Multiple sequence alignment - TraesCS1D01G414400

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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 TraesCS1D01G414400 chr1D 100.000 3741 0 0 1 3741 474351748 474355488 0.000000e+00 6909
1 TraesCS1D01G414400 chr1D 89.076 238 26 0 3219 3456 215863286 215863523 2.830000e-76 296
2 TraesCS1D01G414400 chr1D 86.090 266 32 5 3192 3456 293616986 293617247 7.910000e-72 281
3 TraesCS1D01G414400 chrUn 91.681 2260 137 22 737 2972 8533755 8535987 0.000000e+00 3085
4 TraesCS1D01G414400 chrUn 87.422 2401 219 35 755 3123 8515668 8518017 0.000000e+00 2684
5 TraesCS1D01G414400 chrUn 85.106 658 63 23 11 651 8514617 8515256 1.130000e-179 640
6 TraesCS1D01G414400 chrUn 72.888 1586 357 45 978 2526 26236334 26237883 2.610000e-131 479
7 TraesCS1D01G414400 chrUn 93.238 281 15 3 1 277 8514541 8514821 9.670000e-111 411
8 TraesCS1D01G414400 chrUn 91.111 225 20 0 3232 3456 223002330 223002106 4.690000e-79 305
9 TraesCS1D01G414400 chrUn 79.580 333 50 9 2367 2699 26259225 26259539 4.860000e-54 222
10 TraesCS1D01G414400 chrUn 89.032 155 16 1 2988 3142 8536256 8536409 1.370000e-44 191
11 TraesCS1D01G414400 chrUn 92.174 115 7 2 649 761 8515283 8515397 1.080000e-35 161
12 TraesCS1D01G414400 chr1A 89.487 2007 148 29 1691 3662 568697256 568699234 0.000000e+00 2479
13 TraesCS1D01G414400 chr1A 90.065 765 71 3 880 1640 568696385 568697148 0.000000e+00 987
14 TraesCS1D01G414400 chr2A 73.667 1557 346 40 1005 2526 694839907 694841434 2.540000e-151 545
15 TraesCS1D01G414400 chr2A 85.220 318 47 0 1005 1322 694864578 694864895 1.000000e-85 327
16 TraesCS1D01G414400 chr2A 78.816 321 50 10 2372 2692 694903471 694903773 2.280000e-47 200
17 TraesCS1D01G414400 chr2B 80.062 647 111 8 1005 1642 661175716 661176353 7.320000e-127 464
18 TraesCS1D01G414400 chr2B 86.792 318 42 0 1005 1322 661191856 661192173 4.600000e-94 355
19 TraesCS1D01G414400 chr2B 78.042 378 58 17 2328 2699 661446467 661446825 8.140000e-52 215
20 TraesCS1D01G414400 chr2B 82.000 250 41 4 1032 1279 744178909 744179156 3.790000e-50 209
21 TraesCS1D01G414400 chr3D 91.102 236 21 0 3221 3456 417156491 417156726 1.680000e-83 320
22 TraesCS1D01G414400 chr3D 91.556 225 19 0 3232 3456 29528912 29528688 1.010000e-80 311
23 TraesCS1D01G414400 chr3D 91.111 225 20 0 3232 3456 29493983 29493759 4.690000e-79 305
24 TraesCS1D01G414400 chr3D 90.129 233 22 1 3224 3456 571044467 571044236 6.070000e-78 302
25 TraesCS1D01G414400 chr7B 87.085 271 29 5 3192 3456 28489752 28489482 6.070000e-78 302


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 TraesCS1D01G414400 chr1D 474351748 474355488 3740 False 6909 6909 100.0000 1 3741 1 chr1D.!!$F3 3740
1 TraesCS1D01G414400 chrUn 8533755 8536409 2654 False 1638 3085 90.3565 737 3142 2 chrUn.!!$F4 2405
2 TraesCS1D01G414400 chrUn 8514541 8518017 3476 False 974 2684 89.4850 1 3123 4 chrUn.!!$F3 3122
3 TraesCS1D01G414400 chrUn 26236334 26237883 1549 False 479 479 72.8880 978 2526 1 chrUn.!!$F1 1548
4 TraesCS1D01G414400 chr1A 568696385 568699234 2849 False 1733 2479 89.7760 880 3662 2 chr1A.!!$F1 2782
5 TraesCS1D01G414400 chr2A 694839907 694841434 1527 False 545 545 73.6670 1005 2526 1 chr2A.!!$F1 1521
6 TraesCS1D01G414400 chr2B 661175716 661176353 637 False 464 464 80.0620 1005 1642 1 chr2B.!!$F1 637

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
336 399 0.106708 ACAGTCACGCCATGTTGTCT 59.893 50.000 0.0 0.0 0.00 3.41 F
434 498 1.272704 GGAGGGCTTGGGATTCAAACT 60.273 52.381 0.0 0.0 34.56 2.66 F
2132 2605 0.397535 CCCCAATGCTGGCACCTTAT 60.398 55.000 0.0 0.0 41.99 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2548 0.627451 ATTCTGGCCTCAAGCATCCA 59.373 50.000 3.32 0.0 46.50 3.41 R
2255 2728 1.143889 TGGTAGTTGCACCATGGTTCA 59.856 47.619 16.84 15.1 43.76 3.18 R
3414 4154 0.449786 TATTGGCAATGTTCGTGCGG 59.550 50.000 22.57 0.0 43.18 5.69 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
324 350 3.505680 TGCCATCATGGTTAAACAGTCAC 59.494 43.478 5.31 0.00 40.46 3.67
336 399 0.106708 ACAGTCACGCCATGTTGTCT 59.893 50.000 0.00 0.00 0.00 3.41
355 418 7.589587 TGTTGTCTTGTAACATATTTCGCAAAG 59.410 33.333 0.00 0.00 33.43 2.77
375 439 7.322699 CGCAAAGAAAAATGTTAATACTGTCGT 59.677 33.333 0.00 0.00 0.00 4.34
393 457 4.116238 GTCGTGGCAAATTTTCCAGAAAA 58.884 39.130 10.01 7.94 43.48 2.29
434 498 1.272704 GGAGGGCTTGGGATTCAAACT 60.273 52.381 0.00 0.00 34.56 2.66
445 509 5.513094 TTGGGATTCAAACTCAGGTCTACTG 60.513 44.000 0.00 0.00 39.39 2.74
505 572 2.875296 TGGAATTCAAACCCAGGTCTG 58.125 47.619 7.93 0.00 0.00 3.51
528 595 3.826221 TGCAAAACTCGCACTGCT 58.174 50.000 0.00 0.00 35.78 4.24
529 596 1.356270 TGCAAAACTCGCACTGCTG 59.644 52.632 0.00 0.00 35.78 4.41
532 599 2.896801 AAAACTCGCACTGCTGCCG 61.897 57.895 0.00 0.00 40.73 5.69
592 659 3.119316 CGCTGGGTTTTATGGTATTTGCA 60.119 43.478 0.00 0.00 0.00 4.08
694 790 6.725246 CCTGTTATGATTTCCGTACAAATCC 58.275 40.000 13.31 2.70 40.66 3.01
724 822 2.859929 CCATGGGCAGAGGGACTAT 58.140 57.895 2.85 0.00 41.55 2.12
729 827 3.637821 TGGGCAGAGGGACTATATTCT 57.362 47.619 0.00 0.00 41.55 2.40
781 1155 3.268034 AAGAGGGAGAAGTGGAGAACT 57.732 47.619 0.00 0.00 42.60 3.01
962 1346 4.205792 CGTCCGTATTTTATCCAAGACGAC 59.794 45.833 3.30 0.00 46.41 4.34
971 1355 3.685139 ATCCAAGACGACACACTCAAT 57.315 42.857 0.00 0.00 0.00 2.57
1233 1617 1.745890 CACCGACCTGTTCAGGACA 59.254 57.895 23.45 0.00 36.65 4.02
1278 1662 3.057548 CCCATCAACGCTGCAGCA 61.058 61.111 36.03 18.99 42.21 4.41
1343 1727 2.098831 GGGAGGTTTACGTCTGCGC 61.099 63.158 0.00 0.00 42.83 6.09
1381 1774 4.717629 CCGCGTTCAGCTCCGTCA 62.718 66.667 4.92 0.00 45.59 4.35
1422 1815 2.555199 GGTAGAATCATGACGCAGCTT 58.445 47.619 0.00 0.00 0.00 3.74
1484 1880 4.802051 TGCTTGCGAGGATGGGGC 62.802 66.667 2.37 0.00 0.00 5.80
1685 2146 7.167924 TGCTTTGAGGATTATGCATAAACAA 57.832 32.000 22.37 19.94 0.00 2.83
1686 2147 7.609960 TGCTTTGAGGATTATGCATAAACAAA 58.390 30.769 22.37 23.97 0.00 2.83
1687 2148 8.093307 TGCTTTGAGGATTATGCATAAACAAAA 58.907 29.630 22.37 17.56 0.00 2.44
1688 2149 8.382875 GCTTTGAGGATTATGCATAAACAAAAC 58.617 33.333 22.37 19.43 0.00 2.43
1690 2151 9.941325 TTTGAGGATTATGCATAAACAAAACAT 57.059 25.926 22.37 4.00 0.00 2.71
1691 2152 8.929827 TGAGGATTATGCATAAACAAAACATG 57.070 30.769 22.37 0.00 0.00 3.21
1692 2153 7.492020 TGAGGATTATGCATAAACAAAACATGC 59.508 33.333 22.37 9.17 44.23 4.06
1787 2248 2.874457 GCAGAACCCGTTAACTGGTCAT 60.874 50.000 20.43 10.45 32.01 3.06
1955 2428 1.511887 CGAAGTTGGCGGCGATTTG 60.512 57.895 12.98 2.82 0.00 2.32
2075 2548 1.489649 AGCATAGCTGGAAGTGCTCAT 59.510 47.619 0.00 0.00 43.97 2.90
2131 2604 1.000233 CCCCAATGCTGGCACCTTA 60.000 57.895 0.00 0.00 41.99 2.69
2132 2605 0.397535 CCCCAATGCTGGCACCTTAT 60.398 55.000 0.00 0.00 41.99 1.73
2254 2727 6.343716 TGCAAATCATTACCTTTGTCATGT 57.656 33.333 0.00 0.00 35.33 3.21
2255 2728 6.757237 TGCAAATCATTACCTTTGTCATGTT 58.243 32.000 0.00 0.00 35.33 2.71
2259 2732 8.702438 CAAATCATTACCTTTGTCATGTTGAAC 58.298 33.333 0.00 0.00 29.90 3.18
2298 2771 7.065204 ACCAAAAACGCTATGTCAAAATTTGTT 59.935 29.630 5.56 0.00 0.00 2.83
2321 2794 5.535753 ATGAAAAAGGGAAGACCACAAAG 57.464 39.130 0.00 0.00 43.89 2.77
2349 2822 3.636300 TGAGTTGGATCCAAAAACACCAG 59.364 43.478 28.64 0.00 37.70 4.00
2363 2836 1.279496 CACCAGAGGGAGGATGTGAA 58.721 55.000 0.00 0.00 38.05 3.18
2368 2844 1.836802 AGAGGGAGGATGTGAAGAAGC 59.163 52.381 0.00 0.00 0.00 3.86
2528 3004 3.436761 CCCTTACAAAACCCCAGGTTGTA 60.437 47.826 0.00 0.00 46.20 2.41
2530 3006 4.650131 CCTTACAAAACCCCAGGTTGTAAA 59.350 41.667 12.09 0.29 46.20 2.01
2664 3140 1.123861 AGAGCTGCCTTGGTGACTCA 61.124 55.000 0.00 0.00 0.00 3.41
2741 3223 4.281182 ACCACAGCTTCGGTCTATATTAGG 59.719 45.833 0.00 0.00 0.00 2.69
2767 3249 3.655481 GCACCGTTGCTGCTTAGT 58.345 55.556 0.00 0.00 46.17 2.24
2849 3332 5.538433 TGGTCTTTTGGGTTTTCAGAATAGG 59.462 40.000 0.00 0.00 0.00 2.57
2876 3362 7.753309 AACTGTTGCTATTGTGGTTGTTATA 57.247 32.000 0.00 0.00 0.00 0.98
2877 3363 7.753309 ACTGTTGCTATTGTGGTTGTTATAA 57.247 32.000 0.00 0.00 0.00 0.98
2878 3364 8.348285 ACTGTTGCTATTGTGGTTGTTATAAT 57.652 30.769 0.00 0.00 0.00 1.28
2885 3371 8.338259 GCTATTGTGGTTGTTATAATCTCACTG 58.662 37.037 10.36 0.00 0.00 3.66
2895 3381 0.326264 AATCTCACTGGGCTGTGGTC 59.674 55.000 10.25 0.00 38.40 4.02
2896 3382 1.557269 ATCTCACTGGGCTGTGGTCC 61.557 60.000 10.25 0.00 38.40 4.46
2897 3383 3.596066 CTCACTGGGCTGTGGTCCG 62.596 68.421 10.25 0.00 40.80 4.79
2899 3385 2.203728 ACTGGGCTGTGGTCCGTA 60.204 61.111 0.00 0.00 40.80 4.02
2903 3389 2.577593 GGCTGTGGTCCGTACTCC 59.422 66.667 0.00 0.00 0.00 3.85
2979 3465 1.900498 GCTTCCAGTGTGCAAGCCT 60.900 57.895 7.24 0.00 37.20 4.58
3018 3757 6.980593 TGTTTACTGCATTGCTCATAACTTT 58.019 32.000 10.49 0.00 0.00 2.66
3100 3839 4.075682 GCTATGAAGGATTAAAGGAGCCC 58.924 47.826 0.00 0.00 0.00 5.19
3149 3888 1.943340 GCTCCCAGATCGAACAAATCC 59.057 52.381 0.00 0.00 0.00 3.01
3150 3889 2.205074 CTCCCAGATCGAACAAATCCG 58.795 52.381 0.00 0.00 0.00 4.18
3154 3893 1.933853 CAGATCGAACAAATCCGTCCC 59.066 52.381 0.00 0.00 0.00 4.46
3178 3917 3.189910 GGGGACCGATTGTTTGAGTAAAC 59.810 47.826 0.00 0.00 42.51 2.01
3351 4091 9.418045 GGTATCAATCTCTGCTAGAAGAAATAC 57.582 37.037 1.01 5.42 37.89 1.89
3368 4108 5.869888 AGAAATACTACAAAGACTTCGGCAG 59.130 40.000 0.00 0.00 0.00 4.85
3375 4115 0.902516 AAGACTTCGGCAGAGAGGCT 60.903 55.000 0.00 0.00 41.46 4.58
3405 4145 2.079158 CTGGAGCAACGATGTTGTCAT 58.921 47.619 10.96 0.00 36.95 3.06
3413 4153 4.379793 GCAACGATGTTGTCATTCTTTCAC 59.620 41.667 10.96 0.00 34.06 3.18
3414 4154 4.749245 ACGATGTTGTCATTCTTTCACC 57.251 40.909 0.00 0.00 34.06 4.02
3427 4167 0.309302 TTTCACCCGCACGAACATTG 59.691 50.000 0.00 0.00 0.00 2.82
3493 4233 2.793933 CATTGCTTTGATCAGCTTCCG 58.206 47.619 8.27 0.00 40.79 4.30
3494 4234 1.167851 TTGCTTTGATCAGCTTCCGG 58.832 50.000 8.27 0.00 40.79 5.14
3504 4244 2.423446 GCTTCCGGCGATGGATCT 59.577 61.111 9.30 0.00 38.00 2.75
3505 4245 1.958205 GCTTCCGGCGATGGATCTG 60.958 63.158 9.30 0.00 38.00 2.90
3506 4246 1.301244 CTTCCGGCGATGGATCTGG 60.301 63.158 9.30 0.00 38.00 3.86
3507 4247 2.032860 CTTCCGGCGATGGATCTGGT 62.033 60.000 9.30 0.00 38.00 4.00
3508 4248 0.757561 TTCCGGCGATGGATCTGGTA 60.758 55.000 9.30 0.00 38.00 3.25
3509 4249 1.006102 CCGGCGATGGATCTGGTAC 60.006 63.158 9.30 0.00 0.00 3.34
3510 4250 1.739667 CGGCGATGGATCTGGTACA 59.260 57.895 0.00 0.00 0.00 2.90
3567 4327 8.741603 ACAAAAAGCCTTAAAACTAGTACTCA 57.258 30.769 0.00 0.00 0.00 3.41
3662 4423 7.046033 GGATCTGATGAAAAATGGCTTCAAAT 58.954 34.615 0.00 0.00 36.43 2.32
3663 4424 8.199449 GGATCTGATGAAAAATGGCTTCAAATA 58.801 33.333 0.00 0.00 36.43 1.40
3664 4425 9.245962 GATCTGATGAAAAATGGCTTCAAATAG 57.754 33.333 0.00 0.00 36.43 1.73
3665 4426 7.549839 TCTGATGAAAAATGGCTTCAAATAGG 58.450 34.615 0.00 0.00 36.43 2.57
3666 4427 7.396907 TCTGATGAAAAATGGCTTCAAATAGGA 59.603 33.333 0.00 0.00 36.43 2.94
3667 4428 7.322664 TGATGAAAAATGGCTTCAAATAGGAC 58.677 34.615 0.00 0.00 36.43 3.85
3668 4429 6.916360 TGAAAAATGGCTTCAAATAGGACT 57.084 33.333 0.00 0.00 29.93 3.85
3669 4430 7.301868 TGAAAAATGGCTTCAAATAGGACTT 57.698 32.000 0.00 0.00 29.93 3.01
3670 4431 8.415950 TGAAAAATGGCTTCAAATAGGACTTA 57.584 30.769 0.00 0.00 29.93 2.24
3671 4432 8.865090 TGAAAAATGGCTTCAAATAGGACTTAA 58.135 29.630 0.00 0.00 29.93 1.85
3672 4433 9.705290 GAAAAATGGCTTCAAATAGGACTTAAA 57.295 29.630 0.00 0.00 0.00 1.52
3677 4438 8.519799 TGGCTTCAAATAGGACTTAAAATAGG 57.480 34.615 0.00 0.00 0.00 2.57
3678 4439 7.559897 TGGCTTCAAATAGGACTTAAAATAGGG 59.440 37.037 0.00 0.00 0.00 3.53
3679 4440 7.778382 GGCTTCAAATAGGACTTAAAATAGGGA 59.222 37.037 0.00 0.00 0.00 4.20
3680 4441 9.185680 GCTTCAAATAGGACTTAAAATAGGGAA 57.814 33.333 0.00 0.00 0.00 3.97
3689 4450 9.826574 AGGACTTAAAATAGGGAAAACAAAAAC 57.173 29.630 0.00 0.00 0.00 2.43
3690 4451 9.826574 GGACTTAAAATAGGGAAAACAAAAACT 57.173 29.630 0.00 0.00 0.00 2.66
3701 4462 9.826574 AGGGAAAACAAAAACTTAAAATAGGAC 57.173 29.630 0.00 0.00 0.00 3.85
3702 4463 9.826574 GGGAAAACAAAAACTTAAAATAGGACT 57.173 29.630 0.00 0.00 0.00 3.85
3718 4479 9.831682 AAAATAGGACTTAAAATAGGGGAAACA 57.168 29.630 0.00 0.00 0.00 2.83
3719 4480 9.831682 AAATAGGACTTAAAATAGGGGAAACAA 57.168 29.630 0.00 0.00 0.00 2.83
3720 4481 9.831682 AATAGGACTTAAAATAGGGGAAACAAA 57.168 29.630 0.00 0.00 0.00 2.83
3721 4482 9.831682 ATAGGACTTAAAATAGGGGAAACAAAA 57.168 29.630 0.00 0.00 0.00 2.44
3722 4483 8.555896 AGGACTTAAAATAGGGGAAACAAAAA 57.444 30.769 0.00 0.00 0.00 1.94
3723 4484 8.426489 AGGACTTAAAATAGGGGAAACAAAAAC 58.574 33.333 0.00 0.00 0.00 2.43
3724 4485 8.426489 GGACTTAAAATAGGGGAAACAAAAACT 58.574 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 225 9.143631 GATGGCATTTTTATATTAAGTGATGGC 57.856 33.333 0.00 11.00 38.73 4.40
303 329 3.426159 CGTGACTGTTTAACCATGATGGC 60.426 47.826 12.25 0.00 42.67 4.40
324 350 3.829886 ATGTTACAAGACAACATGGCG 57.170 42.857 0.00 0.00 43.27 5.69
355 418 6.375377 TGCCACGACAGTATTAACATTTTTC 58.625 36.000 0.00 0.00 0.00 2.29
361 424 5.950758 AATTTGCCACGACAGTATTAACA 57.049 34.783 0.00 0.00 0.00 2.41
367 431 3.215151 TGGAAAATTTGCCACGACAGTA 58.785 40.909 14.43 0.00 0.00 2.74
393 457 7.093771 CCCTCCTATTTTTGCTACATGACTTTT 60.094 37.037 0.00 0.00 0.00 2.27
412 476 1.979809 TTGAATCCCAAGCCCTCCTA 58.020 50.000 0.00 0.00 0.00 2.94
505 572 1.007502 TGCGAGTTTTGCACATGGC 60.008 52.632 0.00 0.00 45.13 4.40
542 609 6.754675 CACTTTACTTTTCAAATCAAACCCGT 59.245 34.615 0.00 0.00 0.00 5.28
592 659 5.746721 GCCACGTCAAATTTTGAACTAGTTT 59.253 36.000 13.21 0.00 42.15 2.66
622 689 1.440893 CACGGATCTCAGAGCAGGG 59.559 63.158 0.00 0.00 0.00 4.45
670 766 6.317642 TGGATTTGTACGGAAATCATAACAGG 59.682 38.462 16.30 0.00 42.04 4.00
672 768 7.689446 TTGGATTTGTACGGAAATCATAACA 57.311 32.000 16.30 6.28 42.04 2.41
712 810 9.699703 CTTAAAGTTAGAATATAGTCCCTCTGC 57.300 37.037 0.00 0.00 0.00 4.26
729 827 7.385205 GCACTGATCTGAGTGTTCTTAAAGTTA 59.615 37.037 13.14 0.00 44.53 2.24
962 1346 1.625870 CGAGCGCGTATTGAGTGTG 59.374 57.895 8.43 0.00 0.00 3.82
1233 1617 1.748122 CATCGCCTTGCAAGCCTCT 60.748 57.895 21.43 2.56 0.00 3.69
1278 1662 1.672881 GTCAACTGACAGCACTGCTTT 59.327 47.619 0.00 0.00 44.18 3.51
1343 1727 1.300465 ACACTGCAGCTCGTGTCAG 60.300 57.895 15.27 2.14 40.06 3.51
1398 1791 0.855349 GCGTCATGATTCTACCGCAG 59.145 55.000 17.97 0.00 40.72 5.18
1404 1797 1.935873 GCAAGCTGCGTCATGATTCTA 59.064 47.619 0.00 0.00 31.71 2.10
1472 1865 1.657751 GACAAAAGCCCCATCCTCGC 61.658 60.000 0.00 0.00 0.00 5.03
1484 1880 6.884280 ACTTCATACCTCCTTTGACAAAAG 57.116 37.500 1.62 0.00 42.17 2.27
1575 1974 2.357569 GGAGGGATCTGGCACTTGAAAT 60.358 50.000 0.00 0.00 0.00 2.17
1787 2248 0.800683 CAGGCGCGACGTCAAGATAA 60.801 55.000 17.16 0.00 32.13 1.75
1955 2428 5.819901 CAGTAATCCAAAGAGAAGATCCACC 59.180 44.000 0.00 0.00 0.00 4.61
2075 2548 0.627451 ATTCTGGCCTCAAGCATCCA 59.373 50.000 3.32 0.00 46.50 3.41
2131 2604 2.781681 ACTAGCACCGTAGCCAAAAT 57.218 45.000 0.00 0.00 34.23 1.82
2132 2605 3.258872 TCTTACTAGCACCGTAGCCAAAA 59.741 43.478 0.00 0.00 34.23 2.44
2254 2727 2.235016 GGTAGTTGCACCATGGTTCAA 58.765 47.619 23.77 23.77 38.55 2.69
2255 2728 1.143889 TGGTAGTTGCACCATGGTTCA 59.856 47.619 16.84 15.10 43.76 3.18
2298 2771 5.010617 GCTTTGTGGTCTTCCCTTTTTCATA 59.989 40.000 0.00 0.00 0.00 2.15
2321 2794 2.479566 TTGGATCCAACTCACAGAGC 57.520 50.000 23.63 0.00 32.04 4.09
2349 2822 1.556911 TGCTTCTTCACATCCTCCCTC 59.443 52.381 0.00 0.00 0.00 4.30
2363 2836 3.881688 CCTGCTTTACATATGCTGCTTCT 59.118 43.478 1.58 0.00 0.00 2.85
2368 2844 2.880890 GGTCCCTGCTTTACATATGCTG 59.119 50.000 1.58 0.00 0.00 4.41
2546 3022 5.828747 TGTGAGGCGAAATGTCTATAGTAC 58.171 41.667 0.00 0.00 27.59 2.73
2547 3023 5.826208 TCTGTGAGGCGAAATGTCTATAGTA 59.174 40.000 0.00 0.00 27.59 1.82
2548 3024 4.645136 TCTGTGAGGCGAAATGTCTATAGT 59.355 41.667 0.00 0.00 27.59 2.12
2549 3025 5.188327 TCTGTGAGGCGAAATGTCTATAG 57.812 43.478 0.00 0.00 27.59 1.31
2550 3026 5.301805 TGATCTGTGAGGCGAAATGTCTATA 59.698 40.000 0.00 0.00 27.59 1.31
2551 3027 4.100035 TGATCTGTGAGGCGAAATGTCTAT 59.900 41.667 0.00 0.00 27.59 1.98
2552 3028 3.447229 TGATCTGTGAGGCGAAATGTCTA 59.553 43.478 0.00 0.00 27.59 2.59
2553 3029 2.234661 TGATCTGTGAGGCGAAATGTCT 59.765 45.455 0.00 0.00 32.87 3.41
2554 3030 2.621338 TGATCTGTGAGGCGAAATGTC 58.379 47.619 0.00 0.00 0.00 3.06
2561 3037 4.033358 GTGAGTTTTATGATCTGTGAGGCG 59.967 45.833 0.00 0.00 0.00 5.52
2654 3130 1.709578 AGAGCTCTGTGAGTCACCAA 58.290 50.000 17.42 7.59 32.73 3.67
2664 3140 2.659800 ACGGTGCTAAGAGCTCTGT 58.340 52.632 19.06 10.16 46.05 3.41
2741 3223 4.504132 CAACGGTGCTAGGAGCTC 57.496 61.111 11.82 4.71 42.97 4.09
2797 3280 1.687563 GCACCCACAACAGGTTAACT 58.312 50.000 5.42 0.00 34.56 2.24
2868 3351 5.065218 CACAGCCCAGTGAGATTATAACAAC 59.935 44.000 0.00 0.00 42.05 3.32
2876 3362 0.326264 GACCACAGCCCAGTGAGATT 59.674 55.000 3.37 0.00 42.05 2.40
2877 3363 1.557269 GGACCACAGCCCAGTGAGAT 61.557 60.000 3.37 0.00 42.05 2.75
2878 3364 2.217038 GGACCACAGCCCAGTGAGA 61.217 63.158 3.37 0.00 42.05 3.27
2885 3371 2.577593 GAGTACGGACCACAGCCC 59.422 66.667 0.00 0.00 0.00 5.19
2895 3381 2.352814 CCAAGTGAACTCTGGAGTACGG 60.353 54.545 3.54 0.00 41.58 4.02
2896 3382 2.557056 TCCAAGTGAACTCTGGAGTACG 59.443 50.000 3.54 0.00 41.58 3.67
2897 3383 4.810191 ATCCAAGTGAACTCTGGAGTAC 57.190 45.455 15.07 0.14 41.58 2.73
2899 3385 4.349342 AGAAATCCAAGTGAACTCTGGAGT 59.651 41.667 15.07 11.71 44.94 3.85
2903 3389 5.009410 AGCAAAGAAATCCAAGTGAACTCTG 59.991 40.000 0.00 0.00 0.00 3.35
2986 3472 3.989167 GCAATGCAGTAAACAATCAGCAA 59.011 39.130 0.00 0.00 35.45 3.91
3027 3766 7.839705 TGAAGGATGTAGTAGAGAACTGGTAAT 59.160 37.037 0.00 0.00 39.39 1.89
3033 3772 7.122715 ACTGATGAAGGATGTAGTAGAGAACT 58.877 38.462 0.00 0.00 42.62 3.01
3100 3839 1.866601 TCAATCGTCAGCGCCATATTG 59.133 47.619 2.29 7.94 38.14 1.90
3154 3893 1.271379 ACTCAAACAATCGGTCCCCAG 60.271 52.381 0.00 0.00 0.00 4.45
3166 3905 7.540299 AGGAAACAATTTCGTTTACTCAAACA 58.460 30.769 1.21 0.00 45.07 2.83
3167 3906 7.980742 AGGAAACAATTTCGTTTACTCAAAC 57.019 32.000 1.21 0.00 45.07 2.93
3201 3941 5.761234 TGTAATTGAAGGTGTTACAGGTGTC 59.239 40.000 0.00 0.00 34.44 3.67
3351 4091 3.506810 CTCTCTGCCGAAGTCTTTGTAG 58.493 50.000 0.00 0.00 0.00 2.74
3368 4108 1.093159 CAGTCCAATTGCAGCCTCTC 58.907 55.000 0.00 0.00 0.00 3.20
3375 4115 0.961019 GTTGCTCCAGTCCAATTGCA 59.039 50.000 0.00 0.00 0.00 4.08
3405 4145 0.462225 TGTTCGTGCGGGTGAAAGAA 60.462 50.000 0.00 0.00 0.00 2.52
3413 4153 2.211619 ATTGGCAATGTTCGTGCGGG 62.212 55.000 12.82 0.00 43.18 6.13
3414 4154 0.449786 TATTGGCAATGTTCGTGCGG 59.550 50.000 22.57 0.00 43.18 5.69
3427 4167 6.372381 AGGTGCTTTCAAAAATCATTATTGGC 59.628 34.615 0.00 0.00 0.00 4.52
3493 4233 2.325583 TTTGTACCAGATCCATCGCC 57.674 50.000 0.00 0.00 0.00 5.54
3494 4234 3.938963 TCTTTTTGTACCAGATCCATCGC 59.061 43.478 0.00 0.00 0.00 4.58
3497 4237 5.185828 GGCTTTCTTTTTGTACCAGATCCAT 59.814 40.000 0.00 0.00 0.00 3.41
3498 4238 4.522789 GGCTTTCTTTTTGTACCAGATCCA 59.477 41.667 0.00 0.00 0.00 3.41
3499 4239 4.082190 GGGCTTTCTTTTTGTACCAGATCC 60.082 45.833 0.00 0.00 0.00 3.36
3500 4240 4.522789 TGGGCTTTCTTTTTGTACCAGATC 59.477 41.667 0.00 0.00 0.00 2.75
3501 4241 4.479158 TGGGCTTTCTTTTTGTACCAGAT 58.521 39.130 0.00 0.00 0.00 2.90
3502 4242 3.888930 CTGGGCTTTCTTTTTGTACCAGA 59.111 43.478 0.00 0.00 45.33 3.86
3504 4244 3.637769 ACTGGGCTTTCTTTTTGTACCA 58.362 40.909 0.00 0.00 0.00 3.25
3505 4245 4.665833 AACTGGGCTTTCTTTTTGTACC 57.334 40.909 0.00 0.00 0.00 3.34
3506 4246 6.978343 AAAAACTGGGCTTTCTTTTTGTAC 57.022 33.333 0.00 0.00 0.00 2.90
3530 4290 6.952773 AAGGCTTTTTGTATTAGTCACACA 57.047 33.333 0.00 0.00 0.00 3.72
3531 4291 9.738832 TTTTAAGGCTTTTTGTATTAGTCACAC 57.261 29.630 4.45 0.00 0.00 3.82
3550 4310 8.524487 AGTCATGTCTGAGTACTAGTTTTAAGG 58.476 37.037 0.00 0.00 33.14 2.69
3616 4377 4.889409 TCCATGCTAAATTTGATGGGAGTC 59.111 41.667 18.46 0.00 36.72 3.36
3631 4392 5.010314 GCCATTTTTCATCAGATCCATGCTA 59.990 40.000 0.00 0.00 0.00 3.49
3663 4424 9.826574 GTTTTTGTTTTCCCTATTTTAAGTCCT 57.173 29.630 0.00 0.00 0.00 3.85
3664 4425 9.826574 AGTTTTTGTTTTCCCTATTTTAAGTCC 57.173 29.630 0.00 0.00 0.00 3.85
3675 4436 9.826574 GTCCTATTTTAAGTTTTTGTTTTCCCT 57.173 29.630 0.00 0.00 0.00 4.20
3676 4437 9.826574 AGTCCTATTTTAAGTTTTTGTTTTCCC 57.173 29.630 0.00 0.00 0.00 3.97
3692 4453 9.831682 TGTTTCCCCTATTTTAAGTCCTATTTT 57.168 29.630 0.00 0.00 0.00 1.82
3693 4454 9.831682 TTGTTTCCCCTATTTTAAGTCCTATTT 57.168 29.630 0.00 0.00 0.00 1.40
3694 4455 9.831682 TTTGTTTCCCCTATTTTAAGTCCTATT 57.168 29.630 0.00 0.00 0.00 1.73
3695 4456 9.831682 TTTTGTTTCCCCTATTTTAAGTCCTAT 57.168 29.630 0.00 0.00 0.00 2.57
3696 4457 9.657728 TTTTTGTTTCCCCTATTTTAAGTCCTA 57.342 29.630 0.00 0.00 0.00 2.94
3697 4458 8.426489 GTTTTTGTTTCCCCTATTTTAAGTCCT 58.574 33.333 0.00 0.00 0.00 3.85
3698 4459 8.426489 AGTTTTTGTTTCCCCTATTTTAAGTCC 58.574 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.