Multiple sequence alignment - TraesCS5D01G082100

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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 TraesCS5D01G082100 chr5D 100.000 2764 0 0 1 2764 84177231 84179994 0.000000e+00 5105.0
1 TraesCS5D01G082100 chr5D 93.401 591 34 5 29 616 119995586 119994998 0.000000e+00 870.0
2 TraesCS5D01G082100 chr5D 82.202 781 122 16 42 813 223546691 223547463 0.000000e+00 656.0
3 TraesCS5D01G082100 chr5D 96.535 202 6 1 616 816 298570303 298570102 1.590000e-87 333.0
4 TraesCS5D01G082100 chr5D 95.631 206 8 1 616 820 14159150 14158945 2.050000e-86 329.0
5 TraesCS5D01G082100 chr5D 96.000 50 2 0 1 50 84171985 84172034 6.340000e-12 82.4
6 TraesCS5D01G082100 chr5A 93.170 1962 114 8 817 2764 78474230 78476185 0.000000e+00 2863.0
7 TraesCS5D01G082100 chr5A 82.798 872 106 29 817 1654 78426324 78427185 0.000000e+00 739.0
8 TraesCS5D01G082100 chr5A 82.771 859 108 22 817 1643 78368744 78369594 0.000000e+00 730.0
9 TraesCS5D01G082100 chr5B 87.357 1487 128 28 817 2251 91108625 91110103 0.000000e+00 1650.0
10 TraesCS5D01G082100 chr5B 84.912 855 84 28 817 1639 90988085 90988926 0.000000e+00 822.0
11 TraesCS5D01G082100 chr5B 96.535 202 6 1 616 816 267188118 267187917 1.590000e-87 333.0
12 TraesCS5D01G082100 chr6D 94.098 593 28 6 29 616 163331968 163331378 0.000000e+00 894.0
13 TraesCS5D01G082100 chr6D 97.778 45 1 0 1 45 202595659 202595615 8.210000e-11 78.7
14 TraesCS5D01G082100 chr6D 97.778 45 1 0 1 45 202605776 202605732 8.210000e-11 78.7
15 TraesCS5D01G082100 chr4D 93.311 598 32 7 29 620 148920008 148920603 0.000000e+00 876.0
16 TraesCS5D01G082100 chr4D 92.953 596 36 6 29 620 396257902 396258495 0.000000e+00 863.0
17 TraesCS5D01G082100 chr4D 97.487 199 4 1 616 813 211393723 211393921 3.410000e-89 339.0
18 TraesCS5D01G082100 chr4D 97.778 45 1 0 1 45 121278644 121278600 8.210000e-11 78.7
19 TraesCS5D01G082100 chr4D 97.778 45 1 0 1 45 225382148 225382104 8.210000e-11 78.7
20 TraesCS5D01G082100 chr4D 97.778 45 1 0 1 45 309582205 309582161 8.210000e-11 78.7
21 TraesCS5D01G082100 chr3D 93.121 596 36 5 29 620 271575391 271574797 0.000000e+00 869.0
22 TraesCS5D01G082100 chr3D 92.965 597 36 5 29 620 48951616 48952211 0.000000e+00 865.0
23 TraesCS5D01G082100 chr3D 100.000 45 0 0 1 45 296834826 296834782 1.760000e-12 84.2
24 TraesCS5D01G082100 chr2D 93.098 594 34 6 29 617 27846457 27847048 0.000000e+00 863.0
25 TraesCS5D01G082100 chr2D 79.507 771 119 27 42 792 367063827 367064578 1.900000e-141 512.0
26 TraesCS5D01G082100 chr2D 77.211 882 134 42 817 1642 547952131 547951261 1.170000e-123 453.0
27 TraesCS5D01G082100 chr2D 81.109 577 82 11 1041 1594 547791256 547790684 1.180000e-118 436.0
28 TraesCS5D01G082100 chr1D 92.953 596 37 5 29 620 64817314 64817908 0.000000e+00 863.0
29 TraesCS5D01G082100 chr1D 97.030 202 5 1 616 816 430226760 430226559 3.410000e-89 339.0
30 TraesCS5D01G082100 chr1D 96.535 202 5 2 616 816 430125456 430125256 1.590000e-87 333.0
31 TraesCS5D01G082100 chr1D 97.778 45 1 0 1 45 134523012 134523056 8.210000e-11 78.7
32 TraesCS5D01G082100 chr1D 97.778 45 1 0 1 45 135438977 135438933 8.210000e-11 78.7
33 TraesCS5D01G082100 chr7D 92.941 595 37 5 29 620 567979677 567980269 0.000000e+00 861.0
34 TraesCS5D01G082100 chr7D 96.985 199 5 1 616 813 331768739 331768937 1.590000e-87 333.0
35 TraesCS5D01G082100 chr2B 79.356 683 92 29 817 1453 654727076 654726397 4.230000e-118 435.0
36 TraesCS5D01G082100 chr2B 79.294 652 89 26 846 1453 654699587 654698938 5.510000e-112 414.0
37 TraesCS5D01G082100 chr2B 83.371 439 64 6 1024 1453 654649253 654648815 5.550000e-107 398.0
38 TraesCS5D01G082100 chrUn 79.063 683 94 29 817 1453 248122929 248122250 9.150000e-115 424.0
39 TraesCS5D01G082100 chrUn 79.560 636 86 24 860 1453 281905488 281906121 5.510000e-112 414.0


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 TraesCS5D01G082100 chr5D 84177231 84179994 2763 False 5105 5105 100.000 1 2764 1 chr5D.!!$F2 2763
1 TraesCS5D01G082100 chr5D 119994998 119995586 588 True 870 870 93.401 29 616 1 chr5D.!!$R2 587
2 TraesCS5D01G082100 chr5D 223546691 223547463 772 False 656 656 82.202 42 813 1 chr5D.!!$F3 771
3 TraesCS5D01G082100 chr5A 78474230 78476185 1955 False 2863 2863 93.170 817 2764 1 chr5A.!!$F3 1947
4 TraesCS5D01G082100 chr5A 78426324 78427185 861 False 739 739 82.798 817 1654 1 chr5A.!!$F2 837
5 TraesCS5D01G082100 chr5A 78368744 78369594 850 False 730 730 82.771 817 1643 1 chr5A.!!$F1 826
6 TraesCS5D01G082100 chr5B 91108625 91110103 1478 False 1650 1650 87.357 817 2251 1 chr5B.!!$F2 1434
7 TraesCS5D01G082100 chr5B 90988085 90988926 841 False 822 822 84.912 817 1639 1 chr5B.!!$F1 822
8 TraesCS5D01G082100 chr6D 163331378 163331968 590 True 894 894 94.098 29 616 1 chr6D.!!$R1 587
9 TraesCS5D01G082100 chr4D 148920008 148920603 595 False 876 876 93.311 29 620 1 chr4D.!!$F1 591
10 TraesCS5D01G082100 chr4D 396257902 396258495 593 False 863 863 92.953 29 620 1 chr4D.!!$F3 591
11 TraesCS5D01G082100 chr3D 271574797 271575391 594 True 869 869 93.121 29 620 1 chr3D.!!$R1 591
12 TraesCS5D01G082100 chr3D 48951616 48952211 595 False 865 865 92.965 29 620 1 chr3D.!!$F1 591
13 TraesCS5D01G082100 chr2D 27846457 27847048 591 False 863 863 93.098 29 617 1 chr2D.!!$F1 588
14 TraesCS5D01G082100 chr2D 367063827 367064578 751 False 512 512 79.507 42 792 1 chr2D.!!$F2 750
15 TraesCS5D01G082100 chr2D 547951261 547952131 870 True 453 453 77.211 817 1642 1 chr2D.!!$R2 825
16 TraesCS5D01G082100 chr2D 547790684 547791256 572 True 436 436 81.109 1041 1594 1 chr2D.!!$R1 553
17 TraesCS5D01G082100 chr1D 64817314 64817908 594 False 863 863 92.953 29 620 1 chr1D.!!$F1 591
18 TraesCS5D01G082100 chr7D 567979677 567980269 592 False 861 861 92.941 29 620 1 chr7D.!!$F2 591
19 TraesCS5D01G082100 chr2B 654726397 654727076 679 True 435 435 79.356 817 1453 1 chr2B.!!$R3 636
20 TraesCS5D01G082100 chr2B 654698938 654699587 649 True 414 414 79.294 846 1453 1 chr2B.!!$R2 607
21 TraesCS5D01G082100 chrUn 248122250 248122929 679 True 424 424 79.063 817 1453 1 chrUn.!!$R1 636
22 TraesCS5D01G082100 chrUn 281905488 281906121 633 False 414 414 79.560 860 1453 1 chrUn.!!$F1 593

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
32 33 0.179124 GCTCTCACCAAGGACGCTAG 60.179 60.0 0.0 0.0 0.00 3.42 F
516 528 0.671472 CCCGAACCTGGGTAAACGAC 60.671 60.0 0.0 0.0 44.76 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1285 0.456221 CACTCAGCCGACGGACTATT 59.544 55.0 20.5 0.0 0.00 1.73 R
2038 2182 0.174845 TACCAATCGAGGAACGCCAG 59.825 55.0 0.0 0.0 42.26 4.85 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
18 19 4.785453 CCACCCGGCAAGGCTCTC 62.785 72.222 0.00 0.00 39.21 3.20
19 20 4.020617 CACCCGGCAAGGCTCTCA 62.021 66.667 0.00 0.00 39.21 3.27
20 21 4.021925 ACCCGGCAAGGCTCTCAC 62.022 66.667 0.00 0.00 39.21 3.51
21 22 4.785453 CCCGGCAAGGCTCTCACC 62.785 72.222 0.00 0.00 39.21 4.02
22 23 4.020617 CCGGCAAGGCTCTCACCA 62.021 66.667 0.00 0.00 0.00 4.17
23 24 2.032528 CGGCAAGGCTCTCACCAA 59.967 61.111 0.00 0.00 0.00 3.67
24 25 2.037136 CGGCAAGGCTCTCACCAAG 61.037 63.158 0.00 0.00 0.00 3.61
25 26 1.676967 GGCAAGGCTCTCACCAAGG 60.677 63.158 0.00 0.00 0.00 3.61
26 27 1.376466 GCAAGGCTCTCACCAAGGA 59.624 57.895 0.00 0.00 0.00 3.36
27 28 0.957888 GCAAGGCTCTCACCAAGGAC 60.958 60.000 0.00 0.00 0.00 3.85
28 29 0.671781 CAAGGCTCTCACCAAGGACG 60.672 60.000 0.00 0.00 0.00 4.79
29 30 2.435059 GGCTCTCACCAAGGACGC 60.435 66.667 0.00 0.00 0.00 5.19
30 31 2.659610 GCTCTCACCAAGGACGCT 59.340 61.111 0.00 0.00 0.00 5.07
31 32 1.605058 GGCTCTCACCAAGGACGCTA 61.605 60.000 0.00 0.00 0.00 4.26
32 33 0.179124 GCTCTCACCAAGGACGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
33 34 0.179124 CTCTCACCAAGGACGCTAGC 60.179 60.000 4.06 4.06 0.00 3.42
34 35 0.898326 TCTCACCAAGGACGCTAGCA 60.898 55.000 16.45 0.00 0.00 3.49
39 40 3.787001 AAGGACGCTAGCAGGGCC 61.787 66.667 16.45 11.18 0.00 5.80
74 75 3.710722 AGCTCCCAGGCCAACTCG 61.711 66.667 5.01 0.00 0.00 4.18
203 206 2.361230 TCGAAGCGAGGAGGAGCA 60.361 61.111 0.00 0.00 35.48 4.26
269 275 4.170062 CACCTCAGCGGCGCATTG 62.170 66.667 35.02 24.14 35.61 2.82
343 350 0.745845 CACCTCCTGTATGCCACTGC 60.746 60.000 0.00 0.00 38.26 4.40
446 456 3.699038 AGCTAGTTCGAGAGCTCAAGAAT 59.301 43.478 21.34 14.60 46.08 2.40
450 460 5.146010 AGTTCGAGAGCTCAAGAATTCTT 57.854 39.130 21.34 15.11 36.45 2.52
452 462 6.692486 AGTTCGAGAGCTCAAGAATTCTTTA 58.308 36.000 18.16 9.84 33.11 1.85
469 481 2.873133 TTAAAACACCCACCAAAGCG 57.127 45.000 0.00 0.00 0.00 4.68
516 528 0.671472 CCCGAACCTGGGTAAACGAC 60.671 60.000 0.00 0.00 44.76 4.34
632 649 5.586243 CACCGACATCTTGGATCACTAAAAT 59.414 40.000 0.00 0.00 0.00 1.82
633 650 5.586243 ACCGACATCTTGGATCACTAAAATG 59.414 40.000 0.00 0.00 0.00 2.32
688 706 2.919602 TCCTTAGCATTTTGAGGGGTCT 59.080 45.455 0.00 0.00 0.00 3.85
689 707 3.333680 TCCTTAGCATTTTGAGGGGTCTT 59.666 43.478 0.00 0.00 0.00 3.01
794 813 7.210873 TGTTGTTATGAATTACCAAAACCACC 58.789 34.615 0.00 0.00 0.00 4.61
799 818 0.778720 ATTACCAAAACCACCCGGGA 59.221 50.000 32.02 0.00 41.15 5.14
807 826 2.209690 AACCACCCGGGAATTAGTTG 57.790 50.000 32.02 13.37 41.15 3.16
813 832 2.306512 ACCCGGGAATTAGTTGCACTTA 59.693 45.455 32.02 0.00 0.00 2.24
814 833 2.681344 CCCGGGAATTAGTTGCACTTAC 59.319 50.000 18.48 0.00 0.00 2.34
815 834 3.340034 CCGGGAATTAGTTGCACTTACA 58.660 45.455 0.00 0.00 0.00 2.41
925 949 3.916776 GTCTAATTGCTTGCTTGCTGAAC 59.083 43.478 3.47 0.00 0.00 3.18
981 1008 6.841601 TCTATAAATAGAGCCCAGCACAAAT 58.158 36.000 0.00 0.00 34.63 2.32
994 1021 5.220989 CCCAGCACAAATATTCATCTCACAG 60.221 44.000 0.00 0.00 0.00 3.66
1011 1038 4.850680 TCACAGAACACCAAGGTAAAACT 58.149 39.130 0.00 0.00 0.00 2.66
1053 1149 1.602311 CAGCATCCATGGCTAAGTCC 58.398 55.000 6.96 0.00 40.23 3.85
1125 1221 4.717877 CAATAGAGGGTGTTCATGGCATA 58.282 43.478 0.00 0.00 0.00 3.14
1216 1312 2.591429 CGGCTGAGTGTTGTGCCA 60.591 61.111 0.00 0.00 45.13 4.92
1229 1325 3.565214 TGCCACGCTTGGGAAGGA 61.565 61.111 11.75 0.00 41.03 3.36
1255 1351 1.943340 TGTTGTGCATTTGTCGCTACA 59.057 42.857 0.00 0.00 0.00 2.74
1446 1557 3.471680 GGCTAAATAAGTGGAGGAGCAG 58.528 50.000 0.00 0.00 0.00 4.24
1485 1612 6.272318 TGTTGTTGTGTGATTTGAATTCTCC 58.728 36.000 7.05 0.00 0.00 3.71
1555 1687 5.131067 GGAAGTGTAAGGAGGACAAAAGTT 58.869 41.667 0.00 0.00 0.00 2.66
1872 2016 3.495331 TGCACAGAAACATATGGTTGGT 58.505 40.909 11.61 6.15 40.35 3.67
1889 2033 4.953579 GGTTGGTTATACATGACCATGGTT 59.046 41.667 20.85 5.29 44.57 3.67
1931 2075 6.727697 ACTTTCCCTCTTCAAATCCATGAAAT 59.272 34.615 0.00 0.00 38.75 2.17
1936 2080 3.381272 TCTTCAAATCCATGAAATCCGGC 59.619 43.478 0.00 0.00 38.75 6.13
1965 2109 5.937540 TCTTCGCACCAATAATCTTTGAGAA 59.062 36.000 0.00 0.00 0.00 2.87
1966 2110 5.801350 TCGCACCAATAATCTTTGAGAAG 57.199 39.130 0.00 0.00 0.00 2.85
2105 2249 5.518847 CACCGCCTTATATATTATGTGACCG 59.481 44.000 0.00 0.00 0.00 4.79
2192 2340 5.754778 TGTCGTCATGTATATGTCCTTACG 58.245 41.667 0.00 2.34 35.73 3.18
2213 2362 5.745227 ACGGATCATGTTCCTATTGTCTTT 58.255 37.500 18.52 0.00 33.30 2.52
2214 2363 5.817816 ACGGATCATGTTCCTATTGTCTTTC 59.182 40.000 18.52 0.00 33.30 2.62
2215 2364 5.817296 CGGATCATGTTCCTATTGTCTTTCA 59.183 40.000 18.52 0.00 33.30 2.69
2280 2429 6.404074 GCTCATTTCCATTCTACAAGAACAGG 60.404 42.308 0.00 0.00 37.00 4.00
2329 2479 2.742053 TGCTGAGCCACTCGAATTTTAC 59.258 45.455 0.23 0.00 32.35 2.01
2333 2483 3.003480 GAGCCACTCGAATTTTACTGCT 58.997 45.455 0.00 0.00 0.00 4.24
2384 2535 6.923199 AACCACAAGGATTTCTCATCATTT 57.077 33.333 0.00 0.00 38.69 2.32
2385 2536 6.923199 ACCACAAGGATTTCTCATCATTTT 57.077 33.333 0.00 0.00 38.69 1.82
2407 2558 2.524306 CACTTTGGGTGGCCTAATTCA 58.476 47.619 3.32 0.00 41.90 2.57
2418 2569 3.074390 TGGCCTAATTCATCCCCATGTAG 59.926 47.826 3.32 0.00 0.00 2.74
2433 2584 5.248870 CCATGTAGAAAAATGGGTGTAGC 57.751 43.478 0.00 0.00 39.82 3.58
2442 2593 2.818274 GGGTGTAGCGCCTTTCGG 60.818 66.667 2.29 0.00 38.94 4.30
2470 2621 5.533154 TGTTACCACCAAGTTTGTATGAAGG 59.467 40.000 0.00 0.00 0.00 3.46
2476 2627 7.507616 ACCACCAAGTTTGTATGAAGGAAATTA 59.492 33.333 0.00 0.00 0.00 1.40
2562 2713 3.146847 CCTTCAGGGAAACAGTTGGTAC 58.853 50.000 0.00 0.00 37.23 3.34
2563 2714 3.434453 CCTTCAGGGAAACAGTTGGTACA 60.434 47.826 0.00 0.00 37.23 2.90
2568 2719 6.548321 TCAGGGAAACAGTTGGTACATAATT 58.452 36.000 0.00 0.00 39.30 1.40
2580 2731 8.367156 AGTTGGTACATAATTTTGCAGTTGAAT 58.633 29.630 0.00 0.00 39.30 2.57
2617 2768 6.041865 TGGGACACAACATTTGATTCTTTCAT 59.958 34.615 0.00 0.00 33.34 2.57
2649 2800 5.688621 TGTTGTTACACTAGCAAAGTACGAG 59.311 40.000 0.00 0.00 35.76 4.18
2673 2824 4.963318 TCCCAGAGCTTCTAATACATGG 57.037 45.455 0.00 0.00 0.00 3.66
2677 2828 5.167121 CCAGAGCTTCTAATACATGGATCG 58.833 45.833 0.00 0.00 0.00 3.69
2681 2832 4.058124 GCTTCTAATACATGGATCGCACA 58.942 43.478 0.00 0.00 0.00 4.57
2705 2856 1.602377 GTGGTGTTCTTCTTTCGTGGG 59.398 52.381 0.00 0.00 0.00 4.61
2730 2881 6.612306 AGATTTTCGTTTTCTATGGACTTGC 58.388 36.000 0.00 0.00 0.00 4.01
2736 2887 6.640518 TCGTTTTCTATGGACTTGCTATCTT 58.359 36.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.020617 TGAGAGCCTTGCCGGGTG 62.021 66.667 2.18 0.00 45.40 4.61
4 5 4.785453 GGTGAGAGCCTTGCCGGG 62.785 72.222 2.18 0.00 0.00 5.73
5 6 3.551496 TTGGTGAGAGCCTTGCCGG 62.551 63.158 0.00 0.00 0.00 6.13
7 8 1.676967 CCTTGGTGAGAGCCTTGCC 60.677 63.158 0.00 0.00 0.00 4.52
8 9 0.957888 GTCCTTGGTGAGAGCCTTGC 60.958 60.000 0.00 0.00 0.00 4.01
9 10 0.671781 CGTCCTTGGTGAGAGCCTTG 60.672 60.000 0.00 0.00 0.00 3.61
10 11 1.674057 CGTCCTTGGTGAGAGCCTT 59.326 57.895 0.00 0.00 0.00 4.35
11 12 2.948720 GCGTCCTTGGTGAGAGCCT 61.949 63.158 0.00 0.00 0.00 4.58
12 13 1.605058 TAGCGTCCTTGGTGAGAGCC 61.605 60.000 0.00 0.00 0.00 4.70
13 14 0.179124 CTAGCGTCCTTGGTGAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
14 15 0.179124 GCTAGCGTCCTTGGTGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
15 16 0.898326 TGCTAGCGTCCTTGGTGAGA 60.898 55.000 10.77 0.00 0.00 3.27
16 17 0.459237 CTGCTAGCGTCCTTGGTGAG 60.459 60.000 10.77 0.00 0.00 3.51
17 18 1.591703 CTGCTAGCGTCCTTGGTGA 59.408 57.895 10.77 0.00 0.00 4.02
18 19 1.448540 CCTGCTAGCGTCCTTGGTG 60.449 63.158 10.77 0.00 0.00 4.17
19 20 2.660064 CCCTGCTAGCGTCCTTGGT 61.660 63.158 10.77 0.00 0.00 3.67
20 21 2.187946 CCCTGCTAGCGTCCTTGG 59.812 66.667 10.77 5.13 0.00 3.61
21 22 2.512515 GCCCTGCTAGCGTCCTTG 60.513 66.667 10.77 0.00 0.00 3.61
22 23 3.787001 GGCCCTGCTAGCGTCCTT 61.787 66.667 10.77 0.00 0.00 3.36
24 25 4.840005 GTGGCCCTGCTAGCGTCC 62.840 72.222 10.77 8.66 0.00 4.79
25 26 3.775654 AGTGGCCCTGCTAGCGTC 61.776 66.667 10.77 0.00 0.00 5.19
26 27 4.087892 CAGTGGCCCTGCTAGCGT 62.088 66.667 10.77 0.00 33.59 5.07
40 41 4.986645 TGCATGTCGCCACGCAGT 62.987 61.111 0.00 0.00 41.33 4.40
174 177 4.717629 CTTCGACACGCGCCCTGA 62.718 66.667 5.73 0.00 40.61 3.86
203 206 3.075005 CCCATCCCGTCCGTCACT 61.075 66.667 0.00 0.00 0.00 3.41
269 275 6.097356 TCGTATTACAGGACAAGACACATTC 58.903 40.000 0.00 0.00 0.00 2.67
446 456 4.678309 CGCTTTGGTGGGTGTTTTAAAGAA 60.678 41.667 0.00 0.00 0.00 2.52
450 460 1.409427 CCGCTTTGGTGGGTGTTTTAA 59.591 47.619 0.00 0.00 39.31 1.52
452 462 1.819905 CCGCTTTGGTGGGTGTTTT 59.180 52.632 0.00 0.00 39.31 2.43
469 481 2.558378 GATGCGTAAAACCCTAGTCCC 58.442 52.381 0.00 0.00 0.00 4.46
516 528 2.565841 GATTAGTAGCCAGCACAAGGG 58.434 52.381 0.00 0.00 0.00 3.95
632 649 6.732154 CAAAAGCTCAAGACTCTTCATTTCA 58.268 36.000 0.00 0.00 0.00 2.69
633 650 5.628606 GCAAAAGCTCAAGACTCTTCATTTC 59.371 40.000 0.00 0.00 0.00 2.17
688 706 3.495629 GCATGGCATGGACTAGAGATGAA 60.496 47.826 27.48 0.00 0.00 2.57
689 707 2.038164 GCATGGCATGGACTAGAGATGA 59.962 50.000 27.48 0.00 0.00 2.92
738 757 8.844244 GCTCATTGAACTAATATCCATTCAAGT 58.156 33.333 11.58 0.00 42.56 3.16
807 826 4.656041 ACGATAACGACTACTGTAAGTGC 58.344 43.478 0.00 0.00 45.54 4.40
813 832 4.913924 GTGTTGAACGATAACGACTACTGT 59.086 41.667 0.00 0.00 42.66 3.55
814 833 4.913345 TGTGTTGAACGATAACGACTACTG 59.087 41.667 0.00 0.00 42.66 2.74
815 834 5.049198 TCTGTGTTGAACGATAACGACTACT 60.049 40.000 0.00 0.00 42.66 2.57
925 949 7.166970 GCAGCTATGTTCATGAAATGTGTATTG 59.833 37.037 10.35 4.07 46.80 1.90
981 1008 5.013079 ACCTTGGTGTTCTGTGAGATGAATA 59.987 40.000 0.00 0.00 0.00 1.75
994 1021 7.443272 TCTTAGCTAAGTTTTACCTTGGTGTTC 59.557 37.037 28.31 0.00 34.93 3.18
1125 1221 5.607939 ATTCATCATTTGACATGCCACAT 57.392 34.783 0.00 0.00 32.84 3.21
1189 1285 0.456221 CACTCAGCCGACGGACTATT 59.544 55.000 20.50 0.00 0.00 1.73
1191 1287 0.892358 AACACTCAGCCGACGGACTA 60.892 55.000 20.50 0.00 0.00 2.59
1216 1312 1.228154 GGTTGTCCTTCCCAAGCGT 60.228 57.895 0.00 0.00 31.54 5.07
1255 1351 1.321474 CATATGCCGGTGATGCCTTT 58.679 50.000 1.90 0.00 34.25 3.11
1446 1557 7.009174 CACACAACAACAATAAGACCTTTCAAC 59.991 37.037 0.00 0.00 0.00 3.18
1485 1612 5.048153 TCGACAGATTAATGAGATAGGCG 57.952 43.478 0.00 0.00 0.00 5.52
1555 1687 6.702449 AATATATGGGACTACATGCAAGGA 57.298 37.500 0.00 0.00 32.39 3.36
1585 1718 6.183360 GGGCAATAAGAAGCTCACCAATTAAT 60.183 38.462 0.00 0.00 0.00 1.40
1590 1723 2.224992 TGGGCAATAAGAAGCTCACCAA 60.225 45.455 0.00 0.00 36.06 3.67
1683 1818 2.877154 AGGATGTCTATGGGTCACCT 57.123 50.000 0.00 0.00 37.76 4.00
1684 1819 5.780793 ACTATAAGGATGTCTATGGGTCACC 59.219 44.000 0.00 0.00 37.24 4.02
1686 1821 7.073208 TCAACTATAAGGATGTCTATGGGTCA 58.927 38.462 0.00 0.00 0.00 4.02
1688 1823 8.511748 AATCAACTATAAGGATGTCTATGGGT 57.488 34.615 0.00 0.00 0.00 4.51
1889 2033 7.410174 AGGGAAAGTTGGTGATCAATGTAATA 58.590 34.615 0.00 0.00 37.73 0.98
1936 2080 3.804325 AGATTATTGGTGCGAAGATGACG 59.196 43.478 0.00 0.00 0.00 4.35
2038 2182 0.174845 TACCAATCGAGGAACGCCAG 59.825 55.000 0.00 0.00 42.26 4.85
2105 2249 6.039270 TGGTATTTGCACAGCCTTATATTGAC 59.961 38.462 0.00 0.00 0.00 3.18
2115 2263 2.493278 ACATCTTGGTATTTGCACAGCC 59.507 45.455 0.00 0.00 0.00 4.85
2192 2340 7.814264 ATGAAAGACAATAGGAACATGATCC 57.186 36.000 13.96 13.96 39.96 3.36
2280 2429 6.425721 CACCATTGGAAATTGATCATATTGCC 59.574 38.462 10.37 15.54 32.14 4.52
2348 2498 6.308015 TCCTTGTGGTTATAGCATAAGTGT 57.692 37.500 12.25 0.00 41.31 3.55
2349 2499 7.807977 AATCCTTGTGGTTATAGCATAAGTG 57.192 36.000 12.25 6.25 41.31 3.16
2350 2500 8.275040 AGAAATCCTTGTGGTTATAGCATAAGT 58.725 33.333 12.25 0.00 41.31 2.24
2351 2501 8.682936 AGAAATCCTTGTGGTTATAGCATAAG 57.317 34.615 7.97 7.97 42.14 1.73
2352 2502 8.271458 TGAGAAATCCTTGTGGTTATAGCATAA 58.729 33.333 0.00 0.00 34.23 1.90
2354 2504 6.662755 TGAGAAATCCTTGTGGTTATAGCAT 58.337 36.000 0.00 0.00 34.23 3.79
2355 2505 6.061022 TGAGAAATCCTTGTGGTTATAGCA 57.939 37.500 0.00 0.00 34.23 3.49
2356 2506 6.767902 TGATGAGAAATCCTTGTGGTTATAGC 59.232 38.462 0.00 0.00 34.23 2.97
2357 2507 8.915057 ATGATGAGAAATCCTTGTGGTTATAG 57.085 34.615 0.00 0.00 34.23 1.31
2359 2509 8.599624 AAATGATGAGAAATCCTTGTGGTTAT 57.400 30.769 0.00 0.00 34.23 1.89
2367 2518 9.918630 CAAAGTGTAAAATGATGAGAAATCCTT 57.081 29.630 0.00 0.00 0.00 3.36
2384 2535 3.818295 ATTAGGCCACCCAAAGTGTAA 57.182 42.857 5.01 0.00 45.74 2.41
2385 2536 3.074687 TGAATTAGGCCACCCAAAGTGTA 59.925 43.478 5.01 0.00 45.74 2.90
2397 2548 2.683211 ACATGGGGATGAATTAGGCC 57.317 50.000 0.00 0.00 0.00 5.19
2418 2569 1.173913 AGGCGCTACACCCATTTTTC 58.826 50.000 7.64 0.00 0.00 2.29
2508 2659 5.897377 ACAATGTGGTAGGAAATAGTTGC 57.103 39.130 0.00 0.00 0.00 4.17
2554 2705 7.283625 TCAACTGCAAAATTATGTACCAACT 57.716 32.000 0.00 0.00 0.00 3.16
2580 2731 3.431673 TGTGTCCCAAGTCAATGCATA 57.568 42.857 0.00 0.00 0.00 3.14
2617 2768 5.051153 TGCTAGTGTAACAACAACGATCAA 58.949 37.500 0.00 0.00 41.43 2.57
2649 2800 5.936956 CCATGTATTAGAAGCTCTGGGAATC 59.063 44.000 0.00 0.00 0.00 2.52
2673 2824 0.874390 AACACCACACATGTGCGATC 59.126 50.000 25.68 0.00 44.34 3.69
2677 2828 1.949525 AGAAGAACACCACACATGTGC 59.050 47.619 25.68 7.49 44.34 4.57
2681 2832 3.312421 CACGAAAGAAGAACACCACACAT 59.688 43.478 0.00 0.00 0.00 3.21
2705 2856 6.743172 GCAAGTCCATAGAAAACGAAAATCTC 59.257 38.462 0.00 0.00 0.00 2.75
2730 2881 8.865090 AGGAATCAAGTGTATCCTACAAGATAG 58.135 37.037 6.04 0.00 40.47 2.08
2736 2887 6.867519 TGAAGGAATCAAGTGTATCCTACA 57.132 37.500 7.69 0.00 41.39 2.74


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

AutoCloner maintained by Alex Coulton.