Multiple sequence alignment - TraesCS3D01G219800

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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 TraesCS3D01G219800 chr3D 100.000 2505 0 0 1 2505 299744268 299746772 0.000000e+00 4626.0
1 TraesCS3D01G219800 chr3D 82.672 1033 123 36 229 1236 29813105 29812104 0.000000e+00 865.0
2 TraesCS3D01G219800 chr3D 81.853 1036 102 35 551 1553 29790079 29789097 0.000000e+00 793.0
3 TraesCS3D01G219800 chr3D 97.030 202 3 3 34 234 500137677 500137876 1.110000e-88 337.0
4 TraesCS3D01G219800 chr3D 97.436 195 5 0 38 232 575732564 575732370 1.440000e-87 333.0
5 TraesCS3D01G219800 chr3D 77.493 351 40 28 1667 1993 29811842 29811507 9.210000e-40 174.0
6 TraesCS3D01G219800 chr3D 80.579 242 28 14 1948 2177 29852995 29852761 4.290000e-38 169.0
7 TraesCS3D01G219800 chr3D 95.455 88 2 1 1324 1409 29861192 29861105 3.360000e-29 139.0
8 TraesCS3D01G219800 chr3D 90.217 92 8 1 2147 2238 29788385 29788295 4.380000e-23 119.0
9 TraesCS3D01G219800 chr3A 96.122 2295 70 8 225 2505 436274726 436272437 0.000000e+00 3727.0
10 TraesCS3D01G219800 chr3A 79.962 1043 125 48 226 1236 40390702 40389712 0.000000e+00 691.0
11 TraesCS3D01G219800 chr3A 80.057 1048 110 44 226 1236 40556821 40555836 0.000000e+00 686.0
12 TraesCS3D01G219800 chr3A 80.321 498 55 27 1766 2244 40389331 40388858 1.110000e-88 337.0
13 TraesCS3D01G219800 chr3A 85.106 141 5 7 1316 1441 40555844 40555705 2.020000e-26 130.0
14 TraesCS3D01G219800 chr3A 95.652 46 0 2 1 45 436274758 436274714 3.460000e-09 73.1
15 TraesCS3D01G219800 chr3B 94.411 2308 95 16 225 2505 421532739 421530439 0.000000e+00 3517.0
16 TraesCS3D01G219800 chr3B 86.319 709 71 16 535 1236 50959678 50958989 0.000000e+00 749.0
17 TraesCS3D01G219800 chr3B 80.096 1045 113 56 228 1236 50655063 50654078 0.000000e+00 689.0
18 TraesCS3D01G219800 chr3B 80.780 692 99 23 226 887 50942477 50943164 6.180000e-141 510.0
19 TraesCS3D01G219800 chr3B 88.103 311 22 9 937 1236 50943174 50943480 3.060000e-94 355.0
20 TraesCS3D01G219800 chr3B 82.990 194 19 10 1833 2021 50943863 50944047 1.990000e-36 163.0
21 TraesCS3D01G219800 chr3B 78.800 250 16 16 1357 1594 50653917 50653693 1.560000e-27 134.0
22 TraesCS3D01G219800 chr3B 81.366 161 15 9 1833 1985 50653395 50653242 1.570000e-22 117.0
23 TraesCS3D01G219800 chr3B 90.625 64 4 2 2165 2227 50952359 50952421 1.600000e-12 84.2
24 TraesCS3D01G219800 chr7B 84.000 700 67 23 551 1236 707946959 707946291 4.550000e-177 630.0
25 TraesCS3D01G219800 chr7B 83.390 295 27 14 1398 1673 707946261 707945970 1.150000e-63 254.0
26 TraesCS3D01G219800 chr7B 78.671 286 34 15 227 491 707947581 707947302 5.540000e-37 165.0
27 TraesCS3D01G219800 chr7B 84.516 155 22 2 2330 2484 746617725 746617573 4.320000e-33 152.0
28 TraesCS3D01G219800 chr7B 75.748 301 41 25 1667 1950 707946070 707945785 3.380000e-24 122.0
29 TraesCS3D01G219800 chr1D 98.930 187 2 0 39 225 471759260 471759074 3.990000e-88 335.0
30 TraesCS3D01G219800 chr6D 98.404 188 3 0 41 228 112815917 112815730 5.160000e-87 331.0
31 TraesCS3D01G219800 chr6D 97.917 192 3 1 33 223 436404215 436404406 5.160000e-87 331.0
32 TraesCS3D01G219800 chr2D 97.872 188 3 1 38 224 6929366 6929553 8.640000e-85 324.0
33 TraesCS3D01G219800 chr2D 96.410 195 7 0 40 234 532608207 532608013 3.110000e-84 322.0
34 TraesCS3D01G219800 chrUn 96.410 195 7 0 40 234 235136223 235136029 3.110000e-84 322.0
35 TraesCS3D01G219800 chrUn 96.410 195 7 0 40 234 395778490 395778296 3.110000e-84 322.0
36 TraesCS3D01G219800 chr5A 82.888 187 21 7 2297 2482 644352751 644352927 9.280000e-35 158.0
37 TraesCS3D01G219800 chr7A 84.967 153 17 6 2326 2476 69522340 69522488 1.550000e-32 150.0
38 TraesCS3D01G219800 chr2A 82.123 179 25 6 2304 2482 638322508 638322337 2.010000e-31 147.0
39 TraesCS3D01G219800 chr1B 83.750 160 21 4 2326 2482 4789399 4789556 2.010000e-31 147.0
40 TraesCS3D01G219800 chr7D 78.537 205 34 8 2302 2505 40649873 40649678 2.620000e-25 126.0
41 TraesCS3D01G219800 chr4A 78.325 203 35 7 2302 2503 618576461 618576267 3.380000e-24 122.0


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 TraesCS3D01G219800 chr3D 299744268 299746772 2504 False 4626.000000 4626 100.000000 1 2505 1 chr3D.!!$F1 2504
1 TraesCS3D01G219800 chr3D 29811507 29813105 1598 True 519.500000 865 80.082500 229 1993 2 chr3D.!!$R5 1764
2 TraesCS3D01G219800 chr3D 29788295 29790079 1784 True 456.000000 793 86.035000 551 2238 2 chr3D.!!$R4 1687
3 TraesCS3D01G219800 chr3A 436272437 436274758 2321 True 1900.050000 3727 95.887000 1 2505 2 chr3A.!!$R3 2504
4 TraesCS3D01G219800 chr3A 40388858 40390702 1844 True 514.000000 691 80.141500 226 2244 2 chr3A.!!$R1 2018
5 TraesCS3D01G219800 chr3A 40555705 40556821 1116 True 408.000000 686 82.581500 226 1441 2 chr3A.!!$R2 1215
6 TraesCS3D01G219800 chr3B 421530439 421532739 2300 True 3517.000000 3517 94.411000 225 2505 1 chr3B.!!$R2 2280
7 TraesCS3D01G219800 chr3B 50958989 50959678 689 True 749.000000 749 86.319000 535 1236 1 chr3B.!!$R1 701
8 TraesCS3D01G219800 chr3B 50942477 50944047 1570 False 342.666667 510 83.957667 226 2021 3 chr3B.!!$F2 1795
9 TraesCS3D01G219800 chr3B 50653242 50655063 1821 True 313.333333 689 80.087333 228 1985 3 chr3B.!!$R3 1757
10 TraesCS3D01G219800 chr7B 707945785 707947581 1796 True 292.750000 630 80.452250 227 1950 4 chr7B.!!$R2 1723

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
565 916 0.471617 CTCCTCCTTGCGATTCCCAT 59.528 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 3273 1.363443 CTTGTTGCAATGCACGGGT 59.637 52.632 7.72 0.0 38.71 5.28 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
33 34 1.633774 AAGACCCTGACACTCATCGT 58.366 50.000 0.00 0.00 0.00 3.73
34 35 2.509166 AGACCCTGACACTCATCGTA 57.491 50.000 0.00 0.00 0.00 3.43
35 36 3.019799 AGACCCTGACACTCATCGTAT 57.980 47.619 0.00 0.00 0.00 3.06
36 37 3.366396 AGACCCTGACACTCATCGTATT 58.634 45.455 0.00 0.00 0.00 1.89
37 38 4.533815 AGACCCTGACACTCATCGTATTA 58.466 43.478 0.00 0.00 0.00 0.98
38 39 4.954202 AGACCCTGACACTCATCGTATTAA 59.046 41.667 0.00 0.00 0.00 1.40
39 40 5.598830 AGACCCTGACACTCATCGTATTAAT 59.401 40.000 0.00 0.00 0.00 1.40
40 41 6.776116 AGACCCTGACACTCATCGTATTAATA 59.224 38.462 0.00 0.00 0.00 0.98
41 42 7.287005 AGACCCTGACACTCATCGTATTAATAA 59.713 37.037 0.00 0.00 0.00 1.40
42 43 7.208080 ACCCTGACACTCATCGTATTAATAAC 58.792 38.462 0.00 0.00 0.00 1.89
43 44 7.147794 ACCCTGACACTCATCGTATTAATAACA 60.148 37.037 0.00 0.00 0.00 2.41
44 45 7.382488 CCCTGACACTCATCGTATTAATAACAG 59.618 40.741 0.00 0.00 0.00 3.16
45 46 7.921214 CCTGACACTCATCGTATTAATAACAGT 59.079 37.037 0.00 0.00 0.00 3.55
46 47 9.302345 CTGACACTCATCGTATTAATAACAGTT 57.698 33.333 0.00 0.00 0.00 3.16
47 48 9.647797 TGACACTCATCGTATTAATAACAGTTT 57.352 29.630 0.00 0.00 0.00 2.66
50 51 9.210426 CACTCATCGTATTAATAACAGTTTTGC 57.790 33.333 0.00 0.00 0.00 3.68
51 52 9.162764 ACTCATCGTATTAATAACAGTTTTGCT 57.837 29.630 0.00 0.00 0.00 3.91
54 55 9.353353 CATCGTATTAATAACAGTTTTGCTACG 57.647 33.333 0.00 0.61 0.00 3.51
55 56 8.464770 TCGTATTAATAACAGTTTTGCTACGT 57.535 30.769 0.00 0.00 32.44 3.57
56 57 8.586273 TCGTATTAATAACAGTTTTGCTACGTC 58.414 33.333 0.00 0.00 32.44 4.34
57 58 8.589629 CGTATTAATAACAGTTTTGCTACGTCT 58.410 33.333 0.00 0.00 0.00 4.18
58 59 9.897349 GTATTAATAACAGTTTTGCTACGTCTC 57.103 33.333 0.00 0.00 0.00 3.36
59 60 7.949903 TTAATAACAGTTTTGCTACGTCTCA 57.050 32.000 0.00 0.00 0.00 3.27
60 61 6.467723 AATAACAGTTTTGCTACGTCTCAG 57.532 37.500 0.00 0.00 0.00 3.35
61 62 3.454371 ACAGTTTTGCTACGTCTCAGT 57.546 42.857 0.00 0.00 0.00 3.41
62 63 3.381949 ACAGTTTTGCTACGTCTCAGTC 58.618 45.455 0.00 0.00 0.00 3.51
63 64 2.405357 CAGTTTTGCTACGTCTCAGTCG 59.595 50.000 0.00 0.00 0.00 4.18
64 65 2.292569 AGTTTTGCTACGTCTCAGTCGA 59.707 45.455 0.00 0.00 0.00 4.20
65 66 2.327081 TTTGCTACGTCTCAGTCGAC 57.673 50.000 7.70 7.70 0.00 4.20
66 67 1.520494 TTGCTACGTCTCAGTCGACT 58.480 50.000 13.58 13.58 0.00 4.18
67 68 1.520494 TGCTACGTCTCAGTCGACTT 58.480 50.000 17.26 2.43 0.00 3.01
68 69 2.691927 TGCTACGTCTCAGTCGACTTA 58.308 47.619 17.26 7.41 0.00 2.24
69 70 2.671888 TGCTACGTCTCAGTCGACTTAG 59.328 50.000 17.26 18.13 38.24 2.18
70 71 2.928757 GCTACGTCTCAGTCGACTTAGA 59.071 50.000 22.49 22.49 37.74 2.10
71 72 3.242059 GCTACGTCTCAGTCGACTTAGAC 60.242 52.174 34.76 34.76 41.46 2.59
83 84 5.867166 GTCGACTTAGACTTCGTTATGTCT 58.133 41.667 8.70 0.00 44.56 3.41
84 85 5.958949 GTCGACTTAGACTTCGTTATGTCTC 59.041 44.000 8.70 0.00 41.92 3.36
85 86 5.640783 TCGACTTAGACTTCGTTATGTCTCA 59.359 40.000 0.00 0.00 41.92 3.27
86 87 5.960683 CGACTTAGACTTCGTTATGTCTCAG 59.039 44.000 0.00 0.00 41.92 3.35
87 88 6.402334 CGACTTAGACTTCGTTATGTCTCAGT 60.402 42.308 8.97 8.97 45.06 3.41
88 89 6.844254 ACTTAGACTTCGTTATGTCTCAGTC 58.156 40.000 0.00 0.00 41.23 3.51
89 90 4.343811 AGACTTCGTTATGTCTCAGTCG 57.656 45.455 0.00 0.00 39.04 4.18
90 91 4.001652 AGACTTCGTTATGTCTCAGTCGA 58.998 43.478 0.00 0.00 39.04 4.20
91 92 4.636648 AGACTTCGTTATGTCTCAGTCGAT 59.363 41.667 0.00 0.00 39.04 3.59
92 93 4.663166 ACTTCGTTATGTCTCAGTCGATG 58.337 43.478 0.00 0.00 0.00 3.84
93 94 4.156190 ACTTCGTTATGTCTCAGTCGATGT 59.844 41.667 0.00 0.00 33.39 3.06
94 95 4.696899 TCGTTATGTCTCAGTCGATGTT 57.303 40.909 0.00 0.00 0.00 2.71
95 96 5.806366 TCGTTATGTCTCAGTCGATGTTA 57.194 39.130 0.00 0.00 0.00 2.41
96 97 6.373186 TCGTTATGTCTCAGTCGATGTTAT 57.627 37.500 0.00 0.00 0.00 1.89
97 98 7.486802 TCGTTATGTCTCAGTCGATGTTATA 57.513 36.000 0.00 0.00 0.00 0.98
98 99 8.095937 TCGTTATGTCTCAGTCGATGTTATAT 57.904 34.615 0.00 0.00 0.00 0.86
99 100 8.565416 TCGTTATGTCTCAGTCGATGTTATATT 58.435 33.333 0.00 0.00 0.00 1.28
100 101 9.181805 CGTTATGTCTCAGTCGATGTTATATTT 57.818 33.333 0.00 0.00 0.00 1.40
104 105 9.770097 ATGTCTCAGTCGATGTTATATTTCATT 57.230 29.630 0.00 0.00 0.00 2.57
105 106 9.034544 TGTCTCAGTCGATGTTATATTTCATTG 57.965 33.333 0.00 0.00 0.00 2.82
106 107 9.249457 GTCTCAGTCGATGTTATATTTCATTGA 57.751 33.333 0.00 5.96 33.63 2.57
107 108 9.987272 TCTCAGTCGATGTTATATTTCATTGAT 57.013 29.630 10.75 2.37 37.00 2.57
109 110 9.987272 TCAGTCGATGTTATATTTCATTGATCT 57.013 29.630 10.75 8.36 37.00 2.75
112 113 9.322776 GTCGATGTTATATTTCATTGATCTTGC 57.677 33.333 10.75 0.00 37.00 4.01
113 114 9.054922 TCGATGTTATATTTCATTGATCTTGCA 57.945 29.630 0.00 0.00 31.83 4.08
114 115 9.836076 CGATGTTATATTTCATTGATCTTGCAT 57.164 29.630 0.00 0.00 0.00 3.96
133 134 9.906660 TCTTGCATTAAGATTCGTACAAAAATT 57.093 25.926 0.00 0.00 40.43 1.82
136 137 9.134734 TGCATTAAGATTCGTACAAAAATTTCC 57.865 29.630 0.00 0.00 0.00 3.13
137 138 9.353999 GCATTAAGATTCGTACAAAAATTTCCT 57.646 29.630 0.00 0.00 0.00 3.36
142 143 9.463443 AAGATTCGTACAAAAATTTCCTTTCAG 57.537 29.630 0.00 0.00 0.00 3.02
143 144 8.630037 AGATTCGTACAAAAATTTCCTTTCAGT 58.370 29.630 0.00 0.00 0.00 3.41
144 145 9.244799 GATTCGTACAAAAATTTCCTTTCAGTT 57.755 29.630 0.00 0.00 0.00 3.16
145 146 8.989653 TTCGTACAAAAATTTCCTTTCAGTTT 57.010 26.923 0.00 0.00 0.00 2.66
146 147 8.989653 TCGTACAAAAATTTCCTTTCAGTTTT 57.010 26.923 0.00 0.00 0.00 2.43
147 148 9.425577 TCGTACAAAAATTTCCTTTCAGTTTTT 57.574 25.926 0.00 0.00 33.63 1.94
205 206 4.240175 ACTTGGTTAAGTCTCAGTCGAC 57.760 45.455 7.70 7.70 43.53 4.20
206 207 3.890147 ACTTGGTTAAGTCTCAGTCGACT 59.110 43.478 13.58 13.58 43.53 4.18
207 208 3.917329 TGGTTAAGTCTCAGTCGACTG 57.083 47.619 34.76 34.76 43.14 3.51
208 209 6.438740 ACTTGGTTAAGTCTCAGTCGACTGA 61.439 44.000 38.24 38.24 45.53 3.41
218 219 2.701107 CAGTCGACTGAGACCTAGACA 58.299 52.381 36.73 0.00 46.59 3.41
219 220 2.417239 CAGTCGACTGAGACCTAGACAC 59.583 54.545 36.73 0.00 46.59 3.67
220 221 2.038689 AGTCGACTGAGACCTAGACACA 59.961 50.000 19.30 0.00 41.83 3.72
221 222 2.160022 GTCGACTGAGACCTAGACACAC 59.840 54.545 8.70 0.00 35.22 3.82
222 223 1.469308 CGACTGAGACCTAGACACACC 59.531 57.143 0.00 0.00 0.00 4.16
223 224 1.819903 GACTGAGACCTAGACACACCC 59.180 57.143 0.00 0.00 0.00 4.61
474 520 1.748493 GACTCCCTGCACTAGTCTCTG 59.252 57.143 9.90 0.00 37.30 3.35
497 543 2.422127 TGATCTGTGTCGACGATGCTAA 59.578 45.455 11.62 0.00 0.00 3.09
565 916 0.471617 CTCCTCCTTGCGATTCCCAT 59.528 55.000 0.00 0.00 0.00 4.00
661 1014 2.031012 CTCACCTGTCAGCGGCAA 59.969 61.111 1.45 0.00 0.00 4.52
978 1364 4.144297 ACTTCAAGCTTGTGATTTGCCTA 58.856 39.130 25.19 0.00 0.00 3.93
1645 2411 6.647334 TCACTTGTTTAATTTGCATCTGGA 57.353 33.333 0.00 0.00 0.00 3.86
1803 2609 5.219343 TCACAAATCTTCTCTCAGCAGAA 57.781 39.130 0.00 0.00 0.00 3.02
2105 2962 5.405935 AAAAGATAAAAATTGAGCGCCCT 57.594 34.783 2.29 0.00 0.00 5.19
2126 3064 6.648725 GCCCTAGACAACTCATATCATTCTTC 59.351 42.308 0.00 0.00 0.00 2.87
2270 3243 3.261981 ACTTATAAGGCGTTGGGACAG 57.738 47.619 16.73 0.00 42.39 3.51
2283 3256 3.228188 TGGGACAGCATTGGGATTATC 57.772 47.619 0.00 0.00 0.00 1.75
2308 3281 3.955551 TGTACTAGATAATGACCCGTGCA 59.044 43.478 0.00 0.00 0.00 4.57
2350 3323 6.925610 TGCATATTCTAGTGGTTCAACATC 57.074 37.500 0.00 0.00 0.00 3.06
2360 3333 4.520492 AGTGGTTCAACATCAATCTTGTCC 59.480 41.667 0.00 0.00 0.00 4.02
2456 3429 7.817418 AGGCAGTGAAATTTTTGACTTAGTA 57.183 32.000 0.00 0.00 32.23 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.509166 TACGATGAGTGTCAGGGTCT 57.491 50.000 0.00 0.00 0.00 3.85
33 34 9.642327 TGAGACGTAGCAAAACTGTTATTAATA 57.358 29.630 0.00 0.00 0.00 0.98
34 35 8.542497 TGAGACGTAGCAAAACTGTTATTAAT 57.458 30.769 0.00 0.00 0.00 1.40
35 36 7.654520 ACTGAGACGTAGCAAAACTGTTATTAA 59.345 33.333 0.00 0.00 0.00 1.40
36 37 7.149973 ACTGAGACGTAGCAAAACTGTTATTA 58.850 34.615 0.00 0.00 0.00 0.98
37 38 5.989777 ACTGAGACGTAGCAAAACTGTTATT 59.010 36.000 0.00 0.00 0.00 1.40
38 39 5.539048 ACTGAGACGTAGCAAAACTGTTAT 58.461 37.500 0.00 0.00 0.00 1.89
39 40 4.940463 ACTGAGACGTAGCAAAACTGTTA 58.060 39.130 0.00 0.00 0.00 2.41
40 41 3.793559 ACTGAGACGTAGCAAAACTGTT 58.206 40.909 0.00 0.00 0.00 3.16
41 42 3.381949 GACTGAGACGTAGCAAAACTGT 58.618 45.455 0.00 0.00 0.00 3.55
42 43 2.405357 CGACTGAGACGTAGCAAAACTG 59.595 50.000 0.00 0.00 0.00 3.16
43 44 2.292569 TCGACTGAGACGTAGCAAAACT 59.707 45.455 4.08 0.00 0.00 2.66
44 45 2.404361 GTCGACTGAGACGTAGCAAAAC 59.596 50.000 8.70 0.00 0.00 2.43
45 46 2.292569 AGTCGACTGAGACGTAGCAAAA 59.707 45.455 19.30 0.00 45.26 2.44
46 47 1.878088 AGTCGACTGAGACGTAGCAAA 59.122 47.619 19.30 0.00 45.26 3.68
47 48 1.520494 AGTCGACTGAGACGTAGCAA 58.480 50.000 19.30 0.00 45.26 3.91
48 49 1.520494 AAGTCGACTGAGACGTAGCA 58.480 50.000 20.85 0.00 45.26 3.49
49 50 2.928757 TCTAAGTCGACTGAGACGTAGC 59.071 50.000 26.12 0.00 45.92 3.58
50 51 4.503767 GTCTAAGTCGACTGAGACGTAG 57.496 50.000 36.15 24.24 46.90 3.51
55 56 3.661944 ACGAAGTCTAAGTCGACTGAGA 58.338 45.455 26.12 26.12 43.14 3.27
56 57 4.407496 AACGAAGTCTAAGTCGACTGAG 57.593 45.455 22.32 22.32 45.00 3.35
57 58 5.410746 ACATAACGAAGTCTAAGTCGACTGA 59.589 40.000 20.85 11.31 45.00 3.41
58 59 5.629097 ACATAACGAAGTCTAAGTCGACTG 58.371 41.667 20.85 7.79 45.00 3.51
59 60 5.642919 AGACATAACGAAGTCTAAGTCGACT 59.357 40.000 13.58 13.58 45.00 4.18
60 61 5.867166 AGACATAACGAAGTCTAAGTCGAC 58.133 41.667 7.70 7.70 45.00 4.20
61 62 5.640783 TGAGACATAACGAAGTCTAAGTCGA 59.359 40.000 0.00 0.00 45.00 4.20
62 63 5.866075 TGAGACATAACGAAGTCTAAGTCG 58.134 41.667 0.00 0.00 45.00 4.18
64 65 6.821031 ACTGAGACATAACGAAGTCTAAGT 57.179 37.500 6.74 6.74 46.82 2.24
65 66 5.960683 CGACTGAGACATAACGAAGTCTAAG 59.039 44.000 5.59 5.59 45.00 2.18
66 67 5.640783 TCGACTGAGACATAACGAAGTCTAA 59.359 40.000 0.00 0.00 45.00 2.10
67 68 5.173664 TCGACTGAGACATAACGAAGTCTA 58.826 41.667 0.00 0.00 45.00 2.59
68 69 4.001652 TCGACTGAGACATAACGAAGTCT 58.998 43.478 0.00 0.00 45.00 3.24
69 70 4.337985 TCGACTGAGACATAACGAAGTC 57.662 45.455 0.00 0.00 45.00 3.01
71 72 4.663166 ACATCGACTGAGACATAACGAAG 58.337 43.478 0.00 0.00 33.77 3.79
72 73 4.696899 ACATCGACTGAGACATAACGAA 57.303 40.909 0.00 0.00 33.77 3.85
73 74 4.696899 AACATCGACTGAGACATAACGA 57.303 40.909 0.00 0.00 0.00 3.85
74 75 8.729529 AATATAACATCGACTGAGACATAACG 57.270 34.615 0.00 0.00 0.00 3.18
78 79 9.770097 AATGAAATATAACATCGACTGAGACAT 57.230 29.630 0.00 0.00 0.00 3.06
79 80 9.034544 CAATGAAATATAACATCGACTGAGACA 57.965 33.333 0.00 0.00 0.00 3.41
80 81 9.249457 TCAATGAAATATAACATCGACTGAGAC 57.751 33.333 0.00 0.00 0.00 3.36
81 82 9.987272 ATCAATGAAATATAACATCGACTGAGA 57.013 29.630 0.00 0.00 0.00 3.27
83 84 9.987272 AGATCAATGAAATATAACATCGACTGA 57.013 29.630 0.00 0.00 0.00 3.41
86 87 9.322776 GCAAGATCAATGAAATATAACATCGAC 57.677 33.333 0.00 0.00 0.00 4.20
87 88 9.054922 TGCAAGATCAATGAAATATAACATCGA 57.945 29.630 0.00 0.00 0.00 3.59
88 89 9.836076 ATGCAAGATCAATGAAATATAACATCG 57.164 29.630 0.00 0.00 0.00 3.84
110 111 9.134734 GGAAATTTTTGTACGAATCTTAATGCA 57.865 29.630 0.00 0.00 0.00 3.96
111 112 9.353999 AGGAAATTTTTGTACGAATCTTAATGC 57.646 29.630 0.00 0.00 0.00 3.56
116 117 9.463443 CTGAAAGGAAATTTTTGTACGAATCTT 57.537 29.630 0.00 0.00 0.00 2.40
117 118 8.630037 ACTGAAAGGAAATTTTTGTACGAATCT 58.370 29.630 0.00 0.00 39.30 2.40
118 119 8.797266 ACTGAAAGGAAATTTTTGTACGAATC 57.203 30.769 0.00 0.00 39.30 2.52
119 120 9.594478 AAACTGAAAGGAAATTTTTGTACGAAT 57.406 25.926 0.00 0.00 39.30 3.34
120 121 8.989653 AAACTGAAAGGAAATTTTTGTACGAA 57.010 26.923 0.00 0.00 39.30 3.85
121 122 8.989653 AAAACTGAAAGGAAATTTTTGTACGA 57.010 26.923 0.00 0.00 39.30 3.43
169 170 7.015292 ACTTAACCAAGTCTCACTCAAGTGATA 59.985 37.037 12.96 3.87 44.28 2.15
170 171 6.183361 ACTTAACCAAGTCTCACTCAAGTGAT 60.183 38.462 12.96 0.00 44.28 3.06
171 172 5.128827 ACTTAACCAAGTCTCACTCAAGTGA 59.871 40.000 12.07 12.07 45.66 3.41
172 173 5.360591 ACTTAACCAAGTCTCACTCAAGTG 58.639 41.667 3.69 3.69 41.25 3.16
173 174 5.615925 ACTTAACCAAGTCTCACTCAAGT 57.384 39.130 0.00 0.00 41.25 3.16
198 199 2.417239 GTGTCTAGGTCTCAGTCGACTG 59.583 54.545 34.76 34.76 45.08 3.51
199 200 2.038689 TGTGTCTAGGTCTCAGTCGACT 59.961 50.000 13.58 13.58 34.38 4.18
200 201 2.160022 GTGTGTCTAGGTCTCAGTCGAC 59.840 54.545 7.70 7.70 0.00 4.20
201 202 2.424557 GTGTGTCTAGGTCTCAGTCGA 58.575 52.381 0.00 0.00 0.00 4.20
202 203 1.469308 GGTGTGTCTAGGTCTCAGTCG 59.531 57.143 0.00 0.00 0.00 4.18
203 204 1.819903 GGGTGTGTCTAGGTCTCAGTC 59.180 57.143 0.00 0.00 0.00 3.51
204 205 1.429687 AGGGTGTGTCTAGGTCTCAGT 59.570 52.381 0.00 0.00 0.00 3.41
205 206 2.223803 AGGGTGTGTCTAGGTCTCAG 57.776 55.000 0.00 0.00 0.00 3.35
206 207 4.332683 AATAGGGTGTGTCTAGGTCTCA 57.667 45.455 0.00 0.00 0.00 3.27
207 208 6.980416 ATTAATAGGGTGTGTCTAGGTCTC 57.020 41.667 0.00 0.00 0.00 3.36
208 209 9.091220 GATTATTAATAGGGTGTGTCTAGGTCT 57.909 37.037 0.00 0.00 0.00 3.85
209 210 8.867097 TGATTATTAATAGGGTGTGTCTAGGTC 58.133 37.037 0.00 0.00 0.00 3.85
210 211 8.792830 TGATTATTAATAGGGTGTGTCTAGGT 57.207 34.615 0.00 0.00 0.00 3.08
211 212 7.819900 GCTGATTATTAATAGGGTGTGTCTAGG 59.180 40.741 0.00 0.00 0.00 3.02
212 213 8.367911 TGCTGATTATTAATAGGGTGTGTCTAG 58.632 37.037 0.00 0.00 0.00 2.43
213 214 8.148351 GTGCTGATTATTAATAGGGTGTGTCTA 58.852 37.037 0.00 0.00 0.00 2.59
214 215 6.992715 GTGCTGATTATTAATAGGGTGTGTCT 59.007 38.462 0.00 0.00 0.00 3.41
215 216 6.204882 GGTGCTGATTATTAATAGGGTGTGTC 59.795 42.308 0.00 0.00 0.00 3.67
216 217 6.062095 GGTGCTGATTATTAATAGGGTGTGT 58.938 40.000 0.00 0.00 0.00 3.72
217 218 6.017109 GTGGTGCTGATTATTAATAGGGTGTG 60.017 42.308 0.00 0.00 0.00 3.82
218 219 6.062095 GTGGTGCTGATTATTAATAGGGTGT 58.938 40.000 0.00 0.00 0.00 4.16
219 220 5.179368 CGTGGTGCTGATTATTAATAGGGTG 59.821 44.000 0.00 0.00 0.00 4.61
220 221 5.163237 ACGTGGTGCTGATTATTAATAGGGT 60.163 40.000 0.00 0.00 0.00 4.34
221 222 5.179368 CACGTGGTGCTGATTATTAATAGGG 59.821 44.000 7.95 0.00 0.00 3.53
222 223 6.228273 CACGTGGTGCTGATTATTAATAGG 57.772 41.667 7.95 0.00 0.00 2.57
248 255 0.175531 GTTGCCCAAAACAGCAGTGT 59.824 50.000 0.00 0.00 40.73 3.55
474 520 1.195347 CATCGTCGACACAGATCAGC 58.805 55.000 17.16 0.00 0.00 4.26
497 543 1.694696 AGCCAGAGAGGACGAAAAAGT 59.305 47.619 0.00 0.00 41.22 2.66
1476 2049 7.164171 CAGTAACAAGTCGATCAAAAACACAAG 59.836 37.037 0.00 0.00 0.00 3.16
1645 2411 2.551270 TGGATAGCCTGTTGACTCCTT 58.449 47.619 0.00 0.00 34.31 3.36
1700 2505 3.181487 ACAAAGTGAAGCGAGCACAAAAT 60.181 39.130 8.85 0.00 38.70 1.82
1704 2509 1.378531 AACAAAGTGAAGCGAGCACA 58.621 45.000 8.85 0.00 38.70 4.57
1803 2609 8.171400 ACAGTGGTTAGATATATAGTAGCCTGT 58.829 37.037 0.00 0.00 0.00 4.00
1940 2785 9.740239 CATACAACTGAATGCATAAATAAGCTT 57.260 29.630 3.48 3.48 0.00 3.74
2031 2882 2.195727 TGCAGAAGTATGGATGTGGGA 58.804 47.619 0.00 0.00 0.00 4.37
2126 3064 4.820284 TCGATGCATCTACACTCACTAG 57.180 45.455 23.73 4.47 0.00 2.57
2283 3256 6.072119 TGCACGGGTCATTATCTAGTACATAG 60.072 42.308 0.00 0.00 0.00 2.23
2300 3273 1.363443 CTTGTTGCAATGCACGGGT 59.637 52.632 7.72 0.00 38.71 5.28
2308 3281 3.530265 CATGTATGCCCTTGTTGCAAT 57.470 42.857 0.59 0.00 42.92 3.56
2350 3323 7.169308 GTGTAAGGTATATGTCGGACAAGATTG 59.831 40.741 15.72 0.00 0.00 2.67
2411 3384 4.911522 CCTTCCCCTACCCATACTCAAATA 59.088 45.833 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.