Multiple sequence alignment - TraesCS6A01G304300

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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 TraesCS6A01G304300 chr6A 100.000 4137 0 0 1 4137 537312220 537316356 0.000000e+00 7640.0
1 TraesCS6A01G304300 chr6D 88.953 2073 140 31 1 2049 390832500 390834507 0.000000e+00 2477.0
2 TraesCS6A01G304300 chr6D 96.740 1227 36 2 1891 3117 390834509 390835731 0.000000e+00 2041.0
3 TraesCS6A01G304300 chr6D 89.346 1117 60 15 3023 4108 390835835 390836923 0.000000e+00 1349.0
4 TraesCS6A01G304300 chr6D 95.833 96 4 0 3022 3117 390835735 390835830 5.540000e-34 156.0
5 TraesCS6A01G304300 chr6B 93.516 1496 64 11 1891 3367 583627980 583626499 0.000000e+00 2194.0
6 TraesCS6A01G304300 chr6B 90.416 1513 93 24 548 2049 583629453 583627982 0.000000e+00 1943.0
7 TraesCS6A01G304300 chr6B 90.608 543 49 2 1 541 583631398 583630856 0.000000e+00 719.0
8 TraesCS6A01G304300 chr6B 95.824 431 18 0 3369 3799 583626422 583625992 0.000000e+00 697.0
9 TraesCS6A01G304300 chr6B 93.311 299 7 4 3840 4137 583625922 583625636 2.950000e-116 429.0
10 TraesCS6A01G304300 chr7D 100.000 28 0 0 330 357 623508939 623508912 7.000000e-03 52.8


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 TraesCS6A01G304300 chr6A 537312220 537316356 4136 False 7640.00 7640 100.000 1 4137 1 chr6A.!!$F1 4136
1 TraesCS6A01G304300 chr6D 390832500 390836923 4423 False 1505.75 2477 92.718 1 4108 4 chr6D.!!$F1 4107
2 TraesCS6A01G304300 chr6B 583625636 583631398 5762 True 1196.40 2194 92.735 1 4137 5 chr6B.!!$R1 4136

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
627 2050 0.464013 GGAGAGAGGGACGATGACGA 60.464 60.0 0.0 0.0 42.66 4.20 F
1522 2951 0.107214 TGGGGAATTGTCGATCTGGC 60.107 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 3053 0.037447 GCTGCTTCTCCTTCCTTGGT 59.963 55.000 0.0 0.0 0.0 3.67 R
3233 5028 1.004628 ACACATATGGCTGGCTTGTCA 59.995 47.619 7.8 0.0 0.0 3.58 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
26 27 7.558081 TCCAACGATTATGAAATCAATTGGGTA 59.442 33.333 20.31 8.53 46.38 3.69
33 34 9.604569 ATTATGAAATCAATTGGGTATGGATCA 57.395 29.630 5.42 0.67 0.00 2.92
111 118 8.308931 AGACATAGATTTACTTGTTTACGACCA 58.691 33.333 0.00 0.00 0.00 4.02
132 139 7.413657 CGACCATCCAAACAGAAAACGTATAAT 60.414 37.037 0.00 0.00 0.00 1.28
288 304 6.902224 AGATCTACTCATCTACGATCATCG 57.098 41.667 5.22 5.22 46.93 3.84
314 330 7.744715 GGAACAGATAATGTACAACACGAAAAG 59.255 37.037 0.00 0.00 43.00 2.27
366 382 8.306761 GTGGTCAAAGAAAATTTCACCTCATAT 58.693 33.333 8.55 0.00 0.00 1.78
380 396 4.940046 CACCTCATATGCTTGAGTTGAACT 59.060 41.667 0.00 0.00 38.12 3.01
388 404 5.474578 TGCTTGAGTTGAACTATGAGTCT 57.525 39.130 0.00 0.00 0.00 3.24
391 407 5.061560 GCTTGAGTTGAACTATGAGTCTTCG 59.938 44.000 0.00 0.00 0.00 3.79
396 412 2.826128 TGAACTATGAGTCTTCGCCTGT 59.174 45.455 0.00 0.00 0.00 4.00
417 433 1.069022 GCTTGAGTTGCATTGCTCGAA 60.069 47.619 10.49 0.00 34.67 3.71
439 455 2.328473 CTGACTCGCTTGAAACGATCA 58.672 47.619 0.00 0.00 39.12 2.92
445 461 5.168569 ACTCGCTTGAAACGATCAATTCTA 58.831 37.500 8.44 1.68 46.62 2.10
481 497 2.625737 CAGACTCGGATGTGCTTCAAT 58.374 47.619 0.00 0.00 0.00 2.57
482 498 3.430790 CCAGACTCGGATGTGCTTCAATA 60.431 47.826 0.00 0.00 0.00 1.90
483 499 3.553511 CAGACTCGGATGTGCTTCAATAC 59.446 47.826 0.00 0.00 0.00 1.89
510 527 6.318648 GTGCCATCCAGACTCAACAATATTTA 59.681 38.462 0.00 0.00 0.00 1.40
526 543 8.641499 ACAATATTTACACACAAACCAAACTG 57.359 30.769 0.00 0.00 0.00 3.16
527 544 7.223777 ACAATATTTACACACAAACCAAACTGC 59.776 33.333 0.00 0.00 0.00 4.40
528 545 3.512033 TTACACACAAACCAAACTGCC 57.488 42.857 0.00 0.00 0.00 4.85
529 546 0.534873 ACACACAAACCAAACTGCCC 59.465 50.000 0.00 0.00 0.00 5.36
530 547 0.534412 CACACAAACCAAACTGCCCA 59.466 50.000 0.00 0.00 0.00 5.36
531 548 1.066573 CACACAAACCAAACTGCCCAA 60.067 47.619 0.00 0.00 0.00 4.12
532 549 1.625818 ACACAAACCAAACTGCCCAAA 59.374 42.857 0.00 0.00 0.00 3.28
533 550 2.278854 CACAAACCAAACTGCCCAAAG 58.721 47.619 0.00 0.00 0.00 2.77
534 551 1.905894 ACAAACCAAACTGCCCAAAGT 59.094 42.857 0.00 0.00 0.00 2.66
535 552 2.278854 CAAACCAAACTGCCCAAAGTG 58.721 47.619 0.00 0.00 0.00 3.16
554 571 0.759060 GGCCCAAAGTCACCCAAAGT 60.759 55.000 0.00 0.00 0.00 2.66
555 572 0.673985 GCCCAAAGTCACCCAAAGTC 59.326 55.000 0.00 0.00 0.00 3.01
583 2006 2.642311 TCAAGGCTGGTTGGACAATCTA 59.358 45.455 0.00 0.00 0.00 1.98
596 2019 6.763715 TGGACAATCTATAGGCTACCAAAT 57.236 37.500 0.00 0.00 0.00 2.32
611 2034 2.102578 CCAAATGCCTACTTTGGGGAG 58.897 52.381 6.87 0.00 45.82 4.30
627 2050 0.464013 GGAGAGAGGGACGATGACGA 60.464 60.000 0.00 0.00 42.66 4.20
636 2059 3.254654 CGATGACGACGGCGCATT 61.255 61.111 12.58 0.00 42.48 3.56
642 2065 2.020836 GACGACGGCGCATTTTCGAT 62.021 55.000 21.04 7.53 42.48 3.59
662 2085 1.311859 CCGCTCCGGTGTATGTAGTA 58.688 55.000 0.00 0.00 42.73 1.82
663 2086 1.677576 CCGCTCCGGTGTATGTAGTAA 59.322 52.381 0.00 0.00 42.73 2.24
1026 2452 2.631580 GGAGAGCCCTAGATCCGCG 61.632 68.421 0.00 0.00 0.00 6.46
1131 2557 1.456705 GGAGTCCATCCTCCTCGCT 60.457 63.158 3.60 0.00 46.34 4.93
1238 2664 4.587684 CGGATCTAACACCAGGTACCTATT 59.412 45.833 15.80 9.38 0.00 1.73
1239 2665 5.070047 CGGATCTAACACCAGGTACCTATTT 59.930 44.000 15.80 7.82 0.00 1.40
1245 2671 1.208776 ACCAGGTACCTATTTCCGCAC 59.791 52.381 15.80 0.00 0.00 5.34
1283 2709 2.399356 CGGCCTTCCTCGCCTTTTC 61.399 63.158 0.00 0.00 44.73 2.29
1284 2710 1.002011 GGCCTTCCTCGCCTTTTCT 60.002 57.895 0.00 0.00 43.48 2.52
1285 2711 1.027255 GGCCTTCCTCGCCTTTTCTC 61.027 60.000 0.00 0.00 43.48 2.87
1288 2714 2.784347 CCTTCCTCGCCTTTTCTCTTT 58.216 47.619 0.00 0.00 0.00 2.52
1289 2715 2.744741 CCTTCCTCGCCTTTTCTCTTTC 59.255 50.000 0.00 0.00 0.00 2.62
1292 2718 3.403038 TCCTCGCCTTTTCTCTTTCTTG 58.597 45.455 0.00 0.00 0.00 3.02
1319 2747 2.445145 TCTTGGTTGGTTTCTGGATCCA 59.555 45.455 15.27 15.27 0.00 3.41
1377 2805 4.899239 GGCAGTCGGCGGATGAGG 62.899 72.222 7.21 0.00 46.16 3.86
1427 2855 1.226323 CGACGACGAGAAGCCGAAT 60.226 57.895 0.00 0.00 42.66 3.34
1431 2859 0.456142 CGACGAGAAGCCGAATGACA 60.456 55.000 0.00 0.00 0.00 3.58
1473 2902 1.449070 GCGTTCTTCCTTACCCCGG 60.449 63.158 0.00 0.00 0.00 5.73
1476 2905 0.251354 GTTCTTCCTTACCCCGGTCC 59.749 60.000 0.00 0.00 0.00 4.46
1491 2920 1.952635 GTCCGTTGAGCGTTTCGGT 60.953 57.895 11.61 0.00 42.95 4.69
1522 2951 0.107214 TGGGGAATTGTCGATCTGGC 60.107 55.000 0.00 0.00 0.00 4.85
1547 2976 6.787043 CGTTAATTTGAAATCTTTGCAGTTGC 59.213 34.615 0.00 0.00 42.50 4.17
1560 2989 1.242076 CAGTTGCCAAGAAGGAGGTG 58.758 55.000 0.00 0.00 41.22 4.00
1677 3106 2.421314 CCGTGCATGGATCGGCTA 59.579 61.111 21.08 0.00 37.90 3.93
1729 3158 1.133216 CTCGCAGATCGTTCTCCTTGA 59.867 52.381 0.00 0.00 39.67 3.02
1736 3165 5.277250 GCAGATCGTTCTCCTTGATTTCATC 60.277 44.000 0.00 0.00 0.00 2.92
1742 3171 5.871524 CGTTCTCCTTGATTTCATCTCTTGA 59.128 40.000 0.00 0.00 0.00 3.02
1743 3172 6.369890 CGTTCTCCTTGATTTCATCTCTTGAA 59.630 38.462 0.00 0.00 42.62 2.69
1776 3205 8.588290 ATGTGATTATCCCTGAGTAGAGTATC 57.412 38.462 0.00 0.00 0.00 2.24
1818 3247 3.192844 CAGATTTGCTTGGATGTCTGCTT 59.807 43.478 0.00 0.00 0.00 3.91
1861 3290 3.067461 GTGGTCACAGGTAAATTTGCACA 59.933 43.478 8.59 0.00 0.00 4.57
1872 3304 6.649557 AGGTAAATTTGCACACTACTGTCTAC 59.350 38.462 8.59 0.00 0.00 2.59
1874 3306 5.924475 AATTTGCACACTACTGTCTACAC 57.076 39.130 0.00 0.00 0.00 2.90
1881 3313 6.431852 TGCACACTACTGTCTACACATAGTTA 59.568 38.462 0.00 0.00 30.60 2.24
1882 3314 7.122204 TGCACACTACTGTCTACACATAGTTAT 59.878 37.037 0.00 0.00 30.60 1.89
1883 3315 7.974501 GCACACTACTGTCTACACATAGTTATT 59.025 37.037 0.00 0.00 30.60 1.40
1884 3316 9.856488 CACACTACTGTCTACACATAGTTATTT 57.144 33.333 0.00 0.00 30.60 1.40
1885 3317 9.856488 ACACTACTGTCTACACATAGTTATTTG 57.144 33.333 0.00 0.00 30.60 2.32
1886 3318 9.856488 CACTACTGTCTACACATAGTTATTTGT 57.144 33.333 0.00 0.00 30.60 2.83
1938 3517 5.902681 AGCCAAGTTTTAACTTCCAGAAAC 58.097 37.500 4.93 0.00 45.65 2.78
1967 3546 9.127006 TGATATTGATTTGTTTCGTGAATTGTG 57.873 29.630 0.00 0.00 0.00 3.33
1968 3547 9.128107 GATATTGATTTGTTTCGTGAATTGTGT 57.872 29.630 0.00 0.00 0.00 3.72
1971 3550 5.746245 TGATTTGTTTCGTGAATTGTGTTCC 59.254 36.000 0.00 0.00 0.00 3.62
1981 3562 5.450688 CGTGAATTGTGTTCCCCTGTTTTTA 60.451 40.000 0.00 0.00 0.00 1.52
1987 3568 2.156917 GTTCCCCTGTTTTTACTCCCG 58.843 52.381 0.00 0.00 0.00 5.14
1998 3579 5.106317 TGTTTTTACTCCCGAGATTCAATGC 60.106 40.000 0.00 0.00 0.00 3.56
2026 3607 8.498575 TGATGTGTATAAACCCCTTATTCATCA 58.501 33.333 0.00 0.00 38.01 3.07
2036 3617 7.633018 ACCCCTTATTCATCACATGTACTAT 57.367 36.000 0.00 0.00 0.00 2.12
2039 3620 7.821359 CCCCTTATTCATCACATGTACTATCAG 59.179 40.741 0.00 0.00 0.00 2.90
2049 3630 8.183104 TCACATGTACTATCAGGAATTAGGAG 57.817 38.462 0.00 0.00 0.00 3.69
2052 3633 6.656632 TGTACTATCAGGAATTAGGAGCTG 57.343 41.667 0.00 0.00 0.00 4.24
2104 3685 5.528043 TGTTGTTAATCACTTGTGGCAAT 57.472 34.783 0.00 0.00 0.00 3.56
2199 3780 5.065218 GTGAAGTGTTGACTGTGACAAAGAT 59.935 40.000 0.00 0.00 30.61 2.40
2200 3781 6.257849 GTGAAGTGTTGACTGTGACAAAGATA 59.742 38.462 0.00 0.00 30.61 1.98
2221 3802 7.227156 AGATATTAGCATCCCTGTTAACTTGG 58.773 38.462 7.22 8.93 31.89 3.61
2388 3970 1.039856 TTGCCCCTTTCTTTCACTGC 58.960 50.000 0.00 0.00 0.00 4.40
2479 4061 6.535508 GTCAGTTAATCAGGTAAGCTTCGATT 59.464 38.462 0.00 10.01 0.00 3.34
2587 4169 5.853936 TCTTGCACTATCAACACAGTACTT 58.146 37.500 0.00 0.00 0.00 2.24
2759 4347 0.886490 CAGCTTCACCACACAGGACC 60.886 60.000 0.00 0.00 41.22 4.46
3022 4610 4.631131 TCATGACGGCTTTCGATAATGAT 58.369 39.130 0.00 0.00 42.43 2.45
3121 4907 0.039074 CAGTTCTCCTTCGTGCTCGT 60.039 55.000 8.17 0.00 38.33 4.18
3233 5028 8.617809 ACTTGTATTGTGTGAAAGTAAAACGAT 58.382 29.630 0.00 0.00 29.56 3.73
3238 5033 6.424176 TGTGTGAAAGTAAAACGATGACAA 57.576 33.333 0.00 0.00 0.00 3.18
3239 5034 6.482835 TGTGTGAAAGTAAAACGATGACAAG 58.517 36.000 0.00 0.00 0.00 3.16
3240 5035 5.395486 GTGTGAAAGTAAAACGATGACAAGC 59.605 40.000 0.00 0.00 0.00 4.01
3241 5036 4.909880 GTGAAAGTAAAACGATGACAAGCC 59.090 41.667 0.00 0.00 0.00 4.35
3335 5134 6.543831 GCATTTTCTCTAGCTGGATTAAGGAA 59.456 38.462 0.00 0.00 0.00 3.36
3343 5142 5.359194 AGCTGGATTAAGGAATTTCTCGA 57.641 39.130 0.00 0.00 0.00 4.04
3345 5144 5.994668 AGCTGGATTAAGGAATTTCTCGATC 59.005 40.000 0.00 0.00 0.00 3.69
3354 5153 4.891756 AGGAATTTCTCGATCCGGTAGTTA 59.108 41.667 0.00 0.00 38.31 2.24
3570 5444 8.273780 AGAAACCTATTGTCATCAACAGAATC 57.726 34.615 0.00 0.00 39.58 2.52
3724 5609 5.617252 ACCAAAACTTCGAGAAATACAGGA 58.383 37.500 0.00 0.00 0.00 3.86
3725 5610 5.469084 ACCAAAACTTCGAGAAATACAGGAC 59.531 40.000 0.00 0.00 0.00 3.85
3778 5674 7.168135 GCAACCAAGTTATTCAAAGAGAAACTG 59.832 37.037 0.00 0.00 40.22 3.16
3928 5875 7.556275 TCCAACACTCAAAATCCAGGTATTATC 59.444 37.037 0.00 0.00 0.00 1.75
3992 5939 4.119862 CCATATGTGTTTCCTGTAGTCCG 58.880 47.826 1.24 0.00 0.00 4.79
4004 5951 4.081309 TCCTGTAGTCCGGACAAATTTAGG 60.081 45.833 35.00 27.86 0.00 2.69
4006 5953 3.262405 TGTAGTCCGGACAAATTTAGGCT 59.738 43.478 35.00 13.71 0.00 4.58
4113 6060 2.799978 CGCATCGATAAACCATGCACTA 59.200 45.455 0.00 0.00 42.65 2.74
4123 6070 8.280497 CGATAAACCATGCACTAATTAAGGTAC 58.720 37.037 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.604569 AATGATCCATACCCAATTGATTTCATA 57.395 29.630 7.12 0.00 0.00 2.15
26 27 3.379372 CAGTCGCCTGAAAAATGATCCAT 59.621 43.478 0.00 0.00 41.50 3.41
50 51 0.030101 AAACGTGTCACAATTGGGCG 59.970 50.000 10.83 7.51 0.00 6.13
95 102 5.821470 TGTTTGGATGGTCGTAAACAAGTAA 59.179 36.000 0.00 0.00 39.31 2.24
100 107 4.074627 TCTGTTTGGATGGTCGTAAACA 57.925 40.909 0.00 0.00 39.79 2.83
132 139 7.654568 TCTCACTCTTTCACACGACTTTTATA 58.345 34.615 0.00 0.00 0.00 0.98
150 158 3.951037 TGACCTCTAGCTTCATCTCACTC 59.049 47.826 0.00 0.00 0.00 3.51
151 159 3.974719 TGACCTCTAGCTTCATCTCACT 58.025 45.455 0.00 0.00 0.00 3.41
288 304 6.715344 TTCGTGTTGTACATTATCTGTTCC 57.285 37.500 0.00 0.00 39.39 3.62
366 382 5.474578 AGACTCATAGTTCAACTCAAGCA 57.525 39.130 0.00 0.00 0.00 3.91
391 407 0.316204 AATGCAACTCAAGCACAGGC 59.684 50.000 0.00 0.00 45.95 4.85
417 433 0.387929 TCGTTTCAAGCGAGTCAGGT 59.612 50.000 0.00 0.00 34.11 4.00
439 455 5.819991 TGGCTCTGAAGGAACAATAGAATT 58.180 37.500 0.00 0.00 0.00 2.17
445 461 2.641815 AGTCTGGCTCTGAAGGAACAAT 59.358 45.455 0.00 0.00 0.00 2.71
510 527 0.534873 GGGCAGTTTGGTTTGTGTGT 59.465 50.000 0.00 0.00 0.00 3.72
527 544 0.758685 TGACTTTGGGCCACTTTGGG 60.759 55.000 5.23 0.00 38.19 4.12
528 545 0.389025 GTGACTTTGGGCCACTTTGG 59.611 55.000 5.23 0.00 41.55 3.28
529 546 0.389025 GGTGACTTTGGGCCACTTTG 59.611 55.000 5.23 0.00 0.00 2.77
530 547 0.759060 GGGTGACTTTGGGCCACTTT 60.759 55.000 5.23 0.00 0.00 2.66
531 548 1.152546 GGGTGACTTTGGGCCACTT 60.153 57.895 5.23 0.00 0.00 3.16
532 549 1.943730 TTGGGTGACTTTGGGCCACT 61.944 55.000 5.23 0.00 0.00 4.00
533 550 1.045911 TTTGGGTGACTTTGGGCCAC 61.046 55.000 5.23 0.00 0.00 5.01
534 551 0.758685 CTTTGGGTGACTTTGGGCCA 60.759 55.000 0.00 0.00 0.00 5.36
535 552 0.759060 ACTTTGGGTGACTTTGGGCC 60.759 55.000 0.00 0.00 0.00 5.80
554 571 0.036732 AACCAGCCTTGAGAATGCGA 59.963 50.000 0.00 0.00 0.00 5.10
555 572 0.169672 CAACCAGCCTTGAGAATGCG 59.830 55.000 0.00 0.00 0.00 4.73
596 2019 1.573108 CTCTCTCCCCAAAGTAGGCA 58.427 55.000 0.00 0.00 0.00 4.75
605 2028 1.075970 CATCGTCCCTCTCTCCCCA 60.076 63.158 0.00 0.00 0.00 4.96
608 2031 0.464013 TCGTCATCGTCCCTCTCTCC 60.464 60.000 0.00 0.00 38.33 3.71
611 2034 1.352404 CGTCGTCATCGTCCCTCTC 59.648 63.158 0.00 0.00 38.33 3.20
627 2050 2.808958 CGGATCGAAAATGCGCCGT 61.809 57.895 4.18 0.00 33.97 5.68
655 2078 5.916661 AGACCACTTGACGATTACTACAT 57.083 39.130 0.00 0.00 0.00 2.29
662 2085 8.964476 ATAAATTCATAGACCACTTGACGATT 57.036 30.769 0.00 0.00 0.00 3.34
663 2086 8.964476 AATAAATTCATAGACCACTTGACGAT 57.036 30.769 0.00 0.00 0.00 3.73
790 2215 6.624423 CCTTCAACTGGGATAACAAAAGATG 58.376 40.000 0.00 0.00 0.00 2.90
1238 2664 3.577334 GATTGGTGGGGGTGCGGAA 62.577 63.158 0.00 0.00 0.00 4.30
1239 2665 4.041762 GATTGGTGGGGGTGCGGA 62.042 66.667 0.00 0.00 0.00 5.54
1280 2706 6.180472 ACCAAGACAAGACAAGAAAGAGAAA 58.820 36.000 0.00 0.00 0.00 2.52
1283 2709 5.220931 CCAACCAAGACAAGACAAGAAAGAG 60.221 44.000 0.00 0.00 0.00 2.85
1284 2710 4.640201 CCAACCAAGACAAGACAAGAAAGA 59.360 41.667 0.00 0.00 0.00 2.52
1285 2711 4.399303 ACCAACCAAGACAAGACAAGAAAG 59.601 41.667 0.00 0.00 0.00 2.62
1288 2714 3.644966 ACCAACCAAGACAAGACAAGA 57.355 42.857 0.00 0.00 0.00 3.02
1289 2715 4.399303 AGAAACCAACCAAGACAAGACAAG 59.601 41.667 0.00 0.00 0.00 3.16
1292 2718 3.066760 CCAGAAACCAACCAAGACAAGAC 59.933 47.826 0.00 0.00 0.00 3.01
1427 2855 2.217750 CAACACCGACCTTCATTGTCA 58.782 47.619 0.00 0.00 32.91 3.58
1431 2859 0.893727 GGGCAACACCGACCTTCATT 60.894 55.000 0.00 0.00 40.62 2.57
1491 2920 3.772025 ACAATTCCCCAAACAGACACAAA 59.228 39.130 0.00 0.00 0.00 2.83
1522 2951 6.787043 GCAACTGCAAAGATTTCAAATTAACG 59.213 34.615 0.00 0.00 41.59 3.18
1547 2976 1.612726 CCTGCTTCACCTCCTTCTTGG 60.613 57.143 0.00 0.00 37.10 3.61
1560 2989 3.077556 TCCTCCTCCGCCTGCTTC 61.078 66.667 0.00 0.00 0.00 3.86
1624 3053 0.037447 GCTGCTTCTCCTTCCTTGGT 59.963 55.000 0.00 0.00 0.00 3.67
1665 3094 0.322975 CCTCCCTTAGCCGATCCATG 59.677 60.000 0.00 0.00 0.00 3.66
1677 3106 1.682257 GCAAGACAGCTCCTCCCTT 59.318 57.895 0.00 0.00 0.00 3.95
1736 3165 9.622004 GGATAATCACATATGCAATTTCAAGAG 57.378 33.333 1.58 0.00 0.00 2.85
1742 3171 7.727186 ACTCAGGGATAATCACATATGCAATTT 59.273 33.333 1.58 0.00 0.00 1.82
1743 3172 7.236529 ACTCAGGGATAATCACATATGCAATT 58.763 34.615 1.58 5.58 0.00 2.32
1776 3205 4.916831 TCTGCGCAAAATCAAACACTAATG 59.083 37.500 13.05 0.00 0.00 1.90
1818 3247 1.302192 GGCGTGGTACTTGGCTGAA 60.302 57.895 0.00 0.00 0.00 3.02
1872 3304 7.322699 GTGAACCAACGAACAAATAACTATGTG 59.677 37.037 0.00 0.00 0.00 3.21
1874 3306 7.356540 TGTGAACCAACGAACAAATAACTATG 58.643 34.615 0.00 0.00 0.00 2.23
1902 3334 0.601558 CTTGGCTCTGTGCTGCAAAT 59.398 50.000 2.77 0.00 42.39 2.32
1948 3527 5.174943 GGGAACACAATTCACGAAACAAATC 59.825 40.000 0.00 0.00 0.00 2.17
1967 3546 2.156917 CGGGAGTAAAAACAGGGGAAC 58.843 52.381 0.00 0.00 0.00 3.62
1968 3547 2.039348 CTCGGGAGTAAAAACAGGGGAA 59.961 50.000 0.00 0.00 0.00 3.97
1971 3550 3.629142 ATCTCGGGAGTAAAAACAGGG 57.371 47.619 0.00 0.00 0.00 4.45
1981 3562 0.537188 ACGCATTGAATCTCGGGAGT 59.463 50.000 0.00 0.00 0.00 3.85
1987 3568 5.663795 ATACACATCACGCATTGAATCTC 57.336 39.130 0.00 0.00 37.92 2.75
1998 3579 6.764085 TGAATAAGGGGTTTATACACATCACG 59.236 38.462 0.00 0.00 31.68 4.35
2026 3607 6.784969 AGCTCCTAATTCCTGATAGTACATGT 59.215 38.462 2.69 2.69 0.00 3.21
2036 3617 4.287067 AGAAACACAGCTCCTAATTCCTGA 59.713 41.667 0.00 0.00 0.00 3.86
2039 3620 3.691609 CCAGAAACACAGCTCCTAATTCC 59.308 47.826 0.00 0.00 0.00 3.01
2049 3630 4.508861 TCGTAAAGTAACCAGAAACACAGC 59.491 41.667 0.00 0.00 0.00 4.40
2052 3633 7.170320 TGAATCTCGTAAAGTAACCAGAAACAC 59.830 37.037 0.00 0.00 0.00 3.32
2104 3685 7.212976 TCAAAAATAAGCATTGCCAAGTACAA 58.787 30.769 4.70 0.00 0.00 2.41
2180 3761 7.095229 TGCTAATATCTTTGTCACAGTCAACAC 60.095 37.037 0.00 0.00 0.00 3.32
2199 3780 6.069905 TGTCCAAGTTAACAGGGATGCTAATA 60.070 38.462 17.88 0.00 0.00 0.98
2200 3781 5.193679 GTCCAAGTTAACAGGGATGCTAAT 58.806 41.667 17.88 0.00 0.00 1.73
2221 3802 6.318648 TCAATATACCAAAACTCATGGCTGTC 59.681 38.462 0.00 0.00 41.89 3.51
2355 3936 1.463674 GGGCAACAGTGTTATGAGGG 58.536 55.000 8.49 0.00 39.74 4.30
2479 4061 6.707440 TTGGAGTAGTGCAAAATCTTGAAA 57.293 33.333 1.46 0.00 34.14 2.69
2759 4347 3.372206 GTGCTGTTGCCTATTCTAGTGTG 59.628 47.826 0.00 0.00 38.71 3.82
2802 4390 3.460648 GGCATACTTCTTCTGCCGT 57.539 52.632 0.00 0.00 45.35 5.68
3121 4907 2.158534 TCAAAACTAAAGAGGCCAGCCA 60.159 45.455 12.03 0.00 38.92 4.75
3233 5028 1.004628 ACACATATGGCTGGCTTGTCA 59.995 47.619 7.80 0.00 0.00 3.58
3238 5033 1.285962 AGGAAACACATATGGCTGGCT 59.714 47.619 7.80 0.00 0.00 4.75
3239 5034 1.406539 CAGGAAACACATATGGCTGGC 59.593 52.381 7.80 0.00 0.00 4.85
3240 5035 2.726821 ACAGGAAACACATATGGCTGG 58.273 47.619 7.80 0.00 0.00 4.85
3241 5036 6.542005 TGTATTACAGGAAACACATATGGCTG 59.458 38.462 7.80 0.00 0.00 4.85
3335 5134 5.768662 TGATCTAACTACCGGATCGAGAAAT 59.231 40.000 9.46 0.00 38.79 2.17
3343 5142 6.608002 AGAGTTCTTTGATCTAACTACCGGAT 59.392 38.462 9.46 0.00 33.72 4.18
3345 5144 6.210287 AGAGTTCTTTGATCTAACTACCGG 57.790 41.667 0.00 0.00 33.72 5.28
3566 5440 6.591935 TGAACATTGGTATAGAGTGGGATTC 58.408 40.000 0.00 0.00 0.00 2.52
3570 5444 5.066505 GCTTTGAACATTGGTATAGAGTGGG 59.933 44.000 0.00 0.00 0.00 4.61
3724 5609 2.888834 AATGCTTTGTTCAAAGGCGT 57.111 40.000 21.56 14.19 0.00 5.68
3725 5610 3.122297 TGAAATGCTTTGTTCAAAGGCG 58.878 40.909 21.56 3.79 30.93 5.52
3841 5737 9.973450 TGCTTGTTATTGTTTGTATAACATGTT 57.027 25.926 16.68 16.68 43.89 2.71
3859 5806 1.979855 ATGTGTGCCACTGCTTGTTA 58.020 45.000 0.00 0.00 38.71 2.41
3860 5807 1.979855 TATGTGTGCCACTGCTTGTT 58.020 45.000 0.00 0.00 38.71 2.83
3861 5808 2.205022 ATATGTGTGCCACTGCTTGT 57.795 45.000 0.00 0.00 38.71 3.16
3928 5875 5.569413 AGCTTGTCGTTGTTTTACTTTCAG 58.431 37.500 0.00 0.00 0.00 3.02
3992 5939 5.644977 AGTAAAGCAGCCTAAATTTGTCC 57.355 39.130 0.00 0.00 0.00 4.02
4004 5951 3.166489 ACCGTCATCTAGTAAAGCAGC 57.834 47.619 0.00 0.00 0.00 5.25
4006 5953 5.452776 CCCATTACCGTCATCTAGTAAAGCA 60.453 44.000 0.00 0.00 30.33 3.91


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

AutoCloner maintained by Alex Coulton.