Multiple sequence alignment - TraesCS2B01G538600

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 TraesCS2B01G538600 chr2B 100.000 3410 0 0 1 3410 733893233 733889824 0.000000e+00 6298.0
1 TraesCS2B01G538600 chr2B 91.397 988 72 11 2253 3233 733859942 733858961 0.000000e+00 1341.0
2 TraesCS2B01G538600 chr2B 88.793 928 74 13 2300 3198 733971650 733970724 0.000000e+00 1110.0
3 TraesCS2B01G538600 chr2B 90.012 861 63 13 2521 3363 734049224 734048369 0.000000e+00 1092.0
4 TraesCS2B01G538600 chr2B 87.209 774 56 19 835 1581 733863026 733862269 0.000000e+00 841.0
5 TraesCS2B01G538600 chr2B 100.000 440 0 0 3696 4135 733889538 733889099 0.000000e+00 813.0
6 TraesCS2B01G538600 chr2B 83.957 829 66 32 801 1581 733973471 733972662 0.000000e+00 732.0
7 TraesCS2B01G538600 chr2B 90.385 260 7 1 286 545 733973978 733973737 3.990000e-85 326.0
8 TraesCS2B01G538600 chr2B 78.261 529 55 26 1 489 733863829 733863321 6.770000e-73 285.0
9 TraesCS2B01G538600 chr2B 81.579 304 37 8 1585 1871 733862237 733861936 2.490000e-57 233.0
10 TraesCS2B01G538600 chr2B 85.263 190 12 6 2087 2261 733861614 733861426 9.130000e-42 182.0
11 TraesCS2B01G538600 chr2B 76.440 382 37 25 1931 2285 733972058 733971703 1.540000e-34 158.0
12 TraesCS2B01G538600 chr2B 77.444 266 40 11 1585 1839 733972611 733972355 1.550000e-29 141.0
13 TraesCS2B01G538600 chr2D 86.277 1370 100 39 2087 3399 603542306 603543644 0.000000e+00 1408.0
14 TraesCS2B01G538600 chr2D 91.538 910 59 3 2515 3409 603501268 603500362 0.000000e+00 1238.0
15 TraesCS2B01G538600 chr2D 86.660 1072 99 24 2087 3136 603379819 603378770 0.000000e+00 1147.0
16 TraesCS2B01G538600 chr2D 87.979 965 90 12 2300 3242 603401347 603400387 0.000000e+00 1116.0
17 TraesCS2B01G538600 chr2D 87.117 978 86 16 929 1884 603541049 603542008 0.000000e+00 1072.0
18 TraesCS2B01G538600 chr2D 87.821 780 55 13 838 1581 603381222 603380447 0.000000e+00 878.0
19 TraesCS2B01G538600 chr2D 84.771 939 57 36 801 1696 603403169 603402274 0.000000e+00 863.0
20 TraesCS2B01G538600 chr2D 92.908 423 30 0 985 1407 603502840 603502418 2.110000e-172 616.0
21 TraesCS2B01G538600 chr2D 85.504 476 41 11 48 499 603539986 603540457 4.840000e-129 472.0
22 TraesCS2B01G538600 chr2D 80.692 549 71 20 1 522 603382178 603381638 1.080000e-105 394.0
23 TraesCS2B01G538600 chr2D 81.166 446 56 13 3700 4123 603500296 603499857 2.380000e-87 333.0
24 TraesCS2B01G538600 chr2D 82.698 341 36 9 3719 4059 603543968 603544285 8.750000e-72 281.0
25 TraesCS2B01G538600 chr2D 80.737 353 56 7 188 538 603404151 603403809 8.810000e-67 265.0
26 TraesCS2B01G538600 chr2D 82.178 303 35 14 1588 1887 603380395 603380109 4.130000e-60 243.0
27 TraesCS2B01G538600 chr2D 89.937 159 12 2 3252 3409 603400146 603399991 7.010000e-48 202.0
28 TraesCS2B01G538600 chr2D 77.835 388 45 25 1931 2289 603401772 603401397 7.010000e-48 202.0
29 TraesCS2B01G538600 chr2D 83.691 233 14 10 1880 2092 603380084 603379856 9.070000e-47 198.0
30 TraesCS2B01G538600 chr2D 83.691 233 14 9 1880 2092 603542036 603542264 9.070000e-47 198.0
31 TraesCS2B01G538600 chr2A 85.161 1368 106 41 2101 3409 735762695 735764024 0.000000e+00 1312.0
32 TraesCS2B01G538600 chr2A 85.437 1133 94 33 2160 3233 735601391 735600271 0.000000e+00 1112.0
33 TraesCS2B01G538600 chr2A 84.731 1133 110 38 2298 3395 735701929 735700825 0.000000e+00 1075.0
34 TraesCS2B01G538600 chr2A 83.393 1126 98 42 821 1869 735603079 735601966 0.000000e+00 961.0
35 TraesCS2B01G538600 chr2A 88.404 664 52 11 929 1567 735761373 735762036 0.000000e+00 776.0
36 TraesCS2B01G538600 chr2A 94.019 418 25 0 990 1407 735703439 735703022 5.830000e-178 634.0
37 TraesCS2B01G538600 chr2A 87.328 363 42 4 3699 4059 735764075 735764435 2.970000e-111 412.0
38 TraesCS2B01G538600 chr2A 81.915 470 50 20 52 499 735760324 735760780 8.450000e-97 364.0
39 TraesCS2B01G538600 chr2A 78.065 465 63 22 117 545 735604023 735603562 1.470000e-64 257.0
40 TraesCS2B01G538600 chr2A 88.199 161 12 1 1932 2092 735762490 735762643 7.060000e-43 185.0
41 TraesCS2B01G538600 chr2A 91.597 119 10 0 1719 1837 735762290 735762408 9.200000e-37 165.0
42 TraesCS2B01G538600 chr7A 84.615 65 4 6 3855 3917 37703497 37703557 4.460000e-05 60.2
43 TraesCS2B01G538600 chr7A 88.679 53 1 3 4009 4059 146676789 146676740 4.460000e-05 60.2
44 TraesCS2B01G538600 chrUn 100.000 30 0 0 4027 4056 55734458 55734429 5.770000e-04 56.5
45 TraesCS2B01G538600 chr4D 100.000 30 0 0 4027 4056 214144909 214144938 5.770000e-04 56.5
46 TraesCS2B01G538600 chr4D 100.000 30 0 0 4027 4056 487215339 487215310 5.770000e-04 56.5
47 TraesCS2B01G538600 chr1A 96.970 33 1 0 4027 4059 23697431 23697399 5.770000e-04 56.5
48 TraesCS2B01G538600 chr3A 88.000 50 1 3 4009 4056 170735979 170736025 2.000000e-03 54.7


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 TraesCS2B01G538600 chr2B 733889099 733893233 4134 True 3555.500000 6298 100.000000 1 4135 2 chr2B.!!$R3 4134
1 TraesCS2B01G538600 chr2B 734048369 734049224 855 True 1092.000000 1092 90.012000 2521 3363 1 chr2B.!!$R1 842
2 TraesCS2B01G538600 chr2B 733858961 733863829 4868 True 576.400000 1341 84.741800 1 3233 5 chr2B.!!$R2 3232
3 TraesCS2B01G538600 chr2B 733970724 733973978 3254 True 493.400000 1110 83.403800 286 3198 5 chr2B.!!$R4 2912
4 TraesCS2B01G538600 chr2D 603499857 603502840 2983 True 729.000000 1238 88.537333 985 4123 3 chr2D.!!$R3 3138
5 TraesCS2B01G538600 chr2D 603539986 603544285 4299 False 686.200000 1408 85.057400 48 4059 5 chr2D.!!$F1 4011
6 TraesCS2B01G538600 chr2D 603378770 603382178 3408 True 572.000000 1147 84.208400 1 3136 5 chr2D.!!$R1 3135
7 TraesCS2B01G538600 chr2D 603399991 603404151 4160 True 529.600000 1116 84.251800 188 3409 5 chr2D.!!$R2 3221
8 TraesCS2B01G538600 chr2A 735700825 735703439 2614 True 854.500000 1075 89.375000 990 3395 2 chr2A.!!$R2 2405
9 TraesCS2B01G538600 chr2A 735600271 735604023 3752 True 776.666667 1112 82.298333 117 3233 3 chr2A.!!$R1 3116
10 TraesCS2B01G538600 chr2A 735760324 735764435 4111 False 535.666667 1312 87.100667 52 4059 6 chr2A.!!$F1 4007

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
737 1413 0.036388 ATAGCGGATACCATTGCGGG 60.036 55.0 0.00 0.0 40.22 6.13 F
1681 2832 0.905337 AAGACCGTCCCTTCCAGAGG 60.905 60.0 0.00 0.0 45.86 3.69 F
2074 3832 0.036105 TCCATCTTGTCGCATGCAGT 60.036 50.0 19.57 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 3146 0.178984 GGGGACGAAAGGAAAACCCA 60.179 55.0 0.00 0.0 39.1 4.51 R
2942 6433 0.618458 GGCCCTTGTACTCCATGACA 59.382 55.0 0.00 0.0 0.0 3.58 R
4069 7847 0.117340 AGGGAGAAGTGCACTAGGGT 59.883 55.0 22.01 3.6 0.0 4.34 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
90 93 1.539065 CCCACGAGAGATTAGCGCATT 60.539 52.381 11.47 0.00 0.00 3.56
100 103 8.435430 CGAGAGATTAGCGCATTATTTAATTCA 58.565 33.333 11.47 0.00 0.00 2.57
132 138 2.576847 GCGGCGCAAAAGATTCCG 60.577 61.111 29.21 0.25 42.68 4.30
193 222 4.514585 TGTGCGGGGTGGCTTGTT 62.515 61.111 0.00 0.00 0.00 2.83
266 314 0.721483 CGACGAAACGCTTCCTTTGC 60.721 55.000 0.00 0.00 0.00 3.68
459 544 9.651913 AACAATTTTAACATTCTTGTCAGTGTT 57.348 25.926 0.00 0.00 38.28 3.32
545 644 3.015327 AGGCACTGAATCTTCTTCATGC 58.985 45.455 10.91 10.91 37.18 4.06
577 803 1.073025 TGCCGTGCTGAATCCAACT 59.927 52.632 0.00 0.00 0.00 3.16
624 1146 6.150976 TGACATTAAGCTGTCGAATCCATTTT 59.849 34.615 5.07 0.00 46.89 1.82
721 1397 0.595053 CTGCGTGCAGTACCGGATAG 60.595 60.000 9.46 0.00 39.10 2.08
724 1400 1.299926 GTGCAGTACCGGATAGCGG 60.300 63.158 9.46 0.00 0.00 5.52
725 1401 1.454295 TGCAGTACCGGATAGCGGA 60.454 57.895 9.46 0.00 0.00 5.54
726 1402 0.826256 TGCAGTACCGGATAGCGGAT 60.826 55.000 9.46 0.00 0.00 4.18
727 1403 1.171308 GCAGTACCGGATAGCGGATA 58.829 55.000 9.46 0.00 0.00 2.59
728 1404 1.135460 GCAGTACCGGATAGCGGATAC 60.135 57.143 9.46 0.00 0.00 2.24
729 1405 1.471684 CAGTACCGGATAGCGGATACC 59.528 57.143 9.46 0.00 0.00 2.73
730 1406 1.074405 AGTACCGGATAGCGGATACCA 59.926 52.381 9.46 0.00 0.00 3.25
732 1408 1.640917 ACCGGATAGCGGATACCATT 58.359 50.000 9.46 0.00 0.00 3.16
734 1410 1.359848 CGGATAGCGGATACCATTGC 58.640 55.000 0.00 0.00 0.00 3.56
735 1411 1.359848 GGATAGCGGATACCATTGCG 58.640 55.000 0.00 0.00 0.00 4.85
737 1413 0.036388 ATAGCGGATACCATTGCGGG 60.036 55.000 0.00 0.00 40.22 6.13
739 1415 2.978010 CGGATACCATTGCGGGGC 60.978 66.667 0.00 0.00 40.22 5.80
740 1416 2.978010 GGATACCATTGCGGGGCG 60.978 66.667 0.00 0.00 40.22 6.13
854 1704 3.707189 CCACCCCTCCCTACCCCT 61.707 72.222 0.00 0.00 0.00 4.79
855 1705 2.338377 CCACCCCTCCCTACCCCTA 61.338 68.421 0.00 0.00 0.00 3.53
859 1709 2.089811 CACCCCTCCCTACCCCTATAAA 60.090 54.545 0.00 0.00 0.00 1.40
860 1710 2.814313 ACCCCTCCCTACCCCTATAAAT 59.186 50.000 0.00 0.00 0.00 1.40
861 1711 4.013380 ACCCCTCCCTACCCCTATAAATA 58.987 47.826 0.00 0.00 0.00 1.40
862 1712 4.202979 ACCCCTCCCTACCCCTATAAATAC 60.203 50.000 0.00 0.00 0.00 1.89
868 1718 2.821430 ACCCCTATAAATACCCCCGT 57.179 50.000 0.00 0.00 0.00 5.28
899 1749 2.918934 TCCCATCCTTCATCTCCAACAA 59.081 45.455 0.00 0.00 0.00 2.83
966 1861 2.556286 GTGCCTTCCACAACCTAGC 58.444 57.895 0.00 0.00 44.06 3.42
978 1873 2.045926 CCTAGCAGCACACCACCC 60.046 66.667 0.00 0.00 0.00 4.61
980 1875 3.628646 CTAGCAGCACACCACCCCC 62.629 68.421 0.00 0.00 0.00 5.40
995 1917 1.002624 CCCCGGCACACACATACTT 60.003 57.895 0.00 0.00 0.00 2.24
1525 2516 8.670135 CAACACATATGAGGACGGTAATTAAAA 58.330 33.333 10.38 0.00 0.00 1.52
1556 2574 6.727824 AATTAGAAAGTTCACGTGATGGAG 57.272 37.500 20.80 0.00 0.00 3.86
1613 2718 3.454587 GACGTGTGGGGCACTGTGA 62.455 63.158 12.86 0.00 45.57 3.58
1681 2832 0.905337 AAGACCGTCCCTTCCAGAGG 60.905 60.000 0.00 0.00 45.86 3.69
1696 2940 2.636830 CAGAGGCGGATCTTCATTTGT 58.363 47.619 0.00 0.00 0.00 2.83
1697 2941 3.432186 CCAGAGGCGGATCTTCATTTGTA 60.432 47.826 0.00 0.00 0.00 2.41
1698 2942 3.557595 CAGAGGCGGATCTTCATTTGTAC 59.442 47.826 0.00 0.00 0.00 2.90
1700 2944 3.535561 AGGCGGATCTTCATTTGTACAG 58.464 45.455 0.00 0.00 0.00 2.74
1701 2945 2.032178 GGCGGATCTTCATTTGTACAGC 59.968 50.000 0.00 0.00 0.00 4.40
1702 2946 2.939103 GCGGATCTTCATTTGTACAGCT 59.061 45.455 0.00 0.00 0.00 4.24
1740 3091 1.989165 CTTTTCGTGCTCTCTCGGAAG 59.011 52.381 0.00 0.00 29.69 3.46
1794 3146 4.041723 GCAAGTTAAAAAGATGCACGTGT 58.958 39.130 18.38 0.00 37.00 4.49
1799 3151 1.398692 AAAAGATGCACGTGTGGGTT 58.601 45.000 18.38 3.53 0.00 4.11
1841 3206 5.298276 TCTTTGGAGAAATGTGTGTACCAAC 59.702 40.000 0.00 0.00 36.00 3.77
1871 3239 1.329906 CTGATTTCGCATCCAGCTGAC 59.670 52.381 17.39 0.25 42.61 3.51
1996 3738 8.538039 ACTACGTATTAAAATTCTAGAAAGCGC 58.462 33.333 9.71 0.00 0.00 5.92
2003 3745 8.542497 TTAAAATTCTAGAAAGCGCAAGAGTA 57.458 30.769 11.47 0.00 43.02 2.59
2050 3807 1.746615 CAGGTAGCAGCCGCACAAT 60.747 57.895 0.00 0.00 42.27 2.71
2074 3832 0.036105 TCCATCTTGTCGCATGCAGT 60.036 50.000 19.57 0.00 0.00 4.40
2540 6031 0.393132 GTTTGCAGGGCCTAGAGGTC 60.393 60.000 5.28 0.00 39.63 3.85
2558 6049 2.480845 GTCGTGGACAACAGCTACTTT 58.519 47.619 0.00 0.00 32.09 2.66
2564 6055 4.994852 GTGGACAACAGCTACTTTATCACA 59.005 41.667 0.00 0.00 0.00 3.58
2579 6070 1.186200 TCACAGAGGAGAACATCGGG 58.814 55.000 0.00 0.00 31.71 5.14
2711 6202 1.745115 CGGCATGGTGATGAACGGT 60.745 57.895 0.00 0.00 31.58 4.83
2735 6226 2.029666 ATCAGCATCTACGCGCCC 59.970 61.111 5.73 0.00 36.85 6.13
2741 6232 2.827190 ATCTACGCGCCCGAGACA 60.827 61.111 5.73 0.00 38.29 3.41
2767 6258 2.490217 CGCGGTGGTGGACTCTAG 59.510 66.667 0.00 0.00 0.00 2.43
2918 6409 2.515071 GGAGGCCATCATCCGCTCT 61.515 63.158 5.01 0.00 0.00 4.09
3156 6647 3.450115 GTACGGGAGCTCAGCCGT 61.450 66.667 31.01 31.01 37.58 5.68
3220 6716 0.659957 GCGATTGCCATCTGGTTCTC 59.340 55.000 0.00 0.00 37.57 2.87
3233 6729 2.362717 CTGGTTCTCGTCTAGGAATCCC 59.637 54.545 0.00 0.00 0.00 3.85
3234 6730 2.024273 TGGTTCTCGTCTAGGAATCCCT 60.024 50.000 0.00 0.00 46.62 4.20
3340 7080 8.622157 CACTTCAATTCTAGACCGTCTATCTTA 58.378 37.037 8.73 0.00 0.00 2.10
3363 7103 2.099427 TCCAACGGCTGTAAACAAAACC 59.901 45.455 0.00 0.00 0.00 3.27
3409 7149 3.186613 GGCTTCTTTTTCCTCACGTGTAG 59.813 47.826 16.51 11.33 0.00 2.74
3715 7459 2.030562 CGACTTGTTCCCACCGCT 59.969 61.111 0.00 0.00 0.00 5.52
3717 7461 0.736325 CGACTTGTTCCCACCGCTAG 60.736 60.000 0.00 0.00 0.00 3.42
3772 7528 3.336138 AAAACAACTCCGGAGATCTCC 57.664 47.619 37.69 29.15 46.18 3.71
3781 7537 2.132300 GGAGATCTCCTGCACTCCC 58.868 63.158 31.11 5.04 46.16 4.30
3782 7538 0.689080 GGAGATCTCCTGCACTCCCA 60.689 60.000 31.11 0.00 46.16 4.37
3806 7562 9.561069 CCACCCCTAATAATATAGATAATGTGC 57.439 37.037 0.00 0.00 0.00 4.57
3822 7578 3.608432 GCCCATGGCTTCAACCTC 58.392 61.111 6.09 0.00 46.69 3.85
3833 7589 5.819991 TGGCTTCAACCTCAGATAGATTTT 58.180 37.500 0.00 0.00 0.00 1.82
3837 7593 6.481644 GCTTCAACCTCAGATAGATTTTCGAT 59.518 38.462 0.00 0.00 0.00 3.59
3859 7625 1.500396 GTCCGCCGTGGCTAAAAAG 59.500 57.895 9.55 0.00 39.32 2.27
3860 7626 1.071814 TCCGCCGTGGCTAAAAAGT 59.928 52.632 9.55 0.00 39.32 2.66
3953 7720 7.814587 GTGAAAACCATTATTGCTAAAGCTTCT 59.185 33.333 0.00 0.00 42.66 2.85
3990 7757 2.159653 GCACCGACTGCTAAATGTTCTG 60.160 50.000 0.00 0.00 43.33 3.02
4007 7774 6.790285 TGTTCTGTTTTTAGGGACGTTATC 57.210 37.500 0.00 0.00 0.00 1.75
4064 7842 7.233144 ACATGCATGCATTAGAATAATAACCCA 59.767 33.333 30.32 0.00 33.90 4.51
4068 7846 7.596248 GCATGCATTAGAATAATAACCCACTTG 59.404 37.037 14.21 0.00 0.00 3.16
4069 7847 8.849168 CATGCATTAGAATAATAACCCACTTGA 58.151 33.333 0.00 0.00 0.00 3.02
4084 7862 2.037772 CACTTGACCCTAGTGCACTTCT 59.962 50.000 27.06 2.95 36.88 2.85
4095 7873 1.478916 GTGCACTTCTCCCTCTAGTCC 59.521 57.143 10.32 0.00 0.00 3.85
4099 7877 2.697751 CACTTCTCCCTCTAGTCCCATG 59.302 54.545 0.00 0.00 0.00 3.66
4100 7878 1.691434 CTTCTCCCTCTAGTCCCATGC 59.309 57.143 0.00 0.00 0.00 4.06
4116 7894 1.371337 ATGCGTGCATGTACTGGCAG 61.371 55.000 14.16 14.16 41.35 4.85
4118 7896 1.091771 GCGTGCATGTACTGGCAGAT 61.092 55.000 23.66 8.18 41.35 2.90
4123 7901 4.142708 CGTGCATGTACTGGCAGATAAAAA 60.143 41.667 23.66 0.00 41.35 1.94
4124 7902 5.335127 GTGCATGTACTGGCAGATAAAAAG 58.665 41.667 23.66 5.70 41.35 2.27
4125 7903 5.123820 GTGCATGTACTGGCAGATAAAAAGA 59.876 40.000 23.66 0.00 41.35 2.52
4126 7904 5.887598 TGCATGTACTGGCAGATAAAAAGAT 59.112 36.000 23.66 0.00 34.58 2.40
4127 7905 6.183360 TGCATGTACTGGCAGATAAAAAGATG 60.183 38.462 23.66 12.83 34.58 2.90
4128 7906 6.038603 GCATGTACTGGCAGATAAAAAGATGA 59.961 38.462 23.66 0.00 0.00 2.92
4129 7907 7.415541 GCATGTACTGGCAGATAAAAAGATGAA 60.416 37.037 23.66 0.00 0.00 2.57
4130 7908 7.615582 TGTACTGGCAGATAAAAAGATGAAG 57.384 36.000 23.66 0.00 0.00 3.02
4131 7909 6.599244 TGTACTGGCAGATAAAAAGATGAAGG 59.401 38.462 23.66 0.00 0.00 3.46
4132 7910 4.400567 ACTGGCAGATAAAAAGATGAAGGC 59.599 41.667 23.66 0.00 0.00 4.35
4133 7911 4.343231 TGGCAGATAAAAAGATGAAGGCA 58.657 39.130 0.00 0.00 0.00 4.75
4134 7912 4.957954 TGGCAGATAAAAAGATGAAGGCAT 59.042 37.500 0.00 0.00 37.47 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.086685 TCAGGGTTAAGTTTCCTATTTGACT 57.913 36.000 0.00 0.00 0.00 3.41
12 13 8.721133 AACATTCAGGGTTAAGTTTCCTATTT 57.279 30.769 0.00 0.00 0.00 1.40
22 23 6.741109 ACCGTTTTTAACATTCAGGGTTAAG 58.259 36.000 0.00 0.00 40.59 1.85
90 93 9.716507 GCAGCTCTCGTTTTATTGAATTAAATA 57.283 29.630 0.00 0.00 0.00 1.40
100 103 0.727398 GCCGCAGCTCTCGTTTTATT 59.273 50.000 4.47 0.00 35.50 1.40
115 121 2.576847 CGGAATCTTTTGCGCCGC 60.577 61.111 4.18 0.00 39.82 6.53
183 212 1.000843 GTGGAATCCAAACAAGCCACC 59.999 52.381 2.31 0.00 39.79 4.61
184 213 1.686052 TGTGGAATCCAAACAAGCCAC 59.314 47.619 2.31 0.00 44.50 5.01
239 272 2.928361 CGTTTCGTCGCTGCTGTT 59.072 55.556 0.00 0.00 0.00 3.16
391 476 6.316319 GCCAAATAATTCCATGCAACAAAAG 58.684 36.000 0.00 0.00 0.00 2.27
459 544 2.292257 ACCTCCACAGTCCATAGCAGTA 60.292 50.000 0.00 0.00 0.00 2.74
577 803 0.037790 GGCTGCGTAATTTTTGCCCA 60.038 50.000 0.00 0.00 34.81 5.36
672 1251 6.147164 GGATTTGATGACTCGTGTGTTTAGAA 59.853 38.462 0.00 0.00 0.00 2.10
673 1252 5.637810 GGATTTGATGACTCGTGTGTTTAGA 59.362 40.000 0.00 0.00 0.00 2.10
674 1253 5.163854 GGGATTTGATGACTCGTGTGTTTAG 60.164 44.000 0.00 0.00 0.00 1.85
675 1254 4.693566 GGGATTTGATGACTCGTGTGTTTA 59.306 41.667 0.00 0.00 0.00 2.01
676 1255 3.502211 GGGATTTGATGACTCGTGTGTTT 59.498 43.478 0.00 0.00 0.00 2.83
678 1257 2.699954 GGGATTTGATGACTCGTGTGT 58.300 47.619 0.00 0.00 0.00 3.72
721 1397 2.978010 CCCCGCAATGGTATCCGC 60.978 66.667 0.00 0.00 35.15 5.54
724 1400 1.507141 CTTCGCCCCGCAATGGTATC 61.507 60.000 0.00 0.00 35.15 2.24
725 1401 1.525995 CTTCGCCCCGCAATGGTAT 60.526 57.895 0.00 0.00 35.15 2.73
726 1402 2.124901 CTTCGCCCCGCAATGGTA 60.125 61.111 0.00 0.00 35.15 3.25
727 1403 2.837031 ATTCTTCGCCCCGCAATGGT 62.837 55.000 0.00 0.00 35.15 3.55
728 1404 2.063541 GATTCTTCGCCCCGCAATGG 62.064 60.000 0.00 0.00 37.55 3.16
729 1405 1.356624 GATTCTTCGCCCCGCAATG 59.643 57.895 0.00 0.00 0.00 2.82
730 1406 1.823899 GGATTCTTCGCCCCGCAAT 60.824 57.895 0.00 0.00 0.00 3.56
732 1408 4.483243 GGGATTCTTCGCCCCGCA 62.483 66.667 0.00 0.00 38.45 5.69
739 1415 1.301009 GCTAGGGCGGGATTCTTCG 60.301 63.158 0.00 0.00 0.00 3.79
740 1416 0.533085 GTGCTAGGGCGGGATTCTTC 60.533 60.000 0.00 0.00 42.25 2.87
767 1594 4.587189 GAATCTCGGGTCCGGCCG 62.587 72.222 21.04 21.04 40.25 6.13
768 1595 4.237207 GGAATCTCGGGTCCGGCC 62.237 72.222 9.68 0.36 40.25 6.13
769 1596 2.530958 TTTGGAATCTCGGGTCCGGC 62.531 60.000 9.68 0.00 40.25 6.13
847 1697 3.771479 GACGGGGGTATTTATAGGGGTAG 59.229 52.174 0.00 0.00 0.00 3.18
849 1699 2.624495 GACGGGGGTATTTATAGGGGT 58.376 52.381 0.00 0.00 0.00 4.95
853 1703 2.836372 GGGAGGACGGGGGTATTTATAG 59.164 54.545 0.00 0.00 0.00 1.31
854 1704 2.181865 TGGGAGGACGGGGGTATTTATA 59.818 50.000 0.00 0.00 0.00 0.98
855 1705 1.061190 TGGGAGGACGGGGGTATTTAT 60.061 52.381 0.00 0.00 0.00 1.40
859 1709 2.041197 GTGGGAGGACGGGGGTAT 60.041 66.667 0.00 0.00 0.00 2.73
860 1710 4.403502 GGTGGGAGGACGGGGGTA 62.404 72.222 0.00 0.00 0.00 3.69
868 1718 1.837533 AAGGATGGGAGGTGGGAGGA 61.838 60.000 0.00 0.00 0.00 3.71
899 1749 2.754552 TGCTCTTTGTTGTTGCTCTGTT 59.245 40.909 0.00 0.00 0.00 3.16
978 1873 1.365699 GTAAGTATGTGTGTGCCGGG 58.634 55.000 2.18 0.00 0.00 5.73
980 1875 0.368907 GCGTAAGTATGTGTGTGCCG 59.631 55.000 0.00 0.00 41.68 5.69
1140 2070 3.371063 GCCTCCACCACGTCGAGA 61.371 66.667 0.00 0.00 0.00 4.04
1332 2262 1.208293 GAGTGAGGGGACTTGTCCATC 59.792 57.143 19.90 16.51 44.43 3.51
1482 2460 1.742831 GTTGATTAGGTCGCCATGCAA 59.257 47.619 0.00 0.00 0.00 4.08
1537 2531 2.417719 GCTCCATCACGTGAACTTTCT 58.582 47.619 24.13 0.98 0.00 2.52
1556 2574 1.591863 GCCATTCTACTCCGTCCGC 60.592 63.158 0.00 0.00 0.00 5.54
1613 2718 0.744414 GCACTCATGGTGTACCGCAT 60.744 55.000 13.59 0.00 46.86 4.73
1681 2832 2.939103 AGCTGTACAAATGAAGATCCGC 59.061 45.455 0.00 0.00 0.00 5.54
1740 3091 5.696724 AGCAAACTGTGTCTTGTACTGTATC 59.303 40.000 0.00 0.00 31.26 2.24
1794 3146 0.178984 GGGGACGAAAGGAAAACCCA 60.179 55.000 0.00 0.00 39.10 4.51
1799 3151 0.399075 GACCAGGGGACGAAAGGAAA 59.601 55.000 0.00 0.00 0.00 3.13
1859 3227 1.863454 CTGTTATCGTCAGCTGGATGC 59.137 52.381 15.13 7.88 43.29 3.91
1871 3239 1.732259 GGCTGTTGTCACCTGTTATCG 59.268 52.381 0.00 0.00 0.00 2.92
1989 3731 5.103000 TGACTAGAATACTCTTGCGCTTTC 58.897 41.667 9.73 0.75 32.70 2.62
1996 3738 6.416455 GCACGATCTTGACTAGAATACTCTTG 59.584 42.308 2.89 0.00 36.22 3.02
2003 3745 3.131933 AGCTGCACGATCTTGACTAGAAT 59.868 43.478 2.89 0.00 36.22 2.40
2050 3807 2.291365 CATGCGACAAGATGGATTCCA 58.709 47.619 8.08 8.08 38.19 3.53
2540 6031 4.091509 GTGATAAAGTAGCTGTTGTCCACG 59.908 45.833 0.00 0.00 0.00 4.94
2558 6049 2.959030 CCCGATGTTCTCCTCTGTGATA 59.041 50.000 0.00 0.00 0.00 2.15
2564 6055 0.755686 GCATCCCGATGTTCTCCTCT 59.244 55.000 6.56 0.00 40.80 3.69
2579 6070 1.712977 CCTTGGCGAGCTTGAGCATC 61.713 60.000 4.70 0.00 45.16 3.91
2735 6226 3.470567 GCGCAACCGACTGTCTCG 61.471 66.667 0.30 3.18 42.54 4.04
2747 6238 4.980805 GAGTCCACCACCGCGCAA 62.981 66.667 8.75 0.00 0.00 4.85
2801 6292 2.936993 GCCCGTCATCTTGTTCATGAGT 60.937 50.000 0.00 0.00 30.72 3.41
2939 6430 1.278985 CCCTTGTACTCCATGACAGCA 59.721 52.381 0.00 0.00 0.00 4.41
2942 6433 0.618458 GGCCCTTGTACTCCATGACA 59.382 55.000 0.00 0.00 0.00 3.58
3156 6647 1.669265 CACTACGTGCGGAGACATCTA 59.331 52.381 11.11 0.00 0.00 1.98
3220 6716 2.848691 ACTACGAGGGATTCCTAGACG 58.151 52.381 7.24 2.36 45.05 4.18
3233 6729 2.683867 AGCTAACCAGTGCTACTACGAG 59.316 50.000 0.00 0.00 37.81 4.18
3234 6730 2.719739 AGCTAACCAGTGCTACTACGA 58.280 47.619 0.00 0.00 37.81 3.43
3309 7046 4.099120 CGGTCTAGAATTGAAGTGACTCG 58.901 47.826 0.00 0.00 0.00 4.18
3340 7080 4.364860 GTTTTGTTTACAGCCGTTGGATT 58.635 39.130 0.00 0.00 0.00 3.01
3381 7121 2.965147 TGAGGAAAAAGAAGCCAAAGGG 59.035 45.455 0.00 0.00 37.18 3.95
3695 7435 1.374252 CGGTGGGAACAAGTCGGAG 60.374 63.158 0.00 0.00 46.06 4.63
3696 7436 2.738480 CGGTGGGAACAAGTCGGA 59.262 61.111 0.00 0.00 46.06 4.55
3697 7437 2.162338 TAGCGGTGGGAACAAGTCGG 62.162 60.000 0.00 0.00 46.06 4.79
3704 7444 2.125106 CAGCCTAGCGGTGGGAAC 60.125 66.667 22.31 3.68 36.27 3.62
3764 7520 0.463620 GTGGGAGTGCAGGAGATCTC 59.536 60.000 14.75 14.75 0.00 2.75
3765 7521 0.980231 GGTGGGAGTGCAGGAGATCT 60.980 60.000 0.00 0.00 0.00 2.75
3766 7522 1.524482 GGTGGGAGTGCAGGAGATC 59.476 63.158 0.00 0.00 0.00 2.75
3767 7523 1.997874 GGGTGGGAGTGCAGGAGAT 60.998 63.158 0.00 0.00 0.00 2.75
3768 7524 2.607750 GGGTGGGAGTGCAGGAGA 60.608 66.667 0.00 0.00 0.00 3.71
3769 7525 2.822643 TAGGGGTGGGAGTGCAGGAG 62.823 65.000 0.00 0.00 0.00 3.69
3770 7526 2.409984 TTAGGGGTGGGAGTGCAGGA 62.410 60.000 0.00 0.00 0.00 3.86
3771 7527 1.281925 ATTAGGGGTGGGAGTGCAGG 61.282 60.000 0.00 0.00 0.00 4.85
3772 7528 1.507140 TATTAGGGGTGGGAGTGCAG 58.493 55.000 0.00 0.00 0.00 4.41
3781 7537 9.561069 GGCACATTATCTATATTATTAGGGGTG 57.439 37.037 0.00 0.00 0.00 4.61
3782 7538 8.724310 GGGCACATTATCTATATTATTAGGGGT 58.276 37.037 0.00 0.00 0.00 4.95
3806 7562 0.329261 TCTGAGGTTGAAGCCATGGG 59.671 55.000 15.13 0.00 0.00 4.00
3822 7578 4.920340 CGGACCTCATCGAAAATCTATCTG 59.080 45.833 0.00 0.00 0.00 2.90
3833 7589 3.822192 CACGGCGGACCTCATCGA 61.822 66.667 13.24 0.00 0.00 3.59
3887 7654 5.155278 TCGGTTTTGCTATTTCTCAGGTA 57.845 39.130 0.00 0.00 0.00 3.08
3923 7690 7.275560 GCTTTAGCAATAATGGTTTTCACGATT 59.724 33.333 0.00 0.00 41.59 3.34
3930 7697 9.559732 AAAAGAAGCTTTAGCAATAATGGTTTT 57.440 25.926 0.00 0.00 45.16 2.43
3945 7712 7.552330 TGCAATCCAACTTTTAAAAGAAGCTTT 59.448 29.630 29.97 13.49 39.31 3.51
3953 7720 5.044558 GTCGGTGCAATCCAACTTTTAAAA 58.955 37.500 0.00 0.00 0.00 1.52
3978 7745 6.084277 CGTCCCTAAAAACAGAACATTTAGC 58.916 40.000 0.00 0.00 36.02 3.09
3984 7751 5.406175 CGATAACGTCCCTAAAAACAGAACA 59.594 40.000 0.00 0.00 34.56 3.18
4007 7774 4.667262 AGAGAAGATGATGAAGTCGTTCG 58.333 43.478 0.00 0.00 35.17 3.95
4059 7837 0.400594 GCACTAGGGTCAAGTGGGTT 59.599 55.000 5.47 0.00 43.71 4.11
4060 7838 0.766674 TGCACTAGGGTCAAGTGGGT 60.767 55.000 5.47 0.00 43.71 4.51
4064 7842 2.300437 GAGAAGTGCACTAGGGTCAAGT 59.700 50.000 22.01 0.00 0.00 3.16
4068 7846 0.537653 GGGAGAAGTGCACTAGGGTC 59.462 60.000 22.01 14.08 0.00 4.46
4069 7847 0.117340 AGGGAGAAGTGCACTAGGGT 59.883 55.000 22.01 3.60 0.00 4.34
4084 7862 1.043116 CACGCATGGGACTAGAGGGA 61.043 60.000 17.76 0.00 0.00 4.20
4099 7877 1.091771 ATCTGCCAGTACATGCACGC 61.092 55.000 5.33 0.00 33.17 5.34
4100 7878 2.223537 TATCTGCCAGTACATGCACG 57.776 50.000 5.33 0.00 33.17 5.34
4112 7890 4.989279 TGCCTTCATCTTTTTATCTGCC 57.011 40.909 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.