Multiple sequence alignment - TraesCS4B01G307200

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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 TraesCS4B01G307200 chr4B 100.000 6411 0 0 1 6411 596647679 596654089 0.000000e+00 11839.0
1 TraesCS4B01G307200 chr4B 95.918 147 5 1 4694 4839 596652232 596652378 2.990000e-58 237.0
2 TraesCS4B01G307200 chr4B 95.918 147 5 1 4554 4700 596652372 596652517 2.990000e-58 237.0
3 TraesCS4B01G307200 chr4B 96.124 129 5 0 6283 6411 596668071 596668199 1.810000e-50 211.0
4 TraesCS4B01G307200 chr4D 92.124 3136 111 47 1 3054 473833545 473836626 0.000000e+00 4298.0
5 TraesCS4B01G307200 chr4D 91.987 3095 105 46 3083 6118 473836626 473839636 0.000000e+00 4209.0
6 TraesCS4B01G307200 chr4D 95.906 171 5 1 6114 6284 473843864 473844032 6.330000e-70 276.0
7 TraesCS4B01G307200 chr4D 96.599 147 4 1 4694 4839 473838051 473838197 6.420000e-60 243.0
8 TraesCS4B01G307200 chr4D 95.918 147 5 1 4554 4700 473838191 473838336 2.990000e-58 237.0
9 TraesCS4B01G307200 chr4A 92.982 2921 119 39 682 3568 680397525 680400393 0.000000e+00 4180.0
10 TraesCS4B01G307200 chr4A 90.861 1499 71 30 3244 4700 680400399 680401873 0.000000e+00 1949.0
11 TraesCS4B01G307200 chr4A 92.668 1282 45 22 4699 5948 680401741 680403005 0.000000e+00 1801.0
12 TraesCS4B01G307200 chr4A 89.157 166 13 2 2564 2729 17978104 17977944 1.090000e-47 202.0
13 TraesCS4B01G307200 chr4A 93.750 112 7 0 6163 6274 680403568 680403679 1.110000e-37 169.0
14 TraesCS4B01G307200 chr4A 100.000 60 0 0 2725 2784 17976545 17976486 1.890000e-20 111.0
15 TraesCS4B01G307200 chr4A 83.193 119 6 6 580 694 680397398 680397506 5.290000e-16 97.1
16 TraesCS4B01G307200 chr7D 93.694 222 11 1 2564 2785 159000671 159000889 4.790000e-86 329.0
17 TraesCS4B01G307200 chr2D 91.031 223 19 1 2564 2785 245669725 245669503 3.760000e-77 300.0


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 TraesCS4B01G307200 chr4B 596647679 596654089 6410 False 4104.333333 11839 97.278667 1 6411 3 chr4B.!!$F2 6410
1 TraesCS4B01G307200 chr4D 473833545 473839636 6091 False 2246.750000 4298 94.157000 1 6118 4 chr4D.!!$F2 6117
2 TraesCS4B01G307200 chr4A 680397398 680403679 6281 False 1639.220000 4180 90.690800 580 6274 5 chr4A.!!$F1 5694

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
635 672 0.249073 CGGTCAGTCGTCCATCCATC 60.249 60.000 0.00 0.00 0.00 3.51 F
637 674 0.249073 GTCAGTCGTCCATCCATCCG 60.249 60.000 0.00 0.00 0.00 4.18 F
2229 2319 0.111061 TTGACCACATGGCAGAGCTT 59.889 50.000 0.00 0.00 39.32 3.74 F
3438 3552 2.749621 CCAGTGGACTAATTTCTGGCAC 59.250 50.000 1.68 0.00 39.02 5.01 F
3477 3924 0.030235 GTTTGGCGTGACCCTTTGAC 59.970 55.000 0.00 0.00 37.83 3.18 F
5226 5717 1.271707 GCCCTTGTTAACAGCAGGGTA 60.272 52.381 32.20 9.72 43.08 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 1887 1.190643 CAACAAACCCCCAGTTGTGT 58.809 50.000 0.00 0.0 39.19 3.72 R
2292 2382 1.449353 GGCGATGATCCTCAGCCTT 59.551 57.895 19.04 0.0 44.06 4.35 R
3450 3897 0.665835 GTCACGCCAAACCAACATCA 59.334 50.000 0.00 0.0 0.00 3.07 R
5193 5684 2.632377 ACAAGGGCAGTATGAATGACG 58.368 47.619 0.00 0.0 39.69 4.35 R
5252 5743 4.142816 GCATGCTGTAGTTTGACCTACTTG 60.143 45.833 11.37 0.0 38.49 3.16 R
6351 7225 0.039074 GGATGGTAGATCGACGGCTG 60.039 60.000 0.00 0.0 0.00 4.85 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
89 91 7.786943 ACTCTTATCTCAACCTATCATCCTCAA 59.213 37.037 0.00 0.00 0.00 3.02
91 93 8.811017 TCTTATCTCAACCTATCATCCTCAATC 58.189 37.037 0.00 0.00 0.00 2.67
116 128 6.894828 TCCTTATTAACTTTCAGTTCGCAAC 58.105 36.000 0.00 0.00 39.51 4.17
117 129 6.708949 TCCTTATTAACTTTCAGTTCGCAACT 59.291 34.615 0.00 0.00 44.06 3.16
148 161 3.761752 GGCCAAAGCATTGAGTTTAGGTA 59.238 43.478 2.61 0.00 42.56 3.08
165 178 9.411189 AGTTTAGGTAGGAAATAGTCAGTCTAG 57.589 37.037 0.00 0.00 31.67 2.43
181 194 2.153247 GTCTAGAAACGTGTTGTGCTCG 59.847 50.000 0.00 0.00 39.66 5.03
182 195 1.455786 CTAGAAACGTGTTGTGCTCGG 59.544 52.381 0.00 0.00 38.28 4.63
201 214 1.700186 GGAGAGTTCACCCTCCTTGTT 59.300 52.381 0.29 0.00 44.23 2.83
203 216 3.435169 GGAGAGTTCACCCTCCTTGTTTT 60.435 47.826 0.29 0.00 44.23 2.43
204 217 3.815962 GAGAGTTCACCCTCCTTGTTTTC 59.184 47.826 0.00 0.00 31.53 2.29
205 218 3.202151 AGAGTTCACCCTCCTTGTTTTCA 59.798 43.478 0.00 0.00 31.53 2.69
233 246 8.655970 CATGATCAATAACTAACACAAAGACGA 58.344 33.333 0.00 0.00 0.00 4.20
274 298 4.681025 GCATAACACAATCACAAACTGGTG 59.319 41.667 0.00 0.00 40.16 4.17
285 309 6.114187 TCACAAACTGGTGTCAAGAGATAT 57.886 37.500 0.00 0.00 39.76 1.63
289 313 7.550551 CACAAACTGGTGTCAAGAGATATGTAT 59.449 37.037 0.00 0.00 34.09 2.29
291 315 5.605534 ACTGGTGTCAAGAGATATGTATGC 58.394 41.667 0.00 0.00 0.00 3.14
320 344 7.859598 CATTTTAAAATGCACAACAAAGGCTA 58.140 30.769 24.00 0.00 39.29 3.93
338 362 2.933906 GCTAGCGTGTTATGTAAGGCAA 59.066 45.455 0.00 0.00 0.00 4.52
355 379 6.934048 AAGGCAAGTTCTATCTCAATTAGC 57.066 37.500 0.00 0.00 0.00 3.09
373 397 7.387397 TCAATTAGCAGCACAAATTTAAAAGGG 59.613 33.333 0.00 0.00 0.00 3.95
374 398 4.687901 AGCAGCACAAATTTAAAAGGGT 57.312 36.364 0.00 0.00 0.00 4.34
375 399 5.799827 AGCAGCACAAATTTAAAAGGGTA 57.200 34.783 0.00 0.00 0.00 3.69
378 402 5.405269 GCAGCACAAATTTAAAAGGGTAGTG 59.595 40.000 0.00 0.00 0.00 2.74
384 408 7.014422 CACAAATTTAAAAGGGTAGTGGTGGTA 59.986 37.037 0.00 0.00 0.00 3.25
402 426 5.007136 GGTGGTAGTAGTACTAGTTGTAGCG 59.993 48.000 15.34 0.00 30.12 4.26
404 428 5.812642 TGGTAGTAGTACTAGTTGTAGCGAC 59.187 44.000 15.34 5.89 30.12 5.19
529 553 3.843985 GCGGATTCCTCGCGTATC 58.156 61.111 5.77 5.43 43.71 2.24
574 598 6.460781 AGATCATCTACGTTTGTTGTTGGTA 58.539 36.000 0.00 0.00 0.00 3.25
576 600 8.255206 AGATCATCTACGTTTGTTGTTGGTATA 58.745 33.333 0.00 0.00 0.00 1.47
577 601 8.958119 ATCATCTACGTTTGTTGTTGGTATAT 57.042 30.769 0.00 0.00 0.00 0.86
634 671 1.676678 CCGGTCAGTCGTCCATCCAT 61.677 60.000 0.00 0.00 0.00 3.41
635 672 0.249073 CGGTCAGTCGTCCATCCATC 60.249 60.000 0.00 0.00 0.00 3.51
637 674 0.249073 GTCAGTCGTCCATCCATCCG 60.249 60.000 0.00 0.00 0.00 4.18
638 675 0.683179 TCAGTCGTCCATCCATCCGT 60.683 55.000 0.00 0.00 0.00 4.69
639 676 0.249073 CAGTCGTCCATCCATCCGTC 60.249 60.000 0.00 0.00 0.00 4.79
641 678 2.027605 CGTCCATCCATCCGTCCG 59.972 66.667 0.00 0.00 0.00 4.79
642 679 2.280186 GTCCATCCATCCGTCCGC 60.280 66.667 0.00 0.00 0.00 5.54
798 871 4.423209 GCCTCCTCCCCTCCACCT 62.423 72.222 0.00 0.00 0.00 4.00
799 872 2.041405 CCTCCTCCCCTCCACCTC 60.041 72.222 0.00 0.00 0.00 3.85
800 873 2.041405 CTCCTCCCCTCCACCTCC 60.041 72.222 0.00 0.00 0.00 4.30
801 874 3.695825 TCCTCCCCTCCACCTCCC 61.696 72.222 0.00 0.00 0.00 4.30
937 1024 1.929836 CGGATTCTCTCTGCTTTTCCG 59.070 52.381 0.00 0.00 38.71 4.30
938 1025 2.417379 CGGATTCTCTCTGCTTTTCCGA 60.417 50.000 2.44 0.00 45.60 4.55
948 1035 1.448013 CTTTTCCGACGCCTCCTCC 60.448 63.158 0.00 0.00 0.00 4.30
959 1046 2.359967 CCTCCTCCCCGTCTTGGTC 61.360 68.421 0.00 0.00 35.15 4.02
961 1048 0.905337 CTCCTCCCCGTCTTGGTCTT 60.905 60.000 0.00 0.00 35.15 3.01
963 1050 1.296715 CTCCCCGTCTTGGTCTTGG 59.703 63.158 0.00 0.00 35.15 3.61
964 1051 1.460689 TCCCCGTCTTGGTCTTGGT 60.461 57.895 0.00 0.00 35.15 3.67
965 1052 1.057851 TCCCCGTCTTGGTCTTGGTT 61.058 55.000 0.00 0.00 35.15 3.67
1797 1887 2.115910 CAGGCTGCCCCAGAACAA 59.884 61.111 16.57 0.00 32.44 2.83
2229 2319 0.111061 TTGACCACATGGCAGAGCTT 59.889 50.000 0.00 0.00 39.32 3.74
2358 2448 3.575687 TGCTGAGAATCTCTGTGAACTCA 59.424 43.478 16.61 14.36 38.66 3.41
2402 2492 9.383519 CTCTTGCCTAAACTGATCAATTAACTA 57.616 33.333 0.00 0.00 0.00 2.24
2447 2546 6.313744 ACTAGCTAACCAATTGTCACAAAC 57.686 37.500 4.43 0.00 0.00 2.93
2541 2641 7.278203 CCATGATGCTTACATTGCAACATAAAA 59.722 33.333 0.00 0.00 46.87 1.52
2549 2649 5.689835 ACATTGCAACATAAAACCCCTTTT 58.310 33.333 0.00 0.00 33.92 2.27
2550 2650 5.530543 ACATTGCAACATAAAACCCCTTTTG 59.469 36.000 0.00 0.00 31.74 2.44
2552 2652 5.104259 TGCAACATAAAACCCCTTTTGTT 57.896 34.783 0.00 0.00 32.88 2.83
2553 2653 6.235231 TGCAACATAAAACCCCTTTTGTTA 57.765 33.333 0.00 0.00 32.16 2.41
2554 2654 6.049790 TGCAACATAAAACCCCTTTTGTTAC 58.950 36.000 0.00 0.00 32.16 2.50
3037 3143 3.661758 ACGTTGTTCCGTGTTTACTTG 57.338 42.857 0.00 0.00 40.08 3.16
3074 3180 3.305064 GCCGGCAGATGAACAAAAACTAA 60.305 43.478 24.80 0.00 0.00 2.24
3089 3195 7.703328 ACAAAAACTAAACCTGTACATCAGTG 58.297 34.615 0.00 0.00 42.19 3.66
3092 3198 4.315803 ACTAAACCTGTACATCAGTGTGC 58.684 43.478 0.00 0.00 42.19 4.57
3100 3206 3.938334 TGTACATCAGTGTGCGCATAATT 59.062 39.130 15.91 0.00 43.01 1.40
3113 3219 8.523464 GTGTGCGCATAATTTTAGAAGTTTATG 58.477 33.333 15.91 0.00 35.90 1.90
3434 3548 4.938226 GGTTCTCCAGTGGACTAATTTCTG 59.062 45.833 8.12 0.00 0.00 3.02
3438 3552 2.749621 CCAGTGGACTAATTTCTGGCAC 59.250 50.000 1.68 0.00 39.02 5.01
3450 3897 9.193806 ACTAATTTCTGGCACAATCATCTTAAT 57.806 29.630 0.00 0.00 38.70 1.40
3477 3924 0.030235 GTTTGGCGTGACCCTTTGAC 59.970 55.000 0.00 0.00 37.83 3.18
3642 4094 7.660030 AGGTTTCTTTTAACATGGGGATATG 57.340 36.000 0.00 0.00 0.00 1.78
3797 4250 7.325821 GCTCAATGTCATTTTGAACGTCATAAA 59.674 33.333 0.00 0.00 32.98 1.40
3830 4292 7.437267 CGGGTAAATTAGTAGTGTGTTATGGAG 59.563 40.741 0.00 0.00 0.00 3.86
4150 4637 7.744087 ACAACATTCTTGCACTATGTCTTTA 57.256 32.000 7.69 0.00 31.63 1.85
4318 4806 3.000041 TCGATATTGTTGCTCGTTGCTT 59.000 40.909 5.00 0.00 43.37 3.91
4423 4911 4.010349 CAACTTGATTAGTCCCTTGACCC 58.990 47.826 0.00 0.00 42.81 4.46
4439 4927 9.387397 TCCCTTGACCCTAAAAATCTTATTTTT 57.613 29.630 13.22 13.22 34.51 1.94
4444 4932 9.160412 TGACCCTAAAAATCTTATTTTTCCCAA 57.840 29.630 12.30 0.00 34.51 4.12
4535 5023 5.904941 TCTGTTTGCATTTCACAGACAATT 58.095 33.333 12.22 0.00 41.60 2.32
4571 5059 5.586243 GCTGATAATGGTATGAACTGTGTGT 59.414 40.000 0.00 0.00 0.00 3.72
4582 5070 8.726988 GGTATGAACTGTGTGTTAATTACATGT 58.273 33.333 2.69 2.69 39.39 3.21
4613 5101 7.906327 ACCTTTGTTGGAATAACTATTTGCAT 58.094 30.769 0.00 0.00 0.00 3.96
4614 5102 7.818930 ACCTTTGTTGGAATAACTATTTGCATG 59.181 33.333 0.00 0.00 0.00 4.06
4683 5171 5.898120 TCCCCAACCTGATTTATCTTTTGA 58.102 37.500 0.00 0.00 0.00 2.69
4822 5310 4.466015 TCCCCAACCTGATTTATCTTTTGC 59.534 41.667 0.00 0.00 0.00 3.68
5157 5648 3.141398 TGACTTGATTTCAGTGCCTCAC 58.859 45.455 0.00 0.00 34.10 3.51
5193 5684 2.350484 GCAAGACCCTTTTGCGAACTAC 60.350 50.000 0.00 0.00 41.16 2.73
5226 5717 1.271707 GCCCTTGTTAACAGCAGGGTA 60.272 52.381 32.20 9.72 43.08 3.69
5233 5724 4.131596 TGTTAACAGCAGGGTAAGTGTTC 58.868 43.478 3.59 0.00 34.92 3.18
5246 5737 5.454187 GGGTAAGTGTTCCGATCCATATGAA 60.454 44.000 3.65 0.00 0.00 2.57
5252 5743 7.707104 AGTGTTCCGATCCATATGAATTTTTC 58.293 34.615 3.65 0.00 0.00 2.29
5258 5749 9.056005 TCCGATCCATATGAATTTTTCAAGTAG 57.944 33.333 3.65 0.00 43.95 2.57
5282 5773 5.163622 GGTCAAACTACAGCATGCATATTGT 60.164 40.000 21.98 17.37 42.53 2.71
5284 5775 6.252015 GTCAAACTACAGCATGCATATTGTTG 59.748 38.462 21.98 17.44 42.53 3.33
5647 6138 8.283291 GTGATGGTGTAGAGTTGTAAAGAAAAG 58.717 37.037 0.00 0.00 0.00 2.27
5710 6202 3.363341 TCGTTTTCCTTTGGATTGTGC 57.637 42.857 0.00 0.00 0.00 4.57
5714 6206 2.214376 TTCCTTTGGATTGTGCGGAT 57.786 45.000 0.00 0.00 0.00 4.18
5727 6219 6.375455 GGATTGTGCGGATGGAGAATAATTAT 59.625 38.462 0.00 0.00 29.37 1.28
5756 6260 8.588290 TGGTGGACAAGTTGCTATATATTTTT 57.412 30.769 1.81 0.00 0.00 1.94
5827 6331 9.734984 AAATAATAGCTCATCATGATCATGTCA 57.265 29.630 30.01 16.12 42.06 3.58
5880 6402 1.247419 CCTGTTTTGTATGGCGGGCA 61.247 55.000 6.74 6.74 0.00 5.36
5887 6409 1.317613 TGTATGGCGGGCATTTCATC 58.682 50.000 22.64 8.86 0.00 2.92
5897 6421 3.431626 CGGGCATTTCATCCAGTACAGTA 60.432 47.826 0.00 0.00 0.00 2.74
5935 6459 7.806960 GGAACAAAGCTGATTGATTATATGAGC 59.193 37.037 5.15 0.00 34.38 4.26
5976 6526 6.153680 ACTTGGTACCAATTGTTTCTTTGACA 59.846 34.615 27.24 0.00 35.20 3.58
5980 6530 7.504238 TGGTACCAATTGTTTCTTTGACATAGT 59.496 33.333 13.60 0.00 0.00 2.12
5984 6534 9.313118 ACCAATTGTTTCTTTGACATAGTTTTC 57.687 29.630 4.43 0.00 0.00 2.29
5988 6538 5.591067 TGTTTCTTTGACATAGTTTTCGGGT 59.409 36.000 0.00 0.00 0.00 5.28
5990 6540 3.991773 TCTTTGACATAGTTTTCGGGTCG 59.008 43.478 0.00 0.00 0.00 4.79
5998 6548 2.207590 AGTTTTCGGGTCGTTGAAGAC 58.792 47.619 0.00 0.00 40.25 3.01
6038 6607 7.217200 TGTATTTTCATAGAGATAGGGTGTGC 58.783 38.462 0.00 0.00 0.00 4.57
6039 6614 5.957771 TTTTCATAGAGATAGGGTGTGCT 57.042 39.130 0.00 0.00 0.00 4.40
6048 6623 7.618019 AGAGATAGGGTGTGCTGATAATTTA 57.382 36.000 0.00 0.00 0.00 1.40
6130 6712 9.255029 ACTTGGCTTGATAAATTTGGTTACTAT 57.745 29.630 0.00 0.00 0.00 2.12
6157 6739 6.434340 GGTTTAAGAGACAATCATTTCCAGGT 59.566 38.462 0.00 0.00 0.00 4.00
6171 7045 2.972348 TCCAGGTCTAGTTGTGGACTT 58.028 47.619 5.83 0.00 39.86 3.01
6179 7053 0.916086 AGTTGTGGACTTGTGGTGGA 59.084 50.000 0.00 0.00 33.92 4.02
6192 7066 1.203052 GTGGTGGATGTGCTGAAATGG 59.797 52.381 0.00 0.00 0.00 3.16
6206 7080 4.925054 GCTGAAATGGTACTACAACGTGTA 59.075 41.667 0.00 0.00 0.00 2.90
6221 7095 9.584839 CTACAACGTGTAATAAAAAGTAACCAC 57.415 33.333 0.00 0.00 31.67 4.16
6227 7101 8.155923 CGTGTAATAAAAAGTAACCACGTAGAC 58.844 37.037 0.00 0.00 39.47 2.59
6274 7148 5.975693 TTTCTTCTTGTGAACCAAACTGT 57.024 34.783 0.00 0.00 31.20 3.55
6275 7149 5.560966 TTCTTCTTGTGAACCAAACTGTC 57.439 39.130 0.00 0.00 31.20 3.51
6276 7150 3.621268 TCTTCTTGTGAACCAAACTGTCG 59.379 43.478 0.00 0.00 31.20 4.35
6277 7151 2.980568 TCTTGTGAACCAAACTGTCGT 58.019 42.857 0.00 0.00 31.20 4.34
6278 7152 2.675844 TCTTGTGAACCAAACTGTCGTG 59.324 45.455 0.00 0.00 31.20 4.35
6279 7153 1.374560 TGTGAACCAAACTGTCGTGG 58.625 50.000 8.50 8.50 41.00 4.94
6284 7158 1.663695 ACCAAACTGTCGTGGTCTTG 58.336 50.000 9.64 0.00 45.18 3.02
6285 7159 1.065709 ACCAAACTGTCGTGGTCTTGT 60.066 47.619 9.64 0.00 45.18 3.16
6286 7160 1.597663 CCAAACTGTCGTGGTCTTGTC 59.402 52.381 3.00 0.00 0.00 3.18
6287 7161 2.276201 CAAACTGTCGTGGTCTTGTCA 58.724 47.619 0.00 0.00 0.00 3.58
6288 7162 2.225068 AACTGTCGTGGTCTTGTCAG 57.775 50.000 0.00 0.00 0.00 3.51
6289 7163 0.389391 ACTGTCGTGGTCTTGTCAGG 59.611 55.000 0.00 0.00 0.00 3.86
6290 7164 0.946221 CTGTCGTGGTCTTGTCAGGC 60.946 60.000 0.00 0.00 0.00 4.85
6291 7165 1.668151 GTCGTGGTCTTGTCAGGCC 60.668 63.158 0.00 0.00 46.40 5.19
6292 7166 1.837051 TCGTGGTCTTGTCAGGCCT 60.837 57.895 0.00 0.00 46.36 5.19
6293 7167 1.669115 CGTGGTCTTGTCAGGCCTG 60.669 63.158 27.87 27.87 46.36 4.85
6294 7168 1.451936 GTGGTCTTGTCAGGCCTGT 59.548 57.895 31.58 0.00 46.36 4.00
6295 7169 0.179018 GTGGTCTTGTCAGGCCTGTT 60.179 55.000 31.58 0.00 46.36 3.16
6296 7170 0.108585 TGGTCTTGTCAGGCCTGTTC 59.891 55.000 31.58 24.16 46.36 3.18
6297 7171 0.398318 GGTCTTGTCAGGCCTGTTCT 59.602 55.000 31.58 0.00 42.30 3.01
6298 7172 1.517242 GTCTTGTCAGGCCTGTTCTG 58.483 55.000 31.58 19.62 0.00 3.02
6299 7173 1.131638 TCTTGTCAGGCCTGTTCTGT 58.868 50.000 31.58 0.00 34.15 3.41
6300 7174 1.070758 TCTTGTCAGGCCTGTTCTGTC 59.929 52.381 31.58 15.81 34.15 3.51
6301 7175 0.249868 TTGTCAGGCCTGTTCTGTCG 60.250 55.000 31.58 4.18 34.15 4.35
6302 7176 1.112916 TGTCAGGCCTGTTCTGTCGA 61.113 55.000 31.58 7.59 34.15 4.20
6303 7177 0.667792 GTCAGGCCTGTTCTGTCGAC 60.668 60.000 31.58 16.29 34.15 4.20
6304 7178 1.112916 TCAGGCCTGTTCTGTCGACA 61.113 55.000 31.58 18.88 34.15 4.35
6305 7179 0.249868 CAGGCCTGTTCTGTCGACAA 60.250 55.000 25.53 7.97 0.00 3.18
6306 7180 0.249911 AGGCCTGTTCTGTCGACAAC 60.250 55.000 20.49 16.07 0.00 3.32
6307 7181 0.531974 GGCCTGTTCTGTCGACAACA 60.532 55.000 20.49 19.73 36.18 3.33
6308 7182 0.582005 GCCTGTTCTGTCGACAACAC 59.418 55.000 20.49 18.12 33.24 3.32
6309 7183 1.217882 CCTGTTCTGTCGACAACACC 58.782 55.000 20.49 8.31 33.24 4.16
6310 7184 1.472552 CCTGTTCTGTCGACAACACCA 60.473 52.381 20.49 12.30 33.24 4.17
6311 7185 1.860950 CTGTTCTGTCGACAACACCAG 59.139 52.381 20.49 17.35 33.24 4.00
6312 7186 1.478916 TGTTCTGTCGACAACACCAGA 59.521 47.619 20.49 9.26 33.24 3.86
6313 7187 2.093921 TGTTCTGTCGACAACACCAGAA 60.094 45.455 20.49 14.82 40.57 3.02
6314 7188 3.131396 GTTCTGTCGACAACACCAGAAT 58.869 45.455 20.49 0.00 43.52 2.40
6315 7189 3.469008 TCTGTCGACAACACCAGAATT 57.531 42.857 20.49 0.00 33.24 2.17
6316 7190 3.130633 TCTGTCGACAACACCAGAATTG 58.869 45.455 20.49 3.17 33.24 2.32
6317 7191 1.601903 TGTCGACAACACCAGAATTGC 59.398 47.619 17.62 0.00 31.20 3.56
6318 7192 1.069227 GTCGACAACACCAGAATTGCC 60.069 52.381 11.55 0.00 0.00 4.52
6319 7193 0.950836 CGACAACACCAGAATTGCCA 59.049 50.000 0.00 0.00 0.00 4.92
6320 7194 1.334960 CGACAACACCAGAATTGCCAC 60.335 52.381 0.00 0.00 0.00 5.01
6321 7195 1.680735 GACAACACCAGAATTGCCACA 59.319 47.619 0.00 0.00 0.00 4.17
6322 7196 1.682854 ACAACACCAGAATTGCCACAG 59.317 47.619 0.00 0.00 0.00 3.66
6323 7197 1.682854 CAACACCAGAATTGCCACAGT 59.317 47.619 0.00 0.00 0.00 3.55
6324 7198 2.884012 CAACACCAGAATTGCCACAGTA 59.116 45.455 0.00 0.00 0.00 2.74
6325 7199 2.504367 ACACCAGAATTGCCACAGTAC 58.496 47.619 0.00 0.00 0.00 2.73
6326 7200 1.812571 CACCAGAATTGCCACAGTACC 59.187 52.381 0.00 0.00 0.00 3.34
6327 7201 1.086696 CCAGAATTGCCACAGTACCG 58.913 55.000 0.00 0.00 0.00 4.02
6328 7202 1.338674 CCAGAATTGCCACAGTACCGA 60.339 52.381 0.00 0.00 0.00 4.69
6329 7203 2.632377 CAGAATTGCCACAGTACCGAT 58.368 47.619 0.00 0.00 0.00 4.18
6330 7204 3.009723 CAGAATTGCCACAGTACCGATT 58.990 45.455 0.00 0.00 0.00 3.34
6331 7205 3.063997 CAGAATTGCCACAGTACCGATTC 59.936 47.826 0.00 0.00 32.16 2.52
6332 7206 1.651987 ATTGCCACAGTACCGATTCG 58.348 50.000 0.00 0.00 0.00 3.34
6343 7217 2.550487 CCGATTCGGTTTGCCAAGA 58.450 52.632 17.08 0.00 42.73 3.02
6344 7218 0.168128 CCGATTCGGTTTGCCAAGAC 59.832 55.000 17.08 0.00 42.73 3.01
6345 7219 0.871722 CGATTCGGTTTGCCAAGACA 59.128 50.000 0.00 0.00 34.09 3.41
6346 7220 1.265635 CGATTCGGTTTGCCAAGACAA 59.734 47.619 0.00 0.00 34.09 3.18
6347 7221 2.287308 CGATTCGGTTTGCCAAGACAAA 60.287 45.455 0.00 0.00 37.20 2.83
6354 7228 2.292103 TTGCCAAGACAAACAACAGC 57.708 45.000 0.00 0.00 0.00 4.40
6355 7229 0.459489 TGCCAAGACAAACAACAGCC 59.541 50.000 0.00 0.00 0.00 4.85
6356 7230 0.594796 GCCAAGACAAACAACAGCCG 60.595 55.000 0.00 0.00 0.00 5.52
6357 7231 0.738389 CCAAGACAAACAACAGCCGT 59.262 50.000 0.00 0.00 0.00 5.68
6358 7232 1.268539 CCAAGACAAACAACAGCCGTC 60.269 52.381 0.00 0.00 0.00 4.79
6359 7233 0.655733 AAGACAAACAACAGCCGTCG 59.344 50.000 0.00 0.00 0.00 5.12
6360 7234 0.179094 AGACAAACAACAGCCGTCGA 60.179 50.000 0.00 0.00 0.00 4.20
6361 7235 0.865769 GACAAACAACAGCCGTCGAT 59.134 50.000 0.00 0.00 0.00 3.59
6362 7236 0.865769 ACAAACAACAGCCGTCGATC 59.134 50.000 0.00 0.00 0.00 3.69
6363 7237 1.148310 CAAACAACAGCCGTCGATCT 58.852 50.000 0.00 0.00 0.00 2.75
6364 7238 2.288579 ACAAACAACAGCCGTCGATCTA 60.289 45.455 0.00 0.00 0.00 1.98
6365 7239 1.992170 AACAACAGCCGTCGATCTAC 58.008 50.000 0.00 0.00 0.00 2.59
6366 7240 0.172803 ACAACAGCCGTCGATCTACC 59.827 55.000 0.00 0.00 0.00 3.18
6367 7241 0.172578 CAACAGCCGTCGATCTACCA 59.827 55.000 0.00 0.00 0.00 3.25
6368 7242 1.112113 AACAGCCGTCGATCTACCAT 58.888 50.000 0.00 0.00 0.00 3.55
6369 7243 0.669077 ACAGCCGTCGATCTACCATC 59.331 55.000 0.00 0.00 0.00 3.51
6370 7244 0.039074 CAGCCGTCGATCTACCATCC 60.039 60.000 0.00 0.00 0.00 3.51
6371 7245 1.081376 GCCGTCGATCTACCATCCG 60.081 63.158 0.00 0.00 0.00 4.18
6372 7246 1.512996 GCCGTCGATCTACCATCCGA 61.513 60.000 0.00 0.00 0.00 4.55
6373 7247 0.517755 CCGTCGATCTACCATCCGAG 59.482 60.000 0.00 0.00 0.00 4.63
6374 7248 0.517755 CGTCGATCTACCATCCGAGG 59.482 60.000 0.00 0.00 0.00 4.63
6375 7249 0.882474 GTCGATCTACCATCCGAGGG 59.118 60.000 0.00 0.00 0.00 4.30
6376 7250 0.769247 TCGATCTACCATCCGAGGGA 59.231 55.000 5.98 0.00 35.55 4.20
6377 7251 0.882474 CGATCTACCATCCGAGGGAC 59.118 60.000 5.98 0.00 32.98 4.46
6378 7252 0.882474 GATCTACCATCCGAGGGACG 59.118 60.000 5.98 0.00 42.18 4.79
6379 7253 1.179814 ATCTACCATCCGAGGGACGC 61.180 60.000 5.98 0.00 41.07 5.19
6380 7254 2.043752 TACCATCCGAGGGACGCA 60.044 61.111 5.98 0.00 41.07 5.24
6381 7255 2.076622 CTACCATCCGAGGGACGCAG 62.077 65.000 5.98 0.00 41.07 5.18
6382 7256 4.227134 CCATCCGAGGGACGCAGG 62.227 72.222 0.00 0.00 41.07 4.85
6383 7257 4.227134 CATCCGAGGGACGCAGGG 62.227 72.222 4.63 0.00 41.07 4.45
6388 7262 3.775654 GAGGGACGCAGGGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
6391 7265 2.682494 GGACGCAGGGGAGTGGTA 60.682 66.667 0.00 0.00 0.00 3.25
6392 7266 2.577593 GACGCAGGGGAGTGGTAC 59.422 66.667 0.00 0.00 0.00 3.34
6393 7267 3.001406 ACGCAGGGGAGTGGTACC 61.001 66.667 4.43 4.43 0.00 3.34
6394 7268 4.143333 CGCAGGGGAGTGGTACCG 62.143 72.222 7.57 0.00 0.00 4.02
6395 7269 4.468689 GCAGGGGAGTGGTACCGC 62.469 72.222 18.11 18.11 40.04 5.68
6397 7271 2.122056 AGGGGAGTGGTACCGCTT 59.878 61.111 28.19 10.48 46.03 4.68
6398 7272 1.988406 AGGGGAGTGGTACCGCTTC 60.988 63.158 28.19 25.92 46.03 3.86
6399 7273 2.183555 GGGAGTGGTACCGCTTCG 59.816 66.667 28.19 0.00 36.86 3.79
6400 7274 2.345760 GGGAGTGGTACCGCTTCGA 61.346 63.158 28.19 0.00 36.86 3.71
6401 7275 1.139095 GGAGTGGTACCGCTTCGAG 59.861 63.158 28.19 0.00 36.86 4.04
6402 7276 1.139095 GAGTGGTACCGCTTCGAGG 59.861 63.158 28.19 0.00 36.86 4.63
6403 7277 2.508663 GTGGTACCGCTTCGAGGC 60.509 66.667 18.49 9.88 0.00 4.70
6404 7278 3.766691 TGGTACCGCTTCGAGGCC 61.767 66.667 14.49 0.00 0.00 5.19
6405 7279 4.525949 GGTACCGCTTCGAGGCCC 62.526 72.222 14.49 5.34 0.00 5.80
6406 7280 4.867599 GTACCGCTTCGAGGCCCG 62.868 72.222 14.49 6.82 40.25 6.13
6410 7284 4.951963 CGCTTCGAGGCCCGGATC 62.952 72.222 14.49 0.00 39.14 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 7.301420 TGAGGATGATAGGTTGAGATAAGAGT 58.699 38.462 0.00 0.00 0.00 3.24
71 73 5.543405 AGGAGATTGAGGATGATAGGTTGAG 59.457 44.000 0.00 0.00 0.00 3.02
127 140 3.942130 ACCTAAACTCAATGCTTTGGC 57.058 42.857 11.99 0.00 39.26 4.52
148 161 6.208994 ACACGTTTCTAGACTGACTATTTCCT 59.791 38.462 0.00 0.00 0.00 3.36
165 178 0.232303 CTCCGAGCACAACACGTTTC 59.768 55.000 0.00 0.00 0.00 2.78
182 195 3.493767 AAACAAGGAGGGTGAACTCTC 57.506 47.619 1.42 1.42 37.63 3.20
191 204 4.951715 TGATCATGATGAAAACAAGGAGGG 59.048 41.667 14.30 0.00 0.00 4.30
246 259 4.576216 TTGTGATTGTGTTATGCGGTTT 57.424 36.364 0.00 0.00 0.00 3.27
251 264 4.681025 CACCAGTTTGTGATTGTGTTATGC 59.319 41.667 0.00 0.00 38.55 3.14
274 298 7.413475 AATGTTCGCATACATATCTCTTGAC 57.587 36.000 1.52 0.00 37.76 3.18
285 309 6.642540 TGTGCATTTTAAAATGTTCGCATACA 59.357 30.769 31.43 22.61 45.77 2.29
289 313 5.291858 TGTTGTGCATTTTAAAATGTTCGCA 59.708 32.000 31.43 25.93 45.77 5.10
291 315 7.372918 CCTTTGTTGTGCATTTTAAAATGTTCG 59.627 33.333 31.43 14.63 45.77 3.95
320 344 3.053831 ACTTGCCTTACATAACACGCT 57.946 42.857 0.00 0.00 0.00 5.07
338 362 5.982356 TGTGCTGCTAATTGAGATAGAACT 58.018 37.500 0.00 0.00 0.00 3.01
353 377 4.687901 ACCCTTTTAAATTTGTGCTGCT 57.312 36.364 0.00 0.00 0.00 4.24
355 379 5.925969 CCACTACCCTTTTAAATTTGTGCTG 59.074 40.000 0.00 0.00 0.00 4.41
373 397 6.881602 ACAACTAGTACTACTACCACCACTAC 59.118 42.308 0.00 0.00 0.00 2.73
374 398 7.020827 ACAACTAGTACTACTACCACCACTA 57.979 40.000 0.00 0.00 0.00 2.74
375 399 5.885465 ACAACTAGTACTACTACCACCACT 58.115 41.667 0.00 0.00 0.00 4.00
378 402 5.007136 CGCTACAACTAGTACTACTACCACC 59.993 48.000 0.00 0.00 0.00 4.61
384 408 3.868077 CCGTCGCTACAACTAGTACTACT 59.132 47.826 0.00 0.00 0.00 2.57
402 426 1.947456 GCTTTGGGTAATCCATCCGTC 59.053 52.381 0.00 0.00 46.52 4.79
404 428 1.318576 GGCTTTGGGTAATCCATCCG 58.681 55.000 0.00 0.00 46.52 4.18
451 475 0.961753 CTTTCCTTTGCCACCAGACC 59.038 55.000 0.00 0.00 0.00 3.85
452 476 0.961753 CCTTTCCTTTGCCACCAGAC 59.038 55.000 0.00 0.00 0.00 3.51
453 477 0.850100 TCCTTTCCTTTGCCACCAGA 59.150 50.000 0.00 0.00 0.00 3.86
454 478 1.703411 TTCCTTTCCTTTGCCACCAG 58.297 50.000 0.00 0.00 0.00 4.00
455 479 2.038659 CTTTCCTTTCCTTTGCCACCA 58.961 47.619 0.00 0.00 0.00 4.17
525 549 2.355363 TACGGCGCGCCATGATAC 60.355 61.111 45.26 20.46 35.37 2.24
678 723 2.131067 GCTTCCTCTCCCCTCCTCG 61.131 68.421 0.00 0.00 0.00 4.63
897 970 1.099879 ATCAGAGATTGCAAGCGGGC 61.100 55.000 9.38 3.13 0.00 6.13
938 1025 4.698625 AAGACGGGGAGGAGGCGT 62.699 66.667 0.00 0.00 0.00 5.68
948 1035 1.235724 GAAACCAAGACCAAGACGGG 58.764 55.000 0.00 0.00 40.22 5.28
959 1046 3.431725 GGGCGAGGCGAAACCAAG 61.432 66.667 0.00 0.00 43.14 3.61
981 1068 3.567585 TCATCGCCAGATCAACAAACAAA 59.432 39.130 0.00 0.00 34.23 2.83
982 1069 3.145286 TCATCGCCAGATCAACAAACAA 58.855 40.909 0.00 0.00 34.23 2.83
983 1070 2.777094 TCATCGCCAGATCAACAAACA 58.223 42.857 0.00 0.00 34.23 2.83
984 1071 3.426695 CCTTCATCGCCAGATCAACAAAC 60.427 47.826 0.00 0.00 34.23 2.93
1395 1485 3.685214 CTGCTTCTCCGGGTCGTCG 62.685 68.421 0.00 0.00 0.00 5.12
1655 1745 2.971598 ATGTTGACCTCCAGGCCGG 61.972 63.158 0.00 0.00 39.32 6.13
1797 1887 1.190643 CAACAAACCCCCAGTTGTGT 58.809 50.000 0.00 0.00 39.19 3.72
2229 2319 4.323417 AGTTGGCAAACGAGTTGATCATA 58.677 39.130 0.00 0.00 41.45 2.15
2292 2382 1.449353 GGCGATGATCCTCAGCCTT 59.551 57.895 19.04 0.00 44.06 4.35
2427 2526 7.524717 AATAGTTTGTGACAATTGGTTAGCT 57.475 32.000 10.83 0.00 0.00 3.32
2447 2546 8.146479 TGCAGCATTCTCAAATACAGTAATAG 57.854 34.615 0.00 0.00 0.00 1.73
2510 2610 3.676598 GCAATGTAAGCATCATGGCACAA 60.677 43.478 9.29 0.00 40.69 3.33
2541 2641 5.568624 GCATGCATTTAGTAACAAAAGGGGT 60.569 40.000 14.21 0.00 0.00 4.95
2549 2649 7.278203 CCAATCATTTGCATGCATTTAGTAACA 59.722 33.333 23.37 0.00 0.00 2.41
2550 2650 7.278424 ACCAATCATTTGCATGCATTTAGTAAC 59.722 33.333 23.37 0.00 0.00 2.50
2552 2652 6.757478 CACCAATCATTTGCATGCATTTAGTA 59.243 34.615 23.37 1.46 0.00 1.82
2553 2653 5.583061 CACCAATCATTTGCATGCATTTAGT 59.417 36.000 23.37 9.12 0.00 2.24
2554 2654 5.813157 TCACCAATCATTTGCATGCATTTAG 59.187 36.000 23.37 12.07 0.00 1.85
2863 2966 4.828939 TCATGGTGCTGATTCTCAAACTTT 59.171 37.500 0.00 0.00 0.00 2.66
3037 3143 3.452474 TGCCGGCAAATTTACATAATGC 58.548 40.909 30.74 0.00 36.31 3.56
3089 3195 8.614994 ACATAAACTTCTAAAATTATGCGCAC 57.385 30.769 14.90 0.00 38.63 5.34
3129 3235 3.368236 GGCTAGCGCATATAAACTGCTAC 59.632 47.826 11.47 0.00 37.48 3.58
3450 3897 0.665835 GTCACGCCAAACCAACATCA 59.334 50.000 0.00 0.00 0.00 3.07
3464 3911 2.033602 GGGGGTCAAAGGGTCACG 59.966 66.667 0.00 0.00 0.00 4.35
3513 3960 8.763984 AGAGAATAGAAAAGGAATGCATGATT 57.236 30.769 0.00 0.00 0.00 2.57
3535 3987 7.170998 AGGTACGTTCAGAAACATGTAAAAGAG 59.829 37.037 0.00 0.00 34.93 2.85
3546 3998 4.495184 CCAACACAAGGTACGTTCAGAAAC 60.495 45.833 0.00 0.00 0.00 2.78
3642 4094 6.978659 TCTGGTACATTAACTTCATGATCGAC 59.021 38.462 0.00 0.00 38.20 4.20
3797 4250 8.480501 ACACACTACTAATTTACCCGACATTAT 58.519 33.333 0.00 0.00 0.00 1.28
4129 4616 6.237901 TGGTAAAGACATAGTGCAAGAATGT 58.762 36.000 9.00 9.00 36.57 2.71
4130 4617 6.741992 TGGTAAAGACATAGTGCAAGAATG 57.258 37.500 0.00 0.00 0.00 2.67
4131 4618 7.944729 ATTGGTAAAGACATAGTGCAAGAAT 57.055 32.000 0.00 0.00 0.00 2.40
4150 4637 5.343307 AACTGCTTCACAAAAGAATTGGT 57.657 34.783 0.00 0.00 0.00 3.67
4249 4736 9.461312 TGGATATTCTTCCCATTAATAAATCCG 57.539 33.333 0.00 0.00 34.67 4.18
4261 4749 6.787458 TCAGTATAAGCTGGATATTCTTCCCA 59.213 38.462 0.00 0.00 37.12 4.37
4439 4927 3.297134 AGAGCAACAGAAACTTTGGGA 57.703 42.857 0.00 0.00 0.00 4.37
4444 4932 6.995091 AGTTGAATCTAGAGCAACAGAAACTT 59.005 34.615 28.56 13.51 43.15 2.66
4535 5023 5.364778 ACCATTATCAGCACGCTTATTGTA 58.635 37.500 0.00 0.00 0.00 2.41
4571 5059 8.480133 AACAAAGGTTGGGTACATGTAATTAA 57.520 30.769 7.25 0.18 35.46 1.40
4683 5171 7.171508 CACACAGTTCATACATTCACTACTTGT 59.828 37.037 0.00 0.00 0.00 3.16
4822 5310 9.159364 CATGATGGATATACATTCACTACTTGG 57.841 37.037 0.86 0.00 0.00 3.61
5157 5648 3.111098 GTCTTGCAGCAGTTGTTCAAAG 58.889 45.455 0.00 0.00 0.00 2.77
5193 5684 2.632377 ACAAGGGCAGTATGAATGACG 58.368 47.619 0.00 0.00 39.69 4.35
5226 5717 7.645058 AAAATTCATATGGATCGGAACACTT 57.355 32.000 2.13 0.00 0.00 3.16
5233 5724 8.292448 CCTACTTGAAAAATTCATATGGATCGG 58.708 37.037 2.13 0.00 39.84 4.18
5246 5737 7.284489 TGCTGTAGTTTGACCTACTTGAAAAAT 59.716 33.333 0.00 0.00 38.49 1.82
5252 5743 4.142816 GCATGCTGTAGTTTGACCTACTTG 60.143 45.833 11.37 0.00 38.49 3.16
5258 5749 5.163622 ACAATATGCATGCTGTAGTTTGACC 60.164 40.000 20.33 0.00 0.00 4.02
5265 5756 5.746307 AGTCAACAATATGCATGCTGTAG 57.254 39.130 20.33 7.65 0.00 2.74
5647 6138 1.329599 ACTCGGAAAGCACACGTTTTC 59.670 47.619 2.48 2.48 40.52 2.29
5710 6202 8.677300 CCACCATTAATAATTATTCTCCATCCG 58.323 37.037 13.95 0.00 0.00 4.18
5714 6206 9.928618 TTGTCCACCATTAATAATTATTCTCCA 57.071 29.630 13.95 0.00 0.00 3.86
5727 6219 9.860650 AATATATAGCAACTTGTCCACCATTAA 57.139 29.630 0.00 0.00 0.00 1.40
5756 6260 3.953612 AGTTCAAGCAAGTTGGATTGACA 59.046 39.130 4.75 0.00 42.28 3.58
5761 6265 4.723309 AGAAGAGTTCAAGCAAGTTGGAT 58.277 39.130 4.75 0.00 36.71 3.41
5850 6354 1.311859 CAAAACAGGTGAGCTCTGCA 58.688 50.000 16.19 0.00 35.78 4.41
5851 6355 1.312815 ACAAAACAGGTGAGCTCTGC 58.687 50.000 16.19 7.78 35.78 4.26
5852 6356 3.438087 CCATACAAAACAGGTGAGCTCTG 59.562 47.826 16.19 7.62 38.16 3.35
5897 6421 5.127194 TCAGCTTTGTTCCGACAGTATATCT 59.873 40.000 0.00 0.00 37.04 1.98
5908 6432 7.864686 TCATATAATCAATCAGCTTTGTTCCG 58.135 34.615 0.00 0.00 0.00 4.30
5912 6436 7.812690 TGCTCATATAATCAATCAGCTTTGT 57.187 32.000 0.00 0.00 0.00 2.83
5935 6459 6.531240 GGTACCAAGTTTGCAATTGTGATATG 59.469 38.462 7.15 0.43 0.00 1.78
5948 6472 7.547370 TCAAAGAAACAATTGGTACCAAGTTTG 59.453 33.333 33.12 30.62 39.47 2.93
5976 6526 3.992427 GTCTTCAACGACCCGAAAACTAT 59.008 43.478 0.00 0.00 0.00 2.12
5980 6530 1.585297 GGTCTTCAACGACCCGAAAA 58.415 50.000 0.00 0.00 46.19 2.29
5988 6538 5.789521 TCAACAGATAATGGTCTTCAACGA 58.210 37.500 0.00 0.00 0.00 3.85
5990 6540 7.820648 ACAATCAACAGATAATGGTCTTCAAC 58.179 34.615 0.00 0.00 0.00 3.18
6034 6603 9.840427 GCTTCTTTTAGTTAAATTATCAGCACA 57.160 29.630 0.00 0.00 0.00 4.57
6048 6623 6.524101 TGAAAACACCAGCTTCTTTTAGTT 57.476 33.333 0.00 0.00 0.00 2.24
6108 6689 9.350951 ACCTATAGTAACCAAATTTATCAAGCC 57.649 33.333 0.00 0.00 0.00 4.35
6130 6712 7.829211 CCTGGAAATGATTGTCTCTTAAACCTA 59.171 37.037 0.00 0.00 0.00 3.08
6131 6713 6.660949 CCTGGAAATGATTGTCTCTTAAACCT 59.339 38.462 0.00 0.00 0.00 3.50
6146 6728 3.907474 TCCACAACTAGACCTGGAAATGA 59.093 43.478 0.00 0.00 29.50 2.57
6157 6739 2.104111 CCACCACAAGTCCACAACTAGA 59.896 50.000 0.00 0.00 37.17 2.43
6171 7045 1.887854 CATTTCAGCACATCCACCACA 59.112 47.619 0.00 0.00 0.00 4.17
6179 7053 4.391830 CGTTGTAGTACCATTTCAGCACAT 59.608 41.667 0.00 0.00 0.00 3.21
6206 7080 5.695816 TGCGTCTACGTGGTTACTTTTTATT 59.304 36.000 0.00 0.00 42.22 1.40
6221 7095 3.400505 TGAATCTACACTGCGTCTACG 57.599 47.619 0.00 0.00 43.27 3.51
6227 7101 5.106555 ACCTTGAAAATGAATCTACACTGCG 60.107 40.000 0.00 0.00 0.00 5.18
6245 7119 5.013547 TGGTTCACAAGAAGAAAACCTTGA 58.986 37.500 8.83 0.00 41.56 3.02
6274 7148 1.837051 AGGCCTGACAAGACCACGA 60.837 57.895 3.11 0.00 0.00 4.35
6275 7149 1.669115 CAGGCCTGACAAGACCACG 60.669 63.158 29.88 0.00 0.00 4.94
6276 7150 0.179018 AACAGGCCTGACAAGACCAC 60.179 55.000 39.19 0.00 0.00 4.16
6277 7151 0.108585 GAACAGGCCTGACAAGACCA 59.891 55.000 39.19 0.00 0.00 4.02
6278 7152 0.398318 AGAACAGGCCTGACAAGACC 59.602 55.000 39.19 17.38 0.00 3.85
6279 7153 1.202698 ACAGAACAGGCCTGACAAGAC 60.203 52.381 39.19 20.26 35.69 3.01
6280 7154 1.070758 GACAGAACAGGCCTGACAAGA 59.929 52.381 39.19 0.00 35.69 3.02
6281 7155 1.517242 GACAGAACAGGCCTGACAAG 58.483 55.000 39.19 25.21 35.69 3.16
6282 7156 0.249868 CGACAGAACAGGCCTGACAA 60.250 55.000 39.19 0.00 35.69 3.18
6283 7157 1.112916 TCGACAGAACAGGCCTGACA 61.113 55.000 39.19 12.70 35.69 3.58
6284 7158 0.667792 GTCGACAGAACAGGCCTGAC 60.668 60.000 39.19 28.53 35.69 3.51
6285 7159 1.112916 TGTCGACAGAACAGGCCTGA 61.113 55.000 39.19 11.44 35.69 3.86
6286 7160 0.249868 TTGTCGACAGAACAGGCCTG 60.250 55.000 31.60 31.60 37.64 4.85
6287 7161 0.249911 GTTGTCGACAGAACAGGCCT 60.250 55.000 19.11 0.00 0.00 5.19
6288 7162 0.531974 TGTTGTCGACAGAACAGGCC 60.532 55.000 19.11 0.00 33.40 5.19
6289 7163 0.582005 GTGTTGTCGACAGAACAGGC 59.418 55.000 20.50 8.77 39.39 4.85
6290 7164 1.217882 GGTGTTGTCGACAGAACAGG 58.782 55.000 20.50 0.00 39.39 4.00
6291 7165 1.860950 CTGGTGTTGTCGACAGAACAG 59.139 52.381 22.84 22.84 39.39 3.16
6292 7166 1.478916 TCTGGTGTTGTCGACAGAACA 59.521 47.619 25.10 21.59 39.39 3.18
6293 7167 2.218953 TCTGGTGTTGTCGACAGAAC 57.781 50.000 19.11 19.14 39.39 3.01
6294 7168 2.971660 TTCTGGTGTTGTCGACAGAA 57.028 45.000 19.11 14.22 44.87 3.02
6295 7169 3.130633 CAATTCTGGTGTTGTCGACAGA 58.869 45.455 19.11 8.59 39.39 3.41
6296 7170 2.349817 GCAATTCTGGTGTTGTCGACAG 60.350 50.000 19.11 6.11 39.39 3.51
6297 7171 1.601903 GCAATTCTGGTGTTGTCGACA 59.398 47.619 15.76 15.76 35.42 4.35
6298 7172 1.069227 GGCAATTCTGGTGTTGTCGAC 60.069 52.381 9.11 9.11 0.00 4.20
6299 7173 1.234821 GGCAATTCTGGTGTTGTCGA 58.765 50.000 0.00 0.00 0.00 4.20
6300 7174 0.950836 TGGCAATTCTGGTGTTGTCG 59.049 50.000 0.00 0.00 32.81 4.35
6301 7175 1.680735 TGTGGCAATTCTGGTGTTGTC 59.319 47.619 0.00 0.00 0.00 3.18
6302 7176 1.682854 CTGTGGCAATTCTGGTGTTGT 59.317 47.619 0.00 0.00 0.00 3.32
6303 7177 1.682854 ACTGTGGCAATTCTGGTGTTG 59.317 47.619 0.00 0.00 0.00 3.33
6304 7178 2.071778 ACTGTGGCAATTCTGGTGTT 57.928 45.000 0.00 0.00 0.00 3.32
6305 7179 2.504367 GTACTGTGGCAATTCTGGTGT 58.496 47.619 0.00 0.00 0.00 4.16
6306 7180 1.812571 GGTACTGTGGCAATTCTGGTG 59.187 52.381 0.00 0.00 0.00 4.17
6307 7181 1.610624 CGGTACTGTGGCAATTCTGGT 60.611 52.381 0.00 0.00 0.00 4.00
6308 7182 1.086696 CGGTACTGTGGCAATTCTGG 58.913 55.000 0.00 0.00 0.00 3.86
6309 7183 2.093306 TCGGTACTGTGGCAATTCTG 57.907 50.000 0.64 0.00 0.00 3.02
6310 7184 3.270877 GAATCGGTACTGTGGCAATTCT 58.729 45.455 0.64 0.00 0.00 2.40
6311 7185 2.030457 CGAATCGGTACTGTGGCAATTC 59.970 50.000 0.64 2.65 0.00 2.17
6312 7186 2.006888 CGAATCGGTACTGTGGCAATT 58.993 47.619 0.64 0.00 0.00 2.32
6313 7187 1.651987 CGAATCGGTACTGTGGCAAT 58.348 50.000 0.64 0.00 0.00 3.56
6314 7188 0.390603 CCGAATCGGTACTGTGGCAA 60.391 55.000 14.46 0.00 42.73 4.52
6315 7189 1.216977 CCGAATCGGTACTGTGGCA 59.783 57.895 14.46 0.00 42.73 4.92
6316 7190 4.104143 CCGAATCGGTACTGTGGC 57.896 61.111 14.46 0.00 42.73 5.01
6326 7200 0.871722 TGTCTTGGCAAACCGAATCG 59.128 50.000 0.00 0.00 39.70 3.34
6327 7201 3.363341 TTTGTCTTGGCAAACCGAATC 57.637 42.857 0.00 0.00 39.70 2.52
6334 7208 2.615869 GCTGTTGTTTGTCTTGGCAAA 58.384 42.857 0.00 0.00 36.17 3.68
6335 7209 1.134848 GGCTGTTGTTTGTCTTGGCAA 60.135 47.619 0.00 0.00 0.00 4.52
6336 7210 0.459489 GGCTGTTGTTTGTCTTGGCA 59.541 50.000 0.00 0.00 0.00 4.92
6337 7211 0.594796 CGGCTGTTGTTTGTCTTGGC 60.595 55.000 0.00 0.00 0.00 4.52
6338 7212 0.738389 ACGGCTGTTGTTTGTCTTGG 59.262 50.000 0.00 0.00 0.00 3.61
6339 7213 1.594518 CGACGGCTGTTGTTTGTCTTG 60.595 52.381 0.00 0.00 0.00 3.02
6340 7214 0.655733 CGACGGCTGTTGTTTGTCTT 59.344 50.000 0.00 0.00 0.00 3.01
6341 7215 0.179094 TCGACGGCTGTTGTTTGTCT 60.179 50.000 12.78 0.00 0.00 3.41
6342 7216 0.865769 ATCGACGGCTGTTGTTTGTC 59.134 50.000 12.78 0.00 0.00 3.18
6343 7217 0.865769 GATCGACGGCTGTTGTTTGT 59.134 50.000 12.78 0.00 0.00 2.83
6344 7218 1.148310 AGATCGACGGCTGTTGTTTG 58.852 50.000 12.78 0.00 0.00 2.93
6345 7219 2.334838 GTAGATCGACGGCTGTTGTTT 58.665 47.619 12.78 2.04 0.00 2.83
6346 7220 1.403780 GGTAGATCGACGGCTGTTGTT 60.404 52.381 12.78 4.42 0.00 2.83
6347 7221 0.172803 GGTAGATCGACGGCTGTTGT 59.827 55.000 12.78 0.46 0.00 3.32
6348 7222 0.172578 TGGTAGATCGACGGCTGTTG 59.827 55.000 6.57 6.57 0.00 3.33
6349 7223 1.067212 GATGGTAGATCGACGGCTGTT 59.933 52.381 0.00 0.00 0.00 3.16
6350 7224 0.669077 GATGGTAGATCGACGGCTGT 59.331 55.000 0.00 0.00 0.00 4.40
6351 7225 0.039074 GGATGGTAGATCGACGGCTG 60.039 60.000 0.00 0.00 0.00 4.85
6352 7226 1.516365 CGGATGGTAGATCGACGGCT 61.516 60.000 0.00 0.00 0.00 5.52
6353 7227 1.081376 CGGATGGTAGATCGACGGC 60.081 63.158 0.00 0.00 0.00 5.68
6354 7228 0.517755 CTCGGATGGTAGATCGACGG 59.482 60.000 0.00 0.00 0.00 4.79
6355 7229 0.517755 CCTCGGATGGTAGATCGACG 59.482 60.000 0.00 0.00 0.00 5.12
6356 7230 0.882474 CCCTCGGATGGTAGATCGAC 59.118 60.000 0.00 0.00 0.00 4.20
6357 7231 0.769247 TCCCTCGGATGGTAGATCGA 59.231 55.000 0.00 0.00 0.00 3.59
6358 7232 0.882474 GTCCCTCGGATGGTAGATCG 59.118 60.000 0.00 0.00 32.73 3.69
6359 7233 0.882474 CGTCCCTCGGATGGTAGATC 59.118 60.000 0.00 0.00 35.25 2.75
6360 7234 1.179814 GCGTCCCTCGGATGGTAGAT 61.180 60.000 2.20 0.00 39.01 1.98
6361 7235 1.826921 GCGTCCCTCGGATGGTAGA 60.827 63.158 2.20 0.00 39.01 2.59
6362 7236 2.076622 CTGCGTCCCTCGGATGGTAG 62.077 65.000 2.20 0.00 39.01 3.18
6363 7237 2.043752 TGCGTCCCTCGGATGGTA 60.044 61.111 2.20 0.00 39.01 3.25
6364 7238 3.461773 CTGCGTCCCTCGGATGGT 61.462 66.667 2.20 0.00 39.01 3.55
6365 7239 4.227134 CCTGCGTCCCTCGGATGG 62.227 72.222 2.20 0.00 39.01 3.51
6366 7240 4.227134 CCCTGCGTCCCTCGGATG 62.227 72.222 0.00 0.00 41.35 3.51
6371 7245 3.775654 CACTCCCCTGCGTCCCTC 61.776 72.222 0.00 0.00 0.00 4.30
6374 7248 2.682494 TACCACTCCCCTGCGTCC 60.682 66.667 0.00 0.00 0.00 4.79
6375 7249 2.577593 GTACCACTCCCCTGCGTC 59.422 66.667 0.00 0.00 0.00 5.19
6376 7250 3.001406 GGTACCACTCCCCTGCGT 61.001 66.667 7.15 0.00 0.00 5.24
6377 7251 4.143333 CGGTACCACTCCCCTGCG 62.143 72.222 13.54 0.00 0.00 5.18
6378 7252 4.468689 GCGGTACCACTCCCCTGC 62.469 72.222 13.54 0.05 0.00 4.85
6379 7253 2.240162 GAAGCGGTACCACTCCCCTG 62.240 65.000 13.54 0.00 0.00 4.45
6380 7254 1.988406 GAAGCGGTACCACTCCCCT 60.988 63.158 13.54 0.00 0.00 4.79
6381 7255 2.582978 GAAGCGGTACCACTCCCC 59.417 66.667 13.54 0.00 0.00 4.81
6382 7256 2.183555 CGAAGCGGTACCACTCCC 59.816 66.667 13.54 2.64 0.00 4.30
6383 7257 1.139095 CTCGAAGCGGTACCACTCC 59.861 63.158 13.54 0.00 0.00 3.85
6384 7258 1.139095 CCTCGAAGCGGTACCACTC 59.861 63.158 13.54 3.79 0.00 3.51
6385 7259 3.003113 GCCTCGAAGCGGTACCACT 62.003 63.158 13.54 4.25 33.07 4.00
6386 7260 2.508663 GCCTCGAAGCGGTACCAC 60.509 66.667 13.54 1.22 33.07 4.16
6387 7261 3.766691 GGCCTCGAAGCGGTACCA 61.767 66.667 13.54 0.00 33.07 3.25
6388 7262 4.525949 GGGCCTCGAAGCGGTACC 62.526 72.222 0.84 0.16 33.07 3.34
6389 7263 4.867599 CGGGCCTCGAAGCGGTAC 62.868 72.222 0.84 0.00 42.43 3.34
6393 7267 4.951963 GATCCGGGCCTCGAAGCG 62.952 72.222 14.30 2.56 42.43 4.68


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

AutoCloner maintained by Alex Coulton.