Multiple sequence alignment - TraesCS3A01G078300

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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 TraesCS3A01G078300 chr3A 100.000 2395 0 0 1 2395 50719217 50721611 0.000000e+00 4423.0
1 TraesCS3A01G078300 chr3B 87.941 1161 61 31 854 1961 62292414 62293548 0.000000e+00 1295.0
2 TraesCS3A01G078300 chr3B 79.431 598 69 23 287 870 62291840 62292397 8.080000e-100 374.0
3 TraesCS3A01G078300 chr3B 91.760 267 21 1 28 294 62301144 62301409 1.050000e-98 370.0
4 TraesCS3A01G078300 chr3B 90.114 263 25 1 28 290 62291513 62291774 8.200000e-90 340.0
5 TraesCS3A01G078300 chr3B 80.707 311 46 10 287 592 62301466 62301767 1.850000e-56 230.0
6 TraesCS3A01G078300 chr3B 90.909 44 3 1 2315 2357 595296547 595296590 9.250000e-05 58.4
7 TraesCS3A01G078300 chr3D 88.204 746 51 20 916 1631 39314717 39315455 0.000000e+00 856.0
8 TraesCS3A01G078300 chr3D 83.191 702 57 25 1627 2277 39315483 39316174 9.540000e-164 586.0
9 TraesCS3A01G078300 chr3D 86.650 397 45 6 287 681 39311577 39311967 1.320000e-117 433.0
10 TraesCS3A01G078300 chr3D 90.530 264 24 1 28 290 39311249 39311512 4.900000e-92 348.0
11 TraesCS3A01G078300 chr3D 89.908 218 20 1 464 681 39312283 39312498 1.810000e-71 279.0
12 TraesCS3A01G078300 chr3D 95.833 120 3 2 808 927 39313689 39313806 2.430000e-45 193.0
13 TraesCS3A01G078300 chr3D 91.566 83 6 1 697 778 39311959 39312041 1.950000e-21 113.0
14 TraesCS3A01G078300 chr3D 91.566 83 6 1 697 778 39312490 39312572 1.950000e-21 113.0
15 TraesCS3A01G078300 chr2A 96.774 31 1 0 2338 2368 773707997 773707967 4.000000e-03 52.8


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 TraesCS3A01G078300 chr3A 50719217 50721611 2394 False 4423.000000 4423 100.000000 1 2395 1 chr3A.!!$F1 2394
1 TraesCS3A01G078300 chr3B 62291513 62293548 2035 False 669.666667 1295 85.828667 28 1961 3 chr3B.!!$F2 1933
2 TraesCS3A01G078300 chr3B 62301144 62301767 623 False 300.000000 370 86.233500 28 592 2 chr3B.!!$F3 564
3 TraesCS3A01G078300 chr3D 39311249 39316174 4925 False 365.125000 856 89.681000 28 2277 8 chr3D.!!$F1 2249

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
960 3636 0.537371 CTTCCACACACCACTTCCCC 60.537 60.0 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 4534 0.901114 ATGCAAGCAGTTGGCATGGA 60.901 50.0 0.0 0.0 45.48 3.41 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
24 25 3.577649 ACACAGATCGGAGTGTTGTAG 57.422 47.619 13.51 0.00 46.04 2.74
25 26 3.154710 ACACAGATCGGAGTGTTGTAGA 58.845 45.455 13.51 0.00 46.04 2.59
26 27 3.057456 ACACAGATCGGAGTGTTGTAGAC 60.057 47.826 13.51 0.00 46.04 2.59
95 96 3.534056 GGCAGCCCACATGCATCC 61.534 66.667 0.00 0.00 45.68 3.51
97 98 2.131709 GCAGCCCACATGCATCCAT 61.132 57.895 0.00 0.00 43.31 3.41
108 109 3.181493 ACATGCATCCATTCGAGCTTTTC 60.181 43.478 0.00 0.00 0.00 2.29
227 229 1.045350 TCTTCTCTGGCGCTGGCTAT 61.045 55.000 7.64 0.00 39.81 2.97
264 266 1.941325 CCAGCTCATTAGGACGGTTC 58.059 55.000 0.00 0.00 0.00 3.62
306 380 5.407995 CCGGTTTTGCAAATACATGTCAATT 59.592 36.000 13.65 0.00 0.00 2.32
753 1363 1.816863 ATGACACTCGGGCTGACGTT 61.817 55.000 0.00 0.00 34.94 3.99
756 1366 1.594293 CACTCGGGCTGACGTTTGT 60.594 57.895 0.00 0.00 34.94 2.83
768 1378 5.342259 GGCTGACGTTTGTGAATCATTTAAC 59.658 40.000 0.00 0.00 0.00 2.01
814 2534 3.959975 CCACAACGGCCACAACGG 61.960 66.667 2.24 0.00 35.23 4.44
898 2651 0.627986 CATCTTCCCCCAAGGCTTCT 59.372 55.000 0.00 0.00 34.51 2.85
928 3604 2.204306 CCCCCACCCCCTTCTTCT 60.204 66.667 0.00 0.00 0.00 2.85
929 3605 1.857348 CCCCCACCCCCTTCTTCTT 60.857 63.158 0.00 0.00 0.00 2.52
930 3606 1.691823 CCCCACCCCCTTCTTCTTC 59.308 63.158 0.00 0.00 0.00 2.87
938 3614 2.460669 CCCCTTCTTCTTCCCCATTTG 58.539 52.381 0.00 0.00 0.00 2.32
960 3636 0.537371 CTTCCACACACCACTTCCCC 60.537 60.000 0.00 0.00 0.00 4.81
1096 3772 1.604308 CAGAGCACCACCATTGCCA 60.604 57.895 0.00 0.00 41.18 4.92
1098 3774 1.604593 GAGCACCACCATTGCCACT 60.605 57.895 0.00 0.00 41.18 4.00
1145 3821 2.832129 AGATCTACAAGAAACTCCGCCA 59.168 45.455 0.00 0.00 0.00 5.69
1162 3838 0.506932 CCACAGCGTACGTGTTCTTG 59.493 55.000 17.90 8.47 32.26 3.02
1415 4094 5.495926 AATCTAATCTAGATGCTGGTGGG 57.504 43.478 5.86 0.00 44.44 4.61
1416 4095 4.199002 TCTAATCTAGATGCTGGTGGGA 57.801 45.455 5.86 0.00 0.00 4.37
1417 4096 4.756564 TCTAATCTAGATGCTGGTGGGAT 58.243 43.478 5.86 0.00 0.00 3.85
1420 4102 1.135094 CTAGATGCTGGTGGGATGGT 58.865 55.000 0.00 0.00 0.00 3.55
1468 4184 2.027837 AGTAGTCCCGCCGTGTTAATTT 60.028 45.455 0.00 0.00 0.00 1.82
1505 4221 2.549754 CGCTATGGGCTTTGATTAGTGG 59.450 50.000 0.00 0.00 39.13 4.00
1506 4222 3.555966 GCTATGGGCTTTGATTAGTGGT 58.444 45.455 0.00 0.00 38.06 4.16
1507 4223 3.565902 GCTATGGGCTTTGATTAGTGGTC 59.434 47.826 0.00 0.00 38.06 4.02
1511 4227 3.330701 TGGGCTTTGATTAGTGGTCTCTT 59.669 43.478 0.00 0.00 0.00 2.85
1513 4229 4.156739 GGGCTTTGATTAGTGGTCTCTTTG 59.843 45.833 0.00 0.00 0.00 2.77
1516 4232 5.470098 GCTTTGATTAGTGGTCTCTTTGTCA 59.530 40.000 0.00 0.00 0.00 3.58
1517 4233 6.017109 GCTTTGATTAGTGGTCTCTTTGTCAA 60.017 38.462 0.00 0.00 0.00 3.18
1518 4234 7.468631 GCTTTGATTAGTGGTCTCTTTGTCAAA 60.469 37.037 0.00 0.00 33.57 2.69
1519 4235 8.463930 TTTGATTAGTGGTCTCTTTGTCAAAT 57.536 30.769 0.00 0.00 30.72 2.32
1521 4237 9.567776 TTGATTAGTGGTCTCTTTGTCAAATTA 57.432 29.630 0.00 0.00 0.00 1.40
1522 4238 9.219603 TGATTAGTGGTCTCTTTGTCAAATTAG 57.780 33.333 0.00 0.44 0.00 1.73
1523 4239 9.220767 GATTAGTGGTCTCTTTGTCAAATTAGT 57.779 33.333 0.00 0.00 0.00 2.24
1524 4240 6.867662 AGTGGTCTCTTTGTCAAATTAGTG 57.132 37.500 0.00 0.00 0.00 2.74
1525 4241 5.239525 AGTGGTCTCTTTGTCAAATTAGTGC 59.760 40.000 0.00 0.00 0.00 4.40
1526 4242 5.008613 GTGGTCTCTTTGTCAAATTAGTGCA 59.991 40.000 0.00 0.00 0.00 4.57
1527 4243 5.239306 TGGTCTCTTTGTCAAATTAGTGCAG 59.761 40.000 0.00 0.00 0.00 4.41
1528 4244 5.239525 GGTCTCTTTGTCAAATTAGTGCAGT 59.760 40.000 0.00 0.00 0.00 4.40
1529 4245 6.366630 GTCTCTTTGTCAAATTAGTGCAGTC 58.633 40.000 0.00 0.00 0.00 3.51
1530 4246 6.203723 GTCTCTTTGTCAAATTAGTGCAGTCT 59.796 38.462 0.00 0.00 0.00 3.24
1531 4247 6.425114 TCTCTTTGTCAAATTAGTGCAGTCTC 59.575 38.462 0.00 0.00 0.00 3.36
1532 4248 6.291377 TCTTTGTCAAATTAGTGCAGTCTCT 58.709 36.000 0.00 0.00 0.00 3.10
1533 4249 7.441836 TCTTTGTCAAATTAGTGCAGTCTCTA 58.558 34.615 0.00 0.00 0.00 2.43
1534 4250 8.097038 TCTTTGTCAAATTAGTGCAGTCTCTAT 58.903 33.333 0.00 0.00 0.00 1.98
1535 4251 7.601073 TTGTCAAATTAGTGCAGTCTCTATG 57.399 36.000 0.00 0.00 0.00 2.23
1536 4252 6.701340 TGTCAAATTAGTGCAGTCTCTATGT 58.299 36.000 0.00 0.00 0.00 2.29
1537 4253 7.836842 TGTCAAATTAGTGCAGTCTCTATGTA 58.163 34.615 0.00 0.00 0.00 2.29
1655 4407 5.237996 CACTATGTAATCCATGAGCACTTGG 59.762 44.000 9.43 9.43 41.06 3.61
1664 4416 6.499106 TCCATGAGCACTTGGATCTAATTA 57.501 37.500 13.64 0.00 42.70 1.40
1665 4417 6.528321 TCCATGAGCACTTGGATCTAATTAG 58.472 40.000 13.64 6.11 42.70 1.73
1666 4418 5.704515 CCATGAGCACTTGGATCTAATTAGG 59.295 44.000 12.54 0.00 41.88 2.69
1691 4443 3.243234 TGGATGTTGTTTGCCAAGTTACG 60.243 43.478 0.00 0.00 32.51 3.18
1692 4444 3.243267 GGATGTTGTTTGCCAAGTTACGT 60.243 43.478 0.00 0.00 32.51 3.57
1700 4452 4.436242 TTGCCAAGTTACGTTTTGTCAA 57.564 36.364 0.00 0.00 0.00 3.18
1707 4459 8.544597 GCCAAGTTACGTTTTGTCAATATTTTT 58.455 29.630 0.00 0.00 0.00 1.94
1732 4484 9.927668 TTCTCTTTTCAAAATATCAAATGACCC 57.072 29.630 0.00 0.00 0.00 4.46
1782 4534 1.271840 TTATTGAGGCGGGCTCCTGT 61.272 55.000 26.34 15.30 36.38 4.00
1805 4557 0.032403 TGCCAACTGCTTGCATTCAC 59.968 50.000 0.00 0.00 42.00 3.18
1895 4671 4.991776 TGGGAATGTTCAAAGGACATGTA 58.008 39.130 0.00 0.00 37.76 2.29
1947 4723 8.601845 TCCCAAATCGAAATACACATGTATAG 57.398 34.615 0.00 1.46 40.10 1.31
2017 4793 4.517453 TGTGGCCTTTATACAAGTGTTCAC 59.483 41.667 3.32 0.00 0.00 3.18
2032 4808 4.873827 AGTGTTCACGCTCTTCAAAAGTAA 59.126 37.500 0.00 0.00 29.29 2.24
2039 4815 3.314080 CGCTCTTCAAAAGTAAACCCACA 59.686 43.478 0.00 0.00 0.00 4.17
2040 4816 4.201970 CGCTCTTCAAAAGTAAACCCACAA 60.202 41.667 0.00 0.00 0.00 3.33
2055 4831 9.535878 GTAAACCCACAACATTTTCAGAAAATA 57.464 29.630 18.84 0.00 38.97 1.40
2134 4938 8.751302 AAATCACACGTTTCAAAACTAAGTTT 57.249 26.923 4.28 0.00 37.34 2.66
2142 4946 9.106070 ACGTTTCAAAACTAAGTTTGAGACTAT 57.894 29.630 15.19 5.18 45.62 2.12
2177 4981 7.655328 TGTCCATACCATTCAAAAACATGTTTC 59.345 33.333 23.47 6.45 31.45 2.78
2180 4984 9.703892 CCATACCATTCAAAAACATGTTTCTTA 57.296 29.630 23.47 9.43 31.45 2.10
2217 5021 5.638657 TGCTTGTGCCATTGAAAACAATATC 59.361 36.000 0.00 0.00 38.71 1.63
2241 5045 7.102346 TCCACATGTTTCAAAAGAATGTTTGT 58.898 30.769 0.00 0.00 39.16 2.83
2244 5048 8.441608 CACATGTTTCAAAAGAATGTTTGTGAA 58.558 29.630 0.00 0.00 39.16 3.18
2286 5090 9.796120 TTCTACAAATGTAAAAAGAGGTTTGTG 57.204 29.630 10.51 3.10 39.34 3.33
2287 5091 8.962679 TCTACAAATGTAAAAAGAGGTTTGTGT 58.037 29.630 10.51 0.00 39.34 3.72
2321 5125 9.981114 AAATCTTGGATTTATTCGAAAAACTGT 57.019 25.926 0.00 0.00 0.00 3.55
2322 5126 9.981114 AATCTTGGATTTATTCGAAAAACTGTT 57.019 25.926 0.00 0.00 0.00 3.16
2323 5127 9.626045 ATCTTGGATTTATTCGAAAAACTGTTC 57.374 29.630 0.00 0.00 0.00 3.18
2324 5128 8.625651 TCTTGGATTTATTCGAAAAACTGTTCA 58.374 29.630 0.00 0.00 0.00 3.18
2325 5129 9.243637 CTTGGATTTATTCGAAAAACTGTTCAA 57.756 29.630 0.00 0.56 0.00 2.69
2326 5130 9.587772 TTGGATTTATTCGAAAAACTGTTCAAA 57.412 25.926 0.00 0.00 0.00 2.69
2327 5131 9.243637 TGGATTTATTCGAAAAACTGTTCAAAG 57.756 29.630 0.00 0.00 0.00 2.77
2328 5132 8.214472 GGATTTATTCGAAAAACTGTTCAAAGC 58.786 33.333 0.00 0.00 0.00 3.51
2329 5133 8.641499 ATTTATTCGAAAAACTGTTCAAAGCA 57.359 26.923 0.00 0.00 0.00 3.91
2330 5134 8.641499 TTTATTCGAAAAACTGTTCAAAGCAT 57.359 26.923 0.00 0.00 0.00 3.79
2331 5135 5.947503 TTCGAAAAACTGTTCAAAGCATG 57.052 34.783 0.00 0.00 0.00 4.06
2332 5136 4.992688 TCGAAAAACTGTTCAAAGCATGT 58.007 34.783 0.00 0.00 0.00 3.21
2333 5137 4.797868 TCGAAAAACTGTTCAAAGCATGTG 59.202 37.500 0.00 0.00 0.00 3.21
2334 5138 4.562394 CGAAAAACTGTTCAAAGCATGTGT 59.438 37.500 0.00 0.00 0.00 3.72
2335 5139 5.062058 CGAAAAACTGTTCAAAGCATGTGTT 59.938 36.000 0.00 0.00 0.00 3.32
2336 5140 6.252441 CGAAAAACTGTTCAAAGCATGTGTTA 59.748 34.615 0.00 0.00 0.00 2.41
2337 5141 7.513505 CGAAAAACTGTTCAAAGCATGTGTTAG 60.514 37.037 0.00 0.00 0.00 2.34
2338 5142 6.449635 AAACTGTTCAAAGCATGTGTTAGA 57.550 33.333 0.00 0.00 0.00 2.10
2339 5143 6.449635 AACTGTTCAAAGCATGTGTTAGAA 57.550 33.333 0.00 0.00 0.00 2.10
2340 5144 6.449635 ACTGTTCAAAGCATGTGTTAGAAA 57.550 33.333 0.00 0.00 0.00 2.52
2341 5145 6.862209 ACTGTTCAAAGCATGTGTTAGAAAA 58.138 32.000 0.00 0.00 0.00 2.29
2342 5146 7.319646 ACTGTTCAAAGCATGTGTTAGAAAAA 58.680 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.335964 ACAACACTCCGATCTGTGTCG 60.336 52.381 13.64 7.76 45.33 4.35
3 4 2.440539 ACAACACTCCGATCTGTGTC 57.559 50.000 13.64 0.00 45.33 3.67
5 6 3.191581 AGTCTACAACACTCCGATCTGTG 59.808 47.826 8.25 8.25 39.80 3.66
6 7 3.422796 AGTCTACAACACTCCGATCTGT 58.577 45.455 0.00 0.00 0.00 3.41
7 8 4.169508 CAAGTCTACAACACTCCGATCTG 58.830 47.826 0.00 0.00 0.00 2.90
8 9 3.827302 ACAAGTCTACAACACTCCGATCT 59.173 43.478 0.00 0.00 0.00 2.75
9 10 4.175787 ACAAGTCTACAACACTCCGATC 57.824 45.455 0.00 0.00 0.00 3.69
10 11 4.158025 CCTACAAGTCTACAACACTCCGAT 59.842 45.833 0.00 0.00 0.00 4.18
11 12 3.504906 CCTACAAGTCTACAACACTCCGA 59.495 47.826 0.00 0.00 0.00 4.55
12 13 3.255149 ACCTACAAGTCTACAACACTCCG 59.745 47.826 0.00 0.00 0.00 4.63
13 14 4.280174 TCACCTACAAGTCTACAACACTCC 59.720 45.833 0.00 0.00 0.00 3.85
14 15 5.449107 TCACCTACAAGTCTACAACACTC 57.551 43.478 0.00 0.00 0.00 3.51
15 16 4.262079 GCTCACCTACAAGTCTACAACACT 60.262 45.833 0.00 0.00 0.00 3.55
16 17 3.988517 GCTCACCTACAAGTCTACAACAC 59.011 47.826 0.00 0.00 0.00 3.32
17 18 3.639561 TGCTCACCTACAAGTCTACAACA 59.360 43.478 0.00 0.00 0.00 3.33
18 19 4.252971 TGCTCACCTACAAGTCTACAAC 57.747 45.455 0.00 0.00 0.00 3.32
19 20 4.948341 TTGCTCACCTACAAGTCTACAA 57.052 40.909 0.00 0.00 0.00 2.41
20 21 4.948341 TTTGCTCACCTACAAGTCTACA 57.052 40.909 0.00 0.00 0.00 2.74
21 22 5.539048 TCTTTTGCTCACCTACAAGTCTAC 58.461 41.667 0.00 0.00 0.00 2.59
22 23 5.801531 TCTTTTGCTCACCTACAAGTCTA 57.198 39.130 0.00 0.00 0.00 2.59
23 24 4.689612 TCTTTTGCTCACCTACAAGTCT 57.310 40.909 0.00 0.00 0.00 3.24
24 25 5.288543 CATCTTTTGCTCACCTACAAGTC 57.711 43.478 0.00 0.00 0.00 3.01
85 86 1.306148 AGCTCGAATGGATGCATGTG 58.694 50.000 2.46 0.00 0.00 3.21
88 89 3.066342 CAGAAAAGCTCGAATGGATGCAT 59.934 43.478 0.00 0.00 0.00 3.96
108 109 1.015109 GCCATGACATGAGTGAGCAG 58.985 55.000 17.24 0.00 0.00 4.24
169 171 4.022762 CGCACTAAGTGATACATAGCTCCT 60.023 45.833 0.00 0.00 35.23 3.69
227 229 0.675522 GGCCTACTAAAGCAACCGCA 60.676 55.000 0.00 0.00 42.27 5.69
264 266 3.199289 ACCGGTATAAAGAACCTTCCCAG 59.801 47.826 4.49 0.00 34.66 4.45
318 392 7.094762 TGCATGTATACGAAAAATGTACAACCA 60.095 33.333 0.00 0.00 29.00 3.67
417 492 9.934190 AAAGTGTTCAATGTGCATTTAAAAATC 57.066 25.926 0.00 0.00 0.00 2.17
574 1184 7.707464 TCGAGAAAAATGTGTCTACACTGTAAA 59.293 33.333 13.95 0.00 46.55 2.01
575 1185 7.204604 TCGAGAAAAATGTGTCTACACTGTAA 58.795 34.615 13.95 0.00 46.55 2.41
576 1186 6.741109 TCGAGAAAAATGTGTCTACACTGTA 58.259 36.000 13.95 0.00 46.55 2.74
577 1187 5.597806 TCGAGAAAAATGTGTCTACACTGT 58.402 37.500 13.95 1.05 46.55 3.55
580 1190 7.766723 CATTTCGAGAAAAATGTGTCTACAC 57.233 36.000 6.29 6.29 40.28 2.90
681 1291 6.261381 ACAAAGTTCGTGTGATTAGCCTAAAA 59.739 34.615 0.00 0.00 0.00 1.52
682 1292 5.761234 ACAAAGTTCGTGTGATTAGCCTAAA 59.239 36.000 0.00 0.00 0.00 1.85
683 1293 5.302360 ACAAAGTTCGTGTGATTAGCCTAA 58.698 37.500 0.00 0.00 0.00 2.69
684 1294 4.890088 ACAAAGTTCGTGTGATTAGCCTA 58.110 39.130 0.00 0.00 0.00 3.93
685 1295 3.740115 ACAAAGTTCGTGTGATTAGCCT 58.260 40.909 0.00 0.00 0.00 4.58
693 1303 3.946402 TGCATTACACAAAGTTCGTGTG 58.054 40.909 9.89 7.90 46.72 3.82
695 1305 2.973224 GCTGCATTACACAAAGTTCGTG 59.027 45.455 0.00 0.00 40.32 4.35
736 1346 1.300697 AAACGTCAGCCCGAGTGTC 60.301 57.895 0.00 0.00 0.00 3.67
753 1363 4.083003 GGTGGCTCGTTAAATGATTCACAA 60.083 41.667 0.00 0.00 0.00 3.33
756 1366 3.013921 GGGTGGCTCGTTAAATGATTCA 58.986 45.455 0.00 0.00 0.00 2.57
768 1378 1.079127 AGATCGTTTGGGTGGCTCG 60.079 57.895 0.00 0.00 0.00 5.03
831 2551 4.883354 CGGCCCAGATCCCTTGCC 62.883 72.222 0.00 3.68 35.46 4.52
862 2615 3.468140 GGGGACGGACAGCTACCC 61.468 72.222 0.00 0.00 39.79 3.69
871 2624 2.366435 GGGGAAGATGGGGACGGA 60.366 66.667 0.00 0.00 0.00 4.69
928 3604 1.337118 GTGGAAGTGCAAATGGGGAA 58.663 50.000 0.00 0.00 0.00 3.97
929 3605 0.187117 TGTGGAAGTGCAAATGGGGA 59.813 50.000 0.00 0.00 0.00 4.81
930 3606 0.318120 GTGTGGAAGTGCAAATGGGG 59.682 55.000 0.00 0.00 0.00 4.96
938 3614 0.663153 GAAGTGGTGTGTGGAAGTGC 59.337 55.000 0.00 0.00 0.00 4.40
960 3636 1.225704 GTGGGGAGGCTCTGGATTG 59.774 63.158 15.23 0.00 0.00 2.67
1120 3796 4.109050 CGGAGTTTCTTGTAGATCTGAGC 58.891 47.826 5.18 0.00 0.00 4.26
1145 3821 1.219522 GCCAAGAACACGTACGCTGT 61.220 55.000 16.72 15.57 0.00 4.40
1162 3838 0.113190 CTAATGGAGGGGAATGGGCC 59.887 60.000 0.00 0.00 0.00 5.80
1415 4094 8.389603 GCTAATACTACTGATACTACGACCATC 58.610 40.741 0.00 0.00 0.00 3.51
1416 4095 7.064371 CGCTAATACTACTGATACTACGACCAT 59.936 40.741 0.00 0.00 0.00 3.55
1417 4096 6.367149 CGCTAATACTACTGATACTACGACCA 59.633 42.308 0.00 0.00 0.00 4.02
1420 4102 6.367149 CCACGCTAATACTACTGATACTACGA 59.633 42.308 0.00 0.00 0.00 3.43
1505 4221 6.203723 AGACTGCACTAATTTGACAAAGAGAC 59.796 38.462 15.90 9.80 0.00 3.36
1506 4222 6.291377 AGACTGCACTAATTTGACAAAGAGA 58.709 36.000 15.90 0.81 0.00 3.10
1507 4223 6.426328 AGAGACTGCACTAATTTGACAAAGAG 59.574 38.462 6.77 8.59 0.00 2.85
1511 4227 7.161404 ACATAGAGACTGCACTAATTTGACAA 58.839 34.615 0.00 0.00 0.00 3.18
1513 4229 8.703604 TTACATAGAGACTGCACTAATTTGAC 57.296 34.615 0.00 0.00 0.00 3.18
1521 4237 7.278868 GCACTAATTTTACATAGAGACTGCACT 59.721 37.037 0.00 0.00 0.00 4.40
1522 4238 7.402640 GCACTAATTTTACATAGAGACTGCAC 58.597 38.462 0.00 0.00 0.00 4.57
1523 4239 6.255670 CGCACTAATTTTACATAGAGACTGCA 59.744 38.462 0.00 0.00 0.00 4.41
1524 4240 6.292381 CCGCACTAATTTTACATAGAGACTGC 60.292 42.308 0.00 0.00 0.00 4.40
1525 4241 6.757010 ACCGCACTAATTTTACATAGAGACTG 59.243 38.462 0.00 0.00 0.00 3.51
1526 4242 6.875076 ACCGCACTAATTTTACATAGAGACT 58.125 36.000 0.00 0.00 0.00 3.24
1527 4243 6.979238 AGACCGCACTAATTTTACATAGAGAC 59.021 38.462 0.00 0.00 0.00 3.36
1528 4244 7.068348 AGAGACCGCACTAATTTTACATAGAGA 59.932 37.037 0.00 0.00 0.00 3.10
1529 4245 7.203910 AGAGACCGCACTAATTTTACATAGAG 58.796 38.462 0.00 0.00 0.00 2.43
1530 4246 7.108841 AGAGACCGCACTAATTTTACATAGA 57.891 36.000 0.00 0.00 0.00 1.98
1531 4247 7.491372 TGAAGAGACCGCACTAATTTTACATAG 59.509 37.037 0.00 0.00 0.00 2.23
1532 4248 7.324935 TGAAGAGACCGCACTAATTTTACATA 58.675 34.615 0.00 0.00 0.00 2.29
1533 4249 6.170506 TGAAGAGACCGCACTAATTTTACAT 58.829 36.000 0.00 0.00 0.00 2.29
1534 4250 5.543714 TGAAGAGACCGCACTAATTTTACA 58.456 37.500 0.00 0.00 0.00 2.41
1535 4251 5.638234 ACTGAAGAGACCGCACTAATTTTAC 59.362 40.000 0.00 0.00 0.00 2.01
1536 4252 5.637810 CACTGAAGAGACCGCACTAATTTTA 59.362 40.000 0.00 0.00 0.00 1.52
1537 4253 4.452455 CACTGAAGAGACCGCACTAATTTT 59.548 41.667 0.00 0.00 0.00 1.82
1576 4292 1.471684 ACACTCCATCGTCGAACCTAC 59.528 52.381 0.00 0.00 0.00 3.18
1578 4294 0.966920 AACACTCCATCGTCGAACCT 59.033 50.000 0.00 0.00 0.00 3.50
1583 4300 0.163788 GCACAAACACTCCATCGTCG 59.836 55.000 0.00 0.00 0.00 5.12
1655 4407 9.956720 CAAACAACATCCATTCCTAATTAGATC 57.043 33.333 14.28 0.00 0.00 2.75
1664 4416 2.607499 TGGCAAACAACATCCATTCCT 58.393 42.857 0.00 0.00 0.00 3.36
1665 4417 3.244181 ACTTGGCAAACAACATCCATTCC 60.244 43.478 0.00 0.00 34.76 3.01
1666 4418 3.993920 ACTTGGCAAACAACATCCATTC 58.006 40.909 0.00 0.00 34.76 2.67
1707 4459 8.531146 GGGGTCATTTGATATTTTGAAAAGAGA 58.469 33.333 0.00 0.00 0.00 3.10
1710 4462 7.319646 TCGGGGTCATTTGATATTTTGAAAAG 58.680 34.615 0.00 0.00 0.00 2.27
1716 4468 5.714806 ACAACTCGGGGTCATTTGATATTTT 59.285 36.000 0.00 0.00 0.00 1.82
1730 4482 2.027625 GCGAAGTGACAACTCGGGG 61.028 63.158 8.92 0.00 34.77 5.73
1732 4484 1.300620 TGGCGAAGTGACAACTCGG 60.301 57.895 8.92 0.00 34.77 4.63
1772 4524 4.864334 GGCATGGACAGGAGCCCG 62.864 72.222 0.00 0.00 41.25 6.13
1782 4534 0.901114 ATGCAAGCAGTTGGCATGGA 60.901 50.000 0.00 0.00 45.48 3.41
1859 4612 7.507829 TGAACATTCCCAACAAAAATCAGATT 58.492 30.769 0.00 0.00 0.00 2.40
1860 4613 7.065120 TGAACATTCCCAACAAAAATCAGAT 57.935 32.000 0.00 0.00 0.00 2.90
1947 4723 5.288804 TGCTTTTGTCAATAGCTTTTGGTC 58.711 37.500 23.09 10.34 35.93 4.02
1998 4774 3.435671 AGCGTGAACACTTGTATAAAGGC 59.564 43.478 3.51 0.00 0.00 4.35
1999 4775 4.929808 AGAGCGTGAACACTTGTATAAAGG 59.070 41.667 3.51 0.00 0.00 3.11
2000 4776 6.145534 TGAAGAGCGTGAACACTTGTATAAAG 59.854 38.462 3.51 0.00 0.00 1.85
2005 4781 3.446310 TGAAGAGCGTGAACACTTGTA 57.554 42.857 3.51 0.00 0.00 2.41
2007 4783 3.673746 TTTGAAGAGCGTGAACACTTG 57.326 42.857 3.51 0.00 0.00 3.16
2017 4793 3.314080 TGTGGGTTTACTTTTGAAGAGCG 59.686 43.478 0.00 0.00 0.00 5.03
2032 4808 9.625747 AAATATTTTCTGAAAATGTTGTGGGTT 57.374 25.926 29.33 15.11 40.03 4.11
2112 4912 6.900189 TCAAACTTAGTTTTGAAACGTGTGA 58.100 32.000 7.71 0.00 41.48 3.58
2113 4913 7.007099 GTCTCAAACTTAGTTTTGAAACGTGTG 59.993 37.037 7.71 0.00 43.29 3.82
2114 4914 7.019418 GTCTCAAACTTAGTTTTGAAACGTGT 58.981 34.615 7.71 0.00 43.29 4.49
2115 4915 7.241376 AGTCTCAAACTTAGTTTTGAAACGTG 58.759 34.615 7.71 0.00 43.29 4.49
2117 4917 9.931210 AATAGTCTCAAACTTAGTTTTGAAACG 57.069 29.630 7.71 0.00 43.29 3.60
2154 4958 8.606040 AAGAAACATGTTTTTGAATGGTATGG 57.394 30.769 24.02 0.00 32.11 2.74
2217 5021 7.064371 TCACAAACATTCTTTTGAAACATGTGG 59.936 33.333 0.00 0.00 42.31 4.17
2295 5099 9.981114 ACAGTTTTTCGAATAAATCCAAGATTT 57.019 25.926 0.00 7.63 0.00 2.17
2296 5100 9.981114 AACAGTTTTTCGAATAAATCCAAGATT 57.019 25.926 0.00 0.00 0.00 2.40
2297 5101 9.626045 GAACAGTTTTTCGAATAAATCCAAGAT 57.374 29.630 0.00 0.00 0.00 2.40
2298 5102 8.625651 TGAACAGTTTTTCGAATAAATCCAAGA 58.374 29.630 0.00 0.00 0.00 3.02
2299 5103 8.795786 TGAACAGTTTTTCGAATAAATCCAAG 57.204 30.769 0.00 0.00 0.00 3.61
2300 5104 9.587772 TTTGAACAGTTTTTCGAATAAATCCAA 57.412 25.926 0.00 1.88 0.00 3.53
2301 5105 9.243637 CTTTGAACAGTTTTTCGAATAAATCCA 57.756 29.630 0.00 0.00 30.08 3.41
2302 5106 8.214472 GCTTTGAACAGTTTTTCGAATAAATCC 58.786 33.333 0.00 0.00 30.08 3.01
2303 5107 8.751335 TGCTTTGAACAGTTTTTCGAATAAATC 58.249 29.630 0.00 0.00 30.08 2.17
2304 5108 8.641499 TGCTTTGAACAGTTTTTCGAATAAAT 57.359 26.923 0.00 0.00 30.08 1.40
2305 5109 8.538856 CATGCTTTGAACAGTTTTTCGAATAAA 58.461 29.630 0.00 0.03 30.08 1.40
2306 5110 7.704472 ACATGCTTTGAACAGTTTTTCGAATAA 59.296 29.630 0.00 0.00 30.08 1.40
2307 5111 7.167302 CACATGCTTTGAACAGTTTTTCGAATA 59.833 33.333 0.00 0.00 30.08 1.75
2308 5112 6.019640 CACATGCTTTGAACAGTTTTTCGAAT 60.020 34.615 0.00 0.00 30.08 3.34
2309 5113 5.288232 CACATGCTTTGAACAGTTTTTCGAA 59.712 36.000 0.00 0.00 0.00 3.71
2310 5114 4.797868 CACATGCTTTGAACAGTTTTTCGA 59.202 37.500 0.00 0.00 0.00 3.71
2311 5115 4.562394 ACACATGCTTTGAACAGTTTTTCG 59.438 37.500 0.00 0.00 0.00 3.46
2312 5116 6.407475 AACACATGCTTTGAACAGTTTTTC 57.593 33.333 0.00 0.00 0.00 2.29
2313 5117 7.319646 TCTAACACATGCTTTGAACAGTTTTT 58.680 30.769 0.00 0.00 0.00 1.94
2314 5118 6.862209 TCTAACACATGCTTTGAACAGTTTT 58.138 32.000 0.00 0.00 0.00 2.43
2315 5119 6.449635 TCTAACACATGCTTTGAACAGTTT 57.550 33.333 0.00 0.00 0.00 2.66
2316 5120 6.449635 TTCTAACACATGCTTTGAACAGTT 57.550 33.333 0.00 0.00 0.00 3.16
2317 5121 6.449635 TTTCTAACACATGCTTTGAACAGT 57.550 33.333 0.00 0.00 0.00 3.55
2318 5122 7.754069 TTTTTCTAACACATGCTTTGAACAG 57.246 32.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.