Multiple sequence alignment - TraesCS1D01G410800

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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 TraesCS1D01G410800 chr1D 100.000 3767 0 0 1 3767 472523451 472519685 0.000000e+00 6957.0
1 TraesCS1D01G410800 chr1A 95.742 2560 76 17 612 3148 566479897 566477348 0.000000e+00 4093.0
2 TraesCS1D01G410800 chr1A 92.259 633 20 2 3163 3767 566477279 566476648 0.000000e+00 870.0
3 TraesCS1D01G410800 chr1A 89.619 289 17 7 1 287 566480434 566480157 4.630000e-94 355.0
4 TraesCS1D01G410800 chr1A 84.043 188 25 4 371 555 566480113 566479928 3.870000e-40 176.0
5 TraesCS1D01G410800 chr1A 90.678 118 11 0 3354 3471 566476895 566476778 1.400000e-34 158.0
6 TraesCS1D01G410800 chr1B 92.486 2808 126 36 371 3152 657172836 657170088 0.000000e+00 3938.0
7 TraesCS1D01G410800 chr1B 94.097 288 8 5 1 287 657173159 657172880 2.690000e-116 429.0
8 TraesCS1D01G410800 chr1B 93.665 221 11 2 3163 3383 657169472 657169255 1.010000e-85 327.0
9 TraesCS1D01G410800 chr1B 86.174 311 25 6 3168 3470 657170018 657169718 1.690000e-83 320.0
10 TraesCS1D01G410800 chr1B 88.272 162 16 2 3382 3540 657169186 657169025 1.380000e-44 191.0
11 TraesCS1D01G410800 chr1B 96.721 61 2 0 3468 3528 657169645 657169585 6.660000e-18 102.0
12 TraesCS1D01G410800 chr1B 94.643 56 3 0 3473 3528 517347803 517347748 1.860000e-13 87.9
13 TraesCS1D01G410800 chr2A 92.279 272 18 1 3468 3739 127993576 127993844 2.120000e-102 383.0
14 TraesCS1D01G410800 chr2A 87.143 210 25 2 3530 3739 127993417 127993624 1.750000e-58 237.0
15 TraesCS1D01G410800 chr2A 96.429 56 2 0 3473 3528 649694691 649694636 4.010000e-15 93.5
16 TraesCS1D01G410800 chr2B 89.333 300 31 1 3468 3767 175897796 175898094 3.550000e-100 375.0
17 TraesCS1D01G410800 chr2B 88.732 213 22 2 3527 3739 175897634 175897844 3.730000e-65 259.0
18 TraesCS1D01G410800 chr2B 87.204 211 23 2 3529 3739 592584157 592583951 1.750000e-58 237.0
19 TraesCS1D01G410800 chr2B 90.476 63 6 0 3473 3535 592583994 592583932 2.410000e-12 84.2
20 TraesCS1D01G410800 chr2D 87.948 307 24 5 3468 3767 123098700 123099000 2.150000e-92 350.0
21 TraesCS1D01G410800 chr2D 90.196 204 18 2 3536 3739 123098547 123098748 8.020000e-67 265.0
22 TraesCS1D01G410800 chr2D 87.907 215 23 3 3536 3748 504194101 504193888 2.250000e-62 250.0


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 TraesCS1D01G410800 chr1D 472519685 472523451 3766 True 6957.0 6957 100.0000 1 3767 1 chr1D.!!$R1 3766
1 TraesCS1D01G410800 chr1A 566476648 566480434 3786 True 1130.4 4093 90.4682 1 3767 5 chr1A.!!$R1 3766
2 TraesCS1D01G410800 chr1B 657169025 657173159 4134 True 884.5 3938 91.9025 1 3540 6 chr1B.!!$R2 3539

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
308 311 0.034059 AGTTTCTCCGTCCTGCAGTG 59.966 55.0 13.81 4.33 0.0 3.66 F
897 933 0.037734 ACCCAAACCCTAAAGCCTCG 59.962 55.0 0.00 0.00 0.0 4.63 F
2346 2388 0.250727 AGGCTTTACTTTCTGGCGCA 60.251 50.0 10.83 0.00 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2100 0.826715 CCGCCTCCTCATTCTCAGAA 59.173 55.000 0.0 0.0 0.0 3.02 R
2733 2775 0.730834 CGTCTGCACTCTTCTCACCG 60.731 60.000 0.0 0.0 0.0 4.94 R
3681 4242 1.607467 GCTCAACCCAACTGCCCAT 60.607 57.895 0.0 0.0 0.0 4.00 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
79 81 8.566260 TCTCGTTGCTCTAGTAATAAGTATTCC 58.434 37.037 0.00 0.00 0.00 3.01
231 234 4.034258 GCACCGAGTGTCGTCCGA 62.034 66.667 6.02 0.00 38.40 4.55
233 236 2.281345 ACCGAGTGTCGTCCGAGT 60.281 61.111 0.00 0.00 38.40 4.18
234 237 2.323580 ACCGAGTGTCGTCCGAGTC 61.324 63.158 0.00 0.00 38.40 3.36
235 238 2.096030 CGAGTGTCGTCCGAGTCG 59.904 66.667 5.29 5.29 34.72 4.18
256 259 2.603560 GGACTCGGACAGAATAAAAGCG 59.396 50.000 0.00 0.00 0.00 4.68
258 261 2.993899 ACTCGGACAGAATAAAAGCGTG 59.006 45.455 0.00 0.00 0.00 5.34
259 262 3.250744 CTCGGACAGAATAAAAGCGTGA 58.749 45.455 0.00 0.00 0.00 4.35
270 273 2.191128 AAAGCGTGAGAGCCTGAAAT 57.809 45.000 0.00 0.00 38.01 2.17
275 278 3.624861 AGCGTGAGAGCCTGAAATTTATG 59.375 43.478 0.00 0.00 38.01 1.90
287 290 5.309323 TGAAATTTATGCTGGTACTGTGC 57.691 39.130 0.00 0.00 0.00 4.57
289 292 6.176896 TGAAATTTATGCTGGTACTGTGCTA 58.823 36.000 0.00 0.00 0.00 3.49
290 293 6.316140 TGAAATTTATGCTGGTACTGTGCTAG 59.684 38.462 4.93 4.93 0.00 3.42
291 294 4.819105 TTTATGCTGGTACTGTGCTAGT 57.181 40.909 10.59 0.12 43.56 2.57
293 296 3.703001 ATGCTGGTACTGTGCTAGTTT 57.297 42.857 10.59 0.00 40.89 2.66
294 297 3.040147 TGCTGGTACTGTGCTAGTTTC 57.960 47.619 10.59 0.00 40.89 2.78
295 298 2.632996 TGCTGGTACTGTGCTAGTTTCT 59.367 45.455 10.59 0.00 40.89 2.52
296 299 3.254892 GCTGGTACTGTGCTAGTTTCTC 58.745 50.000 10.59 0.00 40.89 2.87
297 300 3.851098 CTGGTACTGTGCTAGTTTCTCC 58.149 50.000 1.18 0.78 40.89 3.71
298 301 2.230508 TGGTACTGTGCTAGTTTCTCCG 59.769 50.000 0.00 0.00 40.89 4.63
299 302 2.230750 GGTACTGTGCTAGTTTCTCCGT 59.769 50.000 0.00 0.00 40.89 4.69
301 304 1.272769 ACTGTGCTAGTTTCTCCGTCC 59.727 52.381 0.00 0.00 35.67 4.79
302 305 1.546476 CTGTGCTAGTTTCTCCGTCCT 59.454 52.381 0.00 0.00 0.00 3.85
303 306 1.272490 TGTGCTAGTTTCTCCGTCCTG 59.728 52.381 0.00 0.00 0.00 3.86
304 307 0.246635 TGCTAGTTTCTCCGTCCTGC 59.753 55.000 0.00 0.00 0.00 4.85
305 308 0.246635 GCTAGTTTCTCCGTCCTGCA 59.753 55.000 0.00 0.00 0.00 4.41
306 309 1.737363 GCTAGTTTCTCCGTCCTGCAG 60.737 57.143 6.78 6.78 0.00 4.41
307 310 1.546476 CTAGTTTCTCCGTCCTGCAGT 59.454 52.381 13.81 0.00 0.00 4.40
308 311 0.034059 AGTTTCTCCGTCCTGCAGTG 59.966 55.000 13.81 4.33 0.00 3.66
309 312 1.301716 TTTCTCCGTCCTGCAGTGC 60.302 57.895 13.81 8.58 0.00 4.40
310 313 1.758440 TTTCTCCGTCCTGCAGTGCT 61.758 55.000 17.60 0.00 0.00 4.40
311 314 2.433838 CTCCGTCCTGCAGTGCTG 60.434 66.667 17.60 16.00 0.00 4.41
312 315 2.917227 TCCGTCCTGCAGTGCTGA 60.917 61.111 22.25 13.04 0.00 4.26
313 316 2.740055 CCGTCCTGCAGTGCTGAC 60.740 66.667 22.25 21.72 0.00 3.51
314 317 3.108289 CGTCCTGCAGTGCTGACG 61.108 66.667 31.32 31.32 43.28 4.35
315 318 2.740055 GTCCTGCAGTGCTGACGG 60.740 66.667 22.25 13.85 0.00 4.79
316 319 3.233980 TCCTGCAGTGCTGACGGT 61.234 61.111 22.25 0.00 0.00 4.83
317 320 1.906333 TCCTGCAGTGCTGACGGTA 60.906 57.895 22.25 0.00 0.00 4.02
318 321 1.738099 CCTGCAGTGCTGACGGTAC 60.738 63.158 22.25 0.00 0.00 3.34
319 322 1.738099 CTGCAGTGCTGACGGTACC 60.738 63.158 17.60 0.16 0.00 3.34
320 323 2.809601 GCAGTGCTGACGGTACCG 60.810 66.667 32.22 32.22 46.03 4.02
348 351 1.601759 GGCTGCCTGCTGTCTGAAA 60.602 57.895 12.43 0.00 42.39 2.69
349 352 1.578423 GCTGCCTGCTGTCTGAAAC 59.422 57.895 0.00 0.00 38.95 2.78
350 353 1.860484 GCTGCCTGCTGTCTGAAACC 61.860 60.000 0.00 0.00 38.95 3.27
351 354 0.250640 CTGCCTGCTGTCTGAAACCT 60.251 55.000 0.00 0.00 0.00 3.50
352 355 0.535780 TGCCTGCTGTCTGAAACCTG 60.536 55.000 0.00 0.00 0.00 4.00
353 356 1.239968 GCCTGCTGTCTGAAACCTGG 61.240 60.000 0.00 0.00 0.00 4.45
354 357 0.607489 CCTGCTGTCTGAAACCTGGG 60.607 60.000 0.00 0.00 0.00 4.45
355 358 0.397941 CTGCTGTCTGAAACCTGGGA 59.602 55.000 0.00 0.00 0.00 4.37
356 359 1.004044 CTGCTGTCTGAAACCTGGGAT 59.996 52.381 0.00 0.00 0.00 3.85
357 360 1.271543 TGCTGTCTGAAACCTGGGATG 60.272 52.381 0.00 0.00 0.00 3.51
358 361 1.271597 GCTGTCTGAAACCTGGGATGT 60.272 52.381 0.00 0.00 0.00 3.06
359 362 2.815589 GCTGTCTGAAACCTGGGATGTT 60.816 50.000 0.00 0.00 0.00 2.71
360 363 3.490348 CTGTCTGAAACCTGGGATGTTT 58.510 45.455 0.00 0.00 38.57 2.83
365 368 2.445145 TGAAACCTGGGATGTTTCCTCA 59.555 45.455 11.94 0.00 46.98 3.86
367 370 0.324943 ACCTGGGATGTTTCCTCACG 59.675 55.000 0.00 0.00 42.20 4.35
369 372 0.321564 CTGGGATGTTTCCTCACGCA 60.322 55.000 0.00 0.00 42.20 5.24
381 384 2.158871 TCCTCACGCACTGTAAGGTTTT 60.159 45.455 0.00 0.00 39.30 2.43
383 386 3.131396 CTCACGCACTGTAAGGTTTTCT 58.869 45.455 0.00 0.00 39.30 2.52
391 394 5.515270 GCACTGTAAGGTTTTCTGTTTGAAC 59.485 40.000 0.00 0.00 39.30 3.18
392 395 6.616947 CACTGTAAGGTTTTCTGTTTGAACA 58.383 36.000 0.00 0.00 39.30 3.18
403 408 2.600731 TGTTTGAACAGTGCGGTTTTG 58.399 42.857 0.00 0.00 34.30 2.44
411 416 1.002468 CAGTGCGGTTTTGTGAAGGAG 60.002 52.381 0.00 0.00 0.00 3.69
414 419 0.591659 GCGGTTTTGTGAAGGAGTCC 59.408 55.000 0.00 0.00 0.00 3.85
439 445 1.757682 TCCTGTTTGGTGTGTTGGTC 58.242 50.000 0.00 0.00 37.07 4.02
453 459 2.708861 TGTTGGTCTATGGTGTCTTGGT 59.291 45.455 0.00 0.00 0.00 3.67
473 479 1.435577 ACCACATAACGGTTTCGCTC 58.564 50.000 0.00 0.00 40.63 5.03
479 485 3.434299 ACATAACGGTTTCGCTCGAAATT 59.566 39.130 18.55 12.26 44.52 1.82
480 486 4.083696 ACATAACGGTTTCGCTCGAAATTT 60.084 37.500 18.55 14.28 44.52 1.82
555 564 6.541111 AACAAGATAACTGGAGAACGTTTC 57.459 37.500 0.46 2.05 0.00 2.78
559 568 5.480205 AGATAACTGGAGAACGTTTCTTCC 58.520 41.667 16.20 16.20 40.87 3.46
566 575 3.305608 GGAGAACGTTTCTTCCGGACTTA 60.306 47.826 1.83 0.00 40.87 2.24
570 579 5.184671 AGAACGTTTCTTCCGGACTTATAGT 59.815 40.000 1.83 0.00 36.36 2.12
643 662 8.635765 AAAACATAGCCAAAAGTTGAGAGATA 57.364 30.769 0.00 0.00 0.00 1.98
812 837 3.188786 GCCGACATGCGAGTCCAC 61.189 66.667 10.48 0.00 44.57 4.02
827 852 0.963856 TCCACGGAGTACACGCTGAT 60.964 55.000 9.50 0.00 41.61 2.90
895 931 2.556782 GCTTACCCAAACCCTAAAGCCT 60.557 50.000 0.00 0.00 34.64 4.58
897 933 0.037734 ACCCAAACCCTAAAGCCTCG 59.962 55.000 0.00 0.00 0.00 4.63
923 959 2.833582 TCCTCCTCCATCGCGTCC 60.834 66.667 5.77 0.00 0.00 4.79
941 977 1.076014 CCACCCAACCCTAACCCAC 59.924 63.158 0.00 0.00 0.00 4.61
942 978 1.721093 CCACCCAACCCTAACCCACA 61.721 60.000 0.00 0.00 0.00 4.17
945 981 1.302993 CCAACCCTAACCCACACCG 60.303 63.158 0.00 0.00 0.00 4.94
946 982 1.969589 CAACCCTAACCCACACCGC 60.970 63.158 0.00 0.00 0.00 5.68
948 984 4.770874 CCCTAACCCACACCGCCG 62.771 72.222 0.00 0.00 0.00 6.46
2058 2100 0.328258 ATGAGCCTAACCCGTTTGCT 59.672 50.000 4.54 4.54 33.89 3.91
2157 2199 1.211969 CTGTGAAGTGCATGCTGCC 59.788 57.895 20.33 6.86 44.23 4.85
2193 2235 2.210013 TGCTCGCCAGTTCCTCACT 61.210 57.895 0.00 0.00 35.35 3.41
2265 2307 4.443266 AAGCTCGAGTCCCAGCGC 62.443 66.667 15.13 0.00 40.84 5.92
2346 2388 0.250727 AGGCTTTACTTTCTGGCGCA 60.251 50.000 10.83 0.00 0.00 6.09
2661 2703 1.202417 CGTCCGGCTACAGATGATGTT 60.202 52.381 0.00 0.00 39.96 2.71
2733 2775 1.608283 GCAACTACTCAGGGTGGTGAC 60.608 57.143 0.00 0.00 39.58 3.67
2751 2793 0.315568 ACGGTGAGAAGAGTGCAGAC 59.684 55.000 0.00 0.00 0.00 3.51
2805 2848 9.007901 GCCATCTTGCTTTATCTAGATAATGTT 57.992 33.333 26.79 12.83 33.71 2.71
2982 3033 6.992123 TGACTATGCTGGTAGTTGAATATTGG 59.008 38.462 0.00 0.00 35.14 3.16
3082 3133 2.382882 TCATGAAAACCTTGTGGCACA 58.617 42.857 17.96 17.96 36.63 4.57
3102 3153 5.758784 GCACATAGTAACTTCAGATTACCCC 59.241 44.000 0.00 0.00 33.74 4.95
3148 3199 0.459063 GTGGCAATGGCTAAGCTTGC 60.459 55.000 9.86 10.63 43.47 4.01
3152 3203 0.528924 CAATGGCTAAGCTTGCTGCA 59.471 50.000 9.86 0.00 45.94 4.41
3153 3204 1.067425 CAATGGCTAAGCTTGCTGCAA 60.067 47.619 15.16 15.16 45.94 4.08
3157 3208 2.265683 GGCTAAGCTTGCTGCAATTTC 58.734 47.619 16.38 8.26 45.94 2.17
3158 3209 2.265683 GCTAAGCTTGCTGCAATTTCC 58.734 47.619 16.38 5.10 45.94 3.13
3159 3210 2.353011 GCTAAGCTTGCTGCAATTTCCA 60.353 45.455 16.38 0.03 45.94 3.53
3160 3211 2.450609 AAGCTTGCTGCAATTTCCAG 57.549 45.000 16.38 3.86 45.94 3.86
3206 3311 9.224267 CTGATAGTTTTCCATCCTATACCAATG 57.776 37.037 0.00 0.00 0.00 2.82
3231 3344 4.261614 GGGGAAAGTGAACAGCTTGTTTAG 60.262 45.833 3.56 0.00 41.28 1.85
3433 3587 2.452600 TTCTCCCTTGTTGCCTTTGT 57.547 45.000 0.00 0.00 0.00 2.83
3450 3604 3.945981 TTGTCGGCTAAGTGTGTATCA 57.054 42.857 0.00 0.00 0.00 2.15
3547 4038 2.092753 TGGGATGAGTGCTTCTGAATCC 60.093 50.000 0.00 0.00 36.24 3.01
3563 4124 4.271661 TGAATCCATCTGCTTTGCATACA 58.728 39.130 0.00 0.00 38.13 2.29
3629 4190 5.007682 AGTGTGTATCGGTTAAATGCCTTT 58.992 37.500 0.00 0.00 0.00 3.11
3692 4253 1.631405 TGAGGAAAATGGGCAGTTGG 58.369 50.000 0.00 0.00 0.00 3.77
3741 4302 7.380536 CCAACAATCATTTTCCTCTCATTTCA 58.619 34.615 0.00 0.00 0.00 2.69
3758 4319 7.544217 TCTCATTTCAAATGCATCTCATTGTTG 59.456 33.333 5.12 0.00 44.23 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 3.167945 GGCGTTACACGACGTCCG 61.168 66.667 10.58 7.63 46.05 4.79
131 134 0.878523 GCATAGCGCGGTGGATAACA 60.879 55.000 23.02 0.00 0.00 2.41
231 234 2.414994 TATTCTGTCCGAGTCCGACT 57.585 50.000 12.01 0.00 38.22 4.18
233 236 3.675228 GCTTTTATTCTGTCCGAGTCCGA 60.675 47.826 0.00 0.00 38.22 4.55
234 237 2.603560 GCTTTTATTCTGTCCGAGTCCG 59.396 50.000 0.00 0.00 0.00 4.79
235 238 2.603560 CGCTTTTATTCTGTCCGAGTCC 59.396 50.000 0.00 0.00 0.00 3.85
236 239 3.060895 CACGCTTTTATTCTGTCCGAGTC 59.939 47.826 0.00 0.00 0.00 3.36
237 240 2.993899 CACGCTTTTATTCTGTCCGAGT 59.006 45.455 0.00 0.00 0.00 4.18
238 241 3.250744 TCACGCTTTTATTCTGTCCGAG 58.749 45.455 0.00 0.00 0.00 4.63
256 259 4.201990 CCAGCATAAATTTCAGGCTCTCAC 60.202 45.833 7.86 0.00 31.30 3.51
258 261 3.950395 ACCAGCATAAATTTCAGGCTCTC 59.050 43.478 7.86 0.00 31.30 3.20
259 262 3.973425 ACCAGCATAAATTTCAGGCTCT 58.027 40.909 7.86 0.00 31.30 4.09
270 273 4.819105 ACTAGCACAGTACCAGCATAAA 57.181 40.909 4.85 0.00 34.98 1.40
275 278 3.254892 GAGAAACTAGCACAGTACCAGC 58.745 50.000 0.00 0.00 36.04 4.85
287 290 1.546476 ACTGCAGGACGGAGAAACTAG 59.454 52.381 19.93 0.00 36.36 2.57
289 292 0.034059 CACTGCAGGACGGAGAAACT 59.966 55.000 19.93 0.00 36.36 2.66
290 293 1.569479 GCACTGCAGGACGGAGAAAC 61.569 60.000 19.93 0.00 36.36 2.78
291 294 1.301716 GCACTGCAGGACGGAGAAA 60.302 57.895 19.93 0.00 36.36 2.52
293 296 2.601666 AGCACTGCAGGACGGAGA 60.602 61.111 19.93 0.00 36.36 3.71
294 297 2.433838 CAGCACTGCAGGACGGAG 60.434 66.667 19.93 1.55 39.42 4.63
295 298 2.917227 TCAGCACTGCAGGACGGA 60.917 61.111 19.93 12.52 0.00 4.69
296 299 2.740055 GTCAGCACTGCAGGACGG 60.740 66.667 19.93 10.25 0.00 4.79
297 300 3.108289 CGTCAGCACTGCAGGACG 61.108 66.667 24.46 24.46 45.79 4.79
298 301 2.154798 TACCGTCAGCACTGCAGGAC 62.155 60.000 19.93 14.14 33.80 3.85
299 302 1.906333 TACCGTCAGCACTGCAGGA 60.906 57.895 19.93 2.02 33.34 3.86
301 304 1.738099 GGTACCGTCAGCACTGCAG 60.738 63.158 13.48 13.48 0.00 4.41
302 305 2.342279 GGTACCGTCAGCACTGCA 59.658 61.111 3.30 0.00 0.00 4.41
303 306 2.809601 CGGTACCGTCAGCACTGC 60.810 66.667 26.39 0.00 34.35 4.40
313 316 2.807895 CGGTTCAGCACGGTACCG 60.808 66.667 32.22 32.22 46.22 4.02
314 317 2.433664 CCGGTTCAGCACGGTACC 60.434 66.667 0.16 0.16 44.85 3.34
348 351 0.324943 CGTGAGGAAACATCCCAGGT 59.675 55.000 0.00 0.00 0.00 4.00
349 352 1.026718 GCGTGAGGAAACATCCCAGG 61.027 60.000 0.00 0.00 0.00 4.45
350 353 0.321564 TGCGTGAGGAAACATCCCAG 60.322 55.000 0.00 0.00 0.00 4.45
351 354 0.605319 GTGCGTGAGGAAACATCCCA 60.605 55.000 0.00 0.00 0.00 4.37
352 355 0.321653 AGTGCGTGAGGAAACATCCC 60.322 55.000 0.00 0.00 0.00 3.85
353 356 0.798776 CAGTGCGTGAGGAAACATCC 59.201 55.000 0.00 0.00 0.00 3.51
354 357 1.512926 ACAGTGCGTGAGGAAACATC 58.487 50.000 0.00 0.00 0.00 3.06
355 358 2.831685 TACAGTGCGTGAGGAAACAT 57.168 45.000 0.00 0.00 0.00 2.71
356 359 2.479837 CTTACAGTGCGTGAGGAAACA 58.520 47.619 0.00 0.00 0.00 2.83
365 368 2.914059 ACAGAAAACCTTACAGTGCGT 58.086 42.857 0.00 0.00 0.00 5.24
367 370 5.243426 TCAAACAGAAAACCTTACAGTGC 57.757 39.130 0.00 0.00 0.00 4.40
369 372 6.827586 TGTTCAAACAGAAAACCTTACAGT 57.172 33.333 0.00 0.00 38.13 3.55
383 386 2.029828 ACAAAACCGCACTGTTCAAACA 60.030 40.909 0.00 0.00 37.37 2.83
391 394 1.002468 CTCCTTCACAAAACCGCACTG 60.002 52.381 0.00 0.00 0.00 3.66
392 395 1.308998 CTCCTTCACAAAACCGCACT 58.691 50.000 0.00 0.00 0.00 4.40
393 396 1.002792 GACTCCTTCACAAAACCGCAC 60.003 52.381 0.00 0.00 0.00 5.34
396 399 1.873591 CAGGACTCCTTCACAAAACCG 59.126 52.381 0.00 0.00 0.00 4.44
402 407 3.515502 CAGGATTACAGGACTCCTTCACA 59.484 47.826 0.00 0.00 37.30 3.58
403 408 3.515901 ACAGGATTACAGGACTCCTTCAC 59.484 47.826 0.00 0.00 37.30 3.18
411 416 3.502211 CACACCAAACAGGATTACAGGAC 59.498 47.826 0.00 0.00 41.22 3.85
414 419 4.261572 CCAACACACCAAACAGGATTACAG 60.262 45.833 0.00 0.00 41.22 2.74
439 445 3.973206 TGTGGTACCAAGACACCATAG 57.027 47.619 18.31 0.00 46.15 2.23
453 459 2.609350 GAGCGAAACCGTTATGTGGTA 58.391 47.619 0.00 0.00 39.29 3.25
457 463 2.068837 TTCGAGCGAAACCGTTATGT 57.931 45.000 2.42 0.00 0.00 2.29
458 464 3.651562 ATTTCGAGCGAAACCGTTATG 57.348 42.857 18.81 0.00 45.34 1.90
459 465 4.436451 GGAAATTTCGAGCGAAACCGTTAT 60.436 41.667 18.81 1.13 45.34 1.89
462 468 1.196127 GGAAATTTCGAGCGAAACCGT 59.804 47.619 18.81 8.26 45.34 4.83
473 479 4.087930 CACGTTTGGAATTCGGAAATTTCG 59.912 41.667 11.95 7.72 35.21 3.46
479 485 2.943690 TGAACACGTTTGGAATTCGGAA 59.056 40.909 0.00 0.00 0.00 4.30
480 486 2.562635 TGAACACGTTTGGAATTCGGA 58.437 42.857 0.00 0.00 0.00 4.55
555 564 6.424207 GCTTGGATTTACTATAAGTCCGGAAG 59.576 42.308 5.23 1.06 0.00 3.46
559 568 6.201044 CAGTGCTTGGATTTACTATAAGTCCG 59.799 42.308 5.86 0.00 0.00 4.79
566 575 4.235079 TGGCAGTGCTTGGATTTACTAT 57.765 40.909 16.11 0.00 0.00 2.12
570 579 3.193267 GTGATTGGCAGTGCTTGGATTTA 59.807 43.478 16.11 0.00 0.00 1.40
619 638 8.680903 CATATCTCTCAACTTTTGGCTATGTTT 58.319 33.333 0.00 0.00 0.00 2.83
802 827 1.601477 TGTACTCCGTGGACTCGCA 60.601 57.895 0.00 0.00 0.00 5.10
804 829 1.134075 CGTGTACTCCGTGGACTCG 59.866 63.158 0.00 0.00 0.00 4.18
812 837 2.385315 CACATATCAGCGTGTACTCCG 58.615 52.381 0.00 0.00 0.00 4.63
817 842 0.105964 GGCCCACATATCAGCGTGTA 59.894 55.000 0.00 0.00 0.00 2.90
855 880 8.837389 GGGTAAGCGAATATTTATTTTCTGAGT 58.163 33.333 0.00 0.00 0.00 3.41
923 959 1.076014 GTGGGTTAGGGTTGGGTGG 59.924 63.158 0.00 0.00 0.00 4.61
993 1032 4.812476 TCGAAGCCCATGGTCGCG 62.812 66.667 16.29 10.81 0.00 5.87
994 1033 3.195698 GTCGAAGCCCATGGTCGC 61.196 66.667 16.29 11.09 0.00 5.19
1800 1842 3.474570 GAGAGGATGCTGCGGGGT 61.475 66.667 0.00 0.00 0.00 4.95
2058 2100 0.826715 CCGCCTCCTCATTCTCAGAA 59.173 55.000 0.00 0.00 0.00 3.02
2265 2307 1.357258 CTGTAGCAAGCACAGCTCCG 61.357 60.000 10.20 0.00 42.32 4.63
2346 2388 5.649395 CACATAACCCAACTTCATCATGTCT 59.351 40.000 0.00 0.00 0.00 3.41
2733 2775 0.730834 CGTCTGCACTCTTCTCACCG 60.731 60.000 0.00 0.00 0.00 4.94
2982 3033 4.093998 CACAGCAGATCAACCACATAGAAC 59.906 45.833 0.00 0.00 0.00 3.01
3043 3094 1.481901 ATGCATTTGGTGGCAAGGCA 61.482 50.000 0.00 0.00 44.20 4.75
3082 3133 6.134754 ACTCGGGGTAATCTGAAGTTACTAT 58.865 40.000 0.00 0.00 33.60 2.12
3102 3153 3.624326 TGGAAATTGCAAGACAACTCG 57.376 42.857 4.94 0.00 42.27 4.18
3148 3199 4.326504 AAAGTGTTCCTGGAAATTGCAG 57.673 40.909 11.40 7.56 35.43 4.41
3152 3203 9.143155 AGTACATAAAAAGTGTTCCTGGAAATT 57.857 29.630 11.40 3.94 0.00 1.82
3153 3204 8.576442 CAGTACATAAAAAGTGTTCCTGGAAAT 58.424 33.333 11.40 0.00 0.00 2.17
3157 3208 5.473504 AGCAGTACATAAAAAGTGTTCCTGG 59.526 40.000 0.00 0.00 32.49 4.45
3158 3209 6.204688 TCAGCAGTACATAAAAAGTGTTCCTG 59.795 38.462 0.00 0.00 33.79 3.86
3159 3210 6.296026 TCAGCAGTACATAAAAAGTGTTCCT 58.704 36.000 0.00 0.00 0.00 3.36
3160 3211 6.554334 TCAGCAGTACATAAAAAGTGTTCC 57.446 37.500 0.00 0.00 0.00 3.62
3231 3344 6.207691 TGTTGAAGAAAGCATATAAAGGCC 57.792 37.500 0.00 0.00 31.05 5.19
3347 3460 5.766670 GCATTCATCCCATATGAAGAACAGA 59.233 40.000 3.65 0.00 40.80 3.41
3433 3587 5.648178 TTAACTGATACACACTTAGCCGA 57.352 39.130 0.00 0.00 0.00 5.54
3629 4190 7.140705 CACTTTCAGTAAGAAATGCACATCAA 58.859 34.615 0.00 0.00 44.75 2.57
3642 4203 8.723942 ATATAGCAGGAAACACTTTCAGTAAG 57.276 34.615 0.00 0.00 41.43 2.34
3681 4242 1.607467 GCTCAACCCAACTGCCCAT 60.607 57.895 0.00 0.00 0.00 4.00
3692 4253 5.503194 GCGAAAGAGATTATCAAGCTCAACC 60.503 44.000 6.91 0.00 46.04 3.77


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

AutoCloner maintained by Alex Coulton.