Multiple sequence alignment - TraesCS5D01G169600

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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 TraesCS5D01G169600 chr5D 100.000 2653 0 0 1 2653 266084795 266087447 0.000000e+00 4900.0
1 TraesCS5D01G169600 chr5D 94.401 643 34 1 1242 1884 266325798 266325158 0.000000e+00 987.0
2 TraesCS5D01G169600 chr5D 92.927 509 11 6 712 1217 266326280 266325794 0.000000e+00 717.0
3 TraesCS5D01G169600 chr5D 85.874 269 20 11 438 702 266326482 266326228 1.210000e-68 270.0
4 TraesCS5D01G169600 chr5D 98.413 63 1 0 700 762 266085434 266085496 7.760000e-21 111.0
5 TraesCS5D01G169600 chr5D 98.413 63 1 0 640 702 266085494 266085556 7.760000e-21 111.0
6 TraesCS5D01G169600 chr5D 95.000 40 2 0 3 42 533638128 533638167 2.200000e-06 63.9
7 TraesCS5D01G169600 chr5A 95.798 1285 41 5 720 1995 354315816 354314536 0.000000e+00 2061.0
8 TraesCS5D01G169600 chr5A 94.619 669 33 2 1214 1881 353988793 353989459 0.000000e+00 1033.0
9 TraesCS5D01G169600 chr5A 93.253 667 36 6 1993 2653 354313925 354313262 0.000000e+00 974.0
10 TraesCS5D01G169600 chr5A 91.815 672 46 5 1988 2653 227355484 227354816 0.000000e+00 928.0
11 TraesCS5D01G169600 chr5A 91.815 672 46 5 1988 2653 227520523 227519855 0.000000e+00 928.0
12 TraesCS5D01G169600 chr5A 91.892 666 45 5 1994 2653 227422416 227421754 0.000000e+00 922.0
13 TraesCS5D01G169600 chr5A 93.090 521 28 5 700 1218 353988195 353988709 0.000000e+00 756.0
14 TraesCS5D01G169600 chr5A 91.618 346 17 7 71 411 354316584 354316246 4.000000e-128 468.0
15 TraesCS5D01G169600 chr5A 96.018 226 6 3 439 663 354316252 354316029 5.400000e-97 364.0
16 TraesCS5D01G169600 chr5A 90.909 264 13 9 1 259 354316745 354316488 7.030000e-91 344.0
17 TraesCS5D01G169600 chr5A 87.814 279 28 5 426 702 353987981 353988255 3.290000e-84 322.0
18 TraesCS5D01G169600 chr5A 92.784 97 4 3 71 165 354316489 354316394 1.280000e-28 137.0
19 TraesCS5D01G169600 chr5B 95.367 1295 51 6 700 1989 299847163 299848453 0.000000e+00 2050.0
20 TraesCS5D01G169600 chr5B 94.426 1184 56 3 703 1884 300098470 300097295 0.000000e+00 1812.0
21 TraesCS5D01G169600 chr5B 90.335 269 20 5 438 702 300098675 300098409 5.440000e-92 348.0
22 TraesCS5D01G169600 chr5B 89.441 161 13 3 229 385 130576292 130576132 1.610000e-47 200.0
23 TraesCS5D01G169600 chr5B 93.496 123 6 1 582 702 299847105 299847227 5.830000e-42 182.0
24 TraesCS5D01G169600 chr5B 89.286 56 5 1 3 57 673684716 673684771 4.740000e-08 69.4
25 TraesCS5D01G169600 chr4D 92.773 678 40 6 1982 2653 121764290 121764964 0.000000e+00 972.0
26 TraesCS5D01G169600 chrUn 91.667 672 47 5 1988 2653 184002032 184001364 0.000000e+00 922.0
27 TraesCS5D01G169600 chrUn 91.445 678 49 5 1982 2653 191276481 191277155 0.000000e+00 922.0
28 TraesCS5D01G169600 chrUn 89.441 161 13 3 229 385 45093228 45093388 1.610000e-47 200.0
29 TraesCS5D01G169600 chrUn 89.441 161 13 3 229 385 420975018 420975178 1.610000e-47 200.0
30 TraesCS5D01G169600 chr7A 91.654 671 47 5 1988 2652 730114760 730114093 0.000000e+00 920.0
31 TraesCS5D01G169600 chr7A 91.667 672 45 6 1988 2653 730210551 730209885 0.000000e+00 920.0
32 TraesCS5D01G169600 chr7A 90.625 160 12 3 229 385 211339372 211339213 2.680000e-50 209.0
33 TraesCS5D01G169600 chr7A 90.062 161 12 3 229 385 60299717 60299877 3.460000e-49 206.0
34 TraesCS5D01G169600 chr2A 92.506 387 27 2 1270 1655 30072292 30071907 1.070000e-153 553.0
35 TraesCS5D01G169600 chr2A 92.248 387 28 2 1270 1655 30048481 30048096 4.990000e-152 547.0
36 TraesCS5D01G169600 chr2A 91.969 386 29 2 1270 1654 30079875 30079491 8.350000e-150 540.0
37 TraesCS5D01G169600 chr2A 88.889 153 17 0 998 1150 30127269 30127117 3.490000e-44 189.0
38 TraesCS5D01G169600 chr2A 87.582 153 19 0 998 1150 30086811 30086659 7.550000e-41 178.0
39 TraesCS5D01G169600 chr2D 91.710 386 30 2 1270 1654 27888285 27887901 3.890000e-148 534.0
40 TraesCS5D01G169600 chr6B 90.062 161 12 3 229 385 388157043 388156883 3.460000e-49 206.0
41 TraesCS5D01G169600 chr6B 89.474 57 5 1 1 56 42615815 42615871 1.320000e-08 71.3
42 TraesCS5D01G169600 chr7D 89.441 161 13 3 229 385 381937760 381937600 1.610000e-47 200.0
43 TraesCS5D01G169600 chr3D 89.506 162 11 5 229 385 193370616 193370776 1.610000e-47 200.0
44 TraesCS5D01G169600 chr2B 88.235 153 18 0 998 1150 44361838 44361686 1.620000e-42 183.0
45 TraesCS5D01G169600 chr7B 92.500 40 3 0 2 41 681685779 681685740 1.030000e-04 58.4


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 TraesCS5D01G169600 chr5D 266084795 266087447 2652 False 1707.333333 4900 98.942000 1 2653 3 chr5D.!!$F2 2652
1 TraesCS5D01G169600 chr5D 266325158 266326482 1324 True 658.000000 987 91.067333 438 1884 3 chr5D.!!$R1 1446
2 TraesCS5D01G169600 chr5A 227354816 227355484 668 True 928.000000 928 91.815000 1988 2653 1 chr5A.!!$R1 665
3 TraesCS5D01G169600 chr5A 227519855 227520523 668 True 928.000000 928 91.815000 1988 2653 1 chr5A.!!$R3 665
4 TraesCS5D01G169600 chr5A 227421754 227422416 662 True 922.000000 922 91.892000 1994 2653 1 chr5A.!!$R2 659
5 TraesCS5D01G169600 chr5A 354313262 354316745 3483 True 724.666667 2061 93.396667 1 2653 6 chr5A.!!$R4 2652
6 TraesCS5D01G169600 chr5A 353987981 353989459 1478 False 703.666667 1033 91.841000 426 1881 3 chr5A.!!$F1 1455
7 TraesCS5D01G169600 chr5B 299847105 299848453 1348 False 1116.000000 2050 94.431500 582 1989 2 chr5B.!!$F2 1407
8 TraesCS5D01G169600 chr5B 300097295 300098675 1380 True 1080.000000 1812 92.380500 438 1884 2 chr5B.!!$R2 1446
9 TraesCS5D01G169600 chr4D 121764290 121764964 674 False 972.000000 972 92.773000 1982 2653 1 chr4D.!!$F1 671
10 TraesCS5D01G169600 chrUn 184001364 184002032 668 True 922.000000 922 91.667000 1988 2653 1 chrUn.!!$R1 665
11 TraesCS5D01G169600 chrUn 191276481 191277155 674 False 922.000000 922 91.445000 1982 2653 1 chrUn.!!$F2 671
12 TraesCS5D01G169600 chr7A 730114093 730114760 667 True 920.000000 920 91.654000 1988 2652 1 chr7A.!!$R2 664
13 TraesCS5D01G169600 chr7A 730209885 730210551 666 True 920.000000 920 91.667000 1988 2653 1 chr7A.!!$R3 665

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
692 790 0.394565 GTAGGACCAGCATAGCAGGG 59.605 60.0 5.42 2.16 39.6 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 2143 1.160137 GCTTTCTCGAGCCATGTTGT 58.84 50.0 7.81 0.0 36.66 3.32 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
50 51 6.482898 AAAATATGAAGTGGCCATGCATAA 57.517 33.333 21.40 10.75 0.00 1.90
73 74 5.871465 AAAACAAAAAGGAATGCACGTTT 57.129 30.435 0.00 0.00 0.00 3.60
96 97 9.646336 GTTTATTTGTTGTATGATCATCGGTAC 57.354 33.333 12.53 5.40 0.00 3.34
135 136 2.381752 AGGGACCCAACCAAGAAAAG 57.618 50.000 14.60 0.00 0.00 2.27
136 137 1.573857 AGGGACCCAACCAAGAAAAGT 59.426 47.619 14.60 0.00 0.00 2.66
137 138 2.787035 AGGGACCCAACCAAGAAAAGTA 59.213 45.455 14.60 0.00 0.00 2.24
142 238 3.964688 ACCCAACCAAGAAAAGTAAAGGG 59.035 43.478 0.00 0.00 38.52 3.95
189 285 9.507280 GTTCATTTGTTGTATGATCATTGGTAG 57.493 33.333 14.65 0.00 32.43 3.18
228 324 3.344535 AAGGGACCCAACCAAGAAAAT 57.655 42.857 14.60 0.00 0.00 1.82
256 353 3.353557 GGACCCAACCAAGAAATCTACC 58.646 50.000 0.00 0.00 0.00 3.18
273 370 1.499049 ACCGTCTTGAAGCGAAAGTC 58.501 50.000 9.86 0.00 0.00 3.01
274 371 1.202486 ACCGTCTTGAAGCGAAAGTCA 60.202 47.619 9.86 0.00 0.00 3.41
275 372 1.864711 CCGTCTTGAAGCGAAAGTCAA 59.135 47.619 9.86 0.00 32.91 3.18
286 383 3.433615 AGCGAAAGTCAAGCTTGTATCAC 59.566 43.478 25.19 16.02 38.13 3.06
288 385 3.181530 CGAAAGTCAAGCTTGTATCACGG 60.182 47.826 25.19 7.80 37.52 4.94
305 402 6.642683 ATCACGGAACTAGACGTTTATTTG 57.357 37.500 0.00 0.00 42.04 2.32
317 414 9.529325 CTAGACGTTTATTTGATTGATAGGTCA 57.471 33.333 0.00 0.00 0.00 4.02
320 417 8.197988 ACGTTTATTTGATTGATAGGTCAGAC 57.802 34.615 0.00 0.00 35.39 3.51
351 448 6.426633 GCAAACAAGCAAACCAAATTATAGGT 59.573 34.615 0.00 0.00 40.61 3.08
404 501 2.079925 GCATTGAGACTTGAGACCACC 58.920 52.381 0.00 0.00 0.00 4.61
405 502 2.550855 GCATTGAGACTTGAGACCACCA 60.551 50.000 0.00 0.00 0.00 4.17
406 503 3.871463 GCATTGAGACTTGAGACCACCAT 60.871 47.826 0.00 0.00 0.00 3.55
407 504 4.623886 GCATTGAGACTTGAGACCACCATA 60.624 45.833 0.00 0.00 0.00 2.74
408 505 5.678583 CATTGAGACTTGAGACCACCATAT 58.321 41.667 0.00 0.00 0.00 1.78
409 506 5.762179 TTGAGACTTGAGACCACCATATT 57.238 39.130 0.00 0.00 0.00 1.28
410 507 6.867519 TTGAGACTTGAGACCACCATATTA 57.132 37.500 0.00 0.00 0.00 0.98
411 508 6.222038 TGAGACTTGAGACCACCATATTAC 57.778 41.667 0.00 0.00 0.00 1.89
412 509 5.719563 TGAGACTTGAGACCACCATATTACA 59.280 40.000 0.00 0.00 0.00 2.41
413 510 6.384015 TGAGACTTGAGACCACCATATTACAT 59.616 38.462 0.00 0.00 0.00 2.29
414 511 7.563556 TGAGACTTGAGACCACCATATTACATA 59.436 37.037 0.00 0.00 0.00 2.29
415 512 7.727181 AGACTTGAGACCACCATATTACATAC 58.273 38.462 0.00 0.00 0.00 2.39
416 513 7.565398 AGACTTGAGACCACCATATTACATACT 59.435 37.037 0.00 0.00 0.00 2.12
417 514 7.727181 ACTTGAGACCACCATATTACATACTC 58.273 38.462 0.00 0.00 0.00 2.59
418 515 6.665992 TGAGACCACCATATTACATACTCC 57.334 41.667 0.00 0.00 0.00 3.85
419 516 6.382087 TGAGACCACCATATTACATACTCCT 58.618 40.000 0.00 0.00 0.00 3.69
420 517 7.532199 TGAGACCACCATATTACATACTCCTA 58.468 38.462 0.00 0.00 0.00 2.94
421 518 8.177456 TGAGACCACCATATTACATACTCCTAT 58.823 37.037 0.00 0.00 0.00 2.57
422 519 9.696572 GAGACCACCATATTACATACTCCTATA 57.303 37.037 0.00 0.00 0.00 1.31
425 522 9.610104 ACCACCATATTACATACTCCTATAACA 57.390 33.333 0.00 0.00 0.00 2.41
426 523 9.871238 CCACCATATTACATACTCCTATAACAC 57.129 37.037 0.00 0.00 0.00 3.32
457 554 3.359033 AGCATACTAACCGTGTCAGGTA 58.641 45.455 0.00 0.00 45.21 3.08
477 574 4.142381 GGTAAAGGAAGCTATGTTTGCCAG 60.142 45.833 13.48 0.00 35.44 4.85
483 581 4.515567 GGAAGCTATGTTTGCCAGGTATAC 59.484 45.833 0.00 0.00 0.00 1.47
485 583 4.962155 AGCTATGTTTGCCAGGTATACTC 58.038 43.478 2.25 0.00 0.00 2.59
486 584 4.656112 AGCTATGTTTGCCAGGTATACTCT 59.344 41.667 2.25 0.00 0.00 3.24
487 585 4.752101 GCTATGTTTGCCAGGTATACTCTG 59.248 45.833 12.08 12.08 0.00 3.35
685 783 1.008938 AGGAAGGAGTAGGACCAGCAT 59.991 52.381 0.00 0.00 0.00 3.79
686 784 2.247635 AGGAAGGAGTAGGACCAGCATA 59.752 50.000 0.00 0.00 0.00 3.14
687 785 2.630580 GGAAGGAGTAGGACCAGCATAG 59.369 54.545 0.00 0.00 0.00 2.23
688 786 1.710816 AGGAGTAGGACCAGCATAGC 58.289 55.000 0.00 0.00 0.00 2.97
689 787 1.062886 AGGAGTAGGACCAGCATAGCA 60.063 52.381 0.00 0.00 0.00 3.49
690 788 1.342819 GGAGTAGGACCAGCATAGCAG 59.657 57.143 0.00 0.00 0.00 4.24
691 789 1.342819 GAGTAGGACCAGCATAGCAGG 59.657 57.143 0.00 0.00 41.13 4.85
692 790 0.394565 GTAGGACCAGCATAGCAGGG 59.605 60.000 5.42 2.16 39.60 4.45
693 791 1.410850 TAGGACCAGCATAGCAGGGC 61.411 60.000 5.42 1.31 42.88 5.19
694 792 2.591753 GACCAGCATAGCAGGGCA 59.408 61.111 0.96 0.00 43.12 5.36
695 793 1.821332 GACCAGCATAGCAGGGCAC 60.821 63.158 0.96 0.00 43.12 5.01
697 795 1.822613 CCAGCATAGCAGGGCACAG 60.823 63.158 0.00 0.00 31.34 3.66
698 796 1.822613 CAGCATAGCAGGGCACAGG 60.823 63.158 0.00 0.00 0.00 4.00
699 797 2.517875 GCATAGCAGGGCACAGGG 60.518 66.667 0.00 0.00 0.00 4.45
700 798 2.517875 CATAGCAGGGCACAGGGC 60.518 66.667 0.00 0.00 43.74 5.19
813 1074 3.436704 CGCAGACATGTGGTTGTTTATCT 59.563 43.478 1.15 0.00 33.09 1.98
842 1103 2.974148 GGATGCCGATGATGCGCA 60.974 61.111 14.96 14.96 0.00 6.09
1355 1707 2.045536 GCCCTCCTCAAGCAGGTG 60.046 66.667 0.00 0.00 43.95 4.00
1391 1743 1.833934 CAAGTGGGTGCCTTGCCTT 60.834 57.895 0.00 0.00 33.55 4.35
1430 1782 2.744202 GTTCATCTTCCGTGAGCACAAT 59.256 45.455 1.20 0.00 0.00 2.71
1451 1803 1.432270 CGTCTCCCGGGTACTACGAC 61.432 65.000 22.86 16.06 32.35 4.34
1457 1809 4.559229 GGGTACTACGACGGCCGC 62.559 72.222 28.58 17.52 43.32 6.53
1610 1962 0.886043 TGCAGTGCGTCAGCTTCATT 60.886 50.000 11.20 0.00 45.42 2.57
1738 2090 4.953940 TTGGGTTTTCCTTCTCCATTTG 57.046 40.909 0.00 0.00 40.46 2.32
1748 2100 7.745620 TTCCTTCTCCATTTGTCTTTCTTAC 57.254 36.000 0.00 0.00 0.00 2.34
1786 2143 9.625747 AATATGTGTATGTCCATGTTCATGTAA 57.374 29.630 11.13 0.00 0.00 2.41
1806 2163 0.095935 CAACATGGCTCGAGAAAGCG 59.904 55.000 18.75 2.03 43.45 4.68
1946 2305 1.466866 GCACCTTTTATTTCCGTCGCC 60.467 52.381 0.00 0.00 0.00 5.54
2102 3074 2.838736 TCAAAATGATAGCTCTCCGGC 58.161 47.619 0.00 0.00 0.00 6.13
2171 3143 1.481871 ACCGGGTCGACTCATTACAT 58.518 50.000 17.19 0.00 0.00 2.29
2197 3169 6.655078 AACATTTTGTTGGCTTATGAGAGT 57.345 33.333 0.00 0.00 39.45 3.24
2205 3177 9.851686 TTTGTTGGCTTATGAGAGTATTCATAT 57.148 29.630 0.00 0.00 39.20 1.78
2269 3241 5.335127 CAGTTAAACTGGATATGCACAAGC 58.665 41.667 0.00 0.00 42.35 4.01
2271 3243 2.814805 AACTGGATATGCACAAGCCT 57.185 45.000 6.72 0.00 41.13 4.58
2272 3244 3.931907 AACTGGATATGCACAAGCCTA 57.068 42.857 6.72 0.00 41.13 3.93
2292 3264 6.069963 AGCCTATATGATAGGGTTGAATGGAC 60.070 42.308 10.73 0.00 42.22 4.02
2319 3292 3.251479 AGCAGAATGATGACACGCTTA 57.749 42.857 0.00 0.00 39.69 3.09
2377 3354 6.821665 TGTGTCCAGTCAGTTAAATATAAGGC 59.178 38.462 0.00 0.00 0.00 4.35
2400 3377 7.343833 AGGCCAGATTCAATAATCAAGAAACAT 59.656 33.333 5.01 0.00 43.44 2.71
2511 3489 2.023984 TGGCTCATAGAGAGGAGGTTCA 60.024 50.000 0.00 0.00 44.86 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.420118 TGGCCACTTCATATTTTTATGTCTAAT 57.580 29.630 0.00 0.00 0.00 1.73
20 21 7.685155 GCATGGCCACTTCATATTTTTATGTCT 60.685 37.037 8.16 0.00 0.00 3.41
50 51 5.871465 AACGTGCATTCCTTTTTGTTTTT 57.129 30.435 0.00 0.00 0.00 1.94
55 56 6.942891 ACAAATAAACGTGCATTCCTTTTTG 58.057 32.000 0.00 0.10 0.00 2.44
56 57 7.065204 ACAACAAATAAACGTGCATTCCTTTTT 59.935 29.630 0.00 0.00 0.00 1.94
57 58 6.536941 ACAACAAATAAACGTGCATTCCTTTT 59.463 30.769 0.00 0.00 0.00 2.27
60 61 5.195001 ACAACAAATAAACGTGCATTCCT 57.805 34.783 0.00 0.00 0.00 3.36
61 62 6.804295 TCATACAACAAATAAACGTGCATTCC 59.196 34.615 0.00 0.00 0.00 3.01
62 63 7.789341 TCATACAACAAATAAACGTGCATTC 57.211 32.000 0.00 0.00 0.00 2.67
63 64 8.026026 TGATCATACAACAAATAAACGTGCATT 58.974 29.630 0.00 0.00 0.00 3.56
73 74 6.643360 CCGTACCGATGATCATACAACAAATA 59.357 38.462 8.54 0.00 0.00 1.40
96 97 2.710096 TTGATAAAGGCTCCCTTCCG 57.290 50.000 0.00 0.00 43.92 4.30
135 136 2.963599 TCTTGGTTGGGTCCCTTTAC 57.036 50.000 10.00 4.72 0.00 2.01
136 137 3.975479 TTTCTTGGTTGGGTCCCTTTA 57.025 42.857 10.00 0.00 0.00 1.85
137 138 2.858787 TTTCTTGGTTGGGTCCCTTT 57.141 45.000 10.00 0.00 0.00 3.11
142 238 4.652822 ACAGTAGATTTCTTGGTTGGGTC 58.347 43.478 0.00 0.00 0.00 4.46
178 274 2.224646 GCTCCCTTCCCTACCAATGATC 60.225 54.545 0.00 0.00 0.00 2.92
184 280 1.306997 CAGGCTCCCTTCCCTACCA 60.307 63.158 0.00 0.00 0.00 3.25
189 285 1.213296 TTGATACAGGCTCCCTTCCC 58.787 55.000 0.00 0.00 0.00 3.97
228 324 1.571457 TCTTGGTTGGGTCCCTTTTCA 59.429 47.619 10.00 0.00 0.00 2.69
263 360 4.065088 TGATACAAGCTTGACTTTCGCTT 58.935 39.130 32.50 9.46 44.15 4.68
273 370 4.563184 GTCTAGTTCCGTGATACAAGCTTG 59.437 45.833 24.84 24.84 0.00 4.01
274 371 4.674623 CGTCTAGTTCCGTGATACAAGCTT 60.675 45.833 0.00 0.00 0.00 3.74
275 372 3.181499 CGTCTAGTTCCGTGATACAAGCT 60.181 47.826 0.00 0.00 0.00 3.74
276 373 3.106672 CGTCTAGTTCCGTGATACAAGC 58.893 50.000 0.00 0.00 0.00 4.01
286 383 7.285783 TCAATCAAATAAACGTCTAGTTCCG 57.714 36.000 0.00 0.00 43.37 4.30
305 402 4.141846 TGCTTCCTGTCTGACCTATCAATC 60.142 45.833 5.17 0.00 33.30 2.67
317 414 2.057137 TGCTTGTTTGCTTCCTGTCT 57.943 45.000 0.00 0.00 0.00 3.41
320 417 2.204237 GGTTTGCTTGTTTGCTTCCTG 58.796 47.619 0.00 0.00 0.00 3.86
351 448 5.061179 CCTTTCCGAGTTCTAACTTCCAAA 58.939 41.667 0.00 0.00 39.88 3.28
355 452 5.055144 ACAACCTTTCCGAGTTCTAACTTC 58.945 41.667 0.00 0.00 39.88 3.01
367 464 0.817634 TGCACAGGACAACCTTTCCG 60.818 55.000 0.00 0.00 45.36 4.30
422 519 9.042008 CGGTTAGTATGCTAATTATGAAGTGTT 57.958 33.333 6.54 0.00 39.17 3.32
423 520 8.202137 ACGGTTAGTATGCTAATTATGAAGTGT 58.798 33.333 6.54 0.00 39.17 3.55
424 521 8.487970 CACGGTTAGTATGCTAATTATGAAGTG 58.512 37.037 6.54 6.21 39.17 3.16
425 522 8.202137 ACACGGTTAGTATGCTAATTATGAAGT 58.798 33.333 6.54 0.00 39.17 3.01
426 523 8.589335 ACACGGTTAGTATGCTAATTATGAAG 57.411 34.615 6.54 0.00 39.17 3.02
427 524 8.198778 TGACACGGTTAGTATGCTAATTATGAA 58.801 33.333 6.54 0.00 39.17 2.57
428 525 7.718525 TGACACGGTTAGTATGCTAATTATGA 58.281 34.615 6.54 0.00 39.17 2.15
429 526 7.116376 CCTGACACGGTTAGTATGCTAATTATG 59.884 40.741 6.54 7.68 39.17 1.90
430 527 7.152645 CCTGACACGGTTAGTATGCTAATTAT 58.847 38.462 6.54 0.00 39.17 1.28
431 528 6.097270 ACCTGACACGGTTAGTATGCTAATTA 59.903 38.462 6.54 0.00 39.17 1.40
432 529 5.105064 ACCTGACACGGTTAGTATGCTAATT 60.105 40.000 6.54 0.00 39.17 1.40
433 530 4.404715 ACCTGACACGGTTAGTATGCTAAT 59.595 41.667 6.54 0.00 39.17 1.73
434 531 3.765511 ACCTGACACGGTTAGTATGCTAA 59.234 43.478 0.00 0.00 31.94 3.09
435 532 3.359033 ACCTGACACGGTTAGTATGCTA 58.641 45.455 0.00 0.00 31.94 3.49
436 533 2.176889 ACCTGACACGGTTAGTATGCT 58.823 47.619 0.00 0.00 31.94 3.79
457 554 2.827921 CCTGGCAAACATAGCTTCCTTT 59.172 45.455 0.00 0.00 0.00 3.11
477 574 6.141560 GTACACTACCAACCAGAGTATACC 57.858 45.833 0.00 0.00 0.00 2.73
489 587 7.921139 GCATCCGCATTAGGTACACTACCAA 62.921 48.000 0.00 0.00 44.35 3.67
709 807 1.185618 TCCTGGCTACTTGCACTCGT 61.186 55.000 0.00 0.00 45.15 4.18
711 809 1.677217 CCTTCCTGGCTACTTGCACTC 60.677 57.143 0.00 0.00 45.15 3.51
714 812 0.615331 CTCCTTCCTGGCTACTTGCA 59.385 55.000 0.00 0.00 45.15 4.08
715 813 0.615850 ACTCCTTCCTGGCTACTTGC 59.384 55.000 0.00 0.00 41.94 4.01
716 814 2.432510 CCTACTCCTTCCTGGCTACTTG 59.567 54.545 0.00 0.00 35.26 3.16
718 816 1.930914 TCCTACTCCTTCCTGGCTACT 59.069 52.381 0.00 0.00 35.26 2.57
723 977 1.490574 CTGGTCCTACTCCTTCCTGG 58.509 60.000 0.00 0.00 37.10 4.45
813 1074 0.673985 CGGCATCCTGATAAGGTCGA 59.326 55.000 0.00 0.00 0.00 4.20
1266 1618 2.753043 GATGGGCCACACCTGCAG 60.753 66.667 9.28 6.78 39.10 4.41
1355 1707 0.755698 TGGAGCGGATCAGGTAGTCC 60.756 60.000 0.00 0.00 0.00 3.85
1391 1743 1.371183 CCCGACCTTGCTGAACTCA 59.629 57.895 0.00 0.00 0.00 3.41
1430 1782 1.750399 GTAGTACCCGGGAGACGCA 60.750 63.158 32.02 14.65 42.52 5.24
1433 1785 1.432270 CGTCGTAGTACCCGGGAGAC 61.432 65.000 32.02 24.16 0.00 3.36
1439 1791 4.241999 CGGCCGTCGTAGTACCCG 62.242 72.222 19.50 1.32 0.00 5.28
1451 1803 2.173669 CATTGTCCAGTAGCGGCCG 61.174 63.158 24.05 24.05 0.00 6.13
1457 1809 3.005554 CAGCTTCCACATTGTCCAGTAG 58.994 50.000 0.00 0.00 0.00 2.57
1748 2100 9.046296 GGACATACACATATTCTTAGGAACAAG 57.954 37.037 0.00 0.00 33.96 3.16
1786 2143 1.160137 GCTTTCTCGAGCCATGTTGT 58.840 50.000 7.81 0.00 36.66 3.32
1806 2163 3.611517 GATTGCATTCACATACGAGCAC 58.388 45.455 3.73 0.00 0.00 4.40
2021 2993 2.194271 GTACTGTGTAATGAGCTCGGC 58.806 52.381 9.64 0.00 0.00 5.54
2023 2995 3.439293 CCTGTACTGTGTAATGAGCTCG 58.561 50.000 9.64 0.00 0.00 5.03
2171 3143 9.461312 ACTCTCATAAGCCAACAAAATGTTATA 57.539 29.630 0.00 0.00 38.77 0.98
2269 3241 7.502060 AGTCCATTCAACCCTATCATATAGG 57.498 40.000 6.06 6.06 34.52 2.57
2319 3292 8.299570 CAATTTACAAACTCTACATGAAAGCCT 58.700 33.333 0.00 0.00 0.00 4.58
2400 3377 8.358082 AGTCCCCTTCCAGGAATAAAATATTA 57.642 34.615 1.09 0.00 37.67 0.98
2511 3489 1.617804 CCCTGACACCTTCAATGCCAT 60.618 52.381 0.00 0.00 32.21 4.40


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

AutoCloner maintained by Alex Coulton.