Multiple sequence alignment - TraesCS5A01G516600

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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 TraesCS5A01G516600 chr5A 100.000 2954 0 0 1 2954 679876308 679873355 0.000000e+00 5456.0
1 TraesCS5A01G516600 chr5A 85.657 502 60 5 997 1489 685432310 685432808 4.360000e-143 518.0
2 TraesCS5A01G516600 chr4B 92.899 2887 102 47 122 2954 641892272 641889435 0.000000e+00 4100.0
3 TraesCS5A01G516600 chrUn 92.470 1567 61 25 1368 2895 292521737 292523285 0.000000e+00 2187.0
4 TraesCS5A01G516600 chrUn 93.964 1342 28 13 117 1452 365430903 365429609 0.000000e+00 1980.0
5 TraesCS5A01G516600 chr4D 86.235 494 49 14 997 1473 502396610 502397101 4.360000e-143 518.0
6 TraesCS5A01G516600 chr2D 89.021 337 33 3 1106 1440 500362679 500363013 5.890000e-112 414.0
7 TraesCS5A01G516600 chr2A 89.053 338 31 5 1106 1440 645311419 645311753 5.890000e-112 414.0
8 TraesCS5A01G516600 chr6D 88.034 351 38 3 1093 1441 342472984 342472636 2.120000e-111 412.0
9 TraesCS5A01G516600 chr6A 87.749 351 39 3 1093 1441 482620206 482619858 9.860000e-110 407.0
10 TraesCS5A01G516600 chr2B 88.427 337 35 3 1106 1440 588067415 588067749 1.280000e-108 403.0
11 TraesCS5A01G516600 chr5D 85.714 70 6 1 102 167 332797925 332797856 1.470000e-08 71.3


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 TraesCS5A01G516600 chr5A 679873355 679876308 2953 True 5456 5456 100.000 1 2954 1 chr5A.!!$R1 2953
1 TraesCS5A01G516600 chr4B 641889435 641892272 2837 True 4100 4100 92.899 122 2954 1 chr4B.!!$R1 2832
2 TraesCS5A01G516600 chrUn 292521737 292523285 1548 False 2187 2187 92.470 1368 2895 1 chrUn.!!$F1 1527
3 TraesCS5A01G516600 chrUn 365429609 365430903 1294 True 1980 1980 93.964 117 1452 1 chrUn.!!$R1 1335

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
79 80 0.035739 GCCCTAACAAACCAGGACGA 59.964 55.0 0.00 0.0 33.42 4.20 F
772 789 0.396974 ACAGGTTCCTGCTTTGCCAA 60.397 50.0 17.55 0.0 37.57 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1431 0.529555 GCCAGTCGATGAAGAGCCTC 60.530 60.0 0.00 0.0 0.0 4.70 R
2433 2488 0.032515 TTCCTAGGCTCGGTCATGGA 60.033 55.0 2.96 0.0 0.0 3.41 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
46 47 6.624423 AGTCAAATACATGGTCAAATTGAGC 58.376 36.000 17.29 17.29 44.54 4.26
47 48 5.807011 GTCAAATACATGGTCAAATTGAGCC 59.193 40.000 20.61 13.48 43.72 4.70
48 49 5.105392 TCAAATACATGGTCAAATTGAGCCC 60.105 40.000 20.61 8.94 43.72 5.19
49 50 2.307496 ACATGGTCAAATTGAGCCCA 57.693 45.000 20.61 14.10 43.72 5.36
50 51 2.607499 ACATGGTCAAATTGAGCCCAA 58.393 42.857 20.61 4.60 43.72 4.12
51 52 2.971330 ACATGGTCAAATTGAGCCCAAA 59.029 40.909 20.61 4.25 43.72 3.28
52 53 3.390639 ACATGGTCAAATTGAGCCCAAAA 59.609 39.130 20.61 3.89 43.72 2.44
53 54 4.041938 ACATGGTCAAATTGAGCCCAAAAT 59.958 37.500 20.61 6.01 43.72 1.82
54 55 4.270245 TGGTCAAATTGAGCCCAAAATC 57.730 40.909 20.61 0.00 43.72 2.17
55 56 3.007831 TGGTCAAATTGAGCCCAAAATCC 59.992 43.478 20.61 4.85 43.72 3.01
56 57 3.007831 GGTCAAATTGAGCCCAAAATCCA 59.992 43.478 13.67 0.00 38.84 3.41
57 58 4.504689 GGTCAAATTGAGCCCAAAATCCAA 60.505 41.667 13.67 0.00 38.84 3.53
58 59 5.247862 GTCAAATTGAGCCCAAAATCCAAT 58.752 37.500 0.00 0.00 35.67 3.16
59 60 6.405538 GTCAAATTGAGCCCAAAATCCAATA 58.594 36.000 0.00 0.00 35.67 1.90
60 61 6.536224 GTCAAATTGAGCCCAAAATCCAATAG 59.464 38.462 0.00 0.00 35.67 1.73
61 62 4.677673 ATTGAGCCCAAAATCCAATAGC 57.322 40.909 0.00 0.00 35.67 2.97
62 63 2.387757 TGAGCCCAAAATCCAATAGCC 58.612 47.619 0.00 0.00 0.00 3.93
63 64 1.688735 GAGCCCAAAATCCAATAGCCC 59.311 52.381 0.00 0.00 0.00 5.19
64 65 1.291939 AGCCCAAAATCCAATAGCCCT 59.708 47.619 0.00 0.00 0.00 5.19
65 66 2.517980 AGCCCAAAATCCAATAGCCCTA 59.482 45.455 0.00 0.00 0.00 3.53
66 67 3.052186 AGCCCAAAATCCAATAGCCCTAA 60.052 43.478 0.00 0.00 0.00 2.69
67 68 3.069586 GCCCAAAATCCAATAGCCCTAAC 59.930 47.826 0.00 0.00 0.00 2.34
68 69 4.285863 CCCAAAATCCAATAGCCCTAACA 58.714 43.478 0.00 0.00 0.00 2.41
69 70 4.714308 CCCAAAATCCAATAGCCCTAACAA 59.286 41.667 0.00 0.00 0.00 2.83
70 71 5.188751 CCCAAAATCCAATAGCCCTAACAAA 59.811 40.000 0.00 0.00 0.00 2.83
71 72 6.106003 CCAAAATCCAATAGCCCTAACAAAC 58.894 40.000 0.00 0.00 0.00 2.93
72 73 5.932619 AAATCCAATAGCCCTAACAAACC 57.067 39.130 0.00 0.00 0.00 3.27
73 74 4.601406 ATCCAATAGCCCTAACAAACCA 57.399 40.909 0.00 0.00 0.00 3.67
74 75 3.963129 TCCAATAGCCCTAACAAACCAG 58.037 45.455 0.00 0.00 0.00 4.00
75 76 3.023832 CCAATAGCCCTAACAAACCAGG 58.976 50.000 0.00 0.00 0.00 4.45
76 77 3.308832 CCAATAGCCCTAACAAACCAGGA 60.309 47.826 0.00 0.00 33.42 3.86
77 78 3.646736 ATAGCCCTAACAAACCAGGAC 57.353 47.619 0.00 0.00 33.42 3.85
78 79 0.036306 AGCCCTAACAAACCAGGACG 59.964 55.000 0.00 0.00 33.42 4.79
79 80 0.035739 GCCCTAACAAACCAGGACGA 59.964 55.000 0.00 0.00 33.42 4.20
80 81 1.543871 GCCCTAACAAACCAGGACGAA 60.544 52.381 0.00 0.00 33.42 3.85
81 82 2.878526 GCCCTAACAAACCAGGACGAAT 60.879 50.000 0.00 0.00 33.42 3.34
82 83 2.747446 CCCTAACAAACCAGGACGAATG 59.253 50.000 0.00 0.00 33.42 2.67
83 84 3.408634 CCTAACAAACCAGGACGAATGT 58.591 45.455 0.00 0.00 33.42 2.71
84 85 4.563993 CCCTAACAAACCAGGACGAATGTA 60.564 45.833 0.00 0.00 33.42 2.29
85 86 4.630069 CCTAACAAACCAGGACGAATGTAG 59.370 45.833 0.00 0.00 33.42 2.74
86 87 3.764237 ACAAACCAGGACGAATGTAGT 57.236 42.857 0.00 0.00 0.00 2.73
87 88 4.877378 ACAAACCAGGACGAATGTAGTA 57.123 40.909 0.00 0.00 0.00 1.82
88 89 4.563061 ACAAACCAGGACGAATGTAGTAC 58.437 43.478 0.00 0.00 0.00 2.73
89 90 4.039488 ACAAACCAGGACGAATGTAGTACA 59.961 41.667 5.24 5.24 0.00 2.90
90 91 3.863142 ACCAGGACGAATGTAGTACAC 57.137 47.619 4.80 0.00 0.00 2.90
91 92 3.159472 ACCAGGACGAATGTAGTACACA 58.841 45.455 4.80 0.00 42.69 3.72
92 93 3.575256 ACCAGGACGAATGTAGTACACAA 59.425 43.478 4.80 0.00 41.55 3.33
93 94 3.924686 CCAGGACGAATGTAGTACACAAC 59.075 47.826 4.80 0.00 41.55 3.32
94 95 3.924686 CAGGACGAATGTAGTACACAACC 59.075 47.826 4.80 5.58 41.55 3.77
95 96 3.056322 AGGACGAATGTAGTACACAACCC 60.056 47.826 4.80 4.06 41.55 4.11
96 97 3.306225 GGACGAATGTAGTACACAACCCA 60.306 47.826 4.80 0.00 41.55 4.51
97 98 4.501071 GACGAATGTAGTACACAACCCAT 58.499 43.478 4.80 0.00 41.55 4.00
98 99 4.901868 ACGAATGTAGTACACAACCCATT 58.098 39.130 4.80 0.00 41.55 3.16
99 100 5.310451 ACGAATGTAGTACACAACCCATTT 58.690 37.500 4.80 0.00 41.55 2.32
100 101 5.766174 ACGAATGTAGTACACAACCCATTTT 59.234 36.000 4.80 0.00 41.55 1.82
101 102 6.263617 ACGAATGTAGTACACAACCCATTTTT 59.736 34.615 4.80 0.00 41.55 1.94
102 103 7.444792 ACGAATGTAGTACACAACCCATTTTTA 59.555 33.333 4.80 0.00 41.55 1.52
103 104 8.455682 CGAATGTAGTACACAACCCATTTTTAT 58.544 33.333 4.80 0.00 41.55 1.40
305 306 0.545548 GCCCCACCCTAGCTAGCTAT 60.546 60.000 24.36 7.73 0.00 2.97
419 432 3.742882 CCTCCATCATACAGTACATTGCG 59.257 47.826 0.00 0.00 0.00 4.85
460 473 8.487176 CGTATACGTACACATACATACACACTA 58.513 37.037 17.16 0.00 34.11 2.74
461 474 9.586150 GTATACGTACACATACATACACACTAC 57.414 37.037 0.00 0.00 0.00 2.73
462 475 6.748333 ACGTACACATACATACACACTACT 57.252 37.500 0.00 0.00 0.00 2.57
504 517 4.518249 AGCAAGCTAGGACAATTACCTTC 58.482 43.478 8.36 2.99 38.76 3.46
506 519 4.504858 CAAGCTAGGACAATTACCTTCGT 58.495 43.478 8.36 0.00 38.76 3.85
572 585 4.225573 CTCATCTCCATTTCTCCTCCTCT 58.774 47.826 0.00 0.00 0.00 3.69
573 586 4.222336 TCATCTCCATTTCTCCTCCTCTC 58.778 47.826 0.00 0.00 0.00 3.20
595 608 2.042435 CCTTCCTCCGGCCTCTCT 60.042 66.667 0.00 0.00 0.00 3.10
596 609 2.131067 CCTTCCTCCGGCCTCTCTC 61.131 68.421 0.00 0.00 0.00 3.20
597 610 1.076339 CTTCCTCCGGCCTCTCTCT 60.076 63.158 0.00 0.00 0.00 3.10
598 611 1.076632 TTCCTCCGGCCTCTCTCTC 60.077 63.158 0.00 0.00 0.00 3.20
766 780 0.846693 ACTTCCACAGGTTCCTGCTT 59.153 50.000 17.55 0.00 37.57 3.91
767 781 1.215423 ACTTCCACAGGTTCCTGCTTT 59.785 47.619 17.55 0.00 37.57 3.51
772 789 0.396974 ACAGGTTCCTGCTTTGCCAA 60.397 50.000 17.55 0.00 37.57 4.52
986 1010 4.448054 GGCATCTACCTAACCTACCTCTCT 60.448 50.000 0.00 0.00 0.00 3.10
989 1013 6.366340 CATCTACCTAACCTACCTCTCTTCA 58.634 44.000 0.00 0.00 0.00 3.02
1018 1042 0.734889 CATGGAGTTCACCGCAATCC 59.265 55.000 0.00 0.00 0.00 3.01
1581 1605 3.580193 CCGGCGACCGTCTACGAT 61.580 66.667 9.30 0.00 46.80 3.73
1600 1624 1.525718 TTACGACGCCTACCAGCACA 61.526 55.000 0.00 0.00 0.00 4.57
1853 1883 3.706373 GGAGGACTTCAGCGGGCA 61.706 66.667 0.00 0.00 0.00 5.36
1962 1992 3.059884 TCTTGACTTGTGAAGCGCTAAG 58.940 45.455 12.05 13.66 0.00 2.18
1963 1993 2.812358 TGACTTGTGAAGCGCTAAGA 57.188 45.000 21.37 5.29 0.00 2.10
1975 2006 3.003113 GCTAAGAGTGGGCGGTCGT 62.003 63.158 0.00 0.00 0.00 4.34
1990 2021 2.474359 CGGTCGTACGATCCACTACTAG 59.526 54.545 22.57 1.08 35.47 2.57
2067 2098 4.379499 GCAAAGGAGAAATTAACCTGTCGG 60.379 45.833 0.00 0.00 34.03 4.79
2068 2099 2.987232 AGGAGAAATTAACCTGTCGGC 58.013 47.619 0.00 0.00 32.39 5.54
2166 2200 8.441311 TTCCTTTGGTATATAGCTCATGATCT 57.559 34.615 12.87 4.22 0.00 2.75
2197 2231 1.368641 TTATTAGCCAGTGCAGTGCG 58.631 50.000 16.47 10.45 41.13 5.34
2246 2286 2.490328 TAAGCAGCAGCAACAACAAC 57.510 45.000 3.17 0.00 45.49 3.32
2280 2321 5.716094 TCTTGATTGATGCATGGTTTCTTG 58.284 37.500 2.46 0.00 0.00 3.02
2281 2322 3.852286 TGATTGATGCATGGTTTCTTGC 58.148 40.909 2.46 0.00 42.34 4.01
2282 2323 3.512329 TGATTGATGCATGGTTTCTTGCT 59.488 39.130 2.46 0.00 42.44 3.91
2283 2324 4.705991 TGATTGATGCATGGTTTCTTGCTA 59.294 37.500 2.46 0.00 42.44 3.49
2284 2325 4.707030 TTGATGCATGGTTTCTTGCTAG 57.293 40.909 2.46 0.00 42.44 3.42
2285 2326 3.689347 TGATGCATGGTTTCTTGCTAGT 58.311 40.909 2.46 0.00 42.44 2.57
2286 2327 4.842574 TGATGCATGGTTTCTTGCTAGTA 58.157 39.130 2.46 0.00 42.44 1.82
2287 2328 5.439721 TGATGCATGGTTTCTTGCTAGTAT 58.560 37.500 2.46 0.00 42.44 2.12
2288 2329 5.528690 TGATGCATGGTTTCTTGCTAGTATC 59.471 40.000 2.46 0.00 42.44 2.24
2289 2330 5.102953 TGCATGGTTTCTTGCTAGTATCT 57.897 39.130 0.00 0.00 42.44 1.98
2290 2331 5.500234 TGCATGGTTTCTTGCTAGTATCTT 58.500 37.500 0.00 0.00 42.44 2.40
2291 2332 5.945784 TGCATGGTTTCTTGCTAGTATCTTT 59.054 36.000 0.00 0.00 42.44 2.52
2338 2379 1.273327 CCAATTTCCCCTTGTGTGCTC 59.727 52.381 0.00 0.00 0.00 4.26
2341 2382 0.250295 TTTCCCCTTGTGTGCTCGAG 60.250 55.000 8.45 8.45 0.00 4.04
2356 2407 8.360390 TGTGTGCTCGAGTATAATTAAGATGAT 58.640 33.333 15.13 0.00 0.00 2.45
2388 2439 9.639601 GTTCTTTTCATTTGGGGACTTAAATAG 57.360 33.333 0.00 0.00 0.00 1.73
2393 2444 7.465900 TCATTTGGGGACTTAAATAGAGGAT 57.534 36.000 0.00 0.00 0.00 3.24
2452 2507 0.032515 TCCATGACCGAGCCTAGGAA 60.033 55.000 14.75 0.00 0.00 3.36
2484 2539 6.237901 GTGCTCCCCACATATGATAACAATA 58.762 40.000 10.38 0.00 44.06 1.90
2814 2870 4.689549 ATGCCTGCCTGCCTGCAA 62.690 61.111 6.74 0.00 41.51 4.08
2815 2871 3.976490 ATGCCTGCCTGCCTGCAAT 62.976 57.895 6.74 0.00 41.51 3.56
2818 2889 1.079405 CCTGCCTGCCTGCAATTTG 60.079 57.895 0.00 0.00 41.51 2.32
2842 2913 6.935771 TGCATACATTCATACACATGCATCTA 59.064 34.615 0.00 0.00 42.64 1.98
2893 2966 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2894 2967 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2895 2968 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2896 2969 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2897 2970 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2898 2971 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2899 2972 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2900 2973 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
2901 2974 6.065374 TCTCTCTCTCTCTCTCTCTCTCTAC 58.935 48.000 0.00 0.00 0.00 2.59
2902 2975 4.822350 TCTCTCTCTCTCTCTCTCTCTACG 59.178 50.000 0.00 0.00 0.00 3.51
2903 2976 4.533815 TCTCTCTCTCTCTCTCTCTACGT 58.466 47.826 0.00 0.00 0.00 3.57
2904 2977 5.687780 TCTCTCTCTCTCTCTCTCTACGTA 58.312 45.833 0.00 0.00 0.00 3.57
2908 2981 6.776116 TCTCTCTCTCTCTCTCTACGTATCTT 59.224 42.308 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.243426 GCTCAATTTGACCATGTATTTGACTAA 58.757 33.333 0.00 0.00 0.00 2.24
21 22 7.148086 GGCTCAATTTGACCATGTATTTGACTA 60.148 37.037 11.04 0.00 0.00 2.59
22 23 6.350445 GGCTCAATTTGACCATGTATTTGACT 60.350 38.462 11.04 0.00 0.00 3.41
23 24 5.807011 GGCTCAATTTGACCATGTATTTGAC 59.193 40.000 11.04 0.00 0.00 3.18
24 25 5.105392 GGGCTCAATTTGACCATGTATTTGA 60.105 40.000 15.37 0.00 0.00 2.69
25 26 5.111293 GGGCTCAATTTGACCATGTATTTG 58.889 41.667 15.37 0.00 0.00 2.32
26 27 4.776837 TGGGCTCAATTTGACCATGTATTT 59.223 37.500 15.37 0.00 0.00 1.40
27 28 4.352009 TGGGCTCAATTTGACCATGTATT 58.648 39.130 15.37 0.00 0.00 1.89
28 29 3.979911 TGGGCTCAATTTGACCATGTAT 58.020 40.909 15.37 0.00 0.00 2.29
29 30 3.448093 TGGGCTCAATTTGACCATGTA 57.552 42.857 15.37 2.34 0.00 2.29
30 31 2.307496 TGGGCTCAATTTGACCATGT 57.693 45.000 15.37 0.00 0.00 3.21
31 32 3.681593 TTTGGGCTCAATTTGACCATG 57.318 42.857 0.00 0.00 32.28 3.66
32 33 4.323715 GGATTTTGGGCTCAATTTGACCAT 60.324 41.667 0.00 0.00 32.28 3.55
33 34 3.007831 GGATTTTGGGCTCAATTTGACCA 59.992 43.478 0.00 10.87 32.28 4.02
34 35 3.007831 TGGATTTTGGGCTCAATTTGACC 59.992 43.478 0.00 0.74 32.28 4.02
35 36 4.270245 TGGATTTTGGGCTCAATTTGAC 57.730 40.909 0.00 0.00 32.28 3.18
36 37 4.970860 TTGGATTTTGGGCTCAATTTGA 57.029 36.364 0.00 0.00 32.28 2.69
37 38 5.295045 GCTATTGGATTTTGGGCTCAATTTG 59.705 40.000 0.00 0.00 32.28 2.32
38 39 5.430886 GCTATTGGATTTTGGGCTCAATTT 58.569 37.500 0.00 0.00 32.28 1.82
39 40 4.141642 GGCTATTGGATTTTGGGCTCAATT 60.142 41.667 0.00 0.00 32.28 2.32
40 41 3.389002 GGCTATTGGATTTTGGGCTCAAT 59.611 43.478 0.00 0.00 32.28 2.57
41 42 2.765699 GGCTATTGGATTTTGGGCTCAA 59.234 45.455 0.00 0.00 0.00 3.02
42 43 2.387757 GGCTATTGGATTTTGGGCTCA 58.612 47.619 0.00 0.00 0.00 4.26
43 44 1.688735 GGGCTATTGGATTTTGGGCTC 59.311 52.381 0.00 0.00 0.00 4.70
44 45 1.291939 AGGGCTATTGGATTTTGGGCT 59.708 47.619 0.00 0.00 0.00 5.19
45 46 1.793414 AGGGCTATTGGATTTTGGGC 58.207 50.000 0.00 0.00 0.00 5.36
46 47 4.285863 TGTTAGGGCTATTGGATTTTGGG 58.714 43.478 0.00 0.00 0.00 4.12
47 48 5.930837 TTGTTAGGGCTATTGGATTTTGG 57.069 39.130 0.00 0.00 0.00 3.28
48 49 6.106003 GGTTTGTTAGGGCTATTGGATTTTG 58.894 40.000 0.00 0.00 0.00 2.44
49 50 5.782845 TGGTTTGTTAGGGCTATTGGATTTT 59.217 36.000 0.00 0.00 0.00 1.82
50 51 5.337788 TGGTTTGTTAGGGCTATTGGATTT 58.662 37.500 0.00 0.00 0.00 2.17
51 52 4.941713 TGGTTTGTTAGGGCTATTGGATT 58.058 39.130 0.00 0.00 0.00 3.01
52 53 4.536765 CTGGTTTGTTAGGGCTATTGGAT 58.463 43.478 0.00 0.00 0.00 3.41
53 54 3.308832 CCTGGTTTGTTAGGGCTATTGGA 60.309 47.826 0.00 0.00 0.00 3.53
54 55 3.023832 CCTGGTTTGTTAGGGCTATTGG 58.976 50.000 0.00 0.00 0.00 3.16
55 56 3.694566 GTCCTGGTTTGTTAGGGCTATTG 59.305 47.826 0.00 0.00 35.80 1.90
56 57 3.621461 CGTCCTGGTTTGTTAGGGCTATT 60.621 47.826 0.00 0.00 36.54 1.73
57 58 2.093128 CGTCCTGGTTTGTTAGGGCTAT 60.093 50.000 0.00 0.00 36.54 2.97
58 59 1.276989 CGTCCTGGTTTGTTAGGGCTA 59.723 52.381 0.00 0.00 36.54 3.93
59 60 0.036306 CGTCCTGGTTTGTTAGGGCT 59.964 55.000 0.00 0.00 36.54 5.19
60 61 0.035739 TCGTCCTGGTTTGTTAGGGC 59.964 55.000 0.00 0.00 35.34 5.19
61 62 2.554370 TTCGTCCTGGTTTGTTAGGG 57.446 50.000 0.00 0.00 34.76 3.53
62 63 3.408634 ACATTCGTCCTGGTTTGTTAGG 58.591 45.455 0.00 0.00 35.34 2.69
63 64 5.235516 ACTACATTCGTCCTGGTTTGTTAG 58.764 41.667 0.00 0.00 0.00 2.34
64 65 5.217978 ACTACATTCGTCCTGGTTTGTTA 57.782 39.130 0.00 0.00 0.00 2.41
65 66 4.081322 ACTACATTCGTCCTGGTTTGTT 57.919 40.909 0.00 0.00 0.00 2.83
66 67 3.764237 ACTACATTCGTCCTGGTTTGT 57.236 42.857 0.00 0.00 0.00 2.83
67 68 4.387862 GTGTACTACATTCGTCCTGGTTTG 59.612 45.833 0.00 0.00 0.00 2.93
68 69 4.039488 TGTGTACTACATTCGTCCTGGTTT 59.961 41.667 0.00 0.00 33.42 3.27
69 70 3.575256 TGTGTACTACATTCGTCCTGGTT 59.425 43.478 0.00 0.00 33.42 3.67
70 71 3.159472 TGTGTACTACATTCGTCCTGGT 58.841 45.455 0.00 0.00 33.42 4.00
71 72 3.861276 TGTGTACTACATTCGTCCTGG 57.139 47.619 0.00 0.00 33.42 4.45
72 73 3.924686 GGTTGTGTACTACATTCGTCCTG 59.075 47.826 0.00 0.00 39.48 3.86
73 74 3.056322 GGGTTGTGTACTACATTCGTCCT 60.056 47.826 0.00 0.00 39.48 3.85
74 75 3.256558 GGGTTGTGTACTACATTCGTCC 58.743 50.000 0.00 0.00 39.48 4.79
75 76 3.916761 TGGGTTGTGTACTACATTCGTC 58.083 45.455 0.00 0.00 39.48 4.20
76 77 4.546829 ATGGGTTGTGTACTACATTCGT 57.453 40.909 0.00 0.00 39.48 3.85
77 78 5.873179 AAATGGGTTGTGTACTACATTCG 57.127 39.130 0.00 0.00 39.48 3.34
128 129 7.108841 TGGTAGGTATCAGAACAACTGTATC 57.891 40.000 0.00 0.00 45.86 2.24
140 141 5.308014 TGCATGCTTATTGGTAGGTATCAG 58.692 41.667 20.33 0.00 0.00 2.90
313 326 1.953686 GGTGTGAGAGGAGCTAGCTAG 59.046 57.143 19.38 16.84 0.00 3.42
314 327 1.410365 GGGTGTGAGAGGAGCTAGCTA 60.410 57.143 19.38 0.00 0.00 3.32
315 328 0.686112 GGGTGTGAGAGGAGCTAGCT 60.686 60.000 19.45 19.45 0.00 3.32
316 329 1.681486 GGGGTGTGAGAGGAGCTAGC 61.681 65.000 6.62 6.62 0.00 3.42
317 330 0.324738 TGGGGTGTGAGAGGAGCTAG 60.325 60.000 0.00 0.00 0.00 3.42
318 331 0.339859 ATGGGGTGTGAGAGGAGCTA 59.660 55.000 0.00 0.00 0.00 3.32
319 332 0.980231 GATGGGGTGTGAGAGGAGCT 60.980 60.000 0.00 0.00 0.00 4.09
320 333 1.524482 GATGGGGTGTGAGAGGAGC 59.476 63.158 0.00 0.00 0.00 4.70
321 334 0.326048 AGGATGGGGTGTGAGAGGAG 60.326 60.000 0.00 0.00 0.00 3.69
322 335 0.325671 GAGGATGGGGTGTGAGAGGA 60.326 60.000 0.00 0.00 0.00 3.71
323 336 1.341156 GGAGGATGGGGTGTGAGAGG 61.341 65.000 0.00 0.00 0.00 3.69
419 432 3.058520 CGTATACGTGTGTAGTTGTGTGC 59.941 47.826 17.16 0.00 33.17 4.57
460 473 5.106237 GCTTAGCTAGTGTGTGTAGTGTAGT 60.106 44.000 0.00 0.00 0.00 2.73
461 474 5.106277 TGCTTAGCTAGTGTGTGTAGTGTAG 60.106 44.000 5.60 0.00 0.00 2.74
462 475 4.763279 TGCTTAGCTAGTGTGTGTAGTGTA 59.237 41.667 5.60 0.00 0.00 2.90
504 517 1.004715 CTTGCTTTTGGCTTGCAAACG 60.005 47.619 0.00 0.00 44.49 3.60
506 519 1.015868 GCTTGCTTTTGGCTTGCAAA 58.984 45.000 0.00 0.00 44.49 3.68
595 608 5.187186 GGTACTATGAAGGTTCTTGGTGAGA 59.813 44.000 5.26 0.00 30.70 3.27
596 609 5.420409 GGTACTATGAAGGTTCTTGGTGAG 58.580 45.833 5.26 0.00 30.70 3.51
597 610 4.224370 GGGTACTATGAAGGTTCTTGGTGA 59.776 45.833 5.26 0.00 30.70 4.02
598 611 4.019681 TGGGTACTATGAAGGTTCTTGGTG 60.020 45.833 5.26 0.00 30.70 4.17
741 755 2.832733 AGGAACCTGTGGAAGTAGCTAC 59.167 50.000 16.43 16.43 0.00 3.58
746 760 1.729586 AGCAGGAACCTGTGGAAGTA 58.270 50.000 19.97 0.00 45.24 2.24
748 762 1.610522 CAAAGCAGGAACCTGTGGAAG 59.389 52.381 19.97 5.65 45.24 3.46
772 789 5.200483 TGGAATTTAGAATTCTTGGCCGAT 58.800 37.500 14.36 0.00 0.00 4.18
779 796 8.899887 TTGGGAGATTGGAATTTAGAATTCTT 57.100 30.769 14.36 0.00 0.00 2.52
986 1010 1.271325 ACTCCATGTGCACCGATTGAA 60.271 47.619 15.69 0.00 0.00 2.69
989 1013 1.271325 TGAACTCCATGTGCACCGATT 60.271 47.619 15.69 0.00 0.00 3.34
1063 1087 3.050275 GGCCTTATGATCCGCCGC 61.050 66.667 0.00 0.00 0.00 6.53
1099 1123 1.903877 ATGTGCTCCTTCTCCACCGG 61.904 60.000 0.00 0.00 0.00 5.28
1407 1431 0.529555 GCCAGTCGATGAAGAGCCTC 60.530 60.000 0.00 0.00 0.00 4.70
1476 1500 2.612115 AAGGGCACAGAGGGGAGG 60.612 66.667 0.00 0.00 0.00 4.30
1581 1605 1.213537 GTGCTGGTAGGCGTCGTAA 59.786 57.895 0.00 0.00 34.52 3.18
1623 1647 3.219198 GCCCCGTACCCGTCGTAT 61.219 66.667 0.00 0.00 0.00 3.06
1659 1683 1.516386 CTGCGGCTGGTAGTACACG 60.516 63.158 0.00 2.48 0.00 4.49
1853 1883 3.608662 TTGTCGCCGTTCTCCCGT 61.609 61.111 0.00 0.00 0.00 5.28
1962 1992 2.659017 GATCGTACGACCGCCCACTC 62.659 65.000 22.14 7.83 0.00 3.51
1963 1993 2.753043 ATCGTACGACCGCCCACT 60.753 61.111 22.14 0.00 0.00 4.00
1975 2006 5.620738 AGTGGTACTAGTAGTGGATCGTA 57.379 43.478 13.29 0.00 0.00 3.43
2067 2098 2.727916 CGCATTTGTTTACTTCTCCGGC 60.728 50.000 0.00 0.00 0.00 6.13
2068 2099 2.159572 CCGCATTTGTTTACTTCTCCGG 60.160 50.000 0.00 0.00 0.00 5.14
2166 2200 8.436778 TGCACTGGCTAATAATAATTAAGGAGA 58.563 33.333 0.00 0.00 41.91 3.71
2181 2215 2.358615 CCGCACTGCACTGGCTAA 60.359 61.111 1.11 0.00 41.91 3.09
2182 2216 3.625897 ACCGCACTGCACTGGCTA 61.626 61.111 1.11 0.00 41.91 3.93
2185 2219 3.653009 CACACCGCACTGCACTGG 61.653 66.667 1.11 0.00 0.00 4.00
2186 2220 2.588596 TCACACCGCACTGCACTG 60.589 61.111 1.11 0.00 0.00 3.66
2187 2221 2.280389 CTCACACCGCACTGCACT 60.280 61.111 1.11 0.00 0.00 4.40
2188 2222 1.835483 CTTCTCACACCGCACTGCAC 61.835 60.000 1.11 0.00 0.00 4.57
2189 2223 1.595109 CTTCTCACACCGCACTGCA 60.595 57.895 1.11 0.00 0.00 4.41
2190 2224 0.880278 TTCTTCTCACACCGCACTGC 60.880 55.000 0.00 0.00 0.00 4.40
2197 2231 4.331717 TCTTTTCGTGTTTCTTCTCACACC 59.668 41.667 0.00 0.00 40.27 4.16
2246 2286 9.399403 CATGCATCAATCAAGATAGAAGATTTG 57.601 33.333 0.00 0.00 30.04 2.32
2283 2324 8.742777 TGCAAATCAGAGCAAATAAAAGATACT 58.257 29.630 0.00 0.00 37.90 2.12
2284 2325 8.915871 TGCAAATCAGAGCAAATAAAAGATAC 57.084 30.769 0.00 0.00 37.90 2.24
2286 2327 9.095065 GAATGCAAATCAGAGCAAATAAAAGAT 57.905 29.630 0.00 0.00 44.88 2.40
2287 2328 7.546667 GGAATGCAAATCAGAGCAAATAAAAGA 59.453 33.333 0.00 0.00 44.88 2.52
2288 2329 7.548075 AGGAATGCAAATCAGAGCAAATAAAAG 59.452 33.333 0.00 0.00 44.88 2.27
2289 2330 7.388437 AGGAATGCAAATCAGAGCAAATAAAA 58.612 30.769 0.00 0.00 44.88 1.52
2290 2331 6.938507 AGGAATGCAAATCAGAGCAAATAAA 58.061 32.000 0.00 0.00 44.88 1.40
2291 2332 6.534475 AGGAATGCAAATCAGAGCAAATAA 57.466 33.333 0.00 0.00 44.88 1.40
2356 2407 4.072131 CCCCAAATGAAAAGAACGAGAGA 58.928 43.478 0.00 0.00 0.00 3.10
2426 2479 1.293924 GCTCGGTCATGGACTCATTG 58.706 55.000 0.00 0.00 32.47 2.82
2433 2488 0.032515 TTCCTAGGCTCGGTCATGGA 60.033 55.000 2.96 0.00 0.00 3.41
2452 2507 1.064003 TGTGGGGAGCACACTATGTT 58.936 50.000 0.00 0.00 39.52 2.71
2490 2545 9.062524 GCATGTATTGTATTTGTATAAGGGTGA 57.937 33.333 0.00 0.00 0.00 4.02
2562 2617 3.090790 TCCATGTGCACAATTACAGCAT 58.909 40.909 25.72 0.00 40.78 3.79
2813 2869 7.266400 TGCATGTGTATGAATGTATGCAAATT 58.734 30.769 7.18 0.00 45.28 1.82
2814 2870 6.807789 TGCATGTGTATGAATGTATGCAAAT 58.192 32.000 7.18 0.00 45.28 2.32
2815 2871 6.205101 TGCATGTGTATGAATGTATGCAAA 57.795 33.333 7.18 0.00 45.28 3.68
2818 2889 6.250344 AGATGCATGTGTATGAATGTATGC 57.750 37.500 2.46 0.00 40.81 3.14
2842 2913 3.906846 GAGAGAGAGAGAGAGAGAGGGAT 59.093 52.174 0.00 0.00 0.00 3.85
2893 2966 6.463331 GGAGGAGAGAAAGATACGTAGAGAGA 60.463 46.154 0.08 0.00 0.00 3.10
2894 2967 5.699458 GGAGGAGAGAAAGATACGTAGAGAG 59.301 48.000 0.08 0.00 0.00 3.20
2895 2968 5.613329 GGAGGAGAGAAAGATACGTAGAGA 58.387 45.833 0.08 0.00 0.00 3.10
2896 2969 4.449743 CGGAGGAGAGAAAGATACGTAGAG 59.550 50.000 0.08 0.00 0.00 2.43
2897 2970 4.378774 CGGAGGAGAGAAAGATACGTAGA 58.621 47.826 0.08 0.00 0.00 2.59
2898 2971 3.058777 GCGGAGGAGAGAAAGATACGTAG 60.059 52.174 0.08 0.00 0.00 3.51
2899 2972 2.877168 GCGGAGGAGAGAAAGATACGTA 59.123 50.000 0.00 0.00 0.00 3.57
2900 2973 1.677052 GCGGAGGAGAGAAAGATACGT 59.323 52.381 0.00 0.00 0.00 3.57
2901 2974 1.950909 AGCGGAGGAGAGAAAGATACG 59.049 52.381 0.00 0.00 0.00 3.06
2902 2975 2.952978 TGAGCGGAGGAGAGAAAGATAC 59.047 50.000 0.00 0.00 0.00 2.24
2903 2976 3.298686 TGAGCGGAGGAGAGAAAGATA 57.701 47.619 0.00 0.00 0.00 1.98
2904 2977 2.151502 TGAGCGGAGGAGAGAAAGAT 57.848 50.000 0.00 0.00 0.00 2.40
2908 2981 2.173782 AGAGTATGAGCGGAGGAGAGAA 59.826 50.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.