Multiple sequence alignment - TraesCS6D01G165200

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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 TraesCS6D01G165200 chr6D 100.000 4954 0 0 1 4954 144467564 144472517 0.000000e+00 9149
1 TraesCS6D01G165200 chr6D 82.864 391 47 17 4551 4932 77739085 77738706 2.860000e-87 333
2 TraesCS6D01G165200 chr6B 91.816 5034 203 83 1 4954 257564755 257569659 0.000000e+00 6820
3 TraesCS6D01G165200 chr6B 86.829 205 24 3 4281 4484 704894675 704894877 4.990000e-55 226
4 TraesCS6D01G165200 chr6B 85.185 216 32 0 4269 4484 56071326 56071541 6.450000e-54 222
5 TraesCS6D01G165200 chr6A 93.925 3078 111 33 1373 4414 202356126 202353089 0.000000e+00 4578
6 TraesCS6D01G165200 chr6A 92.255 736 28 10 639 1356 202356900 202356176 0.000000e+00 1016
7 TraesCS6D01G165200 chr6A 92.121 495 27 8 4470 4954 202353075 202352583 0.000000e+00 688
8 TraesCS6D01G165200 chr6A 92.550 349 17 6 1 342 202357957 202357611 4.460000e-135 492
9 TraesCS6D01G165200 chr6A 89.437 284 16 9 349 632 202357436 202357167 3.670000e-91 346
10 TraesCS6D01G165200 chr5D 81.330 391 42 18 4555 4932 46993406 46993034 6.270000e-74 289
11 TraesCS6D01G165200 chr5D 81.074 391 45 18 4555 4932 552449584 552449210 8.120000e-73 285
12 TraesCS6D01G165200 chr5D 80.818 391 43 19 4555 4932 513566896 513566525 1.360000e-70 278
13 TraesCS6D01G165200 chr7D 81.365 381 43 18 4555 4922 535675995 535676360 8.120000e-73 285
14 TraesCS6D01G165200 chr7D 80.720 389 50 20 4548 4920 607202283 607202662 3.780000e-71 279
15 TraesCS6D01G165200 chr4D 80.513 390 47 18 4556 4932 467612277 467611904 6.320000e-69 272


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 TraesCS6D01G165200 chr6D 144467564 144472517 4953 False 9149 9149 100.0000 1 4954 1 chr6D.!!$F1 4953
1 TraesCS6D01G165200 chr6B 257564755 257569659 4904 False 6820 6820 91.8160 1 4954 1 chr6B.!!$F2 4953
2 TraesCS6D01G165200 chr6A 202352583 202357957 5374 True 1424 4578 92.0576 1 4954 5 chr6A.!!$R1 4953

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
988 1446 0.689623 AGCCAAACCCTCTCTCACTG 59.310 55.0 0.0 0.0 0.00 3.66 F
1837 2344 0.117340 AGGGCTGACTACTGAGGGTT 59.883 55.0 0.0 0.0 0.00 4.11 F
1862 2369 0.320374 TTTGCGGGTGACTACTGAGG 59.680 55.0 0.0 0.0 0.00 3.86 F
2227 2737 1.014352 ACGTGAACAACTCTTGGCAC 58.986 50.0 0.0 0.0 36.99 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 2350 0.320374 CCTCAGTAGTCACCCGCAAA 59.680 55.0 0.00 0.00 0.0 3.68 R
3142 3706 0.898320 CGGAGTTGACCAGTGATCCT 59.102 55.0 0.00 0.00 0.0 3.24 R
3831 4398 1.965754 ATGGTGGCGAAGGAGAGCTC 61.966 60.0 5.27 5.27 0.0 4.09 R
4219 4787 0.249868 CCACAAAGGCGAGTCAGACA 60.250 55.0 2.66 0.00 0.0 3.41 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
20 21 2.629022 CGAGCATAAAAGAAATCGCCG 58.371 47.619 0.00 0.00 0.00 6.46
103 109 4.410400 CGGGACTGTGGAAGCCCC 62.410 72.222 0.00 0.00 38.40 5.80
104 110 4.048470 GGGACTGTGGAAGCCCCC 62.048 72.222 0.00 0.00 36.66 5.40
146 152 1.337118 AATGCGGGAAAGGCTTTTGA 58.663 45.000 14.66 0.00 0.00 2.69
147 153 1.337118 ATGCGGGAAAGGCTTTTGAA 58.663 45.000 14.66 2.51 0.00 2.69
255 264 3.861689 GGTTAATTTTGAGCTGCAGCATC 59.138 43.478 38.24 29.63 45.16 3.91
313 322 1.665679 ACGAGTGTCAAGTGTGCAAAG 59.334 47.619 0.00 0.00 0.00 2.77
347 524 3.885901 TGCTTTGTTGCTGGTGTAATACA 59.114 39.130 0.00 0.00 0.00 2.29
354 531 5.878116 TGTTGCTGGTGTAATACAAGTATCC 59.122 40.000 0.00 0.00 32.51 2.59
394 576 8.522830 TGTAAGCATTTTTAATGAGAGAAAGGG 58.477 33.333 3.70 0.00 0.00 3.95
395 577 7.781324 AAGCATTTTTAATGAGAGAAAGGGA 57.219 32.000 3.70 0.00 0.00 4.20
396 578 7.163001 AGCATTTTTAATGAGAGAAAGGGAC 57.837 36.000 3.70 0.00 0.00 4.46
397 579 6.721208 AGCATTTTTAATGAGAGAAAGGGACA 59.279 34.615 3.70 0.00 0.00 4.02
398 580 7.398332 AGCATTTTTAATGAGAGAAAGGGACAT 59.602 33.333 3.70 0.00 0.00 3.06
399 581 8.686334 GCATTTTTAATGAGAGAAAGGGACATA 58.314 33.333 3.70 0.00 0.00 2.29
401 583 9.981460 ATTTTTAATGAGAGAAAGGGACATACT 57.019 29.630 0.00 0.00 0.00 2.12
402 584 9.449719 TTTTTAATGAGAGAAAGGGACATACTC 57.550 33.333 0.00 0.00 0.00 2.59
403 585 5.622346 AATGAGAGAAAGGGACATACTCC 57.378 43.478 0.00 0.00 38.55 3.85
404 586 4.338795 TGAGAGAAAGGGACATACTCCT 57.661 45.455 0.00 0.00 39.39 3.69
405 587 5.467668 TGAGAGAAAGGGACATACTCCTA 57.532 43.478 0.00 0.00 39.39 2.94
406 588 5.202004 TGAGAGAAAGGGACATACTCCTAC 58.798 45.833 0.00 0.00 39.39 3.18
412 594 6.551601 AGAAAGGGACATACTCCTACTACATG 59.448 42.308 0.00 0.00 39.39 3.21
555 738 1.730446 GCAGCAGATTTCTTTGCGTCC 60.730 52.381 0.00 0.00 44.80 4.79
602 785 5.880164 GATCCTAAGGAGCTTACCTTTCT 57.120 43.478 11.68 0.00 46.61 2.52
603 786 6.241882 GATCCTAAGGAGCTTACCTTTCTT 57.758 41.667 11.68 0.00 46.61 2.52
610 793 6.189036 AGGAGCTTACCTTTCTTACAAAGT 57.811 37.500 0.00 0.00 36.86 2.66
616 799 7.660617 AGCTTACCTTTCTTACAAAGTTAGTCC 59.339 37.037 0.00 0.00 0.00 3.85
632 815 6.346096 AGTTAGTCCGAAATGCTAATGCTAA 58.654 36.000 0.00 0.00 40.48 3.09
634 817 5.679734 AGTCCGAAATGCTAATGCTAATG 57.320 39.130 0.00 0.00 40.48 1.90
635 818 4.023707 AGTCCGAAATGCTAATGCTAATGC 60.024 41.667 0.00 0.00 40.48 3.56
676 1119 4.495422 AGTGCAATCTTAGGTCAAGTACG 58.505 43.478 0.00 0.00 35.58 3.67
679 1122 4.219944 TGCAATCTTAGGTCAAGTACGACT 59.780 41.667 0.00 0.00 36.12 4.18
938 1396 1.452108 GCCGTCCAATCCCCTCTTG 60.452 63.158 0.00 0.00 0.00 3.02
988 1446 0.689623 AGCCAAACCCTCTCTCACTG 59.310 55.000 0.00 0.00 0.00 3.66
1010 1468 0.960364 TTGAAGACAATGCCGGCTCC 60.960 55.000 29.70 11.72 0.00 4.70
1068 1529 3.058016 TGCTACTCATTGCTTCACTTTGC 60.058 43.478 0.00 0.00 0.00 3.68
1074 1535 3.192001 TCATTGCTTCACTTTGCCATCTC 59.808 43.478 0.00 0.00 0.00 2.75
1092 1553 0.690192 TCGGTTCTTGCAATGGAGGA 59.310 50.000 0.00 0.00 0.00 3.71
1093 1554 1.089920 CGGTTCTTGCAATGGAGGAG 58.910 55.000 0.00 0.00 0.00 3.69
1094 1555 0.813821 GGTTCTTGCAATGGAGGAGC 59.186 55.000 0.00 0.00 0.00 4.70
1164 1634 0.807496 GTCAGTACTCGGGCTACGTT 59.193 55.000 0.00 0.00 44.69 3.99
1173 1643 1.905512 GGGCTACGTTGAGGTGGAT 59.094 57.895 0.00 0.00 0.00 3.41
1278 1748 0.759346 GAGGTGAGTGTTCCTGGTGT 59.241 55.000 0.00 0.00 33.83 4.16
1286 1756 4.246458 GAGTGTTCCTGGTGTATCTTGTC 58.754 47.826 0.00 0.00 0.00 3.18
1287 1757 3.646162 AGTGTTCCTGGTGTATCTTGTCA 59.354 43.478 0.00 0.00 0.00 3.58
1289 1759 3.646162 TGTTCCTGGTGTATCTTGTCACT 59.354 43.478 0.00 0.00 35.26 3.41
1292 1762 3.646162 TCCTGGTGTATCTTGTCACTTGT 59.354 43.478 0.00 0.00 35.26 3.16
1293 1763 3.748048 CCTGGTGTATCTTGTCACTTGTG 59.252 47.826 0.00 0.00 35.26 3.33
1294 1764 3.138304 TGGTGTATCTTGTCACTTGTGC 58.862 45.455 0.00 0.00 35.26 4.57
1295 1765 2.484264 GGTGTATCTTGTCACTTGTGCC 59.516 50.000 0.00 0.00 35.26 5.01
1296 1766 3.138304 GTGTATCTTGTCACTTGTGCCA 58.862 45.455 0.00 0.00 0.00 4.92
1297 1767 3.753272 GTGTATCTTGTCACTTGTGCCAT 59.247 43.478 0.00 0.00 0.00 4.40
1298 1768 3.752747 TGTATCTTGTCACTTGTGCCATG 59.247 43.478 0.00 0.00 0.00 3.66
1299 1769 1.608055 TCTTGTCACTTGTGCCATGG 58.392 50.000 7.63 7.63 0.00 3.66
1317 1787 4.096081 CCATGGCATTCTCTGAACTCTTTC 59.904 45.833 0.00 0.00 0.00 2.62
1324 1794 3.309388 TCTCTGAACTCTTTCGCTTTCG 58.691 45.455 0.00 0.00 34.04 3.46
1326 1796 3.050619 TCTGAACTCTTTCGCTTTCGTC 58.949 45.455 0.00 0.00 34.04 4.20
1384 1887 8.826765 TCTAATGGAGTAGATTTCTTCTTTGGT 58.173 33.333 0.00 0.00 35.79 3.67
1428 1931 1.949847 ATCCGAACTCTGGTCCTGCG 61.950 60.000 0.00 0.00 0.00 5.18
1435 1938 1.072331 ACTCTGGTCCTGCGTTCATTT 59.928 47.619 0.00 0.00 0.00 2.32
1436 1939 1.734465 CTCTGGTCCTGCGTTCATTTC 59.266 52.381 0.00 0.00 0.00 2.17
1437 1940 1.347707 TCTGGTCCTGCGTTCATTTCT 59.652 47.619 0.00 0.00 0.00 2.52
1438 1941 1.466167 CTGGTCCTGCGTTCATTTCTG 59.534 52.381 0.00 0.00 0.00 3.02
1439 1942 0.804989 GGTCCTGCGTTCATTTCTGG 59.195 55.000 0.00 0.00 0.00 3.86
1440 1943 1.610624 GGTCCTGCGTTCATTTCTGGA 60.611 52.381 0.00 0.00 0.00 3.86
1441 1944 1.464997 GTCCTGCGTTCATTTCTGGAC 59.535 52.381 0.00 0.00 40.10 4.02
1701 2205 1.000060 CATGCCTCACTGTTTTGGTGG 60.000 52.381 0.00 0.00 35.61 4.61
1820 2327 2.567169 TGACAACATGACAGGTAGGAGG 59.433 50.000 0.00 0.00 0.00 4.30
1835 2342 1.045911 GGAGGGCTGACTACTGAGGG 61.046 65.000 0.00 0.00 0.00 4.30
1836 2343 0.324830 GAGGGCTGACTACTGAGGGT 60.325 60.000 0.00 0.00 0.00 4.34
1837 2344 0.117340 AGGGCTGACTACTGAGGGTT 59.883 55.000 0.00 0.00 0.00 4.11
1838 2345 0.984995 GGGCTGACTACTGAGGGTTT 59.015 55.000 0.00 0.00 0.00 3.27
1839 2346 1.351350 GGGCTGACTACTGAGGGTTTT 59.649 52.381 0.00 0.00 0.00 2.43
1840 2347 2.224793 GGGCTGACTACTGAGGGTTTTT 60.225 50.000 0.00 0.00 0.00 1.94
1860 2367 2.623878 TTTTTGCGGGTGACTACTGA 57.376 45.000 0.00 0.00 0.00 3.41
1861 2368 2.163818 TTTTGCGGGTGACTACTGAG 57.836 50.000 0.00 0.00 0.00 3.35
1862 2369 0.320374 TTTGCGGGTGACTACTGAGG 59.680 55.000 0.00 0.00 0.00 3.86
1877 2384 7.334421 TGACTACTGAGGTTTATGATTGAAAGC 59.666 37.037 0.00 0.00 35.10 3.51
1882 2389 6.611381 TGAGGTTTATGATTGAAAGCTTTCG 58.389 36.000 29.03 0.00 42.93 3.46
1935 2442 6.788598 ACTGGATATATAGATGACTGCCTG 57.211 41.667 0.00 0.00 0.00 4.85
2015 2525 7.542130 GGGTTTATGTTTTATCAGCAAGTCTTG 59.458 37.037 8.31 8.31 0.00 3.02
2227 2737 1.014352 ACGTGAACAACTCTTGGCAC 58.986 50.000 0.00 0.00 36.99 5.01
2237 2747 6.360370 ACAACTCTTGGCACTCTCTAAATA 57.640 37.500 0.00 0.00 34.12 1.40
2259 2769 9.472361 AAATATTCAGATATTCTTTGCATGTGC 57.528 29.630 0.00 0.00 37.44 4.57
2375 2885 8.801882 AAACCTCAATCAGAATAAACCGATTA 57.198 30.769 0.00 0.00 0.00 1.75
2404 2914 5.531634 TGATGCATTTTTCTGTTTCTGACC 58.468 37.500 0.00 0.00 0.00 4.02
2420 2930 2.851824 CTGACCGAAACAGTTTTGTTGC 59.148 45.455 11.68 2.48 46.54 4.17
2771 3281 8.815565 TCATAGGGTAGCTATCTCTTATCTTG 57.184 38.462 3.53 0.00 0.00 3.02
2775 3285 7.958088 AGGGTAGCTATCTCTTATCTTGTTTC 58.042 38.462 3.53 0.00 0.00 2.78
2827 3337 1.665599 GGCAACAATGTGGCTGTGC 60.666 57.895 13.00 5.57 40.77 4.57
2906 3416 7.839680 AAACTATTTGAACAGGAAGGATGTT 57.160 32.000 0.00 0.00 43.38 2.71
3023 3533 6.983906 AAAATGTGACCTTTGGAGAAAGAT 57.016 33.333 0.00 0.00 41.12 2.40
3091 3655 7.062839 TGTCATGTTTTTCTGTTTTGTTACAGC 59.937 33.333 0.00 0.00 44.10 4.40
3142 3706 6.883756 TGCAGATTCCAACAATCAACATAGTA 59.116 34.615 0.00 0.00 0.00 1.82
3364 3930 6.978080 GGGCGCTAATTAAGAAATCAATGAAA 59.022 34.615 7.64 0.00 0.00 2.69
3481 4047 6.677781 TGTACTTTGCCAGCTTTATATCAC 57.322 37.500 0.00 0.00 0.00 3.06
3830 4397 2.756760 GTGGACTCAGGTATACGGTGAA 59.243 50.000 7.69 0.00 0.00 3.18
3831 4398 3.021695 TGGACTCAGGTATACGGTGAAG 58.978 50.000 7.69 5.45 0.00 3.02
3857 4424 1.617018 CCTTCGCCACCATCAGAGGA 61.617 60.000 0.00 0.00 0.00 3.71
3890 4457 2.178890 GCCATTCTCGCAGCCTGAG 61.179 63.158 0.00 0.00 34.72 3.35
4101 4668 4.309933 GCAGCATTGCTCTAAAGGTTTTT 58.690 39.130 8.54 0.00 46.95 1.94
4103 4670 4.687483 CAGCATTGCTCTAAAGGTTTTTGG 59.313 41.667 8.54 0.00 36.40 3.28
4104 4671 4.344968 AGCATTGCTCTAAAGGTTTTTGGT 59.655 37.500 5.03 0.00 30.62 3.67
4105 4672 5.056480 GCATTGCTCTAAAGGTTTTTGGTT 58.944 37.500 0.16 0.00 0.00 3.67
4263 4831 6.295292 GGAAGGTTTGAAGCAGGTAAAATCAT 60.295 38.462 0.00 0.00 0.00 2.45
4630 5200 7.857734 TTGTTTTCTTCTACATCAGTTCACA 57.142 32.000 0.00 0.00 0.00 3.58
4676 5246 7.427989 ACCGGTCCTTTTATCACTATTTCTA 57.572 36.000 0.00 0.00 0.00 2.10
4869 5454 8.726068 TCGTTTGAATAGAAAAATGCTCACATA 58.274 29.630 0.00 0.00 34.62 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.429463 AGAGGTTCGTTCGTTCATGC 58.571 50.000 0.00 0.00 0.00 4.06
113 119 2.159296 CCCGCATTACAAAAAGTAGGCC 60.159 50.000 0.00 0.00 33.68 5.19
117 123 4.321378 GCCTTTCCCGCATTACAAAAAGTA 60.321 41.667 0.00 0.00 0.00 2.24
120 126 2.630580 AGCCTTTCCCGCATTACAAAAA 59.369 40.909 0.00 0.00 0.00 1.94
146 152 1.075536 GGGACAAGATGGACCCAAGTT 59.924 52.381 0.00 0.00 37.78 2.66
147 153 0.698818 GGGACAAGATGGACCCAAGT 59.301 55.000 0.00 0.00 37.78 3.16
255 264 7.148188 ACACAATACAGCATCAAACTGATAAGG 60.148 37.037 0.00 0.00 34.28 2.69
271 280 7.639945 TCGTCACATCTATCTACACAATACAG 58.360 38.462 0.00 0.00 0.00 2.74
313 322 3.187022 GCAACAAAGCAAATGACAATCCC 59.813 43.478 0.00 0.00 0.00 3.85
394 576 7.578310 TTGTACCATGTAGTAGGAGTATGTC 57.422 40.000 0.00 0.00 0.00 3.06
395 577 8.548880 AATTGTACCATGTAGTAGGAGTATGT 57.451 34.615 0.00 0.00 0.00 2.29
405 587 9.419297 CACGCTATAATAATTGTACCATGTAGT 57.581 33.333 0.00 0.00 0.00 2.73
406 588 9.419297 ACACGCTATAATAATTGTACCATGTAG 57.581 33.333 0.00 0.00 0.00 2.74
412 594 5.699458 AGGCACACGCTATAATAATTGTACC 59.301 40.000 0.00 0.00 38.60 3.34
555 738 0.249120 TCCACTGTTAGCGGGTGATG 59.751 55.000 4.56 0.00 33.32 3.07
596 779 7.486802 TTTCGGACTAACTTTGTAAGAAAGG 57.513 36.000 0.00 0.00 0.00 3.11
602 785 7.966246 TTAGCATTTCGGACTAACTTTGTAA 57.034 32.000 0.00 0.00 0.00 2.41
603 786 7.413657 GCATTAGCATTTCGGACTAACTTTGTA 60.414 37.037 0.00 0.00 41.58 2.41
610 793 6.293407 GCATTAGCATTAGCATTTCGGACTAA 60.293 38.462 0.00 0.00 45.49 2.24
616 799 6.233430 AGTAGCATTAGCATTAGCATTTCG 57.767 37.500 0.00 0.00 45.49 3.46
632 815 7.763528 GCACTATGAGATTAGCATTAGTAGCAT 59.236 37.037 0.00 0.00 0.00 3.79
634 817 7.093354 TGCACTATGAGATTAGCATTAGTAGC 58.907 38.462 0.00 0.00 0.00 3.58
635 818 9.650539 ATTGCACTATGAGATTAGCATTAGTAG 57.349 33.333 0.00 0.00 0.00 2.57
676 1119 9.585099 TTCATTAATTATGCATGTTTTCCAGTC 57.415 29.630 10.16 0.00 34.06 3.51
938 1396 4.173924 GGAGGAGCTGGCTGGAGC 62.174 72.222 0.00 0.00 39.46 4.70
1041 1502 2.289882 TGAAGCAATGAGTAGCAGCACT 60.290 45.455 0.00 0.00 0.00 4.40
1068 1529 1.402968 CCATTGCAAGAACCGAGATGG 59.597 52.381 4.94 0.00 46.41 3.51
1074 1535 1.089920 CTCCTCCATTGCAAGAACCG 58.910 55.000 4.94 0.00 0.00 4.44
1092 1553 1.765657 GATCCTGCCTCCTCCTGCT 60.766 63.158 0.00 0.00 0.00 4.24
1093 1554 2.068821 TGATCCTGCCTCCTCCTGC 61.069 63.158 0.00 0.00 0.00 4.85
1094 1555 0.979709 TGTGATCCTGCCTCCTCCTG 60.980 60.000 0.00 0.00 0.00 3.86
1131 1601 2.640316 ACTGACCAAAGTTCACCTCC 57.360 50.000 0.00 0.00 0.00 4.30
1164 1634 2.615465 CCCCTTGCCATCCACCTCA 61.615 63.158 0.00 0.00 0.00 3.86
1293 1763 1.674962 GAGTTCAGAGAATGCCATGGC 59.325 52.381 30.54 30.54 42.35 4.40
1294 1764 3.278668 AGAGTTCAGAGAATGCCATGG 57.721 47.619 7.63 7.63 0.00 3.66
1295 1765 4.201792 CGAAAGAGTTCAGAGAATGCCATG 60.202 45.833 0.00 0.00 32.89 3.66
1296 1766 3.937706 CGAAAGAGTTCAGAGAATGCCAT 59.062 43.478 0.00 0.00 32.89 4.40
1297 1767 3.329386 CGAAAGAGTTCAGAGAATGCCA 58.671 45.455 0.00 0.00 32.89 4.92
1298 1768 2.095053 GCGAAAGAGTTCAGAGAATGCC 59.905 50.000 0.00 0.00 32.89 4.40
1299 1769 2.999355 AGCGAAAGAGTTCAGAGAATGC 59.001 45.455 0.00 0.00 32.89 3.56
1317 1787 1.266404 GCAAGATACACGACGAAAGCG 60.266 52.381 0.00 0.00 44.79 4.68
1324 1794 1.927895 CAGGGAGCAAGATACACGAC 58.072 55.000 0.00 0.00 0.00 4.34
1326 1796 2.682893 GCAGGGAGCAAGATACACG 58.317 57.895 0.00 0.00 44.79 4.49
1428 1931 4.543590 TCTCCAGAGTCCAGAAATGAAC 57.456 45.455 0.00 0.00 0.00 3.18
1435 1938 4.837298 CCAATGATATCTCCAGAGTCCAGA 59.163 45.833 3.98 0.00 0.00 3.86
1436 1939 4.592351 ACCAATGATATCTCCAGAGTCCAG 59.408 45.833 3.98 0.00 0.00 3.86
1437 1940 4.560739 ACCAATGATATCTCCAGAGTCCA 58.439 43.478 3.98 0.00 0.00 4.02
1438 1941 5.546526 GAACCAATGATATCTCCAGAGTCC 58.453 45.833 3.98 0.00 0.00 3.85
1439 1942 5.010112 TCGAACCAATGATATCTCCAGAGTC 59.990 44.000 3.98 0.00 0.00 3.36
1440 1943 4.895889 TCGAACCAATGATATCTCCAGAGT 59.104 41.667 3.98 0.00 0.00 3.24
1441 1944 5.459536 TCGAACCAATGATATCTCCAGAG 57.540 43.478 3.98 0.00 0.00 3.35
1701 2205 1.672881 AGCTTCTGCACAACACAAGAC 59.327 47.619 0.00 0.00 42.74 3.01
1820 2327 2.861147 AAAACCCTCAGTAGTCAGCC 57.139 50.000 0.00 0.00 0.00 4.85
1841 2348 2.489971 CTCAGTAGTCACCCGCAAAAA 58.510 47.619 0.00 0.00 0.00 1.94
1842 2349 1.270625 CCTCAGTAGTCACCCGCAAAA 60.271 52.381 0.00 0.00 0.00 2.44
1843 2350 0.320374 CCTCAGTAGTCACCCGCAAA 59.680 55.000 0.00 0.00 0.00 3.68
1844 2351 0.830444 ACCTCAGTAGTCACCCGCAA 60.830 55.000 0.00 0.00 0.00 4.85
1845 2352 0.830444 AACCTCAGTAGTCACCCGCA 60.830 55.000 0.00 0.00 0.00 5.69
1846 2353 0.320697 AAACCTCAGTAGTCACCCGC 59.679 55.000 0.00 0.00 0.00 6.13
1847 2354 3.446161 TCATAAACCTCAGTAGTCACCCG 59.554 47.826 0.00 0.00 0.00 5.28
1848 2355 5.615925 ATCATAAACCTCAGTAGTCACCC 57.384 43.478 0.00 0.00 0.00 4.61
1849 2356 6.640518 TCAATCATAAACCTCAGTAGTCACC 58.359 40.000 0.00 0.00 0.00 4.02
1850 2357 8.547967 TTTCAATCATAAACCTCAGTAGTCAC 57.452 34.615 0.00 0.00 0.00 3.67
1851 2358 7.334421 GCTTTCAATCATAAACCTCAGTAGTCA 59.666 37.037 0.00 0.00 0.00 3.41
1852 2359 7.550906 AGCTTTCAATCATAAACCTCAGTAGTC 59.449 37.037 0.00 0.00 0.00 2.59
1853 2360 7.398024 AGCTTTCAATCATAAACCTCAGTAGT 58.602 34.615 0.00 0.00 0.00 2.73
1854 2361 7.856145 AGCTTTCAATCATAAACCTCAGTAG 57.144 36.000 0.00 0.00 0.00 2.57
1855 2362 8.635765 AAAGCTTTCAATCATAAACCTCAGTA 57.364 30.769 5.69 0.00 0.00 2.74
1856 2363 7.530426 AAAGCTTTCAATCATAAACCTCAGT 57.470 32.000 5.69 0.00 0.00 3.41
1857 2364 6.744537 CGAAAGCTTTCAATCATAAACCTCAG 59.255 38.462 32.52 11.45 37.01 3.35
1858 2365 6.206634 ACGAAAGCTTTCAATCATAAACCTCA 59.793 34.615 32.52 0.00 37.01 3.86
1859 2366 6.524586 CACGAAAGCTTTCAATCATAAACCTC 59.475 38.462 32.52 7.37 37.01 3.85
1860 2367 6.381801 CACGAAAGCTTTCAATCATAAACCT 58.618 36.000 32.52 0.00 37.01 3.50
1861 2368 5.060940 GCACGAAAGCTTTCAATCATAAACC 59.939 40.000 32.52 7.83 37.01 3.27
1862 2369 5.629020 TGCACGAAAGCTTTCAATCATAAAC 59.371 36.000 32.52 14.68 37.01 2.01
1877 2384 3.434641 ACATTCAGACAGATGCACGAAAG 59.565 43.478 0.00 0.00 0.00 2.62
1882 2389 2.486982 AGCAACATTCAGACAGATGCAC 59.513 45.455 0.00 0.00 34.89 4.57
1935 2442 6.567050 TCCTACAAATGGTGTATCTACGAAC 58.433 40.000 0.00 0.00 41.93 3.95
2209 2719 1.261619 GAGTGCCAAGAGTTGTTCACG 59.738 52.381 0.00 0.00 37.34 4.35
2237 2747 5.361571 TGGCACATGCAAAGAATATCTGAAT 59.638 36.000 6.15 0.00 44.36 2.57
2259 2769 2.142356 TGTGGAATGTAATGCCCTGG 57.858 50.000 0.00 0.00 43.77 4.45
2375 2885 7.010738 CAGAAACAGAAAAATGCATCAACAGTT 59.989 33.333 0.00 0.00 0.00 3.16
2404 2914 2.874849 ACCAGCAACAAAACTGTTTCG 58.125 42.857 6.20 0.00 31.76 3.46
2411 2921 4.805219 CCCAACTATACCAGCAACAAAAC 58.195 43.478 0.00 0.00 0.00 2.43
2420 2930 3.117888 ACAGGATTGCCCAACTATACCAG 60.118 47.826 0.00 0.00 37.41 4.00
2771 3281 3.145286 AGCTGCCTTCTTTCTCAGAAAC 58.855 45.455 0.00 0.00 41.25 2.78
2775 3285 4.099881 AGAGATAGCTGCCTTCTTTCTCAG 59.900 45.833 0.00 0.00 39.51 3.35
2827 3337 1.280746 CCAACACGCTTCTGCACAG 59.719 57.895 0.00 0.00 39.64 3.66
2906 3416 2.124983 GCATGGAGCGCTTCCTGA 60.125 61.111 23.48 0.25 46.92 3.86
3091 3655 3.129462 TGAGGAGCTCATACTCAAGAACG 59.871 47.826 17.19 0.00 38.22 3.95
3142 3706 0.898320 CGGAGTTGACCAGTGATCCT 59.102 55.000 0.00 0.00 0.00 3.24
3337 3901 2.875933 TGATTTCTTAATTAGCGCCCCG 59.124 45.455 2.29 0.00 0.00 5.73
3364 3930 3.324846 TGCTACACACCTGATTCTTCACT 59.675 43.478 0.00 0.00 0.00 3.41
3413 3979 6.327386 AGTCCCAATTCTATAGGCTTTTCA 57.673 37.500 0.00 0.00 0.00 2.69
3421 3987 8.432805 ACCTTATGTCAAGTCCCAATTCTATAG 58.567 37.037 0.00 0.00 0.00 1.31
3646 4213 2.875786 GCGCGCTAGATTCTGCACC 61.876 63.158 26.67 0.00 0.00 5.01
3830 4397 2.355193 GGTGGCGAAGGAGAGCTCT 61.355 63.158 18.28 18.28 0.00 4.09
3831 4398 1.965754 ATGGTGGCGAAGGAGAGCTC 61.966 60.000 5.27 5.27 0.00 4.09
3890 4457 0.738762 TGATGAGCACAAGAGAGCGC 60.739 55.000 0.00 0.00 36.39 5.92
4080 4647 4.687483 CCAAAAACCTTTAGAGCAATGCTG 59.313 41.667 14.48 0.00 39.88 4.41
4081 4648 4.344968 ACCAAAAACCTTTAGAGCAATGCT 59.655 37.500 7.79 7.79 43.88 3.79
4101 4668 5.245301 TCGAATACAGGAGAAAGAGAAACCA 59.755 40.000 0.00 0.00 0.00 3.67
4103 4670 5.808030 CCTCGAATACAGGAGAAAGAGAAAC 59.192 44.000 0.00 0.00 31.91 2.78
4104 4671 5.624738 GCCTCGAATACAGGAGAAAGAGAAA 60.625 44.000 0.00 0.00 31.91 2.52
4105 4672 4.142138 GCCTCGAATACAGGAGAAAGAGAA 60.142 45.833 0.00 0.00 31.91 2.87
4219 4787 0.249868 CCACAAAGGCGAGTCAGACA 60.250 55.000 2.66 0.00 0.00 3.41
4474 5042 4.060900 CAGATGGCTATACGAACAATGCT 58.939 43.478 0.00 0.00 0.00 3.79
4838 5423 8.816640 AGCATTTTTCTATTCAAACGAACAAT 57.183 26.923 0.00 0.00 0.00 2.71
4909 5494 8.511321 TGAGCATGTTTCTATTTAAACGAACAT 58.489 29.630 11.46 11.46 41.33 2.71


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

AutoCloner maintained by Alex Coulton.