTTTGCCTCGGGAA 59.523 50.000 0.00 0.00 0.00 3.97
440 452 1.354101 TAAAGACCTTTGCCTCGGGA 58.646 50.000 5.34 0.00 34.23 5.14
441 453 2.420058 ATAAAGACCTTTGCCTCGGG 57.580 50.000 5.34 0.00 34.23 5.14
442 454 5.183228 TCTAAATAAAGACCTTTGCCTCGG 58.817 41.667 5.34 0.00 34.23 4.63
443 455 6.238484 CCATCTAAATAAAGACCTTTGCCTCG 60.238 42.308 5.34 0.00 34.23 4.63
444 456 6.460261 GCCATCTAAATAAAGACCTTTGCCTC 60.460 42.308 5.34 0.00 34.23 4.70
445 457 5.360999 GCCATCTAAATAAAGACCTTTGCCT 59.639 40.000 5.34 0.00 34.23 4.75
446 458 5.360999 AGCCATCTAAATAAAGACCTTTGCC 59.639 40.000 5.34 0.00 34.23 4.52
447 459 6.268566 CAGCCATCTAAATAAAGACCTTTGC 58.731 40.000 5.34 0.00 34.23 3.68
448 460 6.378280 ACCAGCCATCTAAATAAAGACCTTTG 59.622 38.462 5.34 0.00 34.23 2.77
449 461 6.494059 ACCAGCCATCTAAATAAAGACCTTT 58.506 36.000 0.41 0.41 36.63 3.11
450 462 6.079712 ACCAGCCATCTAAATAAAGACCTT 57.920 37.500 0.00 0.00 0.00 3.50
451 463 5.717119 ACCAGCCATCTAAATAAAGACCT 57.283 39.130 0.00 0.00 0.00 3.85
527 970 2.161609 GGTGAGGTGAAAATTACAGCGG 59.838 50.000 8.40 0.00 40.12 5.52
529 972 2.414161 GCGGTGAGGTGAAAATTACAGC 60.414 50.000 6.64 6.64 36.23 4.40
558 1001 6.402658 GGAAAGTGAAAAGATTAGAAGAGCCG 60.403 42.308 0.00 0.00 0.00 5.52
563 1006 6.375736 GGGAGGGAAAGTGAAAAGATTAGAAG 59.624 42.308 0.00 0.00 0.00 2.85
606 1049 1.639298 CTTTTTGGCGCGAGAGGAGG 61.639 60.000 12.10 0.00 0.00 4.30
968 1411 3.626924 GCTCGGCGGGGATGGTAT 61.627 66.667 9.67 0.00 0.00 2.73
1277 1744 3.822192 CCCTGATCGTCGGCGTCA 61.822 66.667 10.18 11.77 39.49 4.35
1288 1755 1.617947 GCCTCGGTCTTCACCCTGAT 61.618 60.000 0.00 0.00 40.01 2.90
1300 1767 4.039357 CACGTCGACAGCCTCGGT 62.039 66.667 17.16 0.00 43.16 4.69
1308 1775 1.300620 CTTCTTGGGCACGTCGACA 60.301 57.895 17.16 0.00 0.00 4.35
1388 1855 0.032217 CTCCTCCTGCTTCTCCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
1389 1856 1.048160 CCTCCTCCTGCTTCTCCTCC 61.048 65.000 0.00 0.00 0.00 4.30
1390 1857 0.032615 TCCTCCTCCTGCTTCTCCTC 60.033 60.000 0.00 0.00 0.00 3.71
1391 1858 0.032217 CTCCTCCTCCTGCTTCTCCT 60.032 60.000 0.00 0.00 0.00 3.69
1392 1859 1.048160 CCTCCTCCTCCTGCTTCTCC 61.048 65.000 0.00 0.00 0.00 3.71
1393 1860 0.032615 TCCTCCTCCTCCTGCTTCTC 60.033 60.000 0.00 0.00 0.00 2.87
1394 1861 0.032217 CTCCTCCTCCTCCTGCTTCT 60.032 60.000 0.00 0.00 0.00 2.85
1395 1862 1.048160 CCTCCTCCTCCTCCTGCTTC 61.048 65.000 0.00 0.00 0.00 3.86
1396 1863 1.002792 CCTCCTCCTCCTCCTGCTT 59.997 63.158 0.00 0.00 0.00 3.91
1397 1864 1.938596 TCCTCCTCCTCCTCCTGCT 60.939 63.158 0.00 0.00 0.00 4.24
1398 1865 1.457455 CTCCTCCTCCTCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
1399 1866 1.232792 CCTCCTCCTCCTCCTCCTG 59.767 68.421 0.00 0.00 0.00 3.86
1400 1867 0.858139 AACCTCCTCCTCCTCCTCCT 60.858 60.000 0.00 0.00 0.00 3.69
1401 1868 0.935194 TAACCTCCTCCTCCTCCTCC 59.065 60.000 0.00 0.00 0.00 4.30
1402 1869 1.411930 GGTAACCTCCTCCTCCTCCTC 60.412 61.905 0.00 0.00 0.00 3.71
1481 1966 1.134530 GTCGTCGCAGTCCATCTTCG 61.135 60.000 0.00 0.00 34.38 3.79
2024 2515 1.134461 GCACCATGAGATGAGAGCAGT 60.134 52.381 0.00 0.00 0.00 4.40
2034 2525 0.804364 GTTCGCAATGCACCATGAGA 59.196 50.000 5.91 0.00 0.00 3.27
2035 2526 0.806868 AGTTCGCAATGCACCATGAG 59.193 50.000 5.91 0.00 0.00 2.90
2041 2541 2.838386 ATCATGAGTTCGCAATGCAC 57.162 45.000 5.91 0.00 0.00 4.57
2088 2588 8.526147 CATCAAAAGTTCCACAGGATTAAGATT 58.474 33.333 0.00 0.00 0.00 2.40
2098 2598 5.634859 GCAATAACCATCAAAAGTTCCACAG 59.365 40.000 0.00 0.00 0.00 3.66
2103 2603 6.470235 CGATCTGCAATAACCATCAAAAGTTC 59.530 38.462 0.00 0.00 0.00 3.01
2109 2609 4.149511 TCCGATCTGCAATAACCATCAA 57.850 40.909 0.00 0.00 0.00 2.57
2187 2687 4.030913 ACACGATCTTCCCCTGAATCTTA 58.969 43.478 0.00 0.00 0.00 2.10
2287 2787 6.441274 ACTAACAAAATCAATCACACAGCAG 58.559 36.000 0.00 0.00 0.00 4.24
2320 2820 4.023279 ACTTGCAGACAAAATTGTGCGATA 60.023 37.500 3.05 0.00 42.43 2.92
2323 2823 2.462889 ACTTGCAGACAAAATTGTGCG 58.537 42.857 3.05 0.00 42.43 5.34
2360 2860 7.607607 TGTGAATGTAGAAGCTGTATGAACAAT 59.392 33.333 0.00 0.00 34.49 2.71
2382 2882 3.342377 TTGGTGAACACTGACTTGTGA 57.658 42.857 4.96 0.00 40.12 3.58
2401 2901 2.154462 CAAGGATGAGTTGTCGCCTTT 58.846 47.619 0.00 0.00 37.76 3.11
2524 3024 9.289303 CCACAATAACTGCATAGTTGAATAAAC 57.711 33.333 1.78 0.00 46.28 2.01
2544 3046 4.773674 ACCATTCATCATGAACACCACAAT 59.226 37.500 0.98 0.00 39.45 2.71
2567 3069 7.541783 GCAAAACAAGCATGTATACTGAATCAA 59.458 33.333 4.17 0.00 39.40 2.57
2698 3201 6.994496 TGCTTTGCTATAGATGCTAAAGACAT 59.006 34.615 3.21 0.00 34.10 3.06
2736 3239 9.045223 GCAACAGAAAACAAGAGGATTTAATTT 57.955 29.630 0.00 0.00 0.00 1.82
2783 3286 8.517878 CATCAAAGACAGATACAGAAACCAAAT 58.482 33.333 0.00 0.00 0.00 2.32
2800 3303 9.578439 AATTTTTAATGAGCTAGCATCAAAGAC 57.422 29.630 18.83 0.00 0.00 3.01
2951 3454 4.677673 AATTTTGTTCAAGGCAGCTTCT 57.322 36.364 0.00 0.00 0.00 2.85
3042 3545 8.220559 ACATTAGTTCCCATGCAAATAGAGTAT 58.779 33.333 0.00 0.00 0.00 2.12
3454 3957 5.835113 AATGTAAACCAGGCACATACATC 57.165 39.130 3.03 0.00 36.47 3.06
3492 3995 5.960202 AGATCCAAGGCAAAATGATAAACCT 59.040 36.000 0.00 0.00 0.00 3.50
3616 4120 2.346766 ACATGCACAGACAGGTTTCA 57.653 45.000 0.00 0.00 28.39 2.69
3620 4124 1.321474 CCAAACATGCACAGACAGGT 58.679 50.000 0.00 0.00 35.80 4.00
3626 4130 1.404748 TGTGTCACCAAACATGCACAG 59.595 47.619 0.00 0.00 32.73 3.66
3646 4150 6.484643 CAGCTAATATCAGTGTGGTAAGCATT 59.515 38.462 10.54 0.00 0.00 3.56
3648 4152 5.128663 TCAGCTAATATCAGTGTGGTAAGCA 59.871 40.000 10.54 0.00 0.00 3.91
3669 4173 9.823647 TCATTTCTTAGGCTTAAAGTCTATCAG 57.176 33.333 0.00 0.00 31.68 2.90
3733 4237 3.322828 AGTGAGGCAAATGAAAGCATTGT 59.677 39.130 0.00 0.00 43.71 2.71
4223 4734 6.310467 AGTGCTCACATTATTTACGTGTAGTG 59.690 38.462 0.00 0.00 32.42 2.74
4415 4928 9.131791 ACATAAAAGACCATTGACAAACTTACT 57.868 29.630 0.00 0.00 0.00 2.24
4477 4991 8.677300 CACATTAGTTAGCAAAATGATACAGGT 58.323 33.333 10.31 0.00 35.18 4.00
4479 4993 8.677300 ACCACATTAGTTAGCAAAATGATACAG 58.323 33.333 10.31 0.00 35.18 2.74
4483 4997 7.834181 AGGTACCACATTAGTTAGCAAAATGAT 59.166 33.333 15.94 0.00 35.18 2.45
4490 5004 5.012251 TGTGAAGGTACCACATTAGTTAGCA 59.988 40.000 15.94 3.16 39.36 3.49
4496 5010 4.819105 TCCTGTGAAGGTACCACATTAG 57.181 45.455 15.94 14.48 42.79 1.73
4497 5011 4.080582 CCATCCTGTGAAGGTACCACATTA 60.081 45.833 15.94 6.74 42.79 1.90
4521 5035 1.055849 TCCTGTGAAAGGCACTGCTA 58.944 50.000 0.00 0.00 46.92 3.49
4682 5196 8.833976 TGTGATGTAATACAAATACAAATGCG 57.166 30.769 0.00 0.00 36.88 4.73
4755 5269 5.799827 TCCAAAAACTACAAAAGGATGGG 57.200 39.130 0.00 0.00 0.00 4.00
4768 5282 9.515226 TCATATAAGCTACTGTTTCCAAAAACT 57.485 29.630 0.00 0.00 44.23 2.66
4928 5443 4.036734 TCAAAACAGCTTGTGAATCAGGTC 59.963 41.667 0.00 0.00 0.00 3.85
4953 5468 1.118838 CTTCTGCCACCTAGAGGGAG 58.881 60.000 13.99 13.99 45.03 4.30
5287 5802 9.182933 CGTAAACTCTTAGAAGCATATACCTTC 57.817 37.037 6.80 6.80 39.13 3.46
5312 5827 4.565022 ACTAATCAACAAAATTTGGCCCG 58.435 39.130 10.71 0.00 34.12 6.13
5499 6014 6.761099 AGACGAAGAAGTAGCTCAAGAATA 57.239 37.500 0.00 0.00 0.00 1.75
5567 6082 3.537580 AGAGTGGTTTTGTTGCGAGTAA 58.462 40.909 0.00 0.00 0.00 2.24
5570 6085 2.213499 AGAGAGTGGTTTTGTTGCGAG 58.787 47.619 0.00 0.00 0.00 5.03
5571 6086 2.325583 AGAGAGTGGTTTTGTTGCGA 57.674 45.000 0.00 0.00 0.00 5.10
5587 6102 2.011947 TGAGGCGATGAAATGCAAGAG 58.988 47.619 0.00 0.00 0.00 2.85
5602 6117 6.094603 TCAGCAAAGAAATTAGAAGATGAGGC 59.905 38.462 0.00 0.00 0.00 4.70
5603 6118 7.621428 TCAGCAAAGAAATTAGAAGATGAGG 57.379 36.000 0.00 0.00 0.00 3.86
5618 6166 7.208777 TGCATATTTTGAAAGTTCAGCAAAGA 58.791 30.769 2.08 0.00 38.61 2.52
5660 6208 2.350522 TCGTCTAGGTCGGTGTACTTC 58.649 52.381 0.00 0.00 0.00 3.01
5710 6258 2.569059 CACGGCATCCAGAATCATTCT 58.431 47.619 0.00 0.00 41.70 2.40
5742 6290 2.180204 CCTCTACAAATGCCCGCGG 61.180 63.158 21.04 21.04 0.00 6.46
5747 6295 2.906354 ACGACATCCTCTACAAATGCC 58.094 47.619 0.00 0.00 0.00 4.40
5906 6454 4.632974 CGGCAGATAGGGCAGGCC 62.633 72.222 4.33 4.33 41.20 5.19
5981 6529 0.878523 TCCAGTTGTTCTTGGCGTCG 60.879 55.000 0.00 0.00 0.00 5.12
6104 6652 2.041620 CTGGTTCAAGGGGATCTCCAAA 59.958 50.000 15.83 1.90 37.91 3.28
6286 6836 4.526970 TCCAGGGATAAAAGATCAGCAAC 58.473 43.478 0.00 0.00 0.00 4.17
6313 6869 4.256920 AGTGACATCAACAGCACCTAATC 58.743 43.478 0.00 0.00 31.85 1.75
6325 6881 3.405831 CTCCAGCTTTGAGTGACATCAA 58.594 45.455 2.42 0.00 37.41 2.57
6409 6969 6.427853 TCACTGAATTTACTGGATTGACACAG 59.572 38.462 0.00 0.00 40.48 3.66
6417 6977 9.574516 AAAAGTAGTTCACTGAATTTACTGGAT 57.425 29.630 14.72 6.69 37.63 3.41
6424 6984 6.980397 CCAAGCAAAAGTAGTTCACTGAATTT 59.020 34.615 0.00 0.00 37.63 1.82
6463 7024 5.276270 GTTATTATCACACATTGCTGCCAG 58.724 41.667 0.00 0.00 0.00 4.85
6467 7028 6.855836 ACTTGGTTATTATCACACATTGCTG 58.144 36.000 0.00 0.00 0.00 4.41
6474 7035 7.527457 GGAACAGAACTTGGTTATTATCACAC 58.473 38.462 0.00 0.00 0.00 3.82
6480 7041 5.613329 ACACGGAACAGAACTTGGTTATTA 58.387 37.500 0.00 0.00 0.00 0.98
6589 7152 1.080093 GACGATGAACCGCCTCACA 60.080 57.895 0.00 0.00 0.00 3.58
6787 7354 0.038166 TTACCAAGGGCCTGAAGCTG 59.962 55.000 6.92 0.00 43.05 4.24
6816 7388 4.021016 GGCCATCTTCCCTACATACTACTG 60.021 50.000 0.00 0.00 0.00 2.74
6922 7619 2.689471 CAAAATATACAGCTGCCTGGCA 59.311 45.455 21.96 21.96 43.53 4.92
6952 7651 9.844257 AGATTTCTCCTTCGAATTCAAGATAAT 57.156 29.630 15.13 3.35 0.00 1.28
7031 7731 8.091385 AGGCTTTCACAAATGATGAATTTTTC 57.909 30.769 0.00 0.00 36.28 2.29
7101 7801 8.729756 CATCACCATGAATCTGTAAACTTGTAA 58.270 33.333 0.00 0.00 30.57 2.41
7171 7871 1.153086 CGCCAAGGCATTCCTAGCT 60.153 57.895 12.19 0.00 43.40 3.32


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

AutoCloner maintained by Alex Coulton.