Multiple sequence alignment - TraesCS6B01G467300

Loading Multiple Alignment...

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 TraesCS6B01G467300 chr6B 100.000 4315 0 0 1 4315 717078125 717073811 0.000000e+00 7969.0
1 TraesCS6B01G467300 chr6B 98.980 784 7 1 3532 4315 717060345 717059563 0.000000e+00 1402.0
2 TraesCS6B01G467300 chr6B 95.639 321 6 1 4003 4315 717026757 717026437 3.850000e-140 508.0
3 TraesCS6B01G467300 chr6B 95.639 321 6 1 4003 4315 717043395 717043075 3.850000e-140 508.0
4 TraesCS6B01G467300 chr6B 79.908 433 79 8 1266 1694 519720394 519720822 1.170000e-80 311.0
5 TraesCS6B01G467300 chr6B 84.021 194 25 6 5 195 236227456 236227646 9.530000e-42 182.0
6 TraesCS6B01G467300 chr6B 89.535 86 9 0 3299 3384 717060186 717060101 4.560000e-20 110.0
7 TraesCS6B01G467300 chr6B 89.535 86 9 0 3299 3384 717074434 717074349 4.560000e-20 110.0
8 TraesCS6B01G467300 chr6B 89.535 86 9 0 3692 3777 717074827 717074742 4.560000e-20 110.0
9 TraesCS6B01G467300 chr6D 90.719 3545 183 68 847 4315 472359337 472355863 0.000000e+00 4590.0
10 TraesCS6B01G467300 chr6D 90.985 843 43 18 1 841 472360210 472359399 0.000000e+00 1105.0
11 TraesCS6B01G467300 chr6D 80.139 433 78 8 1266 1694 344207866 344208294 2.500000e-82 316.0
12 TraesCS6B01G467300 chr6D 84.906 159 22 2 1 158 235206782 235206625 4.470000e-35 159.0
13 TraesCS6B01G467300 chr6D 88.372 86 10 0 3692 3777 472356909 472356824 2.120000e-18 104.0
14 TraesCS6B01G467300 chr6A 92.993 1313 40 28 847 2147 617656675 617657947 0.000000e+00 1868.0
15 TraesCS6B01G467300 chr6A 90.663 1221 65 19 2410 3594 617657965 617659172 0.000000e+00 1578.0
16 TraesCS6B01G467300 chr6A 91.206 705 46 10 1 698 617655641 617656336 0.000000e+00 944.0
17 TraesCS6B01G467300 chr6A 89.451 711 53 12 3621 4315 617659233 617659937 0.000000e+00 878.0
18 TraesCS6B01G467300 chr6A 80.370 433 77 8 1266 1694 484608438 484608866 5.380000e-84 322.0
19 TraesCS6B01G467300 chr6A 92.424 132 6 1 707 838 617656483 617656610 7.370000e-43 185.0
20 TraesCS6B01G467300 chr6A 84.783 92 7 5 3692 3777 617658872 617658962 7.690000e-13 86.1
21 TraesCS6B01G467300 chr2D 84.804 408 62 0 1290 1697 564095486 564095079 1.120000e-110 411.0
22 TraesCS6B01G467300 chr2D 73.978 269 43 19 401 667 450920802 450920559 2.770000e-12 84.2
23 TraesCS6B01G467300 chr2D 81.308 107 13 2 382 487 628273475 628273575 3.580000e-11 80.5
24 TraesCS6B01G467300 chr2B 84.314 408 64 0 1290 1697 675356172 675355765 2.420000e-107 399.0
25 TraesCS6B01G467300 chr2B 85.492 193 24 4 1 191 152875311 152875501 9.460000e-47 198.0
26 TraesCS6B01G467300 chr2B 84.456 193 26 4 1 191 553337185 553337375 2.050000e-43 187.0
27 TraesCS6B01G467300 chr2B 76.423 246 35 17 418 660 200904535 200904760 1.270000e-20 111.0
28 TraesCS6B01G467300 chr2A 84.314 408 64 0 1290 1697 704776741 704776334 2.420000e-107 399.0
29 TraesCS6B01G467300 chr1B 79.795 391 67 12 1310 1694 671202668 671202284 1.530000e-69 274.0
30 TraesCS6B01G467300 chr1B 77.122 271 33 21 388 655 415719802 415720046 3.500000e-26 130.0
31 TraesCS6B01G467300 chr1A 81.457 302 48 6 1801 2098 500342868 500342571 1.550000e-59 241.0
32 TraesCS6B01G467300 chr1A 83.951 81 11 2 583 663 29820207 29820285 4.630000e-10 76.8
33 TraesCS6B01G467300 chr4A 80.132 302 54 6 1801 2099 466926509 466926807 2.020000e-53 220.0
34 TraesCS6B01G467300 chr4A 81.622 185 31 3 1 184 738810525 738810343 2.690000e-32 150.0
35 TraesCS6B01G467300 chr5D 87.500 192 20 4 1 190 100761250 100761061 7.270000e-53 219.0
36 TraesCS6B01G467300 chr5D 83.784 185 28 2 1801 1984 400280928 400280745 1.600000e-39 174.0
37 TraesCS6B01G467300 chr4D 79.801 302 55 6 1801 2099 109911468 109911170 9.400000e-52 215.0
38 TraesCS6B01G467300 chr5B 79.599 299 55 5 1802 2097 259538749 259539044 4.370000e-50 209.0
39 TraesCS6B01G467300 chr5A 79.667 300 53 6 1802 2097 310874436 310874141 4.370000e-50 209.0
40 TraesCS6B01G467300 chr5A 83.784 185 28 2 1801 1984 505612649 505612466 1.600000e-39 174.0
41 TraesCS6B01G467300 chr4B 84.974 193 27 2 1 192 670895966 670896157 1.220000e-45 195.0
42 TraesCS6B01G467300 chr3A 82.075 106 16 2 550 655 722453473 722453371 2.140000e-13 87.9
43 TraesCS6B01G467300 chr3A 74.153 236 42 10 427 661 588838311 588838094 3.580000e-11 80.5
44 TraesCS6B01G467300 chr7A 83.333 90 6 5 389 477 716248552 716248633 1.660000e-09 75.0
45 TraesCS6B01G467300 chr7A 72.727 253 51 8 394 645 116191044 116190809 7.740000e-08 69.4


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 TraesCS6B01G467300 chr6B 717073811 717078125 4314 True 2729.666667 7969 93.023333 1 4315 3 chr6B.!!$R4 4314
1 TraesCS6B01G467300 chr6B 717059563 717060345 782 True 756.000000 1402 94.257500 3299 4315 2 chr6B.!!$R3 1016
2 TraesCS6B01G467300 chr6D 472355863 472360210 4347 True 1933.000000 4590 90.025333 1 4315 3 chr6D.!!$R2 4314
3 TraesCS6B01G467300 chr6A 617655641 617659937 4296 False 923.183333 1868 90.253333 1 4315 6 chr6A.!!$F2 4314

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
730 876 0.460284 GGATGCACGACGTTGAGGAT 60.460 55.0 10.51 8.54 0.00 3.24 F
1728 1945 0.393820 GGAAGGTAACGGTGGTGACA 59.606 55.0 0.00 0.00 46.39 3.58 F
2932 3153 0.102300 TCGGCATCGACGACATCATT 59.898 50.0 0.00 0.00 38.55 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2001 0.173481 TGAGGTTGATCTTCTCGCCG 59.827 55.0 0.0 0.00 0.00 6.46 R
3182 3403 0.107945 GGATGGCCGATGGAGCTATC 60.108 60.0 0.0 0.95 44.80 2.08 R
3830 4135 0.739813 GAACGAGCCATACGTGCCTT 60.740 55.0 0.0 0.00 43.16 4.35 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
203 205 7.039923 GGACGGAGATAGTATTAGATTCCACAA 60.040 40.741 0.00 0.00 0.00 3.33
261 263 0.912006 GGTGAGCCTCCCCTTCTTCT 60.912 60.000 0.00 0.00 0.00 2.85
312 315 6.324819 AGTTTTGATCATGAATTTGTAGGCG 58.675 36.000 0.00 0.00 0.00 5.52
342 345 3.670625 TGTGAACCGACCCTTTCTATTG 58.329 45.455 0.00 0.00 0.00 1.90
626 630 4.553756 AAGCTTTTCGAGGTTTGACTTC 57.446 40.909 0.00 0.00 43.27 3.01
630 634 4.214332 GCTTTTCGAGGTTTGACTTCAGAT 59.786 41.667 0.00 0.00 0.00 2.90
674 682 6.370186 AAAAAGATCCGGGGGATACTATAC 57.630 41.667 0.00 0.00 43.27 1.47
675 683 4.969136 AAGATCCGGGGGATACTATACT 57.031 45.455 0.00 0.00 43.27 2.12
676 684 4.523168 AGATCCGGGGGATACTATACTC 57.477 50.000 0.00 0.00 43.27 2.59
730 876 0.460284 GGATGCACGACGTTGAGGAT 60.460 55.000 10.51 8.54 0.00 3.24
737 883 2.422479 CACGACGTTGAGGATAGGAGAA 59.578 50.000 10.51 0.00 0.00 2.87
744 890 4.187694 GTTGAGGATAGGAGAAACTGCTG 58.812 47.826 3.21 0.00 33.39 4.41
782 928 2.893398 GTGCCGCACCTACTAGCT 59.107 61.111 12.80 0.00 0.00 3.32
783 929 2.112898 GTGCCGCACCTACTAGCTA 58.887 57.895 12.80 0.00 0.00 3.32
900 1103 2.874701 CTCAAATTAGGAGGGACATGCG 59.125 50.000 0.00 0.00 0.00 4.73
927 1134 2.938428 ACAATGGAGAGGAGAGGAGT 57.062 50.000 0.00 0.00 0.00 3.85
939 1146 3.036783 GAGGAGTGGTCGTCGTCCG 62.037 68.421 4.07 0.00 33.99 4.79
940 1147 3.360340 GGAGTGGTCGTCGTCCGT 61.360 66.667 4.07 0.00 37.94 4.69
941 1148 2.175322 GAGTGGTCGTCGTCCGTC 59.825 66.667 4.07 0.17 37.94 4.79
942 1149 3.642008 GAGTGGTCGTCGTCCGTCG 62.642 68.421 4.07 0.05 41.41 5.12
943 1150 4.017877 GTGGTCGTCGTCCGTCGT 62.018 66.667 4.07 0.00 40.80 4.34
944 1151 3.716006 TGGTCGTCGTCCGTCGTC 61.716 66.667 4.07 1.35 40.80 4.20
946 1153 4.064491 GTCGTCGTCCGTCGTCGT 62.064 66.667 13.55 0.00 46.88 4.34
947 1154 3.767230 TCGTCGTCCGTCGTCGTC 61.767 66.667 13.55 1.98 46.88 4.20
948 1155 4.783841 CGTCGTCCGTCGTCGTCC 62.784 72.222 0.71 0.00 43.43 4.79
994 1201 1.079057 GCTCCACCTTCGTCTTCCC 60.079 63.158 0.00 0.00 0.00 3.97
995 1202 1.215647 CTCCACCTTCGTCTTCCCG 59.784 63.158 0.00 0.00 0.00 5.14
996 1203 2.434359 CCACCTTCGTCTTCCCGC 60.434 66.667 0.00 0.00 0.00 6.13
997 1204 2.657237 CACCTTCGTCTTCCCGCT 59.343 61.111 0.00 0.00 0.00 5.52
998 1205 1.446272 CACCTTCGTCTTCCCGCTC 60.446 63.158 0.00 0.00 0.00 5.03
999 1206 2.202623 CCTTCGTCTTCCCGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
1000 1207 2.697761 CCTTCGTCTTCCCGCTCGA 61.698 63.158 0.00 0.00 0.00 4.04
1001 1208 1.433879 CTTCGTCTTCCCGCTCGAT 59.566 57.895 0.00 0.00 32.54 3.59
1002 1209 0.592754 CTTCGTCTTCCCGCTCGATC 60.593 60.000 0.00 0.00 32.54 3.69
1003 1210 2.001361 TTCGTCTTCCCGCTCGATCC 62.001 60.000 0.00 0.00 32.54 3.36
1004 1211 2.417936 GTCTTCCCGCTCGATCCC 59.582 66.667 0.00 0.00 0.00 3.85
1005 1212 2.128507 GTCTTCCCGCTCGATCCCT 61.129 63.158 0.00 0.00 0.00 4.20
1015 1222 0.883814 CTCGATCCCTTGCTGCATCC 60.884 60.000 1.84 0.00 0.00 3.51
1033 1240 0.760567 CCAGGGTCCCTCGATCATCA 60.761 60.000 7.76 0.00 0.00 3.07
1034 1241 1.346062 CAGGGTCCCTCGATCATCAT 58.654 55.000 7.76 0.00 0.00 2.45
1038 1245 2.304180 GGGTCCCTCGATCATCATTGAT 59.696 50.000 0.00 0.00 45.39 2.57
1307 1524 1.828660 CCTGCGGGACCTCTACGAT 60.829 63.158 5.28 0.00 33.58 3.73
1697 1914 2.233922 CCTCAAGCCCGAGAACTTTCTA 59.766 50.000 1.58 0.00 37.73 2.10
1718 1935 8.617290 TTCTATTGAAAGACAAGGAAGGTAAC 57.383 34.615 0.00 0.00 42.02 2.50
1719 1936 5.941948 ATTGAAAGACAAGGAAGGTAACG 57.058 39.130 0.00 0.00 42.02 3.18
1720 1937 3.735591 TGAAAGACAAGGAAGGTAACGG 58.264 45.455 0.00 0.00 46.39 4.44
1721 1938 3.135167 TGAAAGACAAGGAAGGTAACGGT 59.865 43.478 0.00 0.00 46.39 4.83
1722 1939 2.833631 AGACAAGGAAGGTAACGGTG 57.166 50.000 0.00 0.00 46.39 4.94
1723 1940 1.346722 AGACAAGGAAGGTAACGGTGG 59.653 52.381 0.00 0.00 46.39 4.61
1724 1941 1.071228 GACAAGGAAGGTAACGGTGGT 59.929 52.381 0.00 0.00 46.39 4.16
1725 1942 1.202722 ACAAGGAAGGTAACGGTGGTG 60.203 52.381 0.00 0.00 46.39 4.17
1726 1943 1.071071 CAAGGAAGGTAACGGTGGTGA 59.929 52.381 0.00 0.00 46.39 4.02
1727 1944 0.683412 AGGAAGGTAACGGTGGTGAC 59.317 55.000 0.00 0.00 46.39 3.67
1728 1945 0.393820 GGAAGGTAACGGTGGTGACA 59.606 55.000 0.00 0.00 46.39 3.58
1744 1961 2.602660 GTGACACCAACAACAACAATGC 59.397 45.455 0.00 0.00 0.00 3.56
1762 1979 2.639970 CCTCCGGCAACAATGTTGA 58.360 52.632 28.10 7.61 0.00 3.18
1763 1980 1.176527 CCTCCGGCAACAATGTTGAT 58.823 50.000 28.10 0.00 0.00 2.57
1764 1981 1.135315 CCTCCGGCAACAATGTTGATG 60.135 52.381 28.10 18.16 34.51 3.07
1765 1982 1.541147 CTCCGGCAACAATGTTGATGT 59.459 47.619 28.10 0.00 33.98 3.06
1768 1985 3.570125 TCCGGCAACAATGTTGATGTTAA 59.430 39.130 28.10 6.32 38.90 2.01
1775 1992 8.220434 GGCAACAATGTTGATGTTAATGTTAAC 58.780 33.333 28.10 6.23 38.90 2.01
1784 2001 2.483491 TGTTAATGTTAACGAACCGGCC 59.517 45.455 0.00 0.00 44.52 6.13
1958 2175 1.335142 GGCGTCATCGTCTACATCCTC 60.335 57.143 0.00 0.00 38.74 3.71
1961 2178 2.224549 CGTCATCGTCTACATCCTCCTC 59.775 54.545 0.00 0.00 0.00 3.71
2153 2370 5.770162 CCAGGTAACCAAAGATTCACTTTCT 59.230 40.000 0.00 0.00 45.66 2.52
2155 2372 7.611855 CCAGGTAACCAAAGATTCACTTTCTAT 59.388 37.037 0.00 0.00 45.66 1.98
2156 2373 8.669243 CAGGTAACCAAAGATTCACTTTCTATC 58.331 37.037 0.00 0.00 45.66 2.08
2162 2379 7.177216 ACCAAAGATTCACTTTCTATCAATGCA 59.823 33.333 0.00 0.00 45.66 3.96
2168 2385 9.798994 GATTCACTTTCTATCAATGCAAGATTT 57.201 29.630 9.89 0.00 0.00 2.17
2251 2468 7.833786 TCTTTTGCTCAGAATATTTCAGCAAT 58.166 30.769 21.13 0.00 46.59 3.56
2252 2469 8.308931 TCTTTTGCTCAGAATATTTCAGCAATT 58.691 29.630 21.13 0.00 46.59 2.32
2253 2470 8.836268 TTTTGCTCAGAATATTTCAGCAATTT 57.164 26.923 21.13 0.00 46.59 1.82
2254 2471 8.836268 TTTGCTCAGAATATTTCAGCAATTTT 57.164 26.923 21.13 0.00 46.59 1.82
2281 2498 5.284079 GGTAGTACGCAGGAATTCGAATAA 58.716 41.667 11.83 0.00 0.00 1.40
2335 2552 2.482326 CTGAATGTTTCGGCCCTCC 58.518 57.895 0.00 0.00 0.00 4.30
2336 2553 0.322456 CTGAATGTTTCGGCCCTCCA 60.322 55.000 0.00 0.00 0.00 3.86
2337 2554 0.111446 TGAATGTTTCGGCCCTCCAA 59.889 50.000 0.00 0.00 0.00 3.53
2338 2555 1.253100 GAATGTTTCGGCCCTCCAAA 58.747 50.000 0.00 0.00 0.00 3.28
2339 2556 1.202348 GAATGTTTCGGCCCTCCAAAG 59.798 52.381 0.00 0.00 0.00 2.77
2357 2574 1.079888 GGGCCGAAATGCAACTTGG 60.080 57.895 0.00 0.00 0.00 3.61
2358 2575 1.665442 GGCCGAAATGCAACTTGGT 59.335 52.632 0.00 0.00 0.00 3.67
2361 2578 2.479560 GGCCGAAATGCAACTTGGTATC 60.480 50.000 0.00 0.00 0.00 2.24
2396 2613 6.318648 CAGGATTTCAGTGATTTCCGGATTTA 59.681 38.462 4.15 0.00 0.00 1.40
2557 2778 4.000988 GGTTGAAGAAGATGGCTTTACGA 58.999 43.478 0.00 0.00 33.61 3.43
2560 2781 5.654603 TGAAGAAGATGGCTTTACGAGTA 57.345 39.130 0.00 0.00 33.61 2.59
2704 2925 1.979155 CACCGAGCTCAGGGACTCA 60.979 63.158 22.76 0.00 34.60 3.41
2761 2982 2.163010 CCGTAGCGGTACCATCGATTAT 59.837 50.000 18.47 0.00 42.73 1.28
2800 3021 0.110056 CCGTGCACATGAACAAGCTC 60.110 55.000 18.64 0.00 0.00 4.09
2932 3153 0.102300 TCGGCATCGACGACATCATT 59.898 50.000 0.00 0.00 38.55 2.57
2983 3204 9.535878 AGTACTCGATTTTCTCTTCATTAATCC 57.464 33.333 0.00 0.00 0.00 3.01
3064 3285 1.109609 GGATCGACTACGGGGAGTTT 58.890 55.000 0.00 0.00 40.21 2.66
3091 3312 4.737578 CCATGATGAAGAAGGGGATCATT 58.262 43.478 0.00 0.00 34.08 2.57
3100 3321 1.379843 GGGGATCATTGGCAACGGT 60.380 57.895 0.00 0.00 42.51 4.83
3142 3363 1.065928 CGACGGTAGCATCCTCCAC 59.934 63.158 0.00 0.00 0.00 4.02
3182 3403 2.014068 GCAGCTAGCCAACTAACCAGG 61.014 57.143 12.13 0.00 37.23 4.45
3192 3413 3.392616 CCAACTAACCAGGATAGCTCCAT 59.607 47.826 3.60 0.00 44.79 3.41
3205 3426 1.756665 CTCCATCGGCCATCCATCA 59.243 57.895 2.24 0.00 0.00 3.07
3207 3428 0.109153 TCCATCGGCCATCCATCAAG 59.891 55.000 2.24 0.00 0.00 3.02
3208 3429 0.179009 CCATCGGCCATCCATCAAGT 60.179 55.000 2.24 0.00 0.00 3.16
3211 3437 3.415212 CATCGGCCATCCATCAAGTATT 58.585 45.455 2.24 0.00 0.00 1.89
3225 3451 2.220653 AGTATTGCCATGGTTGTGCT 57.779 45.000 14.67 5.45 0.00 4.40
3234 3469 3.313526 GCCATGGTTGTGCTATACTTGAG 59.686 47.826 14.67 0.00 0.00 3.02
3243 3478 9.338622 GGTTGTGCTATACTTGAGGTTTAATAT 57.661 33.333 0.00 0.00 0.00 1.28
3270 3514 5.317733 AGACGAGAACGATGAAGAAGAAT 57.682 39.130 0.00 0.00 42.66 2.40
3333 3589 5.309638 TCATTTACCGTGGATTTGAAGACA 58.690 37.500 0.00 0.00 0.00 3.41
3399 3655 1.555075 CTTAACTAGCAGAGTGGCCCA 59.445 52.381 0.00 0.00 38.87 5.36
3400 3656 0.902531 TAACTAGCAGAGTGGCCCAC 59.097 55.000 5.50 5.50 38.87 4.61
3401 3657 1.127567 AACTAGCAGAGTGGCCCACA 61.128 55.000 17.80 0.00 38.87 4.17
3402 3658 1.127567 ACTAGCAGAGTGGCCCACAA 61.128 55.000 17.80 0.00 36.87 3.33
3446 3702 5.139727 TGGAAATGGATTAAGCATAGTGGG 58.860 41.667 0.00 0.00 0.00 4.61
3454 3710 7.807198 TGGATTAAGCATAGTGGGTATTGTTA 58.193 34.615 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 155 5.238650 CCGGTTTATTGGTCCTCATTGTATC 59.761 44.000 0.00 0.00 0.00 2.24
196 198 0.599204 GGAAGTCGCTCGTTGTGGAA 60.599 55.000 0.00 0.00 0.00 3.53
203 205 2.028930 AGAAAGATTGGAAGTCGCTCGT 60.029 45.455 0.00 0.00 0.00 4.18
261 263 5.473504 GGTAACAAGAGAGAATTGGCTCAAA 59.526 40.000 6.85 0.00 37.37 2.69
312 315 0.667792 GTCGGTTCACAGTCTGCTCC 60.668 60.000 0.00 0.00 0.00 4.70
342 345 1.266867 ACTTTTGGGCATGGCATCCC 61.267 55.000 22.06 21.31 42.93 3.85
556 559 9.353431 ACCAGCATTCATAATATGTGTAATCAA 57.647 29.630 0.00 0.00 0.00 2.57
607 611 3.560068 TCTGAAGTCAAACCTCGAAAAGC 59.440 43.478 0.00 0.00 0.00 3.51
610 614 7.979444 ATTTATCTGAAGTCAAACCTCGAAA 57.021 32.000 0.00 0.00 0.00 3.46
665 673 5.220815 CCGGGCTTCATACGAGTATAGTATC 60.221 48.000 0.00 0.00 34.57 2.24
672 680 1.737816 GCCGGGCTTCATACGAGTA 59.262 57.895 12.87 0.00 0.00 2.59
673 681 2.499685 GCCGGGCTTCATACGAGT 59.500 61.111 12.87 0.00 0.00 4.18
674 682 2.280186 GGCCGGGCTTCATACGAG 60.280 66.667 22.87 0.00 0.00 4.18
675 683 4.215742 CGGCCGGGCTTCATACGA 62.216 66.667 27.04 0.00 0.00 3.43
730 876 3.540211 GCAGCAGCAGTTTCTCCTA 57.460 52.632 0.00 0.00 41.58 2.94
876 1078 3.914426 TGTCCCTCCTAATTTGAGCTC 57.086 47.619 6.82 6.82 0.00 4.09
877 1079 3.686691 GCATGTCCCTCCTAATTTGAGCT 60.687 47.826 0.00 0.00 0.00 4.09
900 1103 1.032114 CCTCTCCATTGTTTCGGGGC 61.032 60.000 0.00 0.00 0.00 5.80
939 1146 1.516603 GCTAAGCAGGGACGACGAC 60.517 63.158 0.00 0.00 0.00 4.34
940 1147 2.707849 GGCTAAGCAGGGACGACGA 61.708 63.158 0.00 0.00 0.00 4.20
941 1148 1.381928 TAGGCTAAGCAGGGACGACG 61.382 60.000 0.00 0.00 0.00 5.12
942 1149 0.102663 GTAGGCTAAGCAGGGACGAC 59.897 60.000 0.00 0.00 0.00 4.34
943 1150 1.041447 GGTAGGCTAAGCAGGGACGA 61.041 60.000 0.00 0.00 0.00 4.20
944 1151 1.327690 TGGTAGGCTAAGCAGGGACG 61.328 60.000 0.00 0.00 0.00 4.79
945 1152 1.070914 GATGGTAGGCTAAGCAGGGAC 59.929 57.143 0.00 0.00 0.00 4.46
946 1153 1.424638 GATGGTAGGCTAAGCAGGGA 58.575 55.000 0.00 0.00 0.00 4.20
947 1154 0.034059 CGATGGTAGGCTAAGCAGGG 59.966 60.000 0.00 0.00 0.00 4.45
948 1155 0.601311 GCGATGGTAGGCTAAGCAGG 60.601 60.000 0.00 0.00 0.00 4.85
994 1201 3.267860 GCAGCAAGGGATCGAGCG 61.268 66.667 0.00 0.00 0.00 5.03
995 1202 1.505477 GATGCAGCAAGGGATCGAGC 61.505 60.000 0.00 0.00 0.00 5.03
996 1203 0.883814 GGATGCAGCAAGGGATCGAG 60.884 60.000 3.51 0.00 36.58 4.04
997 1204 1.146930 GGATGCAGCAAGGGATCGA 59.853 57.895 3.51 0.00 36.58 3.59
998 1205 1.153107 TGGATGCAGCAAGGGATCG 60.153 57.895 3.51 0.00 36.58 3.69
999 1206 0.822532 CCTGGATGCAGCAAGGGATC 60.823 60.000 18.31 0.00 35.16 3.36
1000 1207 1.229359 CCTGGATGCAGCAAGGGAT 59.771 57.895 18.31 0.00 0.00 3.85
1001 1208 2.679092 CCTGGATGCAGCAAGGGA 59.321 61.111 18.31 0.00 0.00 4.20
1002 1209 2.441532 CCCTGGATGCAGCAAGGG 60.442 66.667 29.81 29.81 43.42 3.95
1003 1210 1.751927 GACCCTGGATGCAGCAAGG 60.752 63.158 19.14 19.14 0.00 3.61
1004 1211 1.751927 GGACCCTGGATGCAGCAAG 60.752 63.158 9.03 0.31 0.00 4.01
1005 1212 2.356278 GGACCCTGGATGCAGCAA 59.644 61.111 9.03 0.00 0.00 3.91
1015 1222 1.346062 ATGATGATCGAGGGACCCTG 58.654 55.000 20.90 10.75 31.76 4.45
1033 1240 5.571047 CGATGGATCCTCCTCAATGATCAAT 60.571 44.000 14.23 0.00 37.46 2.57
1034 1241 4.262765 CGATGGATCCTCCTCAATGATCAA 60.263 45.833 14.23 0.00 37.46 2.57
1038 1245 2.682594 ACGATGGATCCTCCTCAATGA 58.317 47.619 14.23 0.00 37.46 2.57
1583 1800 2.776913 GCGCTCGGAGAAGTAGCCT 61.777 63.158 9.69 0.00 34.09 4.58
1586 1803 2.024871 CGGCGCTCGGAGAAGTAG 59.975 66.667 9.69 0.00 34.09 2.57
1697 1914 4.760204 CCGTTACCTTCCTTGTCTTTCAAT 59.240 41.667 0.00 0.00 35.35 2.57
1722 1939 3.186119 CATTGTTGTTGTTGGTGTCACC 58.814 45.455 15.64 15.64 39.22 4.02
1723 1940 2.602660 GCATTGTTGTTGTTGGTGTCAC 59.397 45.455 0.00 0.00 0.00 3.67
1724 1941 2.417924 GGCATTGTTGTTGTTGGTGTCA 60.418 45.455 0.00 0.00 0.00 3.58
1725 1942 2.159114 AGGCATTGTTGTTGTTGGTGTC 60.159 45.455 0.00 0.00 0.00 3.67
1726 1943 1.830477 AGGCATTGTTGTTGTTGGTGT 59.170 42.857 0.00 0.00 0.00 4.16
1727 1944 2.472816 GAGGCATTGTTGTTGTTGGTG 58.527 47.619 0.00 0.00 0.00 4.17
1728 1945 1.412343 GGAGGCATTGTTGTTGTTGGT 59.588 47.619 0.00 0.00 0.00 3.67
1729 1946 1.602668 CGGAGGCATTGTTGTTGTTGG 60.603 52.381 0.00 0.00 0.00 3.77
1744 1961 5.169667 AACATCAACATTGTTGCCGGAGG 62.170 47.826 22.02 10.89 39.44 4.30
1754 1971 8.635124 GGTTCGTTAACATTAACATCAACATTG 58.365 33.333 13.47 0.00 42.34 2.82
1755 1972 7.535940 CGGTTCGTTAACATTAACATCAACATT 59.464 33.333 13.47 0.00 42.34 2.71
1756 1973 7.018826 CGGTTCGTTAACATTAACATCAACAT 58.981 34.615 13.47 0.00 42.34 2.71
1757 1974 6.364261 CGGTTCGTTAACATTAACATCAACA 58.636 36.000 13.47 0.00 42.34 3.33
1758 1975 5.791480 CCGGTTCGTTAACATTAACATCAAC 59.209 40.000 13.47 11.52 42.34 3.18
1759 1976 5.617308 GCCGGTTCGTTAACATTAACATCAA 60.617 40.000 1.90 2.24 42.34 2.57
1760 1977 4.142859 GCCGGTTCGTTAACATTAACATCA 60.143 41.667 1.90 0.00 42.34 3.07
1761 1978 4.336932 GCCGGTTCGTTAACATTAACATC 58.663 43.478 1.90 4.48 42.34 3.06
1762 1979 3.127376 GGCCGGTTCGTTAACATTAACAT 59.873 43.478 1.90 0.00 42.34 2.71
1763 1980 2.483491 GGCCGGTTCGTTAACATTAACA 59.517 45.455 1.90 0.60 42.34 2.41
1764 1981 2.474361 CGGCCGGTTCGTTAACATTAAC 60.474 50.000 20.10 6.66 39.62 2.01
1765 1982 1.731160 CGGCCGGTTCGTTAACATTAA 59.269 47.619 20.10 0.00 37.34 1.40
1768 1985 1.742510 CCGGCCGGTTCGTTAACAT 60.743 57.895 36.64 0.00 37.34 2.71
1784 2001 0.173481 TGAGGTTGATCTTCTCGCCG 59.827 55.000 0.00 0.00 0.00 6.46
1790 2007 2.496899 TGGCCTTGAGGTTGATCTTC 57.503 50.000 3.32 0.00 37.57 2.87
1794 2011 0.911769 TCGATGGCCTTGAGGTTGAT 59.088 50.000 3.32 0.00 37.57 2.57
2226 2443 6.822667 TGCTGAAATATTCTGAGCAAAAGA 57.177 33.333 11.58 0.00 36.24 2.52
2252 2469 3.383620 TTCCTGCGTACTACCGAAAAA 57.616 42.857 0.00 0.00 0.00 1.94
2253 2470 3.598019 ATTCCTGCGTACTACCGAAAA 57.402 42.857 0.00 0.00 0.00 2.29
2254 2471 3.514645 GAATTCCTGCGTACTACCGAAA 58.485 45.455 0.00 0.00 0.00 3.46
2265 2482 7.504922 TTTGAAAATTATTCGAATTCCTGCG 57.495 32.000 17.19 0.00 0.00 5.18
2296 2513 8.654230 TTCAGCTAATGCAACAAAACAAATTA 57.346 26.923 0.00 0.00 42.74 1.40
2317 2534 0.322456 TGGAGGGCCGAAACATTCAG 60.322 55.000 0.00 0.00 36.79 3.02
2334 2551 0.670239 GTTGCATTTCGGCCCTTTGG 60.670 55.000 0.00 0.00 0.00 3.28
2335 2552 0.318120 AGTTGCATTTCGGCCCTTTG 59.682 50.000 0.00 0.00 0.00 2.77
2336 2553 1.047801 AAGTTGCATTTCGGCCCTTT 58.952 45.000 0.00 0.00 0.00 3.11
2337 2554 0.318120 CAAGTTGCATTTCGGCCCTT 59.682 50.000 0.00 0.00 0.00 3.95
2338 2555 1.535204 CCAAGTTGCATTTCGGCCCT 61.535 55.000 0.00 0.00 0.00 5.19
2339 2556 1.079888 CCAAGTTGCATTTCGGCCC 60.080 57.895 0.00 0.00 0.00 5.80
2344 2561 3.126858 TCAGCGATACCAAGTTGCATTTC 59.873 43.478 0.00 0.00 0.00 2.17
2647 2868 2.754658 TCCCGGAGCTCCTCGAAC 60.755 66.667 29.73 3.13 0.00 3.95
2671 2892 4.362476 GTGGACCCGTAACGGCGT 62.362 66.667 6.77 6.77 46.86 5.68
2741 2962 2.975410 TAATCGATGGTACCGCTACG 57.025 50.000 7.57 10.07 0.00 3.51
2742 2963 4.164294 GTCATAATCGATGGTACCGCTAC 58.836 47.826 7.57 0.00 36.08 3.58
2743 2964 3.120095 CGTCATAATCGATGGTACCGCTA 60.120 47.826 7.57 0.00 36.08 4.26
2749 2970 5.761165 TGAACTCGTCATAATCGATGGTA 57.239 39.130 0.00 0.00 36.73 3.25
2932 3153 1.305623 GTCCTGGTCGACCTCCCTA 59.694 63.158 33.39 13.59 36.82 3.53
3026 3247 1.679944 CCGACCATCCTGCATTTCAGT 60.680 52.381 0.00 0.00 41.25 3.41
3029 3250 1.876156 GATCCGACCATCCTGCATTTC 59.124 52.381 0.00 0.00 0.00 2.17
3064 3285 1.341285 CCCTTCTTCATCATGGCCACA 60.341 52.381 8.16 0.00 0.00 4.17
3091 3312 1.297364 GGTAAGCCTACCGTTGCCA 59.703 57.895 0.00 0.00 38.43 4.92
3100 3321 1.209504 GTGTGCCTCATGGTAAGCCTA 59.790 52.381 0.00 0.00 35.27 3.93
3155 3376 2.296365 TTGGCTAGCTGCTGAGGCT 61.296 57.895 15.72 0.00 42.39 4.58
3173 3394 2.894126 CGATGGAGCTATCCTGGTTAGT 59.106 50.000 12.22 1.51 46.80 2.24
3179 3400 1.294780 GGCCGATGGAGCTATCCTG 59.705 63.158 0.00 0.00 46.80 3.86
3182 3403 0.107945 GGATGGCCGATGGAGCTATC 60.108 60.000 0.00 0.95 44.80 2.08
3192 3413 2.849942 CAATACTTGATGGATGGCCGA 58.150 47.619 0.00 0.00 36.79 5.54
3205 3426 2.528564 AGCACAACCATGGCAATACTT 58.471 42.857 13.04 0.00 0.00 2.24
3207 3428 4.821805 AGTATAGCACAACCATGGCAATAC 59.178 41.667 13.04 9.15 0.00 1.89
3208 3429 5.047566 AGTATAGCACAACCATGGCAATA 57.952 39.130 13.04 0.00 0.00 1.90
3211 3437 3.016031 CAAGTATAGCACAACCATGGCA 58.984 45.455 13.04 0.00 0.00 4.92
3234 3469 8.847444 TCGTTCTCGTCTTCTTATATTAAACC 57.153 34.615 0.00 0.00 38.33 3.27
3243 3478 5.874895 TCTTCATCGTTCTCGTCTTCTTA 57.125 39.130 0.00 0.00 38.33 2.10
3251 3495 7.513190 AGTTTATTCTTCTTCATCGTTCTCG 57.487 36.000 0.00 0.00 38.55 4.04
3419 3675 7.420800 CACTATGCTTAATCCATTTCCAAGAC 58.579 38.462 0.00 0.00 0.00 3.01
3515 3775 9.971922 AAAGGCAATCTATGTTAAAGCATATTC 57.028 29.630 0.00 0.00 31.74 1.75
3516 3776 9.754382 CAAAGGCAATCTATGTTAAAGCATATT 57.246 29.630 0.00 0.00 31.74 1.28
3517 3777 9.135189 TCAAAGGCAATCTATGTTAAAGCATAT 57.865 29.630 0.00 0.00 31.74 1.78
3518 3778 8.518430 TCAAAGGCAATCTATGTTAAAGCATA 57.482 30.769 0.00 0.00 0.00 3.14
3830 4135 0.739813 GAACGAGCCATACGTGCCTT 60.740 55.000 0.00 0.00 43.16 4.35


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

AutoCloner maintained by Alex Coulton.