Multiple sequence alignment - TraesCS5A01G456500

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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 TraesCS5A01G456500 chr5A 100.000 2879 0 0 1 2879 636625791 636628669 0.000000e+00 5317
1 TraesCS5A01G456500 chr5A 94.726 474 25 0 1068 1541 559983035 559982562 0.000000e+00 737
2 TraesCS5A01G456500 chr5A 90.517 348 16 11 2005 2339 636636676 636637019 7.320000e-121 444
3 TraesCS5A01G456500 chr5A 84.548 343 37 5 1036 1377 328907304 328907631 2.770000e-85 326
4 TraesCS5A01G456500 chr5A 91.534 189 12 2 2488 2676 636637177 636637361 1.020000e-64 257
5 TraesCS5A01G456500 chr5B 90.925 2942 120 71 1 2879 639960189 639963046 0.000000e+00 3818
6 TraesCS5A01G456500 chr5B 89.201 889 55 23 2005 2877 639970323 639971186 0.000000e+00 1072
7 TraesCS5A01G456500 chr5B 86.047 129 11 3 1503 1631 639973237 639973358 6.470000e-27 132
8 TraesCS5A01G456500 chr5D 92.558 2123 68 39 183 2284 509424419 509426472 0.000000e+00 2963
9 TraesCS5A01G456500 chr5D 87.470 830 55 25 2005 2799 509439823 509440638 0.000000e+00 911
10 TraesCS5A01G456500 chr5D 93.069 606 29 8 2281 2879 509426552 509427151 0.000000e+00 874
11 TraesCS5A01G456500 chr5D 93.038 158 5 6 2728 2879 509434612 509434769 2.890000e-55 226
12 TraesCS5A01G456500 chr5D 90.625 128 4 4 1 127 509424298 509424418 2.300000e-36 163
13 TraesCS5A01G456500 chr5D 91.743 109 9 0 1036 1144 366056733 366056841 4.970000e-33 152
14 TraesCS5A01G456500 chr1A 94.937 474 24 0 1068 1541 574348099 574347626 0.000000e+00 743
15 TraesCS5A01G456500 chr7B 81.601 587 86 8 1002 1586 451329442 451330008 1.560000e-127 466
16 TraesCS5A01G456500 chr3A 91.935 310 25 0 1068 1377 470514729 470515038 4.410000e-118 435
17 TraesCS5A01G456500 chr4B 80.220 546 73 11 1042 1586 3955840 3956351 7.530000e-101 377
18 TraesCS5A01G456500 chr7A 85.079 315 24 11 1067 1374 158673336 158673038 1.680000e-77 300
19 TraesCS5A01G456500 chr3B 98.824 85 0 1 2333 2416 822215995 822215911 1.790000e-32 150


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 TraesCS5A01G456500 chr5A 636625791 636628669 2878 False 5317.000000 5317 100.0000 1 2879 1 chr5A.!!$F2 2878
1 TraesCS5A01G456500 chr5A 636636676 636637361 685 False 350.500000 444 91.0255 2005 2676 2 chr5A.!!$F3 671
2 TraesCS5A01G456500 chr5B 639960189 639963046 2857 False 3818.000000 3818 90.9250 1 2879 1 chr5B.!!$F1 2878
3 TraesCS5A01G456500 chr5B 639970323 639973358 3035 False 602.000000 1072 87.6240 1503 2877 2 chr5B.!!$F2 1374
4 TraesCS5A01G456500 chr5D 509424298 509427151 2853 False 1333.333333 2963 92.0840 1 2879 3 chr5D.!!$F4 2878
5 TraesCS5A01G456500 chr5D 509439823 509440638 815 False 911.000000 911 87.4700 2005 2799 1 chr5D.!!$F3 794
6 TraesCS5A01G456500 chr7B 451329442 451330008 566 False 466.000000 466 81.6010 1002 1586 1 chr7B.!!$F1 584
7 TraesCS5A01G456500 chr4B 3955840 3956351 511 False 377.000000 377 80.2200 1042 1586 1 chr4B.!!$F1 544

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
39 40 0.163788 GACAATTGTCTCCACGCACG 59.836 55.0 27.66 0.0 41.65 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2076 1.480954 TCCCATAGCACTCGGAAGAAC 59.519 52.381 0.0 0.0 41.32 3.01 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
39 40 0.163788 GACAATTGTCTCCACGCACG 59.836 55.000 27.66 0.00 41.65 5.34
40 41 1.154413 CAATTGTCTCCACGCACGC 60.154 57.895 0.00 0.00 0.00 5.34
55 56 0.460987 CACGCACCTCAGGAATCTCC 60.461 60.000 0.00 0.00 36.58 3.71
63 64 0.617535 TCAGGAATCTCCCGCCTCAA 60.618 55.000 0.00 0.00 37.19 3.02
67 68 0.179070 GAATCTCCCGCCTCAACCTC 60.179 60.000 0.00 0.00 0.00 3.85
68 69 1.627297 AATCTCCCGCCTCAACCTCC 61.627 60.000 0.00 0.00 0.00 4.30
69 70 2.537714 ATCTCCCGCCTCAACCTCCT 62.538 60.000 0.00 0.00 0.00 3.69
140 150 2.297315 CAGAAACTCCCCCTGCTTTTTC 59.703 50.000 0.00 0.00 0.00 2.29
141 151 1.618837 GAAACTCCCCCTGCTTTTTCC 59.381 52.381 0.00 0.00 0.00 3.13
143 153 0.860457 ACTCCCCCTGCTTTTTCCTT 59.140 50.000 0.00 0.00 0.00 3.36
145 155 1.620323 CTCCCCCTGCTTTTTCCTTTG 59.380 52.381 0.00 0.00 0.00 2.77
146 156 1.062505 TCCCCCTGCTTTTTCCTTTGT 60.063 47.619 0.00 0.00 0.00 2.83
147 157 1.768275 CCCCCTGCTTTTTCCTTTGTT 59.232 47.619 0.00 0.00 0.00 2.83
148 158 2.485302 CCCCCTGCTTTTTCCTTTGTTG 60.485 50.000 0.00 0.00 0.00 3.33
149 159 2.212652 CCCTGCTTTTTCCTTTGTTGC 58.787 47.619 0.00 0.00 0.00 4.17
150 160 2.158914 CCCTGCTTTTTCCTTTGTTGCT 60.159 45.455 0.00 0.00 0.00 3.91
151 161 2.867975 CCTGCTTTTTCCTTTGTTGCTG 59.132 45.455 0.00 0.00 0.00 4.41
152 162 3.524541 CTGCTTTTTCCTTTGTTGCTGT 58.475 40.909 0.00 0.00 0.00 4.40
153 163 3.520569 TGCTTTTTCCTTTGTTGCTGTC 58.479 40.909 0.00 0.00 0.00 3.51
154 164 3.195396 TGCTTTTTCCTTTGTTGCTGTCT 59.805 39.130 0.00 0.00 0.00 3.41
155 165 3.798878 GCTTTTTCCTTTGTTGCTGTCTC 59.201 43.478 0.00 0.00 0.00 3.36
156 166 4.677779 GCTTTTTCCTTTGTTGCTGTCTCA 60.678 41.667 0.00 0.00 0.00 3.27
157 167 5.398603 TTTTTCCTTTGTTGCTGTCTCAA 57.601 34.783 0.00 0.00 0.00 3.02
177 187 1.701847 AGTCTCAACAGCAATGTCCCT 59.298 47.619 0.00 0.00 0.00 4.20
178 188 2.079925 GTCTCAACAGCAATGTCCCTC 58.920 52.381 0.00 0.00 0.00 4.30
181 191 1.002134 AACAGCAATGTCCCTCCCG 60.002 57.895 0.00 0.00 0.00 5.14
186 196 1.991230 CAATGTCCCTCCCGACCTT 59.009 57.895 0.00 0.00 31.35 3.50
188 198 1.614241 AATGTCCCTCCCGACCTTCG 61.614 60.000 0.00 0.00 40.07 3.79
226 236 0.319211 TGTACTGTAGTGGCACGCAC 60.319 55.000 12.71 14.51 44.14 5.34
231 241 3.041351 TAGTGGCACGCACGCAAG 61.041 61.111 12.71 0.00 44.14 4.01
244 254 3.141038 GCAAGCGCGCAAGAAAAG 58.859 55.556 35.10 14.76 43.02 2.27
245 255 1.370414 GCAAGCGCGCAAGAAAAGA 60.370 52.632 35.10 0.00 43.02 2.52
272 282 0.967380 GGGCAATGGCAGCAGTTACT 60.967 55.000 9.51 0.00 43.71 2.24
274 284 1.401905 GGCAATGGCAGCAGTTACTAC 59.598 52.381 0.58 0.00 43.71 2.73
276 286 2.487762 GCAATGGCAGCAGTTACTACAA 59.512 45.455 0.00 0.00 40.72 2.41
277 287 3.129287 GCAATGGCAGCAGTTACTACAAT 59.871 43.478 0.00 0.00 40.72 2.71
279 289 2.710377 TGGCAGCAGTTACTACAATGG 58.290 47.619 0.00 0.00 0.00 3.16
280 290 1.401905 GGCAGCAGTTACTACAATGGC 59.598 52.381 0.00 0.00 0.00 4.40
305 345 2.252898 ACCTGCTCCTCCTCCTCCT 61.253 63.158 0.00 0.00 0.00 3.69
306 346 1.457455 CCTGCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 0.00 3.71
307 347 1.457455 CTGCTCCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
308 348 2.123033 GCTCCTCCTCCTCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
309 349 2.710826 GCTCCTCCTCCTCCTCCCT 61.711 68.421 0.00 0.00 0.00 4.20
310 350 1.541672 CTCCTCCTCCTCCTCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
311 351 2.015726 TCCTCCTCCTCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
312 352 2.197324 CTCCTCCTCCTCCCTCCG 59.803 72.222 0.00 0.00 0.00 4.63
313 353 2.617538 TCCTCCTCCTCCCTCCGT 60.618 66.667 0.00 0.00 0.00 4.69
314 354 2.123640 CCTCCTCCTCCCTCCGTC 60.124 72.222 0.00 0.00 0.00 4.79
315 355 2.695970 CCTCCTCCTCCCTCCGTCT 61.696 68.421 0.00 0.00 0.00 4.18
316 356 1.308326 CTCCTCCTCCCTCCGTCTT 59.692 63.158 0.00 0.00 0.00 3.01
317 357 0.753848 CTCCTCCTCCCTCCGTCTTC 60.754 65.000 0.00 0.00 0.00 2.87
318 358 1.758906 CCTCCTCCCTCCGTCTTCC 60.759 68.421 0.00 0.00 0.00 3.46
319 359 2.044252 TCCTCCCTCCGTCTTCCG 60.044 66.667 0.00 0.00 0.00 4.30
361 401 4.592192 ACAGTGAGCGCTGCGTGT 62.592 61.111 18.48 16.06 39.96 4.49
376 416 1.651132 GTGTCGTGCTGCGTTGTTG 60.651 57.895 0.00 0.00 42.13 3.33
406 446 1.069668 GCTGCCCCCATTGATTTGATC 59.930 52.381 0.00 0.00 0.00 2.92
442 482 2.645297 GTCTCCTTCCTTTCCTTTCCCT 59.355 50.000 0.00 0.00 0.00 4.20
443 483 3.074687 GTCTCCTTCCTTTCCTTTCCCTT 59.925 47.826 0.00 0.00 0.00 3.95
445 485 2.378886 TCCTTCCTTTCCTTTCCCTTCC 59.621 50.000 0.00 0.00 0.00 3.46
446 486 2.557676 CCTTCCTTTCCTTTCCCTTCCC 60.558 54.545 0.00 0.00 0.00 3.97
447 487 2.149521 TCCTTTCCTTTCCCTTCCCT 57.850 50.000 0.00 0.00 0.00 4.20
448 488 2.439265 TCCTTTCCTTTCCCTTCCCTT 58.561 47.619 0.00 0.00 0.00 3.95
449 489 2.378886 TCCTTTCCTTTCCCTTCCCTTC 59.621 50.000 0.00 0.00 0.00 3.46
450 490 2.557676 CCTTTCCTTTCCCTTCCCTTCC 60.558 54.545 0.00 0.00 0.00 3.46
451 491 1.081481 TTCCTTTCCCTTCCCTTCCC 58.919 55.000 0.00 0.00 0.00 3.97
538 594 3.522731 CTCGCTCCTCCCACCTCG 61.523 72.222 0.00 0.00 0.00 4.63
539 595 4.361971 TCGCTCCTCCCACCTCGT 62.362 66.667 0.00 0.00 0.00 4.18
541 597 3.462678 GCTCCTCCCACCTCGTCC 61.463 72.222 0.00 0.00 0.00 4.79
543 599 3.273654 TCCTCCCACCTCGTCCCT 61.274 66.667 0.00 0.00 0.00 4.20
544 600 2.760385 CCTCCCACCTCGTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
545 601 2.760385 CTCCCACCTCGTCCCTCC 60.760 72.222 0.00 0.00 0.00 4.30
546 602 4.393778 TCCCACCTCGTCCCTCCC 62.394 72.222 0.00 0.00 0.00 4.30
548 604 4.400251 CCACCTCGTCCCTCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
549 605 2.760385 CACCTCGTCCCTCCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
550 606 4.444081 ACCTCGTCCCTCCCCTCG 62.444 72.222 0.00 0.00 0.00 4.63
660 735 2.596851 GCTTGCTCCCCTCTCCACA 61.597 63.158 0.00 0.00 0.00 4.17
697 772 2.811317 CGGTGAAGGTGCGAGCTC 60.811 66.667 2.73 2.73 0.00 4.09
698 773 2.435059 GGTGAAGGTGCGAGCTCC 60.435 66.667 8.47 8.01 0.00 4.70
699 774 2.811317 GTGAAGGTGCGAGCTCCG 60.811 66.667 8.47 4.62 42.21 4.63
700 775 4.069232 TGAAGGTGCGAGCTCCGG 62.069 66.667 8.47 0.00 39.04 5.14
701 776 4.821589 GAAGGTGCGAGCTCCGGG 62.822 72.222 8.47 0.00 39.04 5.73
731 811 1.710339 GAGCTTGATTGCGGTCGAC 59.290 57.895 7.13 7.13 38.13 4.20
743 823 3.308705 GTCGACGGGGGTGAAGGT 61.309 66.667 0.00 0.00 0.00 3.50
854 944 1.227853 CCGGATCGACAAATCCCCC 60.228 63.158 0.00 0.00 41.98 5.40
1379 1499 2.249557 TTCTACGTCGCGCTGGTCTC 62.250 60.000 5.56 0.00 0.00 3.36
1596 1716 2.750350 CTCAAGGACCCGTGCCTT 59.250 61.111 0.00 0.00 46.36 4.35
1956 2076 3.732212 TGTTCCATTCAGTGTCTGTCTG 58.268 45.455 0.00 0.00 32.61 3.51
1978 2098 2.184533 TCTTCCGAGTGCTATGGGAAA 58.815 47.619 6.66 0.00 38.04 3.13
2047 2167 5.266242 GCCATCTTCATAAACGATGTGTTC 58.734 41.667 0.00 0.00 40.84 3.18
2118 2240 0.105709 CCCCTCCCCTGTGTTTTGTT 60.106 55.000 0.00 0.00 0.00 2.83
2258 2394 6.992063 ACAGTATTGTCTGATGATTGTTCC 57.008 37.500 0.65 0.00 38.63 3.62
2261 2397 3.805066 TTGTCTGATGATTGTTCCCCA 57.195 42.857 0.00 0.00 0.00 4.96
2262 2398 3.805066 TGTCTGATGATTGTTCCCCAA 57.195 42.857 0.00 0.00 37.49 4.12
2478 2711 2.898612 GAGGATCATGGAGCTCAGATGA 59.101 50.000 22.91 22.91 33.17 2.92
2616 2917 9.604626 CTCTTGCAGTACTTTTCTTATTTCTTG 57.395 33.333 0.00 0.00 0.00 3.02
2669 2970 2.230660 GTGGGTGCAGCTCTACTTTTT 58.769 47.619 16.65 0.00 0.00 1.94
2670 2971 3.408634 GTGGGTGCAGCTCTACTTTTTA 58.591 45.455 16.65 0.00 0.00 1.52
2676 2977 6.093404 GGTGCAGCTCTACTTTTTATTTTCC 58.907 40.000 9.07 0.00 0.00 3.13
2677 2978 6.093404 GTGCAGCTCTACTTTTTATTTTCCC 58.907 40.000 0.00 0.00 0.00 3.97
2727 3028 5.422145 CCACATCGGCTATGATGATCAATA 58.578 41.667 17.08 0.00 46.98 1.90
2770 3071 0.107456 CTGGACCACTTCAGCTGTGT 59.893 55.000 14.67 11.24 33.92 3.72
2772 3073 1.064758 TGGACCACTTCAGCTGTGTTT 60.065 47.619 14.67 3.74 33.92 2.83
2774 3075 2.223572 GGACCACTTCAGCTGTGTTTTG 60.224 50.000 14.67 5.22 33.92 2.44
2775 3076 2.682856 GACCACTTCAGCTGTGTTTTGA 59.317 45.455 14.67 0.00 33.92 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.460987 GGAGATTCCTGAGGTGCGTG 60.461 60.000 0.00 0.00 32.53 5.34
37 38 1.617947 GGGAGATTCCTGAGGTGCGT 61.618 60.000 0.00 0.00 36.57 5.24
38 39 1.144936 GGGAGATTCCTGAGGTGCG 59.855 63.158 0.00 0.00 36.57 5.34
39 40 1.144936 CGGGAGATTCCTGAGGTGC 59.855 63.158 0.00 0.00 45.95 5.01
40 41 1.144936 GCGGGAGATTCCTGAGGTG 59.855 63.158 8.11 0.00 45.95 4.00
55 56 0.462759 GAATGAGGAGGTTGAGGCGG 60.463 60.000 0.00 0.00 0.00 6.13
63 64 1.566298 GGTGGGCTGAATGAGGAGGT 61.566 60.000 0.00 0.00 0.00 3.85
67 68 0.533755 GATCGGTGGGCTGAATGAGG 60.534 60.000 0.00 0.00 33.10 3.86
68 69 0.533755 GGATCGGTGGGCTGAATGAG 60.534 60.000 0.00 0.00 33.10 2.90
69 70 1.271127 TGGATCGGTGGGCTGAATGA 61.271 55.000 0.00 0.00 33.10 2.57
115 125 0.106967 GCAGGGGGAGTTTCTGATCC 60.107 60.000 0.00 0.00 34.64 3.36
127 137 1.423584 ACAAAGGAAAAAGCAGGGGG 58.576 50.000 0.00 0.00 0.00 5.40
140 150 3.209410 AGACTTGAGACAGCAACAAAGG 58.791 45.455 0.00 0.00 0.00 3.11
141 151 3.873361 TGAGACTTGAGACAGCAACAAAG 59.127 43.478 0.00 0.00 0.00 2.77
143 153 3.541996 TGAGACTTGAGACAGCAACAA 57.458 42.857 0.00 0.00 0.00 2.83
145 155 3.198068 TGTTGAGACTTGAGACAGCAAC 58.802 45.455 0.00 0.00 35.85 4.17
146 156 3.461061 CTGTTGAGACTTGAGACAGCAA 58.539 45.455 0.00 0.00 32.36 3.91
147 157 3.103447 CTGTTGAGACTTGAGACAGCA 57.897 47.619 0.00 0.00 32.36 4.41
149 159 3.103447 TGCTGTTGAGACTTGAGACAG 57.897 47.619 0.00 0.00 40.40 3.51
150 160 3.541996 TTGCTGTTGAGACTTGAGACA 57.458 42.857 0.00 0.00 0.00 3.41
151 161 3.812053 ACATTGCTGTTGAGACTTGAGAC 59.188 43.478 0.00 0.00 28.70 3.36
152 162 4.060900 GACATTGCTGTTGAGACTTGAGA 58.939 43.478 0.00 0.00 35.14 3.27
153 163 3.188048 GGACATTGCTGTTGAGACTTGAG 59.812 47.826 0.00 0.00 35.14 3.02
154 164 3.141398 GGACATTGCTGTTGAGACTTGA 58.859 45.455 0.00 0.00 35.14 3.02
155 165 2.227388 GGGACATTGCTGTTGAGACTTG 59.773 50.000 0.00 0.00 35.14 3.16
156 166 2.107204 AGGGACATTGCTGTTGAGACTT 59.893 45.455 0.00 0.00 35.14 3.01
157 167 1.701847 AGGGACATTGCTGTTGAGACT 59.298 47.619 0.00 0.00 35.14 3.24
197 207 4.211374 GCCACTACAGTACAGTTTCAGTTG 59.789 45.833 0.00 0.00 0.00 3.16
231 241 0.502695 GGTTTTCTTTTCTTGCGCGC 59.497 50.000 27.26 27.26 0.00 6.86
232 242 1.833860 TGGTTTTCTTTTCTTGCGCG 58.166 45.000 0.00 0.00 0.00 6.86
234 244 3.059166 CCCATGGTTTTCTTTTCTTGCG 58.941 45.455 11.73 0.00 0.00 4.85
235 245 2.807967 GCCCATGGTTTTCTTTTCTTGC 59.192 45.455 11.73 0.00 0.00 4.01
236 246 4.070630 TGCCCATGGTTTTCTTTTCTTG 57.929 40.909 11.73 0.00 0.00 3.02
237 247 4.769345 TTGCCCATGGTTTTCTTTTCTT 57.231 36.364 11.73 0.00 0.00 2.52
238 248 4.644498 CATTGCCCATGGTTTTCTTTTCT 58.356 39.130 11.73 0.00 0.00 2.52
272 282 1.184431 CAGGTGCCATTGCCATTGTA 58.816 50.000 0.00 0.00 36.33 2.41
274 284 1.448893 GCAGGTGCCATTGCCATTG 60.449 57.895 0.00 0.00 36.33 2.82
276 286 2.038329 AGCAGGTGCCATTGCCAT 59.962 55.556 0.00 0.00 43.38 4.40
277 287 2.677524 GAGCAGGTGCCATTGCCA 60.678 61.111 0.00 0.00 43.38 4.92
279 289 2.362120 AGGAGCAGGTGCCATTGC 60.362 61.111 0.00 0.00 43.38 3.56
280 290 1.751927 GGAGGAGCAGGTGCCATTG 60.752 63.158 0.00 0.00 43.38 2.82
319 359 3.414700 CCAACTCACGCTCACGGC 61.415 66.667 0.00 0.00 46.04 5.68
364 404 0.179070 TACCAGACAACAACGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
366 406 1.148310 CCTACCAGACAACAACGCAG 58.852 55.000 0.00 0.00 0.00 5.18
376 416 3.798511 GGGGCAGCCCTACCAGAC 61.799 72.222 30.52 7.72 44.66 3.51
442 482 1.850755 GTGGTGAGGGGGAAGGGAA 60.851 63.158 0.00 0.00 0.00 3.97
443 483 2.204090 GTGGTGAGGGGGAAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
445 485 3.081554 CAGTGGTGAGGGGGAAGG 58.918 66.667 0.00 0.00 0.00 3.46
446 486 2.352805 GCAGTGGTGAGGGGGAAG 59.647 66.667 0.00 0.00 0.00 3.46
447 487 3.256960 GGCAGTGGTGAGGGGGAA 61.257 66.667 0.00 0.00 0.00 3.97
451 491 4.767255 GAGCGGCAGTGGTGAGGG 62.767 72.222 1.45 0.00 0.00 4.30
473 513 8.569641 CAAGAAGTGAGAACAAGTAGTAGTAGT 58.430 37.037 0.00 0.00 0.00 2.73
545 601 4.150454 AGAGGAGGGAGGCGAGGG 62.150 72.222 0.00 0.00 0.00 4.30
546 602 2.837291 CAGAGGAGGGAGGCGAGG 60.837 72.222 0.00 0.00 0.00 4.63
547 603 2.837291 CCAGAGGAGGGAGGCGAG 60.837 72.222 0.00 0.00 0.00 5.03
552 608 3.740495 TAGCGGCCAGAGGAGGGAG 62.740 68.421 2.24 0.00 0.00 4.30
553 609 3.740495 CTAGCGGCCAGAGGAGGGA 62.740 68.421 2.24 0.00 0.00 4.20
708 783 3.204827 CGCAATCAAGCTCGGGGG 61.205 66.667 0.00 0.00 0.00 5.40
709 784 3.204827 CCGCAATCAAGCTCGGGG 61.205 66.667 1.46 0.00 38.35 5.73
710 785 2.436646 ACCGCAATCAAGCTCGGG 60.437 61.111 13.18 0.00 45.58 5.14
711 786 2.802667 CGACCGCAATCAAGCTCGG 61.803 63.158 7.66 7.66 46.61 4.63
731 811 2.351276 CTTCCACCTTCACCCCCG 59.649 66.667 0.00 0.00 0.00 5.73
743 823 3.272364 ATCCGGCAGCAAGCTTCCA 62.272 57.895 11.17 0.00 44.79 3.53
1053 1147 4.504916 CTGCTGGAGGAGGACGCG 62.505 72.222 3.53 3.53 0.00 6.01
1357 1477 2.202492 CAGCGCGACGTAGAAGCT 60.202 61.111 12.10 11.86 38.90 3.74
1596 1716 3.695816 CTTCTTGTCGATGCGTATCTCA 58.304 45.455 11.83 7.84 0.00 3.27
1919 2039 3.072330 TGGAACATCTTGTTAGCACTGGA 59.928 43.478 0.00 0.00 41.28 3.86
1956 2076 1.480954 TCCCATAGCACTCGGAAGAAC 59.519 52.381 0.00 0.00 41.32 3.01
2006 2126 3.147629 TGGCGAAACCGAAAAGGAATAA 58.852 40.909 0.00 0.00 45.00 1.40
2047 2167 1.879380 TGGAACTTGCCAGACAATTCG 59.121 47.619 0.00 0.00 37.72 3.34
2118 2240 3.437213 TGGAACCGATCTCACTTAAGGA 58.563 45.455 7.53 0.65 0.00 3.36
2227 2363 9.547753 AATCATCAGACAATACTGTTACCATAC 57.452 33.333 0.00 0.00 38.79 2.39
2258 2394 4.025360 TGATCATCAGGGAACAAATTGGG 58.975 43.478 0.00 0.00 0.00 4.12
2496 2771 5.075858 ACCAAATTGCACAGAATATGGTG 57.924 39.130 0.00 0.00 38.44 4.17
2616 2917 2.096496 GCCACACAATGCAGATGACTAC 59.904 50.000 9.10 0.00 0.00 2.73
2669 2970 5.572885 GCAACCTCCTCACTTAGGGAAAATA 60.573 44.000 0.00 0.00 46.55 1.40
2670 2971 4.811063 GCAACCTCCTCACTTAGGGAAAAT 60.811 45.833 0.00 0.00 46.55 1.82
2677 2978 3.686726 GTCAATGCAACCTCCTCACTTAG 59.313 47.826 0.00 0.00 0.00 2.18
2727 3028 1.745653 GCGGAAAGGCTGCTTAATTCT 59.254 47.619 0.00 0.00 45.70 2.40


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

AutoCloner maintained by Alex Coulton.