Multiple sequence alignment - TraesCS5B01G056000

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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 TraesCS5B01G056000 chr5B 100.000 4164 0 0 1 4164 62030396 62026233 0.000000e+00 7690.0
1 TraesCS5B01G056000 chr5B 93.451 3283 134 29 136 3385 63542169 63545403 0.000000e+00 4796.0
2 TraesCS5B01G056000 chr5B 85.025 995 137 7 2050 3035 72098413 72099404 0.000000e+00 1002.0
3 TraesCS5B01G056000 chr5B 95.714 140 6 0 1 140 63536825 63536964 4.190000e-55 226.0
4 TraesCS5B01G056000 chr5B 85.057 174 23 3 2090 2260 70962123 70961950 1.540000e-39 174.0
5 TraesCS5B01G056000 chr5B 95.652 69 2 1 4096 4164 63546845 63546912 4.400000e-20 110.0
6 TraesCS5B01G056000 chr5A 94.783 3412 127 12 1 3385 46707853 46711240 0.000000e+00 5267.0
7 TraesCS5B01G056000 chr5A 84.857 1017 140 10 2032 3038 47540567 47539555 0.000000e+00 1013.0
8 TraesCS5B01G056000 chr5A 83.350 973 150 8 2073 3038 47460990 47460023 0.000000e+00 889.0
9 TraesCS5B01G056000 chr5A 83.023 483 58 19 3533 4011 46713456 46713918 2.320000e-112 416.0
10 TraesCS5B01G056000 chr5A 74.521 679 149 21 1106 1769 47461967 47461298 1.470000e-69 274.0
11 TraesCS5B01G056000 chr5A 79.167 96 19 1 3757 3851 466571089 466570994 9.660000e-07 65.8
12 TraesCS5B01G056000 chr5D 96.182 2724 74 6 678 3385 58500592 58503301 0.000000e+00 4427.0
13 TraesCS5B01G056000 chr5D 94.215 726 24 6 1 726 58499902 58500609 0.000000e+00 1092.0
14 TraesCS5B01G056000 chr5D 84.464 1017 144 9 2032 3038 59044253 59043241 0.000000e+00 990.0
15 TraesCS5B01G056000 chr5D 91.599 369 26 4 3385 3750 58504205 58504571 4.800000e-139 505.0
16 TraesCS5B01G056000 chr5D 84.000 350 41 9 3385 3722 507140314 507139968 5.190000e-84 322.0
17 TraesCS5B01G056000 chr5D 75.207 726 154 21 1111 1817 59045080 59044362 1.870000e-83 320.0
18 TraesCS5B01G056000 chr5D 80.609 361 53 10 3386 3734 487498933 487498578 3.190000e-66 263.0
19 TraesCS5B01G056000 chr6B 84.594 357 43 9 3385 3734 163224391 163224742 1.110000e-90 344.0
20 TraesCS5B01G056000 chr6A 84.615 338 40 9 3385 3712 103683026 103683361 4.010000e-85 326.0
21 TraesCS5B01G056000 chr1B 84.181 354 36 12 3385 3724 512180081 512179734 4.010000e-85 326.0
22 TraesCS5B01G056000 chr1B 85.185 135 15 4 3385 3516 572882924 572883056 2.610000e-27 134.0
23 TraesCS5B01G056000 chr4D 82.720 353 42 11 3385 3723 51290321 51290668 3.150000e-76 296.0
24 TraesCS5B01G056000 chr3A 82.849 344 42 11 3386 3724 701240677 701240346 4.070000e-75 292.0
25 TraesCS5B01G056000 chr4B 77.447 470 98 6 2464 2926 619364309 619363841 1.470000e-69 274.0
26 TraesCS5B01G056000 chr4B 76.424 509 108 11 2470 2972 42135357 42134855 8.880000e-67 265.0
27 TraesCS5B01G056000 chr1D 81.662 349 39 11 3385 3724 423305100 423305432 2.470000e-67 267.0
28 TraesCS5B01G056000 chr1D 80.556 360 52 12 3385 3734 11976022 11975671 1.150000e-65 261.0
29 TraesCS5B01G056000 chr2B 88.128 219 21 5 3517 3733 753832166 753831951 5.340000e-64 255.0
30 TraesCS5B01G056000 chr2B 76.035 459 98 11 2313 2765 793525816 793525364 1.160000e-55 228.0
31 TraesCS5B01G056000 chr7B 80.537 298 58 0 2464 2761 40887717 40888014 3.240000e-56 230.0
32 TraesCS5B01G056000 chr7A 84.862 218 30 3 3507 3723 101466942 101466727 2.520000e-52 217.0
33 TraesCS5B01G056000 chr7A 71.837 664 151 30 2301 2945 694330643 694329997 1.550000e-34 158.0
34 TraesCS5B01G056000 chr6D 79.006 362 39 13 3385 3734 363798296 363797960 3.260000e-51 213.0
35 TraesCS5B01G056000 chr4A 79.839 124 23 2 2079 2201 573743489 573743611 5.730000e-14 89.8
36 TraesCS5B01G056000 chr3D 82.143 84 14 1 3758 3840 516184036 516184119 2.080000e-08 71.3


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 TraesCS5B01G056000 chr5B 62026233 62030396 4163 True 7690.0 7690 100.000000 1 4164 1 chr5B.!!$R1 4163
1 TraesCS5B01G056000 chr5B 63542169 63546912 4743 False 2453.0 4796 94.551500 136 4164 2 chr5B.!!$F3 4028
2 TraesCS5B01G056000 chr5B 72098413 72099404 991 False 1002.0 1002 85.025000 2050 3035 1 chr5B.!!$F2 985
3 TraesCS5B01G056000 chr5A 46707853 46713918 6065 False 2841.5 5267 88.903000 1 4011 2 chr5A.!!$F1 4010
4 TraesCS5B01G056000 chr5A 47539555 47540567 1012 True 1013.0 1013 84.857000 2032 3038 1 chr5A.!!$R1 1006
5 TraesCS5B01G056000 chr5A 47460023 47461967 1944 True 581.5 889 78.935500 1106 3038 2 chr5A.!!$R3 1932
6 TraesCS5B01G056000 chr5D 58499902 58504571 4669 False 2008.0 4427 93.998667 1 3750 3 chr5D.!!$F1 3749
7 TraesCS5B01G056000 chr5D 59043241 59045080 1839 True 655.0 990 79.835500 1111 3038 2 chr5D.!!$R3 1927
8 TraesCS5B01G056000 chr4B 42134855 42135357 502 True 265.0 265 76.424000 2470 2972 1 chr4B.!!$R1 502

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
29 30 0.394216 TGCGTTATTCTGCCCTGCAT 60.394 50.000 0.00 0.0 38.13 3.96 F
1951 2058 2.045926 AGCTCCATTGGTGCCGTC 60.046 61.111 22.68 0.0 42.42 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2076 0.465460 GACAGGCCAAGACACCAACA 60.465 55.0 5.01 0.0 0.0 3.33 R
3433 5905 0.034756 ACATGCAGCTACCGACACAA 59.965 50.0 0.00 0.0 0.0 3.33 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
29 30 0.394216 TGCGTTATTCTGCCCTGCAT 60.394 50.000 0.00 0.00 38.13 3.96
74 75 6.732896 TTTTGGTTTAGTTTGCCCAAGATA 57.267 33.333 0.00 0.00 38.16 1.98
218 219 9.489084 CTCGTGTTATATCTATTTTTGGGATCA 57.511 33.333 0.00 0.00 0.00 2.92
380 381 9.828039 TTGCCATGCATTTGTTTCATTTATATA 57.172 25.926 0.00 0.00 38.76 0.86
381 382 9.999660 TGCCATGCATTTGTTTCATTTATATAT 57.000 25.926 0.00 0.00 31.71 0.86
465 466 2.076100 TCTTCGCATGACACATGGTTC 58.924 47.619 12.56 0.00 0.00 3.62
605 609 7.159372 GGAGAACTGATAAACAAGGTACAGAA 58.841 38.462 0.00 0.00 0.00 3.02
620 624 7.497925 AGGTACAGAACTTTGAACTGAAATC 57.502 36.000 0.00 0.00 35.85 2.17
737 772 7.927788 TGGGGCAAATACTATACATGATGTAT 58.072 34.615 20.57 20.57 44.89 2.29
1847 1946 3.589735 TGGGGTAGCCTTCTTTCACATAA 59.410 43.478 11.48 0.00 0.00 1.90
1951 2058 2.045926 AGCTCCATTGGTGCCGTC 60.046 61.111 22.68 0.00 42.42 4.79
1969 2076 4.177026 CCGTCTCGTTCTTGATCATTCTT 58.823 43.478 0.00 0.00 0.00 2.52
1983 2090 2.622942 TCATTCTTGTTGGTGTCTTGGC 59.377 45.455 0.00 0.00 0.00 4.52
2647 2754 3.991051 CGGGGCTCACACACGACT 61.991 66.667 0.00 0.00 0.00 4.18
2680 2787 1.055849 CGATGGGGTACATGGATCCA 58.944 55.000 18.88 18.88 40.72 3.41
2698 2805 2.217038 AGAGTGCATGACCACCGGT 61.217 57.895 0.00 0.00 39.44 5.28
2743 2850 0.759346 ACAGCTTCGGAGTTGTCCTT 59.241 50.000 7.49 0.00 42.80 3.36
2890 3003 2.267961 GGGGAGTTTGACGGCGAT 59.732 61.111 16.62 0.00 0.00 4.58
3039 3152 0.744281 CCGGTGGCAACTTTCTTGTT 59.256 50.000 0.00 0.00 37.61 2.83
3124 3250 3.733960 CTGACACGACGGCGGAGA 61.734 66.667 18.49 0.00 43.17 3.71
3125 3251 3.263503 CTGACACGACGGCGGAGAA 62.264 63.158 18.49 0.00 43.17 2.87
3126 3252 2.504244 GACACGACGGCGGAGAAG 60.504 66.667 18.49 1.05 43.17 2.85
3127 3253 3.264866 GACACGACGGCGGAGAAGT 62.265 63.158 18.49 4.96 43.17 3.01
3128 3254 2.504244 CACGACGGCGGAGAAGTC 60.504 66.667 18.49 0.00 43.17 3.01
3131 3257 3.437795 GACGGCGGAGAAGTCGGA 61.438 66.667 13.24 0.00 44.42 4.55
3132 3258 3.398353 GACGGCGGAGAAGTCGGAG 62.398 68.421 13.24 0.00 44.42 4.63
3195 3333 5.009610 ACAAATCACTGGACGCTAAATGTTT 59.990 36.000 0.00 0.00 0.00 2.83
3196 3334 4.685169 ATCACTGGACGCTAAATGTTTG 57.315 40.909 0.00 0.00 0.00 2.93
3199 3337 4.213270 TCACTGGACGCTAAATGTTTGAAG 59.787 41.667 0.00 0.00 0.00 3.02
3396 5866 2.414559 CCGCAAATGGTGATTCTGTGTC 60.415 50.000 0.00 0.00 0.00 3.67
3400 5870 4.676196 GCAAATGGTGATTCTGTGTCATCC 60.676 45.833 0.00 0.00 0.00 3.51
3401 5871 4.305539 AATGGTGATTCTGTGTCATCCA 57.694 40.909 0.00 0.00 34.04 3.41
3436 5908 9.889128 CTCATATTTATGTGGGGAAATTTTTGT 57.111 29.630 0.00 0.00 35.26 2.83
3480 5952 4.682778 TTGGTGCTATACAGTATCACCC 57.317 45.455 21.04 9.14 44.81 4.61
3482 5954 2.889045 GGTGCTATACAGTATCACCCGA 59.111 50.000 16.07 0.00 40.84 5.14
3487 5959 0.671796 TACAGTATCACCCGATGGCG 59.328 55.000 0.00 0.00 32.73 5.69
3526 6000 4.705023 GTGGAGGGTGCACTATGTTTTTAT 59.295 41.667 17.98 0.00 35.71 1.40
3551 6025 4.241681 GCCGGTTTTTGCTGATTGATTTA 58.758 39.130 1.90 0.00 0.00 1.40
3553 6027 5.163963 GCCGGTTTTTGCTGATTGATTTAAG 60.164 40.000 1.90 0.00 0.00 1.85
3633 6108 4.021102 TGAAGAGCTTCAAAACTAGGGG 57.979 45.455 10.30 0.00 45.56 4.79
3689 6164 3.592059 TCCTTAAGAAATTGTCGACCCG 58.408 45.455 14.12 0.00 0.00 5.28
3700 6175 1.079681 TCGACCCGGTCAAAATCGG 60.080 57.895 17.87 0.00 45.29 4.18
3724 6199 8.028938 CGGGTGACTCAATTTTAAATTGAAGAT 58.971 33.333 26.50 17.87 37.55 2.40
3760 6257 9.520515 AAATTAGGAAGCATAGAGAGTTTTGAA 57.479 29.630 0.00 0.00 0.00 2.69
3789 6286 0.953960 ACCCGGTCAAAATCGAGTGC 60.954 55.000 0.00 0.00 0.00 4.40
3798 6295 4.853743 GTCAAAATCGAGTGCTCCAATTTC 59.146 41.667 0.00 0.00 0.00 2.17
3801 6298 5.452078 AAATCGAGTGCTCCAATTTCAAA 57.548 34.783 0.00 0.00 0.00 2.69
3804 6301 3.191162 TCGAGTGCTCCAATTTCAAATGG 59.809 43.478 0.00 0.00 38.09 3.16
3834 6331 9.350357 CATCAATTGATTGTGAGTCCTTTAAAG 57.650 33.333 18.41 8.32 38.84 1.85
3855 6352 7.932683 AAAGTTAGGGAGCCTAGTGTTATAT 57.067 36.000 0.00 0.00 37.42 0.86
3885 6382 2.011947 CAGTGTGGATCGCAATGATGT 58.988 47.619 9.72 0.00 41.52 3.06
3891 6388 3.059325 GTGGATCGCAATGATGTAGAAGC 60.059 47.826 0.00 0.00 37.47 3.86
3903 6400 3.308035 TGTAGAAGCCGAGGGAGATTA 57.692 47.619 0.00 0.00 0.00 1.75
3962 6459 2.361757 TGCCACTTGTCATCACAAAAGG 59.638 45.455 0.00 0.00 42.13 3.11
3968 6465 4.766891 ACTTGTCATCACAAAAGGGGTATG 59.233 41.667 0.00 0.00 42.13 2.39
3970 6467 4.735369 TGTCATCACAAAAGGGGTATGTT 58.265 39.130 0.00 0.00 0.00 2.71
3971 6468 5.882040 TGTCATCACAAAAGGGGTATGTTA 58.118 37.500 0.00 0.00 0.00 2.41
3972 6469 5.708230 TGTCATCACAAAAGGGGTATGTTAC 59.292 40.000 0.00 0.00 0.00 2.50
3973 6470 5.944007 GTCATCACAAAAGGGGTATGTTACT 59.056 40.000 0.00 0.00 0.00 2.24
3974 6471 6.093633 GTCATCACAAAAGGGGTATGTTACTC 59.906 42.308 0.00 0.00 0.00 2.59
3992 6489 7.152645 TGTTACTCCTTGACTAGTGATTTCAC 58.847 38.462 0.00 2.41 46.77 3.18
4043 6540 7.801716 TGTTGAAGTATAATCAATGTAGGCC 57.198 36.000 0.00 0.00 38.89 5.19
4044 6541 6.481976 TGTTGAAGTATAATCAATGTAGGCCG 59.518 38.462 0.00 0.00 38.89 6.13
4045 6542 6.169557 TGAAGTATAATCAATGTAGGCCGT 57.830 37.500 0.00 0.00 0.00 5.68
4046 6543 6.220930 TGAAGTATAATCAATGTAGGCCGTC 58.779 40.000 0.00 0.00 0.00 4.79
4047 6544 5.801531 AGTATAATCAATGTAGGCCGTCA 57.198 39.130 0.00 0.31 0.00 4.35
4048 6545 6.169557 AGTATAATCAATGTAGGCCGTCAA 57.830 37.500 0.00 0.00 0.00 3.18
4049 6546 6.588204 AGTATAATCAATGTAGGCCGTCAAA 58.412 36.000 0.00 0.00 0.00 2.69
4050 6547 7.051623 AGTATAATCAATGTAGGCCGTCAAAA 58.948 34.615 0.00 0.00 0.00 2.44
4051 6548 6.767524 ATAATCAATGTAGGCCGTCAAAAA 57.232 33.333 0.00 0.00 0.00 1.94
4052 6549 4.701956 ATCAATGTAGGCCGTCAAAAAG 57.298 40.909 0.00 0.00 0.00 2.27
4053 6550 3.745799 TCAATGTAGGCCGTCAAAAAGA 58.254 40.909 0.00 0.00 0.00 2.52
4054 6551 4.138290 TCAATGTAGGCCGTCAAAAAGAA 58.862 39.130 0.00 0.00 0.00 2.52
4055 6552 4.215399 TCAATGTAGGCCGTCAAAAAGAAG 59.785 41.667 0.00 0.00 0.00 2.85
4056 6553 3.478857 TGTAGGCCGTCAAAAAGAAGA 57.521 42.857 0.00 0.00 0.00 2.87
4057 6554 3.399330 TGTAGGCCGTCAAAAAGAAGAG 58.601 45.455 0.00 0.00 0.00 2.85
4058 6555 2.930826 AGGCCGTCAAAAAGAAGAGA 57.069 45.000 0.00 0.00 0.00 3.10
4059 6556 3.208747 AGGCCGTCAAAAAGAAGAGAA 57.791 42.857 0.00 0.00 0.00 2.87
4060 6557 3.551846 AGGCCGTCAAAAAGAAGAGAAA 58.448 40.909 0.00 0.00 0.00 2.52
4061 6558 3.951680 AGGCCGTCAAAAAGAAGAGAAAA 59.048 39.130 0.00 0.00 0.00 2.29
4062 6559 4.401202 AGGCCGTCAAAAAGAAGAGAAAAA 59.599 37.500 0.00 0.00 0.00 1.94
4063 6560 4.503007 GGCCGTCAAAAAGAAGAGAAAAAC 59.497 41.667 0.00 0.00 0.00 2.43
4064 6561 5.099575 GCCGTCAAAAAGAAGAGAAAAACA 58.900 37.500 0.00 0.00 0.00 2.83
4065 6562 5.230097 GCCGTCAAAAAGAAGAGAAAAACAG 59.770 40.000 0.00 0.00 0.00 3.16
4066 6563 6.322491 CCGTCAAAAAGAAGAGAAAAACAGT 58.678 36.000 0.00 0.00 0.00 3.55
4067 6564 6.251376 CCGTCAAAAAGAAGAGAAAAACAGTG 59.749 38.462 0.00 0.00 0.00 3.66
4068 6565 6.801862 CGTCAAAAAGAAGAGAAAAACAGTGT 59.198 34.615 0.00 0.00 0.00 3.55
4069 6566 7.326063 CGTCAAAAAGAAGAGAAAAACAGTGTT 59.674 33.333 1.64 1.64 0.00 3.32
4070 6567 9.620660 GTCAAAAAGAAGAGAAAAACAGTGTTA 57.379 29.630 9.37 0.00 0.00 2.41
4081 6578 9.366216 GAGAAAAACAGTGTTAAAATTGAACCT 57.634 29.630 9.37 0.00 0.00 3.50
4153 6664 1.692411 AACCCACTTGAGTTGCCTTC 58.308 50.000 0.00 0.00 0.00 3.46
4155 6666 1.215423 ACCCACTTGAGTTGCCTTCTT 59.785 47.619 0.00 0.00 0.00 2.52
4156 6667 2.310538 CCCACTTGAGTTGCCTTCTTT 58.689 47.619 0.00 0.00 0.00 2.52
4157 6668 3.117663 ACCCACTTGAGTTGCCTTCTTTA 60.118 43.478 0.00 0.00 0.00 1.85
4159 6670 4.524328 CCCACTTGAGTTGCCTTCTTTATT 59.476 41.667 0.00 0.00 0.00 1.40
4160 6671 5.710099 CCCACTTGAGTTGCCTTCTTTATTA 59.290 40.000 0.00 0.00 0.00 0.98
4163 6674 8.306761 CCACTTGAGTTGCCTTCTTTATTATTT 58.693 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.577848 ACAATACAAAATGCAGGGCAGAA 59.422 39.130 0.00 0.00 43.65 3.02
22 23 4.389687 GCAAGAACAATACAAAATGCAGGG 59.610 41.667 0.00 0.00 33.00 4.45
29 30 3.640967 AGCAGGGCAAGAACAATACAAAA 59.359 39.130 0.00 0.00 0.00 2.44
218 219 5.659079 AGAGTTCTCCATCTTCGTTAAGGAT 59.341 40.000 0.00 0.00 33.22 3.24
605 609 5.179555 GGAACTAGCGATTTCAGTTCAAAGT 59.820 40.000 14.71 0.00 46.45 2.66
620 624 2.732619 GGGGTCTGGGGAACTAGCG 61.733 68.421 0.00 0.00 39.11 4.26
1951 2058 5.180117 ACCAACAAGAATGATCAAGAACGAG 59.820 40.000 0.00 0.00 0.00 4.18
1969 2076 0.465460 GACAGGCCAAGACACCAACA 60.465 55.000 5.01 0.00 0.00 3.33
1983 2090 0.677098 TCGTCGGAGAAGGAGACAGG 60.677 60.000 0.00 0.00 39.69 4.00
2225 2332 2.099994 CCTCGAGGTTCGACTCCTC 58.900 63.158 24.04 19.95 44.82 3.71
2371 2478 0.528017 CGTAGACAAGGAGCAGCTCA 59.472 55.000 24.09 0.00 31.08 4.26
2680 2787 2.217038 ACCGGTGGTCATGCACTCT 61.217 57.895 6.12 0.00 0.00 3.24
2698 2805 3.807538 GACTCGGCGCTGGTACGA 61.808 66.667 17.88 11.06 34.06 3.43
2743 2850 2.496341 CCGCAGGCAATCTCGAGA 59.504 61.111 19.19 19.19 46.14 4.04
2890 3003 1.227060 CATCACGCGCTCCATCTCA 60.227 57.895 5.73 0.00 0.00 3.27
3039 3152 0.179234 TGGAACTTGAACCAGCACGA 59.821 50.000 0.00 0.00 0.00 4.35
3124 3250 1.130749 CGACATCGACTTCTCCGACTT 59.869 52.381 0.00 0.00 43.02 3.01
3125 3251 0.727970 CGACATCGACTTCTCCGACT 59.272 55.000 0.00 0.00 43.02 4.18
3126 3252 0.725686 TCGACATCGACTTCTCCGAC 59.274 55.000 0.00 0.00 44.22 4.79
3127 3253 3.148340 TCGACATCGACTTCTCCGA 57.852 52.632 0.00 0.00 44.22 4.55
3195 3333 4.850680 AGCGTATTAATTTGTCCCCTTCA 58.149 39.130 0.00 0.00 0.00 3.02
3196 3334 4.879545 TGAGCGTATTAATTTGTCCCCTTC 59.120 41.667 0.00 0.00 0.00 3.46
3199 3337 4.196971 ACTGAGCGTATTAATTTGTCCCC 58.803 43.478 0.00 0.00 0.00 4.81
3369 3510 3.117888 AGAATCACCATTTGCGGGTAGAT 60.118 43.478 0.00 0.00 36.72 1.98
3433 5905 0.034756 ACATGCAGCTACCGACACAA 59.965 50.000 0.00 0.00 0.00 3.33
3436 5908 1.182667 AGTACATGCAGCTACCGACA 58.817 50.000 0.00 0.00 0.00 4.35
3502 5976 1.362224 AACATAGTGCACCCTCCACT 58.638 50.000 14.63 0.00 44.99 4.00
3526 6000 1.543802 CAATCAGCAAAAACCGGCCTA 59.456 47.619 0.00 0.00 0.00 3.93
3551 6025 6.697019 CGATTTTGATCGGCCAATTATTTCTT 59.303 34.615 2.24 0.00 40.12 2.52
3553 6027 6.438327 CGATTTTGATCGGCCAATTATTTC 57.562 37.500 2.24 0.00 40.12 2.17
3669 6144 2.676342 CCGGGTCGACAATTTCTTAAGG 59.324 50.000 18.91 1.27 0.00 2.69
3689 6164 2.178912 TGAGTCACCCGATTTTGACC 57.821 50.000 0.00 0.00 42.73 4.02
3760 6257 2.131776 TTGACCGGGTCAACACTTTT 57.868 45.000 33.05 0.00 45.88 2.27
3783 6280 3.191162 TCCATTTGAAATTGGAGCACTCG 59.809 43.478 3.15 0.00 37.10 4.18
3784 6281 4.789012 TCCATTTGAAATTGGAGCACTC 57.211 40.909 3.15 0.00 37.10 3.51
3798 6295 7.317390 TCACAATCAATTGATGTCTCCATTTG 58.683 34.615 21.39 14.73 40.14 2.32
3801 6298 6.185511 ACTCACAATCAATTGATGTCTCCAT 58.814 36.000 21.39 1.16 40.14 3.41
3804 6301 5.879223 AGGACTCACAATCAATTGATGTCTC 59.121 40.000 21.39 15.29 40.14 3.36
3809 6306 9.082313 ACTTTAAAGGACTCACAATCAATTGAT 57.918 29.630 15.36 15.36 40.14 2.57
3834 6331 7.180663 TCCTATATAACACTAGGCTCCCTAAC 58.819 42.308 0.00 0.00 35.49 2.34
3838 6335 8.005388 TCATATCCTATATAACACTAGGCTCCC 58.995 40.741 0.00 0.00 35.46 4.30
3855 6352 3.255888 GCGATCCACACTGTCATATCCTA 59.744 47.826 0.00 0.00 0.00 2.94
3870 6367 3.133691 GCTTCTACATCATTGCGATCCA 58.866 45.455 0.00 0.00 29.21 3.41
3885 6382 4.742012 AGAATAATCTCCCTCGGCTTCTA 58.258 43.478 0.00 0.00 0.00 2.10
3891 6388 8.732746 TTTAGAAAAAGAATAATCTCCCTCGG 57.267 34.615 0.00 0.00 33.77 4.63
3962 6459 5.655532 TCACTAGTCAAGGAGTAACATACCC 59.344 44.000 0.00 0.00 0.00 3.69
3968 6465 6.590677 GGTGAAATCACTAGTCAAGGAGTAAC 59.409 42.308 12.87 0.00 45.73 2.50
3970 6467 6.017192 AGGTGAAATCACTAGTCAAGGAGTA 58.983 40.000 12.87 0.00 45.73 2.59
3971 6468 4.841246 AGGTGAAATCACTAGTCAAGGAGT 59.159 41.667 12.87 0.00 45.73 3.85
3972 6469 5.413309 AGGTGAAATCACTAGTCAAGGAG 57.587 43.478 12.87 0.00 45.73 3.69
3973 6470 5.825593 AAGGTGAAATCACTAGTCAAGGA 57.174 39.130 12.87 0.00 45.73 3.36
3974 6471 6.884280 AAAAGGTGAAATCACTAGTCAAGG 57.116 37.500 12.87 0.00 45.73 3.61
4017 6514 8.682710 GGCCTACATTGATTATACTTCAACAAA 58.317 33.333 0.00 0.00 36.02 2.83
4018 6515 7.011950 CGGCCTACATTGATTATACTTCAACAA 59.988 37.037 0.00 0.00 36.02 2.83
4019 6516 6.481976 CGGCCTACATTGATTATACTTCAACA 59.518 38.462 0.00 0.00 36.02 3.33
4020 6517 6.482308 ACGGCCTACATTGATTATACTTCAAC 59.518 38.462 0.00 0.00 36.02 3.18
4021 6518 6.588204 ACGGCCTACATTGATTATACTTCAA 58.412 36.000 0.00 0.97 37.49 2.69
4022 6519 6.169557 ACGGCCTACATTGATTATACTTCA 57.830 37.500 0.00 0.00 0.00 3.02
4023 6520 6.220930 TGACGGCCTACATTGATTATACTTC 58.779 40.000 0.00 0.00 0.00 3.01
4024 6521 6.169557 TGACGGCCTACATTGATTATACTT 57.830 37.500 0.00 0.00 0.00 2.24
4025 6522 5.801531 TGACGGCCTACATTGATTATACT 57.198 39.130 0.00 0.00 0.00 2.12
4026 6523 6.854496 TTTGACGGCCTACATTGATTATAC 57.146 37.500 0.00 0.00 0.00 1.47
4027 6524 7.771361 TCTTTTTGACGGCCTACATTGATTATA 59.229 33.333 0.00 0.00 0.00 0.98
4028 6525 6.601613 TCTTTTTGACGGCCTACATTGATTAT 59.398 34.615 0.00 0.00 0.00 1.28
4029 6526 5.941058 TCTTTTTGACGGCCTACATTGATTA 59.059 36.000 0.00 0.00 0.00 1.75
4030 6527 4.764823 TCTTTTTGACGGCCTACATTGATT 59.235 37.500 0.00 0.00 0.00 2.57
4031 6528 4.331968 TCTTTTTGACGGCCTACATTGAT 58.668 39.130 0.00 0.00 0.00 2.57
4032 6529 3.745799 TCTTTTTGACGGCCTACATTGA 58.254 40.909 0.00 0.00 0.00 2.57
4033 6530 4.215399 TCTTCTTTTTGACGGCCTACATTG 59.785 41.667 0.00 0.00 0.00 2.82
4034 6531 4.394729 TCTTCTTTTTGACGGCCTACATT 58.605 39.130 0.00 0.00 0.00 2.71
4035 6532 4.003648 CTCTTCTTTTTGACGGCCTACAT 58.996 43.478 0.00 0.00 0.00 2.29
4036 6533 3.070446 TCTCTTCTTTTTGACGGCCTACA 59.930 43.478 0.00 0.00 0.00 2.74
4037 6534 3.660865 TCTCTTCTTTTTGACGGCCTAC 58.339 45.455 0.00 0.00 0.00 3.18
4038 6535 4.345859 TTCTCTTCTTTTTGACGGCCTA 57.654 40.909 0.00 0.00 0.00 3.93
4039 6536 2.930826 TCTCTTCTTTTTGACGGCCT 57.069 45.000 0.00 0.00 0.00 5.19
4040 6537 3.982576 TTTCTCTTCTTTTTGACGGCC 57.017 42.857 0.00 0.00 0.00 6.13
4041 6538 5.099575 TGTTTTTCTCTTCTTTTTGACGGC 58.900 37.500 0.00 0.00 0.00 5.68
4042 6539 6.251376 CACTGTTTTTCTCTTCTTTTTGACGG 59.749 38.462 0.00 0.00 0.00 4.79
4043 6540 6.801862 ACACTGTTTTTCTCTTCTTTTTGACG 59.198 34.615 0.00 0.00 0.00 4.35
4044 6541 8.520835 AACACTGTTTTTCTCTTCTTTTTGAC 57.479 30.769 0.00 0.00 0.00 3.18
4054 6551 9.366216 GGTTCAATTTTAACACTGTTTTTCTCT 57.634 29.630 0.00 0.00 0.00 3.10
4055 6552 9.366216 AGGTTCAATTTTAACACTGTTTTTCTC 57.634 29.630 0.00 0.00 0.00 2.87
4056 6553 9.366216 GAGGTTCAATTTTAACACTGTTTTTCT 57.634 29.630 0.00 0.00 0.00 2.52
4057 6554 8.318167 CGAGGTTCAATTTTAACACTGTTTTTC 58.682 33.333 0.00 0.00 0.00 2.29
4058 6555 7.201487 GCGAGGTTCAATTTTAACACTGTTTTT 60.201 33.333 0.00 0.00 0.00 1.94
4059 6556 6.254804 GCGAGGTTCAATTTTAACACTGTTTT 59.745 34.615 0.00 0.00 0.00 2.43
4060 6557 5.746721 GCGAGGTTCAATTTTAACACTGTTT 59.253 36.000 0.00 0.00 0.00 2.83
4061 6558 5.067283 AGCGAGGTTCAATTTTAACACTGTT 59.933 36.000 0.00 0.00 0.00 3.16
4062 6559 4.578928 AGCGAGGTTCAATTTTAACACTGT 59.421 37.500 0.00 0.00 0.00 3.55
4063 6560 5.108385 AGCGAGGTTCAATTTTAACACTG 57.892 39.130 0.00 0.00 0.00 3.66
4064 6561 5.767816 AAGCGAGGTTCAATTTTAACACT 57.232 34.783 0.00 0.00 0.00 3.55
4065 6562 7.917720 TTAAAGCGAGGTTCAATTTTAACAC 57.082 32.000 0.00 0.00 0.00 3.32
4066 6563 8.192110 AGTTTAAAGCGAGGTTCAATTTTAACA 58.808 29.630 0.00 0.00 29.48 2.41
4067 6564 8.476925 CAGTTTAAAGCGAGGTTCAATTTTAAC 58.523 33.333 0.00 0.00 0.00 2.01
4068 6565 8.407064 TCAGTTTAAAGCGAGGTTCAATTTTAA 58.593 29.630 0.00 0.00 0.00 1.52
4069 6566 7.932335 TCAGTTTAAAGCGAGGTTCAATTTTA 58.068 30.769 0.00 0.00 0.00 1.52
4070 6567 6.801575 TCAGTTTAAAGCGAGGTTCAATTTT 58.198 32.000 0.00 0.00 0.00 1.82
4081 6578 0.790207 CGCAGCTCAGTTTAAAGCGA 59.210 50.000 9.38 0.00 45.78 4.93


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

AutoCloner maintained by Alex Coulton.