Multiple sequence alignment - TraesCS6B01G211900

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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 TraesCS6B01G211900 chr6B 100.000 3521 0 0 1 3521 280051041 280047521 0.000000e+00 6503.0
1 TraesCS6B01G211900 chr6A 91.127 3595 197 56 1 3520 215526849 215530396 0.000000e+00 4759.0
2 TraesCS6B01G211900 chr6D 93.167 2005 59 33 716 2675 157168495 157166524 0.000000e+00 2872.0
3 TraesCS6B01G211900 chr6D 91.521 401 9 4 3001 3383 157166171 157165778 2.410000e-146 529.0
4 TraesCS6B01G211900 chr6D 91.946 298 11 7 2686 2970 157166468 157166171 4.230000e-109 405.0
5 TraesCS6B01G211900 chr6D 97.321 112 3 0 3410 3521 157165778 157165667 1.290000e-44 191.0
6 TraesCS6B01G211900 chr7D 75.978 716 151 17 1346 2051 459873478 459872774 2.010000e-92 350.0
7 TraesCS6B01G211900 chr7D 96.970 33 1 0 590 622 45001563 45001531 4.910000e-04 56.5
8 TraesCS6B01G211900 chr7A 75.524 715 154 18 1347 2051 539652067 539652770 7.290000e-87 331.0
9 TraesCS6B01G211900 chr7B 75.522 719 149 22 1346 2051 482175897 482175193 9.420000e-86 327.0
10 TraesCS6B01G211900 chr2D 88.406 69 6 2 590 657 595155778 595155845 8.100000e-12 82.4
11 TraesCS6B01G211900 chr5D 88.889 63 7 0 595 657 482005428 482005490 1.050000e-10 78.7
12 TraesCS6B01G211900 chr1A 100.000 28 0 0 590 617 5827526 5827553 6.000000e-03 52.8


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 TraesCS6B01G211900 chr6B 280047521 280051041 3520 True 6503.00 6503 100.00000 1 3521 1 chr6B.!!$R1 3520
1 TraesCS6B01G211900 chr6A 215526849 215530396 3547 False 4759.00 4759 91.12700 1 3520 1 chr6A.!!$F1 3519
2 TraesCS6B01G211900 chr6D 157165667 157168495 2828 True 999.25 2872 93.48875 716 3521 4 chr6D.!!$R1 2805
3 TraesCS6B01G211900 chr7D 459872774 459873478 704 True 350.00 350 75.97800 1346 2051 1 chr7D.!!$R2 705
4 TraesCS6B01G211900 chr7A 539652067 539652770 703 False 331.00 331 75.52400 1347 2051 1 chr7A.!!$F1 704
5 TraesCS6B01G211900 chr7B 482175193 482175897 704 True 327.00 327 75.52200 1346 2051 1 chr7B.!!$R1 705

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
372 374 0.181350 CCACATTCCTAGGCCTGACC 59.819 60.0 17.99 0.0 39.61 4.02 F
1607 1628 0.037326 ACATGGTGATCAACGCGTCT 60.037 50.0 14.44 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2217 0.179012 GGAGGAGGAGAGGACGTAGG 60.179 65.0 0.0 0.0 0.0 3.18 R
2665 2736 0.264359 AGAGCAGCAGACCCTCCTAT 59.736 55.0 0.0 0.0 0.0 2.57 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 4.605183 AGAAGAGGAAGAAGAAGGATCGA 58.395 43.478 0.00 0.00 0.00 3.59
36 37 1.751924 AGGAAGAAGAAGGATCGACGG 59.248 52.381 0.00 0.00 0.00 4.79
76 77 4.056125 TGTCGCTGACCTGCTCGG 62.056 66.667 6.30 0.00 39.35 4.63
164 166 1.070289 GTGGACGAGGGCTAAATAGGG 59.930 57.143 0.00 0.00 0.00 3.53
187 189 2.787473 TCAAATTGGCGAGAGGTGAT 57.213 45.000 0.00 0.00 0.00 3.06
200 202 2.776536 AGAGGTGATCCAATTCCTCCAG 59.223 50.000 5.27 0.00 45.16 3.86
201 203 2.507471 GAGGTGATCCAATTCCTCCAGT 59.493 50.000 0.00 0.00 40.14 4.00
239 241 3.800833 TGGGCTCGCAGCATCCAT 61.801 61.111 9.78 0.00 44.75 3.41
242 244 2.252346 GGCTCGCAGCATCCATCAG 61.252 63.158 9.78 0.00 44.75 2.90
290 292 2.051345 CGTTGCAAGCCGAACACC 60.051 61.111 0.00 0.00 0.00 4.16
307 309 2.777692 ACACCTGGTTGAGAGGAAAGAA 59.222 45.455 0.00 0.00 34.37 2.52
310 312 3.652869 ACCTGGTTGAGAGGAAAGAATGA 59.347 43.478 0.00 0.00 34.37 2.57
318 320 6.257994 TGAGAGGAAAGAATGAGCCAATAT 57.742 37.500 0.00 0.00 0.00 1.28
340 342 3.567375 TGGATATAGGTCAGGCATCCT 57.433 47.619 0.00 0.00 36.83 3.24
369 371 4.567318 GCCACATTCCTAGGCCTG 57.433 61.111 17.99 5.26 42.58 4.85
372 374 0.181350 CCACATTCCTAGGCCTGACC 59.819 60.000 17.99 0.00 39.61 4.02
398 400 3.429543 GCATACACAAGCAACCAAACATG 59.570 43.478 0.00 0.00 0.00 3.21
479 481 4.467084 GGGGTTGCCGATGCTCGA 62.467 66.667 7.07 0.00 43.74 4.04
484 486 2.032634 TTGCCGATGCTCGACAACC 61.033 57.895 7.07 0.00 43.74 3.77
498 500 1.882623 GACAACCTTTGCTCTTGGGAG 59.117 52.381 0.00 0.00 42.18 4.30
563 565 4.764679 TGCTTGTCATCAATACCACAAC 57.235 40.909 0.00 0.00 32.82 3.32
567 569 2.039216 TGTCATCAATACCACAACCCGT 59.961 45.455 0.00 0.00 0.00 5.28
587 589 2.163810 AATAGGGTAGGGTGTGCGTA 57.836 50.000 0.00 0.00 0.00 4.42
588 590 1.406903 ATAGGGTAGGGTGTGCGTAC 58.593 55.000 0.00 0.00 0.00 3.67
589 591 1.031571 TAGGGTAGGGTGTGCGTACG 61.032 60.000 11.84 11.84 0.00 3.67
590 592 2.639327 GGGTAGGGTGTGCGTACGT 61.639 63.158 17.90 0.00 0.00 3.57
591 593 1.444895 GGTAGGGTGTGCGTACGTG 60.445 63.158 17.90 0.00 0.00 4.49
592 594 2.090524 GTAGGGTGTGCGTACGTGC 61.091 63.158 17.90 10.45 0.00 5.34
593 595 2.562876 TAGGGTGTGCGTACGTGCA 61.563 57.895 17.90 12.99 43.95 4.57
611 613 1.858458 GCATGCGTGCGTTTATAGAGA 59.142 47.619 16.43 0.00 42.28 3.10
628 630 2.123342 GAGATGAGTGTATGCTCGTGC 58.877 52.381 1.71 1.71 38.28 5.34
651 653 3.547746 TGTGAGGGACTTTGGTTGTAAC 58.452 45.455 0.00 0.00 41.55 2.50
665 667 6.592798 TGGTTGTAACGTGTTTAGAAGAAG 57.407 37.500 0.00 0.00 0.00 2.85
670 672 9.545611 GTTGTAACGTGTTTAGAAGAAGAAAAA 57.454 29.630 0.00 0.00 0.00 1.94
691 693 5.986004 AAACTCAAAGTAACCTTGAGTCG 57.014 39.130 18.09 0.00 37.72 4.18
695 697 3.385433 TCAAAGTAACCTTGAGTCGACCA 59.615 43.478 13.01 7.31 0.00 4.02
713 715 1.041726 CAAACGAACGTTCATTGGCG 58.958 50.000 26.71 15.21 37.35 5.69
775 779 5.506686 GGCCAGACCAAGAATAGAAAATC 57.493 43.478 0.00 0.00 38.86 2.17
778 782 6.071391 GGCCAGACCAAGAATAGAAAATCAAA 60.071 38.462 0.00 0.00 38.86 2.69
856 860 2.521105 AATAATACCACCTCGACGGC 57.479 50.000 0.00 0.00 35.61 5.68
884 888 5.252586 TCCTACGTATATAGGCCTTGTCT 57.747 43.478 12.58 0.00 41.51 3.41
887 891 5.711036 CCTACGTATATAGGCCTTGTCTTCT 59.289 44.000 12.58 0.00 35.54 2.85
897 901 1.270305 CCTTGTCTTCTCTTCCACGCA 60.270 52.381 0.00 0.00 0.00 5.24
927 935 3.655384 GGTTGTCCCCTCTCTACCTATT 58.345 50.000 0.00 0.00 0.00 1.73
1122 1133 2.181021 GACCCCTACAGCGTCGTG 59.819 66.667 0.00 0.00 0.00 4.35
1143 1154 3.645975 CACTTCAACCGCGCCGTT 61.646 61.111 8.36 8.36 0.00 4.44
1280 1301 3.827784 GTAGTGAGCGTGCGTGCG 61.828 66.667 0.00 0.00 40.67 5.34
1335 1356 2.095161 TCGGAGAAGAAGTCGAAGAAGC 60.095 50.000 0.00 0.00 39.69 3.86
1487 1508 3.071602 GGCTCAAGGGCAAGATCTACATA 59.928 47.826 0.00 0.00 40.53 2.29
1583 1604 1.815212 CGCTGTGGATCATCTTCGCG 61.815 60.000 0.00 0.00 31.65 5.87
1607 1628 0.037326 ACATGGTGATCAACGCGTCT 60.037 50.000 14.44 0.00 0.00 4.18
1793 1814 1.911766 AACCCACTCCACGATCCGT 60.912 57.895 0.00 0.00 42.36 4.69
1969 1990 3.567797 GATGCTCTTCGGCGCCAC 61.568 66.667 28.98 8.43 34.52 5.01
2194 2215 2.085343 AACATGGCTGCCAAGGAGGT 62.085 55.000 27.24 15.35 36.95 3.85
2195 2216 1.207488 ACATGGCTGCCAAGGAGGTA 61.207 55.000 27.24 0.00 36.95 3.08
2196 2217 0.749454 CATGGCTGCCAAGGAGGTAC 60.749 60.000 27.24 0.00 36.95 3.34
2197 2218 1.926426 ATGGCTGCCAAGGAGGTACC 61.926 60.000 27.24 2.73 36.95 3.34
2223 2248 0.465460 CTCTCCTCCTCCTCACTCCG 60.465 65.000 0.00 0.00 0.00 4.63
2224 2249 0.914902 TCTCCTCCTCCTCACTCCGA 60.915 60.000 0.00 0.00 0.00 4.55
2225 2250 0.184933 CTCCTCCTCCTCACTCCGAT 59.815 60.000 0.00 0.00 0.00 4.18
2226 2251 1.422024 CTCCTCCTCCTCACTCCGATA 59.578 57.143 0.00 0.00 0.00 2.92
2227 2252 1.143277 TCCTCCTCCTCACTCCGATAC 59.857 57.143 0.00 0.00 0.00 2.24
2228 2253 1.133761 CCTCCTCCTCACTCCGATACA 60.134 57.143 0.00 0.00 0.00 2.29
2229 2254 2.489985 CCTCCTCCTCACTCCGATACAT 60.490 54.545 0.00 0.00 0.00 2.29
2230 2255 2.817258 CTCCTCCTCACTCCGATACATC 59.183 54.545 0.00 0.00 0.00 3.06
2231 2256 2.443632 TCCTCCTCACTCCGATACATCT 59.556 50.000 0.00 0.00 0.00 2.90
2232 2257 3.651423 TCCTCCTCACTCCGATACATCTA 59.349 47.826 0.00 0.00 0.00 1.98
2233 2258 4.289934 TCCTCCTCACTCCGATACATCTAT 59.710 45.833 0.00 0.00 0.00 1.98
2234 2259 4.638421 CCTCCTCACTCCGATACATCTATC 59.362 50.000 0.00 0.00 0.00 2.08
2235 2260 4.590918 TCCTCACTCCGATACATCTATCC 58.409 47.826 0.00 0.00 0.00 2.59
2236 2261 4.042934 TCCTCACTCCGATACATCTATCCA 59.957 45.833 0.00 0.00 0.00 3.41
2239 2264 3.193691 CACTCCGATACATCTATCCACCC 59.806 52.174 0.00 0.00 0.00 4.61
2240 2265 3.181422 ACTCCGATACATCTATCCACCCA 60.181 47.826 0.00 0.00 0.00 4.51
2241 2266 3.832490 CTCCGATACATCTATCCACCCAA 59.168 47.826 0.00 0.00 0.00 4.12
2242 2267 3.576982 TCCGATACATCTATCCACCCAAC 59.423 47.826 0.00 0.00 0.00 3.77
2243 2268 3.323691 CCGATACATCTATCCACCCAACA 59.676 47.826 0.00 0.00 0.00 3.33
2244 2269 4.020218 CCGATACATCTATCCACCCAACAT 60.020 45.833 0.00 0.00 0.00 2.71
2351 2391 0.472471 TGGAAGAACTGGGTGTGGAC 59.528 55.000 0.00 0.00 0.00 4.02
2384 2424 2.093658 ACCTGATGATAAACGACGCCTT 60.094 45.455 0.00 0.00 0.00 4.35
2390 2430 3.857052 TGATAAACGACGCCTTCTTCAT 58.143 40.909 0.00 0.00 0.00 2.57
2410 2450 0.797542 CACGTCCGGCGGAAAAATAA 59.202 50.000 32.91 2.96 46.52 1.40
2437 2477 0.108281 GCTCAACGGTAAGGACCTCC 60.108 60.000 0.00 0.00 44.46 4.30
2532 2572 1.939785 CTGCTGATCGTCGCCGTAC 60.940 63.158 0.00 0.00 35.01 3.67
2533 2573 2.654404 GCTGATCGTCGCCGTACC 60.654 66.667 0.00 0.00 35.01 3.34
2534 2574 2.025727 CTGATCGTCGCCGTACCC 59.974 66.667 0.00 0.00 35.01 3.69
2535 2575 2.438975 TGATCGTCGCCGTACCCT 60.439 61.111 0.00 0.00 35.01 4.34
2536 2576 1.153188 TGATCGTCGCCGTACCCTA 60.153 57.895 0.00 0.00 35.01 3.53
2554 2594 2.708861 CCTACCATACCATACCTGCCAA 59.291 50.000 0.00 0.00 0.00 4.52
2657 2728 1.541233 GGCCGTAAGCATGCATAGAGT 60.541 52.381 21.98 0.00 46.50 3.24
2665 2736 5.557576 AAGCATGCATAGAGTGAGGAATA 57.442 39.130 21.98 0.00 0.00 1.75
2696 2812 1.339929 TGCTGCTCTCTGTTCGTGTAA 59.660 47.619 0.00 0.00 0.00 2.41
2727 2870 7.770897 TGTACTTGCTTTTCTTCTTCTTCTTCT 59.229 33.333 0.00 0.00 0.00 2.85
2728 2871 7.637631 ACTTGCTTTTCTTCTTCTTCTTCTT 57.362 32.000 0.00 0.00 0.00 2.52
2729 2872 7.702386 ACTTGCTTTTCTTCTTCTTCTTCTTC 58.298 34.615 0.00 0.00 0.00 2.87
2730 2873 7.555914 ACTTGCTTTTCTTCTTCTTCTTCTTCT 59.444 33.333 0.00 0.00 0.00 2.85
2731 2874 7.872113 TGCTTTTCTTCTTCTTCTTCTTCTT 57.128 32.000 0.00 0.00 0.00 2.52
2732 2875 7.924940 TGCTTTTCTTCTTCTTCTTCTTCTTC 58.075 34.615 0.00 0.00 0.00 2.87
2733 2876 7.772757 TGCTTTTCTTCTTCTTCTTCTTCTTCT 59.227 33.333 0.00 0.00 0.00 2.85
2734 2877 8.620416 GCTTTTCTTCTTCTTCTTCTTCTTCTT 58.380 33.333 0.00 0.00 0.00 2.52
2736 2879 9.898152 TTTTCTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
2737 2880 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
2738 2881 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2739 2882 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2740 2883 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2741 2884 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2742 2885 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2743 2886 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2744 2887 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2745 2888 8.147704 TCTTCTTCTTCTTCTTCTTCTTCTTCC 58.852 37.037 0.00 0.00 0.00 3.46
2746 2889 7.610580 TCTTCTTCTTCTTCTTCTTCTTCCT 57.389 36.000 0.00 0.00 0.00 3.36
2747 2890 7.666623 TCTTCTTCTTCTTCTTCTTCTTCCTC 58.333 38.462 0.00 0.00 0.00 3.71
2967 3114 6.586344 TCTCCCATCTCACATAGACAAAATC 58.414 40.000 0.00 0.00 36.93 2.17
2983 3130 7.480810 AGACAAAATCAACACTCAACTAAACC 58.519 34.615 0.00 0.00 0.00 3.27
2989 3136 5.680619 TCAACACTCAACTAAACCAGTCAT 58.319 37.500 0.00 0.00 36.04 3.06
3073 3220 4.642885 GGCATACCATACAAGCAAGGTTTA 59.357 41.667 0.00 0.00 35.62 2.01
3100 3247 7.096230 GGGTGAAAAATACAGACATTTTGTTCG 60.096 37.037 0.00 0.00 37.97 3.95
3109 3256 6.945072 ACAGACATTTTGTTCGTCTAGTTTC 58.055 36.000 0.00 0.00 37.92 2.78
3213 3378 3.359033 TCCCTGCATCAATTTCCTGAAG 58.641 45.455 0.00 0.00 0.00 3.02
3265 3431 7.061326 GTCGCAGTTTTCTTTTTCTTTTACACA 59.939 33.333 0.00 0.00 0.00 3.72
3266 3432 7.595502 TCGCAGTTTTCTTTTTCTTTTACACAA 59.404 29.630 0.00 0.00 0.00 3.33
3267 3433 7.892731 CGCAGTTTTCTTTTTCTTTTACACAAG 59.107 33.333 0.00 0.00 0.00 3.16
3268 3434 8.168626 GCAGTTTTCTTTTTCTTTTACACAAGG 58.831 33.333 0.00 0.00 0.00 3.61
3269 3435 9.418045 CAGTTTTCTTTTTCTTTTACACAAGGA 57.582 29.630 0.00 0.00 0.00 3.36
3339 3505 8.119226 CAGATTTACTTACAAAGCATGTAGAGC 58.881 37.037 0.00 0.00 43.63 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 4.373116 TTCACCGCCGAGCAGGTC 62.373 66.667 8.54 0.00 43.70 3.85
76 77 2.522638 CGGGCGTATTCTTCACCGC 61.523 63.158 0.00 0.00 45.05 5.68
164 166 0.305922 CCTCTCGCCAATTTGATCGC 59.694 55.000 0.00 0.00 0.00 4.58
187 189 4.301072 AAAATCGACTGGAGGAATTGGA 57.699 40.909 0.00 0.00 0.00 3.53
200 202 1.136057 GCGTGTCCCTGAAAAATCGAC 60.136 52.381 0.00 0.00 0.00 4.20
201 203 1.153353 GCGTGTCCCTGAAAAATCGA 58.847 50.000 0.00 0.00 0.00 3.59
232 234 0.883370 TCATGCGAGCTGATGGATGC 60.883 55.000 0.00 0.00 34.36 3.91
274 276 1.008538 CAGGTGTTCGGCTTGCAAC 60.009 57.895 0.00 0.00 0.00 4.17
290 292 3.688673 GCTCATTCTTTCCTCTCAACCAG 59.311 47.826 0.00 0.00 0.00 4.00
318 320 4.242811 AGGATGCCTGACCTATATCCAAA 58.757 43.478 0.00 0.00 39.76 3.28
369 371 0.391130 TGCTTGTGTATGCCTCGGTC 60.391 55.000 0.00 0.00 0.00 4.79
372 374 0.447801 GGTTGCTTGTGTATGCCTCG 59.552 55.000 0.00 0.00 0.00 4.63
376 378 3.090952 TGTTTGGTTGCTTGTGTATGC 57.909 42.857 0.00 0.00 0.00 3.14
382 384 0.106521 GGGCATGTTTGGTTGCTTGT 59.893 50.000 0.00 0.00 38.88 3.16
398 400 6.152154 TGCTTTTTGTAACCTTATCTTAGGGC 59.848 38.462 0.00 0.00 39.76 5.19
479 481 1.215423 ACTCCCAAGAGCAAAGGTTGT 59.785 47.619 0.00 0.00 44.65 3.32
484 486 5.774498 AAGTTTTACTCCCAAGAGCAAAG 57.226 39.130 0.00 0.00 44.65 2.77
567 569 2.163810 ACGCACACCCTACCCTATTA 57.836 50.000 0.00 0.00 0.00 0.98
592 594 3.735746 TCATCTCTATAAACGCACGCATG 59.264 43.478 0.00 0.00 0.00 4.06
593 595 3.977427 TCATCTCTATAAACGCACGCAT 58.023 40.909 0.00 0.00 0.00 4.73
594 596 3.181490 ACTCATCTCTATAAACGCACGCA 60.181 43.478 0.00 0.00 0.00 5.24
609 611 2.215907 GCACGAGCATACACTCATCT 57.784 50.000 0.00 0.00 41.58 2.90
628 630 2.586425 ACAACCAAAGTCCCTCACATG 58.414 47.619 0.00 0.00 0.00 3.21
632 634 2.171027 ACGTTACAACCAAAGTCCCTCA 59.829 45.455 0.00 0.00 0.00 3.86
670 672 5.048507 GTCGACTCAAGGTTACTTTGAGTT 58.951 41.667 32.74 21.34 41.15 3.01
671 673 4.501058 GGTCGACTCAAGGTTACTTTGAGT 60.501 45.833 32.79 32.79 42.42 3.41
683 685 1.189446 CGTTCGTTTGGTCGACTCAAG 59.811 52.381 16.46 7.44 39.58 3.02
691 693 2.646250 CCAATGAACGTTCGTTTGGTC 58.354 47.619 33.48 12.07 37.85 4.02
695 697 0.040781 CCGCCAATGAACGTTCGTTT 60.041 50.000 28.63 18.99 34.34 3.60
713 715 0.521735 GACAAGGGAACGCATGAACC 59.478 55.000 0.00 0.00 0.00 3.62
775 779 8.016801 GGAGACAAATTGTTTTGCCAATATTTG 58.983 33.333 0.00 0.00 45.01 2.32
778 782 7.008021 AGGAGACAAATTGTTTTGCCAATAT 57.992 32.000 0.00 0.00 45.01 1.28
856 860 3.890147 GGCCTATATACGTAGGAGGATGG 59.110 52.174 19.31 8.63 43.27 3.51
884 888 0.037326 ATCGCTTGCGTGGAAGAGAA 60.037 50.000 14.70 0.00 35.70 2.87
887 891 0.179111 CCTATCGCTTGCGTGGAAGA 60.179 55.000 14.70 0.00 0.00 2.87
1122 1133 3.723348 GCGCGGTTGAAGTGGTCC 61.723 66.667 8.83 0.00 0.00 4.46
1201 1222 5.163913 ACTCGCTACAACGTAACTACAGTAG 60.164 44.000 6.00 6.00 33.04 2.57
1203 1224 3.499918 ACTCGCTACAACGTAACTACAGT 59.500 43.478 0.00 0.00 0.00 3.55
1204 1225 3.844657 CACTCGCTACAACGTAACTACAG 59.155 47.826 0.00 0.00 0.00 2.74
1205 1226 3.498018 TCACTCGCTACAACGTAACTACA 59.502 43.478 0.00 0.00 0.00 2.74
1206 1227 4.070581 TCACTCGCTACAACGTAACTAC 57.929 45.455 0.00 0.00 0.00 2.73
1207 1228 3.748048 ACTCACTCGCTACAACGTAACTA 59.252 43.478 0.00 0.00 0.00 2.24
1208 1229 2.551459 ACTCACTCGCTACAACGTAACT 59.449 45.455 0.00 0.00 0.00 2.24
1209 1230 2.655474 CACTCACTCGCTACAACGTAAC 59.345 50.000 0.00 0.00 0.00 2.50
1210 1231 2.351060 CCACTCACTCGCTACAACGTAA 60.351 50.000 0.00 0.00 0.00 3.18
1280 1301 2.184579 GGGCTAGTCGACCTGCAC 59.815 66.667 24.90 20.49 38.04 4.57
1312 1333 4.739195 CTTCTTCGACTTCTTCTCCGAAT 58.261 43.478 0.00 0.00 39.76 3.34
1313 1334 3.612004 GCTTCTTCGACTTCTTCTCCGAA 60.612 47.826 0.00 0.00 38.49 4.30
1335 1356 2.744709 CGGGCCCGTGTACTTTGG 60.745 66.667 36.64 3.38 34.35 3.28
1487 1508 3.598715 TCGTTGGCGTCGGTCACT 61.599 61.111 0.00 0.00 39.49 3.41
1583 1604 1.656652 CGTTGATCACCATGTCCCTC 58.343 55.000 0.00 0.00 0.00 4.30
1607 1628 2.898612 GCTCTGGATGATGATCTCCTGA 59.101 50.000 14.68 14.68 37.22 3.86
1856 1877 2.808543 GTCCTCGCAATTATCCATGGAC 59.191 50.000 18.99 1.61 36.42 4.02
1969 1990 1.075226 TCCTCCTCCTTCCCATCGG 60.075 63.158 0.00 0.00 0.00 4.18
1973 1994 0.547712 CCTTGTCCTCCTCCTTCCCA 60.548 60.000 0.00 0.00 0.00 4.37
1974 1995 0.547954 ACCTTGTCCTCCTCCTTCCC 60.548 60.000 0.00 0.00 0.00 3.97
1980 2001 0.615331 TGCATCACCTTGTCCTCCTC 59.385 55.000 0.00 0.00 0.00 3.71
1981 2002 0.617413 CTGCATCACCTTGTCCTCCT 59.383 55.000 0.00 0.00 0.00 3.69
2194 2215 1.767681 GAGGAGGAGAGGACGTAGGTA 59.232 57.143 0.00 0.00 0.00 3.08
2195 2216 0.547553 GAGGAGGAGAGGACGTAGGT 59.452 60.000 0.00 0.00 0.00 3.08
2196 2217 0.179012 GGAGGAGGAGAGGACGTAGG 60.179 65.000 0.00 0.00 0.00 3.18
2197 2218 0.841289 AGGAGGAGGAGAGGACGTAG 59.159 60.000 0.00 0.00 0.00 3.51
2223 2248 5.221925 ACCATGTTGGGTGGATAGATGTATC 60.222 44.000 1.18 1.18 43.37 2.24
2224 2249 4.665009 ACCATGTTGGGTGGATAGATGTAT 59.335 41.667 0.00 0.00 43.37 2.29
2225 2250 4.044308 ACCATGTTGGGTGGATAGATGTA 58.956 43.478 0.00 0.00 43.37 2.29
2226 2251 2.852449 ACCATGTTGGGTGGATAGATGT 59.148 45.455 0.00 0.00 43.37 3.06
2227 2252 3.582998 ACCATGTTGGGTGGATAGATG 57.417 47.619 0.00 0.00 43.37 2.90
2228 2253 3.527253 TGAACCATGTTGGGTGGATAGAT 59.473 43.478 0.00 0.00 37.76 1.98
2229 2254 2.916269 TGAACCATGTTGGGTGGATAGA 59.084 45.455 0.00 0.00 37.76 1.98
2230 2255 3.364460 TGAACCATGTTGGGTGGATAG 57.636 47.619 0.00 0.00 37.76 2.08
2231 2256 3.816398 TTGAACCATGTTGGGTGGATA 57.184 42.857 0.00 0.00 37.76 2.59
2232 2257 2.692709 TTGAACCATGTTGGGTGGAT 57.307 45.000 0.00 0.00 37.76 3.41
2233 2258 2.461300 TTTGAACCATGTTGGGTGGA 57.539 45.000 0.00 0.00 37.76 4.02
2234 2259 2.632028 TGATTTGAACCATGTTGGGTGG 59.368 45.455 0.00 0.00 37.76 4.61
2235 2260 4.333913 TTGATTTGAACCATGTTGGGTG 57.666 40.909 0.00 0.00 37.76 4.61
2236 2261 5.071519 TGATTTGATTTGAACCATGTTGGGT 59.928 36.000 0.00 0.00 42.68 4.51
2239 2264 7.892778 TGATGATTTGATTTGAACCATGTTG 57.107 32.000 0.00 0.00 0.00 3.33
2240 2265 9.509956 AATTGATGATTTGATTTGAACCATGTT 57.490 25.926 0.00 0.00 0.00 2.71
2241 2266 9.158233 GAATTGATGATTTGATTTGAACCATGT 57.842 29.630 0.00 0.00 0.00 3.21
2242 2267 9.157104 TGAATTGATGATTTGATTTGAACCATG 57.843 29.630 0.00 0.00 0.00 3.66
2243 2268 9.727859 TTGAATTGATGATTTGATTTGAACCAT 57.272 25.926 0.00 0.00 0.00 3.55
2244 2269 9.557061 TTTGAATTGATGATTTGATTTGAACCA 57.443 25.926 0.00 0.00 0.00 3.67
2283 2308 2.250939 CGCCTGCTCCACGTTTGAA 61.251 57.895 0.00 0.00 0.00 2.69
2284 2309 2.664851 CGCCTGCTCCACGTTTGA 60.665 61.111 0.00 0.00 0.00 2.69
2286 2311 2.665185 GTCGCCTGCTCCACGTTT 60.665 61.111 0.00 0.00 0.00 3.60
2287 2312 4.681978 GGTCGCCTGCTCCACGTT 62.682 66.667 0.00 0.00 0.00 3.99
2384 2424 2.180769 CGCCGGACGTGATGAAGA 59.819 61.111 5.05 0.00 36.87 2.87
2390 2430 0.037512 TATTTTTCCGCCGGACGTGA 60.038 50.000 4.70 5.54 41.42 4.35
2437 2477 2.362120 CCCTGGCTTGGGCTTGAG 60.362 66.667 3.38 0.00 40.84 3.02
2532 2572 1.628846 GGCAGGTATGGTATGGTAGGG 59.371 57.143 0.00 0.00 0.00 3.53
2533 2573 2.334977 TGGCAGGTATGGTATGGTAGG 58.665 52.381 0.00 0.00 0.00 3.18
2534 2574 3.807209 GCTTGGCAGGTATGGTATGGTAG 60.807 52.174 0.00 0.00 0.00 3.18
2535 2575 2.105821 GCTTGGCAGGTATGGTATGGTA 59.894 50.000 0.00 0.00 0.00 3.25
2536 2576 1.133792 GCTTGGCAGGTATGGTATGGT 60.134 52.381 0.00 0.00 0.00 3.55
2657 2728 3.142977 AGCAGACCCTCCTATATTCCTCA 59.857 47.826 0.00 0.00 0.00 3.86
2665 2736 0.264359 AGAGCAGCAGACCCTCCTAT 59.736 55.000 0.00 0.00 0.00 2.57
2696 2812 8.401490 AGAAGAAGAAAAGCAAGTACATTGAT 57.599 30.769 8.63 0.85 41.83 2.57
2727 2870 4.833380 TCCGAGGAAGAAGAAGAAGAAGAA 59.167 41.667 0.00 0.00 0.00 2.52
2728 2871 4.408276 TCCGAGGAAGAAGAAGAAGAAGA 58.592 43.478 0.00 0.00 0.00 2.87
2729 2872 4.792521 TCCGAGGAAGAAGAAGAAGAAG 57.207 45.455 0.00 0.00 0.00 2.85
2730 2873 5.546621 TTTCCGAGGAAGAAGAAGAAGAA 57.453 39.130 4.63 0.00 35.38 2.52
2731 2874 5.746990 ATTTCCGAGGAAGAAGAAGAAGA 57.253 39.130 4.63 0.00 35.38 2.87
2732 2875 6.045955 CCTATTTCCGAGGAAGAAGAAGAAG 58.954 44.000 13.72 2.87 35.99 2.85
2733 2876 5.720041 TCCTATTTCCGAGGAAGAAGAAGAA 59.280 40.000 13.72 0.00 40.25 2.52
2734 2877 5.269991 TCCTATTTCCGAGGAAGAAGAAGA 58.730 41.667 13.72 3.48 40.25 2.87
2735 2878 5.599999 TCCTATTTCCGAGGAAGAAGAAG 57.400 43.478 13.72 5.91 40.25 2.85
2743 2886 4.837093 ACACAATTCCTATTTCCGAGGA 57.163 40.909 0.00 0.00 41.52 3.71
2744 2887 4.814771 GGTACACAATTCCTATTTCCGAGG 59.185 45.833 0.00 0.00 35.17 4.63
2745 2888 5.671493 AGGTACACAATTCCTATTTCCGAG 58.329 41.667 0.00 0.00 0.00 4.63
2746 2889 5.687166 AGGTACACAATTCCTATTTCCGA 57.313 39.130 0.00 0.00 0.00 4.55
2806 2951 2.342910 ACAAGAGCGGTTACAGTACG 57.657 50.000 0.00 0.00 0.00 3.67
2859 3006 4.868067 ACAAGCTGCATTTCTTTCTGAAG 58.132 39.130 1.02 0.00 35.89 3.02
2967 3114 5.527214 TGATGACTGGTTTAGTTGAGTGTTG 59.473 40.000 0.00 0.00 40.53 3.33
2983 3130 6.373495 TCTGGAATTCTGTGAAATGATGACTG 59.627 38.462 5.23 0.00 0.00 3.51
2989 3136 7.949690 ATTCATCTGGAATTCTGTGAAATGA 57.050 32.000 5.23 4.37 43.76 2.57
3017 3164 5.281314 AGGTTCTTGACATGTCCCTAGTAT 58.719 41.667 22.85 2.07 0.00 2.12
3073 3220 7.360113 ACAAAATGTCTGTATTTTTCACCCT 57.640 32.000 0.00 0.00 37.97 4.34
3100 3247 2.658285 TGTCTTGCGTCGAAACTAGAC 58.342 47.619 17.69 17.69 35.41 2.59
3109 3256 1.217882 AGGTTTCTTGTCTTGCGTCG 58.782 50.000 0.00 0.00 0.00 5.12
3114 3261 7.540055 GCATCTGAAATTAGGTTTCTTGTCTTG 59.460 37.037 2.67 0.00 45.22 3.02
3213 3378 9.255304 CAGATTCCTAATACTAGAGTTGCTTTC 57.745 37.037 0.00 0.00 0.00 2.62
3265 3431 4.375313 ACATCCAGACCTATCCTTTCCTT 58.625 43.478 0.00 0.00 0.00 3.36
3266 3432 3.970640 GACATCCAGACCTATCCTTTCCT 59.029 47.826 0.00 0.00 0.00 3.36
3267 3433 3.970640 AGACATCCAGACCTATCCTTTCC 59.029 47.826 0.00 0.00 0.00 3.13
3268 3434 4.651503 TCAGACATCCAGACCTATCCTTTC 59.348 45.833 0.00 0.00 0.00 2.62
3269 3435 4.624913 TCAGACATCCAGACCTATCCTTT 58.375 43.478 0.00 0.00 0.00 3.11
3339 3505 6.015940 GCTCTGTGAAAATCCCCTATATTTGG 60.016 42.308 0.00 0.00 0.00 3.28
3403 3569 6.145858 GCACAACATGTTGATGATGCTAAAAA 59.854 34.615 38.30 0.00 42.93 1.94
3417 3583 3.865011 TGTGACAAAGCACAACATGTT 57.135 38.095 4.92 4.92 45.08 2.71


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

AutoCloner maintained by Alex Coulton.