Multiple sequence alignment - TraesCS3D01G190600

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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 TraesCS3D01G190600 chr3D 100.000 5362 0 0 1 5362 179163037 179168398 0.000000e+00 9902.0
1 TraesCS3D01G190600 chr3D 90.847 732 64 3 1 732 556620465 556621193 0.000000e+00 977.0
2 TraesCS3D01G190600 chr3B 94.283 4635 181 30 763 5362 257240188 257244773 0.000000e+00 7014.0
3 TraesCS3D01G190600 chr3A 94.163 2073 96 13 768 2819 221923264 221925332 0.000000e+00 3134.0
4 TraesCS3D01G190600 chr3A 95.000 1600 66 7 2819 4408 221928823 221930418 0.000000e+00 2499.0
5 TraesCS3D01G190600 chr3A 93.008 944 30 10 4451 5362 221930420 221931359 0.000000e+00 1345.0
6 TraesCS3D01G190600 chr1D 91.951 733 56 3 1 732 411723948 411723218 0.000000e+00 1024.0
7 TraesCS3D01G190600 chr6A 91.429 735 55 7 1 732 570899338 570898609 0.000000e+00 1002.0
8 TraesCS3D01G190600 chr6B 90.514 759 67 5 1 758 180960218 180960972 0.000000e+00 998.0
9 TraesCS3D01G190600 chr6B 89.495 733 61 13 1 732 136519103 136519820 0.000000e+00 913.0
10 TraesCS3D01G190600 chr6B 85.656 732 55 23 1 732 158265982 158265301 0.000000e+00 725.0
11 TraesCS3D01G190600 chr2B 90.164 732 60 3 1 732 728624725 728624006 0.000000e+00 942.0
12 TraesCS3D01G190600 chr2B 88.503 748 82 4 13 758 142604794 142605539 0.000000e+00 902.0
13 TraesCS3D01G190600 chr2B 95.556 45 1 1 714 758 761693201 761693158 2.680000e-08 71.3
14 TraesCS3D01G190600 chr4B 89.632 733 61 9 1 732 419201981 419201263 0.000000e+00 918.0
15 TraesCS3D01G190600 chr7B 88.707 735 67 5 1 732 539992164 539991443 0.000000e+00 883.0
16 TraesCS3D01G190600 chr1A 89.860 641 52 4 1 641 524698854 524699481 0.000000e+00 811.0


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 TraesCS3D01G190600 chr3D 179163037 179168398 5361 False 9902 9902 100.000 1 5362 1 chr3D.!!$F1 5361
1 TraesCS3D01G190600 chr3D 556620465 556621193 728 False 977 977 90.847 1 732 1 chr3D.!!$F2 731
2 TraesCS3D01G190600 chr3B 257240188 257244773 4585 False 7014 7014 94.283 763 5362 1 chr3B.!!$F1 4599
3 TraesCS3D01G190600 chr3A 221923264 221931359 8095 False 2326 3134 94.057 768 5362 3 chr3A.!!$F1 4594
4 TraesCS3D01G190600 chr1D 411723218 411723948 730 True 1024 1024 91.951 1 732 1 chr1D.!!$R1 731
5 TraesCS3D01G190600 chr6A 570898609 570899338 729 True 1002 1002 91.429 1 732 1 chr6A.!!$R1 731
6 TraesCS3D01G190600 chr6B 180960218 180960972 754 False 998 998 90.514 1 758 1 chr6B.!!$F2 757
7 TraesCS3D01G190600 chr6B 136519103 136519820 717 False 913 913 89.495 1 732 1 chr6B.!!$F1 731
8 TraesCS3D01G190600 chr6B 158265301 158265982 681 True 725 725 85.656 1 732 1 chr6B.!!$R1 731
9 TraesCS3D01G190600 chr2B 728624006 728624725 719 True 942 942 90.164 1 732 1 chr2B.!!$R1 731
10 TraesCS3D01G190600 chr2B 142604794 142605539 745 False 902 902 88.503 13 758 1 chr2B.!!$F1 745
11 TraesCS3D01G190600 chr4B 419201263 419201981 718 True 918 918 89.632 1 732 1 chr4B.!!$R1 731
12 TraesCS3D01G190600 chr7B 539991443 539992164 721 True 883 883 88.707 1 732 1 chr7B.!!$R1 731
13 TraesCS3D01G190600 chr1A 524698854 524699481 627 False 811 811 89.860 1 641 1 chr1A.!!$F1 640

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
41 42 0.036952 ACGCCTTCACTGTCATCCTG 60.037 55.000 0.0 0.0 0.00 3.86 F
470 473 0.110486 GCCTGGTGTGAGAAGGGAAA 59.890 55.000 0.0 0.0 0.00 3.13 F
650 655 0.337082 TGAGGGTGGGGTTCGATCTA 59.663 55.000 0.0 0.0 0.00 1.98 F
1026 1035 0.608035 TTGCTGCGTTTTAGGGAGGG 60.608 55.000 0.0 0.0 0.00 4.30 F
2065 2091 1.066215 AGCTCACGTGATTGCCATGTA 60.066 47.619 20.4 0.0 42.82 2.29 F
3080 6601 0.745845 ATAGCTTGCTCTGGGCGTTG 60.746 55.000 0.0 0.0 45.43 4.10 F
3651 7172 1.001974 TGGTGGAACTCGTGGATCTTG 59.998 52.381 0.0 0.0 36.74 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1417 0.032267 GCACCATACGAGGTAGGAGC 59.968 60.0 0.00 0.00 40.77 4.70 R
2044 2070 0.376152 CATGGCAATCACGTGAGCTC 59.624 55.0 24.41 15.53 0.00 4.09 R
2481 2507 0.529378 CCATTCAGCAAACCAGAGCC 59.471 55.0 0.00 0.00 0.00 4.70 R
2737 2766 1.494960 ACTGAAAAGGCCTGCCAAAA 58.505 45.0 5.69 0.00 38.92 2.44 R
3875 7402 2.292569 CTGCCATCAAGATGCATGGTAC 59.707 50.0 2.46 0.00 41.63 3.34 R
4213 7740 0.889186 CCAGTAACTTGCGGCAGGTT 60.889 55.0 29.24 29.24 37.44 3.50 R
5211 8758 0.095245 GTTGTGTGTGATCCATCGCG 59.905 55.0 0.00 0.00 40.07 5.87 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
38 39 2.866762 GGATTACGCCTTCACTGTCATC 59.133 50.000 0.00 0.00 0.00 2.92
41 42 0.036952 ACGCCTTCACTGTCATCCTG 60.037 55.000 0.00 0.00 0.00 3.86
117 118 9.658799 TGGTAAGTTTCAGATCTAAGAAATCAG 57.341 33.333 10.46 0.00 36.29 2.90
141 142 4.002906 CTGCTTGGGTAAGTAGTTCACA 57.997 45.455 0.00 0.00 40.48 3.58
217 219 7.530010 CAATGTGGAGAAACGTTAGATGAAAT 58.470 34.615 0.00 0.00 0.00 2.17
320 322 2.281070 CAGCAGGAGCAACACCGT 60.281 61.111 0.00 0.00 45.49 4.83
322 324 3.414700 GCAGGAGCAACACCGTCG 61.415 66.667 0.00 0.00 41.58 5.12
463 466 1.303561 GCAATGGCCTGGTGTGAGA 60.304 57.895 3.32 0.00 0.00 3.27
468 471 2.224159 GGCCTGGTGTGAGAAGGGA 61.224 63.158 0.00 0.00 0.00 4.20
469 472 1.761174 GCCTGGTGTGAGAAGGGAA 59.239 57.895 0.00 0.00 0.00 3.97
470 473 0.110486 GCCTGGTGTGAGAAGGGAAA 59.890 55.000 0.00 0.00 0.00 3.13
471 474 1.884067 GCCTGGTGTGAGAAGGGAAAG 60.884 57.143 0.00 0.00 0.00 2.62
514 519 1.758906 GGCGGAAGTAGGAGCCTCT 60.759 63.158 0.00 0.00 45.67 3.69
516 521 1.038130 GCGGAAGTAGGAGCCTCTGA 61.038 60.000 0.00 0.00 0.00 3.27
608 613 3.827898 CGAGGTCGGGGCAGAGAC 61.828 72.222 0.00 0.00 36.70 3.36
650 655 0.337082 TGAGGGTGGGGTTCGATCTA 59.663 55.000 0.00 0.00 0.00 1.98
758 767 5.470098 AGATTTCGGTTGCCACATACATATC 59.530 40.000 0.00 0.00 0.00 1.63
759 768 3.120321 TCGGTTGCCACATACATATCC 57.880 47.619 0.00 0.00 0.00 2.59
760 769 2.436173 TCGGTTGCCACATACATATCCA 59.564 45.455 0.00 0.00 0.00 3.41
761 770 2.548057 CGGTTGCCACATACATATCCAC 59.452 50.000 0.00 0.00 0.00 4.02
838 847 0.954449 TTTAAAATGCGGCGGTCGGA 60.954 50.000 9.78 0.00 44.80 4.55
906 915 1.284657 TTACCGACGCAAACGAACAA 58.715 45.000 0.00 0.00 43.93 2.83
915 924 3.680458 ACGCAAACGAACAAAAACCAAAT 59.320 34.783 0.00 0.00 43.93 2.32
934 943 6.983890 ACCAAATAAAATCCATATCGTTTGCC 59.016 34.615 0.00 0.00 0.00 4.52
937 946 3.691049 AAATCCATATCGTTTGCCGTG 57.309 42.857 0.00 0.00 37.94 4.94
963 972 2.418368 TGGTGTTGGCCTTATAGCTG 57.582 50.000 3.32 0.00 0.00 4.24
968 977 3.945285 GTGTTGGCCTTATAGCTGCTTTA 59.055 43.478 7.79 0.65 0.00 1.85
974 983 7.687941 TGGCCTTATAGCTGCTTTATATTTC 57.312 36.000 7.79 0.00 0.00 2.17
1026 1035 0.608035 TTGCTGCGTTTTAGGGAGGG 60.608 55.000 0.00 0.00 0.00 4.30
1055 1078 5.382618 AGAGCTGCTCTAAACCATTTTTG 57.617 39.130 29.57 0.00 39.28 2.44
1061 1084 7.653311 AGCTGCTCTAAACCATTTTTGTTTAAG 59.347 33.333 0.00 0.00 37.63 1.85
1063 1086 9.313118 CTGCTCTAAACCATTTTTGTTTAAGTT 57.687 29.630 0.00 0.00 37.63 2.66
1064 1087 9.308318 TGCTCTAAACCATTTTTGTTTAAGTTC 57.692 29.630 0.00 0.00 37.63 3.01
1065 1088 8.476925 GCTCTAAACCATTTTTGTTTAAGTTCG 58.523 33.333 0.00 0.00 37.63 3.95
1310 1333 1.706575 CTTCTCCTCCTCCCCCTCA 59.293 63.158 0.00 0.00 0.00 3.86
1394 1417 4.899239 GATGACAGCGGCGGAGGG 62.899 72.222 9.78 0.00 0.00 4.30
1430 1453 2.872001 CTGCACGACTCGCTCGAC 60.872 66.667 9.03 2.38 46.14 4.20
1691 1714 2.446802 GGATTCCTCCCGCCCTCT 60.447 66.667 0.00 0.00 35.28 3.69
1694 1717 3.332393 ATTCCTCCCGCCCTCTGGA 62.332 63.158 0.00 0.00 0.00 3.86
1765 1788 5.530915 TCCACAAGGTAATTTGACAGTCAAG 59.469 40.000 15.61 4.93 35.39 3.02
1791 1815 4.368874 TGCGATCATGTTACATTTTGGG 57.631 40.909 0.00 0.00 0.00 4.12
1804 1828 4.947645 ACATTTTGGGATAAATCGGCATG 58.052 39.130 0.00 0.00 0.00 4.06
1878 1902 6.160576 TCAAGCCCTTCATTAAATTATGCC 57.839 37.500 0.00 0.00 0.00 4.40
1879 1903 5.660417 TCAAGCCCTTCATTAAATTATGCCA 59.340 36.000 0.00 0.00 0.00 4.92
1931 1957 4.625972 TCAATTGATGTGCTAGCATGTG 57.374 40.909 22.51 11.03 0.00 3.21
1936 1962 2.092807 TGATGTGCTAGCATGTGACCAT 60.093 45.455 22.51 17.64 0.00 3.55
2024 2050 3.905968 TCACTCGGTATGATTGACCCTA 58.094 45.455 0.00 0.00 31.93 3.53
2025 2051 3.889538 TCACTCGGTATGATTGACCCTAG 59.110 47.826 0.00 0.00 31.93 3.02
2032 2058 4.591072 GGTATGATTGACCCTAGCTTCTCT 59.409 45.833 0.00 0.00 0.00 3.10
2044 2070 4.569966 CCTAGCTTCTCTGCTTTGTATGTG 59.430 45.833 0.00 0.00 43.74 3.21
2046 2072 4.252073 AGCTTCTCTGCTTTGTATGTGAG 58.748 43.478 0.00 0.00 40.93 3.51
2065 2091 1.066215 AGCTCACGTGATTGCCATGTA 60.066 47.619 20.40 0.00 42.82 2.29
2163 2189 8.712363 GCTCTAATGCTTTCGTTGATATATTCA 58.288 33.333 0.00 0.00 0.00 2.57
2167 2193 8.668510 AATGCTTTCGTTGATATATTCAGAGT 57.331 30.769 0.00 0.00 35.27 3.24
2243 2269 1.848388 TCCACATGATCTCAATGGCCT 59.152 47.619 3.32 0.00 36.60 5.19
2455 2481 6.230472 ACTCATTTAATGTTTTTGGGGAAGC 58.770 36.000 4.77 0.00 0.00 3.86
2481 2507 7.149569 TCCTGCAATTGAGAAATCTTAACTG 57.850 36.000 10.34 0.00 0.00 3.16
2672 2701 2.835764 ACATTCCGGACTAGCCTAAACA 59.164 45.455 1.83 0.00 0.00 2.83
2673 2702 3.118738 ACATTCCGGACTAGCCTAAACAG 60.119 47.826 1.83 0.00 0.00 3.16
2720 2749 7.974501 ACTTATCCGTATACAAGTCTTCTGTTG 59.025 37.037 3.32 0.00 0.00 3.33
2722 2751 6.335471 TCCGTATACAAGTCTTCTGTTGAA 57.665 37.500 3.32 0.00 0.00 2.69
2880 6401 4.523558 AGACCCTACAGTTCAGTTACACTC 59.476 45.833 0.00 0.00 0.00 3.51
2946 6467 5.420104 GGTTTTCACCTGATGATTCTGGATT 59.580 40.000 5.98 0.00 42.12 3.01
2959 6480 5.949354 TGATTCTGGATTTTACACCCGATTT 59.051 36.000 0.00 0.00 0.00 2.17
2966 6487 6.543100 TGGATTTTACACCCGATTTGTATACC 59.457 38.462 0.00 0.00 29.60 2.73
2988 6509 4.218417 CCCAGAACCAGAAATTTAGGTGTG 59.782 45.833 13.79 13.42 35.42 3.82
2990 6511 5.048713 CCAGAACCAGAAATTTAGGTGTGAC 60.049 44.000 13.79 7.71 35.42 3.67
3080 6601 0.745845 ATAGCTTGCTCTGGGCGTTG 60.746 55.000 0.00 0.00 45.43 4.10
3141 6662 8.213679 TCTCCTAATGTTAGCTATCATGCTTTT 58.786 33.333 16.25 5.68 43.74 2.27
3211 6732 6.086785 TCTGTTGAATGCAATGACATTTGA 57.913 33.333 0.00 0.00 40.31 2.69
3224 6745 7.970061 GCAATGACATTTGAGCTTACTTTGATA 59.030 33.333 0.00 0.00 0.00 2.15
3601 7122 6.804783 ACAACACTTTTCCGTTTAGTTTCTTG 59.195 34.615 0.00 0.00 0.00 3.02
3619 7140 8.576442 AGTTTCTTGTTAATTTGGAGGTGTATG 58.424 33.333 0.00 0.00 0.00 2.39
3651 7172 1.001974 TGGTGGAACTCGTGGATCTTG 59.998 52.381 0.00 0.00 36.74 3.02
3652 7173 1.002087 GGTGGAACTCGTGGATCTTGT 59.998 52.381 0.00 0.00 36.74 3.16
3667 7188 7.910162 CGTGGATCTTGTGTTAAAATGATTAGG 59.090 37.037 0.00 0.00 0.00 2.69
3812 7336 2.837532 GCCATTGCCTTTCTTTTCCA 57.162 45.000 0.00 0.00 0.00 3.53
3813 7337 2.416747 GCCATTGCCTTTCTTTTCCAC 58.583 47.619 0.00 0.00 0.00 4.02
3814 7338 2.037641 GCCATTGCCTTTCTTTTCCACT 59.962 45.455 0.00 0.00 0.00 4.00
3815 7339 3.656559 CCATTGCCTTTCTTTTCCACTG 58.343 45.455 0.00 0.00 0.00 3.66
3817 7341 4.280677 CCATTGCCTTTCTTTTCCACTGTA 59.719 41.667 0.00 0.00 0.00 2.74
3818 7342 5.047092 CCATTGCCTTTCTTTTCCACTGTAT 60.047 40.000 0.00 0.00 0.00 2.29
3819 7343 6.458210 CATTGCCTTTCTTTTCCACTGTATT 58.542 36.000 0.00 0.00 0.00 1.89
3820 7344 7.309744 CCATTGCCTTTCTTTTCCACTGTATTA 60.310 37.037 0.00 0.00 0.00 0.98
3821 7345 7.589958 TTGCCTTTCTTTTCCACTGTATTAA 57.410 32.000 0.00 0.00 0.00 1.40
3822 7346 7.214467 TGCCTTTCTTTTCCACTGTATTAAG 57.786 36.000 0.00 0.00 0.00 1.85
3823 7347 6.775629 TGCCTTTCTTTTCCACTGTATTAAGT 59.224 34.615 0.00 0.00 0.00 2.24
3824 7348 7.040686 TGCCTTTCTTTTCCACTGTATTAAGTC 60.041 37.037 0.00 0.00 0.00 3.01
3825 7349 7.575155 GCCTTTCTTTTCCACTGTATTAAGTCC 60.575 40.741 0.00 0.00 0.00 3.85
3827 7351 7.979444 TTCTTTTCCACTGTATTAAGTCCTG 57.021 36.000 0.00 0.00 0.00 3.86
3875 7402 2.069273 GTCACTGACCAGGTTCATTCG 58.931 52.381 0.00 0.00 0.00 3.34
4039 7566 7.894753 TGCCATGGTATTTCATCTTCAAATA 57.105 32.000 14.67 0.00 0.00 1.40
4100 7627 5.282055 TGCCACTCTACATCTATTCCTTG 57.718 43.478 0.00 0.00 0.00 3.61
4220 7747 2.564721 GGACAGCCACAAACCTGCC 61.565 63.158 0.00 0.00 32.37 4.85
4400 7930 5.575957 GTTCTCACATGTTTGATATGGCAG 58.424 41.667 0.00 0.00 0.00 4.85
4461 7991 5.060077 CACGACAAATGTAAACTCGTATCGT 59.940 40.000 0.00 0.00 39.46 3.73
4492 8022 6.018180 AGTCTTTTCAGTTATGTTCACCGAAC 60.018 38.462 0.00 0.00 42.26 3.95
5012 8558 3.847602 CTCTGGCCCTCCTCGCAG 61.848 72.222 0.00 0.00 0.00 5.18
5185 8731 7.269477 ACTTGAAGTCTGGAATCAAAAGAAG 57.731 36.000 0.00 0.00 33.08 2.85
5187 8733 7.723172 ACTTGAAGTCTGGAATCAAAAGAAGAT 59.277 33.333 0.00 0.00 33.08 2.40
5188 8734 7.678947 TGAAGTCTGGAATCAAAAGAAGATC 57.321 36.000 0.00 0.00 0.00 2.75
5190 8736 8.597167 TGAAGTCTGGAATCAAAAGAAGATCTA 58.403 33.333 0.00 0.00 0.00 1.98
5211 8758 0.512952 GTTGCAGGACACACGATCAC 59.487 55.000 0.00 0.00 0.00 3.06
5286 8852 6.550108 AGGGAAATGGAAGAAATGATGAGATG 59.450 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 5.246307 ACTTACCCAAGCAGTACTGATTTC 58.754 41.667 27.08 8.56 37.04 2.17
117 118 4.928020 GTGAACTACTTACCCAAGCAGTAC 59.072 45.833 0.00 0.00 37.39 2.73
141 142 0.743688 TGTGGCAGTTGCGAACATTT 59.256 45.000 7.04 0.00 43.26 2.32
217 219 1.410517 CTCGGCCATCTGAAAGCTCTA 59.589 52.381 2.24 0.00 0.00 2.43
291 293 2.749682 CTGCTGCTGGTGGTGGTA 59.250 61.111 0.00 0.00 0.00 3.25
417 419 2.055042 CCTCTACCTCCTGCGTGCT 61.055 63.158 0.00 0.00 0.00 4.40
451 454 0.110486 TTTCCCTTCTCACACCAGGC 59.890 55.000 0.00 0.00 0.00 4.85
572 577 2.122413 TCCGATCCCCATCCCAGG 60.122 66.667 0.00 0.00 0.00 4.45
602 607 3.535561 ACCAATATTGCTTCCGTCTCTG 58.464 45.455 10.11 0.00 0.00 3.35
608 613 5.309323 TGAGAAAACCAATATTGCTTCCG 57.691 39.130 10.11 0.00 0.00 4.30
630 635 0.326618 AGATCGAACCCCACCCTCAT 60.327 55.000 0.00 0.00 0.00 2.90
699 708 2.140792 ACACCAGCTGGGAGACGTT 61.141 57.895 35.42 11.03 41.15 3.99
740 749 2.548057 GTGGATATGTATGTGGCAACCG 59.452 50.000 0.00 0.00 0.00 4.44
809 818 3.993736 GCCGCATTTTAAATGTTTGTCCT 59.006 39.130 17.51 0.00 0.00 3.85
822 831 2.437716 ATCCGACCGCCGCATTTT 60.438 55.556 0.00 0.00 36.84 1.82
838 847 1.662760 CATCCGTCGATGCGCTCAT 60.663 57.895 9.73 0.00 39.59 2.90
876 885 1.777199 GTCGGTAAAACGAGCACGG 59.223 57.895 8.74 0.00 44.42 4.94
881 890 1.928276 GTTTGCGTCGGTAAAACGAG 58.072 50.000 0.00 0.00 44.42 4.18
937 946 4.279043 GGCCAACACCAACGCACC 62.279 66.667 0.00 0.00 0.00 5.01
947 956 2.806945 AAGCAGCTATAAGGCCAACA 57.193 45.000 5.01 0.00 0.00 3.33
963 972 4.202010 TGAGGCAAAGCGGAAATATAAAGC 60.202 41.667 0.00 0.00 0.00 3.51
968 977 4.022849 GCTTATGAGGCAAAGCGGAAATAT 60.023 41.667 0.00 0.00 38.80 1.28
1026 1035 4.116238 GGTTTAGAGCAGCTCTATGACAC 58.884 47.826 29.11 21.68 41.87 3.67
1055 1078 5.108518 GGATGTGAAAAACGCGAACTTAAAC 60.109 40.000 15.93 3.20 0.00 2.01
1061 1084 2.392933 TGGATGTGAAAAACGCGAAC 57.607 45.000 15.93 1.33 0.00 3.95
1063 1086 3.634568 ATTTGGATGTGAAAAACGCGA 57.365 38.095 15.93 0.00 0.00 5.87
1064 1087 4.444468 CAAATTTGGATGTGAAAAACGCG 58.556 39.130 10.49 3.53 0.00 6.01
1090 1113 7.753309 TCAGAATCCAATTTTACGGAGAAAA 57.247 32.000 0.00 0.00 33.97 2.29
1296 1319 1.081092 CAGTTGAGGGGGAGGAGGA 59.919 63.158 0.00 0.00 0.00 3.71
1310 1333 1.447838 CCGTCGCCTGCATACAGTT 60.448 57.895 0.00 0.00 42.81 3.16
1340 1363 0.104304 CACAGGCCCGGATAGTGTAC 59.896 60.000 0.73 0.00 0.00 2.90
1394 1417 0.032267 GCACCATACGAGGTAGGAGC 59.968 60.000 0.00 0.00 40.77 4.70
1406 1429 1.153842 CGAGTCGTGCAGCACCATA 60.154 57.895 20.16 2.80 0.00 2.74
1505 1528 2.651361 CTGGTCTCCGCGTTGAGT 59.349 61.111 4.92 0.00 33.93 3.41
1721 1744 0.529337 CGTAGAGGTAGCGGTCGAGA 60.529 60.000 0.00 0.00 0.00 4.04
1765 1788 6.020440 CCAAAATGTAACATGATCGCATCAAC 60.020 38.462 0.00 0.00 43.50 3.18
1804 1828 3.264104 CCAAAATGTGACCATGGCATTC 58.736 45.455 13.04 2.27 32.38 2.67
1815 1839 9.383519 GAGTCTCAAATAGATACCAAAATGTGA 57.616 33.333 0.00 0.00 36.36 3.58
1931 1957 6.347888 CCTGAATGAAAAATTGCAACATGGTC 60.348 38.462 0.00 0.00 0.00 4.02
1936 1962 3.814283 GCCCTGAATGAAAAATTGCAACA 59.186 39.130 0.00 0.00 0.00 3.33
2025 2051 3.181512 GCTCACATACAAAGCAGAGAAGC 60.182 47.826 0.00 0.00 36.06 3.86
2032 2058 2.068519 CGTGAGCTCACATACAAAGCA 58.931 47.619 38.31 3.40 46.75 3.91
2044 2070 0.376152 CATGGCAATCACGTGAGCTC 59.624 55.000 24.41 15.53 0.00 4.09
2046 2072 1.368641 TACATGGCAATCACGTGAGC 58.631 50.000 24.41 21.26 0.00 4.26
2163 2189 3.573110 ACCGTAGTGTCTTTAGCAACTCT 59.427 43.478 0.00 0.00 0.00 3.24
2167 2193 6.982141 CCATATAACCGTAGTGTCTTTAGCAA 59.018 38.462 0.00 0.00 0.00 3.91
2355 2381 6.204688 AGCAGACTAATGACGTTTGAAAATGA 59.795 34.615 2.08 0.00 0.00 2.57
2455 2481 7.701078 CAGTTAAGATTTCTCAATTGCAGGATG 59.299 37.037 0.00 0.00 40.87 3.51
2481 2507 0.529378 CCATTCAGCAAACCAGAGCC 59.471 55.000 0.00 0.00 0.00 4.70
2722 2751 6.929049 GCCTGCCAAAACTCTAGTTTATTTTT 59.071 34.615 8.45 0.00 46.47 1.94
2737 2766 1.494960 ACTGAAAAGGCCTGCCAAAA 58.505 45.000 5.69 0.00 38.92 2.44
2880 6401 3.495753 GGGGGATACGTAATAACTTTGCG 59.504 47.826 0.00 0.00 37.60 4.85
2946 6467 5.189342 TCTGGGTATACAAATCGGGTGTAAA 59.811 40.000 5.01 0.00 35.21 2.01
2959 6480 7.037153 ACCTAAATTTCTGGTTCTGGGTATACA 60.037 37.037 5.01 0.00 0.00 2.29
2966 6487 5.048713 GTCACACCTAAATTTCTGGTTCTGG 60.049 44.000 11.67 5.40 30.72 3.86
2988 6509 8.575649 TCAGAAAAATACCCAATTAAGAGGTC 57.424 34.615 0.00 0.00 35.02 3.85
3080 6601 5.958955 ATCTTAAGAGAAAAGCAACCATGC 58.041 37.500 11.53 0.00 43.47 4.06
3092 6613 9.646427 GAGAAGAAGCAAACTATCTTAAGAGAA 57.354 33.333 11.53 0.89 35.07 2.87
3168 6689 3.823304 AGATGTCAACTTTTGGAGCCTTC 59.177 43.478 0.00 0.00 0.00 3.46
3211 6732 9.077885 TGGAAAACAGATTTATCAAAGTAAGCT 57.922 29.630 0.00 0.00 0.00 3.74
3283 6804 7.274250 GCATTCAAAAATAAGCTACTTGACTGG 59.726 37.037 0.00 0.00 31.19 4.00
3601 7122 5.417580 TCCTTGCATACACCTCCAAATTAAC 59.582 40.000 0.00 0.00 0.00 2.01
3619 7140 2.981977 TTCCACCACGTCGTCCTTGC 62.982 60.000 0.00 0.00 0.00 4.01
3651 7172 8.021396 GGTGACTTGTCCTAATCATTTTAACAC 58.979 37.037 0.00 0.00 0.00 3.32
3652 7173 7.942341 AGGTGACTTGTCCTAATCATTTTAACA 59.058 33.333 0.00 0.00 37.44 2.41
3667 7188 7.119699 TGTGAATTATCAATGAGGTGACTTGTC 59.880 37.037 0.00 0.00 38.00 3.18
3726 7247 5.667626 AGGTGTGGACAGTTTGGATATATCT 59.332 40.000 12.42 0.00 0.00 1.98
3811 7335 5.875359 GGAGAAACCAGGACTTAATACAGTG 59.125 44.000 0.00 0.00 38.79 3.66
3812 7336 5.546499 TGGAGAAACCAGGACTTAATACAGT 59.454 40.000 0.00 0.00 44.64 3.55
3813 7337 6.049955 TGGAGAAACCAGGACTTAATACAG 57.950 41.667 0.00 0.00 44.64 2.74
3827 7351 5.787380 AGAAAATGCAGATTTGGAGAAACC 58.213 37.500 5.10 0.00 31.83 3.27
3875 7402 2.292569 CTGCCATCAAGATGCATGGTAC 59.707 50.000 2.46 0.00 41.63 3.34
4039 7566 7.116075 AGTATTTACAATGGCTGAATGCAAT 57.884 32.000 0.00 0.00 45.15 3.56
4213 7740 0.889186 CCAGTAACTTGCGGCAGGTT 60.889 55.000 29.24 29.24 37.44 3.50
4220 7747 3.701532 TTTTTGGTCCAGTAACTTGCG 57.298 42.857 0.00 0.00 0.00 4.85
4400 7930 4.214437 CACAAGTCGAGAAAGATGCAAAC 58.786 43.478 0.00 0.00 0.00 2.93
4432 7962 5.079406 CGAGTTTACATTTGTCGTGATTGG 58.921 41.667 0.00 0.00 0.00 3.16
4492 8022 7.533900 CGAGTTTACATCAATGGTTACAAGTTG 59.466 37.037 0.00 0.00 0.00 3.16
4683 8229 2.758979 AGTTCATCCGGTGGTACTAGTG 59.241 50.000 5.39 0.00 0.00 2.74
5185 8731 2.668457 CGTGTGTCCTGCAACTTAGATC 59.332 50.000 0.00 0.00 0.00 2.75
5187 8733 1.684450 TCGTGTGTCCTGCAACTTAGA 59.316 47.619 0.00 0.00 0.00 2.10
5188 8734 2.148916 TCGTGTGTCCTGCAACTTAG 57.851 50.000 0.00 0.00 0.00 2.18
5190 8736 1.202639 TGATCGTGTGTCCTGCAACTT 60.203 47.619 0.00 0.00 0.00 2.66
5211 8758 0.095245 GTTGTGTGTGATCCATCGCG 59.905 55.000 0.00 0.00 40.07 5.87
5286 8852 0.107945 GCTCTGTGAGTCATCCACCC 60.108 60.000 0.00 0.00 33.80 4.61


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

AutoCloner maintained by Alex Coulton.