Multiple sequence alignment - TraesCS2D01G189800

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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 TraesCS2D01G189800 chr2D 100.000 2912 0 0 1 2912 133277154 133274243 0.000000e+00 5378
1 TraesCS2D01G189800 chr2D 92.857 126 9 0 1160 1285 133275941 133275816 1.780000e-42 183
2 TraesCS2D01G189800 chr2D 92.857 126 9 0 1214 1339 133275995 133275870 1.780000e-42 183
3 TraesCS2D01G189800 chr2B 87.012 2433 145 55 545 2881 189749414 189747057 0.000000e+00 2584
4 TraesCS2D01G189800 chr2A 93.201 956 45 4 1160 2113 141285872 141284935 0.000000e+00 1387
5 TraesCS2D01G189800 chr2A 92.247 503 28 3 837 1339 141286238 141285747 0.000000e+00 702
6 TraesCS2D01G189800 chr2A 88.983 236 6 6 551 766 141286472 141286237 1.030000e-69 274
7 TraesCS2D01G189800 chr2A 92.857 126 9 0 1214 1339 141285926 141285801 1.780000e-42 183
8 TraesCS2D01G189800 chr2A 83.756 197 23 3 2724 2912 141284873 141284678 8.290000e-41 178
9 TraesCS2D01G189800 chr1A 93.358 542 36 0 1 542 592085978 592086519 0.000000e+00 802
10 TraesCS2D01G189800 chr7A 92.989 542 38 0 1 542 730485506 730486047 0.000000e+00 791
11 TraesCS2D01G189800 chr5D 88.806 536 60 0 7 542 479880638 479880103 0.000000e+00 658
12 TraesCS2D01G189800 chr1D 88.619 536 61 0 7 542 42015512 42014977 0.000000e+00 652
13 TraesCS2D01G189800 chr1D 88.007 542 65 0 1 542 451108527 451109068 2.450000e-180 641
14 TraesCS2D01G189800 chr5B 87.132 544 69 1 1 543 629783360 629783903 1.480000e-172 616
15 TraesCS2D01G189800 chr7B 87.085 542 70 0 1 542 635014498 635015039 5.330000e-172 614
16 TraesCS2D01G189800 chr3A 87.313 536 68 0 7 542 709506421 709505886 5.330000e-172 614
17 TraesCS2D01G189800 chr1B 87.109 543 68 2 1 542 563464911 563465452 5.330000e-172 614


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 TraesCS2D01G189800 chr2D 133274243 133277154 2911 True 1914.666667 5378 95.2380 1 2912 3 chr2D.!!$R1 2911
1 TraesCS2D01G189800 chr2B 189747057 189749414 2357 True 2584.000000 2584 87.0120 545 2881 1 chr2B.!!$R1 2336
2 TraesCS2D01G189800 chr2A 141284678 141286472 1794 True 544.800000 1387 90.2088 551 2912 5 chr2A.!!$R1 2361
3 TraesCS2D01G189800 chr1A 592085978 592086519 541 False 802.000000 802 93.3580 1 542 1 chr1A.!!$F1 541
4 TraesCS2D01G189800 chr7A 730485506 730486047 541 False 791.000000 791 92.9890 1 542 1 chr7A.!!$F1 541
5 TraesCS2D01G189800 chr5D 479880103 479880638 535 True 658.000000 658 88.8060 7 542 1 chr5D.!!$R1 535
6 TraesCS2D01G189800 chr1D 42014977 42015512 535 True 652.000000 652 88.6190 7 542 1 chr1D.!!$R1 535
7 TraesCS2D01G189800 chr1D 451108527 451109068 541 False 641.000000 641 88.0070 1 542 1 chr1D.!!$F1 541
8 TraesCS2D01G189800 chr5B 629783360 629783903 543 False 616.000000 616 87.1320 1 543 1 chr5B.!!$F1 542
9 TraesCS2D01G189800 chr7B 635014498 635015039 541 False 614.000000 614 87.0850 1 542 1 chr7B.!!$F1 541
10 TraesCS2D01G189800 chr3A 709505886 709506421 535 True 614.000000 614 87.3130 7 542 1 chr3A.!!$R1 535
11 TraesCS2D01G189800 chr1B 563464911 563465452 541 False 614.000000 614 87.1090 1 542 1 chr1B.!!$F1 541

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
144 145 0.603707 CCTTCGCTGCAACCTTCTCA 60.604 55.0 0.0 0.0 0.0 3.27 F
189 190 0.911769 CATCTGGTAGCCCCTTCACA 59.088 55.0 0.0 0.0 0.0 3.58 F
1554 1630 0.035152 TCAACAAGATCATGCCCGCT 60.035 50.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1202 0.753111 GATGGGGGTGGATTGCTGAC 60.753 60.0 0.00 0.0 0.00 3.51 R
1611 1687 1.028330 ACTGGGCAATCGTCTGCATG 61.028 55.0 12.35 0.0 44.52 4.06 R
2839 2998 0.392998 GCAGCGGATTTTCAGGGAGA 60.393 55.0 0.00 0.0 0.00 3.71 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
21 22 4.351131 CTTTAGGGTTATTGGCACGAAC 57.649 45.455 0.00 0.00 0.00 3.95
96 97 2.654385 TGGGTTGATTCTCCCCTCATTT 59.346 45.455 12.56 0.00 42.80 2.32
114 115 4.335315 TCATTTATGATCACGGTGAAAGGC 59.665 41.667 15.72 5.90 0.00 4.35
120 121 3.239253 ACGGTGAAAGGCGGGTCT 61.239 61.111 0.00 0.00 0.00 3.85
144 145 0.603707 CCTTCGCTGCAACCTTCTCA 60.604 55.000 0.00 0.00 0.00 3.27
174 175 2.516227 TCCTTCTCGTGAGACCATCT 57.484 50.000 0.00 0.00 37.14 2.90
189 190 0.911769 CATCTGGTAGCCCCTTCACA 59.088 55.000 0.00 0.00 0.00 3.58
206 207 1.111277 ACACTTGCCCAAACTGGAAC 58.889 50.000 0.00 0.00 40.96 3.62
352 353 4.137543 CTGAACCAGAAACAAGTTAGGCT 58.862 43.478 0.00 0.00 32.44 4.58
381 382 3.168528 AACGTCACCCCCTGTGCT 61.169 61.111 0.00 0.00 45.03 4.40
542 543 1.064906 CCTTCCATGCAGTGTCATCCT 60.065 52.381 0.00 0.00 0.00 3.24
543 544 2.171237 CCTTCCATGCAGTGTCATCCTA 59.829 50.000 0.00 0.00 0.00 2.94
544 545 3.464907 CTTCCATGCAGTGTCATCCTAG 58.535 50.000 0.00 0.00 0.00 3.02
545 546 1.764723 TCCATGCAGTGTCATCCTAGG 59.235 52.381 0.82 0.82 0.00 3.02
546 547 1.764723 CCATGCAGTGTCATCCTAGGA 59.235 52.381 15.46 15.46 0.00 2.94
547 548 2.371179 CCATGCAGTGTCATCCTAGGAT 59.629 50.000 19.18 19.18 34.81 3.24
548 549 3.181447 CCATGCAGTGTCATCCTAGGATT 60.181 47.826 22.29 4.15 31.62 3.01
549 550 3.548745 TGCAGTGTCATCCTAGGATTG 57.451 47.619 22.29 17.44 31.62 2.67
609 610 2.551270 CAAGCACACGTCGGCTTC 59.449 61.111 17.70 0.00 46.82 3.86
703 725 2.749776 CGTAATGGCACGGTGATATCA 58.250 47.619 13.29 0.00 38.26 2.15
773 795 2.343387 GCTGCCGCCACCATTTTT 59.657 55.556 0.00 0.00 0.00 1.94
815 837 0.950836 CGCCTCATCTCAGATCGACT 59.049 55.000 0.00 0.00 0.00 4.18
816 838 2.147150 CGCCTCATCTCAGATCGACTA 58.853 52.381 0.00 0.00 0.00 2.59
817 839 2.550180 CGCCTCATCTCAGATCGACTAA 59.450 50.000 0.00 0.00 0.00 2.24
818 840 3.364864 CGCCTCATCTCAGATCGACTAAG 60.365 52.174 0.00 0.00 0.00 2.18
819 841 3.818210 GCCTCATCTCAGATCGACTAAGA 59.182 47.826 0.00 0.00 0.00 2.10
892 914 1.447317 CCAGTGCTGTTCAAACGCCT 61.447 55.000 0.00 2.99 0.00 5.52
911 933 2.047061 CTTATCTCGTCCCCATTCCCA 58.953 52.381 0.00 0.00 0.00 4.37
966 988 2.829206 CGCACCACAGACCGCAAAA 61.829 57.895 0.00 0.00 0.00 2.44
1099 1121 4.812476 CGTCGGCCGCCATCAGAA 62.812 66.667 23.51 0.00 0.00 3.02
1248 1324 0.962356 CAGTGATCAGCAACCCACCC 60.962 60.000 0.00 0.00 0.00 4.61
1326 1402 2.936032 GTCCCTGCTTCCCCACCT 60.936 66.667 0.00 0.00 0.00 4.00
1485 1561 4.314440 TGCGGCGCCTTCAAGTCT 62.314 61.111 30.82 0.00 0.00 3.24
1554 1630 0.035152 TCAACAAGATCATGCCCGCT 60.035 50.000 0.00 0.00 0.00 5.52
1587 1663 2.910360 CGCATGATGTCCCTCCCA 59.090 61.111 0.00 0.00 0.00 4.37
1661 1737 2.597805 ATCGTAGCCGGCCGATCT 60.598 61.111 27.99 24.53 39.45 2.75
1707 1809 3.398292 AGCATGATTGGAGGAGGATTGAT 59.602 43.478 0.00 0.00 0.00 2.57
1999 2111 7.040686 TCCGATCGAGATGATGAATTAGTTGTA 60.041 37.037 18.66 0.00 37.47 2.41
2180 2296 7.877612 TGATCAATATTAGTCCATACGTGCATT 59.122 33.333 0.00 0.00 0.00 3.56
2220 2346 2.125147 GCATGTGCTCCCTGCGTA 60.125 61.111 0.00 0.00 46.63 4.42
2235 2361 2.799412 CTGCGTATTGGATCAGCTCTTC 59.201 50.000 0.00 0.00 0.00 2.87
2236 2362 1.789464 GCGTATTGGATCAGCTCTTCG 59.211 52.381 0.00 0.00 0.00 3.79
2242 2368 3.616956 TGGATCAGCTCTTCGTTCAAT 57.383 42.857 0.00 0.00 0.00 2.57
2243 2369 3.525537 TGGATCAGCTCTTCGTTCAATC 58.474 45.455 0.00 0.00 0.00 2.67
2244 2370 3.055891 TGGATCAGCTCTTCGTTCAATCA 60.056 43.478 0.00 0.00 0.00 2.57
2245 2371 4.125703 GGATCAGCTCTTCGTTCAATCAT 58.874 43.478 0.00 0.00 0.00 2.45
2293 2421 2.907897 GAATCTGCAGGGTACGCGCT 62.908 60.000 15.13 0.00 38.52 5.92
2295 2423 3.490759 CTGCAGGGTACGCGCTTG 61.491 66.667 20.73 9.81 35.58 4.01
2300 2428 0.110373 CAGGGTACGCGCTTGTTTTC 60.110 55.000 5.73 0.00 35.58 2.29
2301 2429 1.208358 GGGTACGCGCTTGTTTTCC 59.792 57.895 5.73 1.10 0.00 3.13
2303 2431 1.208358 GTACGCGCTTGTTTTCCCC 59.792 57.895 5.73 0.00 0.00 4.81
2325 2453 1.599542 CCTCTAAATTGCAGGCTACGC 59.400 52.381 0.00 0.00 0.00 4.42
2326 2454 1.258982 CTCTAAATTGCAGGCTACGCG 59.741 52.381 3.53 3.53 0.00 6.01
2327 2455 1.006832 CTAAATTGCAGGCTACGCGT 58.993 50.000 19.17 19.17 0.00 6.01
2328 2456 0.724549 TAAATTGCAGGCTACGCGTG 59.275 50.000 24.59 13.17 45.60 5.34
2333 2461 4.178861 CAGGCTACGCGTGCTAAA 57.821 55.556 24.59 0.00 37.60 1.85
2334 2462 1.708027 CAGGCTACGCGTGCTAAAC 59.292 57.895 24.59 10.28 37.60 2.01
2335 2463 0.736325 CAGGCTACGCGTGCTAAACT 60.736 55.000 24.59 12.30 37.60 2.66
2336 2464 0.458025 AGGCTACGCGTGCTAAACTC 60.458 55.000 24.59 9.26 0.00 3.01
2337 2465 0.458025 GGCTACGCGTGCTAAACTCT 60.458 55.000 24.59 0.00 0.00 3.24
2338 2466 1.347320 GCTACGCGTGCTAAACTCTT 58.653 50.000 24.59 0.00 0.00 2.85
2339 2467 2.523015 GCTACGCGTGCTAAACTCTTA 58.477 47.619 24.59 0.00 0.00 2.10
2340 2468 2.919229 GCTACGCGTGCTAAACTCTTAA 59.081 45.455 24.59 0.00 0.00 1.85
2341 2469 3.365820 GCTACGCGTGCTAAACTCTTAAA 59.634 43.478 24.59 0.00 0.00 1.52
2342 2470 3.783111 ACGCGTGCTAAACTCTTAAAC 57.217 42.857 12.93 0.00 0.00 2.01
2343 2471 2.477754 ACGCGTGCTAAACTCTTAAACC 59.522 45.455 12.93 0.00 0.00 3.27
2344 2472 2.477375 CGCGTGCTAAACTCTTAAACCA 59.523 45.455 0.00 0.00 0.00 3.67
2372 2500 1.340017 TGTGAGGTGCTAAAGCCCATC 60.340 52.381 10.76 2.82 41.18 3.51
2374 2502 1.065199 TGAGGTGCTAAAGCCCATCTG 60.065 52.381 10.76 0.00 41.18 2.90
2401 2538 1.516110 AGGTGAATGCTAGAGCCCAT 58.484 50.000 0.00 0.00 41.18 4.00
2414 2551 0.395586 AGCCCATGTGTGTTGTGTGT 60.396 50.000 0.00 0.00 0.00 3.72
2415 2552 0.248990 GCCCATGTGTGTTGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
2420 2557 0.801872 TGTGTGTTGTGTGTGCTGTC 59.198 50.000 0.00 0.00 0.00 3.51
2428 2565 0.320771 GTGTGTGCTGTCCCTCGATT 60.321 55.000 0.00 0.00 0.00 3.34
2458 2595 4.814771 GCTATGATACGTGGGCTTTTTACT 59.185 41.667 0.00 0.00 0.00 2.24
2468 2605 1.472878 GGCTTTTTACTAGGCCAGTGC 59.527 52.381 5.01 5.85 43.59 4.40
2469 2606 2.437413 GCTTTTTACTAGGCCAGTGCT 58.563 47.619 5.01 0.00 38.24 4.40
2484 2621 5.551760 CCAGTGCTGGTTCTATTGTTTAG 57.448 43.478 9.96 0.00 45.53 1.85
2485 2622 4.396166 CCAGTGCTGGTTCTATTGTTTAGG 59.604 45.833 9.96 0.00 45.53 2.69
2486 2623 4.010349 AGTGCTGGTTCTATTGTTTAGGC 58.990 43.478 0.00 0.00 0.00 3.93
2487 2624 3.128764 GTGCTGGTTCTATTGTTTAGGCC 59.871 47.826 0.00 0.00 0.00 5.19
2488 2625 3.010138 TGCTGGTTCTATTGTTTAGGCCT 59.990 43.478 11.78 11.78 0.00 5.19
2489 2626 3.378427 GCTGGTTCTATTGTTTAGGCCTG 59.622 47.826 17.99 0.00 0.00 4.85
2494 2631 1.678101 CTATTGTTTAGGCCTGGCTGC 59.322 52.381 17.99 2.28 0.00 5.25
2518 2655 2.434185 GCAAGTGGGCGACGATGA 60.434 61.111 11.41 0.00 0.00 2.92
2606 2743 0.957888 GAGTTGGCCACTTGGAGAGC 60.958 60.000 3.88 0.00 35.01 4.09
2722 2876 2.125512 GATTCTGTCTGCGGCGGT 60.126 61.111 9.78 0.00 0.00 5.68
2737 2891 1.005394 CGGTGTTTCTAGGTGCGGT 60.005 57.895 0.00 0.00 0.00 5.68
2776 2935 7.840342 ATTCTGTGAAATACTACAAGAGCAG 57.160 36.000 0.00 0.00 0.00 4.24
2787 2946 3.004024 ACAAGAGCAGTGAAATTTGCG 57.996 42.857 0.00 0.00 44.80 4.85
2792 2951 3.503363 AGAGCAGTGAAATTTGCGATGAA 59.497 39.130 0.00 0.00 44.80 2.57
2832 2991 5.752472 AGACGCACTCAAGATAGAATGATTG 59.248 40.000 0.00 0.00 31.55 2.67
2835 2994 5.985530 CGCACTCAAGATAGAATGATTGGTA 59.014 40.000 0.00 0.00 29.74 3.25
2836 2995 6.145209 CGCACTCAAGATAGAATGATTGGTAG 59.855 42.308 0.00 0.00 29.74 3.18
2838 2997 7.687837 GCACTCAAGATAGAATGATTGGTAGGA 60.688 40.741 0.00 0.00 29.74 2.94
2839 2998 8.373981 CACTCAAGATAGAATGATTGGTAGGAT 58.626 37.037 0.00 0.00 0.00 3.24
2840 2999 8.592809 ACTCAAGATAGAATGATTGGTAGGATC 58.407 37.037 0.00 0.00 0.00 3.36
2843 3003 7.732222 AGATAGAATGATTGGTAGGATCTCC 57.268 40.000 0.00 0.00 0.00 3.71
2860 3020 0.677731 TCCCTGAAAATCCGCTGCAG 60.678 55.000 10.11 10.11 0.00 4.41
2861 3021 1.138247 CCTGAAAATCCGCTGCAGC 59.862 57.895 29.12 29.12 37.78 5.25
2896 3063 6.035650 GCGTTTCACTATTAAGAGCATGTGTA 59.964 38.462 0.00 0.00 0.00 2.90
2904 3071 2.586258 AGAGCATGTGTAACGCTAGG 57.414 50.000 0.00 0.00 42.39 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.472552 CCGCCTTTCACCGTGATCATA 60.473 52.381 1.09 0.00 0.00 2.15
120 121 1.896660 GGTTGCAGCGAAGGTTGGA 60.897 57.895 0.00 0.00 33.74 3.53
144 145 2.165437 CACGAGAAGGAAAGAGCTAGCT 59.835 50.000 19.45 19.45 0.00 3.32
174 175 0.400213 CAAGTGTGAAGGGGCTACCA 59.600 55.000 0.97 0.00 43.89 3.25
189 190 2.159179 AAGTTCCAGTTTGGGCAAGT 57.841 45.000 0.00 0.00 38.32 3.16
352 353 4.258543 GGGGTGACGTTCAATATCAAAGA 58.741 43.478 0.00 0.00 0.00 2.52
381 382 2.468670 GCGTAATGCATGGTCGGCA 61.469 57.895 0.00 0.00 46.66 5.69
542 543 4.362677 ACAACTCCCTTCTAGCAATCCTA 58.637 43.478 0.00 0.00 0.00 2.94
543 544 3.185455 ACAACTCCCTTCTAGCAATCCT 58.815 45.455 0.00 0.00 0.00 3.24
544 545 3.636153 ACAACTCCCTTCTAGCAATCC 57.364 47.619 0.00 0.00 0.00 3.01
545 546 4.572795 GCTTACAACTCCCTTCTAGCAATC 59.427 45.833 0.00 0.00 0.00 2.67
546 547 4.518249 GCTTACAACTCCCTTCTAGCAAT 58.482 43.478 0.00 0.00 0.00 3.56
547 548 3.616560 CGCTTACAACTCCCTTCTAGCAA 60.617 47.826 0.00 0.00 0.00 3.91
548 549 2.094182 CGCTTACAACTCCCTTCTAGCA 60.094 50.000 0.00 0.00 0.00 3.49
549 550 2.094130 ACGCTTACAACTCCCTTCTAGC 60.094 50.000 0.00 0.00 0.00 3.42
609 610 2.135664 AAGTCGTCTGTTCGAACCTG 57.864 50.000 24.78 17.15 41.47 4.00
703 725 7.070821 ACTCCTCAAGTTTACGGGATATAACAT 59.929 37.037 0.00 0.00 33.03 2.71
816 838 8.807118 TGTCTTGTGTCACTCTTATCTTATCTT 58.193 33.333 4.27 0.00 0.00 2.40
817 839 8.354711 TGTCTTGTGTCACTCTTATCTTATCT 57.645 34.615 4.27 0.00 0.00 1.98
818 840 8.988064 TTGTCTTGTGTCACTCTTATCTTATC 57.012 34.615 4.27 0.00 0.00 1.75
819 841 9.778741 TTTTGTCTTGTGTCACTCTTATCTTAT 57.221 29.630 4.27 0.00 0.00 1.73
839 861 3.139077 ACATGGGACTCTTCGTTTTGTC 58.861 45.455 0.00 0.00 0.00 3.18
892 914 1.766496 GTGGGAATGGGGACGAGATAA 59.234 52.381 0.00 0.00 0.00 1.75
911 933 2.238521 CATGGCGGCCATTTTATAGGT 58.761 47.619 31.17 5.91 42.23 3.08
966 988 1.030457 CTTACGATCGGCTACTGGGT 58.970 55.000 20.98 0.00 0.00 4.51
1087 1109 1.358046 GCTTGATTCTGATGGCGGC 59.642 57.895 0.00 0.00 0.00 6.53
1120 1142 1.643832 GCGGCGATGGCTTAAGAAG 59.356 57.895 12.98 0.00 39.81 2.85
1123 1145 2.203070 AGGCGGCGATGGCTTAAG 60.203 61.111 12.98 0.00 42.97 1.85
1180 1202 0.753111 GATGGGGGTGGATTGCTGAC 60.753 60.000 0.00 0.00 0.00 3.51
1248 1324 2.190578 GAAGCAGGGACGGATGGG 59.809 66.667 0.00 0.00 0.00 4.00
1280 1356 1.379044 GGGTTGCTGATCACTGGGG 60.379 63.158 0.00 0.00 0.00 4.96
1377 1453 3.626924 GTCAGGCACTCCGTGGGT 61.627 66.667 0.00 0.00 34.60 4.51
1395 1471 2.438434 GTCAGCCCCATCAACGGG 60.438 66.667 0.00 0.00 46.94 5.28
1485 1561 3.948719 GGGGCGTTGTCCACCAGA 61.949 66.667 0.00 0.00 0.00 3.86
1587 1663 4.699522 GGGACGGCGCAGTTTCCT 62.700 66.667 15.89 0.00 0.00 3.36
1611 1687 1.028330 ACTGGGCAATCGTCTGCATG 61.028 55.000 12.35 0.00 44.52 4.06
1661 1737 9.364989 GCTAATAACAATGCCAAAAATACTGAA 57.635 29.630 0.00 0.00 0.00 3.02
2069 2181 2.794910 CGCCAGCACACATGTAGTATAC 59.205 50.000 0.00 0.00 43.42 1.47
2133 2246 7.877612 TGATCACCGCATATATACAGTGAAAAT 59.122 33.333 6.17 0.00 37.74 1.82
2180 2296 5.401376 GCATATAGACACTTACGAATTCGCA 59.599 40.000 27.03 12.71 44.43 5.10
2220 2346 3.616956 TGAACGAAGAGCTGATCCAAT 57.383 42.857 0.00 0.00 0.00 3.16
2235 2361 7.141363 ACTGAAAGAGGAAAAATGATTGAACG 58.859 34.615 0.00 0.00 37.43 3.95
2236 2362 8.877808 AACTGAAAGAGGAAAAATGATTGAAC 57.122 30.769 0.00 0.00 37.43 3.18
2242 2368 6.833416 TCCTGAAACTGAAAGAGGAAAAATGA 59.167 34.615 0.00 0.00 31.04 2.57
2243 2369 7.042797 TCCTGAAACTGAAAGAGGAAAAATG 57.957 36.000 0.00 0.00 31.04 2.32
2244 2370 6.239148 GCTCCTGAAACTGAAAGAGGAAAAAT 60.239 38.462 0.00 0.00 33.40 1.82
2245 2371 5.067805 GCTCCTGAAACTGAAAGAGGAAAAA 59.932 40.000 0.00 0.00 33.40 1.94
2303 2431 2.576615 GTAGCCTGCAATTTAGAGGGG 58.423 52.381 0.00 0.00 0.00 4.79
2325 2453 4.901881 CGTTTGGTTTAAGAGTTTAGCACG 59.098 41.667 0.00 0.00 0.00 5.34
2326 2454 4.673761 GCGTTTGGTTTAAGAGTTTAGCAC 59.326 41.667 0.00 0.00 0.00 4.40
2327 2455 4.335874 TGCGTTTGGTTTAAGAGTTTAGCA 59.664 37.500 0.00 0.00 0.00 3.49
2328 2456 4.673761 GTGCGTTTGGTTTAAGAGTTTAGC 59.326 41.667 0.00 0.00 0.00 3.09
2329 2457 5.907391 CAGTGCGTTTGGTTTAAGAGTTTAG 59.093 40.000 0.00 0.00 0.00 1.85
2330 2458 5.354792 ACAGTGCGTTTGGTTTAAGAGTTTA 59.645 36.000 0.00 0.00 0.00 2.01
2331 2459 4.157105 ACAGTGCGTTTGGTTTAAGAGTTT 59.843 37.500 0.00 0.00 0.00 2.66
2332 2460 3.692593 ACAGTGCGTTTGGTTTAAGAGTT 59.307 39.130 0.00 0.00 0.00 3.01
2333 2461 3.064820 CACAGTGCGTTTGGTTTAAGAGT 59.935 43.478 0.00 0.00 0.00 3.24
2334 2462 3.311322 TCACAGTGCGTTTGGTTTAAGAG 59.689 43.478 0.00 0.00 0.00 2.85
2335 2463 3.271729 TCACAGTGCGTTTGGTTTAAGA 58.728 40.909 0.00 0.00 0.00 2.10
2336 2464 3.548014 CCTCACAGTGCGTTTGGTTTAAG 60.548 47.826 0.00 0.00 0.00 1.85
2337 2465 2.356382 CCTCACAGTGCGTTTGGTTTAA 59.644 45.455 0.00 0.00 0.00 1.52
2338 2466 1.944024 CCTCACAGTGCGTTTGGTTTA 59.056 47.619 0.00 0.00 0.00 2.01
2339 2467 0.738389 CCTCACAGTGCGTTTGGTTT 59.262 50.000 0.00 0.00 0.00 3.27
2340 2468 0.393808 ACCTCACAGTGCGTTTGGTT 60.394 50.000 0.00 0.00 29.02 3.67
2341 2469 1.095228 CACCTCACAGTGCGTTTGGT 61.095 55.000 0.00 0.00 32.48 3.67
2342 2470 1.648720 CACCTCACAGTGCGTTTGG 59.351 57.895 0.00 0.00 0.00 3.28
2381 2509 2.174685 TGGGCTCTAGCATTCACCTA 57.825 50.000 4.07 0.00 44.36 3.08
2387 2524 1.283029 ACACACATGGGCTCTAGCATT 59.717 47.619 4.07 0.00 44.36 3.56
2401 2538 0.801872 GACAGCACACACAACACACA 59.198 50.000 0.00 0.00 0.00 3.72
2414 2551 1.686325 GGCCTAATCGAGGGACAGCA 61.686 60.000 0.00 0.00 46.81 4.41
2415 2552 1.069935 GGCCTAATCGAGGGACAGC 59.930 63.158 0.00 0.00 46.81 4.40
2420 2557 1.258445 ATAGCGGGCCTAATCGAGGG 61.258 60.000 0.84 0.00 46.81 4.30
2428 2565 0.885879 CACGTATCATAGCGGGCCTA 59.114 55.000 0.84 0.00 0.00 3.93
2466 2603 3.010138 AGGCCTAAACAATAGAACCAGCA 59.990 43.478 1.29 0.00 0.00 4.41
2467 2604 3.378427 CAGGCCTAAACAATAGAACCAGC 59.622 47.826 3.98 0.00 0.00 4.85
2468 2605 3.947834 CCAGGCCTAAACAATAGAACCAG 59.052 47.826 3.98 0.00 0.00 4.00
2469 2606 3.876156 GCCAGGCCTAAACAATAGAACCA 60.876 47.826 3.98 0.00 0.00 3.67
2471 2608 3.378427 CAGCCAGGCCTAAACAATAGAAC 59.622 47.826 3.98 0.00 0.00 3.01
2472 2609 3.620488 CAGCCAGGCCTAAACAATAGAA 58.380 45.455 3.98 0.00 0.00 2.10
2474 2611 1.678101 GCAGCCAGGCCTAAACAATAG 59.322 52.381 3.98 0.00 0.00 1.73
2475 2612 1.762708 GCAGCCAGGCCTAAACAATA 58.237 50.000 3.98 0.00 0.00 1.90
2476 2613 1.315257 CGCAGCCAGGCCTAAACAAT 61.315 55.000 3.98 0.00 0.00 2.71
2477 2614 1.971167 CGCAGCCAGGCCTAAACAA 60.971 57.895 3.98 0.00 0.00 2.83
2478 2615 2.359850 CGCAGCCAGGCCTAAACA 60.360 61.111 3.98 0.00 0.00 2.83
2481 2618 4.473520 GCTCGCAGCCAGGCCTAA 62.474 66.667 3.98 0.00 34.48 2.69
2506 2643 4.889856 CGCCATCATCGTCGCCCA 62.890 66.667 0.00 0.00 0.00 5.36
2635 2772 3.130633 TGCGGTTGATGAAATCCTATCG 58.869 45.455 0.00 0.00 44.73 2.92
2722 2876 0.948678 GCAAACCGCACCTAGAAACA 59.051 50.000 0.00 0.00 41.79 2.83
2737 2891 3.190327 CACAGAATTCACCATACGGCAAA 59.810 43.478 8.44 0.00 34.57 3.68
2776 2935 6.695292 AACTCAATTCATCGCAAATTTCAC 57.305 33.333 0.00 0.00 0.00 3.18
2787 2946 7.201299 GCGTCTCATTTTCAAACTCAATTCATC 60.201 37.037 0.00 0.00 0.00 2.92
2792 2951 5.009010 AGTGCGTCTCATTTTCAAACTCAAT 59.991 36.000 0.00 0.00 0.00 2.57
2832 2991 3.244249 CGGATTTTCAGGGAGATCCTACC 60.244 52.174 0.00 0.00 46.12 3.18
2836 2995 1.141858 AGCGGATTTTCAGGGAGATCC 59.858 52.381 0.00 0.00 35.73 3.36
2838 2997 1.748591 GCAGCGGATTTTCAGGGAGAT 60.749 52.381 0.00 0.00 0.00 2.75
2839 2998 0.392998 GCAGCGGATTTTCAGGGAGA 60.393 55.000 0.00 0.00 0.00 3.71
2840 2999 0.677731 TGCAGCGGATTTTCAGGGAG 60.678 55.000 0.00 0.00 0.00 4.30
2843 3003 1.138247 GCTGCAGCGGATTTTCAGG 59.862 57.895 25.23 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.