Multiple sequence alignment - TraesCS3B01G384400

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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 TraesCS3B01G384400 chr3B 100.000 5381 0 0 1 5381 604275689 604270309 0.000000e+00 9937
1 TraesCS3B01G384400 chr3D 94.059 3030 114 25 618 3605 457236104 457233099 0.000000e+00 4538
2 TraesCS3B01G384400 chr3D 90.988 1043 45 25 3616 4655 457233058 457232062 0.000000e+00 1360
3 TraesCS3B01G384400 chr3D 95.894 755 31 0 4627 5381 457231985 457231231 0.000000e+00 1223
4 TraesCS3B01G384400 chr3D 94.481 308 11 3 1 307 457237076 457236774 2.270000e-128 470
5 TraesCS3B01G384400 chr3D 84.865 185 20 6 317 498 457236711 457236532 4.280000e-41 180
6 TraesCS3B01G384400 chr3A 94.808 1772 73 11 3618 5381 600024866 600023106 0.000000e+00 2745
7 TraesCS3B01G384400 chr3A 93.758 1650 58 15 1986 3611 600026531 600024903 0.000000e+00 2435
8 TraesCS3B01G384400 chr3A 93.511 1387 66 12 618 1984 600028028 600026646 0.000000e+00 2041
9 TraesCS3B01G384400 chr3A 92.473 279 11 2 22 294 600029118 600028844 1.820000e-104 390
10 TraesCS3B01G384400 chr5D 90.972 288 16 2 5096 5381 524596978 524597257 3.930000e-101 379
11 TraesCS3B01G384400 chr6B 88.814 295 23 5 5096 5381 257599430 257599137 2.380000e-93 353


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 TraesCS3B01G384400 chr3B 604270309 604275689 5380 True 9937.00 9937 100.0000 1 5381 1 chr3B.!!$R1 5380
1 TraesCS3B01G384400 chr3D 457231231 457237076 5845 True 1554.20 4538 92.0574 1 5381 5 chr3D.!!$R1 5380
2 TraesCS3B01G384400 chr3A 600023106 600029118 6012 True 1902.75 2745 93.6375 22 5381 4 chr3A.!!$R1 5359

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
221 224 2.551459 GGGCAATACAGCATGACATCTC 59.449 50.000 0.0 0.0 39.69 2.75 F
1627 2154 1.200020 CATTTCTGTCTTCGGGTTGGC 59.800 52.381 0.0 0.0 0.00 4.52 F
1771 2298 0.249120 GCCATTTTAGGGTGTTGGGC 59.751 55.000 0.0 0.0 0.00 5.36 F
1881 2408 1.347062 TCAATCCCAAAACAAGGGCC 58.653 50.000 0.0 0.0 46.36 5.80 F
3651 4363 0.320697 GATATCAGCGGGGGTGTACC 59.679 60.000 0.0 0.0 39.11 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2287 0.106116 TTTTTACCGCCCAACACCCT 60.106 50.0 0.00 0.0 0.00 4.34 R
3311 3992 0.901114 TTCATGGCTGGCATTGCACT 60.901 50.0 14.65 0.0 0.00 4.40 R
3410 4091 2.566833 TTGGCGCTATAAGGCATGAT 57.433 45.0 7.64 0.0 43.68 2.45 R
3839 4551 2.241281 TTAGAGGACCGGAACCATGA 57.759 50.0 9.46 0.0 0.00 3.07 R
4921 5744 0.176219 TTACCATGAACGCCTACGGG 59.824 55.0 0.00 0.0 46.04 5.28 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 6.088749 CGTTTTCATTGTTGTTGAGAACACAA 59.911 34.615 7.55 0.00 41.97 3.33
89 90 7.358765 CGTTTTCATTGTTGTTGAGAACACAAA 60.359 33.333 7.55 0.00 41.97 2.83
90 91 7.953158 TTTCATTGTTGTTGAGAACACAAAA 57.047 28.000 0.00 0.00 41.97 2.44
91 92 8.545229 TTTCATTGTTGTTGAGAACACAAAAT 57.455 26.923 0.00 0.00 41.97 1.82
132 134 4.725490 TGCTTACCTAGGCAGAAACTTTT 58.275 39.130 9.30 0.00 33.09 2.27
221 224 2.551459 GGGCAATACAGCATGACATCTC 59.449 50.000 0.00 0.00 39.69 2.75
240 243 7.059156 ACATCTCTGGGAGAAAGGAATATTTG 58.941 38.462 1.26 0.00 42.27 2.32
252 255 3.119029 AGGAATATTTGCTGCAATTGCGT 60.119 39.130 24.58 9.21 45.83 5.24
294 303 8.214364 ACCTGATCCAACTATCTTAATTTCTCC 58.786 37.037 0.00 0.00 0.00 3.71
340 431 3.963428 ATATCCCTAGGAATGCACGTC 57.037 47.619 11.48 0.00 34.34 4.34
411 508 6.276091 CACACATGCAAACTCTAGCTCTATA 58.724 40.000 0.00 0.00 0.00 1.31
471 568 7.661127 TGCTGAAACTAAAAGAATAGCGTAA 57.339 32.000 0.00 0.00 32.88 3.18
517 614 5.827568 AAAAACATGCGAGCACTAAATTG 57.172 34.783 0.00 0.00 0.00 2.32
520 617 3.605634 ACATGCGAGCACTAAATTGGTA 58.394 40.909 0.00 0.00 0.00 3.25
521 618 3.374058 ACATGCGAGCACTAAATTGGTAC 59.626 43.478 0.00 0.00 0.00 3.34
522 619 3.328382 TGCGAGCACTAAATTGGTACT 57.672 42.857 0.00 0.00 0.00 2.73
523 620 3.670625 TGCGAGCACTAAATTGGTACTT 58.329 40.909 0.00 0.00 0.00 2.24
524 621 4.823157 TGCGAGCACTAAATTGGTACTTA 58.177 39.130 0.00 0.00 0.00 2.24
526 623 5.350365 TGCGAGCACTAAATTGGTACTTAAG 59.650 40.000 0.00 0.00 0.00 1.85
527 624 5.220605 GCGAGCACTAAATTGGTACTTAAGG 60.221 44.000 7.53 0.00 0.00 2.69
530 627 7.017319 AGCACTAAATTGGTACTTAAGGTCT 57.983 36.000 7.53 0.00 0.00 3.85
531 628 7.459234 AGCACTAAATTGGTACTTAAGGTCTT 58.541 34.615 7.53 0.00 0.00 3.01
532 629 7.390718 AGCACTAAATTGGTACTTAAGGTCTTG 59.609 37.037 7.53 0.00 0.00 3.02
533 630 7.174426 GCACTAAATTGGTACTTAAGGTCTTGT 59.826 37.037 7.53 0.00 0.00 3.16
534 631 9.063615 CACTAAATTGGTACTTAAGGTCTTGTT 57.936 33.333 7.53 0.00 0.00 2.83
538 635 8.575649 AATTGGTACTTAAGGTCTTGTTATGG 57.424 34.615 7.53 0.00 0.00 2.74
540 637 5.786457 TGGTACTTAAGGTCTTGTTATGGGA 59.214 40.000 7.53 0.00 0.00 4.37
541 638 6.111382 GGTACTTAAGGTCTTGTTATGGGAC 58.889 44.000 7.53 0.00 0.00 4.46
561 1043 5.316987 GGACAGGGGGAGTATGATTTTATG 58.683 45.833 0.00 0.00 0.00 1.90
564 1046 4.763793 CAGGGGGAGTATGATTTTATGCAG 59.236 45.833 0.00 0.00 0.00 4.41
572 1054 6.917533 AGTATGATTTTATGCAGCAATAGCC 58.082 36.000 0.00 0.00 43.56 3.93
606 1088 3.713858 ATTAGCGCAATTTGCATAGCA 57.286 38.095 20.56 2.83 45.36 3.49
667 1173 9.546428 AATGATTTGTCCTTAGAAAACTTTTGG 57.454 29.630 0.00 0.00 0.00 3.28
787 1302 5.613964 AACAAAACAAATTAACACGAGCG 57.386 34.783 0.00 0.00 0.00 5.03
920 1439 2.740714 GCTCGCCAGTTTAGCCGTG 61.741 63.158 0.00 0.00 0.00 4.94
1486 2012 4.074466 GGTACGGAAGATTCGGTTTTTG 57.926 45.455 10.51 0.00 40.55 2.44
1623 2150 1.337823 CGTCCATTTCTGTCTTCGGGT 60.338 52.381 0.00 0.00 0.00 5.28
1627 2154 1.200020 CATTTCTGTCTTCGGGTTGGC 59.800 52.381 0.00 0.00 0.00 4.52
1648 2175 2.484770 CGAATTTGGGATTAGGCGGAGA 60.485 50.000 0.00 0.00 0.00 3.71
1689 2216 3.439129 GGGTGTTCTTCCTGGTTAATTCG 59.561 47.826 0.00 0.00 0.00 3.34
1771 2298 0.249120 GCCATTTTAGGGTGTTGGGC 59.751 55.000 0.00 0.00 0.00 5.36
1818 2345 2.747989 CGAGCACCTAGAGTCACTTGTA 59.252 50.000 0.00 0.00 0.00 2.41
1881 2408 1.347062 TCAATCCCAAAACAAGGGCC 58.653 50.000 0.00 0.00 46.36 5.80
1884 2411 2.903135 CAATCCCAAAACAAGGGCCTAA 59.097 45.455 6.41 0.00 46.36 2.69
1889 2416 3.132824 CCCAAAACAAGGGCCTAATGATC 59.867 47.826 6.41 0.00 39.96 2.92
1890 2417 3.132824 CCAAAACAAGGGCCTAATGATCC 59.867 47.826 6.41 0.00 0.00 3.36
1928 2455 8.649591 ACTGCATTAATCTCATCTCTAGACAAT 58.350 33.333 0.00 0.00 0.00 2.71
1984 2511 6.150976 TGTTGCTACCTTTACTGGATCAAATG 59.849 38.462 0.00 0.00 0.00 2.32
1989 2629 6.824305 ACCTTTACTGGATCAAATGACTTG 57.176 37.500 0.00 0.00 36.25 3.16
2005 2645 9.590451 CAAATGACTTGATTAGCCAATATGTTT 57.410 29.630 0.00 0.00 37.17 2.83
2075 2718 2.526304 ACTTCTTGTCGCTGCTGTTA 57.474 45.000 0.00 0.00 0.00 2.41
2106 2749 1.919600 ATCTGAGCCTGCCCCTCAAC 61.920 60.000 0.00 0.00 38.73 3.18
2165 2808 5.008019 ACGCATTTGGTCATGATAGATGAAC 59.992 40.000 13.96 0.00 36.34 3.18
2326 2975 8.396272 ACATTTAGTGTGAAGTCAGCTTTAAT 57.604 30.769 0.00 0.00 40.28 1.40
2544 3193 4.393062 TCTGCTCTTGCTACTTTATTGTGC 59.607 41.667 0.00 0.00 40.48 4.57
2730 3379 2.525368 GTTTGGAAGGTATGGTGGCTT 58.475 47.619 0.00 0.00 0.00 4.35
2748 3397 9.077885 TGGTGGCTTCTAATATTTTATTCATCC 57.922 33.333 0.00 0.00 0.00 3.51
2789 3444 3.031736 GTCAGCTTCCTCACCATACCTA 58.968 50.000 0.00 0.00 0.00 3.08
2910 3565 5.246677 CGTAAGTGTTACAGAAACTTCCG 57.753 43.478 0.00 0.00 38.99 4.30
3206 3880 6.432783 CCATACAGTGGGTGATTACTGAAAAA 59.567 38.462 10.95 0.00 45.46 1.94
3262 3941 5.438833 AGTAGTGTAAGGATTAGAGCGACT 58.561 41.667 0.00 0.00 0.00 4.18
3263 3942 4.640789 AGTGTAAGGATTAGAGCGACTG 57.359 45.455 0.00 0.00 0.00 3.51
3311 3992 1.607801 CGTGACCCTGGATCTCTGCA 61.608 60.000 0.00 0.00 0.00 4.41
3366 4047 4.242602 GCAGGGTGGCCAGAATAC 57.757 61.111 5.11 0.00 0.00 1.89
3377 4058 4.338400 GTGGCCAGAATACAAGGGATTTAC 59.662 45.833 5.11 0.00 0.00 2.01
3410 4091 2.278657 TGGTCCATCCATACCCTTCA 57.721 50.000 0.00 0.00 41.93 3.02
3442 4123 7.435192 CCTTATAGCGCCAATTTTAGAAAAAGG 59.565 37.037 2.29 2.04 33.11 3.11
3524 4205 8.725405 TTTAGTAATGAATCGATGGTGCTTTA 57.275 30.769 0.00 0.00 0.00 1.85
3527 4208 8.225603 AGTAATGAATCGATGGTGCTTTATTT 57.774 30.769 0.00 0.00 0.00 1.40
3534 4215 3.876914 CGATGGTGCTTTATTTGGCTCTA 59.123 43.478 0.00 0.00 0.00 2.43
3535 4216 4.260784 CGATGGTGCTTTATTTGGCTCTAC 60.261 45.833 0.00 0.00 0.00 2.59
3536 4217 4.027674 TGGTGCTTTATTTGGCTCTACA 57.972 40.909 0.00 0.00 0.00 2.74
3537 4218 4.599041 TGGTGCTTTATTTGGCTCTACAT 58.401 39.130 0.00 0.00 0.00 2.29
3538 4219 4.398988 TGGTGCTTTATTTGGCTCTACATG 59.601 41.667 0.00 0.00 0.00 3.21
3539 4220 4.354587 GTGCTTTATTTGGCTCTACATGC 58.645 43.478 0.00 0.00 0.00 4.06
3540 4221 4.015764 TGCTTTATTTGGCTCTACATGCA 58.984 39.130 0.00 0.00 0.00 3.96
3541 4222 4.646040 TGCTTTATTTGGCTCTACATGCAT 59.354 37.500 0.00 0.00 0.00 3.96
3542 4223 5.827267 TGCTTTATTTGGCTCTACATGCATA 59.173 36.000 0.00 0.00 0.00 3.14
3543 4224 6.320926 TGCTTTATTTGGCTCTACATGCATAA 59.679 34.615 0.00 0.00 0.00 1.90
3544 4225 6.860023 GCTTTATTTGGCTCTACATGCATAAG 59.140 38.462 0.00 0.00 0.00 1.73
3545 4226 7.469181 GCTTTATTTGGCTCTACATGCATAAGT 60.469 37.037 0.00 0.00 0.00 2.24
3546 4227 7.880160 TTATTTGGCTCTACATGCATAAGTT 57.120 32.000 0.00 0.00 0.00 2.66
3547 4228 5.565592 TTTGGCTCTACATGCATAAGTTG 57.434 39.130 0.00 0.00 0.00 3.16
3605 4287 2.616634 AGACTGGCTGATAGTGCATG 57.383 50.000 0.00 0.00 0.00 4.06
3608 4290 3.069300 AGACTGGCTGATAGTGCATGTAG 59.931 47.826 0.00 0.00 0.00 2.74
3611 4293 4.590647 ACTGGCTGATAGTGCATGTAGTAT 59.409 41.667 10.56 10.56 0.00 2.12
3613 4295 6.267699 ACTGGCTGATAGTGCATGTAGTATTA 59.732 38.462 11.84 7.58 0.00 0.98
3614 4296 7.038729 ACTGGCTGATAGTGCATGTAGTATTAT 60.039 37.037 11.84 0.00 0.00 1.28
3651 4363 0.320697 GATATCAGCGGGGGTGTACC 59.679 60.000 0.00 0.00 39.11 3.34
3665 4377 4.141018 GGGGTGTACCATTTCAGGGAATAT 60.141 45.833 3.11 0.00 42.91 1.28
3794 4506 2.665165 TGTGTTCCATTTTCAGCTGGT 58.335 42.857 15.13 0.00 34.03 4.00
3825 4537 8.470805 ACTCAGACGATCAAGTAACTGATAATT 58.529 33.333 0.00 0.00 36.15 1.40
4031 4743 1.144936 CCCTCGAACTGATCAGGCC 59.855 63.158 26.08 15.58 0.00 5.19
4032 4744 1.333636 CCCTCGAACTGATCAGGCCT 61.334 60.000 26.08 0.00 0.00 5.19
4033 4745 0.103937 CCTCGAACTGATCAGGCCTC 59.896 60.000 26.08 17.18 0.00 4.70
4055 4767 6.062258 TCCTAAGAATTGTTTAGGTGGAGG 57.938 41.667 18.26 7.97 44.85 4.30
4056 4768 5.788533 TCCTAAGAATTGTTTAGGTGGAGGA 59.211 40.000 18.26 9.72 44.85 3.71
4057 4769 6.070194 TCCTAAGAATTGTTTAGGTGGAGGAG 60.070 42.308 18.26 0.00 44.85 3.69
4293 5006 8.359060 TGTTGTAAATTTGTTTGTTGATAGCC 57.641 30.769 0.00 0.00 0.00 3.93
4323 5036 4.318332 TCTAATGCACAGTTCAAGGTCTG 58.682 43.478 0.00 0.00 37.65 3.51
4354 5071 4.551702 TGTCAAGAGGCTGCATTAACTA 57.448 40.909 0.50 0.00 0.00 2.24
4355 5072 4.905429 TGTCAAGAGGCTGCATTAACTAA 58.095 39.130 0.50 0.00 0.00 2.24
4356 5073 4.695455 TGTCAAGAGGCTGCATTAACTAAC 59.305 41.667 0.50 0.00 0.00 2.34
4357 5074 4.695455 GTCAAGAGGCTGCATTAACTAACA 59.305 41.667 0.50 0.00 0.00 2.41
4446 5166 3.370672 GGATTTTACCAGCATTTTTGCCG 59.629 43.478 0.00 0.00 34.90 5.69
4545 5267 6.542821 AGGAATGACACAAGACTGGATTTTA 58.457 36.000 0.00 0.00 0.00 1.52
4546 5268 7.004086 AGGAATGACACAAGACTGGATTTTAA 58.996 34.615 0.00 0.00 0.00 1.52
4592 5314 2.504585 TCAGAATCTCTGCAGCCTGAAT 59.495 45.455 9.47 0.00 43.95 2.57
4598 5320 0.034767 TCTGCAGCCTGAATTCTGGG 60.035 55.000 27.06 19.35 35.73 4.45
4623 5345 0.739112 GAGGAGGCACTGAAGCTTCG 60.739 60.000 21.11 17.22 41.55 3.79
4708 5531 1.369625 CCTCGTCAAACCTGTATGCC 58.630 55.000 0.00 0.00 0.00 4.40
4816 5639 1.589113 GTCGAAGTCCTGCTGAGCT 59.411 57.895 5.83 0.00 0.00 4.09
4871 5694 2.357517 AGAACACGCAGCCTTCCG 60.358 61.111 0.00 0.00 0.00 4.30
4921 5744 2.440539 TGTCGAACTCCTTGAGCTTC 57.559 50.000 0.00 0.00 32.04 3.86
5026 5849 3.423154 CGGTGCCGCCTGTTCTTC 61.423 66.667 0.00 0.00 34.25 2.87
5212 6035 1.447489 CAGCCTCTTGGACTGCGAG 60.447 63.158 0.00 0.00 33.30 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.529319 AGGCACCTCTGATCCCTTTATTT 59.471 43.478 0.00 0.00 0.00 1.40
89 90 3.117738 CAGGCACCTCTGATCCCTTTATT 60.118 47.826 0.00 0.00 36.93 1.40
90 91 2.441001 CAGGCACCTCTGATCCCTTTAT 59.559 50.000 0.00 0.00 36.93 1.40
91 92 1.839994 CAGGCACCTCTGATCCCTTTA 59.160 52.381 0.00 0.00 36.93 1.85
124 125 9.803315 AAGTAGGTCATTTTCAGAAAAAGTTTC 57.197 29.630 12.38 4.34 37.76 2.78
161 163 2.287009 CGGCCGATATTTCTTTCTTGGC 60.287 50.000 24.07 0.00 40.48 4.52
221 224 4.202090 GCAGCAAATATTCCTTTCTCCCAG 60.202 45.833 0.00 0.00 0.00 4.45
240 243 4.621034 ACATTTTTACTACGCAATTGCAGC 59.379 37.500 28.77 3.58 42.21 5.25
252 255 9.575868 TTGGATCAGGTGTTTACATTTTTACTA 57.424 29.630 0.00 0.00 0.00 1.82
305 314 7.292356 TCCTAGGGATATAATGTGTGTGTGATT 59.708 37.037 9.46 0.00 0.00 2.57
308 317 6.419484 TCCTAGGGATATAATGTGTGTGTG 57.581 41.667 9.46 0.00 0.00 3.82
309 318 7.453393 CATTCCTAGGGATATAATGTGTGTGT 58.547 38.462 9.46 0.00 0.00 3.72
310 319 6.372659 GCATTCCTAGGGATATAATGTGTGTG 59.627 42.308 17.11 0.00 31.65 3.82
340 431 0.096976 CCTTCATAAGTTGCACGCGG 59.903 55.000 12.47 0.00 0.00 6.46
404 501 5.819825 CCTTTTGGAGGTGTTTATAGAGC 57.180 43.478 0.00 0.00 44.07 4.09
433 530 1.298563 CAGCATTATGCCGCGTTGG 60.299 57.895 14.10 0.00 46.52 3.77
438 535 3.691049 TTAGTTTCAGCATTATGCCGC 57.309 42.857 14.10 0.20 46.52 6.53
441 538 8.962111 GCTATTCTTTTAGTTTCAGCATTATGC 58.038 33.333 9.46 9.46 45.46 3.14
446 543 6.743575 ACGCTATTCTTTTAGTTTCAGCAT 57.256 33.333 0.00 0.00 0.00 3.79
455 552 9.355215 TCAGACTTCTTTACGCTATTCTTTTAG 57.645 33.333 0.00 0.00 0.00 1.85
498 595 2.819608 ACCAATTTAGTGCTCGCATGTT 59.180 40.909 0.00 0.00 0.00 2.71
500 597 3.623060 AGTACCAATTTAGTGCTCGCATG 59.377 43.478 0.00 0.00 0.00 4.06
501 598 3.873910 AGTACCAATTTAGTGCTCGCAT 58.126 40.909 0.00 0.00 0.00 4.73
504 601 5.873164 ACCTTAAGTACCAATTTAGTGCTCG 59.127 40.000 0.97 0.00 29.24 5.03
505 602 7.104290 AGACCTTAAGTACCAATTTAGTGCTC 58.896 38.462 0.97 0.00 29.24 4.26
506 603 7.017319 AGACCTTAAGTACCAATTTAGTGCT 57.983 36.000 0.97 0.00 0.00 4.40
507 604 7.174426 ACAAGACCTTAAGTACCAATTTAGTGC 59.826 37.037 0.97 0.00 0.00 4.40
512 609 9.020731 CCATAACAAGACCTTAAGTACCAATTT 57.979 33.333 0.97 0.00 0.00 1.82
513 610 7.614192 CCCATAACAAGACCTTAAGTACCAATT 59.386 37.037 0.97 0.00 0.00 2.32
514 611 7.037153 TCCCATAACAAGACCTTAAGTACCAAT 60.037 37.037 0.97 0.00 0.00 3.16
515 612 6.272792 TCCCATAACAAGACCTTAAGTACCAA 59.727 38.462 0.97 0.00 0.00 3.67
516 613 5.786457 TCCCATAACAAGACCTTAAGTACCA 59.214 40.000 0.97 0.00 0.00 3.25
517 614 6.111382 GTCCCATAACAAGACCTTAAGTACC 58.889 44.000 0.97 0.00 0.00 3.34
520 617 5.280521 CCTGTCCCATAACAAGACCTTAAGT 60.281 44.000 0.97 0.00 0.00 2.24
521 618 5.186198 CCTGTCCCATAACAAGACCTTAAG 58.814 45.833 0.00 0.00 0.00 1.85
522 619 4.018779 CCCTGTCCCATAACAAGACCTTAA 60.019 45.833 0.00 0.00 0.00 1.85
523 620 3.521937 CCCTGTCCCATAACAAGACCTTA 59.478 47.826 0.00 0.00 0.00 2.69
524 621 2.308866 CCCTGTCCCATAACAAGACCTT 59.691 50.000 0.00 0.00 0.00 3.50
526 623 1.064685 CCCCTGTCCCATAACAAGACC 60.065 57.143 0.00 0.00 0.00 3.85
527 624 1.064685 CCCCCTGTCCCATAACAAGAC 60.065 57.143 0.00 0.00 0.00 3.01
530 627 1.295020 CTCCCCCTGTCCCATAACAA 58.705 55.000 0.00 0.00 0.00 2.83
531 628 0.120377 ACTCCCCCTGTCCCATAACA 59.880 55.000 0.00 0.00 0.00 2.41
532 629 2.185663 TACTCCCCCTGTCCCATAAC 57.814 55.000 0.00 0.00 0.00 1.89
533 630 2.251605 TCATACTCCCCCTGTCCCATAA 59.748 50.000 0.00 0.00 0.00 1.90
534 631 1.870327 TCATACTCCCCCTGTCCCATA 59.130 52.381 0.00 0.00 0.00 2.74
535 632 0.647738 TCATACTCCCCCTGTCCCAT 59.352 55.000 0.00 0.00 0.00 4.00
536 633 0.647738 ATCATACTCCCCCTGTCCCA 59.352 55.000 0.00 0.00 0.00 4.37
537 634 1.821088 AATCATACTCCCCCTGTCCC 58.179 55.000 0.00 0.00 0.00 4.46
538 635 3.953542 AAAATCATACTCCCCCTGTCC 57.046 47.619 0.00 0.00 0.00 4.02
540 637 4.167892 TGCATAAAATCATACTCCCCCTGT 59.832 41.667 0.00 0.00 0.00 4.00
541 638 4.728772 TGCATAAAATCATACTCCCCCTG 58.271 43.478 0.00 0.00 0.00 4.45
542 639 4.751028 GCTGCATAAAATCATACTCCCCCT 60.751 45.833 0.00 0.00 0.00 4.79
543 640 3.507622 GCTGCATAAAATCATACTCCCCC 59.492 47.826 0.00 0.00 0.00 5.40
545 642 5.772825 TTGCTGCATAAAATCATACTCCC 57.227 39.130 1.84 0.00 0.00 4.30
546 643 7.025963 GCTATTGCTGCATAAAATCATACTCC 58.974 38.462 1.84 0.00 36.03 3.85
599 1081 9.688592 ATTAAGATAGAATTTGCTTTGCTATGC 57.311 29.630 0.00 0.00 0.00 3.14
604 1086 9.793252 TGAGAATTAAGATAGAATTTGCTTTGC 57.207 29.630 0.00 0.00 0.00 3.68
643 1149 8.299990 TCCAAAAGTTTTCTAAGGACAAATCA 57.700 30.769 0.00 0.00 0.00 2.57
648 1154 7.889873 TGATTCCAAAAGTTTTCTAAGGACA 57.110 32.000 0.00 0.00 0.00 4.02
656 1162 5.748630 AGCTTCGTTGATTCCAAAAGTTTTC 59.251 36.000 0.00 0.00 33.49 2.29
657 1163 5.660460 AGCTTCGTTGATTCCAAAAGTTTT 58.340 33.333 0.00 0.00 33.49 2.43
659 1165 4.918810 AGCTTCGTTGATTCCAAAAGTT 57.081 36.364 0.00 0.00 33.49 2.66
667 1173 3.814945 CTCCACAAAGCTTCGTTGATTC 58.185 45.455 0.00 0.00 0.00 2.52
787 1302 1.607628 CTGCTGGCTTGATGCTTATCC 59.392 52.381 0.00 0.00 42.39 2.59
955 1474 0.914417 ACAGGGGATCGGTGATTGGT 60.914 55.000 0.00 0.00 0.00 3.67
1372 1897 3.411517 ATGAAGGCCACCTCCGGG 61.412 66.667 5.01 0.00 38.88 5.73
1486 2012 3.584733 ATAGCTCCAAGGAACCCAATC 57.415 47.619 0.00 0.00 0.00 2.67
1517 2043 5.163258 CCAAAGTATCTATTGCTCCCTGACT 60.163 44.000 0.00 0.00 0.00 3.41
1623 2150 1.754226 GCCTAATCCCAAATTCGCCAA 59.246 47.619 0.00 0.00 0.00 4.52
1627 2154 1.873591 CTCCGCCTAATCCCAAATTCG 59.126 52.381 0.00 0.00 0.00 3.34
1648 2175 3.165071 CCCAATTAGCTCAAACCAACCT 58.835 45.455 0.00 0.00 0.00 3.50
1759 2286 0.769873 TTTTACCGCCCAACACCCTA 59.230 50.000 0.00 0.00 0.00 3.53
1760 2287 0.106116 TTTTTACCGCCCAACACCCT 60.106 50.000 0.00 0.00 0.00 4.34
1818 2345 6.453926 AAGCTTTTGTTTTGGATTTGCAAT 57.546 29.167 0.00 0.00 0.00 3.56
1884 2411 3.382546 GCAGTTGTTGGCTAATGGATCAT 59.617 43.478 0.00 0.00 0.00 2.45
1889 2416 3.598019 AATGCAGTTGTTGGCTAATGG 57.402 42.857 0.00 0.00 0.00 3.16
1890 2417 6.567050 AGATTAATGCAGTTGTTGGCTAATG 58.433 36.000 0.00 0.00 0.00 1.90
1928 2455 5.013704 TCCTGTAAATTCTCTAAACCAGCCA 59.986 40.000 0.00 0.00 0.00 4.75
2005 2645 7.670364 TGACTACAAGATCAGTGATCAGAAAA 58.330 34.615 30.05 13.37 41.12 2.29
2075 2718 5.307204 GCAGGCTCAGATATCTTCTCAAAT 58.693 41.667 1.33 0.00 29.93 2.32
2106 2749 1.028330 ATCCAATCACGCTGCCAGTG 61.028 55.000 3.17 3.17 40.71 3.66
2274 2923 8.495148 GGCTTGGATTTAGTTTTAACACAAATG 58.505 33.333 8.84 0.00 30.73 2.32
2356 3005 7.611855 CCTGAAAAGGTAGTCCATATTTGTTCT 59.388 37.037 0.00 0.00 35.89 3.01
2582 3231 5.245531 TCAACATCCTTTACAGATCACACC 58.754 41.667 0.00 0.00 0.00 4.16
2589 3238 6.831353 TGTTTTCCTTCAACATCCTTTACAGA 59.169 34.615 0.00 0.00 0.00 3.41
2748 3397 1.068281 CTGGGATCATGTGACGAGAGG 59.932 57.143 0.00 0.00 0.00 3.69
2789 3444 5.595952 GCATAACCTGAGGAGAAATTTGGAT 59.404 40.000 4.99 0.00 0.00 3.41
2910 3565 8.673711 TGTTACAAAATCACTTGTATCCTATGC 58.326 33.333 0.00 0.00 40.53 3.14
3002 3675 6.554419 TGCATGTAACATTCAACTGATTAGC 58.446 36.000 0.00 0.00 0.00 3.09
3080 3753 7.171630 ACGACCAATCTCTAGTATTGAACTT 57.828 36.000 16.98 6.32 39.80 2.66
3206 3880 5.698545 GCAGATTACCATCTTCGCTCTAATT 59.301 40.000 0.00 0.00 37.71 1.40
3262 3941 5.254339 CAGTGCAGACTGTAGATATCACA 57.746 43.478 5.32 6.65 44.15 3.58
3311 3992 0.901114 TTCATGGCTGGCATTGCACT 60.901 50.000 14.65 0.00 0.00 4.40
3366 4047 6.467677 TGAAGAAGAGACAGTAAATCCCTTG 58.532 40.000 0.00 0.00 0.00 3.61
3377 4058 3.969287 TGGACCATGAAGAAGAGACAG 57.031 47.619 0.00 0.00 0.00 3.51
3410 4091 2.566833 TTGGCGCTATAAGGCATGAT 57.433 45.000 7.64 0.00 43.68 2.45
3442 4123 5.354792 AGAATTGATGAGCTGCTTCTTTCTC 59.645 40.000 2.53 0.00 0.00 2.87
3524 4205 6.140303 CAACTTATGCATGTAGAGCCAAAT 57.860 37.500 10.16 0.00 0.00 2.32
3605 4287 9.331282 AGAAAATGAACTGGCTCATAATACTAC 57.669 33.333 0.00 0.00 34.90 2.73
3608 4290 8.213518 TCAGAAAATGAACTGGCTCATAATAC 57.786 34.615 0.00 0.00 34.90 1.89
3611 4293 8.985315 ATATCAGAAAATGAACTGGCTCATAA 57.015 30.769 0.00 0.00 42.53 1.90
3613 4295 7.058525 TGATATCAGAAAATGAACTGGCTCAT 58.941 34.615 0.00 0.00 42.53 2.90
3614 4296 6.417258 TGATATCAGAAAATGAACTGGCTCA 58.583 36.000 0.00 0.00 42.53 4.26
3651 4363 7.119407 CACATGCTCTCTATATTCCCTGAAATG 59.881 40.741 0.00 0.00 0.00 2.32
3794 4506 5.009710 AGTTACTTGATCGTCTGAGTGTTGA 59.990 40.000 0.00 0.00 0.00 3.18
3839 4551 2.241281 TTAGAGGACCGGAACCATGA 57.759 50.000 9.46 0.00 0.00 3.07
3840 4552 3.560636 AATTAGAGGACCGGAACCATG 57.439 47.619 9.46 0.00 0.00 3.66
3950 4662 3.415087 AGGGCTGGCCTCACATCC 61.415 66.667 18.27 0.00 36.10 3.51
4031 4743 6.070194 TCCTCCACCTAAACAATTCTTAGGAG 60.070 42.308 21.89 16.29 45.74 3.69
4032 4744 5.788533 TCCTCCACCTAAACAATTCTTAGGA 59.211 40.000 21.89 3.27 45.74 2.94
4055 4767 1.742268 GGCAGGCACTTGATTCTTCTC 59.258 52.381 0.00 0.00 34.60 2.87
4056 4768 1.074405 TGGCAGGCACTTGATTCTTCT 59.926 47.619 0.00 0.00 34.60 2.85
4057 4769 1.200948 GTGGCAGGCACTTGATTCTTC 59.799 52.381 19.73 0.00 34.60 2.87
4293 5006 7.703621 CCTTGAACTGTGCATTAGATTAAATGG 59.296 37.037 7.80 0.00 37.34 3.16
4323 5036 4.305769 CAGCCTCTTGACATCATAGCTAC 58.694 47.826 0.00 0.00 0.00 3.58
4354 5071 8.463930 TCTGACTGAAACCTTGATTAAATGTT 57.536 30.769 0.00 0.00 0.00 2.71
4355 5072 8.463930 TTCTGACTGAAACCTTGATTAAATGT 57.536 30.769 0.00 0.00 0.00 2.71
4356 5073 9.918630 ATTTCTGACTGAAACCTTGATTAAATG 57.081 29.630 9.40 0.00 46.08 2.32
4357 5074 9.918630 CATTTCTGACTGAAACCTTGATTAAAT 57.081 29.630 9.40 0.00 46.08 1.40
4425 5145 4.241681 TCGGCAAAAATGCTGGTAAAATC 58.758 39.130 9.55 0.00 41.28 2.17
4510 5232 8.443937 GTCTTGTGTCATTCCTTAGTGATTTAC 58.556 37.037 0.00 0.00 0.00 2.01
4527 5249 6.739112 AGCTTTTAAAATCCAGTCTTGTGTC 58.261 36.000 0.09 0.00 0.00 3.67
4545 5267 6.930667 AAATTTGAATGTCAGCAAGCTTTT 57.069 29.167 0.00 0.00 0.00 2.27
4546 5268 6.316890 ACAAAATTTGAATGTCAGCAAGCTTT 59.683 30.769 13.19 0.00 0.00 3.51
4592 5314 0.839946 GCCTCCTCTAATGCCCAGAA 59.160 55.000 0.00 0.00 0.00 3.02
4598 5320 2.559440 CTTCAGTGCCTCCTCTAATGC 58.441 52.381 0.00 0.00 0.00 3.56
4602 5324 1.827969 GAAGCTTCAGTGCCTCCTCTA 59.172 52.381 21.67 0.00 0.00 2.43
4623 5345 4.425520 CGTCCAGAAACTCAGATAAGGAC 58.574 47.826 0.00 0.00 40.57 3.85
4708 5531 4.253257 GCCGGCGTCTACGAGAGG 62.253 72.222 12.58 6.81 43.02 3.69
4798 5621 0.457681 GAGCTCAGCAGGACTTCGAC 60.458 60.000 9.40 0.00 0.00 4.20
4816 5639 1.153489 GATGCTCAGCTTGCTCGGA 60.153 57.895 0.00 0.00 0.00 4.55
4921 5744 0.176219 TTACCATGAACGCCTACGGG 59.824 55.000 0.00 0.00 46.04 5.28
5199 6022 1.876664 CTCGTCTCGCAGTCCAAGA 59.123 57.895 0.00 0.00 0.00 3.02
5291 6114 0.601311 GCCGCCAAGCTCTTCGATAT 60.601 55.000 0.00 0.00 0.00 1.63
5293 6116 2.512515 GCCGCCAAGCTCTTCGAT 60.513 61.111 0.00 0.00 0.00 3.59
5317 6140 3.119096 GTGAACGCCGGGAAGCTC 61.119 66.667 2.18 0.00 0.00 4.09
5329 6152 0.984230 TCCTGTCCATCTGGGTGAAC 59.016 55.000 0.00 0.00 38.11 3.18


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

AutoCloner maintained by Alex Coulton.