Multiple sequence alignment - TraesCS5D01G143900

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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 TraesCS5D01G143900 chr5D 100.000 2558 0 0 1 2558 230044245 230041688 0.000000e+00 4724.0
1 TraesCS5D01G143900 chr5A 89.703 2185 136 30 363 2505 326649240 326651377 0.000000e+00 2706.0
2 TraesCS5D01G143900 chr5A 90.756 357 31 2 9 363 326648848 326649204 2.300000e-130 475.0
3 TraesCS5D01G143900 chr5B 92.819 1295 52 17 612 1884 275503774 275505049 0.000000e+00 1838.0
4 TraesCS5D01G143900 chr5B 86.792 530 43 12 1874 2389 275505297 275505813 1.330000e-157 566.0
5 TraesCS5D01G143900 chr5B 91.292 356 27 4 9 363 275503002 275503354 1.380000e-132 483.0
6 TraesCS5D01G143900 chr5B 80.100 402 70 8 2158 2558 604222574 604222182 8.950000e-75 291.0
7 TraesCS5D01G143900 chr5B 80.994 342 51 8 2220 2554 354725107 354725441 2.520000e-65 259.0
8 TraesCS5D01G143900 chr5B 82.731 249 25 10 371 609 275503406 275503646 3.340000e-49 206.0
9 TraesCS5D01G143900 chr5B 77.922 154 24 7 2211 2355 422121933 422122085 1.260000e-13 87.9
10 TraesCS5D01G143900 chr3B 80.429 373 57 9 2198 2558 395862473 395862841 1.170000e-68 270.0
11 TraesCS5D01G143900 chr4B 80.712 337 56 8 2220 2554 122314397 122314726 1.170000e-63 254.0
12 TraesCS5D01G143900 chr1B 80.925 346 41 10 2223 2558 573759597 573759267 1.520000e-62 250.0
13 TraesCS5D01G143900 chr6D 79.515 371 59 9 2203 2557 405660165 405659796 5.470000e-62 248.0
14 TraesCS5D01G143900 chr7D 82.955 264 35 1 2295 2558 461093247 461092994 1.980000e-56 230.0
15 TraesCS5D01G143900 chr7A 85.581 215 29 2 2297 2510 479291653 479291440 9.210000e-55 224.0
16 TraesCS5D01G143900 chr7B 79.525 337 50 9 2239 2558 540867780 540868114 3.310000e-54 222.0
17 TraesCS5D01G143900 chr7B 81.818 264 38 6 2295 2558 483536369 483536116 1.990000e-51 213.0
18 TraesCS5D01G143900 chr6B 82.186 247 37 3 2312 2552 689279351 689279106 3.340000e-49 206.0
19 TraesCS5D01G143900 chr2B 88.732 71 7 1 2488 2558 637101874 637101943 4.530000e-13 86.1


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 TraesCS5D01G143900 chr5D 230041688 230044245 2557 True 4724.00 4724 100.0000 1 2558 1 chr5D.!!$R1 2557
1 TraesCS5D01G143900 chr5A 326648848 326651377 2529 False 1590.50 2706 90.2295 9 2505 2 chr5A.!!$F1 2496
2 TraesCS5D01G143900 chr5B 275503002 275505813 2811 False 773.25 1838 88.4085 9 2389 4 chr5B.!!$F3 2380

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
435 482 0.034059 AGAAGTTGGCAGACGTCTGG 59.966 55.0 38.72 24.14 43.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2700 0.1791 CATCCGTGCCCACTGACTAG 60.179 60.0 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
51 52 3.057019 CTCCAAGACGTCGTCATTTGAA 58.943 45.455 26.17 7.09 34.60 2.69
118 119 1.890979 GACGATCGAGGGAGGCGTA 60.891 63.158 24.34 0.00 37.29 4.42
121 122 1.721664 CGATCGAGGGAGGCGTAACA 61.722 60.000 10.26 0.00 0.00 2.41
139 141 2.060980 AGATTCGCTCGAAGCCCCT 61.061 57.895 15.35 5.28 40.95 4.79
142 144 1.617947 ATTCGCTCGAAGCCCCTCTT 61.618 55.000 10.53 0.00 38.18 2.85
161 163 2.489938 TGGATTTGTAGTCCTGGTGC 57.510 50.000 0.00 0.00 36.68 5.01
164 166 2.290323 GGATTTGTAGTCCTGGTGCAGT 60.290 50.000 0.00 0.00 32.85 4.40
178 180 2.743718 CAGTGGAGGCTGTTCCGT 59.256 61.111 0.00 0.00 40.27 4.69
182 184 4.373116 GGAGGCTGTTCCGTGCGA 62.373 66.667 0.00 0.00 40.77 5.10
238 241 1.180029 CCTTGGTCTTCTTGCCCATG 58.820 55.000 0.00 0.00 0.00 3.66
275 278 3.321111 AGGTATTGTGTGTGACGACTCTT 59.679 43.478 0.00 0.00 0.00 2.85
276 279 4.056050 GGTATTGTGTGTGACGACTCTTT 58.944 43.478 0.00 0.00 0.00 2.52
369 372 2.281692 TGCGCCAACATCAGTGCT 60.282 55.556 4.18 0.00 40.18 4.40
374 421 1.379916 CCAACATCAGTGCTGGGGA 59.620 57.895 0.00 0.00 37.83 4.81
384 431 1.127343 GTGCTGGGGATTCTAGAGCT 58.873 55.000 0.00 0.00 0.00 4.09
393 440 2.158385 GGATTCTAGAGCTGGAGAGGGA 60.158 54.545 0.00 0.00 0.00 4.20
397 444 2.788807 TCTAGAGCTGGAGAGGGATTCT 59.211 50.000 0.00 0.00 39.43 2.40
408 455 2.524440 AGAGGGATTCTGGATAGGACCA 59.476 50.000 0.00 0.00 33.93 4.02
432 479 2.750948 TGTTAGAAGTTGGCAGACGTC 58.249 47.619 7.70 7.70 0.00 4.34
435 482 0.034059 AGAAGTTGGCAGACGTCTGG 59.966 55.000 38.72 24.14 43.94 3.86
443 490 2.752238 AGACGTCTGGGCTCCTCG 60.752 66.667 19.30 0.00 0.00 4.63
468 515 2.406616 CCCTGATTTTGGGCCGACG 61.407 63.158 0.00 0.00 37.99 5.12
487 534 4.267928 CGACGTAGAGGATTTCAAACATCC 59.732 45.833 0.00 0.00 40.72 3.51
488 535 5.160607 ACGTAGAGGATTTCAAACATCCA 57.839 39.130 1.89 0.00 42.63 3.41
489 536 5.178797 ACGTAGAGGATTTCAAACATCCAG 58.821 41.667 1.89 0.00 42.63 3.86
497 544 5.067023 GGATTTCAAACATCCAGATCAGTCC 59.933 44.000 0.00 0.00 40.21 3.85
498 545 4.639078 TTCAAACATCCAGATCAGTCCA 57.361 40.909 0.00 0.00 0.00 4.02
508 556 2.606725 CAGATCAGTCCAGTCGATTTGC 59.393 50.000 0.00 0.00 0.00 3.68
544 592 5.622346 AGGCCTAAAAATGTTTTGAACCA 57.378 34.783 1.29 0.00 0.00 3.67
561 609 9.784680 TTTTGAACCATTCATTTCAAACATTTG 57.215 25.926 8.60 0.00 46.37 2.32
597 650 2.420642 CTGCGGATGTCATATTGGGAG 58.579 52.381 0.00 0.00 0.00 4.30
715 906 3.924686 ACAGTTCGTTAAAGCTATCACGG 59.075 43.478 10.56 0.00 33.39 4.94
716 907 4.171005 CAGTTCGTTAAAGCTATCACGGA 58.829 43.478 10.56 0.79 33.39 4.69
717 908 4.265556 CAGTTCGTTAAAGCTATCACGGAG 59.734 45.833 10.56 0.00 33.39 4.63
723 914 0.461961 AAGCTATCACGGAGCACTCC 59.538 55.000 6.62 6.62 46.18 3.85
752 943 2.652530 GTGGTCCCGACACGCTAA 59.347 61.111 0.00 0.00 0.00 3.09
776 968 3.226449 AGTCCCACGTGTCAGTGTGAC 62.226 57.143 15.65 8.80 45.53 3.67
897 1089 3.769300 GGGCCACTGGTTTCATTTATCTT 59.231 43.478 4.39 0.00 0.00 2.40
1016 1208 3.334583 TCCCAAAGAAAGTCATCCGAG 57.665 47.619 0.00 0.00 0.00 4.63
1110 1321 1.972223 CCACCGTCGGTCAGTCTCT 60.972 63.158 15.67 0.00 31.02 3.10
1126 1337 4.400251 CTGTCCCTCGGTCCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
1130 1341 2.285442 CCCTCGGTCCCCCTTTCT 60.285 66.667 0.00 0.00 0.00 2.52
1161 1372 3.021695 TCTCCGATCGGTGTTCTTGTAT 58.978 45.455 32.15 0.00 36.47 2.29
1162 1373 4.201657 TCTCCGATCGGTGTTCTTGTATA 58.798 43.478 32.15 8.75 36.47 1.47
1163 1374 4.275196 TCTCCGATCGGTGTTCTTGTATAG 59.725 45.833 32.15 17.77 36.47 1.31
1164 1375 3.949754 TCCGATCGGTGTTCTTGTATAGT 59.050 43.478 32.15 0.00 36.47 2.12
1165 1376 4.400251 TCCGATCGGTGTTCTTGTATAGTT 59.600 41.667 32.15 0.00 36.47 2.24
1166 1377 4.503007 CCGATCGGTGTTCTTGTATAGTTG 59.497 45.833 26.35 0.00 0.00 3.16
1167 1378 5.100259 CGATCGGTGTTCTTGTATAGTTGT 58.900 41.667 7.38 0.00 0.00 3.32
1168 1379 5.004440 CGATCGGTGTTCTTGTATAGTTGTG 59.996 44.000 7.38 0.00 0.00 3.33
1169 1380 5.456548 TCGGTGTTCTTGTATAGTTGTGA 57.543 39.130 0.00 0.00 0.00 3.58
1170 1381 5.845103 TCGGTGTTCTTGTATAGTTGTGAA 58.155 37.500 0.00 0.00 0.00 3.18
1171 1382 6.460781 TCGGTGTTCTTGTATAGTTGTGAAT 58.539 36.000 0.00 0.00 0.00 2.57
1210 1429 3.438781 GGTACTGATTTTGATTGCCGTGA 59.561 43.478 0.00 0.00 0.00 4.35
1232 1451 2.764128 AGGGGCGATGTGGACGAT 60.764 61.111 0.00 0.00 0.00 3.73
1395 1614 2.017782 CTGGACTTCTACTCGCAGCTA 58.982 52.381 0.00 0.00 0.00 3.32
1612 1834 5.956563 GGGGAAGACGGGATTATCTTATCTA 59.043 44.000 0.00 0.00 35.29 1.98
1630 1856 9.011095 TCTTATCTACTTTGTACTATCCATCCG 57.989 37.037 0.00 0.00 0.00 4.18
1681 1907 3.264845 GTGTGATGGGGGTGGGGT 61.265 66.667 0.00 0.00 0.00 4.95
1682 1908 3.264052 TGTGATGGGGGTGGGGTG 61.264 66.667 0.00 0.00 0.00 4.61
1683 1909 4.060667 GTGATGGGGGTGGGGTGG 62.061 72.222 0.00 0.00 0.00 4.61
1694 1920 1.621205 TGGGGTGGGGGTAGGATTG 60.621 63.158 0.00 0.00 0.00 2.67
1740 1975 3.390175 TGAAGGAACCAAGAAACCCAA 57.610 42.857 0.00 0.00 0.00 4.12
1920 2413 2.742053 CTGGAATCCGTGGTTGTTACAG 59.258 50.000 0.00 0.00 0.00 2.74
1939 2432 2.780010 CAGTATCCATTCAAGGGGTCCT 59.220 50.000 0.00 0.00 33.87 3.85
2122 2615 6.592798 GCAACATGCAACATAATAAAGCAT 57.407 33.333 0.00 0.00 45.92 3.79
2123 2616 7.697352 GCAACATGCAACATAATAAAGCATA 57.303 32.000 0.00 0.00 43.43 3.14
2124 2617 7.558137 GCAACATGCAACATAATAAAGCATAC 58.442 34.615 0.00 0.00 43.43 2.39
2125 2618 7.436080 GCAACATGCAACATAATAAAGCATACT 59.564 33.333 0.00 0.00 43.43 2.12
2126 2619 9.949174 CAACATGCAACATAATAAAGCATACTA 57.051 29.630 0.00 0.00 43.43 1.82
2204 2697 3.294493 CCGTGTGCAAACAGGGGG 61.294 66.667 8.00 0.00 40.76 5.40
2218 2711 4.051932 GGGGGACTAGTCAGTGGG 57.948 66.667 23.91 0.00 34.21 4.61
2219 2712 2.368011 GGGGGACTAGTCAGTGGGC 61.368 68.421 23.91 5.67 34.21 5.36
2275 2768 7.788026 TCCTGTATATGTCCGTCAGTAAATTT 58.212 34.615 0.00 0.00 0.00 1.82
2298 2801 2.537114 TTCAAATGTACGTCGCGCGC 62.537 55.000 27.95 23.91 46.11 6.86
2299 2802 3.845472 AAATGTACGTCGCGCGCC 61.845 61.111 27.95 14.67 46.11 6.53
2343 2848 2.595750 TCCCCGATCACAACCAAAAT 57.404 45.000 0.00 0.00 0.00 1.82
2347 2852 3.081061 CCCGATCACAACCAAAATGAGA 58.919 45.455 0.00 0.00 0.00 3.27
2356 2861 7.950512 TCACAACCAAAATGAGACAAATATGT 58.049 30.769 0.00 0.00 44.25 2.29
2390 2895 4.270245 TGCCCAAATCCAAAAGAACATC 57.730 40.909 0.00 0.00 0.00 3.06
2394 2899 5.742838 GCCCAAATCCAAAAGAACATCAGTT 60.743 40.000 0.00 0.00 41.64 3.16
2404 2909 1.197721 GAACATCAGTTTGGCAGTCCG 59.802 52.381 0.00 0.00 38.30 4.79
2417 2922 3.810896 GTCCGTGCATTTCCGCCC 61.811 66.667 0.00 0.00 0.00 6.13
2420 2925 4.481112 CGTGCATTTCCGCCCTGC 62.481 66.667 0.00 0.00 36.45 4.85
2421 2926 4.133796 GTGCATTTCCGCCCTGCC 62.134 66.667 0.00 0.00 35.02 4.85
2458 2963 0.177604 AAGCTGCTCCTCGATCAAGG 59.822 55.000 1.00 0.00 37.81 3.61
2470 2975 0.526662 GATCAAGGAGGTGTCGTCGT 59.473 55.000 0.00 0.00 0.00 4.34
2471 2976 0.526662 ATCAAGGAGGTGTCGTCGTC 59.473 55.000 0.00 0.00 0.00 4.20
2474 2979 4.773117 GGAGGTGTCGTCGTCGCC 62.773 72.222 13.27 13.27 36.96 5.54
2491 2996 2.654877 CGTGTAGGCAACCTCCGT 59.345 61.111 0.00 0.00 34.61 4.69
2497 3002 4.309950 GGCAACCTCCGTGTCCGT 62.310 66.667 0.00 0.00 0.00 4.69
2498 3003 3.041940 GCAACCTCCGTGTCCGTG 61.042 66.667 0.00 0.00 0.00 4.94
2506 3011 4.657824 CGTGTCCGTGTCCGCCTT 62.658 66.667 0.00 0.00 0.00 4.35
2507 3012 2.737376 GTGTCCGTGTCCGCCTTC 60.737 66.667 0.00 0.00 0.00 3.46
2508 3013 4.351938 TGTCCGTGTCCGCCTTCG 62.352 66.667 0.00 0.00 0.00 3.79
2519 3024 4.742201 GCCTTCGCTGCGTCCTCA 62.742 66.667 22.48 0.00 0.00 3.86
2520 3025 2.185350 CCTTCGCTGCGTCCTCAT 59.815 61.111 22.48 0.00 0.00 2.90
2521 3026 1.880340 CCTTCGCTGCGTCCTCATC 60.880 63.158 22.48 0.00 0.00 2.92
2522 3027 1.140589 CTTCGCTGCGTCCTCATCT 59.859 57.895 22.48 0.00 0.00 2.90
2523 3028 0.459237 CTTCGCTGCGTCCTCATCTT 60.459 55.000 22.48 0.00 0.00 2.40
2524 3029 0.458543 TTCGCTGCGTCCTCATCTTC 60.459 55.000 22.48 0.00 0.00 2.87
2525 3030 1.880340 CGCTGCGTCCTCATCTTCC 60.880 63.158 14.93 0.00 0.00 3.46
2526 3031 1.880340 GCTGCGTCCTCATCTTCCG 60.880 63.158 0.00 0.00 0.00 4.30
2527 3032 1.880340 CTGCGTCCTCATCTTCCGC 60.880 63.158 0.00 0.00 44.27 5.54
2528 3033 2.586357 GCGTCCTCATCTTCCGCC 60.586 66.667 0.00 0.00 38.52 6.13
2529 3034 2.278857 CGTCCTCATCTTCCGCCG 60.279 66.667 0.00 0.00 0.00 6.46
2530 3035 2.586357 GTCCTCATCTTCCGCCGC 60.586 66.667 0.00 0.00 0.00 6.53
2531 3036 3.849951 TCCTCATCTTCCGCCGCC 61.850 66.667 0.00 0.00 0.00 6.13
2533 3038 4.514577 CTCATCTTCCGCCGCCGT 62.515 66.667 0.00 0.00 0.00 5.68
2534 3039 4.508128 TCATCTTCCGCCGCCGTC 62.508 66.667 0.00 0.00 0.00 4.79
2535 3040 4.812476 CATCTTCCGCCGCCGTCA 62.812 66.667 0.00 0.00 0.00 4.35
2536 3041 4.077184 ATCTTCCGCCGCCGTCAA 62.077 61.111 0.00 0.00 0.00 3.18
2542 3047 3.554692 CGCCGCCGTCAACTCATC 61.555 66.667 0.00 0.00 0.00 2.92
2543 3048 2.125512 GCCGCCGTCAACTCATCT 60.126 61.111 0.00 0.00 0.00 2.90
2544 3049 1.741770 GCCGCCGTCAACTCATCTT 60.742 57.895 0.00 0.00 0.00 2.40
2545 3050 1.298859 GCCGCCGTCAACTCATCTTT 61.299 55.000 0.00 0.00 0.00 2.52
2546 3051 0.721718 CCGCCGTCAACTCATCTTTC 59.278 55.000 0.00 0.00 0.00 2.62
2547 3052 1.673033 CCGCCGTCAACTCATCTTTCT 60.673 52.381 0.00 0.00 0.00 2.52
2548 3053 1.391485 CGCCGTCAACTCATCTTTCTG 59.609 52.381 0.00 0.00 0.00 3.02
2549 3054 1.129437 GCCGTCAACTCATCTTTCTGC 59.871 52.381 0.00 0.00 0.00 4.26
2550 3055 1.734465 CCGTCAACTCATCTTTCTGCC 59.266 52.381 0.00 0.00 0.00 4.85
2551 3056 1.391485 CGTCAACTCATCTTTCTGCCG 59.609 52.381 0.00 0.00 0.00 5.69
2552 3057 1.129437 GTCAACTCATCTTTCTGCCGC 59.871 52.381 0.00 0.00 0.00 6.53
2553 3058 1.002430 TCAACTCATCTTTCTGCCGCT 59.998 47.619 0.00 0.00 0.00 5.52
2554 3059 1.129998 CAACTCATCTTTCTGCCGCTG 59.870 52.381 0.00 0.00 0.00 5.18
2555 3060 1.023513 ACTCATCTTTCTGCCGCTGC 61.024 55.000 0.00 0.00 38.26 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.420138 GTGAAGGAGGTGGTGAAGGAA 59.580 52.381 0.00 0.00 0.00 3.36
1 2 1.056660 GTGAAGGAGGTGGTGAAGGA 58.943 55.000 0.00 0.00 0.00 3.36
2 3 0.320771 CGTGAAGGAGGTGGTGAAGG 60.321 60.000 0.00 0.00 0.00 3.46
3 4 0.320771 CCGTGAAGGAGGTGGTGAAG 60.321 60.000 0.00 0.00 45.00 3.02
4 5 1.752198 CCGTGAAGGAGGTGGTGAA 59.248 57.895 0.00 0.00 45.00 3.18
5 6 2.214216 CCCGTGAAGGAGGTGGTGA 61.214 63.158 0.00 0.00 45.00 4.02
6 7 2.347490 CCCGTGAAGGAGGTGGTG 59.653 66.667 0.00 0.00 45.00 4.17
7 8 3.637273 GCCCGTGAAGGAGGTGGT 61.637 66.667 0.00 0.00 45.00 4.16
51 52 0.396811 CCACGAAGGAGGAGTTGGTT 59.603 55.000 0.00 0.00 41.22 3.67
118 119 0.741221 GGGCTTCGAGCGAATCTGTT 60.741 55.000 5.73 0.00 43.62 3.16
121 122 2.022240 GAGGGGCTTCGAGCGAATCT 62.022 60.000 5.73 2.44 43.62 2.40
139 141 3.559171 GCACCAGGACTACAAATCCAAGA 60.559 47.826 0.00 0.00 38.86 3.02
142 144 1.702401 TGCACCAGGACTACAAATCCA 59.298 47.619 0.00 0.00 38.86 3.41
161 163 1.669115 CACGGAACAGCCTCCACTG 60.669 63.158 0.00 0.00 43.59 3.66
164 166 4.680237 CGCACGGAACAGCCTCCA 62.680 66.667 0.00 0.00 34.91 3.86
241 244 1.285962 ACAATACCTCCATTGGCTGCT 59.714 47.619 0.00 0.00 39.71 4.24
244 247 2.041620 ACACACAATACCTCCATTGGCT 59.958 45.455 0.00 0.00 39.71 4.75
248 251 3.007506 TCGTCACACACAATACCTCCATT 59.992 43.478 0.00 0.00 0.00 3.16
275 278 1.219469 TCATCCGACTCCCCCTATCAA 59.781 52.381 0.00 0.00 0.00 2.57
276 279 0.857675 TCATCCGACTCCCCCTATCA 59.142 55.000 0.00 0.00 0.00 2.15
352 355 2.281692 AGCACTGATGTTGGCGCA 60.282 55.556 10.83 0.00 0.00 6.09
363 366 1.202627 GCTCTAGAATCCCCAGCACTG 60.203 57.143 0.00 0.00 0.00 3.66
365 368 1.127343 AGCTCTAGAATCCCCAGCAC 58.873 55.000 0.00 0.00 32.17 4.40
369 372 1.575788 TCTCCAGCTCTAGAATCCCCA 59.424 52.381 0.00 0.00 0.00 4.96
374 421 3.921287 ATCCCTCTCCAGCTCTAGAAT 57.079 47.619 0.00 0.00 0.00 2.40
384 431 2.797765 TCCTATCCAGAATCCCTCTCCA 59.202 50.000 0.00 0.00 29.07 3.86
397 444 3.719871 TCTAACAAGCTGGTCCTATCCA 58.280 45.455 0.00 0.00 36.00 3.41
408 455 3.142174 GTCTGCCAACTTCTAACAAGCT 58.858 45.455 0.00 0.00 0.00 3.74
409 456 2.096218 CGTCTGCCAACTTCTAACAAGC 60.096 50.000 0.00 0.00 0.00 4.01
410 457 3.131396 ACGTCTGCCAACTTCTAACAAG 58.869 45.455 0.00 0.00 0.00 3.16
416 463 0.034059 CCAGACGTCTGCCAACTTCT 59.966 55.000 35.09 0.00 42.47 2.85
453 500 0.609151 TCTACGTCGGCCCAAAATCA 59.391 50.000 0.00 0.00 0.00 2.57
468 515 7.050377 TGATCTGGATGTTTGAAATCCTCTAC 58.950 38.462 4.23 0.00 43.52 2.59
487 534 2.606725 GCAAATCGACTGGACTGATCTG 59.393 50.000 0.00 0.00 0.00 2.90
488 535 2.499289 AGCAAATCGACTGGACTGATCT 59.501 45.455 0.00 0.00 0.00 2.75
489 536 2.606725 CAGCAAATCGACTGGACTGATC 59.393 50.000 0.00 0.00 0.00 2.92
497 544 0.096628 GCAGCTCAGCAAATCGACTG 59.903 55.000 0.00 0.00 35.15 3.51
498 545 1.357258 CGCAGCTCAGCAAATCGACT 61.357 55.000 0.00 0.00 0.00 4.18
508 556 2.684843 GGCCTTCAACGCAGCTCAG 61.685 63.158 0.00 0.00 0.00 3.35
561 609 2.227388 CCGCAGCTCATCAAATTATCCC 59.773 50.000 0.00 0.00 0.00 3.85
675 863 8.297426 ACGAACTGTTTCTTTTCTTTTCTTTCT 58.703 29.630 0.00 0.00 0.00 2.52
676 864 8.449085 ACGAACTGTTTCTTTTCTTTTCTTTC 57.551 30.769 0.00 0.00 0.00 2.62
690 878 6.007677 CGTGATAGCTTTAACGAACTGTTTC 58.992 40.000 8.25 0.00 42.09 2.78
699 887 2.281762 GTGCTCCGTGATAGCTTTAACG 59.718 50.000 7.06 7.06 40.73 3.18
715 906 0.170116 CGTCTGTCTCAGGAGTGCTC 59.830 60.000 0.00 0.00 31.51 4.26
716 907 1.247419 CCGTCTGTCTCAGGAGTGCT 61.247 60.000 0.00 0.00 31.51 4.40
717 908 1.214062 CCGTCTGTCTCAGGAGTGC 59.786 63.158 0.00 0.00 31.51 4.40
723 914 1.587054 GGACCACCGTCTGTCTCAG 59.413 63.158 0.00 0.00 39.15 3.35
752 943 2.367567 ACACTGACACGTGGGACTTAAT 59.632 45.455 21.57 0.00 39.19 1.40
776 968 1.153449 TTATCCAGGTTGCTCGCCG 60.153 57.895 0.00 0.00 0.00 6.46
897 1089 5.957798 TCGATCGTTAGCTAGAAGGAAAAA 58.042 37.500 15.94 0.00 0.00 1.94
912 1104 2.223829 CCACTGGCTTCTATCGATCGTT 60.224 50.000 15.94 9.65 0.00 3.85
1016 1208 2.011540 GGTGGACGAGGTTCTGATTC 57.988 55.000 0.00 0.00 0.00 2.52
1126 1337 1.725557 CGGAGATCGCGGGAGAGAAA 61.726 60.000 6.13 0.00 43.31 2.52
1130 1341 1.966972 GATCGGAGATCGCGGGAGA 60.967 63.158 6.13 0.00 45.12 3.71
1161 1372 6.204688 GGTCTCACATCACAAATTCACAACTA 59.795 38.462 0.00 0.00 0.00 2.24
1162 1373 5.009010 GGTCTCACATCACAAATTCACAACT 59.991 40.000 0.00 0.00 0.00 3.16
1163 1374 5.215160 GGTCTCACATCACAAATTCACAAC 58.785 41.667 0.00 0.00 0.00 3.32
1164 1375 4.886489 TGGTCTCACATCACAAATTCACAA 59.114 37.500 0.00 0.00 0.00 3.33
1165 1376 4.459330 TGGTCTCACATCACAAATTCACA 58.541 39.130 0.00 0.00 0.00 3.58
1166 1377 4.083110 CCTGGTCTCACATCACAAATTCAC 60.083 45.833 0.00 0.00 0.00 3.18
1167 1378 4.074259 CCTGGTCTCACATCACAAATTCA 58.926 43.478 0.00 0.00 0.00 2.57
1168 1379 4.074970 ACCTGGTCTCACATCACAAATTC 58.925 43.478 0.00 0.00 0.00 2.17
1169 1380 4.104383 ACCTGGTCTCACATCACAAATT 57.896 40.909 0.00 0.00 0.00 1.82
1170 1381 3.795688 ACCTGGTCTCACATCACAAAT 57.204 42.857 0.00 0.00 0.00 2.32
1171 1382 3.646162 AGTACCTGGTCTCACATCACAAA 59.354 43.478 0.63 0.00 0.00 2.83
1210 1429 2.440796 CCACATCGCCCCTGCATT 60.441 61.111 0.00 0.00 37.32 3.56
1416 1635 4.069232 CGCTCGTTCTCCTGGCCA 62.069 66.667 4.71 4.71 0.00 5.36
1481 1703 2.435938 TTTCGATCCACGGCTGGC 60.436 61.111 0.00 0.00 42.82 4.85
1482 1704 2.452813 CGTTTCGATCCACGGCTGG 61.453 63.158 0.00 0.00 42.82 4.85
1483 1705 1.413767 CTCGTTTCGATCCACGGCTG 61.414 60.000 11.14 0.00 42.82 4.85
1484 1706 1.153823 CTCGTTTCGATCCACGGCT 60.154 57.895 11.14 0.00 42.82 5.52
1612 1834 2.769663 TGCCGGATGGATAGTACAAAGT 59.230 45.455 5.05 0.00 37.49 2.66
1630 1856 1.299089 GACAACAACGCCACTTGCC 60.299 57.895 0.00 0.00 36.24 4.52
1681 1907 2.717958 GGAACCAATCCTACCCCCA 58.282 57.895 0.00 0.00 45.56 4.96
1848 2083 2.693250 TTCTCACTGTGTGCCGGACG 62.693 60.000 5.05 0.00 32.98 4.79
1920 2413 3.953542 AAGGACCCCTTGAATGGATAC 57.046 47.619 0.00 0.00 42.96 2.24
1939 2432 6.884472 TCCTTCCAGATCCAGTTAACATAA 57.116 37.500 8.61 0.00 0.00 1.90
1976 2469 6.754193 TCTCTCTCTTTTCTCCACTTTCTTC 58.246 40.000 0.00 0.00 0.00 2.87
2152 2645 1.966451 GCTGGTTGCCGTTGTAGCT 60.966 57.895 0.00 0.00 35.15 3.32
2204 2697 1.215647 CGTGCCCACTGACTAGTCC 59.784 63.158 20.11 4.12 34.07 3.85
2205 2698 1.215647 CCGTGCCCACTGACTAGTC 59.784 63.158 16.32 16.32 34.07 2.59
2206 2699 0.614979 ATCCGTGCCCACTGACTAGT 60.615 55.000 0.00 0.00 37.75 2.57
2207 2700 0.179100 CATCCGTGCCCACTGACTAG 60.179 60.000 0.00 0.00 0.00 2.57
2208 2701 1.897423 CATCCGTGCCCACTGACTA 59.103 57.895 0.00 0.00 0.00 2.59
2209 2702 2.665000 CATCCGTGCCCACTGACT 59.335 61.111 0.00 0.00 0.00 3.41
2210 2703 3.127533 GCATCCGTGCCCACTGAC 61.128 66.667 0.00 0.00 45.76 3.51
2238 2731 6.812160 GGACATATACAGGATACGGTTGAATC 59.188 42.308 0.00 0.00 45.15 2.52
2241 2734 4.216902 CGGACATATACAGGATACGGTTGA 59.783 45.833 0.00 0.00 45.15 3.18
2275 2768 3.661819 GCGCGACGTACATTTGAATTTA 58.338 40.909 12.10 0.00 0.00 1.40
2347 2852 9.430623 GGGCATGTAAAAACTAAACATATTTGT 57.569 29.630 0.00 0.00 37.82 2.83
2356 2861 7.067496 TGGATTTGGGCATGTAAAAACTAAA 57.933 32.000 0.00 0.00 0.00 1.85
2362 2867 6.179906 TCTTTTGGATTTGGGCATGTAAAA 57.820 33.333 0.00 0.00 0.00 1.52
2390 2895 1.518056 ATGCACGGACTGCCAAACTG 61.518 55.000 0.00 0.00 46.51 3.16
2394 2899 1.523154 GGAAATGCACGGACTGCCAA 61.523 55.000 0.00 0.00 46.51 4.52
2404 2909 4.133796 GGCAGGGCGGAAATGCAC 62.134 66.667 0.00 0.00 41.78 4.57
2421 2926 3.508840 GCTGGAATTGCCGGTCCG 61.509 66.667 3.60 3.60 45.49 4.79
2422 2927 1.937546 CTTGCTGGAATTGCCGGTCC 61.938 60.000 1.90 1.86 45.49 4.46
2428 2933 4.180496 GCAGCTTGCTGGAATTGC 57.820 55.556 21.98 5.72 40.96 3.56
2449 2954 0.809385 GACGACACCTCCTTGATCGA 59.191 55.000 0.00 0.00 36.64 3.59
2474 2979 1.736645 CACGGAGGTTGCCTACACG 60.737 63.158 0.00 2.23 33.03 4.49
2491 2996 4.351938 CGAAGGCGGACACGGACA 62.352 66.667 0.00 0.00 41.36 4.02
2505 3010 0.458543 GAAGATGAGGACGCAGCGAA 60.459 55.000 24.65 1.34 0.00 4.70
2506 3011 1.139734 GAAGATGAGGACGCAGCGA 59.860 57.895 24.65 0.00 0.00 4.93
2507 3012 1.880340 GGAAGATGAGGACGCAGCG 60.880 63.158 14.82 14.82 0.00 5.18
2508 3013 1.880340 CGGAAGATGAGGACGCAGC 60.880 63.158 0.00 0.00 0.00 5.25
2509 3014 4.409342 CGGAAGATGAGGACGCAG 57.591 61.111 0.00 0.00 0.00 5.18
2512 3017 2.278857 CGGCGGAAGATGAGGACG 60.279 66.667 0.00 0.00 0.00 4.79
2513 3018 2.586357 GCGGCGGAAGATGAGGAC 60.586 66.667 9.78 0.00 0.00 3.85
2514 3019 3.849951 GGCGGCGGAAGATGAGGA 61.850 66.667 9.78 0.00 0.00 3.71
2516 3021 4.514577 ACGGCGGCGGAAGATGAG 62.515 66.667 35.05 4.63 0.00 2.90
2517 3022 4.508128 GACGGCGGCGGAAGATGA 62.508 66.667 35.05 0.00 0.00 2.92
2518 3023 4.812476 TGACGGCGGCGGAAGATG 62.812 66.667 35.05 6.26 0.00 2.90
2519 3024 4.077184 TTGACGGCGGCGGAAGAT 62.077 61.111 35.05 14.34 0.00 2.40
2525 3030 3.554692 GATGAGTTGACGGCGGCG 61.555 66.667 31.06 31.06 0.00 6.46
2526 3031 1.298859 AAAGATGAGTTGACGGCGGC 61.299 55.000 13.24 9.67 0.00 6.53
2527 3032 0.721718 GAAAGATGAGTTGACGGCGG 59.278 55.000 13.24 0.00 0.00 6.13
2528 3033 1.391485 CAGAAAGATGAGTTGACGGCG 59.609 52.381 4.80 4.80 0.00 6.46
2529 3034 1.129437 GCAGAAAGATGAGTTGACGGC 59.871 52.381 0.00 0.00 0.00 5.68
2530 3035 1.734465 GGCAGAAAGATGAGTTGACGG 59.266 52.381 0.00 0.00 0.00 4.79
2531 3036 1.391485 CGGCAGAAAGATGAGTTGACG 59.609 52.381 0.00 0.00 33.61 4.35
2532 3037 1.129437 GCGGCAGAAAGATGAGTTGAC 59.871 52.381 0.00 0.00 0.00 3.18
2533 3038 1.002430 AGCGGCAGAAAGATGAGTTGA 59.998 47.619 1.45 0.00 0.00 3.18
2534 3039 1.129998 CAGCGGCAGAAAGATGAGTTG 59.870 52.381 1.45 0.00 0.00 3.16
2535 3040 1.446907 CAGCGGCAGAAAGATGAGTT 58.553 50.000 1.45 0.00 0.00 3.01
2536 3041 1.023513 GCAGCGGCAGAAAGATGAGT 61.024 55.000 3.18 0.00 40.72 3.41
2537 3042 1.720301 GCAGCGGCAGAAAGATGAG 59.280 57.895 3.18 0.00 40.72 2.90
2538 3043 3.895025 GCAGCGGCAGAAAGATGA 58.105 55.556 3.18 0.00 40.72 2.92


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

AutoCloner maintained by Alex Coulton.