Multiple sequence alignment - TraesCS6A01G111300

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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 TraesCS6A01G111300 chr6A 100.000 4342 0 0 1 4342 80697062 80692721 0.000000e+00 8019.0
1 TraesCS6A01G111300 chr6B 91.648 2203 89 40 523 2693 136511374 136509235 0.000000e+00 2961.0
2 TraesCS6A01G111300 chr6B 83.234 1175 87 46 2692 3795 136509108 136507973 0.000000e+00 977.0
3 TraesCS6A01G111300 chr6B 85.499 531 58 15 1 528 136512198 136511684 1.780000e-148 536.0
4 TraesCS6A01G111300 chr6B 83.934 361 23 22 523 879 136520245 136519916 3.260000e-81 313.0
5 TraesCS6A01G111300 chr6D 93.188 1468 42 20 1253 2695 62895569 62894135 0.000000e+00 2104.0
6 TraesCS6A01G111300 chr6D 86.527 1670 156 30 1433 3071 63043910 63042279 0.000000e+00 1773.0
7 TraesCS6A01G111300 chr6D 92.219 1221 74 11 2797 4006 62893802 62892592 0.000000e+00 1709.0
8 TraesCS6A01G111300 chr6D 84.779 565 57 14 8 568 62896736 62896197 1.370000e-149 540.0
9 TraesCS6A01G111300 chr6D 86.214 457 44 10 941 1396 63117658 63117220 1.090000e-130 477.0
10 TraesCS6A01G111300 chr6D 93.233 266 14 2 4077 4342 62892438 62892177 5.270000e-104 388.0
11 TraesCS6A01G111300 chr6D 82.583 333 22 15 748 1079 62896158 62895861 1.200000e-65 261.0
12 TraesCS6A01G111300 chr6D 96.875 64 1 1 4002 4065 62892563 62892501 5.940000e-19 106.0
13 TraesCS6A01G111300 chr7A 74.947 1413 244 68 1009 2387 28514452 28515788 8.210000e-152 547.0
14 TraesCS6A01G111300 chrUn 73.786 1030 190 53 1471 2460 81878615 81877626 2.500000e-87 333.0
15 TraesCS6A01G111300 chrUn 75.717 593 104 28 1471 2048 81861755 81861188 1.200000e-65 261.0
16 TraesCS6A01G111300 chr4A 81.173 324 50 7 1052 1372 701941264 701941579 2.590000e-62 250.0
17 TraesCS6A01G111300 chr4A 75.936 561 92 25 1488 2028 702029680 702029143 9.320000e-62 248.0
18 TraesCS6A01G111300 chr4A 79.508 366 53 9 1009 1372 702030063 702029718 1.560000e-59 241.0
19 TraesCS6A01G111300 chr5A 81.771 192 35 0 1022 1213 447547026 447546835 1.250000e-35 161.0
20 TraesCS6A01G111300 chr5A 91.667 48 4 0 2312 2359 547404646 547404599 2.800000e-07 67.6
21 TraesCS6A01G111300 chr5A 95.000 40 2 0 2319 2358 547552293 547552332 3.630000e-06 63.9
22 TraesCS6A01G111300 chr5A 94.737 38 2 0 2321 2358 547510065 547510102 4.690000e-05 60.2
23 TraesCS6A01G111300 chr5D 97.500 40 1 0 2319 2358 432996465 432996504 7.790000e-08 69.4
24 TraesCS6A01G111300 chr5D 95.000 40 2 0 2319 2358 432805604 432805565 3.630000e-06 63.9
25 TraesCS6A01G111300 chr5B 97.500 40 1 0 2319 2358 526519026 526519065 7.790000e-08 69.4


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 TraesCS6A01G111300 chr6A 80692721 80697062 4341 True 8019.000000 8019 100.000000 1 4342 1 chr6A.!!$R1 4341
1 TraesCS6A01G111300 chr6B 136507973 136512198 4225 True 1491.333333 2961 86.793667 1 3795 3 chr6B.!!$R2 3794
2 TraesCS6A01G111300 chr6D 63042279 63043910 1631 True 1773.000000 1773 86.527000 1433 3071 1 chr6D.!!$R1 1638
3 TraesCS6A01G111300 chr6D 62892177 62896736 4559 True 851.333333 2104 90.479500 8 4342 6 chr6D.!!$R3 4334
4 TraesCS6A01G111300 chr7A 28514452 28515788 1336 False 547.000000 547 74.947000 1009 2387 1 chr7A.!!$F1 1378
5 TraesCS6A01G111300 chrUn 81877626 81878615 989 True 333.000000 333 73.786000 1471 2460 1 chrUn.!!$R2 989
6 TraesCS6A01G111300 chrUn 81861188 81861755 567 True 261.000000 261 75.717000 1471 2048 1 chrUn.!!$R1 577
7 TraesCS6A01G111300 chr4A 702029143 702030063 920 True 244.500000 248 77.722000 1009 2028 2 chr4A.!!$R1 1019

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
966 1305 0.322546 AGACAACCCATTCGGCTTCC 60.323 55.0 0.0 0.0 33.26 3.46 F
2337 2864 0.689412 TCCATCCCTACGTCATGGCA 60.689 55.0 0.0 0.0 37.57 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2859 3649 1.007238 AGCTTGGGGTAGACAGAGCTA 59.993 52.381 0.00 0.0 38.58 3.32 R
3816 4683 0.529378 GGCTTGTTGCAGGATCAAGG 59.471 55.000 13.05 0.0 45.15 3.61 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
26 27 0.393808 AAACACGCCAGACCAACTGT 60.394 50.000 0.00 0.00 44.40 3.55
27 28 0.393808 AACACGCCAGACCAACTGTT 60.394 50.000 0.00 0.00 44.40 3.16
31 32 1.557443 CGCCAGACCAACTGTTCGAC 61.557 60.000 0.00 0.00 44.40 4.20
41 42 2.794910 CAACTGTTCGACGATCAACACT 59.205 45.455 9.70 0.00 0.00 3.55
47 48 3.066369 TCGACGATCAACACTATGCTC 57.934 47.619 0.00 0.00 0.00 4.26
88 89 5.280499 TCCAAGGAAGGAGATCAACATAGA 58.720 41.667 0.00 0.00 32.77 1.98
95 96 6.407979 GGAAGGAGATCAACATAGAGAAAGCT 60.408 42.308 0.00 0.00 0.00 3.74
119 120 9.507329 GCTGAGAAATAATTATTCCTATCACCA 57.493 33.333 11.08 6.79 0.00 4.17
127 128 1.264749 TTCCTATCACCACCGCTGCT 61.265 55.000 0.00 0.00 0.00 4.24
155 156 0.393537 ACCGACGACGAAGACCCTAT 60.394 55.000 9.28 0.00 42.66 2.57
324 326 6.983474 AAAGGAAATGGTTTCAACTTGTTG 57.017 33.333 7.13 7.13 41.43 3.33
375 378 4.980590 TCTGACAAACACACACACATTTC 58.019 39.130 0.00 0.00 0.00 2.17
382 385 6.255453 ACAAACACACACACATTTCTTTATGC 59.745 34.615 0.00 0.00 0.00 3.14
385 388 6.514947 ACACACACACATTTCTTTATGCATT 58.485 32.000 3.54 0.00 0.00 3.56
390 393 9.142515 CACACACATTTCTTTATGCATTAACAT 57.857 29.630 3.54 0.00 0.00 2.71
649 967 6.488817 ACACGTGAACATTTTTAAGGTACAC 58.511 36.000 25.01 0.00 0.00 2.90
650 968 6.093771 ACACGTGAACATTTTTAAGGTACACA 59.906 34.615 25.01 0.00 0.00 3.72
651 969 7.136119 CACGTGAACATTTTTAAGGTACACAT 58.864 34.615 10.90 0.00 0.00 3.21
860 1185 2.001159 GTCGCAGTTAGAGAGACGAGA 58.999 52.381 0.00 0.00 0.00 4.04
863 1188 2.286713 CGCAGTTAGAGAGACGAGATGG 60.287 54.545 0.00 0.00 0.00 3.51
901 1240 3.930504 GACGGACCTGGGTCGTAT 58.069 61.111 14.67 1.87 45.41 3.06
902 1241 1.732308 GACGGACCTGGGTCGTATC 59.268 63.158 14.67 7.11 45.41 2.24
929 1268 3.877508 GGTGGATAAAAGTCATTCGGGAG 59.122 47.826 0.00 0.00 0.00 4.30
939 1278 1.621814 TCATTCGGGAGTTCTTTCCGT 59.378 47.619 12.40 0.00 43.75 4.69
965 1304 1.087501 GAGACAACCCATTCGGCTTC 58.912 55.000 0.00 0.00 33.26 3.86
966 1305 0.322546 AGACAACCCATTCGGCTTCC 60.323 55.000 0.00 0.00 33.26 3.46
967 1306 1.304134 ACAACCCATTCGGCTTCCC 60.304 57.895 0.00 0.00 33.26 3.97
968 1307 2.052104 CAACCCATTCGGCTTCCCC 61.052 63.158 0.00 0.00 33.26 4.81
969 1308 3.296842 AACCCATTCGGCTTCCCCC 62.297 63.158 0.00 0.00 33.26 5.40
970 1309 3.738481 CCCATTCGGCTTCCCCCA 61.738 66.667 0.00 0.00 0.00 4.96
971 1310 2.124151 CCATTCGGCTTCCCCCAG 60.124 66.667 0.00 0.00 0.00 4.45
972 1311 2.679342 CCATTCGGCTTCCCCCAGA 61.679 63.158 0.00 0.00 0.00 3.86
1489 1956 2.159310 AGCGACGAAGAAGATGAGAAGG 60.159 50.000 0.00 0.00 0.00 3.46
1491 1958 3.690422 CGACGAAGAAGATGAGAAGGAG 58.310 50.000 0.00 0.00 0.00 3.69
1793 2289 2.190578 GGGGAGCACCGAGATTGG 59.809 66.667 0.00 0.00 41.60 3.16
1821 2317 4.465305 CAGATTTTCCCTGAGCCTTTGATT 59.535 41.667 0.00 0.00 33.65 2.57
1824 2320 1.371467 TCCCTGAGCCTTTGATTCCA 58.629 50.000 0.00 0.00 0.00 3.53
2304 2828 3.370366 CGGAGCTGAAAAAGATCTGTGAG 59.630 47.826 0.00 0.00 41.88 3.51
2337 2864 0.689412 TCCATCCCTACGTCATGGCA 60.689 55.000 0.00 0.00 37.57 4.92
2411 2940 6.127394 TGCATGTGAAAATGTTGCTGGTATAT 60.127 34.615 0.00 0.00 34.47 0.86
2412 2941 7.067981 TGCATGTGAAAATGTTGCTGGTATATA 59.932 33.333 0.00 0.00 34.47 0.86
2490 3034 4.016444 GGATTGTTGTGGGAATCTGCTAA 58.984 43.478 0.00 0.00 0.00 3.09
2498 3042 1.559682 GGGAATCTGCTAACCCACTCA 59.440 52.381 0.00 0.00 41.72 3.41
2713 3390 1.133513 TGTTGGGTTCCATTCTGCTGT 60.134 47.619 0.00 0.00 31.53 4.40
2728 3405 1.630244 GCTGTCTGCTTACCGCACTG 61.630 60.000 0.00 0.00 45.47 3.66
2771 3448 2.128853 AACATCGGTGGCTTTGCGTG 62.129 55.000 0.00 0.00 0.00 5.34
2793 3473 7.442657 CGTGTTTTAATACCGAGTAGAAACAG 58.557 38.462 15.21 10.32 33.92 3.16
2812 3596 5.304686 ACAGACTACTTGTTTTGGGATGA 57.695 39.130 0.00 0.00 0.00 2.92
2859 3649 2.502745 TCTTTAGGGCCCCAATGATCT 58.497 47.619 21.43 0.00 0.00 2.75
2927 3717 2.362120 GCCCAACAGAGCCTGCAT 60.362 61.111 0.00 0.00 34.37 3.96
2929 3719 2.110967 CCCAACAGAGCCTGCATCG 61.111 63.158 0.00 0.00 34.37 3.84
2930 3720 2.110967 CCAACAGAGCCTGCATCGG 61.111 63.158 0.00 0.00 34.37 4.18
3014 3808 4.078537 TGATTTGCATAATGGGATACGGG 58.921 43.478 0.00 0.00 37.60 5.28
3016 3810 0.321210 TGCATAATGGGATACGGGCG 60.321 55.000 0.00 0.00 37.60 6.13
3090 3884 4.842948 TCTATAGCCTCTGCATCTCCAAAT 59.157 41.667 0.00 0.00 41.13 2.32
3094 3888 3.194968 AGCCTCTGCATCTCCAAATTTTG 59.805 43.478 1.99 1.99 41.13 2.44
3118 3912 4.454678 AGAATGCGCCTGAGATGATTTTA 58.545 39.130 4.18 0.00 0.00 1.52
3193 4001 2.507407 TGGTACCCTTTTGGATGCTC 57.493 50.000 10.07 0.00 44.07 4.26
3229 4037 6.642683 TTCCTAGCTTTTAAATTCGACTCG 57.357 37.500 0.00 0.00 0.00 4.18
3255 4063 3.795623 AAACATTGCAGGATCAGATGC 57.204 42.857 9.22 9.22 42.86 3.91
3293 4101 8.789762 CAGATTTCCAATGCACTATATTGATGA 58.210 33.333 0.00 0.00 37.65 2.92
3294 4102 9.358406 AGATTTCCAATGCACTATATTGATGAA 57.642 29.630 0.00 0.00 37.65 2.57
3296 4104 9.923143 ATTTCCAATGCACTATATTGATGAATG 57.077 29.630 0.00 0.00 37.65 2.67
3297 4105 8.694581 TTCCAATGCACTATATTGATGAATGA 57.305 30.769 0.00 0.00 37.65 2.57
3298 4106 8.873186 TCCAATGCACTATATTGATGAATGAT 57.127 30.769 0.00 0.00 37.65 2.45
3299 4107 8.736244 TCCAATGCACTATATTGATGAATGATG 58.264 33.333 0.00 0.00 37.65 3.07
3347 4161 7.121463 TGTTCTTGTAGGATCACTTAGAGACTC 59.879 40.741 0.00 0.00 0.00 3.36
3404 4230 6.630444 GGTTGATGATGACTCAAGCAATAT 57.370 37.500 9.60 0.00 45.72 1.28
3405 4231 6.436261 GGTTGATGATGACTCAAGCAATATG 58.564 40.000 9.60 0.00 45.72 1.78
3406 4232 6.039047 GGTTGATGATGACTCAAGCAATATGT 59.961 38.462 9.60 0.00 45.72 2.29
3407 4233 7.227314 GGTTGATGATGACTCAAGCAATATGTA 59.773 37.037 9.60 0.00 45.72 2.29
3408 4234 8.781196 GTTGATGATGACTCAAGCAATATGTAT 58.219 33.333 0.00 0.00 34.41 2.29
3409 4235 8.319143 TGATGATGACTCAAGCAATATGTATG 57.681 34.615 0.00 0.00 34.37 2.39
3410 4236 7.389607 TGATGATGACTCAAGCAATATGTATGG 59.610 37.037 0.00 0.00 34.37 2.74
3411 4237 5.471116 TGATGACTCAAGCAATATGTATGGC 59.529 40.000 0.00 0.00 32.69 4.40
3412 4238 3.809279 TGACTCAAGCAATATGTATGGCG 59.191 43.478 0.00 0.00 37.70 5.69
3413 4239 4.058124 GACTCAAGCAATATGTATGGCGA 58.942 43.478 0.00 0.00 37.70 5.54
3414 4240 4.645535 ACTCAAGCAATATGTATGGCGAT 58.354 39.130 0.00 0.00 37.70 4.58
3415 4241 5.793817 ACTCAAGCAATATGTATGGCGATA 58.206 37.500 0.00 0.00 37.70 2.92
3424 4250 3.469008 TGTATGGCGATACCTTGAAGG 57.531 47.619 10.24 10.24 42.49 3.46
3569 4411 4.941873 GGACCTTGGTACTTTAGATGGTTG 59.058 45.833 0.00 0.00 0.00 3.77
3606 4449 3.126858 TGAACAGCATGGTAATTCGAAGC 59.873 43.478 3.35 0.00 33.00 3.86
3609 4452 1.672881 AGCATGGTAATTCGAAGCTGC 59.327 47.619 3.35 6.19 0.00 5.25
3732 4596 3.876274 TGCTCTGTGGACTATCTTGTC 57.124 47.619 0.00 0.00 36.31 3.18
3774 4641 2.708051 CTCTGAATTCCTGCTGCTTGA 58.292 47.619 2.27 0.00 0.00 3.02
3782 4649 1.734137 CTGCTGCTTGATGATGCCC 59.266 57.895 0.00 0.00 0.00 5.36
3798 4665 1.343377 TGCCCTCTATCTTCTGCCTCA 60.343 52.381 0.00 0.00 0.00 3.86
3804 4671 5.076182 CCTCTATCTTCTGCCTCATGAGTA 58.924 45.833 21.11 9.10 0.00 2.59
3816 4683 4.070716 CCTCATGAGTAAATGGAGATGGC 58.929 47.826 21.11 0.00 0.00 4.40
3836 4703 1.250328 CTTGATCCTGCAACAAGCCA 58.750 50.000 8.76 0.00 44.83 4.75
3842 4709 1.900016 CTGCAACAAGCCAGAGCCA 60.900 57.895 0.00 0.00 44.83 4.75
3849 4716 1.144913 ACAAGCCAGAGCCAAACCTAA 59.855 47.619 0.00 0.00 41.25 2.69
3860 4727 5.045140 AGAGCCAAACCTAAGCCTTGTATTA 60.045 40.000 0.00 0.00 0.00 0.98
3861 4728 5.766590 AGCCAAACCTAAGCCTTGTATTAT 58.233 37.500 0.00 0.00 0.00 1.28
3864 4734 6.459710 GCCAAACCTAAGCCTTGTATTATGTC 60.460 42.308 0.00 0.00 0.00 3.06
3868 4738 5.104652 ACCTAAGCCTTGTATTATGTCCGTT 60.105 40.000 0.00 0.00 0.00 4.44
3877 4747 2.282701 TTATGTCCGTTCGCACTACC 57.717 50.000 0.00 0.00 0.00 3.18
3902 4772 1.271982 TGAGGTAGTCTGTCTCGCCTT 60.272 52.381 0.00 0.00 33.79 4.35
3917 4787 2.069165 GCCTTGGGTCCACTCTTGGT 62.069 60.000 0.00 0.00 44.35 3.67
3942 4812 6.151480 TCAACTCAATTTTCTCATATGCTGCA 59.849 34.615 4.13 4.13 0.00 4.41
3978 4848 6.297582 TGAATGCCTGAATTCAACCATTTTT 58.702 32.000 23.37 11.00 42.22 1.94
4066 4969 2.780595 CCATGTAAGCACGGGAAGG 58.219 57.895 0.00 0.00 0.00 3.46
4067 4970 0.035439 CCATGTAAGCACGGGAAGGT 60.035 55.000 0.00 0.00 0.00 3.50
4069 4972 0.252197 ATGTAAGCACGGGAAGGTCC 59.748 55.000 0.00 0.00 35.23 4.46
4071 4974 0.391263 GTAAGCACGGGAAGGTCCAG 60.391 60.000 0.00 0.00 38.64 3.86
4072 4975 0.543410 TAAGCACGGGAAGGTCCAGA 60.543 55.000 1.22 0.00 38.64 3.86
4074 4977 1.072505 GCACGGGAAGGTCCAGAAA 59.927 57.895 1.22 0.00 38.64 2.52
4075 4978 0.536460 GCACGGGAAGGTCCAGAAAA 60.536 55.000 1.22 0.00 38.64 2.29
4113 5067 0.519961 GCAACGGGCTAACGAACAAT 59.480 50.000 0.00 0.00 40.25 2.71
4246 5200 6.129179 TGACTCCCTGGATTTTTATGGATTC 58.871 40.000 0.00 0.00 0.00 2.52
4251 5205 9.200817 CTCCCTGGATTTTTATGGATTCTAAAA 57.799 33.333 0.00 0.00 0.00 1.52
4277 5231 6.144402 AGTTCATGCTTTCAAAAATGTTAGCG 59.856 34.615 0.00 0.00 0.00 4.26
4284 5238 7.009440 GCTTTCAAAAATGTTAGCGGATTTTC 58.991 34.615 0.00 0.00 31.93 2.29
4292 5246 4.778904 TGTTAGCGGATTTTCAAAGTTCG 58.221 39.130 0.00 0.00 0.00 3.95
4299 5253 4.201391 CGGATTTTCAAAGTTCGCGAATTG 60.201 41.667 26.23 24.29 0.00 2.32
4308 5262 6.640499 TCAAAGTTCGCGAATTGAATTTGAAT 59.360 30.769 27.02 4.79 34.19 2.57
4313 5267 5.806286 TCGCGAATTGAATTTGAATAGGTC 58.194 37.500 6.20 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.237498 GTTGGTCTGGCGTGTTTAGC 59.763 55.000 0.00 0.00 0.00 3.09
6 7 1.588674 CAGTTGGTCTGGCGTGTTTA 58.411 50.000 0.00 0.00 40.23 2.01
26 27 3.435566 GAGCATAGTGTTGATCGTCGAA 58.564 45.455 0.00 0.00 0.00 3.71
27 28 2.223502 GGAGCATAGTGTTGATCGTCGA 60.224 50.000 0.00 0.00 32.84 4.20
31 32 1.491670 CCGGAGCATAGTGTTGATCG 58.508 55.000 0.00 0.00 32.84 3.69
41 42 0.394192 CATCAAGGAGCCGGAGCATA 59.606 55.000 5.05 0.00 43.56 3.14
77 78 7.840342 TTTCTCAGCTTTCTCTATGTTGATC 57.160 36.000 0.00 0.00 0.00 2.92
95 96 9.793259 GGTGGTGATAGGAATAATTATTTCTCA 57.207 33.333 20.24 11.98 33.64 3.27
112 113 1.549243 TTGGAGCAGCGGTGGTGATA 61.549 55.000 25.58 7.08 33.41 2.15
119 120 1.598130 GTGAAGTTGGAGCAGCGGT 60.598 57.895 0.00 0.00 0.00 5.68
127 128 1.008194 CGTCGTCGGTGAAGTTGGA 60.008 57.895 0.00 0.00 0.00 3.53
155 156 2.987547 GTCCCGGTCCGTGTCTCA 60.988 66.667 11.06 0.00 0.00 3.27
246 247 0.749091 CTTGCATCCCATTGAGCCGA 60.749 55.000 0.00 0.00 0.00 5.54
356 359 7.515059 GCATAAAGAAATGTGTGTGTGTTTGTC 60.515 37.037 0.00 0.00 0.00 3.18
362 365 8.427012 GTTAATGCATAAAGAAATGTGTGTGTG 58.573 33.333 0.00 0.00 0.00 3.82
626 944 6.487960 TGTGTACCTTAAAAATGTTCACGTG 58.512 36.000 9.94 9.94 34.30 4.49
639 957 8.693120 TTAAACATGTCCAATGTGTACCTTAA 57.307 30.769 0.00 0.00 31.80 1.85
737 1057 7.701809 TTTCATTTTCGTTTTTATGTCCACC 57.298 32.000 0.00 0.00 0.00 4.61
804 1129 3.698040 CCCAGTTAGAGGTAGCTCGTTTA 59.302 47.826 15.91 0.98 0.00 2.01
899 1238 7.451731 AATGACTTTTATCCACCAGAGGATA 57.548 36.000 0.24 0.24 46.41 2.59
901 1240 5.626809 CGAATGACTTTTATCCACCAGAGGA 60.627 44.000 0.00 0.00 43.01 3.71
902 1241 4.572389 CGAATGACTTTTATCCACCAGAGG 59.428 45.833 0.00 0.00 0.00 3.69
929 1268 1.050767 CTCGTGTCGACGGAAAGAAC 58.949 55.000 11.62 0.21 46.11 3.01
939 1278 0.677288 AATGGGTTGTCTCGTGTCGA 59.323 50.000 0.00 0.00 0.00 4.20
965 1304 2.691252 GTAGTGGGGGTCTGGGGG 60.691 72.222 0.00 0.00 0.00 5.40
966 1305 1.689582 GAGTAGTGGGGGTCTGGGG 60.690 68.421 0.00 0.00 0.00 4.96
967 1306 2.058595 CGAGTAGTGGGGGTCTGGG 61.059 68.421 0.00 0.00 0.00 4.45
968 1307 2.722201 GCGAGTAGTGGGGGTCTGG 61.722 68.421 0.00 0.00 0.00 3.86
969 1308 0.395311 TAGCGAGTAGTGGGGGTCTG 60.395 60.000 0.00 0.00 0.00 3.51
970 1309 0.106619 CTAGCGAGTAGTGGGGGTCT 60.107 60.000 0.00 0.00 0.00 3.85
971 1310 1.108132 CCTAGCGAGTAGTGGGGGTC 61.108 65.000 0.00 0.00 0.00 4.46
972 1311 1.076192 CCTAGCGAGTAGTGGGGGT 60.076 63.158 0.00 0.00 0.00 4.95
1357 1815 1.671054 CATTGTCGCCGTCTGGGTT 60.671 57.895 0.00 0.00 38.44 4.11
1424 1882 2.815647 CTTCTTCGTCGCTGCCCC 60.816 66.667 0.00 0.00 0.00 5.80
1458 1916 2.585170 CTTCGTCGCTGTCCTCCTCG 62.585 65.000 0.00 0.00 0.00 4.63
1489 1956 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1491 1958 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1793 2289 1.467920 CTCAGGGAAAATCTGCCACC 58.532 55.000 0.00 0.00 38.23 4.61
1821 2317 3.005539 GCTCCCACTGCTCCTGGA 61.006 66.667 0.00 0.00 0.00 3.86
2304 2828 3.072184 AGGGATGGAGCTTGTGATCATAC 59.928 47.826 0.00 0.00 0.00 2.39
2337 2864 1.566231 CCTACCAAAGAAGGAGGCCAT 59.434 52.381 5.01 0.00 34.58 4.40
2411 2940 7.011669 CCAGGTTTCAAACGTAGAAAGAAACTA 59.988 37.037 20.37 0.00 44.41 2.24
2412 2941 6.183360 CCAGGTTTCAAACGTAGAAAGAAACT 60.183 38.462 20.37 12.92 44.41 2.66
2457 3001 7.260387 TCCCACAACAATCCACTAAATAGTA 57.740 36.000 0.00 0.00 34.13 1.82
2477 3021 1.559682 GAGTGGGTTAGCAGATTCCCA 59.440 52.381 0.00 0.00 46.34 4.37
2490 3034 5.163301 GGAATGATGTACAGTATGAGTGGGT 60.163 44.000 0.33 0.00 39.69 4.51
2498 3042 5.065988 GCAAAACGGGAATGATGTACAGTAT 59.934 40.000 0.33 0.00 0.00 2.12
2670 3218 8.804688 ACATAAAGAAGTATACGAGAATGCTC 57.195 34.615 0.00 0.00 37.81 4.26
2676 3226 7.414222 ACCCAACATAAAGAAGTATACGAGA 57.586 36.000 0.00 0.00 0.00 4.04
2771 3448 8.754230 AGTCTGTTTCTACTCGGTATTAAAAC 57.246 34.615 0.00 0.00 0.00 2.43
2793 3473 5.705441 TGTGATCATCCCAAAACAAGTAGTC 59.295 40.000 0.00 0.00 0.00 2.59
2859 3649 1.007238 AGCTTGGGGTAGACAGAGCTA 59.993 52.381 0.00 0.00 38.58 3.32
2899 3689 4.284550 GTTGGGCCACCTCCAGCA 62.285 66.667 5.23 0.00 35.86 4.41
2927 3717 2.775384 ACCTATTATGCTTTGGGACCGA 59.225 45.455 0.00 0.00 0.00 4.69
2929 3719 8.573885 GTTAATTACCTATTATGCTTTGGGACC 58.426 37.037 0.00 0.00 0.00 4.46
2930 3720 8.287503 CGTTAATTACCTATTATGCTTTGGGAC 58.712 37.037 0.00 0.00 0.00 4.46
3014 3808 3.764885 ATTTCTAATGAAGGTGCACGC 57.235 42.857 11.45 3.85 33.28 5.34
3016 3810 8.863049 CATTTACAATTTCTAATGAAGGTGCAC 58.137 33.333 8.80 8.80 33.28 4.57
3090 3884 2.503331 TCTCAGGCGCATTCTTCAAAA 58.497 42.857 10.83 0.00 0.00 2.44
3094 3888 1.945387 TCATCTCAGGCGCATTCTTC 58.055 50.000 10.83 0.00 0.00 2.87
3118 3912 1.208776 ACGAAAAGGTAAGGCGGCTAT 59.791 47.619 13.71 5.36 0.00 2.97
3193 4001 1.303309 CTAGGAATGGCAGGCTTTCG 58.697 55.000 14.30 0.53 0.00 3.46
3229 4037 7.380602 GCATCTGATCCTGCAATGTTTAAATAC 59.619 37.037 7.03 0.00 38.28 1.89
3238 4046 3.747010 GTCTAGCATCTGATCCTGCAATG 59.253 47.826 12.73 0.00 40.88 2.82
3255 4063 6.036953 GCATTGGAAATCTGAGTCAAGTCTAG 59.963 42.308 0.00 0.00 0.00 2.43
3294 4102 9.471702 AGATAAAGAAGTGGAAACATTCATCAT 57.528 29.630 0.00 0.00 46.14 2.45
3295 4103 8.868522 AGATAAAGAAGTGGAAACATTCATCA 57.131 30.769 0.00 0.00 46.14 3.07
3296 4104 9.565213 CAAGATAAAGAAGTGGAAACATTCATC 57.435 33.333 0.00 0.00 46.14 2.92
3297 4105 9.082313 ACAAGATAAAGAAGTGGAAACATTCAT 57.918 29.630 0.00 0.00 46.14 2.57
3298 4106 8.463930 ACAAGATAAAGAAGTGGAAACATTCA 57.536 30.769 0.00 0.00 46.14 2.57
3299 4107 9.399403 GAACAAGATAAAGAAGTGGAAACATTC 57.601 33.333 0.00 0.00 46.14 2.67
3340 4154 2.092646 ACAGCTATCTCACCGAGTCTCT 60.093 50.000 0.00 0.00 0.00 3.10
3347 4161 1.330655 ACCCCACAGCTATCTCACCG 61.331 60.000 0.00 0.00 0.00 4.94
3404 4230 3.469008 CCTTCAAGGTATCGCCATACA 57.531 47.619 3.81 0.00 37.24 2.29
3424 4250 5.297029 GCCAGTAGGACATAAGGATTTCAAC 59.703 44.000 0.00 0.00 36.89 3.18
3569 4411 6.925610 TGCTGTTCATAATCTGACCATTAC 57.074 37.500 0.00 0.00 32.17 1.89
3606 4449 2.559840 CAGCAACAAGGCTCGCAG 59.440 61.111 0.00 0.00 43.68 5.18
3609 4452 2.559840 CAGCAGCAACAAGGCTCG 59.440 61.111 0.00 0.00 43.68 5.03
3643 4492 1.135199 CAGCAATCCAGGATGCACAAC 60.135 52.381 19.91 2.40 31.97 3.32
3732 4596 5.408356 AGCACCAACATAACTACTTCGTAG 58.592 41.667 0.00 0.00 41.43 3.51
3774 4641 2.305343 GGCAGAAGATAGAGGGCATCAT 59.695 50.000 0.58 0.00 0.00 2.45
3782 4649 6.647334 TTACTCATGAGGCAGAAGATAGAG 57.353 41.667 26.08 0.00 0.00 2.43
3798 4665 4.166725 TCAAGGCCATCTCCATTTACTCAT 59.833 41.667 5.01 0.00 0.00 2.90
3804 4671 2.517127 AGGATCAAGGCCATCTCCATTT 59.483 45.455 5.01 0.00 0.00 2.32
3816 4683 0.529378 GGCTTGTTGCAGGATCAAGG 59.471 55.000 13.05 0.00 45.15 3.61
3836 4703 1.425448 ACAAGGCTTAGGTTTGGCTCT 59.575 47.619 0.00 0.00 38.14 4.09
3842 4709 5.820947 CGGACATAATACAAGGCTTAGGTTT 59.179 40.000 0.00 0.00 0.00 3.27
3849 4716 3.454375 CGAACGGACATAATACAAGGCT 58.546 45.455 0.00 0.00 0.00 4.58
3860 4727 1.153901 CGGTAGTGCGAACGGACAT 60.154 57.895 19.28 8.36 38.98 3.06
3861 4728 2.191354 CTCGGTAGTGCGAACGGACA 62.191 60.000 19.28 4.65 38.98 4.02
3864 4734 2.879462 GCTCGGTAGTGCGAACGG 60.879 66.667 0.00 0.00 0.00 4.44
3868 4738 2.407428 CCTCAGCTCGGTAGTGCGA 61.407 63.158 0.00 0.00 41.35 5.10
3877 4747 1.668751 GAGACAGACTACCTCAGCTCG 59.331 57.143 0.00 0.00 0.00 5.03
3917 4787 6.151480 TGCAGCATATGAGAAAATTGAGTTGA 59.849 34.615 6.97 0.00 0.00 3.18
3942 4812 4.847198 TCAGGCATTCAACACTCATATGT 58.153 39.130 1.90 0.00 0.00 2.29
3978 4848 7.136822 ACCATATCTATGAACTGCCTTGTAA 57.863 36.000 0.00 0.00 35.75 2.41
4024 4927 9.087871 TGGGATCATACAATTTTCTCAAAAAGA 57.912 29.630 0.00 0.00 37.76 2.52
4025 4928 9.880157 ATGGGATCATACAATTTTCTCAAAAAG 57.120 29.630 0.00 0.00 37.76 2.27
4026 4929 9.656040 CATGGGATCATACAATTTTCTCAAAAA 57.344 29.630 0.00 0.00 34.08 1.94
4069 4972 3.045601 ACGTCTCCAGGATGTTTTCTG 57.954 47.619 0.00 0.00 40.95 3.02
4075 4978 1.338200 GCTTGAACGTCTCCAGGATGT 60.338 52.381 0.00 0.00 45.19 3.06
4107 5061 3.140814 GGGCCGGCCTGATTGTTC 61.141 66.667 42.70 21.56 36.10 3.18
4125 5079 0.935196 CGGCTATTCGGTGCTTAACC 59.065 55.000 0.00 0.00 46.60 2.85
4128 5082 0.808453 GTGCGGCTATTCGGTGCTTA 60.808 55.000 0.00 0.00 0.00 3.09
4181 5135 0.807667 ACCATTAGCAAGCGAGCGAG 60.808 55.000 0.00 0.00 40.15 5.03
4218 5172 5.716703 CCATAAAAATCCAGGGAGTCAGTTT 59.283 40.000 0.00 0.00 0.00 2.66
4219 5173 5.015178 TCCATAAAAATCCAGGGAGTCAGTT 59.985 40.000 0.00 0.00 0.00 3.16
4220 5174 4.540099 TCCATAAAAATCCAGGGAGTCAGT 59.460 41.667 0.00 0.00 0.00 3.41
4251 5205 7.306749 CGCTAACATTTTTGAAAGCATGAACTT 60.307 33.333 0.00 0.00 0.00 2.66
4277 5231 4.915085 TCAATTCGCGAACTTTGAAAATCC 59.085 37.500 27.02 0.00 0.00 3.01
4284 5238 5.804449 TCAAATTCAATTCGCGAACTTTG 57.196 34.783 26.00 24.16 0.00 2.77
4292 5246 5.890334 TGGACCTATTCAAATTCAATTCGC 58.110 37.500 0.00 0.00 0.00 4.70
4299 5253 9.874205 TTCAAATTGATGGACCTATTCAAATTC 57.126 29.630 0.00 0.00 33.45 2.17


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

AutoCloner maintained by Alex Coulton.