Multiple sequence alignment - TraesCS3A01G313600

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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 TraesCS3A01G313600 chr3A 100.000 4242 0 0 1 4242 553001060 552996819 0.000000e+00 7834
1 TraesCS3A01G313600 chr3A 88.148 135 16 0 3710 3844 552997285 552997151 1.220000e-35 161
2 TraesCS3A01G313600 chr3A 88.148 135 16 0 3776 3910 552997351 552997217 1.220000e-35 161
3 TraesCS3A01G313600 chr3D 91.720 3732 202 44 4 3705 102778296 102781950 0.000000e+00 5081
4 TraesCS3A01G313600 chr3D 86.310 504 35 11 3710 4179 102782053 102782556 6.290000e-143 518
5 TraesCS3A01G313600 chr3D 93.989 183 9 2 1753 1935 533336751 533336931 4.180000e-70 276
6 TraesCS3A01G313600 chr3D 88.406 138 16 0 3710 3847 102782119 102782256 2.620000e-37 167
7 TraesCS3A01G313600 chr3B 91.769 3341 161 48 422 3705 153606569 153609852 0.000000e+00 4542
8 TraesCS3A01G313600 chr3B 88.276 145 17 0 290 434 153606403 153606547 1.570000e-39 174
9 TraesCS3A01G313600 chr3B 76.923 260 32 14 1 249 153606149 153606391 5.760000e-24 122


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 TraesCS3A01G313600 chr3A 552996819 553001060 4241 True 2718.666667 7834 92.098667 1 4242 3 chr3A.!!$R1 4241
1 TraesCS3A01G313600 chr3D 102778296 102782556 4260 False 1922.000000 5081 88.812000 4 4179 3 chr3D.!!$F2 4175
2 TraesCS3A01G313600 chr3B 153606149 153609852 3703 False 1612.666667 4542 85.656000 1 3705 3 chr3B.!!$F1 3704

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
484 530 0.025001 CGCGTTATTCCAACTGCTCG 59.975 55.0 0.0 0.0 0.00 5.03 F
994 1067 0.390735 CCCCGTGTTCTTAGTTCCCG 60.391 60.0 0.0 0.0 0.00 5.14 F
1409 1482 0.768221 AGTCAGGGCTCCAACCTTCA 60.768 55.0 0.0 0.0 35.78 3.02 F
2350 2435 0.817654 TATGAGCTGACCACAGTCCG 59.182 55.0 0.0 0.0 45.04 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2457 2542 0.034059 CCGGTCCACATCTATGAGCC 59.966 60.0 0.00 0.00 0.0 4.70 R
2955 3040 2.097791 GGAGAGAACGCGTACATCTTCT 59.902 50.0 14.46 10.94 0.0 2.85 R
3040 3126 0.409876 TCAGGGGTCTCACTACTGCT 59.590 55.0 0.00 0.00 0.0 4.24 R
3707 3812 0.237235 GCCGTCATCTCGCAACAAAA 59.763 50.0 0.00 0.00 0.0 2.44 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
23 24 1.867233 CCATTGTGCTCATAGTACGCC 59.133 52.381 0.00 0.00 33.27 5.68
26 27 0.380733 TGTGCTCATAGTACGCCTCG 59.619 55.000 0.00 0.00 33.27 4.63
31 32 1.407979 CTCATAGTACGCCTCGGGTTT 59.592 52.381 0.00 0.00 0.00 3.27
33 34 2.159198 TCATAGTACGCCTCGGGTTTTC 60.159 50.000 0.00 0.00 0.00 2.29
44 46 0.095762 CGGGTTTTCGATGCCGTTAC 59.904 55.000 0.00 0.00 37.05 2.50
45 47 1.445871 GGGTTTTCGATGCCGTTACT 58.554 50.000 0.00 0.00 37.05 2.24
66 68 2.042831 GCAAATCTGTGCGAGGCCT 61.043 57.895 3.86 3.86 34.21 5.19
100 102 4.114794 CGGATCATTGCCTTTTGGATTTC 58.885 43.478 0.00 0.00 44.07 2.17
104 106 3.193267 TCATTGCCTTTTGGATTTCTCCG 59.807 43.478 0.00 0.00 45.37 4.63
137 139 5.186198 GCCTAGATGAACTTCTTTTGCCTA 58.814 41.667 0.00 0.00 0.00 3.93
138 140 5.065346 GCCTAGATGAACTTCTTTTGCCTAC 59.935 44.000 0.00 0.00 0.00 3.18
139 141 5.586643 CCTAGATGAACTTCTTTTGCCTACC 59.413 44.000 0.00 0.00 0.00 3.18
140 142 4.336280 AGATGAACTTCTTTTGCCTACCC 58.664 43.478 0.00 0.00 0.00 3.69
141 143 3.876309 TGAACTTCTTTTGCCTACCCT 57.124 42.857 0.00 0.00 0.00 4.34
143 145 2.881111 ACTTCTTTTGCCTACCCTCC 57.119 50.000 0.00 0.00 0.00 4.30
144 146 2.062636 ACTTCTTTTGCCTACCCTCCA 58.937 47.619 0.00 0.00 0.00 3.86
147 149 3.085952 TCTTTTGCCTACCCTCCATTG 57.914 47.619 0.00 0.00 0.00 2.82
148 150 2.378547 TCTTTTGCCTACCCTCCATTGT 59.621 45.455 0.00 0.00 0.00 2.71
149 151 2.507407 TTTGCCTACCCTCCATTGTC 57.493 50.000 0.00 0.00 0.00 3.18
150 152 0.251916 TTGCCTACCCTCCATTGTCG 59.748 55.000 0.00 0.00 0.00 4.35
151 153 0.616395 TGCCTACCCTCCATTGTCGA 60.616 55.000 0.00 0.00 0.00 4.20
152 154 0.105039 GCCTACCCTCCATTGTCGAG 59.895 60.000 0.00 0.00 0.00 4.04
153 155 1.486211 CCTACCCTCCATTGTCGAGT 58.514 55.000 0.00 0.00 0.00 4.18
154 156 1.409427 CCTACCCTCCATTGTCGAGTC 59.591 57.143 0.00 0.00 0.00 3.36
168 174 2.471743 GTCGAGTCGAAAAGTTCAGGTG 59.528 50.000 18.42 0.00 37.72 4.00
169 175 1.192534 CGAGTCGAAAAGTTCAGGTGC 59.807 52.381 6.73 0.00 0.00 5.01
172 178 1.940613 GTCGAAAAGTTCAGGTGCTGT 59.059 47.619 0.00 0.00 32.61 4.40
187 193 0.235926 GCTGTTTGCCGAGTCTGAAC 59.764 55.000 0.00 0.00 35.15 3.18
190 196 3.390135 CTGTTTGCCGAGTCTGAACTTA 58.610 45.455 0.00 0.00 35.28 2.24
191 197 3.997021 CTGTTTGCCGAGTCTGAACTTAT 59.003 43.478 0.00 0.00 35.28 1.73
192 198 3.994392 TGTTTGCCGAGTCTGAACTTATC 59.006 43.478 0.00 0.00 35.28 1.75
194 200 2.457598 TGCCGAGTCTGAACTTATCCT 58.542 47.619 0.00 0.00 35.28 3.24
195 201 2.166459 TGCCGAGTCTGAACTTATCCTG 59.834 50.000 0.00 0.00 35.28 3.86
196 202 2.427453 GCCGAGTCTGAACTTATCCTGA 59.573 50.000 0.00 0.00 35.28 3.86
233 244 4.334481 CGTGGTTTGGGAAGTCATAATACC 59.666 45.833 0.00 0.00 0.00 2.73
239 250 1.607251 GGAAGTCATAATACCGGCGGG 60.607 57.143 31.78 11.36 40.11 6.13
251 262 2.360726 GGCGGGGTGTTCGGATTT 60.361 61.111 0.00 0.00 0.00 2.17
253 264 0.677414 GGCGGGGTGTTCGGATTTAA 60.677 55.000 0.00 0.00 0.00 1.52
254 265 1.385528 GCGGGGTGTTCGGATTTAAT 58.614 50.000 0.00 0.00 0.00 1.40
255 266 2.563702 GCGGGGTGTTCGGATTTAATA 58.436 47.619 0.00 0.00 0.00 0.98
256 267 2.944349 GCGGGGTGTTCGGATTTAATAA 59.056 45.455 0.00 0.00 0.00 1.40
257 268 3.566742 GCGGGGTGTTCGGATTTAATAAT 59.433 43.478 0.00 0.00 0.00 1.28
258 269 4.756135 GCGGGGTGTTCGGATTTAATAATA 59.244 41.667 0.00 0.00 0.00 0.98
259 270 5.239087 GCGGGGTGTTCGGATTTAATAATAA 59.761 40.000 0.00 0.00 0.00 1.40
260 271 6.072342 GCGGGGTGTTCGGATTTAATAATAAT 60.072 38.462 0.00 0.00 0.00 1.28
261 272 7.524065 CGGGGTGTTCGGATTTAATAATAATC 58.476 38.462 0.00 0.00 0.00 1.75
262 273 7.389607 CGGGGTGTTCGGATTTAATAATAATCT 59.610 37.037 0.00 0.00 33.51 2.40
263 274 9.074576 GGGGTGTTCGGATTTAATAATAATCTT 57.925 33.333 0.00 0.00 33.51 2.40
264 275 9.893305 GGGTGTTCGGATTTAATAATAATCTTG 57.107 33.333 0.00 0.00 33.51 3.02
265 276 9.893305 GGTGTTCGGATTTAATAATAATCTTGG 57.107 33.333 0.00 0.00 33.51 3.61
297 308 1.128692 GTAGATCTTGCTTTGCGCGTT 59.871 47.619 8.43 0.00 43.27 4.84
300 311 1.383412 GATCTTGCTTTGCGCGTTTTC 59.617 47.619 8.43 0.00 43.27 2.29
333 344 3.550842 GCGAGAATTGTTGCCCCATAATC 60.551 47.826 3.36 0.00 0.00 1.75
369 380 3.736252 CGTGAAAAGTCGATGTCTTCACT 59.264 43.478 20.58 0.00 42.29 3.41
370 381 4.915667 CGTGAAAAGTCGATGTCTTCACTA 59.084 41.667 20.58 0.00 42.29 2.74
416 427 5.226396 TGCTTGTTCGGGTCATAATTTTTG 58.774 37.500 0.00 0.00 0.00 2.44
437 482 2.354199 GCTCCTGCAGTTTCTCTAATGC 59.646 50.000 13.81 0.00 39.41 3.56
443 488 4.645535 TGCAGTTTCTCTAATGCTTCACT 58.354 39.130 0.00 0.00 39.42 3.41
445 490 4.671250 GCAGTTTCTCTAATGCTTCACTGC 60.671 45.833 5.30 5.30 46.45 4.40
447 492 5.049198 CAGTTTCTCTAATGCTTCACTGCAA 60.049 40.000 0.00 0.00 46.61 4.08
453 499 3.308438 AATGCTTCACTGCAATCCAAC 57.692 42.857 0.00 0.00 46.61 3.77
484 530 0.025001 CGCGTTATTCCAACTGCTCG 59.975 55.000 0.00 0.00 0.00 5.03
496 543 0.898320 ACTGCTCGTGCCTGTATTCT 59.102 50.000 7.05 0.00 38.71 2.40
505 554 4.122776 CGTGCCTGTATTCTGCTAATTCT 58.877 43.478 0.00 0.00 0.00 2.40
582 645 4.496341 CCCGCCGATAATGATCAATATTGC 60.496 45.833 10.76 12.09 31.78 3.56
653 717 3.304659 CCGTATAATACTACCGGTTGCGT 60.305 47.826 15.04 10.88 0.00 5.24
684 749 4.999950 TCAGCTCACAATCTTTTCTTCCTC 59.000 41.667 0.00 0.00 0.00 3.71
685 750 3.999663 AGCTCACAATCTTTTCTTCCTCG 59.000 43.478 0.00 0.00 0.00 4.63
735 808 3.121030 CTGCCGCGGGTTCTTCAG 61.121 66.667 29.38 19.98 0.00 3.02
740 813 1.667830 CGCGGGTTCTTCAGCAAGA 60.668 57.895 0.00 0.00 36.82 3.02
758 831 4.643784 GCAAGATTCAGGGATCTGTTTGAT 59.356 41.667 0.00 0.00 41.59 2.57
788 861 1.145738 ACCCTTGACCTCTTTGTGCAT 59.854 47.619 0.00 0.00 0.00 3.96
792 865 1.896220 TGACCTCTTTGTGCATCACC 58.104 50.000 0.00 0.00 32.73 4.02
799 872 3.499338 TCTTTGTGCATCACCCATCTTT 58.501 40.909 0.00 0.00 32.73 2.52
801 874 4.344679 TCTTTGTGCATCACCCATCTTTTT 59.655 37.500 0.00 0.00 32.73 1.94
846 919 0.657840 GCAAATGGGTCGAGGAATCG 59.342 55.000 0.00 0.00 0.00 3.34
848 921 0.541863 AAATGGGTCGAGGAATCGCT 59.458 50.000 0.00 0.00 0.00 4.93
871 944 1.418264 GATTCCTGGCCTAAGGTCTCC 59.582 57.143 3.32 0.00 38.58 3.71
875 948 3.862991 GGCCTAAGGTCTCCCGGC 61.863 72.222 0.00 0.00 39.98 6.13
876 949 4.222847 GCCTAAGGTCTCCCGGCG 62.223 72.222 0.00 0.00 35.12 6.46
976 1049 1.295792 TCACTTGTGACAGCGTTTCC 58.704 50.000 0.00 0.00 0.00 3.13
981 1054 2.280524 TGACAGCGTTTCCCCGTG 60.281 61.111 0.00 0.00 0.00 4.94
983 1056 1.890510 GACAGCGTTTCCCCGTGTT 60.891 57.895 0.00 0.00 0.00 3.32
986 1059 1.147600 AGCGTTTCCCCGTGTTCTT 59.852 52.632 0.00 0.00 0.00 2.52
993 1066 0.978907 TCCCCGTGTTCTTAGTTCCC 59.021 55.000 0.00 0.00 0.00 3.97
994 1067 0.390735 CCCCGTGTTCTTAGTTCCCG 60.391 60.000 0.00 0.00 0.00 5.14
1013 1086 1.583054 GGCAATATGGACACGGAGAC 58.417 55.000 0.00 0.00 0.00 3.36
1063 1136 2.036217 CACACCGTCTACACAAGGGTTA 59.964 50.000 0.00 0.00 32.75 2.85
1135 1208 3.181451 ACTTCAGAGGTTTGTGAGCATGA 60.181 43.478 0.00 0.00 0.00 3.07
1218 1291 3.146104 ACTGCTAGTTTGCCATCACTT 57.854 42.857 0.00 0.00 0.00 3.16
1222 1295 2.349886 GCTAGTTTGCCATCACTTCGAG 59.650 50.000 0.00 0.00 0.00 4.04
1230 1303 1.066573 CCATCACTTCGAGCCTCACTT 60.067 52.381 0.00 0.00 0.00 3.16
1245 1318 4.440880 CCTCACTTCAGCCTAATGAGAAG 58.559 47.826 1.18 0.00 39.33 2.85
1409 1482 0.768221 AGTCAGGGCTCCAACCTTCA 60.768 55.000 0.00 0.00 35.78 3.02
1430 1503 5.380043 TCATCAAAAGGCTAATGGATCTCC 58.620 41.667 0.00 0.00 0.00 3.71
1570 1643 2.024176 AAGCGTCTATGGCAAATCGT 57.976 45.000 0.00 0.00 0.00 3.73
1734 1807 1.136984 GACTGTGAGGAGCCGTACG 59.863 63.158 8.69 8.69 0.00 3.67
1761 1834 2.042831 GGCTCAAGCGGTGCAATCT 61.043 57.895 0.00 0.00 43.26 2.40
1854 1927 4.501921 CGGCTATACAAAGGACTTTACGAC 59.498 45.833 0.00 0.00 0.00 4.34
1855 1928 5.413499 GGCTATACAAAGGACTTTACGACA 58.587 41.667 0.00 0.00 0.00 4.35
1948 2021 7.661437 AGCTTGACAAACAATATAACACTGAGA 59.339 33.333 0.00 0.00 37.88 3.27
2079 2152 5.580297 TGCAGAGTGTTTGGTTTGATTTTTC 59.420 36.000 0.00 0.00 0.00 2.29
2081 2154 6.019559 GCAGAGTGTTTGGTTTGATTTTTCTC 60.020 38.462 0.00 0.00 0.00 2.87
2095 2168 8.980481 TTGATTTTTCTCCCTTAGCCTTATAG 57.020 34.615 0.00 0.00 0.00 1.31
2122 2195 8.190122 TGGTCATGCAATCTAATAAAATCACAC 58.810 33.333 0.00 0.00 0.00 3.82
2171 2244 9.859427 TTGCAATAGAAAAATACTTTGAGGATG 57.141 29.630 0.00 0.00 0.00 3.51
2217 2297 2.229543 TCATGATTGTCTGCCAACTTGC 59.770 45.455 0.00 0.00 35.44 4.01
2293 2378 1.804151 TGCTATTTTCAGTGTGCCGTC 59.196 47.619 0.00 0.00 0.00 4.79
2312 2397 5.088739 CCGTCAAGTGCTCAAAATATTCAC 58.911 41.667 0.00 0.00 0.00 3.18
2350 2435 0.817654 TATGAGCTGACCACAGTCCG 59.182 55.000 0.00 0.00 45.04 4.79
2433 2518 6.849588 AACTTCTGATTTCATTTTGTTGGC 57.150 33.333 0.00 0.00 0.00 4.52
2467 2552 2.447244 GCTTGTAGCGGCTCATAGAT 57.553 50.000 5.39 0.00 0.00 1.98
2468 2553 2.064762 GCTTGTAGCGGCTCATAGATG 58.935 52.381 5.39 0.00 0.00 2.90
2595 2680 2.899339 GCTCTGGAGATTGCCCGC 60.899 66.667 1.35 0.00 0.00 6.13
2623 2708 3.366396 GAGTACATCCACTCTCAGGGAA 58.634 50.000 0.00 0.00 41.49 3.97
2904 2989 3.268013 GCTTATGCCGTTGCGAATAAT 57.732 42.857 0.00 0.00 41.78 1.28
2955 3040 3.188460 GCCTTCTTTGCAGAACGTAATCA 59.812 43.478 0.00 0.00 33.80 2.57
3026 3112 3.064900 ACAAGAAAGTGATGGAGCCTC 57.935 47.619 0.00 0.00 0.00 4.70
3034 3120 4.414337 AGTGATGGAGCCTCAAGATTAC 57.586 45.455 0.00 0.00 0.00 1.89
3040 3126 1.210478 GAGCCTCAAGATTACTGCCCA 59.790 52.381 0.00 0.00 0.00 5.36
3065 3151 1.577736 AGTGAGACCCCTGATTGAGG 58.422 55.000 0.00 0.00 42.38 3.86
3076 3162 2.806856 GATTGAGGAGTGCTGCGCG 61.807 63.158 0.00 0.00 0.00 6.86
3233 3319 0.874390 GAAACTGAAGCCATCGCACA 59.126 50.000 0.00 0.00 37.52 4.57
3259 3345 3.490590 CGTGAGCTCAGTCATCTAGCATT 60.491 47.826 18.89 0.00 38.75 3.56
3323 3410 6.419791 AGTCTAGCCTAGCGTAAGATGATAT 58.580 40.000 0.00 0.00 43.02 1.63
3324 3411 7.566569 AGTCTAGCCTAGCGTAAGATGATATA 58.433 38.462 0.00 0.00 43.02 0.86
3333 3420 9.411801 CTAGCGTAAGATGATATAAGCTTTTCA 57.588 33.333 3.20 6.59 37.83 2.69
3334 3421 8.839310 AGCGTAAGATGATATAAGCTTTTCAT 57.161 30.769 3.20 11.32 33.95 2.57
3340 3427 9.941664 AAGATGATATAAGCTTTTCATTTCGTG 57.058 29.630 3.20 0.00 0.00 4.35
3341 3428 9.113838 AGATGATATAAGCTTTTCATTTCGTGT 57.886 29.630 3.20 0.00 0.00 4.49
3381 3468 4.452455 GGATGCGGATGTTTATTAGGTGAG 59.548 45.833 0.00 0.00 0.00 3.51
3390 3477 8.903820 GGATGTTTATTAGGTGAGCTACAATTT 58.096 33.333 0.00 0.00 0.00 1.82
3397 3484 5.535753 AGGTGAGCTACAATTTGCTTTTT 57.464 34.783 0.00 0.00 39.91 1.94
3467 3560 0.254178 TCTCATTGGCTCTTGCTCCC 59.746 55.000 0.00 0.00 39.59 4.30
3472 3565 2.125350 GGCTCTTGCTCCCTGTCG 60.125 66.667 0.00 0.00 39.59 4.35
3630 3729 1.582968 CGGCATTAGCATCATGGGC 59.417 57.895 0.00 0.00 44.61 5.36
3634 3737 1.684983 GCATTAGCATCATGGGCAAGT 59.315 47.619 11.89 0.00 41.58 3.16
3691 3796 1.297689 TCAGCATGCCACTGACTCC 59.702 57.895 15.66 0.00 39.21 3.85
3705 3810 3.152341 CTGACTCCTCATGGTGCTTTTT 58.848 45.455 0.00 0.00 34.23 1.94
3707 3812 4.922206 TGACTCCTCATGGTGCTTTTTAT 58.078 39.130 0.00 0.00 34.23 1.40
3708 3813 5.324409 TGACTCCTCATGGTGCTTTTTATT 58.676 37.500 0.00 0.00 34.23 1.40
3727 3930 1.573829 TTTGTTGCGAGATGACGGCC 61.574 55.000 0.00 0.00 0.00 6.13
3735 3938 2.046700 GATGACGGCCCGGTTTCA 60.047 61.111 8.57 2.06 0.00 2.69
3742 3945 1.507141 CGGCCCGGTTTCAGATATGC 61.507 60.000 0.00 0.00 0.00 3.14
3751 3954 6.258160 CCGGTTTCAGATATGCTTGTTTTAG 58.742 40.000 0.00 0.00 0.00 1.85
3752 3955 5.739161 CGGTTTCAGATATGCTTGTTTTAGC 59.261 40.000 0.00 0.00 41.59 3.09
3763 3966 2.346099 TGTTTTAGCGCTGCATTTCC 57.654 45.000 22.90 1.63 0.00 3.13
3783 3986 3.498777 TCCGTGATATTTTGTTGTTGCGA 59.501 39.130 0.00 0.00 0.00 5.10
3784 3987 4.155099 TCCGTGATATTTTGTTGTTGCGAT 59.845 37.500 0.00 0.00 0.00 4.58
3791 3994 4.475763 TTTTGTTGTTGCGATATGACGT 57.524 36.364 0.00 0.00 35.59 4.34
3792 3995 4.475763 TTTGTTGTTGCGATATGACGTT 57.524 36.364 0.00 0.00 35.59 3.99
3800 4003 2.737783 TGCGATATGACGTTTCGGTTTT 59.262 40.909 9.16 0.00 33.62 2.43
3801 4004 3.088552 GCGATATGACGTTTCGGTTTTG 58.911 45.455 9.16 0.00 33.62 2.44
3805 4008 5.446741 CGATATGACGTTTCGGTTTTGGATT 60.447 40.000 0.00 0.00 0.00 3.01
3818 4021 6.313164 TCGGTTTTGGATTTGTTTGTTTTACC 59.687 34.615 0.00 0.00 0.00 2.85
3849 4052 3.498777 TCCGTGATATTTTGTTGTTGCGA 59.501 39.130 0.00 0.00 0.00 5.10
3851 4054 3.845775 CGTGATATTTTGTTGTTGCGAGG 59.154 43.478 0.00 0.00 0.00 4.63
3857 4060 0.741574 TTGTTGTTGCGAGGTGACGT 60.742 50.000 0.00 0.00 35.59 4.34
3858 4061 0.741574 TGTTGTTGCGAGGTGACGTT 60.742 50.000 0.00 0.00 35.59 3.99
3866 4069 0.932399 CGAGGTGACGTTTCGGTTTT 59.068 50.000 0.00 0.00 0.00 2.43
3892 4095 7.253422 AGATATGTTTGTTTTACTGCTGCATC 58.747 34.615 1.31 0.00 0.00 3.91
3895 4098 4.229876 GTTTGTTTTACTGCTGCATCTCC 58.770 43.478 1.31 0.00 0.00 3.71
3907 4110 3.851105 GCTGCATCTCCGTGATATTTTGC 60.851 47.826 0.00 0.00 33.36 3.68
3909 4112 3.313249 TGCATCTCCGTGATATTTTGCTG 59.687 43.478 0.00 0.00 33.36 4.41
3910 4113 3.561310 GCATCTCCGTGATATTTTGCTGA 59.439 43.478 0.00 0.00 33.36 4.26
3911 4114 4.035558 GCATCTCCGTGATATTTTGCTGAA 59.964 41.667 0.00 0.00 33.36 3.02
3913 4116 5.084818 TCTCCGTGATATTTTGCTGAAGA 57.915 39.130 0.00 0.00 0.00 2.87
3914 4117 4.870426 TCTCCGTGATATTTTGCTGAAGAC 59.130 41.667 0.00 0.00 0.00 3.01
3935 4153 4.351938 TGTTCGTCCTGGCCGTCG 62.352 66.667 0.00 0.00 0.00 5.12
3965 4183 4.760047 CCCTGACGCGGAAGGTGG 62.760 72.222 22.96 11.02 0.00 4.61
4114 4351 4.329545 TTGCTCGGGGTGCCTGTC 62.330 66.667 0.00 0.00 0.00 3.51
4165 4402 1.405256 GGTCTCATGCTGGTGAGTGAG 60.405 57.143 12.03 0.00 44.66 3.51
4179 4416 3.622163 GTGAGTGAGGCTGAAGAATCATG 59.378 47.826 0.00 0.00 34.37 3.07
4180 4417 2.613133 GAGTGAGGCTGAAGAATCATGC 59.387 50.000 0.00 0.00 34.37 4.06
4181 4418 1.674962 GTGAGGCTGAAGAATCATGCC 59.325 52.381 0.00 9.73 43.97 4.40
4182 4419 0.942962 GAGGCTGAAGAATCATGCCG 59.057 55.000 0.00 0.00 46.11 5.69
4183 4420 0.465097 AGGCTGAAGAATCATGCCGG 60.465 55.000 0.00 0.00 46.11 6.13
4184 4421 1.358046 GCTGAAGAATCATGCCGGC 59.642 57.895 22.73 22.73 34.37 6.13
4185 4422 2.028130 CTGAAGAATCATGCCGGCC 58.972 57.895 26.77 7.06 34.37 6.13
4186 4423 1.450531 CTGAAGAATCATGCCGGCCC 61.451 60.000 26.77 5.95 34.37 5.80
4187 4424 1.453745 GAAGAATCATGCCGGCCCA 60.454 57.895 26.77 6.41 0.00 5.36
4188 4425 1.728490 GAAGAATCATGCCGGCCCAC 61.728 60.000 26.77 9.44 0.00 4.61
4189 4426 3.219198 GAATCATGCCGGCCCACC 61.219 66.667 26.77 4.30 0.00 4.61
4190 4427 4.839706 AATCATGCCGGCCCACCC 62.840 66.667 26.77 0.00 0.00 4.61
4201 4438 4.666253 CCCACCCACCCTGCACAG 62.666 72.222 0.00 0.00 0.00 3.66
4202 4439 3.569210 CCACCCACCCTGCACAGA 61.569 66.667 0.00 0.00 0.00 3.41
4203 4440 2.033141 CACCCACCCTGCACAGAG 59.967 66.667 0.00 0.00 0.00 3.35
4204 4441 3.958860 ACCCACCCTGCACAGAGC 61.959 66.667 0.00 0.00 45.96 4.09
4205 4442 4.729918 CCCACCCTGCACAGAGCC 62.730 72.222 0.00 0.00 44.83 4.70
4206 4443 3.644606 CCACCCTGCACAGAGCCT 61.645 66.667 0.00 0.00 44.83 4.58
4207 4444 2.433446 CACCCTGCACAGAGCCTT 59.567 61.111 0.00 0.00 44.83 4.35
4208 4445 1.228367 CACCCTGCACAGAGCCTTT 60.228 57.895 0.00 0.00 44.83 3.11
4209 4446 1.228367 ACCCTGCACAGAGCCTTTG 60.228 57.895 0.00 0.00 44.83 2.77
4210 4447 2.633509 CCCTGCACAGAGCCTTTGC 61.634 63.158 0.00 6.43 44.83 3.68
4211 4448 2.559840 CTGCACAGAGCCTTTGCG 59.440 61.111 8.25 1.87 44.83 4.85
4212 4449 3.606065 CTGCACAGAGCCTTTGCGC 62.606 63.158 0.00 0.00 44.83 6.09
4213 4450 3.663176 GCACAGAGCCTTTGCGCA 61.663 61.111 5.66 5.66 44.33 6.09
4214 4451 2.253452 CACAGAGCCTTTGCGCAC 59.747 61.111 11.12 0.00 44.33 5.34
4215 4452 2.980233 ACAGAGCCTTTGCGCACC 60.980 61.111 11.12 0.00 44.33 5.01
4216 4453 4.093952 CAGAGCCTTTGCGCACCG 62.094 66.667 11.12 3.35 44.33 4.94
4235 4472 4.988598 CGCCGGTCCTTGTGCTGT 62.989 66.667 1.90 0.00 0.00 4.40
4236 4473 2.594592 GCCGGTCCTTGTGCTGTT 60.595 61.111 1.90 0.00 0.00 3.16
4237 4474 2.193536 GCCGGTCCTTGTGCTGTTT 61.194 57.895 1.90 0.00 0.00 2.83
4238 4475 1.734388 GCCGGTCCTTGTGCTGTTTT 61.734 55.000 1.90 0.00 0.00 2.43
4239 4476 1.600023 CCGGTCCTTGTGCTGTTTTA 58.400 50.000 0.00 0.00 0.00 1.52
4240 4477 2.159382 CCGGTCCTTGTGCTGTTTTAT 58.841 47.619 0.00 0.00 0.00 1.40
4241 4478 2.095263 CCGGTCCTTGTGCTGTTTTATG 60.095 50.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.550978 GCGTACTATGAGCACAATGGT 58.449 47.619 0.00 0.00 0.00 3.55
14 15 1.202336 CGAAAACCCGAGGCGTACTAT 60.202 52.381 0.00 0.00 0.00 2.12
15 16 0.171007 CGAAAACCCGAGGCGTACTA 59.829 55.000 0.00 0.00 0.00 1.82
16 17 1.080298 CGAAAACCCGAGGCGTACT 60.080 57.895 0.00 0.00 0.00 2.73
17 18 0.459063 ATCGAAAACCCGAGGCGTAC 60.459 55.000 0.00 0.00 42.21 3.67
23 24 1.296056 AACGGCATCGAAAACCCGAG 61.296 55.000 18.83 0.17 43.20 4.63
26 27 1.129811 CAGTAACGGCATCGAAAACCC 59.870 52.381 0.00 0.00 40.11 4.11
31 32 0.319986 TGCACAGTAACGGCATCGAA 60.320 50.000 0.00 0.00 40.11 3.71
33 34 0.515127 TTTGCACAGTAACGGCATCG 59.485 50.000 0.00 0.00 37.39 3.84
44 46 0.167470 CCTCGCACAGATTTGCACAG 59.833 55.000 0.00 0.00 43.15 3.66
45 47 1.855213 GCCTCGCACAGATTTGCACA 61.855 55.000 0.00 0.00 43.15 4.57
66 68 0.108186 ATGATCCGAAAGCAGACGCA 60.108 50.000 0.00 0.00 42.27 5.24
71 73 1.386533 AGGCAATGATCCGAAAGCAG 58.613 50.000 0.00 0.00 0.00 4.24
111 113 5.278957 GGCAAAAGAAGTTCATCTAGGCAAA 60.279 40.000 5.50 0.00 0.00 3.68
112 114 4.218417 GGCAAAAGAAGTTCATCTAGGCAA 59.782 41.667 5.50 0.00 0.00 4.52
113 115 3.758554 GGCAAAAGAAGTTCATCTAGGCA 59.241 43.478 5.50 0.00 0.00 4.75
114 116 4.013050 AGGCAAAAGAAGTTCATCTAGGC 58.987 43.478 5.50 3.54 0.00 3.93
115 117 5.586643 GGTAGGCAAAAGAAGTTCATCTAGG 59.413 44.000 5.50 0.00 0.00 3.02
116 118 5.586643 GGGTAGGCAAAAGAAGTTCATCTAG 59.413 44.000 5.50 0.00 0.00 2.43
117 119 5.250774 AGGGTAGGCAAAAGAAGTTCATCTA 59.749 40.000 5.50 0.00 0.00 1.98
118 120 4.043435 AGGGTAGGCAAAAGAAGTTCATCT 59.957 41.667 5.50 0.00 0.00 2.90
119 121 4.336280 AGGGTAGGCAAAAGAAGTTCATC 58.664 43.478 5.50 0.00 0.00 2.92
120 122 4.336280 GAGGGTAGGCAAAAGAAGTTCAT 58.664 43.478 5.50 0.00 0.00 2.57
121 123 3.497942 GGAGGGTAGGCAAAAGAAGTTCA 60.498 47.826 5.50 0.00 0.00 3.18
122 124 3.082548 GGAGGGTAGGCAAAAGAAGTTC 58.917 50.000 0.00 0.00 0.00 3.01
123 125 2.445525 TGGAGGGTAGGCAAAAGAAGTT 59.554 45.455 0.00 0.00 0.00 2.66
124 126 2.062636 TGGAGGGTAGGCAAAAGAAGT 58.937 47.619 0.00 0.00 0.00 3.01
133 135 0.105039 CTCGACAATGGAGGGTAGGC 59.895 60.000 0.00 0.00 0.00 3.93
137 139 0.611062 TCGACTCGACAATGGAGGGT 60.611 55.000 0.00 0.00 35.82 4.34
138 140 0.530744 TTCGACTCGACAATGGAGGG 59.469 55.000 0.00 0.00 34.89 4.30
139 141 2.363788 TTTCGACTCGACAATGGAGG 57.636 50.000 0.00 0.00 34.89 4.30
140 142 3.318017 ACTTTTCGACTCGACAATGGAG 58.682 45.455 0.00 0.00 34.89 3.86
141 143 3.380479 ACTTTTCGACTCGACAATGGA 57.620 42.857 0.00 0.00 34.89 3.41
143 145 4.376413 CCTGAACTTTTCGACTCGACAATG 60.376 45.833 0.00 4.67 34.89 2.82
144 146 3.741344 CCTGAACTTTTCGACTCGACAAT 59.259 43.478 0.00 0.00 34.89 2.71
147 149 2.471743 CACCTGAACTTTTCGACTCGAC 59.528 50.000 0.00 0.00 34.89 4.20
148 150 2.739292 CACCTGAACTTTTCGACTCGA 58.261 47.619 0.00 0.00 0.00 4.04
149 151 1.192534 GCACCTGAACTTTTCGACTCG 59.807 52.381 0.00 0.00 0.00 4.18
150 152 2.221981 CAGCACCTGAACTTTTCGACTC 59.778 50.000 0.00 0.00 32.44 3.36
151 153 2.213499 CAGCACCTGAACTTTTCGACT 58.787 47.619 0.00 0.00 32.44 4.18
152 154 1.940613 ACAGCACCTGAACTTTTCGAC 59.059 47.619 0.00 0.00 35.18 4.20
153 155 2.325583 ACAGCACCTGAACTTTTCGA 57.674 45.000 0.00 0.00 35.18 3.71
154 156 3.108144 CAAACAGCACCTGAACTTTTCG 58.892 45.455 0.00 0.00 35.18 3.46
168 174 0.235926 GTTCAGACTCGGCAAACAGC 59.764 55.000 0.00 0.00 44.65 4.40
169 175 1.871080 AGTTCAGACTCGGCAAACAG 58.129 50.000 0.00 0.00 0.00 3.16
172 178 3.260884 AGGATAAGTTCAGACTCGGCAAA 59.739 43.478 0.00 0.00 34.21 3.68
194 200 0.526211 CACGACCGGAGAACATCTCA 59.474 55.000 9.46 0.00 45.12 3.27
195 201 0.179134 CCACGACCGGAGAACATCTC 60.179 60.000 9.46 0.00 42.66 2.75
196 202 0.898789 ACCACGACCGGAGAACATCT 60.899 55.000 9.46 0.00 0.00 2.90
233 244 2.855880 TAAATCCGAACACCCCGCCG 62.856 60.000 0.00 0.00 0.00 6.46
239 250 9.893305 CCAAGATTATTATTAAATCCGAACACC 57.107 33.333 0.00 0.00 34.50 4.16
261 272 8.831550 GCAAGATCTACTATTCCTTTTACCAAG 58.168 37.037 0.00 0.00 0.00 3.61
262 273 8.548877 AGCAAGATCTACTATTCCTTTTACCAA 58.451 33.333 0.00 0.00 0.00 3.67
263 274 8.090788 AGCAAGATCTACTATTCCTTTTACCA 57.909 34.615 0.00 0.00 0.00 3.25
264 275 8.966069 AAGCAAGATCTACTATTCCTTTTACC 57.034 34.615 0.00 0.00 0.00 2.85
266 277 8.893727 GCAAAGCAAGATCTACTATTCCTTTTA 58.106 33.333 0.00 0.00 0.00 1.52
267 278 7.414540 CGCAAAGCAAGATCTACTATTCCTTTT 60.415 37.037 0.00 0.00 0.00 2.27
268 279 6.037610 CGCAAAGCAAGATCTACTATTCCTTT 59.962 38.462 0.00 0.00 0.00 3.11
269 280 5.525378 CGCAAAGCAAGATCTACTATTCCTT 59.475 40.000 0.00 0.00 0.00 3.36
270 281 5.053145 CGCAAAGCAAGATCTACTATTCCT 58.947 41.667 0.00 0.00 0.00 3.36
271 282 5.335827 CGCAAAGCAAGATCTACTATTCC 57.664 43.478 0.00 0.00 0.00 3.01
307 318 1.573829 GGGCAACAATTCTCGCGACA 61.574 55.000 3.71 0.00 39.74 4.35
308 319 1.134694 GGGCAACAATTCTCGCGAC 59.865 57.895 3.71 0.00 39.74 5.19
333 344 0.933047 TTCACGCAACGAGACGTCAG 60.933 55.000 19.50 13.70 41.32 3.51
369 380 7.201848 GCATCATCCAGACCATTTGATTTTCTA 60.202 37.037 0.00 0.00 0.00 2.10
370 381 6.406624 GCATCATCCAGACCATTTGATTTTCT 60.407 38.462 0.00 0.00 0.00 2.52
416 427 2.354199 GCATTAGAGAAACTGCAGGAGC 59.646 50.000 19.93 6.26 42.57 4.70
437 482 2.880268 TGACAGTTGGATTGCAGTGAAG 59.120 45.455 0.00 0.00 0.00 3.02
474 520 0.391661 ATACAGGCACGAGCAGTTGG 60.392 55.000 7.26 0.00 44.61 3.77
484 530 5.586243 TCAAGAATTAGCAGAATACAGGCAC 59.414 40.000 0.00 0.00 0.00 5.01
496 543 8.627208 ATTTGACTTCTTCTCAAGAATTAGCA 57.373 30.769 0.00 0.00 45.75 3.49
554 604 1.398390 GATCATTATCGGCGGGCATTC 59.602 52.381 7.21 0.00 0.00 2.67
555 605 1.271325 TGATCATTATCGGCGGGCATT 60.271 47.619 7.21 0.00 34.60 3.56
559 609 4.496341 GCAATATTGATCATTATCGGCGGG 60.496 45.833 19.73 0.00 34.60 6.13
590 653 5.957842 AAATGTCCTGTTCAGCGAATAAA 57.042 34.783 0.00 0.00 0.00 1.40
653 717 4.623932 AGATTGTGAGCTGAACTTGGTA 57.376 40.909 0.00 0.00 0.00 3.25
684 749 6.811665 TCTCAAGTATCCTGAAATACAACACG 59.188 38.462 0.00 0.00 35.06 4.49
685 750 8.547967 TTCTCAAGTATCCTGAAATACAACAC 57.452 34.615 0.00 0.00 35.06 3.32
722 787 1.021390 ATCTTGCTGAAGAACCCGCG 61.021 55.000 0.00 0.00 41.64 6.46
735 808 4.012374 TCAAACAGATCCCTGAATCTTGC 58.988 43.478 0.00 0.00 43.02 4.01
740 813 6.566079 TCAGTATCAAACAGATCCCTGAAT 57.434 37.500 0.00 0.00 43.02 2.57
758 831 2.897969 GAGGTCAAGGGTCTGTTCAGTA 59.102 50.000 0.00 0.00 0.00 2.74
799 872 3.784701 TTCTTGCCGCAAGTTGTAAAA 57.215 38.095 28.03 14.14 41.66 1.52
801 874 4.047822 CAAATTCTTGCCGCAAGTTGTAA 58.952 39.130 28.03 17.52 41.66 2.41
846 919 1.153168 TTAGGCCAGGAATCGCAGC 60.153 57.895 5.01 0.00 0.00 5.25
848 921 1.271840 ACCTTAGGCCAGGAATCGCA 61.272 55.000 15.94 0.00 37.39 5.10
871 944 4.383602 CACAAGAAACGCCGCCGG 62.384 66.667 0.00 0.00 39.22 6.13
875 948 1.070577 CAGAAGTCACAAGAAACGCCG 60.071 52.381 0.00 0.00 0.00 6.46
876 949 1.940613 ACAGAAGTCACAAGAAACGCC 59.059 47.619 0.00 0.00 0.00 5.68
976 1049 0.390735 CCGGGAACTAAGAACACGGG 60.391 60.000 0.00 0.00 45.32 5.28
981 1054 3.564225 CCATATTGCCGGGAACTAAGAAC 59.436 47.826 11.88 0.00 0.00 3.01
983 1056 3.042682 TCCATATTGCCGGGAACTAAGA 58.957 45.455 11.88 3.17 0.00 2.10
986 1059 2.120312 TGTCCATATTGCCGGGAACTA 58.880 47.619 11.88 5.43 31.32 2.24
993 1066 0.104120 TCTCCGTGTCCATATTGCCG 59.896 55.000 0.00 0.00 0.00 5.69
994 1067 1.583054 GTCTCCGTGTCCATATTGCC 58.417 55.000 0.00 0.00 0.00 4.52
1135 1208 1.337823 GGGCATCGTCACACACTTACT 60.338 52.381 0.00 0.00 0.00 2.24
1207 1280 0.391661 GAGGCTCGAAGTGATGGCAA 60.392 55.000 0.00 0.00 0.00 4.52
1218 1291 0.323451 TAGGCTGAAGTGAGGCTCGA 60.323 55.000 10.42 0.00 45.35 4.04
1222 1295 2.169352 TCTCATTAGGCTGAAGTGAGGC 59.831 50.000 15.40 0.00 37.49 4.70
1245 1318 0.607489 TCTTCTGCTTGCTGGCCTTC 60.607 55.000 3.32 0.00 0.00 3.46
1409 1482 5.133322 TGAGGAGATCCATTAGCCTTTTGAT 59.867 40.000 0.92 0.00 38.89 2.57
1570 1643 2.780924 ACACCCTTCCCTGCCCAA 60.781 61.111 0.00 0.00 0.00 4.12
1734 1807 1.718757 CCGCTTGAGCCATGCTAACC 61.719 60.000 10.01 0.00 39.88 2.85
1761 1834 5.222027 TGGATCAAGTTCCCAATCAACTGTA 60.222 40.000 0.00 0.00 34.21 2.74
1895 1968 2.868044 GCTATTATCCCACCAGCGTCAG 60.868 54.545 0.00 0.00 0.00 3.51
1948 2021 3.951680 TGCAGATGAGACAATGCATTGAT 59.048 39.130 38.99 27.87 43.34 2.57
2079 2152 4.223953 TGACCACTATAAGGCTAAGGGAG 58.776 47.826 0.00 0.00 0.00 4.30
2081 2154 4.804261 GCATGACCACTATAAGGCTAAGGG 60.804 50.000 0.00 0.00 0.00 3.95
2095 2168 8.190122 TGTGATTTTATTAGATTGCATGACCAC 58.810 33.333 0.00 0.00 0.00 4.16
2122 2195 3.499737 GGAGCATGAACGTGCCCG 61.500 66.667 14.22 0.00 46.19 6.13
2200 2280 4.635765 TGTATAGCAAGTTGGCAGACAATC 59.364 41.667 4.75 0.00 41.95 2.67
2293 2378 8.984891 TTATTGGTGAATATTTTGAGCACTTG 57.015 30.769 0.00 0.00 0.00 3.16
2344 2429 7.148573 GGCATGATTCACTAATATTACGGACTG 60.149 40.741 0.00 0.00 0.00 3.51
2350 2435 7.891183 ACGAGGCATGATTCACTAATATTAC 57.109 36.000 0.00 0.00 0.00 1.89
2433 2518 5.091431 GCTACAAGCTGCATTAAGAAGTTG 58.909 41.667 1.02 0.00 38.45 3.16
2457 2542 0.034059 CCGGTCCACATCTATGAGCC 59.966 60.000 0.00 0.00 0.00 4.70
2467 2552 7.224362 CGTAATAATGTAATAAACCGGTCCACA 59.776 37.037 8.04 8.36 0.00 4.17
2468 2553 7.307337 CCGTAATAATGTAATAAACCGGTCCAC 60.307 40.741 8.04 2.10 0.00 4.02
2706 2791 3.000322 GCAGATCACATAACGTTTCCTCG 60.000 47.826 5.91 0.00 0.00 4.63
2712 2797 4.159693 TCCACTAGCAGATCACATAACGTT 59.840 41.667 5.88 5.88 0.00 3.99
2925 3010 2.358898 TCTGCAAAGAAGGCAAACTCAC 59.641 45.455 0.00 0.00 41.39 3.51
2955 3040 2.097791 GGAGAGAACGCGTACATCTTCT 59.902 50.000 14.46 10.94 0.00 2.85
3015 3101 3.432749 GCAGTAATCTTGAGGCTCCATCA 60.433 47.826 12.86 0.00 0.00 3.07
3040 3126 0.409876 TCAGGGGTCTCACTACTGCT 59.590 55.000 0.00 0.00 0.00 4.24
3076 3162 2.851798 CCTCTTCTCAGGCTGCAAC 58.148 57.895 10.34 0.00 0.00 4.17
3085 3171 1.208052 CAGAAATCCGGCCTCTTCTCA 59.792 52.381 0.00 0.00 0.00 3.27
3097 3183 4.789012 TTTCACAATCTGCCAGAAATCC 57.211 40.909 0.00 0.00 0.00 3.01
3233 3319 2.880719 GATGACTGAGCTCACGCGCT 62.881 60.000 13.74 0.00 44.33 5.92
3238 3324 3.731652 ATGCTAGATGACTGAGCTCAC 57.268 47.619 13.74 4.66 37.12 3.51
3250 3336 3.247006 ACGGTCGAAACAATGCTAGAT 57.753 42.857 0.00 0.00 0.00 1.98
3259 3345 4.329528 CCGGATAAAATAACGGTCGAAACA 59.670 41.667 0.00 0.00 41.34 2.83
3323 3410 9.959749 ATCTTAAAACACGAAATGAAAAGCTTA 57.040 25.926 0.00 0.00 0.00 3.09
3324 3411 8.871686 ATCTTAAAACACGAAATGAAAAGCTT 57.128 26.923 0.00 0.00 0.00 3.74
3333 3420 8.893727 CCATCCTAGAATCTTAAAACACGAAAT 58.106 33.333 0.00 0.00 0.00 2.17
3334 3421 8.098286 TCCATCCTAGAATCTTAAAACACGAAA 58.902 33.333 0.00 0.00 0.00 3.46
3337 3424 7.519008 GCATCCATCCTAGAATCTTAAAACACG 60.519 40.741 0.00 0.00 0.00 4.49
3338 3425 7.519008 CGCATCCATCCTAGAATCTTAAAACAC 60.519 40.741 0.00 0.00 0.00 3.32
3339 3426 6.483307 CGCATCCATCCTAGAATCTTAAAACA 59.517 38.462 0.00 0.00 0.00 2.83
3340 3427 6.073003 CCGCATCCATCCTAGAATCTTAAAAC 60.073 42.308 0.00 0.00 0.00 2.43
3341 3428 5.997746 CCGCATCCATCCTAGAATCTTAAAA 59.002 40.000 0.00 0.00 0.00 1.52
3347 3434 3.055530 ACATCCGCATCCATCCTAGAATC 60.056 47.826 0.00 0.00 0.00 2.52
3438 3529 6.293298 GCAAGAGCCAATGAGATAACACATAG 60.293 42.308 0.00 0.00 33.58 2.23
3439 3530 5.528690 GCAAGAGCCAATGAGATAACACATA 59.471 40.000 0.00 0.00 33.58 2.29
3440 3531 4.337555 GCAAGAGCCAATGAGATAACACAT 59.662 41.667 0.00 0.00 33.58 3.21
3441 3532 3.691118 GCAAGAGCCAATGAGATAACACA 59.309 43.478 0.00 0.00 33.58 3.72
3442 3533 3.944015 AGCAAGAGCCAATGAGATAACAC 59.056 43.478 0.00 0.00 43.56 3.32
3455 3548 2.125350 CGACAGGGAGCAAGAGCC 60.125 66.667 0.00 0.00 43.56 4.70
3472 3565 1.639280 GACTGAGCTTAGCAGACAGC 58.361 55.000 19.38 12.07 46.19 4.40
3691 3796 6.365050 GCAACAAAATAAAAAGCACCATGAG 58.635 36.000 0.00 0.00 0.00 2.90
3705 3810 2.095213 GCCGTCATCTCGCAACAAAATA 59.905 45.455 0.00 0.00 0.00 1.40
3707 3812 0.237235 GCCGTCATCTCGCAACAAAA 59.763 50.000 0.00 0.00 0.00 2.44
3708 3813 1.573829 GGCCGTCATCTCGCAACAAA 61.574 55.000 0.00 0.00 0.00 2.83
3727 3930 4.701956 AAACAAGCATATCTGAAACCGG 57.298 40.909 0.00 0.00 0.00 5.28
3735 3938 3.242870 GCAGCGCTAAAACAAGCATATCT 60.243 43.478 10.99 0.00 42.91 1.98
3742 3945 2.663119 GGAAATGCAGCGCTAAAACAAG 59.337 45.455 10.99 0.00 0.00 3.16
3751 3954 0.588252 ATATCACGGAAATGCAGCGC 59.412 50.000 0.00 0.00 0.00 5.92
3752 3955 3.338818 AAATATCACGGAAATGCAGCG 57.661 42.857 0.00 0.00 0.00 5.18
3763 3966 6.904543 TCATATCGCAACAACAAAATATCACG 59.095 34.615 0.00 0.00 0.00 4.35
3783 3986 5.890424 AATCCAAAACCGAAACGTCATAT 57.110 34.783 0.00 0.00 0.00 1.78
3784 3987 5.008811 ACAAATCCAAAACCGAAACGTCATA 59.991 36.000 0.00 0.00 0.00 2.15
3791 3994 6.803154 AAACAAACAAATCCAAAACCGAAA 57.197 29.167 0.00 0.00 0.00 3.46
3792 3995 6.803154 AAAACAAACAAATCCAAAACCGAA 57.197 29.167 0.00 0.00 0.00 4.30
3800 4003 4.363999 CAGCGGTAAAACAAACAAATCCA 58.636 39.130 0.00 0.00 0.00 3.41
3801 4004 3.183574 GCAGCGGTAAAACAAACAAATCC 59.816 43.478 0.00 0.00 0.00 3.01
3805 4008 2.941453 TGCAGCGGTAAAACAAACAA 57.059 40.000 0.00 0.00 0.00 2.83
3818 4021 3.338818 AAATATCACGGAAATGCAGCG 57.661 42.857 0.00 0.00 0.00 5.18
3849 4052 3.457610 TCTAAAACCGAAACGTCACCT 57.542 42.857 0.00 0.00 0.00 4.00
3851 4054 6.399204 ACATATCTAAAACCGAAACGTCAC 57.601 37.500 0.00 0.00 0.00 3.67
3866 4069 7.680442 TGCAGCAGTAAAACAAACATATCTA 57.320 32.000 0.00 0.00 0.00 1.98
3892 4095 4.259970 CGTCTTCAGCAAAATATCACGGAG 60.260 45.833 0.00 0.00 0.00 4.63
3895 4098 3.242413 CCCGTCTTCAGCAAAATATCACG 60.242 47.826 0.00 0.00 0.00 4.35
3913 4116 4.309950 GCCAGGACGAACACCCGT 62.310 66.667 0.00 0.00 46.43 5.28
3963 4181 4.974438 AACGTCCAGGCCCTCCCA 62.974 66.667 0.00 0.00 35.39 4.37
3965 4183 3.192103 AACAACGTCCAGGCCCTCC 62.192 63.158 0.00 0.00 0.00 4.30
4004 4222 2.464403 AACTGCTGGCCAGGGAACT 61.464 57.895 33.46 0.00 46.14 3.01
4135 4372 1.521010 CATGAGACCTCTGCTGGCG 60.521 63.158 0.00 0.00 0.00 5.69
4138 4375 3.067074 CAGCATGAGACCTCTGCTG 57.933 57.895 23.46 23.46 45.55 4.41
4139 4376 0.908656 ACCAGCATGAGACCTCTGCT 60.909 55.000 14.05 14.05 41.36 4.24
4165 4402 2.028130 CCGGCATGATTCTTCAGCC 58.972 57.895 0.00 0.00 40.17 4.85
4184 4421 4.666253 CTGTGCAGGGTGGGTGGG 62.666 72.222 0.00 0.00 0.00 4.61
4185 4422 3.557903 CTCTGTGCAGGGTGGGTGG 62.558 68.421 0.00 0.00 0.00 4.61
4186 4423 2.033141 CTCTGTGCAGGGTGGGTG 59.967 66.667 0.00 0.00 0.00 4.61
4187 4424 3.958860 GCTCTGTGCAGGGTGGGT 61.959 66.667 0.71 0.00 42.31 4.51
4188 4425 4.729918 GGCTCTGTGCAGGGTGGG 62.730 72.222 3.96 0.00 45.15 4.61
4189 4426 2.703675 AAAGGCTCTGTGCAGGGTGG 62.704 60.000 3.96 0.00 45.15 4.61
4190 4427 1.228367 AAAGGCTCTGTGCAGGGTG 60.228 57.895 3.96 0.00 45.15 4.61
4191 4428 1.228367 CAAAGGCTCTGTGCAGGGT 60.228 57.895 3.96 0.00 45.15 4.34
4192 4429 2.633509 GCAAAGGCTCTGTGCAGGG 61.634 63.158 11.26 0.00 43.62 4.45
4193 4430 2.960170 GCAAAGGCTCTGTGCAGG 59.040 61.111 11.26 0.00 43.62 4.85
4194 4431 2.559840 CGCAAAGGCTCTGTGCAG 59.440 61.111 15.08 6.52 44.32 4.41
4195 4432 3.663176 GCGCAAAGGCTCTGTGCA 61.663 61.111 20.75 0.00 44.32 4.57
4197 4434 2.253452 GTGCGCAAAGGCTCTGTG 59.747 61.111 14.00 0.00 38.10 3.66
4198 4435 2.980233 GGTGCGCAAAGGCTCTGT 60.980 61.111 14.00 0.00 38.10 3.41
4199 4436 4.093952 CGGTGCGCAAAGGCTCTG 62.094 66.667 14.00 0.00 38.10 3.35
4218 4455 4.988598 ACAGCACAAGGACCGGCG 62.989 66.667 0.00 0.00 0.00 6.46
4219 4456 1.734388 AAAACAGCACAAGGACCGGC 61.734 55.000 0.00 0.00 0.00 6.13
4220 4457 1.600023 TAAAACAGCACAAGGACCGG 58.400 50.000 0.00 0.00 0.00 5.28
4221 4458 3.201726 CATAAAACAGCACAAGGACCG 57.798 47.619 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.