Multiple sequence alignment - TraesCS5D01G118200

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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 TraesCS5D01G118200 chr5D 100.000 6357 0 0 1 6357 156579489 156573133 0.000000e+00 11740.0
1 TraesCS5D01G118200 chr5D 91.922 718 53 2 5641 6357 116030902 116030189 0.000000e+00 1000.0
2 TraesCS5D01G118200 chr5D 85.542 83 8 4 5560 5642 186952657 186952735 4.080000e-12 84.2
3 TraesCS5D01G118200 chr5A 95.032 5374 139 40 1 5339 239118862 239124142 0.000000e+00 8327.0
4 TraesCS5D01G118200 chr5A 92.409 303 20 2 5340 5642 239124186 239124485 4.550000e-116 429.0
5 TraesCS5D01G118200 chr5B 96.370 1102 26 6 251 1342 191037733 191036636 0.000000e+00 1801.0
6 TraesCS5D01G118200 chr5B 94.719 890 34 4 4462 5339 191030493 191029605 0.000000e+00 1371.0
7 TraesCS5D01G118200 chr5B 97.233 759 19 1 3709 4467 191031303 191030547 0.000000e+00 1284.0
8 TraesCS5D01G118200 chr5B 91.392 790 47 11 1860 2642 191036028 191035253 0.000000e+00 1062.0
9 TraesCS5D01G118200 chr5B 91.226 718 62 1 5641 6357 1414657 1415374 0.000000e+00 976.0
10 TraesCS5D01G118200 chr5B 96.247 453 17 0 3262 3714 191034164 191033712 0.000000e+00 743.0
11 TraesCS5D01G118200 chr5B 91.304 529 12 6 2735 3256 191034794 191034293 0.000000e+00 691.0
12 TraesCS5D01G118200 chr5B 90.928 485 30 7 1383 1863 191036624 191036150 1.930000e-179 640.0
13 TraesCS5D01G118200 chr5B 93.916 263 13 3 1 262 191038036 191037776 1.660000e-105 394.0
14 TraesCS5D01G118200 chr7D 92.201 718 55 1 5641 6357 453185718 453186435 0.000000e+00 1014.0
15 TraesCS5D01G118200 chr6D 91.933 719 54 4 5641 6357 414205022 414205738 0.000000e+00 1003.0
16 TraesCS5D01G118200 chr6D 91.086 718 63 1 5641 6357 438503379 438502662 0.000000e+00 970.0
17 TraesCS5D01G118200 chr6D 90.665 707 65 1 5652 6357 321759646 321760352 0.000000e+00 939.0
18 TraesCS5D01G118200 chr7A 90.833 720 61 4 5641 6357 149428241 149427524 0.000000e+00 959.0
19 TraesCS5D01G118200 chr7A 79.381 194 28 10 2045 2235 340596958 340596774 6.690000e-25 126.0
20 TraesCS5D01G118200 chr2D 90.808 718 65 1 5641 6357 599459450 599458733 0.000000e+00 959.0
21 TraesCS5D01G118200 chr1B 90.403 719 66 3 5641 6357 65710641 65709924 0.000000e+00 942.0
22 TraesCS5D01G118200 chr1B 90.323 186 18 0 1066 1251 198153439 198153254 1.770000e-60 244.0
23 TraesCS5D01G118200 chr1B 79.275 193 28 10 2045 2235 261655232 261655050 2.410000e-24 124.0
24 TraesCS5D01G118200 chr1B 88.462 78 7 2 5567 5642 160672441 160672518 6.790000e-15 93.5
25 TraesCS5D01G118200 chr4A 90.223 358 26 8 1259 1612 249770764 249771116 5.810000e-125 459.0
26 TraesCS5D01G118200 chr4A 91.429 70 6 0 5573 5642 275333851 275333782 5.250000e-16 97.1
27 TraesCS5D01G118200 chr4A 88.235 68 7 1 5576 5642 269433394 269433327 5.280000e-11 80.5
28 TraesCS5D01G118200 chr3B 90.860 186 17 0 1066 1251 151444539 151444724 3.810000e-62 250.0
29 TraesCS5D01G118200 chr3B 82.468 154 21 5 2084 2235 603040607 603040756 5.170000e-26 130.0
30 TraesCS5D01G118200 chr3B 92.754 69 5 0 5574 5642 342722717 342722785 4.060000e-17 100.0
31 TraesCS5D01G118200 chr3B 85.897 78 8 2 5561 5638 336079127 336079201 5.280000e-11 80.5
32 TraesCS5D01G118200 chr3A 90.860 186 17 0 1066 1251 555042272 555042087 3.810000e-62 250.0
33 TraesCS5D01G118200 chr1A 90.323 186 18 0 1066 1251 150456402 150456217 1.770000e-60 244.0
34 TraesCS5D01G118200 chr1A 83.333 96 8 3 3450 3539 561927998 561928091 1.470000e-11 82.4
35 TraesCS5D01G118200 chr1D 89.785 186 19 0 1066 1251 140519696 140519881 8.240000e-59 239.0
36 TraesCS5D01G118200 chr1D 81.696 224 19 10 3329 3539 468969201 468969415 3.940000e-37 167.0
37 TraesCS5D01G118200 chr6B 88.462 156 11 6 1342 1495 275293843 275293993 1.410000e-41 182.0
38 TraesCS5D01G118200 chr2B 83.117 154 20 5 2084 2235 31909947 31910096 1.110000e-27 135.0
39 TraesCS5D01G118200 chr2B 78.462 195 28 9 2045 2236 117978197 117978380 1.450000e-21 115.0
40 TraesCS5D01G118200 chrUn 81.935 155 20 6 2084 2235 264766451 264766600 2.410000e-24 124.0
41 TraesCS5D01G118200 chr4D 79.275 193 28 9 2045 2235 8392105 8391923 2.410000e-24 124.0
42 TraesCS5D01G118200 chr4D 86.250 80 9 2 5563 5642 210096701 210096778 1.140000e-12 86.1
43 TraesCS5D01G118200 chr4D 84.884 86 5 7 5560 5642 209427666 209427746 5.280000e-11 80.5
44 TraesCS5D01G118200 chr6A 93.939 66 4 0 5577 5642 283699731 283699796 4.060000e-17 100.0
45 TraesCS5D01G118200 chr6A 91.429 70 6 0 5573 5642 301254673 301254742 5.250000e-16 97.1
46 TraesCS5D01G118200 chr3D 90.411 73 6 1 5571 5642 242915984 242916056 1.890000e-15 95.3
47 TraesCS5D01G118200 chr2A 90.278 72 7 0 5571 5642 320793686 320793757 1.890000e-15 95.3
48 TraesCS5D01G118200 chr4B 85.556 90 6 6 5557 5642 245740012 245739926 3.160000e-13 87.9


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 TraesCS5D01G118200 chr5D 156573133 156579489 6356 True 11740.00 11740 100.000000 1 6357 1 chr5D.!!$R2 6356
1 TraesCS5D01G118200 chr5D 116030189 116030902 713 True 1000.00 1000 91.922000 5641 6357 1 chr5D.!!$R1 716
2 TraesCS5D01G118200 chr5A 239118862 239124485 5623 False 4378.00 8327 93.720500 1 5642 2 chr5A.!!$F1 5641
3 TraesCS5D01G118200 chr5B 191029605 191038036 8431 True 998.25 1801 94.013625 1 5339 8 chr5B.!!$R1 5338
4 TraesCS5D01G118200 chr5B 1414657 1415374 717 False 976.00 976 91.226000 5641 6357 1 chr5B.!!$F1 716
5 TraesCS5D01G118200 chr7D 453185718 453186435 717 False 1014.00 1014 92.201000 5641 6357 1 chr7D.!!$F1 716
6 TraesCS5D01G118200 chr6D 414205022 414205738 716 False 1003.00 1003 91.933000 5641 6357 1 chr6D.!!$F2 716
7 TraesCS5D01G118200 chr6D 438502662 438503379 717 True 970.00 970 91.086000 5641 6357 1 chr6D.!!$R1 716
8 TraesCS5D01G118200 chr6D 321759646 321760352 706 False 939.00 939 90.665000 5652 6357 1 chr6D.!!$F1 705
9 TraesCS5D01G118200 chr7A 149427524 149428241 717 True 959.00 959 90.833000 5641 6357 1 chr7A.!!$R1 716
10 TraesCS5D01G118200 chr2D 599458733 599459450 717 True 959.00 959 90.808000 5641 6357 1 chr2D.!!$R1 716
11 TraesCS5D01G118200 chr1B 65709924 65710641 717 True 942.00 942 90.403000 5641 6357 1 chr1B.!!$R1 716

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
664 725 1.682854 TCTGCTTCTTGCTTTGGGTTG 59.317 47.619 0.00 0.0 43.37 3.77 F
1273 1345 1.538512 GTGTGTACGTCTACAGCTCCA 59.461 52.381 5.18 0.0 33.31 3.86 F
1795 1869 0.179059 ACAATGTGTGCGAGTGGTGA 60.179 50.000 0.00 0.0 0.00 4.02 F
2986 3565 0.107508 CTAAAGCTAGCTGCCTGCCA 60.108 55.000 20.16 0.0 44.23 4.92 F
4709 7895 1.439679 GGTTGTTCTACAGGCTTCCG 58.560 55.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 1837 0.405198 ACATTGTCCATGGGTGAGCA 59.595 50.000 13.02 0.94 37.17 4.26 R
2913 3492 1.202806 CCCTTCAGTTCTGGCTGACAA 60.203 52.381 0.00 0.00 44.23 3.18 R
3420 4134 0.178921 AGGAGAGACAGGCAAGGACA 60.179 55.000 0.00 0.00 0.00 4.02 R
4906 8107 0.321564 CTCCGCAATCTGGTCACCAA 60.322 55.000 0.00 0.00 30.80 3.67 R
5670 8920 0.036732 CTGGCCCTGCAAGTACTTGA 59.963 55.000 34.43 19.80 42.93 3.02 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
140 142 4.307432 TGTGTCTCTTTGAGGAAATCGAC 58.693 43.478 0.00 0.00 0.00 4.20
141 143 4.039245 TGTGTCTCTTTGAGGAAATCGACT 59.961 41.667 0.00 0.00 0.00 4.18
142 144 4.623595 GTGTCTCTTTGAGGAAATCGACTC 59.376 45.833 0.00 0.00 0.00 3.36
143 145 4.280929 TGTCTCTTTGAGGAAATCGACTCA 59.719 41.667 0.00 0.00 41.63 3.41
262 323 6.114187 TCTTTCTTGCCATCTAGACTTTGA 57.886 37.500 0.00 0.00 0.00 2.69
263 324 6.169094 TCTTTCTTGCCATCTAGACTTTGAG 58.831 40.000 0.00 0.00 0.00 3.02
426 487 3.492102 TGTTTCTTCTAAGCAGCCACT 57.508 42.857 0.00 0.00 0.00 4.00
647 708 3.304559 CGAACTGGTTCTAAAGCGATCTG 59.695 47.826 11.03 0.00 37.44 2.90
664 725 1.682854 TCTGCTTCTTGCTTTGGGTTG 59.317 47.619 0.00 0.00 43.37 3.77
667 728 3.027412 TGCTTCTTGCTTTGGGTTGTTA 58.973 40.909 0.00 0.00 43.37 2.41
668 729 3.640967 TGCTTCTTGCTTTGGGTTGTTAT 59.359 39.130 0.00 0.00 43.37 1.89
669 730 4.100808 TGCTTCTTGCTTTGGGTTGTTATT 59.899 37.500 0.00 0.00 43.37 1.40
670 731 5.056480 GCTTCTTGCTTTGGGTTGTTATTT 58.944 37.500 0.00 0.00 38.95 1.40
671 732 5.177511 GCTTCTTGCTTTGGGTTGTTATTTC 59.822 40.000 0.00 0.00 38.95 2.17
672 733 5.860941 TCTTGCTTTGGGTTGTTATTTCA 57.139 34.783 0.00 0.00 0.00 2.69
673 734 6.418057 TCTTGCTTTGGGTTGTTATTTCAT 57.582 33.333 0.00 0.00 0.00 2.57
978 1042 7.715686 AGATCCATCACAGCTTGCATATATATG 59.284 37.037 17.01 17.01 36.78 1.78
1003 1075 5.625311 CGTGTAAACTTTTGCTGAATCTTCC 59.375 40.000 0.00 0.00 0.00 3.46
1022 1094 3.514539 TCCTTGATCGATGGATGGATCT 58.485 45.455 0.54 0.00 41.05 2.75
1273 1345 1.538512 GTGTGTACGTCTACAGCTCCA 59.461 52.381 5.18 0.00 33.31 3.86
1315 1387 2.632377 TGTAGCTAAGCTTGGTGATGC 58.368 47.619 9.86 2.46 40.44 3.91
1318 1390 3.565764 AGCTAAGCTTGGTGATGCATA 57.434 42.857 9.86 0.00 33.89 3.14
1635 1707 7.560796 AGGAGTATATGAGGTCAAAATAGGG 57.439 40.000 0.00 0.00 0.00 3.53
1706 1778 8.588290 TTCATTTTGCCTAGAAGCCTTTTATA 57.412 30.769 0.00 0.00 0.00 0.98
1707 1779 8.588290 TCATTTTGCCTAGAAGCCTTTTATAA 57.412 30.769 0.00 0.00 0.00 0.98
1708 1780 8.466798 TCATTTTGCCTAGAAGCCTTTTATAAC 58.533 33.333 0.00 0.00 0.00 1.89
1710 1782 8.417273 TTTTGCCTAGAAGCCTTTTATAACTT 57.583 30.769 0.00 0.00 0.00 2.66
1711 1783 7.391148 TTGCCTAGAAGCCTTTTATAACTTG 57.609 36.000 0.00 0.00 0.00 3.16
1712 1784 5.885912 TGCCTAGAAGCCTTTTATAACTTGG 59.114 40.000 0.00 0.00 0.00 3.61
1715 1787 7.285629 GCCTAGAAGCCTTTTATAACTTGGAAT 59.714 37.037 0.00 0.00 0.00 3.01
1795 1869 0.179059 ACAATGTGTGCGAGTGGTGA 60.179 50.000 0.00 0.00 0.00 4.02
1886 2087 5.204409 TGGAAGTTAGCAAGAGAACGTTA 57.796 39.130 0.00 0.00 0.00 3.18
1900 2103 4.087182 AGAACGTTAGACTGGGAGATTGA 58.913 43.478 0.00 0.00 0.00 2.57
1912 2115 3.657727 TGGGAGATTGAAGTTCCTTCCTT 59.342 43.478 0.00 0.00 39.51 3.36
1937 2140 2.260434 GGTGGCGCTAGACGTTCA 59.740 61.111 7.64 0.00 46.11 3.18
2021 2225 4.654091 CACAATTCTCCTGTGTGGTTTT 57.346 40.909 0.00 0.00 39.48 2.43
2135 2339 1.217882 GGGAGTGTATGCATGCGTAC 58.782 55.000 33.64 33.64 38.52 3.67
2139 2343 4.082408 GGGAGTGTATGCATGCGTACTATA 60.082 45.833 37.07 22.58 38.75 1.31
2273 2478 9.387405 AGAATCTTTCTGGCACTGTATTTGTGC 62.387 40.741 9.99 9.99 44.83 4.57
2284 2492 1.194997 GTATTTGTGCCGTACGTGCAA 59.805 47.619 25.80 18.33 41.06 4.08
2594 2803 8.321353 TGTTAACCAAGTGACATAGATCAGATT 58.679 33.333 2.48 0.00 0.00 2.40
2913 3492 1.247567 GGCAACAGGCTACACAACAT 58.752 50.000 0.00 0.00 44.01 2.71
2964 3543 0.521735 AAACGTACGGTCGTACCTCC 59.478 55.000 21.06 4.03 45.80 4.30
2986 3565 0.107508 CTAAAGCTAGCTGCCTGCCA 60.108 55.000 20.16 0.00 44.23 4.92
3136 3727 3.003585 CACATCAACAACTAGCTTGCACA 59.996 43.478 0.00 0.00 32.41 4.57
3138 3729 3.691049 TCAACAACTAGCTTGCACAAC 57.309 42.857 0.00 0.00 32.41 3.32
3420 4134 4.256920 GCATCAAACTAGGTCACTGATGT 58.743 43.478 17.98 0.00 43.38 3.06
3630 4344 5.609284 AGCTAAGGGTCTAGACTCTAGATCA 59.391 44.000 25.57 8.00 42.33 2.92
3667 4381 4.388773 TGCACTAAATTCGTCAGCTTGTAG 59.611 41.667 0.00 0.00 0.00 2.74
3740 6868 7.587037 TGGCCATGATTTAAATCTTTAGGAG 57.413 36.000 24.77 9.56 36.39 3.69
3920 7048 3.776340 CATGCATATATACCCGCGTACA 58.224 45.455 4.92 0.00 0.00 2.90
3925 7053 5.105837 TGCATATATACCCGCGTACATACAA 60.106 40.000 4.92 0.00 0.00 2.41
4111 7239 5.065731 AGACAGCTCACTCTCTTTGTTTTTG 59.934 40.000 0.00 0.00 0.00 2.44
4415 7543 3.216187 TCAACTTCCCACCGATTTTGA 57.784 42.857 0.00 0.00 0.00 2.69
4506 7692 9.865321 TCCACTAATAAATTGTACAGTAGTGTC 57.135 33.333 6.44 0.05 38.19 3.67
4574 7760 6.470278 TCAATGTTATGCTCCTAGATCCATG 58.530 40.000 0.00 0.00 0.00 3.66
4709 7895 1.439679 GGTTGTTCTACAGGCTTCCG 58.560 55.000 0.00 0.00 0.00 4.30
4723 7909 5.116882 CAGGCTTCCGTTAGCTAATTAACT 58.883 41.667 9.88 0.00 40.99 2.24
4811 8000 4.036734 GGAGATAGAGCTTCAGAGTGACAG 59.963 50.000 0.00 0.00 0.00 3.51
4838 8027 4.464244 TGATCTCAGAACCAAGGTACAGAG 59.536 45.833 0.00 0.63 0.00 3.35
4842 8031 2.832129 CAGAACCAAGGTACAGAGGCTA 59.168 50.000 0.00 0.00 0.00 3.93
4843 8032 3.452627 CAGAACCAAGGTACAGAGGCTAT 59.547 47.826 0.00 0.00 0.00 2.97
4844 8033 4.080863 CAGAACCAAGGTACAGAGGCTATT 60.081 45.833 0.00 0.00 0.00 1.73
4847 8036 6.214819 AGAACCAAGGTACAGAGGCTATTAAA 59.785 38.462 0.00 0.00 0.00 1.52
4848 8037 6.576778 ACCAAGGTACAGAGGCTATTAAAT 57.423 37.500 0.00 0.00 0.00 1.40
4858 8059 8.421673 ACAGAGGCTATTAAATTAACTTCGAC 57.578 34.615 0.00 0.00 0.00 4.20
4906 8107 2.093869 ACTGTCCGCGTTATACATGGTT 60.094 45.455 4.92 0.00 0.00 3.67
4969 8170 4.853142 TATCGCCAGGCCCTCGGT 62.853 66.667 5.63 0.00 0.00 4.69
5400 8650 6.458232 TTTTTGATGAAAAGGAGGTCGAAA 57.542 33.333 0.00 0.00 32.44 3.46
5401 8651 6.648879 TTTTGATGAAAAGGAGGTCGAAAT 57.351 33.333 0.00 0.00 0.00 2.17
5467 8717 3.627577 AGCCTCATAAAGCAAATACACGG 59.372 43.478 0.00 0.00 0.00 4.94
5481 8731 2.183478 ACACGGATCAACTCAATGCA 57.817 45.000 0.00 0.00 0.00 3.96
5492 8742 1.072331 ACTCAATGCAACCTTCCTCGT 59.928 47.619 0.00 0.00 0.00 4.18
5493 8743 1.466167 CTCAATGCAACCTTCCTCGTG 59.534 52.381 0.00 0.00 0.00 4.35
5497 8747 1.371558 GCAACCTTCCTCGTGACCT 59.628 57.895 0.00 0.00 0.00 3.85
5498 8748 0.250338 GCAACCTTCCTCGTGACCTT 60.250 55.000 0.00 0.00 0.00 3.50
5510 8760 1.860676 GTGACCTTTGTCGCTACACA 58.139 50.000 0.00 0.00 46.27 3.72
5554 8804 2.476051 CTCGCACCAACGCACATC 59.524 61.111 0.00 0.00 0.00 3.06
5563 8813 1.259770 CCAACGCACATCATCTGATCG 59.740 52.381 0.00 0.00 31.21 3.69
5565 8815 2.131281 ACGCACATCATCTGATCGAG 57.869 50.000 6.73 0.00 31.21 4.04
5618 8868 1.287038 TTGTTACACCCACACCCCCA 61.287 55.000 0.00 0.00 0.00 4.96
5619 8869 1.287038 TGTTACACCCACACCCCCAA 61.287 55.000 0.00 0.00 0.00 4.12
5630 8880 1.992557 ACACCCCCAACTGTCATACAT 59.007 47.619 0.00 0.00 0.00 2.29
5638 8888 4.162320 CCCAACTGTCATACATACTGGACT 59.838 45.833 0.00 0.00 0.00 3.85
5670 8920 0.251033 TGGCTGCAGCTGATTGAGTT 60.251 50.000 35.82 0.00 41.70 3.01
5731 8981 2.114411 GCGGGGTCCCAGTTTTGA 59.886 61.111 10.98 0.00 35.37 2.69
5822 9072 0.397816 CCAGTTTTGGTTGGACCCCA 60.398 55.000 0.00 0.00 39.79 4.96
5891 9141 2.116827 TTGTGACGACCCAACTGTTT 57.883 45.000 0.00 0.00 0.00 2.83
5966 9216 1.681327 GGACCAGCCGAGGTGTAGA 60.681 63.158 0.00 0.00 43.38 2.59
6005 9256 1.465794 AGTAGTCCGTCTTCCTCTGC 58.534 55.000 0.00 0.00 0.00 4.26
6021 9272 1.308128 TGCCCCAGGATCCTGACAT 60.308 57.895 38.37 3.63 46.30 3.06
6103 9355 2.032528 CAGCTGCCGGTTCTCCAA 59.967 61.111 0.00 0.00 0.00 3.53
6185 9437 4.097286 AGCTTCTCAGAGATCGTTTACCTC 59.903 45.833 0.00 0.00 0.00 3.85
6192 9444 0.826062 GATCGTTTACCTCCGGGGAA 59.174 55.000 0.37 0.00 38.76 3.97
6246 9499 0.593128 CTTTGCCCCTTTGTCTCGTG 59.407 55.000 0.00 0.00 0.00 4.35
6254 9507 2.154462 CCTTTGTCTCGTGCCAGAAAT 58.846 47.619 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 142 4.222588 AGAGAAAGGGTGAGATGAGTTGAG 59.777 45.833 0.00 0.00 0.00 3.02
141 143 4.163427 AGAGAAAGGGTGAGATGAGTTGA 58.837 43.478 0.00 0.00 0.00 3.18
142 144 4.550076 AGAGAAAGGGTGAGATGAGTTG 57.450 45.455 0.00 0.00 0.00 3.16
143 145 4.843516 AGAAGAGAAAGGGTGAGATGAGTT 59.156 41.667 0.00 0.00 0.00 3.01
144 146 4.424842 AGAAGAGAAAGGGTGAGATGAGT 58.575 43.478 0.00 0.00 0.00 3.41
145 147 5.187576 AGAAGAAGAGAAAGGGTGAGATGAG 59.812 44.000 0.00 0.00 0.00 2.90
146 148 5.046735 CAGAAGAAGAGAAAGGGTGAGATGA 60.047 44.000 0.00 0.00 0.00 2.92
284 345 6.928979 TCCAAAACGAAACAACAAGATAGA 57.071 33.333 0.00 0.00 0.00 1.98
426 487 7.094506 TGCTACGATCTCTCTTAACAAAGTACA 60.095 37.037 0.00 0.00 0.00 2.90
544 605 5.009710 AGTTTCATTCCTCGAAGGGAAAAAC 59.990 40.000 17.72 17.72 46.73 2.43
590 651 3.011144 TGGGATGGAATTAACAGCTCCAA 59.989 43.478 0.00 0.00 42.41 3.53
647 708 2.602257 AACAACCCAAAGCAAGAAGC 57.398 45.000 0.00 0.00 46.19 3.86
664 725 7.432545 TCGATCTGTCTCTCGAAATGAAATAAC 59.567 37.037 0.00 0.00 40.64 1.89
667 728 5.895928 TCGATCTGTCTCTCGAAATGAAAT 58.104 37.500 0.00 0.00 40.64 2.17
668 729 5.123979 TCTCGATCTGTCTCTCGAAATGAAA 59.876 40.000 0.00 0.00 42.73 2.69
669 730 4.636206 TCTCGATCTGTCTCTCGAAATGAA 59.364 41.667 0.00 0.00 42.73 2.57
670 731 4.192317 TCTCGATCTGTCTCTCGAAATGA 58.808 43.478 0.00 0.00 42.73 2.57
671 732 4.544242 TCTCGATCTGTCTCTCGAAATG 57.456 45.455 0.00 0.00 42.73 2.32
672 733 4.878971 TCTTCTCGATCTGTCTCTCGAAAT 59.121 41.667 0.00 0.00 42.73 2.17
673 734 4.254492 TCTTCTCGATCTGTCTCTCGAAA 58.746 43.478 0.00 0.00 42.73 3.46
978 1042 4.537015 AGATTCAGCAAAAGTTTACACGC 58.463 39.130 0.00 0.00 0.00 5.34
1003 1075 3.001414 GCAGATCCATCCATCGATCAAG 58.999 50.000 0.00 0.00 37.87 3.02
1022 1094 1.444119 GGAACTCTGCCAAACACGCA 61.444 55.000 0.00 0.00 34.41 5.24
1315 1387 6.484643 CCTAGAAATCAGGGAACACATGTATG 59.515 42.308 0.00 0.00 31.56 2.39
1318 1390 4.289672 ACCTAGAAATCAGGGAACACATGT 59.710 41.667 0.00 0.00 37.51 3.21
1447 1519 8.585881 CCAGCAGCCTAGTATTAATACTTCTTA 58.414 37.037 28.42 13.05 43.06 2.10
1449 1521 6.555360 ACCAGCAGCCTAGTATTAATACTTCT 59.445 38.462 28.42 20.23 43.06 2.85
1450 1522 6.760291 ACCAGCAGCCTAGTATTAATACTTC 58.240 40.000 28.42 18.73 43.06 3.01
1612 1684 6.174049 GCCCTATTTTGACCTCATATACTCC 58.826 44.000 0.00 0.00 0.00 3.85
1613 1685 6.769512 TGCCCTATTTTGACCTCATATACTC 58.230 40.000 0.00 0.00 0.00 2.59
1614 1686 6.763715 TGCCCTATTTTGACCTCATATACT 57.236 37.500 0.00 0.00 0.00 2.12
1615 1687 7.448469 ACATTGCCCTATTTTGACCTCATATAC 59.552 37.037 0.00 0.00 0.00 1.47
1616 1688 7.526041 ACATTGCCCTATTTTGACCTCATATA 58.474 34.615 0.00 0.00 0.00 0.86
1617 1689 6.376248 ACATTGCCCTATTTTGACCTCATAT 58.624 36.000 0.00 0.00 0.00 1.78
1635 1707 9.301153 CTAAATTGATTTTGGGTAGTACATTGC 57.699 33.333 2.06 0.00 0.00 3.56
1763 1837 0.405198 ACATTGTCCATGGGTGAGCA 59.595 50.000 13.02 0.94 37.17 4.26
1886 2087 3.525862 AGGAACTTCAATCTCCCAGTCT 58.474 45.455 0.00 0.00 27.25 3.24
1937 2140 7.230510 TCAATTACAAACTAGGCAGACACAAAT 59.769 33.333 0.00 0.00 0.00 2.32
1991 2194 4.278170 CACAGGAGAATTGTGTGCCTTTTA 59.722 41.667 0.00 0.00 40.73 1.52
2001 2204 6.783708 TTTAAAACCACACAGGAGAATTGT 57.216 33.333 0.00 0.00 41.22 2.71
2078 2282 8.035394 ACTACCTAGAACATATGAAACACACAG 58.965 37.037 10.38 1.15 0.00 3.66
2235 2440 6.003950 CCAGAAAGATTCTCTTGGTTTGGTA 58.996 40.000 0.00 0.00 36.71 3.25
2236 2441 4.829492 CCAGAAAGATTCTCTTGGTTTGGT 59.171 41.667 0.00 0.00 36.71 3.67
2237 2442 4.321527 GCCAGAAAGATTCTCTTGGTTTGG 60.322 45.833 10.80 0.00 36.71 3.28
2238 2443 4.279169 TGCCAGAAAGATTCTCTTGGTTTG 59.721 41.667 10.80 0.00 36.71 2.93
2273 2478 3.262135 AGAAAATGTTTGCACGTACGG 57.738 42.857 21.06 9.73 0.00 4.02
2284 2492 9.601217 AGAGTTATCGCTATACAAGAAAATGTT 57.399 29.630 0.00 0.00 34.75 2.71
2340 2548 9.751542 AGGTGACTTAATGAATATAAGAGTTCG 57.248 33.333 0.67 0.00 37.44 3.95
2561 2770 7.992608 TCTATGTCACTTGGTTAACATGCATAT 59.007 33.333 8.10 0.00 34.39 1.78
2604 2816 8.437274 TCCTACTTCCTTCTTTGTAGAGAATT 57.563 34.615 0.00 0.00 35.27 2.17
2913 3492 1.202806 CCCTTCAGTTCTGGCTGACAA 60.203 52.381 0.00 0.00 44.23 3.18
2964 3543 1.809651 GCAGGCAGCTAGCTTTAGGAG 60.810 57.143 16.46 3.53 44.79 3.69
3136 3727 4.308265 GAAGACGCTCAGTTTCTTAGGTT 58.692 43.478 0.00 0.00 0.00 3.50
3138 3729 3.254892 GGAAGACGCTCAGTTTCTTAGG 58.745 50.000 0.00 0.00 0.00 2.69
3294 4008 8.150296 ACTTAAGCATAAAGTTTGGCAAAAGAT 58.850 29.630 15.29 6.09 33.39 2.40
3420 4134 0.178921 AGGAGAGACAGGCAAGGACA 60.179 55.000 0.00 0.00 0.00 4.02
3604 4318 2.661718 AGAGTCTAGACCCTTAGCTGC 58.338 52.381 19.38 0.00 0.00 5.25
3630 4344 2.867109 AGTGCAAGTAGCCACTGATT 57.133 45.000 0.00 0.00 44.83 2.57
3667 4381 7.849804 AGTGTCAGTTCATTTCATGTATACC 57.150 36.000 0.00 0.00 0.00 2.73
3740 6868 1.872952 GGATTTGCTTTGGTGGTTTGC 59.127 47.619 0.00 0.00 0.00 3.68
3920 7048 6.257849 CGATGTACCAGTAACTGCAATTGTAT 59.742 38.462 7.40 0.00 0.00 2.29
3925 7053 4.081642 AGACGATGTACCAGTAACTGCAAT 60.082 41.667 0.00 0.00 0.00 3.56
4415 7543 5.279156 GGATGCCAAACTTGATGAAAGAGTT 60.279 40.000 0.00 0.00 39.38 3.01
4553 7739 6.692849 TTCATGGATCTAGGAGCATAACAT 57.307 37.500 0.00 0.00 0.00 2.71
4560 7746 9.732130 AAGTAAATAATTCATGGATCTAGGAGC 57.268 33.333 0.00 0.00 0.00 4.70
4723 7909 6.518493 ACGGTCGATAATAAAGCCAAGATTA 58.482 36.000 0.00 0.00 0.00 1.75
4785 7974 5.825679 GTCACTCTGAAGCTCTATCTCCTAA 59.174 44.000 0.00 0.00 0.00 2.69
4811 8000 3.350833 ACCTTGGTTCTGAGATCAATGC 58.649 45.455 0.00 0.00 0.00 3.56
4838 8027 6.594284 ACCGTCGAAGTTAATTTAATAGCC 57.406 37.500 0.00 0.00 0.00 3.93
4842 8031 7.437793 TTGGAACCGTCGAAGTTAATTTAAT 57.562 32.000 2.29 0.00 0.00 1.40
4843 8032 6.857777 TTGGAACCGTCGAAGTTAATTTAA 57.142 33.333 2.29 0.00 0.00 1.52
4844 8033 6.857777 TTTGGAACCGTCGAAGTTAATTTA 57.142 33.333 2.29 0.00 0.00 1.40
4847 8036 5.952526 AATTTGGAACCGTCGAAGTTAAT 57.047 34.783 2.29 0.00 0.00 1.40
4848 8037 6.857777 TTAATTTGGAACCGTCGAAGTTAA 57.142 33.333 2.29 0.00 33.95 2.01
4892 8093 3.181504 GGTCACCAAACCATGTATAACGC 60.182 47.826 0.00 0.00 39.27 4.84
4906 8107 0.321564 CTCCGCAATCTGGTCACCAA 60.322 55.000 0.00 0.00 30.80 3.67
5379 8629 7.067008 GGATATTTCGACCTCCTTTTCATCAAA 59.933 37.037 0.00 0.00 0.00 2.69
5382 8632 6.055588 TGGATATTTCGACCTCCTTTTCATC 58.944 40.000 0.00 0.00 0.00 2.92
5400 8650 6.770286 ATAGTTGTGTGGATCCTTGGATAT 57.230 37.500 14.23 0.52 0.00 1.63
5401 8651 6.575244 AATAGTTGTGTGGATCCTTGGATA 57.425 37.500 14.23 0.00 0.00 2.59
5447 8697 5.527214 TGATCCGTGTATTTGCTTTATGAGG 59.473 40.000 0.00 0.00 0.00 3.86
5450 8700 6.785191 AGTTGATCCGTGTATTTGCTTTATG 58.215 36.000 0.00 0.00 0.00 1.90
5467 8717 3.760684 AGGAAGGTTGCATTGAGTTGATC 59.239 43.478 0.00 0.00 0.00 2.92
5481 8731 1.489230 ACAAAGGTCACGAGGAAGGTT 59.511 47.619 0.00 0.00 0.00 3.50
5492 8742 1.137282 TGTGTGTAGCGACAAAGGTCA 59.863 47.619 0.00 0.00 44.54 4.02
5493 8743 1.525619 GTGTGTGTAGCGACAAAGGTC 59.474 52.381 0.00 0.00 37.31 3.85
5497 8747 1.666700 GGTTGTGTGTGTAGCGACAAA 59.333 47.619 0.00 0.00 37.31 2.83
5498 8748 1.292061 GGTTGTGTGTGTAGCGACAA 58.708 50.000 0.00 0.00 37.31 3.18
5510 8760 5.139727 TCCTTGATGAAAAGATGGTTGTGT 58.860 37.500 0.00 0.00 0.00 3.72
5554 8804 0.101219 TGCGACCACTCGATCAGATG 59.899 55.000 0.00 0.00 43.06 2.90
5571 8821 2.012673 GATGTCCTCATCACTTGGTGC 58.987 52.381 3.72 0.00 46.78 5.01
5596 8846 1.253100 GGGTGTGGGTGTAACAATGG 58.747 55.000 0.00 0.00 39.98 3.16
5618 8868 7.344612 TCCATTAGTCCAGTATGTATGACAGTT 59.655 37.037 0.00 0.00 28.85 3.16
5619 8869 6.839134 TCCATTAGTCCAGTATGTATGACAGT 59.161 38.462 0.00 0.00 28.85 3.55
5630 8880 4.019681 CCACAAACCTCCATTAGTCCAGTA 60.020 45.833 0.00 0.00 0.00 2.74
5638 8888 1.202989 TGCAGCCACAAACCTCCATTA 60.203 47.619 0.00 0.00 0.00 1.90
5670 8920 0.036732 CTGGCCCTGCAAGTACTTGA 59.963 55.000 34.43 19.80 42.93 3.02
5716 8966 3.006859 CAGATTTTCAAAACTGGGACCCC 59.993 47.826 8.45 2.69 35.79 4.95
5783 9033 0.967380 GTCCCAGACCCATTGCCAAG 60.967 60.000 0.00 0.00 0.00 3.61
5858 9108 0.881118 TCACAAATCGCAAAGAGCCC 59.119 50.000 0.00 0.00 41.38 5.19
5891 9141 1.199789 CAAAGCAGCCGCAGATACAAA 59.800 47.619 0.00 0.00 42.27 2.83
5963 9213 2.239654 CCCTCAAGTCTGCCCATTTCTA 59.760 50.000 0.00 0.00 0.00 2.10
5966 9216 1.075601 TCCCTCAAGTCTGCCCATTT 58.924 50.000 0.00 0.00 0.00 2.32
5994 9245 0.985490 ATCCTGGGGCAGAGGAAGAC 60.985 60.000 7.73 0.00 43.01 3.01
6005 9256 0.921896 ACAATGTCAGGATCCTGGGG 59.078 55.000 35.95 23.49 43.75 4.96
6185 9437 0.037590 TTCAACACCTCATTCCCCGG 59.962 55.000 0.00 0.00 0.00 5.73
6192 9444 1.541147 CATGGCGTTTCAACACCTCAT 59.459 47.619 0.00 0.00 32.39 2.90
6240 9493 0.690192 TTCCCATTTCTGGCACGAGA 59.310 50.000 0.00 0.00 41.64 4.04
6246 9499 1.327303 TGTGTGTTCCCATTTCTGGC 58.673 50.000 0.00 0.00 41.64 4.85
6302 9555 2.213499 CCAGAGCTTCACGAACAAAGT 58.787 47.619 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.