Multiple sequence alignment - TraesCS1A01G342100

Loading Multiple Alignment...

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 TraesCS1A01G342100 chr1A 100.000 2384 0 0 1 2384 531368730 531366347 0.000000e+00 4403.0
1 TraesCS1A01G342100 chr1A 90.650 1401 78 29 357 1722 531514517 531513135 0.000000e+00 1812.0
2 TraesCS1A01G342100 chr1A 89.230 1402 96 34 357 1722 531563346 531561964 0.000000e+00 1701.0
3 TraesCS1A01G342100 chr1A 85.330 409 20 21 126 513 531515409 531515020 1.030000e-103 387.0
4 TraesCS1A01G342100 chr1A 88.889 135 11 2 2062 2196 531510437 531510307 1.900000e-36 163.0
5 TraesCS1A01G342100 chr1A 96.809 94 2 1 1 93 49970206 49970299 3.170000e-34 156.0
6 TraesCS1A01G342100 chr1D 90.101 2283 112 48 136 2384 433062135 433059933 0.000000e+00 2859.0
7 TraesCS1A01G342100 chr1D 91.955 1243 68 12 510 1737 433093831 433092606 0.000000e+00 1712.0
8 TraesCS1A01G342100 chr1D 87.730 163 7 6 95 254 433062352 433062200 6.770000e-41 178.0
9 TraesCS1A01G342100 chr1D 92.391 92 5 1 1 92 389546849 389546760 1.920000e-26 130.0
10 TraesCS1A01G342100 chr1D 84.615 130 10 6 1887 2006 433140900 433140771 1.160000e-23 121.0
11 TraesCS1A01G342100 chr1B 89.785 1674 96 32 224 1840 584621938 584620283 0.000000e+00 2074.0
12 TraesCS1A01G342100 chr1B 85.700 2042 159 62 224 2164 584605304 584603295 0.000000e+00 2032.0
13 TraesCS1A01G342100 chr1B 89.895 1623 89 29 275 1840 584576526 584574922 0.000000e+00 2019.0
14 TraesCS1A01G342100 chr1B 85.544 2013 170 60 244 2164 584655712 584653729 0.000000e+00 1993.0
15 TraesCS1A01G342100 chr1B 89.191 1434 72 29 357 1749 584780679 584779288 0.000000e+00 1712.0
16 TraesCS1A01G342100 chr1B 89.030 1422 80 28 357 1741 584799471 584798089 0.000000e+00 1692.0
17 TraesCS1A01G342100 chr1B 91.461 972 58 10 224 1177 584567194 584566230 0.000000e+00 1312.0
18 TraesCS1A01G342100 chr1B 91.667 264 11 5 2121 2384 584564166 584563914 2.910000e-94 355.0
19 TraesCS1A01G342100 chr1B 91.667 264 11 5 2121 2384 584652880 584652628 2.910000e-94 355.0
20 TraesCS1A01G342100 chr1B 87.903 124 13 1 2062 2185 584875488 584875367 6.870000e-31 145.0
21 TraesCS1A01G342100 chr1B 87.903 124 13 1 2062 2185 584901891 584901770 6.870000e-31 145.0
22 TraesCS1A01G342100 chr1B 95.122 82 4 0 1 82 519642530 519642611 1.920000e-26 130.0
23 TraesCS1A01G342100 chr1B 97.561 41 1 0 95 135 584567523 584567483 1.180000e-08 71.3
24 TraesCS1A01G342100 chr1B 97.561 41 1 0 95 135 584605633 584605593 1.180000e-08 71.3
25 TraesCS1A01G342100 chr3B 86.924 1453 128 35 419 1840 647942625 647944046 0.000000e+00 1574.0
26 TraesCS1A01G342100 chr3B 84.544 647 66 20 1203 1840 647968832 647969453 5.630000e-171 610.0
27 TraesCS1A01G342100 chr3A 86.837 1451 130 32 419 1841 628218923 628220340 0.000000e+00 1565.0
28 TraesCS1A01G342100 chr3A 85.294 102 8 2 1 97 435780337 435780238 5.420000e-17 99.0
29 TraesCS1A01G342100 chr3D 88.915 1272 105 18 419 1667 485231140 485232398 0.000000e+00 1535.0
30 TraesCS1A01G342100 chr6A 84.848 561 68 9 1184 1741 616688597 616689143 1.250000e-152 549.0
31 TraesCS1A01G342100 chr7A 97.826 92 2 0 1 92 299256052 299256143 2.450000e-35 159.0
32 TraesCS1A01G342100 chr7A 95.699 93 4 0 1 93 520511204 520511296 1.480000e-32 150.0
33 TraesCS1A01G342100 chr7A 96.512 86 3 0 1 86 296570638 296570553 2.470000e-30 143.0
34 TraesCS1A01G342100 chr2A 92.473 93 6 1 1 93 594583307 594583216 5.350000e-27 132.0
35 TraesCS1A01G342100 chr2A 88.542 96 5 5 1 90 755932719 755932814 6.970000e-21 111.0
36 TraesCS1A01G342100 chr2A 81.905 105 9 7 2053 2157 779164680 779164774 1.960000e-11 80.5
37 TraesCS1A01G342100 chr7D 90.000 50 1 1 2071 2116 54310182 54310133 7.120000e-06 62.1


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 TraesCS1A01G342100 chr1A 531366347 531368730 2383 True 4403.000000 4403 100.000000 1 2384 1 chr1A.!!$R1 2383
1 TraesCS1A01G342100 chr1A 531561964 531563346 1382 True 1701.000000 1701 89.230000 357 1722 1 chr1A.!!$R2 1365
2 TraesCS1A01G342100 chr1A 531510307 531515409 5102 True 787.333333 1812 88.289667 126 2196 3 chr1A.!!$R3 2070
3 TraesCS1A01G342100 chr1D 433092606 433093831 1225 True 1712.000000 1712 91.955000 510 1737 1 chr1D.!!$R2 1227
4 TraesCS1A01G342100 chr1D 433059933 433062352 2419 True 1518.500000 2859 88.915500 95 2384 2 chr1D.!!$R4 2289
5 TraesCS1A01G342100 chr1B 584620283 584621938 1655 True 2074.000000 2074 89.785000 224 1840 1 chr1B.!!$R2 1616
6 TraesCS1A01G342100 chr1B 584574922 584576526 1604 True 2019.000000 2019 89.895000 275 1840 1 chr1B.!!$R1 1565
7 TraesCS1A01G342100 chr1B 584779288 584780679 1391 True 1712.000000 1712 89.191000 357 1749 1 chr1B.!!$R3 1392
8 TraesCS1A01G342100 chr1B 584798089 584799471 1382 True 1692.000000 1692 89.030000 357 1741 1 chr1B.!!$R4 1384
9 TraesCS1A01G342100 chr1B 584652628 584655712 3084 True 1174.000000 1993 88.605500 244 2384 2 chr1B.!!$R9 2140
10 TraesCS1A01G342100 chr1B 584603295 584605633 2338 True 1051.650000 2032 91.630500 95 2164 2 chr1B.!!$R8 2069
11 TraesCS1A01G342100 chr1B 584563914 584567523 3609 True 579.433333 1312 93.563000 95 2384 3 chr1B.!!$R7 2289
12 TraesCS1A01G342100 chr3B 647942625 647944046 1421 False 1574.000000 1574 86.924000 419 1840 1 chr3B.!!$F1 1421
13 TraesCS1A01G342100 chr3B 647968832 647969453 621 False 610.000000 610 84.544000 1203 1840 1 chr3B.!!$F2 637
14 TraesCS1A01G342100 chr3A 628218923 628220340 1417 False 1565.000000 1565 86.837000 419 1841 1 chr3A.!!$F1 1422
15 TraesCS1A01G342100 chr3D 485231140 485232398 1258 False 1535.000000 1535 88.915000 419 1667 1 chr3D.!!$F1 1248
16 TraesCS1A01G342100 chr6A 616688597 616689143 546 False 549.000000 549 84.848000 1184 1741 1 chr6A.!!$F1 557

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
19 20 0.107897 TCATGCCGTGTATGTGGGTC 60.108 55.0 0.0 0.0 0.00 4.46 F
25 26 0.320374 CGTGTATGTGGGTCACCTGT 59.680 55.0 0.0 0.0 37.76 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 2512 0.674895 GCTGTGATGCTTCCGTCCTT 60.675 55.000 0.00 0.0 0.00 3.36 R
1722 4246 1.267806 GTCAAGCAAGCAAGCAAGCTA 59.732 47.619 10.81 0.0 45.89 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
17 18 4.952704 TCATGCCGTGTATGTGGG 57.047 55.556 0.00 0.00 0.00 4.61
18 19 1.987213 TCATGCCGTGTATGTGGGT 59.013 52.632 0.00 0.00 0.00 4.51
19 20 0.107897 TCATGCCGTGTATGTGGGTC 60.108 55.000 0.00 0.00 0.00 4.46
20 21 0.392327 CATGCCGTGTATGTGGGTCA 60.392 55.000 0.00 0.00 0.00 4.02
21 22 0.392461 ATGCCGTGTATGTGGGTCAC 60.392 55.000 0.00 0.00 34.56 3.67
22 23 1.743995 GCCGTGTATGTGGGTCACC 60.744 63.158 0.00 0.00 32.73 4.02
23 24 1.980052 CCGTGTATGTGGGTCACCT 59.020 57.895 0.00 0.00 37.76 4.00
24 25 0.391130 CCGTGTATGTGGGTCACCTG 60.391 60.000 0.00 0.00 37.76 4.00
25 26 0.320374 CGTGTATGTGGGTCACCTGT 59.680 55.000 0.00 0.00 37.76 4.00
26 27 1.546923 CGTGTATGTGGGTCACCTGTA 59.453 52.381 0.00 0.00 37.76 2.74
27 28 2.028839 CGTGTATGTGGGTCACCTGTAA 60.029 50.000 0.00 0.00 37.76 2.41
28 29 3.332034 GTGTATGTGGGTCACCTGTAAC 58.668 50.000 0.00 0.00 37.76 2.50
29 30 2.973406 TGTATGTGGGTCACCTGTAACA 59.027 45.455 0.00 0.00 37.76 2.41
30 31 2.561478 ATGTGGGTCACCTGTAACAC 57.439 50.000 0.00 0.00 37.76 3.32
31 32 1.502690 TGTGGGTCACCTGTAACACT 58.497 50.000 0.00 0.00 37.76 3.55
32 33 1.414919 TGTGGGTCACCTGTAACACTC 59.585 52.381 0.00 0.00 37.76 3.51
33 34 1.692519 GTGGGTCACCTGTAACACTCT 59.307 52.381 0.00 0.00 37.76 3.24
34 35 2.895404 GTGGGTCACCTGTAACACTCTA 59.105 50.000 0.00 0.00 37.76 2.43
35 36 3.322828 GTGGGTCACCTGTAACACTCTAA 59.677 47.826 0.00 0.00 37.76 2.10
36 37 3.968649 TGGGTCACCTGTAACACTCTAAA 59.031 43.478 0.00 0.00 37.76 1.85
37 38 4.202284 TGGGTCACCTGTAACACTCTAAAC 60.202 45.833 0.00 0.00 37.76 2.01
38 39 4.040095 GGGTCACCTGTAACACTCTAAACT 59.960 45.833 0.00 0.00 0.00 2.66
39 40 5.228665 GGTCACCTGTAACACTCTAAACTC 58.771 45.833 0.00 0.00 0.00 3.01
40 41 5.010820 GGTCACCTGTAACACTCTAAACTCT 59.989 44.000 0.00 0.00 0.00 3.24
41 42 6.151004 GTCACCTGTAACACTCTAAACTCTC 58.849 44.000 0.00 0.00 0.00 3.20
42 43 6.016108 GTCACCTGTAACACTCTAAACTCTCT 60.016 42.308 0.00 0.00 0.00 3.10
43 44 6.550108 TCACCTGTAACACTCTAAACTCTCTT 59.450 38.462 0.00 0.00 0.00 2.85
44 45 6.864165 CACCTGTAACACTCTAAACTCTCTTC 59.136 42.308 0.00 0.00 0.00 2.87
45 46 6.778559 ACCTGTAACACTCTAAACTCTCTTCT 59.221 38.462 0.00 0.00 0.00 2.85
46 47 7.288158 ACCTGTAACACTCTAAACTCTCTTCTT 59.712 37.037 0.00 0.00 0.00 2.52
47 48 8.794553 CCTGTAACACTCTAAACTCTCTTCTTA 58.205 37.037 0.00 0.00 0.00 2.10
55 56 9.883142 ACTCTAAACTCTCTTCTTATTCAATGG 57.117 33.333 0.00 0.00 0.00 3.16
60 61 8.961294 AACTCTCTTCTTATTCAATGGATGAG 57.039 34.615 9.71 9.71 39.77 2.90
61 62 7.507829 ACTCTCTTCTTATTCAATGGATGAGG 58.492 38.462 13.25 9.29 39.77 3.86
62 63 6.294473 TCTCTTCTTATTCAATGGATGAGGC 58.706 40.000 13.25 0.00 39.77 4.70
63 64 6.005066 TCTTCTTATTCAATGGATGAGGCA 57.995 37.500 0.00 0.00 39.77 4.75
64 65 6.425735 TCTTCTTATTCAATGGATGAGGCAA 58.574 36.000 0.00 0.00 39.77 4.52
65 66 6.891361 TCTTCTTATTCAATGGATGAGGCAAA 59.109 34.615 0.00 0.00 39.77 3.68
66 67 7.562454 TCTTCTTATTCAATGGATGAGGCAAAT 59.438 33.333 0.00 0.00 39.77 2.32
67 68 7.281040 TCTTATTCAATGGATGAGGCAAATC 57.719 36.000 0.00 0.00 39.77 2.17
68 69 7.064866 TCTTATTCAATGGATGAGGCAAATCT 58.935 34.615 0.00 0.00 39.77 2.40
69 70 7.562454 TCTTATTCAATGGATGAGGCAAATCTT 59.438 33.333 0.00 0.00 39.77 2.40
70 71 8.765488 TTATTCAATGGATGAGGCAAATCTTA 57.235 30.769 0.00 0.00 39.77 2.10
71 72 7.850935 ATTCAATGGATGAGGCAAATCTTAT 57.149 32.000 0.00 0.00 39.77 1.73
72 73 6.644248 TCAATGGATGAGGCAAATCTTATG 57.356 37.500 0.00 0.00 33.04 1.90
73 74 5.010314 TCAATGGATGAGGCAAATCTTATGC 59.990 40.000 0.00 0.00 36.73 3.14
81 82 3.782889 GCAAATCTTATGCCTCCGTTT 57.217 42.857 0.00 0.00 37.85 3.60
82 83 3.695816 GCAAATCTTATGCCTCCGTTTC 58.304 45.455 0.00 0.00 37.85 2.78
83 84 3.788797 GCAAATCTTATGCCTCCGTTTCG 60.789 47.826 0.00 0.00 37.85 3.46
84 85 3.536956 AATCTTATGCCTCCGTTTCGA 57.463 42.857 0.00 0.00 0.00 3.71
85 86 3.536956 ATCTTATGCCTCCGTTTCGAA 57.463 42.857 0.00 0.00 0.00 3.71
86 87 3.322211 TCTTATGCCTCCGTTTCGAAA 57.678 42.857 6.47 6.47 0.00 3.46
87 88 3.666274 TCTTATGCCTCCGTTTCGAAAA 58.334 40.909 13.10 0.00 0.00 2.29
88 89 4.066490 TCTTATGCCTCCGTTTCGAAAAA 58.934 39.130 13.10 0.44 0.00 1.94
212 424 3.896888 TCCCTTTGTTCGTTCCTAGTGTA 59.103 43.478 0.00 0.00 0.00 2.90
213 425 4.021719 TCCCTTTGTTCGTTCCTAGTGTAG 60.022 45.833 0.00 0.00 0.00 2.74
214 426 4.262335 CCCTTTGTTCGTTCCTAGTGTAGT 60.262 45.833 0.00 0.00 0.00 2.73
215 427 5.047802 CCCTTTGTTCGTTCCTAGTGTAGTA 60.048 44.000 0.00 0.00 0.00 1.82
216 428 6.091437 CCTTTGTTCGTTCCTAGTGTAGTAG 58.909 44.000 0.00 0.00 0.00 2.57
217 429 6.294397 CCTTTGTTCGTTCCTAGTGTAGTAGT 60.294 42.308 0.00 0.00 0.00 2.73
218 430 5.618056 TGTTCGTTCCTAGTGTAGTAGTG 57.382 43.478 0.00 0.00 0.00 2.74
219 431 5.065914 TGTTCGTTCCTAGTGTAGTAGTGT 58.934 41.667 0.00 0.00 0.00 3.55
222 434 5.308014 TCGTTCCTAGTGTAGTAGTGTTGA 58.692 41.667 0.00 0.00 0.00 3.18
270 658 1.071071 TCCTTTTCCGGTCATCGTTGT 59.929 47.619 0.00 0.00 37.11 3.32
305 694 1.825090 TGTTTATGCACCAGCTGAGG 58.175 50.000 17.39 7.82 42.74 3.86
306 695 1.350684 TGTTTATGCACCAGCTGAGGA 59.649 47.619 17.39 9.18 42.74 3.71
307 696 2.025981 TGTTTATGCACCAGCTGAGGAT 60.026 45.455 17.39 15.99 42.74 3.24
314 703 3.199727 TGCACCAGCTGAGGATGTAATTA 59.800 43.478 17.39 0.00 42.74 1.40
331 720 6.408869 TGTAATTAAGGAGTAGGTTTTCGGG 58.591 40.000 0.00 0.00 0.00 5.14
465 1553 6.377146 TGGCTAGAATTGAACCAAGAATAACC 59.623 38.462 0.00 0.00 0.00 2.85
469 1557 9.846248 CTAGAATTGAACCAAGAATAACCAAAG 57.154 33.333 0.00 0.00 0.00 2.77
470 1558 7.670364 AGAATTGAACCAAGAATAACCAAAGG 58.330 34.615 0.00 0.00 0.00 3.11
473 1561 7.425224 TTGAACCAAGAATAACCAAAGGAAA 57.575 32.000 0.00 0.00 0.00 3.13
529 1642 1.675483 ACAACATGAACTCGCTTGCAA 59.325 42.857 0.00 0.00 0.00 4.08
624 1762 7.439356 TGCTGCACTTATTAGTAGTGATTGATC 59.561 37.037 0.00 0.00 44.52 2.92
636 1774 2.309764 GATTGATCGCGCGGCAGTTT 62.310 55.000 31.69 15.83 0.00 2.66
849 1987 1.151450 CCTGTCCAGCTTGTTGGGT 59.849 57.895 3.76 0.00 38.81 4.51
867 2005 0.884704 GTGTCACCACGTCCTGCATT 60.885 55.000 0.00 0.00 0.00 3.56
1170 2311 1.679032 GCCGGCATCTGGAAGTTTACT 60.679 52.381 24.80 0.00 33.76 2.24
1329 2481 2.347490 GGCGGGCTGAGTTTCTCA 59.653 61.111 0.00 0.00 38.25 3.27
1359 2512 1.993391 GAATGGGGTCGGGTCCAGA 60.993 63.158 0.00 0.00 36.38 3.86
1394 2547 4.711399 TCACAGCCCTAATCATCATCAAG 58.289 43.478 0.00 0.00 0.00 3.02
1433 2606 7.450074 TCAAATCTGGCTAATCGGTTGTATAT 58.550 34.615 0.00 0.00 0.00 0.86
1434 2607 8.590204 TCAAATCTGGCTAATCGGTTGTATATA 58.410 33.333 0.00 0.00 0.00 0.86
1435 2608 8.656849 CAAATCTGGCTAATCGGTTGTATATAC 58.343 37.037 5.89 5.89 0.00 1.47
1717 4241 4.399303 CCGCCATTTCTATTTCTTGGAAGT 59.601 41.667 0.00 0.00 0.00 3.01
1722 4246 7.148000 GCCATTTCTATTTCTTGGAAGTTAGCT 60.148 37.037 0.00 0.00 0.00 3.32
1736 4272 2.746362 AGTTAGCTAGCTTGCTTGCTTG 59.254 45.455 29.21 8.66 43.74 4.01
1796 4342 1.416813 GAAGTGCTCGATCGGTGCTG 61.417 60.000 25.52 10.55 0.00 4.41
1847 4409 3.240302 ACTTATATAGGTGGCCGAGCTT 58.760 45.455 11.31 0.00 33.31 3.74
1850 4412 1.629043 TATAGGTGGCCGAGCTTAGG 58.371 55.000 11.31 4.94 33.31 2.69
1853 4415 0.105658 AGGTGGCCGAGCTTAGGATA 60.106 55.000 12.70 0.00 0.00 2.59
1874 4461 2.434336 ACATACATAGGTCGGCATGTGT 59.566 45.455 9.42 9.42 36.13 3.72
1875 4462 2.595124 TACATAGGTCGGCATGTGTG 57.405 50.000 14.42 0.00 36.13 3.82
1948 4560 0.038618 GTTGGCACCAATTCGTTCCC 60.039 55.000 5.22 0.00 38.28 3.97
1949 4561 0.468214 TTGGCACCAATTCGTTCCCA 60.468 50.000 0.00 0.00 0.00 4.37
2107 7143 0.719465 GTTACATGCGGTTGACTCGG 59.281 55.000 0.00 0.00 0.00 4.63
2160 7204 6.501781 GCTGGAGCTAGTTATTTCGTAGTAA 58.498 40.000 0.00 0.00 38.21 2.24
2185 8118 3.132160 CGAGATTGAGCAGCTGATTGAT 58.868 45.455 20.43 9.43 0.00 2.57
2187 8120 3.878103 GAGATTGAGCAGCTGATTGATGT 59.122 43.478 20.43 7.90 34.02 3.06
2188 8121 5.032327 AGATTGAGCAGCTGATTGATGTA 57.968 39.130 20.43 0.00 34.02 2.29
2236 8169 4.421365 GCCAGTTGCAGATGGGAA 57.579 55.556 18.03 0.00 40.77 3.97
2338 8271 1.949465 ATCCGTTAGGGCTTTTAGCG 58.051 50.000 0.00 0.00 43.62 4.26
2364 8298 8.545420 GCGAGAAACGAATAAATATACTTCCAA 58.455 33.333 0.00 0.00 45.77 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.107897 GACCCACATACACGGCATGA 60.108 55.000 0.00 0.00 0.00 3.07
1 2 0.392327 TGACCCACATACACGGCATG 60.392 55.000 0.00 0.00 0.00 4.06
2 3 0.392461 GTGACCCACATACACGGCAT 60.392 55.000 0.00 0.00 34.08 4.40
3 4 1.004320 GTGACCCACATACACGGCA 60.004 57.895 0.00 0.00 34.08 5.69
4 5 1.743995 GGTGACCCACATACACGGC 60.744 63.158 0.00 0.00 35.86 5.68
5 6 0.391130 CAGGTGACCCACATACACGG 60.391 60.000 0.00 0.00 35.86 4.94
6 7 0.320374 ACAGGTGACCCACATACACG 59.680 55.000 0.00 0.00 35.86 4.49
7 8 3.244284 TGTTACAGGTGACCCACATACAC 60.244 47.826 0.00 0.00 35.86 2.90
8 9 2.973406 TGTTACAGGTGACCCACATACA 59.027 45.455 0.00 0.00 35.86 2.29
9 10 3.007614 AGTGTTACAGGTGACCCACATAC 59.992 47.826 9.95 0.00 35.86 2.39
10 11 3.244582 AGTGTTACAGGTGACCCACATA 58.755 45.455 9.95 0.00 35.86 2.29
11 12 2.038557 GAGTGTTACAGGTGACCCACAT 59.961 50.000 9.95 0.00 35.86 3.21
12 13 1.414919 GAGTGTTACAGGTGACCCACA 59.585 52.381 9.95 0.91 35.86 4.17
13 14 1.692519 AGAGTGTTACAGGTGACCCAC 59.307 52.381 0.00 0.00 0.00 4.61
14 15 2.097110 AGAGTGTTACAGGTGACCCA 57.903 50.000 0.00 0.00 0.00 4.51
15 16 4.040095 AGTTTAGAGTGTTACAGGTGACCC 59.960 45.833 0.00 0.00 0.00 4.46
16 17 5.010820 AGAGTTTAGAGTGTTACAGGTGACC 59.989 44.000 0.00 0.00 0.00 4.02
17 18 6.016108 AGAGAGTTTAGAGTGTTACAGGTGAC 60.016 42.308 0.00 0.00 0.00 3.67
18 19 6.069331 AGAGAGTTTAGAGTGTTACAGGTGA 58.931 40.000 0.00 0.00 0.00 4.02
19 20 6.334102 AGAGAGTTTAGAGTGTTACAGGTG 57.666 41.667 0.00 0.00 0.00 4.00
20 21 6.778559 AGAAGAGAGTTTAGAGTGTTACAGGT 59.221 38.462 0.00 0.00 0.00 4.00
21 22 7.222000 AGAAGAGAGTTTAGAGTGTTACAGG 57.778 40.000 0.00 0.00 0.00 4.00
29 30 9.883142 CCATTGAATAAGAAGAGAGTTTAGAGT 57.117 33.333 0.00 0.00 0.00 3.24
34 35 9.393512 CTCATCCATTGAATAAGAAGAGAGTTT 57.606 33.333 4.52 0.00 32.78 2.66
35 36 7.992033 CCTCATCCATTGAATAAGAAGAGAGTT 59.008 37.037 9.75 0.00 32.78 3.01
36 37 7.507829 CCTCATCCATTGAATAAGAAGAGAGT 58.492 38.462 9.75 0.00 32.78 3.24
37 38 6.427547 GCCTCATCCATTGAATAAGAAGAGAG 59.572 42.308 9.75 5.29 32.78 3.20
38 39 6.126681 TGCCTCATCCATTGAATAAGAAGAGA 60.127 38.462 9.75 0.00 32.78 3.10
39 40 6.060136 TGCCTCATCCATTGAATAAGAAGAG 58.940 40.000 3.84 3.84 32.78 2.85
40 41 6.005066 TGCCTCATCCATTGAATAAGAAGA 57.995 37.500 0.00 0.00 32.78 2.87
41 42 6.704289 TTGCCTCATCCATTGAATAAGAAG 57.296 37.500 0.00 0.00 32.78 2.85
42 43 7.562454 AGATTTGCCTCATCCATTGAATAAGAA 59.438 33.333 0.00 0.00 32.78 2.52
43 44 7.064866 AGATTTGCCTCATCCATTGAATAAGA 58.935 34.615 0.00 0.00 32.78 2.10
44 45 7.286215 AGATTTGCCTCATCCATTGAATAAG 57.714 36.000 0.00 0.00 32.78 1.73
45 46 7.664552 AAGATTTGCCTCATCCATTGAATAA 57.335 32.000 0.00 0.00 32.78 1.40
46 47 8.799367 CATAAGATTTGCCTCATCCATTGAATA 58.201 33.333 0.00 0.00 32.78 1.75
47 48 7.667557 CATAAGATTTGCCTCATCCATTGAAT 58.332 34.615 0.00 0.00 32.78 2.57
48 49 6.461927 GCATAAGATTTGCCTCATCCATTGAA 60.462 38.462 0.00 0.00 32.78 2.69
49 50 5.010314 GCATAAGATTTGCCTCATCCATTGA 59.990 40.000 0.00 0.00 33.95 2.57
50 51 5.227908 GCATAAGATTTGCCTCATCCATTG 58.772 41.667 0.00 0.00 33.95 2.82
51 52 5.464030 GCATAAGATTTGCCTCATCCATT 57.536 39.130 0.00 0.00 33.95 3.16
61 62 3.695816 GAAACGGAGGCATAAGATTTGC 58.304 45.455 0.00 0.00 39.41 3.68
62 63 3.621268 TCGAAACGGAGGCATAAGATTTG 59.379 43.478 0.00 0.00 0.00 2.32
63 64 3.869065 TCGAAACGGAGGCATAAGATTT 58.131 40.909 0.00 0.00 0.00 2.17
64 65 3.536956 TCGAAACGGAGGCATAAGATT 57.463 42.857 0.00 0.00 0.00 2.40
65 66 3.536956 TTCGAAACGGAGGCATAAGAT 57.463 42.857 0.00 0.00 0.00 2.40
66 67 3.322211 TTTCGAAACGGAGGCATAAGA 57.678 42.857 6.47 0.00 0.00 2.10
67 68 4.413495 TTTTTCGAAACGGAGGCATAAG 57.587 40.909 10.79 0.00 0.00 1.73
88 89 7.766219 GCATGTCTGCTAATGATCAATTTTT 57.234 32.000 0.00 0.00 45.32 1.94
184 194 5.952347 AGGAACGAACAAAGGGACTATAT 57.048 39.130 0.00 0.00 38.49 0.86
216 428 9.467258 CCATTATGATTTTCCATGTATCAACAC 57.533 33.333 0.00 0.00 38.78 3.32
217 429 9.418839 TCCATTATGATTTTCCATGTATCAACA 57.581 29.630 0.00 0.00 40.69 3.33
305 694 7.226128 CCCGAAAACCTACTCCTTAATTACATC 59.774 40.741 0.00 0.00 0.00 3.06
306 695 7.052248 CCCGAAAACCTACTCCTTAATTACAT 58.948 38.462 0.00 0.00 0.00 2.29
307 696 6.213195 TCCCGAAAACCTACTCCTTAATTACA 59.787 38.462 0.00 0.00 0.00 2.41
314 703 1.278413 GCTCCCGAAAACCTACTCCTT 59.722 52.381 0.00 0.00 0.00 3.36
331 720 6.820656 TGAACAGAAAAAGATCTAGGATGCTC 59.179 38.462 0.00 0.00 0.00 4.26
414 808 5.390145 GCTACGGAATTGTTCGTGTATGTTT 60.390 40.000 7.93 0.00 40.05 2.83
415 809 4.092383 GCTACGGAATTGTTCGTGTATGTT 59.908 41.667 7.93 0.00 40.05 2.71
417 811 3.863424 AGCTACGGAATTGTTCGTGTATG 59.137 43.478 7.93 0.03 40.05 2.39
489 1596 8.066668 TGTTGTAAAATTTGGCGATACTTTTG 57.933 30.769 0.00 0.00 0.00 2.44
490 1597 8.707839 CATGTTGTAAAATTTGGCGATACTTTT 58.292 29.630 0.00 0.00 0.00 2.27
495 1602 7.598278 AGTTCATGTTGTAAAATTTGGCGATA 58.402 30.769 0.00 0.00 0.00 2.92
624 1762 4.025401 AGGAAAAACTGCCGCGCG 62.025 61.111 25.67 25.67 0.00 6.86
636 1774 0.846427 ACCAGGGCCAGATCAGGAAA 60.846 55.000 8.61 0.00 0.00 3.13
849 1987 0.682292 TAATGCAGGACGTGGTGACA 59.318 50.000 0.00 0.00 38.70 3.58
867 2005 2.580276 GGCAATGACCCGACGGTA 59.420 61.111 13.94 0.00 44.88 4.02
1151 2292 2.403252 AGTAAACTTCCAGATGCCGG 57.597 50.000 0.00 0.00 0.00 6.13
1170 2311 1.000521 CATCCTCAGCAGGGGCAAA 60.001 57.895 0.00 0.00 44.61 3.68
1329 2481 4.473520 CCATTCAGCCCGACGCCT 62.474 66.667 0.00 0.00 38.78 5.52
1359 2512 0.674895 GCTGTGATGCTTCCGTCCTT 60.675 55.000 0.00 0.00 0.00 3.36
1454 2638 5.407387 GTCGAGGTACTTAATGCAAGAAACA 59.593 40.000 0.00 0.00 41.55 2.83
1465 2649 4.787598 GACTGTTTCGTCGAGGTACTTAA 58.212 43.478 4.85 0.00 41.55 1.85
1531 2717 4.247380 GGAGCAGGCCATCTCCGG 62.247 72.222 22.49 0.00 39.43 5.14
1692 4216 2.223805 CCAAGAAATAGAAATGGCGGCC 60.224 50.000 13.32 13.32 0.00 6.13
1717 4241 1.470098 GCAAGCAAGCAAGCTAGCTAA 59.530 47.619 19.70 0.00 45.89 3.09
1722 4246 1.267806 GTCAAGCAAGCAAGCAAGCTA 59.732 47.619 10.81 0.00 45.89 3.32
1736 4272 7.770897 TCTTCCTATTTCCAATCTTAGTCAAGC 59.229 37.037 0.00 0.00 0.00 4.01
1796 4342 2.860582 GCTCGAGCTATAGCAACAGACC 60.861 54.545 29.88 7.67 45.16 3.85
1847 4409 4.925836 TGCCGACCTATGTATGTATCCTA 58.074 43.478 0.00 0.00 0.00 2.94
1850 4412 4.864806 CACATGCCGACCTATGTATGTATC 59.135 45.833 0.00 0.00 35.94 2.24
1853 4415 2.434336 ACACATGCCGACCTATGTATGT 59.566 45.455 0.00 0.00 38.15 2.29
1883 4470 9.752961 CAATGAAGCCATGATAATCATTGTAAA 57.247 29.630 22.04 0.00 46.12 2.01
1898 4486 3.440173 CAGTAACGTTCCAATGAAGCCAT 59.560 43.478 2.82 0.00 33.66 4.40
1949 4561 4.555709 TTTCGCGCCACTGGGTGT 62.556 61.111 0.00 0.00 46.76 4.16
2025 7057 8.867935 CCAAATATTTGTGTATCATTCGCAAAA 58.132 29.630 23.24 0.00 44.46 2.44
2026 7058 8.031864 ACCAAATATTTGTGTATCATTCGCAAA 58.968 29.630 23.24 5.57 45.05 3.68
2027 7059 7.542890 ACCAAATATTTGTGTATCATTCGCAA 58.457 30.769 23.24 0.00 36.45 4.85
2028 7060 7.094508 ACCAAATATTTGTGTATCATTCGCA 57.905 32.000 23.24 0.00 36.45 5.10
2029 7061 8.342634 ACTACCAAATATTTGTGTATCATTCGC 58.657 33.333 23.24 0.00 36.45 4.70
2049 7081 6.656307 GCTGCTAGCTGTTGGTTACTACCA 62.656 50.000 21.03 0.00 44.78 3.25
2050 7082 3.522553 CTGCTAGCTGTTGGTTACTACC 58.477 50.000 17.23 0.00 45.26 3.18
2107 7143 2.309528 TGACCGGTTCATACATCAGC 57.690 50.000 9.42 0.00 0.00 4.26
2160 7204 1.685517 TCAGCTGCTCAATCTCGCTAT 59.314 47.619 9.47 0.00 0.00 2.97
2185 8118 1.191535 AACACGGAGCTGGCTATACA 58.808 50.000 0.00 0.00 0.00 2.29
2187 8120 2.108168 AGAAACACGGAGCTGGCTATA 58.892 47.619 0.00 0.00 0.00 1.31
2188 8121 0.905357 AGAAACACGGAGCTGGCTAT 59.095 50.000 0.00 0.00 0.00 2.97
2236 8169 1.665599 CGGAAAACCAGGCGTACGT 60.666 57.895 17.90 0.00 0.00 3.57
2237 8170 2.385091 CCGGAAAACCAGGCGTACG 61.385 63.158 11.84 11.84 0.00 3.67
2238 8171 1.293963 GACCGGAAAACCAGGCGTAC 61.294 60.000 9.46 0.00 0.00 3.67
2239 8172 1.004679 GACCGGAAAACCAGGCGTA 60.005 57.895 9.46 0.00 0.00 4.42
2338 8271 8.068893 TGGAAGTATATTTATTCGTTTCTCGC 57.931 34.615 0.00 0.00 39.67 5.03
2339 8272 9.845305 GTTGGAAGTATATTTATTCGTTTCTCG 57.155 33.333 0.00 0.00 41.41 4.04
2340 8273 9.845305 CGTTGGAAGTATATTTATTCGTTTCTC 57.155 33.333 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.