Multiple sequence alignment - TraesCS1A01G330500

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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 TraesCS1A01G330500 chr1A 100.000 8894 0 0 1 8894 519251746 519260639 0.000000e+00 16425.0
1 TraesCS1A01G330500 chr1A 98.182 110 2 0 6108 6217 376145840 376145949 9.110000e-45 193.0
2 TraesCS1A01G330500 chr1A 96.522 115 4 0 6108 6222 441770479 441770365 3.280000e-44 191.0
3 TraesCS1A01G330500 chr1A 87.500 96 11 1 5790 5885 267148640 267148734 9.440000e-20 110.0
4 TraesCS1A01G330500 chr1D 96.603 4533 94 18 1620 6112 423251496 423256008 0.000000e+00 7463.0
5 TraesCS1A01G330500 chr1D 94.878 2538 68 21 6214 8698 423256008 423258536 0.000000e+00 3910.0
6 TraesCS1A01G330500 chr1D 92.308 1638 48 20 1 1593 423249894 423251498 0.000000e+00 2255.0
7 TraesCS1A01G330500 chr1D 86.667 180 18 4 8714 8893 423259489 423259662 2.530000e-45 195.0
8 TraesCS1A01G330500 chr1D 87.500 96 11 1 5790 5885 211689136 211689230 9.440000e-20 110.0
9 TraesCS1A01G330500 chr1B 94.427 2817 92 19 3131 5929 572526588 572529357 0.000000e+00 4272.0
10 TraesCS1A01G330500 chr1B 94.253 2784 93 14 306 3060 572523416 572526161 0.000000e+00 4193.0
11 TraesCS1A01G330500 chr1B 90.677 1802 95 33 7140 8893 572531788 572533564 0.000000e+00 2329.0
12 TraesCS1A01G330500 chr1B 95.642 895 31 5 6216 7107 572529636 572530525 0.000000e+00 1430.0
13 TraesCS1A01G330500 chr1B 95.238 189 8 1 5931 6118 572529456 572529644 1.880000e-76 298.0
14 TraesCS1A01G330500 chr1B 92.473 186 3 10 1 177 572522919 572523102 1.150000e-63 255.0
15 TraesCS1A01G330500 chr1B 96.522 115 4 0 6110 6224 651523698 651523584 3.280000e-44 191.0
16 TraesCS1A01G330500 chr1B 82.394 142 16 6 2378 2518 119126417 119126550 2.030000e-21 115.0
17 TraesCS1A01G330500 chr1B 87.500 96 11 1 5790 5885 305171692 305171598 9.440000e-20 110.0
18 TraesCS1A01G330500 chr5D 81.349 252 46 1 4057 4307 57847452 57847703 4.210000e-48 204.0
19 TraesCS1A01G330500 chr5D 92.233 103 5 2 3243 3343 399614584 399614685 9.310000e-30 143.0
20 TraesCS1A01G330500 chr5D 82.517 143 20 4 8747 8889 221149417 221149554 4.360000e-23 121.0
21 TraesCS1A01G330500 chr5D 81.690 142 17 6 2378 2518 5794790 5794923 9.440000e-20 110.0
22 TraesCS1A01G330500 chr5D 80.519 154 17 10 2378 2518 552050127 552050280 1.220000e-18 106.0
23 TraesCS1A01G330500 chr5D 100.000 31 0 0 3207 3237 209318247 209318217 3.470000e-04 58.4
24 TraesCS1A01G330500 chr5A 81.349 252 46 1 4057 4307 45986157 45986408 4.210000e-48 204.0
25 TraesCS1A01G330500 chr5A 84.564 149 16 6 8742 8889 337822837 337822979 3.350000e-29 141.0
26 TraesCS1A01G330500 chr5A 86.139 101 13 1 3246 3346 270189135 270189036 3.400000e-19 108.0
27 TraesCS1A01G330500 chr4A 81.423 253 44 3 4057 4307 564654239 564653988 4.210000e-48 204.0
28 TraesCS1A01G330500 chr4A 93.846 130 6 2 6111 6238 628491116 628490987 2.530000e-45 195.0
29 TraesCS1A01G330500 chr4A 96.552 116 3 1 6106 6221 594217864 594217978 3.280000e-44 191.0
30 TraesCS1A01G330500 chr4A 94.309 123 6 1 6105 6226 500146078 500145956 4.240000e-43 187.0
31 TraesCS1A01G330500 chr4A 84.167 120 17 2 8741 8860 556244951 556245068 2.030000e-21 115.0
32 TraesCS1A01G330500 chr5B 80.556 252 48 1 4057 4307 60794546 60794295 9.110000e-45 193.0
33 TraesCS1A01G330500 chr5B 91.262 103 6 2 3243 3343 479726897 479726998 4.330000e-28 137.0
34 TraesCS1A01G330500 chr5B 86.555 119 14 2 8742 8860 278886603 278886719 7.250000e-26 130.0
35 TraesCS1A01G330500 chr5B 81.046 153 17 6 2378 2518 291786854 291787006 2.620000e-20 111.0
36 TraesCS1A01G330500 chr5B 91.071 56 5 0 2381 2436 699274538 699274483 9.580000e-10 76.8
37 TraesCS1A01G330500 chr3A 98.182 110 2 0 6111 6220 265543444 265543335 9.110000e-45 193.0
38 TraesCS1A01G330500 chr3A 93.069 101 6 1 3243 3343 675873119 675873020 7.200000e-31 147.0
39 TraesCS1A01G330500 chr3A 85.156 128 17 2 8734 8860 401026576 401026702 7.250000e-26 130.0
40 TraesCS1A01G330500 chr3A 80.128 156 20 5 2377 2521 593355868 593355713 1.220000e-18 106.0
41 TraesCS1A01G330500 chrUn 97.321 112 3 0 6111 6222 352766983 352766872 3.280000e-44 191.0
42 TraesCS1A01G330500 chr2A 97.273 110 3 0 6110 6219 120177666 120177775 4.240000e-43 187.0
43 TraesCS1A01G330500 chr2A 92.784 97 7 0 2734 2830 462313519 462313615 3.350000e-29 141.0
44 TraesCS1A01G330500 chr2A 86.667 120 15 1 8741 8860 141506317 141506435 2.010000e-26 132.0
45 TraesCS1A01G330500 chr2A 91.209 91 6 2 2734 2823 8629592 8629503 1.210000e-23 122.0
46 TraesCS1A01G330500 chr2D 92.157 102 5 2 3243 3342 337850146 337850046 3.350000e-29 141.0
47 TraesCS1A01G330500 chr2D 90.110 91 9 0 2733 2823 532674874 532674784 1.570000e-22 119.0
48 TraesCS1A01G330500 chr2D 80.247 162 18 8 2370 2518 215831807 215831967 9.440000e-20 110.0
49 TraesCS1A01G330500 chr4D 93.407 91 6 0 2734 2824 319247783 319247873 1.560000e-27 135.0
50 TraesCS1A01G330500 chr4D 88.776 98 11 0 2737 2834 280308919 280308822 4.360000e-23 121.0
51 TraesCS1A01G330500 chr4D 88.235 102 9 2 3243 3342 32019514 32019614 1.570000e-22 119.0
52 TraesCS1A01G330500 chr7B 90.099 101 8 2 3244 3343 5919495 5919594 7.250000e-26 130.0
53 TraesCS1A01G330500 chr4B 89.524 105 7 3 3243 3345 277316617 277316515 7.250000e-26 130.0
54 TraesCS1A01G330500 chr6A 82.877 146 21 4 8747 8892 82107501 82107360 2.610000e-25 128.0
55 TraesCS1A01G330500 chr6A 91.304 92 7 1 2734 2824 504315501 504315592 3.370000e-24 124.0
56 TraesCS1A01G330500 chr6D 82.313 147 23 3 8748 8892 83109278 83109133 3.370000e-24 124.0
57 TraesCS1A01G330500 chr2B 92.771 83 6 0 2734 2816 748978121 748978203 4.360000e-23 121.0
58 TraesCS1A01G330500 chr3D 80.645 155 18 6 2376 2518 26165849 26165695 9.440000e-20 110.0
59 TraesCS1A01G330500 chr7A 78.947 133 28 0 2381 2513 360613347 360613215 3.420000e-14 91.6


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 TraesCS1A01G330500 chr1A 519251746 519260639 8893 False 16425.00 16425 100.000 1 8894 1 chr1A.!!$F3 8893
1 TraesCS1A01G330500 chr1D 423249894 423259662 9768 False 3455.75 7463 92.614 1 8893 4 chr1D.!!$F2 8892
2 TraesCS1A01G330500 chr1B 572522919 572533564 10645 False 2129.50 4272 93.785 1 8893 6 chr1B.!!$F2 8892

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
305 347 0.940047 GATTGAGTAGTAGCCGCCGC 60.940 60.000 0.00 0.0 0.00 6.53 F
1685 1900 0.389426 TTGAAAGCCGTCTAGCCGTC 60.389 55.000 0.00 0.0 0.00 4.79 F
3241 3833 1.064825 CTCCCACACAAGGTAGGGTT 58.935 55.000 0.00 0.0 38.35 4.11 F
3489 4094 2.008242 TTACATGCTGGCCTGGTTTT 57.992 45.000 12.06 0.0 0.00 2.43 F
5004 5622 0.032615 TTGGCTTGTCAACTTGGGGT 60.033 50.000 0.00 0.0 0.00 4.95 F
5151 5769 0.179215 CGCTGAAAATGTGTCGGAGC 60.179 55.000 0.00 0.0 0.00 4.70 F
6150 6866 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.0 39.69 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2521 0.742635 GCAAGTAGAGGGAGCACAGC 60.743 60.000 0.00 0.00 0.00 4.40 R
3592 4198 1.022982 GTAACGGGCTAACTGGGCAC 61.023 60.000 0.00 0.00 0.00 5.01 R
4741 5350 1.824230 GCATGAAACCAAGTATGCCCA 59.176 47.619 0.00 0.00 39.88 5.36 R
5331 5949 3.496160 GGTAACTGGGTTTCTTGAGCTGA 60.496 47.826 0.00 0.00 0.00 4.26 R
6878 7594 0.030638 CCACCGTCAGCACCAAAAAG 59.969 55.000 0.00 0.00 0.00 2.27 R
7094 7813 6.539173 TCCCTGTGTCAATTAAGTGTATTGT 58.461 36.000 2.43 0.00 35.13 2.71 R
8109 10077 1.078759 CCATCGCCGAGACTGTCAAC 61.079 60.000 10.88 2.97 0.00 3.18 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
109 123 3.447229 GGTGAAGAGAAGAGAAGAGAGGG 59.553 52.174 0.00 0.00 0.00 4.30
238 280 2.908015 GGCTGTTCCGGATGGCTA 59.092 61.111 4.15 0.00 34.14 3.93
264 306 4.150454 CCGCCTCCCTCCCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
277 319 3.309296 TCCCTCTCTCTCTCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
280 322 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
282 324 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
291 333 4.721274 TCTCTCTCTCTCTCTCTGGATTGA 59.279 45.833 0.00 0.00 0.00 2.57
297 339 6.613679 TCTCTCTCTCTCTGGATTGAGTAGTA 59.386 42.308 0.00 0.00 35.68 1.82
305 347 0.940047 GATTGAGTAGTAGCCGCCGC 60.940 60.000 0.00 0.00 0.00 6.53
396 610 4.605967 GTGCGGTGGCGTGTGTTG 62.606 66.667 0.00 0.00 44.10 3.33
446 660 1.065928 CCTCGTCCTCGATTTCCGG 59.934 63.158 0.00 0.00 45.21 5.14
486 700 1.718757 GAGCCGGCAATGCGATTTCT 61.719 55.000 31.54 1.71 0.00 2.52
659 874 1.228552 GGTTCATGCCCAGTGTGGT 60.229 57.895 0.00 0.00 35.17 4.16
764 979 3.116531 GCCCGTGTAAGTCGTGCC 61.117 66.667 0.00 0.00 0.00 5.01
862 1077 2.783288 CGGGTTCTACGGAGGAGGC 61.783 68.421 0.00 0.00 0.00 4.70
974 1189 7.327275 GTCAATATAATACGCTCTCTGGTCTTG 59.673 40.741 0.00 0.00 0.00 3.02
1143 1358 1.004440 GACCAAGCAGAAGGTCGCT 60.004 57.895 0.00 0.00 44.23 4.93
1335 1550 1.029681 GGAAAACGACAAGCACCCTT 58.970 50.000 0.00 0.00 0.00 3.95
1607 1822 8.204836 ACTACCAGATATGACTTGTAATTGGTC 58.795 37.037 0.00 0.00 37.55 4.02
1685 1900 0.389426 TTGAAAGCCGTCTAGCCGTC 60.389 55.000 0.00 0.00 0.00 4.79
1687 1902 1.946475 GAAAGCCGTCTAGCCGTCCT 61.946 60.000 0.00 0.00 0.00 3.85
1774 1989 5.705609 ACCTGCGTCTGATTGTTTATTTT 57.294 34.783 0.00 0.00 0.00 1.82
1810 2025 7.687941 AAACTTGTATCAACATTACTCCCTG 57.312 36.000 0.00 0.00 34.97 4.45
1935 2150 8.260099 TCATCCTGATCTGATATCTTTGTCTT 57.740 34.615 3.98 0.00 0.00 3.01
2177 2394 5.133221 GTTTAACCTCCTATGTGGCATGAT 58.867 41.667 0.00 0.00 35.26 2.45
2221 2438 7.331026 TGGTTGTCAATAGTAGATTCAGAAGG 58.669 38.462 0.00 0.00 0.00 3.46
2370 2589 3.138884 TCTTTGTCTACAAGCATGCCA 57.861 42.857 15.66 0.00 37.15 4.92
2374 2593 2.794103 TGTCTACAAGCATGCCAATGT 58.206 42.857 15.66 18.85 36.08 2.71
2392 2611 5.047802 CCAATGTGTCATTGTTCTTTAGGCT 60.048 40.000 17.36 0.00 0.00 4.58
2457 2676 3.501950 CGACTAAGGCAGGAAAAATTGC 58.498 45.455 0.00 0.00 39.56 3.56
2462 2681 2.049372 AGGCAGGAAAAATTGCAAGGT 58.951 42.857 4.94 0.00 42.02 3.50
2816 3036 4.202080 GGGACTAAAGGGTTTGTTGTTGTC 60.202 45.833 0.00 0.00 0.00 3.18
2970 3206 4.439968 CGTACTTATGAAAGACTTCCCCC 58.560 47.826 0.00 0.00 36.50 5.40
2992 3228 1.227999 CGAAACATGCGTGAGGTGGT 61.228 55.000 14.17 0.00 0.00 4.16
3068 3304 3.443681 CCCCGACTGCATTATTTCTGTTT 59.556 43.478 0.00 0.00 0.00 2.83
3167 3759 7.645058 ACCAACTCCAATTTATAAGATGGTG 57.355 36.000 14.72 14.53 41.62 4.17
3191 3783 9.286170 GTGGTGAAGTAGAGATATATAGTCACA 57.714 37.037 7.61 0.00 0.00 3.58
3241 3833 1.064825 CTCCCACACAAGGTAGGGTT 58.935 55.000 0.00 0.00 38.35 4.11
3259 3864 2.024414 GTTAGCCTTACCCCTTGCATG 58.976 52.381 0.00 0.00 0.00 4.06
3276 3881 4.784177 TGCATGATAATTCTGCAAGGAGA 58.216 39.130 0.00 0.00 42.53 3.71
3353 3958 2.699954 CCCGCCCTTCATATATCACAC 58.300 52.381 0.00 0.00 0.00 3.82
3382 3987 5.966742 AAAAAGAGTCCCTTCATACAAGC 57.033 39.130 0.00 0.00 33.02 4.01
3434 4039 7.752239 AGAGAACATGAGAATAATGTTTTTGCG 59.248 33.333 0.00 0.00 38.48 4.85
3489 4094 2.008242 TTACATGCTGGCCTGGTTTT 57.992 45.000 12.06 0.00 0.00 2.43
3592 4198 5.913137 TTCCCCTGCACTATAAAAATGTG 57.087 39.130 0.00 0.00 35.08 3.21
3627 4233 3.187842 CCGTTACAGCCCAGTTCTTTTAC 59.812 47.826 0.00 0.00 0.00 2.01
3637 4243 3.683340 CCAGTTCTTTTACCGGCTTCTAC 59.317 47.826 0.00 0.00 0.00 2.59
3791 4397 2.650778 GCCAAAAGAACTGGGCCG 59.349 61.111 0.00 0.00 40.55 6.13
4091 4700 2.349532 CGTCAAAGCCGAAAGAAACCTC 60.350 50.000 0.00 0.00 0.00 3.85
4318 4927 6.278363 ACATTCACAGGTATCGTGTATAACC 58.722 40.000 0.00 0.00 35.79 2.85
4676 5285 5.982890 ACTTATTGATGGTTGGGAAACAG 57.017 39.130 0.00 0.00 0.00 3.16
4855 5466 4.262592 GGATTTGACTGAATTTGGCAAGGT 60.263 41.667 0.00 0.00 0.00 3.50
4863 5474 7.615365 TGACTGAATTTGGCAAGGTATTATCTT 59.385 33.333 0.00 0.00 0.00 2.40
5004 5622 0.032615 TTGGCTTGTCAACTTGGGGT 60.033 50.000 0.00 0.00 0.00 4.95
5012 5630 4.171878 TGTCAACTTGGGGTATCAAACA 57.828 40.909 0.00 0.00 0.00 2.83
5151 5769 0.179215 CGCTGAAAATGTGTCGGAGC 60.179 55.000 0.00 0.00 0.00 4.70
5154 5772 2.939103 GCTGAAAATGTGTCGGAGCTAT 59.061 45.455 0.00 0.00 0.00 2.97
5303 5921 7.433680 GTGTTGAACCTAGTCAAATCCAATTT 58.566 34.615 0.00 0.00 39.18 1.82
5306 5924 8.306761 GTTGAACCTAGTCAAATCCAATTTCAT 58.693 33.333 0.00 0.00 39.18 2.57
5935 6651 5.146010 TGAGGATGTTTATTTGGTTTGGC 57.854 39.130 0.00 0.00 0.00 4.52
5986 6702 2.292569 TCGCACGAGACTGACTTTAGTT 59.707 45.455 0.00 0.00 0.00 2.24
5993 6709 7.410942 GCACGAGACTGACTTTAGTTAAATCTG 60.411 40.741 0.00 0.00 0.00 2.90
6086 6802 6.042552 CCCTGTGGATAGATTCTGATAGTTGT 59.957 42.308 0.00 0.00 0.00 3.32
6112 6828 3.068732 TGGTCACTGCAGCTCATATCTAC 59.931 47.826 15.27 0.00 0.00 2.59
6113 6829 3.320541 GGTCACTGCAGCTCATATCTACT 59.679 47.826 15.27 0.00 0.00 2.57
6114 6830 4.545610 GTCACTGCAGCTCATATCTACTC 58.454 47.826 15.27 0.00 0.00 2.59
6115 6831 3.571828 TCACTGCAGCTCATATCTACTCC 59.428 47.826 15.27 0.00 0.00 3.85
6116 6832 2.896685 ACTGCAGCTCATATCTACTCCC 59.103 50.000 15.27 0.00 0.00 4.30
6117 6833 3.164268 CTGCAGCTCATATCTACTCCCT 58.836 50.000 0.00 0.00 0.00 4.20
6118 6834 3.161067 TGCAGCTCATATCTACTCCCTC 58.839 50.000 0.00 0.00 0.00 4.30
6119 6835 3.181424 TGCAGCTCATATCTACTCCCTCT 60.181 47.826 0.00 0.00 0.00 3.69
6120 6836 3.193267 GCAGCTCATATCTACTCCCTCTG 59.807 52.174 0.00 0.00 0.00 3.35
6121 6837 4.406456 CAGCTCATATCTACTCCCTCTGT 58.594 47.826 0.00 0.00 0.00 3.41
6122 6838 4.832266 CAGCTCATATCTACTCCCTCTGTT 59.168 45.833 0.00 0.00 0.00 3.16
6123 6839 5.048083 CAGCTCATATCTACTCCCTCTGTTC 60.048 48.000 0.00 0.00 0.00 3.18
6124 6840 4.219725 GCTCATATCTACTCCCTCTGTTCC 59.780 50.000 0.00 0.00 0.00 3.62
6125 6841 5.389520 CTCATATCTACTCCCTCTGTTCCA 58.610 45.833 0.00 0.00 0.00 3.53
6126 6842 5.777449 TCATATCTACTCCCTCTGTTCCAA 58.223 41.667 0.00 0.00 0.00 3.53
6127 6843 6.202331 TCATATCTACTCCCTCTGTTCCAAA 58.798 40.000 0.00 0.00 0.00 3.28
6128 6844 6.846505 TCATATCTACTCCCTCTGTTCCAAAT 59.153 38.462 0.00 0.00 0.00 2.32
6129 6845 7.348274 TCATATCTACTCCCTCTGTTCCAAATT 59.652 37.037 0.00 0.00 0.00 1.82
6130 6846 8.651389 CATATCTACTCCCTCTGTTCCAAATTA 58.349 37.037 0.00 0.00 0.00 1.40
6131 6847 6.295719 TCTACTCCCTCTGTTCCAAATTAC 57.704 41.667 0.00 0.00 0.00 1.89
6132 6848 6.023603 TCTACTCCCTCTGTTCCAAATTACT 58.976 40.000 0.00 0.00 0.00 2.24
6133 6849 5.167303 ACTCCCTCTGTTCCAAATTACTC 57.833 43.478 0.00 0.00 0.00 2.59
6134 6850 4.184629 CTCCCTCTGTTCCAAATTACTCG 58.815 47.826 0.00 0.00 0.00 4.18
6135 6851 3.581332 TCCCTCTGTTCCAAATTACTCGT 59.419 43.478 0.00 0.00 0.00 4.18
6136 6852 3.933332 CCCTCTGTTCCAAATTACTCGTC 59.067 47.826 0.00 0.00 0.00 4.20
6137 6853 3.612860 CCTCTGTTCCAAATTACTCGTCG 59.387 47.826 0.00 0.00 0.00 5.12
6138 6854 2.991190 TCTGTTCCAAATTACTCGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
6139 6855 2.734606 CTGTTCCAAATTACTCGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
6140 6856 2.734606 TGTTCCAAATTACTCGTCGCAG 59.265 45.455 0.00 0.00 0.00 5.18
6141 6857 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
6142 6858 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
6143 6859 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
6144 6860 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
6145 6861 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
6146 6862 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
6147 6863 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
6148 6864 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
6149 6865 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
6150 6866 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
6151 6867 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
6152 6868 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
6153 6869 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
6154 6870 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
6155 6871 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
6156 6872 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
6157 6873 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
6158 6874 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
6159 6875 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
6160 6876 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
6161 6877 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
6162 6878 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
6163 6879 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
6190 6906 7.561021 ACATCTAGATACATCTATACCTGCG 57.439 40.000 4.54 0.00 38.60 5.18
6191 6907 7.339482 ACATCTAGATACATCTATACCTGCGA 58.661 38.462 4.54 0.00 38.60 5.10
6192 6908 7.281324 ACATCTAGATACATCTATACCTGCGAC 59.719 40.741 4.54 0.00 38.60 5.19
6193 6909 6.708285 TCTAGATACATCTATACCTGCGACA 58.292 40.000 0.00 0.00 38.60 4.35
6194 6910 7.166167 TCTAGATACATCTATACCTGCGACAA 58.834 38.462 0.00 0.00 38.60 3.18
6195 6911 6.260870 AGATACATCTATACCTGCGACAAG 57.739 41.667 0.00 0.00 34.85 3.16
6196 6912 5.770663 AGATACATCTATACCTGCGACAAGT 59.229 40.000 0.00 0.00 34.85 3.16
6197 6913 6.940867 AGATACATCTATACCTGCGACAAGTA 59.059 38.462 0.00 0.00 34.85 2.24
6198 6914 5.847111 ACATCTATACCTGCGACAAGTAA 57.153 39.130 0.00 0.00 0.00 2.24
6199 6915 6.406692 ACATCTATACCTGCGACAAGTAAT 57.593 37.500 0.00 0.00 0.00 1.89
6200 6916 6.817184 ACATCTATACCTGCGACAAGTAATT 58.183 36.000 0.00 0.00 0.00 1.40
6201 6917 6.924060 ACATCTATACCTGCGACAAGTAATTC 59.076 38.462 0.00 0.00 0.00 2.17
6202 6918 6.459670 TCTATACCTGCGACAAGTAATTCA 57.540 37.500 0.00 0.00 0.00 2.57
6203 6919 6.504398 TCTATACCTGCGACAAGTAATTCAG 58.496 40.000 0.00 0.00 0.00 3.02
6204 6920 3.678056 ACCTGCGACAAGTAATTCAGA 57.322 42.857 0.00 0.00 0.00 3.27
6205 6921 4.002906 ACCTGCGACAAGTAATTCAGAA 57.997 40.909 0.00 0.00 0.00 3.02
6206 6922 3.746492 ACCTGCGACAAGTAATTCAGAAC 59.254 43.478 0.00 0.00 0.00 3.01
6207 6923 3.181530 CCTGCGACAAGTAATTCAGAACG 60.182 47.826 0.00 0.00 0.00 3.95
6208 6924 2.734606 TGCGACAAGTAATTCAGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
6209 6925 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
6210 6926 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
6211 6927 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
6212 6928 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
6213 6929 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
6307 7023 9.268268 TGTTTAGTGTTCTGTAGTAGGAATTTG 57.732 33.333 0.00 0.00 0.00 2.32
6352 7068 4.826733 TGTTCATTGGCACACAGAATACTT 59.173 37.500 0.00 0.00 39.29 2.24
6390 7106 7.827819 AAAATGCAATCTGATCTGTTTGATG 57.172 32.000 21.12 7.59 35.14 3.07
6583 7299 5.818678 TCTACACAGTACACCCTCATTTT 57.181 39.130 0.00 0.00 0.00 1.82
6992 7708 5.005971 GTGCGTTTTATATTTCCGAGCAGTA 59.994 40.000 0.00 0.00 32.51 2.74
7045 7762 4.844349 TGGAAGCTGCTAATAACCTTCT 57.156 40.909 0.90 0.00 34.03 2.85
7074 7791 9.945904 TTTACCTGTTTTCACCTTTTATTTTGT 57.054 25.926 0.00 0.00 0.00 2.83
7095 7814 9.827411 TTTTGTGGTTTGCACTTTTAATTTTAC 57.173 25.926 0.00 0.00 0.00 2.01
7120 7857 7.504238 ACAATACACTTAATTGACACAGGGAAA 59.496 33.333 0.00 0.00 37.68 3.13
7143 7880 7.737972 AAACACAACTTTTAAAATATGGGCC 57.262 32.000 12.72 0.00 0.00 5.80
7223 9170 6.761714 ACTTGAATTAGAACTGTGTCGAAAGT 59.238 34.615 0.00 0.00 0.00 2.66
7424 9388 0.894835 TCAGCTTCATGTCGGCACTA 59.105 50.000 0.00 0.00 0.00 2.74
7429 9393 2.939103 GCTTCATGTCGGCACTAAAGAT 59.061 45.455 10.93 0.00 0.00 2.40
7587 9551 7.310423 GGCCTTGGGATTTTGTATTCTTAGTTT 60.310 37.037 0.00 0.00 0.00 2.66
7804 9770 3.027170 GATGAACCTGTGCACGGCG 62.027 63.158 20.76 15.35 0.00 6.46
7908 9874 7.095774 CGACGTAAATAGGATATGGAGGTTTTG 60.096 40.741 0.00 0.00 0.00 2.44
8109 10077 0.956410 TTGGTTCGCCGTATGTTGGG 60.956 55.000 0.00 0.00 41.18 4.12
8133 10101 3.148279 GTCTCGGCGATGGGTCCT 61.148 66.667 11.27 0.00 0.00 3.85
8169 10137 5.177696 GGCTACAGCATAAGTGTATACTTGC 59.822 44.000 14.53 11.04 44.15 4.01
8313 10281 4.104776 CAATGATGATTTGTGGGTTACGC 58.895 43.478 0.00 0.00 0.00 4.42
8328 10296 3.368495 GTTACGCTTGTTCTGGTTTTGG 58.632 45.455 0.00 0.00 0.00 3.28
8342 10311 1.958579 GTTTTGGCTTACCGAACCCTT 59.041 47.619 0.00 0.00 39.19 3.95
8344 10313 3.505480 TTTGGCTTACCGAACCCTTTA 57.495 42.857 0.00 0.00 39.70 1.85
8345 10314 3.724732 TTGGCTTACCGAACCCTTTAT 57.275 42.857 0.00 0.00 39.70 1.40
8346 10315 3.724732 TGGCTTACCGAACCCTTTATT 57.275 42.857 0.00 0.00 39.70 1.40
8347 10316 3.613030 TGGCTTACCGAACCCTTTATTC 58.387 45.455 0.00 0.00 39.70 1.75
8348 10317 2.947652 GGCTTACCGAACCCTTTATTCC 59.052 50.000 0.00 0.00 0.00 3.01
8349 10318 3.613030 GCTTACCGAACCCTTTATTCCA 58.387 45.455 0.00 0.00 0.00 3.53
8350 10319 4.011698 GCTTACCGAACCCTTTATTCCAA 58.988 43.478 0.00 0.00 0.00 3.53
8351 10320 4.142534 GCTTACCGAACCCTTTATTCCAAC 60.143 45.833 0.00 0.00 0.00 3.77
8352 10321 2.799017 ACCGAACCCTTTATTCCAACC 58.201 47.619 0.00 0.00 0.00 3.77
8353 10322 2.108601 ACCGAACCCTTTATTCCAACCA 59.891 45.455 0.00 0.00 0.00 3.67
8355 10324 3.130340 CCGAACCCTTTATTCCAACCATG 59.870 47.826 0.00 0.00 0.00 3.66
8356 10325 3.761752 CGAACCCTTTATTCCAACCATGT 59.238 43.478 0.00 0.00 0.00 3.21
8357 10326 4.142469 CGAACCCTTTATTCCAACCATGTC 60.142 45.833 0.00 0.00 0.00 3.06
8361 10330 2.799126 TTATTCCAACCATGTCGCCT 57.201 45.000 0.00 0.00 0.00 5.52
8372 10341 0.314935 ATGTCGCCTGTTTGCTTTGG 59.685 50.000 0.00 0.00 0.00 3.28
8379 10348 1.410153 CCTGTTTGCTTTGGTGCTTCT 59.590 47.619 0.00 0.00 0.00 2.85
8380 10349 2.622942 CCTGTTTGCTTTGGTGCTTCTA 59.377 45.455 0.00 0.00 0.00 2.10
8464 10447 3.321396 TGAATGCAAATGCTTGGAACAGA 59.679 39.130 6.97 0.00 42.66 3.41
8465 10448 2.798976 TGCAAATGCTTGGAACAGAC 57.201 45.000 6.97 0.00 42.66 3.51
8471 10454 1.371558 GCTTGGAACAGACGAGGGT 59.628 57.895 0.00 0.00 42.39 4.34
8502 10485 1.726791 CGTGTGTGGAGAGTAACATGC 59.273 52.381 0.00 0.00 0.00 4.06
8513 10496 1.134788 AGTAACATGCTGAGTACGGCC 60.135 52.381 0.00 0.00 46.76 6.13
8519 10502 2.579201 CTGAGTACGGCCCACCAG 59.421 66.667 0.00 2.01 34.57 4.00
8559 10543 2.678443 CGAAGCGAGAAATGTGTACG 57.322 50.000 0.00 0.00 0.00 3.67
8627 10613 3.058639 GCGTCAAAAGAGAACAATGAGCT 60.059 43.478 0.00 0.00 0.00 4.09
8691 10677 1.267806 CACATCGTTTTGCCAGCTTCT 59.732 47.619 0.00 0.00 0.00 2.85
8702 10697 1.811558 GCCAGCTTCTGTCTGTCACAA 60.812 52.381 0.00 0.00 33.31 3.33
8714 10709 6.607600 TCTGTCTGTCACAAGGCTATAATACT 59.392 38.462 0.00 0.00 33.31 2.12
8721 11644 8.315482 TGTCACAAGGCTATAATACTGTACAAA 58.685 33.333 0.00 0.00 0.00 2.83
8750 11673 3.389002 TCATGCATGTATGTACTGCCTCT 59.611 43.478 25.43 0.00 35.02 3.69
8759 11682 3.667497 TGTACTGCCTCTGTTCTGAAG 57.333 47.619 0.00 0.00 0.00 3.02
8832 11755 8.905103 ATAAGTGAACAAACACACTAAAACAC 57.095 30.769 0.00 0.00 44.94 3.32
8833 11756 5.387279 AGTGAACAAACACACTAAAACACG 58.613 37.500 0.00 0.00 44.06 4.49
8843 11766 6.160684 ACACACTAAAACACGTCTATATGCA 58.839 36.000 0.00 0.00 0.00 3.96
8846 11769 7.222805 CACACTAAAACACGTCTATATGCATCT 59.777 37.037 0.19 0.00 0.00 2.90
8847 11770 7.222805 ACACTAAAACACGTCTATATGCATCTG 59.777 37.037 0.19 0.00 0.00 2.90
8852 11775 5.157067 ACACGTCTATATGCATCTGATTCG 58.843 41.667 0.19 5.55 0.00 3.34
8853 11776 5.157067 CACGTCTATATGCATCTGATTCGT 58.843 41.667 0.19 6.21 0.00 3.85
8854 11777 6.072673 ACACGTCTATATGCATCTGATTCGTA 60.073 38.462 0.19 0.00 0.00 3.43
8855 11778 6.801862 CACGTCTATATGCATCTGATTCGTAA 59.198 38.462 0.19 0.00 0.00 3.18
8858 11781 8.699749 CGTCTATATGCATCTGATTCGTAAAAA 58.300 33.333 0.19 0.00 0.00 1.94
8893 11816 5.811399 TGCCTTATAATTTGGAACTGACG 57.189 39.130 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 298 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
257 299 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
258 300 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
259 301 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
260 302 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
261 303 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
262 304 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
263 305 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
264 306 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
277 319 4.518970 GGCTACTACTCAATCCAGAGAGAG 59.481 50.000 0.00 0.00 38.98 3.20
280 322 3.215151 CGGCTACTACTCAATCCAGAGA 58.785 50.000 0.00 0.00 38.98 3.10
282 324 1.681793 GCGGCTACTACTCAATCCAGA 59.318 52.381 0.00 0.00 0.00 3.86
466 680 2.971744 GAAATCGCATTGCCGGCTCG 62.972 60.000 29.70 23.49 0.00 5.03
467 681 1.298638 GAAATCGCATTGCCGGCTC 60.299 57.895 29.70 9.60 0.00 4.70
486 700 0.808453 GATTCGCGGAATTCGACCCA 60.808 55.000 6.13 0.00 42.43 4.51
545 759 2.287251 CCCCACCCCCACCAAAAA 59.713 61.111 0.00 0.00 0.00 1.94
546 760 3.851184 CCCCCACCCCCACCAAAA 61.851 66.667 0.00 0.00 0.00 2.44
630 845 1.516386 CATGAACCCTCCGTCGACG 60.516 63.158 30.33 30.33 39.44 5.12
642 857 1.039856 AAACCACACTGGGCATGAAC 58.960 50.000 0.00 0.00 43.37 3.18
659 874 5.010213 CCCAGTCAAAAATCCCGAAACTAAA 59.990 40.000 0.00 0.00 0.00 1.85
764 979 3.429043 GCACAAGTTGCCATCCATG 57.571 52.632 1.81 0.00 46.63 3.66
862 1077 0.744414 ATCAGATGTCCAAACCGGCG 60.744 55.000 0.00 0.00 33.14 6.46
974 1189 1.607628 GCTCACAATGGCATCATCTCC 59.392 52.381 0.00 0.00 32.24 3.71
1143 1358 1.950216 TCAATGTACTGTTTTGCCGCA 59.050 42.857 0.00 0.00 0.00 5.69
1335 1550 3.603158 TGCTCGGTAATAGCAACAAGA 57.397 42.857 0.00 0.00 46.57 3.02
1356 1571 6.435430 TGTGATGTGTGTTAATAAGCATCC 57.565 37.500 11.79 6.72 33.78 3.51
1365 1580 3.825585 ACATGGCATGTGATGTGTGTTAA 59.174 39.130 30.96 0.00 43.01 2.01
1685 1900 5.979517 GTGTCAACCAAAATCTCTGAAAAGG 59.020 40.000 0.00 0.00 0.00 3.11
1687 1902 5.901552 GGTGTCAACCAAAATCTCTGAAAA 58.098 37.500 0.00 0.00 46.75 2.29
1774 1989 9.168451 TGTTGATACAAGTTTTAACTGAGAACA 57.832 29.630 0.00 0.00 39.66 3.18
1935 2150 2.780595 GCATCCAGCGCCTAAAAGA 58.219 52.632 2.29 0.00 0.00 2.52
2177 2394 7.060421 ACAACCAGAATTAGAAGACCAAGAAA 58.940 34.615 0.00 0.00 0.00 2.52
2304 2521 0.742635 GCAAGTAGAGGGAGCACAGC 60.743 60.000 0.00 0.00 0.00 4.40
2370 2589 5.536161 ACAGCCTAAAGAACAATGACACATT 59.464 36.000 0.00 0.00 0.00 2.71
2374 2593 5.705441 CCTTACAGCCTAAAGAACAATGACA 59.295 40.000 0.00 0.00 0.00 3.58
2392 2611 1.822990 CTCGCCTTAGGTCACCTTACA 59.177 52.381 0.00 0.00 34.61 2.41
2457 2676 2.042831 GCACCCTAGCAGCACCTTG 61.043 63.158 0.00 0.00 0.00 3.61
2462 2681 2.352422 CAAGGCACCCTAGCAGCA 59.648 61.111 0.00 0.00 35.83 4.41
2816 3036 6.721321 TCAATCATCATCATCATCAACAACG 58.279 36.000 0.00 0.00 0.00 4.10
2944 3165 4.439968 GAAGTCTTTCATAAGTACGGGGG 58.560 47.826 0.00 0.00 33.38 5.40
2945 3166 4.439968 GGAAGTCTTTCATAAGTACGGGG 58.560 47.826 0.00 0.00 34.90 5.73
2949 3170 5.695424 AGGGGGAAGTCTTTCATAAGTAC 57.305 43.478 0.00 0.00 34.90 2.73
2957 3193 2.812591 GTTTCGAAGGGGGAAGTCTTTC 59.187 50.000 0.00 0.00 0.00 2.62
2970 3206 1.136252 CACCTCACGCATGTTTCGAAG 60.136 52.381 0.00 0.00 0.00 3.79
2992 3228 4.150897 ACTCAGTCAAACCAACAAGCTA 57.849 40.909 0.00 0.00 0.00 3.32
3199 3791 2.434359 GGCACTGGGTACACGCTC 60.434 66.667 0.00 0.00 0.00 5.03
3241 3833 1.590591 TCATGCAAGGGGTAAGGCTA 58.409 50.000 0.00 0.00 0.00 3.93
3259 3864 4.775236 ACCAGTCTCCTTGCAGAATTATC 58.225 43.478 0.00 0.00 0.00 1.75
3353 3958 5.179452 TGAAGGGACTCTTTTTATCCTGG 57.821 43.478 0.00 0.00 38.49 4.45
3367 3972 4.142381 GGTGAAATGCTTGTATGAAGGGAC 60.142 45.833 0.00 0.00 0.00 4.46
3382 3987 5.636543 GCTGAAAAGGATGAAAGGTGAAATG 59.363 40.000 0.00 0.00 0.00 2.32
3434 4039 2.667473 ATACGGGTCAACTGCACTAC 57.333 50.000 0.00 0.00 0.00 2.73
3489 4094 1.486310 AGAAGAACAGAGCACACCACA 59.514 47.619 0.00 0.00 0.00 4.17
3592 4198 1.022982 GTAACGGGCTAACTGGGCAC 61.023 60.000 0.00 0.00 0.00 5.01
3637 4243 1.152673 GGGAGGGGGCAGCTTATTG 60.153 63.158 0.00 0.00 0.00 1.90
3731 4337 4.969359 CCCTCCCCAACTTATTCTAGAAGA 59.031 45.833 11.53 3.09 0.00 2.87
3791 4397 7.440255 ACTGGCGATGGTTACTTTATTACATAC 59.560 37.037 0.00 0.00 0.00 2.39
4091 4700 1.929836 GCACTATCGACTTCTGCAAGG 59.070 52.381 0.00 0.00 33.37 3.61
4318 4927 8.113062 CAGAATTATTAACAGAGCAAGAGAACG 58.887 37.037 0.00 0.00 0.00 3.95
4676 5285 9.398170 GACATGGCATCATAACATTGTTAATAC 57.602 33.333 12.96 0.00 31.33 1.89
4741 5350 1.824230 GCATGAAACCAAGTATGCCCA 59.176 47.619 0.00 0.00 39.88 5.36
4863 5474 8.791327 TTGATTTGCTATCAACATTAGAGACA 57.209 30.769 9.75 0.00 33.55 3.41
5004 5622 5.989477 CCATAGGGTCTGTCTTGTTTGATA 58.011 41.667 0.00 0.00 0.00 2.15
5047 5665 4.593206 TGGATGCCTAGGAAATACGAAGAT 59.407 41.667 14.75 0.00 0.00 2.40
5154 5772 8.236585 TCCTTGAGAAAGATTCATGTTCAAAA 57.763 30.769 0.00 0.00 0.00 2.44
5331 5949 3.496160 GGTAACTGGGTTTCTTGAGCTGA 60.496 47.826 0.00 0.00 0.00 4.26
5756 6375 7.738847 AGAAATGTGAGACCAAAAATCCATTT 58.261 30.769 0.00 0.00 34.86 2.32
5865 6484 3.196685 AGAGACATACCTTTCTGCAGGTC 59.803 47.826 15.13 10.43 44.63 3.85
5935 6651 3.722147 AGCGTTACATAGGCTGAAGATG 58.278 45.455 0.00 0.00 45.72 2.90
5986 6702 6.631766 GCCCTGTCCTATGTGTTACAGATTTA 60.632 42.308 0.00 0.00 41.47 1.40
5993 6709 3.343941 TTGCCCTGTCCTATGTGTTAC 57.656 47.619 0.00 0.00 0.00 2.50
6112 6828 4.184629 CGAGTAATTTGGAACAGAGGGAG 58.815 47.826 0.00 0.00 42.39 4.30
6113 6829 3.581332 ACGAGTAATTTGGAACAGAGGGA 59.419 43.478 0.00 0.00 42.39 4.20
6114 6830 3.933332 GACGAGTAATTTGGAACAGAGGG 59.067 47.826 0.00 0.00 42.39 4.30
6115 6831 3.612860 CGACGAGTAATTTGGAACAGAGG 59.387 47.826 0.00 0.00 42.39 3.69
6116 6832 3.060895 GCGACGAGTAATTTGGAACAGAG 59.939 47.826 0.00 0.00 42.39 3.35
6117 6833 2.991190 GCGACGAGTAATTTGGAACAGA 59.009 45.455 0.00 0.00 42.39 3.41
6118 6834 2.734606 TGCGACGAGTAATTTGGAACAG 59.265 45.455 0.00 0.00 42.39 3.16
6119 6835 2.734606 CTGCGACGAGTAATTTGGAACA 59.265 45.455 0.00 0.00 0.00 3.18
6120 6836 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
6121 6837 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
6122 6838 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
6123 6839 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
6124 6840 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
6125 6841 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
6126 6842 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
6127 6843 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
6128 6844 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
6129 6845 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
6130 6846 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
6131 6847 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
6132 6848 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
6133 6849 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
6134 6850 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
6135 6851 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
6136 6852 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
6137 6853 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
6164 6880 9.278978 CGCAGGTATAGATGTATCTAGATGTAT 57.721 37.037 15.79 9.11 42.20 2.29
6165 6881 8.483758 TCGCAGGTATAGATGTATCTAGATGTA 58.516 37.037 15.79 4.44 42.20 2.29
6166 6882 7.281324 GTCGCAGGTATAGATGTATCTAGATGT 59.719 40.741 15.79 1.25 42.20 3.06
6167 6883 7.281100 TGTCGCAGGTATAGATGTATCTAGATG 59.719 40.741 15.79 0.00 42.20 2.90
6168 6884 7.339482 TGTCGCAGGTATAGATGTATCTAGAT 58.661 38.462 10.73 10.73 42.20 1.98
6169 6885 6.708285 TGTCGCAGGTATAGATGTATCTAGA 58.292 40.000 7.57 0.00 42.20 2.43
6170 6886 6.986904 TGTCGCAGGTATAGATGTATCTAG 57.013 41.667 7.57 0.00 42.20 2.43
6171 6887 6.940867 ACTTGTCGCAGGTATAGATGTATCTA 59.059 38.462 4.22 4.22 43.00 1.98
6172 6888 5.770663 ACTTGTCGCAGGTATAGATGTATCT 59.229 40.000 0.00 0.00 40.86 1.98
6173 6889 6.015027 ACTTGTCGCAGGTATAGATGTATC 57.985 41.667 0.00 0.00 0.00 2.24
6174 6890 7.520451 TTACTTGTCGCAGGTATAGATGTAT 57.480 36.000 3.46 0.00 0.00 2.29
6175 6891 6.947644 TTACTTGTCGCAGGTATAGATGTA 57.052 37.500 3.46 0.00 0.00 2.29
6176 6892 5.847111 TTACTTGTCGCAGGTATAGATGT 57.153 39.130 3.46 0.00 0.00 3.06
6177 6893 6.923508 TGAATTACTTGTCGCAGGTATAGATG 59.076 38.462 3.46 0.00 0.00 2.90
6178 6894 7.014326 TCTGAATTACTTGTCGCAGGTATAGAT 59.986 37.037 3.46 0.00 0.00 1.98
6179 6895 6.320418 TCTGAATTACTTGTCGCAGGTATAGA 59.680 38.462 3.46 3.80 0.00 1.98
6180 6896 6.504398 TCTGAATTACTTGTCGCAGGTATAG 58.496 40.000 3.46 0.00 0.00 1.31
6181 6897 6.459670 TCTGAATTACTTGTCGCAGGTATA 57.540 37.500 3.46 0.00 0.00 1.47
6182 6898 5.339008 TCTGAATTACTTGTCGCAGGTAT 57.661 39.130 3.46 0.00 0.00 2.73
6183 6899 4.794278 TCTGAATTACTTGTCGCAGGTA 57.206 40.909 0.00 0.00 0.00 3.08
6184 6900 3.678056 TCTGAATTACTTGTCGCAGGT 57.322 42.857 0.00 0.91 0.00 4.00
6185 6901 3.181530 CGTTCTGAATTACTTGTCGCAGG 60.182 47.826 0.00 0.00 0.00 4.85
6186 6902 3.181530 CCGTTCTGAATTACTTGTCGCAG 60.182 47.826 0.00 0.00 0.00 5.18
6187 6903 2.734606 CCGTTCTGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
6188 6904 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
6189 6905 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
6190 6906 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
6191 6907 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
6192 6908 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
6193 6909 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
6194 6910 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
6195 6911 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
6196 6912 4.607239 ACTACTCCCTCCGTTCTGAATTA 58.393 43.478 0.00 0.00 0.00 1.40
6197 6913 3.442076 ACTACTCCCTCCGTTCTGAATT 58.558 45.455 0.00 0.00 0.00 2.17
6198 6914 3.103080 ACTACTCCCTCCGTTCTGAAT 57.897 47.619 0.00 0.00 0.00 2.57
6199 6915 2.599408 ACTACTCCCTCCGTTCTGAA 57.401 50.000 0.00 0.00 0.00 3.02
6200 6916 2.444421 GAACTACTCCCTCCGTTCTGA 58.556 52.381 0.00 0.00 34.47 3.27
6201 6917 1.477295 GGAACTACTCCCTCCGTTCTG 59.523 57.143 0.00 0.00 38.44 3.02
6202 6918 1.849977 GGAACTACTCCCTCCGTTCT 58.150 55.000 0.00 0.00 38.44 3.01
6307 7023 7.448748 ACAAGTTAGGTGAATTGTTGGATAC 57.551 36.000 0.00 0.00 32.10 2.24
6352 7068 9.838975 CAGATTGCATTTTTGTACAGTTATACA 57.161 29.630 0.00 0.00 33.18 2.29
6800 7516 0.972134 TCAAGTGTCTGGAGCAGGAG 59.028 55.000 0.00 0.00 31.51 3.69
6878 7594 0.030638 CCACCGTCAGCACCAAAAAG 59.969 55.000 0.00 0.00 0.00 2.27
7094 7813 6.539173 TCCCTGTGTCAATTAAGTGTATTGT 58.461 36.000 2.43 0.00 35.13 2.71
7095 7814 7.447374 TTCCCTGTGTCAATTAAGTGTATTG 57.553 36.000 2.43 0.00 34.94 1.90
7120 7857 6.831976 TGGCCCATATTTTAAAAGTTGTGTT 58.168 32.000 0.00 0.00 0.00 3.32
7223 9170 6.072175 GGTAAATGTAAGCATGACACCTTGAA 60.072 38.462 0.00 0.00 27.27 2.69
7269 9216 1.486310 TGAACTTGTGCTCCAGTCTGT 59.514 47.619 0.00 0.00 0.00 3.41
7360 9324 7.725251 TCCCATGACATCATTATTTTTAAGCC 58.275 34.615 0.00 0.00 33.61 4.35
7374 9338 5.240713 GAACTCAATGTTCCCATGACATC 57.759 43.478 0.00 0.00 46.89 3.06
7587 9551 8.094798 AGCACGATTCAATTCTAAAACTAACA 57.905 30.769 0.00 0.00 0.00 2.41
7607 9571 1.339711 GGCTGTTGCATAAAAGCACG 58.660 50.000 3.04 0.00 45.61 5.34
7804 9770 5.669164 TGGGGCAACATATTTAAGAAACC 57.331 39.130 0.00 0.00 39.74 3.27
8034 10002 1.216064 TTGGAGACAGGGGATGGATG 58.784 55.000 0.00 0.00 44.54 3.51
8109 10077 1.078759 CCATCGCCGAGACTGTCAAC 61.079 60.000 10.88 2.97 0.00 3.18
8133 10101 1.340248 GCTGTAGCCAGTAATAGCCGA 59.660 52.381 0.00 0.00 41.02 5.54
8313 10281 3.550030 CGGTAAGCCAAAACCAGAACAAG 60.550 47.826 0.00 0.00 35.35 3.16
8328 10296 3.613030 TGGAATAAAGGGTTCGGTAAGC 58.387 45.455 0.00 0.00 0.00 3.09
8342 10311 2.290641 ACAGGCGACATGGTTGGAATAA 60.291 45.455 0.00 0.00 0.00 1.40
8344 10313 0.038166 ACAGGCGACATGGTTGGAAT 59.962 50.000 0.00 0.00 0.00 3.01
8345 10314 0.179004 AACAGGCGACATGGTTGGAA 60.179 50.000 0.00 0.00 0.00 3.53
8346 10315 0.179004 AAACAGGCGACATGGTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
8347 10316 0.039256 CAAACAGGCGACATGGTTGG 60.039 55.000 12.39 0.00 40.84 3.77
8348 10317 0.664166 GCAAACAGGCGACATGGTTG 60.664 55.000 14.87 14.87 46.03 3.77
8349 10318 0.823356 AGCAAACAGGCGACATGGTT 60.823 50.000 0.00 0.00 39.27 3.67
8350 10319 0.823356 AAGCAAACAGGCGACATGGT 60.823 50.000 0.00 0.00 39.27 3.55
8351 10320 0.314935 AAAGCAAACAGGCGACATGG 59.685 50.000 0.00 0.00 39.27 3.66
8352 10321 1.411394 CAAAGCAAACAGGCGACATG 58.589 50.000 0.00 0.00 39.27 3.21
8353 10322 0.314935 CCAAAGCAAACAGGCGACAT 59.685 50.000 0.00 0.00 39.27 3.06
8355 10324 0.594796 CACCAAAGCAAACAGGCGAC 60.595 55.000 0.00 0.00 39.27 5.19
8356 10325 1.732917 CACCAAAGCAAACAGGCGA 59.267 52.632 0.00 0.00 39.27 5.54
8357 10326 1.950630 GCACCAAAGCAAACAGGCG 60.951 57.895 0.00 0.00 39.27 5.52
8361 10330 5.476599 ACATATAGAAGCACCAAAGCAAACA 59.523 36.000 0.00 0.00 36.85 2.83
8372 10341 4.039703 TCGTAACGCACATATAGAAGCAC 58.960 43.478 0.00 0.00 0.00 4.40
8379 10348 5.488645 TCAGAACTCGTAACGCACATATA 57.511 39.130 0.00 0.00 0.00 0.86
8380 10349 4.365899 TCAGAACTCGTAACGCACATAT 57.634 40.909 0.00 0.00 0.00 1.78
8415 10384 3.368571 GCAACTGAGCCAGTGCCC 61.369 66.667 8.37 0.00 44.62 5.36
8464 10447 0.107848 CGGGCAAGAAATACCCTCGT 60.108 55.000 0.00 0.00 41.86 4.18
8465 10448 0.107848 ACGGGCAAGAAATACCCTCG 60.108 55.000 0.00 0.00 41.86 4.63
8471 10454 1.072489 TCCACACACGGGCAAGAAATA 59.928 47.619 0.00 0.00 0.00 1.40
8502 10485 1.827399 AACTGGTGGGCCGTACTCAG 61.827 60.000 17.63 17.63 37.67 3.35
8513 10496 1.608590 ACGAAGAAATGCAACTGGTGG 59.391 47.619 0.00 0.00 0.00 4.61
8519 10502 3.121696 CGCTTTTGACGAAGAAATGCAAC 60.122 43.478 0.00 0.00 34.66 4.17
8544 10527 0.370273 CTGGCGTACACATTTCTCGC 59.630 55.000 0.00 0.00 44.95 5.03
8627 10613 4.308899 GCTCTGGTTAGCTCGAAAGATA 57.691 45.455 0.00 0.00 40.84 1.98
8691 10677 6.154534 ACAGTATTATAGCCTTGTGACAGACA 59.845 38.462 0.00 0.00 0.00 3.41
8714 10709 6.330004 ACATGCATGAACATTCTTTGTACA 57.670 33.333 32.75 0.00 37.68 2.90
8721 11644 6.238566 GCAGTACATACATGCATGAACATTCT 60.239 38.462 32.75 18.75 39.75 2.40
8731 11654 2.501316 ACAGAGGCAGTACATACATGCA 59.499 45.455 6.40 0.00 41.78 3.96
8750 11673 9.739276 ATCCAAAACATCTTATACTTCAGAACA 57.261 29.630 0.00 0.00 0.00 3.18
8802 11725 9.781834 TTTAGTGTGTTTGTTCACTTATTTCAG 57.218 29.630 3.25 0.00 43.39 3.02
8832 11755 7.796958 TTTACGAATCAGATGCATATAGACG 57.203 36.000 0.00 4.71 0.00 4.18


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

AutoCloner maintained by Alex Coulton.