Multiple sequence alignment - TraesCS6B01G144400

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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 TraesCS6B01G144400 chr6B 100.000 3449 0 0 1 3449 143788010 143784562 0.000000e+00 6370.0
1 TraesCS6B01G144400 chr6D 96.597 2645 87 3 808 3449 68870197 68867553 0.000000e+00 4383.0
2 TraesCS6B01G144400 chr6A 93.953 2712 146 11 748 3449 86487413 86484710 0.000000e+00 4084.0
3 TraesCS6B01G144400 chr6A 94.393 107 6 0 85 191 86488435 86488329 7.660000e-37 165.0
4 TraesCS6B01G144400 chr3B 72.546 1202 281 38 1034 2206 5938579 5939760 2.550000e-91 346.0
5 TraesCS6B01G144400 chr4A 76.923 481 89 16 198 664 576926030 576926502 1.590000e-63 254.0
6 TraesCS6B01G144400 chr2D 92.000 75 3 3 424 497 559393317 559393245 6.090000e-18 102.0
7 TraesCS6B01G144400 chr2B 89.610 77 5 3 424 499 668568156 668568082 1.020000e-15 95.3
8 TraesCS6B01G144400 chr2B 89.610 77 5 3 424 499 668568514 668568440 1.020000e-15 95.3
9 TraesCS6B01G144400 chr4D 82.022 89 13 3 576 664 477541838 477541753 4.770000e-09 73.1
10 TraesCS6B01G144400 chr1D 88.333 60 7 0 606 665 347302351 347302292 4.770000e-09 73.1


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 TraesCS6B01G144400 chr6B 143784562 143788010 3448 True 6370.0 6370 100.000 1 3449 1 chr6B.!!$R1 3448
1 TraesCS6B01G144400 chr6D 68867553 68870197 2644 True 4383.0 4383 96.597 808 3449 1 chr6D.!!$R1 2641
2 TraesCS6B01G144400 chr6A 86484710 86488435 3725 True 2124.5 4084 94.173 85 3449 2 chr6A.!!$R1 3364
3 TraesCS6B01G144400 chr3B 5938579 5939760 1181 False 346.0 346 72.546 1034 2206 1 chr3B.!!$F1 1172

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
42 43 0.031585 AGTAACACAACGCTCGCTCA 59.968 50.0 0.0 0.0 0.00 4.26 F
44 45 0.031585 TAACACAACGCTCGCTCAGT 59.968 50.0 0.0 0.0 0.00 3.41 F
262 322 0.033228 CGATGATCCAGACCCAGAGC 59.967 60.0 0.0 0.0 0.00 4.09 F
2022 2413 0.044092 TCCTGCCATCTGGGTTCCTA 59.956 55.0 0.0 0.0 39.65 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 2113 1.517832 GTCAGGCTGCCGTATCACT 59.482 57.895 13.96 0.0 0.0 3.41 R
2202 2593 6.016360 CCTTGGTTTCTTCATGTAACATCACA 60.016 38.462 0.00 0.0 0.0 3.58 R
2409 2800 0.105194 TCCACTTCCTCACCACCTCA 60.105 55.000 0.00 0.0 0.0 3.86 R
3373 3770 0.716591 ATACCCTCCTCCAGACCACA 59.283 55.000 0.00 0.0 0.0 4.17 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
34 35 4.057730 CAGATTCTGCAGTAACACAACG 57.942 45.455 14.67 0.00 0.00 4.10
35 36 2.480419 AGATTCTGCAGTAACACAACGC 59.520 45.455 14.67 0.00 0.00 4.84
36 37 1.948104 TTCTGCAGTAACACAACGCT 58.052 45.000 14.67 0.00 0.00 5.07
37 38 1.497991 TCTGCAGTAACACAACGCTC 58.502 50.000 14.67 0.00 0.00 5.03
38 39 0.161658 CTGCAGTAACACAACGCTCG 59.838 55.000 5.25 0.00 0.00 5.03
39 40 1.154654 GCAGTAACACAACGCTCGC 60.155 57.895 0.00 0.00 0.00 5.03
40 41 1.557443 GCAGTAACACAACGCTCGCT 61.557 55.000 0.00 0.00 0.00 4.93
41 42 0.435008 CAGTAACACAACGCTCGCTC 59.565 55.000 0.00 0.00 0.00 5.03
42 43 0.031585 AGTAACACAACGCTCGCTCA 59.968 50.000 0.00 0.00 0.00 4.26
43 44 0.435008 GTAACACAACGCTCGCTCAG 59.565 55.000 0.00 0.00 0.00 3.35
44 45 0.031585 TAACACAACGCTCGCTCAGT 59.968 50.000 0.00 0.00 0.00 3.41
45 46 1.215655 AACACAACGCTCGCTCAGTC 61.216 55.000 0.00 0.00 0.00 3.51
46 47 1.661509 CACAACGCTCGCTCAGTCA 60.662 57.895 0.00 0.00 0.00 3.41
47 48 1.010935 CACAACGCTCGCTCAGTCAT 61.011 55.000 0.00 0.00 0.00 3.06
48 49 0.526211 ACAACGCTCGCTCAGTCATA 59.474 50.000 0.00 0.00 0.00 2.15
49 50 0.917259 CAACGCTCGCTCAGTCATAC 59.083 55.000 0.00 0.00 0.00 2.39
50 51 0.526211 AACGCTCGCTCAGTCATACA 59.474 50.000 0.00 0.00 0.00 2.29
51 52 0.179161 ACGCTCGCTCAGTCATACAC 60.179 55.000 0.00 0.00 0.00 2.90
52 53 0.179163 CGCTCGCTCAGTCATACACA 60.179 55.000 0.00 0.00 0.00 3.72
53 54 1.732405 CGCTCGCTCAGTCATACACAA 60.732 52.381 0.00 0.00 0.00 3.33
54 55 2.337583 GCTCGCTCAGTCATACACAAA 58.662 47.619 0.00 0.00 0.00 2.83
55 56 2.932614 GCTCGCTCAGTCATACACAAAT 59.067 45.455 0.00 0.00 0.00 2.32
56 57 3.242220 GCTCGCTCAGTCATACACAAATG 60.242 47.826 0.00 0.00 0.00 2.32
57 58 4.176271 CTCGCTCAGTCATACACAAATGA 58.824 43.478 0.00 0.00 33.48 2.57
58 59 4.565022 TCGCTCAGTCATACACAAATGAA 58.435 39.130 0.00 0.00 37.61 2.57
59 60 5.178061 TCGCTCAGTCATACACAAATGAAT 58.822 37.500 0.00 0.00 37.61 2.57
60 61 6.337356 TCGCTCAGTCATACACAAATGAATA 58.663 36.000 0.00 0.00 37.61 1.75
61 62 6.476706 TCGCTCAGTCATACACAAATGAATAG 59.523 38.462 0.00 0.00 37.61 1.73
62 63 6.425504 GCTCAGTCATACACAAATGAATAGC 58.574 40.000 0.00 0.00 37.61 2.97
63 64 6.512415 GCTCAGTCATACACAAATGAATAGCC 60.512 42.308 0.00 0.00 37.61 3.93
64 65 6.653020 TCAGTCATACACAAATGAATAGCCT 58.347 36.000 0.00 0.00 37.61 4.58
65 66 6.763135 TCAGTCATACACAAATGAATAGCCTC 59.237 38.462 0.00 0.00 37.61 4.70
66 67 6.017605 CAGTCATACACAAATGAATAGCCTCC 60.018 42.308 0.00 0.00 37.61 4.30
67 68 5.239525 GTCATACACAAATGAATAGCCTCCC 59.760 44.000 0.00 0.00 37.61 4.30
68 69 5.132648 TCATACACAAATGAATAGCCTCCCT 59.867 40.000 0.00 0.00 32.97 4.20
69 70 4.322057 ACACAAATGAATAGCCTCCCTT 57.678 40.909 0.00 0.00 0.00 3.95
70 71 5.450818 ACACAAATGAATAGCCTCCCTTA 57.549 39.130 0.00 0.00 0.00 2.69
71 72 5.826643 ACACAAATGAATAGCCTCCCTTAA 58.173 37.500 0.00 0.00 0.00 1.85
72 73 6.252995 ACACAAATGAATAGCCTCCCTTAAA 58.747 36.000 0.00 0.00 0.00 1.52
73 74 6.897413 ACACAAATGAATAGCCTCCCTTAAAT 59.103 34.615 0.00 0.00 0.00 1.40
74 75 8.058847 ACACAAATGAATAGCCTCCCTTAAATA 58.941 33.333 0.00 0.00 0.00 1.40
75 76 8.912988 CACAAATGAATAGCCTCCCTTAAATAA 58.087 33.333 0.00 0.00 0.00 1.40
76 77 9.487442 ACAAATGAATAGCCTCCCTTAAATAAA 57.513 29.630 0.00 0.00 0.00 1.40
77 78 9.971922 CAAATGAATAGCCTCCCTTAAATAAAG 57.028 33.333 0.00 0.00 34.73 1.85
78 79 9.936329 AAATGAATAGCCTCCCTTAAATAAAGA 57.064 29.630 0.00 0.00 37.38 2.52
103 104 6.515512 AAAGATACTGTAAGGGCCACATAT 57.484 37.500 6.18 2.90 39.30 1.78
106 107 2.205342 ACTGTAAGGGCCACATATGGT 58.795 47.619 6.18 0.00 43.92 3.55
122 123 6.003950 ACATATGGTGCATGGGTATTTACTC 58.996 40.000 7.80 0.00 0.00 2.59
152 153 2.964464 AGACAAGATCCGATCTGATGCT 59.036 45.455 11.76 6.47 40.13 3.79
176 177 7.268199 TCTTGATTCCAAAGATATGCACATC 57.732 36.000 0.00 0.00 0.00 3.06
191 192 2.416431 GCACATCAAGGCACCTTCAATC 60.416 50.000 0.00 0.00 33.42 2.67
193 194 2.225091 ACATCAAGGCACCTTCAATCCA 60.225 45.455 0.00 0.00 33.42 3.41
194 195 2.905415 TCAAGGCACCTTCAATCCAT 57.095 45.000 0.00 0.00 33.42 3.41
195 196 2.726821 TCAAGGCACCTTCAATCCATC 58.273 47.619 0.00 0.00 33.42 3.51
196 197 1.402968 CAAGGCACCTTCAATCCATCG 59.597 52.381 0.00 0.00 33.42 3.84
197 198 0.749454 AGGCACCTTCAATCCATCGC 60.749 55.000 0.00 0.00 0.00 4.58
199 200 1.728490 GCACCTTCAATCCATCGCCC 61.728 60.000 0.00 0.00 0.00 6.13
201 202 1.146041 CCTTCAATCCATCGCCCGA 59.854 57.895 0.00 0.00 0.00 5.14
213 273 4.530857 GCCCGACCGGTGATGAGG 62.531 72.222 14.63 6.17 0.00 3.86
217 277 1.320344 CCGACCGGTGATGAGGAAGA 61.320 60.000 14.63 0.00 0.00 2.87
234 294 4.946772 AGGAAGAAGAGATTTAAAGGCTGC 59.053 41.667 0.00 0.00 0.00 5.25
236 296 3.274288 AGAAGAGATTTAAAGGCTGCCG 58.726 45.455 13.96 0.00 0.00 5.69
242 302 2.070399 TTTAAAGGCTGCCGGGACCA 62.070 55.000 13.96 0.00 0.00 4.02
243 303 2.757980 TTAAAGGCTGCCGGGACCAC 62.758 60.000 13.96 0.00 0.00 4.16
254 314 1.391933 CGGGACCACGATGATCCAGA 61.392 60.000 0.00 0.00 28.89 3.86
262 322 0.033228 CGATGATCCAGACCCAGAGC 59.967 60.000 0.00 0.00 0.00 4.09
285 345 4.388499 AGCGCCCGTTGAACCGAT 62.388 61.111 2.29 0.00 0.00 4.18
298 358 2.700371 TGAACCGATGCTATGGAGTCAT 59.300 45.455 0.00 0.00 37.40 3.06
305 365 3.885724 TGCTATGGAGTCATGTCGAAA 57.114 42.857 0.00 0.00 34.96 3.46
307 367 4.769688 TGCTATGGAGTCATGTCGAAAAT 58.230 39.130 0.00 0.00 34.96 1.82
313 373 6.849588 TGGAGTCATGTCGAAAATATCATG 57.150 37.500 5.35 5.35 38.96 3.07
318 379 4.574421 TCATGTCGAAAATATCATGCCGTT 59.426 37.500 6.57 0.00 37.95 4.44
344 405 4.154347 GCTGTCCTCTGGGGAGCG 62.154 72.222 0.00 0.00 46.10 5.03
358 419 4.704833 AGCGGCCGAGTGCAATGT 62.705 61.111 33.48 0.00 43.89 2.71
361 422 2.359850 GGCCGAGTGCAATGTGGA 60.360 61.111 6.23 0.00 43.89 4.02
362 423 1.971167 GGCCGAGTGCAATGTGGAA 60.971 57.895 6.23 0.00 43.89 3.53
384 445 0.820891 CCATTGCCTCCTCCAATCCG 60.821 60.000 0.00 0.00 30.90 4.18
388 449 2.989639 CCTCCTCCAATCCGCACA 59.010 61.111 0.00 0.00 0.00 4.57
431 492 3.238788 TCCACACTAGTTGGAGTCAGA 57.761 47.619 17.63 1.19 0.00 3.27
432 493 3.779444 TCCACACTAGTTGGAGTCAGAT 58.221 45.455 17.63 0.00 0.00 2.90
443 504 2.894387 GTCAGATCTGCTGCCCGC 60.894 66.667 18.36 0.00 44.52 6.13
466 527 1.745264 CCAGAGAAGGCCGGAGATC 59.255 63.158 5.05 0.00 0.00 2.75
467 528 0.758685 CCAGAGAAGGCCGGAGATCT 60.759 60.000 5.05 3.94 0.00 2.75
506 581 1.668294 CGGAGTGGAGTGAAGTGCT 59.332 57.895 0.00 0.00 0.00 4.40
509 584 2.288825 CGGAGTGGAGTGAAGTGCTTAA 60.289 50.000 0.00 0.00 0.00 1.85
511 586 3.006967 GGAGTGGAGTGAAGTGCTTAAGA 59.993 47.826 6.67 0.00 0.00 2.10
521 596 3.695830 AGTGCTTAAGATTTGGTCCGA 57.304 42.857 6.67 0.00 0.00 4.55
525 600 2.603560 GCTTAAGATTTGGTCCGACGAG 59.396 50.000 6.67 0.00 0.00 4.18
526 601 2.288961 TAAGATTTGGTCCGACGAGC 57.711 50.000 0.00 0.00 37.01 5.03
536 611 4.903730 CGACGAGCGGATGAGTAG 57.096 61.111 0.00 0.00 36.03 2.57
545 620 5.066634 ACGAGCGGATGAGTAGGAATATATG 59.933 44.000 0.00 0.00 0.00 1.78
558 634 2.112279 ATATATGTGGGTCGGTGGGT 57.888 50.000 0.00 0.00 0.00 4.51
566 642 2.436646 GTCGGTGGGTCAGCATGG 60.437 66.667 0.00 0.00 36.16 3.66
568 644 4.033776 CGGTGGGTCAGCATGGGT 62.034 66.667 0.00 0.00 36.16 4.51
571 647 3.716195 TGGGTCAGCATGGGTCGG 61.716 66.667 0.00 0.00 36.16 4.79
574 650 2.351276 GTCAGCATGGGTCGGGTT 59.649 61.111 0.00 0.00 36.16 4.11
585 661 2.660206 TCGGGTTCGATGTGGTGG 59.340 61.111 0.00 0.00 40.88 4.61
587 663 1.740296 CGGGTTCGATGTGGTGGAC 60.740 63.158 0.00 0.00 39.00 4.02
588 664 1.740296 GGGTTCGATGTGGTGGACG 60.740 63.158 0.00 0.00 0.00 4.79
589 665 1.740296 GGTTCGATGTGGTGGACGG 60.740 63.158 0.00 0.00 0.00 4.79
594 670 2.607750 ATGTGGTGGACGGCTCCT 60.608 61.111 4.84 0.00 37.48 3.69
616 692 2.023414 GACGTGCCATATCCGTCCCA 62.023 60.000 0.00 0.00 43.77 4.37
624 700 5.354234 GTGCCATATCCGTCCCATATTTAAG 59.646 44.000 0.00 0.00 0.00 1.85
627 703 5.586243 CCATATCCGTCCCATATTTAAGCTG 59.414 44.000 0.00 0.00 0.00 4.24
633 709 6.878923 TCCGTCCCATATTTAAGCTGAATATG 59.121 38.462 23.54 23.54 42.78 1.78
637 713 8.103305 GTCCCATATTTAAGCTGAATATGAGGA 58.897 37.037 28.04 26.75 44.51 3.71
640 716 8.944029 CCATATTTAAGCTGAATATGAGGAGTG 58.056 37.037 28.04 15.67 44.51 3.51
644 720 1.875576 GCTGAATATGAGGAGTGCCGG 60.876 57.143 0.00 0.00 39.96 6.13
646 722 1.837439 TGAATATGAGGAGTGCCGGTT 59.163 47.619 1.90 0.00 39.96 4.44
650 726 1.972660 ATGAGGAGTGCCGGTTAGCC 61.973 60.000 1.90 0.00 39.96 3.93
665 741 4.699522 GCCCGGACGTTTGAGGCT 62.700 66.667 0.73 0.00 40.57 4.58
666 742 2.032071 CCCGGACGTTTGAGGCTT 59.968 61.111 0.73 0.00 0.00 4.35
667 743 2.033194 CCCGGACGTTTGAGGCTTC 61.033 63.158 0.73 0.00 0.00 3.86
668 744 1.301401 CCGGACGTTTGAGGCTTCA 60.301 57.895 0.00 0.00 0.00 3.02
670 746 0.721718 CGGACGTTTGAGGCTTCATC 59.278 55.000 0.00 0.00 32.27 2.92
671 747 1.087501 GGACGTTTGAGGCTTCATCC 58.912 55.000 0.00 0.00 32.27 3.51
672 748 0.721718 GACGTTTGAGGCTTCATCCG 59.278 55.000 13.66 13.66 34.71 4.18
683 790 0.807667 CTTCATCCGGACGCTTGAGG 60.808 60.000 6.12 2.91 0.00 3.86
694 801 2.510906 CTTGAGGCGGGTATGGGG 59.489 66.667 0.00 0.00 0.00 4.96
695 802 3.774599 CTTGAGGCGGGTATGGGGC 62.775 68.421 0.00 0.00 0.00 5.80
719 866 1.197721 GGTTGATGACGCTTCCTTGTG 59.802 52.381 0.00 0.00 0.00 3.33
726 873 2.059541 GACGCTTCCTTGTGTCTGTAC 58.940 52.381 0.00 0.00 42.31 2.90
768 1131 2.041928 AGCTAGCCTTCCCCAGCT 59.958 61.111 12.13 0.00 43.20 4.24
837 1200 2.024414 GGAGCAACCACAGTTCTGTTT 58.976 47.619 2.47 0.00 38.79 2.83
869 1232 4.186926 ACAATCAATCAGACACAGATCGG 58.813 43.478 0.00 0.00 0.00 4.18
872 1235 2.159379 TCAATCAGACACAGATCGGTCG 60.159 50.000 0.00 0.00 39.01 4.79
937 1303 3.443681 CCCACGAATTTAAGCCACTGATT 59.556 43.478 0.00 0.00 0.00 2.57
965 1331 1.710919 CTCGACTCGTCTCTCCGTG 59.289 63.158 0.00 0.00 0.00 4.94
1592 1965 4.087892 CCAGGACAGGACCAGCGG 62.088 72.222 0.00 0.00 0.00 5.52
1662 2035 2.032377 CGGCATACTTGTGAACACGTTT 60.032 45.455 0.00 0.00 30.67 3.60
1806 2197 1.227527 CAGGTGGCTCGACACACAA 60.228 57.895 14.53 0.00 43.08 3.33
1876 2267 4.498520 CGGCGCAGATGGACGAGT 62.499 66.667 10.83 0.00 0.00 4.18
1965 2356 2.995547 GACCCCGGTGCCAACTAT 59.004 61.111 0.00 0.00 0.00 2.12
2022 2413 0.044092 TCCTGCCATCTGGGTTCCTA 59.956 55.000 0.00 0.00 39.65 2.94
2273 2664 3.181447 GGAGCAGATGGGATGATTCTTGA 60.181 47.826 0.00 0.00 0.00 3.02
2320 2711 8.480501 TGAATGATATGATGAACAGTGAAGAGA 58.519 33.333 0.00 0.00 0.00 3.10
2327 2718 3.242867 TGAACAGTGAAGAGAGGGATGT 58.757 45.455 0.00 0.00 0.00 3.06
2332 2723 3.197333 CAGTGAAGAGAGGGATGTGATGT 59.803 47.826 0.00 0.00 0.00 3.06
2400 2791 1.202394 GCAAGTGGCATGTCACACAAA 60.202 47.619 30.70 0.00 43.97 2.83
2409 2800 3.548014 GCATGTCACACAAAACGCTTACT 60.548 43.478 0.00 0.00 0.00 2.24
2438 2829 1.757699 GAGGAAGTGGAAGGAGCGTAT 59.242 52.381 0.00 0.00 0.00 3.06
2510 2901 2.535012 TGTACGAGACCAATTGTGCA 57.465 45.000 4.43 0.00 0.00 4.57
2826 3220 7.591795 CGCTATATTGTGAGAGAATTAACGTCT 59.408 37.037 0.00 0.00 0.00 4.18
2842 3236 2.747446 ACGTCTGTGCAAACAAGAAAGT 59.253 40.909 0.00 0.00 0.00 2.66
2939 3333 3.765511 AGTGTGGATCACATTGAATTGGG 59.234 43.478 3.98 0.00 46.32 4.12
3060 3457 2.814805 AGTTAGCTCATGCACCCAAT 57.185 45.000 0.00 0.00 42.74 3.16
3171 3568 3.935315 TGCTGGATTTGAGAGAGAACAG 58.065 45.455 0.00 0.00 0.00 3.16
3178 3575 2.827800 TGAGAGAGAACAGTGGCAAG 57.172 50.000 0.00 0.00 0.00 4.01
3301 3698 3.569701 GGCATGAAGAAACTTGTGGAAGA 59.430 43.478 0.00 0.00 32.98 2.87
3303 3700 4.276926 GCATGAAGAAACTTGTGGAAGAGT 59.723 41.667 0.00 0.00 32.98 3.24
3306 3703 4.876107 TGAAGAAACTTGTGGAAGAGTGAC 59.124 41.667 0.00 0.00 32.98 3.67
3373 3770 5.503927 AGCATGATACTTGATTGTGGACTT 58.496 37.500 0.00 0.00 0.00 3.01
3429 3826 5.505181 AAGGATAGAGTGGTTGTGTTGAT 57.495 39.130 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.665323 GCGTTGTGTTACTGCAGAATCTG 60.665 47.826 23.35 5.78 34.12 2.90
14 15 2.480419 GCGTTGTGTTACTGCAGAATCT 59.520 45.455 23.35 0.00 0.00 2.40
15 16 2.480419 AGCGTTGTGTTACTGCAGAATC 59.520 45.455 23.35 10.07 0.00 2.52
16 17 2.480419 GAGCGTTGTGTTACTGCAGAAT 59.520 45.455 23.35 0.27 0.00 2.40
17 18 1.864711 GAGCGTTGTGTTACTGCAGAA 59.135 47.619 23.35 7.64 0.00 3.02
18 19 1.497991 GAGCGTTGTGTTACTGCAGA 58.502 50.000 23.35 0.48 0.00 4.26
19 20 0.161658 CGAGCGTTGTGTTACTGCAG 59.838 55.000 13.48 13.48 0.00 4.41
20 21 1.827315 GCGAGCGTTGTGTTACTGCA 61.827 55.000 0.00 0.00 0.00 4.41
21 22 1.154654 GCGAGCGTTGTGTTACTGC 60.155 57.895 0.00 0.00 0.00 4.40
22 23 0.435008 GAGCGAGCGTTGTGTTACTG 59.565 55.000 0.00 0.00 0.00 2.74
23 24 0.031585 TGAGCGAGCGTTGTGTTACT 59.968 50.000 0.00 0.00 0.00 2.24
24 25 0.435008 CTGAGCGAGCGTTGTGTTAC 59.565 55.000 0.00 0.00 0.00 2.50
25 26 0.031585 ACTGAGCGAGCGTTGTGTTA 59.968 50.000 0.00 0.00 0.00 2.41
26 27 1.215655 GACTGAGCGAGCGTTGTGTT 61.216 55.000 0.00 0.00 0.00 3.32
27 28 1.661821 GACTGAGCGAGCGTTGTGT 60.662 57.895 0.00 0.00 0.00 3.72
28 29 1.010935 ATGACTGAGCGAGCGTTGTG 61.011 55.000 0.00 0.00 0.00 3.33
29 30 0.526211 TATGACTGAGCGAGCGTTGT 59.474 50.000 0.00 0.00 0.00 3.32
30 31 0.917259 GTATGACTGAGCGAGCGTTG 59.083 55.000 0.00 0.00 0.00 4.10
31 32 0.526211 TGTATGACTGAGCGAGCGTT 59.474 50.000 0.00 0.00 0.00 4.84
32 33 0.179161 GTGTATGACTGAGCGAGCGT 60.179 55.000 0.00 0.00 0.00 5.07
33 34 0.179163 TGTGTATGACTGAGCGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
34 35 1.996292 TTGTGTATGACTGAGCGAGC 58.004 50.000 0.00 0.00 0.00 5.03
35 36 4.176271 TCATTTGTGTATGACTGAGCGAG 58.824 43.478 0.00 0.00 29.82 5.03
36 37 4.186856 TCATTTGTGTATGACTGAGCGA 57.813 40.909 0.00 0.00 29.82 4.93
37 38 4.926860 TTCATTTGTGTATGACTGAGCG 57.073 40.909 0.00 0.00 34.41 5.03
38 39 6.425504 GCTATTCATTTGTGTATGACTGAGC 58.574 40.000 0.00 0.00 34.41 4.26
39 40 6.765036 AGGCTATTCATTTGTGTATGACTGAG 59.235 38.462 0.00 0.00 34.41 3.35
40 41 6.653020 AGGCTATTCATTTGTGTATGACTGA 58.347 36.000 0.00 0.00 34.41 3.41
41 42 6.017605 GGAGGCTATTCATTTGTGTATGACTG 60.018 42.308 0.00 0.00 34.41 3.51
42 43 6.058183 GGAGGCTATTCATTTGTGTATGACT 58.942 40.000 0.00 0.00 34.41 3.41
43 44 5.239525 GGGAGGCTATTCATTTGTGTATGAC 59.760 44.000 0.00 0.00 34.41 3.06
44 45 5.132648 AGGGAGGCTATTCATTTGTGTATGA 59.867 40.000 0.00 0.00 32.87 2.15
45 46 5.380043 AGGGAGGCTATTCATTTGTGTATG 58.620 41.667 0.00 0.00 0.00 2.39
46 47 5.653255 AGGGAGGCTATTCATTTGTGTAT 57.347 39.130 0.00 0.00 0.00 2.29
47 48 5.450818 AAGGGAGGCTATTCATTTGTGTA 57.549 39.130 0.00 0.00 0.00 2.90
48 49 4.322057 AAGGGAGGCTATTCATTTGTGT 57.678 40.909 0.00 0.00 0.00 3.72
49 50 6.773976 TTTAAGGGAGGCTATTCATTTGTG 57.226 37.500 0.00 0.00 0.00 3.33
50 51 9.487442 TTTATTTAAGGGAGGCTATTCATTTGT 57.513 29.630 0.00 0.00 0.00 2.83
51 52 9.971922 CTTTATTTAAGGGAGGCTATTCATTTG 57.028 33.333 0.00 0.00 0.00 2.32
52 53 9.936329 TCTTTATTTAAGGGAGGCTATTCATTT 57.064 29.630 0.00 0.00 34.46 2.32
71 72 9.794719 GGCCCTTACAGTATCTTTATCTTTATT 57.205 33.333 0.00 0.00 0.00 1.40
72 73 8.945193 TGGCCCTTACAGTATCTTTATCTTTAT 58.055 33.333 0.00 0.00 0.00 1.40
73 74 8.208903 GTGGCCCTTACAGTATCTTTATCTTTA 58.791 37.037 0.00 0.00 0.00 1.85
74 75 7.054751 GTGGCCCTTACAGTATCTTTATCTTT 58.945 38.462 0.00 0.00 0.00 2.52
75 76 6.157994 TGTGGCCCTTACAGTATCTTTATCTT 59.842 38.462 0.00 0.00 0.00 2.40
76 77 5.665812 TGTGGCCCTTACAGTATCTTTATCT 59.334 40.000 0.00 0.00 0.00 1.98
77 78 5.925509 TGTGGCCCTTACAGTATCTTTATC 58.074 41.667 0.00 0.00 0.00 1.75
78 79 5.968676 TGTGGCCCTTACAGTATCTTTAT 57.031 39.130 0.00 0.00 0.00 1.40
79 80 5.968676 ATGTGGCCCTTACAGTATCTTTA 57.031 39.130 0.00 0.00 0.00 1.85
80 81 4.862641 ATGTGGCCCTTACAGTATCTTT 57.137 40.909 0.00 0.00 0.00 2.52
81 82 5.221925 CCATATGTGGCCCTTACAGTATCTT 60.222 44.000 0.00 0.00 39.01 2.40
82 83 4.287067 CCATATGTGGCCCTTACAGTATCT 59.713 45.833 0.00 0.00 39.01 1.98
83 84 4.579869 CCATATGTGGCCCTTACAGTATC 58.420 47.826 0.00 0.00 39.01 2.24
103 104 2.237643 ACGAGTAAATACCCATGCACCA 59.762 45.455 0.00 0.00 0.00 4.17
106 107 2.285083 GCACGAGTAAATACCCATGCA 58.715 47.619 0.00 0.00 0.00 3.96
122 123 1.293924 GGATCTTGTCTCATGGCACG 58.706 55.000 0.00 0.00 0.00 5.34
152 153 6.829811 TGATGTGCATATCTTTGGAATCAAGA 59.170 34.615 22.09 0.00 33.98 3.02
176 177 1.402968 CGATGGATTGAAGGTGCCTTG 59.597 52.381 8.38 0.00 36.26 3.61
193 194 4.221422 CATCACCGGTCGGGCGAT 62.221 66.667 2.59 11.67 40.62 4.58
195 196 4.873129 CTCATCACCGGTCGGGCG 62.873 72.222 2.59 4.68 40.62 6.13
196 197 4.530857 CCTCATCACCGGTCGGGC 62.531 72.222 2.59 0.00 40.62 6.13
197 198 2.298158 CTTCCTCATCACCGGTCGGG 62.298 65.000 2.59 2.55 43.62 5.14
199 200 0.530744 TTCTTCCTCATCACCGGTCG 59.469 55.000 2.59 0.00 0.00 4.79
201 202 1.827969 CTCTTCTTCCTCATCACCGGT 59.172 52.381 0.00 0.00 0.00 5.28
211 271 4.946772 GCAGCCTTTAAATCTCTTCTTCCT 59.053 41.667 0.00 0.00 0.00 3.36
213 273 4.201861 CGGCAGCCTTTAAATCTCTTCTTC 60.202 45.833 10.54 0.00 0.00 2.87
217 277 2.369394 CCGGCAGCCTTTAAATCTCTT 58.631 47.619 10.54 0.00 0.00 2.85
234 294 2.421739 GGATCATCGTGGTCCCGG 59.578 66.667 0.00 0.00 41.85 5.73
242 302 1.407936 CTCTGGGTCTGGATCATCGT 58.592 55.000 0.00 0.00 0.00 3.73
243 303 0.033228 GCTCTGGGTCTGGATCATCG 59.967 60.000 0.00 0.00 0.00 3.84
244 304 1.126488 TGCTCTGGGTCTGGATCATC 58.874 55.000 0.00 0.00 0.00 2.92
254 314 3.842923 CGCTCGGATGCTCTGGGT 61.843 66.667 0.00 0.00 0.00 4.51
262 322 4.812476 TCAACGGGCGCTCGGATG 62.812 66.667 35.52 30.05 0.00 3.51
272 332 0.937304 CATAGCATCGGTTCAACGGG 59.063 55.000 0.00 0.00 0.00 5.28
273 333 0.937304 CCATAGCATCGGTTCAACGG 59.063 55.000 0.00 0.00 0.00 4.44
274 334 1.860950 CTCCATAGCATCGGTTCAACG 59.139 52.381 0.00 0.00 0.00 4.10
275 335 2.866762 GACTCCATAGCATCGGTTCAAC 59.133 50.000 0.00 0.00 0.00 3.18
285 345 3.885724 TTTCGACATGACTCCATAGCA 57.114 42.857 0.00 0.00 0.00 3.49
298 358 3.064682 CCAACGGCATGATATTTTCGACA 59.935 43.478 0.00 0.00 0.00 4.35
344 405 1.926511 CTTCCACATTGCACTCGGCC 61.927 60.000 0.00 0.00 43.89 6.13
346 407 1.926511 GCCTTCCACATTGCACTCGG 61.927 60.000 0.00 0.00 0.00 4.63
347 408 1.503542 GCCTTCCACATTGCACTCG 59.496 57.895 0.00 0.00 0.00 4.18
397 458 0.325203 TGTGGATCCATCGACTGGGA 60.325 55.000 19.62 8.91 45.98 4.37
407 468 2.832129 GACTCCAACTAGTGTGGATCCA 59.168 50.000 11.44 11.44 0.00 3.41
414 475 3.194542 GCAGATCTGACTCCAACTAGTGT 59.805 47.826 27.04 0.00 0.00 3.55
415 476 3.446873 AGCAGATCTGACTCCAACTAGTG 59.553 47.826 27.04 0.00 0.00 2.74
450 511 0.469144 GGAGATCTCCGGCCTTCTCT 60.469 60.000 25.78 8.72 40.36 3.10
487 548 2.029844 GCACTTCACTCCACTCCGC 61.030 63.158 0.00 0.00 0.00 5.54
506 581 2.613691 GCTCGTCGGACCAAATCTTAA 58.386 47.619 1.91 0.00 0.00 1.85
509 584 1.153823 CGCTCGTCGGACCAAATCT 60.154 57.895 1.91 0.00 33.78 2.40
521 596 1.693627 ATTCCTACTCATCCGCTCGT 58.306 50.000 0.00 0.00 0.00 4.18
525 600 5.352284 CCACATATATTCCTACTCATCCGC 58.648 45.833 0.00 0.00 0.00 5.54
526 601 5.422331 ACCCACATATATTCCTACTCATCCG 59.578 44.000 0.00 0.00 0.00 4.18
532 607 4.527038 CACCGACCCACATATATTCCTACT 59.473 45.833 0.00 0.00 0.00 2.57
536 611 2.290071 CCCACCGACCCACATATATTCC 60.290 54.545 0.00 0.00 0.00 3.01
545 620 4.699522 GCTGACCCACCGACCCAC 62.700 72.222 0.00 0.00 0.00 4.61
558 634 2.668632 GAACCCGACCCATGCTGA 59.331 61.111 0.00 0.00 0.00 4.26
571 647 1.740296 CCGTCCACCACATCGAACC 60.740 63.158 0.00 0.00 0.00 3.62
574 650 2.994995 AGCCGTCCACCACATCGA 60.995 61.111 0.00 0.00 0.00 3.59
578 654 3.311110 GAGGAGCCGTCCACCACA 61.311 66.667 0.00 0.00 46.80 4.17
579 655 4.436998 CGAGGAGCCGTCCACCAC 62.437 72.222 0.00 0.00 46.80 4.16
582 658 4.131088 GTCCGAGGAGCCGTCCAC 62.131 72.222 0.00 0.00 46.80 4.02
585 661 4.477975 CACGTCCGAGGAGCCGTC 62.478 72.222 5.04 0.00 0.00 4.79
589 665 2.088674 ATATGGCACGTCCGAGGAGC 62.089 60.000 0.00 2.30 37.80 4.70
600 676 3.350219 AATATGGGACGGATATGGCAC 57.650 47.619 0.00 0.00 0.00 5.01
601 677 5.496556 CTTAAATATGGGACGGATATGGCA 58.503 41.667 0.00 0.00 0.00 4.92
616 692 7.609532 GGCACTCCTCATATTCAGCTTAAATAT 59.390 37.037 5.60 5.60 31.08 1.28
624 700 1.506493 CGGCACTCCTCATATTCAGC 58.494 55.000 0.00 0.00 0.00 4.26
627 703 2.622064 AACCGGCACTCCTCATATTC 57.378 50.000 0.00 0.00 0.00 1.75
633 709 2.187163 GGCTAACCGGCACTCCTC 59.813 66.667 0.00 0.00 38.25 3.71
644 720 1.017701 CCTCAAACGTCCGGGCTAAC 61.018 60.000 3.66 0.00 0.00 2.34
646 722 2.975536 CCTCAAACGTCCGGGCTA 59.024 61.111 3.66 0.00 0.00 3.93
650 726 0.673644 ATGAAGCCTCAAACGTCCGG 60.674 55.000 0.00 0.00 34.49 5.14
652 728 1.087501 GGATGAAGCCTCAAACGTCC 58.912 55.000 0.00 0.00 34.49 4.79
656 732 1.087501 GTCCGGATGAAGCCTCAAAC 58.912 55.000 7.81 0.00 34.49 2.93
665 741 1.218047 CCTCAAGCGTCCGGATGAA 59.782 57.895 28.06 7.96 0.00 2.57
666 742 2.892640 CCTCAAGCGTCCGGATGA 59.107 61.111 28.06 16.23 0.00 2.92
667 743 2.892425 GCCTCAAGCGTCCGGATG 60.892 66.667 19.87 19.87 0.00 3.51
699 806 1.197721 CACAAGGAAGCGTCATCAACC 59.802 52.381 1.14 0.00 0.00 3.77
700 807 1.873591 ACACAAGGAAGCGTCATCAAC 59.126 47.619 1.14 0.00 0.00 3.18
701 808 2.143122 GACACAAGGAAGCGTCATCAA 58.857 47.619 1.14 0.00 0.00 2.57
702 809 1.344438 AGACACAAGGAAGCGTCATCA 59.656 47.619 1.14 0.00 0.00 3.07
703 810 1.728971 CAGACACAAGGAAGCGTCATC 59.271 52.381 1.14 0.00 0.00 2.92
708 855 1.429463 GGTACAGACACAAGGAAGCG 58.571 55.000 0.00 0.00 0.00 4.68
737 884 7.667635 GGGAAGGCTAGCTCAATATTATTTCTT 59.332 37.037 15.72 4.22 0.00 2.52
739 886 6.375736 GGGGAAGGCTAGCTCAATATTATTTC 59.624 42.308 15.72 2.59 0.00 2.17
740 887 6.183361 TGGGGAAGGCTAGCTCAATATTATTT 60.183 38.462 15.72 0.00 0.00 1.40
741 888 5.313240 TGGGGAAGGCTAGCTCAATATTATT 59.687 40.000 15.72 0.00 0.00 1.40
742 889 4.852118 TGGGGAAGGCTAGCTCAATATTAT 59.148 41.667 15.72 0.00 0.00 1.28
743 890 4.239495 TGGGGAAGGCTAGCTCAATATTA 58.761 43.478 15.72 0.00 0.00 0.98
744 891 3.056080 TGGGGAAGGCTAGCTCAATATT 58.944 45.455 15.72 0.37 0.00 1.28
745 892 2.641815 CTGGGGAAGGCTAGCTCAATAT 59.358 50.000 15.72 0.00 0.00 1.28
746 893 2.050144 CTGGGGAAGGCTAGCTCAATA 58.950 52.381 15.72 0.00 0.00 1.90
778 1141 5.335976 GGAGAAAGCAATTGTTTAGTGGAGG 60.336 44.000 8.03 0.00 0.00 4.30
837 1200 3.054213 TCTGATTGATTGTCTCATGGCCA 60.054 43.478 8.56 8.56 32.72 5.36
869 1232 1.670967 GGCGCTATATGTAACCCCGAC 60.671 57.143 7.64 0.00 0.00 4.79
872 1235 2.554370 TTGGCGCTATATGTAACCCC 57.446 50.000 7.64 0.00 0.00 4.95
1041 1411 4.760840 GAGAGCAGCGCGACGTGA 62.761 66.667 12.10 0.00 0.00 4.35
1485 1858 1.671742 GAACTCGCCCTCCAGTTCA 59.328 57.895 7.37 0.00 45.38 3.18
1569 1942 2.997897 GTCCTGTCCTGGAGCGGT 60.998 66.667 0.00 0.00 36.69 5.68
1662 2035 3.700970 TTGGGCTCGATGGCGTCA 61.701 61.111 7.60 0.00 42.84 4.35
1740 2113 1.517832 GTCAGGCTGCCGTATCACT 59.482 57.895 13.96 0.00 0.00 3.41
2202 2593 6.016360 CCTTGGTTTCTTCATGTAACATCACA 60.016 38.462 0.00 0.00 0.00 3.58
2273 2664 3.748048 CACAACCTTCGTGATGTCTTCAT 59.252 43.478 0.00 0.00 36.54 2.57
2320 2711 2.168521 CCTTCGTACACATCACATCCCT 59.831 50.000 0.00 0.00 0.00 4.20
2327 2718 2.888414 TCTGTCACCTTCGTACACATCA 59.112 45.455 0.00 0.00 0.00 3.07
2332 2723 1.540267 GAGCTCTGTCACCTTCGTACA 59.460 52.381 6.43 0.00 0.00 2.90
2394 2785 2.612212 CACCTCAGTAAGCGTTTTGTGT 59.388 45.455 0.00 0.00 0.00 3.72
2400 2791 1.000955 CTCACCACCTCAGTAAGCGTT 59.999 52.381 0.00 0.00 0.00 4.84
2409 2800 0.105194 TCCACTTCCTCACCACCTCA 60.105 55.000 0.00 0.00 0.00 3.86
2744 3138 3.749609 GTGGTCTTTATGGTAGCACGTTT 59.250 43.478 0.00 0.00 32.65 3.60
2826 3220 9.979578 ATGAAATAATACTTTCTTGTTTGCACA 57.020 25.926 0.00 0.00 36.34 4.57
2939 3333 1.291132 GGAACGAGTAGATGCTTGGC 58.709 55.000 0.00 0.00 0.00 4.52
3060 3457 9.730420 GTCATGCTTGAAGAAAAGTAAAGTTTA 57.270 29.630 3.51 0.00 32.48 2.01
3171 3568 6.530534 CACATACAACTACTACTACTTGCCAC 59.469 42.308 0.00 0.00 0.00 5.01
3212 3609 0.904649 TGTGTTCCTCGATGCCTCAT 59.095 50.000 0.00 0.00 0.00 2.90
3301 3698 4.667573 TCTTACTCCATCACTCAGTCACT 58.332 43.478 0.00 0.00 0.00 3.41
3303 3700 5.105187 CCAATCTTACTCCATCACTCAGTCA 60.105 44.000 0.00 0.00 0.00 3.41
3306 3703 5.604758 TCCAATCTTACTCCATCACTCAG 57.395 43.478 0.00 0.00 0.00 3.35
3357 3754 4.385825 GACCACAAGTCCACAATCAAGTA 58.614 43.478 0.00 0.00 39.84 2.24
3373 3770 0.716591 ATACCCTCCTCCAGACCACA 59.283 55.000 0.00 0.00 0.00 4.17
3429 3826 3.390521 CACCTACCGCCCTCTGCA 61.391 66.667 0.00 0.00 41.33 4.41


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

AutoCloner maintained by Alex Coulton.