Multiple sequence alignment - TraesCS2D01G488100

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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 TraesCS2D01G488100 chr2D 100.000 2489 0 0 1 2489 587695143 587697631 0.000000e+00 4597
1 TraesCS2D01G488100 chr2D 82.626 495 70 8 1 480 617956432 617956925 8.230000e-115 424
2 TraesCS2D01G488100 chr2D 78.378 370 55 13 1 364 518039508 518039858 1.500000e-52 217
3 TraesCS2D01G488100 chr2B 88.763 2038 112 61 529 2489 710279698 710281695 0.000000e+00 2386
4 TraesCS2D01G488100 chr2B 84.314 459 59 6 67 514 710279142 710279598 1.060000e-118 436
5 TraesCS2D01G488100 chr2A 87.641 1861 97 58 705 2489 722517768 722519571 0.000000e+00 2039
6 TraesCS2D01G488100 chr2A 91.111 180 14 2 1479 1657 32967671 32967849 2.470000e-60 243
7 TraesCS2D01G488100 chr2A 93.798 129 7 1 544 672 722517646 722517773 2.530000e-45 193
8 TraesCS2D01G488100 chr2A 90.984 122 5 2 1652 1773 32974152 32974267 2.560000e-35 159
9 TraesCS2D01G488100 chr4D 86.808 993 47 25 1477 2408 344373768 344372799 0.000000e+00 1031
10 TraesCS2D01G488100 chr4D 81.911 492 72 11 1 480 362801319 362800833 1.390000e-107 399
11 TraesCS2D01G488100 chr4D 79.713 488 84 10 3 478 7941296 7941780 3.070000e-89 339
12 TraesCS2D01G488100 chr4D 89.524 105 11 0 2 106 445699645 445699749 1.550000e-27 134
13 TraesCS2D01G488100 chr3A 83.518 813 40 30 1477 2224 195452298 195451515 0.000000e+00 673
14 TraesCS2D01G488100 chr3A 83.023 483 71 7 9 481 496047271 496047752 6.360000e-116 427
15 TraesCS2D01G488100 chr3A 82.057 457 67 10 6 451 523760330 523759878 2.340000e-100 375
16 TraesCS2D01G488100 chr3A 98.315 178 3 0 2231 2408 195447606 195447429 1.860000e-81 313
17 TraesCS2D01G488100 chr6D 84.836 488 63 7 4 480 337847148 337846661 4.810000e-132 481
18 TraesCS2D01G488100 chr6B 82.281 491 75 4 1 480 482469538 482470027 4.950000e-112 414
19 TraesCS2D01G488100 chr7B 81.837 490 73 9 1 478 464533815 464534300 4.990000e-107 398
20 TraesCS2D01G488100 chr7B 80.840 381 60 8 7 377 164097493 164097870 1.130000e-73 287
21 TraesCS2D01G488100 chr6A 80.392 459 75 8 35 481 544214789 544214334 3.970000e-88 335
22 TraesCS2D01G488100 chr3D 80.909 440 69 3 45 471 55150104 55150541 1.430000e-87 333
23 TraesCS2D01G488100 chr7A 78.647 473 81 7 6 469 241723461 241723000 1.870000e-76 296
24 TraesCS2D01G488100 chr1D 97.987 149 3 0 2260 2408 2480366 2480514 2.460000e-65 259
25 TraesCS2D01G488100 chr7D 80.328 183 25 7 1 174 205493798 205493618 7.230000e-26 128
26 TraesCS2D01G488100 chr5B 89.000 100 11 0 1 100 381720898 381720997 9.350000e-25 124


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 TraesCS2D01G488100 chr2D 587695143 587697631 2488 False 4597 4597 100.0000 1 2489 1 chr2D.!!$F2 2488
1 TraesCS2D01G488100 chr2B 710279142 710281695 2553 False 1411 2386 86.5385 67 2489 2 chr2B.!!$F1 2422
2 TraesCS2D01G488100 chr2A 722517646 722519571 1925 False 1116 2039 90.7195 544 2489 2 chr2A.!!$F3 1945
3 TraesCS2D01G488100 chr4D 344372799 344373768 969 True 1031 1031 86.8080 1477 2408 1 chr4D.!!$R1 931
4 TraesCS2D01G488100 chr3A 195447429 195452298 4869 True 493 673 90.9165 1477 2408 2 chr3A.!!$R2 931

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
422 433 0.180406 AGGCGAATTTATGGGCTCGT 59.82 50.0 0.0 0.0 33.87 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1508 1644 0.035458 CTTAGCTCTAATGGGGGCGG 59.965 60.0 0.0 0.0 0.0 6.13 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
21 22 2.496817 CTGTCGCAGCTCCCCTAC 59.503 66.667 0.00 0.00 0.00 3.18
22 23 3.075005 TGTCGCAGCTCCCCTACC 61.075 66.667 0.00 0.00 0.00 3.18
23 24 4.208686 GTCGCAGCTCCCCTACCG 62.209 72.222 0.00 0.00 0.00 4.02
39 40 2.032071 CGGAGCCGGTTTGACCTT 59.968 61.111 1.90 0.00 35.66 3.50
40 41 2.325082 CGGAGCCGGTTTGACCTTG 61.325 63.158 1.90 0.00 35.66 3.61
41 42 1.228154 GGAGCCGGTTTGACCTTGT 60.228 57.895 1.90 0.00 35.66 3.16
42 43 1.235281 GGAGCCGGTTTGACCTTGTC 61.235 60.000 1.90 0.00 35.66 3.18
43 44 0.534203 GAGCCGGTTTGACCTTGTCA 60.534 55.000 1.90 0.00 41.09 3.58
52 53 1.896220 TGACCTTGTCAATGACAGCC 58.104 50.000 16.10 7.61 43.69 4.85
53 54 0.798776 GACCTTGTCAATGACAGCCG 59.201 55.000 16.10 9.95 43.69 5.52
54 55 0.606401 ACCTTGTCAATGACAGCCGG 60.606 55.000 16.10 18.26 43.69 6.13
55 56 0.321564 CCTTGTCAATGACAGCCGGA 60.322 55.000 16.10 0.32 43.69 5.14
56 57 1.522668 CTTGTCAATGACAGCCGGAA 58.477 50.000 16.10 0.00 43.69 4.30
57 58 1.879380 CTTGTCAATGACAGCCGGAAA 59.121 47.619 16.10 0.00 43.69 3.13
58 59 1.522668 TGTCAATGACAGCCGGAAAG 58.477 50.000 12.63 0.00 37.67 2.62
59 60 1.202758 TGTCAATGACAGCCGGAAAGT 60.203 47.619 12.63 0.00 37.67 2.66
60 61 1.464997 GTCAATGACAGCCGGAAAGTC 59.535 52.381 5.05 10.20 32.09 3.01
61 62 1.347707 TCAATGACAGCCGGAAAGTCT 59.652 47.619 5.05 0.00 33.56 3.24
62 63 2.154462 CAATGACAGCCGGAAAGTCTT 58.846 47.619 5.05 4.75 33.56 3.01
63 64 2.100605 ATGACAGCCGGAAAGTCTTC 57.899 50.000 5.05 0.00 33.56 2.87
64 65 0.756294 TGACAGCCGGAAAGTCTTCA 59.244 50.000 5.05 0.00 32.75 3.02
65 66 1.347707 TGACAGCCGGAAAGTCTTCAT 59.652 47.619 5.05 0.00 32.75 2.57
79 80 0.464373 CTTCATGCACGTGCCCCTAT 60.464 55.000 35.72 20.71 41.18 2.57
116 127 1.732917 CGCTGTTGAACCCTTGCAA 59.267 52.632 0.00 0.00 0.00 4.08
140 151 2.997980 TCTGAAGCACTTGACACCAAA 58.002 42.857 0.00 0.00 0.00 3.28
154 165 1.197721 CACCAAATCTCGCCACAAGAC 59.802 52.381 0.00 0.00 0.00 3.01
163 174 0.234884 CGCCACAAGACGAGAAAACC 59.765 55.000 0.00 0.00 0.00 3.27
173 184 3.006644 AGACGAGAAAACCTAACCTCACC 59.993 47.826 0.00 0.00 0.00 4.02
179 190 4.157120 CCTAACCTCACCGCCCCG 62.157 72.222 0.00 0.00 0.00 5.73
186 197 3.358076 CTCACCGCCCCGAAGAGAC 62.358 68.421 0.00 0.00 32.46 3.36
189 200 4.493747 CCGCCCCGAAGAGACGAC 62.494 72.222 0.00 0.00 35.09 4.34
199 210 3.566322 CCGAAGAGACGACAGGAATCTAT 59.434 47.826 0.00 0.00 35.09 1.98
202 213 2.625790 AGAGACGACAGGAATCTATGCC 59.374 50.000 0.00 0.00 0.00 4.40
203 214 2.362397 GAGACGACAGGAATCTATGCCA 59.638 50.000 0.00 0.00 0.00 4.92
238 249 2.177950 GTCTAGACGGGCGAACTCA 58.822 57.895 7.22 0.00 0.00 3.41
249 260 0.456221 GCGAACTCAAGGAGGATCGA 59.544 55.000 20.39 0.00 41.85 3.59
251 262 2.803451 CGAACTCAAGGAGGATCGAAG 58.197 52.381 14.50 0.00 41.85 3.79
252 263 2.545731 GAACTCAAGGAGGATCGAAGC 58.454 52.381 0.00 0.00 34.37 3.86
253 264 1.561643 ACTCAAGGAGGATCGAAGCA 58.438 50.000 0.00 0.00 34.37 3.91
282 293 0.456312 AACTCGAAGAAGTAGCGCCG 60.456 55.000 2.29 0.00 34.09 6.46
286 297 1.521681 GAAGAAGTAGCGCCGCCAT 60.522 57.895 4.98 0.00 0.00 4.40
347 358 5.473066 AACCTAAACTACTAACCGAAGCA 57.527 39.130 0.00 0.00 0.00 3.91
363 374 0.322546 AGCAAAGACACCGGGATTCC 60.323 55.000 6.32 0.00 0.00 3.01
399 410 2.268280 CCAGAGTGGCAGGCAGAG 59.732 66.667 0.00 0.00 0.00 3.35
411 422 2.592308 GCAGAGGGGAGGCGAATT 59.408 61.111 0.00 0.00 0.00 2.17
412 423 1.077429 GCAGAGGGGAGGCGAATTT 60.077 57.895 0.00 0.00 0.00 1.82
415 426 2.498167 CAGAGGGGAGGCGAATTTATG 58.502 52.381 0.00 0.00 0.00 1.90
422 433 0.180406 AGGCGAATTTATGGGCTCGT 59.820 50.000 0.00 0.00 33.87 4.18
424 435 1.295792 GCGAATTTATGGGCTCGTCA 58.704 50.000 0.00 0.00 33.87 4.35
426 437 1.261619 CGAATTTATGGGCTCGTCAGC 59.738 52.381 0.00 0.00 46.06 4.26
439 450 0.319555 CGTCAGCGAAGTTTGGAGGA 60.320 55.000 0.00 0.00 41.33 3.71
440 451 1.673033 CGTCAGCGAAGTTTGGAGGAT 60.673 52.381 0.00 0.00 41.33 3.24
441 452 2.416836 CGTCAGCGAAGTTTGGAGGATA 60.417 50.000 0.00 0.00 41.33 2.59
459 470 0.976073 TAGAGTTTGCCCTAGCCGCT 60.976 55.000 0.00 0.00 38.69 5.52
481 492 5.183331 GCTTAGGGTTAGGGAAGAAAAACAG 59.817 44.000 0.00 0.00 0.00 3.16
483 494 3.162666 GGGTTAGGGAAGAAAAACAGGG 58.837 50.000 0.00 0.00 0.00 4.45
487 498 1.203063 AGGGAAGAAAAACAGGGAGCC 60.203 52.381 0.00 0.00 0.00 4.70
497 508 3.876309 AACAGGGAGCCAGAGTTTTAA 57.124 42.857 0.00 0.00 0.00 1.52
500 511 5.104259 ACAGGGAGCCAGAGTTTTAATAG 57.896 43.478 0.00 0.00 0.00 1.73
507 518 7.068226 GGGAGCCAGAGTTTTAATAGCAAAATA 59.932 37.037 0.00 0.00 30.56 1.40
530 576 9.598517 AATAAAAATCGTGGACCTATTTACGTA 57.401 29.630 0.00 0.00 37.74 3.57
531 577 9.768662 ATAAAAATCGTGGACCTATTTACGTAT 57.231 29.630 0.00 0.00 37.74 3.06
534 580 9.768662 AAAATCGTGGACCTATTTACGTATATT 57.231 29.630 3.80 0.00 37.74 1.28
535 581 8.752766 AATCGTGGACCTATTTACGTATATTG 57.247 34.615 3.80 2.59 37.74 1.90
536 582 7.275888 TCGTGGACCTATTTACGTATATTGT 57.724 36.000 3.80 2.86 37.74 2.71
537 583 8.389779 TCGTGGACCTATTTACGTATATTGTA 57.610 34.615 3.80 0.00 37.74 2.41
538 584 8.506437 TCGTGGACCTATTTACGTATATTGTAG 58.494 37.037 3.80 0.00 37.74 2.74
540 586 7.272084 GTGGACCTATTTACGTATATTGTAGCG 59.728 40.741 3.80 0.00 0.00 4.26
668 766 1.037493 TTATCCCACACGCGCTAGAT 58.963 50.000 5.73 4.41 0.00 1.98
699 797 3.954030 CGGATCGCTTACGTATCAATG 57.046 47.619 0.00 0.00 41.18 2.82
1246 1361 4.456253 CGTCCTCGTCGTGGTCGG 62.456 72.222 20.28 6.04 37.69 4.79
1370 1506 0.689412 GAGGTGAAGGAGGAGGAGGG 60.689 65.000 0.00 0.00 0.00 4.30
1569 1706 0.782384 CTGTTGTTGCGTAGGACGAC 59.218 55.000 2.65 0.00 46.05 4.34
1743 1887 8.504812 AAATGCAAGATTAGTTTGGTTGTTTT 57.495 26.923 0.00 0.00 0.00 2.43
1746 1890 7.271511 TGCAAGATTAGTTTGGTTGTTTTGAT 58.728 30.769 0.00 0.00 0.00 2.57
1759 1903 2.437281 TGTTTTGATGGCATTGGGTGTT 59.563 40.909 0.00 0.00 0.00 3.32
1773 1917 2.697751 TGGGTGTTTGATTCCAACCTTG 59.302 45.455 0.00 0.00 39.29 3.61
1774 1918 2.698274 GGGTGTTTGATTCCAACCTTGT 59.302 45.455 0.00 0.00 35.47 3.16
1777 1921 5.182487 GGTGTTTGATTCCAACCTTGTTTT 58.818 37.500 0.00 0.00 30.88 2.43
1781 1925 7.119116 GTGTTTGATTCCAACCTTGTTTTCTTT 59.881 33.333 0.00 0.00 30.88 2.52
1784 1928 6.039616 TGATTCCAACCTTGTTTTCTTTTCG 58.960 36.000 0.00 0.00 0.00 3.46
1786 1930 4.989044 TCCAACCTTGTTTTCTTTTCGTC 58.011 39.130 0.00 0.00 0.00 4.20
1789 1933 5.515270 CCAACCTTGTTTTCTTTTCGTCTTC 59.485 40.000 0.00 0.00 0.00 2.87
1792 1961 5.163652 ACCTTGTTTTCTTTTCGTCTTCTGG 60.164 40.000 0.00 0.00 0.00 3.86
1801 1970 5.894393 TCTTTTCGTCTTCTGGGATAGAGAT 59.106 40.000 0.00 0.00 36.61 2.75
1804 1973 5.827326 TCGTCTTCTGGGATAGAGATAGA 57.173 43.478 0.00 0.00 36.61 1.98
1807 1976 6.214615 TCGTCTTCTGGGATAGAGATAGAGAT 59.785 42.308 0.00 0.00 36.61 2.75
1811 1980 6.260700 TCTGGGATAGAGATAGAGATAGGC 57.739 45.833 0.00 0.00 0.00 3.93
1862 2035 3.760151 TGAAGGAAGACATGGCAGAATTG 59.240 43.478 0.00 0.00 0.00 2.32
1881 2054 2.253758 TTTGCAGCGTCAGCCTGTC 61.254 57.895 0.00 0.00 46.67 3.51
1882 2055 2.939133 TTTGCAGCGTCAGCCTGTCA 62.939 55.000 0.00 0.00 46.67 3.58
1883 2056 3.117171 GCAGCGTCAGCCTGTCAG 61.117 66.667 0.00 0.00 46.67 3.51
1884 2057 2.433838 CAGCGTCAGCCTGTCAGG 60.434 66.667 15.15 15.15 46.67 3.86
1885 2058 2.601666 AGCGTCAGCCTGTCAGGA 60.602 61.111 23.77 0.00 46.67 3.86
2041 2230 2.762887 CTCTAGCCTGTGAGGAATGACA 59.237 50.000 0.00 0.00 37.67 3.58
2042 2231 3.378512 TCTAGCCTGTGAGGAATGACAT 58.621 45.455 0.00 0.00 37.67 3.06
2043 2232 4.546674 TCTAGCCTGTGAGGAATGACATA 58.453 43.478 0.00 0.00 37.67 2.29
2137 2352 4.025858 AGTCGCTGGCATGTGGCT 62.026 61.111 8.09 0.00 44.01 4.75
2160 2375 6.009908 TCCATGATCCACATTTCATCTTCT 57.990 37.500 0.00 0.00 37.07 2.85
2434 6557 9.177608 ACATATGCACTACTTTTTCATGTATGT 57.822 29.630 1.58 0.00 0.00 2.29
2448 6571 6.573664 TCATGTATGTGAAAACCTGGAAAG 57.426 37.500 0.00 0.00 0.00 2.62
2452 6575 3.094484 TGTGAAAACCTGGAAAGTGGT 57.906 42.857 0.00 0.00 38.35 4.16
2472 6595 6.268847 AGTGGTAAGACAGAAAAGACATCTCT 59.731 38.462 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.496817 GTAGGGGAGCTGCGACAG 59.503 66.667 0.00 2.92 34.12 3.51
5 6 3.075005 GGTAGGGGAGCTGCGACA 61.075 66.667 0.00 0.00 0.00 4.35
6 7 4.208686 CGGTAGGGGAGCTGCGAC 62.209 72.222 0.00 0.00 0.00 5.19
9 10 3.541713 CTCCGGTAGGGGAGCTGC 61.542 72.222 0.00 0.00 46.53 5.25
22 23 2.032071 AAGGTCAAACCGGCTCCG 59.968 61.111 0.00 0.48 44.90 4.63
23 24 1.228154 ACAAGGTCAAACCGGCTCC 60.228 57.895 0.00 0.00 44.90 4.70
24 25 0.534203 TGACAAGGTCAAACCGGCTC 60.534 55.000 0.00 0.00 44.90 4.70
25 26 1.529796 TGACAAGGTCAAACCGGCT 59.470 52.632 0.00 0.00 44.90 5.52
26 27 4.150994 TGACAAGGTCAAACCGGC 57.849 55.556 0.00 0.00 44.90 6.13
33 34 1.877680 CGGCTGTCATTGACAAGGTCA 60.878 52.381 19.44 0.00 42.26 4.02
34 35 0.798776 CGGCTGTCATTGACAAGGTC 59.201 55.000 19.44 10.18 42.26 3.85
35 36 0.606401 CCGGCTGTCATTGACAAGGT 60.606 55.000 19.44 0.00 42.26 3.50
36 37 0.321564 TCCGGCTGTCATTGACAAGG 60.322 55.000 19.44 20.18 42.26 3.61
37 38 1.522668 TTCCGGCTGTCATTGACAAG 58.477 50.000 19.44 14.19 42.26 3.16
38 39 1.879380 CTTTCCGGCTGTCATTGACAA 59.121 47.619 19.44 2.67 42.26 3.18
39 40 1.202758 ACTTTCCGGCTGTCATTGACA 60.203 47.619 18.08 18.08 40.50 3.58
40 41 1.464997 GACTTTCCGGCTGTCATTGAC 59.535 52.381 9.93 9.93 0.00 3.18
41 42 1.347707 AGACTTTCCGGCTGTCATTGA 59.652 47.619 18.54 0.00 33.56 2.57
42 43 1.813513 AGACTTTCCGGCTGTCATTG 58.186 50.000 18.54 0.00 33.56 2.82
43 44 2.224523 TGAAGACTTTCCGGCTGTCATT 60.225 45.455 18.54 11.88 33.56 2.57
44 45 1.347707 TGAAGACTTTCCGGCTGTCAT 59.652 47.619 18.54 10.19 33.56 3.06
45 46 0.756294 TGAAGACTTTCCGGCTGTCA 59.244 50.000 18.54 4.51 33.56 3.58
46 47 1.734465 CATGAAGACTTTCCGGCTGTC 59.266 52.381 0.00 4.81 32.09 3.51
47 48 1.813513 CATGAAGACTTTCCGGCTGT 58.186 50.000 0.00 0.00 32.09 4.40
48 49 0.449388 GCATGAAGACTTTCCGGCTG 59.551 55.000 0.00 0.00 32.06 4.85
49 50 0.036732 TGCATGAAGACTTTCCGGCT 59.963 50.000 0.00 0.00 34.39 5.52
50 51 0.169009 GTGCATGAAGACTTTCCGGC 59.831 55.000 0.00 0.00 34.08 6.13
51 52 0.443869 CGTGCATGAAGACTTTCCGG 59.556 55.000 0.00 0.00 32.09 5.14
52 53 1.136252 CACGTGCATGAAGACTTTCCG 60.136 52.381 14.17 0.00 32.09 4.30
53 54 1.400242 GCACGTGCATGAAGACTTTCC 60.400 52.381 34.52 0.00 41.59 3.13
54 55 1.400242 GGCACGTGCATGAAGACTTTC 60.400 52.381 38.60 15.36 44.36 2.62
55 56 0.593128 GGCACGTGCATGAAGACTTT 59.407 50.000 38.60 0.00 44.36 2.66
56 57 1.237285 GGGCACGTGCATGAAGACTT 61.237 55.000 38.60 0.00 44.36 3.01
57 58 1.672356 GGGCACGTGCATGAAGACT 60.672 57.895 38.60 0.00 44.36 3.24
58 59 2.690778 GGGGCACGTGCATGAAGAC 61.691 63.158 38.60 20.85 44.36 3.01
59 60 1.549243 TAGGGGCACGTGCATGAAGA 61.549 55.000 38.60 17.55 44.36 2.87
60 61 0.464373 ATAGGGGCACGTGCATGAAG 60.464 55.000 38.60 5.84 44.36 3.02
61 62 0.747644 CATAGGGGCACGTGCATGAA 60.748 55.000 38.60 22.61 44.36 2.57
62 63 1.153188 CATAGGGGCACGTGCATGA 60.153 57.895 38.60 22.15 44.36 3.07
63 64 2.188829 CCATAGGGGCACGTGCATG 61.189 63.158 38.60 30.61 44.36 4.06
64 65 2.192979 CCATAGGGGCACGTGCAT 59.807 61.111 38.60 26.23 44.36 3.96
89 90 3.551496 TTCAACAGCGGCTCCAGGG 62.551 63.158 0.00 0.00 0.00 4.45
101 102 3.318839 CAGATCTTTGCAAGGGTTCAACA 59.681 43.478 8.88 0.00 0.00 3.33
116 127 3.181451 TGGTGTCAAGTGCTTCAGATCTT 60.181 43.478 0.00 0.00 0.00 2.40
129 140 1.197721 GTGGCGAGATTTGGTGTCAAG 59.802 52.381 0.00 0.00 33.98 3.02
130 141 1.234821 GTGGCGAGATTTGGTGTCAA 58.765 50.000 0.00 0.00 0.00 3.18
154 165 2.334838 CGGTGAGGTTAGGTTTTCTCG 58.665 52.381 0.00 0.00 0.00 4.04
163 174 2.573609 CTTCGGGGCGGTGAGGTTAG 62.574 65.000 0.00 0.00 0.00 2.34
173 184 3.685214 CTGTCGTCTCTTCGGGGCG 62.685 68.421 0.00 0.00 0.00 6.13
179 190 4.295051 GCATAGATTCCTGTCGTCTCTTC 58.705 47.826 0.00 0.00 0.00 2.87
186 197 2.865670 GCTCTGGCATAGATTCCTGTCG 60.866 54.545 3.79 0.00 38.54 4.35
188 199 2.368221 GAGCTCTGGCATAGATTCCTGT 59.632 50.000 6.43 0.00 41.70 4.00
189 200 2.289569 GGAGCTCTGGCATAGATTCCTG 60.290 54.545 14.64 0.00 41.70 3.86
199 210 2.814913 TAGTCGACGGAGCTCTGGCA 62.815 60.000 27.90 12.44 41.70 4.92
230 241 0.456221 TCGATCCTCCTTGAGTTCGC 59.544 55.000 8.13 0.00 35.15 4.70
232 243 2.093973 TGCTTCGATCCTCCTTGAGTTC 60.094 50.000 0.00 0.00 0.00 3.01
238 249 0.970937 TCCGTGCTTCGATCCTCCTT 60.971 55.000 3.69 0.00 42.86 3.36
249 260 1.202486 TCGAGTTTGTCTTCCGTGCTT 60.202 47.619 0.00 0.00 0.00 3.91
251 262 1.192534 CTTCGAGTTTGTCTTCCGTGC 59.807 52.381 0.00 0.00 0.00 5.34
252 263 2.739292 TCTTCGAGTTTGTCTTCCGTG 58.261 47.619 0.00 0.00 0.00 4.94
253 264 3.181478 ACTTCTTCGAGTTTGTCTTCCGT 60.181 43.478 0.00 0.00 0.00 4.69
321 332 7.093354 GCTTCGGTTAGTAGTTTAGGTTAGTT 58.907 38.462 0.00 0.00 0.00 2.24
322 333 6.209391 TGCTTCGGTTAGTAGTTTAGGTTAGT 59.791 38.462 0.00 0.00 0.00 2.24
326 337 5.473066 TTGCTTCGGTTAGTAGTTTAGGT 57.527 39.130 0.00 0.00 0.00 3.08
327 338 6.090493 GTCTTTGCTTCGGTTAGTAGTTTAGG 59.910 42.308 0.00 0.00 0.00 2.69
331 342 4.748600 GTGTCTTTGCTTCGGTTAGTAGTT 59.251 41.667 0.00 0.00 0.00 2.24
343 354 1.534729 GAATCCCGGTGTCTTTGCTT 58.465 50.000 0.00 0.00 0.00 3.91
381 392 2.527624 TCTGCCTGCCACTCTGGT 60.528 61.111 0.00 0.00 40.46 4.00
384 395 3.007920 CCCTCTGCCTGCCACTCT 61.008 66.667 0.00 0.00 0.00 3.24
396 407 1.421646 CCATAAATTCGCCTCCCCTCT 59.578 52.381 0.00 0.00 0.00 3.69
399 410 1.179174 GCCCATAAATTCGCCTCCCC 61.179 60.000 0.00 0.00 0.00 4.81
406 417 1.261619 GCTGACGAGCCCATAAATTCG 59.738 52.381 0.00 0.00 39.57 3.34
411 422 3.610976 TCGCTGACGAGCCCATAA 58.389 55.556 0.00 0.00 45.12 1.90
422 433 3.096852 TCTATCCTCCAAACTTCGCTGA 58.903 45.455 0.00 0.00 0.00 4.26
424 435 3.100671 ACTCTATCCTCCAAACTTCGCT 58.899 45.455 0.00 0.00 0.00 4.93
426 437 4.093556 GCAAACTCTATCCTCCAAACTTCG 59.906 45.833 0.00 0.00 0.00 3.79
435 446 2.037902 GGCTAGGGCAAACTCTATCCTC 59.962 54.545 0.00 0.00 40.87 3.71
439 450 0.106894 GCGGCTAGGGCAAACTCTAT 59.893 55.000 0.00 0.00 40.87 1.98
440 451 0.976073 AGCGGCTAGGGCAAACTCTA 60.976 55.000 0.00 0.00 40.87 2.43
441 452 1.842381 AAGCGGCTAGGGCAAACTCT 61.842 55.000 1.35 0.00 40.87 3.24
459 470 5.458508 CCCTGTTTTTCTTCCCTAACCCTAA 60.459 44.000 0.00 0.00 0.00 2.69
468 479 1.257743 GGCTCCCTGTTTTTCTTCCC 58.742 55.000 0.00 0.00 0.00 3.97
481 492 3.886123 TGCTATTAAAACTCTGGCTCCC 58.114 45.455 0.00 0.00 0.00 4.30
483 494 9.855021 TTTATTTTGCTATTAAAACTCTGGCTC 57.145 29.630 0.00 0.00 32.86 4.70
497 508 7.404671 AGGTCCACGATTTTTATTTTGCTAT 57.595 32.000 0.00 0.00 0.00 2.97
500 511 8.474006 AAATAGGTCCACGATTTTTATTTTGC 57.526 30.769 0.00 0.00 31.45 3.68
507 518 9.768662 ATATACGTAAATAGGTCCACGATTTTT 57.231 29.630 0.00 0.00 36.14 1.94
516 562 7.272084 CACGCTACAATATACGTAAATAGGTCC 59.728 40.741 0.00 0.00 36.91 4.46
519 565 7.086376 ACCACGCTACAATATACGTAAATAGG 58.914 38.462 0.00 0.00 36.91 2.57
534 580 8.329583 CGATGTTTATTATAAAACCACGCTACA 58.670 33.333 0.00 0.00 38.35 2.74
535 581 8.330302 ACGATGTTTATTATAAAACCACGCTAC 58.670 33.333 0.00 0.00 38.83 3.58
536 582 8.329583 CACGATGTTTATTATAAAACCACGCTA 58.670 33.333 0.00 0.00 38.83 4.26
537 583 7.184106 CACGATGTTTATTATAAAACCACGCT 58.816 34.615 0.00 0.00 38.83 5.07
538 584 6.412653 CCACGATGTTTATTATAAAACCACGC 59.587 38.462 0.00 0.00 38.83 5.34
540 586 8.671028 ACTCCACGATGTTTATTATAAAACCAC 58.329 33.333 0.00 0.00 38.35 4.16
632 730 7.709182 TGTGGGATAACATGTAGACGATTTTAG 59.291 37.037 0.00 0.00 0.00 1.85
699 797 3.184581 CCGCGTCCTAATAAATCTCAAGC 59.815 47.826 4.92 0.00 0.00 4.01
1219 1334 2.125229 CGAGGACGACGAGGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
1380 1516 2.687566 AACCCTTCCTCCGGCGAT 60.688 61.111 9.30 0.00 0.00 4.58
1508 1644 0.035458 CTTAGCTCTAATGGGGGCGG 59.965 60.000 0.00 0.00 0.00 6.13
1569 1706 3.101428 CGAACCGAACCGTCACCG 61.101 66.667 0.00 0.00 0.00 4.94
1723 1867 7.307337 GCCATCAAAACAACCAAACTAATCTTG 60.307 37.037 0.00 0.00 0.00 3.02
1724 1868 6.705825 GCCATCAAAACAACCAAACTAATCTT 59.294 34.615 0.00 0.00 0.00 2.40
1743 1887 2.006805 TCAAACACCCAATGCCATCA 57.993 45.000 0.00 0.00 0.00 3.07
1746 1890 1.622811 GGAATCAAACACCCAATGCCA 59.377 47.619 0.00 0.00 0.00 4.92
1759 1903 6.533367 CGAAAAGAAAACAAGGTTGGAATCAA 59.467 34.615 0.00 0.00 0.00 2.57
1773 1917 5.690997 ATCCCAGAAGACGAAAAGAAAAC 57.309 39.130 0.00 0.00 0.00 2.43
1774 1918 6.765403 TCTATCCCAGAAGACGAAAAGAAAA 58.235 36.000 0.00 0.00 0.00 2.29
1777 1921 5.262009 TCTCTATCCCAGAAGACGAAAAGA 58.738 41.667 0.00 0.00 31.12 2.52
1781 1925 6.043358 TCTCTATCTCTATCCCAGAAGACGAA 59.957 42.308 0.00 0.00 31.12 3.85
1784 1928 7.993183 CCTATCTCTATCTCTATCCCAGAAGAC 59.007 44.444 0.00 0.00 31.12 3.01
1786 1930 6.772716 GCCTATCTCTATCTCTATCCCAGAAG 59.227 46.154 0.00 0.00 31.12 2.85
1789 1933 6.012337 TGCCTATCTCTATCTCTATCCCAG 57.988 45.833 0.00 0.00 0.00 4.45
1792 1961 4.827284 GCCTGCCTATCTCTATCTCTATCC 59.173 50.000 0.00 0.00 0.00 2.59
1801 1970 0.605083 CATGCGCCTGCCTATCTCTA 59.395 55.000 4.18 0.00 41.78 2.43
1804 1973 2.281345 GCATGCGCCTGCCTATCT 60.281 61.111 24.98 0.00 41.78 1.98
1807 1976 3.473647 AGAGCATGCGCCTGCCTA 61.474 61.111 30.22 0.00 43.33 3.93
1811 1980 1.744368 AGTTCAGAGCATGCGCCTG 60.744 57.895 26.73 26.73 39.83 4.85
1862 2035 2.253452 CAGGCTGACGCTGCAAAC 59.747 61.111 9.42 0.00 36.09 2.93
1881 2054 1.276421 CACCTAACCACTCCTGTCCTG 59.724 57.143 0.00 0.00 0.00 3.86
1882 2055 1.645710 CACCTAACCACTCCTGTCCT 58.354 55.000 0.00 0.00 0.00 3.85
1883 2056 0.036294 GCACCTAACCACTCCTGTCC 60.036 60.000 0.00 0.00 0.00 4.02
1884 2057 0.685097 TGCACCTAACCACTCCTGTC 59.315 55.000 0.00 0.00 0.00 3.51
1885 2058 0.687354 CTGCACCTAACCACTCCTGT 59.313 55.000 0.00 0.00 0.00 4.00
2137 2352 6.009908 AGAAGATGAAATGTGGATCATGGA 57.990 37.500 0.00 0.00 36.45 3.41
2160 2375 6.839124 ATCTCAAATACAAACATCCAGCAA 57.161 33.333 0.00 0.00 0.00 3.91
2192 2407 4.620982 GCAAATGACACCAAAGTTAGCTT 58.379 39.130 0.00 0.00 36.30 3.74
2434 6557 4.885325 GTCTTACCACTTTCCAGGTTTTCA 59.115 41.667 0.00 0.00 39.31 2.69
2448 6571 6.367422 CAGAGATGTCTTTTCTGTCTTACCAC 59.633 42.308 0.00 0.00 34.92 4.16
2452 6575 9.613428 TTTTTCAGAGATGTCTTTTCTGTCTTA 57.387 29.630 6.27 0.00 39.41 2.10


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

AutoCloner maintained by Alex Coulton.