Multiple sequence alignment - TraesCS3B01G273100

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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 TraesCS3B01G273100 chr3B 100.000 4424 0 0 1 4424 440127221 440131644 0.000000e+00 8170
1 TraesCS3B01G273100 chr3A 95.256 4448 148 12 1 4424 461862534 461858126 0.000000e+00 6986
2 TraesCS3B01G273100 chr3A 74.737 380 93 2 2627 3006 461840060 461839684 2.740000e-37 167
3 TraesCS3B01G273100 chr3D 96.085 2248 65 5 2173 4411 341465254 341467487 0.000000e+00 3642
4 TraesCS3B01G273100 chr3D 95.712 1539 36 7 1 1536 341463584 341465095 0.000000e+00 2449
5 TraesCS3B01G273100 chr3D 75.936 374 87 3 2627 3000 341495059 341495429 5.840000e-44 189
6 TraesCS3B01G273100 chr3D 92.308 78 3 1 2102 2176 341465096 341465173 1.680000e-19 108
7 TraesCS3B01G273100 chrUn 96.474 397 14 0 2301 2697 478834782 478835178 0.000000e+00 656
8 TraesCS3B01G273100 chr1D 73.013 604 148 15 2547 3141 443554177 443554774 9.710000e-47 198


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 TraesCS3B01G273100 chr3B 440127221 440131644 4423 False 8170.000000 8170 100.000000 1 4424 1 chr3B.!!$F1 4423
1 TraesCS3B01G273100 chr3A 461858126 461862534 4408 True 6986.000000 6986 95.256000 1 4424 1 chr3A.!!$R2 4423
2 TraesCS3B01G273100 chr3D 341463584 341467487 3903 False 2066.333333 3642 94.701667 1 4411 3 chr3D.!!$F2 4410

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
573 581 0.391228 TGCCAGCTTGTCACTAACGA 59.609 50.0 0.00 0.0 0.00 3.85 F
1576 1591 0.178903 AGGTACAAGGCTGGTCTCCA 60.179 55.0 15.49 0.0 0.00 3.86 F
1679 1694 0.034059 AGTGCAGACTACACAGTGCC 59.966 55.0 8.53 0.0 40.59 5.01 F
2919 3021 0.037303 ATGAGTGCCTTGAGTGGGTG 59.963 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1693 0.108138 CTAGTCCGCCCACTTTGAGG 60.108 60.000 0.00 0.00 0.00 3.86 R
3088 3190 0.038983 TCAACCTTTGCGTCGATCGA 60.039 50.000 15.15 15.15 42.86 3.59 R
3119 3221 1.068748 TCTCGAGAAGTACAACGCCAC 60.069 52.381 14.01 0.00 0.00 5.01 R
3997 4115 2.235016 TGGTGCCAAAATGTAGTGGTC 58.765 47.619 0.00 0.00 37.23 4.02 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
126 128 8.722480 ACAATGATCATATATCAATACACGGG 57.278 34.615 9.04 0.00 0.00 5.28
387 395 0.881796 GCCTAACCACTTGTGGCTTC 59.118 55.000 18.67 1.88 40.36 3.86
406 414 4.394610 GCTTCTCCACCTGATCTTCTTTTC 59.605 45.833 0.00 0.00 0.00 2.29
466 474 2.027192 ACCATAGCATGTCAAAGACGGT 60.027 45.455 0.00 0.00 34.95 4.83
566 574 1.455412 TGGTGATGCCAGCTTGTCA 59.545 52.632 0.00 0.00 43.61 3.58
567 575 0.890542 TGGTGATGCCAGCTTGTCAC 60.891 55.000 12.04 12.04 43.61 3.67
568 576 0.607489 GGTGATGCCAGCTTGTCACT 60.607 55.000 16.80 0.00 40.50 3.41
569 577 1.339055 GGTGATGCCAGCTTGTCACTA 60.339 52.381 16.80 0.00 40.50 2.74
570 578 2.426522 GTGATGCCAGCTTGTCACTAA 58.573 47.619 12.76 0.00 38.29 2.24
571 579 2.160417 GTGATGCCAGCTTGTCACTAAC 59.840 50.000 12.76 0.00 38.29 2.34
572 580 1.394917 GATGCCAGCTTGTCACTAACG 59.605 52.381 0.00 0.00 0.00 3.18
573 581 0.391228 TGCCAGCTTGTCACTAACGA 59.609 50.000 0.00 0.00 0.00 3.85
574 582 1.202592 TGCCAGCTTGTCACTAACGAA 60.203 47.619 0.00 0.00 0.00 3.85
575 583 1.194772 GCCAGCTTGTCACTAACGAAC 59.805 52.381 0.00 0.00 0.00 3.95
576 584 2.755650 CCAGCTTGTCACTAACGAACT 58.244 47.619 0.00 0.00 0.00 3.01
577 585 3.131396 CCAGCTTGTCACTAACGAACTT 58.869 45.455 0.00 0.00 0.00 2.66
578 586 3.184581 CCAGCTTGTCACTAACGAACTTC 59.815 47.826 0.00 0.00 0.00 3.01
579 587 4.051922 CAGCTTGTCACTAACGAACTTCT 58.948 43.478 0.00 0.00 0.00 2.85
580 588 5.220381 CAGCTTGTCACTAACGAACTTCTA 58.780 41.667 0.00 0.00 0.00 2.10
581 589 5.343593 CAGCTTGTCACTAACGAACTTCTAG 59.656 44.000 0.00 0.00 0.00 2.43
582 590 4.090210 GCTTGTCACTAACGAACTTCTAGC 59.910 45.833 0.00 0.00 0.00 3.42
583 591 5.449107 TTGTCACTAACGAACTTCTAGCT 57.551 39.130 0.00 0.00 0.00 3.32
584 592 5.449107 TGTCACTAACGAACTTCTAGCTT 57.551 39.130 0.00 0.00 0.00 3.74
585 593 5.220381 TGTCACTAACGAACTTCTAGCTTG 58.780 41.667 0.00 0.00 0.00 4.01
586 594 5.221130 GTCACTAACGAACTTCTAGCTTGT 58.779 41.667 0.00 0.00 0.00 3.16
587 595 5.342791 GTCACTAACGAACTTCTAGCTTGTC 59.657 44.000 0.00 0.00 0.00 3.18
592 600 5.049398 ACGAACTTCTAGCTTGTCACTAG 57.951 43.478 0.00 0.00 38.79 2.57
1023 1038 8.911662 CACATGCATACATACATGATGAAAATG 58.088 33.333 9.77 2.76 45.23 2.32
1046 1061 4.498682 GGCAAGCATAAATGGAAGCAGTAG 60.499 45.833 0.00 0.00 0.00 2.57
1066 1081 1.429148 CTTCGGCCATACAACTCGCC 61.429 60.000 2.24 0.00 38.07 5.54
1071 1086 1.702491 GCCATACAACTCGCCGAACC 61.702 60.000 0.00 0.00 0.00 3.62
1103 1118 5.983333 ATGGACACATTCCTCTTCCTTAT 57.017 39.130 0.00 0.00 46.10 1.73
1123 1138 3.438216 TCATTCTTCCATTGCTCACCA 57.562 42.857 0.00 0.00 0.00 4.17
1224 1239 6.603201 TCCTTACCTCACCAAATGATGATTTC 59.397 38.462 0.00 0.00 36.48 2.17
1461 1476 2.422945 GGTGGTTTCCCTTCTTGACACT 60.423 50.000 0.00 0.00 0.00 3.55
1484 1499 4.943705 TGGCAACCTCATAATCAAAGACTC 59.056 41.667 0.00 0.00 0.00 3.36
1576 1591 0.178903 AGGTACAAGGCTGGTCTCCA 60.179 55.000 15.49 0.00 0.00 3.86
1596 1611 8.613482 GTCTCCAGTTATTACAGCCTTTATTTC 58.387 37.037 0.00 0.00 0.00 2.17
1602 1617 8.448615 AGTTATTACAGCCTTTATTTCGACAAC 58.551 33.333 0.00 0.00 0.00 3.32
1678 1693 1.528586 CAAGTGCAGACTACACAGTGC 59.471 52.381 8.53 0.00 40.59 4.40
1679 1694 0.034059 AGTGCAGACTACACAGTGCC 59.966 55.000 8.53 0.00 40.59 5.01
1685 1700 3.062763 CAGACTACACAGTGCCTCAAAG 58.937 50.000 0.00 0.00 34.21 2.77
1767 1782 2.681848 CTCAAGTGATGGGCTGAATGTC 59.318 50.000 0.00 0.00 0.00 3.06
1791 1806 1.683385 GCTTCTGATTGGGGTAATGGC 59.317 52.381 0.00 0.00 0.00 4.40
1798 1813 0.693622 TTGGGGTAATGGCGTCAAGA 59.306 50.000 0.00 0.00 0.00 3.02
1806 1821 0.392193 ATGGCGTCAAGAGAAGGCTG 60.392 55.000 0.00 0.00 46.34 4.85
1815 1830 3.152341 CAAGAGAAGGCTGACAATTGGT 58.848 45.455 10.83 0.00 0.00 3.67
1870 1885 7.671819 TGAATGTGTTAAATGGGAGTTGGATAA 59.328 33.333 0.00 0.00 0.00 1.75
1894 1909 2.951642 TCATGGCAGGCTATAGCAAAAC 59.048 45.455 25.53 13.22 44.36 2.43
1921 1936 0.330941 TGTGCATGGGCTATGTGGAA 59.669 50.000 12.66 0.00 41.91 3.53
1993 2008 2.480416 GGATATGAGATGACCGATCCGC 60.480 54.545 0.00 0.00 0.00 5.54
2006 2021 1.265635 CGATCCGCAAAACTGGAACAA 59.734 47.619 0.00 0.00 38.70 2.83
2019 2034 0.463620 GGAACAAAGGTTGCAAGCCA 59.536 50.000 24.26 0.00 43.97 4.75
2028 2043 1.069049 GGTTGCAAGCCACAATTCAGT 59.931 47.619 17.84 0.00 0.00 3.41
2032 2047 4.662468 TGCAAGCCACAATTCAGTAAAA 57.338 36.364 0.00 0.00 0.00 1.52
2080 2095 1.089920 CATCAAGCTCCCTCAAACCG 58.910 55.000 0.00 0.00 0.00 4.44
2138 2156 8.787852 GTCCTCACTTGAAGAATGTAAAAAGAT 58.212 33.333 0.00 0.00 0.00 2.40
2139 2157 8.786898 TCCTCACTTGAAGAATGTAAAAAGATG 58.213 33.333 0.00 0.00 0.00 2.90
2146 2164 7.939782 TGAAGAATGTAAAAAGATGTGCTTGA 58.060 30.769 0.00 0.00 36.80 3.02
2181 2283 1.073216 CAGCTCTCACGTACAAGGCG 61.073 60.000 0.00 0.00 0.00 5.52
2186 2288 0.742505 CTCACGTACAAGGCGGGATA 59.257 55.000 0.00 0.00 41.17 2.59
2233 2335 3.274288 CTCTTCAATGGTTACAGCTCCC 58.726 50.000 0.00 0.00 0.00 4.30
2250 2352 1.194218 CCCCAAATTTTCCTGGCGAT 58.806 50.000 0.00 0.00 0.00 4.58
2265 2367 7.770366 TCCTGGCGATAACTATATCAAACTA 57.230 36.000 0.00 0.00 38.26 2.24
2292 2394 5.883685 AGAATATGAGCATCTCCAGACAA 57.116 39.130 0.00 0.00 34.92 3.18
2299 2401 2.100584 AGCATCTCCAGACAATCTCGTC 59.899 50.000 0.00 0.00 36.08 4.20
2321 2423 3.411446 TCACATGCAATCCGGATATTCC 58.589 45.455 19.48 6.98 0.00 3.01
2326 2428 1.537202 GCAATCCGGATATTCCAGTGC 59.463 52.381 19.48 17.88 35.91 4.40
2327 2429 2.849942 CAATCCGGATATTCCAGTGCA 58.150 47.619 19.48 0.00 35.91 4.57
2369 2471 8.613060 AGTATGTATGGAATGAATGATGTCAC 57.387 34.615 0.00 0.00 0.00 3.67
2469 2571 4.796312 TCGTTTCTTTACAGCAAGCAAAAC 59.204 37.500 0.00 0.00 0.00 2.43
2493 2595 3.956744 ACCTAAGTCAATGGAAGAAGGC 58.043 45.455 0.00 0.00 0.00 4.35
2532 2634 4.411540 AGCCAGTTCAGGATGTTCATCTAT 59.588 41.667 11.73 0.34 37.40 1.98
2550 2652 2.833631 ATAGGGAATTACGGGAAGCG 57.166 50.000 0.00 0.00 0.00 4.68
2589 2691 2.200955 GAGATTGGAAGAGGGGGTTCT 58.799 52.381 0.00 0.00 0.00 3.01
2649 2751 2.552743 GGTGGCAGTGAAGAAACTAACC 59.447 50.000 0.00 0.00 0.00 2.85
2664 2766 3.000727 ACTAACCAGCGTTTCACATAGC 58.999 45.455 0.00 0.00 33.17 2.97
2745 2847 1.257750 GGATGTGGGGGTTTTGCTCC 61.258 60.000 0.00 0.00 36.85 4.70
2751 2853 2.754375 GGGTTTTGCTCCGAGGGA 59.246 61.111 0.00 0.00 0.00 4.20
2778 2880 2.719426 AACTGCTGGTGTACGAGTAC 57.281 50.000 6.46 6.46 36.63 2.73
2793 2895 2.223294 CGAGTACGTGGAGAATGAGTCC 60.223 54.545 0.00 0.00 34.56 3.85
2799 2901 2.169352 CGTGGAGAATGAGTCCCTTGAT 59.831 50.000 0.00 0.00 32.49 2.57
2919 3021 0.037303 ATGAGTGCCTTGAGTGGGTG 59.963 55.000 0.00 0.00 0.00 4.61
3088 3190 2.233271 CAGAGTGGGCACTGAATTTGT 58.767 47.619 0.00 0.00 42.66 2.83
3119 3221 5.106712 ACGCAAAGGTTGATGTATACAGTTG 60.107 40.000 11.91 7.58 0.00 3.16
3258 3360 4.965532 AGTGGAGATGTCAAGGTTATAGCT 59.034 41.667 0.00 0.00 0.00 3.32
3298 3400 3.508762 CATTTCAATCCTGAGCAAGTGC 58.491 45.455 0.00 0.00 42.49 4.40
3382 3484 9.283768 TGAATGAAATTGTAAAAGCTCTACTGA 57.716 29.630 7.29 0.00 36.07 3.41
3513 3615 9.730420 TTTGAAAGTAGAAGAAAATGTTGCTAC 57.270 29.630 0.00 0.00 0.00 3.58
3514 3616 8.445275 TGAAAGTAGAAGAAAATGTTGCTACA 57.555 30.769 2.82 2.82 38.95 2.74
3574 3691 1.593196 TGGAACACTAACTGCACTGC 58.407 50.000 0.00 0.00 0.00 4.40
3626 3743 5.913137 TGAAACATAGTGGGCTTATTTGG 57.087 39.130 0.00 0.00 0.00 3.28
3834 3951 5.895636 AACAACTGACAACATTCACTCAA 57.104 34.783 0.00 0.00 0.00 3.02
3997 4115 3.683822 GTCCATCGATCTAGTACTACGGG 59.316 52.174 10.44 6.13 0.00 5.28
4016 4134 1.544246 GGACCACTACATTTTGGCACC 59.456 52.381 0.00 0.00 36.20 5.01
4214 4340 4.269603 CACTGCTCAAGTTCGGAATATCTG 59.730 45.833 0.00 0.00 36.83 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 0.531200 GTTCCTCACACTAGGTCCCG 59.469 60.000 0.00 0.00 37.91 5.14
126 128 2.028112 TGCATGTTCCTCACACTAGGTC 60.028 50.000 0.00 0.00 38.61 3.85
387 395 5.419239 AGAGAAAAGAAGATCAGGTGGAG 57.581 43.478 0.00 0.00 0.00 3.86
395 403 8.499967 GGACAACTTGTTAGAGAAAAGAAGATC 58.500 37.037 0.00 0.00 34.33 2.75
406 414 4.608948 AGAGGTGGACAACTTGTTAGAG 57.391 45.455 0.00 0.00 0.00 2.43
566 574 5.009811 AGTGACAAGCTAGAAGTTCGTTAGT 59.990 40.000 0.00 0.00 0.00 2.24
567 575 5.462405 AGTGACAAGCTAGAAGTTCGTTAG 58.538 41.667 0.00 0.00 0.00 2.34
568 576 5.449107 AGTGACAAGCTAGAAGTTCGTTA 57.551 39.130 0.00 0.00 0.00 3.18
569 577 4.323553 AGTGACAAGCTAGAAGTTCGTT 57.676 40.909 0.00 0.00 0.00 3.85
570 578 4.616373 GCTAGTGACAAGCTAGAAGTTCGT 60.616 45.833 0.00 0.00 38.47 3.85
571 579 3.854809 GCTAGTGACAAGCTAGAAGTTCG 59.145 47.826 0.00 0.00 38.47 3.95
572 580 3.854809 CGCTAGTGACAAGCTAGAAGTTC 59.145 47.826 0.00 0.00 38.47 3.01
573 581 3.506455 TCGCTAGTGACAAGCTAGAAGTT 59.494 43.478 0.70 0.00 38.47 2.66
574 582 3.082548 TCGCTAGTGACAAGCTAGAAGT 58.917 45.455 0.70 0.00 38.47 3.01
575 583 3.766676 TCGCTAGTGACAAGCTAGAAG 57.233 47.619 0.70 0.00 38.47 2.85
576 584 3.506455 AGTTCGCTAGTGACAAGCTAGAA 59.494 43.478 5.23 0.00 38.47 2.10
577 585 3.082548 AGTTCGCTAGTGACAAGCTAGA 58.917 45.455 5.23 0.00 38.47 2.43
578 586 3.495670 AGTTCGCTAGTGACAAGCTAG 57.504 47.619 5.23 0.00 37.85 3.42
579 587 3.506455 AGAAGTTCGCTAGTGACAAGCTA 59.494 43.478 5.23 0.00 37.85 3.32
580 588 2.297597 AGAAGTTCGCTAGTGACAAGCT 59.702 45.455 5.23 0.00 37.85 3.74
581 589 2.410053 CAGAAGTTCGCTAGTGACAAGC 59.590 50.000 5.23 0.00 36.60 4.01
582 590 3.670991 GTCAGAAGTTCGCTAGTGACAAG 59.329 47.826 5.23 0.00 38.73 3.16
583 591 3.639538 GTCAGAAGTTCGCTAGTGACAA 58.360 45.455 5.23 0.00 38.73 3.18
584 592 2.350484 CGTCAGAAGTTCGCTAGTGACA 60.350 50.000 17.45 0.00 38.77 3.58
585 593 2.243407 CGTCAGAAGTTCGCTAGTGAC 58.757 52.381 5.23 10.63 37.01 3.67
586 594 1.401148 GCGTCAGAAGTTCGCTAGTGA 60.401 52.381 0.70 0.70 45.29 3.41
587 595 0.985549 GCGTCAGAAGTTCGCTAGTG 59.014 55.000 0.00 0.00 45.29 2.74
639 647 4.532126 ACCTTGATGATGTTGGTACTGAGA 59.468 41.667 0.00 0.00 0.00 3.27
830 843 3.570540 CAGAGAGGACTGTGATGGGATA 58.429 50.000 0.00 0.00 39.36 2.59
1023 1038 2.167075 ACTGCTTCCATTTATGCTTGCC 59.833 45.455 0.00 0.00 0.00 4.52
1046 1061 2.006772 CGAGTTGTATGGCCGAAGC 58.993 57.895 0.00 0.00 38.76 3.86
1066 1081 2.625790 TGTCCATTTTTCTTGGGGTTCG 59.374 45.455 0.00 0.00 34.85 3.95
1071 1086 4.568956 GGAATGTGTCCATTTTTCTTGGG 58.431 43.478 0.00 0.00 46.97 4.12
1103 1118 3.084039 GTGGTGAGCAATGGAAGAATGA 58.916 45.455 0.00 0.00 0.00 2.57
1123 1138 1.420514 AGCATATGAGCATGGCAGAGT 59.579 47.619 6.97 0.00 36.85 3.24
1175 1190 3.133003 GGTCTGCCTATGCTCTTCTACAA 59.867 47.826 0.00 0.00 38.71 2.41
1224 1239 2.898705 ACTTCATAGAAGCCGCAAGAG 58.101 47.619 6.67 0.00 43.02 2.85
1356 1371 4.772100 ACCAAGTTTCCATTATGGTTCAGG 59.228 41.667 11.39 9.31 41.47 3.86
1401 1416 1.346068 GTCTTGCTCTCCCAAGTGACT 59.654 52.381 2.31 0.00 42.16 3.41
1404 1419 2.149578 CTTGTCTTGCTCTCCCAAGTG 58.850 52.381 2.31 0.00 42.16 3.16
1431 1446 2.671963 GAAACCACCGTGCCCTCC 60.672 66.667 0.00 0.00 0.00 4.30
1461 1476 4.922206 AGTCTTTGATTATGAGGTTGCCA 58.078 39.130 0.00 0.00 0.00 4.92
1484 1499 1.540797 CCCACAAATTTGCACCAGTGG 60.541 52.381 18.12 15.53 44.58 4.00
1576 1591 8.448615 GTTGTCGAAATAAAGGCTGTAATAACT 58.551 33.333 0.00 0.00 0.00 2.24
1596 1611 1.201661 CGTAGCACATTGTCGTTGTCG 60.202 52.381 0.00 0.00 38.55 4.35
1678 1693 0.108138 CTAGTCCGCCCACTTTGAGG 60.108 60.000 0.00 0.00 0.00 3.86
1679 1694 0.741221 GCTAGTCCGCCCACTTTGAG 60.741 60.000 0.00 0.00 0.00 3.02
1685 1700 0.459759 GTTGTAGCTAGTCCGCCCAC 60.460 60.000 0.00 0.00 0.00 4.61
1767 1782 2.806945 TACCCCAATCAGAAGCCTTG 57.193 50.000 0.00 0.00 0.00 3.61
1791 1806 2.154854 TTGTCAGCCTTCTCTTGACG 57.845 50.000 0.17 0.00 32.68 4.35
1798 1813 3.152341 CAGAACCAATTGTCAGCCTTCT 58.848 45.455 4.43 0.00 0.00 2.85
1806 1821 4.524328 AGGTTTCCATCAGAACCAATTGTC 59.476 41.667 4.43 0.00 32.95 3.18
1853 1868 7.615365 GCCATGATATTATCCAACTCCCATTTA 59.385 37.037 0.00 0.00 0.00 1.40
1870 1885 4.849813 TTGCTATAGCCTGCCATGATAT 57.150 40.909 21.84 0.00 41.18 1.63
1921 1936 6.351286 GGCAAGAACTCACATATCCCATTTTT 60.351 38.462 0.00 0.00 0.00 1.94
1993 2008 3.594134 TGCAACCTTTGTTCCAGTTTTG 58.406 40.909 0.00 0.00 30.42 2.44
2006 2021 1.761784 TGAATTGTGGCTTGCAACCTT 59.238 42.857 15.91 5.29 0.00 3.50
2019 2034 3.318839 TGCTGCAGCTTTTACTGAATTGT 59.681 39.130 36.61 0.00 40.25 2.71
2080 2095 5.415701 TGGTCAGATCAAAGCCATAAAAGTC 59.584 40.000 0.00 0.00 0.00 3.01
2138 2156 2.034939 CAGGAGCAAATGTTCAAGCACA 59.965 45.455 0.00 0.00 0.00 4.57
2139 2157 2.669364 CAGGAGCAAATGTTCAAGCAC 58.331 47.619 0.00 0.00 0.00 4.40
2146 2164 0.886563 GCTGAGCAGGAGCAAATGTT 59.113 50.000 0.00 0.00 45.49 2.71
2181 2283 3.118038 TGGTGTAGCAAAGTCCATATCCC 60.118 47.826 0.00 0.00 0.00 3.85
2186 2288 2.558359 GCTTTGGTGTAGCAAAGTCCAT 59.442 45.455 27.30 0.00 39.74 3.41
2233 2335 4.718940 AGTTATCGCCAGGAAAATTTGG 57.281 40.909 0.00 0.00 37.53 3.28
2265 2367 3.718434 TGGAGATGCTCATATTCTTGGGT 59.282 43.478 0.00 0.00 31.08 4.51
2292 2394 2.800985 CGGATTGCATGTGAGACGAGAT 60.801 50.000 0.00 0.00 0.00 2.75
2299 2401 3.438087 GGAATATCCGGATTGCATGTGAG 59.562 47.826 24.71 0.00 0.00 3.51
2321 2423 2.353889 GCAGATCCTTGTACATGCACTG 59.646 50.000 11.11 14.11 33.92 3.66
2326 2428 5.819379 ACATACTTGCAGATCCTTGTACATG 59.181 40.000 0.00 0.00 0.00 3.21
2327 2429 5.994250 ACATACTTGCAGATCCTTGTACAT 58.006 37.500 0.00 0.00 0.00 2.29
2397 2499 1.006998 AGGGCTCCCAATATTGTTGCA 59.993 47.619 14.25 0.00 38.92 4.08
2401 2503 3.669949 AGACTAGGGCTCCCAATATTGT 58.330 45.455 14.25 0.00 38.92 2.71
2407 2509 0.547712 AGCAAGACTAGGGCTCCCAA 60.548 55.000 7.82 0.00 38.92 4.12
2469 2571 5.529060 GCCTTCTTCCATTGACTTAGGTATG 59.471 44.000 0.00 0.00 0.00 2.39
2493 2595 3.894427 ACTGGCTCATCACAGTCCTATAG 59.106 47.826 0.00 0.00 44.08 1.31
2532 2634 1.410153 GTCGCTTCCCGTAATTCCCTA 59.590 52.381 0.00 0.00 38.35 3.53
2550 2652 4.962155 TCTCTTCCTTGAACTTTCCAGTC 58.038 43.478 0.00 0.00 30.45 3.51
2589 2691 7.183112 TCAAGTACCCCTCTATAAACAATTCCA 59.817 37.037 0.00 0.00 0.00 3.53
2649 2751 0.647410 CCTCGCTATGTGAAACGCTG 59.353 55.000 0.00 0.00 42.39 5.18
2664 2766 0.179062 CTGCCCAGAATTCCTCCTCG 60.179 60.000 0.65 0.00 0.00 4.63
2745 2847 0.307760 GCAGTTTGTGTTGTCCCTCG 59.692 55.000 0.00 0.00 0.00 4.63
2751 2853 1.544724 ACACCAGCAGTTTGTGTTGT 58.455 45.000 0.00 0.00 40.12 3.32
2778 2880 1.550524 TCAAGGGACTCATTCTCCACG 59.449 52.381 0.00 0.00 38.49 4.94
2824 2926 4.682859 GCTCCATGCAAGTAATCTCTCAGT 60.683 45.833 0.00 0.00 42.31 3.41
2919 3021 7.164122 TCTCTGGCTTTATATCACAATGGATC 58.836 38.462 0.00 0.00 0.00 3.36
3088 3190 0.038983 TCAACCTTTGCGTCGATCGA 60.039 50.000 15.15 15.15 42.86 3.59
3119 3221 1.068748 TCTCGAGAAGTACAACGCCAC 60.069 52.381 14.01 0.00 0.00 5.01
3258 3360 1.839354 TGGCCATTCAGTCTAGCATCA 59.161 47.619 0.00 0.00 0.00 3.07
3298 3400 2.099405 AGCCAATTTCACCATTACCGG 58.901 47.619 0.00 0.00 0.00 5.28
3382 3484 4.389992 GTGATTGTCTTCGTCATCACATGT 59.610 41.667 0.00 0.00 38.49 3.21
3499 3601 7.715657 TGACATTTTCTGTAGCAACATTTTCT 58.284 30.769 0.00 0.00 38.54 2.52
3500 3602 7.115378 CCTGACATTTTCTGTAGCAACATTTTC 59.885 37.037 0.00 0.00 38.54 2.29
3501 3603 6.925165 CCTGACATTTTCTGTAGCAACATTTT 59.075 34.615 0.00 0.00 38.54 1.82
3502 3604 6.040842 ACCTGACATTTTCTGTAGCAACATTT 59.959 34.615 0.00 0.00 38.54 2.32
3503 3605 5.536161 ACCTGACATTTTCTGTAGCAACATT 59.464 36.000 0.00 0.00 38.54 2.71
3504 3606 5.072741 ACCTGACATTTTCTGTAGCAACAT 58.927 37.500 0.00 0.00 38.54 2.71
3505 3607 4.460263 ACCTGACATTTTCTGTAGCAACA 58.540 39.130 0.00 0.00 38.54 3.33
3506 3608 5.215160 CAACCTGACATTTTCTGTAGCAAC 58.785 41.667 0.00 0.00 38.54 4.17
3507 3609 4.887071 ACAACCTGACATTTTCTGTAGCAA 59.113 37.500 0.00 0.00 38.54 3.91
3508 3610 4.275689 CACAACCTGACATTTTCTGTAGCA 59.724 41.667 0.00 0.00 38.54 3.49
3509 3611 4.275936 ACACAACCTGACATTTTCTGTAGC 59.724 41.667 0.00 0.00 38.54 3.58
3510 3612 5.296780 ACACACAACCTGACATTTTCTGTAG 59.703 40.000 0.00 0.00 38.54 2.74
3511 3613 5.189928 ACACACAACCTGACATTTTCTGTA 58.810 37.500 0.00 0.00 38.54 2.74
3512 3614 4.016444 ACACACAACCTGACATTTTCTGT 58.984 39.130 0.00 0.00 42.15 3.41
3513 3615 4.637483 ACACACAACCTGACATTTTCTG 57.363 40.909 0.00 0.00 0.00 3.02
3514 3616 4.677779 GCAACACACAACCTGACATTTTCT 60.678 41.667 0.00 0.00 0.00 2.52
3969 4087 3.924918 ACTAGATCGATGGACCATTCG 57.075 47.619 8.78 13.26 0.00 3.34
3997 4115 2.235016 TGGTGCCAAAATGTAGTGGTC 58.765 47.619 0.00 0.00 37.23 4.02
4016 4134 5.345741 CAGCCGAAAGTTTGACCATAAATTG 59.654 40.000 0.00 0.00 0.00 2.32
4028 4146 5.708230 TGATTATGTTACCAGCCGAAAGTTT 59.292 36.000 0.00 0.00 0.00 2.66
4214 4340 5.918011 TCATTTTTGTTACTCCAACGATTGC 59.082 36.000 0.00 0.00 40.26 3.56


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

AutoCloner maintained by Alex Coulton.