Multiple sequence alignment - TraesCS6D01G024800

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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 TraesCS6D01G024800 chr6D 100.000 4177 0 0 1 4177 9386367 9390543 0.000000e+00 7714.0
1 TraesCS6D01G024800 chr6D 90.711 1787 101 29 2384 4110 9366588 9364807 0.000000e+00 2320.0
2 TraesCS6D01G024800 chr6D 91.245 731 46 4 909 1630 9372977 9372256 0.000000e+00 979.0
3 TraesCS6D01G024800 chr6D 94.655 449 22 2 1953 2400 9372154 9371707 0.000000e+00 695.0
4 TraesCS6D01G024800 chr6D 83.086 337 45 8 421 754 9373476 9373149 3.160000e-76 296.0
5 TraesCS6D01G024800 chr6D 95.455 44 2 0 827 870 9373019 9372976 2.080000e-08 71.3
6 TraesCS6D01G024800 chr6A 96.106 1541 44 7 2498 4026 10444605 10446141 0.000000e+00 2499.0
7 TraesCS6D01G024800 chr6A 93.677 1550 74 7 83 1630 10384795 10386322 0.000000e+00 2298.0
8 TraesCS6D01G024800 chr6A 93.624 1537 75 6 96 1630 10421190 10422705 0.000000e+00 2274.0
9 TraesCS6D01G024800 chr6A 94.651 1346 68 3 1952 3296 11158240 11159582 0.000000e+00 2084.0
10 TraesCS6D01G024800 chr6A 94.321 898 46 3 1953 2846 10371283 10370387 0.000000e+00 1371.0
11 TraesCS6D01G024800 chr6A 94.321 898 46 3 1953 2846 10399970 10399074 0.000000e+00 1371.0
12 TraesCS6D01G024800 chr6A 90.987 821 46 6 827 1630 11157266 11158075 0.000000e+00 1081.0
13 TraesCS6D01G024800 chr6A 88.028 852 61 21 3297 4110 11159614 11160462 0.000000e+00 970.0
14 TraesCS6D01G024800 chr6A 90.997 722 55 6 909 1630 10372141 10371430 0.000000e+00 965.0
15 TraesCS6D01G024800 chr6A 90.884 724 53 8 909 1630 10400829 10400117 0.000000e+00 959.0
16 TraesCS6D01G024800 chr6A 95.738 305 13 0 1952 2256 10386470 10386774 3.750000e-135 492.0
17 TraesCS6D01G024800 chr6A 95.410 305 14 0 1952 2256 10422853 10423157 1.750000e-133 486.0
18 TraesCS6D01G024800 chr6A 83.086 337 50 6 421 754 10372647 10372315 2.440000e-77 300.0
19 TraesCS6D01G024800 chr6A 82.789 337 50 7 421 754 10401334 10401003 1.140000e-75 294.0
20 TraesCS6D01G024800 chr6A 94.886 176 6 1 1693 1865 10386312 10386487 5.320000e-69 272.0
21 TraesCS6D01G024800 chr6A 94.220 173 7 1 1693 1862 10422695 10422867 1.150000e-65 261.0
22 TraesCS6D01G024800 chr6A 96.667 150 5 0 4028 4177 10446385 10446534 2.490000e-62 250.0
23 TraesCS6D01G024800 chr6A 85.417 192 8 6 1694 1865 11158066 11158257 9.220000e-42 182.0
24 TraesCS6D01G024800 chr6A 84.091 176 13 5 1696 1863 10371437 10371269 5.590000e-34 156.0
25 TraesCS6D01G024800 chr6A 84.091 176 13 5 1696 1863 10400124 10399956 5.590000e-34 156.0
26 TraesCS6D01G024800 chr6A 97.959 49 1 0 1 49 10383730 10383778 7.440000e-13 86.1
27 TraesCS6D01G024800 chr6A 95.918 49 2 0 1 49 10419899 10419947 3.460000e-11 80.5
28 TraesCS6D01G024800 chr6A 97.727 44 1 0 827 870 10372183 10372140 4.480000e-10 76.8
29 TraesCS6D01G024800 chr6A 97.727 44 1 0 827 870 10400871 10400828 4.480000e-10 76.8
30 TraesCS6D01G024800 chrUn 92.632 190 14 0 1953 2142 479619584 479619773 1.480000e-69 274.0
31 TraesCS6D01G024800 chrUn 84.091 176 13 5 1696 1863 479619430 479619598 5.590000e-34 156.0
32 TraesCS6D01G024800 chrUn 85.714 112 9 6 277 387 466239017 466238912 1.230000e-20 111.0
33 TraesCS6D01G024800 chrUn 76.562 192 33 6 3957 4136 419199465 419199656 1.240000e-15 95.3
34 TraesCS6D01G024800 chrUn 76.562 192 33 6 3957 4136 432494302 432494493 1.240000e-15 95.3
35 TraesCS6D01G024800 chrUn 89.362 47 5 0 1139 1185 95188240 95188286 4.510000e-05 60.2
36 TraesCS6D01G024800 chrUn 100.000 28 0 0 1 28 388420264 388420237 8.000000e-03 52.8
37 TraesCS6D01G024800 chr6B 89.305 187 18 2 72 257 399449411 399449226 2.510000e-57 233.0
38 TraesCS6D01G024800 chr6B 88.043 184 20 2 72 254 294159838 294159656 2.530000e-52 217.0
39 TraesCS6D01G024800 chr6B 77.083 192 32 6 3957 4136 693998745 693998936 2.660000e-17 100.0
40 TraesCS6D01G024800 chr6B 76.562 192 33 6 3957 4136 693952895 693953086 1.240000e-15 95.3
41 TraesCS6D01G024800 chr6B 92.500 40 3 0 1146 1185 31016320 31016281 1.620000e-04 58.4
42 TraesCS6D01G024800 chr6B 100.000 29 0 0 1157 1185 31513271 31513299 2.000000e-03 54.7
43 TraesCS6D01G024800 chr1B 88.587 184 19 2 72 254 271723293 271723475 5.440000e-54 222.0
44 TraesCS6D01G024800 chr1B 93.478 92 5 1 1864 1954 565330966 565331057 7.280000e-28 135.0
45 TraesCS6D01G024800 chr5D 88.525 183 18 3 72 253 152628575 152628395 7.030000e-53 219.0
46 TraesCS6D01G024800 chr4A 88.525 183 18 3 72 253 204814721 204814541 7.030000e-53 219.0
47 TraesCS6D01G024800 chr7B 88.043 184 20 2 72 254 532280497 532280679 2.530000e-52 217.0
48 TraesCS6D01G024800 chr5B 88.043 184 20 2 72 254 244331948 244331766 2.530000e-52 217.0
49 TraesCS6D01G024800 chr5B 95.349 86 4 0 1870 1955 16491846 16491931 2.030000e-28 137.0
50 TraesCS6D01G024800 chr5B 95.349 86 4 0 1870 1955 682420193 682420278 2.030000e-28 137.0
51 TraesCS6D01G024800 chr5B 95.349 86 4 0 1870 1955 682460497 682460582 2.030000e-28 137.0
52 TraesCS6D01G024800 chr2B 70.437 893 221 32 2190 3074 28256913 28257770 3.370000e-31 147.0
53 TraesCS6D01G024800 chr7D 96.552 87 2 1 1870 1955 394836127 394836213 4.350000e-30 143.0
54 TraesCS6D01G024800 chr7D 97.590 83 2 0 1873 1955 576325448 576325530 4.350000e-30 143.0
55 TraesCS6D01G024800 chr7D 95.349 86 4 0 1869 1954 19568680 19568765 2.030000e-28 137.0
56 TraesCS6D01G024800 chr7D 95.349 86 4 0 1870 1955 630038727 630038642 2.030000e-28 137.0
57 TraesCS6D01G024800 chr7D 78.713 202 35 7 3948 4144 89483217 89483019 1.220000e-25 128.0
58 TraesCS6D01G024800 chr7D 78.140 215 31 14 3939 4144 132823649 132823856 5.670000e-24 122.0
59 TraesCS6D01G024800 chr7D 82.653 98 14 3 641 735 538820372 538820275 2.680000e-12 84.2
60 TraesCS6D01G024800 chr4B 97.590 83 2 0 1873 1955 499905267 499905349 4.350000e-30 143.0
61 TraesCS6D01G024800 chr7A 79.618 157 25 6 3940 4092 644005397 644005550 5.710000e-19 106.0
62 TraesCS6D01G024800 chr7A 81.818 110 18 2 628 735 37947398 37947507 1.600000e-14 91.6
63 TraesCS6D01G024800 chr3D 82.906 117 15 5 638 751 564134404 564134518 2.660000e-17 100.0
64 TraesCS6D01G024800 chr3B 81.081 111 19 2 643 751 751750189 751750299 2.070000e-13 87.9


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 TraesCS6D01G024800 chr6D 9386367 9390543 4176 False 7714.000 7714 100.00000 1 4177 1 chr6D.!!$F1 4176
1 TraesCS6D01G024800 chr6D 9364807 9366588 1781 True 2320.000 2320 90.71100 2384 4110 1 chr6D.!!$R1 1726
2 TraesCS6D01G024800 chr6D 9371707 9373476 1769 True 510.325 979 91.11025 421 2400 4 chr6D.!!$R2 1979
3 TraesCS6D01G024800 chr6A 10444605 10446534 1929 False 1374.500 2499 96.38650 2498 4177 2 chr6A.!!$F3 1679
4 TraesCS6D01G024800 chr6A 11157266 11160462 3196 False 1079.250 2084 89.77075 827 4110 4 chr6A.!!$F4 3283
5 TraesCS6D01G024800 chr6A 10383730 10386774 3044 False 787.025 2298 95.56500 1 2256 4 chr6A.!!$F1 2255
6 TraesCS6D01G024800 chr6A 10419899 10423157 3258 False 775.375 2274 94.79300 1 2256 4 chr6A.!!$F2 2255
7 TraesCS6D01G024800 chr6A 10370387 10372647 2260 True 573.760 1371 90.04440 421 2846 5 chr6A.!!$R1 2425
8 TraesCS6D01G024800 chr6A 10399074 10401334 2260 True 571.360 1371 89.96240 421 2846 5 chr6A.!!$R2 2425

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
685 1895 0.108804 TCAGACTTTCCGACGATGCC 60.109 55.0 0.0 0.0 0.00 4.40 F
1895 3218 0.185175 AAGAGTTTCCCCCGCTTTGT 59.815 50.0 0.0 0.0 0.00 2.83 F
1945 3268 0.318762 GATAGGTGCTAGGGCGGAAG 59.681 60.0 0.0 0.0 42.25 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 3262 0.171903 ATGAATTGTGCTGCTTCCGC 59.828 50.0 0.00 0.0 0.00 5.54 R
2783 4111 0.941463 CTATGTCGCAGTCGGCCATC 60.941 60.0 2.24 0.0 40.09 3.51 R
3345 4707 2.375014 TTTTTCCTCGGCCTTTTCCT 57.625 45.0 0.00 0.0 0.00 3.36 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
41 42 1.577328 CCATGCGTTTCTCGTTGGCT 61.577 55.000 0.00 0.00 42.13 4.75
49 192 2.652382 TTCTCGTTGGCTCCACGCAA 62.652 55.000 6.18 0.00 41.67 4.85
51 194 1.781025 CTCGTTGGCTCCACGCAAAA 61.781 55.000 6.18 0.00 41.67 2.44
123 1325 6.301169 AGTGGTGCTAATTAGAGCTAGTTT 57.699 37.500 16.85 0.00 43.27 2.66
125 1327 7.168905 AGTGGTGCTAATTAGAGCTAGTTTTT 58.831 34.615 16.85 0.00 43.27 1.94
153 1355 8.770438 TTTTGCATTTATTGTCAATCTAACCC 57.230 30.769 0.07 0.00 0.00 4.11
155 1357 8.815565 TTGCATTTATTGTCAATCTAACCCTA 57.184 30.769 0.07 0.00 0.00 3.53
158 1360 9.066892 GCATTTATTGTCAATCTAACCCTATCA 57.933 33.333 0.07 0.00 0.00 2.15
188 1390 7.017319 ACACCTATTTGGCTAGAGTTAGTTT 57.983 36.000 0.00 0.00 40.22 2.66
193 1395 6.638021 ATTTGGCTAGAGTTAGTTTAGGGT 57.362 37.500 0.00 0.00 0.00 4.34
194 1396 6.443995 TTTGGCTAGAGTTAGTTTAGGGTT 57.556 37.500 0.00 0.00 0.00 4.11
207 1409 9.583765 GTTAGTTTAGGGTTAGTCATGAGTTAG 57.416 37.037 8.68 0.00 0.00 2.34
252 1454 7.606839 AGTTAAGTTAGAGTATTCAAACAGGGC 59.393 37.037 0.00 0.00 0.00 5.19
268 1470 2.203209 GCCTATGGCCGGTCTTGG 60.203 66.667 7.97 7.95 44.06 3.61
336 1538 3.131396 GCGAAGAGGTTCTTTCTTGTGA 58.869 45.455 0.00 0.00 36.73 3.58
337 1539 3.059529 GCGAAGAGGTTCTTTCTTGTGAC 60.060 47.826 0.00 0.00 36.73 3.67
373 1577 1.106285 GGCACCTAAGCATCCAAAGG 58.894 55.000 0.00 0.00 35.83 3.11
382 1586 2.720915 AGCATCCAAAGGAAGAAGCTC 58.279 47.619 0.00 0.00 34.34 4.09
395 1599 3.840890 AGAAGCTCAGAAGTACAGACG 57.159 47.619 0.00 0.00 0.00 4.18
565 1774 3.747099 ACTCCAAATTGATTTCGCGAG 57.253 42.857 9.59 0.00 0.00 5.03
597 1806 5.295540 GTGATTGAAAGATTAGGAGGACAGC 59.704 44.000 0.00 0.00 0.00 4.40
631 1840 5.749462 ACCCATCAGAGTTTGAATTCTAGG 58.251 41.667 7.05 0.00 39.77 3.02
684 1894 1.710013 TTCAGACTTTCCGACGATGC 58.290 50.000 0.00 0.00 0.00 3.91
685 1895 0.108804 TCAGACTTTCCGACGATGCC 60.109 55.000 0.00 0.00 0.00 4.40
709 1919 2.619931 TCAGTGGGAGAAGATGTTCCA 58.380 47.619 0.00 0.00 35.09 3.53
802 2012 5.832539 AGTAGCATCACTTGGGCTATAAT 57.167 39.130 0.00 0.00 41.66 1.28
871 2140 8.660373 CAGAGGACAACAGAAATGATACTTTAC 58.340 37.037 0.00 0.00 0.00 2.01
924 2201 4.261614 GCAGCACTTGGGCTATAAATTACC 60.262 45.833 0.00 0.00 43.68 2.85
1075 2373 0.689412 CCCTCTTGTCCTCCTCCTCC 60.689 65.000 0.00 0.00 0.00 4.30
1076 2374 0.338120 CCTCTTGTCCTCCTCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
1077 2375 1.687996 CCTCTTGTCCTCCTCCTCCTC 60.688 61.905 0.00 0.00 0.00 3.71
1185 2483 2.610859 ATCGGCCACCTCCACCTT 60.611 61.111 2.24 0.00 0.00 3.50
1477 2775 1.613925 GTTCCAAGAAAGTTGGCTCCC 59.386 52.381 0.00 0.00 39.38 4.30
1621 2920 9.724839 TTTTTCTTCCAAGACAAACTAATAACG 57.275 29.630 0.00 0.00 31.74 3.18
1622 2921 8.665643 TTTCTTCCAAGACAAACTAATAACGA 57.334 30.769 0.00 0.00 34.13 3.85
1623 2922 7.884816 TCTTCCAAGACAAACTAATAACGAG 57.115 36.000 0.00 0.00 0.00 4.18
1624 2923 7.439381 TCTTCCAAGACAAACTAATAACGAGT 58.561 34.615 0.00 0.00 0.00 4.18
1625 2924 7.929785 TCTTCCAAGACAAACTAATAACGAGTT 59.070 33.333 0.00 0.00 38.81 3.01
1626 2925 8.441312 TTCCAAGACAAACTAATAACGAGTTT 57.559 30.769 0.00 0.00 45.75 2.66
1627 2926 8.441312 TCCAAGACAAACTAATAACGAGTTTT 57.559 30.769 0.00 0.00 43.03 2.43
1628 2927 8.339714 TCCAAGACAAACTAATAACGAGTTTTG 58.660 33.333 0.00 0.00 43.03 2.44
1629 2928 8.339714 CCAAGACAAACTAATAACGAGTTTTGA 58.660 33.333 0.00 0.00 43.03 2.69
1630 2929 9.155053 CAAGACAAACTAATAACGAGTTTTGAC 57.845 33.333 0.00 0.00 43.03 3.18
1631 2930 8.658499 AGACAAACTAATAACGAGTTTTGACT 57.342 30.769 0.00 0.00 43.03 3.41
1632 2931 8.762426 AGACAAACTAATAACGAGTTTTGACTC 58.238 33.333 0.00 0.00 43.03 3.36
1633 2932 7.858583 ACAAACTAATAACGAGTTTTGACTCC 58.141 34.615 0.00 0.00 43.03 3.85
1634 2933 6.701432 AACTAATAACGAGTTTTGACTCCG 57.299 37.500 0.00 0.00 33.25 4.63
1635 2934 4.624452 ACTAATAACGAGTTTTGACTCCGC 59.376 41.667 0.00 0.00 33.38 5.54
1636 2935 1.411394 TAACGAGTTTTGACTCCGCG 58.589 50.000 0.00 0.00 33.38 6.46
1637 2936 1.828331 AACGAGTTTTGACTCCGCGC 61.828 55.000 0.00 0.00 33.38 6.86
1638 2937 2.022129 CGAGTTTTGACTCCGCGCT 61.022 57.895 5.56 0.00 33.38 5.92
1639 2938 1.493311 GAGTTTTGACTCCGCGCTG 59.507 57.895 5.56 0.00 0.00 5.18
1640 2939 0.944311 GAGTTTTGACTCCGCGCTGA 60.944 55.000 5.56 2.80 0.00 4.26
1641 2940 0.320771 AGTTTTGACTCCGCGCTGAT 60.321 50.000 5.56 0.00 0.00 2.90
1642 2941 1.067142 AGTTTTGACTCCGCGCTGATA 60.067 47.619 5.56 0.00 0.00 2.15
1643 2942 1.933853 GTTTTGACTCCGCGCTGATAT 59.066 47.619 5.56 0.00 0.00 1.63
1644 2943 3.120792 GTTTTGACTCCGCGCTGATATA 58.879 45.455 5.56 0.00 0.00 0.86
1645 2944 3.660501 TTTGACTCCGCGCTGATATAT 57.339 42.857 5.56 0.00 0.00 0.86
1646 2945 3.660501 TTGACTCCGCGCTGATATATT 57.339 42.857 5.56 0.00 0.00 1.28
1647 2946 2.946564 TGACTCCGCGCTGATATATTG 58.053 47.619 5.56 0.00 0.00 1.90
1648 2947 2.296190 TGACTCCGCGCTGATATATTGT 59.704 45.455 5.56 0.00 0.00 2.71
1649 2948 2.917971 GACTCCGCGCTGATATATTGTC 59.082 50.000 5.56 3.30 0.00 3.18
1650 2949 1.914051 CTCCGCGCTGATATATTGTCG 59.086 52.381 5.56 0.00 0.00 4.35
1651 2950 0.366871 CCGCGCTGATATATTGTCGC 59.633 55.000 5.56 13.09 39.26 5.19
1652 2951 3.838533 GCGCTGATATATTGTCGCG 57.161 52.632 0.00 0.00 39.62 5.87
1653 2952 1.336877 GCGCTGATATATTGTCGCGA 58.663 50.000 3.71 3.71 39.28 5.87
1654 2953 1.318785 GCGCTGATATATTGTCGCGAG 59.681 52.381 10.24 0.00 39.28 5.03
1655 2954 2.585845 CGCTGATATATTGTCGCGAGT 58.414 47.619 10.24 0.58 39.28 4.18
1656 2955 2.980476 CGCTGATATATTGTCGCGAGTT 59.020 45.455 10.24 0.00 39.28 3.01
1657 2956 3.425525 CGCTGATATATTGTCGCGAGTTT 59.574 43.478 10.24 0.00 39.28 2.66
1658 2957 4.085055 CGCTGATATATTGTCGCGAGTTTT 60.085 41.667 10.24 0.00 39.28 2.43
1659 2958 5.366752 GCTGATATATTGTCGCGAGTTTTC 58.633 41.667 10.24 0.00 0.00 2.29
1660 2959 5.175856 GCTGATATATTGTCGCGAGTTTTCT 59.824 40.000 10.24 0.00 0.00 2.52
1661 2960 6.510746 TGATATATTGTCGCGAGTTTTCTG 57.489 37.500 10.24 0.00 0.00 3.02
1662 2961 3.658351 ATATTGTCGCGAGTTTTCTGC 57.342 42.857 10.24 0.00 0.00 4.26
1663 2962 1.225855 ATTGTCGCGAGTTTTCTGCA 58.774 45.000 10.24 0.00 0.00 4.41
1664 2963 1.010580 TTGTCGCGAGTTTTCTGCAA 58.989 45.000 10.24 4.50 0.00 4.08
1665 2964 1.225855 TGTCGCGAGTTTTCTGCAAT 58.774 45.000 10.24 0.00 0.00 3.56
1666 2965 2.409012 TGTCGCGAGTTTTCTGCAATA 58.591 42.857 10.24 0.00 0.00 1.90
1667 2966 3.000041 TGTCGCGAGTTTTCTGCAATAT 59.000 40.909 10.24 0.00 0.00 1.28
1668 2967 3.181521 TGTCGCGAGTTTTCTGCAATATG 60.182 43.478 10.24 0.00 0.00 1.78
1669 2968 3.000041 TCGCGAGTTTTCTGCAATATGT 59.000 40.909 3.71 0.00 0.00 2.29
1670 2969 3.062099 TCGCGAGTTTTCTGCAATATGTC 59.938 43.478 3.71 0.00 0.00 3.06
1671 2970 3.345714 GCGAGTTTTCTGCAATATGTCG 58.654 45.455 0.00 0.00 0.00 4.35
1672 2971 3.345714 CGAGTTTTCTGCAATATGTCGC 58.654 45.455 0.00 0.00 0.00 5.19
1673 2972 3.345714 GAGTTTTCTGCAATATGTCGCG 58.654 45.455 0.00 0.00 0.00 5.87
1674 2973 3.000041 AGTTTTCTGCAATATGTCGCGA 59.000 40.909 3.71 3.71 0.00 5.87
1675 2974 3.062639 AGTTTTCTGCAATATGTCGCGAG 59.937 43.478 10.24 0.00 0.00 5.03
1676 2975 2.293677 TTCTGCAATATGTCGCGAGT 57.706 45.000 10.24 3.67 0.00 4.18
1677 2976 2.293677 TCTGCAATATGTCGCGAGTT 57.706 45.000 10.24 1.71 0.00 3.01
1678 2977 2.616960 TCTGCAATATGTCGCGAGTTT 58.383 42.857 10.24 0.00 0.00 2.66
1679 2978 3.000041 TCTGCAATATGTCGCGAGTTTT 59.000 40.909 10.24 0.00 0.00 2.43
1680 2979 3.062099 TCTGCAATATGTCGCGAGTTTTC 59.938 43.478 10.24 0.00 0.00 2.29
1681 2980 3.000041 TGCAATATGTCGCGAGTTTTCT 59.000 40.909 10.24 0.00 0.00 2.52
1682 2981 3.181521 TGCAATATGTCGCGAGTTTTCTG 60.182 43.478 10.24 4.25 0.00 3.02
1683 2982 3.345714 CAATATGTCGCGAGTTTTCTGC 58.654 45.455 10.24 0.00 0.00 4.26
1684 2983 2.073117 TATGTCGCGAGTTTTCTGCA 57.927 45.000 10.24 0.57 0.00 4.41
1685 2984 1.225855 ATGTCGCGAGTTTTCTGCAA 58.774 45.000 10.24 0.00 0.00 4.08
1686 2985 1.225855 TGTCGCGAGTTTTCTGCAAT 58.774 45.000 10.24 0.00 0.00 3.56
1687 2986 2.409012 TGTCGCGAGTTTTCTGCAATA 58.591 42.857 10.24 0.00 0.00 1.90
1688 2987 3.000041 TGTCGCGAGTTTTCTGCAATAT 59.000 40.909 10.24 0.00 0.00 1.28
1689 2988 3.181521 TGTCGCGAGTTTTCTGCAATATG 60.182 43.478 10.24 0.00 0.00 1.78
1690 2989 3.000041 TCGCGAGTTTTCTGCAATATGT 59.000 40.909 3.71 0.00 0.00 2.29
1691 2990 3.062099 TCGCGAGTTTTCTGCAATATGTC 59.938 43.478 3.71 0.00 0.00 3.06
1701 3000 3.062099 TCTGCAATATGTCGCGAGTTTTC 59.938 43.478 10.24 0.00 0.00 2.29
1775 3098 5.009911 TGTCGACTAGAGAGGCTACTACTAG 59.990 48.000 17.92 12.09 38.56 2.57
1825 3148 3.991121 GAGCTCCAAGTAGTGTTGACTTC 59.009 47.826 0.87 0.00 34.90 3.01
1847 3170 4.918583 TCGTTTTTCGGTATGGAAATTTGC 59.081 37.500 2.22 2.22 40.32 3.68
1848 3171 4.681942 CGTTTTTCGGTATGGAAATTTGCA 59.318 37.500 15.13 15.13 35.95 4.08
1849 3172 5.175856 CGTTTTTCGGTATGGAAATTTGCAA 59.824 36.000 16.71 0.00 35.95 4.08
1850 3173 6.128688 CGTTTTTCGGTATGGAAATTTGCAAT 60.129 34.615 16.71 7.94 35.95 3.56
1851 3174 7.570324 CGTTTTTCGGTATGGAAATTTGCAATT 60.570 33.333 16.71 3.78 35.95 2.32
1852 3175 6.959671 TTTCGGTATGGAAATTTGCAATTC 57.040 33.333 16.71 9.46 31.30 2.17
1853 3176 5.651387 TCGGTATGGAAATTTGCAATTCA 57.349 34.783 16.71 0.00 30.51 2.57
1854 3177 6.219417 TCGGTATGGAAATTTGCAATTCAT 57.781 33.333 16.71 6.37 30.51 2.57
1855 3178 6.041511 TCGGTATGGAAATTTGCAATTCATG 58.958 36.000 16.71 5.29 30.51 3.07
1856 3179 5.234757 CGGTATGGAAATTTGCAATTCATGG 59.765 40.000 16.71 0.00 30.51 3.66
1857 3180 6.114767 GGTATGGAAATTTGCAATTCATGGT 58.885 36.000 16.71 0.08 30.51 3.55
1858 3181 7.271511 GGTATGGAAATTTGCAATTCATGGTA 58.728 34.615 16.71 0.00 30.51 3.25
1859 3182 7.933033 GGTATGGAAATTTGCAATTCATGGTAT 59.067 33.333 16.71 0.00 30.51 2.73
1860 3183 9.979578 GTATGGAAATTTGCAATTCATGGTATA 57.020 29.630 16.71 0.00 30.51 1.47
1861 3184 8.891671 ATGGAAATTTGCAATTCATGGTATAC 57.108 30.769 16.71 0.00 30.51 1.47
1862 3185 6.977502 TGGAAATTTGCAATTCATGGTATACG 59.022 34.615 10.24 0.00 0.00 3.06
1863 3186 6.978080 GGAAATTTGCAATTCATGGTATACGT 59.022 34.615 13.35 0.00 0.00 3.57
1864 3187 7.491048 GGAAATTTGCAATTCATGGTATACGTT 59.509 33.333 13.35 0.00 0.00 3.99
1865 3188 8.770438 AAATTTGCAATTCATGGTATACGTTT 57.230 26.923 0.00 0.00 0.00 3.60
1866 3189 8.770438 AATTTGCAATTCATGGTATACGTTTT 57.230 26.923 0.00 0.00 0.00 2.43
1867 3190 9.862371 AATTTGCAATTCATGGTATACGTTTTA 57.138 25.926 0.00 0.00 0.00 1.52
1868 3191 8.676454 TTTGCAATTCATGGTATACGTTTTAC 57.324 30.769 0.00 0.00 0.00 2.01
1869 3192 7.618502 TGCAATTCATGGTATACGTTTTACT 57.381 32.000 0.00 0.00 0.00 2.24
1870 3193 8.719560 TGCAATTCATGGTATACGTTTTACTA 57.280 30.769 0.00 0.00 0.00 1.82
1871 3194 8.605746 TGCAATTCATGGTATACGTTTTACTAC 58.394 33.333 0.00 0.00 0.00 2.73
1872 3195 7.790673 GCAATTCATGGTATACGTTTTACTACG 59.209 37.037 0.00 0.00 46.52 3.51
1873 3196 9.022915 CAATTCATGGTATACGTTTTACTACGA 57.977 33.333 0.00 0.00 43.99 3.43
1874 3197 9.585099 AATTCATGGTATACGTTTTACTACGAA 57.415 29.630 0.00 0.00 43.99 3.85
1875 3198 8.978564 TTCATGGTATACGTTTTACTACGAAA 57.021 30.769 0.00 0.00 43.99 3.46
1876 3199 8.978564 TCATGGTATACGTTTTACTACGAAAA 57.021 30.769 0.00 0.00 43.99 2.29
1877 3200 9.416794 TCATGGTATACGTTTTACTACGAAAAA 57.583 29.630 0.00 0.00 43.99 1.94
1878 3201 9.679596 CATGGTATACGTTTTACTACGAAAAAG 57.320 33.333 0.00 0.00 43.99 2.27
1879 3202 9.638239 ATGGTATACGTTTTACTACGAAAAAGA 57.362 29.630 0.00 0.00 43.99 2.52
1880 3203 9.128107 TGGTATACGTTTTACTACGAAAAAGAG 57.872 33.333 0.00 0.00 43.99 2.85
1881 3204 9.129209 GGTATACGTTTTACTACGAAAAAGAGT 57.871 33.333 0.00 0.00 43.99 3.24
1885 3208 7.401860 ACGTTTTACTACGAAAAAGAGTTTCC 58.598 34.615 2.93 0.00 43.99 3.13
1886 3209 6.847792 CGTTTTACTACGAAAAAGAGTTTCCC 59.152 38.462 0.00 0.00 43.99 3.97
1887 3210 6.866010 TTTACTACGAAAAAGAGTTTCCCC 57.134 37.500 0.00 0.00 0.00 4.81
1888 3211 3.748083 ACTACGAAAAAGAGTTTCCCCC 58.252 45.455 0.00 0.00 0.00 5.40
1889 3212 1.601166 ACGAAAAAGAGTTTCCCCCG 58.399 50.000 0.00 0.00 0.00 5.73
1890 3213 0.240145 CGAAAAAGAGTTTCCCCCGC 59.760 55.000 0.00 0.00 0.00 6.13
1891 3214 1.617322 GAAAAAGAGTTTCCCCCGCT 58.383 50.000 0.00 0.00 0.00 5.52
1892 3215 1.961394 GAAAAAGAGTTTCCCCCGCTT 59.039 47.619 0.00 0.00 0.00 4.68
1893 3216 2.082140 AAAAGAGTTTCCCCCGCTTT 57.918 45.000 0.00 0.00 34.09 3.51
1894 3217 1.328279 AAAGAGTTTCCCCCGCTTTG 58.672 50.000 0.00 0.00 31.93 2.77
1895 3218 0.185175 AAGAGTTTCCCCCGCTTTGT 59.815 50.000 0.00 0.00 0.00 2.83
1896 3219 1.061546 AGAGTTTCCCCCGCTTTGTA 58.938 50.000 0.00 0.00 0.00 2.41
1897 3220 1.633945 AGAGTTTCCCCCGCTTTGTAT 59.366 47.619 0.00 0.00 0.00 2.29
1898 3221 2.041216 AGAGTTTCCCCCGCTTTGTATT 59.959 45.455 0.00 0.00 0.00 1.89
1899 3222 3.264964 AGAGTTTCCCCCGCTTTGTATTA 59.735 43.478 0.00 0.00 0.00 0.98
1900 3223 3.349927 AGTTTCCCCCGCTTTGTATTAC 58.650 45.455 0.00 0.00 0.00 1.89
1901 3224 3.083293 GTTTCCCCCGCTTTGTATTACA 58.917 45.455 0.00 0.00 0.00 2.41
1902 3225 3.436577 TTCCCCCGCTTTGTATTACAA 57.563 42.857 5.14 5.14 36.11 2.41
1903 3226 3.436577 TCCCCCGCTTTGTATTACAAA 57.563 42.857 18.39 18.39 44.91 2.83
1914 3237 4.955925 TGTATTACAAAGCAACCATCCG 57.044 40.909 0.00 0.00 0.00 4.18
1915 3238 4.580868 TGTATTACAAAGCAACCATCCGA 58.419 39.130 0.00 0.00 0.00 4.55
1916 3239 5.189928 TGTATTACAAAGCAACCATCCGAT 58.810 37.500 0.00 0.00 0.00 4.18
1917 3240 6.350103 TGTATTACAAAGCAACCATCCGATA 58.650 36.000 0.00 0.00 0.00 2.92
1918 3241 5.751243 ATTACAAAGCAACCATCCGATAC 57.249 39.130 0.00 0.00 0.00 2.24
1919 3242 3.066291 ACAAAGCAACCATCCGATACA 57.934 42.857 0.00 0.00 0.00 2.29
1920 3243 3.417101 ACAAAGCAACCATCCGATACAA 58.583 40.909 0.00 0.00 0.00 2.41
1921 3244 3.190535 ACAAAGCAACCATCCGATACAAC 59.809 43.478 0.00 0.00 0.00 3.32
1922 3245 2.038387 AGCAACCATCCGATACAACC 57.962 50.000 0.00 0.00 0.00 3.77
1923 3246 1.280710 AGCAACCATCCGATACAACCA 59.719 47.619 0.00 0.00 0.00 3.67
1924 3247 2.088423 GCAACCATCCGATACAACCAA 58.912 47.619 0.00 0.00 0.00 3.67
1925 3248 2.159435 GCAACCATCCGATACAACCAAC 60.159 50.000 0.00 0.00 0.00 3.77
1926 3249 2.018542 ACCATCCGATACAACCAACG 57.981 50.000 0.00 0.00 0.00 4.10
1927 3250 1.551430 ACCATCCGATACAACCAACGA 59.449 47.619 0.00 0.00 0.00 3.85
1928 3251 2.169769 ACCATCCGATACAACCAACGAT 59.830 45.455 0.00 0.00 0.00 3.73
1929 3252 3.385433 ACCATCCGATACAACCAACGATA 59.615 43.478 0.00 0.00 0.00 2.92
1930 3253 3.987868 CCATCCGATACAACCAACGATAG 59.012 47.826 0.00 0.00 46.19 2.08
1931 3254 3.720949 TCCGATACAACCAACGATAGG 57.279 47.619 0.00 0.00 43.77 2.57
1932 3255 3.025978 TCCGATACAACCAACGATAGGT 58.974 45.455 0.00 0.00 42.34 3.08
1941 3264 1.740285 AACGATAGGTGCTAGGGCG 59.260 57.895 0.00 0.00 40.77 6.13
1942 3265 1.745320 AACGATAGGTGCTAGGGCGG 61.745 60.000 0.00 0.00 40.77 6.13
1943 3266 1.901948 CGATAGGTGCTAGGGCGGA 60.902 63.158 0.00 0.00 42.25 5.54
1944 3267 1.461091 CGATAGGTGCTAGGGCGGAA 61.461 60.000 0.00 0.00 42.25 4.30
1945 3268 0.318762 GATAGGTGCTAGGGCGGAAG 59.681 60.000 0.00 0.00 42.25 3.46
1999 3322 1.414181 GATCGTCCACTCATCCATGGT 59.586 52.381 12.58 0.00 37.27 3.55
2025 3348 0.389426 ATCGACAGGTACAACACGCC 60.389 55.000 0.00 0.00 0.00 5.68
2096 3419 2.393271 AAGCTGCTTAGCTCGTTCAT 57.607 45.000 14.24 0.00 45.54 2.57
2166 3489 2.599659 GGTCGAAACGAGTTATTCCGT 58.400 47.619 0.00 0.00 41.14 4.69
2286 3609 2.769663 TGCTAGGGCGGAGAGAATAAAA 59.230 45.455 0.00 0.00 42.25 1.52
2361 3684 4.522405 ACGATGTTGGACCATGAAATCAAA 59.478 37.500 0.00 0.00 0.00 2.69
2366 3689 4.870123 TGGACCATGAAATCAAACAAGG 57.130 40.909 0.00 0.00 0.00 3.61
2460 3783 0.451383 CCGTGTTGGTGGTATGCATG 59.549 55.000 10.16 0.00 0.00 4.06
2631 3959 4.018050 AGCTAATCCAAAATCCAGAGGTGT 60.018 41.667 0.00 0.00 0.00 4.16
2686 4014 3.563479 GCAGAGGGGAAGGAAATGGTTAA 60.563 47.826 0.00 0.00 0.00 2.01
2783 4111 1.153939 CTTCGTGCCTCACCTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3074 4402 2.418746 CCACTTCAACTGGGATCTACCG 60.419 54.545 0.00 0.00 40.11 4.02
3140 4468 1.886542 GTGGGTCGCAAGGAAAATCTT 59.113 47.619 0.00 0.00 38.47 2.40
3203 4531 8.664669 TGGGATCATGCTATATAAGACTACAA 57.335 34.615 0.00 0.00 0.00 2.41
3205 4533 9.539825 GGGATCATGCTATATAAGACTACAATG 57.460 37.037 0.00 0.00 0.00 2.82
3206 4534 9.539825 GGATCATGCTATATAAGACTACAATGG 57.460 37.037 0.00 0.00 0.00 3.16
3287 4615 6.720112 ATGCATAGATATTGTGCCTTTGTT 57.280 33.333 0.00 0.00 42.69 2.83
3293 4621 8.892723 CATAGATATTGTGCCTTTGTTGTAAGA 58.107 33.333 0.00 0.00 0.00 2.10
3294 4622 7.944729 AGATATTGTGCCTTTGTTGTAAGAT 57.055 32.000 0.00 0.00 0.00 2.40
3563 4930 2.494059 TGAGAGCCGAAAAAGACCAAG 58.506 47.619 0.00 0.00 0.00 3.61
3666 5046 6.627087 TGAGGATTGGATCAGTAGTTTCTT 57.373 37.500 0.00 0.00 0.00 2.52
3726 5109 4.206477 AGTTGCCTGAAATTTATTGGGC 57.794 40.909 13.04 13.04 39.93 5.36
3800 5189 5.486735 TTGTCAATTTTCATGGCTTCCAT 57.513 34.783 0.00 0.00 46.37 3.41
3839 5228 2.942641 GCCTTGAAGCCCGTTACTT 58.057 52.632 0.00 0.00 0.00 2.24
3840 5229 0.803117 GCCTTGAAGCCCGTTACTTC 59.197 55.000 0.00 0.00 43.15 3.01
4101 5750 0.472898 GGGTAATACCAGTGCCCCTC 59.527 60.000 12.03 0.00 41.02 4.30
4121 5770 6.437162 CCCCTCATTCATTCTTCCTTACAAAA 59.563 38.462 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 1301 5.523438 ACTAGCTCTAATTAGCACCACTC 57.477 43.478 7.67 0.00 45.30 3.51
127 1329 9.213799 GGGTTAGATTGACAATAAATGCAAAAA 57.786 29.630 0.00 0.00 31.83 1.94
130 1332 7.716799 AGGGTTAGATTGACAATAAATGCAA 57.283 32.000 0.00 0.00 32.34 4.08
151 1353 6.639632 CAAATAGGTGTTTGGATGATAGGG 57.360 41.667 0.00 0.00 35.86 3.53
188 1390 9.537852 TTAGTTTCTAACTCATGACTAACCCTA 57.462 33.333 0.00 0.00 41.77 3.53
228 1430 6.882678 GGCCCTGTTTGAATACTCTAACTTAA 59.117 38.462 0.00 0.00 37.92 1.85
252 1454 1.153168 CACCAAGACCGGCCATAGG 60.153 63.158 0.00 0.00 0.00 2.57
268 1470 0.249657 CTTCCATCGGGCTAGCTCAC 60.250 60.000 16.47 5.00 0.00 3.51
351 1553 1.505151 TTGGATGCTTAGGTGCCCCA 61.505 55.000 0.00 0.00 34.51 4.96
353 1555 1.106285 CTTTGGATGCTTAGGTGCCC 58.894 55.000 0.00 0.00 0.00 5.36
373 1577 4.162812 CGTCTGTACTTCTGAGCTTCTTC 58.837 47.826 0.00 0.00 0.00 2.87
382 1586 3.252701 AGTGTACCACGTCTGTACTTCTG 59.747 47.826 19.92 0.00 39.64 3.02
518 1722 1.609061 CCTCCTTGTGCGTCACAGATT 60.609 52.381 11.48 0.00 45.39 2.40
519 1723 0.036952 CCTCCTTGTGCGTCACAGAT 60.037 55.000 11.48 0.00 45.39 2.90
561 1770 1.852942 TCAATCACGGATTAGCTCGC 58.147 50.000 0.00 0.00 30.44 5.03
565 1774 6.706270 TCCTAATCTTTCAATCACGGATTAGC 59.294 38.462 12.68 0.00 41.65 3.09
684 1894 0.905357 ATCTTCTCCCACTGAACGGG 59.095 55.000 0.00 0.00 46.03 5.28
685 1895 1.276421 ACATCTTCTCCCACTGAACGG 59.724 52.381 0.00 0.00 0.00 4.44
699 1909 3.162666 TCGTAGTGGACTGGAACATCTT 58.837 45.455 0.00 0.00 38.20 2.40
709 1919 1.002379 AGGCGTCTCGTAGTGGACT 60.002 57.895 0.00 0.00 31.90 3.85
802 2012 4.141937 CGGGAACATCTCCTCTGTGATAAA 60.142 45.833 0.00 0.00 44.68 1.40
825 2035 6.214191 TCTGTGATGATTTCTCTAGTGGAC 57.786 41.667 0.00 0.00 0.00 4.02
924 2201 2.403259 GCTTGGTGTTTGATTTTCCCG 58.597 47.619 0.00 0.00 0.00 5.14
1477 2775 3.851845 TTTCACGGGCGAGACGGTG 62.852 63.158 9.97 9.97 41.41 4.94
1596 2895 9.111613 TCGTTATTAGTTTGTCTTGGAAGAAAA 57.888 29.630 0.00 0.00 36.68 2.29
1600 2899 7.653767 ACTCGTTATTAGTTTGTCTTGGAAG 57.346 36.000 0.00 0.00 0.00 3.46
1622 2921 0.320771 ATCAGCGCGGAGTCAAAACT 60.321 50.000 16.84 0.00 38.88 2.66
1623 2922 1.355971 TATCAGCGCGGAGTCAAAAC 58.644 50.000 16.84 0.00 0.00 2.43
1624 2923 2.309528 ATATCAGCGCGGAGTCAAAA 57.690 45.000 16.84 0.00 0.00 2.44
1625 2924 3.660501 ATATATCAGCGCGGAGTCAAA 57.339 42.857 16.84 0.04 0.00 2.69
1626 2925 3.243737 ACAATATATCAGCGCGGAGTCAA 60.244 43.478 16.84 1.86 0.00 3.18
1627 2926 2.296190 ACAATATATCAGCGCGGAGTCA 59.704 45.455 16.84 4.09 0.00 3.41
1628 2927 2.917971 GACAATATATCAGCGCGGAGTC 59.082 50.000 16.84 12.35 0.00 3.36
1629 2928 2.668556 CGACAATATATCAGCGCGGAGT 60.669 50.000 16.84 6.98 0.00 3.85
1630 2929 1.914051 CGACAATATATCAGCGCGGAG 59.086 52.381 16.84 3.50 0.00 4.63
1631 2930 1.977188 CGACAATATATCAGCGCGGA 58.023 50.000 13.82 13.82 0.00 5.54
1632 2931 0.366871 GCGACAATATATCAGCGCGG 59.633 55.000 8.83 0.00 35.02 6.46
1633 2932 3.838533 GCGACAATATATCAGCGCG 57.161 52.632 0.00 0.00 35.02 6.86
1634 2933 1.318785 CTCGCGACAATATATCAGCGC 59.681 52.381 3.71 0.00 46.07 5.92
1636 2935 4.974103 AAACTCGCGACAATATATCAGC 57.026 40.909 3.71 0.00 0.00 4.26
1637 2936 6.576021 CAGAAAACTCGCGACAATATATCAG 58.424 40.000 3.71 0.00 0.00 2.90
1638 2937 5.051039 GCAGAAAACTCGCGACAATATATCA 60.051 40.000 3.71 0.00 0.00 2.15
1639 2938 5.051039 TGCAGAAAACTCGCGACAATATATC 60.051 40.000 3.71 0.00 0.00 1.63
1640 2939 4.808895 TGCAGAAAACTCGCGACAATATAT 59.191 37.500 3.71 0.00 0.00 0.86
1641 2940 4.177783 TGCAGAAAACTCGCGACAATATA 58.822 39.130 3.71 0.00 0.00 0.86
1642 2941 3.000041 TGCAGAAAACTCGCGACAATAT 59.000 40.909 3.71 0.00 0.00 1.28
1643 2942 2.409012 TGCAGAAAACTCGCGACAATA 58.591 42.857 3.71 0.00 0.00 1.90
1644 2943 1.225855 TGCAGAAAACTCGCGACAAT 58.774 45.000 3.71 0.00 0.00 2.71
1645 2944 1.010580 TTGCAGAAAACTCGCGACAA 58.989 45.000 3.71 2.00 0.00 3.18
1646 2945 1.225855 ATTGCAGAAAACTCGCGACA 58.774 45.000 3.71 0.00 0.00 4.35
1647 2946 3.181520 ACATATTGCAGAAAACTCGCGAC 60.182 43.478 3.71 0.00 0.00 5.19
1648 2947 3.000041 ACATATTGCAGAAAACTCGCGA 59.000 40.909 9.26 9.26 0.00 5.87
1649 2948 3.345714 GACATATTGCAGAAAACTCGCG 58.654 45.455 0.00 0.00 0.00 5.87
1650 2949 3.345714 CGACATATTGCAGAAAACTCGC 58.654 45.455 0.00 0.00 0.00 5.03
1651 2950 3.345714 GCGACATATTGCAGAAAACTCG 58.654 45.455 0.00 0.00 35.01 4.18
1652 2951 3.062099 TCGCGACATATTGCAGAAAACTC 59.938 43.478 3.71 0.00 34.49 3.01
1653 2952 3.000041 TCGCGACATATTGCAGAAAACT 59.000 40.909 3.71 0.00 34.49 2.66
1654 2953 3.181520 ACTCGCGACATATTGCAGAAAAC 60.182 43.478 3.71 0.00 34.49 2.43
1655 2954 3.000041 ACTCGCGACATATTGCAGAAAA 59.000 40.909 3.71 0.00 34.49 2.29
1656 2955 2.616960 ACTCGCGACATATTGCAGAAA 58.383 42.857 3.71 0.00 34.49 2.52
1657 2956 2.293677 ACTCGCGACATATTGCAGAA 57.706 45.000 3.71 0.00 34.49 3.02
1658 2957 2.293677 AACTCGCGACATATTGCAGA 57.706 45.000 3.71 0.00 34.49 4.26
1659 2958 3.062639 AGAAAACTCGCGACATATTGCAG 59.937 43.478 3.71 0.00 34.49 4.41
1660 2959 3.000041 AGAAAACTCGCGACATATTGCA 59.000 40.909 3.71 0.00 34.49 4.08
1661 2960 3.345714 CAGAAAACTCGCGACATATTGC 58.654 45.455 3.71 0.00 0.00 3.56
1662 2961 3.181521 TGCAGAAAACTCGCGACATATTG 60.182 43.478 3.71 0.00 0.00 1.90
1663 2962 3.000041 TGCAGAAAACTCGCGACATATT 59.000 40.909 3.71 0.00 0.00 1.28
1664 2963 2.616960 TGCAGAAAACTCGCGACATAT 58.383 42.857 3.71 0.00 0.00 1.78
1665 2964 2.073117 TGCAGAAAACTCGCGACATA 57.927 45.000 3.71 0.00 0.00 2.29
1666 2965 1.225855 TTGCAGAAAACTCGCGACAT 58.774 45.000 3.71 0.00 0.00 3.06
1667 2966 1.225855 ATTGCAGAAAACTCGCGACA 58.774 45.000 3.71 0.00 0.00 4.35
1668 2967 3.181520 ACATATTGCAGAAAACTCGCGAC 60.182 43.478 3.71 0.00 0.00 5.19
1669 2968 3.000041 ACATATTGCAGAAAACTCGCGA 59.000 40.909 9.26 9.26 0.00 5.87
1670 2969 3.345714 GACATATTGCAGAAAACTCGCG 58.654 45.455 0.00 0.00 0.00 5.87
1671 2970 3.345714 CGACATATTGCAGAAAACTCGC 58.654 45.455 0.00 0.00 0.00 5.03
1672 2971 3.345714 GCGACATATTGCAGAAAACTCG 58.654 45.455 0.00 0.00 35.01 4.18
1673 2972 3.062099 TCGCGACATATTGCAGAAAACTC 59.938 43.478 3.71 0.00 34.49 3.01
1674 2973 3.000041 TCGCGACATATTGCAGAAAACT 59.000 40.909 3.71 0.00 34.49 2.66
1675 2974 3.181520 ACTCGCGACATATTGCAGAAAAC 60.182 43.478 3.71 0.00 34.49 2.43
1676 2975 3.000041 ACTCGCGACATATTGCAGAAAA 59.000 40.909 3.71 0.00 34.49 2.29
1677 2976 2.616960 ACTCGCGACATATTGCAGAAA 58.383 42.857 3.71 0.00 34.49 2.52
1678 2977 2.293677 ACTCGCGACATATTGCAGAA 57.706 45.000 3.71 0.00 34.49 3.02
1679 2978 2.293677 AACTCGCGACATATTGCAGA 57.706 45.000 3.71 0.00 34.49 4.26
1680 2979 3.181521 TGAAAACTCGCGACATATTGCAG 60.182 43.478 3.71 0.00 34.49 4.41
1681 2980 2.739379 TGAAAACTCGCGACATATTGCA 59.261 40.909 3.71 0.00 34.49 4.08
1682 2981 3.383546 TGAAAACTCGCGACATATTGC 57.616 42.857 3.71 0.00 0.00 3.56
1683 2982 9.811655 AATATATTGAAAACTCGCGACATATTG 57.188 29.630 3.71 0.00 0.00 1.90
1688 2987 9.644993 CAATTAATATATTGAAAACTCGCGACA 57.355 29.630 3.71 0.00 37.65 4.35
1689 2988 9.646336 ACAATTAATATATTGAAAACTCGCGAC 57.354 29.630 3.71 0.00 38.56 5.19
1690 2989 9.858247 GACAATTAATATATTGAAAACTCGCGA 57.142 29.630 9.26 9.26 38.56 5.87
1691 2990 9.644993 TGACAATTAATATATTGAAAACTCGCG 57.355 29.630 8.28 0.00 38.56 5.87
1825 3148 4.681942 TGCAAATTTCCATACCGAAAAACG 59.318 37.500 0.00 0.00 35.47 3.60
1847 3170 9.022915 TCGTAGTAAAACGTATACCATGAATTG 57.977 33.333 0.00 0.00 43.31 2.32
1848 3171 9.585099 TTCGTAGTAAAACGTATACCATGAATT 57.415 29.630 0.00 0.00 43.31 2.17
1849 3172 9.585099 TTTCGTAGTAAAACGTATACCATGAAT 57.415 29.630 12.08 0.00 43.31 2.57
1850 3173 8.978564 TTTCGTAGTAAAACGTATACCATGAA 57.021 30.769 0.00 9.08 43.31 2.57
1851 3174 8.978564 TTTTCGTAGTAAAACGTATACCATGA 57.021 30.769 0.00 3.62 43.31 3.07
1852 3175 9.679596 CTTTTTCGTAGTAAAACGTATACCATG 57.320 33.333 7.58 1.63 43.31 3.66
1853 3176 9.638239 TCTTTTTCGTAGTAAAACGTATACCAT 57.362 29.630 7.58 0.00 43.31 3.55
1854 3177 9.128107 CTCTTTTTCGTAGTAAAACGTATACCA 57.872 33.333 7.58 0.00 43.31 3.25
1855 3178 9.129209 ACTCTTTTTCGTAGTAAAACGTATACC 57.871 33.333 7.58 0.00 43.31 2.73
1859 3182 8.539674 GGAAACTCTTTTTCGTAGTAAAACGTA 58.460 33.333 0.00 0.00 43.31 3.57
1860 3183 7.401860 GGAAACTCTTTTTCGTAGTAAAACGT 58.598 34.615 0.00 0.00 43.31 3.99
1861 3184 6.847792 GGGAAACTCTTTTTCGTAGTAAAACG 59.152 38.462 0.00 0.00 44.19 3.60
1862 3185 7.134815 GGGGAAACTCTTTTTCGTAGTAAAAC 58.865 38.462 0.00 0.00 0.00 2.43
1863 3186 6.262944 GGGGGAAACTCTTTTTCGTAGTAAAA 59.737 38.462 0.00 0.00 0.00 1.52
1864 3187 5.764686 GGGGGAAACTCTTTTTCGTAGTAAA 59.235 40.000 0.00 0.00 0.00 2.01
1865 3188 5.308014 GGGGGAAACTCTTTTTCGTAGTAA 58.692 41.667 0.00 0.00 0.00 2.24
1866 3189 4.561326 CGGGGGAAACTCTTTTTCGTAGTA 60.561 45.833 0.00 0.00 0.00 1.82
1867 3190 3.748083 GGGGGAAACTCTTTTTCGTAGT 58.252 45.455 0.00 0.00 0.00 2.73
1868 3191 2.740447 CGGGGGAAACTCTTTTTCGTAG 59.260 50.000 0.00 0.00 0.00 3.51
1869 3192 2.769893 CGGGGGAAACTCTTTTTCGTA 58.230 47.619 0.00 0.00 0.00 3.43
1870 3193 1.601166 CGGGGGAAACTCTTTTTCGT 58.399 50.000 0.00 0.00 0.00 3.85
1871 3194 0.240145 GCGGGGGAAACTCTTTTTCG 59.760 55.000 0.00 0.00 0.00 3.46
1872 3195 1.617322 AGCGGGGGAAACTCTTTTTC 58.383 50.000 0.00 0.00 0.00 2.29
1873 3196 2.082140 AAGCGGGGGAAACTCTTTTT 57.918 45.000 0.00 0.00 0.00 1.94
1874 3197 1.686587 CAAAGCGGGGGAAACTCTTTT 59.313 47.619 0.00 0.00 0.00 2.27
1875 3198 1.328279 CAAAGCGGGGGAAACTCTTT 58.672 50.000 0.00 0.00 0.00 2.52
1876 3199 0.185175 ACAAAGCGGGGGAAACTCTT 59.815 50.000 0.00 0.00 0.00 2.85
1877 3200 1.061546 TACAAAGCGGGGGAAACTCT 58.938 50.000 0.00 0.00 0.00 3.24
1878 3201 2.124277 ATACAAAGCGGGGGAAACTC 57.876 50.000 0.00 0.00 0.00 3.01
1879 3202 2.597578 AATACAAAGCGGGGGAAACT 57.402 45.000 0.00 0.00 0.00 2.66
1880 3203 3.083293 TGTAATACAAAGCGGGGGAAAC 58.917 45.455 0.00 0.00 0.00 2.78
1881 3204 3.436577 TGTAATACAAAGCGGGGGAAA 57.563 42.857 0.00 0.00 0.00 3.13
1882 3205 3.436577 TTGTAATACAAAGCGGGGGAA 57.563 42.857 2.97 0.00 34.76 3.97
1883 3206 3.436577 TTTGTAATACAAAGCGGGGGA 57.563 42.857 13.93 0.00 42.55 4.81
1891 3214 5.473846 TCGGATGGTTGCTTTGTAATACAAA 59.526 36.000 16.57 16.57 44.91 2.83
1892 3215 5.004448 TCGGATGGTTGCTTTGTAATACAA 58.996 37.500 1.08 1.08 36.11 2.41
1893 3216 4.580868 TCGGATGGTTGCTTTGTAATACA 58.419 39.130 0.00 0.00 0.00 2.29
1894 3217 5.751243 ATCGGATGGTTGCTTTGTAATAC 57.249 39.130 0.00 0.00 0.00 1.89
1895 3218 6.350103 TGTATCGGATGGTTGCTTTGTAATA 58.650 36.000 0.00 0.00 0.00 0.98
1896 3219 5.189928 TGTATCGGATGGTTGCTTTGTAAT 58.810 37.500 0.00 0.00 0.00 1.89
1897 3220 4.580868 TGTATCGGATGGTTGCTTTGTAA 58.419 39.130 0.00 0.00 0.00 2.41
1898 3221 4.209307 TGTATCGGATGGTTGCTTTGTA 57.791 40.909 0.00 0.00 0.00 2.41
1899 3222 3.066291 TGTATCGGATGGTTGCTTTGT 57.934 42.857 0.00 0.00 0.00 2.83
1900 3223 3.427503 GGTTGTATCGGATGGTTGCTTTG 60.428 47.826 0.00 0.00 0.00 2.77
1901 3224 2.752903 GGTTGTATCGGATGGTTGCTTT 59.247 45.455 0.00 0.00 0.00 3.51
1902 3225 2.290641 TGGTTGTATCGGATGGTTGCTT 60.291 45.455 0.00 0.00 0.00 3.91
1903 3226 1.280710 TGGTTGTATCGGATGGTTGCT 59.719 47.619 0.00 0.00 0.00 3.91
1904 3227 1.745232 TGGTTGTATCGGATGGTTGC 58.255 50.000 0.00 0.00 0.00 4.17
1905 3228 2.095213 CGTTGGTTGTATCGGATGGTTG 59.905 50.000 0.00 0.00 0.00 3.77
1906 3229 2.027929 TCGTTGGTTGTATCGGATGGTT 60.028 45.455 0.00 0.00 0.00 3.67
1907 3230 1.551430 TCGTTGGTTGTATCGGATGGT 59.449 47.619 0.00 0.00 0.00 3.55
1908 3231 2.303163 TCGTTGGTTGTATCGGATGG 57.697 50.000 0.00 0.00 0.00 3.51
1909 3232 3.987868 CCTATCGTTGGTTGTATCGGATG 59.012 47.826 0.00 0.00 0.00 3.51
1910 3233 3.640029 ACCTATCGTTGGTTGTATCGGAT 59.360 43.478 0.00 0.00 33.34 4.18
1911 3234 3.025978 ACCTATCGTTGGTTGTATCGGA 58.974 45.455 0.00 0.00 33.34 4.55
1912 3235 3.120792 CACCTATCGTTGGTTGTATCGG 58.879 50.000 0.00 0.00 35.28 4.18
1913 3236 2.538449 GCACCTATCGTTGGTTGTATCG 59.462 50.000 0.00 0.00 35.28 2.92
1914 3237 3.793559 AGCACCTATCGTTGGTTGTATC 58.206 45.455 0.00 0.00 35.28 2.24
1915 3238 3.906720 AGCACCTATCGTTGGTTGTAT 57.093 42.857 0.00 0.00 35.28 2.29
1916 3239 3.131577 CCTAGCACCTATCGTTGGTTGTA 59.868 47.826 0.00 0.00 35.28 2.41
1917 3240 2.093658 CCTAGCACCTATCGTTGGTTGT 60.094 50.000 0.00 0.00 35.28 3.32
1918 3241 2.550978 CCTAGCACCTATCGTTGGTTG 58.449 52.381 0.00 0.00 35.28 3.77
1919 3242 1.485066 CCCTAGCACCTATCGTTGGTT 59.515 52.381 0.00 0.00 35.28 3.67
1920 3243 1.120530 CCCTAGCACCTATCGTTGGT 58.879 55.000 0.00 0.00 38.53 3.67
1921 3244 0.249911 GCCCTAGCACCTATCGTTGG 60.250 60.000 0.00 0.00 39.53 3.77
1922 3245 0.597637 CGCCCTAGCACCTATCGTTG 60.598 60.000 0.00 0.00 39.83 4.10
1923 3246 1.740285 CGCCCTAGCACCTATCGTT 59.260 57.895 0.00 0.00 39.83 3.85
1924 3247 2.201022 CCGCCCTAGCACCTATCGT 61.201 63.158 0.00 0.00 39.83 3.73
1925 3248 1.461091 TTCCGCCCTAGCACCTATCG 61.461 60.000 0.00 0.00 39.83 2.92
1926 3249 0.318762 CTTCCGCCCTAGCACCTATC 59.681 60.000 0.00 0.00 39.83 2.08
1927 3250 1.759459 GCTTCCGCCCTAGCACCTAT 61.759 60.000 0.00 0.00 39.83 2.57
1928 3251 2.432300 GCTTCCGCCCTAGCACCTA 61.432 63.158 0.00 0.00 39.83 3.08
1929 3252 3.787001 GCTTCCGCCCTAGCACCT 61.787 66.667 0.00 0.00 39.83 4.00
1930 3253 4.096003 TGCTTCCGCCCTAGCACC 62.096 66.667 0.00 0.00 42.12 5.01
1931 3254 2.512515 CTGCTTCCGCCCTAGCAC 60.513 66.667 0.00 0.00 42.12 4.40
1932 3255 4.473520 GCTGCTTCCGCCCTAGCA 62.474 66.667 0.00 0.00 44.58 3.49
1933 3256 4.473520 TGCTGCTTCCGCCCTAGC 62.474 66.667 0.00 0.00 37.89 3.42
1934 3257 2.512515 GTGCTGCTTCCGCCCTAG 60.513 66.667 0.00 0.00 34.43 3.02
1935 3258 2.196997 ATTGTGCTGCTTCCGCCCTA 62.197 55.000 0.00 0.00 34.43 3.53
1936 3259 3.574074 ATTGTGCTGCTTCCGCCCT 62.574 57.895 0.00 0.00 34.43 5.19
1937 3260 2.548127 GAATTGTGCTGCTTCCGCCC 62.548 60.000 0.00 0.00 34.43 6.13
1938 3261 1.153958 GAATTGTGCTGCTTCCGCC 60.154 57.895 0.00 0.00 34.43 6.13
1939 3262 0.171903 ATGAATTGTGCTGCTTCCGC 59.828 50.000 0.00 0.00 0.00 5.54
1940 3263 1.468565 CCATGAATTGTGCTGCTTCCG 60.469 52.381 0.00 0.00 0.00 4.30
1941 3264 1.547372 ACCATGAATTGTGCTGCTTCC 59.453 47.619 0.00 0.00 0.00 3.46
1942 3265 4.644103 ATACCATGAATTGTGCTGCTTC 57.356 40.909 0.00 0.00 0.00 3.86
1943 3266 4.035558 CGTATACCATGAATTGTGCTGCTT 59.964 41.667 0.00 0.00 0.00 3.91
1944 3267 3.561310 CGTATACCATGAATTGTGCTGCT 59.439 43.478 0.00 0.00 0.00 4.24
1945 3268 3.312421 ACGTATACCATGAATTGTGCTGC 59.688 43.478 0.00 0.00 0.00 5.25
1946 3269 5.064579 TCAACGTATACCATGAATTGTGCTG 59.935 40.000 0.00 0.00 0.00 4.41
1947 3270 5.064707 GTCAACGTATACCATGAATTGTGCT 59.935 40.000 6.78 0.00 0.00 4.40
1948 3271 5.263185 GTCAACGTATACCATGAATTGTGC 58.737 41.667 6.78 0.00 0.00 4.57
1949 3272 5.220777 GGGTCAACGTATACCATGAATTGTG 60.221 44.000 18.09 0.00 37.51 3.33
1950 3273 4.879545 GGGTCAACGTATACCATGAATTGT 59.120 41.667 18.09 0.00 37.51 2.71
1999 3322 4.688879 GTGTTGTACCTGTCGATCATTCAA 59.311 41.667 0.00 0.00 0.00 2.69
2063 3386 2.907042 AGCAGCTTACTAAGGTCCACTT 59.093 45.455 0.00 0.00 43.28 3.16
2096 3419 4.018490 AGCATGGCAAACAATATCAGTGA 58.982 39.130 0.00 0.00 0.00 3.41
2286 3609 4.834496 TCAAGCAAGTCATCCCATTTCTTT 59.166 37.500 0.00 0.00 0.00 2.52
2361 3684 1.270907 AATCTGTCTCTCCGCCTTGT 58.729 50.000 0.00 0.00 0.00 3.16
2366 3689 2.123342 CGATGAAATCTGTCTCTCCGC 58.877 52.381 0.00 0.00 42.58 5.54
2460 3783 8.995220 TCCAAATATGCGGTTATTTAGTATGAC 58.005 33.333 0.00 0.00 32.02 3.06
2686 4014 2.544721 TGCCACTCAGATCCTCTTCTT 58.455 47.619 0.00 0.00 0.00 2.52
2783 4111 0.941463 CTATGTCGCAGTCGGCCATC 60.941 60.000 2.24 0.00 40.09 3.51
3074 4402 6.321181 TCATATTGATTTTTACTGTCCCTGCC 59.679 38.462 0.00 0.00 0.00 4.85
3140 4468 2.436417 GCAAGTGCTGGGACAAGAATA 58.564 47.619 0.00 0.00 38.70 1.75
3203 4531 5.573380 AGCATACATCCAACATACTCCAT 57.427 39.130 0.00 0.00 0.00 3.41
3205 4533 5.368145 TCAAGCATACATCCAACATACTCC 58.632 41.667 0.00 0.00 0.00 3.85
3206 4534 7.502120 AATCAAGCATACATCCAACATACTC 57.498 36.000 0.00 0.00 0.00 2.59
3207 4535 7.445402 GGTAATCAAGCATACATCCAACATACT 59.555 37.037 0.00 0.00 0.00 2.12
3287 4615 6.374333 GCACTCTGAAACCCATAAATCTTACA 59.626 38.462 0.00 0.00 0.00 2.41
3293 4621 4.666512 AGTGCACTCTGAAACCCATAAAT 58.333 39.130 15.25 0.00 0.00 1.40
3294 4622 4.098914 AGTGCACTCTGAAACCCATAAA 57.901 40.909 15.25 0.00 0.00 1.40
3345 4707 2.375014 TTTTTCCTCGGCCTTTTCCT 57.625 45.000 0.00 0.00 0.00 3.36
3666 5046 6.598850 TCTGAGATGTGCACAATATAGCAAAA 59.401 34.615 25.72 5.18 43.20 2.44
3800 5189 4.202441 GCCAATAGAGAAATCTTCAGCCA 58.798 43.478 0.00 0.00 0.00 4.75
3926 5319 8.271458 TGTATATATTCACACTCACCCAACATT 58.729 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.