Multiple sequence alignment - TraesCS5B01G238100

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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 TraesCS5B01G238100 chr5B 100.000 2795 0 0 1 2795 418912240 418909446 0 5162
1 TraesCS5B01G238100 chr5A 90.162 2836 187 48 1 2794 455509020 455506235 0 3607
2 TraesCS5B01G238100 chr5D 92.172 2095 92 35 375 2432 354513288 354511229 0 2894


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 TraesCS5B01G238100 chr5B 418909446 418912240 2794 True 5162 5162 100.000 1 2795 1 chr5B.!!$R1 2794
1 TraesCS5B01G238100 chr5A 455506235 455509020 2785 True 3607 3607 90.162 1 2794 1 chr5A.!!$R1 2793
2 TraesCS5B01G238100 chr5D 354511229 354513288 2059 True 2894 2894 92.172 375 2432 1 chr5D.!!$R1 2057

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
365 378 0.537188 CGATGCCCTGACTTGGTACT 59.463 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1970 0.680061 ACCTGTCCACCGAGAACTTC 59.32 55.0 0.0 0.0 0.0 3.01 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
25 26 3.364442 CCAACAAGGCAATGGCGA 58.636 55.556 0.00 0.00 42.47 5.54
32 33 2.358898 ACAAGGCAATGGCGATAATGAC 59.641 45.455 0.00 0.00 42.47 3.06
39 40 4.213674 CAATGGCGATAATGACATCAACG 58.786 43.478 0.00 0.00 36.28 4.10
41 42 3.526534 TGGCGATAATGACATCAACGAA 58.473 40.909 10.66 0.00 0.00 3.85
48 49 6.691388 CGATAATGACATCAACGAAGTCTACA 59.309 38.462 0.00 0.00 45.00 2.74
81 89 1.990160 AACGGACACCTTTCCAGGCA 61.990 55.000 0.00 0.00 45.56 4.75
91 99 3.782523 ACCTTTCCAGGCATAGAGATCAA 59.217 43.478 0.00 0.00 45.56 2.57
103 111 5.105146 GCATAGAGATCAAATCTATCGGGGT 60.105 44.000 0.00 0.00 40.38 4.95
108 116 6.498651 AGAGATCAAATCTATCGGGGTACATT 59.501 38.462 0.00 0.00 40.38 2.71
109 117 7.674348 AGAGATCAAATCTATCGGGGTACATTA 59.326 37.037 0.00 0.00 40.38 1.90
110 118 7.841956 AGATCAAATCTATCGGGGTACATTAG 58.158 38.462 0.00 0.00 38.00 1.73
111 119 5.790593 TCAAATCTATCGGGGTACATTAGC 58.209 41.667 0.00 0.00 0.00 3.09
116 124 2.803817 CGGGGTACATTAGCGGCCT 61.804 63.158 0.00 0.00 0.00 5.19
129 137 0.811616 GCGGCCTGACTTGGTATCAG 60.812 60.000 0.00 0.00 42.79 2.90
139 147 6.183360 CCTGACTTGGTATCAGAAGTAGGTAC 60.183 46.154 3.58 0.00 45.46 3.34
151 159 1.412710 AGTAGGTACATGATGCGGTGG 59.587 52.381 0.00 0.00 0.00 4.61
168 176 1.628846 GTGGGTCTTGGTAGTGGTGAT 59.371 52.381 0.00 0.00 0.00 3.06
169 177 1.628340 TGGGTCTTGGTAGTGGTGATG 59.372 52.381 0.00 0.00 0.00 3.07
180 188 1.704628 AGTGGTGATGGGTGACAATGA 59.295 47.619 0.00 0.00 0.00 2.57
182 190 1.004628 TGGTGATGGGTGACAATGAGG 59.995 52.381 0.00 0.00 0.00 3.86
190 198 1.009829 GTGACAATGAGGCGATGGAC 58.990 55.000 0.00 0.00 0.00 4.02
226 234 1.220236 AGGAGGAGAAGAGGGATGAGG 59.780 57.143 0.00 0.00 0.00 3.86
233 244 4.227527 GGAGAAGAGGGATGAGGGTTAAAA 59.772 45.833 0.00 0.00 0.00 1.52
256 267 0.631753 AGGGAGGGTTGATCTCGAGA 59.368 55.000 19.19 19.19 32.34 4.04
262 273 1.275291 GGGTTGATCTCGAGACCAACA 59.725 52.381 40.04 24.77 40.26 3.33
263 274 2.289444 GGGTTGATCTCGAGACCAACAA 60.289 50.000 40.04 27.83 40.26 2.83
291 302 1.751924 GAGACAACAGGCGAGGTCTAT 59.248 52.381 0.00 0.00 40.48 1.98
299 311 2.032620 AGGCGAGGTCTATGTTACCAG 58.967 52.381 0.00 0.00 39.64 4.00
300 312 1.755380 GGCGAGGTCTATGTTACCAGT 59.245 52.381 0.00 0.00 39.64 4.00
304 316 2.426024 GAGGTCTATGTTACCAGTGCGA 59.574 50.000 0.00 0.00 39.64 5.10
339 352 9.429359 CATTTTCTATGCTTAGGATCTATCGTT 57.571 33.333 6.78 0.00 0.00 3.85
342 355 8.631480 TTCTATGCTTAGGATCTATCGTTGTA 57.369 34.615 6.78 0.00 0.00 2.41
343 356 8.041829 TCTATGCTTAGGATCTATCGTTGTAC 57.958 38.462 6.78 0.00 0.00 2.90
344 357 5.104562 TGCTTAGGATCTATCGTTGTACG 57.895 43.478 0.00 0.00 44.19 3.67
346 359 5.145759 GCTTAGGATCTATCGTTGTACGTC 58.854 45.833 0.00 0.00 43.14 4.34
365 378 0.537188 CGATGCCCTGACTTGGTACT 59.463 55.000 0.00 0.00 0.00 2.73
409 423 0.691904 TTTGGTAGTGGTTACGGGGG 59.308 55.000 0.00 0.00 32.79 5.40
492 506 3.274690 AGAGGAAGAAGGAGAGGAGGAAT 59.725 47.826 0.00 0.00 0.00 3.01
510 524 4.603610 AGGAATGAGGAAAAAGGAAGAGGA 59.396 41.667 0.00 0.00 0.00 3.71
511 525 4.946772 GGAATGAGGAAAAAGGAAGAGGAG 59.053 45.833 0.00 0.00 0.00 3.69
520 534 4.308526 AAAGGAAGAGGAGGCCTAAAAG 57.691 45.455 4.42 0.00 31.76 2.27
521 535 3.207044 AGGAAGAGGAGGCCTAAAAGA 57.793 47.619 4.42 0.00 31.76 2.52
530 544 2.780592 GAGGCCTAAAAGAGGGAAGGAT 59.219 50.000 4.42 0.00 46.81 3.24
542 556 4.013050 GAGGGAAGGATGAAGAAAACCAG 58.987 47.826 0.00 0.00 0.00 4.00
594 608 2.286418 GCAAGCGACCGAATATTCCTTG 60.286 50.000 19.17 19.17 33.32 3.61
614 630 9.847224 TTCCTTGATAGAAATAAACATAGTCCC 57.153 33.333 0.00 0.00 0.00 4.46
616 632 9.853177 CCTTGATAGAAATAAACATAGTCCCTT 57.147 33.333 0.00 0.00 0.00 3.95
618 634 9.542462 TTGATAGAAATAAACATAGTCCCTTCG 57.458 33.333 0.00 0.00 0.00 3.79
622 638 2.667473 AAACATAGTCCCTTCGTCCG 57.333 50.000 0.00 0.00 0.00 4.79
634 651 2.928116 CCTTCGTCCGAAATACTTGTCC 59.072 50.000 3.52 0.00 33.34 4.02
636 653 1.541147 TCGTCCGAAATACTTGTCCGT 59.459 47.619 0.00 0.00 0.00 4.69
637 654 2.746904 TCGTCCGAAATACTTGTCCGTA 59.253 45.455 0.00 0.00 0.00 4.02
643 660 7.514125 CGTCCGAAATACTTGTCCGTAAAATAG 60.514 40.741 0.00 0.00 0.00 1.73
672 689 7.660617 ACATCTAGATGCATCAATTTCTTCGAT 59.339 33.333 28.86 9.72 42.39 3.59
678 695 9.499479 AGATGCATCAATTTCTTCGATAAGTAT 57.501 29.630 27.81 0.00 34.13 2.12
711 728 4.202326 GGAGGGAGTACTCAACAAGTCAAA 60.202 45.833 23.91 0.00 39.55 2.69
726 743 3.692791 GTCAAAGCTGACCGTTTCTTT 57.307 42.857 0.00 0.00 45.41 2.52
754 771 4.735369 TGGTGTCAAATATGTCCCTGTTT 58.265 39.130 0.00 0.00 0.00 2.83
818 838 2.039480 TCACTTCATCAGCTTGCTCCTT 59.961 45.455 0.00 0.00 0.00 3.36
866 889 4.523083 TGTTTGTCTGTGCTTACCTTCTT 58.477 39.130 0.00 0.00 0.00 2.52
908 931 1.005294 GCTCTTTTGTGCGTGCCATG 61.005 55.000 0.00 0.00 0.00 3.66
1048 1072 0.321564 TCCTCTGTTCATGCCAACCG 60.322 55.000 0.00 0.00 0.00 4.44
1094 1124 2.087857 CTATCCTCCTCGCCCTCCCT 62.088 65.000 0.00 0.00 0.00 4.20
1119 1149 2.428544 TCTCCTTCTCCTTCTCTCCG 57.571 55.000 0.00 0.00 0.00 4.63
1154 1184 1.004918 CACCTTCTCACGTCCACCC 60.005 63.158 0.00 0.00 0.00 4.61
1196 1226 1.139734 CCGTCGACATGTCCAGGAG 59.860 63.158 20.03 5.83 0.00 3.69
1201 1231 1.257750 CGACATGTCCAGGAGACCCA 61.258 60.000 20.03 0.00 45.68 4.51
1230 1260 2.515523 GGCAGCGACATCAGCCAT 60.516 61.111 0.00 0.00 46.26 4.40
1254 1284 0.251165 ACTACGCCAAAGCCAACCAT 60.251 50.000 0.00 0.00 34.57 3.55
1467 1497 1.654105 GTGAAGAAGTACATGGCGTCG 59.346 52.381 0.00 0.00 0.00 5.12
1498 1528 2.283894 TGCTCGCCTCCTTCTCCA 60.284 61.111 0.00 0.00 0.00 3.86
1844 1880 2.037136 GCACAGCCAGGCTAGTGTG 61.037 63.158 29.49 26.41 38.72 3.82
1927 1965 2.449525 GCGTGCGTATTGCTTCCGA 61.450 57.895 0.00 0.00 46.63 4.55
1932 1970 1.933181 TGCGTATTGCTTCCGAATCAG 59.067 47.619 0.00 0.00 46.63 2.90
2062 2107 9.930158 ACTATGGAAAATAGGCAAAATAGGTAA 57.070 29.630 0.00 0.00 0.00 2.85
2148 2198 4.730949 TTCTCACTAATACTTCCGTGGG 57.269 45.455 0.00 0.00 0.00 4.61
2256 2306 0.321653 AATCAACACCGGCTGAGGTC 60.322 55.000 0.00 0.00 43.89 3.85
2351 2407 9.892130 CCTGGTAGTAACTCAATTCTTAATCTT 57.108 33.333 0.00 0.00 0.00 2.40
2433 2498 1.772567 TAACCAGGCCACCACCAGT 60.773 57.895 5.01 0.00 0.00 4.00
2434 2499 2.063015 TAACCAGGCCACCACCAGTG 62.063 60.000 5.01 0.00 46.83 3.66
2443 2508 4.319133 CCACCAGTGGCCACATAC 57.681 61.111 36.39 11.15 44.73 2.39
2444 2509 1.378378 CCACCAGTGGCCACATACA 59.622 57.895 36.39 0.00 44.73 2.29
2445 2510 0.960364 CCACCAGTGGCCACATACAC 60.960 60.000 36.39 9.89 44.73 2.90
2450 2515 2.698855 AGTGGCCACATACACTGATC 57.301 50.000 36.39 6.02 45.54 2.92
2466 2531 0.035152 GATCCACATCACCAGCCACA 60.035 55.000 0.00 0.00 0.00 4.17
2467 2532 0.034767 ATCCACATCACCAGCCACAG 60.035 55.000 0.00 0.00 0.00 3.66
2468 2533 2.338015 CCACATCACCAGCCACAGC 61.338 63.158 0.00 0.00 40.32 4.40
2469 2534 2.034687 ACATCACCAGCCACAGCC 59.965 61.111 0.00 0.00 41.25 4.85
2470 2535 2.034532 CATCACCAGCCACAGCCA 59.965 61.111 0.00 0.00 41.25 4.75
2471 2536 2.044555 CATCACCAGCCACAGCCAG 61.045 63.158 0.00 0.00 41.25 4.85
2472 2537 3.933048 ATCACCAGCCACAGCCAGC 62.933 63.158 0.00 0.00 41.25 4.85
2475 2540 3.720601 CCAGCCACAGCCAGCCTA 61.721 66.667 0.00 0.00 41.25 3.93
2484 2549 3.434167 CCACAGCCAGCCTAGATACAAAT 60.434 47.826 0.00 0.00 0.00 2.32
2528 2594 2.959357 GCAAGTGCACGAGTGGAGC 61.959 63.158 12.01 5.39 41.59 4.70
2550 2616 2.299013 CAAGCTCAGTAGTGGGTGTACA 59.701 50.000 0.00 0.00 0.00 2.90
2562 2628 1.337110 GGTGTACAACGTACCGTCGC 61.337 60.000 0.00 0.00 39.99 5.19
2590 2656 1.068474 CCAGCTTTCGTTGGTACTCG 58.932 55.000 0.00 0.00 36.82 4.18
2597 2663 0.883833 TCGTTGGTACTCGGTCCTTC 59.116 55.000 0.00 0.00 0.00 3.46
2627 2693 2.482142 GCCGATCCGATGTCTTTCTCTT 60.482 50.000 0.00 0.00 0.00 2.85
2659 2725 3.782632 GGGTAGAAGTAGCCTTGCC 57.217 57.895 0.00 0.00 42.71 4.52
2665 2731 1.359459 GAAGTAGCCTTGCCCGTTCG 61.359 60.000 0.00 0.00 0.00 3.95
2666 2732 2.798148 AAGTAGCCTTGCCCGTTCGG 62.798 60.000 4.08 4.08 0.00 4.30
2670 2736 1.747745 GCCTTGCCCGTTCGGTTAT 60.748 57.895 10.36 0.00 0.00 1.89
2671 2737 1.310216 GCCTTGCCCGTTCGGTTATT 61.310 55.000 10.36 0.00 0.00 1.40
2674 2740 2.591133 CTTGCCCGTTCGGTTATTTTG 58.409 47.619 10.36 0.00 0.00 2.44
2675 2741 1.893544 TGCCCGTTCGGTTATTTTGA 58.106 45.000 10.36 0.00 0.00 2.69
2676 2742 1.536331 TGCCCGTTCGGTTATTTTGAC 59.464 47.619 10.36 0.00 0.00 3.18
2694 2762 8.873215 ATTTTGACTAACTAGATGATACGGTG 57.127 34.615 0.00 0.00 0.00 4.94
2696 2764 4.885325 TGACTAACTAGATGATACGGTGCA 59.115 41.667 0.00 0.00 0.00 4.57
2708 2776 3.357079 GGTGCACGTTGCTGAGGG 61.357 66.667 11.45 0.00 45.31 4.30
2715 2783 0.249911 ACGTTGCTGAGGGAACTGTC 60.250 55.000 0.00 0.00 44.43 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.023119 TCATTATCGCCATTGCCTTGTT 58.977 40.909 0.00 0.00 0.00 2.83
12 13 2.358582 TGTCATTATCGCCATTGCCTTG 59.641 45.455 0.00 0.00 0.00 3.61
25 26 7.981789 ACATGTAGACTTCGTTGATGTCATTAT 59.018 33.333 0.00 3.96 38.60 1.28
32 33 6.510157 GCCAATACATGTAGACTTCGTTGATG 60.510 42.308 11.91 0.00 0.00 3.07
39 40 7.464178 CGTTTAGTGCCAATACATGTAGACTTC 60.464 40.741 11.91 0.56 0.00 3.01
41 42 5.810587 CGTTTAGTGCCAATACATGTAGACT 59.189 40.000 11.91 9.77 0.00 3.24
48 49 3.687698 GTGTCCGTTTAGTGCCAATACAT 59.312 43.478 0.00 0.00 0.00 2.29
81 89 7.182760 TGTACCCCGATAGATTTGATCTCTAT 58.817 38.462 3.31 3.31 40.76 1.98
91 99 3.194968 CCGCTAATGTACCCCGATAGATT 59.805 47.826 0.00 0.00 39.76 2.40
103 111 1.134521 CCAAGTCAGGCCGCTAATGTA 60.135 52.381 0.00 0.00 0.00 2.29
108 116 0.750850 GATACCAAGTCAGGCCGCTA 59.249 55.000 0.00 0.00 0.00 4.26
109 117 1.264749 TGATACCAAGTCAGGCCGCT 61.265 55.000 0.00 0.00 0.00 5.52
110 118 0.811616 CTGATACCAAGTCAGGCCGC 60.812 60.000 0.00 0.00 39.48 6.53
111 119 0.824109 TCTGATACCAAGTCAGGCCG 59.176 55.000 0.00 0.00 42.58 6.13
116 124 6.250711 TGTACCTACTTCTGATACCAAGTCA 58.749 40.000 0.00 0.00 34.60 3.41
129 137 3.123804 CACCGCATCATGTACCTACTTC 58.876 50.000 0.00 0.00 0.00 3.01
139 147 1.378882 CCAAGACCCACCGCATCATG 61.379 60.000 0.00 0.00 0.00 3.07
151 159 1.065418 CCCATCACCACTACCAAGACC 60.065 57.143 0.00 0.00 0.00 3.85
168 176 0.392863 CATCGCCTCATTGTCACCCA 60.393 55.000 0.00 0.00 0.00 4.51
169 177 1.097547 CCATCGCCTCATTGTCACCC 61.098 60.000 0.00 0.00 0.00 4.61
192 200 1.153086 CTCCTTCCTCCGCCAATGG 60.153 63.158 0.00 0.00 0.00 3.16
204 212 2.965147 CTCATCCCTCTTCTCCTCCTTC 59.035 54.545 0.00 0.00 0.00 3.46
233 244 2.642807 TCGAGATCAACCCTCCCTTTTT 59.357 45.455 0.00 0.00 0.00 1.94
240 251 1.475403 TGGTCTCGAGATCAACCCTC 58.525 55.000 25.86 6.39 31.17 4.30
256 267 0.321653 GTCTCCATCGCCTTGTTGGT 60.322 55.000 0.00 0.00 38.40 3.67
262 273 0.036010 CCTGTTGTCTCCATCGCCTT 60.036 55.000 0.00 0.00 0.00 4.35
263 274 1.599047 CCTGTTGTCTCCATCGCCT 59.401 57.895 0.00 0.00 0.00 5.52
278 289 1.754803 TGGTAACATAGACCTCGCCTG 59.245 52.381 0.00 0.00 46.17 4.85
279 290 2.154567 TGGTAACATAGACCTCGCCT 57.845 50.000 0.00 0.00 46.17 5.52
291 302 7.585143 ATGCTTATCACTCGCACTGGTAACA 62.585 44.000 0.00 0.00 39.87 2.41
299 311 4.606457 AGAAAATGCTTATCACTCGCAC 57.394 40.909 0.00 0.00 36.37 5.34
300 312 5.277490 GCATAGAAAATGCTTATCACTCGCA 60.277 40.000 2.78 0.00 41.52 5.10
330 343 3.552541 GCATCGACGTACAACGATAGAT 58.447 45.455 18.84 5.14 46.05 1.98
339 352 0.963856 AGTCAGGGCATCGACGTACA 60.964 55.000 0.00 0.00 37.23 2.90
342 355 1.079819 CAAGTCAGGGCATCGACGT 60.080 57.895 0.00 0.00 37.23 4.34
343 356 1.811266 CCAAGTCAGGGCATCGACG 60.811 63.158 0.00 0.00 37.23 5.12
344 357 0.535335 TACCAAGTCAGGGCATCGAC 59.465 55.000 0.00 0.00 0.00 4.20
346 359 0.537188 AGTACCAAGTCAGGGCATCG 59.463 55.000 0.00 0.00 0.00 3.84
365 378 0.824109 CAGATCACCGCCTACTTCCA 59.176 55.000 0.00 0.00 0.00 3.53
372 385 0.110486 AAACAACCAGATCACCGCCT 59.890 50.000 0.00 0.00 0.00 5.52
378 391 4.141287 CCACTACCAAAACAACCAGATCA 58.859 43.478 0.00 0.00 0.00 2.92
409 423 3.508744 ATTTCATCACCGCAAATCCAC 57.491 42.857 0.00 0.00 0.00 4.02
492 506 2.040412 GCCTCCTCTTCCTTTTTCCTCA 59.960 50.000 0.00 0.00 0.00 3.86
510 524 2.361085 TCCTTCCCTCTTTTAGGCCT 57.639 50.000 11.78 11.78 45.03 5.19
511 525 2.509964 TCATCCTTCCCTCTTTTAGGCC 59.490 50.000 0.00 0.00 45.03 5.19
520 534 4.013050 CTGGTTTTCTTCATCCTTCCCTC 58.987 47.826 0.00 0.00 0.00 4.30
521 535 3.245407 CCTGGTTTTCTTCATCCTTCCCT 60.245 47.826 0.00 0.00 0.00 4.20
530 544 0.827507 GCCTGCCCTGGTTTTCTTCA 60.828 55.000 0.00 0.00 0.00 3.02
555 569 2.235016 TGCTTTTAAATGCCACGACCT 58.765 42.857 19.88 0.00 0.00 3.85
594 608 9.194271 GACGAAGGGACTATGTTTATTTCTATC 57.806 37.037 0.00 0.00 38.49 2.08
610 626 2.928116 CAAGTATTTCGGACGAAGGGAC 59.072 50.000 7.25 7.17 35.38 4.46
614 630 2.597305 CGGACAAGTATTTCGGACGAAG 59.403 50.000 7.25 0.00 35.38 3.79
616 632 1.541147 ACGGACAAGTATTTCGGACGA 59.459 47.619 0.00 0.00 0.00 4.20
618 634 5.844301 TTTTACGGACAAGTATTTCGGAC 57.156 39.130 0.00 0.00 0.00 4.79
669 686 5.408604 CCCTCCATCCGAAAAATACTTATCG 59.591 44.000 0.00 0.00 35.19 2.92
672 689 5.427481 ACTCCCTCCATCCGAAAAATACTTA 59.573 40.000 0.00 0.00 0.00 2.24
678 695 3.178865 AGTACTCCCTCCATCCGAAAAA 58.821 45.455 0.00 0.00 0.00 1.94
684 701 2.467880 TGTTGAGTACTCCCTCCATCC 58.532 52.381 20.11 0.30 0.00 3.51
711 728 3.126001 TGATCAAAGAAACGGTCAGCT 57.874 42.857 0.00 0.00 0.00 4.24
726 743 5.103982 AGGGACATATTTGACACCATGATCA 60.104 40.000 0.00 0.00 0.00 2.92
754 771 9.988350 CTAGTATTTAAGTCGGAAAGTAACGTA 57.012 33.333 0.00 0.00 0.00 3.57
818 838 6.663953 ACAGGTGAAGAAGATTAGTACTGCTA 59.336 38.462 5.39 0.00 0.00 3.49
829 849 5.297776 CAGACAAACAACAGGTGAAGAAGAT 59.702 40.000 0.00 0.00 0.00 2.40
880 903 1.867233 GCACAAAAGAGCTGAACGAGA 59.133 47.619 0.00 0.00 0.00 4.04
987 1011 1.509923 GTCCATGGCTTTGAGCTGC 59.490 57.895 6.96 0.00 41.99 5.25
1067 1097 2.844839 AGGAGGATAGCGGTGGCC 60.845 66.667 0.00 0.00 41.24 5.36
1094 1124 3.009695 AGAGAAGGAGAAGGAGAAGTCGA 59.990 47.826 0.00 0.00 0.00 4.20
1119 1149 2.367202 TGGAGGCGATGGAGGGAAC 61.367 63.158 0.00 0.00 0.00 3.62
1181 1211 0.970937 GGGTCTCCTGGACATGTCGA 60.971 60.000 19.33 14.89 46.16 4.20
1230 1260 2.257691 TGGCTTTGGCGTAGTTGTTA 57.742 45.000 0.00 0.00 39.81 2.41
1254 1284 3.611674 TGGCTCGTGGCTTGACGA 61.612 61.111 12.46 0.00 45.84 4.20
1354 1384 3.071206 GTCTCTGCCCTCGCCTGA 61.071 66.667 0.00 0.00 0.00 3.86
1832 1868 2.158900 CCTACCATTCACACTAGCCTGG 60.159 54.545 0.00 0.00 0.00 4.45
1844 1880 0.828677 ACGCCACTACCCTACCATTC 59.171 55.000 0.00 0.00 0.00 2.67
1884 1920 2.907897 GATCGTCGGGAGGGTGCAAG 62.908 65.000 0.00 0.00 0.00 4.01
1891 1927 3.606662 ATGGCGATCGTCGGGAGG 61.607 66.667 15.94 0.00 40.84 4.30
1927 1965 2.632996 TGTCCACCGAGAACTTCTGATT 59.367 45.455 0.00 0.00 0.00 2.57
1932 1970 0.680061 ACCTGTCCACCGAGAACTTC 59.320 55.000 0.00 0.00 0.00 3.01
2148 2198 9.250624 CATACACAAGTAGGAGTAATAAGCTTC 57.749 37.037 0.00 0.00 34.03 3.86
2256 2306 1.803334 TGAAAACCGACGGGAAGATG 58.197 50.000 20.00 0.00 36.97 2.90
2386 2443 5.551760 ATGAGTTGCGGATCAAGTTTAAG 57.448 39.130 0.00 0.00 38.40 1.85
2433 2498 1.065491 GTGGATCAGTGTATGTGGCCA 60.065 52.381 0.00 0.00 0.00 5.36
2434 2499 1.065491 TGTGGATCAGTGTATGTGGCC 60.065 52.381 0.00 0.00 0.00 5.36
2440 2505 3.432749 GCTGGTGATGTGGATCAGTGTAT 60.433 47.826 0.00 0.00 39.36 2.29
2441 2506 2.093500 GCTGGTGATGTGGATCAGTGTA 60.093 50.000 0.00 0.00 39.36 2.90
2442 2507 1.339438 GCTGGTGATGTGGATCAGTGT 60.339 52.381 0.00 0.00 39.36 3.55
2443 2508 1.376543 GCTGGTGATGTGGATCAGTG 58.623 55.000 0.00 0.00 39.36 3.66
2444 2509 0.254178 GGCTGGTGATGTGGATCAGT 59.746 55.000 0.00 0.00 39.36 3.41
2445 2510 0.253894 TGGCTGGTGATGTGGATCAG 59.746 55.000 0.00 0.00 39.36 2.90
2446 2511 0.035152 GTGGCTGGTGATGTGGATCA 60.035 55.000 0.00 0.00 36.16 2.92
2447 2512 0.035152 TGTGGCTGGTGATGTGGATC 60.035 55.000 0.00 0.00 0.00 3.36
2450 2515 2.338015 GCTGTGGCTGGTGATGTGG 61.338 63.158 0.00 0.00 35.22 4.17
2466 2531 4.778213 TGAATTTGTATCTAGGCTGGCT 57.222 40.909 9.28 9.28 0.00 4.75
2467 2532 5.997746 TGTATGAATTTGTATCTAGGCTGGC 59.002 40.000 0.00 0.00 0.00 4.85
2468 2533 8.345565 GTTTGTATGAATTTGTATCTAGGCTGG 58.654 37.037 0.00 0.00 0.00 4.85
2469 2534 9.113838 AGTTTGTATGAATTTGTATCTAGGCTG 57.886 33.333 0.00 0.00 0.00 4.85
2470 2535 9.113838 CAGTTTGTATGAATTTGTATCTAGGCT 57.886 33.333 0.00 0.00 0.00 4.58
2471 2536 8.893727 ACAGTTTGTATGAATTTGTATCTAGGC 58.106 33.333 0.00 0.00 0.00 3.93
2474 2539 9.952030 TGGACAGTTTGTATGAATTTGTATCTA 57.048 29.630 0.00 0.00 0.00 1.98
2475 2540 8.730680 GTGGACAGTTTGTATGAATTTGTATCT 58.269 33.333 0.00 0.00 0.00 1.98
2484 2549 5.863965 TCTCATGTGGACAGTTTGTATGAA 58.136 37.500 0.00 0.00 0.00 2.57
2528 2594 0.687354 ACACCCACTACTGAGCTTGG 59.313 55.000 0.00 0.00 0.00 3.61
2537 2603 2.946564 GGTACGTTGTACACCCACTAC 58.053 52.381 9.12 0.00 0.00 2.73
2562 2628 0.670546 ACGAAAGCTGGATGGACGTG 60.671 55.000 0.00 0.00 0.00 4.49
2590 2656 1.003928 TCGGCTTAAAAGGGAAGGACC 59.996 52.381 0.00 0.00 38.08 4.46
2597 2663 1.873591 CATCGGATCGGCTTAAAAGGG 59.126 52.381 0.00 0.00 0.00 3.95
2644 2710 1.206371 GAACGGGCAAGGCTACTTCTA 59.794 52.381 0.00 0.00 33.81 2.10
2647 2713 1.375523 CGAACGGGCAAGGCTACTT 60.376 57.895 0.00 0.00 37.43 2.24
2651 2717 2.193087 ATAACCGAACGGGCAAGGCT 62.193 55.000 17.44 0.00 40.62 4.58
2658 2724 4.692155 AGTTAGTCAAAATAACCGAACGGG 59.308 41.667 17.44 0.00 43.62 5.28
2659 2725 5.851047 AGTTAGTCAAAATAACCGAACGG 57.149 39.130 11.83 11.83 42.03 4.44
2670 2736 6.755141 GCACCGTATCATCTAGTTAGTCAAAA 59.245 38.462 0.00 0.00 0.00 2.44
2671 2737 6.127563 TGCACCGTATCATCTAGTTAGTCAAA 60.128 38.462 0.00 0.00 0.00 2.69
2674 2740 5.213675 GTGCACCGTATCATCTAGTTAGTC 58.786 45.833 5.22 0.00 0.00 2.59
2675 2741 4.261072 CGTGCACCGTATCATCTAGTTAGT 60.261 45.833 12.15 0.00 0.00 2.24
2676 2742 4.219802 CGTGCACCGTATCATCTAGTTAG 58.780 47.826 12.15 0.00 0.00 2.34
2694 2762 1.598130 AGTTCCCTCAGCAACGTGC 60.598 57.895 0.00 0.00 45.46 5.34
2696 2764 0.249911 GACAGTTCCCTCAGCAACGT 60.250 55.000 0.00 0.00 0.00 3.99
2705 2773 6.001460 TCAAATTATTTGTCGACAGTTCCCT 58.999 36.000 19.11 0.93 41.36 4.20
2708 2776 8.728088 AACATCAAATTATTTGTCGACAGTTC 57.272 30.769 19.11 0.00 41.36 3.01


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

AutoCloner maintained by Alex Coulton.