Multiple sequence alignment - TraesCS2A01G120200

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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 TraesCS2A01G120200 chr2A 100.000 3126 0 0 1 3126 70292797 70289672 0.000000e+00 5773.0
1 TraesCS2A01G120200 chr2A 80.077 778 100 26 1510 2247 70649841 70650603 7.680000e-146 527.0
2 TraesCS2A01G120200 chr2A 82.919 603 63 18 2276 2851 70195333 70195922 1.000000e-139 507.0
3 TraesCS2A01G120200 chr2A 82.527 372 52 7 1604 1969 70144601 70144237 6.510000e-82 315.0
4 TraesCS2A01G120200 chr2A 86.159 289 19 7 1036 1303 70235051 70234763 3.050000e-75 292.0
5 TraesCS2A01G120200 chr2A 82.353 357 44 14 955 1308 70654953 70655293 3.050000e-75 292.0
6 TraesCS2A01G120200 chr2A 80.447 358 50 13 962 1307 70153249 70152900 4.000000e-64 255.0
7 TraesCS2A01G120200 chr2A 83.895 267 31 7 1987 2243 70144253 70143989 8.660000e-61 244.0
8 TraesCS2A01G120200 chr2A 77.014 422 52 24 892 1307 70284516 70284134 1.900000e-47 200.0
9 TraesCS2A01G120200 chr2D 91.124 1183 45 21 1987 3126 71400393 71401558 0.000000e+00 1548.0
10 TraesCS2A01G120200 chr2D 94.710 586 16 6 249 824 71398546 71399126 0.000000e+00 896.0
11 TraesCS2A01G120200 chr2D 93.443 549 28 2 1421 1969 71399869 71400409 0.000000e+00 808.0
12 TraesCS2A01G120200 chr2D 91.284 436 27 5 873 1307 71399238 71399663 4.490000e-163 584.0
13 TraesCS2A01G120200 chr2D 78.491 795 87 34 2249 3001 70794407 70793655 7.960000e-121 444.0
14 TraesCS2A01G120200 chr2D 97.826 230 5 0 1 230 71397766 71397995 6.280000e-107 398.0
15 TraesCS2A01G120200 chr2D 84.543 317 33 10 998 1307 71594175 71594482 1.820000e-77 300.0
16 TraesCS2A01G120200 chr2D 78.750 480 50 19 2602 3038 71393756 71394226 1.100000e-69 274.0
17 TraesCS2A01G120200 chr2D 82.331 266 38 7 1987 2247 71595118 71595379 4.060000e-54 222.0
18 TraesCS2A01G120200 chr2D 77.327 419 62 27 892 1307 71404529 71404917 1.890000e-52 217.0
19 TraesCS2A01G120200 chr2D 84.878 205 31 0 1103 1307 70633388 70633592 1.140000e-49 207.0
20 TraesCS2A01G120200 chr2D 85.366 123 18 0 1183 1305 71578484 71578606 9.100000e-26 128.0
21 TraesCS2A01G120200 chr2D 98.148 54 1 0 1336 1389 71399761 71399708 9.230000e-16 95.3
22 TraesCS2A01G120200 chr2D 95.918 49 2 0 824 872 71399149 71399197 2.580000e-11 80.5
23 TraesCS2A01G120200 chr2D 97.059 34 1 0 1304 1337 71399815 71399782 1.210000e-04 58.4
24 TraesCS2A01G120200 chr2B 91.107 1147 52 17 2009 3126 107559907 107561032 0.000000e+00 1507.0
25 TraesCS2A01G120200 chr2B 82.792 831 109 21 1429 2246 107789691 107790500 0.000000e+00 712.0
26 TraesCS2A01G120200 chr2B 81.599 788 90 24 2249 3001 107533663 107534430 4.460000e-168 601.0
27 TraesCS2A01G120200 chr2B 81.699 459 58 12 1514 1969 106962274 106961839 2.960000e-95 359.0
28 TraesCS2A01G120200 chr2B 85.675 363 27 18 956 1307 107789135 107789483 2.960000e-95 359.0
29 TraesCS2A01G120200 chr2B 83.099 355 45 10 955 1307 107793179 107793520 3.030000e-80 309.0
30 TraesCS2A01G120200 chr2B 83.824 272 32 8 1048 1307 106962775 106962504 6.690000e-62 248.0
31 TraesCS2A01G120200 chr2B 77.512 418 56 23 892 1307 107568460 107568841 1.890000e-52 217.0
32 TraesCS2A01G120200 chr2B 94.444 54 3 0 1336 1389 106962406 106962459 2.000000e-12 84.2
33 TraesCS2A01G120200 chr6B 79.902 204 37 4 17 218 75277788 75277587 2.510000e-31 147.0
34 TraesCS2A01G120200 chr7B 79.612 206 38 4 15 218 42124952 42125155 9.040000e-31 145.0
35 TraesCS2A01G120200 chr1A 76.585 205 42 6 17 218 568315106 568315307 1.190000e-19 108.0


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 TraesCS2A01G120200 chr2A 70289672 70292797 3125 True 5773.0000 5773 100.000000 1 3126 1 chr2A.!!$R4 3125
1 TraesCS2A01G120200 chr2A 70649841 70650603 762 False 527.0000 527 80.077000 1510 2247 1 chr2A.!!$F2 737
2 TraesCS2A01G120200 chr2A 70195333 70195922 589 False 507.0000 507 82.919000 2276 2851 1 chr2A.!!$F1 575
3 TraesCS2A01G120200 chr2A 70143989 70144601 612 True 279.5000 315 83.211000 1604 2243 2 chr2A.!!$R5 639
4 TraesCS2A01G120200 chr2D 71393756 71404917 11161 False 600.6875 1548 90.047750 1 3126 8 chr2D.!!$F3 3125
5 TraesCS2A01G120200 chr2D 70793655 70794407 752 True 444.0000 444 78.491000 2249 3001 1 chr2D.!!$R1 752
6 TraesCS2A01G120200 chr2D 71594175 71595379 1204 False 261.0000 300 83.437000 998 2247 2 chr2D.!!$F4 1249
7 TraesCS2A01G120200 chr2B 107559907 107561032 1125 False 1507.0000 1507 91.107000 2009 3126 1 chr2B.!!$F3 1117
8 TraesCS2A01G120200 chr2B 107533663 107534430 767 False 601.0000 601 81.599000 2249 3001 1 chr2B.!!$F2 752
9 TraesCS2A01G120200 chr2B 107789135 107793520 4385 False 460.0000 712 83.855333 955 2246 3 chr2B.!!$F5 1291
10 TraesCS2A01G120200 chr2B 106961839 106962775 936 True 303.5000 359 82.761500 1048 1969 2 chr2B.!!$R1 921

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
540 5085 0.040058 TTGTCTGGCATGCCCTCAAT 59.960 50.0 33.44 0.0 34.56 2.57 F
957 5574 0.041224 CTCGCTCGTCGCTAATGCTA 60.041 55.0 0.00 0.0 38.27 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 6407 0.033504 TCGCCAACAGAAGACCAGTC 59.966 55.000 0.00 0.00 0.00 3.51 R
2156 6982 1.071385 AGCATATGGTAGGAGCTGCAC 59.929 52.381 8.35 3.59 33.67 4.57 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
38 4049 2.666272 TGACCATGCAACCCTTTACA 57.334 45.000 0.00 0.00 0.00 2.41
49 4060 2.706890 ACCCTTTACATAGCAACACCG 58.293 47.619 0.00 0.00 0.00 4.94
86 4097 7.589958 TCCACTCTATCCTATCAAAGACTTC 57.410 40.000 0.00 0.00 0.00 3.01
105 4116 4.569966 ACTTCAGCAAGATCTATTGAAGCG 59.430 41.667 27.11 15.85 45.27 4.68
219 4230 4.352600 AAAGCTTTGCTGAGATTCATCG 57.647 40.909 11.80 0.00 39.62 3.84
260 4803 6.636454 TCAGGGAGGAGTACATTACAAATT 57.364 37.500 0.00 0.00 0.00 1.82
301 4844 8.181904 TCTTGAAGACTTTTGGCATTATCTTT 57.818 30.769 0.00 0.00 0.00 2.52
302 4845 8.641541 TCTTGAAGACTTTTGGCATTATCTTTT 58.358 29.630 0.00 0.00 0.00 2.27
378 4921 7.264294 ACTCCCTCTGATCCATATTTTATCC 57.736 40.000 0.00 0.00 0.00 2.59
478 5023 0.179081 GGCCATCCGGTACTGAAGAC 60.179 60.000 2.31 0.00 33.28 3.01
490 5035 5.975344 CGGTACTGAAGACGCATTATTCTTA 59.025 40.000 0.00 0.00 32.04 2.10
539 5084 0.178967 TTTGTCTGGCATGCCCTCAA 60.179 50.000 33.44 27.99 34.56 3.02
540 5085 0.040058 TTGTCTGGCATGCCCTCAAT 59.960 50.000 33.44 0.00 34.56 2.57
580 5129 8.276325 GGCGTGAAAGAACATAATGATAACTAG 58.724 37.037 0.00 0.00 0.00 2.57
662 5215 8.328758 TGGTCAAGGATCACACTATTCTATTTT 58.671 33.333 0.00 0.00 0.00 1.82
734 5287 9.498176 GAGAACTAAAAATAAGTGGTGTTCCTA 57.502 33.333 0.00 0.00 34.79 2.94
769 5322 1.978617 AATGCCCGCCCTTTGACTG 60.979 57.895 0.00 0.00 0.00 3.51
777 5330 1.856265 GCCCTTTGACTGAACCTGCG 61.856 60.000 0.00 0.00 0.00 5.18
783 5336 3.896648 TTGACTGAACCTGCGAAATTC 57.103 42.857 0.00 0.00 0.00 2.17
851 5427 9.533253 CTACTCCATCAAAGTTCAAAACAAATT 57.467 29.630 0.00 0.00 0.00 1.82
866 5442 9.672086 TCAAAACAAATTACTTGAATTCTACCG 57.328 29.630 7.05 0.00 36.71 4.02
879 5495 0.543277 TCTACCGTTCGGGCTAGAGA 59.457 55.000 15.66 6.99 40.62 3.10
883 5499 1.553704 ACCGTTCGGGCTAGAGAAAAT 59.446 47.619 15.66 0.00 40.62 1.82
888 5504 1.485066 TCGGGCTAGAGAAAATGGGTC 59.515 52.381 0.00 0.00 0.00 4.46
893 5509 3.942115 GGCTAGAGAAAATGGGTCAGAAC 59.058 47.826 0.00 0.00 0.00 3.01
894 5510 4.565652 GGCTAGAGAAAATGGGTCAGAACA 60.566 45.833 0.00 0.00 0.00 3.18
906 5523 1.002792 GTCAGAACAGAACCCGCAAAC 60.003 52.381 0.00 0.00 0.00 2.93
908 5525 0.179067 AGAACAGAACCCGCAAACGA 60.179 50.000 0.00 0.00 43.93 3.85
954 5571 1.586303 TGCTCGCTCGTCGCTAATG 60.586 57.895 0.00 0.00 38.27 1.90
956 5573 1.298713 CTCGCTCGTCGCTAATGCT 60.299 57.895 0.00 0.00 38.27 3.79
957 5574 0.041224 CTCGCTCGTCGCTAATGCTA 60.041 55.000 0.00 0.00 38.27 3.49
960 5577 1.383744 CGCTCGTCGCTAATGCTAATC 59.616 52.381 0.00 0.00 36.97 1.75
964 5581 1.429463 GTCGCTAATGCTAATCCCCG 58.571 55.000 0.00 0.00 36.97 5.73
965 5582 1.045407 TCGCTAATGCTAATCCCCGT 58.955 50.000 0.00 0.00 36.97 5.28
1025 5644 4.698625 ACTCCGACTCCGCCCCTT 62.699 66.667 0.00 0.00 0.00 3.95
1033 5652 3.316573 CTCCGCCCCTTTCGAAGCT 62.317 63.158 0.00 0.00 0.00 3.74
1034 5653 2.359975 CCGCCCCTTTCGAAGCTT 60.360 61.111 0.00 0.00 0.00 3.74
1311 5948 2.282887 GCTCCGCCCCCTTTTTGA 60.283 61.111 0.00 0.00 0.00 2.69
1312 5949 1.906333 GCTCCGCCCCCTTTTTGAA 60.906 57.895 0.00 0.00 0.00 2.69
1313 5950 1.257750 GCTCCGCCCCCTTTTTGAAT 61.258 55.000 0.00 0.00 0.00 2.57
1314 5951 0.532115 CTCCGCCCCCTTTTTGAATG 59.468 55.000 0.00 0.00 0.00 2.67
1315 5952 1.079197 CCGCCCCCTTTTTGAATGC 60.079 57.895 0.00 0.00 0.00 3.56
1316 5953 1.543944 CCGCCCCCTTTTTGAATGCT 61.544 55.000 0.00 0.00 0.00 3.79
1317 5954 0.390209 CGCCCCCTTTTTGAATGCTG 60.390 55.000 0.00 0.00 0.00 4.41
1319 5956 1.347378 GCCCCCTTTTTGAATGCTGAA 59.653 47.619 0.00 0.00 0.00 3.02
1320 5957 2.871637 GCCCCCTTTTTGAATGCTGAAC 60.872 50.000 0.00 0.00 0.00 3.18
1323 5960 2.610232 CCCTTTTTGAATGCTGAACCGG 60.610 50.000 0.00 0.00 0.00 5.28
1324 5961 2.295909 CCTTTTTGAATGCTGAACCGGA 59.704 45.455 9.46 0.00 0.00 5.14
1325 5962 3.056607 CCTTTTTGAATGCTGAACCGGAT 60.057 43.478 9.46 0.00 0.00 4.18
1326 5963 3.848272 TTTTGAATGCTGAACCGGATC 57.152 42.857 9.46 6.62 0.00 3.36
1328 5965 0.617935 TGAATGCTGAACCGGATCCA 59.382 50.000 9.46 0.00 0.00 3.41
1329 5966 1.303309 GAATGCTGAACCGGATCCAG 58.697 55.000 9.46 13.14 0.00 3.86
1331 5968 1.135094 ATGCTGAACCGGATCCAGAT 58.865 50.000 9.46 0.00 0.00 2.90
1332 5969 1.788229 TGCTGAACCGGATCCAGATA 58.212 50.000 9.46 2.45 0.00 1.98
1335 5972 2.365617 GCTGAACCGGATCCAGATAGAA 59.634 50.000 9.46 0.00 0.00 2.10
1337 5974 3.371034 TGAACCGGATCCAGATAGAACA 58.629 45.455 9.46 0.00 0.00 3.18
1338 5975 3.384789 TGAACCGGATCCAGATAGAACAG 59.615 47.826 9.46 0.00 0.00 3.16
1344 6022 0.975556 TCCAGATAGAACAGGCCGCA 60.976 55.000 0.00 0.00 0.00 5.69
1346 6024 0.108186 CAGATAGAACAGGCCGCACA 60.108 55.000 0.00 0.00 0.00 4.57
1349 6027 2.184020 ATAGAACAGGCCGCACAGCA 62.184 55.000 0.00 0.00 0.00 4.41
1380 6058 3.951332 CGCGAGCAAGACAAGGAA 58.049 55.556 0.00 0.00 0.00 3.36
1383 6061 0.952984 GCGAGCAAGACAAGGAAGCT 60.953 55.000 0.00 0.00 38.43 3.74
1386 6064 2.610479 CGAGCAAGACAAGGAAGCTGTA 60.610 50.000 0.00 0.00 35.36 2.74
1388 6066 2.079925 GCAAGACAAGGAAGCTGTAGG 58.920 52.381 0.00 0.00 0.00 3.18
1390 6068 3.807209 GCAAGACAAGGAAGCTGTAGGAA 60.807 47.826 0.00 0.00 0.00 3.36
1391 6069 4.389374 CAAGACAAGGAAGCTGTAGGAAA 58.611 43.478 0.00 0.00 0.00 3.13
1393 6071 5.248380 AGACAAGGAAGCTGTAGGAAATT 57.752 39.130 0.00 0.00 0.00 1.82
1396 6074 5.006386 ACAAGGAAGCTGTAGGAAATTGAG 58.994 41.667 0.00 0.00 0.00 3.02
1397 6075 4.917906 AGGAAGCTGTAGGAAATTGAGT 57.082 40.909 0.00 0.00 0.00 3.41
1398 6076 6.173339 CAAGGAAGCTGTAGGAAATTGAGTA 58.827 40.000 0.00 0.00 0.00 2.59
1401 6079 4.762289 AGCTGTAGGAAATTGAGTAGGG 57.238 45.455 0.00 0.00 0.00 3.53
1405 6083 3.589735 TGTAGGAAATTGAGTAGGGCCAA 59.410 43.478 6.18 0.00 0.00 4.52
1406 6084 3.372440 AGGAAATTGAGTAGGGCCAAG 57.628 47.619 6.18 0.00 0.00 3.61
1408 6086 3.333680 AGGAAATTGAGTAGGGCCAAGAA 59.666 43.478 6.18 0.00 0.00 2.52
1409 6087 3.696548 GGAAATTGAGTAGGGCCAAGAAG 59.303 47.826 6.18 0.00 0.00 2.85
1410 6088 4.567747 GGAAATTGAGTAGGGCCAAGAAGA 60.568 45.833 6.18 0.00 0.00 2.87
1411 6089 4.870021 AATTGAGTAGGGCCAAGAAGAT 57.130 40.909 6.18 0.00 0.00 2.40
1412 6090 4.870021 ATTGAGTAGGGCCAAGAAGATT 57.130 40.909 6.18 0.00 0.00 2.40
1413 6091 4.657814 TTGAGTAGGGCCAAGAAGATTT 57.342 40.909 6.18 0.00 0.00 2.17
1415 6093 5.099042 TGAGTAGGGCCAAGAAGATTTAC 57.901 43.478 6.18 0.00 0.00 2.01
1416 6094 4.534500 TGAGTAGGGCCAAGAAGATTTACA 59.466 41.667 6.18 0.00 0.00 2.41
1417 6095 5.191722 TGAGTAGGGCCAAGAAGATTTACAT 59.808 40.000 6.18 0.00 0.00 2.29
1418 6096 5.440610 AGTAGGGCCAAGAAGATTTACATG 58.559 41.667 6.18 0.00 0.00 3.21
1461 6192 5.395768 GGATGAGTAGCAGTAGTGTTTCCAT 60.396 44.000 0.00 0.00 0.00 3.41
1560 6291 7.227512 TGTGTTTTTGTTGAAATTGTTGTCCTT 59.772 29.630 0.00 0.00 0.00 3.36
1673 6407 2.704572 CCCTTCTTCCTGCTACTTGTG 58.295 52.381 0.00 0.00 0.00 3.33
1674 6408 2.303022 CCCTTCTTCCTGCTACTTGTGA 59.697 50.000 0.00 0.00 0.00 3.58
1746 6486 5.648092 CAGGGAGAAATGGTTGGTTTAGTAG 59.352 44.000 0.00 0.00 0.00 2.57
1751 6491 3.688694 ATGGTTGGTTTAGTAGTCGCA 57.311 42.857 0.00 0.00 0.00 5.10
1763 6503 1.139058 GTAGTCGCAGATGTGGGGATT 59.861 52.381 7.08 0.00 40.67 3.01
1793 6533 2.410774 GCACGCGATATCTTGCATTCTC 60.411 50.000 15.93 0.00 34.97 2.87
1912 6657 5.483231 TCCCCTTTGATTTGAAATATGCACA 59.517 36.000 0.00 0.00 0.00 4.57
1913 6658 6.156602 TCCCCTTTGATTTGAAATATGCACAT 59.843 34.615 0.00 0.00 0.00 3.21
1914 6659 6.480981 CCCCTTTGATTTGAAATATGCACATC 59.519 38.462 0.00 0.00 0.00 3.06
1915 6660 7.042950 CCCTTTGATTTGAAATATGCACATCA 58.957 34.615 0.00 4.44 32.40 3.07
1916 6661 7.223971 CCCTTTGATTTGAAATATGCACATCAG 59.776 37.037 0.00 0.75 34.89 2.90
1917 6662 7.762615 CCTTTGATTTGAAATATGCACATCAGT 59.237 33.333 0.00 0.00 34.89 3.41
1918 6663 8.692110 TTTGATTTGAAATATGCACATCAGTC 57.308 30.769 0.00 0.00 34.89 3.51
1936 6681 8.242053 ACATCAGTCATCAATTGAAAAGATCAC 58.758 33.333 13.09 2.02 37.92 3.06
1959 6767 6.202379 CACATGACTCACAGATACATGGAATC 59.798 42.308 0.00 0.00 41.41 2.52
1960 6768 5.937975 TGACTCACAGATACATGGAATCA 57.062 39.130 11.54 0.00 0.00 2.57
1961 6769 6.490241 TGACTCACAGATACATGGAATCAT 57.510 37.500 11.54 0.00 0.00 2.45
1962 6770 6.892485 TGACTCACAGATACATGGAATCATT 58.108 36.000 11.54 0.00 0.00 2.57
1963 6771 7.341030 TGACTCACAGATACATGGAATCATTT 58.659 34.615 11.54 0.00 0.00 2.32
1964 6772 8.485392 TGACTCACAGATACATGGAATCATTTA 58.515 33.333 11.54 0.00 0.00 1.40
1965 6773 9.499479 GACTCACAGATACATGGAATCATTTAT 57.501 33.333 11.54 0.00 31.16 1.40
1966 6774 9.499479 ACTCACAGATACATGGAATCATTTATC 57.501 33.333 11.54 0.00 40.61 1.75
1967 6775 9.722184 CTCACAGATACATGGAATCATTTATCT 57.278 33.333 11.54 8.43 46.28 1.98
2138 6962 4.461431 GGGACCGTCATGGAACTTAAATTT 59.539 41.667 0.00 0.00 42.00 1.82
2156 6982 6.377327 AAATTTGTGTGAGTAGACAACTGG 57.623 37.500 0.00 0.00 39.48 4.00
2343 7526 6.947733 TCAAGATGGTTTCCATATGTGAAGTT 59.052 34.615 1.24 0.00 45.26 2.66
2720 8181 5.423015 TCTAGTTTTCTGCAGCTTATCTGG 58.577 41.667 9.47 5.90 43.06 3.86
2924 10039 9.256477 TCAACATTGTAGTGTTCTAGTGTTTAG 57.744 33.333 0.00 0.00 40.17 1.85
3038 10171 3.141398 CGCACTTATGTTGGATGGCTAT 58.859 45.455 0.00 0.00 0.00 2.97
3046 10179 5.894298 ATGTTGGATGGCTATCACTCTAA 57.106 39.130 12.54 0.00 34.90 2.10
3118 10257 1.714899 CGGCGGATGTTAGGGCTTTG 61.715 60.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.163530 TGGTCATTTTGCGCATCTGATATTT 60.164 36.000 12.75 0.00 0.00 1.40
38 4049 1.831106 TCATCAGGACGGTGTTGCTAT 59.169 47.619 0.00 0.00 0.00 2.97
49 4060 1.830477 AGAGTGGAGCTTCATCAGGAC 59.170 52.381 0.00 0.00 0.00 3.85
86 4097 4.871993 AACGCTTCAATAGATCTTGCTG 57.128 40.909 0.00 0.00 0.00 4.41
105 4116 3.243737 CCCTGGAAACACAAAGCCTTAAC 60.244 47.826 0.00 0.00 35.60 2.01
219 4230 7.984050 CCTCCCTGATCACATATATACATGAAC 59.016 40.741 0.00 1.61 0.00 3.18
235 4729 5.871396 TTGTAATGTACTCCTCCCTGATC 57.129 43.478 0.00 0.00 0.00 2.92
417 4962 6.095021 TCTCTCAGCTTGGAAATTGATTGATG 59.905 38.462 0.00 0.00 0.00 3.07
478 5023 7.539712 TCTCAAAGGAACTAAGAATAATGCG 57.460 36.000 0.00 0.00 38.49 4.73
490 5035 5.888982 TTCTACAGGTTCTCAAAGGAACT 57.111 39.130 7.19 0.00 43.43 3.01
539 5084 2.092646 TCACGCCTTGGCAATAACCTAT 60.093 45.455 12.45 0.00 0.00 2.57
540 5085 1.279558 TCACGCCTTGGCAATAACCTA 59.720 47.619 12.45 0.00 0.00 3.08
756 5309 1.073199 AGGTTCAGTCAAAGGGCGG 59.927 57.895 0.00 0.00 0.00 6.13
769 5322 0.171231 GCCTGGAATTTCGCAGGTTC 59.829 55.000 23.49 12.15 37.25 3.62
783 5336 2.744202 GCTGTAATATTCATCCGCCTGG 59.256 50.000 0.00 0.00 0.00 4.45
820 5373 0.541863 ACTTTGATGGAGTAGGGGCG 59.458 55.000 0.00 0.00 0.00 6.13
851 5427 3.676873 GCCCGAACGGTAGAATTCAAGTA 60.677 47.826 8.44 0.00 0.00 2.24
866 5442 2.289565 CCCATTTTCTCTAGCCCGAAC 58.710 52.381 0.00 0.00 0.00 3.95
879 5495 3.230976 GGGTTCTGTTCTGACCCATTTT 58.769 45.455 5.93 0.00 40.26 1.82
883 5499 1.752198 CGGGTTCTGTTCTGACCCA 59.248 57.895 11.04 0.00 40.54 4.51
888 5504 0.041312 CGTTTGCGGGTTCTGTTCTG 60.041 55.000 0.00 0.00 0.00 3.02
893 5509 0.941542 TCTTTCGTTTGCGGGTTCTG 59.058 50.000 0.00 0.00 38.89 3.02
894 5510 1.226746 CTCTTTCGTTTGCGGGTTCT 58.773 50.000 0.00 0.00 38.89 3.01
906 5523 1.289109 TTTTCCGGCGAGCTCTTTCG 61.289 55.000 9.30 12.05 43.23 3.46
908 5525 1.235281 GGTTTTCCGGCGAGCTCTTT 61.235 55.000 9.30 0.00 0.00 2.52
954 5571 0.034863 TGTGGGAAACGGGGATTAGC 60.035 55.000 0.00 0.00 0.00 3.09
956 5573 2.516906 GTTTGTGGGAAACGGGGATTA 58.483 47.619 0.00 0.00 0.00 1.75
957 5574 1.334160 GTTTGTGGGAAACGGGGATT 58.666 50.000 0.00 0.00 0.00 3.01
960 5577 2.204461 GGGTTTGTGGGAAACGGGG 61.204 63.158 0.00 0.00 0.00 5.73
1307 5944 2.091541 GGATCCGGTTCAGCATTCAAA 58.908 47.619 14.36 0.00 0.00 2.69
1308 5945 1.004161 TGGATCCGGTTCAGCATTCAA 59.996 47.619 14.36 0.00 0.00 2.69
1311 5948 0.911769 TCTGGATCCGGTTCAGCATT 59.088 50.000 20.32 0.00 0.00 3.56
1312 5949 1.135094 ATCTGGATCCGGTTCAGCAT 58.865 50.000 20.32 2.38 0.00 3.79
1313 5950 1.688735 CTATCTGGATCCGGTTCAGCA 59.311 52.381 20.32 0.00 0.00 4.41
1314 5951 1.964223 TCTATCTGGATCCGGTTCAGC 59.036 52.381 20.32 0.00 0.00 4.26
1315 5952 3.384789 TGTTCTATCTGGATCCGGTTCAG 59.615 47.826 20.32 14.68 0.00 3.02
1316 5953 3.371034 TGTTCTATCTGGATCCGGTTCA 58.629 45.455 20.32 1.31 0.00 3.18
1317 5954 3.243907 CCTGTTCTATCTGGATCCGGTTC 60.244 52.174 20.32 1.67 0.00 3.62
1319 5956 2.320781 CCTGTTCTATCTGGATCCGGT 58.679 52.381 20.32 10.26 0.00 5.28
1320 5957 1.001406 GCCTGTTCTATCTGGATCCGG 59.999 57.143 15.09 15.09 0.00 5.14
1323 5960 1.606737 GCGGCCTGTTCTATCTGGATC 60.607 57.143 0.00 0.00 0.00 3.36
1324 5961 0.394565 GCGGCCTGTTCTATCTGGAT 59.605 55.000 0.00 0.00 0.00 3.41
1325 5962 0.975556 TGCGGCCTGTTCTATCTGGA 60.976 55.000 0.00 0.00 0.00 3.86
1326 5963 0.811616 GTGCGGCCTGTTCTATCTGG 60.812 60.000 0.00 0.00 0.00 3.86
1328 5965 0.176680 CTGTGCGGCCTGTTCTATCT 59.823 55.000 0.00 0.00 0.00 1.98
1329 5966 1.432270 GCTGTGCGGCCTGTTCTATC 61.432 60.000 0.00 0.00 0.00 2.08
1331 5968 2.047274 GCTGTGCGGCCTGTTCTA 60.047 61.111 0.00 0.00 0.00 2.10
1332 5969 4.254709 TGCTGTGCGGCCTGTTCT 62.255 61.111 0.00 0.00 0.00 3.01
1361 6039 2.715532 TTCCTTGTCTTGCTCGCGCT 62.716 55.000 5.56 0.00 36.97 5.92
1363 6041 1.784062 CTTCCTTGTCTTGCTCGCG 59.216 57.895 0.00 0.00 0.00 5.87
1367 6045 2.289945 CCTACAGCTTCCTTGTCTTGCT 60.290 50.000 0.00 0.00 0.00 3.91
1369 6047 3.685139 TCCTACAGCTTCCTTGTCTTG 57.315 47.619 0.00 0.00 0.00 3.02
1370 6048 4.706842 TTTCCTACAGCTTCCTTGTCTT 57.293 40.909 0.00 0.00 0.00 3.01
1371 6049 4.917906 ATTTCCTACAGCTTCCTTGTCT 57.082 40.909 0.00 0.00 0.00 3.41
1372 6050 5.003804 TCAATTTCCTACAGCTTCCTTGTC 58.996 41.667 0.00 0.00 0.00 3.18
1375 6053 5.248380 ACTCAATTTCCTACAGCTTCCTT 57.752 39.130 0.00 0.00 0.00 3.36
1376 6054 4.917906 ACTCAATTTCCTACAGCTTCCT 57.082 40.909 0.00 0.00 0.00 3.36
1378 6056 5.119694 CCCTACTCAATTTCCTACAGCTTC 58.880 45.833 0.00 0.00 0.00 3.86
1379 6057 4.626529 GCCCTACTCAATTTCCTACAGCTT 60.627 45.833 0.00 0.00 0.00 3.74
1380 6058 3.118223 GCCCTACTCAATTTCCTACAGCT 60.118 47.826 0.00 0.00 0.00 4.24
1383 6061 3.186283 TGGCCCTACTCAATTTCCTACA 58.814 45.455 0.00 0.00 0.00 2.74
1386 6064 2.919602 TCTTGGCCCTACTCAATTTCCT 59.080 45.455 0.00 0.00 0.00 3.36
1388 6066 4.589908 TCTTCTTGGCCCTACTCAATTTC 58.410 43.478 0.00 0.00 0.00 2.17
1390 6068 4.870021 ATCTTCTTGGCCCTACTCAATT 57.130 40.909 0.00 0.00 0.00 2.32
1391 6069 4.870021 AATCTTCTTGGCCCTACTCAAT 57.130 40.909 0.00 0.00 0.00 2.57
1393 6071 4.534500 TGTAAATCTTCTTGGCCCTACTCA 59.466 41.667 0.00 0.00 0.00 3.41
1396 6074 5.437060 TCATGTAAATCTTCTTGGCCCTAC 58.563 41.667 0.00 0.00 0.00 3.18
1397 6075 5.708736 TCATGTAAATCTTCTTGGCCCTA 57.291 39.130 0.00 0.00 0.00 3.53
1398 6076 4.591321 TCATGTAAATCTTCTTGGCCCT 57.409 40.909 0.00 0.00 0.00 5.19
1461 6192 5.532032 TGCAGATGAAAGTGATGAACTCAAA 59.468 36.000 0.00 0.00 38.56 2.69
1574 6308 1.079405 TGACTCCCACGCGATTTCC 60.079 57.895 15.93 0.00 0.00 3.13
1576 6310 1.741770 GCTGACTCCCACGCGATTT 60.742 57.895 15.93 0.00 0.00 2.17
1673 6407 0.033504 TCGCCAACAGAAGACCAGTC 59.966 55.000 0.00 0.00 0.00 3.51
1674 6408 0.687354 ATCGCCAACAGAAGACCAGT 59.313 50.000 0.00 0.00 0.00 4.00
1746 6486 1.463674 AAAATCCCCACATCTGCGAC 58.536 50.000 0.00 0.00 0.00 5.19
1751 6491 3.706086 GCATACCAAAAATCCCCACATCT 59.294 43.478 0.00 0.00 0.00 2.90
1763 6503 3.462982 AGATATCGCGTGCATACCAAAA 58.537 40.909 5.77 0.00 0.00 2.44
1793 6533 3.472283 AGTGCTAGAGCTGGAATGATG 57.528 47.619 2.72 0.00 42.66 3.07
1842 6582 1.577328 AACTGCGATGGTGCTTTCCG 61.577 55.000 0.00 0.00 35.36 4.30
1897 6642 8.002984 TGATGACTGATGTGCATATTTCAAAT 57.997 30.769 0.00 0.00 0.00 2.32
1912 6657 8.344446 TGTGATCTTTTCAATTGATGACTGAT 57.656 30.769 9.40 8.88 37.92 2.90
1913 6658 7.748691 TGTGATCTTTTCAATTGATGACTGA 57.251 32.000 9.40 4.55 37.92 3.41
1914 6659 8.241367 TCATGTGATCTTTTCAATTGATGACTG 58.759 33.333 9.40 0.00 37.92 3.51
1915 6660 8.242053 GTCATGTGATCTTTTCAATTGATGACT 58.758 33.333 17.82 2.35 37.92 3.41
1916 6661 8.242053 AGTCATGTGATCTTTTCAATTGATGAC 58.758 33.333 17.57 17.57 37.92 3.06
1917 6662 8.344446 AGTCATGTGATCTTTTCAATTGATGA 57.656 30.769 9.40 8.65 35.70 2.92
1918 6663 8.241367 TGAGTCATGTGATCTTTTCAATTGATG 58.759 33.333 9.40 3.31 35.70 3.07
1936 6681 6.285990 TGATTCCATGTATCTGTGAGTCATG 58.714 40.000 0.00 0.00 36.60 3.07
1987 6795 9.120538 GGCAGTAAACTAAGATAAATGATTCCA 57.879 33.333 0.00 0.00 0.00 3.53
1988 6796 9.343539 AGGCAGTAAACTAAGATAAATGATTCC 57.656 33.333 0.00 0.00 0.00 3.01
1992 6800 9.817809 CAGTAGGCAGTAAACTAAGATAAATGA 57.182 33.333 0.00 0.00 0.00 2.57
2138 6962 2.483013 GCACCAGTTGTCTACTCACACA 60.483 50.000 0.00 0.00 33.85 3.72
2156 6982 1.071385 AGCATATGGTAGGAGCTGCAC 59.929 52.381 8.35 3.59 33.67 4.57
2684 8144 3.831715 AAACTAGAACTTGAATGCGGC 57.168 42.857 0.00 0.00 0.00 6.53
2720 8181 7.708998 TGTTAATAAAGAAACCAGTGTTCCAC 58.291 34.615 0.00 0.00 32.15 4.02
2924 10039 1.239968 CCAGACTTCCCAGCAGCAAC 61.240 60.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.