Multiple sequence alignment - TraesCS5B01G030900

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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 TraesCS5B01G030900 chr5B 100.000 2169 0 0 1 2169 34066068 34068236 0.000000e+00 4006
1 TraesCS5B01G030900 chr5B 100.000 105 0 0 2383 2487 34068450 34068554 7.020000e-46 195
2 TraesCS5B01G030900 chrUn 97.182 2058 51 3 119 2169 282364579 282362522 0.000000e+00 3472
3 TraesCS5B01G030900 chrUn 96.987 2058 55 3 119 2169 86509895 86507838 0.000000e+00 3450
4 TraesCS5B01G030900 chrUn 99.048 105 1 0 2383 2487 86507741 86507637 3.270000e-44 189
5 TraesCS5B01G030900 chr6B 97.183 2059 49 4 119 2169 596620441 596622498 0.000000e+00 3472
6 TraesCS5B01G030900 chr6B 99.153 118 1 0 1 118 14493184 14493301 1.940000e-51 213
7 TraesCS5B01G030900 chr6B 98.319 119 2 0 1 119 144080345 144080463 2.510000e-50 209
8 TraesCS5B01G030900 chr6A 97.036 2058 54 3 119 2169 84434261 84436318 0.000000e+00 3456
9 TraesCS5B01G030900 chr6A 99.048 105 1 0 2383 2487 608880971 608880867 3.270000e-44 189
10 TraesCS5B01G030900 chr3B 96.986 2057 55 4 119 2169 92317955 92320010 0.000000e+00 3448
11 TraesCS5B01G030900 chr3B 96.124 129 4 1 1 128 426377308 426377180 2.510000e-50 209
12 TraesCS5B01G030900 chr3B 95.349 129 3 3 1 128 291267486 291267612 4.190000e-48 202
13 TraesCS5B01G030900 chr4D 96.933 2054 58 4 119 2169 123423832 123425883 0.000000e+00 3439
14 TraesCS5B01G030900 chr3D 96.889 2057 58 3 119 2169 154704843 154702787 0.000000e+00 3439
15 TraesCS5B01G030900 chr3D 91.156 147 8 5 1 143 576415505 576415360 7.020000e-46 195
16 TraesCS5B01G030900 chr3D 99.048 105 1 0 2383 2487 154702692 154702588 3.270000e-44 189
17 TraesCS5B01G030900 chr3D 99.048 105 1 0 2383 2487 213412734 213412630 3.270000e-44 189
18 TraesCS5B01G030900 chr2B 96.743 2057 58 6 119 2169 30670494 30668441 0.000000e+00 3419
19 TraesCS5B01G030900 chr2B 99.048 105 1 0 2383 2487 30668345 30668241 3.270000e-44 189
20 TraesCS5B01G030900 chr3A 96.500 2057 65 4 119 2169 694375453 694373398 0.000000e+00 3393
21 TraesCS5B01G030900 chr7B 96.825 126 2 1 1 124 30287713 30287838 2.510000e-50 209
22 TraesCS5B01G030900 chr7B 96.063 127 5 0 1 127 538850018 538850144 9.010000e-50 207
23 TraesCS5B01G030900 chr7B 96.721 122 2 1 1 120 342926363 342926484 4.190000e-48 202
24 TraesCS5B01G030900 chr1B 96.774 124 4 0 1 124 509174404 509174527 9.010000e-50 207
25 TraesCS5B01G030900 chr7D 99.048 105 1 0 2383 2487 203543704 203543600 3.270000e-44 189
26 TraesCS5B01G030900 chr7A 99.048 105 1 0 2383 2487 563585449 563585553 3.270000e-44 189
27 TraesCS5B01G030900 chr6D 99.048 105 1 0 2383 2487 168769055 168769159 3.270000e-44 189
28 TraesCS5B01G030900 chr5D 99.048 105 1 0 2383 2487 324422471 324422575 3.270000e-44 189


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 TraesCS5B01G030900 chr5B 34066068 34068554 2486 False 2100.5 4006 100.0000 1 2487 2 chr5B.!!$F1 2486
1 TraesCS5B01G030900 chrUn 282362522 282364579 2057 True 3472.0 3472 97.1820 119 2169 1 chrUn.!!$R1 2050
2 TraesCS5B01G030900 chrUn 86507637 86509895 2258 True 1819.5 3450 98.0175 119 2487 2 chrUn.!!$R2 2368
3 TraesCS5B01G030900 chr6B 596620441 596622498 2057 False 3472.0 3472 97.1830 119 2169 1 chr6B.!!$F3 2050
4 TraesCS5B01G030900 chr6A 84434261 84436318 2057 False 3456.0 3456 97.0360 119 2169 1 chr6A.!!$F1 2050
5 TraesCS5B01G030900 chr3B 92317955 92320010 2055 False 3448.0 3448 96.9860 119 2169 1 chr3B.!!$F1 2050
6 TraesCS5B01G030900 chr4D 123423832 123425883 2051 False 3439.0 3439 96.9330 119 2169 1 chr4D.!!$F1 2050
7 TraesCS5B01G030900 chr3D 154702588 154704843 2255 True 1814.0 3439 97.9685 119 2487 2 chr3D.!!$R3 2368
8 TraesCS5B01G030900 chr2B 30668241 30670494 2253 True 1804.0 3419 97.8955 119 2487 2 chr2B.!!$R1 2368
9 TraesCS5B01G030900 chr3A 694373398 694375453 2055 True 3393.0 3393 96.5000 119 2169 1 chr3A.!!$R1 2050

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
61 62 0.034896 TTCTGCTCCTCGTTGGGTTC 59.965 55.0 0.0 0.0 36.20 3.62 F
69 70 0.314302 CTCGTTGGGTTCGACACTCT 59.686 55.0 0.0 0.0 33.71 3.24 F
1374 1380 0.322906 TGTGCCACAGGTGTTGAACA 60.323 50.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1452 0.396811 CCCGACCTGGAAAAGTGACT 59.603 55.000 0.0 0.0 42.0 3.41 R
1458 1464 0.905357 CCACTTCTTGATCCCGACCT 59.095 55.000 0.0 0.0 0.0 3.85 R
2398 2417 2.216898 GCAGAGAACAAGACAGCAAGT 58.783 47.619 0.0 0.0 0.0 3.16 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
22 23 5.376854 AGTGCTTGCATAAAACCTTACTG 57.623 39.130 0.00 0.00 0.00 2.74
23 24 5.070001 AGTGCTTGCATAAAACCTTACTGA 58.930 37.500 0.00 0.00 0.00 3.41
24 25 5.534654 AGTGCTTGCATAAAACCTTACTGAA 59.465 36.000 0.00 0.00 0.00 3.02
25 26 6.040391 AGTGCTTGCATAAAACCTTACTGAAA 59.960 34.615 0.00 0.00 0.00 2.69
26 27 6.699642 GTGCTTGCATAAAACCTTACTGAAAA 59.300 34.615 0.00 0.00 0.00 2.29
27 28 6.699642 TGCTTGCATAAAACCTTACTGAAAAC 59.300 34.615 0.00 0.00 0.00 2.43
28 29 6.145534 GCTTGCATAAAACCTTACTGAAAACC 59.854 38.462 0.00 0.00 0.00 3.27
29 30 5.764131 TGCATAAAACCTTACTGAAAACCG 58.236 37.500 0.00 0.00 0.00 4.44
30 31 4.619760 GCATAAAACCTTACTGAAAACCGC 59.380 41.667 0.00 0.00 0.00 5.68
31 32 5.564063 GCATAAAACCTTACTGAAAACCGCT 60.564 40.000 0.00 0.00 0.00 5.52
32 33 4.994907 AAAACCTTACTGAAAACCGCTT 57.005 36.364 0.00 0.00 0.00 4.68
33 34 7.586747 CATAAAACCTTACTGAAAACCGCTTA 58.413 34.615 0.00 0.00 0.00 3.09
34 35 6.644248 AAAACCTTACTGAAAACCGCTTAT 57.356 33.333 0.00 0.00 0.00 1.73
35 36 5.874895 AACCTTACTGAAAACCGCTTATC 57.125 39.130 0.00 0.00 0.00 1.75
36 37 4.901868 ACCTTACTGAAAACCGCTTATCA 58.098 39.130 0.00 0.00 0.00 2.15
37 38 5.497474 ACCTTACTGAAAACCGCTTATCAT 58.503 37.500 0.00 0.00 0.00 2.45
38 39 5.944007 ACCTTACTGAAAACCGCTTATCATT 59.056 36.000 0.00 0.00 0.00 2.57
39 40 6.433093 ACCTTACTGAAAACCGCTTATCATTT 59.567 34.615 0.00 0.00 0.00 2.32
40 41 6.967199 CCTTACTGAAAACCGCTTATCATTTC 59.033 38.462 0.00 0.00 0.00 2.17
41 42 5.310720 ACTGAAAACCGCTTATCATTTCC 57.689 39.130 0.00 0.00 30.80 3.13
42 43 5.010282 ACTGAAAACCGCTTATCATTTCCT 58.990 37.500 0.00 0.00 30.80 3.36
43 44 5.476945 ACTGAAAACCGCTTATCATTTCCTT 59.523 36.000 0.00 0.00 30.80 3.36
44 45 5.949735 TGAAAACCGCTTATCATTTCCTTC 58.050 37.500 0.00 0.00 30.80 3.46
45 46 5.710099 TGAAAACCGCTTATCATTTCCTTCT 59.290 36.000 0.00 0.00 30.80 2.85
46 47 5.567138 AAACCGCTTATCATTTCCTTCTG 57.433 39.130 0.00 0.00 0.00 3.02
47 48 2.945668 ACCGCTTATCATTTCCTTCTGC 59.054 45.455 0.00 0.00 0.00 4.26
48 49 3.209410 CCGCTTATCATTTCCTTCTGCT 58.791 45.455 0.00 0.00 0.00 4.24
49 50 3.249559 CCGCTTATCATTTCCTTCTGCTC 59.750 47.826 0.00 0.00 0.00 4.26
50 51 3.249559 CGCTTATCATTTCCTTCTGCTCC 59.750 47.826 0.00 0.00 0.00 4.70
51 52 4.459330 GCTTATCATTTCCTTCTGCTCCT 58.541 43.478 0.00 0.00 0.00 3.69
52 53 4.514816 GCTTATCATTTCCTTCTGCTCCTC 59.485 45.833 0.00 0.00 0.00 3.71
53 54 2.680312 TCATTTCCTTCTGCTCCTCG 57.320 50.000 0.00 0.00 0.00 4.63
54 55 1.902508 TCATTTCCTTCTGCTCCTCGT 59.097 47.619 0.00 0.00 0.00 4.18
55 56 2.303022 TCATTTCCTTCTGCTCCTCGTT 59.697 45.455 0.00 0.00 0.00 3.85
56 57 2.169832 TTTCCTTCTGCTCCTCGTTG 57.830 50.000 0.00 0.00 0.00 4.10
57 58 0.321671 TTCCTTCTGCTCCTCGTTGG 59.678 55.000 0.00 0.00 37.10 3.77
58 59 1.078848 CCTTCTGCTCCTCGTTGGG 60.079 63.158 0.00 0.00 36.20 4.12
59 60 1.674057 CTTCTGCTCCTCGTTGGGT 59.326 57.895 0.00 0.00 36.20 4.51
60 61 0.035458 CTTCTGCTCCTCGTTGGGTT 59.965 55.000 0.00 0.00 36.20 4.11
61 62 0.034896 TTCTGCTCCTCGTTGGGTTC 59.965 55.000 0.00 0.00 36.20 3.62
62 63 1.738099 CTGCTCCTCGTTGGGTTCG 60.738 63.158 0.00 0.00 36.20 3.95
63 64 2.154798 CTGCTCCTCGTTGGGTTCGA 62.155 60.000 0.00 0.00 36.20 3.71
64 65 1.737008 GCTCCTCGTTGGGTTCGAC 60.737 63.158 0.00 0.00 36.20 4.20
65 66 1.663739 CTCCTCGTTGGGTTCGACA 59.336 57.895 0.00 0.00 36.20 4.35
66 67 0.666577 CTCCTCGTTGGGTTCGACAC 60.667 60.000 0.00 0.00 36.20 3.67
67 68 1.111116 TCCTCGTTGGGTTCGACACT 61.111 55.000 0.00 0.00 36.20 3.55
68 69 0.666577 CCTCGTTGGGTTCGACACTC 60.667 60.000 0.00 0.00 33.71 3.51
69 70 0.314302 CTCGTTGGGTTCGACACTCT 59.686 55.000 0.00 0.00 33.71 3.24
70 71 0.748450 TCGTTGGGTTCGACACTCTT 59.252 50.000 0.00 0.00 32.30 2.85
71 72 1.955778 TCGTTGGGTTCGACACTCTTA 59.044 47.619 0.00 0.00 32.30 2.10
72 73 2.056577 CGTTGGGTTCGACACTCTTAC 58.943 52.381 0.00 0.00 0.00 2.34
73 74 2.288030 CGTTGGGTTCGACACTCTTACT 60.288 50.000 0.00 0.00 0.00 2.24
74 75 3.725490 GTTGGGTTCGACACTCTTACTT 58.275 45.455 0.00 0.00 0.00 2.24
75 76 4.557296 CGTTGGGTTCGACACTCTTACTTA 60.557 45.833 0.00 0.00 0.00 2.24
76 77 5.476614 GTTGGGTTCGACACTCTTACTTAT 58.523 41.667 0.00 0.00 0.00 1.73
77 78 5.320549 TGGGTTCGACACTCTTACTTATC 57.679 43.478 0.00 0.00 0.00 1.75
78 79 4.142534 TGGGTTCGACACTCTTACTTATCG 60.143 45.833 0.00 0.00 0.00 2.92
79 80 4.095483 GGGTTCGACACTCTTACTTATCGA 59.905 45.833 0.00 0.00 36.85 3.59
80 81 5.392380 GGGTTCGACACTCTTACTTATCGAA 60.392 44.000 2.99 2.99 43.90 3.71
81 82 6.088824 GGTTCGACACTCTTACTTATCGAAA 58.911 40.000 8.30 0.00 46.48 3.46
82 83 6.250951 GGTTCGACACTCTTACTTATCGAAAG 59.749 42.308 8.30 0.00 46.48 2.62
83 84 5.877031 TCGACACTCTTACTTATCGAAAGG 58.123 41.667 10.65 0.00 35.80 3.11
84 85 5.645067 TCGACACTCTTACTTATCGAAAGGA 59.355 40.000 10.65 1.49 35.80 3.36
85 86 5.738225 CGACACTCTTACTTATCGAAAGGAC 59.262 44.000 10.65 0.00 0.00 3.85
86 87 6.403418 CGACACTCTTACTTATCGAAAGGACT 60.403 42.308 10.65 0.00 0.00 3.85
87 88 7.201591 CGACACTCTTACTTATCGAAAGGACTA 60.202 40.741 10.65 0.00 0.00 2.59
88 89 7.760437 ACACTCTTACTTATCGAAAGGACTAC 58.240 38.462 10.65 0.00 0.00 2.73
89 90 6.906143 CACTCTTACTTATCGAAAGGACTACG 59.094 42.308 10.65 0.00 0.00 3.51
90 91 6.820656 ACTCTTACTTATCGAAAGGACTACGA 59.179 38.462 10.65 0.00 40.18 3.43
91 92 7.498570 ACTCTTACTTATCGAAAGGACTACGAT 59.501 37.037 14.84 14.84 46.07 3.73
92 93 8.893219 TCTTACTTATCGAAAGGACTACGATA 57.107 34.615 13.42 13.42 44.33 2.92
93 94 8.986847 TCTTACTTATCGAAAGGACTACGATAG 58.013 37.037 15.42 13.25 45.19 2.08
94 95 8.893219 TTACTTATCGAAAGGACTACGATAGA 57.107 34.615 15.42 9.84 45.19 1.98
95 96 7.982761 ACTTATCGAAAGGACTACGATAGAT 57.017 36.000 15.42 9.33 45.19 1.98
96 97 8.031848 ACTTATCGAAAGGACTACGATAGATC 57.968 38.462 15.42 0.00 45.19 2.75
97 98 5.883503 ATCGAAAGGACTACGATAGATCC 57.116 43.478 10.82 0.00 43.32 3.36
98 99 4.070716 TCGAAAGGACTACGATAGATCCC 58.929 47.826 0.00 0.00 41.38 3.85
99 100 3.190953 CGAAAGGACTACGATAGATCCCC 59.809 52.174 0.00 0.00 41.38 4.81
100 101 4.409187 GAAAGGACTACGATAGATCCCCT 58.591 47.826 0.00 0.00 41.38 4.79
101 102 5.568392 GAAAGGACTACGATAGATCCCCTA 58.432 45.833 0.00 0.00 41.38 3.53
102 103 4.573021 AGGACTACGATAGATCCCCTAC 57.427 50.000 0.00 0.00 41.38 3.18
103 104 3.915073 AGGACTACGATAGATCCCCTACA 59.085 47.826 0.00 0.00 41.38 2.74
104 105 4.009002 GGACTACGATAGATCCCCTACAC 58.991 52.174 0.00 0.00 41.38 2.90
105 106 4.263418 GGACTACGATAGATCCCCTACACT 60.263 50.000 0.00 0.00 41.38 3.55
106 107 5.315348 GACTACGATAGATCCCCTACACTT 58.685 45.833 0.00 0.00 41.38 3.16
107 108 5.315348 ACTACGATAGATCCCCTACACTTC 58.685 45.833 0.00 0.00 41.38 3.01
108 109 4.456662 ACGATAGATCCCCTACACTTCT 57.543 45.455 0.00 0.00 41.38 2.85
109 110 4.145807 ACGATAGATCCCCTACACTTCTG 58.854 47.826 0.00 0.00 41.38 3.02
110 111 3.508012 CGATAGATCCCCTACACTTCTGG 59.492 52.174 0.00 0.00 39.76 3.86
111 112 2.182516 AGATCCCCTACACTTCTGGG 57.817 55.000 0.00 0.00 40.59 4.45
112 113 1.366435 AGATCCCCTACACTTCTGGGT 59.634 52.381 0.00 0.00 39.31 4.51
113 114 1.763545 GATCCCCTACACTTCTGGGTC 59.236 57.143 0.00 0.00 39.31 4.46
114 115 0.490017 TCCCCTACACTTCTGGGTCA 59.510 55.000 0.00 0.00 39.31 4.02
115 116 1.080498 TCCCCTACACTTCTGGGTCAT 59.920 52.381 0.00 0.00 39.31 3.06
116 117 1.486726 CCCCTACACTTCTGGGTCATC 59.513 57.143 0.00 0.00 39.31 2.92
117 118 2.187958 CCCTACACTTCTGGGTCATCA 58.812 52.381 0.00 0.00 36.32 3.07
473 477 5.977489 TCTTCACGATTTCTAGAGTTCCA 57.023 39.130 0.00 0.00 0.00 3.53
776 780 4.464008 AGCACCATCTTCAAAACTTCTCA 58.536 39.130 0.00 0.00 0.00 3.27
779 783 4.823989 CACCATCTTCAAAACTTCTCAGGT 59.176 41.667 0.00 0.00 0.00 4.00
816 820 5.009010 CGATAAAAGGTCCCATCCTTCAATG 59.991 44.000 0.00 0.00 45.79 2.82
868 872 7.827236 TCATAAGTGAAATAGTTTGATCGGGTT 59.173 33.333 0.00 0.00 0.00 4.11
1003 1008 7.106239 AGTGCTAGCTGAACATAAAGTAATGT 58.894 34.615 17.23 0.00 41.87 2.71
1017 1022 5.493133 AAGTAATGTCTTTTGTGCAACGA 57.507 34.783 0.00 0.00 42.39 3.85
1030 1035 1.289800 GCAACGACGAAAGGGTCCTC 61.290 60.000 0.00 0.00 33.30 3.71
1044 1049 2.398588 GGTCCTCATGTAGTGGGATCA 58.601 52.381 0.00 0.00 31.97 2.92
1120 1126 7.048512 ACCTATTTCACCAAGTAGTGCTAATC 58.951 38.462 0.00 0.00 37.68 1.75
1180 1186 4.329545 GTCTGGTCGCTTGGGCCA 62.330 66.667 0.00 0.00 34.44 5.36
1225 1231 6.228616 TGGTATTGTCAGATCCGAACATAA 57.771 37.500 0.00 0.00 0.00 1.90
1361 1367 2.420687 GGTCAAAAATGGGTTTGTGCCA 60.421 45.455 0.00 0.00 39.16 4.92
1374 1380 0.322906 TGTGCCACAGGTGTTGAACA 60.323 50.000 0.00 0.00 0.00 3.18
1446 1452 4.656100 TCTTTCATTCATCAAGGGGTCA 57.344 40.909 0.00 0.00 0.00 4.02
1458 1464 1.518367 AGGGGTCAGTCACTTTTCCA 58.482 50.000 0.00 0.00 0.00 3.53
1461 1467 1.143073 GGGTCAGTCACTTTTCCAGGT 59.857 52.381 0.00 0.00 0.00 4.00
1469 1475 1.003118 CACTTTTCCAGGTCGGGATCA 59.997 52.381 0.00 0.00 36.67 2.92
1517 1523 4.183865 TGTTTCTCTTCGCACCTCATATG 58.816 43.478 0.00 0.00 0.00 1.78
1541 1547 3.904339 AGAGGAAAGGTAGCTTGTCAAGA 59.096 43.478 16.99 0.00 0.00 3.02
1775 1791 3.039011 AGCGAAGAGGCTTAGGGATAAA 58.961 45.455 0.00 0.00 41.39 1.40
1788 1804 2.904434 AGGGATAAAAGAGTGTCGGTGT 59.096 45.455 0.00 0.00 0.00 4.16
1835 1851 2.755650 ACACAAAGTCACTTAGCTCGG 58.244 47.619 0.00 0.00 0.00 4.63
1837 1853 1.070134 ACAAAGTCACTTAGCTCGGCA 59.930 47.619 0.00 0.00 0.00 5.69
1884 1900 7.365295 GGAATACCCTACATAGAAGAACCACAA 60.365 40.741 0.00 0.00 0.00 3.33
1888 1904 6.012858 ACCCTACATAGAAGAACCACAATTCA 60.013 38.462 0.00 0.00 0.00 2.57
2102 2121 3.571828 TGCATTTCATTCTTTCCGGAACA 59.428 39.130 18.64 3.21 0.00 3.18
2121 2140 7.388500 CCGGAACACAAAGAATTAAAGTACCTA 59.612 37.037 0.00 0.00 0.00 3.08
2162 2181 1.757118 TCTCCTTGTGATCGGGATGAC 59.243 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.070001 TCAGTAAGGTTTTATGCAAGCACT 58.930 37.500 0.00 0.00 0.00 4.40
1 2 5.371115 TCAGTAAGGTTTTATGCAAGCAC 57.629 39.130 0.00 0.00 0.00 4.40
2 3 6.398234 TTTCAGTAAGGTTTTATGCAAGCA 57.602 33.333 0.00 0.00 0.00 3.91
3 4 6.145534 GGTTTTCAGTAAGGTTTTATGCAAGC 59.854 38.462 0.00 0.00 0.00 4.01
4 5 6.362283 CGGTTTTCAGTAAGGTTTTATGCAAG 59.638 38.462 0.00 0.00 0.00 4.01
5 6 6.210078 CGGTTTTCAGTAAGGTTTTATGCAA 58.790 36.000 0.00 0.00 0.00 4.08
6 7 5.764131 CGGTTTTCAGTAAGGTTTTATGCA 58.236 37.500 0.00 0.00 0.00 3.96
7 8 4.619760 GCGGTTTTCAGTAAGGTTTTATGC 59.380 41.667 0.00 0.00 0.00 3.14
8 9 6.009115 AGCGGTTTTCAGTAAGGTTTTATG 57.991 37.500 0.00 0.00 0.00 1.90
9 10 6.644248 AAGCGGTTTTCAGTAAGGTTTTAT 57.356 33.333 0.00 0.00 0.00 1.40
10 11 7.444792 TGATAAGCGGTTTTCAGTAAGGTTTTA 59.555 33.333 15.10 0.00 0.00 1.52
11 12 4.994907 AAGCGGTTTTCAGTAAGGTTTT 57.005 36.364 0.00 0.00 0.00 2.43
12 13 5.766174 TGATAAGCGGTTTTCAGTAAGGTTT 59.234 36.000 15.10 0.00 0.00 3.27
13 14 5.310451 TGATAAGCGGTTTTCAGTAAGGTT 58.690 37.500 15.10 0.00 0.00 3.50
14 15 4.901868 TGATAAGCGGTTTTCAGTAAGGT 58.098 39.130 15.10 0.00 0.00 3.50
15 16 6.436843 AATGATAAGCGGTTTTCAGTAAGG 57.563 37.500 21.70 0.00 0.00 2.69
16 17 6.967199 GGAAATGATAAGCGGTTTTCAGTAAG 59.033 38.462 21.70 0.00 0.00 2.34
17 18 6.657541 AGGAAATGATAAGCGGTTTTCAGTAA 59.342 34.615 21.70 3.01 0.00 2.24
18 19 6.177610 AGGAAATGATAAGCGGTTTTCAGTA 58.822 36.000 21.70 3.33 0.00 2.74
19 20 5.010282 AGGAAATGATAAGCGGTTTTCAGT 58.990 37.500 21.70 17.84 0.00 3.41
20 21 5.567138 AGGAAATGATAAGCGGTTTTCAG 57.433 39.130 21.70 0.00 0.00 3.02
21 22 5.710099 AGAAGGAAATGATAAGCGGTTTTCA 59.290 36.000 20.04 20.04 0.00 2.69
22 23 6.030228 CAGAAGGAAATGATAAGCGGTTTTC 58.970 40.000 4.64 8.11 0.00 2.29
23 24 5.622233 GCAGAAGGAAATGATAAGCGGTTTT 60.622 40.000 4.64 0.00 0.00 2.43
24 25 4.142381 GCAGAAGGAAATGATAAGCGGTTT 60.142 41.667 4.64 0.00 0.00 3.27
25 26 3.378427 GCAGAAGGAAATGATAAGCGGTT 59.622 43.478 4.76 4.76 0.00 4.44
26 27 2.945668 GCAGAAGGAAATGATAAGCGGT 59.054 45.455 0.00 0.00 0.00 5.68
27 28 3.209410 AGCAGAAGGAAATGATAAGCGG 58.791 45.455 0.00 0.00 0.00 5.52
28 29 3.249559 GGAGCAGAAGGAAATGATAAGCG 59.750 47.826 0.00 0.00 0.00 4.68
29 30 4.459330 AGGAGCAGAAGGAAATGATAAGC 58.541 43.478 0.00 0.00 0.00 3.09
30 31 4.749099 CGAGGAGCAGAAGGAAATGATAAG 59.251 45.833 0.00 0.00 0.00 1.73
31 32 4.162320 ACGAGGAGCAGAAGGAAATGATAA 59.838 41.667 0.00 0.00 0.00 1.75
32 33 3.706594 ACGAGGAGCAGAAGGAAATGATA 59.293 43.478 0.00 0.00 0.00 2.15
33 34 2.503356 ACGAGGAGCAGAAGGAAATGAT 59.497 45.455 0.00 0.00 0.00 2.45
34 35 1.902508 ACGAGGAGCAGAAGGAAATGA 59.097 47.619 0.00 0.00 0.00 2.57
35 36 2.393271 ACGAGGAGCAGAAGGAAATG 57.607 50.000 0.00 0.00 0.00 2.32
36 37 2.616510 CCAACGAGGAGCAGAAGGAAAT 60.617 50.000 0.00 0.00 41.22 2.17
37 38 1.270839 CCAACGAGGAGCAGAAGGAAA 60.271 52.381 0.00 0.00 41.22 3.13
38 39 0.321671 CCAACGAGGAGCAGAAGGAA 59.678 55.000 0.00 0.00 41.22 3.36
39 40 1.544825 CCCAACGAGGAGCAGAAGGA 61.545 60.000 0.00 0.00 41.22 3.36
40 41 1.078848 CCCAACGAGGAGCAGAAGG 60.079 63.158 0.00 0.00 41.22 3.46
41 42 0.035458 AACCCAACGAGGAGCAGAAG 59.965 55.000 0.00 0.00 41.22 2.85
42 43 0.034896 GAACCCAACGAGGAGCAGAA 59.965 55.000 0.00 0.00 41.22 3.02
43 44 1.671742 GAACCCAACGAGGAGCAGA 59.328 57.895 0.00 0.00 41.22 4.26
44 45 1.738099 CGAACCCAACGAGGAGCAG 60.738 63.158 0.00 0.00 41.22 4.24
45 46 2.204461 TCGAACCCAACGAGGAGCA 61.204 57.895 0.00 0.00 41.22 4.26
46 47 1.737008 GTCGAACCCAACGAGGAGC 60.737 63.158 0.00 0.00 41.22 4.70
47 48 0.666577 GTGTCGAACCCAACGAGGAG 60.667 60.000 0.00 0.00 41.22 3.69
48 49 1.111116 AGTGTCGAACCCAACGAGGA 61.111 55.000 0.00 0.00 41.22 3.71
49 50 0.666577 GAGTGTCGAACCCAACGAGG 60.667 60.000 0.00 0.00 40.37 4.63
50 51 0.314302 AGAGTGTCGAACCCAACGAG 59.686 55.000 0.00 0.00 40.37 4.18
51 52 0.748450 AAGAGTGTCGAACCCAACGA 59.252 50.000 0.00 0.00 37.43 3.85
52 53 2.056577 GTAAGAGTGTCGAACCCAACG 58.943 52.381 0.00 0.00 0.00 4.10
53 54 3.382048 AGTAAGAGTGTCGAACCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
54 55 5.620654 CGATAAGTAAGAGTGTCGAACCCAA 60.621 44.000 0.00 0.00 0.00 4.12
55 56 4.142534 CGATAAGTAAGAGTGTCGAACCCA 60.143 45.833 0.00 0.00 0.00 4.51
56 57 4.095483 TCGATAAGTAAGAGTGTCGAACCC 59.905 45.833 0.00 0.00 35.48 4.11
57 58 5.227238 TCGATAAGTAAGAGTGTCGAACC 57.773 43.478 0.00 0.00 35.48 3.62
58 59 6.250951 CCTTTCGATAAGTAAGAGTGTCGAAC 59.749 42.308 7.42 0.00 44.53 3.95
59 60 6.149973 TCCTTTCGATAAGTAAGAGTGTCGAA 59.850 38.462 4.17 4.17 43.60 3.71
60 61 5.645067 TCCTTTCGATAAGTAAGAGTGTCGA 59.355 40.000 0.00 0.00 36.46 4.20
61 62 5.738225 GTCCTTTCGATAAGTAAGAGTGTCG 59.262 44.000 0.00 0.00 29.89 4.35
62 63 6.854778 AGTCCTTTCGATAAGTAAGAGTGTC 58.145 40.000 0.00 0.00 29.89 3.67
63 64 6.837471 AGTCCTTTCGATAAGTAAGAGTGT 57.163 37.500 0.00 0.00 29.89 3.55
64 65 6.906143 CGTAGTCCTTTCGATAAGTAAGAGTG 59.094 42.308 0.00 0.00 29.89 3.51
65 66 6.820656 TCGTAGTCCTTTCGATAAGTAAGAGT 59.179 38.462 0.00 0.00 29.89 3.24
66 67 7.244166 TCGTAGTCCTTTCGATAAGTAAGAG 57.756 40.000 0.00 0.00 29.89 2.85
67 68 7.798596 ATCGTAGTCCTTTCGATAAGTAAGA 57.201 36.000 0.00 0.00 41.46 2.10
68 69 8.986847 TCTATCGTAGTCCTTTCGATAAGTAAG 58.013 37.037 7.65 0.00 42.90 2.34
69 70 8.893219 TCTATCGTAGTCCTTTCGATAAGTAA 57.107 34.615 7.65 0.00 42.90 2.24
70 71 9.149225 GATCTATCGTAGTCCTTTCGATAAGTA 57.851 37.037 7.65 0.00 42.90 2.24
71 72 7.119553 GGATCTATCGTAGTCCTTTCGATAAGT 59.880 40.741 7.65 1.07 42.90 2.24
72 73 7.414319 GGGATCTATCGTAGTCCTTTCGATAAG 60.414 44.444 7.65 0.00 42.90 1.73
73 74 6.373774 GGGATCTATCGTAGTCCTTTCGATAA 59.626 42.308 7.65 1.63 42.90 1.75
74 75 5.879223 GGGATCTATCGTAGTCCTTTCGATA 59.121 44.000 0.00 0.00 42.78 2.92
75 76 4.701171 GGGATCTATCGTAGTCCTTTCGAT 59.299 45.833 0.00 0.00 44.53 3.59
76 77 4.070716 GGGATCTATCGTAGTCCTTTCGA 58.929 47.826 0.00 0.00 37.96 3.71
77 78 3.190953 GGGGATCTATCGTAGTCCTTTCG 59.809 52.174 0.00 0.00 0.00 3.46
78 79 4.409187 AGGGGATCTATCGTAGTCCTTTC 58.591 47.826 0.00 0.00 0.00 2.62
79 80 4.472690 AGGGGATCTATCGTAGTCCTTT 57.527 45.455 0.00 0.00 0.00 3.11
80 81 4.353191 TGTAGGGGATCTATCGTAGTCCTT 59.647 45.833 0.00 0.00 0.00 3.36
81 82 3.915073 TGTAGGGGATCTATCGTAGTCCT 59.085 47.826 0.00 0.00 0.00 3.85
82 83 4.009002 GTGTAGGGGATCTATCGTAGTCC 58.991 52.174 0.00 0.00 0.00 3.85
83 84 4.909001 AGTGTAGGGGATCTATCGTAGTC 58.091 47.826 0.00 0.00 0.00 2.59
84 85 4.997545 AGTGTAGGGGATCTATCGTAGT 57.002 45.455 0.00 0.00 0.00 2.73
85 86 5.413213 CAGAAGTGTAGGGGATCTATCGTAG 59.587 48.000 0.00 0.00 0.00 3.51
86 87 5.314529 CAGAAGTGTAGGGGATCTATCGTA 58.685 45.833 0.00 0.00 0.00 3.43
87 88 4.145807 CAGAAGTGTAGGGGATCTATCGT 58.854 47.826 0.00 0.00 0.00 3.73
88 89 3.508012 CCAGAAGTGTAGGGGATCTATCG 59.492 52.174 0.00 0.00 0.00 2.92
89 90 3.835395 CCCAGAAGTGTAGGGGATCTATC 59.165 52.174 0.00 0.00 43.57 2.08
90 91 3.863086 CCCAGAAGTGTAGGGGATCTAT 58.137 50.000 0.00 0.00 43.57 1.98
91 92 3.330126 CCCAGAAGTGTAGGGGATCTA 57.670 52.381 0.00 0.00 43.57 1.98
92 93 2.182516 CCCAGAAGTGTAGGGGATCT 57.817 55.000 0.00 0.00 43.57 2.75
98 99 2.419297 GCTGATGACCCAGAAGTGTAGG 60.419 54.545 0.00 0.00 36.29 3.18
99 100 2.499289 AGCTGATGACCCAGAAGTGTAG 59.501 50.000 0.00 0.00 36.29 2.74
100 101 2.234661 CAGCTGATGACCCAGAAGTGTA 59.765 50.000 8.42 0.00 36.29 2.90
101 102 1.002888 CAGCTGATGACCCAGAAGTGT 59.997 52.381 8.42 0.00 36.29 3.55
102 103 1.735386 CAGCTGATGACCCAGAAGTG 58.265 55.000 8.42 0.00 36.29 3.16
103 104 0.035630 GCAGCTGATGACCCAGAAGT 60.036 55.000 20.43 0.00 36.29 3.01
104 105 0.747283 GGCAGCTGATGACCCAGAAG 60.747 60.000 20.43 0.00 36.29 2.85
105 106 1.300963 GGCAGCTGATGACCCAGAA 59.699 57.895 20.43 0.00 36.29 3.02
106 107 2.993008 GGCAGCTGATGACCCAGA 59.007 61.111 20.43 0.00 36.29 3.86
111 112 2.191641 GAGGGGGCAGCTGATGAC 59.808 66.667 20.43 4.22 35.46 3.06
112 113 1.924939 TTGAGGGGGCAGCTGATGA 60.925 57.895 20.43 0.00 0.00 2.92
113 114 1.751927 GTTGAGGGGGCAGCTGATG 60.752 63.158 20.43 0.00 0.00 3.07
114 115 1.919600 GAGTTGAGGGGGCAGCTGAT 61.920 60.000 20.43 0.00 29.01 2.90
115 116 2.530151 AGTTGAGGGGGCAGCTGA 60.530 61.111 20.43 0.00 0.00 4.26
116 117 2.045536 GAGTTGAGGGGGCAGCTG 60.046 66.667 10.11 10.11 29.01 4.24
117 118 2.156098 TTGAGTTGAGGGGGCAGCT 61.156 57.895 0.00 0.00 31.69 4.24
473 477 9.482627 GAAAATCGATATCAGTGAAGTAATCCT 57.517 33.333 0.00 0.00 0.00 3.24
616 620 6.037786 AGAAAGTGAAATGTCCTATCGTCA 57.962 37.500 0.00 0.00 0.00 4.35
776 780 2.853235 ATCGAAAAACTCCGGAACCT 57.147 45.000 5.23 0.00 0.00 3.50
779 783 5.065235 ACCTTTTATCGAAAAACTCCGGAA 58.935 37.500 5.23 0.00 34.16 4.30
816 820 2.094675 CCTGGTTGACCCAATCATGAC 58.905 52.381 0.00 0.00 44.65 3.06
868 872 3.924013 ATCGGGCCTGACCTGGTCA 62.924 63.158 26.79 26.79 46.01 4.02
1003 1008 2.223157 CCTTTCGTCGTTGCACAAAAGA 60.223 45.455 0.00 0.00 0.00 2.52
1017 1022 2.233922 CACTACATGAGGACCCTTTCGT 59.766 50.000 0.00 0.00 0.00 3.85
1030 1035 3.751479 TCCGAATGATCCCACTACATG 57.249 47.619 0.00 0.00 0.00 3.21
1044 1049 5.116882 GCTAGAGGTTGTAACAATCCGAAT 58.883 41.667 0.00 0.00 0.00 3.34
1120 1126 4.203226 GGAGCCATTCTAAAAAGGGAGAG 58.797 47.826 0.00 0.00 0.00 3.20
1225 1231 7.561356 AGATATGGCAAACAAATAAAGTAGCCT 59.439 33.333 0.00 0.00 39.58 4.58
1361 1367 5.552870 AGAGTAGATTGTTCAACACCTGT 57.447 39.130 0.00 0.00 0.00 4.00
1374 1380 3.769844 CCCACACCTGTGTAGAGTAGATT 59.230 47.826 2.05 0.00 42.83 2.40
1401 1407 2.335933 GGTTTATGAGCCCTAGCCCTA 58.664 52.381 0.00 0.00 41.25 3.53
1446 1452 0.396811 CCCGACCTGGAAAAGTGACT 59.603 55.000 0.00 0.00 42.00 3.41
1458 1464 0.905357 CCACTTCTTGATCCCGACCT 59.095 55.000 0.00 0.00 0.00 3.85
1461 1467 2.233922 GACTTCCACTTCTTGATCCCGA 59.766 50.000 0.00 0.00 0.00 5.14
1517 1523 4.273148 TGACAAGCTACCTTTCCTCTTC 57.727 45.455 0.00 0.00 0.00 2.87
1541 1547 6.995091 GCTAGAATTTCCAATAGTGAGACCAT 59.005 38.462 0.00 0.00 0.00 3.55
1775 1791 1.027357 ACGTACACACCGACACTCTT 58.973 50.000 0.00 0.00 0.00 2.85
1788 1804 5.007039 CGTAGTAGAATGAAGGCTACGTACA 59.993 44.000 12.44 0.00 45.43 2.90
1835 1851 9.614792 TTCCTCCTTTACTCTCTTAATTAATGC 57.385 33.333 0.00 0.00 0.00 3.56
1915 1931 1.325476 GCAAAGCAGCTTAGCCCCAT 61.325 55.000 8.45 0.00 34.23 4.00
1916 1932 1.978617 GCAAAGCAGCTTAGCCCCA 60.979 57.895 8.45 0.00 34.23 4.96
1970 1986 1.001815 GGCTTGCGAAACAAAGTAGCA 60.002 47.619 0.00 0.00 37.96 3.49
2102 2121 6.950041 GGGGGTTAGGTACTTTAATTCTTTGT 59.050 38.462 0.00 0.00 41.75 2.83
2398 2417 2.216898 GCAGAGAACAAGACAGCAAGT 58.783 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.