Multiple sequence alignment - TraesCS1B01G272600

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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 TraesCS1B01G272600 chr1B 100.000 4006 0 0 1 4006 478584855 478580850 0.000000e+00 7398.0
1 TraesCS1B01G272600 chr1B 92.444 622 40 6 3389 4006 51327846 51327228 0.000000e+00 881.0
2 TraesCS1B01G272600 chr1D 94.862 2822 76 37 544 3332 355699399 355696614 0.000000e+00 4344.0
3 TraesCS1B01G272600 chr1D 90.485 515 23 6 58 557 355699973 355699470 0.000000e+00 656.0
4 TraesCS1B01G272600 chr1D 100.000 34 0 0 1 34 355700005 355699972 3.340000e-06 63.9
5 TraesCS1B01G272600 chr1A 94.192 2049 76 28 206 2219 456324509 456322469 0.000000e+00 3085.0
6 TraesCS1B01G272600 chr1A 94.118 969 36 5 2328 3281 456322106 456321144 0.000000e+00 1454.0
7 TraesCS1B01G272600 chr1A 95.192 208 10 0 1 208 456324972 456324765 2.980000e-86 329.0
8 TraesCS1B01G272600 chr5B 95.064 628 28 3 3381 4006 508671025 508671651 0.000000e+00 985.0
9 TraesCS1B01G272600 chr5B 95.323 620 24 4 3389 4006 619291476 619292092 0.000000e+00 979.0
10 TraesCS1B01G272600 chrUn 94.929 631 26 5 3380 4006 65982184 65981556 0.000000e+00 983.0
11 TraesCS1B01G272600 chrUn 96.226 53 1 1 3329 3380 310085719 310085667 7.130000e-13 86.1
12 TraesCS1B01G272600 chr3B 95.122 615 27 2 3392 4005 809080201 809079589 0.000000e+00 966.0
13 TraesCS1B01G272600 chr3B 92.395 263 16 4 1364 1624 675281921 675281661 4.890000e-99 372.0
14 TraesCS1B01G272600 chr3B 92.000 175 13 1 1099 1273 675282185 675282012 1.110000e-60 244.0
15 TraesCS1B01G272600 chr3B 78.125 256 42 13 1359 1609 678548536 678548782 2.490000e-32 150.0
16 TraesCS1B01G272600 chr7B 94.286 630 29 7 3380 4006 583217941 583218566 0.000000e+00 957.0
17 TraesCS1B01G272600 chr7B 94.516 620 25 7 3391 4006 7022365 7022979 0.000000e+00 948.0
18 TraesCS1B01G272600 chr7B 92.405 632 37 6 3380 4006 669182701 669182076 0.000000e+00 891.0
19 TraesCS1B01G272600 chr7B 87.600 250 28 2 1362 1608 410620577 410620328 1.820000e-73 287.0
20 TraesCS1B01G272600 chr7B 89.796 147 15 0 1129 1275 410620930 410620784 5.290000e-44 189.0
21 TraesCS1B01G272600 chr4A 93.087 622 35 6 3389 4006 690112648 690113265 0.000000e+00 904.0
22 TraesCS1B01G272600 chr3D 92.015 263 17 4 1364 1624 512707435 512707175 2.270000e-97 366.0
23 TraesCS1B01G272600 chr3D 92.000 175 13 1 1099 1273 512707699 512707526 1.110000e-60 244.0
24 TraesCS1B01G272600 chr3D 98.305 59 1 0 3322 3380 5679241 5679183 1.970000e-18 104.0
25 TraesCS1B01G272600 chr3D 98.077 52 1 0 3329 3380 571057302 571057353 1.530000e-14 91.6
26 TraesCS1B01G272600 chr3A 92.015 263 17 4 1364 1624 648311910 648311650 2.270000e-97 366.0
27 TraesCS1B01G272600 chr3A 91.429 175 14 1 1099 1273 648312177 648312004 5.170000e-59 239.0
28 TraesCS1B01G272600 chr7D 88.400 250 26 2 1362 1608 401093670 401093421 8.420000e-77 298.0
29 TraesCS1B01G272600 chr7D 90.476 147 14 0 1129 1275 401094022 401093876 1.140000e-45 195.0
30 TraesCS1B01G272600 chr7D 78.014 141 21 10 1128 1263 34151675 34151540 3.320000e-11 80.5
31 TraesCS1B01G272600 chr7A 88.446 251 24 4 1362 1608 458934574 458934325 8.420000e-77 298.0
32 TraesCS1B01G272600 chr7A 90.476 147 14 0 1129 1275 458934922 458934776 1.140000e-45 195.0
33 TraesCS1B01G272600 chr4D 75.732 239 48 6 1378 1608 485764233 485763997 1.180000e-20 111.0
34 TraesCS1B01G272600 chr4D 100.000 50 0 0 3331 3380 357986080 357986129 4.260000e-15 93.5
35 TraesCS1B01G272600 chr2B 100.000 53 0 0 3329 3381 615885366 615885418 9.160000e-17 99.0
36 TraesCS1B01G272600 chr2A 98.148 54 1 0 3327 3380 762575851 762575798 1.190000e-15 95.3
37 TraesCS1B01G272600 chr5D 100.000 50 0 0 3331 3380 24332345 24332296 4.260000e-15 93.5
38 TraesCS1B01G272600 chr5D 98.000 50 1 0 3331 3380 513536434 513536385 1.980000e-13 87.9
39 TraesCS1B01G272600 chr4B 98.113 53 1 0 3328 3380 88938830 88938778 4.260000e-15 93.5


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 TraesCS1B01G272600 chr1B 478580850 478584855 4005 True 7398.000000 7398 100.000000 1 4006 1 chr1B.!!$R2 4005
1 TraesCS1B01G272600 chr1B 51327228 51327846 618 True 881.000000 881 92.444000 3389 4006 1 chr1B.!!$R1 617
2 TraesCS1B01G272600 chr1D 355696614 355700005 3391 True 1687.966667 4344 95.115667 1 3332 3 chr1D.!!$R1 3331
3 TraesCS1B01G272600 chr1A 456321144 456324972 3828 True 1622.666667 3085 94.500667 1 3281 3 chr1A.!!$R1 3280
4 TraesCS1B01G272600 chr5B 508671025 508671651 626 False 985.000000 985 95.064000 3381 4006 1 chr5B.!!$F1 625
5 TraesCS1B01G272600 chr5B 619291476 619292092 616 False 979.000000 979 95.323000 3389 4006 1 chr5B.!!$F2 617
6 TraesCS1B01G272600 chrUn 65981556 65982184 628 True 983.000000 983 94.929000 3380 4006 1 chrUn.!!$R1 626
7 TraesCS1B01G272600 chr3B 809079589 809080201 612 True 966.000000 966 95.122000 3392 4005 1 chr3B.!!$R1 613
8 TraesCS1B01G272600 chr3B 675281661 675282185 524 True 308.000000 372 92.197500 1099 1624 2 chr3B.!!$R2 525
9 TraesCS1B01G272600 chr7B 583217941 583218566 625 False 957.000000 957 94.286000 3380 4006 1 chr7B.!!$F2 626
10 TraesCS1B01G272600 chr7B 7022365 7022979 614 False 948.000000 948 94.516000 3391 4006 1 chr7B.!!$F1 615
11 TraesCS1B01G272600 chr7B 669182076 669182701 625 True 891.000000 891 92.405000 3380 4006 1 chr7B.!!$R1 626
12 TraesCS1B01G272600 chr7B 410620328 410620930 602 True 238.000000 287 88.698000 1129 1608 2 chr7B.!!$R2 479
13 TraesCS1B01G272600 chr4A 690112648 690113265 617 False 904.000000 904 93.087000 3389 4006 1 chr4A.!!$F1 617
14 TraesCS1B01G272600 chr3D 512707175 512707699 524 True 305.000000 366 92.007500 1099 1624 2 chr3D.!!$R2 525
15 TraesCS1B01G272600 chr3A 648311650 648312177 527 True 302.500000 366 91.722000 1099 1624 2 chr3A.!!$R1 525
16 TraesCS1B01G272600 chr7D 401093421 401094022 601 True 246.500000 298 89.438000 1129 1608 2 chr7D.!!$R2 479
17 TraesCS1B01G272600 chr7A 458934325 458934922 597 True 246.500000 298 89.461000 1129 1608 2 chr7A.!!$R1 479

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
43 44 0.179089 ATCGAGTGCTCATCCACTGC 60.179 55.0 0.0 0.0 45.55 4.40 F
1281 1698 0.032416 AGCTCCCCGGTACACTACAT 60.032 55.0 0.0 0.0 0.00 2.29 F
2718 3571 0.248377 GGCAATGAGCTCAACGATGC 60.248 55.0 26.2 26.2 44.79 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1706 0.108709 AAGCGGTGCGTTTATCGGTA 60.109 50.000 0.00 0.0 40.26 4.02 R
2972 3825 0.396811 AACTGCCGTAGTCCTTGCTT 59.603 50.000 0.00 0.0 39.18 3.91 R
3524 4381 1.140252 ACTGTCGCGGCCCTATAAAAT 59.860 47.619 8.89 0.0 0.00 1.82 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
43 44 0.179089 ATCGAGTGCTCATCCACTGC 60.179 55.000 0.00 0.00 45.55 4.40
77 78 1.678970 GCCCAAGTGTCCATCCACC 60.679 63.158 0.00 0.00 35.93 4.61
133 134 1.686587 CGGCCGGCCTATCATATATGA 59.313 52.381 41.01 17.56 41.70 2.15
143 157 9.912634 CGGCCTATCATATATGAATTTTGTTTT 57.087 29.630 19.03 2.56 40.69 2.43
169 183 7.041235 TGCAAAATTCATCCAAAAATCCTTCAC 60.041 33.333 0.00 0.00 0.00 3.18
240 523 5.107133 CGTAACATAACAGGTGGTAGGAAG 58.893 45.833 0.00 0.00 28.69 3.46
287 570 2.613739 GATGCGTGACGGCTCTAGCA 62.614 60.000 7.25 3.36 44.36 3.49
292 575 1.065701 CGTGACGGCTCTAGCAACTAT 59.934 52.381 4.07 0.00 44.36 2.12
399 682 1.757574 CAACAAAGGCACACATCACG 58.242 50.000 0.00 0.00 0.00 4.35
424 707 4.773323 GTAGGAACACTACGTGTACCTT 57.227 45.455 0.00 0.00 46.79 3.50
539 824 7.878644 AGTAGAACTTTCCACATTCCTTCTAAC 59.121 37.037 0.00 0.00 0.00 2.34
707 1081 3.802948 ACATAGCTGTACTACCACTGC 57.197 47.619 0.00 0.00 42.00 4.40
709 1083 3.119101 ACATAGCTGTACTACCACTGCAC 60.119 47.826 0.00 0.00 43.54 4.57
712 1086 3.366396 AGCTGTACTACCACTGCACTAT 58.634 45.455 7.67 0.00 43.54 2.12
713 1087 4.533815 AGCTGTACTACCACTGCACTATA 58.466 43.478 7.67 0.00 43.54 1.31
719 1093 4.794334 ACTACCACTGCACTATAGCTAGT 58.206 43.478 0.00 0.00 38.79 2.57
731 1124 4.844420 GCTAGTGGGCAGCTACTG 57.156 61.111 11.62 0.00 36.07 2.74
928 1337 2.136878 GCCCTAGCTAGCTGGCTCA 61.137 63.158 29.79 13.64 42.97 4.26
931 1340 1.745264 CTAGCTAGCTGGCTCACCC 59.255 63.158 29.31 0.00 42.97 4.61
977 1386 3.021451 GCTATGCGGGCAATAGGTT 57.979 52.632 0.00 0.00 0.00 3.50
1281 1698 0.032416 AGCTCCCCGGTACACTACAT 60.032 55.000 0.00 0.00 0.00 2.29
1289 1706 4.525487 CCCCGGTACACTACATACACATAT 59.475 45.833 0.00 0.00 0.00 1.78
1292 1709 6.349611 CCCGGTACACTACATACACATATACC 60.350 46.154 0.00 0.00 0.00 2.73
1293 1710 6.309436 CGGTACACTACATACACATATACCG 58.691 44.000 4.79 4.79 44.40 4.02
1295 1712 8.048534 GGTACACTACATACACATATACCGAT 57.951 38.462 0.00 0.00 0.00 4.18
1299 1716 9.903682 ACACTACATACACATATACCGATAAAC 57.096 33.333 0.00 0.00 0.00 2.01
1340 1757 2.906268 AATCTTGGCAGATTGGGGC 58.094 52.632 10.16 0.00 46.38 5.80
1698 2242 1.337728 GGTTTTGGAATTTGGAGGCCG 60.338 52.381 0.00 0.00 0.00 6.13
1801 2346 5.286797 CGTTGTTCATGCTGTTAATCATTGG 59.713 40.000 0.00 0.00 0.00 3.16
2127 2674 7.546358 TGAAGCATTTAATTCCATGTTACAGG 58.454 34.615 0.00 0.00 0.00 4.00
2197 2744 6.653020 TCACTCAATTTACTGCATCCTATGT 58.347 36.000 0.00 0.00 0.00 2.29
2243 3076 7.633621 CGTACTCGTGTAAGATCTTTGGTATA 58.366 38.462 14.36 0.00 31.32 1.47
2245 3078 7.642082 ACTCGTGTAAGATCTTTGGTATAGT 57.358 36.000 14.36 8.04 0.00 2.12
2246 3079 8.743085 ACTCGTGTAAGATCTTTGGTATAGTA 57.257 34.615 14.36 0.00 0.00 1.82
2718 3571 0.248377 GGCAATGAGCTCAACGATGC 60.248 55.000 26.20 26.20 44.79 3.91
2720 3573 0.379669 CAATGAGCTCAACGATGCCC 59.620 55.000 22.50 0.00 0.00 5.36
2882 3735 2.685380 AGGCACTTCCTCCCCTCG 60.685 66.667 0.00 0.00 43.20 4.63
2977 3830 3.402186 CTGACACCACAGGAAGCAA 57.598 52.632 0.00 0.00 34.64 3.91
3099 3952 4.638865 GGGCATAATTCGTAGGTTTTCACT 59.361 41.667 0.00 0.00 0.00 3.41
3114 3967 0.753867 TCACTGCCACGGTTAACTCA 59.246 50.000 5.42 0.00 0.00 3.41
3332 4185 3.610911 GGTGATCACCCAAAGTCTAAGG 58.389 50.000 31.37 0.00 45.68 2.69
3333 4186 3.622455 GGTGATCACCCAAAGTCTAAGGG 60.622 52.174 31.37 7.78 45.68 3.95
3334 4187 2.026262 TGATCACCCAAAGTCTAAGGGC 60.026 50.000 9.01 0.00 46.88 5.19
3335 4188 1.440618 TCACCCAAAGTCTAAGGGCA 58.559 50.000 9.01 0.00 46.88 5.36
3336 4189 1.992557 TCACCCAAAGTCTAAGGGCAT 59.007 47.619 9.01 0.00 46.88 4.40
3337 4190 2.026262 TCACCCAAAGTCTAAGGGCATC 60.026 50.000 9.01 0.00 46.88 3.91
3338 4191 2.025887 CACCCAAAGTCTAAGGGCATCT 60.026 50.000 9.01 0.00 46.88 2.90
3339 4192 3.199946 CACCCAAAGTCTAAGGGCATCTA 59.800 47.826 9.01 0.00 46.88 1.98
3340 4193 3.200165 ACCCAAAGTCTAAGGGCATCTAC 59.800 47.826 9.01 0.00 46.88 2.59
3341 4194 3.199946 CCCAAAGTCTAAGGGCATCTACA 59.800 47.826 0.00 0.00 35.44 2.74
3342 4195 4.324254 CCCAAAGTCTAAGGGCATCTACAA 60.324 45.833 0.00 0.00 35.44 2.41
3343 4196 5.440610 CCAAAGTCTAAGGGCATCTACAAT 58.559 41.667 0.00 0.00 0.00 2.71
3344 4197 5.297776 CCAAAGTCTAAGGGCATCTACAATG 59.702 44.000 0.00 0.00 0.00 2.82
3345 4198 4.078639 AGTCTAAGGGCATCTACAATGC 57.921 45.455 1.40 1.40 43.85 3.56
3346 4199 3.455910 AGTCTAAGGGCATCTACAATGCA 59.544 43.478 11.69 0.00 46.21 3.96
3347 4200 4.080356 AGTCTAAGGGCATCTACAATGCAA 60.080 41.667 11.69 0.00 46.21 4.08
3348 4201 4.274459 GTCTAAGGGCATCTACAATGCAAG 59.726 45.833 11.69 4.16 46.21 4.01
3349 4202 3.370840 AAGGGCATCTACAATGCAAGA 57.629 42.857 11.69 0.00 46.21 3.02
3350 4203 2.928334 AGGGCATCTACAATGCAAGAG 58.072 47.619 11.69 0.00 46.21 2.85
3351 4204 1.336125 GGGCATCTACAATGCAAGAGC 59.664 52.381 11.69 0.00 46.21 4.09
3352 4205 1.003116 GGCATCTACAATGCAAGAGCG 60.003 52.381 11.69 0.00 46.21 5.03
3353 4206 1.596464 GCATCTACAATGCAAGAGCGC 60.596 52.381 0.00 0.00 46.23 5.92
3354 4207 1.938577 CATCTACAATGCAAGAGCGCT 59.061 47.619 11.27 11.27 46.23 5.92
3355 4208 2.099141 TCTACAATGCAAGAGCGCTT 57.901 45.000 13.26 0.00 46.23 4.68
3356 4209 3.245518 TCTACAATGCAAGAGCGCTTA 57.754 42.857 13.26 0.00 46.23 3.09
3357 4210 3.797039 TCTACAATGCAAGAGCGCTTAT 58.203 40.909 13.26 0.00 46.23 1.73
3358 4211 4.191544 TCTACAATGCAAGAGCGCTTATT 58.808 39.130 13.26 7.25 46.23 1.40
3359 4212 3.855689 ACAATGCAAGAGCGCTTATTT 57.144 38.095 13.26 3.91 46.23 1.40
3360 4213 3.504863 ACAATGCAAGAGCGCTTATTTG 58.495 40.909 13.26 17.56 46.23 2.32
3361 4214 2.855963 CAATGCAAGAGCGCTTATTTGG 59.144 45.455 22.98 9.58 46.23 3.28
3362 4215 1.819928 TGCAAGAGCGCTTATTTGGA 58.180 45.000 22.98 19.85 46.23 3.53
3363 4216 1.468520 TGCAAGAGCGCTTATTTGGAC 59.531 47.619 22.98 13.01 46.23 4.02
3364 4217 1.529826 GCAAGAGCGCTTATTTGGACG 60.530 52.381 22.98 8.50 31.81 4.79
3371 4224 1.003866 CGCTTATTTGGACGCTTAGGC 60.004 52.381 0.00 0.00 0.00 3.93
3372 4225 2.014128 GCTTATTTGGACGCTTAGGCA 58.986 47.619 0.00 0.00 38.60 4.75
3373 4226 2.422127 GCTTATTTGGACGCTTAGGCAA 59.578 45.455 0.00 0.00 38.60 4.52
3374 4227 3.066760 GCTTATTTGGACGCTTAGGCAAT 59.933 43.478 0.00 0.00 38.60 3.56
3375 4228 4.274950 GCTTATTTGGACGCTTAGGCAATA 59.725 41.667 0.00 0.00 38.60 1.90
3376 4229 5.220970 GCTTATTTGGACGCTTAGGCAATAA 60.221 40.000 0.00 0.00 38.60 1.40
3377 4230 6.679392 GCTTATTTGGACGCTTAGGCAATAAA 60.679 38.462 0.00 0.00 38.60 1.40
3378 4231 5.652994 ATTTGGACGCTTAGGCAATAAAA 57.347 34.783 0.00 0.00 38.60 1.52
3425 4281 1.203052 GGGTTTCTGTCGTCCGTCATA 59.797 52.381 0.00 0.00 0.00 2.15
3611 4470 3.147595 CAGCGATGAGACCGGGGA 61.148 66.667 6.32 0.00 0.00 4.81
3612 4471 2.363795 AGCGATGAGACCGGGGAA 60.364 61.111 6.32 0.00 0.00 3.97
3613 4472 1.987855 AGCGATGAGACCGGGGAAA 60.988 57.895 6.32 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 3.242518 CAGACTGTGCTGCATGATTTTG 58.757 45.455 5.27 0.00 0.00 2.44
143 157 6.996879 TGAAGGATTTTTGGATGAATTTTGCA 59.003 30.769 0.00 0.00 0.00 4.08
169 183 5.422650 ACTTAACTAGCTAGGACCTTTGAGG 59.577 44.000 24.35 0.00 42.49 3.86
208 222 6.261118 CACCTGTTATGTTACGTAGTACTCC 58.739 44.000 0.00 0.00 45.76 3.85
209 223 6.127897 ACCACCTGTTATGTTACGTAGTACTC 60.128 42.308 0.00 0.00 45.76 2.59
210 224 5.711976 ACCACCTGTTATGTTACGTAGTACT 59.288 40.000 0.00 0.00 45.76 2.73
211 225 5.954335 ACCACCTGTTATGTTACGTAGTAC 58.046 41.667 0.00 0.00 45.76 2.73
212 226 6.318648 CCTACCACCTGTTATGTTACGTAGTA 59.681 42.308 0.00 0.00 45.11 1.82
214 228 5.357878 TCCTACCACCTGTTATGTTACGTAG 59.642 44.000 0.00 0.00 0.00 3.51
215 229 5.260424 TCCTACCACCTGTTATGTTACGTA 58.740 41.667 0.00 0.00 0.00 3.57
216 230 4.088634 TCCTACCACCTGTTATGTTACGT 58.911 43.478 0.00 0.00 0.00 3.57
217 231 4.724074 TCCTACCACCTGTTATGTTACG 57.276 45.455 0.00 0.00 0.00 3.18
218 232 4.874396 GCTTCCTACCACCTGTTATGTTAC 59.126 45.833 0.00 0.00 0.00 2.50
240 523 6.401047 GGTTGAACTTGAAGAAAACAACTTGC 60.401 38.462 18.40 7.40 37.09 4.01
424 707 8.950007 AAAATAAAAGGAGAATACAAGGGACA 57.050 30.769 0.00 0.00 0.00 4.02
572 941 4.703575 ACATGGAATATCATGGCATACTGC 59.296 41.667 0.00 0.00 46.33 4.40
670 1039 9.565090 ACAGCTATGTACATGTATTGATTTGAT 57.435 29.630 18.81 0.00 38.09 2.57
693 1064 4.580995 AGCTATAGTGCAGTGGTAGTACAG 59.419 45.833 3.69 0.00 34.99 2.74
719 1093 2.153898 AAATGGCCAGTAGCTGCCCA 62.154 55.000 13.05 5.60 43.17 5.36
720 1094 0.106719 TAAATGGCCAGTAGCTGCCC 60.107 55.000 13.05 0.00 43.05 5.36
721 1095 1.762708 TTAAATGGCCAGTAGCTGCC 58.237 50.000 13.05 5.85 43.05 4.85
723 1097 7.230510 TGGTAATAATTAAATGGCCAGTAGCTG 59.769 37.037 13.05 0.00 43.05 4.24
753 1146 4.665833 TTGAACCGGAGTATCGATGATT 57.334 40.909 9.46 0.00 34.37 2.57
755 1148 3.634910 TGATTGAACCGGAGTATCGATGA 59.365 43.478 9.46 0.00 34.37 2.92
756 1149 3.977427 TGATTGAACCGGAGTATCGATG 58.023 45.455 9.46 0.00 34.37 3.84
757 1150 4.665833 TTGATTGAACCGGAGTATCGAT 57.334 40.909 9.46 2.16 34.37 3.59
758 1151 4.459390 TTTGATTGAACCGGAGTATCGA 57.541 40.909 9.46 2.42 34.37 3.59
759 1152 4.630069 AGTTTTGATTGAACCGGAGTATCG 59.370 41.667 9.46 0.00 34.37 2.92
760 1153 7.413767 GGTTAGTTTTGATTGAACCGGAGTATC 60.414 40.741 9.46 6.06 30.94 2.24
761 1154 6.373495 GGTTAGTTTTGATTGAACCGGAGTAT 59.627 38.462 9.46 0.00 30.94 2.12
762 1155 5.702209 GGTTAGTTTTGATTGAACCGGAGTA 59.298 40.000 9.46 0.00 30.94 2.59
763 1156 4.517832 GGTTAGTTTTGATTGAACCGGAGT 59.482 41.667 9.46 0.00 30.94 3.85
764 1157 4.517453 TGGTTAGTTTTGATTGAACCGGAG 59.483 41.667 9.46 0.00 42.08 4.63
765 1158 4.462133 TGGTTAGTTTTGATTGAACCGGA 58.538 39.130 9.46 0.00 42.08 5.14
766 1159 4.320935 CCTGGTTAGTTTTGATTGAACCGG 60.321 45.833 0.00 0.00 42.08 5.28
1281 1698 5.221880 GGTGCGTTTATCGGTATATGTGTA 58.778 41.667 0.00 0.00 40.26 2.90
1289 1706 0.108709 AAGCGGTGCGTTTATCGGTA 60.109 50.000 0.00 0.00 40.26 4.02
1292 1709 3.660904 GCTAATAAGCGGTGCGTTTATCG 60.661 47.826 0.00 0.00 41.01 2.92
1293 1710 3.795659 GCTAATAAGCGGTGCGTTTATC 58.204 45.455 0.00 0.00 41.01 1.75
1340 1757 5.232463 CCAACACCAAGAAATCAATCAAGG 58.768 41.667 0.00 0.00 0.00 3.61
1698 2242 3.054582 AGGAATTTCCGGGTCTTAAGTCC 60.055 47.826 10.00 10.00 42.75 3.85
1801 2346 5.276536 GCAGTGAACAAAAAGCAGATCAAAC 60.277 40.000 0.00 0.00 0.00 2.93
2120 2667 2.260481 GAAGTGAGCGCTACCTGTAAC 58.740 52.381 11.50 0.00 0.00 2.50
2122 2669 1.541379 TGAAGTGAGCGCTACCTGTA 58.459 50.000 11.50 0.00 0.00 2.74
2127 2674 5.718649 TTTTCATATGAAGTGAGCGCTAC 57.281 39.130 11.50 9.49 35.21 3.58
2197 2744 4.053983 CGTACGTGATACTAGCTAGGTGA 58.946 47.826 24.35 9.93 0.00 4.02
2245 3078 9.340695 CGACATGTCAAAAGCAAAGAAATTATA 57.659 29.630 24.93 0.00 0.00 0.98
2246 3079 7.148755 GCGACATGTCAAAAGCAAAGAAATTAT 60.149 33.333 24.93 0.00 0.00 1.28
2257 3092 3.536158 TTACTGCGACATGTCAAAAGC 57.464 42.857 24.93 19.24 0.00 3.51
2258 3093 6.991485 AAATTTACTGCGACATGTCAAAAG 57.009 33.333 24.93 19.14 0.00 2.27
2259 3094 6.975197 TCAAAATTTACTGCGACATGTCAAAA 59.025 30.769 24.93 15.52 0.00 2.44
2303 3138 2.159156 ACCCTTTGTCGAAAAACCAAGC 60.159 45.455 0.00 0.00 0.00 4.01
2549 3387 2.029288 CTGCTGCGTCGGTGACATT 61.029 57.895 0.00 0.00 32.09 2.71
2702 3555 1.091771 CGGGCATCGTTGAGCTCATT 61.092 55.000 19.04 0.00 0.00 2.57
2831 3684 0.399519 GGTTAGGGTAGGCCTGGCTA 60.400 60.000 17.99 4.18 34.45 3.93
2867 3720 4.475135 GGCGAGGGGAGGAAGTGC 62.475 72.222 0.00 0.00 0.00 4.40
2882 3735 2.858807 GAATTTGCGACGACGACGGC 62.859 60.000 20.21 7.81 45.02 5.68
2933 3786 2.673775 TCCAATCCCAAAGCTTGTCA 57.326 45.000 0.00 0.00 0.00 3.58
2972 3825 0.396811 AACTGCCGTAGTCCTTGCTT 59.603 50.000 0.00 0.00 39.18 3.91
2977 3830 2.510928 ACTAGAACTGCCGTAGTCCT 57.489 50.000 0.00 0.00 39.18 3.85
3099 3952 2.614983 GTTTTCTGAGTTAACCGTGGCA 59.385 45.455 0.88 0.00 0.00 4.92
3114 3967 7.514721 TGTAAAGTCTAGGTTGATGGTTTTCT 58.485 34.615 0.00 0.00 0.00 2.52
3201 4054 8.150296 TGTGCTTACAACATCAGTGCTATATAT 58.850 33.333 0.00 0.00 0.00 0.86
3202 4055 7.496747 TGTGCTTACAACATCAGTGCTATATA 58.503 34.615 0.00 0.00 0.00 0.86
3325 4178 3.808728 TGCATTGTAGATGCCCTTAGAC 58.191 45.455 8.36 0.00 43.94 2.59
3332 4185 1.003116 CGCTCTTGCATTGTAGATGCC 60.003 52.381 8.36 0.00 43.94 4.40
3333 4186 1.596464 GCGCTCTTGCATTGTAGATGC 60.596 52.381 0.00 4.14 44.76 3.91
3334 4187 1.938577 AGCGCTCTTGCATTGTAGATG 59.061 47.619 2.64 0.00 39.64 2.90
3335 4188 2.322355 AGCGCTCTTGCATTGTAGAT 57.678 45.000 2.64 0.00 39.64 1.98
3336 4189 2.099141 AAGCGCTCTTGCATTGTAGA 57.901 45.000 12.06 0.00 39.64 2.59
3337 4190 4.542662 AATAAGCGCTCTTGCATTGTAG 57.457 40.909 12.06 0.00 39.64 2.74
3338 4191 4.438608 CCAAATAAGCGCTCTTGCATTGTA 60.439 41.667 12.06 0.00 39.64 2.41
3339 4192 3.504863 CAAATAAGCGCTCTTGCATTGT 58.495 40.909 12.06 0.00 39.64 2.71
3340 4193 2.855963 CCAAATAAGCGCTCTTGCATTG 59.144 45.455 12.06 10.52 39.64 2.82
3341 4194 2.754552 TCCAAATAAGCGCTCTTGCATT 59.245 40.909 12.06 2.79 39.64 3.56
3342 4195 2.098117 GTCCAAATAAGCGCTCTTGCAT 59.902 45.455 12.06 0.00 39.64 3.96
3343 4196 1.468520 GTCCAAATAAGCGCTCTTGCA 59.531 47.619 12.06 0.00 39.64 4.08
3344 4197 1.529826 CGTCCAAATAAGCGCTCTTGC 60.530 52.381 12.06 2.73 33.85 4.01
3345 4198 1.529826 GCGTCCAAATAAGCGCTCTTG 60.530 52.381 12.06 14.73 45.48 3.02
3346 4199 0.727398 GCGTCCAAATAAGCGCTCTT 59.273 50.000 12.06 4.60 45.48 2.85
3347 4200 2.384203 GCGTCCAAATAAGCGCTCT 58.616 52.632 12.06 3.55 45.48 4.09
3348 4201 4.976619 GCGTCCAAATAAGCGCTC 57.023 55.556 12.06 0.00 45.48 5.03
3351 4204 1.003866 GCCTAAGCGTCCAAATAAGCG 60.004 52.381 0.00 0.00 34.34 4.68
3352 4205 2.014128 TGCCTAAGCGTCCAAATAAGC 58.986 47.619 0.00 0.00 44.31 3.09
3353 4206 4.900635 ATTGCCTAAGCGTCCAAATAAG 57.099 40.909 0.00 0.00 44.31 1.73
3354 4207 6.761099 TTTATTGCCTAAGCGTCCAAATAA 57.239 33.333 0.00 0.00 44.31 1.40
3355 4208 6.761099 TTTTATTGCCTAAGCGTCCAAATA 57.239 33.333 0.00 0.00 44.31 1.40
3356 4209 5.652994 TTTTATTGCCTAAGCGTCCAAAT 57.347 34.783 0.00 0.00 44.31 2.32
3357 4210 5.455056 TTTTTATTGCCTAAGCGTCCAAA 57.545 34.783 0.00 0.00 44.31 3.28
3358 4211 5.417580 AGATTTTTATTGCCTAAGCGTCCAA 59.582 36.000 0.00 0.00 44.31 3.53
3359 4212 4.947388 AGATTTTTATTGCCTAAGCGTCCA 59.053 37.500 0.00 0.00 44.31 4.02
3360 4213 5.500645 AGATTTTTATTGCCTAAGCGTCC 57.499 39.130 0.00 0.00 44.31 4.79
3361 4214 7.431376 GGTAAAGATTTTTATTGCCTAAGCGTC 59.569 37.037 0.00 0.00 34.89 5.19
3362 4215 7.122204 AGGTAAAGATTTTTATTGCCTAAGCGT 59.878 33.333 0.00 0.00 34.89 5.07
3363 4216 7.480810 AGGTAAAGATTTTTATTGCCTAAGCG 58.519 34.615 0.00 0.00 34.89 4.68
3524 4381 1.140252 ACTGTCGCGGCCCTATAAAAT 59.860 47.619 8.89 0.00 0.00 1.82
3611 4470 3.790408 AGATGTGGAAGATGGGGATCTTT 59.210 43.478 0.00 0.00 40.67 2.52
3612 4471 3.401385 AGATGTGGAAGATGGGGATCTT 58.599 45.455 0.00 0.00 43.04 2.40
3613 4472 3.071967 AGATGTGGAAGATGGGGATCT 57.928 47.619 0.00 0.00 0.00 2.75
3903 4771 9.773328 CGAATATGTTTTCAATACACAGTCAAT 57.227 29.630 0.00 0.00 0.00 2.57
3904 4772 8.233868 CCGAATATGTTTTCAATACACAGTCAA 58.766 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.