Multiple sequence alignment - TraesCS7D01G077600

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 TraesCS7D01G077600 chr7D 100.000 2879 0 0 1 2879 45702437 45705315 0.000000e+00 5317.0
1 TraesCS7D01G077600 chr7D 87.976 499 40 11 1723 2220 45605985 45605506 3.220000e-159 571.0
2 TraesCS7D01G077600 chr7D 78.649 740 95 32 2019 2744 32253028 32252338 1.580000e-117 433.0
3 TraesCS7D01G077600 chr7D 95.333 150 5 2 1 148 414953711 414953562 1.330000e-58 237.0
4 TraesCS7D01G077600 chr7D 92.547 161 9 3 1 160 129880586 129880744 8.030000e-56 228.0
5 TraesCS7D01G077600 chr7A 89.273 2200 121 38 138 2288 47899358 47901491 0.000000e+00 2649.0
6 TraesCS7D01G077600 chr7A 93.586 608 22 7 2283 2879 47901800 47902401 0.000000e+00 891.0
7 TraesCS7D01G077600 chr7A 90.444 450 43 0 1429 1878 47781102 47780653 6.870000e-166 593.0
8 TraesCS7D01G077600 chr7A 79.838 739 89 31 2018 2744 32415365 32414675 4.310000e-133 484.0
9 TraesCS7D01G077600 chr7A 85.841 339 28 13 1882 2219 47780392 47780073 2.750000e-90 342.0
10 TraesCS7D01G077600 chr7A 97.887 142 2 1 1 141 271102152 271102011 7.970000e-61 244.0
11 TraesCS7D01G077600 chr7A 94.702 151 6 2 1 150 175344884 175345033 1.720000e-57 233.0
12 TraesCS7D01G077600 chr4A 88.032 2231 170 54 138 2343 658896462 658898620 0.000000e+00 2551.0
13 TraesCS7D01G077600 chr4A 92.659 1008 58 5 907 1909 658343103 658344099 0.000000e+00 1437.0
14 TraesCS7D01G077600 chr4A 87.778 720 67 12 1428 2142 658108879 658108176 0.000000e+00 822.0
15 TraesCS7D01G077600 chr4A 87.639 720 68 12 1428 2142 658069899 658069196 0.000000e+00 817.0
16 TraesCS7D01G077600 chr4A 76.339 896 113 52 2019 2879 694846976 694847807 3.480000e-104 388.0
17 TraesCS7D01G077600 chr4A 90.826 218 15 3 586 799 658342671 658342887 1.310000e-73 287.0
18 TraesCS7D01G077600 chr4A 95.302 149 5 2 1 148 636344606 636344459 4.800000e-58 235.0
19 TraesCS7D01G077600 chr4A 91.803 61 4 1 806 866 658897136 658897195 1.840000e-12 84.2
20 TraesCS7D01G077600 chrUn 90.055 543 27 13 2339 2879 320963602 320963085 0.000000e+00 678.0
21 TraesCS7D01G077600 chr6D 87.389 563 60 6 1310 1865 9973262 9973820 1.130000e-178 636.0
22 TraesCS7D01G077600 chr6A 95.918 147 4 2 1 145 310959528 310959382 1.330000e-58 237.0
23 TraesCS7D01G077600 chr6A 97.101 138 3 1 1 137 5175045 5174908 6.200000e-57 231.0
24 TraesCS7D01G077600 chr3D 93.038 158 7 3 1 157 142007594 142007440 8.030000e-56 228.0
25 TraesCS7D01G077600 chr3D 92.500 160 8 4 1 159 459402958 459402802 2.890000e-55 226.0


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 TraesCS7D01G077600 chr7D 45702437 45705315 2878 False 5317.0 5317 100.0000 1 2879 1 chr7D.!!$F1 2878
1 TraesCS7D01G077600 chr7D 32252338 32253028 690 True 433.0 433 78.6490 2019 2744 1 chr7D.!!$R1 725
2 TraesCS7D01G077600 chr7A 47899358 47902401 3043 False 1770.0 2649 91.4295 138 2879 2 chr7A.!!$F2 2741
3 TraesCS7D01G077600 chr7A 32414675 32415365 690 True 484.0 484 79.8380 2018 2744 1 chr7A.!!$R1 726
4 TraesCS7D01G077600 chr7A 47780073 47781102 1029 True 467.5 593 88.1425 1429 2219 2 chr7A.!!$R3 790
5 TraesCS7D01G077600 chr4A 658896462 658898620 2158 False 1317.6 2551 89.9175 138 2343 2 chr4A.!!$F3 2205
6 TraesCS7D01G077600 chr4A 658342671 658344099 1428 False 862.0 1437 91.7425 586 1909 2 chr4A.!!$F2 1323
7 TraesCS7D01G077600 chr4A 658108176 658108879 703 True 822.0 822 87.7780 1428 2142 1 chr4A.!!$R3 714
8 TraesCS7D01G077600 chr4A 658069196 658069899 703 True 817.0 817 87.6390 1428 2142 1 chr4A.!!$R2 714
9 TraesCS7D01G077600 chr4A 694846976 694847807 831 False 388.0 388 76.3390 2019 2879 1 chr4A.!!$F1 860
10 TraesCS7D01G077600 chrUn 320963085 320963602 517 True 678.0 678 90.0550 2339 2879 1 chrUn.!!$R1 540
11 TraesCS7D01G077600 chr6D 9973262 9973820 558 False 636.0 636 87.3890 1310 1865 1 chr6D.!!$F1 555

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
177 178 0.321475 TCCAACAGCATGCACATCGA 60.321 50.0 21.98 6.58 42.53 3.59 F
432 435 0.838122 ACCACTTGGCAGCTACTCCT 60.838 55.0 0.00 0.00 39.32 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1441 0.677288 TGGGTACTTGTCGGTGACTG 59.323 55.0 0.0 0.0 33.15 3.51 R
2165 2598 0.975887 TAGTCTGATGTGGTGCTGCA 59.024 50.0 0.0 0.0 0.00 4.41 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 6.599437 ACACTTTGTTTGTCTATGTATTCGC 58.401 36.000 0.00 0.00 0.00 4.70
26 27 6.021596 CACTTTGTTTGTCTATGTATTCGCC 58.978 40.000 0.00 0.00 0.00 5.54
27 28 5.703592 ACTTTGTTTGTCTATGTATTCGCCA 59.296 36.000 0.00 0.00 0.00 5.69
28 29 6.374333 ACTTTGTTTGTCTATGTATTCGCCAT 59.626 34.615 0.00 0.00 0.00 4.40
29 30 5.733226 TGTTTGTCTATGTATTCGCCATG 57.267 39.130 0.00 0.00 0.00 3.66
30 31 5.182487 TGTTTGTCTATGTATTCGCCATGT 58.818 37.500 0.00 0.00 0.00 3.21
31 32 6.342111 TGTTTGTCTATGTATTCGCCATGTA 58.658 36.000 0.00 0.00 0.00 2.29
32 33 6.989759 TGTTTGTCTATGTATTCGCCATGTAT 59.010 34.615 0.00 0.00 0.00 2.29
33 34 7.497579 TGTTTGTCTATGTATTCGCCATGTATT 59.502 33.333 0.00 0.00 0.00 1.89
34 35 8.984764 GTTTGTCTATGTATTCGCCATGTATTA 58.015 33.333 0.00 0.00 0.00 0.98
35 36 9.719355 TTTGTCTATGTATTCGCCATGTATTAT 57.281 29.630 0.00 0.00 0.00 1.28
36 37 8.702163 TGTCTATGTATTCGCCATGTATTATG 57.298 34.615 0.00 0.00 0.00 1.90
37 38 8.311109 TGTCTATGTATTCGCCATGTATTATGT 58.689 33.333 0.00 0.00 0.00 2.29
38 39 9.151471 GTCTATGTATTCGCCATGTATTATGTT 57.849 33.333 0.00 0.00 0.00 2.71
39 40 9.719355 TCTATGTATTCGCCATGTATTATGTTT 57.281 29.630 0.00 0.00 0.00 2.83
40 41 9.973246 CTATGTATTCGCCATGTATTATGTTTC 57.027 33.333 0.00 0.00 0.00 2.78
41 42 7.197071 TGTATTCGCCATGTATTATGTTTCC 57.803 36.000 0.00 0.00 0.00 3.13
42 43 4.804608 TTCGCCATGTATTATGTTTCCG 57.195 40.909 0.00 0.00 0.00 4.30
43 44 3.135225 TCGCCATGTATTATGTTTCCGG 58.865 45.455 0.00 0.00 0.00 5.14
44 45 2.875933 CGCCATGTATTATGTTTCCGGT 59.124 45.455 0.00 0.00 0.00 5.28
45 46 3.314080 CGCCATGTATTATGTTTCCGGTT 59.686 43.478 0.00 0.00 0.00 4.44
46 47 4.512198 CGCCATGTATTATGTTTCCGGTTA 59.488 41.667 0.00 0.00 0.00 2.85
47 48 5.007823 CGCCATGTATTATGTTTCCGGTTAA 59.992 40.000 0.00 0.00 0.00 2.01
48 49 6.293735 CGCCATGTATTATGTTTCCGGTTAAT 60.294 38.462 0.00 1.95 0.00 1.40
49 50 7.095144 CGCCATGTATTATGTTTCCGGTTAATA 60.095 37.037 0.00 0.00 0.00 0.98
50 51 8.019094 GCCATGTATTATGTTTCCGGTTAATAC 58.981 37.037 0.00 12.47 37.73 1.89
51 52 9.058174 CCATGTATTATGTTTCCGGTTAATACA 57.942 33.333 22.83 22.83 44.85 2.29
59 60 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
60 61 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
61 62 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
62 63 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
63 64 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
64 65 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
65 66 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
66 67 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
132 133 9.959721 TTATTATTGTCTCTAGGGCATATTTCC 57.040 33.333 0.00 0.00 0.00 3.13
133 134 7.633018 TTATTGTCTCTAGGGCATATTTCCT 57.367 36.000 0.00 0.00 37.18 3.36
134 135 5.975988 TTGTCTCTAGGGCATATTTCCTT 57.024 39.130 0.00 0.00 34.75 3.36
135 136 5.552870 TGTCTCTAGGGCATATTTCCTTC 57.447 43.478 0.00 0.00 34.75 3.46
136 137 4.968719 TGTCTCTAGGGCATATTTCCTTCA 59.031 41.667 0.00 0.00 34.75 3.02
177 178 0.321475 TCCAACAGCATGCACATCGA 60.321 50.000 21.98 6.58 42.53 3.59
181 182 1.346197 CAGCATGCACATCGACGTC 59.654 57.895 21.98 5.18 0.00 4.34
284 285 1.153745 CCGCACGAAGAAGAGGAGG 60.154 63.158 0.00 0.00 0.00 4.30
285 286 1.595993 CCGCACGAAGAAGAGGAGGA 61.596 60.000 0.00 0.00 0.00 3.71
287 288 1.178276 GCACGAAGAAGAGGAGGAGA 58.822 55.000 0.00 0.00 0.00 3.71
288 289 1.135228 GCACGAAGAAGAGGAGGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
289 290 2.163509 CACGAAGAAGAGGAGGAGACA 58.836 52.381 0.00 0.00 0.00 3.41
326 329 2.625790 GAGAGGAAGTGCGACCAGATAT 59.374 50.000 0.00 0.00 0.00 1.63
346 349 2.604046 TTTCTAGGCCTCGCTTCATC 57.396 50.000 9.68 0.00 0.00 2.92
413 416 2.897969 GCCGGACCTTAGATAATGAGGA 59.102 50.000 5.05 0.00 36.79 3.71
432 435 0.838122 ACCACTTGGCAGCTACTCCT 60.838 55.000 0.00 0.00 39.32 3.69
439 442 2.191400 TGGCAGCTACTCCTGAAAGAT 58.809 47.619 0.00 0.00 34.07 2.40
448 451 8.363390 CAGCTACTCCTGAAAGATATGTGAATA 58.637 37.037 0.00 0.00 34.07 1.75
477 480 2.963320 GAACGGTTCACCACGCGT 60.963 61.111 15.70 5.58 34.82 6.01
496 499 2.113986 AGCAGCCAAAACGGAGCT 59.886 55.556 0.00 0.00 41.35 4.09
523 526 2.501223 AAGAATCGAGCGGCCGAACA 62.501 55.000 33.48 9.45 42.22 3.18
574 579 2.859032 GCGGGTAGTCTAGCGAGATTTG 60.859 54.545 0.00 0.00 33.14 2.32
584 592 6.038492 AGTCTAGCGAGATTTGTAGGTTAGAC 59.962 42.308 0.00 5.55 39.92 2.59
655 668 9.880157 AGCTTATACTAAACGACTAAAATCCAA 57.120 29.630 0.00 0.00 0.00 3.53
694 708 8.761497 CGATATGTTGACTAAATTCCGTATGTT 58.239 33.333 0.00 0.00 0.00 2.71
810 865 2.490903 GACGTCTGGGTAAAGCTCTACA 59.509 50.000 8.70 0.00 0.00 2.74
887 1027 1.679944 CCATGACCGAGGCAATCTGTT 60.680 52.381 0.00 0.00 0.00 3.16
895 1035 2.158900 CGAGGCAATCTGTTGGGAGTAT 60.159 50.000 0.00 0.00 35.83 2.12
926 1066 5.843673 AGCATTCTCATCGGTCGATATAT 57.156 39.130 5.50 0.00 32.93 0.86
927 1067 6.944234 AGCATTCTCATCGGTCGATATATA 57.056 37.500 5.50 0.00 32.93 0.86
928 1068 7.517614 AGCATTCTCATCGGTCGATATATAT 57.482 36.000 5.50 0.00 32.93 0.86
929 1069 8.622948 AGCATTCTCATCGGTCGATATATATA 57.377 34.615 5.50 0.00 32.93 0.86
943 1083 2.736144 TATATAAACCCAGAGCGCCG 57.264 50.000 2.29 0.00 0.00 6.46
1027 1173 3.793801 GCTCGTATTCTCTGATGAAGCGT 60.794 47.826 0.00 0.00 33.42 5.07
1136 1282 2.607750 AAGGGAGGAGGAGCGCAA 60.608 61.111 11.47 0.00 0.00 4.85
1146 1292 0.886490 AGGAGCGCAACAAGAACCTG 60.886 55.000 11.47 0.00 0.00 4.00
1150 1296 1.724582 GCGCAACAAGAACCTGGTGT 61.725 55.000 0.30 0.00 36.33 4.16
1234 1385 4.274950 CCGCCATTTTCACGGTATAAGAAT 59.725 41.667 0.00 0.00 42.01 2.40
1238 1393 7.132863 GCCATTTTCACGGTATAAGAATTCTC 58.867 38.462 8.78 0.00 0.00 2.87
1298 1453 3.530265 AACTTACACAGTCACCGACAA 57.470 42.857 0.00 0.00 32.94 3.18
1304 1459 0.677842 ACAGTCACCGACAAGTACCC 59.322 55.000 0.00 0.00 34.60 3.69
1307 1462 0.677842 GTCACCGACAAGTACCCACT 59.322 55.000 0.00 0.00 36.19 4.00
1411 1569 1.078214 CAGATCGTGGTGGGCATGT 60.078 57.895 0.00 0.00 0.00 3.21
1414 1572 2.535485 GATCGTGGTGGGCATGTCCA 62.535 60.000 17.02 17.02 36.21 4.02
1524 1682 4.078516 GTGCCCTACGCCTTCGGT 62.079 66.667 0.00 0.00 40.69 4.69
1527 1685 4.077184 CCCTACGCCTTCGGTGCA 62.077 66.667 0.00 0.00 40.69 4.57
1568 1726 3.141488 CCTCCTCCTCGACACCGG 61.141 72.222 0.00 0.00 36.24 5.28
1717 1875 1.134521 TCTGCTTCTGGAACAACACGT 60.135 47.619 0.00 0.00 38.70 4.49
1894 2313 8.686334 CCCTTAACTAAGCATATTGTGTTTCAT 58.314 33.333 0.00 0.00 33.07 2.57
1960 2380 5.991933 ACCAGGATGCTACTATACATCAG 57.008 43.478 0.00 0.00 43.64 2.90
2062 2491 3.620374 TCGAGCATCTGAGCAATTTCTTC 59.380 43.478 0.00 0.00 36.85 2.87
2064 2493 4.094590 CGAGCATCTGAGCAATTTCTTCTT 59.905 41.667 0.00 0.00 36.85 2.52
2072 2501 7.365741 TCTGAGCAATTTCTTCTTGATGAAAC 58.634 34.615 11.95 3.31 35.40 2.78
2102 2533 0.600057 CAAGGCCTGGCAGAGAAAAC 59.400 55.000 22.05 0.00 0.00 2.43
2108 2540 2.297033 GCCTGGCAGAGAAAACAATTGA 59.703 45.455 17.94 0.00 0.00 2.57
2165 2598 6.959639 ACACCTTGATTTTCTGTACAACAT 57.040 33.333 0.00 0.00 0.00 2.71
2166 2599 6.738114 ACACCTTGATTTTCTGTACAACATG 58.262 36.000 0.00 0.00 0.00 3.21
2167 2600 5.630680 CACCTTGATTTTCTGTACAACATGC 59.369 40.000 0.00 0.00 0.00 4.06
2168 2601 5.301551 ACCTTGATTTTCTGTACAACATGCA 59.698 36.000 0.00 0.00 0.00 3.96
2219 2663 6.404513 GCTTCATCTTCTGCAAGCTTCTATTT 60.405 38.462 0.00 0.00 36.20 1.40
2224 2668 4.558226 TCTGCAAGCTTCTATTTGGAGA 57.442 40.909 0.00 0.00 45.51 3.71
2268 2713 3.251479 ACATCTGCTTCATTCGTGCTA 57.749 42.857 0.00 0.00 0.00 3.49
2281 2726 4.932268 TTCGTGCTAACCGGATTAAAAG 57.068 40.909 9.46 0.00 0.00 2.27
2321 3079 7.012327 GCTAATATTCATAGGCAAGTTGTGTCA 59.988 37.037 4.48 0.00 32.63 3.58
2375 3133 8.746530 AGAAATCAGTGTTGCAATTCAGATTAT 58.253 29.630 17.51 11.02 0.00 1.28
2388 3154 3.198068 TCAGATTATCTTGTCGGCTTGC 58.802 45.455 0.00 0.00 0.00 4.01
2451 3222 3.757493 GTGTACCCCAGATCCGAGTATAG 59.243 52.174 0.00 0.00 0.00 1.31
2457 3228 4.642885 CCCCAGATCCGAGTATAGAAGATC 59.357 50.000 0.00 0.00 34.79 2.75
2458 3229 4.334203 CCCAGATCCGAGTATAGAAGATCG 59.666 50.000 0.00 0.00 38.67 3.69
2459 3230 5.179533 CCAGATCCGAGTATAGAAGATCGA 58.820 45.833 0.00 0.00 38.67 3.59
2460 3231 5.293324 CCAGATCCGAGTATAGAAGATCGAG 59.707 48.000 0.00 0.00 38.67 4.04
2480 3251 5.809562 TCGAGAGAAAGAATGAAATCTCAGC 59.190 40.000 4.65 0.00 40.57 4.26
2516 3289 7.531716 TGAACGAAACCATCATTTATACAACC 58.468 34.615 0.00 0.00 0.00 3.77
2522 3295 9.730420 GAAACCATCATTTATACAACCATGTAC 57.270 33.333 0.00 0.00 44.47 2.90
2583 3356 4.386049 ACGAAAGATCACAGTAAGAAAGCG 59.614 41.667 0.00 0.00 0.00 4.68
2618 3391 4.577875 AGAGAAGATGCAGACCAAGAAAG 58.422 43.478 0.00 0.00 0.00 2.62
2752 3528 9.929180 TGAATGCAGTACAATATAGAGATTACC 57.071 33.333 0.00 0.00 0.00 2.85
2755 3531 7.817641 TGCAGTACAATATAGAGATTACCTCG 58.182 38.462 0.00 0.00 46.49 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.736853 GCGAATACATAGACAAACAAAGTGTC 59.263 38.462 0.00 0.00 44.75 3.67
1 2 6.348213 GGCGAATACATAGACAAACAAAGTGT 60.348 38.462 0.00 0.00 0.00 3.55
2 3 6.021596 GGCGAATACATAGACAAACAAAGTG 58.978 40.000 0.00 0.00 0.00 3.16
3 4 5.703592 TGGCGAATACATAGACAAACAAAGT 59.296 36.000 0.00 0.00 0.00 2.66
4 5 6.176975 TGGCGAATACATAGACAAACAAAG 57.823 37.500 0.00 0.00 0.00 2.77
5 6 6.150307 ACATGGCGAATACATAGACAAACAAA 59.850 34.615 0.00 0.00 0.00 2.83
6 7 5.645929 ACATGGCGAATACATAGACAAACAA 59.354 36.000 0.00 0.00 0.00 2.83
7 8 5.182487 ACATGGCGAATACATAGACAAACA 58.818 37.500 0.00 0.00 0.00 2.83
8 9 5.734855 ACATGGCGAATACATAGACAAAC 57.265 39.130 0.00 0.00 0.00 2.93
9 10 9.719355 ATAATACATGGCGAATACATAGACAAA 57.281 29.630 0.00 0.00 0.00 2.83
10 11 9.150348 CATAATACATGGCGAATACATAGACAA 57.850 33.333 0.00 0.00 0.00 3.18
11 12 8.311109 ACATAATACATGGCGAATACATAGACA 58.689 33.333 0.00 0.00 0.00 3.41
12 13 8.703604 ACATAATACATGGCGAATACATAGAC 57.296 34.615 0.00 0.00 0.00 2.59
13 14 9.719355 AAACATAATACATGGCGAATACATAGA 57.281 29.630 0.00 0.00 0.00 1.98
14 15 9.973246 GAAACATAATACATGGCGAATACATAG 57.027 33.333 0.00 0.00 0.00 2.23
15 16 8.941977 GGAAACATAATACATGGCGAATACATA 58.058 33.333 0.00 0.00 0.00 2.29
16 17 7.360861 CGGAAACATAATACATGGCGAATACAT 60.361 37.037 0.00 0.00 0.00 2.29
17 18 6.073494 CGGAAACATAATACATGGCGAATACA 60.073 38.462 0.00 0.00 0.00 2.29
18 19 6.304126 CGGAAACATAATACATGGCGAATAC 58.696 40.000 0.00 0.00 0.00 1.89
19 20 5.410132 CCGGAAACATAATACATGGCGAATA 59.590 40.000 0.00 0.00 0.00 1.75
20 21 4.215399 CCGGAAACATAATACATGGCGAAT 59.785 41.667 0.00 0.00 0.00 3.34
21 22 3.562141 CCGGAAACATAATACATGGCGAA 59.438 43.478 0.00 0.00 0.00 4.70
22 23 3.135225 CCGGAAACATAATACATGGCGA 58.865 45.455 0.00 0.00 0.00 5.54
23 24 2.875933 ACCGGAAACATAATACATGGCG 59.124 45.455 9.46 0.00 0.00 5.69
24 25 4.911514 AACCGGAAACATAATACATGGC 57.088 40.909 9.46 0.00 0.00 4.40
25 26 9.058174 TGTATTAACCGGAAACATAATACATGG 57.942 33.333 22.31 0.00 42.13 3.66
33 34 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
34 35 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
35 36 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
36 37 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
37 38 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
38 39 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
39 40 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
40 41 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
106 107 9.959721 GGAAATATGCCCTAGAGACAATAATAA 57.040 33.333 0.00 0.00 0.00 1.40
107 108 9.338968 AGGAAATATGCCCTAGAGACAATAATA 57.661 33.333 0.00 0.00 0.00 0.98
108 109 8.224620 AGGAAATATGCCCTAGAGACAATAAT 57.775 34.615 0.00 0.00 0.00 1.28
109 110 7.633018 AGGAAATATGCCCTAGAGACAATAA 57.367 36.000 0.00 0.00 0.00 1.40
110 111 7.292356 TGAAGGAAATATGCCCTAGAGACAATA 59.708 37.037 0.00 0.00 31.36 1.90
111 112 6.101734 TGAAGGAAATATGCCCTAGAGACAAT 59.898 38.462 0.00 0.00 31.36 2.71
112 113 5.428457 TGAAGGAAATATGCCCTAGAGACAA 59.572 40.000 0.00 0.00 31.36 3.18
113 114 4.968719 TGAAGGAAATATGCCCTAGAGACA 59.031 41.667 0.00 0.00 31.36 3.41
114 115 5.552870 TGAAGGAAATATGCCCTAGAGAC 57.447 43.478 0.00 0.00 31.36 3.36
115 116 6.575244 TTTGAAGGAAATATGCCCTAGAGA 57.425 37.500 0.00 0.00 31.36 3.10
116 117 6.830838 AGTTTTGAAGGAAATATGCCCTAGAG 59.169 38.462 0.00 0.00 31.36 2.43
117 118 6.603201 CAGTTTTGAAGGAAATATGCCCTAGA 59.397 38.462 0.00 0.00 31.36 2.43
118 119 6.603201 TCAGTTTTGAAGGAAATATGCCCTAG 59.397 38.462 0.00 0.00 31.36 3.02
119 120 6.489603 TCAGTTTTGAAGGAAATATGCCCTA 58.510 36.000 0.00 0.00 31.36 3.53
120 121 5.332743 TCAGTTTTGAAGGAAATATGCCCT 58.667 37.500 0.00 0.00 0.00 5.19
121 122 5.659440 TCAGTTTTGAAGGAAATATGCCC 57.341 39.130 0.00 0.00 0.00 5.36
177 178 0.767060 ACAAGGGAAAGGGAGGACGT 60.767 55.000 0.00 0.00 0.00 4.34
181 182 2.519013 CAAGAACAAGGGAAAGGGAGG 58.481 52.381 0.00 0.00 0.00 4.30
284 285 1.268283 CCTCCCTCCCACCTTGTCTC 61.268 65.000 0.00 0.00 0.00 3.36
285 286 1.229658 CCTCCCTCCCACCTTGTCT 60.230 63.158 0.00 0.00 0.00 3.41
287 288 1.229658 CTCCTCCCTCCCACCTTGT 60.230 63.158 0.00 0.00 0.00 3.16
288 289 0.980231 CTCTCCTCCCTCCCACCTTG 60.980 65.000 0.00 0.00 0.00 3.61
289 290 1.156322 TCTCTCCTCCCTCCCACCTT 61.156 60.000 0.00 0.00 0.00 3.50
326 329 2.738643 CGATGAAGCGAGGCCTAGAAAA 60.739 50.000 18.16 0.00 0.00 2.29
387 390 4.039973 TCATTATCTAAGGTCCGGCGAATT 59.960 41.667 9.30 0.00 0.00 2.17
392 395 2.897969 TCCTCATTATCTAAGGTCCGGC 59.102 50.000 0.00 0.00 0.00 6.13
413 416 0.838122 AGGAGTAGCTGCCAAGTGGT 60.838 55.000 0.00 0.00 37.57 4.16
463 466 3.403057 CTGACGCGTGGTGAACCG 61.403 66.667 20.70 0.00 39.43 4.44
477 480 2.260869 GCTCCGTTTTGGCTGCTGA 61.261 57.895 0.00 0.00 37.80 4.26
496 499 2.888594 CCGCTCGATTCTTTTCCTGTA 58.111 47.619 0.00 0.00 0.00 2.74
574 579 5.131594 ACTCAAAACCTCGTCTAACCTAC 57.868 43.478 0.00 0.00 0.00 3.18
584 592 2.303175 TCCCCAAAACTCAAAACCTCG 58.697 47.619 0.00 0.00 0.00 4.63
655 668 3.536956 ACATATCGGTCGTTCCATGTT 57.463 42.857 0.00 0.00 29.60 2.71
694 708 1.144276 TTCAAGCCGGACGTGTTCA 59.856 52.632 5.05 0.00 0.00 3.18
820 955 7.584987 TCATCGGACTCTTGAATTTTTCTTTC 58.415 34.615 0.00 0.00 0.00 2.62
825 960 8.335532 TGTAATCATCGGACTCTTGAATTTTT 57.664 30.769 0.00 0.00 0.00 1.94
887 1027 3.040655 TGCTAGCTGGTTATACTCCCA 57.959 47.619 17.23 0.00 0.00 4.37
895 1035 3.243873 CCGATGAGAATGCTAGCTGGTTA 60.244 47.826 17.23 0.00 0.00 2.85
926 1066 1.332144 ACCGGCGCTCTGGGTTTATA 61.332 55.000 7.64 0.00 43.28 0.98
927 1067 2.189521 CCGGCGCTCTGGGTTTAT 59.810 61.111 7.64 0.00 35.00 1.40
928 1068 3.315949 ACCGGCGCTCTGGGTTTA 61.316 61.111 7.64 0.00 43.28 2.01
943 1083 1.893801 AGCAGTGTCTGGTAGTACACC 59.106 52.381 2.06 1.46 45.70 4.16
960 1103 6.932400 TAGTAGTAACTTTGCTTTTGCTAGCA 59.068 34.615 14.93 14.93 41.96 3.49
977 1120 6.866010 TGTCACTGTTCGTTCTAGTAGTAA 57.134 37.500 0.00 0.00 0.00 2.24
1027 1173 2.034999 GGGGACGACAATGGCCAA 59.965 61.111 10.96 0.00 0.00 4.52
1136 1282 1.750682 GCTTGGACACCAGGTTCTTGT 60.751 52.381 0.00 0.00 33.81 3.16
1286 1441 0.677288 TGGGTACTTGTCGGTGACTG 59.323 55.000 0.00 0.00 33.15 3.51
1298 1453 1.185618 TCGAAGCTGCAGTGGGTACT 61.186 55.000 16.64 0.00 37.75 2.73
1304 1459 3.485431 CGCCTCGAAGCTGCAGTG 61.485 66.667 16.64 3.33 0.00 3.66
1307 1462 2.029288 CTTTCGCCTCGAAGCTGCA 61.029 57.895 4.21 0.00 46.43 4.41
1414 1572 4.415150 CTGCCACCCGTCCAGCAT 62.415 66.667 0.00 0.00 34.16 3.79
1524 1682 1.149627 GGGGTGGTTGTACTGTGCA 59.850 57.895 0.00 0.00 0.00 4.57
1527 1685 1.448497 CACGGGGTGGTTGTACTGT 59.552 57.895 0.00 0.00 0.00 3.55
1717 1875 1.363443 GGTGGACGTCGTGGTACAA 59.637 57.895 9.92 0.00 44.16 2.41
1850 2011 4.776322 CTTCCATGGGCCGCACGA 62.776 66.667 13.02 0.00 0.00 4.35
1915 2335 4.641396 TGCATGAGGGAAGGATAAATACG 58.359 43.478 0.00 0.00 0.00 3.06
1980 2400 8.082672 TGCACATGCTCCTATATATATGAACT 57.917 34.615 5.44 0.00 42.66 3.01
2062 2491 3.057104 TGAAGCATGCCAGTTTCATCAAG 60.057 43.478 15.66 0.00 34.46 3.02
2064 2493 2.516906 TGAAGCATGCCAGTTTCATCA 58.483 42.857 15.66 3.72 34.46 3.07
2072 2501 1.681327 AGGCCTTGAAGCATGCCAG 60.681 57.895 15.66 5.44 46.45 4.85
2165 2598 0.975887 TAGTCTGATGTGGTGCTGCA 59.024 50.000 0.00 0.00 0.00 4.41
2166 2599 1.205655 TCTAGTCTGATGTGGTGCTGC 59.794 52.381 0.00 0.00 0.00 5.25
2167 2600 3.815856 ATCTAGTCTGATGTGGTGCTG 57.184 47.619 0.00 0.00 0.00 4.41
2168 2601 4.541705 ACTATCTAGTCTGATGTGGTGCT 58.458 43.478 0.00 0.00 0.00 4.40
2224 2668 7.987458 TGTTTTCTGACTTTTGTAGAGACAGAT 59.013 33.333 7.02 0.00 36.76 2.90
2321 3079 1.542915 GCATGCCAGAGTTTCACACAT 59.457 47.619 6.36 0.00 0.00 3.21
2425 3196 1.033574 CGGATCTGGGGTACACTCTC 58.966 60.000 0.00 0.00 0.00 3.20
2451 3222 8.647143 AGATTTCATTCTTTCTCTCGATCTTC 57.353 34.615 0.00 0.00 0.00 2.87
2457 3228 5.579904 TGCTGAGATTTCATTCTTTCTCTCG 59.420 40.000 0.00 0.00 36.43 4.04
2458 3229 6.457257 GCTGCTGAGATTTCATTCTTTCTCTC 60.457 42.308 0.00 0.00 36.43 3.20
2459 3230 5.354792 GCTGCTGAGATTTCATTCTTTCTCT 59.645 40.000 0.00 0.00 36.43 3.10
2460 3231 5.123502 TGCTGCTGAGATTTCATTCTTTCTC 59.876 40.000 0.00 0.00 36.09 2.87
2463 3234 5.652891 AGATGCTGCTGAGATTTCATTCTTT 59.347 36.000 0.00 0.00 31.68 2.52
2480 3251 4.183865 TGGTTTCGTTCAGATAGATGCTG 58.816 43.478 0.00 0.00 34.71 4.41
2516 3289 6.313905 ACTCTTTCGCTTTAATGGAGTACATG 59.686 38.462 0.00 0.00 40.44 3.21
2522 3295 6.487689 AAGAACTCTTTCGCTTTAATGGAG 57.512 37.500 0.00 0.00 36.78 3.86
2583 3356 8.200792 TCTGCATCTTCTCTTATTTACTTCTCC 58.799 37.037 0.00 0.00 0.00 3.71
2752 3528 8.882415 TTAGTATCCCTTACAAAAATAGCGAG 57.118 34.615 0.00 0.00 32.87 5.03


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

AutoCloner maintained by Alex Coulton.