Multiple sequence alignment - TraesCS3A01G256200

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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 TraesCS3A01G256200 chr3A 100.000 3401 0 0 1 3401 478170512 478167112 0.000000e+00 6281
1 TraesCS3A01G256200 chr3A 79.817 986 166 25 1035 2005 477427551 477428518 0.000000e+00 688
2 TraesCS3A01G256200 chr3D 90.684 2587 131 47 476 3004 358505040 358502506 0.000000e+00 3341
3 TraesCS3A01G256200 chr3D 80.508 985 158 28 1035 2005 358176893 358177857 0.000000e+00 725
4 TraesCS3A01G256200 chr3D 86.853 502 35 15 1 475 358507537 358507040 1.800000e-147 532
5 TraesCS3A01G256200 chr3D 81.105 344 33 17 3077 3401 358502380 358502050 2.620000e-61 246
6 TraesCS3A01G256200 chr3B 90.794 1423 86 27 337 1740 464505874 464504478 0.000000e+00 1860
7 TraesCS3A01G256200 chr3B 80.478 1004 144 31 1025 2011 464617060 464616092 0.000000e+00 721
8 TraesCS3A01G256200 chr3B 80.203 985 161 25 1035 2005 462866386 462867350 0.000000e+00 708
9 TraesCS3A01G256200 chr3B 92.068 353 23 1 1 353 464521791 464521444 3.050000e-135 492
10 TraesCS3A01G256200 chr1A 79.900 1000 157 35 1017 1990 545649156 545648175 0.000000e+00 693
11 TraesCS3A01G256200 chr1D 79.719 996 152 39 1017 1983 450462957 450461983 0.000000e+00 675
12 TraesCS3A01G256200 chr1B 79.065 984 170 29 1025 1987 618543015 618543983 0.000000e+00 643
13 TraesCS3A01G256200 chr1B 77.111 983 176 36 1025 1987 618908031 618907078 1.080000e-144 523


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 TraesCS3A01G256200 chr3A 478167112 478170512 3400 True 6281 6281 100.000 1 3401 1 chr3A.!!$R1 3400
1 TraesCS3A01G256200 chr3A 477427551 477428518 967 False 688 688 79.817 1035 2005 1 chr3A.!!$F1 970
2 TraesCS3A01G256200 chr3D 358502050 358507537 5487 True 1373 3341 86.214 1 3401 3 chr3D.!!$R1 3400
3 TraesCS3A01G256200 chr3D 358176893 358177857 964 False 725 725 80.508 1035 2005 1 chr3D.!!$F1 970
4 TraesCS3A01G256200 chr3B 464504478 464505874 1396 True 1860 1860 90.794 337 1740 1 chr3B.!!$R1 1403
5 TraesCS3A01G256200 chr3B 464616092 464617060 968 True 721 721 80.478 1025 2011 1 chr3B.!!$R3 986
6 TraesCS3A01G256200 chr3B 462866386 462867350 964 False 708 708 80.203 1035 2005 1 chr3B.!!$F1 970
7 TraesCS3A01G256200 chr1A 545648175 545649156 981 True 693 693 79.900 1017 1990 1 chr1A.!!$R1 973
8 TraesCS3A01G256200 chr1D 450461983 450462957 974 True 675 675 79.719 1017 1983 1 chr1D.!!$R1 966
9 TraesCS3A01G256200 chr1B 618543015 618543983 968 False 643 643 79.065 1025 1987 1 chr1B.!!$F1 962
10 TraesCS3A01G256200 chr1B 618907078 618908031 953 True 523 523 77.111 1025 1987 1 chr1B.!!$R1 962

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
883 2926 0.034337 ATACACACACACACCCCGAC 59.966 55.0 0.0 0.0 0.00 4.79 F
2052 4151 0.032678 CATCATCGGGCGAAGTAGCT 59.967 55.0 0.0 0.0 37.29 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 4174 0.170339 CTCCACGTATGCAGACACGA 59.830 55.0 20.85 8.24 40.56 4.35 R
3039 5176 0.034896 AAACGCGGATGAACCAGAGT 59.965 50.0 12.47 0.00 38.90 3.24 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
48 49 6.071221 TGCTCATCAACAATTGCCTAAATTCT 60.071 34.615 5.05 0.00 36.28 2.40
54 55 6.640499 TCAACAATTGCCTAAATTCTTTGACG 59.360 34.615 5.05 0.00 36.28 4.35
74 75 5.998981 TGACGTGTACATTAAAATCCTTGGT 59.001 36.000 0.00 0.00 0.00 3.67
89 90 4.724399 TCCTTGGTTGCAGAAGTATTTGA 58.276 39.130 0.00 0.00 0.00 2.69
101 102 9.598517 TGCAGAAGTATTTGAAAACAAAGAAAT 57.401 25.926 0.00 0.00 0.00 2.17
126 127 0.723981 GGCATTCACGAGAGAAGTGC 59.276 55.000 0.00 3.24 39.31 4.40
150 151 8.865090 TGCCATTTAGAAACTCCAAGAAATAAA 58.135 29.630 0.00 0.00 0.00 1.40
161 162 8.218338 ACTCCAAGAAATAAATACATGCTCAG 57.782 34.615 0.00 0.00 0.00 3.35
170 171 8.814038 AATAAATACATGCTCAGGAAAGAACT 57.186 30.769 0.00 0.00 0.00 3.01
201 202 6.007076 TCTGGTATACATGACCAAGCAAAAA 58.993 36.000 5.01 0.00 46.27 1.94
204 205 5.861787 GGTATACATGACCAAGCAAAAACAC 59.138 40.000 5.01 0.00 36.91 3.32
213 214 3.420576 CCAAGCAAAAACACACGATAACG 59.579 43.478 0.00 0.00 45.75 3.18
225 226 3.259064 CACGATAACGGTCAAGGATTGT 58.741 45.455 0.00 0.00 45.01 2.71
256 257 3.055891 TCATCTTGGAGCACGATTTCAGA 60.056 43.478 0.00 0.00 0.00 3.27
302 303 6.705381 CCACTCATGATGATACCTTTCTTCTC 59.295 42.308 0.00 0.00 0.00 2.87
310 311 8.597167 TGATGATACCTTTCTTCTCTTCTTTCA 58.403 33.333 0.00 0.00 0.00 2.69
315 316 7.977789 ACCTTTCTTCTCTTCTTTCATCTTC 57.022 36.000 0.00 0.00 0.00 2.87
396 420 8.730680 ACAGTTAATCTATGGTTTGTGCTTAAG 58.269 33.333 0.00 0.00 0.00 1.85
460 488 1.483424 GCTCGCGATCTTTTCCTCCG 61.483 60.000 10.36 0.00 0.00 4.63
464 492 1.852895 CGCGATCTTTTCCTCCGTAAG 59.147 52.381 0.00 0.00 0.00 2.34
525 2553 1.263484 GCAATGAGAGCATCGACCATG 59.737 52.381 0.00 0.00 42.67 3.66
526 2554 2.830104 CAATGAGAGCATCGACCATGA 58.170 47.619 0.00 0.00 42.67 3.07
527 2555 2.801111 CAATGAGAGCATCGACCATGAG 59.199 50.000 0.00 0.00 42.67 2.90
587 2617 2.101380 GCGCGAGAGAGACAGGAC 59.899 66.667 12.10 0.00 0.00 3.85
595 2625 0.629058 GAGAGACAGGACCTCTCCCT 59.371 60.000 7.05 0.00 46.71 4.20
609 2647 4.748144 CCCTGCCTCCTGCCCAAC 62.748 72.222 0.00 0.00 40.16 3.77
633 2671 1.021390 CGCCGTTTTCCATCTGCTCT 61.021 55.000 0.00 0.00 0.00 4.09
634 2672 0.449388 GCCGTTTTCCATCTGCTCTG 59.551 55.000 0.00 0.00 0.00 3.35
796 2834 1.757574 CACATGCTTTTCACACCACG 58.242 50.000 0.00 0.00 0.00 4.94
873 2916 2.695359 CCCCGCCATATATACACACAC 58.305 52.381 0.00 0.00 0.00 3.82
874 2917 2.037902 CCCCGCCATATATACACACACA 59.962 50.000 0.00 0.00 0.00 3.72
878 2921 3.493129 CGCCATATATACACACACACACC 59.507 47.826 0.00 0.00 0.00 4.16
883 2926 0.034337 ATACACACACACACCCCGAC 59.966 55.000 0.00 0.00 0.00 4.79
995 3058 2.025418 GAACCGAGCGCCGAGAAAA 61.025 57.895 17.96 0.00 41.76 2.29
996 3059 1.956620 GAACCGAGCGCCGAGAAAAG 61.957 60.000 17.96 4.58 41.76 2.27
997 3060 2.126071 CCGAGCGCCGAGAAAAGA 60.126 61.111 17.96 0.00 41.76 2.52
1006 3069 2.742053 CGCCGAGAAAAGAAAATGGAGA 59.258 45.455 0.00 0.00 0.00 3.71
1776 3854 2.819595 CACCCGTTCCTGGCATCG 60.820 66.667 0.00 0.00 0.00 3.84
1900 3993 2.581354 ACGGCATGTCAGAGAGCC 59.419 61.111 0.00 0.00 43.61 4.70
1901 3994 2.202987 CGGCATGTCAGAGAGCCC 60.203 66.667 0.00 0.00 44.18 5.19
1905 3998 2.364842 ATGTCAGAGAGCCCCGCT 60.365 61.111 0.00 0.00 43.88 5.52
1936 4035 0.822532 CAGAGCATTGGCATCCCCTC 60.823 60.000 0.00 0.00 44.61 4.30
1938 4037 2.908940 GCATTGGCATCCCCTCCG 60.909 66.667 0.00 0.00 40.72 4.63
1992 4091 2.202492 ATCGACGTGCTCAGCGAC 60.202 61.111 0.00 0.00 35.44 5.19
2005 4104 3.482783 GCGACAGCCGTGAAGCTC 61.483 66.667 0.00 0.00 42.61 4.09
2037 4136 4.854784 GAGGACGAGCGCGCATCA 62.855 66.667 35.10 0.00 42.48 3.07
2052 4151 0.032678 CATCATCGGGCGAAGTAGCT 59.967 55.000 0.00 0.00 37.29 3.32
2055 4154 0.931005 CATCGGGCGAAGTAGCTTTC 59.069 55.000 0.00 0.00 37.29 2.62
2098 4197 1.136891 TGTCTGCATACGTGGAGGATG 59.863 52.381 0.00 0.00 43.33 3.51
2128 4227 4.154195 GTGTTGGCACTGTAGGATTAACTG 59.846 45.833 0.00 0.00 42.13 3.16
2139 4238 5.358442 TGTAGGATTAACTGCTCTCTCAGTC 59.642 44.000 0.00 0.00 45.77 3.51
2140 4239 4.609301 AGGATTAACTGCTCTCTCAGTCT 58.391 43.478 0.00 0.00 45.77 3.24
2141 4240 4.644685 AGGATTAACTGCTCTCTCAGTCTC 59.355 45.833 0.00 0.00 45.77 3.36
2142 4241 4.400884 GGATTAACTGCTCTCTCAGTCTCA 59.599 45.833 0.00 0.00 45.77 3.27
2143 4242 5.450412 GGATTAACTGCTCTCTCAGTCTCAG 60.450 48.000 0.00 0.00 45.77 3.35
2178 4277 1.449246 CTTCTGCTCGGGCCTCTTG 60.449 63.158 3.94 0.00 37.74 3.02
2204 4303 2.305927 ACCCACCTGTATTTCCTGTGAG 59.694 50.000 0.00 0.00 0.00 3.51
2228 4327 2.229784 GTGCCTTCCTTGATGAAAGTGG 59.770 50.000 0.00 0.00 33.66 4.00
2239 4338 7.890127 TCCTTGATGAAAGTGGAATAACAGAAT 59.110 33.333 0.00 0.00 33.66 2.40
2258 4357 6.199154 ACAGAATCGTTATTGCATCGAACTAG 59.801 38.462 0.00 0.00 37.16 2.57
2259 4358 6.199154 CAGAATCGTTATTGCATCGAACTAGT 59.801 38.462 0.00 0.00 37.16 2.57
2260 4359 7.378728 CAGAATCGTTATTGCATCGAACTAGTA 59.621 37.037 0.00 0.00 37.16 1.82
2261 4360 6.988109 ATCGTTATTGCATCGAACTAGTAC 57.012 37.500 0.00 0.00 37.16 2.73
2264 4363 6.471198 TCGTTATTGCATCGAACTAGTACAAG 59.529 38.462 0.00 0.00 0.00 3.16
2278 4377 6.739664 ACTAGTACAAGTATTACTGTCCCCT 58.260 40.000 0.00 0.00 31.99 4.79
2280 4379 6.541934 AGTACAAGTATTACTGTCCCCTTC 57.458 41.667 0.00 0.00 0.00 3.46
2281 4380 4.838904 ACAAGTATTACTGTCCCCTTCC 57.161 45.455 0.00 0.00 0.00 3.46
2296 4406 0.648441 CTTCCGTGCGCGCTTAATTA 59.352 50.000 33.29 7.72 36.67 1.40
2297 4407 0.370958 TTCCGTGCGCGCTTAATTAC 59.629 50.000 33.29 19.48 36.67 1.89
2367 4477 3.161067 ACTAGAGATATGCACGAGCCAT 58.839 45.455 1.39 0.00 41.13 4.40
2368 4478 3.576118 ACTAGAGATATGCACGAGCCATT 59.424 43.478 1.39 0.00 41.13 3.16
2369 4479 3.482156 AGAGATATGCACGAGCCATTT 57.518 42.857 1.39 0.00 41.13 2.32
2370 4480 3.136763 AGAGATATGCACGAGCCATTTG 58.863 45.455 1.39 0.00 41.13 2.32
2371 4481 2.224606 AGATATGCACGAGCCATTTGG 58.775 47.619 1.39 0.00 41.13 3.28
2379 4489 1.103398 CGAGCCATTTGGGGATCACC 61.103 60.000 7.20 7.20 43.53 4.02
2380 4490 0.259938 GAGCCATTTGGGGATCACCT 59.740 55.000 16.81 0.00 42.87 4.00
2382 4492 0.324645 GCCATTTGGGGATCACCTGT 60.325 55.000 16.81 0.00 40.03 4.00
2428 4544 4.704540 AGCATATGTCTATCTTCTCCTCCG 59.295 45.833 4.29 0.00 0.00 4.63
2447 4563 0.179034 GGTGTCTCATCTCATGGGGC 60.179 60.000 0.00 0.00 35.44 5.80
2448 4564 0.179034 GTGTCTCATCTCATGGGGCC 60.179 60.000 0.00 0.00 33.39 5.80
2449 4565 1.070445 GTCTCATCTCATGGGGCCG 59.930 63.158 0.00 0.00 25.93 6.13
2450 4566 2.142761 TCTCATCTCATGGGGCCGG 61.143 63.158 0.00 0.00 0.00 6.13
2468 4584 1.306296 GCCACCCATGCCTAAAGGA 59.694 57.895 0.00 0.00 37.39 3.36
2479 4595 4.408182 TGCCTAAAGGAGTTGCTAGATC 57.592 45.455 0.00 0.00 37.39 2.75
2481 4597 4.123506 GCCTAAAGGAGTTGCTAGATCAC 58.876 47.826 0.00 0.00 37.39 3.06
2483 4599 2.301577 AAGGAGTTGCTAGATCACGC 57.698 50.000 0.00 0.00 0.00 5.34
2502 4618 0.325671 CTAGAGAAGGCCACTCCCCA 60.326 60.000 21.07 9.93 35.27 4.96
2514 4630 0.608640 ACTCCCCATTCGACACACTC 59.391 55.000 0.00 0.00 0.00 3.51
2517 4633 1.447838 CCCATTCGACACACTCGGG 60.448 63.158 0.00 0.00 43.16 5.14
2518 4634 1.589630 CCATTCGACACACTCGGGA 59.410 57.895 0.00 0.00 43.16 5.14
2519 4635 0.175760 CCATTCGACACACTCGGGAT 59.824 55.000 0.00 0.00 43.16 3.85
2521 4637 1.135112 CATTCGACACACTCGGGATCA 60.135 52.381 0.00 0.00 43.16 2.92
2548 4666 2.229792 CTTTCTTGGCCTGTGCACTTA 58.770 47.619 19.41 0.00 40.13 2.24
2559 4677 2.668457 CTGTGCACTTATCCGTCAGTTC 59.332 50.000 19.41 0.00 0.00 3.01
2609 4728 7.281991 GCAAAAAGCAGACCATAATAAACAG 57.718 36.000 0.00 0.00 44.79 3.16
2650 4769 1.009829 GCCTGATTAGACCGCACTTG 58.990 55.000 0.00 0.00 0.00 3.16
2674 4793 5.197682 TCTAAACGGCCTCTTATCTTAGC 57.802 43.478 0.00 0.00 0.00 3.09
2678 4797 1.663445 CGGCCTCTTATCTTAGCGACG 60.663 57.143 0.00 0.00 0.00 5.12
2684 4803 4.201930 CCTCTTATCTTAGCGACGAACAGT 60.202 45.833 0.00 0.00 0.00 3.55
2726 4845 1.625315 TGTGACACTGGCTGAAGCTAT 59.375 47.619 7.20 0.00 41.70 2.97
2758 4884 0.182299 TTGGGACATATCGCCATGCA 59.818 50.000 0.00 0.00 39.30 3.96
2759 4885 0.534877 TGGGACATATCGCCATGCAC 60.535 55.000 0.00 0.00 36.97 4.57
2760 4886 1.568612 GGGACATATCGCCATGCACG 61.569 60.000 0.00 0.30 0.00 5.34
2761 4887 1.205064 GACATATCGCCATGCACGC 59.795 57.895 0.00 0.00 0.00 5.34
2823 4949 1.738099 CGCCCAGGTGTTCTTCTCG 60.738 63.158 0.00 0.00 0.00 4.04
2827 4953 0.388649 CCAGGTGTTCTTCTCGGACG 60.389 60.000 0.00 0.00 0.00 4.79
2831 4957 0.031721 GTGTTCTTCTCGGACGGTGT 59.968 55.000 0.00 0.00 0.00 4.16
2886 5014 0.042131 ACGTGGAAGTAGGGATGGGA 59.958 55.000 0.00 0.00 0.00 4.37
2918 5046 5.385198 AGCTTGTTCAAATCCTCAAGGTTA 58.615 37.500 0.00 0.00 43.03 2.85
2939 5067 2.736343 CTTACCGTGACACGCGTCCA 62.736 60.000 22.46 7.94 41.85 4.02
2940 5068 3.541093 TACCGTGACACGCGTCCAC 62.541 63.158 22.46 23.72 41.85 4.02
2943 5071 2.624264 GTGACACGCGTCCACAAC 59.376 61.111 26.79 12.19 41.85 3.32
2944 5072 1.881252 GTGACACGCGTCCACAACT 60.881 57.895 26.79 0.00 41.85 3.16
2958 5086 2.064762 CACAACTCTCGGAAAGCTCTG 58.935 52.381 0.00 0.00 0.00 3.35
2959 5087 1.074752 CAACTCTCGGAAAGCTCTGC 58.925 55.000 0.00 0.00 0.00 4.26
2965 5093 1.667830 CGGAAAGCTCTGCCGTGAA 60.668 57.895 12.21 0.00 40.17 3.18
2971 5099 1.081840 GCTCTGCCGTGAAACTTGC 60.082 57.895 0.00 0.00 33.54 4.01
2977 5105 1.852067 GCCGTGAAACTTGCGTCCAT 61.852 55.000 0.00 0.00 31.75 3.41
3003 5140 1.792006 AGATTTTGCAGCTTGCTTGC 58.208 45.000 9.12 9.09 45.31 4.01
3020 5157 2.673523 CCCAAGTGGCAGGAGGAG 59.326 66.667 0.00 0.00 0.00 3.69
3021 5158 2.045536 CCAAGTGGCAGGAGGAGC 60.046 66.667 0.00 0.00 0.00 4.70
3022 5159 2.435586 CAAGTGGCAGGAGGAGCG 60.436 66.667 0.00 0.00 0.00 5.03
3023 5160 2.925170 AAGTGGCAGGAGGAGCGT 60.925 61.111 0.00 0.00 0.00 5.07
3024 5161 3.245668 AAGTGGCAGGAGGAGCGTG 62.246 63.158 0.00 0.00 35.53 5.34
3029 5166 2.898738 CAGGAGGAGCGTGCATCT 59.101 61.111 0.00 0.00 0.00 2.90
3030 5167 2.119009 CAGGAGGAGCGTGCATCTA 58.881 57.895 0.00 0.00 0.00 1.98
3032 5169 0.396417 AGGAGGAGCGTGCATCTACT 60.396 55.000 3.60 3.60 0.00 2.57
3033 5170 1.133761 AGGAGGAGCGTGCATCTACTA 60.134 52.381 3.92 0.00 0.00 1.82
3036 5173 3.139850 GAGGAGCGTGCATCTACTACTA 58.860 50.000 3.92 0.00 0.00 1.82
3037 5174 3.142951 AGGAGCGTGCATCTACTACTAG 58.857 50.000 2.18 0.00 0.00 2.57
3038 5175 2.879646 GGAGCGTGCATCTACTACTAGT 59.120 50.000 0.00 0.00 0.00 2.57
3039 5176 4.063689 GGAGCGTGCATCTACTACTAGTA 58.936 47.826 1.89 1.89 0.00 1.82
3054 5191 2.688958 ACTAGTACTCTGGTTCATCCGC 59.311 50.000 0.00 0.00 39.52 5.54
3055 5192 0.456221 AGTACTCTGGTTCATCCGCG 59.544 55.000 0.00 0.00 39.52 6.46
3059 5196 1.156736 CTCTGGTTCATCCGCGTTTT 58.843 50.000 4.92 0.00 39.52 2.43
3060 5197 1.535462 CTCTGGTTCATCCGCGTTTTT 59.465 47.619 4.92 0.00 39.52 1.94
3061 5198 1.533731 TCTGGTTCATCCGCGTTTTTC 59.466 47.619 4.92 0.00 39.52 2.29
3062 5199 0.236187 TGGTTCATCCGCGTTTTTCG 59.764 50.000 4.92 0.00 43.12 3.46
3063 5200 0.513820 GGTTCATCCGCGTTTTTCGA 59.486 50.000 4.92 0.00 42.86 3.71
3064 5201 1.069771 GGTTCATCCGCGTTTTTCGAA 60.070 47.619 4.92 0.00 42.86 3.71
3065 5202 2.602694 GGTTCATCCGCGTTTTTCGAAA 60.603 45.455 6.47 6.47 42.86 3.46
3066 5203 3.037324 GTTCATCCGCGTTTTTCGAAAA 58.963 40.909 19.08 19.08 42.86 2.29
3067 5204 3.546002 TCATCCGCGTTTTTCGAAAAT 57.454 38.095 23.05 4.56 42.86 1.82
3069 5206 2.759538 TCCGCGTTTTTCGAAAATGT 57.240 40.000 23.05 0.00 42.86 2.71
3070 5207 3.067721 TCCGCGTTTTTCGAAAATGTT 57.932 38.095 23.05 0.00 42.86 2.71
3071 5208 2.784380 TCCGCGTTTTTCGAAAATGTTG 59.216 40.909 23.05 13.92 42.86 3.33
3075 5257 5.010129 CGCGTTTTTCGAAAATGTTGTTTT 58.990 33.333 23.05 0.00 42.86 2.43
3086 5268 9.959775 TCGAAAATGTTGTTTTATTTTGTGAAC 57.040 25.926 0.00 0.00 36.81 3.18
3108 5290 6.877611 ACCGTGAAATCTGTATTTGTTTCT 57.122 33.333 0.00 0.00 35.41 2.52
3109 5291 6.668323 ACCGTGAAATCTGTATTTGTTTCTG 58.332 36.000 0.00 0.00 35.41 3.02
3110 5292 5.569059 CCGTGAAATCTGTATTTGTTTCTGC 59.431 40.000 0.00 0.00 35.41 4.26
3111 5293 6.142139 CGTGAAATCTGTATTTGTTTCTGCA 58.858 36.000 0.00 0.00 35.41 4.41
3112 5294 6.803320 CGTGAAATCTGTATTTGTTTCTGCAT 59.197 34.615 0.00 0.00 35.41 3.96
3116 5298 5.648178 TCTGTATTTGTTTCTGCATGCAT 57.352 34.783 22.97 6.08 0.00 3.96
3124 5306 2.042686 TTCTGCATGCATACTGGGTC 57.957 50.000 22.97 0.00 0.00 4.46
3126 5308 1.153188 TGCATGCATACTGGGTCCG 60.153 57.895 18.46 0.00 0.00 4.79
3128 5310 0.882042 GCATGCATACTGGGTCCGAG 60.882 60.000 14.21 0.00 0.00 4.63
3136 5318 1.609501 CTGGGTCCGAGAAGGGTGA 60.610 63.158 0.00 0.00 41.52 4.02
3144 5326 1.269166 CGAGAAGGGTGAATTCGTCG 58.731 55.000 0.04 0.00 0.00 5.12
3149 5331 0.034896 AGGGTGAATTCGTCGTGCTT 59.965 50.000 0.04 0.00 0.00 3.91
3150 5332 0.442699 GGGTGAATTCGTCGTGCTTC 59.557 55.000 0.04 0.00 0.00 3.86
3151 5333 0.442699 GGTGAATTCGTCGTGCTTCC 59.557 55.000 0.04 0.00 0.00 3.46
3158 5340 1.942677 TCGTCGTGCTTCCAAAGAAA 58.057 45.000 0.00 0.00 0.00 2.52
3190 5372 5.469421 CCAATACAGCATCTGGATCTTCTTC 59.531 44.000 0.00 0.00 33.27 2.87
3191 5373 6.289834 CAATACAGCATCTGGATCTTCTTCT 58.710 40.000 0.00 0.00 33.27 2.85
3192 5374 4.840716 ACAGCATCTGGATCTTCTTCTT 57.159 40.909 0.00 0.00 35.51 2.52
3193 5375 5.176741 ACAGCATCTGGATCTTCTTCTTT 57.823 39.130 0.00 0.00 35.51 2.52
3251 5455 4.562143 GCATTTCTGCTGGTTCTTCCATTT 60.562 41.667 0.00 0.00 46.12 2.32
3252 5456 4.853924 TTTCTGCTGGTTCTTCCATTTC 57.146 40.909 0.00 0.00 46.12 2.17
3253 5457 2.795329 TCTGCTGGTTCTTCCATTTCC 58.205 47.619 0.00 0.00 46.12 3.13
3258 5462 4.408596 TGCTGGTTCTTCCATTTCCTTTTT 59.591 37.500 0.00 0.00 46.12 1.94
3279 5483 4.751767 TTATTTTGTGATGAATGGGGGC 57.248 40.909 0.00 0.00 0.00 5.80
3280 5484 0.894141 TTTTGTGATGAATGGGGGCG 59.106 50.000 0.00 0.00 0.00 6.13
3281 5485 1.603236 TTTGTGATGAATGGGGGCGC 61.603 55.000 0.00 0.00 0.00 6.53
3298 5502 2.322081 GCGCGCTTTGGTGGTTCTA 61.322 57.895 26.67 0.00 0.00 2.10
3308 5512 1.160137 GGTGGTTCTACAGCTGCAAG 58.840 55.000 15.27 12.07 36.03 4.01
3319 5523 3.289834 CTGCAAGGCCAGCGTTGT 61.290 61.111 21.89 0.00 41.95 3.32
3320 5524 3.547249 CTGCAAGGCCAGCGTTGTG 62.547 63.158 21.89 13.56 41.95 3.33
3323 5527 2.124320 AAGGCCAGCGTTGTGTGT 60.124 55.556 5.01 0.00 0.00 3.72
3324 5528 1.752694 AAGGCCAGCGTTGTGTGTT 60.753 52.632 5.01 0.00 0.00 3.32
3326 5530 0.464735 AGGCCAGCGTTGTGTGTTTA 60.465 50.000 5.01 0.00 0.00 2.01
3327 5531 0.040425 GGCCAGCGTTGTGTGTTTAG 60.040 55.000 0.00 0.00 0.00 1.85
3328 5532 0.660300 GCCAGCGTTGTGTGTTTAGC 60.660 55.000 0.00 0.00 0.00 3.09
3329 5533 0.944386 CCAGCGTTGTGTGTTTAGCT 59.056 50.000 0.00 0.00 35.06 3.32
3330 5534 2.022808 CAGCGTTGTGTGTTTAGCTG 57.977 50.000 0.00 0.80 44.51 4.24
3331 5535 0.944386 AGCGTTGTGTGTTTAGCTGG 59.056 50.000 0.00 0.00 33.31 4.85
3338 5543 2.028112 TGTGTGTTTAGCTGGCTAGGAG 60.028 50.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.434408 TGATGAGCAAGCAGAACATTATCT 58.566 37.500 0.00 0.00 0.00 1.98
48 49 7.013464 ACCAAGGATTTTAATGTACACGTCAAA 59.987 33.333 0.00 0.00 0.00 2.69
54 55 6.451393 TGCAACCAAGGATTTTAATGTACAC 58.549 36.000 0.00 0.00 0.00 2.90
65 66 5.774690 TCAAATACTTCTGCAACCAAGGATT 59.225 36.000 4.88 4.88 35.06 3.01
74 75 8.994429 TTCTTTGTTTTCAAATACTTCTGCAA 57.006 26.923 0.00 0.00 46.72 4.08
89 90 7.226523 GTGAATGCCTTACCATTTCTTTGTTTT 59.773 33.333 0.00 0.00 35.67 2.43
101 102 2.176045 TCTCTCGTGAATGCCTTACCA 58.824 47.619 0.00 0.00 0.00 3.25
103 104 3.614616 CACTTCTCTCGTGAATGCCTTAC 59.385 47.826 0.00 0.00 34.35 2.34
150 151 6.465035 GGGATAGTTCTTTCCTGAGCATGTAT 60.465 42.308 8.67 0.00 32.34 2.29
161 162 4.846168 ACCAGAAGGGATAGTTCTTTCC 57.154 45.455 1.58 1.58 41.15 3.13
170 171 5.722290 TGGTCATGTATACCAGAAGGGATA 58.278 41.667 0.69 0.00 42.10 2.59
172 173 4.002256 TGGTCATGTATACCAGAAGGGA 57.998 45.455 0.69 0.00 42.10 4.20
201 202 1.614903 TCCTTGACCGTTATCGTGTGT 59.385 47.619 0.00 0.00 35.01 3.72
204 205 3.259064 ACAATCCTTGACCGTTATCGTG 58.741 45.455 0.00 0.00 35.01 4.35
213 214 9.566432 AGATGAGAATTAATACAATCCTTGACC 57.434 33.333 0.00 0.00 0.00 4.02
225 226 6.816136 TCGTGCTCCAAGATGAGAATTAATA 58.184 36.000 0.00 0.00 34.11 0.98
272 273 6.566079 AAGGTATCATCATGAGTGGAAGAA 57.434 37.500 0.09 0.00 0.00 2.52
273 274 6.385176 AGAAAGGTATCATCATGAGTGGAAGA 59.615 38.462 0.09 0.00 0.00 2.87
274 275 6.590068 AGAAAGGTATCATCATGAGTGGAAG 58.410 40.000 0.09 0.00 0.00 3.46
275 276 6.566079 AGAAAGGTATCATCATGAGTGGAA 57.434 37.500 0.09 0.00 0.00 3.53
285 286 9.612066 ATGAAAGAAGAGAAGAAAGGTATCATC 57.388 33.333 0.00 0.00 0.00 2.92
302 303 8.538039 GCAAAACAAAGAAGAAGATGAAAGAAG 58.462 33.333 0.00 0.00 0.00 2.85
310 311 6.393171 GCATAGGCAAAACAAAGAAGAAGAT 58.607 36.000 0.00 0.00 40.72 2.40
355 379 8.403606 AGATTAACTGTTCTACGGTATTTTCG 57.596 34.615 0.00 0.00 36.53 3.46
363 387 7.548075 ACAAACCATAGATTAACTGTTCTACGG 59.452 37.037 0.00 0.00 34.69 4.02
525 2553 2.649516 CGTCATCGCTTCTCTCATCTC 58.350 52.381 0.00 0.00 0.00 2.75
526 2554 2.772568 CGTCATCGCTTCTCTCATCT 57.227 50.000 0.00 0.00 0.00 2.90
587 2617 3.478274 GCAGGAGGCAGGGAGAGG 61.478 72.222 0.00 0.00 43.97 3.69
609 2647 1.135972 CAGATGGAAAACGGCGTCAAG 60.136 52.381 15.17 0.00 0.00 3.02
769 2807 2.824071 GAAAAGCATGTGCCCAGCGG 62.824 60.000 0.57 0.00 43.38 5.52
770 2808 1.444895 GAAAAGCATGTGCCCAGCG 60.445 57.895 0.57 0.00 43.38 5.18
803 2841 0.386476 TCGATCCGTACCAATTCCGG 59.614 55.000 0.00 0.00 43.03 5.14
804 2842 2.212869 TTCGATCCGTACCAATTCCG 57.787 50.000 0.00 0.00 0.00 4.30
805 2843 3.183775 CGATTTCGATCCGTACCAATTCC 59.816 47.826 0.00 0.00 43.02 3.01
806 2844 4.046462 TCGATTTCGATCCGTACCAATTC 58.954 43.478 0.00 0.00 44.22 2.17
883 2926 0.035056 ATTTGAAGTGGAGCTCGGGG 60.035 55.000 7.83 0.00 0.00 5.73
995 3058 1.673033 CGACCGCTGTCTCCATTTTCT 60.673 52.381 6.71 0.00 39.47 2.52
996 3059 0.721718 CGACCGCTGTCTCCATTTTC 59.278 55.000 6.71 0.00 39.47 2.29
997 3060 0.673644 CCGACCGCTGTCTCCATTTT 60.674 55.000 6.71 0.00 39.47 1.82
1858 3942 0.959372 TCCTCTTCGGTGTCGGACTC 60.959 60.000 9.88 5.65 36.95 3.36
1859 3943 1.074423 TCCTCTTCGGTGTCGGACT 59.926 57.895 9.88 0.00 36.95 3.85
1860 3944 1.212229 GTCCTCTTCGGTGTCGGAC 59.788 63.158 0.00 0.00 37.57 4.79
1890 3983 4.828925 GCAGCGGGGCTCTCTGAC 62.829 72.222 8.90 0.00 36.40 3.51
1900 3993 4.292178 GATCCTCTCGGCAGCGGG 62.292 72.222 0.00 0.00 0.00 6.13
1901 3994 3.496875 CTGATCCTCTCGGCAGCGG 62.497 68.421 0.00 0.00 0.00 5.52
1905 3998 0.758310 ATGCTCTGATCCTCTCGGCA 60.758 55.000 0.00 0.00 33.37 5.69
1938 4037 2.511600 CAGTCCGGGAATGCCGAC 60.512 66.667 16.49 11.01 33.83 4.79
2037 4136 0.527817 CGAAAGCTACTTCGCCCGAT 60.528 55.000 7.56 0.00 41.46 4.18
2071 4170 2.324860 CACGTATGCAGACACGAAGAA 58.675 47.619 20.85 0.00 40.56 2.52
2075 4174 0.170339 CTCCACGTATGCAGACACGA 59.830 55.000 20.85 8.24 40.56 4.35
2078 4177 1.136891 CATCCTCCACGTATGCAGACA 59.863 52.381 12.67 0.00 0.00 3.41
2128 4227 1.462616 TCAGCTGAGACTGAGAGAGC 58.537 55.000 13.74 0.00 41.72 4.09
2142 4241 5.195546 AGAAGTCATTCTGCTGCTCAGCT 62.196 47.826 20.84 0.00 44.28 4.24
2143 4242 2.936114 AGAAGTCATTCTGCTGCTCAGC 60.936 50.000 14.49 14.49 44.28 4.26
2163 4262 2.186384 CTCAAGAGGCCCGAGCAG 59.814 66.667 0.00 0.00 42.56 4.24
2166 4265 1.216710 GTCACTCAAGAGGCCCGAG 59.783 63.158 0.00 3.02 0.00 4.63
2178 4277 2.572104 AGGAAATACAGGTGGGTCACTC 59.428 50.000 0.00 0.00 34.40 3.51
2204 4303 1.538047 TTCATCAAGGAAGGCACTGC 58.462 50.000 0.00 0.00 40.86 4.40
2228 4327 7.564128 TCGATGCAATAACGATTCTGTTATTC 58.436 34.615 16.58 13.57 46.73 1.75
2239 4338 5.882553 TGTACTAGTTCGATGCAATAACGA 58.117 37.500 0.00 0.00 0.00 3.85
2258 4357 5.668471 GGAAGGGGACAGTAATACTTGTAC 58.332 45.833 0.00 0.00 0.00 2.90
2259 4358 4.403432 CGGAAGGGGACAGTAATACTTGTA 59.597 45.833 0.00 0.00 0.00 2.41
2260 4359 3.197116 CGGAAGGGGACAGTAATACTTGT 59.803 47.826 0.00 0.00 0.00 3.16
2261 4360 3.197116 ACGGAAGGGGACAGTAATACTTG 59.803 47.826 0.00 0.00 0.00 3.16
2264 4363 2.740904 GCACGGAAGGGGACAGTAATAC 60.741 54.545 0.00 0.00 32.68 1.89
2278 4377 0.370958 GTAATTAAGCGCGCACGGAA 59.629 50.000 35.10 20.53 40.57 4.30
2280 4379 0.372334 AAGTAATTAAGCGCGCACGG 59.628 50.000 35.10 0.00 40.57 4.94
2281 4380 1.591394 GGAAGTAATTAAGCGCGCACG 60.591 52.381 35.10 0.00 44.07 5.34
2360 4470 1.103398 GGTGATCCCCAAATGGCTCG 61.103 60.000 0.00 0.00 0.00 5.03
2363 4473 0.324645 ACAGGTGATCCCCAAATGGC 60.325 55.000 0.00 0.00 0.00 4.40
2367 4477 1.682849 CCGACAGGTGATCCCCAAA 59.317 57.895 0.00 0.00 0.00 3.28
2368 4478 2.297895 CCCGACAGGTGATCCCCAA 61.298 63.158 0.00 0.00 35.12 4.12
2369 4479 2.687200 CCCGACAGGTGATCCCCA 60.687 66.667 0.00 0.00 35.12 4.96
2379 4489 0.537188 ACTCCATGCTAACCCGACAG 59.463 55.000 0.00 0.00 0.00 3.51
2380 4490 1.754803 CTACTCCATGCTAACCCGACA 59.245 52.381 0.00 0.00 0.00 4.35
2382 4492 1.063492 TCCTACTCCATGCTAACCCGA 60.063 52.381 0.00 0.00 0.00 5.14
2428 4544 0.179034 GCCCCATGAGATGAGACACC 60.179 60.000 0.00 0.00 0.00 4.16
2454 4570 1.106285 GCAACTCCTTTAGGCATGGG 58.894 55.000 0.00 0.00 34.44 4.00
2462 4578 3.447586 AGCGTGATCTAGCAACTCCTTTA 59.552 43.478 13.78 0.00 35.48 1.85
2468 4584 3.546724 TCTCTAGCGTGATCTAGCAACT 58.453 45.455 13.78 0.00 36.77 3.16
2479 4595 0.179124 GAGTGGCCTTCTCTAGCGTG 60.179 60.000 17.19 0.00 0.00 5.34
2481 4597 1.439644 GGAGTGGCCTTCTCTAGCG 59.560 63.158 21.40 0.00 33.06 4.26
2483 4599 0.325671 TGGGGAGTGGCCTTCTCTAG 60.326 60.000 21.40 0.00 36.66 2.43
2517 4633 5.595952 ACAGGCCAAGAAAGGATAAATGATC 59.404 40.000 5.01 0.00 0.00 2.92
2518 4634 5.361857 CACAGGCCAAGAAAGGATAAATGAT 59.638 40.000 5.01 0.00 0.00 2.45
2519 4635 4.706476 CACAGGCCAAGAAAGGATAAATGA 59.294 41.667 5.01 0.00 0.00 2.57
2521 4637 3.448660 GCACAGGCCAAGAAAGGATAAAT 59.551 43.478 5.01 0.00 0.00 1.40
2532 4650 1.098050 GGATAAGTGCACAGGCCAAG 58.902 55.000 21.04 0.00 40.13 3.61
2538 4656 2.370281 ACTGACGGATAAGTGCACAG 57.630 50.000 21.04 6.62 0.00 3.66
2548 4666 1.831736 CCTAACTGGGAACTGACGGAT 59.168 52.381 0.00 0.00 0.00 4.18
2559 4677 2.100252 CAGCATTGCATTCCTAACTGGG 59.900 50.000 11.91 0.00 36.20 4.45
2590 4708 8.903820 GTTTATCCTGTTTATTATGGTCTGCTT 58.096 33.333 0.00 0.00 0.00 3.91
2593 4711 7.713507 TCGGTTTATCCTGTTTATTATGGTCTG 59.286 37.037 0.00 0.00 0.00 3.51
2609 4728 4.734917 CCTACTCATCGATCGGTTTATCC 58.265 47.826 16.41 0.00 0.00 2.59
2650 4769 5.462729 GCTAAGATAAGAGGCCGTTTAGAAC 59.537 44.000 0.00 0.00 0.00 3.01
2674 4793 1.068541 TGACCAGATCACTGTTCGTCG 60.069 52.381 0.00 0.00 42.05 5.12
2678 4797 2.069273 CCGTTGACCAGATCACTGTTC 58.931 52.381 0.00 0.00 42.05 3.18
2684 4803 0.544357 ACTCCCCGTTGACCAGATCA 60.544 55.000 0.00 0.00 34.65 2.92
2771 4897 4.473520 ACTTGGCCATCGCTCGGG 62.474 66.667 6.09 0.00 34.44 5.14
2802 4928 0.535102 AGAAGAACACCTGGGCGTTG 60.535 55.000 8.31 0.00 0.00 4.10
2823 4949 2.067013 GCAACTTTCTCTACACCGTCC 58.933 52.381 0.00 0.00 0.00 4.79
2827 4953 2.165319 ACGGCAACTTTCTCTACACC 57.835 50.000 0.00 0.00 0.00 4.16
2831 4957 2.294233 ACGTGTACGGCAACTTTCTCTA 59.706 45.455 9.40 0.00 44.95 2.43
2886 5014 4.699257 GGATTTGAACAAGCTCACTCTCAT 59.301 41.667 0.00 0.00 0.00 2.90
2918 5046 2.430244 CGCGTGTCACGGTAAGCT 60.430 61.111 25.70 0.00 42.82 3.74
2939 5067 1.606737 GCAGAGCTTTCCGAGAGTTGT 60.607 52.381 0.00 0.00 0.00 3.32
2940 5068 1.074752 GCAGAGCTTTCCGAGAGTTG 58.925 55.000 0.00 0.00 0.00 3.16
2943 5071 1.518133 CGGCAGAGCTTTCCGAGAG 60.518 63.158 14.56 0.00 45.53 3.20
2944 5072 2.276116 ACGGCAGAGCTTTCCGAGA 61.276 57.895 23.06 0.00 45.53 4.04
2971 5099 5.295431 TGCAAAATCTAGAAACATGGACG 57.705 39.130 0.00 0.00 0.00 4.79
2977 5105 4.549458 GCAAGCTGCAAAATCTAGAAACA 58.451 39.130 1.02 0.00 44.26 2.83
3003 5140 2.673523 CTCCTCCTGCCACTTGGG 59.326 66.667 0.00 0.00 40.85 4.12
3015 5152 1.950909 AGTAGTAGATGCACGCTCCTC 59.049 52.381 0.00 0.00 0.00 3.71
3016 5153 2.060050 AGTAGTAGATGCACGCTCCT 57.940 50.000 0.00 0.00 0.00 3.69
3018 5155 4.751098 AGTACTAGTAGTAGATGCACGCTC 59.249 45.833 10.38 0.00 30.12 5.03
3020 5157 4.751098 AGAGTACTAGTAGTAGATGCACGC 59.249 45.833 10.38 2.64 30.12 5.34
3021 5158 5.177881 CCAGAGTACTAGTAGTAGATGCACG 59.822 48.000 10.38 0.00 30.12 5.34
3022 5159 6.056884 ACCAGAGTACTAGTAGTAGATGCAC 58.943 44.000 10.38 0.59 30.12 4.57
3023 5160 6.249911 ACCAGAGTACTAGTAGTAGATGCA 57.750 41.667 10.38 0.00 30.12 3.96
3024 5161 6.766944 TGAACCAGAGTACTAGTAGTAGATGC 59.233 42.308 10.38 0.00 30.12 3.91
3025 5162 8.911918 ATGAACCAGAGTACTAGTAGTAGATG 57.088 38.462 10.38 9.45 30.12 2.90
3026 5163 8.158789 GGATGAACCAGAGTACTAGTAGTAGAT 58.841 40.741 10.38 2.69 38.79 1.98
3027 5164 7.507829 GGATGAACCAGAGTACTAGTAGTAGA 58.492 42.308 10.38 0.00 38.79 2.59
3028 5165 6.424509 CGGATGAACCAGAGTACTAGTAGTAG 59.575 46.154 10.38 2.87 38.90 2.57
3029 5166 6.286758 CGGATGAACCAGAGTACTAGTAGTA 58.713 44.000 10.28 5.90 38.90 1.82
3030 5167 5.124645 CGGATGAACCAGAGTACTAGTAGT 58.875 45.833 10.09 10.09 38.90 2.73
3032 5169 3.881688 GCGGATGAACCAGAGTACTAGTA 59.118 47.826 0.00 0.00 38.90 1.82
3033 5170 2.688958 GCGGATGAACCAGAGTACTAGT 59.311 50.000 0.00 0.00 38.90 2.57
3036 5173 0.456221 CGCGGATGAACCAGAGTACT 59.544 55.000 0.00 0.00 38.90 2.73
3037 5174 0.172803 ACGCGGATGAACCAGAGTAC 59.827 55.000 12.47 0.00 38.90 2.73
3038 5175 0.892755 AACGCGGATGAACCAGAGTA 59.107 50.000 12.47 0.00 38.90 2.59
3039 5176 0.034896 AAACGCGGATGAACCAGAGT 59.965 50.000 12.47 0.00 38.90 3.24
3060 5197 9.959775 GTTCACAAAATAAAACAACATTTTCGA 57.040 25.926 0.00 0.00 33.23 3.71
3061 5198 9.204792 GGTTCACAAAATAAAACAACATTTTCG 57.795 29.630 0.00 0.00 33.23 3.46
3062 5199 9.204792 CGGTTCACAAAATAAAACAACATTTTC 57.795 29.630 0.00 0.00 33.23 2.29
3063 5200 8.722394 ACGGTTCACAAAATAAAACAACATTTT 58.278 25.926 0.00 0.00 35.30 1.82
3064 5201 8.171840 CACGGTTCACAAAATAAAACAACATTT 58.828 29.630 0.00 0.00 0.00 2.32
3065 5202 7.545965 TCACGGTTCACAAAATAAAACAACATT 59.454 29.630 0.00 0.00 0.00 2.71
3066 5203 7.036220 TCACGGTTCACAAAATAAAACAACAT 58.964 30.769 0.00 0.00 0.00 2.71
3067 5204 6.387465 TCACGGTTCACAAAATAAAACAACA 58.613 32.000 0.00 0.00 0.00 3.33
3069 5206 7.884816 TTTCACGGTTCACAAAATAAAACAA 57.115 28.000 0.00 0.00 0.00 2.83
3070 5207 7.976734 AGATTTCACGGTTCACAAAATAAAACA 59.023 29.630 0.00 0.00 0.00 2.83
3071 5208 8.265998 CAGATTTCACGGTTCACAAAATAAAAC 58.734 33.333 0.00 0.00 0.00 2.43
3075 5257 6.627395 ACAGATTTCACGGTTCACAAAATA 57.373 33.333 0.00 0.00 0.00 1.40
3082 5264 6.627395 AACAAATACAGATTTCACGGTTCA 57.373 33.333 0.00 0.00 32.73 3.18
3086 5268 5.569059 GCAGAAACAAATACAGATTTCACGG 59.431 40.000 0.00 0.00 32.73 4.94
3108 5290 1.153188 CGGACCCAGTATGCATGCA 60.153 57.895 25.04 25.04 31.97 3.96
3109 5291 0.882042 CTCGGACCCAGTATGCATGC 60.882 60.000 11.82 11.82 31.97 4.06
3110 5292 0.752658 TCTCGGACCCAGTATGCATG 59.247 55.000 10.16 0.00 31.97 4.06
3111 5293 1.414181 CTTCTCGGACCCAGTATGCAT 59.586 52.381 3.79 3.79 31.97 3.96
3112 5294 0.824109 CTTCTCGGACCCAGTATGCA 59.176 55.000 0.00 0.00 31.97 3.96
3116 5298 0.613853 CACCCTTCTCGGACCCAGTA 60.614 60.000 0.00 0.00 33.16 2.74
3124 5306 1.641577 GACGAATTCACCCTTCTCGG 58.358 55.000 6.22 0.00 33.89 4.63
3126 5308 1.993370 CACGACGAATTCACCCTTCTC 59.007 52.381 0.00 0.00 0.00 2.87
3128 5310 0.442699 GCACGACGAATTCACCCTTC 59.557 55.000 0.00 0.00 0.00 3.46
3136 5318 2.489971 TCTTTGGAAGCACGACGAATT 58.510 42.857 0.00 0.00 0.00 2.17
3168 5350 6.497624 AGAAGAAGATCCAGATGCTGTATT 57.502 37.500 0.00 0.00 0.00 1.89
3193 5375 4.493547 CTCACAGCAAGGTTGTTGAAAAA 58.506 39.130 12.83 0.00 41.22 1.94
3258 5462 3.131933 CGCCCCCATTCATCACAAAATAA 59.868 43.478 0.00 0.00 0.00 1.40
3260 5464 1.481772 CGCCCCCATTCATCACAAAAT 59.518 47.619 0.00 0.00 0.00 1.82
3263 5467 2.051518 GCGCCCCCATTCATCACAA 61.052 57.895 0.00 0.00 0.00 3.33
3280 5484 2.322081 TAGAACCACCAAAGCGCGC 61.322 57.895 26.66 26.66 0.00 6.86
3281 5485 1.225376 TGTAGAACCACCAAAGCGCG 61.225 55.000 0.00 0.00 0.00 6.86
3293 5497 0.606401 TGGCCTTGCAGCTGTAGAAC 60.606 55.000 16.64 9.54 0.00 3.01
3308 5512 0.040425 CTAAACACACAACGCTGGCC 60.040 55.000 0.00 0.00 0.00 5.36
3319 5523 1.555075 CCTCCTAGCCAGCTAAACACA 59.445 52.381 0.34 0.00 0.00 3.72
3320 5524 1.134371 CCCTCCTAGCCAGCTAAACAC 60.134 57.143 0.34 0.00 0.00 3.32
3323 5527 0.620410 TGCCCTCCTAGCCAGCTAAA 60.620 55.000 0.34 0.00 0.00 1.85
3324 5528 0.620410 TTGCCCTCCTAGCCAGCTAA 60.620 55.000 0.34 0.00 0.00 3.09
3326 5530 2.285668 TTGCCCTCCTAGCCAGCT 60.286 61.111 0.00 0.00 0.00 4.24
3327 5531 2.191641 CTTGCCCTCCTAGCCAGC 59.808 66.667 0.00 0.00 0.00 4.85
3328 5532 2.914289 CCTTGCCCTCCTAGCCAG 59.086 66.667 0.00 0.00 0.00 4.85
3329 5533 3.411517 GCCTTGCCCTCCTAGCCA 61.412 66.667 0.00 0.00 0.00 4.75
3330 5534 3.411517 TGCCTTGCCCTCCTAGCC 61.412 66.667 0.00 0.00 0.00 3.93
3331 5535 2.191641 CTGCCTTGCCCTCCTAGC 59.808 66.667 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.