Multiple sequence alignment - TraesCS4D01G245500

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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 TraesCS4D01G245500 chr4D 100.000 8797 0 0 1 8797 414159117 414150321 0.000000e+00 16246.0
1 TraesCS4D01G245500 chr4D 95.745 47 2 0 544 590 469582318 469582364 9.470000e-10 76.8
2 TraesCS4D01G245500 chr4A 97.002 6270 127 21 1924 8146 49253862 49260117 0.000000e+00 10480.0
3 TraesCS4D01G245500 chr4A 93.213 943 37 13 772 1702 49252483 49253410 0.000000e+00 1362.0
4 TraesCS4D01G245500 chr4A 82.014 278 37 7 5274 5544 705177769 705178040 3.200000e-54 224.0
5 TraesCS4D01G245500 chr4A 93.846 130 8 0 8630 8759 49260145 49260274 6.970000e-46 196.0
6 TraesCS4D01G245500 chr4A 75.413 545 58 33 54 534 49251745 49252277 2.510000e-45 195.0
7 TraesCS4D01G245500 chr4A 81.013 237 24 6 581 815 49252277 49252494 1.520000e-37 169.0
8 TraesCS4D01G245500 chr4A 91.139 79 7 0 1849 1927 49253577 49253655 3.360000e-19 108.0
9 TraesCS4D01G245500 chr4A 96.296 54 2 0 1697 1750 49253468 49253521 1.220000e-13 89.8
10 TraesCS4D01G245500 chr4A 95.652 46 2 0 8568 8613 49260101 49260146 3.410000e-09 75.0
11 TraesCS4D01G245500 chr4A 87.097 62 5 3 524 582 125379917 125379978 5.700000e-07 67.6
12 TraesCS4D01G245500 chr4B 93.179 1818 61 15 1924 3707 510315175 510313387 0.000000e+00 2612.0
13 TraesCS4D01G245500 chr4B 92.149 1554 63 30 102 1615 510317478 510315944 0.000000e+00 2139.0
14 TraesCS4D01G245500 chr4B 93.106 1233 65 9 6931 8146 510310131 510308902 0.000000e+00 1788.0
15 TraesCS4D01G245500 chr4B 88.244 1412 100 20 5554 6921 510311564 510310175 0.000000e+00 1628.0
16 TraesCS4D01G245500 chr4B 88.235 765 48 21 3706 4429 510313227 510312464 0.000000e+00 876.0
17 TraesCS4D01G245500 chr4B 92.932 382 27 0 4424 4805 510312438 510312057 2.770000e-154 556.0
18 TraesCS4D01G245500 chr4B 94.760 229 8 4 1700 1926 510315621 510315395 3.910000e-93 353.0
19 TraesCS4D01G245500 chr4B 91.667 252 17 2 4853 5102 510311820 510311571 6.540000e-91 346.0
20 TraesCS4D01G245500 chr4B 92.553 188 13 1 8611 8797 510308894 510308707 1.460000e-67 268.0
21 TraesCS4D01G245500 chr4B 79.783 277 39 7 6074 6335 493346023 493345749 1.510000e-42 185.0
22 TraesCS4D01G245500 chr4B 93.814 97 5 1 1607 1702 510315778 510315682 2.560000e-30 145.0
23 TraesCS4D01G245500 chr4B 100.000 29 0 0 5111 5139 426969206 426969178 4.000000e-03 54.7
24 TraesCS4D01G245500 chr7D 85.962 520 56 9 7254 7764 58141871 58142382 2.790000e-149 540.0
25 TraesCS4D01G245500 chr7D 80.912 351 47 13 5168 5510 578796696 578797034 8.760000e-65 259.0
26 TraesCS4D01G245500 chr1A 85.000 520 61 9 7254 7764 465247712 465247201 6.090000e-141 512.0
27 TraesCS4D01G245500 chr1A 83.073 384 45 12 5143 5520 36130647 36130278 1.830000e-86 331.0
28 TraesCS4D01G245500 chr2D 85.068 442 57 8 5109 5545 375148700 375149137 8.110000e-120 442.0
29 TraesCS4D01G245500 chr2D 88.843 242 12 8 8173 8400 555550944 555551184 5.200000e-72 283.0
30 TraesCS4D01G245500 chr2D 86.667 150 12 2 8425 8573 555551318 555551460 9.140000e-35 159.0
31 TraesCS4D01G245500 chr2B 84.318 440 58 10 5109 5541 445256858 445257293 3.800000e-113 420.0
32 TraesCS4D01G245500 chr2B 97.468 79 2 0 1804 1882 500741332 500741410 1.540000e-27 135.0
33 TraesCS4D01G245500 chr2B 78.169 142 17 12 5433 5566 331224447 331224312 2.630000e-10 78.7
34 TraesCS4D01G245500 chr2B 94.444 36 1 1 5516 5551 128528893 128528927 4.000000e-03 54.7
35 TraesCS4D01G245500 chr2B 94.444 36 1 1 5516 5551 694002591 694002557 4.000000e-03 54.7
36 TraesCS4D01G245500 chr1D 83.420 386 45 12 5142 5520 36602736 36602363 3.040000e-89 340.0
37 TraesCS4D01G245500 chr1D 95.745 47 1 1 546 592 84780974 84780929 3.410000e-09 75.0
38 TraesCS4D01G245500 chr6A 78.889 450 62 17 5106 5547 74236588 74236164 3.130000e-69 274.0
39 TraesCS4D01G245500 chr6A 86.667 75 3 6 519 590 605786385 605786455 9.470000e-10 76.8
40 TraesCS4D01G245500 chr7B 79.512 410 59 16 5106 5510 642755243 642755632 1.460000e-67 268.0
41 TraesCS4D01G245500 chr7B 96.203 79 3 0 1804 1882 52962130 52962208 7.170000e-26 130.0
42 TraesCS4D01G245500 chr7B 94.286 35 2 0 5106 5140 409503041 409503075 4.000000e-03 54.7
43 TraesCS4D01G245500 chr7B 100.000 29 0 0 5111 5139 548323043 548323071 4.000000e-03 54.7
44 TraesCS4D01G245500 chr7B 100.000 29 0 0 5111 5139 687200968 687200996 4.000000e-03 54.7
45 TraesCS4D01G245500 chr5B 83.966 237 28 3 8163 8389 448887606 448887842 1.490000e-52 219.0
46 TraesCS4D01G245500 chr5B 96.203 79 3 0 1804 1882 533059826 533059904 7.170000e-26 130.0
47 TraesCS4D01G245500 chr5B 96.203 79 3 0 1804 1882 713067911 713067989 7.170000e-26 130.0
48 TraesCS4D01G245500 chr5B 96.774 31 1 0 5106 5136 636700159 636700189 1.600000e-02 52.8
49 TraesCS4D01G245500 chr5A 83.544 237 28 5 8163 8393 513714434 513714665 2.490000e-50 211.0
50 TraesCS4D01G245500 chr5D 96.203 79 3 0 1804 1882 3149184 3149106 7.170000e-26 130.0
51 TraesCS4D01G245500 chr1B 96.203 79 3 0 1804 1882 49811390 49811312 7.170000e-26 130.0
52 TraesCS4D01G245500 chr1B 96.203 79 3 0 1804 1882 338906730 338906652 7.170000e-26 130.0
53 TraesCS4D01G245500 chr1B 96.203 79 3 0 1804 1882 683719836 683719914 7.170000e-26 130.0
54 TraesCS4D01G245500 chr3D 83.571 140 14 9 5150 5286 341490840 341490973 1.200000e-23 122.0
55 TraesCS4D01G245500 chr3D 97.727 44 1 0 544 587 133521059 133521016 9.470000e-10 76.8
56 TraesCS4D01G245500 chr3D 97.778 45 0 1 544 588 464128322 464128365 9.470000e-10 76.8
57 TraesCS4D01G245500 chr3A 79.670 182 27 9 5109 5286 461843853 461843678 1.200000e-23 122.0
58 TraesCS4D01G245500 chr6B 97.826 46 1 0 544 589 64927002 64926957 7.320000e-11 80.5
59 TraesCS4D01G245500 chr6B 100.000 30 0 0 5111 5140 631921498 631921469 1.000000e-03 56.5
60 TraesCS4D01G245500 chr6B 100.000 28 0 0 265 292 718482167 718482140 1.600000e-02 52.8
61 TraesCS4D01G245500 chr7A 94.000 50 2 1 544 593 181833248 181833200 3.410000e-09 75.0
62 TraesCS4D01G245500 chr3B 97.059 34 1 0 5515 5548 249991084 249991051 3.430000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G245500 chr4D 414150321 414159117 8796 True 16246.00 16246 100.00000 1 8797 1 chr4D.!!$R1 8796
1 TraesCS4D01G245500 chr4A 49251745 49260274 8529 False 1584.35 10480 90.44675 54 8759 8 chr4A.!!$F3 8705
2 TraesCS4D01G245500 chr4B 510308707 510317478 8771 True 1071.10 2612 92.06390 102 8797 10 chr4B.!!$R3 8695
3 TraesCS4D01G245500 chr7D 58141871 58142382 511 False 540.00 540 85.96200 7254 7764 1 chr7D.!!$F1 510
4 TraesCS4D01G245500 chr1A 465247201 465247712 511 True 512.00 512 85.00000 7254 7764 1 chr1A.!!$R2 510
5 TraesCS4D01G245500 chr2D 555550944 555551460 516 False 221.00 283 87.75500 8173 8573 2 chr2D.!!$F2 400

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
968 1140 1.697297 CCCCCTGCACCAAATACCT 59.303 57.895 0.00 0.0 0.00 3.08 F
1845 2332 0.036858 GAGACTCGCTTGGAAAGGCT 60.037 55.000 0.00 0.0 46.35 4.58 F
2268 2978 0.329261 ATGCTGGCAGGCAAGAGTAA 59.671 50.000 17.64 0.0 45.68 2.24 F
2492 3202 4.528987 TGCAGGTACTTGTAACTACATCCA 59.471 41.667 6.86 0.0 34.60 3.41 F
3417 4155 0.877743 GAAAGACAGACTGGGCAAGC 59.122 55.000 7.51 0.0 0.00 4.01 F
3828 4732 1.375396 CTGCGTCCGATGTTTCCCA 60.375 57.895 0.00 0.0 0.00 4.37 F
4012 4916 1.546961 CTAGGTCTCTCCGGTTGTGT 58.453 55.000 0.00 0.0 41.99 3.72 F
5310 6477 0.674895 GCATCACCAGAGGACCACAC 60.675 60.000 0.00 0.0 0.00 3.82 F
6554 7768 1.510383 CTCAGTCTCCTGGTCGCAG 59.490 63.158 0.00 0.0 39.31 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2702 0.245539 CTTTTCCTAGGGACGCGTCA 59.754 55.000 37.26 18.77 0.00 4.35 R
2927 3640 1.399727 GGTGGCAATTCGAAGTGAACG 60.400 52.381 28.12 2.97 40.00 3.95 R
3352 4089 4.321974 CCTGGAACATTGGCTTTTACCTTC 60.322 45.833 0.00 0.00 38.20 3.46 R
3828 4732 4.520179 AGAACAAGTTACCTGTTCCGTTT 58.480 39.130 19.50 2.66 41.85 3.60 R
4536 5512 0.034337 GTCTTGAACCTACGGTGCCA 59.966 55.000 0.00 0.00 35.34 4.92 R
5159 6326 1.758783 CAGTGTTTTTGCCTTCTCGC 58.241 50.000 0.00 0.00 0.00 5.03 R
5725 6903 2.325583 GTGTCAAACACCACCTGAGA 57.674 50.000 0.00 0.00 43.05 3.27 R
6629 7844 0.874390 GTTGCGTTCTTCATCTGGCA 59.126 50.000 0.00 0.00 0.00 4.92 R
8395 9673 0.036388 GTAGGCTGTTGCTGCTACCA 60.036 55.000 11.51 0.00 39.59 3.25 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
42 43 7.772721 TTTTTCAAAATGCGTGAAACTTTTG 57.227 28.000 0.00 0.00 42.98 2.44
43 44 6.473397 TTTCAAAATGCGTGAAACTTTTGT 57.527 29.167 0.00 0.00 39.46 2.83
44 45 5.447478 TCAAAATGCGTGAAACTTTTGTG 57.553 34.783 0.00 0.00 38.86 3.33
45 46 5.164233 TCAAAATGCGTGAAACTTTTGTGA 58.836 33.333 0.00 0.00 38.86 3.58
46 47 5.635280 TCAAAATGCGTGAAACTTTTGTGAA 59.365 32.000 0.00 0.00 38.86 3.18
47 48 6.312426 TCAAAATGCGTGAAACTTTTGTGAAT 59.688 30.769 0.00 0.00 38.86 2.57
48 49 6.660887 AAATGCGTGAAACTTTTGTGAATT 57.339 29.167 0.00 0.00 31.75 2.17
49 50 6.660887 AATGCGTGAAACTTTTGTGAATTT 57.339 29.167 0.00 0.00 31.75 1.82
50 51 5.694674 TGCGTGAAACTTTTGTGAATTTC 57.305 34.783 0.00 0.00 31.75 2.17
51 52 5.164233 TGCGTGAAACTTTTGTGAATTTCA 58.836 33.333 0.00 0.00 38.42 2.69
52 53 5.809562 TGCGTGAAACTTTTGTGAATTTCAT 59.190 32.000 1.78 0.00 41.64 2.57
53 54 6.312426 TGCGTGAAACTTTTGTGAATTTCATT 59.688 30.769 1.78 0.00 41.64 2.57
54 55 7.148507 TGCGTGAAACTTTTGTGAATTTCATTT 60.149 29.630 1.78 0.00 41.64 2.32
55 56 7.691877 GCGTGAAACTTTTGTGAATTTCATTTT 59.308 29.630 1.78 0.00 41.64 1.82
56 57 9.540431 CGTGAAACTTTTGTGAATTTCATTTTT 57.460 25.926 1.78 0.00 41.64 1.94
574 712 9.585099 TTAAACGCTCTTATATTTCTTTACGGA 57.415 29.630 0.00 0.00 0.00 4.69
575 713 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
576 714 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
577 715 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
588 726 2.610438 TACGGAGGGAGTAGGTGTTT 57.390 50.000 0.00 0.00 0.00 2.83
599 737 4.281182 GGAGTAGGTGTTTTCTGAGACTGA 59.719 45.833 0.00 0.00 0.00 3.41
968 1140 1.697297 CCCCCTGCACCAAATACCT 59.303 57.895 0.00 0.00 0.00 3.08
1041 1213 2.914289 GCCTCAGCTATGGGCAGT 59.086 61.111 15.88 0.00 44.79 4.40
1145 1317 4.329545 GGACAAGGTCAGCCGCCA 62.330 66.667 0.00 0.00 40.50 5.69
1182 1357 2.124901 CCATTCCGGCAAGGCGTA 60.125 61.111 14.89 3.13 40.77 4.42
1195 1370 2.156102 AGGCGTAGTAAACCCTAGCT 57.844 50.000 0.00 0.00 29.79 3.32
1224 1408 1.457455 ACCTGGTTTGGGTGCTTGG 60.457 57.895 0.00 0.00 35.51 3.61
1396 1580 4.381079 GGCTGTTGTGTTTTGTGGTTTCTA 60.381 41.667 0.00 0.00 0.00 2.10
1403 1587 3.065648 TGTTTTGTGGTTTCTACGCCTTC 59.934 43.478 0.00 0.00 0.00 3.46
1404 1588 1.504359 TTGTGGTTTCTACGCCTTCG 58.496 50.000 0.00 0.00 42.43 3.79
1423 1607 1.268794 CGTTGCGTTGGATTTGTGGAA 60.269 47.619 0.00 0.00 0.00 3.53
1449 1633 3.572584 CAGGGCCGTTAGTATAATCGAC 58.427 50.000 0.00 0.00 0.00 4.20
1456 1640 4.980434 CCGTTAGTATAATCGACTGGGTTG 59.020 45.833 0.00 0.00 0.00 3.77
1567 1751 8.524870 TCTCTATAAGGTTCGTGTTGTAAAAC 57.475 34.615 0.00 0.00 0.00 2.43
1568 1752 8.362639 TCTCTATAAGGTTCGTGTTGTAAAACT 58.637 33.333 0.00 0.00 0.00 2.66
1597 1781 0.698818 AAGGGACCTAGTTGCTTGGG 59.301 55.000 0.00 0.00 30.92 4.12
1686 2046 7.260603 AGTGCATATAAAGAAGCAATTTCACC 58.739 34.615 0.00 0.00 38.91 4.02
1805 2292 1.607628 GCATCTGCCCTGCTTTAGATG 59.392 52.381 0.00 0.00 45.75 2.90
1845 2332 0.036858 GAGACTCGCTTGGAAAGGCT 60.037 55.000 0.00 0.00 46.35 4.58
1992 2702 2.113986 GGTCAAGGCACCTGCTGT 59.886 61.111 0.00 0.00 41.70 4.40
2019 2729 2.093658 GTCCCTAGGAAAAGACGCATGA 60.094 50.000 11.48 0.00 31.38 3.07
2032 2742 1.203928 CGCATGATGACGAAGACTCC 58.796 55.000 0.00 0.00 0.00 3.85
2035 2745 2.819115 CATGATGACGAAGACTCCTGG 58.181 52.381 0.00 0.00 0.00 4.45
2079 2789 3.649981 AGTCCTGGGTCCTGATCATTATG 59.350 47.826 0.00 0.00 0.00 1.90
2129 2839 9.356433 TGTTGCAGAATCACACATAAAAATATG 57.644 29.630 0.00 0.00 0.00 1.78
2192 2902 5.769662 AGTGGTGCATGAGTCTTAATTTGAA 59.230 36.000 0.00 0.00 0.00 2.69
2238 2948 5.731126 GCAATGTGCCCATATTTTGATTTGC 60.731 40.000 0.00 0.00 37.42 3.68
2268 2978 0.329261 ATGCTGGCAGGCAAGAGTAA 59.671 50.000 17.64 0.00 45.68 2.24
2492 3202 4.528987 TGCAGGTACTTGTAACTACATCCA 59.471 41.667 6.86 0.00 34.60 3.41
2874 3587 9.137459 TCTTCTAGATAGTCATTTCTACTTGGG 57.863 37.037 0.00 0.00 0.00 4.12
2924 3637 4.987912 GTGTGTTGGAATATTTGGTTGGTG 59.012 41.667 0.00 0.00 0.00 4.17
2927 3640 5.694458 GTGTTGGAATATTTGGTTGGTGTTC 59.306 40.000 0.00 0.00 0.00 3.18
3143 3880 4.657039 AGGGATTGGAAATTCATGGGAATG 59.343 41.667 0.00 0.00 42.87 2.67
3151 3888 7.059156 TGGAAATTCATGGGAATGTTGTTTTT 58.941 30.769 0.00 0.00 42.87 1.94
3352 4089 7.933396 TGTATGCCAAATGTTTCATATGAGAG 58.067 34.615 5.39 0.00 0.00 3.20
3417 4155 0.877743 GAAAGACAGACTGGGCAAGC 59.122 55.000 7.51 0.00 0.00 4.01
3828 4732 1.375396 CTGCGTCCGATGTTTCCCA 60.375 57.895 0.00 0.00 0.00 4.37
3922 4826 8.585018 ACCCTTATTTCAACCATAAAGAAACAG 58.415 33.333 0.00 0.00 34.47 3.16
4012 4916 1.546961 CTAGGTCTCTCCGGTTGTGT 58.453 55.000 0.00 0.00 41.99 3.72
4027 4931 4.911610 CGGTTGTGTTTGAGCTTCTAAATG 59.088 41.667 0.00 0.00 0.00 2.32
4029 4933 6.293190 CGGTTGTGTTTGAGCTTCTAAATGTA 60.293 38.462 0.00 0.00 0.00 2.29
4122 5030 7.875971 AGCTTCGTTCTGTAGATTTTGATTTT 58.124 30.769 0.00 0.00 0.00 1.82
4154 5062 5.134339 TGGAATATGCTCCTCCAGGTTAAAT 59.866 40.000 0.00 0.00 34.26 1.40
4156 5064 7.147213 TGGAATATGCTCCTCCAGGTTAAATTA 60.147 37.037 0.00 0.00 34.26 1.40
4158 5066 9.301897 GAATATGCTCCTCCAGGTTAAATTATT 57.698 33.333 0.00 0.00 36.34 1.40
4210 5138 7.792374 AGATGACGCTAATACATGAATTTGT 57.208 32.000 0.00 0.00 0.00 2.83
4536 5512 9.066892 TCTGCACAATCTAAAAAGTATGTTCTT 57.933 29.630 0.00 0.00 0.00 2.52
4648 5624 8.630054 TGGAGCATAACACAGTTTAAATAACT 57.370 30.769 0.00 0.00 0.00 2.24
4695 5671 9.109393 TCTGTAGCTTGGTAATGTATTTGATTC 57.891 33.333 0.00 0.00 0.00 2.52
5144 6311 6.781014 AGTAGATGATGTAAAATAGACCGGGA 59.219 38.462 6.32 0.00 0.00 5.14
5159 6326 1.735571 CCGGGACCACTTTTTACATCG 59.264 52.381 0.00 0.00 0.00 3.84
5244 6411 1.263217 GGCGTGATGTAAAATAGGCCG 59.737 52.381 0.00 0.00 34.86 6.13
5310 6477 0.674895 GCATCACCAGAGGACCACAC 60.675 60.000 0.00 0.00 0.00 3.82
5787 6969 6.021030 TCTACCATAAGTACCTTTCTGTGGT 58.979 40.000 0.00 0.00 41.28 4.16
5811 6993 6.561737 AGTCTTAGCTGCCTTTAAGTTTTC 57.438 37.500 0.00 0.00 0.00 2.29
6049 7235 3.378427 GCAGAACACTGAAAAGAGTGGTT 59.622 43.478 0.00 0.00 44.18 3.67
6210 7406 7.606839 CCGTACAGATATAAGGTCTATGTCTCA 59.393 40.741 0.00 0.00 0.00 3.27
6554 7768 1.510383 CTCAGTCTCCTGGTCGCAG 59.490 63.158 0.00 0.00 39.31 5.18
6629 7844 1.003355 CATGTGTTCTGGAGGGCGT 60.003 57.895 0.00 0.00 0.00 5.68
6679 7894 1.691976 ACCCACGTCTTTCACATGAGA 59.308 47.619 0.00 0.00 0.00 3.27
6716 7931 0.673333 CGTGTCACCCAGCAATAGCA 60.673 55.000 0.00 0.00 45.49 3.49
7023 8272 0.107410 TGGCAGTCAACGGTTCAACT 60.107 50.000 0.00 0.00 0.00 3.16
7041 8290 8.262933 GGTTCAACTCTATAACCTAGCCTTTAA 58.737 37.037 0.00 0.00 39.66 1.52
7223 8472 4.910195 TCAGGTATGCTTTCAAGTGTCAT 58.090 39.130 0.00 0.00 0.00 3.06
7306 8555 9.743057 TCCAATGTAAAGTTTCAGTGTTTAATG 57.257 29.630 11.67 0.00 0.00 1.90
7318 8567 7.581213 TCAGTGTTTAATGTTCTTGGTGATT 57.419 32.000 0.00 0.00 0.00 2.57
7453 8703 9.388506 CAAACAAGAAGAGATTGTATCAGGTAT 57.611 33.333 0.00 0.00 39.91 2.73
7486 8737 5.997385 AGTTTTGCTTTGGTAGTACGATTG 58.003 37.500 0.00 0.00 0.00 2.67
7510 8761 0.188342 AAGTGGCCTGGGTGTTCATT 59.812 50.000 3.32 0.00 0.00 2.57
7608 8866 4.139786 CTGTGGCATCAAGCTATGGTTAT 58.860 43.478 0.00 0.00 44.79 1.89
8142 9410 3.334583 AAAGAGGCTAAATCTGTCGCA 57.665 42.857 0.00 0.00 0.00 5.10
8143 9411 2.301577 AGAGGCTAAATCTGTCGCAC 57.698 50.000 0.00 0.00 0.00 5.34
8144 9412 1.827969 AGAGGCTAAATCTGTCGCACT 59.172 47.619 0.00 0.00 0.00 4.40
8145 9413 2.234908 AGAGGCTAAATCTGTCGCACTT 59.765 45.455 0.00 0.00 0.00 3.16
8146 9414 3.003480 GAGGCTAAATCTGTCGCACTTT 58.997 45.455 0.00 0.00 0.00 2.66
8147 9415 3.412386 AGGCTAAATCTGTCGCACTTTT 58.588 40.909 0.00 0.00 0.00 2.27
8148 9416 3.821033 AGGCTAAATCTGTCGCACTTTTT 59.179 39.130 0.00 0.00 0.00 1.94
8168 9436 5.923733 TTTTTGTGTGAATACAAGGGTGT 57.076 34.783 0.00 0.00 41.18 4.16
8169 9437 4.909696 TTTGTGTGAATACAAGGGTGTG 57.090 40.909 0.00 0.00 41.18 3.82
8170 9438 3.569194 TGTGTGAATACAAGGGTGTGT 57.431 42.857 0.00 0.00 38.82 3.72
8171 9439 3.892284 TGTGTGAATACAAGGGTGTGTT 58.108 40.909 0.00 0.00 41.31 3.32
8192 9460 2.698803 TGGTTCATGTCCTCGTCATTG 58.301 47.619 10.06 0.00 0.00 2.82
8200 9468 0.745486 TCCTCGTCATTGCATGCCTG 60.745 55.000 16.68 12.98 0.00 4.85
8220 9488 0.964358 GCCTGAGCTGTGCCTGAAAT 60.964 55.000 0.00 0.00 35.50 2.17
8234 9502 3.737047 GCCTGAAATGTGCCTGATGATTG 60.737 47.826 0.00 0.00 0.00 2.67
8248 9516 3.119531 TGATGATTGTTTGGTTCGCATCC 60.120 43.478 0.00 0.00 32.01 3.51
8256 9524 2.787473 TGGTTCGCATCCTGAGAAAT 57.213 45.000 0.00 0.00 37.88 2.17
8258 9526 3.531538 TGGTTCGCATCCTGAGAAATAC 58.468 45.455 0.00 0.00 37.88 1.89
8259 9527 2.872858 GGTTCGCATCCTGAGAAATACC 59.127 50.000 0.00 0.00 37.88 2.73
8284 9558 3.319198 CCTGGCCGTGGTGGTACT 61.319 66.667 0.00 0.00 41.21 2.73
8301 9575 0.254178 ACTGTGATTAGCCTGGCCAG 59.746 55.000 26.87 26.87 0.00 4.85
8335 9613 6.590234 AATTGAAAAAGTACTTAGCCCAGG 57.410 37.500 8.92 0.00 0.00 4.45
8339 9617 1.657804 AAGTACTTAGCCCAGGCAGT 58.342 50.000 12.03 9.08 44.88 4.40
8426 9806 7.545615 GCAGCAACAGCCTACTATTTAAAAATT 59.454 33.333 0.00 0.00 0.00 1.82
8427 9807 9.076596 CAGCAACAGCCTACTATTTAAAAATTC 57.923 33.333 0.00 0.00 0.00 2.17
8428 9808 9.025041 AGCAACAGCCTACTATTTAAAAATTCT 57.975 29.630 0.00 0.00 0.00 2.40
8446 9837 7.617041 AAATTCTATAAGCACTGACAGGAAC 57.383 36.000 7.51 0.00 0.00 3.62
8490 9881 3.030668 CCTGACCAGGCACAATTTTTC 57.969 47.619 2.75 0.00 42.44 2.29
8500 9891 4.020839 AGGCACAATTTTTCTTCATCCCAG 60.021 41.667 0.00 0.00 0.00 4.45
8504 9895 2.286365 TTTTTCTTCATCCCAGGCGT 57.714 45.000 0.00 0.00 0.00 5.68
8511 9903 4.115199 ATCCCAGGCGTTCCCAGC 62.115 66.667 0.00 0.00 35.39 4.85
8535 9927 4.955811 TCACTTTTTCTCAGGCAGAGTA 57.044 40.909 6.81 0.00 44.98 2.59
8536 9928 5.290493 TCACTTTTTCTCAGGCAGAGTAA 57.710 39.130 6.81 0.73 44.98 2.24
8537 9929 5.057149 TCACTTTTTCTCAGGCAGAGTAAC 58.943 41.667 6.81 0.00 44.98 2.50
8538 9930 4.214332 CACTTTTTCTCAGGCAGAGTAACC 59.786 45.833 6.81 0.00 44.98 2.85
8539 9931 4.141482 ACTTTTTCTCAGGCAGAGTAACCA 60.141 41.667 6.81 0.00 44.98 3.67
8540 9932 3.402628 TTTCTCAGGCAGAGTAACCAC 57.597 47.619 6.81 0.00 44.98 4.16
8541 9933 2.310779 TCTCAGGCAGAGTAACCACT 57.689 50.000 6.81 0.00 44.98 4.00
8557 9949 2.437897 CTGCCCAGGCCTTCAACT 59.562 61.111 0.00 0.00 41.09 3.16
8569 9961 4.347000 AGGCCTTCAACTAAACACACTCTA 59.653 41.667 0.00 0.00 0.00 2.43
8573 9965 7.298854 GCCTTCAACTAAACACACTCTAAATC 58.701 38.462 0.00 0.00 0.00 2.17
8574 9966 7.173390 GCCTTCAACTAAACACACTCTAAATCT 59.827 37.037 0.00 0.00 0.00 2.40
8575 9967 8.499162 CCTTCAACTAAACACACTCTAAATCTG 58.501 37.037 0.00 0.00 0.00 2.90
8576 9968 8.958119 TTCAACTAAACACACTCTAAATCTGT 57.042 30.769 0.00 0.00 0.00 3.41
8577 9969 8.589335 TCAACTAAACACACTCTAAATCTGTC 57.411 34.615 0.00 0.00 0.00 3.51
8578 9970 7.381408 TCAACTAAACACACTCTAAATCTGTCG 59.619 37.037 0.00 0.00 0.00 4.35
8579 9971 4.992381 AAACACACTCTAAATCTGTCGC 57.008 40.909 0.00 0.00 0.00 5.19
8613 10005 2.346545 GTGCTAATTTGACCGGACGTAC 59.653 50.000 9.46 0.00 0.00 3.67
8614 10006 1.585214 GCTAATTTGACCGGACGTACG 59.415 52.381 14.78 14.78 0.00 3.67
8615 10007 1.585214 CTAATTTGACCGGACGTACGC 59.415 52.381 16.58 2.10 0.00 4.42
8616 10008 0.319727 AATTTGACCGGACGTACGCA 60.320 50.000 16.58 5.36 0.00 5.24
8617 10009 1.010419 ATTTGACCGGACGTACGCAC 61.010 55.000 16.58 11.25 0.00 5.34
8618 10010 2.347242 TTTGACCGGACGTACGCACA 62.347 55.000 16.58 13.93 0.00 4.57
8619 10011 2.050168 GACCGGACGTACGCACAA 60.050 61.111 16.58 0.00 0.00 3.33
8620 10012 1.661197 GACCGGACGTACGCACAAA 60.661 57.895 16.58 0.00 0.00 2.83
8621 10013 1.214373 GACCGGACGTACGCACAAAA 61.214 55.000 16.58 0.00 0.00 2.44
8622 10014 0.600782 ACCGGACGTACGCACAAAAT 60.601 50.000 16.58 0.00 0.00 1.82
8623 10015 0.513820 CCGGACGTACGCACAAAATT 59.486 50.000 16.58 0.00 0.00 1.82
8624 10016 1.069771 CCGGACGTACGCACAAAATTT 60.070 47.619 16.58 0.00 0.00 1.82
8625 10017 1.966563 CGGACGTACGCACAAAATTTG 59.033 47.619 16.72 3.89 0.00 2.32
8626 10018 2.348685 CGGACGTACGCACAAAATTTGA 60.349 45.455 16.72 0.00 0.00 2.69
8627 10019 3.619729 GGACGTACGCACAAAATTTGAA 58.380 40.909 16.72 0.00 0.00 2.69
8628 10020 3.419596 GGACGTACGCACAAAATTTGAAC 59.580 43.478 16.72 2.94 0.00 3.18
8629 10021 4.276460 GACGTACGCACAAAATTTGAACT 58.724 39.130 16.72 0.00 0.00 3.01
8630 10022 5.406767 ACGTACGCACAAAATTTGAACTA 57.593 34.783 16.72 0.00 0.00 2.24
8694 10086 0.321671 TAGGAGCTGCCACAACAGAC 59.678 55.000 0.00 0.00 40.25 3.51
8695 10087 1.227943 GGAGCTGCCACAACAGACA 60.228 57.895 0.00 0.00 40.25 3.41
8701 10093 1.002142 CTGCCACAACAGACATGTGTG 60.002 52.381 20.62 20.62 45.23 3.82
8759 10152 7.965655 TGTTGTAATTTATAGTCAAACATGGCG 59.034 33.333 0.00 0.00 0.00 5.69
8762 10155 9.163899 TGTAATTTATAGTCAAACATGGCGTAA 57.836 29.630 0.00 0.00 0.00 3.18
8791 10184 7.441836 TCAACAAGCTCTGTAAGTTAATGAGA 58.558 34.615 14.16 3.55 37.23 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 7.322222 CACAAAAGTTTCACGCATTTTGAAAAA 59.678 29.630 14.21 0.00 42.98 1.94
19 20 6.794158 CACAAAAGTTTCACGCATTTTGAAAA 59.206 30.769 14.21 0.00 42.98 2.29
20 21 6.146184 TCACAAAAGTTTCACGCATTTTGAAA 59.854 30.769 14.21 4.73 42.48 2.69
21 22 5.635280 TCACAAAAGTTTCACGCATTTTGAA 59.365 32.000 14.21 0.00 42.48 2.69
22 23 5.164233 TCACAAAAGTTTCACGCATTTTGA 58.836 33.333 14.21 0.00 42.48 2.69
23 24 5.447478 TCACAAAAGTTTCACGCATTTTG 57.553 34.783 7.49 7.49 44.37 2.44
24 25 6.660887 ATTCACAAAAGTTTCACGCATTTT 57.339 29.167 0.00 0.00 0.00 1.82
25 26 6.660887 AATTCACAAAAGTTTCACGCATTT 57.339 29.167 0.00 0.00 0.00 2.32
26 27 6.312426 TGAAATTCACAAAAGTTTCACGCATT 59.688 30.769 0.00 0.00 36.11 3.56
27 28 5.809562 TGAAATTCACAAAAGTTTCACGCAT 59.190 32.000 0.00 0.00 36.11 4.73
28 29 5.164233 TGAAATTCACAAAAGTTTCACGCA 58.836 33.333 0.00 0.00 36.11 5.24
29 30 5.694674 TGAAATTCACAAAAGTTTCACGC 57.305 34.783 0.00 0.00 36.11 5.34
30 31 9.540431 AAAAATGAAATTCACAAAAGTTTCACG 57.460 25.926 0.00 0.00 41.64 4.35
96 97 9.936759 GGATATGGAAAAGGTTCACAAAATTAA 57.063 29.630 0.00 0.00 35.25 1.40
97 98 8.247562 CGGATATGGAAAAGGTTCACAAAATTA 58.752 33.333 0.00 0.00 35.25 1.40
98 99 7.096551 CGGATATGGAAAAGGTTCACAAAATT 58.903 34.615 0.00 0.00 35.25 1.82
99 100 6.210584 ACGGATATGGAAAAGGTTCACAAAAT 59.789 34.615 0.00 0.00 35.25 1.82
100 101 5.536916 ACGGATATGGAAAAGGTTCACAAAA 59.463 36.000 0.00 0.00 35.25 2.44
101 102 5.048364 CACGGATATGGAAAAGGTTCACAAA 60.048 40.000 0.00 0.00 35.25 2.83
102 103 4.457603 CACGGATATGGAAAAGGTTCACAA 59.542 41.667 0.00 0.00 35.25 3.33
103 104 4.006989 CACGGATATGGAAAAGGTTCACA 58.993 43.478 0.00 0.00 35.25 3.58
104 105 4.258543 TCACGGATATGGAAAAGGTTCAC 58.741 43.478 0.00 0.00 35.25 3.18
105 106 4.561500 TCACGGATATGGAAAAGGTTCA 57.438 40.909 0.00 0.00 35.25 3.18
106 107 6.451064 AAATCACGGATATGGAAAAGGTTC 57.549 37.500 0.00 0.00 0.00 3.62
107 108 6.850752 AAAATCACGGATATGGAAAAGGTT 57.149 33.333 0.00 0.00 0.00 3.50
108 109 6.850752 AAAAATCACGGATATGGAAAAGGT 57.149 33.333 0.00 0.00 0.00 3.50
394 510 8.284557 TGAATGATGTTTGTGAAAGATTTTCG 57.715 30.769 0.00 0.00 0.00 3.46
534 672 3.260884 AGCGTTTAAATCACAGAGGGAGA 59.739 43.478 0.00 0.00 0.00 3.71
566 704 2.454538 ACACCTACTCCCTCCGTAAAG 58.545 52.381 0.00 0.00 0.00 1.85
570 708 1.622312 GAAAACACCTACTCCCTCCGT 59.378 52.381 0.00 0.00 0.00 4.69
571 709 1.900486 AGAAAACACCTACTCCCTCCG 59.100 52.381 0.00 0.00 0.00 4.63
572 710 2.904434 TCAGAAAACACCTACTCCCTCC 59.096 50.000 0.00 0.00 0.00 4.30
573 711 3.833070 TCTCAGAAAACACCTACTCCCTC 59.167 47.826 0.00 0.00 0.00 4.30
574 712 3.579151 GTCTCAGAAAACACCTACTCCCT 59.421 47.826 0.00 0.00 0.00 4.20
575 713 3.579151 AGTCTCAGAAAACACCTACTCCC 59.421 47.826 0.00 0.00 0.00 4.30
576 714 4.281182 TCAGTCTCAGAAAACACCTACTCC 59.719 45.833 0.00 0.00 0.00 3.85
577 715 5.455056 TCAGTCTCAGAAAACACCTACTC 57.545 43.478 0.00 0.00 0.00 2.59
599 737 4.202010 CCATTTGTTGTCGGTCTGAACTTT 60.202 41.667 0.00 0.00 0.00 2.66
745 885 3.014036 CTTCGGCGCGCATGTATT 58.986 55.556 34.42 0.00 0.00 1.89
799 970 1.499007 TGGCCTGGACTTTTCCTCTTT 59.501 47.619 3.32 0.00 43.31 2.52
968 1140 1.280998 GGAGGAAAAGGAATCGGGTCA 59.719 52.381 0.00 0.00 0.00 4.02
1151 1323 1.984288 GAATGGAGGAACGGAGGGGG 61.984 65.000 0.00 0.00 0.00 5.40
1166 1341 0.179094 TACTACGCCTTGCCGGAATG 60.179 55.000 5.05 0.00 33.16 2.67
1167 1342 0.538118 TTACTACGCCTTGCCGGAAT 59.462 50.000 5.05 0.00 33.16 3.01
1182 1357 0.616679 TCGGGCAGCTAGGGTTTACT 60.617 55.000 0.00 0.00 0.00 2.24
1195 1370 1.488705 AAACCAGGTCAGATCGGGCA 61.489 55.000 0.00 0.00 0.00 5.36
1265 1449 0.962855 GAACTCCCCTTTGAGCAGGC 60.963 60.000 0.00 0.00 35.72 4.85
1296 1480 2.341543 CAGCAGTCGAGCACAGGT 59.658 61.111 0.00 0.00 36.85 4.00
1403 1587 0.309302 TCCACAAATCCAACGCAACG 59.691 50.000 0.00 0.00 0.00 4.10
1404 1588 2.500509 TTCCACAAATCCAACGCAAC 57.499 45.000 0.00 0.00 0.00 4.17
1409 1593 3.328505 CTGCCAATTCCACAAATCCAAC 58.671 45.455 0.00 0.00 0.00 3.77
1412 1596 1.207811 CCCTGCCAATTCCACAAATCC 59.792 52.381 0.00 0.00 0.00 3.01
1438 1622 7.005296 AGATCTACAACCCAGTCGATTATACT 58.995 38.462 0.00 0.00 0.00 2.12
1456 1640 3.131396 CCCGTAATGGTTGCAGATCTAC 58.869 50.000 0.00 0.00 35.15 2.59
1471 1655 0.689745 ACAGCCTAGGCATCCCGTAA 60.690 55.000 34.70 0.00 44.88 3.18
1567 1751 6.931840 GCAACTAGGTCCCTTTCATAGATTAG 59.068 42.308 0.00 0.00 0.00 1.73
1568 1752 6.615726 AGCAACTAGGTCCCTTTCATAGATTA 59.384 38.462 0.00 0.00 0.00 1.75
1660 2020 8.405531 GGTGAAATTGCTTCTTTATATGCACTA 58.594 33.333 0.00 0.00 35.01 2.74
1795 2282 3.308832 CCTGTAAACCCCCATCTAAAGCA 60.309 47.826 0.00 0.00 0.00 3.91
1805 2292 0.844660 GGGATCTCCTGTAAACCCCC 59.155 60.000 0.00 0.00 35.95 5.40
1845 2332 9.899661 AGTTAAGTGATAATGTTTGGTATAGCA 57.100 29.630 0.00 0.00 0.00 3.49
1876 2363 6.972328 GCAAACTTAATCACTTCACACTTTCA 59.028 34.615 0.00 0.00 0.00 2.69
1882 2369 7.542890 TCTTTTGCAAACTTAATCACTTCACA 58.457 30.769 12.39 0.00 0.00 3.58
1935 2645 7.976175 GGGATGATCCAATTTTTACTCTTTCAC 59.024 37.037 14.36 0.00 38.64 3.18
1936 2646 7.673504 TGGGATGATCCAATTTTTACTCTTTCA 59.326 33.333 14.36 0.00 38.64 2.69
1992 2702 0.245539 CTTTTCCTAGGGACGCGTCA 59.754 55.000 37.26 18.77 0.00 4.35
2019 2729 1.924731 TGACCAGGAGTCTTCGTCAT 58.075 50.000 0.00 0.00 46.46 3.06
2032 2742 2.704572 GACCCTTGAGATGTTGACCAG 58.295 52.381 0.00 0.00 0.00 4.00
2035 2745 2.743636 TCGACCCTTGAGATGTTGAC 57.256 50.000 0.00 0.00 0.00 3.18
2079 2789 8.893727 ACAAGGTCTAATCAGCATACAATTTAC 58.106 33.333 0.00 0.00 0.00 2.01
2129 2839 4.086457 ACTGGACAATTTTCCCACCATAC 58.914 43.478 8.17 0.00 34.33 2.39
2192 2902 4.806247 GCTCGTAAGTCTTACATGAAGCAT 59.194 41.667 20.16 0.00 35.89 3.79
2238 2948 2.416836 CCTGCCAGCATTCAATTGACAG 60.417 50.000 7.89 9.99 0.00 3.51
2268 2978 5.932303 ACAACATTCAGCTTAGTAATGTCGT 59.068 36.000 11.72 6.43 41.67 4.34
2280 2990 5.518848 TGATTCACAAACAACATTCAGCT 57.481 34.783 0.00 0.00 0.00 4.24
2281 2991 6.586868 TTTGATTCACAAACAACATTCAGC 57.413 33.333 0.00 0.00 42.57 4.26
2492 3202 3.665745 AAACGCAAGAGCAATCCAATT 57.334 38.095 0.00 0.00 42.27 2.32
2641 3353 6.822667 ACATGAATTCAGTTAGCAATGTGA 57.177 33.333 14.54 0.00 0.00 3.58
2874 3587 6.151144 ACAGGACAAACCAAATCAATACTAGC 59.849 38.462 0.00 0.00 42.04 3.42
2927 3640 1.399727 GGTGGCAATTCGAAGTGAACG 60.400 52.381 28.12 2.97 40.00 3.95
3352 4089 4.321974 CCTGGAACATTGGCTTTTACCTTC 60.322 45.833 0.00 0.00 38.20 3.46
3789 4693 9.632416 ACGCAGCGTGTTTGATATTTCAAAGAT 62.632 37.037 22.28 0.00 44.17 2.40
3828 4732 4.520179 AGAACAAGTTACCTGTTCCGTTT 58.480 39.130 19.50 2.66 41.85 3.60
3922 4826 5.350365 ACCACATGACGATAATGTACACAAC 59.650 40.000 0.00 0.00 36.10 3.32
4122 5030 7.092712 CCTGGAGGAGCATATTCCATAAGATTA 60.093 40.741 0.00 0.00 40.06 1.75
4536 5512 0.034337 GTCTTGAACCTACGGTGCCA 59.966 55.000 0.00 0.00 35.34 4.92
4695 5671 3.822167 GAGGAACGGAGGGAGTAAGATAG 59.178 52.174 0.00 0.00 0.00 2.08
5087 6254 7.014905 TGCTCTAAGGTAGACAGACTTGTTTAA 59.985 37.037 0.00 0.00 37.76 1.52
5099 6266 4.211920 ACTGGAGATGCTCTAAGGTAGAC 58.788 47.826 0.00 0.00 0.00 2.59
5144 6311 3.034721 TCTCGCGATGTAAAAAGTGGT 57.965 42.857 10.36 0.00 0.00 4.16
5159 6326 1.758783 CAGTGTTTTTGCCTTCTCGC 58.241 50.000 0.00 0.00 0.00 5.03
5172 6339 7.568349 TCTAAATCATCTATTGGAGCAGTGTT 58.432 34.615 0.00 0.00 0.00 3.32
5725 6903 2.325583 GTGTCAAACACCACCTGAGA 57.674 50.000 0.00 0.00 43.05 3.27
5787 6969 6.367969 CGAAAACTTAAAGGCAGCTAAGACTA 59.632 38.462 6.86 0.00 0.00 2.59
5811 6993 2.422832 AGCTCCTACGAAGTTCCTAACG 59.577 50.000 0.00 0.00 37.78 3.18
6210 7406 1.907255 GGGCTCAACCTACTGTTACCT 59.093 52.381 0.00 0.00 39.10 3.08
6554 7768 3.134127 GCCAACCGGTGCATCCTC 61.134 66.667 8.52 0.00 33.28 3.71
6629 7844 0.874390 GTTGCGTTCTTCATCTGGCA 59.126 50.000 0.00 0.00 0.00 4.92
6679 7894 2.440796 CAGACCCCGCATTGGCAT 60.441 61.111 0.00 0.00 41.24 4.40
7023 8272 7.570132 TGCACAATTAAAGGCTAGGTTATAGA 58.430 34.615 0.00 0.00 0.00 1.98
7223 8472 1.205655 CTGCCAGACTCAGATTTCCGA 59.794 52.381 0.00 0.00 33.54 4.55
7306 8555 7.454260 AAACCTATGAGAAATCACCAAGAAC 57.546 36.000 0.00 0.00 0.00 3.01
7318 8567 8.367660 ACTGAGAACAGATAAACCTATGAGAA 57.632 34.615 0.00 0.00 46.03 2.87
7360 8609 0.933097 GTGCCGTATCTGCAGACATG 59.067 55.000 20.97 13.64 39.87 3.21
7453 8703 3.826157 CCAAAGCAAAACTATCACCCAGA 59.174 43.478 0.00 0.00 0.00 3.86
7486 8737 1.302832 CACCCAGGCCACTTCAGAC 60.303 63.158 5.01 0.00 0.00 3.51
7510 8761 6.220930 ACTTTGAGTACTGCGATGAAAGTTA 58.779 36.000 0.00 0.00 30.00 2.24
7608 8866 2.011122 ACGGTTTCTCTCCCTCTTCA 57.989 50.000 0.00 0.00 0.00 3.02
7830 9090 2.031120 CCCAAACAACACACCTGATGT 58.969 47.619 0.00 0.00 44.81 3.06
7846 9106 4.019411 TCTCTGCATAATGTCTTGTCCCAA 60.019 41.667 0.00 0.00 0.00 4.12
8146 9414 5.186021 ACACACCCTTGTATTCACACAAAAA 59.814 36.000 0.00 0.00 37.93 1.94
8147 9415 4.707448 ACACACCCTTGTATTCACACAAAA 59.293 37.500 0.00 0.00 37.93 2.44
8148 9416 4.274147 ACACACCCTTGTATTCACACAAA 58.726 39.130 0.00 0.00 37.93 2.83
8149 9417 3.892284 ACACACCCTTGTATTCACACAA 58.108 40.909 0.00 0.00 36.94 3.33
8150 9418 3.569194 ACACACCCTTGTATTCACACA 57.431 42.857 0.00 0.00 33.30 3.72
8151 9419 4.499019 CCAAACACACCCTTGTATTCACAC 60.499 45.833 0.00 0.00 33.30 3.82
8152 9420 3.634448 CCAAACACACCCTTGTATTCACA 59.366 43.478 0.00 0.00 33.30 3.58
8153 9421 3.634910 ACCAAACACACCCTTGTATTCAC 59.365 43.478 0.00 0.00 33.30 3.18
8154 9422 3.904717 ACCAAACACACCCTTGTATTCA 58.095 40.909 0.00 0.00 33.30 2.57
8155 9423 4.339814 TGAACCAAACACACCCTTGTATTC 59.660 41.667 0.00 0.00 33.30 1.75
8156 9424 4.282496 TGAACCAAACACACCCTTGTATT 58.718 39.130 0.00 0.00 33.30 1.89
8157 9425 3.904717 TGAACCAAACACACCCTTGTAT 58.095 40.909 0.00 0.00 33.30 2.29
8158 9426 3.367646 TGAACCAAACACACCCTTGTA 57.632 42.857 0.00 0.00 33.30 2.41
8159 9427 2.223803 TGAACCAAACACACCCTTGT 57.776 45.000 0.00 0.00 35.84 3.16
8160 9428 2.430332 ACATGAACCAAACACACCCTTG 59.570 45.455 0.00 0.00 0.00 3.61
8161 9429 2.693074 GACATGAACCAAACACACCCTT 59.307 45.455 0.00 0.00 0.00 3.95
8162 9430 2.306847 GACATGAACCAAACACACCCT 58.693 47.619 0.00 0.00 0.00 4.34
8163 9431 1.339929 GGACATGAACCAAACACACCC 59.660 52.381 0.00 0.00 0.00 4.61
8164 9432 2.293399 GAGGACATGAACCAAACACACC 59.707 50.000 0.00 0.00 0.00 4.16
8165 9433 2.032030 CGAGGACATGAACCAAACACAC 60.032 50.000 0.00 0.00 0.00 3.82
8166 9434 2.217750 CGAGGACATGAACCAAACACA 58.782 47.619 0.00 0.00 0.00 3.72
8167 9435 2.218603 ACGAGGACATGAACCAAACAC 58.781 47.619 0.00 0.00 0.00 3.32
8168 9436 2.158885 TGACGAGGACATGAACCAAACA 60.159 45.455 0.00 0.28 0.00 2.83
8169 9437 2.489971 TGACGAGGACATGAACCAAAC 58.510 47.619 0.00 0.00 0.00 2.93
8170 9438 2.920724 TGACGAGGACATGAACCAAA 57.079 45.000 0.00 0.00 0.00 3.28
8171 9439 3.073678 CAATGACGAGGACATGAACCAA 58.926 45.455 0.00 0.00 0.00 3.67
8192 9460 4.816984 AGCTCAGGCCAGGCATGC 62.817 66.667 21.83 10.91 40.32 4.06
8220 9488 2.596346 ACCAAACAATCATCAGGCACA 58.404 42.857 0.00 0.00 0.00 4.57
8234 9502 1.808411 TCTCAGGATGCGAACCAAAC 58.192 50.000 0.00 0.00 34.76 2.93
8248 9516 1.673168 GCCAGGCAGGTATTTCTCAG 58.327 55.000 6.55 0.00 40.61 3.35
8277 9551 2.906354 CCAGGCTAATCACAGTACCAC 58.094 52.381 0.00 0.00 0.00 4.16
8278 9552 1.209504 GCCAGGCTAATCACAGTACCA 59.790 52.381 3.29 0.00 0.00 3.25
8284 9558 1.486310 CTACTGGCCAGGCTAATCACA 59.514 52.381 35.42 8.59 0.00 3.58
8335 9613 0.671472 GGCCAGGCAAATCAAACTGC 60.671 55.000 15.19 0.00 37.86 4.40
8339 9617 1.193462 CCTGGGCCAGGCAAATCAAA 61.193 55.000 38.22 0.00 45.13 2.69
8395 9673 0.036388 GTAGGCTGTTGCTGCTACCA 60.036 55.000 11.51 0.00 39.59 3.25
8398 9778 4.487714 AAATAGTAGGCTGTTGCTGCTA 57.512 40.909 0.00 0.00 39.59 3.49
8426 9806 4.093743 TGGTTCCTGTCAGTGCTTATAGA 58.906 43.478 0.00 0.00 0.00 1.98
8427 9807 4.471904 TGGTTCCTGTCAGTGCTTATAG 57.528 45.455 0.00 0.00 0.00 1.31
8428 9808 4.901197 TTGGTTCCTGTCAGTGCTTATA 57.099 40.909 0.00 0.00 0.00 0.98
8436 9816 0.868406 GAGCGTTTGGTTCCTGTCAG 59.132 55.000 0.00 0.00 0.00 3.51
8446 9837 2.203280 TGGTGGGTGAGCGTTTGG 60.203 61.111 0.00 0.00 0.00 3.28
8485 9876 2.286365 ACGCCTGGGATGAAGAAAAA 57.714 45.000 0.00 0.00 0.00 1.94
8490 9881 1.452108 GGGAACGCCTGGGATGAAG 60.452 63.158 0.00 0.00 0.00 3.02
8500 9891 3.134127 GTGATGGCTGGGAACGCC 61.134 66.667 0.00 0.00 46.00 5.68
8504 9895 3.157087 GAGAAAAAGTGATGGCTGGGAA 58.843 45.455 0.00 0.00 0.00 3.97
8511 9903 3.415212 TCTGCCTGAGAAAAAGTGATGG 58.585 45.455 0.00 0.00 0.00 3.51
8535 9927 3.511610 AAGGCCTGGGCAGTGGTT 61.512 61.111 23.25 4.36 44.11 3.67
8536 9928 3.971702 GAAGGCCTGGGCAGTGGT 61.972 66.667 23.25 0.00 44.11 4.16
8537 9929 3.512154 TTGAAGGCCTGGGCAGTGG 62.512 63.158 23.25 0.00 44.11 4.00
8538 9930 2.115910 TTGAAGGCCTGGGCAGTG 59.884 61.111 23.25 0.00 44.11 3.66
8539 9931 1.133809 TAGTTGAAGGCCTGGGCAGT 61.134 55.000 23.25 9.70 44.11 4.40
8540 9932 0.038166 TTAGTTGAAGGCCTGGGCAG 59.962 55.000 23.25 0.00 44.11 4.85
8541 9933 0.480690 TTTAGTTGAAGGCCTGGGCA 59.519 50.000 23.25 1.80 44.11 5.36
8557 9949 5.404366 GTGCGACAGATTTAGAGTGTGTTTA 59.596 40.000 0.00 0.00 0.00 2.01
8569 9961 1.238439 CCCACAAGTGCGACAGATTT 58.762 50.000 0.00 0.00 0.00 2.17
8573 9965 2.281070 AGCCCACAAGTGCGACAG 60.281 61.111 0.00 0.00 0.00 3.51
8574 9966 2.591429 CAGCCCACAAGTGCGACA 60.591 61.111 0.00 0.00 0.00 4.35
8575 9967 3.357079 CCAGCCCACAAGTGCGAC 61.357 66.667 0.00 0.00 0.00 5.19
8576 9968 3.872603 ACCAGCCCACAAGTGCGA 61.873 61.111 0.00 0.00 0.00 5.10
8577 9969 3.663176 CACCAGCCCACAAGTGCG 61.663 66.667 0.00 0.00 0.00 5.34
8579 9971 0.537143 TTAGCACCAGCCCACAAGTG 60.537 55.000 0.00 0.00 43.56 3.16
8613 10005 4.915085 ACCGATTAGTTCAAATTTTGTGCG 59.085 37.500 8.89 4.33 0.00 5.34
8614 10006 6.200097 ACAACCGATTAGTTCAAATTTTGTGC 59.800 34.615 8.89 3.88 0.00 4.57
8615 10007 7.692908 ACAACCGATTAGTTCAAATTTTGTG 57.307 32.000 8.89 0.00 0.00 3.33
8616 10008 7.223777 CCAACAACCGATTAGTTCAAATTTTGT 59.776 33.333 8.89 0.00 0.00 2.83
8617 10009 7.436673 TCCAACAACCGATTAGTTCAAATTTTG 59.563 33.333 2.59 2.59 0.00 2.44
8618 10010 7.493367 TCCAACAACCGATTAGTTCAAATTTT 58.507 30.769 0.00 0.00 0.00 1.82
8619 10011 7.045126 TCCAACAACCGATTAGTTCAAATTT 57.955 32.000 0.00 0.00 0.00 1.82
8620 10012 6.642707 TCCAACAACCGATTAGTTCAAATT 57.357 33.333 0.00 0.00 0.00 1.82
8621 10013 5.335661 GCTCCAACAACCGATTAGTTCAAAT 60.336 40.000 0.00 0.00 0.00 2.32
8622 10014 4.023536 GCTCCAACAACCGATTAGTTCAAA 60.024 41.667 0.00 0.00 0.00 2.69
8623 10015 3.500680 GCTCCAACAACCGATTAGTTCAA 59.499 43.478 0.00 0.00 0.00 2.69
8624 10016 3.071479 GCTCCAACAACCGATTAGTTCA 58.929 45.455 0.00 0.00 0.00 3.18
8625 10017 3.071479 TGCTCCAACAACCGATTAGTTC 58.929 45.455 0.00 0.00 0.00 3.01
8626 10018 3.134574 TGCTCCAACAACCGATTAGTT 57.865 42.857 0.00 0.00 0.00 2.24
8627 10019 2.851263 TGCTCCAACAACCGATTAGT 57.149 45.000 0.00 0.00 0.00 2.24
8628 10020 3.074412 ACTTGCTCCAACAACCGATTAG 58.926 45.455 0.00 0.00 0.00 1.73
8629 10021 3.134574 ACTTGCTCCAACAACCGATTA 57.865 42.857 0.00 0.00 0.00 1.75
8630 10022 1.981256 ACTTGCTCCAACAACCGATT 58.019 45.000 0.00 0.00 0.00 3.34
8681 10073 1.002142 CACACATGTCTGTTGTGGCAG 60.002 52.381 0.00 0.00 46.89 4.85
8694 10086 4.019858 TCTCCCTCTCTACTTCACACATG 58.980 47.826 0.00 0.00 0.00 3.21
8695 10087 4.323569 TCTCCCTCTCTACTTCACACAT 57.676 45.455 0.00 0.00 0.00 3.21
8701 10093 6.661805 TCTTCTTTCTTCTCCCTCTCTACTTC 59.338 42.308 0.00 0.00 0.00 3.01
8751 10143 4.606961 CTTGTTGAAGTTTACGCCATGTT 58.393 39.130 0.00 0.00 0.00 2.71
8759 10152 7.247929 ACTTACAGAGCTTGTTGAAGTTTAC 57.752 36.000 6.82 0.00 35.89 2.01
8762 10155 7.859325 TTAACTTACAGAGCTTGTTGAAGTT 57.141 32.000 20.83 20.83 44.65 2.66


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

AutoCloner maintained by Alex Coulton.