Multiple sequence alignment - TraesCS1A01G351600

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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 TraesCS1A01G351600 chr1A 100.000 3796 0 0 1 3796 536069810 536066015 0.000000e+00 7011.0
1 TraesCS1A01G351600 chr1A 80.172 116 17 3 725 834 94459572 94459457 8.740000e-12 82.4
2 TraesCS1A01G351600 chr1D 93.494 3105 137 33 712 3790 442525186 442528251 0.000000e+00 4554.0
3 TraesCS1A01G351600 chr1D 87.844 436 38 5 1 436 442524152 442524572 7.320000e-137 497.0
4 TraesCS1A01G351600 chr1D 94.902 255 12 1 435 688 442524842 442525096 7.640000e-107 398.0
5 TraesCS1A01G351600 chr1B 92.690 2914 125 28 895 3772 602004772 602001911 0.000000e+00 4120.0
6 TraesCS1A01G351600 chr1B 80.800 125 18 2 724 842 392525360 392525236 4.040000e-15 93.5
7 TraesCS1A01G351600 chr6A 80.147 136 19 7 712 840 614851015 614850881 1.120000e-15 95.3
8 TraesCS1A01G351600 chr4B 78.832 137 23 3 712 842 553244886 553245022 1.880000e-13 87.9
9 TraesCS1A01G351600 chr4B 78.226 124 21 4 725 842 134989298 134989175 1.460000e-09 75.0
10 TraesCS1A01G351600 chr2D 79.137 139 20 5 712 842 522538032 522538169 1.880000e-13 87.9
11 TraesCS1A01G351600 chr2D 78.519 135 23 3 714 842 589507148 589507282 2.430000e-12 84.2
12 TraesCS1A01G351600 chr2A 78.626 131 22 4 713 842 544304144 544304019 8.740000e-12 82.4


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 TraesCS1A01G351600 chr1A 536066015 536069810 3795 True 7011.000000 7011 100.00 1 3796 1 chr1A.!!$R2 3795
1 TraesCS1A01G351600 chr1D 442524152 442528251 4099 False 1816.333333 4554 92.08 1 3790 3 chr1D.!!$F1 3789
2 TraesCS1A01G351600 chr1B 602001911 602004772 2861 True 4120.000000 4120 92.69 895 3772 1 chr1B.!!$R2 2877

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
229 230 0.319641 AAACAGGAGCGGACGAAGAC 60.320 55.000 0.00 0.0 0.00 3.01 F
426 427 0.320374 CCGCTGAGTTAGGGAACACA 59.680 55.000 0.01 0.0 41.61 3.72 F
862 1201 0.325296 CAGTGGTACTGGAGGGCCTA 60.325 60.000 5.73 0.0 42.35 3.93 F
1815 2156 1.134788 CGCGAGGAGGTCAAGGTTATT 60.135 52.381 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2387 1.067250 GCTCGTGATCTCCTCCAGC 59.933 63.158 0.0 0.0 0.00 4.85 R
2115 2456 1.215382 CATCCTGCGGAAGTCGTCA 59.785 57.895 0.0 0.0 41.72 4.35 R
2445 2786 1.511850 CCACGAACTTCATCTGCACA 58.488 50.000 0.0 0.0 0.00 4.57 R
3288 3667 0.250989 TTTAGTTTCCCACCCCTGCG 60.251 55.000 0.0 0.0 0.00 5.18 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
33 34 4.097714 CAACGTTGGATGGATTTCAATCG 58.902 43.478 20.71 0.00 36.27 3.34
41 42 8.836413 GTTGGATGGATTTCAATCGTAGATAAA 58.164 33.333 0.00 0.00 45.12 1.40
42 43 8.607441 TGGATGGATTTCAATCGTAGATAAAG 57.393 34.615 0.00 0.00 45.12 1.85
96 97 8.630037 CCTCAGCCCGACTTTAAATTAATAAAT 58.370 33.333 0.00 0.00 0.00 1.40
116 117 9.445786 AATAAATTCAACGTCAACAACAGTAAG 57.554 29.630 0.00 0.00 0.00 2.34
131 132 3.383825 ACAGTAAGAACCGAACAGAGTGT 59.616 43.478 0.00 0.00 0.00 3.55
136 137 4.506886 AGAACCGAACAGAGTGTAAGAG 57.493 45.455 0.00 0.00 0.00 2.85
164 165 2.851263 ATGAAGTTTAGACGGCCACA 57.149 45.000 2.24 0.00 0.00 4.17
209 210 4.021981 GCCAAGACCAAAAGCTAAACATCT 60.022 41.667 0.00 0.00 0.00 2.90
220 221 4.184629 AGCTAAACATCTAAACAGGAGCG 58.815 43.478 0.00 0.00 32.70 5.03
221 222 3.309954 GCTAAACATCTAAACAGGAGCGG 59.690 47.826 0.00 0.00 0.00 5.52
222 223 3.695830 AAACATCTAAACAGGAGCGGA 57.304 42.857 0.00 0.00 0.00 5.54
223 224 2.674796 ACATCTAAACAGGAGCGGAC 57.325 50.000 0.00 0.00 0.00 4.79
224 225 1.135083 ACATCTAAACAGGAGCGGACG 60.135 52.381 0.00 0.00 0.00 4.79
225 226 1.134367 CATCTAAACAGGAGCGGACGA 59.866 52.381 0.00 0.00 0.00 4.20
226 227 1.250328 TCTAAACAGGAGCGGACGAA 58.750 50.000 0.00 0.00 0.00 3.85
227 228 1.201647 TCTAAACAGGAGCGGACGAAG 59.798 52.381 0.00 0.00 0.00 3.79
228 229 1.201647 CTAAACAGGAGCGGACGAAGA 59.798 52.381 0.00 0.00 0.00 2.87
229 230 0.319641 AAACAGGAGCGGACGAAGAC 60.320 55.000 0.00 0.00 0.00 3.01
230 231 1.179814 AACAGGAGCGGACGAAGACT 61.180 55.000 0.00 0.00 0.00 3.24
231 232 1.179814 ACAGGAGCGGACGAAGACTT 61.180 55.000 0.00 0.00 0.00 3.01
232 233 0.809385 CAGGAGCGGACGAAGACTTA 59.191 55.000 0.00 0.00 0.00 2.24
233 234 0.810016 AGGAGCGGACGAAGACTTAC 59.190 55.000 0.00 0.00 0.00 2.34
234 235 0.524862 GGAGCGGACGAAGACTTACA 59.475 55.000 0.00 0.00 0.00 2.41
235 236 1.615502 GAGCGGACGAAGACTTACAC 58.384 55.000 0.00 0.00 0.00 2.90
239 240 1.069703 CGGACGAAGACTTACACGACA 60.070 52.381 2.17 0.00 0.00 4.35
270 271 2.601067 TCCCACAACGGCGACCTA 60.601 61.111 16.62 0.00 0.00 3.08
307 308 4.681942 CGGAGATATAAACAGCAGTAGCAC 59.318 45.833 0.00 0.00 45.49 4.40
313 314 1.498865 AACAGCAGTAGCACGCACAC 61.499 55.000 0.00 0.00 45.49 3.82
324 325 3.803082 CGCACACGGCCAATGAGG 61.803 66.667 10.93 3.99 40.31 3.86
334 335 0.620556 GCCAATGAGGACCTCCAGAA 59.379 55.000 19.11 0.00 41.22 3.02
346 347 0.671781 CTCCAGAACCGCCTTGTCAG 60.672 60.000 0.00 0.00 0.00 3.51
347 348 1.118965 TCCAGAACCGCCTTGTCAGA 61.119 55.000 0.00 0.00 0.00 3.27
371 372 8.482128 AGACTCCTTAATTAGAGATTTCCACTG 58.518 37.037 8.34 0.00 34.13 3.66
372 373 7.051000 ACTCCTTAATTAGAGATTTCCACTGC 58.949 38.462 8.34 0.00 34.13 4.40
383 384 4.397417 AGATTTCCACTGCTGCAAGAATAC 59.603 41.667 3.02 5.08 34.07 1.89
389 390 1.662629 CTGCTGCAAGAATACGGACAG 59.337 52.381 3.02 0.00 34.07 3.51
406 407 7.539712 ACGGACAGTTTGAATATGACATTAG 57.460 36.000 0.00 0.00 0.00 1.73
410 411 5.207768 CAGTTTGAATATGACATTAGCCGC 58.792 41.667 0.00 0.00 0.00 6.53
411 412 5.008019 CAGTTTGAATATGACATTAGCCGCT 59.992 40.000 0.00 0.00 0.00 5.52
412 413 5.008019 AGTTTGAATATGACATTAGCCGCTG 59.992 40.000 2.16 0.00 0.00 5.18
426 427 0.320374 CCGCTGAGTTAGGGAACACA 59.680 55.000 0.01 0.00 41.61 3.72
546 819 1.651987 ACTGCCGAATTATGTGACCG 58.348 50.000 0.00 0.00 0.00 4.79
550 823 1.862827 GCCGAATTATGTGACCGGTAC 59.137 52.381 7.34 7.19 41.95 3.34
552 825 3.724374 CCGAATTATGTGACCGGTACAT 58.276 45.455 23.84 23.84 41.36 2.29
635 908 7.484959 GTGCACTTCAATGGTATTTAAGCTTAC 59.515 37.037 10.32 0.00 0.00 2.34
636 909 6.687105 GCACTTCAATGGTATTTAAGCTTACG 59.313 38.462 5.45 0.00 0.00 3.18
677 950 7.560626 AGAAACGTAATCTACTAATCCTCACCT 59.439 37.037 2.17 0.00 0.00 4.00
689 990 0.464452 CCTCACCTATCACCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
694 995 1.111116 CCTATCACCCGTTCCGGCTA 61.111 60.000 0.00 0.00 46.86 3.93
704 1005 1.067212 CGTTCCGGCTATGCTTCTAGT 59.933 52.381 0.00 0.00 0.00 2.57
714 1015 4.321601 GCTATGCTTCTAGTGTCATCGGAT 60.322 45.833 0.00 0.00 0.00 4.18
716 1017 4.046938 TGCTTCTAGTGTCATCGGATTC 57.953 45.455 0.00 0.00 0.00 2.52
717 1018 3.046390 GCTTCTAGTGTCATCGGATTCG 58.954 50.000 0.00 0.00 37.82 3.34
730 1069 1.529010 CGGATTCGATTGGCGTTTGTC 60.529 52.381 0.00 0.00 41.80 3.18
735 1074 0.787787 CGATTGGCGTTTGTCTTCGA 59.212 50.000 0.00 0.00 30.87 3.71
769 1108 3.184581 GGATCAAGTCTTCGTTGTGTGTC 59.815 47.826 0.00 0.00 0.00 3.67
771 1110 2.093921 TCAAGTCTTCGTTGTGTGTCCA 60.094 45.455 0.00 0.00 0.00 4.02
779 1118 1.872952 CGTTGTGTGTCCATGTGTCAT 59.127 47.619 0.00 0.00 0.00 3.06
783 1122 4.078639 TGTGTGTCCATGTGTCATGTTA 57.921 40.909 8.57 0.00 0.00 2.41
787 1126 6.040278 TGTGTGTCCATGTGTCATGTTAAATT 59.960 34.615 8.57 0.00 0.00 1.82
814 1153 5.831997 TCGATCTATGCTTTTCTTCATCGA 58.168 37.500 0.00 0.00 38.76 3.59
817 1156 4.993905 TCTATGCTTTTCTTCATCGACGA 58.006 39.130 0.00 0.00 0.00 4.20
823 1162 1.693467 TTCTTCATCGACGACGGTTG 58.307 50.000 7.55 6.17 40.21 3.77
824 1163 0.876399 TCTTCATCGACGACGGTTGA 59.124 50.000 7.55 8.40 40.79 3.18
835 1174 2.201732 CGACGGTTGATATTCTGGTGG 58.798 52.381 0.00 0.00 0.00 4.61
842 1181 2.770447 TGATATTCTGGTGGGCTGGTA 58.230 47.619 0.00 0.00 0.00 3.25
843 1182 2.438021 TGATATTCTGGTGGGCTGGTAC 59.562 50.000 0.00 0.00 0.00 3.34
844 1183 1.959710 TATTCTGGTGGGCTGGTACA 58.040 50.000 0.00 0.00 0.00 2.90
860 1199 2.990479 CAGTGGTACTGGAGGGCC 59.010 66.667 0.00 0.00 42.35 5.80
862 1201 0.325296 CAGTGGTACTGGAGGGCCTA 60.325 60.000 5.73 0.00 42.35 3.93
875 1214 3.370633 GGAGGGCCTAAGTGGTTTTCTAG 60.371 52.174 5.73 0.00 38.35 2.43
889 1228 7.713073 AGTGGTTTTCTAGAATTCTATGCTAGC 59.287 37.037 15.47 8.10 33.37 3.42
925 1264 2.203070 CATCGCTTTCCGGGGGAG 60.203 66.667 0.00 0.00 37.59 4.30
1037 1378 3.532102 ACCCTACCTCCTTTGTTCTGAT 58.468 45.455 0.00 0.00 0.00 2.90
1092 1433 4.470462 CTTACATGCTGTGCTTTCAGTTC 58.530 43.478 0.00 0.00 37.70 3.01
1141 1482 1.135257 ACTCGCTTCGATCTGGTTCTG 60.135 52.381 0.00 0.00 34.61 3.02
1358 1699 1.454847 TGGGCAACTTCGGCAACTT 60.455 52.632 0.00 0.00 0.00 2.66
1815 2156 1.134788 CGCGAGGAGGTCAAGGTTATT 60.135 52.381 0.00 0.00 0.00 1.40
1840 2181 1.417288 AGCCGTCATGGATCTCATCA 58.583 50.000 0.00 0.00 42.00 3.07
1941 2282 2.567049 GCCGACGAGGATATCCGG 59.433 66.667 16.21 13.64 45.00 5.14
2362 2703 3.865929 CTGCCGACGGACAGCAACT 62.866 63.158 20.50 0.00 35.79 3.16
2445 2786 2.685999 GGCAGGGAGATGGCCTTT 59.314 61.111 3.32 0.00 44.32 3.11
2463 2804 3.548587 CTTTGTGCAGATGAAGTTCGTG 58.451 45.455 1.31 0.00 0.00 4.35
2606 2950 2.358737 GGAGACCACAGGCAACGG 60.359 66.667 0.00 0.00 46.39 4.44
2631 2975 2.126071 GACGCAGCTACAGCCGAA 60.126 61.111 6.84 0.00 43.38 4.30
2643 2987 1.338674 ACAGCCGAAAACCGATCATCA 60.339 47.619 0.00 0.00 41.76 3.07
2675 3024 2.159382 GTGGTAAATGGTCACACCCTG 58.841 52.381 0.00 0.00 37.50 4.45
2722 3071 7.728847 TCATATACATCCACTTTGTACATGC 57.271 36.000 0.00 0.00 35.45 4.06
2736 3085 7.444183 ACTTTGTACATGCCCATACATACATAC 59.556 37.037 0.00 0.00 31.55 2.39
2770 3119 7.984422 ATGAATCTGATGTACACACAGAAAA 57.016 32.000 26.93 19.15 42.55 2.29
2784 3133 5.630680 CACACAGAAAAGAATTCAATTCCCG 59.369 40.000 8.44 8.08 40.13 5.14
2801 3151 3.482436 TCCCGCACAGAATAAAAACACT 58.518 40.909 0.00 0.00 0.00 3.55
2804 3154 4.082787 CCCGCACAGAATAAAAACACTGAT 60.083 41.667 0.00 0.00 34.88 2.90
2855 3205 0.242555 TCCGGCAAGAAATTTTCGCC 59.757 50.000 14.59 14.59 39.45 5.54
2857 3207 3.489813 GGCAAGAAATTTTCGCCGT 57.510 47.368 10.90 0.00 32.14 5.68
2882 3232 9.750125 GTGGTCCCATCAATTCTATTTTATTTC 57.250 33.333 0.00 0.00 0.00 2.17
2921 3271 6.128634 CCATCAAAGTGAAACGAACTAGTACC 60.129 42.308 0.00 0.00 45.86 3.34
2922 3272 4.977963 TCAAAGTGAAACGAACTAGTACCG 59.022 41.667 13.86 13.86 45.86 4.02
2934 3284 2.165845 ACTAGTACCGGTTGATGTGCTC 59.834 50.000 15.04 0.00 0.00 4.26
2938 3288 2.743752 CCGGTTGATGTGCTCGCAG 61.744 63.158 0.00 0.00 0.00 5.18
2996 3365 5.224562 TGAACACTGTTTGTAAAACGGAG 57.775 39.130 16.49 11.75 37.51 4.63
2998 3367 2.356695 ACACTGTTTGTAAAACGGAGCC 59.643 45.455 16.49 0.00 36.32 4.70
3031 3400 5.797934 GTCAGAGTCAGACGAGATAAACTTG 59.202 44.000 0.00 0.00 36.17 3.16
3055 3424 2.941720 GGAAAGTTCAGGCAGATGCTAG 59.058 50.000 4.59 0.00 41.70 3.42
3056 3425 3.604582 GAAAGTTCAGGCAGATGCTAGT 58.395 45.455 4.59 0.00 41.70 2.57
3057 3426 4.383118 GGAAAGTTCAGGCAGATGCTAGTA 60.383 45.833 4.59 0.00 41.70 1.82
3058 3427 4.399004 AAGTTCAGGCAGATGCTAGTAG 57.601 45.455 4.59 0.00 41.70 2.57
3059 3428 2.697751 AGTTCAGGCAGATGCTAGTAGG 59.302 50.000 4.59 0.00 41.70 3.18
3060 3429 2.695666 GTTCAGGCAGATGCTAGTAGGA 59.304 50.000 4.59 0.00 41.70 2.94
3061 3430 2.591923 TCAGGCAGATGCTAGTAGGAG 58.408 52.381 4.59 0.00 41.70 3.69
3093 3462 9.965902 ATCAATAATTCCTGTCAAGAAACTAGT 57.034 29.630 0.00 0.00 0.00 2.57
3288 3667 1.827969 AGGATGATGTAGCTATCGGGC 59.172 52.381 0.00 0.00 0.00 6.13
3292 3671 0.734253 GATGTAGCTATCGGGCGCAG 60.734 60.000 10.83 1.95 37.29 5.18
3326 3705 3.627714 GCTAGCTGCTGCGAGATG 58.372 61.111 25.75 10.01 43.23 2.90
3327 3706 1.955157 GCTAGCTGCTGCGAGATGG 60.955 63.158 25.75 5.81 43.23 3.51
3395 3774 2.025793 TGAAATATCAAGTTGCCGGGGA 60.026 45.455 2.18 0.00 30.99 4.81
3398 3777 0.619255 TATCAAGTTGCCGGGGAGGA 60.619 55.000 2.18 0.00 45.00 3.71
3402 3782 0.539669 AAGTTGCCGGGGAGGAAAAG 60.540 55.000 2.18 0.00 39.87 2.27
3408 3788 2.228480 CGGGGAGGAAAAGGGGTCA 61.228 63.158 0.00 0.00 0.00 4.02
3412 3792 1.377333 GAGGAAAAGGGGTCAGGCG 60.377 63.158 0.00 0.00 0.00 5.52
3508 3888 0.162933 GACCACGTGCGTAATGTGTG 59.837 55.000 10.91 0.00 43.26 3.82
3661 4043 0.605319 TGTTTCCTCGTGATGTGGCC 60.605 55.000 0.00 0.00 0.00 5.36
3671 4053 2.372264 GTGATGTGGCCACTGAATCAT 58.628 47.619 34.75 19.87 30.52 2.45
3672 4054 3.544684 GTGATGTGGCCACTGAATCATA 58.455 45.455 34.75 14.06 30.52 2.15
3673 4055 3.313526 GTGATGTGGCCACTGAATCATAC 59.686 47.826 34.75 19.72 30.52 2.39
3674 4056 3.054508 TGATGTGGCCACTGAATCATACA 60.055 43.478 34.75 17.52 0.00 2.29
3675 4057 2.989909 TGTGGCCACTGAATCATACAG 58.010 47.619 34.75 0.00 40.68 2.74
3755 4138 2.031683 ACGACAAAAGCTGGAAGAAACG 59.968 45.455 0.00 0.00 34.07 3.60
3756 4139 2.602217 CGACAAAAGCTGGAAGAAACGG 60.602 50.000 0.00 0.00 34.07 4.44
3760 4143 1.398692 AAGCTGGAAGAAACGGCAAA 58.601 45.000 0.00 0.00 42.62 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.398696 TTTAAAGTCGGGCTGAGGCA 59.601 50.000 8.68 0.00 40.87 4.75
70 71 7.562454 TTATTAATTTAAAGTCGGGCTGAGG 57.438 36.000 0.00 0.00 0.00 3.86
96 97 5.163834 GGTTCTTACTGTTGTTGACGTTGAA 60.164 40.000 0.00 0.00 0.00 2.69
101 102 3.117794 TCGGTTCTTACTGTTGTTGACG 58.882 45.455 0.00 0.00 32.23 4.35
106 107 4.142004 ACTCTGTTCGGTTCTTACTGTTGT 60.142 41.667 0.00 0.00 32.23 3.32
116 117 4.500603 TCTCTTACACTCTGTTCGGTTC 57.499 45.455 0.00 0.00 0.00 3.62
131 132 7.597743 GTCTAAACTTCATTCGGTGTTCTCTTA 59.402 37.037 0.00 0.00 0.00 2.10
136 137 4.143179 CCGTCTAAACTTCATTCGGTGTTC 60.143 45.833 0.00 0.00 33.20 3.18
142 143 2.093783 GTGGCCGTCTAAACTTCATTCG 59.906 50.000 0.00 0.00 0.00 3.34
147 148 1.534163 GGTTGTGGCCGTCTAAACTTC 59.466 52.381 0.00 0.00 0.00 3.01
164 165 4.279043 GCGCCTTGTTTGCCGGTT 62.279 61.111 1.90 0.00 0.00 4.44
182 183 0.829182 AGCTTTTGGTCTTGGCCTGG 60.829 55.000 3.32 0.00 0.00 4.45
209 210 1.068055 GTCTTCGTCCGCTCCTGTTTA 60.068 52.381 0.00 0.00 0.00 2.01
220 221 2.693797 TGTCGTGTAAGTCTTCGTCC 57.306 50.000 0.00 0.00 0.00 4.79
221 222 4.285292 TCTTTGTCGTGTAAGTCTTCGTC 58.715 43.478 0.00 0.00 0.00 4.20
222 223 4.297299 TCTTTGTCGTGTAAGTCTTCGT 57.703 40.909 0.00 0.00 0.00 3.85
223 224 4.974275 TCTTCTTTGTCGTGTAAGTCTTCG 59.026 41.667 0.00 0.00 0.00 3.79
224 225 5.402867 CCTCTTCTTTGTCGTGTAAGTCTTC 59.597 44.000 0.00 0.00 0.00 2.87
225 226 5.290386 CCTCTTCTTTGTCGTGTAAGTCTT 58.710 41.667 0.00 0.00 0.00 3.01
226 227 4.262079 CCCTCTTCTTTGTCGTGTAAGTCT 60.262 45.833 0.00 0.00 0.00 3.24
227 228 3.988517 CCCTCTTCTTTGTCGTGTAAGTC 59.011 47.826 0.00 0.00 0.00 3.01
228 229 3.640029 TCCCTCTTCTTTGTCGTGTAAGT 59.360 43.478 0.00 0.00 0.00 2.24
229 230 4.238514 CTCCCTCTTCTTTGTCGTGTAAG 58.761 47.826 0.00 0.00 0.00 2.34
230 231 3.554337 GCTCCCTCTTCTTTGTCGTGTAA 60.554 47.826 0.00 0.00 0.00 2.41
231 232 2.029290 GCTCCCTCTTCTTTGTCGTGTA 60.029 50.000 0.00 0.00 0.00 2.90
232 233 1.270358 GCTCCCTCTTCTTTGTCGTGT 60.270 52.381 0.00 0.00 0.00 4.49
233 234 1.001406 AGCTCCCTCTTCTTTGTCGTG 59.999 52.381 0.00 0.00 0.00 4.35
234 235 1.273886 GAGCTCCCTCTTCTTTGTCGT 59.726 52.381 0.87 0.00 35.16 4.34
235 236 1.404851 GGAGCTCCCTCTTCTTTGTCG 60.405 57.143 23.19 0.00 38.21 4.35
256 257 2.813908 GGCTAGGTCGCCGTTGTG 60.814 66.667 0.00 0.00 40.79 3.33
270 271 2.445845 TCCGGGATTGATCGGGCT 60.446 61.111 0.00 0.00 45.69 5.19
307 308 3.803082 CCTCATTGGCCGTGTGCG 61.803 66.667 0.00 0.00 42.61 5.34
313 314 2.190578 GGAGGTCCTCATTGGCCG 59.809 66.667 20.72 0.00 37.18 6.13
324 325 1.376037 CAAGGCGGTTCTGGAGGTC 60.376 63.158 0.00 0.00 0.00 3.85
334 335 1.122019 AAGGAGTCTGACAAGGCGGT 61.122 55.000 10.88 0.00 31.37 5.68
346 347 7.225734 GCAGTGGAAATCTCTAATTAAGGAGTC 59.774 40.741 0.00 0.00 0.00 3.36
347 348 7.051000 GCAGTGGAAATCTCTAATTAAGGAGT 58.949 38.462 0.00 0.00 0.00 3.85
371 372 1.726853 ACTGTCCGTATTCTTGCAGC 58.273 50.000 0.00 0.00 0.00 5.25
372 373 3.745975 TCAAACTGTCCGTATTCTTGCAG 59.254 43.478 0.00 0.00 0.00 4.41
383 384 6.422223 GCTAATGTCATATTCAAACTGTCCG 58.578 40.000 0.00 0.00 0.00 4.79
389 390 5.007626 TCAGCGGCTAATGTCATATTCAAAC 59.992 40.000 0.26 0.00 0.00 2.93
406 407 1.019805 GTGTTCCCTAACTCAGCGGC 61.020 60.000 0.00 0.00 36.51 6.53
503 776 9.389570 AGTTACAAACTTAATTATTGAACGTGC 57.610 29.630 4.66 0.00 39.04 5.34
539 812 3.478857 AAGACAAATGTACCGGTCACA 57.521 42.857 12.40 14.82 32.79 3.58
657 930 8.741841 GGTGATAGGTGAGGATTAGTAGATTAC 58.258 40.741 0.00 0.00 0.00 1.89
689 990 2.871182 TGACACTAGAAGCATAGCCG 57.129 50.000 0.00 0.00 0.00 5.52
694 995 4.626042 GAATCCGATGACACTAGAAGCAT 58.374 43.478 0.00 0.00 0.00 3.79
714 1015 1.193650 CGAAGACAAACGCCAATCGAA 59.806 47.619 0.00 0.00 41.67 3.71
716 1017 0.787787 TCGAAGACAAACGCCAATCG 59.212 50.000 0.00 0.00 45.38 3.34
717 1018 2.476185 CCATCGAAGACAAACGCCAATC 60.476 50.000 0.00 0.00 42.51 2.67
720 1021 0.034198 TCCATCGAAGACAAACGCCA 59.966 50.000 0.00 0.00 42.51 5.69
721 1022 1.327764 GATCCATCGAAGACAAACGCC 59.672 52.381 0.00 0.00 42.51 5.68
723 1024 2.348666 GTGGATCCATCGAAGACAAACG 59.651 50.000 19.62 0.00 42.51 3.60
730 1069 0.459899 TCCACGTGGATCCATCGAAG 59.540 55.000 33.23 23.44 39.78 3.79
769 1108 9.734620 ATCGAAATAATTTAACATGACACATGG 57.265 29.630 14.70 0.00 0.00 3.66
787 1126 8.703336 CGATGAAGAAAAGCATAGATCGAAATA 58.297 33.333 0.00 0.00 34.75 1.40
804 1143 1.267533 TCAACCGTCGTCGATGAAGAA 59.732 47.619 20.29 2.31 39.71 2.52
806 1145 1.909376 ATCAACCGTCGTCGATGAAG 58.091 50.000 16.06 11.39 39.71 3.02
814 1153 2.418197 CCACCAGAATATCAACCGTCGT 60.418 50.000 0.00 0.00 0.00 4.34
817 1156 1.408266 GCCCACCAGAATATCAACCGT 60.408 52.381 0.00 0.00 0.00 4.83
823 1162 2.438021 TGTACCAGCCCACCAGAATATC 59.562 50.000 0.00 0.00 0.00 1.63
824 1163 2.439507 CTGTACCAGCCCACCAGAATAT 59.560 50.000 0.00 0.00 0.00 1.28
842 1181 1.918800 GGCCCTCCAGTACCACTGT 60.919 63.158 5.65 0.00 44.50 3.55
843 1182 0.325296 TAGGCCCTCCAGTACCACTG 60.325 60.000 0.00 0.00 45.53 3.66
844 1183 0.416231 TTAGGCCCTCCAGTACCACT 59.584 55.000 0.00 0.00 33.74 4.00
845 1184 0.831307 CTTAGGCCCTCCAGTACCAC 59.169 60.000 0.00 0.00 33.74 4.16
846 1185 0.416231 ACTTAGGCCCTCCAGTACCA 59.584 55.000 0.00 0.00 33.74 3.25
847 1186 0.831307 CACTTAGGCCCTCCAGTACC 59.169 60.000 0.00 0.00 33.74 3.34
848 1187 0.831307 CCACTTAGGCCCTCCAGTAC 59.169 60.000 0.00 0.00 33.74 2.73
849 1188 0.416231 ACCACTTAGGCCCTCCAGTA 59.584 55.000 0.00 0.00 43.14 2.74
850 1189 0.475828 AACCACTTAGGCCCTCCAGT 60.476 55.000 0.00 0.00 43.14 4.00
860 1199 9.606631 AGCATAGAATTCTAGAAAACCACTTAG 57.393 33.333 19.51 3.18 0.00 2.18
862 1201 9.606631 CTAGCATAGAATTCTAGAAAACCACTT 57.393 33.333 19.51 0.00 42.77 3.16
889 1228 8.213518 AGCGATGGCCATATATTTATTAAGTG 57.786 34.615 20.84 0.00 41.24 3.16
933 1274 3.130160 CTCGCCCTTTGCTGCTCC 61.130 66.667 0.00 0.00 38.05 4.70
945 1286 0.464452 ATACCAAGTACCTGCTCGCC 59.536 55.000 0.00 0.00 0.00 5.54
1037 1378 8.380867 TCCTGTACCTCGATCTAGTGATTATAA 58.619 37.037 0.00 0.00 32.19 0.98
1764 2105 2.815211 GAGCCGATGTTGAGCGCA 60.815 61.111 11.47 0.00 0.00 6.09
1770 2111 3.257561 CGCTCCGAGCCGATGTTG 61.258 66.667 14.85 0.00 38.18 3.33
1797 2138 3.522553 GTGAATAACCTTGACCTCCTCG 58.477 50.000 0.00 0.00 0.00 4.63
1840 2181 1.973812 GCTCCTTTTTGCGGCTCCT 60.974 57.895 0.00 0.00 0.00 3.69
1883 2224 1.968310 GACAGCAGGTCGTTCCTCT 59.032 57.895 0.00 0.00 46.24 3.69
1941 2282 2.408271 TGAAGCTGATCACCATGTCC 57.592 50.000 0.00 0.00 0.00 4.02
2046 2387 1.067250 GCTCGTGATCTCCTCCAGC 59.933 63.158 0.00 0.00 0.00 4.85
2115 2456 1.215382 CATCCTGCGGAAGTCGTCA 59.785 57.895 0.00 0.00 41.72 4.35
2445 2786 1.511850 CCACGAACTTCATCTGCACA 58.488 50.000 0.00 0.00 0.00 4.57
2613 2957 3.642778 TTCGGCTGTAGCTGCGTCC 62.643 63.158 7.82 0.00 46.62 4.79
2722 3071 9.415544 CATATGATCATCGTATGTATGTATGGG 57.584 37.037 12.53 0.00 40.02 4.00
2736 3085 8.805688 GTGTACATCAGATTCATATGATCATCG 58.194 37.037 12.53 5.06 36.67 3.84
2770 3119 3.071874 TCTGTGCGGGAATTGAATTCT 57.928 42.857 16.58 0.00 39.24 2.40
2784 3133 8.524870 AATCAATCAGTGTTTTTATTCTGTGC 57.475 30.769 0.00 0.00 0.00 4.57
2801 3151 5.409520 CACTCGAGTTTCTTGGAATCAATCA 59.590 40.000 17.26 0.00 31.75 2.57
2804 3154 4.065088 CCACTCGAGTTTCTTGGAATCAA 58.935 43.478 17.26 0.00 0.00 2.57
2855 3205 5.835113 AAAATAGAATTGATGGGACCACG 57.165 39.130 0.00 0.00 0.00 4.94
2857 3207 8.629158 CGAAATAAAATAGAATTGATGGGACCA 58.371 33.333 0.00 0.00 0.00 4.02
2882 3232 1.191535 TGATGGGACCCTACTGTTCG 58.808 55.000 13.00 0.00 0.00 3.95
2890 3240 2.814097 CGTTTCACTTTGATGGGACCCT 60.814 50.000 13.00 0.00 0.00 4.34
2921 3271 0.735978 TACTGCGAGCACATCAACCG 60.736 55.000 0.00 0.00 0.00 4.44
2922 3272 1.438651 TTACTGCGAGCACATCAACC 58.561 50.000 0.00 0.00 0.00 3.77
2996 3365 1.140816 GACTCTGACAAGTTCACGGC 58.859 55.000 0.00 0.00 0.00 5.68
2998 3367 3.046390 GTCTGACTCTGACAAGTTCACG 58.954 50.000 10.39 0.00 33.52 4.35
3031 3400 2.163211 GCATCTGCCTGAACTTTCCTTC 59.837 50.000 0.00 0.00 34.31 3.46
3057 3426 9.213777 TGACAGGAATTATTGATTAGTACTCCT 57.786 33.333 0.00 0.00 0.00 3.69
3058 3427 9.832445 TTGACAGGAATTATTGATTAGTACTCC 57.168 33.333 0.00 0.00 0.00 3.85
3092 3461 6.449448 CGTCCCGCTTTATTCTAATTCTAC 57.551 41.667 0.00 0.00 0.00 2.59
3144 3514 1.935873 GGGCGACGACCTTTTTATACC 59.064 52.381 14.07 0.00 0.00 2.73
3288 3667 0.250989 TTTAGTTTCCCACCCCTGCG 60.251 55.000 0.00 0.00 0.00 5.18
3292 3671 0.251033 AGCGTTTAGTTTCCCACCCC 60.251 55.000 0.00 0.00 0.00 4.95
3379 3758 0.619255 TCCTCCCCGGCAACTTGATA 60.619 55.000 0.00 0.00 0.00 2.15
3385 3764 1.977009 CCTTTTCCTCCCCGGCAAC 60.977 63.158 0.00 0.00 0.00 4.17
3395 3774 1.423794 TTCGCCTGACCCCTTTTCCT 61.424 55.000 0.00 0.00 0.00 3.36
3398 3777 0.611896 CCATTCGCCTGACCCCTTTT 60.612 55.000 0.00 0.00 0.00 2.27
3402 3782 4.506255 CCCCATTCGCCTGACCCC 62.506 72.222 0.00 0.00 0.00 4.95
3412 3792 3.564027 CTCGAACGCGCCCCATTC 61.564 66.667 5.73 0.26 37.46 2.67
3508 3888 3.188786 GCCAGATCACGACACGCC 61.189 66.667 0.00 0.00 0.00 5.68
3623 4004 2.441750 ACAAGTCCAGCTCCCAAAAGTA 59.558 45.455 0.00 0.00 0.00 2.24
3624 4005 1.215423 ACAAGTCCAGCTCCCAAAAGT 59.785 47.619 0.00 0.00 0.00 2.66
3625 4006 1.986882 ACAAGTCCAGCTCCCAAAAG 58.013 50.000 0.00 0.00 0.00 2.27
3626 4007 2.452600 AACAAGTCCAGCTCCCAAAA 57.547 45.000 0.00 0.00 0.00 2.44
3671 4053 3.507786 CAGCTGTTATGTACGCACTGTA 58.492 45.455 5.25 0.00 0.00 2.74
3672 4054 2.337583 CAGCTGTTATGTACGCACTGT 58.662 47.619 5.25 0.00 0.00 3.55
3673 4055 1.660607 CCAGCTGTTATGTACGCACTG 59.339 52.381 13.81 0.00 0.00 3.66
3674 4056 2.007049 GCCAGCTGTTATGTACGCACT 61.007 52.381 13.81 0.00 0.00 4.40
3675 4057 0.373716 GCCAGCTGTTATGTACGCAC 59.626 55.000 13.81 0.00 0.00 5.34
3760 4143 3.500680 TGCGCTCCTTATCTTTTCGTTTT 59.499 39.130 9.73 0.00 0.00 2.43
3764 4147 1.005975 CGTGCGCTCCTTATCTTTTCG 60.006 52.381 9.73 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.