Multiple sequence alignment - TraesCS4A01G333900

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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 TraesCS4A01G333900 chr4A 100.000 5444 0 0 1 5444 617235228 617229785 0.000000e+00 10054.0
1 TraesCS4A01G333900 chr4A 100.000 77 0 0 5053 5129 617230100 617230024 5.680000e-30 143.0
2 TraesCS4A01G333900 chr4A 100.000 77 0 0 5129 5205 617230176 617230100 5.680000e-30 143.0
3 TraesCS4A01G333900 chr5B 92.081 3700 209 43 67 3700 702887916 702891597 0.000000e+00 5132.0
4 TraesCS4A01G333900 chr5B 94.023 1121 43 7 4017 5129 702892022 702893126 0.000000e+00 1677.0
5 TraesCS4A01G333900 chr5B 90.596 319 8 7 5129 5444 702893050 702893349 2.360000e-108 403.0
6 TraesCS4A01G333900 chr5B 93.814 194 10 1 3698 3889 702891658 702891851 1.920000e-74 291.0
7 TraesCS4A01G333900 chr5D 95.217 3115 96 16 2025 5129 550439489 550442560 0.000000e+00 4878.0
8 TraesCS4A01G333900 chr5D 92.261 1809 102 10 61 1843 550437695 550439491 0.000000e+00 2531.0
9 TraesCS4A01G333900 chr5D 96.519 316 7 2 5129 5444 550442484 550442795 2.250000e-143 520.0
10 TraesCS4A01G333900 chr5D 98.077 52 1 0 1 52 550437606 550437657 2.090000e-14 91.6
11 TraesCS4A01G333900 chr3D 91.213 1855 139 18 2051 3891 602328526 602326682 0.000000e+00 2501.0
12 TraesCS4A01G333900 chr3D 86.898 1412 137 28 538 1926 602330074 602328688 0.000000e+00 1539.0
13 TraesCS4A01G333900 chr3D 86.931 857 74 22 4283 5106 602326139 602325288 0.000000e+00 928.0
14 TraesCS4A01G333900 chr3D 82.532 395 39 20 3900 4279 602326594 602326215 2.450000e-83 320.0
15 TraesCS4A01G333900 chr3A 89.740 1881 147 17 2051 3891 732060808 732058934 0.000000e+00 2362.0
16 TraesCS4A01G333900 chr3A 88.330 1311 126 14 667 1962 732062262 732060964 0.000000e+00 1548.0
17 TraesCS4A01G333900 chr3A 87.266 534 37 11 4282 4790 732058361 732057834 1.020000e-161 580.0
18 TraesCS4A01G333900 chr3A 89.030 237 19 4 4045 4279 732058668 732058437 2.480000e-73 287.0
19 TraesCS4A01G333900 chr3B 90.848 1628 127 16 2051 3666 809605254 809603637 0.000000e+00 2161.0
20 TraesCS4A01G333900 chr3B 87.129 1414 131 23 573 1962 809606853 809605467 0.000000e+00 1555.0
21 TraesCS4A01G333900 chr3B 86.211 863 78 18 4282 5113 809602872 809602020 0.000000e+00 896.0
22 TraesCS4A01G333900 chr3B 96.648 179 4 1 3715 3891 809603625 809603447 4.120000e-76 296.0
23 TraesCS4A01G333900 chr7D 83.260 227 24 6 2195 2418 382077122 382076907 4.300000e-46 196.0
24 TraesCS4A01G333900 chr7D 95.652 46 2 0 1928 1973 146621617 146621662 2.100000e-09 75.0
25 TraesCS4A01G333900 chr6B 83.260 227 24 6 2195 2418 307018282 307018067 4.300000e-46 196.0
26 TraesCS4A01G333900 chr2B 83.260 227 24 6 2195 2418 357380885 357380670 4.300000e-46 196.0
27 TraesCS4A01G333900 chr2B 81.938 227 27 6 2195 2418 391135119 391134904 4.330000e-41 180.0
28 TraesCS4A01G333900 chr4D 78.947 247 39 10 5206 5444 446644928 446644687 7.300000e-34 156.0
29 TraesCS4A01G333900 chr4D 80.402 199 32 7 1779 1973 87725960 87725765 1.580000e-30 145.0
30 TraesCS4A01G333900 chr4B 82.857 140 19 5 1838 1976 124044057 124043922 2.660000e-23 121.0
31 TraesCS4A01G333900 chr7B 95.652 46 2 0 1928 1973 109033148 109033193 2.100000e-09 75.0


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 TraesCS4A01G333900 chr4A 617229785 617235228 5443 True 10054.00 10054 100.0000 1 5444 1 chr4A.!!$R1 5443
1 TraesCS4A01G333900 chr5B 702887916 702893349 5433 False 1875.75 5132 92.6285 67 5444 4 chr5B.!!$F1 5377
2 TraesCS4A01G333900 chr5D 550437606 550442795 5189 False 2005.15 4878 95.5185 1 5444 4 chr5D.!!$F1 5443
3 TraesCS4A01G333900 chr3D 602325288 602330074 4786 True 1322.00 2501 86.8935 538 5106 4 chr3D.!!$R1 4568
4 TraesCS4A01G333900 chr3A 732057834 732062262 4428 True 1194.25 2362 88.5915 667 4790 4 chr3A.!!$R1 4123
5 TraesCS4A01G333900 chr3B 809602020 809606853 4833 True 1227.00 2161 90.2090 573 5113 4 chr3B.!!$R1 4540

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
406 467 0.458889 CGTTCCGCCTACCGATTCAA 60.459 55.0 0.00 0.00 40.02 2.69 F
632 698 0.805711 GTTGTGGTTGGTGTTGCTGC 60.806 55.0 0.00 0.00 0.00 5.25 F
1313 1411 0.879400 AGCGACATAGATGCTGCTGC 60.879 55.0 8.89 8.89 39.24 5.25 F
2837 3123 0.251297 CCTTTCATGTCAGGCCACCA 60.251 55.0 5.01 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1409 1.627329 GGCTCCCTATCATCATCAGCA 59.373 52.381 0.0 0.0 0.00 4.41 R
2000 2229 2.466846 TGGGAGTTCTATAGTGCTGCA 58.533 47.619 0.0 0.0 0.00 4.41 R
3229 3516 1.076549 AGAATTTTGCCTCCCCGCA 59.923 52.632 0.0 0.0 36.85 5.69 R
4758 5520 1.808945 CATGTTCTGACTGAAGTGGCC 59.191 52.381 0.0 0.0 35.01 5.36 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
52 53 4.778143 CGAAGGGTGGGGGCGAAG 62.778 72.222 0.00 0.00 0.00 3.79
64 65 3.723922 GCGAAGGGTGGGGGCTTA 61.724 66.667 0.00 0.00 0.00 3.09
161 195 3.864789 TTCCCTTGAAGATATGCCTCC 57.135 47.619 0.00 0.00 0.00 4.30
211 261 6.494842 TGGTTGATATGCTTCTTTTAATCGC 58.505 36.000 0.00 0.00 0.00 4.58
238 292 2.509336 CGATCTTGGGCGAACGCT 60.509 61.111 18.14 0.00 41.60 5.07
259 313 4.577693 GCTGCTTATTGATTCCATGAGTCA 59.422 41.667 0.00 0.00 0.00 3.41
260 314 5.505324 GCTGCTTATTGATTCCATGAGTCAC 60.505 44.000 0.00 0.00 28.38 3.67
261 315 5.748402 TGCTTATTGATTCCATGAGTCACT 58.252 37.500 0.00 0.00 28.38 3.41
262 316 5.587443 TGCTTATTGATTCCATGAGTCACTG 59.413 40.000 0.00 0.00 28.38 3.66
263 317 5.008415 GCTTATTGATTCCATGAGTCACTGG 59.992 44.000 12.77 12.77 28.38 4.00
264 318 4.849813 ATTGATTCCATGAGTCACTGGA 57.150 40.909 16.00 16.00 39.78 3.86
296 354 5.897377 AGAGGGTCAATAAATTTTGTCCG 57.103 39.130 0.00 0.00 36.17 4.79
302 360 3.754323 TCAATAAATTTTGTCCGGTCGCT 59.246 39.130 0.00 0.00 0.00 4.93
354 412 2.988493 CGCTTACTTGGCGTGTAAGTAA 59.012 45.455 21.81 15.28 44.99 2.24
360 418 5.103290 ACTTGGCGTGTAAGTAACATTTG 57.897 39.130 0.00 0.00 41.10 2.32
384 445 1.821332 GAATCCAGCTCCTTGCCGG 60.821 63.158 0.00 0.00 44.23 6.13
406 467 0.458889 CGTTCCGCCTACCGATTCAA 60.459 55.000 0.00 0.00 40.02 2.69
414 475 3.059597 CGCCTACCGATTCAATCACATTC 60.060 47.826 0.00 0.00 40.02 2.67
482 543 5.310451 ACGGTTATGTAACAATCAACACCT 58.690 37.500 5.38 0.00 37.92 4.00
489 550 1.774110 ACAATCAACACCTTGCCACA 58.226 45.000 0.00 0.00 0.00 4.17
494 555 1.457267 AACACCTTGCCACATGCCA 60.457 52.632 0.00 0.00 40.16 4.92
497 558 4.424566 CCTTGCCACATGCCACGC 62.425 66.667 0.00 0.00 40.16 5.34
498 559 4.424566 CTTGCCACATGCCACGCC 62.425 66.667 0.00 0.00 40.16 5.68
502 563 3.434319 CCACATGCCACGCCACTC 61.434 66.667 0.00 0.00 0.00 3.51
511 572 2.016604 GCCACGCCACTCCATGATTTA 61.017 52.381 0.00 0.00 0.00 1.40
571 633 0.973632 ACTCGTACTCAATGGGCACA 59.026 50.000 0.00 0.00 0.00 4.57
612 676 9.289303 TCTACGTTCGTTTTTAATGGTATACTC 57.711 33.333 2.62 0.00 0.00 2.59
627 693 2.695127 TACTCGTTGTGGTTGGTGTT 57.305 45.000 0.00 0.00 0.00 3.32
632 698 0.805711 GTTGTGGTTGGTGTTGCTGC 60.806 55.000 0.00 0.00 0.00 5.25
639 705 2.026014 GGTGTTGCTGCCGTGTTG 59.974 61.111 0.00 0.00 0.00 3.33
696 772 7.910162 ACGTGCTGATTAATATTTGTTGTGATC 59.090 33.333 0.00 0.00 0.00 2.92
715 793 6.818142 TGTGATCACATGAATAATCGACAACT 59.182 34.615 24.56 0.00 36.21 3.16
728 806 3.990092 TCGACAACTGCTACTTGTTGAT 58.010 40.909 11.97 0.00 44.29 2.57
734 812 6.729187 ACAACTGCTACTTGTTGATTTCTTC 58.271 36.000 11.97 0.00 44.29 2.87
738 816 8.089115 ACTGCTACTTGTTGATTTCTTCTTAC 57.911 34.615 0.00 0.00 0.00 2.34
758 836 1.069204 CGGAAGATAGGCTTGCTGCTA 59.931 52.381 0.00 0.00 42.22 3.49
835 921 3.379372 AGCACATTCATTGCAGTGATACC 59.621 43.478 13.14 0.98 42.83 2.73
837 923 4.142315 GCACATTCATTGCAGTGATACCTT 60.142 41.667 13.14 0.00 39.93 3.50
840 926 3.354948 TCATTGCAGTGATACCTTGCT 57.645 42.857 7.97 0.00 38.60 3.91
841 927 3.689347 TCATTGCAGTGATACCTTGCTT 58.311 40.909 7.97 0.00 38.60 3.91
854 940 9.423061 GTGATACCTTGCTTATTTGTTTGATTT 57.577 29.630 0.00 0.00 0.00 2.17
888 974 3.424039 CGCTGTCATGTCTGTTGAATGTC 60.424 47.826 0.00 0.00 0.00 3.06
902 990 7.383300 TCTGTTGAATGTCTTGATGCTATATCG 59.617 37.037 0.00 0.00 0.00 2.92
1083 1181 3.374402 CGGAGGCCGTCTCACACT 61.374 66.667 1.71 0.00 44.19 3.55
1310 1408 3.320626 TGATTAGCGACATAGATGCTGC 58.679 45.455 0.00 0.00 39.73 5.25
1311 1409 3.006217 TGATTAGCGACATAGATGCTGCT 59.994 43.478 12.14 12.14 42.07 4.24
1312 1410 2.428888 TAGCGACATAGATGCTGCTG 57.571 50.000 15.55 0.00 40.38 4.41
1313 1411 0.879400 AGCGACATAGATGCTGCTGC 60.879 55.000 8.89 8.89 39.24 5.25
1551 1649 7.309377 CCAAAAGATCCAAGTGATGTTACACAT 60.309 37.037 0.00 0.00 42.43 3.21
1690 1789 5.984926 TCAAGCAGCAATCCTTTAGTTTTTG 59.015 36.000 0.00 0.00 0.00 2.44
1770 1869 6.868339 GGTGCAGAAATTAGCAAGTTGTTTAT 59.132 34.615 4.48 0.00 43.20 1.40
1784 1883 6.936968 AGTTGTTTATTACTCCCTCTGTCT 57.063 37.500 0.00 0.00 0.00 3.41
2000 2229 3.367087 GCGCACTCTATTATGGTACGGAT 60.367 47.826 0.30 0.00 0.00 4.18
2014 2243 3.005472 GGTACGGATGCAGCACTATAGAA 59.995 47.826 6.78 0.00 0.00 2.10
2021 2250 2.837591 TGCAGCACTATAGAACTCCCAA 59.162 45.455 6.78 0.00 0.00 4.12
2094 2372 2.065899 TCCCGGATTAAGGCAATTGG 57.934 50.000 0.73 0.00 0.00 3.16
2394 2676 2.484889 CTTCCAGTTTATCCGGCTAGC 58.515 52.381 6.04 6.04 0.00 3.42
2508 2790 3.343941 TTTACTGTACCCACTGATGCC 57.656 47.619 0.00 0.00 0.00 4.40
2568 2850 5.546887 AGCTATTCCTACTTATAACACCCCC 59.453 44.000 0.00 0.00 0.00 5.40
2739 3021 5.163663 GGAAAGCATAATCACCATTTCGTCA 60.164 40.000 0.00 0.00 0.00 4.35
2837 3123 0.251297 CCTTTCATGTCAGGCCACCA 60.251 55.000 5.01 0.00 0.00 4.17
2857 3143 3.693085 CCAATGATGTTAAGTCTGCAGCT 59.307 43.478 9.47 6.85 0.00 4.24
3028 3314 5.079643 GCAATTATCCACATATCCAAGGGT 58.920 41.667 0.00 0.00 0.00 4.34
3084 3370 0.822121 GTCGAGGTTTGCCCCTTGTT 60.822 55.000 0.00 0.00 37.30 2.83
3229 3516 3.071747 GGGAAGAAGTTCTGAAGGACAGT 59.928 47.826 6.06 0.00 45.86 3.55
3231 3518 3.118905 AGAAGTTCTGAAGGACAGTGC 57.881 47.619 4.10 0.00 45.86 4.40
3343 3630 6.870971 TTACCTTACAGTCAACAAATCACC 57.129 37.500 0.00 0.00 0.00 4.02
3358 3645 2.037049 ACCCCATTGCGCCATGAA 59.963 55.556 22.08 1.16 0.00 2.57
3384 3671 1.166531 GGTGAAGCTGAGCGTGGTTT 61.167 55.000 0.00 0.00 0.00 3.27
3474 3761 6.323482 TCAATGTCAATTTTCTCTGTTTCCCA 59.677 34.615 0.00 0.00 0.00 4.37
3503 3791 4.687948 CCTTCATAATGAGACGTGCCTATG 59.312 45.833 0.00 0.00 0.00 2.23
3591 3879 3.620966 GCTCCTCATACACTTCAAAGCCT 60.621 47.826 0.00 0.00 0.00 4.58
3954 4444 4.164221 CAGTTCATATGGGGTCCTACTTGT 59.836 45.833 2.13 0.00 0.00 3.16
3956 4446 5.253096 AGTTCATATGGGGTCCTACTTGTTT 59.747 40.000 2.13 0.00 0.00 2.83
3958 4448 5.505780 TCATATGGGGTCCTACTTGTTTTG 58.494 41.667 2.13 0.00 0.00 2.44
3963 4453 2.552743 GGGTCCTACTTGTTTTGTGCTC 59.447 50.000 0.00 0.00 0.00 4.26
4023 4680 9.543783 AAAAGACTAGGTTGTTTTCTACTACTG 57.456 33.333 0.00 0.00 33.68 2.74
4593 5343 4.202111 GCTTGTCTATCTTCCTCAGACTCC 60.202 50.000 0.00 0.00 39.54 3.85
4758 5520 0.918983 TATGGGAGGGGCACTCTTTG 59.081 55.000 17.73 0.00 45.83 2.77
4947 5712 5.815740 TCATCGTTCTTATACTCTTTTGCCC 59.184 40.000 0.00 0.00 0.00 5.36
4948 5713 4.178540 TCGTTCTTATACTCTTTTGCCCG 58.821 43.478 0.00 0.00 0.00 6.13
4953 5719 4.713321 TCTTATACTCTTTTGCCCGTACCT 59.287 41.667 0.00 0.00 0.00 3.08
4983 5750 0.596600 TCTTCAGTCGAACACGTGGC 60.597 55.000 21.57 10.54 0.00 5.01
5096 5869 6.655003 TCATGGTGACCAAGTAGAAATTCTTC 59.345 38.462 9.06 0.00 36.95 2.87
5097 5870 5.935945 TGGTGACCAAGTAGAAATTCTTCA 58.064 37.500 0.00 0.00 33.64 3.02
5098 5871 6.542821 TGGTGACCAAGTAGAAATTCTTCAT 58.457 36.000 0.00 0.00 33.64 2.57
5099 5872 6.430925 TGGTGACCAAGTAGAAATTCTTCATG 59.569 38.462 0.00 0.00 33.64 3.07
5100 5873 6.431234 GGTGACCAAGTAGAAATTCTTCATGT 59.569 38.462 0.00 0.00 33.64 3.21
5101 5874 7.040409 GGTGACCAAGTAGAAATTCTTCATGTT 60.040 37.037 0.00 0.00 33.64 2.71
5102 5875 8.017946 GTGACCAAGTAGAAATTCTTCATGTTC 58.982 37.037 0.00 0.00 33.64 3.18
5103 5876 7.939039 TGACCAAGTAGAAATTCTTCATGTTCT 59.061 33.333 0.00 0.00 33.64 3.01
5104 5877 8.697507 ACCAAGTAGAAATTCTTCATGTTCTT 57.302 30.769 0.00 0.00 33.64 2.52
5105 5878 9.136323 ACCAAGTAGAAATTCTTCATGTTCTTT 57.864 29.630 0.00 0.00 33.64 2.52
5106 5879 9.971922 CCAAGTAGAAATTCTTCATGTTCTTTT 57.028 29.630 0.00 0.00 33.64 2.27
5116 5889 9.918630 ATTCTTCATGTTCTTTTGAAATAGGTG 57.081 29.630 0.00 0.00 40.53 4.00
5117 5890 8.463930 TCTTCATGTTCTTTTGAAATAGGTGT 57.536 30.769 0.00 0.00 40.53 4.16
5118 5891 9.567776 TCTTCATGTTCTTTTGAAATAGGTGTA 57.432 29.630 0.00 0.00 40.53 2.90
5119 5892 9.831737 CTTCATGTTCTTTTGAAATAGGTGTAG 57.168 33.333 0.00 0.00 40.53 2.74
5120 5893 8.918202 TCATGTTCTTTTGAAATAGGTGTAGT 57.082 30.769 0.00 0.00 40.53 2.73
5121 5894 9.349713 TCATGTTCTTTTGAAATAGGTGTAGTT 57.650 29.630 0.00 0.00 40.53 2.24
5156 5929 9.696917 ATTTTAAGAAATCTGTTTCATGGTGAC 57.303 29.630 0.00 0.00 44.92 3.67
5157 5930 5.712152 AAGAAATCTGTTTCATGGTGACC 57.288 39.130 0.00 0.00 44.92 4.02
5158 5931 4.728772 AGAAATCTGTTTCATGGTGACCA 58.271 39.130 6.84 6.84 44.92 4.02
5159 5932 5.139727 AGAAATCTGTTTCATGGTGACCAA 58.860 37.500 9.06 0.00 44.92 3.67
5160 5933 5.242393 AGAAATCTGTTTCATGGTGACCAAG 59.758 40.000 9.06 3.87 44.92 3.61
5161 5934 3.576078 TCTGTTTCATGGTGACCAAGT 57.424 42.857 9.06 0.00 36.95 3.16
5162 5935 4.698201 TCTGTTTCATGGTGACCAAGTA 57.302 40.909 9.06 0.00 36.95 2.24
5163 5936 4.641396 TCTGTTTCATGGTGACCAAGTAG 58.359 43.478 9.06 1.97 36.95 2.57
5164 5937 4.346709 TCTGTTTCATGGTGACCAAGTAGA 59.653 41.667 9.06 4.44 36.95 2.59
5165 5938 5.042463 TGTTTCATGGTGACCAAGTAGAA 57.958 39.130 9.06 8.18 36.95 2.10
5166 5939 5.441500 TGTTTCATGGTGACCAAGTAGAAA 58.558 37.500 9.06 13.66 36.95 2.52
5167 5940 6.068010 TGTTTCATGGTGACCAAGTAGAAAT 58.932 36.000 9.06 0.00 36.95 2.17
5168 5941 6.549364 TGTTTCATGGTGACCAAGTAGAAATT 59.451 34.615 9.06 0.00 36.95 1.82
5169 5942 6.817765 TTCATGGTGACCAAGTAGAAATTC 57.182 37.500 9.06 0.00 36.95 2.17
5170 5943 6.126863 TCATGGTGACCAAGTAGAAATTCT 57.873 37.500 9.06 0.00 36.95 2.40
5171 5944 6.542821 TCATGGTGACCAAGTAGAAATTCTT 58.457 36.000 9.06 0.00 36.95 2.52
5275 6051 1.826720 CATGCTACCCATGCAGGTTTT 59.173 47.619 2.55 0.00 44.34 2.43
5365 6141 3.988379 TGGCAACTTAAAGCAAGACAG 57.012 42.857 0.00 0.00 37.71 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.669440 CCTTCGACTTCCCCGACAA 59.331 57.895 0.00 0.00 35.61 3.18
52 53 0.771755 CCTAGATTAAGCCCCCACCC 59.228 60.000 0.00 0.00 0.00 4.61
55 56 2.296943 AACCCTAGATTAAGCCCCCA 57.703 50.000 0.00 0.00 0.00 4.96
56 57 3.074094 CCTAAACCCTAGATTAAGCCCCC 59.926 52.174 0.00 0.00 0.00 5.40
59 60 5.384145 AACCCTAAACCCTAGATTAAGCC 57.616 43.478 0.00 0.00 0.00 4.35
60 61 5.987953 CGTAACCCTAAACCCTAGATTAAGC 59.012 44.000 0.00 0.00 0.00 3.09
61 62 7.352079 TCGTAACCCTAAACCCTAGATTAAG 57.648 40.000 0.00 0.00 0.00 1.85
63 64 7.919385 AATCGTAACCCTAAACCCTAGATTA 57.081 36.000 0.00 0.00 0.00 1.75
64 65 6.819947 AATCGTAACCCTAAACCCTAGATT 57.180 37.500 0.00 0.00 0.00 2.40
149 183 4.039366 GGTTTCGTAGAGGAGGCATATCTT 59.961 45.833 0.00 0.00 38.43 2.40
155 189 2.097825 GTAGGTTTCGTAGAGGAGGCA 58.902 52.381 0.00 0.00 38.43 4.75
156 190 2.099427 CAGTAGGTTTCGTAGAGGAGGC 59.901 54.545 0.00 0.00 38.43 4.70
159 193 4.025040 TGTCAGTAGGTTTCGTAGAGGA 57.975 45.455 0.00 0.00 38.43 3.71
161 195 5.048224 TCCTTTGTCAGTAGGTTTCGTAGAG 60.048 44.000 3.72 0.00 33.03 2.43
211 261 2.186903 CAAGATCGGGTCGGGTGG 59.813 66.667 0.00 0.00 0.00 4.61
238 292 5.587443 CAGTGACTCATGGAATCAATAAGCA 59.413 40.000 0.00 0.00 0.00 3.91
259 313 7.510675 TTGACCCTCTAAATTAGATTCCAGT 57.489 36.000 2.87 0.00 33.66 4.00
270 324 8.466798 CGGACAAAATTTATTGACCCTCTAAAT 58.533 33.333 5.99 0.00 40.53 1.40
296 354 2.353607 CCGATAGACGCAGCGACC 60.354 66.667 24.65 12.83 41.07 4.79
302 360 2.328235 GGACTAGCCGATAGACGCA 58.672 57.895 0.00 0.00 41.07 5.24
406 467 5.598416 TTAGATCCAGTGACGAATGTGAT 57.402 39.130 0.00 0.00 0.00 3.06
414 475 5.869344 TGTCAAGAAATTAGATCCAGTGACG 59.131 40.000 0.00 0.00 36.50 4.35
489 550 2.274948 ATCATGGAGTGGCGTGGCAT 62.275 55.000 0.00 0.00 0.00 4.40
494 555 1.651987 CGTAAATCATGGAGTGGCGT 58.348 50.000 0.00 0.00 0.00 5.68
497 558 2.036958 TGGCGTAAATCATGGAGTGG 57.963 50.000 0.00 0.00 0.00 4.00
498 559 4.353737 CAATTGGCGTAAATCATGGAGTG 58.646 43.478 0.00 0.00 0.00 3.51
502 563 3.446799 CACCAATTGGCGTAAATCATGG 58.553 45.455 24.79 0.00 39.32 3.66
525 586 1.473257 GGCAAGACACACAGAGTCACA 60.473 52.381 0.00 0.00 38.46 3.58
559 620 8.394971 TGTCTATTAATTATGTGCCCATTGAG 57.605 34.615 0.00 0.00 32.29 3.02
560 621 8.938801 ATGTCTATTAATTATGTGCCCATTGA 57.061 30.769 0.00 0.00 32.29 2.57
564 625 9.502091 GTAGAATGTCTATTAATTATGTGCCCA 57.498 33.333 0.00 0.00 30.76 5.36
589 651 6.586082 ACGAGTATACCATTAAAAACGAACGT 59.414 34.615 0.00 0.00 0.00 3.99
612 676 0.525242 CAGCAACACCAACCACAACG 60.525 55.000 0.00 0.00 0.00 4.10
627 693 0.036164 ATAAGTCCAACACGGCAGCA 59.964 50.000 0.00 0.00 33.14 4.41
632 698 6.312180 GGAAAGTAGTAATAAGTCCAACACGG 59.688 42.308 0.00 0.00 0.00 4.94
639 705 8.768957 AGAAAACGGAAAGTAGTAATAAGTCC 57.231 34.615 0.00 0.00 0.00 3.85
696 772 5.475273 AGCAGTTGTCGATTATTCATGTG 57.525 39.130 0.00 0.00 0.00 3.21
715 793 6.147164 CCGTAAGAAGAAATCAACAAGTAGCA 59.853 38.462 0.00 0.00 43.02 3.49
734 812 3.126831 CAGCAAGCCTATCTTCCGTAAG 58.873 50.000 0.00 0.00 31.27 2.34
738 816 2.315246 GCAGCAAGCCTATCTTCCG 58.685 57.895 0.00 0.00 37.23 4.30
758 836 5.418840 AGTCGGCATTCACCAAGAATAAATT 59.581 36.000 0.00 0.00 45.06 1.82
841 927 9.288124 CGCAGAATGATACAAATCAAACAAATA 57.712 29.630 0.00 0.00 45.12 1.40
854 940 2.671130 TGACAGCGCAGAATGATACA 57.329 45.000 11.47 0.23 39.69 2.29
984 1082 4.631813 GGCTTCATGGTTTACTCACTACAG 59.368 45.833 0.00 0.00 0.00 2.74
1075 1173 1.971357 GGAGGTTTCCTGAGTGTGAGA 59.029 52.381 0.00 0.00 40.58 3.27
1310 1408 2.354906 GGCTCCCTATCATCATCAGCAG 60.355 54.545 0.00 0.00 0.00 4.24
1311 1409 1.627329 GGCTCCCTATCATCATCAGCA 59.373 52.381 0.00 0.00 0.00 4.41
1312 1410 1.907936 AGGCTCCCTATCATCATCAGC 59.092 52.381 0.00 0.00 28.47 4.26
1313 1411 2.905085 ACAGGCTCCCTATCATCATCAG 59.095 50.000 0.00 0.00 29.64 2.90
1770 1869 9.575868 CACTATATTTAGAGACAGAGGGAGTAA 57.424 37.037 0.00 0.00 0.00 2.24
1859 1961 9.941664 CATTGATTTGGTATTCTAGATGTTGAC 57.058 33.333 0.00 0.00 0.00 3.18
1962 2066 4.870363 AGTGCGCATTAATTTGACAAAGT 58.130 34.783 15.91 6.44 0.00 2.66
1963 2067 5.156355 AGAGTGCGCATTAATTTGACAAAG 58.844 37.500 15.91 0.00 0.00 2.77
1964 2068 5.119931 AGAGTGCGCATTAATTTGACAAA 57.880 34.783 15.91 2.48 0.00 2.83
1965 2069 4.764679 AGAGTGCGCATTAATTTGACAA 57.235 36.364 15.91 0.00 0.00 3.18
1966 2070 6.435430 AATAGAGTGCGCATTAATTTGACA 57.565 33.333 15.91 0.00 0.00 3.58
1968 2072 7.228507 ACCATAATAGAGTGCGCATTAATTTGA 59.771 33.333 15.91 0.00 0.00 2.69
1969 2073 7.362662 ACCATAATAGAGTGCGCATTAATTTG 58.637 34.615 15.91 12.52 0.00 2.32
2000 2229 2.466846 TGGGAGTTCTATAGTGCTGCA 58.533 47.619 0.00 0.00 0.00 4.41
2340 2622 5.671493 AGTATAATGGTTGGAGGAAGTTCG 58.329 41.667 0.00 0.00 0.00 3.95
2394 2676 4.744137 GCATCTGACACTGAGTATAAGCTG 59.256 45.833 0.00 0.00 0.00 4.24
2568 2850 4.946157 ACCAATAGCTCTCCTGAACATTTG 59.054 41.667 0.00 0.00 0.00 2.32
2837 3123 4.155462 CACAGCTGCAGACTTAACATCATT 59.845 41.667 20.43 0.00 0.00 2.57
2986 3272 4.948341 TGCCTTAGACTTATTCCGCATA 57.052 40.909 0.00 0.00 0.00 3.14
3054 3340 3.005554 CAAACCTCGACAAGCTCATCAT 58.994 45.455 0.00 0.00 0.00 2.45
3229 3516 1.076549 AGAATTTTGCCTCCCCGCA 59.923 52.632 0.00 0.00 36.85 5.69
3231 3518 1.948721 GCCAGAATTTTGCCTCCCCG 61.949 60.000 0.00 0.00 0.00 5.73
3343 3630 0.037512 TTTGTTCATGGCGCAATGGG 60.038 50.000 24.33 0.00 0.00 4.00
3358 3645 0.538287 GCTCAGCTTCACCCCTTTGT 60.538 55.000 0.00 0.00 0.00 2.83
3384 3671 4.119862 GCTGCTACGAGGAAATACATTCA 58.880 43.478 0.00 0.00 39.98 2.57
3474 3761 5.171476 CACGTCTCATTATGAAGGTCAACT 58.829 41.667 0.00 0.00 0.00 3.16
3526 3814 2.636403 CAGCCTGATGGAGGATATCACA 59.364 50.000 4.83 0.81 46.33 3.58
3591 3879 4.042311 TCAGTTGCAACCTACCTTCCATAA 59.958 41.667 25.62 0.00 0.00 1.90
3733 4142 7.062605 CAGTGGATCAGCAAAATGAAATACAAC 59.937 37.037 0.00 0.00 31.76 3.32
3925 4415 3.714798 GGACCCCATATGAACTGGAGTTA 59.285 47.826 3.65 0.00 38.56 2.24
3926 4416 2.509964 GGACCCCATATGAACTGGAGTT 59.490 50.000 3.65 0.00 41.64 3.01
3954 4444 8.579850 AATGGACTTGATATTAGAGCACAAAA 57.420 30.769 0.00 0.00 0.00 2.44
3956 4446 8.486210 ACTAATGGACTTGATATTAGAGCACAA 58.514 33.333 9.46 0.00 37.66 3.33
4003 4577 7.837863 TCCATCAGTAGTAGAAAACAACCTAG 58.162 38.462 0.00 0.00 0.00 3.02
4149 4812 4.469657 TCCTGTACAAAGGTTGCTTCAAT 58.530 39.130 0.00 0.00 38.58 2.57
4256 4919 8.719645 TGGTAAGTAAAAGTAACCTACCTACA 57.280 34.615 3.45 0.00 0.00 2.74
4593 5343 3.378112 CACACAAGTATAGCCATGGTTGG 59.622 47.826 14.67 5.70 46.66 3.77
4715 5465 2.874701 GGCGAACATATCAGCAATCAGT 59.125 45.455 0.00 0.00 31.84 3.41
4758 5520 1.808945 CATGTTCTGACTGAAGTGGCC 59.191 52.381 0.00 0.00 35.01 5.36
4947 5712 7.096436 CGACTGAAGATTATCAATCAAGGTACG 60.096 40.741 0.00 0.00 40.42 3.67
4948 5713 7.921214 TCGACTGAAGATTATCAATCAAGGTAC 59.079 37.037 0.00 0.00 40.42 3.34
4953 5719 7.201435 CGTGTTCGACTGAAGATTATCAATCAA 60.201 37.037 0.00 0.00 38.65 2.57
4997 5765 1.202867 TGTAGCCACCATGCAGAACAA 60.203 47.619 0.00 0.00 0.00 2.83
5130 5903 9.696917 GTCACCATGAAACAGATTTCTTAAAAT 57.303 29.630 0.00 0.00 44.02 1.82
5131 5904 8.141268 GGTCACCATGAAACAGATTTCTTAAAA 58.859 33.333 0.00 0.00 44.02 1.52
5132 5905 7.286546 TGGTCACCATGAAACAGATTTCTTAAA 59.713 33.333 0.00 0.00 44.02 1.52
5133 5906 6.775142 TGGTCACCATGAAACAGATTTCTTAA 59.225 34.615 0.00 0.00 44.02 1.85
5134 5907 6.303054 TGGTCACCATGAAACAGATTTCTTA 58.697 36.000 0.00 0.00 44.02 2.10
5135 5908 5.139727 TGGTCACCATGAAACAGATTTCTT 58.860 37.500 0.00 0.00 44.02 2.52
5136 5909 4.728772 TGGTCACCATGAAACAGATTTCT 58.271 39.130 0.00 0.00 44.02 2.52
5137 5910 5.010012 ACTTGGTCACCATGAAACAGATTTC 59.990 40.000 16.54 0.00 43.96 2.17
5138 5911 4.895297 ACTTGGTCACCATGAAACAGATTT 59.105 37.500 16.54 0.00 33.58 2.17
5139 5912 4.473444 ACTTGGTCACCATGAAACAGATT 58.527 39.130 16.54 0.00 33.58 2.40
5140 5913 4.104383 ACTTGGTCACCATGAAACAGAT 57.896 40.909 16.54 0.00 33.58 2.90
5141 5914 3.576078 ACTTGGTCACCATGAAACAGA 57.424 42.857 16.54 0.00 33.58 3.41
5142 5915 4.641396 TCTACTTGGTCACCATGAAACAG 58.359 43.478 16.54 2.95 33.58 3.16
5143 5916 4.698201 TCTACTTGGTCACCATGAAACA 57.302 40.909 16.54 0.00 33.58 2.83
5144 5917 6.575162 ATTTCTACTTGGTCACCATGAAAC 57.425 37.500 16.54 0.00 33.58 2.78
5145 5918 7.004086 AGAATTTCTACTTGGTCACCATGAAA 58.996 34.615 16.54 14.75 33.58 2.69
5146 5919 6.542821 AGAATTTCTACTTGGTCACCATGAA 58.457 36.000 16.54 7.26 33.58 2.57
5147 5920 6.126863 AGAATTTCTACTTGGTCACCATGA 57.873 37.500 16.54 1.25 33.58 3.07
5148 5921 6.430925 TGAAGAATTTCTACTTGGTCACCATG 59.569 38.462 8.20 8.20 33.68 3.66
5149 5922 6.542821 TGAAGAATTTCTACTTGGTCACCAT 58.457 36.000 0.00 0.00 34.31 3.55
5150 5923 5.935945 TGAAGAATTTCTACTTGGTCACCA 58.064 37.500 0.00 0.00 34.31 4.17
5151 5924 6.431234 ACATGAAGAATTTCTACTTGGTCACC 59.569 38.462 0.00 0.00 34.31 4.02
5152 5925 7.440523 ACATGAAGAATTTCTACTTGGTCAC 57.559 36.000 0.00 0.00 34.31 3.67
5153 5926 7.939039 AGAACATGAAGAATTTCTACTTGGTCA 59.061 33.333 16.42 9.58 34.31 4.02
5154 5927 8.329203 AGAACATGAAGAATTTCTACTTGGTC 57.671 34.615 0.00 5.96 34.31 4.02
5155 5928 8.697507 AAGAACATGAAGAATTTCTACTTGGT 57.302 30.769 0.00 0.00 34.31 3.67
5156 5929 9.971922 AAAAGAACATGAAGAATTTCTACTTGG 57.028 29.630 0.00 0.00 34.31 3.61
5166 5939 9.918630 CACCTATTTCAAAAGAACATGAAGAAT 57.081 29.630 0.00 0.00 36.93 2.40
5167 5940 8.912988 ACACCTATTTCAAAAGAACATGAAGAA 58.087 29.630 0.00 0.00 36.93 2.52
5168 5941 8.463930 ACACCTATTTCAAAAGAACATGAAGA 57.536 30.769 0.00 0.00 36.93 2.87
5169 5942 9.831737 CTACACCTATTTCAAAAGAACATGAAG 57.168 33.333 0.00 0.00 36.93 3.02
5170 5943 9.349713 ACTACACCTATTTCAAAAGAACATGAA 57.650 29.630 0.00 0.00 33.93 2.57
5171 5944 8.918202 ACTACACCTATTTCAAAAGAACATGA 57.082 30.769 0.00 0.00 0.00 3.07
5214 5987 3.216985 TTCATGGGCGGGGCTTTCA 62.217 57.895 0.00 0.00 0.00 2.69
5275 6051 4.202641 GGGGGAGTAAAGAAGGAAAAAGGA 60.203 45.833 0.00 0.00 0.00 3.36
5365 6141 1.723220 GGCGGTACCTGTTTTCTCTC 58.277 55.000 10.90 0.00 34.51 3.20
5396 6172 4.581409 GCTTGTAAGGAGGTGTTGGTAAAA 59.419 41.667 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.