Multiple sequence alignment - TraesCS3D01G060300

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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 TraesCS3D01G060300 chr3D 100.000 5150 0 0 1 5150 26270027 26275176 0.000000e+00 9511.0
1 TraesCS3D01G060300 chr3D 82.534 3252 510 37 925 4147 26300699 26303921 0.000000e+00 2806.0
2 TraesCS3D01G060300 chr3D 81.899 3160 515 42 995 4133 26222573 26219450 0.000000e+00 2614.0
3 TraesCS3D01G060300 chr3D 81.856 3125 529 30 1026 4137 26218395 26215296 0.000000e+00 2595.0
4 TraesCS3D01G060300 chr3D 89.058 329 8 10 4800 5122 26227075 26226769 2.910000e-102 383.0
5 TraesCS3D01G060300 chr3D 86.992 246 28 4 4223 4465 26228109 26227865 1.830000e-69 274.0
6 TraesCS3D01G060300 chr3D 81.515 330 22 13 4498 4802 26227470 26227155 8.620000e-58 235.0
7 TraesCS3D01G060300 chr3D 94.340 53 1 2 146 198 550247610 550247560 4.270000e-11 80.5
8 TraesCS3D01G060300 chr3D 83.951 81 11 2 36 115 509080231 509080310 5.530000e-10 76.8
9 TraesCS3D01G060300 chr3D 96.774 31 1 0 4177 4207 26228881 26228851 9.000000e-03 52.8
10 TraesCS3D01G060300 chr3A 94.690 3277 163 6 873 4147 36246274 36249541 0.000000e+00 5077.0
11 TraesCS3D01G060300 chr3A 81.467 3135 534 37 1026 4142 36289053 36292158 0.000000e+00 2527.0
12 TraesCS3D01G060300 chr3A 82.885 1227 189 12 2923 4137 36480710 36479493 0.000000e+00 1083.0
13 TraesCS3D01G060300 chr3A 90.625 416 26 6 1 409 36245186 36245595 1.630000e-149 540.0
14 TraesCS3D01G060300 chr3A 81.395 602 99 10 3539 4138 36286067 36286657 3.610000e-131 479.0
15 TraesCS3D01G060300 chr3A 88.860 386 25 5 526 893 36245651 36246036 4.700000e-125 459.0
16 TraesCS3D01G060300 chr3A 88.966 290 19 7 4823 5102 36273799 36274085 3.820000e-91 346.0
17 TraesCS3D01G060300 chr3A 91.935 186 14 1 4280 4465 36249717 36249901 5.120000e-65 259.0
18 TraesCS3D01G060300 chr3A 84.091 220 14 2 4529 4727 36250131 36250350 5.260000e-45 193.0
19 TraesCS3D01G060300 chr3B 93.835 3163 181 8 976 4135 43818566 43821717 0.000000e+00 4748.0
20 TraesCS3D01G060300 chr3B 86.522 1751 205 14 2396 4138 43850362 43852089 0.000000e+00 1897.0
21 TraesCS3D01G060300 chr3B 82.803 1884 306 15 2102 3979 44038654 44040525 0.000000e+00 1668.0
22 TraesCS3D01G060300 chr3B 82.749 1884 307 15 2102 3979 43933175 43935046 0.000000e+00 1663.0
23 TraesCS3D01G060300 chr3B 82.656 1822 291 19 2323 4138 43836572 43838374 0.000000e+00 1591.0
24 TraesCS3D01G060300 chr3B 77.494 391 31 31 125 467 43817719 43818100 1.140000e-41 182.0
25 TraesCS3D01G060300 chr3B 100.000 28 0 0 4177 4204 43820656 43820683 9.000000e-03 52.8
26 TraesCS3D01G060300 chr4D 83.861 3191 463 34 966 4133 1398096 1401257 0.000000e+00 2992.0
27 TraesCS3D01G060300 chrUn 81.599 3239 536 40 933 4144 245875289 245872084 0.000000e+00 2625.0
28 TraesCS3D01G060300 chrUn 81.627 3233 534 40 933 4138 260283630 260286829 0.000000e+00 2625.0
29 TraesCS3D01G060300 chrUn 81.728 405 47 10 3752 4138 432523112 432523507 3.870000e-81 313.0
30 TraesCS3D01G060300 chrUn 100.000 31 0 0 4177 4207 75443540 75443570 2.000000e-04 58.4
31 TraesCS3D01G060300 chr6D 82.118 3031 491 35 1121 4125 387430 390435 0.000000e+00 2547.0
32 TraesCS3D01G060300 chr6D 78.998 419 64 11 3716 4120 2290725 2290317 1.100000e-66 265.0


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 TraesCS3D01G060300 chr3D 26270027 26275176 5149 False 9511.000000 9511 100.00000 1 5150 1 chr3D.!!$F1 5149
1 TraesCS3D01G060300 chr3D 26300699 26303921 3222 False 2806.000000 2806 82.53400 925 4147 1 chr3D.!!$F2 3222
2 TraesCS3D01G060300 chr3D 26215296 26222573 7277 True 2604.500000 2614 81.87750 995 4137 2 chr3D.!!$R2 3142
3 TraesCS3D01G060300 chr3D 26226769 26228881 2112 True 236.200000 383 88.58475 4177 5122 4 chr3D.!!$R3 945
4 TraesCS3D01G060300 chr3A 36286067 36292158 6091 False 1503.000000 2527 81.43100 1026 4142 2 chr3A.!!$F3 3116
5 TraesCS3D01G060300 chr3A 36245186 36250350 5164 False 1305.600000 5077 90.04020 1 4727 5 chr3A.!!$F2 4726
6 TraesCS3D01G060300 chr3A 36479493 36480710 1217 True 1083.000000 1083 82.88500 2923 4137 1 chr3A.!!$R1 1214
7 TraesCS3D01G060300 chr3B 43850362 43852089 1727 False 1897.000000 1897 86.52200 2396 4138 1 chr3B.!!$F2 1742
8 TraesCS3D01G060300 chr3B 44038654 44040525 1871 False 1668.000000 1668 82.80300 2102 3979 1 chr3B.!!$F4 1877
9 TraesCS3D01G060300 chr3B 43933175 43935046 1871 False 1663.000000 1663 82.74900 2102 3979 1 chr3B.!!$F3 1877
10 TraesCS3D01G060300 chr3B 43817719 43821717 3998 False 1660.933333 4748 90.44300 125 4204 3 chr3B.!!$F5 4079
11 TraesCS3D01G060300 chr3B 43836572 43838374 1802 False 1591.000000 1591 82.65600 2323 4138 1 chr3B.!!$F1 1815
12 TraesCS3D01G060300 chr4D 1398096 1401257 3161 False 2992.000000 2992 83.86100 966 4133 1 chr4D.!!$F1 3167
13 TraesCS3D01G060300 chrUn 245872084 245875289 3205 True 2625.000000 2625 81.59900 933 4144 1 chrUn.!!$R1 3211
14 TraesCS3D01G060300 chrUn 260283630 260286829 3199 False 2625.000000 2625 81.62700 933 4138 1 chrUn.!!$F2 3205
15 TraesCS3D01G060300 chr6D 387430 390435 3005 False 2547.000000 2547 82.11800 1121 4125 1 chr6D.!!$F1 3004

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
350 403 1.326328 GGAGATCCCCAGGTACGTAC 58.674 60.000 17.56 17.56 0.00 3.67 F
748 916 1.419762 ACATGGCATATCTGGGCGTTA 59.580 47.619 0.00 0.00 0.00 3.18 F
1392 3367 1.675310 CCTGCATCGCCTCCAAACA 60.675 57.895 0.00 0.00 0.00 2.83 F
1762 3737 2.307686 GGTCTTGACCTTGGTCCCAATA 59.692 50.000 16.23 0.00 35.20 1.90 F
3382 9508 0.532573 GATGCGAGGAGGTGACTTGA 59.467 55.000 0.00 0.00 44.43 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 4054 0.035439 AACTTGGTACATGCCCCGAG 60.035 55.0 14.29 14.29 39.30 4.63 R
2220 4201 0.534652 CCGGAACCACACCCGTAAAA 60.535 55.0 0.00 0.00 43.93 1.52 R
3094 5077 1.961793 TGTGTTGCTTTCGCTAGGTT 58.038 45.0 0.00 0.00 36.97 3.50 R
3394 9520 0.608130 TCATGGTCCTGGTTCGAGTG 59.392 55.0 0.00 0.00 0.00 3.51 R
4495 12169 0.035820 TTGTCAATACGGGTGCCTCC 60.036 55.0 0.00 0.00 0.00 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
21 22 1.563111 TTAAACGCCGATCCACGATC 58.437 50.000 8.85 0.00 45.77 3.69
30 31 1.571919 GATCCACGATCGAAACCCAG 58.428 55.000 24.34 1.96 29.12 4.45
43 44 4.819630 TCGAAACCCAGGTATAATGCATTC 59.180 41.667 16.86 1.13 0.00 2.67
54 57 7.397476 CAGGTATAATGCATTCTACTCCCTCTA 59.603 40.741 25.40 4.21 0.00 2.43
271 307 3.900855 CCTTGCAGCTGTAGGCAG 58.099 61.111 19.68 9.07 44.79 4.85
282 318 2.287608 GCTGTAGGCAGTCCAAAACAAC 60.288 50.000 0.00 0.00 44.32 3.32
350 403 1.326328 GGAGATCCCCAGGTACGTAC 58.674 60.000 17.56 17.56 0.00 3.67
391 444 6.146184 ACACGATCGATCCATGAATAAATGAC 59.854 38.462 24.34 0.00 0.00 3.06
437 490 4.081586 ACTTCCTCCGTCCTTGTTTCTATC 60.082 45.833 0.00 0.00 0.00 2.08
438 491 3.437213 TCCTCCGTCCTTGTTTCTATCA 58.563 45.455 0.00 0.00 0.00 2.15
442 495 1.659098 CGTCCTTGTTTCTATCACGCC 59.341 52.381 0.00 0.00 0.00 5.68
450 503 4.883083 TGTTTCTATCACGCCCAGATATC 58.117 43.478 0.00 0.00 0.00 1.63
496 599 8.375493 TGTGTCATAAAAGTTATACTCCCTCT 57.625 34.615 0.00 0.00 0.00 3.69
500 603 9.968870 GTCATAAAAGTTATACTCCCTCTGTAG 57.031 37.037 0.00 0.00 0.00 2.74
501 604 8.639761 TCATAAAAGTTATACTCCCTCTGTAGC 58.360 37.037 0.00 0.00 0.00 3.58
509 612 8.738106 GTTATACTCCCTCTGTAGCGTAATATT 58.262 37.037 0.00 0.00 0.00 1.28
510 613 7.778185 ATACTCCCTCTGTAGCGTAATATTT 57.222 36.000 0.00 0.00 0.00 1.40
512 615 5.363005 ACTCCCTCTGTAGCGTAATATTTGT 59.637 40.000 0.00 0.00 0.00 2.83
513 616 5.839621 TCCCTCTGTAGCGTAATATTTGTC 58.160 41.667 0.00 0.00 0.00 3.18
514 617 4.680110 CCCTCTGTAGCGTAATATTTGTCG 59.320 45.833 0.00 0.00 0.00 4.35
515 618 5.279384 CCTCTGTAGCGTAATATTTGTCGT 58.721 41.667 0.00 0.00 0.00 4.34
517 620 6.291637 CCTCTGTAGCGTAATATTTGTCGTTG 60.292 42.308 0.00 0.00 0.00 4.10
659 808 2.419667 AGCTGCAACATGGCAATTTTC 58.580 42.857 1.02 0.00 44.40 2.29
696 864 4.599047 TTGAAACATGGCGAATCCTTTT 57.401 36.364 0.00 0.00 35.26 2.27
733 901 9.874205 ATGGTAAATTTATCTGTTTTCACATGG 57.126 29.630 9.79 0.00 30.39 3.66
748 916 1.419762 ACATGGCATATCTGGGCGTTA 59.580 47.619 0.00 0.00 0.00 3.18
749 917 2.040278 ACATGGCATATCTGGGCGTTAT 59.960 45.455 0.00 0.00 0.00 1.89
750 918 2.183478 TGGCATATCTGGGCGTTATG 57.817 50.000 0.00 0.00 0.00 1.90
776 944 6.759356 TGAGAAACACTAAAAATCTGACGTCA 59.241 34.615 18.88 18.88 0.00 4.35
798 966 9.916397 CGTCAGACTTTAACATTTACCATAATC 57.084 33.333 0.00 0.00 0.00 1.75
846 1014 6.564557 ATGGTCCAATTATTGCTCCAATTT 57.435 33.333 17.64 5.11 35.54 1.82
852 1020 9.598517 GTCCAATTATTGCTCCAATTTAATCAA 57.401 29.630 0.00 0.00 35.54 2.57
882 1050 5.368145 TGATGGCACCATGTAAATAGAGAC 58.632 41.667 6.96 0.00 36.70 3.36
902 1328 8.735692 AGAGACGTAGGGAGTATTATATTAGC 57.264 38.462 0.00 0.00 0.00 3.09
1098 3063 2.122768 AGCTCCTCCTTCTTACATGGG 58.877 52.381 0.00 0.00 0.00 4.00
1230 3198 3.240606 CTTGTGCACGGTGAAGGCG 62.241 63.158 13.29 0.00 0.00 5.52
1392 3367 1.675310 CCTGCATCGCCTCCAAACA 60.675 57.895 0.00 0.00 0.00 2.83
1486 3461 9.755804 TGTTTCATGTTGCATTTAACAATCTAA 57.244 25.926 0.00 0.00 43.13 2.10
1503 3478 3.439154 TCTAATTGGCCAATTTCCTGCA 58.561 40.909 40.69 24.48 40.99 4.41
1626 3601 9.664332 ATTACCTTCTCATATAATCACATCAGC 57.336 33.333 0.00 0.00 0.00 4.26
1628 3603 6.015095 ACCTTCTCATATAATCACATCAGCGA 60.015 38.462 0.00 0.00 0.00 4.93
1743 3718 6.378564 TCTTGAATCTTTCTACTCTCATCGGT 59.621 38.462 0.00 0.00 0.00 4.69
1762 3737 2.307686 GGTCTTGACCTTGGTCCCAATA 59.692 50.000 16.23 0.00 35.20 1.90
2076 4054 3.193691 TCTCCTTGAGTTGGAATCGTCTC 59.806 47.826 0.00 0.00 32.61 3.36
2220 4201 7.529534 TCTATTATCATTGGGGGCTAATCAT 57.470 36.000 0.00 0.00 0.00 2.45
2272 4253 5.975344 GGGACTGTTAAAACTTTGCAACTAC 59.025 40.000 0.00 0.00 0.00 2.73
2645 4626 6.376018 AGTTTAGAAGACATCGAGCTAGACTT 59.624 38.462 0.00 0.00 0.00 3.01
2740 4721 7.122715 TGCCAATAACTTAACTGGGTCAATAT 58.877 34.615 0.00 0.00 0.00 1.28
2931 4914 9.638239 TGTTCTGTTATGCCTTTAAATTCAATC 57.362 29.630 0.00 0.00 0.00 2.67
3042 5025 4.068599 GGAGAGGAAAACACAAGAGGAAG 58.931 47.826 0.00 0.00 0.00 3.46
3061 5044 3.533606 AGTCTGTATCACTGCCATCAC 57.466 47.619 0.00 0.00 0.00 3.06
3072 5055 2.816087 ACTGCCATCACTTGCTACAAAG 59.184 45.455 0.00 0.00 0.00 2.77
3094 5077 8.555361 CAAAGTTTCCAAAAGTTTCTTTCAACA 58.445 29.630 2.97 0.00 0.00 3.33
3188 9314 5.770162 ACAAAGGAAAACTAGTGGAAGATGG 59.230 40.000 0.00 0.00 0.00 3.51
3213 9339 4.015872 TGAGGTCGCCATAAAAGTCTTT 57.984 40.909 0.00 0.00 0.00 2.52
3368 9494 1.598183 CCTAGTGTACGAGCTGATGCG 60.598 57.143 0.00 0.00 45.42 4.73
3375 9501 2.780094 CGAGCTGATGCGAGGAGGT 61.780 63.158 0.00 0.00 45.42 3.85
3382 9508 0.532573 GATGCGAGGAGGTGACTTGA 59.467 55.000 0.00 0.00 44.43 3.02
3394 9520 5.351740 GGAGGTGACTTGAATAAACTGCTAC 59.648 44.000 0.00 0.00 44.43 3.58
3482 9608 3.719268 TTTGGTGGATGTAGCAGATGT 57.281 42.857 0.00 0.00 0.00 3.06
3618 9744 4.507756 GCAAGATTCAAAGTTGGTTCAACC 59.492 41.667 0.00 0.00 44.49 3.77
3694 9820 2.610727 GGATACGCTGCTCCAGGTAATC 60.611 54.545 0.00 0.00 31.21 1.75
3702 9828 3.628008 TGCTCCAGGTAATCGACTCTTA 58.372 45.455 0.00 0.00 0.00 2.10
3744 9872 7.281774 ACCACATTCTTTTCTGCATCTATGTAG 59.718 37.037 1.99 1.99 41.16 2.74
3767 9895 7.951530 AGACCAATGAAAGCAAAATTAACTG 57.048 32.000 0.00 0.00 0.00 3.16
3909 10037 7.092891 ACTGATGACATGTTTAAGGATGGACTA 60.093 37.037 0.00 0.00 0.00 2.59
3924 10052 6.431234 AGGATGGACTAAACATTGTGAAGTTC 59.569 38.462 0.00 0.00 0.00 3.01
4104 10233 2.138320 CGTATCACCATGCATGAGGTC 58.862 52.381 28.31 11.40 35.52 3.85
4108 10237 0.179076 CACCATGCATGAGGTCGCTA 60.179 55.000 28.31 0.00 35.52 4.26
4147 10276 4.141321 TCAGGGATGCATATTTGAGAAGCT 60.141 41.667 0.00 0.00 0.00 3.74
4148 10277 5.072193 TCAGGGATGCATATTTGAGAAGCTA 59.928 40.000 0.00 0.00 0.00 3.32
4149 10278 5.766670 CAGGGATGCATATTTGAGAAGCTAA 59.233 40.000 0.00 0.00 0.00 3.09
4150 10279 6.433404 CAGGGATGCATATTTGAGAAGCTAAT 59.567 38.462 0.00 0.00 0.00 1.73
4151 10280 6.658391 AGGGATGCATATTTGAGAAGCTAATC 59.342 38.462 0.00 0.00 0.00 1.75
4152 10281 6.658391 GGGATGCATATTTGAGAAGCTAATCT 59.342 38.462 0.00 0.00 0.00 2.40
4153 10282 7.148272 GGGATGCATATTTGAGAAGCTAATCTC 60.148 40.741 0.00 8.27 44.96 2.75
4154 10283 7.607223 GGATGCATATTTGAGAAGCTAATCTCT 59.393 37.037 14.90 1.24 44.98 3.10
4155 10284 7.725818 TGCATATTTGAGAAGCTAATCTCTG 57.274 36.000 14.90 6.99 44.98 3.35
4156 10285 7.278135 TGCATATTTGAGAAGCTAATCTCTGT 58.722 34.615 14.90 5.42 44.98 3.41
4157 10286 8.424133 TGCATATTTGAGAAGCTAATCTCTGTA 58.576 33.333 14.90 7.04 44.98 2.74
4158 10287 8.707839 GCATATTTGAGAAGCTAATCTCTGTAC 58.292 37.037 14.90 0.00 44.98 2.90
4159 10288 9.979578 CATATTTGAGAAGCTAATCTCTGTACT 57.020 33.333 14.90 1.29 44.98 2.73
4160 10289 9.979578 ATATTTGAGAAGCTAATCTCTGTACTG 57.020 33.333 14.90 0.00 44.98 2.74
4161 10290 6.842437 TTGAGAAGCTAATCTCTGTACTGT 57.158 37.500 14.90 0.00 44.98 3.55
4162 10291 7.939784 TTGAGAAGCTAATCTCTGTACTGTA 57.060 36.000 14.90 0.00 44.98 2.74
4163 10292 8.526667 TTGAGAAGCTAATCTCTGTACTGTAT 57.473 34.615 14.90 0.00 44.98 2.29
4164 10293 7.935520 TGAGAAGCTAATCTCTGTACTGTATG 58.064 38.462 14.90 0.00 44.98 2.39
4165 10294 7.775561 TGAGAAGCTAATCTCTGTACTGTATGA 59.224 37.037 14.90 0.00 44.98 2.15
4166 10295 8.526667 AGAAGCTAATCTCTGTACTGTATGAA 57.473 34.615 0.00 0.00 0.00 2.57
4167 10296 8.972127 AGAAGCTAATCTCTGTACTGTATGAAA 58.028 33.333 0.00 0.00 0.00 2.69
4168 10297 9.243637 GAAGCTAATCTCTGTACTGTATGAAAG 57.756 37.037 0.00 0.00 0.00 2.62
4169 10298 7.721402 AGCTAATCTCTGTACTGTATGAAAGG 58.279 38.462 0.00 0.00 0.00 3.11
4170 10299 7.561722 AGCTAATCTCTGTACTGTATGAAAGGA 59.438 37.037 0.00 0.00 0.00 3.36
4171 10300 7.650104 GCTAATCTCTGTACTGTATGAAAGGAC 59.350 40.741 0.00 0.00 0.00 3.85
4172 10301 5.916661 TCTCTGTACTGTATGAAAGGACC 57.083 43.478 0.00 0.00 0.00 4.46
4173 10302 4.710375 TCTCTGTACTGTATGAAAGGACCC 59.290 45.833 0.00 0.00 0.00 4.46
4174 10303 3.446161 TCTGTACTGTATGAAAGGACCCG 59.554 47.826 0.00 0.00 0.00 5.28
4175 10304 2.498481 TGTACTGTATGAAAGGACCCGG 59.502 50.000 0.00 0.00 0.00 5.73
4204 10333 5.240844 CCCAAAGTTTCTTTCAACGACCTAT 59.759 40.000 0.00 0.00 0.00 2.57
4207 10336 4.243270 AGTTTCTTTCAACGACCTATCCG 58.757 43.478 0.00 0.00 0.00 4.18
4208 10337 2.953466 TCTTTCAACGACCTATCCGG 57.047 50.000 0.00 0.00 39.35 5.14
4210 10339 3.028850 TCTTTCAACGACCTATCCGGAT 58.971 45.455 22.95 22.95 36.31 4.18
4211 10340 3.449737 TCTTTCAACGACCTATCCGGATT 59.550 43.478 24.71 4.08 36.31 3.01
4212 10341 3.899052 TTCAACGACCTATCCGGATTT 57.101 42.857 24.71 6.62 36.31 2.17
4215 10344 3.047796 CAACGACCTATCCGGATTTACG 58.952 50.000 24.71 22.86 36.31 3.18
4216 10345 2.301346 ACGACCTATCCGGATTTACGT 58.699 47.619 24.71 23.46 36.31 3.57
4217 10346 2.689983 ACGACCTATCCGGATTTACGTT 59.310 45.455 24.71 10.97 36.31 3.99
4218 10347 3.882888 ACGACCTATCCGGATTTACGTTA 59.117 43.478 24.71 0.71 36.31 3.18
4220 10349 4.233005 GACCTATCCGGATTTACGTTAGC 58.767 47.826 24.71 0.00 36.31 3.09
4311 11608 3.089284 CAAGGACCCAGATTTACAACCC 58.911 50.000 0.00 0.00 0.00 4.11
4380 11677 8.400947 ACTGTGATGAATAGCATTTTCATGTAC 58.599 33.333 11.91 10.94 42.38 2.90
4393 11690 9.248291 GCATTTTCATGTACCAATATTACCAAG 57.752 33.333 0.00 0.00 32.28 3.61
4427 11724 9.708092 ATATTTTATTTACTACTCCCTTCGAGC 57.292 33.333 0.00 0.00 43.01 5.03
4433 11730 3.158676 ACTACTCCCTTCGAGCCATATC 58.841 50.000 0.00 0.00 43.01 1.63
4448 11745 4.214971 AGCCATATCAATTGTCGCTGATTC 59.785 41.667 5.13 0.00 34.21 2.52
4451 11748 5.237996 CCATATCAATTGTCGCTGATTCAGT 59.762 40.000 14.90 0.00 34.21 3.41
4453 11750 7.041848 CCATATCAATTGTCGCTGATTCAGTAA 60.042 37.037 14.90 6.44 34.21 2.24
4459 11756 6.371809 TTGTCGCTGATTCAGTAAAAAGTT 57.628 33.333 14.90 0.00 33.43 2.66
4465 11762 7.868922 TCGCTGATTCAGTAAAAAGTTGTACTA 59.131 33.333 14.90 0.00 33.43 1.82
4466 11763 8.492748 CGCTGATTCAGTAAAAAGTTGTACTAA 58.507 33.333 14.90 0.00 33.43 2.24
4491 11788 8.519492 AAATCAGTGACAATTTTTATGGAACG 57.481 30.769 0.00 0.00 0.00 3.95
4495 12169 5.183140 AGTGACAATTTTTATGGAACGGAGG 59.817 40.000 0.00 0.00 0.00 4.30
4496 12170 4.461081 TGACAATTTTTATGGAACGGAGGG 59.539 41.667 0.00 0.00 0.00 4.30
4533 12207 5.156804 ACAATCAAACAGACAAAGACGAC 57.843 39.130 0.00 0.00 0.00 4.34
4545 12220 4.420168 ACAAAGACGACCACACATTTTTG 58.580 39.130 0.00 0.00 0.00 2.44
4580 12256 1.804601 TGACAGTGAGCAAGCATCAG 58.195 50.000 0.00 0.00 0.00 2.90
4659 12354 4.749310 CTGCTTCAGGCGCCGAGT 62.749 66.667 23.20 0.00 45.43 4.18
4676 12371 2.744202 CGAGTAGCTTTGTGCCTTTGAT 59.256 45.455 0.00 0.00 44.23 2.57
4687 12382 4.431809 TGTGCCTTTGATGTTTGAAGTTG 58.568 39.130 0.00 0.00 0.00 3.16
4702 12397 4.028490 TTGGTCTGCCGCGGGATT 62.028 61.111 29.38 0.00 37.67 3.01
4727 12422 3.151554 TGCAGCAAGAACACAGATTCAT 58.848 40.909 0.00 0.00 0.00 2.57
4741 12436 8.821686 ACACAGATTCATAATATCACCCAAAA 57.178 30.769 0.00 0.00 0.00 2.44
4778 12473 7.228314 TCAGATCCCCTATTGTATTTCTACG 57.772 40.000 0.00 0.00 0.00 3.51
4827 12608 3.945921 GGCGCTTACCCTCTCTTTTAAAT 59.054 43.478 7.64 0.00 0.00 1.40
4862 12643 3.140325 TGGAAAGAGTAGGCAAGGTTG 57.860 47.619 0.00 0.00 0.00 3.77
4943 12730 8.555361 GTCTGAAATGCATAACCTAAAGAGATC 58.445 37.037 0.00 0.00 0.00 2.75
4988 12775 6.112734 TGCACAACAAAAGAGAGTCTCTAAA 58.887 36.000 22.93 0.00 40.28 1.85
5013 12800 0.317854 GCGGGCAGTTGTTTTGAGAC 60.318 55.000 0.00 0.00 0.00 3.36
5020 12807 0.928451 GTTGTTTTGAGACGGCGCAC 60.928 55.000 10.83 0.76 0.00 5.34
5030 12817 3.185365 CGGCGCACGCAGATGTTA 61.185 61.111 17.69 0.00 44.11 2.41
5031 12818 2.399611 GGCGCACGCAGATGTTAC 59.600 61.111 17.69 0.00 44.11 2.50
5032 12819 2.387445 GGCGCACGCAGATGTTACA 61.387 57.895 17.69 0.00 44.11 2.41
5033 12820 1.225745 GCGCACGCAGATGTTACAC 60.226 57.895 10.65 0.00 41.49 2.90
5034 12821 1.896339 GCGCACGCAGATGTTACACA 61.896 55.000 10.65 0.00 41.49 3.72
5035 12822 0.721154 CGCACGCAGATGTTACACAT 59.279 50.000 0.00 0.00 42.43 3.21
5076 12863 1.821136 CTGGTTCTGGCAAAGGAATCC 59.179 52.381 0.00 0.00 0.00 3.01
5099 12886 3.360867 TGTTTCTTTTCTGCCACTTGGA 58.639 40.909 0.00 0.00 37.39 3.53
5126 12913 3.786516 TGCATGTGAAAGCATACCATG 57.213 42.857 0.00 0.00 35.51 3.66
5127 12914 3.090790 TGCATGTGAAAGCATACCATGT 58.909 40.909 0.00 0.00 35.51 3.21
5128 12915 4.268359 TGCATGTGAAAGCATACCATGTA 58.732 39.130 0.00 0.00 35.51 2.29
5129 12916 4.336153 TGCATGTGAAAGCATACCATGTAG 59.664 41.667 0.00 0.00 35.51 2.74
5130 12917 4.336433 GCATGTGAAAGCATACCATGTAGT 59.664 41.667 0.00 0.00 0.00 2.73
5131 12918 5.527214 GCATGTGAAAGCATACCATGTAGTA 59.473 40.000 0.00 0.00 0.00 1.82
5132 12919 6.511767 GCATGTGAAAGCATACCATGTAGTAC 60.512 42.308 0.00 0.00 0.00 2.73
5133 12920 5.106442 TGTGAAAGCATACCATGTAGTACG 58.894 41.667 0.00 0.00 0.00 3.67
5134 12921 5.107133 GTGAAAGCATACCATGTAGTACGT 58.893 41.667 0.00 0.00 0.00 3.57
5135 12922 6.127675 TGTGAAAGCATACCATGTAGTACGTA 60.128 38.462 0.00 0.00 0.00 3.57
5136 12923 6.197842 GTGAAAGCATACCATGTAGTACGTAC 59.802 42.308 18.10 18.10 0.00 3.67
5137 12924 4.478843 AGCATACCATGTAGTACGTACG 57.521 45.455 19.49 15.01 33.87 3.67
5138 12925 3.879295 AGCATACCATGTAGTACGTACGT 59.121 43.478 25.98 25.98 33.87 3.57
5139 12926 3.970610 GCATACCATGTAGTACGTACGTG 59.029 47.826 30.25 13.41 45.13 4.49
5146 12933 4.014847 TGTAGTACGTACGTGGTATTGC 57.985 45.455 30.25 11.68 33.87 3.56
5147 12934 3.438434 TGTAGTACGTACGTGGTATTGCA 59.562 43.478 30.25 14.10 33.87 4.08
5148 12935 3.141002 AGTACGTACGTGGTATTGCAG 57.859 47.619 30.25 0.00 0.00 4.41
5149 12936 2.749076 AGTACGTACGTGGTATTGCAGA 59.251 45.455 30.25 3.44 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.533491 TACCTGGGTTTCGATCGTGG 59.467 55.000 15.94 9.27 0.00 4.94
15 16 2.596904 ATACCTGGGTTTCGATCGTG 57.403 50.000 15.94 0.00 0.00 4.35
16 17 4.628074 CATTATACCTGGGTTTCGATCGT 58.372 43.478 15.94 0.00 0.00 3.73
21 22 4.821805 AGAATGCATTATACCTGGGTTTCG 59.178 41.667 12.97 0.00 0.00 3.46
22 23 6.998673 AGTAGAATGCATTATACCTGGGTTTC 59.001 38.462 30.85 11.15 35.63 2.78
23 24 6.911308 AGTAGAATGCATTATACCTGGGTTT 58.089 36.000 30.85 14.71 35.63 3.27
30 31 6.613153 AGAGGGAGTAGAATGCATTATACC 57.387 41.667 30.85 23.60 35.63 2.73
102 105 4.837298 ACCCCCTCCGTAGAAATATAAGAC 59.163 45.833 0.00 0.00 0.00 3.01
271 307 6.386654 TGTTCTTCTTCTTGTTGTTTTGGAC 58.613 36.000 0.00 0.00 0.00 4.02
282 318 7.088589 TCCTTTCTTGTTGTTCTTCTTCTTG 57.911 36.000 0.00 0.00 0.00 3.02
330 383 0.179009 TACGTACCTGGGGATCTCCG 60.179 60.000 7.25 1.55 36.71 4.63
398 451 7.106239 CGGAGGAAGTATATATTTTGGCAGAT 58.894 38.462 0.00 0.00 0.00 2.90
404 457 7.931948 ACAAGGACGGAGGAAGTATATATTTTG 59.068 37.037 0.00 0.00 0.00 2.44
409 462 6.837568 AGAAACAAGGACGGAGGAAGTATATA 59.162 38.462 0.00 0.00 0.00 0.86
417 470 3.194968 GTGATAGAAACAAGGACGGAGGA 59.805 47.826 0.00 0.00 0.00 3.71
437 490 0.250467 CCTTGGGATATCTGGGCGTG 60.250 60.000 2.05 0.00 0.00 5.34
438 491 0.694444 ACCTTGGGATATCTGGGCGT 60.694 55.000 2.05 0.00 0.00 5.68
442 495 6.155049 ACAAAATTGAACCTTGGGATATCTGG 59.845 38.462 2.05 3.30 0.00 3.86
450 503 6.765512 ACACATAAACAAAATTGAACCTTGGG 59.234 34.615 0.00 0.00 0.00 4.12
495 598 5.517411 TCCAACGACAAATATTACGCTACAG 59.483 40.000 0.00 0.00 0.00 2.74
496 599 5.409211 TCCAACGACAAATATTACGCTACA 58.591 37.500 0.00 0.00 0.00 2.74
500 603 3.001939 CCCTCCAACGACAAATATTACGC 59.998 47.826 0.00 0.00 0.00 4.42
501 604 4.435425 TCCCTCCAACGACAAATATTACG 58.565 43.478 0.00 7.66 0.00 3.18
509 612 2.005370 ACTACTCCCTCCAACGACAA 57.995 50.000 0.00 0.00 0.00 3.18
510 613 2.005370 AACTACTCCCTCCAACGACA 57.995 50.000 0.00 0.00 0.00 4.35
512 615 1.897802 GGAAACTACTCCCTCCAACGA 59.102 52.381 0.00 0.00 0.00 3.85
513 616 1.621814 TGGAAACTACTCCCTCCAACG 59.378 52.381 0.00 0.00 35.02 4.10
514 617 3.782656 TTGGAAACTACTCCCTCCAAC 57.217 47.619 0.00 0.00 41.83 3.77
515 618 3.782656 GTTGGAAACTACTCCCTCCAA 57.217 47.619 0.00 0.00 45.32 3.53
623 772 2.542411 GCAGCTACTAATTGCCATGCAC 60.542 50.000 0.00 0.00 38.71 4.57
659 808 8.071368 CCATGTTTCAAAATGAAAATTGTCAGG 58.929 33.333 4.31 3.43 46.53 3.86
696 864 8.826710 CAGATAAATTTACCATGCTTACGAAGA 58.173 33.333 0.00 0.00 0.00 2.87
733 901 2.738846 CTCACATAACGCCCAGATATGC 59.261 50.000 0.00 0.00 38.65 3.14
750 918 6.945072 ACGTCAGATTTTTAGTGTTTCTCAC 58.055 36.000 0.00 0.00 46.46 3.51
768 936 6.422701 TGGTAAATGTTAAAGTCTGACGTCAG 59.577 38.462 34.76 34.76 45.08 3.51
772 940 9.916397 GATTATGGTAAATGTTAAAGTCTGACG 57.084 33.333 1.52 0.00 0.00 4.35
824 992 7.487822 TTAAATTGGAGCAATAATTGGACCA 57.512 32.000 0.00 0.00 32.43 4.02
846 1014 5.015515 TGGTGCCATCATGTTTCTTGATTA 58.984 37.500 0.00 0.00 31.50 1.75
1068 3033 0.616964 AGGAGGAGCTGCAGATGACA 60.617 55.000 20.43 0.00 0.00 3.58
1098 3063 5.287274 CAGTGACAATCTATCTGTGTCGTTC 59.713 44.000 0.00 0.00 43.73 3.95
1230 3198 2.799916 GAGACGACACGACGTGGC 60.800 66.667 29.86 27.19 46.52 5.01
1243 3214 6.251655 TCGACTTGTAAGGTTTAGAGAGAC 57.748 41.667 0.00 0.00 0.00 3.36
1486 3461 3.724732 ATTTGCAGGAAATTGGCCAAT 57.275 38.095 25.73 25.73 29.22 3.16
1503 3478 5.324832 TCTGAAGGTGAGGAGGAAAATTT 57.675 39.130 0.00 0.00 0.00 1.82
1626 3601 5.095490 GCAAACTCACTTGGGATATTTTCG 58.905 41.667 0.00 0.00 0.00 3.46
1628 3603 5.774690 TCTGCAAACTCACTTGGGATATTTT 59.225 36.000 0.00 0.00 0.00 1.82
1743 3718 3.256704 ACTATTGGGACCAAGGTCAAGA 58.743 45.455 20.03 4.95 46.20 3.02
2076 4054 0.035439 AACTTGGTACATGCCCCGAG 60.035 55.000 14.29 14.29 39.30 4.63
2220 4201 0.534652 CCGGAACCACACCCGTAAAA 60.535 55.000 0.00 0.00 43.93 1.52
2247 4228 3.701532 TGCAAAGTTTTAACAGTCCCG 57.298 42.857 0.00 0.00 0.00 5.14
2272 4253 8.198778 GGTGAAGTAGTTTCCTCCTAAATCTAG 58.801 40.741 0.00 0.00 34.77 2.43
2740 4721 5.545063 TGTAGGTTGACAAGAGATGTTGA 57.455 39.130 0.00 0.00 44.12 3.18
2931 4914 2.756840 TCACAGATCTCTTGTGCCTG 57.243 50.000 8.36 0.00 33.93 4.85
2995 4978 9.410556 CCAAAGAAGTAAAACAAATATGACCAG 57.589 33.333 0.00 0.00 0.00 4.00
3042 5025 3.533606 AGTGATGGCAGTGATACAGAC 57.466 47.619 0.00 0.00 0.00 3.51
3061 5044 7.545615 AGAAACTTTTGGAAACTTTGTAGCAAG 59.454 33.333 0.00 0.00 0.00 4.01
3072 5055 7.172532 AGGTTGTTGAAAGAAACTTTTGGAAAC 59.827 33.333 0.00 0.00 0.00 2.78
3094 5077 1.961793 TGTGTTGCTTTCGCTAGGTT 58.038 45.000 0.00 0.00 36.97 3.50
3188 9314 4.636206 AGACTTTTATGGCGACCTCATTTC 59.364 41.667 0.00 0.00 0.00 2.17
3213 9339 3.280295 CGCTCCTCTTGTCTCTAGGTTA 58.720 50.000 0.00 0.00 0.00 2.85
3368 9494 4.393371 GCAGTTTATTCAAGTCACCTCCTC 59.607 45.833 0.00 0.00 0.00 3.71
3375 9501 5.633601 CGAGTGTAGCAGTTTATTCAAGTCA 59.366 40.000 0.00 0.00 0.00 3.41
3382 9508 4.890088 TGGTTCGAGTGTAGCAGTTTATT 58.110 39.130 0.00 0.00 0.00 1.40
3394 9520 0.608130 TCATGGTCCTGGTTCGAGTG 59.392 55.000 0.00 0.00 0.00 3.51
3482 9608 4.894705 TGTTGTGGTGTAAGTACTCCAGTA 59.105 41.667 11.56 3.36 46.73 2.74
3585 9711 1.714541 TGAATCTTGCCAGGCCAAAA 58.285 45.000 9.64 0.00 0.00 2.44
3618 9744 6.162079 ACTTGAGTTACACTGAGATGATGTG 58.838 40.000 0.00 0.00 37.67 3.21
3726 9852 7.496920 TCATTGGTCTACATAGATGCAGAAAAG 59.503 37.037 0.00 0.00 32.35 2.27
3744 9872 6.593072 GCAGTTAATTTTGCTTTCATTGGTC 58.407 36.000 3.24 0.00 37.35 4.02
3782 9910 7.667219 CACCCCTTGCATATTCTACAGATTATT 59.333 37.037 0.00 0.00 0.00 1.40
3924 10052 4.686191 ATCAGGGAAGCTAATCTCTGTG 57.314 45.455 13.76 0.00 46.14 3.66
4108 10237 2.092212 CCCTGATTCCATGTAGCTTGGT 60.092 50.000 2.88 0.00 35.64 3.67
4147 10276 7.069578 GGGTCCTTTCATACAGTACAGAGATTA 59.930 40.741 0.00 0.00 0.00 1.75
4148 10277 6.127026 GGGTCCTTTCATACAGTACAGAGATT 60.127 42.308 0.00 0.00 0.00 2.40
4149 10278 5.364157 GGGTCCTTTCATACAGTACAGAGAT 59.636 44.000 0.00 0.00 0.00 2.75
4150 10279 4.710375 GGGTCCTTTCATACAGTACAGAGA 59.290 45.833 0.00 0.00 0.00 3.10
4151 10280 4.440250 CGGGTCCTTTCATACAGTACAGAG 60.440 50.000 0.00 0.00 0.00 3.35
4152 10281 3.446161 CGGGTCCTTTCATACAGTACAGA 59.554 47.826 0.00 0.00 0.00 3.41
4153 10282 3.430374 CCGGGTCCTTTCATACAGTACAG 60.430 52.174 0.00 0.00 0.00 2.74
4154 10283 2.498481 CCGGGTCCTTTCATACAGTACA 59.502 50.000 0.00 0.00 0.00 2.90
4155 10284 2.762327 TCCGGGTCCTTTCATACAGTAC 59.238 50.000 0.00 0.00 0.00 2.73
4156 10285 3.104519 TCCGGGTCCTTTCATACAGTA 57.895 47.619 0.00 0.00 0.00 2.74
4157 10286 1.946984 TCCGGGTCCTTTCATACAGT 58.053 50.000 0.00 0.00 0.00 3.55
4158 10287 3.560636 AATCCGGGTCCTTTCATACAG 57.439 47.619 0.00 0.00 0.00 2.74
4159 10288 3.371166 GGAAATCCGGGTCCTTTCATACA 60.371 47.826 0.00 0.00 31.91 2.29
4160 10289 3.211865 GGAAATCCGGGTCCTTTCATAC 58.788 50.000 0.00 0.00 31.91 2.39
4161 10290 2.173996 GGGAAATCCGGGTCCTTTCATA 59.826 50.000 16.31 0.00 36.71 2.15
4162 10291 1.063942 GGGAAATCCGGGTCCTTTCAT 60.064 52.381 16.31 0.00 36.71 2.57
4163 10292 0.330267 GGGAAATCCGGGTCCTTTCA 59.670 55.000 16.31 0.00 36.71 2.69
4164 10293 0.330267 TGGGAAATCCGGGTCCTTTC 59.670 55.000 16.31 12.87 38.76 2.62
4165 10294 0.781278 TTGGGAAATCCGGGTCCTTT 59.219 50.000 16.31 5.97 38.76 3.11
4166 10295 0.781278 TTTGGGAAATCCGGGTCCTT 59.219 50.000 16.31 0.00 38.76 3.36
4167 10296 0.331616 CTTTGGGAAATCCGGGTCCT 59.668 55.000 16.31 0.00 38.76 3.85
4168 10297 0.039180 ACTTTGGGAAATCCGGGTCC 59.961 55.000 0.00 6.39 38.76 4.46
4169 10298 1.919240 AACTTTGGGAAATCCGGGTC 58.081 50.000 0.00 0.00 38.76 4.46
4170 10299 2.158370 AGAAACTTTGGGAAATCCGGGT 60.158 45.455 0.00 0.00 38.76 5.28
4171 10300 2.525368 AGAAACTTTGGGAAATCCGGG 58.475 47.619 0.00 0.00 38.76 5.73
4172 10301 4.038642 TGAAAGAAACTTTGGGAAATCCGG 59.961 41.667 0.00 0.00 38.76 5.14
4173 10302 5.195001 TGAAAGAAACTTTGGGAAATCCG 57.805 39.130 1.41 0.00 38.76 4.18
4174 10303 5.462068 CGTTGAAAGAAACTTTGGGAAATCC 59.538 40.000 1.41 0.00 0.00 3.01
4175 10304 6.198403 GTCGTTGAAAGAAACTTTGGGAAATC 59.802 38.462 1.41 0.00 0.00 2.17
4204 10333 4.505808 TGAAATGCTAACGTAAATCCGGA 58.494 39.130 6.61 6.61 0.00 5.14
4207 10336 7.745015 TGTTACTGAAATGCTAACGTAAATCC 58.255 34.615 0.00 0.00 0.00 3.01
4208 10337 9.769093 AATGTTACTGAAATGCTAACGTAAATC 57.231 29.630 0.00 0.00 0.00 2.17
4211 10340 8.385111 GCTAATGTTACTGAAATGCTAACGTAA 58.615 33.333 0.00 0.00 0.00 3.18
4212 10341 7.762615 AGCTAATGTTACTGAAATGCTAACGTA 59.237 33.333 0.00 0.00 0.00 3.57
4215 10344 8.336080 GGTAGCTAATGTTACTGAAATGCTAAC 58.664 37.037 0.00 0.00 33.26 2.34
4216 10345 8.265055 AGGTAGCTAATGTTACTGAAATGCTAA 58.735 33.333 0.00 0.00 33.26 3.09
4217 10346 7.710907 CAGGTAGCTAATGTTACTGAAATGCTA 59.289 37.037 0.00 0.00 31.73 3.49
4218 10347 6.540189 CAGGTAGCTAATGTTACTGAAATGCT 59.460 38.462 0.00 0.00 31.73 3.79
4220 10349 8.492673 TTCAGGTAGCTAATGTTACTGAAATG 57.507 34.615 14.45 0.00 31.55 2.32
4275 11473 8.664992 TCTGGGTCCTTGCATACATTATATTTA 58.335 33.333 0.00 0.00 0.00 1.40
4276 11474 7.526041 TCTGGGTCCTTGCATACATTATATTT 58.474 34.615 0.00 0.00 0.00 1.40
4277 11475 7.090319 TCTGGGTCCTTGCATACATTATATT 57.910 36.000 0.00 0.00 0.00 1.28
4278 11476 6.702449 TCTGGGTCCTTGCATACATTATAT 57.298 37.500 0.00 0.00 0.00 0.86
4290 11587 3.089284 GGGTTGTAAATCTGGGTCCTTG 58.911 50.000 0.00 0.00 0.00 3.61
4311 11608 3.541632 ACAGTAACACACAGAGGGTTTG 58.458 45.455 0.00 0.00 42.51 2.93
4358 11655 7.878547 TGGTACATGAAAATGCTATTCATCA 57.121 32.000 0.00 5.16 43.72 3.07
4422 11719 2.135139 GCGACAATTGATATGGCTCGA 58.865 47.619 13.59 0.00 0.00 4.04
4426 11723 4.023792 TGAATCAGCGACAATTGATATGGC 60.024 41.667 13.59 2.80 33.09 4.40
4427 11724 5.237996 ACTGAATCAGCGACAATTGATATGG 59.762 40.000 13.59 0.00 34.37 2.74
4433 11730 6.857964 ACTTTTTACTGAATCAGCGACAATTG 59.142 34.615 10.62 3.24 34.37 2.32
4465 11762 8.977505 CGTTCCATAAAAATTGTCACTGATTTT 58.022 29.630 0.00 0.00 37.12 1.82
4466 11763 7.598493 CCGTTCCATAAAAATTGTCACTGATTT 59.402 33.333 0.00 0.00 0.00 2.17
4467 11764 7.040062 TCCGTTCCATAAAAATTGTCACTGATT 60.040 33.333 0.00 0.00 0.00 2.57
4470 11767 6.007936 TCCGTTCCATAAAAATTGTCACTG 57.992 37.500 0.00 0.00 0.00 3.66
4472 11769 5.399013 CCTCCGTTCCATAAAAATTGTCAC 58.601 41.667 0.00 0.00 0.00 3.67
4473 11770 4.461081 CCCTCCGTTCCATAAAAATTGTCA 59.539 41.667 0.00 0.00 0.00 3.58
4474 11771 4.703093 TCCCTCCGTTCCATAAAAATTGTC 59.297 41.667 0.00 0.00 0.00 3.18
4476 11773 4.097892 CCTCCCTCCGTTCCATAAAAATTG 59.902 45.833 0.00 0.00 0.00 2.32
4477 11774 4.278310 CCTCCCTCCGTTCCATAAAAATT 58.722 43.478 0.00 0.00 0.00 1.82
4479 11776 2.619590 GCCTCCCTCCGTTCCATAAAAA 60.620 50.000 0.00 0.00 0.00 1.94
4480 11777 1.064979 GCCTCCCTCCGTTCCATAAAA 60.065 52.381 0.00 0.00 0.00 1.52
4481 11778 0.544697 GCCTCCCTCCGTTCCATAAA 59.455 55.000 0.00 0.00 0.00 1.40
4482 11779 0.619255 TGCCTCCCTCCGTTCCATAA 60.619 55.000 0.00 0.00 0.00 1.90
4483 11780 1.002403 TGCCTCCCTCCGTTCCATA 59.998 57.895 0.00 0.00 0.00 2.74
4484 11781 2.285368 TGCCTCCCTCCGTTCCAT 60.285 61.111 0.00 0.00 0.00 3.41
4485 11782 3.319198 GTGCCTCCCTCCGTTCCA 61.319 66.667 0.00 0.00 0.00 3.53
4486 11783 4.097361 GGTGCCTCCCTCCGTTCC 62.097 72.222 0.00 0.00 0.00 3.62
4495 12169 0.035820 TTGTCAATACGGGTGCCTCC 60.036 55.000 0.00 0.00 0.00 4.30
4496 12170 1.940613 GATTGTCAATACGGGTGCCTC 59.059 52.381 0.00 0.00 0.00 4.70
4504 12178 7.321271 GTCTTTGTCTGTTTGATTGTCAATACG 59.679 37.037 0.00 0.00 36.11 3.06
4508 12182 5.352846 TCGTCTTTGTCTGTTTGATTGTCAA 59.647 36.000 0.00 0.00 34.03 3.18
4533 12207 5.649557 TCAAGTTCTGACAAAAATGTGTGG 58.350 37.500 0.00 0.00 0.00 4.17
4659 12354 4.340666 TCAAACATCAAAGGCACAAAGCTA 59.659 37.500 0.00 0.00 44.79 3.32
4676 12371 1.021202 CGGCAGACCAACTTCAAACA 58.979 50.000 0.00 0.00 34.57 2.83
4687 12382 4.467084 TCAATCCCGCGGCAGACC 62.467 66.667 22.85 0.00 0.00 3.85
4702 12397 1.134431 TCTGTGTTCTTGCTGCAGTCA 60.134 47.619 16.64 11.11 0.00 3.41
4727 12422 7.227873 TGTTCAGAGTGTTTTGGGTGATATTA 58.772 34.615 0.00 0.00 0.00 0.98
4760 12455 4.957296 AGCACGTAGAAATACAATAGGGG 58.043 43.478 0.00 0.00 0.00 4.79
4862 12643 6.019318 ACCACGCACAAGTACGATAATTAATC 60.019 38.462 0.00 0.00 0.00 1.75
4943 12730 1.670811 GAGAGAGAGAGCGGAGAAGTG 59.329 57.143 0.00 0.00 0.00 3.16
4953 12740 3.657015 TTGTTGTGCAGAGAGAGAGAG 57.343 47.619 0.00 0.00 0.00 3.20
4954 12741 4.100035 TCTTTTGTTGTGCAGAGAGAGAGA 59.900 41.667 0.00 0.00 0.00 3.10
4988 12775 1.398958 AAACAACTGCCCGCAATGGT 61.399 50.000 6.97 0.00 35.15 3.55
5013 12800 3.185365 TAACATCTGCGTGCGCCG 61.185 61.111 14.16 9.69 41.09 6.46
5027 12814 4.757149 GCCTCCTCCATATTGATGTGTAAC 59.243 45.833 0.00 0.00 37.35 2.50
5028 12815 4.202461 GGCCTCCTCCATATTGATGTGTAA 60.202 45.833 0.00 0.00 0.00 2.41
5030 12817 2.107204 GGCCTCCTCCATATTGATGTGT 59.893 50.000 0.00 0.00 0.00 3.72
5031 12818 2.553904 GGGCCTCCTCCATATTGATGTG 60.554 54.545 0.84 0.00 0.00 3.21
5032 12819 1.707427 GGGCCTCCTCCATATTGATGT 59.293 52.381 0.84 0.00 0.00 3.06
5033 12820 1.706866 TGGGCCTCCTCCATATTGATG 59.293 52.381 4.53 0.00 0.00 3.07
5034 12821 2.138535 TGGGCCTCCTCCATATTGAT 57.861 50.000 4.53 0.00 0.00 2.57
5035 12822 2.138535 ATGGGCCTCCTCCATATTGA 57.861 50.000 4.53 0.00 42.69 2.57
5036 12823 2.377869 AGAATGGGCCTCCTCCATATTG 59.622 50.000 4.53 0.00 43.61 1.90
5037 12824 2.377869 CAGAATGGGCCTCCTCCATATT 59.622 50.000 4.53 0.00 43.61 1.28
5038 12825 1.991070 CAGAATGGGCCTCCTCCATAT 59.009 52.381 4.53 0.00 43.61 1.78
5039 12826 1.438469 CAGAATGGGCCTCCTCCATA 58.562 55.000 4.53 0.00 43.61 2.74
5040 12827 2.238530 CAGAATGGGCCTCCTCCAT 58.761 57.895 4.53 0.00 46.11 3.41
5041 12828 3.745546 CAGAATGGGCCTCCTCCA 58.254 61.111 4.53 0.00 38.82 3.86
5076 12863 4.053295 CCAAGTGGCAGAAAAGAAACATG 58.947 43.478 0.00 0.00 0.00 3.21
5099 12886 2.380941 TGCTTTCACATGCATGGCTAT 58.619 42.857 29.41 6.68 33.94 2.97
5122 12909 4.818534 ATACCACGTACGTACTACATGG 57.181 45.455 22.34 22.81 0.00 3.66
5123 12910 4.438797 GCAATACCACGTACGTACTACATG 59.561 45.833 22.34 16.01 0.00 3.21
5124 12911 4.096231 TGCAATACCACGTACGTACTACAT 59.904 41.667 22.34 7.40 0.00 2.29
5125 12912 3.438434 TGCAATACCACGTACGTACTACA 59.562 43.478 22.34 10.19 0.00 2.74
5126 12913 4.014847 TGCAATACCACGTACGTACTAC 57.985 45.455 22.34 7.68 0.00 2.73
5127 12914 3.938334 TCTGCAATACCACGTACGTACTA 59.062 43.478 22.34 13.18 0.00 1.82
5128 12915 2.749076 TCTGCAATACCACGTACGTACT 59.251 45.455 22.34 11.28 0.00 2.73
5129 12916 3.135414 TCTGCAATACCACGTACGTAC 57.865 47.619 22.34 15.90 0.00 3.67


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

AutoCloner maintained by Alex Coulton.