Multiple sequence alignment - TraesCS1A01G006000

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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 TraesCS1A01G006000 chr1A 100.000 5539 0 0 1 5539 3455772 3450234 0.000000e+00 10229.0
1 TraesCS1A01G006000 chr1A 89.862 3324 295 20 2238 5539 2975203 2978506 0.000000e+00 4233.0
2 TraesCS1A01G006000 chr1A 89.103 3368 286 38 2213 5539 3680272 3676945 0.000000e+00 4111.0
3 TraesCS1A01G006000 chr1A 85.780 3453 473 17 1006 4451 3582485 3579044 0.000000e+00 3640.0
4 TraesCS1A01G006000 chr1A 82.592 2045 249 57 20 2013 3504824 3502836 0.000000e+00 1705.0
5 TraesCS1A01G006000 chr1A 83.925 1437 193 23 513 1941 2982196 2983602 0.000000e+00 1339.0
6 TraesCS1A01G006000 chr1A 78.191 188 28 8 5043 5222 3668766 3668584 2.110000e-19 108.0
7 TraesCS1A01G006000 chr1D 87.705 3717 365 52 1882 5539 620313 616630 0.000000e+00 4248.0
8 TraesCS1A01G006000 chr1D 84.354 3937 547 46 941 4853 447070 450961 0.000000e+00 3794.0
9 TraesCS1A01G006000 chr1D 90.446 2020 169 20 1 2013 622112 620110 0.000000e+00 2639.0
10 TraesCS1A01G006000 chr1D 84.516 1311 174 18 783 2085 458555 459844 0.000000e+00 1269.0
11 TraesCS1A01G006000 chr1D 85.593 118 16 1 5229 5345 494550842 494550959 7.540000e-24 122.0
12 TraesCS1A01G006000 chr1B 87.924 3594 369 22 1989 5539 4560707 4557136 0.000000e+00 4172.0
13 TraesCS1A01G006000 chr1B 88.681 3101 316 19 1882 4961 4115362 4118448 0.000000e+00 3749.0
14 TraesCS1A01G006000 chr1B 88.631 3105 302 31 1882 4964 4482843 4479768 0.000000e+00 3731.0
15 TraesCS1A01G006000 chr1B 85.825 2702 372 7 1878 4574 3951975 3954670 0.000000e+00 2857.0
16 TraesCS1A01G006000 chr1B 85.688 2697 372 8 1882 4570 4510009 4507319 0.000000e+00 2830.0
17 TraesCS1A01G006000 chr1B 85.736 2685 357 21 1882 4556 3943209 3945877 0.000000e+00 2813.0
18 TraesCS1A01G006000 chr1B 88.999 1909 176 23 119 2013 4857243 4855355 0.000000e+00 2331.0
19 TraesCS1A01G006000 chr1B 83.232 1813 232 53 249 2013 4094820 4096608 0.000000e+00 1598.0
20 TraesCS1A01G006000 chr1B 86.177 1172 153 7 844 2013 4591761 4590597 0.000000e+00 1258.0
21 TraesCS1A01G006000 chr1B 85.520 1174 153 10 843 2013 4483799 4482640 0.000000e+00 1210.0
22 TraesCS1A01G006000 chr1B 84.786 1170 168 8 845 2013 4114405 4115565 0.000000e+00 1166.0
23 TraesCS1A01G006000 chr1B 84.760 1168 161 10 840 2004 3951020 3952173 0.000000e+00 1155.0
24 TraesCS1A01G006000 chr1B 83.576 1236 184 15 786 2013 687785307 687786531 0.000000e+00 1140.0
25 TraesCS1A01G006000 chr1B 92.007 538 30 7 5014 5539 4479758 4479222 0.000000e+00 743.0
26 TraesCS1A01G006000 chr1B 89.572 537 39 10 5014 5539 4118461 4118991 0.000000e+00 665.0
27 TraesCS1A01G006000 chr1B 80.857 700 97 18 821 1510 4825184 4824512 2.960000e-142 516.0
28 TraesCS1A01G006000 chr1B 78.481 316 22 27 4658 4934 687788995 687789303 1.230000e-36 165.0
29 TraesCS1A01G006000 chr1B 89.796 49 3 1 414 460 4830432 4830480 1.670000e-05 62.1
30 TraesCS1A01G006000 chr1B 94.444 36 2 0 441 476 4113999 4114034 7.750000e-04 56.5
31 TraesCS1A01G006000 chr3D 86.325 1170 154 4 845 2013 560058246 560057082 0.000000e+00 1269.0
32 TraesCS1A01G006000 chr3D 81.443 97 14 4 5122 5218 560072697 560072605 5.950000e-10 76.8
33 TraesCS1A01G006000 chr3D 100.000 30 0 0 447 476 560061336 560061307 7.750000e-04 56.5


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 TraesCS1A01G006000 chr1A 3450234 3455772 5538 True 10229.000000 10229 100.000000 1 5539 1 chr1A.!!$R1 5538
1 TraesCS1A01G006000 chr1A 3676945 3680272 3327 True 4111.000000 4111 89.103000 2213 5539 1 chr1A.!!$R5 3326
2 TraesCS1A01G006000 chr1A 3579044 3582485 3441 True 3640.000000 3640 85.780000 1006 4451 1 chr1A.!!$R3 3445
3 TraesCS1A01G006000 chr1A 2975203 2983602 8399 False 2786.000000 4233 86.893500 513 5539 2 chr1A.!!$F1 5026
4 TraesCS1A01G006000 chr1A 3502836 3504824 1988 True 1705.000000 1705 82.592000 20 2013 1 chr1A.!!$R2 1993
5 TraesCS1A01G006000 chr1D 447070 450961 3891 False 3794.000000 3794 84.354000 941 4853 1 chr1D.!!$F1 3912
6 TraesCS1A01G006000 chr1D 616630 622112 5482 True 3443.500000 4248 89.075500 1 5539 2 chr1D.!!$R1 5538
7 TraesCS1A01G006000 chr1D 458555 459844 1289 False 1269.000000 1269 84.516000 783 2085 1 chr1D.!!$F2 1302
8 TraesCS1A01G006000 chr1B 4557136 4560707 3571 True 4172.000000 4172 87.924000 1989 5539 1 chr1B.!!$R2 3550
9 TraesCS1A01G006000 chr1B 4507319 4510009 2690 True 2830.000000 2830 85.688000 1882 4570 1 chr1B.!!$R1 2688
10 TraesCS1A01G006000 chr1B 3943209 3945877 2668 False 2813.000000 2813 85.736000 1882 4556 1 chr1B.!!$F1 2674
11 TraesCS1A01G006000 chr1B 4855355 4857243 1888 True 2331.000000 2331 88.999000 119 2013 1 chr1B.!!$R5 1894
12 TraesCS1A01G006000 chr1B 3951020 3954670 3650 False 2006.000000 2857 85.292500 840 4574 2 chr1B.!!$F4 3734
13 TraesCS1A01G006000 chr1B 4479222 4483799 4577 True 1894.666667 3731 88.719333 843 5539 3 chr1B.!!$R6 4696
14 TraesCS1A01G006000 chr1B 4094820 4096608 1788 False 1598.000000 1598 83.232000 249 2013 1 chr1B.!!$F2 1764
15 TraesCS1A01G006000 chr1B 4113999 4118991 4992 False 1409.125000 3749 89.370750 441 5539 4 chr1B.!!$F5 5098
16 TraesCS1A01G006000 chr1B 4590597 4591761 1164 True 1258.000000 1258 86.177000 844 2013 1 chr1B.!!$R3 1169
17 TraesCS1A01G006000 chr1B 687785307 687789303 3996 False 652.500000 1140 81.028500 786 4934 2 chr1B.!!$F6 4148
18 TraesCS1A01G006000 chr1B 4824512 4825184 672 True 516.000000 516 80.857000 821 1510 1 chr1B.!!$R4 689
19 TraesCS1A01G006000 chr3D 560057082 560061336 4254 True 662.750000 1269 93.162500 447 2013 2 chr3D.!!$R2 1566

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
894 3697 1.065199 TGAGGACCTCATGACAATGGC 60.065 52.381 20.74 0.0 35.39 4.40 F
2230 5276 0.035458 GATAACCGGCTCCATCCCTG 59.965 60.000 0.00 0.0 0.00 4.45 F
2258 5304 0.659957 GGCAATCTGATGAACCTCGC 59.340 55.000 0.00 0.0 0.00 5.03 F
3631 6678 0.773644 ACAACTCCAAGATGGGCAGT 59.226 50.000 0.00 0.0 38.32 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 5899 0.106419 GGGCCCGGATAATTGGTTGA 60.106 55.000 5.69 0.0 0.00 3.18 R
4152 7206 0.104855 AGTTCTGCACAGAAGCGTCA 59.895 50.000 13.21 0.0 46.93 4.35 R
4295 7349 7.500227 TCCAGAATATCTTTCACCATCATTGAC 59.500 37.037 0.00 0.0 0.00 3.18 R
4723 7805 0.827368 AAAAACCACGGGCACACAAT 59.173 45.000 0.00 0.0 0.00 2.71 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
48 49 7.012327 GGAGCAATACTAATCATTTGCACACTA 59.988 37.037 8.92 0.00 45.26 2.74
117 119 2.987821 GGAAGACGTACAGAAAGTGCTC 59.012 50.000 0.00 0.00 0.00 4.26
155 157 6.588719 TTACCAAATCAAATCCACTTGAGG 57.411 37.500 0.00 0.00 38.66 3.86
559 3296 8.019656 AGATACCATCCGATAAAAACTGTACT 57.980 34.615 0.00 0.00 0.00 2.73
894 3697 1.065199 TGAGGACCTCATGACAATGGC 60.065 52.381 20.74 0.00 35.39 4.40
897 3700 1.077501 ACCTCATGACAATGGCCGG 60.078 57.895 0.00 0.00 34.30 6.13
925 3729 9.319143 ACACTGTTAAATACTCATCAATAGAGC 57.681 33.333 0.00 0.00 36.58 4.09
966 3779 2.182516 TCCCCCAACCAAACACATTT 57.817 45.000 0.00 0.00 0.00 2.32
969 3782 1.765314 CCCCAACCAAACACATTTCCA 59.235 47.619 0.00 0.00 0.00 3.53
992 3805 6.128472 CCAAAATTCCAGATGCAAAAACTAGC 60.128 38.462 0.00 0.00 0.00 3.42
993 3806 5.726980 AATTCCAGATGCAAAAACTAGCA 57.273 34.783 0.00 0.00 45.92 3.49
996 3809 3.507233 TCCAGATGCAAAAACTAGCAAGG 59.493 43.478 0.00 0.00 44.88 3.61
1011 3836 3.569250 GCAAGGAAAATGCGACCTTTA 57.431 42.857 0.00 0.00 41.33 1.85
1033 3861 0.179097 GTACCTCTGCCTACTGCTGC 60.179 60.000 0.00 0.00 42.00 5.25
1139 3967 3.066621 CACTGGAAAGCTACACTTGCAAA 59.933 43.478 0.00 0.00 39.09 3.68
1167 3995 2.693762 GCGCATGAGCTCTTGGCAA 61.694 57.895 25.89 0.00 44.79 4.52
1185 4013 1.688197 CAAGAAAACACCAGCCCATGT 59.312 47.619 0.00 0.00 0.00 3.21
1251 4079 3.180282 CCCTGGGTGGTGACCAAT 58.820 61.111 5.57 0.00 45.25 3.16
1330 4158 5.625426 GCTCTTCCATTCCTCGCATATATCA 60.625 44.000 0.00 0.00 0.00 2.15
1376 4204 3.181478 GGTGCACTACCCACTAGTATCAC 60.181 52.174 17.98 0.00 44.15 3.06
1397 4225 0.250467 TCCCTGTCAGCACTTTCAGC 60.250 55.000 0.00 0.00 0.00 4.26
1439 4268 4.400567 CCAGCTCAAAGGGAAAATTCCTAG 59.599 45.833 11.75 4.16 46.72 3.02
1484 4313 0.540923 AGGGTGCTTGAGCTCTCATC 59.459 55.000 16.19 10.20 42.66 2.92
1755 4584 1.396653 GCAGGCTAGTCCATTTGCAT 58.603 50.000 1.72 0.00 34.63 3.96
1782 4611 7.168796 GTCTTGCGCTTAATTCAAATGATTTG 58.831 34.615 11.54 11.54 41.96 2.32
1913 4742 6.649557 GCTAAGCTAAACCAACTTGTTCTCTA 59.350 38.462 0.00 0.00 0.00 2.43
1923 4752 8.103948 ACCAACTTGTTCTCTATGAAAATCAG 57.896 34.615 0.00 0.00 36.30 2.90
1953 4782 3.720002 GTCCAATACCCCCAGAAATAGGA 59.280 47.826 0.00 0.00 0.00 2.94
1961 4790 6.668133 ACCCCCAGAAATAGGAAATCTTAA 57.332 37.500 0.00 0.00 0.00 1.85
1962 4791 6.673583 ACCCCCAGAAATAGGAAATCTTAAG 58.326 40.000 0.00 0.00 0.00 1.85
1987 4816 5.183228 TGCTAAACCAACTTATGCTCTACC 58.817 41.667 0.00 0.00 0.00 3.18
1998 4827 9.294030 CAACTTATGCTCTACCAAAATCAAATC 57.706 33.333 0.00 0.00 0.00 2.17
2000 4829 9.193806 ACTTATGCTCTACCAAAATCAAATCAT 57.806 29.630 0.00 0.00 0.00 2.45
2004 4833 6.039717 TGCTCTACCAAAATCAAATCATAGGC 59.960 38.462 0.00 0.00 0.00 3.93
2016 4845 2.815357 TCATAGGCTCAATACCCCCT 57.185 50.000 0.00 0.00 0.00 4.79
2029 4930 0.770557 ACCCCCTGAACTAGGCAACA 60.771 55.000 0.00 0.00 45.89 3.33
2129 5174 8.160106 ACTGAATCTCCAGAATTTAGAGTTGTT 58.840 33.333 0.00 0.00 37.59 2.83
2160 5205 4.647564 AATATCTGGCACTATTCCTGGG 57.352 45.455 0.00 0.00 0.00 4.45
2164 5209 1.149401 GGCACTATTCCTGGGAGCC 59.851 63.158 0.00 1.93 0.00 4.70
2204 5249 3.766591 CTGGTAGCACTATCCCTCTATGG 59.233 52.174 0.00 0.00 0.00 2.74
2230 5276 0.035458 GATAACCGGCTCCATCCCTG 59.965 60.000 0.00 0.00 0.00 4.45
2258 5304 0.659957 GGCAATCTGATGAACCTCGC 59.340 55.000 0.00 0.00 0.00 5.03
2272 5318 8.147704 TGATGAACCTCGCATATTTATACTTGA 58.852 33.333 0.00 0.00 0.00 3.02
2275 5321 8.773645 TGAACCTCGCATATTTATACTTGAATG 58.226 33.333 0.00 0.00 0.00 2.67
2322 5368 4.808895 CCTAAAACTTTTGGGAAGTTGCAC 59.191 41.667 10.45 0.00 40.10 4.57
2324 5370 3.971245 AACTTTTGGGAAGTTGCACAA 57.029 38.095 3.57 0.00 38.88 3.33
2386 5432 5.890419 GGTGATCTTCCTCAAGAATTTGGAT 59.110 40.000 0.00 0.00 42.14 3.41
2465 5511 3.304659 CCCGCAAATATATGTTCAGGTGC 60.305 47.826 0.00 0.00 0.00 5.01
2492 5538 5.237815 ACTTCAAACTCTCAATGTCGCATA 58.762 37.500 0.00 0.00 0.00 3.14
2536 5582 8.576442 CCATTCCAAGTAGTTTAAAGACATGTT 58.424 33.333 0.00 0.00 0.00 2.71
2574 5620 3.971032 GACCTTGAGTCAAACCAACTG 57.029 47.619 7.06 0.00 45.55 3.16
2621 5667 4.134563 GGTGTTTATCCACAACTCACAGT 58.865 43.478 0.00 0.00 37.06 3.55
2654 5700 2.738587 TCGAATAGACTCTCTGGGCT 57.261 50.000 0.00 0.00 0.00 5.19
2658 5704 4.075682 CGAATAGACTCTCTGGGCTGATA 58.924 47.826 0.00 0.00 0.00 2.15
2686 5732 5.604231 TCCAATCTAGGTGCATCTACTCAAT 59.396 40.000 1.47 0.00 0.00 2.57
2689 5735 7.601886 CCAATCTAGGTGCATCTACTCAATTAG 59.398 40.741 1.47 0.00 0.00 1.73
2693 5739 3.561725 GGTGCATCTACTCAATTAGTGGC 59.438 47.826 0.00 0.00 39.39 5.01
2725 5771 3.627577 AGCACAAAATATGATCACGGGTC 59.372 43.478 0.00 0.00 0.00 4.46
2764 5810 8.221944 TCCTTTCTAAATTGTCCAACCTAGAAA 58.778 33.333 16.61 16.61 36.04 2.52
2778 5825 7.713942 TCCAACCTAGAAAAACTAAGACTTGAC 59.286 37.037 0.00 0.00 0.00 3.18
2827 5874 5.335191 CCACCAGAAATCTGCAGTTTAACTC 60.335 44.000 14.67 6.60 42.47 3.01
2868 5915 6.490040 ACTTATCATTCAACCAATTATCCGGG 59.510 38.462 0.00 0.00 0.00 5.73
2869 5916 2.955660 TCATTCAACCAATTATCCGGGC 59.044 45.455 0.00 0.00 0.00 6.13
2900 5947 4.252073 ACACAGATAGAAAAGCTGAGCAG 58.748 43.478 7.39 0.00 33.94 4.24
2972 6019 1.202818 GGAACTAGGGGCCTGCATAAG 60.203 57.143 0.84 0.00 0.00 1.73
2974 6021 1.893315 ACTAGGGGCCTGCATAAGAA 58.107 50.000 0.84 0.00 0.00 2.52
3072 6119 5.122869 GCAGATCAAGTTAGATGTGAGCAAA 59.877 40.000 13.12 0.00 40.61 3.68
3124 6171 2.113860 TGGGAAGTTGCTGATGCTAC 57.886 50.000 0.00 0.00 43.42 3.58
3127 6174 2.162408 GGGAAGTTGCTGATGCTACAAC 59.838 50.000 5.56 0.00 45.02 3.32
3200 6247 2.226962 AGCATGGTGAGCCTTTCAAT 57.773 45.000 0.00 0.00 37.61 2.57
3228 6275 2.631062 TGTGTCCTACAACGACTTGGAT 59.369 45.455 0.00 0.00 36.06 3.41
3270 6317 2.476854 GCTACTCCAAAATGCTTCAGCG 60.477 50.000 0.00 0.00 45.83 5.18
3307 6354 5.313712 CCAATAAAGGTCTGTGTGGTAACT 58.686 41.667 0.00 0.00 37.61 2.24
3315 6362 3.069729 GTCTGTGTGGTAACTTCTCTGGT 59.930 47.826 0.00 0.00 37.61 4.00
3548 6595 8.921205 ACTAGTATTTGACGATATTGTAAGGGT 58.079 33.333 0.00 0.00 0.00 4.34
3631 6678 0.773644 ACAACTCCAAGATGGGCAGT 59.226 50.000 0.00 0.00 38.32 4.40
3798 6845 9.653287 AAATTTCTCGTCTATGACTACATTCAA 57.347 29.630 0.00 0.00 37.87 2.69
3918 6965 7.416817 CAATATCTTATTTGCACCACGAATGA 58.583 34.615 0.00 0.00 34.09 2.57
4295 7349 2.673833 AGTCTTTCTAACGGCGAACAG 58.326 47.619 16.62 7.39 0.00 3.16
4335 7389 2.517402 TGGACCAACGGCCAACAC 60.517 61.111 2.24 0.00 0.00 3.32
4371 7425 5.068987 ACTGAAGAGAATAGCTTAGCTCTGG 59.931 44.000 11.09 0.00 40.44 3.86
4391 7445 2.421952 GGTCATCAAGCTGGCCTTATCA 60.422 50.000 3.32 0.00 37.93 2.15
4550 7615 5.186021 GTCTGAATCCTAGTGAGAAACCAGA 59.814 44.000 0.00 0.00 0.00 3.86
4589 7654 8.255905 AGAGGCCAATTCAGATTTCTAATTTTG 58.744 33.333 5.01 0.00 0.00 2.44
4642 7720 9.373450 CCTATATATACCTCTTGCCATATGACT 57.627 37.037 3.65 0.00 0.00 3.41
4723 7805 5.248248 TCTCCTGATACAACAAAGATCACCA 59.752 40.000 0.00 0.00 0.00 4.17
4745 7827 1.076632 TGTGCCCGTGGTTTTTCCT 60.077 52.632 0.00 0.00 37.07 3.36
5100 8224 5.159925 CAATCACAATGCATAAACGGAACA 58.840 37.500 0.00 0.00 0.00 3.18
5102 8226 4.541779 TCACAATGCATAAACGGAACAAC 58.458 39.130 0.00 0.00 0.00 3.32
5295 8445 5.723492 TCATGTCATCTCGCTTATTGTTG 57.277 39.130 0.00 0.00 0.00 3.33
5322 8472 7.832187 TCTGGGTATCAAAGTAAAATACCTTGG 59.168 37.037 9.85 0.00 42.94 3.61
5405 8562 6.037830 ACACGGATATAGGTGCATAAAACAAC 59.962 38.462 0.00 0.00 37.68 3.32
5415 8576 6.754675 AGGTGCATAAAACAACAAAAGTACAC 59.245 34.615 0.00 0.00 0.00 2.90
5476 8643 2.541178 CGCATACGTAGTCCTTGTCCTC 60.541 54.545 0.08 0.00 43.93 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.175641 GCAAATGATTAGTATTGCTCCCATACT 59.824 37.037 2.33 0.00 43.58 2.12
55 57 7.113437 TGCCCAGCACTTTATAAATACAAGTA 58.887 34.615 0.00 0.00 31.71 2.24
67 69 2.819608 GAGTTGATTGCCCAGCACTTTA 59.180 45.455 0.00 0.00 38.71 1.85
144 146 3.884037 AAGTTCCAACCTCAAGTGGAT 57.116 42.857 0.00 0.00 0.00 3.41
155 157 3.626217 ACTGACCGAAGAAAAGTTCCAAC 59.374 43.478 0.00 0.00 0.00 3.77
476 510 9.423061 GTTTGACCATAACTGCTTGAATATTTT 57.577 29.630 0.00 0.00 0.00 1.82
894 3697 3.331150 TGAGTATTTAACAGTGTGCCGG 58.669 45.455 0.00 0.00 0.00 6.13
897 3700 9.098355 TCTATTGATGAGTATTTAACAGTGTGC 57.902 33.333 0.00 0.00 0.00 4.57
966 3779 5.927819 AGTTTTTGCATCTGGAATTTTGGA 58.072 33.333 0.00 0.00 0.00 3.53
969 3782 6.523840 TGCTAGTTTTTGCATCTGGAATTTT 58.476 32.000 0.00 0.00 33.94 1.82
992 3805 4.023193 ACAGTAAAGGTCGCATTTTCCTTG 60.023 41.667 0.00 0.00 40.80 3.61
993 3806 4.142038 ACAGTAAAGGTCGCATTTTCCTT 58.858 39.130 0.00 0.00 42.47 3.36
996 3809 4.694037 AGGTACAGTAAAGGTCGCATTTTC 59.306 41.667 0.00 0.00 0.00 2.29
1011 3836 1.187087 GCAGTAGGCAGAGGTACAGT 58.813 55.000 0.00 0.00 43.97 3.55
1033 3861 2.064762 CAAGAGAAGAAGGCACGACAG 58.935 52.381 0.00 0.00 0.00 3.51
1151 3979 1.171308 TTCTTGCCAAGAGCTCATGC 58.829 50.000 17.77 15.17 44.23 4.06
1152 3980 3.005050 TGTTTTCTTGCCAAGAGCTCATG 59.995 43.478 17.77 14.73 44.23 3.07
1167 3995 2.890945 GTTACATGGGCTGGTGTTTTCT 59.109 45.455 0.00 0.00 0.00 2.52
1185 4013 0.908910 ACATGATGCCCGTCCAGTTA 59.091 50.000 0.00 0.00 0.00 2.24
1227 4055 2.285069 ACCACCCAGGGCATACGA 60.285 61.111 4.91 0.00 43.89 3.43
1251 4079 3.538614 GCGTCTGGCAGGGAGATA 58.461 61.111 15.73 0.00 42.87 1.98
1330 4158 4.340617 TGGAGACTGTTGTTTTGAAGGTT 58.659 39.130 0.00 0.00 0.00 3.50
1376 4204 0.397941 TGAAAGTGCTGACAGGGAGG 59.602 55.000 4.26 0.00 0.00 4.30
1397 4225 3.476552 TGGTTGAAGCTAAGGTCAAGTG 58.523 45.455 0.00 0.00 34.52 3.16
1439 4268 0.895100 TTGCAGGCCACCAATCTCAC 60.895 55.000 5.01 0.00 0.00 3.51
1613 4442 0.167689 GCTGTTGCTTAGCTGCAGAC 59.832 55.000 20.43 9.11 44.27 3.51
1755 4584 4.217334 TCATTTGAATTAAGCGCAAGACCA 59.783 37.500 11.47 0.00 43.02 4.02
1763 4592 6.808212 ACCTGACAAATCATTTGAATTAAGCG 59.192 34.615 17.30 4.15 43.26 4.68
1782 4611 3.282885 GGAGATTGGAATTGGACCTGAC 58.717 50.000 0.00 0.00 0.00 3.51
1913 4742 5.183530 TGGACCTGTGATCTGATTTTCAT 57.816 39.130 0.00 0.00 0.00 2.57
1961 4790 5.749462 AGAGCATAAGTTGGTTTAGCATCT 58.251 37.500 0.00 0.00 35.82 2.90
1962 4791 6.017852 GGTAGAGCATAAGTTGGTTTAGCATC 60.018 42.308 0.00 0.00 39.42 3.91
1978 4807 7.255730 GCCTATGATTTGATTTTGGTAGAGCAT 60.256 37.037 0.00 0.00 0.00 3.79
1980 4809 6.264067 AGCCTATGATTTGATTTTGGTAGAGC 59.736 38.462 0.00 0.00 0.00 4.09
1987 4816 7.869429 GGGTATTGAGCCTATGATTTGATTTTG 59.131 37.037 0.00 0.00 40.35 2.44
1998 4827 2.338809 TCAGGGGGTATTGAGCCTATG 58.661 52.381 0.00 0.00 43.31 2.23
2000 4829 2.124411 GTTCAGGGGGTATTGAGCCTA 58.876 52.381 0.00 0.00 43.31 3.93
2004 4833 2.104963 GCCTAGTTCAGGGGGTATTGAG 59.895 54.545 0.00 0.00 45.66 3.02
2016 4845 4.080919 AGCATAGTGATGTTGCCTAGTTCA 60.081 41.667 0.00 0.00 37.07 3.18
2029 4930 9.270640 GAGAGAAATTACATTGAGCATAGTGAT 57.729 33.333 0.00 0.00 0.00 3.06
2065 5038 3.473113 AGGTATTGGGCCTGTGATTTT 57.527 42.857 4.53 0.00 34.56 1.82
2129 5174 3.006940 GTGCCAGATATTTGGTTGTCGA 58.993 45.455 13.50 0.00 40.49 4.20
2160 5205 5.703130 CAGCTTGGTAATATTTCCTAGGCTC 59.297 44.000 19.04 7.32 0.00 4.70
2189 5234 6.924913 TCTGATTTCCATAGAGGGATAGTG 57.075 41.667 0.00 0.00 36.67 2.74
2204 5249 3.194005 TGGAGCCGGTTATCTGATTTC 57.806 47.619 1.90 0.00 0.00 2.17
2230 5276 5.221009 GGTTCATCAGATTGCCAATCTCTTC 60.221 44.000 16.92 5.32 46.20 2.87
2275 5321 8.160106 AGGTATTGATCCTGATATTTGGTTCTC 58.840 37.037 0.00 0.00 33.62 2.87
2286 5332 8.971073 CCAAAAGTTTTAGGTATTGATCCTGAT 58.029 33.333 0.00 0.00 36.60 2.90
2322 5368 4.990257 AGATTCGCATTTCTTGGATGTTG 58.010 39.130 0.00 0.00 0.00 3.33
2324 5370 4.701651 TGAAGATTCGCATTTCTTGGATGT 59.298 37.500 0.00 0.00 32.46 3.06
2365 5411 9.218440 GAGATATCCAAATTCTTGAGGAAGATC 57.782 37.037 0.00 0.00 38.05 2.75
2366 5412 8.721479 TGAGATATCCAAATTCTTGAGGAAGAT 58.279 33.333 0.00 0.00 38.05 2.40
2386 5432 8.334263 TCAAGCACAACAATGTTTATGAGATA 57.666 30.769 10.39 0.00 37.82 1.98
2398 5444 2.787994 AGCTAGCTCAAGCACAACAAT 58.212 42.857 12.68 0.00 45.30 2.71
2406 5452 3.369451 GTGAGTTGTTAGCTAGCTCAAGC 59.631 47.826 23.26 14.54 43.11 4.01
2465 5511 3.403038 ACATTGAGAGTTTGAAGTCCGG 58.597 45.455 0.00 0.00 0.00 5.14
2492 5538 5.484998 GGAATGGGGCCATTGAACATATTAT 59.515 40.000 4.39 0.00 45.50 1.28
2536 5582 8.287439 TCAAGGTCAATTTCAACTAAACTTGA 57.713 30.769 0.00 0.00 34.95 3.02
2604 5650 5.482163 TCATCACTGTGAGTTGTGGATAA 57.518 39.130 16.46 0.00 35.15 1.75
2621 5667 6.057533 AGTCTATTCGATGCCAAATTCATCA 58.942 36.000 6.47 0.00 40.11 3.07
2654 5700 6.442885 AGATGCACCTAGATTGGATGATATCA 59.557 38.462 8.10 8.10 0.00 2.15
2658 5704 5.784390 AGTAGATGCACCTAGATTGGATGAT 59.216 40.000 0.00 0.00 0.00 2.45
2686 5732 3.767131 TGTGCTAGATGTAGTGCCACTAA 59.233 43.478 6.06 0.00 31.62 2.24
2689 5735 2.672961 TGTGCTAGATGTAGTGCCAC 57.327 50.000 0.00 0.00 0.00 5.01
2693 5739 9.264719 TGATCATATTTTGTGCTAGATGTAGTG 57.735 33.333 0.00 0.00 0.00 2.74
2725 5771 8.850156 CAATTTAGAAAGGATTGTAGGTATGGG 58.150 37.037 0.00 0.00 0.00 4.00
2734 5780 6.782494 AGGTTGGACAATTTAGAAAGGATTGT 59.218 34.615 1.00 1.00 44.25 2.71
2852 5899 0.106419 GGGCCCGGATAATTGGTTGA 60.106 55.000 5.69 0.00 0.00 3.18
2853 5900 0.396417 TGGGCCCGGATAATTGGTTG 60.396 55.000 19.37 0.00 0.00 3.77
2865 5912 1.046472 TCTGTGTAGGTATGGGCCCG 61.046 60.000 19.37 0.00 0.00 6.13
2868 5915 5.546621 TTTCTATCTGTGTAGGTATGGGC 57.453 43.478 0.00 0.00 0.00 5.36
2869 5916 5.992217 GCTTTTCTATCTGTGTAGGTATGGG 59.008 44.000 0.00 0.00 0.00 4.00
2900 5947 8.282982 TCCCAGATATATCAAGGTATCCTAGAC 58.717 40.741 15.08 0.00 31.13 2.59
2972 6019 7.173218 TGTTGTTGATCTTCAAGGACTGTATTC 59.827 37.037 0.00 0.00 37.00 1.75
2974 6021 6.533730 TGTTGTTGATCTTCAAGGACTGTAT 58.466 36.000 0.00 0.00 37.00 2.29
3022 6069 4.400567 GCCTGCTAAATTTCCAATCTCACT 59.599 41.667 0.00 0.00 0.00 3.41
3026 6073 3.703052 CAGGCCTGCTAAATTTCCAATCT 59.297 43.478 22.33 0.00 0.00 2.40
3056 6103 7.665559 TGAGGTTATTTTTGCTCACATCTAACT 59.334 33.333 0.00 0.00 0.00 2.24
3116 6163 8.668353 GTGATAAATTCAGAAGTTGTAGCATCA 58.332 33.333 6.10 4.25 34.17 3.07
3200 6247 2.036604 TCGTTGTAGGACACATCAAGCA 59.963 45.455 0.00 0.00 36.90 3.91
3240 6287 0.394938 TTTGGAGTAGCCGTGCTGAA 59.605 50.000 8.44 0.00 40.10 3.02
3241 6288 0.394938 TTTTGGAGTAGCCGTGCTGA 59.605 50.000 8.44 0.00 40.10 4.26
3315 6362 3.153919 GGTTGAATAACAAGGTGGCAGA 58.846 45.455 0.00 0.00 39.30 4.26
3631 6678 2.057137 AGCTTCTTCACAGCAACCAA 57.943 45.000 0.00 0.00 39.99 3.67
3740 6787 4.090761 TGGGAGCAGAATCCATACATTC 57.909 45.455 0.00 0.00 41.52 2.67
3798 6845 0.768221 TTCTGTGGAGGCTTCCCTGT 60.768 55.000 13.07 0.00 43.12 4.00
3918 6965 5.394738 TCTCGATGGATTATAGGTGGACTT 58.605 41.667 0.00 0.00 0.00 3.01
4152 7206 0.104855 AGTTCTGCACAGAAGCGTCA 59.895 50.000 13.21 0.00 46.93 4.35
4295 7349 7.500227 TCCAGAATATCTTTCACCATCATTGAC 59.500 37.037 0.00 0.00 0.00 3.18
4335 7389 7.041508 GCTATTCTCTTCAGTTGATATTGGTGG 60.042 40.741 0.00 0.00 0.00 4.61
4371 7425 2.923121 TGATAAGGCCAGCTTGATGAC 58.077 47.619 5.01 0.00 0.00 3.06
4391 7445 4.347607 CTTGGGGAGAAGATTCCAAACAT 58.652 43.478 0.00 0.00 38.60 2.71
4550 7615 1.324005 GGCCTCTGCTTCGGTAGACT 61.324 60.000 0.00 0.00 37.74 3.24
4589 7654 9.811995 TGGTGTATGAGTGATGTATAAGTAAAC 57.188 33.333 0.00 0.00 0.00 2.01
4596 7666 9.990868 ATATAGGTGGTGTATGAGTGATGTATA 57.009 33.333 0.00 0.00 0.00 1.47
4597 7667 8.901472 ATATAGGTGGTGTATGAGTGATGTAT 57.099 34.615 0.00 0.00 0.00 2.29
4601 7671 9.422681 GGTATATATAGGTGGTGTATGAGTGAT 57.577 37.037 0.00 0.00 0.00 3.06
4642 7720 1.077086 ATCCTGTGTGGCATGGCAA 59.923 52.632 25.11 11.55 35.26 4.52
4723 7805 0.827368 AAAAACCACGGGCACACAAT 59.173 45.000 0.00 0.00 0.00 2.71
5069 8193 1.068402 TGCATTGTGATTGTTCCTGCG 60.068 47.619 0.00 0.00 0.00 5.18
5100 8224 5.711506 TCTCCAATGTGCTTACATTCATGTT 59.288 36.000 2.88 0.00 41.97 2.71
5102 8226 5.823209 TCTCCAATGTGCTTACATTCATG 57.177 39.130 2.88 0.00 38.16 3.07
5212 8350 4.479158 GTTCATGGGGGCAATAATAAGGA 58.521 43.478 0.00 0.00 0.00 3.36
5283 8432 2.851263 ACCCAGACAACAATAAGCGA 57.149 45.000 0.00 0.00 0.00 4.93
5295 8445 8.674607 CAAGGTATTTTACTTTGATACCCAGAC 58.325 37.037 7.86 0.00 45.37 3.51
5322 8472 1.079503 GTGATCGTTCCTGCTTGGTC 58.920 55.000 0.00 0.00 37.07 4.02
5364 8521 3.004210 TCCGTGTGTTCACATTCATTTGG 59.996 43.478 8.87 3.89 44.02 3.28
5415 8576 5.809051 CGTAAGCCCTTTTACTTAGTACTGG 59.191 44.000 5.39 0.69 32.58 4.00
5476 8643 3.079578 GGACCACATATGCTCCATCATG 58.920 50.000 1.58 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.