Multiple sequence alignment - TraesCS7D01G449000

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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 TraesCS7D01G449000 chr7D 100.000 2387 0 0 1 2387 568421915 568419529 0.000000e+00 4409.0
1 TraesCS7D01G449000 chr7D 81.057 776 86 46 1526 2249 7465502 7466268 1.600000e-156 562.0
2 TraesCS7D01G449000 chr7D 81.453 647 95 16 883 1518 568698536 568699168 7.610000e-140 507.0
3 TraesCS7D01G449000 chr7D 80.804 448 44 20 1540 1961 7458080 7458511 1.780000e-81 313.0
4 TraesCS7D01G449000 chr7D 92.727 165 11 1 403 566 522510312 522510476 1.100000e-58 237.0
5 TraesCS7D01G449000 chr7D 91.489 94 7 1 1919 2012 9304773 9304865 6.930000e-26 128.0
6 TraesCS7D01G449000 chr7D 96.154 78 3 0 1926 2003 10507782 10507705 6.930000e-26 128.0
7 TraesCS7D01G449000 chr7D 84.783 92 9 4 279 370 596112583 596112497 1.180000e-13 87.9
8 TraesCS7D01G449000 chr7A 93.209 1502 74 12 892 2387 657156294 657154815 0.000000e+00 2183.0
9 TraesCS7D01G449000 chr7A 85.577 520 49 15 1525 2018 8403689 8404208 2.720000e-144 521.0
10 TraesCS7D01G449000 chr7A 85.577 520 49 15 1525 2018 8410501 8411020 2.720000e-144 521.0
11 TraesCS7D01G449000 chr7A 82.394 568 81 16 883 1440 657431510 657430952 5.970000e-131 477.0
12 TraesCS7D01G449000 chr7A 89.206 315 19 6 575 889 657156796 657156497 1.730000e-101 379.0
13 TraesCS7D01G449000 chr7A 88.841 233 18 4 1 233 657157159 657156935 1.810000e-71 279.0
14 TraesCS7D01G449000 chr7A 83.193 238 31 5 1471 1703 657424760 657424527 2.400000e-50 209.0
15 TraesCS7D01G449000 chr7A 88.235 85 6 3 279 363 689268891 689268811 5.430000e-17 99.0
16 TraesCS7D01G449000 chr7B 93.849 943 37 6 1448 2387 624247001 624246077 0.000000e+00 1400.0
17 TraesCS7D01G449000 chr7B 85.106 470 65 3 883 1350 624791784 624791318 2.150000e-130 475.0
18 TraesCS7D01G449000 chr7B 92.195 205 13 1 1249 1453 624247680 624247479 1.080000e-73 287.0
19 TraesCS7D01G449000 chr7B 83.708 178 22 2 1428 1605 624791285 624791115 6.830000e-36 161.0
20 TraesCS7D01G449000 chr4A 81.398 758 86 38 1530 2249 732788795 732789535 3.440000e-158 568.0
21 TraesCS7D01G449000 chr5D 87.361 269 31 2 1 267 277630914 277631181 2.980000e-79 305.0
22 TraesCS7D01G449000 chr5D 86.166 253 26 5 2 251 553012028 553012274 5.060000e-67 265.0
23 TraesCS7D01G449000 chr5D 93.373 166 10 1 402 566 60139910 60139745 6.590000e-61 244.0
24 TraesCS7D01G449000 chr5A 79.140 465 80 11 883 1341 60246374 60246827 2.980000e-79 305.0
25 TraesCS7D01G449000 chr5B 87.132 272 29 4 1 267 315832014 315832284 1.070000e-78 303.0
26 TraesCS7D01G449000 chr2D 86.486 259 24 9 1 253 453785383 453785636 8.410000e-70 274.0
27 TraesCS7D01G449000 chr2D 92.216 167 12 1 402 567 595489269 595489435 3.970000e-58 235.0
28 TraesCS7D01G449000 chr6D 87.069 232 25 4 41 267 83059152 83058921 8.470000e-65 257.0
29 TraesCS7D01G449000 chr6D 92.090 177 11 3 403 576 79346849 79347025 1.830000e-61 246.0
30 TraesCS7D01G449000 chr6D 80.827 266 45 6 1 262 69296948 69297211 1.120000e-48 204.0
31 TraesCS7D01G449000 chr6D 80.556 252 37 9 2 243 82465788 82466037 1.460000e-42 183.0
32 TraesCS7D01G449000 chr3D 93.373 166 10 1 403 567 560940499 560940664 6.590000e-61 244.0
33 TraesCS7D01G449000 chr3D 92.857 168 11 1 401 567 396430333 396430166 2.370000e-60 243.0
34 TraesCS7D01G449000 chr3D 91.765 170 13 1 403 571 94507526 94507357 3.970000e-58 235.0
35 TraesCS7D01G449000 chr3D 82.573 241 34 4 1 237 526986246 526986482 3.110000e-49 206.0
36 TraesCS7D01G449000 chr3A 92.771 166 11 1 402 566 40915055 40914890 3.070000e-59 239.0
37 TraesCS7D01G449000 chr3A 83.401 247 35 4 1 243 661491136 661491380 8.590000e-55 224.0
38 TraesCS7D01G449000 chr4D 92.262 168 12 1 400 566 316527354 316527521 1.100000e-58 237.0


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 TraesCS7D01G449000 chr7D 568419529 568421915 2386 True 4409.0 4409 100.000000 1 2387 1 chr7D.!!$R2 2386
1 TraesCS7D01G449000 chr7D 7465502 7466268 766 False 562.0 562 81.057000 1526 2249 1 chr7D.!!$F2 723
2 TraesCS7D01G449000 chr7D 568698536 568699168 632 False 507.0 507 81.453000 883 1518 1 chr7D.!!$F5 635
3 TraesCS7D01G449000 chr7A 657154815 657157159 2344 True 947.0 2183 90.418667 1 2387 3 chr7A.!!$R4 2386
4 TraesCS7D01G449000 chr7A 8403689 8404208 519 False 521.0 521 85.577000 1525 2018 1 chr7A.!!$F1 493
5 TraesCS7D01G449000 chr7A 8410501 8411020 519 False 521.0 521 85.577000 1525 2018 1 chr7A.!!$F2 493
6 TraesCS7D01G449000 chr7A 657430952 657431510 558 True 477.0 477 82.394000 883 1440 1 chr7A.!!$R2 557
7 TraesCS7D01G449000 chr7B 624246077 624247680 1603 True 843.5 1400 93.022000 1249 2387 2 chr7B.!!$R1 1138
8 TraesCS7D01G449000 chr7B 624791115 624791784 669 True 318.0 475 84.407000 883 1605 2 chr7B.!!$R2 722
9 TraesCS7D01G449000 chr4A 732788795 732789535 740 False 568.0 568 81.398000 1530 2249 1 chr4A.!!$F1 719

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
784 792 0.528017 GAGTCGTGTGAGATCTGCCA 59.472 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2773 1.592743 GCAGCAATGGTGGCAATGA 59.407 52.632 14.61 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
149 150 7.881775 AAATAGGTTTCCAGTGGAATATGTC 57.118 36.000 25.12 12.51 41.71 3.06
151 152 2.943033 GGTTTCCAGTGGAATATGTCGG 59.057 50.000 25.12 0.00 41.71 4.79
157 158 4.080582 TCCAGTGGAATATGTCGGTTTCAT 60.081 41.667 10.20 0.00 0.00 2.57
244 245 8.596380 GGAATGTGAAACGTCAAAAATTAAACA 58.404 29.630 0.00 0.00 42.39 2.83
246 247 9.913451 AATGTGAAACGTCAAAAATTAAACATG 57.087 25.926 0.00 0.00 42.39 3.21
253 254 9.965748 AACGTCAAAAATTAAACATGTTTCAAG 57.034 25.926 26.46 11.18 34.23 3.02
264 265 7.823745 AAACATGTTTCAAGTGAATCTAGGT 57.176 32.000 18.13 0.00 33.54 3.08
265 266 7.823745 AACATGTTTCAAGTGAATCTAGGTT 57.176 32.000 4.92 0.00 33.54 3.50
266 267 7.823745 ACATGTTTCAAGTGAATCTAGGTTT 57.176 32.000 0.00 0.00 33.54 3.27
267 268 8.237811 ACATGTTTCAAGTGAATCTAGGTTTT 57.762 30.769 0.00 0.00 33.54 2.43
268 269 8.695456 ACATGTTTCAAGTGAATCTAGGTTTTT 58.305 29.630 0.00 0.00 33.54 1.94
290 291 5.873179 TTTTCCGGCAAAAGTGTATCTAG 57.127 39.130 0.00 0.00 30.07 2.43
291 292 3.536956 TCCGGCAAAAGTGTATCTAGG 57.463 47.619 0.00 0.00 0.00 3.02
319 320 7.453393 TGATCTTGTTCTAAAGGTCTTGATGT 58.547 34.615 0.00 0.00 38.02 3.06
332 333 6.251471 AGGTCTTGATGTCAGGAATTCAAAT 58.749 36.000 7.93 0.00 33.66 2.32
333 334 7.405292 AGGTCTTGATGTCAGGAATTCAAATA 58.595 34.615 7.93 0.00 33.66 1.40
334 335 8.057623 AGGTCTTGATGTCAGGAATTCAAATAT 58.942 33.333 7.93 0.00 33.66 1.28
335 336 9.342308 GGTCTTGATGTCAGGAATTCAAATATA 57.658 33.333 7.93 0.00 33.66 0.86
418 426 4.594123 TGATGTACTCACTCCGTTTCAA 57.406 40.909 0.00 0.00 0.00 2.69
419 427 4.951254 TGATGTACTCACTCCGTTTCAAA 58.049 39.130 0.00 0.00 0.00 2.69
420 428 5.361427 TGATGTACTCACTCCGTTTCAAAA 58.639 37.500 0.00 0.00 0.00 2.44
421 429 5.995282 TGATGTACTCACTCCGTTTCAAAAT 59.005 36.000 0.00 0.00 0.00 1.82
422 430 7.156000 TGATGTACTCACTCCGTTTCAAAATA 58.844 34.615 0.00 0.00 0.00 1.40
423 431 7.822334 TGATGTACTCACTCCGTTTCAAAATAT 59.178 33.333 0.00 0.00 0.00 1.28
424 432 9.309516 GATGTACTCACTCCGTTTCAAAATATA 57.690 33.333 0.00 0.00 0.00 0.86
425 433 9.661563 ATGTACTCACTCCGTTTCAAAATATAA 57.338 29.630 0.00 0.00 0.00 0.98
426 434 9.146984 TGTACTCACTCCGTTTCAAAATATAAG 57.853 33.333 0.00 0.00 0.00 1.73
427 435 9.148104 GTACTCACTCCGTTTCAAAATATAAGT 57.852 33.333 0.00 0.00 0.00 2.24
428 436 8.252964 ACTCACTCCGTTTCAAAATATAAGTC 57.747 34.615 0.00 0.00 0.00 3.01
429 437 8.095169 ACTCACTCCGTTTCAAAATATAAGTCT 58.905 33.333 0.00 0.00 0.00 3.24
430 438 8.842358 TCACTCCGTTTCAAAATATAAGTCTT 57.158 30.769 0.00 0.00 0.00 3.01
431 439 9.280174 TCACTCCGTTTCAAAATATAAGTCTTT 57.720 29.630 0.00 0.00 0.00 2.52
432 440 9.329913 CACTCCGTTTCAAAATATAAGTCTTTG 57.670 33.333 0.00 0.00 0.00 2.77
433 441 9.063615 ACTCCGTTTCAAAATATAAGTCTTTGT 57.936 29.630 0.00 0.00 32.92 2.83
461 469 9.347934 GAGATTTCAATAGATGACTACATACGG 57.652 37.037 0.00 0.00 37.92 4.02
462 470 9.078990 AGATTTCAATAGATGACTACATACGGA 57.921 33.333 0.00 0.00 37.92 4.69
463 471 9.347934 GATTTCAATAGATGACTACATACGGAG 57.652 37.037 0.00 0.00 37.92 4.63
464 472 6.255596 TCAATAGATGACTACATACGGAGC 57.744 41.667 0.00 0.00 36.82 4.70
465 473 5.768164 TCAATAGATGACTACATACGGAGCA 59.232 40.000 0.00 0.00 36.82 4.26
466 474 6.264518 TCAATAGATGACTACATACGGAGCAA 59.735 38.462 0.00 0.00 36.82 3.91
467 475 6.650427 ATAGATGACTACATACGGAGCAAA 57.350 37.500 0.00 0.00 36.82 3.68
468 476 5.339008 AGATGACTACATACGGAGCAAAA 57.661 39.130 0.00 0.00 36.82 2.44
469 477 5.918608 AGATGACTACATACGGAGCAAAAT 58.081 37.500 0.00 0.00 36.82 1.82
470 478 5.755375 AGATGACTACATACGGAGCAAAATG 59.245 40.000 0.00 0.00 36.82 2.32
471 479 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
472 480 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
473 481 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
474 482 6.127563 TGACTACATACGGAGCAAAATGAGTA 60.128 38.462 0.00 0.00 0.00 2.59
475 483 6.636705 ACTACATACGGAGCAAAATGAGTAA 58.363 36.000 0.00 0.00 0.00 2.24
476 484 7.101054 ACTACATACGGAGCAAAATGAGTAAA 58.899 34.615 0.00 0.00 0.00 2.01
477 485 7.769044 ACTACATACGGAGCAAAATGAGTAAAT 59.231 33.333 0.00 0.00 0.00 1.40
478 486 7.016361 ACATACGGAGCAAAATGAGTAAATC 57.984 36.000 0.00 0.00 0.00 2.17
479 487 6.823689 ACATACGGAGCAAAATGAGTAAATCT 59.176 34.615 0.00 0.00 0.00 2.40
480 488 7.985184 ACATACGGAGCAAAATGAGTAAATCTA 59.015 33.333 0.00 0.00 0.00 1.98
481 489 6.663944 ACGGAGCAAAATGAGTAAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
482 490 5.585047 ACGGAGCAAAATGAGTAAATCTACC 59.415 40.000 0.00 0.00 0.00 3.18
483 491 5.007724 CGGAGCAAAATGAGTAAATCTACCC 59.992 44.000 0.00 0.00 0.00 3.69
484 492 6.122964 GGAGCAAAATGAGTAAATCTACCCT 58.877 40.000 0.00 0.00 0.00 4.34
485 493 6.261158 GGAGCAAAATGAGTAAATCTACCCTC 59.739 42.308 0.00 0.00 0.00 4.30
486 494 6.963322 AGCAAAATGAGTAAATCTACCCTCT 58.037 36.000 0.00 0.00 0.00 3.69
487 495 8.090788 AGCAAAATGAGTAAATCTACCCTCTA 57.909 34.615 0.00 0.00 0.00 2.43
488 496 8.548877 AGCAAAATGAGTAAATCTACCCTCTAA 58.451 33.333 0.00 0.00 0.00 2.10
489 497 9.174166 GCAAAATGAGTAAATCTACCCTCTAAA 57.826 33.333 0.00 0.00 0.00 1.85
573 581 4.946445 GGAACGGAGGGAGTATTTAAGAG 58.054 47.826 0.00 0.00 0.00 2.85
604 612 7.011857 AGAGAGTTTGTGCTTAAGTCAGAAAAG 59.988 37.037 17.42 0.00 30.24 2.27
605 613 6.823689 AGAGTTTGTGCTTAAGTCAGAAAAGA 59.176 34.615 17.42 1.86 30.24 2.52
606 614 7.011857 AGAGTTTGTGCTTAAGTCAGAAAAGAG 59.988 37.037 17.42 0.00 30.24 2.85
607 615 6.823689 AGTTTGTGCTTAAGTCAGAAAAGAGA 59.176 34.615 17.42 1.34 30.24 3.10
608 616 6.851222 TTGTGCTTAAGTCAGAAAAGAGAG 57.149 37.500 4.02 0.00 0.00 3.20
665 673 4.920640 ATGATACTAGAACCTGTGTCCG 57.079 45.455 0.00 0.00 0.00 4.79
666 674 2.426024 TGATACTAGAACCTGTGTCCGC 59.574 50.000 0.00 0.00 0.00 5.54
728 736 0.773644 ATACATCTGGGTGGGCCATC 59.226 55.000 10.70 9.68 36.17 3.51
735 743 2.590092 GGTGGGCCATCGCTACTT 59.410 61.111 10.70 0.00 34.44 2.24
748 756 1.336332 CGCTACTTCCATAGCTCGCAT 60.336 52.381 0.00 0.00 44.60 4.73
758 766 2.688364 TAGCTCGCATGTATCTCACG 57.312 50.000 0.00 0.00 0.00 4.35
784 792 0.528017 GAGTCGTGTGAGATCTGCCA 59.472 55.000 0.00 0.00 0.00 4.92
801 809 1.672356 CACTTGGCCACCTTCCTCG 60.672 63.158 3.88 0.00 0.00 4.63
904 1112 2.663196 CGAGGTGTTCCTGTCCCC 59.337 66.667 0.00 0.00 45.24 4.81
985 1193 3.443045 GTGCCATTCGCCCTGGTG 61.443 66.667 0.00 0.00 36.10 4.17
1049 1259 4.008933 GACCTGCGCCTGGTCACT 62.009 66.667 31.68 10.07 46.90 3.41
1102 1312 1.803922 CGTTCGTGCTCATGCCGTA 60.804 57.895 0.00 0.00 38.71 4.02
1138 1348 4.446413 GACCTGTGTACCCGCCCG 62.446 72.222 0.00 0.00 0.00 6.13
1185 1395 4.702081 ACAGCCGTCGACGCTGTC 62.702 66.667 38.19 25.46 45.85 3.51
1211 1421 1.602605 TCACCGACTTCTGCCTCGA 60.603 57.895 0.00 0.00 31.24 4.04
1415 1641 6.140786 TCAATCAATCGTAGCATCGTACTAC 58.859 40.000 0.00 0.00 37.29 2.73
1416 1642 5.943706 ATCAATCGTAGCATCGTACTACT 57.056 39.130 9.42 0.00 38.27 2.57
1417 1643 7.172019 TCAATCAATCGTAGCATCGTACTACTA 59.828 37.037 9.42 1.64 38.27 1.82
1458 2174 4.299155 ACTGTCATTGACGAACACTACAG 58.701 43.478 11.97 0.00 38.05 2.74
1524 2240 5.822584 TGTGCGTAATTAATCTGCTATCG 57.177 39.130 7.69 0.00 0.00 2.92
1525 2241 4.149922 TGTGCGTAATTAATCTGCTATCGC 59.850 41.667 0.00 0.00 41.17 4.58
1699 2439 4.128388 TCGATGAAGAGGCGCGCA 62.128 61.111 34.42 11.89 0.00 6.09
2140 2943 5.482908 TCTTATTCCTCAGCTCAACTTGTC 58.517 41.667 0.00 0.00 0.00 3.18
2287 3092 2.125350 CTCCTCTCGCTTGGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
2309 3114 5.050490 GCTAATCTCAGCCGTTGATTTCTA 58.950 41.667 0.00 0.00 35.40 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 8.533569 ACCTATTTACCCCAAATATGAAACTG 57.466 34.615 0.00 0.00 38.21 3.16
110 111 8.983789 GGAAACCTATTTACCCCAAATATGAAA 58.016 33.333 0.00 0.00 38.21 2.69
111 112 8.123130 TGGAAACCTATTTACCCCAAATATGAA 58.877 33.333 0.00 0.00 38.21 2.57
112 113 7.653503 TGGAAACCTATTTACCCCAAATATGA 58.346 34.615 0.00 0.00 38.21 2.15
113 114 7.563556 ACTGGAAACCTATTTACCCCAAATATG 59.436 37.037 0.00 0.00 38.21 1.78
114 115 7.563556 CACTGGAAACCTATTTACCCCAAATAT 59.436 37.037 0.00 0.00 38.21 1.28
115 116 6.893005 CACTGGAAACCTATTTACCCCAAATA 59.107 38.462 0.00 0.00 37.93 1.40
116 117 5.719563 CACTGGAAACCTATTTACCCCAAAT 59.280 40.000 0.00 0.00 40.10 2.32
229 230 9.407514 CACTTGAAACATGTTTAATTTTTGACG 57.592 29.630 23.33 6.28 32.11 4.35
267 268 5.182380 CCTAGATACACTTTTGCCGGAAAAA 59.818 40.000 19.47 19.47 33.04 1.94
268 269 4.698304 CCTAGATACACTTTTGCCGGAAAA 59.302 41.667 5.05 3.64 32.44 2.29
269 270 4.258543 CCTAGATACACTTTTGCCGGAAA 58.741 43.478 5.05 0.00 0.00 3.13
270 271 3.262405 ACCTAGATACACTTTTGCCGGAA 59.738 43.478 5.05 0.00 0.00 4.30
271 272 2.835764 ACCTAGATACACTTTTGCCGGA 59.164 45.455 5.05 0.00 0.00 5.14
272 273 3.261981 ACCTAGATACACTTTTGCCGG 57.738 47.619 0.00 0.00 0.00 6.13
273 274 4.693566 TCAAACCTAGATACACTTTTGCCG 59.306 41.667 0.00 0.00 0.00 5.69
274 275 6.599638 AGATCAAACCTAGATACACTTTTGCC 59.400 38.462 0.00 0.00 0.00 4.52
275 276 7.617041 AGATCAAACCTAGATACACTTTTGC 57.383 36.000 0.00 0.00 0.00 3.68
276 277 9.003658 ACAAGATCAAACCTAGATACACTTTTG 57.996 33.333 0.00 0.00 0.00 2.44
277 278 9.574516 AACAAGATCAAACCTAGATACACTTTT 57.425 29.630 0.00 0.00 0.00 2.27
278 279 9.220767 GAACAAGATCAAACCTAGATACACTTT 57.779 33.333 0.00 0.00 0.00 2.66
279 280 8.598041 AGAACAAGATCAAACCTAGATACACTT 58.402 33.333 0.00 0.00 0.00 3.16
280 281 8.140112 AGAACAAGATCAAACCTAGATACACT 57.860 34.615 0.00 0.00 0.00 3.55
281 282 9.871238 TTAGAACAAGATCAAACCTAGATACAC 57.129 33.333 0.00 0.00 0.00 2.90
285 286 8.606830 ACCTTTAGAACAAGATCAAACCTAGAT 58.393 33.333 0.00 0.00 0.00 1.98
286 287 7.974504 ACCTTTAGAACAAGATCAAACCTAGA 58.025 34.615 0.00 0.00 0.00 2.43
287 288 8.097662 AGACCTTTAGAACAAGATCAAACCTAG 58.902 37.037 0.00 0.00 0.00 3.02
288 289 7.974504 AGACCTTTAGAACAAGATCAAACCTA 58.025 34.615 0.00 0.00 0.00 3.08
289 290 6.842676 AGACCTTTAGAACAAGATCAAACCT 58.157 36.000 0.00 0.00 0.00 3.50
290 291 7.228706 TCAAGACCTTTAGAACAAGATCAAACC 59.771 37.037 0.00 0.00 0.00 3.27
291 292 8.154649 TCAAGACCTTTAGAACAAGATCAAAC 57.845 34.615 0.00 0.00 0.00 2.93
404 412 8.480643 AGACTTATATTTTGAAACGGAGTGAG 57.519 34.615 0.00 0.00 45.00 3.51
406 414 9.329913 CAAAGACTTATATTTTGAAACGGAGTG 57.670 33.333 0.00 0.00 35.82 3.51
435 443 9.347934 CCGTATGTAGTCATCTATTGAAATCTC 57.652 37.037 0.00 0.00 35.70 2.75
436 444 9.078990 TCCGTATGTAGTCATCTATTGAAATCT 57.921 33.333 0.00 0.00 35.70 2.40
437 445 9.347934 CTCCGTATGTAGTCATCTATTGAAATC 57.652 37.037 0.00 0.00 35.70 2.17
438 446 7.815068 GCTCCGTATGTAGTCATCTATTGAAAT 59.185 37.037 0.00 0.00 35.70 2.17
439 447 7.145985 GCTCCGTATGTAGTCATCTATTGAAA 58.854 38.462 0.00 0.00 35.70 2.69
440 448 6.264518 TGCTCCGTATGTAGTCATCTATTGAA 59.735 38.462 0.00 0.00 35.70 2.69
441 449 5.768164 TGCTCCGTATGTAGTCATCTATTGA 59.232 40.000 0.00 0.00 35.70 2.57
442 450 6.013842 TGCTCCGTATGTAGTCATCTATTG 57.986 41.667 0.00 0.00 35.70 1.90
443 451 6.650427 TTGCTCCGTATGTAGTCATCTATT 57.350 37.500 0.00 0.00 35.70 1.73
444 452 6.650427 TTTGCTCCGTATGTAGTCATCTAT 57.350 37.500 0.00 0.00 35.70 1.98
445 453 6.459670 TTTTGCTCCGTATGTAGTCATCTA 57.540 37.500 0.00 0.00 35.70 1.98
446 454 5.339008 TTTTGCTCCGTATGTAGTCATCT 57.661 39.130 0.00 0.00 35.70 2.90
447 455 5.753438 TCATTTTGCTCCGTATGTAGTCATC 59.247 40.000 0.00 0.00 35.70 2.92
448 456 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
449 457 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
450 458 5.109903 ACTCATTTTGCTCCGTATGTAGTC 58.890 41.667 0.00 0.00 0.00 2.59
451 459 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
452 460 7.534085 TTTACTCATTTTGCTCCGTATGTAG 57.466 36.000 0.00 0.00 0.00 2.74
453 461 7.985184 AGATTTACTCATTTTGCTCCGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
454 462 6.823689 AGATTTACTCATTTTGCTCCGTATGT 59.176 34.615 0.00 0.00 0.00 2.29
455 463 7.251704 AGATTTACTCATTTTGCTCCGTATG 57.748 36.000 0.00 0.00 0.00 2.39
456 464 7.441458 GGTAGATTTACTCATTTTGCTCCGTAT 59.559 37.037 0.00 0.00 0.00 3.06
457 465 6.759827 GGTAGATTTACTCATTTTGCTCCGTA 59.240 38.462 0.00 0.00 0.00 4.02
458 466 5.585047 GGTAGATTTACTCATTTTGCTCCGT 59.415 40.000 0.00 0.00 0.00 4.69
459 467 5.007724 GGGTAGATTTACTCATTTTGCTCCG 59.992 44.000 0.00 0.00 30.20 4.63
460 468 6.122964 AGGGTAGATTTACTCATTTTGCTCC 58.877 40.000 0.00 0.00 32.35 4.70
461 469 7.051000 AGAGGGTAGATTTACTCATTTTGCTC 58.949 38.462 0.00 0.00 32.35 4.26
462 470 6.963322 AGAGGGTAGATTTACTCATTTTGCT 58.037 36.000 0.00 0.00 32.35 3.91
463 471 8.732746 TTAGAGGGTAGATTTACTCATTTTGC 57.267 34.615 0.00 0.00 32.35 3.68
532 540 9.434420 TCCGTTCCGAAATATAAGTCTTTTTAA 57.566 29.630 0.00 0.00 0.00 1.52
533 541 9.090692 CTCCGTTCCGAAATATAAGTCTTTTTA 57.909 33.333 0.00 0.00 0.00 1.52
534 542 7.065443 CCTCCGTTCCGAAATATAAGTCTTTTT 59.935 37.037 0.00 0.00 0.00 1.94
535 543 6.537660 CCTCCGTTCCGAAATATAAGTCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
536 544 6.047231 CCTCCGTTCCGAAATATAAGTCTTT 58.953 40.000 0.00 0.00 0.00 2.52
537 545 5.452917 CCCTCCGTTCCGAAATATAAGTCTT 60.453 44.000 0.00 0.00 0.00 3.01
538 546 4.038883 CCCTCCGTTCCGAAATATAAGTCT 59.961 45.833 0.00 0.00 0.00 3.24
539 547 4.038402 TCCCTCCGTTCCGAAATATAAGTC 59.962 45.833 0.00 0.00 0.00 3.01
540 548 3.962718 TCCCTCCGTTCCGAAATATAAGT 59.037 43.478 0.00 0.00 0.00 2.24
541 549 4.038883 ACTCCCTCCGTTCCGAAATATAAG 59.961 45.833 0.00 0.00 0.00 1.73
542 550 3.962718 ACTCCCTCCGTTCCGAAATATAA 59.037 43.478 0.00 0.00 0.00 0.98
543 551 3.569491 ACTCCCTCCGTTCCGAAATATA 58.431 45.455 0.00 0.00 0.00 0.86
544 552 2.395619 ACTCCCTCCGTTCCGAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
545 553 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
546 554 1.856629 TACTCCCTCCGTTCCGAAAT 58.143 50.000 0.00 0.00 0.00 2.17
547 555 1.856629 ATACTCCCTCCGTTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
548 556 1.856629 AATACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
549 557 1.856629 AAATACTCCCTCCGTTCCGA 58.143 50.000 0.00 0.00 0.00 4.55
550 558 3.382546 TCTTAAATACTCCCTCCGTTCCG 59.617 47.826 0.00 0.00 0.00 4.30
551 559 4.648307 TCTCTTAAATACTCCCTCCGTTCC 59.352 45.833 0.00 0.00 0.00 3.62
552 560 5.593502 TCTCTCTTAAATACTCCCTCCGTTC 59.406 44.000 0.00 0.00 0.00 3.95
553 561 5.516984 TCTCTCTTAAATACTCCCTCCGTT 58.483 41.667 0.00 0.00 0.00 4.44
554 562 5.104024 TCTCTCTCTTAAATACTCCCTCCGT 60.104 44.000 0.00 0.00 0.00 4.69
555 563 5.378332 TCTCTCTCTTAAATACTCCCTCCG 58.622 45.833 0.00 0.00 0.00 4.63
556 564 6.607019 TCTCTCTCTCTTAAATACTCCCTCC 58.393 44.000 0.00 0.00 0.00 4.30
557 565 7.514721 TCTCTCTCTCTCTTAAATACTCCCTC 58.485 42.308 0.00 0.00 0.00 4.30
558 566 7.128883 ACTCTCTCTCTCTCTTAAATACTCCCT 59.871 40.741 0.00 0.00 0.00 4.20
559 567 7.287810 ACTCTCTCTCTCTCTTAAATACTCCC 58.712 42.308 0.00 0.00 0.00 4.30
560 568 8.747538 AACTCTCTCTCTCTCTTAAATACTCC 57.252 38.462 0.00 0.00 0.00 3.85
562 570 9.528489 ACAAACTCTCTCTCTCTCTTAAATACT 57.472 33.333 0.00 0.00 0.00 2.12
563 571 9.567848 CACAAACTCTCTCTCTCTCTTAAATAC 57.432 37.037 0.00 0.00 0.00 1.89
564 572 8.247562 GCACAAACTCTCTCTCTCTCTTAAATA 58.752 37.037 0.00 0.00 0.00 1.40
565 573 7.039082 AGCACAAACTCTCTCTCTCTCTTAAAT 60.039 37.037 0.00 0.00 0.00 1.40
566 574 6.266558 AGCACAAACTCTCTCTCTCTCTTAAA 59.733 38.462 0.00 0.00 0.00 1.52
567 575 5.772672 AGCACAAACTCTCTCTCTCTCTTAA 59.227 40.000 0.00 0.00 0.00 1.85
568 576 5.321102 AGCACAAACTCTCTCTCTCTCTTA 58.679 41.667 0.00 0.00 0.00 2.10
569 577 4.151883 AGCACAAACTCTCTCTCTCTCTT 58.848 43.478 0.00 0.00 0.00 2.85
570 578 3.766545 AGCACAAACTCTCTCTCTCTCT 58.233 45.455 0.00 0.00 0.00 3.10
571 579 4.519540 AAGCACAAACTCTCTCTCTCTC 57.480 45.455 0.00 0.00 0.00 3.20
572 580 5.538433 ACTTAAGCACAAACTCTCTCTCTCT 59.462 40.000 1.29 0.00 0.00 3.10
573 581 5.778862 ACTTAAGCACAAACTCTCTCTCTC 58.221 41.667 1.29 0.00 0.00 3.20
639 647 7.228108 CGGACACAGGTTCTAGTATCATAGTAA 59.772 40.741 0.00 0.00 0.00 2.24
640 648 6.709397 CGGACACAGGTTCTAGTATCATAGTA 59.291 42.308 0.00 0.00 0.00 1.82
641 649 5.531659 CGGACACAGGTTCTAGTATCATAGT 59.468 44.000 0.00 0.00 0.00 2.12
642 650 5.563085 GCGGACACAGGTTCTAGTATCATAG 60.563 48.000 0.00 0.00 0.00 2.23
643 651 4.277672 GCGGACACAGGTTCTAGTATCATA 59.722 45.833 0.00 0.00 0.00 2.15
644 652 3.068307 GCGGACACAGGTTCTAGTATCAT 59.932 47.826 0.00 0.00 0.00 2.45
645 653 2.426024 GCGGACACAGGTTCTAGTATCA 59.574 50.000 0.00 0.00 0.00 2.15
646 654 2.223758 GGCGGACACAGGTTCTAGTATC 60.224 54.545 0.00 0.00 0.00 2.24
647 655 1.755380 GGCGGACACAGGTTCTAGTAT 59.245 52.381 0.00 0.00 0.00 2.12
648 656 1.180029 GGCGGACACAGGTTCTAGTA 58.820 55.000 0.00 0.00 0.00 1.82
649 657 0.542232 AGGCGGACACAGGTTCTAGT 60.542 55.000 0.00 0.00 0.00 2.57
650 658 1.405821 CTAGGCGGACACAGGTTCTAG 59.594 57.143 0.00 0.00 0.00 2.43
660 668 3.767673 AGAGTTAAATCACTAGGCGGACA 59.232 43.478 5.62 0.00 0.00 4.02
661 669 4.113354 CAGAGTTAAATCACTAGGCGGAC 58.887 47.826 5.62 0.00 0.00 4.79
665 673 7.491696 ACGTATTTCAGAGTTAAATCACTAGGC 59.508 37.037 5.62 0.00 0.00 3.93
666 674 8.928270 ACGTATTTCAGAGTTAAATCACTAGG 57.072 34.615 5.62 0.00 0.00 3.02
707 715 0.258484 TGGCCCACCCAGATGTATTG 59.742 55.000 0.00 0.00 39.18 1.90
735 743 3.057245 GTGAGATACATGCGAGCTATGGA 60.057 47.826 0.00 0.00 0.00 3.41
758 766 4.325741 CAGATCTCACACGACTCACATTTC 59.674 45.833 0.00 0.00 0.00 2.17
768 776 0.969149 AAGTGGCAGATCTCACACGA 59.031 50.000 14.93 0.00 38.78 4.35
784 792 2.113243 GACGAGGAAGGTGGCCAAGT 62.113 60.000 7.24 0.00 0.00 3.16
983 1191 4.947147 TGTCTGTTGGGCGGGCAC 62.947 66.667 3.27 0.00 32.28 5.01
984 1192 3.965258 ATGTCTGTTGGGCGGGCA 61.965 61.111 3.27 0.00 42.98 5.36
985 1193 3.443045 CATGTCTGTTGGGCGGGC 61.443 66.667 0.00 0.00 0.00 6.13
989 1197 2.345760 CCAGCCATGTCTGTTGGGC 61.346 63.158 2.64 0.00 46.77 5.36
1049 1259 2.122413 ACCCCAGAGCAGACCACA 60.122 61.111 0.00 0.00 0.00 4.17
1125 1335 3.518419 GAACACGGGCGGGTACACA 62.518 63.158 0.00 0.00 0.00 3.72
1138 1348 1.949465 AACGACAGGGAGTTGAACAC 58.051 50.000 0.00 0.00 35.47 3.32
1193 1403 0.965866 ATCGAGGCAGAAGTCGGTGA 60.966 55.000 0.00 0.00 36.81 4.02
1299 1512 3.288308 CTCCTGCTCGCCGTTGTCT 62.288 63.158 0.00 0.00 0.00 3.41
1351 1577 0.532573 AGTTCCATCGACGATGCTGT 59.467 50.000 28.45 12.15 38.59 4.40
1352 1578 1.325640 CAAGTTCCATCGACGATGCTG 59.674 52.381 28.45 17.69 38.59 4.41
1415 1641 9.090692 GACAGTCTCAAGTTACTAGTAGTCTAG 57.909 40.741 5.96 2.67 46.43 2.43
1416 1642 8.591940 TGACAGTCTCAAGTTACTAGTAGTCTA 58.408 37.037 5.96 0.00 0.00 2.59
1417 1643 7.451732 TGACAGTCTCAAGTTACTAGTAGTCT 58.548 38.462 5.96 3.59 0.00 3.24
1437 1670 3.675225 CCTGTAGTGTTCGTCAATGACAG 59.325 47.826 14.24 6.55 31.94 3.51
1705 2445 2.282958 ACCGTCTCCTTCTGCCGA 60.283 61.111 0.00 0.00 0.00 5.54
2033 2773 1.592743 GCAGCAATGGTGGCAATGA 59.407 52.632 14.61 0.00 0.00 2.57
2140 2943 5.853936 TGGGATTAACCAACAGATAGATCG 58.146 41.667 0.00 0.00 41.20 3.69
2287 3092 6.199908 CACTAGAAATCAACGGCTGAGATTAG 59.800 42.308 15.04 12.21 37.52 1.73
2309 3114 1.676529 CCGTACGTCCTCATGATCACT 59.323 52.381 15.21 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.