Multiple sequence alignment - TraesCS3D01G302900

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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 TraesCS3D01G302900 chr3D 100.000 4819 0 0 1 4819 417737448 417742266 0.000000e+00 8900.0
1 TraesCS3D01G302900 chr3D 86.441 59 6 2 1265 1321 581116035 581115977 4.030000e-06 63.9
2 TraesCS3D01G302900 chr3B 95.059 4837 170 29 6 4817 544108305 544113097 0.000000e+00 7544.0
3 TraesCS3D01G302900 chr3B 97.297 37 1 0 1265 1301 777578791 777578827 4.030000e-06 63.9
4 TraesCS3D01G302900 chr3A 92.936 4374 211 46 226 4562 532938366 532934054 0.000000e+00 6276.0
5 TraesCS3D01G302900 chr3A 86.667 195 23 3 4 196 532938557 532938364 3.780000e-51 213.0
6 TraesCS3D01G302900 chr3A 97.297 37 1 0 1265 1301 716756784 716756820 4.030000e-06 63.9
7 TraesCS3D01G302900 chr7A 93.385 257 17 0 4561 4817 11265233 11264977 9.790000e-102 381.0
8 TraesCS3D01G302900 chr6B 93.385 257 15 2 4561 4817 189138370 189138116 3.520000e-101 379.0
9 TraesCS3D01G302900 chr6A 92.996 257 18 0 4561 4817 32503388 32503644 4.550000e-100 375.0
10 TraesCS3D01G302900 chr6A 92.607 257 19 0 4561 4817 32382324 32382580 2.120000e-98 370.0
11 TraesCS3D01G302900 chr5A 92.607 257 19 0 4561 4817 47463286 47463030 2.120000e-98 370.0
12 TraesCS3D01G302900 chr5A 84.615 104 16 0 4389 4492 429513002 429512899 2.370000e-18 104.0
13 TraesCS3D01G302900 chr1D 92.607 257 19 0 4561 4817 253191034 253190778 2.120000e-98 370.0
14 TraesCS3D01G302900 chr7B 92.607 257 17 2 4561 4817 328517039 328516785 7.620000e-98 368.0
15 TraesCS3D01G302900 chr1A 92.607 257 18 1 4561 4816 517900225 517899969 7.620000e-98 368.0
16 TraesCS3D01G302900 chr1A 87.500 104 13 0 4390 4493 489238922 489239025 2.360000e-23 121.0
17 TraesCS3D01G302900 chr1A 85.246 61 7 2 4433 4492 415638100 415638041 1.450000e-05 62.1
18 TraesCS3D01G302900 chr6D 91.923 260 20 1 4558 4817 455663776 455664034 3.550000e-96 363.0
19 TraesCS3D01G302900 chr5B 84.615 104 16 0 4389 4492 379815595 379815698 2.370000e-18 104.0
20 TraesCS3D01G302900 chr5D 84.524 84 13 0 4409 4492 327055988 327056071 3.090000e-12 84.2
21 TraesCS3D01G302900 chr2D 78.571 112 20 4 4383 4492 114769904 114770013 2.410000e-08 71.3
22 TraesCS3D01G302900 chr1B 83.333 60 10 0 4433 4492 439444780 439444721 6.740000e-04 56.5


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 TraesCS3D01G302900 chr3D 417737448 417742266 4818 False 8900.0 8900 100.0000 1 4819 1 chr3D.!!$F1 4818
1 TraesCS3D01G302900 chr3B 544108305 544113097 4792 False 7544.0 7544 95.0590 6 4817 1 chr3B.!!$F1 4811
2 TraesCS3D01G302900 chr3A 532934054 532938557 4503 True 3244.5 6276 89.8015 4 4562 2 chr3A.!!$R1 4558

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
452 500 0.036306 TCTTCTCCGACCCCAAAAGC 59.964 55.000 0.0 0.0 0.00 3.51 F
1163 1231 0.170116 GTCGAGGCTGTGAGTCTGAG 59.830 60.000 0.0 0.0 24.78 3.35 F
1644 1718 1.450312 GTTCCAGGTGAGGGATGCG 60.450 63.158 0.0 0.0 33.63 4.73 F
2800 2899 0.039764 CCTCTCCCAAAAAGTCCCCC 59.960 60.000 0.0 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1785 1.339055 TGCCATGTCTGTAGCCAAGAC 60.339 52.381 4.50 4.5 0.00 3.01 R
2781 2880 0.039764 GGGGGACTTTTTGGGAGAGG 59.960 60.000 0.00 0.0 0.00 3.69 R
3146 3245 3.004944 GCACCGGACAAAGTAAAATTGGA 59.995 43.478 9.46 0.0 32.02 3.53 R
4792 4898 0.467804 GGAGGACATTCAGAGGGAGC 59.532 60.000 0.00 0.0 0.00 4.70 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 1.644786 CGATTGGGTCCAAAGTCGCC 61.645 60.000 6.52 0.00 39.55 5.54
26 27 4.324991 GGTCCAAAGTCGCCCCGT 62.325 66.667 0.00 0.00 0.00 5.28
32 33 1.663695 CAAAGTCGCCCCGTCAATAT 58.336 50.000 0.00 0.00 0.00 1.28
40 42 3.005050 TCGCCCCGTCAATATAACTACAG 59.995 47.826 0.00 0.00 0.00 2.74
105 108 5.155905 TCTTACAAAAAGGGCCCCAAATAA 58.844 37.500 21.43 9.29 0.00 1.40
108 111 3.977326 ACAAAAAGGGCCCCAAATAAAGA 59.023 39.130 21.43 0.00 0.00 2.52
109 112 4.041567 ACAAAAAGGGCCCCAAATAAAGAG 59.958 41.667 21.43 0.51 0.00 2.85
184 187 1.945580 AGGGGAAGGAGAGAGAACAC 58.054 55.000 0.00 0.00 0.00 3.32
187 190 0.533032 GGAAGGAGAGAGAACACGGG 59.467 60.000 0.00 0.00 0.00 5.28
189 192 1.893801 GAAGGAGAGAGAACACGGGAA 59.106 52.381 0.00 0.00 0.00 3.97
190 193 1.551452 AGGAGAGAGAACACGGGAAG 58.449 55.000 0.00 0.00 0.00 3.46
191 194 1.075698 AGGAGAGAGAACACGGGAAGA 59.924 52.381 0.00 0.00 0.00 2.87
192 195 1.474879 GGAGAGAGAACACGGGAAGAG 59.525 57.143 0.00 0.00 0.00 2.85
193 196 2.438411 GAGAGAGAACACGGGAAGAGA 58.562 52.381 0.00 0.00 0.00 3.10
194 197 2.422127 GAGAGAGAACACGGGAAGAGAG 59.578 54.545 0.00 0.00 0.00 3.20
195 198 2.040545 AGAGAGAACACGGGAAGAGAGA 59.959 50.000 0.00 0.00 0.00 3.10
196 199 2.820787 GAGAGAACACGGGAAGAGAGAA 59.179 50.000 0.00 0.00 0.00 2.87
197 200 3.231818 AGAGAACACGGGAAGAGAGAAA 58.768 45.455 0.00 0.00 0.00 2.52
198 201 3.641906 AGAGAACACGGGAAGAGAGAAAA 59.358 43.478 0.00 0.00 0.00 2.29
199 202 4.284746 AGAGAACACGGGAAGAGAGAAAAT 59.715 41.667 0.00 0.00 0.00 1.82
200 203 4.570930 AGAACACGGGAAGAGAGAAAATC 58.429 43.478 0.00 0.00 0.00 2.17
201 204 3.336138 ACACGGGAAGAGAGAAAATCC 57.664 47.619 0.00 0.00 0.00 3.01
202 205 2.907042 ACACGGGAAGAGAGAAAATCCT 59.093 45.455 0.00 0.00 32.41 3.24
203 206 3.055747 ACACGGGAAGAGAGAAAATCCTC 60.056 47.826 0.00 0.00 32.41 3.71
204 207 2.502130 ACGGGAAGAGAGAAAATCCTCC 59.498 50.000 0.00 0.00 33.76 4.30
205 208 2.158885 CGGGAAGAGAGAAAATCCTCCC 60.159 54.545 0.28 0.28 33.76 4.30
206 209 2.846827 GGGAAGAGAGAAAATCCTCCCA 59.153 50.000 5.00 0.00 35.13 4.37
207 210 3.118075 GGGAAGAGAGAAAATCCTCCCAG 60.118 52.174 5.00 0.00 35.13 4.45
208 211 3.540617 GAAGAGAGAAAATCCTCCCAGC 58.459 50.000 0.00 0.00 33.76 4.85
209 212 2.555664 AGAGAGAAAATCCTCCCAGCA 58.444 47.619 0.00 0.00 33.76 4.41
210 213 3.121688 AGAGAGAAAATCCTCCCAGCAT 58.878 45.455 0.00 0.00 33.76 3.79
211 214 4.302067 AGAGAGAAAATCCTCCCAGCATA 58.698 43.478 0.00 0.00 33.76 3.14
212 215 4.347583 AGAGAGAAAATCCTCCCAGCATAG 59.652 45.833 0.00 0.00 33.76 2.23
213 216 4.302067 AGAGAAAATCCTCCCAGCATAGA 58.698 43.478 0.00 0.00 33.76 1.98
214 217 4.102367 AGAGAAAATCCTCCCAGCATAGAC 59.898 45.833 0.00 0.00 33.76 2.59
215 218 3.782523 AGAAAATCCTCCCAGCATAGACA 59.217 43.478 0.00 0.00 0.00 3.41
216 219 3.853355 AAATCCTCCCAGCATAGACAG 57.147 47.619 0.00 0.00 0.00 3.51
217 220 1.055040 ATCCTCCCAGCATAGACAGC 58.945 55.000 0.00 0.00 0.00 4.40
218 221 1.068753 CCTCCCAGCATAGACAGCG 59.931 63.158 0.00 0.00 37.01 5.18
219 222 1.068753 CTCCCAGCATAGACAGCGG 59.931 63.158 0.00 0.00 37.01 5.52
220 223 1.381191 TCCCAGCATAGACAGCGGA 60.381 57.895 0.00 0.00 37.01 5.54
221 224 1.068753 CCCAGCATAGACAGCGGAG 59.931 63.158 0.00 0.00 37.01 4.63
222 225 1.395045 CCCAGCATAGACAGCGGAGA 61.395 60.000 0.00 0.00 37.01 3.71
223 226 0.249238 CCAGCATAGACAGCGGAGAC 60.249 60.000 0.00 0.00 37.01 3.36
224 227 0.457443 CAGCATAGACAGCGGAGACA 59.543 55.000 0.00 0.00 37.01 3.41
262 297 0.902531 TCACAAGTCTTCCCCCGATC 59.097 55.000 0.00 0.00 0.00 3.69
287 322 3.838795 CGTGTGGAGCTTACGCGC 61.839 66.667 19.98 13.50 43.68 6.86
288 323 3.838795 GTGTGGAGCTTACGCGCG 61.839 66.667 30.96 30.96 42.32 6.86
309 344 2.495939 CTACGTTTTGTCATCGCAAGC 58.504 47.619 0.00 0.00 37.18 4.01
329 364 3.062763 GCTGCGACATGTAGAGCAATAT 58.937 45.455 19.24 0.00 39.26 1.28
378 415 4.775058 TGTACTTTGCAAACGCCAATAT 57.225 36.364 8.05 0.00 0.00 1.28
398 435 1.145571 TGGTATTCTATGGGGTGGCC 58.854 55.000 0.00 0.00 0.00 5.36
409 446 2.740438 GGTGGCCCGTGCAATTTT 59.260 55.556 0.00 0.00 40.13 1.82
410 447 1.536943 GGGTGGCCCGTGCAATTTTA 61.537 55.000 0.00 0.00 40.13 1.52
411 448 0.389296 GGTGGCCCGTGCAATTTTAC 60.389 55.000 0.00 0.00 40.13 2.01
412 449 0.389296 GTGGCCCGTGCAATTTTACC 60.389 55.000 0.00 0.00 40.13 2.85
413 450 1.216977 GGCCCGTGCAATTTTACCC 59.783 57.895 0.00 0.00 40.13 3.69
414 451 1.153920 GCCCGTGCAATTTTACCCG 60.154 57.895 0.00 0.00 37.47 5.28
415 452 1.153920 CCCGTGCAATTTTACCCGC 60.154 57.895 0.00 0.00 0.00 6.13
416 453 1.513160 CCGTGCAATTTTACCCGCG 60.513 57.895 0.00 0.00 0.00 6.46
417 454 1.513160 CGTGCAATTTTACCCGCGG 60.513 57.895 21.04 21.04 0.00 6.46
418 455 1.582461 GTGCAATTTTACCCGCGGT 59.418 52.632 26.12 14.84 40.16 5.68
419 456 0.803740 GTGCAATTTTACCCGCGGTA 59.196 50.000 26.12 13.74 37.09 4.02
451 499 2.038557 TCTTCTTCTCCGACCCCAAAAG 59.961 50.000 0.00 0.00 0.00 2.27
452 500 0.036306 TCTTCTCCGACCCCAAAAGC 59.964 55.000 0.00 0.00 0.00 3.51
453 501 0.960861 CTTCTCCGACCCCAAAAGCC 60.961 60.000 0.00 0.00 0.00 4.35
481 536 3.254060 CCTGATCGAAGAAAGCGAAGAA 58.746 45.455 0.00 0.00 43.58 2.52
817 879 3.068691 CCGTCCCTTCTCCGCTGA 61.069 66.667 0.00 0.00 0.00 4.26
830 892 2.124695 GCTGAGTTTAGGCGGGGG 60.125 66.667 0.00 0.00 0.00 5.40
1158 1226 2.986413 AGCGTCGAGGCTGTGAGT 60.986 61.111 30.10 6.64 42.86 3.41
1163 1231 0.170116 GTCGAGGCTGTGAGTCTGAG 59.830 60.000 0.00 0.00 24.78 3.35
1389 1463 3.090532 GGAGCGGGAGGGGATGTT 61.091 66.667 0.00 0.00 0.00 2.71
1644 1718 1.450312 GTTCCAGGTGAGGGATGCG 60.450 63.158 0.00 0.00 33.63 4.73
1929 2027 8.331730 TGCTAATCATGGTTAAGATGATCATG 57.668 34.615 14.30 0.00 39.21 3.07
2122 2220 6.132056 CCGAAATCGCTGATGAGATAAAAAG 58.868 40.000 0.00 0.00 38.18 2.27
2175 2273 2.169769 GACACCATCATTTCGGACCCTA 59.830 50.000 0.00 0.00 0.00 3.53
2231 2329 4.035324 GCACTGGATTCTGATGATGTTGAG 59.965 45.833 0.00 0.00 0.00 3.02
2724 2822 7.699391 CCTTTTATGCAATGATAGTGACACTTG 59.301 37.037 14.50 6.64 0.00 3.16
2781 2880 1.627329 AGGTCGAGAAAAAGTACCCCC 59.373 52.381 0.00 0.00 0.00 5.40
2800 2899 0.039764 CCTCTCCCAAAAAGTCCCCC 59.960 60.000 0.00 0.00 0.00 5.40
2801 2900 1.076438 CTCTCCCAAAAAGTCCCCCT 58.924 55.000 0.00 0.00 0.00 4.79
2802 2901 1.429299 CTCTCCCAAAAAGTCCCCCTT 59.571 52.381 0.00 0.00 33.79 3.95
2829 2928 2.196742 TCCCCTCTCCAGTGCATATT 57.803 50.000 0.00 0.00 0.00 1.28
3111 3210 0.324368 TCGAGGGTGGATGCACTAGT 60.324 55.000 17.44 1.86 0.00 2.57
3123 3222 3.275617 TGCACTAGTGAAAACAGGTGT 57.724 42.857 27.08 0.00 0.00 4.16
3138 3237 3.641436 ACAGGTGTGAACATGAGTAGTCA 59.359 43.478 1.95 1.95 37.02 3.41
3139 3238 4.284490 ACAGGTGTGAACATGAGTAGTCAT 59.716 41.667 7.27 7.27 44.85 3.06
3140 3239 4.867047 CAGGTGTGAACATGAGTAGTCATC 59.133 45.833 10.23 1.57 41.85 2.92
3141 3240 4.774726 AGGTGTGAACATGAGTAGTCATCT 59.225 41.667 10.23 0.92 41.85 2.90
3143 3242 5.578727 GGTGTGAACATGAGTAGTCATCTTC 59.421 44.000 17.20 17.20 41.85 2.87
3146 3245 7.332926 GTGTGAACATGAGTAGTCATCTTCATT 59.667 37.037 25.00 10.62 44.79 2.57
3147 3246 7.547019 TGTGAACATGAGTAGTCATCTTCATTC 59.453 37.037 25.00 17.22 44.79 2.67
3232 3333 7.151308 TGGATAAAATGTTGGCTAAACTGTTG 58.849 34.615 0.00 0.00 39.70 3.33
3258 3359 9.477484 GCTAGCTGTTAATACAACTATGTACAT 57.523 33.333 13.93 13.93 44.47 2.29
3316 3417 5.300034 TGGGTTCATTGATATTCTGTGCATC 59.700 40.000 0.00 0.00 0.00 3.91
3397 3500 1.001068 CATTCTGGCATGTGGCACAAA 59.999 47.619 25.95 13.49 46.12 2.83
3454 3557 4.994852 TGCAACTTGTCATTGTAGGTACTC 59.005 41.667 0.00 0.00 41.75 2.59
3459 3562 4.801330 TGTCATTGTAGGTACTCTGGTG 57.199 45.455 0.00 0.00 41.75 4.17
3468 3571 3.629142 GGTACTCTGGTGCCTTGTAAT 57.371 47.619 0.00 0.00 43.47 1.89
4023 4127 6.021030 CCCATTCCAGATTCCCAATATCAAT 58.979 40.000 0.00 0.00 0.00 2.57
4397 4503 6.674760 GCAACAAAATAACGACATACTCCCTC 60.675 42.308 0.00 0.00 0.00 4.30
4400 4506 2.425143 TAACGACATACTCCCTCCGT 57.575 50.000 0.00 0.00 0.00 4.69
4416 4522 4.069304 CCTCCGTTCCAAACTAATTGTCA 58.931 43.478 0.00 0.00 37.32 3.58
4430 4536 8.951787 AACTAATTGTCACACACTTAGTACAA 57.048 30.769 15.70 0.93 46.79 2.41
4504 4610 1.577328 AACATTTCTCGCTGCCCACG 61.577 55.000 0.00 0.00 0.00 4.94
4653 4759 7.657761 ACAATATCATTCATAGGTTCCTCGAAC 59.342 37.037 0.00 0.00 41.32 3.95
4664 4770 1.358152 TCCTCGAACCAATCCCTTGT 58.642 50.000 0.00 0.00 0.00 3.16
4719 4825 7.344612 TCATGAGCTACTTTATTTGTCTCCCTA 59.655 37.037 0.00 0.00 0.00 3.53
4732 4838 7.921786 TTTGTCTCCCTATTACAATGTTCAG 57.078 36.000 0.00 0.00 33.44 3.02
4765 4871 4.462483 ACGGAACATCACAAGCCATAAAAT 59.538 37.500 0.00 0.00 0.00 1.82
4792 4898 1.859427 ATCAAACACAGCAGCCGCAG 61.859 55.000 0.00 0.00 42.27 5.18
4811 4917 0.467804 GCTCCCTCTGAATGTCCTCC 59.532 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.876416 CGACTTTGGACCCAATCGTGT 60.876 52.381 13.66 6.74 35.70 4.49
1 2 0.796312 CGACTTTGGACCCAATCGTG 59.204 55.000 13.66 4.29 35.70 4.35
2 3 0.953960 GCGACTTTGGACCCAATCGT 60.954 55.000 19.63 12.71 35.70 3.73
7 8 3.961414 GGGGCGACTTTGGACCCA 61.961 66.667 0.00 0.00 44.76 4.51
22 23 7.597743 GGTTATGTCTGTAGTTATATTGACGGG 59.402 40.741 0.00 0.00 0.00 5.28
26 27 8.555896 TGGGGTTATGTCTGTAGTTATATTGA 57.444 34.615 0.00 0.00 0.00 2.57
71 74 6.627287 GCCCTTTTTGTAAGATTATGGTCCAC 60.627 42.308 0.00 0.00 0.00 4.02
105 108 0.663568 CGACCGCGTTCTTCACTCTT 60.664 55.000 4.92 0.00 0.00 2.85
150 153 4.566697 CCTTCCCCTTTCCTTCTCTTCTTC 60.567 50.000 0.00 0.00 0.00 2.87
184 187 2.158885 GGGAGGATTTTCTCTCTTCCCG 60.159 54.545 4.93 0.00 32.90 5.14
187 190 3.054802 TGCTGGGAGGATTTTCTCTCTTC 60.055 47.826 0.00 0.00 35.37 2.87
189 192 2.555664 TGCTGGGAGGATTTTCTCTCT 58.444 47.619 0.00 0.00 35.37 3.10
190 193 3.574354 ATGCTGGGAGGATTTTCTCTC 57.426 47.619 0.00 0.00 34.92 3.20
191 194 4.102367 GTCTATGCTGGGAGGATTTTCTCT 59.898 45.833 0.00 0.00 34.39 3.10
192 195 4.141620 TGTCTATGCTGGGAGGATTTTCTC 60.142 45.833 0.00 0.00 0.00 2.87
193 196 3.782523 TGTCTATGCTGGGAGGATTTTCT 59.217 43.478 0.00 0.00 0.00 2.52
194 197 4.133078 CTGTCTATGCTGGGAGGATTTTC 58.867 47.826 0.00 0.00 0.00 2.29
195 198 3.686691 GCTGTCTATGCTGGGAGGATTTT 60.687 47.826 0.00 0.00 0.00 1.82
196 199 2.158696 GCTGTCTATGCTGGGAGGATTT 60.159 50.000 0.00 0.00 0.00 2.17
197 200 1.419387 GCTGTCTATGCTGGGAGGATT 59.581 52.381 0.00 0.00 0.00 3.01
198 201 1.055040 GCTGTCTATGCTGGGAGGAT 58.945 55.000 0.00 0.00 0.00 3.24
199 202 1.395045 CGCTGTCTATGCTGGGAGGA 61.395 60.000 0.00 0.00 0.00 3.71
200 203 1.068753 CGCTGTCTATGCTGGGAGG 59.931 63.158 0.00 0.00 0.00 4.30
201 204 1.068753 CCGCTGTCTATGCTGGGAG 59.931 63.158 0.00 0.00 0.00 4.30
202 205 1.381191 TCCGCTGTCTATGCTGGGA 60.381 57.895 0.00 0.00 0.00 4.37
203 206 1.068753 CTCCGCTGTCTATGCTGGG 59.931 63.158 0.00 0.00 0.00 4.45
204 207 0.249238 GTCTCCGCTGTCTATGCTGG 60.249 60.000 0.00 0.00 0.00 4.85
205 208 0.457443 TGTCTCCGCTGTCTATGCTG 59.543 55.000 0.00 0.00 0.00 4.41
206 209 1.135915 CTTGTCTCCGCTGTCTATGCT 59.864 52.381 0.00 0.00 0.00 3.79
207 210 1.135139 TCTTGTCTCCGCTGTCTATGC 59.865 52.381 0.00 0.00 0.00 3.14
208 211 2.223688 CCTCTTGTCTCCGCTGTCTATG 60.224 54.545 0.00 0.00 0.00 2.23
209 212 2.028130 CCTCTTGTCTCCGCTGTCTAT 58.972 52.381 0.00 0.00 0.00 1.98
210 213 1.464734 CCTCTTGTCTCCGCTGTCTA 58.535 55.000 0.00 0.00 0.00 2.59
211 214 1.882989 GCCTCTTGTCTCCGCTGTCT 61.883 60.000 0.00 0.00 0.00 3.41
212 215 1.446966 GCCTCTTGTCTCCGCTGTC 60.447 63.158 0.00 0.00 0.00 3.51
213 216 1.910772 AGCCTCTTGTCTCCGCTGT 60.911 57.895 0.00 0.00 0.00 4.40
214 217 1.447489 CAGCCTCTTGTCTCCGCTG 60.447 63.158 0.00 0.00 40.81 5.18
215 218 2.654079 CCAGCCTCTTGTCTCCGCT 61.654 63.158 0.00 0.00 0.00 5.52
216 219 2.125350 CCAGCCTCTTGTCTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
217 220 2.125350 GCCAGCCTCTTGTCTCCG 60.125 66.667 0.00 0.00 0.00 4.63
218 221 0.676151 CTTGCCAGCCTCTTGTCTCC 60.676 60.000 0.00 0.00 0.00 3.71
219 222 0.036022 ACTTGCCAGCCTCTTGTCTC 59.964 55.000 0.00 0.00 0.00 3.36
220 223 0.250640 CACTTGCCAGCCTCTTGTCT 60.251 55.000 0.00 0.00 0.00 3.41
221 224 1.239968 CCACTTGCCAGCCTCTTGTC 61.240 60.000 0.00 0.00 0.00 3.18
222 225 1.228367 CCACTTGCCAGCCTCTTGT 60.228 57.895 0.00 0.00 0.00 3.16
223 226 1.975407 CCCACTTGCCAGCCTCTTG 60.975 63.158 0.00 0.00 0.00 3.02
224 227 1.504275 ATCCCACTTGCCAGCCTCTT 61.504 55.000 0.00 0.00 0.00 2.85
262 297 3.406361 GCTCCACACGTCACTGCG 61.406 66.667 0.00 0.00 37.94 5.18
287 322 0.436913 TGCGATGACAAAACGTAGCG 59.563 50.000 0.00 0.00 31.83 4.26
288 323 2.495939 CTTGCGATGACAAAACGTAGC 58.504 47.619 0.00 0.00 0.00 3.58
309 344 5.663795 AAATATTGCTCTACATGTCGCAG 57.336 39.130 0.00 0.00 33.48 5.18
329 364 5.049680 GCGCGGAGATCATTAGGAAATTAAA 60.050 40.000 8.83 0.00 0.00 1.52
378 415 1.497286 GGCCACCCCATAGAATACCAA 59.503 52.381 0.00 0.00 0.00 3.67
398 435 1.513160 CGCGGGTAAAATTGCACGG 60.513 57.895 7.94 0.00 40.13 4.94
409 446 1.402107 GGGAAGGAATACCGCGGGTA 61.402 60.000 31.76 19.22 42.80 3.69
410 447 2.738938 GGGAAGGAATACCGCGGGT 61.739 63.158 31.76 17.55 41.83 5.28
411 448 1.979619 AAGGGAAGGAATACCGCGGG 61.980 60.000 31.76 11.88 36.96 6.13
412 449 0.532196 GAAGGGAAGGAATACCGCGG 60.532 60.000 26.86 26.86 36.96 6.46
413 450 0.464452 AGAAGGGAAGGAATACCGCG 59.536 55.000 0.00 0.00 36.96 6.46
414 451 2.170817 AGAAGAAGGGAAGGAATACCGC 59.829 50.000 0.00 0.00 36.96 5.68
415 452 4.162509 AGAAGAAGAAGGGAAGGAATACCG 59.837 45.833 0.00 0.00 36.96 4.02
416 453 5.396996 GGAGAAGAAGAAGGGAAGGAATACC 60.397 48.000 0.00 0.00 0.00 2.73
417 454 5.676552 GGAGAAGAAGAAGGGAAGGAATAC 58.323 45.833 0.00 0.00 0.00 1.89
418 455 4.406003 CGGAGAAGAAGAAGGGAAGGAATA 59.594 45.833 0.00 0.00 0.00 1.75
419 456 3.198853 CGGAGAAGAAGAAGGGAAGGAAT 59.801 47.826 0.00 0.00 0.00 3.01
451 499 1.478510 TCTTCGATCAGGTTCTCTGGC 59.521 52.381 0.00 0.00 43.53 4.85
452 500 3.876274 TTCTTCGATCAGGTTCTCTGG 57.124 47.619 0.00 0.00 43.53 3.86
453 501 3.616379 GCTTTCTTCGATCAGGTTCTCTG 59.384 47.826 0.00 0.00 44.68 3.35
481 536 1.907255 CTCCCGTCCCTACCTTTCTTT 59.093 52.381 0.00 0.00 0.00 2.52
729 791 2.058675 CCGGGAGCTTTCGGGATAT 58.941 57.895 17.57 0.00 42.32 1.63
830 892 1.302271 GAAACTCCCCCACGTCACC 60.302 63.158 0.00 0.00 0.00 4.02
831 893 1.302271 GGAAACTCCCCCACGTCAC 60.302 63.158 0.00 0.00 0.00 3.67
947 1009 3.055719 GCCGGACCACCATGTGTG 61.056 66.667 5.05 7.20 45.01 3.82
1163 1231 3.426568 GGTTGCTGCTGAGGCGAC 61.427 66.667 0.00 0.00 41.80 5.19
1261 1329 2.507944 GAGGATGCAGCGGTGGAT 59.492 61.111 21.99 21.99 37.46 3.41
1644 1718 5.220873 GCTAAACAAGCCAATAAGAGCCTAC 60.221 44.000 0.00 0.00 46.25 3.18
1701 1785 1.339055 TGCCATGTCTGTAGCCAAGAC 60.339 52.381 4.50 4.50 0.00 3.01
1711 1795 1.654954 GCCTGAAGCTGCCATGTCTG 61.655 60.000 0.00 0.00 38.99 3.51
1713 1797 3.194719 GCCTGAAGCTGCCATGTC 58.805 61.111 0.00 0.00 38.99 3.06
2095 2193 1.480545 TCTCATCAGCGATTTCGGGAA 59.519 47.619 1.75 0.00 40.23 3.97
2099 2197 6.937457 TCTTTTTATCTCATCAGCGATTTCG 58.063 36.000 0.00 0.00 43.27 3.46
2105 2203 5.463392 TCGGATTCTTTTTATCTCATCAGCG 59.537 40.000 0.00 0.00 0.00 5.18
2122 2220 2.485657 GGGGGAGATTTCTGTCGGATTC 60.486 54.545 0.00 0.00 0.00 2.52
2175 2273 9.575783 GATTCTTCTTACTCTTTTCTCGTGTAT 57.424 33.333 0.00 0.00 0.00 2.29
2231 2329 5.762045 TCATTAAGAAGCAACTTCACAAGC 58.238 37.500 9.80 0.00 42.37 4.01
2315 2413 6.932960 GGCCTAACAACTCTGTAAGAACTTTA 59.067 38.462 0.00 0.00 46.34 1.85
2781 2880 0.039764 GGGGGACTTTTTGGGAGAGG 59.960 60.000 0.00 0.00 0.00 3.69
2829 2928 9.824216 AGTGTTATAGCCACCTATTTCTATAGA 57.176 33.333 0.00 0.00 36.62 1.98
3111 3210 4.269183 ACTCATGTTCACACCTGTTTTCA 58.731 39.130 0.00 0.00 0.00 2.69
3138 3237 8.028938 CGGACAAAGTAAAATTGGAATGAAGAT 58.971 33.333 0.00 0.00 32.02 2.40
3139 3238 7.367285 CGGACAAAGTAAAATTGGAATGAAGA 58.633 34.615 0.00 0.00 32.02 2.87
3140 3239 6.586082 CCGGACAAAGTAAAATTGGAATGAAG 59.414 38.462 0.00 0.00 32.02 3.02
3141 3240 6.041069 ACCGGACAAAGTAAAATTGGAATGAA 59.959 34.615 9.46 0.00 32.02 2.57
3143 3242 5.633182 CACCGGACAAAGTAAAATTGGAATG 59.367 40.000 9.46 0.00 32.02 2.67
3146 3245 3.004944 GCACCGGACAAAGTAAAATTGGA 59.995 43.478 9.46 0.00 32.02 3.53
3147 3246 3.005367 AGCACCGGACAAAGTAAAATTGG 59.995 43.478 9.46 0.00 32.02 3.16
3282 3383 9.768662 GAATATCAATGAACCCAATAAGCAATT 57.231 29.630 0.00 0.00 0.00 2.32
3287 3388 7.864379 GCACAGAATATCAATGAACCCAATAAG 59.136 37.037 0.00 0.00 0.00 1.73
3316 3417 6.441093 ACAACACATGCTATCAATAGGTTG 57.559 37.500 0.00 0.00 35.52 3.77
3426 3529 5.359576 ACCTACAATGACAAGTTGCAAAGAA 59.640 36.000 0.00 0.00 0.00 2.52
3454 3557 3.879295 CACCTATGATTACAAGGCACCAG 59.121 47.826 0.00 0.00 33.42 4.00
3459 3562 5.065218 CACTGAACACCTATGATTACAAGGC 59.935 44.000 0.00 0.00 33.42 4.35
3468 3571 4.415881 ACACAACACTGAACACCTATGA 57.584 40.909 0.00 0.00 0.00 2.15
3928 4031 5.193728 TCATCTTCTACTATTTTGGGGCCTT 59.806 40.000 0.84 0.00 0.00 4.35
4004 4108 6.554605 GGGAAAATTGATATTGGGAATCTGGA 59.445 38.462 0.00 0.00 0.00 3.86
4139 4243 7.665145 CCTCAATAACCTACTACTCCCTAGTAC 59.335 44.444 0.00 0.00 36.95 2.73
4142 4246 5.477637 GCCTCAATAACCTACTACTCCCTAG 59.522 48.000 0.00 0.00 0.00 3.02
4143 4247 5.135705 AGCCTCAATAACCTACTACTCCCTA 59.864 44.000 0.00 0.00 0.00 3.53
4144 4248 4.078513 AGCCTCAATAACCTACTACTCCCT 60.079 45.833 0.00 0.00 0.00 4.20
4274 4380 3.491104 GCACTGGCGCTATACTAGTCTTT 60.491 47.826 7.64 0.00 0.00 2.52
4397 4503 4.035792 TGTGTGACAATTAGTTTGGAACGG 59.964 41.667 0.00 0.00 39.80 4.44
4400 4506 6.767524 AAGTGTGTGACAATTAGTTTGGAA 57.232 33.333 0.00 0.00 34.36 3.53
4463 4569 6.014840 TGTTACTCCCTCCGATCCATATTAAC 60.015 42.308 0.00 0.00 0.00 2.01
4628 4734 8.023050 GTTCGAGGAACCTATGAATGATATTG 57.977 38.462 9.94 0.00 36.65 1.90
4653 4759 5.990120 AATTTTCTGAGACAAGGGATTGG 57.010 39.130 0.00 0.00 0.00 3.16
4732 4838 7.126398 GCTTGTGATGTTCCGTTAATTAGATC 58.874 38.462 0.00 0.00 0.00 2.75
4765 4871 4.321156 GGCTGCTGTGTTTGATGATTGTTA 60.321 41.667 0.00 0.00 0.00 2.41
4792 4898 0.467804 GGAGGACATTCAGAGGGAGC 59.532 60.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.