Multiple sequence alignment - TraesCS4B01G362400

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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 TraesCS4B01G362400 chr4B 100.000 2489 0 0 1 2489 651734240 651736728 0.000000e+00 4597
1 TraesCS4B01G362400 chr4B 90.192 2498 206 30 4 2489 131332847 131330377 0.000000e+00 3219
2 TraesCS4B01G362400 chr5B 88.599 2526 227 36 1 2489 575801390 575803891 0.000000e+00 3013
3 TraesCS4B01G362400 chr5B 88.680 2500 220 34 4 2489 192372348 192369898 0.000000e+00 2990
4 TraesCS4B01G362400 chr5B 88.160 2500 229 41 7 2489 69065297 69062848 0.000000e+00 2915
5 TraesCS4B01G362400 chr4A 86.863 2512 275 43 4 2489 500424074 500421592 0.000000e+00 2760
6 TraesCS4B01G362400 chr7B 88.088 2359 226 38 4 2341 220107752 220105428 0.000000e+00 2748
7 TraesCS4B01G362400 chr2D 88.342 2316 225 33 1 2294 412482554 412484846 0.000000e+00 2739
8 TraesCS4B01G362400 chr6D 86.725 2516 270 45 6 2489 347424746 347427229 0.000000e+00 2737
9 TraesCS4B01G362400 chr7D 86.117 2521 282 48 1 2489 535917335 535919819 0.000000e+00 2654
10 TraesCS4B01G362400 chr6B 88.556 367 35 6 2124 2489 670220935 670220575 2.940000e-119 438


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 TraesCS4B01G362400 chr4B 651734240 651736728 2488 False 4597 4597 100.000 1 2489 1 chr4B.!!$F1 2488
1 TraesCS4B01G362400 chr4B 131330377 131332847 2470 True 3219 3219 90.192 4 2489 1 chr4B.!!$R1 2485
2 TraesCS4B01G362400 chr5B 575801390 575803891 2501 False 3013 3013 88.599 1 2489 1 chr5B.!!$F1 2488
3 TraesCS4B01G362400 chr5B 192369898 192372348 2450 True 2990 2990 88.680 4 2489 1 chr5B.!!$R2 2485
4 TraesCS4B01G362400 chr5B 69062848 69065297 2449 True 2915 2915 88.160 7 2489 1 chr5B.!!$R1 2482
5 TraesCS4B01G362400 chr4A 500421592 500424074 2482 True 2760 2760 86.863 4 2489 1 chr4A.!!$R1 2485
6 TraesCS4B01G362400 chr7B 220105428 220107752 2324 True 2748 2748 88.088 4 2341 1 chr7B.!!$R1 2337
7 TraesCS4B01G362400 chr2D 412482554 412484846 2292 False 2739 2739 88.342 1 2294 1 chr2D.!!$F1 2293
8 TraesCS4B01G362400 chr6D 347424746 347427229 2483 False 2737 2737 86.725 6 2489 1 chr6D.!!$F1 2483
9 TraesCS4B01G362400 chr7D 535917335 535919819 2484 False 2654 2654 86.117 1 2489 1 chr7D.!!$F1 2488

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
708 731 0.097674 GGCAATAGCTGTCGTGCAAG 59.902 55.0 9.06 0.0 41.7 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1829 0.60478 GCATGTCTGCTGTCACACCT 60.605 55.0 0.0 0.0 45.32 4.0 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
50 51 1.406887 GGTAGTTCACGCACCATCCAT 60.407 52.381 0.00 0.00 32.32 3.41
196 199 5.243730 CCACACCACATAACCTCTCATTTTT 59.756 40.000 0.00 0.00 0.00 1.94
240 245 9.614792 GTTCCTCCTTTTGCTATTTCTAGATAA 57.385 33.333 0.00 0.00 0.00 1.75
263 268 9.937175 ATAAGCTCTATTTGCGTTTTATTTCTC 57.063 29.630 0.00 0.00 35.28 2.87
352 358 2.945008 CCAAGGTCATACAATGCGATGT 59.055 45.455 0.00 0.00 37.32 3.06
386 392 0.321564 TGGGTGATCTTGCCAAGTCG 60.322 55.000 4.04 0.00 0.00 4.18
430 436 3.398406 TGACGAATGTAGTTGCATGTGT 58.602 40.909 0.00 0.00 0.00 3.72
483 489 5.695851 GTCTCCTGACAAAACAATCATGT 57.304 39.130 0.00 0.00 42.48 3.21
495 506 3.942829 ACAATCATGTAGTGTGACCTGG 58.057 45.455 0.00 0.00 38.24 4.45
504 515 6.121776 TGTAGTGTGACCTGGAAAATATGT 57.878 37.500 0.00 0.00 0.00 2.29
560 572 2.730006 TTTGCGCGCATGGTGACTTG 62.730 55.000 36.83 0.00 38.46 3.16
570 582 2.936919 TGGTGACTTGAAGCTCACAT 57.063 45.000 20.93 0.00 38.89 3.21
575 587 4.036734 GGTGACTTGAAGCTCACATTGAAA 59.963 41.667 20.93 0.00 38.89 2.69
576 588 5.450412 GGTGACTTGAAGCTCACATTGAAAA 60.450 40.000 20.93 0.00 38.89 2.29
577 589 6.035843 GTGACTTGAAGCTCACATTGAAAAA 58.964 36.000 17.15 0.00 37.36 1.94
621 637 4.703379 TTTGCACATTTTTCCTCCCATT 57.297 36.364 0.00 0.00 0.00 3.16
634 653 4.815269 TCCTCCCATTTTATGTTTTTGCG 58.185 39.130 0.00 0.00 0.00 4.85
639 658 6.982852 TCCCATTTTATGTTTTTGCGAGTAA 58.017 32.000 0.00 0.00 0.00 2.24
640 659 7.434492 TCCCATTTTATGTTTTTGCGAGTAAA 58.566 30.769 0.00 0.00 0.00 2.01
652 671 5.469373 TTGCGAGTAAATATGCTTCACAG 57.531 39.130 0.00 0.00 0.00 3.66
656 675 5.109210 CGAGTAAATATGCTTCACAGGTGA 58.891 41.667 0.00 0.00 37.91 4.02
677 699 7.133891 GTGAGCTACACTATTTTTGTGACAT 57.866 36.000 8.50 0.00 45.13 3.06
678 700 8.251750 GTGAGCTACACTATTTTTGTGACATA 57.748 34.615 8.50 0.00 45.13 2.29
680 702 9.448438 TGAGCTACACTATTTTTGTGACATATT 57.552 29.630 0.00 0.00 38.65 1.28
694 717 6.699366 TGTGACATATTTTTCATGTGGCAAT 58.301 32.000 0.00 0.00 36.76 3.56
700 723 4.870123 TTTTTCATGTGGCAATAGCTGT 57.130 36.364 0.00 0.00 41.70 4.40
705 728 1.298157 TGTGGCAATAGCTGTCGTGC 61.298 55.000 0.00 0.00 41.70 5.34
708 731 0.097674 GGCAATAGCTGTCGTGCAAG 59.902 55.000 9.06 0.00 41.70 4.01
711 734 2.270923 CAATAGCTGTCGTGCAAGCTA 58.729 47.619 17.75 17.75 42.92 3.32
713 736 2.672961 TAGCTGTCGTGCAAGCTAAT 57.327 45.000 14.07 0.00 37.00 1.73
742 766 9.558396 TTTGATTTTTGCTTCCTCATACAAAAT 57.442 25.926 0.00 0.00 40.53 1.82
744 768 8.991026 TGATTTTTGCTTCCTCATACAAAATTG 58.009 29.630 0.00 0.00 40.53 2.32
756 780 7.043961 TCATACAAAATTGTGTGGCAACTTA 57.956 32.000 18.82 0.34 46.31 2.24
766 790 7.583860 TTGTGTGGCAACTTAAAACTAAAAC 57.416 32.000 0.00 0.00 37.61 2.43
804 828 4.454678 TCATACATGGATGGCAACTTCTC 58.545 43.478 18.06 0.00 40.47 2.87
811 835 5.902613 TGGATGGCAACTTCTCTTAATTG 57.097 39.130 0.00 0.00 40.47 2.32
913 940 4.134563 GCAACCGGTGATATCCTTACATT 58.865 43.478 8.52 0.00 0.00 2.71
916 943 4.628074 ACCGGTGATATCCTTACATTTCG 58.372 43.478 6.12 0.00 0.00 3.46
932 959 9.418045 CTTACATTTCGTTTTTCCCAATTACAT 57.582 29.630 0.00 0.00 0.00 2.29
963 990 5.610398 TGTTCTTCATGTGAACTCTGCTTA 58.390 37.500 23.68 8.77 42.86 3.09
993 1025 5.833131 TCCTTCATTTTACTTGCAGGTCTTT 59.167 36.000 4.04 0.00 30.59 2.52
1030 1063 1.821759 CTTGCACCACACGACCCAA 60.822 57.895 0.00 0.00 0.00 4.12
1106 1139 2.516906 TGAGGTGCTTGATTCAATGCA 58.483 42.857 15.15 15.15 0.00 3.96
1114 1147 4.142116 TGCTTGATTCAATGCATTCGGAAT 60.142 37.500 19.52 19.52 32.97 3.01
1116 1149 4.572985 TGATTCAATGCATTCGGAATCC 57.427 40.909 30.47 20.66 43.00 3.01
1117 1150 3.952967 TGATTCAATGCATTCGGAATCCA 59.047 39.130 30.47 22.07 43.00 3.41
1120 1153 6.264970 TGATTCAATGCATTCGGAATCCAATA 59.735 34.615 30.47 19.11 43.00 1.90
1121 1154 5.694231 TCAATGCATTCGGAATCCAATAG 57.306 39.130 9.53 0.00 0.00 1.73
1205 1238 6.148480 CACTATGAAAACTCAAAGGTCCAGAG 59.852 42.308 0.00 0.00 35.56 3.35
1227 1260 6.888632 AGAGCAGACATTTTCCAATTGAGTAT 59.111 34.615 7.12 0.00 0.00 2.12
1236 1269 2.027653 TCCAATTGAGTATGTGGCGACA 60.028 45.455 7.12 3.31 36.22 4.35
1262 1295 2.486592 AGCAAGGAAACCGGTATTTTCG 59.513 45.455 8.00 0.00 34.34 3.46
1275 1310 5.028375 CGGTATTTTCGCATCTTTTCTTCC 58.972 41.667 0.00 0.00 0.00 3.46
1304 1339 1.271871 CCACACCAATGCTAACCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
1334 1379 9.565213 CACCTCTGAATTGAAGTTTATGATTTC 57.435 33.333 0.00 0.00 0.00 2.17
1376 1423 6.038603 TGAGTTCACCTGATTCTTTTCTTGTG 59.961 38.462 0.00 0.00 0.00 3.33
1386 1433 2.555325 TCTTTTCTTGTGCAGGCATGAG 59.445 45.455 0.62 0.00 0.00 2.90
1419 1466 3.381908 ACACGTTGGAATACCTTGCAAAA 59.618 39.130 0.00 0.00 43.21 2.44
1434 1481 2.039216 TGCAAAATGGGAAGGTAGACGA 59.961 45.455 0.00 0.00 0.00 4.20
1439 1486 2.297698 TGGGAAGGTAGACGAGTTCA 57.702 50.000 0.00 0.00 0.00 3.18
1461 1508 2.009774 GTCGTCATAGCTGCAATGGTT 58.990 47.619 1.02 0.00 0.00 3.67
1473 1520 1.238439 CAATGGTTGTTGAGCTCCGT 58.762 50.000 12.15 0.00 0.00 4.69
1486 1534 6.205853 TGTTGAGCTCCGTAAAATTACACATT 59.794 34.615 12.15 0.00 33.28 2.71
1517 1565 6.038161 AGTTGACGAATGAAGATTTCAACACA 59.962 34.615 13.17 0.00 43.95 3.72
1535 1583 2.962786 CGGTCCAACGCACGTGAA 60.963 61.111 22.23 0.00 0.00 3.18
1603 1651 0.390603 CGTGGTGCTCCATACCGAAA 60.391 55.000 11.31 0.00 46.20 3.46
1642 1690 3.746045 TGCCGAGGAATGTAAGGTATC 57.254 47.619 0.00 0.00 0.00 2.24
1702 1750 0.459899 ATGACTGCATCTCCGCGTAA 59.540 50.000 4.92 0.00 33.35 3.18
1746 1794 6.425417 TGTGTGAGCGACATTTGAATAGTTTA 59.575 34.615 0.00 0.00 36.78 2.01
1777 1828 5.726980 ATGTGTGCATGTGAACCTATTTT 57.273 34.783 0.00 0.00 33.37 1.82
1778 1829 6.832520 ATGTGTGCATGTGAACCTATTTTA 57.167 33.333 0.00 0.00 33.37 1.52
1793 1844 4.631813 CCTATTTTAGGTGTGACAGCAGAC 59.368 45.833 17.69 0.00 41.18 3.51
1868 1922 1.717645 GTGTTTCGAATGCGTCTACGT 59.282 47.619 0.00 0.00 42.22 3.57
1870 1924 2.796031 TGTTTCGAATGCGTCTACGTTT 59.204 40.909 0.00 0.00 42.22 3.60
1909 1963 4.022935 GGCAAATGAAGTTCATCAGACACA 60.023 41.667 18.52 0.00 35.76 3.72
1911 1965 5.152097 CAAATGAAGTTCATCAGACACAGC 58.848 41.667 18.52 0.00 35.76 4.40
2020 2075 2.545106 CGTAGCCGTAACCTTTTTGTGT 59.455 45.455 0.00 0.00 0.00 3.72
2030 2085 2.289320 ACCTTTTTGTGTTTGCTGCACA 60.289 40.909 0.00 0.00 44.05 4.57
2056 2112 6.553100 TGACCTTTTCAACTTGTTTCCCATAT 59.447 34.615 0.00 0.00 0.00 1.78
2059 2115 7.714813 ACCTTTTCAACTTGTTTCCCATATTTG 59.285 33.333 0.00 0.00 0.00 2.32
2121 2179 2.665649 ACGGAAATCTACGTGATGCA 57.334 45.000 0.00 0.00 42.39 3.96
2122 2180 2.540515 ACGGAAATCTACGTGATGCAG 58.459 47.619 0.00 0.09 42.39 4.41
2123 2181 2.094182 ACGGAAATCTACGTGATGCAGT 60.094 45.455 0.00 0.65 42.39 4.40
2124 2182 2.535984 CGGAAATCTACGTGATGCAGTC 59.464 50.000 0.00 0.00 35.21 3.51
2125 2183 3.521560 GGAAATCTACGTGATGCAGTCA 58.478 45.455 0.00 0.00 35.21 3.41
2126 2184 4.122776 GGAAATCTACGTGATGCAGTCAT 58.877 43.478 0.00 0.00 39.48 3.06
2127 2185 4.572389 GGAAATCTACGTGATGCAGTCATT 59.428 41.667 0.00 0.00 39.48 2.57
2128 2186 5.753438 GGAAATCTACGTGATGCAGTCATTA 59.247 40.000 0.00 0.00 39.48 1.90
2129 2187 6.292381 GGAAATCTACGTGATGCAGTCATTAC 60.292 42.308 0.00 0.00 39.48 1.89
2130 2188 4.712122 TCTACGTGATGCAGTCATTACA 57.288 40.909 0.00 0.00 38.63 2.41
2131 2189 5.066968 TCTACGTGATGCAGTCATTACAA 57.933 39.130 0.00 0.00 38.63 2.41
2132 2190 5.474825 TCTACGTGATGCAGTCATTACAAA 58.525 37.500 0.00 0.00 38.63 2.83
2133 2191 6.106003 TCTACGTGATGCAGTCATTACAAAT 58.894 36.000 0.00 0.00 38.63 2.32
2134 2192 7.262048 TCTACGTGATGCAGTCATTACAAATA 58.738 34.615 0.00 0.00 38.63 1.40
2135 2193 6.735678 ACGTGATGCAGTCATTACAAATAA 57.264 33.333 0.00 0.00 38.63 1.40
2136 2194 6.542852 ACGTGATGCAGTCATTACAAATAAC 58.457 36.000 0.00 0.00 38.63 1.89
2137 2195 6.148645 ACGTGATGCAGTCATTACAAATAACA 59.851 34.615 0.00 0.00 38.63 2.41
2138 2196 7.148255 ACGTGATGCAGTCATTACAAATAACAT 60.148 33.333 0.00 0.00 38.63 2.71
2139 2197 7.164662 CGTGATGCAGTCATTACAAATAACATG 59.835 37.037 0.00 0.00 38.63 3.21
2185 2266 9.710900 CATGGCATATTCAGTAGAACTAACATA 57.289 33.333 0.00 0.00 36.39 2.29
2201 2352 8.934507 AACTAACATAGCAGATTCAGTAGAAC 57.065 34.615 0.00 0.00 36.39 3.01
2223 2374 5.911752 ACTAACATGGCAGATTCAGTAGAG 58.088 41.667 0.00 0.00 0.00 2.43
2247 2398 7.215789 AGAATAACATGGCAGATTCAGTAGAG 58.784 38.462 13.38 0.00 31.92 2.43
2266 2417 7.496920 CAGTAGAGAATAACATGGCAGATTCAA 59.503 37.037 13.38 1.22 31.92 2.69
2271 2422 8.618702 AGAATAACATGGCAGATTCAATAGAG 57.381 34.615 13.38 0.00 31.92 2.43
2306 2458 8.682710 GGCAGATTTAGTACAAAATAACATGGA 58.317 33.333 0.00 0.00 0.00 3.41
2333 2508 9.331282 AGATTTAGTAGAGAATAACATGGCAAC 57.669 33.333 0.00 0.00 0.00 4.17
2351 2526 4.328169 GGCAACTTAAGTACCATACACGTC 59.672 45.833 18.35 0.00 0.00 4.34
2425 2602 6.886459 CCTCAAGAGTCATTCTCCCATTTTAA 59.114 38.462 0.00 0.00 43.71 1.52
2486 2666 2.470990 AGGACCATGTCATAGTGCTCA 58.529 47.619 0.00 0.00 33.68 4.26
2488 2668 3.457380 AGGACCATGTCATAGTGCTCAAT 59.543 43.478 0.00 0.00 33.68 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.911525 CCTCACAGATCCAGGGGTGT 60.912 60.000 0.00 0.00 33.17 4.16
50 51 2.766263 ACTTCTGGCTCGTAATCATCCA 59.234 45.455 0.00 0.00 0.00 3.41
166 167 2.159382 GGTTATGTGGTGTGGTCCTTG 58.841 52.381 0.00 0.00 0.00 3.61
169 170 1.628846 AGAGGTTATGTGGTGTGGTCC 59.371 52.381 0.00 0.00 0.00 4.46
196 199 6.072342 GGAGGAACGGTAAAAAGAGCAAATAA 60.072 38.462 0.00 0.00 0.00 1.40
197 200 5.413523 GGAGGAACGGTAAAAAGAGCAAATA 59.586 40.000 0.00 0.00 0.00 1.40
198 201 4.217767 GGAGGAACGGTAAAAAGAGCAAAT 59.782 41.667 0.00 0.00 0.00 2.32
214 218 9.614792 TTATCTAGAAATAGCAAAAGGAGGAAC 57.385 33.333 0.00 0.00 0.00 3.62
240 245 7.617041 AGAGAAATAAAACGCAAATAGAGCT 57.383 32.000 0.00 0.00 0.00 4.09
298 304 7.222031 CCAAACATGAGCTGTATGAAAATGATG 59.778 37.037 13.05 0.00 36.98 3.07
352 358 2.327343 CCCAGGTCGACGTACGTCA 61.327 63.158 38.60 26.24 44.77 4.35
386 392 0.035739 TTTTACCGAGTGGCCTCACC 59.964 55.000 3.32 0.00 44.64 4.02
467 473 6.238621 GGTCACACTACATGATTGTTTTGTCA 60.239 38.462 0.00 0.00 37.28 3.58
483 489 6.367374 TCACATATTTTCCAGGTCACACTA 57.633 37.500 0.00 0.00 0.00 2.74
495 506 6.555315 GTGGAAGTCACCATCACATATTTTC 58.445 40.000 0.00 0.00 42.17 2.29
575 587 3.916989 AGGAAGGAGTACTCACCCATTTT 59.083 43.478 23.91 6.56 0.00 1.82
576 588 3.532102 AGGAAGGAGTACTCACCCATTT 58.468 45.455 23.91 8.15 0.00 2.32
577 589 3.207044 AGGAAGGAGTACTCACCCATT 57.793 47.619 23.91 10.10 0.00 3.16
621 637 9.632807 AAGCATATTTACTCGCAAAAACATAAA 57.367 25.926 0.00 0.00 0.00 1.40
634 653 5.007136 GCTCACCTGTGAAGCATATTTACTC 59.993 44.000 13.30 0.00 39.39 2.59
639 658 3.641434 AGCTCACCTGTGAAGCATATT 57.359 42.857 17.69 2.13 39.39 1.28
640 659 3.452264 TGTAGCTCACCTGTGAAGCATAT 59.548 43.478 17.69 6.12 39.39 1.78
665 684 8.505625 GCCACATGAAAAATATGTCACAAAAAT 58.494 29.630 0.00 0.00 36.67 1.82
677 699 6.528537 ACAGCTATTGCCACATGAAAAATA 57.471 33.333 0.00 0.00 40.80 1.40
678 700 5.410355 ACAGCTATTGCCACATGAAAAAT 57.590 34.783 0.00 0.00 40.80 1.82
680 702 3.119884 CGACAGCTATTGCCACATGAAAA 60.120 43.478 0.00 0.00 40.80 2.29
694 717 2.672961 ATTAGCTTGCACGACAGCTA 57.327 45.000 12.74 12.74 35.35 3.32
718 741 8.991026 CAATTTTGTATGAGGAAGCAAAAATCA 58.009 29.630 0.00 0.00 41.89 2.57
719 742 8.992073 ACAATTTTGTATGAGGAAGCAAAAATC 58.008 29.630 0.00 0.00 41.89 2.17
720 743 8.776470 CACAATTTTGTATGAGGAAGCAAAAAT 58.224 29.630 0.00 0.00 41.89 1.82
721 744 7.768120 ACACAATTTTGTATGAGGAAGCAAAAA 59.232 29.630 0.00 0.00 41.89 1.94
722 745 7.224362 CACACAATTTTGTATGAGGAAGCAAAA 59.776 33.333 0.00 0.00 37.79 2.44
738 762 8.779354 TTAGTTTTAAGTTGCCACACAATTTT 57.221 26.923 0.00 0.00 41.27 1.82
742 766 7.116519 GTGTTTTAGTTTTAAGTTGCCACACAA 59.883 33.333 0.00 0.00 35.33 3.33
744 768 6.586844 TGTGTTTTAGTTTTAAGTTGCCACAC 59.413 34.615 0.00 0.00 0.00 3.82
756 780 5.414789 AAGTTGCCCTGTGTTTTAGTTTT 57.585 34.783 0.00 0.00 0.00 2.43
766 790 3.317711 TGTATGAACAAAGTTGCCCTGTG 59.682 43.478 0.00 0.00 34.25 3.66
858 883 3.125829 ACATGAGTGACATAAAAGCAGCG 59.874 43.478 0.00 0.00 37.46 5.18
913 940 8.894768 AAAATGATGTAATTGGGAAAAACGAA 57.105 26.923 0.00 0.00 0.00 3.85
916 943 9.271828 ACAGAAAATGATGTAATTGGGAAAAAC 57.728 29.630 0.00 0.00 0.00 2.43
932 959 7.500227 AGAGTTCACATGAAGAACAGAAAATGA 59.500 33.333 25.92 4.65 45.93 2.57
963 990 7.015584 ACCTGCAAGTAAAATGAAGGAAAGAAT 59.984 33.333 7.55 0.00 45.29 2.40
993 1025 0.039618 GCTCCTGGAACATGGGGAAA 59.960 55.000 0.00 0.00 38.20 3.13
1030 1063 2.727123 TGGTGACCACACTTGTCATT 57.273 45.000 0.00 0.00 43.98 2.57
1106 1139 5.896073 AAGGTCTCTATTGGATTCCGAAT 57.104 39.130 0.00 0.00 0.00 3.34
1114 1147 6.183360 GCATGTGTAGTAAGGTCTCTATTGGA 60.183 42.308 0.00 0.00 0.00 3.53
1116 1149 6.699204 CAGCATGTGTAGTAAGGTCTCTATTG 59.301 42.308 0.00 0.00 0.00 1.90
1117 1150 6.607600 TCAGCATGTGTAGTAAGGTCTCTATT 59.392 38.462 0.00 0.00 37.40 1.73
1120 1153 4.344978 TCAGCATGTGTAGTAAGGTCTCT 58.655 43.478 0.00 0.00 37.40 3.10
1121 1154 4.720649 TCAGCATGTGTAGTAAGGTCTC 57.279 45.455 0.00 0.00 37.40 3.36
1205 1238 6.529125 CACATACTCAATTGGAAAATGTCTGC 59.471 38.462 5.42 0.00 31.81 4.26
1227 1260 0.100325 CTTGCTTTGTTGTCGCCACA 59.900 50.000 0.00 0.00 0.00 4.17
1236 1269 1.480789 ACCGGTTTCCTTGCTTTGTT 58.519 45.000 0.00 0.00 0.00 2.83
1262 1295 3.416156 AGGACACAGGAAGAAAAGATGC 58.584 45.455 0.00 0.00 0.00 3.91
1304 1339 7.884877 TCATAAACTTCAATTCAGAGGTGACAT 59.115 33.333 0.00 0.00 30.10 3.06
1334 1379 6.909357 GTGAACTCACAAAAGAACAGAATGAG 59.091 38.462 4.96 0.00 45.75 2.90
1376 1423 1.530013 AAAGCCACACTCATGCCTGC 61.530 55.000 0.00 0.00 0.00 4.85
1419 1466 2.816411 TGAACTCGTCTACCTTCCCAT 58.184 47.619 0.00 0.00 0.00 4.00
1434 1481 2.094026 TGCAGCTATGACGACATGAACT 60.094 45.455 10.69 2.44 37.87 3.01
1439 1486 2.216046 CCATTGCAGCTATGACGACAT 58.784 47.619 17.36 5.56 40.16 3.06
1448 1495 1.541147 GCTCAACAACCATTGCAGCTA 59.459 47.619 0.00 0.00 33.57 3.32
1461 1508 5.057819 TGTGTAATTTTACGGAGCTCAACA 58.942 37.500 17.19 2.50 36.45 3.33
1486 1534 7.655732 TGAAATCTTCATTCGTCAACTAGTTCA 59.344 33.333 4.77 0.00 34.08 3.18
1517 1565 2.981977 ATTCACGTGCGTTGGACCGT 62.982 55.000 11.67 0.00 0.00 4.83
1535 1583 8.160106 ACTTTCTTGACAACTTCCTCTATGAAT 58.840 33.333 0.00 0.00 0.00 2.57
1603 1651 4.503296 CGGCAATAGAATGTAAGGTAGCCT 60.503 45.833 0.00 0.00 36.33 4.58
1605 1653 4.628074 TCGGCAATAGAATGTAAGGTAGC 58.372 43.478 0.00 0.00 0.00 3.58
1620 1668 4.102524 TGATACCTTACATTCCTCGGCAAT 59.897 41.667 0.00 0.00 0.00 3.56
1642 1690 9.150348 ACATAGTTTTGAAAAGAACAAAAGGTG 57.850 29.630 0.00 0.00 44.21 4.00
1646 1694 9.883142 ATGGACATAGTTTTGAAAAGAACAAAA 57.117 25.926 0.00 0.00 42.37 2.44
1702 1750 3.767673 CACACCACCACTACATACTAGGT 59.232 47.826 0.00 0.00 0.00 3.08
1746 1794 7.720957 AGGTTCACATGCACACATATATTACAT 59.279 33.333 0.00 0.00 33.67 2.29
1777 1828 1.338105 GCATGTCTGCTGTCACACCTA 60.338 52.381 0.00 0.00 45.32 3.08
1778 1829 0.604780 GCATGTCTGCTGTCACACCT 60.605 55.000 0.00 0.00 45.32 4.00
1846 1900 2.063266 GTAGACGCATTCGAAACACCA 58.937 47.619 0.00 0.00 39.41 4.17
1878 1932 6.766944 TGATGAACTTCATTTGCCATGTTTTT 59.233 30.769 5.73 0.00 37.20 1.94
1894 1948 4.281941 TCACTAGCTGTGTCTGATGAACTT 59.718 41.667 13.59 0.00 46.27 2.66
1909 1963 9.771534 GAAAAAGGATGATAACTATCACTAGCT 57.228 33.333 1.53 0.00 44.66 3.32
2020 2075 2.429971 TGAAAAGGTCATGTGCAGCAAA 59.570 40.909 0.00 0.00 0.00 3.68
2030 2085 4.714308 TGGGAAACAAGTTGAAAAGGTCAT 59.286 37.500 10.54 0.00 35.70 3.06
2119 2177 5.649557 TGCCATGTTATTTGTAATGACTGC 58.350 37.500 0.00 0.00 0.00 4.40
2120 2178 7.087409 TCTGCCATGTTATTTGTAATGACTG 57.913 36.000 0.00 0.00 0.00 3.51
2121 2179 7.886629 ATCTGCCATGTTATTTGTAATGACT 57.113 32.000 0.00 0.00 0.00 3.41
2122 2180 8.190122 TGAATCTGCCATGTTATTTGTAATGAC 58.810 33.333 0.00 0.00 0.00 3.06
2123 2181 8.291191 TGAATCTGCCATGTTATTTGTAATGA 57.709 30.769 0.00 0.00 0.00 2.57
2124 2182 8.192774 ACTGAATCTGCCATGTTATTTGTAATG 58.807 33.333 0.00 0.00 0.00 1.90
2125 2183 8.297470 ACTGAATCTGCCATGTTATTTGTAAT 57.703 30.769 0.00 0.00 0.00 1.89
2126 2184 7.701539 ACTGAATCTGCCATGTTATTTGTAA 57.298 32.000 0.00 0.00 0.00 2.41
2127 2185 7.826744 TGTACTGAATCTGCCATGTTATTTGTA 59.173 33.333 0.00 0.00 0.00 2.41
2128 2186 6.658816 TGTACTGAATCTGCCATGTTATTTGT 59.341 34.615 0.00 0.00 0.00 2.83
2129 2187 7.087409 TGTACTGAATCTGCCATGTTATTTG 57.913 36.000 0.00 0.00 0.00 2.32
2130 2188 7.701539 TTGTACTGAATCTGCCATGTTATTT 57.298 32.000 0.00 0.00 0.00 1.40
2131 2189 7.701539 TTTGTACTGAATCTGCCATGTTATT 57.298 32.000 0.00 0.00 0.00 1.40
2132 2190 7.886629 ATTTGTACTGAATCTGCCATGTTAT 57.113 32.000 0.00 0.00 0.00 1.89
2133 2191 8.673711 GTTATTTGTACTGAATCTGCCATGTTA 58.326 33.333 0.00 0.00 0.00 2.41
2134 2192 7.176515 TGTTATTTGTACTGAATCTGCCATGTT 59.823 33.333 0.00 0.00 0.00 2.71
2135 2193 6.658816 TGTTATTTGTACTGAATCTGCCATGT 59.341 34.615 0.00 0.00 0.00 3.21
2136 2194 7.087409 TGTTATTTGTACTGAATCTGCCATG 57.913 36.000 0.00 0.00 0.00 3.66
2137 2195 7.201848 CCATGTTATTTGTACTGAATCTGCCAT 60.202 37.037 0.00 0.00 0.00 4.40
2138 2196 6.095300 CCATGTTATTTGTACTGAATCTGCCA 59.905 38.462 0.00 0.00 0.00 4.92
2139 2197 6.498304 CCATGTTATTTGTACTGAATCTGCC 58.502 40.000 0.00 0.00 0.00 4.85
2185 2266 6.344500 CCATGTTAGTTCTACTGAATCTGCT 58.656 40.000 0.00 0.00 34.40 4.24
2201 2352 6.154203 TCTCTACTGAATCTGCCATGTTAG 57.846 41.667 0.00 0.00 0.00 2.34
2223 2374 7.212976 TCTCTACTGAATCTGCCATGTTATTC 58.787 38.462 0.00 0.00 0.00 1.75
2247 2398 8.613060 TCTCTATTGAATCTGCCATGTTATTC 57.387 34.615 0.00 0.00 0.00 1.75
2306 2458 9.905713 TTGCCATGTTATTCTCTACTAAATCTT 57.094 29.630 0.00 0.00 0.00 2.40
2312 2464 9.817809 CTTAAGTTGCCATGTTATTCTCTACTA 57.182 33.333 0.00 0.00 0.00 1.82
2319 2494 7.385778 TGGTACTTAAGTTGCCATGTTATTC 57.614 36.000 20.82 1.13 30.66 1.75
2320 2495 7.954666 ATGGTACTTAAGTTGCCATGTTATT 57.045 32.000 28.64 14.59 39.42 1.40
2333 2508 3.761657 TGCGACGTGTATGGTACTTAAG 58.238 45.455 0.00 0.00 0.00 1.85
2351 2526 5.741425 CATGAATGGATAACTACAGTTGCG 58.259 41.667 4.86 0.00 38.90 4.85
2457 2637 1.704628 TGACATGGTCCTTGGTGACAT 59.295 47.619 9.44 0.00 42.32 3.06


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

AutoCloner maintained by Alex Coulton.