Multiple sequence alignment - TraesCS3D01G272800

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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 TraesCS3D01G272800 chr3D 100.000 5930 0 0 1 5930 378238323 378244252 0.000000e+00 10951.0
1 TraesCS3D01G272800 chr3D 82.927 82 14 0 406 487 543884567 543884486 2.290000e-09 75.0
2 TraesCS3D01G272800 chr3A 93.811 5235 206 47 749 5930 502398578 502403747 0.000000e+00 7764.0
3 TraesCS3D01G272800 chr3A 89.628 646 49 6 126 757 502397658 502398299 0.000000e+00 806.0
4 TraesCS3D01G272800 chr3B 93.823 4549 173 38 717 5214 493162724 493167215 0.000000e+00 6745.0
5 TraesCS3D01G272800 chr3B 91.096 730 33 11 5214 5930 493167296 493168006 0.000000e+00 959.0
6 TraesCS3D01G272800 chr3B 87.470 830 50 25 4961 5785 493273957 493274737 0.000000e+00 907.0
7 TraesCS3D01G272800 chr3B 86.789 545 57 4 195 725 493159575 493160118 1.420000e-165 593.0
8 TraesCS3D01G272800 chr3B 94.656 131 6 1 1 131 493125982 493126111 1.010000e-47 202.0
9 TraesCS3D01G272800 chr3B 94.958 119 2 1 5816 5930 493274732 493274850 3.650000e-42 183.0
10 TraesCS3D01G272800 chr4D 100.000 28 0 0 53 80 455262058 455262031 1.100000e-02 52.8
11 TraesCS3D01G272800 chr1A 100.000 28 0 0 56 83 321413611 321413584 1.100000e-02 52.8


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 TraesCS3D01G272800 chr3D 378238323 378244252 5929 False 10951.000000 10951 100.000000 1 5930 1 chr3D.!!$F1 5929
1 TraesCS3D01G272800 chr3A 502397658 502403747 6089 False 4285.000000 7764 91.719500 126 5930 2 chr3A.!!$F1 5804
2 TraesCS3D01G272800 chr3B 493159575 493168006 8431 False 2765.666667 6745 90.569333 195 5930 3 chr3B.!!$F2 5735
3 TraesCS3D01G272800 chr3B 493273957 493274850 893 False 545.000000 907 91.214000 4961 5930 2 chr3B.!!$F3 969

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
821 3738 0.180878 TCGATGCATCATCCTGGCAA 59.819 50.000 25.70 0.0 41.43 4.52 F
822 3739 0.309922 CGATGCATCATCCTGGCAAC 59.690 55.000 25.70 0.0 41.43 4.17 F
2322 5261 0.034337 TTCCAAAGGACCGAGGAACG 59.966 55.000 10.21 0.0 35.35 3.95 F
4116 7064 1.675116 CCTGATCTGCCGGCTGATATG 60.675 57.143 38.84 31.9 35.29 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 5261 2.464865 CGGAACTCGTCATTGGAGATC 58.535 52.381 0.0 0.0 35.49 2.75 R
2663 5602 5.473504 AGAAATGTTACGCAAGGACAGATTT 59.526 36.000 0.0 0.0 46.39 2.17 R
4158 7106 0.527565 CATGTCTTTTCCTTGCCCCG 59.472 55.000 0.0 0.0 0.00 5.73 R
5530 8588 0.036010 GTGACAGGGTGATGGACAGG 60.036 60.000 0.0 0.0 0.00 4.00 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
25 26 2.599408 AGGAGACCAACCTTCGTAGA 57.401 50.000 0.00 0.00 33.55 2.59
26 27 2.448453 AGGAGACCAACCTTCGTAGAG 58.552 52.381 0.00 0.00 38.43 2.43
27 28 2.041350 AGGAGACCAACCTTCGTAGAGA 59.959 50.000 0.00 0.00 38.43 3.10
28 29 2.424246 GGAGACCAACCTTCGTAGAGAG 59.576 54.545 0.00 0.00 38.43 3.20
29 30 3.083293 GAGACCAACCTTCGTAGAGAGT 58.917 50.000 0.00 0.00 38.43 3.24
30 31 4.260170 GAGACCAACCTTCGTAGAGAGTA 58.740 47.826 0.00 0.00 38.43 2.59
31 32 4.857679 AGACCAACCTTCGTAGAGAGTAT 58.142 43.478 0.00 0.00 38.43 2.12
32 33 4.641094 AGACCAACCTTCGTAGAGAGTATG 59.359 45.833 0.00 0.00 38.43 2.39
33 34 4.597004 ACCAACCTTCGTAGAGAGTATGA 58.403 43.478 0.00 0.00 38.43 2.15
34 35 4.641094 ACCAACCTTCGTAGAGAGTATGAG 59.359 45.833 0.00 0.00 38.43 2.90
35 36 4.036971 CCAACCTTCGTAGAGAGTATGAGG 59.963 50.000 0.00 0.00 38.43 3.86
36 37 3.822940 ACCTTCGTAGAGAGTATGAGGG 58.177 50.000 1.84 1.84 38.43 4.30
37 38 3.150767 CCTTCGTAGAGAGTATGAGGGG 58.849 54.545 0.00 0.00 38.43 4.79
38 39 2.273538 TCGTAGAGAGTATGAGGGGC 57.726 55.000 0.00 0.00 0.00 5.80
39 40 1.202903 TCGTAGAGAGTATGAGGGGCC 60.203 57.143 0.00 0.00 0.00 5.80
40 41 1.249407 GTAGAGAGTATGAGGGGCCG 58.751 60.000 0.00 0.00 0.00 6.13
41 42 0.539901 TAGAGAGTATGAGGGGCCGC 60.540 60.000 12.88 12.88 0.00 6.53
42 43 2.041922 AGAGTATGAGGGGCCGCA 60.042 61.111 23.39 8.39 0.00 5.69
43 44 1.686325 GAGAGTATGAGGGGCCGCAA 61.686 60.000 23.39 10.26 0.00 4.85
44 45 1.523938 GAGTATGAGGGGCCGCAAC 60.524 63.158 23.39 15.53 0.00 4.17
45 46 2.252072 GAGTATGAGGGGCCGCAACA 62.252 60.000 23.39 20.53 0.00 3.33
46 47 1.819632 GTATGAGGGGCCGCAACAG 60.820 63.158 23.39 0.00 0.00 3.16
47 48 3.697439 TATGAGGGGCCGCAACAGC 62.697 63.158 23.39 6.16 0.00 4.40
63 64 4.596180 GCGAACGCGGCATGGATG 62.596 66.667 12.47 0.00 38.16 3.51
64 65 3.940640 CGAACGCGGCATGGATGG 61.941 66.667 12.47 0.00 0.00 3.51
76 77 3.823330 GGATGGCGTCCGACGAGT 61.823 66.667 24.78 8.83 46.05 4.18
77 78 2.579787 GATGGCGTCCGACGAGTG 60.580 66.667 24.78 0.00 46.05 3.51
78 79 3.047718 GATGGCGTCCGACGAGTGA 62.048 63.158 24.78 4.74 46.05 3.41
79 80 2.337749 GATGGCGTCCGACGAGTGAT 62.338 60.000 24.78 9.25 46.05 3.06
80 81 1.945354 ATGGCGTCCGACGAGTGATT 61.945 55.000 24.78 0.00 46.05 2.57
81 82 1.872679 GGCGTCCGACGAGTGATTC 60.873 63.158 24.78 4.60 46.05 2.52
82 83 1.154093 GCGTCCGACGAGTGATTCA 60.154 57.895 24.78 0.00 46.05 2.57
83 84 0.525668 GCGTCCGACGAGTGATTCAT 60.526 55.000 24.78 0.00 46.05 2.57
84 85 1.467875 CGTCCGACGAGTGATTCATC 58.532 55.000 16.03 0.00 46.05 2.92
85 86 1.064208 CGTCCGACGAGTGATTCATCT 59.936 52.381 16.03 0.00 46.05 2.90
86 87 2.478031 CGTCCGACGAGTGATTCATCTT 60.478 50.000 16.03 0.00 46.05 2.40
87 88 3.512680 GTCCGACGAGTGATTCATCTTT 58.487 45.455 0.00 0.00 0.00 2.52
88 89 3.927142 GTCCGACGAGTGATTCATCTTTT 59.073 43.478 0.00 0.00 0.00 2.27
89 90 4.389077 GTCCGACGAGTGATTCATCTTTTT 59.611 41.667 0.00 0.00 0.00 1.94
149 150 7.707464 TGTAATGTCTCTTCAAAAACAGACGTA 59.293 33.333 0.00 0.00 38.52 3.57
151 152 4.807304 TGTCTCTTCAAAAACAGACGTACC 59.193 41.667 0.00 0.00 38.52 3.34
160 161 6.596497 TCAAAAACAGACGTACCTCTCTTTTT 59.404 34.615 11.82 11.82 32.00 1.94
162 163 8.557029 CAAAAACAGACGTACCTCTCTTTTTAT 58.443 33.333 15.06 0.11 30.83 1.40
166 167 5.581085 CAGACGTACCTCTCTTTTTATTGGG 59.419 44.000 0.00 0.00 0.00 4.12
173 174 5.420104 ACCTCTCTTTTTATTGGGCATCAAG 59.580 40.000 0.00 0.00 38.95 3.02
180 181 0.333993 ATTGGGCATCAAGGTGCTCT 59.666 50.000 6.75 0.00 45.87 4.09
184 185 1.340017 GGGCATCAAGGTGCTCTAACA 60.340 52.381 5.18 0.00 42.38 2.41
198 199 5.125417 GTGCTCTAACATCTTTGGGCAAATA 59.875 40.000 0.00 0.00 39.84 1.40
199 200 5.893255 TGCTCTAACATCTTTGGGCAAATAT 59.107 36.000 0.00 0.00 35.91 1.28
244 245 1.271217 GGTTTCTTCAGCCTACCGGTT 60.271 52.381 15.04 0.00 0.00 4.44
295 296 1.737793 CATGCCCCTTCTCGTTAACAC 59.262 52.381 6.39 0.00 0.00 3.32
362 363 0.819259 TGTGCTTGAGCCTGTTGGAC 60.819 55.000 0.00 0.00 41.18 4.02
387 388 7.029563 CCTACTCCAAATGTGTTTTAAGATGC 58.970 38.462 0.00 0.00 0.00 3.91
403 404 1.876156 GATGCGCCCTTCTTGATTAGG 59.124 52.381 4.18 0.00 0.00 2.69
452 453 5.069318 TGGCATGTCTGAATTGTTGAACTA 58.931 37.500 0.00 0.00 0.00 2.24
456 457 6.744537 GCATGTCTGAATTGTTGAACTATGAC 59.255 38.462 0.00 0.00 0.00 3.06
515 516 7.294676 TCGTGATGAATTTGTGTTCTATGAG 57.705 36.000 0.00 0.00 0.00 2.90
525 526 2.096496 GTGTTCTATGAGCCATGTGCAC 59.904 50.000 10.75 10.75 44.83 4.57
528 529 1.153188 TATGAGCCATGTGCACGGG 60.153 57.895 19.95 19.95 44.83 5.28
608 623 0.937304 CCGTTTGACACAGTGTGGAG 59.063 55.000 26.40 10.66 37.94 3.86
627 642 3.503412 GGAGGTTTAGGGGGTTGGATTTT 60.503 47.826 0.00 0.00 0.00 1.82
672 687 0.827368 CTACCCCAGGAGAGAACTGC 59.173 60.000 0.00 0.00 34.65 4.40
716 731 1.059913 AGAAACTGTGAGACCAGGGG 58.940 55.000 0.00 0.00 36.75 4.79
723 3352 1.536418 TGAGACCAGGGGGAGTGTG 60.536 63.158 0.00 0.00 38.05 3.82
809 3726 3.964221 GACGCGTGACCTCGATGCA 62.964 63.158 20.70 0.00 0.00 3.96
810 3727 2.583319 CGCGTGACCTCGATGCAT 60.583 61.111 0.00 0.00 0.00 3.96
811 3728 2.580470 CGCGTGACCTCGATGCATC 61.580 63.158 17.10 17.10 0.00 3.91
812 3729 1.519234 GCGTGACCTCGATGCATCA 60.519 57.895 25.70 12.22 0.00 3.07
813 3730 0.877649 GCGTGACCTCGATGCATCAT 60.878 55.000 25.70 8.37 0.00 2.45
815 3732 1.506493 GTGACCTCGATGCATCATCC 58.494 55.000 25.70 10.34 37.57 3.51
816 3733 1.069823 GTGACCTCGATGCATCATCCT 59.930 52.381 25.70 5.62 37.57 3.24
817 3734 1.069668 TGACCTCGATGCATCATCCTG 59.930 52.381 25.70 9.64 37.57 3.86
818 3735 0.395686 ACCTCGATGCATCATCCTGG 59.604 55.000 25.70 19.29 37.57 4.45
819 3736 0.954449 CCTCGATGCATCATCCTGGC 60.954 60.000 25.70 0.00 37.57 4.85
820 3737 0.250166 CTCGATGCATCATCCTGGCA 60.250 55.000 25.70 0.00 42.43 4.92
821 3738 0.180878 TCGATGCATCATCCTGGCAA 59.819 50.000 25.70 0.00 41.43 4.52
822 3739 0.309922 CGATGCATCATCCTGGCAAC 59.690 55.000 25.70 0.00 41.43 4.17
823 3740 1.395635 GATGCATCATCCTGGCAACA 58.604 50.000 21.92 0.00 41.43 3.33
824 3741 1.752498 GATGCATCATCCTGGCAACAA 59.248 47.619 21.92 0.00 41.43 2.83
825 3742 2.166870 GATGCATCATCCTGGCAACAAA 59.833 45.455 21.92 0.00 41.43 2.83
826 3743 3.368635 GATGCATCATCCTGGCAACAAAA 60.369 43.478 21.92 0.00 41.43 2.44
827 3744 5.208655 GATGCATCATCCTGGCAACAAAAG 61.209 45.833 21.92 0.00 41.43 2.27
862 3779 2.049063 CGATTCGAGATCGGCCCC 60.049 66.667 16.96 0.00 40.29 5.80
869 3786 1.458588 GAGATCGGCCCCTCTCCTT 60.459 63.158 15.39 0.00 33.30 3.36
871 3788 1.147153 GATCGGCCCCTCTCCTTTG 59.853 63.158 0.00 0.00 0.00 2.77
874 3791 0.326238 TCGGCCCCTCTCCTTTGTAT 60.326 55.000 0.00 0.00 0.00 2.29
876 3793 1.766496 CGGCCCCTCTCCTTTGTATAA 59.234 52.381 0.00 0.00 0.00 0.98
877 3794 2.224305 CGGCCCCTCTCCTTTGTATAAG 60.224 54.545 0.00 0.00 0.00 1.73
935 3859 0.895559 CACTCTGCAACCCTTTCCCC 60.896 60.000 0.00 0.00 0.00 4.81
1212 4146 0.832135 TCCCGGAGATAGTGGCCATC 60.832 60.000 9.72 1.70 0.00 3.51
1576 4510 3.518998 CGAGTCGCACCTCCGGAT 61.519 66.667 3.57 0.00 0.00 4.18
1713 4652 6.119536 ACTTCAGTGATTGTTTGGTCAGTTA 58.880 36.000 0.00 0.00 0.00 2.24
1714 4653 6.601613 ACTTCAGTGATTGTTTGGTCAGTTAA 59.398 34.615 0.00 0.00 0.00 2.01
1722 4661 9.126151 TGATTGTTTGGTCAGTTAATCAGTTTA 57.874 29.630 0.00 0.00 32.58 2.01
1787 4726 4.753610 GGGTAGTGGTTGTTTAGTCTGTTC 59.246 45.833 0.00 0.00 0.00 3.18
1959 4898 4.559229 TCGCTCTGGCTCGATGCG 62.559 66.667 0.00 0.00 46.71 4.73
2133 5072 7.147966 TGGTACTGTGTCTTATGATATTGTCGT 60.148 37.037 0.00 0.00 0.00 4.34
2139 5078 7.488150 TGTGTCTTATGATATTGTCGTCTGTTC 59.512 37.037 0.00 0.00 0.00 3.18
2199 5138 3.119637 TCGTGTCTTCTGATATTGTCGCA 60.120 43.478 0.00 0.00 0.00 5.10
2322 5261 0.034337 TTCCAAAGGACCGAGGAACG 59.966 55.000 10.21 0.00 35.35 3.95
2551 5490 1.832600 CAGTGATGTCTCGATGGACG 58.167 55.000 0.94 0.00 44.09 4.79
2703 5642 9.685828 GTAACATTTCTTTGTAATTAGGTTGCA 57.314 29.630 0.00 0.00 0.00 4.08
2736 5675 4.282195 ACTGGAGCTAACTGGCACTATATC 59.718 45.833 0.00 0.00 34.17 1.63
2923 5863 3.624861 CGGCTTTTGAGAGAGTAATGCAT 59.375 43.478 0.00 0.00 0.00 3.96
2983 5923 3.829601 AGGTGTCAAGAGAGAAGGTACAG 59.170 47.826 0.00 0.00 0.00 2.74
3078 6018 5.523552 TCATCAGGTTGCGAACATATTACTG 59.476 40.000 0.00 0.00 0.00 2.74
3274 6214 8.761575 TTCAAGATGTAAGATTTGGCATTTTC 57.238 30.769 0.00 0.00 0.00 2.29
3363 6306 3.955471 TCTAATGACAAAAGGGAGCCAG 58.045 45.455 0.00 0.00 0.00 4.85
3401 6346 3.648339 AATGTGTGCCATCAAGTGTTC 57.352 42.857 0.00 0.00 31.75 3.18
3450 6398 5.023533 TCCCTATTACTGTTGATCACTGC 57.976 43.478 0.00 0.00 0.00 4.40
3585 6533 8.562892 CAAGATACCATATCATCAGTTTTGTCC 58.437 37.037 0.00 0.00 0.00 4.02
3665 6613 9.708092 ATACTTTTAGAAGTTCTTGGAGTACAC 57.292 33.333 11.40 0.00 43.48 2.90
3685 6633 4.832266 ACACCAGGATCAATTTGCTAAACA 59.168 37.500 0.00 0.00 0.00 2.83
3692 6640 6.716628 AGGATCAATTTGCTAAACAGTTCTCA 59.283 34.615 0.00 0.00 0.00 3.27
3966 6914 5.879223 AGTTGCATCTTTTGACCTATCAGAG 59.121 40.000 0.00 0.00 35.83 3.35
4116 7064 1.675116 CCTGATCTGCCGGCTGATATG 60.675 57.143 38.84 31.90 35.29 1.78
4143 7091 4.459337 GGTGGTAAGAAGAAAGACAATGGG 59.541 45.833 0.00 0.00 0.00 4.00
4158 7106 5.479375 AGACAATGGGAATATGAATGATGGC 59.521 40.000 0.00 0.00 0.00 4.40
4260 7208 1.185618 TGGTCTCAAGGTCAGGGTCG 61.186 60.000 0.00 0.00 0.00 4.79
4302 7250 6.238566 GCTCAATATCTGCTCAGTATTTTGCA 60.239 38.462 0.00 0.00 0.00 4.08
4388 7337 3.427503 CCATGGTATGTTCGAACTTTGGC 60.428 47.826 27.32 14.58 0.00 4.52
4400 7349 6.659745 TCGAACTTTGGCCTATAGCTATAA 57.340 37.500 14.30 0.00 43.05 0.98
4405 7354 9.892130 GAACTTTGGCCTATAGCTATAATACAT 57.108 33.333 14.30 0.00 43.05 2.29
4442 7391 4.967084 TGTTTAGCCCTGAAGTGAACTA 57.033 40.909 0.00 0.00 0.00 2.24
4446 7395 1.065126 AGCCCTGAAGTGAACTATGGC 60.065 52.381 0.00 0.00 0.00 4.40
4466 7415 7.886629 ATGGCATCTAACTTGTAATTCATGT 57.113 32.000 0.00 0.00 36.24 3.21
4477 7426 9.502091 AACTTGTAATTCATGTCTAAGTTAGCA 57.498 29.630 4.93 7.18 35.75 3.49
4521 7471 7.039993 GGGACTGAAAAATAGGCAGTTCTTTTA 60.040 37.037 0.00 0.00 42.47 1.52
4525 7475 9.143631 CTGAAAAATAGGCAGTTCTTTTAATGG 57.856 33.333 0.00 0.00 0.00 3.16
4555 7509 2.551459 AGATGAGCACAAACTGAGCAAC 59.449 45.455 0.00 0.00 36.40 4.17
4848 7819 3.604772 GCGCGATTGATTGTATCCAGAAC 60.605 47.826 12.10 0.00 0.00 3.01
4887 7858 5.334105 GCTGAAACGTCAAAAGATTCTGCTA 60.334 40.000 14.64 0.00 39.93 3.49
5037 8009 5.120830 TGGTTGTTTTATTGTTGTTGCACAC 59.879 36.000 0.00 0.00 0.00 3.82
5331 8387 8.724310 AGGGCCAAATCTGTATTTTATACTAGT 58.276 33.333 6.18 0.00 32.87 2.57
5358 8414 0.250901 ATGTGGTCTGGTTGGACTGC 60.251 55.000 0.00 0.00 36.55 4.40
5530 8588 4.965119 ATCTTTCTGGCCGTATTTTCAC 57.035 40.909 0.00 0.00 0.00 3.18
5593 8661 3.686016 TCTTCTACCATGTTTTCTGCCC 58.314 45.455 0.00 0.00 0.00 5.36
5598 8666 1.133513 ACCATGTTTTCTGCCCTGTCA 60.134 47.619 0.00 0.00 0.00 3.58
5599 8667 1.962807 CCATGTTTTCTGCCCTGTCAA 59.037 47.619 0.00 0.00 0.00 3.18
5756 8840 1.351017 TCTGTCGAGGAATTGGGCTTT 59.649 47.619 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.826725 CTCTACGAAGGTTGGTCTCCTT 59.173 50.000 0.00 0.00 46.44 3.36
6 7 2.041350 TCTCTACGAAGGTTGGTCTCCT 59.959 50.000 0.00 0.00 36.81 3.69
7 8 2.424246 CTCTCTACGAAGGTTGGTCTCC 59.576 54.545 0.00 0.00 0.00 3.71
8 9 3.083293 ACTCTCTACGAAGGTTGGTCTC 58.917 50.000 0.00 0.00 0.00 3.36
9 10 3.157750 ACTCTCTACGAAGGTTGGTCT 57.842 47.619 0.00 0.00 0.00 3.85
10 11 4.639310 TCATACTCTCTACGAAGGTTGGTC 59.361 45.833 0.00 0.00 0.00 4.02
11 12 4.597004 TCATACTCTCTACGAAGGTTGGT 58.403 43.478 0.00 0.00 0.00 3.67
12 13 4.036971 CCTCATACTCTCTACGAAGGTTGG 59.963 50.000 0.00 0.00 0.00 3.77
13 14 4.036971 CCCTCATACTCTCTACGAAGGTTG 59.963 50.000 0.00 0.00 0.00 3.77
14 15 4.208746 CCCTCATACTCTCTACGAAGGTT 58.791 47.826 0.00 0.00 0.00 3.50
15 16 3.435313 CCCCTCATACTCTCTACGAAGGT 60.435 52.174 0.00 0.00 0.00 3.50
16 17 3.150767 CCCCTCATACTCTCTACGAAGG 58.849 54.545 0.00 0.00 0.00 3.46
17 18 2.554893 GCCCCTCATACTCTCTACGAAG 59.445 54.545 0.00 0.00 0.00 3.79
18 19 2.584236 GCCCCTCATACTCTCTACGAA 58.416 52.381 0.00 0.00 0.00 3.85
19 20 1.202903 GGCCCCTCATACTCTCTACGA 60.203 57.143 0.00 0.00 0.00 3.43
20 21 1.249407 GGCCCCTCATACTCTCTACG 58.751 60.000 0.00 0.00 0.00 3.51
21 22 1.249407 CGGCCCCTCATACTCTCTAC 58.751 60.000 0.00 0.00 0.00 2.59
22 23 0.539901 GCGGCCCCTCATACTCTCTA 60.540 60.000 0.00 0.00 0.00 2.43
23 24 1.834822 GCGGCCCCTCATACTCTCT 60.835 63.158 0.00 0.00 0.00 3.10
24 25 1.686325 TTGCGGCCCCTCATACTCTC 61.686 60.000 0.00 0.00 0.00 3.20
25 26 1.689233 TTGCGGCCCCTCATACTCT 60.689 57.895 0.00 0.00 0.00 3.24
26 27 1.523938 GTTGCGGCCCCTCATACTC 60.524 63.158 0.00 0.00 0.00 2.59
27 28 2.257409 CTGTTGCGGCCCCTCATACT 62.257 60.000 0.00 0.00 0.00 2.12
28 29 1.819632 CTGTTGCGGCCCCTCATAC 60.820 63.158 0.00 0.00 0.00 2.39
29 30 2.589540 CTGTTGCGGCCCCTCATA 59.410 61.111 0.00 0.00 0.00 2.15
41 42 4.088762 ATGCCGCGTTCGCTGTTG 62.089 61.111 14.92 0.00 0.00 3.33
42 43 4.088762 CATGCCGCGTTCGCTGTT 62.089 61.111 14.92 0.00 0.00 3.16
45 46 4.838152 ATCCATGCCGCGTTCGCT 62.838 61.111 14.92 0.00 0.00 4.93
46 47 4.596180 CATCCATGCCGCGTTCGC 62.596 66.667 4.92 7.14 0.00 4.70
47 48 3.940640 CCATCCATGCCGCGTTCG 61.941 66.667 4.92 0.00 0.00 3.95
48 49 4.256090 GCCATCCATGCCGCGTTC 62.256 66.667 4.92 0.00 0.00 3.95
59 60 3.823330 ACTCGTCGGACGCCATCC 61.823 66.667 24.76 0.00 42.21 3.51
60 61 2.337749 ATCACTCGTCGGACGCCATC 62.338 60.000 24.76 0.00 42.21 3.51
61 62 1.945354 AATCACTCGTCGGACGCCAT 61.945 55.000 24.76 10.09 42.21 4.40
62 63 2.537792 GAATCACTCGTCGGACGCCA 62.538 60.000 24.76 8.65 42.21 5.69
63 64 1.872679 GAATCACTCGTCGGACGCC 60.873 63.158 24.76 4.84 42.21 5.68
64 65 0.525668 ATGAATCACTCGTCGGACGC 60.526 55.000 24.76 10.03 42.21 5.19
65 66 1.064208 AGATGAATCACTCGTCGGACG 59.936 52.381 23.73 23.73 43.83 4.79
66 67 2.853731 AGATGAATCACTCGTCGGAC 57.146 50.000 0.00 0.00 43.83 4.79
67 68 3.868757 AAAGATGAATCACTCGTCGGA 57.131 42.857 0.00 0.00 43.83 4.55
68 69 4.928661 AAAAAGATGAATCACTCGTCGG 57.071 40.909 0.00 0.00 43.83 4.79
121 122 8.070171 CGTCTGTTTTTGAAGAGACATTACAAT 58.930 33.333 14.26 0.00 41.54 2.71
122 123 7.065324 ACGTCTGTTTTTGAAGAGACATTACAA 59.935 33.333 14.26 0.00 41.54 2.41
123 124 6.537301 ACGTCTGTTTTTGAAGAGACATTACA 59.463 34.615 14.26 0.00 41.54 2.41
124 125 6.945072 ACGTCTGTTTTTGAAGAGACATTAC 58.055 36.000 14.26 0.00 41.54 1.89
131 132 5.290386 AGAGGTACGTCTGTTTTTGAAGAG 58.710 41.667 16.96 0.00 0.00 2.85
146 147 4.258543 TGCCCAATAAAAAGAGAGGTACG 58.741 43.478 0.00 0.00 0.00 3.67
149 150 4.934356 TGATGCCCAATAAAAAGAGAGGT 58.066 39.130 0.00 0.00 0.00 3.85
151 152 5.420104 ACCTTGATGCCCAATAAAAAGAGAG 59.580 40.000 0.00 0.00 33.68 3.20
166 167 3.539604 AGATGTTAGAGCACCTTGATGC 58.460 45.455 0.00 0.00 46.50 3.91
173 174 1.745653 GCCCAAAGATGTTAGAGCACC 59.254 52.381 0.00 0.00 0.00 5.01
198 199 1.136305 GCACATGCTTTCAGGATGCAT 59.864 47.619 0.00 0.00 46.39 3.96
199 200 0.528924 GCACATGCTTTCAGGATGCA 59.471 50.000 5.25 0.00 46.39 3.96
203 204 2.275134 TTCTGCACATGCTTTCAGGA 57.725 45.000 5.31 0.00 42.66 3.86
204 205 2.352421 CCTTTCTGCACATGCTTTCAGG 60.352 50.000 5.31 2.38 42.66 3.86
214 215 2.358898 GCTGAAGAAACCTTTCTGCACA 59.641 45.455 4.55 4.22 45.58 4.57
244 245 5.344743 TGACAAATTTTGCCCAAACTGTA 57.655 34.783 9.04 0.00 0.00 2.74
295 296 2.549754 GACAGGGTCAACACAAGACATG 59.450 50.000 0.00 0.00 37.74 3.21
362 363 7.029563 GCATCTTAAAACACATTTGGAGTAGG 58.970 38.462 0.00 0.00 32.27 3.18
380 381 3.281727 AATCAAGAAGGGCGCATCTTA 57.718 42.857 19.15 9.73 34.24 2.10
420 421 8.674263 ACAATTCAGACATGCCAAAATAAAAA 57.326 26.923 0.00 0.00 0.00 1.94
493 494 6.127925 TGGCTCATAGAACACAAATTCATCAC 60.128 38.462 0.00 0.00 0.00 3.06
506 507 1.328680 CGTGCACATGGCTCATAGAAC 59.671 52.381 18.64 0.00 45.15 3.01
509 510 1.162181 CCCGTGCACATGGCTCATAG 61.162 60.000 18.64 0.00 45.15 2.23
525 526 2.425569 CCCCAATCCATGCAACCCG 61.426 63.158 0.00 0.00 0.00 5.28
528 529 0.983467 AAACCCCCAATCCATGCAAC 59.017 50.000 0.00 0.00 0.00 4.17
587 588 1.011242 CACACTGTGTCAAACGGCG 60.011 57.895 11.12 4.80 38.92 6.46
608 623 3.904965 TGAAAAATCCAACCCCCTAAACC 59.095 43.478 0.00 0.00 0.00 3.27
627 642 1.475280 GCATCTGCAGCTGGATTTGAA 59.525 47.619 18.62 0.00 41.59 2.69
672 687 7.775397 TTTGCTCAAAAGAAGAAAAATCTGG 57.225 32.000 0.00 0.00 0.00 3.86
716 731 1.455383 CCCACAAAGCACCACACTCC 61.455 60.000 0.00 0.00 0.00 3.85
723 3352 1.244019 CCAGTAGCCCACAAAGCACC 61.244 60.000 0.00 0.00 0.00 5.01
809 3726 2.181975 CCCTTTTGTTGCCAGGATGAT 58.818 47.619 0.00 0.00 39.69 2.45
810 3727 1.631405 CCCTTTTGTTGCCAGGATGA 58.369 50.000 0.00 0.00 39.69 2.92
811 3728 0.609662 CCCCTTTTGTTGCCAGGATG 59.390 55.000 0.00 0.00 0.00 3.51
812 3729 0.486879 TCCCCTTTTGTTGCCAGGAT 59.513 50.000 0.00 0.00 0.00 3.24
813 3730 0.178964 CTCCCCTTTTGTTGCCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
815 3732 1.820010 GCCTCCCCTTTTGTTGCCAG 61.820 60.000 0.00 0.00 0.00 4.85
816 3733 1.836604 GCCTCCCCTTTTGTTGCCA 60.837 57.895 0.00 0.00 0.00 4.92
817 3734 2.931068 CGCCTCCCCTTTTGTTGCC 61.931 63.158 0.00 0.00 0.00 4.52
818 3735 2.200337 ACGCCTCCCCTTTTGTTGC 61.200 57.895 0.00 0.00 0.00 4.17
819 3736 1.659794 CACGCCTCCCCTTTTGTTG 59.340 57.895 0.00 0.00 0.00 3.33
820 3737 1.530655 CCACGCCTCCCCTTTTGTT 60.531 57.895 0.00 0.00 0.00 2.83
821 3738 2.002018 TTCCACGCCTCCCCTTTTGT 62.002 55.000 0.00 0.00 0.00 2.83
822 3739 1.228429 TTCCACGCCTCCCCTTTTG 60.228 57.895 0.00 0.00 0.00 2.44
823 3740 1.074951 CTTCCACGCCTCCCCTTTT 59.925 57.895 0.00 0.00 0.00 2.27
824 3741 1.846124 TCTTCCACGCCTCCCCTTT 60.846 57.895 0.00 0.00 0.00 3.11
825 3742 2.203938 TCTTCCACGCCTCCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
826 3743 3.003763 GTCTTCCACGCCTCCCCT 61.004 66.667 0.00 0.00 0.00 4.79
827 3744 3.319198 TGTCTTCCACGCCTCCCC 61.319 66.667 0.00 0.00 0.00 4.81
874 3791 7.201750 GCCGTTTGGGATTGTGATATTTACTTA 60.202 37.037 0.00 0.00 38.47 2.24
876 3793 5.067283 GCCGTTTGGGATTGTGATATTTACT 59.933 40.000 0.00 0.00 38.47 2.24
877 3794 5.067283 AGCCGTTTGGGATTGTGATATTTAC 59.933 40.000 0.00 0.00 38.47 2.01
935 3859 0.321564 TGAAATGCGGGAGAGGTGTG 60.322 55.000 0.00 0.00 0.00 3.82
1194 4128 1.674057 GATGGCCACTATCTCCGGG 59.326 63.158 8.16 0.00 0.00 5.73
1395 4329 1.916777 GTGAGGGGAACGAAGGGGA 60.917 63.158 0.00 0.00 0.00 4.81
1538 4472 1.742880 GCGCTGCTTGATGAGGTCA 60.743 57.895 0.00 0.00 34.25 4.02
1576 4510 3.315142 GACACAGCGGCCTGGATCA 62.315 63.158 0.00 0.00 43.53 2.92
1705 4644 6.595716 ACAGCTGATAAACTGATTAACTGACC 59.404 38.462 23.35 0.00 37.35 4.02
1713 4652 7.692460 TCATCAAACAGCTGATAAACTGATT 57.308 32.000 23.35 0.00 37.35 2.57
1714 4653 7.692460 TTCATCAAACAGCTGATAAACTGAT 57.308 32.000 23.35 11.71 37.35 2.90
1722 4661 4.081309 CCCCAAATTCATCAAACAGCTGAT 60.081 41.667 23.35 5.41 36.45 2.90
1757 4696 4.994907 AAACAACCACTACCCTTTGTTC 57.005 40.909 0.00 0.00 40.44 3.18
1787 4726 3.725895 CGAATTCCATCAAACAGCTGACG 60.726 47.826 23.35 8.11 0.00 4.35
1959 4898 5.975693 AAGTGGGATCGATCTCTCTAATC 57.024 43.478 25.77 7.72 31.39 1.75
2133 5072 8.413309 AAATTCCTTGAAATGATCAGAACAGA 57.587 30.769 0.09 0.00 39.77 3.41
2322 5261 2.464865 CGGAACTCGTCATTGGAGATC 58.535 52.381 0.00 0.00 35.49 2.75
2663 5602 5.473504 AGAAATGTTACGCAAGGACAGATTT 59.526 36.000 0.00 0.00 46.39 2.17
2736 5675 6.086222 AGTAATGCACGCTTTCATACAAAAG 58.914 36.000 0.00 0.00 38.91 2.27
2983 5923 8.387190 AGTACCTACAACTTTCCAATGTAAAC 57.613 34.615 0.00 0.00 0.00 2.01
3274 6214 1.475280 CAGATGAACCCCAGCACAATG 59.525 52.381 0.00 0.00 32.59 2.82
3346 6286 2.619074 GCTACTGGCTCCCTTTTGTCAT 60.619 50.000 0.00 0.00 38.06 3.06
3352 6292 2.907458 AAATGCTACTGGCTCCCTTT 57.093 45.000 0.00 0.00 42.39 3.11
3363 6306 7.359181 GCACACATTTGGTTTAGAAAATGCTAC 60.359 37.037 7.78 0.00 44.15 3.58
3401 6346 4.196626 TGTGTGTAAGTTAAGGGATCCG 57.803 45.455 5.45 0.00 0.00 4.18
3450 6398 7.921786 TGACTGAATAAACTTTGTATGGAGG 57.078 36.000 0.00 0.00 0.00 4.30
3559 6507 8.562892 GGACAAAACTGATGATATGGTATCTTG 58.437 37.037 0.00 0.00 0.00 3.02
3665 6613 5.649782 ACTGTTTAGCAAATTGATCCTGG 57.350 39.130 0.00 0.00 0.00 4.45
3709 6657 8.560355 TTTTCGACATTTTGATCTGATAGGAA 57.440 30.769 0.00 0.00 0.00 3.36
3710 6658 8.737168 ATTTTCGACATTTTGATCTGATAGGA 57.263 30.769 0.00 0.00 0.00 2.94
3729 6677 6.151648 AGCCAACATATCCATCCATATTTTCG 59.848 38.462 0.00 0.00 0.00 3.46
3966 6914 1.484240 CCTTCCTCCAGTGATCCACTC 59.516 57.143 0.00 0.00 43.43 3.51
4116 7064 4.072131 TGTCTTTCTTCTTACCACCATGC 58.928 43.478 0.00 0.00 0.00 4.06
4143 7091 1.474077 GCCCCGCCATCATTCATATTC 59.526 52.381 0.00 0.00 0.00 1.75
4158 7106 0.527565 CATGTCTTTTCCTTGCCCCG 59.472 55.000 0.00 0.00 0.00 5.73
4302 7250 4.761739 TCAATCAGGACTTCTCGCATTTTT 59.238 37.500 0.00 0.00 0.00 1.94
4400 7349 7.516198 AACAAGCAGAAAGAGAAACATGTAT 57.484 32.000 0.00 0.00 0.00 2.29
4430 7379 6.344500 AGTTAGATGCCATAGTTCACTTCAG 58.656 40.000 0.00 0.00 0.00 3.02
4431 7380 6.299805 AGTTAGATGCCATAGTTCACTTCA 57.700 37.500 0.00 0.00 0.00 3.02
4442 7391 7.776969 AGACATGAATTACAAGTTAGATGCCAT 59.223 33.333 0.00 0.00 30.32 4.40
4477 7426 2.106566 CCCTGACTACTCAGCAGATGT 58.893 52.381 0.00 0.00 42.55 3.06
4486 7435 6.342111 CCTATTTTTCAGTCCCTGACTACTC 58.658 44.000 0.00 0.00 41.37 2.59
4489 7438 4.534500 TGCCTATTTTTCAGTCCCTGACTA 59.466 41.667 0.00 0.00 41.37 2.59
4495 7444 4.336280 AGAACTGCCTATTTTTCAGTCCC 58.664 43.478 0.00 0.00 39.86 4.46
4496 7445 5.966742 AAGAACTGCCTATTTTTCAGTCC 57.033 39.130 0.00 0.00 39.86 3.85
4501 7450 9.489084 AACCATTAAAAGAACTGCCTATTTTTC 57.511 29.630 0.00 0.00 0.00 2.29
4521 7471 5.804639 TGTGCTCATCTAGTTACAACCATT 58.195 37.500 0.00 0.00 0.00 3.16
4525 7475 6.423905 TCAGTTTGTGCTCATCTAGTTACAAC 59.576 38.462 0.00 0.00 35.53 3.32
4569 7528 8.950208 ATTTATGCCTAGAGTTAGTGTCTTTC 57.050 34.615 0.00 0.00 0.00 2.62
4570 7529 9.384764 GAATTTATGCCTAGAGTTAGTGTCTTT 57.615 33.333 0.00 0.00 0.00 2.52
4579 7538 9.553064 CTGAACATAGAATTTATGCCTAGAGTT 57.447 33.333 0.00 0.00 0.00 3.01
4580 7539 8.709308 ACTGAACATAGAATTTATGCCTAGAGT 58.291 33.333 0.00 0.00 0.00 3.24
4848 7819 4.127040 AGCAGAGACTGGCGCTCG 62.127 66.667 7.64 0.30 37.46 5.03
4887 7858 4.894784 TCTTGAACTCGCTTAAACAGGAT 58.105 39.130 0.00 0.00 0.00 3.24
5037 8009 3.117452 GCATGGAGGCTCAGGAGGG 62.117 68.421 17.69 0.35 0.00 4.30
5207 8180 7.757097 TTCGAGATCACAAAATCTAGTAAGC 57.243 36.000 0.00 0.00 36.13 3.09
5287 8343 3.275143 CCCTAACATACGAATTGTGCCA 58.725 45.455 0.00 0.00 0.00 4.92
5329 8385 1.552337 CCAGACCACATGCTGAGTACT 59.448 52.381 0.00 0.00 34.06 2.73
5330 8386 1.276421 ACCAGACCACATGCTGAGTAC 59.724 52.381 0.00 0.00 34.06 2.73
5331 8387 1.644509 ACCAGACCACATGCTGAGTA 58.355 50.000 0.00 0.00 34.06 2.59
5332 8388 0.767375 AACCAGACCACATGCTGAGT 59.233 50.000 0.00 0.00 34.06 3.41
5333 8389 1.162698 CAACCAGACCACATGCTGAG 58.837 55.000 0.00 0.00 34.06 3.35
5334 8390 0.250858 CCAACCAGACCACATGCTGA 60.251 55.000 0.00 0.00 34.06 4.26
5358 8414 7.822658 TCTCATATTAAAACCAAAACGGGAAG 58.177 34.615 0.00 0.00 40.22 3.46
5530 8588 0.036010 GTGACAGGGTGATGGACAGG 60.036 60.000 0.00 0.00 0.00 4.00
5756 8840 6.017109 GTCTGTCCAAAATGAACTAGAAAGCA 60.017 38.462 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.