Multiple sequence alignment - TraesCS2D01G438900

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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 TraesCS2D01G438900 chr2D 100.000 4717 0 0 1 4717 548087620 548082904 0.000000e+00 8711.0
1 TraesCS2D01G438900 chr2D 80.105 191 21 10 16 189 418993383 418993573 4.960000e-25 126.0
2 TraesCS2D01G438900 chr2B 93.680 2927 116 34 944 3821 655017212 655014306 0.000000e+00 4316.0
3 TraesCS2D01G438900 chr2B 88.131 792 42 22 194 952 655020264 655019492 0.000000e+00 894.0
4 TraesCS2D01G438900 chr2B 97.436 156 4 0 2 157 655020419 655020264 2.800000e-67 267.0
5 TraesCS2D01G438900 chr2B 80.000 190 21 7 15 187 596106994 596107183 1.780000e-24 124.0
6 TraesCS2D01G438900 chr2A 91.516 2935 182 28 1352 4244 690923966 690926875 0.000000e+00 3978.0
7 TraesCS2D01G438900 chr2A 88.222 433 30 6 922 1349 690923508 690923924 9.120000e-137 497.0
8 TraesCS2D01G438900 chr2A 83.387 313 41 9 4316 4623 690927006 690927312 3.590000e-71 279.0
9 TraesCS2D01G438900 chr2A 87.121 132 17 0 60 191 634022299 634022168 2.940000e-32 150.0
10 TraesCS2D01G438900 chr2A 87.903 124 13 1 567 690 93459036 93459157 1.370000e-30 145.0
11 TraesCS2D01G438900 chr2A 79.381 194 23 5 13 189 159095047 159095240 2.310000e-23 121.0
12 TraesCS2D01G438900 chr2A 77.957 186 24 10 17 185 168314082 168313897 3.000000e-17 100.0
13 TraesCS2D01G438900 chr6D 88.445 476 49 6 1350 1822 251262180 251261708 1.900000e-158 569.0
14 TraesCS2D01G438900 chr6D 82.313 147 20 5 1209 1350 251262364 251262219 6.410000e-24 122.0
15 TraesCS2D01G438900 chr6D 94.444 54 3 0 1199 1252 447841025 447841078 3.020000e-12 84.2
16 TraesCS2D01G438900 chr1B 89.062 128 13 1 564 690 8417154 8417281 1.760000e-34 158.0
17 TraesCS2D01G438900 chr1B 88.189 127 15 0 60 186 116154453 116154327 8.180000e-33 152.0
18 TraesCS2D01G438900 chr5A 90.598 117 11 0 568 684 163619207 163619323 6.320000e-34 156.0
19 TraesCS2D01G438900 chr5A 87.597 129 16 0 60 188 413706343 413706471 2.940000e-32 150.0
20 TraesCS2D01G438900 chr5A 84.783 138 19 2 60 196 178721491 178721627 2.290000e-28 137.0
21 TraesCS2D01G438900 chr5A 83.333 78 9 4 183 259 660317871 660317797 8.470000e-08 69.4
22 TraesCS2D01G438900 chr4D 90.517 116 11 0 568 683 378301393 378301508 2.270000e-33 154.0
23 TraesCS2D01G438900 chr3A 87.879 132 15 1 60 191 550749629 550749759 2.270000e-33 154.0
24 TraesCS2D01G438900 chr3A 87.500 128 16 0 61 188 484444367 484444494 1.060000e-31 148.0
25 TraesCS2D01G438900 chr3A 88.889 117 13 0 568 684 578879844 578879960 1.370000e-30 145.0
26 TraesCS2D01G438900 chr6A 88.189 127 15 0 60 186 600657109 600656983 8.180000e-33 152.0
27 TraesCS2D01G438900 chr6A 88.136 118 14 0 567 684 12327780 12327897 1.770000e-29 141.0
28 TraesCS2D01G438900 chr6A 94.444 54 3 0 1199 1252 594430434 594430487 3.020000e-12 84.2
29 TraesCS2D01G438900 chr5B 87.805 123 13 2 569 690 179244645 179244524 4.920000e-30 143.0
30 TraesCS2D01G438900 chr7A 85.294 136 20 0 60 195 387485114 387484979 1.770000e-29 141.0
31 TraesCS2D01G438900 chr7A 80.000 165 27 6 205 368 103218711 103218552 2.980000e-22 117.0
32 TraesCS2D01G438900 chr5D 87.097 124 13 3 568 690 323283741 323283620 2.290000e-28 137.0
33 TraesCS2D01G438900 chr5D 77.949 195 26 9 15 192 297206155 297205961 6.460000e-19 106.0
34 TraesCS2D01G438900 chr7D 79.894 189 21 3 15 186 541421283 541421095 6.410000e-24 122.0
35 TraesCS2D01G438900 chr6B 77.228 202 28 7 9 193 564572493 564572693 8.350000e-18 102.0
36 TraesCS2D01G438900 chr6B 94.444 54 3 0 1199 1252 678661345 678661398 3.020000e-12 84.2
37 TraesCS2D01G438900 chr1D 78.409 176 21 9 15 173 105380126 105380301 1.080000e-16 99.0


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 TraesCS2D01G438900 chr2D 548082904 548087620 4716 True 8711.000000 8711 100.000000 1 4717 1 chr2D.!!$R1 4716
1 TraesCS2D01G438900 chr2B 655014306 655020419 6113 True 1825.666667 4316 93.082333 2 3821 3 chr2B.!!$R1 3819
2 TraesCS2D01G438900 chr2A 690923508 690927312 3804 False 1584.666667 3978 87.708333 922 4623 3 chr2A.!!$F3 3701
3 TraesCS2D01G438900 chr6D 251261708 251262364 656 True 345.500000 569 85.379000 1209 1822 2 chr6D.!!$R1 613

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
191 192 0.179059 TTCTGACAACCTTGCTCGCA 60.179 50.0 0.0 0.0 0.0 5.10 F
192 193 0.601046 TCTGACAACCTTGCTCGCAG 60.601 55.0 0.0 0.0 0.0 5.18 F
700 718 0.707616 AGCTACTCCCTCTGTCTGGT 59.292 55.0 0.0 0.0 0.0 4.00 F
1915 4302 0.752658 AGTTGGTGAAGCAAAAGGGC 59.247 50.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 4049 0.041839 GCACTATCGATTTGCTGCGG 60.042 55.0 19.38 0.0 33.26 5.69 R
1898 4285 0.753479 TCGCCCTTTTGCTTCACCAA 60.753 50.0 0.00 0.0 0.00 3.67 R
2519 4910 2.056094 AAAAGATTCAGCTTGCGCAC 57.944 45.0 11.12 0.0 39.10 5.34 R
3844 6276 0.174617 GGCTTCTCAGAGAACTCCGG 59.825 60.0 8.95 0.0 29.89 5.14 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
157 158 6.517605 TGGATCGTAAAATCGTGGAATCATA 58.482 36.000 0.00 0.00 0.00 2.15
158 159 7.158697 TGGATCGTAAAATCGTGGAATCATAT 58.841 34.615 0.00 0.00 0.00 1.78
159 160 8.308207 TGGATCGTAAAATCGTGGAATCATATA 58.692 33.333 0.00 0.00 0.00 0.86
160 161 9.146984 GGATCGTAAAATCGTGGAATCATATAA 57.853 33.333 0.00 0.00 0.00 0.98
161 162 9.953825 GATCGTAAAATCGTGGAATCATATAAC 57.046 33.333 0.00 0.00 0.00 1.89
162 163 8.874744 TCGTAAAATCGTGGAATCATATAACA 57.125 30.769 0.00 0.00 0.00 2.41
163 164 8.974408 TCGTAAAATCGTGGAATCATATAACAG 58.026 33.333 0.00 0.00 0.00 3.16
164 165 8.974408 CGTAAAATCGTGGAATCATATAACAGA 58.026 33.333 0.00 0.00 0.00 3.41
168 169 9.559732 AAATCGTGGAATCATATAACAGAATCA 57.440 29.630 0.00 0.00 0.00 2.57
169 170 7.946655 TCGTGGAATCATATAACAGAATCAC 57.053 36.000 0.00 0.00 0.00 3.06
170 171 6.640907 TCGTGGAATCATATAACAGAATCACG 59.359 38.462 0.00 0.00 0.00 4.35
171 172 6.640907 CGTGGAATCATATAACAGAATCACGA 59.359 38.462 0.00 0.00 0.00 4.35
172 173 7.329471 CGTGGAATCATATAACAGAATCACGAT 59.671 37.037 0.00 0.00 0.00 3.73
173 174 8.993121 GTGGAATCATATAACAGAATCACGATT 58.007 33.333 0.00 0.00 0.00 3.34
174 175 9.208022 TGGAATCATATAACAGAATCACGATTC 57.792 33.333 11.11 11.11 45.66 2.52
185 186 4.962693 GAATCACGATTCTGACAACCTTG 58.037 43.478 11.68 0.00 42.85 3.61
186 187 2.143122 TCACGATTCTGACAACCTTGC 58.857 47.619 0.00 0.00 0.00 4.01
187 188 2.146342 CACGATTCTGACAACCTTGCT 58.854 47.619 0.00 0.00 0.00 3.91
188 189 2.158449 CACGATTCTGACAACCTTGCTC 59.842 50.000 0.00 0.00 0.00 4.26
189 190 1.391485 CGATTCTGACAACCTTGCTCG 59.609 52.381 0.00 0.00 0.00 5.03
190 191 1.129437 GATTCTGACAACCTTGCTCGC 59.871 52.381 0.00 0.00 0.00 5.03
191 192 0.179059 TTCTGACAACCTTGCTCGCA 60.179 50.000 0.00 0.00 0.00 5.10
192 193 0.601046 TCTGACAACCTTGCTCGCAG 60.601 55.000 0.00 0.00 0.00 5.18
193 194 0.882042 CTGACAACCTTGCTCGCAGT 60.882 55.000 0.00 0.00 0.00 4.40
274 275 1.391157 TTGTGGGCACTTCCAAGCAC 61.391 55.000 0.00 0.00 38.72 4.40
511 529 9.647797 AAGTTAAGTTTTAAAAGGGTTCACTTG 57.352 29.630 0.00 0.00 0.00 3.16
512 530 7.762615 AGTTAAGTTTTAAAAGGGTTCACTTGC 59.237 33.333 0.00 0.00 0.00 4.01
550 568 5.356291 CTCAGGATTGAGGAGTTCAGAAT 57.644 43.478 0.00 0.00 45.79 2.40
557 575 2.573462 TGAGGAGTTCAGAATTGAGGGG 59.427 50.000 0.00 0.00 34.15 4.79
560 578 1.004745 GAGTTCAGAATTGAGGGGGCA 59.995 52.381 0.00 0.00 34.15 5.36
590 608 5.457686 AGGGCATGTACAATGGTTGATAAT 58.542 37.500 0.00 0.00 0.00 1.28
672 690 6.352016 TGGGTCATCTCTTAGCATTATCTC 57.648 41.667 0.00 0.00 0.00 2.75
674 692 5.483583 GGGTCATCTCTTAGCATTATCTCCT 59.516 44.000 0.00 0.00 0.00 3.69
699 717 2.092103 ACTAGCTACTCCCTCTGTCTGG 60.092 54.545 0.00 0.00 0.00 3.86
700 718 0.707616 AGCTACTCCCTCTGTCTGGT 59.292 55.000 0.00 0.00 0.00 4.00
701 719 1.107945 GCTACTCCCTCTGTCTGGTC 58.892 60.000 0.00 0.00 0.00 4.02
767 800 7.921786 ATCCATTTGTAAGATTTTCAGACGA 57.078 32.000 0.00 0.00 0.00 4.20
770 803 7.023575 CCATTTGTAAGATTTTCAGACGAAGG 58.976 38.462 0.00 0.00 31.28 3.46
789 822 8.376889 ACGAAGGGAGTATTTTTAAAAACGTA 57.623 30.769 15.35 3.00 0.00 3.57
791 824 9.830294 CGAAGGGAGTATTTTTAAAAACGTAAT 57.170 29.630 15.35 4.92 0.00 1.89
882 916 3.323691 TGATTTCTTTCTCCTCCACGTCA 59.676 43.478 0.00 0.00 0.00 4.35
897 931 4.097135 TCCACGTCATCATTTCTCTCTCTC 59.903 45.833 0.00 0.00 0.00 3.20
898 932 4.097741 CCACGTCATCATTTCTCTCTCTCT 59.902 45.833 0.00 0.00 0.00 3.10
899 933 5.394005 CCACGTCATCATTTCTCTCTCTCTT 60.394 44.000 0.00 0.00 0.00 2.85
900 934 6.098679 CACGTCATCATTTCTCTCTCTCTTT 58.901 40.000 0.00 0.00 0.00 2.52
936 970 3.254470 TCTCTCTCTAGTCCACGTCTG 57.746 52.381 0.00 0.00 0.00 3.51
1266 3593 1.187087 AGGTCCTCCTCGCTTACTTG 58.813 55.000 0.00 0.00 40.58 3.16
1312 3644 1.269998 CCTGGAGCGTGTAGGCTATAC 59.730 57.143 11.03 11.03 44.93 1.47
1319 3651 3.446161 AGCGTGTAGGCTATACAAGTCAA 59.554 43.478 19.51 0.00 42.62 3.18
1320 3652 3.797256 GCGTGTAGGCTATACAAGTCAAG 59.203 47.826 19.51 5.20 29.52 3.02
1675 4054 7.195646 ACATTGTTTGATATTATGTTCCGCAG 58.804 34.615 0.00 0.00 0.00 5.18
1786 4173 3.245229 TGCAGTTTGGTGAGGTGGATATT 60.245 43.478 0.00 0.00 0.00 1.28
1798 4185 5.011431 TGAGGTGGATATTGATAGCTCACTG 59.989 44.000 0.00 0.00 41.21 3.66
1858 4245 2.493278 GGTGAATAATGGCTGCTTGTGT 59.507 45.455 0.00 0.00 0.00 3.72
1915 4302 0.752658 AGTTGGTGAAGCAAAAGGGC 59.247 50.000 0.00 0.00 0.00 5.19
1936 4323 4.034048 GGCGACAAGTTTGATCATATCGTT 59.966 41.667 0.00 0.00 0.00 3.85
1989 4376 8.880750 GTTCAAAATCTACCAGACTACCAATAC 58.119 37.037 0.00 0.00 0.00 1.89
2030 4418 6.750148 AGTCTAAAGATGTGTCGAAGTTCTT 58.250 36.000 0.56 0.00 0.00 2.52
2033 4421 9.784680 GTCTAAAGATGTGTCGAAGTTCTTATA 57.215 33.333 0.56 0.00 0.00 0.98
2439 4830 6.353323 TGATGACACAGAACTTGAGGTTTTA 58.647 36.000 0.00 0.00 38.41 1.52
2464 4855 3.073274 ACAAGATCAAGGTAGGTTGGC 57.927 47.619 0.00 0.00 0.00 4.52
2519 4910 7.288317 TGTCAAGTGCAAACTTATTTTGTTG 57.712 32.000 0.00 0.00 45.70 3.33
2523 4914 4.267452 AGTGCAAACTTATTTTGTTGTGCG 59.733 37.500 0.00 0.00 45.70 5.34
2667 5058 9.556030 GGTTAGTATCTTTATTTTCTTGTGTGC 57.444 33.333 0.00 0.00 0.00 4.57
2690 5081 5.125417 GCTAAAGAATGTTGGGCTGTAATCA 59.875 40.000 0.00 0.00 0.00 2.57
2694 5085 4.885907 AGAATGTTGGGCTGTAATCATGAG 59.114 41.667 0.09 0.00 0.00 2.90
2695 5086 3.998913 TGTTGGGCTGTAATCATGAGA 57.001 42.857 0.09 0.00 0.00 3.27
2825 5227 2.240667 AGCATGGTAATGTTCAGGCTCT 59.759 45.455 0.00 0.00 46.09 4.09
2846 5248 3.879295 CTGGTATCCATGCGTTCTGAATT 59.121 43.478 0.00 0.00 30.82 2.17
2870 5272 7.373617 TCCACCATATTAGAGACATGCTAAA 57.626 36.000 0.00 0.00 32.16 1.85
2914 5316 3.256631 CAGCATTTAGTGGCTTCCTTTGT 59.743 43.478 0.00 0.00 38.56 2.83
3015 5417 8.025445 CAGTTTGCTCTAAATTTTCTGTATGCT 58.975 33.333 0.00 0.00 0.00 3.79
3081 5483 4.357918 ACTTTGCTGACTTGTAGGACAT 57.642 40.909 0.00 0.00 0.00 3.06
3233 5638 4.590850 ACTTTTCCTCAGCAAATGAACC 57.409 40.909 0.00 0.00 37.52 3.62
3247 5652 7.538678 CAGCAAATGAACCAGTTTATCACTAAC 59.461 37.037 0.00 0.00 32.76 2.34
3292 5697 0.908198 ATTGGCTGGAGAGACTGGTC 59.092 55.000 0.00 0.00 0.00 4.02
3304 5709 2.494073 GAGACTGGTCGATGAGAAAGGT 59.506 50.000 0.00 0.00 34.09 3.50
3410 5815 1.266989 CCTCGGCAAAGAAACCAGTTC 59.733 52.381 0.00 0.00 36.38 3.01
3455 5863 2.724977 TGCTTGAACGAAGTCGATCT 57.275 45.000 7.87 0.00 45.00 2.75
3479 5887 5.047377 TGTGTGATCAGAGCTATGTGTTGTA 60.047 40.000 8.44 0.00 0.00 2.41
3516 5924 2.560542 TCCTTGTGTTGCCGCATAAAAT 59.439 40.909 0.00 0.00 0.00 1.82
3555 5963 2.129607 TGCAGTTTCGACCGTTCTAAC 58.870 47.619 0.00 0.00 0.00 2.34
3556 5964 2.129607 GCAGTTTCGACCGTTCTAACA 58.870 47.619 0.00 0.00 0.00 2.41
3758 6182 2.627515 ATCTCATTGGGATCGTGGTG 57.372 50.000 0.00 0.00 0.00 4.17
3760 6184 0.464373 CTCATTGGGATCGTGGTGGG 60.464 60.000 0.00 0.00 0.00 4.61
3770 6194 2.971598 CGTGGTGGGGGCTGAGAAT 61.972 63.158 0.00 0.00 0.00 2.40
3778 6207 3.007398 GTGGGGGCTGAGAATGACTATAG 59.993 52.174 0.00 0.00 0.00 1.31
3844 6276 0.392336 TTTGGTGCTGATGTTTGCCC 59.608 50.000 0.00 0.00 0.00 5.36
3846 6278 2.568090 GTGCTGATGTTTGCCCCG 59.432 61.111 0.00 0.00 0.00 5.73
3861 6293 0.820871 CCCCGGAGTTCTCTGAGAAG 59.179 60.000 19.85 8.62 34.42 2.85
3880 6312 3.784701 AGCCGAGTAGTGTATCTTGTG 57.215 47.619 0.00 0.00 0.00 3.33
3902 6337 4.070009 GGACTAGGCTAGAAGTAGAGAGC 58.930 52.174 27.59 4.01 0.00 4.09
3920 6355 1.559682 AGCCGAATTGTGTGGTATCCT 59.440 47.619 0.00 0.00 0.00 3.24
3940 6375 5.734720 TCCTTGTCTTGATGAGAACCATAC 58.265 41.667 0.00 0.00 35.79 2.39
3949 6384 3.838244 TGAGAACCATACCTGTATGCC 57.162 47.619 11.05 3.95 41.10 4.40
3956 6391 3.181469 ACCATACCTGTATGCCGTTGTAG 60.181 47.826 11.05 0.00 41.10 2.74
3974 6409 7.634817 CCGTTGTAGTTTTCTTGCGATTTATAG 59.365 37.037 0.00 0.00 0.00 1.31
3975 6410 7.634817 CGTTGTAGTTTTCTTGCGATTTATAGG 59.365 37.037 0.00 0.00 0.00 2.57
3976 6411 8.448615 GTTGTAGTTTTCTTGCGATTTATAGGT 58.551 33.333 0.00 0.00 0.00 3.08
3977 6412 8.556213 TGTAGTTTTCTTGCGATTTATAGGTT 57.444 30.769 0.00 0.00 0.00 3.50
3978 6413 9.656040 TGTAGTTTTCTTGCGATTTATAGGTTA 57.344 29.630 0.00 0.00 0.00 2.85
4049 6487 2.125753 GTCAGCTCAGCCGTCTGG 60.126 66.667 0.00 0.00 40.69 3.86
4064 6502 3.172050 CGTCTGGAACTCTGAATACGTG 58.828 50.000 0.00 0.00 0.00 4.49
4110 6548 4.405358 TGTCATTCTATTGGAATTTGGCCC 59.595 41.667 0.00 0.00 42.20 5.80
4115 6553 1.278537 ATTGGAATTTGGCCCTGTGG 58.721 50.000 0.00 0.00 0.00 4.17
4140 6579 5.454187 CCGGCTCTATTTACCTCCAAATACA 60.454 44.000 0.00 0.00 30.84 2.29
4152 6591 6.194235 ACCTCCAAATACAGGATATTTTGCA 58.806 36.000 0.00 0.00 33.99 4.08
4180 6621 2.856760 AGACCCTCTTATCTGGCTGA 57.143 50.000 0.00 0.00 0.00 4.26
4185 6626 2.093447 CCCTCTTATCTGGCTGACGTTT 60.093 50.000 0.00 0.00 0.00 3.60
4186 6627 3.132289 CCCTCTTATCTGGCTGACGTTTA 59.868 47.826 0.00 0.00 0.00 2.01
4189 6630 5.067413 CCTCTTATCTGGCTGACGTTTACTA 59.933 44.000 0.00 0.00 0.00 1.82
4190 6631 6.132791 TCTTATCTGGCTGACGTTTACTAG 57.867 41.667 0.00 0.00 0.00 2.57
4192 6633 2.522185 TCTGGCTGACGTTTACTAGGT 58.478 47.619 0.00 0.00 0.00 3.08
4193 6634 2.895404 TCTGGCTGACGTTTACTAGGTT 59.105 45.455 0.00 0.00 0.00 3.50
4200 6641 1.348696 ACGTTTACTAGGTTGGGGTGG 59.651 52.381 0.00 0.00 0.00 4.61
4208 6649 2.216331 GGTTGGGGTGGCATTTGCT 61.216 57.895 2.12 0.00 41.70 3.91
4210 6651 0.532115 GTTGGGGTGGCATTTGCTAG 59.468 55.000 2.12 0.00 41.70 3.42
4216 6657 1.617740 GTGGCATTTGCTAGCGTTTC 58.382 50.000 10.77 0.00 41.70 2.78
4220 6661 2.187707 GCATTTGCTAGCGTTTCCATG 58.812 47.619 10.77 6.72 38.21 3.66
4221 6662 2.159393 GCATTTGCTAGCGTTTCCATGA 60.159 45.455 10.77 0.00 38.21 3.07
4222 6663 3.673052 GCATTTGCTAGCGTTTCCATGAA 60.673 43.478 10.77 0.00 38.21 2.57
4231 6672 5.767816 AGCGTTTCCATGAAAGTTTTAGT 57.232 34.783 0.00 0.00 31.87 2.24
4233 6674 6.206498 AGCGTTTCCATGAAAGTTTTAGTTC 58.794 36.000 0.00 0.00 31.87 3.01
4237 6678 7.165812 CGTTTCCATGAAAGTTTTAGTTCTGTG 59.834 37.037 0.00 0.00 31.87 3.66
4240 6681 6.039270 TCCATGAAAGTTTTAGTTCTGTGTGG 59.961 38.462 0.00 0.00 0.00 4.17
4244 6685 4.245251 AGTTTTAGTTCTGTGTGGGGTT 57.755 40.909 0.00 0.00 0.00 4.11
4245 6686 3.951680 AGTTTTAGTTCTGTGTGGGGTTG 59.048 43.478 0.00 0.00 0.00 3.77
4246 6687 3.935818 TTTAGTTCTGTGTGGGGTTGA 57.064 42.857 0.00 0.00 0.00 3.18
4247 6688 3.935818 TTAGTTCTGTGTGGGGTTGAA 57.064 42.857 0.00 0.00 0.00 2.69
4249 6690 1.843851 AGTTCTGTGTGGGGTTGAAGA 59.156 47.619 0.00 0.00 0.00 2.87
4250 6691 2.241176 AGTTCTGTGTGGGGTTGAAGAA 59.759 45.455 0.00 0.00 0.00 2.52
4251 6692 3.020984 GTTCTGTGTGGGGTTGAAGAAA 58.979 45.455 0.00 0.00 0.00 2.52
4254 6695 2.358898 CTGTGTGGGGTTGAAGAAACTG 59.641 50.000 0.00 0.00 38.92 3.16
4255 6696 2.291282 TGTGTGGGGTTGAAGAAACTGT 60.291 45.455 0.00 0.00 38.92 3.55
4256 6697 2.357952 GTGTGGGGTTGAAGAAACTGTC 59.642 50.000 0.00 0.00 38.92 3.51
4257 6698 2.025793 TGTGGGGTTGAAGAAACTGTCA 60.026 45.455 0.00 0.00 38.92 3.58
4258 6699 2.357952 GTGGGGTTGAAGAAACTGTCAC 59.642 50.000 0.00 0.00 38.92 3.67
4259 6700 1.954382 GGGGTTGAAGAAACTGTCACC 59.046 52.381 0.00 0.00 38.92 4.02
4260 6701 2.650322 GGGTTGAAGAAACTGTCACCA 58.350 47.619 0.00 0.00 38.92 4.17
4261 6702 2.357952 GGGTTGAAGAAACTGTCACCAC 59.642 50.000 0.00 0.00 38.92 4.16
4262 6703 2.357952 GGTTGAAGAAACTGTCACCACC 59.642 50.000 0.00 0.00 38.92 4.61
4263 6704 1.948104 TGAAGAAACTGTCACCACCG 58.052 50.000 0.00 0.00 0.00 4.94
4268 6709 3.162666 AGAAACTGTCACCACCGATAGA 58.837 45.455 0.00 0.00 39.76 1.98
4269 6710 3.769844 AGAAACTGTCACCACCGATAGAT 59.230 43.478 0.00 0.00 39.76 1.98
4270 6711 4.954202 AGAAACTGTCACCACCGATAGATA 59.046 41.667 0.00 0.00 39.76 1.98
4271 6712 4.920640 AACTGTCACCACCGATAGATAG 57.079 45.455 0.00 0.00 39.76 2.08
4274 6756 3.883489 CTGTCACCACCGATAGATAGTCA 59.117 47.826 0.00 0.00 39.76 3.41
4276 6758 4.135306 GTCACCACCGATAGATAGTCAGA 58.865 47.826 0.00 0.00 39.76 3.27
4292 6774 7.934120 AGATAGTCAGATACAACTAAAATGGCC 59.066 37.037 0.00 0.00 32.08 5.36
4306 6788 6.995091 ACTAAAATGGCCAGCAAAAACATTTA 59.005 30.769 13.05 4.79 39.89 1.40
4311 6793 6.311055 TGGCCAGCAAAAACATTTAAAATC 57.689 33.333 0.00 0.00 0.00 2.17
4312 6794 6.060788 TGGCCAGCAAAAACATTTAAAATCT 58.939 32.000 0.00 0.00 0.00 2.40
4314 6796 6.298853 GCCAGCAAAAACATTTAAAATCTCG 58.701 36.000 0.00 0.00 0.00 4.04
4321 6821 4.361451 ACATTTAAAATCTCGCAGCCAG 57.639 40.909 0.00 0.00 0.00 4.85
4332 6832 2.805099 CTCGCAGCCAGATAAGATTTCC 59.195 50.000 0.00 0.00 0.00 3.13
4333 6833 2.170397 TCGCAGCCAGATAAGATTTCCA 59.830 45.455 0.00 0.00 0.00 3.53
4335 6835 3.567164 CGCAGCCAGATAAGATTTCCAAT 59.433 43.478 0.00 0.00 0.00 3.16
4341 6843 8.139989 CAGCCAGATAAGATTTCCAATAAAAGG 58.860 37.037 0.00 0.00 0.00 3.11
4343 6845 8.864087 GCCAGATAAGATTTCCAATAAAAGGAT 58.136 33.333 0.00 0.00 34.56 3.24
4364 6866 4.576216 TTACACATGAATTTTGCCGTGT 57.424 36.364 0.00 0.00 40.46 4.49
4376 6878 0.107897 TGCCGTGTGACAGACTTGTT 60.108 50.000 0.82 0.00 37.76 2.83
4379 6881 1.860950 CCGTGTGACAGACTTGTTCAG 59.139 52.381 0.82 0.00 37.76 3.02
4384 6886 3.118629 TGTGACAGACTTGTTCAGCTCTT 60.119 43.478 0.00 0.00 37.76 2.85
4385 6887 3.247173 GTGACAGACTTGTTCAGCTCTTG 59.753 47.826 0.00 0.00 37.76 3.02
4389 6891 0.475906 ACTTGTTCAGCTCTTGGCCT 59.524 50.000 3.32 0.00 43.05 5.19
4395 6897 0.322975 TCAGCTCTTGGCCTGAAGTC 59.677 55.000 3.32 0.00 43.05 3.01
4399 6901 0.390472 CTCTTGGCCTGAAGTCGTCC 60.390 60.000 3.32 0.00 0.00 4.79
4411 6913 0.529378 AGTCGTCCCGCGTTTCTATT 59.471 50.000 4.92 0.00 42.13 1.73
4414 6916 0.523968 CGTCCCGCGTTTCTATTCGA 60.524 55.000 4.92 0.00 35.54 3.71
4421 6923 3.173599 CGCGTTTCTATTCGACCTAACA 58.826 45.455 0.00 0.00 0.00 2.41
4435 6937 4.201970 CGACCTAACAAACACACCACAAAT 60.202 41.667 0.00 0.00 0.00 2.32
4436 6938 5.257082 ACCTAACAAACACACCACAAATC 57.743 39.130 0.00 0.00 0.00 2.17
4438 6940 4.098654 CCTAACAAACACACCACAAATCCA 59.901 41.667 0.00 0.00 0.00 3.41
4446 6948 2.159028 ACACCACAAATCCAAAAACCGG 60.159 45.455 0.00 0.00 0.00 5.28
4447 6949 1.414550 ACCACAAATCCAAAAACCGGG 59.585 47.619 6.32 0.00 0.00 5.73
4453 6955 3.973206 AATCCAAAAACCGGGGATTTC 57.027 42.857 14.22 0.00 46.51 2.17
4454 6956 2.383442 TCCAAAAACCGGGGATTTCA 57.617 45.000 6.32 0.00 0.00 2.69
4457 6959 2.547007 CCAAAAACCGGGGATTTCACAC 60.547 50.000 6.32 0.00 0.00 3.82
4458 6960 1.334160 AAAACCGGGGATTTCACACC 58.666 50.000 6.32 0.00 0.00 4.16
4468 6970 3.498018 GGGATTTCACACCAATTTTGCAC 59.502 43.478 0.00 0.00 0.00 4.57
4473 6975 3.443037 TCACACCAATTTTGCACGAAAG 58.557 40.909 0.00 0.00 0.00 2.62
4476 6978 2.033832 CACCAATTTTGCACGAAAGCAC 60.034 45.455 0.00 0.00 45.61 4.40
4477 6979 1.526464 CCAATTTTGCACGAAAGCACC 59.474 47.619 0.00 0.00 45.61 5.01
4478 6980 1.189884 CAATTTTGCACGAAAGCACCG 59.810 47.619 0.00 0.00 45.61 4.94
4483 6985 0.237235 TGCACGAAAGCACCGAAATC 59.763 50.000 0.00 0.00 40.11 2.17
4486 6988 1.128692 CACGAAAGCACCGAAATCCTC 59.871 52.381 0.00 0.00 0.00 3.71
4489 6991 2.675317 CGAAAGCACCGAAATCCTCTCT 60.675 50.000 0.00 0.00 0.00 3.10
4491 6993 1.859302 AGCACCGAAATCCTCTCTCT 58.141 50.000 0.00 0.00 0.00 3.10
4492 6994 1.754226 AGCACCGAAATCCTCTCTCTC 59.246 52.381 0.00 0.00 0.00 3.20
4493 6995 1.478510 GCACCGAAATCCTCTCTCTCA 59.521 52.381 0.00 0.00 0.00 3.27
4494 6996 2.737039 GCACCGAAATCCTCTCTCTCAC 60.737 54.545 0.00 0.00 0.00 3.51
4495 6997 1.746220 ACCGAAATCCTCTCTCTCACG 59.254 52.381 0.00 0.00 0.00 4.35
4496 6998 2.017782 CCGAAATCCTCTCTCTCACGA 58.982 52.381 0.00 0.00 0.00 4.35
4497 6999 2.423892 CCGAAATCCTCTCTCTCACGAA 59.576 50.000 0.00 0.00 0.00 3.85
4498 7000 3.119459 CCGAAATCCTCTCTCTCACGAAA 60.119 47.826 0.00 0.00 0.00 3.46
4499 7001 4.440802 CCGAAATCCTCTCTCTCACGAAAT 60.441 45.833 0.00 0.00 0.00 2.17
4500 7002 4.737765 CGAAATCCTCTCTCTCACGAAATC 59.262 45.833 0.00 0.00 0.00 2.17
4501 7003 5.449862 CGAAATCCTCTCTCTCACGAAATCT 60.450 44.000 0.00 0.00 0.00 2.40
4502 7004 4.916983 ATCCTCTCTCTCACGAAATCTG 57.083 45.455 0.00 0.00 0.00 2.90
4504 7006 4.336280 TCCTCTCTCTCACGAAATCTGAA 58.664 43.478 0.00 0.00 0.00 3.02
4505 7007 4.767409 TCCTCTCTCTCACGAAATCTGAAA 59.233 41.667 0.00 0.00 0.00 2.69
4506 7008 5.243954 TCCTCTCTCTCACGAAATCTGAAAA 59.756 40.000 0.00 0.00 0.00 2.29
4554 7056 0.736325 AACCGAATTCCGCGAGACAG 60.736 55.000 8.23 0.00 36.84 3.51
4569 7072 3.786635 GAGACAGTGCTCGTATGGAATT 58.213 45.455 0.00 0.00 0.00 2.17
4589 7092 0.527817 CCATGCGGGAGAACGAGTAC 60.528 60.000 0.00 0.00 40.01 2.73
4591 7094 0.456221 ATGCGGGAGAACGAGTACTG 59.544 55.000 0.00 0.00 35.47 2.74
4593 7096 1.880894 CGGGAGAACGAGTACTGCA 59.119 57.895 0.00 0.00 35.47 4.41
4619 7122 4.179579 GGCGTCCGCTGATTTGCC 62.180 66.667 11.82 3.89 41.60 4.52
4623 7126 2.031919 TCCGCTGATTTGCCGTGT 59.968 55.556 0.00 0.00 0.00 4.49
4624 7127 2.032634 TCCGCTGATTTGCCGTGTC 61.033 57.895 0.00 0.00 0.00 3.67
4625 7128 2.480555 CGCTGATTTGCCGTGTCC 59.519 61.111 0.00 0.00 0.00 4.02
4626 7129 2.480555 GCTGATTTGCCGTGTCCG 59.519 61.111 0.00 0.00 0.00 4.79
4627 7130 2.325082 GCTGATTTGCCGTGTCCGT 61.325 57.895 0.00 0.00 0.00 4.69
4628 7131 1.497278 CTGATTTGCCGTGTCCGTG 59.503 57.895 0.00 0.00 0.00 4.94
4629 7132 2.175811 GATTTGCCGTGTCCGTGC 59.824 61.111 0.00 0.00 0.00 5.34
4630 7133 3.645157 GATTTGCCGTGTCCGTGCG 62.645 63.158 0.00 0.00 34.36 5.34
4649 7152 4.814294 GCTACGAGGGTGCCCGTG 62.814 72.222 0.98 1.09 41.95 4.94
4650 7153 4.143333 CTACGAGGGTGCCCGTGG 62.143 72.222 0.98 0.00 41.95 4.94
4661 7164 2.989639 CCCGTGGCATCCAGAGAA 59.010 61.111 0.00 0.00 32.34 2.87
4662 7165 1.299648 CCCGTGGCATCCAGAGAAA 59.700 57.895 0.00 0.00 32.34 2.52
4663 7166 0.322456 CCCGTGGCATCCAGAGAAAA 60.322 55.000 0.00 0.00 32.34 2.29
4664 7167 0.804989 CCGTGGCATCCAGAGAAAAC 59.195 55.000 0.00 0.00 32.34 2.43
4665 7168 0.443869 CGTGGCATCCAGAGAAAACG 59.556 55.000 0.00 0.00 32.34 3.60
4666 7169 0.169009 GTGGCATCCAGAGAAAACGC 59.831 55.000 0.00 0.00 32.34 4.84
4667 7170 1.298157 TGGCATCCAGAGAAAACGCG 61.298 55.000 3.53 3.53 0.00 6.01
4668 7171 1.425428 GCATCCAGAGAAAACGCGG 59.575 57.895 12.47 0.00 0.00 6.46
4669 7172 1.298859 GCATCCAGAGAAAACGCGGT 61.299 55.000 12.47 0.00 0.00 5.68
4670 7173 2.004583 CATCCAGAGAAAACGCGGTA 57.995 50.000 12.47 0.00 0.00 4.02
4671 7174 1.659098 CATCCAGAGAAAACGCGGTAC 59.341 52.381 12.47 1.34 0.00 3.34
4672 7175 0.037975 TCCAGAGAAAACGCGGTACC 60.038 55.000 12.47 0.16 0.00 3.34
4673 7176 1.017701 CCAGAGAAAACGCGGTACCC 61.018 60.000 12.47 0.00 0.00 3.69
4716 7219 4.864704 TTTTACACCCTTCCATCTTTGC 57.135 40.909 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.813210 CCTTGGCTGCGAGGAATCTC 60.813 60.000 13.58 0.00 34.91 2.75
7 8 1.572085 CTGACAACCTTGGCTGCGAG 61.572 60.000 0.00 0.00 37.03 5.03
8 9 1.597854 CTGACAACCTTGGCTGCGA 60.598 57.895 0.00 0.00 37.03 5.10
10 11 1.200948 GATTCTGACAACCTTGGCTGC 59.799 52.381 0.00 0.00 37.03 5.25
109 110 1.790818 AACCCCTCCGATTCTAGGAC 58.209 55.000 4.04 0.00 34.58 3.85
163 164 4.670221 GCAAGGTTGTCAGAATCGTGATTC 60.670 45.833 13.46 13.46 45.66 2.52
164 165 3.189287 GCAAGGTTGTCAGAATCGTGATT 59.811 43.478 0.00 0.00 0.00 2.57
165 166 2.744202 GCAAGGTTGTCAGAATCGTGAT 59.256 45.455 0.00 0.00 0.00 3.06
166 167 2.143122 GCAAGGTTGTCAGAATCGTGA 58.857 47.619 0.00 0.00 0.00 4.35
167 168 2.146342 AGCAAGGTTGTCAGAATCGTG 58.854 47.619 0.00 0.00 0.00 4.35
168 169 2.417719 GAGCAAGGTTGTCAGAATCGT 58.582 47.619 0.00 0.00 0.00 3.73
169 170 1.391485 CGAGCAAGGTTGTCAGAATCG 59.609 52.381 0.00 0.00 0.00 3.34
170 171 1.129437 GCGAGCAAGGTTGTCAGAATC 59.871 52.381 0.00 0.00 0.00 2.52
171 172 1.160137 GCGAGCAAGGTTGTCAGAAT 58.840 50.000 0.00 0.00 0.00 2.40
172 173 0.179059 TGCGAGCAAGGTTGTCAGAA 60.179 50.000 0.00 0.00 0.00 3.02
173 174 0.601046 CTGCGAGCAAGGTTGTCAGA 60.601 55.000 0.00 0.00 0.00 3.27
174 175 0.882042 ACTGCGAGCAAGGTTGTCAG 60.882 55.000 0.00 8.42 0.00 3.51
175 176 1.146041 ACTGCGAGCAAGGTTGTCA 59.854 52.632 0.00 0.00 0.00 3.58
176 177 1.571460 CACTGCGAGCAAGGTTGTC 59.429 57.895 0.00 0.00 0.00 3.18
177 178 2.546494 GCACTGCGAGCAAGGTTGT 61.546 57.895 0.00 0.00 0.00 3.32
178 179 1.859427 ATGCACTGCGAGCAAGGTTG 61.859 55.000 0.00 0.00 46.27 3.77
179 180 1.580845 GATGCACTGCGAGCAAGGTT 61.581 55.000 0.00 0.00 46.27 3.50
180 181 2.033141 ATGCACTGCGAGCAAGGT 59.967 55.556 0.00 0.00 46.27 3.50
181 182 2.789917 GATGCACTGCGAGCAAGG 59.210 61.111 0.00 0.00 46.27 3.61
182 183 1.629345 TTCGATGCACTGCGAGCAAG 61.629 55.000 7.96 0.00 46.27 4.01
183 184 1.629345 CTTCGATGCACTGCGAGCAA 61.629 55.000 7.96 0.00 46.27 3.91
185 186 0.802222 TACTTCGATGCACTGCGAGC 60.802 55.000 7.96 0.00 37.85 5.03
186 187 1.783711 GATACTTCGATGCACTGCGAG 59.216 52.381 7.96 6.04 37.85 5.03
187 188 1.840181 GATACTTCGATGCACTGCGA 58.160 50.000 4.28 4.28 34.32 5.10
274 275 5.356190 ACATGATAGGAGCACAACAATCAAG 59.644 40.000 0.00 0.00 0.00 3.02
379 395 6.952773 AACTTGCTAATTAAGGTTCACACA 57.047 33.333 0.00 0.00 0.00 3.72
495 513 4.468153 AGGTTTGCAAGTGAACCCTTTTAA 59.532 37.500 13.28 0.00 45.08 1.52
502 520 6.745116 AGTTAAATAGGTTTGCAAGTGAACC 58.255 36.000 9.60 9.60 44.47 3.62
511 529 5.497474 TCCTGAGGAGTTAAATAGGTTTGC 58.503 41.667 0.00 0.00 0.00 3.68
512 530 7.829211 TCAATCCTGAGGAGTTAAATAGGTTTG 59.171 37.037 7.50 2.06 36.80 2.93
539 557 1.683319 GCCCCCTCAATTCTGAACTCC 60.683 57.143 0.00 0.00 0.00 3.85
545 563 1.688772 CAGATGCCCCCTCAATTCTG 58.311 55.000 0.00 0.00 0.00 3.02
550 568 1.348008 CCTAGCAGATGCCCCCTCAA 61.348 60.000 0.14 0.00 43.38 3.02
638 656 7.715249 GCTAAGAGATGACCCATTGTAAACATA 59.285 37.037 0.00 0.00 0.00 2.29
672 690 5.883180 ACAGAGGGAGTAGCTAGTTATAGG 58.117 45.833 1.78 0.00 0.00 2.57
674 692 6.466038 CCAGACAGAGGGAGTAGCTAGTTATA 60.466 46.154 1.78 0.00 0.00 0.98
751 778 5.480205 ACTCCCTTCGTCTGAAAATCTTAC 58.520 41.667 0.00 0.00 32.66 2.34
754 781 5.941555 ATACTCCCTTCGTCTGAAAATCT 57.058 39.130 0.00 0.00 32.66 2.40
755 782 6.986904 AAATACTCCCTTCGTCTGAAAATC 57.013 37.500 0.00 0.00 32.66 2.17
761 794 7.532884 CGTTTTTAAAAATACTCCCTTCGTCTG 59.467 37.037 16.02 0.00 0.00 3.51
762 795 7.227314 ACGTTTTTAAAAATACTCCCTTCGTCT 59.773 33.333 16.02 0.00 0.00 4.18
765 798 9.830294 ATTACGTTTTTAAAAATACTCCCTTCG 57.170 29.630 16.02 13.04 0.00 3.79
851 884 9.586732 TGGAGGAGAAAGAAATCATAAGAAAAA 57.413 29.630 0.00 0.00 0.00 1.94
856 889 6.109359 ACGTGGAGGAGAAAGAAATCATAAG 58.891 40.000 0.00 0.00 0.00 1.73
860 894 3.323691 TGACGTGGAGGAGAAAGAAATCA 59.676 43.478 0.00 0.00 0.00 2.57
868 902 3.515502 AGAAATGATGACGTGGAGGAGAA 59.484 43.478 0.00 0.00 0.00 2.87
869 903 3.099905 AGAAATGATGACGTGGAGGAGA 58.900 45.455 0.00 0.00 0.00 3.71
936 970 1.418755 GGGTTTCGACGATTCGTGC 59.581 57.895 17.75 7.43 46.01 5.34
1253 3575 1.338769 GGAAAGGCAAGTAAGCGAGGA 60.339 52.381 0.00 0.00 34.64 3.71
1266 3593 1.613925 GAACTTCACAAGGGGAAAGGC 59.386 52.381 0.00 0.00 0.00 4.35
1312 3644 2.805099 GACTTCAGACTGGCTTGACTTG 59.195 50.000 1.81 0.00 0.00 3.16
1319 3651 2.324541 AGTTCAGACTTCAGACTGGCT 58.675 47.619 1.81 3.47 38.15 4.75
1320 3652 2.829741 AGTTCAGACTTCAGACTGGC 57.170 50.000 1.81 1.57 38.15 4.85
1670 4049 0.041839 GCACTATCGATTTGCTGCGG 60.042 55.000 19.38 0.00 33.26 5.69
1675 4054 4.034394 TGATTCAGTGCACTATCGATTTGC 59.966 41.667 21.20 19.69 36.76 3.68
1786 4173 2.052782 TAGCGACCAGTGAGCTATCA 57.947 50.000 9.74 0.00 41.88 2.15
1858 4245 1.899437 GATCCCCTCGGACAGTGCAA 61.899 60.000 0.00 0.00 42.48 4.08
1894 4281 2.825205 CCCTTTTGCTTCACCAACTTG 58.175 47.619 0.00 0.00 0.00 3.16
1898 4285 0.753479 TCGCCCTTTTGCTTCACCAA 60.753 50.000 0.00 0.00 0.00 3.67
1915 4302 8.539674 TCAATAACGATATGATCAAACTTGTCG 58.460 33.333 10.48 10.48 35.78 4.35
1936 4323 9.166173 CAATGAGATTTACCTGTTGTCTCAATA 57.834 33.333 7.37 0.00 45.71 1.90
1998 4385 9.970395 TTCGACACATCTTTAGACTAAAAAGTA 57.030 29.630 8.92 0.00 35.79 2.24
2000 4387 8.979574 ACTTCGACACATCTTTAGACTAAAAAG 58.020 33.333 8.92 8.36 35.66 2.27
2052 4440 2.289694 GGCTTTGCAAGACCTAGACAGA 60.290 50.000 11.51 0.00 0.00 3.41
2439 4830 4.724279 ACCTACCTTGATCTTGTTGGTT 57.276 40.909 9.04 0.00 35.10 3.67
2507 4898 2.794350 GCTTGCGCACAACAAAATAAGT 59.206 40.909 11.12 0.00 35.78 2.24
2519 4910 2.056094 AAAAGATTCAGCTTGCGCAC 57.944 45.000 11.12 0.00 39.10 5.34
2523 4914 4.152607 ACGAGAAAAAGATTCAGCTTGC 57.847 40.909 0.00 0.00 0.00 4.01
2528 4919 3.910767 GCTGCAACGAGAAAAAGATTCAG 59.089 43.478 0.00 0.00 0.00 3.02
2533 4924 2.560504 TGAGCTGCAACGAGAAAAAGA 58.439 42.857 1.02 0.00 0.00 2.52
2534 4925 3.549299 ATGAGCTGCAACGAGAAAAAG 57.451 42.857 1.02 0.00 0.00 2.27
2535 4926 5.431420 TTTATGAGCTGCAACGAGAAAAA 57.569 34.783 1.02 0.00 0.00 1.94
2584 4975 3.560105 TCCATGTCAACATCACCAAACA 58.440 40.909 0.00 0.00 33.61 2.83
2667 5058 6.757897 TGATTACAGCCCAACATTCTTTAG 57.242 37.500 0.00 0.00 0.00 1.85
2690 5081 7.600231 ACAAGATATGACATCTGACTCTCAT 57.400 36.000 0.00 0.00 0.00 2.90
2694 5085 6.481644 GGGAAACAAGATATGACATCTGACTC 59.518 42.308 0.00 0.00 0.00 3.36
2695 5086 6.157645 AGGGAAACAAGATATGACATCTGACT 59.842 38.462 0.00 0.00 0.00 3.41
2793 5193 3.448093 TTACCATGCTCATGTCCCAAA 57.552 42.857 8.81 0.00 37.11 3.28
2825 5227 3.558931 ATTCAGAACGCATGGATACCA 57.441 42.857 0.00 0.00 38.19 3.25
2846 5248 6.994421 TTAGCATGTCTCTAATATGGTGGA 57.006 37.500 0.00 0.00 37.69 4.02
2870 5272 8.660435 TGCTGTCTTAAGCCCTAGATATAAAAT 58.340 33.333 0.00 0.00 42.83 1.82
2921 5323 8.482943 TCTCCATCAGAATTTCGATAAAAGGTA 58.517 33.333 0.00 0.00 0.00 3.08
2967 5369 1.270907 AGTCTGGGTGTGTCATCTCC 58.729 55.000 0.00 0.00 0.00 3.71
3081 5483 4.394729 CATCATGGACATGGTCATGATGA 58.605 43.478 37.49 22.86 46.32 2.92
3304 5709 5.546499 ACCCTTTAATCTGTACAGGTCTTCA 59.454 40.000 22.48 2.45 0.00 3.02
3410 5815 5.104859 AGGGATAGCATAGCAGAAGATGATG 60.105 44.000 0.00 0.00 0.00 3.07
3455 5863 4.248058 CAACACATAGCTCTGATCACACA 58.752 43.478 6.05 0.00 0.00 3.72
3479 5887 7.823745 ACACAAGGATGATCAAAAGTTTAGT 57.176 32.000 0.00 0.00 0.00 2.24
3516 5924 0.472471 AGAGGCACCGGAACAAAAGA 59.528 50.000 9.46 0.00 0.00 2.52
3545 5953 2.878406 GCATGGCATATGTTAGAACGGT 59.122 45.455 0.00 0.00 0.00 4.83
3555 5963 2.473609 GCAATTTCGTGCATGGCATATG 59.526 45.455 5.98 0.00 44.29 1.78
3556 5964 2.746269 GCAATTTCGTGCATGGCATAT 58.254 42.857 5.98 0.00 44.29 1.78
3758 6182 2.569404 CCTATAGTCATTCTCAGCCCCC 59.431 54.545 0.00 0.00 0.00 5.40
3760 6184 2.634940 TGCCTATAGTCATTCTCAGCCC 59.365 50.000 0.00 0.00 0.00 5.19
3770 6194 5.611374 GCCTGATTTACTTGCCTATAGTCA 58.389 41.667 0.00 0.00 0.00 3.41
3778 6207 3.501950 CTTTTCGCCTGATTTACTTGCC 58.498 45.455 0.00 0.00 0.00 4.52
3832 6264 0.609131 AACTCCGGGGCAAACATCAG 60.609 55.000 0.00 0.00 0.00 2.90
3844 6276 0.174617 GGCTTCTCAGAGAACTCCGG 59.825 60.000 8.95 0.00 29.89 5.14
3846 6278 1.134175 CTCGGCTTCTCAGAGAACTCC 59.866 57.143 8.95 11.69 39.01 3.85
3861 6293 2.426024 TCCACAAGATACACTACTCGGC 59.574 50.000 0.00 0.00 0.00 5.54
3880 6312 4.070009 GCTCTCTACTTCTAGCCTAGTCC 58.930 52.174 0.00 0.00 0.00 3.85
3902 6337 3.343617 ACAAGGATACCACACAATTCGG 58.656 45.455 0.00 0.00 37.17 4.30
3920 6355 5.013079 ACAGGTATGGTTCTCATCAAGACAA 59.987 40.000 0.00 0.00 37.30 3.18
3940 6375 4.000988 AGAAAACTACAACGGCATACAGG 58.999 43.478 0.00 0.00 0.00 4.00
3979 6414 7.093333 ACAGGAAACTCTTCATGGTTTCTTTTT 60.093 33.333 18.61 4.80 45.53 1.94
4049 6487 2.030946 GGCATGCACGTATTCAGAGTTC 59.969 50.000 21.36 0.00 0.00 3.01
4096 6534 1.278537 CCACAGGGCCAAATTCCAAT 58.721 50.000 6.18 0.00 0.00 3.16
4110 6548 1.583054 GTAAATAGAGCCGGCCACAG 58.417 55.000 26.15 0.00 0.00 3.66
4115 6553 0.756903 TGGAGGTAAATAGAGCCGGC 59.243 55.000 21.89 21.89 0.00 6.13
4159 6598 3.198853 GTCAGCCAGATAAGAGGGTCTTT 59.801 47.826 0.00 0.00 37.89 2.52
4180 6621 1.348696 CCACCCCAACCTAGTAAACGT 59.651 52.381 0.00 0.00 0.00 3.99
4185 6626 1.676248 AATGCCACCCCAACCTAGTA 58.324 50.000 0.00 0.00 0.00 1.82
4186 6627 0.783850 AAATGCCACCCCAACCTAGT 59.216 50.000 0.00 0.00 0.00 2.57
4189 6630 2.216331 GCAAATGCCACCCCAACCT 61.216 57.895 0.00 0.00 34.31 3.50
4190 6631 0.902516 TAGCAAATGCCACCCCAACC 60.903 55.000 0.94 0.00 43.38 3.77
4192 6633 1.257055 GCTAGCAAATGCCACCCCAA 61.257 55.000 10.63 0.00 43.38 4.12
4193 6634 1.682005 GCTAGCAAATGCCACCCCA 60.682 57.895 10.63 0.00 43.38 4.96
4200 6641 2.159393 TCATGGAAACGCTAGCAAATGC 60.159 45.455 16.45 5.39 42.49 3.56
4208 6649 6.870971 ACTAAAACTTTCATGGAAACGCTA 57.129 33.333 0.00 0.00 0.00 4.26
4210 6651 6.142320 CAGAACTAAAACTTTCATGGAAACGC 59.858 38.462 0.00 0.00 0.00 4.84
4216 6657 6.208644 CCACACAGAACTAAAACTTTCATGG 58.791 40.000 0.00 0.00 0.00 3.66
4220 6661 4.643334 ACCCCACACAGAACTAAAACTTTC 59.357 41.667 0.00 0.00 0.00 2.62
4221 6662 4.606210 ACCCCACACAGAACTAAAACTTT 58.394 39.130 0.00 0.00 0.00 2.66
4222 6663 4.245251 ACCCCACACAGAACTAAAACTT 57.755 40.909 0.00 0.00 0.00 2.66
4231 6672 3.020984 GTTTCTTCAACCCCACACAGAA 58.979 45.455 0.00 0.00 0.00 3.02
4233 6674 2.358898 CAGTTTCTTCAACCCCACACAG 59.641 50.000 0.00 0.00 35.77 3.66
4237 6678 2.357952 GTGACAGTTTCTTCAACCCCAC 59.642 50.000 0.00 0.00 35.77 4.61
4240 6681 2.357952 GTGGTGACAGTTTCTTCAACCC 59.642 50.000 0.00 0.00 44.46 4.11
4244 6685 1.483004 TCGGTGGTGACAGTTTCTTCA 59.517 47.619 0.00 0.00 44.46 3.02
4245 6686 2.234300 TCGGTGGTGACAGTTTCTTC 57.766 50.000 0.00 0.00 44.46 2.87
4246 6687 2.930826 ATCGGTGGTGACAGTTTCTT 57.069 45.000 0.00 0.00 44.46 2.52
4247 6688 3.162666 TCTATCGGTGGTGACAGTTTCT 58.837 45.455 0.00 0.00 44.46 2.52
4249 6690 4.710375 ACTATCTATCGGTGGTGACAGTTT 59.290 41.667 0.00 0.00 44.46 2.66
4250 6691 4.279145 ACTATCTATCGGTGGTGACAGTT 58.721 43.478 0.00 0.00 44.46 3.16
4251 6692 3.884091 GACTATCTATCGGTGGTGACAGT 59.116 47.826 0.00 0.00 44.46 3.55
4254 6695 4.135306 TCTGACTATCTATCGGTGGTGAC 58.865 47.826 0.00 0.00 0.00 3.67
4255 6696 4.432980 TCTGACTATCTATCGGTGGTGA 57.567 45.455 0.00 0.00 0.00 4.02
4256 6697 5.705905 TGTATCTGACTATCTATCGGTGGTG 59.294 44.000 0.00 0.00 0.00 4.17
4257 6698 5.877491 TGTATCTGACTATCTATCGGTGGT 58.123 41.667 0.00 0.00 0.00 4.16
4258 6699 6.431543 AGTTGTATCTGACTATCTATCGGTGG 59.568 42.308 0.00 0.00 0.00 4.61
4259 6700 7.441890 AGTTGTATCTGACTATCTATCGGTG 57.558 40.000 0.00 0.00 0.00 4.94
4260 6701 9.570468 TTTAGTTGTATCTGACTATCTATCGGT 57.430 33.333 0.00 0.00 0.00 4.69
4268 6709 7.573710 TGGCCATTTTAGTTGTATCTGACTAT 58.426 34.615 0.00 0.00 0.00 2.12
4269 6710 6.953101 TGGCCATTTTAGTTGTATCTGACTA 58.047 36.000 0.00 0.00 0.00 2.59
4270 6711 5.815581 TGGCCATTTTAGTTGTATCTGACT 58.184 37.500 0.00 0.00 0.00 3.41
4271 6712 5.449177 GCTGGCCATTTTAGTTGTATCTGAC 60.449 44.000 5.51 0.00 0.00 3.51
4274 6756 4.599041 TGCTGGCCATTTTAGTTGTATCT 58.401 39.130 5.51 0.00 0.00 1.98
4276 6758 5.736951 TTTGCTGGCCATTTTAGTTGTAT 57.263 34.783 5.51 0.00 0.00 2.29
4288 6770 6.060788 AGATTTTAAATGTTTTTGCTGGCCA 58.939 32.000 4.71 4.71 0.00 5.36
4289 6771 6.558771 AGATTTTAAATGTTTTTGCTGGCC 57.441 33.333 0.00 0.00 0.00 5.36
4292 6774 6.875753 TGCGAGATTTTAAATGTTTTTGCTG 58.124 32.000 0.00 0.00 0.00 4.41
4306 6788 4.142609 TCTTATCTGGCTGCGAGATTTT 57.857 40.909 27.99 11.28 31.71 1.82
4311 6793 2.805099 GGAAATCTTATCTGGCTGCGAG 59.195 50.000 5.20 5.20 0.00 5.03
4312 6794 2.170397 TGGAAATCTTATCTGGCTGCGA 59.830 45.455 0.00 0.00 0.00 5.10
4314 6796 6.639632 TTATTGGAAATCTTATCTGGCTGC 57.360 37.500 0.00 0.00 0.00 5.25
4335 6835 7.543868 CGGCAAAATTCATGTGTAATCCTTTTA 59.456 33.333 0.00 0.00 0.00 1.52
4341 6843 5.060816 CACACGGCAAAATTCATGTGTAATC 59.939 40.000 0.00 0.00 38.40 1.75
4343 6845 4.036852 TCACACGGCAAAATTCATGTGTAA 59.963 37.500 0.00 0.00 38.40 2.41
4345 6847 2.360483 TCACACGGCAAAATTCATGTGT 59.640 40.909 0.00 0.00 40.87 3.72
4354 6856 1.400142 CAAGTCTGTCACACGGCAAAA 59.600 47.619 0.00 0.00 0.00 2.44
4364 6866 3.461061 CAAGAGCTGAACAAGTCTGTCA 58.539 45.455 0.00 0.00 33.45 3.58
4376 6878 0.322975 GACTTCAGGCCAAGAGCTGA 59.677 55.000 5.01 0.00 43.05 4.26
4379 6881 1.004440 ACGACTTCAGGCCAAGAGC 60.004 57.895 5.01 0.00 42.60 4.09
4399 6901 2.480224 TAGGTCGAATAGAAACGCGG 57.520 50.000 12.47 0.00 0.00 6.46
4411 6913 2.093606 TGTGGTGTGTTTGTTAGGTCGA 60.094 45.455 0.00 0.00 0.00 4.20
4414 6916 4.098807 GGATTTGTGGTGTGTTTGTTAGGT 59.901 41.667 0.00 0.00 0.00 3.08
4421 6923 4.697828 GGTTTTTGGATTTGTGGTGTGTTT 59.302 37.500 0.00 0.00 0.00 2.83
4435 6937 1.964933 GTGAAATCCCCGGTTTTTGGA 59.035 47.619 0.00 0.00 0.00 3.53
4436 6938 1.689273 TGTGAAATCCCCGGTTTTTGG 59.311 47.619 0.00 0.00 0.00 3.28
4438 6940 1.689813 GGTGTGAAATCCCCGGTTTTT 59.310 47.619 0.00 0.00 0.00 1.94
4446 6948 3.498018 GTGCAAAATTGGTGTGAAATCCC 59.502 43.478 0.00 0.00 0.00 3.85
4447 6949 3.184178 CGTGCAAAATTGGTGTGAAATCC 59.816 43.478 0.00 0.00 0.00 3.01
4453 6955 2.033832 GCTTTCGTGCAAAATTGGTGTG 60.034 45.455 0.00 0.00 0.00 3.82
4454 6956 2.200899 GCTTTCGTGCAAAATTGGTGT 58.799 42.857 0.00 0.00 0.00 4.16
4457 6959 1.526464 GGTGCTTTCGTGCAAAATTGG 59.474 47.619 0.00 0.00 45.12 3.16
4458 6960 1.189884 CGGTGCTTTCGTGCAAAATTG 59.810 47.619 0.00 0.00 45.12 2.32
4468 6970 1.661112 GAGAGGATTTCGGTGCTTTCG 59.339 52.381 0.00 0.00 0.00 3.46
4473 6975 1.478510 TGAGAGAGAGGATTTCGGTGC 59.521 52.381 0.00 0.00 0.00 5.01
4476 6978 2.017782 TCGTGAGAGAGAGGATTTCGG 58.982 52.381 0.00 0.00 34.84 4.30
4477 6979 3.766676 TTCGTGAGAGAGAGGATTTCG 57.233 47.619 0.00 0.00 43.69 3.46
4478 6980 5.748152 CAGATTTCGTGAGAGAGAGGATTTC 59.252 44.000 0.00 0.00 43.69 2.17
4483 6985 4.710423 TTCAGATTTCGTGAGAGAGAGG 57.290 45.455 0.00 0.00 43.69 3.69
4486 6988 7.413475 TTTCTTTTCAGATTTCGTGAGAGAG 57.587 36.000 0.00 0.00 43.69 3.20
4489 6991 7.170828 TCGATTTTCTTTTCAGATTTCGTGAGA 59.829 33.333 0.00 0.00 39.20 3.27
4491 6993 7.184800 TCGATTTTCTTTTCAGATTTCGTGA 57.815 32.000 0.00 0.00 31.71 4.35
4492 6994 8.440021 AATCGATTTTCTTTTCAGATTTCGTG 57.560 30.769 4.39 0.00 31.71 4.35
4493 6995 9.118236 GAAATCGATTTTCTTTTCAGATTTCGT 57.882 29.630 23.49 0.00 40.98 3.85
4495 6997 9.329913 TCGAAATCGATTTTCTTTTCAGATTTC 57.670 29.630 23.49 14.41 44.22 2.17
4569 7072 0.681887 TACTCGTTCTCCCGCATGGA 60.682 55.000 0.00 0.00 42.41 3.41
4573 7076 1.880894 CAGTACTCGTTCTCCCGCA 59.119 57.895 0.00 0.00 0.00 5.69
4574 7077 1.516603 GCAGTACTCGTTCTCCCGC 60.517 63.158 0.00 0.00 0.00 6.13
4644 7147 0.322456 TTTTCTCTGGATGCCACGGG 60.322 55.000 0.00 0.00 0.00 5.28
4645 7148 0.804989 GTTTTCTCTGGATGCCACGG 59.195 55.000 0.00 0.00 0.00 4.94
4646 7149 0.443869 CGTTTTCTCTGGATGCCACG 59.556 55.000 0.00 0.00 0.00 4.94
4647 7150 0.169009 GCGTTTTCTCTGGATGCCAC 59.831 55.000 0.00 0.00 0.00 5.01
4648 7151 1.298157 CGCGTTTTCTCTGGATGCCA 61.298 55.000 0.00 0.00 0.00 4.92
4649 7152 1.425428 CGCGTTTTCTCTGGATGCC 59.575 57.895 0.00 0.00 0.00 4.40
4650 7153 1.298859 ACCGCGTTTTCTCTGGATGC 61.299 55.000 4.92 0.00 0.00 3.91
4651 7154 1.659098 GTACCGCGTTTTCTCTGGATG 59.341 52.381 4.92 0.00 0.00 3.51
4652 7155 1.405121 GGTACCGCGTTTTCTCTGGAT 60.405 52.381 4.92 0.00 0.00 3.41
4653 7156 0.037975 GGTACCGCGTTTTCTCTGGA 60.038 55.000 4.92 0.00 0.00 3.86
4654 7157 1.017701 GGGTACCGCGTTTTCTCTGG 61.018 60.000 4.92 0.00 40.86 3.86
4655 7158 2.452767 GGGTACCGCGTTTTCTCTG 58.547 57.895 4.92 0.00 40.86 3.35
4694 7197 5.208463 GCAAAGATGGAAGGGTGTAAAAA 57.792 39.130 0.00 0.00 0.00 1.94
4695 7198 4.864704 GCAAAGATGGAAGGGTGTAAAA 57.135 40.909 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.