Multiple sequence alignment - TraesCS2D01G267300

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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 TraesCS2D01G267300 chr2D 100.000 4484 0 0 1 4484 326460209 326455726 0.000000e+00 8281.0
1 TraesCS2D01G267300 chr2A 96.381 3841 103 14 663 4484 390881977 390885800 0.000000e+00 6290.0
2 TraesCS2D01G267300 chr2A 95.495 111 5 0 360 470 390881242 390881352 1.280000e-40 178.0
3 TraesCS2D01G267300 chr2A 96.000 50 1 1 615 664 390881626 390881674 3.720000e-11 80.5
4 TraesCS2D01G267300 chr2B 96.213 3776 106 16 726 4484 396193490 396189735 0.000000e+00 6146.0
5 TraesCS2D01G267300 chr5D 77.033 492 57 34 3283 3768 68893812 68893371 9.700000e-57 231.0


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 TraesCS2D01G267300 chr2D 326455726 326460209 4483 True 8281.000000 8281 100.000000 1 4484 1 chr2D.!!$R1 4483
1 TraesCS2D01G267300 chr2A 390881242 390885800 4558 False 2182.833333 6290 95.958667 360 4484 3 chr2A.!!$F1 4124
2 TraesCS2D01G267300 chr2B 396189735 396193490 3755 True 6146.000000 6146 96.213000 726 4484 1 chr2B.!!$R1 3758

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
307 308 0.102300 GCCGGCCCAATACATTTCAC 59.898 55.0 18.11 0.00 0.00 3.18 F
1351 1833 0.106149 CACCTACTACCATTCCGGCC 59.894 60.0 0.00 0.00 39.03 6.13 F
1629 2112 0.827507 TCCCTTTGACTTGCAAGCCC 60.828 55.0 26.27 17.96 37.87 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 2093 0.827507 GGGCTTGCAAGTCAAAGGGA 60.828 55.0 30.67 0.0 33.65 4.20 R
2616 3101 0.962356 AAGCAATCTCCTGTTGGGCG 60.962 55.0 0.00 0.0 34.39 6.13 R
3598 4083 1.758440 AAGAACTCCTCTGTGCGGCA 61.758 55.0 0.00 0.0 33.37 5.69 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
123 124 8.300495 TGTTACAAAACAAGTTTCCAGAAAAC 57.700 30.769 0.00 0.00 42.60 2.43
124 125 8.145122 TGTTACAAAACAAGTTTCCAGAAAACT 58.855 29.630 0.00 0.00 44.77 2.66
136 137 8.045176 GTTTCCAGAAAACTTCATATACAGCT 57.955 34.615 0.00 0.00 43.30 4.24
137 138 9.162764 GTTTCCAGAAAACTTCATATACAGCTA 57.837 33.333 0.00 0.00 43.30 3.32
138 139 8.948631 TTCCAGAAAACTTCATATACAGCTAG 57.051 34.615 0.00 0.00 0.00 3.42
139 140 8.306313 TCCAGAAAACTTCATATACAGCTAGA 57.694 34.615 0.00 0.00 0.00 2.43
140 141 8.928448 TCCAGAAAACTTCATATACAGCTAGAT 58.072 33.333 0.00 0.00 0.00 1.98
141 142 9.202273 CCAGAAAACTTCATATACAGCTAGATC 57.798 37.037 0.00 0.00 0.00 2.75
142 143 9.202273 CAGAAAACTTCATATACAGCTAGATCC 57.798 37.037 0.00 0.00 0.00 3.36
143 144 8.928448 AGAAAACTTCATATACAGCTAGATCCA 58.072 33.333 0.00 0.00 0.00 3.41
144 145 9.717942 GAAAACTTCATATACAGCTAGATCCAT 57.282 33.333 0.00 0.00 0.00 3.41
177 178 8.730680 ACACTTTCATACAAATGTTGACTATCC 58.269 33.333 0.00 0.00 34.50 2.59
178 179 8.184192 CACTTTCATACAAATGTTGACTATCCC 58.816 37.037 0.00 0.00 34.50 3.85
179 180 7.339466 ACTTTCATACAAATGTTGACTATCCCC 59.661 37.037 0.00 0.00 34.50 4.81
180 181 5.690865 TCATACAAATGTTGACTATCCCCC 58.309 41.667 0.00 0.00 34.50 5.40
260 261 8.801882 AAAATCCGGATAAAAAGTGATACAGA 57.198 30.769 19.48 0.00 0.00 3.41
261 262 8.801882 AAATCCGGATAAAAAGTGATACAGAA 57.198 30.769 19.48 0.00 0.00 3.02
262 263 8.801882 AATCCGGATAAAAAGTGATACAGAAA 57.198 30.769 19.48 0.00 0.00 2.52
263 264 8.801882 ATCCGGATAAAAAGTGATACAGAAAA 57.198 30.769 17.43 0.00 0.00 2.29
264 265 8.036273 TCCGGATAAAAAGTGATACAGAAAAC 57.964 34.615 0.00 0.00 0.00 2.43
265 266 7.881232 TCCGGATAAAAAGTGATACAGAAAACT 59.119 33.333 0.00 0.00 0.00 2.66
266 267 8.175716 CCGGATAAAAAGTGATACAGAAAACTC 58.824 37.037 0.00 0.00 0.00 3.01
267 268 8.175716 CGGATAAAAAGTGATACAGAAAACTCC 58.824 37.037 0.00 0.00 0.00 3.85
268 269 8.175716 GGATAAAAAGTGATACAGAAAACTCCG 58.824 37.037 0.00 0.00 0.00 4.63
269 270 5.941948 AAAAGTGATACAGAAAACTCCGG 57.058 39.130 0.00 0.00 0.00 5.14
270 271 4.884668 AAGTGATACAGAAAACTCCGGA 57.115 40.909 2.93 2.93 0.00 5.14
271 272 4.884668 AGTGATACAGAAAACTCCGGAA 57.115 40.909 5.23 0.00 0.00 4.30
272 273 5.223449 AGTGATACAGAAAACTCCGGAAA 57.777 39.130 5.23 0.00 0.00 3.13
273 274 5.617252 AGTGATACAGAAAACTCCGGAAAA 58.383 37.500 5.23 0.00 0.00 2.29
274 275 6.059484 AGTGATACAGAAAACTCCGGAAAAA 58.941 36.000 5.23 0.00 0.00 1.94
275 276 6.715264 AGTGATACAGAAAACTCCGGAAAAAT 59.285 34.615 5.23 0.00 0.00 1.82
276 277 6.801862 GTGATACAGAAAACTCCGGAAAAATG 59.198 38.462 5.23 2.49 0.00 2.32
277 278 6.488683 TGATACAGAAAACTCCGGAAAAATGT 59.511 34.615 5.23 8.63 0.00 2.71
278 279 5.183014 ACAGAAAACTCCGGAAAAATGTC 57.817 39.130 5.23 0.00 0.00 3.06
279 280 4.219033 CAGAAAACTCCGGAAAAATGTCG 58.781 43.478 5.23 0.00 0.00 4.35
280 281 2.699251 AAACTCCGGAAAAATGTCGC 57.301 45.000 5.23 0.00 0.00 5.19
281 282 1.892209 AACTCCGGAAAAATGTCGCT 58.108 45.000 5.23 0.00 0.00 4.93
282 283 2.754946 ACTCCGGAAAAATGTCGCTA 57.245 45.000 5.23 0.00 0.00 4.26
283 284 2.344025 ACTCCGGAAAAATGTCGCTAC 58.656 47.619 5.23 0.00 0.00 3.58
284 285 2.289195 ACTCCGGAAAAATGTCGCTACA 60.289 45.455 5.23 0.00 40.69 2.74
291 292 4.124910 ATGTCGCTACATTGGCCG 57.875 55.556 0.00 0.00 44.07 6.13
292 293 1.523711 ATGTCGCTACATTGGCCGG 60.524 57.895 0.00 0.00 44.07 6.13
293 294 3.573491 GTCGCTACATTGGCCGGC 61.573 66.667 21.18 21.18 0.00 6.13
294 295 4.849310 TCGCTACATTGGCCGGCC 62.849 66.667 39.40 39.40 0.00 6.13
296 297 4.813235 GCTACATTGGCCGGCCCA 62.813 66.667 41.75 33.21 43.51 5.36
303 304 2.686632 TGGCCGGCCCAATACATT 59.313 55.556 41.75 0.00 41.82 2.71
304 305 1.000993 TGGCCGGCCCAATACATTT 59.999 52.632 41.75 0.00 41.82 2.32
305 306 1.040339 TGGCCGGCCCAATACATTTC 61.040 55.000 41.75 13.62 41.82 2.17
306 307 1.040339 GGCCGGCCCAATACATTTCA 61.040 55.000 36.64 0.00 0.00 2.69
307 308 0.102300 GCCGGCCCAATACATTTCAC 59.898 55.000 18.11 0.00 0.00 3.18
308 309 1.468985 CCGGCCCAATACATTTCACA 58.531 50.000 0.00 0.00 0.00 3.58
309 310 1.821753 CCGGCCCAATACATTTCACAA 59.178 47.619 0.00 0.00 0.00 3.33
310 311 2.430332 CCGGCCCAATACATTTCACAAT 59.570 45.455 0.00 0.00 0.00 2.71
311 312 3.118811 CCGGCCCAATACATTTCACAATT 60.119 43.478 0.00 0.00 0.00 2.32
312 313 4.502962 CGGCCCAATACATTTCACAATTT 58.497 39.130 0.00 0.00 0.00 1.82
313 314 4.934602 CGGCCCAATACATTTCACAATTTT 59.065 37.500 0.00 0.00 0.00 1.82
314 315 5.411053 CGGCCCAATACATTTCACAATTTTT 59.589 36.000 0.00 0.00 0.00 1.94
315 316 6.402011 CGGCCCAATACATTTCACAATTTTTC 60.402 38.462 0.00 0.00 0.00 2.29
316 317 6.654582 GGCCCAATACATTTCACAATTTTTCT 59.345 34.615 0.00 0.00 0.00 2.52
317 318 7.174772 GGCCCAATACATTTCACAATTTTTCTT 59.825 33.333 0.00 0.00 0.00 2.52
318 319 9.213799 GCCCAATACATTTCACAATTTTTCTTA 57.786 29.630 0.00 0.00 0.00 2.10
561 732 9.476202 AAATAAATGAGAAGAAAAGAAAACCGG 57.524 29.630 0.00 0.00 0.00 5.28
567 738 6.874134 TGAGAAGAAAAGAAAACCGGATAGAG 59.126 38.462 9.46 0.00 0.00 2.43
568 739 6.174049 AGAAGAAAAGAAAACCGGATAGAGG 58.826 40.000 9.46 0.00 0.00 3.69
569 740 5.500546 AGAAAAGAAAACCGGATAGAGGT 57.499 39.130 9.46 0.00 45.29 3.85
577 748 3.629142 ACCGGATAGAGGTTCTTTTGG 57.371 47.619 9.46 0.00 39.29 3.28
578 749 2.238898 ACCGGATAGAGGTTCTTTTGGG 59.761 50.000 9.46 0.00 39.29 4.12
579 750 2.504175 CCGGATAGAGGTTCTTTTGGGA 59.496 50.000 0.00 0.00 0.00 4.37
580 751 3.136626 CCGGATAGAGGTTCTTTTGGGAT 59.863 47.826 0.00 0.00 0.00 3.85
581 752 4.347000 CCGGATAGAGGTTCTTTTGGGATA 59.653 45.833 0.00 0.00 0.00 2.59
582 753 5.163237 CCGGATAGAGGTTCTTTTGGGATAA 60.163 44.000 0.00 0.00 0.00 1.75
583 754 6.354130 CGGATAGAGGTTCTTTTGGGATAAA 58.646 40.000 0.00 0.00 0.00 1.40
584 755 6.826741 CGGATAGAGGTTCTTTTGGGATAAAA 59.173 38.462 0.00 0.00 0.00 1.52
585 756 7.338449 CGGATAGAGGTTCTTTTGGGATAAAAA 59.662 37.037 0.00 0.00 0.00 1.94
586 757 8.687242 GGATAGAGGTTCTTTTGGGATAAAAAG 58.313 37.037 3.56 3.56 44.84 2.27
587 758 6.918067 AGAGGTTCTTTTGGGATAAAAAGG 57.082 37.500 8.98 0.00 44.02 3.11
588 759 6.620429 AGAGGTTCTTTTGGGATAAAAAGGA 58.380 36.000 8.98 0.00 44.02 3.36
595 766 9.594936 TTCTTTTGGGATAAAAAGGACATAGAA 57.405 29.630 8.98 0.00 44.02 2.10
596 767 9.594936 TCTTTTGGGATAAAAAGGACATAGAAA 57.405 29.630 8.98 0.00 44.02 2.52
598 769 9.990360 TTTTGGGATAAAAAGGACATAGAAAAC 57.010 29.630 0.00 0.00 0.00 2.43
599 770 7.712204 TGGGATAAAAAGGACATAGAAAACC 57.288 36.000 0.00 0.00 0.00 3.27
600 771 6.666113 TGGGATAAAAAGGACATAGAAAACCC 59.334 38.462 0.00 0.00 0.00 4.11
601 772 6.097839 GGGATAAAAAGGACATAGAAAACCCC 59.902 42.308 0.00 0.00 0.00 4.95
602 773 6.183360 GGATAAAAAGGACATAGAAAACCCCG 60.183 42.308 0.00 0.00 0.00 5.73
603 774 4.376225 AAAAGGACATAGAAAACCCCGA 57.624 40.909 0.00 0.00 0.00 5.14
604 775 4.376225 AAAGGACATAGAAAACCCCGAA 57.624 40.909 0.00 0.00 0.00 4.30
605 776 4.376225 AAGGACATAGAAAACCCCGAAA 57.624 40.909 0.00 0.00 0.00 3.46
606 777 4.376225 AGGACATAGAAAACCCCGAAAA 57.624 40.909 0.00 0.00 0.00 2.29
607 778 4.732065 AGGACATAGAAAACCCCGAAAAA 58.268 39.130 0.00 0.00 0.00 1.94
608 779 5.330233 AGGACATAGAAAACCCCGAAAAAT 58.670 37.500 0.00 0.00 0.00 1.82
609 780 5.185056 AGGACATAGAAAACCCCGAAAAATG 59.815 40.000 0.00 0.00 0.00 2.32
610 781 5.047590 GGACATAGAAAACCCCGAAAAATGT 60.048 40.000 0.00 0.00 0.00 2.71
611 782 6.413783 ACATAGAAAACCCCGAAAAATGTT 57.586 33.333 0.00 0.00 0.00 2.71
612 783 6.220201 ACATAGAAAACCCCGAAAAATGTTG 58.780 36.000 0.00 0.00 0.00 3.33
613 784 4.746535 AGAAAACCCCGAAAAATGTTGT 57.253 36.364 0.00 0.00 0.00 3.32
651 822 7.155328 CCCATGTAGGAGTACTAAGCTTTATG 58.845 42.308 3.20 0.00 41.22 1.90
656 827 6.062258 AGGAGTACTAAGCTTTATGGCAAA 57.938 37.500 3.20 0.00 34.17 3.68
657 828 5.880887 AGGAGTACTAAGCTTTATGGCAAAC 59.119 40.000 3.20 0.00 34.17 2.93
658 829 5.880887 GGAGTACTAAGCTTTATGGCAAACT 59.119 40.000 3.20 0.00 34.17 2.66
660 831 7.551617 GGAGTACTAAGCTTTATGGCAAACTAA 59.448 37.037 3.20 0.00 34.17 2.24
894 1371 1.213926 CCCTCCCTCCTCCAAATTCAG 59.786 57.143 0.00 0.00 0.00 3.02
931 1408 0.613292 ACGCACACAGAGGGAGAGAT 60.613 55.000 0.00 0.00 0.00 2.75
932 1409 1.341089 ACGCACACAGAGGGAGAGATA 60.341 52.381 0.00 0.00 0.00 1.98
950 1427 7.280205 GGAGAGATAGAGATAGAAAGACGATCC 59.720 44.444 0.00 0.00 32.35 3.36
955 1432 9.405587 GATAGAGATAGAAAGACGATCCAAAAG 57.594 37.037 0.00 0.00 32.35 2.27
1045 1527 2.525629 CCAACCCCAACCCCAACC 60.526 66.667 0.00 0.00 0.00 3.77
1218 1700 1.336240 GCCAAGACCAGCAACAACATC 60.336 52.381 0.00 0.00 0.00 3.06
1221 1703 1.967319 AGACCAGCAACAACATCGTT 58.033 45.000 0.00 0.00 0.00 3.85
1224 1706 0.240945 CCAGCAACAACATCGTTCCC 59.759 55.000 0.00 0.00 0.00 3.97
1351 1833 0.106149 CACCTACTACCATTCCGGCC 59.894 60.000 0.00 0.00 39.03 6.13
1498 1980 0.957395 CGCTCTTTCACCCTGTGCAT 60.957 55.000 0.00 0.00 32.98 3.96
1610 2093 8.727100 ATCTTTTAGGGGAGAATTTTGAACTT 57.273 30.769 0.00 0.00 0.00 2.66
1629 2112 0.827507 TCCCTTTGACTTGCAAGCCC 60.828 55.000 26.27 17.96 37.87 5.19
1642 2125 5.089461 TTGCAAGCCCATGGTTTGGAAAT 62.089 43.478 22.40 0.00 46.65 2.17
1713 2196 8.812329 GTTTCTGAACTGCACTGTTAGATATAG 58.188 37.037 0.00 0.00 32.91 1.31
1726 2209 6.486056 TGTTAGATATAGTTTGGGCCACAAA 58.514 36.000 5.23 10.26 46.34 2.83
1955 2440 2.912956 AGTATTTCTCCTCCAACTGCCA 59.087 45.455 0.00 0.00 0.00 4.92
1978 2463 2.362736 CACATGCAGCCTAGTCATGTT 58.637 47.619 11.84 0.00 45.86 2.71
1985 2470 6.233905 TGCAGCCTAGTCATGTTCTATTAA 57.766 37.500 0.00 0.00 0.00 1.40
2013 2498 5.261209 GCTTTTGCCATCCATACATTGTA 57.739 39.130 0.00 0.00 40.15 2.41
2281 2766 2.877168 CCTCCAAGAGAATATGTGCTGC 59.123 50.000 0.00 0.00 0.00 5.25
2288 2773 1.208052 AGAATATGTGCTGCACCGTCT 59.792 47.619 28.17 20.49 32.73 4.18
2460 2945 5.126222 TGAACATTCAGTGGTTGCAAAACTA 59.874 36.000 14.00 2.92 30.66 2.24
2531 3016 6.015856 CAGTCTCAAGTCAGTTCTTCTCCTTA 60.016 42.308 0.00 0.00 0.00 2.69
2616 3101 2.229792 TCTGTGGTTCCAAATGCTCAC 58.770 47.619 0.00 0.00 0.00 3.51
2760 3245 3.726557 AAATCAAGCACCCAGAGATCA 57.273 42.857 0.00 0.00 0.00 2.92
3032 3517 5.237815 TCAAAGGTATGCTACTGTGTTCTG 58.762 41.667 0.00 0.00 0.00 3.02
3268 3753 6.736794 GCACTGTCTTGATTTTGTTCATCCTT 60.737 38.462 0.00 0.00 0.00 3.36
3572 4057 7.544804 TGATCTAGATGGCTAGCTAATTTGA 57.455 36.000 15.72 8.07 43.13 2.69
3598 4083 2.760092 ACATGCTGTTTTGACCAACTGT 59.240 40.909 0.00 0.00 0.00 3.55
3717 4202 9.770503 CTTCATGTATAGCTGATATTGAATTGC 57.229 33.333 0.00 0.00 30.64 3.56
3773 4258 8.398665 GGTCAGAAGTTTGCTATATTAAACCTG 58.601 37.037 7.84 8.77 37.47 4.00
3824 4309 5.076873 AGCTTTTGGTGCTCCTAAAATGTA 58.923 37.500 13.91 0.00 37.81 2.29
3825 4310 5.716703 AGCTTTTGGTGCTCCTAAAATGTAT 59.283 36.000 13.91 0.00 37.81 2.29
3826 4311 5.807011 GCTTTTGGTGCTCCTAAAATGTATG 59.193 40.000 13.91 4.60 37.81 2.39
3829 4314 6.909550 TTGGTGCTCCTAAAATGTATGTTT 57.090 33.333 6.34 0.00 34.23 2.83
3830 4315 6.266168 TGGTGCTCCTAAAATGTATGTTTG 57.734 37.500 6.34 0.00 34.23 2.93
3831 4316 5.102313 GGTGCTCCTAAAATGTATGTTTGC 58.898 41.667 0.00 0.00 0.00 3.68
3833 4318 6.030228 GTGCTCCTAAAATGTATGTTTGCTC 58.970 40.000 0.00 0.00 0.00 4.26
3918 4403 6.115446 TGTTCTTGAGCCAATATAGAAGTGG 58.885 40.000 0.00 0.00 35.39 4.00
4067 4557 2.748461 TTGTTTGCCTTCTTCGTTCG 57.252 45.000 0.00 0.00 0.00 3.95
4071 4561 0.531974 TTGCCTTCTTCGTTCGTGCT 60.532 50.000 0.00 0.00 0.00 4.40
4106 4596 8.196771 GCATCATGTAAATTTCTATGGTTTCCA 58.803 33.333 12.16 0.00 38.19 3.53
4140 4630 2.278245 TGTGGATGGTTCCCTCTGATT 58.722 47.619 0.00 0.00 41.83 2.57
4162 4652 6.755542 TTTTCCTGTTGGGGTTCAAATTAT 57.244 33.333 0.00 0.00 37.08 1.28
4170 4660 3.194542 TGGGGTTCAAATTATTGGCTTCG 59.805 43.478 0.00 0.00 37.15 3.79
4264 4754 7.640597 ACAAGCTTAAAACTAGAAAACAGGT 57.359 32.000 0.00 0.00 0.00 4.00
4429 4919 4.402056 AAATACCAGTGGTACCATCTCG 57.598 45.455 24.38 12.02 41.31 4.04
4471 4972 3.685058 GCAAACGGCAGAATATGTCTTC 58.315 45.455 0.00 0.00 43.97 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 9.598517 ACTTGTTTTGTAACATGAACATGATTT 57.401 25.926 19.56 8.39 43.43 2.17
87 88 9.598517 AACTTGTTTTGTAACATGAACATGATT 57.401 25.926 19.56 12.53 43.43 2.57
88 89 9.598517 AAACTTGTTTTGTAACATGAACATGAT 57.401 25.926 19.56 11.45 43.43 2.45
89 90 8.994429 AAACTTGTTTTGTAACATGAACATGA 57.006 26.923 19.56 0.00 43.43 3.07
90 91 8.327429 GGAAACTTGTTTTGTAACATGAACATG 58.673 33.333 12.43 12.43 43.43 3.21
91 92 8.037758 TGGAAACTTGTTTTGTAACATGAACAT 58.962 29.630 0.00 0.00 43.43 2.71
92 93 7.378966 TGGAAACTTGTTTTGTAACATGAACA 58.621 30.769 0.00 0.00 43.43 3.18
93 94 7.757624 TCTGGAAACTTGTTTTGTAACATGAAC 59.242 33.333 0.00 0.00 43.43 3.18
94 95 7.831753 TCTGGAAACTTGTTTTGTAACATGAA 58.168 30.769 0.00 0.00 43.43 2.57
95 96 7.397892 TCTGGAAACTTGTTTTGTAACATGA 57.602 32.000 0.00 0.00 43.43 3.07
96 97 8.472683 TTTCTGGAAACTTGTTTTGTAACATG 57.527 30.769 0.06 0.00 43.43 3.21
97 98 8.931775 GTTTTCTGGAAACTTGTTTTGTAACAT 58.068 29.630 4.28 0.00 43.44 2.71
98 99 8.300495 GTTTTCTGGAAACTTGTTTTGTAACA 57.700 30.769 4.28 0.00 43.44 2.41
111 112 8.045176 AGCTGTATATGAAGTTTTCTGGAAAC 57.955 34.615 3.27 3.27 46.42 2.78
112 113 9.383519 CTAGCTGTATATGAAGTTTTCTGGAAA 57.616 33.333 0.00 0.00 0.00 3.13
113 114 8.758829 TCTAGCTGTATATGAAGTTTTCTGGAA 58.241 33.333 0.00 0.00 0.00 3.53
114 115 8.306313 TCTAGCTGTATATGAAGTTTTCTGGA 57.694 34.615 0.00 0.00 0.00 3.86
115 116 9.202273 GATCTAGCTGTATATGAAGTTTTCTGG 57.798 37.037 0.00 0.00 0.00 3.86
116 117 9.202273 GGATCTAGCTGTATATGAAGTTTTCTG 57.798 37.037 0.00 0.00 0.00 3.02
117 118 8.928448 TGGATCTAGCTGTATATGAAGTTTTCT 58.072 33.333 0.00 0.00 0.00 2.52
118 119 9.717942 ATGGATCTAGCTGTATATGAAGTTTTC 57.282 33.333 0.00 0.00 0.00 2.29
151 152 8.730680 GGATAGTCAACATTTGTATGAAAGTGT 58.269 33.333 0.00 0.00 35.65 3.55
152 153 8.184192 GGGATAGTCAACATTTGTATGAAAGTG 58.816 37.037 0.00 0.00 35.65 3.16
153 154 7.339466 GGGGATAGTCAACATTTGTATGAAAGT 59.661 37.037 0.00 0.00 35.65 2.66
154 155 7.201821 GGGGGATAGTCAACATTTGTATGAAAG 60.202 40.741 0.00 0.00 35.65 2.62
155 156 6.605594 GGGGGATAGTCAACATTTGTATGAAA 59.394 38.462 0.00 0.00 35.65 2.69
156 157 6.126409 GGGGGATAGTCAACATTTGTATGAA 58.874 40.000 0.00 0.00 35.65 2.57
157 158 5.690865 GGGGGATAGTCAACATTTGTATGA 58.309 41.667 0.00 0.00 35.65 2.15
178 179 4.662278 TCATAGTTTCACTTTCTTGGGGG 58.338 43.478 0.00 0.00 0.00 5.40
179 180 5.770162 ACTTCATAGTTTCACTTTCTTGGGG 59.230 40.000 0.00 0.00 0.00 4.96
180 181 6.884280 ACTTCATAGTTTCACTTTCTTGGG 57.116 37.500 0.00 0.00 0.00 4.12
234 235 9.238368 TCTGTATCACTTTTTATCCGGATTTTT 57.762 29.630 24.71 0.15 0.00 1.94
235 236 8.801882 TCTGTATCACTTTTTATCCGGATTTT 57.198 30.769 24.71 0.61 0.00 1.82
236 237 8.801882 TTCTGTATCACTTTTTATCCGGATTT 57.198 30.769 24.71 1.54 0.00 2.17
237 238 8.801882 TTTCTGTATCACTTTTTATCCGGATT 57.198 30.769 24.71 6.96 0.00 3.01
238 239 8.674607 GTTTTCTGTATCACTTTTTATCCGGAT 58.325 33.333 22.95 22.95 0.00 4.18
239 240 7.881232 AGTTTTCTGTATCACTTTTTATCCGGA 59.119 33.333 6.61 6.61 0.00 5.14
240 241 8.040716 AGTTTTCTGTATCACTTTTTATCCGG 57.959 34.615 0.00 0.00 0.00 5.14
241 242 8.175716 GGAGTTTTCTGTATCACTTTTTATCCG 58.824 37.037 0.00 0.00 0.00 4.18
242 243 8.175716 CGGAGTTTTCTGTATCACTTTTTATCC 58.824 37.037 0.00 0.00 0.00 2.59
243 244 8.175716 CCGGAGTTTTCTGTATCACTTTTTATC 58.824 37.037 0.00 0.00 0.00 1.75
244 245 7.881232 TCCGGAGTTTTCTGTATCACTTTTTAT 59.119 33.333 0.00 0.00 0.00 1.40
245 246 7.218614 TCCGGAGTTTTCTGTATCACTTTTTA 58.781 34.615 0.00 0.00 0.00 1.52
246 247 6.059484 TCCGGAGTTTTCTGTATCACTTTTT 58.941 36.000 0.00 0.00 0.00 1.94
247 248 5.617252 TCCGGAGTTTTCTGTATCACTTTT 58.383 37.500 0.00 0.00 0.00 2.27
248 249 5.223449 TCCGGAGTTTTCTGTATCACTTT 57.777 39.130 0.00 0.00 0.00 2.66
249 250 4.884668 TCCGGAGTTTTCTGTATCACTT 57.115 40.909 0.00 0.00 0.00 3.16
250 251 4.884668 TTCCGGAGTTTTCTGTATCACT 57.115 40.909 3.34 0.00 0.00 3.41
251 252 5.934935 TTTTCCGGAGTTTTCTGTATCAC 57.065 39.130 3.34 0.00 0.00 3.06
252 253 6.488683 ACATTTTTCCGGAGTTTTCTGTATCA 59.511 34.615 3.34 0.00 0.00 2.15
253 254 6.909909 ACATTTTTCCGGAGTTTTCTGTATC 58.090 36.000 3.34 0.00 0.00 2.24
254 255 6.348213 CGACATTTTTCCGGAGTTTTCTGTAT 60.348 38.462 3.34 0.00 0.00 2.29
255 256 5.049954 CGACATTTTTCCGGAGTTTTCTGTA 60.050 40.000 3.34 0.00 0.00 2.74
256 257 4.261031 CGACATTTTTCCGGAGTTTTCTGT 60.261 41.667 3.34 5.22 0.00 3.41
257 258 4.219033 CGACATTTTTCCGGAGTTTTCTG 58.781 43.478 3.34 1.79 0.00 3.02
258 259 3.304458 GCGACATTTTTCCGGAGTTTTCT 60.304 43.478 3.34 0.00 0.00 2.52
259 260 2.977829 GCGACATTTTTCCGGAGTTTTC 59.022 45.455 3.34 0.00 0.00 2.29
260 261 2.621526 AGCGACATTTTTCCGGAGTTTT 59.378 40.909 3.34 0.00 0.00 2.43
261 262 2.227194 AGCGACATTTTTCCGGAGTTT 58.773 42.857 3.34 0.00 0.00 2.66
262 263 1.892209 AGCGACATTTTTCCGGAGTT 58.108 45.000 3.34 0.00 0.00 3.01
263 264 2.289195 TGTAGCGACATTTTTCCGGAGT 60.289 45.455 3.34 0.00 0.00 3.85
264 265 2.343101 TGTAGCGACATTTTTCCGGAG 58.657 47.619 3.34 0.00 0.00 4.63
265 266 2.459060 TGTAGCGACATTTTTCCGGA 57.541 45.000 0.00 0.00 0.00 5.14
275 276 2.125310 CCGGCCAATGTAGCGACA 60.125 61.111 2.24 0.95 40.72 4.35
276 277 3.573491 GCCGGCCAATGTAGCGAC 61.573 66.667 18.11 0.00 0.00 5.19
277 278 4.849310 GGCCGGCCAATGTAGCGA 62.849 66.667 40.73 0.00 35.81 4.93
279 280 4.813235 TGGGCCGGCCAATGTAGC 62.813 66.667 44.46 26.57 37.98 3.58
280 281 0.179004 TATTGGGCCGGCCAATGTAG 60.179 55.000 44.46 0.00 38.21 2.74
281 282 0.466555 GTATTGGGCCGGCCAATGTA 60.467 55.000 44.46 26.85 38.21 2.29
282 283 1.756561 GTATTGGGCCGGCCAATGT 60.757 57.895 44.46 27.94 38.21 2.71
283 284 1.114722 ATGTATTGGGCCGGCCAATG 61.115 55.000 44.46 0.00 38.21 2.82
284 285 0.398381 AATGTATTGGGCCGGCCAAT 60.398 50.000 44.46 36.94 40.43 3.16
285 286 0.616111 AAATGTATTGGGCCGGCCAA 60.616 50.000 44.46 35.30 37.98 4.52
286 287 1.000993 AAATGTATTGGGCCGGCCA 59.999 52.632 44.46 28.13 37.98 5.36
287 288 1.040339 TGAAATGTATTGGGCCGGCC 61.040 55.000 38.57 38.57 0.00 6.13
288 289 0.102300 GTGAAATGTATTGGGCCGGC 59.898 55.000 21.18 21.18 0.00 6.13
289 290 1.468985 TGTGAAATGTATTGGGCCGG 58.531 50.000 0.00 0.00 0.00 6.13
290 291 3.799281 ATTGTGAAATGTATTGGGCCG 57.201 42.857 0.00 0.00 0.00 6.13
291 292 6.654582 AGAAAAATTGTGAAATGTATTGGGCC 59.345 34.615 0.00 0.00 0.00 5.80
292 293 7.671495 AGAAAAATTGTGAAATGTATTGGGC 57.329 32.000 0.00 0.00 0.00 5.36
339 340 9.802039 TGTTACTTTGTAGGAAAGACCAAATAT 57.198 29.630 0.00 0.00 42.04 1.28
340 341 9.629878 TTGTTACTTTGTAGGAAAGACCAAATA 57.370 29.630 0.00 0.00 42.04 1.40
341 342 8.528044 TTGTTACTTTGTAGGAAAGACCAAAT 57.472 30.769 0.00 0.00 42.04 2.32
342 343 7.941431 TTGTTACTTTGTAGGAAAGACCAAA 57.059 32.000 0.00 0.00 42.04 3.28
343 344 7.941431 TTTGTTACTTTGTAGGAAAGACCAA 57.059 32.000 0.00 0.00 42.04 3.67
344 345 9.802039 ATATTTGTTACTTTGTAGGAAAGACCA 57.198 29.630 0.00 0.00 42.04 4.02
408 409 6.260050 ACGTCTTCTTTGTACACATGAACATT 59.740 34.615 0.00 0.00 0.00 2.71
426 427 9.107367 CACTTTCTGAAATAAATGAACGTCTTC 57.893 33.333 2.88 0.00 0.00 2.87
538 709 7.811117 TCCGGTTTTCTTTTCTTCTCATTTA 57.189 32.000 0.00 0.00 0.00 1.40
542 713 6.765403 TCTATCCGGTTTTCTTTTCTTCTCA 58.235 36.000 0.00 0.00 0.00 3.27
545 716 5.938710 ACCTCTATCCGGTTTTCTTTTCTTC 59.061 40.000 0.00 0.00 0.00 2.87
548 719 5.938710 AGAACCTCTATCCGGTTTTCTTTTC 59.061 40.000 0.00 0.00 44.41 2.29
549 720 5.877491 AGAACCTCTATCCGGTTTTCTTTT 58.123 37.500 0.00 0.00 44.41 2.27
553 724 5.106277 CCAAAAGAACCTCTATCCGGTTTTC 60.106 44.000 0.00 0.00 44.41 2.29
558 729 2.504175 TCCCAAAAGAACCTCTATCCGG 59.496 50.000 0.00 0.00 0.00 5.14
559 730 3.906720 TCCCAAAAGAACCTCTATCCG 57.093 47.619 0.00 0.00 0.00 4.18
560 731 8.589701 TTTTTATCCCAAAAGAACCTCTATCC 57.410 34.615 0.00 0.00 0.00 2.59
561 732 8.687242 CCTTTTTATCCCAAAAGAACCTCTATC 58.313 37.037 7.36 0.00 43.70 2.08
567 738 6.413783 TGTCCTTTTTATCCCAAAAGAACC 57.586 37.500 7.36 0.00 43.70 3.62
568 739 9.020731 TCTATGTCCTTTTTATCCCAAAAGAAC 57.979 33.333 7.36 0.00 43.70 3.01
569 740 9.594936 TTCTATGTCCTTTTTATCCCAAAAGAA 57.405 29.630 7.36 0.00 43.70 2.52
570 741 9.594936 TTTCTATGTCCTTTTTATCCCAAAAGA 57.405 29.630 7.36 0.00 43.70 2.52
572 743 9.990360 GTTTTCTATGTCCTTTTTATCCCAAAA 57.010 29.630 0.00 0.00 0.00 2.44
573 744 8.590204 GGTTTTCTATGTCCTTTTTATCCCAAA 58.410 33.333 0.00 0.00 0.00 3.28
574 745 7.179516 GGGTTTTCTATGTCCTTTTTATCCCAA 59.820 37.037 0.00 0.00 0.00 4.12
575 746 6.666113 GGGTTTTCTATGTCCTTTTTATCCCA 59.334 38.462 0.00 0.00 0.00 4.37
576 747 6.097839 GGGGTTTTCTATGTCCTTTTTATCCC 59.902 42.308 0.00 0.00 0.00 3.85
577 748 6.183360 CGGGGTTTTCTATGTCCTTTTTATCC 60.183 42.308 0.00 0.00 0.00 2.59
578 749 6.600427 TCGGGGTTTTCTATGTCCTTTTTATC 59.400 38.462 0.00 0.00 0.00 1.75
579 750 6.486941 TCGGGGTTTTCTATGTCCTTTTTAT 58.513 36.000 0.00 0.00 0.00 1.40
580 751 5.878627 TCGGGGTTTTCTATGTCCTTTTTA 58.121 37.500 0.00 0.00 0.00 1.52
581 752 4.732065 TCGGGGTTTTCTATGTCCTTTTT 58.268 39.130 0.00 0.00 0.00 1.94
582 753 4.376225 TCGGGGTTTTCTATGTCCTTTT 57.624 40.909 0.00 0.00 0.00 2.27
583 754 4.376225 TTCGGGGTTTTCTATGTCCTTT 57.624 40.909 0.00 0.00 0.00 3.11
584 755 4.376225 TTTCGGGGTTTTCTATGTCCTT 57.624 40.909 0.00 0.00 0.00 3.36
585 756 4.376225 TTTTCGGGGTTTTCTATGTCCT 57.624 40.909 0.00 0.00 0.00 3.85
586 757 5.047590 ACATTTTTCGGGGTTTTCTATGTCC 60.048 40.000 0.00 0.00 0.00 4.02
587 758 6.020971 ACATTTTTCGGGGTTTTCTATGTC 57.979 37.500 0.00 0.00 0.00 3.06
588 759 6.183360 ACAACATTTTTCGGGGTTTTCTATGT 60.183 34.615 0.00 0.00 0.00 2.29
589 760 6.220201 ACAACATTTTTCGGGGTTTTCTATG 58.780 36.000 0.00 0.00 0.00 2.23
590 761 6.413783 ACAACATTTTTCGGGGTTTTCTAT 57.586 33.333 0.00 0.00 0.00 1.98
591 762 5.855740 ACAACATTTTTCGGGGTTTTCTA 57.144 34.783 0.00 0.00 0.00 2.10
592 763 4.746535 ACAACATTTTTCGGGGTTTTCT 57.253 36.364 0.00 0.00 0.00 2.52
593 764 5.811100 TGTAACAACATTTTTCGGGGTTTTC 59.189 36.000 0.00 0.00 0.00 2.29
594 765 5.731591 TGTAACAACATTTTTCGGGGTTTT 58.268 33.333 0.00 0.00 0.00 2.43
595 766 5.340439 TGTAACAACATTTTTCGGGGTTT 57.660 34.783 0.00 0.00 0.00 3.27
596 767 5.293560 CATGTAACAACATTTTTCGGGGTT 58.706 37.500 0.00 0.00 0.00 4.11
597 768 4.262249 CCATGTAACAACATTTTTCGGGGT 60.262 41.667 0.00 0.00 0.00 4.95
598 769 4.241681 CCATGTAACAACATTTTTCGGGG 58.758 43.478 0.00 0.00 0.00 5.73
599 770 4.241681 CCCATGTAACAACATTTTTCGGG 58.758 43.478 0.00 0.00 0.00 5.14
600 771 3.677596 GCCCATGTAACAACATTTTTCGG 59.322 43.478 0.00 0.00 0.00 4.30
601 772 3.677596 GGCCCATGTAACAACATTTTTCG 59.322 43.478 0.00 0.00 0.00 3.46
602 773 3.677596 CGGCCCATGTAACAACATTTTTC 59.322 43.478 0.00 0.00 0.00 2.29
603 774 3.556004 CCGGCCCATGTAACAACATTTTT 60.556 43.478 0.00 0.00 0.00 1.94
604 775 2.028567 CCGGCCCATGTAACAACATTTT 60.029 45.455 0.00 0.00 0.00 1.82
605 776 1.548269 CCGGCCCATGTAACAACATTT 59.452 47.619 0.00 0.00 0.00 2.32
606 777 1.181786 CCGGCCCATGTAACAACATT 58.818 50.000 0.00 0.00 0.00 2.71
607 778 1.319614 GCCGGCCCATGTAACAACAT 61.320 55.000 18.11 0.00 0.00 2.71
608 779 1.974343 GCCGGCCCATGTAACAACA 60.974 57.895 18.11 0.00 0.00 3.33
609 780 2.706834 GGCCGGCCCATGTAACAAC 61.707 63.158 36.64 4.38 0.00 3.32
610 781 2.361865 GGCCGGCCCATGTAACAA 60.362 61.111 36.64 0.00 0.00 2.83
656 827 5.063880 CCTAGCCCGCAAAGATTAATTAGT 58.936 41.667 0.00 0.00 0.00 2.24
657 828 5.305585 TCCTAGCCCGCAAAGATTAATTAG 58.694 41.667 0.00 0.00 0.00 1.73
658 829 5.071250 TCTCCTAGCCCGCAAAGATTAATTA 59.929 40.000 0.00 0.00 0.00 1.40
660 831 3.391296 TCTCCTAGCCCGCAAAGATTAAT 59.609 43.478 0.00 0.00 0.00 1.40
667 1141 1.964223 CTCTATCTCCTAGCCCGCAAA 59.036 52.381 0.00 0.00 0.00 3.68
894 1371 0.933047 GTCTCGGCGGTTTTTGTTGC 60.933 55.000 7.21 0.00 0.00 4.17
931 1408 8.521170 TCTTTTGGATCGTCTTTCTATCTCTA 57.479 34.615 0.00 0.00 0.00 2.43
932 1409 7.411486 TCTTTTGGATCGTCTTTCTATCTCT 57.589 36.000 0.00 0.00 0.00 3.10
950 1427 6.147864 AGATCTCGATCTCTCCTTCTTTTG 57.852 41.667 3.63 0.00 44.37 2.44
955 1432 5.160607 TCCTAGATCTCGATCTCTCCTTC 57.839 47.826 12.39 0.00 44.37 3.46
1045 1527 3.732849 GGAGGAGTTGGGGCTGGG 61.733 72.222 0.00 0.00 0.00 4.45
1186 1668 2.747855 CTTGGCGAAGAGGTGGGC 60.748 66.667 1.62 0.00 0.00 5.36
1498 1980 2.679450 CATAACGTCGAACAAGTGGGA 58.321 47.619 0.00 0.00 0.00 4.37
1554 2037 1.069049 CAAGCAAACAAGGGGTTGGAG 59.931 52.381 0.00 0.00 40.35 3.86
1610 2093 0.827507 GGGCTTGCAAGTCAAAGGGA 60.828 55.000 30.67 0.00 33.65 4.20
1629 2112 6.016360 TGACAGTAGACAATTTCCAAACCATG 60.016 38.462 0.00 0.00 0.00 3.66
1646 2129 8.391106 GGCAAGAATTACAACTTATGACAGTAG 58.609 37.037 0.00 0.00 0.00 2.57
1726 2209 8.807118 CATCTACTATCCATGTAACTGGTATGT 58.193 37.037 0.00 0.00 37.57 2.29
1729 2212 6.210784 GCCATCTACTATCCATGTAACTGGTA 59.789 42.308 0.00 0.00 37.57 3.25
1955 2440 1.206878 TGACTAGGCTGCATGTGGAT 58.793 50.000 0.50 0.00 0.00 3.41
1978 2463 6.542370 GGATGGCAAAAGCTACACTTAATAGA 59.458 38.462 0.00 0.00 37.75 1.98
1985 2470 2.584835 TGGATGGCAAAAGCTACACT 57.415 45.000 0.00 0.00 0.00 3.55
2013 2498 8.109634 ACCAGGTGATAAACTGAAATCTAATGT 58.890 33.333 0.00 0.00 36.86 2.71
2281 2766 1.798813 GGTTCAAGCTTGTAGACGGTG 59.201 52.381 25.19 0.00 0.00 4.94
2322 2807 8.480643 AAATGACTGTCAAGTTATGCTAGTAC 57.519 34.615 15.31 0.00 36.52 2.73
2616 3101 0.962356 AAGCAATCTCCTGTTGGGCG 60.962 55.000 0.00 0.00 34.39 6.13
2760 3245 5.221702 CCCTTTCACATGTTCCCTTTTTGAT 60.222 40.000 0.00 0.00 0.00 2.57
3237 3722 4.520111 ACAAAATCAAGACAGTGCAGCATA 59.480 37.500 0.00 0.00 0.00 3.14
3598 4083 1.758440 AAGAACTCCTCTGTGCGGCA 61.758 55.000 0.00 0.00 33.37 5.69
3745 4230 7.407337 GTTTAATATAGCAAACTTCTGACCCG 58.593 38.462 5.23 0.00 32.96 5.28
3773 4258 4.869861 GCAAACCATGGAAAATACCATCAC 59.130 41.667 21.47 0.00 46.24 3.06
3824 4309 4.331168 GCTCTAATTCACTCGAGCAAACAT 59.669 41.667 13.61 2.95 46.06 2.71
3825 4310 3.679980 GCTCTAATTCACTCGAGCAAACA 59.320 43.478 13.61 0.00 46.06 2.83
3826 4311 4.251960 GCTCTAATTCACTCGAGCAAAC 57.748 45.455 13.61 0.00 46.06 2.93
3830 4315 5.751028 ACTTTATGCTCTAATTCACTCGAGC 59.249 40.000 13.61 0.00 46.74 5.03
3831 4316 7.159437 CACTTTATGCTCTAATTCACTCGAG 57.841 40.000 11.84 11.84 0.00 4.04
3874 4359 7.674120 AGAACATCACATCTGCATTAGCTATA 58.326 34.615 0.00 0.00 42.74 1.31
3878 4363 5.065602 TCAAGAACATCACATCTGCATTAGC 59.934 40.000 0.00 0.00 42.57 3.09
3918 4403 3.002348 GCACAAATACCTACGATTCTGCC 59.998 47.826 0.00 0.00 0.00 4.85
4062 4552 0.368227 GCAAGAGATGAGCACGAACG 59.632 55.000 0.00 0.00 0.00 3.95
4067 4557 2.943690 ACATGATGCAAGAGATGAGCAC 59.056 45.455 0.00 0.00 41.60 4.40
4071 4561 8.515695 AGAAATTTACATGATGCAAGAGATGA 57.484 30.769 0.00 0.00 0.00 2.92
4106 4596 3.708631 CCATCCACATAAGGAGAGAGTGT 59.291 47.826 0.00 0.00 41.90 3.55
4140 4630 6.465035 CCAATAATTTGAACCCCAACAGGAAA 60.465 38.462 0.00 0.00 34.10 3.13
4162 4652 4.344102 AGCCATAAGTATCTACGAAGCCAA 59.656 41.667 0.00 0.00 0.00 4.52
4264 4754 4.209538 CCCATATGCTTTTCATCTGGACA 58.790 43.478 9.89 0.00 46.67 4.02
4403 4893 4.107127 TGGTACCACTGGTATTTTTGCT 57.893 40.909 11.60 0.00 40.54 3.91


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

AutoCloner maintained by Alex Coulton.