Multiple sequence alignment - TraesCS4D01G111000

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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 TraesCS4D01G111000 chr4D 100.000 2894 0 0 1 2894 91523866 91520973 0.000000e+00 5345.0
1 TraesCS4D01G111000 chr4A 95.125 1641 53 13 560 2185 503684472 503682844 0.000000e+00 2562.0
2 TraesCS4D01G111000 chr4A 94.224 277 12 4 30 305 503685366 503685093 1.240000e-113 420.0
3 TraesCS4D01G111000 chr4A 89.899 297 17 5 295 580 503685007 503684713 1.270000e-98 370.0
4 TraesCS4D01G111000 chr4A 89.637 193 16 4 2441 2629 572708416 572708608 2.880000e-60 243.0
5 TraesCS4D01G111000 chr4A 87.778 180 22 0 1604 1783 503683468 503683289 8.120000e-51 211.0
6 TraesCS4D01G111000 chr4A 85.915 142 18 2 1553 1693 503683384 503683244 1.800000e-32 150.0
7 TraesCS4D01G111000 chr4B 90.520 1308 91 21 742 2034 128260342 128259053 0.000000e+00 1698.0
8 TraesCS4D01G111000 chr4B 87.150 607 38 20 198 792 128260922 128260344 0.000000e+00 652.0
9 TraesCS4D01G111000 chr4B 80.373 912 98 42 2026 2894 128228102 128227229 4.100000e-173 617.0
10 TraesCS4D01G111000 chr4B 96.454 282 10 0 1502 1783 128259637 128259356 1.570000e-127 466.0
11 TraesCS4D01G111000 chr4B 88.172 186 22 0 1553 1738 128259496 128259311 3.750000e-54 222.0
12 TraesCS4D01G111000 chr4B 88.889 180 20 0 1604 1783 128259580 128259401 3.750000e-54 222.0
13 TraesCS4D01G111000 chr4B 85.294 136 18 2 1559 1693 128259445 128259311 3.890000e-29 139.0
14 TraesCS4D01G111000 chr7D 90.155 193 15 4 2441 2629 614107453 614107645 6.190000e-62 248.0
15 TraesCS4D01G111000 chr6B 89.796 196 17 3 2437 2629 634640631 634640436 6.190000e-62 248.0
16 TraesCS4D01G111000 chr3B 90.104 192 16 3 2441 2629 32447520 32447711 2.230000e-61 246.0
17 TraesCS4D01G111000 chr3B 86.636 217 23 6 2416 2629 776355694 776355481 4.820000e-58 235.0
18 TraesCS4D01G111000 chr3B 87.302 63 8 0 1 63 674670852 674670914 4.000000e-09 73.1
19 TraesCS4D01G111000 chr3B 93.750 48 0 3 17 63 403346069 403346024 5.170000e-08 69.4
20 TraesCS4D01G111000 chr3B 89.796 49 1 3 17 63 403220175 403220129 3.110000e-05 60.2
21 TraesCS4D01G111000 chr2B 89.637 193 16 4 2436 2625 593006298 593006107 2.880000e-60 243.0
22 TraesCS4D01G111000 chr5B 88.614 202 18 5 2433 2629 609892260 609892059 1.040000e-59 241.0
23 TraesCS4D01G111000 chr2A 87.923 207 18 7 2428 2629 780721064 780720860 1.340000e-58 237.0
24 TraesCS4D01G111000 chr1A 79.216 255 37 13 2198 2439 240557638 240557889 2.310000e-36 163.0
25 TraesCS4D01G111000 chr5D 85.714 126 15 3 9 132 343078545 343078421 2.340000e-26 130.0
26 TraesCS4D01G111000 chr5D 83.333 102 11 4 24 124 433939105 433939009 3.970000e-14 89.8
27 TraesCS4D01G111000 chr5D 82.812 64 10 1 17 79 232595570 232595507 4.030000e-04 56.5
28 TraesCS4D01G111000 chr1B 82.569 109 15 3 18 126 688688077 688688181 3.070000e-15 93.5
29 TraesCS4D01G111000 chr2D 100.000 28 0 0 67 94 648544269 648544296 5.000000e-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 TraesCS4D01G111000 chr4D 91520973 91523866 2893 True 5345.0 5345 100.000000 1 2894 1 chr4D.!!$R1 2893
1 TraesCS4D01G111000 chr4A 503682844 503685366 2522 True 742.6 2562 90.588200 30 2185 5 chr4A.!!$R1 2155
2 TraesCS4D01G111000 chr4B 128227229 128228102 873 True 617.0 617 80.373000 2026 2894 1 chr4B.!!$R1 868
3 TraesCS4D01G111000 chr4B 128259053 128260922 1869 True 566.5 1698 89.413167 198 2034 6 chr4B.!!$R2 1836

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
347 442 0.036388 TGAAACGGAGGGCTTAGCTG 60.036 55.0 3.59 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2606 0.037046 TTCGGTAGGCGGTCCTTTTC 60.037 55.0 0.0 0.0 40.66 2.29 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
133 134 7.989826 AGTTGACATCAAAATATAGTCTTGGC 58.010 34.615 0.00 0.00 37.63 4.52
143 144 0.830444 TAGTCTTGGCGAGGGTGTGT 60.830 55.000 0.97 0.00 0.00 3.72
169 170 4.148838 CTGTTAACCCTCCATTTGGTGAA 58.851 43.478 2.48 0.00 34.34 3.18
289 291 8.927675 TGTAAACAAGGCCTAAGAATAAAGAA 57.072 30.769 5.16 0.00 0.00 2.52
290 292 9.010029 TGTAAACAAGGCCTAAGAATAAAGAAG 57.990 33.333 5.16 0.00 0.00 2.85
293 295 6.181190 ACAAGGCCTAAGAATAAAGAAGACC 58.819 40.000 5.16 0.00 0.00 3.85
340 435 3.254903 ACACTTATTTTGAAACGGAGGGC 59.745 43.478 0.00 0.00 0.00 5.19
341 436 3.506067 CACTTATTTTGAAACGGAGGGCT 59.494 43.478 0.00 0.00 0.00 5.19
345 440 1.530323 TTTGAAACGGAGGGCTTAGC 58.470 50.000 0.00 0.00 0.00 3.09
347 442 0.036388 TGAAACGGAGGGCTTAGCTG 60.036 55.000 3.59 0.00 0.00 4.24
348 443 0.744771 GAAACGGAGGGCTTAGCTGG 60.745 60.000 3.59 0.00 0.00 4.85
369 464 6.531594 GCTGGAAAAATATCTGTTTTACCAGC 59.468 38.462 22.13 22.13 46.70 4.85
399 494 6.882678 ACTACGCCAAATTTAACTTATCCACT 59.117 34.615 0.00 0.00 0.00 4.00
582 948 5.982890 AATGAAGTTCGATGGTGGATTTT 57.017 34.783 0.00 0.00 0.00 1.82
624 990 5.276348 GCATGCACAAACACAAGACTTTTAC 60.276 40.000 14.21 0.00 0.00 2.01
758 1130 4.929808 TCTCTAAATTCAACGAGCCAAGAC 59.070 41.667 0.00 0.00 0.00 3.01
849 1273 9.590451 AATGTTCAAATCTAAATGGCTACATTG 57.410 29.630 0.00 0.00 46.25 2.82
851 1275 6.772360 TCAAATCTAAATGGCTACATTGCA 57.228 33.333 0.00 0.00 46.25 4.08
866 1290 1.592064 TTGCACATGCGAGTTCTCAA 58.408 45.000 0.00 0.00 45.83 3.02
980 1411 4.713946 GGTTGTCATCAAGCGGGA 57.286 55.556 0.00 0.00 41.15 5.14
1320 1751 2.281761 CCTGGCAAACACGCTCCT 60.282 61.111 0.00 0.00 0.00 3.69
1407 1838 4.778143 GGCCCGCACGACCAGAAT 62.778 66.667 0.00 0.00 0.00 2.40
1413 1844 2.264480 CACGACCAGAATCCGCCA 59.736 61.111 0.00 0.00 0.00 5.69
1840 2322 2.617274 GCACTGTCTTTCCACGGCC 61.617 63.158 0.00 0.00 0.00 6.13
2084 2574 6.874134 GGAGAAGAGAAATTACTGCACACTTA 59.126 38.462 0.00 0.00 0.00 2.24
2087 2577 7.880195 AGAAGAGAAATTACTGCACACTTACAT 59.120 33.333 0.00 0.00 0.00 2.29
2088 2578 7.602517 AGAGAAATTACTGCACACTTACATC 57.397 36.000 0.00 0.00 0.00 3.06
2089 2579 7.390027 AGAGAAATTACTGCACACTTACATCT 58.610 34.615 0.00 0.00 0.00 2.90
2090 2580 7.880195 AGAGAAATTACTGCACACTTACATCTT 59.120 33.333 0.00 0.00 0.00 2.40
2091 2581 8.396272 AGAAATTACTGCACACTTACATCTTT 57.604 30.769 0.00 0.00 0.00 2.52
2094 2584 7.986085 ATTACTGCACACTTACATCTTTTCT 57.014 32.000 0.00 0.00 0.00 2.52
2105 2595 6.207614 ACTTACATCTTTTCTTTTGGAGAGCC 59.792 38.462 0.00 0.00 35.37 4.70
2125 2616 3.305110 CCAATTTTGTCGAAAAGGACCG 58.695 45.455 0.00 0.00 34.53 4.79
2172 2664 2.496470 ACCACCTCTAGATCCAAACGAC 59.504 50.000 0.00 0.00 0.00 4.34
2173 2665 2.159085 CCACCTCTAGATCCAAACGACC 60.159 54.545 0.00 0.00 0.00 4.79
2181 2673 3.939066 AGATCCAAACGACCGAAAAGAT 58.061 40.909 0.00 0.00 0.00 2.40
2185 2677 2.412847 CCAAACGACCGAAAAGATCAGC 60.413 50.000 0.00 0.00 0.00 4.26
2188 2680 1.000955 ACGACCGAAAAGATCAGCTGT 59.999 47.619 14.67 0.42 0.00 4.40
2189 2681 1.391485 CGACCGAAAAGATCAGCTGTG 59.609 52.381 14.67 0.00 0.00 3.66
2192 2684 1.446907 CGAAAAGATCAGCTGTGCCT 58.553 50.000 14.67 6.53 0.00 4.75
2193 2685 1.129998 CGAAAAGATCAGCTGTGCCTG 59.870 52.381 14.67 0.00 0.00 4.85
2203 2696 1.150567 GCTGTGCCTGATAGCAGACG 61.151 60.000 10.19 0.00 45.14 4.18
2204 2697 1.150567 CTGTGCCTGATAGCAGACGC 61.151 60.000 10.19 5.04 45.14 5.19
2252 2745 3.303135 TCGCAGACGGCAAGACCT 61.303 61.111 0.00 0.00 45.17 3.85
2253 2746 3.114616 CGCAGACGGCAAGACCTG 61.115 66.667 0.00 0.00 45.17 4.00
2283 2776 2.670934 AAGCGGCAGGTTGAGCAG 60.671 61.111 1.45 0.00 36.62 4.24
2296 2789 0.664761 TGAGCAGCACAACTTCAAGC 59.335 50.000 0.00 0.00 0.00 4.01
2332 2826 0.537371 AAAGAAAGACGTGGGGCCTG 60.537 55.000 0.84 0.00 0.00 4.85
2333 2827 3.056328 GAAAGACGTGGGGCCTGC 61.056 66.667 0.84 0.00 0.00 4.85
2349 2849 2.516930 GCCGCCACATGCTATGGT 60.517 61.111 3.05 0.00 39.63 3.55
2356 2856 0.394762 CACATGCTATGGTGGCACCT 60.395 55.000 34.69 22.73 42.69 4.00
2358 2858 0.742505 CATGCTATGGTGGCACCTTG 59.257 55.000 34.69 24.27 42.69 3.61
2375 2875 5.115480 CACCTTGTGTGGTTTGCTTTATTT 58.885 37.500 0.00 0.00 41.52 1.40
2387 2887 8.934825 TGGTTTGCTTTATTTTATCAAATGAGC 58.065 29.630 12.19 12.19 40.18 4.26
2401 2901 4.577693 TCAAATGAGCAGATAGGATTGCAC 59.422 41.667 0.00 0.00 42.67 4.57
2466 2966 1.217882 AACGCAGTACAGACACAAGC 58.782 50.000 0.00 0.00 45.00 4.01
2490 2990 3.049912 ACATACATACGCGCATACACTG 58.950 45.455 5.73 0.00 0.00 3.66
2496 2996 1.317431 ACGCGCATACACTGACCCTA 61.317 55.000 5.73 0.00 0.00 3.53
2497 2997 0.032130 CGCGCATACACTGACCCTAT 59.968 55.000 8.75 0.00 0.00 2.57
2498 2998 1.502231 GCGCATACACTGACCCTATG 58.498 55.000 0.30 0.00 0.00 2.23
2499 2999 1.068588 GCGCATACACTGACCCTATGA 59.931 52.381 0.30 0.00 0.00 2.15
2501 3001 3.384668 CGCATACACTGACCCTATGAAG 58.615 50.000 0.00 0.00 0.00 3.02
2502 3002 3.733337 GCATACACTGACCCTATGAAGG 58.267 50.000 0.00 0.00 43.25 3.46
2503 3003 3.733337 CATACACTGACCCTATGAAGGC 58.267 50.000 0.00 0.00 42.14 4.35
2504 3004 1.656587 ACACTGACCCTATGAAGGCA 58.343 50.000 0.00 0.00 42.14 4.75
2513 3013 1.372582 CTATGAAGGCACACACGCAT 58.627 50.000 0.00 0.00 0.00 4.73
2519 3019 1.182667 AGGCACACACGCATACTCTA 58.817 50.000 0.00 0.00 0.00 2.43
2537 3037 2.693591 TCTACCCTTATGAGCACCTTCG 59.306 50.000 0.00 0.00 0.00 3.79
2543 3043 3.490078 CCTTATGAGCACCTTCGAGAGAC 60.490 52.174 0.00 0.00 41.84 3.36
2544 3044 1.846007 ATGAGCACCTTCGAGAGACT 58.154 50.000 0.00 0.00 41.84 3.24
2551 3051 1.431440 CTTCGAGAGACTGAGCCGG 59.569 63.158 0.00 0.00 41.84 6.13
2569 3069 4.223700 AGCCGGCATATCATCTTGAGATTA 59.776 41.667 31.54 0.00 31.21 1.75
2572 3072 5.062683 CCGGCATATCATCTTGAGATTAACG 59.937 44.000 0.00 0.00 31.21 3.18
2580 3080 8.954950 ATCATCTTGAGATTAACGAAGTCATT 57.045 30.769 0.00 0.00 32.87 2.57
2592 3092 3.227147 CGAAGTCATTATAGACGCCTCG 58.773 50.000 0.00 0.00 43.24 4.63
2625 3125 1.900486 ACGTCTCCTCCCACTAAAAGG 59.100 52.381 0.00 0.00 0.00 3.11
2630 3130 1.106285 CCTCCCACTAAAAGGCATGC 58.894 55.000 9.90 9.90 0.00 4.06
2631 3131 1.341383 CCTCCCACTAAAAGGCATGCT 60.341 52.381 18.92 0.00 0.00 3.79
2632 3132 2.450476 CTCCCACTAAAAGGCATGCTT 58.550 47.619 18.92 7.19 0.00 3.91
2634 3134 4.210331 CTCCCACTAAAAGGCATGCTTAT 58.790 43.478 18.92 5.44 0.00 1.73
2635 3135 3.953612 TCCCACTAAAAGGCATGCTTATG 59.046 43.478 18.92 8.57 0.00 1.90
2659 3159 0.936600 TGACTGTGTGTGTTCGCATG 59.063 50.000 0.00 0.00 36.45 4.06
2665 3165 2.112928 TGTGTTCGCATGGCTGGT 59.887 55.556 0.00 0.00 0.00 4.00
2667 3167 1.081242 GTGTTCGCATGGCTGGTTG 60.081 57.895 0.00 0.00 0.00 3.77
2685 3185 1.468985 TGGCTAGCTCTGTGTCTCTC 58.531 55.000 15.72 0.00 0.00 3.20
2687 3187 1.134175 GGCTAGCTCTGTGTCTCTCAC 59.866 57.143 15.72 0.00 46.31 3.51
2700 3200 3.196469 TGTCTCTCACCCATCAACTCATC 59.804 47.826 0.00 0.00 0.00 2.92
2708 3208 4.575236 CACCCATCAACTCATCATTCTCTG 59.425 45.833 0.00 0.00 0.00 3.35
2709 3209 3.564644 CCCATCAACTCATCATTCTCTGC 59.435 47.826 0.00 0.00 0.00 4.26
2710 3210 4.196971 CCATCAACTCATCATTCTCTGCA 58.803 43.478 0.00 0.00 0.00 4.41
2711 3211 4.822350 CCATCAACTCATCATTCTCTGCAT 59.178 41.667 0.00 0.00 0.00 3.96
2740 3240 0.753867 TGCTCCACGGTCACTTTACA 59.246 50.000 0.00 0.00 0.00 2.41
2748 3248 3.741344 CACGGTCACTTTACAAAGAGAGG 59.259 47.826 8.65 4.28 36.52 3.69
2759 3289 3.863086 ACAAAGAGAGGGAGGAAGAGAA 58.137 45.455 0.00 0.00 0.00 2.87
2760 3290 3.837731 ACAAAGAGAGGGAGGAAGAGAAG 59.162 47.826 0.00 0.00 0.00 2.85
2764 3294 0.618968 GAGGGAGGAAGAGAAGGGCA 60.619 60.000 0.00 0.00 0.00 5.36
2767 3297 2.127708 GGGAGGAAGAGAAGGGCAATA 58.872 52.381 0.00 0.00 0.00 1.90
2772 3302 3.325135 AGGAAGAGAAGGGCAATATACCG 59.675 47.826 0.00 0.00 0.00 4.02
2775 3305 5.513267 GGAAGAGAAGGGCAATATACCGATT 60.513 44.000 0.00 0.00 0.00 3.34
2779 3309 5.491982 AGAAGGGCAATATACCGATTGATC 58.508 41.667 0.40 0.00 38.83 2.92
2781 3311 4.836825 AGGGCAATATACCGATTGATCAG 58.163 43.478 0.00 0.00 38.83 2.90
2856 3387 2.831526 GGCCCACCAAATAGTCATTGTT 59.168 45.455 0.00 0.00 35.26 2.83
2858 3389 3.763897 GCCCACCAAATAGTCATTGTTCT 59.236 43.478 0.00 0.00 0.00 3.01
2867 3398 8.023128 CCAAATAGTCATTGTTCTGTTACAAGG 58.977 37.037 0.00 0.00 40.99 3.61
2873 3404 1.771854 TGTTCTGTTACAAGGGCTGGA 59.228 47.619 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 9.683069 ATGTCAACTTTCTTTTCATACACATTC 57.317 29.630 0.00 0.00 0.00 2.67
143 144 3.501385 CCAAATGGAGGGTTAACAGGGAA 60.501 47.826 8.10 0.00 37.39 3.97
289 291 8.746530 TGATTTAGTCGAAATTAGTAGTGGTCT 58.253 33.333 0.00 0.00 37.90 3.85
290 292 8.805688 GTGATTTAGTCGAAATTAGTAGTGGTC 58.194 37.037 0.00 0.00 37.90 4.02
293 295 8.521860 GTCGTGATTTAGTCGAAATTAGTAGTG 58.478 37.037 0.00 0.00 37.90 2.74
301 396 8.475331 AATAAGTGTCGTGATTTAGTCGAAAT 57.525 30.769 0.00 0.00 40.62 2.17
305 400 7.726079 TCAAAATAAGTGTCGTGATTTAGTCG 58.274 34.615 0.00 0.00 0.00 4.18
340 435 9.788960 GGTAAAACAGATATTTTTCCAGCTAAG 57.211 33.333 0.00 0.00 38.32 2.18
341 436 9.303116 TGGTAAAACAGATATTTTTCCAGCTAA 57.697 29.630 5.52 0.00 41.41 3.09
347 442 6.338146 GGGCTGGTAAAACAGATATTTTTCC 58.662 40.000 0.00 0.00 40.97 3.13
348 443 6.338146 GGGGCTGGTAAAACAGATATTTTTC 58.662 40.000 0.00 0.00 40.97 2.29
369 464 2.131776 TAAATTTGGCGTAGTGGGGG 57.868 50.000 0.00 0.00 0.00 5.40
399 494 2.813754 GCACCAGAGCAATACAAAGTGA 59.186 45.455 0.00 0.00 0.00 3.41
582 948 2.027385 TGCGCATGGTGGCAAATAATA 58.973 42.857 5.66 0.00 35.98 0.98
610 976 8.616076 CAAATCTCTCTTGTAAAAGTCTTGTGT 58.384 33.333 0.00 0.00 0.00 3.72
758 1130 2.472695 TGTAGCTAGTGGCCTTGTTG 57.527 50.000 3.32 0.00 43.05 3.33
794 1218 0.606673 GGTGGGTGTGAGAAGGAAGC 60.607 60.000 0.00 0.00 0.00 3.86
849 1273 0.166814 GGTTGAGAACTCGCATGTGC 59.833 55.000 0.00 0.00 37.78 4.57
851 1275 0.396435 TGGGTTGAGAACTCGCATGT 59.604 50.000 0.00 0.00 33.43 3.21
866 1290 2.430694 TGAGTGATCGATCGATTTGGGT 59.569 45.455 29.89 14.17 34.60 4.51
980 1411 2.194212 TTAGCTAGCTAGGCGCGCT 61.194 57.895 32.29 19.12 45.59 5.92
1249 1680 4.767075 CGCTTTTTCTTCTCAGACTGAAC 58.233 43.478 6.61 0.00 0.00 3.18
1710 2141 2.677875 GGCCACTGCTTTCCTGGG 60.678 66.667 0.00 0.00 37.74 4.45
1826 2308 2.111999 CTCCTGGCCGTGGAAAGACA 62.112 60.000 16.67 0.00 32.61 3.41
1840 2322 0.798776 GATGCGTGTTGTTCCTCCTG 59.201 55.000 0.00 0.00 0.00 3.86
2051 2541 7.308830 GCAGTAATTTCTCTTCTCCAATGTTGT 60.309 37.037 0.00 0.00 0.00 3.32
2071 2561 7.801716 AAGAAAAGATGTAAGTGTGCAGTAA 57.198 32.000 0.00 0.00 0.00 2.24
2084 2574 4.473444 TGGCTCTCCAAAAGAAAAGATGT 58.527 39.130 0.00 0.00 39.99 3.06
2105 2595 2.724174 GCGGTCCTTTTCGACAAAATTG 59.276 45.455 0.00 0.00 34.24 2.32
2115 2606 0.037046 TTCGGTAGGCGGTCCTTTTC 60.037 55.000 0.00 0.00 40.66 2.29
2125 2616 1.748493 TGGCAATTCAATTCGGTAGGC 59.252 47.619 0.00 0.00 0.00 3.93
2160 2652 3.396260 TCTTTTCGGTCGTTTGGATCT 57.604 42.857 0.00 0.00 0.00 2.75
2161 2653 3.682858 TGATCTTTTCGGTCGTTTGGATC 59.317 43.478 0.00 0.00 0.00 3.36
2169 2661 1.391485 CACAGCTGATCTTTTCGGTCG 59.609 52.381 23.35 0.00 32.85 4.79
2172 2664 0.449388 GGCACAGCTGATCTTTTCGG 59.551 55.000 23.35 0.00 0.00 4.30
2173 2665 1.129998 CAGGCACAGCTGATCTTTTCG 59.870 52.381 23.35 0.00 0.00 3.46
2181 2673 0.177373 CTGCTATCAGGCACAGCTGA 59.823 55.000 23.35 0.00 37.29 4.26
2185 2677 1.150567 GCGTCTGCTATCAGGCACAG 61.151 60.000 0.00 0.00 44.95 3.66
2188 2680 2.104928 CGCGTCTGCTATCAGGCA 59.895 61.111 0.00 0.00 44.95 4.75
2189 2681 3.333969 GCGCGTCTGCTATCAGGC 61.334 66.667 8.43 0.00 41.40 4.85
2192 2684 4.569023 CCGGCGCGTCTGCTATCA 62.569 66.667 9.90 0.00 39.65 2.15
2231 2724 3.114616 CTTGCCGTCTGCGACCTG 61.115 66.667 0.00 0.00 45.60 4.00
2232 2725 3.303135 TCTTGCCGTCTGCGACCT 61.303 61.111 0.00 0.00 45.60 3.85
2233 2726 3.112709 GTCTTGCCGTCTGCGACC 61.113 66.667 0.00 0.00 45.60 4.79
2235 2728 3.303135 AGGTCTTGCCGTCTGCGA 61.303 61.111 0.00 0.00 45.60 5.10
2236 2729 3.114616 CAGGTCTTGCCGTCTGCG 61.115 66.667 0.00 0.00 45.60 5.18
2251 2744 3.052082 CTTGCGTCCCTGTGGCAG 61.052 66.667 0.00 0.00 38.04 4.85
2261 2754 4.389576 CAACCTGCCGCTTGCGTC 62.390 66.667 13.97 1.20 45.60 5.19
2262 2755 4.927782 TCAACCTGCCGCTTGCGT 62.928 61.111 13.97 0.00 45.60 5.24
2263 2756 4.093952 CTCAACCTGCCGCTTGCG 62.094 66.667 8.14 8.14 45.60 4.85
2264 2757 4.410743 GCTCAACCTGCCGCTTGC 62.411 66.667 0.00 0.00 41.77 4.01
2265 2758 2.974489 CTGCTCAACCTGCCGCTTG 61.974 63.158 0.00 0.00 0.00 4.01
2266 2759 2.670934 CTGCTCAACCTGCCGCTT 60.671 61.111 0.00 0.00 0.00 4.68
2283 2776 3.983344 CCATACAAAGCTTGAAGTTGTGC 59.017 43.478 10.33 0.00 36.23 4.57
2315 2809 2.750350 CAGGCCCCACGTCTTTCT 59.250 61.111 0.00 0.00 0.00 2.52
2349 2849 1.954362 GCAAACCACACAAGGTGCCA 61.954 55.000 0.00 0.00 46.50 4.92
2356 2856 8.948631 TTGATAAAATAAAGCAAACCACACAA 57.051 26.923 0.00 0.00 0.00 3.33
2358 2858 9.810231 CATTTGATAAAATAAAGCAAACCACAC 57.190 29.630 0.00 0.00 32.09 3.82
2375 2875 6.999871 TGCAATCCTATCTGCTCATTTGATAA 59.000 34.615 0.00 0.00 39.38 1.75
2386 2886 2.701073 GCATGTGCAATCCTATCTGC 57.299 50.000 0.00 0.00 41.59 4.26
2450 2950 1.221466 TGCGCTTGTGTCTGTACTGC 61.221 55.000 9.73 0.00 0.00 4.40
2452 2952 0.104120 TGTGCGCTTGTGTCTGTACT 59.896 50.000 9.73 0.00 0.00 2.73
2456 2956 1.147473 TGTATGTGCGCTTGTGTCTG 58.853 50.000 9.73 0.00 0.00 3.51
2461 2961 0.650512 GCGTATGTATGTGCGCTTGT 59.349 50.000 9.73 0.00 45.48 3.16
2480 2980 3.384668 CTTCATAGGGTCAGTGTATGCG 58.615 50.000 0.00 0.00 0.00 4.73
2490 2990 1.739067 GTGTGTGCCTTCATAGGGTC 58.261 55.000 0.00 0.00 42.25 4.46
2496 2996 1.086696 GTATGCGTGTGTGCCTTCAT 58.913 50.000 0.00 0.00 0.00 2.57
2497 2997 0.034756 AGTATGCGTGTGTGCCTTCA 59.965 50.000 0.00 0.00 0.00 3.02
2498 2998 0.721718 GAGTATGCGTGTGTGCCTTC 59.278 55.000 0.00 0.00 0.00 3.46
2499 2999 0.321671 AGAGTATGCGTGTGTGCCTT 59.678 50.000 0.00 0.00 0.00 4.35
2501 3001 1.278238 GTAGAGTATGCGTGTGTGCC 58.722 55.000 0.00 0.00 0.00 5.01
2502 3002 1.278238 GGTAGAGTATGCGTGTGTGC 58.722 55.000 0.00 0.00 0.00 4.57
2503 3003 1.476891 AGGGTAGAGTATGCGTGTGTG 59.523 52.381 0.00 0.00 0.00 3.82
2504 3004 1.848652 AGGGTAGAGTATGCGTGTGT 58.151 50.000 0.00 0.00 0.00 3.72
2513 3013 4.537945 AGGTGCTCATAAGGGTAGAGTA 57.462 45.455 0.00 0.00 0.00 2.59
2519 3019 1.482593 CTCGAAGGTGCTCATAAGGGT 59.517 52.381 0.00 0.00 0.00 4.34
2537 3037 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
2543 3043 2.074576 CAAGATGATATGCCGGCTCAG 58.925 52.381 29.70 7.35 0.00 3.35
2544 3044 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
2551 3051 8.304202 ACTTCGTTAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
2569 3069 4.608951 GAGGCGTCTATAATGACTTCGTT 58.391 43.478 0.00 0.00 29.84 3.85
2572 3072 4.226113 ACGAGGCGTCTATAATGACTTC 57.774 45.455 4.69 0.00 33.69 3.01
2592 3092 2.177778 GACGTTCCCCTCGACGAC 59.822 66.667 0.00 0.00 41.53 4.34
2625 3125 2.485426 ACAGTCACACACATAAGCATGC 59.515 45.455 10.51 10.51 35.39 4.06
2630 3130 3.871006 ACACACACAGTCACACACATAAG 59.129 43.478 0.00 0.00 0.00 1.73
2631 3131 3.867857 ACACACACAGTCACACACATAA 58.132 40.909 0.00 0.00 0.00 1.90
2632 3132 3.535280 ACACACACAGTCACACACATA 57.465 42.857 0.00 0.00 0.00 2.29
2634 3134 2.073056 GAACACACACAGTCACACACA 58.927 47.619 0.00 0.00 0.00 3.72
2635 3135 1.060553 CGAACACACACAGTCACACAC 59.939 52.381 0.00 0.00 0.00 3.82
2659 3159 1.451028 CAGAGCTAGCCAACCAGCC 60.451 63.158 12.13 0.00 38.61 4.85
2665 3165 1.821753 GAGAGACACAGAGCTAGCCAA 59.178 52.381 12.13 0.00 0.00 4.52
2667 3167 1.468985 TGAGAGACACAGAGCTAGCC 58.531 55.000 12.13 2.81 0.00 3.93
2685 3185 4.575236 CAGAGAATGATGAGTTGATGGGTG 59.425 45.833 0.00 0.00 0.00 4.61
2687 3187 3.564644 GCAGAGAATGATGAGTTGATGGG 59.435 47.826 0.00 0.00 0.00 4.00
2700 3200 1.002792 CACCGATGCATGCAGAGAATG 60.003 52.381 26.69 17.50 0.00 2.67
2740 3240 3.449918 CCTTCTCTTCCTCCCTCTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
2748 3248 4.263112 GGTATATTGCCCTTCTCTTCCTCC 60.263 50.000 0.00 0.00 0.00 4.30
2759 3289 4.836825 CTGATCAATCGGTATATTGCCCT 58.163 43.478 0.00 0.00 36.89 5.19
2760 3290 3.375299 GCTGATCAATCGGTATATTGCCC 59.625 47.826 0.00 0.00 36.89 5.36
2764 3294 7.386059 TGTACATGCTGATCAATCGGTATATT 58.614 34.615 0.00 0.00 36.54 1.28
2767 3297 5.213891 TGTACATGCTGATCAATCGGTAT 57.786 39.130 0.00 0.00 38.76 2.73
2856 3387 1.623811 GAGTCCAGCCCTTGTAACAGA 59.376 52.381 0.00 0.00 0.00 3.41
2858 3389 1.429930 TGAGTCCAGCCCTTGTAACA 58.570 50.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.