Multiple sequence alignment - TraesCS1D01G365600

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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 TraesCS1D01G365600 chr1D 100.000 5858 0 0 1 5858 446272548 446266691 0.000000e+00 10818
1 TraesCS1D01G365600 chr1A 93.927 4446 152 62 300 4700 541998006 541993634 0.000000e+00 6606
2 TraesCS1D01G365600 chr1A 90.304 691 36 13 5172 5858 541992715 541992052 0.000000e+00 876
3 TraesCS1D01G365600 chr1A 94.191 482 18 6 4701 5181 541993605 541993133 0.000000e+00 726
4 TraesCS1D01G365600 chr1A 92.760 221 12 3 1 219 541998257 541998039 3.410000e-82 316
5 TraesCS1D01G365600 chr1B 93.468 4118 149 52 1092 5116 610169295 610165205 0.000000e+00 6004
6 TraesCS1D01G365600 chr1B 91.440 736 28 12 300 1021 610170047 610169333 0.000000e+00 977
7 TraesCS1D01G365600 chr1B 90.677 665 36 15 5203 5858 610165047 610164400 0.000000e+00 861
8 TraesCS1D01G365600 chr1B 92.760 221 12 3 1 219 610170298 610170080 3.410000e-82 316


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 TraesCS1D01G365600 chr1D 446266691 446272548 5857 True 10818.0 10818 100.00000 1 5858 1 chr1D.!!$R1 5857
1 TraesCS1D01G365600 chr1A 541992052 541998257 6205 True 2131.0 6606 92.79550 1 5858 4 chr1A.!!$R1 5857
2 TraesCS1D01G365600 chr1B 610164400 610170298 5898 True 2039.5 6004 92.08625 1 5858 4 chr1B.!!$R1 5857

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
263 265 0.106268 ACATGCCACAGTGGGAAACA 60.106 50.000 19.03 9.0 42.59 2.83 F
292 294 0.108186 TCAGCGGCATTACACAGGAG 60.108 55.000 1.45 0.0 0.00 3.69 F
293 295 0.391661 CAGCGGCATTACACAGGAGT 60.392 55.000 1.45 0.0 0.00 3.85 F
894 915 0.541063 GGGGGCGGAAAGGAAAAGAA 60.541 55.000 0.00 0.0 0.00 2.52 F
1373 1416 0.823356 TGGGCCAGAGTTTTGTGCTC 60.823 55.000 0.00 0.0 0.00 4.26 F
2353 2423 1.059913 AGGCAGTAGAGGTTTGCTGT 58.940 50.000 0.00 0.0 37.93 4.40 F
3531 3605 1.079819 CATTCGTCAGCACGGGTCT 60.080 57.895 0.00 0.0 46.70 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1517 0.600255 CTGTCACCACACGAGGGTTC 60.600 60.000 0.00 0.0 36.19 3.62 R
1452 1518 1.335132 ACTGTCACCACACGAGGGTT 61.335 55.000 0.00 0.0 36.19 4.11 R
1568 1637 3.938963 AGAACACACAACTTATATGCCCG 59.061 43.478 0.00 0.0 0.00 6.13 R
1960 2030 5.184864 TGTCCAAGAAAAAGAAAGAAGCACA 59.815 36.000 0.00 0.0 0.00 4.57 R
3049 3123 3.487372 AGGGTGAAAACAAGAAGGTAGC 58.513 45.455 0.00 0.0 0.00 3.58 R
4058 4139 1.612199 GGCCTACATGAAACCCACGAA 60.612 52.381 0.00 0.0 0.00 3.85 R
4857 5001 0.318275 TTTTGTTCGCGCATCCAACC 60.318 50.000 8.75 0.0 0.00 3.77 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
110 111 5.006386 AGTACTTCTCCTGCTCCAAAAATG 58.994 41.667 0.00 0.00 0.00 2.32
114 115 3.167485 TCTCCTGCTCCAAAAATGCAAT 58.833 40.909 0.00 0.00 36.22 3.56
135 136 2.224606 AGCAACACACAATCAGGTGAG 58.775 47.619 0.00 0.00 41.32 3.51
136 137 1.335324 GCAACACACAATCAGGTGAGC 60.335 52.381 0.00 0.00 41.32 4.26
152 153 2.042464 TGAGCTCCAGAGGCGATTTAT 58.958 47.619 12.15 0.00 34.52 1.40
153 154 3.005897 GTGAGCTCCAGAGGCGATTTATA 59.994 47.826 12.15 0.00 34.52 0.98
184 186 1.030488 CCAGCCTCTCCAATGCAGTG 61.030 60.000 7.29 7.29 0.00 3.66
192 194 4.514441 CCTCTCCAATGCAGTGTCATAATC 59.486 45.833 13.82 0.00 0.00 1.75
193 195 5.363562 TCTCCAATGCAGTGTCATAATCT 57.636 39.130 13.82 0.00 0.00 2.40
208 210 6.863645 TGTCATAATCTCGATCTTCCGATTTC 59.136 38.462 1.28 0.00 37.96 2.17
209 211 6.863645 GTCATAATCTCGATCTTCCGATTTCA 59.136 38.462 1.28 0.00 37.96 2.69
212 214 8.715998 CATAATCTCGATCTTCCGATTTCAAAT 58.284 33.333 1.28 0.00 37.96 2.32
213 215 5.973651 TCTCGATCTTCCGATTTCAAATG 57.026 39.130 0.00 0.00 37.96 2.32
214 216 5.660460 TCTCGATCTTCCGATTTCAAATGA 58.340 37.500 0.00 0.00 37.96 2.57
216 218 6.763135 TCTCGATCTTCCGATTTCAAATGAAT 59.237 34.615 0.00 0.00 37.96 2.57
218 220 7.409697 TCGATCTTCCGATTTCAAATGAATTC 58.590 34.615 0.00 0.00 31.93 2.17
219 221 7.065683 TCGATCTTCCGATTTCAAATGAATTCA 59.934 33.333 11.26 11.26 35.37 2.57
220 222 7.859377 CGATCTTCCGATTTCAAATGAATTCAT 59.141 33.333 15.36 15.36 35.37 2.57
248 250 2.684881 AGCCTAAATTCGAAGCCACATG 59.315 45.455 3.35 0.00 0.00 3.21
249 251 2.796032 GCCTAAATTCGAAGCCACATGC 60.796 50.000 3.35 0.00 41.71 4.06
253 255 0.608856 ATTCGAAGCCACATGCCACA 60.609 50.000 3.35 0.00 42.71 4.17
256 258 1.582968 GAAGCCACATGCCACAGTG 59.417 57.895 0.00 0.00 42.71 3.66
260 262 4.498346 CACATGCCACAGTGGGAA 57.502 55.556 19.03 0.00 42.59 3.97
262 264 0.314935 CACATGCCACAGTGGGAAAC 59.685 55.000 19.03 2.74 42.59 2.78
263 265 0.106268 ACATGCCACAGTGGGAAACA 60.106 50.000 19.03 9.00 42.59 2.83
264 266 1.259609 CATGCCACAGTGGGAAACAT 58.740 50.000 19.03 11.02 42.59 2.71
265 267 1.619827 CATGCCACAGTGGGAAACATT 59.380 47.619 19.03 0.00 42.59 2.71
266 268 1.327303 TGCCACAGTGGGAAACATTC 58.673 50.000 21.77 2.19 33.84 2.67
267 269 0.240945 GCCACAGTGGGAAACATTCG 59.759 55.000 21.77 0.00 38.19 3.34
268 270 1.604604 CCACAGTGGGAAACATTCGT 58.395 50.000 12.40 0.00 32.67 3.85
269 271 1.953686 CCACAGTGGGAAACATTCGTT 59.046 47.619 12.40 0.00 32.79 3.85
270 272 2.287547 CCACAGTGGGAAACATTCGTTG 60.288 50.000 12.40 0.00 32.12 4.10
271 273 2.357637 CACAGTGGGAAACATTCGTTGT 59.642 45.455 0.00 0.00 41.53 3.32
272 274 2.357637 ACAGTGGGAAACATTCGTTGTG 59.642 45.455 0.00 0.00 38.99 3.33
273 275 2.357637 CAGTGGGAAACATTCGTTGTGT 59.642 45.455 0.00 0.00 38.99 3.72
274 276 2.616842 AGTGGGAAACATTCGTTGTGTC 59.383 45.455 3.69 3.69 41.26 3.67
275 277 2.356382 GTGGGAAACATTCGTTGTGTCA 59.644 45.455 11.67 0.60 43.43 3.58
276 278 2.616376 TGGGAAACATTCGTTGTGTCAG 59.384 45.455 11.67 0.00 43.43 3.51
277 279 2.604614 GGGAAACATTCGTTGTGTCAGC 60.605 50.000 11.67 0.00 43.43 4.26
278 280 2.298300 GAAACATTCGTTGTGTCAGCG 58.702 47.619 6.57 0.00 41.56 5.18
279 281 0.586319 AACATTCGTTGTGTCAGCGG 59.414 50.000 6.21 0.00 38.99 5.52
280 282 1.154413 CATTCGTTGTGTCAGCGGC 60.154 57.895 6.21 0.00 38.53 6.53
281 283 1.596752 ATTCGTTGTGTCAGCGGCA 60.597 52.632 1.45 0.00 38.53 5.69
282 284 0.955428 ATTCGTTGTGTCAGCGGCAT 60.955 50.000 1.45 0.00 38.53 4.40
283 285 1.163420 TTCGTTGTGTCAGCGGCATT 61.163 50.000 1.45 0.00 38.53 3.56
284 286 0.319986 TCGTTGTGTCAGCGGCATTA 60.320 50.000 1.45 0.00 38.53 1.90
285 287 0.179225 CGTTGTGTCAGCGGCATTAC 60.179 55.000 1.45 0.00 34.62 1.89
286 288 0.871722 GTTGTGTCAGCGGCATTACA 59.128 50.000 1.45 0.00 0.00 2.41
287 289 0.871722 TTGTGTCAGCGGCATTACAC 59.128 50.000 19.29 19.29 42.00 2.90
288 290 2.539003 GTGTCAGCGGCATTACACA 58.461 52.632 20.46 6.53 41.43 3.72
289 291 0.443869 GTGTCAGCGGCATTACACAG 59.556 55.000 20.46 0.00 41.43 3.66
290 292 0.673333 TGTCAGCGGCATTACACAGG 60.673 55.000 1.45 0.00 0.00 4.00
291 293 0.391130 GTCAGCGGCATTACACAGGA 60.391 55.000 1.45 0.00 0.00 3.86
292 294 0.108186 TCAGCGGCATTACACAGGAG 60.108 55.000 1.45 0.00 0.00 3.69
293 295 0.391661 CAGCGGCATTACACAGGAGT 60.392 55.000 1.45 0.00 0.00 3.85
319 321 1.555075 TCAGTGGAATCTGGCCAGTAC 59.445 52.381 31.58 21.79 36.96 2.73
398 410 1.830279 CTGAGCAAGGAGGCATTTCA 58.170 50.000 0.00 0.00 35.83 2.69
411 423 2.156504 GGCATTTCATCGAGCATCTACG 59.843 50.000 0.00 0.00 0.00 3.51
634 646 0.606604 GCACCGTCTTCTCCCACTTA 59.393 55.000 0.00 0.00 0.00 2.24
871 892 1.017387 GCGCTCCCAGAATACAAAGG 58.983 55.000 0.00 0.00 0.00 3.11
894 915 0.541063 GGGGGCGGAAAGGAAAAGAA 60.541 55.000 0.00 0.00 0.00 2.52
897 918 2.288825 GGGGCGGAAAGGAAAAGAAAAG 60.289 50.000 0.00 0.00 0.00 2.27
900 921 4.442332 GGGCGGAAAGGAAAAGAAAAGAAA 60.442 41.667 0.00 0.00 0.00 2.52
901 922 5.113383 GGCGGAAAGGAAAAGAAAAGAAAA 58.887 37.500 0.00 0.00 0.00 2.29
902 923 5.234329 GGCGGAAAGGAAAAGAAAAGAAAAG 59.766 40.000 0.00 0.00 0.00 2.27
943 964 2.131067 GCCTCTTCTCCCCCTCTCG 61.131 68.421 0.00 0.00 0.00 4.04
944 965 2.131067 CCTCTTCTCCCCCTCTCGC 61.131 68.421 0.00 0.00 0.00 5.03
945 966 2.042843 TCTTCTCCCCCTCTCGCC 60.043 66.667 0.00 0.00 0.00 5.54
946 967 3.532155 CTTCTCCCCCTCTCGCCG 61.532 72.222 0.00 0.00 0.00 6.46
1055 1076 3.160748 GCCTGAGCCTCCTCCTCC 61.161 72.222 0.00 0.00 37.29 4.30
1085 1106 6.421202 GTGGATTTTGAGTATCGTATCCTGTC 59.579 42.308 0.00 0.00 38.76 3.51
1307 1346 1.229625 TGACCCACATGGCCTCTCT 60.230 57.895 3.32 0.00 37.83 3.10
1373 1416 0.823356 TGGGCCAGAGTTTTGTGCTC 60.823 55.000 0.00 0.00 0.00 4.26
1451 1517 3.035363 AGGTTGGGTTTAGGGTTTTGTG 58.965 45.455 0.00 0.00 0.00 3.33
1452 1518 3.032459 GGTTGGGTTTAGGGTTTTGTGA 58.968 45.455 0.00 0.00 0.00 3.58
1568 1637 2.282783 AAATTTGCGCCCACCCCTC 61.283 57.895 4.18 0.00 0.00 4.30
1583 1652 1.420138 CCCCTCGGGCATATAAGTTGT 59.580 52.381 0.00 0.00 35.35 3.32
1735 1805 6.539649 TGTTAACAAGCAGTTGTGAGATAC 57.460 37.500 5.64 0.00 46.68 2.24
1874 1944 4.162320 TGATGTCACCAGGTTTAGATCTCC 59.838 45.833 0.00 0.00 0.00 3.71
1901 1971 8.466617 TCTCTCTCTCCAACCATACTTAATAC 57.533 38.462 0.00 0.00 0.00 1.89
1962 2032 9.368416 AGTCCTAGTATGTATGTATGTTCATGT 57.632 33.333 0.00 0.00 0.00 3.21
1963 2033 9.411801 GTCCTAGTATGTATGTATGTTCATGTG 57.588 37.037 0.00 0.00 0.00 3.21
1964 2034 8.088365 TCCTAGTATGTATGTATGTTCATGTGC 58.912 37.037 0.00 0.00 0.00 4.57
2205 2275 5.238868 AGAAGGACGAGCTTTTAAAAAGGTC 59.761 40.000 2.00 2.00 40.35 3.85
2233 2303 3.117663 TCCTTTGGTTGTTTCCTAGCACT 60.118 43.478 0.00 0.00 0.00 4.40
2234 2304 3.636764 CCTTTGGTTGTTTCCTAGCACTT 59.363 43.478 0.00 0.00 0.00 3.16
2353 2423 1.059913 AGGCAGTAGAGGTTTGCTGT 58.940 50.000 0.00 0.00 37.93 4.40
3049 3123 8.365647 AGGTAATATTAACATAGTGGACTTCCG 58.634 37.037 12.96 0.00 39.43 4.30
3314 3388 2.937799 CTGCAGATTCTTGAGGAGCTTC 59.062 50.000 8.42 0.00 0.00 3.86
3531 3605 1.079819 CATTCGTCAGCACGGGTCT 60.080 57.895 0.00 0.00 46.70 3.85
3680 3754 1.463056 TCCGCTTTAAAGTCATGCACG 59.537 47.619 16.38 9.16 0.00 5.34
3744 3823 3.541996 TCGCATGTGTCCATTGTCTAT 57.458 42.857 6.09 0.00 0.00 1.98
3949 4028 3.327404 TTTCCCCAGGGCCTCGTC 61.327 66.667 0.95 0.00 34.68 4.20
4009 4088 3.560896 GTGTGACAAAGGCATGCATTTTT 59.439 39.130 26.39 21.00 0.00 1.94
4463 4575 2.678336 GCCTAGTGTGTCACTATTTGGC 59.322 50.000 16.79 16.79 44.49 4.52
4467 4579 3.600388 AGTGTGTCACTATTTGGCTAGC 58.400 45.455 6.04 6.04 43.46 3.42
4479 4591 0.670706 TGGCTAGCGCTAGACATCAG 59.329 55.000 42.21 21.54 45.67 2.90
4525 4637 5.755861 GCCCTAGTTTGAACTGTAGATGATC 59.244 44.000 6.64 0.00 40.07 2.92
4529 4641 5.491982 AGTTTGAACTGTAGATGATCCCAC 58.508 41.667 0.00 0.00 37.98 4.61
4551 4663 2.031516 GCAGCGCGCCTGATATCAT 61.032 57.895 30.33 1.73 44.64 2.45
4572 4684 1.395954 CATCACCACAAGACAGATGCG 59.604 52.381 0.00 0.00 30.96 4.73
4585 4697 1.067706 CAGATGCGCATTTCCCAACAA 60.068 47.619 26.12 0.00 0.00 2.83
4740 4884 7.115095 GGTAGTACTGCTATATCTTTTTCTGCG 59.885 40.741 10.95 0.00 31.50 5.18
4792 4936 3.950397 TGGTATGAATCGCAGGAAACTT 58.050 40.909 0.00 0.00 40.21 2.66
4809 4953 1.301677 CTTCGGAGAAACCAGCCAGC 61.302 60.000 0.00 0.00 45.90 4.85
4857 5001 1.134491 ACCCGCGGAAGGAAGAAATAG 60.134 52.381 30.73 7.25 0.00 1.73
4908 5052 2.627221 GCATCCTCAGCTAGATCAGTCA 59.373 50.000 0.00 0.00 0.00 3.41
5060 5204 2.559668 TGTAGGGTCGTACTTTCCTGTG 59.440 50.000 7.68 0.00 0.00 3.66
5135 5283 8.756376 CAATTTGTGCAGTGAAATTTTAGTTG 57.244 30.769 7.84 0.00 30.94 3.16
5147 5295 1.611519 TTTAGTTGGACGGGCAAAGG 58.388 50.000 0.00 0.00 0.00 3.11
5156 5304 1.106944 ACGGGCAAAGGTTGGACTTG 61.107 55.000 0.00 0.00 0.00 3.16
5163 5311 3.320826 GCAAAGGTTGGACTTGTACCAAT 59.679 43.478 0.00 0.00 46.78 3.16
5210 5881 5.206299 CACGCCACAAAACGTTAGAATTTA 58.794 37.500 0.00 0.00 41.32 1.40
5252 5923 2.788786 CCAGTGACGTGAACAAAATTGC 59.211 45.455 0.00 0.00 0.00 3.56
5273 5944 6.983474 TGCGAAACATCTAAGATGAATTCA 57.017 33.333 11.26 11.26 0.00 2.57
5276 5947 8.124823 TGCGAAACATCTAAGATGAATTCATTC 58.875 33.333 21.57 14.27 36.57 2.67
5278 5949 8.834465 CGAAACATCTAAGATGAATTCATTCCT 58.166 33.333 21.57 12.42 36.57 3.36
5281 5952 7.938715 ACATCTAAGATGAATTCATTCCTTGC 58.061 34.615 21.57 8.24 36.57 4.01
5282 5953 7.558807 ACATCTAAGATGAATTCATTCCTTGCA 59.441 33.333 21.57 11.88 36.57 4.08
5283 5954 7.325660 TCTAAGATGAATTCATTCCTTGCAC 57.674 36.000 21.57 6.86 36.57 4.57
5316 5991 9.723601 AAGCAAAATCACACCATTTACAATTAT 57.276 25.926 0.00 0.00 0.00 1.28
5317 5992 9.153721 AGCAAAATCACACCATTTACAATTATG 57.846 29.630 0.00 0.00 0.00 1.90
5430 6107 3.245016 TGAGCATTGATCCCACAAGTTCT 60.245 43.478 0.00 0.00 33.22 3.01
5432 6109 4.154942 AGCATTGATCCCACAAGTTCTTT 58.845 39.130 0.00 0.00 33.22 2.52
5436 6113 3.754965 TGATCCCACAAGTTCTTTGAGG 58.245 45.455 0.00 0.00 44.40 3.86
5438 6115 3.943671 TCCCACAAGTTCTTTGAGGAA 57.056 42.857 5.16 0.00 46.80 3.36
5439 6116 3.551846 TCCCACAAGTTCTTTGAGGAAC 58.448 45.455 5.16 0.00 46.80 3.62
5440 6117 2.623416 CCCACAAGTTCTTTGAGGAACC 59.377 50.000 5.16 0.00 46.80 3.62
5451 6128 0.391597 TGAGGAACCGGACACTGAAC 59.608 55.000 9.46 0.00 0.00 3.18
5564 6247 1.923006 TTCCCACGGGACCAACAACA 61.923 55.000 3.66 0.00 45.11 3.33
5657 6340 2.620585 GCTATTTGTCCCAGCCATCTTC 59.379 50.000 0.00 0.00 0.00 2.87
5748 6431 0.386858 TGACGTCGTAGTGCTTCTGC 60.387 55.000 11.62 0.00 40.20 4.26
5799 6482 2.746375 GGAGGTGTCGATGGCCCAT 61.746 63.158 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 2.104170 CAGGAGAAGTACTGGGAGGAC 58.896 57.143 0.00 0.00 0.00 3.85
110 111 3.057315 ACCTGATTGTGTGTTGCTATTGC 60.057 43.478 0.00 0.00 40.20 3.56
114 115 3.402110 CTCACCTGATTGTGTGTTGCTA 58.598 45.455 0.00 0.00 37.51 3.49
135 136 2.739379 GCTTATAAATCGCCTCTGGAGC 59.261 50.000 0.00 0.00 0.00 4.70
136 137 3.743396 GTGCTTATAAATCGCCTCTGGAG 59.257 47.826 0.00 0.00 0.00 3.86
152 153 1.953686 GAGGCTGGTTTTGTGTGCTTA 59.046 47.619 0.00 0.00 0.00 3.09
153 154 0.746659 GAGGCTGGTTTTGTGTGCTT 59.253 50.000 0.00 0.00 0.00 3.91
221 223 4.279671 TGGCTTCGAATTTAGGCTGAAAAA 59.720 37.500 9.48 0.00 37.78 1.94
222 224 3.823873 TGGCTTCGAATTTAGGCTGAAAA 59.176 39.130 9.48 0.00 37.78 2.29
223 225 3.190535 GTGGCTTCGAATTTAGGCTGAAA 59.809 43.478 9.48 0.00 37.78 2.69
224 226 2.747446 GTGGCTTCGAATTTAGGCTGAA 59.253 45.455 9.48 0.00 37.78 3.02
225 227 2.290008 TGTGGCTTCGAATTTAGGCTGA 60.290 45.455 9.48 0.00 37.78 4.26
226 228 2.083774 TGTGGCTTCGAATTTAGGCTG 58.916 47.619 9.48 0.00 37.78 4.85
227 229 2.489938 TGTGGCTTCGAATTTAGGCT 57.510 45.000 9.48 0.00 37.78 4.58
228 230 2.796032 GCATGTGGCTTCGAATTTAGGC 60.796 50.000 0.00 0.00 40.25 3.93
237 239 1.968017 ACTGTGGCATGTGGCTTCG 60.968 57.895 8.09 0.00 44.01 3.79
248 250 0.240945 CGAATGTTTCCCACTGTGGC 59.759 55.000 21.47 8.20 35.79 5.01
249 251 1.604604 ACGAATGTTTCCCACTGTGG 58.395 50.000 20.01 20.01 37.25 4.17
253 255 2.616842 GACACAACGAATGTTTCCCACT 59.383 45.455 0.00 0.00 41.46 4.00
256 258 2.604614 GCTGACACAACGAATGTTTCCC 60.605 50.000 8.86 0.04 41.46 3.97
260 262 0.586319 CCGCTGACACAACGAATGTT 59.414 50.000 0.00 0.00 41.46 2.71
262 264 1.154413 GCCGCTGACACAACGAATG 60.154 57.895 0.00 0.00 0.00 2.67
263 265 0.955428 ATGCCGCTGACACAACGAAT 60.955 50.000 0.00 0.00 0.00 3.34
264 266 1.163420 AATGCCGCTGACACAACGAA 61.163 50.000 0.00 0.00 0.00 3.85
265 267 0.319986 TAATGCCGCTGACACAACGA 60.320 50.000 0.00 0.00 0.00 3.85
266 268 0.179225 GTAATGCCGCTGACACAACG 60.179 55.000 0.00 0.00 0.00 4.10
267 269 0.871722 TGTAATGCCGCTGACACAAC 59.128 50.000 0.00 0.00 0.00 3.32
268 270 0.871722 GTGTAATGCCGCTGACACAA 59.128 50.000 14.35 0.00 41.46 3.33
269 271 2.539003 GTGTAATGCCGCTGACACA 58.461 52.632 14.35 2.20 41.46 3.72
270 272 0.443869 CTGTGTAATGCCGCTGACAC 59.556 55.000 13.06 13.06 42.04 3.67
271 273 0.673333 CCTGTGTAATGCCGCTGACA 60.673 55.000 0.00 0.00 0.00 3.58
272 274 0.391130 TCCTGTGTAATGCCGCTGAC 60.391 55.000 0.00 0.00 0.00 3.51
273 275 0.108186 CTCCTGTGTAATGCCGCTGA 60.108 55.000 0.00 0.00 0.00 4.26
274 276 0.391661 ACTCCTGTGTAATGCCGCTG 60.392 55.000 0.00 0.00 0.00 5.18
275 277 0.391661 CACTCCTGTGTAATGCCGCT 60.392 55.000 0.00 0.00 39.24 5.52
276 278 0.391130 TCACTCCTGTGTAATGCCGC 60.391 55.000 0.00 0.00 44.14 6.53
277 279 1.935873 CATCACTCCTGTGTAATGCCG 59.064 52.381 0.00 0.00 44.14 5.69
278 280 2.292267 CCATCACTCCTGTGTAATGCC 58.708 52.381 0.00 0.00 44.14 4.40
279 281 2.939103 GACCATCACTCCTGTGTAATGC 59.061 50.000 0.00 0.00 44.14 3.56
280 282 4.186926 CTGACCATCACTCCTGTGTAATG 58.813 47.826 0.00 0.00 44.14 1.90
281 283 3.840666 ACTGACCATCACTCCTGTGTAAT 59.159 43.478 0.00 0.00 44.14 1.89
282 284 3.006859 CACTGACCATCACTCCTGTGTAA 59.993 47.826 0.00 0.00 44.14 2.41
283 285 2.562738 CACTGACCATCACTCCTGTGTA 59.437 50.000 0.00 0.00 44.14 2.90
284 286 1.345741 CACTGACCATCACTCCTGTGT 59.654 52.381 0.00 0.00 44.14 3.72
285 287 1.338484 CCACTGACCATCACTCCTGTG 60.338 57.143 0.00 0.00 45.07 3.66
286 288 0.979665 CCACTGACCATCACTCCTGT 59.020 55.000 0.00 0.00 0.00 4.00
287 289 1.269958 TCCACTGACCATCACTCCTG 58.730 55.000 0.00 0.00 0.00 3.86
288 290 2.030027 TTCCACTGACCATCACTCCT 57.970 50.000 0.00 0.00 0.00 3.69
289 291 2.503356 AGATTCCACTGACCATCACTCC 59.497 50.000 0.00 0.00 0.00 3.85
290 292 3.529533 CAGATTCCACTGACCATCACTC 58.470 50.000 0.00 0.00 39.94 3.51
291 293 2.238144 CCAGATTCCACTGACCATCACT 59.762 50.000 0.00 0.00 39.94 3.41
292 294 2.636830 CCAGATTCCACTGACCATCAC 58.363 52.381 0.00 0.00 39.94 3.06
293 295 1.065199 GCCAGATTCCACTGACCATCA 60.065 52.381 0.00 0.00 39.94 3.07
294 296 1.673168 GCCAGATTCCACTGACCATC 58.327 55.000 0.00 0.00 39.94 3.51
295 297 0.257039 GGCCAGATTCCACTGACCAT 59.743 55.000 0.00 0.00 39.60 3.55
296 298 1.133181 TGGCCAGATTCCACTGACCA 61.133 55.000 0.00 0.00 45.38 4.02
297 299 0.393537 CTGGCCAGATTCCACTGACC 60.394 60.000 29.88 0.00 40.11 4.02
298 300 0.326264 ACTGGCCAGATTCCACTGAC 59.674 55.000 39.19 0.00 39.94 3.51
398 410 2.049985 GCGCCGTAGATGCTCGAT 60.050 61.111 0.00 0.00 0.00 3.59
428 440 3.322466 CCCCCTTCCTGTCTGCGT 61.322 66.667 0.00 0.00 0.00 5.24
603 615 3.434319 CGGTGCTGTGGGACATGC 61.434 66.667 0.00 0.00 44.52 4.06
634 646 4.778143 GCGGACCGGCAGTTCCAT 62.778 66.667 17.22 0.00 34.01 3.41
744 757 1.141234 GATCTCGGACCGAACCCAC 59.859 63.158 18.93 4.44 34.74 4.61
745 758 1.304630 TGATCTCGGACCGAACCCA 60.305 57.895 18.93 12.25 34.74 4.51
746 759 1.437986 CTGATCTCGGACCGAACCC 59.562 63.158 18.93 9.78 34.74 4.11
747 760 1.321074 ACCTGATCTCGGACCGAACC 61.321 60.000 18.93 10.13 34.74 3.62
833 854 1.743391 CGTGGTACATATGGGCCGA 59.257 57.895 7.80 0.00 44.52 5.54
1037 1058 3.535962 GAGGAGGAGGCTCAGGCG 61.536 72.222 17.69 0.00 39.81 5.52
1055 1076 4.261801 ACGATACTCAAAATCCACAAGGG 58.738 43.478 0.00 0.00 34.83 3.95
1085 1106 2.171725 GGAAAGCGTCCCCGAATCG 61.172 63.158 0.00 0.00 41.10 3.34
1102 1139 1.095228 CCATTCGAATGTGACGGGGG 61.095 60.000 30.71 13.65 34.60 5.40
1307 1346 6.687081 ACGAGAAACAAACAGTAAATGGAA 57.313 33.333 0.00 0.00 0.00 3.53
1451 1517 0.600255 CTGTCACCACACGAGGGTTC 60.600 60.000 0.00 0.00 36.19 3.62
1452 1518 1.335132 ACTGTCACCACACGAGGGTT 61.335 55.000 0.00 0.00 36.19 4.11
1514 1580 8.484641 TGCAACAATCTTCTTCTAAGAGTATG 57.515 34.615 0.00 0.00 36.22 2.39
1568 1637 3.938963 AGAACACACAACTTATATGCCCG 59.061 43.478 0.00 0.00 0.00 6.13
1583 1652 4.150897 ACTCAGGCAAACTAAGAACACA 57.849 40.909 0.00 0.00 0.00 3.72
1874 1944 5.930837 AAGTATGGTTGGAGAGAGAGAAG 57.069 43.478 0.00 0.00 0.00 2.85
1906 1976 7.945134 ACTTTGAGCAGTACTTCAAATCAAAT 58.055 30.769 18.53 7.87 35.39 2.32
1907 1977 7.333528 ACTTTGAGCAGTACTTCAAATCAAA 57.666 32.000 18.53 15.52 34.87 2.69
1908 1978 6.942532 ACTTTGAGCAGTACTTCAAATCAA 57.057 33.333 18.53 10.51 32.60 2.57
1909 1979 6.942532 AACTTTGAGCAGTACTTCAAATCA 57.057 33.333 18.53 5.88 32.60 2.57
1912 1982 9.555727 ACTATAAACTTTGAGCAGTACTTCAAA 57.444 29.630 17.62 17.62 0.00 2.69
1953 2023 7.495055 AGAAAAAGAAAGAAGCACATGAACAT 58.505 30.769 0.00 0.00 0.00 2.71
1954 2024 6.866480 AGAAAAAGAAAGAAGCACATGAACA 58.134 32.000 0.00 0.00 0.00 3.18
1955 2025 7.254218 CCAAGAAAAAGAAAGAAGCACATGAAC 60.254 37.037 0.00 0.00 0.00 3.18
1957 2027 6.096705 TCCAAGAAAAAGAAAGAAGCACATGA 59.903 34.615 0.00 0.00 0.00 3.07
1959 2029 6.127366 TGTCCAAGAAAAAGAAAGAAGCACAT 60.127 34.615 0.00 0.00 0.00 3.21
1960 2030 5.184864 TGTCCAAGAAAAAGAAAGAAGCACA 59.815 36.000 0.00 0.00 0.00 4.57
1961 2031 5.650543 TGTCCAAGAAAAAGAAAGAAGCAC 58.349 37.500 0.00 0.00 0.00 4.40
1962 2032 5.418840 ACTGTCCAAGAAAAAGAAAGAAGCA 59.581 36.000 0.00 0.00 0.00 3.91
1963 2033 5.895928 ACTGTCCAAGAAAAAGAAAGAAGC 58.104 37.500 0.00 0.00 0.00 3.86
1964 2034 7.088589 TGACTGTCCAAGAAAAAGAAAGAAG 57.911 36.000 5.17 0.00 0.00 2.85
2205 2275 7.035612 GCTAGGAAACAACCAAAGGATAAATG 58.964 38.462 0.00 0.00 0.00 2.32
2382 2452 7.386299 GTCAAAAGAGAGAGCATAGAAGAACAA 59.614 37.037 0.00 0.00 0.00 2.83
3049 3123 3.487372 AGGGTGAAAACAAGAAGGTAGC 58.513 45.455 0.00 0.00 0.00 3.58
3284 3358 7.795047 TCCTCAAGAATCTGCAGTATGAAATA 58.205 34.615 14.67 0.00 39.69 1.40
3314 3388 7.703621 GTCAATGAATTGGTCCATAGTGAATTG 59.296 37.037 0.00 0.00 38.30 2.32
3531 3605 9.653516 TTAATATTTTCCAGAATGCCCTCAATA 57.346 29.630 0.00 0.00 31.97 1.90
3680 3754 2.229784 CCAGAATTTCACTGGCCAAGAC 59.770 50.000 7.01 0.00 46.30 3.01
3744 3823 8.206867 CAGTCCTCAGGAATTTGATATCTACAA 58.793 37.037 0.00 0.00 31.38 2.41
4009 4088 2.558795 CTGGAACGGAGAGAGACAAGAA 59.441 50.000 0.00 0.00 36.31 2.52
4058 4139 1.612199 GGCCTACATGAAACCCACGAA 60.612 52.381 0.00 0.00 0.00 3.85
4155 4237 8.236586 GCACACATGTATTATTCTTGAGAACAA 58.763 33.333 0.00 0.00 36.80 2.83
4156 4238 7.390162 TGCACACATGTATTATTCTTGAGAACA 59.610 33.333 0.00 0.00 36.80 3.18
4162 4244 8.006027 CGACTATGCACACATGTATTATTCTTG 58.994 37.037 0.00 0.00 37.04 3.02
4359 4452 5.244626 AGAAAATGATGTTTCTGGACAAGGG 59.755 40.000 0.00 0.00 44.35 3.95
4412 4509 4.797471 TGAATTGCATGCACAGTTCTAAC 58.203 39.130 22.58 4.75 37.23 2.34
4463 4575 2.498807 TTGCTGATGTCTAGCGCTAG 57.501 50.000 33.92 33.92 44.01 3.42
4467 4579 2.286294 GGTGAATTGCTGATGTCTAGCG 59.714 50.000 0.00 0.00 44.01 4.26
4479 4591 0.811281 GTAGCCTGGTGGTGAATTGC 59.189 55.000 0.00 0.00 35.27 3.56
4551 4663 2.703416 GCATCTGTCTTGTGGTGATGA 58.297 47.619 0.00 0.00 37.33 2.92
4572 4684 8.728833 TCATTTGAAAATATTGTTGGGAAATGC 58.271 29.630 0.00 0.00 31.40 3.56
4585 4697 7.710475 CCCGGTTGCTTATTCATTTGAAAATAT 59.290 33.333 0.00 0.00 37.61 1.28
4716 4859 7.648112 CACGCAGAAAAAGATATAGCAGTACTA 59.352 37.037 0.00 0.00 34.64 1.82
4723 4867 5.718649 TGTCACGCAGAAAAAGATATAGC 57.281 39.130 0.00 0.00 0.00 2.97
4740 4884 4.227512 TCATGTGCTGAAATGTTGTCAC 57.772 40.909 0.00 0.00 0.00 3.67
4792 4936 2.347490 GCTGGCTGGTTTCTCCGA 59.653 61.111 0.00 0.00 39.52 4.55
4794 4938 3.435186 GCGCTGGCTGGTTTCTCC 61.435 66.667 0.00 0.00 35.83 3.71
4857 5001 0.318275 TTTTGTTCGCGCATCCAACC 60.318 50.000 8.75 0.00 0.00 3.77
4908 5052 4.497291 TTTGAGTTACACAACAGGAGGT 57.503 40.909 0.00 0.00 37.10 3.85
5060 5204 6.097412 ACCCTAAAATTGCTGAATTCTCCATC 59.903 38.462 7.05 0.00 30.02 3.51
5135 5283 2.114411 TCCAACCTTTGCCCGTCC 59.886 61.111 0.00 0.00 0.00 4.79
5156 5304 4.773209 GGCCTAGCCGATTGGTAC 57.227 61.111 0.00 0.00 39.62 3.34
5228 5899 1.295792 TTTGTTCACGTCACTGGAGC 58.704 50.000 0.00 0.00 0.00 4.70
5252 5923 8.834465 AGGAATGAATTCATCTTAGATGTTTCG 58.166 33.333 20.95 0.00 38.53 3.46
5273 5944 4.137116 TGCTTATCTACGTGCAAGGAAT 57.863 40.909 4.26 0.00 32.12 3.01
5276 5947 4.678509 TTTTGCTTATCTACGTGCAAGG 57.321 40.909 4.26 0.00 44.52 3.61
5278 5949 5.180304 TGTGATTTTGCTTATCTACGTGCAA 59.820 36.000 0.00 0.61 42.60 4.08
5279 5950 4.693095 TGTGATTTTGCTTATCTACGTGCA 59.307 37.500 0.00 0.00 0.00 4.57
5280 5951 5.022021 GTGTGATTTTGCTTATCTACGTGC 58.978 41.667 0.00 0.00 0.00 5.34
5281 5952 5.121611 TGGTGTGATTTTGCTTATCTACGTG 59.878 40.000 0.00 0.00 0.00 4.49
5282 5953 5.242434 TGGTGTGATTTTGCTTATCTACGT 58.758 37.500 0.00 0.00 0.00 3.57
5283 5954 5.794687 TGGTGTGATTTTGCTTATCTACG 57.205 39.130 0.00 0.00 0.00 3.51
5315 5990 5.936956 TGTTCTTTTTGCACTTGTTTTCCAT 59.063 32.000 0.00 0.00 0.00 3.41
5316 5991 5.300752 TGTTCTTTTTGCACTTGTTTTCCA 58.699 33.333 0.00 0.00 0.00 3.53
5317 5992 5.854431 TGTTCTTTTTGCACTTGTTTTCC 57.146 34.783 0.00 0.00 0.00 3.13
5322 5997 7.229306 TCTCATAGATGTTCTTTTTGCACTTGT 59.771 33.333 0.00 0.00 0.00 3.16
5355 6030 6.211184 TCAATTGGATTGTATGCCTGTCTTTT 59.789 34.615 5.42 0.00 41.02 2.27
5356 6031 5.716228 TCAATTGGATTGTATGCCTGTCTTT 59.284 36.000 5.42 0.00 41.02 2.52
5358 6033 4.858850 TCAATTGGATTGTATGCCTGTCT 58.141 39.130 5.42 0.00 41.02 3.41
5359 6034 5.581126 TTCAATTGGATTGTATGCCTGTC 57.419 39.130 5.42 0.00 41.02 3.51
5361 6036 6.401047 AGATTCAATTGGATTGTATGCCTG 57.599 37.500 5.42 0.00 41.02 4.85
5362 6037 7.255730 GCTAAGATTCAATTGGATTGTATGCCT 60.256 37.037 5.42 0.00 41.02 4.75
5363 6038 6.865205 GCTAAGATTCAATTGGATTGTATGCC 59.135 38.462 5.42 0.00 41.02 4.40
5372 6047 4.734402 GCAATGCGCTAAGATTCAATTGGA 60.734 41.667 9.73 0.00 37.77 3.53
5430 6107 1.124780 TCAGTGTCCGGTTCCTCAAA 58.875 50.000 0.00 0.00 0.00 2.69
5432 6109 0.391597 GTTCAGTGTCCGGTTCCTCA 59.608 55.000 0.00 0.00 0.00 3.86
5436 6113 2.028930 AGATCTGTTCAGTGTCCGGTTC 60.029 50.000 0.00 0.00 0.00 3.62
5438 6115 1.633774 AGATCTGTTCAGTGTCCGGT 58.366 50.000 0.00 0.00 0.00 5.28
5439 6116 2.029020 TCAAGATCTGTTCAGTGTCCGG 60.029 50.000 0.00 0.00 0.00 5.14
5440 6117 3.303881 TCAAGATCTGTTCAGTGTCCG 57.696 47.619 0.00 0.00 0.00 4.79
5451 6128 5.518848 AGAGTGCAGTAGATCAAGATCTG 57.481 43.478 20.01 7.85 46.80 2.90
5583 6266 4.870363 GTACACAACCAACAGATGCAAAT 58.130 39.130 0.00 0.00 0.00 2.32
5584 6267 4.300189 GTACACAACCAACAGATGCAAA 57.700 40.909 0.00 0.00 0.00 3.68
5606 6289 4.181010 CAGTGGGGGCGGGAGATG 62.181 72.222 0.00 0.00 0.00 2.90
5657 6340 2.747855 GGGAGTTTGGCAGGCGAG 60.748 66.667 0.00 0.00 0.00 5.03
5694 6377 4.242811 TGGCCAAGTTCTCCTCCATATAT 58.757 43.478 0.61 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.