Multiple sequence alignment - TraesCS5B01G351400

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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 TraesCS5B01G351400 chr5B 100.000 3437 0 0 1 3437 531614442 531611006 0.000000e+00 6348.0
1 TraesCS5B01G351400 chr5B 90.488 1987 123 25 840 2810 100039270 100037334 0.000000e+00 2562.0
2 TraesCS5B01G351400 chr5B 85.161 775 74 19 81 848 100040029 100039289 0.000000e+00 756.0
3 TraesCS5B01G351400 chr5B 96.000 50 2 0 2 51 100040078 100040029 7.910000e-12 82.4
4 TraesCS5B01G351400 chr6B 95.317 1986 66 11 1 1973 607125851 607123880 0.000000e+00 3127.0
5 TraesCS5B01G351400 chr6B 95.055 991 38 6 1973 2956 607123716 607122730 0.000000e+00 1548.0
6 TraesCS5B01G351400 chr6B 79.780 727 141 6 879 1602 711333433 711332710 1.090000e-144 523.0
7 TraesCS5B01G351400 chr6B 76.447 743 150 19 862 1594 711360212 711360939 2.500000e-101 379.0
8 TraesCS5B01G351400 chr6B 74.963 683 121 30 1618 2263 711332725 711332056 5.650000e-68 268.0
9 TraesCS5B01G351400 chr6B 74.961 639 112 26 1618 2241 711757168 711757773 2.050000e-62 250.0
10 TraesCS5B01G351400 chr6B 73.832 642 118 30 1618 2220 710682873 710682243 3.480000e-50 209.0
11 TraesCS5B01G351400 chr6B 77.941 204 42 3 628 830 705520825 705520624 1.300000e-24 124.0
12 TraesCS5B01G351400 chr5D 95.825 1892 64 8 840 2726 437530451 437528570 0.000000e+00 3042.0
13 TraesCS5B01G351400 chr5D 96.269 268 9 1 3170 3436 437526233 437525966 4.070000e-119 438.0
14 TraesCS5B01G351400 chr5D 97.541 244 4 2 2714 2956 437526709 437526467 1.910000e-112 416.0
15 TraesCS5B01G351400 chr5D 91.787 207 14 3 645 848 437530682 437530476 5.610000e-73 285.0
16 TraesCS5B01G351400 chr5D 85.161 155 23 0 647 801 24615323 24615169 3.550000e-35 159.0
17 TraesCS5B01G351400 chr5A 90.625 1888 116 26 840 2724 396225408 396223579 0.000000e+00 2449.0
18 TraesCS5B01G351400 chr5A 85.277 523 50 12 2 521 396226331 396225833 6.580000e-142 514.0
19 TraesCS5B01G351400 chr5A 89.262 298 16 8 65 353 552599061 552598771 3.260000e-95 359.0
20 TraesCS5B01G351400 chr6D 78.600 743 145 13 862 1598 465966319 465965585 2.400000e-131 479.0
21 TraesCS5B01G351400 chr6D 81.279 219 33 7 1618 1833 465965596 465965383 1.640000e-38 171.0
22 TraesCS5B01G351400 chr6D 78.641 206 36 7 628 830 462839812 462840012 2.780000e-26 130.0
23 TraesCS5B01G351400 chr6A 78.078 739 148 13 862 1594 612300514 612301244 4.040000e-124 455.0
24 TraesCS5B01G351400 chr6A 80.788 203 34 4 629 830 612109057 612108859 1.650000e-33 154.0
25 TraesCS5B01G351400 chr6A 81.218 197 32 5 1618 1811 612301237 612301431 1.650000e-33 154.0


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 TraesCS5B01G351400 chr5B 531611006 531614442 3436 True 6348.000000 6348 100.000000 1 3437 1 chr5B.!!$R1 3436
1 TraesCS5B01G351400 chr5B 100037334 100040078 2744 True 1133.466667 2562 90.549667 2 2810 3 chr5B.!!$R2 2808
2 TraesCS5B01G351400 chr6B 607122730 607125851 3121 True 2337.500000 3127 95.186000 1 2956 2 chr6B.!!$R3 2955
3 TraesCS5B01G351400 chr6B 711332056 711333433 1377 True 395.500000 523 77.371500 879 2263 2 chr6B.!!$R4 1384
4 TraesCS5B01G351400 chr6B 711360212 711360939 727 False 379.000000 379 76.447000 862 1594 1 chr6B.!!$F1 732
5 TraesCS5B01G351400 chr6B 711757168 711757773 605 False 250.000000 250 74.961000 1618 2241 1 chr6B.!!$F2 623
6 TraesCS5B01G351400 chr6B 710682243 710682873 630 True 209.000000 209 73.832000 1618 2220 1 chr6B.!!$R2 602
7 TraesCS5B01G351400 chr5D 437525966 437530682 4716 True 1045.250000 3042 95.355500 645 3436 4 chr5D.!!$R2 2791
8 TraesCS5B01G351400 chr5A 396223579 396226331 2752 True 1481.500000 2449 87.951000 2 2724 2 chr5A.!!$R2 2722
9 TraesCS5B01G351400 chr6D 465965383 465966319 936 True 325.000000 479 79.939500 862 1833 2 chr6D.!!$R1 971
10 TraesCS5B01G351400 chr6A 612300514 612301431 917 False 304.500000 455 79.648000 862 1811 2 chr6A.!!$F1 949

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
643 749 0.584396 CGTTTTTGCGACTGGTGCTA 59.416 50.000 0.0 0.0 0.0 3.49 F
1558 1704 1.837439 AGGTAAGTCGGGATGATTGCA 59.163 47.619 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2630 1.134699 CCTTCAGATTCACCGCTGCTA 60.135 52.381 0.00 0.0 32.27 3.49 R
2658 3088 0.036105 ATGCGCTCATCACCAAGACA 60.036 50.000 9.73 0.0 0.00 3.41 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
108 109 1.742768 CTAGACGGGAGCCATGGAC 59.257 63.158 18.40 8.46 0.00 4.02
177 180 5.612351 AGACACTTCTTCCTCTAAAACCAC 58.388 41.667 0.00 0.00 0.00 4.16
188 191 5.646360 TCCTCTAAAACCACGGATCAAAATC 59.354 40.000 0.00 0.00 0.00 2.17
203 206 3.571828 TCAAAATCCAATCTTTCACGCCA 59.428 39.130 0.00 0.00 0.00 5.69
214 217 7.354257 CAATCTTTCACGCCAAATCAAAATTT 58.646 30.769 0.00 0.00 35.43 1.82
268 272 9.997482 TTCGATGCAGTAAAATAAAATAGAACC 57.003 29.630 0.00 0.00 0.00 3.62
270 274 9.950680 CGATGCAGTAAAATAAAATAGAACCAT 57.049 29.630 0.00 0.00 0.00 3.55
369 385 2.212752 ATCTTAGGGGAGCCATGGAA 57.787 50.000 18.40 0.00 0.00 3.53
386 407 4.008074 TGGAAGTGAGTTCATTGTCCTC 57.992 45.455 2.06 0.00 36.82 3.71
412 433 1.674221 GCATCTAGCTAGGCCCATTCG 60.674 57.143 20.58 2.35 41.15 3.34
469 490 9.408648 AGGGGAAAGTTATATATCAAGTTTGTG 57.591 33.333 7.27 0.00 30.55 3.33
540 646 9.393249 CAAAATAGCTTCTTTCACGATTACAAA 57.607 29.630 0.00 0.00 0.00 2.83
642 748 1.355210 CGTTTTTGCGACTGGTGCT 59.645 52.632 0.00 0.00 0.00 4.40
643 749 0.584396 CGTTTTTGCGACTGGTGCTA 59.416 50.000 0.00 0.00 0.00 3.49
669 775 3.138304 CAACTCTGATTTGTTCCCGTGA 58.862 45.455 0.03 0.00 0.00 4.35
689 795 2.721090 GACAAATGCAGAAAGTCAACGC 59.279 45.455 0.00 0.00 0.00 4.84
834 943 3.323979 TCCCTCGACTTATCATAAAGCCC 59.676 47.826 0.00 0.00 0.00 5.19
1382 1526 2.551887 CAACGTTCACATGTTGGATGGA 59.448 45.455 0.00 0.00 43.63 3.41
1558 1704 1.837439 AGGTAAGTCGGGATGATTGCA 59.163 47.619 0.00 0.00 0.00 4.08
1598 1745 9.647918 ACTTGTTCTCTACTCATCCTATTATGA 57.352 33.333 0.00 0.00 34.72 2.15
1833 1992 9.463443 CTTACCTAAATCCACTTGTTCTTTTTG 57.537 33.333 0.00 0.00 0.00 2.44
1876 2061 2.229302 ACGTCACCTAGAGCTTGTTCTC 59.771 50.000 0.00 0.00 0.00 2.87
2204 2630 3.118629 AGTTATGTCAGGCGTGTCATGAT 60.119 43.478 23.32 10.34 37.84 2.45
2413 2839 1.676635 GCTGACCATGCTGCAAGGA 60.677 57.895 28.63 7.95 40.11 3.36
2554 2982 3.648067 TCAGAAGTCAGAACCACTTGGAT 59.352 43.478 1.14 0.00 34.10 3.41
2956 5266 5.142635 TGAAATATGCGACACAATCTTCG 57.857 39.130 0.00 0.00 38.31 3.79
2958 5268 5.350091 TGAAATATGCGACACAATCTTCGAA 59.650 36.000 0.00 0.00 37.43 3.71
2959 5269 5.395325 AATATGCGACACAATCTTCGAAG 57.605 39.130 19.35 19.35 37.43 3.79
2960 5270 1.428448 TGCGACACAATCTTCGAAGG 58.572 50.000 24.37 11.47 37.43 3.46
2961 5271 1.270094 TGCGACACAATCTTCGAAGGT 60.270 47.619 24.37 15.92 37.43 3.50
2962 5272 1.390463 GCGACACAATCTTCGAAGGTC 59.610 52.381 24.37 19.99 37.43 3.85
2963 5273 1.993370 CGACACAATCTTCGAAGGTCC 59.007 52.381 24.37 8.19 37.43 4.46
2965 5275 2.996621 GACACAATCTTCGAAGGTCCTG 59.003 50.000 24.37 15.93 0.00 3.86
2966 5276 2.368875 ACACAATCTTCGAAGGTCCTGT 59.631 45.455 24.37 16.58 0.00 4.00
2967 5277 3.181454 ACACAATCTTCGAAGGTCCTGTT 60.181 43.478 24.37 8.29 0.00 3.16
2968 5278 4.039973 ACACAATCTTCGAAGGTCCTGTTA 59.960 41.667 24.37 3.32 0.00 2.41
2969 5279 4.389077 CACAATCTTCGAAGGTCCTGTTAC 59.611 45.833 24.37 0.00 0.00 2.50
2970 5280 3.889520 ATCTTCGAAGGTCCTGTTACC 57.110 47.619 24.37 0.00 40.06 2.85
2971 5281 1.542915 TCTTCGAAGGTCCTGTTACCG 59.457 52.381 24.37 0.00 44.77 4.02
2972 5282 1.542915 CTTCGAAGGTCCTGTTACCGA 59.457 52.381 17.70 0.00 44.77 4.69
2973 5283 1.171308 TCGAAGGTCCTGTTACCGAG 58.829 55.000 0.00 0.00 44.77 4.63
2974 5284 0.458025 CGAAGGTCCTGTTACCGAGC 60.458 60.000 0.00 0.00 44.77 5.03
2976 5286 0.834687 AAGGTCCTGTTACCGAGCCA 60.835 55.000 0.00 0.00 44.77 4.75
2977 5287 0.617820 AGGTCCTGTTACCGAGCCAT 60.618 55.000 0.00 0.00 44.77 4.40
2978 5288 0.462047 GGTCCTGTTACCGAGCCATG 60.462 60.000 0.00 0.00 0.00 3.66
2979 5289 0.535335 GTCCTGTTACCGAGCCATGA 59.465 55.000 0.00 0.00 0.00 3.07
2980 5290 0.824109 TCCTGTTACCGAGCCATGAG 59.176 55.000 0.00 0.00 0.00 2.90
2981 5291 0.537188 CCTGTTACCGAGCCATGAGT 59.463 55.000 0.00 0.00 0.00 3.41
2982 5292 1.471676 CCTGTTACCGAGCCATGAGTC 60.472 57.143 0.00 0.00 0.00 3.36
2983 5293 0.172578 TGTTACCGAGCCATGAGTCG 59.827 55.000 9.10 9.10 35.91 4.18
2984 5294 0.454600 GTTACCGAGCCATGAGTCGA 59.545 55.000 15.75 0.00 38.50 4.20
2985 5295 0.454600 TTACCGAGCCATGAGTCGAC 59.545 55.000 7.70 7.70 38.50 4.20
2986 5296 1.712018 TACCGAGCCATGAGTCGACG 61.712 60.000 10.46 0.00 38.50 5.12
2987 5297 2.761195 CCGAGCCATGAGTCGACGA 61.761 63.158 10.46 0.77 38.50 4.20
2988 5298 1.297967 CGAGCCATGAGTCGACGAG 60.298 63.158 10.46 1.29 38.50 4.18
2989 5299 1.587613 GAGCCATGAGTCGACGAGC 60.588 63.158 10.46 9.78 0.00 5.03
2990 5300 2.583593 GCCATGAGTCGACGAGCC 60.584 66.667 10.46 1.74 0.00 4.70
2991 5301 2.885113 CCATGAGTCGACGAGCCA 59.115 61.111 10.46 7.61 0.00 4.75
2992 5302 1.215382 CCATGAGTCGACGAGCCAA 59.785 57.895 10.46 0.00 0.00 4.52
2993 5303 0.803768 CCATGAGTCGACGAGCCAAG 60.804 60.000 10.46 4.50 0.00 3.61
2994 5304 1.153745 ATGAGTCGACGAGCCAAGC 60.154 57.895 10.46 0.00 0.00 4.01
2995 5305 2.507324 GAGTCGACGAGCCAAGCC 60.507 66.667 10.46 0.00 0.00 4.35
2996 5306 3.282745 GAGTCGACGAGCCAAGCCA 62.283 63.158 10.46 0.00 0.00 4.75
2997 5307 2.357034 GTCGACGAGCCAAGCCAA 60.357 61.111 0.00 0.00 0.00 4.52
2998 5308 2.357034 TCGACGAGCCAAGCCAAC 60.357 61.111 0.00 0.00 0.00 3.77
3000 5310 3.056328 GACGAGCCAAGCCAACCC 61.056 66.667 0.00 0.00 0.00 4.11
3001 5311 3.553095 GACGAGCCAAGCCAACCCT 62.553 63.158 0.00 0.00 0.00 4.34
3002 5312 2.747855 CGAGCCAAGCCAACCCTC 60.748 66.667 0.00 0.00 0.00 4.30
3004 5314 2.860971 AGCCAAGCCAACCCTCCT 60.861 61.111 0.00 0.00 0.00 3.69
3005 5315 2.361737 GCCAAGCCAACCCTCCTC 60.362 66.667 0.00 0.00 0.00 3.71
3006 5316 2.356667 CCAAGCCAACCCTCCTCC 59.643 66.667 0.00 0.00 0.00 4.30
3007 5317 2.538141 CCAAGCCAACCCTCCTCCA 61.538 63.158 0.00 0.00 0.00 3.86
3008 5318 1.303643 CAAGCCAACCCTCCTCCAC 60.304 63.158 0.00 0.00 0.00 4.02
3009 5319 2.539081 AAGCCAACCCTCCTCCACC 61.539 63.158 0.00 0.00 0.00 4.61
3010 5320 3.256960 GCCAACCCTCCTCCACCA 61.257 66.667 0.00 0.00 0.00 4.17
3011 5321 2.757077 CCAACCCTCCTCCACCAC 59.243 66.667 0.00 0.00 0.00 4.16
3012 5322 2.153401 CCAACCCTCCTCCACCACA 61.153 63.158 0.00 0.00 0.00 4.17
3014 5324 0.322816 CAACCCTCCTCCACCACATG 60.323 60.000 0.00 0.00 0.00 3.21
3015 5325 2.142292 AACCCTCCTCCACCACATGC 62.142 60.000 0.00 0.00 0.00 4.06
3016 5326 2.304056 CCCTCCTCCACCACATGCT 61.304 63.158 0.00 0.00 0.00 3.79
3017 5327 1.687612 CCTCCTCCACCACATGCTT 59.312 57.895 0.00 0.00 0.00 3.91
3018 5328 0.393537 CCTCCTCCACCACATGCTTC 60.394 60.000 0.00 0.00 0.00 3.86
3019 5329 0.742281 CTCCTCCACCACATGCTTCG 60.742 60.000 0.00 0.00 0.00 3.79
3020 5330 2.401766 CCTCCACCACATGCTTCGC 61.402 63.158 0.00 0.00 0.00 4.70
3021 5331 2.359850 TCCACCACATGCTTCGCC 60.360 61.111 0.00 0.00 0.00 5.54
3022 5332 2.360350 CCACCACATGCTTCGCCT 60.360 61.111 0.00 0.00 0.00 5.52
3023 5333 2.693762 CCACCACATGCTTCGCCTG 61.694 63.158 0.00 0.00 0.00 4.85
3024 5334 3.058160 ACCACATGCTTCGCCTGC 61.058 61.111 0.00 0.00 0.00 4.85
3025 5335 4.170062 CCACATGCTTCGCCTGCG 62.170 66.667 4.92 4.92 41.35 5.18
3026 5336 4.824166 CACATGCTTCGCCTGCGC 62.824 66.667 6.67 0.00 39.59 6.09
3028 5338 3.884350 CATGCTTCGCCTGCGCAT 61.884 61.111 12.24 1.89 44.53 4.73
3030 5340 2.537560 ATGCTTCGCCTGCGCATAC 61.538 57.895 12.24 4.91 42.12 2.39
3031 5341 4.285149 GCTTCGCCTGCGCATACG 62.285 66.667 21.99 21.99 44.07 3.06
3032 5342 2.582226 CTTCGCCTGCGCATACGA 60.582 61.111 25.29 25.29 43.93 3.43
3033 5343 2.860628 CTTCGCCTGCGCATACGAC 61.861 63.158 27.84 9.28 43.93 4.34
3034 5344 4.865761 TCGCCTGCGCATACGACC 62.866 66.667 25.29 5.20 43.93 4.79
3036 5346 4.830765 GCCTGCGCATACGACCCA 62.831 66.667 12.24 0.00 43.93 4.51
3038 5348 2.586079 CTGCGCATACGACCCAGG 60.586 66.667 12.24 0.00 43.93 4.45
3040 5350 2.011741 CTGCGCATACGACCCAGGTA 62.012 60.000 12.24 0.00 43.93 3.08
3041 5351 1.590792 GCGCATACGACCCAGGTAC 60.591 63.158 0.30 0.00 43.93 3.34
3042 5352 1.811195 CGCATACGACCCAGGTACA 59.189 57.895 0.00 0.00 43.93 2.90
3043 5353 0.387929 CGCATACGACCCAGGTACAT 59.612 55.000 0.00 0.00 43.93 2.29
3044 5354 1.865865 GCATACGACCCAGGTACATG 58.134 55.000 0.00 0.00 0.00 3.21
3045 5355 1.138266 GCATACGACCCAGGTACATGT 59.862 52.381 6.79 2.69 0.00 3.21
3046 5356 2.419574 GCATACGACCCAGGTACATGTT 60.420 50.000 2.30 0.00 0.00 2.71
3047 5357 3.869065 CATACGACCCAGGTACATGTTT 58.131 45.455 2.30 0.00 0.00 2.83
3048 5358 2.943036 ACGACCCAGGTACATGTTTT 57.057 45.000 2.30 0.00 0.00 2.43
3050 5360 1.810151 CGACCCAGGTACATGTTTTGG 59.190 52.381 2.30 9.68 0.00 3.28
3051 5361 2.551287 CGACCCAGGTACATGTTTTGGA 60.551 50.000 19.02 0.00 0.00 3.53
3052 5362 3.081804 GACCCAGGTACATGTTTTGGAG 58.918 50.000 19.02 13.28 0.00 3.86
3053 5363 1.818674 CCCAGGTACATGTTTTGGAGC 59.181 52.381 19.02 5.76 36.89 4.70
3055 5365 3.157087 CCAGGTACATGTTTTGGAGCTT 58.843 45.455 2.30 0.00 44.88 3.74
3056 5366 3.573967 CCAGGTACATGTTTTGGAGCTTT 59.426 43.478 2.30 0.00 44.88 3.51
3057 5367 4.039124 CCAGGTACATGTTTTGGAGCTTTT 59.961 41.667 2.30 0.00 44.88 2.27
3059 5369 5.463061 CAGGTACATGTTTTGGAGCTTTTTG 59.537 40.000 2.30 0.00 44.88 2.44
3060 5370 4.749598 GGTACATGTTTTGGAGCTTTTTGG 59.250 41.667 2.30 0.00 33.61 3.28
3061 5371 3.807553 ACATGTTTTGGAGCTTTTTGGG 58.192 40.909 0.00 0.00 0.00 4.12
3062 5372 3.199727 ACATGTTTTGGAGCTTTTTGGGT 59.800 39.130 0.00 0.00 0.00 4.51
3065 5375 3.118811 TGTTTTGGAGCTTTTTGGGTCTG 60.119 43.478 0.00 0.00 34.55 3.51
3066 5376 1.703411 TTGGAGCTTTTTGGGTCTGG 58.297 50.000 0.00 0.00 34.55 3.86
3067 5377 0.850100 TGGAGCTTTTTGGGTCTGGA 59.150 50.000 0.00 0.00 34.55 3.86
3068 5378 1.428912 TGGAGCTTTTTGGGTCTGGAT 59.571 47.619 0.00 0.00 34.55 3.41
3069 5379 2.095461 GGAGCTTTTTGGGTCTGGATC 58.905 52.381 0.00 0.00 34.55 3.36
3070 5380 2.095461 GAGCTTTTTGGGTCTGGATCC 58.905 52.381 4.20 4.20 0.00 3.36
3071 5381 1.713078 AGCTTTTTGGGTCTGGATCCT 59.287 47.619 14.23 0.00 31.21 3.24
3072 5382 2.110721 AGCTTTTTGGGTCTGGATCCTT 59.889 45.455 14.23 0.00 31.21 3.36
3073 5383 2.493675 GCTTTTTGGGTCTGGATCCTTC 59.506 50.000 14.23 3.17 31.21 3.46
3074 5384 3.766545 CTTTTTGGGTCTGGATCCTTCA 58.233 45.455 14.23 1.36 31.21 3.02
3076 5386 1.741028 TTGGGTCTGGATCCTTCACA 58.259 50.000 14.23 7.72 31.21 3.58
3077 5387 1.279496 TGGGTCTGGATCCTTCACAG 58.721 55.000 14.23 1.02 31.21 3.66
3078 5388 1.280457 GGGTCTGGATCCTTCACAGT 58.720 55.000 14.23 0.00 34.02 3.55
3079 5389 1.065854 GGGTCTGGATCCTTCACAGTG 60.066 57.143 14.23 0.00 34.02 3.66
3080 5390 1.065854 GGTCTGGATCCTTCACAGTGG 60.066 57.143 14.23 0.00 34.02 4.00
3081 5391 1.902508 GTCTGGATCCTTCACAGTGGA 59.097 52.381 14.23 0.00 36.72 4.02
3082 5392 2.503356 GTCTGGATCCTTCACAGTGGAT 59.497 50.000 14.23 0.00 44.91 3.41
3087 5397 2.479566 TCCTTCACAGTGGATCAAGC 57.520 50.000 0.00 0.00 0.00 4.01
3088 5398 1.081892 CCTTCACAGTGGATCAAGCG 58.918 55.000 0.00 0.00 0.00 4.68
3089 5399 1.609061 CCTTCACAGTGGATCAAGCGT 60.609 52.381 0.00 0.00 0.00 5.07
3090 5400 1.462283 CTTCACAGTGGATCAAGCGTG 59.538 52.381 0.00 0.00 0.00 5.34
3091 5401 0.320683 TCACAGTGGATCAAGCGTGG 60.321 55.000 0.00 0.00 0.00 4.94
3095 5405 4.015406 TGGATCAAGCGTGGCCGT 62.015 61.111 0.00 0.00 36.15 5.68
3097 5407 1.448893 GGATCAAGCGTGGCCGTAA 60.449 57.895 0.00 0.00 36.15 3.18
3101 5411 2.096220 TCAAGCGTGGCCGTAATTAA 57.904 45.000 0.00 0.00 36.15 1.40
3104 5414 0.107848 AGCGTGGCCGTAATTAAGCT 60.108 50.000 0.00 0.00 36.15 3.74
3105 5415 0.027586 GCGTGGCCGTAATTAAGCTG 59.972 55.000 0.00 2.06 36.15 4.24
3107 5417 1.326548 CGTGGCCGTAATTAAGCTGTC 59.673 52.381 0.00 0.00 0.00 3.51
3111 5421 3.189702 TGGCCGTAATTAAGCTGTCAAAC 59.810 43.478 0.00 0.00 0.00 2.93
3112 5422 3.439129 GGCCGTAATTAAGCTGTCAAACT 59.561 43.478 8.26 0.00 0.00 2.66
3114 5424 4.083484 GCCGTAATTAAGCTGTCAAACTGT 60.083 41.667 0.00 0.00 0.00 3.55
3115 5425 5.562113 GCCGTAATTAAGCTGTCAAACTGTT 60.562 40.000 0.00 0.00 0.00 3.16
3116 5426 5.851177 CCGTAATTAAGCTGTCAAACTGTTG 59.149 40.000 0.00 0.00 35.95 3.33
3118 5428 5.520376 AATTAAGCTGTCAAACTGTTGCT 57.480 34.783 0.00 0.00 34.50 3.91
3119 5429 4.981806 TTAAGCTGTCAAACTGTTGCTT 57.018 36.364 16.10 16.10 42.36 3.91
3120 5430 6.633500 ATTAAGCTGTCAAACTGTTGCTTA 57.367 33.333 14.53 14.53 40.55 3.09
3121 5431 4.558538 AAGCTGTCAAACTGTTGCTTAG 57.441 40.909 11.81 3.01 38.71 2.18
3122 5432 3.545703 AGCTGTCAAACTGTTGCTTAGT 58.454 40.909 0.00 0.00 34.50 2.24
3123 5433 4.703897 AGCTGTCAAACTGTTGCTTAGTA 58.296 39.130 0.00 0.00 34.50 1.82
3124 5434 4.752101 AGCTGTCAAACTGTTGCTTAGTAG 59.248 41.667 0.00 0.00 34.50 2.57
3138 5448 5.330271 GCTTAGTAGCCAAATACATGACG 57.670 43.478 0.00 0.00 41.74 4.35
3139 5449 4.211374 GCTTAGTAGCCAAATACATGACGG 59.789 45.833 0.00 0.00 41.74 4.79
3140 5450 5.597806 CTTAGTAGCCAAATACATGACGGA 58.402 41.667 0.00 0.00 0.00 4.69
3141 5451 3.793559 AGTAGCCAAATACATGACGGAC 58.206 45.455 0.00 0.00 0.00 4.79
3142 5452 2.779755 AGCCAAATACATGACGGACA 57.220 45.000 0.00 0.00 0.00 4.02
3143 5453 3.066291 AGCCAAATACATGACGGACAA 57.934 42.857 0.00 0.00 0.00 3.18
3144 5454 3.009723 AGCCAAATACATGACGGACAAG 58.990 45.455 0.00 0.00 0.00 3.16
3145 5455 3.006940 GCCAAATACATGACGGACAAGA 58.993 45.455 0.00 0.00 0.00 3.02
3146 5456 3.627577 GCCAAATACATGACGGACAAGAT 59.372 43.478 0.00 0.00 0.00 2.40
3152 5462 8.830580 CAAATACATGACGGACAAGATTAGAAT 58.169 33.333 0.00 0.00 0.00 2.40
3153 5463 8.964476 AATACATGACGGACAAGATTAGAATT 57.036 30.769 0.00 0.00 0.00 2.17
3154 5464 8.964476 ATACATGACGGACAAGATTAGAATTT 57.036 30.769 0.00 0.00 0.00 1.82
3156 5466 8.425577 ACATGACGGACAAGATTAGAATTTAG 57.574 34.615 0.00 0.00 0.00 1.85
3157 5467 8.258007 ACATGACGGACAAGATTAGAATTTAGA 58.742 33.333 0.00 0.00 0.00 2.10
3158 5468 9.098355 CATGACGGACAAGATTAGAATTTAGAA 57.902 33.333 0.00 0.00 0.00 2.10
3159 5469 8.703604 TGACGGACAAGATTAGAATTTAGAAG 57.296 34.615 0.00 0.00 0.00 2.85
3160 5470 7.277981 TGACGGACAAGATTAGAATTTAGAAGC 59.722 37.037 0.00 0.00 0.00 3.86
3161 5471 7.103641 ACGGACAAGATTAGAATTTAGAAGCA 58.896 34.615 0.00 0.00 0.00 3.91
3162 5472 7.064728 ACGGACAAGATTAGAATTTAGAAGCAC 59.935 37.037 0.00 0.00 0.00 4.40
3163 5473 7.402640 GGACAAGATTAGAATTTAGAAGCACG 58.597 38.462 0.00 0.00 0.00 5.34
3164 5474 7.277981 GGACAAGATTAGAATTTAGAAGCACGA 59.722 37.037 0.00 0.00 0.00 4.35
3166 5476 9.817809 ACAAGATTAGAATTTAGAAGCACGATA 57.182 29.630 0.00 0.00 0.00 2.92
3204 5534 8.140112 ACTAAATTGACTCTGATACCTTCACT 57.860 34.615 0.00 0.00 0.00 3.41
3225 5555 2.110213 TGACAACACCTCCACCGC 59.890 61.111 0.00 0.00 0.00 5.68
3247 5577 3.253188 CCAAGGACACATAAACCACACAG 59.747 47.826 0.00 0.00 0.00 3.66
3255 5585 6.593807 ACACATAAACCACACAGTTAAGGTA 58.406 36.000 0.00 0.00 33.15 3.08
3276 5606 6.978659 AGGTATGACTATGTATGTGAAACGTG 59.021 38.462 0.00 0.00 42.39 4.49
3298 5629 6.253727 CGTGGTTCTTTACTCTATGACACATC 59.746 42.308 0.00 0.00 0.00 3.06
3378 5709 3.308323 CGTAATTCTTCTTGCCTCTCAGC 59.692 47.826 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 2.232452 AGGAGATGACAAGGAACTCACG 59.768 50.000 0.00 0.00 38.49 4.35
177 180 5.030295 CGTGAAAGATTGGATTTTGATCCG 58.970 41.667 1.37 0.00 43.62 4.18
188 191 3.574284 TGATTTGGCGTGAAAGATTGG 57.426 42.857 0.00 0.00 0.00 3.16
200 203 6.347969 GCTGGAAGAAGAAATTTTGATTTGGC 60.348 38.462 0.00 0.00 34.07 4.52
203 206 9.428097 GTATGCTGGAAGAAGAAATTTTGATTT 57.572 29.630 0.00 0.00 34.07 2.17
246 250 9.533253 GCATGGTTCTATTTTATTTTACTGCAT 57.467 29.630 0.00 0.00 0.00 3.96
267 271 4.754372 AAAGATATACGTGCATGCATGG 57.246 40.909 36.26 26.75 37.27 3.66
268 272 6.578545 GGTTAAAAGATATACGTGCATGCATG 59.421 38.462 33.18 33.18 38.78 4.06
270 274 5.820423 AGGTTAAAAGATATACGTGCATGCA 59.180 36.000 18.46 18.46 0.00 3.96
369 385 2.894126 ACGAGAGGACAATGAACTCACT 59.106 45.455 10.38 0.00 33.76 3.41
386 407 1.604185 GGCCTAGCTAGATGCAACGAG 60.604 57.143 22.70 3.00 45.94 4.18
444 465 9.185680 ACACAAACTTGATATATAACTTTCCCC 57.814 33.333 0.00 0.00 0.00 4.81
666 772 3.725740 CGTTGACTTTCTGCATTTGTCAC 59.274 43.478 10.18 6.62 37.38 3.67
669 775 2.098934 TGCGTTGACTTTCTGCATTTGT 59.901 40.909 0.00 0.00 0.00 2.83
689 795 4.213694 GCAAGGTGCTGATTCTATCATCTG 59.786 45.833 0.00 0.00 40.96 2.90
834 943 0.679002 CCAAGTCACCATCAGGCTGG 60.679 60.000 15.73 1.55 42.35 4.85
1382 1526 5.209818 TGACAGTGGTAGTTCTTCGAAAT 57.790 39.130 0.00 0.00 0.00 2.17
1558 1704 2.561478 ACAAGTGAAGCCGGTACAAT 57.439 45.000 1.90 0.00 0.00 2.71
1598 1745 9.692325 ATATGATGTTCTTTAAAAAGGAGAGCT 57.308 29.630 2.77 0.00 36.67 4.09
1616 1766 8.087136 TGCAACAACAAACACATAATATGATGT 58.913 29.630 7.33 0.00 40.78 3.06
1634 1786 3.451141 TGAACCCAAATCTGCAACAAC 57.549 42.857 0.00 0.00 0.00 3.32
1833 1992 5.290386 GTCATGTAGCAGAGTAACCCATAC 58.710 45.833 0.00 0.00 34.52 2.39
1876 2061 7.976175 AGCAACTCCTCAAACTAAAAAGAAAAG 59.024 33.333 0.00 0.00 0.00 2.27
1995 2402 7.093068 TGCATTCCAACCATATATAGGACGTAT 60.093 37.037 0.00 0.00 0.00 3.06
1998 2405 5.487433 TGCATTCCAACCATATATAGGACG 58.513 41.667 0.00 0.00 0.00 4.79
2204 2630 1.134699 CCTTCAGATTCACCGCTGCTA 60.135 52.381 0.00 0.00 32.27 3.49
2655 3085 1.063174 GCGCTCATCACCAAGACAATC 59.937 52.381 0.00 0.00 0.00 2.67
2658 3088 0.036105 ATGCGCTCATCACCAAGACA 60.036 50.000 9.73 0.00 0.00 3.41
2805 5114 4.590850 AGCCAGGACAAAACTTCATTTC 57.409 40.909 0.00 0.00 0.00 2.17
2956 5266 0.108281 GGCTCGGTAACAGGACCTTC 60.108 60.000 0.00 0.00 37.34 3.46
2958 5268 0.617820 ATGGCTCGGTAACAGGACCT 60.618 55.000 0.00 0.00 37.34 3.85
2959 5269 0.462047 CATGGCTCGGTAACAGGACC 60.462 60.000 0.00 0.00 36.00 4.46
2960 5270 0.535335 TCATGGCTCGGTAACAGGAC 59.465 55.000 0.00 0.00 0.00 3.85
2961 5271 0.824109 CTCATGGCTCGGTAACAGGA 59.176 55.000 0.00 0.00 0.00 3.86
2962 5272 0.537188 ACTCATGGCTCGGTAACAGG 59.463 55.000 0.00 0.00 0.00 4.00
2963 5273 1.799181 CGACTCATGGCTCGGTAACAG 60.799 57.143 0.00 0.00 0.00 3.16
2965 5275 0.454600 TCGACTCATGGCTCGGTAAC 59.545 55.000 11.51 0.00 0.00 2.50
2966 5276 0.454600 GTCGACTCATGGCTCGGTAA 59.545 55.000 8.70 0.00 0.00 2.85
2967 5277 1.712018 CGTCGACTCATGGCTCGGTA 61.712 60.000 14.70 0.00 0.00 4.02
2968 5278 2.885861 GTCGACTCATGGCTCGGT 59.114 61.111 8.70 0.00 0.00 4.69
2969 5279 2.278206 CGTCGACTCATGGCTCGG 60.278 66.667 14.70 0.00 0.00 4.63
2970 5280 1.297967 CTCGTCGACTCATGGCTCG 60.298 63.158 14.70 6.61 0.00 5.03
2971 5281 1.587613 GCTCGTCGACTCATGGCTC 60.588 63.158 14.70 0.00 0.00 4.70
2972 5282 2.492090 GCTCGTCGACTCATGGCT 59.508 61.111 14.70 0.00 0.00 4.75
2973 5283 2.583593 GGCTCGTCGACTCATGGC 60.584 66.667 14.70 9.08 0.00 4.40
2974 5284 0.803768 CTTGGCTCGTCGACTCATGG 60.804 60.000 14.70 0.00 0.00 3.66
2976 5286 1.153745 GCTTGGCTCGTCGACTCAT 60.154 57.895 14.70 0.00 0.00 2.90
2977 5287 2.258591 GCTTGGCTCGTCGACTCA 59.741 61.111 14.70 3.96 0.00 3.41
2978 5288 2.507324 GGCTTGGCTCGTCGACTC 60.507 66.667 14.70 2.42 0.00 3.36
2979 5289 2.867855 TTGGCTTGGCTCGTCGACT 61.868 57.895 14.70 0.00 0.00 4.18
2980 5290 2.357034 TTGGCTTGGCTCGTCGAC 60.357 61.111 5.18 5.18 0.00 4.20
2981 5291 2.357034 GTTGGCTTGGCTCGTCGA 60.357 61.111 0.00 0.00 0.00 4.20
2982 5292 3.423154 GGTTGGCTTGGCTCGTCG 61.423 66.667 0.00 0.00 0.00 5.12
2983 5293 3.056328 GGGTTGGCTTGGCTCGTC 61.056 66.667 0.00 0.00 0.00 4.20
2984 5294 3.553095 GAGGGTTGGCTTGGCTCGT 62.553 63.158 0.00 0.00 0.00 4.18
2985 5295 2.747855 GAGGGTTGGCTTGGCTCG 60.748 66.667 0.00 0.00 0.00 5.03
2986 5296 2.361737 GGAGGGTTGGCTTGGCTC 60.362 66.667 0.00 0.00 0.00 4.70
2987 5297 2.860971 AGGAGGGTTGGCTTGGCT 60.861 61.111 0.00 0.00 0.00 4.75
2988 5298 2.361737 GAGGAGGGTTGGCTTGGC 60.362 66.667 0.00 0.00 0.00 4.52
2989 5299 2.356667 GGAGGAGGGTTGGCTTGG 59.643 66.667 0.00 0.00 0.00 3.61
2990 5300 1.303643 GTGGAGGAGGGTTGGCTTG 60.304 63.158 0.00 0.00 0.00 4.01
2991 5301 2.539081 GGTGGAGGAGGGTTGGCTT 61.539 63.158 0.00 0.00 0.00 4.35
2992 5302 2.936032 GGTGGAGGAGGGTTGGCT 60.936 66.667 0.00 0.00 0.00 4.75
2993 5303 3.256960 TGGTGGAGGAGGGTTGGC 61.257 66.667 0.00 0.00 0.00 4.52
2994 5304 1.500783 ATGTGGTGGAGGAGGGTTGG 61.501 60.000 0.00 0.00 0.00 3.77
2995 5305 0.322816 CATGTGGTGGAGGAGGGTTG 60.323 60.000 0.00 0.00 0.00 3.77
2996 5306 2.078452 CATGTGGTGGAGGAGGGTT 58.922 57.895 0.00 0.00 0.00 4.11
2997 5307 2.606587 GCATGTGGTGGAGGAGGGT 61.607 63.158 0.00 0.00 0.00 4.34
2998 5308 1.856539 AAGCATGTGGTGGAGGAGGG 61.857 60.000 0.00 0.00 0.00 4.30
3000 5310 0.742281 CGAAGCATGTGGTGGAGGAG 60.742 60.000 0.00 0.00 0.00 3.69
3001 5311 1.296392 CGAAGCATGTGGTGGAGGA 59.704 57.895 0.00 0.00 0.00 3.71
3002 5312 3.895025 CGAAGCATGTGGTGGAGG 58.105 61.111 0.00 0.00 0.00 4.30
3015 5325 2.582226 TCGTATGCGCAGGCGAAG 60.582 61.111 28.40 12.27 44.10 3.79
3016 5326 2.883730 GTCGTATGCGCAGGCGAA 60.884 61.111 30.85 17.67 44.10 4.70
3017 5327 4.865761 GGTCGTATGCGCAGGCGA 62.866 66.667 27.36 27.36 44.10 5.54
3019 5329 4.830765 TGGGTCGTATGCGCAGGC 62.831 66.667 18.32 10.22 38.14 4.85
3020 5330 2.586079 CTGGGTCGTATGCGCAGG 60.586 66.667 18.32 7.98 41.38 4.85
3021 5331 2.011741 TACCTGGGTCGTATGCGCAG 62.012 60.000 18.32 1.66 43.65 5.18
3022 5332 2.053277 TACCTGGGTCGTATGCGCA 61.053 57.895 14.96 14.96 38.14 6.09
3023 5333 1.590792 GTACCTGGGTCGTATGCGC 60.591 63.158 0.00 0.00 38.14 6.09
3024 5334 0.387929 ATGTACCTGGGTCGTATGCG 59.612 55.000 0.00 0.00 39.92 4.73
3025 5335 1.138266 ACATGTACCTGGGTCGTATGC 59.862 52.381 0.00 0.00 0.00 3.14
3026 5336 3.536956 AACATGTACCTGGGTCGTATG 57.463 47.619 0.00 2.93 0.00 2.39
3027 5337 4.258543 CAAAACATGTACCTGGGTCGTAT 58.741 43.478 0.00 0.00 0.00 3.06
3028 5338 3.557475 CCAAAACATGTACCTGGGTCGTA 60.557 47.826 0.00 0.00 0.00 3.43
3030 5340 1.810151 CCAAAACATGTACCTGGGTCG 59.190 52.381 0.00 0.00 0.00 4.79
3031 5341 3.081804 CTCCAAAACATGTACCTGGGTC 58.918 50.000 16.63 0.00 0.00 4.46
3032 5342 2.817839 GCTCCAAAACATGTACCTGGGT 60.818 50.000 16.63 0.00 0.00 4.51
3033 5343 1.818674 GCTCCAAAACATGTACCTGGG 59.181 52.381 16.63 7.87 0.00 4.45
3034 5344 2.795329 AGCTCCAAAACATGTACCTGG 58.205 47.619 12.47 12.47 0.00 4.45
3036 5346 5.453198 CCAAAAAGCTCCAAAACATGTACCT 60.453 40.000 0.00 0.00 0.00 3.08
3038 5348 4.749598 CCCAAAAAGCTCCAAAACATGTAC 59.250 41.667 0.00 0.00 0.00 2.90
3040 5350 3.199727 ACCCAAAAAGCTCCAAAACATGT 59.800 39.130 0.00 0.00 0.00 3.21
3041 5351 3.807553 ACCCAAAAAGCTCCAAAACATG 58.192 40.909 0.00 0.00 0.00 3.21
3042 5352 3.711190 AGACCCAAAAAGCTCCAAAACAT 59.289 39.130 0.00 0.00 0.00 2.71
3043 5353 3.103742 AGACCCAAAAAGCTCCAAAACA 58.896 40.909 0.00 0.00 0.00 2.83
3044 5354 3.457234 CAGACCCAAAAAGCTCCAAAAC 58.543 45.455 0.00 0.00 0.00 2.43
3045 5355 2.433970 CCAGACCCAAAAAGCTCCAAAA 59.566 45.455 0.00 0.00 0.00 2.44
3046 5356 2.038659 CCAGACCCAAAAAGCTCCAAA 58.961 47.619 0.00 0.00 0.00 3.28
3047 5357 1.216678 TCCAGACCCAAAAAGCTCCAA 59.783 47.619 0.00 0.00 0.00 3.53
3048 5358 0.850100 TCCAGACCCAAAAAGCTCCA 59.150 50.000 0.00 0.00 0.00 3.86
3050 5360 2.095461 GGATCCAGACCCAAAAAGCTC 58.905 52.381 6.95 0.00 0.00 4.09
3051 5361 1.713078 AGGATCCAGACCCAAAAAGCT 59.287 47.619 15.82 0.00 0.00 3.74
3052 5362 2.222227 AGGATCCAGACCCAAAAAGC 57.778 50.000 15.82 0.00 0.00 3.51
3053 5363 3.507622 GTGAAGGATCCAGACCCAAAAAG 59.492 47.826 15.82 0.00 0.00 2.27
3054 5364 3.117322 TGTGAAGGATCCAGACCCAAAAA 60.117 43.478 15.82 0.00 0.00 1.94
3055 5365 2.445145 TGTGAAGGATCCAGACCCAAAA 59.555 45.455 15.82 0.00 0.00 2.44
3056 5366 2.040278 CTGTGAAGGATCCAGACCCAAA 59.960 50.000 15.82 0.00 0.00 3.28
3057 5367 1.630369 CTGTGAAGGATCCAGACCCAA 59.370 52.381 15.82 0.00 0.00 4.12
3059 5369 1.065854 CACTGTGAAGGATCCAGACCC 60.066 57.143 15.82 0.00 31.89 4.46
3060 5370 1.065854 CCACTGTGAAGGATCCAGACC 60.066 57.143 15.82 0.00 31.89 3.85
3061 5371 1.902508 TCCACTGTGAAGGATCCAGAC 59.097 52.381 15.82 7.67 31.89 3.51
3062 5372 2.325661 TCCACTGTGAAGGATCCAGA 57.674 50.000 15.82 0.00 31.89 3.86
3067 5377 2.679059 CGCTTGATCCACTGTGAAGGAT 60.679 50.000 9.86 3.44 46.98 3.24
3068 5378 1.338105 CGCTTGATCCACTGTGAAGGA 60.338 52.381 9.86 0.00 38.50 3.36
3069 5379 1.081892 CGCTTGATCCACTGTGAAGG 58.918 55.000 9.86 0.00 0.00 3.46
3070 5380 1.462283 CACGCTTGATCCACTGTGAAG 59.538 52.381 9.86 6.01 0.00 3.02
3071 5381 1.511850 CACGCTTGATCCACTGTGAA 58.488 50.000 9.86 0.00 0.00 3.18
3072 5382 0.320683 CCACGCTTGATCCACTGTGA 60.321 55.000 9.86 0.00 0.00 3.58
3073 5383 1.915614 GCCACGCTTGATCCACTGTG 61.916 60.000 0.00 0.00 0.00 3.66
3074 5384 1.672356 GCCACGCTTGATCCACTGT 60.672 57.895 0.00 0.00 0.00 3.55
3076 5386 2.045926 GGCCACGCTTGATCCACT 60.046 61.111 0.00 0.00 0.00 4.00
3077 5387 2.845752 TACGGCCACGCTTGATCCAC 62.846 60.000 2.24 0.00 46.04 4.02
3078 5388 2.173758 TTACGGCCACGCTTGATCCA 62.174 55.000 2.24 0.00 46.04 3.41
3079 5389 0.814010 ATTACGGCCACGCTTGATCC 60.814 55.000 2.24 0.00 46.04 3.36
3080 5390 1.014352 AATTACGGCCACGCTTGATC 58.986 50.000 2.24 0.00 46.04 2.92
3081 5391 2.319136 TAATTACGGCCACGCTTGAT 57.681 45.000 2.24 0.00 46.04 2.57
3082 5392 2.004017 CTTAATTACGGCCACGCTTGA 58.996 47.619 2.24 0.00 46.04 3.02
3083 5393 1.531058 GCTTAATTACGGCCACGCTTG 60.531 52.381 2.24 0.00 46.04 4.01
3084 5394 0.730840 GCTTAATTACGGCCACGCTT 59.269 50.000 2.24 0.00 46.04 4.68
3088 5398 2.352388 TGACAGCTTAATTACGGCCAC 58.648 47.619 2.24 1.12 0.00 5.01
3089 5399 2.772077 TGACAGCTTAATTACGGCCA 57.228 45.000 2.24 0.00 0.00 5.36
3090 5400 3.439129 AGTTTGACAGCTTAATTACGGCC 59.561 43.478 0.00 0.00 0.00 6.13
3091 5401 4.083484 ACAGTTTGACAGCTTAATTACGGC 60.083 41.667 0.00 2.42 0.00 5.68
3095 5405 6.633500 AGCAACAGTTTGACAGCTTAATTA 57.367 33.333 0.00 0.00 34.24 1.40
3097 5407 5.520376 AAGCAACAGTTTGACAGCTTAAT 57.480 34.783 6.11 0.00 40.19 1.40
3101 5411 3.545703 ACTAAGCAACAGTTTGACAGCT 58.454 40.909 0.00 0.00 34.24 4.24
3118 5428 5.105269 TGTCCGTCATGTATTTGGCTACTAA 60.105 40.000 0.00 0.00 0.00 2.24
3119 5429 4.403113 TGTCCGTCATGTATTTGGCTACTA 59.597 41.667 0.00 0.00 0.00 1.82
3120 5430 3.196901 TGTCCGTCATGTATTTGGCTACT 59.803 43.478 0.00 0.00 0.00 2.57
3121 5431 3.527533 TGTCCGTCATGTATTTGGCTAC 58.472 45.455 0.00 0.00 0.00 3.58
3122 5432 3.897141 TGTCCGTCATGTATTTGGCTA 57.103 42.857 0.00 0.00 0.00 3.93
3123 5433 2.779755 TGTCCGTCATGTATTTGGCT 57.220 45.000 0.00 0.00 0.00 4.75
3124 5434 3.006940 TCTTGTCCGTCATGTATTTGGC 58.993 45.455 0.00 0.00 0.00 4.52
3125 5435 5.818136 AATCTTGTCCGTCATGTATTTGG 57.182 39.130 0.00 0.00 0.00 3.28
3126 5436 7.770801 TCTAATCTTGTCCGTCATGTATTTG 57.229 36.000 0.00 0.00 0.00 2.32
3127 5437 8.964476 ATTCTAATCTTGTCCGTCATGTATTT 57.036 30.769 0.00 0.00 0.00 1.40
3129 5439 8.964476 AAATTCTAATCTTGTCCGTCATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
3130 5440 9.529325 CTAAATTCTAATCTTGTCCGTCATGTA 57.471 33.333 0.00 0.00 0.00 2.29
3132 5442 8.648557 TCTAAATTCTAATCTTGTCCGTCATG 57.351 34.615 0.00 0.00 0.00 3.07
3133 5443 9.319143 CTTCTAAATTCTAATCTTGTCCGTCAT 57.681 33.333 0.00 0.00 0.00 3.06
3135 5445 7.277981 TGCTTCTAAATTCTAATCTTGTCCGTC 59.722 37.037 0.00 0.00 0.00 4.79
3137 5447 7.402640 GTGCTTCTAAATTCTAATCTTGTCCG 58.597 38.462 0.00 0.00 0.00 4.79
3138 5448 7.277981 TCGTGCTTCTAAATTCTAATCTTGTCC 59.722 37.037 0.00 0.00 0.00 4.02
3139 5449 8.186178 TCGTGCTTCTAAATTCTAATCTTGTC 57.814 34.615 0.00 0.00 0.00 3.18
3140 5450 8.723942 ATCGTGCTTCTAAATTCTAATCTTGT 57.276 30.769 0.00 0.00 0.00 3.16
3143 5453 9.469807 CAGTATCGTGCTTCTAAATTCTAATCT 57.530 33.333 0.00 0.00 0.00 2.40
3144 5454 9.250624 ACAGTATCGTGCTTCTAAATTCTAATC 57.749 33.333 0.00 0.00 0.00 1.75
3145 5455 9.035607 CACAGTATCGTGCTTCTAAATTCTAAT 57.964 33.333 0.00 0.00 0.00 1.73
3146 5456 8.033038 ACACAGTATCGTGCTTCTAAATTCTAA 58.967 33.333 0.00 0.00 40.73 2.10
3152 5462 5.128992 TCACACAGTATCGTGCTTCTAAA 57.871 39.130 0.00 0.00 40.73 1.85
3153 5463 4.776795 TCACACAGTATCGTGCTTCTAA 57.223 40.909 0.00 0.00 40.73 2.10
3154 5464 4.983671 ATCACACAGTATCGTGCTTCTA 57.016 40.909 0.00 0.00 40.73 2.10
3156 5466 3.482472 CGTATCACACAGTATCGTGCTTC 59.518 47.826 0.00 0.00 40.73 3.86
3157 5467 3.128068 TCGTATCACACAGTATCGTGCTT 59.872 43.478 0.00 0.00 40.73 3.91
3158 5468 2.681344 TCGTATCACACAGTATCGTGCT 59.319 45.455 0.00 0.00 40.73 4.40
3159 5469 2.782192 GTCGTATCACACAGTATCGTGC 59.218 50.000 0.00 0.00 40.73 5.34
3160 5470 4.274421 AGTCGTATCACACAGTATCGTG 57.726 45.455 0.00 0.00 42.81 4.35
3161 5471 6.426980 TTTAGTCGTATCACACAGTATCGT 57.573 37.500 0.00 0.00 0.00 3.73
3162 5472 7.642586 TCAATTTAGTCGTATCACACAGTATCG 59.357 37.037 0.00 0.00 0.00 2.92
3163 5473 8.744011 GTCAATTTAGTCGTATCACACAGTATC 58.256 37.037 0.00 0.00 0.00 2.24
3164 5474 8.467598 AGTCAATTTAGTCGTATCACACAGTAT 58.532 33.333 0.00 0.00 0.00 2.12
3166 5476 6.688578 AGTCAATTTAGTCGTATCACACAGT 58.311 36.000 0.00 0.00 0.00 3.55
3167 5477 7.008719 CAGAGTCAATTTAGTCGTATCACACAG 59.991 40.741 0.00 0.00 0.00 3.66
3168 5478 6.806739 CAGAGTCAATTTAGTCGTATCACACA 59.193 38.462 0.00 0.00 0.00 3.72
3204 5534 0.468226 GGTGGAGGTGTTGTCACAGA 59.532 55.000 0.98 0.00 45.45 3.41
3225 5555 3.218453 TGTGTGGTTTATGTGTCCTTGG 58.782 45.455 0.00 0.00 0.00 3.61
3255 5585 5.730550 ACCACGTTTCACATACATAGTCAT 58.269 37.500 0.00 0.00 0.00 3.06
3272 5602 5.010314 TGTGTCATAGAGTAAAGAACCACGT 59.990 40.000 0.00 0.00 0.00 4.49
3276 5606 6.981559 GGAGATGTGTCATAGAGTAAAGAACC 59.018 42.308 0.00 0.00 0.00 3.62
3368 5699 1.346062 AGTTTCAGAGCTGAGAGGCA 58.654 50.000 0.00 0.00 41.13 4.75
3378 5709 6.593382 CCTTGTCTCCAATAGAAGTTTCAGAG 59.407 42.308 0.00 0.00 35.47 3.35


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

AutoCloner maintained by Alex Coulton.