Multiple sequence alignment - TraesCS3A01G032200

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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 TraesCS3A01G032200 chr3A 100.000 3265 0 0 1 3265 17623776 17620512 0.000000e+00 6030.0
1 TraesCS3A01G032200 chr3A 81.139 790 138 8 1249 2027 16458027 16457238 9.950000e-175 623.0
2 TraesCS3A01G032200 chr3A 80.253 790 145 8 1249 2027 16455319 16454530 4.690000e-163 584.0
3 TraesCS3A01G032200 chr3A 95.349 43 2 0 572 614 17607169 17607127 5.850000e-08 69.4
4 TraesCS3A01G032200 chr3A 90.909 44 4 0 406 449 16456086 16456043 3.520000e-05 60.2
5 TraesCS3A01G032200 chr3B 90.682 2758 170 36 30 2753 26589460 26586756 0.000000e+00 3589.0
6 TraesCS3A01G032200 chr3B 88.758 1272 89 25 1 1241 15052764 15054012 0.000000e+00 1507.0
7 TraesCS3A01G032200 chr3B 82.834 501 46 17 207 686 14708869 14709350 2.340000e-111 412.0
8 TraesCS3A01G032200 chr3B 86.404 228 23 5 2810 3037 26586387 26586168 3.250000e-60 243.0
9 TraesCS3A01G032200 chr3D 91.678 2199 133 21 636 2809 10642847 10645020 0.000000e+00 3001.0
10 TraesCS3A01G032200 chr3D 97.662 727 14 1 952 1675 10376678 10375952 0.000000e+00 1245.0
11 TraesCS3A01G032200 chr3D 87.633 752 46 23 223 961 10377858 10377141 0.000000e+00 830.0
12 TraesCS3A01G032200 chr3D 97.158 387 11 0 1667 2053 10366125 10365739 0.000000e+00 654.0
13 TraesCS3A01G032200 chr3D 92.636 258 12 4 1 257 10378842 10378591 6.660000e-97 364.0
14 TraesCS3A01G032200 chrUn 81.139 790 138 8 1249 2027 358413536 358412747 9.950000e-175 623.0
15 TraesCS3A01G032200 chrUn 80.253 790 145 8 1249 2027 254254659 254255448 4.690000e-163 584.0
16 TraesCS3A01G032200 chrUn 80.253 790 145 8 1249 2027 290074119 290073330 4.690000e-163 584.0
17 TraesCS3A01G032200 chrUn 80.253 790 145 8 1249 2027 360302543 360301754 4.690000e-163 584.0


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 TraesCS3A01G032200 chr3A 17620512 17623776 3264 True 6030.0 6030 100.000000 1 3265 1 chr3A.!!$R2 3264
1 TraesCS3A01G032200 chr3A 16454530 16458027 3497 True 422.4 623 84.100333 406 2027 3 chr3A.!!$R3 1621
2 TraesCS3A01G032200 chr3B 26586168 26589460 3292 True 1916.0 3589 88.543000 30 3037 2 chr3B.!!$R1 3007
3 TraesCS3A01G032200 chr3B 15052764 15054012 1248 False 1507.0 1507 88.758000 1 1241 1 chr3B.!!$F2 1240
4 TraesCS3A01G032200 chr3D 10642847 10645020 2173 False 3001.0 3001 91.678000 636 2809 1 chr3D.!!$F1 2173
5 TraesCS3A01G032200 chr3D 10375952 10378842 2890 True 813.0 1245 92.643667 1 1675 3 chr3D.!!$R2 1674
6 TraesCS3A01G032200 chrUn 358412747 358413536 789 True 623.0 623 81.139000 1249 2027 1 chrUn.!!$R2 778
7 TraesCS3A01G032200 chrUn 254254659 254255448 789 False 584.0 584 80.253000 1249 2027 1 chrUn.!!$F1 778
8 TraesCS3A01G032200 chrUn 290073330 290074119 789 True 584.0 584 80.253000 1249 2027 1 chrUn.!!$R1 778
9 TraesCS3A01G032200 chrUn 360301754 360302543 789 True 584.0 584 80.253000 1249 2027 1 chrUn.!!$R3 778

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
915 2500 0.250770 GGAGAAAGGAGCGGTGGTTT 60.251 55.0 0.00 0.0 0.0 3.27 F
1499 3623 0.038618 TGGAACATGTCGTCCAGTCG 60.039 55.0 14.15 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 4278 0.762418 TTTTGAGAGGAAGTCGGGCA 59.238 50.0 0.0 0.0 0.0 5.36 R
3142 5578 0.035739 GGCAGGACCCGTTTGTTAGA 59.964 55.0 0.0 0.0 0.0 2.10 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
28 29 0.671781 CTGCGGCTCTTAGCAAGTGT 60.672 55.000 0.00 0.00 44.75 3.55
120 122 1.112281 CAACGCGCGAACATTACACG 61.112 55.000 39.36 4.08 0.00 4.49
257 291 3.328050 TCTCAGAGAAAGAGGGGGAAAAC 59.672 47.826 0.00 0.00 33.92 2.43
384 1186 1.229082 TCACCGGTAAGGGAGCAGT 60.229 57.895 6.87 0.00 46.96 4.40
484 2021 2.931713 CTAGTTCAGGTACGGCCGCG 62.932 65.000 28.58 9.04 43.70 6.46
522 2062 1.005394 GAACTTTCCTCCGTCGCCA 60.005 57.895 0.00 0.00 0.00 5.69
524 2064 2.815647 CTTTCCTCCGTCGCCAGC 60.816 66.667 0.00 0.00 0.00 4.85
658 2199 3.637911 TTATCCCAGTAACGTGGCAAT 57.362 42.857 0.00 0.00 36.11 3.56
742 2283 3.689649 ACCACTCGATTAATTTGCCTGTC 59.310 43.478 0.00 0.00 0.00 3.51
915 2500 0.250770 GGAGAAAGGAGCGGTGGTTT 60.251 55.000 0.00 0.00 0.00 3.27
916 2501 1.157585 GAGAAAGGAGCGGTGGTTTC 58.842 55.000 9.29 9.29 0.00 2.78
917 2502 0.472471 AGAAAGGAGCGGTGGTTTCA 59.528 50.000 16.46 0.00 32.38 2.69
918 2503 0.875059 GAAAGGAGCGGTGGTTTCAG 59.125 55.000 11.53 0.00 0.00 3.02
919 2504 0.537371 AAAGGAGCGGTGGTTTCAGG 60.537 55.000 0.00 0.00 0.00 3.86
920 2505 1.705997 AAGGAGCGGTGGTTTCAGGT 61.706 55.000 0.00 0.00 0.00 4.00
921 2506 1.228154 GGAGCGGTGGTTTCAGGTT 60.228 57.895 0.00 0.00 0.00 3.50
957 3018 2.338500 GTCTGTAGTACCAGCAGCAAC 58.662 52.381 0.00 0.00 32.32 4.17
1305 3413 6.436218 TGTGTAGCAGTAACCTATCTTCTTGA 59.564 38.462 0.00 0.00 0.00 3.02
1308 3416 5.363939 AGCAGTAACCTATCTTCTTGATGC 58.636 41.667 0.00 0.00 36.65 3.91
1319 3443 8.719648 CCTATCTTCTTGATGCAGTATTCATTC 58.280 37.037 0.00 0.00 36.65 2.67
1499 3623 0.038618 TGGAACATGTCGTCCAGTCG 60.039 55.000 14.15 0.00 0.00 4.18
1838 3962 0.892755 TCGTCTGCGTCCAACCTAAT 59.107 50.000 0.00 0.00 39.49 1.73
2053 4177 2.655090 TCAAGTGTCAGCAAATCCCA 57.345 45.000 0.00 0.00 0.00 4.37
2103 4227 2.076863 CATTGACCCTGTTTCCTCGTC 58.923 52.381 0.00 0.00 0.00 4.20
2154 4278 5.189180 GCAGATCCTGTATTGAAGGAAAGT 58.811 41.667 0.00 0.00 46.76 2.66
2219 4343 2.103601 TGATGACGATGATGATGTGCCT 59.896 45.455 0.00 0.00 0.00 4.75
2241 4365 0.528017 AAGATTCGAGCGTGCTCTCA 59.472 50.000 18.79 6.33 40.69 3.27
2266 4390 3.433031 CGGGTGTCCCTGCTTGATTAATA 60.433 47.826 3.25 0.00 42.67 0.98
2347 4471 1.594836 GGTGTGTGGACGCCGTTAA 60.595 57.895 0.00 0.00 42.86 2.01
2348 4472 0.952010 GGTGTGTGGACGCCGTTAAT 60.952 55.000 0.00 0.00 42.86 1.40
2349 4473 1.672441 GGTGTGTGGACGCCGTTAATA 60.672 52.381 0.00 0.00 42.86 0.98
2416 4540 4.639135 TGACGAGAACCTGTATGATCTG 57.361 45.455 0.00 0.00 0.00 2.90
2458 4582 7.254852 TGACCTTCTTTATGTGTTTTGTTGTC 58.745 34.615 0.00 0.00 0.00 3.18
2488 4612 3.807538 CGTGGCATGTGAGGCTGC 61.808 66.667 0.00 0.00 37.66 5.25
2553 4677 5.416083 TGTATCGATGAACCACTAACTTGG 58.584 41.667 8.54 0.00 43.04 3.61
2580 4704 8.903820 AGTTATCCTGTTTTATAATCTTGCACC 58.096 33.333 0.00 0.00 0.00 5.01
2588 4712 9.019656 TGTTTTATAATCTTGCACCATAACAGT 57.980 29.630 0.00 0.00 0.00 3.55
2635 4759 3.194116 GTGCATTCATGAGTTCCCAATGT 59.806 43.478 0.00 0.00 0.00 2.71
2636 4760 3.833650 TGCATTCATGAGTTCCCAATGTT 59.166 39.130 0.00 0.00 0.00 2.71
2637 4761 4.178540 GCATTCATGAGTTCCCAATGTTG 58.821 43.478 0.00 0.00 0.00 3.33
2638 4762 3.940209 TTCATGAGTTCCCAATGTTGC 57.060 42.857 0.00 0.00 0.00 4.17
2639 4763 2.874014 TCATGAGTTCCCAATGTTGCA 58.126 42.857 0.00 0.00 0.00 4.08
2640 4764 3.433343 TCATGAGTTCCCAATGTTGCAT 58.567 40.909 0.00 0.00 0.00 3.96
2641 4765 4.598022 TCATGAGTTCCCAATGTTGCATA 58.402 39.130 0.00 0.00 0.00 3.14
2642 4766 5.202765 TCATGAGTTCCCAATGTTGCATAT 58.797 37.500 0.00 0.00 0.00 1.78
2643 4767 6.363882 TCATGAGTTCCCAATGTTGCATATA 58.636 36.000 0.00 0.00 0.00 0.86
2734 4858 2.100584 TGTGCACAAAAACCAAGCTAGG 59.899 45.455 19.28 0.00 0.00 3.02
2742 4866 4.301072 AAAACCAAGCTAGGCATAGTGA 57.699 40.909 7.32 0.00 0.00 3.41
2766 4890 0.962356 ACTGCCAGGCACAATACTGC 60.962 55.000 11.22 0.00 33.79 4.40
2792 5063 7.040201 CCTGCTACTATATGATGGCAAAATTGT 60.040 37.037 0.00 0.00 0.00 2.71
2815 5251 7.127405 TGTAACAGGTTACCATGTCTAGGATA 58.873 38.462 17.12 0.00 43.47 2.59
2822 5258 7.039644 AGGTTACCATGTCTAGGATAAAGATCG 60.040 40.741 3.51 0.00 32.28 3.69
2827 5263 8.142551 ACCATGTCTAGGATAAAGATCGTAAAC 58.857 37.037 0.00 0.00 33.24 2.01
2831 5267 9.798994 TGTCTAGGATAAAGATCGTAAACTTTC 57.201 33.333 0.00 0.00 37.49 2.62
2836 5272 9.372369 AGGATAAAGATCGTAAACTTTCTGAAG 57.628 33.333 0.00 0.00 37.49 3.02
2837 5273 9.152595 GGATAAAGATCGTAAACTTTCTGAAGT 57.847 33.333 0.00 0.00 39.16 3.01
2839 5275 9.706691 ATAAAGATCGTAAACTTTCTGAAGTCA 57.293 29.630 0.00 0.00 45.18 3.41
2847 5283 9.931210 CGTAAACTTTCTGAAGTCATTTAAAGT 57.069 29.630 9.21 9.21 45.18 2.66
2901 5337 3.817647 GAGGTTCTGCTGAAAGTCACAAT 59.182 43.478 7.68 0.00 35.30 2.71
2904 5340 1.800586 TCTGCTGAAAGTCACAATCGC 59.199 47.619 0.00 0.00 35.30 4.58
2919 5355 5.468409 TCACAATCGCTTCAAGTTTGTATGA 59.532 36.000 3.24 0.00 0.00 2.15
2930 5366 5.243507 TCAAGTTTGTATGATGTGGCAATGT 59.756 36.000 0.00 0.00 0.00 2.71
2936 5372 5.468592 TGTATGATGTGGCAATGTTGAAAC 58.531 37.500 0.00 0.00 0.00 2.78
3004 5440 4.515944 TGCATTCCCTGAAATTGCAAAAAG 59.484 37.500 1.71 0.00 0.00 2.27
3005 5441 4.756135 GCATTCCCTGAAATTGCAAAAAGA 59.244 37.500 1.71 0.00 0.00 2.52
3007 5443 6.238703 GCATTCCCTGAAATTGCAAAAAGAAA 60.239 34.615 1.71 0.00 0.00 2.52
3008 5444 7.681543 GCATTCCCTGAAATTGCAAAAAGAAAA 60.682 33.333 1.71 0.00 0.00 2.29
3009 5445 7.693969 TTCCCTGAAATTGCAAAAAGAAAAA 57.306 28.000 1.71 0.00 0.00 1.94
3010 5446 7.878547 TCCCTGAAATTGCAAAAAGAAAAAT 57.121 28.000 1.71 0.00 0.00 1.82
3011 5447 7.705214 TCCCTGAAATTGCAAAAAGAAAAATG 58.295 30.769 1.71 0.00 0.00 2.32
3012 5448 7.555554 TCCCTGAAATTGCAAAAAGAAAAATGA 59.444 29.630 1.71 0.00 0.00 2.57
3022 5458 9.504710 TGCAAAAAGAAAAATGAATGTGAAATG 57.495 25.926 0.00 0.00 0.00 2.32
3037 5473 9.161684 GAATGTGAAATGAAGCAATTGTTTTTC 57.838 29.630 9.04 9.41 0.00 2.29
3038 5474 7.846644 TGTGAAATGAAGCAATTGTTTTTCT 57.153 28.000 9.04 0.00 0.00 2.52
3039 5475 8.266392 TGTGAAATGAAGCAATTGTTTTTCTT 57.734 26.923 9.04 2.12 0.00 2.52
3040 5476 8.728833 TGTGAAATGAAGCAATTGTTTTTCTTT 58.271 25.926 9.04 8.93 0.00 2.52
3041 5477 9.558648 GTGAAATGAAGCAATTGTTTTTCTTTT 57.441 25.926 20.17 20.17 32.81 2.27
3044 5480 7.974243 ATGAAGCAATTGTTTTTCTTTTTGC 57.026 28.000 9.04 0.00 39.68 3.68
3045 5481 6.906659 TGAAGCAATTGTTTTTCTTTTTGCA 58.093 28.000 9.04 0.00 41.33 4.08
3046 5482 7.365741 TGAAGCAATTGTTTTTCTTTTTGCAA 58.634 26.923 9.04 0.00 41.33 4.08
3047 5483 8.027771 TGAAGCAATTGTTTTTCTTTTTGCAAT 58.972 25.926 9.04 0.00 41.33 3.56
3048 5484 8.760103 AAGCAATTGTTTTTCTTTTTGCAATT 57.240 23.077 7.40 0.00 41.33 2.32
3049 5485 9.852091 AAGCAATTGTTTTTCTTTTTGCAATTA 57.148 22.222 7.40 0.00 41.33 1.40
3050 5486 9.505995 AGCAATTGTTTTTCTTTTTGCAATTAG 57.494 25.926 7.40 0.55 41.33 1.73
3051 5487 8.744923 GCAATTGTTTTTCTTTTTGCAATTAGG 58.255 29.630 7.40 0.00 39.30 2.69
3052 5488 9.235537 CAATTGTTTTTCTTTTTGCAATTAGGG 57.764 29.630 0.00 0.00 35.58 3.53
3053 5489 8.744568 ATTGTTTTTCTTTTTGCAATTAGGGA 57.255 26.923 0.00 0.00 0.00 4.20
3054 5490 8.744568 TTGTTTTTCTTTTTGCAATTAGGGAT 57.255 26.923 0.00 0.00 0.00 3.85
3055 5491 8.152309 TGTTTTTCTTTTTGCAATTAGGGATG 57.848 30.769 0.00 0.00 0.00 3.51
3056 5492 7.228308 TGTTTTTCTTTTTGCAATTAGGGATGG 59.772 33.333 0.00 0.00 0.00 3.51
3057 5493 5.419239 TTCTTTTTGCAATTAGGGATGGG 57.581 39.130 0.00 0.00 0.00 4.00
3058 5494 4.682563 TCTTTTTGCAATTAGGGATGGGA 58.317 39.130 0.00 0.00 0.00 4.37
3059 5495 4.711355 TCTTTTTGCAATTAGGGATGGGAG 59.289 41.667 0.00 0.00 0.00 4.30
3060 5496 4.329638 TTTTGCAATTAGGGATGGGAGA 57.670 40.909 0.00 0.00 0.00 3.71
3061 5497 3.582998 TTGCAATTAGGGATGGGAGAG 57.417 47.619 0.00 0.00 0.00 3.20
3062 5498 2.492025 TGCAATTAGGGATGGGAGAGT 58.508 47.619 0.00 0.00 0.00 3.24
3063 5499 2.852449 TGCAATTAGGGATGGGAGAGTT 59.148 45.455 0.00 0.00 0.00 3.01
3064 5500 3.217626 GCAATTAGGGATGGGAGAGTTG 58.782 50.000 0.00 0.00 0.00 3.16
3065 5501 3.217626 CAATTAGGGATGGGAGAGTTGC 58.782 50.000 0.00 0.00 0.00 4.17
3066 5502 2.270434 TTAGGGATGGGAGAGTTGCT 57.730 50.000 0.00 0.00 0.00 3.91
3067 5503 1.500474 TAGGGATGGGAGAGTTGCTG 58.500 55.000 0.00 0.00 0.00 4.41
3068 5504 1.225704 GGGATGGGAGAGTTGCTGG 59.774 63.158 0.00 0.00 0.00 4.85
3069 5505 1.274703 GGGATGGGAGAGTTGCTGGA 61.275 60.000 0.00 0.00 0.00 3.86
3070 5506 0.620556 GGATGGGAGAGTTGCTGGAA 59.379 55.000 0.00 0.00 0.00 3.53
3071 5507 1.680249 GGATGGGAGAGTTGCTGGAAC 60.680 57.143 3.63 3.63 34.40 3.62
3072 5508 0.036010 ATGGGAGAGTTGCTGGAACG 60.036 55.000 6.39 0.00 39.80 3.95
3073 5509 1.371558 GGGAGAGTTGCTGGAACGT 59.628 57.895 6.39 0.00 39.80 3.99
3074 5510 0.951040 GGGAGAGTTGCTGGAACGTG 60.951 60.000 6.39 0.00 39.80 4.49
3075 5511 0.951040 GGAGAGTTGCTGGAACGTGG 60.951 60.000 6.39 0.00 39.80 4.94
3076 5512 0.951040 GAGAGTTGCTGGAACGTGGG 60.951 60.000 6.39 0.00 39.80 4.61
3077 5513 1.966451 GAGTTGCTGGAACGTGGGG 60.966 63.158 6.39 0.00 39.80 4.96
3078 5514 3.670377 GTTGCTGGAACGTGGGGC 61.670 66.667 0.00 0.00 0.00 5.80
3079 5515 4.966787 TTGCTGGAACGTGGGGCC 62.967 66.667 0.00 0.00 0.00 5.80
3082 5518 3.953775 CTGGAACGTGGGGCCTGT 61.954 66.667 0.84 0.00 0.00 4.00
3083 5519 4.263572 TGGAACGTGGGGCCTGTG 62.264 66.667 0.84 0.00 0.00 3.66
3089 5525 3.897122 GTGGGGCCTGTGGGTTGA 61.897 66.667 0.84 0.00 34.45 3.18
3090 5526 3.897122 TGGGGCCTGTGGGTTGAC 61.897 66.667 0.84 0.00 34.45 3.18
3091 5527 3.580319 GGGGCCTGTGGGTTGACT 61.580 66.667 0.84 0.00 34.45 3.41
3092 5528 2.520968 GGGCCTGTGGGTTGACTT 59.479 61.111 0.84 0.00 34.45 3.01
3093 5529 1.765074 GGGCCTGTGGGTTGACTTA 59.235 57.895 0.84 0.00 34.45 2.24
3094 5530 0.608308 GGGCCTGTGGGTTGACTTAC 60.608 60.000 0.84 0.00 34.45 2.34
3095 5531 0.109723 GGCCTGTGGGTTGACTTACA 59.890 55.000 0.00 0.00 34.45 2.41
3096 5532 1.235724 GCCTGTGGGTTGACTTACAC 58.764 55.000 0.00 0.00 34.45 2.90
3097 5533 1.202770 GCCTGTGGGTTGACTTACACT 60.203 52.381 0.00 0.00 35.02 3.55
3098 5534 2.494059 CCTGTGGGTTGACTTACACTG 58.506 52.381 0.00 0.00 35.02 3.66
3099 5535 2.158813 CCTGTGGGTTGACTTACACTGT 60.159 50.000 0.00 0.00 35.02 3.55
3100 5536 2.872245 CTGTGGGTTGACTTACACTGTG 59.128 50.000 6.19 6.19 35.02 3.66
3101 5537 1.602377 GTGGGTTGACTTACACTGTGC 59.398 52.381 7.90 0.00 0.00 4.57
3102 5538 1.488812 TGGGTTGACTTACACTGTGCT 59.511 47.619 7.90 0.00 0.00 4.40
3103 5539 2.701423 TGGGTTGACTTACACTGTGCTA 59.299 45.455 7.90 0.00 0.00 3.49
3104 5540 3.134985 TGGGTTGACTTACACTGTGCTAA 59.865 43.478 7.90 5.37 0.00 3.09
3105 5541 4.131596 GGGTTGACTTACACTGTGCTAAA 58.868 43.478 7.90 0.00 0.00 1.85
3106 5542 4.577283 GGGTTGACTTACACTGTGCTAAAA 59.423 41.667 7.90 0.00 0.00 1.52
3107 5543 5.066764 GGGTTGACTTACACTGTGCTAAAAA 59.933 40.000 7.90 0.00 0.00 1.94
3121 5557 3.115556 AAAAAGGCTTGCGCGTCA 58.884 50.000 8.43 3.08 36.88 4.35
3122 5558 1.299089 AAAAAGGCTTGCGCGTCAC 60.299 52.632 8.43 0.00 36.88 3.67
3123 5559 2.677573 AAAAAGGCTTGCGCGTCACC 62.678 55.000 8.43 4.59 36.88 4.02
3124 5560 4.626081 AAGGCTTGCGCGTCACCT 62.626 61.111 8.43 7.16 36.88 4.00
3125 5561 4.626081 AGGCTTGCGCGTCACCTT 62.626 61.111 8.43 0.00 36.88 3.50
3126 5562 4.389576 GGCTTGCGCGTCACCTTG 62.390 66.667 8.43 0.00 36.88 3.61
3127 5563 3.649986 GCTTGCGCGTCACCTTGT 61.650 61.111 8.43 0.00 0.00 3.16
3128 5564 2.249309 CTTGCGCGTCACCTTGTG 59.751 61.111 8.43 0.00 34.45 3.33
3129 5565 3.862063 CTTGCGCGTCACCTTGTGC 62.862 63.158 8.43 0.00 41.81 4.57
3135 5571 2.672996 GTCACCTTGTGCGGCCAT 60.673 61.111 2.24 0.00 32.98 4.40
3136 5572 1.376683 GTCACCTTGTGCGGCCATA 60.377 57.895 2.24 0.00 32.98 2.74
3137 5573 1.376683 TCACCTTGTGCGGCCATAC 60.377 57.895 2.24 0.63 32.98 2.39
3138 5574 2.045340 ACCTTGTGCGGCCATACC 60.045 61.111 2.24 0.00 0.00 2.73
3139 5575 2.045438 CCTTGTGCGGCCATACCA 60.045 61.111 2.24 0.00 39.03 3.25
3140 5576 1.453745 CCTTGTGCGGCCATACCAT 60.454 57.895 2.24 0.00 39.03 3.55
3141 5577 1.447317 CCTTGTGCGGCCATACCATC 61.447 60.000 2.24 0.00 39.03 3.51
3142 5578 0.464373 CTTGTGCGGCCATACCATCT 60.464 55.000 2.24 0.00 39.03 2.90
3143 5579 0.463654 TTGTGCGGCCATACCATCTC 60.464 55.000 2.24 0.00 39.03 2.75
3144 5580 1.337384 TGTGCGGCCATACCATCTCT 61.337 55.000 2.24 0.00 39.03 3.10
3145 5581 0.679505 GTGCGGCCATACCATCTCTA 59.320 55.000 2.24 0.00 39.03 2.43
3146 5582 1.070134 GTGCGGCCATACCATCTCTAA 59.930 52.381 2.24 0.00 39.03 2.10
3147 5583 1.070134 TGCGGCCATACCATCTCTAAC 59.930 52.381 2.24 0.00 39.03 2.34
3148 5584 1.070134 GCGGCCATACCATCTCTAACA 59.930 52.381 2.24 0.00 39.03 2.41
3149 5585 2.484770 GCGGCCATACCATCTCTAACAA 60.485 50.000 2.24 0.00 39.03 2.83
3150 5586 3.804036 CGGCCATACCATCTCTAACAAA 58.196 45.455 2.24 0.00 39.03 2.83
3151 5587 3.560068 CGGCCATACCATCTCTAACAAAC 59.440 47.826 2.24 0.00 39.03 2.93
3152 5588 3.560068 GGCCATACCATCTCTAACAAACG 59.440 47.826 0.00 0.00 38.86 3.60
3153 5589 3.560068 GCCATACCATCTCTAACAAACGG 59.440 47.826 0.00 0.00 0.00 4.44
3154 5590 4.127171 CCATACCATCTCTAACAAACGGG 58.873 47.826 0.00 0.00 0.00 5.28
3155 5591 4.383770 CCATACCATCTCTAACAAACGGGT 60.384 45.833 0.00 0.00 0.00 5.28
3156 5592 3.329929 ACCATCTCTAACAAACGGGTC 57.670 47.619 0.00 0.00 0.00 4.46
3157 5593 2.027469 ACCATCTCTAACAAACGGGTCC 60.027 50.000 0.00 0.00 0.00 4.46
3158 5594 2.236395 CCATCTCTAACAAACGGGTCCT 59.764 50.000 0.00 0.00 0.00 3.85
3159 5595 3.262420 CATCTCTAACAAACGGGTCCTG 58.738 50.000 0.00 0.00 0.00 3.86
3160 5596 1.001633 TCTCTAACAAACGGGTCCTGC 59.998 52.381 0.00 0.00 0.00 4.85
3161 5597 0.035739 TCTAACAAACGGGTCCTGCC 59.964 55.000 0.00 0.00 0.00 4.85
3162 5598 0.250553 CTAACAAACGGGTCCTGCCA 60.251 55.000 0.00 0.00 39.65 4.92
3163 5599 0.250553 TAACAAACGGGTCCTGCCAG 60.251 55.000 0.00 0.00 39.65 4.85
3165 5601 1.966451 CAAACGGGTCCTGCCAGTC 60.966 63.158 0.00 0.00 44.94 3.51
3166 5602 2.448582 AAACGGGTCCTGCCAGTCA 61.449 57.895 0.00 0.00 44.94 3.41
3167 5603 2.397413 AAACGGGTCCTGCCAGTCAG 62.397 60.000 0.00 0.00 44.94 3.51
3177 5613 3.451141 CTGCCAGTCAGGAACTCTATC 57.549 52.381 0.00 0.00 41.22 2.08
3178 5614 2.762887 CTGCCAGTCAGGAACTCTATCA 59.237 50.000 0.00 0.00 41.22 2.15
3179 5615 3.173151 TGCCAGTCAGGAACTCTATCAA 58.827 45.455 0.00 0.00 41.22 2.57
3180 5616 3.582647 TGCCAGTCAGGAACTCTATCAAA 59.417 43.478 0.00 0.00 41.22 2.69
3181 5617 4.187694 GCCAGTCAGGAACTCTATCAAAG 58.812 47.826 0.00 0.00 41.22 2.77
3182 5618 4.323104 GCCAGTCAGGAACTCTATCAAAGT 60.323 45.833 0.00 0.00 41.22 2.66
3183 5619 5.415221 CCAGTCAGGAACTCTATCAAAGTC 58.585 45.833 0.00 0.00 41.22 3.01
3184 5620 5.415221 CAGTCAGGAACTCTATCAAAGTCC 58.585 45.833 0.00 0.00 34.60 3.85
3185 5621 4.468153 AGTCAGGAACTCTATCAAAGTCCC 59.532 45.833 0.00 0.00 34.60 4.46
3186 5622 4.223032 GTCAGGAACTCTATCAAAGTCCCA 59.777 45.833 0.00 0.00 34.60 4.37
3187 5623 5.032846 TCAGGAACTCTATCAAAGTCCCAT 58.967 41.667 0.00 0.00 34.60 4.00
3188 5624 5.488919 TCAGGAACTCTATCAAAGTCCCATT 59.511 40.000 0.00 0.00 34.60 3.16
3189 5625 6.672218 TCAGGAACTCTATCAAAGTCCCATTA 59.328 38.462 0.00 0.00 34.60 1.90
3190 5626 7.182026 TCAGGAACTCTATCAAAGTCCCATTAA 59.818 37.037 0.00 0.00 34.60 1.40
3191 5627 7.497249 CAGGAACTCTATCAAAGTCCCATTAAG 59.503 40.741 0.00 0.00 34.60 1.85
3192 5628 6.768381 GGAACTCTATCAAAGTCCCATTAAGG 59.232 42.308 0.00 0.00 37.03 2.69
3203 5639 2.240493 CCATTAAGGGGTCGCTAGTG 57.760 55.000 0.00 0.00 0.00 2.74
3204 5640 1.583054 CATTAAGGGGTCGCTAGTGC 58.417 55.000 0.00 0.00 0.00 4.40
3205 5641 1.139058 CATTAAGGGGTCGCTAGTGCT 59.861 52.381 0.00 0.00 36.97 4.40
3206 5642 2.148446 TTAAGGGGTCGCTAGTGCTA 57.852 50.000 0.00 0.00 36.97 3.49
3207 5643 2.376695 TAAGGGGTCGCTAGTGCTAT 57.623 50.000 0.00 0.00 36.97 2.97
3208 5644 1.497161 AAGGGGTCGCTAGTGCTATT 58.503 50.000 0.00 0.00 36.97 1.73
3209 5645 1.497161 AGGGGTCGCTAGTGCTATTT 58.503 50.000 0.00 0.00 36.97 1.40
3210 5646 1.139058 AGGGGTCGCTAGTGCTATTTG 59.861 52.381 0.00 0.00 36.97 2.32
3211 5647 1.138266 GGGGTCGCTAGTGCTATTTGA 59.862 52.381 0.00 0.00 36.97 2.69
3212 5648 2.419574 GGGGTCGCTAGTGCTATTTGAA 60.420 50.000 0.00 0.00 36.97 2.69
3213 5649 3.267483 GGGTCGCTAGTGCTATTTGAAA 58.733 45.455 0.00 0.00 36.97 2.69
3214 5650 3.063588 GGGTCGCTAGTGCTATTTGAAAC 59.936 47.826 0.00 0.00 36.97 2.78
3215 5651 3.682858 GGTCGCTAGTGCTATTTGAAACA 59.317 43.478 0.00 0.00 36.97 2.83
3216 5652 4.153475 GGTCGCTAGTGCTATTTGAAACAA 59.847 41.667 0.00 0.00 36.97 2.83
3217 5653 5.334569 GGTCGCTAGTGCTATTTGAAACAAA 60.335 40.000 0.00 0.00 36.97 2.83
3218 5654 6.140110 GTCGCTAGTGCTATTTGAAACAAAA 58.860 36.000 0.00 0.00 36.97 2.44
3219 5655 6.086371 GTCGCTAGTGCTATTTGAAACAAAAC 59.914 38.462 0.00 0.00 36.97 2.43
3220 5656 6.017440 TCGCTAGTGCTATTTGAAACAAAACT 60.017 34.615 0.00 0.00 36.97 2.66
3221 5657 6.086765 CGCTAGTGCTATTTGAAACAAAACTG 59.913 38.462 0.00 0.00 36.97 3.16
3222 5658 6.918022 GCTAGTGCTATTTGAAACAAAACTGT 59.082 34.615 0.00 0.00 36.03 3.55
3223 5659 7.435192 GCTAGTGCTATTTGAAACAAAACTGTT 59.565 33.333 0.00 0.00 36.03 3.16
3224 5660 9.301153 CTAGTGCTATTTGAAACAAAACTGTTT 57.699 29.630 0.00 0.00 43.77 2.83
3236 5672 6.966435 ACAAAACTGTTTGGAGATTTTGTG 57.034 33.333 14.37 4.05 46.38 3.33
3237 5673 6.463360 ACAAAACTGTTTGGAGATTTTGTGT 58.537 32.000 14.37 4.64 46.38 3.72
3238 5674 6.368516 ACAAAACTGTTTGGAGATTTTGTGTG 59.631 34.615 14.37 3.40 46.38 3.82
3239 5675 5.659440 AACTGTTTGGAGATTTTGTGTGT 57.341 34.783 0.00 0.00 0.00 3.72
3240 5676 5.659440 ACTGTTTGGAGATTTTGTGTGTT 57.341 34.783 0.00 0.00 0.00 3.32
3241 5677 6.036577 ACTGTTTGGAGATTTTGTGTGTTT 57.963 33.333 0.00 0.00 0.00 2.83
3242 5678 5.868801 ACTGTTTGGAGATTTTGTGTGTTTG 59.131 36.000 0.00 0.00 0.00 2.93
3243 5679 5.788450 TGTTTGGAGATTTTGTGTGTTTGT 58.212 33.333 0.00 0.00 0.00 2.83
3244 5680 6.226787 TGTTTGGAGATTTTGTGTGTTTGTT 58.773 32.000 0.00 0.00 0.00 2.83
3245 5681 6.708054 TGTTTGGAGATTTTGTGTGTTTGTTT 59.292 30.769 0.00 0.00 0.00 2.83
3246 5682 6.718454 TTGGAGATTTTGTGTGTTTGTTTG 57.282 33.333 0.00 0.00 0.00 2.93
3247 5683 4.629200 TGGAGATTTTGTGTGTTTGTTTGC 59.371 37.500 0.00 0.00 0.00 3.68
3248 5684 4.629200 GGAGATTTTGTGTGTTTGTTTGCA 59.371 37.500 0.00 0.00 0.00 4.08
3249 5685 5.121454 GGAGATTTTGTGTGTTTGTTTGCAA 59.879 36.000 0.00 0.00 0.00 4.08
3250 5686 6.348050 GGAGATTTTGTGTGTTTGTTTGCAAA 60.348 34.615 8.05 8.05 41.77 3.68
3251 5687 6.963796 AGATTTTGTGTGTTTGTTTGCAAAA 58.036 28.000 14.67 1.61 45.01 2.44
3252 5688 7.420800 AGATTTTGTGTGTTTGTTTGCAAAAA 58.579 26.923 14.67 5.49 45.01 1.94
3253 5689 8.081025 AGATTTTGTGTGTTTGTTTGCAAAAAT 58.919 25.926 14.67 5.27 45.01 1.82
3254 5690 6.981379 TTTGTGTGTTTGTTTGCAAAAATG 57.019 29.167 14.67 0.00 45.01 2.32
3255 5691 5.929697 TGTGTGTTTGTTTGCAAAAATGA 57.070 30.435 14.67 0.00 45.01 2.57
3256 5692 6.492007 TGTGTGTTTGTTTGCAAAAATGAT 57.508 29.167 14.67 0.00 45.01 2.45
3257 5693 6.312487 TGTGTGTTTGTTTGCAAAAATGATG 58.688 32.000 14.67 0.00 45.01 3.07
3258 5694 5.738225 GTGTGTTTGTTTGCAAAAATGATGG 59.262 36.000 14.67 0.00 45.01 3.51
3259 5695 4.734370 GTGTTTGTTTGCAAAAATGATGGC 59.266 37.500 14.67 0.00 45.01 4.40
3260 5696 4.639310 TGTTTGTTTGCAAAAATGATGGCT 59.361 33.333 14.67 0.00 45.01 4.75
3261 5697 5.819379 TGTTTGTTTGCAAAAATGATGGCTA 59.181 32.000 14.67 0.00 45.01 3.93
3262 5698 6.485984 TGTTTGTTTGCAAAAATGATGGCTAT 59.514 30.769 14.67 0.00 45.01 2.97
3263 5699 6.483385 TTGTTTGCAAAAATGATGGCTATG 57.517 33.333 14.67 0.00 0.00 2.23
3264 5700 5.549347 TGTTTGCAAAAATGATGGCTATGT 58.451 33.333 14.67 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.894387 GCTAAGAGCCGCAGCCTG 60.894 66.667 0.00 0.00 41.25 4.85
6 7 2.866085 CTTGCTAAGAGCCGCAGCCT 62.866 60.000 0.00 0.00 41.51 4.58
84 86 1.673920 GTTGCAACGGAACAGAAGGAA 59.326 47.619 14.90 0.00 0.00 3.36
86 88 3.845625 GTTGCAACGGAACAGAAGG 57.154 52.632 14.90 0.00 0.00 3.46
120 122 9.541143 TTGATGAATTCAACTTTTCTTTTACCC 57.459 29.630 13.09 0.00 39.44 3.69
384 1186 2.970639 CCGTCGAAGAAGAGGCCA 59.029 61.111 5.01 0.00 38.59 5.36
484 2021 1.599240 GAATCGGGAGGGATGCAGC 60.599 63.158 0.00 0.00 0.00 5.25
522 2062 3.081133 CATTAGCAACGCGACGCT 58.919 55.556 25.32 25.32 42.34 5.07
524 2064 2.021380 GGCATTAGCAACGCGACG 59.979 61.111 15.93 3.67 44.61 5.12
530 2070 0.536260 TGGGCATTGGCATTAGCAAC 59.464 50.000 12.70 2.31 44.61 4.17
658 2199 5.105106 TCGGGACAGTAAATATTGAGCTGAA 60.105 40.000 16.25 0.00 0.00 3.02
742 2283 2.467305 GCACAAGCACAAATTACACACG 59.533 45.455 0.00 0.00 41.58 4.49
915 2500 3.146066 CGAAACCAAGATCCAAACCTGA 58.854 45.455 0.00 0.00 0.00 3.86
916 2501 2.228822 CCGAAACCAAGATCCAAACCTG 59.771 50.000 0.00 0.00 0.00 4.00
917 2502 2.158519 ACCGAAACCAAGATCCAAACCT 60.159 45.455 0.00 0.00 0.00 3.50
918 2503 2.228103 GACCGAAACCAAGATCCAAACC 59.772 50.000 0.00 0.00 0.00 3.27
919 2504 3.058224 CAGACCGAAACCAAGATCCAAAC 60.058 47.826 0.00 0.00 0.00 2.93
920 2505 3.146066 CAGACCGAAACCAAGATCCAAA 58.854 45.455 0.00 0.00 0.00 3.28
921 2506 2.105821 ACAGACCGAAACCAAGATCCAA 59.894 45.455 0.00 0.00 0.00 3.53
957 3018 3.256631 ACCAGAACTAAATTGCTTGCTGG 59.743 43.478 0.00 0.00 45.36 4.85
1032 3095 0.395036 CTCCCTCTCTCGGAGCTTCA 60.395 60.000 0.00 0.00 40.55 3.02
1838 3962 3.618171 GAACTTGGGTTCCGTAGCA 57.382 52.632 0.00 0.00 44.24 3.49
2053 4177 3.076032 AGTCAGGCCCTTTCCTTTAACAT 59.924 43.478 0.00 0.00 33.25 2.71
2103 4227 1.856802 TCGCCATCATCATCAGAACG 58.143 50.000 0.00 0.00 0.00 3.95
2154 4278 0.762418 TTTTGAGAGGAAGTCGGGCA 59.238 50.000 0.00 0.00 0.00 5.36
2219 4343 1.067565 AGAGCACGCTCGAATCTTGAA 60.068 47.619 13.12 0.00 46.90 2.69
2266 4390 2.050144 AGGTACATCATCAATCGGCCT 58.950 47.619 0.00 0.00 0.00 5.19
2347 4471 3.206412 TGAAACCCACCCAGGCATATTAT 59.794 43.478 0.00 0.00 35.39 1.28
2348 4472 2.583101 TGAAACCCACCCAGGCATATTA 59.417 45.455 0.00 0.00 35.39 0.98
2349 4473 1.360852 TGAAACCCACCCAGGCATATT 59.639 47.619 0.00 0.00 35.39 1.28
2416 4540 2.930682 GGTCAAAACAGCTCCGATACTC 59.069 50.000 0.00 0.00 0.00 2.59
2522 4646 5.815740 AGTGGTTCATCGATACAAATGTACC 59.184 40.000 0.00 0.14 41.28 3.34
2553 4677 9.937175 GTGCAAGATTATAAAACAGGATAACTC 57.063 33.333 0.00 0.00 0.00 3.01
2580 4704 3.834489 AGAGAGGGCATCACTGTTATG 57.166 47.619 0.58 0.00 0.00 1.90
2588 4712 3.328931 AGAAACTGAAAGAGAGGGCATCA 59.671 43.478 0.58 0.00 37.43 3.07
2723 4847 5.630415 TTATCACTATGCCTAGCTTGGTT 57.370 39.130 15.85 6.55 0.00 3.67
2734 4858 3.686726 GCCTGGCAGTATTATCACTATGC 59.313 47.826 15.17 0.62 0.00 3.14
2742 4866 5.065914 CAGTATTGTGCCTGGCAGTATTAT 58.934 41.667 24.10 12.95 40.08 1.28
2766 4890 7.040201 ACAATTTTGCCATCATATAGTAGCAGG 60.040 37.037 0.00 0.00 0.00 4.85
2792 5063 8.612486 TTTATCCTAGACATGGTAACCTGTTA 57.388 34.615 0.00 0.00 46.10 2.41
2815 5251 8.608844 ATGACTTCAGAAAGTTTACGATCTTT 57.391 30.769 0.00 0.00 45.80 2.52
2855 5291 9.513906 CTCACAATCTGATTACTATCCTCTCTA 57.486 37.037 1.98 0.00 0.00 2.43
2856 5292 7.451255 CCTCACAATCTGATTACTATCCTCTCT 59.549 40.741 1.98 0.00 0.00 3.10
2857 5293 7.232534 ACCTCACAATCTGATTACTATCCTCTC 59.767 40.741 1.98 0.00 0.00 3.20
2901 5337 4.154015 CCACATCATACAAACTTGAAGCGA 59.846 41.667 0.00 0.00 0.00 4.93
2904 5340 5.375417 TGCCACATCATACAAACTTGAAG 57.625 39.130 0.00 0.00 0.00 3.02
2919 5355 7.467131 GCTTTTTAAGTTTCAACATTGCCACAT 60.467 33.333 0.00 0.00 0.00 3.21
2955 5391 9.588096 AATTAGTTTCAAAACTCCTAATCAGGT 57.412 29.630 11.22 0.00 45.65 4.00
2967 5403 6.928492 TCAGGGAATGCAATTAGTTTCAAAAC 59.072 34.615 0.00 0.00 36.07 2.43
2983 5419 6.864360 TTCTTTTTGCAATTTCAGGGAATG 57.136 33.333 0.00 0.00 0.00 2.67
2984 5420 7.878547 TTTTCTTTTTGCAATTTCAGGGAAT 57.121 28.000 0.00 0.00 0.00 3.01
2988 5424 9.738832 ATTCATTTTTCTTTTTGCAATTTCAGG 57.261 25.926 0.00 0.00 0.00 3.86
3004 5440 9.887406 AATTGCTTCATTTCACATTCATTTTTC 57.113 25.926 0.00 0.00 0.00 2.29
3005 5441 9.672086 CAATTGCTTCATTTCACATTCATTTTT 57.328 25.926 0.00 0.00 0.00 1.94
3007 5443 8.385898 ACAATTGCTTCATTTCACATTCATTT 57.614 26.923 5.05 0.00 0.00 2.32
3008 5444 7.972832 ACAATTGCTTCATTTCACATTCATT 57.027 28.000 5.05 0.00 0.00 2.57
3009 5445 7.972832 AACAATTGCTTCATTTCACATTCAT 57.027 28.000 5.05 0.00 0.00 2.57
3010 5446 7.789273 AAACAATTGCTTCATTTCACATTCA 57.211 28.000 5.05 0.00 0.00 2.57
3011 5447 9.161684 GAAAAACAATTGCTTCATTTCACATTC 57.838 29.630 5.05 0.00 0.00 2.67
3012 5448 8.895737 AGAAAAACAATTGCTTCATTTCACATT 58.104 25.926 5.05 0.00 0.00 2.71
3022 5458 7.793907 TTGCAAAAAGAAAAACAATTGCTTC 57.206 28.000 5.05 6.40 42.59 3.86
3024 5460 9.505995 CTAATTGCAAAAAGAAAAACAATTGCT 57.494 25.926 1.71 0.00 42.59 3.91
3037 5473 4.711355 TCTCCCATCCCTAATTGCAAAAAG 59.289 41.667 1.71 3.65 0.00 2.27
3038 5474 4.682563 TCTCCCATCCCTAATTGCAAAAA 58.317 39.130 1.71 0.00 0.00 1.94
3039 5475 4.264352 ACTCTCCCATCCCTAATTGCAAAA 60.264 41.667 1.71 0.00 0.00 2.44
3040 5476 3.269381 ACTCTCCCATCCCTAATTGCAAA 59.731 43.478 1.71 0.00 0.00 3.68
3041 5477 2.852449 ACTCTCCCATCCCTAATTGCAA 59.148 45.455 0.00 0.00 0.00 4.08
3042 5478 2.492025 ACTCTCCCATCCCTAATTGCA 58.508 47.619 0.00 0.00 0.00 4.08
3043 5479 3.217626 CAACTCTCCCATCCCTAATTGC 58.782 50.000 0.00 0.00 0.00 3.56
3044 5480 3.117738 AGCAACTCTCCCATCCCTAATTG 60.118 47.826 0.00 0.00 0.00 2.32
3045 5481 3.117738 CAGCAACTCTCCCATCCCTAATT 60.118 47.826 0.00 0.00 0.00 1.40
3046 5482 2.441001 CAGCAACTCTCCCATCCCTAAT 59.559 50.000 0.00 0.00 0.00 1.73
3047 5483 1.839994 CAGCAACTCTCCCATCCCTAA 59.160 52.381 0.00 0.00 0.00 2.69
3048 5484 1.500474 CAGCAACTCTCCCATCCCTA 58.500 55.000 0.00 0.00 0.00 3.53
3049 5485 1.277580 CCAGCAACTCTCCCATCCCT 61.278 60.000 0.00 0.00 0.00 4.20
3050 5486 1.225704 CCAGCAACTCTCCCATCCC 59.774 63.158 0.00 0.00 0.00 3.85
3051 5487 0.620556 TTCCAGCAACTCTCCCATCC 59.379 55.000 0.00 0.00 0.00 3.51
3052 5488 1.743996 GTTCCAGCAACTCTCCCATC 58.256 55.000 0.00 0.00 31.50 3.51
3053 5489 0.036010 CGTTCCAGCAACTCTCCCAT 60.036 55.000 0.00 0.00 32.09 4.00
3054 5490 1.371183 CGTTCCAGCAACTCTCCCA 59.629 57.895 0.00 0.00 32.09 4.37
3055 5491 0.951040 CACGTTCCAGCAACTCTCCC 60.951 60.000 0.00 0.00 32.09 4.30
3056 5492 0.951040 CCACGTTCCAGCAACTCTCC 60.951 60.000 0.00 0.00 32.09 3.71
3057 5493 0.951040 CCCACGTTCCAGCAACTCTC 60.951 60.000 0.00 0.00 32.09 3.20
3058 5494 1.071471 CCCACGTTCCAGCAACTCT 59.929 57.895 0.00 0.00 32.09 3.24
3059 5495 1.966451 CCCCACGTTCCAGCAACTC 60.966 63.158 0.00 0.00 32.09 3.01
3060 5496 2.113139 CCCCACGTTCCAGCAACT 59.887 61.111 0.00 0.00 32.09 3.16
3061 5497 3.670377 GCCCCACGTTCCAGCAAC 61.670 66.667 0.00 0.00 0.00 4.17
3062 5498 4.966787 GGCCCCACGTTCCAGCAA 62.967 66.667 0.00 0.00 0.00 3.91
3065 5501 3.953775 ACAGGCCCCACGTTCCAG 61.954 66.667 0.00 0.00 0.00 3.86
3066 5502 4.263572 CACAGGCCCCACGTTCCA 62.264 66.667 0.00 0.00 0.00 3.53
3072 5508 3.897122 TCAACCCACAGGCCCCAC 61.897 66.667 0.00 0.00 36.11 4.61
3073 5509 3.897122 GTCAACCCACAGGCCCCA 61.897 66.667 0.00 0.00 36.11 4.96
3074 5510 1.785353 TAAGTCAACCCACAGGCCCC 61.785 60.000 0.00 0.00 36.11 5.80
3075 5511 0.608308 GTAAGTCAACCCACAGGCCC 60.608 60.000 0.00 0.00 36.11 5.80
3076 5512 0.109723 TGTAAGTCAACCCACAGGCC 59.890 55.000 0.00 0.00 36.11 5.19
3077 5513 1.202770 AGTGTAAGTCAACCCACAGGC 60.203 52.381 0.00 0.00 36.11 4.85
3078 5514 2.158813 ACAGTGTAAGTCAACCCACAGG 60.159 50.000 0.00 0.00 40.04 4.00
3079 5515 2.872245 CACAGTGTAAGTCAACCCACAG 59.128 50.000 0.00 0.00 0.00 3.66
3080 5516 2.912771 CACAGTGTAAGTCAACCCACA 58.087 47.619 0.00 0.00 0.00 4.17
3081 5517 1.602377 GCACAGTGTAAGTCAACCCAC 59.398 52.381 1.61 0.00 0.00 4.61
3082 5518 1.488812 AGCACAGTGTAAGTCAACCCA 59.511 47.619 1.61 0.00 0.00 4.51
3083 5519 2.256117 AGCACAGTGTAAGTCAACCC 57.744 50.000 1.61 0.00 0.00 4.11
3084 5520 5.744666 TTTTAGCACAGTGTAAGTCAACC 57.255 39.130 1.61 0.00 0.00 3.77
3111 5547 2.249309 CACAAGGTGACGCGCAAG 59.751 61.111 5.73 0.00 35.23 4.01
3112 5548 3.947841 GCACAAGGTGACGCGCAA 61.948 61.111 5.73 0.00 35.23 4.85
3118 5554 1.376683 TATGGCCGCACAAGGTGAC 60.377 57.895 0.00 0.00 35.23 3.67
3119 5555 1.376683 GTATGGCCGCACAAGGTGA 60.377 57.895 0.00 0.00 35.23 4.02
3120 5556 2.406616 GGTATGGCCGCACAAGGTG 61.407 63.158 8.63 0.00 36.51 4.00
3121 5557 2.045340 GGTATGGCCGCACAAGGT 60.045 61.111 8.63 0.00 0.00 3.50
3122 5558 1.447317 GATGGTATGGCCGCACAAGG 61.447 60.000 8.63 0.00 41.21 3.61
3123 5559 0.464373 AGATGGTATGGCCGCACAAG 60.464 55.000 8.63 0.00 41.21 3.16
3124 5560 0.463654 GAGATGGTATGGCCGCACAA 60.464 55.000 8.63 0.00 41.21 3.33
3125 5561 1.146041 GAGATGGTATGGCCGCACA 59.854 57.895 8.63 0.55 41.21 4.57
3126 5562 0.679505 TAGAGATGGTATGGCCGCAC 59.320 55.000 0.00 0.00 41.21 5.34
3127 5563 1.070134 GTTAGAGATGGTATGGCCGCA 59.930 52.381 0.00 0.00 41.21 5.69
3128 5564 1.070134 TGTTAGAGATGGTATGGCCGC 59.930 52.381 0.00 0.00 41.21 6.53
3129 5565 3.469008 TTGTTAGAGATGGTATGGCCG 57.531 47.619 0.00 0.00 41.21 6.13
3130 5566 3.560068 CGTTTGTTAGAGATGGTATGGCC 59.440 47.826 0.00 0.00 37.90 5.36
3131 5567 3.560068 CCGTTTGTTAGAGATGGTATGGC 59.440 47.826 0.00 0.00 0.00 4.40
3132 5568 4.127171 CCCGTTTGTTAGAGATGGTATGG 58.873 47.826 0.00 0.00 0.00 2.74
3133 5569 4.766375 ACCCGTTTGTTAGAGATGGTATG 58.234 43.478 0.00 0.00 0.00 2.39
3134 5570 4.141779 GGACCCGTTTGTTAGAGATGGTAT 60.142 45.833 0.00 0.00 0.00 2.73
3135 5571 3.196254 GGACCCGTTTGTTAGAGATGGTA 59.804 47.826 0.00 0.00 0.00 3.25
3136 5572 2.027469 GGACCCGTTTGTTAGAGATGGT 60.027 50.000 0.00 0.00 0.00 3.55
3137 5573 2.236395 AGGACCCGTTTGTTAGAGATGG 59.764 50.000 0.00 0.00 0.00 3.51
3138 5574 3.262420 CAGGACCCGTTTGTTAGAGATG 58.738 50.000 0.00 0.00 0.00 2.90
3139 5575 2.354805 GCAGGACCCGTTTGTTAGAGAT 60.355 50.000 0.00 0.00 0.00 2.75
3140 5576 1.001633 GCAGGACCCGTTTGTTAGAGA 59.998 52.381 0.00 0.00 0.00 3.10
3141 5577 1.439679 GCAGGACCCGTTTGTTAGAG 58.560 55.000 0.00 0.00 0.00 2.43
3142 5578 0.035739 GGCAGGACCCGTTTGTTAGA 59.964 55.000 0.00 0.00 0.00 2.10
3143 5579 0.250553 TGGCAGGACCCGTTTGTTAG 60.251 55.000 0.00 0.00 37.83 2.34
3144 5580 0.250553 CTGGCAGGACCCGTTTGTTA 60.251 55.000 6.61 0.00 37.83 2.41
3145 5581 1.528309 CTGGCAGGACCCGTTTGTT 60.528 57.895 6.61 0.00 37.83 2.83
3146 5582 2.113139 CTGGCAGGACCCGTTTGT 59.887 61.111 6.61 0.00 37.83 2.83
3147 5583 1.966451 GACTGGCAGGACCCGTTTG 60.966 63.158 20.34 0.00 35.74 2.93
3148 5584 2.397413 CTGACTGGCAGGACCCGTTT 62.397 60.000 20.34 0.00 41.07 3.60
3149 5585 2.847234 TGACTGGCAGGACCCGTT 60.847 61.111 20.34 0.00 35.74 4.44
3150 5586 3.314331 CTGACTGGCAGGACCCGT 61.314 66.667 20.34 0.00 41.07 5.28
3157 5593 2.762887 TGATAGAGTTCCTGACTGGCAG 59.237 50.000 14.16 14.16 44.49 4.85
3158 5594 2.820178 TGATAGAGTTCCTGACTGGCA 58.180 47.619 0.00 0.00 39.19 4.92
3159 5595 3.895232 TTGATAGAGTTCCTGACTGGC 57.105 47.619 0.00 0.00 39.19 4.85
3160 5596 5.413309 ACTTTGATAGAGTTCCTGACTGG 57.587 43.478 0.00 0.00 39.19 4.00
3161 5597 5.415221 GGACTTTGATAGAGTTCCTGACTG 58.585 45.833 0.00 0.00 39.19 3.51
3162 5598 4.468153 GGGACTTTGATAGAGTTCCTGACT 59.532 45.833 0.00 0.00 39.34 3.41
3163 5599 4.223032 TGGGACTTTGATAGAGTTCCTGAC 59.777 45.833 3.44 0.00 42.37 3.51
3164 5600 4.425772 TGGGACTTTGATAGAGTTCCTGA 58.574 43.478 3.44 0.00 42.37 3.86
3165 5601 4.826274 TGGGACTTTGATAGAGTTCCTG 57.174 45.455 3.44 0.00 42.37 3.86
3166 5602 7.366011 CCTTAATGGGACTTTGATAGAGTTCCT 60.366 40.741 3.44 0.00 42.37 3.36
3167 5603 6.768381 CCTTAATGGGACTTTGATAGAGTTCC 59.232 42.308 0.00 0.00 42.25 3.62
3168 5604 7.793927 CCTTAATGGGACTTTGATAGAGTTC 57.206 40.000 0.00 0.00 0.00 3.01
3184 5620 1.810412 GCACTAGCGACCCCTTAATGG 60.810 57.143 0.00 0.00 0.00 3.16
3185 5621 1.583054 GCACTAGCGACCCCTTAATG 58.417 55.000 0.00 0.00 0.00 1.90
3196 5632 8.201703 ACAGTTTTGTTTCAAATAGCACTAGCG 61.202 37.037 0.00 0.00 39.34 4.26
3197 5633 6.918022 ACAGTTTTGTTTCAAATAGCACTAGC 59.082 34.615 0.00 0.00 35.83 3.42
3198 5634 8.856490 AACAGTTTTGTTTCAAATAGCACTAG 57.144 30.769 0.00 0.00 45.01 2.57
3214 5650 6.368516 ACACACAAAATCTCCAAACAGTTTTG 59.631 34.615 0.00 7.18 42.43 2.44
3215 5651 6.463360 ACACACAAAATCTCCAAACAGTTTT 58.537 32.000 0.00 0.00 0.00 2.43
3216 5652 6.036577 ACACACAAAATCTCCAAACAGTTT 57.963 33.333 0.00 0.00 0.00 2.66
3217 5653 5.659440 ACACACAAAATCTCCAAACAGTT 57.341 34.783 0.00 0.00 0.00 3.16
3218 5654 5.659440 AACACACAAAATCTCCAAACAGT 57.341 34.783 0.00 0.00 0.00 3.55
3219 5655 5.868801 ACAAACACACAAAATCTCCAAACAG 59.131 36.000 0.00 0.00 0.00 3.16
3220 5656 5.788450 ACAAACACACAAAATCTCCAAACA 58.212 33.333 0.00 0.00 0.00 2.83
3221 5657 6.720012 AACAAACACACAAAATCTCCAAAC 57.280 33.333 0.00 0.00 0.00 2.93
3222 5658 6.348050 GCAAACAAACACACAAAATCTCCAAA 60.348 34.615 0.00 0.00 0.00 3.28
3223 5659 5.121454 GCAAACAAACACACAAAATCTCCAA 59.879 36.000 0.00 0.00 0.00 3.53
3224 5660 4.629200 GCAAACAAACACACAAAATCTCCA 59.371 37.500 0.00 0.00 0.00 3.86
3225 5661 4.629200 TGCAAACAAACACACAAAATCTCC 59.371 37.500 0.00 0.00 0.00 3.71
3226 5662 5.776519 TGCAAACAAACACACAAAATCTC 57.223 34.783 0.00 0.00 0.00 2.75
3227 5663 6.551385 TTTGCAAACAAACACACAAAATCT 57.449 29.167 8.05 0.00 40.84 2.40
3228 5664 7.614674 TTTTTGCAAACAAACACACAAAATC 57.385 28.000 12.39 0.00 45.29 2.17
3229 5665 7.864379 TCATTTTTGCAAACAAACACACAAAAT 59.136 25.926 12.39 1.48 45.29 1.82
3230 5666 7.195646 TCATTTTTGCAAACAAACACACAAAA 58.804 26.923 12.39 0.00 45.29 2.44
3231 5667 6.728200 TCATTTTTGCAAACAAACACACAAA 58.272 28.000 12.39 0.00 45.29 2.83
3232 5668 6.304356 TCATTTTTGCAAACAAACACACAA 57.696 29.167 12.39 0.15 45.29 3.33
3233 5669 5.929697 TCATTTTTGCAAACAAACACACA 57.070 30.435 12.39 0.00 45.29 3.72
3234 5670 5.738225 CCATCATTTTTGCAAACAAACACAC 59.262 36.000 12.39 0.00 45.29 3.82
3235 5671 5.675575 GCCATCATTTTTGCAAACAAACACA 60.676 36.000 12.39 0.00 45.29 3.72
3236 5672 4.734370 GCCATCATTTTTGCAAACAAACAC 59.266 37.500 12.39 0.00 45.29 3.32
3237 5673 4.639310 AGCCATCATTTTTGCAAACAAACA 59.361 33.333 12.39 0.00 45.29 2.83
3238 5674 5.172460 AGCCATCATTTTTGCAAACAAAC 57.828 34.783 12.39 0.00 45.29 2.93
3239 5675 6.485984 ACATAGCCATCATTTTTGCAAACAAA 59.514 30.769 12.39 4.95 43.97 2.83
3240 5676 5.996513 ACATAGCCATCATTTTTGCAAACAA 59.003 32.000 12.39 9.98 0.00 2.83
3241 5677 5.549347 ACATAGCCATCATTTTTGCAAACA 58.451 33.333 12.39 5.81 0.00 2.83


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

AutoCloner maintained by Alex Coulton.