Multiple sequence alignment - TraesCS7D01G376100

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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 TraesCS7D01G376100 chr7D 100.000 3826 0 0 1 3826 486170101 486166276 0.000000e+00 7066.0
1 TraesCS7D01G376100 chr7D 78.069 953 160 25 955 1882 486107992 486107064 1.200000e-154 556.0
2 TraesCS7D01G376100 chr7D 77.518 685 127 21 2200 2863 486106940 486106262 1.670000e-103 387.0
3 TraesCS7D01G376100 chr7D 74.875 800 158 30 1088 1874 486242833 486242064 1.330000e-84 324.0
4 TraesCS7D01G376100 chr7D 90.909 198 12 3 3520 3711 179484935 179485132 1.050000e-65 261.0
5 TraesCS7D01G376100 chr7B 96.345 1286 37 5 871 2155 513958419 513957143 0.000000e+00 2106.0
6 TraesCS7D01G376100 chr7B 96.350 822 30 0 2137 2958 513957071 513956250 0.000000e+00 1352.0
7 TraesCS7D01G376100 chr7B 94.154 804 37 5 48 849 513959198 513958403 0.000000e+00 1216.0
8 TraesCS7D01G376100 chr7B 93.646 661 36 3 2952 3610 513956143 513955487 0.000000e+00 983.0
9 TraesCS7D01G376100 chr7B 79.087 942 159 23 955 1885 513771622 513770708 7.020000e-172 614.0
10 TraesCS7D01G376100 chr7B 90.228 307 23 7 3525 3825 513955516 513955211 9.960000e-106 394.0
11 TraesCS7D01G376100 chr7B 79.691 517 92 13 2355 2863 513770331 513769820 1.010000e-95 361.0
12 TraesCS7D01G376100 chr7B 86.154 195 22 5 3520 3711 482245666 482245858 5.010000e-49 206.0
13 TraesCS7D01G376100 chr2A 94.088 1184 59 7 976 2155 137565953 137564777 0.000000e+00 1788.0
14 TraesCS7D01G376100 chr2A 94.767 707 33 4 2137 2840 137564705 137564000 0.000000e+00 1098.0
15 TraesCS7D01G376100 chr2A 87.926 323 35 3 350 672 356675588 356675906 1.000000e-100 377.0
16 TraesCS7D01G376100 chr7A 88.450 1013 87 10 890 1886 554502879 554501881 0.000000e+00 1195.0
17 TraesCS7D01G376100 chr7A 84.672 822 113 10 2135 2948 554501809 554500993 0.000000e+00 808.0
18 TraesCS7D01G376100 chr7A 86.649 382 35 7 3127 3502 554787645 554787274 3.560000e-110 409.0
19 TraesCS7D01G376100 chr7A 78.107 507 100 10 2355 2854 554490297 554489795 1.030000e-80 311.0
20 TraesCS7D01G376100 chr7A 94.068 118 6 1 3709 3825 554787276 554787159 1.090000e-40 178.0
21 TraesCS7D01G376100 chr7A 88.525 61 5 2 1960 2019 554501898 554501839 5.300000e-09 73.1
22 TraesCS7D01G376100 chr2D 86.337 344 37 5 19 352 444756528 444756871 2.170000e-97 366.0
23 TraesCS7D01G376100 chr2D 87.313 268 25 9 1 266 638382755 638382495 8.040000e-77 298.0
24 TraesCS7D01G376100 chr2D 89.552 67 6 1 200 266 627645309 627645244 2.450000e-12 84.2
25 TraesCS7D01G376100 chr2B 85.882 340 47 1 366 705 321713702 321713364 1.010000e-95 361.0
26 TraesCS7D01G376100 chr6A 79.348 460 72 14 1013 1464 522044504 522044948 6.210000e-78 302.0
27 TraesCS7D01G376100 chr6A 76.950 282 49 12 1012 1280 51480139 51479861 3.080000e-31 147.0
28 TraesCS7D01G376100 chr6A 82.738 168 23 2 3520 3686 263912577 263912415 1.110000e-30 145.0
29 TraesCS7D01G376100 chr1A 86.940 268 28 4 1 264 471884474 471884210 1.040000e-75 294.0
30 TraesCS7D01G376100 chr1B 92.228 193 14 1 3520 3711 87972973 87973165 4.870000e-69 272.0
31 TraesCS7D01G376100 chr3B 92.063 189 9 3 3524 3711 296186793 296186610 1.050000e-65 261.0
32 TraesCS7D01G376100 chr1D 91.579 190 15 1 3525 3713 465781363 465781552 1.050000e-65 261.0
33 TraesCS7D01G376100 chr1D 88.060 67 6 2 199 264 372458923 372458988 1.140000e-10 78.7
34 TraesCS7D01G376100 chr1D 100.000 29 0 0 3740 3768 22034246 22034218 2.000000e-03 54.7
35 TraesCS7D01G376100 chr3D 92.073 164 7 2 3549 3711 209682237 209682079 3.850000e-55 226.0
36 TraesCS7D01G376100 chr4B 86.364 176 21 3 76 249 591092176 591092350 5.050000e-44 189.0
37 TraesCS7D01G376100 chr6B 88.889 63 6 1 204 266 160672140 160672201 4.100000e-10 76.8
38 TraesCS7D01G376100 chr6D 94.872 39 1 1 1243 1280 39673254 39673216 4.130000e-05 60.2


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 TraesCS7D01G376100 chr7D 486166276 486170101 3825 True 7066.000000 7066 100.000000 1 3826 1 chr7D.!!$R1 3825
1 TraesCS7D01G376100 chr7D 486106262 486107992 1730 True 471.500000 556 77.793500 955 2863 2 chr7D.!!$R3 1908
2 TraesCS7D01G376100 chr7D 486242064 486242833 769 True 324.000000 324 74.875000 1088 1874 1 chr7D.!!$R2 786
3 TraesCS7D01G376100 chr7B 513955211 513959198 3987 True 1210.200000 2106 94.144600 48 3825 5 chr7B.!!$R2 3777
4 TraesCS7D01G376100 chr7B 513769820 513771622 1802 True 487.500000 614 79.389000 955 2863 2 chr7B.!!$R1 1908
5 TraesCS7D01G376100 chr2A 137564000 137565953 1953 True 1443.000000 1788 94.427500 976 2840 2 chr2A.!!$R1 1864
6 TraesCS7D01G376100 chr7A 554500993 554502879 1886 True 692.033333 1195 87.215667 890 2948 3 chr7A.!!$R2 2058
7 TraesCS7D01G376100 chr7A 554489795 554490297 502 True 311.000000 311 78.107000 2355 2854 1 chr7A.!!$R1 499

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
333 336 0.105408 CCGGTTATAAGGGTCACGGG 59.895 60.0 0.0 0.0 36.45 5.28 F
725 728 0.339859 ACCCATCAGTCTGCCCTAGA 59.660 55.0 0.0 0.0 0.00 2.43 F
2162 2303 0.170339 TGTGTATCTGTCTCGGTGCG 59.830 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1597 0.685097 CAAGGGTCTTCAGAACGGGA 59.315 55.0 0.00 0.0 30.99 5.14 R
2621 2857 0.459489 GTGGCACAAGCACCAAAGAA 59.541 50.0 13.86 0.0 44.16 2.52 R
3326 3685 0.322816 AACAGCATCATGCCGGAAGT 60.323 50.0 5.05 0.0 46.52 3.01 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
27 28 2.601067 TGGTGCTGCCAATGGTGG 60.601 61.111 0.00 0.00 45.94 4.61
36 37 3.743714 CCAATGGTGGTGGTGAAGA 57.256 52.632 0.00 0.00 40.42 2.87
37 38 2.220653 CCAATGGTGGTGGTGAAGAT 57.779 50.000 0.00 0.00 40.42 2.40
38 39 2.528564 CCAATGGTGGTGGTGAAGATT 58.471 47.619 0.00 0.00 40.42 2.40
39 40 2.899256 CCAATGGTGGTGGTGAAGATTT 59.101 45.455 0.00 0.00 40.42 2.17
40 41 3.056607 CCAATGGTGGTGGTGAAGATTTC 60.057 47.826 0.00 0.00 40.42 2.17
41 42 3.524095 ATGGTGGTGGTGAAGATTTCA 57.476 42.857 0.00 0.00 37.33 2.69
42 43 3.524095 TGGTGGTGGTGAAGATTTCAT 57.476 42.857 0.00 0.00 42.47 2.57
43 44 3.420893 TGGTGGTGGTGAAGATTTCATC 58.579 45.455 0.00 0.00 42.47 2.92
44 45 2.420022 GGTGGTGGTGAAGATTTCATCG 59.580 50.000 0.00 0.00 43.77 3.84
45 46 3.074412 GTGGTGGTGAAGATTTCATCGT 58.926 45.455 0.00 0.00 43.77 3.73
46 47 3.073678 TGGTGGTGAAGATTTCATCGTG 58.926 45.455 0.00 0.00 43.77 4.35
107 108 2.203437 GGGTTGTGGCCCGAAACT 60.203 61.111 0.00 0.00 39.17 2.66
108 109 1.073548 GGGTTGTGGCCCGAAACTA 59.926 57.895 0.00 0.00 39.17 2.24
109 110 0.323087 GGGTTGTGGCCCGAAACTAT 60.323 55.000 0.00 0.00 39.17 2.12
110 111 0.808755 GGTTGTGGCCCGAAACTATG 59.191 55.000 0.00 0.00 0.00 2.23
111 112 1.530323 GTTGTGGCCCGAAACTATGT 58.470 50.000 0.00 0.00 0.00 2.29
113 114 1.816074 TGTGGCCCGAAACTATGTTC 58.184 50.000 0.00 0.00 0.00 3.18
121 123 4.647964 CCCGAAACTATGTTCAAATGACG 58.352 43.478 0.00 0.00 0.00 4.35
143 145 4.207019 CGCCAAAACTGTGTTTGAATTCTC 59.793 41.667 7.05 0.00 40.29 2.87
145 147 5.659463 CCAAAACTGTGTTTGAATTCTCCA 58.341 37.500 7.05 0.00 40.29 3.86
177 180 7.271653 GTGTTTATTTATCAAAATCGCGGTCAA 59.728 33.333 6.13 0.00 36.67 3.18
184 187 3.127721 TCAAAATCGCGGTCAATTGCATA 59.872 39.130 6.13 0.00 0.00 3.14
188 191 0.726827 CGCGGTCAATTGCATAGTGT 59.273 50.000 0.00 0.00 0.00 3.55
197 200 5.567534 GTCAATTGCATAGTGTGGTTTTACG 59.432 40.000 0.00 0.00 0.00 3.18
268 271 3.135530 AGCGGCAAAAGAGAATATCCTCT 59.864 43.478 1.45 0.00 44.84 3.69
292 295 4.380128 GCAACCGATTTCGACCCTTAAAAT 60.380 41.667 0.67 0.00 43.02 1.82
305 308 3.365969 CCCTTAAAATGCGCTTTTCTCGT 60.366 43.478 20.02 8.50 38.09 4.18
333 336 0.105408 CCGGTTATAAGGGTCACGGG 59.895 60.000 0.00 0.00 36.45 5.28
346 349 0.688487 TCACGGGTTTAAGGGGTCTG 59.312 55.000 0.00 0.00 0.00 3.51
386 389 1.202818 CCCCTTGAGCTAGCCCATTAC 60.203 57.143 12.13 0.00 0.00 1.89
490 493 1.066587 CCTCGGTCGCTTCAGATCC 59.933 63.158 0.00 0.00 0.00 3.36
493 496 2.586357 GGTCGCTTCAGATCCCGC 60.586 66.667 0.00 0.00 0.00 6.13
494 497 2.184322 GTCGCTTCAGATCCCGCA 59.816 61.111 0.00 0.00 0.00 5.69
517 520 2.732619 CCCTTCGCCTCCCTGGTAC 61.733 68.421 0.00 0.00 38.35 3.34
603 606 3.126001 GGATGCCATCCGAGTGAAATA 57.874 47.619 8.21 0.00 40.13 1.40
704 707 6.015772 GGAGATGTCTACTTCTTGACCCTATC 60.016 46.154 0.63 0.00 31.50 2.08
722 725 2.362369 CGACCCATCAGTCTGCCCT 61.362 63.158 0.00 0.00 34.46 5.19
725 728 0.339859 ACCCATCAGTCTGCCCTAGA 59.660 55.000 0.00 0.00 0.00 2.43
726 729 1.061812 ACCCATCAGTCTGCCCTAGAT 60.062 52.381 0.00 0.00 37.83 1.98
727 730 2.180086 ACCCATCAGTCTGCCCTAGATA 59.820 50.000 0.00 0.00 37.83 1.98
728 731 3.242867 CCCATCAGTCTGCCCTAGATAA 58.757 50.000 0.00 0.00 37.83 1.75
751 754 6.841781 AATATATCGGGCAATATAAGGGGT 57.158 37.500 3.78 0.00 30.07 4.95
752 755 2.879103 ATCGGGCAATATAAGGGGTG 57.121 50.000 0.00 0.00 0.00 4.61
753 756 0.768622 TCGGGCAATATAAGGGGTGG 59.231 55.000 0.00 0.00 0.00 4.61
841 844 8.850007 AAAAGAGAGGAATTTCACTAACCTAC 57.150 34.615 0.00 0.00 0.00 3.18
842 845 6.547930 AGAGAGGAATTTCACTAACCTACC 57.452 41.667 0.00 0.00 0.00 3.18
843 846 6.023603 AGAGAGGAATTTCACTAACCTACCA 58.976 40.000 0.00 0.00 0.00 3.25
844 847 6.674419 AGAGAGGAATTTCACTAACCTACCAT 59.326 38.462 0.00 0.00 0.00 3.55
845 848 7.844779 AGAGAGGAATTTCACTAACCTACCATA 59.155 37.037 0.00 0.00 0.00 2.74
846 849 8.024145 AGAGGAATTTCACTAACCTACCATAG 57.976 38.462 0.00 0.00 0.00 2.23
847 850 7.844779 AGAGGAATTTCACTAACCTACCATAGA 59.155 37.037 0.00 0.00 0.00 1.98
848 851 8.568617 AGGAATTTCACTAACCTACCATAGAT 57.431 34.615 0.00 0.00 0.00 1.98
849 852 9.004231 AGGAATTTCACTAACCTACCATAGATT 57.996 33.333 0.00 0.00 0.00 2.40
850 853 9.628500 GGAATTTCACTAACCTACCATAGATTT 57.372 33.333 0.00 0.00 0.00 2.17
1228 1253 1.384989 CCGTGACGCCATAGTCTCCT 61.385 60.000 0.00 0.00 41.47 3.69
1233 1258 1.330655 ACGCCATAGTCTCCTGGGTG 61.331 60.000 0.00 0.00 34.76 4.61
1571 1596 1.547372 GGAGTGTTTGATTGCTGCCAT 59.453 47.619 0.00 0.00 0.00 4.40
1572 1597 2.028748 GGAGTGTTTGATTGCTGCCATT 60.029 45.455 0.00 0.00 0.00 3.16
1658 1689 3.649096 CCATTGCGTGGTCGTTGA 58.351 55.556 0.00 0.00 43.44 3.18
1659 1690 1.206578 CCATTGCGTGGTCGTTGAC 59.793 57.895 0.00 0.00 43.44 3.18
1888 1939 8.260099 TCTCCATCTCTATCTCAACATGATTT 57.740 34.615 0.00 0.00 0.00 2.17
1889 1940 8.712103 TCTCCATCTCTATCTCAACATGATTTT 58.288 33.333 0.00 0.00 0.00 1.82
1890 1941 9.339850 CTCCATCTCTATCTCAACATGATTTTT 57.660 33.333 0.00 0.00 0.00 1.94
1940 1991 7.774625 TGCATATGTTCATAAATCTTGTCAGGA 59.225 33.333 4.29 0.00 0.00 3.86
2030 2081 2.974794 CCACTGAGATCCATCCACCATA 59.025 50.000 0.00 0.00 0.00 2.74
2055 2106 8.859517 AGTCTTCTCTACGATTATAAAACTGC 57.140 34.615 0.00 0.00 0.00 4.40
2155 2206 6.378280 TGTGTGAGTATGATGTGTATCTGTCT 59.622 38.462 0.00 0.00 34.31 3.41
2156 2207 6.915300 GTGTGAGTATGATGTGTATCTGTCTC 59.085 42.308 0.00 0.00 34.31 3.36
2162 2303 0.170339 TGTGTATCTGTCTCGGTGCG 59.830 55.000 0.00 0.00 0.00 5.34
2185 2326 3.490590 CCGCATTGCAGCCAAACATAATA 60.491 43.478 9.69 0.00 34.05 0.98
2189 2330 5.653507 CATTGCAGCCAAACATAATAGTGT 58.346 37.500 0.00 0.00 34.05 3.55
2232 2373 2.289002 GCGTCAAGATATTGGCCTTGAG 59.711 50.000 3.32 0.39 46.33 3.02
2609 2845 2.686915 CAAGTTCATCTCCAAGGATGCC 59.313 50.000 0.00 0.00 41.83 4.40
2685 2921 5.281727 CGAACGAGGTGAATGAGATGATAA 58.718 41.667 0.00 0.00 0.00 1.75
2696 2932 6.156775 TGAATGAGATGATAAACAGACTGGGA 59.843 38.462 7.51 0.00 0.00 4.37
2708 2944 0.899720 GACTGGGATGTCCACGGTTA 59.100 55.000 0.86 0.00 41.46 2.85
2711 2947 1.153509 GGGATGTCCACGGTTACGG 60.154 63.158 0.86 0.00 46.48 4.02
2981 3340 7.581213 TGTTTCAAGTTTCAACTACCATGAT 57.419 32.000 0.00 0.00 38.57 2.45
3032 3391 4.218852 AGAACTACTGAACTGGCTAGTGTC 59.781 45.833 2.40 4.58 37.19 3.67
3035 3394 3.601443 ACTGAACTGGCTAGTGTCATC 57.399 47.619 2.40 0.00 37.19 2.92
3038 3397 3.930336 TGAACTGGCTAGTGTCATCTTG 58.070 45.455 2.40 0.00 37.19 3.02
3048 3407 6.589523 GGCTAGTGTCATCTTGTCATGATATC 59.410 42.308 0.00 0.00 35.23 1.63
3049 3408 7.150640 GCTAGTGTCATCTTGTCATGATATCA 58.849 38.462 8.10 8.10 35.23 2.15
3128 3487 5.730296 ATCTGAATATAGTACGCCTGCTT 57.270 39.130 0.00 0.00 0.00 3.91
3150 3509 2.026356 TGTAGCATGTGTTAGGTGCCAT 60.026 45.455 0.00 0.00 39.62 4.40
3189 3548 2.843701 CTTCTGCAGAGTGTCACCTTT 58.156 47.619 17.43 0.00 0.00 3.11
3274 3633 3.697166 AGGTTGACAAGTTTTCTGGTGT 58.303 40.909 0.00 0.00 33.62 4.16
3278 3637 7.057894 AGGTTGACAAGTTTTCTGGTGTTATA 58.942 34.615 0.00 0.00 33.62 0.98
3308 3667 8.872845 ACAGAAAGAAAAATTAAACTTGTGCTG 58.127 29.630 0.00 0.00 0.00 4.41
3314 3673 7.492344 AGAAAAATTAAACTTGTGCTGGAACTG 59.508 33.333 0.00 0.00 0.00 3.16
3326 3685 4.997395 GTGCTGGAACTGAATTGAGTAAGA 59.003 41.667 0.00 0.00 0.00 2.10
3331 3690 6.231211 TGGAACTGAATTGAGTAAGACTTCC 58.769 40.000 0.00 1.21 0.00 3.46
3359 3718 3.781079 TGCTGTTATATGCACAAAGGC 57.219 42.857 0.00 0.00 33.94 4.35
3389 3748 2.032071 CCGCGGAAGGTGTCCTTT 59.968 61.111 24.07 0.00 44.82 3.11
3469 3828 6.043243 TCCCAGAAGAAGATTTCAACTACACT 59.957 38.462 0.00 0.00 0.00 3.55
3491 3850 1.915266 CCTGACTGGCTCCTCCACA 60.915 63.158 0.00 0.00 40.72 4.17
3508 3867 4.098155 TCCACATGGTAAGTAAGTGCCTA 58.902 43.478 0.00 0.00 36.34 3.93
3512 3871 6.112734 CACATGGTAAGTAAGTGCCTATTCA 58.887 40.000 0.00 0.00 0.00 2.57
3515 3874 4.127907 GGTAAGTAAGTGCCTATTCAGCC 58.872 47.826 0.00 0.00 0.00 4.85
3585 3946 1.924939 TTGGCTCCATGCTCTCCCA 60.925 57.895 0.00 0.00 42.39 4.37
3626 4047 3.255642 TGTAGGCCATTTTTCAGAGTTGC 59.744 43.478 5.01 0.00 0.00 4.17
3631 4052 4.024641 GGCCATTTTTCAGAGTTGCAAAAG 60.025 41.667 0.00 0.00 33.93 2.27
3680 4101 1.882623 GGAGCTGGGAGTTGAAAAGTG 59.117 52.381 0.00 0.00 0.00 3.16
3688 4109 2.230660 GAGTTGAAAAGTGGGGAGTGG 58.769 52.381 0.00 0.00 0.00 4.00
3738 4159 7.556275 TCTTGTTCTGAAACTTGACCTTTGTAT 59.444 33.333 0.00 0.00 36.30 2.29
3789 4210 3.192466 GACACGTTAGGAACAACACAGT 58.808 45.455 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.534769 TGAAATCTTCACCACCACCATTGG 61.535 45.833 0.00 0.00 41.07 3.16
19 20 3.573538 TGAAATCTTCACCACCACCATTG 59.426 43.478 0.00 0.00 34.08 2.82
20 21 3.843422 TGAAATCTTCACCACCACCATT 58.157 40.909 0.00 0.00 34.08 3.16
21 22 3.524095 TGAAATCTTCACCACCACCAT 57.476 42.857 0.00 0.00 34.08 3.55
22 23 3.420893 GATGAAATCTTCACCACCACCA 58.579 45.455 0.00 0.00 43.48 4.17
23 24 2.420022 CGATGAAATCTTCACCACCACC 59.580 50.000 0.00 0.00 42.58 4.61
24 25 3.074412 ACGATGAAATCTTCACCACCAC 58.926 45.455 0.00 0.00 42.58 4.16
25 26 3.073678 CACGATGAAATCTTCACCACCA 58.926 45.455 0.00 0.00 42.58 4.17
26 27 3.074412 ACACGATGAAATCTTCACCACC 58.926 45.455 0.00 0.00 42.58 4.61
27 28 3.745975 TCACACGATGAAATCTTCACCAC 59.254 43.478 0.00 0.00 42.58 4.16
28 29 4.001618 TCACACGATGAAATCTTCACCA 57.998 40.909 0.00 0.00 42.58 4.17
41 42 5.790593 TCATCATCATCATCATCACACGAT 58.209 37.500 0.00 0.00 0.00 3.73
42 43 5.204409 TCATCATCATCATCATCACACGA 57.796 39.130 0.00 0.00 0.00 4.35
43 44 5.465724 ACTTCATCATCATCATCATCACACG 59.534 40.000 0.00 0.00 0.00 4.49
44 45 6.482308 TCACTTCATCATCATCATCATCACAC 59.518 38.462 0.00 0.00 0.00 3.82
45 46 6.588204 TCACTTCATCATCATCATCATCACA 58.412 36.000 0.00 0.00 0.00 3.58
46 47 7.387948 TCATCACTTCATCATCATCATCATCAC 59.612 37.037 0.00 0.00 0.00 3.06
101 102 4.088648 GGCGTCATTTGAACATAGTTTCG 58.911 43.478 0.00 0.00 0.00 3.46
106 107 5.343058 CAGTTTTGGCGTCATTTGAACATAG 59.657 40.000 0.00 0.00 0.00 2.23
107 108 5.218885 CAGTTTTGGCGTCATTTGAACATA 58.781 37.500 0.00 0.00 0.00 2.29
108 109 4.050553 CAGTTTTGGCGTCATTTGAACAT 58.949 39.130 0.00 0.00 0.00 2.71
109 110 3.119316 ACAGTTTTGGCGTCATTTGAACA 60.119 39.130 0.00 0.00 0.00 3.18
110 111 3.242712 CACAGTTTTGGCGTCATTTGAAC 59.757 43.478 0.00 0.00 0.00 3.18
111 112 3.119316 ACACAGTTTTGGCGTCATTTGAA 60.119 39.130 0.00 0.00 0.00 2.69
113 114 2.808244 ACACAGTTTTGGCGTCATTTG 58.192 42.857 0.00 0.00 0.00 2.32
121 123 4.507756 GGAGAATTCAAACACAGTTTTGGC 59.492 41.667 8.44 0.00 37.13 4.52
161 164 2.094803 TGCAATTGACCGCGATTTTGAT 60.095 40.909 8.23 0.00 0.00 2.57
177 180 4.076394 ACCGTAAAACCACACTATGCAAT 58.924 39.130 0.00 0.00 0.00 3.56
184 187 2.946990 CCTCAAACCGTAAAACCACACT 59.053 45.455 0.00 0.00 0.00 3.55
188 191 1.984066 CCCCTCAAACCGTAAAACCA 58.016 50.000 0.00 0.00 0.00 3.67
197 200 1.654023 CCGATTTCGCCCCTCAAACC 61.654 60.000 0.00 0.00 38.18 3.27
237 240 3.492311 TTTTGCCGCTCGGGTTTGC 62.492 57.895 10.57 0.00 38.44 3.68
238 241 1.371635 CTTTTGCCGCTCGGGTTTG 60.372 57.895 10.57 0.00 38.44 2.93
251 254 5.220739 CGGTTGCAGAGGATATTCTCTTTTG 60.221 44.000 11.14 2.71 41.76 2.44
268 271 0.250553 AAGGGTCGAAATCGGTTGCA 60.251 50.000 2.63 0.00 40.29 4.08
292 295 0.319083 TAAGGGACGAGAAAAGCGCA 59.681 50.000 11.47 0.00 0.00 6.09
305 308 2.693210 CCTTATAACCGGGGTAAGGGA 58.307 52.381 23.65 0.00 40.37 4.20
330 333 0.906775 TAGCAGACCCCTTAAACCCG 59.093 55.000 0.00 0.00 0.00 5.28
333 336 7.778185 TCTATATCTAGCAGACCCCTTAAAC 57.222 40.000 0.00 0.00 0.00 2.01
346 349 4.048241 GGCGACCCATTCTATATCTAGC 57.952 50.000 0.00 0.00 0.00 3.42
386 389 3.071602 ACATATTCATCAACCCCTCCTCG 59.928 47.826 0.00 0.00 0.00 4.63
493 496 4.452733 GGAGGCGAAGGGACCGTG 62.453 72.222 0.00 0.00 0.00 4.94
512 515 3.243053 CCACCCACACCCGTACCA 61.243 66.667 0.00 0.00 0.00 3.25
517 520 3.250734 TTACCCCACCCACACCCG 61.251 66.667 0.00 0.00 0.00 5.28
526 529 1.734163 CATTCACTCGGTTACCCCAC 58.266 55.000 0.00 0.00 0.00 4.61
537 540 2.125512 ACCGCTCCGCATTCACTC 60.126 61.111 0.00 0.00 0.00 3.51
560 563 1.078759 CGCTCGGATGTTGTCTGGTC 61.079 60.000 0.00 0.00 33.78 4.02
562 565 1.811266 CCGCTCGGATGTTGTCTGG 60.811 63.158 1.35 0.00 37.50 3.86
588 591 7.228507 TCACCAATAATTATTTCACTCGGATGG 59.771 37.037 8.01 6.04 0.00 3.51
704 707 1.043116 TAGGGCAGACTGATGGGTCG 61.043 60.000 6.65 0.00 40.76 4.79
725 728 8.955794 ACCCCTTATATTGCCCGATATATTTAT 58.044 33.333 0.00 0.00 0.00 1.40
726 729 8.215050 CACCCCTTATATTGCCCGATATATTTA 58.785 37.037 0.00 0.00 0.00 1.40
727 730 7.060421 CACCCCTTATATTGCCCGATATATTT 58.940 38.462 0.00 0.00 0.00 1.40
728 731 6.410388 CCACCCCTTATATTGCCCGATATATT 60.410 42.308 0.00 0.00 0.00 1.28
858 861 9.280174 CTATGGTAGGTTAGTTCAACTCAAAAA 57.720 33.333 0.00 0.00 37.30 1.94
859 862 8.653191 TCTATGGTAGGTTAGTTCAACTCAAAA 58.347 33.333 0.00 0.00 37.30 2.44
860 863 8.197592 TCTATGGTAGGTTAGTTCAACTCAAA 57.802 34.615 0.00 0.00 37.30 2.69
861 864 7.786046 TCTATGGTAGGTTAGTTCAACTCAA 57.214 36.000 0.00 0.00 37.30 3.02
862 865 7.973048 ATCTATGGTAGGTTAGTTCAACTCA 57.027 36.000 0.00 0.00 37.30 3.41
1571 1596 1.071699 CAAGGGTCTTCAGAACGGGAA 59.928 52.381 0.00 0.00 30.99 3.97
1572 1597 0.685097 CAAGGGTCTTCAGAACGGGA 59.315 55.000 0.00 0.00 30.99 5.14
1940 1991 4.279145 AGATCACCTATCCACTTGTACGT 58.721 43.478 0.00 0.00 34.90 3.57
2030 2081 8.688151 AGCAGTTTTATAATCGTAGAGAAGACT 58.312 33.333 0.00 0.00 43.63 3.24
2074 2125 9.213799 TGGAATAATTTGCACCAAAAGAAATAC 57.786 29.630 0.00 0.00 36.90 1.89
2185 2326 3.100545 CACAGTTCTTGGGCACACT 57.899 52.632 0.00 0.00 0.00 3.55
2232 2373 4.048241 TCGAAAACACCAAAATTCACCC 57.952 40.909 0.00 0.00 0.00 4.61
2397 2632 1.332375 GCCAGTGCGTAAACAGTTCAA 59.668 47.619 0.00 0.00 0.00 2.69
2609 2845 0.815734 CCAAAGAATGCAGCTCCAGG 59.184 55.000 0.00 0.00 0.00 4.45
2621 2857 0.459489 GTGGCACAAGCACCAAAGAA 59.541 50.000 13.86 0.00 44.16 2.52
2654 2890 2.712057 TCACCTCGTTCGGTAAAGAC 57.288 50.000 0.00 0.00 34.94 3.01
2696 2932 1.906105 ATGCCCGTAACCGTGGACAT 61.906 55.000 0.00 0.00 0.00 3.06
2795 3031 0.179032 TTGAGCAGCGAAAAGGGTCA 60.179 50.000 0.00 0.00 37.28 4.02
3021 3380 3.599730 TGACAAGATGACACTAGCCAG 57.400 47.619 0.00 0.00 0.00 4.85
3022 3381 3.515104 TCATGACAAGATGACACTAGCCA 59.485 43.478 0.00 0.00 0.00 4.75
3023 3382 4.128925 TCATGACAAGATGACACTAGCC 57.871 45.455 0.00 0.00 0.00 3.93
3032 3391 6.037500 ACCACGTTTGATATCATGACAAGATG 59.962 38.462 6.17 5.22 0.00 2.90
3035 3394 5.122239 ACACCACGTTTGATATCATGACAAG 59.878 40.000 6.17 4.36 0.00 3.16
3038 3397 6.844696 ATACACCACGTTTGATATCATGAC 57.155 37.500 6.17 7.83 0.00 3.06
3128 3487 2.224646 TGGCACCTAACACATGCTACAA 60.225 45.455 0.00 0.00 39.38 2.41
3189 3548 8.514330 AGAGGTGTTTGTTAAATTAACTGACA 57.486 30.769 15.80 15.61 39.38 3.58
3278 3637 9.435688 ACAAGTTTAATTTTTCTTTCTGTTGCT 57.564 25.926 0.00 0.00 0.00 3.91
3285 3644 8.419076 TCCAGCACAAGTTTAATTTTTCTTTC 57.581 30.769 0.00 0.00 0.00 2.62
3308 3667 5.348997 CGGAAGTCTTACTCAATTCAGTTCC 59.651 44.000 0.00 0.00 0.00 3.62
3314 3673 3.596214 TGCCGGAAGTCTTACTCAATTC 58.404 45.455 5.05 0.00 0.00 2.17
3326 3685 0.322816 AACAGCATCATGCCGGAAGT 60.323 50.000 5.05 0.00 46.52 3.01
3331 3690 2.485038 TGCATATAACAGCATCATGCCG 59.515 45.455 5.84 0.00 46.52 5.69
3359 3718 1.665916 CCGCGGCTCAGTCATATGG 60.666 63.158 14.67 0.00 0.00 2.74
3400 3759 0.593128 AAACCTGCATTGACTCACGC 59.407 50.000 0.00 0.00 0.00 5.34
3428 3787 2.485814 CTGGGACTAGCTCAGTTTTTGC 59.514 50.000 0.00 0.00 40.40 3.68
3436 3795 3.458044 TCTTCTTCTGGGACTAGCTCA 57.542 47.619 0.00 0.00 0.00 4.26
3469 3828 1.610673 GAGGAGCCAGTCAGGTCCA 60.611 63.158 11.93 0.00 38.99 4.02
3491 3850 5.368989 GCTGAATAGGCACTTACTTACCAT 58.631 41.667 0.00 0.00 41.75 3.55
3548 3907 4.980805 GCGTTCGGTGCCACTCCA 62.981 66.667 0.00 0.00 0.00 3.86
3590 3951 3.068691 TACAAGCCGCTCCGCTCT 61.069 61.111 0.00 0.00 38.44 4.09
3607 3968 2.318908 TGCAACTCTGAAAAATGGCCT 58.681 42.857 3.32 0.00 0.00 5.19
3610 3971 6.039781 CACTTTTGCAACTCTGAAAAATGG 57.960 37.500 0.00 0.00 39.01 3.16
3640 4061 4.671569 CTAGATGGGGAGCGCGCC 62.672 72.222 30.33 23.29 46.73 6.53
3641 4062 2.936912 ATCTAGATGGGGAGCGCGC 61.937 63.158 26.66 26.66 0.00 6.86
3654 4075 2.392662 TCAACTCCCAGCTCCATCTAG 58.607 52.381 0.00 0.00 0.00 2.43
3738 4159 0.983467 TGTGCAGGATAACAGCAGGA 59.017 50.000 0.00 0.00 39.21 3.86


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

AutoCloner maintained by Alex Coulton.