Multiple sequence alignment - TraesCS5A01G438000

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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 TraesCS5A01G438000 chr5A 100.000 2886 0 0 1 2886 619695637 619692752 0.000000e+00 5330.0
1 TraesCS5A01G438000 chr5A 96.126 826 25 2 1 826 285636056 285635238 0.000000e+00 1341.0
2 TraesCS5A01G438000 chr5A 87.682 617 31 21 1 604 673510937 673510353 0.000000e+00 676.0
3 TraesCS5A01G438000 chr5A 89.091 385 40 2 997 1380 619754641 619754258 7.230000e-131 477.0
4 TraesCS5A01G438000 chr5A 95.111 225 10 1 602 826 48185560 48185337 1.270000e-93 353.0
5 TraesCS5A01G438000 chr5A 95.067 223 11 0 603 825 673510318 673510096 4.580000e-93 351.0
6 TraesCS5A01G438000 chr5A 89.848 197 20 0 1709 1905 619754009 619753813 1.330000e-63 254.0
7 TraesCS5A01G438000 chr5A 84.186 215 27 4 1677 1887 619720137 619719926 4.880000e-48 202.0
8 TraesCS5A01G438000 chr5A 83.636 110 16 2 712 820 651935585 651935477 5.090000e-18 102.0
9 TraesCS5A01G438000 chr5A 82.609 115 17 2 713 826 521724770 521724658 6.580000e-17 99.0
10 TraesCS5A01G438000 chr5A 100.000 37 0 0 568 604 48185630 48185594 5.160000e-08 69.4
11 TraesCS5A01G438000 chr5D 89.486 1265 69 27 1665 2886 495630238 495628995 0.000000e+00 1541.0
12 TraesCS5A01G438000 chr5D 90.555 667 46 10 835 1487 495631067 495630404 0.000000e+00 867.0
13 TraesCS5A01G438000 chr5D 89.005 382 35 6 997 1373 495785117 495784738 1.570000e-127 466.0
14 TraesCS5A01G438000 chr5D 87.826 230 22 3 1677 1902 495783244 495783017 6.130000e-67 265.0
15 TraesCS5A01G438000 chr5B 90.549 656 47 6 837 1487 612685071 612684426 0.000000e+00 854.0
16 TraesCS5A01G438000 chr5B 92.264 349 26 1 1001 1348 613110766 613110418 7.180000e-136 494.0
17 TraesCS5A01G438000 chr5B 79.339 484 72 23 2421 2886 612683443 612682970 6.000000e-82 315.0
18 TraesCS5A01G438000 chr5B 87.407 270 30 3 1665 1932 612684260 612683993 1.000000e-79 307.0
19 TraesCS5A01G438000 chr5B 85.514 214 21 7 1684 1889 613110219 613110008 6.260000e-52 215.0
20 TraesCS5A01G438000 chr6A 90.065 614 29 14 1 604 562751900 562751309 0.000000e+00 767.0
21 TraesCS5A01G438000 chr6A 94.924 197 8 1 603 797 562751274 562751078 1.000000e-79 307.0
22 TraesCS5A01G438000 chr1B 93.805 226 13 1 602 827 170823865 170824089 3.560000e-89 339.0
23 TraesCS5A01G438000 chr7A 81.538 195 30 5 636 827 723071979 723072170 3.850000e-34 156.0


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 TraesCS5A01G438000 chr5A 619692752 619695637 2885 True 5330.0 5330 100.0000 1 2886 1 chr5A.!!$R3 2885
1 TraesCS5A01G438000 chr5A 285635238 285636056 818 True 1341.0 1341 96.1260 1 826 1 chr5A.!!$R1 825
2 TraesCS5A01G438000 chr5A 673510096 673510937 841 True 513.5 676 91.3745 1 825 2 chr5A.!!$R8 824
3 TraesCS5A01G438000 chr5A 619753813 619754641 828 True 365.5 477 89.4695 997 1905 2 chr5A.!!$R7 908
4 TraesCS5A01G438000 chr5D 495628995 495631067 2072 True 1204.0 1541 90.0205 835 2886 2 chr5D.!!$R1 2051
5 TraesCS5A01G438000 chr5D 495783017 495785117 2100 True 365.5 466 88.4155 997 1902 2 chr5D.!!$R2 905
6 TraesCS5A01G438000 chr5B 612682970 612685071 2101 True 492.0 854 85.7650 837 2886 3 chr5B.!!$R1 2049
7 TraesCS5A01G438000 chr5B 613110008 613110766 758 True 354.5 494 88.8890 1001 1889 2 chr5B.!!$R2 888
8 TraesCS5A01G438000 chr6A 562751078 562751900 822 True 537.0 767 92.4945 1 797 2 chr6A.!!$R1 796

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
269 276 1.128188 GGGACACCCTGACAGGAACT 61.128 60.0 23.77 3.74 41.34 3.01 F
1356 1436 0.109913 TCTCGGCCTCCTCGCTAATA 59.890 55.0 0.00 0.00 0.00 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 2780 0.873054 GCTGCATCGGATTGGATCAG 59.127 55.0 0.0 0.0 0.0 2.9 R
2750 4376 0.184933 TAGTTGGGTTGCTTGCCACT 59.815 50.0 0.0 0.0 0.0 4.0 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
128 135 6.543100 AGATGGTCAGTAGCTACTACTAACAC 59.457 42.308 25.63 15.49 44.37 3.32
269 276 1.128188 GGGACACCCTGACAGGAACT 61.128 60.000 23.77 3.74 41.34 3.01
283 290 3.876589 GAACTTCCAGCCACGCCGA 62.877 63.158 0.00 0.00 0.00 5.54
444 451 1.153369 CGGTCAACGCTGGATCCAT 60.153 57.895 16.63 0.00 34.82 3.41
623 682 9.294614 AGAGCTCTGTTTTTCTATTTTCTCATT 57.705 29.630 17.42 0.00 0.00 2.57
975 1036 3.589654 ATCACGCACCCACGACCAG 62.590 63.158 0.00 0.00 36.70 4.00
1057 1130 1.362584 TCCTCTTCTCCCTCACCATCA 59.637 52.381 0.00 0.00 0.00 3.07
1339 1413 1.486211 CATGGTAACCCCGTCTCTCT 58.514 55.000 0.00 0.00 35.15 3.10
1348 1426 2.124487 CGTCTCTCTCGGCCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
1353 1433 2.203224 CTCTCGGCCTCCTCGCTA 60.203 66.667 0.00 0.00 0.00 4.26
1354 1434 1.824329 CTCTCGGCCTCCTCGCTAA 60.824 63.158 0.00 0.00 0.00 3.09
1355 1435 1.152735 TCTCGGCCTCCTCGCTAAT 60.153 57.895 0.00 0.00 0.00 1.73
1356 1436 0.109913 TCTCGGCCTCCTCGCTAATA 59.890 55.000 0.00 0.00 0.00 0.98
1358 1438 1.546476 CTCGGCCTCCTCGCTAATATT 59.454 52.381 0.00 0.00 0.00 1.28
1413 1496 4.460263 TGAGATTAAATGTGCCGCCTATT 58.540 39.130 0.00 0.00 0.00 1.73
1415 1498 3.821033 AGATTAAATGTGCCGCCTATTCC 59.179 43.478 0.00 0.00 0.00 3.01
1425 1508 0.962489 CGCCTATTCCTCGGATCTGT 59.038 55.000 0.42 0.00 0.00 3.41
1517 2768 4.156455 ACGATGTGGATCTGCCTAATTT 57.844 40.909 0.00 0.00 37.63 1.82
1518 2769 4.526970 ACGATGTGGATCTGCCTAATTTT 58.473 39.130 0.00 0.00 37.63 1.82
1523 2774 4.832266 TGTGGATCTGCCTAATTTTTGTGT 59.168 37.500 0.00 0.00 37.63 3.72
1527 2778 5.979517 GGATCTGCCTAATTTTTGTGTATGC 59.020 40.000 0.00 0.00 0.00 3.14
1528 2779 6.183360 GGATCTGCCTAATTTTTGTGTATGCT 60.183 38.462 0.00 0.00 0.00 3.79
1529 2780 6.194796 TCTGCCTAATTTTTGTGTATGCTC 57.805 37.500 0.00 0.00 0.00 4.26
1536 2787 6.839124 AATTTTTGTGTATGCTCTGATCCA 57.161 33.333 0.00 0.00 0.00 3.41
1547 2853 2.414806 CTCTGATCCAATCCGATGCAG 58.585 52.381 0.00 0.00 0.00 4.41
1549 2855 0.881600 TGATCCAATCCGATGCAGCG 60.882 55.000 19.16 19.16 0.00 5.18
1551 2857 0.035881 ATCCAATCCGATGCAGCGAT 59.964 50.000 28.29 14.45 0.00 4.58
1552 2858 0.179048 TCCAATCCGATGCAGCGATT 60.179 50.000 28.29 19.41 0.00 3.34
1556 2862 1.139989 ATCCGATGCAGCGATTTACG 58.860 50.000 28.29 7.93 45.66 3.18
1558 2864 0.504384 CCGATGCAGCGATTTACGAG 59.496 55.000 28.29 1.65 45.77 4.18
1562 2868 2.293677 TGCAGCGATTTACGAGTCAT 57.706 45.000 0.00 0.00 45.77 3.06
1567 2873 4.435518 GCAGCGATTTACGAGTCATTTTGA 60.436 41.667 0.00 0.00 45.77 2.69
1569 2875 5.898606 CAGCGATTTACGAGTCATTTTGATC 59.101 40.000 0.00 0.00 45.77 2.92
1570 2876 5.580691 AGCGATTTACGAGTCATTTTGATCA 59.419 36.000 0.00 0.00 45.77 2.92
1572 2878 6.237835 GCGATTTACGAGTCATTTTGATCAGA 60.238 38.462 0.00 0.00 45.77 3.27
1574 2880 8.168626 CGATTTACGAGTCATTTTGATCAGAAA 58.831 33.333 2.39 4.43 45.77 2.52
1587 2893 9.822185 ATTTTGATCAGAAATAAATAGGCAACC 57.178 29.630 2.39 0.00 37.17 3.77
1589 2895 7.572523 TGATCAGAAATAAATAGGCAACCAG 57.427 36.000 0.00 0.00 37.17 4.00
1590 2896 7.118723 TGATCAGAAATAAATAGGCAACCAGT 58.881 34.615 0.00 0.00 37.17 4.00
1591 2897 7.283127 TGATCAGAAATAAATAGGCAACCAGTC 59.717 37.037 0.00 0.00 37.17 3.51
1592 2898 6.721318 TCAGAAATAAATAGGCAACCAGTCT 58.279 36.000 0.00 0.00 35.44 3.24
1593 2899 6.599244 TCAGAAATAAATAGGCAACCAGTCTG 59.401 38.462 0.00 0.00 31.94 3.51
1594 2900 5.888161 AGAAATAAATAGGCAACCAGTCTGG 59.112 40.000 17.88 17.88 45.02 3.86
1595 2901 5.450818 AATAAATAGGCAACCAGTCTGGA 57.549 39.130 26.18 1.63 40.96 3.86
1596 2902 2.789409 AATAGGCAACCAGTCTGGAC 57.211 50.000 26.18 13.45 40.96 4.02
1597 2903 1.958288 ATAGGCAACCAGTCTGGACT 58.042 50.000 26.18 17.77 40.96 3.85
1613 2919 8.785329 AGTCTGGACTGAGAAGATTTAATTTC 57.215 34.615 2.15 0.00 40.75 2.17
1614 2920 7.826744 AGTCTGGACTGAGAAGATTTAATTTCC 59.173 37.037 2.15 0.00 40.75 3.13
1615 2921 7.607991 GTCTGGACTGAGAAGATTTAATTTCCA 59.392 37.037 0.00 0.00 0.00 3.53
1616 2922 7.607991 TCTGGACTGAGAAGATTTAATTTCCAC 59.392 37.037 0.00 0.00 0.00 4.02
1617 2923 7.461749 TGGACTGAGAAGATTTAATTTCCACT 58.538 34.615 0.00 0.00 0.00 4.00
1618 2924 7.944554 TGGACTGAGAAGATTTAATTTCCACTT 59.055 33.333 0.00 0.00 0.00 3.16
1619 2925 9.449719 GGACTGAGAAGATTTAATTTCCACTTA 57.550 33.333 0.00 0.00 0.00 2.24
1628 2934 7.619302 AGATTTAATTTCCACTTAGATTGGCCA 59.381 33.333 0.00 0.00 33.71 5.36
1629 2935 6.773976 TTAATTTCCACTTAGATTGGCCAG 57.226 37.500 5.11 0.00 33.71 4.85
1630 2936 4.591321 ATTTCCACTTAGATTGGCCAGA 57.409 40.909 5.11 0.00 33.71 3.86
1633 2939 4.963318 TCCACTTAGATTGGCCAGATAG 57.037 45.455 5.11 3.21 33.71 2.08
1660 2966 6.314896 CCTTCTTACTTGGCAGTTGAATAGAG 59.685 42.308 0.00 0.00 34.06 2.43
1663 2969 3.077359 ACTTGGCAGTTGAATAGAGCAC 58.923 45.455 0.00 0.00 0.00 4.40
1674 3070 3.133542 TGAATAGAGCACATCACTCTGGG 59.866 47.826 3.60 0.00 44.20 4.45
1682 3078 3.808618 GCACATCACTCTGGGGATTATCC 60.809 52.174 1.91 1.91 35.23 2.59
1690 3086 4.977739 ACTCTGGGGATTATCCTGATTTCA 59.022 41.667 11.40 0.71 36.57 2.69
1705 3104 9.956640 ATCCTGATTTCATTCCTAATAGTGATC 57.043 33.333 0.00 0.00 0.00 2.92
1706 3105 9.163894 TCCTGATTTCATTCCTAATAGTGATCT 57.836 33.333 0.00 0.00 0.00 2.75
1707 3106 9.434420 CCTGATTTCATTCCTAATAGTGATCTC 57.566 37.037 0.00 0.00 0.00 2.75
1712 3111 6.216569 TCATTCCTAATAGTGATCTCGCAAC 58.783 40.000 0.00 0.00 0.00 4.17
1801 3204 4.168014 TGTATGTTCCATACGTCGTGTTC 58.832 43.478 8.47 0.00 0.00 3.18
1802 3205 3.587797 ATGTTCCATACGTCGTGTTCT 57.412 42.857 8.47 0.00 0.00 3.01
1808 3211 0.095935 ATACGTCGTGTTCTCCGTCG 59.904 55.000 8.47 0.00 41.35 5.12
1840 3243 1.227205 CGGTCTCTGCTCATGCTCC 60.227 63.158 0.00 0.00 40.48 4.70
1999 3535 6.127479 GGAATGTAAATGTCCATACTGCCAAA 60.127 38.462 0.00 0.00 0.00 3.28
2020 3560 8.063630 GCCAAAGTTATTGTTCACATTTTGAAG 58.936 33.333 0.00 0.00 45.23 3.02
2051 3598 7.652727 TGTACTGCATCTGTTCTATGATAGAC 58.347 38.462 0.78 0.00 33.84 2.59
2063 3610 5.289595 TCTATGATAGACCATGTTCAACGC 58.710 41.667 0.00 0.00 0.00 4.84
2069 3616 0.961019 ACCATGTTCAACGCAGCATT 59.039 45.000 0.00 0.00 0.00 3.56
2082 3629 2.476821 GCAGCATTGGTTTGCCATATC 58.523 47.619 0.00 0.00 45.56 1.63
2084 3631 3.431207 GCAGCATTGGTTTGCCATATCTT 60.431 43.478 0.00 0.00 45.56 2.40
2085 3632 4.761975 CAGCATTGGTTTGCCATATCTTT 58.238 39.130 0.00 0.00 45.56 2.52
2086 3633 5.180271 CAGCATTGGTTTGCCATATCTTTT 58.820 37.500 0.00 0.00 45.56 2.27
2087 3634 5.064198 CAGCATTGGTTTGCCATATCTTTTG 59.936 40.000 0.00 0.00 45.56 2.44
2088 3635 4.937015 GCATTGGTTTGCCATATCTTTTGT 59.063 37.500 0.00 0.00 45.56 2.83
2089 3636 5.412286 GCATTGGTTTGCCATATCTTTTGTT 59.588 36.000 0.00 0.00 45.56 2.83
2090 3637 6.072563 GCATTGGTTTGCCATATCTTTTGTTT 60.073 34.615 0.00 0.00 45.56 2.83
2091 3638 7.118971 GCATTGGTTTGCCATATCTTTTGTTTA 59.881 33.333 0.00 0.00 45.56 2.01
2200 3750 7.033791 TCAGAAGATAAACAACGAGGACATAC 58.966 38.462 0.00 0.00 0.00 2.39
2216 3766 7.380870 CGAGGACATACATCAACTCTTCATTAG 59.619 40.741 0.00 0.00 0.00 1.73
2217 3767 6.989169 AGGACATACATCAACTCTTCATTAGC 59.011 38.462 0.00 0.00 0.00 3.09
2218 3768 6.989169 GGACATACATCAACTCTTCATTAGCT 59.011 38.462 0.00 0.00 0.00 3.32
2294 3844 5.646360 TGCAACCTAGTTTATGGAAGTAAGC 59.354 40.000 0.00 0.00 0.00 3.09
2295 3845 5.646360 GCAACCTAGTTTATGGAAGTAAGCA 59.354 40.000 0.00 0.00 0.00 3.91
2304 3854 8.088365 AGTTTATGGAAGTAAGCATTTTGTTCC 58.912 33.333 0.00 0.00 35.09 3.62
2337 3887 8.359060 AGCAAATAAATTTTAACTCGCACAAA 57.641 26.923 0.00 0.00 0.00 2.83
2361 3911 9.768662 AAATAAAGCAATGTGAGAGAAAACAAT 57.231 25.926 0.00 0.00 0.00 2.71
2367 3917 8.632679 AGCAATGTGAGAGAAAACAATAGAAAA 58.367 29.630 0.00 0.00 0.00 2.29
2397 3947 6.040878 ACATACTCCGTGATAAACTTACAGC 58.959 40.000 0.00 0.00 0.00 4.40
2441 3991 7.309805 GGGTTTACAAGTCAGGAATTAATGCTT 60.310 37.037 0.00 0.00 0.00 3.91
2472 4027 9.766277 CTTCTGATAAACTTTCTTAATGTGAGC 57.234 33.333 0.00 0.00 0.00 4.26
2528 4083 2.772515 GGATACAGTACAAAGCCTCCCT 59.227 50.000 0.00 0.00 0.00 4.20
2543 4099 2.087646 CTCCCTAAGGAAGCAACAAGC 58.912 52.381 0.00 0.00 43.40 4.01
2573 4131 3.879892 CCTAAAAGAAGATGGTAGCAGGC 59.120 47.826 0.00 0.00 0.00 4.85
2587 4145 2.923121 AGCAGGCACATTACACATAGG 58.077 47.619 0.00 0.00 0.00 2.57
2745 4371 3.188460 TCCGACTAAAATCTTTGCACAGC 59.812 43.478 0.00 0.00 0.00 4.40
2746 4372 3.058293 CCGACTAAAATCTTTGCACAGCA 60.058 43.478 0.00 0.00 36.47 4.41
2747 4373 4.153986 CGACTAAAATCTTTGCACAGCAG 58.846 43.478 0.00 0.00 40.61 4.24
2748 4374 4.083855 CGACTAAAATCTTTGCACAGCAGA 60.084 41.667 0.00 0.00 40.61 4.26
2749 4375 5.113502 ACTAAAATCTTTGCACAGCAGAC 57.886 39.130 0.00 0.00 40.61 3.51
2750 4376 4.580167 ACTAAAATCTTTGCACAGCAGACA 59.420 37.500 0.00 0.00 40.61 3.41
2751 4377 3.637998 AAATCTTTGCACAGCAGACAG 57.362 42.857 0.00 0.00 40.61 3.51
2752 4378 2.267174 ATCTTTGCACAGCAGACAGT 57.733 45.000 0.00 0.00 40.61 3.55
2817 4466 4.394920 ACACGGCATTGACGAAAATAAGAT 59.605 37.500 20.74 0.00 35.20 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.255687 TGGCTGTGATCACAACAAGATTAT 58.744 37.500 27.63 0.00 41.33 1.28
128 135 1.129998 CAGAGGCTCATTTGAACGCAG 59.870 52.381 18.26 0.00 0.00 5.18
283 290 4.619227 CACTGTTGGGTCGGCCGT 62.619 66.667 27.15 0.00 34.97 5.68
562 584 2.435693 CCCAACCCTAGAGGAGGCG 61.436 68.421 0.00 0.00 45.17 5.52
563 585 2.073101 CCCCAACCCTAGAGGAGGC 61.073 68.421 0.00 0.00 45.17 4.70
564 586 0.399233 CTCCCCAACCCTAGAGGAGG 60.399 65.000 0.00 5.70 46.25 4.30
565 587 0.637195 TCTCCCCAACCCTAGAGGAG 59.363 60.000 0.00 0.00 44.59 3.69
566 588 1.098589 TTCTCCCCAACCCTAGAGGA 58.901 55.000 0.00 0.00 39.89 3.71
567 589 1.840635 CTTTCTCCCCAACCCTAGAGG 59.159 57.143 0.00 0.00 43.78 3.69
623 682 3.694072 CGAAATTGCCCTTGTCCATAAGA 59.306 43.478 0.00 0.00 0.00 2.10
826 887 5.749462 AGCATGTGAAAGCCTCTTATAAGT 58.251 37.500 12.19 0.00 0.00 2.24
827 888 6.054295 AGAGCATGTGAAAGCCTCTTATAAG 58.946 40.000 6.11 6.11 0.00 1.73
828 889 5.994250 AGAGCATGTGAAAGCCTCTTATAA 58.006 37.500 0.00 0.00 0.00 0.98
829 890 5.620738 AGAGCATGTGAAAGCCTCTTATA 57.379 39.130 0.00 0.00 0.00 0.98
830 891 4.500499 AGAGCATGTGAAAGCCTCTTAT 57.500 40.909 0.00 0.00 0.00 1.73
831 892 3.988976 AGAGCATGTGAAAGCCTCTTA 57.011 42.857 0.00 0.00 0.00 2.10
832 893 2.875094 AGAGCATGTGAAAGCCTCTT 57.125 45.000 0.00 0.00 0.00 2.85
833 894 2.305343 AGAAGAGCATGTGAAAGCCTCT 59.695 45.455 0.00 0.00 0.00 3.69
1339 1413 1.629043 AATATTAGCGAGGAGGCCGA 58.371 50.000 0.00 0.00 0.00 5.54
1393 1473 3.821033 GGAATAGGCGGCACATTTAATCT 59.179 43.478 13.08 0.00 0.00 2.40
1413 1496 5.521906 CTCTGATTTTACAGATCCGAGGA 57.478 43.478 0.00 0.00 44.32 3.71
1415 1498 5.163509 TGACCTCTGATTTTACAGATCCGAG 60.164 44.000 0.00 0.00 44.32 4.63
1425 1508 5.071788 ACTGTGGAGTTGACCTCTGATTTTA 59.928 40.000 0.00 0.00 40.30 1.52
1462 1546 4.458295 AGAAATTTCTCTACCGAGACGTGA 59.542 41.667 15.11 0.00 45.61 4.35
1480 1674 7.726216 TCCACATCGTTGTCATCTATAGAAAT 58.274 34.615 6.52 0.00 32.34 2.17
1484 1678 6.805760 CAGATCCACATCGTTGTCATCTATAG 59.194 42.308 13.59 0.00 33.54 1.31
1488 1682 3.790091 CAGATCCACATCGTTGTCATCT 58.210 45.455 10.11 10.11 34.75 2.90
1489 1683 2.286294 GCAGATCCACATCGTTGTCATC 59.714 50.000 0.00 2.12 32.34 2.92
1517 2768 4.883585 GGATTGGATCAGAGCATACACAAA 59.116 41.667 0.00 0.00 0.00 2.83
1518 2769 4.454678 GGATTGGATCAGAGCATACACAA 58.545 43.478 0.00 0.00 0.00 3.33
1523 2774 3.618263 GCATCGGATTGGATCAGAGCATA 60.618 47.826 0.00 0.00 36.94 3.14
1527 2778 2.414806 CTGCATCGGATTGGATCAGAG 58.585 52.381 0.00 0.00 36.94 3.35
1528 2779 1.541889 GCTGCATCGGATTGGATCAGA 60.542 52.381 0.00 0.00 37.86 3.27
1529 2780 0.873054 GCTGCATCGGATTGGATCAG 59.127 55.000 0.00 0.00 0.00 2.90
1536 2787 1.526887 CGTAAATCGCTGCATCGGATT 59.473 47.619 10.42 8.06 0.00 3.01
1547 2853 5.795766 TGATCAAAATGACTCGTAAATCGC 58.204 37.500 0.00 0.00 39.67 4.58
1549 2855 9.994432 ATTTCTGATCAAAATGACTCGTAAATC 57.006 29.630 12.24 0.00 0.00 2.17
1562 2868 8.811017 TGGTTGCCTATTTATTTCTGATCAAAA 58.189 29.630 0.00 1.39 0.00 2.44
1567 2873 7.284034 CAGACTGGTTGCCTATTTATTTCTGAT 59.716 37.037 0.00 0.00 0.00 2.90
1569 2875 6.183360 CCAGACTGGTTGCCTATTTATTTCTG 60.183 42.308 13.84 0.00 31.35 3.02
1570 2876 5.888161 CCAGACTGGTTGCCTATTTATTTCT 59.112 40.000 13.84 0.00 31.35 2.52
1572 2878 5.652452 GTCCAGACTGGTTGCCTATTTATTT 59.348 40.000 21.06 0.00 39.03 1.40
1574 2880 4.475016 AGTCCAGACTGGTTGCCTATTTAT 59.525 41.667 21.06 0.00 40.75 1.40
1577 2883 2.269940 AGTCCAGACTGGTTGCCTATT 58.730 47.619 21.06 0.00 40.75 1.73
1578 2884 1.958288 AGTCCAGACTGGTTGCCTAT 58.042 50.000 21.06 0.00 40.75 2.57
1579 2885 3.475932 AGTCCAGACTGGTTGCCTA 57.524 52.632 21.06 0.00 40.75 3.93
1580 2886 4.320844 AGTCCAGACTGGTTGCCT 57.679 55.556 21.06 10.05 40.75 4.75
1589 2895 7.607991 TGGAAATTAAATCTTCTCAGTCCAGAC 59.392 37.037 0.00 0.00 0.00 3.51
1590 2896 7.607991 GTGGAAATTAAATCTTCTCAGTCCAGA 59.392 37.037 0.00 0.00 32.32 3.86
1591 2897 7.609532 AGTGGAAATTAAATCTTCTCAGTCCAG 59.390 37.037 0.00 0.00 32.32 3.86
1592 2898 7.461749 AGTGGAAATTAAATCTTCTCAGTCCA 58.538 34.615 0.00 0.00 0.00 4.02
1593 2899 7.929941 AGTGGAAATTAAATCTTCTCAGTCC 57.070 36.000 0.00 0.00 0.00 3.85
1600 2906 9.521503 GCCAATCTAAGTGGAAATTAAATCTTC 57.478 33.333 0.00 0.00 38.54 2.87
1601 2907 8.478066 GGCCAATCTAAGTGGAAATTAAATCTT 58.522 33.333 0.00 0.00 38.54 2.40
1602 2908 7.619302 TGGCCAATCTAAGTGGAAATTAAATCT 59.381 33.333 0.61 0.00 38.54 2.40
1603 2909 7.781056 TGGCCAATCTAAGTGGAAATTAAATC 58.219 34.615 0.61 0.00 38.54 2.17
1604 2910 7.619302 TCTGGCCAATCTAAGTGGAAATTAAAT 59.381 33.333 7.01 0.00 38.54 1.40
1605 2911 6.951198 TCTGGCCAATCTAAGTGGAAATTAAA 59.049 34.615 7.01 0.00 38.54 1.52
1606 2912 6.489603 TCTGGCCAATCTAAGTGGAAATTAA 58.510 36.000 7.01 0.00 38.54 1.40
1607 2913 6.073447 TCTGGCCAATCTAAGTGGAAATTA 57.927 37.500 7.01 0.00 38.54 1.40
1608 2914 4.934356 TCTGGCCAATCTAAGTGGAAATT 58.066 39.130 7.01 0.00 38.54 1.82
1609 2915 4.591321 TCTGGCCAATCTAAGTGGAAAT 57.409 40.909 7.01 0.00 38.54 2.17
1610 2916 4.591321 ATCTGGCCAATCTAAGTGGAAA 57.409 40.909 7.01 0.00 38.54 3.13
1611 2917 4.103153 CCTATCTGGCCAATCTAAGTGGAA 59.897 45.833 7.01 0.00 38.54 3.53
1612 2918 3.648067 CCTATCTGGCCAATCTAAGTGGA 59.352 47.826 7.01 0.00 38.54 4.02
1613 2919 4.013267 CCTATCTGGCCAATCTAAGTGG 57.987 50.000 7.01 0.00 39.33 4.00
1628 2934 3.847671 GCCAAGTAAGAAGGCCTATCT 57.152 47.619 5.16 8.77 42.58 1.98
1636 2942 6.183360 GCTCTATTCAACTGCCAAGTAAGAAG 60.183 42.308 0.00 0.00 35.37 2.85
1650 2956 4.569966 CCAGAGTGATGTGCTCTATTCAAC 59.430 45.833 0.00 0.00 40.97 3.18
1660 2966 3.406764 GATAATCCCCAGAGTGATGTGC 58.593 50.000 0.00 0.00 0.00 4.57
1663 2969 3.906218 TCAGGATAATCCCCAGAGTGATG 59.094 47.826 0.00 0.00 37.19 3.07
1682 3078 9.138062 CGAGATCACTATTAGGAATGAAATCAG 57.862 37.037 0.00 0.00 0.00 2.90
1690 3086 6.183360 ACAGTTGCGAGATCACTATTAGGAAT 60.183 38.462 0.00 0.00 0.00 3.01
1705 3104 1.070309 GCAGACTGAAACAGTTGCGAG 60.070 52.381 6.65 0.00 45.44 5.03
1706 3105 0.937304 GCAGACTGAAACAGTTGCGA 59.063 50.000 6.65 0.00 45.44 5.10
1707 3106 3.444657 GCAGACTGAAACAGTTGCG 57.555 52.632 6.65 7.21 45.44 4.85
1712 3111 3.369147 CCAAGTATCGCAGACTGAAACAG 59.631 47.826 6.65 0.00 42.51 3.16
1801 3204 1.970917 GCAGAATGGCAACGACGGAG 61.971 60.000 0.00 0.00 42.51 4.63
1802 3205 2.032634 GCAGAATGGCAACGACGGA 61.033 57.895 0.00 0.00 42.51 4.69
1808 3211 3.667429 GACCGCGCAGAATGGCAAC 62.667 63.158 8.75 0.00 35.86 4.17
2020 3560 7.708322 TCATAGAACAGATGCAGTACAATCTTC 59.292 37.037 0.00 0.00 0.00 2.87
2051 3598 1.342555 CAATGCTGCGTTGAACATGG 58.657 50.000 26.26 0.31 32.66 3.66
2115 3662 6.515200 GCCAGTCGCCAGGTATATATATGTAG 60.515 46.154 5.44 0.00 0.00 2.74
2118 3665 4.342378 AGCCAGTCGCCAGGTATATATATG 59.658 45.833 5.44 0.00 38.78 1.78
2200 3750 8.657729 CATATAGCAGCTAATGAAGAGTTGATG 58.342 37.037 6.13 0.00 0.00 3.07
2216 3766 6.992063 ATACATTGCTTACCATATAGCAGC 57.008 37.500 0.00 0.00 46.95 5.25
2217 3767 8.607459 GCTTATACATTGCTTACCATATAGCAG 58.393 37.037 0.00 0.00 46.95 4.24
2218 3768 8.321353 AGCTTATACATTGCTTACCATATAGCA 58.679 33.333 0.00 0.00 45.06 3.49
2330 3880 4.475028 TCTCACATTGCTTTATTTGTGCG 58.525 39.130 0.00 0.00 39.39 5.34
2331 3881 5.702865 TCTCTCACATTGCTTTATTTGTGC 58.297 37.500 0.00 0.00 39.39 4.57
2361 3911 6.693466 TCACGGAGTATGTCACAATTTTCTA 58.307 36.000 0.00 0.00 41.61 2.10
2367 3917 6.640518 AGTTTATCACGGAGTATGTCACAAT 58.359 36.000 0.00 0.00 41.61 2.71
2454 4009 9.736023 CTAAAGTTGCTCACATTAAGAAAGTTT 57.264 29.630 0.00 0.00 38.15 2.66
2472 4027 9.667107 TCACTAAGGAATTGGTATCTAAAGTTG 57.333 33.333 0.00 0.00 0.00 3.16
2528 4083 2.930950 ACTGTGCTTGTTGCTTCCTTA 58.069 42.857 0.00 0.00 43.37 2.69
2573 4131 5.123661 TCATGTTGTGCCTATGTGTAATGTG 59.876 40.000 0.00 0.00 0.00 3.21
2587 4145 6.074835 CGATGTACAGTAGTATCATGTTGTGC 60.075 42.308 0.33 0.00 31.84 4.57
2691 4307 8.018537 TGTATGCCTAGTTTTCTGATAGCTAA 57.981 34.615 0.00 0.00 0.00 3.09
2745 4371 1.656441 GGTTGCTTGCCACTGTCTG 59.344 57.895 0.00 0.00 0.00 3.51
2746 4372 1.529244 GGGTTGCTTGCCACTGTCT 60.529 57.895 0.00 0.00 0.00 3.41
2747 4373 1.391157 TTGGGTTGCTTGCCACTGTC 61.391 55.000 0.00 0.00 0.00 3.51
2748 4374 1.381056 TTGGGTTGCTTGCCACTGT 60.381 52.632 0.00 0.00 0.00 3.55
2749 4375 1.067916 GTTGGGTTGCTTGCCACTG 59.932 57.895 0.00 0.00 0.00 3.66
2750 4376 0.184933 TAGTTGGGTTGCTTGCCACT 59.815 50.000 0.00 0.00 0.00 4.00
2751 4377 0.598065 CTAGTTGGGTTGCTTGCCAC 59.402 55.000 0.00 0.00 0.00 5.01
2752 4378 0.476338 TCTAGTTGGGTTGCTTGCCA 59.524 50.000 0.00 0.00 0.00 4.92
2817 4466 5.305902 TGCCACCCTATTATCTTATTGTCGA 59.694 40.000 0.00 0.00 0.00 4.20
2823 4472 7.341805 GTGATGATGCCACCCTATTATCTTAT 58.658 38.462 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.