Multiple sequence alignment - TraesCS5B01G016600

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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 TraesCS5B01G016600 chr5B 100.000 2675 0 0 1 2675 15270265 15272939 0.000000e+00 4940
1 TraesCS5B01G016600 chr5B 96.124 774 26 2 1 770 15339106 15338333 0.000000e+00 1260
2 TraesCS5B01G016600 chr5B 85.672 1012 62 34 848 1792 15338296 15337301 0.000000e+00 989
3 TraesCS5B01G016600 chr5B 82.895 228 16 7 1832 2036 15337307 15337080 1.640000e-42 183
4 TraesCS5B01G016600 chr5D 85.722 1849 107 51 185 1922 21559845 21558043 0.000000e+00 1807
5 TraesCS5B01G016600 chr5D 90.222 767 57 9 1 762 21560653 21559900 0.000000e+00 985
6 TraesCS5B01G016600 chr5D 87.622 307 22 11 2376 2675 21555081 21554784 2.550000e-90 342
7 TraesCS5B01G016600 chr5D 98.551 69 1 0 2216 2284 21557157 21557089 3.620000e-24 122
8 TraesCS5B01G016600 chr5A 87.370 863 51 20 654 1479 14923593 14922752 0.000000e+00 937
9 TraesCS5B01G016600 chr5A 84.005 744 45 24 1475 2185 14922724 14922022 0.000000e+00 647
10 TraesCS5B01G016600 chr5A 82.212 416 41 14 1 395 14923997 14923594 7.140000e-86 327
11 TraesCS5B01G016600 chr5A 93.182 88 6 0 2376 2463 14914168 14914081 2.160000e-26 130
12 TraesCS5B01G016600 chr5A 98.387 62 1 0 2216 2277 14921491 14921430 2.820000e-20 110
13 TraesCS5B01G016600 chr4D 91.667 96 7 1 1044 1139 6969474 6969568 6.010000e-27 132
14 TraesCS5B01G016600 chr4B 91.667 96 7 1 1044 1139 12251716 12251810 6.010000e-27 132
15 TraesCS5B01G016600 chr4A 90.625 96 8 1 1044 1139 596571775 596571681 2.800000e-25 126
16 TraesCS5B01G016600 chr7B 95.588 68 1 2 2286 2353 59336062 59336127 1.010000e-19 108
17 TraesCS5B01G016600 chr7B 95.522 67 1 2 2286 2352 484901904 484901840 3.640000e-19 106
18 TraesCS5B01G016600 chr7B 95.522 67 1 2 2286 2352 484902160 484902096 3.640000e-19 106
19 TraesCS5B01G016600 chr7A 94.444 72 1 3 2282 2353 643964867 643964799 1.010000e-19 108
20 TraesCS5B01G016600 chr6B 95.588 68 1 2 2286 2353 191443981 191443916 1.010000e-19 108
21 TraesCS5B01G016600 chr3D 95.588 68 1 2 2286 2353 385437968 385437903 1.010000e-19 108
22 TraesCS5B01G016600 chr2A 96.923 65 0 2 2286 2350 588288041 588288103 1.010000e-19 108
23 TraesCS5B01G016600 chr1B 96.923 65 1 1 2286 2350 625208618 625208681 1.010000e-19 108
24 TraesCS5B01G016600 chr2B 95.522 67 1 2 2286 2352 503222734 503222798 3.640000e-19 106


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 TraesCS5B01G016600 chr5B 15270265 15272939 2674 False 4940.000000 4940 100.000000 1 2675 1 chr5B.!!$F1 2674
1 TraesCS5B01G016600 chr5B 15337080 15339106 2026 True 810.666667 1260 88.230333 1 2036 3 chr5B.!!$R1 2035
2 TraesCS5B01G016600 chr5D 21554784 21560653 5869 True 814.000000 1807 90.529250 1 2675 4 chr5D.!!$R1 2674
3 TraesCS5B01G016600 chr5A 14921430 14923997 2567 True 505.250000 937 87.993500 1 2277 4 chr5A.!!$R2 2276

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
914 1569 1.214175 TCCAAAGCCAAAGTGGAGACA 59.786 47.619 0.0 0.0 40.96 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 3016 0.243365 TGAATTCAACATGCCGCACC 59.757 50.0 5.45 0.0 0.0 5.01 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
108 109 6.483385 TTGTGGCAAATTTTTCATGCTATG 57.517 33.333 0.00 0.00 39.94 2.23
160 183 6.264744 AGGACCAATGCATCATATCTTTTCAG 59.735 38.462 0.00 0.00 0.00 3.02
221 249 3.620427 TTAATGTCGCAAGGAGCCTTA 57.380 42.857 0.66 0.00 41.38 2.69
294 322 4.452114 GCGAATGTGACATAATCAGCCATA 59.548 41.667 0.00 0.00 38.28 2.74
468 496 5.336690 GCATAGCATCACAAAAGAAAAGGGA 60.337 40.000 0.00 0.00 0.00 4.20
469 497 4.861102 AGCATCACAAAAGAAAAGGGAG 57.139 40.909 0.00 0.00 0.00 4.30
571 599 6.702972 TTGAACGTTTATGATGGCAAATTG 57.297 33.333 0.46 0.00 0.00 2.32
572 600 5.167121 TGAACGTTTATGATGGCAAATTGG 58.833 37.500 0.46 0.00 0.00 3.16
616 648 4.202040 TGCTAAATCAAAATGCCATCCTCG 60.202 41.667 0.00 0.00 0.00 4.63
625 657 2.887568 CCATCCTCGCGACAGCAC 60.888 66.667 3.71 0.00 45.49 4.40
686 718 9.142515 CAAAAATCTAATGCTCAATTTGCAGTA 57.857 29.630 8.56 8.87 44.04 2.74
812 1448 4.677584 TGTAGACCAAATGCACACAAAAC 58.322 39.130 0.00 0.00 0.00 2.43
846 1482 7.596749 ATTTTGTAATCCTACTTCACTCACG 57.403 36.000 0.00 0.00 0.00 4.35
865 1520 1.463056 CGAAATGTTTGCACTAGCGGA 59.537 47.619 0.00 0.00 46.23 5.54
871 1526 1.607148 GTTTGCACTAGCGGAGGTTTT 59.393 47.619 0.00 0.00 46.23 2.43
907 1562 2.955660 TCACGAAATCCAAAGCCAAAGT 59.044 40.909 0.00 0.00 0.00 2.66
908 1563 3.052036 CACGAAATCCAAAGCCAAAGTG 58.948 45.455 0.00 0.00 0.00 3.16
909 1564 2.035832 ACGAAATCCAAAGCCAAAGTGG 59.964 45.455 0.00 0.00 41.55 4.00
910 1565 2.295909 CGAAATCCAAAGCCAAAGTGGA 59.704 45.455 0.00 0.00 45.29 4.02
911 1566 3.612479 CGAAATCCAAAGCCAAAGTGGAG 60.612 47.826 0.00 0.00 44.45 3.86
912 1567 2.978156 ATCCAAAGCCAAAGTGGAGA 57.022 45.000 0.00 0.00 44.45 3.71
913 1568 1.981256 TCCAAAGCCAAAGTGGAGAC 58.019 50.000 0.00 0.00 40.96 3.36
914 1569 1.214175 TCCAAAGCCAAAGTGGAGACA 59.786 47.619 0.00 0.00 40.96 3.41
915 1570 2.031120 CCAAAGCCAAAGTGGAGACAA 58.969 47.619 0.00 0.00 46.06 3.18
916 1571 2.430332 CCAAAGCCAAAGTGGAGACAAA 59.570 45.455 0.00 0.00 46.06 2.83
917 1572 3.491447 CCAAAGCCAAAGTGGAGACAAAG 60.491 47.826 0.00 0.00 46.06 2.77
974 1663 1.507140 TCCCACTTCACACTCCACTT 58.493 50.000 0.00 0.00 0.00 3.16
977 1666 2.487934 CCACTTCACACTCCACTTCTG 58.512 52.381 0.00 0.00 0.00 3.02
1224 1913 2.090437 GGAGGTAGGGGAGATTCCTTCT 60.090 54.545 0.00 0.00 36.57 2.85
1234 1923 1.205893 AGATTCCTTCTCTGCCGACAC 59.794 52.381 0.00 0.00 0.00 3.67
1262 1951 3.825833 CTCTATCGCCGGTGGTCGC 62.826 68.421 16.49 0.00 37.59 5.19
1281 1970 3.462678 GAGGACTCCTCGGCACCC 61.463 72.222 9.44 0.00 41.08 4.61
1514 2267 2.930562 AGGTGGAAGAAGCGCCCT 60.931 61.111 2.29 0.00 0.00 5.19
1700 2510 0.809385 CGAGCCAGTTAGAACCGAGA 59.191 55.000 0.00 0.00 0.00 4.04
1702 2512 0.526662 AGCCAGTTAGAACCGAGACG 59.473 55.000 0.00 0.00 0.00 4.18
1711 2521 1.201880 AGAACCGAGACGTTTCTAGCC 59.798 52.381 4.43 0.00 29.47 3.93
1716 2526 1.736032 CGAGACGTTTCTAGCCCCTTG 60.736 57.143 4.43 0.00 29.47 3.61
1717 2527 1.275573 GAGACGTTTCTAGCCCCTTGT 59.724 52.381 0.00 0.00 29.47 3.16
1718 2528 1.697982 AGACGTTTCTAGCCCCTTGTT 59.302 47.619 0.00 0.00 0.00 2.83
1719 2529 2.105993 AGACGTTTCTAGCCCCTTGTTT 59.894 45.455 0.00 0.00 0.00 2.83
1831 2647 1.153628 GTTCGTCCCGGTGATCCTG 60.154 63.158 0.00 0.00 0.00 3.86
1922 2749 1.215647 CGTGGAGCGAGTTTAGGCT 59.784 57.895 0.00 0.00 44.77 4.58
1923 2750 0.454600 CGTGGAGCGAGTTTAGGCTA 59.545 55.000 0.00 0.00 44.77 3.93
1924 2751 1.534175 CGTGGAGCGAGTTTAGGCTAG 60.534 57.143 0.00 0.00 44.77 3.42
1925 2752 1.112113 TGGAGCGAGTTTAGGCTAGG 58.888 55.000 0.00 0.00 40.16 3.02
1926 2753 0.249531 GGAGCGAGTTTAGGCTAGGC 60.250 60.000 8.55 8.55 40.16 3.93
1977 2806 0.909623 ATCAATCCCCTCGAAACCGT 59.090 50.000 0.00 0.00 0.00 4.83
1978 2807 0.248289 TCAATCCCCTCGAAACCGTC 59.752 55.000 0.00 0.00 0.00 4.79
1979 2808 0.743345 CAATCCCCTCGAAACCGTCC 60.743 60.000 0.00 0.00 0.00 4.79
2028 2907 6.578023 AGACGGAAGAAGAAGAAATCCATAG 58.422 40.000 0.00 0.00 0.00 2.23
2046 2925 4.458295 CCATAGATGCTGAATGTTGATCCC 59.542 45.833 0.00 0.00 0.00 3.85
2061 2940 4.038080 CCCGCTTTTCCACCGTGC 62.038 66.667 0.00 0.00 0.00 5.34
2062 2941 2.978010 CCGCTTTTCCACCGTGCT 60.978 61.111 0.00 0.00 0.00 4.40
2068 2947 1.002468 CTTTTCCACCGTGCTCTTGTG 60.002 52.381 0.00 0.00 0.00 3.33
2070 2949 0.107410 TTCCACCGTGCTCTTGTGTT 60.107 50.000 0.00 0.00 0.00 3.32
2071 2950 0.813610 TCCACCGTGCTCTTGTGTTG 60.814 55.000 0.00 0.00 0.00 3.33
2072 2951 1.095228 CCACCGTGCTCTTGTGTTGT 61.095 55.000 0.00 0.00 0.00 3.32
2075 2954 1.013596 CCGTGCTCTTGTGTTGTTGA 58.986 50.000 0.00 0.00 0.00 3.18
2078 2957 3.291585 CGTGCTCTTGTGTTGTTGAATC 58.708 45.455 0.00 0.00 0.00 2.52
2079 2958 3.291585 GTGCTCTTGTGTTGTTGAATCG 58.708 45.455 0.00 0.00 0.00 3.34
2080 2959 2.290367 TGCTCTTGTGTTGTTGAATCGG 59.710 45.455 0.00 0.00 0.00 4.18
2081 2960 2.350772 GCTCTTGTGTTGTTGAATCGGG 60.351 50.000 0.00 0.00 0.00 5.14
2084 2963 2.932855 TGTGTTGTTGAATCGGGGTA 57.067 45.000 0.00 0.00 0.00 3.69
2085 2964 2.773487 TGTGTTGTTGAATCGGGGTAG 58.227 47.619 0.00 0.00 0.00 3.18
2097 2989 1.017387 CGGGGTAGAAATTCTGCTGC 58.983 55.000 10.71 0.00 29.49 5.25
2099 2991 1.017387 GGGTAGAAATTCTGCTGCCG 58.983 55.000 10.71 0.00 37.72 5.69
2124 3016 3.558505 CTGAATTTCTTTCCTGTGTGCG 58.441 45.455 0.00 0.00 33.04 5.34
2142 3034 0.798009 CGGTGCGGCATGTTGAATTC 60.798 55.000 5.72 0.00 0.00 2.17
2144 3036 1.336702 GGTGCGGCATGTTGAATTCAA 60.337 47.619 16.91 16.91 0.00 2.69
2185 3077 1.398705 GCGATCGTGCAAAACCGTTAA 60.399 47.619 17.81 0.00 34.15 2.01
2187 3079 2.348685 CGATCGTGCAAAACCGTTAACA 60.349 45.455 7.03 0.00 0.00 2.41
2188 3080 3.619729 GATCGTGCAAAACCGTTAACAA 58.380 40.909 6.39 0.00 0.00 2.83
2189 3081 3.482722 TCGTGCAAAACCGTTAACAAA 57.517 38.095 6.39 0.00 0.00 2.83
2190 3082 3.829948 TCGTGCAAAACCGTTAACAAAA 58.170 36.364 6.39 0.00 0.00 2.44
2193 3085 4.501198 CGTGCAAAACCGTTAACAAAAGAT 59.499 37.500 6.39 0.00 0.00 2.40
2196 3088 6.035112 GTGCAAAACCGTTAACAAAAGATCAA 59.965 34.615 6.39 0.00 0.00 2.57
2199 3091 7.412020 GCAAAACCGTTAACAAAAGATCAAACA 60.412 33.333 6.39 0.00 0.00 2.83
2200 3092 7.749539 AAACCGTTAACAAAAGATCAAACAG 57.250 32.000 6.39 0.00 0.00 3.16
2214 3617 6.413052 AGATCAAACAGCAGTGATGAACTAT 58.587 36.000 16.72 3.19 36.83 2.12
2284 3720 9.534565 TTCAGTTAGTTGCACAGATAGATAATC 57.465 33.333 0.00 0.00 34.52 1.75
2285 3721 8.695456 TCAGTTAGTTGCACAGATAGATAATCA 58.305 33.333 0.00 0.00 37.03 2.57
2286 3722 9.317936 CAGTTAGTTGCACAGATAGATAATCAA 57.682 33.333 0.00 0.00 37.03 2.57
2287 3723 9.890629 AGTTAGTTGCACAGATAGATAATCAAA 57.109 29.630 0.00 0.00 37.03 2.69
2288 3724 9.922305 GTTAGTTGCACAGATAGATAATCAAAC 57.078 33.333 0.00 0.00 37.03 2.93
2289 3725 9.890629 TTAGTTGCACAGATAGATAATCAAACT 57.109 29.630 0.00 0.00 37.03 2.66
2290 3726 8.798859 AGTTGCACAGATAGATAATCAAACTT 57.201 30.769 0.00 0.00 37.03 2.66
2293 3729 9.890629 TTGCACAGATAGATAATCAAACTTAGT 57.109 29.630 0.00 0.00 37.03 2.24
2294 3730 9.534565 TGCACAGATAGATAATCAAACTTAGTC 57.465 33.333 0.00 0.00 37.03 2.59
2295 3731 9.534565 GCACAGATAGATAATCAAACTTAGTCA 57.465 33.333 0.00 0.00 37.03 3.41
2324 3760 8.888579 TTAAACAAAAGTTTGACTTTGACCAA 57.111 26.923 10.66 0.00 46.78 3.67
2325 3761 7.793927 AAACAAAAGTTTGACTTTGACCAAA 57.206 28.000 10.66 0.00 46.78 3.28
2326 3762 7.977789 AACAAAAGTTTGACTTTGACCAAAT 57.022 28.000 10.66 0.00 46.78 2.32
2327 3763 7.595311 ACAAAAGTTTGACTTTGACCAAATC 57.405 32.000 10.66 0.00 46.78 2.17
2328 3764 7.386059 ACAAAAGTTTGACTTTGACCAAATCT 58.614 30.769 10.66 0.00 46.78 2.40
2329 3765 7.877612 ACAAAAGTTTGACTTTGACCAAATCTT 59.122 29.630 10.66 0.00 46.78 2.40
2330 3766 9.364989 CAAAAGTTTGACTTTGACCAAATCTTA 57.635 29.630 6.81 0.00 46.78 2.10
2335 3771 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
2337 3773 7.988737 TGACTTTGACCAAATCTTATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
2342 3778 9.679661 TTTGACCAAATCTTATATGCAGACTAA 57.320 29.630 0.00 0.00 0.00 2.24
2343 3779 9.679661 TTGACCAAATCTTATATGCAGACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
2344 3780 9.679661 TGACCAAATCTTATATGCAGACTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
2359 4151 6.128145 GCAGACTAAAAAGAAATGGTCTCTCC 60.128 42.308 0.00 0.00 34.56 3.71
2417 5769 4.761739 GGATTCATGTTCTTGGAGTTGACA 59.238 41.667 0.00 0.00 0.00 3.58
2457 5816 2.131023 AGGATCCTTGGATTCTGGTCC 58.869 52.381 9.02 3.48 38.81 4.46
2459 5818 3.051032 AGGATCCTTGGATTCTGGTCCTA 60.051 47.826 9.02 0.00 39.12 2.94
2467 5826 4.570926 TGGATTCTGGTCCTATGGATTCT 58.429 43.478 0.00 0.00 39.12 2.40
2470 5829 6.270927 TGGATTCTGGTCCTATGGATTCTAAG 59.729 42.308 0.00 0.00 39.12 2.18
2516 5875 1.341080 CAATGGTTGGGCTTTCAGGT 58.659 50.000 0.00 0.00 0.00 4.00
2517 5876 1.693606 CAATGGTTGGGCTTTCAGGTT 59.306 47.619 0.00 0.00 0.00 3.50
2524 5883 2.758130 TGGGCTTTCAGGTTTTTCCTT 58.242 42.857 0.00 0.00 45.67 3.36
2526 5885 4.290942 TGGGCTTTCAGGTTTTTCCTTTA 58.709 39.130 0.00 0.00 45.67 1.85
2527 5886 4.100344 TGGGCTTTCAGGTTTTTCCTTTAC 59.900 41.667 0.00 0.00 45.67 2.01
2570 5929 4.215330 GTTTTCCCGAAAACGGCG 57.785 55.556 15.21 4.80 46.90 6.46
2594 5953 0.178767 ATGCAATCAGCCTCTGCGTA 59.821 50.000 0.00 0.00 44.83 4.42
2595 5954 0.460811 TGCAATCAGCCTCTGCGTAG 60.461 55.000 0.00 0.00 44.83 3.51
2596 5955 0.460987 GCAATCAGCCTCTGCGTAGT 60.461 55.000 0.00 0.00 44.33 2.73
2597 5956 1.565305 CAATCAGCCTCTGCGTAGTC 58.435 55.000 0.00 0.00 44.33 2.59
2598 5957 0.101399 AATCAGCCTCTGCGTAGTCG 59.899 55.000 0.00 0.00 44.33 4.18
2618 5977 1.670674 GCGTAGACCGTGACCAATCAA 60.671 52.381 0.00 0.00 36.31 2.57
2620 5979 2.603110 CGTAGACCGTGACCAATCAATG 59.397 50.000 0.00 0.00 36.31 2.82
2626 5985 2.162208 CCGTGACCAATCAATGAACCAG 59.838 50.000 0.00 0.00 36.31 4.00
2634 5993 4.406069 CAATCAATGAACCAGTAGTTGCG 58.594 43.478 0.00 0.00 39.40 4.85
2649 6008 3.664025 TGCGTTGCATCCGAGAGGG 62.664 63.158 10.15 0.00 42.98 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 236 6.483640 ACTTAAGAAATATAAGGCTCCTTGCG 59.516 38.462 10.09 0.00 44.05 4.85
210 238 8.738645 ACACTTAAGAAATATAAGGCTCCTTG 57.261 34.615 10.09 0.00 37.47 3.61
571 599 3.088532 TGACAAATGCTATGGACAACCC 58.911 45.455 0.00 0.00 34.81 4.11
572 600 4.675510 CATGACAAATGCTATGGACAACC 58.324 43.478 0.00 0.00 0.00 3.77
605 637 2.107750 CTGTCGCGAGGATGGCAT 59.892 61.111 10.24 0.00 41.24 4.40
625 657 3.181503 CGAACTCCTGAGATGGCAAATTG 60.182 47.826 0.22 0.00 0.00 2.32
726 759 4.516321 GCCATTCAAAATTCTTGTTGGCTT 59.484 37.500 23.05 0.00 41.71 4.35
727 760 4.067192 GCCATTCAAAATTCTTGTTGGCT 58.933 39.130 23.05 2.51 41.71 4.75
841 1477 3.482786 GCTAGTGCAAACATTTCGTGAG 58.517 45.455 0.00 0.00 39.41 3.51
842 1478 2.096466 CGCTAGTGCAAACATTTCGTGA 60.096 45.455 0.00 0.00 39.64 4.35
843 1479 2.233355 CGCTAGTGCAAACATTTCGTG 58.767 47.619 0.00 0.00 39.64 4.35
845 1481 1.463056 TCCGCTAGTGCAAACATTTCG 59.537 47.619 0.00 0.00 39.64 3.46
846 1482 2.159517 CCTCCGCTAGTGCAAACATTTC 60.160 50.000 0.00 0.00 39.64 2.17
865 1520 4.398044 TGAGCGAAGAAAACAAGAAAACCT 59.602 37.500 0.00 0.00 0.00 3.50
871 1526 2.816689 TCGTGAGCGAAGAAAACAAGA 58.183 42.857 0.00 0.00 44.92 3.02
907 1562 1.965414 TATGGCCTCCTTTGTCTCCA 58.035 50.000 3.32 0.00 0.00 3.86
908 1563 3.366052 TTTATGGCCTCCTTTGTCTCC 57.634 47.619 3.32 0.00 0.00 3.71
909 1564 3.129462 GCTTTTATGGCCTCCTTTGTCTC 59.871 47.826 3.32 0.00 0.00 3.36
910 1565 3.092301 GCTTTTATGGCCTCCTTTGTCT 58.908 45.455 3.32 0.00 0.00 3.41
911 1566 2.166459 GGCTTTTATGGCCTCCTTTGTC 59.834 50.000 3.32 0.00 45.57 3.18
912 1567 2.179427 GGCTTTTATGGCCTCCTTTGT 58.821 47.619 3.32 0.00 45.57 2.83
913 1568 2.967599 GGCTTTTATGGCCTCCTTTG 57.032 50.000 3.32 0.00 45.57 2.77
947 1613 1.625818 GTGTGAAGTGGGATGGTCTCT 59.374 52.381 0.00 0.00 0.00 3.10
974 1663 1.816537 GGCGAGCATACAGGACAGA 59.183 57.895 0.00 0.00 0.00 3.41
1202 1891 0.188834 AGGAATCTCCCCTACCTCCG 59.811 60.000 0.00 0.00 37.19 4.63
1407 2096 2.125512 AGCGAGGCGATGGTGAAC 60.126 61.111 0.00 0.00 0.00 3.18
1514 2267 2.184322 GTCGGAATCGGAGCAGCA 59.816 61.111 0.00 0.00 36.95 4.41
1585 2368 0.898789 TCCTCGCTTTCCTCTTCGGT 60.899 55.000 0.00 0.00 0.00 4.69
1700 2510 2.501261 GAAACAAGGGGCTAGAAACGT 58.499 47.619 0.00 0.00 0.00 3.99
1702 2512 1.199327 GCGAAACAAGGGGCTAGAAAC 59.801 52.381 0.00 0.00 0.00 2.78
1711 2521 2.668212 TGCTCGGCGAAACAAGGG 60.668 61.111 12.13 0.00 0.00 3.95
1716 2526 4.135493 GCGTCTGCTCGGCGAAAC 62.135 66.667 12.13 6.86 38.39 2.78
1825 2641 4.925861 GCGAGGCCTGCCAGGATC 62.926 72.222 16.85 10.60 37.67 3.36
1914 2730 0.253327 ACTGCCTGCCTAGCCTAAAC 59.747 55.000 0.00 0.00 0.00 2.01
1922 2749 3.390521 CCGGTCACTGCCTGCCTA 61.391 66.667 0.00 0.00 0.00 3.93
1940 2767 2.054140 ATCGGAACTCTCTCGCTCGC 62.054 60.000 0.00 0.00 0.00 5.03
1945 2772 2.287909 GGGATTGATCGGAACTCTCTCG 60.288 54.545 0.00 0.00 0.00 4.04
1977 2806 0.387202 TTTACAAACGGACGGACGGA 59.613 50.000 6.00 0.00 38.39 4.69
1978 2807 1.216122 TTTTACAAACGGACGGACGG 58.784 50.000 6.00 0.00 38.39 4.79
2008 2884 6.997476 AGCATCTATGGATTTCTTCTTCTTCC 59.003 38.462 0.00 0.00 0.00 3.46
2028 2907 1.002033 GCGGGATCAACATTCAGCATC 60.002 52.381 0.00 0.00 0.00 3.91
2061 2940 2.226437 CCCCGATTCAACAACACAAGAG 59.774 50.000 0.00 0.00 0.00 2.85
2062 2941 2.226330 CCCCGATTCAACAACACAAGA 58.774 47.619 0.00 0.00 0.00 3.02
2068 2947 5.414765 AGAATTTCTACCCCGATTCAACAAC 59.585 40.000 0.00 0.00 32.35 3.32
2070 2949 4.941263 CAGAATTTCTACCCCGATTCAACA 59.059 41.667 0.00 0.00 32.35 3.33
2071 2950 4.201920 GCAGAATTTCTACCCCGATTCAAC 60.202 45.833 0.00 0.00 32.35 3.18
2072 2951 3.945285 GCAGAATTTCTACCCCGATTCAA 59.055 43.478 0.00 0.00 32.35 2.69
2075 2954 3.545703 CAGCAGAATTTCTACCCCGATT 58.454 45.455 0.00 0.00 0.00 3.34
2078 2957 1.017387 GCAGCAGAATTTCTACCCCG 58.983 55.000 0.00 0.00 0.00 5.73
2079 2958 1.393603 GGCAGCAGAATTTCTACCCC 58.606 55.000 0.00 0.00 0.00 4.95
2080 2959 1.017387 CGGCAGCAGAATTTCTACCC 58.983 55.000 0.00 0.00 0.00 3.69
2081 2960 1.398390 CACGGCAGCAGAATTTCTACC 59.602 52.381 0.00 0.00 0.00 3.18
2084 2963 1.589716 GGCACGGCAGCAGAATTTCT 61.590 55.000 0.00 0.00 35.83 2.52
2085 2964 1.153958 GGCACGGCAGCAGAATTTC 60.154 57.895 0.00 0.00 35.83 2.17
2097 2989 2.095059 CAGGAAAGAAATTCAGGCACGG 60.095 50.000 0.00 0.00 39.98 4.94
2099 2991 3.319122 ACACAGGAAAGAAATTCAGGCAC 59.681 43.478 0.00 0.00 39.98 5.01
2124 3016 0.243365 TGAATTCAACATGCCGCACC 59.757 50.000 5.45 0.00 0.00 5.01
2138 3030 5.302568 TCAGCCAAGAAGTGTTCATTGAATT 59.697 36.000 1.78 0.00 0.00 2.17
2142 3034 3.316029 TGTCAGCCAAGAAGTGTTCATTG 59.684 43.478 0.00 0.00 0.00 2.82
2144 3036 3.144506 CTGTCAGCCAAGAAGTGTTCAT 58.855 45.455 0.00 0.00 0.00 2.57
2185 3077 5.300034 TCATCACTGCTGTTTGATCTTTTGT 59.700 36.000 0.00 0.00 29.64 2.83
2187 3079 6.040166 AGTTCATCACTGCTGTTTGATCTTTT 59.960 34.615 6.88 0.00 32.83 2.27
2188 3080 5.533903 AGTTCATCACTGCTGTTTGATCTTT 59.466 36.000 6.88 0.00 32.83 2.52
2189 3081 5.068636 AGTTCATCACTGCTGTTTGATCTT 58.931 37.500 6.88 0.00 32.83 2.40
2190 3082 4.649692 AGTTCATCACTGCTGTTTGATCT 58.350 39.130 6.88 8.31 32.83 2.75
2193 3085 5.550290 TGATAGTTCATCACTGCTGTTTGA 58.450 37.500 0.00 0.00 38.79 2.69
2196 3088 6.175471 TGATTGATAGTTCATCACTGCTGTT 58.825 36.000 0.00 0.00 43.49 3.16
2199 3091 4.815308 GCTGATTGATAGTTCATCACTGCT 59.185 41.667 0.00 0.00 43.49 4.24
2200 3092 4.024218 GGCTGATTGATAGTTCATCACTGC 60.024 45.833 0.00 0.00 43.49 4.40
2214 3617 1.519246 CAGAGGCGAGGCTGATTGA 59.481 57.895 3.24 0.00 34.06 2.57
2301 3737 8.389779 ATTTGGTCAAAGTCAAACTTTTGTTT 57.610 26.923 2.42 0.00 45.38 2.83
2304 3740 7.832503 AGATTTGGTCAAAGTCAAACTTTTG 57.167 32.000 2.42 0.00 45.38 2.44
2310 3746 8.801299 TGCATATAAGATTTGGTCAAAGTCAAA 58.199 29.630 2.55 0.00 37.29 2.69
2311 3747 8.347004 TGCATATAAGATTTGGTCAAAGTCAA 57.653 30.769 2.55 0.00 33.32 3.18
2315 3751 8.218338 AGTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
2316 3752 9.679661 TTAGTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
2317 3753 9.679661 TTTAGTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
2318 3754 9.679661 TTTTAGTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
2329 3765 9.905713 AGACCATTTCTTTTTAGTCTGCATATA 57.094 29.630 0.00 0.00 33.50 0.86
2330 3766 8.814038 AGACCATTTCTTTTTAGTCTGCATAT 57.186 30.769 0.00 0.00 33.50 1.78
2331 3767 8.103305 AGAGACCATTTCTTTTTAGTCTGCATA 58.897 33.333 0.00 0.00 34.84 3.14
2332 3768 6.944862 AGAGACCATTTCTTTTTAGTCTGCAT 59.055 34.615 0.00 0.00 34.84 3.96
2333 3769 6.299141 AGAGACCATTTCTTTTTAGTCTGCA 58.701 36.000 0.00 0.00 34.84 4.41
2334 3770 6.128145 GGAGAGACCATTTCTTTTTAGTCTGC 60.128 42.308 0.00 0.00 34.84 4.26
2335 3771 7.164803 AGGAGAGACCATTTCTTTTTAGTCTG 58.835 38.462 0.00 0.00 42.04 3.51
2337 3773 7.987750 AAGGAGAGACCATTTCTTTTTAGTC 57.012 36.000 0.00 0.00 42.04 2.59
2368 4160 8.896744 CACTGATGCAGATATTTCCTTTTCTAA 58.103 33.333 0.82 0.00 35.18 2.10
2369 4161 7.500227 CCACTGATGCAGATATTTCCTTTTCTA 59.500 37.037 0.82 0.00 35.18 2.10
2370 4162 6.320672 CCACTGATGCAGATATTTCCTTTTCT 59.679 38.462 0.82 0.00 35.18 2.52
2371 4163 6.319658 TCCACTGATGCAGATATTTCCTTTTC 59.680 38.462 0.82 0.00 35.18 2.29
2372 4164 6.189859 TCCACTGATGCAGATATTTCCTTTT 58.810 36.000 0.82 0.00 35.18 2.27
2373 4165 5.759059 TCCACTGATGCAGATATTTCCTTT 58.241 37.500 0.82 0.00 35.18 3.11
2390 5742 4.330250 ACTCCAAGAACATGAATCCACTG 58.670 43.478 0.00 0.00 0.00 3.66
2417 5769 5.261216 TCCTTTTCCTCTTGCGGATATTTT 58.739 37.500 0.00 0.00 32.02 1.82
2459 5818 9.383519 CAAACGCCATATATACTTAGAATCCAT 57.616 33.333 0.00 0.00 0.00 3.41
2467 5826 9.811995 GGTATGATCAAACGCCATATATACTTA 57.188 33.333 0.00 0.00 0.00 2.24
2470 5829 7.254455 GCAGGTATGATCAAACGCCATATATAC 60.254 40.741 0.00 0.00 0.00 1.47
2480 5839 3.243168 CCATTGGCAGGTATGATCAAACG 60.243 47.826 0.00 0.00 0.00 3.60
2570 5929 2.928116 GCAGAGGCTGATTGCATTTTTC 59.072 45.455 9.58 0.00 45.15 2.29
2600 5959 3.857052 TCATTGATTGGTCACGGTCTAC 58.143 45.455 0.00 0.00 33.11 2.59
2601 5960 4.250464 GTTCATTGATTGGTCACGGTCTA 58.750 43.478 0.00 0.00 33.11 2.59
2602 5961 3.074412 GTTCATTGATTGGTCACGGTCT 58.926 45.455 0.00 0.00 33.11 3.85
2603 5962 2.161609 GGTTCATTGATTGGTCACGGTC 59.838 50.000 0.00 0.00 33.11 4.79
2604 5963 2.159382 GGTTCATTGATTGGTCACGGT 58.841 47.619 0.00 0.00 33.11 4.83
2605 5964 2.158559 TGGTTCATTGATTGGTCACGG 58.841 47.619 0.00 0.00 33.11 4.94
2606 5965 2.813754 ACTGGTTCATTGATTGGTCACG 59.186 45.455 0.00 0.00 33.11 4.35
2607 5966 5.003804 ACTACTGGTTCATTGATTGGTCAC 58.996 41.667 0.00 0.00 33.11 3.67
2608 5967 5.241403 ACTACTGGTTCATTGATTGGTCA 57.759 39.130 0.00 0.00 0.00 4.02
2618 5977 1.535462 GCAACGCAACTACTGGTTCAT 59.465 47.619 0.00 0.00 35.74 2.57
2620 5979 0.941542 TGCAACGCAACTACTGGTTC 59.058 50.000 0.00 0.00 34.76 3.62
2626 5985 0.370273 CTCGGATGCAACGCAACTAC 59.630 55.000 9.06 0.00 43.62 2.73
2634 5993 1.087501 GTTTCCCTCTCGGATGCAAC 58.912 55.000 0.00 0.00 41.63 4.17
2649 6008 2.225019 CACACACATCTGCTCTGGTTTC 59.775 50.000 0.00 0.00 0.00 2.78
2653 6012 1.888215 AACACACACATCTGCTCTGG 58.112 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.