Multiple sequence alignment - TraesCS1A01G419700

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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 TraesCS1A01G419700 chr1A 100.000 2400 0 0 1 2400 576492867 576490468 0.000000e+00 4433.0
1 TraesCS1A01G419700 chr1A 86.970 1274 98 32 867 2122 576561493 576562716 0.000000e+00 1371.0
2 TraesCS1A01G419700 chr1A 87.259 518 45 10 301 813 576560968 576561469 3.300000e-159 571.0
3 TraesCS1A01G419700 chr1A 100.000 221 0 0 2727 2947 576490141 576489921 2.730000e-110 409.0
4 TraesCS1A01G419700 chr1B 95.678 1018 36 5 989 1999 668182985 668184001 0.000000e+00 1629.0
5 TraesCS1A01G419700 chr1B 90.435 1035 89 6 974 1999 668200043 668201076 0.000000e+00 1354.0
6 TraesCS1A01G419700 chr1B 84.881 1131 100 27 880 1999 668186305 668187375 0.000000e+00 1075.0
7 TraesCS1A01G419700 chr1B 87.352 593 58 13 49 627 668199271 668199860 0.000000e+00 664.0
8 TraesCS1A01G419700 chr1B 82.812 704 93 20 1306 1999 668429802 668429117 3.250000e-169 604.0
9 TraesCS1A01G419700 chr1B 85.219 548 52 16 301 838 668185782 668186310 1.200000e-148 536.0
10 TraesCS1A01G419700 chr1B 83.738 535 56 16 208 718 668182176 668182703 7.390000e-131 477.0
11 TraesCS1A01G419700 chr1B 81.185 574 55 28 999 1544 668540328 668539780 2.110000e-111 412.0
12 TraesCS1A01G419700 chr1B 92.453 212 9 5 1942 2152 668184263 668184468 2.220000e-76 296.0
13 TraesCS1A01G419700 chr1B 83.273 275 41 4 1695 1967 668545152 668544881 6.310000e-62 248.0
14 TraesCS1A01G419700 chr1B 91.919 99 7 1 879 976 668199874 668199972 1.420000e-28 137.0
15 TraesCS1A01G419700 chr1B 98.630 73 1 0 879 951 668182910 668182982 2.380000e-26 130.0
16 TraesCS1A01G419700 chr1D 89.695 1048 80 13 974 1999 478755723 478754682 0.000000e+00 1312.0
17 TraesCS1A01G419700 chr1D 88.856 1005 91 13 974 1963 480155560 480156558 0.000000e+00 1216.0
18 TraesCS1A01G419700 chr1D 91.573 356 19 4 868 1213 480063555 480063909 5.710000e-132 481.0
19 TraesCS1A01G419700 chr1D 88.354 395 35 5 1414 1798 480076418 480076811 5.750000e-127 464.0
20 TraesCS1A01G419700 chr1D 86.936 421 43 8 303 718 478756503 478756090 2.070000e-126 462.0
21 TraesCS1A01G419700 chr1D 87.887 388 25 3 867 1254 480075580 480075945 1.250000e-118 436.0
22 TraesCS1A01G419700 chr1D 93.033 244 17 0 2151 2394 474094051 474094294 1.000000e-94 357.0
23 TraesCS1A01G419700 chr1D 92.000 250 20 0 2151 2400 15758620 15758371 4.670000e-93 351.0
24 TraesCS1A01G419700 chr1D 92.000 250 19 1 2151 2400 457574565 457574317 1.680000e-92 350.0
25 TraesCS1A01G419700 chr1D 94.570 221 6 3 2727 2947 15758330 15758116 1.310000e-88 337.0
26 TraesCS1A01G419700 chr1D 84.424 321 35 6 504 823 480075264 480075570 4.770000e-78 302.0
27 TraesCS1A01G419700 chr1D 90.404 198 19 0 1802 1999 480099280 480099477 8.100000e-66 261.0
28 TraesCS1A01G419700 chr1D 89.655 203 13 5 1212 1408 480075935 480076135 4.880000e-63 252.0
29 TraesCS1A01G419700 chr1D 85.782 211 23 3 301 506 480064117 480064325 1.780000e-52 217.0
30 TraesCS1A01G419700 chr1D 92.437 119 5 1 709 823 478756032 478755914 1.820000e-37 167.0
31 TraesCS1A01G419700 chr1D 87.970 133 10 3 701 828 480155264 480155395 5.090000e-33 152.0
32 TraesCS1A01G419700 chr1D 90.476 105 10 0 709 813 478710495 478710391 3.960000e-29 139.0
33 TraesCS1A01G419700 chr1D 91.919 99 7 1 879 976 478755892 478755794 1.420000e-28 137.0
34 TraesCS1A01G419700 chr1D 85.385 130 17 1 321 450 480063370 480063497 1.840000e-27 134.0
35 TraesCS1A01G419700 chr1D 91.753 97 5 1 880 976 480155395 480155488 6.630000e-27 132.0
36 TraesCS1A01G419700 chr7D 97.285 221 6 0 2727 2947 629770462 629770242 2.770000e-100 375.0
37 TraesCS1A01G419700 chr7D 92.308 247 19 0 2151 2397 141204075 141204321 4.670000e-93 351.0
38 TraesCS1A01G419700 chr7A 96.380 221 8 0 2727 2947 486874286 486874506 6.000000e-97 364.0
39 TraesCS1A01G419700 chr6D 92.126 254 20 0 2147 2400 12394887 12394634 2.790000e-95 359.0
40 TraesCS1A01G419700 chr6D 92.000 250 20 0 2148 2397 38652862 38653111 4.670000e-93 351.0
41 TraesCS1A01G419700 chr6D 95.455 220 4 2 2728 2947 316822276 316822063 2.170000e-91 346.0
42 TraesCS1A01G419700 chr6D 95.735 211 9 0 2737 2947 38648167 38648377 1.010000e-89 340.0
43 TraesCS1A01G419700 chr6D 94.118 221 13 0 2727 2947 38653161 38653381 1.310000e-88 337.0
44 TraesCS1A01G419700 chr4D 92.430 251 18 1 2148 2397 501979682 501979932 1.000000e-94 357.0
45 TraesCS1A01G419700 chr4D 91.633 251 21 0 2147 2397 449793585 449793835 6.050000e-92 348.0
46 TraesCS1A01G419700 chr4D 94.118 221 7 3 2727 2947 449793865 449794079 6.090000e-87 331.0
47 TraesCS1A01G419700 chr3D 92.308 247 19 0 2151 2397 20061385 20061631 4.670000e-93 351.0
48 TraesCS1A01G419700 chr3D 94.118 221 13 0 2727 2947 569004508 569004288 1.310000e-88 337.0
49 TraesCS1A01G419700 chr3A 94.884 215 11 0 2727 2941 48967343 48967557 1.310000e-88 337.0
50 TraesCS1A01G419700 chr2D 100.000 30 0 0 208 237 333283040 333283011 4.100000e-04 56.5
51 TraesCS1A01G419700 chr5B 100.000 28 0 0 539 566 680544589 680544562 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G419700 chr1A 576489921 576492867 2946 True 2421.000000 4433 100.000000 1 2947 2 chr1A.!!$R1 2946
1 TraesCS1A01G419700 chr1A 576560968 576562716 1748 False 971.000000 1371 87.114500 301 2122 2 chr1A.!!$F1 1821
2 TraesCS1A01G419700 chr1B 668199271 668201076 1805 False 718.333333 1354 89.902000 49 1999 3 chr1B.!!$F2 1950
3 TraesCS1A01G419700 chr1B 668182176 668187375 5199 False 690.500000 1629 90.099833 208 2152 6 chr1B.!!$F1 1944
4 TraesCS1A01G419700 chr1B 668429117 668429802 685 True 604.000000 604 82.812000 1306 1999 1 chr1B.!!$R1 693
5 TraesCS1A01G419700 chr1B 668539780 668540328 548 True 412.000000 412 81.185000 999 1544 1 chr1B.!!$R2 545
6 TraesCS1A01G419700 chr1D 478754682 478756503 1821 True 519.500000 1312 90.246750 303 1999 4 chr1D.!!$R4 1696
7 TraesCS1A01G419700 chr1D 480155264 480156558 1294 False 500.000000 1216 89.526333 701 1963 3 chr1D.!!$F5 1262
8 TraesCS1A01G419700 chr1D 480075264 480076811 1547 False 363.500000 464 87.580000 504 1798 4 chr1D.!!$F4 1294
9 TraesCS1A01G419700 chr1D 15758116 15758620 504 True 344.000000 351 93.285000 2151 2947 2 chr1D.!!$R3 796
10 TraesCS1A01G419700 chr1D 480063370 480064325 955 False 277.333333 481 87.580000 301 1213 3 chr1D.!!$F3 912
11 TraesCS1A01G419700 chr6D 38652862 38653381 519 False 344.000000 351 93.059000 2148 2947 2 chr6D.!!$F2 799

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
153 154 0.251073 AAGGGCCAAATTGCTCATGC 59.749 50.0 6.18 0.0 32.74 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 3168 0.798159 GTGCGTTCATGTCAGATGCA 59.202 50.0 0.0 0.0 0.0 3.96 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
24 25 7.692460 AGGATGTATATGTATTGCCATGTTG 57.308 36.000 0.00 0.00 0.00 3.33
25 26 7.460910 AGGATGTATATGTATTGCCATGTTGA 58.539 34.615 0.00 0.00 0.00 3.18
26 27 8.111545 AGGATGTATATGTATTGCCATGTTGAT 58.888 33.333 0.00 0.00 0.00 2.57
27 28 8.400947 GGATGTATATGTATTGCCATGTTGATC 58.599 37.037 0.00 0.00 0.00 2.92
28 29 7.363205 TGTATATGTATTGCCATGTTGATCG 57.637 36.000 0.00 0.00 0.00 3.69
29 30 7.158021 TGTATATGTATTGCCATGTTGATCGA 58.842 34.615 0.00 0.00 0.00 3.59
30 31 6.732531 ATATGTATTGCCATGTTGATCGAG 57.267 37.500 0.00 0.00 0.00 4.04
31 32 3.872696 TGTATTGCCATGTTGATCGAGT 58.127 40.909 0.00 0.00 0.00 4.18
32 33 4.260985 TGTATTGCCATGTTGATCGAGTT 58.739 39.130 0.00 0.00 0.00 3.01
33 34 4.699735 TGTATTGCCATGTTGATCGAGTTT 59.300 37.500 0.00 0.00 0.00 2.66
34 35 3.557577 TTGCCATGTTGATCGAGTTTG 57.442 42.857 0.00 0.00 0.00 2.93
35 36 1.199789 TGCCATGTTGATCGAGTTTGC 59.800 47.619 0.00 0.00 0.00 3.68
36 37 1.199789 GCCATGTTGATCGAGTTTGCA 59.800 47.619 0.00 0.00 0.00 4.08
37 38 2.351641 GCCATGTTGATCGAGTTTGCAA 60.352 45.455 0.00 0.00 0.00 4.08
38 39 3.856638 GCCATGTTGATCGAGTTTGCAAA 60.857 43.478 8.05 8.05 0.00 3.68
39 40 4.487948 CCATGTTGATCGAGTTTGCAAAT 58.512 39.130 16.21 4.49 0.00 2.32
40 41 4.925054 CCATGTTGATCGAGTTTGCAAATT 59.075 37.500 16.21 11.56 0.00 1.82
41 42 6.092092 CCATGTTGATCGAGTTTGCAAATTA 58.908 36.000 16.21 0.00 0.00 1.40
42 43 6.033831 CCATGTTGATCGAGTTTGCAAATTAC 59.966 38.462 16.21 3.08 0.00 1.89
43 44 5.457140 TGTTGATCGAGTTTGCAAATTACC 58.543 37.500 16.21 2.00 0.00 2.85
44 45 5.240623 TGTTGATCGAGTTTGCAAATTACCT 59.759 36.000 16.21 7.47 0.00 3.08
45 46 5.957842 TGATCGAGTTTGCAAATTACCTT 57.042 34.783 16.21 0.00 0.00 3.50
46 47 5.698832 TGATCGAGTTTGCAAATTACCTTG 58.301 37.500 16.21 11.28 0.00 3.61
47 48 5.240623 TGATCGAGTTTGCAAATTACCTTGT 59.759 36.000 16.21 3.05 0.00 3.16
50 51 6.607689 TCGAGTTTGCAAATTACCTTGTATG 58.392 36.000 16.21 0.00 0.00 2.39
58 59 6.318648 TGCAAATTACCTTGTATGGAGATGAC 59.681 38.462 0.00 0.00 0.00 3.06
62 63 1.138859 CCTTGTATGGAGATGACCGCA 59.861 52.381 0.00 0.00 0.00 5.69
74 75 3.256631 AGATGACCGCAAAAGCAAATCTT 59.743 39.130 0.00 0.00 36.34 2.40
84 85 5.220378 GCAAAAGCAAATCTTGTTGTTTCGA 60.220 36.000 0.00 0.00 31.60 3.71
97 98 4.202101 TGTTGTTTCGATGAGGCAAACAAT 60.202 37.500 11.28 0.00 46.36 2.71
107 108 5.987777 TGAGGCAAACAATTTTCATGTTG 57.012 34.783 0.00 0.00 39.98 3.33
108 109 5.668471 TGAGGCAAACAATTTTCATGTTGA 58.332 33.333 1.16 0.00 39.98 3.18
113 114 5.231991 GCAAACAATTTTCATGTTGACGAGT 59.768 36.000 1.16 0.00 39.98 4.18
123 124 9.574458 TTTTCATGTTGACGAGTTTTTGATTTA 57.426 25.926 0.00 0.00 0.00 1.40
129 130 4.580995 TGACGAGTTTTTGATTTAAGGCCA 59.419 37.500 5.01 0.00 0.00 5.36
134 135 7.175990 ACGAGTTTTTGATTTAAGGCCATCTTA 59.824 33.333 5.01 0.00 36.93 2.10
153 154 0.251073 AAGGGCCAAATTGCTCATGC 59.749 50.000 6.18 0.00 32.74 4.06
155 156 1.597989 GGCCAAATTGCTCATGCCA 59.402 52.632 0.00 0.00 38.73 4.92
159 160 1.342555 CAAATTGCTCATGCCACACG 58.657 50.000 0.00 0.00 38.71 4.49
187 188 8.497910 AGACAAGTATCATTATATGTCTGGGT 57.502 34.615 5.51 0.00 44.10 4.51
188 189 8.589338 AGACAAGTATCATTATATGTCTGGGTC 58.411 37.037 5.51 0.00 44.10 4.46
221 223 7.369542 CCAAATTTTGAATTTGTTCGTTTCGAC 59.630 33.333 19.13 0.00 37.32 4.20
284 289 5.858581 GCCATGTTAAACTCTGTTAGCAAAG 59.141 40.000 0.00 0.00 29.53 2.77
294 299 1.811965 TGTTAGCAAAGCATCACGCAT 59.188 42.857 0.00 0.00 46.13 4.73
298 303 0.451383 GCAAAGCATCACGCATACCA 59.549 50.000 0.00 0.00 46.13 3.25
307 337 1.760029 TCACGCATACCAGAAGGCATA 59.240 47.619 0.00 0.00 39.06 3.14
314 344 4.885907 GCATACCAGAAGGCATATGCATAT 59.114 41.667 28.07 13.63 43.86 1.78
321 351 6.239092 CCAGAAGGCATATGCATATTGTTCAA 60.239 38.462 28.07 0.00 44.36 2.69
322 352 7.204604 CAGAAGGCATATGCATATTGTTCAAA 58.795 34.615 28.07 0.00 44.36 2.69
406 440 2.680841 CTGACCGACAAACAAGAAACCA 59.319 45.455 0.00 0.00 0.00 3.67
426 464 1.069204 ACATCACGTCAAGACTGCACT 59.931 47.619 0.00 0.00 0.00 4.40
443 481 6.413052 ACTGCACTGACAATGAATCTAGATT 58.587 36.000 17.96 17.96 0.00 2.40
461 500 1.327303 TTGACCATTTGGACCTGCAC 58.673 50.000 3.01 0.00 38.94 4.57
518 557 5.829924 ACTGGCATATCATAACTTGGGAAAG 59.170 40.000 0.00 0.00 0.00 2.62
531 570 1.886886 GGGAAAGCACGTTTACCTGA 58.113 50.000 0.00 0.00 45.12 3.86
577 620 9.965824 GTTCATGAATTAAAATATACTGTGGGG 57.034 33.333 12.12 0.00 0.00 4.96
789 981 3.053291 GCGGGCCACGTTCATTCA 61.053 61.111 4.39 0.00 46.52 2.57
809 1001 6.866010 TTCATTGGATGACGATGGATAAAG 57.134 37.500 0.00 0.00 40.73 1.85
823 1019 7.550906 ACGATGGATAAAGGAAAGAGAAGAAAG 59.449 37.037 0.00 0.00 0.00 2.62
824 1020 7.766278 CGATGGATAAAGGAAAGAGAAGAAAGA 59.234 37.037 0.00 0.00 0.00 2.52
826 1022 9.813826 ATGGATAAAGGAAAGAGAAGAAAGAAA 57.186 29.630 0.00 0.00 0.00 2.52
827 1023 9.289782 TGGATAAAGGAAAGAGAAGAAAGAAAG 57.710 33.333 0.00 0.00 0.00 2.62
831 1027 6.852858 AGGAAAGAGAAGAAAGAAAGAACG 57.147 37.500 0.00 0.00 0.00 3.95
832 1028 5.760743 AGGAAAGAGAAGAAAGAAAGAACGG 59.239 40.000 0.00 0.00 0.00 4.44
833 1029 5.425577 AAAGAGAAGAAAGAAAGAACGGC 57.574 39.130 0.00 0.00 0.00 5.68
834 1030 4.073293 AGAGAAGAAAGAAAGAACGGCA 57.927 40.909 0.00 0.00 0.00 5.69
835 1031 4.646572 AGAGAAGAAAGAAAGAACGGCAT 58.353 39.130 0.00 0.00 0.00 4.40
836 1032 5.066593 AGAGAAGAAAGAAAGAACGGCATT 58.933 37.500 0.00 0.00 0.00 3.56
837 1033 5.532779 AGAGAAGAAAGAAAGAACGGCATTT 59.467 36.000 0.00 0.00 0.00 2.32
838 1034 5.523369 AGAAGAAAGAAAGAACGGCATTTG 58.477 37.500 0.00 0.00 0.00 2.32
839 1035 4.918810 AGAAAGAAAGAACGGCATTTGT 57.081 36.364 0.00 0.00 0.00 2.83
840 1036 5.262588 AGAAAGAAAGAACGGCATTTGTT 57.737 34.783 0.00 0.00 0.00 2.83
841 1037 5.660460 AGAAAGAAAGAACGGCATTTGTTT 58.340 33.333 4.18 4.18 35.37 2.83
842 1038 6.106003 AGAAAGAAAGAACGGCATTTGTTTT 58.894 32.000 5.52 0.00 33.55 2.43
843 1039 6.593770 AGAAAGAAAGAACGGCATTTGTTTTT 59.406 30.769 5.52 0.00 33.55 1.94
875 1071 3.326836 TTTTTGCGGGGGAATGAAATC 57.673 42.857 0.00 0.00 0.00 2.17
962 1171 2.700371 TCAGAGAAGAAGAACAGGTGCA 59.300 45.455 0.00 0.00 0.00 4.57
967 1176 2.954753 GAAGAACAGGTGCACGCCG 61.955 63.158 11.45 3.91 0.00 6.46
1074 1430 2.753029 GTGGCTGTGGAGAAGGCT 59.247 61.111 0.00 0.00 40.70 4.58
1102 1458 2.440430 TCTTCCCGAGGCTCTCCG 60.440 66.667 13.50 0.00 37.47 4.63
1128 1487 4.189188 CGGGCTAGGTCGACCACG 62.189 72.222 35.00 24.91 38.89 4.94
1138 1497 4.052229 CGACCACGTCCTCCGCTT 62.052 66.667 0.00 0.00 41.42 4.68
1208 1598 4.055360 CGTCGGCTCACCAATTTCATATA 58.945 43.478 0.00 0.00 34.57 0.86
1244 1682 4.588899 TGTTTCTGCAACCTAGCATATGT 58.411 39.130 4.29 0.00 44.68 2.29
1270 1708 5.856986 GTGCTAATAGCTCGTTCGATAATCA 59.143 40.000 13.88 0.00 42.97 2.57
1272 1710 6.362551 TGCTAATAGCTCGTTCGATAATCAAC 59.637 38.462 13.88 0.00 42.97 3.18
1276 1742 3.130516 AGCTCGTTCGATAATCAACCTCA 59.869 43.478 0.00 0.00 0.00 3.86
1284 1750 7.526608 GTTCGATAATCAACCTCAATGTTTCA 58.473 34.615 0.00 0.00 0.00 2.69
1408 1893 0.675837 GGACCGAGTAGCAAAACCCC 60.676 60.000 0.00 0.00 0.00 4.95
1469 2231 3.788333 ATTTTCCCGTTGCATGATCAG 57.212 42.857 0.09 0.00 0.00 2.90
1763 2540 4.536090 AGTTATCTCATCTGAACCCAACCA 59.464 41.667 0.00 0.00 0.00 3.67
1847 2624 3.243535 CCTTCAGCTCGTATGTGCTCATA 60.244 47.826 8.52 4.38 42.73 2.15
1897 2675 6.555463 ATTGGATCCAGATGAAAAGCAATT 57.445 33.333 15.53 0.00 0.00 2.32
1898 2676 7.664552 ATTGGATCCAGATGAAAAGCAATTA 57.335 32.000 15.53 0.00 0.00 1.40
1940 2719 1.583404 GCACACAAGCAAAGTGAAACG 59.417 47.619 9.71 0.00 45.86 3.60
1969 3068 4.200838 TGAGAGCCATGTTTATGAACGA 57.799 40.909 0.00 0.00 38.65 3.85
2023 3122 3.951563 AAATGCTAGTAATGGAGGCCA 57.048 42.857 5.01 0.00 38.19 5.36
2069 3168 0.921896 AGCACCTGGGCATCTTACAT 59.078 50.000 9.36 0.00 35.83 2.29
2117 3216 2.025155 TCGCTGTAGAACTCCTGATCC 58.975 52.381 0.00 0.00 0.00 3.36
2155 3653 0.999406 CGTACCTGTGCATGCACTAC 59.001 55.000 41.43 33.45 46.30 2.73
2192 3728 2.203153 CCCGGTTCATAAGGCCCG 60.203 66.667 0.00 0.00 40.12 6.13
2385 4540 1.661509 CGCGTCAGCAGTTCAGTGA 60.662 57.895 0.00 0.00 45.49 3.41
2397 4558 4.023963 GCAGTTCAGTGACTAGGGTTTTTC 60.024 45.833 0.00 0.00 0.00 2.29
2896 5057 5.579718 ACCATTAAGTACAGAAGATCGTCG 58.420 41.667 2.87 1.59 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.118607 CGATCAACATGGCAATACATATACATC 58.881 37.037 0.00 0.00 0.00 3.06
3 4 7.823799 TCGATCAACATGGCAATACATATACAT 59.176 33.333 0.00 0.00 0.00 2.29
4 5 7.158021 TCGATCAACATGGCAATACATATACA 58.842 34.615 0.00 0.00 0.00 2.29
6 7 7.386059 ACTCGATCAACATGGCAATACATATA 58.614 34.615 0.00 0.00 0.00 0.86
7 8 6.233434 ACTCGATCAACATGGCAATACATAT 58.767 36.000 0.00 0.00 0.00 1.78
8 9 5.610398 ACTCGATCAACATGGCAATACATA 58.390 37.500 0.00 0.00 0.00 2.29
9 10 4.454678 ACTCGATCAACATGGCAATACAT 58.545 39.130 0.00 0.00 0.00 2.29
10 11 3.872696 ACTCGATCAACATGGCAATACA 58.127 40.909 0.00 0.00 0.00 2.29
11 12 4.882671 AACTCGATCAACATGGCAATAC 57.117 40.909 0.00 0.00 0.00 1.89
12 13 4.438608 GCAAACTCGATCAACATGGCAATA 60.439 41.667 0.00 0.00 0.00 1.90
13 14 3.674138 GCAAACTCGATCAACATGGCAAT 60.674 43.478 0.00 0.00 0.00 3.56
14 15 2.351641 GCAAACTCGATCAACATGGCAA 60.352 45.455 0.00 0.00 0.00 4.52
15 16 1.199789 GCAAACTCGATCAACATGGCA 59.800 47.619 0.00 0.00 0.00 4.92
16 17 1.199789 TGCAAACTCGATCAACATGGC 59.800 47.619 0.00 0.00 0.00 4.40
17 18 3.557577 TTGCAAACTCGATCAACATGG 57.442 42.857 0.00 0.00 0.00 3.66
18 19 6.033831 GGTAATTTGCAAACTCGATCAACATG 59.966 38.462 15.41 0.00 0.00 3.21
19 20 6.071952 AGGTAATTTGCAAACTCGATCAACAT 60.072 34.615 15.41 0.00 0.00 2.71
20 21 5.240623 AGGTAATTTGCAAACTCGATCAACA 59.759 36.000 15.41 0.00 0.00 3.33
21 22 5.699839 AGGTAATTTGCAAACTCGATCAAC 58.300 37.500 15.41 0.00 0.00 3.18
22 23 5.957842 AGGTAATTTGCAAACTCGATCAA 57.042 34.783 15.41 0.00 0.00 2.57
23 24 5.240623 ACAAGGTAATTTGCAAACTCGATCA 59.759 36.000 15.41 0.00 0.00 2.92
24 25 5.699839 ACAAGGTAATTTGCAAACTCGATC 58.300 37.500 15.41 0.31 0.00 3.69
25 26 5.705609 ACAAGGTAATTTGCAAACTCGAT 57.294 34.783 15.41 0.00 0.00 3.59
26 27 6.348950 CCATACAAGGTAATTTGCAAACTCGA 60.349 38.462 15.41 0.00 0.00 4.04
27 28 5.799936 CCATACAAGGTAATTTGCAAACTCG 59.200 40.000 15.41 0.00 0.00 4.18
28 29 6.919721 TCCATACAAGGTAATTTGCAAACTC 58.080 36.000 15.41 7.70 0.00 3.01
29 30 6.719370 TCTCCATACAAGGTAATTTGCAAACT 59.281 34.615 15.41 6.12 0.00 2.66
30 31 6.919721 TCTCCATACAAGGTAATTTGCAAAC 58.080 36.000 15.41 2.12 0.00 2.93
31 32 7.395772 TCATCTCCATACAAGGTAATTTGCAAA 59.604 33.333 15.44 15.44 0.00 3.68
32 33 6.889177 TCATCTCCATACAAGGTAATTTGCAA 59.111 34.615 0.00 0.00 0.00 4.08
33 34 6.318648 GTCATCTCCATACAAGGTAATTTGCA 59.681 38.462 0.00 0.00 0.00 4.08
34 35 6.238759 GGTCATCTCCATACAAGGTAATTTGC 60.239 42.308 0.00 0.00 0.00 3.68
35 36 6.017934 CGGTCATCTCCATACAAGGTAATTTG 60.018 42.308 0.00 0.00 0.00 2.32
36 37 6.055588 CGGTCATCTCCATACAAGGTAATTT 58.944 40.000 0.00 0.00 0.00 1.82
37 38 5.611374 CGGTCATCTCCATACAAGGTAATT 58.389 41.667 0.00 0.00 0.00 1.40
38 39 4.503296 GCGGTCATCTCCATACAAGGTAAT 60.503 45.833 0.00 0.00 0.00 1.89
39 40 3.181469 GCGGTCATCTCCATACAAGGTAA 60.181 47.826 0.00 0.00 0.00 2.85
40 41 2.364324 GCGGTCATCTCCATACAAGGTA 59.636 50.000 0.00 0.00 0.00 3.08
41 42 1.139058 GCGGTCATCTCCATACAAGGT 59.861 52.381 0.00 0.00 0.00 3.50
42 43 1.138859 TGCGGTCATCTCCATACAAGG 59.861 52.381 0.00 0.00 0.00 3.61
43 44 2.602257 TGCGGTCATCTCCATACAAG 57.398 50.000 0.00 0.00 0.00 3.16
44 45 3.342377 TTTGCGGTCATCTCCATACAA 57.658 42.857 0.00 0.00 0.00 2.41
45 46 3.270027 CTTTTGCGGTCATCTCCATACA 58.730 45.455 0.00 0.00 0.00 2.29
46 47 2.032178 GCTTTTGCGGTCATCTCCATAC 59.968 50.000 0.00 0.00 34.86 2.39
47 48 2.288666 GCTTTTGCGGTCATCTCCATA 58.711 47.619 0.00 0.00 34.86 2.74
62 63 6.756074 TCATCGAAACAACAAGATTTGCTTTT 59.244 30.769 0.00 0.00 33.60 2.27
74 75 2.685388 TGTTTGCCTCATCGAAACAACA 59.315 40.909 0.00 0.00 36.81 3.33
84 85 6.203338 GTCAACATGAAAATTGTTTGCCTCAT 59.797 34.615 0.00 0.00 35.18 2.90
97 98 8.472683 AAATCAAAAACTCGTCAACATGAAAA 57.527 26.923 0.00 0.00 0.00 2.29
107 108 5.116069 TGGCCTTAAATCAAAAACTCGTC 57.884 39.130 3.32 0.00 0.00 4.20
108 109 5.476945 AGATGGCCTTAAATCAAAAACTCGT 59.523 36.000 3.32 0.00 0.00 4.18
113 114 7.619965 CCCTTAAGATGGCCTTAAATCAAAAA 58.380 34.615 3.32 0.00 44.25 1.94
129 130 3.711863 TGAGCAATTTGGCCCTTAAGAT 58.288 40.909 3.36 0.00 0.00 2.40
134 135 0.251073 GCATGAGCAATTTGGCCCTT 59.749 50.000 0.00 0.00 41.58 3.95
153 154 2.412870 TGATACTTGTCTTGCGTGTGG 58.587 47.619 0.00 0.00 0.00 4.17
155 156 7.710907 ACATATAATGATACTTGTCTTGCGTGT 59.289 33.333 0.00 0.00 0.00 4.49
159 160 8.715998 CCAGACATATAATGATACTTGTCTTGC 58.284 37.037 4.22 0.00 41.22 4.01
187 188 1.464376 TTCAAAATTTGGGCGCCCGA 61.464 50.000 39.00 36.02 39.42 5.14
188 189 0.390998 ATTCAAAATTTGGGCGCCCG 60.391 50.000 39.00 23.48 39.42 6.13
195 197 7.369542 GTCGAAACGAACAAATTCAAAATTTGG 59.630 33.333 22.30 11.70 41.80 3.28
221 223 6.312426 ACTCAGCATAAAAGTTCTTCATCTCG 59.688 38.462 0.00 0.00 0.00 4.04
267 272 5.107104 CGTGATGCTTTGCTAACAGAGTTTA 60.107 40.000 0.00 0.00 30.72 2.01
276 281 2.354510 GGTATGCGTGATGCTTTGCTAA 59.645 45.455 0.00 0.00 46.63 3.09
284 289 0.940126 CCTTCTGGTATGCGTGATGC 59.060 55.000 0.00 0.00 46.70 3.91
294 299 5.879763 ACAATATGCATATGCCTTCTGGTA 58.120 37.500 24.54 3.84 41.18 3.25
298 303 6.964807 TTGAACAATATGCATATGCCTTCT 57.035 33.333 24.54 9.44 41.18 2.85
322 352 3.369546 GCCGTATGCATATGCCTTTTT 57.630 42.857 24.54 7.24 41.18 1.94
345 375 2.987125 GGAGCCCGTACCATGTGT 59.013 61.111 0.00 0.00 0.00 3.72
376 410 3.513912 TGTTTGTCGGTCAGAGATGGTAT 59.486 43.478 0.00 0.00 0.00 2.73
377 411 2.894765 TGTTTGTCGGTCAGAGATGGTA 59.105 45.455 0.00 0.00 0.00 3.25
406 440 1.069204 AGTGCAGTCTTGACGTGATGT 59.931 47.619 0.00 0.00 0.00 3.06
426 464 8.680001 CAAATGGTCAATCTAGATTCATTGTCA 58.320 33.333 22.13 13.84 32.67 3.58
443 481 0.539438 GGTGCAGGTCCAAATGGTCA 60.539 55.000 0.00 0.00 36.34 4.02
461 500 7.054751 TGAGATCTATGTAGGTATCGGTATGG 58.945 42.308 0.00 0.00 27.44 2.74
518 557 4.742438 TCTCAAAATCAGGTAAACGTGC 57.258 40.909 0.00 0.00 0.00 5.34
789 981 5.567037 TCCTTTATCCATCGTCATCCAAT 57.433 39.130 0.00 0.00 0.00 3.16
809 1001 5.561145 GCCGTTCTTTCTTTCTTCTCTTTCC 60.561 44.000 0.00 0.00 0.00 3.13
855 1051 2.634940 TGATTTCATTCCCCCGCAAAAA 59.365 40.909 0.00 0.00 0.00 1.94
856 1052 2.028567 GTGATTTCATTCCCCCGCAAAA 60.029 45.455 0.00 0.00 0.00 2.44
857 1053 1.548269 GTGATTTCATTCCCCCGCAAA 59.452 47.619 0.00 0.00 0.00 3.68
858 1054 1.181786 GTGATTTCATTCCCCCGCAA 58.818 50.000 0.00 0.00 0.00 4.85
859 1055 1.029408 CGTGATTTCATTCCCCCGCA 61.029 55.000 0.00 0.00 0.00 5.69
860 1056 1.724582 CCGTGATTTCATTCCCCCGC 61.725 60.000 0.00 0.00 0.00 6.13
861 1057 1.724582 GCCGTGATTTCATTCCCCCG 61.725 60.000 0.00 0.00 0.00 5.73
862 1058 0.682855 TGCCGTGATTTCATTCCCCC 60.683 55.000 0.00 0.00 0.00 5.40
863 1059 1.402787 ATGCCGTGATTTCATTCCCC 58.597 50.000 0.00 0.00 0.00 4.81
864 1060 3.525268 AAATGCCGTGATTTCATTCCC 57.475 42.857 0.00 0.00 30.84 3.97
865 1061 3.618150 CCAAAATGCCGTGATTTCATTCC 59.382 43.478 0.00 0.00 30.84 3.01
869 1065 1.617850 AGCCAAAATGCCGTGATTTCA 59.382 42.857 0.00 0.00 0.00 2.69
874 1070 1.976474 GGGAGCCAAAATGCCGTGA 60.976 57.895 0.00 0.00 0.00 4.35
875 1071 2.573340 GGGAGCCAAAATGCCGTG 59.427 61.111 0.00 0.00 0.00 4.94
962 1171 4.398598 GCACGGAATTTGCGGCGT 62.399 61.111 14.84 0.00 34.75 5.68
967 1176 1.846175 GCGAAATAGCACGGAATTTGC 59.154 47.619 0.00 0.00 40.52 3.68
1074 1430 4.388499 GGGAAGAGCCGGCGTTGA 62.388 66.667 23.20 0.00 37.63 3.18
1102 1458 3.217743 CCTAGCCCGGTCGACCTC 61.218 72.222 30.92 19.38 0.00 3.85
1122 1481 2.126031 GAAGCGGAGGACGTGGTC 60.126 66.667 0.00 0.00 46.52 4.02
1244 1682 3.497297 TCGAACGAGCTATTAGCACAA 57.503 42.857 17.59 0.00 45.56 3.33
1284 1750 1.607467 GATGCCCTGGCTGTTTGGT 60.607 57.895 9.97 0.00 42.51 3.67
1367 1844 4.502087 CCTCGGATTATGCATCTTGTCAGA 60.502 45.833 0.19 3.11 31.67 3.27
1408 1893 5.745294 CCATGGATCAAAGCATTTAGAAACG 59.255 40.000 5.56 0.00 35.03 3.60
1469 2231 8.251721 ACAGTGTAAGATGAGTTCCTACATAAC 58.748 37.037 0.00 0.00 34.56 1.89
1518 2291 2.418884 GGAGTTTCTCCCGATCTTCACC 60.419 54.545 4.60 0.00 44.36 4.02
1897 2675 5.573707 GCCTCCCCTCTTTTCTTCTTGATTA 60.574 44.000 0.00 0.00 0.00 1.75
1898 2676 4.812442 GCCTCCCCTCTTTTCTTCTTGATT 60.812 45.833 0.00 0.00 0.00 2.57
1940 2719 7.709947 TCATAAACATGGCTCTCAATCATTTC 58.290 34.615 0.00 0.00 0.00 2.17
1969 3068 4.542697 ACAACCTTTTATTGGACCTGTGT 58.457 39.130 0.00 0.00 0.00 3.72
2069 3168 0.798159 GTGCGTTCATGTCAGATGCA 59.202 50.000 0.00 0.00 0.00 3.96
2117 3216 1.390123 CGTAAAGTCTCCACACGCATG 59.610 52.381 0.00 0.00 0.00 4.06
2236 3778 4.533001 ACCGGGACTAAAGGTATAGAGT 57.467 45.455 6.32 0.00 36.34 3.24
2896 5057 6.983307 ACTTCTCTCTGTATGCATATGTTCAC 59.017 38.462 10.16 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.