Multiple sequence alignment - TraesCS5D01G211000

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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 TraesCS5D01G211000 chr5D 100.000 5314 0 0 1 5314 319316216 319321529 0.000000e+00 9814.0
1 TraesCS5D01G211000 chr5B 91.163 5013 221 107 170 5096 369611681 369616557 0.000000e+00 6599.0
2 TraesCS5D01G211000 chr5B 94.954 218 8 1 5097 5314 369616715 369616929 6.590000e-89 339.0
3 TraesCS5D01G211000 chr5A 95.510 3118 107 15 2216 5314 414779665 414776562 0.000000e+00 4951.0
4 TraesCS5D01G211000 chr5A 90.838 1539 54 39 527 2035 414781349 414779868 0.000000e+00 1980.0
5 TraesCS5D01G211000 chr5A 86.306 555 44 17 1 551 414781904 414781378 4.620000e-160 575.0
6 TraesCS5D01G211000 chr6D 81.194 335 41 11 843 1162 273187250 273186923 3.180000e-62 250.0
7 TraesCS5D01G211000 chr2D 91.111 45 4 0 1495 1539 644375532 644375488 1.600000e-05 62.1
8 TraesCS5D01G211000 chr2B 97.222 36 1 0 1495 1530 791471289 791471324 1.600000e-05 62.1
9 TraesCS5D01G211000 chr2A 91.111 45 4 0 1495 1539 769501867 769501823 1.600000e-05 62.1


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 TraesCS5D01G211000 chr5D 319316216 319321529 5313 False 9814 9814 100.000000 1 5314 1 chr5D.!!$F1 5313
1 TraesCS5D01G211000 chr5B 369611681 369616929 5248 False 3469 6599 93.058500 170 5314 2 chr5B.!!$F1 5144
2 TraesCS5D01G211000 chr5A 414776562 414781904 5342 True 2502 4951 90.884667 1 5314 3 chr5A.!!$R1 5313

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
525 536 1.102222 CGACGAACTAGCCCTAGCCT 61.102 60.000 2.31 0.00 41.25 4.58 F
583 641 1.134228 ACCAAGACCCGGTAAACAGT 58.866 50.000 0.00 0.00 34.02 3.55 F
1404 1506 1.267121 ACCTGTCCTACAGCGTCATT 58.733 50.000 1.43 0.00 44.63 2.57 F
1905 2035 0.322546 GGTCTGCAGGTAACCCCTTG 60.323 60.000 15.13 0.00 42.73 3.61 F
2135 2338 0.996462 GCAACTATGCGACGCAACTA 59.004 50.000 28.24 14.64 43.62 2.24 F
2136 2339 1.392168 GCAACTATGCGACGCAACTAA 59.608 47.619 28.24 11.63 43.62 2.24 F
4034 4241 0.035739 TCAAGTACCCGTTTGAGGCC 59.964 55.000 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1840 0.601558 GTAGCTCGTGGTGACCTGAA 59.398 55.000 2.11 0.0 0.00 3.02 R
1804 1934 0.964358 GCCTGACCTCAGCTGCAAAT 60.964 55.000 9.47 0.0 42.47 2.32 R
2714 2920 1.403814 TCAGTCGCCCTCTGGATAAG 58.596 55.000 0.00 0.0 34.15 1.73 R
3521 3728 0.678366 ACAGCGTCGAGAGGATGAGT 60.678 55.000 16.31 0.0 36.28 3.41 R
3959 4166 1.066143 GGGATCTTGTTCCGCTTCAGA 60.066 52.381 0.00 0.0 36.58 3.27 R
4121 4328 3.087031 CAGTTGATCATGAAGGCCACTT 58.913 45.455 5.01 0.0 40.34 3.16 R
4882 5101 5.009811 GTGTGAGTCTGTACCTTGTTCTACT 59.990 44.000 0.00 0.0 0.00 2.57 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 6.791887 TCTAAAGAGAACTGATGCAAACAG 57.208 37.500 18.41 18.41 43.16 3.16
109 110 1.945387 CCGCTACAGTACTAGACCGA 58.055 55.000 0.00 0.00 0.00 4.69
175 176 2.770164 AGGCGATAAACAGCTCTTGT 57.230 45.000 0.00 0.00 43.45 3.16
219 222 2.112297 GCTCCAACACCCAACGGA 59.888 61.111 0.00 0.00 0.00 4.69
279 282 2.373169 AGGAGAAATGCTGGACAAGACA 59.627 45.455 0.00 0.00 0.00 3.41
285 288 4.785767 CTGGACAAGACAGCAGCA 57.214 55.556 0.00 0.00 0.00 4.41
398 409 2.051971 CCAACGACGACGACGACA 60.052 61.111 25.15 0.00 42.66 4.35
428 439 1.139095 GTCCGTACGCTCCTCAAGG 59.861 63.158 10.49 0.00 0.00 3.61
432 443 1.226717 GTACGCTCCTCAAGGCTCG 60.227 63.158 0.00 7.80 36.33 5.03
435 446 3.780173 GCTCCTCAAGGCTCGGCT 61.780 66.667 0.00 0.00 34.44 5.52
436 447 2.186384 CTCCTCAAGGCTCGGCTG 59.814 66.667 0.00 0.00 34.44 4.85
437 448 4.087892 TCCTCAAGGCTCGGCTGC 62.088 66.667 0.00 0.00 34.44 5.25
482 493 4.212913 TCGGCGGCAGATCAGAGC 62.213 66.667 10.53 0.00 0.00 4.09
521 532 3.518003 GGCGACGAACTAGCCCTA 58.482 61.111 0.00 0.00 44.80 3.53
522 533 1.359475 GGCGACGAACTAGCCCTAG 59.641 63.158 0.00 0.88 44.80 3.02
523 534 1.299240 GCGACGAACTAGCCCTAGC 60.299 63.158 0.00 0.00 36.66 3.42
525 536 1.102222 CGACGAACTAGCCCTAGCCT 61.102 60.000 2.31 0.00 41.25 4.58
536 594 1.139256 GCCCTAGCCTAGTTCAGTTCC 59.861 57.143 0.00 0.00 0.00 3.62
551 609 1.904537 AGTTCCCTTCCCGTCGTTAAT 59.095 47.619 0.00 0.00 0.00 1.40
552 610 2.303890 AGTTCCCTTCCCGTCGTTAATT 59.696 45.455 0.00 0.00 0.00 1.40
553 611 3.515104 AGTTCCCTTCCCGTCGTTAATTA 59.485 43.478 0.00 0.00 0.00 1.40
554 612 4.020307 AGTTCCCTTCCCGTCGTTAATTAA 60.020 41.667 0.00 0.00 0.00 1.40
555 613 3.860641 TCCCTTCCCGTCGTTAATTAAC 58.139 45.455 16.87 16.87 0.00 2.01
556 614 3.515104 TCCCTTCCCGTCGTTAATTAACT 59.485 43.478 22.57 0.00 34.12 2.24
557 615 3.619929 CCCTTCCCGTCGTTAATTAACTG 59.380 47.826 22.57 16.63 34.12 3.16
566 624 6.291385 CGTCGTTAATTAACTGTGTGTAACC 58.709 40.000 22.57 0.00 32.46 2.85
568 626 7.516470 CGTCGTTAATTAACTGTGTGTAACCAA 60.516 37.037 22.57 0.00 32.46 3.67
573 631 2.632987 ACTGTGTGTAACCAAGACCC 57.367 50.000 0.00 0.00 34.36 4.46
579 637 2.437281 TGTGTAACCAAGACCCGGTAAA 59.563 45.455 0.00 0.00 34.99 2.01
580 638 2.807967 GTGTAACCAAGACCCGGTAAAC 59.192 50.000 0.00 0.00 34.99 2.01
581 639 2.437281 TGTAACCAAGACCCGGTAAACA 59.563 45.455 0.00 0.00 34.99 2.83
582 640 2.265589 AACCAAGACCCGGTAAACAG 57.734 50.000 0.00 0.00 34.99 3.16
583 641 1.134228 ACCAAGACCCGGTAAACAGT 58.866 50.000 0.00 0.00 34.02 3.55
584 642 1.491754 ACCAAGACCCGGTAAACAGTT 59.508 47.619 0.00 0.00 34.02 3.16
603 671 1.300971 TGCTCTGCATTCTCCGTTGC 61.301 55.000 0.00 0.00 39.33 4.17
608 676 2.409870 GCATTCTCCGTTGCCCCAG 61.410 63.158 0.00 0.00 32.66 4.45
609 677 2.044946 ATTCTCCGTTGCCCCAGC 60.045 61.111 0.00 0.00 40.48 4.85
656 725 1.576356 GCCCTGAATCAGTCATCGTC 58.424 55.000 9.63 0.00 35.07 4.20
657 726 1.845266 CCCTGAATCAGTCATCGTCG 58.155 55.000 9.63 0.00 35.07 5.12
676 745 4.704833 TCTGCGCCAGTCCAAGCC 62.705 66.667 4.18 0.00 32.61 4.35
733 813 2.914097 AAGCACAGGCCAAGGCAC 60.914 61.111 13.87 2.47 44.11 5.01
734 814 3.736996 AAGCACAGGCCAAGGCACA 62.737 57.895 13.87 0.00 44.11 4.57
735 815 3.225798 GCACAGGCCAAGGCACAA 61.226 61.111 13.87 0.00 44.11 3.33
736 816 3.045142 CACAGGCCAAGGCACAAG 58.955 61.111 13.87 1.84 44.11 3.16
737 817 2.203538 ACAGGCCAAGGCACAAGG 60.204 61.111 13.87 0.00 44.11 3.61
1404 1506 1.267121 ACCTGTCCTACAGCGTCATT 58.733 50.000 1.43 0.00 44.63 2.57
1476 1578 3.140814 GACATTTCCGGGCAGGCC 61.141 66.667 0.00 1.81 40.77 5.19
1634 1737 2.915738 ACACTCGACTCGATGGTTAC 57.084 50.000 0.62 0.00 34.61 2.50
1695 1825 1.806542 ACGGTGCAGTTTCTTATGCTG 59.193 47.619 0.00 0.00 42.98 4.41
1710 1840 7.801716 TCTTATGCTGTAAACTGAAACTTGT 57.198 32.000 0.00 0.00 0.00 3.16
1804 1934 2.340078 GTGCTGGAGACGCTCACA 59.660 61.111 8.71 4.37 31.08 3.58
1905 2035 0.322546 GGTCTGCAGGTAACCCCTTG 60.323 60.000 15.13 0.00 42.73 3.61
2035 2166 6.925211 TGGTGAGAATACTAGTTCAGAACTG 58.075 40.000 23.92 16.01 42.84 3.16
2061 2192 5.638596 AAACCTCATGTTTCCCGATTTAC 57.361 39.130 0.00 0.00 43.74 2.01
2063 2194 5.687166 ACCTCATGTTTCCCGATTTACTA 57.313 39.130 0.00 0.00 0.00 1.82
2064 2195 6.057321 ACCTCATGTTTCCCGATTTACTAA 57.943 37.500 0.00 0.00 0.00 2.24
2067 2198 7.282450 ACCTCATGTTTCCCGATTTACTAATTC 59.718 37.037 0.00 0.00 0.00 2.17
2068 2199 7.241663 TCATGTTTCCCGATTTACTAATTCG 57.758 36.000 6.24 6.24 0.00 3.34
2069 2200 6.259167 TCATGTTTCCCGATTTACTAATTCGG 59.741 38.462 19.00 19.00 42.91 4.30
2113 2316 2.295885 GATCCAATGCCCTCTCACTTG 58.704 52.381 0.00 0.00 0.00 3.16
2120 2323 1.569479 GCCCTCTCACTTGACGCAAC 61.569 60.000 0.00 0.00 0.00 4.17
2135 2338 0.996462 GCAACTATGCGACGCAACTA 59.004 50.000 28.24 14.64 43.62 2.24
2136 2339 1.392168 GCAACTATGCGACGCAACTAA 59.608 47.619 28.24 11.63 43.62 2.24
2139 2342 2.955614 ACTATGCGACGCAACTAAACT 58.044 42.857 28.24 10.99 43.62 2.66
2157 2360 7.923888 ACTAAACTAATAGTAGCGACGAATCA 58.076 34.615 0.00 0.00 34.40 2.57
2178 2381 3.065371 CACAACCGAACTTCAGAAGCTTT 59.935 43.478 10.33 0.00 0.00 3.51
2179 2382 4.272504 CACAACCGAACTTCAGAAGCTTTA 59.727 41.667 10.33 0.00 0.00 1.85
2180 2383 4.511826 ACAACCGAACTTCAGAAGCTTTAG 59.488 41.667 10.33 0.00 0.00 1.85
2181 2384 3.067833 ACCGAACTTCAGAAGCTTTAGC 58.932 45.455 10.33 0.00 42.49 3.09
2205 2408 2.542595 CCAAAGCAAAAGCTGAAGCAAG 59.457 45.455 4.90 0.00 45.16 4.01
2271 2476 4.095483 ACATGAAAAATAGCGCCTGAGAAG 59.905 41.667 2.29 0.00 0.00 2.85
2276 2481 1.876322 ATAGCGCCTGAGAAGATTGC 58.124 50.000 2.29 0.00 0.00 3.56
2319 2524 2.361757 CCTTGCCAAATGACAGACAACA 59.638 45.455 0.00 0.00 0.00 3.33
2340 2545 2.017049 GCTCACACATACATTGGGGAC 58.983 52.381 0.00 0.00 30.69 4.46
2388 2593 1.929806 AACGCCGCAGAGTGTCGATA 61.930 55.000 0.00 0.00 0.00 2.92
2633 2838 6.206829 GTGTTCTCAGGCCTGTTAATAACTTT 59.793 38.462 31.58 0.00 0.00 2.66
2645 2850 9.391006 CCTGTTAATAACTTTCTATTGTGGCTA 57.609 33.333 4.67 0.00 0.00 3.93
2668 2874 9.659830 GCTATTTTAGTGGTTAATTACATTCCG 57.340 33.333 0.00 0.00 0.00 4.30
2671 2877 7.999450 TTTAGTGGTTAATTACATTCCGGTT 57.001 32.000 0.00 0.00 0.00 4.44
2726 2933 6.253946 AGTTCCAATAACTTATCCAGAGGG 57.746 41.667 0.00 0.00 0.00 4.30
3113 3320 6.231211 TCTTGAGAGAAAAATACAGACACCC 58.769 40.000 0.00 0.00 0.00 4.61
3521 3728 2.358615 GTGCTCACGGTCATGGCA 60.359 61.111 0.00 0.00 0.00 4.92
3782 3989 3.966215 ACCTTTGCGGTGATCACG 58.034 55.556 19.33 15.06 46.80 4.35
3908 4115 1.615883 CCGAGCTACATCACTGGCTAT 59.384 52.381 0.00 0.00 35.01 2.97
3959 4166 0.984230 TCCTCACCTGCGGATTCTTT 59.016 50.000 0.00 0.00 0.00 2.52
4034 4241 0.035739 TCAAGTACCCGTTTGAGGCC 59.964 55.000 0.00 0.00 0.00 5.19
4080 4287 1.466856 CCATTGCTACACTGGCACAT 58.533 50.000 0.00 0.00 39.55 3.21
4081 4288 1.820519 CCATTGCTACACTGGCACATT 59.179 47.619 0.00 0.00 39.55 2.71
4082 4289 2.159338 CCATTGCTACACTGGCACATTC 60.159 50.000 0.00 0.00 39.55 2.67
4094 4301 1.133790 GGCACATTCAATCAGCTGTCC 59.866 52.381 14.67 0.00 0.00 4.02
4119 4326 2.092699 GGACCTCTGGGAGAAATCAAGG 60.093 54.545 0.00 0.00 36.25 3.61
4121 4328 3.260205 ACCTCTGGGAGAAATCAAGGAA 58.740 45.455 0.00 0.00 36.25 3.36
4163 4370 2.818130 ACCCAAACATCACAACATGC 57.182 45.000 0.00 0.00 0.00 4.06
4167 4374 1.619827 CAAACATCACAACATGCCCCT 59.380 47.619 0.00 0.00 0.00 4.79
4374 4584 6.309494 CCATATCTCTTTGTGTGCATTTGTTG 59.691 38.462 0.00 0.00 0.00 3.33
4484 4694 4.992951 GCCTTCAAAAGCATCAAGTGAAAT 59.007 37.500 0.00 0.00 0.00 2.17
4566 4776 4.629634 CGTGCAGTATTTCATTGTAGGTCA 59.370 41.667 0.00 0.00 0.00 4.02
4579 4789 2.305635 TGTAGGTCACCATGCAGTCATT 59.694 45.455 0.00 0.00 0.00 2.57
4585 4795 1.741706 CACCATGCAGTCATTCAGGAC 59.258 52.381 0.00 0.00 38.08 3.85
4642 4859 9.801873 AGAATATGTAATTGCACACATTTTACC 57.198 29.630 11.75 2.80 36.74 2.85
4668 4885 7.995463 TGAATAACTTACAAAACAAAGGTGC 57.005 32.000 0.00 0.00 0.00 5.01
4846 5063 7.120873 CAGAGATCAAATGAGGAATGTTGAAGT 59.879 37.037 0.00 0.00 33.93 3.01
4847 5064 8.324306 AGAGATCAAATGAGGAATGTTGAAGTA 58.676 33.333 0.00 0.00 33.93 2.24
4853 5070 9.793252 CAAATGAGGAATGTTGAAGTAATTAGG 57.207 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.203530 TCACTGTTTGCATCAGTTCTCTTTAG 59.796 38.462 18.28 8.35 43.14 1.85
29 30 6.054941 TCACTGTTTGCATCAGTTCTCTTTA 58.945 36.000 18.28 1.72 43.14 1.85
35 36 5.112220 TCAATCACTGTTTGCATCAGTTC 57.888 39.130 18.28 0.00 43.14 3.01
91 92 1.596727 GGTCGGTCTAGTACTGTAGCG 59.403 57.143 19.03 19.03 35.78 4.26
124 125 3.972276 CTCCGGCTCGCCTCTAGC 61.972 72.222 6.35 0.00 39.33 3.42
154 155 3.522553 ACAAGAGCTGTTTATCGCCTAC 58.477 45.455 0.00 0.00 32.99 3.18
161 162 5.008415 GCTATGCATGACAAGAGCTGTTTAT 59.992 40.000 10.16 0.00 38.84 1.40
241 244 3.119709 CTCTCCTCTCGCAGGTCGC 62.120 68.421 0.63 0.00 43.95 5.19
242 245 2.477176 CCTCTCCTCTCGCAGGTCG 61.477 68.421 0.63 0.00 43.95 4.79
243 246 1.077357 TCCTCTCCTCTCGCAGGTC 60.077 63.158 0.63 0.00 43.95 3.85
244 247 1.077068 CTCCTCTCCTCTCGCAGGT 60.077 63.158 0.63 0.00 43.95 4.00
245 248 0.395036 TTCTCCTCTCCTCTCGCAGG 60.395 60.000 0.00 0.00 45.15 4.85
246 249 1.468985 TTTCTCCTCTCCTCTCGCAG 58.531 55.000 0.00 0.00 0.00 5.18
247 250 1.753649 CATTTCTCCTCTCCTCTCGCA 59.246 52.381 0.00 0.00 0.00 5.10
248 251 1.537990 GCATTTCTCCTCTCCTCTCGC 60.538 57.143 0.00 0.00 0.00 5.03
249 252 2.031120 AGCATTTCTCCTCTCCTCTCG 58.969 52.381 0.00 0.00 0.00 4.04
250 253 2.102925 CCAGCATTTCTCCTCTCCTCTC 59.897 54.545 0.00 0.00 0.00 3.20
251 254 2.117865 CCAGCATTTCTCCTCTCCTCT 58.882 52.381 0.00 0.00 0.00 3.69
252 255 2.114616 TCCAGCATTTCTCCTCTCCTC 58.885 52.381 0.00 0.00 0.00 3.71
253 256 1.836802 GTCCAGCATTTCTCCTCTCCT 59.163 52.381 0.00 0.00 0.00 3.69
254 257 1.556911 TGTCCAGCATTTCTCCTCTCC 59.443 52.381 0.00 0.00 0.00 3.71
279 282 4.400961 GCCCGGTCTCTTGCTGCT 62.401 66.667 0.00 0.00 0.00 4.24
375 380 1.062258 GTCGTCGTCGTTGGCAATAA 58.938 50.000 1.92 0.00 38.33 1.40
428 439 3.435186 GTTGGAAGGCAGCCGAGC 61.435 66.667 5.55 0.00 0.00 5.03
432 443 1.508088 CATTCGTTGGAAGGCAGCC 59.492 57.895 1.84 1.84 35.19 4.85
437 448 1.243342 TGCTGGCATTCGTTGGAAGG 61.243 55.000 0.00 0.00 37.03 3.46
462 473 2.279120 CTGATCTGCCGCCGAGTC 60.279 66.667 0.00 0.00 0.00 3.36
482 493 3.978723 CTCCTCGCGAGCAGTGTGG 62.979 68.421 30.49 16.13 43.37 4.17
507 518 1.978454 TAGGCTAGGGCTAGTTCGTC 58.022 55.000 0.00 0.00 39.70 4.20
518 529 2.753247 AGGGAACTGAACTAGGCTAGG 58.247 52.381 24.57 9.89 41.13 3.02
520 531 3.105283 GGAAGGGAACTGAACTAGGCTA 58.895 50.000 0.00 0.00 42.68 3.93
521 532 1.909986 GGAAGGGAACTGAACTAGGCT 59.090 52.381 0.00 0.00 42.68 4.58
522 533 1.065345 GGGAAGGGAACTGAACTAGGC 60.065 57.143 0.00 0.00 42.68 3.93
523 534 1.207329 CGGGAAGGGAACTGAACTAGG 59.793 57.143 0.00 0.00 42.68 3.02
525 536 1.897802 GACGGGAAGGGAACTGAACTA 59.102 52.381 0.00 0.00 42.68 2.24
536 594 4.092383 CACAGTTAATTAACGACGGGAAGG 59.908 45.833 19.92 7.31 40.96 3.46
551 609 4.453751 GGGTCTTGGTTACACACAGTTAA 58.546 43.478 0.00 0.00 0.00 2.01
552 610 3.493002 CGGGTCTTGGTTACACACAGTTA 60.493 47.826 0.00 0.00 0.00 2.24
553 611 2.743838 CGGGTCTTGGTTACACACAGTT 60.744 50.000 0.00 0.00 0.00 3.16
554 612 1.202604 CGGGTCTTGGTTACACACAGT 60.203 52.381 0.00 0.00 0.00 3.55
555 613 1.508632 CGGGTCTTGGTTACACACAG 58.491 55.000 0.00 0.00 0.00 3.66
556 614 0.107081 CCGGGTCTTGGTTACACACA 59.893 55.000 0.00 0.00 0.00 3.72
557 615 0.107268 ACCGGGTCTTGGTTACACAC 59.893 55.000 6.32 0.00 35.82 3.82
566 624 1.265905 GCAACTGTTTACCGGGTCTTG 59.734 52.381 6.32 0.00 0.00 3.02
568 626 0.763035 AGCAACTGTTTACCGGGTCT 59.237 50.000 6.32 0.00 0.00 3.85
580 638 0.725686 CGGAGAATGCAGAGCAACTG 59.274 55.000 6.57 6.57 43.62 3.16
581 639 0.322975 ACGGAGAATGCAGAGCAACT 59.677 50.000 0.00 0.00 43.62 3.16
582 640 1.135859 CAACGGAGAATGCAGAGCAAC 60.136 52.381 0.00 0.00 43.62 4.17
583 641 1.159285 CAACGGAGAATGCAGAGCAA 58.841 50.000 0.00 0.00 43.62 3.91
584 642 1.300971 GCAACGGAGAATGCAGAGCA 61.301 55.000 0.00 0.00 44.86 4.26
591 659 2.409870 GCTGGGGCAACGGAGAATG 61.410 63.158 0.00 0.00 38.54 2.67
639 708 2.568696 ACGACGATGACTGATTCAGG 57.431 50.000 17.66 2.35 37.77 3.86
657 726 2.970974 GCTTGGACTGGCGCAGAAC 61.971 63.158 10.83 4.43 35.18 3.01
758 838 2.092968 TGATATTGAGGCAGTGGTGGAC 60.093 50.000 0.00 0.00 0.00 4.02
759 839 2.195727 TGATATTGAGGCAGTGGTGGA 58.804 47.619 0.00 0.00 0.00 4.02
760 840 2.684881 GTTGATATTGAGGCAGTGGTGG 59.315 50.000 0.00 0.00 0.00 4.61
761 841 2.352651 CGTTGATATTGAGGCAGTGGTG 59.647 50.000 0.00 0.00 0.00 4.17
762 842 2.027192 ACGTTGATATTGAGGCAGTGGT 60.027 45.455 0.00 0.00 0.00 4.16
805 885 1.896660 GCCTTGGTTTCGCAGGTGA 60.897 57.895 0.00 0.00 0.00 4.02
840 926 2.042831 CCAGAAGCTTTGGAGGCGG 61.043 63.158 17.72 0.00 37.96 6.13
1404 1506 2.233922 CCCGTCCTTCTTCTGCTTCTTA 59.766 50.000 0.00 0.00 0.00 2.10
1552 1654 4.918201 GCTCCCCTTGGCGATCCG 62.918 72.222 0.00 0.00 34.14 4.18
1602 1704 7.140705 TCGAGTCGAGTGTTAAAAATCTTACA 58.859 34.615 12.09 0.00 0.00 2.41
1634 1737 7.621832 TTCTTCTTGTAATGAAAATGCAACG 57.378 32.000 0.00 0.00 28.96 4.10
1664 1794 1.816224 ACTGCACCGTTTGTTCTTGTT 59.184 42.857 0.00 0.00 0.00 2.83
1665 1795 1.459450 ACTGCACCGTTTGTTCTTGT 58.541 45.000 0.00 0.00 0.00 3.16
1666 1796 2.559998 AACTGCACCGTTTGTTCTTG 57.440 45.000 0.00 0.00 0.00 3.02
1695 1825 6.255950 GTGACCTGAACAAGTTTCAGTTTAC 58.744 40.000 11.94 2.81 43.19 2.01
1710 1840 0.601558 GTAGCTCGTGGTGACCTGAA 59.398 55.000 2.11 0.00 0.00 3.02
1804 1934 0.964358 GCCTGACCTCAGCTGCAAAT 60.964 55.000 9.47 0.00 42.47 2.32
1905 2035 4.102367 AGGAATGCTTGAGTAGGGAGAATC 59.898 45.833 0.00 0.00 0.00 2.52
2040 2171 4.918588 AGTAAATCGGGAAACATGAGGTT 58.081 39.130 0.00 0.00 42.98 3.50
2061 2192 7.486802 ACCGTAATGGAAAATACCGAATTAG 57.513 36.000 0.00 0.00 42.00 1.73
2063 2194 7.274447 TCTACCGTAATGGAAAATACCGAATT 58.726 34.615 0.00 0.00 42.00 2.17
2064 2195 6.819284 TCTACCGTAATGGAAAATACCGAAT 58.181 36.000 0.00 0.00 42.00 3.34
2067 2198 6.480981 ACAATCTACCGTAATGGAAAATACCG 59.519 38.462 0.00 0.00 42.00 4.02
2068 2199 7.496591 TCACAATCTACCGTAATGGAAAATACC 59.503 37.037 0.00 0.00 42.00 2.73
2069 2200 8.428186 TCACAATCTACCGTAATGGAAAATAC 57.572 34.615 0.00 0.00 42.00 1.89
2120 2323 5.637104 ATTAGTTTAGTTGCGTCGCATAG 57.363 39.130 22.41 0.00 38.76 2.23
2135 2338 6.558009 TGTGATTCGTCGCTACTATTAGTTT 58.442 36.000 0.85 0.00 0.00 2.66
2136 2339 6.127810 TGTGATTCGTCGCTACTATTAGTT 57.872 37.500 0.85 0.00 0.00 2.24
2139 2342 5.276270 GGTTGTGATTCGTCGCTACTATTA 58.724 41.667 4.23 0.00 0.00 0.98
2157 2360 2.622064 AGCTTCTGAAGTTCGGTTGT 57.378 45.000 17.97 0.00 0.00 3.32
2190 2393 4.430137 TGCTATCTTGCTTCAGCTTTTG 57.570 40.909 0.00 0.00 42.66 2.44
2191 2394 5.458041 TTTGCTATCTTGCTTCAGCTTTT 57.542 34.783 0.00 0.00 42.66 2.27
2192 2395 5.458041 TTTTGCTATCTTGCTTCAGCTTT 57.542 34.783 0.00 0.00 42.66 3.51
2271 2476 5.224888 TGCTTGTCAAAAATCTGAGCAATC 58.775 37.500 0.00 0.00 0.00 2.67
2276 2481 5.416952 AGGGTATGCTTGTCAAAAATCTGAG 59.583 40.000 0.00 0.00 0.00 3.35
2319 2524 1.915489 TCCCCAATGTATGTGTGAGCT 59.085 47.619 0.00 0.00 0.00 4.09
2388 2593 3.746751 GCTTATGGATGATGTCTGTGCCT 60.747 47.826 0.00 0.00 0.00 4.75
2633 2838 9.914834 ATTAACCACTAAAATAGCCACAATAGA 57.085 29.630 0.00 0.00 0.00 1.98
2645 2850 8.584063 ACCGGAATGTAATTAACCACTAAAAT 57.416 30.769 9.46 0.00 36.07 1.82
2646 2851 7.999450 ACCGGAATGTAATTAACCACTAAAA 57.001 32.000 9.46 0.00 36.07 1.52
2647 2852 7.447853 ACAACCGGAATGTAATTAACCACTAAA 59.552 33.333 9.46 0.00 36.07 1.85
2651 2856 5.632244 ACAACCGGAATGTAATTAACCAC 57.368 39.130 9.46 0.00 36.07 4.16
2714 2920 1.403814 TCAGTCGCCCTCTGGATAAG 58.596 55.000 0.00 0.00 34.15 1.73
2726 2933 3.570559 GTTGCCTAGATAGATCAGTCGC 58.429 50.000 0.00 0.00 0.00 5.19
3521 3728 0.678366 ACAGCGTCGAGAGGATGAGT 60.678 55.000 16.31 0.00 36.28 3.41
3710 3917 3.534357 ATGAGGGAGGAGATCACGTAT 57.466 47.619 0.00 0.00 35.97 3.06
3782 3989 5.049543 GCTATTCAGATGGAGCATGAACTTC 60.050 44.000 0.00 0.00 35.89 3.01
3908 4115 2.942879 GTTGCAATCACGACGGCA 59.057 55.556 0.59 0.00 0.00 5.69
3959 4166 1.066143 GGGATCTTGTTCCGCTTCAGA 60.066 52.381 0.00 0.00 36.58 3.27
4119 4326 3.760684 AGTTGATCATGAAGGCCACTTTC 59.239 43.478 5.01 0.00 36.97 2.62
4121 4328 3.087031 CAGTTGATCATGAAGGCCACTT 58.913 45.455 5.01 0.00 40.34 3.16
4163 4370 0.403271 CATCCTGGCCTATCAAGGGG 59.597 60.000 3.32 0.00 43.87 4.79
4167 4374 1.141657 GAGCACATCCTGGCCTATCAA 59.858 52.381 3.32 0.00 0.00 2.57
4374 4584 7.721286 TCTGTCAAAAGAGAATGAGAAAGAC 57.279 36.000 0.00 0.00 0.00 3.01
4484 4694 9.912634 GTCAAAATAAGAAAGAATGATGTTGGA 57.087 29.630 0.00 0.00 0.00 3.53
4550 4760 5.504853 TGCATGGTGACCTACAATGAAATA 58.495 37.500 2.11 0.00 42.39 1.40
4556 4766 2.305635 TGACTGCATGGTGACCTACAAT 59.694 45.455 2.11 0.00 0.00 2.71
4566 4776 1.676916 CGTCCTGAATGACTGCATGGT 60.677 52.381 0.00 0.00 34.26 3.55
4579 4789 1.472878 GAGCACAGTATGACGTCCTGA 59.527 52.381 22.12 2.05 39.69 3.86
4585 4795 7.807680 TCTATATGTAAGAGCACAGTATGACG 58.192 38.462 0.00 0.00 39.69 4.35
4642 4859 8.487176 GCACCTTTGTTTTGTAAGTTATTCATG 58.513 33.333 0.00 0.00 0.00 3.07
4828 5045 9.533831 ACCTAATTACTTCAACATTCCTCATTT 57.466 29.630 0.00 0.00 0.00 2.32
4882 5101 5.009811 GTGTGAGTCTGTACCTTGTTCTACT 59.990 44.000 0.00 0.00 0.00 2.57
4938 5160 6.089150 GCTCTTGCAGATTCTTTTAGCTTTTG 59.911 38.462 0.00 0.00 39.41 2.44
5168 5550 6.701145 TGTACTCATATGGACTCAACTCTC 57.299 41.667 2.13 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.