Multiple sequence alignment - TraesCS4B01G125900

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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 TraesCS4B01G125900 chr4B 100.000 2510 0 0 1 2510 157887190 157889699 0.000000e+00 4636
1 TraesCS4B01G125900 chr4B 92.760 221 14 2 2292 2510 347858876 347859096 4.030000e-83 318
2 TraesCS4B01G125900 chr6D 91.816 1564 97 9 1 1533 303615593 303614030 0.000000e+00 2150
3 TraesCS4B01G125900 chr6D 91.432 1564 103 9 1 1533 131934959 131933396 0.000000e+00 2117
4 TraesCS4B01G125900 chr6D 87.887 776 88 5 1536 2306 407535589 407536363 0.000000e+00 907
5 TraesCS4B01G125900 chr6D 94.118 578 34 0 957 1534 296684803 296685380 0.000000e+00 880
6 TraesCS4B01G125900 chr2D 91.752 1564 97 10 1 1533 314365844 314367406 0.000000e+00 2145
7 TraesCS4B01G125900 chr4D 91.598 1571 100 10 1 1539 486778043 486776473 0.000000e+00 2141
8 TraesCS4B01G125900 chr4D 93.772 578 35 1 957 1533 112970063 112969486 0.000000e+00 867
9 TraesCS4B01G125900 chr5D 91.677 1562 99 9 3 1533 482813496 482815057 0.000000e+00 2135
10 TraesCS4B01G125900 chr7D 91.496 1564 102 9 1 1533 188545867 188544304 0.000000e+00 2122
11 TraesCS4B01G125900 chr1D 91.443 1566 101 11 1 1535 272539875 272538312 0.000000e+00 2119
12 TraesCS4B01G125900 chr5B 94.363 958 50 3 1 954 34044774 34043817 0.000000e+00 1467
13 TraesCS4B01G125900 chr5B 93.717 955 58 2 1 954 245600824 245599871 0.000000e+00 1430
14 TraesCS4B01G125900 chr5B 85.770 766 106 2 1536 2298 69538256 69537491 0.000000e+00 808
15 TraesCS4B01G125900 chr3A 94.346 955 53 1 1 954 312003740 312002786 0.000000e+00 1463
16 TraesCS4B01G125900 chr1B 94.044 957 52 4 1 954 14853889 14854843 0.000000e+00 1447
17 TraesCS4B01G125900 chr1B 85.935 775 94 9 1536 2306 329278910 329278147 0.000000e+00 813
18 TraesCS4B01G125900 chr1B 84.000 775 118 5 1536 2306 411410058 411409286 0.000000e+00 739
19 TraesCS4B01G125900 chr1B 95.631 206 9 0 2305 2510 446871212 446871417 5.180000e-87 331
20 TraesCS4B01G125900 chr1B 94.787 211 11 0 2300 2510 271666244 271666034 1.860000e-86 329
21 TraesCS4B01G125900 chr1B 94.313 211 12 0 2300 2510 120089527 120089317 8.660000e-85 324
22 TraesCS4B01G125900 chr2A 93.521 957 57 5 1 954 619837809 619838763 0.000000e+00 1419
23 TraesCS4B01G125900 chr6B 86.216 769 98 6 1536 2300 476207215 476207979 0.000000e+00 826
24 TraesCS4B01G125900 chr6B 84.000 775 119 5 1536 2306 304217333 304218106 0.000000e+00 739
25 TraesCS4B01G125900 chr6B 94.787 211 11 0 2300 2510 484550481 484550271 1.860000e-86 329
26 TraesCS4B01G125900 chr3B 85.695 755 97 6 1536 2283 719098207 719098957 0.000000e+00 785
27 TraesCS4B01G125900 chr3B 84.129 775 117 5 1536 2306 441356480 441357252 0.000000e+00 745
28 TraesCS4B01G125900 chr7B 83.742 775 122 3 1536 2306 672054329 672053555 0.000000e+00 730
29 TraesCS4B01G125900 chr7B 95.238 210 9 1 2302 2510 248405854 248406063 5.180000e-87 331
30 TraesCS4B01G125900 chr7B 95.192 208 9 1 2299 2505 133007624 133007417 6.690000e-86 327
31 TraesCS4B01G125900 chr2B 94.787 211 11 0 2300 2510 512545745 512545535 1.860000e-86 329
32 TraesCS4B01G125900 chr2B 94.787 211 11 0 2300 2510 554775361 554775571 1.860000e-86 329


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 TraesCS4B01G125900 chr4B 157887190 157889699 2509 False 4636 4636 100.000 1 2510 1 chr4B.!!$F1 2509
1 TraesCS4B01G125900 chr6D 303614030 303615593 1563 True 2150 2150 91.816 1 1533 1 chr6D.!!$R2 1532
2 TraesCS4B01G125900 chr6D 131933396 131934959 1563 True 2117 2117 91.432 1 1533 1 chr6D.!!$R1 1532
3 TraesCS4B01G125900 chr6D 407535589 407536363 774 False 907 907 87.887 1536 2306 1 chr6D.!!$F2 770
4 TraesCS4B01G125900 chr6D 296684803 296685380 577 False 880 880 94.118 957 1534 1 chr6D.!!$F1 577
5 TraesCS4B01G125900 chr2D 314365844 314367406 1562 False 2145 2145 91.752 1 1533 1 chr2D.!!$F1 1532
6 TraesCS4B01G125900 chr4D 486776473 486778043 1570 True 2141 2141 91.598 1 1539 1 chr4D.!!$R2 1538
7 TraesCS4B01G125900 chr4D 112969486 112970063 577 True 867 867 93.772 957 1533 1 chr4D.!!$R1 576
8 TraesCS4B01G125900 chr5D 482813496 482815057 1561 False 2135 2135 91.677 3 1533 1 chr5D.!!$F1 1530
9 TraesCS4B01G125900 chr7D 188544304 188545867 1563 True 2122 2122 91.496 1 1533 1 chr7D.!!$R1 1532
10 TraesCS4B01G125900 chr1D 272538312 272539875 1563 True 2119 2119 91.443 1 1535 1 chr1D.!!$R1 1534
11 TraesCS4B01G125900 chr5B 34043817 34044774 957 True 1467 1467 94.363 1 954 1 chr5B.!!$R1 953
12 TraesCS4B01G125900 chr5B 245599871 245600824 953 True 1430 1430 93.717 1 954 1 chr5B.!!$R3 953
13 TraesCS4B01G125900 chr5B 69537491 69538256 765 True 808 808 85.770 1536 2298 1 chr5B.!!$R2 762
14 TraesCS4B01G125900 chr3A 312002786 312003740 954 True 1463 1463 94.346 1 954 1 chr3A.!!$R1 953
15 TraesCS4B01G125900 chr1B 14853889 14854843 954 False 1447 1447 94.044 1 954 1 chr1B.!!$F1 953
16 TraesCS4B01G125900 chr1B 329278147 329278910 763 True 813 813 85.935 1536 2306 1 chr1B.!!$R3 770
17 TraesCS4B01G125900 chr1B 411409286 411410058 772 True 739 739 84.000 1536 2306 1 chr1B.!!$R4 770
18 TraesCS4B01G125900 chr2A 619837809 619838763 954 False 1419 1419 93.521 1 954 1 chr2A.!!$F1 953
19 TraesCS4B01G125900 chr6B 476207215 476207979 764 False 826 826 86.216 1536 2300 1 chr6B.!!$F2 764
20 TraesCS4B01G125900 chr6B 304217333 304218106 773 False 739 739 84.000 1536 2306 1 chr6B.!!$F1 770
21 TraesCS4B01G125900 chr3B 719098207 719098957 750 False 785 785 85.695 1536 2283 1 chr3B.!!$F2 747
22 TraesCS4B01G125900 chr3B 441356480 441357252 772 False 745 745 84.129 1536 2306 1 chr3B.!!$F1 770
23 TraesCS4B01G125900 chr7B 672053555 672054329 774 True 730 730 83.742 1536 2306 1 chr7B.!!$R2 770

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
166 169 0.313987 GGCAAAGTATTATGGCGGGC 59.686 55.0 0.0 0.0 32.19 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2189 0.177141 CCCGGCAGAGGATTTTCGTA 59.823 55.0 0.0 0.0 0.0 3.43 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
100 101 2.484889 CGAGCTAAGTATTTCCCTGGC 58.515 52.381 0.00 0.00 0.00 4.85
121 122 4.857037 GGCGGAGATTTATTGAACACAAAC 59.143 41.667 0.00 0.00 0.00 2.93
166 169 0.313987 GGCAAAGTATTATGGCGGGC 59.686 55.000 0.00 0.00 32.19 6.13
169 173 1.263217 CAAAGTATTATGGCGGGCGTC 59.737 52.381 0.00 0.00 0.00 5.19
187 191 4.439563 GGCGTCAATACCTTAAAACATGGG 60.440 45.833 0.00 0.00 0.00 4.00
241 246 2.827921 GACATTTGGGAAGATGCTTGGT 59.172 45.455 0.00 0.00 0.00 3.67
243 248 3.647590 ACATTTGGGAAGATGCTTGGTTT 59.352 39.130 0.00 0.00 0.00 3.27
265 270 8.957466 GGTTTCCTAACTGTGCTAATAGAAAAT 58.043 33.333 0.00 0.00 34.59 1.82
276 281 8.049117 TGTGCTAATAGAAAATTCATCACTCCT 58.951 33.333 0.00 0.00 0.00 3.69
286 291 2.492025 TCATCACTCCTAAGGGGCAAT 58.508 47.619 0.00 0.00 34.39 3.56
324 329 1.211949 TCGGATTTCATTGACCCCTCC 59.788 52.381 0.00 0.00 0.00 4.30
367 372 3.390967 TCTCATCAGACAAACCTTGTGGA 59.609 43.478 0.00 0.00 45.52 4.02
382 387 2.857483 TGTGGACCGTTGATTCACAAT 58.143 42.857 0.00 0.00 40.76 2.71
513 518 7.147689 TGGGATTATCAACATGGAAGGAAATTG 60.148 37.037 0.00 0.00 0.00 2.32
516 521 4.870123 TCAACATGGAAGGAAATTGTGG 57.130 40.909 0.00 0.00 0.00 4.17
535 540 4.215109 GTGGCATACTAATGGAATGGGTT 58.785 43.478 0.00 0.00 33.38 4.11
588 593 4.365514 TTGGAAGTTATCTTGTCCAGCA 57.634 40.909 0.00 0.00 31.96 4.41
752 761 2.868899 CCAGAAGGCAAAAGAGGTCTT 58.131 47.619 0.00 0.00 37.91 3.01
882 891 1.887797 TGGGGTCCCAGAATATTCGT 58.112 50.000 10.98 0.00 41.89 3.85
885 894 2.484947 GGGGTCCCAGAATATTCGTGAC 60.485 54.545 10.98 18.74 35.81 3.67
889 898 3.809832 GTCCCAGAATATTCGTGACATGG 59.190 47.826 20.58 16.18 0.00 3.66
954 963 1.815003 GTGCACAAGGAGGGAATTCAG 59.185 52.381 13.17 0.00 0.00 3.02
955 964 0.813821 GCACAAGGAGGGAATTCAGC 59.186 55.000 7.93 0.00 0.00 4.26
971 1010 7.040823 GGGAATTCAGCCTCTTATGACTAATTG 60.041 40.741 7.93 0.00 0.00 2.32
1016 1056 4.344978 GCTTCTATGAAAAGAGGGGGTTT 58.655 43.478 0.00 0.00 0.00 3.27
1026 1066 0.618981 GAGGGGGTTTGATTCGTCCT 59.381 55.000 0.00 0.00 0.00 3.85
1075 1115 8.283699 TGTTGATGCTTCTTTTGATCATGATA 57.716 30.769 8.54 0.00 0.00 2.15
1081 1121 9.967346 ATGCTTCTTTTGATCATGATATTCTTG 57.033 29.630 8.54 0.00 0.00 3.02
1090 1130 7.951591 TGATCATGATATTCTTGAAGGTACGA 58.048 34.615 8.54 0.00 34.79 3.43
1160 1200 3.928375 ACTTGGAAAATTGATCATTGCGC 59.072 39.130 0.00 0.00 0.00 6.09
1214 1254 0.731514 TTCGGTCTTTCACTAGCGCG 60.732 55.000 0.00 0.00 36.60 6.86
1248 1288 7.954788 TTGCAAACACCTTGTTATTAATTCC 57.045 32.000 0.00 0.00 40.14 3.01
1249 1289 7.055667 TGCAAACACCTTGTTATTAATTCCA 57.944 32.000 0.00 0.00 40.14 3.53
1325 1365 2.282290 CGGCGGCAATTTTTGATGATTC 59.718 45.455 10.53 0.00 0.00 2.52
1352 1392 5.461032 TTTTTGGCGTGTGATTTTCCTAT 57.539 34.783 0.00 0.00 0.00 2.57
1398 1438 1.134946 GAAGCCAATAAGGTTGCGCAT 59.865 47.619 12.75 0.00 40.61 4.73
1403 1443 1.132834 CAATAAGGTTGCGCATGAGCA 59.867 47.619 20.84 20.84 46.54 4.26
1515 1555 6.177610 TGTTATTTCGGCTGAATAAAGTCCT 58.822 36.000 9.22 0.00 33.20 3.85
1648 1688 4.618920 AAATGACTAAGACCGTCACCTT 57.381 40.909 0.40 0.00 43.44 3.50
1651 1691 2.696707 TGACTAAGACCGTCACCTTGTT 59.303 45.455 0.40 0.00 36.54 2.83
1717 1757 1.349688 TGTTCAAATGGGCGTCCTAGT 59.650 47.619 7.97 0.00 0.00 2.57
1730 1770 5.130292 GCGTCCTAGTAGCCAAATATGTA 57.870 43.478 0.00 0.00 0.00 2.29
1731 1771 5.721232 GCGTCCTAGTAGCCAAATATGTAT 58.279 41.667 0.00 0.00 0.00 2.29
1762 1806 1.239347 GTTCCAAGGCCAGAAGTCAC 58.761 55.000 5.01 0.00 0.00 3.67
1797 1841 5.153950 AGAAGGCGAAGTCATAGTCTTTT 57.846 39.130 0.00 0.00 29.09 2.27
1824 1868 3.434453 CCATATAAACCGGGGCTTCTCAA 60.434 47.826 6.32 0.00 0.00 3.02
1850 1894 4.537015 CTGGGTCAAAATTCTTTCGTGAC 58.463 43.478 0.00 0.00 38.28 3.67
1916 1960 4.147321 ACTCTGTTTCCAACATCTGCAAT 58.853 39.130 0.00 0.00 41.26 3.56
1958 2005 1.402787 ACCTTCAAAAGCCCAGTGTG 58.597 50.000 0.00 0.00 0.00 3.82
1969 2016 1.823250 GCCCAGTGTGGACCTTTTCAT 60.823 52.381 0.00 0.00 40.96 2.57
1979 2026 7.444487 AGTGTGGACCTTTTCATAGAGTTTTAC 59.556 37.037 0.00 0.00 0.00 2.01
2013 2060 4.629200 GCCAGACTGAATTTACAGACAGAG 59.371 45.833 3.32 0.00 40.63 3.35
2027 2074 2.495669 AGACAGAGCCAGCTTAGAACTC 59.504 50.000 0.00 0.00 0.00 3.01
2034 2081 0.103208 CAGCTTAGAACTCGGCGGAT 59.897 55.000 7.21 0.00 0.00 4.18
2043 2090 0.460311 ACTCGGCGGATTCTCGATTT 59.540 50.000 7.21 0.00 32.32 2.17
2045 2092 2.287668 ACTCGGCGGATTCTCGATTTAG 60.288 50.000 7.21 0.00 32.32 1.85
2059 2106 2.554462 CGATTTAGAGGCGAGGAGATGA 59.446 50.000 0.00 0.00 0.00 2.92
2122 2169 5.546499 ACTGGAATCAGACCTGGTTTTACTA 59.454 40.000 0.00 0.00 43.49 1.82
2137 2184 5.347907 GGTTTTACTACCAAGACACATCTCG 59.652 44.000 0.00 0.00 38.12 4.04
2141 2188 4.017126 ACTACCAAGACACATCTCGATCA 58.983 43.478 0.00 0.00 32.34 2.92
2142 2189 4.646945 ACTACCAAGACACATCTCGATCAT 59.353 41.667 0.00 0.00 32.34 2.45
2181 2228 4.717629 TCCGCGACTGTCGGCTTG 62.718 66.667 28.92 15.22 46.05 4.01
2301 2348 1.024579 CGGAGTTGATTTGGTCCGGG 61.025 60.000 0.00 0.00 46.68 5.73
2302 2349 1.313091 GGAGTTGATTTGGTCCGGGC 61.313 60.000 0.00 0.00 0.00 6.13
2303 2350 0.322546 GAGTTGATTTGGTCCGGGCT 60.323 55.000 5.77 0.00 0.00 5.19
2304 2351 0.609131 AGTTGATTTGGTCCGGGCTG 60.609 55.000 5.77 0.00 0.00 4.85
2306 2353 2.075355 TTGATTTGGTCCGGGCTGGT 62.075 55.000 13.14 0.00 39.52 4.00
2307 2354 2.035626 ATTTGGTCCGGGCTGGTG 59.964 61.111 13.14 0.00 39.52 4.17
2308 2355 2.478335 GATTTGGTCCGGGCTGGTGA 62.478 60.000 13.14 0.00 39.52 4.02
2309 2356 2.484287 ATTTGGTCCGGGCTGGTGAG 62.484 60.000 13.14 0.00 39.52 3.51
2315 2362 3.775654 CGGGCTGGTGAGGGAGTC 61.776 72.222 0.00 0.00 0.00 3.36
2316 2363 3.403558 GGGCTGGTGAGGGAGTCC 61.404 72.222 0.00 0.00 0.00 3.85
2318 2365 2.664081 GGCTGGTGAGGGAGTCCTG 61.664 68.421 9.58 0.00 45.05 3.86
2319 2366 2.664081 GCTGGTGAGGGAGTCCTGG 61.664 68.421 9.58 0.00 45.05 4.45
2320 2367 1.079256 CTGGTGAGGGAGTCCTGGA 59.921 63.158 9.58 0.00 45.05 3.86
2321 2368 0.326048 CTGGTGAGGGAGTCCTGGAT 60.326 60.000 9.58 0.00 45.05 3.41
2322 2369 0.119155 TGGTGAGGGAGTCCTGGATT 59.881 55.000 9.58 0.00 45.05 3.01
2323 2370 1.364678 TGGTGAGGGAGTCCTGGATTA 59.635 52.381 9.58 0.00 45.05 1.75
2324 2371 2.043227 GGTGAGGGAGTCCTGGATTAG 58.957 57.143 9.58 0.00 45.05 1.73
2325 2372 2.043227 GTGAGGGAGTCCTGGATTAGG 58.957 57.143 9.58 0.00 45.05 2.69
2333 2380 3.359669 CCTGGATTAGGGGGTCCTT 57.640 57.895 0.00 0.00 41.56 3.36
2334 2381 2.507478 CCTGGATTAGGGGGTCCTTA 57.493 55.000 0.00 0.00 41.56 2.69
2335 2382 2.339769 CCTGGATTAGGGGGTCCTTAG 58.660 57.143 0.00 0.00 41.56 2.18
2336 2383 2.090153 CCTGGATTAGGGGGTCCTTAGA 60.090 54.545 0.00 0.00 41.56 2.10
2337 2384 2.973406 CTGGATTAGGGGGTCCTTAGAC 59.027 54.545 0.00 0.00 41.56 2.59
2338 2385 2.319747 TGGATTAGGGGGTCCTTAGACA 59.680 50.000 0.00 0.00 45.48 3.41
2339 2386 2.973406 GGATTAGGGGGTCCTTAGACAG 59.027 54.545 0.00 0.00 45.48 3.51
2340 2387 1.875488 TTAGGGGGTCCTTAGACAGC 58.125 55.000 0.00 0.00 45.48 4.40
2341 2388 0.031414 TAGGGGGTCCTTAGACAGCC 60.031 60.000 0.00 0.00 45.48 4.85
2342 2389 2.732619 GGGGGTCCTTAGACAGCCG 61.733 68.421 0.00 0.00 45.48 5.52
2343 2390 2.732619 GGGGTCCTTAGACAGCCGG 61.733 68.421 0.00 0.00 45.48 6.13
2344 2391 1.684734 GGGTCCTTAGACAGCCGGA 60.685 63.158 5.05 0.00 45.48 5.14
2345 2392 1.516423 GGTCCTTAGACAGCCGGAC 59.484 63.158 5.05 0.00 45.48 4.79
2346 2393 0.971447 GGTCCTTAGACAGCCGGACT 60.971 60.000 5.05 0.00 45.48 3.85
2347 2394 1.684248 GGTCCTTAGACAGCCGGACTA 60.684 57.143 5.05 0.00 45.48 2.59
2348 2395 2.308690 GTCCTTAGACAGCCGGACTAT 58.691 52.381 5.05 0.00 42.99 2.12
2349 2396 2.034812 GTCCTTAGACAGCCGGACTATG 59.965 54.545 5.05 0.00 42.99 2.23
2350 2397 2.032620 CCTTAGACAGCCGGACTATGT 58.967 52.381 5.05 3.22 0.00 2.29
2351 2398 3.117776 TCCTTAGACAGCCGGACTATGTA 60.118 47.826 5.05 0.00 0.00 2.29
2352 2399 3.004524 CCTTAGACAGCCGGACTATGTAC 59.995 52.174 5.05 0.00 0.00 2.90
2353 2400 2.438800 AGACAGCCGGACTATGTACT 57.561 50.000 5.05 1.19 0.00 2.73
2354 2401 2.736347 AGACAGCCGGACTATGTACTT 58.264 47.619 5.05 0.00 0.00 2.24
2355 2402 3.894759 AGACAGCCGGACTATGTACTTA 58.105 45.455 5.05 0.00 0.00 2.24
2356 2403 4.471548 AGACAGCCGGACTATGTACTTAT 58.528 43.478 5.05 0.00 0.00 1.73
2357 2404 4.278669 AGACAGCCGGACTATGTACTTATG 59.721 45.833 5.05 0.00 0.00 1.90
2358 2405 3.243771 ACAGCCGGACTATGTACTTATGC 60.244 47.826 5.05 0.00 0.00 3.14
2359 2406 2.299297 AGCCGGACTATGTACTTATGCC 59.701 50.000 5.05 0.00 0.00 4.40
2360 2407 2.925306 GCCGGACTATGTACTTATGCCG 60.925 54.545 5.05 16.22 37.41 5.69
2361 2408 2.942710 CGGACTATGTACTTATGCCGG 58.057 52.381 15.73 0.00 34.29 6.13
2362 2409 2.555325 CGGACTATGTACTTATGCCGGA 59.445 50.000 5.05 0.00 34.29 5.14
2363 2410 3.611057 CGGACTATGTACTTATGCCGGAC 60.611 52.174 5.05 0.00 34.29 4.79
2364 2411 3.573110 GGACTATGTACTTATGCCGGACT 59.427 47.826 5.05 0.00 0.00 3.85
2365 2412 4.547532 GACTATGTACTTATGCCGGACTG 58.452 47.826 5.05 0.00 0.00 3.51
2366 2413 3.958798 ACTATGTACTTATGCCGGACTGT 59.041 43.478 5.05 0.00 0.00 3.55
2367 2414 3.906720 ATGTACTTATGCCGGACTGTT 57.093 42.857 5.05 0.00 0.00 3.16
2368 2415 2.967362 TGTACTTATGCCGGACTGTTG 58.033 47.619 5.05 0.00 0.00 3.33
2369 2416 2.277084 GTACTTATGCCGGACTGTTGG 58.723 52.381 5.05 0.00 0.00 3.77
2370 2417 0.981183 ACTTATGCCGGACTGTTGGA 59.019 50.000 5.05 0.00 0.00 3.53
2371 2418 1.338769 ACTTATGCCGGACTGTTGGAC 60.339 52.381 5.05 0.00 0.00 4.02
2372 2419 0.981183 TTATGCCGGACTGTTGGACT 59.019 50.000 5.05 0.00 0.00 3.85
2373 2420 1.855295 TATGCCGGACTGTTGGACTA 58.145 50.000 5.05 0.00 0.00 2.59
2374 2421 1.204146 ATGCCGGACTGTTGGACTAT 58.796 50.000 5.05 0.00 0.00 2.12
2375 2422 0.249120 TGCCGGACTGTTGGACTATG 59.751 55.000 5.05 0.00 0.00 2.23
2376 2423 0.535335 GCCGGACTGTTGGACTATGA 59.465 55.000 5.05 0.00 0.00 2.15
2377 2424 1.066430 GCCGGACTGTTGGACTATGAA 60.066 52.381 5.05 0.00 0.00 2.57
2378 2425 2.893637 CCGGACTGTTGGACTATGAAG 58.106 52.381 0.00 0.00 0.00 3.02
2379 2426 2.496070 CCGGACTGTTGGACTATGAAGA 59.504 50.000 0.00 0.00 0.00 2.87
2380 2427 3.133003 CCGGACTGTTGGACTATGAAGAT 59.867 47.826 0.00 0.00 0.00 2.40
2381 2428 4.341235 CCGGACTGTTGGACTATGAAGATA 59.659 45.833 0.00 0.00 0.00 1.98
2382 2429 5.282510 CGGACTGTTGGACTATGAAGATAC 58.717 45.833 0.00 0.00 0.00 2.24
2383 2430 5.163550 CGGACTGTTGGACTATGAAGATACA 60.164 44.000 0.00 0.00 0.00 2.29
2384 2431 6.627287 CGGACTGTTGGACTATGAAGATACAA 60.627 42.308 0.00 0.00 0.00 2.41
2385 2432 6.758886 GGACTGTTGGACTATGAAGATACAAG 59.241 42.308 0.00 0.00 0.00 3.16
2386 2433 7.363880 GGACTGTTGGACTATGAAGATACAAGA 60.364 40.741 0.00 0.00 0.00 3.02
2387 2434 8.083828 ACTGTTGGACTATGAAGATACAAGAT 57.916 34.615 0.00 0.00 0.00 2.40
2388 2435 8.543774 ACTGTTGGACTATGAAGATACAAGATT 58.456 33.333 0.00 0.00 0.00 2.40
2389 2436 8.722480 TGTTGGACTATGAAGATACAAGATTG 57.278 34.615 0.00 0.00 0.00 2.67
2390 2437 8.539544 TGTTGGACTATGAAGATACAAGATTGA 58.460 33.333 0.00 0.00 0.00 2.57
2391 2438 9.383519 GTTGGACTATGAAGATACAAGATTGAA 57.616 33.333 0.00 0.00 0.00 2.69
2392 2439 9.605275 TTGGACTATGAAGATACAAGATTGAAG 57.395 33.333 0.00 0.00 0.00 3.02
2393 2440 8.981659 TGGACTATGAAGATACAAGATTGAAGA 58.018 33.333 0.00 0.00 0.00 2.87
2394 2441 9.255304 GGACTATGAAGATACAAGATTGAAGAC 57.745 37.037 0.00 0.00 0.00 3.01
2398 2445 7.818493 TGAAGATACAAGATTGAAGACTTCG 57.182 36.000 10.56 0.00 34.37 3.79
2399 2446 7.378966 TGAAGATACAAGATTGAAGACTTCGT 58.621 34.615 10.56 1.87 34.37 3.85
2400 2447 7.542477 TGAAGATACAAGATTGAAGACTTCGTC 59.458 37.037 10.56 10.67 34.37 4.20
2401 2448 7.164230 AGATACAAGATTGAAGACTTCGTCT 57.836 36.000 14.05 14.05 45.64 4.18
2402 2449 7.254852 AGATACAAGATTGAAGACTTCGTCTC 58.745 38.462 18.03 11.38 42.59 3.36
2403 2450 4.230657 ACAAGATTGAAGACTTCGTCTCG 58.769 43.478 18.03 12.49 42.59 4.04
2404 2451 4.230657 CAAGATTGAAGACTTCGTCTCGT 58.769 43.478 18.03 8.11 42.59 4.18
2405 2452 3.827625 AGATTGAAGACTTCGTCTCGTG 58.172 45.455 14.05 0.00 42.59 4.35
2406 2453 3.253677 AGATTGAAGACTTCGTCTCGTGT 59.746 43.478 14.05 0.00 42.59 4.49
2407 2454 2.682952 TGAAGACTTCGTCTCGTGTC 57.317 50.000 10.56 8.76 42.59 3.67
2408 2455 1.266175 TGAAGACTTCGTCTCGTGTCC 59.734 52.381 10.56 0.00 42.59 4.02
2409 2456 0.237761 AAGACTTCGTCTCGTGTCCG 59.762 55.000 0.00 0.00 42.59 4.79
2410 2457 1.154263 GACTTCGTCTCGTGTCCGG 60.154 63.158 0.00 0.00 33.95 5.14
2411 2458 2.178521 CTTCGTCTCGTGTCCGGG 59.821 66.667 0.00 0.00 35.26 5.73
2412 2459 2.595463 TTCGTCTCGTGTCCGGGT 60.595 61.111 0.00 0.00 35.53 5.28
2413 2460 2.797866 CTTCGTCTCGTGTCCGGGTG 62.798 65.000 0.00 0.00 35.53 4.61
2414 2461 4.415332 CGTCTCGTGTCCGGGTGG 62.415 72.222 0.00 0.00 35.53 4.61
2415 2462 4.065281 GTCTCGTGTCCGGGTGGG 62.065 72.222 0.00 0.00 35.53 4.61
2416 2463 4.289101 TCTCGTGTCCGGGTGGGA 62.289 66.667 0.00 0.00 44.68 4.37
2423 2470 3.273654 TCCGGGTGGGACTCTCCT 61.274 66.667 0.00 0.00 40.94 3.69
2424 2471 2.284699 CCGGGTGGGACTCTCCTT 60.285 66.667 0.00 0.00 38.47 3.36
2425 2472 1.918800 CCGGGTGGGACTCTCCTTT 60.919 63.158 0.00 0.00 38.47 3.11
2426 2473 1.296715 CGGGTGGGACTCTCCTTTG 59.703 63.158 0.00 0.00 36.57 2.77
2427 2474 1.002011 GGGTGGGACTCTCCTTTGC 60.002 63.158 0.00 0.00 36.57 3.68
2428 2475 1.376037 GGTGGGACTCTCCTTTGCG 60.376 63.158 0.00 0.00 36.57 4.85
2429 2476 1.371558 GTGGGACTCTCCTTTGCGT 59.628 57.895 0.00 0.00 36.57 5.24
2430 2477 0.951040 GTGGGACTCTCCTTTGCGTG 60.951 60.000 0.00 0.00 36.57 5.34
2431 2478 1.376037 GGGACTCTCCTTTGCGTGG 60.376 63.158 0.00 0.00 36.57 4.94
2432 2479 1.671742 GGACTCTCCTTTGCGTGGA 59.328 57.895 0.00 0.00 32.53 4.02
2433 2480 0.034896 GGACTCTCCTTTGCGTGGAA 59.965 55.000 0.00 0.00 32.53 3.53
2434 2481 1.433534 GACTCTCCTTTGCGTGGAAG 58.566 55.000 0.00 0.00 32.61 3.46
2435 2482 0.035458 ACTCTCCTTTGCGTGGAAGG 59.965 55.000 7.12 7.12 44.06 3.46
2444 2491 2.956987 CGTGGAAGGCAAGCTTGG 59.043 61.111 27.10 9.80 0.00 3.61
2452 2499 4.173971 GCAAGCTTGGCAATTCGG 57.826 55.556 27.10 0.00 0.00 4.30
2453 2500 1.586028 GCAAGCTTGGCAATTCGGA 59.414 52.632 27.10 0.00 0.00 4.55
2454 2501 0.174162 GCAAGCTTGGCAATTCGGAT 59.826 50.000 27.10 0.00 0.00 4.18
2455 2502 1.405105 GCAAGCTTGGCAATTCGGATA 59.595 47.619 27.10 0.00 0.00 2.59
2456 2503 2.035066 GCAAGCTTGGCAATTCGGATAT 59.965 45.455 27.10 0.00 0.00 1.63
2457 2504 3.635331 CAAGCTTGGCAATTCGGATATG 58.365 45.455 19.14 0.00 0.00 1.78
2458 2505 2.936202 AGCTTGGCAATTCGGATATGT 58.064 42.857 0.00 0.00 0.00 2.29
2459 2506 4.085357 AGCTTGGCAATTCGGATATGTA 57.915 40.909 0.00 0.00 0.00 2.29
2460 2507 4.067896 AGCTTGGCAATTCGGATATGTAG 58.932 43.478 0.00 0.00 0.00 2.74
2461 2508 4.065088 GCTTGGCAATTCGGATATGTAGA 58.935 43.478 0.00 0.00 0.00 2.59
2462 2509 4.697352 GCTTGGCAATTCGGATATGTAGAT 59.303 41.667 0.00 0.00 0.00 1.98
2463 2510 5.182001 GCTTGGCAATTCGGATATGTAGATT 59.818 40.000 0.00 0.00 0.00 2.40
2464 2511 6.294176 GCTTGGCAATTCGGATATGTAGATTT 60.294 38.462 0.00 0.00 0.00 2.17
2465 2512 6.801539 TGGCAATTCGGATATGTAGATTTC 57.198 37.500 0.00 0.00 0.00 2.17
2466 2513 5.705441 TGGCAATTCGGATATGTAGATTTCC 59.295 40.000 0.00 0.00 0.00 3.13
2467 2514 5.940470 GGCAATTCGGATATGTAGATTTCCT 59.060 40.000 7.58 0.00 29.66 3.36
2468 2515 6.431234 GGCAATTCGGATATGTAGATTTCCTT 59.569 38.462 7.58 0.00 29.66 3.36
2469 2516 7.361286 GGCAATTCGGATATGTAGATTTCCTTC 60.361 40.741 7.58 0.00 29.66 3.46
2470 2517 7.389053 GCAATTCGGATATGTAGATTTCCTTCT 59.611 37.037 7.58 0.00 29.66 2.85
2471 2518 9.277783 CAATTCGGATATGTAGATTTCCTTCTT 57.722 33.333 7.58 0.00 29.66 2.52
2472 2519 9.853177 AATTCGGATATGTAGATTTCCTTCTTT 57.147 29.630 7.58 0.00 29.66 2.52
2473 2520 8.662781 TTCGGATATGTAGATTTCCTTCTTTG 57.337 34.615 7.58 0.00 29.66 2.77
2474 2521 7.792032 TCGGATATGTAGATTTCCTTCTTTGT 58.208 34.615 7.58 0.00 29.66 2.83
2475 2522 8.920174 TCGGATATGTAGATTTCCTTCTTTGTA 58.080 33.333 7.58 0.00 29.66 2.41
2476 2523 9.542462 CGGATATGTAGATTTCCTTCTTTGTAA 57.458 33.333 7.58 0.00 29.66 2.41
2479 2526 7.611213 ATGTAGATTTCCTTCTTTGTAACCG 57.389 36.000 0.00 0.00 0.00 4.44
2480 2527 6.761312 TGTAGATTTCCTTCTTTGTAACCGA 58.239 36.000 0.00 0.00 0.00 4.69
2481 2528 6.647895 TGTAGATTTCCTTCTTTGTAACCGAC 59.352 38.462 0.00 0.00 0.00 4.79
2482 2529 5.866207 AGATTTCCTTCTTTGTAACCGACT 58.134 37.500 0.00 0.00 0.00 4.18
2483 2530 6.296803 AGATTTCCTTCTTTGTAACCGACTT 58.703 36.000 0.00 0.00 0.00 3.01
2484 2531 6.771267 AGATTTCCTTCTTTGTAACCGACTTT 59.229 34.615 0.00 0.00 0.00 2.66
2485 2532 5.744666 TTCCTTCTTTGTAACCGACTTTG 57.255 39.130 0.00 0.00 0.00 2.77
2486 2533 4.131596 TCCTTCTTTGTAACCGACTTTGG 58.868 43.478 0.00 0.00 0.00 3.28
2487 2534 3.252458 CCTTCTTTGTAACCGACTTTGGG 59.748 47.826 0.00 0.00 0.00 4.12
2488 2535 3.564053 TCTTTGTAACCGACTTTGGGT 57.436 42.857 0.00 0.00 40.20 4.51
2489 2536 4.686191 TCTTTGTAACCGACTTTGGGTA 57.314 40.909 0.00 0.00 36.57 3.69
2490 2537 5.033589 TCTTTGTAACCGACTTTGGGTAA 57.966 39.130 0.00 0.00 36.57 2.85
2491 2538 4.815846 TCTTTGTAACCGACTTTGGGTAAC 59.184 41.667 0.00 0.00 36.57 2.50
2504 2551 2.837411 GGTAACCCTAGCCCTCTCC 58.163 63.158 0.00 0.00 0.00 3.71
2505 2552 0.031414 GGTAACCCTAGCCCTCTCCA 60.031 60.000 0.00 0.00 0.00 3.86
2506 2553 1.415200 GTAACCCTAGCCCTCTCCAG 58.585 60.000 0.00 0.00 0.00 3.86
2507 2554 1.016415 TAACCCTAGCCCTCTCCAGT 58.984 55.000 0.00 0.00 0.00 4.00
2508 2555 0.618968 AACCCTAGCCCTCTCCAGTG 60.619 60.000 0.00 0.00 0.00 3.66
2509 2556 1.002274 CCCTAGCCCTCTCCAGTGT 59.998 63.158 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 9.672086 TTTAAGTTTGTGTTCAATAAATCTCCG 57.328 29.630 0.00 0.00 33.32 4.63
166 169 5.890424 ACCCATGTTTTAAGGTATTGACG 57.110 39.130 0.00 0.00 0.00 4.35
187 191 6.605594 TGACCATTTCCAACTCCCAAATATAC 59.394 38.462 0.00 0.00 0.00 1.47
243 248 9.905713 ATGAATTTTCTATTAGCACAGTTAGGA 57.094 29.630 0.00 0.00 0.00 2.94
265 270 1.965414 TGCCCCTTAGGAGTGATGAA 58.035 50.000 0.00 0.00 38.24 2.57
276 281 9.041354 ACTTTTGATAACAAATATTGCCCCTTA 57.959 29.630 0.00 0.00 43.99 2.69
286 291 9.834628 GAAATCCGACACTTTTGATAACAAATA 57.165 29.630 0.00 0.00 43.99 1.40
324 329 0.176680 CCTCATCCCACCTGTTCGAG 59.823 60.000 0.00 0.00 0.00 4.04
367 372 2.159382 GACCCATTGTGAATCAACGGT 58.841 47.619 0.00 0.00 41.68 4.83
382 387 0.343372 AGAGGGATAGCAAGGACCCA 59.657 55.000 0.00 0.00 44.25 4.51
466 471 5.125900 CCCACTCAACAAAATATGCAGATCA 59.874 40.000 0.00 0.00 0.00 2.92
513 518 3.832527 ACCCATTCCATTAGTATGCCAC 58.167 45.455 0.00 0.00 0.00 5.01
516 521 5.359576 TGTTCAACCCATTCCATTAGTATGC 59.640 40.000 0.00 0.00 0.00 3.14
535 540 8.043710 ACACCAAATTGGATTAAAGTTTGTTCA 58.956 29.630 20.25 0.00 40.96 3.18
613 620 0.727398 GGAAGAGTACCATGCAACGC 59.273 55.000 0.00 0.00 0.00 4.84
752 761 1.066858 CGTCTAAGCCAAGCCTTCTCA 60.067 52.381 0.00 0.00 0.00 3.27
882 891 2.080693 GACGTAATGGCAACCATGTCA 58.919 47.619 0.00 0.00 44.40 3.58
885 894 2.159393 CCAAGACGTAATGGCAACCATG 60.159 50.000 6.19 0.00 44.40 3.66
889 898 3.332034 AGTACCAAGACGTAATGGCAAC 58.668 45.455 16.78 14.81 40.51 4.17
954 963 6.743575 ACAACACAATTAGTCATAAGAGGC 57.256 37.500 0.00 0.00 0.00 4.70
955 964 7.023575 GCAACAACACAATTAGTCATAAGAGG 58.976 38.462 0.00 0.00 0.00 3.69
971 1010 1.388547 TGGACTGGAAGCAACAACAC 58.611 50.000 0.00 0.00 37.60 3.32
1026 1066 1.104630 GTTTCACAAAACCCACCGGA 58.895 50.000 9.46 0.00 39.10 5.14
1075 1115 2.236395 CCCCAGTCGTACCTTCAAGAAT 59.764 50.000 0.00 0.00 0.00 2.40
1081 1121 1.218316 CAGCCCCAGTCGTACCTTC 59.782 63.158 0.00 0.00 0.00 3.46
1090 1130 2.608988 CCTCAGGACAGCCCCAGT 60.609 66.667 0.00 0.00 34.66 4.00
1248 1288 9.801873 ATCGTTTCAATAACCTCCAAATTATTG 57.198 29.630 9.44 9.44 44.66 1.90
1249 1289 9.801873 CATCGTTTCAATAACCTCCAAATTATT 57.198 29.630 0.00 0.00 32.43 1.40
1352 1392 8.265055 CCCTATTACAATGTTCAAACCTAGAGA 58.735 37.037 0.00 0.00 0.00 3.10
1398 1438 1.139654 CTAGCCAACCTAGCATGCTCA 59.860 52.381 26.57 10.00 37.34 4.26
1403 1443 5.379706 AGAAAATCTAGCCAACCTAGCAT 57.620 39.130 0.00 0.00 42.73 3.79
1566 1606 4.940654 TCAAATTCGTGATGATAAGCCACA 59.059 37.500 0.00 0.00 0.00 4.17
1648 1688 4.097741 CAGTTGAAGTGACCCAATTGAACA 59.902 41.667 7.12 1.12 37.82 3.18
1651 1691 3.882888 GACAGTTGAAGTGACCCAATTGA 59.117 43.478 7.12 0.00 35.09 2.57
1717 1757 7.523293 CACCAATGGAATACATATTTGGCTA 57.477 36.000 6.16 0.00 38.15 3.93
1762 1806 1.001378 CGCCTTCTTTTGGTTGAGGTG 60.001 52.381 0.00 0.00 0.00 4.00
1797 1841 1.050204 CCCCGGTTTATATGGTCGGA 58.950 55.000 0.00 0.00 42.94 4.55
1824 1868 1.995376 AAGAATTTTGACCCAGGCGT 58.005 45.000 0.00 0.00 0.00 5.68
1916 1960 8.429641 AGGTATACTTCACAAAAGACTTGAAGA 58.570 33.333 17.57 5.78 46.16 2.87
1947 1991 0.261696 AAAAGGTCCACACTGGGCTT 59.738 50.000 0.00 0.00 43.05 4.35
1969 2016 6.465948 TGGCGGTTCAAATAGTAAAACTCTA 58.534 36.000 0.00 0.00 0.00 2.43
1979 2026 2.972625 TCAGTCTGGCGGTTCAAATAG 58.027 47.619 0.00 0.00 0.00 1.73
2013 2060 2.167861 CGCCGAGTTCTAAGCTGGC 61.168 63.158 0.00 0.00 39.10 4.85
2027 2074 2.320367 CTCTAAATCGAGAATCCGCCG 58.680 52.381 0.00 0.00 32.74 6.46
2043 2090 4.853468 AGATATCATCTCCTCGCCTCTA 57.147 45.455 5.32 0.00 33.42 2.43
2045 2092 3.130340 GGAAGATATCATCTCCTCGCCTC 59.870 52.174 5.32 0.00 39.08 4.70
2052 2099 4.323409 GGCTGAAGGGAAGATATCATCTCC 60.323 50.000 4.20 7.02 39.08 3.71
2059 2106 1.131638 TGCGGCTGAAGGGAAGATAT 58.868 50.000 0.00 0.00 0.00 1.63
2122 2169 4.498177 CGTATGATCGAGATGTGTCTTGGT 60.498 45.833 0.00 0.00 36.64 3.67
2137 2184 3.430218 CGGCAGAGGATTTTCGTATGATC 59.570 47.826 0.00 0.00 0.00 2.92
2141 2188 1.202651 CCCGGCAGAGGATTTTCGTAT 60.203 52.381 0.00 0.00 0.00 3.06
2142 2189 0.177141 CCCGGCAGAGGATTTTCGTA 59.823 55.000 0.00 0.00 0.00 3.43
2181 2228 1.313091 GGAAGTGGATGTTTCGGGCC 61.313 60.000 0.00 0.00 0.00 5.80
2301 2348 2.664081 CCAGGACTCCCTCACCAGC 61.664 68.421 0.00 0.00 42.02 4.85
2302 2349 0.326048 ATCCAGGACTCCCTCACCAG 60.326 60.000 0.00 0.00 42.02 4.00
2303 2350 0.119155 AATCCAGGACTCCCTCACCA 59.881 55.000 0.00 0.00 42.02 4.17
2304 2351 2.043227 CTAATCCAGGACTCCCTCACC 58.957 57.143 0.00 0.00 42.02 4.02
2314 2361 6.498785 GTCTAAGGACCCCCTAATCCAGGA 62.499 54.167 0.00 0.00 43.48 3.86
2315 2362 2.090153 TCTAAGGACCCCCTAATCCAGG 60.090 54.545 0.00 0.00 43.48 4.45
2316 2363 2.973406 GTCTAAGGACCCCCTAATCCAG 59.027 54.545 0.00 0.00 43.48 3.86
2317 2364 2.319747 TGTCTAAGGACCCCCTAATCCA 59.680 50.000 0.00 0.00 43.48 3.41
2318 2365 2.973406 CTGTCTAAGGACCCCCTAATCC 59.027 54.545 0.00 0.00 43.48 3.01
2319 2366 2.369203 GCTGTCTAAGGACCCCCTAATC 59.631 54.545 0.00 0.00 43.48 1.75
2320 2367 2.409570 GCTGTCTAAGGACCCCCTAAT 58.590 52.381 0.00 0.00 43.48 1.73
2321 2368 1.624391 GGCTGTCTAAGGACCCCCTAA 60.624 57.143 0.00 0.00 43.48 2.69
2322 2369 0.031414 GGCTGTCTAAGGACCCCCTA 60.031 60.000 0.00 0.00 43.48 3.53
2324 2371 2.732619 CGGCTGTCTAAGGACCCCC 61.733 68.421 0.00 0.00 41.47 5.40
2325 2372 2.732619 CCGGCTGTCTAAGGACCCC 61.733 68.421 0.00 0.00 41.47 4.95
2326 2373 1.684734 TCCGGCTGTCTAAGGACCC 60.685 63.158 0.00 0.00 41.47 4.46
2327 2374 1.516423 GTCCGGCTGTCTAAGGACC 59.484 63.158 0.00 0.00 45.39 4.46
2329 2376 2.307768 CATAGTCCGGCTGTCTAAGGA 58.692 52.381 0.00 0.00 0.00 3.36
2330 2377 2.032620 ACATAGTCCGGCTGTCTAAGG 58.967 52.381 0.00 0.00 0.00 2.69
2331 2378 3.884091 AGTACATAGTCCGGCTGTCTAAG 59.116 47.826 0.00 0.00 0.00 2.18
2332 2379 3.894759 AGTACATAGTCCGGCTGTCTAA 58.105 45.455 0.00 0.00 0.00 2.10
2333 2380 3.572632 AGTACATAGTCCGGCTGTCTA 57.427 47.619 0.00 0.00 0.00 2.59
2334 2381 2.438800 AGTACATAGTCCGGCTGTCT 57.561 50.000 0.00 0.00 0.00 3.41
2335 2382 4.547532 CATAAGTACATAGTCCGGCTGTC 58.452 47.826 0.00 0.00 0.00 3.51
2336 2383 3.243771 GCATAAGTACATAGTCCGGCTGT 60.244 47.826 0.00 0.00 0.00 4.40
2337 2384 3.318017 GCATAAGTACATAGTCCGGCTG 58.682 50.000 0.00 0.00 0.00 4.85
2338 2385 2.299297 GGCATAAGTACATAGTCCGGCT 59.701 50.000 0.00 0.00 0.00 5.52
2339 2386 2.685100 GGCATAAGTACATAGTCCGGC 58.315 52.381 0.00 0.00 0.00 6.13
2340 2387 2.942710 CGGCATAAGTACATAGTCCGG 58.057 52.381 0.00 0.00 32.75 5.14
2341 2388 2.555325 TCCGGCATAAGTACATAGTCCG 59.445 50.000 0.00 11.56 35.80 4.79
2342 2389 3.573110 AGTCCGGCATAAGTACATAGTCC 59.427 47.826 0.00 0.00 0.00 3.85
2343 2390 4.037684 ACAGTCCGGCATAAGTACATAGTC 59.962 45.833 0.00 0.00 0.00 2.59
2344 2391 3.958798 ACAGTCCGGCATAAGTACATAGT 59.041 43.478 0.00 0.00 0.00 2.12
2345 2392 4.585955 ACAGTCCGGCATAAGTACATAG 57.414 45.455 0.00 0.00 0.00 2.23
2346 2393 4.442332 CCAACAGTCCGGCATAAGTACATA 60.442 45.833 0.00 0.00 0.00 2.29
2347 2394 3.531538 CAACAGTCCGGCATAAGTACAT 58.468 45.455 0.00 0.00 0.00 2.29
2348 2395 2.354303 CCAACAGTCCGGCATAAGTACA 60.354 50.000 0.00 0.00 0.00 2.90
2349 2396 2.093869 TCCAACAGTCCGGCATAAGTAC 60.094 50.000 0.00 0.00 0.00 2.73
2350 2397 2.093869 GTCCAACAGTCCGGCATAAGTA 60.094 50.000 0.00 0.00 0.00 2.24
2351 2398 0.981183 TCCAACAGTCCGGCATAAGT 59.019 50.000 0.00 0.00 0.00 2.24
2352 2399 1.066143 AGTCCAACAGTCCGGCATAAG 60.066 52.381 0.00 0.00 0.00 1.73
2353 2400 0.981183 AGTCCAACAGTCCGGCATAA 59.019 50.000 0.00 0.00 0.00 1.90
2354 2401 1.855295 TAGTCCAACAGTCCGGCATA 58.145 50.000 0.00 0.00 0.00 3.14
2355 2402 1.134401 CATAGTCCAACAGTCCGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
2356 2403 0.249120 CATAGTCCAACAGTCCGGCA 59.751 55.000 0.00 0.00 0.00 5.69
2357 2404 0.535335 TCATAGTCCAACAGTCCGGC 59.465 55.000 0.00 0.00 0.00 6.13
2358 2405 2.496070 TCTTCATAGTCCAACAGTCCGG 59.504 50.000 0.00 0.00 0.00 5.14
2359 2406 3.868757 TCTTCATAGTCCAACAGTCCG 57.131 47.619 0.00 0.00 0.00 4.79
2360 2407 6.222038 TGTATCTTCATAGTCCAACAGTCC 57.778 41.667 0.00 0.00 0.00 3.85
2361 2408 7.548097 TCTTGTATCTTCATAGTCCAACAGTC 58.452 38.462 0.00 0.00 0.00 3.51
2362 2409 7.482169 TCTTGTATCTTCATAGTCCAACAGT 57.518 36.000 0.00 0.00 0.00 3.55
2363 2410 8.824781 CAATCTTGTATCTTCATAGTCCAACAG 58.175 37.037 0.00 0.00 0.00 3.16
2364 2411 8.539544 TCAATCTTGTATCTTCATAGTCCAACA 58.460 33.333 0.00 0.00 0.00 3.33
2365 2412 8.948631 TCAATCTTGTATCTTCATAGTCCAAC 57.051 34.615 0.00 0.00 0.00 3.77
2366 2413 9.605275 CTTCAATCTTGTATCTTCATAGTCCAA 57.395 33.333 0.00 0.00 0.00 3.53
2367 2414 8.981659 TCTTCAATCTTGTATCTTCATAGTCCA 58.018 33.333 0.00 0.00 0.00 4.02
2368 2415 9.255304 GTCTTCAATCTTGTATCTTCATAGTCC 57.745 37.037 0.00 0.00 0.00 3.85
2372 2419 9.521503 CGAAGTCTTCAATCTTGTATCTTCATA 57.478 33.333 12.99 0.00 32.10 2.15
2373 2420 8.037758 ACGAAGTCTTCAATCTTGTATCTTCAT 58.962 33.333 12.99 0.00 29.74 2.57
2374 2421 7.378966 ACGAAGTCTTCAATCTTGTATCTTCA 58.621 34.615 12.99 0.00 29.74 3.02
2375 2422 7.820044 ACGAAGTCTTCAATCTTGTATCTTC 57.180 36.000 12.99 0.00 29.74 2.87
2393 2440 2.623915 CCCGGACACGAGACGAAGT 61.624 63.158 0.73 0.00 45.45 3.01
2394 2441 2.178521 CCCGGACACGAGACGAAG 59.821 66.667 0.73 0.00 44.60 3.79
2395 2442 2.595463 ACCCGGACACGAGACGAA 60.595 61.111 0.73 0.00 44.60 3.85
2396 2443 3.359523 CACCCGGACACGAGACGA 61.360 66.667 0.73 0.00 44.60 4.20
2397 2444 4.415332 CCACCCGGACACGAGACG 62.415 72.222 0.73 0.00 44.60 4.18
2398 2445 4.065281 CCCACCCGGACACGAGAC 62.065 72.222 0.73 0.00 44.60 3.36
2399 2446 4.289101 TCCCACCCGGACACGAGA 62.289 66.667 0.73 0.00 44.60 4.04
2406 2453 2.396651 AAAGGAGAGTCCCACCCGGA 62.397 60.000 0.73 0.00 37.19 5.14
2407 2454 1.918800 AAAGGAGAGTCCCACCCGG 60.919 63.158 0.00 0.00 37.19 5.73
2408 2455 1.296715 CAAAGGAGAGTCCCACCCG 59.703 63.158 1.17 0.00 37.19 5.28
2409 2456 1.002011 GCAAAGGAGAGTCCCACCC 60.002 63.158 1.17 0.00 37.19 4.61
2410 2457 1.376037 CGCAAAGGAGAGTCCCACC 60.376 63.158 1.17 0.00 37.19 4.61
2411 2458 0.951040 CACGCAAAGGAGAGTCCCAC 60.951 60.000 1.17 0.00 37.19 4.61
2412 2459 1.371183 CACGCAAAGGAGAGTCCCA 59.629 57.895 1.17 0.00 37.19 4.37
2413 2460 1.376037 CCACGCAAAGGAGAGTCCC 60.376 63.158 0.00 0.00 37.19 4.46
2414 2461 0.034896 TTCCACGCAAAGGAGAGTCC 59.965 55.000 0.00 0.00 36.33 3.85
2415 2462 1.433534 CTTCCACGCAAAGGAGAGTC 58.566 55.000 0.00 0.00 36.33 3.36
2416 2463 0.035458 CCTTCCACGCAAAGGAGAGT 59.965 55.000 5.37 0.00 45.15 3.24
2417 2464 1.301677 GCCTTCCACGCAAAGGAGAG 61.302 60.000 13.57 3.40 45.15 3.20
2418 2465 1.302511 GCCTTCCACGCAAAGGAGA 60.303 57.895 13.57 0.00 45.15 3.71
2419 2466 1.172180 TTGCCTTCCACGCAAAGGAG 61.172 55.000 13.57 0.00 45.15 3.69
2420 2467 1.152860 TTGCCTTCCACGCAAAGGA 60.153 52.632 13.57 0.00 45.15 3.36
2421 2468 1.286880 CTTGCCTTCCACGCAAAGG 59.713 57.895 6.69 6.69 45.11 3.11
2422 2469 1.372128 GCTTGCCTTCCACGCAAAG 60.372 57.895 0.00 0.00 45.11 2.77
2423 2470 1.391157 AAGCTTGCCTTCCACGCAAA 61.391 50.000 0.00 0.00 45.11 3.68
2424 2471 1.827789 AAGCTTGCCTTCCACGCAA 60.828 52.632 0.00 0.00 43.71 4.85
2425 2472 2.203337 AAGCTTGCCTTCCACGCA 60.203 55.556 0.00 0.00 40.87 5.24
2426 2473 2.256461 CAAGCTTGCCTTCCACGC 59.744 61.111 14.65 0.00 38.87 5.34
2427 2474 2.956987 CCAAGCTTGCCTTCCACG 59.043 61.111 21.43 0.62 0.00 4.94
2428 2475 1.747325 TTGCCAAGCTTGCCTTCCAC 61.747 55.000 21.43 4.32 0.00 4.02
2429 2476 0.832983 ATTGCCAAGCTTGCCTTCCA 60.833 50.000 21.43 9.04 0.00 3.53
2430 2477 0.322648 AATTGCCAAGCTTGCCTTCC 59.677 50.000 21.43 6.63 0.00 3.46
2431 2478 1.718396 GAATTGCCAAGCTTGCCTTC 58.282 50.000 21.43 14.81 0.00 3.46
2432 2479 0.037975 CGAATTGCCAAGCTTGCCTT 60.038 50.000 21.43 10.35 0.00 4.35
2433 2480 1.588082 CGAATTGCCAAGCTTGCCT 59.412 52.632 21.43 2.43 0.00 4.75
2434 2481 1.446618 CCGAATTGCCAAGCTTGCC 60.447 57.895 21.43 11.17 0.00 4.52
2435 2482 0.174162 ATCCGAATTGCCAAGCTTGC 59.826 50.000 21.43 16.17 0.00 4.01
2436 2483 3.067180 ACATATCCGAATTGCCAAGCTTG 59.933 43.478 19.93 19.93 0.00 4.01
2437 2484 3.290710 ACATATCCGAATTGCCAAGCTT 58.709 40.909 0.00 0.00 0.00 3.74
2438 2485 2.936202 ACATATCCGAATTGCCAAGCT 58.064 42.857 0.00 0.00 0.00 3.74
2439 2486 4.065088 TCTACATATCCGAATTGCCAAGC 58.935 43.478 0.00 0.00 0.00 4.01
2440 2487 6.808008 AATCTACATATCCGAATTGCCAAG 57.192 37.500 0.00 0.00 0.00 3.61
2441 2488 6.206634 GGAAATCTACATATCCGAATTGCCAA 59.793 38.462 0.00 0.00 0.00 4.52
2442 2489 5.705441 GGAAATCTACATATCCGAATTGCCA 59.295 40.000 0.00 0.00 0.00 4.92
2443 2490 5.940470 AGGAAATCTACATATCCGAATTGCC 59.060 40.000 0.00 0.00 37.05 4.52
2444 2491 7.389053 AGAAGGAAATCTACATATCCGAATTGC 59.611 37.037 0.00 0.00 37.05 3.56
2445 2492 8.839310 AGAAGGAAATCTACATATCCGAATTG 57.161 34.615 0.00 0.00 37.05 2.32
2446 2493 9.853177 AAAGAAGGAAATCTACATATCCGAATT 57.147 29.630 0.00 0.00 37.05 2.17
2447 2494 9.277783 CAAAGAAGGAAATCTACATATCCGAAT 57.722 33.333 0.00 0.00 37.05 3.34
2448 2495 8.265055 ACAAAGAAGGAAATCTACATATCCGAA 58.735 33.333 0.00 0.00 37.05 4.30
2449 2496 7.792032 ACAAAGAAGGAAATCTACATATCCGA 58.208 34.615 0.00 0.00 37.05 4.55
2450 2497 9.542462 TTACAAAGAAGGAAATCTACATATCCG 57.458 33.333 0.00 0.00 37.05 4.18
2453 2500 9.326413 CGGTTACAAAGAAGGAAATCTACATAT 57.674 33.333 0.00 0.00 0.00 1.78
2454 2501 8.533657 TCGGTTACAAAGAAGGAAATCTACATA 58.466 33.333 0.00 0.00 0.00 2.29
2455 2502 7.333672 GTCGGTTACAAAGAAGGAAATCTACAT 59.666 37.037 0.00 0.00 0.00 2.29
2456 2503 6.647895 GTCGGTTACAAAGAAGGAAATCTACA 59.352 38.462 0.00 0.00 0.00 2.74
2457 2504 6.872547 AGTCGGTTACAAAGAAGGAAATCTAC 59.127 38.462 0.00 0.00 0.00 2.59
2458 2505 7.001099 AGTCGGTTACAAAGAAGGAAATCTA 57.999 36.000 0.00 0.00 0.00 1.98
2459 2506 5.866207 AGTCGGTTACAAAGAAGGAAATCT 58.134 37.500 0.00 0.00 0.00 2.40
2460 2507 6.555812 AAGTCGGTTACAAAGAAGGAAATC 57.444 37.500 0.00 0.00 0.00 2.17
2461 2508 6.238925 CCAAAGTCGGTTACAAAGAAGGAAAT 60.239 38.462 0.00 0.00 0.00 2.17
2462 2509 5.066764 CCAAAGTCGGTTACAAAGAAGGAAA 59.933 40.000 0.00 0.00 0.00 3.13
2463 2510 4.577283 CCAAAGTCGGTTACAAAGAAGGAA 59.423 41.667 0.00 0.00 0.00 3.36
2464 2511 4.131596 CCAAAGTCGGTTACAAAGAAGGA 58.868 43.478 0.00 0.00 0.00 3.36
2465 2512 3.252458 CCCAAAGTCGGTTACAAAGAAGG 59.748 47.826 0.00 0.00 0.00 3.46
2466 2513 3.881089 ACCCAAAGTCGGTTACAAAGAAG 59.119 43.478 0.00 0.00 0.00 2.85
2467 2514 3.888583 ACCCAAAGTCGGTTACAAAGAA 58.111 40.909 0.00 0.00 0.00 2.52
2468 2515 3.564053 ACCCAAAGTCGGTTACAAAGA 57.436 42.857 0.00 0.00 0.00 2.52
2469 2516 4.023792 GGTTACCCAAAGTCGGTTACAAAG 60.024 45.833 0.00 0.00 35.16 2.77
2470 2517 3.882288 GGTTACCCAAAGTCGGTTACAAA 59.118 43.478 0.00 0.00 35.16 2.83
2471 2518 3.475575 GGTTACCCAAAGTCGGTTACAA 58.524 45.455 0.00 0.00 35.16 2.41
2472 2519 2.224499 GGGTTACCCAAAGTCGGTTACA 60.224 50.000 16.81 0.00 44.65 2.41
2473 2520 2.426522 GGGTTACCCAAAGTCGGTTAC 58.573 52.381 16.81 0.00 44.65 2.50
2474 2521 2.857186 GGGTTACCCAAAGTCGGTTA 57.143 50.000 16.81 0.00 44.65 2.85
2475 2522 3.731716 GGGTTACCCAAAGTCGGTT 57.268 52.632 16.81 0.00 44.65 4.44
2485 2532 0.763604 GGAGAGGGCTAGGGTTACCC 60.764 65.000 13.56 13.56 45.90 3.69
2486 2533 0.031414 TGGAGAGGGCTAGGGTTACC 60.031 60.000 0.00 0.00 0.00 2.85
2487 2534 1.343176 ACTGGAGAGGGCTAGGGTTAC 60.343 57.143 0.00 0.00 0.00 2.50
2488 2535 1.016415 ACTGGAGAGGGCTAGGGTTA 58.984 55.000 0.00 0.00 0.00 2.85
2489 2536 0.618968 CACTGGAGAGGGCTAGGGTT 60.619 60.000 0.00 0.00 0.00 4.11
2490 2537 1.002274 CACTGGAGAGGGCTAGGGT 59.998 63.158 0.00 0.00 0.00 4.34
2491 2538 1.002274 ACACTGGAGAGGGCTAGGG 59.998 63.158 0.00 0.00 0.00 3.53
2492 2539 4.796408 ACACTGGAGAGGGCTAGG 57.204 61.111 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.