Multiple sequence alignment - TraesCS2B01G497800

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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 TraesCS2B01G497800 chr2B 100.000 4611 0 0 1 4611 694276662 694272052 0.000000e+00 8516.0
1 TraesCS2B01G497800 chr2B 82.258 186 28 4 2954 3138 430750009 430749828 6.180000e-34 156.0
2 TraesCS2B01G497800 chr2A 89.264 2785 169 52 51 2798 715416949 715414258 0.000000e+00 3367.0
3 TraesCS2B01G497800 chr2A 89.626 935 77 13 2819 3746 715414184 715413263 0.000000e+00 1171.0
4 TraesCS2B01G497800 chr2A 87.827 764 60 15 3841 4596 715413263 715412525 0.000000e+00 865.0
5 TraesCS2B01G497800 chr2D 92.234 1777 87 19 330 2088 577338910 577337167 0.000000e+00 2470.0
6 TraesCS2B01G497800 chr2D 89.597 1711 143 23 2922 4611 577335622 577333926 0.000000e+00 2141.0
7 TraesCS2B01G497800 chr2D 85.696 762 61 13 2088 2819 577336554 577335811 0.000000e+00 760.0
8 TraesCS2B01G497800 chr2D 88.000 200 23 1 330 528 600340786 600340985 7.710000e-58 235.0
9 TraesCS2B01G497800 chr2D 95.652 46 2 0 1 46 334075441 334075486 1.780000e-09 75.0
10 TraesCS2B01G497800 chr7A 89.952 209 19 2 321 528 293302425 293302632 7.600000e-68 268.0
11 TraesCS2B01G497800 chr7A 100.000 41 0 0 4 44 53297030 53296990 4.950000e-10 76.8
12 TraesCS2B01G497800 chr6B 87.981 208 24 1 325 531 468029667 468029460 1.280000e-60 244.0
13 TraesCS2B01G497800 chr6B 86.486 74 10 0 1160 1233 688372548 688372621 1.060000e-11 82.4
14 TraesCS2B01G497800 chr4B 86.603 209 26 2 332 539 525268371 525268164 3.590000e-56 230.0
15 TraesCS2B01G497800 chr4B 86.124 209 27 2 332 539 525304558 525304765 1.670000e-54 224.0
16 TraesCS2B01G497800 chr4B 86.124 209 27 2 332 539 525390125 525389918 1.670000e-54 224.0
17 TraesCS2B01G497800 chr4B 73.061 245 51 10 80 318 500523278 500523513 6.400000e-09 73.1
18 TraesCS2B01G497800 chr4B 93.617 47 3 0 1 47 426431805 426431851 2.300000e-08 71.3
19 TraesCS2B01G497800 chr4B 100.000 28 0 0 82 109 500523499 500523472 8.000000e-03 52.8
20 TraesCS2B01G497800 chr1D 86.893 206 24 2 324 528 486144660 486144863 1.290000e-55 228.0
21 TraesCS2B01G497800 chr1D 82.162 185 33 0 2949 3133 42589971 42590155 4.780000e-35 159.0
22 TraesCS2B01G497800 chr1D 90.000 70 6 1 83 151 203454221 203454152 6.350000e-14 89.8
23 TraesCS2B01G497800 chr6A 86.022 186 22 4 2950 3132 187900185 187900369 3.640000e-46 196.0
24 TraesCS2B01G497800 chr6A 86.486 74 10 0 1160 1233 599059731 599059804 1.060000e-11 82.4
25 TraesCS2B01G497800 chr1A 87.662 154 19 0 2971 3124 532763088 532762935 3.670000e-41 180.0
26 TraesCS2B01G497800 chr7D 85.799 169 20 1 2950 3114 5094468 5094636 4.740000e-40 176.0
27 TraesCS2B01G497800 chr7D 82.564 195 29 3 2950 3144 429573584 429573395 2.850000e-37 167.0
28 TraesCS2B01G497800 chr7D 100.000 28 0 0 82 109 448509765 448509738 8.000000e-03 52.8
29 TraesCS2B01G497800 chrUn 80.000 210 35 7 2947 3156 15316243 15316445 1.030000e-31 148.0
30 TraesCS2B01G497800 chr6D 86.486 74 10 0 1160 1233 453021921 453021994 1.060000e-11 82.4
31 TraesCS2B01G497800 chr3B 95.918 49 2 0 1 49 75767901 75767949 3.820000e-11 80.5
32 TraesCS2B01G497800 chr5A 97.727 44 0 1 1 44 592671764 592671806 1.780000e-09 75.0
33 TraesCS2B01G497800 chr3D 95.556 45 2 0 4 48 504494808 504494764 6.400000e-09 73.1
34 TraesCS2B01G497800 chr3D 94.444 36 0 2 82 115 505570265 505570300 2.000000e-03 54.7
35 TraesCS2B01G497800 chr4D 95.455 44 2 0 1 44 487352391 487352434 2.300000e-08 71.3
36 TraesCS2B01G497800 chr1B 93.617 47 3 0 1 47 273460537 273460583 2.300000e-08 71.3
37 TraesCS2B01G497800 chr1B 93.617 47 3 0 1 47 273562694 273562740 2.300000e-08 71.3
38 TraesCS2B01G497800 chr7B 96.970 33 0 1 82 113 732698168 732698200 2.000000e-03 54.7
39 TraesCS2B01G497800 chr5D 96.875 32 0 1 82 112 57575824 57575855 8.000000e-03 52.8


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 TraesCS2B01G497800 chr2B 694272052 694276662 4610 True 8516.000000 8516 100.000000 1 4611 1 chr2B.!!$R2 4610
1 TraesCS2B01G497800 chr2A 715412525 715416949 4424 True 1801.000000 3367 88.905667 51 4596 3 chr2A.!!$R1 4545
2 TraesCS2B01G497800 chr2D 577333926 577338910 4984 True 1790.333333 2470 89.175667 330 4611 3 chr2D.!!$R1 4281

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
447 449 0.524414 AATTTTTGCTCCCGCCGTAC 59.476 50.0 0.00 0.0 34.43 3.67 F
1479 1487 0.305313 GCAACGCCACTGTTTTCGTA 59.695 50.0 0.00 0.0 34.50 3.43 F
2501 3151 0.942962 GTGGCACATGATAGCTCAGC 59.057 55.0 13.86 0.0 44.52 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 1932 0.323629 CGGTAGGTGTGGATGGTTGT 59.676 55.0 0.0 0.0 0.0 3.32 R
3343 4102 0.034896 GGTCGAAGTCTGCCCAAGAA 59.965 55.0 0.0 0.0 36.4 2.52 R
3784 4552 0.539438 ACATGGGCATCACAAACCGT 60.539 50.0 0.0 0.0 0.0 4.83 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
37 38 6.698359 TTTTAAAATTGCATGCTACGTTCC 57.302 33.333 20.33 0.00 0.00 3.62
38 39 5.637006 TTAAAATTGCATGCTACGTTCCT 57.363 34.783 20.33 0.00 0.00 3.36
39 40 3.764885 AAATTGCATGCTACGTTCCTC 57.235 42.857 20.33 0.00 0.00 3.71
40 41 2.401583 ATTGCATGCTACGTTCCTCA 57.598 45.000 20.33 0.00 0.00 3.86
41 42 2.177394 TTGCATGCTACGTTCCTCAA 57.823 45.000 20.33 0.00 0.00 3.02
42 43 1.438651 TGCATGCTACGTTCCTCAAC 58.561 50.000 20.33 0.00 0.00 3.18
43 44 1.270571 TGCATGCTACGTTCCTCAACA 60.271 47.619 20.33 0.00 32.14 3.33
44 45 1.128692 GCATGCTACGTTCCTCAACAC 59.871 52.381 11.37 0.00 32.14 3.32
45 46 2.688507 CATGCTACGTTCCTCAACACT 58.311 47.619 0.00 0.00 32.14 3.55
46 47 2.902705 TGCTACGTTCCTCAACACTT 57.097 45.000 0.00 0.00 32.14 3.16
47 48 3.188159 TGCTACGTTCCTCAACACTTT 57.812 42.857 0.00 0.00 32.14 2.66
48 49 3.537580 TGCTACGTTCCTCAACACTTTT 58.462 40.909 0.00 0.00 32.14 2.27
49 50 3.311322 TGCTACGTTCCTCAACACTTTTG 59.689 43.478 0.00 0.00 32.14 2.44
50 51 3.558418 GCTACGTTCCTCAACACTTTTGA 59.442 43.478 0.00 0.00 32.14 2.69
51 52 4.552184 GCTACGTTCCTCAACACTTTTGAC 60.552 45.833 0.00 0.00 32.14 3.18
52 53 3.606687 ACGTTCCTCAACACTTTTGACT 58.393 40.909 0.00 0.00 32.14 3.41
53 54 4.007659 ACGTTCCTCAACACTTTTGACTT 58.992 39.130 0.00 0.00 32.14 3.01
54 55 4.094442 ACGTTCCTCAACACTTTTGACTTC 59.906 41.667 0.00 0.00 32.14 3.01
55 56 4.332819 CGTTCCTCAACACTTTTGACTTCT 59.667 41.667 0.00 0.00 32.14 2.85
61 62 5.182487 TCAACACTTTTGACTTCTACTGCA 58.818 37.500 0.00 0.00 0.00 4.41
78 79 8.008513 TCTACTGCAGGACTAAAACTATTAGG 57.991 38.462 19.93 0.00 0.00 2.69
79 80 5.429130 ACTGCAGGACTAAAACTATTAGGC 58.571 41.667 19.93 0.00 0.00 3.93
94 95 6.525629 ACTATTAGGCCATGATAAGTGACAC 58.474 40.000 5.01 0.00 0.00 3.67
116 117 2.316237 TGTGGCACGAACACATGAC 58.684 52.632 13.77 0.00 43.35 3.06
123 124 3.549827 GGCACGAACACATGACAATTTCA 60.550 43.478 0.00 0.00 39.11 2.69
127 128 5.514559 CACGAACACATGACAATTTCAAACA 59.485 36.000 0.00 0.00 37.92 2.83
166 167 1.135721 GTAACCTAACGCGAGGATGGT 59.864 52.381 19.78 13.21 39.15 3.55
172 173 2.005971 AACGCGAGGATGGTAACTTC 57.994 50.000 15.93 0.00 39.93 3.01
202 203 5.009510 TGAAGCATGACAATTTCCTTTTCGA 59.990 36.000 0.00 0.00 0.00 3.71
208 209 7.063780 GCATGACAATTTCCTTTTCGAATTCAT 59.936 33.333 6.22 0.00 0.00 2.57
253 254 3.552604 TCGGATTGCAACTTTAACTGC 57.447 42.857 0.00 0.00 39.09 4.40
269 270 2.927028 ACTGCAAAAACGTTAGGTCCT 58.073 42.857 0.00 0.00 0.00 3.85
278 279 7.597369 GCAAAAACGTTAGGTCCTGATTATTTT 59.403 33.333 0.00 1.62 0.00 1.82
279 280 8.911662 CAAAAACGTTAGGTCCTGATTATTTTG 58.088 33.333 0.00 9.92 0.00 2.44
281 282 6.737254 ACGTTAGGTCCTGATTATTTTGTG 57.263 37.500 0.00 0.00 0.00 3.33
286 287 4.403432 AGGTCCTGATTATTTTGTGCCATG 59.597 41.667 0.00 0.00 0.00 3.66
288 289 3.768215 TCCTGATTATTTTGTGCCATGCA 59.232 39.130 0.00 0.00 35.60 3.96
327 329 4.825085 TGGGAAACTATTTTCACGCTTTCT 59.175 37.500 7.73 0.00 46.74 2.52
334 336 7.440523 ACTATTTTCACGCTTTCTGAGATTT 57.559 32.000 0.00 0.00 0.00 2.17
367 369 4.434593 CGTAAATTTAACCAACGAGACCGG 60.435 45.833 0.00 0.00 40.78 5.28
377 379 4.221422 GAGACCGGCTGCGGCATA 62.221 66.667 21.31 0.00 40.87 3.14
380 382 2.124320 ACCGGCTGCGGCATAAAT 60.124 55.556 21.31 0.00 40.87 1.40
414 416 7.900782 ACCACGGAATTATATCGAAAATAGG 57.099 36.000 0.00 0.00 0.00 2.57
415 417 7.673180 ACCACGGAATTATATCGAAAATAGGA 58.327 34.615 0.00 0.00 0.00 2.94
416 418 8.152246 ACCACGGAATTATATCGAAAATAGGAA 58.848 33.333 0.00 0.00 0.00 3.36
417 419 9.162764 CCACGGAATTATATCGAAAATAGGAAT 57.837 33.333 0.00 0.00 0.00 3.01
445 447 1.470051 ATAATTTTTGCTCCCGCCGT 58.530 45.000 0.00 0.00 34.43 5.68
447 449 0.524414 AATTTTTGCTCCCGCCGTAC 59.476 50.000 0.00 0.00 34.43 3.67
478 480 6.968250 TCGTTGGTTAAATTTACGGTCAAAT 58.032 32.000 9.79 0.00 33.37 2.32
482 484 9.032420 GTTGGTTAAATTTACGGTCAAATTTGA 57.968 29.630 16.91 16.91 44.08 2.69
501 503 1.231958 AATCTCGAAAAACGCGGGCA 61.232 50.000 12.47 0.00 42.26 5.36
547 549 4.813161 AGTAGCATCATGACAAATCCTTCG 59.187 41.667 0.00 0.00 0.00 3.79
592 594 3.192633 ACACTCACAAACCCTGACAAAAC 59.807 43.478 0.00 0.00 0.00 2.43
610 612 1.015868 ACGCGTCCTAGTAGCTTCTC 58.984 55.000 5.58 0.00 0.00 2.87
638 640 7.215789 TGACAAAATGCAAACATTCTACCAAT 58.784 30.769 0.00 0.00 45.90 3.16
655 657 0.676782 AATGCTCGAAAAGGACGGGG 60.677 55.000 0.00 0.00 0.00 5.73
688 690 0.804933 GAATCGCCGGTACACTCCAC 60.805 60.000 1.90 0.00 0.00 4.02
879 881 4.528504 CGGTTGATAGTACATCTCTGTCG 58.471 47.826 0.00 0.00 36.79 4.35
941 947 1.266175 ACGTACTGTGTTCTCGTCCTG 59.734 52.381 0.00 0.00 0.00 3.86
956 962 3.470888 CTGGGAAGGGCGTCCGAT 61.471 66.667 0.00 0.00 38.72 4.18
957 963 3.447025 CTGGGAAGGGCGTCCGATC 62.447 68.421 0.00 2.90 38.72 3.69
958 964 4.237207 GGGAAGGGCGTCCGATCC 62.237 72.222 21.63 21.63 40.78 3.36
959 965 4.587189 GGAAGGGCGTCCGATCCG 62.587 72.222 16.60 0.00 35.35 4.18
1102 1108 4.304048 ACTAGGACTAGCTAGTGTGTGT 57.696 45.455 30.70 19.17 36.50 3.72
1119 1125 6.095300 AGTGTGTGTGTTTCTGAATTTGATCA 59.905 34.615 0.00 0.00 0.00 2.92
1121 1127 7.436080 GTGTGTGTGTTTCTGAATTTGATCATT 59.564 33.333 0.00 0.00 0.00 2.57
1270 1276 2.040544 CGCTCACGGGGAATGCTTT 61.041 57.895 0.00 0.00 34.97 3.51
1296 1302 3.832527 AGCTGGGTAAACATTTCAGTGT 58.167 40.909 0.00 0.00 0.00 3.55
1345 1351 4.666253 TTGCCTGCCTGCCTGACC 62.666 66.667 0.00 0.00 0.00 4.02
1347 1353 4.437587 GCCTGCCTGCCTGACCAT 62.438 66.667 0.00 0.00 0.00 3.55
1348 1354 2.357836 CCTGCCTGCCTGACCATT 59.642 61.111 0.00 0.00 0.00 3.16
1349 1355 1.304713 CCTGCCTGCCTGACCATTT 60.305 57.895 0.00 0.00 0.00 2.32
1350 1356 0.901580 CCTGCCTGCCTGACCATTTT 60.902 55.000 0.00 0.00 0.00 1.82
1478 1486 1.063488 GCAACGCCACTGTTTTCGT 59.937 52.632 0.00 0.00 36.67 3.85
1479 1487 0.305313 GCAACGCCACTGTTTTCGTA 59.695 50.000 0.00 0.00 34.50 3.43
1499 1507 4.979197 CGTATATGGAGTGAGAGCAGTTTC 59.021 45.833 0.00 0.00 0.00 2.78
1518 1526 1.080434 GTGTCTCCTGTCTCGGCAC 60.080 63.158 0.00 0.00 0.00 5.01
1539 1547 4.096984 CACAATTCTCTATTTGGTCTGGCC 59.903 45.833 0.00 0.00 37.90 5.36
1566 1574 4.159321 TCTTGTGATTGTGCCTTGTTTTGA 59.841 37.500 0.00 0.00 0.00 2.69
1719 1727 3.803082 CGCCCGGAGCACATGTTG 61.803 66.667 0.73 0.00 44.04 3.33
1796 1806 8.697846 CATGTTTTGCAGACATCTTGATAAAT 57.302 30.769 13.10 0.00 35.64 1.40
1797 1807 9.146984 CATGTTTTGCAGACATCTTGATAAATT 57.853 29.630 13.10 0.00 35.64 1.82
1804 1814 9.638239 TGCAGACATCTTGATAAATTAAAAACC 57.362 29.630 0.00 0.00 0.00 3.27
1849 1859 5.537188 AGTACCGATAAAACCAACGTTACA 58.463 37.500 0.00 0.00 0.00 2.41
1853 1863 6.144175 ACCGATAAAACCAACGTTACATTTG 58.856 36.000 0.00 0.00 0.00 2.32
1894 1905 2.422479 GGCAAGAGTTTCCGGGTTAATC 59.578 50.000 0.00 0.00 0.00 1.75
1921 1932 7.506261 TGGAAAACCAGGCTAAAACTATAACAA 59.494 33.333 0.00 0.00 0.00 2.83
1936 1947 2.452600 AACAACAACCATCCACACCT 57.547 45.000 0.00 0.00 0.00 4.00
2161 2793 3.458857 AGGGATCACTCAAATCATGCTCT 59.541 43.478 0.00 0.00 0.00 4.09
2221 2869 5.983118 CGACAACAACATGCTAGGATACATA 59.017 40.000 0.00 0.00 41.41 2.29
2222 2870 6.646653 CGACAACAACATGCTAGGATACATAT 59.353 38.462 0.00 0.00 41.41 1.78
2263 2911 5.135383 AGGCATACATTGTCTGCATTACAT 58.865 37.500 23.44 4.67 39.37 2.29
2265 2913 5.221106 GGCATACATTGTCTGCATTACATGT 60.221 40.000 23.44 2.69 37.38 3.21
2275 2923 4.858140 TCTGCATTACATGTTTTTCGCATG 59.142 37.500 2.30 4.02 46.51 4.06
2297 2945 5.250200 TGTTTAGGACATGTTGGGTACATC 58.750 41.667 0.00 0.00 45.71 3.06
2324 2972 3.854809 GCTTCTTCAGTGATCAGACGTAC 59.145 47.826 0.00 0.00 0.00 3.67
2343 2993 5.188359 ACGTACACATTAGGAAAGGGTGTAT 59.812 40.000 0.00 0.00 44.05 2.29
2369 3019 4.902443 TGGTCTCTCAACTATTAGCGAG 57.098 45.455 0.00 4.93 0.00 5.03
2395 3045 6.854578 TCAAAATTTGACCCCCTAACTCTAA 58.145 36.000 4.03 0.00 34.08 2.10
2429 3079 5.098893 TCTTGGTCACAAAAATGTCAAACG 58.901 37.500 0.00 0.00 35.89 3.60
2501 3151 0.942962 GTGGCACATGATAGCTCAGC 59.057 55.000 13.86 0.00 44.52 4.26
2510 3160 5.297527 CACATGATAGCTCAGCCAATACAAA 59.702 40.000 0.00 0.00 34.12 2.83
2513 3163 6.624352 TGATAGCTCAGCCAATACAAATTC 57.376 37.500 0.00 0.00 0.00 2.17
2546 3196 8.727910 ACAAAAATAAGAAAGATAGGAACGACC 58.272 33.333 0.00 0.00 39.35 4.79
2776 3440 9.603921 ATCAGGATACAAAAATGCCTTAAAATG 57.396 29.630 0.00 0.00 41.41 2.32
2777 3441 7.548780 TCAGGATACAAAAATGCCTTAAAATGC 59.451 33.333 0.00 0.00 41.41 3.56
2798 3462 3.735514 GCGTGGAGCCTAAAAACACAAAA 60.736 43.478 0.00 0.00 40.81 2.44
2799 3463 4.616953 CGTGGAGCCTAAAAACACAAAAT 58.383 39.130 0.00 0.00 32.58 1.82
2801 3465 6.386654 CGTGGAGCCTAAAAACACAAAATAT 58.613 36.000 0.00 0.00 32.58 1.28
2802 3466 7.531716 CGTGGAGCCTAAAAACACAAAATATA 58.468 34.615 0.00 0.00 32.58 0.86
2882 3602 6.797454 TGCGTACATTTTTCCTTACTTTTGT 58.203 32.000 0.00 0.00 0.00 2.83
2885 3605 8.684655 GCGTACATTTTTCCTTACTTTTGTTAC 58.315 33.333 0.00 0.00 0.00 2.50
2929 3682 9.880157 ATTTATGATTGATTTTTCAACCCTCAG 57.120 29.630 0.00 0.00 31.89 3.35
2932 3685 4.935352 TTGATTTTTCAACCCTCAGTGG 57.065 40.909 0.00 0.00 0.00 4.00
2943 3696 2.111255 ACCCTCAGTGGTAACTAGGTCA 59.889 50.000 0.00 0.00 36.67 4.02
2963 3716 2.510768 CCACTAGTGGCGATTCTACC 57.489 55.000 28.48 0.00 44.73 3.18
2969 3723 2.111251 GGCGATTCTACCAGGGGC 59.889 66.667 0.00 0.00 0.00 5.80
3004 3758 3.825908 AAGCCTACCCTCCAAAAATCA 57.174 42.857 0.00 0.00 0.00 2.57
3012 3766 8.360390 GCCTACCCTCCAAAAATCATATTTTAG 58.640 37.037 0.00 0.00 31.54 1.85
3051 3805 9.398170 CTTGACAATTGTATTGAGGTGTTTTAG 57.602 33.333 11.95 0.00 0.00 1.85
3064 3818 6.160576 AGGTGTTTTAGATGCAACAATTGT 57.839 33.333 4.92 4.92 34.70 2.71
3134 3888 4.375272 CTCCATTGTCATGCTAGATTCGT 58.625 43.478 0.00 0.00 0.00 3.85
3138 3892 3.165058 TGTCATGCTAGATTCGTCACC 57.835 47.619 0.00 0.00 0.00 4.02
3139 3893 2.495669 TGTCATGCTAGATTCGTCACCA 59.504 45.455 0.00 0.00 0.00 4.17
3140 3894 2.860735 GTCATGCTAGATTCGTCACCAC 59.139 50.000 0.00 0.00 0.00 4.16
3142 3896 2.654749 TGCTAGATTCGTCACCACTG 57.345 50.000 0.00 0.00 0.00 3.66
3175 3930 2.425143 ACCACCGCATCATCAAAGAT 57.575 45.000 0.00 0.00 0.00 2.40
3177 3932 1.335810 CCACCGCATCATCAAAGATGG 59.664 52.381 7.11 0.00 44.33 3.51
3197 3952 2.551032 GGTTTTGGTGAAGTAAGGGACG 59.449 50.000 0.00 0.00 0.00 4.79
3206 3961 4.883006 GTGAAGTAAGGGACGAGATCTAGT 59.117 45.833 8.35 8.35 0.00 2.57
3207 3962 5.357596 GTGAAGTAAGGGACGAGATCTAGTT 59.642 44.000 10.02 0.00 0.00 2.24
3214 3969 3.933332 GGGACGAGATCTAGTTGTTTTGG 59.067 47.826 10.02 0.00 0.00 3.28
3225 3980 1.480545 GTTGTTTTGGCACTTGAGGGT 59.519 47.619 0.00 0.00 0.00 4.34
3227 3982 1.341482 TGTTTTGGCACTTGAGGGTCA 60.341 47.619 0.00 0.00 0.00 4.02
3231 3986 1.691196 TGGCACTTGAGGGTCAAAAG 58.309 50.000 0.00 0.00 35.73 2.27
3232 3987 1.064017 TGGCACTTGAGGGTCAAAAGT 60.064 47.619 0.00 0.00 35.73 2.66
3234 3989 2.034685 GGCACTTGAGGGTCAAAAGTTC 59.965 50.000 0.00 0.00 35.73 3.01
3236 3991 3.319122 GCACTTGAGGGTCAAAAGTTCAT 59.681 43.478 0.00 0.00 35.73 2.57
3237 3992 4.794003 GCACTTGAGGGTCAAAAGTTCATG 60.794 45.833 0.00 0.00 35.73 3.07
3238 3993 3.319122 ACTTGAGGGTCAAAAGTTCATGC 59.681 43.478 0.00 0.00 35.73 4.06
3260 4017 9.921637 CATGCTTTAAAATGGGTCTAAACTTAA 57.078 29.630 0.00 0.00 0.00 1.85
3261 4018 9.923143 ATGCTTTAAAATGGGTCTAAACTTAAC 57.077 29.630 0.00 0.00 0.00 2.01
3324 4081 2.542020 TTTCTTGTCACCGATGAGCA 57.458 45.000 0.00 0.00 34.75 4.26
3361 4120 2.003301 GATTCTTGGGCAGACTTCGAC 58.997 52.381 0.00 0.00 0.00 4.20
3382 4141 2.425592 CAGCACCAACTCCCACGA 59.574 61.111 0.00 0.00 0.00 4.35
3419 4178 2.968574 GGGATAGCTTCAGAGATCACCA 59.031 50.000 0.00 0.00 0.00 4.17
3477 4236 2.125512 CCCGCCACCGAGAAAGAG 60.126 66.667 0.00 0.00 36.29 2.85
3500 4259 2.940410 AGGCGAAAGAAGAAAACAACGA 59.060 40.909 0.00 0.00 0.00 3.85
3511 4270 3.499918 AGAAAACAACGATTGGCTCTCTG 59.500 43.478 0.00 0.00 34.12 3.35
3566 4325 2.664851 CCTCGACGGCAGCAACAA 60.665 61.111 0.00 0.00 0.00 2.83
3568 4327 2.954753 CTCGACGGCAGCAACAACC 61.955 63.158 0.00 0.00 0.00 3.77
3581 4340 3.249999 CAACCGTCGTTGCCGATT 58.750 55.556 0.00 0.00 46.30 3.34
3605 4364 0.250684 TGACACCAATGGCGTGATGT 60.251 50.000 0.00 0.00 36.14 3.06
3606 4365 0.168788 GACACCAATGGCGTGATGTG 59.831 55.000 0.00 0.00 35.17 3.21
3643 4410 3.119637 GCAAAGTGTGTTGTAAGTGTGGT 60.120 43.478 0.00 0.00 0.00 4.16
3649 4416 2.162608 GTGTTGTAAGTGTGGTTGTGCA 59.837 45.455 0.00 0.00 0.00 4.57
3708 4476 6.747414 TCATAGGTAGCTGAATACAATGGT 57.253 37.500 4.27 0.00 0.00 3.55
3738 4506 2.514205 AGCGTGCATTGCTTCTTTTT 57.486 40.000 10.49 0.00 40.48 1.94
3810 4578 0.174162 GTGATGCCCATGTTCTTGCC 59.826 55.000 0.00 0.00 0.00 4.52
3822 4590 1.728971 GTTCTTGCCACGAGATGACAG 59.271 52.381 0.00 0.00 0.00 3.51
3825 4593 2.146342 CTTGCCACGAGATGACAGTTT 58.854 47.619 0.00 0.00 0.00 2.66
3885 4654 6.699575 AACAAGTTGGGATAGCATGAATAC 57.300 37.500 7.96 0.00 0.00 1.89
3919 4688 9.753674 TCCTGATAAGATTTAAAGTTCCAACAT 57.246 29.630 0.00 0.00 0.00 2.71
3944 4713 7.230747 TGGTCTTTTGATGTCTCCATTTCTAA 58.769 34.615 0.00 0.00 0.00 2.10
3953 4722 8.277197 TGATGTCTCCATTTCTAATTGGATCTT 58.723 33.333 6.75 3.46 41.09 2.40
3955 4724 8.511604 TGTCTCCATTTCTAATTGGATCTTTC 57.488 34.615 6.75 0.00 41.09 2.62
3968 4737 8.529424 AATTGGATCTTTCTGCATCTCAATAA 57.471 30.769 0.00 0.00 0.00 1.40
3976 4746 9.234827 TCTTTCTGCATCTCAATAATTCTCAAA 57.765 29.630 0.00 0.00 0.00 2.69
3986 4756 9.224267 TCTCAATAATTCTCAAACTTCTGAAGG 57.776 33.333 20.61 4.31 0.00 3.46
3996 4766 1.421646 ACTTCTGAAGGAACCCCACAG 59.578 52.381 20.61 0.00 39.06 3.66
4014 4785 4.298332 CACAGTGAACCAACAAAATAGGC 58.702 43.478 0.00 0.00 0.00 3.93
4030 4801 5.977489 AATAGGCCAGAAGTTAAAACACC 57.023 39.130 5.01 0.00 0.00 4.16
4040 4811 4.677673 AGTTAAAACACCGTGACCTAGT 57.322 40.909 5.28 0.00 0.00 2.57
4095 4867 9.893305 ATTTCTTTCACCGAAAACTATACAAAG 57.107 29.630 0.00 0.00 34.42 2.77
4129 4901 3.820467 ACCAATGATCAAAGCAAACTCGA 59.180 39.130 0.00 0.00 0.00 4.04
4135 4907 3.878086 TCAAAGCAAACTCGACATCAC 57.122 42.857 0.00 0.00 0.00 3.06
4147 4919 0.792640 GACATCACAGTTGTCGCTGG 59.207 55.000 0.00 0.00 40.59 4.85
4196 4968 3.388308 CCTCAATCTGCACTATCGGAAG 58.612 50.000 0.00 0.00 0.00 3.46
4210 4982 3.618171 GGAAGGCCGTTAACTCACA 57.382 52.632 3.71 0.00 0.00 3.58
4331 5103 1.682344 GCCCCTAGCCCACAAAAGG 60.682 63.158 0.00 0.00 34.35 3.11
4393 5167 5.869888 CCTAGTGTTGATAAATAGATCGCCC 59.130 44.000 0.00 0.00 0.00 6.13
4409 5183 2.146342 CGCCCAAGACTATTATGGCAG 58.854 52.381 0.00 0.00 38.81 4.85
4428 5203 2.266376 GAAATCGCGTCCTTTGCCCC 62.266 60.000 5.77 0.00 0.00 5.80
4437 5212 2.282462 CTTTGCCCCGCTCCAACT 60.282 61.111 0.00 0.00 0.00 3.16
4460 5235 3.380320 AGGTTTGTTGTTTGCCTCACTAC 59.620 43.478 0.00 0.00 0.00 2.73
4479 5254 7.175797 TCACTACTTGTTCTCTCTATGGAAGA 58.824 38.462 0.00 0.00 0.00 2.87
4498 5275 7.453393 TGGAAGATTTAGAGAACACAACAGAT 58.547 34.615 0.00 0.00 0.00 2.90
4510 5287 3.057736 ACACAACAGATGCATCTTTGAGC 60.058 43.478 33.84 12.75 34.22 4.26
4517 5294 5.416639 ACAGATGCATCTTTGAGCAATGTAA 59.583 36.000 26.70 0.00 44.88 2.41
4569 5346 0.957362 AGAACAAAGCTGCTCTTGGC 59.043 50.000 20.54 14.75 42.22 4.52
4575 5352 3.782244 GCTGCTCTTGGCGTGACG 61.782 66.667 0.00 0.00 45.43 4.35
4606 5383 0.400213 TGGTCTCGGTGCTTTGGATT 59.600 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.926272 AGGAACGTAGCATGCAATTTTAAAAA 59.074 30.769 21.98 0.00 0.00 1.94
14 15 6.451393 AGGAACGTAGCATGCAATTTTAAAA 58.549 32.000 21.98 2.51 0.00 1.52
15 16 6.019779 AGGAACGTAGCATGCAATTTTAAA 57.980 33.333 21.98 0.00 0.00 1.52
16 17 5.182190 TGAGGAACGTAGCATGCAATTTTAA 59.818 36.000 21.98 0.00 0.00 1.52
17 18 4.697828 TGAGGAACGTAGCATGCAATTTTA 59.302 37.500 21.98 0.00 0.00 1.52
18 19 3.505680 TGAGGAACGTAGCATGCAATTTT 59.494 39.130 21.98 7.41 0.00 1.82
19 20 3.081061 TGAGGAACGTAGCATGCAATTT 58.919 40.909 21.98 7.02 0.00 1.82
20 21 2.710377 TGAGGAACGTAGCATGCAATT 58.290 42.857 21.98 7.96 0.00 2.32
21 22 2.401583 TGAGGAACGTAGCATGCAAT 57.598 45.000 21.98 1.90 0.00 3.56
22 23 1.804151 GTTGAGGAACGTAGCATGCAA 59.196 47.619 21.98 0.00 0.00 4.08
23 24 1.270571 TGTTGAGGAACGTAGCATGCA 60.271 47.619 21.98 2.77 34.49 3.96
24 25 1.128692 GTGTTGAGGAACGTAGCATGC 59.871 52.381 10.51 10.51 34.49 4.06
25 26 2.688507 AGTGTTGAGGAACGTAGCATG 58.311 47.619 0.00 0.00 34.49 4.06
26 27 3.402628 AAGTGTTGAGGAACGTAGCAT 57.597 42.857 0.00 0.00 34.49 3.79
27 28 2.902705 AAGTGTTGAGGAACGTAGCA 57.097 45.000 0.00 0.00 34.49 3.49
28 29 3.558418 TCAAAAGTGTTGAGGAACGTAGC 59.442 43.478 0.00 0.00 34.49 3.58
29 30 4.809426 AGTCAAAAGTGTTGAGGAACGTAG 59.191 41.667 0.00 0.00 34.49 3.51
30 31 4.761975 AGTCAAAAGTGTTGAGGAACGTA 58.238 39.130 0.00 0.00 34.49 3.57
31 32 3.606687 AGTCAAAAGTGTTGAGGAACGT 58.393 40.909 0.00 0.00 34.49 3.99
32 33 4.332819 AGAAGTCAAAAGTGTTGAGGAACG 59.667 41.667 0.00 0.00 34.49 3.95
33 34 5.819825 AGAAGTCAAAAGTGTTGAGGAAC 57.180 39.130 0.00 0.00 0.00 3.62
34 35 6.538742 CAGTAGAAGTCAAAAGTGTTGAGGAA 59.461 38.462 0.00 0.00 0.00 3.36
35 36 6.049149 CAGTAGAAGTCAAAAGTGTTGAGGA 58.951 40.000 0.00 0.00 0.00 3.71
36 37 5.277538 GCAGTAGAAGTCAAAAGTGTTGAGG 60.278 44.000 0.00 0.00 0.00 3.86
37 38 5.294306 TGCAGTAGAAGTCAAAAGTGTTGAG 59.706 40.000 0.00 0.00 0.00 3.02
38 39 5.182487 TGCAGTAGAAGTCAAAAGTGTTGA 58.818 37.500 0.00 0.00 0.00 3.18
39 40 5.484173 TGCAGTAGAAGTCAAAAGTGTTG 57.516 39.130 0.00 0.00 0.00 3.33
40 41 4.576463 CCTGCAGTAGAAGTCAAAAGTGTT 59.424 41.667 13.81 0.00 0.00 3.32
41 42 4.130118 CCTGCAGTAGAAGTCAAAAGTGT 58.870 43.478 13.81 0.00 0.00 3.55
42 43 4.212214 GTCCTGCAGTAGAAGTCAAAAGTG 59.788 45.833 13.81 0.00 0.00 3.16
43 44 4.101741 AGTCCTGCAGTAGAAGTCAAAAGT 59.898 41.667 13.81 0.00 0.00 2.66
44 45 4.636249 AGTCCTGCAGTAGAAGTCAAAAG 58.364 43.478 13.81 0.00 0.00 2.27
45 46 4.689612 AGTCCTGCAGTAGAAGTCAAAA 57.310 40.909 13.81 0.00 0.00 2.44
46 47 5.801531 TTAGTCCTGCAGTAGAAGTCAAA 57.198 39.130 13.81 0.00 0.00 2.69
47 48 5.801531 TTTAGTCCTGCAGTAGAAGTCAA 57.198 39.130 13.81 0.00 0.00 3.18
48 49 5.304614 AGTTTTAGTCCTGCAGTAGAAGTCA 59.695 40.000 13.81 0.00 0.00 3.41
49 50 5.785243 AGTTTTAGTCCTGCAGTAGAAGTC 58.215 41.667 13.81 0.00 0.00 3.01
50 51 5.810080 AGTTTTAGTCCTGCAGTAGAAGT 57.190 39.130 13.81 0.63 0.00 3.01
51 52 9.522804 CTAATAGTTTTAGTCCTGCAGTAGAAG 57.477 37.037 13.81 0.00 0.00 2.85
52 53 8.475639 CCTAATAGTTTTAGTCCTGCAGTAGAA 58.524 37.037 13.81 0.00 0.00 2.10
53 54 7.417570 GCCTAATAGTTTTAGTCCTGCAGTAGA 60.418 40.741 13.81 0.01 0.00 2.59
54 55 6.702282 GCCTAATAGTTTTAGTCCTGCAGTAG 59.298 42.308 13.81 2.75 0.00 2.57
55 56 6.407752 GGCCTAATAGTTTTAGTCCTGCAGTA 60.408 42.308 13.81 0.00 0.00 2.74
61 62 6.824958 TCATGGCCTAATAGTTTTAGTCCT 57.175 37.500 3.32 0.00 0.00 3.85
78 79 2.094258 CACGTGTGTCACTTATCATGGC 59.906 50.000 7.58 0.00 31.34 4.40
79 80 3.123453 CACACGTGTGTCACTTATCATGG 59.877 47.826 35.03 9.31 42.83 3.66
150 151 1.407979 AGTTACCATCCTCGCGTTAGG 59.592 52.381 5.77 6.78 38.06 2.69
151 152 2.865343 AGTTACCATCCTCGCGTTAG 57.135 50.000 5.77 0.00 0.00 2.34
152 153 2.492881 TGAAGTTACCATCCTCGCGTTA 59.507 45.455 5.77 0.00 0.00 3.18
153 154 1.274167 TGAAGTTACCATCCTCGCGTT 59.726 47.619 5.77 0.00 0.00 4.84
154 155 0.892755 TGAAGTTACCATCCTCGCGT 59.107 50.000 5.77 0.00 0.00 6.01
155 156 1.135083 ACTGAAGTTACCATCCTCGCG 60.135 52.381 0.00 0.00 0.00 5.87
172 173 4.682860 GGAAATTGTCATGCTTCACAACTG 59.317 41.667 0.23 0.00 35.37 3.16
187 188 9.546428 AAAGAATGAATTCGAAAAGGAAATTGT 57.454 25.926 0.00 0.00 41.56 2.71
228 229 5.402270 CAGTTAAAGTTGCAATCCGAAAAGG 59.598 40.000 0.59 0.00 42.97 3.11
253 254 8.911662 CAAAATAATCAGGACCTAACGTTTTTG 58.088 33.333 5.91 12.77 0.00 2.44
259 260 5.448632 GGCACAAAATAATCAGGACCTAACG 60.449 44.000 0.00 0.00 0.00 3.18
278 279 1.268066 AATTCCACATGCATGGCACA 58.732 45.000 29.41 11.95 43.04 4.57
279 280 3.068448 TGATAATTCCACATGCATGGCAC 59.932 43.478 29.41 10.86 43.04 5.01
281 282 4.530710 ATGATAATTCCACATGCATGGC 57.469 40.909 29.41 8.33 39.85 4.40
286 287 5.534207 TCCCAAATGATAATTCCACATGC 57.466 39.130 0.00 0.00 0.00 4.06
288 289 7.738437 AGTTTCCCAAATGATAATTCCACAT 57.262 32.000 0.00 0.00 0.00 3.21
334 336 7.854916 CGTTGGTTAAATTTACGGTCAAACTTA 59.145 33.333 0.00 0.00 0.00 2.24
367 369 7.596995 TGGTATAATTTTTATTTATGCCGCAGC 59.403 33.333 0.00 0.00 41.83 5.25
415 417 9.965824 CGGGAGCAAAAATTATATCACTAAATT 57.034 29.630 0.00 0.00 0.00 1.82
445 447 4.789012 ATTTAACCAACGAGACCGAGTA 57.211 40.909 0.00 0.00 39.50 2.59
447 449 5.443693 CGTAAATTTAACCAACGAGACCGAG 60.444 44.000 4.77 0.00 39.50 4.63
478 480 2.350007 CCCGCGTTTTTCGAGATTCAAA 60.350 45.455 4.92 0.00 41.61 2.69
482 484 1.231958 TGCCCGCGTTTTTCGAGATT 61.232 50.000 4.92 0.00 41.61 2.40
501 503 3.587061 TCCTCCATTCCACAATGTAGTGT 59.413 43.478 0.00 0.00 38.22 3.55
523 525 5.295292 CGAAGGATTTGTCATGATGCTACTT 59.705 40.000 0.00 0.00 0.00 2.24
547 549 0.761802 GACAGGGATGAGATGGACCC 59.238 60.000 0.00 0.00 42.36 4.46
592 594 1.015109 TGAGAAGCTACTAGGACGCG 58.985 55.000 3.53 3.53 0.00 6.01
610 612 7.171167 TGGTAGAATGTTTGCATTTTGTCATTG 59.829 33.333 0.00 0.00 44.61 2.82
638 640 2.345991 CCCCGTCCTTTTCGAGCA 59.654 61.111 0.00 0.00 0.00 4.26
655 657 1.915983 GATTCCTGTCCCCTCACCC 59.084 63.158 0.00 0.00 0.00 4.61
661 663 4.547367 CCGGCGATTCCTGTCCCC 62.547 72.222 9.30 0.00 0.00 4.81
688 690 3.902881 AGCTCCTACTGAAAGATGGTG 57.097 47.619 0.00 0.00 37.43 4.17
941 947 4.237207 GGATCGGACGCCCTTCCC 62.237 72.222 0.00 0.00 31.03 3.97
978 984 1.399744 CGATGGCACCCTGCTAGGTA 61.400 60.000 0.00 0.00 44.28 3.08
979 985 2.735772 CGATGGCACCCTGCTAGGT 61.736 63.158 0.00 0.00 44.28 3.08
980 986 1.762522 ATCGATGGCACCCTGCTAGG 61.763 60.000 0.00 0.00 44.28 3.02
981 987 0.969149 TATCGATGGCACCCTGCTAG 59.031 55.000 8.54 0.00 44.28 3.42
982 988 1.276138 CATATCGATGGCACCCTGCTA 59.724 52.381 8.54 0.00 44.28 3.49
1005 1011 4.911390 ACCCTTTCATCTTGTAGTTGGAG 58.089 43.478 0.00 0.00 0.00 3.86
1119 1125 3.007398 GTCTGTCTGTCCCTGTTCTGAAT 59.993 47.826 0.00 0.00 0.00 2.57
1121 1127 1.964223 GTCTGTCTGTCCCTGTTCTGA 59.036 52.381 0.00 0.00 0.00 3.27
1151 1157 1.067250 GGCCGCTGCAAGAACAAAA 59.933 52.632 1.55 0.00 40.13 2.44
1270 1276 4.219115 TGAAATGTTTACCCAGCTTGGAA 58.781 39.130 11.55 0.00 40.96 3.53
1285 1291 4.625742 GCGTGTACTATCACACTGAAATGT 59.374 41.667 5.00 0.00 45.40 2.71
1296 1302 4.827692 ACCAGAATTTGCGTGTACTATCA 58.172 39.130 0.00 0.00 0.00 2.15
1417 1425 2.765807 CAGGAGGTCCCCGCTGAT 60.766 66.667 0.00 0.00 36.42 2.90
1478 1486 4.645136 ACGAAACTGCTCTCACTCCATATA 59.355 41.667 0.00 0.00 0.00 0.86
1479 1487 3.449018 ACGAAACTGCTCTCACTCCATAT 59.551 43.478 0.00 0.00 0.00 1.78
1499 1507 2.179517 GCCGAGACAGGAGACACG 59.820 66.667 0.00 0.00 0.00 4.49
1518 1526 3.313526 CGGCCAGACCAAATAGAGAATTG 59.686 47.826 2.24 0.00 39.03 2.32
1539 1547 0.877071 AGGCACAATCACAAGAAGCG 59.123 50.000 0.00 0.00 0.00 4.68
1566 1574 9.039870 GTCTCAGACGATGAATCATAATCTTTT 57.960 33.333 0.00 0.00 37.52 2.27
1657 1665 9.206870 TCAAGATCAAGCCAATAAAATTTGTTC 57.793 29.630 0.00 0.00 0.00 3.18
1719 1727 3.364621 CACAAGCATGCGAATTGTTTACC 59.635 43.478 18.20 0.00 35.04 2.85
1843 1853 6.754675 AGTTTGAAAAAGGGACAAATGTAACG 59.245 34.615 0.00 0.00 36.25 3.18
1849 1859 6.823182 CCTTCAAGTTTGAAAAAGGGACAAAT 59.177 34.615 8.48 0.00 45.61 2.32
1853 1863 4.119862 GCCTTCAAGTTTGAAAAAGGGAC 58.880 43.478 12.28 3.62 45.61 4.46
1921 1932 0.323629 CGGTAGGTGTGGATGGTTGT 59.676 55.000 0.00 0.00 0.00 3.32
2017 2036 1.421485 GATGAAGGTGACGCTTGCG 59.579 57.895 13.70 13.70 0.00 4.85
2061 2080 2.262211 GATGGCCATTTGAAACGAAGC 58.738 47.619 21.84 0.00 0.00 3.86
2263 2911 4.902443 TGTCCTAAACATGCGAAAAACA 57.098 36.364 0.00 0.00 31.20 2.83
2297 2945 3.195182 TCTGATCACTGAAGAAGCTCTGG 59.805 47.826 0.00 0.00 0.00 3.86
2369 3019 5.952347 AGAGTTAGGGGGTCAAATTTTGATC 59.048 40.000 14.54 13.75 42.47 2.92
2429 3079 2.280628 CAAAGGACCGAACCTAGATGC 58.719 52.381 0.00 0.00 39.62 3.91
2534 3184 1.269998 CCTCCATCGGTCGTTCCTATC 59.730 57.143 0.00 0.00 0.00 2.08
2535 3185 1.329256 CCTCCATCGGTCGTTCCTAT 58.671 55.000 0.00 0.00 0.00 2.57
2546 3196 5.534654 TCTTTAATTTAATGCCCCTCCATCG 59.465 40.000 0.00 0.00 0.00 3.84
2757 3415 5.406780 CCACGCATTTTAAGGCATTTTTGTA 59.593 36.000 0.00 0.00 34.99 2.41
2758 3416 4.213059 CCACGCATTTTAAGGCATTTTTGT 59.787 37.500 0.00 0.00 34.99 2.83
2759 3417 4.450419 TCCACGCATTTTAAGGCATTTTTG 59.550 37.500 0.00 0.00 34.99 2.44
2776 3440 0.948678 TGTGTTTTTAGGCTCCACGC 59.051 50.000 0.00 0.00 38.13 5.34
2777 3441 3.701532 TTTGTGTTTTTAGGCTCCACG 57.298 42.857 0.00 0.00 0.00 4.94
2963 3716 2.029666 CCTATCGAAGCGCCCCTG 59.970 66.667 2.29 0.00 0.00 4.45
3030 3784 8.028354 TGCATCTAAAACACCTCAATACAATTG 58.972 33.333 3.24 3.24 0.00 2.32
3035 3789 6.908825 TGTTGCATCTAAAACACCTCAATAC 58.091 36.000 0.00 0.00 31.52 1.89
3051 3805 5.849858 CAAGTGCATTACAATTGTTGCATC 58.150 37.500 30.46 24.26 46.61 3.91
3092 3846 1.551883 GGGCAGGCTCAAAACATCAAT 59.448 47.619 0.00 0.00 0.00 2.57
3134 3888 1.627834 TCATACATGTGGCAGTGGTGA 59.372 47.619 9.11 5.71 0.00 4.02
3138 3892 2.819019 TGGTTTCATACATGTGGCAGTG 59.181 45.455 9.11 0.00 0.00 3.66
3139 3893 2.819608 GTGGTTTCATACATGTGGCAGT 59.180 45.455 9.11 0.00 0.00 4.40
3140 3894 2.164219 GGTGGTTTCATACATGTGGCAG 59.836 50.000 9.11 0.00 0.00 4.85
3142 3896 1.132262 CGGTGGTTTCATACATGTGGC 59.868 52.381 9.11 0.00 0.00 5.01
3175 3930 3.558033 GTCCCTTACTTCACCAAAACCA 58.442 45.455 0.00 0.00 0.00 3.67
3177 3932 3.469739 TCGTCCCTTACTTCACCAAAAC 58.530 45.455 0.00 0.00 0.00 2.43
3197 3952 5.470098 TCAAGTGCCAAAACAACTAGATCTC 59.530 40.000 0.00 0.00 0.00 2.75
3206 3961 1.754226 GACCCTCAAGTGCCAAAACAA 59.246 47.619 0.00 0.00 0.00 2.83
3207 3962 1.341482 TGACCCTCAAGTGCCAAAACA 60.341 47.619 0.00 0.00 0.00 2.83
3214 3969 2.687935 TGAACTTTTGACCCTCAAGTGC 59.312 45.455 0.00 0.00 37.70 4.40
3225 3980 7.278875 ACCCATTTTAAAGCATGAACTTTTGA 58.721 30.769 0.00 0.00 40.32 2.69
3227 3982 7.508687 AGACCCATTTTAAAGCATGAACTTTT 58.491 30.769 0.00 0.00 40.32 2.27
3231 3986 8.088365 AGTTTAGACCCATTTTAAAGCATGAAC 58.912 33.333 0.00 0.00 0.00 3.18
3232 3987 8.189119 AGTTTAGACCCATTTTAAAGCATGAA 57.811 30.769 0.00 0.00 0.00 2.57
3234 3989 9.921637 TTAAGTTTAGACCCATTTTAAAGCATG 57.078 29.630 0.00 0.00 0.00 4.06
3236 3991 8.915036 TGTTAAGTTTAGACCCATTTTAAAGCA 58.085 29.630 0.00 0.00 0.00 3.91
3237 3992 9.923143 ATGTTAAGTTTAGACCCATTTTAAAGC 57.077 29.630 0.00 0.00 0.00 3.51
3291 4048 8.690840 CGGTGACAAGAAAATAACTGAAAAATC 58.309 33.333 0.00 0.00 0.00 2.17
3292 4049 8.410141 TCGGTGACAAGAAAATAACTGAAAAAT 58.590 29.630 0.00 0.00 0.00 1.82
3293 4050 7.763356 TCGGTGACAAGAAAATAACTGAAAAA 58.237 30.769 0.00 0.00 0.00 1.94
3294 4051 7.323049 TCGGTGACAAGAAAATAACTGAAAA 57.677 32.000 0.00 0.00 0.00 2.29
3303 4060 3.411446 TGCTCATCGGTGACAAGAAAAT 58.589 40.909 0.00 0.00 0.00 1.82
3343 4102 0.034896 GGTCGAAGTCTGCCCAAGAA 59.965 55.000 0.00 0.00 36.40 2.52
3361 4120 2.674380 GGGAGTTGGTGCTGCTGG 60.674 66.667 0.00 0.00 0.00 4.85
3419 4178 3.241530 TGCTGCCACGTCTTCCCT 61.242 61.111 0.00 0.00 0.00 4.20
3477 4236 3.724257 CGTTGTTTTCTTCTTTCGCCTTC 59.276 43.478 0.00 0.00 0.00 3.46
3500 4259 2.026822 ACGAATTCACCAGAGAGCCAAT 60.027 45.455 6.22 0.00 0.00 3.16
3511 4270 3.296322 TTTGGCATTGACGAATTCACC 57.704 42.857 6.22 0.00 32.26 4.02
3605 4364 4.648626 GCAGCCTGCCTGTCACCA 62.649 66.667 5.06 0.00 43.71 4.17
3606 4365 4.648626 TGCAGCCTGCCTGTCACC 62.649 66.667 15.29 0.00 44.23 4.02
3708 4476 3.489047 GCAATGCACGCTTTTAGAACAAA 59.511 39.130 0.00 0.00 0.00 2.83
3762 4530 8.287503 ACCGTGAATGAGAATAAAGTAAAACAC 58.712 33.333 0.00 0.00 0.00 3.32
3764 4532 9.673454 AAACCGTGAATGAGAATAAAGTAAAAC 57.327 29.630 0.00 0.00 0.00 2.43
3766 4534 8.842280 ACAAACCGTGAATGAGAATAAAGTAAA 58.158 29.630 0.00 0.00 0.00 2.01
3784 4552 0.539438 ACATGGGCATCACAAACCGT 60.539 50.000 0.00 0.00 0.00 4.83
3810 4578 3.906998 AGAGTCAAACTGTCATCTCGTG 58.093 45.455 0.00 0.00 0.00 4.35
3905 4674 7.411486 TCAAAAGACCATGTTGGAACTTTAA 57.589 32.000 16.69 10.11 41.93 1.52
3913 4682 4.082571 GGAGACATCAAAAGACCATGTTGG 60.083 45.833 0.00 0.00 45.02 3.77
3944 4713 8.707796 ATTATTGAGATGCAGAAAGATCCAAT 57.292 30.769 0.00 0.00 0.00 3.16
3953 4722 8.571461 AGTTTGAGAATTATTGAGATGCAGAA 57.429 30.769 0.00 0.00 0.00 3.02
3955 4724 8.675504 AGAAGTTTGAGAATTATTGAGATGCAG 58.324 33.333 0.00 0.00 0.00 4.41
3968 4737 5.073428 GGGTTCCTTCAGAAGTTTGAGAAT 58.927 41.667 9.41 0.00 34.29 2.40
3976 4746 1.421646 CTGTGGGGTTCCTTCAGAAGT 59.578 52.381 9.41 0.00 37.65 3.01
3984 4754 0.991355 TGGTTCACTGTGGGGTTCCT 60.991 55.000 8.11 0.00 0.00 3.36
3986 4756 1.029681 GTTGGTTCACTGTGGGGTTC 58.970 55.000 8.11 0.00 0.00 3.62
3996 4766 3.572255 TCTGGCCTATTTTGTTGGTTCAC 59.428 43.478 3.32 0.00 0.00 3.18
4014 4785 3.002965 GGTCACGGTGTTTTAACTTCTGG 59.997 47.826 8.17 0.00 0.00 3.86
4094 4866 9.485206 CTTTGATCATTGGTTCTTTCATTTTCT 57.515 29.630 0.00 0.00 0.00 2.52
4095 4867 8.225777 GCTTTGATCATTGGTTCTTTCATTTTC 58.774 33.333 0.00 0.00 0.00 2.29
4129 4901 1.230635 GCCAGCGACAACTGTGATGT 61.231 55.000 0.00 0.00 35.83 3.06
4135 4907 2.661537 TGACGCCAGCGACAACTG 60.662 61.111 20.32 0.00 40.53 3.16
4147 4919 2.946762 GGCTTGACTTGGTGACGC 59.053 61.111 0.00 0.00 0.00 5.19
4196 4968 1.800681 GCCATGTGAGTTAACGGCC 59.199 57.895 8.32 0.00 33.31 6.13
4206 4978 3.894427 ACTGTTGTATTTTGGCCATGTGA 59.106 39.130 6.09 0.00 0.00 3.58
4210 4982 4.406456 TGAGACTGTTGTATTTTGGCCAT 58.594 39.130 6.09 0.00 0.00 4.40
4284 5056 7.067129 TGCCTTAGCGGTAGAGATACATAATAG 59.933 40.741 0.00 0.00 44.31 1.73
4316 5088 4.643334 GGTTTATACCTTTTGTGGGCTAGG 59.357 45.833 0.00 0.00 41.53 3.02
4331 5103 6.043411 GTGTGGATCTCTGTGAGGTTTATAC 58.957 44.000 0.00 0.00 0.00 1.47
4393 5167 5.613360 CGCGATTTCTGCCATAATAGTCTTG 60.613 44.000 0.00 0.00 0.00 3.02
4409 5183 1.136774 GGGCAAAGGACGCGATTTC 59.863 57.895 15.93 0.00 0.00 2.17
4428 5203 2.969443 CAACAAACCTAGTTGGAGCG 57.031 50.000 0.00 0.00 41.92 5.03
4437 5212 3.626930 AGTGAGGCAAACAACAAACCTA 58.373 40.909 0.00 0.00 0.00 3.08
4460 5235 9.748708 CTCTAAATCTTCCATAGAGAGAACAAG 57.251 37.037 3.53 0.00 43.39 3.16
4479 5254 6.883217 AGATGCATCTGTTGTGTTCTCTAAAT 59.117 34.615 28.21 0.00 35.42 1.40
4484 5261 5.049198 TCAAAGATGCATCTGTTGTGTTCTC 60.049 40.000 29.34 0.00 37.19 2.87
4498 5275 3.506844 TGCTTACATTGCTCAAAGATGCA 59.493 39.130 0.00 0.00 37.42 3.96
4510 5287 8.697846 ATTTCAGATGTTGATTGCTTACATTG 57.302 30.769 0.00 0.00 35.27 2.82
4517 5294 4.401519 CCAGGATTTCAGATGTTGATTGCT 59.598 41.667 0.00 0.00 35.27 3.91
4569 5346 1.724623 CCAACACTAACCATCGTCACG 59.275 52.381 0.00 0.00 0.00 4.35
4575 5352 2.028385 ACCGAGACCAACACTAACCATC 60.028 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.