Multiple sequence alignment - TraesCS6A01G330300

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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 TraesCS6A01G330300 chr6A 100.000 3644 0 0 1 3644 562932982 562936625 0.000000e+00 6730.0
1 TraesCS6A01G330300 chr6D 94.513 2260 95 13 618 2864 419882034 419884277 0.000000e+00 3459.0
2 TraesCS6A01G330300 chr6D 94.814 617 29 3 2924 3537 419884286 419884902 0.000000e+00 959.0
3 TraesCS6A01G330300 chr6D 88.690 504 39 8 106 608 419881407 419881893 1.870000e-167 599.0
4 TraesCS6A01G330300 chr6D 92.857 56 2 2 3589 3644 419884914 419884967 3.020000e-11 80.5
5 TraesCS6A01G330300 chr6B 92.291 1349 61 16 607 1942 632877764 632879082 0.000000e+00 1875.0
6 TraesCS6A01G330300 chr6B 96.076 892 31 4 2699 3586 632880127 632881018 0.000000e+00 1450.0
7 TraesCS6A01G330300 chr6B 96.530 634 15 4 2030 2660 632879499 632880128 0.000000e+00 1042.0
8 TraesCS6A01G330300 chr6B 86.018 329 32 7 19 334 632851094 632851421 1.250000e-89 340.0
9 TraesCS6A01G330300 chr6B 84.477 277 32 6 332 608 632877209 632877474 2.790000e-66 263.0
10 TraesCS6A01G330300 chr6B 92.982 57 4 0 3588 3644 632881055 632881111 2.330000e-12 84.2
11 TraesCS6A01G330300 chr6B 94.118 51 3 0 2866 2916 632880374 632880424 1.080000e-10 78.7
12 TraesCS6A01G330300 chr6B 95.122 41 2 0 2395 2435 632879830 632879870 8.450000e-07 65.8


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 TraesCS6A01G330300 chr6A 562932982 562936625 3643 False 6730.000 6730 100.000000 1 3644 1 chr6A.!!$F1 3643
1 TraesCS6A01G330300 chr6D 419881407 419884967 3560 False 1274.375 3459 92.718500 106 3644 4 chr6D.!!$F1 3538
2 TraesCS6A01G330300 chr6B 632877209 632881111 3902 False 694.100 1875 93.085143 332 3644 7 chr6B.!!$F2 3312

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
32 33 0.030908 CTCGGCCTCTCGGTTATGAC 59.969 60.0 0.0 0.0 0.0 3.06 F
755 1055 0.033601 TTCCCAATTCCCATCCACCG 60.034 55.0 0.0 0.0 0.0 4.94 F
1289 1600 0.318441 GCTATCTCCAGCCATGCGTA 59.682 55.0 0.0 0.0 35.4 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1600 1.707427 AGACATGGAGCTTTGGAAGGT 59.293 47.619 0.00 0.0 42.93 3.50 R
1935 2248 1.909302 TCCTCAATCAGTCCCCTCAAC 59.091 52.381 0.00 0.0 0.00 3.18 R
3023 3676 0.829182 CTGGGAGGCCTGCTTTTGTT 60.829 55.000 24.77 0.0 0.00 2.83 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
17 18 3.539842 GCCCTTACCTCCTCTCGG 58.460 66.667 0.00 0.00 0.00 4.63
18 19 2.798364 GCCCTTACCTCCTCTCGGC 61.798 68.421 0.00 0.00 0.00 5.54
19 20 2.134933 CCCTTACCTCCTCTCGGCC 61.135 68.421 0.00 0.00 0.00 6.13
20 21 1.075896 CCTTACCTCCTCTCGGCCT 60.076 63.158 0.00 0.00 0.00 5.19
21 22 1.110518 CCTTACCTCCTCTCGGCCTC 61.111 65.000 0.00 0.00 0.00 4.70
22 23 0.106419 CTTACCTCCTCTCGGCCTCT 60.106 60.000 0.00 0.00 0.00 3.69
23 24 0.106619 TTACCTCCTCTCGGCCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
24 25 2.326773 TACCTCCTCTCGGCCTCTCG 62.327 65.000 0.00 0.00 0.00 4.04
25 26 2.904866 CTCCTCTCGGCCTCTCGG 60.905 72.222 0.00 0.00 0.00 4.63
26 27 3.707640 CTCCTCTCGGCCTCTCGGT 62.708 68.421 0.00 0.00 0.00 4.69
27 28 2.756283 CCTCTCGGCCTCTCGGTT 60.756 66.667 0.00 0.00 0.00 4.44
28 29 1.453379 CCTCTCGGCCTCTCGGTTA 60.453 63.158 0.00 0.00 0.00 2.85
29 30 0.824182 CCTCTCGGCCTCTCGGTTAT 60.824 60.000 0.00 0.00 0.00 1.89
30 31 0.312416 CTCTCGGCCTCTCGGTTATG 59.688 60.000 0.00 0.00 0.00 1.90
31 32 0.106868 TCTCGGCCTCTCGGTTATGA 60.107 55.000 0.00 0.00 0.00 2.15
32 33 0.030908 CTCGGCCTCTCGGTTATGAC 59.969 60.000 0.00 0.00 0.00 3.06
33 34 1.299165 CGGCCTCTCGGTTATGACG 60.299 63.158 0.00 0.00 0.00 4.35
34 35 1.721664 CGGCCTCTCGGTTATGACGA 61.722 60.000 0.00 0.00 38.79 4.20
42 43 1.395954 TCGGTTATGACGAGTCAGACG 59.604 52.381 11.74 12.00 43.61 4.18
43 44 1.531264 CGGTTATGACGAGTCAGACGG 60.531 57.143 11.74 11.99 43.61 4.79
44 45 1.741706 GGTTATGACGAGTCAGACGGA 59.258 52.381 11.74 0.00 43.61 4.69
45 46 2.358267 GGTTATGACGAGTCAGACGGAT 59.642 50.000 11.74 0.00 43.61 4.18
46 47 3.181489 GGTTATGACGAGTCAGACGGATT 60.181 47.826 11.74 0.00 43.61 3.01
47 48 2.568696 ATGACGAGTCAGACGGATTG 57.431 50.000 11.74 0.00 43.61 2.67
48 49 1.244816 TGACGAGTCAGACGGATTGT 58.755 50.000 1.24 0.00 34.14 2.71
49 50 2.429478 TGACGAGTCAGACGGATTGTA 58.571 47.619 1.24 0.00 34.14 2.41
50 51 2.815503 TGACGAGTCAGACGGATTGTAA 59.184 45.455 1.24 0.00 34.14 2.41
51 52 3.442625 TGACGAGTCAGACGGATTGTAAT 59.557 43.478 1.24 0.00 34.14 1.89
52 53 3.770666 ACGAGTCAGACGGATTGTAATG 58.229 45.455 0.00 0.00 34.93 1.90
53 54 3.192844 ACGAGTCAGACGGATTGTAATGT 59.807 43.478 0.00 0.00 34.93 2.71
54 55 4.397103 ACGAGTCAGACGGATTGTAATGTA 59.603 41.667 0.00 0.00 34.93 2.29
55 56 5.106038 ACGAGTCAGACGGATTGTAATGTAA 60.106 40.000 0.00 0.00 34.93 2.41
56 57 5.455849 CGAGTCAGACGGATTGTAATGTAAG 59.544 44.000 0.00 0.00 0.00 2.34
57 58 5.109903 AGTCAGACGGATTGTAATGTAAGC 58.890 41.667 0.00 0.00 0.00 3.09
58 59 5.105310 AGTCAGACGGATTGTAATGTAAGCT 60.105 40.000 0.00 0.00 0.00 3.74
59 60 5.005779 GTCAGACGGATTGTAATGTAAGCTG 59.994 44.000 0.00 0.00 0.00 4.24
60 61 3.871594 AGACGGATTGTAATGTAAGCTGC 59.128 43.478 0.00 0.00 0.00 5.25
61 62 2.607635 ACGGATTGTAATGTAAGCTGCG 59.392 45.455 0.00 0.00 0.00 5.18
62 63 2.032894 CGGATTGTAATGTAAGCTGCGG 60.033 50.000 0.00 0.00 0.00 5.69
63 64 3.202906 GGATTGTAATGTAAGCTGCGGA 58.797 45.455 0.00 0.00 0.00 5.54
64 65 3.625764 GGATTGTAATGTAAGCTGCGGAA 59.374 43.478 0.00 0.00 0.00 4.30
65 66 4.275936 GGATTGTAATGTAAGCTGCGGAAT 59.724 41.667 0.00 0.00 0.00 3.01
66 67 5.221048 GGATTGTAATGTAAGCTGCGGAATT 60.221 40.000 0.00 0.00 0.00 2.17
67 68 6.017440 GGATTGTAATGTAAGCTGCGGAATTA 60.017 38.462 0.00 0.00 0.00 1.40
68 69 5.984233 TGTAATGTAAGCTGCGGAATTAG 57.016 39.130 0.00 0.00 0.00 1.73
69 70 5.424757 TGTAATGTAAGCTGCGGAATTAGT 58.575 37.500 0.00 0.00 0.00 2.24
70 71 6.575267 TGTAATGTAAGCTGCGGAATTAGTA 58.425 36.000 0.00 0.00 0.00 1.82
71 72 6.700081 TGTAATGTAAGCTGCGGAATTAGTAG 59.300 38.462 0.00 0.00 0.00 2.57
72 73 3.454375 TGTAAGCTGCGGAATTAGTAGC 58.546 45.455 13.16 13.16 45.58 3.58
74 75 2.973420 GCTGCGGAATTAGTAGCGT 58.027 52.632 0.00 0.00 37.56 5.07
75 76 0.577269 GCTGCGGAATTAGTAGCGTG 59.423 55.000 0.00 0.00 37.56 5.34
76 77 1.209128 CTGCGGAATTAGTAGCGTGG 58.791 55.000 0.00 0.00 0.00 4.94
77 78 0.533491 TGCGGAATTAGTAGCGTGGT 59.467 50.000 0.00 0.00 0.00 4.16
78 79 0.928229 GCGGAATTAGTAGCGTGGTG 59.072 55.000 0.00 0.00 0.00 4.17
79 80 1.567504 CGGAATTAGTAGCGTGGTGG 58.432 55.000 0.00 0.00 0.00 4.61
80 81 1.296727 GGAATTAGTAGCGTGGTGGC 58.703 55.000 0.00 0.00 0.00 5.01
81 82 1.406341 GGAATTAGTAGCGTGGTGGCA 60.406 52.381 0.00 0.00 34.64 4.92
82 83 2.561569 GAATTAGTAGCGTGGTGGCAT 58.438 47.619 0.00 0.00 34.64 4.40
83 84 2.240493 ATTAGTAGCGTGGTGGCATC 57.760 50.000 0.00 0.00 34.64 3.91
84 85 1.191535 TTAGTAGCGTGGTGGCATCT 58.808 50.000 0.00 0.00 34.64 2.90
85 86 1.191535 TAGTAGCGTGGTGGCATCTT 58.808 50.000 0.00 0.00 34.64 2.40
86 87 0.324943 AGTAGCGTGGTGGCATCTTT 59.675 50.000 0.00 0.00 34.64 2.52
87 88 1.165270 GTAGCGTGGTGGCATCTTTT 58.835 50.000 0.00 0.00 34.64 2.27
88 89 2.027561 AGTAGCGTGGTGGCATCTTTTA 60.028 45.455 0.00 0.00 34.64 1.52
89 90 1.904287 AGCGTGGTGGCATCTTTTAA 58.096 45.000 0.00 0.00 34.64 1.52
90 91 1.539827 AGCGTGGTGGCATCTTTTAAC 59.460 47.619 0.00 0.00 34.64 2.01
91 92 1.268352 GCGTGGTGGCATCTTTTAACA 59.732 47.619 0.00 0.00 0.00 2.41
92 93 2.287909 GCGTGGTGGCATCTTTTAACAA 60.288 45.455 0.00 0.00 0.00 2.83
93 94 3.797184 GCGTGGTGGCATCTTTTAACAAA 60.797 43.478 0.00 0.00 0.00 2.83
94 95 4.555262 CGTGGTGGCATCTTTTAACAAAT 58.445 39.130 0.00 0.00 0.00 2.32
95 96 4.987912 CGTGGTGGCATCTTTTAACAAATT 59.012 37.500 0.00 0.00 0.00 1.82
96 97 5.107530 CGTGGTGGCATCTTTTAACAAATTG 60.108 40.000 0.00 0.00 0.00 2.32
97 98 5.757808 GTGGTGGCATCTTTTAACAAATTGT 59.242 36.000 0.00 0.00 0.00 2.71
98 99 6.926272 GTGGTGGCATCTTTTAACAAATTGTA 59.074 34.615 0.00 0.00 0.00 2.41
99 100 7.602265 GTGGTGGCATCTTTTAACAAATTGTAT 59.398 33.333 0.00 0.00 0.00 2.29
100 101 8.153550 TGGTGGCATCTTTTAACAAATTGTATT 58.846 29.630 0.00 0.00 0.00 1.89
101 102 9.646427 GGTGGCATCTTTTAACAAATTGTATTA 57.354 29.630 0.00 0.00 0.00 0.98
141 142 5.934625 AGCACTCGTGTAAAGAAATCAGATT 59.065 36.000 0.00 0.00 0.00 2.40
173 174 1.743995 GCACCGGCCAAATACGAGT 60.744 57.895 0.00 0.00 0.00 4.18
183 184 5.220700 CGGCCAAATACGAGTAAGCATTTTA 60.221 40.000 2.24 0.00 0.00 1.52
233 234 6.535150 ACATGAAGTCATCCTGTACGTTTATG 59.465 38.462 0.00 0.00 35.44 1.90
343 344 2.977405 AGAATGCGAGCAAAGTGAAC 57.023 45.000 0.57 0.00 0.00 3.18
436 437 2.197465 AGGGTTCCACTATCAAGGGAC 58.803 52.381 0.00 0.00 32.29 4.46
462 463 2.851824 GACCAAACAACAAAACAGAGCG 59.148 45.455 0.00 0.00 0.00 5.03
474 475 0.534877 ACAGAGCGTCCAAATGTGCA 60.535 50.000 0.00 0.00 0.00 4.57
550 551 3.143338 TGGTACAACGCTGCCTCA 58.857 55.556 0.00 0.00 31.92 3.86
556 557 1.726853 ACAACGCTGCCTCATCTAAC 58.273 50.000 0.00 0.00 0.00 2.34
563 564 2.038295 GCTGCCTCATCTAACCTAGCAT 59.962 50.000 0.00 0.00 0.00 3.79
564 565 3.259374 GCTGCCTCATCTAACCTAGCATA 59.741 47.826 0.00 0.00 0.00 3.14
565 566 4.620332 GCTGCCTCATCTAACCTAGCATAG 60.620 50.000 0.00 0.00 38.80 2.23
566 567 3.259374 TGCCTCATCTAACCTAGCATAGC 59.741 47.826 0.00 0.00 37.37 2.97
567 568 3.259374 GCCTCATCTAACCTAGCATAGCA 59.741 47.826 0.00 0.00 37.37 3.49
574 575 0.824109 ACCTAGCATAGCAGCACGAA 59.176 50.000 0.00 0.00 37.37 3.85
576 577 1.594862 CCTAGCATAGCAGCACGAAAC 59.405 52.381 0.00 0.00 37.37 2.78
577 578 2.544685 CTAGCATAGCAGCACGAAACT 58.455 47.619 0.00 0.00 36.85 2.66
608 609 7.681939 TTCCGTTTCTTTCTGCATTAACTAT 57.318 32.000 0.00 0.00 0.00 2.12
609 610 7.072177 TCCGTTTCTTTCTGCATTAACTATG 57.928 36.000 0.00 0.00 37.31 2.23
610 611 6.653320 TCCGTTTCTTTCTGCATTAACTATGT 59.347 34.615 0.00 0.00 36.57 2.29
611 612 6.742718 CCGTTTCTTTCTGCATTAACTATGTG 59.257 38.462 0.00 0.00 36.57 3.21
612 613 6.742718 CGTTTCTTTCTGCATTAACTATGTGG 59.257 38.462 0.00 0.00 36.57 4.17
622 922 5.801947 GCATTAACTATGTGGCAAAGACAAG 59.198 40.000 0.00 0.00 36.57 3.16
755 1055 0.033601 TTCCCAATTCCCATCCACCG 60.034 55.000 0.00 0.00 0.00 4.94
764 1064 1.488812 TCCCATCCACCGTTCCTAATG 59.511 52.381 0.00 0.00 0.00 1.90
772 1072 1.817941 CGTTCCTAATGCCCACCCG 60.818 63.158 0.00 0.00 0.00 5.28
804 1104 7.396540 AAACAAGGCCTGATGATTTTACTAG 57.603 36.000 5.69 0.00 0.00 2.57
955 1266 6.295249 TCTGATGATCTCTACCTACACTGAG 58.705 44.000 0.00 0.00 0.00 3.35
957 1268 5.825151 TGATGATCTCTACCTACACTGAGTG 59.175 44.000 11.70 11.70 39.75 3.51
961 1272 5.100344 TCTCTACCTACACTGAGTGGTAG 57.900 47.826 17.92 17.47 44.55 3.18
1020 1331 4.002797 GGCAAGAAAGCCGGTGAT 57.997 55.556 1.90 0.00 46.12 3.06
1119 1430 1.216710 GGCTCTCAGCGCTAAGTGT 59.783 57.895 10.99 0.00 43.62 3.55
1289 1600 0.318441 GCTATCTCCAGCCATGCGTA 59.682 55.000 0.00 0.00 35.40 4.42
1670 1983 4.439289 GGCATTATTCCTGAGTTTCACTGC 60.439 45.833 0.00 0.00 0.00 4.40
1771 2084 1.002430 TCCAGCTTACACTTCAGCAGG 59.998 52.381 0.00 0.00 42.62 4.85
1825 2138 3.541996 ATCCATTGTGCGTACAGATGA 57.458 42.857 21.17 13.71 38.23 2.92
1935 2248 1.063616 CTTGACATGAGCATTCGCCAG 59.936 52.381 0.00 0.00 39.83 4.85
2029 2343 7.516450 CCCCCTTTCTATATCTCATATGGTT 57.484 40.000 2.13 0.00 0.00 3.67
2093 2734 6.480524 TGACATAAAGTGACAACATGCTAC 57.519 37.500 0.00 0.00 29.67 3.58
2275 2919 1.338136 CCTTGGCCTAGACCCATCGT 61.338 60.000 16.43 0.00 31.26 3.73
2331 2975 3.121030 CTGCAAGCCCTCGTTCCG 61.121 66.667 0.00 0.00 0.00 4.30
2385 3029 0.816825 CATCCACTTCCATGCCTCCG 60.817 60.000 0.00 0.00 0.00 4.63
2501 3145 5.689514 TGAAACTAAATGCAACCAATTCACG 59.310 36.000 0.00 0.00 0.00 4.35
2625 3269 1.153524 AGCACCAACCTCCATTGCA 59.846 52.632 0.00 0.00 35.57 4.08
2693 3340 8.962679 GGGTTTACCAATGTAGTCATTAAATCA 58.037 33.333 0.69 0.00 41.66 2.57
2831 3480 7.345422 ACGCCTTTACCTAACCTTTTAAAAA 57.655 32.000 1.66 0.00 0.00 1.94
2883 3534 7.984391 ACAAAGATGGTTTGAATTTTGTTTCC 58.016 30.769 4.55 0.00 35.83 3.13
2912 3563 5.929992 TGAATTTTCTCCAGGTACTTGTACG 59.070 40.000 4.10 0.00 34.60 3.67
2988 3641 6.039270 TGTTGAATTTTCTCCAGGTACTTGTG 59.961 38.462 4.10 0.00 34.60 3.33
3016 3669 5.241506 TCGAGCAAGATTCAAGTTCCAATTT 59.758 36.000 0.00 0.00 0.00 1.82
3039 3692 1.039856 TTCAACAAAAGCAGGCCTCC 58.960 50.000 0.00 0.00 0.00 4.30
3077 3730 8.887717 AGATCAGAATTTGCATGTTAAGACTAC 58.112 33.333 0.00 0.00 0.00 2.73
3431 4085 6.562608 AGAGCCCCTTGGATATTGATTTACTA 59.437 38.462 0.00 0.00 0.00 1.82
3579 4246 6.688578 ACTATCAGCTAAACATGTATACCCG 58.311 40.000 0.00 0.00 0.00 5.28
3581 4248 2.806244 CAGCTAAACATGTATACCCGCC 59.194 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.395954 CGTCTGACTCGTCATAACCGA 59.604 52.381 6.21 0.00 39.13 4.69
23 24 1.531264 CCGTCTGACTCGTCATAACCG 60.531 57.143 6.21 1.56 39.13 4.44
24 25 1.741706 TCCGTCTGACTCGTCATAACC 59.258 52.381 6.21 0.00 39.13 2.85
25 26 3.694535 ATCCGTCTGACTCGTCATAAC 57.305 47.619 6.21 2.14 39.13 1.89
26 27 3.442625 ACAATCCGTCTGACTCGTCATAA 59.557 43.478 6.21 0.00 39.13 1.90
27 28 3.014623 ACAATCCGTCTGACTCGTCATA 58.985 45.455 6.21 0.00 39.13 2.15
28 29 1.819288 ACAATCCGTCTGACTCGTCAT 59.181 47.619 6.21 0.00 39.13 3.06
29 30 1.244816 ACAATCCGTCTGACTCGTCA 58.755 50.000 6.21 0.00 38.06 4.35
30 31 3.482722 TTACAATCCGTCTGACTCGTC 57.517 47.619 6.21 0.00 0.00 4.20
31 32 3.192844 ACATTACAATCCGTCTGACTCGT 59.807 43.478 6.21 0.00 0.00 4.18
32 33 3.770666 ACATTACAATCCGTCTGACTCG 58.229 45.455 6.21 0.00 0.00 4.18
33 34 5.232414 GCTTACATTACAATCCGTCTGACTC 59.768 44.000 6.21 0.00 0.00 3.36
34 35 5.105310 AGCTTACATTACAATCCGTCTGACT 60.105 40.000 6.21 0.00 0.00 3.41
35 36 5.005779 CAGCTTACATTACAATCCGTCTGAC 59.994 44.000 0.00 0.00 0.00 3.51
36 37 5.109210 CAGCTTACATTACAATCCGTCTGA 58.891 41.667 0.00 0.00 0.00 3.27
37 38 4.260375 GCAGCTTACATTACAATCCGTCTG 60.260 45.833 0.00 0.00 0.00 3.51
38 39 3.871594 GCAGCTTACATTACAATCCGTCT 59.128 43.478 0.00 0.00 0.00 4.18
39 40 3.302480 CGCAGCTTACATTACAATCCGTC 60.302 47.826 0.00 0.00 0.00 4.79
40 41 2.607635 CGCAGCTTACATTACAATCCGT 59.392 45.455 0.00 0.00 0.00 4.69
41 42 2.032894 CCGCAGCTTACATTACAATCCG 60.033 50.000 0.00 0.00 0.00 4.18
42 43 3.202906 TCCGCAGCTTACATTACAATCC 58.797 45.455 0.00 0.00 0.00 3.01
43 44 4.875544 TTCCGCAGCTTACATTACAATC 57.124 40.909 0.00 0.00 0.00 2.67
44 45 5.835113 AATTCCGCAGCTTACATTACAAT 57.165 34.783 0.00 0.00 0.00 2.71
45 46 5.878116 ACTAATTCCGCAGCTTACATTACAA 59.122 36.000 0.00 0.00 0.00 2.41
46 47 5.424757 ACTAATTCCGCAGCTTACATTACA 58.575 37.500 0.00 0.00 0.00 2.41
47 48 5.986004 ACTAATTCCGCAGCTTACATTAC 57.014 39.130 0.00 0.00 0.00 1.89
48 49 5.694910 GCTACTAATTCCGCAGCTTACATTA 59.305 40.000 0.00 0.00 0.00 1.90
49 50 4.511826 GCTACTAATTCCGCAGCTTACATT 59.488 41.667 0.00 0.00 0.00 2.71
50 51 4.058817 GCTACTAATTCCGCAGCTTACAT 58.941 43.478 0.00 0.00 0.00 2.29
51 52 3.454375 GCTACTAATTCCGCAGCTTACA 58.546 45.455 0.00 0.00 0.00 2.41
52 53 2.471743 CGCTACTAATTCCGCAGCTTAC 59.528 50.000 0.00 0.00 0.00 2.34
53 54 2.100252 ACGCTACTAATTCCGCAGCTTA 59.900 45.455 0.00 0.00 0.00 3.09
54 55 1.134788 ACGCTACTAATTCCGCAGCTT 60.135 47.619 0.00 0.00 0.00 3.74
55 56 0.460311 ACGCTACTAATTCCGCAGCT 59.540 50.000 0.00 0.00 0.00 4.24
56 57 0.577269 CACGCTACTAATTCCGCAGC 59.423 55.000 0.00 0.00 0.00 5.25
57 58 1.209128 CCACGCTACTAATTCCGCAG 58.791 55.000 0.00 0.00 0.00 5.18
58 59 0.533491 ACCACGCTACTAATTCCGCA 59.467 50.000 0.00 0.00 0.00 5.69
59 60 0.928229 CACCACGCTACTAATTCCGC 59.072 55.000 0.00 0.00 0.00 5.54
60 61 1.567504 CCACCACGCTACTAATTCCG 58.432 55.000 0.00 0.00 0.00 4.30
61 62 1.296727 GCCACCACGCTACTAATTCC 58.703 55.000 0.00 0.00 0.00 3.01
62 63 2.018542 TGCCACCACGCTACTAATTC 57.981 50.000 0.00 0.00 0.00 2.17
63 64 2.170607 AGATGCCACCACGCTACTAATT 59.829 45.455 0.00 0.00 0.00 1.40
64 65 1.762957 AGATGCCACCACGCTACTAAT 59.237 47.619 0.00 0.00 0.00 1.73
65 66 1.191535 AGATGCCACCACGCTACTAA 58.808 50.000 0.00 0.00 0.00 2.24
66 67 1.191535 AAGATGCCACCACGCTACTA 58.808 50.000 0.00 0.00 0.00 1.82
67 68 0.324943 AAAGATGCCACCACGCTACT 59.675 50.000 0.00 0.00 0.00 2.57
68 69 1.165270 AAAAGATGCCACCACGCTAC 58.835 50.000 0.00 0.00 0.00 3.58
69 70 2.745281 GTTAAAAGATGCCACCACGCTA 59.255 45.455 0.00 0.00 0.00 4.26
70 71 1.539827 GTTAAAAGATGCCACCACGCT 59.460 47.619 0.00 0.00 0.00 5.07
71 72 1.268352 TGTTAAAAGATGCCACCACGC 59.732 47.619 0.00 0.00 0.00 5.34
72 73 3.634568 TTGTTAAAAGATGCCACCACG 57.365 42.857 0.00 0.00 0.00 4.94
73 74 5.757808 ACAATTTGTTAAAAGATGCCACCAC 59.242 36.000 0.00 0.00 0.00 4.16
74 75 5.923204 ACAATTTGTTAAAAGATGCCACCA 58.077 33.333 0.00 0.00 0.00 4.17
75 76 8.546597 AATACAATTTGTTAAAAGATGCCACC 57.453 30.769 7.45 0.00 0.00 4.61
88 89 8.134895 CCGCATCACCTATTAATACAATTTGTT 58.865 33.333 7.45 0.00 0.00 2.83
89 90 7.284489 ACCGCATCACCTATTAATACAATTTGT 59.716 33.333 7.30 7.30 0.00 2.83
90 91 7.648142 ACCGCATCACCTATTAATACAATTTG 58.352 34.615 0.00 0.00 0.00 2.32
91 92 7.817418 ACCGCATCACCTATTAATACAATTT 57.183 32.000 0.00 0.00 0.00 1.82
92 93 8.911918 TTACCGCATCACCTATTAATACAATT 57.088 30.769 0.00 0.00 0.00 2.32
93 94 7.119262 GCTTACCGCATCACCTATTAATACAAT 59.881 37.037 0.00 0.00 38.92 2.71
94 95 6.425721 GCTTACCGCATCACCTATTAATACAA 59.574 38.462 0.00 0.00 38.92 2.41
95 96 5.929992 GCTTACCGCATCACCTATTAATACA 59.070 40.000 0.00 0.00 38.92 2.29
96 97 5.929992 TGCTTACCGCATCACCTATTAATAC 59.070 40.000 0.00 0.00 45.47 1.89
97 98 6.104146 TGCTTACCGCATCACCTATTAATA 57.896 37.500 0.00 0.00 45.47 0.98
98 99 4.968259 TGCTTACCGCATCACCTATTAAT 58.032 39.130 0.00 0.00 45.47 1.40
99 100 4.409718 TGCTTACCGCATCACCTATTAA 57.590 40.909 0.00 0.00 45.47 1.40
113 114 5.407387 TGATTTCTTTACACGAGTGCTTACC 59.593 40.000 2.76 0.00 0.00 2.85
158 159 0.935196 GCTTACTCGTATTTGGCCGG 59.065 55.000 0.00 0.00 0.00 6.13
214 215 6.534475 TTACCATAAACGTACAGGATGACT 57.466 37.500 0.00 0.00 39.69 3.41
219 220 5.813672 GCAAGATTACCATAAACGTACAGGA 59.186 40.000 0.00 0.00 0.00 3.86
221 222 6.757010 AGAGCAAGATTACCATAAACGTACAG 59.243 38.462 0.00 0.00 0.00 2.74
287 288 3.139077 AGTCGGAAAGCAAGGTTAGTTG 58.861 45.455 0.00 0.00 0.00 3.16
292 293 0.472471 TGGAGTCGGAAAGCAAGGTT 59.528 50.000 0.00 0.00 0.00 3.50
317 318 5.063944 TCACTTTGCTCGCATTCTTATCTTC 59.936 40.000 0.00 0.00 0.00 2.87
343 344 0.531657 TTTGCCATCCCTTTCATGCG 59.468 50.000 0.00 0.00 0.00 4.73
416 417 2.197465 GTCCCTTGATAGTGGAACCCT 58.803 52.381 0.00 0.00 37.80 4.34
436 437 3.318017 TGTTTTGTTGTTTGGTCCGTTG 58.682 40.909 0.00 0.00 0.00 4.10
462 463 6.473455 GCTTATTATGTTCTGCACATTTGGAC 59.527 38.462 0.00 0.00 44.40 4.02
535 536 2.579207 TAGATGAGGCAGCGTTGTAC 57.421 50.000 0.00 0.00 0.00 2.90
538 539 1.009829 GGTTAGATGAGGCAGCGTTG 58.990 55.000 0.00 0.00 0.00 4.10
550 551 3.305676 CGTGCTGCTATGCTAGGTTAGAT 60.306 47.826 0.00 0.00 0.00 1.98
556 557 1.594862 GTTTCGTGCTGCTATGCTAGG 59.405 52.381 0.00 0.00 0.00 3.02
563 564 5.277634 GGAAAACTTTAGTTTCGTGCTGCTA 60.278 40.000 8.21 0.00 46.47 3.49
564 565 4.497507 GGAAAACTTTAGTTTCGTGCTGCT 60.498 41.667 8.21 0.00 46.47 4.24
565 566 3.729217 GGAAAACTTTAGTTTCGTGCTGC 59.271 43.478 8.21 0.00 46.47 5.25
566 567 3.966218 CGGAAAACTTTAGTTTCGTGCTG 59.034 43.478 8.21 1.64 46.47 4.41
567 568 3.624410 ACGGAAAACTTTAGTTTCGTGCT 59.376 39.130 16.40 0.34 46.47 4.40
574 575 6.750501 GCAGAAAGAAACGGAAAACTTTAGTT 59.249 34.615 0.00 0.00 40.50 2.24
576 577 6.262601 TGCAGAAAGAAACGGAAAACTTTAG 58.737 36.000 0.00 0.00 33.61 1.85
577 578 6.197364 TGCAGAAAGAAACGGAAAACTTTA 57.803 33.333 0.00 0.00 33.61 1.85
588 589 6.528072 GCCACATAGTTAATGCAGAAAGAAAC 59.472 38.462 0.00 0.00 39.39 2.78
590 591 5.709631 TGCCACATAGTTAATGCAGAAAGAA 59.290 36.000 0.00 0.00 39.39 2.52
608 609 3.490439 TCATCTCTTGTCTTTGCCACA 57.510 42.857 0.00 0.00 0.00 4.17
609 610 4.005650 TCATCATCTCTTGTCTTTGCCAC 58.994 43.478 0.00 0.00 0.00 5.01
610 611 4.290711 TCATCATCTCTTGTCTTTGCCA 57.709 40.909 0.00 0.00 0.00 4.92
611 612 5.831702 AATCATCATCTCTTGTCTTTGCC 57.168 39.130 0.00 0.00 0.00 4.52
612 613 9.286946 CTAAAAATCATCATCTCTTGTCTTTGC 57.713 33.333 0.00 0.00 0.00 3.68
622 922 7.507733 ACTGGCATCTAAAAATCATCATCTC 57.492 36.000 0.00 0.00 0.00 2.75
696 996 3.179048 GCTGTTTTGACTTTTGCTCGTT 58.821 40.909 0.00 0.00 0.00 3.85
732 1032 0.105504 GGATGGGAATTGGGAAGGGG 60.106 60.000 0.00 0.00 0.00 4.79
755 1055 2.119029 GCGGGTGGGCATTAGGAAC 61.119 63.158 0.00 0.00 0.00 3.62
772 1072 1.602605 AGGCCTTGTTTACACCGGC 60.603 57.895 0.00 11.83 40.18 6.13
804 1104 1.963515 ACAATCAAAACTGGAGGGCAC 59.036 47.619 0.00 0.00 0.00 5.01
955 1266 3.075005 TGGCTCCGAGGCTACCAC 61.075 66.667 21.49 0.00 41.96 4.16
957 1268 2.442272 TCTGGCTCCGAGGCTACC 60.442 66.667 21.49 3.40 41.96 3.18
961 1272 2.441164 TCTCTCTGGCTCCGAGGC 60.441 66.667 14.94 14.94 41.77 4.70
1020 1331 4.383861 CGTCCAGCCTGCTCAGCA 62.384 66.667 0.00 0.00 36.92 4.41
1119 1430 3.547249 GAGGACCAACGCGACGACA 62.547 63.158 15.93 0.00 0.00 4.35
1289 1600 1.707427 AGACATGGAGCTTTGGAAGGT 59.293 47.619 0.00 0.00 42.93 3.50
1340 1651 7.679453 TGAAGGGGGTTCTAGTATTTTACTGTA 59.321 37.037 0.00 0.00 35.34 2.74
1341 1652 6.502863 TGAAGGGGGTTCTAGTATTTTACTGT 59.497 38.462 0.00 0.00 35.34 3.55
1342 1653 6.954232 TGAAGGGGGTTCTAGTATTTTACTG 58.046 40.000 0.00 0.00 35.34 2.74
1343 1654 6.734281 ACTGAAGGGGGTTCTAGTATTTTACT 59.266 38.462 0.00 0.00 36.64 2.24
1353 1664 4.226620 GGTTGATTACTGAAGGGGGTTCTA 59.773 45.833 0.00 0.00 35.99 2.10
1360 1671 5.989477 TGACTATGGTTGATTACTGAAGGG 58.011 41.667 0.00 0.00 0.00 3.95
1670 1983 7.148340 GGTCAGGAAGAACATCAAATTCTACAG 60.148 40.741 0.00 0.00 35.31 2.74
1771 2084 4.837567 GATGGTGTCAGCGATAAATTCAC 58.162 43.478 0.00 0.00 0.00 3.18
1935 2248 1.909302 TCCTCAATCAGTCCCCTCAAC 59.091 52.381 0.00 0.00 0.00 3.18
2034 2675 9.447157 AGGAAAGATGTTAATCAGAAGAAGAAG 57.553 33.333 0.00 0.00 35.03 2.85
2093 2734 7.410120 TCTATGTATATGTCCTGCATGTAGG 57.590 40.000 22.87 22.87 38.47 3.18
2331 2975 4.057432 GAGATGAGCTAGGAGCAAATGAC 58.943 47.826 0.64 0.00 45.56 3.06
2385 3029 3.316308 GGGATGACATTGGCTGTGAATAC 59.684 47.826 0.00 0.00 38.54 1.89
2625 3269 4.104738 CCTTACTATGGTTGGGATGATGGT 59.895 45.833 0.00 0.00 0.00 3.55
2662 3309 6.375830 TGACTACATTGGTAAACCCATACA 57.624 37.500 0.00 0.00 44.74 2.29
2663 3310 7.875327 AATGACTACATTGGTAAACCCATAC 57.125 36.000 0.00 0.00 44.74 2.39
2665 3312 8.887264 TTTAATGACTACATTGGTAAACCCAT 57.113 30.769 0.00 0.00 44.74 4.00
2883 3534 6.824305 AGTACCTGGAGAAAATTCAACATG 57.176 37.500 0.00 0.00 0.00 3.21
2988 3641 2.072298 ACTTGAATCTTGCTCGACTGC 58.928 47.619 0.00 0.00 0.00 4.40
3016 3669 2.699846 AGGCCTGCTTTTGTTGAATTCA 59.300 40.909 3.11 3.38 0.00 2.57
3023 3676 0.829182 CTGGGAGGCCTGCTTTTGTT 60.829 55.000 24.77 0.00 0.00 2.83
3077 3730 6.122850 TGCACTGTAATATAAGCTGCAAAG 57.877 37.500 1.02 0.00 31.85 2.77
3248 3901 7.241042 TGCTAATTCTACTATACATGGACCC 57.759 40.000 0.00 0.00 0.00 4.46
3296 3949 5.110814 TGTCTTTAGGAACATATGGTGGG 57.889 43.478 7.80 0.00 0.00 4.61
3383 4037 3.776969 TGGAGATAAGAGCAATGTCTGGT 59.223 43.478 0.00 0.00 38.89 4.00
3431 4085 4.450053 GACTCATAAGCAAGATTCAGGCT 58.550 43.478 0.00 0.00 40.14 4.58
3581 4248 2.280797 CTGTGTGTGTGTCGGGGG 60.281 66.667 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.