Multiple sequence alignment - TraesCS5D01G297900

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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 TraesCS5D01G297900 chr5D 100.000 2714 0 0 1 2714 395692934 395690221 0.000000e+00 5012
1 TraesCS5D01G297900 chr5B 95.705 2049 59 11 680 2714 475958472 475956439 0.000000e+00 3269
2 TraesCS5D01G297900 chr5B 91.304 851 31 15 1 844 475959089 475958275 0.000000e+00 1122
3 TraesCS5D01G297900 chr5B 89.116 147 10 5 2465 2607 476000752 476000608 7.720000e-41 178
4 TraesCS5D01G297900 chr5B 81.395 172 20 9 2530 2690 476017346 476017176 2.190000e-26 130
5 TraesCS5D01G297900 chr5A 86.905 252 20 6 2465 2714 501847284 501847044 1.240000e-68 270


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 TraesCS5D01G297900 chr5D 395690221 395692934 2713 True 5012.0 5012 100.0000 1 2714 1 chr5D.!!$R1 2713
1 TraesCS5D01G297900 chr5B 475956439 475959089 2650 True 2195.5 3269 93.5045 1 2714 2 chr5B.!!$R3 2713

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
351 352 0.250858 CATGGGCCGGCTCAATATGA 60.251 55.0 36.68 9.18 0.0 2.15 F
978 983 0.800012 TTCAGGTTTTACGCCGCATC 59.200 50.0 0.00 0.00 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1584 0.235926 GCAGCTGTGGAAGAACGAAC 59.764 55.0 16.64 0.0 0.00 3.95 R
2645 2663 6.075984 ACCACTAGGAGGACGATGTATATTT 58.924 40.0 10.16 0.0 38.69 1.40 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
58 59 6.480763 AGTTGGAGAAAATGTTTGGGTTTTT 58.519 32.000 0.00 0.00 0.00 1.94
59 60 7.625469 AGTTGGAGAAAATGTTTGGGTTTTTA 58.375 30.769 0.00 0.00 0.00 1.52
60 61 8.103935 AGTTGGAGAAAATGTTTGGGTTTTTAA 58.896 29.630 0.00 0.00 0.00 1.52
115 116 2.846193 TCAGTTTCTCTTCCCGTTTGG 58.154 47.619 0.00 0.00 0.00 3.28
267 268 2.207229 ACTGACCGCTACAGTGCCA 61.207 57.895 0.00 0.00 45.19 4.92
320 321 8.067751 AGAAGATTGTGAATGTAGCTACACTA 57.932 34.615 28.28 14.58 39.30 2.74
326 327 4.298763 GTAGCTACACTACGCCGC 57.701 61.111 19.15 0.00 41.88 6.53
327 328 1.726265 GTAGCTACACTACGCCGCT 59.274 57.895 19.15 0.00 41.88 5.52
328 329 0.591741 GTAGCTACACTACGCCGCTG 60.592 60.000 19.15 0.00 41.88 5.18
329 330 2.332362 TAGCTACACTACGCCGCTGC 62.332 60.000 0.00 0.00 32.49 5.25
330 331 2.490217 CTACACTACGCCGCTGCT 59.510 61.111 0.00 0.00 34.43 4.24
331 332 1.725665 CTACACTACGCCGCTGCTA 59.274 57.895 0.00 0.00 34.43 3.49
332 333 0.591741 CTACACTACGCCGCTGCTAC 60.592 60.000 0.00 0.00 34.43 3.58
333 334 1.307355 TACACTACGCCGCTGCTACA 61.307 55.000 0.00 0.00 34.43 2.74
334 335 1.226974 CACTACGCCGCTGCTACAT 60.227 57.895 0.00 0.00 34.43 2.29
335 336 1.226974 ACTACGCCGCTGCTACATG 60.227 57.895 0.00 0.00 34.43 3.21
336 337 1.951130 CTACGCCGCTGCTACATGG 60.951 63.158 0.00 0.00 34.43 3.66
337 338 3.439513 TACGCCGCTGCTACATGGG 62.440 63.158 0.00 0.00 34.43 4.00
343 344 4.181010 CTGCTACATGGGCCGGCT 62.181 66.667 28.56 8.66 0.00 5.52
344 345 4.175337 TGCTACATGGGCCGGCTC 62.175 66.667 28.56 25.91 0.00 4.70
345 346 4.175337 GCTACATGGGCCGGCTCA 62.175 66.667 35.14 35.14 0.00 4.26
351 352 0.250858 CATGGGCCGGCTCAATATGA 60.251 55.000 36.68 9.18 0.00 2.15
508 511 3.852536 CACGACTTTACTCACGAAGGATC 59.147 47.826 0.00 0.00 0.00 3.36
530 533 7.119553 GGATCGTTTCCTACTACTAGGTATCTG 59.880 44.444 0.00 0.00 41.78 2.90
531 534 6.893583 TCGTTTCCTACTACTAGGTATCTGT 58.106 40.000 0.00 0.00 40.71 3.41
532 535 7.341805 TCGTTTCCTACTACTAGGTATCTGTT 58.658 38.462 0.00 0.00 40.71 3.16
570 575 7.884816 CGCTAGGATCGGAAATTCTTATAAA 57.115 36.000 0.00 0.00 0.00 1.40
778 783 4.803908 CCGCCTTGGCTTCCCCTC 62.804 72.222 10.12 0.00 0.00 4.30
779 784 4.803908 CGCCTTGGCTTCCCCTCC 62.804 72.222 10.12 0.00 0.00 4.30
780 785 3.342477 GCCTTGGCTTCCCCTCCT 61.342 66.667 4.11 0.00 0.00 3.69
781 786 3.002371 CCTTGGCTTCCCCTCCTC 58.998 66.667 0.00 0.00 0.00 3.71
782 787 2.684499 CCTTGGCTTCCCCTCCTCC 61.684 68.421 0.00 0.00 0.00 4.30
783 788 2.614013 TTGGCTTCCCCTCCTCCC 60.614 66.667 0.00 0.00 0.00 4.30
813 818 2.124695 CCGCCTTGGCTTACCCTC 60.125 66.667 10.12 0.00 33.59 4.30
823 828 3.081409 TTACCCTCCTCCTGCGGC 61.081 66.667 0.00 0.00 0.00 6.53
959 964 3.720193 CTGCTGCAAAGTCGCGCT 61.720 61.111 5.56 0.00 34.17 5.92
973 978 1.154282 GCGCTTCAGGTTTTACGCC 60.154 57.895 0.00 0.00 40.43 5.68
975 980 1.154282 GCTTCAGGTTTTACGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
978 983 0.800012 TTCAGGTTTTACGCCGCATC 59.200 50.000 0.00 0.00 0.00 3.91
1069 1075 7.604657 TTTAGGTTTTCACACCATTTACCAT 57.395 32.000 0.00 0.00 39.62 3.55
1141 1147 3.552132 TGTTAAGATAGCGATTGGGCA 57.448 42.857 0.00 0.00 34.64 5.36
1157 1163 3.992999 TGGGCATTCCTTTTATCATGGT 58.007 40.909 0.00 0.00 36.20 3.55
1213 1219 1.508088 CAAGTGCGGCCTCATTTCC 59.492 57.895 0.00 0.00 0.00 3.13
1224 1230 1.818060 CCTCATTTCCAACGCCATTGA 59.182 47.619 0.00 0.00 41.23 2.57
1235 1241 4.862018 CCAACGCCATTGAAAAATTACGAT 59.138 37.500 0.00 0.00 41.23 3.73
1236 1242 5.220191 CCAACGCCATTGAAAAATTACGATG 60.220 40.000 0.00 0.00 41.23 3.84
1241 1247 6.099341 GCCATTGAAAAATTACGATGTCCTT 58.901 36.000 0.00 0.00 0.00 3.36
1245 1251 7.737972 TTGAAAAATTACGATGTCCTTCTGA 57.262 32.000 0.00 0.00 0.00 3.27
1246 1252 7.364522 TGAAAAATTACGATGTCCTTCTGAG 57.635 36.000 0.00 0.00 0.00 3.35
1257 1263 4.645535 TGTCCTTCTGAGTTTTCCAGATG 58.354 43.478 0.00 0.00 40.02 2.90
1282 1288 4.706842 AAGAGTTCTTTTACCCTGCAGA 57.293 40.909 17.39 0.00 30.82 4.26
1300 1306 3.004106 GCAGAAAGCGCTATCCAAATCAT 59.996 43.478 12.05 0.00 0.00 2.45
1301 1307 4.781071 CAGAAAGCGCTATCCAAATCATC 58.219 43.478 12.05 0.00 0.00 2.92
1302 1308 3.817647 AGAAAGCGCTATCCAAATCATCC 59.182 43.478 12.05 0.00 0.00 3.51
1303 1309 2.936919 AGCGCTATCCAAATCATCCA 57.063 45.000 8.99 0.00 0.00 3.41
1304 1310 3.213206 AGCGCTATCCAAATCATCCAA 57.787 42.857 8.99 0.00 0.00 3.53
1305 1311 3.554934 AGCGCTATCCAAATCATCCAAA 58.445 40.909 8.99 0.00 0.00 3.28
1306 1312 4.147321 AGCGCTATCCAAATCATCCAAAT 58.853 39.130 8.99 0.00 0.00 2.32
1307 1313 4.217118 AGCGCTATCCAAATCATCCAAATC 59.783 41.667 8.99 0.00 0.00 2.17
1308 1314 4.022935 GCGCTATCCAAATCATCCAAATCA 60.023 41.667 0.00 0.00 0.00 2.57
1329 1335 5.588240 TCACAGACGGTATTGCTGTAATAG 58.412 41.667 0.00 0.00 40.63 1.73
1340 1346 3.489355 TGCTGTAATAGAATGCCATGGG 58.511 45.455 15.13 0.00 0.00 4.00
1343 1349 4.728772 CTGTAATAGAATGCCATGGGGAA 58.271 43.478 15.13 0.00 35.59 3.97
1347 1353 1.600058 AGAATGCCATGGGGAAGAGA 58.400 50.000 15.13 0.00 35.59 3.10
1353 1359 3.055328 TGCCATGGGGAAGAGATTGATA 58.945 45.455 15.13 0.00 35.59 2.15
1364 1370 6.454795 GGAAGAGATTGATACAGATCTGGTC 58.545 44.000 26.08 21.69 32.96 4.02
1381 1387 2.271800 GGTCGAGGCACTTCAAGTATG 58.728 52.381 0.00 0.00 41.55 2.39
1384 1390 2.002586 CGAGGCACTTCAAGTATGTGG 58.997 52.381 0.00 0.00 41.55 4.17
1390 1396 4.065088 GCACTTCAAGTATGTGGAGAACA 58.935 43.478 0.00 0.00 44.79 3.18
1392 1398 5.334414 GCACTTCAAGTATGTGGAGAACAAG 60.334 44.000 0.00 0.00 43.61 3.16
1432 1438 9.355215 AGAAGTGTATACATATAATGCTTACGC 57.645 33.333 9.18 0.00 34.39 4.42
1433 1439 9.355215 GAAGTGTATACATATAATGCTTACGCT 57.645 33.333 9.18 8.77 40.46 5.07
1449 1455 1.493950 CGCTGAGGGCATAGAAAGCG 61.494 60.000 0.12 0.12 46.09 4.68
1508 1514 6.424683 CGTAAGAAAATTACTTATTCCCCGC 58.575 40.000 7.83 0.00 43.02 6.13
1559 1565 4.757149 ACTAACTTGCCTCTTTACAAGCAG 59.243 41.667 2.80 3.71 45.74 4.24
1569 1579 5.705441 CCTCTTTACAAGCAGGTCAATACAA 59.295 40.000 0.00 0.00 0.00 2.41
1574 1584 4.573900 ACAAGCAGGTCAATACAAGAGAG 58.426 43.478 0.00 0.00 0.00 3.20
1599 1609 1.302271 CTTCCACAGCTGCTCTGCA 60.302 57.895 15.27 0.00 46.76 4.41
1614 1624 3.632189 CTCTGCAGGTTTAACTTTGCAC 58.368 45.455 15.13 0.00 41.23 4.57
1730 1740 9.540538 ACTAGCATAAGTAGATCCTGATTACAT 57.459 33.333 0.00 0.00 0.00 2.29
1740 1750 7.259088 AGATCCTGATTACATATACCCAACC 57.741 40.000 0.00 0.00 0.00 3.77
1956 1973 7.119846 GCATGTACCTTGTTTCAAAGATCTAGT 59.880 37.037 0.00 0.00 0.00 2.57
2467 2485 0.321564 CCCACATTCTTCAGCCGTGA 60.322 55.000 0.00 0.00 0.00 4.35
2640 2658 4.044426 GCTTCTGTGGTTGCTAGTTTTTG 58.956 43.478 0.00 0.00 0.00 2.44
2645 2663 7.159322 TCTGTGGTTGCTAGTTTTTGTTAAA 57.841 32.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.209391 CCCAAACATTTTCTCCAACTACAGAT 59.791 38.462 0.00 0.00 0.00 2.90
35 36 6.751514 AAAAACCCAAACATTTTCTCCAAC 57.248 33.333 0.00 0.00 0.00 3.77
60 61 9.990360 ACATATTGTAAAATTCCGGTTTTTCTT 57.010 25.926 17.21 5.28 33.62 2.52
84 85 3.531538 AGAGAAACTGAAAGCACGAACA 58.468 40.909 0.00 0.00 37.60 3.18
122 123 9.541143 CAGTAATGTTTTTGTAAAACCCAAGAT 57.459 29.630 11.30 0.00 0.00 2.40
226 227 3.370209 GGACAGTAGCTCCCGGTTTTTAT 60.370 47.826 0.00 0.00 0.00 1.40
244 245 0.826256 ACTGTAGCGGTCAGTGGACA 60.826 55.000 15.61 2.79 46.17 4.02
264 265 5.609088 CGATTCAATTAGTATAGCGTTGGC 58.391 41.667 0.00 0.00 40.37 4.52
267 268 6.585322 GGTAGCGATTCAATTAGTATAGCGTT 59.415 38.462 0.00 0.00 32.37 4.84
326 327 4.181010 AGCCGGCCCATGTAGCAG 62.181 66.667 26.15 3.17 0.00 4.24
327 328 4.175337 GAGCCGGCCCATGTAGCA 62.175 66.667 26.15 0.00 0.00 3.49
328 329 2.965716 ATTGAGCCGGCCCATGTAGC 62.966 60.000 26.15 2.96 0.00 3.58
329 330 0.396435 TATTGAGCCGGCCCATGTAG 59.604 55.000 26.15 0.00 0.00 2.74
330 331 1.064003 ATATTGAGCCGGCCCATGTA 58.936 50.000 26.15 14.32 0.00 2.29
331 332 0.538057 CATATTGAGCCGGCCCATGT 60.538 55.000 26.15 12.36 0.00 3.21
332 333 0.250858 TCATATTGAGCCGGCCCATG 60.251 55.000 26.15 18.50 0.00 3.66
333 334 0.478072 TTCATATTGAGCCGGCCCAT 59.522 50.000 26.15 15.39 0.00 4.00
334 335 0.179020 CTTCATATTGAGCCGGCCCA 60.179 55.000 26.15 17.08 0.00 5.36
335 336 1.518903 GCTTCATATTGAGCCGGCCC 61.519 60.000 26.15 13.59 0.00 5.80
336 337 1.845809 CGCTTCATATTGAGCCGGCC 61.846 60.000 26.15 15.80 0.00 6.13
337 338 1.571460 CGCTTCATATTGAGCCGGC 59.429 57.895 21.89 21.89 0.00 6.13
338 339 1.571460 GCGCTTCATATTGAGCCGG 59.429 57.895 0.00 0.00 0.00 6.13
339 340 1.571460 GGCGCTTCATATTGAGCCG 59.429 57.895 7.64 0.00 39.15 5.52
340 341 0.880278 TCGGCGCTTCATATTGAGCC 60.880 55.000 7.64 0.00 43.95 4.70
341 342 1.136141 CATCGGCGCTTCATATTGAGC 60.136 52.381 7.64 0.00 0.00 4.26
342 343 2.096565 CACATCGGCGCTTCATATTGAG 60.097 50.000 7.64 0.00 0.00 3.02
343 344 1.866601 CACATCGGCGCTTCATATTGA 59.133 47.619 7.64 0.00 0.00 2.57
344 345 1.661178 GCACATCGGCGCTTCATATTG 60.661 52.381 7.64 0.00 0.00 1.90
345 346 0.588252 GCACATCGGCGCTTCATATT 59.412 50.000 7.64 0.00 0.00 1.28
520 523 5.923204 AGAAGGCATGAAACAGATACCTAG 58.077 41.667 0.00 0.00 0.00 3.02
524 527 3.879892 GGGAGAAGGCATGAAACAGATAC 59.120 47.826 0.00 0.00 0.00 2.24
525 528 3.432186 CGGGAGAAGGCATGAAACAGATA 60.432 47.826 0.00 0.00 0.00 1.98
526 529 2.681976 CGGGAGAAGGCATGAAACAGAT 60.682 50.000 0.00 0.00 0.00 2.90
527 530 1.339055 CGGGAGAAGGCATGAAACAGA 60.339 52.381 0.00 0.00 0.00 3.41
530 533 0.678048 AGCGGGAGAAGGCATGAAAC 60.678 55.000 0.00 0.00 0.00 2.78
531 534 0.908910 TAGCGGGAGAAGGCATGAAA 59.091 50.000 0.00 0.00 0.00 2.69
532 535 0.465705 CTAGCGGGAGAAGGCATGAA 59.534 55.000 0.00 0.00 0.00 2.57
570 575 0.107654 CAACTAGCGGCTTTAGGGCT 60.108 55.000 8.26 0.00 40.68 5.19
696 701 2.614013 GGGAGGAGGGGAAGCCAA 60.614 66.667 0.00 0.00 0.00 4.52
798 803 1.224870 GAGGAGGGTAAGCCAAGGC 59.775 63.158 2.02 2.02 42.33 4.35
799 804 0.621862 AGGAGGAGGGTAAGCCAAGG 60.622 60.000 0.00 0.00 36.17 3.61
800 805 0.543749 CAGGAGGAGGGTAAGCCAAG 59.456 60.000 0.00 0.00 36.17 3.61
801 806 1.562672 GCAGGAGGAGGGTAAGCCAA 61.563 60.000 0.00 0.00 36.17 4.52
802 807 1.995626 GCAGGAGGAGGGTAAGCCA 60.996 63.158 0.00 0.00 36.17 4.75
803 808 2.911928 GCAGGAGGAGGGTAAGCC 59.088 66.667 0.00 0.00 0.00 4.35
804 809 2.501610 CGCAGGAGGAGGGTAAGC 59.498 66.667 0.00 0.00 0.00 3.09
959 964 0.800012 GATGCGGCGTAAAACCTGAA 59.200 50.000 9.37 0.00 0.00 3.02
973 978 0.744414 ATCGTTGAACCAGGGATGCG 60.744 55.000 0.00 0.00 0.00 4.73
975 980 3.505680 TCAAAATCGTTGAACCAGGGATG 59.494 43.478 0.00 0.00 0.00 3.51
978 983 3.505680 TGATCAAAATCGTTGAACCAGGG 59.494 43.478 0.00 0.00 34.39 4.45
1020 1025 1.829222 GGACGGAACAGATAGTGGGAA 59.171 52.381 0.00 0.00 0.00 3.97
1021 1026 1.481871 GGACGGAACAGATAGTGGGA 58.518 55.000 0.00 0.00 0.00 4.37
1141 1147 9.492973 CAGAAACAAAACCATGATAAAAGGAAT 57.507 29.630 0.00 0.00 0.00 3.01
1157 1163 5.392919 CCGTGGCATGATATCAGAAACAAAA 60.393 40.000 11.78 0.00 0.00 2.44
1213 1219 5.344665 ACATCGTAATTTTTCAATGGCGTTG 59.655 36.000 13.28 13.28 39.25 4.10
1224 1230 7.745620 AACTCAGAAGGACATCGTAATTTTT 57.254 32.000 0.00 0.00 0.00 1.94
1235 1241 4.505566 CCATCTGGAAAACTCAGAAGGACA 60.506 45.833 9.03 0.00 46.93 4.02
1236 1242 4.006319 CCATCTGGAAAACTCAGAAGGAC 58.994 47.826 9.03 0.00 46.93 3.85
1260 1266 9.290218 GCTTTCTGCAGGGTAAAAGAACTCTTT 62.290 40.741 22.92 0.00 43.63 2.52
1261 1267 4.706842 TCTGCAGGGTAAAAGAACTCTT 57.293 40.909 15.13 0.00 37.91 2.85
1262 1268 4.706842 TTCTGCAGGGTAAAAGAACTCT 57.293 40.909 15.13 0.00 0.00 3.24
1263 1269 4.320567 GCTTTCTGCAGGGTAAAAGAACTC 60.321 45.833 22.92 7.25 42.31 3.01
1282 1288 3.554934 TGGATGATTTGGATAGCGCTTT 58.445 40.909 18.68 8.03 0.00 3.51
1300 1306 3.006940 GCAATACCGTCTGTGATTTGGA 58.993 45.455 0.00 0.00 0.00 3.53
1301 1307 3.009723 AGCAATACCGTCTGTGATTTGG 58.990 45.455 0.00 0.00 0.00 3.28
1302 1308 3.436704 ACAGCAATACCGTCTGTGATTTG 59.563 43.478 0.00 0.00 39.36 2.32
1303 1309 3.674997 ACAGCAATACCGTCTGTGATTT 58.325 40.909 0.00 0.00 39.36 2.17
1304 1310 3.334583 ACAGCAATACCGTCTGTGATT 57.665 42.857 0.00 0.00 39.36 2.57
1305 1311 4.465632 TTACAGCAATACCGTCTGTGAT 57.534 40.909 4.56 0.00 40.80 3.06
1306 1312 3.945981 TTACAGCAATACCGTCTGTGA 57.054 42.857 4.56 0.00 40.80 3.58
1307 1313 5.588240 TCTATTACAGCAATACCGTCTGTG 58.412 41.667 4.56 0.00 40.80 3.66
1308 1314 5.847111 TCTATTACAGCAATACCGTCTGT 57.153 39.130 0.00 0.00 42.89 3.41
1329 1335 2.626743 CAATCTCTTCCCCATGGCATTC 59.373 50.000 6.09 0.00 0.00 2.67
1340 1346 6.418057 ACCAGATCTGTATCAATCTCTTCC 57.582 41.667 21.11 0.00 34.28 3.46
1343 1349 5.380900 TCGACCAGATCTGTATCAATCTCT 58.619 41.667 21.11 0.00 34.28 3.10
1347 1353 3.006323 GCCTCGACCAGATCTGTATCAAT 59.994 47.826 21.11 0.00 34.28 2.57
1353 1359 0.613292 AGTGCCTCGACCAGATCTGT 60.613 55.000 21.11 9.51 0.00 3.41
1364 1370 2.002586 CCACATACTTGAAGTGCCTCG 58.997 52.381 8.33 0.00 32.09 4.63
1381 1387 7.672983 TCAGATATTGAAACTTGTTCTCCAC 57.327 36.000 0.00 0.00 31.34 4.02
1432 1438 1.162800 GGCGCTTTCTATGCCCTCAG 61.163 60.000 7.64 0.00 43.06 3.35
1433 1439 1.153168 GGCGCTTTCTATGCCCTCA 60.153 57.895 7.64 0.00 43.06 3.86
1520 1526 8.443937 GGCAAGTTAGTGTTTGAGAATAAGTAG 58.556 37.037 0.00 0.00 0.00 2.57
1559 1565 5.471257 AGAACGAACTCTCTTGTATTGACC 58.529 41.667 0.00 0.00 0.00 4.02
1569 1579 2.288518 GCTGTGGAAGAACGAACTCTCT 60.289 50.000 0.00 0.00 0.00 3.10
1574 1584 0.235926 GCAGCTGTGGAAGAACGAAC 59.764 55.000 16.64 0.00 0.00 3.95
1599 1609 2.091555 TCCCAGGTGCAAAGTTAAACCT 60.092 45.455 0.00 0.00 43.92 3.50
1604 1614 0.476338 TGCTCCCAGGTGCAAAGTTA 59.524 50.000 10.85 0.00 40.89 2.24
1610 1620 2.036098 CCAATGCTCCCAGGTGCA 59.964 61.111 15.19 15.19 46.35 4.57
1614 1624 2.689983 GTTAATGACCAATGCTCCCAGG 59.310 50.000 0.00 0.00 0.00 4.45
1715 1725 7.123697 CGGTTGGGTATATGTAATCAGGATCTA 59.876 40.741 0.00 0.00 0.00 1.98
1730 1740 4.895668 AAACAGTCTTCGGTTGGGTATA 57.104 40.909 0.00 0.00 32.81 1.47
1792 1809 7.437267 GCATTAATTCAAAGCATGCTCTAACAT 59.563 33.333 22.93 9.29 37.78 2.71
2467 2485 6.538945 AAAAATAACAAAGGTGTCACCAGT 57.461 33.333 24.02 15.52 41.95 4.00
2640 2658 9.978044 ACTAGGAGGACGATGTATATTTTTAAC 57.022 33.333 0.00 0.00 0.00 2.01
2645 2663 6.075984 ACCACTAGGAGGACGATGTATATTT 58.924 40.000 10.16 0.00 38.69 1.40


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

AutoCloner maintained by Alex Coulton.