Multiple sequence alignment - TraesCS2B01G148600

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 TraesCS2B01G148600 chr2B 100.000 4903 0 0 821 5723 114654059 114649157 0.000000e+00 9055.0
1 TraesCS2B01G148600 chr2B 100.000 552 0 0 1 552 114654879 114654328 0.000000e+00 1020.0
2 TraesCS2B01G148600 chr2D 94.415 4405 187 19 824 5196 75005776 75001399 0.000000e+00 6717.0
3 TraesCS2B01G148600 chr2D 92.174 345 21 3 5349 5693 74140909 74141247 3.100000e-132 483.0
4 TraesCS2B01G148600 chr2D 87.826 345 36 3 2034 2374 80248850 80248508 3.210000e-107 399.0
5 TraesCS2B01G148600 chr2D 80.270 593 26 18 1 552 75006332 75005790 4.210000e-96 363.0
6 TraesCS2B01G148600 chr2A 94.727 4343 181 22 874 5205 74792253 74787948 0.000000e+00 6708.0
7 TraesCS2B01G148600 chr2A 84.936 551 36 21 1 520 74793169 74792635 1.100000e-141 514.0
8 TraesCS2B01G148600 chr2A 81.595 326 22 15 5196 5507 424508830 424509131 9.590000e-58 235.0
9 TraesCS2B01G148600 chr2A 85.333 75 10 1 5195 5269 277174661 277174734 6.150000e-10 76.8
10 TraesCS2B01G148600 chr1A 78.191 1692 258 69 2175 3810 540197710 540196074 0.000000e+00 977.0
11 TraesCS2B01G148600 chr1A 84.262 305 29 12 4131 4420 540195707 540195407 4.370000e-71 279.0
12 TraesCS2B01G148600 chr1A 84.733 131 19 1 2001 2131 540197911 540197782 4.650000e-26 130.0
13 TraesCS2B01G148600 chr1B 77.987 1649 256 68 2207 3813 605443313 605441730 0.000000e+00 935.0
14 TraesCS2B01G148600 chr1B 92.000 100 7 1 2001 2100 605443546 605443448 7.730000e-29 139.0
15 TraesCS2B01G148600 chr3B 96.468 538 15 4 5186 5723 594665900 594665367 0.000000e+00 885.0
16 TraesCS2B01G148600 chr3B 95.817 526 19 3 5198 5723 581253249 581253771 0.000000e+00 846.0
17 TraesCS2B01G148600 chr3B 86.905 84 10 1 5186 5269 213216108 213216026 6.110000e-15 93.5
18 TraesCS2B01G148600 chr7B 95.167 538 19 7 5192 5723 84293801 84293265 0.000000e+00 843.0
19 TraesCS2B01G148600 chr4B 91.064 470 40 2 5196 5664 462204293 462203825 8.090000e-178 634.0
20 TraesCS2B01G148600 chr7D 94.203 345 20 0 5349 5693 221989789 221989445 1.410000e-145 527.0
21 TraesCS2B01G148600 chr7D 89.450 218 19 3 5294 5507 249484848 249484631 7.310000e-69 272.0
22 TraesCS2B01G148600 chr7D 87.273 165 20 1 5331 5495 122531332 122531169 2.720000e-43 187.0
23 TraesCS2B01G148600 chr3D 91.507 365 24 4 5330 5693 53779620 53779978 3.980000e-136 496.0
24 TraesCS2B01G148600 chr1D 92.754 345 19 3 5349 5693 319557971 319558309 1.430000e-135 494.0
25 TraesCS2B01G148600 chr1D 80.480 666 105 22 2175 2824 444907756 444907100 2.400000e-133 486.0
26 TraesCS2B01G148600 chr1D 81.702 470 67 16 4270 4727 444898364 444897902 1.950000e-99 374.0
27 TraesCS2B01G148600 chr1D 91.099 191 17 0 5503 5693 6743449 6743639 5.690000e-65 259.0
28 TraesCS2B01G148600 chr1D 87.023 131 16 1 2001 2131 444907957 444907828 4.620000e-31 147.0
29 TraesCS2B01G148600 chr4A 85.526 76 10 1 5194 5269 701708170 701708244 1.710000e-10 78.7


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 TraesCS2B01G148600 chr2B 114649157 114654879 5722 True 5037.5 9055 100.000000 1 5723 2 chr2B.!!$R1 5722
1 TraesCS2B01G148600 chr2D 75001399 75006332 4933 True 3540.0 6717 87.342500 1 5196 2 chr2D.!!$R2 5195
2 TraesCS2B01G148600 chr2A 74787948 74793169 5221 True 3611.0 6708 89.831500 1 5205 2 chr2A.!!$R1 5204
3 TraesCS2B01G148600 chr1A 540195407 540197911 2504 True 462.0 977 82.395333 2001 4420 3 chr1A.!!$R1 2419
4 TraesCS2B01G148600 chr1B 605441730 605443546 1816 True 537.0 935 84.993500 2001 3813 2 chr1B.!!$R1 1812
5 TraesCS2B01G148600 chr3B 594665367 594665900 533 True 885.0 885 96.468000 5186 5723 1 chr3B.!!$R2 537
6 TraesCS2B01G148600 chr3B 581253249 581253771 522 False 846.0 846 95.817000 5198 5723 1 chr3B.!!$F1 525
7 TraesCS2B01G148600 chr7B 84293265 84293801 536 True 843.0 843 95.167000 5192 5723 1 chr7B.!!$R1 531
8 TraesCS2B01G148600 chr1D 444907100 444907957 857 True 316.5 486 83.751500 2001 2824 2 chr1D.!!$R2 823

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
285 312 0.030705 TTCCCCTCCATCTCCTCCAG 60.031 60.000 0.00 0.00 0.00 3.86 F
1194 1272 0.533032 AGAGAAGCACGGTAGGAAGC 59.467 55.000 0.00 0.00 0.00 3.86 F
1968 2048 0.037697 TTACATTCAGCGCACTCCGT 60.038 50.000 11.47 3.31 39.71 4.69 F
3002 3159 1.135460 GCTGAGCACAATGCCTTTCTC 60.135 52.381 0.00 0.00 46.52 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1335 0.665670 CTGAGATACTCATGGCCGCG 60.666 60.000 0.0 0.0 39.92 6.46 R
2741 2882 1.269569 TGAAGTGTCCGTGTAGCTGTG 60.270 52.381 0.0 0.0 0.00 3.66 R
3555 3729 0.238289 CCCGAACAACATGTCTGCAC 59.762 55.000 0.0 0.0 0.00 4.57 R
4992 5241 0.176680 CTTCCATCGGTAGCAGCAGT 59.823 55.000 0.0 0.0 0.00 4.40 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
63 64 1.315690 GGGCTTATACGGGCCTTTTC 58.684 55.000 0.84 0.00 46.80 2.29
64 65 1.315690 GGCTTATACGGGCCTTTTCC 58.684 55.000 0.84 0.00 44.48 3.13
65 66 1.133884 GGCTTATACGGGCCTTTTCCT 60.134 52.381 0.84 0.00 44.48 3.36
66 67 1.947456 GCTTATACGGGCCTTTTCCTG 59.053 52.381 0.84 0.00 38.47 3.86
67 68 1.947456 CTTATACGGGCCTTTTCCTGC 59.053 52.381 0.84 0.00 35.90 4.85
72 73 3.062466 GGCCTTTTCCTGCCGTCC 61.062 66.667 0.00 0.00 38.00 4.79
73 74 2.282180 GCCTTTTCCTGCCGTCCA 60.282 61.111 0.00 0.00 0.00 4.02
74 75 2.626780 GCCTTTTCCTGCCGTCCAC 61.627 63.158 0.00 0.00 0.00 4.02
75 76 1.228124 CCTTTTCCTGCCGTCCACA 60.228 57.895 0.00 0.00 0.00 4.17
76 77 1.515521 CCTTTTCCTGCCGTCCACAC 61.516 60.000 0.00 0.00 0.00 3.82
77 78 0.817634 CTTTTCCTGCCGTCCACACA 60.818 55.000 0.00 0.00 0.00 3.72
78 79 1.098712 TTTTCCTGCCGTCCACACAC 61.099 55.000 0.00 0.00 0.00 3.82
79 80 3.800685 TTCCTGCCGTCCACACACG 62.801 63.158 0.00 0.00 39.61 4.49
163 167 1.545759 GATCGCGACGTGATTCTTCA 58.454 50.000 23.57 0.00 32.57 3.02
165 169 1.990799 TCGCGACGTGATTCTTCATT 58.009 45.000 3.71 0.00 33.56 2.57
183 187 7.820648 TCTTCATTGAGAGCAAAAAGAATACC 58.179 34.615 0.00 0.00 37.14 2.73
225 235 4.824515 CCGCCCTCCTCTCCTCGT 62.825 72.222 0.00 0.00 0.00 4.18
226 236 2.756283 CGCCCTCCTCTCCTCGTT 60.756 66.667 0.00 0.00 0.00 3.85
227 237 1.453379 CGCCCTCCTCTCCTCGTTA 60.453 63.158 0.00 0.00 0.00 3.18
229 239 0.683504 GCCCTCCTCTCCTCGTTACA 60.684 60.000 0.00 0.00 0.00 2.41
285 312 0.030705 TTCCCCTCCATCTCCTCCAG 60.031 60.000 0.00 0.00 0.00 3.86
289 316 1.623557 CCCTCCATCTCCTCCAGTTCA 60.624 57.143 0.00 0.00 0.00 3.18
295 322 3.710677 CCATCTCCTCCAGTTCATCTCTT 59.289 47.826 0.00 0.00 0.00 2.85
307 334 1.648568 TCATCTCTTCCCCTCTCACCT 59.351 52.381 0.00 0.00 0.00 4.00
354 403 4.695231 CACGTCTCCGTCGCCGTT 62.695 66.667 0.00 0.00 46.28 4.44
374 423 2.046314 CTTGATTCCGGCCACCGT 60.046 61.111 2.24 0.00 46.80 4.83
406 455 3.965026 CTCTCCCCGCACCTCCTCA 62.965 68.421 0.00 0.00 0.00 3.86
483 532 0.595053 CGTATCGGCCTACAGCAGTG 60.595 60.000 0.00 0.00 46.50 3.66
538 587 1.341802 GCGACGACAGATTTGAGCG 59.658 57.895 0.00 0.00 33.93 5.03
540 589 1.344226 CGACGACAGATTTGAGCGCA 61.344 55.000 11.47 0.00 32.05 6.09
844 893 0.676782 ACCACGCAGCAAGGTAATCC 60.677 55.000 3.95 0.00 32.92 3.01
851 929 2.856222 CAGCAAGGTAATCCCCATCTC 58.144 52.381 0.00 0.00 0.00 2.75
1157 1235 4.324267 CAACCGAACACCCTCTTAATCTT 58.676 43.478 0.00 0.00 0.00 2.40
1194 1272 0.533032 AGAGAAGCACGGTAGGAAGC 59.467 55.000 0.00 0.00 0.00 3.86
1466 1545 1.133041 TCAGATCTCCCCGACCATGAT 60.133 52.381 0.00 0.00 0.00 2.45
1478 1557 3.582780 CGACCATGATGATGATGACGAT 58.417 45.455 0.00 0.00 0.00 3.73
1580 1659 0.549950 ATGTTCAGGGCATGCTAGCT 59.450 50.000 18.92 0.00 34.17 3.32
1586 1665 2.029623 CAGGGCATGCTAGCTCAATTT 58.970 47.619 18.92 0.00 37.50 1.82
1612 1691 2.203252 CGCTCATGGGTCATGGGG 60.203 66.667 9.47 4.99 42.15 4.96
1613 1692 2.745308 CGCTCATGGGTCATGGGGA 61.745 63.158 9.47 0.00 42.15 4.81
1614 1693 1.614711 GCTCATGGGTCATGGGGAA 59.385 57.895 9.47 0.00 42.15 3.97
1615 1694 0.186873 GCTCATGGGTCATGGGGAAT 59.813 55.000 9.47 0.00 42.15 3.01
1616 1695 1.412074 GCTCATGGGTCATGGGGAATT 60.412 52.381 9.47 0.00 42.15 2.17
1692 1771 8.989131 ACTTCTGGCCTAGAAAATTATACACTA 58.011 33.333 15.54 0.00 44.47 2.74
1693 1772 9.262358 CTTCTGGCCTAGAAAATTATACACTAC 57.738 37.037 15.54 0.00 44.47 2.73
1754 1833 6.646267 TCACCTGGTTTAGTATTGTCATACC 58.354 40.000 0.00 0.00 36.63 2.73
1930 2010 2.285083 TGATAAACGTGGTGCTATGCC 58.715 47.619 0.00 0.00 0.00 4.40
1960 2040 7.962918 AGTTATTTGCTTACTTTACATTCAGCG 59.037 33.333 0.00 0.00 0.00 5.18
1968 2048 0.037697 TTACATTCAGCGCACTCCGT 60.038 50.000 11.47 3.31 39.71 4.69
2339 2465 1.918262 AGGATTGGATCTGCACAGGAA 59.082 47.619 0.00 0.00 0.00 3.36
2393 2522 8.902806 CATCTTCAGTAGTCTAGTGAGATTTCT 58.097 37.037 15.42 1.81 39.16 2.52
2396 2525 7.384439 TCAGTAGTCTAGTGAGATTTCTGTG 57.616 40.000 12.58 0.00 37.77 3.66
2459 2589 2.871022 GCTTCATCACCTATCACTGCTG 59.129 50.000 0.00 0.00 0.00 4.41
2741 2882 6.998074 TGGATGGACAGATAAATGTATGGAAC 59.002 38.462 0.00 0.00 32.25 3.62
2858 3002 2.799126 TCCATAGCCGTTTCCATTGT 57.201 45.000 0.00 0.00 0.00 2.71
2899 3056 4.604976 ACGCGGTGTAACTATATGTCTTC 58.395 43.478 12.47 0.00 36.74 2.87
2987 3144 2.804527 CGTATGGATGTGGAATGCTGAG 59.195 50.000 0.00 0.00 0.00 3.35
3002 3159 1.135460 GCTGAGCACAATGCCTTTCTC 60.135 52.381 0.00 0.00 46.52 2.87
3195 3359 4.868195 GCCTCGGCATGAAAACAC 57.132 55.556 2.41 0.00 41.49 3.32
3208 3372 5.655488 CATGAAAACACACCCTTGTTTGTA 58.345 37.500 2.16 0.00 46.68 2.41
3283 3455 5.311265 TCAGAGAAACATATGGATCATGGC 58.689 41.667 7.80 0.00 0.00 4.40
3347 3519 7.678947 ATTTCTGTTGAACTAGAAGTGATGG 57.321 36.000 0.00 0.00 34.68 3.51
3380 3553 3.196254 AGCAAGGGCAAATAACAGAATGG 59.804 43.478 0.00 0.00 42.02 3.16
3555 3729 1.817099 GGATCCCAGAAGCGCACAG 60.817 63.158 11.47 0.00 0.00 3.66
4376 4614 1.079543 CTGGGACCTTGCTCGTCAG 60.080 63.158 0.00 0.00 31.55 3.51
4394 4632 4.184629 GTCAGGCAATTCGATCTACTTGT 58.815 43.478 0.00 0.00 0.00 3.16
4424 4662 7.838771 TGATGTGAGTGTAGAAATCAATCTG 57.161 36.000 0.00 0.00 32.27 2.90
4515 4753 2.282391 GGTGTGACATGCCTGGCA 60.282 61.111 25.65 25.65 44.86 4.92
4557 4795 4.891727 GCGTCGGGGTGCATCGAT 62.892 66.667 11.68 0.00 37.73 3.59
4635 4873 2.910479 AGGGACGTCGTGCAGTCA 60.910 61.111 18.92 0.00 39.01 3.41
4641 4879 3.044305 GTCGTGCAGTCACTGGCC 61.044 66.667 7.00 0.00 40.99 5.36
4770 5009 4.520111 TGATTGATTTGGTTGGTCAGTCAG 59.480 41.667 0.00 0.00 34.86 3.51
4773 5012 3.117701 TGATTTGGTTGGTCAGTCAGGAA 60.118 43.478 0.00 0.00 0.00 3.36
4776 5015 1.168714 GGTTGGTCAGTCAGGAATGC 58.831 55.000 0.00 0.00 0.00 3.56
4847 5086 1.133199 TCATGGGGGCACTCAAACTTT 60.133 47.619 0.00 0.00 0.00 2.66
4849 5088 0.758685 TGGGGGCACTCAAACTTTGG 60.759 55.000 0.00 0.00 0.00 3.28
4860 5099 6.389906 CACTCAAACTTTGGACTTGTTCTTT 58.610 36.000 1.62 0.00 0.00 2.52
4867 5106 8.514330 AACTTTGGACTTGTTCTTTACATGTA 57.486 30.769 0.08 0.08 43.06 2.29
4871 5110 5.924254 TGGACTTGTTCTTTACATGTAGTCG 59.076 40.000 5.56 0.00 43.06 4.18
4926 5172 2.830321 CCTAAGTTGAGGGTAGTCGGTT 59.170 50.000 0.00 0.00 32.39 4.44
4992 5241 3.719268 TTCTGCTGCATTTCCTCCTTA 57.281 42.857 1.31 0.00 0.00 2.69
5096 5345 1.747206 GCCCATACTTCGTGCTGGATT 60.747 52.381 0.00 0.00 0.00 3.01
5105 5354 4.578928 ACTTCGTGCTGGATTAAGTTGTTT 59.421 37.500 0.00 0.00 0.00 2.83
5123 5372 8.877864 AGTTGTTTATTCTCCATGGTTGATTA 57.122 30.769 12.58 9.28 0.00 1.75
5184 5433 3.384702 GCTTGAAAGCGCAACCTAC 57.615 52.632 11.47 0.00 42.88 3.18
5282 5531 8.956533 TCGAGAACATAAATATCATTTGGTCA 57.043 30.769 0.00 0.00 0.00 4.02
5499 5754 5.925397 TCCAATGTGTCAATACAAACATTGC 59.075 36.000 17.64 0.00 42.78 3.56
5610 5865 8.277270 TCATTAATCAAACAGTATAGCGTACG 57.723 34.615 11.84 11.84 0.00 3.67
5661 5916 6.294473 TCTCAAGAAAATCAGCTTCACTCTT 58.706 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.000557 CTGCGTGCGTGTGTGGAC 62.001 66.667 0.00 0.00 0.00 4.02
72 73 3.705638 CTCCTGCGTGCGTGTGTG 61.706 66.667 0.00 0.00 0.00 3.82
75 76 4.908687 TTGCTCCTGCGTGCGTGT 62.909 61.111 0.00 0.00 43.34 4.49
76 77 2.660553 TTTTTGCTCCTGCGTGCGTG 62.661 55.000 0.00 0.00 43.34 5.34
77 78 2.477176 TTTTTGCTCCTGCGTGCGT 61.477 52.632 0.00 0.00 43.34 5.24
78 79 2.010817 GTTTTTGCTCCTGCGTGCG 61.011 57.895 0.00 0.00 43.34 5.34
79 80 0.936297 CTGTTTTTGCTCCTGCGTGC 60.936 55.000 0.00 0.00 43.34 5.34
163 167 7.309438 GGAGTTGGTATTCTTTTTGCTCTCAAT 60.309 37.037 0.00 0.00 31.33 2.57
165 169 5.473504 GGAGTTGGTATTCTTTTTGCTCTCA 59.526 40.000 0.00 0.00 0.00 3.27
183 187 1.986413 CTGTCCAGGGAGGGAGTTG 59.014 63.158 0.00 0.00 37.71 3.16
224 234 0.673644 ATGGAGGCGTGTGCTGTAAC 60.674 55.000 0.00 0.00 42.25 2.50
225 235 0.391130 GATGGAGGCGTGTGCTGTAA 60.391 55.000 0.00 0.00 42.25 2.41
226 236 1.218047 GATGGAGGCGTGTGCTGTA 59.782 57.895 0.00 0.00 42.25 2.74
227 237 2.046892 GATGGAGGCGTGTGCTGT 60.047 61.111 0.00 0.00 42.25 4.40
229 239 4.101448 GGGATGGAGGCGTGTGCT 62.101 66.667 0.00 0.00 42.25 4.40
285 312 2.169561 GGTGAGAGGGGAAGAGATGAAC 59.830 54.545 0.00 0.00 0.00 3.18
289 316 1.062505 GGAGGTGAGAGGGGAAGAGAT 60.063 57.143 0.00 0.00 0.00 2.75
295 322 2.684104 CGAGGAGGTGAGAGGGGA 59.316 66.667 0.00 0.00 0.00 4.81
307 334 3.948719 GTTGGTGGGTGGCGAGGA 61.949 66.667 0.00 0.00 0.00 3.71
406 455 4.996434 GGAGGTGCTGCGTGCTGT 62.996 66.667 0.00 0.00 43.37 4.40
461 510 0.101759 TGCTGTAGGCCGATACGTTC 59.898 55.000 0.00 0.00 40.92 3.95
867 945 9.255304 GGCAACAGTTCATGTAAAGAAAATTAA 57.745 29.630 0.00 0.00 43.00 1.40
868 946 8.417106 TGGCAACAGTTCATGTAAAGAAAATTA 58.583 29.630 0.00 0.00 46.17 1.40
871 949 6.214191 TGGCAACAGTTCATGTAAAGAAAA 57.786 33.333 0.00 0.00 46.17 2.29
889 967 3.181488 CCATATCAAGCGAAACATGGCAA 60.181 43.478 0.00 0.00 0.00 4.52
946 1024 1.280066 CACCACAAGCAAACAACTGC 58.720 50.000 0.00 0.00 42.97 4.40
950 1028 5.330455 TCATAAACACCACAAGCAAACAA 57.670 34.783 0.00 0.00 0.00 2.83
1042 1120 1.507520 CACGTACGACGACATGAATCG 59.492 52.381 24.41 8.07 46.05 3.34
1183 1261 1.108132 GGATCCTCGCTTCCTACCGT 61.108 60.000 3.84 0.00 0.00 4.83
1194 1272 1.519455 GAACAGTGGCGGATCCTCG 60.519 63.158 10.75 0.00 35.26 4.63
1205 1283 1.374758 GTGGCCGGAGAGAACAGTG 60.375 63.158 5.05 0.00 0.00 3.66
1257 1335 0.665670 CTGAGATACTCATGGCCGCG 60.666 60.000 0.00 0.00 39.92 6.46
1466 1545 3.304928 CCTCATCGTCATCGTCATCATCA 60.305 47.826 0.00 0.00 38.33 3.07
1478 1557 2.493675 CTCTTGGTCTTCCTCATCGTCA 59.506 50.000 0.00 0.00 34.23 4.35
1580 1659 6.152661 ACCCATGAGCGAAGATTAAAAATTGA 59.847 34.615 0.00 0.00 0.00 2.57
1586 1665 4.214986 TGACCCATGAGCGAAGATTAAA 57.785 40.909 0.00 0.00 0.00 1.52
1692 1771 0.750182 CGGTGGGTGAAGTTTGGTGT 60.750 55.000 0.00 0.00 0.00 4.16
1693 1772 0.750182 ACGGTGGGTGAAGTTTGGTG 60.750 55.000 0.00 0.00 0.00 4.17
1754 1833 5.062934 TCGAAATATGTTAGCCTTGTGAACG 59.937 40.000 0.00 0.00 0.00 3.95
1848 1927 5.643777 GGCTGAGCTCACTTACAAAAAGATA 59.356 40.000 13.74 0.00 0.00 1.98
1960 2040 7.569591 GCAAGTATTTCAGATTATACGGAGTGC 60.570 40.741 0.00 0.00 45.73 4.40
1968 2048 9.317936 CTCACAGTGCAAGTATTTCAGATTATA 57.682 33.333 0.00 0.00 0.00 0.98
2339 2465 3.118112 CCATACCAGTCAGCTCCTGAAAT 60.118 47.826 10.79 2.52 42.46 2.17
2393 2522 3.797451 TGCACAGAAAAATCAAGCACA 57.203 38.095 0.00 0.00 0.00 4.57
2396 2525 3.551485 ACGTTTGCACAGAAAAATCAAGC 59.449 39.130 0.00 0.00 0.00 4.01
2459 2589 9.860898 ATCAGAAATAGAAACAGGCATTTTAAC 57.139 29.630 0.00 0.00 0.00 2.01
2741 2882 1.269569 TGAAGTGTCCGTGTAGCTGTG 60.270 52.381 0.00 0.00 0.00 3.66
2858 3002 4.913345 CGCGTAACTAATCATCGATTACCA 59.087 41.667 0.00 0.00 33.95 3.25
2899 3056 3.438087 CCATCTGAGCCACTACAAAACAG 59.562 47.826 0.00 0.00 0.00 3.16
2987 3144 4.439305 TGTATTGAGAAAGGCATTGTGC 57.561 40.909 0.00 0.00 44.08 4.57
3002 3159 4.771590 ACTGTGACCAGCAAATGTATTG 57.228 40.909 0.00 0.00 42.81 1.90
3231 3395 5.893824 TGAACTGATATGAAGGAGCTCTGTA 59.106 40.000 14.64 0.00 0.00 2.74
3380 3553 8.190784 ACTAAAATGTTAAAGCATCATACAGGC 58.809 33.333 0.00 0.00 0.00 4.85
3555 3729 0.238289 CCCGAACAACATGTCTGCAC 59.762 55.000 0.00 0.00 0.00 4.57
4376 4614 3.001736 GCTCACAAGTAGATCGAATTGCC 59.998 47.826 14.68 0.00 0.00 4.52
4394 4632 4.806640 TTCTACACTCACATCATGCTCA 57.193 40.909 0.00 0.00 0.00 4.26
4515 4753 2.579201 CTCGACGAACCCAGCCAT 59.421 61.111 0.00 0.00 0.00 4.40
4557 4795 3.135457 CAGATGCGCACCATGCCA 61.135 61.111 14.90 0.00 41.12 4.92
4587 4825 4.329545 GTGCGAGCCAAGTCCCCA 62.330 66.667 0.00 0.00 0.00 4.96
4695 4933 7.386025 CACTTGAACATAGAGATGTCAAAGACA 59.614 37.037 14.66 1.95 45.93 3.41
4770 5009 3.119495 ACAAGCTGAATAAACCGCATTCC 60.119 43.478 0.00 0.00 32.46 3.01
4773 5012 4.036734 CCATACAAGCTGAATAAACCGCAT 59.963 41.667 0.00 0.00 0.00 4.73
4776 5015 4.634004 TGACCATACAAGCTGAATAAACCG 59.366 41.667 0.00 0.00 0.00 4.44
4847 5086 5.924254 CGACTACATGTAAAGAACAAGTCCA 59.076 40.000 7.06 0.00 42.70 4.02
4849 5088 5.924825 ACCGACTACATGTAAAGAACAAGTC 59.075 40.000 7.06 8.79 42.70 3.01
4860 5099 1.140161 GCGCCACCGACTACATGTA 59.860 57.895 5.25 5.25 36.29 2.29
4867 5106 4.988598 CCACTTGCGCCACCGACT 62.989 66.667 4.18 0.00 36.29 4.18
4871 5110 1.852067 CTTGTACCACTTGCGCCACC 61.852 60.000 4.18 0.00 0.00 4.61
4926 5172 8.717821 GTTAGATAAATGAAGTGCTTGTACACA 58.282 33.333 0.00 0.00 43.23 3.72
4941 5190 5.575218 GCAAAACCCCAACGTTAGATAAATG 59.425 40.000 0.00 0.00 0.00 2.32
4947 5196 2.351706 AGCAAAACCCCAACGTTAGA 57.648 45.000 0.00 0.00 0.00 2.10
4992 5241 0.176680 CTTCCATCGGTAGCAGCAGT 59.823 55.000 0.00 0.00 0.00 4.40
5063 5312 3.408634 AGTATGGGCGCAACATATAACC 58.591 45.455 21.71 12.13 33.77 2.85
5096 5345 8.877864 ATCAACCATGGAGAATAAACAACTTA 57.122 30.769 21.47 0.00 0.00 2.24
5170 5419 1.732405 GCCAATGTAGGTTGCGCTTTC 60.732 52.381 9.73 0.00 0.00 2.62
5174 5423 1.091537 TAAGCCAATGTAGGTTGCGC 58.908 50.000 0.00 0.00 0.00 6.09
5184 5433 5.170748 CCCTTTTGCTAGTTTAAGCCAATG 58.829 41.667 0.00 0.00 42.05 2.82
5222 5471 5.010719 TGAACGTTGCAATTTTATTACCCCA 59.989 36.000 5.00 0.00 0.00 4.96
5469 5724 7.758980 TGTTTGTATTGACACATTGGATAATGC 59.241 33.333 0.00 0.00 46.05 3.56
5650 5905 4.810191 ATAAGACCGAAAGAGTGAAGCT 57.190 40.909 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.