Multiple sequence alignment - TraesCS5B01G241200

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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 TraesCS5B01G241200 chr5B 100.000 2291 0 0 1 2291 421186671 421188961 0.000000e+00 4231.0
1 TraesCS5B01G241200 chr5B 84.066 546 51 18 830 1373 421275455 421275966 5.690000e-136 494.0
2 TraesCS5B01G241200 chr5B 96.154 52 2 0 1590 1641 421188163 421188214 4.060000e-13 86.1
3 TraesCS5B01G241200 chr5B 96.154 52 2 0 1493 1544 421188260 421188311 4.060000e-13 86.1
4 TraesCS5B01G241200 chr5D 89.721 1576 93 30 1 1545 356205696 356207233 0.000000e+00 1949.0
5 TraesCS5B01G241200 chr5D 88.433 683 68 6 1590 2271 356207180 356207852 0.000000e+00 813.0
6 TraesCS5B01G241200 chr5D 79.424 695 68 35 816 1487 356320370 356321012 2.720000e-114 422.0
7 TraesCS5B01G241200 chr5A 86.436 811 63 16 848 1641 457908243 457909023 0.000000e+00 845.0
8 TraesCS5B01G241200 chr5A 89.000 600 28 16 1 592 457904710 457905279 0.000000e+00 708.0
9 TraesCS5B01G241200 chr5A 83.799 716 54 32 115 809 457907568 457908242 6.950000e-175 623.0
10 TraesCS5B01G241200 chr5A 83.701 589 68 13 1644 2227 457909260 457909825 4.330000e-147 531.0
11 TraesCS5B01G241200 chr5A 80.938 682 65 34 840 1487 457915124 457915774 1.590000e-131 479.0
12 TraesCS5B01G241200 chr5A 87.273 220 14 6 592 809 457905474 457905681 2.940000e-59 239.0
13 TraesCS5B01G241200 chr5A 93.966 116 4 2 1 116 457906354 457906466 3.030000e-39 172.0
14 TraesCS5B01G241200 chr3B 83.505 97 15 1 1647 1743 126456991 126456896 3.130000e-14 89.8


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 TraesCS5B01G241200 chr5B 421186671 421188961 2290 False 1467.733333 4231 97.4360 1 2291 3 chr5B.!!$F2 2290
1 TraesCS5B01G241200 chr5B 421275455 421275966 511 False 494.000000 494 84.0660 830 1373 1 chr5B.!!$F1 543
2 TraesCS5B01G241200 chr5D 356205696 356207852 2156 False 1381.000000 1949 89.0770 1 2271 2 chr5D.!!$F2 2270
3 TraesCS5B01G241200 chr5D 356320370 356321012 642 False 422.000000 422 79.4240 816 1487 1 chr5D.!!$F1 671
4 TraesCS5B01G241200 chr5A 457904710 457909825 5115 False 519.666667 845 87.3625 1 2227 6 chr5A.!!$F2 2226
5 TraesCS5B01G241200 chr5A 457915124 457915774 650 False 479.000000 479 80.9380 840 1487 1 chr5A.!!$F1 647

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
795 1015 0.179 CATGGTCTAGTGTCCTGGCC 59.821 60.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 4974 0.106708 AGCAGTTGTTCGCTCCTCAA 59.893 50.0 0.0 0.0 31.16 3.02 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
243 244 4.335315 CCTTGCAGTAAGTGTTTCTCAACA 59.665 41.667 0.00 0.00 35.70 3.33
283 284 8.329203 ACTTTTCCTTTCTGATGATGTTAGTC 57.671 34.615 0.00 0.00 0.00 2.59
301 306 4.383850 AGTCTTCACTCCATGAGAATCG 57.616 45.455 0.00 0.00 38.99 3.34
306 311 4.645762 TCACTCCATGAGAATCGAAGAG 57.354 45.455 0.00 0.00 38.61 2.85
310 315 4.141756 ACTCCATGAGAATCGAAGAGCAAT 60.142 41.667 0.00 0.00 38.61 3.56
360 373 5.366460 CATCTGTCCATGCAATACTCTTCT 58.634 41.667 0.00 0.00 0.00 2.85
387 400 6.560003 TTCTGAAGCACTAATCTCCCATAA 57.440 37.500 0.00 0.00 0.00 1.90
390 403 5.541845 TGAAGCACTAATCTCCCATAATCG 58.458 41.667 0.00 0.00 0.00 3.34
405 418 5.197549 CCATAATCGAATGTGCACGTTTAG 58.802 41.667 24.49 20.24 30.94 1.85
433 446 9.512588 AGATGAACATTTAGTTTCTTGATGACT 57.487 29.630 0.00 0.00 41.51 3.41
434 447 9.552114 GATGAACATTTAGTTTCTTGATGACTG 57.448 33.333 0.00 0.00 41.51 3.51
435 448 7.362662 TGAACATTTAGTTTCTTGATGACTGC 58.637 34.615 0.00 0.00 41.51 4.40
455 468 1.203052 CGGCAGAGGCATGTGAAAATT 59.797 47.619 0.00 0.00 43.71 1.82
466 479 4.151157 GCATGTGAAAATTTTGGACTCTGC 59.849 41.667 8.47 12.83 0.00 4.26
467 480 4.320608 TGTGAAAATTTTGGACTCTGCC 57.679 40.909 8.47 0.00 0.00 4.85
483 496 3.277715 TCTGCCGAAAATGACATGCATA 58.722 40.909 0.00 0.00 35.78 3.14
540 553 1.538047 TGCTTCTTCATGTGGCCTTC 58.462 50.000 3.32 0.00 0.00 3.46
561 574 2.810852 CTGAGTTTTGAGGAGCCTTCAC 59.189 50.000 0.00 0.00 0.00 3.18
607 818 6.556974 ACCTTTCTACTTTGTATACCCCTC 57.443 41.667 0.00 0.00 0.00 4.30
614 825 5.070823 ACTTTGTATACCCCTCGGATCTA 57.929 43.478 0.00 0.00 0.00 1.98
615 826 5.078256 ACTTTGTATACCCCTCGGATCTAG 58.922 45.833 0.00 0.00 0.00 2.43
616 827 4.736611 TTGTATACCCCTCGGATCTAGT 57.263 45.455 0.00 0.00 0.00 2.57
618 829 6.398655 TTGTATACCCCTCGGATCTAGTAT 57.601 41.667 0.00 0.00 0.00 2.12
620 831 6.893583 TGTATACCCCTCGGATCTAGTATAC 58.106 44.000 0.00 14.48 41.09 1.47
621 832 3.347077 ACCCCTCGGATCTAGTATACG 57.653 52.381 0.00 1.64 0.00 3.06
622 833 2.015587 CCCCTCGGATCTAGTATACGC 58.984 57.143 0.00 0.00 0.00 4.42
623 834 2.355920 CCCCTCGGATCTAGTATACGCT 60.356 54.545 0.00 0.00 0.00 5.07
624 835 3.118482 CCCCTCGGATCTAGTATACGCTA 60.118 52.174 0.00 0.00 0.00 4.26
625 836 4.121317 CCCTCGGATCTAGTATACGCTAG 58.879 52.174 0.00 0.00 39.70 3.42
633 844 6.649973 GGATCTAGTATACGCTAGTCTTGTCA 59.350 42.308 0.00 0.00 39.44 3.58
721 932 3.579302 CTGCCCACCCAGGTTGGA 61.579 66.667 4.07 0.00 40.96 3.53
781 1001 1.830477 ACAAAAATATGCCGCCATGGT 59.170 42.857 14.67 0.00 41.21 3.55
795 1015 0.179000 CATGGTCTAGTGTCCTGGCC 59.821 60.000 0.00 0.00 0.00 5.36
846 1852 4.641645 TGCCACAGCACTTCCCCG 62.642 66.667 0.00 0.00 46.52 5.73
863 3607 2.218603 CCCGCCTATAAATTGACGCTT 58.781 47.619 0.00 0.00 0.00 4.68
866 3610 3.498397 CCGCCTATAAATTGACGCTTGAT 59.502 43.478 0.00 0.00 0.00 2.57
887 3631 3.225104 TGCAAACCTCTCAAATCAAGCT 58.775 40.909 0.00 0.00 0.00 3.74
888 3632 4.397420 TGCAAACCTCTCAAATCAAGCTA 58.603 39.130 0.00 0.00 0.00 3.32
889 3633 4.826733 TGCAAACCTCTCAAATCAAGCTAA 59.173 37.500 0.00 0.00 0.00 3.09
890 3634 5.477984 TGCAAACCTCTCAAATCAAGCTAAT 59.522 36.000 0.00 0.00 0.00 1.73
948 3714 1.228245 GCACTGCCTCAAACCCTGA 60.228 57.895 0.00 0.00 0.00 3.86
954 3720 3.170362 CTCAAACCCTGAGCCCCA 58.830 61.111 0.00 0.00 45.11 4.96
971 3739 2.559931 CCCCAGGAGAGTCTTAGACCAA 60.560 54.545 8.96 0.00 32.18 3.67
973 3741 3.436243 CCAGGAGAGTCTTAGACCAACT 58.564 50.000 8.96 6.41 32.18 3.16
974 3742 3.835395 CCAGGAGAGTCTTAGACCAACTT 59.165 47.826 8.96 0.00 32.18 2.66
975 3743 5.017490 CCAGGAGAGTCTTAGACCAACTTA 58.983 45.833 8.96 0.00 32.18 2.24
976 3744 5.480772 CCAGGAGAGTCTTAGACCAACTTAA 59.519 44.000 8.96 0.00 32.18 1.85
980 3748 8.751242 AGGAGAGTCTTAGACCAACTTAATTAC 58.249 37.037 8.96 0.00 32.18 1.89
1120 3888 3.913573 CGGCGTCGGCAAAGATCG 61.914 66.667 19.59 0.00 42.47 3.69
1302 4076 0.179222 GCCGTTGAGCGAAACTAAGC 60.179 55.000 0.00 0.91 44.77 3.09
1336 4111 2.111384 GGATGGGTACAGAGCTCTTGA 58.889 52.381 15.27 1.15 0.00 3.02
1396 4196 6.264832 TCGTTCATTGTATTCCATTTCATGC 58.735 36.000 0.00 0.00 0.00 4.06
1487 4295 3.054878 GTTTGTGCATTGCCTTCTCTTG 58.945 45.455 6.12 0.00 0.00 3.02
1489 4297 1.610038 TGTGCATTGCCTTCTCTTGTG 59.390 47.619 6.12 0.00 0.00 3.33
1491 4299 0.599558 GCATTGCCTTCTCTTGTGCA 59.400 50.000 0.00 0.00 0.00 4.57
1516 4324 4.217767 AGTGCTACTGTGTTATTGTCTCGA 59.782 41.667 0.00 0.00 0.00 4.04
1532 4340 4.464951 TGTCTCGACAATATAAGGGTGTGT 59.535 41.667 0.00 0.00 38.56 3.72
1533 4341 5.046878 TGTCTCGACAATATAAGGGTGTGTT 60.047 40.000 0.00 0.00 38.56 3.32
1534 4342 5.873164 GTCTCGACAATATAAGGGTGTGTTT 59.127 40.000 0.00 0.00 0.00 2.83
1535 4343 5.872617 TCTCGACAATATAAGGGTGTGTTTG 59.127 40.000 0.00 0.00 0.00 2.93
1536 4344 4.938832 TCGACAATATAAGGGTGTGTTTGG 59.061 41.667 0.00 0.00 0.00 3.28
1537 4345 4.438200 CGACAATATAAGGGTGTGTTTGGC 60.438 45.833 0.00 0.00 0.00 4.52
1538 4346 4.411927 ACAATATAAGGGTGTGTTTGGCA 58.588 39.130 0.00 0.00 0.00 4.92
1539 4347 4.835615 ACAATATAAGGGTGTGTTTGGCAA 59.164 37.500 0.00 0.00 0.00 4.52
1540 4348 5.167845 CAATATAAGGGTGTGTTTGGCAAC 58.832 41.667 0.00 0.00 0.00 4.17
1565 4373 3.043999 ATCCTAGCGTGGTTGCCCC 62.044 63.158 0.00 0.00 34.65 5.80
1567 4375 2.125106 CTAGCGTGGTTGCCCCTC 60.125 66.667 0.00 0.00 34.65 4.30
1587 4395 1.344496 CCCCCTCTCCCTAAGACATGT 60.344 57.143 0.00 0.00 0.00 3.21
1641 4453 7.685641 AACATAAGGGTGTGTTTGGTAACATTG 60.686 37.037 0.00 0.00 45.41 2.82
1668 4714 5.405935 ACATGCTGAGTGTAGACATGTTA 57.594 39.130 0.00 0.00 46.80 2.41
1692 4738 5.522456 AGTACATGCATCTGTTGTTGTTTG 58.478 37.500 0.00 0.00 0.00 2.93
1726 4772 0.879090 TGCTGAAACATGCTGAGCTG 59.121 50.000 5.83 4.14 0.00 4.24
1731 4778 2.224354 TGAAACATGCTGAGCTGAGACA 60.224 45.455 3.62 1.75 0.00 3.41
1738 4785 4.006780 TGCTGAGCTGAGACATTGTTTA 57.993 40.909 3.62 0.00 0.00 2.01
1744 4791 5.480422 TGAGCTGAGACATTGTTTAGTAGGA 59.520 40.000 0.00 0.00 0.00 2.94
1760 4807 1.002502 GGAAGCGGGTTAGTTGCCT 60.003 57.895 0.00 0.00 0.00 4.75
1765 4812 1.078426 CGGGTTAGTTGCCTGAGGG 60.078 63.158 0.00 0.00 34.35 4.30
1766 4813 1.303282 GGGTTAGTTGCCTGAGGGG 59.697 63.158 0.00 0.00 38.36 4.79
1769 4816 0.391263 GTTAGTTGCCTGAGGGGTCG 60.391 60.000 0.00 0.00 37.43 4.79
1799 4846 0.033405 CTACCACCGAGGAGAAGGGA 60.033 60.000 0.00 0.00 41.22 4.20
1800 4847 0.410663 TACCACCGAGGAGAAGGGAA 59.589 55.000 0.00 0.00 41.22 3.97
1801 4848 0.905337 ACCACCGAGGAGAAGGGAAG 60.905 60.000 0.00 0.00 41.22 3.46
1802 4849 1.617947 CCACCGAGGAGAAGGGAAGG 61.618 65.000 0.00 0.00 41.22 3.46
1803 4850 0.614979 CACCGAGGAGAAGGGAAGGA 60.615 60.000 0.00 0.00 0.00 3.36
1804 4851 0.324830 ACCGAGGAGAAGGGAAGGAG 60.325 60.000 0.00 0.00 0.00 3.69
1805 4852 1.045911 CCGAGGAGAAGGGAAGGAGG 61.046 65.000 0.00 0.00 0.00 4.30
1848 4895 2.300967 TGGCTGGTAGGGAGCTTGG 61.301 63.158 0.00 0.00 36.63 3.61
1860 4907 3.225235 GCTTGGGAGCGAGAGGAT 58.775 61.111 0.00 0.00 39.48 3.24
1865 4912 3.745797 GCTTGGGAGCGAGAGGATAAATT 60.746 47.826 0.00 0.00 39.48 1.82
1867 4914 2.104792 TGGGAGCGAGAGGATAAATTGG 59.895 50.000 0.00 0.00 0.00 3.16
1873 4920 3.181454 GCGAGAGGATAAATTGGGAGGAA 60.181 47.826 0.00 0.00 0.00 3.36
1876 4923 5.163301 CGAGAGGATAAATTGGGAGGAAAGA 60.163 44.000 0.00 0.00 0.00 2.52
1886 4933 3.046374 TGGGAGGAAAGATAACCCTAGC 58.954 50.000 0.00 0.00 40.98 3.42
1900 4947 1.997874 CTAGCAGGCCTCCTTGGGT 60.998 63.158 0.00 0.00 36.00 4.51
1902 4949 4.432741 GCAGGCCTCCTTGGGTCC 62.433 72.222 0.00 0.00 36.00 4.46
1905 4952 2.610859 GGCCTCCTTGGGTCCTGA 60.611 66.667 0.00 0.00 36.00 3.86
1939 4986 1.129437 GAAGCATGTTGAGGAGCGAAC 59.871 52.381 0.00 0.00 0.00 3.95
1940 4987 0.035317 AGCATGTTGAGGAGCGAACA 59.965 50.000 0.00 0.00 36.54 3.18
1942 4989 1.400242 GCATGTTGAGGAGCGAACAAC 60.400 52.381 0.00 0.00 42.51 3.32
1945 4992 0.235926 GTTGAGGAGCGAACAACTGC 59.764 55.000 0.00 0.00 40.13 4.40
1970 5017 1.153939 CGTTCTCTCCTCGTGCAGG 60.154 63.158 0.00 0.00 45.15 4.85
2002 5049 4.980805 TGGGCCGAGTTCGTGCAC 62.981 66.667 6.82 6.82 38.69 4.57
2008 5055 2.876879 CGAGTTCGTGCACGCCAAA 61.877 57.895 33.63 20.33 39.60 3.28
2061 5112 1.259507 CGATTTGTGGTCGTGTTTCGT 59.740 47.619 0.00 0.00 40.80 3.85
2062 5113 2.635444 GATTTGTGGTCGTGTTTCGTG 58.365 47.619 0.00 0.00 40.80 4.35
2065 5116 0.108756 TGTGGTCGTGTTTCGTGTGA 60.109 50.000 0.00 0.00 40.80 3.58
2088 5139 2.603652 GGGCCTCCGTTCCTTCCTT 61.604 63.158 0.84 0.00 0.00 3.36
2104 5155 6.428295 TCCTTCCTTTGGTGTTTTCTTCTTA 58.572 36.000 0.00 0.00 0.00 2.10
2111 5162 3.181458 TGGTGTTTTCTTCTTAGCCTCGT 60.181 43.478 0.00 0.00 0.00 4.18
2112 5163 3.186613 GGTGTTTTCTTCTTAGCCTCGTG 59.813 47.826 0.00 0.00 0.00 4.35
2117 5168 0.175989 CTTCTTAGCCTCGTGGGGAC 59.824 60.000 5.54 0.00 35.12 4.46
2134 5185 3.145551 CCCCCTGGTAGTCGGTCG 61.146 72.222 0.00 0.00 0.00 4.79
2145 5196 0.462789 AGTCGGTCGTGGTTGACTTT 59.537 50.000 0.00 0.00 38.48 2.66
2149 5200 1.516161 GGTCGTGGTTGACTTTACCC 58.484 55.000 0.00 0.00 38.91 3.69
2153 5204 1.000060 CGTGGTTGACTTTACCCTCGA 60.000 52.381 0.00 0.00 35.53 4.04
2188 5239 2.402564 CTCCTGCTCCCCTCTGATTTA 58.597 52.381 0.00 0.00 0.00 1.40
2228 5279 4.585526 CTTCTATGGCGCGGGCGA 62.586 66.667 18.30 15.71 42.83 5.54
2239 5290 3.151710 CGGGCGATGGGTGGTCTA 61.152 66.667 0.00 0.00 0.00 2.59
2283 5334 3.999051 GACGCCGTGTCTATGCTC 58.001 61.111 0.00 0.00 44.58 4.26
2284 5335 1.939785 GACGCCGTGTCTATGCTCG 60.940 63.158 0.00 0.00 44.58 5.03
2285 5336 2.102357 CGCCGTGTCTATGCTCGT 59.898 61.111 0.00 0.00 0.00 4.18
2286 5337 2.224217 CGCCGTGTCTATGCTCGTG 61.224 63.158 0.00 0.00 0.00 4.35
2287 5338 2.517450 GCCGTGTCTATGCTCGTGC 61.517 63.158 1.71 1.71 40.20 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 6.009908 AGGAAAAGTAACCCACACTTAAGT 57.990 37.500 1.12 1.12 35.19 2.24
249 250 4.885325 TCAGAAAGGAAAAGTAACCCACAC 59.115 41.667 0.00 0.00 0.00 3.82
250 251 5.118729 TCAGAAAGGAAAAGTAACCCACA 57.881 39.130 0.00 0.00 0.00 4.17
283 284 5.003692 TCTTCGATTCTCATGGAGTGAAG 57.996 43.478 0.00 4.81 36.14 3.02
301 306 7.589221 CAGTCTGTTAAACTCAAATTGCTCTTC 59.411 37.037 0.00 0.00 0.00 2.87
306 311 5.280945 TGCAGTCTGTTAAACTCAAATTGC 58.719 37.500 0.93 0.00 0.00 3.56
310 315 4.580167 AGCATGCAGTCTGTTAAACTCAAA 59.420 37.500 21.98 0.00 0.00 2.69
387 400 4.242475 TCTTCTAAACGTGCACATTCGAT 58.758 39.130 18.64 0.00 0.00 3.59
390 403 5.530519 TCATCTTCTAAACGTGCACATTC 57.469 39.130 18.64 0.00 0.00 2.67
429 442 3.709633 ATGCCTCTGCCGCAGTCA 61.710 61.111 19.77 15.54 40.15 3.41
430 443 3.200593 CATGCCTCTGCCGCAGTC 61.201 66.667 19.77 10.83 40.15 3.51
431 444 4.025858 ACATGCCTCTGCCGCAGT 62.026 61.111 19.77 0.00 40.15 4.40
432 445 3.506096 CACATGCCTCTGCCGCAG 61.506 66.667 14.62 14.62 40.15 5.18
433 446 3.549900 TTCACATGCCTCTGCCGCA 62.550 57.895 0.00 0.00 41.28 5.69
434 447 1.865788 TTTTCACATGCCTCTGCCGC 61.866 55.000 0.00 0.00 36.33 6.53
435 448 0.813184 ATTTTCACATGCCTCTGCCG 59.187 50.000 0.00 0.00 36.33 5.69
455 468 2.552315 GTCATTTTCGGCAGAGTCCAAA 59.448 45.455 0.00 0.00 0.00 3.28
466 479 4.621068 ACACTATGCATGTCATTTTCGG 57.379 40.909 10.16 0.00 36.63 4.30
467 480 5.286797 CCAAACACTATGCATGTCATTTTCG 59.713 40.000 10.16 0.00 36.63 3.46
540 553 2.810852 GTGAAGGCTCCTCAAAACTCAG 59.189 50.000 0.00 0.00 0.00 3.35
561 574 3.818787 GCCCAGCTCCGTGCAATG 61.819 66.667 0.00 0.00 45.94 2.82
607 818 5.638657 ACAAGACTAGCGTATACTAGATCCG 59.361 44.000 0.00 0.00 41.92 4.18
614 825 6.885952 ATGATGACAAGACTAGCGTATACT 57.114 37.500 0.56 0.00 0.00 2.12
615 826 7.932120 AAATGATGACAAGACTAGCGTATAC 57.068 36.000 0.00 0.00 0.00 1.47
618 829 8.766000 TTTTAAATGATGACAAGACTAGCGTA 57.234 30.769 0.00 0.00 0.00 4.42
633 844 9.142515 CATATGGCGTGCAATATTTTAAATGAT 57.857 29.630 0.00 0.00 0.00 2.45
719 930 2.725008 CGCTGGATCCGAGACTCC 59.275 66.667 7.39 0.00 0.00 3.85
721 932 1.682684 AACCGCTGGATCCGAGACT 60.683 57.895 7.39 0.00 0.00 3.24
781 1001 1.681327 GACCGGCCAGGACACTAGA 60.681 63.158 18.74 0.00 45.00 2.43
817 1037 1.203052 GCTGTGGCACTGCAATGTATT 59.797 47.619 35.13 0.00 41.83 1.89
834 1840 0.468226 TTATAGGCGGGGAAGTGCTG 59.532 55.000 0.00 0.00 0.00 4.41
846 1852 4.222114 GCATCAAGCGTCAATTTATAGGC 58.778 43.478 0.00 0.00 0.00 3.93
863 3607 4.321452 GCTTGATTTGAGAGGTTTGCATCA 60.321 41.667 0.00 0.00 0.00 3.07
866 3610 3.225104 AGCTTGATTTGAGAGGTTTGCA 58.775 40.909 0.00 0.00 0.00 4.08
887 3631 6.668645 TCCTCTTGCTTGGGCTTATTAATTA 58.331 36.000 0.00 0.00 39.59 1.40
888 3632 5.518865 TCCTCTTGCTTGGGCTTATTAATT 58.481 37.500 0.00 0.00 39.59 1.40
889 3633 5.129368 TCCTCTTGCTTGGGCTTATTAAT 57.871 39.130 0.00 0.00 39.59 1.40
890 3634 4.018415 ACTCCTCTTGCTTGGGCTTATTAA 60.018 41.667 0.00 0.00 39.59 1.40
938 3703 3.170362 CTGGGGCTCAGGGTTTGA 58.830 61.111 6.45 0.00 39.76 2.69
948 3714 1.011595 TCTAAGACTCTCCTGGGGCT 58.988 55.000 0.00 0.00 0.00 5.19
949 3715 1.116308 GTCTAAGACTCTCCTGGGGC 58.884 60.000 0.00 0.00 0.00 5.80
950 3716 1.007238 TGGTCTAAGACTCTCCTGGGG 59.993 57.143 0.00 0.00 32.47 4.96
951 3717 2.498078 GTTGGTCTAAGACTCTCCTGGG 59.502 54.545 0.00 0.00 32.47 4.45
952 3718 3.436243 AGTTGGTCTAAGACTCTCCTGG 58.564 50.000 0.00 0.00 32.47 4.45
953 3719 6.591750 TTAAGTTGGTCTAAGACTCTCCTG 57.408 41.667 0.00 0.00 32.47 3.86
954 3720 7.800300 AATTAAGTTGGTCTAAGACTCTCCT 57.200 36.000 0.00 0.00 32.47 3.69
957 3723 9.930693 CAAGTAATTAAGTTGGTCTAAGACTCT 57.069 33.333 0.00 0.00 35.24 3.24
971 3739 8.747538 ACTGAAGAACCAACAAGTAATTAAGT 57.252 30.769 0.00 0.00 0.00 2.24
974 3742 9.616156 TGTAACTGAAGAACCAACAAGTAATTA 57.384 29.630 0.00 0.00 0.00 1.40
975 3743 8.514330 TGTAACTGAAGAACCAACAAGTAATT 57.486 30.769 0.00 0.00 0.00 1.40
976 3744 8.567948 CATGTAACTGAAGAACCAACAAGTAAT 58.432 33.333 0.00 0.00 0.00 1.89
980 3748 5.762045 CCATGTAACTGAAGAACCAACAAG 58.238 41.667 0.00 0.00 0.00 3.16
1120 3888 3.643978 GCATGCCTCATCGCCGTC 61.644 66.667 6.36 0.00 0.00 4.79
1194 3968 1.450312 GGTGGTCGCCATCTTCCAG 60.450 63.158 1.90 0.00 35.28 3.86
1218 3992 4.351938 CCAGGCGACGTTCCACGA 62.352 66.667 2.75 0.00 46.05 4.35
1309 4083 0.909133 TCTGTACCCATCCAGCAGCA 60.909 55.000 0.00 0.00 0.00 4.41
1310 4084 0.179062 CTCTGTACCCATCCAGCAGC 60.179 60.000 0.00 0.00 0.00 5.25
1311 4085 0.179062 GCTCTGTACCCATCCAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
1365 4144 7.969536 ATGGAATACAATGAACGAGGAATAG 57.030 36.000 0.00 0.00 0.00 1.73
1489 4297 3.997021 ACAATAACACAGTAGCACTCTGC 59.003 43.478 3.38 0.00 45.46 4.26
1491 4299 5.620205 CGAGACAATAACACAGTAGCACTCT 60.620 44.000 0.00 0.00 0.00 3.24
1516 4324 4.411927 TGCCAAACACACCCTTATATTGT 58.588 39.130 0.00 0.00 0.00 2.71
1520 4328 3.833732 TGTTGCCAAACACACCCTTATA 58.166 40.909 0.00 0.00 41.41 0.98
1535 4343 1.322442 GCTAGGATGGGAATGTTGCC 58.678 55.000 0.00 0.00 39.41 4.52
1536 4344 0.947244 CGCTAGGATGGGAATGTTGC 59.053 55.000 0.00 0.00 0.00 4.17
1537 4345 1.942657 CACGCTAGGATGGGAATGTTG 59.057 52.381 0.00 0.00 0.00 3.33
1538 4346 1.134098 CCACGCTAGGATGGGAATGTT 60.134 52.381 0.00 0.00 31.83 2.71
1539 4347 0.469917 CCACGCTAGGATGGGAATGT 59.530 55.000 0.00 0.00 31.83 2.71
1540 4348 0.469917 ACCACGCTAGGATGGGAATG 59.530 55.000 0.00 0.00 40.59 2.67
1541 4349 1.134098 CAACCACGCTAGGATGGGAAT 60.134 52.381 0.00 0.00 40.59 3.01
1542 4350 0.251916 CAACCACGCTAGGATGGGAA 59.748 55.000 0.00 0.00 40.59 3.97
1543 4351 1.904771 CAACCACGCTAGGATGGGA 59.095 57.895 0.00 0.00 40.59 4.37
1544 4352 1.819632 GCAACCACGCTAGGATGGG 60.820 63.158 0.00 0.00 40.59 4.00
1565 4373 0.637195 TGTCTTAGGGAGAGGGGGAG 59.363 60.000 0.00 0.00 34.31 4.30
1567 4375 1.344496 ACATGTCTTAGGGAGAGGGGG 60.344 57.143 0.00 0.00 34.31 5.40
1572 4380 3.055819 GCACTCAACATGTCTTAGGGAGA 60.056 47.826 0.00 0.00 0.00 3.71
1587 4395 5.853936 AGACAATAACACAGTAGCACTCAA 58.146 37.500 0.00 0.00 0.00 3.02
1641 4453 5.060662 TGTCTACACTCAGCATGTCTTAC 57.939 43.478 0.00 0.00 37.40 2.34
1668 4714 5.772825 AACAACAACAGATGCATGTACTT 57.227 34.783 2.46 0.00 33.45 2.24
1692 4738 3.819564 TCAGCACATACATCACTACCC 57.180 47.619 0.00 0.00 0.00 3.69
1726 4772 4.567159 CCGCTTCCTACTAAACAATGTCTC 59.433 45.833 0.00 0.00 0.00 3.36
1731 4778 3.994931 ACCCGCTTCCTACTAAACAAT 57.005 42.857 0.00 0.00 0.00 2.71
1738 4785 1.066358 GCAACTAACCCGCTTCCTACT 60.066 52.381 0.00 0.00 0.00 2.57
1760 4807 4.051167 TACTCCGGCGACCCCTCA 62.051 66.667 9.30 0.00 0.00 3.86
1782 4829 0.905337 CTTCCCTTCTCCTCGGTGGT 60.905 60.000 0.00 0.00 37.07 4.16
1786 4833 1.045911 CCTCCTTCCCTTCTCCTCGG 61.046 65.000 0.00 0.00 0.00 4.63
1848 4895 2.368875 TCCCAATTTATCCTCTCGCTCC 59.631 50.000 0.00 0.00 0.00 4.70
1860 4907 6.668133 AGGGTTATCTTTCCTCCCAATTTA 57.332 37.500 0.00 0.00 40.48 1.40
1865 4912 3.046374 GCTAGGGTTATCTTTCCTCCCA 58.954 50.000 0.00 0.00 40.48 4.37
1867 4914 3.071747 CCTGCTAGGGTTATCTTTCCTCC 59.928 52.174 0.00 0.00 32.46 4.30
1873 4920 2.050918 GAGGCCTGCTAGGGTTATCTT 58.949 52.381 12.00 0.00 35.37 2.40
1876 4923 0.269173 AGGAGGCCTGCTAGGGTTAT 59.731 55.000 27.45 0.00 35.37 1.89
1886 4933 2.612115 AGGACCCAAGGAGGCCTG 60.612 66.667 12.00 0.00 33.70 4.85
1900 4947 0.826715 CGCTTGAAGGATCCTCAGGA 59.173 55.000 16.52 0.00 35.55 3.86
1902 4949 2.548875 CTTCGCTTGAAGGATCCTCAG 58.451 52.381 16.52 12.58 44.42 3.35
1927 4974 0.106708 AGCAGTTGTTCGCTCCTCAA 59.893 50.000 0.00 0.00 31.16 3.02
1928 4975 0.106708 AAGCAGTTGTTCGCTCCTCA 59.893 50.000 0.00 0.00 37.54 3.86
1939 4986 1.856265 GAGAACGCCCCAAGCAGTTG 61.856 60.000 0.00 0.00 44.04 3.16
1940 4987 1.600916 GAGAACGCCCCAAGCAGTT 60.601 57.895 0.00 0.00 44.04 3.16
1942 4989 1.743252 GAGAGAACGCCCCAAGCAG 60.743 63.158 0.00 0.00 44.04 4.24
1945 4992 1.219393 GAGGAGAGAACGCCCCAAG 59.781 63.158 0.00 0.00 36.64 3.61
1970 5017 0.110678 GCCCAAATACCCCTCCTAGC 59.889 60.000 0.00 0.00 0.00 3.42
2006 5053 2.361771 CCTGCATGGGGCCTCTTT 59.638 61.111 3.07 0.00 43.89 2.52
2078 5129 5.127194 AGAAGAAAACACCAAAGGAAGGAAC 59.873 40.000 0.00 0.00 0.00 3.62
2088 5139 3.813166 CGAGGCTAAGAAGAAAACACCAA 59.187 43.478 0.00 0.00 0.00 3.67
2117 5168 3.145551 CGACCGACTACCAGGGGG 61.146 72.222 0.00 0.00 41.29 5.40
2134 5185 2.825861 TCGAGGGTAAAGTCAACCAC 57.174 50.000 0.00 0.00 38.87 4.16
2188 5239 0.251341 GGCAAGGAGGTGGACAACAT 60.251 55.000 0.00 0.00 0.00 2.71
2228 5279 3.849951 CGCCGCTAGACCACCCAT 61.850 66.667 0.00 0.00 0.00 4.00
2252 5303 2.738521 CGTCACCGAGCCACAAGG 60.739 66.667 0.00 0.00 35.63 3.61
2267 5318 2.102357 CGAGCATAGACACGGCGT 59.898 61.111 6.77 6.77 0.00 5.68


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

AutoCloner maintained by Alex Coulton.