Multiple sequence alignment - TraesCS3A01G185700

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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 TraesCS3A01G185700 chr3A 100.000 5529 0 0 1 5529 217987298 217981770 0.000000e+00 10211.0
1 TraesCS3A01G185700 chr3D 96.043 5383 137 30 1 5367 177374027 177368705 0.000000e+00 8691.0
2 TraesCS3A01G185700 chr3D 98.324 179 3 0 5330 5508 177368704 177368526 1.160000e-81 315.0
3 TraesCS3A01G185700 chr3D 100.000 34 0 0 5496 5529 177368527 177368494 4.620000e-06 63.9
4 TraesCS3A01G185700 chr3B 96.022 2363 67 8 3012 5367 256252462 256250120 0.000000e+00 3818.0
5 TraesCS3A01G185700 chr3B 94.981 1335 48 10 693 2021 256255127 256253806 0.000000e+00 2076.0
6 TraesCS3A01G185700 chr3B 91.250 720 30 9 2323 3026 256253289 256252587 0.000000e+00 950.0
7 TraesCS3A01G185700 chr3B 87.102 566 66 4 1 560 491522949 491522385 7.810000e-178 634.0
8 TraesCS3A01G185700 chr3B 92.880 309 16 4 2020 2324 256253712 256253406 1.410000e-120 444.0
9 TraesCS3A01G185700 chr3B 97.500 200 5 0 5330 5529 256250119 256249920 5.300000e-90 342.0
10 TraesCS3A01G185700 chr3B 93.714 175 10 1 501 675 256255430 256255257 1.530000e-65 261.0
11 TraesCS3A01G185700 chr5B 86.926 566 67 4 1 560 672843461 672844025 3.640000e-176 628.0
12 TraesCS3A01G185700 chr7B 86.572 566 66 5 1 560 678853676 678854237 2.830000e-172 616.0
13 TraesCS3A01G185700 chr7B 86.551 461 60 2 1 459 520113338 520112878 1.780000e-139 507.0
14 TraesCS3A01G185700 chr6B 88.254 315 34 3 1 313 42760438 42760751 1.880000e-99 374.0
15 TraesCS3A01G185700 chr2A 74.265 272 57 10 124 387 468286474 468286208 9.800000e-18 102.0


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 TraesCS3A01G185700 chr3A 217981770 217987298 5528 True 10211.000000 10211 100.000000 1 5529 1 chr3A.!!$R1 5528
1 TraesCS3A01G185700 chr3D 177368494 177374027 5533 True 3023.300000 8691 98.122333 1 5529 3 chr3D.!!$R1 5528
2 TraesCS3A01G185700 chr3B 256249920 256255430 5510 True 1315.166667 3818 94.391167 501 5529 6 chr3B.!!$R2 5028
3 TraesCS3A01G185700 chr3B 491522385 491522949 564 True 634.000000 634 87.102000 1 560 1 chr3B.!!$R1 559
4 TraesCS3A01G185700 chr5B 672843461 672844025 564 False 628.000000 628 86.926000 1 560 1 chr5B.!!$F1 559
5 TraesCS3A01G185700 chr7B 678853676 678854237 561 False 616.000000 616 86.572000 1 560 1 chr7B.!!$F1 559

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
88 89 0.687354 AACTCTCCACATGCGTCCTT 59.313 50.000 0.00 0.00 0.00 3.36 F
165 166 0.899720 TCGGACCCGCTTTCAGTAAT 59.100 50.000 3.13 0.00 39.59 1.89 F
908 1033 1.299089 GTGCCTCCAACGTGTTTGC 60.299 57.895 0.00 0.00 33.34 3.68 F
1554 1680 1.005037 GGACAGCACACATCGGTCA 60.005 57.895 0.00 0.00 31.70 4.02 F
2495 2852 2.061220 CCAGTCACAGCCCTTCTCA 58.939 57.895 0.00 0.00 0.00 3.27 F
2750 3107 1.030488 ATTACCTGCTGCTGCTGCTG 61.030 55.000 27.67 25.97 40.48 4.41 F
3197 3697 4.895297 ACCCAACAATCAACATTCTCTTGT 59.105 37.500 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 1336 0.030603 GAGGAGTTGGGGGAGAGGAT 60.031 60.0 0.00 0.00 0.00 3.24 R
1236 1362 0.764890 CTGTGGTTGAGGGAGGACAA 59.235 55.0 0.00 0.00 0.00 3.18 R
2750 3107 0.607489 TTCCCTCTTGAAGCAGCAGC 60.607 55.0 0.00 0.00 42.56 5.25 R
2751 3108 1.901591 TTTCCCTCTTGAAGCAGCAG 58.098 50.0 0.00 0.00 0.00 4.24 R
3724 4225 0.391927 TTCCCGTAAAGGCATCGGTG 60.392 55.0 0.00 0.00 42.30 4.94 R
4169 4674 5.182001 ACATGTACAATTCAGTTCTGAAGCC 59.818 40.0 18.03 6.94 0.00 4.35 R
4775 5286 0.620556 GGATCCAAGCAGGTCTGGAA 59.379 55.0 6.95 0.00 39.02 3.53 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
32 33 2.028190 CGGACTGCTAGGCATCCG 59.972 66.667 19.77 19.77 45.17 4.18
61 62 4.403432 CCTCCCATATGTTGACATTTGCTT 59.597 41.667 1.46 0.00 37.76 3.91
78 79 2.037251 TGCTTCAGTACCAACTCTCCAC 59.963 50.000 0.00 0.00 31.97 4.02
82 83 2.028112 TCAGTACCAACTCTCCACATGC 60.028 50.000 0.00 0.00 31.97 4.06
88 89 0.687354 AACTCTCCACATGCGTCCTT 59.313 50.000 0.00 0.00 0.00 3.36
96 97 3.438781 TCCACATGCGTCCTTTCATAAAC 59.561 43.478 0.00 0.00 0.00 2.01
122 123 5.386958 CGTAGCCCAACTATTATGCTCTA 57.613 43.478 0.00 0.00 32.15 2.43
140 141 5.483937 TGCTCTACCAAGTAAAAGAGGATCA 59.516 40.000 0.00 0.00 37.82 2.92
143 144 7.171630 TCTACCAAGTAAAAGAGGATCACTC 57.828 40.000 0.00 0.00 46.98 3.51
165 166 0.899720 TCGGACCCGCTTTCAGTAAT 59.100 50.000 3.13 0.00 39.59 1.89
186 189 6.758806 AATTCCATCGGGGTAATACTTAGT 57.241 37.500 0.00 0.00 38.11 2.24
192 195 6.014499 CCATCGGGGTAATACTTAGTTCTGAT 60.014 42.308 0.00 0.00 0.00 2.90
268 271 4.745125 GCTAACATAGCGAGACTAAATGCA 59.255 41.667 0.00 0.00 42.62 3.96
274 277 2.749076 AGCGAGACTAAATGCATGCAAA 59.251 40.909 26.68 12.36 0.00 3.68
275 278 3.191162 AGCGAGACTAAATGCATGCAAAA 59.809 39.130 26.68 11.98 0.00 2.44
277 280 4.726416 CGAGACTAAATGCATGCAAAACT 58.274 39.130 26.68 17.00 0.00 2.66
285 288 4.870123 ATGCATGCAAAACTCTAAACCA 57.130 36.364 26.68 0.00 0.00 3.67
294 297 4.373156 AAACTCTAAACCACATGCCTCT 57.627 40.909 0.00 0.00 0.00 3.69
304 307 5.904362 ACCACATGCCTCTATTCTTTTTC 57.096 39.130 0.00 0.00 0.00 2.29
308 311 4.396166 ACATGCCTCTATTCTTTTTCGGTG 59.604 41.667 0.00 0.00 0.00 4.94
313 316 4.396166 CCTCTATTCTTTTTCGGTGCACAT 59.604 41.667 20.43 2.33 0.00 3.21
322 325 4.855715 TTTCGGTGCACATATTTTCCAA 57.144 36.364 20.43 0.00 0.00 3.53
336 339 2.498644 TTCCAACACGCCCATCAATA 57.501 45.000 0.00 0.00 0.00 1.90
337 340 2.727123 TCCAACACGCCCATCAATAT 57.273 45.000 0.00 0.00 0.00 1.28
387 390 5.774690 TCCACCAAAAGCTAGACATTTCATT 59.225 36.000 0.00 0.00 0.00 2.57
465 468 5.669164 AGGAGAGACTGGATAACAACTTC 57.331 43.478 0.00 0.00 0.00 3.01
473 476 8.567285 AGACTGGATAACAACTTCCAATAAAG 57.433 34.615 0.00 0.00 41.36 1.85
484 487 5.528870 ACTTCCAATAAAGTTTCTTTGCCG 58.471 37.500 5.19 0.00 36.02 5.69
503 510 2.550606 CCGTCCACCGAAATTTTTCTCA 59.449 45.455 0.00 0.00 39.56 3.27
507 514 3.954904 TCCACCGAAATTTTTCTCACCAA 59.045 39.130 0.00 0.00 35.07 3.67
509 516 5.069781 TCCACCGAAATTTTTCTCACCAAAT 59.930 36.000 0.00 0.00 35.07 2.32
514 521 6.088085 CCGAAATTTTTCTCACCAAATCTTCG 59.912 38.462 0.00 0.00 35.50 3.79
620 627 6.761312 TGAAAAACTGCCATCATTTGATCTT 58.239 32.000 0.00 0.00 31.21 2.40
672 679 5.368523 TGAGTTTCTTCCCAGAGAACCTTTA 59.631 40.000 0.00 0.00 35.50 1.85
673 680 5.622180 AGTTTCTTCCCAGAGAACCTTTAC 58.378 41.667 0.00 0.00 35.50 2.01
674 681 4.635699 TTCTTCCCAGAGAACCTTTACC 57.364 45.455 0.00 0.00 30.98 2.85
675 682 3.870559 TCTTCCCAGAGAACCTTTACCT 58.129 45.455 0.00 0.00 0.00 3.08
676 683 5.019657 TCTTCCCAGAGAACCTTTACCTA 57.980 43.478 0.00 0.00 0.00 3.08
677 684 5.600749 TCTTCCCAGAGAACCTTTACCTAT 58.399 41.667 0.00 0.00 0.00 2.57
678 685 6.748969 TCTTCCCAGAGAACCTTTACCTATA 58.251 40.000 0.00 0.00 0.00 1.31
873 998 3.482722 CAGCAGCTGGAAACAAGTATG 57.517 47.619 17.12 0.00 42.06 2.39
874 999 3.076621 CAGCAGCTGGAAACAAGTATGA 58.923 45.455 17.12 0.00 42.06 2.15
875 1000 3.693085 CAGCAGCTGGAAACAAGTATGAT 59.307 43.478 17.12 0.00 42.06 2.45
876 1001 3.944015 AGCAGCTGGAAACAAGTATGATC 59.056 43.478 17.12 0.00 42.06 2.92
877 1002 3.944015 GCAGCTGGAAACAAGTATGATCT 59.056 43.478 17.12 0.00 42.06 2.75
878 1003 4.397417 GCAGCTGGAAACAAGTATGATCTT 59.603 41.667 17.12 0.00 42.06 2.40
879 1004 5.675575 GCAGCTGGAAACAAGTATGATCTTG 60.676 44.000 17.12 5.12 46.89 3.02
880 1005 4.397417 AGCTGGAAACAAGTATGATCTTGC 59.603 41.667 6.38 0.00 45.86 4.01
908 1033 1.299089 GTGCCTCCAACGTGTTTGC 60.299 57.895 0.00 0.00 33.34 3.68
1210 1336 3.607299 TCCCTTCCGTCCCCTCCA 61.607 66.667 0.00 0.00 0.00 3.86
1219 1345 1.460497 GTCCCCTCCATCCTCTCCC 60.460 68.421 0.00 0.00 0.00 4.30
1222 1348 2.705410 CCTCCATCCTCTCCCCCA 59.295 66.667 0.00 0.00 0.00 4.96
1236 1362 2.204151 CCCAACTCCTCCACCCCT 60.204 66.667 0.00 0.00 0.00 4.79
1239 1365 1.427072 CCAACTCCTCCACCCCTTGT 61.427 60.000 0.00 0.00 0.00 3.16
1242 1368 1.229658 CTCCTCCACCCCTTGTCCT 60.230 63.158 0.00 0.00 0.00 3.85
1243 1369 1.229529 TCCTCCACCCCTTGTCCTC 60.230 63.158 0.00 0.00 0.00 3.71
1257 1383 2.224159 TCCTCCCTCAACCACAGCC 61.224 63.158 0.00 0.00 0.00 4.85
1263 1389 1.079543 CTCAACCACAGCCTCCTCG 60.080 63.158 0.00 0.00 0.00 4.63
1473 1599 2.529389 AAGAGCGTGGAAGGGGGT 60.529 61.111 0.00 0.00 0.00 4.95
1554 1680 1.005037 GGACAGCACACATCGGTCA 60.005 57.895 0.00 0.00 31.70 4.02
1653 1779 2.125512 GCCGCATCGTCTTCTGGT 60.126 61.111 0.00 0.00 0.00 4.00
1781 1907 3.511699 CGTAAGAGCATGCTCAAGTGTA 58.488 45.455 40.91 24.17 44.99 2.90
1914 2041 3.062639 ACTCATGCGAGAAATTGCTAACG 59.937 43.478 0.00 0.00 42.34 3.18
2495 2852 2.061220 CCAGTCACAGCCCTTCTCA 58.939 57.895 0.00 0.00 0.00 3.27
2750 3107 1.030488 ATTACCTGCTGCTGCTGCTG 61.030 55.000 27.67 25.97 40.48 4.41
3122 3622 5.769662 TGTTTATTTGCCTCTGAGTGATGTT 59.230 36.000 3.66 0.00 0.00 2.71
3197 3697 4.895297 ACCCAACAATCAACATTCTCTTGT 59.105 37.500 0.00 0.00 0.00 3.16
3620 4120 5.695851 AGTGTTTACTTTTCTGCATCTGG 57.304 39.130 0.00 0.00 31.66 3.86
3724 4225 6.605194 TCATGATATATCTGTCTACTCCCTGC 59.395 42.308 13.79 0.00 0.00 4.85
4169 4674 2.372504 AGGATTCTGGCTCATCATGGAG 59.627 50.000 0.00 0.00 37.97 3.86
4306 4814 2.363788 TCGTTGTGTCTGATGTAGGC 57.636 50.000 0.00 0.00 0.00 3.93
4635 5143 3.286329 TCATTGCACATGGAGCTGTAT 57.714 42.857 12.69 2.87 0.00 2.29
4775 5286 9.662545 CACATCAAAACTTTTGAAACAGTTTTT 57.337 25.926 18.57 10.03 46.42 1.94
4923 5435 1.338105 TGGTCACATTCTCTGCGGAAG 60.338 52.381 0.00 0.00 0.00 3.46
5042 5554 4.647424 TGGCTTTCGTTTTGAAGTTCAT 57.353 36.364 6.36 0.00 37.99 2.57
5083 5595 1.529244 GGCTTGGTCAAGGTGCACT 60.529 57.895 17.98 0.00 38.80 4.40
5301 5814 3.670359 CGTTGATGGTTGTATGGCTTGTG 60.670 47.826 0.00 0.00 0.00 3.33
5337 5850 2.483877 TGTTACTGCACAAGCTACATGC 59.516 45.455 9.28 9.28 42.74 4.06
5424 5975 3.044156 ACTACTGGTCTGATGCATCCAT 58.956 45.455 23.67 7.94 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.028112 GCATGTGGAGAGTTGGTACTGA 60.028 50.000 0.00 0.00 33.84 3.41
78 79 3.416277 CACGTTTATGAAAGGACGCATG 58.584 45.455 0.00 0.00 38.97 4.06
82 83 1.458064 ACGCACGTTTATGAAAGGACG 59.542 47.619 0.00 0.00 41.00 4.79
88 89 1.337917 TGGGCTACGCACGTTTATGAA 60.338 47.619 0.00 0.00 32.76 2.57
96 97 2.212869 TAATAGTTGGGCTACGCACG 57.787 50.000 0.00 0.00 32.76 5.34
140 141 0.320508 GAAAGCGGGTCCGAAAGAGT 60.321 55.000 14.15 0.00 42.83 3.24
143 144 0.602905 ACTGAAAGCGGGTCCGAAAG 60.603 55.000 14.15 4.92 41.75 2.62
165 166 5.901276 AGAACTAAGTATTACCCCGATGGAA 59.099 40.000 0.00 0.00 38.00 3.53
186 189 5.588246 TCTTTGTGTGCAACTGTTATCAGAA 59.412 36.000 7.81 0.00 43.76 3.02
192 195 5.809562 CCAAATTCTTTGTGTGCAACTGTTA 59.190 36.000 0.00 0.00 38.98 2.41
265 268 3.382865 TGTGGTTTAGAGTTTTGCATGCA 59.617 39.130 18.46 18.46 0.00 3.96
268 271 4.559153 GCATGTGGTTTAGAGTTTTGCAT 58.441 39.130 0.00 0.00 0.00 3.96
274 277 5.700402 ATAGAGGCATGTGGTTTAGAGTT 57.300 39.130 0.00 0.00 0.00 3.01
275 278 5.426833 AGAATAGAGGCATGTGGTTTAGAGT 59.573 40.000 0.00 0.00 0.00 3.24
277 280 5.957771 AGAATAGAGGCATGTGGTTTAGA 57.042 39.130 0.00 0.00 0.00 2.10
285 288 4.396166 CACCGAAAAAGAATAGAGGCATGT 59.604 41.667 0.00 0.00 0.00 3.21
294 297 7.757624 GGAAAATATGTGCACCGAAAAAGAATA 59.242 33.333 15.69 2.21 0.00 1.75
304 307 3.241701 GTGTTGGAAAATATGTGCACCG 58.758 45.455 15.69 0.00 0.00 4.94
308 311 2.258755 GGCGTGTTGGAAAATATGTGC 58.741 47.619 0.00 0.00 0.00 4.57
313 316 2.796557 TGATGGGCGTGTTGGAAAATA 58.203 42.857 0.00 0.00 0.00 1.40
322 325 5.489792 AGAGAATATATTGATGGGCGTGT 57.510 39.130 1.78 0.00 0.00 4.49
363 366 4.724399 TGAAATGTCTAGCTTTTGGTGGA 58.276 39.130 0.00 0.00 35.08 4.02
440 443 7.310485 GGAAGTTGTTATCCAGTCTCTCCTTAA 60.310 40.741 0.00 0.00 35.71 1.85
441 444 6.154706 GGAAGTTGTTATCCAGTCTCTCCTTA 59.845 42.308 0.00 0.00 35.71 2.69
443 446 4.468153 GGAAGTTGTTATCCAGTCTCTCCT 59.532 45.833 0.00 0.00 35.71 3.69
465 468 4.234574 GGACGGCAAAGAAACTTTATTGG 58.765 43.478 0.00 0.00 0.00 3.16
473 476 1.161563 TCGGTGGACGGCAAAGAAAC 61.162 55.000 0.00 0.00 44.45 2.78
484 487 3.316868 TGGTGAGAAAAATTTCGGTGGAC 59.683 43.478 0.00 0.00 41.92 4.02
503 510 2.457366 AAGCGACTCGAAGATTTGGT 57.543 45.000 1.63 0.00 32.57 3.67
507 514 6.797454 AGAGTAATAAAGCGACTCGAAGATT 58.203 36.000 1.63 0.00 43.57 2.40
509 516 5.220815 GGAGAGTAATAAAGCGACTCGAAGA 60.221 44.000 1.63 0.00 43.57 2.87
514 521 4.650754 TGGGAGAGTAATAAAGCGACTC 57.349 45.455 0.00 0.00 39.96 3.36
584 591 7.071014 TGGCAGTTTTTCAAAAGAAAATGTC 57.929 32.000 4.45 3.82 36.38 3.06
620 627 1.300971 GCCTCGCAGCTGTTTGATCA 61.301 55.000 16.64 0.00 0.00 2.92
672 679 4.648307 GGTATAATGCTAGCCGGTATAGGT 59.352 45.833 13.29 0.00 0.00 3.08
673 680 4.261489 CGGTATAATGCTAGCCGGTATAGG 60.261 50.000 13.29 3.42 38.86 2.57
674 681 4.856664 CGGTATAATGCTAGCCGGTATAG 58.143 47.826 13.29 7.42 38.86 1.31
675 682 4.906065 CGGTATAATGCTAGCCGGTATA 57.094 45.455 13.29 8.43 38.86 1.47
676 683 3.795623 CGGTATAATGCTAGCCGGTAT 57.204 47.619 13.29 9.40 38.86 2.73
854 979 3.423539 TCATACTTGTTTCCAGCTGCT 57.576 42.857 8.66 0.00 0.00 4.24
861 986 4.702131 AGTGGCAAGATCATACTTGTTTCC 59.298 41.667 0.00 0.00 45.98 3.13
862 987 5.412594 TCAGTGGCAAGATCATACTTGTTTC 59.587 40.000 0.00 0.00 45.98 2.78
865 990 4.511527 CTCAGTGGCAAGATCATACTTGT 58.488 43.478 0.00 0.00 45.98 3.16
867 992 3.199508 AGCTCAGTGGCAAGATCATACTT 59.800 43.478 0.00 0.00 34.17 2.24
868 993 2.770802 AGCTCAGTGGCAAGATCATACT 59.229 45.455 0.00 0.00 34.17 2.12
870 995 2.502947 ACAGCTCAGTGGCAAGATCATA 59.497 45.455 0.00 0.00 34.17 2.15
871 996 1.281287 ACAGCTCAGTGGCAAGATCAT 59.719 47.619 0.00 0.00 34.17 2.45
872 997 0.689055 ACAGCTCAGTGGCAAGATCA 59.311 50.000 0.00 0.00 34.17 2.92
873 998 1.085091 CACAGCTCAGTGGCAAGATC 58.915 55.000 6.40 0.00 35.88 2.75
874 999 0.959372 GCACAGCTCAGTGGCAAGAT 60.959 55.000 6.35 0.00 39.87 2.40
875 1000 1.598962 GCACAGCTCAGTGGCAAGA 60.599 57.895 6.35 0.00 39.87 3.02
876 1001 2.952245 GCACAGCTCAGTGGCAAG 59.048 61.111 6.35 0.00 39.87 4.01
880 1005 2.046507 GGAGGCACAGCTCAGTGG 60.047 66.667 6.35 0.00 39.87 4.00
908 1033 4.465512 GCCACCTGCGCATTCACG 62.466 66.667 12.24 0.00 0.00 4.35
1030 1156 1.485066 GATGGTTGGGTAGTCGTCCAT 59.515 52.381 0.00 0.00 38.21 3.41
1210 1336 0.030603 GAGGAGTTGGGGGAGAGGAT 60.031 60.000 0.00 0.00 0.00 3.24
1219 1345 1.852626 AAGGGGTGGAGGAGTTGGG 60.853 63.158 0.00 0.00 0.00 4.12
1222 1348 1.134438 GGACAAGGGGTGGAGGAGTT 61.134 60.000 0.00 0.00 0.00 3.01
1236 1362 0.764890 CTGTGGTTGAGGGAGGACAA 59.235 55.000 0.00 0.00 0.00 3.18
1239 1365 2.224159 GGCTGTGGTTGAGGGAGGA 61.224 63.158 0.00 0.00 0.00 3.71
1242 1368 2.224159 GGAGGCTGTGGTTGAGGGA 61.224 63.158 0.00 0.00 0.00 4.20
1243 1369 2.190488 GAGGAGGCTGTGGTTGAGGG 62.190 65.000 0.00 0.00 0.00 4.30
1275 1401 4.840288 TCGACGGCGGTGTATGCG 62.840 66.667 12.58 0.00 38.28 4.73
1473 1599 2.180086 ACCATCCCAGTAGATGAGGCTA 59.820 50.000 3.14 0.00 45.43 3.93
1554 1680 6.893020 TCCCTAAGATTAAGCTTCTCCTTT 57.107 37.500 9.67 0.00 0.00 3.11
1653 1779 1.127567 CGCCCTCCCCATCCTTATCA 61.128 60.000 0.00 0.00 0.00 2.15
1860 1987 3.801307 TGATCATAATCTGCCATGGCT 57.199 42.857 35.53 19.28 42.51 4.75
1914 2041 3.491792 GGGTCTTGATTCCATCTCTCGTC 60.492 52.174 0.00 0.00 0.00 4.20
2416 2771 7.094118 ACCAGAGTCTAAGTATCAAAGAGTCAC 60.094 40.741 8.62 0.00 40.61 3.67
2417 2772 6.948886 ACCAGAGTCTAAGTATCAAAGAGTCA 59.051 38.462 8.62 0.00 40.61 3.41
2418 2773 7.399245 ACCAGAGTCTAAGTATCAAAGAGTC 57.601 40.000 0.00 0.00 39.14 3.36
2495 2852 8.860088 GCTTAAATTTTATCATACCTGGTCCAT 58.140 33.333 0.63 0.00 0.00 3.41
2750 3107 0.607489 TTCCCTCTTGAAGCAGCAGC 60.607 55.000 0.00 0.00 42.56 5.25
2751 3108 1.901591 TTTCCCTCTTGAAGCAGCAG 58.098 50.000 0.00 0.00 0.00 4.24
2752 3109 2.158623 TCTTTTCCCTCTTGAAGCAGCA 60.159 45.455 0.00 0.00 0.00 4.41
2753 3110 2.508526 TCTTTTCCCTCTTGAAGCAGC 58.491 47.619 0.00 0.00 0.00 5.25
2754 3111 3.119566 GCATCTTTTCCCTCTTGAAGCAG 60.120 47.826 0.00 0.00 0.00 4.24
2755 3112 2.821969 GCATCTTTTCCCTCTTGAAGCA 59.178 45.455 0.00 0.00 0.00 3.91
2756 3113 2.821969 TGCATCTTTTCCCTCTTGAAGC 59.178 45.455 0.00 0.00 0.00 3.86
2757 3114 4.077822 ACTGCATCTTTTCCCTCTTGAAG 58.922 43.478 0.00 0.00 0.00 3.02
2758 3115 3.822735 CACTGCATCTTTTCCCTCTTGAA 59.177 43.478 0.00 0.00 0.00 2.69
3007 3366 5.047731 TCAGTATCATTCTTATCCTGAGCGG 60.048 44.000 0.00 0.00 0.00 5.52
3008 3367 5.861251 GTCAGTATCATTCTTATCCTGAGCG 59.139 44.000 0.00 0.00 0.00 5.03
3009 3368 6.991938 AGTCAGTATCATTCTTATCCTGAGC 58.008 40.000 0.00 0.00 0.00 4.26
3051 3551 2.115427 TCTGGGAATCGACCTAATGCA 58.885 47.619 0.00 0.00 0.00 3.96
3122 3622 4.454678 CAGATCCCTAACTAAAGCATGCA 58.545 43.478 21.98 0.00 0.00 3.96
3197 3697 6.482308 GCCTATATAACGCTTCTTTTCCTGAA 59.518 38.462 0.00 0.00 0.00 3.02
3307 3807 6.764276 TCAAGTTTGAGTCTGAAGCATCAGC 61.764 44.000 14.07 9.28 41.39 4.26
3620 4120 4.439305 TCAAATGCAGTTGTTCCTATGC 57.561 40.909 24.60 0.00 39.14 3.14
3704 4205 5.020132 GGTGCAGGGAGTAGACAGATATAT 58.980 45.833 0.00 0.00 0.00 0.86
3724 4225 0.391927 TTCCCGTAAAGGCATCGGTG 60.392 55.000 0.00 0.00 42.30 4.94
4119 4620 7.417911 CCTGTATCTCCTGCAAGTACAGAAATA 60.418 40.741 19.17 0.00 42.90 1.40
4169 4674 5.182001 ACATGTACAATTCAGTTCTGAAGCC 59.818 40.000 18.03 6.94 0.00 4.35
4306 4814 8.610896 CAAGTAAATGAAGAGCTAATCTCCAAG 58.389 37.037 0.00 0.00 42.90 3.61
4635 5143 9.967346 GCACACTGAGATAACTATGAGTAAATA 57.033 33.333 0.00 0.00 0.00 1.40
4775 5286 0.620556 GGATCCAAGCAGGTCTGGAA 59.379 55.000 6.95 0.00 39.02 3.53
4917 5429 1.226746 GCACCATATGTACCTTCCGC 58.773 55.000 1.24 0.00 0.00 5.54
4923 5435 4.279922 GGGTTATTTGGCACCATATGTACC 59.720 45.833 1.24 13.21 34.36 3.34
5155 5667 1.889829 CCCTGCGGAAAATAACAACCA 59.110 47.619 0.00 0.00 0.00 3.67
5201 5713 9.330063 CTAAAATGCCTTCATGTATCTTCTGTA 57.670 33.333 0.00 0.00 32.23 2.74
5216 5728 4.275936 GGTGCGATGTATCTAAAATGCCTT 59.724 41.667 0.00 0.00 0.00 4.35
5269 5782 0.944386 ACCATCAACGTTGTCTGTGC 59.056 50.000 26.47 0.00 0.00 4.57
5337 5850 1.616872 GCAACAAATGAAAGGCGCCG 61.617 55.000 23.20 6.46 0.00 6.46


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

AutoCloner maintained by Alex Coulton.