Multiple sequence alignment - TraesCS5A01G384100

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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 TraesCS5A01G384100 chr5A 100.000 2884 0 0 1 2884 581925267 581928150 0.000000e+00 5326.0
1 TraesCS5A01G384100 chr5A 83.573 487 47 7 2368 2834 572368095 572367622 2.660000e-115 425.0
2 TraesCS5A01G384100 chr5A 75.714 420 80 20 1437 1845 619683190 619682782 1.050000e-44 191.0
3 TraesCS5A01G384100 chr5A 92.188 64 2 3 2037 2098 577717560 577717622 1.420000e-13 87.9
4 TraesCS5A01G384100 chr5D 91.950 2062 82 40 1 2039 461911569 461913569 0.000000e+00 2811.0
5 TraesCS5A01G384100 chr5D 75.952 420 79 20 1437 1845 495619053 495618645 2.270000e-46 196.0
6 TraesCS5A01G384100 chr5B 92.993 1527 70 23 516 2039 567873453 567874945 0.000000e+00 2193.0
7 TraesCS5A01G384100 chr5B 96.005 851 31 3 2037 2884 109412392 109413242 0.000000e+00 1380.0
8 TraesCS5A01G384100 chr5B 83.778 487 46 9 2368 2834 483525156 483524683 5.710000e-117 431.0
9 TraesCS5A01G384100 chr5B 76.190 420 78 20 1437 1845 612674208 612673800 4.870000e-48 202.0
10 TraesCS5A01G384100 chr2D 85.039 381 43 10 2468 2834 366141205 366141585 2.710000e-100 375.0
11 TraesCS5A01G384100 chr3B 79.228 544 70 21 2368 2884 41084822 41085349 3.560000e-89 339.0
12 TraesCS5A01G384100 chr6B 83.038 395 41 11 2289 2678 595122733 595123106 4.600000e-88 335.0
13 TraesCS5A01G384100 chr6B 78.860 544 72 21 2368 2884 720914116 720914643 7.710000e-86 327.0
14 TraesCS5A01G384100 chr6B 95.349 86 2 2 2037 2121 222856031 222856115 5.010000e-28 135.0
15 TraesCS5A01G384100 chr6B 93.548 62 4 0 2037 2098 720913654 720913715 3.060000e-15 93.5
16 TraesCS5A01G384100 chr1A 78.860 544 72 21 2368 2884 10647541 10647014 7.710000e-86 327.0
17 TraesCS5A01G384100 chr1A 85.496 131 15 4 2040 2168 335045168 335045040 1.800000e-27 134.0
18 TraesCS5A01G384100 chr7B 84.962 133 13 7 2032 2161 32000055 31999927 8.390000e-26 128.0
19 TraesCS5A01G384100 chr2A 84.559 136 14 7 2029 2161 337771968 337772099 8.390000e-26 128.0
20 TraesCS5A01G384100 chr2A 84.559 136 14 7 2029 2161 337888976 337889107 8.390000e-26 128.0
21 TraesCS5A01G384100 chr7A 88.710 62 6 1 2038 2098 611288116 611288177 1.110000e-09 75.0


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 TraesCS5A01G384100 chr5A 581925267 581928150 2883 False 5326.00 5326 100.000 1 2884 1 chr5A.!!$F2 2883
1 TraesCS5A01G384100 chr5D 461911569 461913569 2000 False 2811.00 2811 91.950 1 2039 1 chr5D.!!$F1 2038
2 TraesCS5A01G384100 chr5B 567873453 567874945 1492 False 2193.00 2193 92.993 516 2039 1 chr5B.!!$F2 1523
3 TraesCS5A01G384100 chr5B 109412392 109413242 850 False 1380.00 1380 96.005 2037 2884 1 chr5B.!!$F1 847
4 TraesCS5A01G384100 chr3B 41084822 41085349 527 False 339.00 339 79.228 2368 2884 1 chr3B.!!$F1 516
5 TraesCS5A01G384100 chr6B 720913654 720914643 989 False 210.25 327 86.204 2037 2884 2 chr6B.!!$F3 847
6 TraesCS5A01G384100 chr1A 10647014 10647541 527 True 327.00 327 78.860 2368 2884 1 chr1A.!!$R1 516

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
950 970 1.010935 CGAGCCATCCCATTCGATCG 61.011 60.0 9.36 9.36 35.19 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2435 0.036448 AGACACGGGAGTCTTCGAGA 59.964 55.0 12.01 0.0 46.26 4.04 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
47 48 6.148480 AGCATGCAAAAACTGTTGTAAAAACA 59.852 30.769 21.98 0.00 0.00 2.83
65 66 7.603963 AAAAACAAACGGACTTGCTAAAAAT 57.396 28.000 0.00 0.00 0.00 1.82
245 247 8.211629 AGATTAACATAGAAGATTGTACCCCAC 58.788 37.037 0.00 0.00 0.00 4.61
259 261 4.283978 TGTACCCCACACGATAAGAGAAAA 59.716 41.667 0.00 0.00 30.04 2.29
302 304 9.045223 AGTAAAGAGAAATTGTTTTCCATTTGC 57.955 29.630 7.93 7.06 41.86 3.68
303 305 7.862512 AAAGAGAAATTGTTTTCCATTTGCA 57.137 28.000 0.00 0.00 41.86 4.08
305 307 8.454570 AAGAGAAATTGTTTTCCATTTGCAAT 57.545 26.923 0.00 0.00 41.86 3.56
307 309 9.729281 AGAGAAATTGTTTTCCATTTGCAATAT 57.271 25.926 0.00 0.00 41.86 1.28
560 577 2.814280 AATAGGTCGCCCGATACTTG 57.186 50.000 0.00 0.00 35.12 3.16
690 708 2.530701 CCACCAGAGACCAGACTTACT 58.469 52.381 0.00 0.00 0.00 2.24
691 709 3.698289 CCACCAGAGACCAGACTTACTA 58.302 50.000 0.00 0.00 0.00 1.82
692 710 3.444388 CCACCAGAGACCAGACTTACTAC 59.556 52.174 0.00 0.00 0.00 2.73
805 824 4.292178 CCTCTCTCGCGCCATCCC 62.292 72.222 0.00 0.00 0.00 3.85
897 917 3.098555 CCGCACCGGCAAAGATAC 58.901 61.111 0.00 0.00 41.17 2.24
950 970 1.010935 CGAGCCATCCCATTCGATCG 61.011 60.000 9.36 9.36 35.19 3.69
1289 1321 1.293757 GTACGTTACGTTTCGCGCG 60.294 57.895 26.76 26.76 46.11 6.86
1292 1324 2.128054 GTTACGTTTCGCGCGCAA 60.128 55.556 32.61 19.90 46.11 4.85
1293 1325 1.508332 GTTACGTTTCGCGCGCAAT 60.508 52.632 32.61 9.47 46.11 3.56
1298 1330 1.578618 GTTTCGCGCGCAATCTCAG 60.579 57.895 32.61 13.04 0.00 3.35
1307 1339 2.349249 CGCGCAATCTCAGATCAATTCC 60.349 50.000 8.75 0.00 0.00 3.01
1308 1340 2.031333 GCGCAATCTCAGATCAATTCCC 60.031 50.000 0.30 0.00 0.00 3.97
1313 1345 5.368145 CAATCTCAGATCAATTCCCCGTTA 58.632 41.667 0.00 0.00 0.00 3.18
1314 1346 4.402056 TCTCAGATCAATTCCCCGTTAC 57.598 45.455 0.00 0.00 0.00 2.50
1315 1347 3.134081 TCTCAGATCAATTCCCCGTTACC 59.866 47.826 0.00 0.00 0.00 2.85
1317 1349 3.458118 TCAGATCAATTCCCCGTTACCAT 59.542 43.478 0.00 0.00 0.00 3.55
1318 1350 4.080015 TCAGATCAATTCCCCGTTACCATT 60.080 41.667 0.00 0.00 0.00 3.16
1319 1351 4.036734 CAGATCAATTCCCCGTTACCATTG 59.963 45.833 0.00 0.00 0.00 2.82
1320 1352 2.096248 TCAATTCCCCGTTACCATTGC 58.904 47.619 0.00 0.00 0.00 3.56
1321 1353 2.099405 CAATTCCCCGTTACCATTGCT 58.901 47.619 0.00 0.00 0.00 3.91
1322 1354 2.495669 CAATTCCCCGTTACCATTGCTT 59.504 45.455 0.00 0.00 0.00 3.91
1323 1355 1.540267 TTCCCCGTTACCATTGCTTG 58.460 50.000 0.00 0.00 0.00 4.01
1324 1356 0.402504 TCCCCGTTACCATTGCTTGT 59.597 50.000 0.00 0.00 0.00 3.16
1325 1357 0.808755 CCCCGTTACCATTGCTTGTC 59.191 55.000 0.00 0.00 0.00 3.18
1326 1358 1.529226 CCCGTTACCATTGCTTGTCA 58.471 50.000 0.00 0.00 0.00 3.58
1327 1359 1.468520 CCCGTTACCATTGCTTGTCAG 59.531 52.381 0.00 0.00 0.00 3.51
1328 1360 2.422597 CCGTTACCATTGCTTGTCAGA 58.577 47.619 0.00 0.00 0.00 3.27
1329 1361 2.159627 CCGTTACCATTGCTTGTCAGAC 59.840 50.000 0.00 0.00 0.00 3.51
1330 1362 2.805671 CGTTACCATTGCTTGTCAGACA 59.194 45.455 0.00 0.00 0.00 3.41
1331 1363 3.436704 CGTTACCATTGCTTGTCAGACAT 59.563 43.478 3.45 0.00 0.00 3.06
1332 1364 4.669965 CGTTACCATTGCTTGTCAGACATG 60.670 45.833 3.45 8.12 0.00 3.21
1333 1365 3.144657 ACCATTGCTTGTCAGACATGA 57.855 42.857 18.43 0.00 0.00 3.07
1334 1366 3.693807 ACCATTGCTTGTCAGACATGAT 58.306 40.909 18.43 3.32 37.87 2.45
1335 1367 3.693085 ACCATTGCTTGTCAGACATGATC 59.307 43.478 18.43 4.35 37.87 2.92
1336 1368 3.242641 CCATTGCTTGTCAGACATGATCG 60.243 47.826 18.43 5.08 37.87 3.69
1337 1369 3.317603 TTGCTTGTCAGACATGATCGA 57.682 42.857 18.43 0.00 37.87 3.59
1338 1370 3.531934 TGCTTGTCAGACATGATCGAT 57.468 42.857 18.43 0.00 37.87 3.59
1339 1371 3.451526 TGCTTGTCAGACATGATCGATC 58.548 45.455 18.72 18.72 37.87 3.69
1340 1372 2.470628 GCTTGTCAGACATGATCGATCG 59.529 50.000 20.03 9.36 37.87 3.69
1341 1373 2.125461 TGTCAGACATGATCGATCGC 57.875 50.000 20.03 9.61 37.87 4.58
1342 1374 1.678101 TGTCAGACATGATCGATCGCT 59.322 47.619 20.03 11.60 37.87 4.93
1392 1424 3.036084 CTCACCGTGTCCGTGTGC 61.036 66.667 0.00 0.00 36.12 4.57
1400 1432 0.814010 GTGTCCGTGTGCTTGGAACT 60.814 55.000 0.00 0.00 35.67 3.01
1893 1925 1.699656 CGATTCCTGAAGTGCCTGCG 61.700 60.000 0.00 0.00 0.00 5.18
1930 1962 3.218974 CGTAGCCCCTCCTCCTAAA 57.781 57.895 0.00 0.00 0.00 1.85
1931 1963 1.041437 CGTAGCCCCTCCTCCTAAAG 58.959 60.000 0.00 0.00 0.00 1.85
1933 1965 2.040939 GTAGCCCCTCCTCCTAAAGTC 58.959 57.143 0.00 0.00 0.00 3.01
1936 1968 1.062352 GCCCCTCCTCCTAAAGTCCTA 60.062 57.143 0.00 0.00 0.00 2.94
1938 1970 2.680251 CCCTCCTCCTAAAGTCCTACC 58.320 57.143 0.00 0.00 0.00 3.18
1939 1971 2.680251 CCTCCTCCTAAAGTCCTACCC 58.320 57.143 0.00 0.00 0.00 3.69
1940 1972 2.247897 CCTCCTCCTAAAGTCCTACCCT 59.752 54.545 0.00 0.00 0.00 4.34
1941 1973 3.466344 CCTCCTCCTAAAGTCCTACCCTA 59.534 52.174 0.00 0.00 0.00 3.53
1942 1974 4.472496 CTCCTCCTAAAGTCCTACCCTAC 58.528 52.174 0.00 0.00 0.00 3.18
1943 1975 3.206185 TCCTCCTAAAGTCCTACCCTACC 59.794 52.174 0.00 0.00 0.00 3.18
1944 1976 3.574749 CTCCTAAAGTCCTACCCTACCC 58.425 54.545 0.00 0.00 0.00 3.69
1945 1977 2.248423 TCCTAAAGTCCTACCCTACCCC 59.752 54.545 0.00 0.00 0.00 4.95
1946 1978 2.249478 CCTAAAGTCCTACCCTACCCCT 59.751 54.545 0.00 0.00 0.00 4.79
1956 1988 1.368558 ACCCTACCCCTGTAATCCTGT 59.631 52.381 0.00 0.00 0.00 4.00
1987 2019 1.812571 ACATCACGAATGTGCTTTCCC 59.187 47.619 7.27 0.00 47.00 3.97
1989 2021 2.270352 TCACGAATGTGCTTTCCCTT 57.730 45.000 0.00 0.00 46.01 3.95
1990 2022 3.410631 TCACGAATGTGCTTTCCCTTA 57.589 42.857 0.00 0.00 46.01 2.69
1997 2029 2.513753 TGTGCTTTCCCTTATGTGTGG 58.486 47.619 0.00 0.00 0.00 4.17
2163 2251 2.909965 TTTGCCACGTTCTGCCCC 60.910 61.111 0.00 0.00 0.00 5.80
2164 2252 3.723097 TTTGCCACGTTCTGCCCCA 62.723 57.895 0.00 0.00 0.00 4.96
2165 2253 4.947147 TGCCACGTTCTGCCCCAC 62.947 66.667 0.00 0.00 0.00 4.61
2295 2400 2.189342 GATTGGCTTCGTTCTCTCTCG 58.811 52.381 0.00 0.00 0.00 4.04
2304 2409 3.886549 TCGTTCTCTCTCGTTTCAGTTC 58.113 45.455 0.00 0.00 0.00 3.01
2314 2419 0.868406 GTTTCAGTTCGCTCCACCTG 59.132 55.000 0.00 0.00 0.00 4.00
2330 2435 0.617249 CCTGTCCTCTTGGGCTCTCT 60.617 60.000 0.00 0.00 39.11 3.10
2491 2678 2.243774 ATCCCCGCTCCTTCTCTCCA 62.244 60.000 0.00 0.00 0.00 3.86
2540 2727 2.282462 CTGCCCTGTTGGTGTCCC 60.282 66.667 0.00 0.00 36.04 4.46
2546 2733 0.112218 CCTGTTGGTGTCCCATCCAA 59.888 55.000 0.00 0.00 41.49 3.53
2747 2934 0.464554 CGATGGCTTTCTCCCCCTTC 60.465 60.000 0.00 0.00 0.00 3.46
2750 2937 0.776080 TGGCTTTCTCCCCCTTCCTT 60.776 55.000 0.00 0.00 0.00 3.36
2786 2977 5.665360 TCTCCCAATTTTTCCTTTTCCTTGT 59.335 36.000 0.00 0.00 0.00 3.16
2796 2987 0.589223 TTTTCCTTGTAGCCGCAACG 59.411 50.000 0.00 0.00 0.00 4.10
2797 2988 0.533308 TTTCCTTGTAGCCGCAACGT 60.533 50.000 0.00 0.00 0.00 3.99
2821 3018 0.824109 CAGGGACACATTAGGAGCGA 59.176 55.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 5.656480 ACACAATTTTTAGCAAGTCCGTTT 58.344 33.333 0.00 0.00 0.00 3.60
162 164 2.827800 TGCGCAATTGATTTTTGGGA 57.172 40.000 8.16 0.00 38.81 4.37
171 173 4.495911 TGACAAAAGTATGCGCAATTGA 57.504 36.364 17.11 0.00 0.00 2.57
277 279 8.825745 TGCAAATGGAAAACAATTTCTCTTTAC 58.174 29.630 1.80 0.00 43.65 2.01
355 357 7.676004 TGTTCCATATATGATGTACCGTTGAT 58.324 34.615 14.54 0.00 0.00 2.57
356 358 7.056844 TGTTCCATATATGATGTACCGTTGA 57.943 36.000 14.54 0.00 0.00 3.18
374 376 1.306141 AGCGGGAGAGGATGTTCCA 60.306 57.895 0.00 0.00 39.61 3.53
386 388 4.373116 GCCTTGTCGACAGCGGGA 62.373 66.667 27.12 11.34 38.28 5.14
405 407 4.475135 GCCTCCACTTCCTCCGCC 62.475 72.222 0.00 0.00 0.00 6.13
491 508 9.950680 AACATTTCAGTTTCATAACAGTTACTG 57.049 29.630 11.21 11.21 36.70 2.74
514 531 3.194062 GCCTGCTTTGCAAAACTAAACA 58.806 40.909 13.84 4.28 38.41 2.83
520 537 2.749280 ATAGGCCTGCTTTGCAAAAC 57.251 45.000 17.99 9.61 38.41 2.43
551 568 2.678336 GCCTTCTGTTTCCAAGTATCGG 59.322 50.000 0.00 0.00 0.00 4.18
560 577 2.678336 CGATTACCTGCCTTCTGTTTCC 59.322 50.000 0.00 0.00 0.00 3.13
589 606 3.379057 CGGGGTTATCCGTATTTTGCTTT 59.621 43.478 0.00 0.00 44.60 3.51
692 710 0.179073 CGGTATGGCTGACCTTCTGG 60.179 60.000 6.79 0.00 36.63 3.86
751 770 3.546714 CTTCTCGGCGGTTGGGGTT 62.547 63.158 7.21 0.00 0.00 4.11
809 828 4.400251 AGAGGGGACAGGACGGGG 62.400 72.222 0.00 0.00 0.00 5.73
825 844 3.429684 GCGGAGAGTTTTAAGGAGAGGAG 60.430 52.174 0.00 0.00 0.00 3.69
895 915 0.876777 CACGTGTCGCCTTGGTTGTA 60.877 55.000 7.58 0.00 0.00 2.41
896 916 2.177580 CACGTGTCGCCTTGGTTGT 61.178 57.895 7.58 0.00 0.00 3.32
897 917 2.631428 CACGTGTCGCCTTGGTTG 59.369 61.111 7.58 0.00 0.00 3.77
950 970 4.814294 CCTCTACGGCGGTGCACC 62.814 72.222 26.78 26.78 0.00 5.01
1128 1148 2.632028 CTGGATGGAGAGGATGGTGTAG 59.368 54.545 0.00 0.00 0.00 2.74
1176 1196 2.426261 CGCACGAAGACGACGACA 60.426 61.111 0.00 0.00 41.77 4.35
1236 1256 6.185114 AGGATGATGAGGAAAATGTAGAGG 57.815 41.667 0.00 0.00 0.00 3.69
1245 1265 2.594536 AGGGGAGGATGATGAGGAAA 57.405 50.000 0.00 0.00 0.00 3.13
1281 1313 1.083806 ATCTGAGATTGCGCGCGAAA 61.084 50.000 37.18 32.54 0.00 3.46
1283 1315 1.946156 GATCTGAGATTGCGCGCGA 60.946 57.895 37.18 25.63 0.00 5.87
1289 1321 2.551459 CGGGGAATTGATCTGAGATTGC 59.449 50.000 0.00 0.00 0.00 3.56
1292 1324 4.202367 GGTAACGGGGAATTGATCTGAGAT 60.202 45.833 0.00 0.00 0.00 2.75
1293 1325 3.134081 GGTAACGGGGAATTGATCTGAGA 59.866 47.826 0.00 0.00 0.00 3.27
1298 1330 3.243401 GCAATGGTAACGGGGAATTGATC 60.243 47.826 0.00 0.00 42.51 2.92
1307 1339 1.468520 CTGACAAGCAATGGTAACGGG 59.531 52.381 0.00 0.00 42.51 5.28
1308 1340 2.159627 GTCTGACAAGCAATGGTAACGG 59.840 50.000 2.24 0.00 42.51 4.44
1313 1345 3.144657 TCATGTCTGACAAGCAATGGT 57.855 42.857 15.31 0.00 0.00 3.55
1314 1346 3.242641 CGATCATGTCTGACAAGCAATGG 60.243 47.826 15.31 4.10 33.22 3.16
1315 1347 3.619929 TCGATCATGTCTGACAAGCAATG 59.380 43.478 15.31 8.22 33.22 2.82
1317 1349 3.317603 TCGATCATGTCTGACAAGCAA 57.682 42.857 15.31 1.16 33.22 3.91
1318 1350 3.451526 GATCGATCATGTCTGACAAGCA 58.548 45.455 20.52 1.92 33.22 3.91
1319 1351 2.470628 CGATCGATCATGTCTGACAAGC 59.529 50.000 24.40 0.90 33.22 4.01
1320 1352 2.470628 GCGATCGATCATGTCTGACAAG 59.529 50.000 24.40 10.77 33.22 3.16
1321 1353 2.099756 AGCGATCGATCATGTCTGACAA 59.900 45.455 24.40 0.00 33.22 3.18
1322 1354 1.678101 AGCGATCGATCATGTCTGACA 59.322 47.619 24.40 13.60 33.22 3.58
1323 1355 2.414058 AGCGATCGATCATGTCTGAC 57.586 50.000 24.40 0.00 33.22 3.51
1324 1356 3.142174 AGTAGCGATCGATCATGTCTGA 58.858 45.455 24.40 0.00 35.41 3.27
1325 1357 3.188254 AGAGTAGCGATCGATCATGTCTG 59.812 47.826 24.40 8.61 0.00 3.51
1326 1358 3.188254 CAGAGTAGCGATCGATCATGTCT 59.812 47.826 24.40 15.88 0.00 3.41
1327 1359 3.487536 CAGAGTAGCGATCGATCATGTC 58.512 50.000 24.40 12.75 0.00 3.06
1328 1360 2.351253 GCAGAGTAGCGATCGATCATGT 60.351 50.000 24.40 10.75 0.00 3.21
1329 1361 2.095314 AGCAGAGTAGCGATCGATCATG 60.095 50.000 24.40 10.70 40.15 3.07
1330 1362 2.158559 AGCAGAGTAGCGATCGATCAT 58.841 47.619 24.40 14.68 40.15 2.45
1331 1363 1.533299 GAGCAGAGTAGCGATCGATCA 59.467 52.381 24.40 2.91 40.15 2.92
1332 1364 1.804151 AGAGCAGAGTAGCGATCGATC 59.196 52.381 21.57 15.68 40.15 3.69
1333 1365 1.535028 CAGAGCAGAGTAGCGATCGAT 59.465 52.381 21.57 16.78 40.15 3.59
1334 1366 0.940833 CAGAGCAGAGTAGCGATCGA 59.059 55.000 21.57 0.00 40.15 3.59
1335 1367 0.660488 ACAGAGCAGAGTAGCGATCG 59.340 55.000 11.69 11.69 40.15 3.69
1336 1368 2.861462 AACAGAGCAGAGTAGCGATC 57.139 50.000 0.00 0.00 40.15 3.69
1337 1369 3.194542 AGAAAACAGAGCAGAGTAGCGAT 59.805 43.478 0.00 0.00 40.15 4.58
1338 1370 2.558795 AGAAAACAGAGCAGAGTAGCGA 59.441 45.455 0.00 0.00 40.15 4.93
1339 1371 2.953020 AGAAAACAGAGCAGAGTAGCG 58.047 47.619 0.00 0.00 40.15 4.26
1340 1372 3.366422 CGAAGAAAACAGAGCAGAGTAGC 59.634 47.826 0.00 0.00 0.00 3.58
1341 1373 4.799678 TCGAAGAAAACAGAGCAGAGTAG 58.200 43.478 0.00 0.00 0.00 2.57
1342 1374 4.848562 TCGAAGAAAACAGAGCAGAGTA 57.151 40.909 0.00 0.00 0.00 2.59
1392 1424 0.309922 CACAGCACTGCAGTTCCAAG 59.690 55.000 18.94 6.70 0.00 3.61
1400 1432 1.070275 CAGAGGACACAGCACTGCA 59.930 57.895 3.30 0.00 0.00 4.41
1499 1531 2.281484 TTGGTGAAGGCGCAGGTC 60.281 61.111 10.83 3.15 0.00 3.85
1598 1630 4.717629 CTGAAGTCGTGCCCGCGA 62.718 66.667 8.23 0.00 38.68 5.87
1893 1925 0.319125 GCTACGCTATGGCAGGAGAC 60.319 60.000 8.83 0.00 38.60 3.36
1903 1935 1.228490 AGGGGCTACGCTACGCTAT 60.228 57.895 0.00 0.00 38.23 2.97
1929 1961 1.099456 ACAGGGGTAGGGTAGGACTT 58.901 55.000 0.00 0.00 0.00 3.01
1930 1962 2.006213 TACAGGGGTAGGGTAGGACT 57.994 55.000 0.00 0.00 0.00 3.85
1931 1963 2.854736 TTACAGGGGTAGGGTAGGAC 57.145 55.000 0.00 0.00 0.00 3.85
1933 1965 2.181642 AGGATTACAGGGGTAGGGTAGG 59.818 54.545 0.00 0.00 0.00 3.18
1936 1968 1.368558 ACAGGATTACAGGGGTAGGGT 59.631 52.381 0.00 0.00 0.00 4.34
1938 1970 2.047830 GGACAGGATTACAGGGGTAGG 58.952 57.143 0.00 0.00 0.00 3.18
1939 1971 2.047830 GGGACAGGATTACAGGGGTAG 58.952 57.143 0.00 0.00 0.00 3.18
1940 1972 1.654997 AGGGACAGGATTACAGGGGTA 59.345 52.381 0.00 0.00 0.00 3.69
1941 1973 0.421904 AGGGACAGGATTACAGGGGT 59.578 55.000 0.00 0.00 0.00 4.95
1942 1974 0.839946 CAGGGACAGGATTACAGGGG 59.160 60.000 0.00 0.00 0.00 4.79
1943 1975 0.181350 GCAGGGACAGGATTACAGGG 59.819 60.000 0.00 0.00 0.00 4.45
1944 1976 0.181350 GGCAGGGACAGGATTACAGG 59.819 60.000 0.00 0.00 0.00 4.00
1945 1977 0.179073 CGGCAGGGACAGGATTACAG 60.179 60.000 0.00 0.00 0.00 2.74
1946 1978 0.907704 ACGGCAGGGACAGGATTACA 60.908 55.000 0.00 0.00 0.00 2.41
1956 1988 1.216977 CGTGATGTAACGGCAGGGA 59.783 57.895 0.00 0.00 39.89 4.20
2034 2066 5.534278 ACGGGCCTAGTCTTCTTAGTATTAC 59.466 44.000 0.84 0.00 0.00 1.89
2163 2251 1.990563 CGGTAGACAGTTAAAGCGGTG 59.009 52.381 0.00 0.00 0.00 4.94
2164 2252 1.067354 CCGGTAGACAGTTAAAGCGGT 60.067 52.381 11.28 0.00 45.37 5.68
2165 2253 1.636988 CCGGTAGACAGTTAAAGCGG 58.363 55.000 0.00 6.89 45.21 5.52
2295 2400 0.868406 CAGGTGGAGCGAACTGAAAC 59.132 55.000 0.00 0.00 32.86 2.78
2304 2409 1.079543 CAAGAGGACAGGTGGAGCG 60.080 63.158 0.00 0.00 0.00 5.03
2314 2419 1.111277 GAGAGAGAGCCCAAGAGGAC 58.889 60.000 0.00 0.00 38.24 3.85
2330 2435 0.036448 AGACACGGGAGTCTTCGAGA 59.964 55.000 12.01 0.00 46.26 4.04
2491 2678 2.363795 TCGATGGAAGGGGCGTCT 60.364 61.111 0.00 0.00 0.00 4.18
2747 2934 4.844349 TGGGAGATGAGTAGGAAAAAGG 57.156 45.455 0.00 0.00 0.00 3.11
2750 2937 7.178451 GGAAAAATTGGGAGATGAGTAGGAAAA 59.822 37.037 0.00 0.00 0.00 2.29
2786 2977 1.445410 CTGCTACACGTTGCGGCTA 60.445 57.895 0.00 0.00 34.11 3.93
2796 2987 2.500098 TCCTAATGTGTCCCTGCTACAC 59.500 50.000 0.00 0.00 45.96 2.90
2797 2988 2.766263 CTCCTAATGTGTCCCTGCTACA 59.234 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.