Multiple sequence alignment - TraesCS4B01G122300

Loading Multiple Alignment...

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 TraesCS4B01G122300 chr4B 100.000 3924 0 0 1 3924 145377968 145374045 0.000000e+00 7247.0
1 TraesCS4B01G122300 chr4B 94.444 54 3 0 202 255 145377725 145377672 2.510000e-12 84.2
2 TraesCS4B01G122300 chr4D 93.617 2820 98 24 523 3264 101443350 101440535 0.000000e+00 4135.0
3 TraesCS4B01G122300 chr4D 84.576 590 55 22 3360 3922 101439967 101439387 1.590000e-153 553.0
4 TraesCS4B01G122300 chr4D 88.168 262 25 5 1 257 101444001 101443741 1.370000e-79 307.0
5 TraesCS4B01G122300 chr4A 95.143 2594 91 12 523 3089 473939598 473942183 0.000000e+00 4060.0
6 TraesCS4B01G122300 chr4A 86.381 257 29 5 3 257 473938626 473938878 3.860000e-70 276.0
7 TraesCS4B01G122300 chr4A 93.671 79 4 1 3151 3229 473942298 473942375 2.480000e-22 117.0
8 TraesCS4B01G122300 chr4A 92.754 69 2 1 3091 3156 473942208 473942276 3.230000e-16 97.1
9 TraesCS4B01G122300 chr4A 84.507 71 5 4 3377 3444 453010100 453010167 9.100000e-07 65.8
10 TraesCS4B01G122300 chr7B 95.876 388 16 0 2387 2774 452266115 452265728 2.570000e-176 628.0
11 TraesCS4B01G122300 chr7B 93.557 388 23 1 2387 2774 452300060 452299675 9.450000e-161 577.0
12 TraesCS4B01G122300 chr7B 95.000 40 2 0 3377 3416 150258876 150258915 3.270000e-06 63.9
13 TraesCS4B01G122300 chr7D 96.542 347 12 0 1982 2328 519190713 519191059 3.400000e-160 575.0
14 TraesCS4B01G122300 chrUn 92.542 295 21 1 1912 2206 1831895 1831602 4.690000e-114 422.0
15 TraesCS4B01G122300 chr2D 94.186 86 5 0 2029 2114 114664722 114664807 8.850000e-27 132.0
16 TraesCS4B01G122300 chr2D 91.837 49 3 1 3369 3416 11614672 11614624 2.530000e-07 67.6
17 TraesCS4B01G122300 chr3B 94.340 53 3 0 2032 2084 744559454 744559402 9.040000e-12 82.4
18 TraesCS4B01G122300 chr6A 95.918 49 2 0 2029 2077 143008591 143008639 3.250000e-11 80.5
19 TraesCS4B01G122300 chr7A 92.000 50 2 2 3369 3416 19966962 19966913 7.040000e-08 69.4
20 TraesCS4B01G122300 chr5A 93.478 46 2 1 3371 3416 371024458 371024502 2.530000e-07 67.6
21 TraesCS4B01G122300 chr3A 90.566 53 2 3 3366 3416 70655027 70655078 2.530000e-07 67.6
22 TraesCS4B01G122300 chr2B 92.000 50 1 3 3369 3416 18144679 18144631 2.530000e-07 67.6
23 TraesCS4B01G122300 chr1A 91.667 48 4 0 3369 3416 287694044 287693997 2.530000e-07 67.6


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 TraesCS4B01G122300 chr4B 145374045 145377968 3923 True 3665.600 7247 97.22200 1 3924 2 chr4B.!!$R1 3923
1 TraesCS4B01G122300 chr4D 101439387 101444001 4614 True 1665.000 4135 88.78700 1 3922 3 chr4D.!!$R1 3921
2 TraesCS4B01G122300 chr4A 473938626 473942375 3749 False 1137.525 4060 91.98725 3 3229 4 chr4A.!!$F2 3226

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
729 1243 0.038251 CAGAGCCACAGCGAACACTA 60.038 55.000 0.0 0.0 46.67 2.74 F
1318 1861 1.135402 GGGCACAACTAAATGCTTCCG 60.135 52.381 0.0 0.0 41.74 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 2252 0.663153 AAAAGCACCTCGTTGCAGAC 59.337 50.0 8.68 0.0 45.62 3.51 R
3307 4335 0.107459 GCTAGGGGGTGAAGAAGCAG 60.107 60.0 0.00 0.0 0.00 4.24 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
69 75 7.812648 TGTTATTAACAGTGTGATTGTAAGGC 58.187 34.615 5.14 0.00 36.25 4.35
88 94 2.233922 GGCACTAGCTAGAAACCAGTCA 59.766 50.000 27.45 0.00 41.70 3.41
100 106 4.402155 AGAAACCAGTCAACTGAAAATGCA 59.598 37.500 11.70 0.00 46.59 3.96
103 109 6.403866 AACCAGTCAACTGAAAATGCAATA 57.596 33.333 11.70 0.00 46.59 1.90
105 111 7.701539 ACCAGTCAACTGAAAATGCAATATA 57.298 32.000 11.70 0.00 46.59 0.86
108 114 6.694411 CAGTCAACTGAAAATGCAATATAGGC 59.306 38.462 4.05 0.00 46.59 3.93
149 155 1.076332 CCGATGGAAAACAGACGTCC 58.924 55.000 13.01 0.00 33.24 4.79
260 267 4.699522 GCCACCACCACCCTCGAC 62.700 72.222 0.00 0.00 0.00 4.20
261 268 2.923035 CCACCACCACCCTCGACT 60.923 66.667 0.00 0.00 0.00 4.18
262 269 2.343758 CACCACCACCCTCGACTG 59.656 66.667 0.00 0.00 0.00 3.51
263 270 2.923035 ACCACCACCCTCGACTGG 60.923 66.667 0.00 0.00 0.00 4.00
264 271 4.394712 CCACCACCCTCGACTGGC 62.395 72.222 0.00 0.00 0.00 4.85
265 272 4.742201 CACCACCCTCGACTGGCG 62.742 72.222 0.00 0.00 42.69 5.69
268 275 4.742201 CACCCTCGACTGGCGGTG 62.742 72.222 2.25 0.00 39.85 4.94
271 278 4.803426 CCTCGACTGGCGGTGCTC 62.803 72.222 2.25 0.00 41.33 4.26
272 279 4.803426 CTCGACTGGCGGTGCTCC 62.803 72.222 2.25 0.00 41.33 4.70
353 361 0.179045 CCGCCAACCATCCCTCTAAG 60.179 60.000 0.00 0.00 0.00 2.18
368 376 1.714899 CTAAGCCCGGCCATGAAACG 61.715 60.000 5.55 0.00 0.00 3.60
375 384 1.156736 CGGCCATGAAACGTTTCTCT 58.843 50.000 33.94 21.92 38.02 3.10
400 409 0.766674 ACCTGCACCCCTCTAACACA 60.767 55.000 0.00 0.00 0.00 3.72
402 411 0.396435 CTGCACCCCTCTAACACACA 59.604 55.000 0.00 0.00 0.00 3.72
403 412 0.396435 TGCACCCCTCTAACACACAG 59.604 55.000 0.00 0.00 0.00 3.66
405 414 1.338200 GCACCCCTCTAACACACAGAG 60.338 57.143 0.00 0.00 39.44 3.35
406 415 1.971357 CACCCCTCTAACACACAGAGT 59.029 52.381 0.00 0.00 38.29 3.24
407 416 2.028930 CACCCCTCTAACACACAGAGTC 60.029 54.545 0.00 0.00 38.29 3.36
409 418 2.232452 CCCCTCTAACACACAGAGTCTG 59.768 54.545 18.83 18.83 38.29 3.51
410 419 2.353208 CCCTCTAACACACAGAGTCTGC 60.353 54.545 20.31 0.00 38.29 4.26
411 420 2.353208 CCTCTAACACACAGAGTCTGCC 60.353 54.545 20.31 0.00 38.29 4.85
412 421 2.297315 CTCTAACACACAGAGTCTGCCA 59.703 50.000 20.31 0.00 35.75 4.92
413 422 2.035961 TCTAACACACAGAGTCTGCCAC 59.964 50.000 20.31 0.00 34.37 5.01
414 423 0.179045 AACACACAGAGTCTGCCACC 60.179 55.000 20.31 0.00 34.37 4.61
429 455 7.501844 AGTCTGCCACCTTAAAGATAGATAAC 58.498 38.462 0.00 0.00 0.00 1.89
431 457 6.097839 TCTGCCACCTTAAAGATAGATAACGT 59.902 38.462 0.00 0.00 0.00 3.99
433 459 5.465724 GCCACCTTAAAGATAGATAACGTGG 59.534 44.000 0.00 0.00 39.32 4.94
443 469 2.741145 AGATAACGTGGGAGCTTCTCT 58.259 47.619 0.00 0.00 0.00 3.10
458 484 0.613292 TCTCTGGCGAGCTTCTTCCT 60.613 55.000 0.00 0.00 37.19 3.36
459 485 0.248843 CTCTGGCGAGCTTCTTCCTT 59.751 55.000 0.00 0.00 0.00 3.36
460 486 0.247736 TCTGGCGAGCTTCTTCCTTC 59.752 55.000 0.00 0.00 0.00 3.46
462 488 0.687354 TGGCGAGCTTCTTCCTTCTT 59.313 50.000 0.00 0.00 0.00 2.52
464 490 1.735018 GGCGAGCTTCTTCCTTCTTTC 59.265 52.381 0.00 0.00 0.00 2.62
465 491 1.735018 GCGAGCTTCTTCCTTCTTTCC 59.265 52.381 0.00 0.00 0.00 3.13
466 492 1.996191 CGAGCTTCTTCCTTCTTTCCG 59.004 52.381 0.00 0.00 0.00 4.30
467 493 2.352814 CGAGCTTCTTCCTTCTTTCCGA 60.353 50.000 0.00 0.00 0.00 4.55
468 494 2.997303 GAGCTTCTTCCTTCTTTCCGAC 59.003 50.000 0.00 0.00 0.00 4.79
469 495 2.368875 AGCTTCTTCCTTCTTTCCGACA 59.631 45.455 0.00 0.00 0.00 4.35
470 496 2.739379 GCTTCTTCCTTCTTTCCGACAG 59.261 50.000 0.00 0.00 0.00 3.51
471 497 3.555168 GCTTCTTCCTTCTTTCCGACAGA 60.555 47.826 0.00 0.00 0.00 3.41
478 834 3.614616 CCTTCTTTCCGACAGATTCTTCG 59.385 47.826 9.75 9.75 34.93 3.79
482 838 2.257974 TCCGACAGATTCTTCGTTCG 57.742 50.000 13.42 6.97 33.23 3.95
501 857 4.188247 TCGATCAAAAATCGACTGACCT 57.812 40.909 6.06 0.00 44.42 3.85
514 870 6.737254 TCGACTGACCTAAATTCCAAATTC 57.263 37.500 0.00 0.00 0.00 2.17
516 872 6.884295 TCGACTGACCTAAATTCCAAATTCAT 59.116 34.615 0.00 0.00 0.00 2.57
519 875 6.211184 ACTGACCTAAATTCCAAATTCATGCA 59.789 34.615 0.00 0.00 0.00 3.96
525 881 8.872845 CCTAAATTCCAAATTCATGCAACTTAC 58.127 33.333 0.00 0.00 0.00 2.34
526 882 9.421806 CTAAATTCCAAATTCATGCAACTTACA 57.578 29.630 0.00 0.00 0.00 2.41
527 883 8.851541 AAATTCCAAATTCATGCAACTTACAT 57.148 26.923 0.00 0.00 0.00 2.29
528 884 9.941325 AAATTCCAAATTCATGCAACTTACATA 57.059 25.926 0.00 0.00 0.00 2.29
532 888 9.625747 TCCAAATTCATGCAACTTACATATAGA 57.374 29.630 0.00 0.00 0.00 1.98
729 1243 0.038251 CAGAGCCACAGCGAACACTA 60.038 55.000 0.00 0.00 46.67 2.74
740 1254 1.201647 GCGAACACTAGCCACTAGTCA 59.798 52.381 4.31 0.00 44.37 3.41
748 1262 3.960755 ACTAGCCACTAGTCACATGCATA 59.039 43.478 0.00 0.00 42.87 3.14
772 1312 3.953612 TCCAATCCAATCAAATTCCCGAG 59.046 43.478 0.00 0.00 0.00 4.63
834 1374 2.460757 ACACCAGCCATGCAAAAATC 57.539 45.000 0.00 0.00 0.00 2.17
835 1375 1.693062 ACACCAGCCATGCAAAAATCA 59.307 42.857 0.00 0.00 0.00 2.57
865 1405 4.155826 CCGCCATCACAAGAAAATACTTGA 59.844 41.667 14.00 0.00 46.85 3.02
1054 1595 4.792087 CCAGCCAGTGGTACGTTT 57.208 55.556 11.74 0.00 42.17 3.60
1084 1626 1.444895 CCAGTGCGAATTGCTTGCC 60.445 57.895 0.00 0.00 46.63 4.52
1095 1637 2.045926 GCTTGCCCGTCCATGTCT 60.046 61.111 0.00 0.00 0.00 3.41
1113 1655 3.696548 TGTCTCTCGTATGCTCATGTCTT 59.303 43.478 0.00 0.00 0.00 3.01
1115 1657 2.793790 CTCTCGTATGCTCATGTCTTGC 59.206 50.000 0.00 0.00 0.00 4.01
1116 1658 1.863454 CTCGTATGCTCATGTCTTGCC 59.137 52.381 0.00 0.00 0.00 4.52
1128 1670 5.072055 TCATGTCTTGCCTCTTTGAATTGA 58.928 37.500 0.00 0.00 0.00 2.57
1318 1861 1.135402 GGGCACAACTAAATGCTTCCG 60.135 52.381 0.00 0.00 41.74 4.30
2114 2657 3.362399 CTCGATGGCGCTGGTGAGT 62.362 63.158 7.64 0.00 37.46 3.41
2398 2941 0.833287 ACATCTACCTCAAGGCGCAT 59.167 50.000 10.83 0.00 39.32 4.73
2860 3403 2.483745 GACACGTCGAGCATCCGA 59.516 61.111 0.00 0.00 36.06 4.55
2898 3441 1.475280 CATGAATGTGGTGAAGCCCAG 59.525 52.381 0.00 0.00 34.43 4.45
2929 3472 3.322541 GGTCCTCCATAAGCTAAGACTCC 59.677 52.174 0.00 0.00 0.00 3.85
2933 3476 6.013379 TCCTCCATAAGCTAAGACTCCATAG 58.987 44.000 0.00 0.00 0.00 2.23
2935 3478 6.495181 CCTCCATAAGCTAAGACTCCATAGAA 59.505 42.308 0.00 0.00 0.00 2.10
3058 3601 5.163364 TGCTAGTTCTCATGATTCTTCCCTC 60.163 44.000 0.00 0.00 0.00 4.30
3068 3613 7.689299 TCATGATTCTTCCCTCTTTCAGTTAA 58.311 34.615 0.00 0.00 0.00 2.01
3119 3693 8.450578 TGTTGGGCATTGTATATTAGAAAGAG 57.549 34.615 0.00 0.00 0.00 2.85
3120 3694 7.502226 TGTTGGGCATTGTATATTAGAAAGAGG 59.498 37.037 0.00 0.00 0.00 3.69
3121 3695 7.387265 TGGGCATTGTATATTAGAAAGAGGA 57.613 36.000 0.00 0.00 0.00 3.71
3125 3699 8.994170 GGCATTGTATATTAGAAAGAGGAAGTC 58.006 37.037 0.00 0.00 0.00 3.01
3156 3730 5.424252 TCAACTATACTTCCTCCGTGGATTT 59.576 40.000 0.00 0.00 45.68 2.17
3157 3731 5.532664 ACTATACTTCCTCCGTGGATTTC 57.467 43.478 0.00 0.00 45.68 2.17
3158 3732 4.960469 ACTATACTTCCTCCGTGGATTTCA 59.040 41.667 0.00 0.00 45.68 2.69
3159 3733 2.474410 ACTTCCTCCGTGGATTTCAC 57.526 50.000 0.00 0.00 45.68 3.18
3211 3811 6.187727 TCAGATCTTGTAACTGAAAAGGGT 57.812 37.500 0.00 0.00 37.66 4.34
3230 3830 3.556423 GGGTAGATTCAGTTCGGTTGTGT 60.556 47.826 0.00 0.00 0.00 3.72
3236 3836 2.557317 TCAGTTCGGTTGTGTTTCCTC 58.443 47.619 0.00 0.00 0.00 3.71
3237 3837 1.602377 CAGTTCGGTTGTGTTTCCTCC 59.398 52.381 0.00 0.00 0.00 4.30
3239 3839 0.533308 TTCGGTTGTGTTTCCTCCGG 60.533 55.000 0.00 0.00 41.27 5.14
3258 3858 5.047847 TCCGGAAAGAAATATAAGAGCGTG 58.952 41.667 0.00 0.00 0.00 5.34
3264 3864 5.854010 AGAAATATAAGAGCGTGTGGAGA 57.146 39.130 0.00 0.00 0.00 3.71
3266 3866 5.361285 AGAAATATAAGAGCGTGTGGAGAGT 59.639 40.000 0.00 0.00 0.00 3.24
3274 4302 0.589708 CGTGTGGAGAGTGTACGTGA 59.410 55.000 0.00 0.00 0.00 4.35
3278 4306 4.438336 CGTGTGGAGAGTGTACGTGATAAT 60.438 45.833 0.00 0.00 0.00 1.28
3318 4346 6.924629 CTTGAATAAAAGCTGCTTCTTCAC 57.075 37.500 23.23 14.11 0.00 3.18
3319 4347 5.376854 TGAATAAAAGCTGCTTCTTCACC 57.623 39.130 16.28 4.76 0.00 4.02
3320 4348 4.218417 TGAATAAAAGCTGCTTCTTCACCC 59.782 41.667 16.28 3.23 0.00 4.61
3321 4349 1.332195 AAAAGCTGCTTCTTCACCCC 58.668 50.000 16.28 0.00 0.00 4.95
3322 4350 0.540597 AAAGCTGCTTCTTCACCCCC 60.541 55.000 16.28 0.00 0.00 5.40
3323 4351 1.430369 AAGCTGCTTCTTCACCCCCT 61.430 55.000 9.53 0.00 0.00 4.79
3324 4352 0.547712 AGCTGCTTCTTCACCCCCTA 60.548 55.000 0.00 0.00 0.00 3.53
3359 4417 4.092279 TGATGGCCATTCATTGTGGTTTA 58.908 39.130 21.84 0.00 39.01 2.01
3386 4474 7.663827 AGAGATCGATATATAGTACTCCCTCG 58.336 42.308 0.00 2.91 0.00 4.63
3416 4504 9.573133 CCTTTTTAGTCTGCATATAAGTTTTGG 57.427 33.333 0.00 0.00 0.00 3.28
3433 4521 3.451141 TTGGAATGTTTGACTTGGCAC 57.549 42.857 0.00 0.00 0.00 5.01
3463 4551 9.199982 TCTTATACACGAAGTAAAAAGAACTGG 57.800 33.333 13.20 0.00 41.61 4.00
3512 4600 7.944061 TGTTGATCAACATGAAACTCAAGAAT 58.056 30.769 32.36 0.00 45.42 2.40
3540 4628 5.178061 CACTAGATGGTCAACATACAAGCA 58.822 41.667 0.00 0.00 40.72 3.91
3578 4666 9.667989 TCGCATAGAAATTAATTGTGAATCATG 57.332 29.630 0.39 4.00 0.00 3.07
3591 4679 9.961265 AATTGTGAATCATGCAATATGAACTAG 57.039 29.630 0.00 0.00 33.13 2.57
3754 4872 1.018910 AACGGGTTTTCTCGGTTGTG 58.981 50.000 0.00 0.00 43.33 3.33
3756 4874 1.440938 CGGGTTTTCTCGGTTGTGCA 61.441 55.000 0.00 0.00 40.55 4.57
3764 4882 1.148310 CTCGGTTGTGCATTCGTTCT 58.852 50.000 0.00 0.00 0.00 3.01
3766 4884 1.529438 TCGGTTGTGCATTCGTTCTTC 59.471 47.619 0.00 0.00 0.00 2.87
3767 4885 1.531149 CGGTTGTGCATTCGTTCTTCT 59.469 47.619 0.00 0.00 0.00 2.85
3768 4886 2.662791 CGGTTGTGCATTCGTTCTTCTG 60.663 50.000 0.00 0.00 0.00 3.02
3769 4887 2.290641 GGTTGTGCATTCGTTCTTCTGT 59.709 45.455 0.00 0.00 0.00 3.41
3771 4889 3.607422 TGTGCATTCGTTCTTCTGTTG 57.393 42.857 0.00 0.00 0.00 3.33
3772 4890 3.202097 TGTGCATTCGTTCTTCTGTTGA 58.798 40.909 0.00 0.00 0.00 3.18
3773 4891 3.814842 TGTGCATTCGTTCTTCTGTTGAT 59.185 39.130 0.00 0.00 0.00 2.57
3774 4892 4.083855 TGTGCATTCGTTCTTCTGTTGATC 60.084 41.667 0.00 0.00 0.00 2.92
3775 4893 3.123453 TGCATTCGTTCTTCTGTTGATCG 59.877 43.478 0.00 0.00 0.00 3.69
3776 4894 3.663908 CATTCGTTCTTCTGTTGATCGC 58.336 45.455 0.00 0.00 0.00 4.58
3792 4911 1.577468 TCGCTGATGTGTTTGTTCGT 58.423 45.000 0.00 0.00 0.00 3.85
3885 5005 8.836413 TCTCTACATGTACTTTGGTTTTCTTTG 58.164 33.333 0.08 0.00 0.00 2.77
3892 5012 9.719355 ATGTACTTTGGTTTTCTTTGTTTTTCT 57.281 25.926 0.00 0.00 0.00 2.52
3893 5013 9.198837 TGTACTTTGGTTTTCTTTGTTTTTCTC 57.801 29.630 0.00 0.00 0.00 2.87
3894 5014 7.667043 ACTTTGGTTTTCTTTGTTTTTCTCC 57.333 32.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 53 7.165485 AGTGCCTTACAATCACACTGTTAATA 58.835 34.615 0.00 0.00 39.97 0.98
55 61 3.600388 AGCTAGTGCCTTACAATCACAC 58.400 45.455 0.00 0.00 40.80 3.82
69 75 4.926238 CAGTTGACTGGTTTCTAGCTAGTG 59.074 45.833 20.10 2.97 40.20 2.74
88 94 6.543430 TTGGCCTATATTGCATTTTCAGTT 57.457 33.333 3.32 0.00 0.00 3.16
100 106 4.706842 AACCAGTCGATTGGCCTATATT 57.293 40.909 25.45 9.39 42.18 1.28
103 109 2.238646 TGAAACCAGTCGATTGGCCTAT 59.761 45.455 25.45 10.08 42.18 2.57
105 111 0.400213 TGAAACCAGTCGATTGGCCT 59.600 50.000 25.45 13.44 42.18 5.19
108 114 0.804989 GGCTGAAACCAGTCGATTGG 59.195 55.000 24.11 24.11 44.09 3.16
251 258 4.742201 CACCGCCAGTCGAGGGTG 62.742 72.222 9.17 9.17 43.41 4.61
255 262 4.803426 GGAGCACCGCCAGTCGAG 62.803 72.222 0.00 0.00 41.67 4.04
290 297 4.547367 GATTGGCGGGAGGTCGGG 62.547 72.222 0.00 0.00 0.00 5.14
291 298 4.891727 CGATTGGCGGGAGGTCGG 62.892 72.222 0.00 0.00 36.03 4.79
333 340 2.265467 TTAGAGGGATGGTTGGCGGC 62.265 60.000 0.00 0.00 0.00 6.53
336 344 0.466372 GGCTTAGAGGGATGGTTGGC 60.466 60.000 0.00 0.00 0.00 4.52
340 348 1.766461 CCGGGCTTAGAGGGATGGT 60.766 63.158 0.00 0.00 0.00 3.55
353 361 2.812542 GAAACGTTTCATGGCCGGGC 62.813 60.000 30.99 23.42 37.15 6.13
368 376 3.873805 GCAGGTTTGCCAGAGAAAC 57.126 52.632 0.00 0.00 44.74 2.78
390 399 2.353208 GGCAGACTCTGTGTGTTAGAGG 60.353 54.545 7.89 0.00 44.65 3.69
392 401 2.035961 GTGGCAGACTCTGTGTGTTAGA 59.964 50.000 7.89 0.00 33.43 2.10
400 409 2.972713 TCTTTAAGGTGGCAGACTCTGT 59.027 45.455 7.89 0.00 33.43 3.41
402 411 5.273208 TCTATCTTTAAGGTGGCAGACTCT 58.727 41.667 0.00 0.00 0.00 3.24
403 412 5.599999 TCTATCTTTAAGGTGGCAGACTC 57.400 43.478 0.00 0.00 0.00 3.36
405 414 6.421202 CGTTATCTATCTTTAAGGTGGCAGAC 59.579 42.308 0.00 0.00 0.00 3.51
406 415 6.097839 ACGTTATCTATCTTTAAGGTGGCAGA 59.902 38.462 0.00 0.00 0.00 4.26
407 416 6.201044 CACGTTATCTATCTTTAAGGTGGCAG 59.799 42.308 0.00 0.00 39.08 4.85
409 418 6.526566 CACGTTATCTATCTTTAAGGTGGC 57.473 41.667 7.33 0.00 39.08 5.01
411 420 6.812998 TCCCACGTTATCTATCTTTAAGGTG 58.187 40.000 7.98 7.98 40.90 4.00
412 421 6.462628 GCTCCCACGTTATCTATCTTTAAGGT 60.463 42.308 0.00 0.00 0.00 3.50
413 422 5.927115 GCTCCCACGTTATCTATCTTTAAGG 59.073 44.000 0.00 0.00 0.00 2.69
414 423 6.750148 AGCTCCCACGTTATCTATCTTTAAG 58.250 40.000 0.00 0.00 0.00 1.85
429 455 2.125350 GCCAGAGAAGCTCCCACG 60.125 66.667 0.00 0.00 0.00 4.94
431 457 2.283894 TCGCCAGAGAAGCTCCCA 60.284 61.111 0.00 0.00 0.00 4.37
443 469 0.687354 AAGAAGGAAGAAGCTCGCCA 59.313 50.000 0.00 0.00 0.00 5.69
458 484 4.252971 ACGAAGAATCTGTCGGAAAGAA 57.747 40.909 1.21 0.00 41.56 2.52
459 485 3.936372 ACGAAGAATCTGTCGGAAAGA 57.064 42.857 15.31 0.00 41.56 2.52
460 486 3.059570 CGAACGAAGAATCTGTCGGAAAG 59.940 47.826 15.31 0.00 41.56 2.62
462 488 2.227149 TCGAACGAAGAATCTGTCGGAA 59.773 45.455 15.31 1.07 41.56 4.30
464 490 2.257974 TCGAACGAAGAATCTGTCGG 57.742 50.000 15.31 3.19 41.56 4.79
465 491 3.426323 TGATCGAACGAAGAATCTGTCG 58.574 45.455 11.32 11.32 42.91 4.35
466 492 5.763444 TTTGATCGAACGAAGAATCTGTC 57.237 39.130 0.12 0.00 0.00 3.51
467 493 6.539649 TTTTTGATCGAACGAAGAATCTGT 57.460 33.333 0.12 0.00 0.00 3.41
468 494 6.406327 CGATTTTTGATCGAACGAAGAATCTG 59.594 38.462 17.78 12.38 43.59 2.90
469 495 6.310467 TCGATTTTTGATCGAACGAAGAATCT 59.690 34.615 8.49 0.00 46.01 2.40
470 496 6.466812 TCGATTTTTGATCGAACGAAGAATC 58.533 36.000 8.49 14.01 46.01 2.52
471 497 6.403333 TCGATTTTTGATCGAACGAAGAAT 57.597 33.333 8.49 0.00 46.01 2.40
482 838 7.910683 GGAATTTAGGTCAGTCGATTTTTGATC 59.089 37.037 0.00 0.00 0.00 2.92
495 851 6.632909 TGCATGAATTTGGAATTTAGGTCAG 58.367 36.000 0.00 0.00 0.00 3.51
498 854 7.008021 AGTTGCATGAATTTGGAATTTAGGT 57.992 32.000 0.00 0.00 29.37 3.08
501 857 9.941325 ATGTAAGTTGCATGAATTTGGAATTTA 57.059 25.926 5.58 0.00 31.29 1.40
532 888 9.801873 GGCTTTACATTTACAATCACACAATAT 57.198 29.630 0.00 0.00 0.00 1.28
692 1206 1.052124 TGTTCCGTGGAAGGAGGTGT 61.052 55.000 0.53 0.00 41.98 4.16
694 1208 0.471211 TCTGTTCCGTGGAAGGAGGT 60.471 55.000 0.53 0.00 41.98 3.85
695 1209 0.247736 CTCTGTTCCGTGGAAGGAGG 59.752 60.000 17.15 4.60 41.98 4.30
729 1243 2.768527 AGTATGCATGTGACTAGTGGCT 59.231 45.455 10.16 0.00 0.00 4.75
740 1254 4.795469 TGATTGGATTGGAGTATGCATGT 58.205 39.130 10.16 0.00 35.22 3.21
748 1262 3.701040 CGGGAATTTGATTGGATTGGAGT 59.299 43.478 0.00 0.00 0.00 3.85
772 1312 4.101790 CGTGCATGTGTTCGGGGC 62.102 66.667 0.00 0.00 0.00 5.80
834 1374 2.825836 GTGATGGCGGAGGGCTTG 60.826 66.667 0.00 0.00 42.94 4.01
835 1375 2.826777 CTTGTGATGGCGGAGGGCTT 62.827 60.000 0.00 0.00 42.94 4.35
865 1405 9.853177 ATAGAGATTCCATTAAAATTCTCCGTT 57.147 29.630 0.00 0.00 0.00 4.44
1053 1594 0.961019 GCACTGGCAAAGACATGGAA 59.039 50.000 0.00 0.00 40.72 3.53
1054 1595 1.236616 CGCACTGGCAAAGACATGGA 61.237 55.000 0.00 0.00 41.24 3.41
1084 1626 1.600663 GCATACGAGAGACATGGACGG 60.601 57.143 0.00 0.00 0.00 4.79
1095 1637 2.481969 GGCAAGACATGAGCATACGAGA 60.482 50.000 0.00 0.00 0.00 4.04
1113 1655 3.827876 TGCTCAATCAATTCAAAGAGGCA 59.172 39.130 0.00 0.00 0.00 4.75
1115 1657 4.142227 CCCTGCTCAATCAATTCAAAGAGG 60.142 45.833 0.00 0.00 0.00 3.69
1116 1658 4.461781 ACCCTGCTCAATCAATTCAAAGAG 59.538 41.667 0.00 0.00 0.00 2.85
1128 1670 1.079819 CGACGACACCCTGCTCAAT 60.080 57.895 0.00 0.00 0.00 2.57
1318 1861 4.722700 ACCATCACCGCCTGCACC 62.723 66.667 0.00 0.00 0.00 5.01
1621 2164 4.314440 TCACAGGACCGCAGCACC 62.314 66.667 0.00 0.00 0.00 5.01
1709 2252 0.663153 AAAAGCACCTCGTTGCAGAC 59.337 50.000 8.68 0.00 45.62 3.51
1909 2452 1.153997 GACAACGGACTCGAGGAGC 60.154 63.158 18.41 5.51 40.11 4.70
2077 2620 4.704833 GCCAAGGCGAGCAGGTCA 62.705 66.667 0.00 0.00 0.00 4.02
2114 2657 1.656594 CGATTCGGTGTTAATGACGCA 59.343 47.619 0.00 0.00 40.59 5.24
2155 2698 1.741770 GGACTCGCGCTCCACAAAT 60.742 57.895 15.57 0.00 0.00 2.32
2398 2941 1.824329 GATCTCGTCCAGCTCCGGA 60.824 63.158 2.93 2.93 0.00 5.14
2758 3301 0.980423 AGAAGCTCGCTTTCTTCCCT 59.020 50.000 5.53 0.00 39.48 4.20
2797 3340 4.021925 GGGTTCAGCCGGCTCAGT 62.022 66.667 30.29 1.77 38.44 3.41
2890 3433 2.069430 CCTCCTCCTCCTGGGCTTC 61.069 68.421 0.00 0.00 34.39 3.86
2929 3472 6.679327 ATCGCATCATGGATGATTTCTATG 57.321 37.500 10.24 0.00 44.70 2.23
2933 3476 4.940046 ACCTATCGCATCATGGATGATTTC 59.060 41.667 10.24 0.00 44.70 2.17
2935 3478 4.259356 CACCTATCGCATCATGGATGATT 58.741 43.478 10.24 0.00 44.70 2.57
3068 3613 9.890629 ATACACAGTACAATAGATGACACAAAT 57.109 29.630 0.00 0.00 0.00 2.32
3089 3634 8.615878 TCTAATATACAATGCCCAACATACAC 57.384 34.615 0.00 0.00 38.34 2.90
3120 3694 9.660180 AGGAAGTATAGTTGAATTGAAGACTTC 57.340 33.333 8.34 8.34 39.54 3.01
3121 3695 9.660180 GAGGAAGTATAGTTGAATTGAAGACTT 57.340 33.333 0.00 0.00 0.00 3.01
3125 3699 7.010552 CACGGAGGAAGTATAGTTGAATTGAAG 59.989 40.741 0.00 0.00 0.00 3.02
3211 3811 4.753107 GGAAACACAACCGAACTGAATCTA 59.247 41.667 0.00 0.00 0.00 1.98
3236 3836 4.809426 ACACGCTCTTATATTTCTTTCCGG 59.191 41.667 0.00 0.00 0.00 5.14
3237 3837 5.276868 CCACACGCTCTTATATTTCTTTCCG 60.277 44.000 0.00 0.00 0.00 4.30
3239 3839 6.757010 TCTCCACACGCTCTTATATTTCTTTC 59.243 38.462 0.00 0.00 0.00 2.62
3258 3858 6.963049 AAAATTATCACGTACACTCTCCAC 57.037 37.500 0.00 0.00 0.00 4.02
3304 4332 1.075659 GGGGGTGAAGAAGCAGCTT 59.924 57.895 7.60 7.60 36.56 3.74
3307 4335 0.107459 GCTAGGGGGTGAAGAAGCAG 60.107 60.000 0.00 0.00 0.00 4.24
3309 4337 1.497161 TAGCTAGGGGGTGAAGAAGC 58.503 55.000 0.00 0.00 0.00 3.86
3310 4338 3.375699 TCTTAGCTAGGGGGTGAAGAAG 58.624 50.000 2.65 0.00 0.00 2.85
3311 4339 3.246021 ACTCTTAGCTAGGGGGTGAAGAA 60.246 47.826 7.75 0.00 0.00 2.52
3312 4340 2.315155 ACTCTTAGCTAGGGGGTGAAGA 59.685 50.000 7.75 0.00 0.00 2.87
3313 4341 2.696187 GACTCTTAGCTAGGGGGTGAAG 59.304 54.545 7.75 0.00 0.00 3.02
3314 4342 2.043939 TGACTCTTAGCTAGGGGGTGAA 59.956 50.000 7.75 0.00 0.00 3.18
3315 4343 1.644337 TGACTCTTAGCTAGGGGGTGA 59.356 52.381 7.75 0.00 0.00 4.02
3316 4344 2.160721 TGACTCTTAGCTAGGGGGTG 57.839 55.000 7.75 0.00 0.00 4.61
3317 4345 3.041946 CAATGACTCTTAGCTAGGGGGT 58.958 50.000 7.75 4.43 0.00 4.95
3318 4346 3.309296 TCAATGACTCTTAGCTAGGGGG 58.691 50.000 7.75 1.08 0.00 5.40
3319 4347 4.262808 CCATCAATGACTCTTAGCTAGGGG 60.263 50.000 0.23 0.23 0.00 4.79
3320 4348 4.802248 GCCATCAATGACTCTTAGCTAGGG 60.802 50.000 2.65 0.00 0.00 3.53
3321 4349 4.314121 GCCATCAATGACTCTTAGCTAGG 58.686 47.826 0.00 0.00 0.00 3.02
3322 4350 4.202295 TGGCCATCAATGACTCTTAGCTAG 60.202 45.833 0.00 0.00 0.00 3.42
3323 4351 3.711190 TGGCCATCAATGACTCTTAGCTA 59.289 43.478 0.00 0.00 0.00 3.32
3324 4352 2.507058 TGGCCATCAATGACTCTTAGCT 59.493 45.455 0.00 0.00 0.00 3.32
3359 4417 9.841295 GAGGGAGTACTATATATCGATCTCTTT 57.159 37.037 0.00 0.00 0.00 2.52
3382 4470 2.737252 GCAGACTAAAAAGGACACGAGG 59.263 50.000 0.00 0.00 0.00 4.63
3386 4474 8.494016 ACTTATATGCAGACTAAAAAGGACAC 57.506 34.615 0.00 0.00 0.00 3.67
3416 4504 5.291971 AGATTTGTGCCAAGTCAAACATTC 58.708 37.500 11.17 0.00 36.58 2.67
3419 4507 4.734398 AAGATTTGTGCCAAGTCAAACA 57.266 36.364 11.17 0.00 36.58 2.83
3444 4532 5.983720 TCTCTCCAGTTCTTTTTACTTCGTG 59.016 40.000 0.00 0.00 0.00 4.35
3445 4533 6.158023 TCTCTCCAGTTCTTTTTACTTCGT 57.842 37.500 0.00 0.00 0.00 3.85
3447 4535 9.145865 CATACTCTCTCCAGTTCTTTTTACTTC 57.854 37.037 0.00 0.00 0.00 3.01
3448 4536 8.871125 TCATACTCTCTCCAGTTCTTTTTACTT 58.129 33.333 0.00 0.00 0.00 2.24
3458 4546 6.013379 TCTTCACTTCATACTCTCTCCAGTT 58.987 40.000 0.00 0.00 0.00 3.16
3461 4549 8.595362 TTTATCTTCACTTCATACTCTCTCCA 57.405 34.615 0.00 0.00 0.00 3.86
3462 4550 9.474920 CATTTATCTTCACTTCATACTCTCTCC 57.525 37.037 0.00 0.00 0.00 3.71
3554 4642 9.251792 TGCATGATTCACAATTAATTTCTATGC 57.748 29.630 16.83 16.83 36.25 3.14
3603 4691 8.541234 TGTCCACATATACTTATACCAAACACA 58.459 33.333 0.00 0.00 0.00 3.72
3665 4777 8.710239 ACCAAACACATAGTATATGTCCACATA 58.290 33.333 1.89 1.89 42.38 2.29
3710 4828 2.375345 CCGGCCCATCACCTAACCT 61.375 63.158 0.00 0.00 0.00 3.50
3719 4837 3.857038 TTACTCGGCCGGCCCATC 61.857 66.667 39.24 15.59 0.00 3.51
3747 4865 1.531149 AGAAGAACGAATGCACAACCG 59.469 47.619 0.00 0.00 0.00 4.44
3754 4872 3.663908 CGATCAACAGAAGAACGAATGC 58.336 45.455 0.00 0.00 33.80 3.56
3756 4874 3.369147 CAGCGATCAACAGAAGAACGAAT 59.631 43.478 0.00 0.00 33.80 3.34
3764 4882 3.044235 ACACATCAGCGATCAACAGAA 57.956 42.857 0.00 0.00 0.00 3.02
3766 4884 3.058708 ACAAACACATCAGCGATCAACAG 60.059 43.478 0.00 0.00 0.00 3.16
3767 4885 2.877786 ACAAACACATCAGCGATCAACA 59.122 40.909 0.00 0.00 0.00 3.33
3768 4886 3.542712 ACAAACACATCAGCGATCAAC 57.457 42.857 0.00 0.00 0.00 3.18
3769 4887 3.363871 CGAACAAACACATCAGCGATCAA 60.364 43.478 0.00 0.00 0.00 2.57
3771 4889 2.157668 ACGAACAAACACATCAGCGATC 59.842 45.455 0.00 0.00 0.00 3.69
3772 4890 2.143122 ACGAACAAACACATCAGCGAT 58.857 42.857 0.00 0.00 0.00 4.58
3773 4891 1.577468 ACGAACAAACACATCAGCGA 58.423 45.000 0.00 0.00 0.00 4.93
3774 4892 2.032894 AGAACGAACAAACACATCAGCG 60.033 45.455 0.00 0.00 0.00 5.18
3775 4893 3.609103 AGAACGAACAAACACATCAGC 57.391 42.857 0.00 0.00 0.00 4.26
3776 4894 5.568482 TGAAAGAACGAACAAACACATCAG 58.432 37.500 0.00 0.00 0.00 2.90
3863 4982 9.930693 AAAACAAAGAAAACCAAAGTACATGTA 57.069 25.926 0.08 0.08 0.00 2.29
3864 4983 8.840833 AAAACAAAGAAAACCAAAGTACATGT 57.159 26.923 2.69 2.69 0.00 3.21
3866 4985 9.719355 AGAAAAACAAAGAAAACCAAAGTACAT 57.281 25.926 0.00 0.00 0.00 2.29
3868 4987 8.653338 GGAGAAAAACAAAGAAAACCAAAGTAC 58.347 33.333 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.