Multiple sequence alignment - TraesCS6B01G471500

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 TraesCS6B01G471500 chr6B 100.000 3191 0 0 1 3191 719507577 719510767 0.000000e+00 5893.0
1 TraesCS6B01G471500 chr6B 91.613 310 16 2 2891 3191 719515753 719516061 1.370000e-113 420.0
2 TraesCS6B01G471500 chr6B 78.497 386 73 8 89 468 601340840 601340459 8.840000e-61 244.0
3 TraesCS6B01G471500 chr6B 96.364 55 2 0 2521 2575 719515373 719515427 1.220000e-14 91.6
4 TraesCS6B01G471500 chr6D 93.476 2575 131 17 18 2575 471072656 471070102 0.000000e+00 3790.0
5 TraesCS6B01G471500 chr6D 94.737 114 6 0 2891 3004 471069854 471069741 9.100000e-41 178.0
6 TraesCS6B01G471500 chr6D 90.580 138 5 3 3062 3191 471069739 471069602 3.270000e-40 176.0
7 TraesCS6B01G471500 chr6A 91.475 2604 161 27 7 2575 615891386 615888809 0.000000e+00 3522.0
8 TraesCS6B01G471500 chr6A 88.818 313 23 7 2891 3191 615888540 615888228 1.080000e-99 374.0
9 TraesCS6B01G471500 chr2D 78.526 475 84 14 6 469 388057211 388057678 2.410000e-76 296.0
10 TraesCS6B01G471500 chr7A 77.215 474 94 11 5 469 149029325 149028857 6.790000e-67 265.0
11 TraesCS6B01G471500 chr5B 76.923 442 96 6 12 451 707438053 707437616 2.460000e-61 246.0
12 TraesCS6B01G471500 chr1B 76.682 446 97 7 12 453 623897588 623897146 1.140000e-59 241.0
13 TraesCS6B01G471500 chr1D 76.871 441 89 12 18 453 212424113 212424545 1.480000e-58 237.0
14 TraesCS6B01G471500 chr1D 76.596 423 91 7 32 452 416468158 416467742 3.200000e-55 226.0


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 TraesCS6B01G471500 chr6B 719507577 719510767 3190 False 5893.000000 5893 100.0000 1 3191 1 chr6B.!!$F1 3190
1 TraesCS6B01G471500 chr6B 719515373 719516061 688 False 255.800000 420 93.9885 2521 3191 2 chr6B.!!$F2 670
2 TraesCS6B01G471500 chr6D 471069602 471072656 3054 True 1381.333333 3790 92.9310 18 3191 3 chr6D.!!$R1 3173
3 TraesCS6B01G471500 chr6A 615888228 615891386 3158 True 1948.000000 3522 90.1465 7 3191 2 chr6A.!!$R1 3184

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
368 372 0.109735 CGCTTCAGTGCTCGTAGTCA 60.110 55.0 0.0 0.0 0.0 3.41 F
679 701 0.472161 GATAGTCCCCCTCCACCTCC 60.472 65.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1481 0.182299 TGACATCACCACCAACAGCA 59.818 50.0 0.0 0.0 0.0 4.41 R
2650 2689 0.178992 TCAGCCACCCAAGACCAAAG 60.179 55.0 0.0 0.0 0.0 2.77 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
44 47 2.764547 GAGGTTCCCCGCCTAGCT 60.765 66.667 0.00 0.00 36.29 3.32
68 71 2.816083 CCGGCGGTGCGTTTCATA 60.816 61.111 19.97 0.00 0.00 2.15
76 79 1.593006 GGTGCGTTTCATATCGTCAGG 59.407 52.381 0.00 0.00 0.00 3.86
168 171 0.594284 GATCCGGTCATCGTTCGTCC 60.594 60.000 0.00 0.00 37.11 4.79
170 173 2.177531 CGGTCATCGTTCGTCCGT 59.822 61.111 0.00 0.00 36.99 4.69
184 187 1.134367 CGTCCGTGGTCATGTGTCTAT 59.866 52.381 0.00 0.00 0.00 1.98
192 195 4.081087 GTGGTCATGTGTCTATAGGTTGGT 60.081 45.833 0.00 0.00 0.00 3.67
195 198 5.104900 GGTCATGTGTCTATAGGTTGGTTCT 60.105 44.000 0.00 0.00 0.00 3.01
226 229 2.270923 CATTTCTCTTCATCGGCGACA 58.729 47.619 13.76 0.00 0.00 4.35
278 281 0.242825 CTTAGCACGACGACTTCCCA 59.757 55.000 0.00 0.00 0.00 4.37
300 303 6.463331 CCCAACTGTCTACTACAACAAGGTAA 60.463 42.308 0.00 0.00 37.74 2.85
353 357 2.736236 CACGCACTCTGCTCGCTT 60.736 61.111 0.00 0.00 42.25 4.68
361 365 1.077645 CTCTGCTCGCTTCAGTGCTC 61.078 60.000 0.00 0.00 33.48 4.26
368 372 0.109735 CGCTTCAGTGCTCGTAGTCA 60.110 55.000 0.00 0.00 0.00 3.41
371 375 2.416027 GCTTCAGTGCTCGTAGTCATCA 60.416 50.000 0.00 0.00 0.00 3.07
376 380 3.623510 CAGTGCTCGTAGTCATCACTAGA 59.376 47.826 0.00 0.00 35.67 2.43
414 418 5.010112 TGGATGCAATTTCCGTTACTTTTCA 59.990 36.000 0.00 0.00 35.94 2.69
461 465 9.992910 TGTTTGATGAATAGATCAGATTTTTCG 57.007 29.630 0.00 0.00 42.53 3.46
523 537 8.308931 TCCATTACTACCACTGTTTGTACTTAG 58.691 37.037 0.00 0.00 0.00 2.18
590 604 8.099364 TGTTGAGAAAAGACAGGCTTAATAAG 57.901 34.615 0.00 0.00 35.24 1.73
675 697 1.122019 ATGCGATAGTCCCCCTCCAC 61.122 60.000 0.00 0.00 39.35 4.02
676 698 2.508751 GCGATAGTCCCCCTCCACC 61.509 68.421 0.00 0.00 39.35 4.61
677 699 1.233369 CGATAGTCCCCCTCCACCT 59.767 63.158 0.00 0.00 0.00 4.00
678 700 0.828343 CGATAGTCCCCCTCCACCTC 60.828 65.000 0.00 0.00 0.00 3.85
679 701 0.472161 GATAGTCCCCCTCCACCTCC 60.472 65.000 0.00 0.00 0.00 4.30
680 702 2.313749 ATAGTCCCCCTCCACCTCCG 62.314 65.000 0.00 0.00 0.00 4.63
749 772 3.009115 CCCCCTTCTTCCTCGCCA 61.009 66.667 0.00 0.00 0.00 5.69
886 909 2.165845 GCTAGCCTAGGTCGTTTCTTCA 59.834 50.000 11.31 0.00 0.00 3.02
888 911 3.528597 AGCCTAGGTCGTTTCTTCATC 57.471 47.619 11.31 0.00 0.00 2.92
904 927 0.761187 CATCCATCCATCCGTCCAGT 59.239 55.000 0.00 0.00 0.00 4.00
909 932 3.770040 CCATCCGTCCAGTGCCGA 61.770 66.667 2.39 0.00 0.00 5.54
1458 1481 1.535202 GATCGAGGGGGCAGAGGAT 60.535 63.158 0.00 0.00 0.00 3.24
1572 1595 1.303282 GCCCCGGATTTCCTTCACT 59.697 57.895 0.73 0.00 0.00 3.41
1611 1634 1.499049 GTATCGCCGATGGGAAAGAC 58.501 55.000 10.41 0.00 36.96 3.01
1757 1783 1.054406 TCCAAGATTAGGGCTCCGGG 61.054 60.000 0.00 0.00 0.00 5.73
1758 1784 1.451936 CAAGATTAGGGCTCCGGGG 59.548 63.158 0.00 0.00 0.00 5.73
1761 1787 1.539124 GATTAGGGCTCCGGGGGAT 60.539 63.158 1.90 0.00 0.00 3.85
1764 1790 2.340909 TTAGGGCTCCGGGGGATGAT 62.341 60.000 1.90 0.00 0.00 2.45
1923 1949 5.482908 GGTGAACAGAGAGAAGAGCATAAA 58.517 41.667 0.00 0.00 0.00 1.40
1955 1981 0.543749 CAATCCAGAGACCCTCCCAC 59.456 60.000 0.00 0.00 0.00 4.61
1983 2012 2.555325 CTGCAATGAGCTCAAGTCCAAA 59.445 45.455 22.50 2.20 45.94 3.28
2154 2183 2.341846 TGTTGTGTTCCTCCAGTTCC 57.658 50.000 0.00 0.00 0.00 3.62
2328 2363 0.673985 CCGGACAGACAGACAGACAA 59.326 55.000 0.00 0.00 0.00 3.18
2330 2365 1.067060 CGGACAGACAGACAGACAACA 59.933 52.381 0.00 0.00 0.00 3.33
2341 2376 0.397941 CAGACAACAAGAGGAGGCCA 59.602 55.000 5.01 0.00 0.00 5.36
2343 2378 2.237143 CAGACAACAAGAGGAGGCCATA 59.763 50.000 5.01 0.00 0.00 2.74
2448 2487 2.921754 CGAATCGTTCCTGTTCTGTACC 59.078 50.000 0.00 0.00 0.00 3.34
2570 2609 7.147724 TGCCATATAAACTTGTAGCTACTGTCT 60.148 37.037 23.84 12.32 0.00 3.41
2575 2614 8.764524 ATAAACTTGTAGCTACTGTCTTCTTG 57.235 34.615 23.84 6.71 0.00 3.02
2576 2615 5.793030 ACTTGTAGCTACTGTCTTCTTGT 57.207 39.130 23.84 7.25 0.00 3.16
2577 2616 5.533482 ACTTGTAGCTACTGTCTTCTTGTG 58.467 41.667 23.84 4.14 0.00 3.33
2578 2617 5.302059 ACTTGTAGCTACTGTCTTCTTGTGA 59.698 40.000 23.84 0.00 0.00 3.58
2579 2618 5.378292 TGTAGCTACTGTCTTCTTGTGAG 57.622 43.478 23.84 0.00 0.00 3.51
2580 2619 4.827835 TGTAGCTACTGTCTTCTTGTGAGT 59.172 41.667 23.84 0.00 0.00 3.41
2581 2620 6.002082 TGTAGCTACTGTCTTCTTGTGAGTA 58.998 40.000 23.84 0.00 0.00 2.59
2582 2621 6.489022 TGTAGCTACTGTCTTCTTGTGAGTAA 59.511 38.462 23.84 0.00 0.00 2.24
2583 2622 6.406692 AGCTACTGTCTTCTTGTGAGTAAA 57.593 37.500 0.00 0.00 0.00 2.01
2584 2623 6.217294 AGCTACTGTCTTCTTGTGAGTAAAC 58.783 40.000 0.00 0.00 0.00 2.01
2585 2624 5.983720 GCTACTGTCTTCTTGTGAGTAAACA 59.016 40.000 0.00 0.00 0.00 2.83
2586 2625 6.479001 GCTACTGTCTTCTTGTGAGTAAACAA 59.521 38.462 0.00 0.00 37.71 2.83
2587 2626 6.663944 ACTGTCTTCTTGTGAGTAAACAAC 57.336 37.500 0.00 0.00 35.16 3.32
2588 2627 5.585047 ACTGTCTTCTTGTGAGTAAACAACC 59.415 40.000 0.00 0.00 35.16 3.77
2589 2628 5.741011 TGTCTTCTTGTGAGTAAACAACCT 58.259 37.500 0.00 0.00 35.16 3.50
2590 2629 5.815740 TGTCTTCTTGTGAGTAAACAACCTC 59.184 40.000 0.00 0.00 35.16 3.85
2591 2630 6.049790 GTCTTCTTGTGAGTAAACAACCTCT 58.950 40.000 0.00 0.00 35.16 3.69
2592 2631 6.018669 GTCTTCTTGTGAGTAAACAACCTCTG 60.019 42.308 0.00 0.00 35.16 3.35
2593 2632 5.353394 TCTTGTGAGTAAACAACCTCTGT 57.647 39.130 0.00 0.00 41.27 3.41
2605 2644 2.810852 CAACCTCTGTTCTTCTTGCCTC 59.189 50.000 0.00 0.00 30.42 4.70
2606 2645 2.334023 ACCTCTGTTCTTCTTGCCTCT 58.666 47.619 0.00 0.00 0.00 3.69
2610 2649 4.221703 CCTCTGTTCTTCTTGCCTCTCTTA 59.778 45.833 0.00 0.00 0.00 2.10
2614 2653 6.493802 TCTGTTCTTCTTGCCTCTCTTACTTA 59.506 38.462 0.00 0.00 0.00 2.24
2626 2665 9.863650 TGCCTCTCTTACTTACTTACAGTATAT 57.136 33.333 0.00 0.00 29.64 0.86
2655 2694 8.424274 AATTCAGCTTGTTCTTAAAACTTTGG 57.576 30.769 0.00 0.00 0.00 3.28
2656 2695 6.524101 TCAGCTTGTTCTTAAAACTTTGGT 57.476 33.333 0.00 0.00 0.00 3.67
2657 2696 6.560711 TCAGCTTGTTCTTAAAACTTTGGTC 58.439 36.000 0.00 0.00 0.00 4.02
2658 2697 6.377146 TCAGCTTGTTCTTAAAACTTTGGTCT 59.623 34.615 0.00 0.00 0.00 3.85
2659 2698 7.035612 CAGCTTGTTCTTAAAACTTTGGTCTT 58.964 34.615 0.00 0.00 0.00 3.01
2660 2699 7.009540 CAGCTTGTTCTTAAAACTTTGGTCTTG 59.990 37.037 0.00 0.00 0.00 3.02
2681 2720 3.209410 GGGTGGCTGACATAAATCTCTG 58.791 50.000 0.00 0.00 0.00 3.35
2685 2724 5.183904 GGTGGCTGACATAAATCTCTGTTTT 59.816 40.000 0.00 0.00 0.00 2.43
2745 2784 1.568504 TCCACCCGTCATCTTTAGCT 58.431 50.000 0.00 0.00 0.00 3.32
2751 2790 2.224066 CCCGTCATCTTTAGCTGTAGGG 60.224 54.545 0.00 0.00 0.00 3.53
2752 2791 2.431057 CCGTCATCTTTAGCTGTAGGGT 59.569 50.000 0.00 0.00 0.00 4.34
2757 2796 6.116126 GTCATCTTTAGCTGTAGGGTCAATT 58.884 40.000 0.00 0.00 0.00 2.32
2764 2803 9.573133 CTTTAGCTGTAGGGTCAATTTTAATTG 57.427 33.333 8.55 8.55 45.49 2.32
2766 2805 6.924111 AGCTGTAGGGTCAATTTTAATTGTG 58.076 36.000 13.28 0.00 44.66 3.33
2778 2817 9.838339 TCAATTTTAATTGTGTAAACCAACCAT 57.162 25.926 13.28 0.00 44.66 3.55
2800 2839 3.052944 TCAGATCCCCACCCTTTAATTGG 60.053 47.826 0.00 0.00 0.00 3.16
2819 2858 2.568062 TGGGACGGTGAAAGTTATAGCA 59.432 45.455 0.00 0.00 0.00 3.49
2854 2893 6.183360 GCATTTTTATTGGAGAAAATGGGCAG 60.183 38.462 17.90 0.07 46.05 4.85
2855 2894 5.419239 TTTTATTGGAGAAAATGGGCAGG 57.581 39.130 0.00 0.00 0.00 4.85
2858 2897 0.039618 TGGAGAAAATGGGCAGGACC 59.960 55.000 0.00 0.00 37.93 4.46
2888 2927 9.460019 TCATTCATTTATAACCTGTTCATCACA 57.540 29.630 0.00 0.00 0.00 3.58
2927 3062 3.055602 TGATCTCCTCAGGTGACACATTG 60.056 47.826 8.08 5.51 0.00 2.82
2948 3083 0.179018 GCCAACAGGACTCAACACCT 60.179 55.000 0.00 0.00 36.92 4.00
2972 3107 4.641541 TGTTCTGCAGATTAACATGGATGG 59.358 41.667 19.04 0.00 0.00 3.51
2980 3115 7.506599 TGCAGATTAACATGGATGGAATTACAT 59.493 33.333 1.71 1.71 0.00 2.29
3121 3265 1.675641 GGGCCTGACAAACAGCGAT 60.676 57.895 0.84 0.00 44.52 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.884579 TCTTTAGAGACTCGCCGTTGT 59.115 47.619 0.00 0.00 0.00 3.32
1 2 2.631418 TCTTTAGAGACTCGCCGTTG 57.369 50.000 0.00 0.00 0.00 4.10
2 3 2.159226 CCATCTTTAGAGACTCGCCGTT 60.159 50.000 0.00 0.00 33.99 4.44
3 4 1.405821 CCATCTTTAGAGACTCGCCGT 59.594 52.381 0.00 0.00 33.99 5.68
4 5 1.676529 TCCATCTTTAGAGACTCGCCG 59.323 52.381 0.00 0.00 33.99 6.46
5 6 3.802948 TTCCATCTTTAGAGACTCGCC 57.197 47.619 0.00 0.00 33.99 5.54
63 66 1.067060 CACGCTCCCTGACGATATGAA 59.933 52.381 0.00 0.00 0.00 2.57
68 71 2.885861 GACACGCTCCCTGACGAT 59.114 61.111 0.00 0.00 0.00 3.73
76 79 2.430921 CACACCTCGACACGCTCC 60.431 66.667 0.00 0.00 0.00 4.70
110 113 6.635641 CGAAGACAAATACCGATCGAATCTTA 59.364 38.462 18.66 0.00 0.00 2.10
111 114 5.459107 CGAAGACAAATACCGATCGAATCTT 59.541 40.000 18.66 13.14 0.00 2.40
117 120 2.534349 CACCGAAGACAAATACCGATCG 59.466 50.000 8.51 8.51 0.00 3.69
119 122 2.498481 TCCACCGAAGACAAATACCGAT 59.502 45.455 0.00 0.00 0.00 4.18
129 132 1.409427 CCAGGTAGATCCACCGAAGAC 59.591 57.143 4.56 0.00 43.84 3.01
168 171 4.112634 CAACCTATAGACACATGACCACG 58.887 47.826 0.00 0.00 0.00 4.94
170 173 4.101114 ACCAACCTATAGACACATGACCA 58.899 43.478 0.00 0.00 0.00 4.02
184 187 2.829023 AGATCGGGAAGAACCAACCTA 58.171 47.619 0.00 0.00 41.20 3.08
192 195 6.154534 TGAAGAGAAATGTAGATCGGGAAGAA 59.845 38.462 0.00 0.00 0.00 2.52
195 198 5.932619 TGAAGAGAAATGTAGATCGGGAA 57.067 39.130 0.00 0.00 0.00 3.97
226 229 1.032014 AGCGCACCAGAACAACAATT 58.968 45.000 11.47 0.00 0.00 2.32
278 281 6.221659 GCTTACCTTGTTGTAGTAGACAGTT 58.778 40.000 0.00 0.00 39.88 3.16
313 316 2.359975 GTCAACGCCCCTCCCTTG 60.360 66.667 0.00 0.00 0.00 3.61
342 346 1.077645 GAGCACTGAAGCGAGCAGAG 61.078 60.000 9.89 4.11 40.15 3.35
345 349 1.862602 TACGAGCACTGAAGCGAGCA 61.863 55.000 0.00 0.00 40.15 4.26
353 357 2.437413 AGTGATGACTACGAGCACTGA 58.563 47.619 0.00 0.00 38.30 3.41
368 372 4.520874 CACATCCGTAGACCATCTAGTGAT 59.479 45.833 0.00 0.00 27.77 3.06
371 375 3.117625 TCCACATCCGTAGACCATCTAGT 60.118 47.826 0.00 0.00 28.01 2.57
376 380 1.070758 GCATCCACATCCGTAGACCAT 59.929 52.381 0.00 0.00 0.00 3.55
388 392 3.417101 AGTAACGGAAATTGCATCCACA 58.583 40.909 5.70 0.00 36.74 4.17
426 430 8.833493 TGATCTATTCATCAAACATCATGACAC 58.167 33.333 0.00 0.00 29.41 3.67
523 537 3.011119 TGATTAACGCCATTACACCCAC 58.989 45.455 0.00 0.00 0.00 4.61
590 604 1.392589 CCTCTCTGTCTCTCTCCAGC 58.607 60.000 0.00 0.00 0.00 4.85
842 865 3.539604 AGCTGCTCATACCTCAATCAAC 58.460 45.455 0.00 0.00 0.00 3.18
886 909 0.761187 CACTGGACGGATGGATGGAT 59.239 55.000 0.00 0.00 0.00 3.41
888 911 1.524621 GCACTGGACGGATGGATGG 60.525 63.158 0.00 0.00 0.00 3.51
979 1002 1.000171 TGCTAGATCATGCGCGATTCT 60.000 47.619 12.10 6.11 0.00 2.40
1458 1481 0.182299 TGACATCACCACCAACAGCA 59.818 50.000 0.00 0.00 0.00 4.41
1572 1595 2.606519 CGGGGTCTCTTGGGTCCA 60.607 66.667 0.00 0.00 0.00 4.02
1707 1733 1.278127 GTTCTCTCACCGGATTTCCCA 59.722 52.381 9.46 0.00 34.14 4.37
1757 1783 4.278975 GGATACTCTTCACCATCATCCC 57.721 50.000 0.00 0.00 0.00 3.85
1800 1826 7.448161 CCATCTCCATTATTAACAATGTGCCTA 59.552 37.037 5.77 0.00 34.67 3.93
1923 1949 4.070716 CTCTGGATTGCTCTGTTTCTTGT 58.929 43.478 0.00 0.00 0.00 3.16
1955 1981 3.189618 TGAGCTCATTGCAGTATCCTG 57.810 47.619 13.74 0.00 45.94 3.86
2057 2086 2.347630 ACGGACGTGATCTTGGTCA 58.652 52.632 0.00 0.00 32.39 4.02
2154 2183 3.793144 GCAGAGGTTTCAGCCGCG 61.793 66.667 0.00 0.00 33.40 6.46
2232 2265 9.588096 AGGACACACATCTGACAACTATATATA 57.412 33.333 0.00 0.00 0.00 0.86
2233 2266 8.484214 AGGACACACATCTGACAACTATATAT 57.516 34.615 0.00 0.00 0.00 0.86
2251 2284 8.595362 ACAAGCATATATATAGCTAGGACACA 57.405 34.615 15.53 0.00 37.70 3.72
2328 2363 3.342926 AGAGATATGGCCTCCTCTTGT 57.657 47.619 3.32 0.00 32.55 3.16
2330 2365 2.978278 CCAAGAGATATGGCCTCCTCTT 59.022 50.000 17.59 17.59 44.19 2.85
2341 2376 5.731924 AGGTGGGAATCTACCAAGAGATAT 58.268 41.667 9.21 0.00 45.75 1.63
2343 2378 4.014273 AGGTGGGAATCTACCAAGAGAT 57.986 45.455 9.21 0.00 45.75 2.75
2448 2487 8.704849 TCATTACTGACATATAAAAATGGGGG 57.295 34.615 0.00 0.00 0.00 5.40
2570 2609 5.741011 ACAGAGGTTGTTTACTCACAAGAA 58.259 37.500 0.00 0.00 37.33 2.52
2583 2622 2.173569 AGGCAAGAAGAACAGAGGTTGT 59.826 45.455 0.00 0.00 43.45 3.32
2584 2623 2.810852 GAGGCAAGAAGAACAGAGGTTG 59.189 50.000 0.00 0.00 37.36 3.77
2585 2624 2.708325 AGAGGCAAGAAGAACAGAGGTT 59.292 45.455 0.00 0.00 40.76 3.50
2586 2625 2.301583 GAGAGGCAAGAAGAACAGAGGT 59.698 50.000 0.00 0.00 0.00 3.85
2587 2626 2.566724 AGAGAGGCAAGAAGAACAGAGG 59.433 50.000 0.00 0.00 0.00 3.69
2588 2627 3.959535 AGAGAGGCAAGAAGAACAGAG 57.040 47.619 0.00 0.00 0.00 3.35
2589 2628 4.835615 AGTAAGAGAGGCAAGAAGAACAGA 59.164 41.667 0.00 0.00 0.00 3.41
2590 2629 5.146010 AGTAAGAGAGGCAAGAAGAACAG 57.854 43.478 0.00 0.00 0.00 3.16
2591 2630 5.552870 AAGTAAGAGAGGCAAGAAGAACA 57.447 39.130 0.00 0.00 0.00 3.18
2592 2631 6.693466 AGTAAGTAAGAGAGGCAAGAAGAAC 58.307 40.000 0.00 0.00 0.00 3.01
2593 2632 6.919775 AGTAAGTAAGAGAGGCAAGAAGAA 57.080 37.500 0.00 0.00 0.00 2.52
2594 2633 6.919775 AAGTAAGTAAGAGAGGCAAGAAGA 57.080 37.500 0.00 0.00 0.00 2.87
2595 2634 7.603651 TGTAAGTAAGTAAGAGAGGCAAGAAG 58.396 38.462 0.00 0.00 0.00 2.85
2596 2635 7.534723 TGTAAGTAAGTAAGAGAGGCAAGAA 57.465 36.000 0.00 0.00 0.00 2.52
2597 2636 7.159322 CTGTAAGTAAGTAAGAGAGGCAAGA 57.841 40.000 0.00 0.00 0.00 3.02
2629 2668 8.882736 CCAAAGTTTTAAGAACAAGCTGAATTT 58.117 29.630 0.00 0.00 0.00 1.82
2630 2669 8.040727 ACCAAAGTTTTAAGAACAAGCTGAATT 58.959 29.630 0.00 0.00 0.00 2.17
2631 2670 7.555965 ACCAAAGTTTTAAGAACAAGCTGAAT 58.444 30.769 0.00 0.00 0.00 2.57
2632 2671 6.930731 ACCAAAGTTTTAAGAACAAGCTGAA 58.069 32.000 0.00 0.00 0.00 3.02
2633 2672 6.377146 AGACCAAAGTTTTAAGAACAAGCTGA 59.623 34.615 0.00 0.00 0.00 4.26
2634 2673 6.564328 AGACCAAAGTTTTAAGAACAAGCTG 58.436 36.000 0.00 0.00 0.00 4.24
2635 2674 6.775594 AGACCAAAGTTTTAAGAACAAGCT 57.224 33.333 0.00 0.00 0.00 3.74
2636 2675 6.255670 CCAAGACCAAAGTTTTAAGAACAAGC 59.744 38.462 0.00 0.00 0.00 4.01
2637 2676 6.756542 CCCAAGACCAAAGTTTTAAGAACAAG 59.243 38.462 0.00 0.00 0.00 3.16
2638 2677 6.211785 ACCCAAGACCAAAGTTTTAAGAACAA 59.788 34.615 0.00 0.00 0.00 2.83
2639 2678 5.717654 ACCCAAGACCAAAGTTTTAAGAACA 59.282 36.000 0.00 0.00 0.00 3.18
2640 2679 6.040247 CACCCAAGACCAAAGTTTTAAGAAC 58.960 40.000 0.00 0.00 0.00 3.01
2641 2680 5.128008 CCACCCAAGACCAAAGTTTTAAGAA 59.872 40.000 0.00 0.00 0.00 2.52
2642 2681 4.647399 CCACCCAAGACCAAAGTTTTAAGA 59.353 41.667 0.00 0.00 0.00 2.10
2643 2682 4.739436 GCCACCCAAGACCAAAGTTTTAAG 60.739 45.833 0.00 0.00 0.00 1.85
2644 2683 3.133183 GCCACCCAAGACCAAAGTTTTAA 59.867 43.478 0.00 0.00 0.00 1.52
2645 2684 2.696187 GCCACCCAAGACCAAAGTTTTA 59.304 45.455 0.00 0.00 0.00 1.52
2646 2685 1.484653 GCCACCCAAGACCAAAGTTTT 59.515 47.619 0.00 0.00 0.00 2.43
2647 2686 1.119684 GCCACCCAAGACCAAAGTTT 58.880 50.000 0.00 0.00 0.00 2.66
2648 2687 0.261696 AGCCACCCAAGACCAAAGTT 59.738 50.000 0.00 0.00 0.00 2.66
2649 2688 0.468029 CAGCCACCCAAGACCAAAGT 60.468 55.000 0.00 0.00 0.00 2.66
2650 2689 0.178992 TCAGCCACCCAAGACCAAAG 60.179 55.000 0.00 0.00 0.00 2.77
2651 2690 0.467290 GTCAGCCACCCAAGACCAAA 60.467 55.000 0.00 0.00 0.00 3.28
2652 2691 1.150536 GTCAGCCACCCAAGACCAA 59.849 57.895 0.00 0.00 0.00 3.67
2653 2692 1.426251 ATGTCAGCCACCCAAGACCA 61.426 55.000 0.00 0.00 0.00 4.02
2654 2693 0.618458 TATGTCAGCCACCCAAGACC 59.382 55.000 0.00 0.00 0.00 3.85
2655 2694 2.489938 TTATGTCAGCCACCCAAGAC 57.510 50.000 0.00 0.00 0.00 3.01
2656 2695 3.266772 AGATTTATGTCAGCCACCCAAGA 59.733 43.478 0.00 0.00 0.00 3.02
2657 2696 3.624777 AGATTTATGTCAGCCACCCAAG 58.375 45.455 0.00 0.00 0.00 3.61
2658 2697 3.266772 AGAGATTTATGTCAGCCACCCAA 59.733 43.478 0.00 0.00 0.00 4.12
2659 2698 2.846206 AGAGATTTATGTCAGCCACCCA 59.154 45.455 0.00 0.00 0.00 4.51
2660 2699 3.209410 CAGAGATTTATGTCAGCCACCC 58.791 50.000 0.00 0.00 0.00 4.61
2688 2727 4.037684 GCGCTAGGAGTCTATTCAGGTAAA 59.962 45.833 0.00 0.00 0.00 2.01
2690 2729 3.147629 GCGCTAGGAGTCTATTCAGGTA 58.852 50.000 0.00 0.00 0.00 3.08
2692 2731 1.957177 TGCGCTAGGAGTCTATTCAGG 59.043 52.381 9.73 0.00 0.00 3.86
2693 2732 2.606795 GCTGCGCTAGGAGTCTATTCAG 60.607 54.545 9.73 0.00 38.17 3.02
2694 2733 1.338337 GCTGCGCTAGGAGTCTATTCA 59.662 52.381 9.73 0.00 38.17 2.57
2695 2734 1.338337 TGCTGCGCTAGGAGTCTATTC 59.662 52.381 9.73 0.00 38.17 1.75
2696 2735 1.403814 TGCTGCGCTAGGAGTCTATT 58.596 50.000 9.73 0.00 38.17 1.73
2697 2736 1.067821 GTTGCTGCGCTAGGAGTCTAT 59.932 52.381 9.73 0.00 38.17 1.98
2698 2737 0.456221 GTTGCTGCGCTAGGAGTCTA 59.544 55.000 9.73 0.00 38.17 2.59
2699 2738 1.216710 GTTGCTGCGCTAGGAGTCT 59.783 57.895 9.73 0.00 38.17 3.24
2723 2762 2.872858 GCTAAAGATGACGGGTGGATTC 59.127 50.000 0.00 0.00 0.00 2.52
2745 2784 9.968870 GTTTACACAATTAAAATTGACCCTACA 57.031 29.630 19.53 0.00 46.72 2.74
2751 2790 9.099454 TGGTTGGTTTACACAATTAAAATTGAC 57.901 29.630 19.53 8.49 46.72 3.18
2752 2791 9.838339 ATGGTTGGTTTACACAATTAAAATTGA 57.162 25.926 19.53 0.00 46.72 2.57
2757 2796 8.239038 TCTGATGGTTGGTTTACACAATTAAA 57.761 30.769 0.00 0.00 0.00 1.52
2764 2803 3.694566 GGGATCTGATGGTTGGTTTACAC 59.305 47.826 0.00 0.00 0.00 2.90
2766 2805 3.288092 GGGGATCTGATGGTTGGTTTAC 58.712 50.000 0.00 0.00 0.00 2.01
2778 2817 3.052944 CCAATTAAAGGGTGGGGATCTGA 60.053 47.826 0.00 0.00 0.00 3.27
2800 2839 5.616488 TTTTGCTATAACTTTCACCGTCC 57.384 39.130 0.00 0.00 0.00 4.79
2819 2858 8.393671 TCTCCAATAAAAATGCTGCAATTTTT 57.606 26.923 27.39 25.74 46.37 1.94
2829 2868 5.647225 TGCCCATTTTCTCCAATAAAAATGC 59.353 36.000 12.71 5.81 45.21 3.56
2837 2876 2.460669 GTCCTGCCCATTTTCTCCAAT 58.539 47.619 0.00 0.00 0.00 3.16
2840 2879 2.887790 GGTCCTGCCCATTTTCTCC 58.112 57.895 0.00 0.00 0.00 3.71
2854 2893 7.342026 ACAGGTTATAAATGAATGAAAGGGTCC 59.658 37.037 6.06 0.00 0.00 4.46
2855 2894 8.293699 ACAGGTTATAAATGAATGAAAGGGTC 57.706 34.615 6.06 0.00 0.00 4.46
2862 2901 9.460019 TGTGATGAACAGGTTATAAATGAATGA 57.540 29.630 6.06 0.00 33.78 2.57
2888 2927 6.560304 AGGAGATCAGGACCATTACATGTAAT 59.440 38.462 22.70 22.70 36.27 1.89
2889 2928 5.905331 AGGAGATCAGGACCATTACATGTAA 59.095 40.000 20.14 20.14 0.00 2.41
2927 3062 1.230324 GTGTTGAGTCCTGTTGGCTC 58.770 55.000 0.00 0.00 37.17 4.70
2948 3083 5.125900 CCATCCATGTTAATCTGCAGAACAA 59.874 40.000 22.50 14.53 36.70 2.83
2980 3115 6.659668 AGTCTGCCGCTATAGAGTATTTATCA 59.340 38.462 3.21 0.00 0.00 2.15
2993 3128 3.056250 CAGGATATCAAGTCTGCCGCTAT 60.056 47.826 4.83 0.00 0.00 2.97
3121 3265 1.683011 GCCCAGAAATGGCTGAAGCTA 60.683 52.381 1.74 0.00 45.70 3.32


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

AutoCloner maintained by Alex Coulton.