Multiple sequence alignment - TraesCS3A01G048400

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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 TraesCS3A01G048400 chr3A 100.000 3678 0 0 1 3678 25894926 25898603 0.000000e+00 6793.0
1 TraesCS3A01G048400 chr3A 85.592 1402 189 11 1193 2590 8910261 8908869 0.000000e+00 1458.0
2 TraesCS3A01G048400 chr3A 83.032 831 129 7 1773 2603 25770245 25771063 0.000000e+00 743.0
3 TraesCS3A01G048400 chr3A 75.615 447 87 15 3161 3593 14810804 14810366 6.230000e-48 202.0
4 TraesCS3A01G048400 chr3D 92.702 1932 107 21 865 2771 11418098 11416176 0.000000e+00 2756.0
5 TraesCS3A01G048400 chr3D 88.136 1416 154 11 1199 2613 11795147 11796549 0.000000e+00 1672.0
6 TraesCS3A01G048400 chr3D 85.735 1381 195 2 1211 2590 707944 709323 0.000000e+00 1458.0
7 TraesCS3A01G048400 chr3D 82.468 462 57 13 3145 3593 403939080 403939530 2.070000e-102 383.0
8 TraesCS3A01G048400 chr3D 84.483 290 27 8 511 784 11418383 11418096 1.680000e-68 270.0
9 TraesCS3A01G048400 chr3B 90.937 1975 129 35 868 2825 16080033 16078092 0.000000e+00 2610.0
10 TraesCS3A01G048400 chr3B 90.657 1980 114 29 868 2827 25219632 25221560 0.000000e+00 2566.0
11 TraesCS3A01G048400 chr3B 87.535 1412 163 6 1193 2603 16758153 16756754 0.000000e+00 1620.0
12 TraesCS3A01G048400 chr3B 85.654 1422 191 10 1192 2603 5938554 5939972 0.000000e+00 1483.0
13 TraesCS3A01G048400 chr3B 86.048 1412 160 12 1193 2603 16692623 16693998 0.000000e+00 1482.0
14 TraesCS3A01G048400 chr3B 86.859 936 110 6 1193 2127 16958593 16959516 0.000000e+00 1035.0
15 TraesCS3A01G048400 chr3B 84.172 815 79 19 2887 3678 25239673 25240460 0.000000e+00 745.0
16 TraesCS3A01G048400 chr3B 83.246 382 44 10 2886 3257 16077402 16077031 2.120000e-87 333.0
17 TraesCS3A01G048400 chr3B 89.823 226 18 5 184 408 16080631 16080410 6.010000e-73 285.0
18 TraesCS3A01G048400 chr3B 80.781 333 31 10 1 323 25217581 25217890 2.860000e-56 230.0
19 TraesCS3A01G048400 chr3B 92.308 91 7 0 781 871 432332944 432333034 2.980000e-26 130.0
20 TraesCS3A01G048400 chr3B 88.542 96 11 0 775 870 188484071 188484166 2.320000e-22 117.0
21 TraesCS3A01G048400 chr4B 85.112 356 38 9 3137 3486 435432963 435433309 2.100000e-92 350.0
22 TraesCS3A01G048400 chr4B 88.288 111 10 1 3483 3590 435433629 435433739 2.980000e-26 130.0
23 TraesCS3A01G048400 chr7A 76.975 443 85 13 3161 3593 299255701 299256136 1.710000e-58 237.0
24 TraesCS3A01G048400 chr1A 76.524 443 87 14 3161 3593 531369081 531368646 3.700000e-55 226.0
25 TraesCS3A01G048400 chr7B 76.092 435 84 13 3173 3593 497895860 497896288 3.720000e-50 209.0
26 TraesCS3A01G048400 chr1B 75.391 447 87 14 3160 3591 22927117 22927555 1.040000e-45 195.0
27 TraesCS3A01G048400 chr1B 92.045 88 7 0 780 867 392432443 392432530 1.390000e-24 124.0
28 TraesCS3A01G048400 chr6B 74.945 451 87 17 3160 3593 500295144 500294703 2.260000e-42 183.0
29 TraesCS3A01G048400 chr5A 93.258 89 6 0 782 870 698143645 698143557 8.290000e-27 132.0
30 TraesCS3A01G048400 chr6A 92.222 90 6 1 779 867 595071420 595071509 3.860000e-25 126.0
31 TraesCS3A01G048400 chr6D 90.526 95 7 1 782 876 34581493 34581585 1.390000e-24 124.0
32 TraesCS3A01G048400 chr6D 88.776 98 9 2 773 868 367006975 367006878 6.450000e-23 119.0
33 TraesCS3A01G048400 chr7D 92.941 85 3 1 424 508 10466242 10466161 1.790000e-23 121.0
34 TraesCS3A01G048400 chr2A 88.776 98 11 0 774 871 227622789 227622692 1.790000e-23 121.0
35 TraesCS3A01G048400 chr2A 91.111 90 7 1 782 871 694958719 694958631 1.790000e-23 121.0
36 TraesCS3A01G048400 chr2A 100.000 36 0 0 473 508 778247620 778247655 2.370000e-07 67.6
37 TraesCS3A01G048400 chr1D 90.000 90 4 3 424 513 335042116 335042200 1.080000e-20 111.0
38 TraesCS3A01G048400 chr4A 85.227 88 9 4 424 511 655078071 655078154 1.820000e-13 87.9
39 TraesCS3A01G048400 chr4D 100.000 28 0 0 3562 3589 335892512 335892539 7.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G048400 chr3A 25894926 25898603 3677 False 6793 6793 100.0000 1 3678 1 chr3A.!!$F2 3677
1 TraesCS3A01G048400 chr3A 8908869 8910261 1392 True 1458 1458 85.5920 1193 2590 1 chr3A.!!$R1 1397
2 TraesCS3A01G048400 chr3A 25770245 25771063 818 False 743 743 83.0320 1773 2603 1 chr3A.!!$F1 830
3 TraesCS3A01G048400 chr3D 11795147 11796549 1402 False 1672 1672 88.1360 1199 2613 1 chr3D.!!$F2 1414
4 TraesCS3A01G048400 chr3D 11416176 11418383 2207 True 1513 2756 88.5925 511 2771 2 chr3D.!!$R1 2260
5 TraesCS3A01G048400 chr3D 707944 709323 1379 False 1458 1458 85.7350 1211 2590 1 chr3D.!!$F1 1379
6 TraesCS3A01G048400 chr3B 16756754 16758153 1399 True 1620 1620 87.5350 1193 2603 1 chr3B.!!$R1 1410
7 TraesCS3A01G048400 chr3B 5938554 5939972 1418 False 1483 1483 85.6540 1192 2603 1 chr3B.!!$F1 1411
8 TraesCS3A01G048400 chr3B 16692623 16693998 1375 False 1482 1482 86.0480 1193 2603 1 chr3B.!!$F2 1410
9 TraesCS3A01G048400 chr3B 25217581 25221560 3979 False 1398 2566 85.7190 1 2827 2 chr3B.!!$F7 2826
10 TraesCS3A01G048400 chr3B 16077031 16080631 3600 True 1076 2610 88.0020 184 3257 3 chr3B.!!$R2 3073
11 TraesCS3A01G048400 chr3B 16958593 16959516 923 False 1035 1035 86.8590 1193 2127 1 chr3B.!!$F3 934
12 TraesCS3A01G048400 chr3B 25239673 25240460 787 False 745 745 84.1720 2887 3678 1 chr3B.!!$F4 791
13 TraesCS3A01G048400 chr4B 435432963 435433739 776 False 240 350 86.7000 3137 3590 2 chr4B.!!$F1 453

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
193 210 0.026285 CGATCATCCGGCGTTTTGAC 59.974 55.0 6.01 0.85 0.00 3.18 F
499 1799 0.038526 CCGTTGGTCTACACGAAGCT 60.039 55.0 0.00 0.00 0.00 3.74 F
1075 2417 0.179100 CCCGTAGCACATCACTCCAG 60.179 60.0 0.00 0.00 0.00 3.86 F
1931 3287 1.344942 GCATCGGTCCGATCATACGC 61.345 60.0 24.03 19.10 45.19 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1062 2404 0.242017 GTTTGGCTGGAGTGATGTGC 59.758 55.000 0.00 0.0 0.0 4.57 R
1904 3260 1.872234 CGGACCGATGCTGTACACG 60.872 63.158 8.64 0.0 0.0 4.49 R
2643 4047 0.040204 ACAGAATTGGAGGGGGCAAG 59.960 55.000 0.00 0.0 0.0 4.01 R
3415 5505 0.029167 GTAAGGAGAGTAGACGGCGC 59.971 60.000 6.90 0.0 0.0 6.53 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
28 29 5.059710 AGAGTCGTTAAAAATACGTACACGC 59.940 40.000 0.00 0.00 44.43 5.34
37 38 1.651240 TACGTACACGCTGAGAGGCC 61.651 60.000 0.00 0.00 44.43 5.19
57 61 4.504864 GGCCAGCCTTAAACTCCAATTTTT 60.505 41.667 0.00 0.00 0.00 1.94
63 67 6.098266 AGCCTTAAACTCCAATTTTTGACACT 59.902 34.615 0.00 0.00 0.00 3.55
99 103 6.881065 TCAGAACTGATCTTCCGAATCAAATT 59.119 34.615 0.00 0.00 35.73 1.82
106 110 7.656412 TGATCTTCCGAATCAAATTGTTTCAA 58.344 30.769 14.72 4.33 0.00 2.69
108 112 7.038154 TCTTCCGAATCAAATTGTTTCAAGT 57.962 32.000 14.72 0.00 0.00 3.16
109 113 7.488322 TCTTCCGAATCAAATTGTTTCAAGTT 58.512 30.769 14.72 0.00 0.00 2.66
110 114 7.434897 TCTTCCGAATCAAATTGTTTCAAGTTG 59.565 33.333 14.72 13.86 0.00 3.16
111 115 5.461737 TCCGAATCAAATTGTTTCAAGTTGC 59.538 36.000 14.72 4.21 0.00 4.17
115 119 7.528182 CGAATCAAATTGTTTCAAGTTGCATTC 59.472 33.333 20.66 20.66 0.00 2.67
117 121 9.545105 AATCAAATTGTTTCAAGTTGCATTCTA 57.455 25.926 14.82 1.54 0.00 2.10
118 122 8.939201 TCAAATTGTTTCAAGTTGCATTCTAA 57.061 26.923 14.82 0.00 0.00 2.10
150 167 9.614792 AGAACAAAAGTACAGAAGAACATAACT 57.385 29.630 0.00 0.00 0.00 2.24
193 210 0.026285 CGATCATCCGGCGTTTTGAC 59.974 55.000 6.01 0.85 0.00 3.18
251 268 1.278637 GCGTTTGTCCGTTCCACAG 59.721 57.895 0.00 0.00 0.00 3.66
271 288 1.598962 CCTGTGGCTGTCACCTGTG 60.599 63.158 10.27 0.00 45.48 3.66
317 334 4.276431 TCTCCACGGCTATTTTTCGTTTTT 59.724 37.500 0.00 0.00 34.73 1.94
323 340 7.115095 CCACGGCTATTTTTCGTTTTTGATTTA 59.885 33.333 0.00 0.00 34.73 1.40
332 349 7.470289 TTTCGTTTTTGATTTATGTTGTGGG 57.530 32.000 0.00 0.00 0.00 4.61
341 1641 6.638610 TGATTTATGTTGTGGGCATTTTAGG 58.361 36.000 0.00 0.00 0.00 2.69
350 1650 4.841246 TGTGGGCATTTTAGGTTTGGTAAT 59.159 37.500 0.00 0.00 0.00 1.89
382 1682 8.865590 TTTTTGGACACTTTAGAAATTGTAGC 57.134 30.769 0.00 0.00 32.79 3.58
383 1683 5.856126 TGGACACTTTAGAAATTGTAGCG 57.144 39.130 0.00 0.00 32.79 4.26
404 1704 2.704572 CTGGCTTCCGAGAATTCTTGT 58.295 47.619 19.34 0.00 0.00 3.16
408 1708 3.067106 GCTTCCGAGAATTCTTGTCACA 58.933 45.455 19.34 0.45 0.00 3.58
409 1709 3.498397 GCTTCCGAGAATTCTTGTCACAA 59.502 43.478 19.34 7.43 0.00 3.33
410 1710 4.611581 GCTTCCGAGAATTCTTGTCACAAC 60.612 45.833 19.34 0.00 0.00 3.32
411 1711 4.336889 TCCGAGAATTCTTGTCACAACT 57.663 40.909 19.34 0.00 0.00 3.16
412 1712 4.703897 TCCGAGAATTCTTGTCACAACTT 58.296 39.130 19.34 0.00 0.00 2.66
413 1713 5.123227 TCCGAGAATTCTTGTCACAACTTT 58.877 37.500 19.34 0.00 0.00 2.66
414 1714 5.588648 TCCGAGAATTCTTGTCACAACTTTT 59.411 36.000 19.34 0.00 0.00 2.27
416 1716 5.682862 CGAGAATTCTTGTCACAACTTTTGG 59.317 40.000 9.87 0.00 34.12 3.28
417 1717 6.458206 CGAGAATTCTTGTCACAACTTTTGGA 60.458 38.462 9.87 0.00 34.12 3.53
418 1718 6.799512 AGAATTCTTGTCACAACTTTTGGAG 58.200 36.000 0.88 0.00 34.12 3.86
421 1721 5.560966 TCTTGTCACAACTTTTGGAGTTC 57.439 39.130 0.00 0.00 45.40 3.01
424 1724 4.505808 TGTCACAACTTTTGGAGTTCGTA 58.494 39.130 0.00 0.00 45.40 3.43
428 1728 6.970613 GTCACAACTTTTGGAGTTCGTAAAAT 59.029 34.615 0.00 0.00 45.40 1.82
430 1730 8.842280 TCACAACTTTTGGAGTTCGTAAAATAT 58.158 29.630 0.00 0.00 45.40 1.28
468 1768 7.727578 ATGGTTGTAATAAAAGTTAAGGGGG 57.272 36.000 0.00 0.00 0.00 5.40
488 1788 3.068064 CCATTGCCCCCGTTGGTC 61.068 66.667 0.00 0.00 0.00 4.02
491 1791 1.029947 CATTGCCCCCGTTGGTCTAC 61.030 60.000 0.00 0.00 0.00 2.59
492 1792 1.493854 ATTGCCCCCGTTGGTCTACA 61.494 55.000 0.00 0.00 0.00 2.74
494 1794 2.263540 CCCCCGTTGGTCTACACG 59.736 66.667 0.00 0.00 0.00 4.49
495 1795 2.277591 CCCCCGTTGGTCTACACGA 61.278 63.158 0.00 0.00 0.00 4.35
496 1796 1.667151 CCCCGTTGGTCTACACGAA 59.333 57.895 0.00 0.00 0.00 3.85
497 1797 0.389426 CCCCGTTGGTCTACACGAAG 60.389 60.000 0.00 0.00 0.00 3.79
498 1798 1.012486 CCCGTTGGTCTACACGAAGC 61.012 60.000 0.00 0.00 0.00 3.86
499 1799 0.038526 CCGTTGGTCTACACGAAGCT 60.039 55.000 0.00 0.00 0.00 3.74
500 1800 1.337821 CGTTGGTCTACACGAAGCTC 58.662 55.000 0.00 0.00 0.00 4.09
501 1801 1.711206 GTTGGTCTACACGAAGCTCC 58.289 55.000 0.00 0.00 0.00 4.70
502 1802 0.242825 TTGGTCTACACGAAGCTCCG 59.757 55.000 0.00 0.00 0.00 4.63
503 1803 1.516603 GGTCTACACGAAGCTCCGC 60.517 63.158 0.00 0.00 0.00 5.54
504 1804 1.516603 GTCTACACGAAGCTCCGCC 60.517 63.158 0.00 0.00 0.00 6.13
505 1805 1.974875 TCTACACGAAGCTCCGCCA 60.975 57.895 0.00 0.00 0.00 5.69
506 1806 1.805945 CTACACGAAGCTCCGCCAC 60.806 63.158 0.00 0.00 0.00 5.01
507 1807 2.214181 CTACACGAAGCTCCGCCACT 62.214 60.000 0.00 0.00 0.00 4.00
508 1808 1.812686 TACACGAAGCTCCGCCACTT 61.813 55.000 0.00 0.00 0.00 3.16
509 1809 2.357517 ACGAAGCTCCGCCACTTG 60.358 61.111 0.00 0.00 0.00 3.16
520 1820 2.907179 GCCACTTGCCCCACCTAGT 61.907 63.158 0.00 0.00 0.00 2.57
524 1824 2.618045 CCACTTGCCCCACCTAGTAAAG 60.618 54.545 0.00 0.00 0.00 1.85
525 1825 2.304761 CACTTGCCCCACCTAGTAAAGA 59.695 50.000 0.00 0.00 0.00 2.52
536 1836 5.592688 CCACCTAGTAAAGAGAAGAGGAGAG 59.407 48.000 0.00 0.00 0.00 3.20
542 1842 7.849322 AGTAAAGAGAAGAGGAGAGAAAGTT 57.151 36.000 0.00 0.00 0.00 2.66
544 1844 8.710239 AGTAAAGAGAAGAGGAGAGAAAGTTTT 58.290 33.333 0.00 0.00 0.00 2.43
625 1944 7.519032 TTGTAAAATAGAACTGTTGGAAGGG 57.481 36.000 0.00 0.00 0.00 3.95
658 1978 7.063662 GCACCAAAAACTTATAATAAAACCCCG 59.936 37.037 0.00 0.00 0.00 5.73
662 1982 8.865978 CAAAAACTTATAATAAAACCCCGAAGC 58.134 33.333 0.00 0.00 0.00 3.86
697 2017 1.591863 GTAGCCGCCGGTGAGAATC 60.592 63.158 18.79 0.00 0.00 2.52
722 2042 6.105397 TCCGTATAAATGGTTGGTATCTCC 57.895 41.667 0.00 0.00 33.06 3.71
723 2043 5.842328 TCCGTATAAATGGTTGGTATCTCCT 59.158 40.000 0.00 0.00 33.55 3.69
724 2044 6.014840 TCCGTATAAATGGTTGGTATCTCCTC 60.015 42.308 0.00 0.00 33.55 3.71
736 2056 8.437575 GGTTGGTATCTCCTCTAATTATTTGGA 58.562 37.037 0.00 0.00 37.07 3.53
763 2084 7.741027 AAAACTAGAACTTTTGGTAGGTAGC 57.259 36.000 0.00 0.00 0.00 3.58
784 2105 4.766891 AGCAATGCACCACAAACTTATACT 59.233 37.500 8.35 0.00 0.00 2.12
785 2106 5.095490 GCAATGCACCACAAACTTATACTC 58.905 41.667 0.00 0.00 0.00 2.59
786 2107 5.106157 GCAATGCACCACAAACTTATACTCT 60.106 40.000 0.00 0.00 0.00 3.24
787 2108 6.546395 CAATGCACCACAAACTTATACTCTC 58.454 40.000 0.00 0.00 0.00 3.20
788 2109 5.483685 TGCACCACAAACTTATACTCTCT 57.516 39.130 0.00 0.00 0.00 3.10
789 2110 5.479306 TGCACCACAAACTTATACTCTCTC 58.521 41.667 0.00 0.00 0.00 3.20
790 2111 4.870991 GCACCACAAACTTATACTCTCTCC 59.129 45.833 0.00 0.00 0.00 3.71
791 2112 5.568825 GCACCACAAACTTATACTCTCTCCA 60.569 44.000 0.00 0.00 0.00 3.86
792 2113 6.644347 CACCACAAACTTATACTCTCTCCAT 58.356 40.000 0.00 0.00 0.00 3.41
793 2114 7.632898 GCACCACAAACTTATACTCTCTCCATA 60.633 40.741 0.00 0.00 0.00 2.74
794 2115 8.258007 CACCACAAACTTATACTCTCTCCATAA 58.742 37.037 0.00 0.00 0.00 1.90
795 2116 8.822805 ACCACAAACTTATACTCTCTCCATAAA 58.177 33.333 0.00 0.00 0.00 1.40
796 2117 9.099454 CCACAAACTTATACTCTCTCCATAAAC 57.901 37.037 0.00 0.00 0.00 2.01
797 2118 9.877178 CACAAACTTATACTCTCTCCATAAACT 57.123 33.333 0.00 0.00 0.00 2.66
875 2196 8.532819 AGTTTACAGAGGGAGTACAAAATAGAG 58.467 37.037 0.00 0.00 0.00 2.43
897 2218 3.191371 GCTGTTGGAAGTTGGGAATACAG 59.809 47.826 0.00 0.00 35.92 2.74
901 2222 3.420893 TGGAAGTTGGGAATACAGCAAG 58.579 45.455 0.00 0.00 0.00 4.01
905 2226 2.644798 AGTTGGGAATACAGCAAGGACT 59.355 45.455 0.00 0.00 0.00 3.85
915 2240 3.596214 ACAGCAAGGACTTTGTATACCG 58.404 45.455 0.00 0.00 39.08 4.02
966 2291 1.976045 CGCGGAGAAATTTCGTTTTGG 59.024 47.619 12.42 2.24 0.00 3.28
980 2316 4.006989 TCGTTTTGGTGATTGGTATCTGG 58.993 43.478 0.00 0.00 0.00 3.86
982 2318 4.094887 CGTTTTGGTGATTGGTATCTGGAG 59.905 45.833 0.00 0.00 0.00 3.86
984 2320 6.177610 GTTTTGGTGATTGGTATCTGGAGTA 58.822 40.000 0.00 0.00 0.00 2.59
986 2322 5.353394 TGGTGATTGGTATCTGGAGTAAC 57.647 43.478 0.00 0.00 0.00 2.50
991 2327 7.711339 GGTGATTGGTATCTGGAGTAACTTTAG 59.289 40.741 0.00 0.00 0.00 1.85
997 2333 6.817140 GGTATCTGGAGTAACTTTAGTTGGTG 59.183 42.308 5.41 0.00 38.90 4.17
1017 2356 9.908152 GTTGGTGCAGTATAAAAATAGAACTTT 57.092 29.630 0.00 0.00 0.00 2.66
1062 2404 4.492494 ACTTATAAAACCCCACCCGTAG 57.508 45.455 0.00 0.00 0.00 3.51
1063 2405 3.208594 CTTATAAAACCCCACCCGTAGC 58.791 50.000 0.00 0.00 0.00 3.58
1064 2406 0.993470 ATAAAACCCCACCCGTAGCA 59.007 50.000 0.00 0.00 0.00 3.49
1070 2412 1.449601 CCCACCCGTAGCACATCAC 60.450 63.158 0.00 0.00 0.00 3.06
1075 2417 0.179100 CCCGTAGCACATCACTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
1107 2451 1.593006 CCCGCGTACATCAAATCAGAC 59.407 52.381 4.92 0.00 0.00 3.51
1130 2474 2.892425 CACGCCCGGAGAATCTGC 60.892 66.667 0.73 0.00 41.22 4.26
1131 2475 3.077556 ACGCCCGGAGAATCTGCT 61.078 61.111 0.73 0.00 41.22 4.24
1188 2538 3.864686 CAATGGAGGCGAACGGCG 61.865 66.667 4.80 4.80 44.92 6.46
1931 3287 1.344942 GCATCGGTCCGATCATACGC 61.345 60.000 24.03 19.10 45.19 4.42
2186 3560 4.394712 AAGAAGGACCCGCTGGCG 62.395 66.667 8.08 8.08 39.44 5.69
2596 3994 4.803426 GGACGAGGTGGCGAGCAG 62.803 72.222 0.00 0.00 34.83 4.24
2603 4001 4.008933 GTGGCGAGCAGGTGGACT 62.009 66.667 0.00 0.00 0.00 3.85
2634 4038 4.111016 CGTGAGTAGGCGTCGGCA 62.111 66.667 21.79 4.20 42.47 5.69
2635 4039 2.260434 GTGAGTAGGCGTCGGCAA 59.740 61.111 21.79 0.00 42.47 4.52
2637 4041 1.373748 TGAGTAGGCGTCGGCAAAC 60.374 57.895 21.79 17.41 42.47 2.93
2638 4042 2.047560 AGTAGGCGTCGGCAAACC 60.048 61.111 21.79 5.32 42.47 3.27
2639 4043 2.047560 GTAGGCGTCGGCAAACCT 60.048 61.111 21.79 7.56 42.47 3.50
2641 4045 1.669760 TAGGCGTCGGCAAACCTTG 60.670 57.895 21.79 0.00 42.47 3.61
2669 4079 2.689983 CCCCTCCAATTCTGTTGTATGC 59.310 50.000 0.00 0.00 0.00 3.14
2728 4155 8.132362 TGTTTGTAAGTTGCTTTCGAAATGTAT 58.868 29.630 11.70 0.00 0.00 2.29
2730 4157 8.500837 TTGTAAGTTGCTTTCGAAATGTATTG 57.499 30.769 11.70 0.00 0.00 1.90
2731 4158 6.580791 TGTAAGTTGCTTTCGAAATGTATTGC 59.419 34.615 11.70 10.59 0.00 3.56
2732 4159 4.158384 AGTTGCTTTCGAAATGTATTGCG 58.842 39.130 11.70 0.00 40.16 4.85
2733 4160 3.129852 TGCTTTCGAAATGTATTGCGG 57.870 42.857 11.70 0.00 39.29 5.69
2734 4161 2.486203 TGCTTTCGAAATGTATTGCGGT 59.514 40.909 11.70 0.00 39.29 5.68
2735 4162 3.685272 TGCTTTCGAAATGTATTGCGGTA 59.315 39.130 11.70 0.00 39.29 4.02
2736 4163 4.201773 TGCTTTCGAAATGTATTGCGGTAG 60.202 41.667 11.70 4.59 39.29 3.18
2737 4164 4.201783 GCTTTCGAAATGTATTGCGGTAGT 60.202 41.667 11.70 0.00 39.29 2.73
2738 4165 5.672819 GCTTTCGAAATGTATTGCGGTAGTT 60.673 40.000 11.70 0.00 39.29 2.24
2739 4166 4.850859 TCGAAATGTATTGCGGTAGTTG 57.149 40.909 5.23 0.00 39.29 3.16
2740 4167 4.496360 TCGAAATGTATTGCGGTAGTTGA 58.504 39.130 5.23 0.00 39.29 3.18
2806 4240 3.148279 GCCCGTCTCCGTCTGGAT 61.148 66.667 0.00 0.00 45.33 3.41
2827 4261 3.853487 ATGCGATGCCAGAGCCGA 61.853 61.111 0.00 0.00 38.69 5.54
2828 4262 3.174507 ATGCGATGCCAGAGCCGAT 62.175 57.895 0.00 0.00 38.69 4.18
2832 4266 3.762429 GATGCCAGAGCCGATGCCA 62.762 63.158 0.00 0.00 38.69 4.92
2834 4268 4.166888 GCCAGAGCCGATGCCAGA 62.167 66.667 0.00 0.00 38.69 3.86
2835 4269 2.108566 CCAGAGCCGATGCCAGAG 59.891 66.667 0.00 0.00 38.69 3.35
2836 4270 2.588314 CAGAGCCGATGCCAGAGC 60.588 66.667 0.00 0.00 38.69 4.09
2860 4844 0.607489 GCCCAGTGCATGTCTCTTGT 60.607 55.000 0.00 0.00 40.77 3.16
2861 4845 1.339055 GCCCAGTGCATGTCTCTTGTA 60.339 52.381 0.00 0.00 40.77 2.41
2871 4927 4.503910 CATGTCTCTTGTAATGGTCCGAA 58.496 43.478 0.00 0.00 0.00 4.30
2877 4933 1.184431 TGTAATGGTCCGAACGCCTA 58.816 50.000 0.00 0.00 0.00 3.93
2883 4939 1.152383 GGTCCGAACGCCTATGCTTC 61.152 60.000 0.00 0.00 34.43 3.86
2884 4940 0.179108 GTCCGAACGCCTATGCTTCT 60.179 55.000 0.00 0.00 34.43 2.85
2889 4952 0.179108 AACGCCTATGCTTCTCCGTC 60.179 55.000 0.00 0.00 34.43 4.79
2897 4960 0.836400 TGCTTCTCCGTCCCCTCTTT 60.836 55.000 0.00 0.00 0.00 2.52
2908 4971 2.815647 CCTCTTTCCGGCGCACTC 60.816 66.667 10.83 0.00 0.00 3.51
2923 4994 0.944311 CACTCGAACCTGTCAACCCG 60.944 60.000 0.00 0.00 0.00 5.28
2924 4995 2.027625 CTCGAACCTGTCAACCCGC 61.028 63.158 0.00 0.00 0.00 6.13
2925 4996 3.411351 CGAACCTGTCAACCCGCG 61.411 66.667 0.00 0.00 0.00 6.46
2926 4997 2.029964 GAACCTGTCAACCCGCGA 59.970 61.111 8.23 0.00 0.00 5.87
2927 4998 2.280592 AACCTGTCAACCCGCGAC 60.281 61.111 8.23 0.00 0.00 5.19
2928 4999 2.710724 GAACCTGTCAACCCGCGACT 62.711 60.000 8.23 0.00 34.37 4.18
2929 5000 2.432628 CCTGTCAACCCGCGACTC 60.433 66.667 8.23 0.00 34.37 3.36
2972 5050 4.383861 GTGTCGTCCCCCGGTTCC 62.384 72.222 0.00 0.00 37.11 3.62
2982 5060 3.636231 CCGGTTCCAGGGTGCTCA 61.636 66.667 0.00 0.00 0.00 4.26
2988 5066 1.792757 TTCCAGGGTGCTCATGGCTT 61.793 55.000 6.47 0.00 42.39 4.35
3026 5105 0.463204 CTGTCCATCTCAGGATGCGT 59.537 55.000 0.94 0.00 45.73 5.24
3035 5114 5.752472 CCATCTCAGGATGCGTATATTGATC 59.248 44.000 0.94 0.00 45.73 2.92
3037 5116 4.700213 TCTCAGGATGCGTATATTGATCGA 59.300 41.667 0.00 0.00 34.76 3.59
3059 5138 1.689273 ACCGGTTGCAAATTTAGGCAA 59.311 42.857 0.00 10.87 46.84 4.52
3077 5156 3.860536 GGCAAAACTTGTCGTTAGCAAAA 59.139 39.130 0.00 0.00 38.06 2.44
3140 5219 1.000274 GAAGGGTTGTTTGAGCGCAAT 60.000 47.619 11.47 0.00 33.25 3.56
3163 5242 0.743688 TTGCAAAGAGGAAGCGCAAA 59.256 45.000 11.47 0.00 39.47 3.68
3189 5270 4.335315 ACACGTGCTCATCTTTTCTTCAAA 59.665 37.500 17.22 0.00 0.00 2.69
3194 5275 6.567321 CGTGCTCATCTTTTCTTCAAATGTCT 60.567 38.462 0.00 0.00 0.00 3.41
3196 5277 6.487668 TGCTCATCTTTTCTTCAAATGTCTCA 59.512 34.615 0.00 0.00 0.00 3.27
3206 5287 7.117241 TCTTCAAATGTCTCAACACGATTAC 57.883 36.000 0.00 0.00 38.48 1.89
3283 5364 0.165944 GCACCTTGATGAAACCGTCG 59.834 55.000 0.00 0.00 0.00 5.12
3288 5369 0.597898 TTGATGAAACCGTCGACGCA 60.598 50.000 31.73 23.38 38.18 5.24
3289 5370 1.279527 TGATGAAACCGTCGACGCAC 61.280 55.000 31.73 20.34 38.18 5.34
3306 5387 2.147387 ACGGTGGGGCAAGAGAACT 61.147 57.895 0.00 0.00 0.00 3.01
3312 5397 1.527433 GGGGCAAGAGAACTGGCAAC 61.527 60.000 0.00 0.00 44.32 4.17
3329 5414 2.923020 GCAACAACAATCCTAATTGGCG 59.077 45.455 3.45 0.00 45.48 5.69
3386 5475 6.269538 TGGACCATTTGGAATGAAAGAAATGA 59.730 34.615 3.01 0.00 37.80 2.57
3400 5489 6.368791 TGAAAGAAATGATAGAGTGTTCCACG 59.631 38.462 0.00 0.00 39.64 4.94
3410 5500 1.130955 GTGTTCCACGCAAAAGCATG 58.869 50.000 0.00 0.00 0.00 4.06
3412 5502 1.006337 TTCCACGCAAAAGCATGCC 60.006 52.632 15.66 0.00 43.47 4.40
3413 5503 2.745906 TTCCACGCAAAAGCATGCCG 62.746 55.000 15.66 12.98 43.47 5.69
3414 5504 3.472298 CACGCAAAAGCATGCCGC 61.472 61.111 15.66 11.37 43.47 6.53
3445 5535 6.547880 GTCTACTCTCCTTACCATCATCTTGA 59.452 42.308 0.00 0.00 0.00 3.02
3493 5906 4.201685 CGGGTGCTAAGAAACTTGTTATCG 60.202 45.833 0.00 0.00 0.00 2.92
3496 5909 4.694037 GTGCTAAGAAACTTGTTATCGGGT 59.306 41.667 0.00 0.00 0.00 5.28
3590 6006 3.184379 GCCAAATCTTTTGCCTTCGTTTC 59.816 43.478 0.00 0.00 0.00 2.78
3592 6008 4.286910 CAAATCTTTTGCCTTCGTTTCGA 58.713 39.130 0.00 0.00 0.00 3.71
3597 6013 5.344884 TCTTTTGCCTTCGTTTCGATTTTT 58.655 33.333 0.00 0.00 35.23 1.94
3638 6054 8.141268 AGAAACACCAGTTGTATATTTGTTTGG 58.859 33.333 1.76 0.00 37.51 3.28
3654 6070 7.440523 TTTGTTTGGAATAAGAAGAGAGAGC 57.559 36.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.202268 GCCTCTCAGCGTGTACGTATT 60.202 52.381 0.00 0.00 42.22 1.89
37 38 6.200854 GTGTCAAAAATTGGAGTTTAAGGCTG 59.799 38.462 0.00 0.00 0.00 4.85
50 54 6.592798 ATGCAACTTGAGTGTCAAAAATTG 57.407 33.333 0.00 0.00 35.73 2.32
57 61 3.807553 TCTGAATGCAACTTGAGTGTCA 58.192 40.909 0.00 0.00 0.00 3.58
63 67 5.311265 AGATCAGTTCTGAATGCAACTTGA 58.689 37.500 6.60 0.00 31.79 3.02
124 141 9.614792 AGTTATGTTCTTCTGTACTTTTGTTCT 57.385 29.630 0.00 0.00 0.00 3.01
147 164 7.970102 TCACTGGTACTCCATTAGTTTTAGTT 58.030 34.615 0.00 0.00 43.43 2.24
148 165 7.549147 TCACTGGTACTCCATTAGTTTTAGT 57.451 36.000 0.00 0.00 43.43 2.24
149 166 7.435488 CGATCACTGGTACTCCATTAGTTTTAG 59.565 40.741 0.00 0.00 43.43 1.85
150 167 7.123098 TCGATCACTGGTACTCCATTAGTTTTA 59.877 37.037 0.00 0.00 43.43 1.52
151 168 6.070995 TCGATCACTGGTACTCCATTAGTTTT 60.071 38.462 0.00 0.00 43.43 2.43
152 169 5.421056 TCGATCACTGGTACTCCATTAGTTT 59.579 40.000 0.00 0.00 43.43 2.66
167 184 1.005804 CGCCGGATGATCGATCACTG 61.006 60.000 29.49 24.12 40.03 3.66
193 210 5.922544 CACCACTGCCATTTCTTTCTTTTAG 59.077 40.000 0.00 0.00 0.00 1.85
295 312 3.824414 AAACGAAAAATAGCCGTGGAG 57.176 42.857 0.00 0.00 36.58 3.86
317 334 6.212388 ACCTAAAATGCCCACAACATAAATCA 59.788 34.615 0.00 0.00 0.00 2.57
323 340 4.504689 CCAAACCTAAAATGCCCACAACAT 60.505 41.667 0.00 0.00 0.00 2.71
327 344 2.683768 ACCAAACCTAAAATGCCCACA 58.316 42.857 0.00 0.00 0.00 4.17
341 1641 9.497030 GTGTCCAAAAATGAAAAATTACCAAAC 57.503 29.630 0.00 0.00 0.00 2.93
363 1663 5.316770 CAGCGCTACAATTTCTAAAGTGTC 58.683 41.667 10.99 0.00 42.81 3.67
382 1682 0.460987 AGAATTCTCGGAAGCCAGCG 60.461 55.000 0.88 0.00 0.00 5.18
383 1683 1.399791 CAAGAATTCTCGGAAGCCAGC 59.600 52.381 8.78 0.00 0.00 4.85
442 1742 9.257428 CCCCCTTAACTTTTATTACAACCATTA 57.743 33.333 0.00 0.00 0.00 1.90
477 1777 1.818959 TTCGTGTAGACCAACGGGGG 61.819 60.000 0.26 0.00 42.91 5.40
478 1778 0.389426 CTTCGTGTAGACCAACGGGG 60.389 60.000 0.00 0.00 44.81 5.73
479 1779 1.012486 GCTTCGTGTAGACCAACGGG 61.012 60.000 0.00 0.00 41.29 5.28
480 1780 0.038526 AGCTTCGTGTAGACCAACGG 60.039 55.000 0.00 0.00 0.00 4.44
481 1781 1.337821 GAGCTTCGTGTAGACCAACG 58.662 55.000 0.00 0.00 0.00 4.10
482 1782 1.711206 GGAGCTTCGTGTAGACCAAC 58.289 55.000 0.00 0.00 0.00 3.77
483 1783 0.242825 CGGAGCTTCGTGTAGACCAA 59.757 55.000 6.14 0.00 0.00 3.67
484 1784 1.880894 CGGAGCTTCGTGTAGACCA 59.119 57.895 6.14 0.00 0.00 4.02
485 1785 4.787999 CGGAGCTTCGTGTAGACC 57.212 61.111 6.14 0.00 0.00 3.85
501 1801 3.976701 CTAGGTGGGGCAAGTGGCG 62.977 68.421 0.00 0.00 46.16 5.69
502 1802 1.559065 TACTAGGTGGGGCAAGTGGC 61.559 60.000 0.00 0.00 43.74 5.01
503 1803 0.988832 TTACTAGGTGGGGCAAGTGG 59.011 55.000 0.00 0.00 0.00 4.00
504 1804 2.304761 TCTTTACTAGGTGGGGCAAGTG 59.695 50.000 0.00 0.00 0.00 3.16
505 1805 2.572104 CTCTTTACTAGGTGGGGCAAGT 59.428 50.000 0.00 0.00 0.00 3.16
506 1806 2.838202 TCTCTTTACTAGGTGGGGCAAG 59.162 50.000 0.00 0.00 0.00 4.01
507 1807 2.910544 TCTCTTTACTAGGTGGGGCAA 58.089 47.619 0.00 0.00 0.00 4.52
508 1808 2.634639 TCTCTTTACTAGGTGGGGCA 57.365 50.000 0.00 0.00 0.00 5.36
509 1809 3.105283 TCTTCTCTTTACTAGGTGGGGC 58.895 50.000 0.00 0.00 0.00 5.80
524 1824 7.715686 TGGTTTAAAACTTTCTCTCCTCTTCTC 59.284 37.037 4.60 0.00 0.00 2.87
525 1825 7.499563 GTGGTTTAAAACTTTCTCTCCTCTTCT 59.500 37.037 4.60 0.00 0.00 2.85
536 1836 5.347620 AAGGGTGGTGGTTTAAAACTTTC 57.652 39.130 4.60 0.00 0.00 2.62
542 1842 2.814842 CGGCTAAGGGTGGTGGTTTAAA 60.815 50.000 0.00 0.00 0.00 1.52
544 1844 0.325602 CGGCTAAGGGTGGTGGTTTA 59.674 55.000 0.00 0.00 0.00 2.01
602 1921 6.843752 TCCCTTCCAACAGTTCTATTTTACA 58.156 36.000 0.00 0.00 0.00 2.41
611 1930 2.505405 GTTCCTCCCTTCCAACAGTTC 58.495 52.381 0.00 0.00 0.00 3.01
625 1944 2.863401 AAGTTTTTGGTGCGTTCCTC 57.137 45.000 0.40 0.00 0.00 3.71
688 2008 6.289064 ACCATTTATACGGAAGATTCTCACC 58.711 40.000 0.00 0.00 0.00 4.02
697 2017 6.649557 GGAGATACCAACCATTTATACGGAAG 59.350 42.308 0.00 0.00 38.79 3.46
763 2084 6.372659 AGAGAGTATAAGTTTGTGGTGCATTG 59.627 38.462 0.00 0.00 0.00 2.82
848 2169 9.537852 TCTATTTTGTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
849 2170 8.431910 TCTATTTTGTACTCCCTCTGTAAACT 57.568 34.615 0.00 0.00 0.00 2.66
850 2171 7.278203 GCTCTATTTTGTACTCCCTCTGTAAAC 59.722 40.741 0.00 0.00 0.00 2.01
851 2172 7.180408 AGCTCTATTTTGTACTCCCTCTGTAAA 59.820 37.037 0.00 0.00 0.00 2.01
852 2173 6.668283 AGCTCTATTTTGTACTCCCTCTGTAA 59.332 38.462 0.00 0.00 0.00 2.41
853 2174 6.096987 CAGCTCTATTTTGTACTCCCTCTGTA 59.903 42.308 0.00 0.00 0.00 2.74
854 2175 5.026790 AGCTCTATTTTGTACTCCCTCTGT 58.973 41.667 0.00 0.00 0.00 3.41
855 2176 5.105146 ACAGCTCTATTTTGTACTCCCTCTG 60.105 44.000 0.00 0.00 0.00 3.35
856 2177 5.026790 ACAGCTCTATTTTGTACTCCCTCT 58.973 41.667 0.00 0.00 0.00 3.69
857 2178 5.346181 ACAGCTCTATTTTGTACTCCCTC 57.654 43.478 0.00 0.00 0.00 4.30
858 2179 5.491982 CAACAGCTCTATTTTGTACTCCCT 58.508 41.667 0.00 0.00 0.00 4.20
859 2180 4.636206 CCAACAGCTCTATTTTGTACTCCC 59.364 45.833 0.00 0.00 0.00 4.30
860 2181 5.488341 TCCAACAGCTCTATTTTGTACTCC 58.512 41.667 0.00 0.00 0.00 3.85
861 2182 6.651225 ACTTCCAACAGCTCTATTTTGTACTC 59.349 38.462 0.00 0.00 0.00 2.59
862 2183 6.534634 ACTTCCAACAGCTCTATTTTGTACT 58.465 36.000 0.00 0.00 0.00 2.73
863 2184 6.803154 ACTTCCAACAGCTCTATTTTGTAC 57.197 37.500 0.00 0.00 0.00 2.90
864 2185 6.206634 CCAACTTCCAACAGCTCTATTTTGTA 59.793 38.462 0.00 0.00 0.00 2.41
865 2186 5.010012 CCAACTTCCAACAGCTCTATTTTGT 59.990 40.000 0.00 0.00 0.00 2.83
866 2187 5.464168 CCAACTTCCAACAGCTCTATTTTG 58.536 41.667 0.00 0.00 0.00 2.44
875 2196 3.153919 TGTATTCCCAACTTCCAACAGC 58.846 45.455 0.00 0.00 0.00 4.40
897 2218 2.352388 TGCGGTATACAAAGTCCTTGC 58.648 47.619 5.01 0.00 38.75 4.01
947 2272 2.724174 CACCAAAACGAAATTTCTCCGC 59.276 45.455 15.92 0.00 0.00 5.54
966 2291 8.258708 ACTAAAGTTACTCCAGATACCAATCAC 58.741 37.037 1.00 0.00 34.28 3.06
980 2316 8.767478 TTATACTGCACCAACTAAAGTTACTC 57.233 34.615 0.00 0.00 36.32 2.59
991 2327 9.908152 AAAGTTCTATTTTTATACTGCACCAAC 57.092 29.630 0.00 0.00 0.00 3.77
1017 2356 0.963355 GGCGCATTCCTACCAACCAA 60.963 55.000 10.83 0.00 0.00 3.67
1022 2361 0.250945 TTTGTGGCGCATTCCTACCA 60.251 50.000 10.83 0.00 0.00 3.25
1062 2404 0.242017 GTTTGGCTGGAGTGATGTGC 59.758 55.000 0.00 0.00 0.00 4.57
1063 2405 0.883833 GGTTTGGCTGGAGTGATGTG 59.116 55.000 0.00 0.00 0.00 3.21
1064 2406 0.478072 TGGTTTGGCTGGAGTGATGT 59.522 50.000 0.00 0.00 0.00 3.06
1070 2412 3.365265 GCGGTGGTTTGGCTGGAG 61.365 66.667 0.00 0.00 0.00 3.86
1090 2432 3.060272 CGATGGTCTGATTTGATGTACGC 60.060 47.826 0.00 0.00 0.00 4.42
1130 2474 1.474879 GTGTCTCTTTCTCGGGAGGAG 59.525 57.143 10.06 10.06 44.58 3.69
1131 2475 1.546961 GTGTCTCTTTCTCGGGAGGA 58.453 55.000 0.00 0.00 0.00 3.71
1168 2518 1.501741 CCGTTCGCCTCCATTGTTG 59.498 57.895 0.00 0.00 0.00 3.33
1499 2855 2.755876 TCCATGAGCCGCGAGAGT 60.756 61.111 8.23 0.00 0.00 3.24
1904 3260 1.872234 CGGACCGATGCTGTACACG 60.872 63.158 8.64 0.00 0.00 4.49
2618 4022 1.373748 TTTGCCGACGCCTACTCAC 60.374 57.895 0.00 0.00 0.00 3.51
2634 4038 2.526624 GGGGGCAAGGCAAGGTTT 60.527 61.111 0.00 0.00 0.00 3.27
2635 4039 3.521452 AGGGGGCAAGGCAAGGTT 61.521 61.111 0.00 0.00 0.00 3.50
2637 4041 4.766632 GGAGGGGGCAAGGCAAGG 62.767 72.222 0.00 0.00 0.00 3.61
2638 4042 2.810488 ATTGGAGGGGGCAAGGCAAG 62.810 60.000 0.00 0.00 0.00 4.01
2639 4043 2.399600 AATTGGAGGGGGCAAGGCAA 62.400 55.000 0.00 0.00 0.00 4.52
2641 4045 2.039462 AATTGGAGGGGGCAAGGC 59.961 61.111 0.00 0.00 0.00 4.35
2642 4046 0.685458 CAGAATTGGAGGGGGCAAGG 60.685 60.000 0.00 0.00 0.00 3.61
2643 4047 0.040204 ACAGAATTGGAGGGGGCAAG 59.960 55.000 0.00 0.00 0.00 4.01
2649 4053 3.624777 AGCATACAACAGAATTGGAGGG 58.375 45.455 0.00 0.00 0.00 4.30
2728 4155 2.226912 CCGGAAAAATCAACTACCGCAA 59.773 45.455 0.00 0.00 39.19 4.85
2730 4157 1.466866 GCCGGAAAAATCAACTACCGC 60.467 52.381 5.05 0.00 39.19 5.68
2731 4158 1.807742 TGCCGGAAAAATCAACTACCG 59.192 47.619 5.05 0.00 40.03 4.02
2732 4159 2.817844 AGTGCCGGAAAAATCAACTACC 59.182 45.455 5.05 0.00 0.00 3.18
2733 4160 3.365969 CCAGTGCCGGAAAAATCAACTAC 60.366 47.826 5.05 0.00 0.00 2.73
2734 4161 2.817258 CCAGTGCCGGAAAAATCAACTA 59.183 45.455 5.05 0.00 0.00 2.24
2735 4162 1.613437 CCAGTGCCGGAAAAATCAACT 59.387 47.619 5.05 0.00 0.00 3.16
2736 4163 1.611491 TCCAGTGCCGGAAAAATCAAC 59.389 47.619 5.05 0.00 29.93 3.18
2737 4164 1.988293 TCCAGTGCCGGAAAAATCAA 58.012 45.000 5.05 0.00 29.93 2.57
2738 4165 2.214376 ATCCAGTGCCGGAAAAATCA 57.786 45.000 5.05 0.00 38.95 2.57
2739 4166 2.159240 GGAATCCAGTGCCGGAAAAATC 60.159 50.000 5.05 0.00 38.95 2.17
2740 4167 1.824852 GGAATCCAGTGCCGGAAAAAT 59.175 47.619 5.05 0.00 38.95 1.82
2797 4231 3.274586 CGCATGGCATCCAGACGG 61.275 66.667 0.00 0.00 36.75 4.79
2798 4232 1.596203 ATCGCATGGCATCCAGACG 60.596 57.895 0.00 0.00 36.75 4.18
2827 4261 4.575973 GGGCATCGGCTCTGGCAT 62.576 66.667 10.92 0.00 40.70 4.40
2832 4266 4.479993 GCACTGGGCATCGGCTCT 62.480 66.667 0.00 0.00 42.67 4.09
2846 4830 3.375299 GGACCATTACAAGAGACATGCAC 59.625 47.826 0.00 0.00 0.00 4.57
2854 4838 1.659098 GCGTTCGGACCATTACAAGAG 59.341 52.381 0.00 0.00 0.00 2.85
2855 4839 1.673626 GGCGTTCGGACCATTACAAGA 60.674 52.381 0.00 0.00 0.00 3.02
2856 4840 0.725117 GGCGTTCGGACCATTACAAG 59.275 55.000 0.00 0.00 0.00 3.16
2857 4841 0.322322 AGGCGTTCGGACCATTACAA 59.678 50.000 0.00 0.00 0.00 2.41
2860 4844 1.539496 GCATAGGCGTTCGGACCATTA 60.539 52.381 0.00 0.00 0.00 1.90
2861 4845 0.814010 GCATAGGCGTTCGGACCATT 60.814 55.000 0.00 0.00 0.00 3.16
2877 4933 0.618968 AAGAGGGGACGGAGAAGCAT 60.619 55.000 0.00 0.00 0.00 3.79
2883 4939 2.893398 CGGAAAGAGGGGACGGAG 59.107 66.667 0.00 0.00 0.00 4.63
2908 4971 3.411351 CGCGGGTTGACAGGTTCG 61.411 66.667 0.00 0.00 0.00 3.95
2966 5037 1.746615 CATGAGCACCCTGGAACCG 60.747 63.158 0.00 0.00 0.00 4.44
3021 5100 3.242518 CGGTGTCGATCAATATACGCAT 58.757 45.455 0.00 0.00 39.00 4.73
3024 5103 3.278367 ACCGGTGTCGATCAATATACG 57.722 47.619 6.12 0.00 39.00 3.06
3026 5105 3.181474 TGCAACCGGTGTCGATCAATATA 60.181 43.478 8.52 0.00 39.00 0.86
3035 5114 2.580589 CTAAATTTGCAACCGGTGTCG 58.419 47.619 8.52 0.10 0.00 4.35
3037 5116 1.000394 GCCTAAATTTGCAACCGGTGT 60.000 47.619 8.52 0.00 0.00 4.16
3087 5166 7.720515 TGGAATGACAATGAGAATACATGCATA 59.279 33.333 0.00 0.00 0.00 3.14
3088 5167 6.548251 TGGAATGACAATGAGAATACATGCAT 59.452 34.615 0.00 0.00 0.00 3.96
3089 5168 5.887035 TGGAATGACAATGAGAATACATGCA 59.113 36.000 0.00 0.00 0.00 3.96
3090 5169 6.381481 TGGAATGACAATGAGAATACATGC 57.619 37.500 0.00 0.00 0.00 4.06
3104 5183 4.739793 ACCCTTCTCAAAATGGAATGACA 58.260 39.130 0.00 0.00 0.00 3.58
3140 5219 1.808411 CGCTTCCTCTTTGCAAGGTA 58.192 50.000 8.56 0.00 35.29 3.08
3163 5242 4.900635 AGAAAAGATGAGCACGTGTTTT 57.099 36.364 18.38 14.02 39.85 2.43
3169 5248 5.455392 ACATTTGAAGAAAAGATGAGCACG 58.545 37.500 0.00 0.00 0.00 5.34
3177 5256 6.315144 TCGTGTTGAGACATTTGAAGAAAAGA 59.685 34.615 0.00 0.00 38.23 2.52
3189 5270 3.232213 AGCGTAATCGTGTTGAGACAT 57.768 42.857 0.00 0.00 38.23 3.06
3194 5275 2.734606 CTCCAAAGCGTAATCGTGTTGA 59.265 45.455 0.00 0.00 39.49 3.18
3196 5277 2.073816 CCTCCAAAGCGTAATCGTGTT 58.926 47.619 0.00 0.00 39.49 3.32
3261 5342 1.176527 CGGTTTCATCAAGGTGCCAT 58.823 50.000 0.00 0.00 0.00 4.40
3288 5369 2.147387 AGTTCTCTTGCCCCACCGT 61.147 57.895 0.00 0.00 0.00 4.83
3289 5370 1.672356 CAGTTCTCTTGCCCCACCG 60.672 63.158 0.00 0.00 0.00 4.94
3296 5377 1.405105 TGTTGTTGCCAGTTCTCTTGC 59.595 47.619 0.00 0.00 33.63 4.01
3306 5387 3.306641 GCCAATTAGGATTGTTGTTGCCA 60.307 43.478 0.00 0.00 40.85 4.92
3312 5397 2.529151 GCACGCCAATTAGGATTGTTG 58.471 47.619 0.00 0.00 40.85 3.33
3314 5399 1.102978 GGCACGCCAATTAGGATTGT 58.897 50.000 2.36 0.00 40.85 2.71
3329 5414 3.667217 ATGTGGGAGGCCATGGCAC 62.667 63.158 36.56 27.63 44.11 5.01
3344 5432 3.341823 GTCCAAGAGACAAGCATGATGT 58.658 45.455 0.00 0.00 45.55 3.06
3413 5503 4.908877 GGAGAGTAGACGGCGCGC 62.909 72.222 25.94 25.94 0.00 6.86
3414 5504 1.434622 TAAGGAGAGTAGACGGCGCG 61.435 60.000 6.90 0.00 0.00 6.86
3415 5505 0.029167 GTAAGGAGAGTAGACGGCGC 59.971 60.000 6.90 0.00 0.00 6.53
3416 5506 0.662085 GGTAAGGAGAGTAGACGGCG 59.338 60.000 4.80 4.80 0.00 6.46
3425 5515 5.365025 TCCTTCAAGATGATGGTAAGGAGAG 59.635 44.000 10.87 0.00 41.12 3.20
3445 5535 4.527426 CCAAAGCTTGGCCTCCTT 57.473 55.556 3.32 0.27 45.17 3.36
3493 5906 2.607187 CGACATGACAACTACTCACCC 58.393 52.381 0.00 0.00 0.00 4.61
3496 5909 3.660501 AAGCGACATGACAACTACTCA 57.339 42.857 0.00 0.00 0.00 3.41
3548 5961 3.181470 GGCTCATCCACTAAAGGAGAGAC 60.181 52.174 11.20 6.60 41.90 3.36
3560 5976 3.256558 GCAAAAGATTTGGCTCATCCAC 58.743 45.455 5.12 0.00 46.55 4.02
3599 6015 9.796120 CAACTGGTGTTTCTAAGAAAAACATAA 57.204 29.630 11.54 4.55 45.42 1.90
3600 6016 8.962679 ACAACTGGTGTTTCTAAGAAAAACATA 58.037 29.630 11.54 5.39 45.42 2.29
3601 6017 7.836842 ACAACTGGTGTTTCTAAGAAAAACAT 58.163 30.769 11.54 0.00 45.42 2.71
3602 6018 7.222000 ACAACTGGTGTTTCTAAGAAAAACA 57.778 32.000 8.75 8.75 42.63 2.83
3608 6024 9.787435 ACAAATATACAACTGGTGTTTCTAAGA 57.213 29.630 2.56 0.00 41.98 2.10
3636 6052 8.762645 TCTTTATTGCTCTCTCTTCTTATTCCA 58.237 33.333 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.