Multiple sequence alignment - TraesCS1A01G238800

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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 TraesCS1A01G238800 chr1A 100.000 2570 0 0 1 2570 425682767 425680198 0.000000e+00 4747.0
1 TraesCS1A01G238800 chr1D 87.561 2685 123 80 1 2570 328799234 328796646 0.000000e+00 2913.0
2 TraesCS1A01G238800 chr1B 86.738 1870 80 70 93 1901 442971833 442970071 0.000000e+00 1925.0
3 TraesCS1A01G238800 chr1B 91.403 221 15 4 1953 2172 442970049 442969832 1.490000e-77 300.0
4 TraesCS1A01G238800 chr1B 91.935 62 5 0 1 62 442971895 442971834 1.270000e-13 87.9
5 TraesCS1A01G238800 chr3B 85.366 410 58 2 1117 1525 776195217 776195625 8.500000e-115 424.0
6 TraesCS1A01G238800 chr3B 84.615 416 62 2 1117 1531 777997583 777997169 1.840000e-111 412.0
7 TraesCS1A01G238800 chr3D 85.194 412 55 3 1117 1525 580713774 580714182 3.960000e-113 418.0
8 TraesCS1A01G238800 chr3D 84.487 419 57 5 1117 1531 581834193 581833779 8.560000e-110 407.0
9 TraesCS1A01G238800 chr3A 84.466 412 58 4 1117 1525 716258966 716259374 3.980000e-108 401.0


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 TraesCS1A01G238800 chr1A 425680198 425682767 2569 True 4747.000000 4747 100.000000 1 2570 1 chr1A.!!$R1 2569
1 TraesCS1A01G238800 chr1D 328796646 328799234 2588 True 2913.000000 2913 87.561000 1 2570 1 chr1D.!!$R1 2569
2 TraesCS1A01G238800 chr1B 442969832 442971895 2063 True 770.966667 1925 90.025333 1 2172 3 chr1B.!!$R1 2171

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
419 446 0.10852 GTACGGCCGAATCTTCACCA 60.109 55.0 35.9 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2200 0.040067 CAAGTTCGGGCTGCAACTTC 60.04 55.0 16.1 0.0 40.19 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
40 41 1.593787 CCGTGCAGTCATGTCTCCT 59.406 57.895 0.00 0.00 0.00 3.69
44 45 2.352715 CGTGCAGTCATGTCTCCTAACA 60.353 50.000 0.00 0.00 0.00 2.41
51 52 5.352569 CAGTCATGTCTCCTAACAAATCCAC 59.647 44.000 0.00 0.00 31.81 4.02
52 53 5.013079 AGTCATGTCTCCTAACAAATCCACA 59.987 40.000 0.00 0.00 31.81 4.17
75 76 3.647026 GACGACGACGACGACATG 58.353 61.111 25.15 3.03 42.66 3.21
76 77 1.862147 GACGACGACGACGACATGG 60.862 63.158 25.15 0.00 42.66 3.66
77 78 3.238241 CGACGACGACGACATGGC 61.238 66.667 15.32 0.00 42.66 4.40
80 81 2.277949 CGACGACGACATGGCGAT 60.278 61.111 31.27 12.39 42.66 4.58
87 88 1.359117 CGACATGGCGATAGGACGT 59.641 57.895 18.41 0.00 35.59 4.34
91 92 2.431454 ATGGCGATAGGACGTGGCA 61.431 57.895 0.00 0.00 41.33 4.92
102 103 3.314331 CGTGGCACCACCTCCTCT 61.314 66.667 12.86 0.00 43.49 3.69
190 202 2.903357 CGACCCACAGATCCCAGG 59.097 66.667 0.00 0.00 0.00 4.45
191 203 1.685765 CGACCCACAGATCCCAGGA 60.686 63.158 0.00 0.00 0.00 3.86
266 278 3.412879 GAGAGCGTACGGAGCACCC 62.413 68.421 18.39 0.00 37.01 4.61
268 280 3.291101 GAGCGTACGGAGCACCCAA 62.291 63.158 18.39 0.00 37.01 4.12
269 281 2.813908 GCGTACGGAGCACCCAAG 60.814 66.667 18.39 0.00 34.14 3.61
270 282 2.813908 CGTACGGAGCACCCAAGC 60.814 66.667 7.57 0.00 34.14 4.01
272 284 1.895238 GTACGGAGCACCCAAGCTA 59.105 57.895 0.00 0.00 46.75 3.32
273 285 0.179108 GTACGGAGCACCCAAGCTAG 60.179 60.000 0.00 0.00 46.75 3.42
274 286 0.613853 TACGGAGCACCCAAGCTAGT 60.614 55.000 0.00 0.00 46.75 2.57
280 293 3.460648 CACCCAAGCTAGTGCCTAC 57.539 57.895 0.00 0.00 40.80 3.18
317 332 1.755008 AGAGAGACCTGGTAGCCGC 60.755 63.158 0.00 0.00 0.00 6.53
318 333 1.755008 GAGAGACCTGGTAGCCGCT 60.755 63.158 0.00 0.00 0.00 5.52
319 334 2.010582 GAGAGACCTGGTAGCCGCTG 62.011 65.000 2.16 0.00 0.00 5.18
320 335 3.724914 GAGACCTGGTAGCCGCTGC 62.725 68.421 2.16 0.39 37.95 5.25
358 384 3.248171 GCTCACGGTCGCGATCAC 61.248 66.667 21.02 9.20 0.00 3.06
382 408 3.702048 GTAGGCCCGGCACAGTGA 61.702 66.667 12.58 0.00 0.00 3.41
383 409 3.390521 TAGGCCCGGCACAGTGAG 61.391 66.667 12.58 0.00 0.00 3.51
387 413 3.052082 CCCGGCACAGTGAGCAAG 61.052 66.667 14.66 7.48 0.00 4.01
388 414 2.281070 CCGGCACAGTGAGCAAGT 60.281 61.111 14.66 0.00 0.00 3.16
412 438 3.317795 GACGCGTACGGCCGAATC 61.318 66.667 35.90 19.50 43.48 2.52
419 446 0.108520 GTACGGCCGAATCTTCACCA 60.109 55.000 35.90 0.00 0.00 4.17
421 448 2.106683 CGGCCGAATCTTCACCACC 61.107 63.158 24.07 0.00 0.00 4.61
426 457 1.475280 CCGAATCTTCACCACCTCGTA 59.525 52.381 0.00 0.00 0.00 3.43
479 518 1.772063 GCGTGTGACAAACGAGGCTT 61.772 55.000 22.24 0.00 43.68 4.35
515 558 4.712425 GCACGCGTGGTCGGTAGT 62.712 66.667 37.47 0.00 37.56 2.73
516 559 2.049802 CACGCGTGGTCGGTAGTT 60.050 61.111 31.15 0.00 37.56 2.24
534 578 4.463515 AGTTCGCGGTAAAGAAAGAAAC 57.536 40.909 6.13 0.00 0.00 2.78
555 607 2.271944 AAGAAACAAAGGAGTCCCGG 57.728 50.000 5.25 0.00 37.58 5.73
627 679 3.122369 CGGTAGTCGGTATTCCCCT 57.878 57.895 0.00 0.00 34.75 4.79
630 682 1.411041 GTAGTCGGTATTCCCCTGCT 58.589 55.000 0.00 0.00 0.00 4.24
631 683 1.340568 GTAGTCGGTATTCCCCTGCTC 59.659 57.143 0.00 0.00 0.00 4.26
632 684 1.049289 AGTCGGTATTCCCCTGCTCC 61.049 60.000 0.00 0.00 0.00 4.70
633 685 1.049289 GTCGGTATTCCCCTGCTCCT 61.049 60.000 0.00 0.00 0.00 3.69
777 839 0.459759 GAAAGGTTAGGCGTCGGGAG 60.460 60.000 0.00 0.00 0.00 4.30
778 840 2.517484 AAAGGTTAGGCGTCGGGAGC 62.517 60.000 0.00 0.00 0.00 4.70
874 939 3.053896 CCAAAACCGCGTCCTCCC 61.054 66.667 4.92 0.00 0.00 4.30
875 940 3.419759 CAAAACCGCGTCCTCCCG 61.420 66.667 4.92 0.00 0.00 5.14
900 965 1.481802 CCCTCCTATAAGTACGCCCCA 60.482 57.143 0.00 0.00 0.00 4.96
957 1026 3.630769 CCTCACAACATCATCCAATCCAG 59.369 47.826 0.00 0.00 0.00 3.86
968 1037 0.543749 CCAATCCAGACCTCCCACTC 59.456 60.000 0.00 0.00 0.00 3.51
1074 1156 1.194781 GCTCCTCCTCCACCAAGTCA 61.195 60.000 0.00 0.00 0.00 3.41
1082 1164 0.242825 TCCACCAAGTCATCGTCGAC 59.757 55.000 5.18 5.18 36.08 4.20
1575 1657 3.723348 GTCCGCGCCTGAACCAAC 61.723 66.667 0.00 0.00 0.00 3.77
1582 1664 0.250295 CGCCTGAACCAACCTCAAGA 60.250 55.000 0.00 0.00 0.00 3.02
1608 1690 4.430765 CGGCTACCGGTCGCTTGT 62.431 66.667 27.90 0.00 44.15 3.16
1632 1714 2.162408 CCTTCATTCTTTTGCGAGACCC 59.838 50.000 0.00 0.00 0.00 4.46
1648 1744 0.253894 ACCCTGTAAATACCACCGCC 59.746 55.000 0.00 0.00 0.00 6.13
1662 1758 2.861935 CCACCGCCAAATACTTACTACG 59.138 50.000 0.00 0.00 0.00 3.51
1664 1760 3.305094 CACCGCCAAATACTTACTACGTG 59.695 47.826 0.00 0.00 0.00 4.49
1722 1829 2.995258 GGTGTGCCATTATTTTGCTGTG 59.005 45.455 0.00 0.00 34.09 3.66
1823 1936 3.476552 TGGCGTCAGATTTTCACTTCTT 58.523 40.909 0.00 0.00 0.00 2.52
1825 1938 3.748568 GGCGTCAGATTTTCACTTCTTCT 59.251 43.478 0.00 0.00 0.00 2.85
1826 1939 4.143009 GGCGTCAGATTTTCACTTCTTCTC 60.143 45.833 0.00 0.00 0.00 2.87
1827 1940 4.449068 GCGTCAGATTTTCACTTCTTCTCA 59.551 41.667 0.00 0.00 0.00 3.27
1828 1941 5.121454 GCGTCAGATTTTCACTTCTTCTCAT 59.879 40.000 0.00 0.00 0.00 2.90
1845 1958 8.026396 TCTTCTCATTCATCAGATAATGTCCA 57.974 34.615 10.16 0.00 35.16 4.02
1846 1959 7.930325 TCTTCTCATTCATCAGATAATGTCCAC 59.070 37.037 10.16 0.00 35.16 4.02
1853 1966 4.902443 TCAGATAATGTCCACGAGTCTC 57.098 45.455 0.00 0.00 0.00 3.36
1854 1967 3.312697 TCAGATAATGTCCACGAGTCTCG 59.687 47.826 20.57 20.57 46.93 4.04
1940 2067 6.368791 CGGATGACTTTGTGAAGTTATGAAGA 59.631 38.462 1.91 0.00 45.88 2.87
1960 2087 0.809241 GGGAGCGAGCTTCATGTGAG 60.809 60.000 5.66 0.00 0.00 3.51
1978 2105 7.919091 TCATGTGAGATATACGAACCTGTAAAC 59.081 37.037 0.00 0.00 0.00 2.01
1980 2107 5.684626 GTGAGATATACGAACCTGTAAACGG 59.315 44.000 0.00 0.00 0.00 4.44
2035 2163 1.329292 TGCCGTTGTTTTCGTCAAGAG 59.671 47.619 0.00 0.00 0.00 2.85
2039 2167 4.788521 GCCGTTGTTTTCGTCAAGAGAATT 60.789 41.667 0.00 0.00 0.00 2.17
2072 2200 2.559998 AGCGTGAACAACAAAACCTG 57.440 45.000 0.00 0.00 0.00 4.00
2079 2207 4.091365 GTGAACAACAAAACCTGAAGTTGC 59.909 41.667 0.00 0.00 43.74 4.17
2085 2213 1.455383 AAACCTGAAGTTGCAGCCCG 61.455 55.000 0.00 0.00 39.19 6.13
2114 2242 5.065090 TGCAATACCTCTGATGAAATTGACG 59.935 40.000 12.80 0.00 0.00 4.35
2191 2320 9.189723 AGATTCCGTTAATTTTATACTCGTAGC 57.810 33.333 0.00 0.00 0.00 3.58
2192 2321 8.876275 ATTCCGTTAATTTTATACTCGTAGCA 57.124 30.769 0.00 0.00 0.00 3.49
2193 2322 8.700722 TTCCGTTAATTTTATACTCGTAGCAA 57.299 30.769 0.00 0.00 0.00 3.91
2194 2323 8.876275 TCCGTTAATTTTATACTCGTAGCAAT 57.124 30.769 0.00 0.00 0.00 3.56
2195 2324 8.757789 TCCGTTAATTTTATACTCGTAGCAATG 58.242 33.333 0.00 0.00 0.00 2.82
2196 2325 8.545420 CCGTTAATTTTATACTCGTAGCAATGT 58.455 33.333 0.00 0.00 0.00 2.71
2337 2466 8.529424 TGCATAGGTTGTATACTTGTAGTACT 57.471 34.615 0.00 0.00 32.84 2.73
2338 2467 9.631257 TGCATAGGTTGTATACTTGTAGTACTA 57.369 33.333 4.17 0.00 32.84 1.82
2464 2612 0.939577 CCATGATACCGCGTCCGAAG 60.940 60.000 4.92 0.00 36.29 3.79
2476 2624 2.414161 GCGTCCGAAGAAAAGGGAAATG 60.414 50.000 0.00 0.00 0.00 2.32
2477 2625 2.161609 CGTCCGAAGAAAAGGGAAATGG 59.838 50.000 0.00 0.00 0.00 3.16
2478 2626 3.418047 GTCCGAAGAAAAGGGAAATGGA 58.582 45.455 0.00 0.00 0.00 3.41
2479 2627 3.440522 GTCCGAAGAAAAGGGAAATGGAG 59.559 47.826 0.00 0.00 0.00 3.86
2480 2628 3.073946 TCCGAAGAAAAGGGAAATGGAGT 59.926 43.478 0.00 0.00 0.00 3.85
2493 2641 5.071788 GGGAAATGGAGTAGTACCATGATCA 59.928 44.000 0.00 0.00 45.89 2.92
2521 2669 0.826715 ACATGCAGATGACGCTACCT 59.173 50.000 0.00 0.00 33.36 3.08
2522 2670 2.031870 ACATGCAGATGACGCTACCTA 58.968 47.619 0.00 0.00 33.36 3.08
2523 2671 2.430694 ACATGCAGATGACGCTACCTAA 59.569 45.455 0.00 0.00 33.36 2.69
2524 2672 2.871182 TGCAGATGACGCTACCTAAG 57.129 50.000 0.00 0.00 0.00 2.18
2525 2673 2.375146 TGCAGATGACGCTACCTAAGA 58.625 47.619 0.00 0.00 0.00 2.10
2526 2674 2.359214 TGCAGATGACGCTACCTAAGAG 59.641 50.000 0.00 0.00 0.00 2.85
2528 2676 3.215151 CAGATGACGCTACCTAAGAGGA 58.785 50.000 0.00 0.00 37.67 3.71
2529 2677 3.823873 CAGATGACGCTACCTAAGAGGAT 59.176 47.826 0.00 0.00 37.67 3.24
2547 2702 4.077108 AGGATATATCAGACCACGCGTAA 58.923 43.478 13.44 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.472115 CGTCGTCGTTGTGGATTTGTTA 59.528 45.455 0.00 0.00 0.00 2.41
44 45 1.134226 GTCGTCGTCGTTGTGGATTT 58.866 50.000 1.33 0.00 38.33 2.17
51 52 2.128017 TCGTCGTCGTCGTCGTTG 60.128 61.111 18.44 5.92 45.27 4.10
52 53 2.127980 GTCGTCGTCGTCGTCGTT 60.128 61.111 18.44 0.00 45.27 3.85
67 68 0.660595 CGTCCTATCGCCATGTCGTC 60.661 60.000 0.00 0.00 0.00 4.20
68 69 1.359117 CGTCCTATCGCCATGTCGT 59.641 57.895 0.00 0.00 0.00 4.34
69 70 0.934901 CACGTCCTATCGCCATGTCG 60.935 60.000 0.00 0.00 0.00 4.35
70 71 0.597637 CCACGTCCTATCGCCATGTC 60.598 60.000 0.00 0.00 0.00 3.06
73 74 2.421739 GCCACGTCCTATCGCCAT 59.578 61.111 0.00 0.00 0.00 4.40
75 76 2.585247 GTGCCACGTCCTATCGCC 60.585 66.667 0.00 0.00 0.00 5.54
76 77 2.585247 GGTGCCACGTCCTATCGC 60.585 66.667 0.00 0.00 0.00 4.58
77 78 1.518572 GTGGTGCCACGTCCTATCG 60.519 63.158 5.53 0.00 37.19 2.92
87 88 2.607750 GGAGAGGAGGTGGTGCCA 60.608 66.667 0.00 0.00 40.61 4.92
91 92 2.037527 GACGGGAGAGGAGGTGGT 59.962 66.667 0.00 0.00 0.00 4.16
102 103 2.987547 GGGTGTGAGACGACGGGA 60.988 66.667 0.00 0.00 0.00 5.14
270 282 3.912907 CCGGGCGGTAGGCACTAG 61.913 72.222 0.00 0.00 45.36 2.57
276 288 3.436924 GTTTTGCCGGGCGGTAGG 61.437 66.667 15.40 0.00 37.65 3.18
370 396 3.052082 CTTGCTCACTGTGCCGGG 61.052 66.667 2.18 0.00 0.00 5.73
371 397 2.281070 ACTTGCTCACTGTGCCGG 60.281 61.111 2.12 0.00 0.00 6.13
372 398 2.610694 CCACTTGCTCACTGTGCCG 61.611 63.158 2.12 0.00 0.00 5.69
373 399 1.103398 AACCACTTGCTCACTGTGCC 61.103 55.000 2.12 0.00 0.00 5.01
374 400 0.740737 AAACCACTTGCTCACTGTGC 59.259 50.000 2.12 0.00 0.00 4.57
375 401 1.066002 CCAAACCACTTGCTCACTGTG 59.934 52.381 0.17 0.17 33.27 3.66
376 402 1.064758 TCCAAACCACTTGCTCACTGT 60.065 47.619 0.00 0.00 33.27 3.55
377 403 1.334869 GTCCAAACCACTTGCTCACTG 59.665 52.381 0.00 0.00 33.27 3.66
378 404 1.680338 GTCCAAACCACTTGCTCACT 58.320 50.000 0.00 0.00 33.27 3.41
379 405 0.307760 CGTCCAAACCACTTGCTCAC 59.692 55.000 0.00 0.00 33.27 3.51
380 406 1.444119 GCGTCCAAACCACTTGCTCA 61.444 55.000 0.00 0.00 33.27 4.26
381 407 1.282875 GCGTCCAAACCACTTGCTC 59.717 57.895 0.00 0.00 33.27 4.26
382 408 2.542907 CGCGTCCAAACCACTTGCT 61.543 57.895 0.00 0.00 33.27 3.91
383 409 1.500512 TACGCGTCCAAACCACTTGC 61.501 55.000 18.63 0.00 33.27 4.01
384 410 0.233848 GTACGCGTCCAAACCACTTG 59.766 55.000 18.63 0.00 34.52 3.16
385 411 1.216941 CGTACGCGTCCAAACCACTT 61.217 55.000 18.63 0.00 0.00 3.16
386 412 1.662446 CGTACGCGTCCAAACCACT 60.662 57.895 18.63 0.00 0.00 4.00
387 413 2.660612 CCGTACGCGTCCAAACCAC 61.661 63.158 18.63 5.32 36.15 4.16
388 414 2.356075 CCGTACGCGTCCAAACCA 60.356 61.111 18.63 0.00 36.15 3.67
410 436 5.670792 TTACAATACGAGGTGGTGAAGAT 57.329 39.130 0.00 0.00 0.00 2.40
412 438 6.348213 CCTTTTTACAATACGAGGTGGTGAAG 60.348 42.308 0.00 0.00 0.00 3.02
419 446 4.886579 ACGACCTTTTTACAATACGAGGT 58.113 39.130 0.00 0.00 40.04 3.85
421 448 4.489841 GCGACGACCTTTTTACAATACGAG 60.490 45.833 0.00 0.00 0.00 4.18
426 457 1.461897 CCGCGACGACCTTTTTACAAT 59.538 47.619 8.23 0.00 0.00 2.71
479 518 1.891919 GGTGCAAGCCAAGTCGTCA 60.892 57.895 0.00 0.00 0.00 4.35
511 554 5.050837 TGTTTCTTTCTTTACCGCGAACTAC 60.051 40.000 8.23 0.00 0.00 2.73
513 556 3.872771 TGTTTCTTTCTTTACCGCGAACT 59.127 39.130 8.23 0.00 0.00 3.01
515 558 4.879104 TTGTTTCTTTCTTTACCGCGAA 57.121 36.364 8.23 0.00 0.00 4.70
516 559 4.571580 TCTTTGTTTCTTTCTTTACCGCGA 59.428 37.500 8.23 0.00 0.00 5.87
534 578 2.293399 CCGGGACTCCTTTGTTTCTTTG 59.707 50.000 0.00 0.00 0.00 2.77
555 607 0.964700 GGTGGCGGTACCTATCCTAC 59.035 60.000 10.90 8.86 40.22 3.18
630 682 4.272511 TTTTTGCGGCGGGGAGGA 62.273 61.111 9.78 0.00 0.00 3.71
631 683 4.050934 GTTTTTGCGGCGGGGAGG 62.051 66.667 9.78 0.00 0.00 4.30
632 684 3.267597 CTGTTTTTGCGGCGGGGAG 62.268 63.158 9.78 0.00 0.00 4.30
633 685 3.291383 CTGTTTTTGCGGCGGGGA 61.291 61.111 9.78 0.00 0.00 4.81
691 743 1.900545 GCTCCCATACGGATAGGGCC 61.901 65.000 9.61 0.00 41.00 5.80
692 744 1.192146 TGCTCCCATACGGATAGGGC 61.192 60.000 9.61 2.84 41.00 5.19
697 749 1.409661 GGGTTTTGCTCCCATACGGAT 60.410 52.381 0.00 0.00 44.05 4.18
874 939 2.743126 CGTACTTATAGGAGGGAGAGCG 59.257 54.545 0.00 0.00 0.00 5.03
875 940 2.488937 GCGTACTTATAGGAGGGAGAGC 59.511 54.545 0.00 0.00 0.00 4.09
877 942 2.224967 GGGCGTACTTATAGGAGGGAGA 60.225 54.545 0.00 0.00 0.00 3.71
900 965 0.419459 AGGATCTGGAGGTTGGAGGT 59.581 55.000 0.00 0.00 0.00 3.85
957 1026 2.413765 GCGATCGAGTGGGAGGTC 59.586 66.667 21.57 0.00 0.00 3.85
1239 1321 2.976903 GCCTCCTCCATCATGCGC 60.977 66.667 0.00 0.00 0.00 6.09
1574 1656 1.007271 CGAGTGCACGTCTTGAGGT 60.007 57.895 12.01 0.00 0.00 3.85
1575 1657 1.734477 CCGAGTGCACGTCTTGAGG 60.734 63.158 12.01 4.66 0.00 3.86
1576 1658 2.375766 GCCGAGTGCACGTCTTGAG 61.376 63.158 12.01 0.00 40.77 3.02
1596 1678 0.883370 GAAGGAAACAAGCGACCGGT 60.883 55.000 6.92 6.92 0.00 5.28
1602 1684 4.084900 GCAAAAGAATGAAGGAAACAAGCG 60.085 41.667 0.00 0.00 0.00 4.68
1604 1686 5.280945 TCGCAAAAGAATGAAGGAAACAAG 58.719 37.500 0.00 0.00 0.00 3.16
1605 1687 5.067153 TCTCGCAAAAGAATGAAGGAAACAA 59.933 36.000 0.00 0.00 0.00 2.83
1606 1688 4.578516 TCTCGCAAAAGAATGAAGGAAACA 59.421 37.500 0.00 0.00 0.00 2.83
1607 1689 4.912187 GTCTCGCAAAAGAATGAAGGAAAC 59.088 41.667 0.00 0.00 0.00 2.78
1608 1690 4.023193 GGTCTCGCAAAAGAATGAAGGAAA 60.023 41.667 0.00 0.00 0.00 3.13
1632 1714 4.879545 AGTATTTGGCGGTGGTATTTACAG 59.120 41.667 0.00 0.00 0.00 2.74
1722 1829 9.661187 CCGACAGTTCCGATACATTATATATAC 57.339 37.037 0.00 0.00 0.00 1.47
1823 1936 6.040842 TCGTGGACATTATCTGATGAATGAGA 59.959 38.462 18.31 10.78 36.69 3.27
1825 1938 6.160576 TCGTGGACATTATCTGATGAATGA 57.839 37.500 18.31 0.29 36.69 2.57
1826 1939 5.987953 ACTCGTGGACATTATCTGATGAATG 59.012 40.000 0.00 8.78 38.70 2.67
1827 1940 6.041409 AGACTCGTGGACATTATCTGATGAAT 59.959 38.462 0.00 0.00 0.00 2.57
1828 1941 5.360999 AGACTCGTGGACATTATCTGATGAA 59.639 40.000 0.00 0.00 0.00 2.57
1846 1959 2.796304 ACTACGACTCTACGAGACTCG 58.204 52.381 22.97 22.97 46.93 4.18
1853 1966 6.305639 GGAAGCATTATACTACGACTCTACG 58.694 44.000 0.00 0.00 39.31 3.51
1854 1967 6.305639 CGGAAGCATTATACTACGACTCTAC 58.694 44.000 0.00 0.00 0.00 2.59
1855 1968 6.477669 CGGAAGCATTATACTACGACTCTA 57.522 41.667 0.00 0.00 0.00 2.43
1856 1969 5.359716 CGGAAGCATTATACTACGACTCT 57.640 43.478 0.00 0.00 0.00 3.24
1940 2067 1.220206 CACATGAAGCTCGCTCCCT 59.780 57.895 0.00 0.00 0.00 4.20
1960 2087 5.689068 CCTTCCGTTTACAGGTTCGTATATC 59.311 44.000 0.00 0.00 0.00 1.63
1978 2105 0.175760 ACATCGACATGTCCCTTCCG 59.824 55.000 20.03 8.11 39.15 4.30
1980 2107 2.271800 GTCACATCGACATGTCCCTTC 58.728 52.381 20.03 0.00 41.69 3.46
2035 2163 2.731976 CGCTACTCGGGCAGAATAATTC 59.268 50.000 0.00 0.00 33.78 2.17
2039 2167 0.384309 CACGCTACTCGGGCAGAATA 59.616 55.000 0.00 0.00 43.86 1.75
2072 2200 0.040067 CAAGTTCGGGCTGCAACTTC 60.040 55.000 16.10 0.00 40.19 3.01
2079 2207 0.451783 GGTATTGCAAGTTCGGGCTG 59.548 55.000 4.94 0.00 0.00 4.85
2085 2213 6.500684 TTTCATCAGAGGTATTGCAAGTTC 57.499 37.500 4.94 0.00 0.00 3.01
2223 2352 1.880027 CCAACAGTAAACTCCACCTGC 59.120 52.381 0.00 0.00 0.00 4.85
2325 2454 4.719773 TCGGGGGTACTAGTACTACAAGTA 59.280 45.833 27.71 9.20 36.36 2.24
2337 2466 3.181452 GCCATTAATTGTCGGGGGTACTA 60.181 47.826 0.00 0.00 0.00 1.82
2338 2467 2.422377 GCCATTAATTGTCGGGGGTACT 60.422 50.000 0.00 0.00 0.00 2.73
2339 2468 1.951602 GCCATTAATTGTCGGGGGTAC 59.048 52.381 0.00 0.00 0.00 3.34
2340 2469 1.847737 AGCCATTAATTGTCGGGGGTA 59.152 47.619 0.00 0.00 0.00 3.69
2341 2470 0.629058 AGCCATTAATTGTCGGGGGT 59.371 50.000 0.00 0.00 0.00 4.95
2342 2471 1.318576 GAGCCATTAATTGTCGGGGG 58.681 55.000 0.00 0.00 0.00 5.40
2421 2553 6.349363 GGGTACTCCATCAATTTGTTTCTGAC 60.349 42.308 0.00 0.00 35.00 3.51
2425 2557 5.975693 TGGGTACTCCATCAATTTGTTTC 57.024 39.130 0.00 0.00 41.46 2.78
2464 2612 5.812286 TGGTACTACTCCATTTCCCTTTTC 58.188 41.667 0.00 0.00 0.00 2.29
2476 2624 6.943146 TCTACAGATGATCATGGTACTACTCC 59.057 42.308 14.30 0.00 0.00 3.85
2477 2625 7.987750 TCTACAGATGATCATGGTACTACTC 57.012 40.000 14.30 0.00 0.00 2.59
2478 2626 7.780271 TGTTCTACAGATGATCATGGTACTACT 59.220 37.037 14.30 0.00 0.00 2.57
2479 2627 7.941919 TGTTCTACAGATGATCATGGTACTAC 58.058 38.462 14.30 12.67 0.00 2.73
2480 2628 8.579863 CATGTTCTACAGATGATCATGGTACTA 58.420 37.037 14.30 2.36 37.69 1.82
2521 2669 4.395231 CGCGTGGTCTGATATATCCTCTTA 59.605 45.833 10.25 0.00 0.00 2.10
2522 2670 3.191581 CGCGTGGTCTGATATATCCTCTT 59.808 47.826 10.25 0.00 0.00 2.85
2523 2671 2.750166 CGCGTGGTCTGATATATCCTCT 59.250 50.000 10.25 0.00 0.00 3.69
2524 2672 2.488545 ACGCGTGGTCTGATATATCCTC 59.511 50.000 12.93 1.11 0.00 3.71
2525 2673 2.515854 ACGCGTGGTCTGATATATCCT 58.484 47.619 12.93 0.00 0.00 3.24
2526 2674 4.413087 CTTACGCGTGGTCTGATATATCC 58.587 47.826 24.59 0.00 0.00 2.59
2528 2676 4.077108 TCCTTACGCGTGGTCTGATATAT 58.923 43.478 24.59 0.00 0.00 0.86
2529 2677 3.251729 GTCCTTACGCGTGGTCTGATATA 59.748 47.826 24.59 0.00 0.00 0.86
2547 2702 2.203640 TCGTGGGCTGTCTGTCCT 60.204 61.111 1.75 0.00 42.07 3.85


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

AutoCloner maintained by Alex Coulton.