Multiple sequence alignment - TraesCS7D01G363700

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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 TraesCS7D01G363700 chr7D 100.000 3748 0 0 1 3748 467989528 467993275 0.000000e+00 6922.0
1 TraesCS7D01G363700 chr7D 93.023 86 5 1 2023 2108 467991426 467991510 1.410000e-24 124.0
2 TraesCS7D01G363700 chr7D 93.023 86 5 1 1899 1983 467991550 467991635 1.410000e-24 124.0
3 TraesCS7D01G363700 chr7D 88.571 70 6 1 2260 2327 568233267 568233336 2.400000e-12 84.2
4 TraesCS7D01G363700 chr7B 96.915 2820 66 10 937 3748 491391628 491394434 0.000000e+00 4706.0
5 TraesCS7D01G363700 chr7B 77.882 746 110 21 1 742 491390277 491390971 2.690000e-111 412.0
6 TraesCS7D01G363700 chr7B 85.616 146 17 1 795 936 491391337 491391482 2.330000e-32 150.0
7 TraesCS7D01G363700 chr7B 93.023 86 5 1 1899 1983 491392711 491392796 1.410000e-24 124.0
8 TraesCS7D01G363700 chr7A 92.518 989 42 5 795 1779 532685628 532684668 0.000000e+00 1387.0
9 TraesCS7D01G363700 chr7A 87.269 432 53 2 2328 2757 532679926 532679495 3.360000e-135 492.0
10 TraesCS7D01G363700 chr7A 90.909 77 7 0 178 254 532686439 532686363 1.840000e-18 104.0
11 TraesCS7D01G363700 chr2D 86.557 729 83 6 1049 1771 40803 40084 0.000000e+00 789.0
12 TraesCS7D01G363700 chr2B 85.852 728 86 12 1049 1772 10992924 10992210 0.000000e+00 758.0
13 TraesCS7D01G363700 chr2A 85.379 725 91 7 1053 1771 389295 390010 0.000000e+00 737.0
14 TraesCS7D01G363700 chr3B 83.121 314 51 2 1427 1739 579427752 579428064 6.130000e-73 285.0
15 TraesCS7D01G363700 chr4D 87.654 81 6 3 2249 2327 8594010 8593932 1.430000e-14 91.6
16 TraesCS7D01G363700 chr1B 80.992 121 18 3 2215 2331 675952174 675952293 1.430000e-14 91.6
17 TraesCS7D01G363700 chr1B 87.500 80 7 3 2249 2327 8563664 8563741 5.160000e-14 89.8
18 TraesCS7D01G363700 chr3A 85.882 85 8 4 2249 2331 46569133 46569215 1.850000e-13 87.9
19 TraesCS7D01G363700 chr4B 85.542 83 10 2 2249 2331 373979773 373979693 6.670000e-13 86.1
20 TraesCS7D01G363700 chr5B 83.951 81 11 2 2248 2327 654926937 654927016 4.010000e-10 76.8
21 TraesCS7D01G363700 chr1A 83.750 80 11 2 2249 2327 575387093 575387171 1.440000e-09 75.0


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 TraesCS7D01G363700 chr7D 467989528 467993275 3747 False 2390.0 6922 95.348667 1 3748 3 chr7D.!!$F2 3747
1 TraesCS7D01G363700 chr7B 491390277 491394434 4157 False 1348.0 4706 88.359000 1 3748 4 chr7B.!!$F1 3747
2 TraesCS7D01G363700 chr7A 532684668 532686439 1771 True 745.5 1387 91.713500 178 1779 2 chr7A.!!$R2 1601
3 TraesCS7D01G363700 chr2D 40084 40803 719 True 789.0 789 86.557000 1049 1771 1 chr2D.!!$R1 722
4 TraesCS7D01G363700 chr2B 10992210 10992924 714 True 758.0 758 85.852000 1049 1772 1 chr2B.!!$R1 723
5 TraesCS7D01G363700 chr2A 389295 390010 715 False 737.0 737 85.379000 1053 1771 1 chr2A.!!$F1 718

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
619 830 0.324275 CACCCCCAACACCCCTAATG 60.324 60.0 0.0 0.0 0.0 1.90 F
1930 2611 0.034477 ATTAGGCAAAGACGGGGTGG 60.034 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2902 0.440758 TTTTTGCGCGGATCTACACG 59.559 50.0 8.83 0.0 0.0 4.49 R
3129 3816 0.377203 GCTGTAATACTTGGCGTGGC 59.623 55.0 0.00 0.0 0.0 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.635030 TTCAAACTTTAGCCTTTTCTCTCC 57.365 37.500 0.00 0.00 0.00 3.71
31 32 4.724279 ACTTTAGCCTTTTCTCTCCCAA 57.276 40.909 0.00 0.00 0.00 4.12
33 34 3.721087 TTAGCCTTTTCTCTCCCAAGG 57.279 47.619 0.00 0.00 40.24 3.61
36 37 2.986728 AGCCTTTTCTCTCCCAAGGTTA 59.013 45.455 0.00 0.00 39.55 2.85
41 42 5.012768 CCTTTTCTCTCCCAAGGTTAGTACA 59.987 44.000 0.00 0.00 33.57 2.90
43 44 5.934402 TTCTCTCCCAAGGTTAGTACATC 57.066 43.478 0.00 0.00 0.00 3.06
59 64 4.949856 AGTACATCCTAATGCAAACCCTTG 59.050 41.667 0.00 0.00 36.26 3.61
76 81 7.552050 AACCCTTGGAAAATGATCAAACATA 57.448 32.000 0.00 0.00 0.00 2.29
131 136 9.685276 TGATGGGCTACTATAAAATATCATTGG 57.315 33.333 0.00 0.00 0.00 3.16
135 140 8.957466 GGGCTACTATAAAATATCATTGGTTCC 58.043 37.037 0.00 0.00 0.00 3.62
147 152 5.682943 TCATTGGTTCCGAAGTTTAACAG 57.317 39.130 0.00 0.00 0.00 3.16
149 154 3.564053 TGGTTCCGAAGTTTAACAGGT 57.436 42.857 0.00 0.00 0.00 4.00
154 159 4.139859 TCCGAAGTTTAACAGGTCAACA 57.860 40.909 0.00 0.00 0.00 3.33
155 160 4.515361 TCCGAAGTTTAACAGGTCAACAA 58.485 39.130 0.00 0.00 0.00 2.83
156 161 5.127491 TCCGAAGTTTAACAGGTCAACAAT 58.873 37.500 0.00 0.00 0.00 2.71
157 162 6.289834 TCCGAAGTTTAACAGGTCAACAATA 58.710 36.000 0.00 0.00 0.00 1.90
158 163 6.766944 TCCGAAGTTTAACAGGTCAACAATAA 59.233 34.615 0.00 0.00 0.00 1.40
159 164 7.041644 TCCGAAGTTTAACAGGTCAACAATAAG 60.042 37.037 0.00 0.00 0.00 1.73
160 165 7.041644 CCGAAGTTTAACAGGTCAACAATAAGA 60.042 37.037 0.00 0.00 0.00 2.10
161 166 8.339714 CGAAGTTTAACAGGTCAACAATAAGAA 58.660 33.333 0.00 0.00 0.00 2.52
166 171 8.810652 TTAACAGGTCAACAATAAGAAAATGC 57.189 30.769 0.00 0.00 0.00 3.56
167 172 6.403866 ACAGGTCAACAATAAGAAAATGCA 57.596 33.333 0.00 0.00 0.00 3.96
168 173 6.996509 ACAGGTCAACAATAAGAAAATGCAT 58.003 32.000 0.00 0.00 0.00 3.96
169 174 7.092716 ACAGGTCAACAATAAGAAAATGCATC 58.907 34.615 0.00 0.00 0.00 3.91
170 175 6.532657 CAGGTCAACAATAAGAAAATGCATCC 59.467 38.462 0.00 0.00 0.00 3.51
171 176 6.438425 AGGTCAACAATAAGAAAATGCATCCT 59.562 34.615 0.00 0.00 0.00 3.24
172 177 7.615365 AGGTCAACAATAAGAAAATGCATCCTA 59.385 33.333 0.00 0.00 0.00 2.94
173 178 8.250332 GGTCAACAATAAGAAAATGCATCCTAA 58.750 33.333 0.00 0.00 0.00 2.69
174 179 9.638239 GTCAACAATAAGAAAATGCATCCTAAA 57.362 29.630 0.00 0.00 0.00 1.85
248 253 1.002087 AGCCCACTCCTAACAAGAACG 59.998 52.381 0.00 0.00 0.00 3.95
256 261 3.656559 TCCTAACAAGAACGCTACAACC 58.343 45.455 0.00 0.00 0.00 3.77
257 262 2.740447 CCTAACAAGAACGCTACAACCC 59.260 50.000 0.00 0.00 0.00 4.11
258 263 2.632987 AACAAGAACGCTACAACCCT 57.367 45.000 0.00 0.00 0.00 4.34
285 298 6.371809 AAAAACAAGAATGCTACAACGAGA 57.628 33.333 0.00 0.00 0.00 4.04
287 300 5.786401 AACAAGAATGCTACAACGAGATC 57.214 39.130 0.00 0.00 0.00 2.75
288 301 3.859961 ACAAGAATGCTACAACGAGATCG 59.140 43.478 0.00 0.00 46.33 3.69
289 302 2.464865 AGAATGCTACAACGAGATCGC 58.535 47.619 1.39 0.00 44.43 4.58
290 303 2.099921 AGAATGCTACAACGAGATCGCT 59.900 45.455 1.39 0.00 44.43 4.93
291 304 2.126914 ATGCTACAACGAGATCGCTC 57.873 50.000 1.39 0.00 44.43 5.03
306 495 0.364515 CGCTCGTAAACGCTACAACC 59.635 55.000 0.00 0.00 39.60 3.77
308 497 1.997606 GCTCGTAAACGCTACAACCAT 59.002 47.619 0.00 0.00 39.60 3.55
323 512 5.784578 ACAACCATAAAAACAAGGGAGTC 57.215 39.130 0.00 0.00 0.00 3.36
324 513 5.205056 ACAACCATAAAAACAAGGGAGTCA 58.795 37.500 0.00 0.00 0.00 3.41
337 526 5.419471 ACAAGGGAGTCACTAGATGTAAGTC 59.581 44.000 0.00 0.00 0.00 3.01
338 527 5.194473 AGGGAGTCACTAGATGTAAGTCA 57.806 43.478 0.00 0.00 0.00 3.41
349 538 9.429359 CACTAGATGTAAGTCAAGTCTGAAAAT 57.571 33.333 0.00 0.00 31.88 1.82
363 552 9.323985 CAAGTCTGAAAATTTAATTTGGGTCAA 57.676 29.630 3.51 0.00 31.77 3.18
367 556 8.580720 TCTGAAAATTTAATTTGGGTCAATCGA 58.419 29.630 3.51 0.00 31.77 3.59
397 586 4.946784 AGCCGTCAGATGTAAAATGAAC 57.053 40.909 0.00 0.00 0.00 3.18
400 589 4.391830 GCCGTCAGATGTAAAATGAACAGA 59.608 41.667 0.00 0.00 0.00 3.41
413 602 3.126001 TGAACAGACGGATGCTTTCTT 57.874 42.857 0.00 0.00 0.00 2.52
414 603 3.476552 TGAACAGACGGATGCTTTCTTT 58.523 40.909 0.00 0.00 0.00 2.52
423 612 3.756434 CGGATGCTTTCTTTAACCTTCCA 59.244 43.478 0.00 0.00 0.00 3.53
428 617 7.093945 GGATGCTTTCTTTAACCTTCCAATGTA 60.094 37.037 0.00 0.00 0.00 2.29
442 631 2.687935 CCAATGTATTCTTCCCCAACCG 59.312 50.000 0.00 0.00 0.00 4.44
448 637 1.137594 TTCTTCCCCAACCGTCCCAT 61.138 55.000 0.00 0.00 0.00 4.00
470 660 3.931247 CACCGACCCGACCACCAA 61.931 66.667 0.00 0.00 0.00 3.67
536 726 1.915769 GCCACACTCTCCCCTCAGT 60.916 63.158 0.00 0.00 0.00 3.41
541 752 3.522731 CTCTCCCCTCAGTCGCCG 61.523 72.222 0.00 0.00 0.00 6.46
548 759 4.504916 CTCAGTCGCCGCCTCCAG 62.505 72.222 0.00 0.00 0.00 3.86
559 770 1.460305 GCCTCCAGCCATCCCTCTA 60.460 63.158 0.00 0.00 34.35 2.43
560 771 1.056700 GCCTCCAGCCATCCCTCTAA 61.057 60.000 0.00 0.00 34.35 2.10
567 778 2.041206 GCCATCCCTCTAACCCCGAC 62.041 65.000 0.00 0.00 0.00 4.79
568 779 0.689745 CCATCCCTCTAACCCCGACA 60.690 60.000 0.00 0.00 0.00 4.35
580 791 2.115266 CCGACAAGGGCCAGGTTT 59.885 61.111 6.18 0.00 35.97 3.27
606 817 4.678743 GGAACCTGCACCACCCCC 62.679 72.222 0.00 0.00 0.00 5.40
608 819 3.434179 AACCTGCACCACCCCCAA 61.434 61.111 0.00 0.00 0.00 4.12
609 820 3.749284 AACCTGCACCACCCCCAAC 62.749 63.158 0.00 0.00 0.00 3.77
610 821 4.217210 CCTGCACCACCCCCAACA 62.217 66.667 0.00 0.00 0.00 3.33
614 825 4.614036 CACCACCCCCAACACCCC 62.614 72.222 0.00 0.00 0.00 4.95
615 826 4.875301 ACCACCCCCAACACCCCT 62.875 66.667 0.00 0.00 0.00 4.79
616 827 2.533232 CCACCCCCAACACCCCTA 60.533 66.667 0.00 0.00 0.00 3.53
617 828 2.164279 CCACCCCCAACACCCCTAA 61.164 63.158 0.00 0.00 0.00 2.69
618 829 1.514864 CCACCCCCAACACCCCTAAT 61.515 60.000 0.00 0.00 0.00 1.73
619 830 0.324275 CACCCCCAACACCCCTAATG 60.324 60.000 0.00 0.00 0.00 1.90
630 841 6.498651 CCAACACCCCTAATGAGATAGATAGT 59.501 42.308 0.00 0.00 0.00 2.12
646 857 0.844661 TAGTGGGGTCCATTGCCACT 60.845 55.000 18.32 18.32 43.04 4.00
649 860 1.379044 GGGGTCCATTGCCACTCTG 60.379 63.158 0.00 0.00 0.00 3.35
659 870 5.479724 TCCATTGCCACTCTGAGATAGATAG 59.520 44.000 12.44 0.00 34.21 2.08
716 927 2.028203 GCTTCTCTTGTGAGCTCCTTCT 60.028 50.000 12.15 0.00 40.03 2.85
720 931 2.992543 CTCTTGTGAGCTCCTTCTTTCG 59.007 50.000 12.15 0.00 33.12 3.46
721 932 2.365617 TCTTGTGAGCTCCTTCTTTCGT 59.634 45.455 12.15 0.00 0.00 3.85
728 939 1.352156 CTCCTTCTTTCGTTCCGGCG 61.352 60.000 0.00 0.00 0.00 6.46
729 940 2.388232 CCTTCTTTCGTTCCGGCGG 61.388 63.158 22.51 22.51 0.00 6.13
737 948 4.717313 GTTCCGGCGGGCTCCTTT 62.717 66.667 27.98 0.00 0.00 3.11
745 977 0.606673 GCGGGCTCCTTTCTTCAAGT 60.607 55.000 0.00 0.00 0.00 3.16
753 985 5.149977 GCTCCTTTCTTCAAGTGAAATTCG 58.850 41.667 0.00 0.00 33.65 3.34
791 1023 7.323420 TCTAAATTCAGGTGACTCACATGTAG 58.677 38.462 20.29 14.97 44.86 2.74
792 1024 3.319137 TTCAGGTGACTCACATGTAGC 57.681 47.619 20.29 0.00 44.86 3.58
793 1025 2.529632 TCAGGTGACTCACATGTAGCT 58.470 47.619 20.29 0.00 44.86 3.32
797 1321 1.998315 GTGACTCACATGTAGCTGCTG 59.002 52.381 13.43 0.00 34.08 4.41
800 1324 3.122297 GACTCACATGTAGCTGCTGATC 58.878 50.000 13.43 3.50 0.00 2.92
809 1333 3.433274 TGTAGCTGCTGATCGTGAAAAAG 59.567 43.478 13.43 0.00 0.00 2.27
810 1334 1.198637 AGCTGCTGATCGTGAAAAAGC 59.801 47.619 0.00 0.00 0.00 3.51
843 1367 0.739813 GCCTACACGTCGCTTGGATT 60.740 55.000 0.00 0.00 0.00 3.01
901 1429 0.957395 CAGACAATCCGTGCTTGGCT 60.957 55.000 0.00 0.00 42.76 4.75
902 1430 0.957395 AGACAATCCGTGCTTGGCTG 60.957 55.000 0.00 0.00 40.47 4.85
916 1444 4.486503 GCTGAGCAGGCAGGAGGG 62.487 72.222 0.00 0.00 36.41 4.30
1145 1818 4.778143 GGCGGACCTGGCGAACAT 62.778 66.667 0.00 0.00 0.00 2.71
1929 2610 1.834188 AATTAGGCAAAGACGGGGTG 58.166 50.000 0.00 0.00 0.00 4.61
1930 2611 0.034477 ATTAGGCAAAGACGGGGTGG 60.034 55.000 0.00 0.00 0.00 4.61
1931 2612 2.132089 TTAGGCAAAGACGGGGTGGG 62.132 60.000 0.00 0.00 0.00 4.61
1932 2613 4.280019 GGCAAAGACGGGGTGGGT 62.280 66.667 0.00 0.00 0.00 4.51
1936 2617 1.889262 GCAAAGACGGGGTGGGTAAAT 60.889 52.381 0.00 0.00 0.00 1.40
1947 2628 4.490743 GGGTGGGTAAATCACAAATTTCG 58.509 43.478 0.00 0.00 36.90 3.46
2180 2861 7.827236 AGTTTATGTTGGATCGGTAAATCTCAA 59.173 33.333 0.00 0.00 0.00 3.02
2221 2902 6.253727 CCAATGTTACACTCGTGAGATCTTAC 59.746 42.308 7.56 7.56 40.84 2.34
2232 2913 4.608667 CGTGAGATCTTACGTGTAGATCCG 60.609 50.000 26.80 21.22 39.24 4.18
2271 2954 9.649167 CCATTTTCTTTCTCTTTTGAATATGCT 57.351 29.630 0.00 0.00 31.40 3.79
2347 3030 7.388500 CACACCTTTTGCAAATTTGAATCCTAT 59.612 33.333 22.31 0.00 0.00 2.57
2382 3065 7.615403 AGAAGCGGAATAATAGATTCTATGCA 58.385 34.615 6.96 0.00 38.62 3.96
2389 3072 8.515414 GGAATAATAGATTCTATGCACCCAAAC 58.485 37.037 6.96 0.00 0.00 2.93
2625 3308 2.755655 GAGATCTTCGACTGGGAGTTGA 59.244 50.000 0.00 0.00 36.86 3.18
2631 3314 1.216710 GACTGGGAGTTGAGCGAGG 59.783 63.158 0.00 0.00 0.00 4.63
2765 3448 9.924650 GATATATGAATATATGTACCCGGTTCC 57.075 37.037 0.00 0.00 36.38 3.62
2779 3462 2.674357 CCGGTTCCGAAATATTTGACGT 59.326 45.455 13.08 0.00 0.00 4.34
2884 3570 2.867333 TAAAGCGCTCGCCGACAGAG 62.867 60.000 12.06 0.00 43.17 3.35
2926 3612 0.476771 AAAGGATGTCACCGTGGGTT 59.523 50.000 0.00 0.00 31.02 4.11
3129 3816 2.286833 TCCTTCTTTGAGACAAAACGCG 59.713 45.455 3.53 3.53 0.00 6.01
3180 3867 6.094742 TGCAACACTATGACTTGAACAAGAAA 59.905 34.615 19.35 8.49 40.79 2.52
3223 3910 0.037605 AGAGCAGAAACGTAACCCCG 60.038 55.000 0.00 0.00 0.00 5.73
3242 3929 3.250040 CCCGAAACACAGTAAAGGACAAG 59.750 47.826 0.00 0.00 0.00 3.16
3363 4050 3.042682 TCCTAAACTCACCACCAGACAA 58.957 45.455 0.00 0.00 0.00 3.18
3364 4051 3.456644 TCCTAAACTCACCACCAGACAAA 59.543 43.478 0.00 0.00 0.00 2.83
3393 4080 3.997021 CAGGAACGCAAGAGTATCAGTTT 59.003 43.478 0.00 0.00 43.62 2.66
3411 4098 2.679642 CGGGGAAATTGCCTGCCA 60.680 61.111 1.41 0.00 0.00 4.92
3444 4131 4.499183 TCTTTGCTTCGCCAAAAGAAAAA 58.501 34.783 0.00 0.00 34.18 1.94
3445 4132 4.566360 TCTTTGCTTCGCCAAAAGAAAAAG 59.434 37.500 0.00 0.00 34.18 2.27
3450 4137 3.726291 TCGCCAAAAGAAAAAGAAGGG 57.274 42.857 0.00 0.00 0.00 3.95
3451 4138 2.364002 TCGCCAAAAGAAAAAGAAGGGG 59.636 45.455 0.00 0.00 0.00 4.79
3522 4209 1.830477 ACCACCAAAGCAAGAAAGCAA 59.170 42.857 0.00 0.00 36.85 3.91
3525 4212 2.286025 CACCAAAGCAAGAAAGCAAAGC 59.714 45.455 0.00 0.00 36.85 3.51
3526 4213 2.093553 ACCAAAGCAAGAAAGCAAAGCA 60.094 40.909 0.00 0.00 36.85 3.91
3545 4232 2.093711 GCAAACAAGTCACAGGGGTTTT 60.094 45.455 0.00 0.00 29.89 2.43
3546 4233 3.780902 CAAACAAGTCACAGGGGTTTTC 58.219 45.455 0.00 0.00 29.89 2.29
3678 4365 2.001872 CAGCATGCACACAAGATACGA 58.998 47.619 21.98 0.00 0.00 3.43
3695 4382 2.607187 ACGATGATGTGAGAACGGAAC 58.393 47.619 0.00 0.00 0.00 3.62
3716 4403 4.016444 ACATACGACAGGGAAAATGCATT 58.984 39.130 5.99 5.99 0.00 3.56
3724 4411 6.912591 CGACAGGGAAAATGCATTATTAACTC 59.087 38.462 13.39 3.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.087007 GGAGAGAAAAGGCTAAAGTTTGAATG 58.913 38.462 0.00 0.00 0.00 2.67
8 9 5.061721 TGGGAGAGAAAAGGCTAAAGTTT 57.938 39.130 0.00 0.00 0.00 2.66
28 29 5.680619 TGCATTAGGATGTACTAACCTTGG 58.319 41.667 10.27 0.00 35.90 3.61
31 32 6.120220 GGTTTGCATTAGGATGTACTAACCT 58.880 40.000 9.98 9.98 35.90 3.50
33 34 6.120220 AGGGTTTGCATTAGGATGTACTAAC 58.880 40.000 0.00 0.00 35.90 2.34
36 37 4.862641 AGGGTTTGCATTAGGATGTACT 57.137 40.909 0.00 0.00 35.63 2.73
41 42 3.756082 TCCAAGGGTTTGCATTAGGAT 57.244 42.857 0.00 0.00 32.79 3.24
43 44 4.615588 TTTTCCAAGGGTTTGCATTAGG 57.384 40.909 0.00 0.00 32.79 2.69
76 81 8.697507 AGTGGACATCTTTTATCTGAAAAAGT 57.302 30.769 16.92 6.57 43.72 2.66
85 90 7.255381 CCCATCATGAAGTGGACATCTTTTATC 60.255 40.741 15.66 0.00 37.72 1.75
91 96 2.422519 GCCCATCATGAAGTGGACATCT 60.423 50.000 15.66 0.00 37.72 2.90
128 133 3.878699 GACCTGTTAAACTTCGGAACCAA 59.121 43.478 0.00 0.00 0.00 3.67
130 135 3.469739 TGACCTGTTAAACTTCGGAACC 58.530 45.455 0.00 0.00 0.00 3.62
131 136 4.333372 TGTTGACCTGTTAAACTTCGGAAC 59.667 41.667 0.00 0.00 0.00 3.62
135 140 7.857569 TCTTATTGTTGACCTGTTAAACTTCG 58.142 34.615 0.00 0.00 0.00 3.79
147 152 6.633856 AGGATGCATTTTCTTATTGTTGACC 58.366 36.000 0.00 0.00 0.00 4.02
174 179 4.958581 CCATCCCAGCCTTCTCTTATTTTT 59.041 41.667 0.00 0.00 0.00 1.94
175 180 4.230502 TCCATCCCAGCCTTCTCTTATTTT 59.769 41.667 0.00 0.00 0.00 1.82
176 181 3.788142 TCCATCCCAGCCTTCTCTTATTT 59.212 43.478 0.00 0.00 0.00 1.40
184 189 0.323725 TGCTTTCCATCCCAGCCTTC 60.324 55.000 0.00 0.00 32.11 3.46
266 279 3.859961 CGATCTCGTTGTAGCATTCTTGT 59.140 43.478 0.00 0.00 34.11 3.16
267 280 3.302092 GCGATCTCGTTGTAGCATTCTTG 60.302 47.826 1.14 0.00 42.22 3.02
269 282 2.099921 AGCGATCTCGTTGTAGCATTCT 59.900 45.455 1.14 0.00 42.22 2.40
270 283 2.464865 AGCGATCTCGTTGTAGCATTC 58.535 47.619 1.14 0.00 42.22 2.67
282 295 2.035503 GTAGCGTTTACGAGCGATCTC 58.964 52.381 6.44 0.00 43.02 2.75
284 297 1.818850 TGTAGCGTTTACGAGCGATC 58.181 50.000 6.44 0.00 43.02 3.69
285 298 1.916000 GTTGTAGCGTTTACGAGCGAT 59.084 47.619 6.44 0.00 43.02 4.58
287 300 0.364515 GGTTGTAGCGTTTACGAGCG 59.635 55.000 6.44 0.00 43.02 5.03
288 301 1.421382 TGGTTGTAGCGTTTACGAGC 58.579 50.000 6.44 10.07 43.02 5.03
289 302 5.766702 TTTATGGTTGTAGCGTTTACGAG 57.233 39.130 6.44 0.00 43.02 4.18
290 303 6.018425 TGTTTTTATGGTTGTAGCGTTTACGA 60.018 34.615 6.44 0.00 43.02 3.43
291 304 6.134730 TGTTTTTATGGTTGTAGCGTTTACG 58.865 36.000 0.00 0.00 43.27 3.18
292 305 7.113825 CCTTGTTTTTATGGTTGTAGCGTTTAC 59.886 37.037 0.00 0.00 0.00 2.01
293 306 7.140048 CCTTGTTTTTATGGTTGTAGCGTTTA 58.860 34.615 0.00 0.00 0.00 2.01
294 307 5.980715 CCTTGTTTTTATGGTTGTAGCGTTT 59.019 36.000 0.00 0.00 0.00 3.60
295 308 5.508320 CCCTTGTTTTTATGGTTGTAGCGTT 60.508 40.000 0.00 0.00 0.00 4.84
296 309 4.022676 CCCTTGTTTTTATGGTTGTAGCGT 60.023 41.667 0.00 0.00 0.00 5.07
306 495 7.607991 ACATCTAGTGACTCCCTTGTTTTTATG 59.392 37.037 0.00 0.00 0.00 1.90
308 497 7.074653 ACATCTAGTGACTCCCTTGTTTTTA 57.925 36.000 0.00 0.00 0.00 1.52
323 512 8.818141 TTTTCAGACTTGACTTACATCTAGTG 57.182 34.615 0.00 0.00 35.25 2.74
337 526 8.885494 TGACCCAAATTAAATTTTCAGACTTG 57.115 30.769 0.00 0.00 0.00 3.16
363 552 5.707242 TCTGACGGCTAGAAATAATCGAT 57.293 39.130 0.00 0.00 0.00 3.59
367 556 8.958119 TTTTACATCTGACGGCTAGAAATAAT 57.042 30.769 0.00 0.00 0.00 1.28
397 586 4.003648 AGGTTAAAGAAAGCATCCGTCTG 58.996 43.478 0.00 0.00 38.08 3.51
400 589 3.756963 GGAAGGTTAAAGAAAGCATCCGT 59.243 43.478 0.00 0.00 41.89 4.69
413 602 6.192044 GGGGAAGAATACATTGGAAGGTTAA 58.808 40.000 0.00 0.00 0.00 2.01
414 603 5.254267 TGGGGAAGAATACATTGGAAGGTTA 59.746 40.000 0.00 0.00 0.00 2.85
423 612 3.617284 GACGGTTGGGGAAGAATACATT 58.383 45.455 0.00 0.00 0.00 2.71
428 617 1.137594 TGGGACGGTTGGGGAAGAAT 61.138 55.000 0.00 0.00 0.00 2.40
521 711 1.979693 GCGACTGAGGGGAGAGTGT 60.980 63.158 0.00 0.00 0.00 3.55
541 752 1.056700 TTAGAGGGATGGCTGGAGGC 61.057 60.000 0.00 0.00 41.50 4.70
544 755 0.694444 GGGTTAGAGGGATGGCTGGA 60.694 60.000 0.00 0.00 0.00 3.86
545 756 1.709994 GGGGTTAGAGGGATGGCTGG 61.710 65.000 0.00 0.00 0.00 4.85
548 759 1.764854 TCGGGGTTAGAGGGATGGC 60.765 63.158 0.00 0.00 0.00 4.40
549 760 0.689745 TGTCGGGGTTAGAGGGATGG 60.690 60.000 0.00 0.00 0.00 3.51
586 797 2.034221 GGTGGTGCAGGTTCCCTC 59.966 66.667 0.00 0.00 0.00 4.30
587 798 3.580319 GGGTGGTGCAGGTTCCCT 61.580 66.667 8.40 0.00 35.63 4.20
588 799 4.678743 GGGGTGGTGCAGGTTCCC 62.679 72.222 7.42 7.42 37.59 3.97
589 800 4.678743 GGGGGTGGTGCAGGTTCC 62.679 72.222 0.00 0.00 0.00 3.62
602 813 0.258774 CTCATTAGGGGTGTTGGGGG 59.741 60.000 0.00 0.00 0.00 5.40
606 817 7.382110 CACTATCTATCTCATTAGGGGTGTTG 58.618 42.308 0.00 0.00 0.00 3.33
608 819 6.019748 CCACTATCTATCTCATTAGGGGTGT 58.980 44.000 0.00 0.00 31.75 4.16
609 820 5.423610 CCCACTATCTATCTCATTAGGGGTG 59.576 48.000 0.00 0.00 34.07 4.61
610 821 5.521068 CCCCACTATCTATCTCATTAGGGGT 60.521 48.000 0.00 0.00 45.63 4.95
614 825 6.256819 TGGACCCCACTATCTATCTCATTAG 58.743 44.000 0.00 0.00 0.00 1.73
615 826 6.227624 TGGACCCCACTATCTATCTCATTA 57.772 41.667 0.00 0.00 0.00 1.90
616 827 5.093236 TGGACCCCACTATCTATCTCATT 57.907 43.478 0.00 0.00 0.00 2.57
617 828 4.767000 TGGACCCCACTATCTATCTCAT 57.233 45.455 0.00 0.00 0.00 2.90
618 829 4.767000 ATGGACCCCACTATCTATCTCA 57.233 45.455 0.00 0.00 35.80 3.27
619 830 4.323104 GCAATGGACCCCACTATCTATCTC 60.323 50.000 0.00 0.00 35.80 2.75
630 841 1.852157 AGAGTGGCAATGGACCCCA 60.852 57.895 0.00 0.00 38.19 4.96
646 857 3.811098 GCGACCCCACTATCTATCTCAGA 60.811 52.174 0.00 0.00 37.79 3.27
649 860 2.797786 AGCGACCCCACTATCTATCTC 58.202 52.381 0.00 0.00 0.00 2.75
678 889 2.577772 AGCCCTCTGGGTCTATCTTT 57.422 50.000 4.42 0.00 46.51 2.52
703 914 2.548067 GGAACGAAAGAAGGAGCTCACA 60.548 50.000 17.19 0.00 0.00 3.58
705 916 2.457366 GGAACGAAAGAAGGAGCTCA 57.543 50.000 17.19 0.00 0.00 4.26
720 931 4.717313 AAAGGAGCCCGCCGGAAC 62.717 66.667 5.05 0.00 0.00 3.62
721 932 4.404098 GAAAGGAGCCCGCCGGAA 62.404 66.667 5.05 0.00 0.00 4.30
728 939 2.568623 TCACTTGAAGAAAGGAGCCC 57.431 50.000 0.00 0.00 40.51 5.19
729 940 5.459536 AATTTCACTTGAAGAAAGGAGCC 57.540 39.130 0.00 0.00 40.51 4.70
737 948 3.739300 GTCGGTCGAATTTCACTTGAAGA 59.261 43.478 0.00 0.00 35.21 2.87
745 977 2.257691 TTTGGGTCGGTCGAATTTCA 57.742 45.000 0.00 0.00 0.00 2.69
753 985 5.163652 CCTGAATTTAGAATTTGGGTCGGTC 60.164 44.000 0.00 0.00 0.00 4.79
791 1023 1.069022 TGCTTTTTCACGATCAGCAGC 60.069 47.619 0.00 0.00 35.56 5.25
792 1024 2.975410 TGCTTTTTCACGATCAGCAG 57.025 45.000 0.00 0.00 35.56 4.24
793 1025 3.921119 ATTGCTTTTTCACGATCAGCA 57.079 38.095 0.00 0.00 38.72 4.41
797 1321 7.412853 AGATGTGATATTGCTTTTTCACGATC 58.587 34.615 0.00 0.00 41.02 3.69
800 1324 5.674148 CGAGATGTGATATTGCTTTTTCACG 59.326 40.000 0.00 0.00 41.02 4.35
809 1333 3.430218 GTGTAGGCGAGATGTGATATTGC 59.570 47.826 0.00 0.00 0.00 3.56
810 1334 3.670523 CGTGTAGGCGAGATGTGATATTG 59.329 47.826 0.00 0.00 0.00 1.90
902 1430 3.695747 GAAGCCCTCCTGCCTGCTC 62.696 68.421 0.00 0.00 32.62 4.26
916 1444 2.125350 CGCAGGACAGGAGGAAGC 60.125 66.667 0.00 0.00 0.00 3.86
922 1450 0.321564 CAATGGAACGCAGGACAGGA 60.322 55.000 0.00 0.00 0.00 3.86
924 1452 0.518636 CACAATGGAACGCAGGACAG 59.481 55.000 0.00 0.00 0.00 3.51
926 1454 1.210155 GCACAATGGAACGCAGGAC 59.790 57.895 0.00 0.00 0.00 3.85
1141 1814 2.739704 CGGCGTGCACGATGATGTT 61.740 57.895 41.19 0.00 43.02 2.71
1688 2367 4.821589 CGTCGGAGCCCCAGAAGC 62.822 72.222 0.00 0.00 0.00 3.86
1929 2610 8.036273 TCTCTTACGAAATTTGTGATTTACCC 57.964 34.615 0.00 0.00 0.00 3.69
1936 2617 8.148807 TGTTGATTCTCTTACGAAATTTGTGA 57.851 30.769 0.00 0.00 0.00 3.58
2112 2793 3.553511 CGAGATTCAGTGTGCTAATGTCC 59.446 47.826 0.00 0.00 0.00 4.02
2180 2861 8.308931 TGTAACATTGGTTAAGTCTTAGTCGAT 58.691 33.333 0.00 0.00 40.95 3.59
2221 2902 0.440758 TTTTTGCGCGGATCTACACG 59.559 50.000 8.83 0.00 0.00 4.49
2303 2986 5.047660 AGGTGTGGCTAGATCTTAATCGATC 60.048 44.000 0.00 0.00 40.04 3.69
2347 3030 9.006839 TCTATTATTCCGCTTCTAAACGATCTA 57.993 33.333 0.00 0.00 0.00 1.98
2382 3065 1.416030 GTGATTTTGCAGGGTTTGGGT 59.584 47.619 0.00 0.00 0.00 4.51
2389 3072 5.712152 AGTTTCTTAGTGATTTTGCAGGG 57.288 39.130 0.00 0.00 0.00 4.45
2625 3308 1.955458 ATCCCCTTCTCCTCCTCGCT 61.955 60.000 0.00 0.00 0.00 4.93
2631 3314 2.774234 TGTCAATCATCCCCTTCTCCTC 59.226 50.000 0.00 0.00 0.00 3.71
2765 3448 7.799447 TGAACTAAAACCACGTCAAATATTTCG 59.201 33.333 0.00 2.79 0.00 3.46
2779 3462 5.701224 ACCCTCAAATCTGAACTAAAACCA 58.299 37.500 0.00 0.00 0.00 3.67
2860 3543 2.023320 GGCGAGCGCTTTACATGC 59.977 61.111 13.26 9.20 41.60 4.06
2937 3624 1.675310 CAATGCTTCCAGTCCGGCA 60.675 57.895 0.00 0.00 39.06 5.69
3036 3723 2.494530 GGTTGGCGCTTGGTTGGAA 61.495 57.895 7.64 0.00 0.00 3.53
3104 3791 5.575218 GCGTTTTGTCTCAAAGAAGGAAAAA 59.425 36.000 0.00 0.00 0.00 1.94
3129 3816 0.377203 GCTGTAATACTTGGCGTGGC 59.623 55.000 0.00 0.00 0.00 5.01
3135 3822 3.683989 CATGTTGCGCTGTAATACTTGG 58.316 45.455 9.73 0.00 0.00 3.61
3223 3910 7.279313 TGAACTACTTGTCCTTTACTGTGTTTC 59.721 37.037 0.00 0.00 0.00 2.78
3242 3929 6.743575 AGTGGTAGCAAATTGATGAACTAC 57.256 37.500 0.00 0.00 0.00 2.73
3393 4080 2.362375 GGCAGGCAATTTCCCCGA 60.362 61.111 0.00 0.00 0.00 5.14
3460 4147 3.578688 GCTTAACAAACATGAAGCCTGG 58.421 45.455 0.00 0.00 38.68 4.45
3522 4209 1.341976 ACCCCTGTGACTTGTTTGCTT 60.342 47.619 0.00 0.00 0.00 3.91
3525 4212 3.430236 GGAAAACCCCTGTGACTTGTTTG 60.430 47.826 0.00 0.00 0.00 2.93
3526 4213 2.764010 GGAAAACCCCTGTGACTTGTTT 59.236 45.455 0.00 0.00 0.00 2.83
3549 4236 1.734655 ACCTCCTGAAGCCTGAAGAA 58.265 50.000 0.00 0.00 0.00 2.52
3678 4365 4.112634 CGTATGTTCCGTTCTCACATCAT 58.887 43.478 0.00 0.00 33.19 2.45
3695 4382 4.637483 AATGCATTTTCCCTGTCGTATG 57.363 40.909 5.99 0.00 0.00 2.39
3724 4411 6.521151 AGATGCCTTTGACTTTCCTATTTG 57.479 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.