Multiple sequence alignment - TraesCS4D01G322000

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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 TraesCS4D01G322000 chr4D 100.000 5107 0 0 1 5107 484289017 484294123 0.000000e+00 9431.0
1 TraesCS4D01G322000 chr4B 93.693 4598 153 50 2 4523 615829715 615834251 0.000000e+00 6758.0
2 TraesCS4D01G322000 chr4B 92.969 4409 120 50 856 5107 615830534 615834909 0.000000e+00 6250.0
3 TraesCS4D01G322000 chr4B 94.118 85 3 2 2614 2698 272036192 272036274 1.490000e-25 128.0
4 TraesCS4D01G322000 chr5A 92.988 1369 39 19 2095 3422 664551489 664552841 0.000000e+00 1943.0
5 TraesCS4D01G322000 chr5A 94.586 1256 40 11 856 2095 664549922 664551165 0.000000e+00 1917.0
6 TraesCS4D01G322000 chr5A 94.414 913 40 8 3409 4319 664553028 664553931 0.000000e+00 1393.0
7 TraesCS4D01G322000 chr5A 92.974 854 46 3 2 841 664549085 664549938 0.000000e+00 1232.0
8 TraesCS4D01G322000 chr5A 85.308 844 52 25 4330 5107 664554275 664555112 0.000000e+00 806.0
9 TraesCS4D01G322000 chr5A 85.366 123 12 3 3046 3168 641111031 641111147 6.940000e-24 122.0
10 TraesCS4D01G322000 chr4A 94.138 290 17 0 27 316 738881609 738881320 4.690000e-120 442.0
11 TraesCS4D01G322000 chr5B 93.793 290 18 0 27 316 321629352 321629641 2.180000e-118 436.0
12 TraesCS4D01G322000 chr5B 84.553 123 13 3 3046 3168 710172079 710171963 3.230000e-22 117.0
13 TraesCS4D01G322000 chr6B 93.448 290 19 0 27 316 44820809 44821098 1.020000e-116 431.0
14 TraesCS4D01G322000 chr6B 85.366 123 12 3 3046 3168 690992447 690992331 6.940000e-24 122.0
15 TraesCS4D01G322000 chr6B 87.255 102 10 2 3046 3146 282852037 282852136 4.180000e-21 113.0
16 TraesCS4D01G322000 chr1A 87.821 156 13 5 3221 3371 1314419 1314573 1.460000e-40 178.0
17 TraesCS4D01G322000 chr1D 87.582 153 13 3 3219 3367 2194143 2194293 6.800000e-39 172.0
18 TraesCS4D01G322000 chr2B 85.366 123 12 3 3046 3168 793126461 793126577 6.940000e-24 122.0
19 TraesCS4D01G322000 chr7A 84.553 123 13 3 3046 3168 87021639 87021523 3.230000e-22 117.0
20 TraesCS4D01G322000 chr3A 84.553 123 13 3 3046 3168 565343963 565344079 3.230000e-22 117.0
21 TraesCS4D01G322000 chr5D 86.538 52 7 0 2726 2777 225256896 225256845 1.990000e-04 58.4


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 TraesCS4D01G322000 chr4D 484289017 484294123 5106 False 9431.0 9431 100.000 1 5107 1 chr4D.!!$F1 5106
1 TraesCS4D01G322000 chr4B 615829715 615834909 5194 False 6504.0 6758 93.331 2 5107 2 chr4B.!!$F2 5105
2 TraesCS4D01G322000 chr5A 664549085 664555112 6027 False 1458.2 1943 92.054 2 5107 5 chr5A.!!$F2 5105

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
901 923 0.247460 CATCGGCAGTCTCACCAAGA 59.753 55.000 0.00 0.0 0.0 3.02 F
915 937 1.457346 CCAAGAGGTCATGAGCCAAC 58.543 55.000 20.92 12.7 0.0 3.77 F
927 949 2.768698 TGAGCCAACCATGCAAAAATG 58.231 42.857 0.00 0.0 0.0 2.32 F
1554 1586 5.163713 GCAAATCCAGTCCTATGTCTTTGAC 60.164 44.000 0.00 0.0 0.0 3.18 F
2978 3374 1.483004 GCCTACTCCCTCTGTTTCTCC 59.517 57.143 0.00 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2593 2.390306 TTACAGCGCTGTGGCAGGAA 62.390 55.000 44.69 30.13 44.63 3.36 R
2828 3207 7.952671 TCATGTATCTAAGGTTAAGCGAAGAT 58.047 34.615 20.89 20.89 0.00 2.40 R
2833 3212 8.470805 AGGATATCATGTATCTAAGGTTAAGCG 58.529 37.037 4.83 0.00 0.00 4.68 R
3216 3612 1.564818 TCTCCATAGAGGACGGACAGT 59.435 52.381 0.00 0.00 43.07 3.55 R
4809 5847 0.030235 GGTTTCGACAGGTTGTTGCC 59.970 55.000 0.00 0.00 31.81 4.52 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
114 115 0.613260 ATAAGACGCTGGCAAGTGGA 59.387 50.000 6.61 0.00 38.30 4.02
143 145 8.089115 ACAGCTTATTCTTGTTTACTTGTCTC 57.911 34.615 0.00 0.00 0.00 3.36
214 216 6.480320 GCTGATTGATTATTAGTTGGACGAGT 59.520 38.462 0.00 0.00 0.00 4.18
252 254 7.736447 ACATTTGACTTTTGACCAAAACAAA 57.264 28.000 18.00 18.00 38.93 2.83
294 296 0.328926 TGGCATCATCCTGCAGACAA 59.671 50.000 17.39 0.00 44.12 3.18
300 302 1.872952 TCATCCTGCAGACAACGTTTG 59.127 47.619 17.39 0.00 0.00 2.93
316 318 4.130118 ACGTTTGGGATGAGCATTATCTC 58.870 43.478 0.00 0.00 0.00 2.75
318 320 4.212847 CGTTTGGGATGAGCATTATCTCTG 59.787 45.833 0.00 0.00 34.29 3.35
344 346 6.954102 TCTCCCACTATATATGTATGTGCAGT 59.046 38.462 0.00 0.00 0.00 4.40
358 360 2.230266 TGTGCAGTGTGCTTCGTATAGA 59.770 45.455 0.00 0.00 45.31 1.98
359 361 2.599082 GTGCAGTGTGCTTCGTATAGAC 59.401 50.000 0.00 0.00 45.31 2.59
571 577 6.369065 GTCGTTCAGATTCCTTTGAAGTATGT 59.631 38.462 0.00 0.00 34.25 2.29
684 702 4.764679 TGACATGCTGTTCCAACATAAC 57.235 40.909 0.00 0.00 38.41 1.89
689 707 1.885887 GCTGTTCCAACATAACCTGCA 59.114 47.619 0.00 0.00 38.41 4.41
818 836 5.234329 CGTTATGTAGGTAAAGCCATGACTG 59.766 44.000 0.00 0.00 40.61 3.51
833 851 5.568825 GCCATGACTGTCTGGTTTAGTTCTA 60.569 44.000 20.09 0.00 34.86 2.10
834 852 6.644347 CCATGACTGTCTGGTTTAGTTCTAT 58.356 40.000 9.51 0.00 0.00 1.98
835 853 6.536582 CCATGACTGTCTGGTTTAGTTCTATG 59.463 42.308 9.51 0.00 0.00 2.23
836 854 6.911250 TGACTGTCTGGTTTAGTTCTATGA 57.089 37.500 9.51 0.00 0.00 2.15
837 855 7.482169 TGACTGTCTGGTTTAGTTCTATGAT 57.518 36.000 9.51 0.00 0.00 2.45
838 856 7.323420 TGACTGTCTGGTTTAGTTCTATGATG 58.677 38.462 9.51 0.00 0.00 3.07
839 857 6.109359 ACTGTCTGGTTTAGTTCTATGATGC 58.891 40.000 0.00 0.00 0.00 3.91
840 858 6.070538 ACTGTCTGGTTTAGTTCTATGATGCT 60.071 38.462 0.00 0.00 0.00 3.79
841 859 7.124298 ACTGTCTGGTTTAGTTCTATGATGCTA 59.876 37.037 0.00 0.00 0.00 3.49
842 860 8.023021 TGTCTGGTTTAGTTCTATGATGCTAT 57.977 34.615 0.00 0.00 0.00 2.97
843 861 8.144478 TGTCTGGTTTAGTTCTATGATGCTATC 58.856 37.037 0.00 0.00 0.00 2.08
844 862 8.144478 GTCTGGTTTAGTTCTATGATGCTATCA 58.856 37.037 2.05 2.05 44.55 2.15
891 909 3.448686 CTCTCGTTTATTCATCGGCAGT 58.551 45.455 0.00 0.00 0.00 4.40
892 910 3.444916 TCTCGTTTATTCATCGGCAGTC 58.555 45.455 0.00 0.00 0.00 3.51
895 913 3.119280 TCGTTTATTCATCGGCAGTCTCA 60.119 43.478 0.00 0.00 0.00 3.27
897 915 2.890808 TATTCATCGGCAGTCTCACC 57.109 50.000 0.00 0.00 0.00 4.02
898 916 0.904649 ATTCATCGGCAGTCTCACCA 59.095 50.000 0.00 0.00 0.00 4.17
901 923 0.247460 CATCGGCAGTCTCACCAAGA 59.753 55.000 0.00 0.00 0.00 3.02
915 937 1.457346 CCAAGAGGTCATGAGCCAAC 58.543 55.000 20.92 12.70 0.00 3.77
927 949 2.768698 TGAGCCAACCATGCAAAAATG 58.231 42.857 0.00 0.00 0.00 2.32
1359 1391 7.609097 TCTATGCTTTCTCATCTGAATAGGT 57.391 36.000 0.00 0.00 0.00 3.08
1437 1469 8.557592 TGAATATCATGATTAATCTGCAGGAC 57.442 34.615 14.65 0.23 0.00 3.85
1554 1586 5.163713 GCAAATCCAGTCCTATGTCTTTGAC 60.164 44.000 0.00 0.00 0.00 3.18
2060 2092 7.719633 TCAACTGTCTAGTTTTCCAGCTAAAAT 59.280 33.333 0.00 0.00 44.57 1.82
2198 2556 5.316167 AGTGGTCAGCAAATTGAGTAATCA 58.684 37.500 0.00 0.00 0.00 2.57
2854 3233 7.952671 TCTTCGCTTAACCTTAGATACATGAT 58.047 34.615 0.00 0.00 0.00 2.45
2978 3374 1.483004 GCCTACTCCCTCTGTTTCTCC 59.517 57.143 0.00 0.00 0.00 3.71
3013 3409 6.790319 ACTCCCTTCTACCACAATTACATTT 58.210 36.000 0.00 0.00 0.00 2.32
3017 3413 6.659242 CCCTTCTACCACAATTACATTTGACT 59.341 38.462 0.00 0.00 0.00 3.41
3113 3509 7.148407 CCCTCAAGTATGTGTAATTCTGTGAAC 60.148 40.741 0.00 0.00 0.00 3.18
3133 3529 8.821894 TGTGAACCACAAATTAAATTTTGTAGC 58.178 29.630 6.82 0.21 45.54 3.58
3134 3530 9.040939 GTGAACCACAAATTAAATTTTGTAGCT 57.959 29.630 6.82 0.00 45.54 3.32
3213 3609 5.726980 ATTATGTTCATGCTGTGGTTGTT 57.273 34.783 0.00 0.00 0.00 2.83
3214 3610 3.648339 ATGTTCATGCTGTGGTTGTTC 57.352 42.857 0.00 0.00 0.00 3.18
3215 3611 1.333308 TGTTCATGCTGTGGTTGTTCG 59.667 47.619 0.00 0.00 0.00 3.95
3216 3612 1.601903 GTTCATGCTGTGGTTGTTCGA 59.398 47.619 0.00 0.00 0.00 3.71
3217 3613 1.225855 TCATGCTGTGGTTGTTCGAC 58.774 50.000 0.00 0.00 0.00 4.20
3218 3614 1.202639 TCATGCTGTGGTTGTTCGACT 60.203 47.619 0.00 0.00 0.00 4.18
3219 3615 1.069703 CATGCTGTGGTTGTTCGACTG 60.070 52.381 0.00 0.00 0.00 3.51
3220 3616 0.107897 TGCTGTGGTTGTTCGACTGT 60.108 50.000 0.00 0.00 0.00 3.55
3317 3713 4.813027 TGCTTTTGAAATGAGAATGGCTC 58.187 39.130 0.00 0.00 44.21 4.70
3367 3767 8.732746 TTAATAAGAGGGCTTGTACTTGATTC 57.267 34.615 0.00 0.00 35.56 2.52
3377 3777 4.301072 TGTACTTGATTCCCTCCCAAAG 57.699 45.455 0.00 0.00 0.00 2.77
3393 3810 9.147732 CCCTCCCAAAGCTAATATTTTTCTTAT 57.852 33.333 0.00 0.00 0.00 1.73
3460 4078 9.635520 TTTAGTTTTTCATTCACGTTGGTTTTA 57.364 25.926 0.00 0.00 0.00 1.52
3497 4115 6.069673 TGAGTATGGAAATGAGTGGGTTACAT 60.070 38.462 0.00 0.00 0.00 2.29
3561 4180 6.656003 ACTGCAGTTTACTTTACGTTTGATC 58.344 36.000 15.25 0.00 0.00 2.92
3638 4257 8.716646 TCACGATTGTTATATCTGTTTCATGT 57.283 30.769 0.00 0.00 0.00 3.21
3639 4258 9.161629 TCACGATTGTTATATCTGTTTCATGTT 57.838 29.630 0.00 0.00 0.00 2.71
3640 4259 9.773328 CACGATTGTTATATCTGTTTCATGTTT 57.227 29.630 0.00 0.00 0.00 2.83
3641 4260 9.773328 ACGATTGTTATATCTGTTTCATGTTTG 57.227 29.630 0.00 0.00 0.00 2.93
3642 4261 9.773328 CGATTGTTATATCTGTTTCATGTTTGT 57.227 29.630 0.00 0.00 0.00 2.83
3785 4404 2.684843 GGCAGCCACTGAGAAAGCG 61.685 63.158 6.55 0.00 32.44 4.68
3788 4407 0.603707 CAGCCACTGAGAAAGCGGAA 60.604 55.000 0.00 0.00 32.44 4.30
3803 4422 2.409152 CGGAAGCGGAGAAGATACTC 57.591 55.000 0.00 0.00 36.31 2.59
3839 4458 2.275318 GAAGGTGAGGCAGAATCGAAG 58.725 52.381 0.00 0.00 0.00 3.79
4138 4757 6.872920 TGGAAAATGGATGCCACTTTTATAC 58.127 36.000 0.00 0.00 32.91 1.47
4228 4852 7.715249 GGATGTTAATATCAGTACTTGCTTGGA 59.285 37.037 13.45 0.00 0.00 3.53
4279 4903 1.798223 GTTGTGCTATCACTGCGTTCA 59.202 47.619 0.00 0.00 43.49 3.18
4281 4905 0.721718 GTGCTATCACTGCGTTCACC 59.278 55.000 0.00 0.00 40.03 4.02
4480 5451 4.475763 TTTTGTGTGCGTTCATCGTATT 57.524 36.364 0.00 0.00 42.13 1.89
4481 5452 3.447752 TTGTGTGCGTTCATCGTATTG 57.552 42.857 0.00 0.00 42.13 1.90
4482 5453 2.409012 TGTGTGCGTTCATCGTATTGT 58.591 42.857 0.00 0.00 42.13 2.71
4483 5454 2.410392 TGTGTGCGTTCATCGTATTGTC 59.590 45.455 0.00 0.00 42.13 3.18
4484 5455 2.410392 GTGTGCGTTCATCGTATTGTCA 59.590 45.455 0.00 0.00 42.13 3.58
4491 5462 5.484085 CGTTCATCGTATTGTCATGTGAAG 58.516 41.667 0.00 0.00 34.52 3.02
4493 5464 3.551485 TCATCGTATTGTCATGTGAAGCG 59.449 43.478 0.00 0.00 0.00 4.68
4519 5490 5.706833 AGTTCATTGTATTGTCATGTGAGCA 59.293 36.000 0.00 0.00 0.00 4.26
4523 5494 3.410508 TGTATTGTCATGTGAGCAGCAA 58.589 40.909 0.00 0.00 0.00 3.91
4526 5497 1.170442 TGTCATGTGAGCAGCAATGG 58.830 50.000 0.00 0.00 0.00 3.16
4527 5498 0.179145 GTCATGTGAGCAGCAATGGC 60.179 55.000 0.00 0.00 41.61 4.40
4536 5528 1.677966 CAGCAATGGCCAGCAGAGT 60.678 57.895 18.35 0.00 42.56 3.24
4544 5536 0.536006 GGCCAGCAGAGTTTCACACT 60.536 55.000 0.00 0.00 39.07 3.55
4562 5554 3.834813 ACACTCTGCTCCTCACTTAATGA 59.165 43.478 0.00 0.00 35.45 2.57
4587 5579 7.763172 AAAAACAAATGCAAACTTCGATACA 57.237 28.000 0.00 0.00 0.00 2.29
4588 5580 7.945033 AAAACAAATGCAAACTTCGATACAT 57.055 28.000 0.00 0.00 0.00 2.29
4599 5614 7.429340 GCAAACTTCGATACATCAATACCAAAG 59.571 37.037 0.00 0.00 0.00 2.77
4641 5656 1.467342 GCCACAGTTTACCACGGATTC 59.533 52.381 0.00 0.00 0.00 2.52
4658 5673 3.118738 GGATTCGATACAAGGTGGACACT 60.119 47.826 2.13 0.00 0.00 3.55
4741 5761 9.748708 GAAGATTAAAGCACAATAATATGCCAA 57.251 29.630 0.00 0.00 43.12 4.52
4809 5847 6.732154 TGAAAGCTGTTTCATTCTTCTCAAG 58.268 36.000 0.00 0.00 45.82 3.02
4819 5858 3.297134 TTCTTCTCAAGGCAACAACCT 57.703 42.857 0.00 0.00 43.91 3.50
4820 5859 2.575532 TCTTCTCAAGGCAACAACCTG 58.424 47.619 0.00 0.00 39.93 4.00
4919 5958 0.320771 GCTTCTTCGCCTTCAGGTCA 60.321 55.000 0.00 0.00 37.57 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 9.284968 ACAAGTAAACAAGAATAAGCTGTACAT 57.715 29.630 0.00 0.00 0.00 2.29
143 145 4.864633 ACAGCGATATACATCTGTGTCTG 58.135 43.478 0.00 0.00 38.25 3.51
214 216 0.112995 AAATGTTCAGCCCCAGCAGA 59.887 50.000 0.00 0.00 43.56 4.26
252 254 0.179034 GGGGAAGCGCTTCTGATCAT 60.179 55.000 40.11 12.06 39.45 2.45
294 296 4.130118 GAGATAATGCTCATCCCAAACGT 58.870 43.478 0.00 0.00 35.01 3.99
300 302 4.322650 GGAGACAGAGATAATGCTCATCCC 60.323 50.000 0.00 0.00 37.37 3.85
316 318 7.093771 TGCACATACATATATAGTGGGAGACAG 60.094 40.741 0.00 0.00 0.00 3.51
318 320 7.093727 ACTGCACATACATATATAGTGGGAGAC 60.094 40.741 0.00 0.00 0.00 3.36
344 346 1.855295 TGGGGTCTATACGAAGCACA 58.145 50.000 0.00 0.00 0.00 4.57
358 360 0.930726 TGTTCTTGGGAAGTTGGGGT 59.069 50.000 0.00 0.00 31.46 4.95
359 361 1.328279 GTGTTCTTGGGAAGTTGGGG 58.672 55.000 0.00 0.00 31.46 4.96
717 735 5.547666 TGCAATATGTAGTCATATCAGGGGT 59.452 40.000 1.96 0.00 43.80 4.95
759 777 6.368791 TGCATACACTGACTAATGTCTCAAAC 59.631 38.462 0.00 0.00 43.29 2.93
803 821 2.290323 ACCAGACAGTCATGGCTTTACC 60.290 50.000 15.33 0.00 44.99 2.85
818 836 8.144478 TGATAGCATCATAGAACTAAACCAGAC 58.856 37.037 0.00 0.00 33.59 3.51
845 863 9.817809 AGCGTCATGAGACTAAAATCTAATAAA 57.182 29.630 0.00 0.00 42.73 1.40
846 864 9.464714 GAGCGTCATGAGACTAAAATCTAATAA 57.535 33.333 0.00 0.00 42.73 1.40
847 865 8.851145 AGAGCGTCATGAGACTAAAATCTAATA 58.149 33.333 0.00 0.00 42.73 0.98
848 866 7.721402 AGAGCGTCATGAGACTAAAATCTAAT 58.279 34.615 0.00 0.00 42.73 1.73
849 867 7.101652 AGAGCGTCATGAGACTAAAATCTAA 57.898 36.000 0.00 0.00 42.73 2.10
850 868 6.511929 CGAGAGCGTCATGAGACTAAAATCTA 60.512 42.308 0.00 0.00 42.73 1.98
851 869 5.587289 GAGAGCGTCATGAGACTAAAATCT 58.413 41.667 0.00 0.00 42.73 2.40
852 870 4.439449 CGAGAGCGTCATGAGACTAAAATC 59.561 45.833 0.00 0.00 42.73 2.17
853 871 4.355437 CGAGAGCGTCATGAGACTAAAAT 58.645 43.478 0.00 0.00 42.73 1.82
854 872 3.759418 CGAGAGCGTCATGAGACTAAAA 58.241 45.455 0.00 0.00 42.73 1.52
855 873 3.406728 CGAGAGCGTCATGAGACTAAA 57.593 47.619 0.00 0.00 42.73 1.85
885 903 1.079543 CCTCTTGGTGAGACTGCCG 60.080 63.158 0.00 0.00 45.39 5.69
897 915 1.271543 TGGTTGGCTCATGACCTCTTG 60.272 52.381 13.32 0.00 34.52 3.02
898 916 1.067295 TGGTTGGCTCATGACCTCTT 58.933 50.000 13.32 0.00 34.52 2.85
901 923 0.682209 GCATGGTTGGCTCATGACCT 60.682 55.000 16.08 0.00 43.25 3.85
1041 1063 4.326826 CAAAAGTCTCCTTGATGGCTACA 58.673 43.478 0.00 0.00 35.26 2.74
1134 1156 2.337583 TGCACACGCAGAGAAAGATAC 58.662 47.619 0.00 0.00 45.36 2.24
1437 1469 3.790820 CCACAACGTTGACAAAGACATTG 59.209 43.478 33.66 16.69 44.95 2.82
1554 1586 8.559536 AGTTCAAATCATACAGCAATATTACCG 58.440 33.333 0.00 0.00 0.00 4.02
2060 2092 7.867305 TGTGAAATGTAAAACCAGACAGTTA 57.133 32.000 0.00 0.00 34.29 2.24
2231 2593 2.390306 TTACAGCGCTGTGGCAGGAA 62.390 55.000 44.69 30.13 44.63 3.36
2359 2733 9.831737 CAAAAATTACACATTTGACACCAAAAA 57.168 25.926 0.00 0.00 44.49 1.94
2392 2766 9.280174 TCCAAAGTAACTCAGTTTATTGGTTAG 57.720 33.333 19.94 4.24 35.19 2.34
2828 3207 7.952671 TCATGTATCTAAGGTTAAGCGAAGAT 58.047 34.615 20.89 20.89 0.00 2.40
2833 3212 8.470805 AGGATATCATGTATCTAAGGTTAAGCG 58.529 37.037 4.83 0.00 0.00 4.68
2854 3233 8.852894 TGGTCTACCATCCACTATATAAGGATA 58.147 37.037 13.37 2.20 42.01 2.59
2978 3374 1.981495 AGAAGGGAGTCCAAGAACAGG 59.019 52.381 12.30 0.00 34.83 4.00
3013 3409 6.096987 GTCTGGAATGTAAGATCTACCAGTCA 59.903 42.308 18.15 8.20 42.44 3.41
3017 3413 5.958380 ACAGTCTGGAATGTAAGATCTACCA 59.042 40.000 4.53 0.00 37.91 3.25
3061 3457 7.285069 CAACGTTTCAATTAACTACACATCGA 58.715 34.615 0.00 0.00 0.00 3.59
3191 3587 5.619757 CGAACAACCACAGCATGAACATAAT 60.620 40.000 0.00 0.00 39.69 1.28
3215 3611 4.301295 CTCTCCATAGAGGACGGACAGTC 61.301 56.522 0.00 0.00 44.82 3.51
3216 3612 1.564818 TCTCCATAGAGGACGGACAGT 59.435 52.381 0.00 0.00 43.07 3.55
3217 3613 2.226330 CTCTCCATAGAGGACGGACAG 58.774 57.143 0.00 0.00 44.82 3.51
3218 3614 2.350057 CTCTCCATAGAGGACGGACA 57.650 55.000 0.00 0.00 44.82 4.02
3317 3713 4.616181 AAATCAAAACGATAGCCTTCCG 57.384 40.909 0.00 0.00 42.67 4.30
3329 3725 8.531982 AGCCCTCTTATTAAGGAAAATCAAAAC 58.468 33.333 3.66 0.00 35.83 2.43
3367 3767 7.423844 AAGAAAAATATTAGCTTTGGGAGGG 57.576 36.000 0.00 0.00 0.00 4.30
3451 4067 7.937649 ACTCAACTATGACCTTTAAAACCAAC 58.062 34.615 0.00 0.00 0.00 3.77
3460 4078 8.328758 TCATTTCCATACTCAACTATGACCTTT 58.671 33.333 0.00 0.00 0.00 3.11
3497 4115 8.518430 AGCCATTCAAAACACATATGTACATA 57.482 30.769 17.65 17.65 38.45 2.29
3561 4180 6.780706 ATTGACTAGGAACAGTTTGTTACG 57.219 37.500 0.00 0.00 45.67 3.18
3575 4194 9.360093 CTTGTTCTTGAGTAGTAATTGACTAGG 57.640 37.037 0.00 0.00 41.47 3.02
3638 4257 8.682710 GCACATACTTTTCATAGGGATAACAAA 58.317 33.333 0.00 0.00 0.00 2.83
3639 4258 8.052748 AGCACATACTTTTCATAGGGATAACAA 58.947 33.333 0.00 0.00 0.00 2.83
3640 4259 7.498900 CAGCACATACTTTTCATAGGGATAACA 59.501 37.037 0.00 0.00 0.00 2.41
3641 4260 7.499232 ACAGCACATACTTTTCATAGGGATAAC 59.501 37.037 0.00 0.00 0.00 1.89
3642 4261 7.573710 ACAGCACATACTTTTCATAGGGATAA 58.426 34.615 0.00 0.00 0.00 1.75
3734 4353 6.700081 TCCTAGCAGCTGTAACATAAATTACG 59.300 38.462 16.64 0.00 37.79 3.18
3785 4404 2.804697 GGAGTATCTTCTCCGCTTCC 57.195 55.000 0.00 0.00 43.42 3.46
3794 4413 4.262420 GCCCTCTTGATCTGGAGTATCTTC 60.262 50.000 12.19 0.00 33.73 2.87
3800 4419 1.202330 CAGCCCTCTTGATCTGGAGT 58.798 55.000 12.19 0.00 0.00 3.85
3803 4422 1.134159 CCTTCAGCCCTCTTGATCTGG 60.134 57.143 0.00 0.00 0.00 3.86
3839 4458 0.688487 TACCCACACCAGCCAAGTAC 59.312 55.000 0.00 0.00 0.00 2.73
4138 4757 7.464830 AGCTGTATGTACTTAAAAGTATGCG 57.535 36.000 5.90 0.00 42.88 4.73
4228 4852 1.967319 ACAGAAACGAGTGGCACAAT 58.033 45.000 21.41 0.00 44.16 2.71
4257 4881 2.480419 GAACGCAGTGATAGCACAACTT 59.520 45.455 14.51 0.00 45.00 2.66
4344 5300 9.059260 CAAGGTTTCCAAGATTTGAATGAAAAT 57.941 29.630 0.00 0.00 32.43 1.82
4356 5312 5.606329 TCCAAAATTCCAAGGTTTCCAAGAT 59.394 36.000 0.00 0.00 0.00 2.40
4361 5317 5.745312 ATCTCCAAAATTCCAAGGTTTCC 57.255 39.130 0.00 0.00 0.00 3.13
4445 5416 6.861055 ACGCACACAAAATCTAAATACCAAAG 59.139 34.615 0.00 0.00 0.00 2.77
4480 5451 0.867746 GAACTGCGCTTCACATGACA 59.132 50.000 9.73 0.00 0.00 3.58
4481 5452 0.867746 TGAACTGCGCTTCACATGAC 59.132 50.000 9.73 0.00 0.00 3.06
4482 5453 1.812235 ATGAACTGCGCTTCACATGA 58.188 45.000 13.58 0.00 32.95 3.07
4483 5454 2.247637 CAATGAACTGCGCTTCACATG 58.752 47.619 13.58 11.83 32.95 3.21
4484 5455 1.881973 ACAATGAACTGCGCTTCACAT 59.118 42.857 13.58 9.08 32.95 3.21
4491 5462 3.469899 TGACAATACAATGAACTGCGC 57.530 42.857 0.00 0.00 0.00 6.09
4493 5464 5.941733 TCACATGACAATACAATGAACTGC 58.058 37.500 0.00 0.00 0.00 4.40
4519 5490 0.541296 AAACTCTGCTGGCCATTGCT 60.541 50.000 17.08 0.00 37.74 3.91
4523 5494 0.111061 TGTGAAACTCTGCTGGCCAT 59.889 50.000 5.51 0.00 38.04 4.40
4526 5497 3.012560 AGTGTGAAACTCTGCTGGC 57.987 52.632 0.00 0.00 39.54 4.85
4536 5528 2.042464 AGTGAGGAGCAGAGTGTGAAA 58.958 47.619 0.00 0.00 0.00 2.69
4576 5568 8.964476 ATCTTTGGTATTGATGTATCGAAGTT 57.036 30.769 0.00 0.00 31.08 2.66
4588 5580 9.886132 GTACCTCTTAAAGATCTTTGGTATTGA 57.114 33.333 25.97 16.14 33.15 2.57
4599 5614 6.767902 TGGCATGAATGTACCTCTTAAAGATC 59.232 38.462 0.00 0.00 0.00 2.75
4641 5656 2.736721 CACAAGTGTCCACCTTGTATCG 59.263 50.000 5.56 0.00 39.01 2.92
4658 5673 4.650734 TCATCTAGATTTGGTGCACACAA 58.349 39.130 20.43 16.88 0.00 3.33
4660 5675 4.877823 TGATCATCTAGATTTGGTGCACAC 59.122 41.667 20.43 8.79 37.00 3.82
4665 5680 6.628919 TTGCATGATCATCTAGATTTGGTG 57.371 37.500 4.86 0.49 37.00 4.17
4666 5681 6.294564 GCATTGCATGATCATCTAGATTTGGT 60.295 38.462 4.86 0.00 37.00 3.67
4668 5683 6.803807 CAGCATTGCATGATCATCTAGATTTG 59.196 38.462 11.91 0.00 37.00 2.32
4755 5775 4.514441 GCATGCAGCTAGTGACATCTTATT 59.486 41.667 14.21 0.00 41.15 1.40
4756 5776 4.063689 GCATGCAGCTAGTGACATCTTAT 58.936 43.478 14.21 0.00 41.15 1.73
4757 5777 3.118665 TGCATGCAGCTAGTGACATCTTA 60.119 43.478 18.46 0.00 45.94 2.10
4758 5778 2.286872 GCATGCAGCTAGTGACATCTT 58.713 47.619 14.21 0.00 41.15 2.40
4759 5779 1.208776 TGCATGCAGCTAGTGACATCT 59.791 47.619 18.46 0.00 45.94 2.90
4760 5780 1.660167 TGCATGCAGCTAGTGACATC 58.340 50.000 18.46 0.00 45.94 3.06
4762 5782 1.741145 CAATGCATGCAGCTAGTGACA 59.259 47.619 26.69 0.00 45.94 3.58
4763 5783 2.470196 CAATGCATGCAGCTAGTGAC 57.530 50.000 26.69 0.00 45.94 3.67
4809 5847 0.030235 GGTTTCGACAGGTTGTTGCC 59.970 55.000 0.00 0.00 31.81 4.52
4819 5858 2.357034 GCGGCTGAGGTTTCGACA 60.357 61.111 0.00 0.00 0.00 4.35
4820 5859 2.048127 AGCGGCTGAGGTTTCGAC 60.048 61.111 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.