Multiple sequence alignment - TraesCS2B01G606000

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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 TraesCS2B01G606000 chr2B 100.000 2432 0 0 1 2432 787097355 787099786 0.000000e+00 4492.0
1 TraesCS2B01G606000 chr2B 86.385 1491 110 34 81 1536 787232407 787233839 0.000000e+00 1543.0
2 TraesCS2B01G606000 chr2B 92.537 670 35 9 856 1525 787154266 787154920 0.000000e+00 946.0
3 TraesCS2B01G606000 chr2B 94.089 203 8 4 1773 1974 787156158 787156357 3.040000e-79 305.0
4 TraesCS2B01G606000 chr2B 86.694 248 22 1 2081 2328 787156971 787157207 5.160000e-67 265.0
5 TraesCS2B01G606000 chr2A 86.913 1490 128 44 48 1516 773779713 773778270 0.000000e+00 1609.0
6 TraesCS2B01G606000 chr2A 81.141 806 105 27 905 1707 771933996 771934757 9.620000e-169 603.0
7 TraesCS2B01G606000 chr2A 92.606 284 14 5 1540 1823 773778277 773778001 3.770000e-108 401.0
8 TraesCS2B01G606000 chr2A 90.283 247 21 3 2090 2334 773776544 773776299 1.080000e-83 320.0
9 TraesCS2B01G606000 chr2A 92.357 157 10 1 1821 1977 773777958 773777804 3.150000e-54 222.0
10 TraesCS2B01G606000 chr2A 82.500 200 31 4 321 517 19162842 19162644 3.210000e-39 172.0
11 TraesCS2B01G606000 chr2A 89.773 88 5 4 2085 2170 147477768 147477683 2.560000e-20 110.0
12 TraesCS2B01G606000 chr2A 85.859 99 9 3 822 918 771933887 771933982 1.540000e-17 100.0
13 TraesCS2B01G606000 chr2A 77.500 160 20 13 397 546 569007471 569007318 5.570000e-12 82.4
14 TraesCS2B01G606000 chr2A 75.758 165 30 9 223 381 357066881 357066721 9.330000e-10 75.0
15 TraesCS2B01G606000 chr2D 90.577 1231 77 22 602 1818 650565119 650566324 0.000000e+00 1594.0
16 TraesCS2B01G606000 chr2D 80.373 805 115 24 905 1707 650585352 650586115 2.710000e-159 571.0
17 TraesCS2B01G606000 chr2D 93.590 156 8 1 1822 1977 650566378 650566531 5.230000e-57 231.0
18 TraesCS2B01G606000 chr7B 75.159 471 66 32 20 449 689980409 689980869 8.940000e-40 174.0
19 TraesCS2B01G606000 chr7B 93.684 95 4 2 1984 2077 664550864 664550771 9.070000e-30 141.0
20 TraesCS2B01G606000 chr7B 93.407 91 5 1 1984 2073 664355432 664355342 1.520000e-27 134.0
21 TraesCS2B01G606000 chr7B 76.613 248 43 11 265 502 339242079 339242321 3.280000e-24 122.0
22 TraesCS2B01G606000 chr7A 85.065 154 22 1 23 175 339756305 339756458 3.240000e-34 156.0
23 TraesCS2B01G606000 chr7A 90.385 52 4 1 2125 2176 546702071 546702021 1.560000e-07 67.6
24 TraesCS2B01G606000 chr6B 78.455 246 40 12 265 502 500601082 500601322 5.420000e-32 148.0
25 TraesCS2B01G606000 chr6B 80.473 169 19 12 359 518 282979043 282979206 1.530000e-22 117.0
26 TraesCS2B01G606000 chr6B 73.881 268 55 12 1001 1266 20667646 20667392 2.570000e-15 93.5
27 TraesCS2B01G606000 chr5B 84.314 153 20 3 25 174 700953620 700953771 1.950000e-31 147.0
28 TraesCS2B01G606000 chr5B 78.235 170 28 7 23 185 292172578 292172745 1.540000e-17 100.0
29 TraesCS2B01G606000 chr1B 78.903 237 31 16 23 255 684116304 684116525 2.520000e-30 143.0
30 TraesCS2B01G606000 chr1B 97.222 36 1 0 2085 2120 117459594 117459559 7.260000e-06 62.1
31 TraesCS2B01G606000 chr6D 72.261 429 92 18 840 1266 10815410 10815007 9.190000e-20 108.0
32 TraesCS2B01G606000 chr6D 76.730 159 23 14 352 499 412385781 412385626 2.590000e-10 76.8
33 TraesCS2B01G606000 chr3B 88.235 85 10 0 231 315 791401826 791401742 4.280000e-18 102.0
34 TraesCS2B01G606000 chr3B 84.416 77 11 1 659 735 465672816 465672891 9.330000e-10 75.0
35 TraesCS2B01G606000 chr6A 74.349 269 52 13 1001 1266 12378336 12378082 5.530000e-17 99.0
36 TraesCS2B01G606000 chr6A 94.444 36 0 2 670 704 549054671 549054637 1.000000e-03 54.7
37 TraesCS2B01G606000 chr5A 89.873 79 4 4 2081 2157 641586570 641586646 5.530000e-17 99.0
38 TraesCS2B01G606000 chr3A 89.610 77 8 0 665 741 131355520 131355444 5.530000e-17 99.0
39 TraesCS2B01G606000 chr3A 100.000 33 0 0 660 692 744386701 744386669 7.260000e-06 62.1
40 TraesCS2B01G606000 chr1D 89.744 78 5 1 1743 1817 18197565 18197642 1.990000e-16 97.1
41 TraesCS2B01G606000 chr1D 85.263 95 10 4 2082 2174 81173675 81173767 7.160000e-16 95.3
42 TraesCS2B01G606000 chr1D 94.545 55 2 1 2121 2175 383254474 383254421 1.550000e-12 84.2
43 TraesCS2B01G606000 chr1D 88.889 54 4 2 2121 2173 83689024 83689076 5.610000e-07 65.8
44 TraesCS2B01G606000 chr7D 84.524 84 9 3 660 741 32375072 32374991 2.000000e-11 80.5
45 TraesCS2B01G606000 chr7D 87.500 64 4 3 674 735 37101656 37101595 1.210000e-08 71.3
46 TraesCS2B01G606000 chr3D 79.646 113 15 7 397 502 350119168 350119279 9.330000e-10 75.0
47 TraesCS2B01G606000 chr3D 85.000 60 5 4 2100 2157 27931791 27931848 9.390000e-05 58.4
48 TraesCS2B01G606000 chr1A 93.617 47 1 2 2115 2160 503370648 503370693 4.340000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G606000 chr2B 787097355 787099786 2431 False 4492.000000 4492 100.000000 1 2432 1 chr2B.!!$F1 2431
1 TraesCS2B01G606000 chr2B 787232407 787233839 1432 False 1543.000000 1543 86.385000 81 1536 1 chr2B.!!$F2 1455
2 TraesCS2B01G606000 chr2B 787154266 787157207 2941 False 505.333333 946 91.106667 856 2328 3 chr2B.!!$F3 1472
3 TraesCS2B01G606000 chr2A 773776299 773779713 3414 True 638.000000 1609 90.539750 48 2334 4 chr2A.!!$R5 2286
4 TraesCS2B01G606000 chr2A 771933887 771934757 870 False 351.500000 603 83.500000 822 1707 2 chr2A.!!$F1 885
5 TraesCS2B01G606000 chr2D 650565119 650566531 1412 False 912.500000 1594 92.083500 602 1977 2 chr2D.!!$F2 1375
6 TraesCS2B01G606000 chr2D 650585352 650586115 763 False 571.000000 571 80.373000 905 1707 1 chr2D.!!$F1 802

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
90 92 0.382636 CGTTCAAACGTTGGAGCGAC 60.383 55.0 30.92 14.7 46.63 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 3252 0.339859 AGCTACCTCACAGGGATCCA 59.66 55.0 15.23 0.0 40.58 3.41 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
23 24 2.550830 CGCCAATTAGGAGCCATAGT 57.449 50.000 0.00 0.00 41.22 2.12
24 25 2.417719 CGCCAATTAGGAGCCATAGTC 58.582 52.381 0.00 0.00 41.22 2.59
25 26 2.417719 GCCAATTAGGAGCCATAGTCG 58.582 52.381 0.00 0.00 41.22 4.18
26 27 2.037251 GCCAATTAGGAGCCATAGTCGA 59.963 50.000 0.00 0.00 41.22 4.20
27 28 3.862642 GCCAATTAGGAGCCATAGTCGAG 60.863 52.174 0.00 0.00 41.22 4.04
28 29 3.306364 CCAATTAGGAGCCATAGTCGAGG 60.306 52.174 0.00 0.00 41.22 4.63
35 36 4.569023 CATAGTCGAGGCGGCGCA 62.569 66.667 34.36 11.73 36.23 6.09
36 37 4.570663 ATAGTCGAGGCGGCGCAC 62.571 66.667 34.36 22.52 36.23 5.34
46 47 3.849951 CGGCGCACAGGGGTAGAT 61.850 66.667 10.83 0.00 0.00 1.98
90 92 0.382636 CGTTCAAACGTTGGAGCGAC 60.383 55.000 30.92 14.70 46.63 5.19
116 118 6.062258 TGGTTTTAGGAATCTTCTAGGTGG 57.938 41.667 0.00 0.00 0.00 4.61
153 156 6.367374 TTTTCTGGTTTTGGAAACCTTCTT 57.633 33.333 19.85 0.00 40.88 2.52
225 257 5.660460 TGTTTCTTTTCTTTCCTTTGCTCC 58.340 37.500 0.00 0.00 0.00 4.70
392 424 8.797266 AAATATCCGTGTTTCAAAAAGTCTTC 57.203 30.769 0.00 0.00 0.00 2.87
393 425 5.828299 ATCCGTGTTTCAAAAAGTCTTCA 57.172 34.783 0.00 0.00 0.00 3.02
402 434 8.983724 TGTTTCAAAAAGTCTTCAACGAATTTT 58.016 25.926 0.00 0.00 41.30 1.82
403 435 9.249844 GTTTCAAAAAGTCTTCAACGAATTTTG 57.750 29.630 0.00 0.00 39.41 2.44
597 636 8.602328 GTCATTCACAAAATGTTCATGTTTCAA 58.398 29.630 0.00 0.00 0.00 2.69
600 639 7.895975 TCACAAAATGTTCATGTTTCAAACA 57.104 28.000 5.18 5.18 46.94 2.83
626 665 0.684535 TGAGATGGAACTTGGCACGA 59.315 50.000 0.00 0.00 0.00 4.35
639 678 1.337354 TGGCACGAATATCACACACGT 60.337 47.619 0.00 0.00 37.68 4.49
646 685 5.457473 CACGAATATCACACACGTAAGCATA 59.543 40.000 0.00 0.00 45.62 3.14
648 687 6.143919 ACGAATATCACACACGTAAGCATATG 59.856 38.462 0.00 0.00 45.62 1.78
658 697 4.025730 CACGTAAGCATATGTCACCACATC 60.026 45.833 4.29 0.00 41.70 3.06
663 705 5.571784 AGCATATGTCACCACATCTTTTG 57.428 39.130 4.29 0.00 42.66 2.44
717 767 4.081642 TGTTCACAGGGTGTAGATTAGCTC 60.082 45.833 0.00 0.00 34.79 4.09
718 768 3.708451 TCACAGGGTGTAGATTAGCTCA 58.292 45.455 0.00 0.00 34.79 4.26
737 787 5.033589 CTCAGGAGCAGAATTGGATACTT 57.966 43.478 0.00 0.00 37.61 2.24
768 825 1.339929 ACCATTTTCCAAACACGCCTC 59.660 47.619 0.00 0.00 0.00 4.70
776 833 4.481368 TCCAAACACGCCTCTATACAAT 57.519 40.909 0.00 0.00 0.00 2.71
833 890 6.035220 CACATCCATGCACATTTCAACATTAC 59.965 38.462 0.00 0.00 0.00 1.89
867 924 6.018913 GCATATCTTCAAGATAGGATCATGCG 60.019 42.308 20.80 0.11 40.38 4.73
871 928 3.642705 TCAAGATAGGATCATGCGAACG 58.357 45.455 0.00 0.00 0.00 3.95
882 939 6.366332 AGGATCATGCGAACGTTATATCTTTC 59.634 38.462 0.00 0.00 0.00 2.62
916 974 2.988010 TAGGTCACATCATCAGTGCC 57.012 50.000 0.00 0.00 36.93 5.01
1121 1225 4.308526 AGGCACTTCTTCCATGCG 57.691 55.556 0.00 0.00 40.37 4.73
1165 1269 8.730680 AGTCATATGTGAAGTTTTGTATTCCAC 58.269 33.333 1.90 0.00 35.80 4.02
1192 1296 6.749118 CCACTTCTTTCTGTCTTGTTTTTCTG 59.251 38.462 0.00 0.00 0.00 3.02
1208 1316 8.547967 TGTTTTTCTGTAGAACATCATAGGTC 57.452 34.615 0.00 0.00 33.13 3.85
1210 1318 8.874816 GTTTTTCTGTAGAACATCATAGGTCTC 58.125 37.037 0.00 0.00 33.13 3.36
1313 1423 0.468226 TATACCGGCAAGGCTTCCTG 59.532 55.000 0.00 0.00 46.52 3.86
1341 1451 2.362120 GCTCCATGTGCCAAGGCT 60.362 61.111 12.96 0.00 42.51 4.58
1356 1466 1.533994 GGCTTGCCAAAAGGAGGGT 60.534 57.895 6.79 0.00 0.00 4.34
1438 1549 5.410746 TGCAAGAAAGAGTGCTAAATGAGAG 59.589 40.000 0.00 0.00 41.48 3.20
1463 1574 2.412937 GCAAGTTGCAACTGCCGT 59.587 55.556 31.73 14.21 44.26 5.68
1559 2288 9.678260 ATGAAATAAGTTGAGACTCTAGCAAAT 57.322 29.630 3.68 0.00 34.21 2.32
1616 2348 1.274069 ACTGGATGGAGTGGAGTGGAT 60.274 52.381 0.00 0.00 0.00 3.41
1646 2378 6.391055 AGGAGATCTGAAAATATCAAGGGGAA 59.609 38.462 0.00 0.00 37.67 3.97
1647 2379 6.714356 GGAGATCTGAAAATATCAAGGGGAAG 59.286 42.308 0.00 0.00 37.67 3.46
1712 2458 3.244249 GCTTGGTAACCAGAGTCTGAACT 60.244 47.826 22.09 7.67 38.88 3.01
1713 2459 4.310769 CTTGGTAACCAGAGTCTGAACTG 58.689 47.826 22.09 7.13 35.28 3.16
1714 2460 2.037251 TGGTAACCAGAGTCTGAACTGC 59.963 50.000 22.09 8.40 35.28 4.40
1715 2461 2.613223 GGTAACCAGAGTCTGAACTGCC 60.613 54.545 22.09 13.30 35.28 4.85
1716 2462 0.034059 AACCAGAGTCTGAACTGCCG 59.966 55.000 22.09 5.28 35.28 5.69
1723 2473 0.320421 GTCTGAACTGCCGGTGCTAA 60.320 55.000 1.90 0.00 38.71 3.09
1740 2490 6.700081 CGGTGCTAATTTCTACATGTAAGCTA 59.300 38.462 20.16 8.76 0.00 3.32
1766 2583 8.685838 TGGCTAAAATCACTGTACTTTTACTT 57.314 30.769 0.00 0.00 0.00 2.24
1908 3104 4.159879 GGCTAACTAACTAGCTGAGTTCCA 59.840 45.833 10.58 0.00 45.81 3.53
1909 3105 5.344884 GCTAACTAACTAGCTGAGTTCCAG 58.655 45.833 10.58 7.61 45.81 3.86
1927 3123 6.268847 AGTTCCAGAGATCTGTCTGTAAACTT 59.731 38.462 16.35 7.84 41.37 2.66
1988 3184 3.863407 GGAGTCATCCAGGTGAACC 57.137 57.895 0.00 0.00 45.87 3.62
1992 3188 2.167487 GAGTCATCCAGGTGAACCTCTC 59.833 54.545 0.00 0.00 46.65 3.20
1993 3189 2.183679 GTCATCCAGGTGAACCTCTCT 58.816 52.381 0.00 0.00 46.65 3.10
1994 3190 2.167487 GTCATCCAGGTGAACCTCTCTC 59.833 54.545 0.00 0.00 46.65 3.20
1997 3193 1.150135 TCCAGGTGAACCTCTCTCCTT 59.850 52.381 0.00 0.00 44.14 3.36
1998 3194 1.552792 CCAGGTGAACCTCTCTCCTTC 59.447 57.143 0.00 0.00 44.14 3.46
1999 3195 2.534990 CAGGTGAACCTCTCTCCTTCT 58.465 52.381 0.00 0.00 44.14 2.85
2000 3196 2.903135 CAGGTGAACCTCTCTCCTTCTT 59.097 50.000 0.00 0.00 44.14 2.52
2001 3197 2.903135 AGGTGAACCTCTCTCCTTCTTG 59.097 50.000 0.00 0.00 44.14 3.02
2002 3198 2.614229 GGTGAACCTCTCTCCTTCTTGC 60.614 54.545 0.00 0.00 35.21 4.01
2003 3199 2.301583 GTGAACCTCTCTCCTTCTTGCT 59.698 50.000 0.00 0.00 0.00 3.91
2007 3203 2.708325 ACCTCTCTCCTTCTTGCTGTTT 59.292 45.455 0.00 0.00 0.00 2.83
2009 3205 3.495806 CCTCTCTCCTTCTTGCTGTTTGT 60.496 47.826 0.00 0.00 0.00 2.83
2010 3206 4.133078 CTCTCTCCTTCTTGCTGTTTGTT 58.867 43.478 0.00 0.00 0.00 2.83
2011 3207 4.526970 TCTCTCCTTCTTGCTGTTTGTTT 58.473 39.130 0.00 0.00 0.00 2.83
2012 3208 4.949856 TCTCTCCTTCTTGCTGTTTGTTTT 59.050 37.500 0.00 0.00 0.00 2.43
2013 3209 5.066505 TCTCTCCTTCTTGCTGTTTGTTTTC 59.933 40.000 0.00 0.00 0.00 2.29
2014 3210 4.704540 TCTCCTTCTTGCTGTTTGTTTTCA 59.295 37.500 0.00 0.00 0.00 2.69
2015 3211 4.997565 TCCTTCTTGCTGTTTGTTTTCAG 58.002 39.130 0.00 0.00 35.12 3.02
2038 3234 4.675510 CACATTTGTGCTTGTATCCATCC 58.324 43.478 0.00 0.00 39.39 3.51
2039 3235 4.400251 CACATTTGTGCTTGTATCCATCCT 59.600 41.667 0.00 0.00 39.39 3.24
2040 3236 5.018809 ACATTTGTGCTTGTATCCATCCTT 58.981 37.500 0.00 0.00 0.00 3.36
2041 3237 5.105635 ACATTTGTGCTTGTATCCATCCTTG 60.106 40.000 0.00 0.00 0.00 3.61
2042 3238 3.719268 TGTGCTTGTATCCATCCTTGT 57.281 42.857 0.00 0.00 0.00 3.16
2043 3239 4.835284 TGTGCTTGTATCCATCCTTGTA 57.165 40.909 0.00 0.00 0.00 2.41
2044 3240 4.513442 TGTGCTTGTATCCATCCTTGTAC 58.487 43.478 0.00 0.00 0.00 2.90
2045 3241 4.225042 TGTGCTTGTATCCATCCTTGTACT 59.775 41.667 0.00 0.00 0.00 2.73
2046 3242 4.811557 GTGCTTGTATCCATCCTTGTACTC 59.188 45.833 0.00 0.00 0.00 2.59
2047 3243 4.716784 TGCTTGTATCCATCCTTGTACTCT 59.283 41.667 0.00 0.00 0.00 3.24
2048 3244 5.053145 GCTTGTATCCATCCTTGTACTCTG 58.947 45.833 0.00 0.00 0.00 3.35
2049 3245 5.163405 GCTTGTATCCATCCTTGTACTCTGA 60.163 44.000 0.00 0.00 0.00 3.27
2050 3246 6.630413 GCTTGTATCCATCCTTGTACTCTGAA 60.630 42.308 0.00 0.00 0.00 3.02
2051 3247 7.437713 TTGTATCCATCCTTGTACTCTGAAT 57.562 36.000 0.00 0.00 0.00 2.57
2054 3250 6.566079 ATCCATCCTTGTACTCTGAATTGA 57.434 37.500 0.00 0.00 0.00 2.57
2058 3254 5.152623 TCCTTGTACTCTGAATTGAGTGG 57.847 43.478 8.35 2.38 45.70 4.00
2060 3256 5.485353 TCCTTGTACTCTGAATTGAGTGGAT 59.515 40.000 8.35 0.00 45.70 3.41
2061 3257 5.814705 CCTTGTACTCTGAATTGAGTGGATC 59.185 44.000 8.35 0.00 45.70 3.36
2062 3258 5.344743 TGTACTCTGAATTGAGTGGATCC 57.655 43.478 4.20 4.20 45.70 3.36
2064 3260 3.458831 ACTCTGAATTGAGTGGATCCCT 58.541 45.455 9.90 5.82 44.64 4.20
2065 3261 3.199508 ACTCTGAATTGAGTGGATCCCTG 59.800 47.826 9.90 0.00 44.64 4.45
2066 3262 3.184628 TCTGAATTGAGTGGATCCCTGT 58.815 45.455 9.90 0.00 0.00 4.00
2067 3263 3.054875 TCTGAATTGAGTGGATCCCTGTG 60.055 47.826 9.90 0.00 0.00 3.66
2068 3264 2.912295 TGAATTGAGTGGATCCCTGTGA 59.088 45.455 9.90 0.00 0.00 3.58
2069 3265 3.054875 TGAATTGAGTGGATCCCTGTGAG 60.055 47.826 9.90 0.00 0.00 3.51
2071 3267 0.117140 TGAGTGGATCCCTGTGAGGT 59.883 55.000 9.90 0.00 31.93 3.85
2073 3269 2.035632 GAGTGGATCCCTGTGAGGTAG 58.964 57.143 9.90 0.00 31.93 3.18
2074 3270 0.466124 GTGGATCCCTGTGAGGTAGC 59.534 60.000 9.90 0.00 31.93 3.58
2075 3271 0.339859 TGGATCCCTGTGAGGTAGCT 59.660 55.000 9.90 0.00 31.93 3.32
2076 3272 1.573857 TGGATCCCTGTGAGGTAGCTA 59.426 52.381 9.90 0.00 31.93 3.32
2077 3273 2.023404 TGGATCCCTGTGAGGTAGCTAA 60.023 50.000 9.90 0.00 31.93 3.09
2078 3274 2.365941 GGATCCCTGTGAGGTAGCTAAC 59.634 54.545 0.00 0.00 31.93 2.34
2079 3275 2.615986 TCCCTGTGAGGTAGCTAACA 57.384 50.000 12.26 11.67 31.93 2.41
2080 3276 3.116096 TCCCTGTGAGGTAGCTAACAT 57.884 47.619 12.58 0.00 31.93 2.71
2081 3277 3.450904 TCCCTGTGAGGTAGCTAACATT 58.549 45.455 12.58 0.00 31.93 2.71
2082 3278 3.451178 TCCCTGTGAGGTAGCTAACATTC 59.549 47.826 12.58 0.94 31.93 2.67
2083 3279 3.197766 CCCTGTGAGGTAGCTAACATTCA 59.802 47.826 12.58 3.94 31.93 2.57
2084 3280 4.437239 CCTGTGAGGTAGCTAACATTCAG 58.563 47.826 12.58 14.27 0.00 3.02
2085 3281 4.081420 CCTGTGAGGTAGCTAACATTCAGT 60.081 45.833 12.58 0.00 0.00 3.41
2086 3282 5.073311 TGTGAGGTAGCTAACATTCAGTC 57.927 43.478 12.26 0.00 0.00 3.51
2087 3283 4.772624 TGTGAGGTAGCTAACATTCAGTCT 59.227 41.667 12.26 0.00 0.00 3.24
2088 3284 5.105716 TGTGAGGTAGCTAACATTCAGTCTC 60.106 44.000 12.26 0.35 0.00 3.36
2102 4501 8.316640 ACATTCAGTCTCAAAATAAGTGTCTC 57.683 34.615 0.00 0.00 0.00 3.36
2164 4563 7.947890 AGTTAAGACACTTATTTTGGGATGGAA 59.052 33.333 0.00 0.00 0.00 3.53
2175 4574 6.648879 TTTTGGGATGGAAAGAGTACTTTG 57.351 37.500 0.00 0.00 44.97 2.77
2222 4621 2.169352 TCTGTTATCTGAGGCCTCTTGC 59.831 50.000 32.28 16.50 40.16 4.01
2246 4645 2.009774 GGTCGGGATTCACACAGATTG 58.990 52.381 0.00 0.00 0.00 2.67
2261 4660 2.494471 CAGATTGGACCAACATGCATGT 59.506 45.455 26.61 26.61 44.20 3.21
2303 4703 4.712337 AGTCTGTTTCTAGGGATCGATGTT 59.288 41.667 0.54 0.00 0.00 2.71
2307 4707 4.120589 GTTTCTAGGGATCGATGTTCCAC 58.879 47.826 0.54 0.00 34.77 4.02
2328 4728 4.569966 CACTGATCTCTGTAGCACATTTCC 59.430 45.833 0.00 0.00 0.00 3.13
2329 4729 4.469227 ACTGATCTCTGTAGCACATTTCCT 59.531 41.667 0.00 0.00 0.00 3.36
2330 4730 5.016051 TGATCTCTGTAGCACATTTCCTC 57.984 43.478 0.00 0.00 0.00 3.71
2334 4734 6.544928 TCTCTGTAGCACATTTCCTCATTA 57.455 37.500 0.00 0.00 0.00 1.90
2335 4735 6.341316 TCTCTGTAGCACATTTCCTCATTAC 58.659 40.000 0.00 0.00 0.00 1.89
2336 4736 6.155221 TCTCTGTAGCACATTTCCTCATTACT 59.845 38.462 0.00 0.00 0.00 2.24
2337 4737 6.108687 TCTGTAGCACATTTCCTCATTACTG 58.891 40.000 0.00 0.00 0.00 2.74
2338 4738 4.635765 TGTAGCACATTTCCTCATTACTGC 59.364 41.667 0.00 0.00 0.00 4.40
2339 4739 3.689347 AGCACATTTCCTCATTACTGCA 58.311 40.909 0.00 0.00 0.00 4.41
2340 4740 4.275810 AGCACATTTCCTCATTACTGCAT 58.724 39.130 0.00 0.00 0.00 3.96
2341 4741 5.439721 AGCACATTTCCTCATTACTGCATA 58.560 37.500 0.00 0.00 0.00 3.14
2342 4742 5.530171 AGCACATTTCCTCATTACTGCATAG 59.470 40.000 0.00 0.00 0.00 2.23
2343 4743 5.297776 GCACATTTCCTCATTACTGCATAGT 59.702 40.000 0.00 0.00 40.99 2.12
2344 4744 6.183360 GCACATTTCCTCATTACTGCATAGTT 60.183 38.462 0.00 0.00 38.36 2.24
2345 4745 7.012327 GCACATTTCCTCATTACTGCATAGTTA 59.988 37.037 0.00 0.00 38.36 2.24
2346 4746 8.554528 CACATTTCCTCATTACTGCATAGTTAG 58.445 37.037 0.00 0.00 38.36 2.34
2347 4747 8.267894 ACATTTCCTCATTACTGCATAGTTAGT 58.732 33.333 0.00 0.00 38.36 2.24
2348 4748 8.768955 CATTTCCTCATTACTGCATAGTTAGTC 58.231 37.037 0.00 0.00 38.36 2.59
2349 4749 7.418337 TTCCTCATTACTGCATAGTTAGTCA 57.582 36.000 0.00 0.00 38.36 3.41
2350 4750 6.806751 TCCTCATTACTGCATAGTTAGTCAC 58.193 40.000 0.00 0.00 38.36 3.67
2351 4751 5.687730 CCTCATTACTGCATAGTTAGTCACG 59.312 44.000 0.00 0.00 38.36 4.35
2352 4752 5.041287 TCATTACTGCATAGTTAGTCACGC 58.959 41.667 0.00 0.00 38.36 5.34
2353 4753 4.713824 TTACTGCATAGTTAGTCACGCT 57.286 40.909 0.00 0.00 38.36 5.07
2354 4754 3.152261 ACTGCATAGTTAGTCACGCTC 57.848 47.619 0.00 0.00 31.66 5.03
2355 4755 2.112522 CTGCATAGTTAGTCACGCTCG 58.887 52.381 0.00 0.00 0.00 5.03
2356 4756 1.471287 TGCATAGTTAGTCACGCTCGT 59.529 47.619 0.00 0.00 0.00 4.18
2357 4757 1.846782 GCATAGTTAGTCACGCTCGTG 59.153 52.381 15.49 15.49 46.64 4.35
2358 4758 2.451132 CATAGTTAGTCACGCTCGTGG 58.549 52.381 20.36 4.41 45.43 4.94
2359 4759 0.806868 TAGTTAGTCACGCTCGTGGG 59.193 55.000 20.36 0.00 45.43 4.61
2360 4760 2.092882 GTTAGTCACGCTCGTGGGC 61.093 63.158 20.36 14.00 45.43 5.36
2361 4761 3.291101 TTAGTCACGCTCGTGGGCC 62.291 63.158 20.36 0.00 45.43 5.80
2373 4773 4.815973 TGGGCCGGCCTCCTGTAT 62.816 66.667 42.70 0.00 36.10 2.29
2374 4774 3.942439 GGGCCGGCCTCCTGTATC 61.942 72.222 42.70 21.56 36.10 2.24
2375 4775 2.844839 GGCCGGCCTCCTGTATCT 60.845 66.667 38.76 0.00 0.00 1.98
2376 4776 2.423446 GCCGGCCTCCTGTATCTG 59.577 66.667 18.11 0.00 0.00 2.90
2377 4777 2.435693 GCCGGCCTCCTGTATCTGT 61.436 63.158 18.11 0.00 0.00 3.41
2378 4778 1.113517 GCCGGCCTCCTGTATCTGTA 61.114 60.000 18.11 0.00 0.00 2.74
2379 4779 1.633774 CCGGCCTCCTGTATCTGTAT 58.366 55.000 0.00 0.00 0.00 2.29
2380 4780 1.273606 CCGGCCTCCTGTATCTGTATG 59.726 57.143 0.00 0.00 0.00 2.39
2381 4781 1.337260 CGGCCTCCTGTATCTGTATGC 60.337 57.143 0.00 0.00 0.00 3.14
2382 4782 1.694150 GGCCTCCTGTATCTGTATGCA 59.306 52.381 0.00 0.00 0.00 3.96
2383 4783 2.304180 GGCCTCCTGTATCTGTATGCAT 59.696 50.000 3.79 3.79 0.00 3.96
2384 4784 3.515502 GGCCTCCTGTATCTGTATGCATA 59.484 47.826 1.16 1.16 0.00 3.14
2385 4785 4.163078 GGCCTCCTGTATCTGTATGCATAT 59.837 45.833 10.16 0.00 0.00 1.78
2386 4786 5.355596 GCCTCCTGTATCTGTATGCATATC 58.644 45.833 10.16 4.65 0.00 1.63
2387 4787 5.586339 CCTCCTGTATCTGTATGCATATCG 58.414 45.833 10.16 4.37 0.00 2.92
2388 4788 5.358160 CCTCCTGTATCTGTATGCATATCGA 59.642 44.000 10.16 9.74 0.00 3.59
2389 4789 6.196079 TCCTGTATCTGTATGCATATCGAC 57.804 41.667 10.16 0.00 0.00 4.20
2390 4790 5.030936 CCTGTATCTGTATGCATATCGACG 58.969 45.833 10.16 0.00 0.00 5.12
2391 4791 4.981794 TGTATCTGTATGCATATCGACGG 58.018 43.478 10.16 4.72 0.00 4.79
2392 4792 2.347697 TCTGTATGCATATCGACGGC 57.652 50.000 10.16 0.00 0.00 5.68
2393 4793 1.611491 TCTGTATGCATATCGACGGCA 59.389 47.619 10.16 9.52 42.43 5.69
2394 4794 1.988467 CTGTATGCATATCGACGGCAG 59.012 52.381 10.16 6.76 41.40 4.85
2395 4795 0.716108 GTATGCATATCGACGGCAGC 59.284 55.000 10.16 2.61 41.40 5.25
2396 4796 0.389817 TATGCATATCGACGGCAGCC 60.390 55.000 1.16 0.00 41.40 4.85
2397 4797 2.029666 GCATATCGACGGCAGCCT 59.970 61.111 10.54 0.00 0.00 4.58
2398 4798 1.595382 GCATATCGACGGCAGCCTT 60.595 57.895 10.54 0.00 0.00 4.35
2399 4799 1.160329 GCATATCGACGGCAGCCTTT 61.160 55.000 10.54 0.00 0.00 3.11
2400 4800 1.299541 CATATCGACGGCAGCCTTTT 58.700 50.000 10.54 0.00 0.00 2.27
2401 4801 1.670811 CATATCGACGGCAGCCTTTTT 59.329 47.619 10.54 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.189499 GGCTCCTAATTGGCGCTGG 61.189 63.158 7.64 0.49 45.39 4.85
1 2 0.820891 ATGGCTCCTAATTGGCGCTG 60.821 55.000 7.64 0.00 45.39 5.18
2 3 0.764890 TATGGCTCCTAATTGGCGCT 59.235 50.000 7.64 0.00 45.39 5.92
4 5 2.417719 GACTATGGCTCCTAATTGGCG 58.582 52.381 0.00 0.00 35.26 5.69
5 6 2.037251 TCGACTATGGCTCCTAATTGGC 59.963 50.000 0.00 0.00 35.26 4.52
6 7 3.306364 CCTCGACTATGGCTCCTAATTGG 60.306 52.174 0.00 0.00 37.10 3.16
7 8 3.862642 GCCTCGACTATGGCTCCTAATTG 60.863 52.174 6.18 0.00 45.26 2.32
8 9 2.300437 GCCTCGACTATGGCTCCTAATT 59.700 50.000 6.18 0.00 45.26 1.40
9 10 1.896465 GCCTCGACTATGGCTCCTAAT 59.104 52.381 6.18 0.00 45.26 1.73
10 11 1.329256 GCCTCGACTATGGCTCCTAA 58.671 55.000 6.18 0.00 45.26 2.69
11 12 0.889638 CGCCTCGACTATGGCTCCTA 60.890 60.000 11.21 0.00 46.42 2.94
12 13 2.196925 CGCCTCGACTATGGCTCCT 61.197 63.158 11.21 0.00 46.42 3.69
13 14 2.336809 CGCCTCGACTATGGCTCC 59.663 66.667 11.21 0.00 46.42 4.70
14 15 2.336809 CCGCCTCGACTATGGCTC 59.663 66.667 11.21 0.00 46.42 4.70
15 16 3.917760 GCCGCCTCGACTATGGCT 61.918 66.667 11.21 0.00 46.42 4.75
18 19 4.569023 TGCGCCGCCTCGACTATG 62.569 66.667 6.63 0.00 0.00 2.23
19 20 4.570663 GTGCGCCGCCTCGACTAT 62.571 66.667 6.63 0.00 0.00 2.12
29 30 3.792053 GATCTACCCCTGTGCGCCG 62.792 68.421 4.18 0.00 0.00 6.46
30 31 2.109181 GATCTACCCCTGTGCGCC 59.891 66.667 4.18 0.00 0.00 6.53
31 32 2.279517 CGATCTACCCCTGTGCGC 60.280 66.667 0.00 0.00 0.00 6.09
32 33 1.065928 GTCGATCTACCCCTGTGCG 59.934 63.158 0.00 0.00 0.00 5.34
33 34 1.065928 CGTCGATCTACCCCTGTGC 59.934 63.158 0.00 0.00 0.00 4.57
34 35 1.100510 TTCGTCGATCTACCCCTGTG 58.899 55.000 0.00 0.00 0.00 3.66
35 36 1.101331 GTTCGTCGATCTACCCCTGT 58.899 55.000 0.00 0.00 0.00 4.00
36 37 0.029035 CGTTCGTCGATCTACCCCTG 59.971 60.000 0.00 0.00 42.86 4.45
37 38 0.393537 ACGTTCGTCGATCTACCCCT 60.394 55.000 0.00 0.00 42.86 4.79
38 39 0.453390 AACGTTCGTCGATCTACCCC 59.547 55.000 0.00 0.00 42.86 4.95
39 40 1.820092 GAACGTTCGTCGATCTACCC 58.180 55.000 13.36 0.00 42.86 3.69
40 41 1.450717 CGAACGTTCGTCGATCTACC 58.549 55.000 35.92 3.94 45.09 3.18
90 92 7.044798 CACCTAGAAGATTCCTAAAACCAGAG 58.955 42.308 0.00 0.00 0.00 3.35
198 208 8.032952 AGCAAAGGAAAGAAAAGAAACAAAAG 57.967 30.769 0.00 0.00 0.00 2.27
202 212 5.422012 AGGAGCAAAGGAAAGAAAAGAAACA 59.578 36.000 0.00 0.00 0.00 2.83
203 213 5.907207 AGGAGCAAAGGAAAGAAAAGAAAC 58.093 37.500 0.00 0.00 0.00 2.78
335 367 2.103263 TGAACAAAATTTGGGAACGGGG 59.897 45.455 10.71 0.00 34.12 5.73
339 371 7.756558 TGAAATTGTGAACAAAATTTGGGAAC 58.243 30.769 17.02 5.50 39.55 3.62
342 374 8.976986 TTTTGAAATTGTGAACAAAATTTGGG 57.023 26.923 17.02 0.00 39.55 4.12
371 403 5.828299 TGAAGACTTTTTGAAACACGGAT 57.172 34.783 0.00 0.00 0.00 4.18
392 424 9.540431 AACAAGAACATTTTTCAAAATTCGTTG 57.460 25.926 5.78 5.59 36.52 4.10
567 606 7.267128 ACATGAACATTTTGTGAATGACAGTT 58.733 30.769 0.00 0.00 35.44 3.16
569 608 7.703298 AACATGAACATTTTGTGAATGACAG 57.297 32.000 0.00 3.75 35.44 3.51
597 636 4.494091 AGTTCCATCTCATTCGGATGTT 57.506 40.909 3.00 0.00 38.95 2.71
600 639 3.813443 CCAAGTTCCATCTCATTCGGAT 58.187 45.455 0.00 0.00 0.00 4.18
626 665 6.983890 TGACATATGCTTACGTGTGTGATATT 59.016 34.615 1.58 0.00 37.28 1.28
639 678 6.095300 CCAAAAGATGTGGTGACATATGCTTA 59.905 38.462 1.58 0.00 42.81 3.09
646 685 4.834496 ACATTCCAAAAGATGTGGTGACAT 59.166 37.500 0.00 0.00 46.01 3.06
648 687 4.853924 ACATTCCAAAAGATGTGGTGAC 57.146 40.909 0.00 0.00 37.43 3.67
717 767 3.881688 CCAAGTATCCAATTCTGCTCCTG 59.118 47.826 0.00 0.00 0.00 3.86
718 768 3.782523 TCCAAGTATCCAATTCTGCTCCT 59.217 43.478 0.00 0.00 0.00 3.69
724 774 7.331791 GTTCTGTACTCCAAGTATCCAATTCT 58.668 38.462 0.00 0.00 32.65 2.40
735 785 5.070001 TGGAAAATGGTTCTGTACTCCAAG 58.930 41.667 0.00 0.00 34.80 3.61
737 787 4.715534 TGGAAAATGGTTCTGTACTCCA 57.284 40.909 0.00 0.00 35.64 3.86
768 825 4.212004 CCATGTCGGTGCTCAATTGTATAG 59.788 45.833 5.13 0.00 0.00 1.31
776 833 2.749682 AGCCATGTCGGTGCTCAA 59.250 55.556 0.00 0.00 36.97 3.02
833 890 4.625028 TCTTGAAGATATGCATGACGGAG 58.375 43.478 10.16 0.00 0.00 4.63
916 974 4.817464 ACTAGGCTACACGATCTCTTGTAG 59.183 45.833 15.72 15.72 45.76 2.74
1121 1225 6.668541 ATGACTAGCAAATGTGTACATCAC 57.331 37.500 0.00 0.00 46.31 3.06
1165 1269 2.213499 ACAAGACAGAAAGAAGTGGCG 58.787 47.619 0.00 0.00 0.00 5.69
1192 1296 8.261522 AGAAAAAGGAGACCTATGATGTTCTAC 58.738 37.037 0.00 0.00 31.13 2.59
1341 1451 2.701423 GGTAAAACCCTCCTTTTGGCAA 59.299 45.455 0.00 0.00 33.64 4.52
1356 1466 1.970092 CACACACCCCTTCGGTAAAA 58.030 50.000 0.00 0.00 46.14 1.52
1455 1566 3.196901 TCATACTACATCCAACGGCAGTT 59.803 43.478 0.00 0.00 42.15 3.16
1456 1567 2.764010 TCATACTACATCCAACGGCAGT 59.236 45.455 0.00 0.00 0.00 4.40
1457 1568 3.452755 TCATACTACATCCAACGGCAG 57.547 47.619 0.00 0.00 0.00 4.85
1458 1569 3.133901 ACATCATACTACATCCAACGGCA 59.866 43.478 0.00 0.00 0.00 5.69
1459 1570 3.728845 ACATCATACTACATCCAACGGC 58.271 45.455 0.00 0.00 0.00 5.68
1460 1571 6.277605 TGTTACATCATACTACATCCAACGG 58.722 40.000 0.00 0.00 0.00 4.44
1461 1572 7.516785 GCTTGTTACATCATACTACATCCAACG 60.517 40.741 0.00 0.00 0.00 4.10
1462 1573 7.279981 TGCTTGTTACATCATACTACATCCAAC 59.720 37.037 0.00 0.00 0.00 3.77
1463 1574 7.334858 TGCTTGTTACATCATACTACATCCAA 58.665 34.615 0.00 0.00 0.00 3.53
1468 1579 9.884636 ACTTATTGCTTGTTACATCATACTACA 57.115 29.630 0.00 0.00 0.00 2.74
1525 1636 9.171877 GAGTCTCAACTTATTTCATTCCTCATT 57.828 33.333 0.00 0.00 35.28 2.57
1616 2348 9.618890 CCTTGATATTTTCAGATCTCCTGTAAA 57.381 33.333 0.00 0.00 43.22 2.01
1712 2458 2.772077 TGTAGAAATTAGCACCGGCA 57.228 45.000 0.00 0.00 44.61 5.69
1713 2459 2.943033 ACATGTAGAAATTAGCACCGGC 59.057 45.455 0.00 0.00 41.61 6.13
1714 2460 5.277345 GCTTACATGTAGAAATTAGCACCGG 60.277 44.000 16.48 0.00 0.00 5.28
1715 2461 5.523916 AGCTTACATGTAGAAATTAGCACCG 59.476 40.000 21.18 0.00 0.00 4.94
1716 2462 6.927294 AGCTTACATGTAGAAATTAGCACC 57.073 37.500 21.18 0.00 0.00 5.01
1740 2490 8.863872 AGTAAAAGTACAGTGATTTTAGCCAT 57.136 30.769 0.00 0.00 31.10 4.40
1908 3104 4.284490 TGCCAAGTTTACAGACAGATCTCT 59.716 41.667 0.00 0.00 30.42 3.10
1909 3105 4.390297 GTGCCAAGTTTACAGACAGATCTC 59.610 45.833 0.00 0.00 30.42 2.75
1981 3177 2.614229 GCAAGAAGGAGAGAGGTTCACC 60.614 54.545 0.00 0.00 36.86 4.02
1982 3178 2.301583 AGCAAGAAGGAGAGAGGTTCAC 59.698 50.000 0.00 0.00 0.00 3.18
1985 3181 2.334023 ACAGCAAGAAGGAGAGAGGTT 58.666 47.619 0.00 0.00 0.00 3.50
1986 3182 2.022718 ACAGCAAGAAGGAGAGAGGT 57.977 50.000 0.00 0.00 0.00 3.85
1987 3183 3.072944 CAAACAGCAAGAAGGAGAGAGG 58.927 50.000 0.00 0.00 0.00 3.69
1988 3184 3.737850 ACAAACAGCAAGAAGGAGAGAG 58.262 45.455 0.00 0.00 0.00 3.20
1989 3185 3.845781 ACAAACAGCAAGAAGGAGAGA 57.154 42.857 0.00 0.00 0.00 3.10
1992 3188 4.997565 TGAAAACAAACAGCAAGAAGGAG 58.002 39.130 0.00 0.00 0.00 3.69
1993 3189 4.997565 CTGAAAACAAACAGCAAGAAGGA 58.002 39.130 0.00 0.00 0.00 3.36
2002 3198 5.552807 CACAAATGTGCTGAAAACAAACAG 58.447 37.500 0.00 0.00 39.39 3.16
2003 3199 5.527511 CACAAATGTGCTGAAAACAAACA 57.472 34.783 0.00 0.00 39.39 2.83
2029 3225 7.500992 TCAATTCAGAGTACAAGGATGGATAC 58.499 38.462 0.00 0.00 0.00 2.24
2031 3227 6.157645 ACTCAATTCAGAGTACAAGGATGGAT 59.842 38.462 0.00 0.00 46.52 3.41
2032 3228 5.485353 ACTCAATTCAGAGTACAAGGATGGA 59.515 40.000 0.00 0.00 46.52 3.41
2033 3229 5.583854 CACTCAATTCAGAGTACAAGGATGG 59.416 44.000 0.00 0.00 46.65 3.51
2034 3230 5.583854 CCACTCAATTCAGAGTACAAGGATG 59.416 44.000 0.00 0.00 46.65 3.51
2035 3231 5.485353 TCCACTCAATTCAGAGTACAAGGAT 59.515 40.000 0.00 0.00 46.65 3.24
2036 3232 4.838423 TCCACTCAATTCAGAGTACAAGGA 59.162 41.667 0.00 0.00 46.65 3.36
2038 3234 5.814705 GGATCCACTCAATTCAGAGTACAAG 59.185 44.000 6.95 0.00 46.65 3.16
2039 3235 5.338381 GGGATCCACTCAATTCAGAGTACAA 60.338 44.000 15.23 0.00 46.65 2.41
2040 3236 4.162320 GGGATCCACTCAATTCAGAGTACA 59.838 45.833 15.23 0.00 46.65 2.90
2041 3237 4.407296 AGGGATCCACTCAATTCAGAGTAC 59.593 45.833 15.23 0.00 46.65 2.73
2042 3238 4.406972 CAGGGATCCACTCAATTCAGAGTA 59.593 45.833 15.23 0.00 46.65 2.59
2044 3240 3.199508 ACAGGGATCCACTCAATTCAGAG 59.800 47.826 15.23 0.00 41.44 3.35
2045 3241 3.054875 CACAGGGATCCACTCAATTCAGA 60.055 47.826 15.23 0.00 0.00 3.27
2046 3242 3.054875 TCACAGGGATCCACTCAATTCAG 60.055 47.826 15.23 0.00 0.00 3.02
2047 3243 2.912295 TCACAGGGATCCACTCAATTCA 59.088 45.455 15.23 0.00 0.00 2.57
2048 3244 3.539604 CTCACAGGGATCCACTCAATTC 58.460 50.000 15.23 0.00 0.00 2.17
2049 3245 2.240667 CCTCACAGGGATCCACTCAATT 59.759 50.000 15.23 0.00 0.00 2.32
2050 3246 1.842562 CCTCACAGGGATCCACTCAAT 59.157 52.381 15.23 0.00 0.00 2.57
2051 3247 1.279496 CCTCACAGGGATCCACTCAA 58.721 55.000 15.23 0.00 0.00 3.02
2054 3250 1.967274 GCTACCTCACAGGGATCCACT 60.967 57.143 15.23 5.45 40.58 4.00
2056 3252 0.339859 AGCTACCTCACAGGGATCCA 59.660 55.000 15.23 0.00 40.58 3.41
2058 3254 3.031736 TGTTAGCTACCTCACAGGGATC 58.968 50.000 0.00 0.00 40.58 3.36
2060 3256 2.615986 TGTTAGCTACCTCACAGGGA 57.384 50.000 0.00 0.00 40.58 4.20
2061 3257 3.197766 TGAATGTTAGCTACCTCACAGGG 59.802 47.826 0.00 0.00 40.58 4.45
2062 3258 4.081420 ACTGAATGTTAGCTACCTCACAGG 60.081 45.833 15.73 0.00 42.49 4.00
2064 3260 4.772624 AGACTGAATGTTAGCTACCTCACA 59.227 41.667 0.00 0.00 30.40 3.58
2065 3261 5.105716 TGAGACTGAATGTTAGCTACCTCAC 60.106 44.000 0.00 0.00 0.00 3.51
2066 3262 5.016831 TGAGACTGAATGTTAGCTACCTCA 58.983 41.667 0.00 0.00 0.00 3.86
2067 3263 5.584253 TGAGACTGAATGTTAGCTACCTC 57.416 43.478 0.00 0.00 0.00 3.85
2068 3264 6.360370 TTTGAGACTGAATGTTAGCTACCT 57.640 37.500 0.00 0.00 0.00 3.08
2069 3265 7.617041 ATTTTGAGACTGAATGTTAGCTACC 57.383 36.000 0.00 0.00 0.00 3.18
2071 3267 9.944376 ACTTATTTTGAGACTGAATGTTAGCTA 57.056 29.630 0.00 0.00 0.00 3.32
2073 3269 8.507249 ACACTTATTTTGAGACTGAATGTTAGC 58.493 33.333 0.00 0.00 0.00 3.09
2075 3271 9.778741 AGACACTTATTTTGAGACTGAATGTTA 57.221 29.630 0.00 0.00 0.00 2.41
2076 3272 8.682936 AGACACTTATTTTGAGACTGAATGTT 57.317 30.769 0.00 0.00 0.00 2.71
2077 3273 7.933577 TGAGACACTTATTTTGAGACTGAATGT 59.066 33.333 0.00 0.00 0.00 2.71
2078 3274 8.315391 TGAGACACTTATTTTGAGACTGAATG 57.685 34.615 0.00 0.00 0.00 2.67
2079 3275 8.778358 GTTGAGACACTTATTTTGAGACTGAAT 58.222 33.333 0.00 0.00 0.00 2.57
2080 3276 7.987458 AGTTGAGACACTTATTTTGAGACTGAA 59.013 33.333 0.00 0.00 0.00 3.02
2081 3277 7.500992 AGTTGAGACACTTATTTTGAGACTGA 58.499 34.615 0.00 0.00 0.00 3.41
2082 3278 7.721286 AGTTGAGACACTTATTTTGAGACTG 57.279 36.000 0.00 0.00 0.00 3.51
2083 3279 7.169982 CGAAGTTGAGACACTTATTTTGAGACT 59.830 37.037 0.00 0.00 37.11 3.24
2084 3280 7.284351 CGAAGTTGAGACACTTATTTTGAGAC 58.716 38.462 0.00 0.00 37.11 3.36
2085 3281 6.423905 CCGAAGTTGAGACACTTATTTTGAGA 59.576 38.462 0.00 0.00 37.11 3.27
2086 3282 6.202954 ACCGAAGTTGAGACACTTATTTTGAG 59.797 38.462 0.00 0.00 37.11 3.02
2087 3283 6.053005 ACCGAAGTTGAGACACTTATTTTGA 58.947 36.000 0.00 0.00 37.11 2.69
2088 3284 6.300354 ACCGAAGTTGAGACACTTATTTTG 57.700 37.500 0.00 0.00 37.11 2.44
2102 4501 3.064820 AGCACAAAGTTGTACCGAAGTTG 59.935 43.478 0.00 0.00 39.91 3.16
2134 4533 8.391075 TCCCAAAATAAGTGTCTTAACTTCAG 57.609 34.615 0.00 0.00 40.77 3.02
2136 4535 8.244113 CCATCCCAAAATAAGTGTCTTAACTTC 58.756 37.037 0.00 0.00 40.77 3.01
2156 4555 6.051179 AGTACAAAGTACTCTTTCCATCCC 57.949 41.667 4.09 0.00 41.31 3.85
2164 4563 6.821665 TGCTTGAACAAGTACAAAGTACTCTT 59.178 34.615 14.62 5.40 40.45 2.85
2175 4574 7.549488 AGGTTATCAGTATGCTTGAACAAGTAC 59.451 37.037 14.62 10.45 40.45 2.73
2222 4621 2.100631 GTGTGAATCCCGACCGCAG 61.101 63.158 0.00 0.00 0.00 5.18
2246 4645 3.813443 AGAGATACATGCATGTTGGTCC 58.187 45.455 35.45 21.56 41.97 4.46
2303 4703 2.807676 TGTGCTACAGAGATCAGTGGA 58.192 47.619 0.00 0.00 0.00 4.02
2307 4707 5.021033 AGGAAATGTGCTACAGAGATCAG 57.979 43.478 0.00 0.00 0.00 2.90
2328 4728 5.174035 GCGTGACTAACTATGCAGTAATGAG 59.826 44.000 0.00 0.00 33.48 2.90
2329 4729 5.041287 GCGTGACTAACTATGCAGTAATGA 58.959 41.667 0.00 0.00 33.48 2.57
2330 4730 5.043903 AGCGTGACTAACTATGCAGTAATG 58.956 41.667 0.00 0.00 33.48 1.90
2334 4734 2.478031 CGAGCGTGACTAACTATGCAGT 60.478 50.000 0.00 0.00 36.19 4.40
2335 4735 2.112522 CGAGCGTGACTAACTATGCAG 58.887 52.381 0.00 0.00 0.00 4.41
2336 4736 1.471287 ACGAGCGTGACTAACTATGCA 59.529 47.619 0.00 0.00 0.00 3.96
2337 4737 2.190325 ACGAGCGTGACTAACTATGC 57.810 50.000 0.00 0.00 0.00 3.14
2356 4756 4.815973 ATACAGGAGGCCGGCCCA 62.816 66.667 41.72 19.97 36.58 5.36
2357 4757 3.942439 GATACAGGAGGCCGGCCC 61.942 72.222 41.72 30.78 36.58 5.80
2358 4758 2.844839 AGATACAGGAGGCCGGCC 60.845 66.667 39.29 39.29 0.00 6.13
2359 4759 1.113517 TACAGATACAGGAGGCCGGC 61.114 60.000 21.18 21.18 0.00 6.13
2360 4760 1.273606 CATACAGATACAGGAGGCCGG 59.726 57.143 0.00 0.00 0.00 6.13
2361 4761 1.337260 GCATACAGATACAGGAGGCCG 60.337 57.143 0.00 0.00 0.00 6.13
2362 4762 1.694150 TGCATACAGATACAGGAGGCC 59.306 52.381 0.00 0.00 0.00 5.19
2363 4763 3.692257 ATGCATACAGATACAGGAGGC 57.308 47.619 0.00 0.00 0.00 4.70
2364 4764 5.358160 TCGATATGCATACAGATACAGGAGG 59.642 44.000 8.99 0.00 0.00 4.30
2365 4765 6.261859 GTCGATATGCATACAGATACAGGAG 58.738 44.000 8.99 0.00 0.00 3.69
2366 4766 5.163754 CGTCGATATGCATACAGATACAGGA 60.164 44.000 8.99 0.00 0.00 3.86
2367 4767 5.030936 CGTCGATATGCATACAGATACAGG 58.969 45.833 8.99 0.00 0.00 4.00
2368 4768 5.030936 CCGTCGATATGCATACAGATACAG 58.969 45.833 8.99 5.20 0.00 2.74
2369 4769 4.674362 GCCGTCGATATGCATACAGATACA 60.674 45.833 8.99 0.00 0.00 2.29
2370 4770 3.791887 GCCGTCGATATGCATACAGATAC 59.208 47.826 8.99 2.88 0.00 2.24
2371 4771 3.442273 TGCCGTCGATATGCATACAGATA 59.558 43.478 8.99 0.00 0.00 1.98
2372 4772 2.231235 TGCCGTCGATATGCATACAGAT 59.769 45.455 8.99 0.00 0.00 2.90
2373 4773 1.611491 TGCCGTCGATATGCATACAGA 59.389 47.619 8.99 8.64 0.00 3.41
2374 4774 1.988467 CTGCCGTCGATATGCATACAG 59.012 52.381 8.99 6.22 33.97 2.74
2375 4775 1.934849 GCTGCCGTCGATATGCATACA 60.935 52.381 8.99 0.00 33.97 2.29
2376 4776 0.716108 GCTGCCGTCGATATGCATAC 59.284 55.000 8.99 0.00 33.97 2.39
2377 4777 0.389817 GGCTGCCGTCGATATGCATA 60.390 55.000 9.27 9.27 33.97 3.14
2378 4778 1.669115 GGCTGCCGTCGATATGCAT 60.669 57.895 1.35 3.79 33.97 3.96
2379 4779 2.280119 GGCTGCCGTCGATATGCA 60.280 61.111 1.35 6.35 0.00 3.96
2380 4780 1.160329 AAAGGCTGCCGTCGATATGC 61.160 55.000 13.96 0.00 0.00 3.14
2381 4781 1.299541 AAAAGGCTGCCGTCGATATG 58.700 50.000 13.96 0.00 0.00 1.78
2382 4782 2.038387 AAAAAGGCTGCCGTCGATAT 57.962 45.000 13.96 0.00 0.00 1.63
2383 4783 3.543884 AAAAAGGCTGCCGTCGATA 57.456 47.368 13.96 0.00 0.00 2.92
2384 4784 4.397348 AAAAAGGCTGCCGTCGAT 57.603 50.000 13.96 0.00 0.00 3.59
2409 4809 4.335400 TGCCCTTTGCCTTTAGAAAAAG 57.665 40.909 0.00 0.00 41.57 2.27
2410 4810 4.762289 TTGCCCTTTGCCTTTAGAAAAA 57.238 36.364 0.00 0.00 40.16 1.94


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

AutoCloner maintained by Alex Coulton.