Multiple sequence alignment - TraesCS5D01G529300

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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 TraesCS5D01G529300 chr5D 100.000 4612 0 0 1 4612 545966583 545971194 0 8517
1 TraesCS5D01G529300 chr5D 91.470 2204 155 28 1576 3757 424144164 424141972 0 2998
2 TraesCS5D01G529300 chr5D 94.148 1572 88 4 1 1571 333242654 333241086 0 2390
3 TraesCS5D01G529300 chr5D 92.134 1551 105 9 1 1544 526641938 526640398 0 2172
4 TraesCS5D01G529300 chr5D 92.130 864 60 6 3754 4612 526638161 526637301 0 1212
5 TraesCS5D01G529300 chr6D 95.444 4631 170 17 1 4612 118587540 118592148 0 7345
6 TraesCS5D01G529300 chr1D 95.334 3965 159 15 1 3954 479066218 479070167 0 6274
7 TraesCS5D01G529300 chr1D 92.111 862 60 6 3754 4609 58472084 58472943 0 1208
8 TraesCS5D01G529300 chr2D 96.194 3048 102 9 1576 4612 374134315 374131271 0 4974
9 TraesCS5D01G529300 chr2D 91.119 2207 162 28 1573 3757 594637706 594639900 0 2959
10 TraesCS5D01G529300 chr2D 96.249 1573 56 3 1 1571 374135858 374134287 0 2575
11 TraesCS5D01G529300 chr2D 92.023 865 62 5 3754 4612 536213463 536212600 0 1208
12 TraesCS5D01G529300 chr4D 91.265 2198 158 30 1580 3757 19166629 19168812 0 2964
13 TraesCS5D01G529300 chr4D 93.270 1575 99 6 1 1571 47164126 47162555 0 2314
14 TraesCS5D01G529300 chr4D 93.003 1572 99 7 1 1565 285386681 285388248 0 2283
15 TraesCS5D01G529300 chr4D 92.334 861 57 7 3754 4609 19168856 19169712 0 1216
16 TraesCS5D01G529300 chrUn 90.385 2205 177 27 1576 3757 52480492 52478300 0 2865
17 TraesCS5D01G529300 chr2B 89.287 2203 194 34 1577 3751 747114357 747116545 0 2723
18 TraesCS5D01G529300 chr2B 88.307 2215 206 41 1576 3757 608461526 608459332 0 2606
19 TraesCS5D01G529300 chr1B 88.984 2215 201 33 1573 3757 588833111 588835312 0 2699
20 TraesCS5D01G529300 chr3D 93.830 1572 94 3 1 1571 610715369 610713800 0 2362
21 TraesCS5D01G529300 chr3D 93.575 1572 99 2 1 1571 341449007 341447437 0 2342
22 TraesCS5D01G529300 chr3D 92.218 861 59 6 3754 4609 500620677 500621534 0 1212
23 TraesCS5D01G529300 chr7D 93.953 860 47 4 3754 4611 59515196 59514340 0 1295
24 TraesCS5D01G529300 chr7D 92.370 865 58 6 3754 4612 30317744 30316882 0 1225


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 TraesCS5D01G529300 chr5D 545966583 545971194 4611 False 8517.0 8517 100.0000 1 4612 1 chr5D.!!$F1 4611
1 TraesCS5D01G529300 chr5D 424141972 424144164 2192 True 2998.0 2998 91.4700 1576 3757 1 chr5D.!!$R2 2181
2 TraesCS5D01G529300 chr5D 333241086 333242654 1568 True 2390.0 2390 94.1480 1 1571 1 chr5D.!!$R1 1570
3 TraesCS5D01G529300 chr5D 526637301 526641938 4637 True 1692.0 2172 92.1320 1 4612 2 chr5D.!!$R3 4611
4 TraesCS5D01G529300 chr6D 118587540 118592148 4608 False 7345.0 7345 95.4440 1 4612 1 chr6D.!!$F1 4611
5 TraesCS5D01G529300 chr1D 479066218 479070167 3949 False 6274.0 6274 95.3340 1 3954 1 chr1D.!!$F2 3953
6 TraesCS5D01G529300 chr1D 58472084 58472943 859 False 1208.0 1208 92.1110 3754 4609 1 chr1D.!!$F1 855
7 TraesCS5D01G529300 chr2D 374131271 374135858 4587 True 3774.5 4974 96.2215 1 4612 2 chr2D.!!$R2 4611
8 TraesCS5D01G529300 chr2D 594637706 594639900 2194 False 2959.0 2959 91.1190 1573 3757 1 chr2D.!!$F1 2184
9 TraesCS5D01G529300 chr2D 536212600 536213463 863 True 1208.0 1208 92.0230 3754 4612 1 chr2D.!!$R1 858
10 TraesCS5D01G529300 chr4D 47162555 47164126 1571 True 2314.0 2314 93.2700 1 1571 1 chr4D.!!$R1 1570
11 TraesCS5D01G529300 chr4D 285386681 285388248 1567 False 2283.0 2283 93.0030 1 1565 1 chr4D.!!$F1 1564
12 TraesCS5D01G529300 chr4D 19166629 19169712 3083 False 2090.0 2964 91.7995 1580 4609 2 chr4D.!!$F2 3029
13 TraesCS5D01G529300 chrUn 52478300 52480492 2192 True 2865.0 2865 90.3850 1576 3757 1 chrUn.!!$R1 2181
14 TraesCS5D01G529300 chr2B 747114357 747116545 2188 False 2723.0 2723 89.2870 1577 3751 1 chr2B.!!$F1 2174
15 TraesCS5D01G529300 chr2B 608459332 608461526 2194 True 2606.0 2606 88.3070 1576 3757 1 chr2B.!!$R1 2181
16 TraesCS5D01G529300 chr1B 588833111 588835312 2201 False 2699.0 2699 88.9840 1573 3757 1 chr1B.!!$F1 2184
17 TraesCS5D01G529300 chr3D 610713800 610715369 1569 True 2362.0 2362 93.8300 1 1571 1 chr3D.!!$R2 1570
18 TraesCS5D01G529300 chr3D 341447437 341449007 1570 True 2342.0 2342 93.5750 1 1571 1 chr3D.!!$R1 1570
19 TraesCS5D01G529300 chr3D 500620677 500621534 857 False 1212.0 1212 92.2180 3754 4609 1 chr3D.!!$F1 855
20 TraesCS5D01G529300 chr7D 59514340 59515196 856 True 1295.0 1295 93.9530 3754 4611 1 chr7D.!!$R2 857
21 TraesCS5D01G529300 chr7D 30316882 30317744 862 True 1225.0 1225 92.3700 3754 4612 1 chr7D.!!$R1 858

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
251 266 1.138069 TGACAACGCTCTTGGTTCTGA 59.862 47.619 0.0 0.0 0.0 3.27 F
1550 1567 0.321919 TGATGCTCCAACACCTGCTC 60.322 55.000 0.0 0.0 0.0 4.26 F
2115 2174 0.257328 TTGGTTGCTGTGACCCTTCA 59.743 50.000 0.0 0.0 36.3 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1585 0.312102 GCTGGAGCAGGTGTTGTTTC 59.688 55.000 0.0 0.00 41.59 2.78 R
2871 2959 1.227674 CTTCCTCCATAGGTGGCGC 60.228 63.158 0.0 0.00 45.63 6.53 R
3930 4111 0.698886 ATTGGAGGCTGCATCCCCTA 60.699 55.000 28.3 15.21 35.86 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
121 130 4.375313 AGGGGGAGAAGACAAAGATACAT 58.625 43.478 0.00 0.00 0.00 2.29
240 255 2.798847 CGATGATGATGATGACAACGCT 59.201 45.455 0.00 0.00 0.00 5.07
242 257 3.531934 TGATGATGATGACAACGCTCT 57.468 42.857 0.00 0.00 0.00 4.09
251 266 1.138069 TGACAACGCTCTTGGTTCTGA 59.862 47.619 0.00 0.00 0.00 3.27
366 381 5.070770 TGTTGATTGACAAAACTTGCTGT 57.929 34.783 0.00 0.00 40.36 4.40
381 397 7.817418 AACTTGCTGTAAAGACAAGGATTTA 57.183 32.000 16.54 0.00 44.01 1.40
384 400 5.626142 TGCTGTAAAGACAAGGATTTACCA 58.374 37.500 5.62 0.00 39.87 3.25
435 451 3.634504 TCAGGGCAGCATTGATATGTTT 58.365 40.909 0.00 0.00 34.12 2.83
672 689 4.217334 CCAGATATAAGCTCGAGCAAGAGA 59.783 45.833 36.87 19.79 45.16 3.10
676 693 2.533266 AAGCTCGAGCAAGAGAAACA 57.467 45.000 36.87 0.00 45.16 2.83
677 694 2.077413 AGCTCGAGCAAGAGAAACAG 57.923 50.000 36.87 0.00 45.16 3.16
733 750 2.555325 TGCAAAGCAGTCTCAATGAAGG 59.445 45.455 0.00 0.00 33.32 3.46
742 759 5.732633 CAGTCTCAATGAAGGAGAATCTGT 58.267 41.667 0.00 0.00 42.63 3.41
798 815 5.047164 TGCAGATGCTGAAATAAATGTGGTT 60.047 36.000 6.35 0.00 42.66 3.67
961 978 2.604382 CCAAGGGCACAAAGGGGG 60.604 66.667 0.00 0.00 0.00 5.40
1166 1183 2.900106 GCTCAGGGAGGCACCACTT 61.900 63.158 2.69 0.00 41.20 3.16
1361 1378 5.755849 ACATTATAAGTAGGTGCAAGCCTT 58.244 37.500 0.51 0.00 39.94 4.35
1522 1539 1.963515 GCACCATCTTTTGACCTTGGT 59.036 47.619 0.00 0.00 39.25 3.67
1524 1541 3.572255 GCACCATCTTTTGACCTTGGTAA 59.428 43.478 0.00 0.00 37.27 2.85
1539 1556 3.281727 TGGTAAAGATGGTGATGCTCC 57.718 47.619 0.00 0.00 0.00 4.70
1540 1557 2.575735 TGGTAAAGATGGTGATGCTCCA 59.424 45.455 0.00 0.00 39.41 3.86
1541 1558 3.010027 TGGTAAAGATGGTGATGCTCCAA 59.990 43.478 0.00 0.00 38.52 3.53
1542 1559 3.378427 GGTAAAGATGGTGATGCTCCAAC 59.622 47.826 0.00 0.00 38.52 3.77
1543 1560 2.885135 AAGATGGTGATGCTCCAACA 57.115 45.000 0.00 0.00 38.23 3.33
1544 1561 2.119801 AGATGGTGATGCTCCAACAC 57.880 50.000 0.00 0.00 36.47 3.32
1548 1565 1.878775 GTGATGCTCCAACACCTGC 59.121 57.895 0.00 0.00 32.27 4.85
1549 1566 0.607489 GTGATGCTCCAACACCTGCT 60.607 55.000 0.00 0.00 32.27 4.24
1550 1567 0.321919 TGATGCTCCAACACCTGCTC 60.322 55.000 0.00 0.00 0.00 4.26
1551 1568 1.001641 ATGCTCCAACACCTGCTCC 60.002 57.895 0.00 0.00 0.00 4.70
1552 1569 1.782201 ATGCTCCAACACCTGCTCCA 61.782 55.000 0.00 0.00 0.00 3.86
1553 1570 1.673665 GCTCCAACACCTGCTCCAG 60.674 63.158 0.00 0.00 0.00 3.86
1554 1571 1.673665 CTCCAACACCTGCTCCAGC 60.674 63.158 0.00 0.00 42.50 4.85
1566 1583 1.874562 CTCCAGCAGCAGAAACAGC 59.125 57.895 0.00 0.00 0.00 4.40
1567 1584 0.887836 CTCCAGCAGCAGAAACAGCA 60.888 55.000 0.00 0.00 0.00 4.41
1568 1585 0.887836 TCCAGCAGCAGAAACAGCAG 60.888 55.000 0.00 0.00 0.00 4.24
1569 1586 0.887836 CCAGCAGCAGAAACAGCAGA 60.888 55.000 0.00 0.00 0.00 4.26
1570 1587 0.949397 CAGCAGCAGAAACAGCAGAA 59.051 50.000 0.00 0.00 0.00 3.02
1571 1588 1.335810 CAGCAGCAGAAACAGCAGAAA 59.664 47.619 0.00 0.00 0.00 2.52
1574 1591 2.480073 GCAGCAGAAACAGCAGAAACAA 60.480 45.455 0.00 0.00 0.00 2.83
1649 1700 0.835971 TGAGTTGGACCCAGCAGCTA 60.836 55.000 0.00 0.00 0.00 3.32
1650 1701 0.324943 GAGTTGGACCCAGCAGCTAA 59.675 55.000 0.00 0.00 0.00 3.09
1651 1702 0.771127 AGTTGGACCCAGCAGCTAAA 59.229 50.000 0.00 0.00 0.00 1.85
1819 1870 2.104963 GAGGAGGGTAATAAGGCCTGTG 59.895 54.545 5.69 0.00 0.00 3.66
1933 1986 2.606587 GGTCAGGCATCACCCAGGT 61.607 63.158 0.00 0.00 40.58 4.00
1946 1999 0.458669 CCCAGGTGCAAATGATGAGC 59.541 55.000 0.00 0.00 0.00 4.26
1947 2000 1.471119 CCAGGTGCAAATGATGAGCT 58.529 50.000 0.00 0.00 0.00 4.09
2029 2082 2.618709 GCCACTTAGTTGCACAGAAAGT 59.381 45.455 3.44 0.00 0.00 2.66
2073 2126 3.441922 TGCTTTTAGTTGCACACTGTTCA 59.558 39.130 10.59 0.00 35.97 3.18
2084 2138 7.602265 AGTTGCACACTGTTCAGTTTTAATTTT 59.398 29.630 2.47 0.00 32.83 1.82
2115 2174 0.257328 TTGGTTGCTGTGACCCTTCA 59.743 50.000 0.00 0.00 36.30 3.02
2240 2304 2.350772 CGGTTCAATGGCTGTCAAGAAC 60.351 50.000 17.37 17.37 40.57 3.01
2339 2403 9.290483 GAGGTTTTCTGTAAGTTTCTTCAAAAG 57.710 33.333 0.00 0.00 33.76 2.27
2558 2638 5.163269 CCCACATGATCCATCTCTTAGTTGA 60.163 44.000 0.00 0.00 0.00 3.18
2591 2671 2.097304 TGTTCAGTTGCACATGACACAC 59.903 45.455 0.00 0.00 0.00 3.82
2610 2690 3.135895 ACACCTGTTAGTTGGCAAGTACT 59.864 43.478 14.17 4.91 0.00 2.73
2640 2721 5.725362 CCAACCTGTTTTAACTTCACCAAA 58.275 37.500 0.00 0.00 0.00 3.28
2855 2942 1.202580 GCTCATGAACACCGCCTCTAT 60.203 52.381 0.00 0.00 0.00 1.98
2867 2955 0.818296 GCCTCTATCATCGCGGGTAT 59.182 55.000 6.13 0.00 0.00 2.73
2871 2959 3.065510 CCTCTATCATCGCGGGTATAGTG 59.934 52.174 6.13 11.04 0.00 2.74
2937 3025 6.832384 AGCACTTCCAGATTATTGACATTGAT 59.168 34.615 0.00 0.00 0.00 2.57
3120 3238 7.568349 TCAAGGATTATCTAGTCAGTTTGCAT 58.432 34.615 0.00 0.00 0.00 3.96
3134 3252 4.156556 CAGTTTGCATAGTGCCACATAAGT 59.843 41.667 0.00 0.00 44.23 2.24
3175 3293 3.480470 AGCAGTTGCACAGTAGAACATT 58.520 40.909 6.90 0.00 45.16 2.71
3732 3865 3.281727 TCCTGAATATGTCCACTTGGC 57.718 47.619 0.00 0.00 34.44 4.52
3927 4108 4.562143 GGGCACAAAATCATCAGAAGCTTT 60.562 41.667 0.00 0.00 0.00 3.51
3930 4111 5.464389 GCACAAAATCATCAGAAGCTTTTGT 59.536 36.000 15.90 12.41 45.73 2.83
3969 4150 1.363280 TGGGGTAGTAGGACCATCACA 59.637 52.381 0.00 0.00 41.73 3.58
4306 4497 5.102967 TGGAGTTGGGGTAGGTATTTTACT 58.897 41.667 0.00 0.00 0.00 2.24
4416 4607 0.482446 TTGAGGGTTGCCATCACCTT 59.518 50.000 1.74 0.00 44.22 3.50
4423 4614 1.892474 GTTGCCATCACCTTTAGCCAA 59.108 47.619 0.00 0.00 0.00 4.52
4488 4680 4.152625 CAGCGTGCGCAACTAGGC 62.153 66.667 14.00 11.18 44.88 3.93
4549 4743 7.986320 TGCAACTAAAGTTACACACCTAGTTAA 59.014 33.333 0.00 0.00 34.74 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 130 1.078918 CCTCGCTGCCATCAACTGA 60.079 57.895 0.00 0.00 0.00 3.41
240 255 2.027192 GCCTGTACCATCAGAACCAAGA 60.027 50.000 0.00 0.00 37.61 3.02
242 257 1.338674 CGCCTGTACCATCAGAACCAA 60.339 52.381 0.00 0.00 37.61 3.67
251 266 0.394938 TGTGTTGTCGCCTGTACCAT 59.605 50.000 0.00 0.00 0.00 3.55
263 278 1.734655 AGTCCTCCTGGATGTGTTGT 58.265 50.000 0.00 0.00 45.29 3.32
366 381 8.754991 TTGACTTTGGTAAATCCTTGTCTTTA 57.245 30.769 0.00 0.00 37.07 1.85
381 397 6.202516 TCGTCATTTTTCTTTGACTTTGGT 57.797 33.333 0.00 0.00 40.05 3.67
384 400 6.329496 TGCTTCGTCATTTTTCTTTGACTTT 58.671 32.000 0.00 0.00 40.05 2.66
435 451 2.154462 GGCTTCAAGTTGCAGAGCTTA 58.846 47.619 18.63 0.00 0.00 3.09
676 693 4.580580 GTGAGGGTTTGAAACAGATGTTCT 59.419 41.667 10.53 0.00 37.25 3.01
677 694 4.554723 CGTGAGGGTTTGAAACAGATGTTC 60.555 45.833 10.53 0.00 37.25 3.18
798 815 3.882888 CAGTTTGAACCACAGCTTCCTTA 59.117 43.478 0.00 0.00 0.00 2.69
961 978 0.759060 ACCCTTTTGTGCCCTGTTCC 60.759 55.000 0.00 0.00 0.00 3.62
1061 1078 4.530553 TGTAGTTGGCATCTTTCCAGTCTA 59.469 41.667 2.98 0.00 34.66 2.59
1166 1183 1.531365 CCTTGGGGCTTGCAGTTGA 60.531 57.895 0.00 0.00 0.00 3.18
1361 1378 1.133945 TGTTGTAGTTGGCAGCCTTGA 60.134 47.619 14.15 0.00 0.00 3.02
1368 1385 2.489971 GCAGTAGTGTTGTAGTTGGCA 58.510 47.619 0.00 0.00 0.00 4.92
1522 1539 4.009675 GTGTTGGAGCATCACCATCTTTA 58.990 43.478 0.00 0.00 37.26 1.85
1524 1541 2.440409 GTGTTGGAGCATCACCATCTT 58.560 47.619 0.00 0.00 37.26 2.40
1548 1565 0.887836 TGCTGTTTCTGCTGCTGGAG 60.888 55.000 5.73 5.73 34.93 3.86
1549 1566 0.887836 CTGCTGTTTCTGCTGCTGGA 60.888 55.000 6.69 0.00 34.93 3.86
1550 1567 0.887836 TCTGCTGTTTCTGCTGCTGG 60.888 55.000 6.69 0.00 34.69 4.85
1551 1568 0.949397 TTCTGCTGTTTCTGCTGCTG 59.051 50.000 0.00 0.00 34.93 4.41
1552 1569 1.336125 GTTTCTGCTGTTTCTGCTGCT 59.664 47.619 0.00 0.00 34.93 4.24
1553 1570 1.066002 TGTTTCTGCTGTTTCTGCTGC 59.934 47.619 0.00 0.00 0.00 5.25
1554 1571 3.111098 GTTGTTTCTGCTGTTTCTGCTG 58.889 45.455 0.00 0.00 0.00 4.41
1555 1572 2.754552 TGTTGTTTCTGCTGTTTCTGCT 59.245 40.909 0.00 0.00 0.00 4.24
1556 1573 2.854185 GTGTTGTTTCTGCTGTTTCTGC 59.146 45.455 0.00 0.00 0.00 4.26
1557 1574 3.129287 AGGTGTTGTTTCTGCTGTTTCTG 59.871 43.478 0.00 0.00 0.00 3.02
1558 1575 3.129287 CAGGTGTTGTTTCTGCTGTTTCT 59.871 43.478 0.00 0.00 0.00 2.52
1559 1576 3.438360 CAGGTGTTGTTTCTGCTGTTTC 58.562 45.455 0.00 0.00 0.00 2.78
1560 1577 3.508744 CAGGTGTTGTTTCTGCTGTTT 57.491 42.857 0.00 0.00 0.00 2.83
1566 1583 1.605710 CTGGAGCAGGTGTTGTTTCTG 59.394 52.381 0.00 0.00 0.00 3.02
1567 1584 1.972872 CTGGAGCAGGTGTTGTTTCT 58.027 50.000 0.00 0.00 0.00 2.52
1568 1585 0.312102 GCTGGAGCAGGTGTTGTTTC 59.688 55.000 0.00 0.00 41.59 2.78
1569 1586 2.419057 GCTGGAGCAGGTGTTGTTT 58.581 52.632 0.00 0.00 41.59 2.83
1570 1587 4.164258 GCTGGAGCAGGTGTTGTT 57.836 55.556 0.00 0.00 41.59 2.83
1649 1700 1.547372 AGCAGCGCATCCTTCATTTTT 59.453 42.857 11.47 0.00 0.00 1.94
1650 1701 1.135199 CAGCAGCGCATCCTTCATTTT 60.135 47.619 11.47 0.00 0.00 1.82
1651 1702 0.454600 CAGCAGCGCATCCTTCATTT 59.545 50.000 11.47 0.00 0.00 2.32
1819 1870 5.359194 TGAATGGAGACCTTTGAGATACC 57.641 43.478 0.00 0.00 0.00 2.73
1933 1986 3.018856 CCTGGTAAGCTCATCATTTGCA 58.981 45.455 0.00 0.00 0.00 4.08
1946 1999 3.560668 GGGGAGTTGGTTTACCTGGTAAG 60.561 52.174 18.02 0.00 36.82 2.34
1947 2000 2.376181 GGGGAGTTGGTTTACCTGGTAA 59.624 50.000 15.15 15.15 36.82 2.85
2029 2082 4.872124 CACAGTTCTATGCAACATGCTCTA 59.128 41.667 3.78 0.00 45.31 2.43
2098 2157 0.954452 CTTGAAGGGTCACAGCAACC 59.046 55.000 0.00 0.00 31.90 3.77
2240 2304 7.819415 TGTGTAAGATTCCAGTCTCAATAACAG 59.181 37.037 0.00 0.00 0.00 3.16
2339 2403 5.163405 ACAGAAAAAGAAGAGGGGAAAAAGC 60.163 40.000 0.00 0.00 0.00 3.51
2558 2638 4.821260 TGCAACTGAACATGTTATGAGTGT 59.179 37.500 11.95 1.85 0.00 3.55
2591 2671 5.531287 AGAAAAGTACTTGCCAACTAACAGG 59.469 40.000 9.34 0.00 0.00 4.00
2610 2690 5.669164 AGTTAAAACAGGTTGGCAGAAAA 57.331 34.783 0.00 0.00 0.00 2.29
2664 2749 2.882927 TCAGACACAGTTACACGCTT 57.117 45.000 0.00 0.00 0.00 4.68
2673 2758 2.738846 GCGTGAATGATTCAGACACAGT 59.261 45.455 8.33 0.00 41.01 3.55
2867 2955 1.399744 CCTCCATAGGTGGCGCACTA 61.400 60.000 10.83 9.05 45.63 2.74
2871 2959 1.227674 CTTCCTCCATAGGTGGCGC 60.228 63.158 0.00 0.00 45.63 6.53
3120 3238 4.250464 GTGCAACTACTTATGTGGCACTA 58.750 43.478 19.83 5.69 44.80 2.74
3134 3252 2.849294 TATGTGCCACTGTGCAACTA 57.151 45.000 1.29 0.00 44.11 2.24
3175 3293 1.414550 TGTGCCACTGTGCAACTACTA 59.585 47.619 1.29 0.00 44.11 1.82
3315 3439 1.358152 TAGTTGGGCAGTTGGCTACT 58.642 50.000 14.50 14.50 44.01 2.57
3555 3683 5.630680 CCTAATGTGTCAACAAAAGTGATGC 59.369 40.000 0.00 0.00 40.46 3.91
3732 3865 2.158842 TGGTTTTTGAGCAATGTTGGGG 60.159 45.455 0.00 0.00 31.67 4.96
3862 4042 1.177401 CAAAGGGTAGGGCAAAGAGC 58.823 55.000 0.00 0.00 44.65 4.09
3927 4108 1.635817 GGAGGCTGCATCCCCTACAA 61.636 60.000 22.05 0.00 32.01 2.41
3930 4111 0.698886 ATTGGAGGCTGCATCCCCTA 60.699 55.000 28.30 15.21 35.86 3.53
3969 4150 5.744171 TGTATGACTATTGCACAGGTGATT 58.256 37.500 3.10 0.00 0.00 2.57
4306 4497 0.547471 TCAGGAGGCTCATCACCCAA 60.547 55.000 17.69 0.00 0.00 4.12
4389 4580 0.110486 GGCAACCCTCAAAGACCTCA 59.890 55.000 0.00 0.00 0.00 3.86
4416 4607 4.464597 ACTTGTTTGTCCTGTTTTGGCTAA 59.535 37.500 0.00 0.00 0.00 3.09
4423 4614 6.015772 ACACAACTAACTTGTTTGTCCTGTTT 60.016 34.615 1.60 0.00 41.50 2.83
4488 4680 1.200716 CCAGTTGCACATAACAGGCTG 59.799 52.381 14.16 14.16 31.74 4.85
4549 4743 0.776080 ACCTGACCCAACTCCCCATT 60.776 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.