Multiple sequence alignment - TraesCS2A01G161700

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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 TraesCS2A01G161700 chr2A 100.000 3110 0 0 1 3110 114302530 114299421 0.000000e+00 5744.0
1 TraesCS2A01G161700 chr2D 90.348 3191 146 48 1 3108 112867216 112864105 0.000000e+00 4037.0
2 TraesCS2A01G161700 chr2B 93.659 2271 109 19 1 2249 163233404 163231147 0.000000e+00 3363.0
3 TraesCS2A01G161700 chr2B 83.612 897 48 21 2257 3108 163230707 163229865 0.000000e+00 750.0
4 TraesCS2A01G161700 chr2B 75.522 335 72 10 1 333 53941935 53941609 4.150000e-34 156.0
5 TraesCS2A01G161700 chr5D 73.998 973 194 46 1157 2095 456751303 456752250 1.070000e-89 340.0
6 TraesCS2A01G161700 chr5D 73.006 652 155 18 6 648 339722235 339722874 3.140000e-50 209.0
7 TraesCS2A01G161700 chr5D 75.165 455 85 11 1 443 118220645 118221083 4.090000e-44 189.0
8 TraesCS2A01G161700 chr5B 73.429 971 203 44 1157 2095 558686569 558687516 2.330000e-81 313.0
9 TraesCS2A01G161700 chr5B 73.192 567 132 18 90 645 176585092 176584535 1.470000e-43 187.0
10 TraesCS2A01G161700 chr5A 73.306 974 199 47 1157 2095 574784847 574785794 5.040000e-78 302.0
11 TraesCS2A01G161700 chr4B 84.211 190 28 2 9 197 651510522 651510710 1.900000e-42 183.0
12 TraesCS2A01G161700 chr4A 79.310 261 46 6 9 265 477793710 477793454 3.190000e-40 176.0
13 TraesCS2A01G161700 chr6D 79.151 259 48 3 1 254 108191089 108191346 1.150000e-39 174.0
14 TraesCS2A01G161700 chr6D 86.154 65 6 3 718 781 470900969 470901031 2.000000e-07 67.6
15 TraesCS2A01G161700 chr3B 71.628 645 170 12 9 647 637025190 637024553 6.900000e-37 165.0
16 TraesCS2A01G161700 chr3D 78.059 237 41 11 32 263 548962530 548962300 4.180000e-29 139.0


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 TraesCS2A01G161700 chr2A 114299421 114302530 3109 True 5744.0 5744 100.0000 1 3110 1 chr2A.!!$R1 3109
1 TraesCS2A01G161700 chr2D 112864105 112867216 3111 True 4037.0 4037 90.3480 1 3108 1 chr2D.!!$R1 3107
2 TraesCS2A01G161700 chr2B 163229865 163233404 3539 True 2056.5 3363 88.6355 1 3108 2 chr2B.!!$R2 3107
3 TraesCS2A01G161700 chr5D 456751303 456752250 947 False 340.0 340 73.9980 1157 2095 1 chr5D.!!$F3 938
4 TraesCS2A01G161700 chr5D 339722235 339722874 639 False 209.0 209 73.0060 6 648 1 chr5D.!!$F2 642
5 TraesCS2A01G161700 chr5B 558686569 558687516 947 False 313.0 313 73.4290 1157 2095 1 chr5B.!!$F1 938
6 TraesCS2A01G161700 chr5A 574784847 574785794 947 False 302.0 302 73.3060 1157 2095 1 chr5A.!!$F1 938

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
620 624 0.175989 CTCCCTCCTAAGGACGTTGC 59.824 60.0 0.0 0.0 46.67 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 2998 0.109132 CCCTTTTCATCCTTGCGTGC 60.109 55.0 0.0 0.0 0.0 5.34 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
83 84 3.633094 CTGGAGACGCAGGTGTCGG 62.633 68.421 7.28 0.00 43.70 4.79
120 121 2.368875 AGGTGTTGATCCAGACTTCGTT 59.631 45.455 0.00 0.00 0.00 3.85
189 190 1.732941 GTGGTTGGTGCATCGTGATA 58.267 50.000 0.00 0.00 0.00 2.15
195 196 0.534877 GGTGCATCGTGATATGGGCA 60.535 55.000 0.00 0.00 0.00 5.36
198 199 1.151668 GCATCGTGATATGGGCAGAC 58.848 55.000 0.00 0.00 0.00 3.51
224 225 1.284491 TGGCTTGGACATGGATGCTAA 59.716 47.619 0.00 0.00 0.00 3.09
265 267 1.136147 CTGCATGTTGGCTCTTCGC 59.864 57.895 0.00 0.00 38.13 4.70
290 292 3.133464 CATTGCGGCGGTGGTGAT 61.133 61.111 9.78 0.00 0.00 3.06
309 311 1.184431 TTATCCGTCTTGGGCGTGTA 58.816 50.000 0.00 0.00 38.76 2.90
381 384 1.153309 TAGTGACGCTCCGATCCGA 60.153 57.895 0.00 0.00 0.00 4.55
385 388 1.877165 GACGCTCCGATCCGAAACC 60.877 63.158 0.00 0.00 0.00 3.27
406 409 2.621055 CGGAGATCTTTCCTCATCGAGT 59.379 50.000 0.00 0.00 34.96 4.18
443 446 1.482593 GTAGTAGCATGGGTGAGCTGT 59.517 52.381 0.00 0.00 41.97 4.40
545 548 0.178921 TCCTCTCTGTGACAGGGCTT 60.179 55.000 13.33 0.00 30.92 4.35
572 576 2.038387 AGACCTTTGTTCGTTGCAGT 57.962 45.000 0.00 0.00 0.00 4.40
575 579 2.354821 GACCTTTGTTCGTTGCAGTCTT 59.645 45.455 0.00 0.00 0.00 3.01
588 592 2.280797 GTCTTGGCAGCGGTGACA 60.281 61.111 21.42 21.42 41.34 3.58
614 618 0.686769 GCCGTTCTCCCTCCTAAGGA 60.687 60.000 0.00 0.00 46.67 3.36
620 624 0.175989 CTCCCTCCTAAGGACGTTGC 59.824 60.000 0.00 0.00 46.67 4.17
633 637 2.006772 CGTTGCCGTGGAGCTTATC 58.993 57.895 0.00 0.00 0.00 1.75
649 653 3.555168 GCTTATCTGTGCTAGGGCGTAAT 60.555 47.826 0.00 0.00 42.25 1.89
654 684 1.002659 TGTGCTAGGGCGTAATGTTGT 59.997 47.619 0.00 0.00 42.25 3.32
673 703 3.135225 TGTGTAGTGTTTTGCGTATGCT 58.865 40.909 8.69 0.00 43.34 3.79
723 753 5.281314 AGGGTCACCTCAGTATCTTGTATT 58.719 41.667 0.00 0.00 46.95 1.89
729 759 5.520288 CACCTCAGTATCTTGTATTGTTCGG 59.480 44.000 0.00 0.00 0.00 4.30
730 760 4.508124 CCTCAGTATCTTGTATTGTTCGGC 59.492 45.833 0.00 0.00 0.00 5.54
737 767 2.676632 TGTATTGTTCGGCCGTGTAT 57.323 45.000 27.15 16.21 0.00 2.29
745 775 0.892755 TCGGCCGTGTATCTTGTTCT 59.107 50.000 27.15 0.00 0.00 3.01
759 789 8.629158 TGTATCTTGTTCTGCTGTTGTTTTATT 58.371 29.630 0.00 0.00 0.00 1.40
811 842 8.402326 ACCTCGAAAAACAAGAATACAAAAAC 57.598 30.769 0.00 0.00 0.00 2.43
858 890 6.726258 ACCTTGCAAAAGAAAACAAGAAAG 57.274 33.333 0.00 0.00 41.59 2.62
983 1019 2.118404 CACACACCCACACACCCAC 61.118 63.158 0.00 0.00 0.00 4.61
1614 1656 2.097038 CGAGCTGCCGGAGAACTTG 61.097 63.158 5.05 0.00 0.00 3.16
1644 1689 2.887568 GCCTCGGTCATCGTGCTG 60.888 66.667 0.00 0.00 40.32 4.41
1863 1908 2.433838 CTGGAGCAGCTGGACGTG 60.434 66.667 17.12 0.00 0.00 4.49
2131 2248 3.492011 GCGGAAATCATCATTCATTTGGC 59.508 43.478 0.00 0.00 0.00 4.52
2151 2268 1.293963 GGTGTAAAACGGGCGGAGAC 61.294 60.000 0.00 0.00 0.00 3.36
2251 2371 9.898152 TCAATGGAATTTGTAGACATACATACA 57.102 29.630 0.00 0.00 41.49 2.29
2255 2807 8.201464 TGGAATTTGTAGACATACATACACGAT 58.799 33.333 0.00 0.00 41.49 3.73
2320 2872 1.144057 GGCTGTCCGTCCGATGATT 59.856 57.895 0.00 0.00 0.00 2.57
2377 2939 7.446625 GCATCTTGTTGGTGGAGAGATTATTAT 59.553 37.037 0.00 0.00 0.00 1.28
2380 2942 9.832445 TCTTGTTGGTGGAGAGATTATTATTAC 57.168 33.333 0.00 0.00 0.00 1.89
2381 2943 9.838339 CTTGTTGGTGGAGAGATTATTATTACT 57.162 33.333 0.00 0.00 0.00 2.24
2387 2949 9.930693 GGTGGAGAGATTATTATTACTACTTGG 57.069 37.037 0.00 0.00 0.00 3.61
2388 2950 9.425577 GTGGAGAGATTATTATTACTACTTGGC 57.574 37.037 0.00 0.00 0.00 4.52
2403 2965 3.972403 ACTTGGCGTATTGTTTTTGGTC 58.028 40.909 0.00 0.00 0.00 4.02
2404 2966 3.381908 ACTTGGCGTATTGTTTTTGGTCA 59.618 39.130 0.00 0.00 0.00 4.02
2453 3015 2.256174 CATGCACGCAAGGATGAAAAG 58.744 47.619 0.00 0.00 46.39 2.27
2465 3027 4.620723 AGGATGAAAAGGGGGAATTAACC 58.379 43.478 0.00 0.00 0.00 2.85
2489 3051 2.108952 AGAATGTGTGGCTTCCTTTCCT 59.891 45.455 0.00 0.00 0.00 3.36
2513 3075 1.889170 CCTTGGCTTGAAAGGGAGTTC 59.111 52.381 0.00 0.00 40.54 3.01
2516 3078 0.875059 GGCTTGAAAGGGAGTTCACG 59.125 55.000 0.00 0.00 37.24 4.35
2517 3079 1.542547 GGCTTGAAAGGGAGTTCACGA 60.543 52.381 0.00 0.00 37.24 4.35
2518 3080 2.218603 GCTTGAAAGGGAGTTCACGAA 58.781 47.619 0.00 0.00 37.24 3.85
2519 3081 2.224314 GCTTGAAAGGGAGTTCACGAAG 59.776 50.000 0.00 0.00 37.24 3.79
2520 3082 2.543777 TGAAAGGGAGTTCACGAAGG 57.456 50.000 0.00 0.00 32.56 3.46
2521 3083 1.766496 TGAAAGGGAGTTCACGAAGGT 59.234 47.619 0.00 0.00 32.56 3.50
2522 3084 2.143925 GAAAGGGAGTTCACGAAGGTG 58.856 52.381 0.00 0.00 45.78 4.00
2523 3085 1.129058 AAGGGAGTTCACGAAGGTGT 58.871 50.000 0.00 0.00 44.68 4.16
2524 3086 1.129058 AGGGAGTTCACGAAGGTGTT 58.871 50.000 0.00 0.00 44.68 3.32
2548 3119 1.216710 GGCTGTCCTCTCCAAGTCG 59.783 63.158 0.00 0.00 0.00 4.18
2557 3128 3.382865 TCCTCTCCAAGTCGAATGATGAG 59.617 47.826 1.21 7.52 0.00 2.90
2580 3151 3.791586 GAGCAGGGGAGGAGGCAC 61.792 72.222 0.00 0.00 0.00 5.01
2594 3165 1.450312 GGCACGGTCAAGGATGAGG 60.450 63.158 0.00 0.00 35.88 3.86
2608 3179 8.208993 GTCAAGGATGAGGTGATAACGATAGTG 61.209 44.444 0.00 0.00 43.09 2.74
2646 3217 3.490419 GGAGAAGAATCAATGCCATGCAC 60.490 47.826 0.00 0.00 43.04 4.57
2680 3265 0.773644 CCTAGGTGGATGGGATTGGG 59.226 60.000 0.00 0.00 38.35 4.12
2806 3391 5.692654 GCTTAGCTTAGGAGTAGTACATTGC 59.307 44.000 2.52 0.00 0.00 3.56
2808 3393 3.700038 AGCTTAGGAGTAGTACATTGCGT 59.300 43.478 2.52 0.00 0.00 5.24
2813 3398 3.954904 AGGAGTAGTACATTGCGTCTGAT 59.045 43.478 2.52 0.00 0.00 2.90
2814 3399 5.131067 AGGAGTAGTACATTGCGTCTGATA 58.869 41.667 2.52 0.00 0.00 2.15
2815 3400 5.008811 AGGAGTAGTACATTGCGTCTGATAC 59.991 44.000 2.52 0.00 0.00 2.24
2816 3401 5.220989 GGAGTAGTACATTGCGTCTGATACA 60.221 44.000 2.52 0.00 0.00 2.29
2820 3405 5.212934 AGTACATTGCGTCTGATACATACG 58.787 41.667 0.00 0.00 37.10 3.06
2906 3511 2.330231 TGCTTTCCAAATTTCGAGCG 57.670 45.000 0.00 0.00 33.03 5.03
2920 3535 3.092334 TCGAGCGCATGTTATGTATGT 57.908 42.857 11.47 0.00 0.00 2.29
2921 3536 2.794350 TCGAGCGCATGTTATGTATGTG 59.206 45.455 11.47 0.00 38.67 3.21
2922 3537 2.539688 CGAGCGCATGTTATGTATGTGT 59.460 45.455 11.47 0.00 38.10 3.72
2965 3585 2.437716 CGGGATGGGGTTTGACGG 60.438 66.667 0.00 0.00 0.00 4.79
3015 3641 2.317609 CGAACGTGGGCTGTGGAAG 61.318 63.158 0.00 0.00 0.00 3.46
3031 3657 2.818296 GAAGCTTTCTCGTTGCCGCG 62.818 60.000 0.00 0.00 0.00 6.46
3080 3710 2.264794 CCGGACCGGTCAAGAAGG 59.735 66.667 34.40 23.28 42.73 3.46
3093 3723 0.606673 AAGAAGGAGCGGACAAAGGC 60.607 55.000 0.00 0.00 0.00 4.35
3094 3724 1.302511 GAAGGAGCGGACAAAGGCA 60.303 57.895 0.00 0.00 0.00 4.75
3108 3738 3.112709 GGCAACCAGACGACTCGC 61.113 66.667 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 1.690283 TCCTAGCCTGGCATCAGCA 60.690 57.895 22.65 0.00 44.61 4.41
165 166 1.599518 GATGCACCAACCACGGTCA 60.600 57.895 0.00 0.00 37.07 4.02
189 190 1.228063 GCCATCATCGTCTGCCCAT 60.228 57.895 0.00 0.00 0.00 4.00
195 196 0.904649 TGTCCAAGCCATCATCGTCT 59.095 50.000 0.00 0.00 0.00 4.18
198 199 0.949397 CCATGTCCAAGCCATCATCG 59.051 55.000 0.00 0.00 0.00 3.84
265 267 2.176546 CGCCGCAATGTTGTCTGG 59.823 61.111 0.00 0.00 0.00 3.86
290 292 1.135527 CTACACGCCCAAGACGGATAA 59.864 52.381 0.00 0.00 36.56 1.75
353 355 1.743958 GAGCGTCACTAGTGCTAAGGA 59.256 52.381 18.45 0.00 39.49 3.36
381 384 3.430929 CGATGAGGAAAGATCTCCGGTTT 60.431 47.826 0.00 0.00 40.75 3.27
385 388 2.621055 ACTCGATGAGGAAAGATCTCCG 59.379 50.000 0.00 0.00 40.75 4.63
469 472 0.437295 GCAAGCGTCGTTGTTATCGT 59.563 50.000 0.00 0.00 0.00 3.73
504 507 1.142060 ACCCACCACGACATCTTCAAA 59.858 47.619 0.00 0.00 0.00 2.69
518 521 1.757699 GTCACAGAGAGGATACCCACC 59.242 57.143 0.00 0.00 33.88 4.61
545 548 1.539496 CGAACAAAGGTCTTCACCCGA 60.539 52.381 0.00 0.00 45.12 5.14
572 576 2.280797 GTGTCACCGCTGCCAAGA 60.281 61.111 0.00 0.00 0.00 3.02
575 579 2.186160 CAAAGTGTCACCGCTGCCA 61.186 57.895 0.00 0.00 0.00 4.92
588 592 2.668550 GGGAGAACGGCGCAAAGT 60.669 61.111 10.83 2.59 0.00 2.66
620 624 0.176680 AGCACAGATAAGCTCCACGG 59.823 55.000 0.00 0.00 36.00 4.94
633 637 1.665679 CAACATTACGCCCTAGCACAG 59.334 52.381 0.00 0.00 39.83 3.66
649 653 4.786927 GCATACGCAAAACACTACACAACA 60.787 41.667 0.00 0.00 38.36 3.33
654 684 2.095969 GCAGCATACGCAAAACACTACA 60.096 45.455 0.00 0.00 42.27 2.74
673 703 0.827925 AGCCGATCCGAGGATAAGCA 60.828 55.000 20.92 0.00 36.06 3.91
723 753 0.319083 ACAAGATACACGGCCGAACA 59.681 50.000 35.90 16.27 0.00 3.18
729 759 1.394917 CAGCAGAACAAGATACACGGC 59.605 52.381 0.00 0.00 0.00 5.68
730 760 2.688507 ACAGCAGAACAAGATACACGG 58.311 47.619 0.00 0.00 0.00 4.94
759 789 7.197901 TCTGGTTTTCCCCTCGTTTTATATA 57.802 36.000 0.00 0.00 39.73 0.86
770 800 2.751816 CGAGGTTTTCTGGTTTTCCCCT 60.752 50.000 0.00 0.00 39.73 4.79
778 809 4.703093 TCTTGTTTTTCGAGGTTTTCTGGT 59.297 37.500 0.00 0.00 0.00 4.00
811 842 1.114722 TGCTGGCTTTCCCACCTTTG 61.115 55.000 0.00 0.00 39.18 2.77
858 890 1.529826 GCGTCATGATTTCGTTCTGGC 60.530 52.381 0.00 0.00 0.00 4.85
983 1019 2.046313 GCATGTTTGCGTGTCTTTCTG 58.954 47.619 0.00 0.00 39.49 3.02
2110 2227 3.732219 CGCCAAATGAATGATGATTTCCG 59.268 43.478 0.00 0.00 0.00 4.30
2115 2232 3.025978 ACACCGCCAAATGAATGATGAT 58.974 40.909 0.00 0.00 0.00 2.45
2116 2233 2.445427 ACACCGCCAAATGAATGATGA 58.555 42.857 0.00 0.00 0.00 2.92
2117 2234 2.945447 ACACCGCCAAATGAATGATG 57.055 45.000 0.00 0.00 0.00 3.07
2131 2248 2.357275 TCCGCCCGTTTTACACCG 60.357 61.111 0.00 0.00 0.00 4.94
2226 2346 9.935682 GTGTATGTATGTCTACAAATTCCATTG 57.064 33.333 0.00 0.00 41.09 2.82
2227 2347 8.826710 CGTGTATGTATGTCTACAAATTCCATT 58.173 33.333 0.00 0.00 41.09 3.16
2228 2348 8.201464 TCGTGTATGTATGTCTACAAATTCCAT 58.799 33.333 0.00 0.00 41.09 3.41
2229 2349 7.548967 TCGTGTATGTATGTCTACAAATTCCA 58.451 34.615 0.00 0.00 41.09 3.53
2249 2369 7.148738 GCAGAATGATCGATAATGTAATCGTGT 60.149 37.037 0.00 0.00 43.81 4.49
2250 2370 7.169455 GCAGAATGATCGATAATGTAATCGTG 58.831 38.462 0.00 0.00 43.81 4.35
2251 2371 6.033937 CGCAGAATGATCGATAATGTAATCGT 59.966 38.462 0.00 0.00 43.81 3.73
2255 2807 4.929211 CCCGCAGAATGATCGATAATGTAA 59.071 41.667 0.00 0.00 39.69 2.41
2264 2816 2.874694 CGCACCCGCAGAATGATCG 61.875 63.158 0.00 0.00 39.69 3.69
2268 2820 1.089481 ATGTACGCACCCGCAGAATG 61.089 55.000 0.00 0.00 38.40 2.67
2272 2824 0.529773 ATGTATGTACGCACCCGCAG 60.530 55.000 0.00 0.00 38.40 5.18
2317 2869 9.173939 CGCACAAGAAAGAATGGAATAATAATC 57.826 33.333 0.00 0.00 0.00 1.75
2320 2872 7.335673 TGTCGCACAAGAAAGAATGGAATAATA 59.664 33.333 0.00 0.00 0.00 0.98
2377 2939 6.262720 ACCAAAAACAATACGCCAAGTAGTAA 59.737 34.615 0.00 0.00 38.94 2.24
2379 2941 4.581409 ACCAAAAACAATACGCCAAGTAGT 59.419 37.500 0.00 0.00 38.94 2.73
2380 2942 5.116069 ACCAAAAACAATACGCCAAGTAG 57.884 39.130 0.00 0.00 38.94 2.57
2381 2943 4.579340 TGACCAAAAACAATACGCCAAGTA 59.421 37.500 0.00 0.00 40.03 2.24
2382 2944 3.381908 TGACCAAAAACAATACGCCAAGT 59.618 39.130 0.00 0.00 0.00 3.16
2383 2945 3.971150 TGACCAAAAACAATACGCCAAG 58.029 40.909 0.00 0.00 0.00 3.61
2384 2946 4.302455 CATGACCAAAAACAATACGCCAA 58.698 39.130 0.00 0.00 0.00 4.52
2385 2947 3.305676 CCATGACCAAAAACAATACGCCA 60.306 43.478 0.00 0.00 0.00 5.69
2386 2948 3.249917 CCATGACCAAAAACAATACGCC 58.750 45.455 0.00 0.00 0.00 5.68
2387 2949 3.672867 CACCATGACCAAAAACAATACGC 59.327 43.478 0.00 0.00 0.00 4.42
2388 2950 4.233789 CCACCATGACCAAAAACAATACG 58.766 43.478 0.00 0.00 0.00 3.06
2432 2994 0.109179 TTTCATCCTTGCGTGCATGC 60.109 50.000 24.20 24.20 0.00 4.06
2433 2995 2.256174 CTTTTCATCCTTGCGTGCATG 58.744 47.619 0.09 0.09 0.00 4.06
2434 2996 1.203052 CCTTTTCATCCTTGCGTGCAT 59.797 47.619 0.00 0.00 0.00 3.96
2435 2997 0.597568 CCTTTTCATCCTTGCGTGCA 59.402 50.000 0.00 0.00 0.00 4.57
2436 2998 0.109132 CCCTTTTCATCCTTGCGTGC 60.109 55.000 0.00 0.00 0.00 5.34
2437 2999 0.527565 CCCCTTTTCATCCTTGCGTG 59.472 55.000 0.00 0.00 0.00 5.34
2438 3000 0.611896 CCCCCTTTTCATCCTTGCGT 60.612 55.000 0.00 0.00 0.00 5.24
2439 3001 0.323360 TCCCCCTTTTCATCCTTGCG 60.323 55.000 0.00 0.00 0.00 4.85
2453 3015 3.881089 CACATTCTACGGTTAATTCCCCC 59.119 47.826 0.00 0.00 0.00 5.40
2465 3027 2.386661 AGGAAGCCACACATTCTACG 57.613 50.000 0.00 0.00 0.00 3.51
2489 3051 2.965147 CTCCCTTTCAAGCCAAGGAAAA 59.035 45.455 0.00 0.00 43.32 2.29
2513 3075 0.868406 GCCTCTTGAACACCTTCGTG 59.132 55.000 0.00 0.00 46.11 4.35
2516 3078 2.147150 GACAGCCTCTTGAACACCTTC 58.853 52.381 0.00 0.00 0.00 3.46
2517 3079 1.202818 GGACAGCCTCTTGAACACCTT 60.203 52.381 0.00 0.00 0.00 3.50
2518 3080 0.398318 GGACAGCCTCTTGAACACCT 59.602 55.000 0.00 0.00 0.00 4.00
2519 3081 0.398318 AGGACAGCCTCTTGAACACC 59.602 55.000 0.00 0.00 42.19 4.16
2548 3119 2.552591 CCTGCTCATCCCCTCATCATTC 60.553 54.545 0.00 0.00 0.00 2.67
2557 3128 3.174265 CCTCCCCTGCTCATCCCC 61.174 72.222 0.00 0.00 0.00 4.81
2580 3151 3.458189 GTTATCACCTCATCCTTGACCG 58.542 50.000 0.00 0.00 0.00 4.79
2594 3165 7.013529 GGAAACACAAACACTATCGTTATCAC 58.986 38.462 0.00 0.00 0.00 3.06
2608 3179 4.398044 TCTTCTCCAACTGGAAACACAAAC 59.602 41.667 0.00 0.00 44.91 2.93
2613 3184 5.047566 TGATTCTTCTCCAACTGGAAACA 57.952 39.130 0.00 0.00 44.91 2.83
2646 3217 5.070981 TCCACCTAGGCTTTCTTATCAGATG 59.929 44.000 9.30 0.00 37.29 2.90
2786 3371 3.700038 ACGCAATGTACTACTCCTAAGCT 59.300 43.478 0.00 0.00 0.00 3.74
2787 3372 4.043037 ACGCAATGTACTACTCCTAAGC 57.957 45.455 0.00 0.00 0.00 3.09
2788 3373 5.066117 TCAGACGCAATGTACTACTCCTAAG 59.934 44.000 0.00 0.00 0.00 2.18
2789 3374 4.945543 TCAGACGCAATGTACTACTCCTAA 59.054 41.667 0.00 0.00 0.00 2.69
2790 3375 4.520179 TCAGACGCAATGTACTACTCCTA 58.480 43.478 0.00 0.00 0.00 2.94
2806 3391 4.404324 GCTGTATCCGTATGTATCAGACG 58.596 47.826 9.44 9.44 46.56 4.18
2808 3393 4.663334 AGGCTGTATCCGTATGTATCAGA 58.337 43.478 0.00 0.00 0.00 3.27
2813 3398 4.398358 GCATCTAGGCTGTATCCGTATGTA 59.602 45.833 0.00 0.00 0.00 2.29
2814 3399 3.193691 GCATCTAGGCTGTATCCGTATGT 59.806 47.826 0.00 0.00 0.00 2.29
2815 3400 3.445450 AGCATCTAGGCTGTATCCGTATG 59.555 47.826 0.00 0.00 43.89 2.39
2816 3401 3.702792 AGCATCTAGGCTGTATCCGTAT 58.297 45.455 0.00 0.00 43.89 3.06
2840 3425 6.370718 CACCCACCTAACAGTACTTGATAAAC 59.629 42.308 0.00 0.00 0.00 2.01
2954 3574 2.046700 TCATCGCCGTCAAACCCC 60.047 61.111 0.00 0.00 0.00 4.95
3007 3633 1.069636 GCAACGAGAAAGCTTCCACAG 60.070 52.381 0.00 0.00 0.00 3.66
3023 3649 4.389576 CCTGTCTTGCGCGGCAAC 62.390 66.667 8.83 3.41 43.99 4.17
3031 3657 3.745803 GCTGCCAGCCTGTCTTGC 61.746 66.667 5.06 0.00 34.48 4.01
3067 3697 2.657237 CGCTCCTTCTTGACCGGT 59.343 61.111 6.92 6.92 0.00 5.28
3069 3699 1.446272 GTCCGCTCCTTCTTGACCG 60.446 63.158 0.00 0.00 0.00 4.79
3070 3700 0.034896 TTGTCCGCTCCTTCTTGACC 59.965 55.000 0.00 0.00 0.00 4.02
3071 3701 1.801178 CTTTGTCCGCTCCTTCTTGAC 59.199 52.381 0.00 0.00 0.00 3.18
3072 3702 1.270839 CCTTTGTCCGCTCCTTCTTGA 60.271 52.381 0.00 0.00 0.00 3.02
3073 3703 1.160137 CCTTTGTCCGCTCCTTCTTG 58.840 55.000 0.00 0.00 0.00 3.02
3074 3704 0.606673 GCCTTTGTCCGCTCCTTCTT 60.607 55.000 0.00 0.00 0.00 2.52
3075 3705 1.003233 GCCTTTGTCCGCTCCTTCT 60.003 57.895 0.00 0.00 0.00 2.85
3076 3706 0.889186 TTGCCTTTGTCCGCTCCTTC 60.889 55.000 0.00 0.00 0.00 3.46
3080 3710 1.856265 CTGGTTGCCTTTGTCCGCTC 61.856 60.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.