Multiple sequence alignment - TraesCS7A01G188400

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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 TraesCS7A01G188400 chr7A 100.000 3064 0 0 1 3064 144608441 144605378 0.000000e+00 5659.0
1 TraesCS7A01G188400 chr7A 76.943 386 51 21 2612 2963 510729198 510728817 5.220000e-43 185.0
2 TraesCS7A01G188400 chr7A 83.333 180 19 6 2710 2879 510729187 510729009 4.090000e-34 156.0
3 TraesCS7A01G188400 chr7A 82.667 150 16 6 2544 2684 538297549 538297697 1.150000e-24 124.0
4 TraesCS7A01G188400 chr7A 78.443 167 21 12 2719 2883 144605811 144605658 9.040000e-16 95.3
5 TraesCS7A01G188400 chr7A 85.106 94 12 2 2786 2879 510729155 510729064 9.040000e-16 95.3
6 TraesCS7A01G188400 chr7A 92.857 42 3 0 2257 2298 75161433 75161392 9.170000e-06 62.1
7 TraesCS7A01G188400 chr7D 94.897 1450 58 5 630 2072 142614068 142612628 0.000000e+00 2254.0
8 TraesCS7A01G188400 chr7D 88.950 543 30 13 1 536 142616381 142615862 0.000000e+00 643.0
9 TraesCS7A01G188400 chr7D 96.262 107 4 0 2100 2206 142612630 142612524 3.140000e-40 176.0
10 TraesCS7A01G188400 chr7D 95.385 65 3 0 561 625 142615271 142615207 1.500000e-18 104.0
11 TraesCS7A01G188400 chr7B 94.635 1454 63 8 630 2082 106948125 106949564 0.000000e+00 2239.0
12 TraesCS7A01G188400 chr7B 93.939 66 3 1 561 625 106948022 106948087 6.990000e-17 99.0
13 TraesCS7A01G188400 chr3A 94.682 677 27 3 2296 2963 743942650 743943326 0.000000e+00 1042.0
14 TraesCS7A01G188400 chr3A 97.619 42 1 0 2257 2298 743942558 743942599 4.240000e-09 73.1
15 TraesCS7A01G188400 chr2A 94.551 679 26 5 2296 2966 631656527 631655852 0.000000e+00 1038.0
16 TraesCS7A01G188400 chr2A 93.235 680 33 5 2296 2966 778820613 778819938 0.000000e+00 989.0
17 TraesCS7A01G188400 chr2A 78.571 168 20 13 2719 2883 631656188 631656034 2.510000e-16 97.1
18 TraesCS7A01G188400 chr2A 97.727 44 1 0 2255 2298 631656621 631656578 3.280000e-10 76.8
19 TraesCS7A01G188400 chr1A 94.895 666 26 2 2296 2954 496292564 496293228 0.000000e+00 1035.0
20 TraesCS7A01G188400 chr1A 90.909 66 6 0 2716 2781 496292903 496292968 4.210000e-14 89.8
21 TraesCS7A01G188400 chr6B 85.348 273 31 5 2449 2713 8818448 8818719 1.080000e-69 274.0
22 TraesCS7A01G188400 chr6B 82.895 304 37 11 2449 2742 8858982 8859280 3.030000e-65 259.0
23 TraesCS7A01G188400 chr6B 96.875 64 2 0 2719 2782 8818637 8818700 1.160000e-19 108.0
24 TraesCS7A01G188400 chr2D 76.848 514 80 19 2444 2949 153358168 153357686 1.410000e-63 254.0
25 TraesCS7A01G188400 chr2D 81.714 175 18 8 2711 2874 153357984 153357813 1.920000e-27 134.0
26 TraesCS7A01G188400 chr4D 83.094 278 36 9 2444 2713 445741807 445741533 3.050000e-60 243.0
27 TraesCS7A01G188400 chr4D 82.123 179 20 4 2711 2879 445741622 445741446 3.180000e-30 143.0
28 TraesCS7A01G188400 chr4D 92.308 52 4 0 2836 2887 445741597 445741546 1.180000e-09 75.0


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 TraesCS7A01G188400 chr7A 144605378 144608441 3063 True 2877.150000 5659 89.2215 1 3064 2 chr7A.!!$R2 3063
1 TraesCS7A01G188400 chr7D 142612524 142616381 3857 True 794.250000 2254 93.8735 1 2206 4 chr7D.!!$R1 2205
2 TraesCS7A01G188400 chr7B 106948022 106949564 1542 False 1169.000000 2239 94.2870 561 2082 2 chr7B.!!$F1 1521
3 TraesCS7A01G188400 chr3A 743942558 743943326 768 False 557.550000 1042 96.1505 2257 2963 2 chr3A.!!$F1 706
4 TraesCS7A01G188400 chr2A 778819938 778820613 675 True 989.000000 989 93.2350 2296 2966 1 chr2A.!!$R1 670
5 TraesCS7A01G188400 chr2A 631655852 631656621 769 True 403.966667 1038 90.2830 2255 2966 3 chr2A.!!$R2 711
6 TraesCS7A01G188400 chr1A 496292564 496293228 664 False 562.400000 1035 92.9020 2296 2954 2 chr1A.!!$F1 658

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
271 273 0.036164 TGACTCGTTCAATGGTGGGG 59.964 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 3978 0.103026 CGGCCGTCTGATCTGAATCA 59.897 55.0 19.5 0.0 39.63 2.57 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
47 49 9.268268 GTTAAAATCCCATATTGTAGATCGTCA 57.732 33.333 0.00 0.00 0.00 4.35
49 51 6.672266 AATCCCATATTGTAGATCGTCACT 57.328 37.500 0.00 0.00 0.00 3.41
77 79 9.624697 GTAATTTCAACATGCTATTCTGAAACA 57.375 29.630 0.00 0.00 38.45 2.83
78 80 8.752766 AATTTCAACATGCTATTCTGAAACAG 57.247 30.769 0.00 0.00 38.45 3.16
99 101 3.499737 CATGCTTCCGTCGCACCC 61.500 66.667 0.00 0.00 40.65 4.61
130 132 5.295540 AGCTTTGATCTTTTCTTATCCGCTC 59.704 40.000 0.00 0.00 0.00 5.03
192 194 3.215151 TCTATCTTCTCTGGTGCTACGG 58.785 50.000 0.00 0.00 0.00 4.02
193 195 2.145397 ATCTTCTCTGGTGCTACGGA 57.855 50.000 0.00 0.00 0.00 4.69
194 196 1.919240 TCTTCTCTGGTGCTACGGAA 58.081 50.000 0.00 0.00 0.00 4.30
195 197 1.819288 TCTTCTCTGGTGCTACGGAAG 59.181 52.381 0.00 0.00 33.65 3.46
196 198 0.895530 TTCTCTGGTGCTACGGAAGG 59.104 55.000 0.00 0.00 0.00 3.46
197 199 0.039180 TCTCTGGTGCTACGGAAGGA 59.961 55.000 0.00 0.00 0.00 3.36
202 204 3.723554 GTGCTACGGAAGGACAGAG 57.276 57.895 6.78 0.00 45.40 3.35
224 226 4.003788 CACCTCGGTTGGGCGAGT 62.004 66.667 0.00 0.00 0.00 4.18
225 227 2.283388 ACCTCGGTTGGGCGAGTA 60.283 61.111 0.00 0.00 0.00 2.59
226 228 2.348888 ACCTCGGTTGGGCGAGTAG 61.349 63.158 0.00 0.00 0.00 2.57
227 229 2.348888 CCTCGGTTGGGCGAGTAGT 61.349 63.158 0.00 0.00 0.00 2.73
228 230 1.033746 CCTCGGTTGGGCGAGTAGTA 61.034 60.000 0.00 0.00 0.00 1.82
229 231 0.813184 CTCGGTTGGGCGAGTAGTAA 59.187 55.000 0.00 0.00 0.00 2.24
230 232 0.527565 TCGGTTGGGCGAGTAGTAAC 59.472 55.000 0.00 0.00 0.00 2.50
231 233 0.459063 CGGTTGGGCGAGTAGTAACC 60.459 60.000 0.00 0.00 37.90 2.85
232 234 0.459063 GGTTGGGCGAGTAGTAACCG 60.459 60.000 0.00 0.00 32.42 4.44
233 235 0.459063 GTTGGGCGAGTAGTAACCGG 60.459 60.000 0.00 0.00 0.00 5.28
234 236 0.611618 TTGGGCGAGTAGTAACCGGA 60.612 55.000 9.46 0.00 0.00 5.14
235 237 1.033746 TGGGCGAGTAGTAACCGGAG 61.034 60.000 9.46 0.00 0.00 4.63
264 266 1.523758 GGGTGCTTGACTCGTTCAAT 58.476 50.000 3.25 0.00 43.54 2.57
270 272 1.806542 CTTGACTCGTTCAATGGTGGG 59.193 52.381 3.25 0.00 43.54 4.61
271 273 0.036164 TGACTCGTTCAATGGTGGGG 59.964 55.000 0.00 0.00 0.00 4.96
273 275 0.991920 ACTCGTTCAATGGTGGGGAT 59.008 50.000 0.00 0.00 0.00 3.85
284 286 0.552848 GGTGGGGATGATGGATGTGT 59.447 55.000 0.00 0.00 0.00 3.72
294 296 5.649395 GGATGATGGATGTGTTTTCTTCTCA 59.351 40.000 0.00 0.00 0.00 3.27
356 364 4.154015 CACCAAGATTCAGTCAATTACGCA 59.846 41.667 0.00 0.00 0.00 5.24
360 368 5.078411 AGATTCAGTCAATTACGCAGAGT 57.922 39.130 0.00 0.00 0.00 3.24
369 377 0.806868 TTACGCAGAGTACGGAGGTG 59.193 55.000 0.00 0.00 34.56 4.00
390 398 2.125912 ACTGCACATCCGACTCGC 60.126 61.111 0.00 0.00 0.00 5.03
397 405 2.180862 CATCCGACTCGCTCGAGGA 61.181 63.158 21.34 11.76 46.14 3.71
400 408 2.352915 CGACTCGCTCGAGGATGC 60.353 66.667 21.34 0.00 46.14 3.91
452 460 5.061920 ACTTAGTTGAAGACGAGGATGAC 57.938 43.478 0.00 0.00 38.65 3.06
456 464 3.193691 AGTTGAAGACGAGGATGACGAAT 59.806 43.478 0.00 0.00 34.70 3.34
469 477 4.504461 GGATGACGAATGTGATGACTACAC 59.496 45.833 0.00 0.00 38.55 2.90
517 525 2.893398 GAGGTCTAGGTGCCACCG 59.107 66.667 8.52 0.00 44.90 4.94
543 551 3.712907 GGGCGCCCAGGAGTAACA 61.713 66.667 40.73 0.00 35.81 2.41
544 552 2.590092 GGCGCCCAGGAGTAACAT 59.410 61.111 18.11 0.00 0.00 2.71
545 553 1.692173 GGGCGCCCAGGAGTAACATA 61.692 60.000 40.73 0.00 35.81 2.29
547 555 0.464452 GCGCCCAGGAGTAACATACT 59.536 55.000 0.00 0.00 42.86 2.12
564 1138 2.089600 ACTCCCCACTATGGCTAGTC 57.910 55.000 0.00 0.00 35.99 2.59
571 1145 3.643792 CCCACTATGGCTAGTCTAAAGCT 59.356 47.826 0.00 0.00 39.97 3.74
590 1164 2.223479 GCTGAACAGGAGCGAAAACAAA 60.223 45.455 3.99 0.00 0.00 2.83
696 2404 4.013267 ACAAAACATGCAGACTCTAGCT 57.987 40.909 0.00 0.00 0.00 3.32
702 2410 3.999663 ACATGCAGACTCTAGCTGAAAAC 59.000 43.478 0.00 0.00 35.39 2.43
729 2437 0.459899 TAGCCATACTCAGTGCACGG 59.540 55.000 12.01 11.52 0.00 4.94
847 2555 9.920946 TCCATTAGCTACTCTTGGAATTAATTT 57.079 29.630 1.43 0.00 33.66 1.82
971 2679 4.202264 CGTCTCCCATAAGAGTATTTGGCT 60.202 45.833 0.00 0.00 35.28 4.75
1010 2718 7.358770 TCTCTCTAGAAAGAATGGATTCCAG 57.641 40.000 11.78 0.00 36.75 3.86
1081 2789 5.839262 TTGACAAAGTAAGATAGTGCACG 57.161 39.130 12.01 0.00 0.00 5.34
1118 2833 7.611855 AGAAAGTAGTGCCTTTGTTATTGCTAT 59.388 33.333 0.00 0.00 34.87 2.97
1119 2834 8.801882 AAAGTAGTGCCTTTGTTATTGCTATA 57.198 30.769 0.00 0.00 33.50 1.31
1140 2855 8.608317 GCTATAAGTTGATCCAGTTCTTCTTTC 58.392 37.037 0.00 0.00 0.00 2.62
1206 2921 3.511477 AGTTACCTGCTTGAAGAGGAGA 58.489 45.455 14.72 3.22 45.96 3.71
1219 2934 2.183046 GGAGACGCTCCTCTGCAC 59.817 66.667 15.90 0.00 46.41 4.57
1323 3038 0.320247 ACGCAGAGCAACTTCTGGAG 60.320 55.000 5.30 0.00 43.80 3.86
1324 3039 0.320247 CGCAGAGCAACTTCTGGAGT 60.320 55.000 5.30 0.00 43.80 3.85
1325 3040 1.067565 CGCAGAGCAACTTCTGGAGTA 60.068 52.381 5.30 0.00 43.80 2.59
1326 3041 2.342179 GCAGAGCAACTTCTGGAGTAC 58.658 52.381 5.30 0.00 43.80 2.73
1327 3042 2.028567 GCAGAGCAACTTCTGGAGTACT 60.029 50.000 0.00 0.00 43.80 2.73
1403 3118 1.138069 TCTTGTTCCTTGCGACACAGA 59.862 47.619 0.00 0.00 0.00 3.41
1520 3235 2.094182 CACTACTGTGTTATGGCGAGGT 60.094 50.000 0.00 0.00 39.24 3.85
1674 3389 0.979665 TCCTGAAGAAGAGGTGCAGG 59.020 55.000 0.00 0.00 45.77 4.85
1681 3396 0.905357 GAAGAGGTGCAGGGAGCTTA 59.095 55.000 0.00 0.00 45.94 3.09
1772 3488 7.225011 CCCTCTTTATCCATACTAGTTTTCCC 58.775 42.308 0.00 0.00 0.00 3.97
1798 3514 3.118000 TCTGATTCTGAATCTGCCAGCAT 60.118 43.478 25.83 0.00 38.72 3.79
1830 3546 4.853196 CGTTGTTTCTCCATGTAAATGCTG 59.147 41.667 0.00 0.00 0.00 4.41
2021 3737 1.464997 GCCAGCTACAAAAAGAGACGG 59.535 52.381 0.00 0.00 0.00 4.79
2070 3786 5.178996 GCATCCAAGTACTATTGATGCAGAG 59.821 44.000 30.12 11.30 40.06 3.35
2096 3812 7.776464 CGTCTCGCATATAGTAGTAGTATAGC 58.224 42.308 9.93 11.21 0.00 2.97
2097 3813 7.096106 CGTCTCGCATATAGTAGTAGTATAGCC 60.096 44.444 9.93 3.84 0.00 3.93
2098 3814 7.171337 GTCTCGCATATAGTAGTAGTATAGCCC 59.829 44.444 9.93 1.96 0.00 5.19
2099 3815 6.892485 TCGCATATAGTAGTAGTATAGCCCA 58.108 40.000 9.93 2.12 0.00 5.36
2139 3855 5.882557 CCATGTTTTATTAGAGTCTGGTGCT 59.117 40.000 1.86 0.00 0.00 4.40
2189 3905 4.320788 GCTCTGGGAGAAGAACACAAATTG 60.321 45.833 0.00 0.00 0.00 2.32
2206 3922 7.230849 ACAAATTGTGATGGCAGAAGAATTA 57.769 32.000 0.00 0.00 30.18 1.40
2207 3923 7.844009 ACAAATTGTGATGGCAGAAGAATTAT 58.156 30.769 0.00 0.00 30.18 1.28
2208 3924 7.762615 ACAAATTGTGATGGCAGAAGAATTATG 59.237 33.333 0.00 9.62 41.00 1.90
2209 3925 5.840243 TTGTGATGGCAGAAGAATTATGG 57.160 39.130 0.00 0.00 37.87 2.74
2220 3936 8.707938 GCAGAAGAATTATGGCAAAAATTACT 57.292 30.769 10.16 8.12 37.87 2.24
2221 3937 9.801873 GCAGAAGAATTATGGCAAAAATTACTA 57.198 29.630 10.16 0.00 37.87 1.82
2233 3949 8.458843 TGGCAAAAATTACTAGTTCTATCAAGC 58.541 33.333 0.00 0.00 0.00 4.01
2234 3950 8.458843 GGCAAAAATTACTAGTTCTATCAAGCA 58.541 33.333 0.00 0.00 0.00 3.91
2239 3955 9.890629 AAATTACTAGTTCTATCAAGCATGTGA 57.109 29.630 0.00 0.00 0.00 3.58
2240 3956 9.539825 AATTACTAGTTCTATCAAGCATGTGAG 57.460 33.333 0.00 0.00 0.00 3.51
2241 3957 5.911752 ACTAGTTCTATCAAGCATGTGAGG 58.088 41.667 0.00 0.00 0.00 3.86
2242 3958 3.539604 AGTTCTATCAAGCATGTGAGGC 58.460 45.455 0.00 0.00 0.00 4.70
2243 3959 3.054875 AGTTCTATCAAGCATGTGAGGCA 60.055 43.478 0.00 0.00 0.00 4.75
2244 3960 2.910199 TCTATCAAGCATGTGAGGCAC 58.090 47.619 0.00 0.00 34.56 5.01
2246 3962 3.706086 TCTATCAAGCATGTGAGGCACTA 59.294 43.478 0.00 0.00 41.55 2.74
2247 3963 3.572632 ATCAAGCATGTGAGGCACTAT 57.427 42.857 0.00 0.00 41.55 2.12
2248 3964 4.694760 ATCAAGCATGTGAGGCACTATA 57.305 40.909 0.00 0.00 41.55 1.31
2249 3965 4.694760 TCAAGCATGTGAGGCACTATAT 57.305 40.909 0.00 0.00 41.55 0.86
2250 3966 5.806654 TCAAGCATGTGAGGCACTATATA 57.193 39.130 0.00 0.00 41.55 0.86
2251 3967 6.364568 TCAAGCATGTGAGGCACTATATAT 57.635 37.500 0.00 0.00 41.55 0.86
2252 3968 7.480760 TCAAGCATGTGAGGCACTATATATA 57.519 36.000 0.00 0.00 41.55 0.86
2253 3969 7.323420 TCAAGCATGTGAGGCACTATATATAC 58.677 38.462 0.00 0.00 41.55 1.47
2262 3978 9.672673 GTGAGGCACTATATATACATGGAAAAT 57.327 33.333 0.00 0.00 41.55 1.82
2313 4082 5.352284 CGAGCATCTGTATGGAGTAGTTTT 58.648 41.667 0.00 0.00 33.38 2.43
2367 4136 5.454062 TCAACCTTTTCCTTTCTTCCATGA 58.546 37.500 0.00 0.00 0.00 3.07
2455 4224 1.341852 TGTAGCTAGTGCGTGGTTCAA 59.658 47.619 0.00 0.00 45.42 2.69
2482 4251 1.404181 GCGACTGCATACAAGACCTCA 60.404 52.381 0.00 0.00 42.15 3.86
2637 4413 4.312443 ACATGGCAAAAGAATTCTGCAAG 58.688 39.130 17.06 9.91 37.83 4.01
2905 4685 2.359850 GGCCACTCGATGCACCAA 60.360 61.111 0.00 0.00 0.00 3.67
2910 4690 0.734889 CACTCGATGCACCAAATCCC 59.265 55.000 0.00 0.00 0.00 3.85
2966 4746 4.764336 CGGCGGACGCGTAGTTGA 62.764 66.667 13.97 0.00 43.06 3.18
2967 4747 2.431260 GGCGGACGCGTAGTTGAA 60.431 61.111 13.97 0.00 43.06 2.69
2968 4748 2.023223 GGCGGACGCGTAGTTGAAA 61.023 57.895 13.97 0.00 43.06 2.69
2969 4749 1.356527 GGCGGACGCGTAGTTGAAAT 61.357 55.000 13.97 0.00 43.06 2.17
2970 4750 0.441145 GCGGACGCGTAGTTGAAATT 59.559 50.000 13.97 0.00 0.00 1.82
2971 4751 1.136169 GCGGACGCGTAGTTGAAATTT 60.136 47.619 13.97 0.00 0.00 1.82
2972 4752 2.092524 GCGGACGCGTAGTTGAAATTTA 59.907 45.455 13.97 0.00 0.00 1.40
2973 4753 3.652478 CGGACGCGTAGTTGAAATTTAC 58.348 45.455 13.97 0.00 0.00 2.01
2974 4754 3.121611 CGGACGCGTAGTTGAAATTTACA 59.878 43.478 13.97 0.00 0.00 2.41
2975 4755 4.201647 CGGACGCGTAGTTGAAATTTACAT 60.202 41.667 13.97 0.00 0.00 2.29
2976 4756 5.253335 GGACGCGTAGTTGAAATTTACATC 58.747 41.667 13.97 0.00 0.00 3.06
2977 4757 5.163933 GGACGCGTAGTTGAAATTTACATCA 60.164 40.000 13.97 0.00 0.00 3.07
2978 4758 5.614760 ACGCGTAGTTGAAATTTACATCAC 58.385 37.500 11.67 0.00 0.00 3.06
2979 4759 4.717299 CGCGTAGTTGAAATTTACATCACG 59.283 41.667 0.00 8.79 0.00 4.35
2980 4760 4.490890 GCGTAGTTGAAATTTACATCACGC 59.509 41.667 17.56 17.56 32.73 5.34
2981 4761 5.670341 GCGTAGTTGAAATTTACATCACGCT 60.670 40.000 21.86 8.25 35.65 5.07
2982 4762 6.454583 GCGTAGTTGAAATTTACATCACGCTA 60.455 38.462 21.86 7.55 35.65 4.26
2983 4763 7.618442 CGTAGTTGAAATTTACATCACGCTAT 58.382 34.615 0.00 0.00 0.00 2.97
2984 4764 8.748582 CGTAGTTGAAATTTACATCACGCTATA 58.251 33.333 0.00 0.00 0.00 1.31
2990 4770 8.664798 TGAAATTTACATCACGCTATATATGCC 58.335 33.333 0.00 0.00 0.00 4.40
2991 4771 8.560355 AAATTTACATCACGCTATATATGCCA 57.440 30.769 0.00 0.00 0.00 4.92
2992 4772 8.737168 AATTTACATCACGCTATATATGCCAT 57.263 30.769 0.00 0.00 0.00 4.40
2993 4773 7.770801 TTTACATCACGCTATATATGCCATC 57.229 36.000 0.00 0.00 0.00 3.51
2994 4774 4.363138 ACATCACGCTATATATGCCATCG 58.637 43.478 0.00 0.00 0.00 3.84
2995 4775 4.142160 ACATCACGCTATATATGCCATCGT 60.142 41.667 0.00 0.00 0.00 3.73
2996 4776 4.028852 TCACGCTATATATGCCATCGTC 57.971 45.455 0.00 0.00 0.00 4.20
2997 4777 3.116300 CACGCTATATATGCCATCGTCC 58.884 50.000 0.00 0.00 0.00 4.79
2998 4778 2.100916 ACGCTATATATGCCATCGTCCC 59.899 50.000 0.00 0.00 0.00 4.46
2999 4779 2.100749 CGCTATATATGCCATCGTCCCA 59.899 50.000 0.00 0.00 0.00 4.37
3000 4780 3.458189 GCTATATATGCCATCGTCCCAC 58.542 50.000 0.00 0.00 0.00 4.61
3001 4781 3.118775 GCTATATATGCCATCGTCCCACA 60.119 47.826 0.00 0.00 0.00 4.17
3002 4782 3.616956 ATATATGCCATCGTCCCACAG 57.383 47.619 0.00 0.00 0.00 3.66
3003 4783 1.131638 ATATGCCATCGTCCCACAGT 58.868 50.000 0.00 0.00 0.00 3.55
3004 4784 0.464036 TATGCCATCGTCCCACAGTC 59.536 55.000 0.00 0.00 0.00 3.51
3005 4785 1.267574 ATGCCATCGTCCCACAGTCT 61.268 55.000 0.00 0.00 0.00 3.24
3006 4786 1.296715 GCCATCGTCCCACAGTCTT 59.703 57.895 0.00 0.00 0.00 3.01
3007 4787 1.021390 GCCATCGTCCCACAGTCTTG 61.021 60.000 0.00 0.00 0.00 3.02
3008 4788 1.021390 CCATCGTCCCACAGTCTTGC 61.021 60.000 0.00 0.00 0.00 4.01
3009 4789 0.320683 CATCGTCCCACAGTCTTGCA 60.321 55.000 0.00 0.00 0.00 4.08
3010 4790 0.320771 ATCGTCCCACAGTCTTGCAC 60.321 55.000 0.00 0.00 0.00 4.57
3011 4791 1.069765 CGTCCCACAGTCTTGCACT 59.930 57.895 0.00 0.00 34.67 4.40
3012 4792 0.317160 CGTCCCACAGTCTTGCACTA 59.683 55.000 0.00 0.00 32.21 2.74
3013 4793 1.797025 GTCCCACAGTCTTGCACTAC 58.203 55.000 0.00 0.00 32.21 2.73
3014 4794 1.070134 GTCCCACAGTCTTGCACTACA 59.930 52.381 0.00 0.00 32.21 2.74
3015 4795 1.070134 TCCCACAGTCTTGCACTACAC 59.930 52.381 0.00 0.00 32.21 2.90
3016 4796 1.202639 CCCACAGTCTTGCACTACACA 60.203 52.381 0.00 0.00 32.21 3.72
3017 4797 2.560504 CCACAGTCTTGCACTACACAA 58.439 47.619 0.00 0.00 32.21 3.33
3018 4798 3.141398 CCACAGTCTTGCACTACACAAT 58.859 45.455 0.00 0.00 32.21 2.71
3019 4799 3.565482 CCACAGTCTTGCACTACACAATT 59.435 43.478 0.00 0.00 32.21 2.32
3020 4800 4.319766 CCACAGTCTTGCACTACACAATTC 60.320 45.833 0.00 0.00 32.21 2.17
3021 4801 4.512944 CACAGTCTTGCACTACACAATTCT 59.487 41.667 0.00 0.00 32.21 2.40
3022 4802 5.696270 CACAGTCTTGCACTACACAATTCTA 59.304 40.000 0.00 0.00 32.21 2.10
3023 4803 5.696724 ACAGTCTTGCACTACACAATTCTAC 59.303 40.000 0.00 0.00 32.21 2.59
3024 4804 5.696270 CAGTCTTGCACTACACAATTCTACA 59.304 40.000 0.00 0.00 32.21 2.74
3025 4805 5.696724 AGTCTTGCACTACACAATTCTACAC 59.303 40.000 0.00 0.00 31.37 2.90
3026 4806 5.696724 GTCTTGCACTACACAATTCTACACT 59.303 40.000 0.00 0.00 0.00 3.55
3027 4807 6.202954 GTCTTGCACTACACAATTCTACACTT 59.797 38.462 0.00 0.00 0.00 3.16
3028 4808 6.765989 TCTTGCACTACACAATTCTACACTTT 59.234 34.615 0.00 0.00 0.00 2.66
3029 4809 6.935741 TGCACTACACAATTCTACACTTTT 57.064 33.333 0.00 0.00 0.00 2.27
3030 4810 6.724263 TGCACTACACAATTCTACACTTTTG 58.276 36.000 0.00 0.00 0.00 2.44
3031 4811 6.540551 TGCACTACACAATTCTACACTTTTGA 59.459 34.615 0.00 0.00 0.00 2.69
3032 4812 7.066404 TGCACTACACAATTCTACACTTTTGAA 59.934 33.333 0.00 0.00 0.00 2.69
3033 4813 7.587757 GCACTACACAATTCTACACTTTTGAAG 59.412 37.037 0.00 0.00 0.00 3.02
3034 4814 8.612619 CACTACACAATTCTACACTTTTGAAGT 58.387 33.333 0.00 0.00 44.06 3.01
3035 4815 9.174166 ACTACACAATTCTACACTTTTGAAGTT 57.826 29.630 0.00 0.00 40.46 2.66
3037 4817 8.911247 ACACAATTCTACACTTTTGAAGTTTC 57.089 30.769 0.00 0.00 40.46 2.78
3038 4818 8.519526 ACACAATTCTACACTTTTGAAGTTTCA 58.480 29.630 0.00 0.00 40.46 2.69
3039 4819 9.352784 CACAATTCTACACTTTTGAAGTTTCAA 57.647 29.630 3.28 3.28 44.78 2.69
3040 4820 9.573133 ACAATTCTACACTTTTGAAGTTTCAAG 57.427 29.630 7.30 0.67 46.68 3.02
3041 4821 8.534778 CAATTCTACACTTTTGAAGTTTCAAGC 58.465 33.333 7.30 0.00 46.68 4.01
3042 4822 6.751514 TCTACACTTTTGAAGTTTCAAGCA 57.248 33.333 7.30 0.00 46.68 3.91
3043 4823 6.785191 TCTACACTTTTGAAGTTTCAAGCAG 58.215 36.000 7.30 9.72 46.68 4.24
3044 4824 5.391312 ACACTTTTGAAGTTTCAAGCAGT 57.609 34.783 7.30 10.23 46.68 4.40
3045 4825 5.691508 CACTTTTGAAGTTTCAAGCAGTG 57.308 39.130 21.80 21.80 46.68 3.66
3046 4826 5.643379 ACTTTTGAAGTTTCAAGCAGTGA 57.357 34.783 15.33 0.00 46.68 3.41
3047 4827 5.402398 ACTTTTGAAGTTTCAAGCAGTGAC 58.598 37.500 15.33 0.00 46.68 3.67
3048 4828 4.370364 TTTGAAGTTTCAAGCAGTGACC 57.630 40.909 7.30 0.00 46.68 4.02
3049 4829 2.997980 TGAAGTTTCAAGCAGTGACCA 58.002 42.857 0.00 0.00 35.39 4.02
3050 4830 3.554934 TGAAGTTTCAAGCAGTGACCAT 58.445 40.909 0.00 0.00 35.39 3.55
3051 4831 3.316029 TGAAGTTTCAAGCAGTGACCATG 59.684 43.478 0.00 0.00 35.39 3.66
3052 4832 2.936202 AGTTTCAAGCAGTGACCATGT 58.064 42.857 0.00 0.00 35.39 3.21
3053 4833 2.880890 AGTTTCAAGCAGTGACCATGTC 59.119 45.455 0.00 0.00 35.39 3.06
3054 4834 2.880890 GTTTCAAGCAGTGACCATGTCT 59.119 45.455 0.00 0.00 35.39 3.41
3055 4835 2.174363 TCAAGCAGTGACCATGTCTG 57.826 50.000 0.00 0.00 33.15 3.51
3056 4836 1.417517 TCAAGCAGTGACCATGTCTGT 59.582 47.619 0.00 0.00 33.15 3.41
3057 4837 1.802960 CAAGCAGTGACCATGTCTGTC 59.197 52.381 0.00 0.00 33.15 3.51
3058 4838 0.322975 AGCAGTGACCATGTCTGTCC 59.677 55.000 0.00 0.00 33.15 4.02
3059 4839 0.322975 GCAGTGACCATGTCTGTCCT 59.677 55.000 0.00 0.00 33.15 3.85
3060 4840 1.674221 GCAGTGACCATGTCTGTCCTC 60.674 57.143 0.00 0.00 33.15 3.71
3061 4841 0.891373 AGTGACCATGTCTGTCCTCG 59.109 55.000 0.00 0.00 33.15 4.63
3062 4842 0.737715 GTGACCATGTCTGTCCTCGC 60.738 60.000 0.00 0.00 33.15 5.03
3063 4843 1.517257 GACCATGTCTGTCCTCGCG 60.517 63.158 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.364142 TGGGATTTTAACCAAAGTCAAATACTG 58.636 33.333 0.00 0.00 38.88 2.74
7 8 8.485578 TGGGATTTTAACCAAAGTCAAATACT 57.514 30.769 0.00 0.00 41.49 2.12
21 23 9.268268 TGACGATCTACAATATGGGATTTTAAC 57.732 33.333 0.00 0.00 0.00 2.01
23 25 8.647796 AGTGACGATCTACAATATGGGATTTTA 58.352 33.333 0.00 0.00 0.00 1.52
47 49 9.013229 TCAGAATAGCATGTTGAAATTACAAGT 57.987 29.630 0.00 0.00 0.00 3.16
77 79 1.153745 GCGACGGAAGCATGTCTCT 60.154 57.895 0.00 0.00 32.93 3.10
78 80 1.446099 TGCGACGGAAGCATGTCTC 60.446 57.895 0.00 0.00 40.01 3.36
99 101 0.883833 AAAGATCAAAGCTGGCGTGG 59.116 50.000 0.00 0.00 0.00 4.94
130 132 0.038526 AGACAAAGCGGTGGTAGACG 60.039 55.000 0.00 0.00 0.00 4.18
192 194 1.446966 GGTGAGCGCTCTGTCCTTC 60.447 63.158 35.27 16.81 0.00 3.46
193 195 1.882989 GAGGTGAGCGCTCTGTCCTT 61.883 60.000 35.27 21.99 0.00 3.36
194 196 2.283532 AGGTGAGCGCTCTGTCCT 60.284 61.111 35.27 31.75 0.00 3.85
195 197 2.183046 GAGGTGAGCGCTCTGTCC 59.817 66.667 35.27 30.36 0.00 4.02
196 198 2.202544 CGAGGTGAGCGCTCTGTC 60.203 66.667 35.27 25.86 0.00 3.51
197 199 3.753434 CCGAGGTGAGCGCTCTGT 61.753 66.667 35.27 20.90 0.00 3.41
224 226 0.749454 GTCCTCGCCTCCGGTTACTA 60.749 60.000 0.00 0.00 34.56 1.82
225 227 2.050934 GTCCTCGCCTCCGGTTACT 61.051 63.158 0.00 0.00 34.56 2.24
226 228 2.493501 GTCCTCGCCTCCGGTTAC 59.506 66.667 0.00 0.00 34.56 2.50
227 229 2.757099 GGTCCTCGCCTCCGGTTA 60.757 66.667 0.00 0.00 34.56 2.85
237 239 3.691342 TCAAGCACCCGGTCCTCG 61.691 66.667 0.00 0.00 38.88 4.63
238 240 2.047179 GTCAAGCACCCGGTCCTC 60.047 66.667 0.00 0.00 0.00 3.71
239 241 2.526873 AGTCAAGCACCCGGTCCT 60.527 61.111 0.00 0.00 0.00 3.85
240 242 2.047179 GAGTCAAGCACCCGGTCC 60.047 66.667 0.00 0.00 0.00 4.46
243 245 2.027625 GAACGAGTCAAGCACCCGG 61.028 63.158 0.00 0.00 0.00 5.73
264 266 0.552363 CACATCCATCATCCCCACCA 59.448 55.000 0.00 0.00 0.00 4.17
270 272 5.649395 TGAGAAGAAAACACATCCATCATCC 59.351 40.000 0.00 0.00 0.00 3.51
271 273 6.404074 GGTGAGAAGAAAACACATCCATCATC 60.404 42.308 0.00 0.00 36.42 2.92
273 275 4.761739 GGTGAGAAGAAAACACATCCATCA 59.238 41.667 0.00 0.00 36.42 3.07
284 286 3.480470 CCTCAAGCAGGTGAGAAGAAAA 58.520 45.455 12.25 0.00 46.76 2.29
319 327 1.314534 TTGGTGCCCAATCATCGCAG 61.315 55.000 2.84 0.00 38.75 5.18
322 330 1.683943 ATCTTGGTGCCCAATCATCG 58.316 50.000 7.06 0.00 43.07 3.84
356 364 2.370349 CAGTCATCACCTCCGTACTCT 58.630 52.381 0.00 0.00 0.00 3.24
360 368 0.530744 GTGCAGTCATCACCTCCGTA 59.469 55.000 0.00 0.00 0.00 4.02
369 377 1.565305 GAGTCGGATGTGCAGTCATC 58.435 55.000 8.44 8.44 42.20 2.92
390 398 0.037512 CTAGGCATGGCATCCTCGAG 60.038 60.000 22.64 5.13 34.02 4.04
397 405 0.250209 CTCGCTTCTAGGCATGGCAT 60.250 55.000 22.64 9.12 0.00 4.40
400 408 4.766970 CCTCGCTTCTAGGCATGG 57.233 61.111 0.00 0.00 0.00 3.66
418 426 0.321653 AACTAAGTTGAGCGCCCAGG 60.322 55.000 2.29 0.00 0.00 4.45
421 429 3.226884 TCAACTAAGTTGAGCGCCC 57.773 52.632 2.29 0.00 45.88 6.13
452 460 1.588404 GCCGTGTAGTCATCACATTCG 59.412 52.381 0.00 0.00 35.79 3.34
456 464 0.037697 GTGGCCGTGTAGTCATCACA 60.038 55.000 0.00 0.00 35.79 3.58
469 477 2.740826 CCACCGTTAGTGTGGCCG 60.741 66.667 0.00 0.00 46.13 6.13
517 525 4.467084 TGGGCGCCCGACTCATTC 62.467 66.667 39.00 13.87 39.42 2.67
536 544 4.262506 GCCATAGTGGGGAGTATGTTACTC 60.263 50.000 6.20 6.20 44.99 2.59
537 545 3.646637 GCCATAGTGGGGAGTATGTTACT 59.353 47.826 0.00 0.00 38.90 2.24
538 546 3.646637 AGCCATAGTGGGGAGTATGTTAC 59.353 47.826 0.00 0.00 38.19 2.50
540 548 2.776665 AGCCATAGTGGGGAGTATGTT 58.223 47.619 0.00 0.00 38.19 2.71
541 549 2.496679 AGCCATAGTGGGGAGTATGT 57.503 50.000 0.00 0.00 38.19 2.29
543 551 3.403051 AGACTAGCCATAGTGGGGAGTAT 59.597 47.826 0.00 0.00 42.46 2.12
544 552 2.789992 AGACTAGCCATAGTGGGGAGTA 59.210 50.000 0.00 0.00 42.46 2.59
545 553 1.576272 AGACTAGCCATAGTGGGGAGT 59.424 52.381 0.00 0.00 42.46 3.85
547 555 3.985553 TTAGACTAGCCATAGTGGGGA 57.014 47.619 0.00 0.00 42.46 4.81
548 556 3.244249 GCTTTAGACTAGCCATAGTGGGG 60.244 52.174 0.00 0.00 42.46 4.96
551 559 5.521906 TCAGCTTTAGACTAGCCATAGTG 57.478 43.478 0.00 0.00 42.46 2.74
552 560 5.422331 TGTTCAGCTTTAGACTAGCCATAGT 59.578 40.000 0.00 0.00 45.16 2.12
553 561 5.907207 TGTTCAGCTTTAGACTAGCCATAG 58.093 41.667 0.00 0.00 39.47 2.23
554 562 5.163405 CCTGTTCAGCTTTAGACTAGCCATA 60.163 44.000 0.00 0.00 39.47 2.74
555 563 4.383552 CCTGTTCAGCTTTAGACTAGCCAT 60.384 45.833 0.00 0.00 39.47 4.40
556 564 3.055819 CCTGTTCAGCTTTAGACTAGCCA 60.056 47.826 0.00 0.00 39.47 4.75
557 565 3.195825 TCCTGTTCAGCTTTAGACTAGCC 59.804 47.826 0.00 0.00 39.47 3.93
558 566 4.429108 CTCCTGTTCAGCTTTAGACTAGC 58.571 47.826 0.00 0.00 38.93 3.42
564 1138 2.370281 TCGCTCCTGTTCAGCTTTAG 57.630 50.000 0.00 0.00 34.45 1.85
571 1145 4.647424 AATTTGTTTTCGCTCCTGTTCA 57.353 36.364 0.00 0.00 0.00 3.18
625 1199 5.551233 TGGAACTGTAAGACTTTCATGGAG 58.449 41.667 0.00 0.00 37.43 3.86
626 1200 5.560722 TGGAACTGTAAGACTTTCATGGA 57.439 39.130 0.00 0.00 37.43 3.41
627 1201 5.997746 TCTTGGAACTGTAAGACTTTCATGG 59.002 40.000 0.00 0.00 37.43 3.66
628 1202 7.227512 ACTTCTTGGAACTGTAAGACTTTCATG 59.772 37.037 0.00 0.00 37.43 3.07
696 2404 8.402798 TGAGTATGGCTAATCAAAAGTTTTCA 57.597 30.769 0.00 0.00 29.52 2.69
702 2410 5.355071 TGCACTGAGTATGGCTAATCAAAAG 59.645 40.000 0.00 0.00 32.04 2.27
729 2437 2.043953 GGAACATGCCTGGGGGTC 60.044 66.667 0.00 0.00 34.45 4.46
971 2679 3.921104 AGAGAGATCTAGAACATGGGCA 58.079 45.455 0.00 0.00 0.00 5.36
1081 2789 3.187700 CACTACTTTCTGATGTACGCCC 58.812 50.000 0.00 0.00 0.00 6.13
1118 2833 6.837312 TGGAAAGAAGAACTGGATCAACTTA 58.163 36.000 0.00 0.00 0.00 2.24
1119 2834 5.694995 TGGAAAGAAGAACTGGATCAACTT 58.305 37.500 0.00 0.00 0.00 2.66
1140 2855 3.599584 CCAGAAGCTGGTGCATGG 58.400 61.111 5.31 0.00 45.82 3.66
1206 2921 1.316706 GGTAGAGTGCAGAGGAGCGT 61.317 60.000 0.00 0.00 37.31 5.07
1219 2934 1.320507 GTAGCTCGGGAAGGGTAGAG 58.679 60.000 0.00 0.00 0.00 2.43
1360 3075 2.511829 AGCTGCATGCGAGCTCTG 60.512 61.111 28.01 4.51 43.54 3.35
1403 3118 2.028112 TCAAAGCTTGTATCCAGCTCGT 60.028 45.455 0.00 0.00 38.01 4.18
1520 3235 0.944311 GTTCGAAGCTGCTCCGTTCA 60.944 55.000 8.43 0.00 0.00 3.18
1674 3389 1.141858 CACCTGGGAATCCTAAGCTCC 59.858 57.143 0.00 0.00 0.00 4.70
1681 3396 3.411517 CGGCCACCTGGGAATCCT 61.412 66.667 2.24 0.00 40.01 3.24
1772 3488 4.704965 TGGCAGATTCAGAATCAGAGATG 58.295 43.478 22.70 13.59 40.42 2.90
1798 3514 5.533154 ACATGGAGAAACAACGGATGTAAAA 59.467 36.000 0.00 0.00 42.99 1.52
1830 3546 1.421410 GACCATGACCGACATCGCAC 61.421 60.000 0.00 0.00 37.07 5.34
2021 3737 1.163554 CAGGTTCAAGAGCCAAGAGC 58.836 55.000 5.74 0.00 44.25 4.09
2082 3798 3.659195 TGGGCTGGGCTATACTACTACTA 59.341 47.826 0.00 0.00 0.00 1.82
2083 3799 2.449730 TGGGCTGGGCTATACTACTACT 59.550 50.000 0.00 0.00 0.00 2.57
2084 3800 2.885616 TGGGCTGGGCTATACTACTAC 58.114 52.381 0.00 0.00 0.00 2.73
2085 3801 3.116862 ACTTGGGCTGGGCTATACTACTA 60.117 47.826 0.00 0.00 0.00 1.82
2086 3802 2.330216 CTTGGGCTGGGCTATACTACT 58.670 52.381 0.00 0.00 0.00 2.57
2087 3803 2.047830 ACTTGGGCTGGGCTATACTAC 58.952 52.381 0.00 0.00 0.00 2.73
2088 3804 2.047061 CACTTGGGCTGGGCTATACTA 58.953 52.381 0.00 0.00 0.00 1.82
2089 3805 0.839946 CACTTGGGCTGGGCTATACT 59.160 55.000 0.00 0.00 0.00 2.12
2090 3806 0.546598 ACACTTGGGCTGGGCTATAC 59.453 55.000 0.00 0.00 0.00 1.47
2091 3807 1.295020 AACACTTGGGCTGGGCTATA 58.705 50.000 0.00 0.00 0.00 1.31
2092 3808 0.409484 AAACACTTGGGCTGGGCTAT 59.591 50.000 0.00 0.00 0.00 2.97
2093 3809 0.251165 GAAACACTTGGGCTGGGCTA 60.251 55.000 0.00 0.00 0.00 3.93
2094 3810 1.531602 GAAACACTTGGGCTGGGCT 60.532 57.895 0.00 0.00 0.00 5.19
2095 3811 1.115326 AAGAAACACTTGGGCTGGGC 61.115 55.000 0.00 0.00 37.45 5.36
2096 3812 0.961753 GAAGAAACACTTGGGCTGGG 59.038 55.000 0.00 0.00 39.13 4.45
2097 3813 0.961753 GGAAGAAACACTTGGGCTGG 59.038 55.000 0.00 0.00 39.13 4.85
2098 3814 1.691196 TGGAAGAAACACTTGGGCTG 58.309 50.000 0.00 0.00 39.13 4.85
2099 3815 2.242043 CATGGAAGAAACACTTGGGCT 58.758 47.619 0.00 0.00 39.13 5.19
2139 3855 6.599244 CAGGGATGCATAGTAGAAACTGAAAA 59.401 38.462 0.00 0.00 36.36 2.29
2189 3905 3.633525 TGCCATAATTCTTCTGCCATCAC 59.366 43.478 0.00 0.00 0.00 3.06
2194 3910 6.990341 AATTTTTGCCATAATTCTTCTGCC 57.010 33.333 0.00 0.00 0.00 4.85
2207 3923 8.458843 GCTTGATAGAACTAGTAATTTTTGCCA 58.541 33.333 0.00 0.00 0.00 4.92
2208 3924 8.458843 TGCTTGATAGAACTAGTAATTTTTGCC 58.541 33.333 0.00 0.00 0.00 4.52
2213 3929 9.890629 TCACATGCTTGATAGAACTAGTAATTT 57.109 29.630 6.60 0.00 0.00 1.82
2214 3930 9.539825 CTCACATGCTTGATAGAACTAGTAATT 57.460 33.333 6.60 0.00 0.00 1.40
2215 3931 8.147058 CCTCACATGCTTGATAGAACTAGTAAT 58.853 37.037 6.60 0.00 0.00 1.89
2216 3932 7.492524 CCTCACATGCTTGATAGAACTAGTAA 58.507 38.462 6.60 0.00 0.00 2.24
2217 3933 6.461648 GCCTCACATGCTTGATAGAACTAGTA 60.462 42.308 6.60 0.00 0.00 1.82
2218 3934 5.683509 GCCTCACATGCTTGATAGAACTAGT 60.684 44.000 6.60 0.00 0.00 2.57
2219 3935 4.749099 GCCTCACATGCTTGATAGAACTAG 59.251 45.833 6.60 0.00 0.00 2.57
2220 3936 4.162131 TGCCTCACATGCTTGATAGAACTA 59.838 41.667 6.60 0.00 0.00 2.24
2221 3937 3.054875 TGCCTCACATGCTTGATAGAACT 60.055 43.478 6.60 0.00 0.00 3.01
2222 3938 3.064545 GTGCCTCACATGCTTGATAGAAC 59.935 47.826 6.60 2.52 34.08 3.01
2223 3939 3.054875 AGTGCCTCACATGCTTGATAGAA 60.055 43.478 6.60 0.00 36.74 2.10
2224 3940 2.502947 AGTGCCTCACATGCTTGATAGA 59.497 45.455 6.60 0.99 36.74 1.98
2225 3941 2.915349 AGTGCCTCACATGCTTGATAG 58.085 47.619 6.60 3.20 36.74 2.08
2226 3942 4.694760 ATAGTGCCTCACATGCTTGATA 57.305 40.909 6.60 0.00 36.74 2.15
2227 3943 3.572632 ATAGTGCCTCACATGCTTGAT 57.427 42.857 6.60 0.00 36.74 2.57
2228 3944 4.694760 ATATAGTGCCTCACATGCTTGA 57.305 40.909 6.60 0.00 36.74 3.02
2229 3945 7.099120 TGTATATATAGTGCCTCACATGCTTG 58.901 38.462 0.00 0.00 36.74 4.01
2230 3946 7.244886 TGTATATATAGTGCCTCACATGCTT 57.755 36.000 0.00 0.00 36.74 3.91
2231 3947 6.857437 TGTATATATAGTGCCTCACATGCT 57.143 37.500 0.00 0.00 36.74 3.79
2232 3948 6.481313 CCATGTATATATAGTGCCTCACATGC 59.519 42.308 12.49 0.00 40.25 4.06
2233 3949 7.785033 TCCATGTATATATAGTGCCTCACATG 58.215 38.462 11.53 11.53 40.91 3.21
2234 3950 7.978099 TCCATGTATATATAGTGCCTCACAT 57.022 36.000 0.00 0.00 36.74 3.21
2235 3951 7.790782 TTCCATGTATATATAGTGCCTCACA 57.209 36.000 0.00 0.00 36.74 3.58
2236 3952 9.672673 ATTTTCCATGTATATATAGTGCCTCAC 57.327 33.333 0.00 0.00 34.10 3.51
2237 3953 9.671279 CATTTTCCATGTATATATAGTGCCTCA 57.329 33.333 0.00 0.00 0.00 3.86
2238 3954 9.890629 TCATTTTCCATGTATATATAGTGCCTC 57.109 33.333 0.00 0.00 0.00 4.70
2250 3966 9.064706 GTCTGATCTGAATCATTTTCCATGTAT 57.935 33.333 3.59 0.00 41.05 2.29
2251 3967 7.225341 CGTCTGATCTGAATCATTTTCCATGTA 59.775 37.037 3.59 0.00 41.05 2.29
2252 3968 6.037940 CGTCTGATCTGAATCATTTTCCATGT 59.962 38.462 3.59 0.00 41.05 3.21
2253 3969 6.427974 CGTCTGATCTGAATCATTTTCCATG 58.572 40.000 3.59 0.00 41.05 3.66
2262 3978 0.103026 CGGCCGTCTGATCTGAATCA 59.897 55.000 19.50 0.00 39.63 2.57
2313 4082 5.338381 GGTGTGGGTGAGATAAAGATGAAGA 60.338 44.000 0.00 0.00 0.00 2.87
2367 4136 4.138487 AGGTTTGAGAGAGACAAAACGT 57.862 40.909 0.00 0.00 45.78 3.99
2385 4154 2.192263 GGTGGGAGATTGAGAGAAGGT 58.808 52.381 0.00 0.00 0.00 3.50
2472 4241 0.107508 CGGCATGGATGAGGTCTTGT 60.108 55.000 0.00 0.00 0.00 3.16
2482 4251 4.195334 GTCAGGGGCGGCATGGAT 62.195 66.667 12.47 0.00 0.00 3.41
2809 4589 3.553508 GCATCGCCCTTCATTATTGCAAT 60.554 43.478 17.56 17.56 0.00 3.56
2821 4601 3.064324 GCAACCAGCATCGCCCTT 61.064 61.111 0.00 0.00 44.79 3.95
2966 4746 8.560355 TGGCATATATAGCGTGATGTAAATTT 57.440 30.769 0.00 0.00 0.00 1.82
2967 4747 8.737168 ATGGCATATATAGCGTGATGTAAATT 57.263 30.769 0.00 0.00 0.00 1.82
2968 4748 7.169813 CGATGGCATATATAGCGTGATGTAAAT 59.830 37.037 0.00 0.00 0.00 1.40
2969 4749 6.475402 CGATGGCATATATAGCGTGATGTAAA 59.525 38.462 0.00 0.00 0.00 2.01
2970 4750 5.977129 CGATGGCATATATAGCGTGATGTAA 59.023 40.000 0.00 0.00 0.00 2.41
2971 4751 5.067283 ACGATGGCATATATAGCGTGATGTA 59.933 40.000 0.00 0.00 0.00 2.29
2972 4752 4.142160 ACGATGGCATATATAGCGTGATGT 60.142 41.667 0.00 0.00 0.00 3.06
2973 4753 4.363138 ACGATGGCATATATAGCGTGATG 58.637 43.478 0.00 0.00 0.00 3.07
2974 4754 4.499865 GGACGATGGCATATATAGCGTGAT 60.500 45.833 13.36 0.00 0.00 3.06
2975 4755 3.181490 GGACGATGGCATATATAGCGTGA 60.181 47.826 13.36 0.00 0.00 4.35
2976 4756 3.116300 GGACGATGGCATATATAGCGTG 58.884 50.000 13.36 0.00 0.00 5.34
2977 4757 2.100916 GGGACGATGGCATATATAGCGT 59.899 50.000 9.06 9.06 0.00 5.07
2978 4758 2.100749 TGGGACGATGGCATATATAGCG 59.899 50.000 0.00 0.57 0.00 4.26
2979 4759 3.118775 TGTGGGACGATGGCATATATAGC 60.119 47.826 0.00 0.00 0.00 2.97
2980 4760 4.160439 ACTGTGGGACGATGGCATATATAG 59.840 45.833 0.00 0.00 0.00 1.31
2981 4761 4.093743 ACTGTGGGACGATGGCATATATA 58.906 43.478 0.00 0.00 0.00 0.86
2982 4762 2.906389 ACTGTGGGACGATGGCATATAT 59.094 45.455 0.00 0.00 0.00 0.86
2983 4763 2.299013 GACTGTGGGACGATGGCATATA 59.701 50.000 0.00 0.00 0.00 0.86
2984 4764 1.070758 GACTGTGGGACGATGGCATAT 59.929 52.381 0.00 0.00 0.00 1.78
2985 4765 0.464036 GACTGTGGGACGATGGCATA 59.536 55.000 0.00 0.00 0.00 3.14
2986 4766 1.221840 GACTGTGGGACGATGGCAT 59.778 57.895 0.00 0.00 0.00 4.40
2987 4767 1.480212 AAGACTGTGGGACGATGGCA 61.480 55.000 0.00 0.00 0.00 4.92
2988 4768 1.021390 CAAGACTGTGGGACGATGGC 61.021 60.000 0.00 0.00 0.00 4.40
2989 4769 1.021390 GCAAGACTGTGGGACGATGG 61.021 60.000 0.00 0.00 0.00 3.51
2990 4770 0.320683 TGCAAGACTGTGGGACGATG 60.321 55.000 0.00 0.00 0.00 3.84
2991 4771 0.320771 GTGCAAGACTGTGGGACGAT 60.321 55.000 0.00 0.00 0.00 3.73
2992 4772 1.069090 GTGCAAGACTGTGGGACGA 59.931 57.895 0.00 0.00 0.00 4.20
2993 4773 0.317160 TAGTGCAAGACTGTGGGACG 59.683 55.000 0.00 0.00 35.96 4.79
2994 4774 1.070134 TGTAGTGCAAGACTGTGGGAC 59.930 52.381 0.00 0.00 35.96 4.46
2995 4775 1.070134 GTGTAGTGCAAGACTGTGGGA 59.930 52.381 0.00 0.00 35.96 4.37
2996 4776 1.202639 TGTGTAGTGCAAGACTGTGGG 60.203 52.381 0.00 0.00 35.96 4.61
2997 4777 2.238942 TGTGTAGTGCAAGACTGTGG 57.761 50.000 0.00 0.00 35.96 4.17
2998 4778 4.512944 AGAATTGTGTAGTGCAAGACTGTG 59.487 41.667 0.00 0.00 35.96 3.66
2999 4779 4.708177 AGAATTGTGTAGTGCAAGACTGT 58.292 39.130 0.00 0.00 35.96 3.55
3000 4780 5.696270 TGTAGAATTGTGTAGTGCAAGACTG 59.304 40.000 0.00 0.00 35.96 3.51
3001 4781 5.696724 GTGTAGAATTGTGTAGTGCAAGACT 59.303 40.000 0.00 0.00 38.88 3.24
3002 4782 5.696724 AGTGTAGAATTGTGTAGTGCAAGAC 59.303 40.000 0.00 0.00 0.00 3.01
3003 4783 5.853936 AGTGTAGAATTGTGTAGTGCAAGA 58.146 37.500 0.00 0.00 0.00 3.02
3004 4784 6.545504 AAGTGTAGAATTGTGTAGTGCAAG 57.454 37.500 0.00 0.00 0.00 4.01
3005 4785 6.935741 AAAGTGTAGAATTGTGTAGTGCAA 57.064 33.333 0.00 0.00 0.00 4.08
3006 4786 6.540551 TCAAAAGTGTAGAATTGTGTAGTGCA 59.459 34.615 0.00 0.00 0.00 4.57
3007 4787 6.954944 TCAAAAGTGTAGAATTGTGTAGTGC 58.045 36.000 0.00 0.00 0.00 4.40
3008 4788 8.612619 ACTTCAAAAGTGTAGAATTGTGTAGTG 58.387 33.333 2.41 0.00 41.01 2.74
3009 4789 8.732746 ACTTCAAAAGTGTAGAATTGTGTAGT 57.267 30.769 0.00 0.00 41.01 2.73
3011 4791 9.997482 GAAACTTCAAAAGTGTAGAATTGTGTA 57.003 29.630 0.00 0.00 41.91 2.90
3012 4792 8.519526 TGAAACTTCAAAAGTGTAGAATTGTGT 58.480 29.630 0.00 0.00 41.91 3.72
3013 4793 8.909708 TGAAACTTCAAAAGTGTAGAATTGTG 57.090 30.769 0.00 0.00 41.91 3.33
3014 4794 9.573133 CTTGAAACTTCAAAAGTGTAGAATTGT 57.427 29.630 6.36 0.00 45.61 2.71
3015 4795 8.534778 GCTTGAAACTTCAAAAGTGTAGAATTG 58.465 33.333 6.36 0.00 45.61 2.32
3016 4796 8.250332 TGCTTGAAACTTCAAAAGTGTAGAATT 58.750 29.630 6.36 0.00 45.61 2.17
3017 4797 7.771183 TGCTTGAAACTTCAAAAGTGTAGAAT 58.229 30.769 6.36 0.00 45.61 2.40
3018 4798 7.094377 ACTGCTTGAAACTTCAAAAGTGTAGAA 60.094 33.333 14.71 0.00 45.61 2.10
3019 4799 6.374333 ACTGCTTGAAACTTCAAAAGTGTAGA 59.626 34.615 14.71 0.00 45.61 2.59
3020 4800 6.470235 CACTGCTTGAAACTTCAAAAGTGTAG 59.530 38.462 23.80 15.90 45.42 2.74
3021 4801 6.321717 CACTGCTTGAAACTTCAAAAGTGTA 58.678 36.000 23.80 8.53 45.42 2.90
3022 4802 5.163513 CACTGCTTGAAACTTCAAAAGTGT 58.836 37.500 23.80 12.55 45.42 3.55
3023 4803 5.691508 CACTGCTTGAAACTTCAAAAGTG 57.308 39.130 21.40 21.40 45.61 3.16
3024 4804 5.402398 GTCACTGCTTGAAACTTCAAAAGT 58.598 37.500 6.36 9.43 45.61 2.66
3025 4805 4.800471 GGTCACTGCTTGAAACTTCAAAAG 59.200 41.667 6.36 8.91 45.61 2.27
3026 4806 4.219507 TGGTCACTGCTTGAAACTTCAAAA 59.780 37.500 6.36 0.00 45.61 2.44
3027 4807 3.761218 TGGTCACTGCTTGAAACTTCAAA 59.239 39.130 6.36 0.00 45.61 2.69
3028 4808 3.351740 TGGTCACTGCTTGAAACTTCAA 58.648 40.909 4.87 4.87 44.31 2.69
3029 4809 2.997980 TGGTCACTGCTTGAAACTTCA 58.002 42.857 0.00 0.00 35.39 3.02
3030 4810 3.316308 ACATGGTCACTGCTTGAAACTTC 59.684 43.478 0.00 0.00 35.39 3.01
3031 4811 3.290710 ACATGGTCACTGCTTGAAACTT 58.709 40.909 0.00 0.00 35.39 2.66
3032 4812 2.880890 GACATGGTCACTGCTTGAAACT 59.119 45.455 0.00 0.00 35.39 2.66
3033 4813 2.880890 AGACATGGTCACTGCTTGAAAC 59.119 45.455 0.00 0.00 35.39 2.78
3034 4814 2.880268 CAGACATGGTCACTGCTTGAAA 59.120 45.455 0.00 0.00 35.39 2.69
3035 4815 2.158769 ACAGACATGGTCACTGCTTGAA 60.159 45.455 0.00 0.00 35.39 2.69
3036 4816 1.417517 ACAGACATGGTCACTGCTTGA 59.582 47.619 0.00 0.00 34.60 3.02
3037 4817 1.802960 GACAGACATGGTCACTGCTTG 59.197 52.381 0.00 0.00 34.60 4.01
3038 4818 1.271054 GGACAGACATGGTCACTGCTT 60.271 52.381 0.00 0.00 37.00 3.91
3039 4819 0.322975 GGACAGACATGGTCACTGCT 59.677 55.000 0.00 0.00 37.00 4.24
3040 4820 0.322975 AGGACAGACATGGTCACTGC 59.677 55.000 0.00 0.00 37.00 4.40
3041 4821 1.403382 CGAGGACAGACATGGTCACTG 60.403 57.143 0.00 3.95 37.00 3.66
3042 4822 0.891373 CGAGGACAGACATGGTCACT 59.109 55.000 0.00 0.00 37.00 3.41
3043 4823 0.737715 GCGAGGACAGACATGGTCAC 60.738 60.000 0.00 0.00 37.00 3.67
3044 4824 1.591703 GCGAGGACAGACATGGTCA 59.408 57.895 0.00 0.00 37.00 4.02
3045 4825 1.517257 CGCGAGGACAGACATGGTC 60.517 63.158 0.00 0.00 34.52 4.02
3046 4826 2.573869 CGCGAGGACAGACATGGT 59.426 61.111 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.