Multiple sequence alignment - TraesCS1B01G388200

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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 TraesCS1B01G388200 chr1B 100.000 2798 0 0 1 2798 622217327 622220124 0.000000e+00 5168
1 TraesCS1B01G388200 chr1B 93.204 2163 109 22 667 2798 622358399 622360554 0.000000e+00 3145
2 TraesCS1B01G388200 chr1B 92.635 2159 113 14 667 2795 622312759 622314901 0.000000e+00 3064
3 TraesCS1B01G388200 chr1B 83.621 116 11 3 341 448 622345704 622345819 4.930000e-18 102
4 TraesCS1B01G388200 chr1A 91.835 1886 93 24 559 2388 547238969 547237089 0.000000e+00 2573
5 TraesCS1B01G388200 chr1A 91.737 1888 93 24 559 2388 547217073 547215191 0.000000e+00 2564
6 TraesCS1B01G388200 chr1A 90.667 450 38 3 1 448 547217517 547217070 1.860000e-166 595
7 TraesCS1B01G388200 chr1A 90.667 450 38 3 1 448 547239413 547238966 1.860000e-166 595
8 TraesCS1B01G388200 chr1A 86.429 140 17 2 445 583 584805231 584805093 4.830000e-33 152
9 TraesCS1B01G388200 chr1D 91.194 1851 111 19 573 2388 452262617 452260784 0.000000e+00 2468
10 TraesCS1B01G388200 chr1D 94.100 1356 56 9 667 2002 452270297 452268946 0.000000e+00 2039
11 TraesCS1B01G388200 chr1D 92.265 1448 83 16 577 2002 452265493 452264053 0.000000e+00 2026
12 TraesCS1B01G388200 chr1D 93.230 1034 58 7 977 2002 452337936 452336907 0.000000e+00 1511
13 TraesCS1B01G388200 chr1D 89.749 439 36 4 12 448 452338550 452338119 1.130000e-153 553
14 TraesCS1B01G388200 chr1D 94.203 138 7 1 1963 2099 452264047 452263910 2.820000e-50 209
15 TraesCS1B01G388200 chr1D 92.857 140 7 2 1963 2099 452268940 452268801 1.700000e-47 200
16 TraesCS1B01G388200 chr1D 92.373 118 8 1 445 562 171522513 171522629 1.720000e-37 167
17 TraesCS1B01G388200 chrUn 92.648 1605 73 16 559 2121 246249996 246248395 0.000000e+00 2268
18 TraesCS1B01G388200 chrUn 92.539 1032 53 8 1379 2388 416393732 416394761 0.000000e+00 1458
19 TraesCS1B01G388200 chrUn 93.256 519 23 8 871 1377 474453545 474454063 0.000000e+00 754
20 TraesCS1B01G388200 chrUn 90.889 450 37 3 1 448 362687884 362688331 3.990000e-168 601
21 TraesCS1B01G388200 chrUn 92.203 295 19 3 156 448 246250285 246249993 5.580000e-112 414
22 TraesCS1B01G388200 chrUn 89.426 331 22 7 559 877 362688328 362688657 3.360000e-109 405
23 TraesCS1B01G388200 chr6D 83.974 312 49 1 2488 2798 381007737 381008048 5.860000e-77 298
24 TraesCS1B01G388200 chr6D 83.596 317 45 4 2483 2798 428978509 428978819 9.800000e-75 291
25 TraesCS1B01G388200 chr5D 83.758 314 50 1 2486 2798 536239838 536240151 2.110000e-76 296
26 TraesCS1B01G388200 chr5D 85.240 271 39 1 2486 2755 499616058 499615788 7.630000e-71 278
27 TraesCS1B01G388200 chr6B 83.067 313 52 1 2487 2798 518677005 518676693 1.640000e-72 283
28 TraesCS1B01G388200 chr6B 91.736 121 10 0 446 566 601043176 601043056 4.790000e-38 169
29 TraesCS1B01G388200 chr6A 82.965 317 51 3 2483 2798 573641598 573641912 1.640000e-72 283
30 TraesCS1B01G388200 chr3A 82.803 314 52 2 2486 2798 134257369 134257057 2.120000e-71 279
31 TraesCS1B01G388200 chr3A 91.667 120 8 2 444 562 120804775 120804893 6.200000e-37 165
32 TraesCS1B01G388200 chr5A 92.742 124 8 1 445 567 594645673 594645796 7.960000e-41 178
33 TraesCS1B01G388200 chr5A 90.476 126 10 2 447 571 440806841 440806965 6.200000e-37 165
34 TraesCS1B01G388200 chr3B 92.683 123 8 1 445 566 173371473 173371595 2.860000e-40 176
35 TraesCS1B01G388200 chr4A 91.200 125 8 3 439 562 514351535 514351657 1.720000e-37 167
36 TraesCS1B01G388200 chr3D 92.241 116 9 0 447 562 341502408 341502523 6.200000e-37 165


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 TraesCS1B01G388200 chr1B 622217327 622220124 2797 False 5168.0 5168 100.0000 1 2798 1 chr1B.!!$F1 2797
1 TraesCS1B01G388200 chr1B 622358399 622360554 2155 False 3145.0 3145 93.2040 667 2798 1 chr1B.!!$F4 2131
2 TraesCS1B01G388200 chr1B 622312759 622314901 2142 False 3064.0 3064 92.6350 667 2795 1 chr1B.!!$F2 2128
3 TraesCS1B01G388200 chr1A 547237089 547239413 2324 True 1584.0 2573 91.2510 1 2388 2 chr1A.!!$R3 2387
4 TraesCS1B01G388200 chr1A 547215191 547217517 2326 True 1579.5 2564 91.2020 1 2388 2 chr1A.!!$R2 2387
5 TraesCS1B01G388200 chr1D 452260784 452270297 9513 True 1388.4 2468 92.9238 573 2388 5 chr1D.!!$R1 1815
6 TraesCS1B01G388200 chr1D 452336907 452338550 1643 True 1032.0 1511 91.4895 12 2002 2 chr1D.!!$R2 1990
7 TraesCS1B01G388200 chrUn 416393732 416394761 1029 False 1458.0 1458 92.5390 1379 2388 1 chrUn.!!$F1 1009
8 TraesCS1B01G388200 chrUn 246248395 246250285 1890 True 1341.0 2268 92.4255 156 2121 2 chrUn.!!$R1 1965
9 TraesCS1B01G388200 chrUn 474453545 474454063 518 False 754.0 754 93.2560 871 1377 1 chrUn.!!$F2 506
10 TraesCS1B01G388200 chrUn 362687884 362688657 773 False 503.0 601 90.1575 1 877 2 chrUn.!!$F3 876

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
462 465 0.038744 AAGTACTTCCTCCGTCCGGA 59.961 55.0 0.00 0.0 42.90 5.14 F
463 466 0.038744 AGTACTTCCTCCGTCCGGAA 59.961 55.0 5.23 0.0 44.66 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1416 0.105964 CCTCACCGAACTTGACACCA 59.894 55.0 0.00 0.00 0.0 4.17 R
2117 9965 0.953960 CTCTGTACAACGTTGGGGCC 60.954 60.0 30.34 15.61 0.0 5.80 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
46 47 4.749598 GCAACGGGAATCTTTTGTTGAAAT 59.250 37.500 7.51 0.00 41.76 2.17
49 50 6.843069 ACGGGAATCTTTTGTTGAAATTTG 57.157 33.333 0.00 0.00 0.00 2.32
73 74 5.113502 AGGCGCTCAAATTTATGCTAATC 57.886 39.130 7.64 0.00 0.00 1.75
79 80 6.145535 GCTCAAATTTATGCTAATCGGGAAG 58.854 40.000 7.17 0.00 0.00 3.46
83 84 7.500892 TCAAATTTATGCTAATCGGGAAGCTTA 59.499 33.333 0.00 0.00 39.53 3.09
106 107 9.543018 CTTACGAGGCTTAACTTCTTAAATTTG 57.457 33.333 0.00 0.00 0.00 2.32
108 109 7.937649 ACGAGGCTTAACTTCTTAAATTTGTT 58.062 30.769 0.00 0.00 0.00 2.83
194 195 5.758924 AGTTAGGCGTTTTTGAGAATTCAC 58.241 37.500 8.44 1.50 31.71 3.18
195 196 5.298276 AGTTAGGCGTTTTTGAGAATTCACA 59.702 36.000 8.44 4.65 31.71 3.58
257 258 1.375098 GATGCTCTCTGTGGGCAAGC 61.375 60.000 8.49 0.56 39.46 4.01
269 270 1.036707 GGGCAAGCTTGTGTTTACCA 58.963 50.000 26.55 0.00 0.00 3.25
382 385 7.179076 AGTAGGAATAAAAGAGGCGAACTTA 57.821 36.000 0.00 0.00 0.00 2.24
436 439 5.815581 AGGCTTTCATGTATAGTTCACCAA 58.184 37.500 0.00 0.00 0.00 3.67
437 440 6.245408 AGGCTTTCATGTATAGTTCACCAAA 58.755 36.000 0.00 0.00 0.00 3.28
459 462 3.957591 AAGAAAGTACTTCCTCCGTCC 57.042 47.619 8.95 0.00 34.21 4.79
460 463 1.817447 AGAAAGTACTTCCTCCGTCCG 59.183 52.381 8.95 0.00 34.21 4.79
461 464 0.893447 AAAGTACTTCCTCCGTCCGG 59.107 55.000 8.95 0.00 0.00 5.14
462 465 0.038744 AAGTACTTCCTCCGTCCGGA 59.961 55.000 0.00 0.00 42.90 5.14
463 466 0.038744 AGTACTTCCTCCGTCCGGAA 59.961 55.000 5.23 0.00 44.66 4.30
464 467 0.890683 GTACTTCCTCCGTCCGGAAA 59.109 55.000 5.23 1.47 44.66 3.13
465 468 1.479730 GTACTTCCTCCGTCCGGAAAT 59.520 52.381 5.23 0.00 44.66 2.17
466 469 1.856629 ACTTCCTCCGTCCGGAAATA 58.143 50.000 5.23 0.00 44.66 1.40
467 470 1.479730 ACTTCCTCCGTCCGGAAATAC 59.520 52.381 5.23 0.00 44.66 1.89
468 471 1.755380 CTTCCTCCGTCCGGAAATACT 59.245 52.381 5.23 0.00 44.66 2.12
469 472 1.856629 TCCTCCGTCCGGAAATACTT 58.143 50.000 5.23 0.00 44.66 2.24
470 473 1.479323 TCCTCCGTCCGGAAATACTTG 59.521 52.381 5.23 0.00 44.66 3.16
471 474 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
472 475 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
473 476 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
474 477 1.648504 CGTCCGGAAATACTTGTCCC 58.351 55.000 5.23 0.00 0.00 4.46
475 478 1.066716 CGTCCGGAAATACTTGTCCCA 60.067 52.381 5.23 0.00 0.00 4.37
476 479 2.629051 GTCCGGAAATACTTGTCCCAG 58.371 52.381 5.23 0.00 0.00 4.45
477 480 2.235402 GTCCGGAAATACTTGTCCCAGA 59.765 50.000 5.23 0.00 0.00 3.86
478 481 2.907696 TCCGGAAATACTTGTCCCAGAA 59.092 45.455 0.00 0.00 0.00 3.02
479 482 3.328343 TCCGGAAATACTTGTCCCAGAAA 59.672 43.478 0.00 0.00 0.00 2.52
480 483 4.018779 TCCGGAAATACTTGTCCCAGAAAT 60.019 41.667 0.00 0.00 0.00 2.17
481 484 4.096382 CCGGAAATACTTGTCCCAGAAATG 59.904 45.833 0.00 0.00 0.00 2.32
482 485 4.941263 CGGAAATACTTGTCCCAGAAATGA 59.059 41.667 0.00 0.00 0.00 2.57
483 486 5.414454 CGGAAATACTTGTCCCAGAAATGAA 59.586 40.000 0.00 0.00 0.00 2.57
484 487 6.095440 CGGAAATACTTGTCCCAGAAATGAAT 59.905 38.462 0.00 0.00 0.00 2.57
485 488 7.282224 CGGAAATACTTGTCCCAGAAATGAATA 59.718 37.037 0.00 0.00 0.00 1.75
486 489 8.966868 GGAAATACTTGTCCCAGAAATGAATAA 58.033 33.333 0.00 0.00 0.00 1.40
491 494 8.421249 ACTTGTCCCAGAAATGAATAAAATGA 57.579 30.769 0.00 0.00 0.00 2.57
492 495 8.869109 ACTTGTCCCAGAAATGAATAAAATGAA 58.131 29.630 0.00 0.00 0.00 2.57
493 496 9.880157 CTTGTCCCAGAAATGAATAAAATGAAT 57.120 29.630 0.00 0.00 0.00 2.57
494 497 9.656040 TTGTCCCAGAAATGAATAAAATGAATG 57.344 29.630 0.00 0.00 0.00 2.67
495 498 8.814931 TGTCCCAGAAATGAATAAAATGAATGT 58.185 29.630 0.00 0.00 0.00 2.71
538 541 9.739276 AATCTAGATACAACAATTTTCAGGACA 57.261 29.630 5.46 0.00 0.00 4.02
539 542 9.739276 ATCTAGATACAACAATTTTCAGGACAA 57.261 29.630 2.53 0.00 0.00 3.18
540 543 9.219603 TCTAGATACAACAATTTTCAGGACAAG 57.780 33.333 0.00 0.00 0.00 3.16
541 544 7.823745 AGATACAACAATTTTCAGGACAAGT 57.176 32.000 0.00 0.00 0.00 3.16
542 545 8.918202 AGATACAACAATTTTCAGGACAAGTA 57.082 30.769 0.00 0.00 0.00 2.24
543 546 9.520515 AGATACAACAATTTTCAGGACAAGTAT 57.479 29.630 0.00 0.00 0.00 2.12
546 549 8.871686 ACAACAATTTTCAGGACAAGTATTTC 57.128 30.769 0.00 0.00 0.00 2.17
547 550 7.926018 ACAACAATTTTCAGGACAAGTATTTCC 59.074 33.333 0.00 0.00 0.00 3.13
548 551 6.677913 ACAATTTTCAGGACAAGTATTTCCG 58.322 36.000 0.00 0.00 36.95 4.30
549 552 5.897377 ATTTTCAGGACAAGTATTTCCGG 57.103 39.130 0.00 0.00 36.95 5.14
550 553 4.627284 TTTCAGGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 36.95 5.14
551 554 4.837093 TTCAGGACAAGTATTTCCGGAT 57.163 40.909 4.15 0.00 36.20 4.18
552 555 4.137116 TCAGGACAAGTATTTCCGGATG 57.863 45.455 4.15 0.97 36.95 3.51
553 556 3.118408 TCAGGACAAGTATTTCCGGATGG 60.118 47.826 4.15 0.00 36.95 3.51
554 557 3.112263 AGGACAAGTATTTCCGGATGGA 58.888 45.455 4.15 0.00 44.61 3.41
590 593 5.376854 AAATAAGCAATGATCGTATGGCC 57.623 39.130 0.00 0.00 0.00 5.36
591 594 2.645838 AAGCAATGATCGTATGGCCT 57.354 45.000 3.32 0.00 0.00 5.19
593 596 1.417517 AGCAATGATCGTATGGCCTCA 59.582 47.619 3.32 0.00 0.00 3.86
596 599 3.254166 GCAATGATCGTATGGCCTCAAAT 59.746 43.478 3.32 0.00 0.00 2.32
597 600 4.261741 GCAATGATCGTATGGCCTCAAATT 60.262 41.667 3.32 0.00 0.00 1.82
598 601 5.217393 CAATGATCGTATGGCCTCAAATTG 58.783 41.667 3.32 0.00 0.00 2.32
599 602 2.618241 TGATCGTATGGCCTCAAATTGC 59.382 45.455 3.32 0.00 0.00 3.56
607 610 2.531522 GCCTCAAATTGCCAACACTT 57.468 45.000 0.00 0.00 0.00 3.16
608 611 2.837498 GCCTCAAATTGCCAACACTTT 58.163 42.857 0.00 0.00 0.00 2.66
609 612 2.802247 GCCTCAAATTGCCAACACTTTC 59.198 45.455 0.00 0.00 0.00 2.62
610 613 3.493176 GCCTCAAATTGCCAACACTTTCT 60.493 43.478 0.00 0.00 0.00 2.52
612 615 4.508861 CCTCAAATTGCCAACACTTTCTTG 59.491 41.667 0.00 0.00 0.00 3.02
615 618 3.733443 ATTGCCAACACTTTCTTGACC 57.267 42.857 0.00 0.00 0.00 4.02
618 621 1.268539 GCCAACACTTTCTTGACCACG 60.269 52.381 0.00 0.00 0.00 4.94
629 632 2.432628 GACCACGCTTGCGCTACT 60.433 61.111 15.21 0.00 0.00 2.57
637 640 1.059264 CGCTTGCGCTACTTACTTCAC 59.941 52.381 9.73 0.00 0.00 3.18
641 644 1.616865 TGCGCTACTTACTTCACCAGT 59.383 47.619 9.73 0.00 39.87 4.00
657 660 4.161565 TCACCAGTGACAAGTTTACTGTCT 59.838 41.667 13.68 1.63 40.04 3.41
662 665 5.041940 AGTGACAAGTTTACTGTCTCGTTC 58.958 41.667 4.74 0.00 34.03 3.95
680 694 1.963172 TCCATGTGAGCTGATGATGC 58.037 50.000 0.00 0.00 0.00 3.91
832 847 2.279741 TGCACCAATAGCATCGAAGAC 58.720 47.619 0.00 0.00 42.51 3.01
955 993 2.069273 CGTCTCAAACCATCTCCACAC 58.931 52.381 0.00 0.00 0.00 3.82
956 994 2.427506 GTCTCAAACCATCTCCACACC 58.572 52.381 0.00 0.00 0.00 4.16
957 995 1.351017 TCTCAAACCATCTCCACACCC 59.649 52.381 0.00 0.00 0.00 4.61
958 996 1.073763 CTCAAACCATCTCCACACCCA 59.926 52.381 0.00 0.00 0.00 4.51
994 1048 2.692741 ACCTCCCCTGCCTTAGCC 60.693 66.667 0.00 0.00 38.69 3.93
1089 1143 3.003173 CTCCTTGGTGAGGCCCGA 61.003 66.667 0.00 0.00 45.87 5.14
1365 1419 1.174712 AGCTTCTTGCACGCAATGGT 61.175 50.000 4.68 2.20 45.94 3.55
1377 1431 0.951558 GCAATGGTGTCAAGTTCGGT 59.048 50.000 0.00 0.00 0.00 4.69
1401 1455 3.670377 GTGTGGTTCAAGGCCGGC 61.670 66.667 21.18 21.18 0.00 6.13
1407 1461 3.575247 TTCAAGGCCGGCTCCCAA 61.575 61.111 28.56 11.80 0.00 4.12
1410 1464 1.984026 CAAGGCCGGCTCCCAAATT 60.984 57.895 28.56 7.13 0.00 1.82
1422 1476 0.108662 CCCAAATTTTCAGCGAGGGC 60.109 55.000 0.00 0.00 40.37 5.19
1506 1560 1.003355 CCAAGTCGTGCTCATGGGT 60.003 57.895 0.00 0.00 0.00 4.51
1551 1605 1.002134 CGGCCCACTTGGTGAGATT 60.002 57.895 0.00 0.00 35.23 2.40
1726 1780 2.283529 GGCCCACTCGAGAACCTCA 61.284 63.158 21.68 0.00 0.00 3.86
2111 9955 1.668628 CCCGTTTGCTTGTATGGTTGC 60.669 52.381 0.00 0.00 0.00 4.17
2117 9965 0.526096 GCTTGTATGGTTGCATGCCG 60.526 55.000 16.68 0.00 34.10 5.69
2134 9982 2.322081 CGGCCCCAACGTTGTACAG 61.322 63.158 25.63 11.01 0.00 2.74
2149 9997 5.854866 CGTTGTACAGAGAGTCATTTTCGTA 59.145 40.000 0.00 0.00 0.00 3.43
2150 9998 6.032565 CGTTGTACAGAGAGTCATTTTCGTAG 59.967 42.308 0.00 0.00 0.00 3.51
2151 9999 6.570672 TGTACAGAGAGTCATTTTCGTAGT 57.429 37.500 0.00 0.00 0.00 2.73
2167 10015 6.939551 TTCGTAGTGTTTTACTAGTGCATC 57.060 37.500 5.39 0.00 42.37 3.91
2169 10017 4.259292 CGTAGTGTTTTACTAGTGCATCGC 60.259 45.833 5.39 0.92 42.37 4.58
2170 10018 3.659786 AGTGTTTTACTAGTGCATCGCA 58.340 40.909 5.39 0.00 38.04 5.10
2360 10213 5.989777 GCATAGACGTATTTTATGGACAGGT 59.010 40.000 0.00 0.00 0.00 4.00
2367 10224 9.355215 GACGTATTTTATGGACAGGTATATCTG 57.645 37.037 11.62 11.62 40.40 2.90
2431 10288 4.858935 TGCAACGGAAGAAAAAGATTGAG 58.141 39.130 0.00 0.00 0.00 3.02
2446 10303 6.801539 AAGATTGAGAACGCTTGATTACAA 57.198 33.333 0.00 0.00 34.65 2.41
2499 10356 3.461773 ACCACCAGATCCGAGCGG 61.462 66.667 1.74 1.74 0.00 5.52
2574 10431 1.681793 CTAGACACACCACCGGGATAG 59.318 57.143 6.32 0.00 38.05 2.08
2603 10460 5.403512 AGACGGGGAGAATCTTATTCCATA 58.596 41.667 0.00 0.00 33.73 2.74
2636 10494 2.288273 CCTTCGTCTCGTCTTCCAAAGT 60.288 50.000 0.00 0.00 0.00 2.66
2691 10549 2.104281 TCTAAAAATAGAGCCCTCCCGC 59.896 50.000 0.00 0.00 0.00 6.13
2739 10597 1.306654 ATGGCCCTAAGACCACCGA 60.307 57.895 0.00 0.00 39.19 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.579684 ATTCCCGTTGCTCCTCTCGC 62.580 60.000 0.00 0.00 0.00 5.03
29 30 6.073058 GCCTCCAAATTTCAACAAAAGATTCC 60.073 38.462 0.00 0.00 0.00 3.01
46 47 3.675775 GCATAAATTTGAGCGCCTCCAAA 60.676 43.478 18.19 18.19 0.00 3.28
49 50 1.678101 AGCATAAATTTGAGCGCCTCC 59.322 47.619 2.29 0.00 0.00 4.30
73 74 2.893398 AGCCTCGTAAGCTTCCCG 59.107 61.111 0.00 7.22 37.24 5.14
79 80 6.716898 TTTAAGAAGTTAAGCCTCGTAAGC 57.283 37.500 0.00 0.00 29.71 3.09
83 84 7.506328 ACAAATTTAAGAAGTTAAGCCTCGT 57.494 32.000 0.00 0.00 29.71 4.18
106 107 7.541162 ACCAAAACCTCAAACAGTTAACTAAC 58.459 34.615 8.04 0.00 36.46 2.34
108 109 7.706100 AACCAAAACCTCAAACAGTTAACTA 57.294 32.000 8.04 0.00 0.00 2.24
148 149 8.469309 ACTCTTCAAAGGATTTCATTTTGAGA 57.531 30.769 13.81 8.29 40.63 3.27
176 177 3.964909 ACTGTGAATTCTCAAAAACGCC 58.035 40.909 11.11 0.00 31.88 5.68
194 195 4.331168 GGCAACTTAGAGCATCACTAACTG 59.669 45.833 4.24 0.00 37.82 3.16
195 196 4.020218 TGGCAACTTAGAGCATCACTAACT 60.020 41.667 4.24 0.00 35.07 2.24
257 258 9.187455 GTAAATAACACCAATGGTAAACACAAG 57.813 33.333 3.85 0.00 32.11 3.16
314 316 1.676006 AGCCACGTCTTGAAAACAAGG 59.324 47.619 9.54 0.00 33.26 3.61
382 385 9.832445 ATCTGAGAATACACCACGTAAAAATAT 57.168 29.630 0.00 0.00 32.59 1.28
436 439 5.061853 GGACGGAGGAAGTACTTTCTTTTT 58.938 41.667 17.72 4.98 36.03 1.94
437 440 4.639334 GGACGGAGGAAGTACTTTCTTTT 58.361 43.478 17.72 5.33 36.03 2.27
450 453 1.479323 CAAGTATTTCCGGACGGAGGA 59.521 52.381 13.64 7.39 46.06 3.71
451 454 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
452 455 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
453 456 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
454 457 1.648504 GGACAAGTATTTCCGGACGG 58.351 55.000 1.83 3.96 0.00 4.79
455 458 1.066716 TGGGACAAGTATTTCCGGACG 60.067 52.381 1.83 0.00 31.92 4.79
456 459 2.235402 TCTGGGACAAGTATTTCCGGAC 59.765 50.000 1.83 0.00 38.70 4.79
457 460 2.542550 TCTGGGACAAGTATTTCCGGA 58.457 47.619 0.00 0.00 38.70 5.14
458 461 3.343941 TTCTGGGACAAGTATTTCCGG 57.656 47.619 0.00 0.00 38.70 5.14
459 462 4.941263 TCATTTCTGGGACAAGTATTTCCG 59.059 41.667 0.00 0.00 38.70 4.30
460 463 6.834168 TTCATTTCTGGGACAAGTATTTCC 57.166 37.500 0.00 0.00 38.70 3.13
465 468 9.527157 TCATTTTATTCATTTCTGGGACAAGTA 57.473 29.630 0.00 0.00 38.70 2.24
466 469 8.421249 TCATTTTATTCATTTCTGGGACAAGT 57.579 30.769 0.00 0.00 38.70 3.16
467 470 9.880157 ATTCATTTTATTCATTTCTGGGACAAG 57.120 29.630 0.00 0.00 38.70 3.16
468 471 9.656040 CATTCATTTTATTCATTTCTGGGACAA 57.344 29.630 0.00 0.00 38.70 3.18
469 472 8.814931 ACATTCATTTTATTCATTTCTGGGACA 58.185 29.630 0.00 0.00 0.00 4.02
515 518 9.003658 ACTTGTCCTGAAAATTGTTGTATCTAG 57.996 33.333 0.00 0.00 0.00 2.43
516 519 8.918202 ACTTGTCCTGAAAATTGTTGTATCTA 57.082 30.769 0.00 0.00 0.00 1.98
517 520 7.823745 ACTTGTCCTGAAAATTGTTGTATCT 57.176 32.000 0.00 0.00 0.00 1.98
520 523 9.959749 GAAATACTTGTCCTGAAAATTGTTGTA 57.040 29.630 0.00 0.00 0.00 2.41
521 524 7.926018 GGAAATACTTGTCCTGAAAATTGTTGT 59.074 33.333 0.00 0.00 0.00 3.32
522 525 7.114811 CGGAAATACTTGTCCTGAAAATTGTTG 59.885 37.037 0.00 0.00 0.00 3.33
523 526 7.145323 CGGAAATACTTGTCCTGAAAATTGTT 58.855 34.615 0.00 0.00 0.00 2.83
524 527 6.294508 CCGGAAATACTTGTCCTGAAAATTGT 60.295 38.462 0.00 0.00 0.00 2.71
525 528 6.072175 TCCGGAAATACTTGTCCTGAAAATTG 60.072 38.462 0.00 0.00 0.00 2.32
526 529 6.007703 TCCGGAAATACTTGTCCTGAAAATT 58.992 36.000 0.00 0.00 0.00 1.82
527 530 5.566469 TCCGGAAATACTTGTCCTGAAAAT 58.434 37.500 0.00 0.00 0.00 1.82
528 531 4.975631 TCCGGAAATACTTGTCCTGAAAA 58.024 39.130 0.00 0.00 0.00 2.29
529 532 4.627284 TCCGGAAATACTTGTCCTGAAA 57.373 40.909 0.00 0.00 0.00 2.69
530 533 4.513442 CATCCGGAAATACTTGTCCTGAA 58.487 43.478 9.01 0.00 31.85 3.02
531 534 3.118408 CCATCCGGAAATACTTGTCCTGA 60.118 47.826 9.01 0.00 32.51 3.86
532 535 3.118408 TCCATCCGGAAATACTTGTCCTG 60.118 47.826 9.01 0.00 38.83 3.86
533 536 3.112263 TCCATCCGGAAATACTTGTCCT 58.888 45.455 9.01 0.00 38.83 3.85
534 537 3.467803 CTCCATCCGGAAATACTTGTCC 58.532 50.000 9.01 0.00 42.21 4.02
535 538 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
536 539 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
537 540 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
538 541 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
539 542 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
540 543 2.047830 ACTCCCTCCATCCGGAAATAC 58.952 52.381 9.01 0.00 42.21 1.89
541 544 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
542 545 2.489528 TACTCCCTCCATCCGGAAAT 57.510 50.000 9.01 0.00 42.21 2.17
543 546 2.257391 TTACTCCCTCCATCCGGAAA 57.743 50.000 9.01 0.00 42.21 3.13
544 547 2.489528 ATTACTCCCTCCATCCGGAA 57.510 50.000 9.01 0.00 42.21 4.30
545 548 3.623466 TTATTACTCCCTCCATCCGGA 57.377 47.619 6.61 6.61 39.79 5.14
546 549 4.699925 TTTTATTACTCCCTCCATCCGG 57.300 45.455 0.00 0.00 0.00 5.14
572 575 2.158769 TGAGGCCATACGATCATTGCTT 60.159 45.455 5.01 0.00 0.00 3.91
574 577 1.882912 TGAGGCCATACGATCATTGC 58.117 50.000 5.01 0.00 0.00 3.56
576 579 4.261741 GCAATTTGAGGCCATACGATCATT 60.262 41.667 5.01 0.00 0.00 2.57
577 580 3.254166 GCAATTTGAGGCCATACGATCAT 59.746 43.478 5.01 0.00 0.00 2.45
578 581 2.618241 GCAATTTGAGGCCATACGATCA 59.382 45.455 5.01 0.00 0.00 2.92
579 582 3.273919 GCAATTTGAGGCCATACGATC 57.726 47.619 5.01 0.00 0.00 3.69
588 591 2.531522 AAGTGTTGGCAATTTGAGGC 57.468 45.000 1.92 0.00 27.29 4.70
589 592 4.326504 AGAAAGTGTTGGCAATTTGAGG 57.673 40.909 1.92 0.00 42.06 3.86
590 593 5.232838 GTCAAGAAAGTGTTGGCAATTTGAG 59.767 40.000 1.92 0.00 42.06 3.02
591 594 5.108517 GTCAAGAAAGTGTTGGCAATTTGA 58.891 37.500 1.92 3.27 42.06 2.69
593 596 4.081198 TGGTCAAGAAAGTGTTGGCAATTT 60.081 37.500 1.92 0.00 44.25 1.82
596 599 2.165437 GTGGTCAAGAAAGTGTTGGCAA 59.835 45.455 0.00 0.00 30.75 4.52
597 600 1.748493 GTGGTCAAGAAAGTGTTGGCA 59.252 47.619 0.00 0.00 30.75 4.92
598 601 1.268539 CGTGGTCAAGAAAGTGTTGGC 60.269 52.381 0.00 0.00 0.00 4.52
599 602 1.268539 GCGTGGTCAAGAAAGTGTTGG 60.269 52.381 0.00 0.00 0.00 3.77
600 603 1.670811 AGCGTGGTCAAGAAAGTGTTG 59.329 47.619 0.00 0.00 0.00 3.33
601 604 2.038387 AGCGTGGTCAAGAAAGTGTT 57.962 45.000 0.00 0.00 0.00 3.32
602 605 1.670811 CAAGCGTGGTCAAGAAAGTGT 59.329 47.619 0.00 0.00 0.00 3.55
603 606 1.597937 GCAAGCGTGGTCAAGAAAGTG 60.598 52.381 0.79 0.00 0.00 3.16
604 607 0.663153 GCAAGCGTGGTCAAGAAAGT 59.337 50.000 0.79 0.00 0.00 2.66
605 608 0.384725 CGCAAGCGTGGTCAAGAAAG 60.385 55.000 6.25 0.00 34.35 2.62
606 609 1.646540 CGCAAGCGTGGTCAAGAAA 59.353 52.632 6.25 0.00 34.35 2.52
607 610 3.329231 CGCAAGCGTGGTCAAGAA 58.671 55.556 6.25 0.00 34.35 2.52
629 632 6.537301 CAGTAAACTTGTCACTGGTGAAGTAA 59.463 38.462 4.92 1.63 41.85 2.24
637 640 3.736252 CGAGACAGTAAACTTGTCACTGG 59.264 47.826 15.27 3.67 43.18 4.00
641 644 4.142116 TGGAACGAGACAGTAAACTTGTCA 60.142 41.667 7.96 0.00 35.23 3.58
657 660 1.550072 TCATCAGCTCACATGGAACGA 59.450 47.619 0.00 0.00 0.00 3.85
662 665 0.586802 CGCATCATCAGCTCACATGG 59.413 55.000 0.00 0.00 0.00 3.66
680 694 1.135046 GGATCACATGTCGATGCTCG 58.865 55.000 16.72 0.00 42.10 5.03
845 860 9.610705 GTACCGACAAGATAGATATATACAGGA 57.389 37.037 0.00 0.00 0.00 3.86
849 864 9.985318 GTGTGTACCGACAAGATAGATATATAC 57.015 37.037 0.00 0.00 37.31 1.47
955 993 2.291741 GCAGTGAAAACTGAAGAGTGGG 59.708 50.000 9.97 0.00 39.99 4.61
956 994 2.945008 TGCAGTGAAAACTGAAGAGTGG 59.055 45.455 9.97 0.00 39.99 4.00
957 995 3.242870 GGTGCAGTGAAAACTGAAGAGTG 60.243 47.826 9.97 0.00 39.99 3.51
958 996 2.945668 GGTGCAGTGAAAACTGAAGAGT 59.054 45.455 9.97 0.00 39.99 3.24
976 1014 2.592308 GCTAAGGCAGGGGAGGTG 59.408 66.667 0.00 0.00 38.54 4.00
977 1015 2.692741 GGCTAAGGCAGGGGAGGT 60.693 66.667 0.00 0.00 40.87 3.85
978 1016 3.866582 CGGCTAAGGCAGGGGAGG 61.867 72.222 0.00 0.00 40.87 4.30
979 1017 4.554036 GCGGCTAAGGCAGGGGAG 62.554 72.222 0.00 0.00 40.87 4.30
1075 1129 2.266055 GACTCGGGCCTCACCAAG 59.734 66.667 0.84 0.00 42.05 3.61
1089 1143 0.458543 CGGTCTTGCGCATAGTGACT 60.459 55.000 12.75 0.00 0.00 3.41
1362 1416 0.105964 CCTCACCGAACTTGACACCA 59.894 55.000 0.00 0.00 0.00 4.17
1365 1419 1.070786 GGCCTCACCGAACTTGACA 59.929 57.895 0.00 0.00 0.00 3.58
1377 1431 1.227823 CTTGAACCACACGGCCTCA 60.228 57.895 0.00 0.00 34.57 3.86
1386 1440 3.056328 GAGCCGGCCTTGAACCAC 61.056 66.667 26.15 0.00 0.00 4.16
1401 1455 1.474077 CCCTCGCTGAAAATTTGGGAG 59.526 52.381 11.81 11.81 39.48 4.30
1407 1461 2.700773 GCCGCCCTCGCTGAAAATT 61.701 57.895 0.00 0.00 0.00 1.82
1422 1476 3.528370 CCCAGGTAGTCGAGGCCG 61.528 72.222 0.00 0.00 37.07 6.13
1506 1560 3.697747 CGGTACCCCTCAACGGCA 61.698 66.667 6.25 0.00 0.00 5.69
1551 1605 1.304713 GGGGTAGAGTGGGTCGACA 60.305 63.158 18.91 0.00 32.61 4.35
1596 1650 3.838271 GCCTCTGGATCGTCGGCA 61.838 66.667 8.51 0.00 40.41 5.69
1726 1780 2.675772 GTCGGAGAGGTGGTCGGT 60.676 66.667 0.00 0.00 36.95 4.69
2117 9965 0.953960 CTCTGTACAACGTTGGGGCC 60.954 60.000 30.34 15.61 0.00 5.80
2134 9982 8.295569 AGTAAAACACTACGAAAATGACTCTC 57.704 34.615 0.00 0.00 34.98 3.20
2149 9997 3.659786 TGCGATGCACTAGTAAAACACT 58.340 40.909 0.00 0.00 35.85 3.55
2150 9998 4.398549 TTGCGATGCACTAGTAAAACAC 57.601 40.909 0.00 0.00 38.71 3.32
2151 9999 4.968626 CATTGCGATGCACTAGTAAAACA 58.031 39.130 0.00 0.00 38.71 2.83
2167 10015 3.245754 ACTTTGACAAACATTGCATTGCG 59.754 39.130 8.48 0.85 0.00 4.85
2169 10017 5.005586 ACGAACTTTGACAAACATTGCATTG 59.994 36.000 7.04 7.04 0.00 2.82
2170 10018 5.108517 ACGAACTTTGACAAACATTGCATT 58.891 33.333 0.00 0.00 0.00 3.56
2203 10051 2.482494 CCTCTAGGTTCAGGGGTGATT 58.518 52.381 0.00 0.00 30.77 2.57
2367 10224 7.577107 GCTAGTACAAGCAAAATTATAGAGCC 58.423 38.462 0.00 0.00 42.30 4.70
2446 10303 2.261671 GTGTCGCCACGTCCATCT 59.738 61.111 0.00 0.00 0.00 2.90
2476 10333 0.400213 TCGGATCTGGTGGTGCTTTT 59.600 50.000 0.62 0.00 0.00 2.27
2574 10431 1.459730 ATTCTCCCCGTCTAGCCCC 60.460 63.158 0.00 0.00 0.00 5.80
2603 10460 2.187946 CGAAGGCGGCTCCTGAAT 59.812 61.111 13.70 0.00 46.94 2.57
2636 10494 4.101430 AGTTTTGTTAGGTTCCGTGTCCTA 59.899 41.667 0.00 0.00 35.51 2.94
2691 10549 2.123982 GATCCTGGCCCTTGCAGG 60.124 66.667 0.00 0.00 40.13 4.85
2739 10597 1.211969 CATCGGTCCACGTCGTCTT 59.788 57.895 0.00 0.00 44.69 3.01


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

AutoCloner maintained by Alex Coulton.