Multiple sequence alignment - TraesCS1A01G428100

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 TraesCS1A01G428100 chr1A 100.000 4604 0 0 1 4604 582222953 582218350 0.000000e+00 8503.0
1 TraesCS1A01G428100 chr1A 87.215 219 14 10 4109 4323 581916614 581916406 2.140000e-58 237.0
2 TraesCS1A01G428100 chr1A 83.182 220 14 13 4112 4324 581960400 581960197 3.660000e-41 180.0
3 TraesCS1A01G428100 chr1A 97.872 47 1 0 4112 4158 581880499 581880453 1.060000e-11 82.4
4 TraesCS1A01G428100 chr1D 93.636 2860 102 24 1 2807 485024771 485021939 0.000000e+00 4200.0
5 TraesCS1A01G428100 chr1D 89.442 1667 71 31 2901 4489 485021795 485020156 0.000000e+00 2006.0
6 TraesCS1A01G428100 chr1D 88.073 218 17 8 4109 4323 484796984 484796773 2.750000e-62 250.0
7 TraesCS1A01G428100 chr1D 82.192 219 16 12 4112 4323 484871407 484871205 2.850000e-37 167.0
8 TraesCS1A01G428100 chr1D 89.831 118 11 1 4478 4594 485020134 485020017 2.870000e-32 150.0
9 TraesCS1A01G428100 chr1D 95.000 80 4 0 4244 4323 484739393 484739314 4.840000e-25 126.0
10 TraesCS1A01G428100 chr1D 97.872 47 1 0 4112 4158 484566414 484566368 1.060000e-11 82.4
11 TraesCS1A01G428100 chr1B 93.064 2624 111 20 1339 3905 675314505 675311896 0.000000e+00 3771.0
12 TraesCS1A01G428100 chr1B 94.974 1333 33 5 1 1300 675315827 675314496 0.000000e+00 2060.0
13 TraesCS1A01G428100 chr1B 82.270 564 41 15 3972 4489 675311895 675311345 2.540000e-117 433.0
14 TraesCS1A01G428100 chr1B 81.982 222 17 12 4109 4323 674895157 674894952 2.850000e-37 167.0
15 TraesCS1A01G428100 chr1B 81.982 222 17 12 4109 4323 675220740 675220945 2.850000e-37 167.0
16 TraesCS1A01G428100 chr1B 80.088 226 20 11 4109 4323 646687345 646687134 1.340000e-30 145.0
17 TraesCS1A01G428100 chr1B 80.269 223 19 11 4112 4323 646776596 646776388 1.340000e-30 145.0
18 TraesCS1A01G428100 chr1B 90.217 92 9 0 4223 4314 675227265 675227356 2.250000e-23 121.0
19 TraesCS1A01G428100 chr1B 97.872 47 1 0 4112 4158 674821357 674821311 1.060000e-11 82.4


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 TraesCS1A01G428100 chr1A 582218350 582222953 4603 True 8503.000000 8503 100.000000 1 4604 1 chr1A.!!$R4 4603
1 TraesCS1A01G428100 chr1D 485020017 485024771 4754 True 2118.666667 4200 90.969667 1 4594 3 chr1D.!!$R5 4593
2 TraesCS1A01G428100 chr1B 675311345 675315827 4482 True 2088.000000 3771 90.102667 1 4489 3 chr1B.!!$R5 4488

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
813 848 1.400142 CAGTGAGCACGGTGTGAAAAA 59.600 47.619 10.24 0.0 35.23 1.94 F
1876 1923 0.320771 GTCCTGTCGACCACTGCATT 60.321 55.000 14.12 0.0 35.23 3.56 F
3049 3177 0.172127 GATCACTCTCAGCGCAGTCA 59.828 55.000 11.47 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2127 0.452184 CAGCTTCCTGCAGCAGATTG 59.548 55.0 24.90 13.19 45.94 2.67 R
3324 3464 0.457851 GCTGCACGAGTAGAGGTCAT 59.542 55.0 1.52 0.00 0.00 3.06 R
4565 4840 0.040425 GACCGCGCACTTGTGATTTT 60.040 50.0 8.75 0.00 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
259 264 6.385759 TCTTGATAGGTACTCCTGGCAAAATA 59.614 38.462 0.00 0.00 44.81 1.40
279 284 1.622811 AGTCACTCTTCCTTGGCTCTG 59.377 52.381 0.00 0.00 0.00 3.35
352 357 3.258872 TGAAATTCCACCAGCAGAAATGG 59.741 43.478 0.00 0.00 43.87 3.16
432 438 8.731275 TTCATCTCTAGGAAATAAAATTCGCA 57.269 30.769 0.00 0.00 0.00 5.10
526 533 2.930950 GCAGTGGGCATTAATACTCCA 58.069 47.619 0.00 0.00 43.97 3.86
531 538 3.636300 GTGGGCATTAATACTCCATGCAA 59.364 43.478 5.77 0.00 44.37 4.08
565 572 4.599047 TTCTTGGTTGGCTGTAAAATGG 57.401 40.909 0.00 0.00 0.00 3.16
617 624 3.662759 TTTTTGTTCCCTCTCCACTGT 57.337 42.857 0.00 0.00 0.00 3.55
715 746 2.646930 TGTGCCAGATGCTTCCTTATG 58.353 47.619 0.00 0.00 42.00 1.90
813 848 1.400142 CAGTGAGCACGGTGTGAAAAA 59.600 47.619 10.24 0.00 35.23 1.94
1094 1133 1.868713 TGCTCCATGGATGCCAAAAT 58.131 45.000 24.48 0.00 36.95 1.82
1269 1309 5.066593 ACTTCTTTCTTTAACTCTGCCTGG 58.933 41.667 0.00 0.00 0.00 4.45
1300 1340 1.490910 CCCCTCCAGGACTTAACATCC 59.509 57.143 0.00 0.00 38.24 3.51
1303 1343 2.092914 CCTCCAGGACTTAACATCCCAC 60.093 54.545 0.00 0.00 36.86 4.61
1305 1345 1.369625 CAGGACTTAACATCCCACGC 58.630 55.000 0.00 0.00 36.86 5.34
1320 1360 0.865111 CACGCGTCTGGTTTTGATCA 59.135 50.000 9.86 0.00 0.00 2.92
1323 1363 1.267038 CGCGTCTGGTTTTGATCATCG 60.267 52.381 0.00 0.00 0.00 3.84
1327 1367 3.001634 CGTCTGGTTTTGATCATCGGATG 59.998 47.826 11.79 11.79 32.67 3.51
1336 1376 5.806654 TTGATCATCGGATGGATCTAACA 57.193 39.130 17.42 0.88 40.41 2.41
1344 1384 4.115516 CGGATGGATCTAACACACTTCAG 58.884 47.826 0.00 0.00 0.00 3.02
1347 1387 5.352569 GGATGGATCTAACACACTTCAGTTG 59.647 44.000 0.00 0.00 0.00 3.16
1476 1516 3.181487 GCAAGAAACCACACATGTCAACT 60.181 43.478 0.00 0.00 0.00 3.16
1643 1683 3.861276 TGTCCTACATCACACCTAACG 57.139 47.619 0.00 0.00 0.00 3.18
1678 1718 5.591877 GGACATCAATATGCCTCTCACTTTT 59.408 40.000 0.00 0.00 36.50 2.27
1695 1735 6.054941 TCACTTTTCTTCATGCAGTAAGTGA 58.945 36.000 25.44 25.44 40.33 3.41
1712 1752 8.660373 CAGTAAGTGAAGAGGAATGTCAAATAC 58.340 37.037 0.00 0.00 0.00 1.89
1713 1753 8.598041 AGTAAGTGAAGAGGAATGTCAAATACT 58.402 33.333 0.00 0.00 0.00 2.12
1714 1754 9.220767 GTAAGTGAAGAGGAATGTCAAATACTT 57.779 33.333 0.00 0.00 0.00 2.24
1837 1884 8.938801 ATGCCATGTATAATTTATCACAAGGA 57.061 30.769 16.15 8.58 32.78 3.36
1875 1922 1.293498 GTCCTGTCGACCACTGCAT 59.707 57.895 14.12 0.00 35.23 3.96
1876 1923 0.320771 GTCCTGTCGACCACTGCATT 60.321 55.000 14.12 0.00 35.23 3.56
1888 1935 5.675538 GACCACTGCATTAGAGTCCTTAAT 58.324 41.667 0.00 0.00 31.43 1.40
1926 1973 8.408743 CTTGCTAACTAAGTAAGCGTTAAGAT 57.591 34.615 0.00 0.00 40.43 2.40
1927 1974 7.982371 TGCTAACTAAGTAAGCGTTAAGATC 57.018 36.000 0.00 0.00 39.14 2.75
1928 1975 7.541162 TGCTAACTAAGTAAGCGTTAAGATCA 58.459 34.615 0.00 0.00 39.14 2.92
1929 1976 7.487189 TGCTAACTAAGTAAGCGTTAAGATCAC 59.513 37.037 0.00 0.00 39.14 3.06
1930 1977 7.701501 GCTAACTAAGTAAGCGTTAAGATCACT 59.298 37.037 0.00 0.00 0.00 3.41
1933 1980 9.918630 AACTAAGTAAGCGTTAAGATCACTAAA 57.081 29.630 0.00 0.00 0.00 1.85
1934 1981 9.918630 ACTAAGTAAGCGTTAAGATCACTAAAA 57.081 29.630 0.00 0.00 0.00 1.52
1986 2033 6.099159 AGGTGTCTTTCTAACAAGTAGGAC 57.901 41.667 0.00 0.00 0.00 3.85
1992 2039 9.485206 TGTCTTTCTAACAAGTAGGACAATAAC 57.515 33.333 0.00 0.00 30.26 1.89
2000 2047 5.309806 ACAAGTAGGACAATAACAAGACCCT 59.690 40.000 0.00 0.00 0.00 4.34
2001 2048 5.422214 AGTAGGACAATAACAAGACCCTG 57.578 43.478 0.00 0.00 0.00 4.45
2046 2111 6.265422 GGTGGTAAGAGCATAATTTTAGGCAT 59.735 38.462 9.34 0.00 42.42 4.40
2085 2152 1.664321 GCTGCAGGAAGCTGGAATGG 61.664 60.000 17.12 0.00 45.94 3.16
2270 2337 4.568152 ATTCTGTGGTTACAAAGTGCAC 57.432 40.909 9.40 9.40 36.14 4.57
2273 2340 4.771903 TCTGTGGTTACAAAGTGCACTAA 58.228 39.130 22.01 7.84 36.14 2.24
2315 2382 4.666512 AGATTAGTCCTGTTGCAACCAAT 58.333 39.130 26.14 14.58 32.75 3.16
2473 2540 0.398381 TGGTTTTGAGGCCCTGCTTT 60.398 50.000 0.00 0.00 0.00 3.51
2572 2639 6.569780 AGCGGTGAATTTTGAAAACTTACTT 58.430 32.000 0.00 0.00 0.00 2.24
2712 2779 2.294791 CCGAGCCTTCTGATGGTACTAG 59.705 54.545 10.85 0.00 0.00 2.57
2794 2864 1.377333 GTGCTAGGCCCAGTGTTCC 60.377 63.158 0.00 0.00 0.00 3.62
2815 2886 8.647796 TGTTCCTTTTCTATCTCTAAGAACACA 58.352 33.333 0.00 0.00 32.81 3.72
2842 2931 3.438087 AGAATCTCAAAGCATTGTGGTCG 59.562 43.478 1.04 0.00 37.79 4.79
2852 2941 0.941542 ATTGTGGTCGTGTTGGTTCG 59.058 50.000 0.00 0.00 0.00 3.95
2861 2950 1.790623 CGTGTTGGTTCGTTAGACTGG 59.209 52.381 0.00 0.00 0.00 4.00
2873 2962 4.038763 TCGTTAGACTGGAACTGAACACAT 59.961 41.667 0.00 0.00 0.00 3.21
2874 2963 4.150627 CGTTAGACTGGAACTGAACACATG 59.849 45.833 0.00 0.00 0.00 3.21
2913 3041 7.715265 AAGTATATGGCTAACTGATTGTTCG 57.285 36.000 0.00 0.00 39.89 3.95
2949 3077 3.682292 GAAGCTTGGGATCGGCGGT 62.682 63.158 2.10 0.00 0.00 5.68
3049 3177 0.172127 GATCACTCTCAGCGCAGTCA 59.828 55.000 11.47 0.00 0.00 3.41
3090 3222 2.540265 CTTGCTCAAGGTCAGTCAGT 57.460 50.000 1.79 0.00 34.87 3.41
3091 3223 2.411904 CTTGCTCAAGGTCAGTCAGTC 58.588 52.381 1.79 0.00 34.87 3.51
3092 3224 1.413118 TGCTCAAGGTCAGTCAGTCA 58.587 50.000 0.00 0.00 0.00 3.41
3093 3225 1.342496 TGCTCAAGGTCAGTCAGTCAG 59.658 52.381 0.00 0.00 0.00 3.51
3159 3291 6.552008 TCCTAAACAAACCCTGATGATCTTT 58.448 36.000 0.00 0.00 0.00 2.52
3289 3429 1.134461 ACAGGCTAGCTGCTGATTCAG 60.134 52.381 22.92 9.40 42.39 3.02
3292 3432 1.219646 GCTAGCTGCTGATTCAGAGC 58.780 55.000 17.87 19.78 38.95 4.09
3299 3439 4.100653 AGCTGCTGATTCAGAGCTGTATTA 59.899 41.667 26.13 0.00 40.54 0.98
3317 3457 7.279981 GCTGTATTACATGGTGTCACTGAATTA 59.720 37.037 2.35 0.00 0.00 1.40
3324 3464 4.967036 TGGTGTCACTGAATTATGTGTGA 58.033 39.130 2.35 0.00 37.14 3.58
3371 3511 2.267961 GTGCCCTACAGGAACGGG 59.732 66.667 0.00 0.00 33.06 5.28
3447 3587 2.756760 TCCTACAACGGGTACACATCTC 59.243 50.000 0.00 0.00 0.00 2.75
3455 3595 1.671850 GGGTACACATCTCACACCACG 60.672 57.143 0.00 0.00 0.00 4.94
3576 3724 3.243816 TGCAGGTGGCTCAGCTCA 61.244 61.111 0.00 0.00 40.40 4.26
3904 4082 5.541845 TCATACTATTCATGCTACCAGTGC 58.458 41.667 0.00 0.00 0.00 4.40
3908 4086 3.641434 ATTCATGCTACCAGTGCTCTT 57.359 42.857 0.00 0.00 0.00 2.85
3909 4087 3.423539 TTCATGCTACCAGTGCTCTTT 57.576 42.857 0.00 0.00 0.00 2.52
3911 4089 3.076621 TCATGCTACCAGTGCTCTTTTG 58.923 45.455 0.00 0.00 0.00 2.44
3912 4090 1.896220 TGCTACCAGTGCTCTTTTGG 58.104 50.000 0.00 0.00 37.98 3.28
3935 4128 5.519927 GGGTTTCAAAGACTTTGTCACAATG 59.480 40.000 23.78 1.89 41.36 2.82
4006 4199 3.136443 CCTTTCCAGGCAGTATATGGACA 59.864 47.826 0.00 0.00 42.72 4.02
4011 4204 3.497405 CCAGGCAGTATATGGACAGCAAT 60.497 47.826 0.00 0.00 36.09 3.56
4016 4209 7.006509 AGGCAGTATATGGACAGCAATTATTT 58.993 34.615 0.00 0.00 33.77 1.40
4042 4235 9.529325 TTGCTGTATGTATATTCTCAAGTGTAC 57.471 33.333 0.00 0.00 0.00 2.90
4044 4237 8.141909 GCTGTATGTATATTCTCAAGTGTACCA 58.858 37.037 0.00 0.00 0.00 3.25
4082 4275 0.725686 CAACTGAAGCATCTGAGGCG 59.274 55.000 8.79 0.00 36.08 5.52
4175 4378 3.118531 AGGAACATACAGGAATCTGGCT 58.881 45.455 0.00 0.00 44.99 4.75
4179 4382 1.945394 CATACAGGAATCTGGCTGTGC 59.055 52.381 0.00 0.00 44.99 4.57
4200 4403 4.469586 TGCTTACAGTGGGATATCTGAACA 59.530 41.667 2.05 0.00 35.84 3.18
4210 4413 3.258123 GGATATCTGAACAGGAGGAGAGC 59.742 52.174 2.05 0.00 0.00 4.09
4211 4414 2.244486 ATCTGAACAGGAGGAGAGCA 57.756 50.000 1.93 0.00 0.00 4.26
4212 4415 1.554836 TCTGAACAGGAGGAGAGCAG 58.445 55.000 1.93 0.00 0.00 4.24
4213 4416 1.076187 TCTGAACAGGAGGAGAGCAGA 59.924 52.381 1.93 0.00 0.00 4.26
4214 4417 1.898472 CTGAACAGGAGGAGAGCAGAA 59.102 52.381 0.00 0.00 0.00 3.02
4218 4421 0.179051 CAGGAGGAGAGCAGAATGGC 60.179 60.000 0.00 0.00 35.86 4.40
4219 4422 0.619832 AGGAGGAGAGCAGAATGGCA 60.620 55.000 0.00 0.00 35.86 4.92
4221 4424 1.133853 GGAGGAGAGCAGAATGGCAAT 60.134 52.381 0.00 0.00 35.86 3.56
4231 4434 3.192001 GCAGAATGGCAATTGTCTTGAGA 59.808 43.478 12.01 0.00 35.86 3.27
4235 4438 5.713389 AGAATGGCAATTGTCTTGAGAATGA 59.287 36.000 12.01 0.00 0.00 2.57
4236 4439 5.988310 ATGGCAATTGTCTTGAGAATGAA 57.012 34.783 12.01 0.00 0.00 2.57
4239 4442 5.984926 TGGCAATTGTCTTGAGAATGAAAAC 59.015 36.000 12.01 0.00 0.00 2.43
4273 4476 1.601166 TGCATCATGCTCTGGTATGC 58.399 50.000 11.84 6.38 45.31 3.14
4300 4510 2.871637 GCCTACTGTCATCACTGCACAA 60.872 50.000 0.00 0.00 0.00 3.33
4305 4515 1.955778 TGTCATCACTGCACAAAAGGG 59.044 47.619 0.00 0.00 0.00 3.95
4316 4526 0.779997 ACAAAAGGGGCAGATCACCT 59.220 50.000 0.00 0.00 35.78 4.00
4347 4572 6.830838 ACCAACTCTGAACTTTGATTTCTCTT 59.169 34.615 0.00 0.00 0.00 2.85
4398 4623 0.807667 CTCACCTCGAATCTTGGCCG 60.808 60.000 0.00 0.00 0.00 6.13
4416 4655 0.108804 CGTTAGCACCAGTCGTCCAT 60.109 55.000 0.00 0.00 0.00 3.41
4429 4668 1.498865 CGTCCATAGATTGTGCGGGC 61.499 60.000 0.00 0.00 0.00 6.13
4447 4686 2.338381 CTGCTCCAGCCAATATGCC 58.662 57.895 0.00 0.00 41.18 4.40
4476 4717 2.283298 GCTGCTGCTGCTAGTATCAAA 58.717 47.619 22.10 0.00 40.48 2.69
4485 4726 1.943340 GCTAGTATCAAACTGCCCTGC 59.057 52.381 0.00 0.00 39.39 4.85
4494 4768 2.044806 AACTGCCCTGCTTCGTCAGT 62.045 55.000 0.00 0.00 39.42 3.41
4498 4772 1.828595 TGCCCTGCTTCGTCAGTTATA 59.171 47.619 0.00 0.00 32.32 0.98
4529 4803 0.397675 ATCAGCACCTCCTGATCCGA 60.398 55.000 0.00 0.00 46.75 4.55
4532 4806 0.689080 AGCACCTCCTGATCCGATGT 60.689 55.000 0.00 0.00 0.00 3.06
4540 4814 1.269309 CCTGATCCGATGTTCGACTCC 60.269 57.143 0.00 0.00 43.74 3.85
4542 4816 1.033574 GATCCGATGTTCGACTCCCT 58.966 55.000 0.00 0.00 43.74 4.20
4543 4817 0.747255 ATCCGATGTTCGACTCCCTG 59.253 55.000 0.00 0.00 43.74 4.45
4544 4818 1.519455 CCGATGTTCGACTCCCTGC 60.519 63.158 0.00 0.00 43.74 4.85
4545 4819 1.513158 CGATGTTCGACTCCCTGCT 59.487 57.895 0.00 0.00 43.74 4.24
4548 4822 1.734465 GATGTTCGACTCCCTGCTTTG 59.266 52.381 0.00 0.00 0.00 2.77
4549 4823 0.884704 TGTTCGACTCCCTGCTTTGC 60.885 55.000 0.00 0.00 0.00 3.68
4565 4840 2.700329 TGCACACGCAGAACAATGA 58.300 47.368 0.00 0.00 45.36 2.57
4576 4851 4.977963 CGCAGAACAATGAAAATCACAAGT 59.022 37.500 0.00 0.00 0.00 3.16
4580 4855 3.052036 ACAATGAAAATCACAAGTGCGC 58.948 40.909 0.00 0.00 0.00 6.09
4591 4866 0.229753 CAAGTGCGCGGTCGATTATC 59.770 55.000 8.83 0.00 38.10 1.75
4594 4869 1.142097 TGCGCGGTCGATTATCCAA 59.858 52.632 8.83 0.00 38.10 3.53
4595 4870 0.460459 TGCGCGGTCGATTATCCAAA 60.460 50.000 8.83 0.00 38.10 3.28
4596 4871 0.865769 GCGCGGTCGATTATCCAAAT 59.134 50.000 8.83 0.00 38.10 2.32
4597 4872 1.136336 GCGCGGTCGATTATCCAAATC 60.136 52.381 8.83 0.00 38.10 2.17
4598 4873 1.459592 CGCGGTCGATTATCCAAATCC 59.540 52.381 0.00 0.00 38.10 3.01
4599 4874 1.459592 GCGGTCGATTATCCAAATCCG 59.540 52.381 0.00 0.00 39.71 4.18
4600 4875 2.066262 CGGTCGATTATCCAAATCCGG 58.934 52.381 0.00 0.00 34.24 5.14
4601 4876 1.804748 GGTCGATTATCCAAATCCGGC 59.195 52.381 0.00 0.00 0.00 6.13
4602 4877 2.550208 GGTCGATTATCCAAATCCGGCT 60.550 50.000 0.00 0.00 0.00 5.52
4603 4878 2.737252 GTCGATTATCCAAATCCGGCTC 59.263 50.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.509575 TGGCGCAAATGGTTAAAAGATCT 59.490 39.130 10.83 0.00 0.00 2.75
259 264 1.622811 CAGAGCCAAGGAAGAGTGACT 59.377 52.381 0.00 0.00 0.00 3.41
279 284 7.770897 ACTTGTTTCAGGATACAATCAGGATAC 59.229 37.037 5.90 0.00 41.41 2.24
352 357 6.655003 TCACTAATCCATGGACTTTCAGAAAC 59.345 38.462 18.99 0.00 0.00 2.78
432 438 3.221771 TGGCAAGGAATATAAAGCGCAT 58.778 40.909 11.47 0.00 0.00 4.73
531 538 2.962859 ACCAAGAATTTCCCTGCTTGT 58.037 42.857 0.00 0.00 36.81 3.16
565 572 3.721087 TGTTTCCTCTCCCTTTGATCC 57.279 47.619 0.00 0.00 0.00 3.36
617 624 7.541162 CAAAGGTTGATAAGATGCATCTTTGA 58.459 34.615 39.03 26.30 44.28 2.69
743 778 3.200825 CCTGGAAAGCTCTTGGGATTAGA 59.799 47.826 0.00 0.00 0.00 2.10
752 787 2.057922 TCTGGAACCTGGAAAGCTCTT 58.942 47.619 0.00 0.00 0.00 2.85
1094 1133 2.034558 TGCGACGATCTCAGCATTGATA 59.965 45.455 0.00 0.00 34.39 2.15
1269 1309 2.262774 CTGGAGGGGCATCACCTGAC 62.263 65.000 0.00 0.00 38.79 3.51
1300 1340 0.165944 GATCAAAACCAGACGCGTGG 59.834 55.000 20.70 16.51 44.01 4.94
1303 1343 1.267038 CGATGATCAAAACCAGACGCG 60.267 52.381 3.53 3.53 0.00 6.01
1305 1345 2.616960 TCCGATGATCAAAACCAGACG 58.383 47.619 0.00 0.00 0.00 4.18
1320 1360 4.405680 TGAAGTGTGTTAGATCCATCCGAT 59.594 41.667 0.00 0.00 0.00 4.18
1323 1363 5.091261 ACTGAAGTGTGTTAGATCCATCC 57.909 43.478 0.00 0.00 0.00 3.51
1327 1367 5.542779 AGACAACTGAAGTGTGTTAGATCC 58.457 41.667 0.00 0.00 0.00 3.36
1344 1384 7.803659 GGAAGTTTAGCATTCAGTTAAGACAAC 59.196 37.037 0.00 0.00 0.00 3.32
1347 1387 7.674471 AGGAAGTTTAGCATTCAGTTAAGAC 57.326 36.000 0.00 0.00 0.00 3.01
1427 1467 6.936335 TCCCTATTACATTCACACAGCATATG 59.064 38.462 0.00 0.00 0.00 1.78
1428 1468 7.078249 TCCCTATTACATTCACACAGCATAT 57.922 36.000 0.00 0.00 0.00 1.78
1476 1516 7.142021 GCGATCATCTACTCATGTCTTTTCTA 58.858 38.462 0.00 0.00 0.00 2.10
1643 1683 6.149142 GGCATATTGATGTCCTTGAGAAGATC 59.851 42.308 0.00 0.00 35.30 2.75
1695 1735 8.954350 CATCAAGAAGTATTTGACATTCCTCTT 58.046 33.333 0.00 0.00 37.38 2.85
1712 1752 4.264253 TGTCATTAGCCCACATCAAGAAG 58.736 43.478 0.00 0.00 0.00 2.85
1713 1753 4.299586 TGTCATTAGCCCACATCAAGAA 57.700 40.909 0.00 0.00 0.00 2.52
1714 1754 3.998913 TGTCATTAGCCCACATCAAGA 57.001 42.857 0.00 0.00 0.00 3.02
1779 1819 0.761802 GCCAAGACAGGGGATAGGAG 59.238 60.000 0.00 0.00 0.00 3.69
1832 1879 3.713764 AGATACTCCCATCCACTTCCTTG 59.286 47.826 0.00 0.00 0.00 3.61
1837 1884 3.375699 ACGAAGATACTCCCATCCACTT 58.624 45.455 0.00 0.00 0.00 3.16
1875 1922 4.568072 TGCTTGCCATTAAGGACTCTAA 57.432 40.909 0.00 0.00 41.22 2.10
1876 1923 4.778213 ATGCTTGCCATTAAGGACTCTA 57.222 40.909 0.00 0.00 41.22 2.43
1933 1980 9.802039 TCCTTGTAGGTGTTATTGTCTTTTATT 57.198 29.630 0.00 0.00 36.53 1.40
1934 1981 9.975218 ATCCTTGTAGGTGTTATTGTCTTTTAT 57.025 29.630 0.00 0.00 36.53 1.40
1935 1982 9.444600 GATCCTTGTAGGTGTTATTGTCTTTTA 57.555 33.333 0.00 0.00 36.53 1.52
1954 2001 6.936279 TGTTAGAAAGACACCTAGATCCTTG 58.064 40.000 0.00 0.00 0.00 3.61
1967 2014 9.485206 TGTTATTGTCCTACTTGTTAGAAAGAC 57.515 33.333 0.00 0.00 0.00 3.01
1986 2033 1.094785 CGGCCAGGGTCTTGTTATTG 58.905 55.000 2.24 0.00 0.00 1.90
1992 2039 1.244019 CCTTTTCGGCCAGGGTCTTG 61.244 60.000 2.24 0.00 0.00 3.02
2000 2047 1.061546 AGGTTAGTCCTTTTCGGCCA 58.938 50.000 2.24 0.00 45.67 5.36
2001 2048 1.450025 CAGGTTAGTCCTTTTCGGCC 58.550 55.000 0.00 0.00 45.67 6.13
2023 2088 7.341769 ACAATGCCTAAAATTATGCTCTTACCA 59.658 33.333 2.85 0.00 0.00 3.25
2025 2090 8.190784 ACACAATGCCTAAAATTATGCTCTTAC 58.809 33.333 2.85 0.00 0.00 2.34
2032 2097 7.095910 TGAACCACACAATGCCTAAAATTATG 58.904 34.615 0.00 0.00 0.00 1.90
2033 2098 7.238486 TGAACCACACAATGCCTAAAATTAT 57.762 32.000 0.00 0.00 0.00 1.28
2060 2127 0.452184 CAGCTTCCTGCAGCAGATTG 59.548 55.000 24.90 13.19 45.94 2.67
2085 2152 6.374565 ACAGAATTGCAGCAGAAGATATTC 57.625 37.500 7.02 7.02 0.00 1.75
2168 2235 0.750911 GCAAGGGAAGAGCATCCAGG 60.751 60.000 5.69 0.00 41.55 4.45
2257 2324 7.075741 CAGGTTACATTAGTGCACTTTGTAAC 58.924 38.462 39.29 39.29 43.84 2.50
2270 2337 5.466819 TCTGAACACGACAGGTTACATTAG 58.533 41.667 0.00 0.00 36.22 1.73
2273 2340 3.572682 TCTCTGAACACGACAGGTTACAT 59.427 43.478 0.00 0.00 36.22 2.29
2405 2472 1.303888 ACATGCAGTGCAGGGGAAG 60.304 57.895 30.98 14.84 45.01 3.46
2473 2540 3.680490 TCATGAAAAGTTCCCGCATACA 58.320 40.909 0.00 0.00 0.00 2.29
2587 2654 3.127895 CGTCAAACCCTGTTTCAGTTCAA 59.872 43.478 0.00 0.00 0.00 2.69
2794 2864 8.818141 TGTGTGTGTTCTTAGAGATAGAAAAG 57.182 34.615 0.00 0.00 33.71 2.27
2815 2886 5.508489 CCACAATGCTTTGAGATTCTTGTGT 60.508 40.000 18.35 0.00 40.00 3.72
2842 2931 3.102052 TCCAGTCTAACGAACCAACAC 57.898 47.619 0.00 0.00 0.00 3.32
2852 2941 5.050091 CACATGTGTTCAGTTCCAGTCTAAC 60.050 44.000 18.03 0.00 0.00 2.34
2861 2950 4.572389 AGTTCTGACACATGTGTTCAGTTC 59.428 41.667 33.25 28.52 45.05 3.01
2873 2962 7.710907 GCCATATACTTTCATAGTTCTGACACA 59.289 37.037 0.00 0.00 38.33 3.72
2874 2963 7.928706 AGCCATATACTTTCATAGTTCTGACAC 59.071 37.037 0.00 0.00 38.33 3.67
2913 3041 2.728690 TCACTGCATCCACAAATTGC 57.271 45.000 0.00 0.00 36.91 3.56
3000 3128 2.979676 CCGCTGCTGAACTTGCCA 60.980 61.111 0.00 0.00 0.00 4.92
3159 3291 2.038952 CCTCAGTGTCCTGAATTCACCA 59.961 50.000 3.38 0.00 46.79 4.17
3289 3429 4.568359 CAGTGACACCATGTAATACAGCTC 59.432 45.833 0.84 0.00 0.00 4.09
3292 3432 7.615582 AATTCAGTGACACCATGTAATACAG 57.384 36.000 0.84 0.00 0.00 2.74
3299 3439 5.181811 CACACATAATTCAGTGACACCATGT 59.818 40.000 14.88 0.00 39.03 3.21
3317 3457 3.129462 CACGAGTAGAGGTCATCACACAT 59.871 47.826 0.00 0.00 0.00 3.21
3324 3464 0.457851 GCTGCACGAGTAGAGGTCAT 59.542 55.000 1.52 0.00 0.00 3.06
3353 3493 2.125673 CCGTTCCTGTAGGGCACG 60.126 66.667 13.44 13.44 40.03 5.34
3356 3496 2.686106 TCCCCGTTCCTGTAGGGC 60.686 66.667 0.00 0.00 43.74 5.19
3447 3587 1.648720 CTTTGTCAGGCGTGGTGTG 59.351 57.895 6.56 0.00 0.00 3.82
3455 3595 1.003003 AGAGGAAGAGCTTTGTCAGGC 59.997 52.381 0.00 0.00 0.00 4.85
3513 3660 4.028490 TAGTGGCCCAACCTGCGG 62.028 66.667 0.00 0.00 40.22 5.69
3882 4060 5.545588 AGCACTGGTAGCATGAATAGTATG 58.454 41.667 0.00 0.00 0.00 2.39
3904 4082 6.398095 ACAAAGTCTTTGAAACCCAAAAGAG 58.602 36.000 28.07 0.84 43.50 2.85
3908 4086 5.011125 TGTGACAAAGTCTTTGAAACCCAAA 59.989 36.000 28.07 11.74 43.26 3.28
3909 4087 4.524714 TGTGACAAAGTCTTTGAAACCCAA 59.475 37.500 28.07 9.78 43.26 4.12
3911 4089 4.712122 TGTGACAAAGTCTTTGAAACCC 57.288 40.909 28.07 12.59 43.26 4.11
3912 4090 6.099341 ACATTGTGACAAAGTCTTTGAAACC 58.901 36.000 28.07 15.21 43.26 3.27
3935 4128 9.674068 AAGGTTTTTCTCTGATATTCTAGGAAC 57.326 33.333 0.00 0.00 0.00 3.62
3958 4151 4.821805 TGCTTCAGTTCCTTCTTACAAAGG 59.178 41.667 0.00 0.00 46.11 3.11
3970 4163 1.248486 GAAAGGGGTGCTTCAGTTCC 58.752 55.000 0.00 0.00 0.00 3.62
4016 4209 9.529325 GTACACTTGAGAATATACATACAGCAA 57.471 33.333 0.00 0.00 0.00 3.91
4042 4235 5.604758 TGACCTAGATCTGATCAAAGTGG 57.395 43.478 19.12 14.06 0.00 4.00
4044 4237 6.438741 TCAGTTGACCTAGATCTGATCAAAGT 59.561 38.462 19.12 12.18 31.45 2.66
4047 4240 6.629068 GCTTCAGTTGACCTAGATCTGATCAA 60.629 42.308 19.12 9.47 35.54 2.57
4082 4275 2.470286 CTCGGCGTCGCAAAGTTC 59.530 61.111 20.50 0.00 36.13 3.01
4121 4320 2.892334 GAAGCAAGCACGGCGACAA 61.892 57.895 16.62 0.00 36.08 3.18
4123 4322 4.430423 CGAAGCAAGCACGGCGAC 62.430 66.667 16.62 5.01 36.08 5.19
4175 4378 4.030216 TCAGATATCCCACTGTAAGCACA 58.970 43.478 0.00 0.00 37.60 4.57
4179 4382 5.363868 TCCTGTTCAGATATCCCACTGTAAG 59.636 44.000 0.00 0.00 42.29 2.34
4200 4403 0.619832 TGCCATTCTGCTCTCCTCCT 60.620 55.000 0.00 0.00 0.00 3.69
4210 4413 5.381174 TTCTCAAGACAATTGCCATTCTG 57.619 39.130 5.05 0.00 0.00 3.02
4211 4414 5.713389 TCATTCTCAAGACAATTGCCATTCT 59.287 36.000 5.05 0.00 0.00 2.40
4212 4415 5.957798 TCATTCTCAAGACAATTGCCATTC 58.042 37.500 5.05 0.00 0.00 2.67
4213 4416 5.988310 TCATTCTCAAGACAATTGCCATT 57.012 34.783 5.05 0.00 0.00 3.16
4214 4417 5.988310 TTCATTCTCAAGACAATTGCCAT 57.012 34.783 5.05 0.00 0.00 4.40
4218 4421 9.956720 ACTTAGTTTTCATTCTCAAGACAATTG 57.043 29.630 3.24 3.24 0.00 2.32
4231 4434 7.284489 TGCAAGTCACCTTACTTAGTTTTCATT 59.716 33.333 0.00 0.00 37.61 2.57
4235 4438 6.770785 TGATGCAAGTCACCTTACTTAGTTTT 59.229 34.615 0.00 0.00 37.61 2.43
4236 4439 6.296026 TGATGCAAGTCACCTTACTTAGTTT 58.704 36.000 0.00 0.00 37.61 2.66
4239 4442 5.220739 GCATGATGCAAGTCACCTTACTTAG 60.221 44.000 13.36 0.00 44.26 2.18
4273 4476 2.499289 AGTGATGACAGTAGGCTTCAGG 59.501 50.000 0.00 0.00 0.00 3.86
4300 4510 1.693640 CCAGGTGATCTGCCCCTTT 59.306 57.895 0.00 0.00 42.05 3.11
4305 4515 0.107165 GGTAACCCAGGTGATCTGCC 60.107 60.000 0.00 0.00 42.05 4.85
4316 4526 4.080243 TCAAAGTTCAGAGTTGGTAACCCA 60.080 41.667 0.00 0.00 39.65 4.51
4347 4572 1.725641 CTTATCTGTGCAGTTCGCCA 58.274 50.000 0.00 0.00 41.33 5.69
4398 4623 2.426024 TCTATGGACGACTGGTGCTAAC 59.574 50.000 0.00 0.00 37.93 2.34
4416 4655 1.153369 GAGCAGCCCGCACAATCTA 60.153 57.895 0.00 0.00 46.13 1.98
4429 4668 0.466739 TGGCATATTGGCTGGAGCAG 60.467 55.000 0.20 0.00 44.10 4.24
4476 4717 2.044806 AACTGACGAAGCAGGGCAGT 62.045 55.000 4.52 4.52 41.19 4.40
4485 4726 4.148348 GCGTAGGCAATATAACTGACGAAG 59.852 45.833 1.75 0.00 39.62 3.79
4529 4803 1.813513 CAAAGCAGGGAGTCGAACAT 58.186 50.000 0.00 0.00 0.00 2.71
4532 4806 0.884704 GTGCAAAGCAGGGAGTCGAA 60.885 55.000 0.00 0.00 40.08 3.71
4548 4822 2.118228 TTTCATTGTTCTGCGTGTGC 57.882 45.000 0.00 0.00 43.20 4.57
4549 4823 4.146961 GTGATTTTCATTGTTCTGCGTGTG 59.853 41.667 0.00 0.00 0.00 3.82
4565 4840 0.040425 GACCGCGCACTTGTGATTTT 60.040 50.000 8.75 0.00 0.00 1.82
4576 4851 0.460459 TTTGGATAATCGACCGCGCA 60.460 50.000 8.75 0.00 37.46 6.09
4580 4855 2.066262 CCGGATTTGGATAATCGACCG 58.934 52.381 0.00 0.00 39.02 4.79


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

AutoCloner maintained by Alex Coulton.