Multiple sequence alignment - TraesCS1A01G161400

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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 TraesCS1A01G161400 chr1A 100.000 4512 0 0 1 4512 290205903 290201392 0.000000e+00 8333
1 TraesCS1A01G161400 chr1B 94.056 4088 129 53 479 4512 322487046 322483019 0.000000e+00 6098
2 TraesCS1A01G161400 chr1B 90.428 491 39 7 1 488 322487931 322487446 1.370000e-179 640
3 TraesCS1A01G161400 chr7D 93.170 3397 110 41 515 3838 617975293 617971946 0.000000e+00 4876
4 TraesCS1A01G161400 chr7D 94.883 684 23 7 3840 4512 617971896 617971214 0.000000e+00 1059
5 TraesCS1A01G161400 chr7D 91.887 530 33 6 1 523 617976001 617975475 0.000000e+00 732
6 TraesCS1A01G161400 chr1D 93.045 3393 117 38 515 3838 223174472 223171130 0.000000e+00 4848
7 TraesCS1A01G161400 chr1D 94.737 684 24 7 3840 4512 223171080 223170398 0.000000e+00 1053
8 TraesCS1A01G161400 chr1D 92.264 530 34 4 1 523 223175183 223174654 0.000000e+00 745
9 TraesCS1A01G161400 chrUn 92.926 311 9 9 3534 3838 480384364 480384061 1.490000e-119 440


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 TraesCS1A01G161400 chr1A 290201392 290205903 4511 True 8333.000000 8333 100.000000 1 4512 1 chr1A.!!$R1 4511
1 TraesCS1A01G161400 chr1B 322483019 322487931 4912 True 3369.000000 6098 92.242000 1 4512 2 chr1B.!!$R1 4511
2 TraesCS1A01G161400 chr7D 617971214 617976001 4787 True 2222.333333 4876 93.313333 1 4512 3 chr7D.!!$R1 4511
3 TraesCS1A01G161400 chr1D 223170398 223175183 4785 True 2215.333333 4848 93.348667 1 4512 3 chr1D.!!$R1 4511

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
694 1309 0.096628 GCGCAAGAAGCAGATCAGTG 59.903 55.000 0.30 0.0 46.13 3.66 F
776 1391 1.301677 GCTCGAGGAAGGCCACAAAG 61.302 60.000 15.58 0.0 36.29 2.77 F
986 1630 6.205464 CACCTTTATCTGCATATCCAAATCGT 59.795 38.462 0.00 0.0 0.00 3.73 F
2624 3289 2.357637 CTGCTAGTCTGCTACTGAGGTC 59.642 54.545 2.92 0.0 39.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2621 0.108281 GGAACTTGTCCGAGTAGGCC 60.108 60.0 0.00 0.00 40.77 5.19 R
2058 2702 0.694771 TGAGCAGCCAGAAGAACCAT 59.305 50.0 0.00 0.00 0.00 3.55 R
2697 3363 0.731417 AGCTTCACGATGATGCAAGC 59.269 50.0 19.88 11.99 46.27 4.01 R
3529 4214 0.106719 ACTTGGGAACACACCACCAG 60.107 55.0 0.00 0.00 42.67 4.00 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
32 33 3.194329 TGCCACAGAGATGAGAGTTGTAG 59.806 47.826 0.00 0.00 0.00 2.74
148 150 5.592282 TGCTAAGTCACAAATTTCAACTCCA 59.408 36.000 0.00 0.00 0.00 3.86
178 180 4.278170 CCTCAAACATCCAAAAGTGCAGTA 59.722 41.667 0.00 0.00 0.00 2.74
234 237 2.874701 CCATAGCTGGATTTGTTCCTCG 59.125 50.000 0.00 0.00 46.37 4.63
255 258 6.697892 CCTCGGACTTAGAAATGACATTCTAC 59.302 42.308 0.05 0.00 40.62 2.59
270 273 5.933617 ACATTCTACCATGCACATCATACT 58.066 37.500 0.00 0.00 33.19 2.12
272 275 3.732212 TCTACCATGCACATCATACTGC 58.268 45.455 0.00 0.00 33.19 4.40
286 289 3.711190 TCATACTGCACATGTATCCACCT 59.289 43.478 0.00 0.00 0.00 4.00
345 348 6.045955 TGGTTTTTGACATAGTTTTCCTTGC 58.954 36.000 0.00 0.00 0.00 4.01
347 350 6.420903 GGTTTTTGACATAGTTTTCCTTGCTC 59.579 38.462 0.00 0.00 0.00 4.26
368 371 8.425577 TGCTCTAGAGTATTGCATAAAGTTTC 57.574 34.615 20.75 0.00 0.00 2.78
381 387 8.060020 TGCATAAAGTTTCGATGTTTTTCTTG 57.940 30.769 0.00 0.00 0.00 3.02
382 388 7.003648 GCATAAAGTTTCGATGTTTTTCTTGC 58.996 34.615 0.00 0.00 0.00 4.01
395 403 5.359576 TGTTTTTCTTGCCTCATTGTGTACT 59.640 36.000 0.00 0.00 0.00 2.73
429 437 4.020839 AGTGCACCTTATTTACTGGTACGT 60.021 41.667 14.63 0.00 32.13 3.57
469 477 8.702163 ATACACTTTGAACAGGAAAACAAAAG 57.298 30.769 0.00 0.00 33.05 2.27
471 479 4.935205 ACTTTGAACAGGAAAACAAAAGGC 59.065 37.500 0.00 0.00 33.05 4.35
523 938 5.619625 CAAACTTTGCCAAAACCAGAAAA 57.380 34.783 0.00 0.00 0.00 2.29
547 1153 1.537202 GGCACAAATCTCGAAGCAACT 59.463 47.619 0.00 0.00 0.00 3.16
560 1166 3.309138 CGAAGCAACTGAGAGAATCCATG 59.691 47.826 0.00 0.00 33.66 3.66
561 1167 3.996921 AGCAACTGAGAGAATCCATGT 57.003 42.857 0.00 0.00 33.66 3.21
562 1168 5.423015 GAAGCAACTGAGAGAATCCATGTA 58.577 41.667 0.00 0.00 33.66 2.29
604 1215 5.479124 TGGTAGAAAAACCACTCTCCTAC 57.521 43.478 0.00 0.00 44.68 3.18
694 1309 0.096628 GCGCAAGAAGCAGATCAGTG 59.903 55.000 0.30 0.00 46.13 3.66
731 1346 3.332034 CGGGATTAAACCGTTGAGAGTT 58.668 45.455 12.36 0.00 46.03 3.01
761 1376 1.344942 CGGGTCAAAAGAGTCGCTCG 61.345 60.000 1.98 0.00 35.36 5.03
776 1391 1.301677 GCTCGAGGAAGGCCACAAAG 61.302 60.000 15.58 0.00 36.29 2.77
984 1628 6.491403 ACCACCTTTATCTGCATATCCAAATC 59.509 38.462 0.00 0.00 0.00 2.17
985 1629 6.348786 CCACCTTTATCTGCATATCCAAATCG 60.349 42.308 0.00 0.00 0.00 3.34
986 1630 6.205464 CACCTTTATCTGCATATCCAAATCGT 59.795 38.462 0.00 0.00 0.00 3.73
987 1631 7.387673 CACCTTTATCTGCATATCCAAATCGTA 59.612 37.037 0.00 0.00 0.00 3.43
2318 2965 5.117897 CGTATAATACGTACATGCATGCACA 59.882 40.000 25.37 8.58 46.41 4.57
2475 3137 5.543507 TGAGGAAATTAAAGCAAGCCAAA 57.456 34.783 0.00 0.00 0.00 3.28
2504 3166 5.277828 GCTTCTCCTACAACAAAACAACGAT 60.278 40.000 0.00 0.00 0.00 3.73
2584 3249 6.931838 AGTCAAATAGGAACGATGACAAGTA 58.068 36.000 6.94 0.00 42.12 2.24
2607 3272 3.523564 ACTGGGTTATTGTGGATACTGCT 59.476 43.478 0.00 0.00 37.61 4.24
2608 3273 4.719773 ACTGGGTTATTGTGGATACTGCTA 59.280 41.667 0.00 0.00 37.61 3.49
2609 3274 5.163301 ACTGGGTTATTGTGGATACTGCTAG 60.163 44.000 0.00 0.00 37.61 3.42
2610 3275 4.719773 TGGGTTATTGTGGATACTGCTAGT 59.280 41.667 0.00 0.00 37.61 2.57
2611 3276 5.163343 TGGGTTATTGTGGATACTGCTAGTC 60.163 44.000 0.00 0.00 37.61 2.59
2612 3277 5.070580 GGGTTATTGTGGATACTGCTAGTCT 59.929 44.000 0.00 0.00 37.61 3.24
2613 3278 5.986135 GGTTATTGTGGATACTGCTAGTCTG 59.014 44.000 0.00 0.00 37.61 3.51
2614 3279 3.526931 TTGTGGATACTGCTAGTCTGC 57.473 47.619 0.00 0.00 37.61 4.26
2615 3280 2.739943 TGTGGATACTGCTAGTCTGCT 58.260 47.619 0.00 0.00 37.61 4.24
2624 3289 2.357637 CTGCTAGTCTGCTACTGAGGTC 59.642 54.545 2.92 0.00 39.39 3.85
2697 3363 4.752101 CACCTCACTAACTGGAGTTTTGAG 59.248 45.833 16.77 16.77 41.62 3.02
2709 3375 3.423571 GAGTTTTGAGCTTGCATCATCG 58.576 45.455 0.00 0.00 0.00 3.84
2732 3398 5.614382 CGTGAAGCTAACGTGTAAAAAGAAC 59.386 40.000 12.46 0.00 36.31 3.01
2758 3424 9.395707 CTTACGCAAGATTTATACTACTAGGTG 57.604 37.037 0.00 0.00 43.62 4.00
2893 3570 8.942338 TGTGCTCAGGTTTACTATACTTAATG 57.058 34.615 0.00 0.00 0.00 1.90
2938 3615 3.746940 TGCCAACAAGGGTACTCTTTAC 58.253 45.455 4.88 0.00 38.09 2.01
2949 3626 5.184671 AGGGTACTCTTTACCTTGTTCGTAG 59.815 44.000 0.00 0.00 37.71 3.51
2955 3632 6.481313 ACTCTTTACCTTGTTCGTAGAAAACC 59.519 38.462 0.00 0.00 45.90 3.27
2962 3639 4.295857 TGTTCGTAGAAAACCCAAAAGC 57.704 40.909 0.00 0.00 45.90 3.51
2966 3643 3.562557 TCGTAGAAAACCCAAAAGCAGAC 59.437 43.478 0.00 0.00 0.00 3.51
2986 3671 3.929610 GACCACAGCATCTTTAGTCAGAC 59.070 47.826 0.00 0.00 0.00 3.51
2997 3682 4.771054 TCTTTAGTCAGACCACCTAACCTC 59.229 45.833 0.00 0.00 0.00 3.85
3020 3705 2.025226 TCTACCTGGACTGGAGTAGGTG 60.025 54.545 10.40 3.15 43.11 4.00
3022 3707 1.149288 ACCTGGACTGGAGTAGGTGAA 59.851 52.381 0.00 0.00 41.76 3.18
3091 3776 5.738619 TGTCACCATGATAACTGTACTGT 57.261 39.130 0.00 0.00 0.00 3.55
3092 3777 5.478407 TGTCACCATGATAACTGTACTGTG 58.522 41.667 6.13 0.00 0.00 3.66
3219 3904 0.346574 TCCATGGGGAGGATGGAGAA 59.653 55.000 13.02 0.00 43.71 2.87
3253 3938 2.203922 TGCAGGGAGTACAGGCCA 60.204 61.111 5.01 0.00 0.00 5.36
3521 4206 2.507484 CCAAGCTCTGAACCACATCAA 58.493 47.619 0.00 0.00 0.00 2.57
3522 4207 2.886523 CCAAGCTCTGAACCACATCAAA 59.113 45.455 0.00 0.00 0.00 2.69
3524 4209 3.213206 AGCTCTGAACCACATCAAACA 57.787 42.857 0.00 0.00 0.00 2.83
3525 4210 3.759581 AGCTCTGAACCACATCAAACAT 58.240 40.909 0.00 0.00 0.00 2.71
3526 4211 3.755378 AGCTCTGAACCACATCAAACATC 59.245 43.478 0.00 0.00 0.00 3.06
3527 4212 3.119708 GCTCTGAACCACATCAAACATCC 60.120 47.826 0.00 0.00 0.00 3.51
3528 4213 4.330250 CTCTGAACCACATCAAACATCCT 58.670 43.478 0.00 0.00 0.00 3.24
3529 4214 4.326826 TCTGAACCACATCAAACATCCTC 58.673 43.478 0.00 0.00 0.00 3.71
3530 4215 4.042062 TCTGAACCACATCAAACATCCTCT 59.958 41.667 0.00 0.00 0.00 3.69
3532 4217 3.077484 ACCACATCAAACATCCTCTGG 57.923 47.619 0.00 0.00 0.00 3.86
3533 4218 2.376518 ACCACATCAAACATCCTCTGGT 59.623 45.455 0.00 0.00 0.00 4.00
3534 4219 2.751259 CCACATCAAACATCCTCTGGTG 59.249 50.000 0.00 0.00 0.00 4.17
3535 4220 2.751259 CACATCAAACATCCTCTGGTGG 59.249 50.000 0.00 0.00 0.00 4.61
3536 4221 2.376518 ACATCAAACATCCTCTGGTGGT 59.623 45.455 0.00 0.00 0.00 4.16
3537 4222 2.566833 TCAAACATCCTCTGGTGGTG 57.433 50.000 0.00 0.00 0.00 4.17
3538 4223 1.774254 TCAAACATCCTCTGGTGGTGT 59.226 47.619 0.00 0.00 0.00 4.16
3539 4224 1.881973 CAAACATCCTCTGGTGGTGTG 59.118 52.381 0.00 0.00 0.00 3.82
3540 4225 1.140312 AACATCCTCTGGTGGTGTGT 58.860 50.000 0.00 0.00 0.00 3.72
3541 4226 1.140312 ACATCCTCTGGTGGTGTGTT 58.860 50.000 0.00 0.00 0.00 3.32
3542 4227 1.072331 ACATCCTCTGGTGGTGTGTTC 59.928 52.381 0.00 0.00 0.00 3.18
3543 4228 0.693049 ATCCTCTGGTGGTGTGTTCC 59.307 55.000 0.00 0.00 0.00 3.62
3544 4229 1.073199 CCTCTGGTGGTGTGTTCCC 59.927 63.158 0.00 0.00 0.00 3.97
3545 4230 1.705002 CCTCTGGTGGTGTGTTCCCA 61.705 60.000 0.00 0.00 0.00 4.37
3546 4231 0.182537 CTCTGGTGGTGTGTTCCCAA 59.817 55.000 0.00 0.00 32.72 4.12
3547 4232 0.182537 TCTGGTGGTGTGTTCCCAAG 59.817 55.000 0.00 0.00 32.72 3.61
3548 4233 0.106719 CTGGTGGTGTGTTCCCAAGT 60.107 55.000 0.00 0.00 32.72 3.16
3549 4234 0.395036 TGGTGGTGTGTTCCCAAGTG 60.395 55.000 0.00 0.00 32.72 3.16
3550 4235 1.106944 GGTGGTGTGTTCCCAAGTGG 61.107 60.000 0.00 0.00 32.72 4.00
3578 4279 2.544685 CTCTCCGGTGATACTTTGCAG 58.455 52.381 6.68 0.00 0.00 4.41
3811 4518 0.938713 TGTTGTTGTTACCGGCGAAG 59.061 50.000 9.30 0.00 0.00 3.79
4102 4861 7.174253 GGTAATCCATGGCTTTTTATCGATGTA 59.826 37.037 6.96 0.00 0.00 2.29
4113 4872 7.270579 GCTTTTTATCGATGTAAGTTGGTGAAC 59.729 37.037 8.54 0.00 0.00 3.18
4215 4974 8.587608 TCTTCATAGAATTCAGCCACAAAATTT 58.412 29.630 8.44 0.00 0.00 1.82
4315 5074 4.139786 ACATAATGGAAGGCTACAGCATG 58.860 43.478 3.24 1.25 44.36 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.909550 ACTTTCTACAACTCTCATCTCTGT 57.090 37.500 0.00 0.00 0.00 3.41
32 33 9.614792 TTTGGAGGCTCTCTTATTATAACTTTC 57.385 33.333 15.23 0.00 0.00 2.62
65 67 6.436847 TCATCCCAAATTTGTGAAAGCTCATA 59.563 34.615 16.73 0.00 33.05 2.15
148 150 4.463050 TTTGGATGTTTGAGGGTAGGTT 57.537 40.909 0.00 0.00 0.00 3.50
234 237 7.254932 GCATGGTAGAATGTCATTTCTAAGTCC 60.255 40.741 0.00 2.67 39.31 3.85
286 289 8.677300 GGCATGAATCTCAAAGTAACTATGAAA 58.323 33.333 0.00 0.00 0.00 2.69
333 336 7.042335 GCAATACTCTAGAGCAAGGAAAACTA 58.958 38.462 19.97 0.94 0.00 2.24
340 343 6.989169 ACTTTATGCAATACTCTAGAGCAAGG 59.011 38.462 19.97 8.49 38.85 3.61
345 348 8.858003 TCGAAACTTTATGCAATACTCTAGAG 57.142 34.615 18.49 18.49 0.00 2.43
347 350 9.035607 ACATCGAAACTTTATGCAATACTCTAG 57.964 33.333 0.00 0.00 0.00 2.43
368 371 4.383649 CACAATGAGGCAAGAAAAACATCG 59.616 41.667 0.00 0.00 0.00 3.84
381 387 0.804989 GCCACAGTACACAATGAGGC 59.195 55.000 5.72 5.72 44.10 4.70
382 388 2.183478 TGCCACAGTACACAATGAGG 57.817 50.000 0.00 0.00 0.00 3.86
395 403 2.477176 GGTGCACTCGTTTGCCACA 61.477 57.895 17.98 0.00 42.25 4.17
429 437 3.860641 AGTGTATCACAATGCATCGTCA 58.139 40.909 0.00 0.00 36.74 4.35
469 477 4.505191 CACAGTATTGCATATTGCTTTGCC 59.495 41.667 0.75 0.00 45.31 4.52
471 479 8.562052 TCTATCACAGTATTGCATATTGCTTTG 58.438 33.333 0.75 0.00 45.31 2.77
523 938 1.148310 CTTCGAGATTTGTGCCACGT 58.852 50.000 0.00 0.00 0.00 4.49
547 1153 9.907229 ATATATCGTACTACATGGATTCTCTCA 57.093 33.333 0.00 0.00 0.00 3.27
560 1166 4.952262 TGCCCGTGATATATCGTACTAC 57.048 45.455 8.19 0.00 0.00 2.73
561 1167 4.337274 CCATGCCCGTGATATATCGTACTA 59.663 45.833 8.19 0.00 0.00 1.82
562 1168 3.130516 CCATGCCCGTGATATATCGTACT 59.869 47.826 8.19 0.00 0.00 2.73
600 1211 6.676456 GCAAGCACTTATCACAATCTTGTAGG 60.676 42.308 0.00 0.00 39.91 3.18
604 1215 5.050644 TGCAAGCACTTATCACAATCTTG 57.949 39.130 0.00 0.00 34.32 3.02
673 1288 0.651551 CTGATCTGCTTCTTGCGCTC 59.348 55.000 9.73 0.00 46.63 5.03
694 1309 1.450312 CCGAGGTGGCTTCATGGAC 60.450 63.158 0.00 0.00 0.00 4.02
731 1346 0.181587 TTTGACCCGAACCTTGAGCA 59.818 50.000 0.00 0.00 0.00 4.26
743 1358 0.038526 TCGAGCGACTCTTTTGACCC 60.039 55.000 5.53 0.00 0.00 4.46
761 1376 2.646121 CACCTTTGTGGCCTTCCTC 58.354 57.895 3.32 0.00 38.90 3.71
776 1391 3.663493 GCGACAACGAACTAATCAACACC 60.663 47.826 0.00 0.00 42.66 4.16
1125 1769 1.212688 TGGATGGCCACGAAGATGAAT 59.787 47.619 8.16 0.00 39.92 2.57
1977 2621 0.108281 GGAACTTGTCCGAGTAGGCC 60.108 60.000 0.00 0.00 40.77 5.19
2058 2702 0.694771 TGAGCAGCCAGAAGAACCAT 59.305 50.000 0.00 0.00 0.00 3.55
2146 2790 4.787280 CTCCTCCACCTCCCCGCT 62.787 72.222 0.00 0.00 0.00 5.52
2318 2965 5.696270 CCATGTATAGCATCGTGTGTGTATT 59.304 40.000 0.00 0.00 35.19 1.89
2348 2999 1.462283 CAAGGTCGCAACATGAGACAG 59.538 52.381 14.56 2.52 46.79 3.51
2475 3137 5.163237 TGTTTTGTTGTAGGAGAAGCTACCT 60.163 40.000 10.96 10.96 39.95 3.08
2584 3249 4.018415 AGCAGTATCCACAATAACCCAGTT 60.018 41.667 0.00 0.00 0.00 3.16
2607 3272 2.236644 AGTCGACCTCAGTAGCAGACTA 59.763 50.000 13.01 0.00 35.64 2.59
2608 3273 1.003812 AGTCGACCTCAGTAGCAGACT 59.996 52.381 13.01 0.00 39.82 3.24
2609 3274 1.399089 GAGTCGACCTCAGTAGCAGAC 59.601 57.143 13.01 0.00 40.17 3.51
2610 3275 1.279558 AGAGTCGACCTCAGTAGCAGA 59.720 52.381 13.01 0.00 43.12 4.26
2611 3276 1.745232 AGAGTCGACCTCAGTAGCAG 58.255 55.000 13.01 0.00 43.12 4.24
2612 3277 2.201921 AAGAGTCGACCTCAGTAGCA 57.798 50.000 13.01 0.00 43.12 3.49
2613 3278 2.355444 GGTAAGAGTCGACCTCAGTAGC 59.645 54.545 13.01 10.74 43.12 3.58
2614 3279 2.944349 GGGTAAGAGTCGACCTCAGTAG 59.056 54.545 13.01 0.00 43.12 2.57
2615 3280 2.306805 TGGGTAAGAGTCGACCTCAGTA 59.693 50.000 13.01 3.67 43.12 2.74
2697 3363 0.731417 AGCTTCACGATGATGCAAGC 59.269 50.000 19.88 11.99 46.27 4.01
2709 3375 6.712549 AGTTCTTTTTACACGTTAGCTTCAC 58.287 36.000 0.00 0.00 0.00 3.18
2732 3398 9.395707 CACCTAGTAGTATAAATCTTGCGTAAG 57.604 37.037 6.95 6.95 43.44 2.34
2758 3424 5.105837 CCAACTGACAACCTACTACTCTACC 60.106 48.000 0.00 0.00 0.00 3.18
2893 3570 7.433425 GCAATCAACTTAATTTGCAGACCTATC 59.567 37.037 0.83 0.00 43.00 2.08
2938 3615 4.904253 TTTGGGTTTTCTACGAACAAGG 57.096 40.909 0.00 0.00 0.00 3.61
2943 3620 4.035909 GTCTGCTTTTGGGTTTTCTACGAA 59.964 41.667 0.00 0.00 0.00 3.85
2945 3622 3.304458 GGTCTGCTTTTGGGTTTTCTACG 60.304 47.826 0.00 0.00 0.00 3.51
2949 3626 2.167487 TGTGGTCTGCTTTTGGGTTTTC 59.833 45.455 0.00 0.00 0.00 2.29
2955 3632 0.963962 ATGCTGTGGTCTGCTTTTGG 59.036 50.000 0.00 0.00 38.91 3.28
2962 3639 3.930336 TGACTAAAGATGCTGTGGTCTG 58.070 45.455 0.00 0.00 0.00 3.51
2966 3643 3.265791 GGTCTGACTAAAGATGCTGTGG 58.734 50.000 7.85 0.00 0.00 4.17
2986 3671 2.700897 CCAGGTAGATGAGGTTAGGTGG 59.299 54.545 0.00 0.00 0.00 4.61
2997 3682 3.226777 CCTACTCCAGTCCAGGTAGATG 58.773 54.545 0.00 0.00 35.13 2.90
3020 3705 7.358683 GCTTCAGTTTTGTTATGATGTGCTTTC 60.359 37.037 0.00 0.00 0.00 2.62
3022 3707 5.922544 GCTTCAGTTTTGTTATGATGTGCTT 59.077 36.000 0.00 0.00 0.00 3.91
3084 3769 7.920160 TCATGAGAAAATTATGCACAGTACA 57.080 32.000 0.00 0.00 0.00 2.90
3085 3770 8.072567 GGATCATGAGAAAATTATGCACAGTAC 58.927 37.037 0.09 0.00 0.00 2.73
3086 3771 7.041848 CGGATCATGAGAAAATTATGCACAGTA 60.042 37.037 0.09 0.00 0.00 2.74
3087 3772 6.238566 CGGATCATGAGAAAATTATGCACAGT 60.239 38.462 0.09 0.00 0.00 3.55
3088 3773 6.140786 CGGATCATGAGAAAATTATGCACAG 58.859 40.000 0.09 0.00 0.00 3.66
3089 3774 5.589855 ACGGATCATGAGAAAATTATGCACA 59.410 36.000 0.09 0.00 0.00 4.57
3090 3775 6.064846 ACGGATCATGAGAAAATTATGCAC 57.935 37.500 0.09 0.00 0.00 4.57
3091 3776 5.239306 GGACGGATCATGAGAAAATTATGCA 59.761 40.000 0.09 0.00 0.00 3.96
3092 3777 5.239306 TGGACGGATCATGAGAAAATTATGC 59.761 40.000 0.09 0.00 0.00 3.14
3521 4206 1.140312 ACACACCACCAGAGGATGTT 58.860 50.000 0.00 0.00 30.80 2.71
3522 4207 1.072331 GAACACACCACCAGAGGATGT 59.928 52.381 0.00 0.00 34.51 3.06
3524 4209 0.693049 GGAACACACCACCAGAGGAT 59.307 55.000 0.00 0.00 0.00 3.24
3525 4210 1.415672 GGGAACACACCACCAGAGGA 61.416 60.000 0.00 0.00 0.00 3.71
3526 4211 1.073199 GGGAACACACCACCAGAGG 59.927 63.158 0.00 0.00 0.00 3.69
3527 4212 0.182537 TTGGGAACACACCACCAGAG 59.817 55.000 0.00 0.00 42.67 3.35
3528 4213 0.182537 CTTGGGAACACACCACCAGA 59.817 55.000 0.00 0.00 42.67 3.86
3529 4214 0.106719 ACTTGGGAACACACCACCAG 60.107 55.000 0.00 0.00 42.67 4.00
3530 4215 0.395036 CACTTGGGAACACACCACCA 60.395 55.000 0.00 0.00 42.67 4.17
3532 4217 0.395173 ACCACTTGGGAACACACCAC 60.395 55.000 0.00 0.00 42.67 4.16
3533 4218 0.395036 CACCACTTGGGAACACACCA 60.395 55.000 0.00 0.00 42.67 4.17
3534 4219 1.106944 CCACCACTTGGGAACACACC 61.107 60.000 0.00 0.00 42.54 4.16
3535 4220 2.414750 CCACCACTTGGGAACACAC 58.585 57.895 0.00 0.00 42.54 3.82
3536 4221 4.997884 CCACCACTTGGGAACACA 57.002 55.556 0.00 0.00 42.54 3.72
3544 4229 0.886490 GGAGAGCACACCACCACTTG 60.886 60.000 0.00 0.00 0.00 3.16
3545 4230 1.451936 GGAGAGCACACCACCACTT 59.548 57.895 0.00 0.00 0.00 3.16
3546 4231 2.872388 CGGAGAGCACACCACCACT 61.872 63.158 0.00 0.00 0.00 4.00
3547 4232 2.357517 CGGAGAGCACACCACCAC 60.358 66.667 0.00 0.00 0.00 4.16
3548 4233 3.625897 CCGGAGAGCACACCACCA 61.626 66.667 0.00 0.00 0.00 4.17
3549 4234 3.626924 ACCGGAGAGCACACCACC 61.627 66.667 9.46 0.00 0.00 4.61
3550 4235 2.172483 ATCACCGGAGAGCACACCAC 62.172 60.000 9.46 0.00 0.00 4.16
3610 4315 3.712016 AGAAAGAAGGGAGGAAAGCTC 57.288 47.619 0.00 0.00 0.00 4.09
3689 4396 4.503741 AGATGCTAACAATGCAAAACGT 57.496 36.364 0.00 0.00 44.01 3.99
4024 4783 1.825474 TGAAACTTTCCCCAAAACGCA 59.175 42.857 0.00 0.00 0.00 5.24
4102 4861 1.474879 CCAACCAACGTTCACCAACTT 59.525 47.619 0.00 0.00 0.00 2.66
4215 4974 3.960102 AGAAAAGGCACAAGTTCATGGAA 59.040 39.130 0.00 0.00 0.00 3.53
4315 5074 5.118203 GGTTCTCAGTACAAACATGACGTAC 59.882 44.000 0.00 7.76 36.57 3.67
4432 5192 5.759059 AGTTGATGGTCATAATGTCATGGT 58.241 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.