Multiple sequence alignment - TraesCS1A01G398300

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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 TraesCS1A01G398300 chr1A 100.000 4918 0 0 1 4918 563679807 563684724 0.000000e+00 9082.0
1 TraesCS1A01G398300 chr1A 89.873 79 8 0 2185 2263 563682072 563682150 8.710000e-18 102.0
2 TraesCS1A01G398300 chr1B 93.219 4911 202 58 75 4918 652452939 652457785 0.000000e+00 7103.0
3 TraesCS1A01G398300 chr1B 91.509 106 9 0 2239 2344 652455048 652455153 3.970000e-31 147.0
4 TraesCS1A01G398300 chr1D 95.212 3070 106 7 15 3084 470070516 470073544 0.000000e+00 4817.0
5 TraesCS1A01G398300 chr1D 97.810 1187 21 3 3082 4263 470073647 470074833 0.000000e+00 2043.0
6 TraesCS1A01G398300 chr1D 87.336 687 44 18 4253 4918 470074853 470075517 0.000000e+00 747.0
7 TraesCS1A01G398300 chr1D 92.952 454 22 5 15 463 354747472 354747920 0.000000e+00 652.0
8 TraesCS1A01G398300 chr1D 91.257 183 13 1 281 463 135062860 135063039 3.800000e-61 246.0
9 TraesCS1A01G398300 chr1D 93.671 79 5 0 2266 2344 470072674 470072752 8.650000e-23 119.0
10 TraesCS1A01G398300 chr5D 92.731 454 23 5 15 463 563497541 563497093 0.000000e+00 647.0
11 TraesCS1A01G398300 chr3D 92.511 454 24 4 15 463 549966027 549966475 4.150000e-180 641.0
12 TraesCS1A01G398300 chr3D 92.291 454 25 5 15 463 550030437 550029989 1.930000e-178 636.0
13 TraesCS1A01G398300 chr3D 94.872 39 2 0 3221 3259 339850947 339850909 1.480000e-05 62.1
14 TraesCS1A01G398300 chr2D 91.410 454 29 5 15 463 496894512 496894960 9.050000e-172 614.0
15 TraesCS1A01G398300 chr7B 87.448 239 24 5 196 433 78680687 78680920 2.260000e-68 270.0
16 TraesCS1A01G398300 chr7D 92.708 96 7 0 196 291 134508548 134508643 6.640000e-29 139.0
17 TraesCS1A01G398300 chr5B 83.206 131 21 1 3711 3841 6524252 6524123 8.650000e-23 119.0
18 TraesCS1A01G398300 chr6B 81.915 94 13 4 4293 4384 4295806 4295715 5.280000e-10 76.8
19 TraesCS1A01G398300 chr3B 94.872 39 2 0 3221 3259 438542726 438542688 1.480000e-05 62.1
20 TraesCS1A01G398300 chr3A 94.872 39 2 0 3221 3259 464910653 464910691 1.480000e-05 62.1


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 TraesCS1A01G398300 chr1A 563679807 563684724 4917 False 4592.0 9082 94.93650 1 4918 2 chr1A.!!$F1 4917
1 TraesCS1A01G398300 chr1B 652452939 652457785 4846 False 3625.0 7103 92.36400 75 4918 2 chr1B.!!$F1 4843
2 TraesCS1A01G398300 chr1D 470070516 470075517 5001 False 1931.5 4817 93.50725 15 4918 4 chr1D.!!$F3 4903

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
167 168 0.622154 TATTCGGGTGGGGGATGTGT 60.622 55.0 0.0 0.0 0.00 3.72 F
1546 1558 0.405198 TCCTGCACAATGGACATGGT 59.595 50.0 0.0 0.0 0.00 3.55 F
2259 2272 0.032540 GCAAGGCACAAACCCTTCTG 59.967 55.0 0.0 0.0 40.63 3.02 F
2275 2288 0.251297 TCTGGAATGGTGCAAGGTGG 60.251 55.0 0.0 0.0 0.00 4.61 F
3748 3923 0.175760 GCTGTCAATGCCCGTCTCTA 59.824 55.0 0.0 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1621 0.618458 GGGTGAGTAGCCATTGGTGA 59.382 55.000 4.26 0.0 44.02 4.02 R
3302 3476 0.519519 CATGCAAACCCGCGAAAGTA 59.480 50.000 8.23 0.0 33.35 2.24 R
3395 3569 1.472480 CCTTTCTGGCAAACCGGTATG 59.528 52.381 8.00 0.0 43.58 2.39 R
3803 3978 1.893801 CAGTCGAGGGTTCCTACAAGT 59.106 52.381 0.00 0.0 31.76 3.16 R
4859 5107 2.284190 GTCTTAGCTCAAGATGGTGGC 58.716 52.381 0.00 0.0 45.00 5.01 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 3.804329 AACCGTGGTGTGGGCACT 61.804 61.111 0.00 0.00 44.65 4.40
83 84 0.832983 TGCTCTTGGCTGGGCATTTT 60.833 50.000 1.72 0.00 42.39 1.82
124 125 9.905713 TGGCTTTTAGATTAGTTACTGATGAAT 57.094 29.630 0.00 0.00 0.00 2.57
167 168 0.622154 TATTCGGGTGGGGGATGTGT 60.622 55.000 0.00 0.00 0.00 3.72
258 259 5.116882 GGTACAGGGTAGAACTGCTTAATG 58.883 45.833 0.00 0.00 39.55 1.90
287 288 2.373169 TCAGTCTGATTTTCAGGTGGCT 59.627 45.455 0.00 0.00 44.39 4.75
312 313 6.980051 AACACTCTTGTTTTTACTCTTCGT 57.020 33.333 0.00 0.00 43.89 3.85
313 314 6.585389 ACACTCTTGTTTTTACTCTTCGTC 57.415 37.500 0.00 0.00 28.43 4.20
314 315 5.231568 ACACTCTTGTTTTTACTCTTCGTCG 59.768 40.000 0.00 0.00 28.43 5.12
327 328 3.136763 TCTTCGTCGTCTAAGTGACAGT 58.863 45.455 0.00 0.00 45.60 3.55
333 334 5.696270 TCGTCGTCTAAGTGACAGTAAACTA 59.304 40.000 0.00 0.00 45.60 2.24
354 355 5.870978 ACTATTTCAATTGCCAATTGCTGTC 59.129 36.000 22.42 0.00 46.09 3.51
364 365 3.672808 CCAATTGCTGTCTGTTCTCTCT 58.327 45.455 0.00 0.00 0.00 3.10
377 378 6.974622 GTCTGTTCTCTCTCTCATCTTGATTC 59.025 42.308 0.00 0.00 0.00 2.52
473 474 9.806203 TTCTAAATCTGCCATCATGTTTAATTG 57.194 29.630 0.00 0.00 0.00 2.32
708 710 1.480137 GCTGGCACTAGATCTGTGTCT 59.520 52.381 22.04 0.00 40.33 3.41
755 763 5.460646 CAGTTTTCTGTCGCCATTATGTTT 58.539 37.500 0.00 0.00 42.48 2.83
825 833 7.325660 TGTTCTTGCCAAATTGATATCTCTC 57.674 36.000 3.98 0.00 0.00 3.20
841 849 8.037758 TGATATCTCTCTGAAGTTTTTGTCCTC 58.962 37.037 3.98 0.00 0.00 3.71
926 935 5.053145 GGACTGACTGCTGACCATATTTAG 58.947 45.833 0.00 0.00 0.00 1.85
984 993 2.378038 TGTTGATCCATAAGCAAGGGC 58.622 47.619 0.00 0.00 41.61 5.19
1169 1178 6.550108 GGAAATACTACTAGTGATGGAGTCCA 59.450 42.308 15.88 15.88 38.19 4.02
1384 1396 2.189594 TCATCAAGTTGCCACAGGAG 57.810 50.000 0.00 0.00 0.00 3.69
1394 1406 1.341156 GCCACAGGAGCTAGGGATGT 61.341 60.000 0.00 0.00 0.00 3.06
1537 1549 1.005097 TGCCTCAGAATCCTGCACAAT 59.995 47.619 0.00 0.00 40.20 2.71
1546 1558 0.405198 TCCTGCACAATGGACATGGT 59.595 50.000 0.00 0.00 0.00 3.55
1606 1618 0.895100 TGCTGATGGACCAAACAGGC 60.895 55.000 23.97 18.51 43.14 4.85
1776 1788 5.726793 AGTCCACAATCCTTCAGGTAAGTAT 59.273 40.000 0.00 0.00 36.34 2.12
1831 1843 3.065925 GCTAAGTGATGATTCAAGGCACC 59.934 47.826 11.62 0.00 32.48 5.01
1860 1873 3.820467 TGGCTGTCAGTAGTTTTCATTGG 59.180 43.478 0.93 0.00 0.00 3.16
1975 1988 4.404073 GTGAGTGAGATGTGGAGAGGTAAT 59.596 45.833 0.00 0.00 0.00 1.89
2032 2045 1.259142 CCAGGAACAATGGGCATGCA 61.259 55.000 21.36 0.00 33.94 3.96
2233 2246 0.675633 CAAGGTGCAAACCCTTCTGG 59.324 55.000 4.16 0.00 40.35 3.86
2244 2257 2.877975 CCTTCTGGGATGGTGCAAG 58.122 57.895 0.00 0.00 37.23 4.01
2245 2258 0.682209 CCTTCTGGGATGGTGCAAGG 60.682 60.000 0.00 0.00 37.23 3.61
2246 2259 1.304381 TTCTGGGATGGTGCAAGGC 60.304 57.895 0.00 0.00 0.00 4.35
2247 2260 2.036098 CTGGGATGGTGCAAGGCA 59.964 61.111 0.00 0.00 35.60 4.75
2256 2269 4.371699 TGCAAGGCACAAACCCTT 57.628 50.000 0.00 0.00 43.29 3.95
2257 2270 2.123409 TGCAAGGCACAAACCCTTC 58.877 52.632 0.00 0.00 40.63 3.46
2258 2271 0.396974 TGCAAGGCACAAACCCTTCT 60.397 50.000 0.00 0.00 40.63 2.85
2259 2272 0.032540 GCAAGGCACAAACCCTTCTG 59.967 55.000 0.00 0.00 40.63 3.02
2275 2288 0.251297 TCTGGAATGGTGCAAGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
2445 2512 5.707298 ACAGATCAAGTTTACAATGGGAGTG 59.293 40.000 0.00 0.00 0.00 3.51
2608 2675 5.243954 TGCGAGGCATAGAAGATGTATTACT 59.756 40.000 0.00 0.00 31.71 2.24
2697 2764 5.233902 TGCTGGAAACACAATTTCATTTTCG 59.766 36.000 2.14 0.00 35.60 3.46
3019 3087 2.880890 CTGTTGTCTTGCTTGCCTACTT 59.119 45.455 0.00 0.00 0.00 2.24
3076 3144 5.507482 CCATCCGTACCTCACTAATACTGTG 60.507 48.000 0.00 0.00 36.82 3.66
3395 3569 3.376546 GCAAGAACAGATTGGAGATGTCC 59.623 47.826 0.83 0.83 44.24 4.02
3570 3744 9.391006 TGTTAATAACACCACTGGATCTTAATC 57.609 33.333 0.71 0.00 36.25 1.75
3748 3923 0.175760 GCTGTCAATGCCCGTCTCTA 59.824 55.000 0.00 0.00 0.00 2.43
3759 3934 3.830755 TGCCCGTCTCTAGTTTCTAAAGT 59.169 43.478 0.00 0.00 0.00 2.66
3803 3978 1.546476 GAGGAGTTTGAGGCGAGAGAA 59.454 52.381 0.00 0.00 0.00 2.87
3988 4168 4.499183 AGATTCAGCTCCGTTTCTTGTAG 58.501 43.478 0.00 0.00 0.00 2.74
4216 4407 4.605640 TCCCTTTGCCAAAAATCAGAAG 57.394 40.909 0.00 0.00 0.00 2.85
4248 4439 5.047802 TCAAATGGTTCTTTCTTCTGGATGC 60.048 40.000 0.00 0.00 0.00 3.91
4254 4445 5.526846 GGTTCTTTCTTCTGGATGCTCTATG 59.473 44.000 0.00 0.00 0.00 2.23
4255 4446 5.287674 TCTTTCTTCTGGATGCTCTATGG 57.712 43.478 0.00 0.00 0.00 2.74
4256 4447 4.718774 TCTTTCTTCTGGATGCTCTATGGT 59.281 41.667 0.00 0.00 0.00 3.55
4257 4448 5.190528 TCTTTCTTCTGGATGCTCTATGGTT 59.809 40.000 0.00 0.00 0.00 3.67
4263 4486 6.560003 TCTGGATGCTCTATGGTTTTCTTA 57.440 37.500 0.00 0.00 0.00 2.10
4267 4490 6.823689 TGGATGCTCTATGGTTTTCTTAGTTC 59.176 38.462 0.00 0.00 0.00 3.01
4271 4494 5.220491 GCTCTATGGTTTTCTTAGTTCTGCG 60.220 44.000 0.00 0.00 0.00 5.18
4276 4499 4.399934 TGGTTTTCTTAGTTCTGCGGTTTT 59.600 37.500 0.00 0.00 0.00 2.43
4278 4501 5.449451 GGTTTTCTTAGTTCTGCGGTTTTGA 60.449 40.000 0.00 0.00 0.00 2.69
4282 4505 6.385649 TCTTAGTTCTGCGGTTTTGATTTT 57.614 33.333 0.00 0.00 0.00 1.82
4283 4506 6.205784 TCTTAGTTCTGCGGTTTTGATTTTG 58.794 36.000 0.00 0.00 0.00 2.44
4288 4511 1.269309 TGCGGTTTTGATTTTGACGGG 60.269 47.619 0.00 0.00 0.00 5.28
4289 4512 1.933052 GCGGTTTTGATTTTGACGGGG 60.933 52.381 0.00 0.00 0.00 5.73
4320 4543 2.521126 TGGTTAGGCTTAACTTTGGCC 58.479 47.619 17.16 0.00 45.57 5.36
4330 4553 4.279922 GCTTAACTTTGGCCTTTGGAGTTA 59.720 41.667 3.32 8.39 33.13 2.24
4341 4564 6.185511 GGCCTTTGGAGTTAGGTTTATAACT 58.814 40.000 0.00 0.00 46.23 2.24
4393 4619 3.883830 TGGCTTTTTGCTTTTGACTGA 57.116 38.095 0.00 0.00 42.39 3.41
4424 4652 5.520376 ACATGATGGTATAAGCCAAAAGC 57.480 39.130 0.00 0.00 42.48 3.51
4442 4686 9.116054 GCCAAAAGCACAAAAATATATGTTTTG 57.884 29.630 20.04 20.04 46.63 2.44
4443 4687 9.609950 CCAAAAGCACAAAAATATATGTTTTGG 57.390 29.630 22.71 16.42 45.89 3.28
4470 4714 7.033791 GGCTTATAAACCAAACTCTAAAAGCC 58.966 38.462 0.00 0.00 45.78 4.35
4474 4718 4.665833 AACCAAACTCTAAAAGCCCAAC 57.334 40.909 0.00 0.00 0.00 3.77
4491 4735 4.707934 GCCCAACTTTTGCCTAACCTATAA 59.292 41.667 0.00 0.00 0.00 0.98
4501 4745 9.640952 TTTTGCCTAACCTATAATCTAGCAATT 57.359 29.630 0.00 0.00 0.00 2.32
4519 4763 7.389803 AGCAATTGTTTTTGGCTTTTAACTT 57.610 28.000 7.40 0.00 0.00 2.66
4562 4807 8.301002 GTCAGCCAAAATATTTGGTACAGTAAA 58.699 33.333 19.82 0.00 42.39 2.01
4564 4809 9.651913 CAGCCAAAATATTTGGTACAGTAAAAT 57.348 29.630 19.82 0.00 42.39 1.82
4587 4834 8.664669 AATAGTTTACAACAAATCCCCTGAAT 57.335 30.769 0.00 0.00 0.00 2.57
4605 4852 6.153340 CCCTGAATGAAATGGAACTGTGTAAT 59.847 38.462 0.00 0.00 0.00 1.89
4606 4853 7.339212 CCCTGAATGAAATGGAACTGTGTAATA 59.661 37.037 0.00 0.00 0.00 0.98
4613 4860 8.243426 TGAAATGGAACTGTGTAATAAATCAGC 58.757 33.333 0.00 0.00 0.00 4.26
4614 4861 7.701539 AATGGAACTGTGTAATAAATCAGCA 57.298 32.000 0.00 0.00 0.00 4.41
4627 4874 9.202273 GTAATAAATCAGCAGACTCAGGAATAG 57.798 37.037 0.00 0.00 0.00 1.73
4859 5107 4.593206 TCCCCTACAGTATAAGATGCCAAG 59.407 45.833 0.00 0.00 0.00 3.61
4864 5114 2.880890 CAGTATAAGATGCCAAGCCACC 59.119 50.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.438087 CAGAAATCAACTCTGAACGGCAT 59.562 43.478 0.00 0.00 42.51 4.40
3 4 2.807967 CAGAAATCAACTCTGAACGGCA 59.192 45.455 0.00 0.00 42.51 5.69
4 5 2.413371 GCAGAAATCAACTCTGAACGGC 60.413 50.000 4.06 0.00 42.51 5.68
5 6 2.807967 TGCAGAAATCAACTCTGAACGG 59.192 45.455 4.06 0.00 42.51 4.44
6 7 4.214437 GTTGCAGAAATCAACTCTGAACG 58.786 43.478 4.06 0.00 42.51 3.95
7 8 4.540824 GGTTGCAGAAATCAACTCTGAAC 58.459 43.478 4.06 5.64 42.51 3.18
8 9 3.250762 CGGTTGCAGAAATCAACTCTGAA 59.749 43.478 4.06 0.00 42.51 3.02
9 10 2.807967 CGGTTGCAGAAATCAACTCTGA 59.192 45.455 4.06 0.00 42.51 3.27
10 11 2.549754 ACGGTTGCAGAAATCAACTCTG 59.450 45.455 5.94 0.00 42.40 3.35
11 12 2.549754 CACGGTTGCAGAAATCAACTCT 59.450 45.455 5.94 0.00 42.40 3.24
12 13 2.350772 CCACGGTTGCAGAAATCAACTC 60.351 50.000 5.94 0.00 42.40 3.01
13 14 1.608590 CCACGGTTGCAGAAATCAACT 59.391 47.619 5.94 0.00 42.40 3.16
83 84 1.065600 GCCAGCACGCTGTGAAAAA 59.934 52.632 17.31 0.00 42.15 1.94
124 125 9.743581 ATAATCTGCATCCATACATCATGTTAA 57.256 29.630 0.00 0.00 32.21 2.01
139 140 2.154462 CCCACCCGAATAATCTGCATC 58.846 52.381 0.00 0.00 0.00 3.91
167 168 0.321387 ACTACACTCGCTCGTCCAGA 60.321 55.000 0.00 0.00 0.00 3.86
354 355 7.104043 AGAATCAAGATGAGAGAGAGAACAG 57.896 40.000 0.00 0.00 0.00 3.16
364 365 7.070447 ACCTGCAGTAATAGAATCAAGATGAGA 59.930 37.037 13.81 0.00 0.00 3.27
377 378 7.103641 TCCAGACTTAAAACCTGCAGTAATAG 58.896 38.462 13.81 4.77 0.00 1.73
577 578 6.290294 AGCATTTTGGAATAGTTTGCAGAT 57.710 33.333 0.00 0.00 34.44 2.90
663 664 8.798153 GCATAAGAACATACACAAAGCATAAAC 58.202 33.333 0.00 0.00 0.00 2.01
742 744 6.262944 AGCAATCTTGATAAACATAATGGCGA 59.737 34.615 0.00 0.00 30.14 5.54
743 745 6.361481 CAGCAATCTTGATAAACATAATGGCG 59.639 38.462 0.00 0.00 30.14 5.69
744 746 7.428020 TCAGCAATCTTGATAAACATAATGGC 58.572 34.615 0.00 0.00 0.00 4.40
745 747 9.406828 CATCAGCAATCTTGATAAACATAATGG 57.593 33.333 0.00 0.00 0.00 3.16
746 748 8.912658 GCATCAGCAATCTTGATAAACATAATG 58.087 33.333 0.00 0.00 41.58 1.90
747 749 8.857098 AGCATCAGCAATCTTGATAAACATAAT 58.143 29.630 0.00 0.00 45.49 1.28
755 763 4.758674 GGCTTAGCATCAGCAATCTTGATA 59.241 41.667 6.53 0.00 45.49 2.15
825 833 5.997746 TCATGGTAGAGGACAAAAACTTCAG 59.002 40.000 0.00 0.00 0.00 3.02
841 849 9.436957 ACATGTTTTCTTAAGTAGTCATGGTAG 57.563 33.333 22.85 9.94 36.68 3.18
926 935 6.749923 ACTCTTCCTGCAAATCAGATTAAC 57.250 37.500 0.00 0.00 45.72 2.01
984 993 1.647346 GCATGATGCCAACCACAATG 58.353 50.000 6.04 0.00 37.42 2.82
1169 1178 6.515862 GCTCTCATAGTAACTCCGTGAATCAT 60.516 42.308 0.00 0.00 0.00 2.45
1384 1396 1.270041 GCTGCTACTCACATCCCTAGC 60.270 57.143 0.00 0.00 33.56 3.42
1394 1406 1.550327 ACTGCTACTGCTGCTACTCA 58.450 50.000 0.00 0.00 41.07 3.41
1432 1444 4.107622 GCATTCCTCGTTTTCATGGATTG 58.892 43.478 0.00 0.00 34.77 2.67
1537 1549 2.291209 AATGAAGCACACCATGTCCA 57.709 45.000 0.00 0.00 0.00 4.02
1609 1621 0.618458 GGGTGAGTAGCCATTGGTGA 59.382 55.000 4.26 0.00 44.02 4.02
1831 1843 7.648142 TGAAAACTACTGACAGCCATAAAAAG 58.352 34.615 1.25 0.00 0.00 2.27
2239 2252 0.396974 AGAAGGGTTTGTGCCTTGCA 60.397 50.000 0.00 0.00 35.60 4.08
2240 2253 0.032540 CAGAAGGGTTTGTGCCTTGC 59.967 55.000 0.00 0.00 0.00 4.01
2241 2254 0.675633 CCAGAAGGGTTTGTGCCTTG 59.324 55.000 0.00 0.00 0.00 3.61
2242 2255 0.555769 TCCAGAAGGGTTTGTGCCTT 59.444 50.000 0.00 0.00 38.11 4.35
2243 2256 0.555769 TTCCAGAAGGGTTTGTGCCT 59.444 50.000 0.00 0.00 38.11 4.75
2244 2257 1.273327 CATTCCAGAAGGGTTTGTGCC 59.727 52.381 0.00 0.00 38.11 5.01
2245 2258 1.273327 CCATTCCAGAAGGGTTTGTGC 59.727 52.381 2.91 0.00 37.47 4.57
2252 2265 1.180029 CTTGCACCATTCCAGAAGGG 58.820 55.000 9.45 9.45 46.81 3.95
2253 2266 1.180029 CCTTGCACCATTCCAGAAGG 58.820 55.000 0.00 0.00 0.00 3.46
2254 2267 1.542915 CACCTTGCACCATTCCAGAAG 59.457 52.381 0.00 0.00 0.00 2.85
2255 2268 1.619654 CACCTTGCACCATTCCAGAA 58.380 50.000 0.00 0.00 0.00 3.02
2256 2269 0.251297 CCACCTTGCACCATTCCAGA 60.251 55.000 0.00 0.00 0.00 3.86
2257 2270 0.251297 TCCACCTTGCACCATTCCAG 60.251 55.000 0.00 0.00 0.00 3.86
2258 2271 0.187117 TTCCACCTTGCACCATTCCA 59.813 50.000 0.00 0.00 0.00 3.53
2259 2272 1.000843 GTTTCCACCTTGCACCATTCC 59.999 52.381 0.00 0.00 0.00 3.01
2306 2319 1.601419 CTTGCACCATTCCAGCAGGG 61.601 60.000 0.00 0.00 39.72 4.45
2335 2402 1.014564 GGTGAACGCCCTTCGAGAAG 61.015 60.000 5.90 5.90 41.67 2.85
2445 2512 6.223852 TGTGAATCACCTGAAGAAGTCTTAC 58.776 40.000 11.24 0.00 32.89 2.34
2539 2606 9.793252 CAAACAAAGTATCCAAGGAAGATAATG 57.207 33.333 0.00 0.00 0.00 1.90
2541 2608 7.361713 CGCAAACAAAGTATCCAAGGAAGATAA 60.362 37.037 0.00 0.00 0.00 1.75
2608 2675 6.751514 AGTCCAAATTATACATGCAAACGA 57.248 33.333 0.00 0.00 0.00 3.85
3076 3144 4.833390 AGTAAGCCCAGTCATGTAGAAAC 58.167 43.478 0.00 0.00 0.00 2.78
3302 3476 0.519519 CATGCAAACCCGCGAAAGTA 59.480 50.000 8.23 0.00 33.35 2.24
3395 3569 1.472480 CCTTTCTGGCAAACCGGTATG 59.528 52.381 8.00 0.00 43.58 2.39
3441 3615 2.711542 CCCTGGGAACAACATACTGAC 58.288 52.381 7.01 0.00 42.06 3.51
3748 3923 5.413523 ACGGAACAAACACACTTTAGAAACT 59.586 36.000 0.00 0.00 0.00 2.66
3759 3934 2.414824 GCAAAGACACGGAACAAACACA 60.415 45.455 0.00 0.00 0.00 3.72
3803 3978 1.893801 CAGTCGAGGGTTCCTACAAGT 59.106 52.381 0.00 0.00 31.76 3.16
3936 4113 3.119209 TGCTGCGGCAAATGATTTATTGA 60.119 39.130 20.23 0.00 46.36 2.57
3977 4157 7.759886 TCCAACATCTCTTATCTACAAGAAACG 59.240 37.037 0.00 0.00 34.22 3.60
3988 4168 7.798596 ACACAATCATCCAACATCTCTTATC 57.201 36.000 0.00 0.00 0.00 1.75
4248 4439 5.292101 CCGCAGAACTAAGAAAACCATAGAG 59.708 44.000 0.00 0.00 0.00 2.43
4254 4445 4.563337 AAACCGCAGAACTAAGAAAACC 57.437 40.909 0.00 0.00 0.00 3.27
4255 4446 5.575019 TCAAAACCGCAGAACTAAGAAAAC 58.425 37.500 0.00 0.00 0.00 2.43
4256 4447 5.821516 TCAAAACCGCAGAACTAAGAAAA 57.178 34.783 0.00 0.00 0.00 2.29
4257 4448 6.385649 AATCAAAACCGCAGAACTAAGAAA 57.614 33.333 0.00 0.00 0.00 2.52
4263 4486 4.359706 GTCAAAATCAAAACCGCAGAACT 58.640 39.130 0.00 0.00 0.00 3.01
4267 4490 2.050691 CCGTCAAAATCAAAACCGCAG 58.949 47.619 0.00 0.00 0.00 5.18
4271 4494 3.057104 CCTACCCCGTCAAAATCAAAACC 60.057 47.826 0.00 0.00 0.00 3.27
4276 4499 0.621609 CCCCTACCCCGTCAAAATCA 59.378 55.000 0.00 0.00 0.00 2.57
4278 4501 0.330267 CACCCCTACCCCGTCAAAAT 59.670 55.000 0.00 0.00 0.00 1.82
4282 4505 1.461849 AAACACCCCTACCCCGTCA 60.462 57.895 0.00 0.00 0.00 4.35
4283 4506 1.002990 CAAACACCCCTACCCCGTC 60.003 63.158 0.00 0.00 0.00 4.79
4288 4511 1.615116 GCCTAACCAAACACCCCTACC 60.615 57.143 0.00 0.00 0.00 3.18
4289 4512 1.353358 AGCCTAACCAAACACCCCTAC 59.647 52.381 0.00 0.00 0.00 3.18
4377 4603 9.296400 GTAACAGTATTCAGTCAAAAGCAAAAA 57.704 29.630 0.00 0.00 0.00 1.94
4378 4604 8.462811 TGTAACAGTATTCAGTCAAAAGCAAAA 58.537 29.630 0.00 0.00 0.00 2.44
4379 4605 7.990917 TGTAACAGTATTCAGTCAAAAGCAAA 58.009 30.769 0.00 0.00 0.00 3.68
4380 4606 7.561021 TGTAACAGTATTCAGTCAAAAGCAA 57.439 32.000 0.00 0.00 0.00 3.91
4381 4607 7.443879 TCATGTAACAGTATTCAGTCAAAAGCA 59.556 33.333 0.00 0.00 0.00 3.91
4382 4608 7.806690 TCATGTAACAGTATTCAGTCAAAAGC 58.193 34.615 0.00 0.00 0.00 3.51
4383 4609 9.764870 CATCATGTAACAGTATTCAGTCAAAAG 57.235 33.333 0.00 0.00 0.00 2.27
4393 4619 8.436778 TGGCTTATACCATCATGTAACAGTATT 58.563 33.333 0.00 0.00 33.75 1.89
4424 4652 6.413892 AGCCCCCAAAACATATATTTTTGTG 58.586 36.000 19.94 14.15 40.76 3.33
4425 4653 6.634889 AGCCCCCAAAACATATATTTTTGT 57.365 33.333 19.94 2.91 40.76 2.83
4430 4658 8.876181 GGTTTATAAGCCCCCAAAACATATATT 58.124 33.333 7.10 0.00 32.89 1.28
4431 4659 8.013667 TGGTTTATAAGCCCCCAAAACATATAT 58.986 33.333 15.03 0.00 32.89 0.86
4432 4660 7.363031 TGGTTTATAAGCCCCCAAAACATATA 58.637 34.615 15.03 0.00 32.89 0.86
4442 4686 3.977312 AGAGTTTGGTTTATAAGCCCCC 58.023 45.455 15.03 3.90 0.00 5.40
4443 4687 7.470935 TTTTAGAGTTTGGTTTATAAGCCCC 57.529 36.000 15.03 4.22 0.00 5.80
4444 4688 7.033791 GCTTTTAGAGTTTGGTTTATAAGCCC 58.966 38.462 15.03 6.16 29.53 5.19
4470 4714 7.881775 AGATTATAGGTTAGGCAAAAGTTGG 57.118 36.000 0.00 0.00 0.00 3.77
4474 4718 8.677148 TTGCTAGATTATAGGTTAGGCAAAAG 57.323 34.615 0.00 0.00 34.87 2.27
4491 4735 8.773645 GTTAAAAGCCAAAAACAATTGCTAGAT 58.226 29.630 5.05 0.00 0.00 1.98
4501 4745 9.490379 TCAAACTAAAGTTAAAAGCCAAAAACA 57.510 25.926 0.00 0.00 37.25 2.83
4519 4763 4.517285 GCTGACTCCCATCATCAAACTAA 58.483 43.478 0.00 0.00 0.00 2.24
4526 4770 2.425143 TTTGGCTGACTCCCATCATC 57.575 50.000 0.00 0.00 31.26 2.92
4570 4815 5.280113 CCATTTCATTCAGGGGATTTGTTGT 60.280 40.000 0.00 0.00 0.00 3.32
4587 4834 8.243426 GCTGATTTATTACACAGTTCCATTTCA 58.757 33.333 0.00 0.00 33.57 2.69
4605 4852 6.381133 TGTCTATTCCTGAGTCTGCTGATTTA 59.619 38.462 0.00 0.00 0.00 1.40
4606 4853 5.188555 TGTCTATTCCTGAGTCTGCTGATTT 59.811 40.000 0.00 0.00 0.00 2.17
4612 4859 4.261994 GGATCTGTCTATTCCTGAGTCTGC 60.262 50.000 0.00 0.00 0.00 4.26
4613 4860 4.892345 TGGATCTGTCTATTCCTGAGTCTG 59.108 45.833 0.00 0.00 0.00 3.51
4614 4861 5.136068 TGGATCTGTCTATTCCTGAGTCT 57.864 43.478 0.00 0.00 0.00 3.24
4627 4874 5.794894 TGTTTTCTACCTCTTGGATCTGTC 58.205 41.667 0.00 0.00 37.04 3.51
4677 4925 4.038763 TGAAAGTGTGAGTGAGGTTATCGT 59.961 41.667 0.00 0.00 0.00 3.73
4859 5107 2.284190 GTCTTAGCTCAAGATGGTGGC 58.716 52.381 0.00 0.00 45.00 5.01


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

AutoCloner maintained by Alex Coulton.