Multiple sequence alignment - TraesCS1B01G065100

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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 TraesCS1B01G065100 chr1B 100.000 4052 0 0 1 4052 49662065 49666116 0.000000e+00 7483.0
1 TraesCS1B01G065100 chr1B 86.894 1381 154 16 1516 2889 49676058 49677418 0.000000e+00 1522.0
2 TraesCS1B01G065100 chr1B 83.985 1561 239 9 1515 3069 48997366 48998921 0.000000e+00 1487.0
3 TraesCS1B01G065100 chr1B 83.883 1545 238 9 1515 3053 48933205 48934744 0.000000e+00 1463.0
4 TraesCS1B01G065100 chr1B 86.199 913 91 14 597 1478 49144572 49145480 0.000000e+00 955.0
5 TraesCS1B01G065100 chr1B 86.007 829 107 7 2232 3053 48984447 48985273 0.000000e+00 880.0
6 TraesCS1B01G065100 chr1B 83.696 552 71 12 941 1478 49674550 49675096 1.680000e-138 503.0
7 TraesCS1B01G065100 chr1B 83.804 531 77 6 952 1478 49633868 49634393 2.810000e-136 496.0
8 TraesCS1B01G065100 chr1B 79.851 670 87 26 155 781 49524314 49524978 2.870000e-121 446.0
9 TraesCS1B01G065100 chr1B 81.644 523 70 11 958 1478 49525136 49525634 1.050000e-110 411.0
10 TraesCS1B01G065100 chr1B 80.128 624 59 39 206 793 49639657 49640251 4.880000e-109 405.0
11 TraesCS1B01G065100 chr1B 80.347 173 18 9 3075 3232 49677425 49677596 2.560000e-22 117.0
12 TraesCS1B01G065100 chr1B 88.636 88 8 2 3441 3528 49862712 49862797 5.540000e-19 106.0
13 TraesCS1B01G065100 chr1B 87.500 88 11 0 3952 4039 49843128 49843215 7.170000e-18 102.0
14 TraesCS1B01G065100 chr1B 86.207 87 7 5 3144 3227 49478563 49478647 5.580000e-14 89.8
15 TraesCS1B01G065100 chr1B 91.045 67 4 1 66 132 49522921 49522985 5.580000e-14 89.8
16 TraesCS1B01G065100 chr1B 97.674 43 0 1 3292 3334 49089696 49089737 5.620000e-09 73.1
17 TraesCS1B01G065100 chr1D 84.167 1800 223 38 1515 3269 30666831 30668613 0.000000e+00 1688.0
18 TraesCS1B01G065100 chr1D 83.646 1810 255 19 1516 3297 31060419 31062215 0.000000e+00 1664.0
19 TraesCS1B01G065100 chr1D 84.357 1547 225 13 1515 3053 30652147 30653684 0.000000e+00 1500.0
20 TraesCS1B01G065100 chr1D 82.340 1376 213 15 1544 2912 31038504 31039856 0.000000e+00 1168.0
21 TraesCS1B01G065100 chr1D 83.635 1216 182 13 1866 3074 30430693 30431898 0.000000e+00 1127.0
22 TraesCS1B01G065100 chr1D 94.976 637 30 2 2661 3297 30381011 30381645 0.000000e+00 998.0
23 TraesCS1B01G065100 chr1D 89.301 701 58 11 791 1478 30537276 30537972 0.000000e+00 863.0
24 TraesCS1B01G065100 chr1D 90.893 549 40 3 3514 4052 30381857 30382405 0.000000e+00 728.0
25 TraesCS1B01G065100 chr1D 85.314 606 71 14 887 1478 30264912 30265513 9.630000e-171 610.0
26 TraesCS1B01G065100 chr1D 79.780 910 96 38 597 1475 31058775 31059627 7.550000e-162 580.0
27 TraesCS1B01G065100 chr1D 83.275 568 44 24 66 594 31058175 31058730 3.660000e-130 475.0
28 TraesCS1B01G065100 chr1D 80.826 605 93 17 887 1478 30428821 30429415 1.720000e-123 453.0
29 TraesCS1B01G065100 chr1D 85.593 354 29 5 246 584 30536256 30536602 6.440000e-93 351.0
30 TraesCS1B01G065100 chr1D 79.406 539 72 24 949 1478 31029417 31029925 1.080000e-90 344.0
31 TraesCS1B01G065100 chr1D 84.665 313 36 10 887 1189 30372539 30372849 6.580000e-78 302.0
32 TraesCS1B01G065100 chr1D 76.393 610 105 22 887 1474 30642460 30643052 3.960000e-75 292.0
33 TraesCS1B01G065100 chr1D 92.045 176 14 0 3291 3466 30381681 30381856 8.700000e-62 248.0
34 TraesCS1B01G065100 chr1D 88.800 125 11 3 1354 1477 30373275 30373397 2.520000e-32 150.0
35 TraesCS1B01G065100 chr1D 88.750 80 7 1 3531 3610 31062490 31062567 3.330000e-16 97.1
36 TraesCS1B01G065100 chr1D 75.089 281 31 17 3778 4039 31328666 31328926 1.200000e-15 95.3
37 TraesCS1B01G065100 chr1D 89.855 69 7 0 3971 4039 31334157 31334225 5.580000e-14 89.8
38 TraesCS1B01G065100 chr1D 92.982 57 4 0 3971 4027 31322726 31322782 2.600000e-12 84.2
39 TraesCS1B01G065100 chr1D 93.878 49 3 0 91 139 30535936 30535984 1.560000e-09 75.0
40 TraesCS1B01G065100 chr1A 84.133 1771 231 26 1568 3297 30334404 30336165 0.000000e+00 1668.0
41 TraesCS1B01G065100 chr1A 86.297 1226 162 6 1833 3053 30389379 30390603 0.000000e+00 1328.0
42 TraesCS1B01G065100 chr1A 80.308 325 58 6 1516 1838 30388677 30388997 1.460000e-59 241.0
43 TraesCS1B01G065100 chr1A 84.884 172 26 0 1307 1478 30572467 30572638 1.500000e-39 174.0
44 TraesCS1B01G065100 chr1A 86.364 88 12 0 3952 4039 30637587 30637674 3.330000e-16 97.1
45 TraesCS1B01G065100 chr1A 89.333 75 6 2 3441 3515 30780474 30780546 4.310000e-15 93.5


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 TraesCS1B01G065100 chr1B 49662065 49666116 4051 False 7483.000000 7483 100.000000 1 4052 1 chr1B.!!$F9 4051
1 TraesCS1B01G065100 chr1B 48997366 48998921 1555 False 1487.000000 1487 83.985000 1515 3069 1 chr1B.!!$F3 1554
2 TraesCS1B01G065100 chr1B 48933205 48934744 1539 False 1463.000000 1463 83.883000 1515 3053 1 chr1B.!!$F1 1538
3 TraesCS1B01G065100 chr1B 49144572 49145480 908 False 955.000000 955 86.199000 597 1478 1 chr1B.!!$F5 881
4 TraesCS1B01G065100 chr1B 48984447 48985273 826 False 880.000000 880 86.007000 2232 3053 1 chr1B.!!$F2 821
5 TraesCS1B01G065100 chr1B 49674550 49677596 3046 False 714.000000 1522 83.645667 941 3232 3 chr1B.!!$F13 2291
6 TraesCS1B01G065100 chr1B 49633868 49634393 525 False 496.000000 496 83.804000 952 1478 1 chr1B.!!$F7 526
7 TraesCS1B01G065100 chr1B 49639657 49640251 594 False 405.000000 405 80.128000 206 793 1 chr1B.!!$F8 587
8 TraesCS1B01G065100 chr1B 49522921 49525634 2713 False 315.600000 446 84.180000 66 1478 3 chr1B.!!$F12 1412
9 TraesCS1B01G065100 chr1D 30666831 30668613 1782 False 1688.000000 1688 84.167000 1515 3269 1 chr1D.!!$F4 1754
10 TraesCS1B01G065100 chr1D 30652147 30653684 1537 False 1500.000000 1500 84.357000 1515 3053 1 chr1D.!!$F3 1538
11 TraesCS1B01G065100 chr1D 31038504 31039856 1352 False 1168.000000 1168 82.340000 1544 2912 1 chr1D.!!$F6 1368
12 TraesCS1B01G065100 chr1D 30428821 30431898 3077 False 790.000000 1127 82.230500 887 3074 2 chr1D.!!$F12 2187
13 TraesCS1B01G065100 chr1D 31058175 31062567 4392 False 704.025000 1664 83.862750 66 3610 4 chr1D.!!$F14 3544
14 TraesCS1B01G065100 chr1D 30381011 30382405 1394 False 658.000000 998 92.638000 2661 4052 3 chr1D.!!$F11 1391
15 TraesCS1B01G065100 chr1D 30264912 30265513 601 False 610.000000 610 85.314000 887 1478 1 chr1D.!!$F1 591
16 TraesCS1B01G065100 chr1D 30535936 30537972 2036 False 429.666667 863 89.590667 91 1478 3 chr1D.!!$F13 1387
17 TraesCS1B01G065100 chr1D 31029417 31029925 508 False 344.000000 344 79.406000 949 1478 1 chr1D.!!$F5 529
18 TraesCS1B01G065100 chr1D 30642460 30643052 592 False 292.000000 292 76.393000 887 1474 1 chr1D.!!$F2 587
19 TraesCS1B01G065100 chr1D 30372539 30373397 858 False 226.000000 302 86.732500 887 1477 2 chr1D.!!$F10 590
20 TraesCS1B01G065100 chr1A 30334404 30336165 1761 False 1668.000000 1668 84.133000 1568 3297 1 chr1A.!!$F1 1729
21 TraesCS1B01G065100 chr1A 30388677 30390603 1926 False 784.500000 1328 83.302500 1516 3053 2 chr1A.!!$F5 1537

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
177 1554 0.034089 CTTCCCATTCCCCACCACTC 60.034 60.0 0.00 0.0 0.00 3.51 F
590 2005 0.182299 GGATTGCAGGAAGGAGGAGG 59.818 60.0 0.00 0.0 0.00 4.30 F
1824 5443 0.317770 CGCCATGTGACACACCAAAC 60.318 55.0 11.22 0.0 32.73 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 4738 0.393077 CTCAGGTGGTAATAGGCCGG 59.607 60.000 0.00 0.0 0.0 6.13 R
2328 6340 1.071385 CTGTTGGTCCAGTTCAGCTCT 59.929 52.381 7.52 0.0 0.0 4.09 R
3768 7915 0.034863 TTGGGGTCGCCTTTCCATAC 60.035 55.000 7.55 0.0 0.0 2.39 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
25 26 8.897872 AAAATCAACTGATTGCAGATTCTTTT 57.102 26.923 5.72 0.00 45.17 2.27
26 27 9.985730 AAAATCAACTGATTGCAGATTCTTTTA 57.014 25.926 5.72 0.00 45.17 1.52
27 28 9.635520 AAATCAACTGATTGCAGATTCTTTTAG 57.364 29.630 5.72 0.00 45.17 1.85
28 29 7.750229 TCAACTGATTGCAGATTCTTTTAGT 57.250 32.000 0.00 0.00 45.17 2.24
29 30 8.169977 TCAACTGATTGCAGATTCTTTTAGTT 57.830 30.769 0.00 0.00 45.17 2.24
30 31 9.283768 TCAACTGATTGCAGATTCTTTTAGTTA 57.716 29.630 0.00 0.00 45.17 2.24
31 32 9.552114 CAACTGATTGCAGATTCTTTTAGTTAG 57.448 33.333 0.00 0.00 45.17 2.34
32 33 8.854614 ACTGATTGCAGATTCTTTTAGTTAGT 57.145 30.769 0.00 0.00 45.17 2.24
33 34 9.289782 ACTGATTGCAGATTCTTTTAGTTAGTT 57.710 29.630 0.00 0.00 45.17 2.24
34 35 9.552114 CTGATTGCAGATTCTTTTAGTTAGTTG 57.448 33.333 0.00 0.00 45.17 3.16
35 36 9.066892 TGATTGCAGATTCTTTTAGTTAGTTGT 57.933 29.630 0.00 0.00 0.00 3.32
36 37 9.899226 GATTGCAGATTCTTTTAGTTAGTTGTT 57.101 29.630 0.00 0.00 0.00 2.83
51 52 8.203681 AGTTAGTTGTTAAATACTCCCTCAGT 57.796 34.615 0.00 0.00 39.41 3.41
52 53 8.312564 AGTTAGTTGTTAAATACTCCCTCAGTC 58.687 37.037 0.00 0.00 36.43 3.51
53 54 6.051179 AGTTGTTAAATACTCCCTCAGTCC 57.949 41.667 0.00 0.00 36.43 3.85
54 55 4.730949 TGTTAAATACTCCCTCAGTCCG 57.269 45.455 0.00 0.00 36.43 4.79
55 56 3.449737 TGTTAAATACTCCCTCAGTCCGG 59.550 47.826 0.00 0.00 36.43 5.14
56 57 2.544844 AAATACTCCCTCAGTCCGGA 57.455 50.000 0.00 0.00 36.43 5.14
98 99 6.032985 GCGATAATAGAGTTGTTATCTCTGCG 59.967 42.308 5.82 0.00 41.57 5.18
101 102 0.924090 GAGTTGTTATCTCTGCGGCG 59.076 55.000 0.51 0.51 0.00 6.46
134 135 2.493675 GTCATGACTCTAGCACCTCACA 59.506 50.000 18.83 0.00 0.00 3.58
139 140 1.552337 ACTCTAGCACCTCACACATGG 59.448 52.381 0.00 0.00 0.00 3.66
143 144 1.609208 AGCACCTCACACATGGTTTC 58.391 50.000 0.00 0.00 33.75 2.78
147 148 1.494721 ACCTCACACATGGTTTCCAGT 59.505 47.619 0.00 0.00 36.75 4.00
148 149 2.091885 ACCTCACACATGGTTTCCAGTT 60.092 45.455 0.00 0.00 36.75 3.16
156 1533 3.213506 CATGGTTTCCAGTTCTGTGTCA 58.786 45.455 0.00 0.00 36.75 3.58
164 1541 2.038952 CCAGTTCTGTGTCATCTTCCCA 59.961 50.000 0.00 0.00 0.00 4.37
177 1554 0.034089 CTTCCCATTCCCCACCACTC 60.034 60.000 0.00 0.00 0.00 3.51
183 1560 0.545787 ATTCCCCACCACTCACCGTA 60.546 55.000 0.00 0.00 0.00 4.02
277 1665 1.454539 CGTCACCCCCTTTGTCCTT 59.545 57.895 0.00 0.00 0.00 3.36
280 1668 0.476771 TCACCCCCTTTGTCCTTGAC 59.523 55.000 0.00 0.00 0.00 3.18
334 1722 2.565841 GCTCGAATAGCCAATCCAAGT 58.434 47.619 0.00 0.00 46.25 3.16
433 1821 4.200283 GAGGCGCAGAGGTCGGAG 62.200 72.222 10.83 0.00 0.00 4.63
435 1823 3.760035 GGCGCAGAGGTCGGAGAA 61.760 66.667 10.83 0.00 39.69 2.87
463 1851 2.487762 GCAGGTTAGCAGTGCAATTACA 59.512 45.455 19.20 0.00 37.16 2.41
466 1854 4.156556 CAGGTTAGCAGTGCAATTACACAT 59.843 41.667 19.20 0.00 43.23 3.21
491 1885 2.165234 CAGCTCCTCGAATCAGTCAAGA 59.835 50.000 0.00 0.00 0.00 3.02
565 1980 1.475751 CCCACATCACATGGCCTACTC 60.476 57.143 3.32 0.00 35.74 2.59
587 2002 1.283029 TGAAGGATTGCAGGAAGGAGG 59.717 52.381 0.00 0.00 0.00 4.30
590 2005 0.182299 GGATTGCAGGAAGGAGGAGG 59.818 60.000 0.00 0.00 0.00 4.30
616 2078 5.772672 AGTATTCGATGAATCTAGAGCCTGT 59.227 40.000 0.00 0.00 33.95 4.00
694 2162 2.973899 CCAGCAGGCTGTACTCGT 59.026 61.111 17.16 0.00 42.15 4.18
705 2176 1.293963 TGTACTCGTCTGTCGGTCCG 61.294 60.000 4.39 4.39 40.32 4.79
706 2177 1.004560 TACTCGTCTGTCGGTCCGT 60.005 57.895 11.88 0.00 40.32 4.69
708 2179 1.018226 ACTCGTCTGTCGGTCCGTAG 61.018 60.000 11.88 11.17 40.32 3.51
709 2180 0.738762 CTCGTCTGTCGGTCCGTAGA 60.739 60.000 11.88 13.31 40.32 2.59
710 2181 1.016130 TCGTCTGTCGGTCCGTAGAC 61.016 60.000 27.00 27.00 42.73 2.59
715 2190 1.331138 CTGTCGGTCCGTAGACTCATC 59.669 57.143 11.88 0.00 43.05 2.92
717 2192 0.545171 TCGGTCCGTAGACTCATCCT 59.455 55.000 11.88 0.00 43.05 3.24
754 2229 1.956170 ACGCGGTGCTTCAGACTTG 60.956 57.895 12.47 0.00 0.00 3.16
785 2269 8.417106 TCTTCTTCAGTCAATGATACATACCTC 58.583 37.037 0.00 0.00 37.89 3.85
853 2854 1.818060 TCCTGGCAATGTGTGTAATGC 59.182 47.619 0.00 0.00 38.06 3.56
939 2956 3.490031 AACACACGGCATCAGGGCA 62.490 57.895 0.00 0.00 43.60 5.36
1145 3193 1.068121 AGCCTAAGCAGTTGGTCCTT 58.932 50.000 0.00 0.00 43.56 3.36
1192 3433 1.427072 AAGCAGCCCCTGTAACTGGT 61.427 55.000 0.00 0.00 43.54 4.00
1261 3511 0.400213 TCCTGCCTTAGTTGTGTGGG 59.600 55.000 0.00 0.00 0.00 4.61
1268 3518 3.191371 GCCTTAGTTGTGTGGGAGATTTG 59.809 47.826 0.00 0.00 0.00 2.32
1478 4064 9.962783 ATCGCTAGGTAATTGTACTAAACTAAG 57.037 33.333 0.00 0.00 0.00 2.18
1493 4723 2.222027 ACTAAGAACACTGGCACTTGC 58.778 47.619 0.00 0.00 41.14 4.01
1497 4727 1.202855 AGAACACTGGCACTTGCATCT 60.203 47.619 3.15 0.00 44.36 2.90
1504 4734 3.054875 ACTGGCACTTGCATCTAATCAGA 60.055 43.478 3.15 0.00 44.36 3.27
1508 4738 5.528690 TGGCACTTGCATCTAATCAGATTAC 59.471 40.000 3.15 0.00 39.62 1.89
1550 5134 6.951971 AGATAGGATATTGCCGCTCTTTATT 58.048 36.000 0.00 0.00 0.00 1.40
1562 5146 5.266242 CCGCTCTTTATTGTCATTACTTGC 58.734 41.667 0.00 0.00 0.00 4.01
1614 5198 5.070001 CCACAAGAACTTGGGTATCTTTCA 58.930 41.667 17.05 0.00 42.21 2.69
1657 5241 9.841295 ATTTGAGTAGAAACAGTTTAAGTGGTA 57.159 29.630 0.00 0.00 0.00 3.25
1670 5254 2.270434 AGTGGTACCATCCCAGTGAT 57.730 50.000 19.72 0.00 34.31 3.06
1683 5267 6.206243 CCATCCCAGTGATTCTTTATAAGCTG 59.794 42.308 0.00 0.00 0.00 4.24
1689 5273 8.821894 CCAGTGATTCTTTATAAGCTGAACTAC 58.178 37.037 0.00 0.00 0.00 2.73
1699 5285 3.425162 AGCTGAACTACCTTTTCAGGG 57.575 47.619 12.70 0.00 46.84 4.45
1741 5327 2.683211 AGGTGGCAAAGTTCCATCTT 57.317 45.000 0.00 0.00 42.13 2.40
1748 5334 3.305608 GGCAAAGTTCCATCTTTCACTGG 60.306 47.826 0.00 0.00 35.77 4.00
1754 5340 3.920231 TCCATCTTTCACTGGATCCTG 57.080 47.619 16.56 16.56 36.63 3.86
1759 5357 2.432146 TCTTTCACTGGATCCTGGATCG 59.568 50.000 26.04 17.50 39.72 3.69
1760 5358 2.159179 TTCACTGGATCCTGGATCGA 57.841 50.000 26.04 22.40 39.72 3.59
1761 5359 2.388526 TCACTGGATCCTGGATCGAT 57.611 50.000 26.04 13.72 39.72 3.59
1787 5385 8.154203 TCTTGACCATAATAAGGATTTATGCGA 58.846 33.333 0.00 0.00 36.27 5.10
1824 5443 0.317770 CGCCATGTGACACACCAAAC 60.318 55.000 11.22 0.00 32.73 2.93
1825 5444 0.743688 GCCATGTGACACACCAAACA 59.256 50.000 11.22 0.00 32.73 2.83
1908 5920 0.670546 TTTCCTTCGCTTGCCTCTCG 60.671 55.000 0.00 0.00 0.00 4.04
1968 5980 9.699703 AAGTGTGTAAAAAGTAAAAGCAAAAGA 57.300 25.926 0.00 0.00 0.00 2.52
1981 5993 5.702349 AAGCAAAAGAAAGTCTGGAGATG 57.298 39.130 0.00 0.00 0.00 2.90
2110 6122 6.291377 ACTGTATTCAGAGTTGAGCTTGAAA 58.709 36.000 6.32 0.00 43.76 2.69
2247 6259 3.012518 GCTGTATGGCTTCTGTTCACAT 58.987 45.455 0.00 0.00 0.00 3.21
2328 6340 2.032030 GCACGAACAAGAGCTAGCAAAA 60.032 45.455 18.83 0.00 0.00 2.44
2341 6353 2.645838 AGCAAAAGAGCTGAACTGGA 57.354 45.000 0.00 0.00 44.66 3.86
2424 6436 4.647399 TGTGATGATCCTATTGTACACCGA 59.353 41.667 0.00 0.00 0.00 4.69
2573 6585 6.420913 CTACATAGCACCTGGTATTTACCT 57.579 41.667 0.00 0.00 46.58 3.08
2575 6587 6.420913 ACATAGCACCTGGTATTTACCTAG 57.579 41.667 0.00 4.36 46.58 3.02
2577 6589 2.438392 AGCACCTGGTATTTACCTAGGC 59.562 50.000 9.30 12.04 46.58 3.93
2581 6593 3.454812 ACCTGGTATTTACCTAGGCACTG 59.545 47.826 9.30 0.00 46.58 3.66
2584 6596 5.511545 CCTGGTATTTACCTAGGCACTGATC 60.512 48.000 9.30 0.00 46.58 2.92
2586 6598 4.347000 GGTATTTACCTAGGCACTGATCCA 59.653 45.833 9.30 0.00 43.10 3.41
2594 6613 5.006386 CCTAGGCACTGATCCATTTTATCC 58.994 45.833 0.00 0.00 41.52 2.59
2624 6645 9.745018 ATGAAATGTTATTCAGAAAGAGAGGAA 57.255 29.630 0.00 0.00 42.21 3.36
2631 6658 6.890979 ATTCAGAAAGAGAGGAAAACAAGG 57.109 37.500 0.00 0.00 0.00 3.61
2636 6663 4.445557 AAGAGAGGAAAACAAGGCTCTT 57.554 40.909 0.00 0.00 37.75 2.85
2703 6737 3.576078 ACCATGGTGTTGACTGAGAAA 57.424 42.857 18.99 0.00 0.00 2.52
3134 7186 5.429762 TCAAGGACAGAAGGATGGATAACAT 59.570 40.000 0.00 0.00 44.18 2.71
3230 7294 7.510001 TGTTGGATGAAAATATATGCATTCCCT 59.490 33.333 3.54 0.00 0.00 4.20
3241 7305 3.098774 TGCATTCCCTTTATCTTGCCA 57.901 42.857 0.00 0.00 0.00 4.92
3335 7443 2.108250 ACAGGCTGGATGTTTAACAGGT 59.892 45.455 20.34 0.00 32.98 4.00
3367 7475 2.160205 GGACCGAAGCTTTTTAGCCTT 58.840 47.619 0.00 0.00 34.90 4.35
3371 7479 5.117355 ACCGAAGCTTTTTAGCCTTTAAC 57.883 39.130 0.00 0.00 34.90 2.01
3397 7505 2.099263 AGATGTGACGATCCCACTTACG 59.901 50.000 12.38 0.00 35.66 3.18
3408 7516 3.266636 TCCCACTTACGTATGTGCATTG 58.733 45.455 27.53 17.42 33.26 2.82
3426 7534 4.621510 GCATTGCTTTCTTTTCTTAGGGGG 60.622 45.833 0.16 0.00 0.00 5.40
3487 7595 4.530161 AGTAGCAGATCTCAAGTTCAACCT 59.470 41.667 0.00 0.00 0.00 3.50
3494 7602 7.308830 GCAGATCTCAAGTTCAACCTGTTTTAT 60.309 37.037 0.00 0.00 0.00 1.40
3499 7607 7.228706 TCTCAAGTTCAACCTGTTTTATTCTCC 59.771 37.037 0.00 0.00 0.00 3.71
3500 7608 5.941948 AGTTCAACCTGTTTTATTCTCCG 57.058 39.130 0.00 0.00 0.00 4.63
3501 7609 5.374071 AGTTCAACCTGTTTTATTCTCCGT 58.626 37.500 0.00 0.00 0.00 4.69
3502 7610 5.469084 AGTTCAACCTGTTTTATTCTCCGTC 59.531 40.000 0.00 0.00 0.00 4.79
3503 7611 5.223449 TCAACCTGTTTTATTCTCCGTCT 57.777 39.130 0.00 0.00 0.00 4.18
3510 7623 7.284716 ACCTGTTTTATTCTCCGTCTTTTTCTT 59.715 33.333 0.00 0.00 0.00 2.52
3548 7685 2.307392 ACTAGCTCTCACACTCCAGAGA 59.693 50.000 0.70 0.00 38.85 3.10
3560 7697 0.894141 TCCAGAGAGTGCTGAAGCTC 59.106 55.000 3.61 0.00 42.66 4.09
3578 7715 4.348486 AGCTCCAGACTGAACTCTGAATA 58.652 43.478 3.32 0.00 40.28 1.75
3627 7764 2.237393 TTGCTTTGGACAAACATGCC 57.763 45.000 0.00 0.00 0.00 4.40
3676 7813 2.033801 CCTTGTCTGGTTGCAGTTTCTG 59.966 50.000 0.00 0.00 34.12 3.02
3719 7856 0.733150 GTTTCTGAATACTGGCCGGC 59.267 55.000 21.18 21.18 0.00 6.13
3743 7880 6.263392 GCTCTCCCTCTTTTCTTTTGTAAACT 59.737 38.462 0.00 0.00 0.00 2.66
3768 7915 0.107703 TTTATGGGAGCACTGCCTCG 60.108 55.000 9.75 0.00 42.12 4.63
3784 7931 0.529992 CTCGTATGGAAAGGCGACCC 60.530 60.000 0.00 0.00 0.00 4.46
3786 7933 1.605453 GTATGGAAAGGCGACCCCA 59.395 57.895 0.00 0.00 35.39 4.96
3815 7962 7.413438 CCATTGCACATTCTACTTCACTAGTTC 60.413 40.741 0.00 0.00 38.33 3.01
3853 8000 7.685532 AGAAGAAAAATGACGAAAAGAAAGC 57.314 32.000 0.00 0.00 0.00 3.51
3857 8004 5.949233 AAAATGACGAAAAGAAAGCACAC 57.051 34.783 0.00 0.00 0.00 3.82
3858 8005 4.900635 AATGACGAAAAGAAAGCACACT 57.099 36.364 0.00 0.00 0.00 3.55
3881 8028 7.860872 CACTAAAACCTGAAGCTTCGTATTTTT 59.139 33.333 26.14 23.78 0.00 1.94
3888 8035 0.170339 GCTTCGTATTTTTGGCGGCT 59.830 50.000 11.43 0.00 0.00 5.52
3905 8052 2.728922 GGCTAACTTCTCCATACGTCG 58.271 52.381 0.00 0.00 0.00 5.12
3909 8056 4.023878 GCTAACTTCTCCATACGTCGATCT 60.024 45.833 0.00 0.00 0.00 2.75
3937 8084 7.175641 GTGCTGCATTCTCAACCCTAATAATAT 59.824 37.037 5.27 0.00 0.00 1.28
3950 8097 9.678260 AACCCTAATAATATCATCAATCTCAGC 57.322 33.333 0.00 0.00 0.00 4.26
3955 8102 8.929827 AATAATATCATCAATCTCAGCTCTCG 57.070 34.615 0.00 0.00 0.00 4.04
3958 8105 2.100418 TCATCAATCTCAGCTCTCGTGG 59.900 50.000 0.00 0.00 0.00 4.94
3961 8108 0.829333 AATCTCAGCTCTCGTGGCAT 59.171 50.000 0.00 0.00 0.00 4.40
3965 8112 2.125229 AGCTCTCGTGGCATGCTG 60.125 61.111 18.92 8.20 32.32 4.41
3966 8113 2.435586 GCTCTCGTGGCATGCTGT 60.436 61.111 18.92 0.00 0.00 4.40
3967 8114 2.459442 GCTCTCGTGGCATGCTGTC 61.459 63.158 18.92 7.39 0.00 3.51
4020 8167 9.045223 CATTTATCATCTACATTTTCTCGACCA 57.955 33.333 0.00 0.00 0.00 4.02
4029 8176 3.485463 TTTTCTCGACCATGTCCAAGT 57.515 42.857 0.00 0.00 0.00 3.16
4035 8182 1.275291 CGACCATGTCCAAGTACCTGT 59.725 52.381 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.897872 AAAAGAATCTGCAATCAGTTGATTTT 57.102 26.923 4.66 0.00 42.41 1.82
1 2 9.635520 CTAAAAGAATCTGCAATCAGTTGATTT 57.364 29.630 4.66 0.00 42.41 2.17
2 3 8.800332 ACTAAAAGAATCTGCAATCAGTTGATT 58.200 29.630 1.58 1.58 44.93 2.57
3 4 8.345724 ACTAAAAGAATCTGCAATCAGTTGAT 57.654 30.769 0.00 0.00 41.10 2.57
4 5 7.750229 ACTAAAAGAATCTGCAATCAGTTGA 57.250 32.000 0.00 0.00 41.10 3.18
5 6 9.552114 CTAACTAAAAGAATCTGCAATCAGTTG 57.448 33.333 0.00 0.00 41.10 3.16
6 7 9.289782 ACTAACTAAAAGAATCTGCAATCAGTT 57.710 29.630 0.00 0.00 41.10 3.16
7 8 8.854614 ACTAACTAAAAGAATCTGCAATCAGT 57.145 30.769 0.00 0.00 41.10 3.41
8 9 9.552114 CAACTAACTAAAAGAATCTGCAATCAG 57.448 33.333 0.00 0.00 41.67 2.90
9 10 9.066892 ACAACTAACTAAAAGAATCTGCAATCA 57.933 29.630 0.00 0.00 0.00 2.57
10 11 9.899226 AACAACTAACTAAAAGAATCTGCAATC 57.101 29.630 0.00 0.00 0.00 2.67
25 26 9.317827 ACTGAGGGAGTATTTAACAACTAACTA 57.682 33.333 0.00 0.00 30.86 2.24
26 27 8.203681 ACTGAGGGAGTATTTAACAACTAACT 57.796 34.615 0.00 0.00 30.86 2.24
27 28 7.548427 GGACTGAGGGAGTATTTAACAACTAAC 59.452 40.741 0.00 0.00 33.83 2.34
28 29 7.578189 CGGACTGAGGGAGTATTTAACAACTAA 60.578 40.741 0.00 0.00 33.83 2.24
29 30 6.127535 CGGACTGAGGGAGTATTTAACAACTA 60.128 42.308 0.00 0.00 33.83 2.24
30 31 5.337330 CGGACTGAGGGAGTATTTAACAACT 60.337 44.000 0.00 0.00 33.83 3.16
31 32 4.868734 CGGACTGAGGGAGTATTTAACAAC 59.131 45.833 0.00 0.00 33.83 3.32
32 33 4.081309 CCGGACTGAGGGAGTATTTAACAA 60.081 45.833 0.00 0.00 33.83 2.83
33 34 3.449737 CCGGACTGAGGGAGTATTTAACA 59.550 47.826 0.00 0.00 33.83 2.41
34 35 3.703052 TCCGGACTGAGGGAGTATTTAAC 59.297 47.826 0.00 0.00 33.83 2.01
35 36 3.958798 CTCCGGACTGAGGGAGTATTTAA 59.041 47.826 0.00 0.00 43.91 1.52
36 37 3.563223 CTCCGGACTGAGGGAGTATTTA 58.437 50.000 0.00 0.00 43.91 1.40
37 38 2.389715 CTCCGGACTGAGGGAGTATTT 58.610 52.381 0.00 0.00 43.91 1.40
38 39 1.411787 CCTCCGGACTGAGGGAGTATT 60.412 57.143 0.00 0.00 46.83 1.89
39 40 0.186386 CCTCCGGACTGAGGGAGTAT 59.814 60.000 0.00 0.00 46.83 2.12
40 41 1.613610 CCTCCGGACTGAGGGAGTA 59.386 63.158 0.00 0.00 46.83 2.59
41 42 2.360980 CCTCCGGACTGAGGGAGT 59.639 66.667 0.00 0.00 46.83 3.85
46 47 0.256464 AGTACTCCCTCCGGACTGAG 59.744 60.000 19.33 19.33 33.32 3.35
47 48 1.489649 CTAGTACTCCCTCCGGACTGA 59.510 57.143 0.00 0.00 33.32 3.41
48 49 1.970092 CTAGTACTCCCTCCGGACTG 58.030 60.000 0.00 0.00 33.32 3.51
49 50 0.183252 GCTAGTACTCCCTCCGGACT 59.817 60.000 0.00 0.00 33.32 3.85
50 51 0.106819 TGCTAGTACTCCCTCCGGAC 60.107 60.000 0.00 0.00 33.32 4.79
51 52 0.627451 TTGCTAGTACTCCCTCCGGA 59.373 55.000 2.93 2.93 36.45 5.14
52 53 1.033574 CTTGCTAGTACTCCCTCCGG 58.966 60.000 0.00 0.00 0.00 5.14
53 54 1.405821 CACTTGCTAGTACTCCCTCCG 59.594 57.143 0.00 0.00 31.96 4.63
54 55 1.137282 GCACTTGCTAGTACTCCCTCC 59.863 57.143 0.00 0.00 38.21 4.30
55 56 1.202313 CGCACTTGCTAGTACTCCCTC 60.202 57.143 0.00 0.00 39.32 4.30
56 57 0.818296 CGCACTTGCTAGTACTCCCT 59.182 55.000 0.00 0.00 39.32 4.20
57 58 0.815734 TCGCACTTGCTAGTACTCCC 59.184 55.000 0.00 0.00 39.32 4.30
58 59 2.873133 ATCGCACTTGCTAGTACTCC 57.127 50.000 0.00 0.00 39.32 3.85
59 60 6.900189 TCTATTATCGCACTTGCTAGTACTC 58.100 40.000 0.00 0.00 39.32 2.59
60 61 6.487331 ACTCTATTATCGCACTTGCTAGTACT 59.513 38.462 0.00 0.00 39.32 2.73
61 62 6.670233 ACTCTATTATCGCACTTGCTAGTAC 58.330 40.000 0.00 0.00 39.32 2.73
62 63 6.879276 ACTCTATTATCGCACTTGCTAGTA 57.121 37.500 0.00 0.00 39.32 1.82
63 64 5.776173 ACTCTATTATCGCACTTGCTAGT 57.224 39.130 0.00 0.00 39.32 2.57
64 65 5.980116 ACAACTCTATTATCGCACTTGCTAG 59.020 40.000 0.00 0.00 39.32 3.42
87 88 2.280186 CCCCGCCGCAGAGATAAC 60.280 66.667 0.00 0.00 0.00 1.89
98 99 4.796495 GACATGTGGGTCCCCGCC 62.796 72.222 13.24 0.00 45.42 6.13
101 102 0.394352 GTCATGACATGTGGGTCCCC 60.394 60.000 21.07 0.00 36.97 4.81
134 135 3.214328 GACACAGAACTGGAAACCATGT 58.786 45.455 6.76 0.02 30.82 3.21
139 140 4.214332 GGAAGATGACACAGAACTGGAAAC 59.786 45.833 6.76 0.00 34.19 2.78
143 144 2.038952 TGGGAAGATGACACAGAACTGG 59.961 50.000 6.76 0.00 34.19 4.00
147 148 3.308402 GGGAATGGGAAGATGACACAGAA 60.308 47.826 0.00 0.00 0.00 3.02
148 149 2.239654 GGGAATGGGAAGATGACACAGA 59.760 50.000 0.00 0.00 0.00 3.41
156 1533 0.631212 GTGGTGGGGAATGGGAAGAT 59.369 55.000 0.00 0.00 0.00 2.40
164 1541 0.545787 TACGGTGAGTGGTGGGGAAT 60.546 55.000 0.00 0.00 0.00 3.01
186 1563 1.410882 GCAGAGGAAGAAGAGGCGTAT 59.589 52.381 0.00 0.00 0.00 3.06
187 1564 0.818296 GCAGAGGAAGAAGAGGCGTA 59.182 55.000 0.00 0.00 0.00 4.42
432 1820 1.618837 TGCTAACCTGCTCGAAGTTCT 59.381 47.619 0.56 0.00 0.00 3.01
433 1821 1.996191 CTGCTAACCTGCTCGAAGTTC 59.004 52.381 0.00 0.00 0.00 3.01
435 1823 0.969894 ACTGCTAACCTGCTCGAAGT 59.030 50.000 0.00 0.00 0.00 3.01
436 1824 1.354040 CACTGCTAACCTGCTCGAAG 58.646 55.000 0.00 0.00 0.00 3.79
437 1825 0.670546 GCACTGCTAACCTGCTCGAA 60.671 55.000 0.00 0.00 0.00 3.71
438 1826 1.079819 GCACTGCTAACCTGCTCGA 60.080 57.895 0.00 0.00 0.00 4.04
439 1827 0.950555 TTGCACTGCTAACCTGCTCG 60.951 55.000 1.98 0.00 0.00 5.03
463 1851 1.591703 TTCGAGGAGCTGCGAATGT 59.408 52.632 10.51 0.00 41.07 2.71
491 1885 7.849804 ACTGTAATTAGCATTGAATCGACTT 57.150 32.000 0.00 0.00 0.00 3.01
587 2002 7.027161 GCTCTAGATTCATCGAATACTTCCTC 58.973 42.308 0.00 0.00 31.89 3.71
590 2005 6.806249 CAGGCTCTAGATTCATCGAATACTTC 59.194 42.308 0.00 0.00 31.89 3.01
616 2078 9.494271 GATATATTTGACCAGATGCAAGACTTA 57.506 33.333 0.00 0.00 0.00 2.24
684 2152 0.179194 GACCGACAGACGAGTACAGC 60.179 60.000 0.00 0.00 45.77 4.40
694 2162 0.322648 TGAGTCTACGGACCGACAGA 59.677 55.000 23.38 18.75 43.05 3.41
705 2176 4.642437 TCATCAGTGACAGGATGAGTCTAC 59.358 45.833 13.60 0.00 43.56 2.59
706 2177 4.860022 TCATCAGTGACAGGATGAGTCTA 58.140 43.478 13.60 0.00 43.56 2.59
734 2209 2.644555 AAGTCTGAAGCACCGCGTGT 62.645 55.000 4.92 0.00 35.75 4.49
754 2229 8.939201 TGTATCATTGACTGAAGAAGAATCTC 57.061 34.615 0.00 0.00 37.44 2.75
781 2265 6.365970 AAGTCATATCACTTTCACAGAGGT 57.634 37.500 0.00 0.00 32.34 3.85
853 2854 2.584418 CGTCTCTGCCTGCCGATG 60.584 66.667 0.00 0.00 0.00 3.84
882 2887 0.889186 CCAGGCTTGCCGTGTAAACT 60.889 55.000 5.95 0.00 0.00 2.66
1145 3193 3.330405 TGTCCATGAGTCCAGGAAATCAA 59.670 43.478 9.24 0.00 32.30 2.57
1228 3478 4.741239 AGGATGACCCCGGCCACT 62.741 66.667 2.24 0.00 36.73 4.00
1240 3490 2.086869 CCACACAACTAAGGCAGGATG 58.913 52.381 0.00 0.00 40.87 3.51
1261 3511 2.098117 CACAATCCGGAAGCCAAATCTC 59.902 50.000 9.01 0.00 0.00 2.75
1268 3518 3.140814 GGCCACAATCCGGAAGCC 61.141 66.667 9.01 12.64 0.00 4.35
1393 3651 2.740981 CCAAGTGAGTGAGATCAGCAAC 59.259 50.000 0.00 0.00 0.00 4.17
1398 3656 5.538053 GGATAGATCCAAGTGAGTGAGATCA 59.462 44.000 3.54 0.00 46.38 2.92
1449 3782 7.919621 AGTTTAGTACAATTACCTAGCGATGTC 59.080 37.037 0.00 0.00 0.00 3.06
1478 4064 1.242076 AGATGCAAGTGCCAGTGTTC 58.758 50.000 0.00 0.00 41.18 3.18
1493 4723 4.543590 AGGCCGGTAATCTGATTAGATG 57.456 45.455 10.26 3.97 42.80 2.90
1497 4727 5.781306 TGGTAATAGGCCGGTAATCTGATTA 59.219 40.000 1.90 6.01 0.00 1.75
1504 4734 2.370849 CAGGTGGTAATAGGCCGGTAAT 59.629 50.000 1.90 0.00 0.00 1.89
1508 4738 0.393077 CTCAGGTGGTAATAGGCCGG 59.607 60.000 0.00 0.00 0.00 6.13
1541 5125 7.475015 TGATGCAAGTAATGACAATAAAGAGC 58.525 34.615 0.00 0.00 0.00 4.09
1550 5134 5.308014 AGTTGTCTGATGCAAGTAATGACA 58.692 37.500 0.00 0.00 0.00 3.58
1562 5146 5.934043 TGTCCTGTCAATAAGTTGTCTGATG 59.066 40.000 0.00 0.00 36.69 3.07
1614 5198 9.606631 CTACTCAAATCTAGCTCATTTAGGTTT 57.393 33.333 0.00 0.00 37.13 3.27
1657 5241 6.064717 GCTTATAAAGAATCACTGGGATGGT 58.935 40.000 0.00 0.00 36.02 3.55
1670 5254 9.787435 TGAAAAGGTAGTTCAGCTTATAAAGAA 57.213 29.630 0.00 0.00 44.18 2.52
1683 5267 6.650427 AAATTCACCCTGAAAAGGTAGTTC 57.350 37.500 0.00 0.00 40.12 3.01
1722 5308 2.683211 AAGATGGAACTTTGCCACCT 57.317 45.000 0.00 0.00 38.44 4.00
1724 5310 3.319122 AGTGAAAGATGGAACTTTGCCAC 59.681 43.478 0.00 0.00 39.71 5.01
1741 5327 2.159179 TCGATCCAGGATCCAGTGAA 57.841 50.000 22.02 0.00 35.83 3.18
1748 5334 2.630098 TGGTCAAGATCGATCCAGGATC 59.370 50.000 21.66 18.69 40.45 3.36
1754 5340 6.936279 TCCTTATTATGGTCAAGATCGATCC 58.064 40.000 21.66 7.46 0.00 3.36
1760 5358 8.950210 CGCATAAATCCTTATTATGGTCAAGAT 58.050 33.333 8.00 0.00 39.84 2.40
1761 5359 8.154203 TCGCATAAATCCTTATTATGGTCAAGA 58.846 33.333 8.00 0.00 39.84 3.02
1824 5443 2.094894 GCTCTTGTGTTCCATGTCGATG 59.905 50.000 0.00 0.00 0.00 3.84
1825 5444 2.289631 TGCTCTTGTGTTCCATGTCGAT 60.290 45.455 0.00 0.00 0.00 3.59
1840 5846 5.106555 CCATACGTGAATGTTTTCTGCTCTT 60.107 40.000 0.00 0.00 32.78 2.85
1842 5848 4.154195 ACCATACGTGAATGTTTTCTGCTC 59.846 41.667 0.00 0.00 32.78 4.26
1908 5920 2.009774 ACAACCGTGATGCTTGCTATC 58.990 47.619 0.00 0.00 0.00 2.08
1981 5993 7.115947 CCCGTCGAAATTCCATATAGAAAGTAC 59.884 40.741 0.00 0.00 0.00 2.73
2031 6043 5.830912 TCATCGAAATTTTCTGTTGCAGTT 58.169 33.333 7.50 0.00 32.61 3.16
2110 6122 3.958860 AGCAAAGACAGCCCCGCT 61.959 61.111 0.00 0.00 40.77 5.52
2162 6174 2.419159 TCAGCATGAAATGTCTCCTCGG 60.419 50.000 0.00 0.00 45.97 4.63
2247 6259 3.320541 ACACGAGAAATTTGCATTGGGAA 59.679 39.130 0.00 0.00 0.00 3.97
2328 6340 1.071385 CTGTTGGTCCAGTTCAGCTCT 59.929 52.381 7.52 0.00 0.00 4.09
2335 6347 3.864789 AGTGATTCTGTTGGTCCAGTT 57.135 42.857 0.00 0.00 34.02 3.16
2383 6395 3.628942 TCACAATCATGATGCAAGTAGGC 59.371 43.478 9.46 0.00 0.00 3.93
2424 6436 6.336842 AGAATGTTGCTGCTTTTTATGTCT 57.663 33.333 0.00 0.00 0.00 3.41
2529 6541 2.173519 CCACATGTCCCTGCAAAGATT 58.826 47.619 0.00 0.00 0.00 2.40
2567 6579 5.450818 AAATGGATCAGTGCCTAGGTAAA 57.549 39.130 11.31 0.00 0.00 2.01
2572 6584 5.874093 AGGATAAAATGGATCAGTGCCTAG 58.126 41.667 0.00 0.00 0.00 3.02
2573 6585 5.912149 AGGATAAAATGGATCAGTGCCTA 57.088 39.130 0.00 0.00 0.00 3.93
2575 6587 5.859205 AAAGGATAAAATGGATCAGTGCC 57.141 39.130 0.00 0.00 0.00 5.01
2622 6643 9.988815 TCTATATCAGATAAGAGCCTTGTTTTC 57.011 33.333 0.00 0.00 0.00 2.29
2703 6737 1.071019 CGAAGCTGTACACGTCGCAT 61.071 55.000 15.88 2.45 32.66 4.73
3134 7186 9.787435 ACAATACTAAGTCAACATACAAAAGGA 57.213 29.630 0.00 0.00 0.00 3.36
3187 7251 3.980775 CCAACAGTTTTGCCAAACGATAG 59.019 43.478 7.67 3.07 46.14 2.08
3188 7252 3.632604 TCCAACAGTTTTGCCAAACGATA 59.367 39.130 7.67 0.00 46.14 2.92
3230 7294 7.776500 TCAGATGAATGAAGATGGCAAGATAAA 59.224 33.333 0.00 0.00 0.00 1.40
3281 7345 9.185680 AGTTTCCACTAAAACATAACCATATCC 57.814 33.333 2.73 0.00 40.77 2.59
3288 7352 9.685828 TTGCATAAGTTTCCACTAAAACATAAC 57.314 29.630 0.00 0.00 40.77 1.89
3290 7354 8.851145 TGTTGCATAAGTTTCCACTAAAACATA 58.149 29.630 0.00 0.00 40.77 2.29
3295 7403 5.278758 GCCTGTTGCATAAGTTTCCACTAAA 60.279 40.000 0.00 0.00 40.77 1.85
3335 7443 3.143728 GCTTCGGTCCTTTCAGGTTTTA 58.856 45.455 0.00 0.00 36.53 1.52
3347 7455 1.822506 AGGCTAAAAAGCTTCGGTCC 58.177 50.000 0.00 0.00 34.73 4.46
3367 7475 7.287005 AGTGGGATCGTCACATCTATAAGTTAA 59.713 37.037 16.64 0.00 37.58 2.01
3371 7479 5.713792 AGTGGGATCGTCACATCTATAAG 57.286 43.478 16.64 0.00 37.58 1.73
3378 7486 2.579207 CGTAAGTGGGATCGTCACAT 57.421 50.000 16.64 9.63 37.58 3.21
3397 7505 7.274250 CCTAAGAAAAGAAAGCAATGCACATAC 59.726 37.037 8.35 0.00 0.00 2.39
3408 7516 1.472878 CGCCCCCTAAGAAAAGAAAGC 59.527 52.381 0.00 0.00 0.00 3.51
3434 7542 1.234821 TTGCAAGTAAAGCCGACCTG 58.765 50.000 0.00 0.00 0.00 4.00
3468 7576 3.406764 ACAGGTTGAACTTGAGATCTGC 58.593 45.455 14.60 0.00 0.00 4.26
3494 7602 8.943002 GGAACATTATAAGAAAAAGACGGAGAA 58.057 33.333 0.00 0.00 0.00 2.87
3548 7685 0.321021 CAGTCTGGAGCTTCAGCACT 59.679 55.000 17.99 17.29 45.16 4.40
3560 7697 5.982516 GCACTATATTCAGAGTTCAGTCTGG 59.017 44.000 11.06 0.00 43.69 3.86
3578 7715 4.508551 TCTTCCATGTTCATGGCACTAT 57.491 40.909 22.60 0.00 41.43 2.12
3599 7736 8.776470 CATGTTTGTCCAAAGCAAATATTCTTT 58.224 29.630 0.00 0.00 36.16 2.52
3627 7764 7.393234 TGGAAATTAACTTCAGTTATGACCCAG 59.607 37.037 0.00 0.00 39.89 4.45
3699 7836 1.679032 GCCGGCCAGTATTCAGAAACT 60.679 52.381 18.11 0.00 0.00 2.66
3719 7856 7.809546 AGTTTACAAAAGAAAAGAGGGAGAG 57.190 36.000 0.00 0.00 0.00 3.20
3743 7880 2.094078 GCAGTGCTCCCATAAATTGCAA 60.094 45.455 8.18 0.00 35.34 4.08
3752 7889 1.050988 ATACGAGGCAGTGCTCCCAT 61.051 55.000 16.11 0.00 0.00 4.00
3768 7915 0.034863 TTGGGGTCGCCTTTCCATAC 60.035 55.000 7.55 0.00 0.00 2.39
3784 7931 5.125900 TGAAGTAGAATGTGCAATGGATTGG 59.874 40.000 0.00 0.00 38.21 3.16
3786 7933 5.948162 AGTGAAGTAGAATGTGCAATGGATT 59.052 36.000 0.00 0.00 0.00 3.01
3815 7962 6.861065 TTTTTCTTCTAGTGTTGCTAGTGG 57.139 37.500 0.00 0.00 45.65 4.00
3836 7983 5.248870 AGTGTGCTTTCTTTTCGTCATTT 57.751 34.783 0.00 0.00 0.00 2.32
3853 8000 3.560068 ACGAAGCTTCAGGTTTTAGTGTG 59.440 43.478 25.47 7.35 35.69 3.82
3857 8004 7.326063 CCAAAAATACGAAGCTTCAGGTTTTAG 59.674 37.037 25.47 16.56 35.69 1.85
3858 8005 7.142680 CCAAAAATACGAAGCTTCAGGTTTTA 58.857 34.615 25.47 7.20 35.69 1.52
3881 8028 1.138266 GTATGGAGAAGTTAGCCGCCA 59.862 52.381 0.00 0.00 36.71 5.69
3888 8035 4.275196 CCAGATCGACGTATGGAGAAGTTA 59.725 45.833 9.23 0.00 34.60 2.24
3905 8052 2.034104 TGAGAATGCAGCACCAGATC 57.966 50.000 0.00 0.00 0.00 2.75
3909 8056 0.895100 GGGTTGAGAATGCAGCACCA 60.895 55.000 0.00 0.00 0.00 4.17
3937 8084 2.100418 CCACGAGAGCTGAGATTGATGA 59.900 50.000 0.00 0.00 0.00 2.92
3950 8097 0.671472 TTGACAGCATGCCACGAGAG 60.671 55.000 15.66 0.00 42.53 3.20
3965 8112 2.126346 GGCAATGCGGCTGTTGAC 60.126 61.111 18.31 13.65 37.17 3.18
3966 8113 3.372730 GGGCAATGCGGCTGTTGA 61.373 61.111 18.31 0.00 40.90 3.18
3967 8114 3.009192 ATGGGCAATGCGGCTGTTG 62.009 57.895 12.29 12.29 40.90 3.33
4020 8167 2.334977 TGTGGACAGGTACTTGGACAT 58.665 47.619 10.04 0.00 34.60 3.06
4029 8176 2.028476 CGTTTCTCCATGTGGACAGGTA 60.028 50.000 0.00 0.00 39.78 3.08


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

AutoCloner maintained by Alex Coulton.