Multiple sequence alignment - TraesCS6B01G035200

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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 TraesCS6B01G035200 chr6B 100.000 3212 0 0 1 3212 20922986 20926197 0.000000e+00 5932
1 TraesCS6B01G035200 chr6B 88.346 2171 226 20 147 2307 20783765 20785918 0.000000e+00 2582
2 TraesCS6B01G035200 chr6B 87.582 2142 246 13 169 2307 20826216 20828340 0.000000e+00 2464
3 TraesCS6B01G035200 chr6B 87.577 1948 211 25 175 2115 21043600 21045523 0.000000e+00 2228
4 TraesCS6B01G035200 chr6B 85.779 1976 267 11 147 2116 21004274 21006241 0.000000e+00 2080
5 TraesCS6B01G035200 chr6B 83.974 2134 314 20 164 2293 20976724 20978833 0.000000e+00 2021
6 TraesCS6B01G035200 chr6B 85.417 960 121 14 1351 2306 20695658 20696602 0.000000e+00 979
7 TraesCS6B01G035200 chr6B 90.037 271 15 5 2534 2794 20697178 20697446 1.100000e-89 340
8 TraesCS6B01G035200 chr6D 90.379 2214 198 12 1 2207 11046278 11048483 0.000000e+00 2894
9 TraesCS6B01G035200 chr6D 87.058 2233 248 27 184 2389 11089651 11091869 0.000000e+00 2484
10 TraesCS6B01G035200 chr6D 88.421 2064 198 25 152 2207 10943910 10945940 0.000000e+00 2449
11 TraesCS6B01G035200 chr6D 87.532 1925 232 6 194 2116 11113391 11115309 0.000000e+00 2218
12 TraesCS6B01G035200 chr6D 85.787 1977 247 23 147 2116 10921316 10923265 0.000000e+00 2063
13 TraesCS6B01G035200 chr6D 92.035 113 9 0 2682 2794 11048806 11048918 3.320000e-35 159
14 TraesCS6B01G035200 chr6A 88.616 2117 229 7 1 2116 12410178 12412283 0.000000e+00 2564
15 TraesCS6B01G035200 chr6A 95.455 66 3 0 3147 3212 12418250 12418315 4.380000e-19 106
16 TraesCS6B01G035200 chr7B 99.157 356 3 0 2790 3145 129548006 129548361 2.700000e-180 641
17 TraesCS6B01G035200 chr7B 98.588 354 4 1 2793 3145 129542667 129543020 2.720000e-175 625
18 TraesCS6B01G035200 chr7B 98.295 352 6 0 2794 3145 665685445 665685094 4.550000e-173 617
19 TraesCS6B01G035200 chr7B 96.884 353 9 1 2794 3146 284147065 284147415 9.920000e-165 590
20 TraesCS6B01G035200 chr3B 98.596 356 5 0 2790 3145 691361489 691361844 5.850000e-177 630
21 TraesCS6B01G035200 chr3B 97.727 352 5 1 2794 3145 691358457 691358805 1.270000e-168 603
22 TraesCS6B01G035200 chr5B 97.479 357 9 0 2790 3146 493651053 493651409 7.620000e-171 610
23 TraesCS6B01G035200 chr5B 97.721 351 7 1 2795 3145 493636946 493637295 1.270000e-168 603
24 TraesCS6B01G035200 chr1B 96.348 356 13 0 2790 3145 36563375 36563730 1.280000e-163 586


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 TraesCS6B01G035200 chr6B 20922986 20926197 3211 False 5932.0 5932 100.0000 1 3212 1 chr6B.!!$F3 3211
1 TraesCS6B01G035200 chr6B 20783765 20785918 2153 False 2582.0 2582 88.3460 147 2307 1 chr6B.!!$F1 2160
2 TraesCS6B01G035200 chr6B 20826216 20828340 2124 False 2464.0 2464 87.5820 169 2307 1 chr6B.!!$F2 2138
3 TraesCS6B01G035200 chr6B 21043600 21045523 1923 False 2228.0 2228 87.5770 175 2115 1 chr6B.!!$F6 1940
4 TraesCS6B01G035200 chr6B 21004274 21006241 1967 False 2080.0 2080 85.7790 147 2116 1 chr6B.!!$F5 1969
5 TraesCS6B01G035200 chr6B 20976724 20978833 2109 False 2021.0 2021 83.9740 164 2293 1 chr6B.!!$F4 2129
6 TraesCS6B01G035200 chr6B 20695658 20697446 1788 False 659.5 979 87.7270 1351 2794 2 chr6B.!!$F7 1443
7 TraesCS6B01G035200 chr6D 11089651 11091869 2218 False 2484.0 2484 87.0580 184 2389 1 chr6D.!!$F3 2205
8 TraesCS6B01G035200 chr6D 10943910 10945940 2030 False 2449.0 2449 88.4210 152 2207 1 chr6D.!!$F2 2055
9 TraesCS6B01G035200 chr6D 11113391 11115309 1918 False 2218.0 2218 87.5320 194 2116 1 chr6D.!!$F4 1922
10 TraesCS6B01G035200 chr6D 10921316 10923265 1949 False 2063.0 2063 85.7870 147 2116 1 chr6D.!!$F1 1969
11 TraesCS6B01G035200 chr6D 11046278 11048918 2640 False 1526.5 2894 91.2070 1 2794 2 chr6D.!!$F5 2793
12 TraesCS6B01G035200 chr6A 12410178 12412283 2105 False 2564.0 2564 88.6160 1 2116 1 chr6A.!!$F1 2115
13 TraesCS6B01G035200 chr3B 691358457 691361844 3387 False 616.5 630 98.1615 2790 3145 2 chr3B.!!$F1 355

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
462 463 0.602372 GGAGGAAGATGAGCGATGGC 60.602 60.000 0.0 0.0 40.37 4.40 F
1261 1271 2.346803 CAGATGATCGTTTGGACCGTT 58.653 47.619 0.0 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1275 0.470341 GGCATCCTCTCCCCTAACAC 59.530 60.0 0.00 0.0 0.00 3.32 R
3172 3740 0.038159 GGAACAGGTCTGTGAGGACG 60.038 60.0 4.22 0.0 44.13 4.79 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
142 143 4.779993 ACCCATGGAGAGGATAGTTTTC 57.220 45.455 15.22 0.00 0.00 2.29
155 156 6.044682 AGGATAGTTTTCCGTAAACATACCG 58.955 40.000 11.48 0.00 46.93 4.02
304 305 8.978874 ATTATGTATGTTGCAGGTATTCAAGA 57.021 30.769 0.00 0.00 0.00 3.02
340 341 4.078639 ACAGATTTAGTCCCAGCTATGC 57.921 45.455 0.00 0.00 0.00 3.14
437 438 4.465886 TCCACTAAGCCAAAAACTGCTAA 58.534 39.130 0.00 0.00 36.66 3.09
462 463 0.602372 GGAGGAAGATGAGCGATGGC 60.602 60.000 0.00 0.00 40.37 4.40
468 469 3.397482 GAAGATGAGCGATGGCATTAGT 58.603 45.455 0.00 0.00 43.41 2.24
492 493 7.937942 AGTATTGAATTGGAGATGAATCCTGAG 59.062 37.037 0.00 0.00 40.29 3.35
736 737 2.451493 TGCCAGGGGAAGGGACAA 60.451 61.111 0.00 0.00 0.00 3.18
899 900 3.138884 TCTTGTCATTGGCAGCAACTA 57.861 42.857 0.00 0.00 0.00 2.24
1215 1216 2.593346 TGCCAACAACAATCACCAAC 57.407 45.000 0.00 0.00 0.00 3.77
1261 1271 2.346803 CAGATGATCGTTTGGACCGTT 58.653 47.619 0.00 0.00 0.00 4.44
1262 1272 2.742053 CAGATGATCGTTTGGACCGTTT 59.258 45.455 0.00 0.00 0.00 3.60
1265 1275 0.452122 GATCGTTTGGACCGTTTGCG 60.452 55.000 0.00 0.00 37.95 4.85
1283 1296 0.105039 CGTGTTAGGGGAGAGGATGC 59.895 60.000 0.00 0.00 0.00 3.91
1599 1615 1.958288 AAGTGGGTGGTCTGAGCTAT 58.042 50.000 8.47 0.00 0.00 2.97
1787 1806 4.811557 GCTAGTCAATGTAACAGGATGGAC 59.188 45.833 0.00 0.00 43.62 4.02
1875 1894 3.563479 CCATACAAGCCCTTGGGTTACTT 60.563 47.826 12.22 0.00 41.85 2.24
1914 1933 0.676782 GTCTGGGGGTGGATTCGTTG 60.677 60.000 0.00 0.00 0.00 4.10
1978 1997 2.941064 CTCATGGTGCTGGAGTTGTATG 59.059 50.000 0.00 0.00 0.00 2.39
2145 2164 7.067372 AGTCATTGTCTCAGTGAAACATTGAAA 59.933 33.333 20.28 3.26 41.43 2.69
2169 2188 1.219393 GGTGCAGAGTCAGGTAGCC 59.781 63.158 0.00 0.00 0.00 3.93
2197 2216 6.238676 GCATATGAAGCATGTCAGAGTGAATT 60.239 38.462 6.97 0.00 0.00 2.17
2206 2226 6.732154 CATGTCAGAGTGAATTTTGTTGACT 58.268 36.000 3.76 0.00 35.66 3.41
2208 2228 6.554419 TGTCAGAGTGAATTTTGTTGACTTG 58.446 36.000 3.76 0.00 35.66 3.16
2213 2233 9.520204 CAGAGTGAATTTTGTTGACTTGTAAAT 57.480 29.630 0.00 0.00 0.00 1.40
2298 2442 3.008049 ACTCGCTCTTGTAATTGTCCCTT 59.992 43.478 0.00 0.00 0.00 3.95
2313 2457 1.211949 TCCCTTTGGTACTATGCTGGC 59.788 52.381 0.00 0.00 0.00 4.85
2323 2483 6.701340 TGGTACTATGCTGGCAGATAATTAG 58.299 40.000 20.86 12.34 0.00 1.73
2355 2516 3.695830 TCTCCCACGCTAATTCAGTTT 57.304 42.857 0.00 0.00 0.00 2.66
2389 2550 3.787785 TGTGTTGACTCTGCGTTTCTTA 58.212 40.909 0.00 0.00 0.00 2.10
2390 2551 4.185394 TGTGTTGACTCTGCGTTTCTTAA 58.815 39.130 0.00 0.00 0.00 1.85
2391 2552 4.814234 TGTGTTGACTCTGCGTTTCTTAAT 59.186 37.500 0.00 0.00 0.00 1.40
2393 2554 5.846473 GTGTTGACTCTGCGTTTCTTAATTC 59.154 40.000 0.00 0.00 0.00 2.17
2394 2555 5.758296 TGTTGACTCTGCGTTTCTTAATTCT 59.242 36.000 0.00 0.00 0.00 2.40
2429 2591 2.224784 GGCATTTCTTTGCTTTTGGCTG 59.775 45.455 0.00 0.00 42.38 4.85
2458 2620 3.067180 CAGTAATGGTTGATGGCATGTCC 59.933 47.826 3.81 4.96 0.00 4.02
2464 2626 2.100252 GGTTGATGGCATGTCCTTGATG 59.900 50.000 3.81 0.00 35.26 3.07
2482 2644 2.489938 TGATGTGGCCTAACTGAACC 57.510 50.000 3.32 0.00 0.00 3.62
2483 2645 1.004277 TGATGTGGCCTAACTGAACCC 59.996 52.381 3.32 0.00 0.00 4.11
2485 2647 1.072266 TGTGGCCTAACTGAACCCAT 58.928 50.000 3.32 0.00 0.00 4.00
2487 2649 2.645297 TGTGGCCTAACTGAACCCATTA 59.355 45.455 3.32 0.00 0.00 1.90
2488 2650 3.014623 GTGGCCTAACTGAACCCATTAC 58.985 50.000 3.32 0.00 0.00 1.89
2507 2669 6.239430 CCATTACTGCTCCTCTGCTCTTAATA 60.239 42.308 0.00 0.00 0.00 0.98
2534 2699 1.467678 CCCGCTACTGCTGCCTATCT 61.468 60.000 0.00 0.00 36.97 1.98
2535 2700 1.248486 CCGCTACTGCTGCCTATCTA 58.752 55.000 0.00 0.00 36.97 1.98
2551 3111 5.460419 GCCTATCTAAAACAGACATGTCGAG 59.540 44.000 19.85 18.01 39.29 4.04
2560 3121 1.364626 GACATGTCGAGGCAGGCTTG 61.365 60.000 10.69 4.73 0.00 4.01
2562 3123 1.088340 CATGTCGAGGCAGGCTTGAG 61.088 60.000 14.36 0.00 0.00 3.02
2583 3144 1.658994 TCACAGTTGAACCACGTTCC 58.341 50.000 2.26 0.00 41.35 3.62
2584 3145 1.066071 TCACAGTTGAACCACGTTCCA 60.066 47.619 2.26 0.00 41.35 3.53
2597 3165 0.802494 CGTTCCAATACACCAGGTGC 59.198 55.000 20.48 0.00 36.98 5.01
2631 3199 2.618709 GTGTAACAGCTCAGCTTTTGGT 59.381 45.455 8.40 0.00 36.40 3.67
2691 3259 1.895131 GTGTGGGCCTTCATGTTGAAT 59.105 47.619 4.53 0.00 35.59 2.57
2697 3265 3.629398 GGGCCTTCATGTTGAATAGTGAG 59.371 47.826 0.84 0.00 35.59 3.51
2706 3274 6.697455 TCATGTTGAATAGTGAGAGCGAATAC 59.303 38.462 0.00 0.00 0.00 1.89
2729 3297 2.039462 AATTCCCAGCCCCTTGCC 59.961 61.111 0.00 0.00 42.71 4.52
2737 3305 2.118294 GCCCCTTGCCCTGTTTCT 59.882 61.111 0.00 0.00 0.00 2.52
2768 3336 1.346068 GAACCTTGAGGAGCTGACAGT 59.654 52.381 3.59 0.00 38.94 3.55
2777 3345 2.945668 AGGAGCTGACAGTCAACAAAAC 59.054 45.455 4.41 0.00 0.00 2.43
2782 3350 4.811557 AGCTGACAGTCAACAAAACTCTAC 59.188 41.667 4.41 0.00 0.00 2.59
2784 3352 5.277058 GCTGACAGTCAACAAAACTCTACAG 60.277 44.000 4.41 0.00 0.00 2.74
2866 3434 4.787280 AGGGAGACGAGGGCTGGG 62.787 72.222 0.00 0.00 0.00 4.45
3106 3674 1.339727 GCCCCTAATACTAATGCCCGG 60.340 57.143 0.00 0.00 0.00 5.73
3148 3716 3.552604 CCAAACCGGTCATAACACAAG 57.447 47.619 8.04 0.00 0.00 3.16
3149 3717 2.882137 CCAAACCGGTCATAACACAAGT 59.118 45.455 8.04 0.00 0.00 3.16
3150 3718 4.066490 CCAAACCGGTCATAACACAAGTA 58.934 43.478 8.04 0.00 0.00 2.24
3151 3719 4.153475 CCAAACCGGTCATAACACAAGTAG 59.847 45.833 8.04 0.00 0.00 2.57
3152 3720 4.877378 AACCGGTCATAACACAAGTAGA 57.123 40.909 8.04 0.00 0.00 2.59
3153 3721 4.451629 ACCGGTCATAACACAAGTAGAG 57.548 45.455 0.00 0.00 0.00 2.43
3154 3722 3.187700 CCGGTCATAACACAAGTAGAGC 58.812 50.000 0.00 0.00 0.00 4.09
3155 3723 3.368013 CCGGTCATAACACAAGTAGAGCA 60.368 47.826 0.00 0.00 0.00 4.26
3156 3724 4.242475 CGGTCATAACACAAGTAGAGCAA 58.758 43.478 0.00 0.00 0.00 3.91
3157 3725 4.327357 CGGTCATAACACAAGTAGAGCAAG 59.673 45.833 0.00 0.00 0.00 4.01
3158 3726 4.093556 GGTCATAACACAAGTAGAGCAAGC 59.906 45.833 0.00 0.00 0.00 4.01
3159 3727 4.690748 GTCATAACACAAGTAGAGCAAGCA 59.309 41.667 0.00 0.00 0.00 3.91
3160 3728 5.179368 GTCATAACACAAGTAGAGCAAGCAA 59.821 40.000 0.00 0.00 0.00 3.91
3161 3729 3.971032 AACACAAGTAGAGCAAGCAAC 57.029 42.857 0.00 0.00 0.00 4.17
3162 3730 2.917933 ACACAAGTAGAGCAAGCAACA 58.082 42.857 0.00 0.00 0.00 3.33
3163 3731 2.874701 ACACAAGTAGAGCAAGCAACAG 59.125 45.455 0.00 0.00 0.00 3.16
3164 3732 3.133691 CACAAGTAGAGCAAGCAACAGA 58.866 45.455 0.00 0.00 0.00 3.41
3165 3733 3.186001 CACAAGTAGAGCAAGCAACAGAG 59.814 47.826 0.00 0.00 0.00 3.35
3166 3734 3.070159 ACAAGTAGAGCAAGCAACAGAGA 59.930 43.478 0.00 0.00 0.00 3.10
3167 3735 3.591196 AGTAGAGCAAGCAACAGAGAG 57.409 47.619 0.00 0.00 0.00 3.20
3168 3736 3.161067 AGTAGAGCAAGCAACAGAGAGA 58.839 45.455 0.00 0.00 0.00 3.10
3169 3737 3.768757 AGTAGAGCAAGCAACAGAGAGAT 59.231 43.478 0.00 0.00 0.00 2.75
3170 3738 4.952957 AGTAGAGCAAGCAACAGAGAGATA 59.047 41.667 0.00 0.00 0.00 1.98
3171 3739 5.598005 AGTAGAGCAAGCAACAGAGAGATAT 59.402 40.000 0.00 0.00 0.00 1.63
3172 3740 4.947645 AGAGCAAGCAACAGAGAGATATC 58.052 43.478 0.00 0.00 0.00 1.63
3173 3741 3.715495 AGCAAGCAACAGAGAGATATCG 58.285 45.455 0.00 0.00 0.00 2.92
3174 3742 3.131933 AGCAAGCAACAGAGAGATATCGT 59.868 43.478 0.00 0.00 0.00 3.73
3175 3743 3.489047 GCAAGCAACAGAGAGATATCGTC 59.511 47.826 0.00 0.00 0.00 4.20
3176 3744 4.047822 CAAGCAACAGAGAGATATCGTCC 58.952 47.826 0.00 0.00 0.00 4.79
3177 3745 3.561143 AGCAACAGAGAGATATCGTCCT 58.439 45.455 0.00 0.00 0.00 3.85
3178 3746 3.568007 AGCAACAGAGAGATATCGTCCTC 59.432 47.826 12.11 12.11 0.00 3.71
3179 3747 3.316588 GCAACAGAGAGATATCGTCCTCA 59.683 47.826 18.38 0.00 30.82 3.86
3180 3748 4.791411 GCAACAGAGAGATATCGTCCTCAC 60.791 50.000 18.38 3.41 30.82 3.51
3181 3749 4.157849 ACAGAGAGATATCGTCCTCACA 57.842 45.455 18.38 0.00 30.82 3.58
3182 3750 4.133820 ACAGAGAGATATCGTCCTCACAG 58.866 47.826 18.38 12.63 30.82 3.66
3183 3751 4.141597 ACAGAGAGATATCGTCCTCACAGA 60.142 45.833 18.38 0.00 30.82 3.41
3184 3752 4.213270 CAGAGAGATATCGTCCTCACAGAC 59.787 50.000 18.38 0.00 30.82 3.51
3185 3753 3.482436 AGAGATATCGTCCTCACAGACC 58.518 50.000 0.00 0.00 32.91 3.85
3186 3754 3.137544 AGAGATATCGTCCTCACAGACCT 59.862 47.826 0.00 0.00 32.91 3.85
3187 3755 3.218453 AGATATCGTCCTCACAGACCTG 58.782 50.000 0.00 0.00 32.91 4.00
3188 3756 2.509166 TATCGTCCTCACAGACCTGT 57.491 50.000 0.00 0.00 46.17 4.00
3189 3757 1.633774 ATCGTCCTCACAGACCTGTT 58.366 50.000 0.00 0.00 42.83 3.16
3190 3758 0.959553 TCGTCCTCACAGACCTGTTC 59.040 55.000 0.00 0.00 42.83 3.18
3191 3759 0.038159 CGTCCTCACAGACCTGTTCC 60.038 60.000 0.00 0.00 42.83 3.62
3192 3760 1.343069 GTCCTCACAGACCTGTTCCT 58.657 55.000 0.00 0.00 42.83 3.36
3193 3761 1.694696 GTCCTCACAGACCTGTTCCTT 59.305 52.381 0.00 0.00 42.83 3.36
3194 3762 2.104963 GTCCTCACAGACCTGTTCCTTT 59.895 50.000 0.00 0.00 42.83 3.11
3195 3763 2.777692 TCCTCACAGACCTGTTCCTTTT 59.222 45.455 0.00 0.00 42.83 2.27
3196 3764 3.202151 TCCTCACAGACCTGTTCCTTTTT 59.798 43.478 0.00 0.00 42.83 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.394767 TGTGCACAAAACTGTAATCATAGATAT 57.605 29.630 19.28 0.00 0.00 1.63
106 107 9.408648 CTCTCCATGGGTTTAACATTTACTAAT 57.591 33.333 13.02 0.00 0.00 1.73
122 123 3.495100 CGGAAAACTATCCTCTCCATGGG 60.495 52.174 13.02 2.57 37.34 4.00
142 143 2.204237 GCCCTAACGGTATGTTTACGG 58.796 52.381 0.00 0.00 42.09 4.02
155 156 0.965866 GTCAAAGCCCTGGCCCTAAC 60.966 60.000 4.13 0.00 43.17 2.34
286 287 6.594788 ATTGTTCTTGAATACCTGCAACAT 57.405 33.333 0.00 0.00 0.00 2.71
340 341 0.106819 ATAGGCCTTGCTTGCTCCAG 60.107 55.000 12.58 0.00 0.00 3.86
354 355 1.952296 CCACATTTCTGCAGGATAGGC 59.048 52.381 15.13 0.00 0.00 3.93
437 438 2.702478 TCGCTCATCTTCCTCCATTCAT 59.298 45.455 0.00 0.00 0.00 2.57
468 469 6.713903 GCTCAGGATTCATCTCCAATTCAATA 59.286 38.462 0.00 0.00 37.81 1.90
616 617 4.767255 CTCTGCAGTCCACCGCCC 62.767 72.222 14.67 0.00 0.00 6.13
736 737 8.031277 GGAATTGATTTTCTGACTGTATTGCTT 58.969 33.333 0.00 0.00 0.00 3.91
899 900 4.952335 CCAGCACATCTTTATCCCTTTTCT 59.048 41.667 0.00 0.00 0.00 2.52
1215 1216 1.277557 AGGTGCTGTAGCTTCAGAAGG 59.722 52.381 23.06 0.00 42.66 3.46
1261 1271 0.543410 TCCTCTCCCCTAACACGCAA 60.543 55.000 0.00 0.00 0.00 4.85
1262 1272 0.325296 ATCCTCTCCCCTAACACGCA 60.325 55.000 0.00 0.00 0.00 5.24
1265 1275 0.470341 GGCATCCTCTCCCCTAACAC 59.530 60.000 0.00 0.00 0.00 3.32
1570 1586 3.393278 AGACCACCCACTTTAAGCTTACA 59.607 43.478 5.45 0.00 0.00 2.41
1599 1615 7.323420 CAGACCATAACTCACTGATGTTTCTA 58.677 38.462 0.00 0.00 0.00 2.10
1787 1806 3.553922 GGAGAGATTCTGAAGCGTATGGG 60.554 52.174 0.00 0.00 0.00 4.00
1875 1894 3.994392 GACGTAGAACTGCAAGATTTGGA 59.006 43.478 0.00 0.00 37.43 3.53
1914 1933 3.374058 CGAAATGGAGTTGTGTCCCATAC 59.626 47.826 0.00 0.00 39.58 2.39
2145 2164 1.701847 ACCTGACTCTGCACCAATTCT 59.298 47.619 0.00 0.00 0.00 2.40
2169 2188 3.387397 TCTGACATGCTTCATATGCTCG 58.613 45.455 0.00 0.00 0.00 5.03
2236 2376 6.015282 TGTGCTCTGATGATGGAGTCTATAT 58.985 40.000 0.00 0.00 32.67 0.86
2237 2377 5.388654 TGTGCTCTGATGATGGAGTCTATA 58.611 41.667 0.00 0.00 32.67 1.31
2238 2378 4.221530 TGTGCTCTGATGATGGAGTCTAT 58.778 43.478 0.00 0.00 32.67 1.98
2239 2379 3.635591 TGTGCTCTGATGATGGAGTCTA 58.364 45.455 0.00 0.00 32.67 2.59
2240 2380 2.464782 TGTGCTCTGATGATGGAGTCT 58.535 47.619 0.00 0.00 32.67 3.24
2241 2381 2.975732 TGTGCTCTGATGATGGAGTC 57.024 50.000 0.00 0.00 32.67 3.36
2242 2382 3.262660 TCTTTGTGCTCTGATGATGGAGT 59.737 43.478 0.00 0.00 32.67 3.85
2243 2383 3.870274 TCTTTGTGCTCTGATGATGGAG 58.130 45.455 0.00 0.00 0.00 3.86
2244 2384 3.986996 TCTTTGTGCTCTGATGATGGA 57.013 42.857 0.00 0.00 0.00 3.41
2247 2387 4.398358 CACCAATCTTTGTGCTCTGATGAT 59.602 41.667 0.00 0.00 0.00 2.45
2248 2388 3.754850 CACCAATCTTTGTGCTCTGATGA 59.245 43.478 0.00 0.00 0.00 2.92
2257 2397 2.548057 AGTACACGCACCAATCTTTGTG 59.452 45.455 0.00 0.00 0.00 3.33
2298 2442 5.567037 ATTATCTGCCAGCATAGTACCAA 57.433 39.130 0.00 0.00 0.00 3.67
2313 2457 8.341173 GGAGAACAAGCAATGACTAATTATCTG 58.659 37.037 0.00 0.00 0.00 2.90
2323 2483 1.197721 CGTGGGAGAACAAGCAATGAC 59.802 52.381 0.00 0.00 0.00 3.06
2355 2516 6.090763 CAGAGTCAACACATAAATACTTGCGA 59.909 38.462 0.00 0.00 0.00 5.10
2389 2550 4.843728 TGCCTATTCGGTCAAAGAGAATT 58.156 39.130 0.00 0.00 36.23 2.17
2390 2551 4.487714 TGCCTATTCGGTCAAAGAGAAT 57.512 40.909 0.00 0.00 38.12 2.40
2391 2552 3.973206 TGCCTATTCGGTCAAAGAGAA 57.027 42.857 0.00 0.00 34.25 2.87
2393 2554 4.878397 AGAAATGCCTATTCGGTCAAAGAG 59.122 41.667 0.00 0.00 34.25 2.85
2394 2555 4.843728 AGAAATGCCTATTCGGTCAAAGA 58.156 39.130 0.00 0.00 34.25 2.52
2429 2591 1.167851 TCAACCATTACTGCAGCAGC 58.832 50.000 23.05 0.00 42.57 5.25
2458 2620 3.877559 TCAGTTAGGCCACATCATCAAG 58.122 45.455 5.01 0.00 0.00 3.02
2464 2626 1.004277 TGGGTTCAGTTAGGCCACATC 59.996 52.381 5.01 0.00 0.00 3.06
2482 2644 1.761784 AGAGCAGAGGAGCAGTAATGG 59.238 52.381 0.00 0.00 36.85 3.16
2483 2645 3.540314 AAGAGCAGAGGAGCAGTAATG 57.460 47.619 0.00 0.00 36.85 1.90
2485 2647 6.780031 AGATATTAAGAGCAGAGGAGCAGTAA 59.220 38.462 0.00 0.00 36.85 2.24
2487 2649 5.147032 AGATATTAAGAGCAGAGGAGCAGT 58.853 41.667 0.00 0.00 36.85 4.40
2488 2650 5.726980 AGATATTAAGAGCAGAGGAGCAG 57.273 43.478 0.00 0.00 36.85 4.24
2534 2699 3.325870 CTGCCTCGACATGTCTGTTTTA 58.674 45.455 22.95 5.08 35.14 1.52
2535 2700 2.146342 CTGCCTCGACATGTCTGTTTT 58.854 47.619 22.95 0.00 35.14 2.43
2551 3111 0.536006 ACTGTGAACTCAAGCCTGCC 60.536 55.000 0.00 0.00 0.00 4.85
2575 3136 1.271163 ACCTGGTGTATTGGAACGTGG 60.271 52.381 0.00 0.00 0.00 4.94
2576 3137 1.804151 CACCTGGTGTATTGGAACGTG 59.196 52.381 18.76 0.00 0.00 4.49
2577 3138 1.880646 GCACCTGGTGTATTGGAACGT 60.881 52.381 26.48 0.00 35.75 3.99
2578 3139 0.802494 GCACCTGGTGTATTGGAACG 59.198 55.000 26.48 0.00 35.75 3.95
2579 3140 1.173913 GGCACCTGGTGTATTGGAAC 58.826 55.000 26.48 8.31 35.75 3.62
2580 3141 1.072266 AGGCACCTGGTGTATTGGAA 58.928 50.000 26.48 0.00 35.75 3.53
2581 3142 0.327924 CAGGCACCTGGTGTATTGGA 59.672 55.000 26.48 0.00 40.17 3.53
2582 3143 1.315257 GCAGGCACCTGGTGTATTGG 61.315 60.000 26.48 13.55 43.77 3.16
2583 3144 1.315257 GGCAGGCACCTGGTGTATTG 61.315 60.000 26.48 21.17 43.77 1.90
2584 3145 1.000896 GGCAGGCACCTGGTGTATT 60.001 57.895 26.48 10.81 43.77 1.89
2597 3165 3.545124 TTACACCGTGGCAGGCAGG 62.545 63.158 9.66 9.66 33.69 4.85
2631 3199 3.141398 GAGGCATTCATTCTTCGGCATA 58.859 45.455 0.00 0.00 0.00 3.14
2691 3259 6.641169 ATTCAGATGTATTCGCTCTCACTA 57.359 37.500 0.00 0.00 0.00 2.74
2697 3265 4.380531 TGGGAATTCAGATGTATTCGCTC 58.619 43.478 21.30 9.53 41.70 5.03
2706 3274 0.554792 AGGGGCTGGGAATTCAGATG 59.445 55.000 7.93 0.00 36.93 2.90
2729 3297 0.247736 CAGTCGGGAGGAGAAACAGG 59.752 60.000 0.00 0.00 0.00 4.00
2737 3305 0.178944 TCAAGGTTCAGTCGGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
2768 3336 6.318648 ACTTGAATGCTGTAGAGTTTTGTTGA 59.681 34.615 0.00 0.00 0.00 3.18
2777 3345 4.872691 CCTACCAACTTGAATGCTGTAGAG 59.127 45.833 0.00 0.00 0.00 2.43
2782 3350 3.679389 AGTCCTACCAACTTGAATGCTG 58.321 45.455 0.00 0.00 0.00 4.41
2784 3352 4.192317 CCTAGTCCTACCAACTTGAATGC 58.808 47.826 0.00 0.00 0.00 3.56
3106 3674 3.637694 GTCTATACCAGGAAGAGTCCCAC 59.362 52.174 0.00 0.00 46.30 4.61
3145 3713 3.657634 TCTCTGTTGCTTGCTCTACTTG 58.342 45.455 0.00 0.00 0.00 3.16
3146 3714 3.576118 TCTCTCTGTTGCTTGCTCTACTT 59.424 43.478 0.00 0.00 0.00 2.24
3147 3715 3.161067 TCTCTCTGTTGCTTGCTCTACT 58.839 45.455 0.00 0.00 0.00 2.57
3148 3716 3.584406 TCTCTCTGTTGCTTGCTCTAC 57.416 47.619 0.00 0.00 0.00 2.59
3149 3717 5.278218 CGATATCTCTCTGTTGCTTGCTCTA 60.278 44.000 0.34 0.00 0.00 2.43
3150 3718 4.499526 CGATATCTCTCTGTTGCTTGCTCT 60.500 45.833 0.34 0.00 0.00 4.09
3151 3719 3.735240 CGATATCTCTCTGTTGCTTGCTC 59.265 47.826 0.34 0.00 0.00 4.26
3152 3720 3.131933 ACGATATCTCTCTGTTGCTTGCT 59.868 43.478 0.34 0.00 0.00 3.91
3153 3721 3.452474 ACGATATCTCTCTGTTGCTTGC 58.548 45.455 0.34 0.00 0.00 4.01
3154 3722 4.047822 GGACGATATCTCTCTGTTGCTTG 58.952 47.826 0.34 0.00 0.00 4.01
3155 3723 3.957497 AGGACGATATCTCTCTGTTGCTT 59.043 43.478 0.34 0.00 0.00 3.91
3156 3724 3.561143 AGGACGATATCTCTCTGTTGCT 58.439 45.455 0.34 0.00 0.00 3.91
3157 3725 3.316588 TGAGGACGATATCTCTCTGTTGC 59.683 47.826 14.40 0.00 0.00 4.17
3158 3726 4.336713 TGTGAGGACGATATCTCTCTGTTG 59.663 45.833 14.40 0.00 0.00 3.33
3159 3727 4.527944 TGTGAGGACGATATCTCTCTGTT 58.472 43.478 14.40 0.00 0.00 3.16
3160 3728 4.133820 CTGTGAGGACGATATCTCTCTGT 58.866 47.826 14.40 0.94 0.00 3.41
3161 3729 4.213270 GTCTGTGAGGACGATATCTCTCTG 59.787 50.000 14.40 6.03 0.00 3.35
3162 3730 4.385825 GTCTGTGAGGACGATATCTCTCT 58.614 47.826 14.40 4.50 0.00 3.10
3163 3731 3.500680 GGTCTGTGAGGACGATATCTCTC 59.499 52.174 0.34 6.01 37.12 3.20
3164 3732 3.137544 AGGTCTGTGAGGACGATATCTCT 59.862 47.826 0.34 0.00 37.12 3.10
3165 3733 3.252215 CAGGTCTGTGAGGACGATATCTC 59.748 52.174 0.34 0.00 37.12 2.75
3166 3734 3.218453 CAGGTCTGTGAGGACGATATCT 58.782 50.000 0.34 0.00 37.12 1.98
3167 3735 2.952978 ACAGGTCTGTGAGGACGATATC 59.047 50.000 2.46 0.00 43.11 1.63
3168 3736 3.019799 ACAGGTCTGTGAGGACGATAT 57.980 47.619 2.46 0.00 43.11 1.63
3169 3737 2.509166 ACAGGTCTGTGAGGACGATA 57.491 50.000 2.46 0.00 43.11 2.92
3170 3738 1.546476 GAACAGGTCTGTGAGGACGAT 59.454 52.381 4.22 0.00 44.13 3.73
3171 3739 0.959553 GAACAGGTCTGTGAGGACGA 59.040 55.000 4.22 0.00 44.13 4.20
3172 3740 0.038159 GGAACAGGTCTGTGAGGACG 60.038 60.000 4.22 0.00 44.13 4.79
3173 3741 1.343069 AGGAACAGGTCTGTGAGGAC 58.657 55.000 4.22 0.00 44.13 3.85
3174 3742 2.103153 AAGGAACAGGTCTGTGAGGA 57.897 50.000 4.22 0.00 44.13 3.71
3175 3743 2.938956 AAAGGAACAGGTCTGTGAGG 57.061 50.000 4.22 0.00 44.13 3.86


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

AutoCloner maintained by Alex Coulton.