Multiple sequence alignment - TraesCS4A01G458500

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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 TraesCS4A01G458500 chr4A 100.000 2698 0 0 1 2698 723708354 723711051 0.000000e+00 4983.0
1 TraesCS4A01G458500 chr4A 83.893 1161 129 23 1553 2690 723735700 723736825 0.000000e+00 1055.0
2 TraesCS4A01G458500 chr7A 89.615 1300 83 22 1 1255 12810920 12809628 0.000000e+00 1605.0
3 TraesCS4A01G458500 chr7A 89.384 1055 80 10 1647 2697 12809038 12808012 0.000000e+00 1299.0
4 TraesCS4A01G458500 chr7A 89.223 566 53 6 2139 2697 12804698 12804134 0.000000e+00 701.0
5 TraesCS4A01G458500 chr7A 95.093 428 21 0 1372 1799 12809626 12809199 0.000000e+00 675.0
6 TraesCS4A01G458500 chr7A 100.000 31 0 0 1594 1624 12803956 12803926 1.040000e-04 58.4
7 TraesCS4A01G458500 chr7D 87.393 1285 102 37 3 1257 13411884 13410630 0.000000e+00 1421.0
8 TraesCS4A01G458500 chr7D 93.068 577 38 1 1371 1947 13410631 13410057 0.000000e+00 843.0
9 TraesCS4A01G458500 chr6B 94.488 127 6 1 1253 1378 164883037 164882911 7.620000e-46 195.0
10 TraesCS4A01G458500 chr5D 93.798 129 7 1 1251 1378 47283879 47284007 2.740000e-45 193.0
11 TraesCS4A01G458500 chr5B 94.444 126 5 2 1252 1375 446529750 446529625 2.740000e-45 193.0
12 TraesCS4A01G458500 chr5B 92.366 131 9 1 1247 1376 614065035 614065165 4.590000e-43 185.0
13 TraesCS4A01G458500 chr3B 95.763 118 5 0 1256 1373 655032862 655032745 9.860000e-45 191.0
14 TraesCS4A01G458500 chr3A 94.400 125 6 1 1252 1376 511599581 511599458 9.860000e-45 191.0
15 TraesCS4A01G458500 chr3D 93.077 130 7 2 1253 1381 66262963 66262835 3.550000e-44 189.0
16 TraesCS4A01G458500 chr1A 93.077 130 6 3 1253 1381 539977572 539977699 1.280000e-43 187.0
17 TraesCS4A01G458500 chr2B 89.865 148 10 5 1252 1399 500592374 500592516 4.590000e-43 185.0
18 TraesCS4A01G458500 chr7B 80.247 162 30 1 1802 1963 578744701 578744542 1.310000e-23 121.0
19 TraesCS4A01G458500 chr7B 80.247 162 30 1 1802 1963 578778031 578777872 1.310000e-23 121.0


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 TraesCS4A01G458500 chr4A 723708354 723711051 2697 False 4983.00 4983 100.0000 1 2698 1 chr4A.!!$F1 2697
1 TraesCS4A01G458500 chr4A 723735700 723736825 1125 False 1055.00 1055 83.8930 1553 2690 1 chr4A.!!$F2 1137
2 TraesCS4A01G458500 chr7A 12803926 12810920 6994 True 867.68 1605 92.6630 1 2697 5 chr7A.!!$R1 2696
3 TraesCS4A01G458500 chr7D 13410057 13411884 1827 True 1132.00 1421 90.2305 3 1947 2 chr7D.!!$R1 1944

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
881 920 1.205064 CTTTTCACTGCCACGCTCG 59.795 57.895 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2681 0.108615 AGATGTTTCTCAGGACGGCG 60.109 55.0 4.8 4.8 0.0 6.46 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
42 45 2.582728 TGCTGCTGTTTCAGTTTTGG 57.417 45.000 0.00 0.00 36.49 3.28
104 114 9.594478 TCCTTTTTCTTTTCCTTATTTGAACAC 57.406 29.630 0.00 0.00 0.00 3.32
183 213 2.000048 TCAACCTCCCTGCCCTTTAAT 59.000 47.619 0.00 0.00 0.00 1.40
242 272 6.094742 TGTGCAAGTTTGTCTAGTTCAAATGA 59.905 34.615 14.84 0.00 37.18 2.57
273 303 4.341806 TCAAAACGGTGTGGAAGAGTAGTA 59.658 41.667 0.00 0.00 0.00 1.82
318 349 7.177878 TCCTGAAATGAGGATTCTTAGCTTTT 58.822 34.615 0.00 0.00 37.20 2.27
319 350 7.671398 TCCTGAAATGAGGATTCTTAGCTTTTT 59.329 33.333 0.00 0.00 37.20 1.94
361 392 9.591792 TCAATATTTGATCTAACTGAGTCAGTG 57.408 33.333 26.12 14.72 38.62 3.66
362 393 9.376075 CAATATTTGATCTAACTGAGTCAGTGT 57.624 33.333 26.12 17.36 44.62 3.55
386 417 4.081752 GGTGCCATGTGATTTTCCATGTTA 60.082 41.667 0.00 0.00 37.37 2.41
442 473 8.772705 TCATTTAAATGCATTTGTCCAAGAAAC 58.227 29.630 30.43 0.00 36.36 2.78
444 475 4.686191 AATGCATTTGTCCAAGAAACCA 57.314 36.364 5.99 0.00 0.00 3.67
511 543 9.456797 GTTTTTAAACGTATCTACAGATCAACG 57.543 33.333 11.23 11.23 40.43 4.10
512 544 8.969121 TTTTAAACGTATCTACAGATCAACGA 57.031 30.769 17.18 0.00 38.23 3.85
550 587 2.488153 GTCCCAGGCTTTATGACAACAC 59.512 50.000 0.00 0.00 0.00 3.32
631 670 7.707624 TGATGAGCAATTTCAGGTCTTATTT 57.292 32.000 0.00 0.00 34.73 1.40
744 783 8.299570 ACGAGAGATTGATTTGTTGCTAATTTT 58.700 29.630 0.00 0.00 0.00 1.82
827 866 2.695585 ACTCCTCCCTCTTTCACTGTT 58.304 47.619 0.00 0.00 0.00 3.16
831 870 4.168101 TCCTCCCTCTTTCACTGTTATGT 58.832 43.478 0.00 0.00 0.00 2.29
863 902 7.856145 AATGACTCAAATGAGGACAGATAAC 57.144 36.000 14.50 0.00 46.13 1.89
872 911 7.678947 AATGAGGACAGATAACTTTTCACTG 57.321 36.000 0.00 0.00 35.14 3.66
873 912 4.997395 TGAGGACAGATAACTTTTCACTGC 59.003 41.667 0.00 0.00 32.67 4.40
876 915 4.083271 GGACAGATAACTTTTCACTGCCAC 60.083 45.833 0.00 0.00 32.67 5.01
881 920 1.205064 CTTTTCACTGCCACGCTCG 59.795 57.895 0.00 0.00 0.00 5.03
907 946 6.498304 TGTCAAGATCAAAGCTTTTTCTGTC 58.502 36.000 17.82 12.83 0.00 3.51
931 970 9.362539 GTCGTACAGATTCATAGGAAGTTTTTA 57.637 33.333 0.00 0.00 36.25 1.52
932 971 9.582431 TCGTACAGATTCATAGGAAGTTTTTAG 57.418 33.333 0.00 0.00 36.25 1.85
933 972 9.582431 CGTACAGATTCATAGGAAGTTTTTAGA 57.418 33.333 0.00 0.00 36.25 2.10
936 975 9.401058 ACAGATTCATAGGAAGTTTTTAGATGG 57.599 33.333 0.00 0.00 36.25 3.51
937 976 9.618890 CAGATTCATAGGAAGTTTTTAGATGGA 57.381 33.333 0.00 0.00 36.25 3.41
947 1009 7.648112 GGAAGTTTTTAGATGGAGTCACAAAAC 59.352 37.037 0.00 0.00 39.22 2.43
977 1039 4.215613 GGAGTTGACATTAACAGTGGGAAC 59.784 45.833 0.00 0.00 33.02 3.62
984 1046 5.630121 ACATTAACAGTGGGAACTTGATCA 58.370 37.500 0.00 0.00 0.00 2.92
1033 1095 2.211250 ATGTCCATCAAAGCAGCTGT 57.789 45.000 16.64 0.00 0.00 4.40
1088 1150 1.032794 TGCGAGAACTCACTGTCACT 58.967 50.000 2.78 0.00 0.00 3.41
1101 1163 1.755959 CTGTCACTAGCTCCAGATGCT 59.244 52.381 0.00 0.00 43.79 3.79
1102 1164 1.753649 TGTCACTAGCTCCAGATGCTC 59.246 52.381 0.00 0.00 41.46 4.26
1104 1166 0.743688 CACTAGCTCCAGATGCTCGT 59.256 55.000 0.00 0.00 41.46 4.18
1142 1204 1.451504 CACTCTCCTGCAACCACCA 59.548 57.895 0.00 0.00 0.00 4.17
1165 1227 1.134699 TCTTCACCATCATCCTGTCGC 60.135 52.381 0.00 0.00 0.00 5.19
1168 1230 0.460109 CACCATCATCCTGTCGCGAA 60.460 55.000 12.06 0.00 0.00 4.70
1217 1279 5.412594 TGGTATGAGACAGCAACAAATTCTC 59.587 40.000 0.00 0.00 34.48 2.87
1221 1283 4.276678 TGAGACAGCAACAAATTCTCCAAG 59.723 41.667 0.00 0.00 33.17 3.61
1226 1288 5.594317 ACAGCAACAAATTCTCCAAGTACTT 59.406 36.000 1.12 1.12 0.00 2.24
1249 1312 3.440173 AGTATTGCAGAAATGACCCGTTG 59.560 43.478 0.00 0.00 0.00 4.10
1255 1318 3.864921 GCAGAAATGACCCGTTGACTACT 60.865 47.826 0.00 0.00 0.00 2.57
1256 1319 4.619863 GCAGAAATGACCCGTTGACTACTA 60.620 45.833 0.00 0.00 0.00 1.82
1257 1320 4.863131 CAGAAATGACCCGTTGACTACTAC 59.137 45.833 0.00 0.00 0.00 2.73
1258 1321 4.771054 AGAAATGACCCGTTGACTACTACT 59.229 41.667 0.00 0.00 0.00 2.57
1259 1322 4.715527 AATGACCCGTTGACTACTACTC 57.284 45.455 0.00 0.00 0.00 2.59
1260 1323 2.440409 TGACCCGTTGACTACTACTCC 58.560 52.381 0.00 0.00 0.00 3.85
1261 1324 1.747924 GACCCGTTGACTACTACTCCC 59.252 57.143 0.00 0.00 0.00 4.30
1262 1325 1.357079 ACCCGTTGACTACTACTCCCT 59.643 52.381 0.00 0.00 0.00 4.20
1263 1326 2.022934 CCCGTTGACTACTACTCCCTC 58.977 57.143 0.00 0.00 0.00 4.30
1264 1327 2.022934 CCGTTGACTACTACTCCCTCC 58.977 57.143 0.00 0.00 0.00 4.30
1265 1328 1.669779 CGTTGACTACTACTCCCTCCG 59.330 57.143 0.00 0.00 0.00 4.63
1266 1329 2.720915 GTTGACTACTACTCCCTCCGT 58.279 52.381 0.00 0.00 0.00 4.69
1267 1330 2.682352 GTTGACTACTACTCCCTCCGTC 59.318 54.545 0.00 0.00 0.00 4.79
1268 1331 1.211457 TGACTACTACTCCCTCCGTCC 59.789 57.143 0.00 0.00 0.00 4.79
1269 1332 0.179936 ACTACTACTCCCTCCGTCCG 59.820 60.000 0.00 0.00 0.00 4.79
1270 1333 0.467384 CTACTACTCCCTCCGTCCGA 59.533 60.000 0.00 0.00 0.00 4.55
1271 1334 0.911769 TACTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
1272 1335 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1273 1336 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
1274 1337 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
1275 1338 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1276 1339 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1277 1340 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1278 1341 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1279 1342 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1280 1343 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1281 1344 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1282 1345 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1283 1346 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1284 1347 4.571919 TCCGTCCGAAAATACTTGTCATT 58.428 39.130 0.00 0.00 0.00 2.57
1285 1348 4.390603 TCCGTCCGAAAATACTTGTCATTG 59.609 41.667 0.00 0.00 0.00 2.82
1286 1349 4.390603 CCGTCCGAAAATACTTGTCATTGA 59.609 41.667 0.00 0.00 0.00 2.57
1287 1350 5.106869 CCGTCCGAAAATACTTGTCATTGAA 60.107 40.000 0.00 0.00 0.00 2.69
1288 1351 6.367421 CGTCCGAAAATACTTGTCATTGAAA 58.633 36.000 0.00 0.00 0.00 2.69
1289 1352 7.021196 CGTCCGAAAATACTTGTCATTGAAAT 58.979 34.615 0.00 0.00 0.00 2.17
1290 1353 7.007367 CGTCCGAAAATACTTGTCATTGAAATG 59.993 37.037 0.00 0.00 37.75 2.32
1291 1354 7.273381 GTCCGAAAATACTTGTCATTGAAATGG 59.727 37.037 3.31 0.00 37.03 3.16
1292 1355 7.175816 TCCGAAAATACTTGTCATTGAAATGGA 59.824 33.333 3.31 0.00 37.03 3.41
1293 1356 7.975616 CCGAAAATACTTGTCATTGAAATGGAT 59.024 33.333 3.31 0.00 37.03 3.41
1294 1357 8.800972 CGAAAATACTTGTCATTGAAATGGATG 58.199 33.333 3.31 0.00 37.03 3.51
1295 1358 9.643693 GAAAATACTTGTCATTGAAATGGATGT 57.356 29.630 3.31 2.77 37.03 3.06
1299 1362 9.857656 ATACTTGTCATTGAAATGGATGTATCT 57.142 29.630 3.31 0.00 37.03 1.98
1301 1364 9.334947 ACTTGTCATTGAAATGGATGTATCTAG 57.665 33.333 3.31 0.00 37.03 2.43
1302 1365 9.551734 CTTGTCATTGAAATGGATGTATCTAGA 57.448 33.333 0.00 0.00 37.03 2.43
1304 1367 9.498176 TGTCATTGAAATGGATGTATCTAGATG 57.502 33.333 15.79 0.00 37.03 2.90
1305 1368 9.499479 GTCATTGAAATGGATGTATCTAGATGT 57.501 33.333 15.79 1.25 37.03 3.06
1358 1421 6.851609 TCCATTTTGATGACAAGTAATTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1359 1422 6.035843 CCATTTTGATGACAAGTAATTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1360 1423 6.127758 CCATTTTGATGACAAGTAATTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1361 1424 7.416664 CCATTTTGATGACAAGTAATTCCGGAT 60.417 37.037 4.15 0.00 37.32 4.18
1362 1425 6.435430 TTTGATGACAAGTAATTCCGGATG 57.565 37.500 4.15 0.97 37.32 3.51
1363 1426 4.450976 TGATGACAAGTAATTCCGGATGG 58.549 43.478 4.15 0.00 0.00 3.51
1364 1427 4.163268 TGATGACAAGTAATTCCGGATGGA 59.837 41.667 4.15 0.00 44.61 3.41
1365 1428 8.543352 TTTGATGACAAGTAATTCCGGATGGAG 61.543 40.741 4.15 0.00 40.39 3.86
1396 1459 2.358582 TGATGTTGCTTTGTGTCCAGTG 59.641 45.455 0.00 0.00 0.00 3.66
1448 1511 4.008933 GAGCGCACCTCCACCACT 62.009 66.667 11.47 0.00 34.35 4.00
1475 1538 3.716195 CGTGGGAGGTCATGGGCA 61.716 66.667 0.00 0.00 0.00 5.36
1480 1543 1.380246 GGAGGTCATGGGCAATGCA 60.380 57.895 7.79 0.00 36.11 3.96
1487 1550 0.101759 CATGGGCAATGCACTACTGC 59.898 55.000 9.57 0.00 44.52 4.40
1507 1570 1.259507 CGGCGACTTGAAGACGAAAAA 59.740 47.619 20.08 0.00 35.52 1.94
1548 1611 3.141522 TTCGCTGTCGACAACCGGT 62.142 57.895 27.40 0.00 45.43 5.28
1559 1622 0.467290 ACAACCGGTTGCAGGTCAAT 60.467 50.000 40.39 20.36 44.03 2.57
1565 1628 0.179156 GGTTGCAGGTCAATGATGCG 60.179 55.000 4.62 0.00 42.92 4.73
1777 1844 2.908626 GCGCTGTTAAAATCTGGTTTCG 59.091 45.455 0.00 0.00 0.00 3.46
1810 2190 3.754850 AGCGTATTTTGGGTCAGTTTACC 59.245 43.478 0.00 0.00 38.94 2.85
1822 2202 3.057526 GTCAGTTTACCAACAGAATGGGC 60.058 47.826 0.00 0.00 45.18 5.36
1837 2217 1.000396 GGGCTTGGAAGGTGATGCT 60.000 57.895 0.00 0.00 0.00 3.79
1865 2245 3.732048 TTCTGACCTTGTAATTCCCCC 57.268 47.619 0.00 0.00 0.00 5.40
1866 2246 1.557832 TCTGACCTTGTAATTCCCCCG 59.442 52.381 0.00 0.00 0.00 5.73
1888 2269 6.586082 CCCGAACAATTTGGTAATGAGAAAAG 59.414 38.462 0.78 0.00 31.82 2.27
1889 2270 7.367285 CCGAACAATTTGGTAATGAGAAAAGA 58.633 34.615 0.78 0.00 0.00 2.52
1953 2334 1.480137 CTGTTGGGTTTTGTCTGGCAA 59.520 47.619 0.00 0.00 34.87 4.52
1979 2360 3.119602 GGAAACCCCTTCGCTTTAATCAC 60.120 47.826 0.00 0.00 34.56 3.06
2021 2402 1.144708 TGGATGGAGTCAACTTTGGCA 59.855 47.619 0.00 0.00 34.61 4.92
2034 2415 7.014615 AGTCAACTTTGGCATCTTTCTAACAAT 59.985 33.333 0.00 0.00 34.61 2.71
2067 2448 7.510549 TTTCCTGAGTAGAAGTTCCATTTTG 57.489 36.000 0.00 0.00 0.00 2.44
2083 2464 7.789273 TCCATTTTGTTAAGTGAAGTCGTTA 57.211 32.000 0.00 0.00 0.00 3.18
2103 2484 5.233689 CGTTAACTCATCCCGGAATAAAGAC 59.766 44.000 0.73 0.00 0.00 3.01
2106 2487 4.770795 ACTCATCCCGGAATAAAGACAAG 58.229 43.478 0.73 0.00 0.00 3.16
2129 2510 7.613551 AGAAGGAACTACTTTGACTAAAGGA 57.386 36.000 4.96 0.00 42.88 3.36
2130 2511 8.030913 AGAAGGAACTACTTTGACTAAAGGAA 57.969 34.615 4.96 0.00 42.88 3.36
2160 2541 2.677914 AGGCTTACTTTGGCTTTTGGT 58.322 42.857 0.00 0.00 36.97 3.67
2161 2542 3.038280 AGGCTTACTTTGGCTTTTGGTT 58.962 40.909 0.00 0.00 36.97 3.67
2162 2543 3.454447 AGGCTTACTTTGGCTTTTGGTTT 59.546 39.130 0.00 0.00 36.97 3.27
2163 2544 3.559655 GGCTTACTTTGGCTTTTGGTTTG 59.440 43.478 0.00 0.00 0.00 2.93
2164 2545 3.559655 GCTTACTTTGGCTTTTGGTTTGG 59.440 43.478 0.00 0.00 0.00 3.28
2278 2659 6.961359 TTTCATTATTGTAGACGACAGGTG 57.039 37.500 0.00 0.00 39.88 4.00
2300 2681 1.207329 AGATGAACCTAGGCACCGAAC 59.793 52.381 9.30 0.00 0.00 3.95
2347 2730 0.680618 CAGGCTCATCTGCTCCCTAG 59.319 60.000 0.00 0.00 0.00 3.02
2351 2734 2.903135 GGCTCATCTGCTCCCTAGTTAT 59.097 50.000 0.00 0.00 0.00 1.89
2358 2741 6.156949 TCATCTGCTCCCTAGTTATTGAACTT 59.843 38.462 0.00 0.00 43.70 2.66
2422 2810 4.067896 CCAAAGAAGCTCAAGTCTGCTAA 58.932 43.478 0.00 0.00 38.75 3.09
2587 2986 0.324943 TTGGAAGCTCCTAGCACACC 59.675 55.000 1.22 2.50 45.56 4.16
2607 6866 4.396166 CACCCGAGCATCTTTAGTGAAAAT 59.604 41.667 0.00 0.00 0.00 1.82
2613 6872 9.226345 CCGAGCATCTTTAGTGAAAATAATTTC 57.774 33.333 0.00 0.00 44.27 2.17
2650 6909 9.768215 TTCTATTTTCTGGAATTTACCCTTCAT 57.232 29.630 0.00 0.00 0.00 2.57
2680 6939 1.101331 GATGAGCCTGGGCAAGAAAG 58.899 55.000 14.39 0.00 44.88 2.62
2697 6956 1.911057 AAGGGCAGGTTAGTTTGAGC 58.089 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 24 3.260740 CCAAAACTGAAACAGCAGCAAA 58.739 40.909 0.00 0.00 39.51 3.68
42 45 4.664150 ACCAAGAGAGAGCATAACTAGC 57.336 45.455 0.00 0.00 0.00 3.42
141 167 5.997746 TGAACATTTCTTAAGAGAGGGTGTG 59.002 40.000 11.75 2.99 32.44 3.82
183 213 5.487488 ACAGGGTTCAGTCTGTAATGGAATA 59.513 40.000 0.00 0.00 41.81 1.75
242 272 5.838531 TCCACACCGTTTTGAACTTATTT 57.161 34.783 0.00 0.00 0.00 1.40
256 286 3.005050 TGTGTTACTACTCTTCCACACCG 59.995 47.826 0.00 0.00 34.81 4.94
258 288 5.989777 ACAATGTGTTACTACTCTTCCACAC 59.010 40.000 0.00 0.00 35.84 3.82
361 392 1.617850 TGGAAAATCACATGGCACCAC 59.382 47.619 0.00 0.00 0.00 4.16
362 393 2.006805 TGGAAAATCACATGGCACCA 57.993 45.000 0.00 0.00 0.00 4.17
410 441 9.153721 TGGACAAATGCATTTAAATGATTTCTC 57.846 29.630 28.33 22.45 38.70 2.87
417 448 8.016801 GGTTTCTTGGACAAATGCATTTAAATG 58.983 33.333 23.69 21.54 39.40 2.32
421 452 6.166984 TGGTTTCTTGGACAAATGCATTTA 57.833 33.333 23.69 6.31 0.00 1.40
427 458 3.328505 GGCATGGTTTCTTGGACAAATG 58.671 45.455 0.00 0.00 0.00 2.32
442 473 2.109517 ATCCTAGAGCAGCGGCATGG 62.110 60.000 12.44 7.30 44.61 3.66
444 475 1.370437 CATCCTAGAGCAGCGGCAT 59.630 57.895 12.44 1.29 44.61 4.40
511 543 7.764443 GCCTGGGACTAAATTTAGGAAATTTTC 59.236 37.037 25.25 13.53 46.01 2.29
512 544 7.457852 AGCCTGGGACTAAATTTAGGAAATTTT 59.542 33.333 25.25 6.13 46.01 1.82
606 645 7.707624 AATAAGACCTGAAATTGCTCATCAA 57.292 32.000 0.00 0.00 39.32 2.57
616 655 6.206634 TGAGAACGCAAAATAAGACCTGAAAT 59.793 34.615 0.00 0.00 0.00 2.17
623 662 8.408743 AGTACTATGAGAACGCAAAATAAGAC 57.591 34.615 0.00 0.00 0.00 3.01
631 670 4.927425 GGTGAAAGTACTATGAGAACGCAA 59.073 41.667 0.00 0.00 0.00 4.85
744 783 2.787473 CTTGTACATCTGCCAAGGGA 57.213 50.000 0.00 0.00 33.57 4.20
831 870 7.285172 TGTCCTCATTTGAGTCATTTCAGAAAA 59.715 33.333 0.00 0.00 40.48 2.29
863 902 1.205064 CGAGCGTGGCAGTGAAAAG 59.795 57.895 0.00 0.00 0.00 2.27
872 911 3.782244 CTTGACAGCGAGCGTGGC 61.782 66.667 0.00 0.00 0.00 5.01
873 912 1.416813 GATCTTGACAGCGAGCGTGG 61.417 60.000 0.00 0.00 0.00 4.94
876 915 1.060266 CTTTGATCTTGACAGCGAGCG 59.940 52.381 0.00 0.00 0.00 5.03
881 920 5.401674 CAGAAAAAGCTTTGATCTTGACAGC 59.598 40.000 19.77 0.00 0.00 4.40
907 946 9.582431 TCTAAAAACTTCCTATGAATCTGTACG 57.418 33.333 0.00 0.00 0.00 3.67
931 970 2.158623 TGCAGGTTTTGTGACTCCATCT 60.159 45.455 0.00 0.00 0.00 2.90
932 971 2.229792 TGCAGGTTTTGTGACTCCATC 58.770 47.619 0.00 0.00 0.00 3.51
933 972 2.363306 TGCAGGTTTTGTGACTCCAT 57.637 45.000 0.00 0.00 0.00 3.41
934 973 1.955778 CATGCAGGTTTTGTGACTCCA 59.044 47.619 0.00 0.00 0.00 3.86
935 974 1.270550 CCATGCAGGTTTTGTGACTCC 59.729 52.381 0.00 0.00 0.00 3.85
936 975 2.227388 CTCCATGCAGGTTTTGTGACTC 59.773 50.000 0.00 0.00 39.02 3.36
937 976 2.233271 CTCCATGCAGGTTTTGTGACT 58.767 47.619 0.00 0.00 39.02 3.41
947 1009 3.758023 TGTTAATGTCAACTCCATGCAGG 59.242 43.478 0.00 0.00 39.47 4.85
1033 1095 1.846712 TTGATGGGGTGTGCATCCGA 61.847 55.000 0.00 0.00 30.36 4.55
1088 1150 1.406898 CTTCACGAGCATCTGGAGCTA 59.593 52.381 0.00 0.00 43.58 3.32
1101 1163 2.288825 GGTGGTCTCACAATCTTCACGA 60.289 50.000 0.00 0.00 45.32 4.35
1102 1164 2.069273 GGTGGTCTCACAATCTTCACG 58.931 52.381 0.00 0.00 45.32 4.35
1104 1166 1.351017 GGGGTGGTCTCACAATCTTCA 59.649 52.381 0.00 0.00 45.32 3.02
1142 1204 3.368843 CGACAGGATGATGGTGAAGAAGT 60.369 47.826 0.00 0.00 39.69 3.01
1168 1230 2.550830 AACGGCTTCTGAACATGAGT 57.449 45.000 0.00 0.00 0.00 3.41
1217 1279 8.391106 GTCATTTCTGCAATACTAAGTACTTGG 58.609 37.037 18.56 17.57 0.00 3.61
1221 1283 6.018994 CGGGTCATTTCTGCAATACTAAGTAC 60.019 42.308 0.00 0.00 0.00 2.73
1226 1288 4.481368 ACGGGTCATTTCTGCAATACTA 57.519 40.909 0.00 0.00 0.00 1.82
1249 1312 1.809651 CGGACGGAGGGAGTAGTAGTC 60.810 61.905 0.00 0.00 0.00 2.59
1255 1318 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1256 1319 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1257 1320 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1258 1321 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1259 1322 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1260 1323 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1261 1324 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1262 1325 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1263 1326 4.390603 TCAATGACAAGTATTTTCGGACGG 59.609 41.667 0.00 0.00 0.00 4.79
1264 1327 5.524511 TCAATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1265 1328 7.273381 CCATTTCAATGACAAGTATTTTCGGAC 59.727 37.037 0.81 0.00 38.70 4.79
1266 1329 7.175816 TCCATTTCAATGACAAGTATTTTCGGA 59.824 33.333 0.81 0.00 38.70 4.55
1267 1330 7.312154 TCCATTTCAATGACAAGTATTTTCGG 58.688 34.615 0.81 0.00 38.70 4.30
1268 1331 8.800972 CATCCATTTCAATGACAAGTATTTTCG 58.199 33.333 0.81 0.00 38.70 3.46
1269 1332 9.643693 ACATCCATTTCAATGACAAGTATTTTC 57.356 29.630 0.81 0.00 38.70 2.29
1273 1336 9.857656 AGATACATCCATTTCAATGACAAGTAT 57.142 29.630 0.81 4.50 38.70 2.12
1275 1338 9.334947 CTAGATACATCCATTTCAATGACAAGT 57.665 33.333 0.81 0.00 38.70 3.16
1276 1339 9.551734 TCTAGATACATCCATTTCAATGACAAG 57.448 33.333 0.81 0.00 38.70 3.16
1278 1341 9.498176 CATCTAGATACATCCATTTCAATGACA 57.502 33.333 4.54 0.00 38.70 3.58
1279 1342 9.499479 ACATCTAGATACATCCATTTCAATGAC 57.501 33.333 4.54 0.00 38.70 3.06
1332 1395 8.620416 CGGAATTACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1333 1396 7.416664 CCGGAATTACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1334 1397 6.127758 CCGGAATTACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1335 1398 6.035843 CCGGAATTACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1336 1399 6.851609 TCCGGAATTACTTGTCATCAAAATG 58.148 36.000 0.00 0.00 32.87 2.32
1337 1400 7.416664 CCATCCGGAATTACTTGTCATCAAAAT 60.417 37.037 9.01 0.00 32.87 1.82
1338 1401 6.127758 CCATCCGGAATTACTTGTCATCAAAA 60.128 38.462 9.01 0.00 32.87 2.44
1339 1402 5.356751 CCATCCGGAATTACTTGTCATCAAA 59.643 40.000 9.01 0.00 32.87 2.69
1340 1403 4.881273 CCATCCGGAATTACTTGTCATCAA 59.119 41.667 9.01 0.00 0.00 2.57
1341 1404 4.163268 TCCATCCGGAATTACTTGTCATCA 59.837 41.667 9.01 0.00 38.83 3.07
1342 1405 4.703897 TCCATCCGGAATTACTTGTCATC 58.296 43.478 9.01 0.00 38.83 2.92
1343 1406 4.444876 CCTCCATCCGGAATTACTTGTCAT 60.445 45.833 9.01 0.00 42.21 3.06
1344 1407 3.118408 CCTCCATCCGGAATTACTTGTCA 60.118 47.826 9.01 0.00 42.21 3.58
1345 1408 3.467803 CCTCCATCCGGAATTACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
1346 1409 2.172717 CCCTCCATCCGGAATTACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
1347 1410 2.438021 TCCCTCCATCCGGAATTACTTG 59.562 50.000 9.01 0.00 42.21 3.16
1348 1411 2.706190 CTCCCTCCATCCGGAATTACTT 59.294 50.000 9.01 0.00 42.21 2.24
1349 1412 2.330216 CTCCCTCCATCCGGAATTACT 58.670 52.381 9.01 0.00 42.21 2.24
1350 1413 2.047830 ACTCCCTCCATCCGGAATTAC 58.952 52.381 9.01 0.00 42.21 1.89
1351 1414 2.489528 ACTCCCTCCATCCGGAATTA 57.510 50.000 9.01 0.00 42.21 1.40
1352 1415 2.489528 TACTCCCTCCATCCGGAATT 57.510 50.000 9.01 0.00 42.21 2.17
1353 1416 2.723530 ATACTCCCTCCATCCGGAAT 57.276 50.000 9.01 0.00 42.21 3.01
1354 1417 2.489528 AATACTCCCTCCATCCGGAA 57.510 50.000 9.01 0.00 42.21 4.30
1355 1418 3.076937 TCATAATACTCCCTCCATCCGGA 59.923 47.826 6.61 6.61 39.79 5.14
1356 1419 3.441101 TCATAATACTCCCTCCATCCGG 58.559 50.000 0.00 0.00 0.00 5.14
1357 1420 4.467795 ACATCATAATACTCCCTCCATCCG 59.532 45.833 0.00 0.00 0.00 4.18
1358 1421 6.176183 CAACATCATAATACTCCCTCCATCC 58.824 44.000 0.00 0.00 0.00 3.51
1359 1422 5.645497 GCAACATCATAATACTCCCTCCATC 59.355 44.000 0.00 0.00 0.00 3.51
1360 1423 5.311649 AGCAACATCATAATACTCCCTCCAT 59.688 40.000 0.00 0.00 0.00 3.41
1361 1424 4.660303 AGCAACATCATAATACTCCCTCCA 59.340 41.667 0.00 0.00 0.00 3.86
1362 1425 5.234466 AGCAACATCATAATACTCCCTCC 57.766 43.478 0.00 0.00 0.00 4.30
1363 1426 6.543831 ACAAAGCAACATCATAATACTCCCTC 59.456 38.462 0.00 0.00 0.00 4.30
1364 1427 6.319658 CACAAAGCAACATCATAATACTCCCT 59.680 38.462 0.00 0.00 0.00 4.20
1365 1428 6.095440 ACACAAAGCAACATCATAATACTCCC 59.905 38.462 0.00 0.00 0.00 4.30
1366 1429 7.088589 ACACAAAGCAACATCATAATACTCC 57.911 36.000 0.00 0.00 0.00 3.85
1367 1430 7.148255 TGGACACAAAGCAACATCATAATACTC 60.148 37.037 0.00 0.00 0.00 2.59
1368 1431 6.658816 TGGACACAAAGCAACATCATAATACT 59.341 34.615 0.00 0.00 0.00 2.12
1369 1432 6.851609 TGGACACAAAGCAACATCATAATAC 58.148 36.000 0.00 0.00 0.00 1.89
1396 1459 1.377202 TGGAAGCGACCTGGAATGC 60.377 57.895 0.00 0.60 0.00 3.56
1439 1502 0.177604 GGCAGATGAGAGTGGTGGAG 59.822 60.000 0.00 0.00 0.00 3.86
1443 1506 1.593787 CACGGCAGATGAGAGTGGT 59.406 57.895 0.00 0.00 0.00 4.16
1448 1511 2.060383 CCTCCCACGGCAGATGAGA 61.060 63.158 0.00 0.00 0.00 3.27
1480 1543 0.388649 CTTCAAGTCGCCGCAGTAGT 60.389 55.000 0.00 0.00 0.00 2.73
1487 1550 0.856641 TTTTCGTCTTCAAGTCGCCG 59.143 50.000 0.00 0.00 0.00 6.46
1490 1553 3.535860 CAGCTTTTTCGTCTTCAAGTCG 58.464 45.455 0.00 0.00 0.00 4.18
1507 1570 1.478837 CCATCCAATCTGCATCCAGCT 60.479 52.381 0.00 0.00 45.94 4.24
1548 1611 0.522626 CACGCATCATTGACCTGCAA 59.477 50.000 11.64 0.00 41.53 4.08
1559 1622 1.008875 GCTCGAAGACACACGCATCA 61.009 55.000 0.00 0.00 0.00 3.07
1565 1628 1.523095 GTCACAAGCTCGAAGACACAC 59.477 52.381 0.00 0.00 0.00 3.82
1810 2190 1.547372 CCTTCCAAGCCCATTCTGTTG 59.453 52.381 0.00 0.00 0.00 3.33
1822 2202 2.029649 CCAACAAGCATCACCTTCCAAG 60.030 50.000 0.00 0.00 0.00 3.61
1837 2217 6.208599 GGAATTACAAGGTCAGAATCCAACAA 59.791 38.462 0.00 0.00 0.00 2.83
1865 2245 8.795786 TTCTTTTCTCATTACCAAATTGTTCG 57.204 30.769 0.00 0.00 0.00 3.95
1931 2312 2.303175 GCCAGACAAAACCCAACAGTA 58.697 47.619 0.00 0.00 0.00 2.74
1973 2354 9.223099 CCAGCAATATCATACATTCAGTGATTA 57.777 33.333 0.00 0.00 34.62 1.75
1979 2360 6.882678 TCCATCCAGCAATATCATACATTCAG 59.117 38.462 0.00 0.00 0.00 3.02
2067 2448 6.090493 GGGATGAGTTAACGACTTCACTTAAC 59.910 42.308 16.64 0.00 39.19 2.01
2083 2464 4.837093 TGTCTTTATTCCGGGATGAGTT 57.163 40.909 5.13 0.00 0.00 3.01
2103 2484 7.931948 TCCTTTAGTCAAAGTAGTTCCTTCTTG 59.068 37.037 0.00 0.00 39.70 3.02
2106 2487 8.722394 CATTCCTTTAGTCAAAGTAGTTCCTTC 58.278 37.037 0.00 0.00 39.70 3.46
2129 2510 5.510690 GCCAAAGTAAGCCTAACCAAACATT 60.511 40.000 0.00 0.00 0.00 2.71
2130 2511 4.021456 GCCAAAGTAAGCCTAACCAAACAT 60.021 41.667 0.00 0.00 0.00 2.71
2259 2640 7.284716 TCATCTACACCTGTCGTCTACAATAAT 59.715 37.037 0.00 0.00 37.74 1.28
2263 2644 4.329392 TCATCTACACCTGTCGTCTACAA 58.671 43.478 0.00 0.00 37.74 2.41
2267 2648 2.492484 GGTTCATCTACACCTGTCGTCT 59.508 50.000 0.00 0.00 0.00 4.18
2274 2655 2.766828 GTGCCTAGGTTCATCTACACCT 59.233 50.000 11.31 0.00 45.85 4.00
2278 2659 2.029623 TCGGTGCCTAGGTTCATCTAC 58.970 52.381 11.31 0.00 0.00 2.59
2300 2681 0.108615 AGATGTTTCTCAGGACGGCG 60.109 55.000 4.80 4.80 0.00 6.46
2309 2690 4.133078 CCTGGGCTCATTAGATGTTTCTC 58.867 47.826 0.00 0.00 33.17 2.87
2396 2784 1.268079 GACTTGAGCTTCTTTGGTGCC 59.732 52.381 0.00 0.00 0.00 5.01
2402 2790 5.220710 TCTTAGCAGACTTGAGCTTCTTT 57.779 39.130 0.00 0.00 42.05 2.52
2422 2810 5.815581 TCACCATGTAATTTTGTAGGCTCT 58.184 37.500 0.00 0.00 0.00 4.09
2455 2851 2.290323 TGTTTTTGGCTAGAGCTCCTCC 60.290 50.000 10.93 9.75 41.70 4.30
2531 2930 4.642466 TGATATTCGAGGAGCTCTAGGA 57.358 45.455 14.64 5.39 0.00 2.94
2532 2931 4.704540 ACATGATATTCGAGGAGCTCTAGG 59.295 45.833 14.64 2.89 0.00 3.02
2587 2986 9.226345 GAAATTATTTTCACTAAAGATGCTCGG 57.774 33.333 5.43 0.00 40.82 4.63
2644 6903 0.469917 ATCTACACCCGCCATGAAGG 59.530 55.000 0.00 0.00 41.84 3.46
2645 6904 1.138859 TCATCTACACCCGCCATGAAG 59.861 52.381 0.00 0.00 0.00 3.02
2650 6909 2.731571 GGCTCATCTACACCCGCCA 61.732 63.158 0.00 0.00 37.48 5.69


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

AutoCloner maintained by Alex Coulton.