Multiple sequence alignment - TraesCS7A01G288500

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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 TraesCS7A01G288500 chr7A 100.000 4733 0 0 1 4733 347282077 347286809 0.000000e+00 8741.0
1 TraesCS7A01G288500 chr7A 83.456 949 120 25 3812 4733 587165977 587166915 0.000000e+00 848.0
2 TraesCS7A01G288500 chr7A 92.233 309 17 6 3555 3861 458679464 458679767 9.410000e-117 431.0
3 TraesCS7A01G288500 chr7A 95.169 207 6 4 3364 3568 715758642 715758438 1.640000e-84 324.0
4 TraesCS7A01G288500 chr7A 98.361 183 2 1 3374 3555 332425546 332425364 2.130000e-83 320.0
5 TraesCS7A01G288500 chr6A 94.549 1431 73 5 1 1427 347329127 347327698 0.000000e+00 2206.0
6 TraesCS7A01G288500 chr6A 92.710 1454 78 8 1 1427 347465326 347463874 0.000000e+00 2073.0
7 TraesCS7A01G288500 chr6A 94.085 1251 66 6 182 1427 533016594 533015347 0.000000e+00 1893.0
8 TraesCS7A01G288500 chr6A 91.872 1218 51 13 3555 4731 533015013 533013803 0.000000e+00 1657.0
9 TraesCS7A01G288500 chr6A 90.835 1222 64 24 3555 4733 347327366 347326150 0.000000e+00 1592.0
10 TraesCS7A01G288500 chr6A 90.612 1225 63 18 3555 4733 347463602 347462384 0.000000e+00 1578.0
11 TraesCS7A01G288500 chr6A 94.633 354 15 2 3022 3373 533015349 533014998 3.220000e-151 545.0
12 TraesCS7A01G288500 chr6A 92.090 354 22 3 3022 3373 347327700 347327351 1.180000e-135 494.0
13 TraesCS7A01G288500 chr3A 93.994 1432 80 4 1 1427 23156536 23157966 0.000000e+00 2163.0
14 TraesCS7A01G288500 chr3A 91.482 1221 56 20 3555 4733 23158300 23159514 0.000000e+00 1635.0
15 TraesCS7A01G288500 chr3A 93.803 355 16 4 3022 3373 23157964 23158315 3.240000e-146 529.0
16 TraesCS7A01G288500 chr2D 93.385 1421 66 7 34 1427 397651917 397650498 0.000000e+00 2078.0
17 TraesCS7A01G288500 chr2D 92.015 814 40 12 3558 4349 397650160 397649350 0.000000e+00 1120.0
18 TraesCS7A01G288500 chr2D 94.915 354 15 2 3022 3373 397650500 397650148 6.920000e-153 551.0
19 TraesCS7A01G288500 chr2D 91.243 354 11 5 4399 4733 397614887 397614535 9.280000e-127 464.0
20 TraesCS7A01G288500 chr4A 90.859 1466 69 20 1535 2971 157568690 157567261 0.000000e+00 1905.0
21 TraesCS7A01G288500 chr4A 95.192 208 6 4 3362 3565 646314391 646314598 4.570000e-85 326.0
22 TraesCS7A01G288500 chr4A 93.388 121 8 0 1425 1545 157568839 157568719 3.760000e-41 180.0
23 TraesCS7A01G288500 chr4A 98.000 50 1 0 2973 3022 157567175 157567126 2.350000e-13 87.9
24 TraesCS7A01G288500 chr3D 94.932 1184 51 5 248 1427 260289445 260290623 0.000000e+00 1845.0
25 TraesCS7A01G288500 chr3D 93.244 1199 57 8 3555 4733 260290961 260292155 0.000000e+00 1744.0
26 TraesCS7A01G288500 chr3D 93.521 355 19 2 3022 3372 260290621 260290975 4.200000e-145 525.0
27 TraesCS7A01G288500 chr3D 93.676 253 15 1 1 252 260285235 260285487 1.240000e-100 377.0
28 TraesCS7A01G288500 chr6B 90.056 1418 105 14 1 1396 312258122 312259525 0.000000e+00 1805.0
29 TraesCS7A01G288500 chr6B 91.854 356 25 3 3022 3373 312260082 312260437 1.180000e-135 494.0
30 TraesCS7A01G288500 chr4B 92.373 944 48 7 1425 2366 394381123 394382044 0.000000e+00 1323.0
31 TraesCS7A01G288500 chr4B 90.831 698 33 8 2339 3022 394382046 394382726 0.000000e+00 905.0
32 TraesCS7A01G288500 chr4B 94.762 210 8 3 3374 3580 146013653 146013444 1.640000e-84 324.0
33 TraesCS7A01G288500 chr4B 93.274 223 7 7 3345 3562 494584893 494584674 5.910000e-84 322.0
34 TraesCS7A01G288500 chr1B 88.953 1032 87 9 1 1007 10263400 10262371 0.000000e+00 1249.0
35 TraesCS7A01G288500 chr1B 88.760 1032 88 11 1 1007 224177300 224176272 0.000000e+00 1238.0
36 TraesCS7A01G288500 chr1B 91.854 356 25 3 3022 3373 224175445 224175090 1.180000e-135 494.0
37 TraesCS7A01G288500 chr1B 90.037 271 14 3 1123 1392 10262374 10262116 5.870000e-89 339.0
38 TraesCS7A01G288500 chr1B 95.305 213 4 6 3357 3565 301282192 301282402 2.730000e-87 333.0
39 TraesCS7A01G288500 chr1B 95.652 207 7 2 3364 3568 263618813 263619019 9.820000e-87 331.0
40 TraesCS7A01G288500 chr1B 88.848 269 19 3 1125 1393 224176273 224176016 2.130000e-83 320.0
41 TraesCS7A01G288500 chr1B 91.176 102 7 1 2495 2594 229963142 229963243 2.300000e-28 137.0
42 TraesCS7A01G288500 chr4D 90.805 870 48 16 1814 2677 317187910 317188753 0.000000e+00 1134.0
43 TraesCS7A01G288500 chr4D 92.327 391 25 4 1425 1814 317186971 317187357 6.920000e-153 551.0
44 TraesCS7A01G288500 chr5B 92.416 356 23 3 3022 3373 457446576 457446221 5.470000e-139 505.0
45 TraesCS7A01G288500 chr5B 84.892 139 14 6 4576 4707 304145100 304145238 2.970000e-27 134.0
46 TraesCS7A01G288500 chr3B 92.416 356 23 3 3022 3373 151852265 151852620 5.470000e-139 505.0
47 TraesCS7A01G288500 chr3B 84.454 238 32 4 4072 4308 327922244 327922477 3.680000e-56 230.0
48 TraesCS7A01G288500 chr3B 77.644 416 47 20 4334 4707 327922471 327922882 1.330000e-50 211.0
49 TraesCS7A01G288500 chr6D 84.486 477 62 10 4072 4545 331180065 331180532 1.200000e-125 460.0
50 TraesCS7A01G288500 chr6D 86.331 139 12 6 4576 4707 331181013 331181151 1.370000e-30 145.0
51 TraesCS7A01G288500 chr1A 92.233 309 16 6 3555 3861 86681731 86681429 9.410000e-117 431.0
52 TraesCS7A01G288500 chr2A 91.909 309 18 6 3555 3861 388042438 388042741 4.380000e-115 425.0
53 TraesCS7A01G288500 chr2A 94.836 213 5 6 3345 3555 334889460 334889668 1.270000e-85 327.0
54 TraesCS7A01G288500 chr2A 96.721 61 2 0 1336 1396 260683911 260683971 8.380000e-18 102.0
55 TraesCS7A01G288500 chr2B 81.064 470 78 8 4072 4538 278321810 278322271 9.680000e-97 364.0
56 TraesCS7A01G288500 chr2B 97.927 193 3 1 3373 3564 48048714 48048522 2.730000e-87 333.0


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 TraesCS7A01G288500 chr7A 347282077 347286809 4732 False 8741.000000 8741 100.000000 1 4733 1 chr7A.!!$F1 4732
1 TraesCS7A01G288500 chr7A 587165977 587166915 938 False 848.000000 848 83.456000 3812 4733 1 chr7A.!!$F3 921
2 TraesCS7A01G288500 chr6A 347462384 347465326 2942 True 1825.500000 2073 91.661000 1 4733 2 chr6A.!!$R2 4732
3 TraesCS7A01G288500 chr6A 347326150 347329127 2977 True 1430.666667 2206 92.491333 1 4733 3 chr6A.!!$R1 4732
4 TraesCS7A01G288500 chr6A 533013803 533016594 2791 True 1365.000000 1893 93.530000 182 4731 3 chr6A.!!$R3 4549
5 TraesCS7A01G288500 chr3A 23156536 23159514 2978 False 1442.333333 2163 93.093000 1 4733 3 chr3A.!!$F1 4732
6 TraesCS7A01G288500 chr2D 397649350 397651917 2567 True 1249.666667 2078 93.438333 34 4349 3 chr2D.!!$R2 4315
7 TraesCS7A01G288500 chr4A 157567126 157568839 1713 True 724.300000 1905 94.082333 1425 3022 3 chr4A.!!$R1 1597
8 TraesCS7A01G288500 chr3D 260285235 260292155 6920 False 1122.750000 1845 93.843250 1 4733 4 chr3D.!!$F1 4732
9 TraesCS7A01G288500 chr6B 312258122 312260437 2315 False 1149.500000 1805 90.955000 1 3373 2 chr6B.!!$F1 3372
10 TraesCS7A01G288500 chr4B 394381123 394382726 1603 False 1114.000000 1323 91.602000 1425 3022 2 chr4B.!!$F1 1597
11 TraesCS7A01G288500 chr1B 10262116 10263400 1284 True 794.000000 1249 89.495000 1 1392 2 chr1B.!!$R1 1391
12 TraesCS7A01G288500 chr1B 224175090 224177300 2210 True 684.000000 1238 89.820667 1 3373 3 chr1B.!!$R2 3372
13 TraesCS7A01G288500 chr4D 317186971 317188753 1782 False 842.500000 1134 91.566000 1425 2677 2 chr4D.!!$F1 1252
14 TraesCS7A01G288500 chr3B 327922244 327922882 638 False 220.500000 230 81.049000 4072 4707 2 chr3B.!!$F2 635
15 TraesCS7A01G288500 chr6D 331180065 331181151 1086 False 302.500000 460 85.408500 4072 4707 2 chr6D.!!$F1 635

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
186 190 1.071471 CACCTGTTTCCTCCTGCGT 59.929 57.895 0.00 0.0 0.00 5.24 F
1046 5081 1.303888 CTGGTGCAGCATCCAACCT 60.304 57.895 20.52 0.0 33.06 3.50 F
2859 8102 0.409092 ATTCATGCCAAGGTGGTCCA 59.591 50.000 0.00 0.0 40.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 6049 0.816825 CTATGCAGCGCCAATCAGGT 60.817 55.000 2.29 0.00 40.61 4.00 R
2991 8326 0.467804 GGAGAGAAGCACCAGGATCC 59.532 60.000 2.48 2.48 0.00 3.36 R
4261 9638 1.003355 CAGCCGACATCCTTGTGGT 60.003 57.895 0.00 0.00 35.79 4.16 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
27 29 1.995626 CAACCTCCCGGATCCTGGT 60.996 63.158 20.59 14.30 0.00 4.00
54 56 3.120191 CCCCTACCTCCTCCCTGT 58.880 66.667 0.00 0.00 0.00 4.00
186 190 1.071471 CACCTGTTTCCTCCTGCGT 59.929 57.895 0.00 0.00 0.00 5.24
297 4265 6.533730 TCATTGTCAGTACAGGTTCTGAAAT 58.466 36.000 9.84 9.25 41.41 2.17
346 4314 4.404394 TCTGGAATCACGTATCCTTGCTAA 59.596 41.667 13.45 0.00 36.64 3.09
354 4322 3.262420 CGTATCCTTGCTAACTTGCAGT 58.738 45.455 0.00 0.00 44.27 4.40
381 4349 8.518702 TGTAATTTTGATTGCATAGCAGTACAA 58.481 29.630 0.00 0.00 40.61 2.41
389 4357 9.389755 TGATTGCATAGCAGTACAATTTAGTTA 57.610 29.630 0.00 0.00 40.61 2.24
415 4383 4.276678 TCTGAAGTTTTGATTCACAGCAGG 59.723 41.667 0.00 0.00 33.28 4.85
459 4427 2.512485 TTCTGCAAACCATTGTGCTG 57.488 45.000 0.00 0.00 41.48 4.41
684 4658 8.761689 ACTATCAAAATGGAAGCCACAATAAAT 58.238 29.630 0.00 0.00 35.80 1.40
727 4701 6.272318 TGATTCAACCATGTTTTCTTGTGTC 58.728 36.000 0.00 0.00 0.00 3.67
730 4704 7.581213 TTCAACCATGTTTTCTTGTGTCTAT 57.419 32.000 0.00 0.00 0.00 1.98
786 4760 2.159734 CGCTGATTCTGAACTGTTGCTC 60.160 50.000 0.00 0.00 0.00 4.26
1029 5064 4.731612 CGACCACTGCGAGCTGCT 62.732 66.667 0.00 0.00 46.63 4.24
1046 5081 1.303888 CTGGTGCAGCATCCAACCT 60.304 57.895 20.52 0.00 33.06 3.50
1072 5107 1.713005 ATGCGCCTCCATCCCTCAAT 61.713 55.000 4.18 0.00 0.00 2.57
1101 5136 2.991728 CGTCGTCGCGAACTCTTTA 58.008 52.632 12.06 0.00 37.72 1.85
1187 5222 5.924356 TCAGTTCAGACCACACTAAAATGA 58.076 37.500 0.00 0.00 0.00 2.57
1259 5295 4.321230 GGAAACAAAGTCGCAGAATGGATT 60.321 41.667 0.00 0.00 39.69 3.01
1461 6049 2.378547 ACTGCCTTGACCAATTAAGGGA 59.621 45.455 6.82 3.38 42.92 4.20
1568 6195 2.524569 TGACAAGCATCGTCAAGTCA 57.475 45.000 0.89 0.00 40.34 3.41
1590 6217 4.825634 CACATCATCCAATGGTCTATGCTT 59.174 41.667 0.00 0.00 0.00 3.91
1661 6291 5.470437 TGTTATTCATGTTGGTCGTTTGCTA 59.530 36.000 0.00 0.00 0.00 3.49
1709 6339 3.475566 AGCTGTGAGCACTCTGTTAAA 57.524 42.857 1.99 0.00 45.56 1.52
1734 6364 5.532406 CAGGTTTATCATGTGTAATCCCAGG 59.468 44.000 12.80 0.00 0.00 4.45
1770 6400 9.129209 GGAAAAATATTTGTACTGTTGCTTCTC 57.871 33.333 0.39 0.00 0.00 2.87
1773 6403 9.683069 AAAATATTTGTACTGTTGCTTCTCTTG 57.317 29.630 0.39 0.00 0.00 3.02
1790 6420 5.684704 TCTCTTGGAATGAAAGTGTTGTCT 58.315 37.500 0.00 0.00 0.00 3.41
1903 7087 9.330063 TGCAGTACCAATTTATTTCTGAGATAG 57.670 33.333 0.00 0.00 0.00 2.08
1904 7088 9.331282 GCAGTACCAATTTATTTCTGAGATAGT 57.669 33.333 0.00 0.00 0.00 2.12
1998 7185 4.768448 TGATTTTGACTCTTGCATGGACAT 59.232 37.500 0.00 0.00 0.00 3.06
2049 7236 6.588719 TGATAAATTGTGGTTAGCTGCTTT 57.411 33.333 7.79 0.00 0.00 3.51
2063 7250 3.900446 GCTTTTGCATGGTCAAGCT 57.100 47.368 0.00 0.00 46.58 3.74
2137 7324 2.687935 AGTTTGTGGGTTGCAGTACTTG 59.312 45.455 0.00 0.00 0.00 3.16
2146 7333 5.057149 GGGTTGCAGTACTTGTGGATATAG 58.943 45.833 0.00 0.00 0.00 1.31
2147 7334 4.511826 GGTTGCAGTACTTGTGGATATAGC 59.488 45.833 0.00 0.00 0.00 2.97
2202 7391 4.508461 TGATCTGTTCTGTTTGCCAATG 57.492 40.909 0.00 0.00 0.00 2.82
2203 7392 3.890756 TGATCTGTTCTGTTTGCCAATGT 59.109 39.130 0.00 0.00 0.00 2.71
2204 7393 3.988379 TCTGTTCTGTTTGCCAATGTC 57.012 42.857 0.00 0.00 0.00 3.06
2205 7394 3.286353 TCTGTTCTGTTTGCCAATGTCA 58.714 40.909 0.00 0.00 0.00 3.58
2206 7395 3.890756 TCTGTTCTGTTTGCCAATGTCAT 59.109 39.130 0.00 0.00 0.00 3.06
2207 7396 3.979948 TGTTCTGTTTGCCAATGTCATG 58.020 40.909 0.00 0.00 0.00 3.07
2208 7397 3.384146 TGTTCTGTTTGCCAATGTCATGT 59.616 39.130 0.00 0.00 0.00 3.21
2246 7435 3.874383 TCTCACCATTTTCCTTGACCA 57.126 42.857 0.00 0.00 0.00 4.02
2327 7520 7.281100 ACATGCCTTTTTAGACTATTCAGCTAC 59.719 37.037 0.00 0.00 0.00 3.58
2374 7596 9.743057 TTTGGTTATTTGATTGTTAACTGACAG 57.257 29.630 7.22 0.00 0.00 3.51
2432 7656 1.903860 ACGGTGAGTTTAGTGCCCATA 59.096 47.619 0.00 0.00 0.00 2.74
2434 7658 3.707611 ACGGTGAGTTTAGTGCCCATATA 59.292 43.478 0.00 0.00 0.00 0.86
2477 7701 9.083080 GTTTGCAAATCATGGGTTATTACTTAC 57.917 33.333 16.21 0.00 0.00 2.34
2478 7702 8.588290 TTGCAAATCATGGGTTATTACTTACT 57.412 30.769 0.00 0.00 0.00 2.24
2479 7703 9.688091 TTGCAAATCATGGGTTATTACTTACTA 57.312 29.630 0.00 0.00 0.00 1.82
2522 7746 4.202388 GGGGACTACTTGGTTCAGTTTACA 60.202 45.833 0.00 0.00 0.00 2.41
2537 7761 6.611381 TCAGTTTACATTTTATGCTCACTGC 58.389 36.000 0.00 0.00 43.25 4.40
2606 7830 5.353394 AGATTTTAATCCCACGTGCTCTA 57.647 39.130 10.91 0.00 36.04 2.43
2626 7850 9.920946 TGCTCTATATTTCCCTTTCAAAAGTAT 57.079 29.630 2.09 0.00 34.20 2.12
2859 8102 0.409092 ATTCATGCCAAGGTGGTCCA 59.591 50.000 0.00 0.00 40.46 4.02
2862 8105 1.638070 TCATGCCAAGGTGGTCCAATA 59.362 47.619 0.00 0.00 40.46 1.90
2875 8118 3.266772 TGGTCCAATAGAGCCAACAGATT 59.733 43.478 0.00 0.00 42.62 2.40
2880 8123 6.995091 GTCCAATAGAGCCAACAGATTAATCT 59.005 38.462 12.37 12.37 37.72 2.40
2932 8183 1.079405 ATCGTGGGCGTCGACATTT 60.079 52.632 17.16 0.00 40.07 2.32
2946 8197 1.537202 GACATTTGTGAGGTGACCAGC 59.463 52.381 3.63 0.00 0.00 4.85
3022 8357 0.336392 TTCTCTCCCTCTGCTGCCTA 59.664 55.000 0.00 0.00 0.00 3.93
3023 8358 0.560193 TCTCTCCCTCTGCTGCCTAT 59.440 55.000 0.00 0.00 0.00 2.57
3036 8371 4.697514 TGCTGCCTATGTTCTCAAGATAC 58.302 43.478 0.00 0.00 0.00 2.24
3050 8385 5.071923 TCTCAAGATACGAGAGAGTGGGATA 59.928 44.000 0.00 0.00 34.59 2.59
3359 8701 8.757982 ATCCTGAAAAATTATATGTGCACTCT 57.242 30.769 19.41 8.06 0.00 3.24
3360 8702 7.988737 TCCTGAAAAATTATATGTGCACTCTG 58.011 34.615 19.41 6.83 0.00 3.35
3361 8703 7.611467 TCCTGAAAAATTATATGTGCACTCTGT 59.389 33.333 19.41 6.45 0.00 3.41
3362 8704 8.892723 CCTGAAAAATTATATGTGCACTCTGTA 58.107 33.333 19.41 5.45 0.00 2.74
3373 8715 6.741992 TGTGCACTCTGTATTTTCTTATGG 57.258 37.500 19.41 0.00 0.00 2.74
3374 8716 6.472016 TGTGCACTCTGTATTTTCTTATGGA 58.528 36.000 19.41 0.00 0.00 3.41
3375 8717 6.939730 TGTGCACTCTGTATTTTCTTATGGAA 59.060 34.615 19.41 0.00 0.00 3.53
3376 8718 7.119699 TGTGCACTCTGTATTTTCTTATGGAAG 59.880 37.037 19.41 0.00 35.16 3.46
3377 8719 6.599244 TGCACTCTGTATTTTCTTATGGAAGG 59.401 38.462 0.00 0.00 35.16 3.46
3378 8720 6.038714 GCACTCTGTATTTTCTTATGGAAGGG 59.961 42.308 0.00 0.00 35.16 3.95
3379 8721 6.543831 CACTCTGTATTTTCTTATGGAAGGGG 59.456 42.308 0.00 0.00 35.16 4.79
3380 8722 6.447084 ACTCTGTATTTTCTTATGGAAGGGGA 59.553 38.462 0.00 0.00 35.16 4.81
3381 8723 6.900194 TCTGTATTTTCTTATGGAAGGGGAG 58.100 40.000 0.00 0.00 35.16 4.30
3382 8724 5.445964 TGTATTTTCTTATGGAAGGGGAGC 58.554 41.667 0.00 0.00 35.16 4.70
3383 8725 3.382083 TTTTCTTATGGAAGGGGAGCC 57.618 47.619 0.00 0.00 35.16 4.70
3384 8726 2.286935 TTCTTATGGAAGGGGAGCCT 57.713 50.000 0.00 0.00 33.09 4.58
3385 8727 2.286935 TCTTATGGAAGGGGAGCCTT 57.713 50.000 0.00 0.00 33.09 4.35
3386 8728 1.846439 TCTTATGGAAGGGGAGCCTTG 59.154 52.381 0.00 0.00 33.09 3.61
3387 8729 0.926293 TTATGGAAGGGGAGCCTTGG 59.074 55.000 0.00 0.00 0.00 3.61
3388 8730 1.645402 TATGGAAGGGGAGCCTTGGC 61.645 60.000 2.97 2.97 0.00 4.52
3389 8731 4.803908 GGAAGGGGAGCCTTGGCG 62.804 72.222 5.95 0.00 0.00 5.69
3397 8739 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
3398 8740 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
3399 8741 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
3400 8742 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
3401 8743 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
3402 8744 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
3403 8745 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
3417 8759 3.677527 GCTGCTGCTTGTGACCAT 58.322 55.556 8.53 0.00 36.03 3.55
3418 8760 1.211969 GCTGCTGCTTGTGACCATG 59.788 57.895 8.53 0.00 36.03 3.66
3419 8761 1.239296 GCTGCTGCTTGTGACCATGA 61.239 55.000 8.53 0.00 36.03 3.07
3420 8762 0.803117 CTGCTGCTTGTGACCATGAG 59.197 55.000 0.00 0.00 0.00 2.90
3421 8763 0.607217 TGCTGCTTGTGACCATGAGG 60.607 55.000 0.00 0.00 42.21 3.86
3435 8777 3.968265 CCATGAGGTTATGGGTTCAAGT 58.032 45.455 0.00 0.00 43.16 3.16
3436 8778 3.947834 CCATGAGGTTATGGGTTCAAGTC 59.052 47.826 0.00 0.00 43.16 3.01
3437 8779 3.713826 TGAGGTTATGGGTTCAAGTCC 57.286 47.619 0.00 0.00 0.00 3.85
3438 8780 3.256704 TGAGGTTATGGGTTCAAGTCCT 58.743 45.455 0.00 0.00 0.00 3.85
3439 8781 3.009033 TGAGGTTATGGGTTCAAGTCCTG 59.991 47.826 0.00 0.00 0.00 3.86
3440 8782 2.308866 AGGTTATGGGTTCAAGTCCTGG 59.691 50.000 0.00 0.00 0.00 4.45
3441 8783 2.307686 GGTTATGGGTTCAAGTCCTGGA 59.692 50.000 0.00 0.00 0.00 3.86
3442 8784 3.245122 GGTTATGGGTTCAAGTCCTGGAA 60.245 47.826 0.00 0.00 0.00 3.53
3443 8785 4.403734 GTTATGGGTTCAAGTCCTGGAAA 58.596 43.478 0.00 0.00 0.00 3.13
3444 8786 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
3445 8787 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
3459 8801 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3460 8802 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3461 8803 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3462 8804 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3463 8805 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3464 8806 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3465 8807 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3466 8808 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3467 8809 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3468 8810 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3469 8811 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3470 8812 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3471 8813 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3472 8814 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3473 8815 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3474 8816 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3475 8817 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3476 8818 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3477 8819 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3478 8820 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3479 8821 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3480 8822 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
3481 8823 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
3482 8824 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
3483 8825 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
3484 8826 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
3485 8827 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
3486 8828 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
3487 8829 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
3488 8830 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
3489 8831 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
3490 8832 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
3491 8833 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
3492 8834 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
3493 8835 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
3494 8836 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
3495 8837 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
3496 8838 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
3501 8843 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3502 8844 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3503 8845 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3504 8846 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3505 8847 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3506 8848 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3507 8849 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3508 8850 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3509 8851 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
3510 8852 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
3511 8853 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
3512 8854 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
3513 8855 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
3514 8856 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
3515 8857 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
3516 8858 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
3517 8859 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
3518 8860 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3519 8861 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3520 8862 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3542 8884 2.910205 CGGGAGCTACATGCATCAG 58.090 57.895 0.00 0.00 45.94 2.90
3543 8885 0.602106 CGGGAGCTACATGCATCAGG 60.602 60.000 0.00 0.00 45.94 3.86
3544 8886 0.471617 GGGAGCTACATGCATCAGGT 59.528 55.000 8.83 8.83 45.94 4.00
3545 8887 1.133976 GGGAGCTACATGCATCAGGTT 60.134 52.381 10.11 0.00 45.94 3.50
3546 8888 1.945394 GGAGCTACATGCATCAGGTTG 59.055 52.381 10.11 2.66 45.94 3.77
3547 8889 1.332997 GAGCTACATGCATCAGGTTGC 59.667 52.381 12.12 12.12 44.17 4.17
3548 8890 0.383231 GCTACATGCATCAGGTTGCC 59.617 55.000 9.81 0.00 39.88 4.52
3549 8891 1.027357 CTACATGCATCAGGTTGCCC 58.973 55.000 0.00 0.00 42.06 5.36
3550 8892 0.625316 TACATGCATCAGGTTGCCCT 59.375 50.000 0.00 0.00 44.02 5.19
3551 8893 0.251922 ACATGCATCAGGTTGCCCTT 60.252 50.000 0.00 0.00 39.89 3.95
3552 8894 0.899720 CATGCATCAGGTTGCCCTTT 59.100 50.000 0.00 0.00 39.89 3.11
3553 8895 1.276989 CATGCATCAGGTTGCCCTTTT 59.723 47.619 0.00 0.00 39.89 2.27
3687 9029 4.998033 TCACCCAAAAGTTTGAAAAACCAC 59.002 37.500 5.34 0.00 40.55 4.16
3689 9031 6.014499 TCACCCAAAAGTTTGAAAAACCACTA 60.014 34.615 5.34 0.00 40.55 2.74
3953 9303 6.442513 AAAAGTTCAGACTCTTGTTTCCTG 57.557 37.500 0.00 0.00 34.21 3.86
3975 9325 5.897050 TGAAGTGTTTGTTTTGGTATGTCC 58.103 37.500 0.00 0.00 0.00 4.02
3989 9339 2.610438 ATGTCCAGCCCAAACAATCT 57.390 45.000 0.00 0.00 0.00 2.40
3999 9349 6.709846 CCAGCCCAAACAATCTTCAAATTTTA 59.290 34.615 0.00 0.00 0.00 1.52
4068 9420 7.867305 TGGACATGTTCAGTACAAACTTTTA 57.133 32.000 1.52 0.00 40.89 1.52
4230 9585 4.074259 TCTCATCAGTTCAACAACATGGG 58.926 43.478 0.00 0.00 34.60 4.00
4261 9638 1.872234 GTAGTGATCTTGCGCGCGA 60.872 57.895 37.18 24.92 0.00 5.87
4458 9838 1.405105 GAAAATGCAGGAAGCCGCATA 59.595 47.619 13.28 0.00 44.83 3.14
4533 9916 2.224090 TGAAGGTAAGCTTGTGCGTGTA 60.224 45.455 9.86 0.00 45.42 2.90
4682 10523 2.157668 CCTGCACGTACTTGTTGCTAAG 59.842 50.000 0.93 0.00 0.00 2.18
4714 10557 6.079424 TGTTAAACTTGTTATGAAGCCACC 57.921 37.500 0.00 0.00 0.00 4.61
4715 10558 5.594725 TGTTAAACTTGTTATGAAGCCACCA 59.405 36.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 169 0.606673 GCAGGAGGAAACAGGTGGAC 60.607 60.000 0.00 0.00 0.00 4.02
186 190 2.126228 GATTCGCACCGTCCGACA 60.126 61.111 0.00 0.00 34.01 4.35
255 4222 3.976793 TGAACTATGGATCGACGGTAC 57.023 47.619 0.00 0.00 0.00 3.34
297 4265 3.264964 GTCCCCCAACATGTACTAGGAAA 59.735 47.826 0.00 0.00 0.00 3.13
354 4322 8.518702 TGTACTGCTATGCAATCAAAATTACAA 58.481 29.630 0.00 0.00 38.41 2.41
389 4357 5.766670 TGCTGTGAATCAAAACTTCAGAGAT 59.233 36.000 12.66 0.00 43.20 2.75
415 4383 1.745653 GGCAGCTGGGACTAAATTGTC 59.254 52.381 17.12 0.00 36.31 3.18
588 4557 2.818432 AGCTCCTTGTCAGCATTTCAAG 59.182 45.455 0.00 0.00 39.56 3.02
710 4684 7.936847 TCAGTAATAGACACAAGAAAACATGGT 59.063 33.333 0.00 0.00 0.00 3.55
719 4693 7.284919 TGTCAGTTCAGTAATAGACACAAGA 57.715 36.000 0.00 0.00 30.83 3.02
730 4704 9.826574 AGTTTAGTAACATTGTCAGTTCAGTAA 57.173 29.630 0.00 0.00 36.70 2.24
1013 5026 3.117171 CAGCAGCTCGCAGTGGTC 61.117 66.667 10.16 0.00 46.13 4.02
1029 5064 1.604308 CAGGTTGGATGCTGCACCA 60.604 57.895 16.47 16.47 0.00 4.17
1072 5107 2.761195 CGACGACGCATCTGGGAGA 61.761 63.158 0.00 0.00 0.00 3.71
1096 5131 1.476833 GGCAGCGATGGGGAATAAAGA 60.477 52.381 1.46 0.00 0.00 2.52
1101 5136 2.512896 GAGGCAGCGATGGGGAAT 59.487 61.111 1.46 0.00 0.00 3.01
1259 5295 6.620877 ACCATGGAAGTATACTCTGTTCAA 57.379 37.500 21.47 0.00 0.00 2.69
1436 6024 4.082571 CCTTAATTGGTCAAGGCAGTCAAG 60.083 45.833 0.00 0.00 35.24 3.02
1437 6025 3.826157 CCTTAATTGGTCAAGGCAGTCAA 59.174 43.478 0.00 0.00 35.24 3.18
1461 6049 0.816825 CTATGCAGCGCCAATCAGGT 60.817 55.000 2.29 0.00 40.61 4.00
1515 6103 6.471146 GGTCTGTGATAAGCCATATGAGAAT 58.529 40.000 3.65 0.00 0.00 2.40
1518 6106 4.285517 AGGGTCTGTGATAAGCCATATGAG 59.714 45.833 3.65 0.00 35.46 2.90
1568 6195 4.719026 AGCATAGACCATTGGATGATGT 57.281 40.909 10.37 0.00 0.00 3.06
1590 6217 2.553602 TGTACTCTTCGTGCCGAACTTA 59.446 45.455 6.01 0.00 41.05 2.24
1607 6237 6.944096 AGAGTAAATAAAGGGTCTGGTGTAC 58.056 40.000 0.00 0.00 0.00 2.90
1608 6238 7.016858 ACAAGAGTAAATAAAGGGTCTGGTGTA 59.983 37.037 0.00 0.00 0.00 2.90
1609 6239 6.183361 ACAAGAGTAAATAAAGGGTCTGGTGT 60.183 38.462 0.00 0.00 0.00 4.16
1661 6291 2.035704 TGGATTGTGCGCTGAAACATTT 59.964 40.909 9.73 0.00 0.00 2.32
1709 6339 6.073447 TGGGATTACACATGATAAACCTGT 57.927 37.500 0.00 0.00 0.00 4.00
1734 6364 9.869757 AGTACAAATATTTTTCCCAAATACAGC 57.130 29.630 0.00 0.00 0.00 4.40
1770 6400 4.741676 GCAAGACAACACTTTCATTCCAAG 59.258 41.667 0.00 0.00 0.00 3.61
1773 6403 4.276926 AGAGCAAGACAACACTTTCATTCC 59.723 41.667 0.00 0.00 0.00 3.01
1811 6441 3.950395 GGGAGAAAGAACAGATTGGATGG 59.050 47.826 0.00 0.00 0.00 3.51
2040 7227 1.908344 TGACCATGCAAAAGCAGCTA 58.092 45.000 0.00 0.00 0.00 3.32
2049 7236 1.302752 AGCGAGCTTGACCATGCAA 60.303 52.632 4.70 0.00 34.33 4.08
2063 7250 6.835819 AAGTATATAGTGCCTTATCAGCGA 57.164 37.500 0.00 0.00 0.00 4.93
2137 7324 6.260936 AGCAACACATTTACAGCTATATCCAC 59.739 38.462 0.00 0.00 0.00 4.02
2146 7333 1.270550 AGCCAGCAACACATTTACAGC 59.729 47.619 0.00 0.00 0.00 4.40
2147 7334 2.923605 GCAGCCAGCAACACATTTACAG 60.924 50.000 0.00 0.00 44.79 2.74
2292 7481 2.531522 AAAAGGCATGTGTTTGGAGC 57.468 45.000 0.00 0.00 0.00 4.70
2343 7536 8.919145 AGTTAACAATCAAATAACCAAACAGGA 58.081 29.630 8.61 0.00 41.22 3.86
2413 7637 2.684001 TATGGGCACTAAACTCACCG 57.316 50.000 0.00 0.00 0.00 4.94
2432 7656 9.938280 TTGCAAACAACAGTATTACTACTCTAT 57.062 29.630 0.00 0.00 35.99 1.98
2434 7658 8.671384 TTTGCAAACAACAGTATTACTACTCT 57.329 30.769 8.05 0.00 35.99 3.24
2477 7701 8.375506 TCCCCAATATTCTGCAGTAACTAATAG 58.624 37.037 14.67 0.00 0.00 1.73
2478 7702 8.154856 GTCCCCAATATTCTGCAGTAACTAATA 58.845 37.037 14.67 10.19 0.00 0.98
2479 7703 6.998673 GTCCCCAATATTCTGCAGTAACTAAT 59.001 38.462 14.67 8.17 0.00 1.73
2606 7830 8.366359 ACAGCATACTTTTGAAAGGGAAATAT 57.634 30.769 8.23 0.00 40.31 1.28
2626 7850 7.124147 TGCCATATGTAGCTATAATCTACAGCA 59.876 37.037 15.49 15.29 46.39 4.41
2627 7851 7.492524 TGCCATATGTAGCTATAATCTACAGC 58.507 38.462 15.49 13.73 46.39 4.40
2678 7902 4.696899 AGCGTAATTCCTTTTTACCAGC 57.303 40.909 0.00 0.00 0.00 4.85
2772 8000 7.505923 TGCGCTGGGAGTATATATCTATATTGT 59.494 37.037 9.73 0.00 31.69 2.71
2777 8005 5.300539 CAGTGCGCTGGGAGTATATATCTAT 59.699 44.000 19.78 0.00 39.01 1.98
2880 8123 3.650950 GTCCTGCTGGCCTTCCCA 61.651 66.667 3.32 0.00 42.79 4.37
2904 8155 1.234615 CGCCCACGATGTCAACCTTT 61.235 55.000 0.00 0.00 43.93 3.11
2932 8183 2.421314 CGTGCTGGTCACCTCACA 59.579 61.111 16.58 1.04 42.69 3.58
2946 8197 2.279120 GCGCTCTCCTCATCCGTG 60.279 66.667 0.00 0.00 0.00 4.94
2991 8326 0.467804 GGAGAGAAGCACCAGGATCC 59.532 60.000 2.48 2.48 0.00 3.36
3022 8357 5.067153 CCACTCTCTCGTATCTTGAGAACAT 59.933 44.000 0.00 0.00 41.66 2.71
3023 8358 4.396478 CCACTCTCTCGTATCTTGAGAACA 59.604 45.833 0.00 0.00 41.66 3.18
3036 8371 1.609072 TGCGAATATCCCACTCTCTCG 59.391 52.381 0.00 0.00 0.00 4.04
3050 8385 0.742505 CCAGCCACAATCATGCGAAT 59.257 50.000 0.00 0.00 0.00 3.34
3099 8435 7.409697 ACATCGTGTCATAAGCAAATAACATC 58.590 34.615 0.00 0.00 0.00 3.06
3359 8701 5.445964 GCTCCCCTTCCATAAGAAAATACA 58.554 41.667 0.00 0.00 34.37 2.29
3360 8702 4.827835 GGCTCCCCTTCCATAAGAAAATAC 59.172 45.833 0.00 0.00 34.37 1.89
3361 8703 4.731929 AGGCTCCCCTTCCATAAGAAAATA 59.268 41.667 0.00 0.00 38.74 1.40
3362 8704 3.533487 AGGCTCCCCTTCCATAAGAAAAT 59.467 43.478 0.00 0.00 38.74 1.82
3363 8705 2.926329 AGGCTCCCCTTCCATAAGAAAA 59.074 45.455 0.00 0.00 38.74 2.29
3364 8706 2.573463 AGGCTCCCCTTCCATAAGAAA 58.427 47.619 0.00 0.00 38.74 2.52
3365 8707 2.286935 AGGCTCCCCTTCCATAAGAA 57.713 50.000 0.00 0.00 38.74 2.52
3379 8721 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
3380 8722 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
3381 8723 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
3382 8724 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
3383 8725 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
3384 8726 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
3385 8727 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
3386 8728 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
3400 8742 1.211969 CATGGTCACAAGCAGCAGC 59.788 57.895 0.00 0.00 42.56 5.25
3401 8743 0.803117 CTCATGGTCACAAGCAGCAG 59.197 55.000 0.00 0.00 36.11 4.24
3402 8744 0.607217 CCTCATGGTCACAAGCAGCA 60.607 55.000 0.00 0.00 36.11 4.41
3403 8745 0.607489 ACCTCATGGTCACAAGCAGC 60.607 55.000 0.00 0.00 44.78 5.25
3404 8746 3.639099 ACCTCATGGTCACAAGCAG 57.361 52.632 0.00 0.00 44.78 4.24
3414 8756 3.947834 GACTTGAACCCATAACCTCATGG 59.052 47.826 0.00 0.00 44.44 3.66
3415 8757 3.947834 GGACTTGAACCCATAACCTCATG 59.052 47.826 0.00 0.00 0.00 3.07
3416 8758 3.852578 AGGACTTGAACCCATAACCTCAT 59.147 43.478 0.00 0.00 0.00 2.90
3417 8759 3.009033 CAGGACTTGAACCCATAACCTCA 59.991 47.826 0.00 0.00 0.00 3.86
3418 8760 3.610911 CAGGACTTGAACCCATAACCTC 58.389 50.000 0.00 0.00 0.00 3.85
3419 8761 2.308866 CCAGGACTTGAACCCATAACCT 59.691 50.000 0.00 0.00 0.00 3.50
3420 8762 2.307686 TCCAGGACTTGAACCCATAACC 59.692 50.000 0.00 0.00 0.00 2.85
3421 8763 3.713826 TCCAGGACTTGAACCCATAAC 57.286 47.619 0.00 0.00 0.00 1.89
3422 8764 4.141135 TGTTTCCAGGACTTGAACCCATAA 60.141 41.667 0.00 0.00 0.00 1.90
3423 8765 3.396276 TGTTTCCAGGACTTGAACCCATA 59.604 43.478 0.00 0.00 0.00 2.74
3424 8766 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
3425 8767 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
3426 8768 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3427 8769 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3428 8770 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3429 8771 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3430 8772 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3431 8773 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3432 8774 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3433 8775 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3434 8776 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3435 8777 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
3436 8778 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3437 8779 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3449 8791 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
3450 8792 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3451 8793 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3452 8794 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3453 8795 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3454 8796 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3455 8797 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3456 8798 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3457 8799 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3458 8800 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3459 8801 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3460 8802 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3461 8803 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
3462 8804 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
3463 8805 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
3464 8806 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
3465 8807 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
3466 8808 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
3467 8809 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
3468 8810 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
3469 8811 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
3470 8812 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
3471 8813 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
3472 8814 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
3473 8815 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
3474 8816 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
3475 8817 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
3485 8827 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3486 8828 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3487 8829 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3488 8830 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3489 8831 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3490 8832 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3491 8833 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3492 8834 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
3493 8835 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
3494 8836 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
3495 8837 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
3496 8838 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
3497 8839 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
3498 8840 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
3499 8841 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
3500 8842 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
3501 8843 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
3502 8844 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
3503 8845 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
3515 8857 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3518 8860 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3519 8861 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3520 8862 0.816825 ATGCATGTAGCTCCCGCTTG 60.817 55.000 0.00 0.00 46.47 4.01
3521 8863 0.533755 GATGCATGTAGCTCCCGCTT 60.534 55.000 2.46 0.00 46.47 4.68
3523 8865 1.226686 CTGATGCATGTAGCTCCCGC 61.227 60.000 2.46 0.00 45.94 6.13
3524 8866 0.602106 CCTGATGCATGTAGCTCCCG 60.602 60.000 2.46 0.00 45.94 5.14
3525 8867 0.471617 ACCTGATGCATGTAGCTCCC 59.528 55.000 2.46 0.00 45.94 4.30
3526 8868 1.945394 CAACCTGATGCATGTAGCTCC 59.055 52.381 2.46 0.00 45.94 4.70
3527 8869 1.332997 GCAACCTGATGCATGTAGCTC 59.667 52.381 2.46 0.00 45.70 4.09
3528 8870 1.386533 GCAACCTGATGCATGTAGCT 58.613 50.000 2.46 0.00 45.70 3.32
3529 8871 3.932459 GCAACCTGATGCATGTAGC 57.068 52.632 2.46 0.00 45.70 3.58
3544 8886 9.377312 GCATAAGAAAATACATAAAAAGGGCAA 57.623 29.630 0.00 0.00 0.00 4.52
3545 8887 8.757877 AGCATAAGAAAATACATAAAAAGGGCA 58.242 29.630 0.00 0.00 0.00 5.36
3546 8888 9.599866 AAGCATAAGAAAATACATAAAAAGGGC 57.400 29.630 0.00 0.00 0.00 5.19
3687 9029 9.436957 AACATATGTTACCAGAACTGAAAGTAG 57.563 33.333 19.51 0.00 41.36 2.57
3689 9031 8.691661 AAACATATGTTACCAGAACTGAAAGT 57.308 30.769 21.07 0.00 44.09 2.66
3953 9303 5.897050 TGGACATACCAAAACAAACACTTC 58.103 37.500 0.00 0.00 46.75 3.01
3975 9325 6.622833 AAAATTTGAAGATTGTTTGGGCTG 57.377 33.333 0.00 0.00 0.00 4.85
4043 9394 6.767524 AAAGTTTGTACTGAACATGTCCAA 57.232 33.333 0.00 0.00 38.10 3.53
4207 9562 4.703575 CCCATGTTGTTGAACTGATGAGAT 59.296 41.667 0.00 0.00 32.79 2.75
4242 9597 2.615618 GCGCGCAAGATCACTACG 59.384 61.111 29.10 0.00 43.02 3.51
4261 9638 1.003355 CAGCCGACATCCTTGTGGT 60.003 57.895 0.00 0.00 35.79 4.16
4298 9676 3.495806 GCCAGGCAGAATGTAGATAGCTT 60.496 47.826 6.55 0.00 39.31 3.74
4458 9838 4.339247 GGTGTGCATTAGCTCCACATAAAT 59.661 41.667 11.08 0.00 41.77 1.40
4533 9916 3.312736 ACCAACCACCTCAGACAAATT 57.687 42.857 0.00 0.00 0.00 1.82
4682 10523 9.509855 TTCATAACAAGTTTAACAACACACATC 57.490 29.630 0.00 0.00 35.05 3.06


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

AutoCloner maintained by Alex Coulton.