Multiple sequence alignment - TraesCS1D01G029800

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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 TraesCS1D01G029800 chr1D 100.000 2723 0 0 1 2723 11642365 11639643 0.000000e+00 5029.0
1 TraesCS1D01G029800 chr1D 93.333 420 22 1 928 1347 14149005 14148592 1.390000e-172 616.0
2 TraesCS1D01G029800 chr1D 81.938 609 100 9 2115 2721 383363090 383363690 8.700000e-140 507.0
3 TraesCS1D01G029800 chr7A 93.525 1220 61 6 679 1892 189431922 189433129 0.000000e+00 1799.0
4 TraesCS1D01G029800 chr7A 84.884 172 24 2 176 346 62556299 62556469 3.600000e-39 172.0
5 TraesCS1D01G029800 chr1A 95.385 845 25 4 1889 2723 13806955 13806115 0.000000e+00 1332.0
6 TraesCS1D01G029800 chr1A 85.420 679 74 12 1 675 13817724 13817067 0.000000e+00 682.0
7 TraesCS1D01G029800 chr1A 86.828 577 62 4 9 584 13816709 13816146 1.380000e-177 632.0
8 TraesCS1D01G029800 chr1A 81.403 613 102 11 2112 2721 483133390 483133993 8.760000e-135 490.0
9 TraesCS1D01G029800 chr1A 81.373 612 102 10 2112 2721 483195500 483196101 3.150000e-134 488.0
10 TraesCS1D01G029800 chr1A 83.402 241 34 4 678 916 549330855 549330619 4.570000e-53 219.0
11 TraesCS1D01G029800 chr1A 94.355 124 2 2 1889 2011 13807101 13806982 4.630000e-43 185.0
12 TraesCS1D01G029800 chr1A 89.655 87 5 1 1889 1975 13817073 13816991 1.030000e-19 108.0
13 TraesCS1D01G029800 chr1A 90.741 54 5 0 1 54 557420949 557421002 3.760000e-09 73.1
14 TraesCS1D01G029800 chr1B 93.333 795 20 4 1952 2723 17536307 17537091 0.000000e+00 1144.0
15 TraesCS1D01G029800 chr1B 82.219 613 97 11 2112 2721 514076431 514077034 4.020000e-143 518.0
16 TraesCS1D01G029800 chr1B 80.750 613 106 11 2112 2721 513673696 513674299 4.110000e-128 468.0
17 TraesCS1D01G029800 chr3A 83.495 1236 153 23 679 1888 698744278 698743068 0.000000e+00 1105.0
18 TraesCS1D01G029800 chr3A 91.826 575 29 7 678 1243 665978904 665978339 0.000000e+00 785.0
19 TraesCS1D01G029800 chr3A 90.573 541 45 5 1355 1892 665969362 665968825 0.000000e+00 712.0
20 TraesCS1D01G029800 chr3A 93.144 423 23 1 925 1347 715408322 715408738 1.390000e-172 616.0
21 TraesCS1D01G029800 chr3A 88.789 223 23 2 1239 1461 665969514 665969294 3.450000e-69 272.0
22 TraesCS1D01G029800 chr5D 82.982 1234 148 36 677 1890 113489694 113490885 0.000000e+00 1059.0
23 TraesCS1D01G029800 chr3B 82.658 1234 157 30 679 1888 751947682 751946482 0.000000e+00 1040.0
24 TraesCS1D01G029800 chr3B 80.753 478 80 7 2249 2723 672706662 672706194 1.990000e-96 363.0
25 TraesCS1D01G029800 chr3B 83.217 286 33 10 1606 1890 546204954 546205225 5.820000e-62 248.0
26 TraesCS1D01G029800 chr3B 82.119 302 43 7 2424 2723 672609328 672609036 5.820000e-62 248.0
27 TraesCS1D01G029800 chr3B 89.922 129 12 1 1281 1409 732426372 732426499 6.030000e-37 165.0
28 TraesCS1D01G029800 chr3B 85.039 127 13 4 1283 1409 662471473 662471353 1.020000e-24 124.0
29 TraesCS1D01G029800 chr3D 83.821 717 75 18 1188 1888 564174780 564174089 0.000000e+00 643.0
30 TraesCS1D01G029800 chr3D 88.889 63 7 0 1 63 350874482 350874544 8.080000e-11 78.7
31 TraesCS1D01G029800 chr6D 93.381 423 22 1 925 1347 454585287 454585703 2.980000e-174 621.0
32 TraesCS1D01G029800 chr6D 80.645 186 29 7 146 325 452827990 452827806 1.310000e-28 137.0
33 TraesCS1D01G029800 chr6A 93.396 424 21 2 925 1347 524317489 524317906 2.980000e-174 621.0
34 TraesCS1D01G029800 chr6A 93.510 416 21 1 932 1347 521552231 521552640 4.980000e-172 614.0
35 TraesCS1D01G029800 chr2D 92.908 423 24 3 925 1347 524269695 524270111 6.450000e-171 610.0
36 TraesCS1D01G029800 chr2D 81.223 229 39 3 172 397 447249723 447249950 5.990000e-42 182.0
37 TraesCS1D01G029800 chr2B 87.273 275 26 7 673 946 88231407 88231141 3.410000e-79 305.0
38 TraesCS1D01G029800 chr2B 85.000 200 26 4 193 390 90404282 90404085 1.650000e-47 200.0
39 TraesCS1D01G029800 chr2A 88.755 249 22 5 678 924 759840765 759840521 1.580000e-77 300.0
40 TraesCS1D01G029800 chr7D 79.587 436 72 15 676 1104 180970911 180971336 2.050000e-76 296.0
41 TraesCS1D01G029800 chr7D 85.294 272 27 10 679 947 1523921 1524182 4.470000e-68 268.0
42 TraesCS1D01G029800 chr7D 82.609 276 43 4 1613 1888 180972014 180972284 3.500000e-59 239.0
43 TraesCS1D01G029800 chr7D 78.859 298 48 10 1 296 76261495 76261779 1.290000e-43 187.0
44 TraesCS1D01G029800 chr5A 75.987 608 113 28 2117 2708 671092879 671093469 1.600000e-72 283.0
45 TraesCS1D01G029800 chr5A 83.688 282 42 4 1609 1888 638815310 638815031 2.080000e-66 263.0
46 TraesCS1D01G029800 chr5A 81.215 181 32 2 193 371 361904252 361904072 7.860000e-31 145.0
47 TraesCS1D01G029800 chr5A 86.614 127 17 0 1283 1409 493832701 493832575 1.020000e-29 141.0
48 TraesCS1D01G029800 chr5B 83.172 309 36 10 1592 1896 458926616 458926320 4.470000e-68 268.0
49 TraesCS1D01G029800 chr5B 80.870 230 40 3 135 362 593438386 593438613 7.750000e-41 178.0
50 TraesCS1D01G029800 chr4D 82.168 286 42 8 1607 1888 196878149 196878429 1.260000e-58 237.0
51 TraesCS1D01G029800 chr4D 84.082 245 30 3 678 916 196877012 196877253 7.590000e-56 228.0
52 TraesCS1D01G029800 chr4D 81.951 205 35 2 176 378 132218155 132217951 3.600000e-39 172.0
53 TraesCS1D01G029800 chr7B 82.014 278 44 5 1613 1888 192018516 192018789 5.860000e-57 231.0
54 TraesCS1D01G029800 chr6B 80.727 275 43 6 1268 1535 235608552 235608281 3.550000e-49 206.0


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 TraesCS1D01G029800 chr1D 11639643 11642365 2722 True 5029.0 5029 100.000 1 2723 1 chr1D.!!$R1 2722
1 TraesCS1D01G029800 chr1D 383363090 383363690 600 False 507.0 507 81.938 2115 2721 1 chr1D.!!$F1 606
2 TraesCS1D01G029800 chr7A 189431922 189433129 1207 False 1799.0 1799 93.525 679 1892 1 chr7A.!!$F2 1213
3 TraesCS1D01G029800 chr1A 13806115 13807101 986 True 758.5 1332 94.870 1889 2723 2 chr1A.!!$R2 834
4 TraesCS1D01G029800 chr1A 483133390 483133993 603 False 490.0 490 81.403 2112 2721 1 chr1A.!!$F1 609
5 TraesCS1D01G029800 chr1A 483195500 483196101 601 False 488.0 488 81.373 2112 2721 1 chr1A.!!$F2 609
6 TraesCS1D01G029800 chr1A 13816146 13817724 1578 True 474.0 682 87.301 1 1975 3 chr1A.!!$R3 1974
7 TraesCS1D01G029800 chr1B 17536307 17537091 784 False 1144.0 1144 93.333 1952 2723 1 chr1B.!!$F1 771
8 TraesCS1D01G029800 chr1B 514076431 514077034 603 False 518.0 518 82.219 2112 2721 1 chr1B.!!$F3 609
9 TraesCS1D01G029800 chr1B 513673696 513674299 603 False 468.0 468 80.750 2112 2721 1 chr1B.!!$F2 609
10 TraesCS1D01G029800 chr3A 698743068 698744278 1210 True 1105.0 1105 83.495 679 1888 1 chr3A.!!$R2 1209
11 TraesCS1D01G029800 chr3A 665978339 665978904 565 True 785.0 785 91.826 678 1243 1 chr3A.!!$R1 565
12 TraesCS1D01G029800 chr3A 665968825 665969514 689 True 492.0 712 89.681 1239 1892 2 chr3A.!!$R3 653
13 TraesCS1D01G029800 chr5D 113489694 113490885 1191 False 1059.0 1059 82.982 677 1890 1 chr5D.!!$F1 1213
14 TraesCS1D01G029800 chr3B 751946482 751947682 1200 True 1040.0 1040 82.658 679 1888 1 chr3B.!!$R4 1209
15 TraesCS1D01G029800 chr3D 564174089 564174780 691 True 643.0 643 83.821 1188 1888 1 chr3D.!!$R1 700
16 TraesCS1D01G029800 chr7D 180970911 180972284 1373 False 267.5 296 81.098 676 1888 2 chr7D.!!$F3 1212
17 TraesCS1D01G029800 chr5A 671092879 671093469 590 False 283.0 283 75.987 2117 2708 1 chr5A.!!$F1 591
18 TraesCS1D01G029800 chr4D 196877012 196878429 1417 False 232.5 237 83.125 678 1888 2 chr4D.!!$F1 1210

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
96 97 0.036388 GCACGGACTTTCTCCATGGA 60.036 55.0 15.27 15.27 39.39 3.41 F
402 404 0.036732 CTGAGCTGGCCAGGTTACAA 59.963 55.0 36.40 21.24 39.57 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1320 0.247460 CTCCAGGACGACTGCATTGA 59.753 55.000 6.40 0.0 46.14 2.57 R
2042 2890 2.050714 CGGTGTAGTGTCGCGTGT 60.051 61.111 5.77 0.0 0.00 4.49 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
28 29 1.807165 CTGCAGTCGTCATGGTCCG 60.807 63.158 5.25 0.00 0.00 4.79
33 34 3.766432 TCGTCATGGTCCGACACA 58.234 55.556 0.00 0.00 32.72 3.72
38 39 0.756294 TCATGGTCCGACACACACTT 59.244 50.000 0.00 0.00 0.00 3.16
46 47 3.184581 GTCCGACACACACTTCATTTCTC 59.815 47.826 0.00 0.00 0.00 2.87
54 55 1.635487 CACTTCATTTCTCCTCCCCCA 59.365 52.381 0.00 0.00 0.00 4.96
59 60 2.252676 TCATTTCTCCTCCCCCATCCTA 59.747 50.000 0.00 0.00 0.00 2.94
89 90 0.605589 CTCCTCTGCACGGACTTTCT 59.394 55.000 0.00 0.00 0.00 2.52
90 91 0.603569 TCCTCTGCACGGACTTTCTC 59.396 55.000 0.00 0.00 0.00 2.87
91 92 0.390472 CCTCTGCACGGACTTTCTCC 60.390 60.000 0.00 0.00 35.33 3.71
92 93 0.318441 CTCTGCACGGACTTTCTCCA 59.682 55.000 0.00 0.00 39.39 3.86
93 94 0.976641 TCTGCACGGACTTTCTCCAT 59.023 50.000 0.00 0.00 39.39 3.41
96 97 0.036388 GCACGGACTTTCTCCATGGA 60.036 55.000 15.27 15.27 39.39 3.41
118 119 1.059264 GCAACGCTAGCAACTAGTTCG 59.941 52.381 16.45 8.57 36.53 3.95
121 122 0.179134 CGCTAGCAACTAGTTCGCCT 60.179 55.000 16.45 13.02 36.53 5.52
122 123 1.562017 GCTAGCAACTAGTTCGCCTC 58.438 55.000 19.73 10.16 36.53 4.70
124 125 0.454600 TAGCAACTAGTTCGCCTCGG 59.545 55.000 19.73 4.90 0.00 4.63
125 126 1.810030 GCAACTAGTTCGCCTCGGG 60.810 63.158 4.77 0.00 0.00 5.14
164 165 2.042259 ACCGTCCATCGTAGTCGCA 61.042 57.895 0.00 0.00 37.94 5.10
185 186 5.502382 CGCAAGGCATAGTATGTGTGTTAAG 60.502 44.000 11.73 0.00 0.00 1.85
186 187 5.354234 GCAAGGCATAGTATGTGTGTTAAGT 59.646 40.000 11.73 0.00 0.00 2.24
187 188 6.675486 GCAAGGCATAGTATGTGTGTTAAGTG 60.675 42.308 11.73 0.22 0.00 3.16
188 189 4.876107 AGGCATAGTATGTGTGTTAAGTGC 59.124 41.667 11.73 0.00 0.00 4.40
190 191 5.447279 GGCATAGTATGTGTGTTAAGTGCAC 60.447 44.000 9.40 9.40 37.37 4.57
191 192 5.121611 GCATAGTATGTGTGTTAAGTGCACA 59.878 40.000 21.04 8.50 45.48 4.57
212 213 8.152898 TGCACATGTTAGCTCTTAATCATATCT 58.847 33.333 9.33 0.00 0.00 1.98
233 234 3.058450 TCGTGTATACAACCAAACACCG 58.942 45.455 7.25 3.85 39.20 4.94
249 250 2.028112 ACACCGTGTAGTTGCATGATCT 60.028 45.455 1.18 0.00 0.00 2.75
250 251 3.002791 CACCGTGTAGTTGCATGATCTT 58.997 45.455 0.00 0.00 0.00 2.40
260 261 1.605232 TGCATGATCTTAGCCAATGCG 59.395 47.619 0.00 0.00 44.33 4.73
263 264 0.836606 TGATCTTAGCCAATGCGGGA 59.163 50.000 0.00 0.00 44.33 5.14
291 292 2.297880 ACGCTAACCCAAAATTGTTCCC 59.702 45.455 0.00 0.00 0.00 3.97
301 302 5.312079 CCAAAATTGTTCCCCTAATGCAAA 58.688 37.500 0.00 0.00 0.00 3.68
303 304 6.264067 CCAAAATTGTTCCCCTAATGCAAAAA 59.736 34.615 0.00 0.00 0.00 1.94
324 325 2.028112 AGACTAGATGCGAGCAACCAAA 60.028 45.455 0.57 0.00 0.00 3.28
325 326 2.076863 ACTAGATGCGAGCAACCAAAC 58.923 47.619 0.57 0.00 0.00 2.93
329 330 3.081061 AGATGCGAGCAACCAAACAATA 58.919 40.909 0.57 0.00 0.00 1.90
334 335 3.173599 CGAGCAACCAAACAATATGCAG 58.826 45.455 0.00 0.00 39.42 4.41
338 339 3.307782 GCAACCAAACAATATGCAGATGC 59.692 43.478 0.00 0.00 42.50 3.91
348 350 4.739046 ATATGCAGATGCTAGTTTTCGC 57.261 40.909 6.35 0.00 42.66 4.70
350 352 0.378610 GCAGATGCTAGTTTTCGCCC 59.621 55.000 0.00 0.00 38.21 6.13
360 362 2.353323 AGTTTTCGCCCGTATTTCCTC 58.647 47.619 0.00 0.00 0.00 3.71
364 366 0.108041 TCGCCCGTATTTCCTCAACC 60.108 55.000 0.00 0.00 0.00 3.77
375 377 1.672356 CCTCAACCAGCCTCCGTTG 60.672 63.158 0.00 0.00 40.58 4.10
378 380 1.071471 CAACCAGCCTCCGTTGAGT 59.929 57.895 0.00 0.00 41.53 3.41
380 382 2.113243 AACCAGCCTCCGTTGAGTCC 62.113 60.000 0.00 0.00 36.86 3.85
397 399 3.699894 CGACTGAGCTGGCCAGGT 61.700 66.667 36.72 36.72 42.58 4.00
399 401 1.888436 CGACTGAGCTGGCCAGGTTA 61.888 60.000 36.40 30.92 39.57 2.85
402 404 0.036732 CTGAGCTGGCCAGGTTACAA 59.963 55.000 36.40 21.24 39.57 2.41
421 423 2.844122 ACGAGAAAGCAACCAAACAC 57.156 45.000 0.00 0.00 0.00 3.32
426 428 2.621371 AAAGCAACCAAACACGCCCG 62.621 55.000 0.00 0.00 0.00 6.13
448 450 8.457348 CCCGTAATGGTGATACAGAGATCTGG 62.457 50.000 14.09 0.00 41.61 3.86
460 463 3.581770 CAGAGATCTGGAGCCCATATTCA 59.418 47.826 0.00 0.00 40.20 2.57
479 482 0.179062 AGTGATCCTCGCTGATTGCC 60.179 55.000 0.00 0.00 35.63 4.52
537 540 3.056678 TGTGCCAGCAATATCCTTTGTTG 60.057 43.478 0.00 0.00 37.51 3.33
546 549 6.595716 AGCAATATCCTTTGTTGACTGTAGAC 59.404 38.462 0.00 0.00 0.00 2.59
547 550 6.371548 GCAATATCCTTTGTTGACTGTAGACA 59.628 38.462 0.00 0.00 0.00 3.41
555 558 7.331193 CCTTTGTTGACTGTAGACATAGTAACC 59.669 40.741 10.34 0.00 0.00 2.85
556 559 5.946298 TGTTGACTGTAGACATAGTAACCG 58.054 41.667 0.00 0.00 0.00 4.44
573 576 2.942710 ACCGACTATTCGTCACTGTTG 58.057 47.619 1.61 0.00 44.28 3.33
585 588 3.194861 GTCACTGTTGAACACTGTAGCA 58.805 45.455 0.00 0.00 35.87 3.49
590 593 2.285083 GTTGAACACTGTAGCACCACA 58.715 47.619 0.00 0.00 0.00 4.17
598 601 0.821711 TGTAGCACCACAGTTTGCCC 60.822 55.000 0.84 0.00 39.75 5.36
627 630 0.251916 ATTGGCTGGCTACGCAACTA 59.748 50.000 2.00 0.00 0.00 2.24
629 632 1.218316 GGCTGGCTACGCAACTACT 59.782 57.895 0.00 0.00 0.00 2.57
635 638 2.000447 GGCTACGCAACTACTTTCAGG 59.000 52.381 0.00 0.00 0.00 3.86
717 720 5.134661 CCACCACTTTGAAGGTTAGGTTTA 58.865 41.667 0.00 0.00 35.52 2.01
767 777 5.100259 CAGAAAACACCGTGTCTATCGTAT 58.900 41.667 4.23 0.00 0.00 3.06
769 779 6.090358 CAGAAAACACCGTGTCTATCGTATTT 59.910 38.462 4.23 0.00 0.00 1.40
956 986 1.305381 CTCCCTCCCTCGAACCAGT 60.305 63.158 0.00 0.00 0.00 4.00
1048 1202 1.732259 CAATTAACCAGCTCTCGCGTT 59.268 47.619 5.77 0.00 42.32 4.84
1713 2548 5.593010 TGTAAAATGTTAAGTGTTGCCACC 58.407 37.500 0.00 0.00 42.88 4.61
1892 2731 5.757320 TGGTTTTGTGCAATTTACTCCATTG 59.243 36.000 0.00 0.00 35.12 2.82
1937 2776 2.924290 CACACGCCTTAGCTAGAAGTTC 59.076 50.000 0.00 0.00 36.60 3.01
1940 2779 3.614616 CACGCCTTAGCTAGAAGTTCTTG 59.385 47.826 11.40 10.42 36.60 3.02
1947 2786 7.327214 CCTTAGCTAGAAGTTCTTGTGATTCT 58.673 38.462 11.40 3.97 36.11 2.40
1948 2787 8.470805 CCTTAGCTAGAAGTTCTTGTGATTCTA 58.529 37.037 11.40 3.05 34.08 2.10
1949 2788 9.862371 CTTAGCTAGAAGTTCTTGTGATTCTAA 57.138 33.333 11.40 10.01 34.71 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.107993 CCATGACGACTGCAGTGGAT 60.108 55.000 32.20 17.72 0.00 3.41
8 9 1.016130 GGACCATGACGACTGCAGTG 61.016 60.000 27.27 18.48 0.00 3.66
11 12 2.261361 CGGACCATGACGACTGCA 59.739 61.111 0.00 0.00 0.00 4.41
28 29 3.748568 GGAGGAGAAATGAAGTGTGTGTC 59.251 47.826 0.00 0.00 0.00 3.67
33 34 1.636003 GGGGGAGGAGAAATGAAGTGT 59.364 52.381 0.00 0.00 0.00 3.55
38 39 1.011293 AGGATGGGGGAGGAGAAATGA 59.989 52.381 0.00 0.00 0.00 2.57
46 47 1.151721 AGGCATAGGATGGGGGAGG 60.152 63.158 0.00 0.00 0.00 4.30
54 55 1.670590 GAGCGCTCAGGCATAGGAT 59.329 57.895 31.91 0.00 38.60 3.24
59 60 2.763292 AGAGGAGCGCTCAGGCAT 60.763 61.111 36.27 17.53 38.60 4.40
89 90 1.522092 CTAGCGTTGCCTCCATGGA 59.478 57.895 15.27 15.27 38.35 3.41
90 91 2.182842 GCTAGCGTTGCCTCCATGG 61.183 63.158 4.97 4.97 39.35 3.66
91 92 1.026182 TTGCTAGCGTTGCCTCCATG 61.026 55.000 10.77 0.00 0.00 3.66
92 93 1.026718 GTTGCTAGCGTTGCCTCCAT 61.027 55.000 10.77 0.00 0.00 3.41
93 94 1.671054 GTTGCTAGCGTTGCCTCCA 60.671 57.895 10.77 0.00 0.00 3.86
96 97 0.608640 ACTAGTTGCTAGCGTTGCCT 59.391 50.000 10.77 3.64 37.57 4.75
154 155 1.100510 ACTATGCCTTGCGACTACGA 58.899 50.000 0.00 0.00 42.66 3.43
156 157 3.736252 CACATACTATGCCTTGCGACTAC 59.264 47.826 0.00 0.00 0.00 2.73
164 165 5.354234 GCACTTAACACACATACTATGCCTT 59.646 40.000 0.00 0.00 0.00 4.35
185 186 5.801350 TGATTAAGAGCTAACATGTGCAC 57.199 39.130 10.75 10.75 0.00 4.57
186 187 8.152898 AGATATGATTAAGAGCTAACATGTGCA 58.847 33.333 10.46 0.00 0.00 4.57
187 188 8.545229 AGATATGATTAAGAGCTAACATGTGC 57.455 34.615 0.00 0.00 0.00 4.57
188 189 8.858186 CGAGATATGATTAAGAGCTAACATGTG 58.142 37.037 0.00 0.00 0.00 3.21
190 191 8.858186 CACGAGATATGATTAAGAGCTAACATG 58.142 37.037 0.00 0.00 0.00 3.21
191 192 8.580720 ACACGAGATATGATTAAGAGCTAACAT 58.419 33.333 0.00 0.00 0.00 2.71
212 213 3.058450 CGGTGTTTGGTTGTATACACGA 58.942 45.455 4.68 0.00 41.28 4.35
233 234 4.191544 TGGCTAAGATCATGCAACTACAC 58.808 43.478 0.00 0.00 0.00 2.90
249 250 0.251386 TGGTTTCCCGCATTGGCTAA 60.251 50.000 0.00 0.00 38.10 3.09
250 251 0.251386 TTGGTTTCCCGCATTGGCTA 60.251 50.000 0.00 0.00 38.10 3.93
260 261 0.599558 GGGTTAGCGTTTGGTTTCCC 59.400 55.000 0.00 0.00 32.87 3.97
263 264 3.889520 TTTTGGGTTAGCGTTTGGTTT 57.110 38.095 0.00 0.00 0.00 3.27
273 274 6.639563 CATTAGGGGAACAATTTTGGGTTAG 58.360 40.000 0.00 0.00 0.00 2.34
276 277 3.263170 GCATTAGGGGAACAATTTTGGGT 59.737 43.478 0.00 0.00 0.00 4.51
277 278 3.262915 TGCATTAGGGGAACAATTTTGGG 59.737 43.478 0.00 0.00 0.00 4.12
291 292 5.294306 TCGCATCTAGTCTTTTTGCATTAGG 59.706 40.000 0.00 0.00 32.94 2.69
301 302 2.028112 TGGTTGCTCGCATCTAGTCTTT 60.028 45.455 0.00 0.00 0.00 2.52
303 304 1.186200 TGGTTGCTCGCATCTAGTCT 58.814 50.000 0.00 0.00 0.00 3.24
324 325 5.504665 GCGAAAACTAGCATCTGCATATTGT 60.505 40.000 4.79 0.00 45.16 2.71
325 326 4.908156 GCGAAAACTAGCATCTGCATATTG 59.092 41.667 4.79 0.00 45.16 1.90
329 330 1.672881 GGCGAAAACTAGCATCTGCAT 59.327 47.619 4.79 0.00 45.16 3.96
334 335 1.930567 TACGGGCGAAAACTAGCATC 58.069 50.000 0.00 0.00 34.54 3.91
338 339 3.528532 AGGAAATACGGGCGAAAACTAG 58.471 45.455 0.00 0.00 0.00 2.57
348 350 1.379527 GCTGGTTGAGGAAATACGGG 58.620 55.000 0.00 0.00 0.00 5.28
350 352 2.280628 GAGGCTGGTTGAGGAAATACG 58.719 52.381 0.00 0.00 0.00 3.06
360 362 0.951040 GACTCAACGGAGGCTGGTTG 60.951 60.000 17.52 17.52 46.33 3.77
375 377 2.183046 GCCAGCTCAGTCGGACTC 59.817 66.667 7.89 0.00 0.00 3.36
378 380 3.385384 CTGGCCAGCTCAGTCGGA 61.385 66.667 22.33 0.00 0.00 4.55
380 382 1.888436 TAACCTGGCCAGCTCAGTCG 61.888 60.000 28.39 14.16 0.00 4.18
397 399 4.156190 TGTTTGGTTGCTTTCTCGTTGTAA 59.844 37.500 0.00 0.00 0.00 2.41
399 401 2.490115 TGTTTGGTTGCTTTCTCGTTGT 59.510 40.909 0.00 0.00 0.00 3.32
402 404 1.063469 CGTGTTTGGTTGCTTTCTCGT 59.937 47.619 0.00 0.00 0.00 4.18
421 423 1.067974 TCTGTATCACCATTACGGGCG 59.932 52.381 0.00 0.00 40.22 6.13
426 428 6.656632 TCCAGATCTCTGTATCACCATTAC 57.343 41.667 6.46 0.00 42.27 1.89
448 450 3.616076 CGAGGATCACTGAATATGGGCTC 60.616 52.174 0.00 0.00 33.17 4.70
450 452 2.693069 CGAGGATCACTGAATATGGGC 58.307 52.381 0.00 0.00 33.17 5.36
460 463 3.376218 GCAATCAGCGAGGATCACT 57.624 52.632 0.00 0.00 33.17 3.41
479 482 1.539827 CTTGTTACCTTGGGCCTTTCG 59.460 52.381 4.53 0.00 0.00 3.46
511 514 1.842562 AGGATATTGCTGGCACACTCT 59.157 47.619 0.00 0.00 0.00 3.24
585 588 4.514585 TGCCGGGCAAACTGTGGT 62.515 61.111 21.55 0.00 34.76 4.16
590 593 4.660938 GGTCCTGCCGGGCAAACT 62.661 66.667 23.94 0.00 38.41 2.66
591 594 4.966787 TGGTCCTGCCGGGCAAAC 62.967 66.667 23.94 21.88 38.41 2.93
592 595 3.521765 AATGGTCCTGCCGGGCAAA 62.522 57.895 23.94 11.45 38.41 3.68
593 596 3.978193 AATGGTCCTGCCGGGCAA 61.978 61.111 23.94 8.11 38.41 4.52
594 597 4.738998 CAATGGTCCTGCCGGGCA 62.739 66.667 22.39 22.39 41.21 5.36
598 601 3.136123 CAGCCAATGGTCCTGCCG 61.136 66.667 0.00 0.00 41.21 5.69
627 630 1.192146 TCCGGCAGCTACCTGAAAGT 61.192 55.000 0.42 0.00 41.77 2.66
629 632 0.618458 AATCCGGCAGCTACCTGAAA 59.382 50.000 0.69 0.00 41.77 2.69
635 638 0.308993 GATGCAAATCCGGCAGCTAC 59.691 55.000 0.00 0.00 45.68 3.58
775 785 2.006888 ACGCCGATCAGTGTTATTTGG 58.993 47.619 0.00 0.00 0.00 3.28
956 986 1.145598 GCTCCTGCATGCTGCTCTA 59.854 57.895 20.33 3.44 45.31 2.43
1048 1202 1.473965 GCTCGATTCTTGCTGGATCCA 60.474 52.381 15.27 15.27 0.00 3.41
1160 1320 0.247460 CTCCAGGACGACTGCATTGA 59.753 55.000 6.40 0.00 46.14 2.57
1612 2445 7.221452 CACCTGTCATTGAAACAAAAGAAGAAG 59.779 37.037 0.00 0.00 0.00 2.85
1828 2667 5.511729 GCTTTGCGAAAATCACTACAATACC 59.488 40.000 0.00 0.00 0.00 2.73
1840 2679 4.846779 TGAAGGTTAGCTTTGCGAAAAT 57.153 36.364 0.00 0.00 0.00 1.82
1892 2731 5.163652 GCCACACCATTTACTTATCTTGGAC 60.164 44.000 0.00 0.00 0.00 4.02
1937 2776 7.164826 GCTGCACGATTTATTTAGAATCACAAG 59.835 37.037 0.00 0.00 34.02 3.16
1940 2779 6.630443 CAGCTGCACGATTTATTTAGAATCAC 59.370 38.462 0.00 0.00 34.02 3.06
2042 2890 2.050714 CGGTGTAGTGTCGCGTGT 60.051 61.111 5.77 0.00 0.00 4.49
2380 3266 4.011517 GAACGCTGGGTCCGGGAA 62.012 66.667 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.