Multiple sequence alignment - TraesCS5D01G545500

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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 TraesCS5D01G545500 chr5D 100.000 4192 0 0 1 4192 554503747 554507938 0.000000e+00 7742.0
1 TraesCS5D01G545500 chr5D 79.836 610 83 26 1906 2507 6111498 6110921 3.900000e-110 409.0
2 TraesCS5D01G545500 chr5B 91.588 2449 143 28 1757 4192 696177705 696175307 0.000000e+00 3323.0
3 TraesCS5D01G545500 chr5B 87.986 1132 48 28 610 1691 696178806 696177713 0.000000e+00 1256.0
4 TraesCS5D01G545500 chr5B 80.592 608 71 32 1906 2507 690650186 690649620 3.870000e-115 425.0
5 TraesCS5D01G545500 chr5B 84.839 310 18 12 3 292 696179353 696179053 6.860000e-73 285.0
6 TraesCS5D01G545500 chr5B 90.000 110 10 1 337 445 696178912 696178803 1.570000e-29 141.0
7 TraesCS5D01G545500 chr4A 93.192 2071 110 8 2127 4192 614028558 614026514 0.000000e+00 3014.0
8 TraesCS5D01G545500 chr4A 92.188 768 33 7 842 1589 614029925 614029165 0.000000e+00 1061.0
9 TraesCS5D01G545500 chr4A 85.062 810 58 31 1 747 614030783 614029974 0.000000e+00 767.0
10 TraesCS5D01G545500 chr4A 92.473 279 12 3 1858 2135 614028980 614028710 1.410000e-104 390.0
11 TraesCS5D01G545500 chr1A 81.291 604 68 30 1910 2507 590841639 590841075 8.270000e-122 448.0
12 TraesCS5D01G545500 chr1A 94.118 51 3 0 2519 2569 446542858 446542808 1.250000e-10 78.7
13 TraesCS5D01G545500 chr1A 86.111 72 8 2 2589 2660 590841046 590840977 4.490000e-10 76.8
14 TraesCS5D01G545500 chr4D 94.444 54 3 0 2516 2569 165260820 165260873 2.690000e-12 84.2
15 TraesCS5D01G545500 chr2B 96.078 51 2 0 2516 2566 458853936 458853986 2.690000e-12 84.2
16 TraesCS5D01G545500 chr5A 97.872 47 1 0 2520 2566 76958143 76958189 9.660000e-12 82.4
17 TraesCS5D01G545500 chr7A 95.918 49 2 0 2516 2564 50054298 50054346 3.470000e-11 80.5
18 TraesCS5D01G545500 chr1D 94.118 51 3 0 2519 2569 122770132 122770082 1.250000e-10 78.7
19 TraesCS5D01G545500 chr1D 95.833 48 2 0 2519 2566 202564391 202564344 1.250000e-10 78.7


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 TraesCS5D01G545500 chr5D 554503747 554507938 4191 False 7742.00 7742 100.00000 1 4192 1 chr5D.!!$F1 4191
1 TraesCS5D01G545500 chr5D 6110921 6111498 577 True 409.00 409 79.83600 1906 2507 1 chr5D.!!$R1 601
2 TraesCS5D01G545500 chr5B 696175307 696179353 4046 True 1251.25 3323 88.60325 3 4192 4 chr5B.!!$R2 4189
3 TraesCS5D01G545500 chr5B 690649620 690650186 566 True 425.00 425 80.59200 1906 2507 1 chr5B.!!$R1 601
4 TraesCS5D01G545500 chr4A 614026514 614030783 4269 True 1308.00 3014 90.72875 1 4192 4 chr4A.!!$R1 4191
5 TraesCS5D01G545500 chr1A 590840977 590841639 662 True 262.40 448 83.70100 1910 2660 2 chr1A.!!$R2 750

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
313 355 0.033109 GATGACCCCCTTCCCTTTGG 60.033 60.0 0.0 0.0 0.0 3.28 F
578 716 0.036294 GACCACCTTCTTCTTCCCGG 60.036 60.0 0.0 0.0 0.0 5.73 F
974 1187 0.247460 CGCTTGGACTCATCTGACCA 59.753 55.0 0.0 0.0 0.0 4.02 F
1515 1737 0.655733 CCAAGCTGTTCAACGTCGTT 59.344 50.0 4.4 4.4 0.0 3.85 F
2071 2313 1.016627 TCTGCACAAACTGACACTGC 58.983 50.0 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2260 0.972983 TCTCCCTTTCCTCAGGCGAG 60.973 60.000 0.0 0.28 39.16 5.03 R
2322 2733 3.334691 ACGCAGCAGTTCTAGCATTTAA 58.665 40.909 0.0 0.00 0.00 1.52 R
2600 3011 0.607489 AGGACACAACCAGCATCAGC 60.607 55.000 0.0 0.00 42.56 4.26 R
2832 3245 1.203050 CCAGGAAACAACCAGGACCAT 60.203 52.381 0.0 0.00 38.63 3.55 R
3928 4346 0.107703 TGTAGGAAGAGCCATTGCCG 60.108 55.000 0.0 0.00 40.02 5.69 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
41 42 5.245531 TGTGGATCTGGATTGTTGAACTAC 58.754 41.667 0.00 0.00 0.00 2.73
60 61 9.002600 TGAACTACATGATGATTATTATGTGCC 57.997 33.333 15.56 5.26 41.80 5.01
76 77 1.128692 GTGCCGTTTGCTGTCATAGAC 59.871 52.381 0.00 0.00 42.00 2.59
105 108 6.625362 AGTAGTAGTCATCATGTGTGTTCTG 58.375 40.000 0.00 0.00 0.00 3.02
168 179 2.564062 CCAAAATGAGGCAAGGTCATGT 59.436 45.455 0.00 0.00 34.78 3.21
231 257 9.931210 GTAGCAATTAAGGTGTGATAATAACAC 57.069 33.333 0.00 0.00 45.81 3.32
260 293 6.259387 GGTGGTAAATAACATGTACTGTAGGC 59.741 42.308 0.00 0.00 36.98 3.93
272 308 6.169557 TGTACTGTAGGCGGAATTATTCAT 57.830 37.500 7.29 0.00 0.00 2.57
292 328 0.926155 CACGAGCCGATGAACATCTG 59.074 55.000 12.05 7.38 35.72 2.90
294 330 0.877649 CGAGCCGATGAACATCTGGG 60.878 60.000 18.91 12.74 35.72 4.45
301 343 2.808202 CGATGAACATCTGGGATGACCC 60.808 54.545 13.51 0.00 42.69 4.46
302 344 5.927512 CGATGAACATCTGGGATGACCCC 62.928 56.522 13.51 0.00 42.22 4.95
313 355 0.033109 GATGACCCCCTTCCCTTTGG 60.033 60.000 0.00 0.00 0.00 3.28
454 592 4.789075 GCCGCGGCGTAGAACTCA 62.789 66.667 37.24 0.00 0.00 3.41
458 596 2.202570 CGGCGTAGAACTCACGGG 60.203 66.667 0.00 0.00 39.75 5.28
460 598 1.153881 GGCGTAGAACTCACGGGAC 60.154 63.158 0.00 0.00 39.75 4.46
461 599 1.153881 GCGTAGAACTCACGGGACC 60.154 63.158 0.00 0.00 39.75 4.46
499 637 4.746309 TCGTCGTCGGGGATGGGT 62.746 66.667 1.55 0.00 37.69 4.51
526 664 0.538746 TGTAGGGGCTCGCGATCATA 60.539 55.000 10.36 1.66 0.00 2.15
531 669 1.080995 GGGCTCGCGATCATATGCTC 61.081 60.000 10.36 4.16 0.00 4.26
532 670 1.080995 GGCTCGCGATCATATGCTCC 61.081 60.000 10.36 0.00 0.00 4.70
564 702 1.373748 TTAGCCGCGTCTTGACCAC 60.374 57.895 4.92 0.00 0.00 4.16
572 710 1.270358 GCGTCTTGACCACCTTCTTCT 60.270 52.381 0.00 0.00 0.00 2.85
574 712 3.060602 CGTCTTGACCACCTTCTTCTTC 58.939 50.000 0.00 0.00 0.00 2.87
575 713 3.403968 GTCTTGACCACCTTCTTCTTCC 58.596 50.000 0.00 0.00 0.00 3.46
576 714 2.372172 TCTTGACCACCTTCTTCTTCCC 59.628 50.000 0.00 0.00 0.00 3.97
577 715 0.685097 TGACCACCTTCTTCTTCCCG 59.315 55.000 0.00 0.00 0.00 5.14
578 716 0.036294 GACCACCTTCTTCTTCCCGG 60.036 60.000 0.00 0.00 0.00 5.73
579 717 1.377333 CCACCTTCTTCTTCCCGGC 60.377 63.158 0.00 0.00 0.00 6.13
581 719 2.125106 CCTTCTTCTTCCCGGCCG 60.125 66.667 21.04 21.04 0.00 6.13
584 722 3.291101 TTCTTCTTCCCGGCCGTCG 62.291 63.158 26.12 14.11 38.88 5.12
585 723 3.755628 CTTCTTCCCGGCCGTCGA 61.756 66.667 26.12 16.47 42.43 4.20
604 766 2.281208 TTCGTGCCCGGTGAAAGG 60.281 61.111 0.00 0.00 33.95 3.11
637 799 1.066587 CGCCTCCGTCATCTCCTTC 59.933 63.158 0.00 0.00 0.00 3.46
684 846 4.200283 CGCCTCCCTCTCGAGCAC 62.200 72.222 7.81 0.00 0.00 4.40
689 851 4.504916 CCCTCTCGAGCACAGCGG 62.505 72.222 7.81 0.55 0.00 5.52
690 852 3.753434 CCTCTCGAGCACAGCGGT 61.753 66.667 7.81 0.00 0.00 5.68
788 962 2.610859 GGAGGTGAGGAAGGCCCA 60.611 66.667 0.00 0.00 37.41 5.36
845 1019 3.335534 GCAACGTGACGGTTCGCT 61.336 61.111 10.66 0.00 0.00 4.93
846 1020 2.544359 CAACGTGACGGTTCGCTG 59.456 61.111 10.66 0.00 0.00 5.18
847 1021 2.105528 AACGTGACGGTTCGCTGT 59.894 55.556 10.66 0.00 39.90 4.40
888 1088 1.321743 CACTTCTTTCGCTCGATTCGG 59.678 52.381 6.18 0.00 0.00 4.30
973 1186 0.460987 CCGCTTGGACTCATCTGACC 60.461 60.000 0.00 0.00 33.02 4.02
974 1187 0.247460 CGCTTGGACTCATCTGACCA 59.753 55.000 0.00 0.00 0.00 4.02
975 1188 1.338105 CGCTTGGACTCATCTGACCAA 60.338 52.381 0.00 0.00 38.87 3.67
976 1189 2.679059 CGCTTGGACTCATCTGACCAAT 60.679 50.000 0.00 0.00 39.96 3.16
977 1190 3.350833 GCTTGGACTCATCTGACCAATT 58.649 45.455 0.00 0.00 39.96 2.32
978 1191 3.760684 GCTTGGACTCATCTGACCAATTT 59.239 43.478 0.00 0.00 39.96 1.82
1443 1665 4.847444 GAGCGGCTGGAGAAGGGC 62.847 72.222 7.50 0.00 0.00 5.19
1446 1668 4.168291 CGGCTGGAGAAGGGCCTC 62.168 72.222 6.46 0.00 43.29 4.70
1515 1737 0.655733 CCAAGCTGTTCAACGTCGTT 59.344 50.000 4.40 4.40 0.00 3.85
1551 1773 3.877508 CCATGTTCGGGAAGAAGGATTAC 59.122 47.826 0.00 0.00 39.95 1.89
1643 1865 4.874396 TCTGAATATGCTTCTTCAGTGCAG 59.126 41.667 20.26 0.00 45.49 4.41
1646 1868 1.166129 ATGCTTCTTCAGTGCAGCTG 58.834 50.000 10.11 10.11 46.34 4.24
1649 1871 1.875009 CTTCTTCAGTGCAGCTGTCA 58.125 50.000 16.64 11.11 45.23 3.58
1668 1890 7.451429 GCTGTCAGCTTGATTTACATATATCG 58.549 38.462 17.89 0.00 38.45 2.92
1669 1891 7.329471 GCTGTCAGCTTGATTTACATATATCGA 59.671 37.037 17.89 0.00 38.45 3.59
1691 1915 3.327464 AGCACATAGTTTTTGGCCCATTT 59.673 39.130 0.00 0.00 0.00 2.32
1692 1916 3.436359 GCACATAGTTTTTGGCCCATTTG 59.564 43.478 0.00 0.00 0.00 2.32
1693 1917 4.802248 GCACATAGTTTTTGGCCCATTTGA 60.802 41.667 0.00 0.00 0.00 2.69
1696 1920 5.012975 ACATAGTTTTTGGCCCATTTGATGT 59.987 36.000 0.00 0.00 0.00 3.06
1697 1921 4.006780 AGTTTTTGGCCCATTTGATGTC 57.993 40.909 0.00 0.00 0.00 3.06
1699 1923 2.323999 TTTGGCCCATTTGATGTCCT 57.676 45.000 0.00 0.00 0.00 3.85
1700 1924 2.323999 TTGGCCCATTTGATGTCCTT 57.676 45.000 0.00 0.00 0.00 3.36
1702 1926 1.076841 TGGCCCATTTGATGTCCTTGA 59.923 47.619 0.00 0.00 0.00 3.02
1703 1927 2.292389 TGGCCCATTTGATGTCCTTGAT 60.292 45.455 0.00 0.00 0.00 2.57
1704 1928 2.363359 GGCCCATTTGATGTCCTTGATC 59.637 50.000 0.00 0.00 0.00 2.92
1705 1929 3.025978 GCCCATTTGATGTCCTTGATCA 58.974 45.455 0.00 0.00 0.00 2.92
1706 1930 3.640029 GCCCATTTGATGTCCTTGATCAT 59.360 43.478 0.00 0.00 29.96 2.45
1707 1931 4.261909 GCCCATTTGATGTCCTTGATCATC 60.262 45.833 0.00 0.00 40.29 2.92
1721 1945 7.011857 GTCCTTGATCATCTTTGATAACCTGAC 59.988 40.741 0.00 0.00 42.73 3.51
1730 1958 8.517878 CATCTTTGATAACCTGACACATTCTTT 58.482 33.333 0.00 0.00 0.00 2.52
1735 1963 3.312736 ACCTGACACATTCTTTTGGGT 57.687 42.857 0.00 0.00 35.46 4.51
1744 1972 5.772672 ACACATTCTTTTGGGTAGTGCATAA 59.227 36.000 0.00 0.00 29.44 1.90
1745 1973 6.437162 ACACATTCTTTTGGGTAGTGCATAAT 59.563 34.615 0.00 0.00 29.44 1.28
1746 1974 6.753279 CACATTCTTTTGGGTAGTGCATAATG 59.247 38.462 0.00 0.00 0.00 1.90
1747 1975 4.981806 TCTTTTGGGTAGTGCATAATGC 57.018 40.909 0.00 0.00 45.29 3.56
1801 2029 5.827797 AGTTTTTGCTCCATTTCAGTACTCA 59.172 36.000 0.00 0.00 0.00 3.41
1842 2078 2.223203 CGATGCTTCATGCCTTCAGTTC 60.223 50.000 0.08 0.00 42.00 3.01
1849 2085 2.552315 TCATGCCTTCAGTTCCGTTTTC 59.448 45.455 0.00 0.00 0.00 2.29
1852 2088 1.679153 GCCTTCAGTTCCGTTTTCCAA 59.321 47.619 0.00 0.00 0.00 3.53
1903 2140 7.750229 TTCAATTGCTTCAGTTACTGAGATT 57.250 32.000 14.99 11.03 41.75 2.40
2018 2256 1.877576 ATGAGCTCTCGCAACGTCCA 61.878 55.000 16.19 0.00 39.10 4.02
2022 2260 1.444553 CTCTCGCAACGTCCACCTC 60.445 63.158 0.00 0.00 0.00 3.85
2071 2313 1.016627 TCTGCACAAACTGACACTGC 58.983 50.000 0.00 0.00 0.00 4.40
2097 2339 5.673337 TGCACACTTGTATTCTGACTTTC 57.327 39.130 0.00 0.00 0.00 2.62
2130 2372 9.102757 TGCATTTACAAAAGACAGCAAAATTTA 57.897 25.926 0.00 0.00 0.00 1.40
2322 2733 7.236432 AGGCATTATCCATTAGTAGATCACTGT 59.764 37.037 0.00 0.00 38.24 3.55
2438 2849 5.820423 TCGGGTTGATTATGTTGAGGTAATG 59.180 40.000 0.00 0.00 0.00 1.90
2484 2895 8.621286 CAAGTGTCCTTAGTGTTTTCTGTAAAT 58.379 33.333 0.00 0.00 0.00 1.40
2584 2995 4.815269 AGTAGCTCACTGTGATTCACTTC 58.185 43.478 17.26 5.16 35.62 3.01
2597 3008 4.580167 TGATTCACTTCCTTTCCTGTTGTG 59.420 41.667 0.00 0.00 0.00 3.33
2600 3011 4.136796 TCACTTCCTTTCCTGTTGTGATG 58.863 43.478 0.00 0.00 0.00 3.07
2654 3065 8.985315 TTGAAATCTCCATGATGTTAGCTATT 57.015 30.769 0.00 0.00 35.21 1.73
2667 3079 5.782047 TGTTAGCTATTGTTTGCATTTGCT 58.218 33.333 3.94 0.00 42.66 3.91
2762 3174 5.099484 ACCGTTCGAGTTTTGGTTATTTC 57.901 39.130 0.00 0.00 0.00 2.17
2800 3212 7.441890 GCTATACTGAGCATCTCAAGTAGTA 57.558 40.000 0.00 0.00 40.18 1.82
2808 3221 9.593134 CTGAGCATCTCAAGTAGTATAACTTTT 57.407 33.333 0.00 0.00 40.18 2.27
2832 3245 8.707796 TTTATGGTCCCTTTATGTTGTAACAA 57.292 30.769 1.10 0.00 43.03 2.83
2837 3250 6.349860 GGTCCCTTTATGTTGTAACAATGGTC 60.350 42.308 1.10 0.00 43.03 4.02
2924 3337 7.281774 CAGACAGTCCAATTCAGCATAATTAGT 59.718 37.037 0.00 0.00 0.00 2.24
2926 3339 7.765307 ACAGTCCAATTCAGCATAATTAGTTG 58.235 34.615 0.00 0.00 0.00 3.16
2971 3384 5.908341 ACCGCTGATTTTGGTAAAAAGAAA 58.092 33.333 0.00 0.00 38.62 2.52
3164 3578 6.318900 GGTTTGGAAAGGTTAGATTGATCGAT 59.681 38.462 0.00 0.00 0.00 3.59
3215 3629 4.275936 GGATTTTGCTGTCGCCTTGTATAT 59.724 41.667 0.00 0.00 34.43 0.86
3296 3710 6.259638 ACAATGTAAGTTTGTAACAACCACG 58.740 36.000 0.00 0.00 35.61 4.94
3331 3745 8.299570 ACTTGCAAAATCTTCGATAAATGTCTT 58.700 29.630 0.00 0.00 0.00 3.01
3332 3746 8.673626 TTGCAAAATCTTCGATAAATGTCTTC 57.326 30.769 0.00 0.00 0.00 2.87
3376 3790 6.982141 AGATATGTTGCTATGCCAAAAACATG 59.018 34.615 12.87 0.00 40.62 3.21
3496 3911 2.093764 AGAGGCAGTGATACTCAAGTGC 60.094 50.000 11.04 4.80 37.69 4.40
3560 3975 4.326826 TGAAGTCACTAATTCCTGCCTTG 58.673 43.478 0.00 0.00 0.00 3.61
3574 3989 1.545582 TGCCTTGCTGCTATTCCAAAC 59.454 47.619 0.00 0.00 0.00 2.93
3576 3991 2.167075 GCCTTGCTGCTATTCCAAACAT 59.833 45.455 0.00 0.00 0.00 2.71
3579 3994 4.439700 CCTTGCTGCTATTCCAAACATCTG 60.440 45.833 0.00 0.00 0.00 2.90
3826 4244 3.135712 TCAAGTTACTTGCAGTTCTCCCA 59.864 43.478 19.24 0.00 40.84 4.37
3830 4248 0.839946 ACTTGCAGTTCTCCCAGTGT 59.160 50.000 0.00 0.00 0.00 3.55
3851 4269 5.807011 GTGTTCTTCTTGAGTTTTGCAATGT 59.193 36.000 0.00 0.00 0.00 2.71
3928 4346 2.577593 GTACCTGACTGGGACGCC 59.422 66.667 0.00 0.00 40.38 5.68
3953 4371 2.202756 GCTCTTCCTACACCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
4012 4430 2.603247 GCATGGCGTGTTCGTGTCA 61.603 57.895 8.75 0.00 39.49 3.58
4020 4438 0.796312 GTGTTCGTGTCAATCGGCAT 59.204 50.000 0.00 0.00 0.00 4.40
4061 4479 3.611674 TCCTTGCGCTCGACACCA 61.612 61.111 9.73 0.00 0.00 4.17
4062 4480 2.664851 CCTTGCGCTCGACACCAA 60.665 61.111 9.73 0.00 0.00 3.67
4098 4517 0.599991 GTGATGTGTGAGCCGTGTCA 60.600 55.000 0.00 0.00 0.00 3.58
4099 4518 0.599991 TGATGTGTGAGCCGTGTCAC 60.600 55.000 7.31 7.31 46.08 3.67
4105 4524 3.936203 GAGCCGTGTCACCCACCA 61.936 66.667 0.00 0.00 41.26 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.088483 GCAAACGGCACATAATAATCATCATG 59.912 38.462 0.00 0.00 43.97 3.07
60 61 4.923871 ACTAGTTGTCTATGACAGCAAACG 59.076 41.667 14.87 4.83 44.24 3.60
76 77 7.539436 ACACACATGATGACTACTACTAGTTG 58.461 38.462 0.00 0.59 32.96 3.16
105 108 2.088950 ATTGCAGCAAAAGCATCACC 57.911 45.000 12.97 0.00 42.33 4.02
168 179 4.931002 GCTATTTTGGCAGCAAGAAATTGA 59.069 37.500 0.00 0.00 37.73 2.57
231 257 5.588648 CAGTACATGTTATTTACCACCCTGG 59.411 44.000 2.30 0.00 45.02 4.45
260 293 2.155732 CGGCTCGTGATGAATAATTCCG 59.844 50.000 0.00 0.00 0.00 4.30
272 308 0.817654 AGATGTTCATCGGCTCGTGA 59.182 50.000 7.08 0.00 0.00 4.35
294 330 0.033109 CCAAAGGGAAGGGGGTCATC 60.033 60.000 0.00 0.00 35.59 2.92
301 343 1.820010 GCAGCAACCAAAGGGAAGGG 61.820 60.000 0.00 0.00 38.05 3.95
302 344 0.829182 AGCAGCAACCAAAGGGAAGG 60.829 55.000 0.00 0.00 38.05 3.46
303 345 1.815003 CTAGCAGCAACCAAAGGGAAG 59.185 52.381 0.00 0.00 38.05 3.46
304 346 1.144913 ACTAGCAGCAACCAAAGGGAA 59.855 47.619 0.00 0.00 38.05 3.97
305 347 0.771127 ACTAGCAGCAACCAAAGGGA 59.229 50.000 0.00 0.00 38.05 4.20
313 355 1.737363 CGGAGGAGAACTAGCAGCAAC 60.737 57.143 0.00 0.00 0.00 4.17
439 577 3.238241 CGTGAGTTCTACGCCGCG 61.238 66.667 12.14 12.14 34.56 6.46
441 579 2.202570 CCCGTGAGTTCTACGCCG 60.203 66.667 0.00 0.00 40.04 6.46
458 596 4.394712 CAGGCGTCCCAGGTGGTC 62.395 72.222 0.00 0.00 34.77 4.02
531 669 2.511373 TAACGCAGGCGCTCATGG 60.511 61.111 14.32 1.53 44.19 3.66
532 670 3.009140 CTAACGCAGGCGCTCATG 58.991 61.111 14.32 5.32 44.19 3.07
546 684 1.373748 GTGGTCAAGACGCGGCTAA 60.374 57.895 18.71 3.05 0.00 3.09
552 690 1.149148 GAAGAAGGTGGTCAAGACGC 58.851 55.000 0.00 0.00 0.00 5.19
559 697 0.036294 CCGGGAAGAAGAAGGTGGTC 60.036 60.000 0.00 0.00 0.00 4.02
564 702 2.125106 CGGCCGGGAAGAAGAAGG 60.125 66.667 20.10 0.00 0.00 3.46
572 710 4.060038 GAAGTCGACGGCCGGGAA 62.060 66.667 31.76 11.14 39.14 3.97
581 719 4.353437 ACCGGGCACGAAGTCGAC 62.353 66.667 11.66 7.70 41.61 4.20
584 722 1.566018 CTTTCACCGGGCACGAAGTC 61.566 60.000 11.66 0.00 41.61 3.01
618 780 2.962697 GAAGGAGATGACGGAGGCGC 62.963 65.000 0.00 0.00 0.00 6.53
626 788 3.370104 TGAGGAGGAAGAAGGAGATGAC 58.630 50.000 0.00 0.00 0.00 3.06
706 880 4.379243 AACAGCAGGAGGTCGGCG 62.379 66.667 0.00 0.00 41.48 6.46
707 881 2.743928 CAACAGCAGGAGGTCGGC 60.744 66.667 0.00 0.00 36.81 5.54
708 882 2.743928 GCAACAGCAGGAGGTCGG 60.744 66.667 0.00 0.00 0.00 4.79
710 884 2.743928 CCGCAACAGCAGGAGGTC 60.744 66.667 0.00 0.00 0.00 3.85
753 927 2.104530 GGTTAGGGCTCGAGCGAC 59.895 66.667 29.81 24.22 43.26 5.19
754 928 3.515286 CGGTTAGGGCTCGAGCGA 61.515 66.667 29.81 15.66 43.26 4.93
755 929 4.570663 CCGGTTAGGGCTCGAGCG 62.571 72.222 29.81 14.63 43.26 5.03
756 930 3.140225 CTCCGGTTAGGGCTCGAGC 62.140 68.421 29.38 29.38 41.52 5.03
757 931 2.491022 CCTCCGGTTAGGGCTCGAG 61.491 68.421 8.45 8.45 41.52 4.04
758 932 2.441532 CCTCCGGTTAGGGCTCGA 60.442 66.667 0.00 0.00 41.52 4.04
776 950 2.688666 ATCGCTGGGCCTTCCTCA 60.689 61.111 4.53 0.00 36.20 3.86
780 954 2.203126 CCTGATCGCTGGGCCTTC 60.203 66.667 4.53 0.00 0.00 3.46
803 977 2.202878 CCGTCGGTCGATGCCAAT 60.203 61.111 2.08 0.00 42.86 3.16
896 1096 2.063541 ATAAGATTGCGGCGGCTTGC 62.064 55.000 17.76 4.42 45.38 4.01
973 1186 1.471684 GGGAGCAGAGCAGTCAAATTG 59.528 52.381 0.00 0.00 0.00 2.32
974 1187 1.831580 GGGAGCAGAGCAGTCAAATT 58.168 50.000 0.00 0.00 0.00 1.82
975 1188 0.392193 CGGGAGCAGAGCAGTCAAAT 60.392 55.000 0.00 0.00 0.00 2.32
976 1189 1.004560 CGGGAGCAGAGCAGTCAAA 60.005 57.895 0.00 0.00 0.00 2.69
977 1190 1.260538 ATCGGGAGCAGAGCAGTCAA 61.261 55.000 0.00 0.00 0.00 3.18
978 1191 1.670949 GATCGGGAGCAGAGCAGTCA 61.671 60.000 0.00 0.00 0.00 3.41
1071 1293 3.703127 ACCGTCTTTCCCTCCGCC 61.703 66.667 0.00 0.00 0.00 6.13
1074 1296 1.003718 CACCACCGTCTTTCCCTCC 60.004 63.158 0.00 0.00 0.00 4.30
1080 1302 1.594293 CACGAGCACCACCGTCTTT 60.594 57.895 0.00 0.00 36.83 2.52
1368 1590 4.093291 AGGCAGGAAGAGGCAGCG 62.093 66.667 0.00 0.00 0.00 5.18
1371 1593 2.203983 TCCAGGCAGGAAGAGGCA 60.204 61.111 0.00 0.00 45.65 4.75
1413 1635 3.781307 CGCTCCACCCGGATCCAA 61.781 66.667 13.41 0.00 41.79 3.53
1551 1773 4.790962 ATGAGGCGCCACTGCTGG 62.791 66.667 31.54 0.00 41.13 4.85
1643 1865 7.329471 TCGATATATGTAAATCAAGCTGACAGC 59.671 37.037 20.12 20.12 42.84 4.40
1646 1868 7.329471 TGCTCGATATATGTAAATCAAGCTGAC 59.671 37.037 0.00 0.00 0.00 3.51
1649 1871 7.154656 TGTGCTCGATATATGTAAATCAAGCT 58.845 34.615 0.00 0.00 0.00 3.74
1665 1887 2.423538 GGCCAAAAACTATGTGCTCGAT 59.576 45.455 0.00 0.00 0.00 3.59
1667 1889 1.135402 GGGCCAAAAACTATGTGCTCG 60.135 52.381 4.39 0.00 0.00 5.03
1668 1890 1.892474 TGGGCCAAAAACTATGTGCTC 59.108 47.619 2.13 0.00 0.00 4.26
1669 1891 2.008242 TGGGCCAAAAACTATGTGCT 57.992 45.000 2.13 0.00 0.00 4.40
1691 1915 7.500227 GGTTATCAAAGATGATCAAGGACATCA 59.500 37.037 0.00 0.00 42.75 3.07
1692 1916 7.718753 AGGTTATCAAAGATGATCAAGGACATC 59.281 37.037 0.00 0.00 42.75 3.06
1693 1917 7.501559 CAGGTTATCAAAGATGATCAAGGACAT 59.498 37.037 0.00 0.00 42.75 3.06
1696 1920 7.050377 GTCAGGTTATCAAAGATGATCAAGGA 58.950 38.462 0.00 0.00 42.75 3.36
1697 1921 6.825213 TGTCAGGTTATCAAAGATGATCAAGG 59.175 38.462 0.00 0.00 42.75 3.61
1699 1923 7.167535 TGTGTCAGGTTATCAAAGATGATCAA 58.832 34.615 0.00 0.00 42.75 2.57
1700 1924 6.710278 TGTGTCAGGTTATCAAAGATGATCA 58.290 36.000 0.00 0.00 42.75 2.92
1703 1927 7.397221 AGAATGTGTCAGGTTATCAAAGATGA 58.603 34.615 0.00 0.00 40.57 2.92
1704 1928 7.621428 AGAATGTGTCAGGTTATCAAAGATG 57.379 36.000 0.00 0.00 0.00 2.90
1705 1929 8.641498 AAAGAATGTGTCAGGTTATCAAAGAT 57.359 30.769 0.00 0.00 0.00 2.40
1706 1930 8.352201 CAAAAGAATGTGTCAGGTTATCAAAGA 58.648 33.333 0.00 0.00 0.00 2.52
1707 1931 7.596248 CCAAAAGAATGTGTCAGGTTATCAAAG 59.404 37.037 0.00 0.00 0.00 2.77
1721 1945 4.789012 ATGCACTACCCAAAAGAATGTG 57.211 40.909 0.00 0.00 0.00 3.21
1744 1972 9.089601 CAATTCAACATTGTGTACATTATGCAT 57.910 29.630 15.93 3.79 0.00 3.96
1745 1973 7.544915 CCAATTCAACATTGTGTACATTATGCA 59.455 33.333 15.93 0.00 0.00 3.96
1746 1974 7.010367 CCCAATTCAACATTGTGTACATTATGC 59.990 37.037 15.93 0.00 0.00 3.14
1747 1975 7.492020 CCCCAATTCAACATTGTGTACATTATG 59.508 37.037 14.92 14.92 0.00 1.90
1748 1976 7.398618 TCCCCAATTCAACATTGTGTACATTAT 59.601 33.333 0.00 0.00 0.00 1.28
1749 1977 6.721668 TCCCCAATTCAACATTGTGTACATTA 59.278 34.615 0.00 0.00 0.00 1.90
1750 1978 5.541868 TCCCCAATTCAACATTGTGTACATT 59.458 36.000 0.00 0.00 0.00 2.71
1751 1979 5.083122 TCCCCAATTCAACATTGTGTACAT 58.917 37.500 0.00 0.00 0.00 2.29
1752 1980 4.474394 TCCCCAATTCAACATTGTGTACA 58.526 39.130 0.00 0.00 0.00 2.90
1753 1981 4.618227 GCTCCCCAATTCAACATTGTGTAC 60.618 45.833 0.00 0.00 0.00 2.90
1754 1982 3.509575 GCTCCCCAATTCAACATTGTGTA 59.490 43.478 0.00 0.00 0.00 2.90
1755 1983 2.299867 GCTCCCCAATTCAACATTGTGT 59.700 45.455 0.00 0.00 0.00 3.72
1756 1984 2.299582 TGCTCCCCAATTCAACATTGTG 59.700 45.455 0.00 0.00 0.00 3.33
1757 1985 2.564062 CTGCTCCCCAATTCAACATTGT 59.436 45.455 0.00 0.00 0.00 2.71
1758 1986 2.564062 ACTGCTCCCCAATTCAACATTG 59.436 45.455 0.00 0.00 0.00 2.82
1798 2026 7.851508 TCGAAACAGAAACAGACTAAAATGAG 58.148 34.615 0.00 0.00 0.00 2.90
1801 2029 7.041098 AGCATCGAAACAGAAACAGACTAAAAT 60.041 33.333 0.00 0.00 0.00 1.82
1842 2078 4.815269 TGGAATTAGCATTTGGAAAACGG 58.185 39.130 0.00 0.00 0.00 4.44
2022 2260 0.972983 TCTCCCTTTCCTCAGGCGAG 60.973 60.000 0.00 0.28 39.16 5.03
2071 2313 6.064846 AGTCAGAATACAAGTGTGCAAAAG 57.935 37.500 0.00 0.00 0.00 2.27
2097 2339 4.226761 GTCTTTTGTAAATGCACCCTTCG 58.773 43.478 0.00 0.00 0.00 3.79
2130 2372 6.670695 AGGTAAGGCATTGTGAGAAATTTT 57.329 33.333 0.00 0.00 0.00 1.82
2322 2733 3.334691 ACGCAGCAGTTCTAGCATTTAA 58.665 40.909 0.00 0.00 0.00 1.52
2453 2864 8.836413 CAGAAAACACTAAGGACACTTGAATAA 58.164 33.333 0.00 0.00 37.53 1.40
2584 2995 2.507484 TCAGCATCACAACAGGAAAGG 58.493 47.619 0.00 0.00 0.00 3.11
2597 3008 1.131883 GACACAACCAGCATCAGCATC 59.868 52.381 0.00 0.00 45.49 3.91
2600 3011 0.607489 AGGACACAACCAGCATCAGC 60.607 55.000 0.00 0.00 42.56 4.26
2667 3079 4.020751 GCTGATATTAGGATCTCTGGTGCA 60.021 45.833 0.00 0.00 0.00 4.57
2808 3221 8.744652 CATTGTTACAACATAAAGGGACCATAA 58.255 33.333 0.00 0.00 38.95 1.90
2821 3234 4.112634 ACCAGGACCATTGTTACAACAT 57.887 40.909 0.00 0.00 38.95 2.71
2832 3245 1.203050 CCAGGAAACAACCAGGACCAT 60.203 52.381 0.00 0.00 38.63 3.55
2837 3250 2.230660 GTTCTCCAGGAAACAACCAGG 58.769 52.381 8.75 0.00 37.85 4.45
2926 3339 7.428472 GCGGTATGCTGTTCTAAGAAATAAAAC 59.572 37.037 0.00 0.00 41.73 2.43
2971 3384 4.082125 CTGAGATGCCCCACTTAGTTTTT 58.918 43.478 0.00 0.00 0.00 1.94
3215 3629 8.146412 CAGATTGGTGATACTTCATGAGATACA 58.854 37.037 0.00 0.00 33.56 2.29
3283 3697 4.652421 TCTCTGTACGTGGTTGTTACAA 57.348 40.909 0.00 0.00 0.00 2.41
3296 3710 6.073765 TCGAAGATTTTGCAAGTTCTCTGTAC 60.074 38.462 12.11 0.00 0.00 2.90
3376 3790 5.508994 CCTTCTGGTGGTCCAAACATTTAAC 60.509 44.000 0.00 0.00 43.81 2.01
3393 3807 9.007901 CATTTATAAAGCTAGAATCCCTTCTGG 57.992 37.037 3.94 0.00 41.83 3.86
3496 3911 3.584406 TCCAAACAATAAATGCCGGTG 57.416 42.857 1.90 0.00 0.00 4.94
3560 3975 4.708726 AACAGATGTTTGGAATAGCAGC 57.291 40.909 0.00 0.00 33.93 5.25
3574 3989 4.533919 TGGCCCAAACATTTAACAGATG 57.466 40.909 0.00 0.00 0.00 2.90
3576 3991 3.706594 TGTTGGCCCAAACATTTAACAGA 59.293 39.130 0.00 0.00 35.16 3.41
3579 3994 4.329462 TCTGTTGGCCCAAACATTTAAC 57.671 40.909 8.95 0.00 39.25 2.01
3774 4192 5.532406 GTGGCTCAGGAATTCAAGCATATAA 59.468 40.000 21.15 5.64 36.47 0.98
3826 4244 5.643379 TTGCAAAACTCAAGAAGAACACT 57.357 34.783 0.00 0.00 0.00 3.55
3830 4248 6.206395 TGACATTGCAAAACTCAAGAAGAA 57.794 33.333 1.71 0.00 0.00 2.52
3928 4346 0.107703 TGTAGGAAGAGCCATTGCCG 60.108 55.000 0.00 0.00 40.02 5.69
3953 4371 2.825836 CAATGGGCGCAGGTCCTC 60.826 66.667 10.83 0.00 39.29 3.71
3977 4395 1.227263 GCACATAGTCGGACGGCAT 60.227 57.895 1.89 0.00 0.00 4.40
3978 4396 1.955495 ATGCACATAGTCGGACGGCA 61.955 55.000 13.56 13.56 0.00 5.69
4012 4430 1.819632 GCCTTGTCCGATGCCGATT 60.820 57.895 0.00 0.00 38.22 3.34
4061 4479 3.049674 CCATGACGTGCTGGCGTT 61.050 61.111 0.00 0.00 45.79 4.84
4098 4517 0.185901 AACTTGATGCAGTGGTGGGT 59.814 50.000 0.00 0.00 0.00 4.51
4099 4518 0.599558 CAACTTGATGCAGTGGTGGG 59.400 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.