Multiple sequence alignment - TraesCS5D01G309200

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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 TraesCS5D01G309200 chr5D 100.000 3893 0 0 1 3893 406396233 406392341 0.000000e+00 7190
1 TraesCS5D01G309200 chr5D 96.572 671 23 0 1 671 296957387 296958057 0.000000e+00 1112
2 TraesCS5D01G309200 chr5D 97.959 343 5 1 329 671 296950875 296951215 9.310000e-166 593
3 TraesCS5D01G309200 chr5D 97.674 344 8 0 333 676 406401018 406400675 3.350000e-165 592
4 TraesCS5D01G309200 chr5B 94.147 2785 95 28 674 3442 487346542 487343810 0.000000e+00 4178
5 TraesCS5D01G309200 chr5B 90.000 220 9 7 3438 3646 487342980 487342763 4.960000e-69 272
6 TraesCS5D01G309200 chr5B 90.780 141 10 1 3749 3889 487342583 487342446 6.640000e-43 185
7 TraesCS5D01G309200 chr5A 94.470 2640 82 27 674 3287 512052432 512049831 0.000000e+00 4008
8 TraesCS5D01G309200 chr5A 85.714 413 15 21 3289 3699 512049797 512049427 2.820000e-106 396
9 TraesCS5D01G309200 chr3D 86.378 1960 202 42 988 2894 613056905 613058852 0.000000e+00 2080
10 TraesCS5D01G309200 chr3A 88.208 1696 171 19 1224 2893 747723739 747725431 0.000000e+00 1997
11 TraesCS5D01G309200 chr3B 84.140 2150 246 68 809 2893 825994469 825992350 0.000000e+00 1993
12 TraesCS5D01G309200 chr6B 93.304 672 42 3 2 673 2257145 2256477 0.000000e+00 989
13 TraesCS5D01G309200 chr6B 91.014 345 29 1 332 676 2263511 2263169 7.620000e-127 464
14 TraesCS5D01G309200 chr1D 85.633 703 77 19 1407 2094 104593964 104594657 0.000000e+00 717
15 TraesCS5D01G309200 chr1D 82.595 316 42 11 1233 1543 440718648 440718955 2.310000e-67 267
16 TraesCS5D01G309200 chr1D 84.247 146 23 0 2472 2617 265986820 265986675 4.050000e-30 143
17 TraesCS5D01G309200 chr7D 84.906 530 76 4 2371 2898 555233265 555232738 2.060000e-147 532
18 TraesCS5D01G309200 chr7D 77.091 550 113 12 1717 2258 509631640 509631096 4.890000e-79 305
19 TraesCS5D01G309200 chr1A 75.770 714 142 30 1717 2413 537346917 537346218 8.060000e-87 331
20 TraesCS5D01G309200 chr1A 81.646 316 45 11 1233 1543 537347602 537347295 2.320000e-62 250
21 TraesCS5D01G309200 chr1B 75.417 720 140 34 1714 2413 598191549 598192251 8.120000e-82 315
22 TraesCS5D01G309200 chr1B 90.129 233 23 0 1179 1411 616824823 616825055 1.760000e-78 303
23 TraesCS5D01G309200 chr1B 92.697 178 13 0 2274 2451 616824819 616824642 1.390000e-64 257
24 TraesCS5D01G309200 chr1B 95.890 146 6 0 2307 2452 616963177 616963032 1.810000e-58 237
25 TraesCS5D01G309200 chr1B 91.083 157 11 2 2307 2462 616958867 616959021 3.940000e-50 209
26 TraesCS5D01G309200 chr1B 83.938 193 27 4 167 357 646234821 646235011 8.590000e-42 182
27 TraesCS5D01G309200 chr7B 80.723 332 54 8 1233 1562 685360922 685360599 2.320000e-62 250


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 TraesCS5D01G309200 chr5D 406392341 406396233 3892 True 7190.0 7190 100.000000 1 3893 1 chr5D.!!$R1 3892
1 TraesCS5D01G309200 chr5D 296957387 296958057 670 False 1112.0 1112 96.572000 1 671 1 chr5D.!!$F2 670
2 TraesCS5D01G309200 chr5B 487342446 487346542 4096 True 1545.0 4178 91.642333 674 3889 3 chr5B.!!$R1 3215
3 TraesCS5D01G309200 chr5A 512049427 512052432 3005 True 2202.0 4008 90.092000 674 3699 2 chr5A.!!$R1 3025
4 TraesCS5D01G309200 chr3D 613056905 613058852 1947 False 2080.0 2080 86.378000 988 2894 1 chr3D.!!$F1 1906
5 TraesCS5D01G309200 chr3A 747723739 747725431 1692 False 1997.0 1997 88.208000 1224 2893 1 chr3A.!!$F1 1669
6 TraesCS5D01G309200 chr3B 825992350 825994469 2119 True 1993.0 1993 84.140000 809 2893 1 chr3B.!!$R1 2084
7 TraesCS5D01G309200 chr6B 2256477 2257145 668 True 989.0 989 93.304000 2 673 1 chr6B.!!$R1 671
8 TraesCS5D01G309200 chr1D 104593964 104594657 693 False 717.0 717 85.633000 1407 2094 1 chr1D.!!$F1 687
9 TraesCS5D01G309200 chr7D 555232738 555233265 527 True 532.0 532 84.906000 2371 2898 1 chr7D.!!$R2 527
10 TraesCS5D01G309200 chr7D 509631096 509631640 544 True 305.0 305 77.091000 1717 2258 1 chr7D.!!$R1 541
11 TraesCS5D01G309200 chr1A 537346218 537347602 1384 True 290.5 331 78.708000 1233 2413 2 chr1A.!!$R1 1180
12 TraesCS5D01G309200 chr1B 598191549 598192251 702 False 315.0 315 75.417000 1714 2413 1 chr1B.!!$F1 699

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
754 755 0.327924 AGCCACAAATGATCCCGTGA 59.672 50.000 0.00 0.0 0.0 4.35 F
834 841 1.279271 CACAAAGGATCCCGGACTCTT 59.721 52.381 8.55 0.0 0.0 2.85 F
2100 2480 0.905357 AGTACAAGCAGGCCTTCGAT 59.095 50.000 0.00 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2480 0.666274 CGCCTGACTTGTCGTGCTTA 60.666 55.0 10.85 0.0 0.00 3.09 R
2552 2935 1.386533 CATCATGTCCTTGGACAGCC 58.613 55.0 24.22 0.0 38.59 4.85 R
3060 3462 0.653636 GACGGTTCAAACAGTCGCAA 59.346 50.0 9.76 0.0 42.47 4.85 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
21 22 4.072088 GTTTGCCGTGGAGCGTCG 62.072 66.667 0.00 0.00 39.32 5.12
63 64 2.849162 GGATCAGATCCGGGGGCA 60.849 66.667 14.02 0.00 40.13 5.36
341 342 3.579586 TCTGATACCAAGTTGTAACGGGT 59.420 43.478 15.11 15.11 41.85 5.28
605 606 2.692557 CACAGCTCTAGCCACTACTCAT 59.307 50.000 0.00 0.00 43.38 2.90
684 685 2.069273 GTCATGACACTCCAGTTTCCG 58.931 52.381 21.07 0.00 0.00 4.30
717 718 4.523813 CCTGTAGTGCTAAACGTGTTTTG 58.476 43.478 2.97 3.05 34.23 2.44
718 719 4.271533 CCTGTAGTGCTAAACGTGTTTTGA 59.728 41.667 10.38 0.00 34.23 2.69
744 745 5.997746 AGAATATACATACGCAGCCACAAAT 59.002 36.000 0.00 0.00 0.00 2.32
754 755 0.327924 AGCCACAAATGATCCCGTGA 59.672 50.000 0.00 0.00 0.00 4.35
834 841 1.279271 CACAAAGGATCCCGGACTCTT 59.721 52.381 8.55 0.00 0.00 2.85
1286 1351 4.452733 CTTCCAGGTCGTCCCGGC 62.453 72.222 0.00 0.00 38.74 6.13
2100 2480 0.905357 AGTACAAGCAGGCCTTCGAT 59.095 50.000 0.00 0.00 0.00 3.59
2115 2495 3.242518 CTTCGATAAGCACGACAAGTCA 58.757 45.455 0.72 0.00 39.46 3.41
2909 3298 1.228184 GAGAGCCCAGCCATGATGG 60.228 63.158 7.21 7.21 39.04 3.51
2932 3321 3.577667 TCATCGATTTGCTTTGCCTTTG 58.422 40.909 0.00 0.00 0.00 2.77
2933 3322 3.005684 TCATCGATTTGCTTTGCCTTTGT 59.994 39.130 0.00 0.00 0.00 2.83
2934 3323 3.451141 TCGATTTGCTTTGCCTTTGTT 57.549 38.095 0.00 0.00 0.00 2.83
2936 3325 3.801594 TCGATTTGCTTTGCCTTTGTTTC 59.198 39.130 0.00 0.00 0.00 2.78
2938 3327 1.933247 TTGCTTTGCCTTTGTTTCCG 58.067 45.000 0.00 0.00 0.00 4.30
2939 3328 0.820871 TGCTTTGCCTTTGTTTCCGT 59.179 45.000 0.00 0.00 0.00 4.69
2941 3330 2.427453 TGCTTTGCCTTTGTTTCCGTTA 59.573 40.909 0.00 0.00 0.00 3.18
2948 3338 3.040099 CCTTTGTTTCCGTTAGTTTGCG 58.960 45.455 0.00 0.00 0.00 4.85
2990 3391 1.222115 GAAGCTGTGAACCGAACGCT 61.222 55.000 0.00 0.00 0.00 5.07
2992 3393 0.814010 AGCTGTGAACCGAACGCTTT 60.814 50.000 0.00 0.00 0.00 3.51
3059 3461 3.581755 TCTGAATGAATTGCTTGCTTGC 58.418 40.909 0.00 0.00 0.00 4.01
3060 3462 3.257375 TCTGAATGAATTGCTTGCTTGCT 59.743 39.130 3.47 0.00 0.00 3.91
3061 3463 3.994392 CTGAATGAATTGCTTGCTTGCTT 59.006 39.130 3.47 0.00 0.00 3.91
3062 3464 3.743911 TGAATGAATTGCTTGCTTGCTTG 59.256 39.130 3.47 0.00 0.00 4.01
3063 3465 1.504359 TGAATTGCTTGCTTGCTTGC 58.496 45.000 3.47 0.00 0.00 4.01
3076 3478 0.380378 TGCTTGCGACTGTTTGAACC 59.620 50.000 0.00 0.00 0.00 3.62
3121 3523 9.250624 CTTCAGTTACAGCCTTTACTCATATAC 57.749 37.037 0.00 0.00 0.00 1.47
3122 3524 8.534954 TCAGTTACAGCCTTTACTCATATACT 57.465 34.615 0.00 0.00 0.00 2.12
3123 3525 9.636789 TCAGTTACAGCCTTTACTCATATACTA 57.363 33.333 0.00 0.00 0.00 1.82
3124 3526 9.900710 CAGTTACAGCCTTTACTCATATACTAG 57.099 37.037 0.00 0.00 0.00 2.57
3125 3527 9.643735 AGTTACAGCCTTTACTCATATACTAGT 57.356 33.333 0.00 0.00 0.00 2.57
3151 3554 4.691685 TGAAATCCAATTGCATGCTGAAAC 59.308 37.500 20.33 1.16 0.00 2.78
3249 3653 6.888105 ACCTCCAAAATGATTCAGTTTTGTT 58.112 32.000 20.44 0.57 41.43 2.83
3280 3704 0.251474 TTCTGGCTGGCTGAAATGCT 60.251 50.000 18.67 0.00 0.00 3.79
3305 3762 4.339814 AGTTCGTTCTATAGCTTCTCCTGG 59.660 45.833 0.00 0.00 0.00 4.45
3336 3793 0.396435 AGCGGTTCACCACTCATGAA 59.604 50.000 0.00 0.00 35.14 2.57
3341 3798 0.404040 TTCACCACTCATGAACCCCC 59.596 55.000 0.00 0.00 31.11 5.40
3370 3827 5.710513 AAGTGCAGCATTACAATTTCTGA 57.289 34.783 0.00 0.00 0.00 3.27
3371 3828 5.909621 AGTGCAGCATTACAATTTCTGAT 57.090 34.783 0.00 0.00 0.00 2.90
3372 3829 5.888105 AGTGCAGCATTACAATTTCTGATC 58.112 37.500 0.00 0.00 0.00 2.92
3373 3830 4.731961 GTGCAGCATTACAATTTCTGATCG 59.268 41.667 0.00 0.00 0.00 3.69
3374 3831 4.395854 TGCAGCATTACAATTTCTGATCGT 59.604 37.500 0.00 0.00 0.00 3.73
3375 3832 4.731961 GCAGCATTACAATTTCTGATCGTG 59.268 41.667 0.00 0.00 0.00 4.35
3376 3833 5.447683 GCAGCATTACAATTTCTGATCGTGA 60.448 40.000 0.00 0.00 0.00 4.35
3377 3834 6.545508 CAGCATTACAATTTCTGATCGTGAA 58.454 36.000 0.00 0.00 0.00 3.18
3378 3835 6.685828 CAGCATTACAATTTCTGATCGTGAAG 59.314 38.462 0.00 0.00 0.00 3.02
3379 3836 6.372659 AGCATTACAATTTCTGATCGTGAAGT 59.627 34.615 0.00 0.00 0.00 3.01
3380 3837 7.023575 GCATTACAATTTCTGATCGTGAAGTT 58.976 34.615 4.12 4.12 0.00 2.66
3381 3838 7.538678 GCATTACAATTTCTGATCGTGAAGTTT 59.461 33.333 6.37 1.73 0.00 2.66
3382 3839 9.055248 CATTACAATTTCTGATCGTGAAGTTTC 57.945 33.333 6.37 0.00 0.00 2.78
3383 3840 6.618287 ACAATTTCTGATCGTGAAGTTTCA 57.382 33.333 6.37 0.00 34.20 2.69
3384 3841 7.026631 ACAATTTCTGATCGTGAAGTTTCAA 57.973 32.000 0.00 0.00 39.21 2.69
3385 3842 7.651808 ACAATTTCTGATCGTGAAGTTTCAAT 58.348 30.769 0.00 0.00 39.21 2.57
3386 3843 7.805071 ACAATTTCTGATCGTGAAGTTTCAATC 59.195 33.333 0.00 0.00 39.21 2.67
3387 3844 5.862924 TTCTGATCGTGAAGTTTCAATCC 57.137 39.130 0.00 0.00 39.21 3.01
3388 3845 4.893608 TCTGATCGTGAAGTTTCAATCCA 58.106 39.130 0.00 0.00 39.21 3.41
3394 3861 7.336679 TGATCGTGAAGTTTCAATCCATAACAT 59.663 33.333 0.00 0.00 39.21 2.71
3539 4840 5.567138 AAAGCAATGCAACCTGAGTATAC 57.433 39.130 8.35 0.00 0.00 1.47
3546 4847 3.134458 GCAACCTGAGTATACATGGAGC 58.866 50.000 5.50 9.51 0.00 4.70
3562 4864 7.625828 ACATGGAGCACTATAAAAAGGTTAC 57.374 36.000 0.00 0.00 0.00 2.50
3596 4898 7.488187 TTCTCTCAATCAAACTGTTCTGAAG 57.512 36.000 0.00 0.00 0.00 3.02
3611 4920 9.736023 ACTGTTCTGAAGATATTTTGTTTTCAC 57.264 29.630 0.00 0.00 0.00 3.18
3642 4954 4.568359 TCTTACGATGTACTCCGTACTCAC 59.432 45.833 16.03 0.00 40.41 3.51
3674 4986 5.305585 TCGTTGCCTACATTCTTCTTCTTT 58.694 37.500 0.00 0.00 0.00 2.52
3701 5104 2.108075 TCTCTCTCAGCCCATCCTAGAG 59.892 54.545 0.00 0.00 35.97 2.43
3710 5113 2.487934 CCCATCCTAGAGTCAAATGCG 58.512 52.381 0.00 0.00 0.00 4.73
3712 5115 1.524355 CATCCTAGAGTCAAATGCGCG 59.476 52.381 0.00 0.00 0.00 6.86
3719 5122 1.859135 GTCAAATGCGCGCTTCGTC 60.859 57.895 33.29 14.13 41.07 4.20
3731 5134 2.652172 GCGCTTCGTCATTTTTCACTTC 59.348 45.455 0.00 0.00 0.00 3.01
3734 5137 4.222114 GCTTCGTCATTTTTCACTTCTGG 58.778 43.478 0.00 0.00 0.00 3.86
3735 5138 4.024048 GCTTCGTCATTTTTCACTTCTGGA 60.024 41.667 0.00 0.00 0.00 3.86
3736 5139 5.505654 GCTTCGTCATTTTTCACTTCTGGAA 60.506 40.000 0.00 0.00 0.00 3.53
3737 5140 6.443934 TTCGTCATTTTTCACTTCTGGAAA 57.556 33.333 0.00 0.00 32.74 3.13
3738 5141 6.633500 TCGTCATTTTTCACTTCTGGAAAT 57.367 33.333 0.00 0.00 34.50 2.17
3739 5142 7.737972 TCGTCATTTTTCACTTCTGGAAATA 57.262 32.000 0.00 0.00 34.50 1.40
3740 5143 8.160521 TCGTCATTTTTCACTTCTGGAAATAA 57.839 30.769 0.00 0.00 34.50 1.40
3741 5144 8.073768 TCGTCATTTTTCACTTCTGGAAATAAC 58.926 33.333 0.00 0.00 34.50 1.89
3742 5145 7.059488 CGTCATTTTTCACTTCTGGAAATAACG 59.941 37.037 0.00 0.00 34.50 3.18
3743 5146 8.073768 GTCATTTTTCACTTCTGGAAATAACGA 58.926 33.333 0.00 0.00 34.50 3.85
3744 5147 8.625651 TCATTTTTCACTTCTGGAAATAACGAA 58.374 29.630 0.00 0.00 34.50 3.85
3745 5148 9.243637 CATTTTTCACTTCTGGAAATAACGAAA 57.756 29.630 0.00 0.00 34.50 3.46
3746 5149 9.810545 ATTTTTCACTTCTGGAAATAACGAAAA 57.189 25.926 0.00 0.00 34.50 2.29
3747 5150 9.640963 TTTTTCACTTCTGGAAATAACGAAAAA 57.359 25.926 0.00 0.00 37.44 1.94
3821 5224 7.041372 TGACTTCAGTTTTGGTTATGTTCTAGC 60.041 37.037 0.00 0.00 0.00 3.42
3842 5245 8.952278 TCTAGCGGTGTTTTTCATACATTTATT 58.048 29.630 0.00 0.00 0.00 1.40
3884 5287 7.384115 TGTTGAAGACGGTATTTGTTCTAAGAG 59.616 37.037 0.00 0.00 0.00 2.85
3889 5292 7.097834 AGACGGTATTTGTTCTAAGAGGAAAG 58.902 38.462 0.00 0.00 0.00 2.62
3890 5293 5.642491 ACGGTATTTGTTCTAAGAGGAAAGC 59.358 40.000 0.00 0.00 0.00 3.51
3891 5294 5.220416 CGGTATTTGTTCTAAGAGGAAAGCG 60.220 44.000 0.00 0.00 0.00 4.68
3892 5295 5.642491 GGTATTTGTTCTAAGAGGAAAGCGT 59.358 40.000 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 232 2.729479 CGATGGAGGAGCAGCTGGT 61.729 63.158 20.31 20.31 0.00 4.00
341 342 3.654517 GCCCTAGGCTAGATCGAGA 57.345 57.895 22.99 0.00 46.69 4.04
394 395 0.689412 CCTCTTCCTCCTCCCCAGAC 60.689 65.000 0.00 0.00 0.00 3.51
684 685 1.798813 GCACTACAGGCTGTGTTACAC 59.201 52.381 29.65 8.76 40.94 2.90
717 718 4.859798 GTGGCTGCGTATGTATATTCTCTC 59.140 45.833 0.00 0.00 0.00 3.20
718 719 4.280929 TGTGGCTGCGTATGTATATTCTCT 59.719 41.667 0.00 0.00 0.00 3.10
744 745 4.312443 GAAGTTGTACTTTCACGGGATCA 58.688 43.478 0.00 0.00 38.80 2.92
834 841 1.508808 GCCACCGCAACCGACTTAAA 61.509 55.000 0.00 0.00 36.29 1.52
984 1004 3.068691 ATGGCTGGCTTGCTGCTG 61.069 61.111 0.00 0.00 42.39 4.41
985 1005 3.068691 CATGGCTGGCTTGCTGCT 61.069 61.111 0.00 0.00 42.39 4.24
1144 1200 3.519930 GCCCTCGGAGTCGGAGTC 61.520 72.222 22.09 12.25 36.95 3.36
1383 1448 4.125695 GACTTACCGAGCCCGCGT 62.126 66.667 4.92 0.00 0.00 6.01
1395 1460 2.043652 CCCTCCCGGTCGGACTTA 60.044 66.667 11.39 0.00 34.86 2.24
1656 1778 1.446966 GTGCTCCGTCTCCTTCTGC 60.447 63.158 0.00 0.00 0.00 4.26
2100 2480 0.666274 CGCCTGACTTGTCGTGCTTA 60.666 55.000 10.85 0.00 0.00 3.09
2184 2564 2.184322 GCGGCCAAGATCTCGTGA 59.816 61.111 2.24 0.00 0.00 4.35
2552 2935 1.386533 CATCATGTCCTTGGACAGCC 58.613 55.000 24.22 0.00 38.59 4.85
2909 3298 3.705043 AGGCAAAGCAAATCGATGATC 57.295 42.857 0.00 0.00 0.00 2.92
2932 3321 3.422732 GCTAGTCGCAAACTAACGGAAAC 60.423 47.826 0.00 0.00 39.98 2.78
2933 3322 2.733026 GCTAGTCGCAAACTAACGGAAA 59.267 45.455 0.00 0.00 39.98 3.13
2934 3323 2.029649 AGCTAGTCGCAAACTAACGGAA 60.030 45.455 0.00 0.00 39.98 4.30
2936 3325 1.992170 AGCTAGTCGCAAACTAACGG 58.008 50.000 0.00 0.00 39.98 4.44
2938 3327 3.858238 CACCTAGCTAGTCGCAAACTAAC 59.142 47.826 19.31 0.00 39.98 2.34
2939 3328 3.760151 TCACCTAGCTAGTCGCAAACTAA 59.240 43.478 19.31 0.00 39.98 2.24
2941 3330 2.168496 TCACCTAGCTAGTCGCAAACT 58.832 47.619 19.31 0.00 42.61 2.66
2948 3338 5.825679 TCAGAGAGATTTCACCTAGCTAGTC 59.174 44.000 19.31 9.08 0.00 2.59
2990 3391 7.864108 TTCAGTTCAGAGATTCAGAACAAAA 57.136 32.000 14.16 7.03 42.89 2.44
2992 3393 7.219322 TCATTCAGTTCAGAGATTCAGAACAA 58.781 34.615 14.16 4.27 42.89 2.83
3059 3461 0.655733 ACGGTTCAAACAGTCGCAAG 59.344 50.000 0.00 0.00 31.70 4.01
3060 3462 0.653636 GACGGTTCAAACAGTCGCAA 59.346 50.000 9.76 0.00 42.47 4.85
3061 3463 2.303452 GACGGTTCAAACAGTCGCA 58.697 52.632 9.76 0.00 42.47 5.10
3076 3478 4.033932 TGAAGAATAACCATGCAATCGACG 59.966 41.667 0.00 0.00 0.00 5.12
3121 3523 7.381408 CAGCATGCAATTGGATTTCATTACTAG 59.619 37.037 21.98 0.00 0.00 2.57
3122 3524 7.068470 TCAGCATGCAATTGGATTTCATTACTA 59.932 33.333 21.98 0.00 34.76 1.82
3123 3525 6.046593 CAGCATGCAATTGGATTTCATTACT 58.953 36.000 21.98 0.57 0.00 2.24
3124 3526 6.044046 TCAGCATGCAATTGGATTTCATTAC 58.956 36.000 21.98 0.00 34.76 1.89
3125 3527 6.223351 TCAGCATGCAATTGGATTTCATTA 57.777 33.333 21.98 0.00 34.76 1.90
3126 3528 5.092554 TCAGCATGCAATTGGATTTCATT 57.907 34.783 21.98 0.00 34.76 2.57
3127 3529 4.746535 TCAGCATGCAATTGGATTTCAT 57.253 36.364 21.98 0.00 34.76 2.57
3128 3530 4.538746 TTCAGCATGCAATTGGATTTCA 57.461 36.364 21.98 0.00 34.76 2.69
3129 3531 4.093850 GGTTTCAGCATGCAATTGGATTTC 59.906 41.667 21.98 5.38 34.76 2.17
3130 3532 4.004982 GGTTTCAGCATGCAATTGGATTT 58.995 39.130 21.98 0.00 34.76 2.17
3131 3533 3.008157 TGGTTTCAGCATGCAATTGGATT 59.992 39.130 21.98 0.00 34.76 3.01
3132 3534 2.568062 TGGTTTCAGCATGCAATTGGAT 59.432 40.909 21.98 6.63 34.76 3.41
3151 3554 8.447924 ACACTTGATTGAGAATAGATGAATGG 57.552 34.615 0.00 0.00 0.00 3.16
3204 3608 7.361286 GGAGGTCTGAAATCAACAGTTACAATC 60.361 40.741 0.00 0.00 36.81 2.67
3222 3626 5.972107 AACTGAATCATTTTGGAGGTCTG 57.028 39.130 0.00 0.00 0.00 3.51
3249 3653 5.048083 CAGCCAGCCAGAATACAAAGTTAAA 60.048 40.000 0.00 0.00 0.00 1.52
3280 3704 6.039493 CCAGGAGAAGCTATAGAACGAACTAA 59.961 42.308 3.21 0.00 0.00 2.24
3305 3762 2.870411 GTGAACCGCTACATTCATACCC 59.130 50.000 0.00 0.00 37.19 3.69
3336 3793 2.357593 CTGCACTTTGGTGAGGGGGT 62.358 60.000 0.00 0.00 45.61 4.95
3341 3798 2.553602 TGTAATGCTGCACTTTGGTGAG 59.446 45.455 3.57 0.00 45.61 3.51
3370 3827 7.336679 TCATGTTATGGATTGAAACTTCACGAT 59.663 33.333 0.00 0.00 36.83 3.73
3371 3828 6.652900 TCATGTTATGGATTGAAACTTCACGA 59.347 34.615 0.00 0.00 36.83 4.35
3372 3829 6.841119 TCATGTTATGGATTGAAACTTCACG 58.159 36.000 0.00 0.00 36.83 4.35
3373 3830 9.474920 TTTTCATGTTATGGATTGAAACTTCAC 57.525 29.630 0.00 0.00 37.69 3.18
3384 3841 9.645128 TCCATCTACATTTTTCATGTTATGGAT 57.355 29.630 18.65 6.92 42.25 3.41
3385 3842 9.123902 CTCCATCTACATTTTTCATGTTATGGA 57.876 33.333 20.05 20.05 43.40 3.41
3386 3843 8.906867 ACTCCATCTACATTTTTCATGTTATGG 58.093 33.333 16.05 16.05 41.15 2.74
3394 3861 9.958180 TCTTATGAACTCCATCTACATTTTTCA 57.042 29.630 0.00 0.00 36.71 2.69
3462 4763 3.287222 CAATTGTAACGGGGTGGATGAT 58.713 45.455 0.00 0.00 0.00 2.45
3463 4764 2.717390 CAATTGTAACGGGGTGGATGA 58.283 47.619 0.00 0.00 0.00 2.92
3464 4765 1.134175 GCAATTGTAACGGGGTGGATG 59.866 52.381 7.40 0.00 0.00 3.51
3539 4840 7.552687 TCAGTAACCTTTTTATAGTGCTCCATG 59.447 37.037 0.00 0.00 0.00 3.66
3562 4864 8.965172 CAGTTTGATTGAGAGAAAATGTTTCAG 58.035 33.333 3.74 0.00 0.00 3.02
3642 4954 1.204704 TGTAGGCAACGAGTCTCATGG 59.795 52.381 0.00 0.00 46.39 3.66
3652 4964 5.613358 AAAGAAGAAGAATGTAGGCAACG 57.387 39.130 0.00 0.00 46.39 4.10
3674 4986 3.054802 GGATGGGCTGAGAGAGAGAAAAA 60.055 47.826 0.00 0.00 0.00 1.94
3679 4991 2.108075 TCTAGGATGGGCTGAGAGAGAG 59.892 54.545 0.00 0.00 0.00 3.20
3701 5104 1.859135 GACGAAGCGCGCATTTGAC 60.859 57.895 35.10 21.78 46.04 3.18
3710 5113 2.316119 AGTGAAAAATGACGAAGCGC 57.684 45.000 0.00 0.00 0.00 5.92
3712 5115 4.024048 TCCAGAAGTGAAAAATGACGAAGC 60.024 41.667 0.00 0.00 0.00 3.86
3719 5122 8.795786 TTCGTTATTTCCAGAAGTGAAAAATG 57.204 30.769 0.00 0.00 35.52 2.32
3790 5193 8.458573 ACATAACCAAAACTGAAGTCAACATA 57.541 30.769 0.00 0.00 0.00 2.29
3791 5194 7.346751 ACATAACCAAAACTGAAGTCAACAT 57.653 32.000 0.00 0.00 0.00 2.71
3792 5195 6.767524 ACATAACCAAAACTGAAGTCAACA 57.232 33.333 0.00 0.00 0.00 3.33
3801 5204 4.454504 ACCGCTAGAACATAACCAAAACTG 59.545 41.667 0.00 0.00 0.00 3.16
3808 5211 5.049267 TGAAAAACACCGCTAGAACATAACC 60.049 40.000 0.00 0.00 0.00 2.85
3809 5212 5.992729 TGAAAAACACCGCTAGAACATAAC 58.007 37.500 0.00 0.00 0.00 1.89
3842 5245 3.291584 TCAACAGCAACCCAACACAATA 58.708 40.909 0.00 0.00 0.00 1.90
3843 5246 2.106566 TCAACAGCAACCCAACACAAT 58.893 42.857 0.00 0.00 0.00 2.71
3844 5247 1.550327 TCAACAGCAACCCAACACAA 58.450 45.000 0.00 0.00 0.00 3.33
3845 5248 1.476085 CTTCAACAGCAACCCAACACA 59.524 47.619 0.00 0.00 0.00 3.72
3854 5257 3.880490 ACAAATACCGTCTTCAACAGCAA 59.120 39.130 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.