Multiple sequence alignment - TraesCS1A01G285300

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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 TraesCS1A01G285300 chr1A 100.000 2645 0 0 1 2645 482766916 482769560 0.000000e+00 4885
1 TraesCS1A01G285300 chr1D 92.034 2335 129 28 336 2645 382719048 382721350 0.000000e+00 3229
2 TraesCS1A01G285300 chr1D 89.677 310 23 5 1 310 382718756 382719056 1.150000e-103 387
3 TraesCS1A01G285300 chr1B 91.848 1791 97 20 871 2645 512630449 512632206 0.000000e+00 2453
4 TraesCS1A01G285300 chr1B 87.018 285 28 5 4 288 512623303 512623578 1.980000e-81 313
5 TraesCS1A01G285300 chr1B 96.689 151 5 0 722 872 512623994 512624144 4.370000e-63 252
6 TraesCS1A01G285300 chr4B 89.286 448 36 10 1090 1533 43061248 43061687 3.850000e-153 551
7 TraesCS1A01G285300 chrUn 89.333 450 31 9 1090 1526 249353767 249353322 1.380000e-152 549
8 TraesCS1A01G285300 chrUn 89.333 450 31 9 1090 1526 249358135 249357690 1.380000e-152 549
9 TraesCS1A01G285300 chrUn 89.333 450 31 9 1090 1526 249362503 249362058 1.380000e-152 549
10 TraesCS1A01G285300 chrUn 89.333 450 31 10 1090 1526 249942943 249943388 1.380000e-152 549
11 TraesCS1A01G285300 chrUn 89.333 450 31 10 1090 1526 249947311 249947756 1.380000e-152 549
12 TraesCS1A01G285300 chrUn 89.333 450 31 10 1090 1526 249951679 249952124 1.380000e-152 549


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 TraesCS1A01G285300 chr1A 482766916 482769560 2644 False 4885.0 4885 100.0000 1 2645 1 chr1A.!!$F1 2644
1 TraesCS1A01G285300 chr1D 382718756 382721350 2594 False 1808.0 3229 90.8555 1 2645 2 chr1D.!!$F1 2644
2 TraesCS1A01G285300 chr1B 512630449 512632206 1757 False 2453.0 2453 91.8480 871 2645 1 chr1B.!!$F1 1774
3 TraesCS1A01G285300 chr1B 512623303 512624144 841 False 282.5 313 91.8535 4 872 2 chr1B.!!$F2 868
4 TraesCS1A01G285300 chrUn 249353322 249362503 9181 True 549.0 549 89.3330 1090 1526 3 chrUn.!!$R1 436
5 TraesCS1A01G285300 chrUn 249942943 249952124 9181 False 549.0 549 89.3330 1090 1526 3 chrUn.!!$F1 436

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
51 52 0.107214 CCAACCAGTACCATCCGCAT 60.107 55.0 0.00 0.00 0.00 4.73 F
58 59 0.179094 GTACCATCCGCATCCGACAA 60.179 55.0 0.00 0.00 36.29 3.18 F
124 125 0.318762 GAAGGTCTGGCTCGACAAGT 59.681 55.0 9.15 0.00 35.63 3.16 F
264 265 0.322975 ACTGCACAGGGCTAGTCTTG 59.677 55.0 4.69 4.69 45.15 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 4525 0.321671 TCTTGGCCTTCTTGTCCGAG 59.678 55.000 3.32 0.0 33.58 4.63 R
1549 4862 0.456142 CATCAAACGCGAGGAGACGA 60.456 55.000 15.93 0.0 35.09 4.20 R
1550 4863 0.456142 TCATCAAACGCGAGGAGACG 60.456 55.000 15.93 0.0 0.00 4.18 R
1945 9187 1.080839 CAACCCGGCCAAATTCGTG 60.081 57.895 2.24 0.0 0.00 4.35 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
49 50 0.538118 TACCAACCAGTACCATCCGC 59.462 55.000 0.00 0.00 0.00 5.54
51 52 0.107214 CCAACCAGTACCATCCGCAT 60.107 55.000 0.00 0.00 0.00 4.73
55 56 1.739667 CAGTACCATCCGCATCCGA 59.260 57.895 0.00 0.00 36.29 4.55
57 58 1.040893 AGTACCATCCGCATCCGACA 61.041 55.000 0.00 0.00 36.29 4.35
58 59 0.179094 GTACCATCCGCATCCGACAA 60.179 55.000 0.00 0.00 36.29 3.18
59 60 0.537653 TACCATCCGCATCCGACAAA 59.462 50.000 0.00 0.00 36.29 2.83
99 100 8.160106 GGTCATATCCCTAGAGTGAAAATGAAT 58.840 37.037 0.00 0.00 0.00 2.57
124 125 0.318762 GAAGGTCTGGCTCGACAAGT 59.681 55.000 9.15 0.00 35.63 3.16
130 131 0.952497 CTGGCTCGACAAGTGTGCAT 60.952 55.000 0.00 0.00 0.00 3.96
132 133 0.950555 GGCTCGACAAGTGTGCATGA 60.951 55.000 0.00 0.00 0.00 3.07
197 198 3.119101 TGGAAGAGGCGAGAAATAGTGAC 60.119 47.826 0.00 0.00 0.00 3.67
230 231 1.683917 ACATGATCGTAGAGAGTGCCC 59.316 52.381 0.00 0.00 43.63 5.36
256 257 2.754552 TGAAATTATCACTGCACAGGGC 59.245 45.455 2.21 0.00 36.58 5.19
264 265 0.322975 ACTGCACAGGGCTAGTCTTG 59.677 55.000 4.69 4.69 45.15 3.02
296 297 1.140252 AGTGTAAACGAAGGGCACTGT 59.860 47.619 0.00 0.00 38.74 3.55
297 298 2.366266 AGTGTAAACGAAGGGCACTGTA 59.634 45.455 0.00 0.00 38.74 2.74
300 301 2.922740 AAACGAAGGGCACTGTAGAA 57.077 45.000 0.00 0.00 0.00 2.10
301 302 2.165319 AACGAAGGGCACTGTAGAAC 57.835 50.000 0.00 0.00 0.00 3.01
302 303 1.045407 ACGAAGGGCACTGTAGAACA 58.955 50.000 0.00 0.00 0.00 3.18
303 304 1.414919 ACGAAGGGCACTGTAGAACAA 59.585 47.619 0.00 0.00 0.00 2.83
304 305 2.038557 ACGAAGGGCACTGTAGAACAAT 59.961 45.455 0.00 0.00 0.00 2.71
305 306 2.416547 CGAAGGGCACTGTAGAACAATG 59.583 50.000 0.00 0.00 0.00 2.82
306 307 3.674997 GAAGGGCACTGTAGAACAATGA 58.325 45.455 0.00 0.00 24.12 2.57
307 308 3.340814 AGGGCACTGTAGAACAATGAG 57.659 47.619 0.00 0.00 24.12 2.90
308 309 2.906389 AGGGCACTGTAGAACAATGAGA 59.094 45.455 0.00 0.00 24.12 3.27
309 310 3.055530 AGGGCACTGTAGAACAATGAGAG 60.056 47.826 0.00 0.00 24.12 3.20
311 312 3.307059 GGCACTGTAGAACAATGAGAGGT 60.307 47.826 0.00 0.00 24.12 3.85
314 315 3.515901 ACTGTAGAACAATGAGAGGTCCC 59.484 47.826 0.00 0.00 0.00 4.46
315 316 3.772025 CTGTAGAACAATGAGAGGTCCCT 59.228 47.826 0.00 0.00 0.00 4.20
317 318 3.990959 AGAACAATGAGAGGTCCCTTC 57.009 47.619 0.00 0.00 0.00 3.46
318 319 3.251484 AGAACAATGAGAGGTCCCTTCA 58.749 45.455 0.00 0.00 0.00 3.02
319 320 3.262915 AGAACAATGAGAGGTCCCTTCAG 59.737 47.826 0.00 0.00 0.00 3.02
320 321 1.912043 ACAATGAGAGGTCCCTTCAGG 59.088 52.381 0.00 0.00 0.00 3.86
321 322 2.191400 CAATGAGAGGTCCCTTCAGGA 58.809 52.381 0.00 0.00 44.91 3.86
329 330 3.392066 TCCCTTCAGGAACATCCGA 57.608 52.632 0.00 0.00 43.78 4.55
330 331 1.879575 TCCCTTCAGGAACATCCGAT 58.120 50.000 0.00 0.00 43.78 4.18
332 333 3.380393 TCCCTTCAGGAACATCCGATAA 58.620 45.455 0.00 0.00 43.78 1.75
333 334 3.778075 TCCCTTCAGGAACATCCGATAAA 59.222 43.478 0.00 0.00 43.78 1.40
348 349 7.390440 ACATCCGATAAAACAATGAGAGAAACA 59.610 33.333 0.00 0.00 0.00 2.83
359 360 5.551760 ATGAGAGAAACAACAATAAGGCG 57.448 39.130 0.00 0.00 0.00 5.52
371 372 2.163810 ATAAGGCGTACCCACTGGTA 57.836 50.000 3.60 0.00 45.45 3.25
388 389 5.049405 CACTGGTAGTTGTGTGGAGATTTTC 60.049 44.000 0.00 0.00 0.00 2.29
408 409 3.963129 TCCAGGGCTCACGAAAAATATT 58.037 40.909 0.00 0.00 0.00 1.28
414 415 7.134815 CAGGGCTCACGAAAAATATTGATAAG 58.865 38.462 0.00 0.00 0.00 1.73
461 462 1.686355 TGCCACCAACGTGAAAGAAT 58.314 45.000 0.00 0.00 43.14 2.40
462 463 2.852449 TGCCACCAACGTGAAAGAATA 58.148 42.857 0.00 0.00 43.14 1.75
479 480 5.178096 AGAATAACATGGATGTGACACCA 57.822 39.130 2.45 8.85 41.61 4.17
512 513 1.595382 CGGAGCCATCGGTGGATTC 60.595 63.158 21.83 11.01 46.08 2.52
621 623 7.066284 GGAAATCAATACTTGTGTAGAGCATGT 59.934 37.037 0.00 0.00 31.51 3.21
647 650 5.560966 AATCCTTGTATTTACCTGCAACG 57.439 39.130 0.00 0.00 0.00 4.10
649 652 4.839121 TCCTTGTATTTACCTGCAACGAT 58.161 39.130 0.00 0.00 0.00 3.73
650 653 5.250200 TCCTTGTATTTACCTGCAACGATT 58.750 37.500 0.00 0.00 0.00 3.34
651 654 5.708230 TCCTTGTATTTACCTGCAACGATTT 59.292 36.000 0.00 0.00 0.00 2.17
652 655 6.207810 TCCTTGTATTTACCTGCAACGATTTT 59.792 34.615 0.00 0.00 0.00 1.82
653 656 6.526674 CCTTGTATTTACCTGCAACGATTTTC 59.473 38.462 0.00 0.00 0.00 2.29
654 657 6.811253 TGTATTTACCTGCAACGATTTTCT 57.189 33.333 0.00 0.00 0.00 2.52
657 660 8.138712 TGTATTTACCTGCAACGATTTTCTTTT 58.861 29.630 0.00 0.00 0.00 2.27
664 690 7.065283 CCTGCAACGATTTTCTTTTCAATTTC 58.935 34.615 0.00 0.00 0.00 2.17
666 692 8.864069 TGCAACGATTTTCTTTTCAATTTCTA 57.136 26.923 0.00 0.00 0.00 2.10
668 694 7.939386 GCAACGATTTTCTTTTCAATTTCTACG 59.061 33.333 0.00 0.00 0.00 3.51
670 696 8.488979 ACGATTTTCTTTTCAATTTCTACGTG 57.511 30.769 0.00 0.00 0.00 4.49
671 697 8.126700 ACGATTTTCTTTTCAATTTCTACGTGT 58.873 29.630 0.00 0.00 0.00 4.49
713 739 8.754991 TCTTTTCTTTTGGTGTATAAACTCCA 57.245 30.769 0.00 0.00 45.28 3.86
744 787 4.324267 AGACTTTTGACGGTGGATTAAGG 58.676 43.478 0.00 0.00 0.00 2.69
1002 1046 0.394216 CCATCTCATCCCACCGCAAA 60.394 55.000 0.00 0.00 0.00 3.68
1030 1074 2.256764 CGCCCTCTCCGATCATCG 59.743 66.667 0.00 0.00 40.07 3.84
1040 1084 1.528292 CCGATCATCGTCCTCCTCCC 61.528 65.000 6.25 0.00 38.40 4.30
1042 1086 0.470080 GATCATCGTCCTCCTCCCCA 60.470 60.000 0.00 0.00 0.00 4.96
1048 1092 4.649705 TCCTCCTCCCCACCGCAA 62.650 66.667 0.00 0.00 0.00 4.85
1049 1093 4.410400 CCTCCTCCCCACCGCAAC 62.410 72.222 0.00 0.00 0.00 4.17
1076 1120 3.210528 ACCTCTCGATCCGTCCGC 61.211 66.667 0.00 0.00 0.00 5.54
1125 4390 2.202810 GAGAAGAAGCCGGCGGAG 60.203 66.667 33.44 3.96 0.00 4.63
1126 4391 3.724914 GAGAAGAAGCCGGCGGAGG 62.725 68.421 33.44 3.04 0.00 4.30
1127 4392 3.771160 GAAGAAGCCGGCGGAGGA 61.771 66.667 33.44 0.00 0.00 3.71
1128 4393 3.724914 GAAGAAGCCGGCGGAGGAG 62.725 68.421 33.44 2.12 0.00 3.69
1129 4394 4.761058 AGAAGCCGGCGGAGGAGA 62.761 66.667 33.44 0.00 0.00 3.71
1130 4395 3.771160 GAAGCCGGCGGAGGAGAA 61.771 66.667 33.44 0.00 0.00 2.87
1131 4396 3.724914 GAAGCCGGCGGAGGAGAAG 62.725 68.421 33.44 0.00 0.00 2.85
1531 4844 1.153127 ACCTCCTCCTAGACGCTCG 60.153 63.158 0.00 0.00 0.00 5.03
1549 4862 3.684628 TCCCCCGCCCTTCTCTCT 61.685 66.667 0.00 0.00 0.00 3.10
1550 4863 3.157949 CCCCCGCCCTTCTCTCTC 61.158 72.222 0.00 0.00 0.00 3.20
1654 5197 3.836365 TGGATGAATGGAATCGCTACA 57.164 42.857 0.00 0.00 0.00 2.74
1682 5225 6.321717 TGGTTGCAATATTTCGTCTCAATTC 58.678 36.000 0.59 0.00 0.00 2.17
1697 5240 3.571571 TCAATTCTCGTTCGATCGTTGT 58.428 40.909 15.94 0.00 0.00 3.32
1698 5241 4.725359 TCAATTCTCGTTCGATCGTTGTA 58.275 39.130 15.94 5.01 0.00 2.41
1737 6752 9.710900 ATGAAGTTAAAAGAAACCAAATGATCC 57.289 29.630 0.00 0.00 0.00 3.36
1885 9127 4.530946 TCGAGGTATTTCTGGTTCTCCTTT 59.469 41.667 0.00 0.00 34.23 3.11
1945 9187 3.793888 CCGTACCCCTTGAGCCCC 61.794 72.222 0.00 0.00 0.00 5.80
1951 9193 2.677228 CCCTTGAGCCCCACGAAT 59.323 61.111 0.00 0.00 0.00 3.34
2002 9244 3.803082 CGCACGCCAATGTCCCTG 61.803 66.667 0.00 0.00 0.00 4.45
2022 9264 1.656095 GAGAATCTGAAACGGACAGCG 59.344 52.381 0.00 0.00 35.61 5.18
2024 9266 2.066262 GAATCTGAAACGGACAGCGAA 58.934 47.619 0.00 0.00 35.61 4.70
2026 9268 2.163818 TCTGAAACGGACAGCGAAAT 57.836 45.000 0.00 0.00 35.61 2.17
2087 9329 4.362279 CAAGAATGTTAAATCCGCCATGG 58.638 43.478 7.63 7.63 40.09 3.66
2102 9347 3.531538 GCCATGGAGAATTCAAGTACGA 58.468 45.455 18.40 0.00 0.00 3.43
2266 9511 4.409218 GTACACGAGGACGCCGCA 62.409 66.667 0.00 0.00 43.96 5.69
2393 9638 1.215382 CACGTCTTCTCCATCGCCA 59.785 57.895 0.00 0.00 0.00 5.69
2399 9644 3.552890 CGTCTTCTCCATCGCCAATATCA 60.553 47.826 0.00 0.00 0.00 2.15
2404 9649 2.567169 CTCCATCGCCAATATCACCCTA 59.433 50.000 0.00 0.00 0.00 3.53
2415 9660 2.897271 ATCACCCTACACATTTGCCA 57.103 45.000 0.00 0.00 0.00 4.92
2481 9745 0.036022 GGCTCACTGGTTTCTGCTCT 59.964 55.000 0.00 0.00 0.00 4.09
2514 9778 7.121168 TCTGTCAGAGAAACACAACAAGAATTT 59.879 33.333 0.00 0.00 0.00 1.82
2619 9884 2.603110 GCAAACGAGATACAGCGATCAA 59.397 45.455 0.00 0.00 0.00 2.57
2629 9894 0.379669 CAGCGATCAATTCCACCAGC 59.620 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.292267 CTTCCCCTGATTTGTCGGATG 58.708 52.381 0.00 0.00 0.00 3.51
51 52 0.618458 CCTTCCCCTGATTTGTCGGA 59.382 55.000 0.00 0.00 0.00 4.55
55 56 1.503347 ACCAACCTTCCCCTGATTTGT 59.497 47.619 0.00 0.00 0.00 2.83
57 58 1.786441 TGACCAACCTTCCCCTGATTT 59.214 47.619 0.00 0.00 0.00 2.17
58 59 1.455822 TGACCAACCTTCCCCTGATT 58.544 50.000 0.00 0.00 0.00 2.57
59 60 1.686236 ATGACCAACCTTCCCCTGAT 58.314 50.000 0.00 0.00 0.00 2.90
99 100 0.824109 CGAGCCAGACCTTCCATGTA 59.176 55.000 0.00 0.00 0.00 2.29
124 125 1.270571 TGTACTTCCGCTTCATGCACA 60.271 47.619 0.00 0.00 43.06 4.57
130 131 5.049267 GGTGTAAAATTGTACTTCCGCTTCA 60.049 40.000 7.31 0.00 0.00 3.02
132 133 4.822896 TGGTGTAAAATTGTACTTCCGCTT 59.177 37.500 7.31 0.00 0.00 4.68
197 198 4.563524 CGATCATGTCACATCATCATCG 57.436 45.455 2.26 3.53 40.84 3.84
230 231 5.327616 TGTGCAGTGATAATTTCATTGGG 57.672 39.130 0.00 0.00 41.18 4.12
256 257 0.035056 CCACCTTGGGCCAAGACTAG 60.035 60.000 40.88 27.90 43.42 2.57
264 265 0.111639 TTTACACTCCACCTTGGGCC 59.888 55.000 0.00 0.00 38.32 5.80
296 297 4.425772 TGAAGGGACCTCTCATTGTTCTA 58.574 43.478 0.00 0.00 0.00 2.10
297 298 3.251484 TGAAGGGACCTCTCATTGTTCT 58.749 45.455 0.00 0.00 0.00 3.01
300 301 1.912043 CCTGAAGGGACCTCTCATTGT 59.088 52.381 0.00 0.00 37.23 2.71
301 302 2.191400 TCCTGAAGGGACCTCTCATTG 58.809 52.381 0.00 0.00 39.58 2.82
302 303 2.573915 GTTCCTGAAGGGACCTCTCATT 59.426 50.000 0.00 0.00 45.03 2.57
303 304 2.192263 GTTCCTGAAGGGACCTCTCAT 58.808 52.381 0.00 0.00 45.03 2.90
304 305 1.132849 TGTTCCTGAAGGGACCTCTCA 60.133 52.381 5.29 0.00 43.30 3.27
305 306 1.645710 TGTTCCTGAAGGGACCTCTC 58.354 55.000 5.29 0.00 43.30 3.20
306 307 2.192263 GATGTTCCTGAAGGGACCTCT 58.808 52.381 5.29 0.00 43.30 3.69
307 308 1.210722 GGATGTTCCTGAAGGGACCTC 59.789 57.143 5.29 5.04 43.30 3.85
308 309 1.290134 GGATGTTCCTGAAGGGACCT 58.710 55.000 5.29 0.00 43.30 3.85
309 310 0.107654 CGGATGTTCCTGAAGGGACC 60.108 60.000 5.29 0.00 43.30 4.46
311 312 1.879575 ATCGGATGTTCCTGAAGGGA 58.120 50.000 0.00 0.00 43.41 4.20
314 315 6.494893 TTGTTTTATCGGATGTTCCTGAAG 57.505 37.500 0.00 0.00 33.30 3.02
315 316 6.657117 TCATTGTTTTATCGGATGTTCCTGAA 59.343 34.615 0.00 0.00 33.30 3.02
317 318 6.316140 TCTCATTGTTTTATCGGATGTTCCTG 59.684 38.462 0.00 0.00 33.30 3.86
318 319 6.414732 TCTCATTGTTTTATCGGATGTTCCT 58.585 36.000 0.00 0.00 33.30 3.36
319 320 6.538742 TCTCTCATTGTTTTATCGGATGTTCC 59.461 38.462 0.00 0.00 0.00 3.62
320 321 7.539712 TCTCTCATTGTTTTATCGGATGTTC 57.460 36.000 0.00 0.00 0.00 3.18
321 322 7.921786 TTCTCTCATTGTTTTATCGGATGTT 57.078 32.000 0.00 0.00 0.00 2.71
323 324 7.751732 TGTTTCTCTCATTGTTTTATCGGATG 58.248 34.615 0.00 0.00 0.00 3.51
324 325 7.921786 TGTTTCTCTCATTGTTTTATCGGAT 57.078 32.000 0.00 0.00 0.00 4.18
325 326 7.227711 TGTTGTTTCTCTCATTGTTTTATCGGA 59.772 33.333 0.00 0.00 0.00 4.55
326 327 7.359595 TGTTGTTTCTCTCATTGTTTTATCGG 58.640 34.615 0.00 0.00 0.00 4.18
327 328 8.781067 TTGTTGTTTCTCTCATTGTTTTATCG 57.219 30.769 0.00 0.00 0.00 2.92
332 333 7.653311 GCCTTATTGTTGTTTCTCTCATTGTTT 59.347 33.333 0.00 0.00 0.00 2.83
333 334 7.147976 GCCTTATTGTTGTTTCTCTCATTGTT 58.852 34.615 0.00 0.00 0.00 2.83
348 349 2.617021 CCAGTGGGTACGCCTTATTGTT 60.617 50.000 7.55 0.00 34.45 2.83
388 389 3.694072 TCAATATTTTTCGTGAGCCCTGG 59.306 43.478 0.00 0.00 0.00 4.45
408 409 5.358922 TCATGTCGCATGATGAACTTATCA 58.641 37.500 15.52 0.00 43.67 2.15
414 415 4.330894 TCTCTTTCATGTCGCATGATGAAC 59.669 41.667 18.73 0.00 38.11 3.18
461 462 3.072330 ACAGTGGTGTCACATCCATGTTA 59.928 43.478 5.12 0.00 45.91 2.41
462 463 2.158623 ACAGTGGTGTCACATCCATGTT 60.159 45.455 5.12 0.00 45.91 2.71
479 480 0.606401 CTCCGCCCAACAATGACAGT 60.606 55.000 0.00 0.00 0.00 3.55
512 513 2.014068 GCGGGTTTGAAGATGGAGAGG 61.014 57.143 0.00 0.00 0.00 3.69
563 564 1.136305 GTGGCGCATCTCACCTTAGTA 59.864 52.381 10.83 0.00 0.00 1.82
565 566 2.682893 GTGGCGCATCTCACCTTAG 58.317 57.895 10.83 0.00 0.00 2.18
566 567 4.932789 GTGGCGCATCTCACCTTA 57.067 55.556 10.83 0.00 0.00 2.69
621 623 5.979993 TGCAGGTAAATACAAGGATTCGTA 58.020 37.500 0.00 0.00 0.00 3.43
699 725 9.257651 GTCTACACAATATGGAGTTTATACACC 57.742 37.037 0.00 0.00 40.65 4.16
706 732 8.784043 GTCAAAAGTCTACACAATATGGAGTTT 58.216 33.333 0.00 0.00 40.65 2.66
707 733 7.117812 CGTCAAAAGTCTACACAATATGGAGTT 59.882 37.037 0.00 0.00 40.65 3.01
708 734 6.590292 CGTCAAAAGTCTACACAATATGGAGT 59.410 38.462 0.00 0.00 40.65 3.85
709 735 6.036083 CCGTCAAAAGTCTACACAATATGGAG 59.964 42.308 0.00 0.00 41.27 3.86
711 737 5.642063 ACCGTCAAAAGTCTACACAATATGG 59.358 40.000 0.00 0.00 0.00 2.74
712 738 6.402118 CCACCGTCAAAAGTCTACACAATATG 60.402 42.308 0.00 0.00 0.00 1.78
713 739 5.642063 CCACCGTCAAAAGTCTACACAATAT 59.358 40.000 0.00 0.00 0.00 1.28
715 741 3.813166 CCACCGTCAAAAGTCTACACAAT 59.187 43.478 0.00 0.00 0.00 2.71
717 743 2.431419 TCCACCGTCAAAAGTCTACACA 59.569 45.455 0.00 0.00 0.00 3.72
718 744 3.102052 TCCACCGTCAAAAGTCTACAC 57.898 47.619 0.00 0.00 0.00 2.90
801 844 2.263540 GCGGTTTAGGCGGTGAGA 59.736 61.111 0.00 0.00 0.00 3.27
960 1003 4.506802 GGAATTGGATTTATAGAGGGGCGT 60.507 45.833 0.00 0.00 0.00 5.68
1002 1046 4.101448 GAGGGCGCTGGTGATGGT 62.101 66.667 8.56 0.00 0.00 3.55
1047 1091 2.856000 AGAGGTGGCTGGCTGGTT 60.856 61.111 2.00 0.00 0.00 3.67
1048 1092 3.325753 GAGAGGTGGCTGGCTGGT 61.326 66.667 2.00 0.00 0.00 4.00
1049 1093 4.463879 CGAGAGGTGGCTGGCTGG 62.464 72.222 2.00 0.00 0.00 4.85
1125 4390 2.188207 GCCTTCTCCGCCTTCTCC 59.812 66.667 0.00 0.00 0.00 3.71
1126 4391 2.202810 CGCCTTCTCCGCCTTCTC 60.203 66.667 0.00 0.00 0.00 2.87
1127 4392 4.459089 GCGCCTTCTCCGCCTTCT 62.459 66.667 0.00 0.00 45.30 2.85
1213 4523 2.436824 GGCCTTCTTGTCCGAGCC 60.437 66.667 0.00 0.00 0.00 4.70
1214 4524 1.301677 CTTGGCCTTCTTGTCCGAGC 61.302 60.000 3.32 0.00 0.00 5.03
1215 4525 0.321671 TCTTGGCCTTCTTGTCCGAG 59.678 55.000 3.32 0.00 33.58 4.63
1531 4844 3.471806 GAGAGAAGGGCGGGGGAC 61.472 72.222 0.00 0.00 0.00 4.46
1549 4862 0.456142 CATCAAACGCGAGGAGACGA 60.456 55.000 15.93 0.00 35.09 4.20
1550 4863 0.456142 TCATCAAACGCGAGGAGACG 60.456 55.000 15.93 0.00 0.00 4.18
1654 5197 5.647658 TGAGACGAAATATTGCAACCAATCT 59.352 36.000 0.00 0.00 41.68 2.40
1682 5225 5.676953 TCTGATATACAACGATCGAACGAG 58.323 41.667 24.34 15.12 37.03 4.18
1722 6737 3.433306 TCCACGGATCATTTGGTTTCT 57.567 42.857 0.00 0.00 0.00 2.52
1945 9187 1.080839 CAACCCGGCCAAATTCGTG 60.081 57.895 2.24 0.00 0.00 4.35
1951 9193 2.124236 ACGAACAACCCGGCCAAA 60.124 55.556 2.24 0.00 0.00 3.28
2002 9244 1.656095 CGCTGTCCGTTTCAGATTCTC 59.344 52.381 0.00 0.00 35.20 2.87
2022 9264 6.211587 TGATGATTGATGGTGGTGAATTTC 57.788 37.500 0.00 0.00 0.00 2.17
2024 9266 5.953548 TCTTGATGATTGATGGTGGTGAATT 59.046 36.000 0.00 0.00 0.00 2.17
2026 9268 4.920999 TCTTGATGATTGATGGTGGTGAA 58.079 39.130 0.00 0.00 0.00 3.18
2087 9329 3.933332 CCCAGGTTCGTACTTGAATTCTC 59.067 47.826 7.05 0.00 33.45 2.87
2246 9491 2.108514 CGGCGTCCTCGTGTACCTA 61.109 63.158 0.00 0.00 39.49 3.08
2266 9511 2.759973 TGATCGAGAAGGCCGGCT 60.760 61.111 28.56 7.30 0.00 5.52
2393 9638 4.644685 GTGGCAAATGTGTAGGGTGATATT 59.355 41.667 0.00 0.00 0.00 1.28
2399 9644 2.364002 GTTTGTGGCAAATGTGTAGGGT 59.636 45.455 0.00 0.00 0.00 4.34
2404 9649 4.576216 TTATCGTTTGTGGCAAATGTGT 57.424 36.364 11.90 6.67 0.00 3.72
2436 9681 3.543494 CGTTTGATTGTGCGATTCAATCC 59.457 43.478 17.97 7.92 45.88 3.01
2481 9745 4.202111 TGTGTTTCTCTGACAGAACGATCA 60.202 41.667 6.61 2.26 41.13 2.92
2514 9778 2.499197 TCGCTGTTGCAAAGGTAATGA 58.501 42.857 0.00 0.00 39.64 2.57
2575 9840 2.132686 ACTAAATGGGGCCTATTCCGT 58.867 47.619 16.07 12.42 0.00 4.69
2581 9846 2.199927 TGCCTACTAAATGGGGCCTA 57.800 50.000 0.84 0.00 43.50 3.93
2619 9884 1.376649 AAGGGAGAAGCTGGTGGAAT 58.623 50.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.