Multiple sequence alignment - TraesCS5A01G388700

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 TraesCS5A01G388700 chr5A 100.000 3971 0 0 1 3971 585098840 585094870 0.000000e+00 7334.0
1 TraesCS5A01G388700 chr5D 94.896 3977 176 16 1 3971 464694381 464690426 0.000000e+00 6194.0
2 TraesCS5A01G388700 chr5B 95.773 3170 112 11 807 3971 571613878 571617030 0.000000e+00 5092.0
3 TraesCS5A01G388700 chr3B 76.749 486 91 19 47 522 449737283 449736810 6.590000e-63 252.0
4 TraesCS5A01G388700 chr3B 94.286 35 1 1 1039 1073 531730354 531730387 7.000000e-03 52.8
5 TraesCS5A01G388700 chr4B 78.167 371 64 13 61 424 134205414 134205054 1.860000e-53 220.0
6 TraesCS5A01G388700 chr6B 77.515 338 60 12 55 388 705390744 705390419 5.240000e-44 189.0
7 TraesCS5A01G388700 chr4A 74.941 427 84 18 86 504 449406372 449406783 1.470000e-39 174.0
8 TraesCS5A01G388700 chr4A 93.750 48 3 0 3661 3708 575026761 575026714 5.500000e-09 73.1
9 TraesCS5A01G388700 chr4D 77.193 285 60 5 229 510 15434716 15434434 1.140000e-35 161.0
10 TraesCS5A01G388700 chr2B 79.253 241 36 10 92 329 233554790 233555019 5.310000e-34 156.0
11 TraesCS5A01G388700 chr3A 79.149 235 38 9 198 426 713709292 713709521 6.870000e-33 152.0
12 TraesCS5A01G388700 chr3A 88.889 63 6 1 662 723 600310261 600310323 4.260000e-10 76.8
13 TraesCS5A01G388700 chr7A 77.395 261 54 5 229 488 549788391 549788647 2.470000e-32 150.0
14 TraesCS5A01G388700 chr7A 96.000 50 2 0 667 716 418604967 418604918 9.150000e-12 82.4
15 TraesCS5A01G388700 chr2A 91.667 60 3 2 658 715 659185149 659185090 9.150000e-12 82.4
16 TraesCS5A01G388700 chr1A 95.349 43 2 0 3666 3708 238670242 238670284 7.120000e-08 69.4
17 TraesCS5A01G388700 chr1A 94.595 37 2 0 3671 3707 130911682 130911646 1.540000e-04 58.4
18 TraesCS5A01G388700 chr1D 97.222 36 1 0 3666 3701 192564974 192565009 1.190000e-05 62.1


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 TraesCS5A01G388700 chr5A 585094870 585098840 3970 True 7334 7334 100.000 1 3971 1 chr5A.!!$R1 3970
1 TraesCS5A01G388700 chr5D 464690426 464694381 3955 True 6194 6194 94.896 1 3971 1 chr5D.!!$R1 3970
2 TraesCS5A01G388700 chr5B 571613878 571617030 3152 False 5092 5092 95.773 807 3971 1 chr5B.!!$F1 3164

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
393 395 0.108138 GGTATCTGAGTGTGCCGCTT 60.108 55.0 0.00 0.0 0.00 4.68 F
455 457 0.249031 GCAAGCTTGGTTTTGCTCGT 60.249 50.0 27.10 0.0 44.70 4.18 F
1732 1739 0.034670 AAGGGATGCAGTCTCTTGGC 60.035 55.0 9.58 0.0 46.01 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1675 1.202976 GCAGCCATATGAACCATCCCT 60.203 52.381 3.65 0.0 0.0 4.20 R
2805 2812 1.137404 CTTGGCCAATTCTTCCGCG 59.863 57.895 20.85 0.0 0.0 6.46 R
3313 3322 2.259012 AGAATGGCCAGGCAAATTTGA 58.741 42.857 22.31 0.0 0.0 2.69 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
88 89 3.327757 ACTGGCTGAAGGTGAACTATTCA 59.672 43.478 0.00 0.00 37.33 2.57
100 101 3.130516 TGAACTATTCAGCGATCTTCCGT 59.869 43.478 0.00 0.00 34.08 4.69
103 104 0.811616 ATTCAGCGATCTTCCGTGGC 60.812 55.000 0.00 0.00 0.00 5.01
137 138 4.626172 CCTAGTTTTGTCCTTCGTAGCTTC 59.374 45.833 0.00 0.00 0.00 3.86
145 146 0.447011 CTTCGTAGCTTCGTCGGAGT 59.553 55.000 12.66 0.00 0.00 3.85
187 188 1.153208 GCTGGCTGAGCTGTAGCAT 60.153 57.895 18.29 0.00 45.21 3.79
211 212 1.833630 TCGGGATCTTCATGCAACTCT 59.166 47.619 0.00 0.00 0.00 3.24
227 228 4.378874 GCAACTCTCTGATGCCTTTACAAC 60.379 45.833 0.00 0.00 38.34 3.32
247 248 1.604438 CGTGGGTTGAGTTGACGATCA 60.604 52.381 0.00 0.00 31.71 2.92
252 253 3.251571 GGTTGAGTTGACGATCACCTAC 58.748 50.000 0.00 0.00 0.00 3.18
256 257 0.108992 GTTGACGATCACCTACGGCA 60.109 55.000 0.00 0.00 45.87 5.69
292 293 1.210478 GCTCAGGGTTTAGAGATGGCA 59.790 52.381 0.00 0.00 33.74 4.92
296 297 2.360165 CAGGGTTTAGAGATGGCAATGC 59.640 50.000 0.00 0.00 0.00 3.56
320 322 3.321950 CCTTTAGGGGAGGAGTGATGAT 58.678 50.000 0.00 0.00 36.33 2.45
322 324 3.706389 TTAGGGGAGGAGTGATGATGA 57.294 47.619 0.00 0.00 0.00 2.92
338 340 1.955495 ATGATGACGCCCGTGTGCTA 61.955 55.000 0.00 0.00 0.00 3.49
344 346 2.279517 GCCCGTGTGCTATCTCGG 60.280 66.667 9.38 9.38 41.97 4.63
345 347 2.279517 CCCGTGTGCTATCTCGGC 60.280 66.667 10.38 0.00 41.29 5.54
348 350 0.739462 CCGTGTGCTATCTCGGCAAA 60.739 55.000 0.00 0.00 41.54 3.68
353 355 0.618458 TGCTATCTCGGCAAAACCCT 59.382 50.000 0.00 0.00 36.71 4.34
357 359 2.115343 ATCTCGGCAAAACCCTCTTC 57.885 50.000 0.00 0.00 33.26 2.87
359 361 1.298859 CTCGGCAAAACCCTCTTCGG 61.299 60.000 0.00 0.00 33.26 4.30
364 366 1.542547 GCAAAACCCTCTTCGGAGTGA 60.543 52.381 0.00 0.00 40.29 3.41
371 373 1.416813 CTCTTCGGAGTGATGTGCGC 61.417 60.000 0.00 0.00 37.31 6.09
393 395 0.108138 GGTATCTGAGTGTGCCGCTT 60.108 55.000 0.00 0.00 0.00 4.68
423 425 3.367743 GGTTTCGCCCGGGTTTCC 61.368 66.667 24.63 13.88 0.00 3.13
426 428 1.676303 TTTCGCCCGGGTTTCCATC 60.676 57.895 24.63 1.44 0.00 3.51
427 429 3.961838 TTCGCCCGGGTTTCCATCG 62.962 63.158 24.63 15.43 0.00 3.84
443 445 3.388024 TCCATCGATAACTAGGCAAGCTT 59.612 43.478 0.00 0.00 0.00 3.74
445 447 3.179443 TCGATAACTAGGCAAGCTTGG 57.821 47.619 27.10 13.18 0.00 3.61
454 456 0.940991 GGCAAGCTTGGTTTTGCTCG 60.941 55.000 27.10 0.00 46.69 5.03
455 457 0.249031 GCAAGCTTGGTTTTGCTCGT 60.249 50.000 27.10 0.00 44.70 4.18
461 463 3.119137 AGCTTGGTTTTGCTCGTTTTCTT 60.119 39.130 0.00 0.00 33.90 2.52
462 464 3.242944 GCTTGGTTTTGCTCGTTTTCTTC 59.757 43.478 0.00 0.00 0.00 2.87
479 481 9.612620 CGTTTTCTTCTAATTAATCAAGCAACT 57.387 29.630 0.00 0.00 0.00 3.16
552 554 4.250305 ACGGGCACACAGGACCAC 62.250 66.667 0.00 0.00 0.00 4.16
554 556 3.936203 GGGCACACAGGACCACGA 61.936 66.667 0.00 0.00 0.00 4.35
558 560 1.949133 CACACAGGACCACGACACG 60.949 63.158 0.00 0.00 0.00 4.49
578 580 3.142838 ATCCATGCTGCAACCGGC 61.143 61.111 6.36 0.00 43.83 6.13
663 665 1.190103 CGATTACGCGACCATGTCATG 59.810 52.381 15.93 5.79 32.09 3.07
700 705 9.205916 GCAATACTTATAACACATTTACACGTG 57.794 33.333 15.48 15.48 39.10 4.49
731 736 9.333724 AGCAAAACTGAAGAAAAATCAAATGAT 57.666 25.926 0.00 0.00 36.07 2.45
733 738 9.377383 CAAAACTGAAGAAAAATCAAATGATGC 57.623 29.630 0.00 0.00 34.49 3.91
734 739 8.665643 AAACTGAAGAAAAATCAAATGATGCA 57.334 26.923 0.00 0.00 34.49 3.96
765 770 8.496707 AAGTATTATTTTTGGGTACGTACTGG 57.503 34.615 24.07 0.00 0.00 4.00
766 771 7.623630 AGTATTATTTTTGGGTACGTACTGGT 58.376 34.615 24.07 7.41 0.00 4.00
767 772 8.757877 AGTATTATTTTTGGGTACGTACTGGTA 58.242 33.333 24.07 6.66 0.00 3.25
768 773 7.848223 ATTATTTTTGGGTACGTACTGGTAC 57.152 36.000 24.07 7.92 41.58 3.34
838 843 1.982073 GAGAAGAATGGCAACGGCGG 61.982 60.000 13.24 0.00 42.47 6.13
993 1000 0.804989 GATTGGCACGAAGAAGTGGG 59.195 55.000 0.00 0.00 42.09 4.61
1051 1058 1.658686 CCTCGTCTCGTCCCTCAAGG 61.659 65.000 0.00 0.00 0.00 3.61
1143 1150 1.004918 CTTCGTCCGCAACTCCCTT 60.005 57.895 0.00 0.00 0.00 3.95
1157 1164 1.035932 TCCCTTCTCGCCTTCTACGG 61.036 60.000 0.00 0.00 0.00 4.02
1220 1227 1.066645 GTTCGACGAAATACCCCTGGT 60.067 52.381 12.67 0.00 40.16 4.00
1260 1267 3.077556 AACATCCTCCTCGCCGCT 61.078 61.111 0.00 0.00 0.00 5.52
1355 1362 4.308458 CACCGTCTTGACCGCCCA 62.308 66.667 0.00 0.00 0.00 5.36
1589 1596 0.941542 GCAGCGTCACAGGTTTGTTA 59.058 50.000 0.00 0.00 34.62 2.41
1617 1624 2.237893 TGAGATCTTTGAGCAGATGCCA 59.762 45.455 0.00 0.00 43.38 4.92
1653 1660 3.193267 TCACTTGGAATGCCATGCTTAAC 59.807 43.478 5.49 0.00 45.46 2.01
1656 1663 0.249031 GGAATGCCATGCTTAACGGC 60.249 55.000 0.00 0.00 46.43 5.68
1668 1675 3.194755 TGCTTAACGGCTATCTGAAGACA 59.805 43.478 0.00 0.00 0.00 3.41
1695 1702 2.104792 GGTTCATATGGCTGCTGAGGTA 59.895 50.000 2.13 0.00 0.00 3.08
1732 1739 0.034670 AAGGGATGCAGTCTCTTGGC 60.035 55.000 9.58 0.00 46.01 4.52
1765 1772 3.196469 AGATGGGTATATCCGTGCAGATG 59.804 47.826 0.00 0.00 37.00 2.90
1768 1775 2.829720 GGGTATATCCGTGCAGATGGTA 59.170 50.000 0.00 0.00 37.00 3.25
2031 2038 1.866601 TCAGACAAGTCACACATTGCG 59.133 47.619 2.72 0.00 0.00 4.85
2185 2192 3.118665 ACATTCAAACAAGGCTTTGCAGT 60.119 39.130 8.71 0.00 37.85 4.40
2447 2454 3.055819 TCTGTGTCTCCTTGGAATGCTAC 60.056 47.826 0.00 0.00 0.00 3.58
2483 2490 2.842188 ATCCACGGCCATGCACACAT 62.842 55.000 2.24 0.00 36.79 3.21
2510 2517 4.149046 GCTTGAACTGTTCTCAGAACTACG 59.851 45.833 18.49 9.33 43.76 3.51
2556 2563 4.996758 TCAGTCACATACATTGGTGTCTTG 59.003 41.667 0.00 0.00 39.77 3.02
2567 2574 1.814394 TGGTGTCTTGAATGCATGCTC 59.186 47.619 20.33 9.72 0.00 4.26
2925 2932 0.193574 TGAGGAAGGAACTCCAGGGT 59.806 55.000 0.00 0.00 38.49 4.34
3061 3068 5.931146 GTGTGATTATTCATTTGGTTTGCCA 59.069 36.000 0.00 0.00 37.30 4.92
3063 3070 6.817641 TGTGATTATTCATTTGGTTTGCCATC 59.182 34.615 0.00 0.00 38.24 3.51
3302 3311 6.323739 TCCTAAAAACATTGTCTTGCTTCCTT 59.676 34.615 0.00 0.00 0.00 3.36
3311 3320 4.277476 TGTCTTGCTTCCTTTCCTTTTGA 58.723 39.130 0.00 0.00 0.00 2.69
3313 3322 5.363580 TGTCTTGCTTCCTTTCCTTTTGAAT 59.636 36.000 0.00 0.00 31.67 2.57
3329 3338 1.976404 TGAATCAAATTTGCCTGGCCA 59.024 42.857 17.53 4.71 0.00 5.36
3419 3428 9.539825 GCTATGAGAAATATCAGTCTTTCTTCA 57.460 33.333 0.00 0.00 40.77 3.02
3483 3492 7.419518 CCTTCTAAATGGTATCCTCACATCACT 60.420 40.741 0.00 0.00 0.00 3.41
3499 3508 4.704540 ACATCACTGGTTTTGTGTTCAGAA 59.295 37.500 0.00 0.00 36.83 3.02
3793 3803 1.237285 TGCTCCCTTTCTTTCTGCGC 61.237 55.000 0.00 0.00 0.00 6.09
3834 3844 2.416547 TCGCAAGCTAGCATTCAGTTTC 59.583 45.455 18.83 0.00 37.18 2.78
3892 3902 6.555463 TTCCTAGTTCCCTTTATGTACAGG 57.445 41.667 0.33 0.00 0.00 4.00
3947 3958 6.480320 GTGCTCGTCATTGTATTAGAAGGAAT 59.520 38.462 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 1.797933 CGCAACTCTGACTCCGACG 60.798 63.158 0.00 0.00 0.00 5.12
145 146 1.668751 GACCAAACAACGCAACTCTGA 59.331 47.619 0.00 0.00 0.00 3.27
187 188 1.130777 TGCATGAAGATCCCGATCCA 58.869 50.000 0.00 0.00 38.58 3.41
211 212 2.422597 CCACGTTGTAAAGGCATCAGA 58.577 47.619 0.00 0.00 34.48 3.27
227 228 1.068474 GATCGTCAACTCAACCCACG 58.932 55.000 0.00 0.00 0.00 4.94
252 253 1.219522 AAACGACTCCGACTTTGCCG 61.220 55.000 0.00 0.00 39.50 5.69
256 257 1.202486 TGAGCAAACGACTCCGACTTT 60.202 47.619 0.00 0.00 39.50 2.66
292 293 1.227383 CTCCCCTAAAGGCGGCATT 59.773 57.895 13.08 8.50 0.00 3.56
296 297 1.689582 ACTCCTCCCCTAAAGGCGG 60.690 63.158 0.00 0.00 33.65 6.13
298 299 1.141858 CATCACTCCTCCCCTAAAGGC 59.858 57.143 0.00 0.00 33.65 4.35
306 308 2.288702 CGTCATCATCATCACTCCTCCC 60.289 54.545 0.00 0.00 0.00 4.30
320 322 1.955495 ATAGCACACGGGCGTCATCA 61.955 55.000 0.00 0.00 39.27 3.07
322 324 1.227263 GATAGCACACGGGCGTCAT 60.227 57.895 0.00 0.00 39.27 3.06
338 340 1.676014 CGAAGAGGGTTTTGCCGAGAT 60.676 52.381 0.00 0.00 38.44 2.75
344 346 0.875059 CACTCCGAAGAGGGTTTTGC 59.125 55.000 0.00 0.00 45.11 3.68
345 347 2.543777 TCACTCCGAAGAGGGTTTTG 57.456 50.000 0.00 0.00 44.57 2.44
348 350 1.276421 CACATCACTCCGAAGAGGGTT 59.724 52.381 0.00 0.00 44.57 4.11
353 355 1.446099 GCGCACATCACTCCGAAGA 60.446 57.895 0.30 0.00 0.00 2.87
357 359 3.842126 CACGCGCACATCACTCCG 61.842 66.667 5.73 0.00 0.00 4.63
359 361 0.806102 ATACCACGCGCACATCACTC 60.806 55.000 5.73 0.00 0.00 3.51
364 366 0.528466 CTCAGATACCACGCGCACAT 60.528 55.000 5.73 0.00 0.00 3.21
371 373 0.802222 CGGCACACTCAGATACCACG 60.802 60.000 0.00 0.00 0.00 4.94
423 425 3.496130 CCAAGCTTGCCTAGTTATCGATG 59.504 47.826 21.43 0.00 0.00 3.84
426 428 2.906354 ACCAAGCTTGCCTAGTTATCG 58.094 47.619 21.43 5.74 0.00 2.92
427 429 5.402398 CAAAACCAAGCTTGCCTAGTTATC 58.598 41.667 21.43 0.00 0.00 1.75
443 445 5.821516 TTAGAAGAAAACGAGCAAAACCA 57.178 34.783 0.00 0.00 0.00 3.67
483 485 9.850628 CAGAATTTCTGCATTTATCAAGAAGAA 57.149 29.630 13.20 0.00 37.72 2.52
528 530 1.172180 CCTGTGTGCCCGTCAATTGT 61.172 55.000 5.13 0.00 0.00 2.71
529 531 0.888736 TCCTGTGTGCCCGTCAATTG 60.889 55.000 0.00 0.00 0.00 2.32
532 534 2.110213 GTCCTGTGTGCCCGTCAA 59.890 61.111 0.00 0.00 0.00 3.18
541 543 2.415843 CGTGTCGTGGTCCTGTGT 59.584 61.111 0.00 0.00 0.00 3.72
542 544 3.036084 GCGTGTCGTGGTCCTGTG 61.036 66.667 0.00 0.00 0.00 3.66
552 554 2.512286 AGCATGGATGGCGTGTCG 60.512 61.111 0.00 0.00 36.08 4.35
554 556 3.136123 GCAGCATGGATGGCGTGT 61.136 61.111 0.00 0.00 35.86 4.49
558 560 2.497770 GGTTGCAGCATGGATGGC 59.502 61.111 2.05 0.00 35.22 4.40
578 580 0.945813 CGTAGAGGCTTCCTACTCCG 59.054 60.000 10.56 0.00 35.54 4.63
610 612 1.588674 TTGATTTGTCGGTCGCAACT 58.411 45.000 0.00 0.00 0.00 3.16
618 620 5.162794 TGATTGCATCTTTTGATTTGTCGG 58.837 37.500 0.00 0.00 36.97 4.79
619 621 5.220154 GCTGATTGCATCTTTTGATTTGTCG 60.220 40.000 0.00 0.00 42.31 4.35
653 655 5.195185 TGCACATCTAAATCATGACATGGT 58.805 37.500 15.37 5.35 0.00 3.55
685 687 4.533222 GCTAAAGCACGTGTAAATGTGTT 58.467 39.130 18.38 0.00 41.59 3.32
700 705 8.130307 TGATTTTTCTTCAGTTTTGCTAAAGC 57.870 30.769 0.00 0.00 42.50 3.51
717 722 8.031277 ACTTACTCCTGCATCATTTGATTTTTC 58.969 33.333 0.00 0.00 31.21 2.29
731 736 7.179269 ACCCAAAAATAATACTTACTCCTGCA 58.821 34.615 0.00 0.00 0.00 4.41
733 738 8.823818 CGTACCCAAAAATAATACTTACTCCTG 58.176 37.037 0.00 0.00 0.00 3.86
734 739 8.542926 ACGTACCCAAAAATAATACTTACTCCT 58.457 33.333 0.00 0.00 0.00 3.69
762 767 0.377554 CGCTCCTCACTACGTACCAG 59.622 60.000 0.00 0.00 0.00 4.00
763 768 0.321919 ACGCTCCTCACTACGTACCA 60.322 55.000 0.00 0.00 36.91 3.25
764 769 0.098376 CACGCTCCTCACTACGTACC 59.902 60.000 0.00 0.00 36.91 3.34
765 770 0.801251 ACACGCTCCTCACTACGTAC 59.199 55.000 0.00 0.00 36.91 3.67
766 771 0.800631 CACACGCTCCTCACTACGTA 59.199 55.000 0.00 0.00 36.91 3.57
767 772 1.579932 CACACGCTCCTCACTACGT 59.420 57.895 0.00 0.00 39.78 3.57
768 773 1.801913 GCACACGCTCCTCACTACG 60.802 63.158 0.00 0.00 34.30 3.51
769 774 4.170723 GCACACGCTCCTCACTAC 57.829 61.111 0.00 0.00 34.30 2.73
838 843 1.656095 CTCTCGCTTTGGTGAACGATC 59.344 52.381 0.00 0.00 33.53 3.69
865 872 0.955919 CCTCACCGCCTTCCTTGTTC 60.956 60.000 0.00 0.00 0.00 3.18
993 1000 3.818787 CCGCTGGGCATGTGCTTC 61.819 66.667 4.84 0.00 41.70 3.86
1589 1596 1.745141 GCTCAAAGATCTCACGGGCAT 60.745 52.381 0.00 0.00 0.00 4.40
1617 1624 7.066284 GCATTCCAAGTGACTGTGTTCTTATAT 59.934 37.037 0.00 0.00 0.00 0.86
1653 1660 1.403814 TCCCTGTCTTCAGATAGCCG 58.596 55.000 0.00 0.00 43.76 5.52
1656 1663 4.406972 TGAACCATCCCTGTCTTCAGATAG 59.593 45.833 0.00 0.00 43.76 2.08
1668 1675 1.202976 GCAGCCATATGAACCATCCCT 60.203 52.381 3.65 0.00 0.00 4.20
1722 1729 1.550327 TCATCGTCAGCCAAGAGACT 58.450 50.000 0.00 0.00 32.68 3.24
1732 1739 6.293680 CGGATATACCCATCTATCATCGTCAG 60.294 46.154 0.00 0.00 34.64 3.51
1971 1978 1.728971 GCAAGGTCAAGACGATCACAG 59.271 52.381 0.00 0.00 0.00 3.66
2031 2038 3.622163 CAGACATGAGAGCATTCCAAGAC 59.378 47.826 0.00 0.00 30.68 3.01
2185 2192 4.199310 GCACCCAGCATCAAGTAGAATAA 58.801 43.478 0.00 0.00 44.79 1.40
2220 2227 2.290641 ACTTGCCAAAGTGACGTCATTC 59.709 45.455 23.12 9.96 45.12 2.67
2223 2230 2.159014 AGTACTTGCCAAAGTGACGTCA 60.159 45.455 15.76 15.76 46.30 4.35
2447 2454 1.952296 GGATGGCTAAACTGCAGATGG 59.048 52.381 23.35 11.81 34.04 3.51
2483 2490 2.100749 TCTGAGAACAGTTCAAGCGACA 59.899 45.455 15.85 5.02 43.81 4.35
2510 2517 4.402474 AGTTGGGCTTAATATTGGTGCTTC 59.598 41.667 0.00 0.00 0.00 3.86
2567 2574 0.749454 GGTTACCAGCCCAGCATGAG 60.749 60.000 0.00 0.00 39.69 2.90
2805 2812 1.137404 CTTGGCCAATTCTTCCGCG 59.863 57.895 20.85 0.00 0.00 6.46
2925 2932 6.789268 TCCAGAAAACCTCTCCATATTTTCA 58.211 36.000 10.06 0.00 41.44 2.69
3033 3040 7.798052 GCAAACCAAATGAATAATCACACAAAC 59.202 33.333 0.00 0.00 38.69 2.93
3061 3068 8.192774 TCTTTAACGAATCATAACTGTACGGAT 58.807 33.333 9.17 0.00 0.00 4.18
3063 3070 7.745022 TCTTTAACGAATCATAACTGTACGG 57.255 36.000 0.00 0.00 0.00 4.02
3227 3236 9.900710 AGTAACGTGCAATTAAATATTTTGTCA 57.099 25.926 5.91 0.00 0.00 3.58
3302 3311 5.764192 CCAGGCAAATTTGATTCAAAAGGAA 59.236 36.000 22.31 0.00 36.90 3.36
3311 3320 3.264964 AGAATGGCCAGGCAAATTTGATT 59.735 39.130 22.31 10.14 0.00 2.57
3313 3322 2.259012 AGAATGGCCAGGCAAATTTGA 58.741 42.857 22.31 0.00 0.00 2.69
3329 3338 4.340381 AGTGCAGAAAGTGAAAGCAAGAAT 59.660 37.500 0.00 0.00 36.91 2.40
3483 3492 5.534278 TGCATAGATTCTGAACACAAAACCA 59.466 36.000 0.00 0.00 0.00 3.67
3499 3508 9.393512 GATAATCTTAAATCAGCCTGCATAGAT 57.606 33.333 0.00 0.00 0.00 1.98
3693 3703 7.556996 TGTAAACTTCTTTAGTGGCCTAAAACA 59.443 33.333 3.32 0.00 41.41 2.83
3702 3712 6.110411 TCCCTCTGTAAACTTCTTTAGTGG 57.890 41.667 0.00 0.00 37.12 4.00
3776 3786 0.801251 CTGCGCAGAAAGAAAGGGAG 59.199 55.000 33.66 0.00 0.00 4.30
3793 3803 4.377022 GCGACAATGTACCACTGTAAACTG 60.377 45.833 0.00 0.00 0.00 3.16
3814 3824 2.417933 AGAAACTGAATGCTAGCTTGCG 59.582 45.455 17.23 7.48 35.36 4.85
3841 3851 4.446889 CCAATTCTTCCCTCCTAAGGATGG 60.447 50.000 0.90 0.90 46.67 3.51
3947 3958 0.842030 AGACTCCCACCATCTTGGCA 60.842 55.000 0.00 0.00 42.67 4.92


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

AutoCloner maintained by Alex Coulton.