Multiple sequence alignment - TraesCS1B01G122000

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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 TraesCS1B01G122000 chr1B 100.000 6660 0 0 1 6660 145458756 145452097 0.000000e+00 12299.0
1 TraesCS1B01G122000 chr1B 84.571 175 23 2 318 492 322488002 322488172 3.190000e-38 171.0
2 TraesCS1B01G122000 chr1B 97.143 70 1 1 5968 6036 145452754 145452685 4.220000e-22 117.0
3 TraesCS1B01G122000 chr1B 97.143 70 1 1 6003 6072 145452789 145452721 4.220000e-22 117.0
4 TraesCS1B01G122000 chr1B 95.714 70 3 0 2122 2191 145456569 145456500 5.460000e-21 113.0
5 TraesCS1B01G122000 chr1B 95.714 70 3 0 2188 2257 145456635 145456566 5.460000e-21 113.0
6 TraesCS1B01G122000 chr1D 97.472 5498 102 18 544 6036 90650487 90645022 0.000000e+00 9348.0
7 TraesCS1B01G122000 chr1D 94.991 539 16 5 6003 6536 90645091 90644559 0.000000e+00 835.0
8 TraesCS1B01G122000 chr1D 93.097 536 36 1 1 536 90651180 90650646 0.000000e+00 784.0
9 TraesCS1B01G122000 chr1D 95.714 70 3 0 2188 2257 90648909 90648840 5.460000e-21 113.0
10 TraesCS1B01G122000 chr1D 94.286 70 4 0 2122 2191 90648843 90648774 2.540000e-19 108.0
11 TraesCS1B01G122000 chr1A 96.714 5478 134 10 570 6036 86649495 86644053 0.000000e+00 9077.0
12 TraesCS1B01G122000 chr1A 89.159 535 27 10 6003 6536 86644122 86643618 7.280000e-179 638.0
13 TraesCS1B01G122000 chr1A 90.448 335 30 2 1 333 86649823 86649489 2.200000e-119 440.0
14 TraesCS1B01G122000 chr1A 95.714 70 3 0 2188 2257 86647942 86647873 5.460000e-21 113.0
15 TraesCS1B01G122000 chr4D 84.118 170 23 3 323 492 442397276 442397441 1.920000e-35 161.0
16 TraesCS1B01G122000 chr2A 84.118 170 23 3 323 492 680277627 680277462 1.920000e-35 161.0
17 TraesCS1B01G122000 chr2A 83.636 165 21 5 323 487 267885449 267885291 4.160000e-32 150.0
18 TraesCS1B01G122000 chr2A 100.000 30 0 0 323 352 527378723 527378752 1.000000e-03 56.5
19 TraesCS1B01G122000 chr5B 84.431 167 21 3 323 488 83902775 83902613 6.910000e-35 159.0
20 TraesCS1B01G122000 chr2B 85.235 149 16 5 323 470 550876474 550876331 1.500000e-31 148.0
21 TraesCS1B01G122000 chr2D 83.766 154 20 3 327 480 14695273 14695125 2.500000e-29 141.0
22 TraesCS1B01G122000 chr7D 84.956 113 16 1 374 486 3095342 3095231 5.460000e-21 113.0


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 TraesCS1B01G122000 chr1B 145452097 145458756 6659 True 12299.0 12299 100.00000 1 6660 1 chr1B.!!$R1 6659
1 TraesCS1B01G122000 chr1D 90644559 90651180 6621 True 2237.6 9348 95.11200 1 6536 5 chr1D.!!$R1 6535
2 TraesCS1B01G122000 chr1A 86643618 86649823 6205 True 2567.0 9077 93.00875 1 6536 4 chr1A.!!$R1 6535

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
90 93 0.389817 CGACTTGAAGTGCCCGATGA 60.390 55.000 0.90 0.00 0.00 2.92 F
938 1098 1.152139 CCCTCCATCTCCTCCTCCC 60.152 68.421 0.00 0.00 0.00 4.30 F
2117 2277 1.165270 AGCAGGTTGTTGATAACGGC 58.835 50.000 0.00 0.00 34.05 5.68 F
2884 3048 1.264557 GCTGCAGCTGCTAATGATCAG 59.735 52.381 36.61 24.05 42.66 2.90 F
2941 3105 1.280421 GGTGAGGAGAATGAAGGTGCT 59.720 52.381 0.00 0.00 0.00 4.40 F
3920 4084 1.146263 GATACACCAGGCCTTCGGG 59.854 63.158 13.51 9.95 36.74 5.14 F
4948 5112 1.679944 GCAAGGCCTGTTCTAGATGCA 60.680 52.381 5.69 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1672 1.654220 CACGTTGCCCACTTCCTTG 59.346 57.895 0.00 0.00 0.00 3.61 R
2896 3060 0.318120 TGTCTTCGTCATCAGCTGCA 59.682 50.000 9.47 0.00 0.00 4.41 R
3013 3177 0.178068 CACCCTCATTACCACTCCCG 59.822 60.000 0.00 0.00 0.00 5.14 R
3920 4084 0.819582 CCTTGGTCCATCACATTGGC 59.180 55.000 0.00 0.00 36.66 4.52 R
4339 4503 2.289882 TGAGTAGCACAAGAGCAGCATT 60.290 45.455 0.00 0.00 36.85 3.56 R
5290 5454 1.021390 CCACTAACGCCAGCCTCTTG 61.021 60.000 0.00 0.00 0.00 3.02 R
6025 6190 0.252558 TCTGGGTTGGTACTCCCTCC 60.253 60.000 17.33 4.96 41.88 4.30 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
54 55 1.603455 CCTGGGTGTGAATTGCGGT 60.603 57.895 0.00 0.00 0.00 5.68
90 93 0.389817 CGACTTGAAGTGCCCGATGA 60.390 55.000 0.90 0.00 0.00 2.92
140 143 8.847196 GGTTGTAGTCAGTTTTCCTTTAAGAAT 58.153 33.333 0.00 0.00 0.00 2.40
151 154 9.594478 GTTTTCCTTTAAGAATTTGAGTTTCCA 57.406 29.630 0.00 0.00 0.00 3.53
210 213 9.319143 TGTTTTTGTTATAAATTGGTCAACTGG 57.681 29.630 0.00 0.00 0.00 4.00
251 254 9.874215 CTACTATATCTCGTTGTTATCGTTGAA 57.126 33.333 0.00 0.00 0.00 2.69
262 265 4.637977 TGTTATCGTTGAATGGCTATTGCA 59.362 37.500 0.00 0.00 41.91 4.08
300 303 5.481122 TGTATAGTGTAGGTGTTTGCAGGTA 59.519 40.000 0.00 0.00 0.00 3.08
307 310 1.544246 GGTGTTTGCAGGTATTCCCAC 59.456 52.381 0.00 0.00 34.66 4.61
347 350 5.951747 AGCAATTTTAACATGCTCCCTCTTA 59.048 36.000 0.00 0.00 46.98 2.10
381 384 6.593382 CCCTCTTCACATGAGAAGTAAGAAAG 59.407 42.308 25.81 16.98 44.18 2.62
401 404 9.722184 AAGAAAGTAAGAGTTAATTAGACCCAC 57.278 33.333 0.00 0.00 0.00 4.61
536 539 4.702392 GCAGACGCCGAATAATCAAATAG 58.298 43.478 0.00 0.00 0.00 1.73
537 540 4.447724 GCAGACGCCGAATAATCAAATAGA 59.552 41.667 0.00 0.00 0.00 1.98
538 541 5.050363 GCAGACGCCGAATAATCAAATAGAA 60.050 40.000 0.00 0.00 0.00 2.10
539 542 6.347725 GCAGACGCCGAATAATCAAATAGAAT 60.348 38.462 0.00 0.00 0.00 2.40
541 544 8.708742 CAGACGCCGAATAATCAAATAGAATAA 58.291 33.333 0.00 0.00 0.00 1.40
542 545 8.926710 AGACGCCGAATAATCAAATAGAATAAG 58.073 33.333 0.00 0.00 0.00 1.73
703 860 8.159344 ACACAGAACAGAAAATAGAAAAGGAG 57.841 34.615 0.00 0.00 0.00 3.69
717 874 5.995446 AGAAAAGGAGTAAGGAGGCAATAG 58.005 41.667 0.00 0.00 0.00 1.73
861 1021 6.354883 CGAATTGAGCTATATATACTCGCGAC 59.645 42.308 3.71 0.00 32.98 5.19
938 1098 1.152139 CCCTCCATCTCCTCCTCCC 60.152 68.421 0.00 0.00 0.00 4.30
1072 1232 3.120105 CTGATGCGGACGAGGCTA 58.880 61.111 0.00 0.00 0.00 3.93
1640 1800 2.570181 CGAGAAGGCGGTTACGGT 59.430 61.111 0.00 0.00 41.36 4.83
1642 1802 2.047560 AGAAGGCGGTTACGGTGC 60.048 61.111 0.00 0.00 41.36 5.01
1973 2133 1.800805 ACCGTGCTGATGTTGAAGAG 58.199 50.000 0.00 0.00 0.00 2.85
2117 2277 1.165270 AGCAGGTTGTTGATAACGGC 58.835 50.000 0.00 0.00 34.05 5.68
2275 2435 3.127548 GTGGTAAGTGGACATGCTCAATG 59.872 47.826 0.00 0.00 42.48 2.82
2306 2466 5.747197 CGTTGCTACTACCTAGTAATGTTGG 59.253 44.000 0.00 0.00 38.24 3.77
2487 2651 6.816640 TGCTAGTAGTGTTCATTAATGTGGAC 59.183 38.462 14.97 12.25 0.00 4.02
2674 2838 1.798813 GTTGGTGTTGAGAAGCCTACG 59.201 52.381 0.00 0.00 0.00 3.51
2871 3035 2.693069 TCAGAAAACTCTAGCTGCAGC 58.307 47.619 31.53 31.53 42.49 5.25
2883 3047 1.306148 GCTGCAGCTGCTAATGATCA 58.694 50.000 36.61 15.14 42.66 2.92
2884 3048 1.264557 GCTGCAGCTGCTAATGATCAG 59.735 52.381 36.61 24.05 42.66 2.90
2885 3049 2.835027 CTGCAGCTGCTAATGATCAGA 58.165 47.619 36.61 13.65 42.66 3.27
2886 3050 3.203716 CTGCAGCTGCTAATGATCAGAA 58.796 45.455 36.61 13.13 42.66 3.02
2887 3051 3.613030 TGCAGCTGCTAATGATCAGAAA 58.387 40.909 36.61 11.32 42.66 2.52
2888 3052 4.011698 TGCAGCTGCTAATGATCAGAAAA 58.988 39.130 36.61 10.85 42.66 2.29
2889 3053 4.142534 TGCAGCTGCTAATGATCAGAAAAC 60.143 41.667 36.61 4.71 42.66 2.43
2890 3054 4.096081 GCAGCTGCTAATGATCAGAAAACT 59.904 41.667 31.33 0.00 38.21 2.66
2891 3055 5.730010 GCAGCTGCTAATGATCAGAAAACTC 60.730 44.000 31.33 0.00 38.21 3.01
2892 3056 5.585445 CAGCTGCTAATGATCAGAAAACTCT 59.415 40.000 0.00 0.00 32.26 3.24
2893 3057 6.760298 CAGCTGCTAATGATCAGAAAACTCTA 59.240 38.462 0.00 0.00 32.26 2.43
2894 3058 6.985645 AGCTGCTAATGATCAGAAAACTCTAG 59.014 38.462 0.00 0.00 32.26 2.43
2895 3059 6.292811 GCTGCTAATGATCAGAAAACTCTAGC 60.293 42.308 0.09 4.22 32.26 3.42
2896 3060 6.882656 TGCTAATGATCAGAAAACTCTAGCT 58.117 36.000 0.09 0.00 32.40 3.32
2897 3061 6.760298 TGCTAATGATCAGAAAACTCTAGCTG 59.240 38.462 0.09 0.00 32.40 4.24
2898 3062 6.292811 GCTAATGATCAGAAAACTCTAGCTGC 60.293 42.308 0.09 0.00 0.00 5.25
2899 3063 4.541973 TGATCAGAAAACTCTAGCTGCA 57.458 40.909 1.02 0.00 0.00 4.41
2900 3064 4.502016 TGATCAGAAAACTCTAGCTGCAG 58.498 43.478 10.11 10.11 0.00 4.41
2941 3105 1.280421 GGTGAGGAGAATGAAGGTGCT 59.720 52.381 0.00 0.00 0.00 4.40
2951 3115 4.458295 AGAATGAAGGTGCTCAAGATGTTG 59.542 41.667 0.00 0.00 34.67 3.33
3013 3177 1.654317 CTGCAGCTGATGAGGAAGAC 58.346 55.000 20.43 0.00 0.00 3.01
3082 3246 1.803519 GAGTCCTGCTCGAGTTGCG 60.804 63.158 15.13 0.00 42.69 4.85
3691 3855 1.664649 CAGCCTTGAGAACGCACGA 60.665 57.895 0.00 0.00 0.00 4.35
3886 4050 3.153130 TGTTGGTAATGTGGATGGTGTG 58.847 45.455 0.00 0.00 0.00 3.82
3920 4084 1.146263 GATACACCAGGCCTTCGGG 59.854 63.158 13.51 9.95 36.74 5.14
3964 4128 3.441572 CCAACAGGAAAATTCTCGCATCT 59.558 43.478 0.00 0.00 0.00 2.90
4363 4527 2.191802 CTGCTCTTGTGCTACTCATCG 58.808 52.381 0.00 0.00 0.00 3.84
4948 5112 1.679944 GCAAGGCCTGTTCTAGATGCA 60.680 52.381 5.69 0.00 0.00 3.96
5065 5229 5.183331 GGTTACCAAGGACAAGAAGGAATTC 59.817 44.000 0.00 0.00 0.00 2.17
5880 6044 9.736414 ATGATCCTTCTACCATTCTATCAATTG 57.264 33.333 0.00 0.00 0.00 2.32
5893 6057 0.597118 TCAATTGCCGTTGTTGCTGC 60.597 50.000 0.00 0.00 0.00 5.25
5943 6107 6.500684 TGATGAGGAAATAAGCACTGTTTC 57.499 37.500 0.00 0.00 0.00 2.78
5994 6159 6.223120 CCAGAACTTGTTTTATTTTGGGAGG 58.777 40.000 0.00 0.00 0.00 4.30
5995 6160 6.223120 CAGAACTTGTTTTATTTTGGGAGGG 58.777 40.000 0.00 0.00 0.00 4.30
5996 6161 6.041523 CAGAACTTGTTTTATTTTGGGAGGGA 59.958 38.462 0.00 0.00 0.00 4.20
5997 6162 6.267699 AGAACTTGTTTTATTTTGGGAGGGAG 59.732 38.462 0.00 0.00 0.00 4.30
5998 6163 5.464069 ACTTGTTTTATTTTGGGAGGGAGT 58.536 37.500 0.00 0.00 0.00 3.85
5999 6164 6.616577 ACTTGTTTTATTTTGGGAGGGAGTA 58.383 36.000 0.00 0.00 0.00 2.59
6000 6165 6.492429 ACTTGTTTTATTTTGGGAGGGAGTAC 59.508 38.462 0.00 0.00 0.00 2.73
6001 6166 5.326900 TGTTTTATTTTGGGAGGGAGTACC 58.673 41.667 0.00 0.00 40.67 3.34
6002 6167 5.162969 TGTTTTATTTTGGGAGGGAGTACCA 60.163 40.000 0.00 0.00 43.89 3.25
6003 6168 5.602291 TTTATTTTGGGAGGGAGTACCAA 57.398 39.130 0.00 0.00 43.89 3.67
6004 6169 2.963599 TTTTGGGAGGGAGTACCAAC 57.036 50.000 0.00 0.00 43.43 3.77
6005 6170 1.069775 TTTGGGAGGGAGTACCAACC 58.930 55.000 0.00 0.00 43.43 3.77
6006 6171 3.737122 GGGAGGGAGTACCAACCC 58.263 66.667 10.40 10.40 45.85 4.11
6011 6176 3.950869 GGGAGTACCAACCCAGAAC 57.049 57.895 13.37 0.00 44.96 3.01
6012 6177 1.359168 GGGAGTACCAACCCAGAACT 58.641 55.000 13.37 0.00 44.96 3.01
6013 6178 1.703513 GGGAGTACCAACCCAGAACTT 59.296 52.381 13.37 0.00 44.96 2.66
6014 6179 2.552373 GGGAGTACCAACCCAGAACTTG 60.552 54.545 13.37 0.00 44.96 3.16
6015 6180 2.105993 GGAGTACCAACCCAGAACTTGT 59.894 50.000 0.00 0.00 35.97 3.16
6016 6181 3.434596 GGAGTACCAACCCAGAACTTGTT 60.435 47.826 0.00 0.00 35.97 2.83
6017 6182 4.204799 GAGTACCAACCCAGAACTTGTTT 58.795 43.478 0.00 0.00 0.00 2.83
6018 6183 4.606210 AGTACCAACCCAGAACTTGTTTT 58.394 39.130 0.00 0.00 0.00 2.43
6019 6184 5.757988 AGTACCAACCCAGAACTTGTTTTA 58.242 37.500 0.00 0.00 0.00 1.52
6020 6185 6.370453 AGTACCAACCCAGAACTTGTTTTAT 58.630 36.000 0.00 0.00 0.00 1.40
6021 6186 6.837048 AGTACCAACCCAGAACTTGTTTTATT 59.163 34.615 0.00 0.00 0.00 1.40
6022 6187 6.553953 ACCAACCCAGAACTTGTTTTATTT 57.446 33.333 0.00 0.00 0.00 1.40
6023 6188 6.953101 ACCAACCCAGAACTTGTTTTATTTT 58.047 32.000 0.00 0.00 0.00 1.82
6024 6189 6.821160 ACCAACCCAGAACTTGTTTTATTTTG 59.179 34.615 0.00 0.00 0.00 2.44
6025 6190 6.259829 CCAACCCAGAACTTGTTTTATTTTGG 59.740 38.462 0.00 0.00 0.00 3.28
6026 6191 5.924356 ACCCAGAACTTGTTTTATTTTGGG 58.076 37.500 9.60 9.60 46.39 4.12
6027 6192 5.663556 ACCCAGAACTTGTTTTATTTTGGGA 59.336 36.000 16.35 0.00 44.32 4.37
6028 6193 6.183360 ACCCAGAACTTGTTTTATTTTGGGAG 60.183 38.462 16.35 0.00 44.32 4.30
6092 6257 2.232208 CTCCCCCTCTTTTCACAAATGC 59.768 50.000 0.00 0.00 0.00 3.56
6155 6321 6.721571 ACAAGTTGTATCATACTGGTTTCG 57.278 37.500 6.75 0.00 0.00 3.46
6185 6351 8.304596 TCAATCTCAGGTAGTGTTACTTGTTAG 58.695 37.037 0.00 0.00 37.90 2.34
6476 6647 7.792736 TGGATTACTGATACCTGTAACCCTATT 59.207 37.037 0.00 0.00 39.69 1.73
6506 6677 3.470709 CAGTTCTGCTTTCTTCTGGTGA 58.529 45.455 0.00 0.00 0.00 4.02
6507 6678 4.070716 CAGTTCTGCTTTCTTCTGGTGAT 58.929 43.478 0.00 0.00 0.00 3.06
6508 6679 4.518211 CAGTTCTGCTTTCTTCTGGTGATT 59.482 41.667 0.00 0.00 0.00 2.57
6536 6710 7.453141 AACTATTACCTGGCTCCTAAAATCT 57.547 36.000 0.00 0.00 0.00 2.40
6537 6711 8.562949 AACTATTACCTGGCTCCTAAAATCTA 57.437 34.615 0.00 0.00 0.00 1.98
6538 6712 7.964624 ACTATTACCTGGCTCCTAAAATCTAC 58.035 38.462 0.00 0.00 0.00 2.59
6539 6713 6.824958 ATTACCTGGCTCCTAAAATCTACA 57.175 37.500 0.00 0.00 0.00 2.74
6540 6714 6.630203 TTACCTGGCTCCTAAAATCTACAA 57.370 37.500 0.00 0.00 0.00 2.41
6541 6715 5.104259 ACCTGGCTCCTAAAATCTACAAG 57.896 43.478 0.00 0.00 0.00 3.16
6542 6716 4.536489 ACCTGGCTCCTAAAATCTACAAGT 59.464 41.667 0.00 0.00 0.00 3.16
6543 6717 4.878397 CCTGGCTCCTAAAATCTACAAGTG 59.122 45.833 0.00 0.00 0.00 3.16
6544 6718 4.261801 TGGCTCCTAAAATCTACAAGTGC 58.738 43.478 0.00 0.00 0.00 4.40
6545 6719 4.261801 GGCTCCTAAAATCTACAAGTGCA 58.738 43.478 0.00 0.00 0.00 4.57
6546 6720 4.884164 GGCTCCTAAAATCTACAAGTGCAT 59.116 41.667 0.00 0.00 0.00 3.96
6547 6721 5.220931 GGCTCCTAAAATCTACAAGTGCATG 60.221 44.000 0.00 0.00 0.00 4.06
6548 6722 5.731686 GCTCCTAAAATCTACAAGTGCATGC 60.732 44.000 11.82 11.82 0.00 4.06
6549 6723 5.500234 TCCTAAAATCTACAAGTGCATGCT 58.500 37.500 20.33 0.00 0.00 3.79
6550 6724 5.586243 TCCTAAAATCTACAAGTGCATGCTC 59.414 40.000 20.33 15.94 0.00 4.26
6551 6725 5.587844 CCTAAAATCTACAAGTGCATGCTCT 59.412 40.000 20.33 18.23 0.00 4.09
6552 6726 6.763135 CCTAAAATCTACAAGTGCATGCTCTA 59.237 38.462 21.70 7.14 0.00 2.43
6553 6727 7.443575 CCTAAAATCTACAAGTGCATGCTCTAT 59.556 37.037 21.70 15.30 0.00 1.98
6554 6728 6.857777 AAATCTACAAGTGCATGCTCTATC 57.142 37.500 21.70 6.08 0.00 2.08
6555 6729 4.327982 TCTACAAGTGCATGCTCTATCC 57.672 45.455 21.70 1.82 0.00 2.59
6556 6730 3.706086 TCTACAAGTGCATGCTCTATCCA 59.294 43.478 21.70 7.67 0.00 3.41
6557 6731 3.354948 ACAAGTGCATGCTCTATCCAA 57.645 42.857 21.70 0.00 0.00 3.53
6558 6732 3.894759 ACAAGTGCATGCTCTATCCAAT 58.105 40.909 21.70 3.24 0.00 3.16
6559 6733 3.630769 ACAAGTGCATGCTCTATCCAATG 59.369 43.478 21.70 16.68 0.00 2.82
6560 6734 2.228059 AGTGCATGCTCTATCCAATGC 58.772 47.619 20.22 0.00 35.77 3.56
6561 6735 1.951602 GTGCATGCTCTATCCAATGCA 59.048 47.619 20.33 5.13 41.91 3.96
6562 6736 2.359848 GTGCATGCTCTATCCAATGCAA 59.640 45.455 20.33 0.00 44.98 4.08
6563 6737 2.359848 TGCATGCTCTATCCAATGCAAC 59.640 45.455 20.33 0.00 41.32 4.17
6564 6738 2.359848 GCATGCTCTATCCAATGCAACA 59.640 45.455 11.37 0.00 38.96 3.33
6565 6739 3.181484 GCATGCTCTATCCAATGCAACAA 60.181 43.478 11.37 0.00 38.96 2.83
6566 6740 4.678574 GCATGCTCTATCCAATGCAACAAA 60.679 41.667 11.37 0.00 38.96 2.83
6567 6741 5.412640 CATGCTCTATCCAATGCAACAAAA 58.587 37.500 0.00 0.00 38.96 2.44
6568 6742 5.063180 TGCTCTATCCAATGCAACAAAAG 57.937 39.130 0.00 0.00 32.12 2.27
6569 6743 4.766373 TGCTCTATCCAATGCAACAAAAGA 59.234 37.500 0.00 0.00 32.12 2.52
6570 6744 5.098211 GCTCTATCCAATGCAACAAAAGAC 58.902 41.667 0.00 0.00 0.00 3.01
6571 6745 5.643379 TCTATCCAATGCAACAAAAGACC 57.357 39.130 0.00 0.00 0.00 3.85
6572 6746 2.791383 TCCAATGCAACAAAAGACCG 57.209 45.000 0.00 0.00 0.00 4.79
6573 6747 2.302260 TCCAATGCAACAAAAGACCGA 58.698 42.857 0.00 0.00 0.00 4.69
6574 6748 2.890311 TCCAATGCAACAAAAGACCGAT 59.110 40.909 0.00 0.00 0.00 4.18
6575 6749 3.057596 TCCAATGCAACAAAAGACCGATC 60.058 43.478 0.00 0.00 0.00 3.69
6576 6750 3.057315 CCAATGCAACAAAAGACCGATCT 60.057 43.478 0.00 0.00 36.42 2.75
6577 6751 3.837213 ATGCAACAAAAGACCGATCTG 57.163 42.857 0.00 0.00 34.48 2.90
6578 6752 2.844946 TGCAACAAAAGACCGATCTGA 58.155 42.857 0.00 0.00 34.48 3.27
6579 6753 3.411446 TGCAACAAAAGACCGATCTGAT 58.589 40.909 0.00 0.00 34.48 2.90
6580 6754 3.189080 TGCAACAAAAGACCGATCTGATG 59.811 43.478 0.00 0.00 34.48 3.07
6581 6755 3.436704 GCAACAAAAGACCGATCTGATGA 59.563 43.478 0.00 0.00 34.48 2.92
6582 6756 4.083324 GCAACAAAAGACCGATCTGATGAA 60.083 41.667 0.00 0.00 34.48 2.57
6583 6757 5.562696 GCAACAAAAGACCGATCTGATGAAA 60.563 40.000 0.00 0.00 34.48 2.69
6584 6758 5.869753 ACAAAAGACCGATCTGATGAAAG 57.130 39.130 0.00 0.00 34.48 2.62
6585 6759 5.551233 ACAAAAGACCGATCTGATGAAAGA 58.449 37.500 0.00 0.00 34.48 2.52
6586 6760 5.641209 ACAAAAGACCGATCTGATGAAAGAG 59.359 40.000 0.00 0.00 34.48 2.85
6587 6761 5.667539 AAAGACCGATCTGATGAAAGAGA 57.332 39.130 0.00 0.00 34.48 3.10
6588 6762 5.667539 AAGACCGATCTGATGAAAGAGAA 57.332 39.130 0.00 0.00 34.48 2.87
6589 6763 5.261209 AGACCGATCTGATGAAAGAGAAG 57.739 43.478 0.00 0.00 32.29 2.85
6590 6764 4.952957 AGACCGATCTGATGAAAGAGAAGA 59.047 41.667 0.00 0.00 32.29 2.87
6591 6765 5.004922 ACCGATCTGATGAAAGAGAAGAC 57.995 43.478 0.00 0.00 0.00 3.01
6592 6766 4.709397 ACCGATCTGATGAAAGAGAAGACT 59.291 41.667 0.00 0.00 0.00 3.24
6593 6767 5.888724 ACCGATCTGATGAAAGAGAAGACTA 59.111 40.000 0.00 0.00 0.00 2.59
6594 6768 6.183360 ACCGATCTGATGAAAGAGAAGACTAC 60.183 42.308 0.00 0.00 0.00 2.73
6595 6769 6.183360 CCGATCTGATGAAAGAGAAGACTACA 60.183 42.308 0.00 0.00 0.00 2.74
6596 6770 6.690957 CGATCTGATGAAAGAGAAGACTACAC 59.309 42.308 0.00 0.00 0.00 2.90
6597 6771 6.901081 TCTGATGAAAGAGAAGACTACACA 57.099 37.500 0.00 0.00 0.00 3.72
6598 6772 7.473735 TCTGATGAAAGAGAAGACTACACAT 57.526 36.000 0.00 0.00 0.00 3.21
6599 6773 7.901029 TCTGATGAAAGAGAAGACTACACATT 58.099 34.615 0.00 0.00 0.00 2.71
6600 6774 8.370940 TCTGATGAAAGAGAAGACTACACATTT 58.629 33.333 0.00 0.00 0.00 2.32
6601 6775 9.645059 CTGATGAAAGAGAAGACTACACATTTA 57.355 33.333 0.00 0.00 0.00 1.40
6605 6779 9.569167 TGAAAGAGAAGACTACACATTTATACG 57.431 33.333 0.00 0.00 0.00 3.06
6606 6780 9.570488 GAAAGAGAAGACTACACATTTATACGT 57.430 33.333 0.00 0.00 0.00 3.57
6607 6781 9.570488 AAAGAGAAGACTACACATTTATACGTC 57.430 33.333 0.00 0.00 0.00 4.34
6608 6782 8.277490 AGAGAAGACTACACATTTATACGTCA 57.723 34.615 0.00 0.00 0.00 4.35
6609 6783 8.737175 AGAGAAGACTACACATTTATACGTCAA 58.263 33.333 0.00 0.00 0.00 3.18
6610 6784 8.684973 AGAAGACTACACATTTATACGTCAAC 57.315 34.615 0.00 0.00 0.00 3.18
6611 6785 8.301720 AGAAGACTACACATTTATACGTCAACA 58.698 33.333 0.00 0.00 0.00 3.33
6612 6786 8.462143 AAGACTACACATTTATACGTCAACAG 57.538 34.615 0.00 0.00 0.00 3.16
6613 6787 7.600065 AGACTACACATTTATACGTCAACAGT 58.400 34.615 0.00 0.00 0.00 3.55
6614 6788 8.086522 AGACTACACATTTATACGTCAACAGTT 58.913 33.333 0.00 0.00 0.00 3.16
6615 6789 9.345517 GACTACACATTTATACGTCAACAGTTA 57.654 33.333 0.00 0.00 0.00 2.24
6616 6790 9.865321 ACTACACATTTATACGTCAACAGTTAT 57.135 29.630 0.00 0.00 0.00 1.89
6618 6792 8.542497 ACACATTTATACGTCAACAGTTATGT 57.458 30.769 0.00 0.00 43.15 2.29
6619 6793 9.642327 ACACATTTATACGTCAACAGTTATGTA 57.358 29.630 0.00 0.00 39.29 2.29
6631 6805 5.835113 ACAGTTATGTATGTTGGAATGCC 57.165 39.130 0.00 0.00 38.09 4.40
6632 6806 5.260424 ACAGTTATGTATGTTGGAATGCCA 58.740 37.500 0.00 0.00 39.40 4.92
6633 6807 5.714333 ACAGTTATGTATGTTGGAATGCCAA 59.286 36.000 0.00 0.00 44.47 4.52
6642 6816 1.668826 TGGAATGCCAACTACTCCCT 58.331 50.000 0.00 0.00 42.49 4.20
6643 6817 1.559682 TGGAATGCCAACTACTCCCTC 59.440 52.381 0.00 0.00 42.49 4.30
6644 6818 1.134068 GGAATGCCAACTACTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
6645 6819 0.541863 AATGCCAACTACTCCCTCCG 59.458 55.000 0.00 0.00 0.00 4.63
6646 6820 0.617820 ATGCCAACTACTCCCTCCGT 60.618 55.000 0.00 0.00 0.00 4.69
6647 6821 1.255667 TGCCAACTACTCCCTCCGTC 61.256 60.000 0.00 0.00 0.00 4.79
6648 6822 1.957765 GCCAACTACTCCCTCCGTCC 61.958 65.000 0.00 0.00 0.00 4.79
6649 6823 1.328430 CCAACTACTCCCTCCGTCCC 61.328 65.000 0.00 0.00 0.00 4.46
6650 6824 1.379576 AACTACTCCCTCCGTCCCG 60.380 63.158 0.00 0.00 0.00 5.14
6651 6825 2.147433 AACTACTCCCTCCGTCCCGT 62.147 60.000 0.00 0.00 0.00 5.28
6652 6826 1.379576 CTACTCCCTCCGTCCCGTT 60.380 63.158 0.00 0.00 0.00 4.44
6653 6827 0.107017 CTACTCCCTCCGTCCCGTTA 60.107 60.000 0.00 0.00 0.00 3.18
6654 6828 0.552848 TACTCCCTCCGTCCCGTTAT 59.447 55.000 0.00 0.00 0.00 1.89
6655 6829 0.552848 ACTCCCTCCGTCCCGTTATA 59.447 55.000 0.00 0.00 0.00 0.98
6656 6830 1.146566 ACTCCCTCCGTCCCGTTATAT 59.853 52.381 0.00 0.00 0.00 0.86
6657 6831 2.245582 CTCCCTCCGTCCCGTTATATT 58.754 52.381 0.00 0.00 0.00 1.28
6658 6832 3.181429 ACTCCCTCCGTCCCGTTATATTA 60.181 47.826 0.00 0.00 0.00 0.98
6659 6833 4.021916 CTCCCTCCGTCCCGTTATATTAT 58.978 47.826 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.602323 GGACCGCAATTCACACCCA 60.602 57.895 0.00 0.00 0.00 4.51
98 101 0.617820 AACCTCGCCACCACCTAGAT 60.618 55.000 0.00 0.00 0.00 1.98
164 167 8.519799 AAAACAGGACCGAAAATCATACATAT 57.480 30.769 0.00 0.00 0.00 1.78
166 169 6.834168 AAAACAGGACCGAAAATCATACAT 57.166 33.333 0.00 0.00 0.00 2.29
179 182 8.145122 TGACCAATTTATAACAAAAACAGGACC 58.855 33.333 0.00 0.00 0.00 4.46
210 213 0.889306 AGTAGTCGTGGAAGGAGCAC 59.111 55.000 0.00 0.00 0.00 4.40
251 254 3.129988 GCTTTGAAGACTGCAATAGCCAT 59.870 43.478 14.65 0.00 41.13 4.40
262 265 5.539048 ACACTATACAACGCTTTGAAGACT 58.461 37.500 10.27 0.00 36.48 3.24
300 303 4.016479 TCCTAGACAGTAAGAGGTGGGAAT 60.016 45.833 0.00 0.00 0.00 3.01
307 310 5.606348 AATTGCTCCTAGACAGTAAGAGG 57.394 43.478 0.00 0.00 0.00 3.69
462 465 3.895232 TGACATGCTTCCTCTTACCTC 57.105 47.619 0.00 0.00 0.00 3.85
488 491 6.183360 CGAAGCTTGAAAAATTACTAGGGAGG 60.183 42.308 2.10 0.00 0.00 4.30
489 492 6.183360 CCGAAGCTTGAAAAATTACTAGGGAG 60.183 42.308 2.10 0.00 0.00 4.30
490 493 5.646360 CCGAAGCTTGAAAAATTACTAGGGA 59.354 40.000 2.10 0.00 0.00 4.20
536 539 4.620184 ACTACACGCGTTGACTTCTTATTC 59.380 41.667 10.22 0.00 0.00 1.75
537 540 4.553323 ACTACACGCGTTGACTTCTTATT 58.447 39.130 10.22 0.00 0.00 1.40
538 541 4.170292 ACTACACGCGTTGACTTCTTAT 57.830 40.909 10.22 0.00 0.00 1.73
539 542 3.631145 ACTACACGCGTTGACTTCTTA 57.369 42.857 10.22 0.00 0.00 2.10
541 544 2.503920 AACTACACGCGTTGACTTCT 57.496 45.000 10.22 0.00 0.00 2.85
542 545 2.283351 ACAAACTACACGCGTTGACTTC 59.717 45.455 10.22 0.00 0.00 3.01
549 703 6.897259 AATTATATCACAAACTACACGCGT 57.103 33.333 5.58 5.58 0.00 6.01
600 754 8.433421 AACGATAGAAAAGAAGAAGAACAACA 57.567 30.769 0.00 0.00 41.38 3.33
663 818 4.729227 TCTGTGTTTGGGGTTTTTCTTC 57.271 40.909 0.00 0.00 0.00 2.87
672 828 4.670896 ATTTTCTGTTCTGTGTTTGGGG 57.329 40.909 0.00 0.00 0.00 4.96
703 860 4.730903 GCGCTTTTTCTATTGCCTCCTTAC 60.731 45.833 0.00 0.00 0.00 2.34
717 874 2.732282 GCTGGTGATAAGGCGCTTTTTC 60.732 50.000 11.00 12.99 0.00 2.29
861 1021 8.762426 GTTTTAGGTTAGGCTACTCGATTTATG 58.238 37.037 0.00 0.00 0.00 1.90
1126 1286 2.528708 CTCCTCGCCCTCCCCTAT 59.471 66.667 0.00 0.00 0.00 2.57
1438 1598 3.466791 CTACCAGCGCATCAGGGGG 62.467 68.421 11.47 1.31 0.00 5.40
1508 1668 4.659172 TGCCCACTTCCTTGGCCG 62.659 66.667 0.00 0.00 44.72 6.13
1512 1672 1.654220 CACGTTGCCCACTTCCTTG 59.346 57.895 0.00 0.00 0.00 3.61
1640 1800 4.343323 CCATGGTCGTGGTGGGCA 62.343 66.667 2.57 0.00 34.46 5.36
1642 1802 2.268920 CTCCATGGTCGTGGTGGG 59.731 66.667 12.58 0.00 40.27 4.61
1992 2152 2.510238 AGTTGCATCGCTCTCCGC 60.510 61.111 0.00 0.00 36.73 5.54
2275 2435 5.648572 ACTAGGTAGTAGCAACGAAATCAC 58.351 41.667 1.58 0.00 34.13 3.06
2277 2437 7.919621 ACATTACTAGGTAGTAGCAACGAAATC 59.080 37.037 1.58 0.00 39.69 2.17
2306 2466 9.738832 TTTATTTGTTTTAAACTCCAGTAGTGC 57.261 29.630 9.33 0.00 38.88 4.40
2405 2565 2.738521 GCGTCGCTTTCTGGCTCA 60.739 61.111 10.68 0.00 0.00 4.26
2674 2838 1.604278 GCAACAACACTCTCAACCTCC 59.396 52.381 0.00 0.00 0.00 4.30
2804 2968 2.842496 TCTCATCATCACCAGCCTCTTT 59.158 45.455 0.00 0.00 0.00 2.52
2871 3035 6.985645 AGCTAGAGTTTTCTGATCATTAGCAG 59.014 38.462 0.00 0.00 40.61 4.24
2872 3036 6.760298 CAGCTAGAGTTTTCTGATCATTAGCA 59.240 38.462 0.00 0.00 34.79 3.49
2873 3037 6.292811 GCAGCTAGAGTTTTCTGATCATTAGC 60.293 42.308 0.00 1.04 34.79 3.09
2874 3038 6.760298 TGCAGCTAGAGTTTTCTGATCATTAG 59.240 38.462 0.00 0.00 34.79 1.73
2875 3039 6.643388 TGCAGCTAGAGTTTTCTGATCATTA 58.357 36.000 0.00 0.00 34.79 1.90
2876 3040 5.494724 TGCAGCTAGAGTTTTCTGATCATT 58.505 37.500 0.00 0.00 34.79 2.57
2877 3041 5.095145 TGCAGCTAGAGTTTTCTGATCAT 57.905 39.130 0.00 0.00 34.79 2.45
2878 3042 4.502016 CTGCAGCTAGAGTTTTCTGATCA 58.498 43.478 0.00 0.00 34.79 2.92
2879 3043 3.309410 GCTGCAGCTAGAGTTTTCTGATC 59.691 47.826 31.33 0.00 38.21 2.92
2880 3044 3.269178 GCTGCAGCTAGAGTTTTCTGAT 58.731 45.455 31.33 0.00 38.21 2.90
2881 3045 2.693069 GCTGCAGCTAGAGTTTTCTGA 58.307 47.619 31.33 0.00 38.21 3.27
2894 3058 0.738762 TCTTCGTCATCAGCTGCAGC 60.739 55.000 31.53 31.53 42.49 5.25
2895 3059 0.997932 GTCTTCGTCATCAGCTGCAG 59.002 55.000 10.11 10.11 0.00 4.41
2896 3060 0.318120 TGTCTTCGTCATCAGCTGCA 59.682 50.000 9.47 0.00 0.00 4.41
2897 3061 0.718343 GTGTCTTCGTCATCAGCTGC 59.282 55.000 9.47 0.00 0.00 5.25
2898 3062 1.991264 CTGTGTCTTCGTCATCAGCTG 59.009 52.381 7.63 7.63 0.00 4.24
2899 3063 1.067283 CCTGTGTCTTCGTCATCAGCT 60.067 52.381 0.00 0.00 0.00 4.24
2900 3064 1.337260 ACCTGTGTCTTCGTCATCAGC 60.337 52.381 0.00 0.00 0.00 4.26
2941 3105 1.069978 TCACGGTCAGCAACATCTTGA 59.930 47.619 0.00 0.00 0.00 3.02
2951 3115 0.458716 GCCTCTACTTCACGGTCAGC 60.459 60.000 0.00 0.00 0.00 4.26
3013 3177 0.178068 CACCCTCATTACCACTCCCG 59.822 60.000 0.00 0.00 0.00 5.14
3082 3246 4.984161 GCAGCTTCAGAGTTCTCTATGATC 59.016 45.833 1.83 0.00 40.81 2.92
3115 3279 2.376518 TCCTTCACCAAGCTCCTTCATT 59.623 45.455 0.00 0.00 0.00 2.57
3886 4050 6.455647 TGGTGTATCAATGATCCGTATCTTC 58.544 40.000 0.00 0.00 32.93 2.87
3920 4084 0.819582 CCTTGGTCCATCACATTGGC 59.180 55.000 0.00 0.00 36.66 4.52
3964 4128 7.987458 GGACATCTCTTGGTATATTTCTTGACA 59.013 37.037 0.00 0.00 0.00 3.58
4339 4503 2.289882 TGAGTAGCACAAGAGCAGCATT 60.290 45.455 0.00 0.00 36.85 3.56
4363 4527 7.930865 AGTGAGTTGGCTTCTGATAATATCTTC 59.069 37.037 1.66 0.00 0.00 2.87
4948 5112 1.213678 CAGTCATGATCCCACCCATGT 59.786 52.381 0.00 0.00 40.59 3.21
5290 5454 1.021390 CCACTAACGCCAGCCTCTTG 61.021 60.000 0.00 0.00 0.00 3.02
5880 6044 3.631487 GATGGGCAGCAACAACGGC 62.631 63.158 0.00 0.00 0.00 5.68
5893 6057 6.530181 GCGGTAAAGAACATTAAAAAGATGGG 59.470 38.462 0.00 0.00 0.00 4.00
5994 6159 2.105993 ACAAGTTCTGGGTTGGTACTCC 59.894 50.000 0.00 0.00 0.00 3.85
5995 6160 3.487120 ACAAGTTCTGGGTTGGTACTC 57.513 47.619 0.00 0.00 0.00 2.59
5996 6161 3.945640 AACAAGTTCTGGGTTGGTACT 57.054 42.857 0.00 0.00 0.00 2.73
5997 6162 4.994907 AAAACAAGTTCTGGGTTGGTAC 57.005 40.909 0.00 0.00 0.00 3.34
5998 6163 7.663043 AAATAAAACAAGTTCTGGGTTGGTA 57.337 32.000 0.00 0.00 0.00 3.25
5999 6164 6.553953 AAATAAAACAAGTTCTGGGTTGGT 57.446 33.333 0.00 0.00 0.00 3.67
6000 6165 6.259829 CCAAAATAAAACAAGTTCTGGGTTGG 59.740 38.462 0.00 0.00 0.00 3.77
6001 6166 6.259829 CCCAAAATAAAACAAGTTCTGGGTTG 59.740 38.462 0.00 0.00 36.91 3.77
6002 6167 6.157123 TCCCAAAATAAAACAAGTTCTGGGTT 59.843 34.615 3.38 0.00 41.50 4.11
6003 6168 5.663556 TCCCAAAATAAAACAAGTTCTGGGT 59.336 36.000 3.38 0.00 41.50 4.51
6004 6169 6.168270 TCCCAAAATAAAACAAGTTCTGGG 57.832 37.500 0.00 0.00 42.03 4.45
6005 6170 6.223120 CCTCCCAAAATAAAACAAGTTCTGG 58.777 40.000 0.00 0.00 0.00 3.86
6006 6171 6.041523 TCCCTCCCAAAATAAAACAAGTTCTG 59.958 38.462 0.00 0.00 0.00 3.02
6007 6172 6.140377 TCCCTCCCAAAATAAAACAAGTTCT 58.860 36.000 0.00 0.00 0.00 3.01
6008 6173 6.041637 ACTCCCTCCCAAAATAAAACAAGTTC 59.958 38.462 0.00 0.00 0.00 3.01
6009 6174 5.903010 ACTCCCTCCCAAAATAAAACAAGTT 59.097 36.000 0.00 0.00 0.00 2.66
6010 6175 5.464069 ACTCCCTCCCAAAATAAAACAAGT 58.536 37.500 0.00 0.00 0.00 3.16
6011 6176 6.071560 GGTACTCCCTCCCAAAATAAAACAAG 60.072 42.308 0.00 0.00 0.00 3.16
6012 6177 5.776208 GGTACTCCCTCCCAAAATAAAACAA 59.224 40.000 0.00 0.00 0.00 2.83
6013 6178 5.162969 TGGTACTCCCTCCCAAAATAAAACA 60.163 40.000 0.00 0.00 0.00 2.83
6014 6179 5.326900 TGGTACTCCCTCCCAAAATAAAAC 58.673 41.667 0.00 0.00 0.00 2.43
6015 6180 5.602291 TGGTACTCCCTCCCAAAATAAAA 57.398 39.130 0.00 0.00 0.00 1.52
6016 6181 5.326900 GTTGGTACTCCCTCCCAAAATAAA 58.673 41.667 0.00 0.00 39.79 1.40
6017 6182 4.264038 GGTTGGTACTCCCTCCCAAAATAA 60.264 45.833 0.00 0.00 39.79 1.40
6018 6183 3.267551 GGTTGGTACTCCCTCCCAAAATA 59.732 47.826 0.00 0.00 39.79 1.40
6019 6184 2.042569 GGTTGGTACTCCCTCCCAAAAT 59.957 50.000 0.00 0.00 39.79 1.82
6020 6185 1.426215 GGTTGGTACTCCCTCCCAAAA 59.574 52.381 0.00 0.00 39.79 2.44
6021 6186 1.069775 GGTTGGTACTCCCTCCCAAA 58.930 55.000 0.00 0.00 39.79 3.28
6022 6187 0.843343 GGGTTGGTACTCCCTCCCAA 60.843 60.000 11.94 0.00 43.19 4.12
6023 6188 1.229723 GGGTTGGTACTCCCTCCCA 60.230 63.158 11.94 0.00 43.19 4.37
6024 6189 1.229723 TGGGTTGGTACTCCCTCCC 60.230 63.158 17.33 11.66 43.64 4.30
6025 6190 0.252558 TCTGGGTTGGTACTCCCTCC 60.253 60.000 17.33 4.96 41.88 4.30
6026 6191 1.278413 GTTCTGGGTTGGTACTCCCTC 59.722 57.143 17.33 6.70 41.88 4.30
6027 6192 1.132495 AGTTCTGGGTTGGTACTCCCT 60.132 52.381 17.33 0.78 41.88 4.20
6028 6193 1.359168 AGTTCTGGGTTGGTACTCCC 58.641 55.000 12.20 12.20 41.76 4.30
6075 6240 4.301628 GTCTTGCATTTGTGAAAAGAGGG 58.698 43.478 0.00 0.00 0.00 4.30
6076 6241 3.976942 CGTCTTGCATTTGTGAAAAGAGG 59.023 43.478 0.00 0.00 0.00 3.69
6081 6246 4.328440 CCAAAACGTCTTGCATTTGTGAAA 59.672 37.500 0.00 0.00 32.29 2.69
6092 6257 4.859798 TGTTTAAACTGCCAAAACGTCTTG 59.140 37.500 18.72 0.00 36.19 3.02
6135 6301 5.187186 AGACCGAAACCAGTATGATACAACT 59.813 40.000 5.28 0.00 39.69 3.16
6155 6321 4.810191 AACACTACCTGAGATTGAGACC 57.190 45.455 0.00 0.00 0.00 3.85
6185 6351 4.697352 AGATATTAAGCATGATTGTCGCCC 59.303 41.667 6.43 0.00 0.00 6.13
6536 6710 4.486125 TTGGATAGAGCATGCACTTGTA 57.514 40.909 22.83 5.74 34.26 2.41
6537 6711 3.354948 TTGGATAGAGCATGCACTTGT 57.645 42.857 22.83 12.13 34.26 3.16
6538 6712 3.550233 GCATTGGATAGAGCATGCACTTG 60.550 47.826 22.83 14.29 41.47 3.16
6539 6713 2.621998 GCATTGGATAGAGCATGCACTT 59.378 45.455 22.83 10.73 41.47 3.16
6540 6714 2.228059 GCATTGGATAGAGCATGCACT 58.772 47.619 21.45 21.45 41.47 4.40
6541 6715 1.951602 TGCATTGGATAGAGCATGCAC 59.048 47.619 21.98 14.59 45.50 4.57
6543 6717 2.359848 TGTTGCATTGGATAGAGCATGC 59.640 45.455 10.51 10.51 42.07 4.06
6544 6718 4.642445 TTGTTGCATTGGATAGAGCATG 57.358 40.909 0.00 0.00 36.80 4.06
6545 6719 5.419788 TCTTTTGTTGCATTGGATAGAGCAT 59.580 36.000 0.00 0.00 36.80 3.79
6546 6720 4.766373 TCTTTTGTTGCATTGGATAGAGCA 59.234 37.500 0.00 0.00 34.79 4.26
6547 6721 5.098211 GTCTTTTGTTGCATTGGATAGAGC 58.902 41.667 0.00 0.00 0.00 4.09
6548 6722 5.644644 GGTCTTTTGTTGCATTGGATAGAG 58.355 41.667 0.00 0.00 0.00 2.43
6549 6723 4.155826 CGGTCTTTTGTTGCATTGGATAGA 59.844 41.667 0.00 0.00 0.00 1.98
6550 6724 4.155826 TCGGTCTTTTGTTGCATTGGATAG 59.844 41.667 0.00 0.00 0.00 2.08
6551 6725 4.075682 TCGGTCTTTTGTTGCATTGGATA 58.924 39.130 0.00 0.00 0.00 2.59
6552 6726 2.890311 TCGGTCTTTTGTTGCATTGGAT 59.110 40.909 0.00 0.00 0.00 3.41
6553 6727 2.302260 TCGGTCTTTTGTTGCATTGGA 58.698 42.857 0.00 0.00 0.00 3.53
6554 6728 2.791383 TCGGTCTTTTGTTGCATTGG 57.209 45.000 0.00 0.00 0.00 3.16
6555 6729 3.916172 CAGATCGGTCTTTTGTTGCATTG 59.084 43.478 0.00 0.00 30.42 2.82
6556 6730 3.820467 TCAGATCGGTCTTTTGTTGCATT 59.180 39.130 0.00 0.00 30.42 3.56
6557 6731 3.411446 TCAGATCGGTCTTTTGTTGCAT 58.589 40.909 0.00 0.00 30.42 3.96
6558 6732 2.844946 TCAGATCGGTCTTTTGTTGCA 58.155 42.857 0.00 0.00 30.42 4.08
6559 6733 3.436704 TCATCAGATCGGTCTTTTGTTGC 59.563 43.478 0.00 0.00 30.42 4.17
6560 6734 5.611796 TTCATCAGATCGGTCTTTTGTTG 57.388 39.130 0.00 0.00 30.42 3.33
6561 6735 5.997746 TCTTTCATCAGATCGGTCTTTTGTT 59.002 36.000 0.00 0.00 30.42 2.83
6562 6736 5.551233 TCTTTCATCAGATCGGTCTTTTGT 58.449 37.500 0.00 0.00 30.42 2.83
6563 6737 5.871524 TCTCTTTCATCAGATCGGTCTTTTG 59.128 40.000 0.00 0.00 30.42 2.44
6564 6738 6.042638 TCTCTTTCATCAGATCGGTCTTTT 57.957 37.500 0.00 0.00 30.42 2.27
6565 6739 5.667539 TCTCTTTCATCAGATCGGTCTTT 57.332 39.130 0.00 0.00 30.42 2.52
6566 6740 5.420421 TCTTCTCTTTCATCAGATCGGTCTT 59.580 40.000 0.00 0.00 30.42 3.01
6567 6741 4.952957 TCTTCTCTTTCATCAGATCGGTCT 59.047 41.667 0.00 0.00 34.14 3.85
6568 6742 5.040635 GTCTTCTCTTTCATCAGATCGGTC 58.959 45.833 0.00 0.00 0.00 4.79
6569 6743 4.709397 AGTCTTCTCTTTCATCAGATCGGT 59.291 41.667 0.00 0.00 0.00 4.69
6570 6744 5.261209 AGTCTTCTCTTTCATCAGATCGG 57.739 43.478 0.00 0.00 0.00 4.18
6571 6745 6.690957 GTGTAGTCTTCTCTTTCATCAGATCG 59.309 42.308 0.00 0.00 0.00 3.69
6572 6746 7.542890 TGTGTAGTCTTCTCTTTCATCAGATC 58.457 38.462 0.00 0.00 0.00 2.75
6573 6747 7.473735 TGTGTAGTCTTCTCTTTCATCAGAT 57.526 36.000 0.00 0.00 0.00 2.90
6574 6748 6.901081 TGTGTAGTCTTCTCTTTCATCAGA 57.099 37.500 0.00 0.00 0.00 3.27
6575 6749 8.545229 AAATGTGTAGTCTTCTCTTTCATCAG 57.455 34.615 0.00 0.00 0.00 2.90
6579 6753 9.569167 CGTATAAATGTGTAGTCTTCTCTTTCA 57.431 33.333 0.00 0.00 0.00 2.69
6580 6754 9.570488 ACGTATAAATGTGTAGTCTTCTCTTTC 57.430 33.333 0.00 0.00 0.00 2.62
6581 6755 9.570488 GACGTATAAATGTGTAGTCTTCTCTTT 57.430 33.333 0.00 0.00 0.00 2.52
6582 6756 8.737175 TGACGTATAAATGTGTAGTCTTCTCTT 58.263 33.333 0.00 0.00 0.00 2.85
6583 6757 8.277490 TGACGTATAAATGTGTAGTCTTCTCT 57.723 34.615 0.00 0.00 0.00 3.10
6584 6758 8.796278 GTTGACGTATAAATGTGTAGTCTTCTC 58.204 37.037 0.00 0.00 0.00 2.87
6585 6759 8.301720 TGTTGACGTATAAATGTGTAGTCTTCT 58.698 33.333 0.00 0.00 0.00 2.85
6586 6760 8.456904 TGTTGACGTATAAATGTGTAGTCTTC 57.543 34.615 0.00 0.00 0.00 2.87
6587 6761 8.086522 ACTGTTGACGTATAAATGTGTAGTCTT 58.913 33.333 0.00 0.00 0.00 3.01
6588 6762 7.600065 ACTGTTGACGTATAAATGTGTAGTCT 58.400 34.615 0.00 0.00 0.00 3.24
6589 6763 7.807687 ACTGTTGACGTATAAATGTGTAGTC 57.192 36.000 0.00 0.00 0.00 2.59
6590 6764 9.865321 ATAACTGTTGACGTATAAATGTGTAGT 57.135 29.630 2.69 0.00 0.00 2.73
6592 6766 9.642327 ACATAACTGTTGACGTATAAATGTGTA 57.358 29.630 2.69 0.00 28.70 2.90
6593 6767 8.542497 ACATAACTGTTGACGTATAAATGTGT 57.458 30.769 2.69 0.00 28.70 3.72
6607 6781 7.790415 TTGGCATTCCAACATACATAACTGTTG 60.790 37.037 2.69 8.13 46.89 3.33
6608 6782 5.714333 TGGCATTCCAACATACATAACTGTT 59.286 36.000 0.00 0.00 39.99 3.16
6609 6783 5.260424 TGGCATTCCAACATACATAACTGT 58.740 37.500 0.00 0.00 39.99 3.55
6610 6784 5.833406 TGGCATTCCAACATACATAACTG 57.167 39.130 0.00 0.00 39.99 3.16
6623 6797 1.559682 GAGGGAGTAGTTGGCATTCCA 59.440 52.381 0.00 0.00 41.55 3.53
6624 6798 1.134068 GGAGGGAGTAGTTGGCATTCC 60.134 57.143 0.00 0.00 0.00 3.01
6625 6799 1.473434 CGGAGGGAGTAGTTGGCATTC 60.473 57.143 0.00 0.00 0.00 2.67
6626 6800 0.541863 CGGAGGGAGTAGTTGGCATT 59.458 55.000 0.00 0.00 0.00 3.56
6627 6801 0.617820 ACGGAGGGAGTAGTTGGCAT 60.618 55.000 0.00 0.00 0.00 4.40
6628 6802 1.229082 ACGGAGGGAGTAGTTGGCA 60.229 57.895 0.00 0.00 0.00 4.92
6629 6803 1.516423 GACGGAGGGAGTAGTTGGC 59.484 63.158 0.00 0.00 0.00 4.52
6630 6804 1.328430 GGGACGGAGGGAGTAGTTGG 61.328 65.000 0.00 0.00 0.00 3.77
6631 6805 2.200052 GGGACGGAGGGAGTAGTTG 58.800 63.158 0.00 0.00 0.00 3.16
6632 6806 4.781264 GGGACGGAGGGAGTAGTT 57.219 61.111 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.