Multiple sequence alignment - TraesCS5D01G270000

Loading Multiple Alignment...

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 TraesCS5D01G270000 chr5D 100.000 2414 0 0 1 2414 373773151 373775564 0.000000e+00 4458.0
1 TraesCS5D01G270000 chr5A 93.032 2253 115 12 176 2411 475632041 475634268 0.000000e+00 3253.0
2 TraesCS5D01G270000 chr5A 91.525 118 8 2 63 179 475619373 475619489 6.910000e-36 161.0
3 TraesCS5D01G270000 chr5B 92.500 1920 95 15 514 2414 445193509 445195398 0.000000e+00 2702.0
4 TraesCS5D01G270000 chr5B 78.144 334 51 11 176 497 445191404 445191727 2.450000e-45 193.0
5 TraesCS5D01G270000 chr2D 89.136 359 36 2 1799 2154 626672600 626672958 6.120000e-121 444.0
6 TraesCS5D01G270000 chr7D 98.387 62 1 0 5 66 485321739 485321800 2.540000e-20 110.0
7 TraesCS5D01G270000 chr7D 94.030 67 4 0 1 67 621738300 621738234 4.250000e-18 102.0
8 TraesCS5D01G270000 chr1A 94.203 69 3 1 5 73 148610383 148610450 1.180000e-18 104.0
9 TraesCS5D01G270000 chr1A 94.030 67 4 0 1 67 384334508 384334442 4.250000e-18 102.0
10 TraesCS5D01G270000 chr4B 94.030 67 4 0 5 71 89839923 89839989 4.250000e-18 102.0
11 TraesCS5D01G270000 chr2B 95.312 64 3 0 1 64 76928480 76928417 4.250000e-18 102.0
12 TraesCS5D01G270000 chr1B 92.958 71 3 2 5 73 224373827 224373897 4.250000e-18 102.0
13 TraesCS5D01G270000 chr3A 92.754 69 5 0 1 69 614468472 614468540 1.530000e-17 100.0
14 TraesCS5D01G270000 chr6A 89.333 75 8 0 6 80 479885304 479885230 7.100000e-16 95.3


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 TraesCS5D01G270000 chr5D 373773151 373775564 2413 False 4458.0 4458 100.000 1 2414 1 chr5D.!!$F1 2413
1 TraesCS5D01G270000 chr5A 475632041 475634268 2227 False 3253.0 3253 93.032 176 2411 1 chr5A.!!$F2 2235
2 TraesCS5D01G270000 chr5B 445191404 445195398 3994 False 1447.5 2702 85.322 176 2414 2 chr5B.!!$F1 2238

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
154 155 0.040058 AATTCCAGTGGGCATGCTCA 59.960 50.0 18.52 18.52 0.00 4.26 F
845 2625 0.108615 CCACAGGCTACTTCTGACCG 60.109 60.0 0.00 0.00 36.22 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 2944 0.384725 CAACGCCAAAGTGCTTCTCG 60.385 55.000 0.00 0.0 0.0 4.04 R
2315 4112 1.469308 GAGCTCGAGGAGAAGAACGAA 59.531 52.381 15.58 0.0 34.5 3.85 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
25 26 5.969741 CAGTTTTGCACATTGTCTGAAATG 58.030 37.500 0.00 9.50 42.21 2.32
27 28 5.750067 AGTTTTGCACATTGTCTGAAATGTC 59.250 36.000 12.25 9.51 45.47 3.06
28 29 5.518848 TTTGCACATTGTCTGAAATGTCT 57.481 34.783 12.25 0.00 45.47 3.41
29 30 5.518848 TTGCACATTGTCTGAAATGTCTT 57.481 34.783 12.25 0.00 45.47 3.01
30 31 5.112220 TGCACATTGTCTGAAATGTCTTC 57.888 39.130 12.25 7.82 45.47 2.87
31 32 4.579753 TGCACATTGTCTGAAATGTCTTCA 59.420 37.500 12.25 9.40 45.47 3.02
32 33 5.067544 TGCACATTGTCTGAAATGTCTTCAA 59.932 36.000 12.25 0.00 45.47 2.69
33 34 5.628193 GCACATTGTCTGAAATGTCTTCAAG 59.372 40.000 12.25 5.42 45.47 3.02
34 35 6.147581 CACATTGTCTGAAATGTCTTCAAGG 58.852 40.000 12.25 0.00 45.47 3.61
35 36 4.836125 TTGTCTGAAATGTCTTCAAGGC 57.164 40.909 0.00 0.00 0.00 4.35
36 37 3.149196 TGTCTGAAATGTCTTCAAGGCC 58.851 45.455 0.00 0.00 0.00 5.19
37 38 3.181440 TGTCTGAAATGTCTTCAAGGCCT 60.181 43.478 0.00 0.00 0.00 5.19
38 39 3.823304 GTCTGAAATGTCTTCAAGGCCTT 59.177 43.478 13.78 13.78 0.00 4.35
39 40 5.003804 GTCTGAAATGTCTTCAAGGCCTTA 58.996 41.667 20.00 2.00 0.00 2.69
40 41 5.649831 GTCTGAAATGTCTTCAAGGCCTTAT 59.350 40.000 20.00 3.68 0.00 1.73
41 42 6.823689 GTCTGAAATGTCTTCAAGGCCTTATA 59.176 38.462 20.00 6.65 0.00 0.98
42 43 7.336931 GTCTGAAATGTCTTCAAGGCCTTATAA 59.663 37.037 20.00 14.54 0.00 0.98
43 44 7.888021 TCTGAAATGTCTTCAAGGCCTTATAAA 59.112 33.333 20.00 11.96 0.00 1.40
44 45 8.415950 TGAAATGTCTTCAAGGCCTTATAAAA 57.584 30.769 20.00 9.43 0.00 1.52
45 46 8.522830 TGAAATGTCTTCAAGGCCTTATAAAAG 58.477 33.333 20.00 18.05 0.00 2.27
46 47 8.422577 AAATGTCTTCAAGGCCTTATAAAAGT 57.577 30.769 20.00 0.00 0.00 2.66
47 48 6.817765 TGTCTTCAAGGCCTTATAAAAGTG 57.182 37.500 20.00 3.72 0.00 3.16
48 49 6.539173 TGTCTTCAAGGCCTTATAAAAGTGA 58.461 36.000 20.00 6.54 0.00 3.41
49 50 7.001674 TGTCTTCAAGGCCTTATAAAAGTGAA 58.998 34.615 20.00 14.48 0.00 3.18
50 51 7.040686 TGTCTTCAAGGCCTTATAAAAGTGAAC 60.041 37.037 20.00 13.04 0.00 3.18
51 52 7.001674 TCTTCAAGGCCTTATAAAAGTGAACA 58.998 34.615 20.00 0.21 0.00 3.18
52 53 6.817765 TCAAGGCCTTATAAAAGTGAACAG 57.182 37.500 20.00 0.00 0.00 3.16
53 54 6.539173 TCAAGGCCTTATAAAAGTGAACAGA 58.461 36.000 20.00 2.74 0.00 3.41
54 55 6.655003 TCAAGGCCTTATAAAAGTGAACAGAG 59.345 38.462 20.00 0.00 0.00 3.35
55 56 5.501156 AGGCCTTATAAAAGTGAACAGAGG 58.499 41.667 0.00 0.00 0.00 3.69
56 57 5.250774 AGGCCTTATAAAAGTGAACAGAGGA 59.749 40.000 0.00 0.00 0.00 3.71
57 58 5.944007 GGCCTTATAAAAGTGAACAGAGGAA 59.056 40.000 0.00 0.00 0.00 3.36
58 59 6.094186 GGCCTTATAAAAGTGAACAGAGGAAG 59.906 42.308 0.00 0.00 0.00 3.46
59 60 6.655425 GCCTTATAAAAGTGAACAGAGGAAGT 59.345 38.462 0.00 0.00 0.00 3.01
60 61 7.822822 GCCTTATAAAAGTGAACAGAGGAAGTA 59.177 37.037 0.00 0.00 0.00 2.24
61 62 9.892130 CCTTATAAAAGTGAACAGAGGAAGTAT 57.108 33.333 0.00 0.00 0.00 2.12
89 90 9.322773 ACATATAACTTCACTCAACTGATCATG 57.677 33.333 0.00 0.00 0.00 3.07
90 91 9.322773 CATATAACTTCACTCAACTGATCATGT 57.677 33.333 0.00 0.00 0.00 3.21
93 94 7.664082 AACTTCACTCAACTGATCATGTAAG 57.336 36.000 0.00 1.79 0.00 2.34
94 95 6.997655 ACTTCACTCAACTGATCATGTAAGA 58.002 36.000 0.00 0.00 0.00 2.10
95 96 7.445121 ACTTCACTCAACTGATCATGTAAGAA 58.555 34.615 0.00 0.00 0.00 2.52
96 97 8.099537 ACTTCACTCAACTGATCATGTAAGAAT 58.900 33.333 0.00 0.00 0.00 2.40
97 98 8.484641 TTCACTCAACTGATCATGTAAGAATC 57.515 34.615 0.00 0.00 0.00 2.52
98 99 6.753744 TCACTCAACTGATCATGTAAGAATCG 59.246 38.462 0.00 0.00 0.00 3.34
99 100 6.753744 CACTCAACTGATCATGTAAGAATCGA 59.246 38.462 0.00 0.00 0.00 3.59
100 101 7.437565 CACTCAACTGATCATGTAAGAATCGAT 59.562 37.037 0.00 0.00 0.00 3.59
101 102 7.984050 ACTCAACTGATCATGTAAGAATCGATT 59.016 33.333 11.20 11.20 0.00 3.34
102 103 8.722480 TCAACTGATCATGTAAGAATCGATTT 57.278 30.769 12.81 0.00 0.00 2.17
103 104 9.166173 TCAACTGATCATGTAAGAATCGATTTT 57.834 29.630 12.81 3.29 0.00 1.82
110 111 9.669353 ATCATGTAAGAATCGATTTTAATGTGC 57.331 29.630 12.81 0.00 0.00 4.57
111 112 8.892723 TCATGTAAGAATCGATTTTAATGTGCT 58.107 29.630 12.81 0.00 0.00 4.40
112 113 8.950961 CATGTAAGAATCGATTTTAATGTGCTG 58.049 33.333 12.81 0.00 0.00 4.41
113 114 7.471721 TGTAAGAATCGATTTTAATGTGCTGG 58.528 34.615 12.81 0.00 0.00 4.85
114 115 6.515272 AAGAATCGATTTTAATGTGCTGGT 57.485 33.333 12.81 0.00 0.00 4.00
115 116 6.515272 AGAATCGATTTTAATGTGCTGGTT 57.485 33.333 12.81 0.00 0.00 3.67
116 117 6.324819 AGAATCGATTTTAATGTGCTGGTTG 58.675 36.000 12.81 0.00 0.00 3.77
117 118 3.832276 TCGATTTTAATGTGCTGGTTGC 58.168 40.909 0.00 0.00 43.25 4.17
129 130 3.155093 GCTGGTTGCAATGGTATCTTG 57.845 47.619 0.59 0.00 42.31 3.02
130 131 2.754552 GCTGGTTGCAATGGTATCTTGA 59.245 45.455 0.59 0.00 42.31 3.02
131 132 3.193267 GCTGGTTGCAATGGTATCTTGAA 59.807 43.478 0.59 0.00 42.31 2.69
132 133 4.142093 GCTGGTTGCAATGGTATCTTGAAT 60.142 41.667 0.59 0.00 42.31 2.57
133 134 5.625197 GCTGGTTGCAATGGTATCTTGAATT 60.625 40.000 0.59 0.00 42.31 2.17
134 135 6.357579 TGGTTGCAATGGTATCTTGAATTT 57.642 33.333 0.59 0.00 0.00 1.82
135 136 7.473735 TGGTTGCAATGGTATCTTGAATTTA 57.526 32.000 0.59 0.00 0.00 1.40
136 137 7.901029 TGGTTGCAATGGTATCTTGAATTTAA 58.099 30.769 0.59 0.00 0.00 1.52
137 138 8.538701 TGGTTGCAATGGTATCTTGAATTTAAT 58.461 29.630 0.59 0.00 0.00 1.40
138 139 9.382275 GGTTGCAATGGTATCTTGAATTTAATT 57.618 29.630 0.59 0.00 0.00 1.40
140 141 9.598517 TTGCAATGGTATCTTGAATTTAATTCC 57.401 29.630 14.22 0.00 38.50 3.01
141 142 8.756927 TGCAATGGTATCTTGAATTTAATTCCA 58.243 29.630 14.22 5.09 38.50 3.53
142 143 9.252962 GCAATGGTATCTTGAATTTAATTCCAG 57.747 33.333 14.22 12.63 38.50 3.86
145 146 8.292444 TGGTATCTTGAATTTAATTCCAGTGG 57.708 34.615 14.22 1.40 38.50 4.00
146 147 7.341769 TGGTATCTTGAATTTAATTCCAGTGGG 59.658 37.037 9.92 0.00 38.50 4.61
147 148 5.659440 TCTTGAATTTAATTCCAGTGGGC 57.341 39.130 9.92 0.00 38.50 5.36
148 149 5.083122 TCTTGAATTTAATTCCAGTGGGCA 58.917 37.500 9.92 0.00 38.50 5.36
149 150 5.721000 TCTTGAATTTAATTCCAGTGGGCAT 59.279 36.000 9.92 0.00 38.50 4.40
150 151 5.341872 TGAATTTAATTCCAGTGGGCATG 57.658 39.130 9.92 0.00 38.50 4.06
151 152 3.825143 ATTTAATTCCAGTGGGCATGC 57.175 42.857 9.90 9.90 0.00 4.06
152 153 2.530460 TTAATTCCAGTGGGCATGCT 57.470 45.000 18.92 0.00 0.00 3.79
153 154 2.057137 TAATTCCAGTGGGCATGCTC 57.943 50.000 18.92 15.59 0.00 4.26
154 155 0.040058 AATTCCAGTGGGCATGCTCA 59.960 50.000 18.52 18.52 0.00 4.26
155 156 0.395311 ATTCCAGTGGGCATGCTCAG 60.395 55.000 23.56 10.54 0.00 3.35
156 157 3.138798 CCAGTGGGCATGCTCAGC 61.139 66.667 23.56 15.95 0.00 4.26
157 158 2.045242 CAGTGGGCATGCTCAGCT 60.045 61.111 23.56 18.04 0.00 4.24
158 159 1.222661 CAGTGGGCATGCTCAGCTA 59.777 57.895 23.56 0.00 0.00 3.32
159 160 0.814410 CAGTGGGCATGCTCAGCTAG 60.814 60.000 23.56 7.32 0.00 3.42
160 161 1.525535 GTGGGCATGCTCAGCTAGG 60.526 63.158 23.56 0.00 0.00 3.02
161 162 1.997311 TGGGCATGCTCAGCTAGGT 60.997 57.895 18.52 0.00 0.00 3.08
162 163 1.525535 GGGCATGCTCAGCTAGGTG 60.526 63.158 18.92 15.93 0.00 4.00
163 164 2.185494 GGCATGCTCAGCTAGGTGC 61.185 63.158 18.92 7.18 43.29 5.01
183 184 1.071385 CTATGCCTAGGTCCTTGCCTG 59.929 57.143 11.31 0.00 39.60 4.85
184 185 2.124529 GCCTAGGTCCTTGCCTGC 60.125 66.667 11.31 0.00 39.60 4.85
188 189 0.835941 CTAGGTCCTTGCCTGCATCT 59.164 55.000 0.00 0.00 39.60 2.90
202 203 4.337555 GCCTGCATCTGTGAATCTAACAAT 59.662 41.667 0.00 0.00 0.00 2.71
223 224 7.182060 ACAATATATTCTTGGAACCAACAGGT 58.818 34.615 1.83 0.00 37.19 4.00
254 256 9.020813 CAGATCAATGTTATTGAATTCAAGCAG 57.979 33.333 24.17 12.58 39.47 4.24
269 271 9.274065 GAATTCAAGCAGGTAAATTAAACTACG 57.726 33.333 0.00 0.00 0.00 3.51
272 274 6.091713 TCAAGCAGGTAAATTAAACTACGCTC 59.908 38.462 0.00 0.00 0.00 5.03
357 359 6.966021 TGTGTTACTATGCTTTGAAAACTCC 58.034 36.000 0.00 0.00 0.00 3.85
371 373 5.130350 TGAAAACTCCCTCAAACCTAAGTG 58.870 41.667 0.00 0.00 0.00 3.16
378 380 2.224450 CCTCAAACCTAAGTGGACCGTT 60.224 50.000 0.00 0.00 39.71 4.44
383 385 4.420522 AACCTAAGTGGACCGTTTGTTA 57.579 40.909 0.00 0.00 39.71 2.41
469 475 7.174253 CGGGGCAAGCTATGAATTTTAAGTATA 59.826 37.037 0.00 0.00 0.00 1.47
498 508 6.353323 TCCATAACGATTTAGCAAGATTCCA 58.647 36.000 0.00 0.00 0.00 3.53
519 2294 0.538057 AACATGCACCACCAGGACAG 60.538 55.000 0.00 0.00 38.69 3.51
551 2326 1.400494 GGGTGCATTTTCGTATTCGCT 59.600 47.619 0.00 0.00 36.96 4.93
607 2383 6.524101 TTGGGATAAAATAAGTTGCTCCAC 57.476 37.500 0.00 0.00 0.00 4.02
617 2393 2.202395 TTGCTCCACTGCCAAAGCC 61.202 57.895 0.00 0.00 38.69 4.35
623 2399 3.884774 ACTGCCAAAGCCGGGTGA 61.885 61.111 7.07 0.00 38.69 4.02
628 2404 2.561037 CCAAAGCCGGGTGAACCAC 61.561 63.158 7.07 0.00 40.22 4.16
633 2409 3.148084 CCGGGTGAACCACAGACT 58.852 61.111 1.16 0.00 40.22 3.24
634 2410 1.450211 CCGGGTGAACCACAGACTT 59.550 57.895 1.16 0.00 40.22 3.01
635 2411 0.179029 CCGGGTGAACCACAGACTTT 60.179 55.000 1.16 0.00 40.22 2.66
636 2412 1.675552 CGGGTGAACCACAGACTTTT 58.324 50.000 1.16 0.00 40.22 2.27
637 2413 2.021457 CGGGTGAACCACAGACTTTTT 58.979 47.619 1.16 0.00 40.22 1.94
661 2440 4.685169 TTCTCAGATTTCGCAAATGACC 57.315 40.909 0.00 0.00 0.00 4.02
680 2459 6.761731 TGACCGCTTGAAACAAATTAAATG 57.238 33.333 0.00 0.00 0.00 2.32
735 2515 4.389374 GCCCATAGCATACAACATACTGT 58.611 43.478 0.00 0.00 42.97 3.55
736 2516 5.547465 GCCCATAGCATACAACATACTGTA 58.453 41.667 0.00 0.00 42.97 2.74
737 2517 5.408604 GCCCATAGCATACAACATACTGTAC 59.591 44.000 0.00 0.00 42.97 2.90
738 2518 6.741521 GCCCATAGCATACAACATACTGTACT 60.742 42.308 0.00 0.00 42.97 2.73
779 2559 3.093814 TCACCACCGAAGCTAGTGATAA 58.906 45.455 11.85 0.00 36.01 1.75
845 2625 0.108615 CCACAGGCTACTTCTGACCG 60.109 60.000 0.00 0.00 36.22 4.79
848 2628 1.078710 AGGCTACTTCTGACCGGGT 59.921 57.895 6.32 0.00 0.00 5.28
1065 2845 2.125106 GACGAAGGCGCCTTCCAT 60.125 61.111 46.84 38.98 47.00 3.41
1164 2944 1.138661 CTCATGAGCCTCAGGGTTCTC 59.861 57.143 10.38 0.00 42.35 2.87
1368 3148 2.584391 GGTGGTCGAGGAAGGCAGT 61.584 63.158 0.00 0.00 0.00 4.40
1414 3194 0.598419 GCTGGCCAAAGCAACTTGAC 60.598 55.000 7.01 0.00 43.01 3.18
1559 3339 2.498167 ACAGAAGCCACAACATCAGTC 58.502 47.619 0.00 0.00 0.00 3.51
1641 3421 6.233434 TGGATGCCTACATGAGAAATATCAC 58.767 40.000 0.00 0.00 36.35 3.06
1679 3459 6.371271 AGAATTTGGGTGTTTTGTTTTCACTG 59.629 34.615 0.00 0.00 33.30 3.66
1687 3467 5.576384 GTGTTTTGTTTTCACTGCAGAATCA 59.424 36.000 23.35 7.00 0.00 2.57
1752 3532 5.528690 CAGAACAGTCACCAAGAAGAATCAA 59.471 40.000 0.00 0.00 0.00 2.57
1764 3544 9.883142 ACCAAGAAGAATCAAATTAACACAAAA 57.117 25.926 0.00 0.00 0.00 2.44
1784 3564 5.607119 AAATGAATCAACCGCGTATATCC 57.393 39.130 4.92 0.00 0.00 2.59
1818 3598 7.404671 AAAGTACATTTCACTTCAACACCTT 57.595 32.000 0.00 0.00 35.19 3.50
1946 3727 5.105554 CCAGAGCTAACACTGTCAGAATAGT 60.106 44.000 6.91 0.00 33.10 2.12
1958 3739 6.870965 ACTGTCAGAATAGTTCATCAACTGAC 59.129 38.462 6.91 1.27 46.91 3.51
1989 3770 2.159043 TCTTCCGTCTGATTCATCTGCC 60.159 50.000 0.00 0.00 0.00 4.85
1990 3771 1.489481 TCCGTCTGATTCATCTGCCT 58.511 50.000 0.00 0.00 0.00 4.75
1991 3772 1.137675 TCCGTCTGATTCATCTGCCTG 59.862 52.381 0.00 0.00 0.00 4.85
1996 3777 2.237893 TCTGATTCATCTGCCTGCTCAA 59.762 45.455 0.00 0.00 0.00 3.02
2016 3797 8.132995 TGCTCAAATGTCTCATGCATAATTTAG 58.867 33.333 0.00 0.00 0.00 1.85
2088 3869 2.056223 CCCATGCTGCCCTTTCTGG 61.056 63.158 0.00 0.00 0.00 3.86
2105 3886 7.232737 CCCTTTCTGGATAAAGTTTAACACCTT 59.767 37.037 0.00 0.00 38.35 3.50
2126 3907 6.761242 ACCTTCCAAAATGTTCTTTTGCTAAC 59.239 34.615 5.18 0.00 37.89 2.34
2265 4062 5.091261 AGCCATATACTGCTAATACTGCC 57.909 43.478 0.00 0.00 35.69 4.85
2266 4063 4.780021 AGCCATATACTGCTAATACTGCCT 59.220 41.667 0.00 0.00 35.69 4.75
2267 4064 5.958380 AGCCATATACTGCTAATACTGCCTA 59.042 40.000 0.00 0.00 35.69 3.93
2315 4112 2.885135 TCACAAACCCATGAGCTCAT 57.115 45.000 23.75 23.75 36.96 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.129607 CAGACAATGTGCAAAACTGCC 58.870 47.619 0.00 0.00 0.00 4.85
1 2 3.082698 TCAGACAATGTGCAAAACTGC 57.917 42.857 0.00 0.00 0.00 4.40
2 3 5.521010 ACATTTCAGACAATGTGCAAAACTG 59.479 36.000 0.00 0.00 44.19 3.16
3 4 5.663456 ACATTTCAGACAATGTGCAAAACT 58.337 33.333 0.00 0.00 44.19 2.66
4 5 5.750067 AGACATTTCAGACAATGTGCAAAAC 59.250 36.000 12.82 2.36 45.55 2.43
5 6 5.904941 AGACATTTCAGACAATGTGCAAAA 58.095 33.333 12.82 0.00 45.55 2.44
6 7 5.518848 AGACATTTCAGACAATGTGCAAA 57.481 34.783 12.82 0.00 45.55 3.68
7 8 5.067544 TGAAGACATTTCAGACAATGTGCAA 59.932 36.000 12.82 0.00 45.55 4.08
8 9 4.579753 TGAAGACATTTCAGACAATGTGCA 59.420 37.500 12.82 0.00 45.55 4.57
9 10 5.112220 TGAAGACATTTCAGACAATGTGC 57.888 39.130 12.82 7.29 45.55 4.57
10 11 6.147581 CCTTGAAGACATTTCAGACAATGTG 58.852 40.000 12.82 2.31 45.55 3.21
12 13 5.159209 GCCTTGAAGACATTTCAGACAATG 58.841 41.667 0.00 0.00 39.67 2.82
13 14 4.219288 GGCCTTGAAGACATTTCAGACAAT 59.781 41.667 0.00 0.00 0.00 2.71
14 15 3.569701 GGCCTTGAAGACATTTCAGACAA 59.430 43.478 0.00 0.00 0.00 3.18
15 16 3.149196 GGCCTTGAAGACATTTCAGACA 58.851 45.455 0.00 0.00 0.00 3.41
16 17 3.416156 AGGCCTTGAAGACATTTCAGAC 58.584 45.455 0.00 0.00 0.00 3.51
17 18 3.795688 AGGCCTTGAAGACATTTCAGA 57.204 42.857 0.00 0.00 0.00 3.27
18 19 7.630242 TTATAAGGCCTTGAAGACATTTCAG 57.370 36.000 28.77 0.00 0.00 3.02
19 20 8.415950 TTTTATAAGGCCTTGAAGACATTTCA 57.584 30.769 28.77 3.15 0.00 2.69
20 21 8.523658 ACTTTTATAAGGCCTTGAAGACATTTC 58.476 33.333 28.77 0.00 35.61 2.17
21 22 8.306761 CACTTTTATAAGGCCTTGAAGACATTT 58.693 33.333 28.77 0.00 35.61 2.32
22 23 7.669722 TCACTTTTATAAGGCCTTGAAGACATT 59.330 33.333 28.77 0.00 35.61 2.71
23 24 7.175104 TCACTTTTATAAGGCCTTGAAGACAT 58.825 34.615 28.77 14.50 35.61 3.06
24 25 6.539173 TCACTTTTATAAGGCCTTGAAGACA 58.461 36.000 28.77 7.10 35.61 3.41
25 26 7.040686 TGTTCACTTTTATAAGGCCTTGAAGAC 60.041 37.037 28.77 17.56 35.61 3.01
26 27 7.001674 TGTTCACTTTTATAAGGCCTTGAAGA 58.998 34.615 28.77 15.87 35.61 2.87
27 28 7.174946 TCTGTTCACTTTTATAAGGCCTTGAAG 59.825 37.037 28.77 24.09 35.61 3.02
28 29 7.001674 TCTGTTCACTTTTATAAGGCCTTGAA 58.998 34.615 28.77 17.44 35.61 2.69
29 30 6.539173 TCTGTTCACTTTTATAAGGCCTTGA 58.461 36.000 28.77 11.98 35.61 3.02
30 31 6.127897 CCTCTGTTCACTTTTATAAGGCCTTG 60.128 42.308 28.77 12.48 35.61 3.61
31 32 5.946377 CCTCTGTTCACTTTTATAAGGCCTT 59.054 40.000 24.18 24.18 35.61 4.35
32 33 5.250774 TCCTCTGTTCACTTTTATAAGGCCT 59.749 40.000 0.00 0.00 35.61 5.19
33 34 5.497474 TCCTCTGTTCACTTTTATAAGGCC 58.503 41.667 0.00 0.00 35.61 5.19
34 35 6.655425 ACTTCCTCTGTTCACTTTTATAAGGC 59.345 38.462 0.00 0.00 35.61 4.35
35 36 9.892130 ATACTTCCTCTGTTCACTTTTATAAGG 57.108 33.333 0.00 0.00 35.61 2.69
63 64 9.322773 CATGATCAGTTGAGTGAAGTTATATGT 57.677 33.333 0.09 0.00 0.00 2.29
64 65 9.322773 ACATGATCAGTTGAGTGAAGTTATATG 57.677 33.333 0.00 0.00 0.00 1.78
67 68 9.376075 CTTACATGATCAGTTGAGTGAAGTTAT 57.624 33.333 0.00 0.00 0.00 1.89
68 69 8.585018 TCTTACATGATCAGTTGAGTGAAGTTA 58.415 33.333 0.00 0.00 0.00 2.24
69 70 7.445121 TCTTACATGATCAGTTGAGTGAAGTT 58.555 34.615 0.00 0.00 0.00 2.66
70 71 6.997655 TCTTACATGATCAGTTGAGTGAAGT 58.002 36.000 0.00 0.00 0.00 3.01
71 72 7.895975 TTCTTACATGATCAGTTGAGTGAAG 57.104 36.000 0.00 0.72 0.00 3.02
72 73 7.276438 CGATTCTTACATGATCAGTTGAGTGAA 59.724 37.037 0.00 3.93 0.00 3.18
73 74 6.753744 CGATTCTTACATGATCAGTTGAGTGA 59.246 38.462 0.00 0.00 0.00 3.41
74 75 6.753744 TCGATTCTTACATGATCAGTTGAGTG 59.246 38.462 0.00 0.00 0.00 3.51
75 76 6.867550 TCGATTCTTACATGATCAGTTGAGT 58.132 36.000 0.00 0.00 0.00 3.41
76 77 7.943413 ATCGATTCTTACATGATCAGTTGAG 57.057 36.000 0.00 0.00 0.00 3.02
77 78 8.722480 AAATCGATTCTTACATGATCAGTTGA 57.278 30.769 11.83 0.27 0.00 3.18
84 85 9.669353 GCACATTAAAATCGATTCTTACATGAT 57.331 29.630 11.83 1.44 0.00 2.45
85 86 8.892723 AGCACATTAAAATCGATTCTTACATGA 58.107 29.630 11.83 0.00 0.00 3.07
86 87 8.950961 CAGCACATTAAAATCGATTCTTACATG 58.049 33.333 11.83 16.39 0.00 3.21
87 88 8.131100 CCAGCACATTAAAATCGATTCTTACAT 58.869 33.333 11.83 6.55 0.00 2.29
88 89 7.120579 ACCAGCACATTAAAATCGATTCTTACA 59.879 33.333 11.83 4.88 0.00 2.41
89 90 7.472543 ACCAGCACATTAAAATCGATTCTTAC 58.527 34.615 11.83 1.64 0.00 2.34
90 91 7.624360 ACCAGCACATTAAAATCGATTCTTA 57.376 32.000 11.83 9.41 0.00 2.10
91 92 6.515272 ACCAGCACATTAAAATCGATTCTT 57.485 33.333 11.83 10.34 0.00 2.52
92 93 6.324819 CAACCAGCACATTAAAATCGATTCT 58.675 36.000 11.83 0.00 0.00 2.40
93 94 5.004726 GCAACCAGCACATTAAAATCGATTC 59.995 40.000 11.83 0.00 44.79 2.52
94 95 4.864247 GCAACCAGCACATTAAAATCGATT 59.136 37.500 4.39 4.39 44.79 3.34
95 96 4.423732 GCAACCAGCACATTAAAATCGAT 58.576 39.130 0.00 0.00 44.79 3.59
96 97 3.832276 GCAACCAGCACATTAAAATCGA 58.168 40.909 0.00 0.00 44.79 3.59
109 110 2.754552 TCAAGATACCATTGCAACCAGC 59.245 45.455 0.00 0.00 45.96 4.85
110 111 5.587388 ATTCAAGATACCATTGCAACCAG 57.413 39.130 0.00 0.00 0.00 4.00
111 112 5.999205 AATTCAAGATACCATTGCAACCA 57.001 34.783 0.00 0.00 0.00 3.67
112 113 8.947055 ATTAAATTCAAGATACCATTGCAACC 57.053 30.769 0.00 0.00 0.00 3.77
114 115 9.598517 GGAATTAAATTCAAGATACCATTGCAA 57.401 29.630 0.00 0.00 41.03 4.08
115 116 8.756927 TGGAATTAAATTCAAGATACCATTGCA 58.243 29.630 0.00 0.00 41.03 4.08
116 117 9.252962 CTGGAATTAAATTCAAGATACCATTGC 57.747 33.333 0.00 0.00 41.88 3.56
119 120 8.917088 CCACTGGAATTAAATTCAAGATACCAT 58.083 33.333 0.00 0.00 41.88 3.55
120 121 7.341769 CCCACTGGAATTAAATTCAAGATACCA 59.658 37.037 0.00 0.00 41.88 3.25
121 122 7.684428 GCCCACTGGAATTAAATTCAAGATACC 60.684 40.741 0.00 0.00 41.88 2.73
122 123 7.147915 TGCCCACTGGAATTAAATTCAAGATAC 60.148 37.037 0.00 0.00 41.88 2.24
123 124 6.894654 TGCCCACTGGAATTAAATTCAAGATA 59.105 34.615 0.00 0.00 41.88 1.98
124 125 5.721000 TGCCCACTGGAATTAAATTCAAGAT 59.279 36.000 0.00 0.00 41.88 2.40
125 126 5.083122 TGCCCACTGGAATTAAATTCAAGA 58.917 37.500 0.00 0.00 41.88 3.02
126 127 5.404466 TGCCCACTGGAATTAAATTCAAG 57.596 39.130 0.00 0.00 44.30 3.02
127 128 5.732633 CATGCCCACTGGAATTAAATTCAA 58.267 37.500 0.00 0.00 41.03 2.69
128 129 4.382901 GCATGCCCACTGGAATTAAATTCA 60.383 41.667 6.36 0.00 41.03 2.57
129 130 4.122046 GCATGCCCACTGGAATTAAATTC 58.878 43.478 6.36 0.00 38.55 2.17
130 131 3.776417 AGCATGCCCACTGGAATTAAATT 59.224 39.130 15.66 0.00 0.00 1.82
131 132 3.377573 AGCATGCCCACTGGAATTAAAT 58.622 40.909 15.66 0.00 0.00 1.40
132 133 2.760092 GAGCATGCCCACTGGAATTAAA 59.240 45.455 15.66 0.00 0.00 1.52
133 134 2.291475 TGAGCATGCCCACTGGAATTAA 60.291 45.455 15.66 0.00 0.00 1.40
134 135 1.284491 TGAGCATGCCCACTGGAATTA 59.716 47.619 15.66 0.00 0.00 1.40
135 136 0.040058 TGAGCATGCCCACTGGAATT 59.960 50.000 15.66 0.00 0.00 2.17
136 137 0.395311 CTGAGCATGCCCACTGGAAT 60.395 55.000 15.66 0.00 0.00 3.01
137 138 1.001764 CTGAGCATGCCCACTGGAA 60.002 57.895 15.66 0.00 0.00 3.53
138 139 2.672908 CTGAGCATGCCCACTGGA 59.327 61.111 15.66 0.00 0.00 3.86
139 140 2.261430 TAGCTGAGCATGCCCACTGG 62.261 60.000 15.66 0.00 0.00 4.00
140 141 0.814410 CTAGCTGAGCATGCCCACTG 60.814 60.000 15.66 11.27 0.00 3.66
141 142 1.525923 CTAGCTGAGCATGCCCACT 59.474 57.895 15.66 11.36 0.00 4.00
142 143 1.525535 CCTAGCTGAGCATGCCCAC 60.526 63.158 15.66 7.14 0.00 4.61
143 144 1.997311 ACCTAGCTGAGCATGCCCA 60.997 57.895 15.66 8.18 0.00 5.36
144 145 1.525535 CACCTAGCTGAGCATGCCC 60.526 63.158 15.66 2.04 0.00 5.36
145 146 2.185494 GCACCTAGCTGAGCATGCC 61.185 63.158 15.66 6.65 41.15 4.40
146 147 3.418714 GCACCTAGCTGAGCATGC 58.581 61.111 10.51 10.51 41.15 4.06
157 158 1.503784 AGGACCTAGGCATAGCACCTA 59.496 52.381 9.30 0.00 38.81 3.08
158 159 0.266152 AGGACCTAGGCATAGCACCT 59.734 55.000 9.30 13.25 41.57 4.00
159 160 1.132500 AAGGACCTAGGCATAGCACC 58.868 55.000 9.30 5.51 0.00 5.01
160 161 1.811941 GCAAGGACCTAGGCATAGCAC 60.812 57.143 9.30 0.00 0.00 4.40
161 162 0.469917 GCAAGGACCTAGGCATAGCA 59.530 55.000 9.30 0.00 0.00 3.49
162 163 0.250510 GGCAAGGACCTAGGCATAGC 60.251 60.000 9.30 6.98 0.00 2.97
163 164 1.071385 CAGGCAAGGACCTAGGCATAG 59.929 57.143 9.30 0.00 38.26 2.23
164 165 1.131638 CAGGCAAGGACCTAGGCATA 58.868 55.000 9.30 0.00 38.26 3.14
165 166 1.918253 CAGGCAAGGACCTAGGCAT 59.082 57.895 9.30 9.41 38.26 4.40
166 167 2.971598 GCAGGCAAGGACCTAGGCA 61.972 63.158 9.30 0.00 38.26 4.75
167 168 2.124529 GCAGGCAAGGACCTAGGC 60.125 66.667 9.30 9.12 38.26 3.93
168 169 0.179034 GATGCAGGCAAGGACCTAGG 60.179 60.000 7.41 7.41 38.26 3.02
169 170 0.835941 AGATGCAGGCAAGGACCTAG 59.164 55.000 0.00 0.00 38.26 3.02
170 171 0.543277 CAGATGCAGGCAAGGACCTA 59.457 55.000 0.00 0.00 38.26 3.08
171 172 1.302285 CAGATGCAGGCAAGGACCT 59.698 57.895 0.00 0.00 42.30 3.85
172 173 1.001641 ACAGATGCAGGCAAGGACC 60.002 57.895 0.00 0.00 0.00 4.46
173 174 0.321919 TCACAGATGCAGGCAAGGAC 60.322 55.000 0.00 0.00 0.00 3.85
174 175 0.401356 TTCACAGATGCAGGCAAGGA 59.599 50.000 0.00 0.00 0.00 3.36
254 256 9.143631 TCTTACTTGAGCGTAGTTTAATTTACC 57.856 33.333 0.00 0.00 0.00 2.85
269 271 4.579869 TCCACTTCCATTCTTACTTGAGC 58.420 43.478 0.00 0.00 0.00 4.26
272 274 7.391554 TCATTCTTCCACTTCCATTCTTACTTG 59.608 37.037 0.00 0.00 0.00 3.16
357 359 1.346722 ACGGTCCACTTAGGTTTGAGG 59.653 52.381 0.00 0.00 39.02 3.86
371 373 4.132336 AGGAAAGTTCTAACAAACGGTCC 58.868 43.478 0.00 0.00 37.29 4.46
378 380 8.143193 TCGTATACACAAGGAAAGTTCTAACAA 58.857 33.333 3.32 0.00 0.00 2.83
383 385 6.817140 GGATTCGTATACACAAGGAAAGTTCT 59.183 38.462 3.32 0.00 0.00 3.01
442 444 2.435372 AAATTCATAGCTTGCCCCGA 57.565 45.000 0.00 0.00 0.00 5.14
469 475 6.591935 TCTTGCTAAATCGTTATGGAATCCT 58.408 36.000 0.00 0.00 0.00 3.24
498 508 1.354031 TGTCCTGGTGGTGCATGTTAT 59.646 47.619 0.00 0.00 34.23 1.89
519 2294 2.821991 ATGCACCCGCTCTAACTATC 57.178 50.000 0.00 0.00 39.64 2.08
590 2366 4.402829 TGGCAGTGGAGCAACTTATTTTA 58.597 39.130 0.00 0.00 35.83 1.52
607 2383 2.597217 TTCACCCGGCTTTGGCAG 60.597 61.111 0.00 0.00 40.87 4.85
617 2393 1.675552 AAAAGTCTGTGGTTCACCCG 58.324 50.000 0.00 0.00 35.15 5.28
637 2413 5.920273 GGTCATTTGCGAAATCTGAGAAAAA 59.080 36.000 0.00 0.00 0.00 1.94
644 2420 1.131126 AGCGGTCATTTGCGAAATCTG 59.869 47.619 0.00 0.00 35.87 2.90
661 2440 7.159437 TGTGACATTTAATTTGTTTCAAGCG 57.841 32.000 0.00 0.00 0.00 4.68
680 2459 1.396301 GCAGATGCTAGCTGTTGTGAC 59.604 52.381 17.23 3.28 38.21 3.67
734 2514 1.669265 GCGGCCTGTGGATTTTAGTAC 59.331 52.381 0.00 0.00 0.00 2.73
735 2515 1.557832 AGCGGCCTGTGGATTTTAGTA 59.442 47.619 0.00 0.00 0.00 1.82
736 2516 0.328258 AGCGGCCTGTGGATTTTAGT 59.672 50.000 0.00 0.00 0.00 2.24
737 2517 1.401905 GAAGCGGCCTGTGGATTTTAG 59.598 52.381 0.00 0.00 0.00 1.85
738 2518 1.004277 AGAAGCGGCCTGTGGATTTTA 59.996 47.619 0.00 0.00 0.00 1.52
743 2523 2.922503 TGAGAAGCGGCCTGTGGA 60.923 61.111 0.00 0.00 0.00 4.02
845 2625 1.270678 ACTGCTAACTGGTTTCGACCC 60.271 52.381 0.00 0.00 0.00 4.46
848 2628 2.489971 CCAACTGCTAACTGGTTTCGA 58.510 47.619 0.00 0.00 0.00 3.71
1164 2944 0.384725 CAACGCCAAAGTGCTTCTCG 60.385 55.000 0.00 0.00 0.00 4.04
1368 3148 1.214175 TCCACAGCCACCTTCAGAAAA 59.786 47.619 0.00 0.00 0.00 2.29
1414 3194 1.217882 AGTCGTTCCAAGCAGTTTCG 58.782 50.000 0.00 0.00 0.00 3.46
1573 3353 9.520204 CATTTCCCTTTACATAAATAGCTTGTG 57.480 33.333 0.00 0.00 32.63 3.33
1616 3396 6.712095 GTGATATTTCTCATGTAGGCATCCAA 59.288 38.462 0.00 0.00 31.99 3.53
1641 3421 6.016276 ACACCCAAATTCTAAAACTGCTAGTG 60.016 38.462 0.00 0.00 0.00 2.74
1679 3459 7.383572 AGTCGTCATAACATAATCTGATTCTGC 59.616 37.037 13.72 0.00 0.00 4.26
1719 3499 6.650807 TCTTGGTGACTGTTCTGAACATATTC 59.349 38.462 22.28 17.96 41.26 1.75
1752 3532 6.128956 CGCGGTTGATTCATTTTGTGTTAATT 60.129 34.615 0.00 0.00 0.00 1.40
1764 3544 4.265904 TGGATATACGCGGTTGATTCAT 57.734 40.909 12.47 0.00 0.00 2.57
1877 3658 5.376625 ACCAATTCTGCAACCGATACATAT 58.623 37.500 0.00 0.00 0.00 1.78
1946 3727 5.833406 ACAACACAATGTCAGTTGATGAA 57.167 34.783 19.18 0.00 43.93 2.57
1958 3739 3.130633 TCAGACGGAAGACAACACAATG 58.869 45.455 0.00 0.00 0.00 2.82
1989 3770 5.494632 TTATGCATGAGACATTTGAGCAG 57.505 39.130 10.16 0.00 33.69 4.24
1990 3771 6.459670 AATTATGCATGAGACATTTGAGCA 57.540 33.333 10.16 0.00 34.78 4.26
1991 3772 8.133627 ACTAAATTATGCATGAGACATTTGAGC 58.866 33.333 10.16 0.00 0.00 4.26
1996 3777 9.399797 TCTTGACTAAATTATGCATGAGACATT 57.600 29.630 10.16 0.00 0.00 2.71
2016 3797 2.930682 GGTCTAGAAACGGCATCTTGAC 59.069 50.000 15.28 15.28 43.99 3.18
2088 3869 9.758651 ACATTTTGGAAGGTGTTAAACTTTATC 57.241 29.630 0.00 0.00 0.00 1.75
2105 3886 7.106439 TCTGTTAGCAAAAGAACATTTTGGA 57.894 32.000 13.27 0.98 39.19 3.53
2126 3907 5.515797 AATTGCACATCAGGATTGATCTG 57.484 39.130 0.00 0.00 42.12 2.90
2282 4079 4.351192 GGTTTGTGATCATATTGGCGTTC 58.649 43.478 0.00 0.00 0.00 3.95
2293 4090 2.040145 TGAGCTCATGGGTTTGTGATCA 59.960 45.455 13.74 0.00 34.33 2.92
2298 4095 2.086869 CGAATGAGCTCATGGGTTTGT 58.913 47.619 29.34 12.22 36.56 2.83
2300 4097 2.496899 ACGAATGAGCTCATGGGTTT 57.503 45.000 29.34 14.54 36.56 3.27
2315 4112 1.469308 GAGCTCGAGGAGAAGAACGAA 59.531 52.381 15.58 0.00 34.50 3.85
2387 4184 4.745649 CCTACTTTAACTTCCTGAGGTCG 58.254 47.826 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.