Multiple sequence alignment - TraesCS2B01G134100

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 TraesCS2B01G134100 chr2B 100.000 3295 0 0 1 3295 100324769 100328063 0.000000e+00 6085.0
1 TraesCS2B01G134100 chr2A 90.204 3328 166 61 58 3295 65651843 65655100 0.000000e+00 4193.0
2 TraesCS2B01G134100 chr2D 89.754 3299 154 78 71 3295 64156381 64159569 0.000000e+00 4050.0
3 TraesCS2B01G134100 chr4D 94.444 72 4 0 2028 2099 291587224 291587295 9.670000e-21 111.0
4 TraesCS2B01G134100 chr5D 92.105 76 4 2 2033 2107 40183814 40183888 4.500000e-19 106.0
5 TraesCS2B01G134100 chr5B 92.105 76 4 2 2033 2107 33556623 33556549 4.500000e-19 106.0
6 TraesCS2B01G134100 chr5A 92.000 75 6 0 2025 2099 28228880 28228954 4.500000e-19 106.0
7 TraesCS2B01G134100 chr1D 94.915 59 3 0 1177 1235 87776235 87776293 3.500000e-15 93.5
8 TraesCS2B01G134100 chr1A 93.220 59 4 0 1177 1235 84022813 84022871 1.630000e-13 87.9
9 TraesCS2B01G134100 chr1B 91.379 58 5 0 1177 1234 141722165 141722222 2.730000e-11 80.5


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 TraesCS2B01G134100 chr2B 100324769 100328063 3294 False 6085 6085 100.000 1 3295 1 chr2B.!!$F1 3294
1 TraesCS2B01G134100 chr2A 65651843 65655100 3257 False 4193 4193 90.204 58 3295 1 chr2A.!!$F1 3237
2 TraesCS2B01G134100 chr2D 64156381 64159569 3188 False 4050 4050 89.754 71 3295 1 chr2D.!!$F1 3224

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
35 36 0.031449 AACCCGCATGTTTCGTTTGG 59.969 50.0 0.00 0.0 0.0 3.28 F
142 146 0.169672 AACCAGACGTCGTGTATCCG 59.830 55.0 10.46 0.0 0.0 4.18 F
188 193 0.254178 TAGCCCTACGTCGAGAAGGT 59.746 55.0 0.00 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1754 1.618837 TCTCTGAACCTTCGTCCTTGG 59.381 52.381 0.0 0.0 0.0 3.61 R
2042 2160 0.973632 TGTTGTAGCTCATCACCGGT 59.026 50.000 0.0 0.0 0.0 5.28 R
2352 2476 2.285743 AAGCCTCCTCTCCCACCC 60.286 66.667 0.0 0.0 0.0 4.61 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
19 20 0.643820 CGAACGAATAGCGGACAACC 59.356 55.000 0.00 0.00 46.49 3.77
20 21 1.004595 GAACGAATAGCGGACAACCC 58.995 55.000 0.00 0.00 46.49 4.11
30 31 1.209127 GGACAACCCGCATGTTTCG 59.791 57.895 0.00 0.00 0.00 3.46
31 32 1.512156 GGACAACCCGCATGTTTCGT 61.512 55.000 0.00 0.00 0.00 3.85
32 33 0.309612 GACAACCCGCATGTTTCGTT 59.690 50.000 0.00 0.00 0.00 3.85
33 34 0.741915 ACAACCCGCATGTTTCGTTT 59.258 45.000 0.00 0.00 0.00 3.60
34 35 1.127701 CAACCCGCATGTTTCGTTTG 58.872 50.000 0.00 0.00 0.00 2.93
35 36 0.031449 AACCCGCATGTTTCGTTTGG 59.969 50.000 0.00 0.00 0.00 3.28
36 37 1.080839 CCCGCATGTTTCGTTTGGG 60.081 57.895 0.00 0.00 0.00 4.12
37 38 1.657556 CCGCATGTTTCGTTTGGGT 59.342 52.632 0.00 0.00 0.00 4.51
38 39 0.386731 CCGCATGTTTCGTTTGGGTC 60.387 55.000 0.00 0.00 0.00 4.46
39 40 0.724453 CGCATGTTTCGTTTGGGTCG 60.724 55.000 0.00 0.00 0.00 4.79
40 41 1.001745 GCATGTTTCGTTTGGGTCGC 61.002 55.000 0.00 0.00 0.00 5.19
41 42 0.386731 CATGTTTCGTTTGGGTCGCC 60.387 55.000 0.00 0.00 0.00 5.54
42 43 1.520600 ATGTTTCGTTTGGGTCGCCC 61.521 55.000 7.87 7.87 45.71 6.13
52 53 4.368543 GGTCGCCCCGTTCGAGTT 62.369 66.667 0.00 0.00 36.56 3.01
53 54 3.110178 GTCGCCCCGTTCGAGTTG 61.110 66.667 0.00 0.00 36.56 3.16
56 57 3.119096 GCCCCGTTCGAGTTGCTC 61.119 66.667 0.00 0.00 0.00 4.26
69 73 3.237660 CGAGTTGCTCTTACGAACATACG 59.762 47.826 0.00 0.00 39.31 3.06
73 77 3.239254 TGCTCTTACGAACATACGTGTG 58.761 45.455 11.09 11.09 46.02 3.82
104 108 4.686972 TGATCTGCGGATAAGAACAAGAG 58.313 43.478 8.35 0.00 31.46 2.85
141 145 1.468736 GGAACCAGACGTCGTGTATCC 60.469 57.143 10.46 14.97 0.00 2.59
142 146 0.169672 AACCAGACGTCGTGTATCCG 59.830 55.000 10.46 0.00 0.00 4.18
188 193 0.254178 TAGCCCTACGTCGAGAAGGT 59.746 55.000 0.00 0.00 0.00 3.50
235 240 1.378531 GCACATTGATGGAACGCCTA 58.621 50.000 0.00 0.00 34.31 3.93
263 268 1.150536 AGGTTTCCGAAAGCCAGCA 59.849 52.632 17.39 0.00 38.18 4.41
266 275 0.668535 GTTTCCGAAAGCCAGCAAGT 59.331 50.000 0.00 0.00 0.00 3.16
281 296 3.542704 CAGCAAGTAAGCTTACTCGTACG 59.457 47.826 33.50 21.39 43.70 3.67
333 348 6.315642 GCACTGAAAGGAACCCTAGTTATTAC 59.684 42.308 0.00 0.00 39.30 1.89
334 349 7.391620 CACTGAAAGGAACCCTAGTTATTACA 58.608 38.462 0.00 0.00 39.30 2.41
423 438 0.964358 CTAACGACCCGTCCACCTCT 60.964 60.000 0.00 0.00 39.99 3.69
425 440 1.405272 AACGACCCGTCCACCTCTTT 61.405 55.000 0.00 0.00 39.99 2.52
468 484 2.965831 AGCAGCCGGATTAGTTATGAGA 59.034 45.455 5.05 0.00 0.00 3.27
469 485 3.006323 AGCAGCCGGATTAGTTATGAGAG 59.994 47.826 5.05 0.00 0.00 3.20
470 486 3.005897 GCAGCCGGATTAGTTATGAGAGA 59.994 47.826 5.05 0.00 0.00 3.10
471 487 4.322349 GCAGCCGGATTAGTTATGAGAGAT 60.322 45.833 5.05 0.00 0.00 2.75
472 488 5.167121 CAGCCGGATTAGTTATGAGAGATG 58.833 45.833 5.05 0.00 0.00 2.90
473 489 3.929610 GCCGGATTAGTTATGAGAGATGC 59.070 47.826 5.05 0.00 0.00 3.91
474 490 4.169508 CCGGATTAGTTATGAGAGATGCG 58.830 47.826 0.00 0.00 0.00 4.73
475 491 4.169508 CGGATTAGTTATGAGAGATGCGG 58.830 47.826 0.00 0.00 0.00 5.69
476 492 4.082733 CGGATTAGTTATGAGAGATGCGGA 60.083 45.833 0.00 0.00 0.00 5.54
477 493 5.164954 GGATTAGTTATGAGAGATGCGGAC 58.835 45.833 0.00 0.00 0.00 4.79
478 494 5.279006 GGATTAGTTATGAGAGATGCGGACA 60.279 44.000 0.00 0.00 0.00 4.02
479 495 5.791336 TTAGTTATGAGAGATGCGGACAT 57.209 39.130 0.00 0.00 39.98 3.06
480 496 3.987547 AGTTATGAGAGATGCGGACATG 58.012 45.455 0.00 0.00 36.35 3.21
481 497 2.445565 TATGAGAGATGCGGACATGC 57.554 50.000 0.00 0.00 36.35 4.06
518 540 3.616956 TCTGAAGGCAAACGAGATCAT 57.383 42.857 0.00 0.00 0.00 2.45
523 545 5.614308 TGAAGGCAAACGAGATCATATCAT 58.386 37.500 0.00 0.00 0.00 2.45
540 562 1.002257 ATGTCGATGTGGCCTTGCA 60.002 52.632 3.32 0.24 0.00 4.08
546 568 1.733389 CGATGTGGCCTTGCACAATTC 60.733 52.381 3.32 0.00 34.78 2.17
548 570 1.117994 TGTGGCCTTGCACAATTCAA 58.882 45.000 3.32 0.00 0.00 2.69
554 576 2.417787 GCCTTGCACAATTCAAGATCCC 60.418 50.000 6.88 0.00 42.52 3.85
563 585 6.462500 CACAATTCAAGATCCCTATCGAGAT 58.538 40.000 0.00 0.00 37.19 2.75
564 586 6.589523 CACAATTCAAGATCCCTATCGAGATC 59.410 42.308 4.62 4.62 39.38 2.75
565 587 6.268617 ACAATTCAAGATCCCTATCGAGATCA 59.731 38.462 13.11 0.00 41.16 2.92
619 645 4.576053 CAGCCCGAGTGAAAATTCATCATA 59.424 41.667 0.00 0.00 39.73 2.15
623 649 6.348050 GCCCGAGTGAAAATTCATCATAGATC 60.348 42.308 0.00 0.00 39.73 2.75
644 670 2.026542 CCATCATGGACCGATCATGGAT 60.027 50.000 0.00 0.00 40.96 3.41
674 700 1.308069 ATGATGTGGAGGCGTTGTGC 61.308 55.000 0.00 0.00 45.38 4.57
860 906 0.484655 AGCAAAGGCCCCTTCTTTCT 59.515 50.000 0.00 0.00 42.56 2.52
861 907 0.891373 GCAAAGGCCCCTTCTTTCTC 59.109 55.000 0.00 0.00 34.84 2.87
978 1039 1.190643 ACCCTGCTCTCTGTAGCTTC 58.809 55.000 0.00 0.00 43.19 3.86
999 1060 2.351455 GCTCCCTTTCTCCTTCTTTCG 58.649 52.381 0.00 0.00 0.00 3.46
1074 1153 1.673329 GCTTCACCGTCTTCTTCCTCC 60.673 57.143 0.00 0.00 0.00 4.30
1077 1156 0.533032 CACCGTCTTCTTCCTCCTCC 59.467 60.000 0.00 0.00 0.00 4.30
1080 1159 1.107945 CGTCTTCTTCCTCCTCCTCC 58.892 60.000 0.00 0.00 0.00 4.30
1134 1231 2.863704 GCTGACATTGTGTTTGGGCTTC 60.864 50.000 0.00 0.00 0.00 3.86
1191 1288 3.785859 TCCATCCACTGCGAGGGC 61.786 66.667 0.00 0.00 33.63 5.19
1249 1346 4.221924 TCGAAGGTACCAACTCATGAATCA 59.778 41.667 15.94 0.00 0.00 2.57
1281 1378 9.912634 GGTTAATTGATTGAACTTTCATTCTCA 57.087 29.630 12.66 5.73 38.03 3.27
1306 1403 2.069273 AGTTCATTCTTCTTGCGACGG 58.931 47.619 0.00 0.00 0.00 4.79
1322 1419 2.147958 GACGGCAATTAACTGGTGTGA 58.852 47.619 0.00 0.00 0.00 3.58
1324 1421 3.153919 ACGGCAATTAACTGGTGTGAAT 58.846 40.909 0.00 0.00 0.00 2.57
1325 1422 3.057596 ACGGCAATTAACTGGTGTGAATG 60.058 43.478 0.00 0.00 28.09 2.67
1327 1424 4.320861 CGGCAATTAACTGGTGTGAATGAA 60.321 41.667 0.00 0.00 28.09 2.57
1328 1425 5.537188 GGCAATTAACTGGTGTGAATGAAA 58.463 37.500 0.00 0.00 28.09 2.69
1329 1426 6.165577 GGCAATTAACTGGTGTGAATGAAAT 58.834 36.000 0.00 0.00 28.09 2.17
1330 1427 6.650390 GGCAATTAACTGGTGTGAATGAAATT 59.350 34.615 0.00 0.00 40.93 1.82
1372 1469 5.861251 TGTGGTTTTGATTAATCGAATGTGC 59.139 36.000 17.11 9.95 30.68 4.57
1626 1738 2.752238 ACGAGGCAGAGTCGGAGG 60.752 66.667 0.00 0.00 41.88 4.30
1772 1884 2.674380 CCGCCAGCCAAAGAAGCT 60.674 61.111 0.00 0.00 42.70 3.74
1777 1889 2.113986 AGCCAAAGAAGCTGCGGT 59.886 55.556 0.00 0.00 39.69 5.68
1780 1892 2.680913 CCAAAGAAGCTGCGGTCGG 61.681 63.158 0.00 0.00 0.00 4.79
1859 1971 2.645838 AGAACAAGCAGCAGAAGGAA 57.354 45.000 0.00 0.00 0.00 3.36
1952 2064 4.254709 ACGAAGCAGCCACAGCCA 62.255 61.111 0.00 0.00 41.25 4.75
2213 2334 3.075641 TACATGTACGGCCCGCCA 61.076 61.111 1.23 0.00 35.37 5.69
2350 2474 3.978672 AGTCTGTAGTTAAAAGTGGGGGT 59.021 43.478 0.00 0.00 0.00 4.95
2351 2475 4.070009 GTCTGTAGTTAAAAGTGGGGGTG 58.930 47.826 0.00 0.00 0.00 4.61
2352 2476 3.073356 TCTGTAGTTAAAAGTGGGGGTGG 59.927 47.826 0.00 0.00 0.00 4.61
2353 2477 2.108601 TGTAGTTAAAAGTGGGGGTGGG 59.891 50.000 0.00 0.00 0.00 4.61
2481 2614 8.567948 TCTTCAAATTTTCGACTTGATTAGCTT 58.432 29.630 0.00 0.00 0.00 3.74
2556 2689 9.994432 CTACTAGCTTGTTTCAATAATTTCCAG 57.006 33.333 6.03 0.00 0.00 3.86
2564 2697 9.757227 TTGTTTCAATAATTTCCAGTTTGGTAG 57.243 29.630 0.00 0.00 39.03 3.18
2582 2716 8.616076 GTTTGGTAGTATCCATTTGAGAAGATG 58.384 37.037 0.00 0.00 37.33 2.90
2588 2722 7.961351 AGTATCCATTTGAGAAGATGGTCTAG 58.039 38.462 2.64 0.00 42.72 2.43
2591 2725 5.721480 TCCATTTGAGAAGATGGTCTAGTCA 59.279 40.000 2.64 0.00 42.72 3.41
2616 2750 6.428159 AGTCTCACATGAATTTGGTACTGAAC 59.572 38.462 0.00 0.00 0.00 3.18
2646 2781 7.680982 TCGAATCATGTCTACAAAAATAACCG 58.319 34.615 0.00 0.00 0.00 4.44
2648 2783 7.391148 AATCATGTCTACAAAAATAACCGCT 57.609 32.000 0.00 0.00 0.00 5.52
2657 2792 4.022416 ACAAAAATAACCGCTGATGCAGAA 60.022 37.500 0.00 0.00 39.64 3.02
2660 2795 3.764885 ATAACCGCTGATGCAGAAAAC 57.235 42.857 0.00 0.00 39.64 2.43
2661 2796 1.609208 AACCGCTGATGCAGAAAACT 58.391 45.000 0.00 0.00 39.64 2.66
2663 2798 0.449388 CCGCTGATGCAGAAAACTCC 59.551 55.000 0.00 0.00 39.64 3.85
2664 2799 1.159285 CGCTGATGCAGAAAACTCCA 58.841 50.000 0.00 0.00 39.64 3.86
2665 2800 1.135859 CGCTGATGCAGAAAACTCCAC 60.136 52.381 0.00 0.00 39.64 4.02
2666 2801 1.881973 GCTGATGCAGAAAACTCCACA 59.118 47.619 0.00 0.00 39.41 4.17
2667 2802 2.294233 GCTGATGCAGAAAACTCCACAA 59.706 45.455 0.00 0.00 39.41 3.33
2668 2803 3.611057 GCTGATGCAGAAAACTCCACAAG 60.611 47.826 0.00 0.00 39.41 3.16
2669 2804 3.554934 TGATGCAGAAAACTCCACAAGT 58.445 40.909 0.00 0.00 41.10 3.16
2670 2805 4.037208 CTGATGCAGAAAACTCCACAAGTT 59.963 41.667 0.00 0.00 40.98 2.66
2671 2806 5.239306 CTGATGCAGAAAACTCCACAAGTTA 59.761 40.000 0.00 0.00 39.46 2.24
2672 2807 6.567321 CTGATGCAGAAAACTCCACAAGTTAG 60.567 42.308 0.00 0.00 39.46 2.34
2673 2808 9.835390 CTGATGCAGAAAACTCCACAAGTTAGC 62.835 44.444 0.00 0.00 39.46 3.09
2706 2841 7.906611 TGTGTACAAATTCATTTTGAACTCG 57.093 32.000 0.00 0.00 46.36 4.18
2708 2843 7.642194 TGTGTACAAATTCATTTTGAACTCGTC 59.358 33.333 0.00 0.00 46.36 4.20
2731 2871 7.011950 CGTCCCTACAAGATAACATATGCAAAA 59.988 37.037 1.58 0.00 0.00 2.44
2734 2874 7.425606 CCTACAAGATAACATATGCAAAACCC 58.574 38.462 1.58 0.00 0.00 4.11
2742 2882 4.384940 ACATATGCAAAACCCCACAAAAC 58.615 39.130 1.58 0.00 0.00 2.43
2745 2885 1.625818 TGCAAAACCCCACAAAACAGT 59.374 42.857 0.00 0.00 0.00 3.55
2747 2887 3.452627 TGCAAAACCCCACAAAACAGTAT 59.547 39.130 0.00 0.00 0.00 2.12
2760 2900 7.678194 ACAAAACAGTATCAAATTTGTGTCG 57.322 32.000 17.47 9.19 41.27 4.35
2797 2938 3.245229 TGCAGTATCTGAATTTGGTGGGT 60.245 43.478 0.66 0.00 32.44 4.51
2811 2952 1.247567 GTGGGTGTGCTGCTTACATT 58.752 50.000 0.00 0.00 0.00 2.71
2910 3054 2.993863 AGTGGGGTCCCTTCACTTAATT 59.006 45.455 12.75 0.00 38.44 1.40
2965 3109 0.173935 TAAGCTGGCATGCATGTTGC 59.826 50.000 26.79 24.73 45.29 4.17
3009 3153 3.072038 TCCTGCTATGATGATTGTCCTGG 59.928 47.826 0.00 0.00 0.00 4.45
3072 3219 7.280876 AGTGTTGTACTACTAATGCAATGATGG 59.719 37.037 8.88 0.00 38.04 3.51
3079 3226 5.002464 ACTAATGCAATGATGGTTCTTGC 57.998 39.130 0.00 0.00 44.25 4.01
3109 3259 4.737578 TGTGGTGGTACTCTACTCTCTTT 58.262 43.478 0.00 0.00 34.45 2.52
3223 3379 1.635817 GCCTGCCAGTCCTCCCAATA 61.636 60.000 0.00 0.00 0.00 1.90
3234 3390 5.949354 CAGTCCTCCCAATACCATTGTTAAA 59.051 40.000 0.00 0.00 0.00 1.52
3239 3395 6.493458 CCTCCCAATACCATTGTTAAATAGGG 59.507 42.308 0.00 0.00 0.00 3.53
3262 3418 1.392589 ACCACTGGCTTCAACTTGTG 58.607 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.643820 GGTTGTCCGCTATTCGTTCG 59.356 55.000 0.00 0.00 36.19 3.95
1 2 1.004595 GGGTTGTCCGCTATTCGTTC 58.995 55.000 0.00 0.00 36.19 3.95
2 3 3.148340 GGGTTGTCCGCTATTCGTT 57.852 52.632 0.00 0.00 36.19 3.85
3 4 4.926207 GGGTTGTCCGCTATTCGT 57.074 55.556 0.00 0.00 36.19 3.85
12 13 1.209127 CGAAACATGCGGGTTGTCC 59.791 57.895 0.00 0.00 0.00 4.02
13 14 0.309612 AACGAAACATGCGGGTTGTC 59.690 50.000 0.00 0.00 0.00 3.18
14 15 0.741915 AAACGAAACATGCGGGTTGT 59.258 45.000 0.00 0.00 0.00 3.32
15 16 1.127701 CAAACGAAACATGCGGGTTG 58.872 50.000 0.00 0.00 0.00 3.77
16 17 0.031449 CCAAACGAAACATGCGGGTT 59.969 50.000 0.00 0.00 0.00 4.11
17 18 1.657556 CCAAACGAAACATGCGGGT 59.342 52.632 0.00 0.00 0.00 5.28
18 19 1.080839 CCCAAACGAAACATGCGGG 60.081 57.895 0.00 0.00 0.00 6.13
19 20 0.386731 GACCCAAACGAAACATGCGG 60.387 55.000 0.00 0.00 0.00 5.69
20 21 0.724453 CGACCCAAACGAAACATGCG 60.724 55.000 0.00 0.00 0.00 4.73
21 22 1.001745 GCGACCCAAACGAAACATGC 61.002 55.000 0.00 0.00 0.00 4.06
22 23 0.386731 GGCGACCCAAACGAAACATG 60.387 55.000 0.00 0.00 0.00 3.21
23 24 1.953772 GGCGACCCAAACGAAACAT 59.046 52.632 0.00 0.00 0.00 2.71
24 25 3.423179 GGCGACCCAAACGAAACA 58.577 55.556 0.00 0.00 0.00 2.83
36 37 3.110178 CAACTCGAACGGGGCGAC 61.110 66.667 0.00 0.00 33.71 5.19
39 40 3.119096 GAGCAACTCGAACGGGGC 61.119 66.667 0.00 0.00 0.00 5.80
40 41 0.245539 TAAGAGCAACTCGAACGGGG 59.754 55.000 0.00 0.00 35.36 5.73
41 42 1.347320 GTAAGAGCAACTCGAACGGG 58.653 55.000 0.00 0.00 35.36 5.28
42 43 0.982673 CGTAAGAGCAACTCGAACGG 59.017 55.000 13.49 0.00 38.68 4.44
43 44 1.959747 TCGTAAGAGCAACTCGAACG 58.040 50.000 14.54 14.54 45.01 3.95
56 57 2.091588 GCACCACACGTATGTTCGTAAG 59.908 50.000 0.00 0.00 42.27 2.34
69 73 2.223112 CGCAGATCAAATAGCACCACAC 60.223 50.000 0.00 0.00 0.00 3.82
73 77 1.953559 TCCGCAGATCAAATAGCACC 58.046 50.000 0.00 0.00 0.00 5.01
141 145 2.277692 TCCAATCGTCTACGCGCG 60.278 61.111 30.96 30.96 39.60 6.86
142 146 1.074319 TTGTCCAATCGTCTACGCGC 61.074 55.000 5.73 0.00 39.60 6.86
188 193 3.262405 CCAAGTAGGGTTAGTTAGGTGCA 59.738 47.826 0.00 0.00 0.00 4.57
235 240 1.254026 TCGGAAACCTGATCTGACGT 58.746 50.000 0.38 0.00 0.00 4.34
263 268 2.489329 TGGCGTACGAGTAAGCTTACTT 59.511 45.455 33.78 23.60 43.64 2.24
266 275 2.684374 TCATGGCGTACGAGTAAGCTTA 59.316 45.455 21.65 0.86 39.82 3.09
281 296 1.100510 TCTGCTGCTTGATTCATGGC 58.899 50.000 0.00 3.98 0.00 4.40
333 348 1.202348 TCATGGACGTACAGCTGAGTG 59.798 52.381 23.35 11.40 0.00 3.51
334 349 1.545841 TCATGGACGTACAGCTGAGT 58.454 50.000 23.35 16.82 0.00 3.41
423 438 1.691196 CTGCAGGGTTTGGTGAGAAA 58.309 50.000 5.57 0.00 0.00 2.52
425 440 1.228245 GCTGCAGGGTTTGGTGAGA 60.228 57.895 17.12 0.00 0.00 3.27
472 488 4.241999 GACGCCATGCATGTCCGC 62.242 66.667 26.85 21.12 0.00 5.54
473 489 2.512286 AGACGCCATGCATGTCCG 60.512 61.111 25.88 25.88 33.09 4.79
474 490 0.461870 TACAGACGCCATGCATGTCC 60.462 55.000 24.58 14.13 33.09 4.02
475 491 1.586422 ATACAGACGCCATGCATGTC 58.414 50.000 24.58 15.70 0.00 3.06
476 492 1.942657 GAATACAGACGCCATGCATGT 59.057 47.619 24.58 8.96 0.00 3.21
477 493 2.216046 AGAATACAGACGCCATGCATG 58.784 47.619 20.19 20.19 0.00 4.06
478 494 2.627515 AGAATACAGACGCCATGCAT 57.372 45.000 0.00 0.00 0.00 3.96
479 495 2.093500 AGAAGAATACAGACGCCATGCA 60.093 45.455 0.00 0.00 0.00 3.96
480 496 2.286294 CAGAAGAATACAGACGCCATGC 59.714 50.000 0.00 0.00 0.00 4.06
481 497 3.785486 TCAGAAGAATACAGACGCCATG 58.215 45.455 0.00 0.00 0.00 3.66
482 498 4.437239 CTTCAGAAGAATACAGACGCCAT 58.563 43.478 3.82 0.00 32.31 4.40
483 499 3.368427 CCTTCAGAAGAATACAGACGCCA 60.368 47.826 12.14 0.00 32.31 5.69
518 540 2.837498 CAAGGCCACATCGACATGATA 58.163 47.619 5.01 0.00 34.83 2.15
523 545 1.965930 GTGCAAGGCCACATCGACA 60.966 57.895 5.01 0.00 35.80 4.35
554 576 1.003866 TCGCGTGTGTGATCTCGATAG 60.004 52.381 5.77 0.00 0.00 2.08
563 585 0.031449 TGTGAAGATCGCGTGTGTGA 59.969 50.000 5.77 0.00 39.32 3.58
564 586 0.858583 TTGTGAAGATCGCGTGTGTG 59.141 50.000 5.77 0.00 0.00 3.82
565 587 1.139989 CTTGTGAAGATCGCGTGTGT 58.860 50.000 5.77 0.00 0.00 3.72
577 602 3.696051 GCTGCCTCCAAATATCTTGTGAA 59.304 43.478 0.00 0.00 0.00 3.18
623 649 1.348696 TCCATGATCGGTCCATGATGG 59.651 52.381 4.74 4.74 42.89 3.51
633 659 1.597742 GACAACCCATCCATGATCGG 58.402 55.000 0.00 0.00 0.00 4.18
635 661 2.734755 TGGACAACCCATCCATGATC 57.265 50.000 0.00 0.00 41.47 2.92
644 670 1.426983 TCCACATCATTGGACAACCCA 59.573 47.619 0.00 0.00 41.00 4.51
674 700 1.078759 GGCGACGGTGACATCAGAAG 61.079 60.000 0.00 0.00 0.00 2.85
860 906 3.691342 CGAGTGGCAACCGAGGGA 61.691 66.667 4.04 0.00 0.00 4.20
943 999 1.183549 GGGTAGCTTCGAGAGTGGAA 58.816 55.000 0.00 0.00 0.00 3.53
978 1039 2.351455 GAAAGAAGGAGAAAGGGAGCG 58.649 52.381 0.00 0.00 0.00 5.03
999 1060 2.514824 GCTTCCCCTGACGCCATC 60.515 66.667 0.00 0.00 29.89 3.51
1074 1153 3.761752 ACGAAGAAGAAGAAGAGGAGGAG 59.238 47.826 0.00 0.00 0.00 3.69
1077 1156 4.233789 CACACGAAGAAGAAGAAGAGGAG 58.766 47.826 0.00 0.00 0.00 3.69
1080 1159 2.734079 GCCACACGAAGAAGAAGAAGAG 59.266 50.000 0.00 0.00 0.00 2.85
1191 1288 3.501445 CCTTCTTGACCTTCTTCTTGCAG 59.499 47.826 0.00 0.00 0.00 4.41
1249 1346 6.575162 AAGTTCAATCAATTAACCGAAGCT 57.425 33.333 0.00 0.00 0.00 3.74
1306 1403 7.599998 AGAATTTCATTCACACCAGTTAATTGC 59.400 33.333 0.00 0.00 41.71 3.56
1327 1424 7.877612 ACCACAAACAAAGAAACAGAAAGAATT 59.122 29.630 0.00 0.00 0.00 2.17
1328 1425 7.386059 ACCACAAACAAAGAAACAGAAAGAAT 58.614 30.769 0.00 0.00 0.00 2.40
1329 1426 6.754193 ACCACAAACAAAGAAACAGAAAGAA 58.246 32.000 0.00 0.00 0.00 2.52
1330 1427 6.339587 ACCACAAACAAAGAAACAGAAAGA 57.660 33.333 0.00 0.00 0.00 2.52
1372 1469 3.067106 GTCACCTTGTACACACCTGATG 58.933 50.000 0.00 0.00 0.00 3.07
1448 1557 2.983930 GAGCAGCCGTCTGACGAGT 61.984 63.158 29.93 14.34 46.05 4.18
1565 1677 4.083862 ACCTTCTCCGCGCCCTTC 62.084 66.667 0.00 0.00 0.00 3.46
1620 1732 2.440430 CTTCTCCGAGCCCTCCGA 60.440 66.667 0.00 0.00 0.00 4.55
1642 1754 1.618837 TCTCTGAACCTTCGTCCTTGG 59.381 52.381 0.00 0.00 0.00 3.61
2042 2160 0.973632 TGTTGTAGCTCATCACCGGT 59.026 50.000 0.00 0.00 0.00 5.28
2350 2474 4.741239 GCCTCCTCTCCCACCCCA 62.741 72.222 0.00 0.00 0.00 4.96
2351 2475 3.952799 AAGCCTCCTCTCCCACCCC 62.953 68.421 0.00 0.00 0.00 4.95
2352 2476 2.285743 AAGCCTCCTCTCCCACCC 60.286 66.667 0.00 0.00 0.00 4.61
2353 2477 2.726351 CGAAGCCTCCTCTCCCACC 61.726 68.421 0.00 0.00 0.00 4.61
2556 2689 8.616076 CATCTTCTCAAATGGATACTACCAAAC 58.384 37.037 0.00 0.00 43.47 2.93
2564 2697 7.731054 ACTAGACCATCTTCTCAAATGGATAC 58.269 38.462 8.31 0.62 44.37 2.24
2582 2716 5.590530 ATTCATGTGAGACTGACTAGACC 57.409 43.478 0.00 0.00 0.00 3.85
2588 2722 5.934625 AGTACCAAATTCATGTGAGACTGAC 59.065 40.000 0.00 0.00 0.00 3.51
2591 2725 6.114187 TCAGTACCAAATTCATGTGAGACT 57.886 37.500 0.00 0.00 0.00 3.24
2657 2792 5.652994 TTTGTTGCTAACTTGTGGAGTTT 57.347 34.783 0.00 0.00 46.34 2.66
2660 2795 6.019640 CACAAATTTGTTGCTAACTTGTGGAG 60.020 38.462 21.10 0.79 39.91 3.86
2661 2796 5.809562 CACAAATTTGTTGCTAACTTGTGGA 59.190 36.000 21.10 0.00 39.91 4.02
2663 2798 6.645700 ACACAAATTTGTTGCTAACTTGTG 57.354 33.333 21.10 18.80 39.91 3.33
2664 2799 7.316640 TGTACACAAATTTGTTGCTAACTTGT 58.683 30.769 21.10 14.22 39.91 3.16
2665 2800 7.748031 TGTACACAAATTTGTTGCTAACTTG 57.252 32.000 21.10 9.26 39.91 3.16
2666 2801 8.764524 TTTGTACACAAATTTGTTGCTAACTT 57.235 26.923 21.10 3.58 40.55 2.66
2699 2834 4.768448 TGTTATCTTGTAGGGACGAGTTCA 59.232 41.667 0.00 0.00 38.17 3.18
2706 2841 7.801716 TTTGCATATGTTATCTTGTAGGGAC 57.198 36.000 4.29 0.00 0.00 4.46
2708 2843 7.425606 GGTTTTGCATATGTTATCTTGTAGGG 58.574 38.462 4.29 0.00 0.00 3.53
2731 2871 6.126911 ACAAATTTGATACTGTTTTGTGGGGT 60.127 34.615 24.64 0.00 38.64 4.95
2742 2882 7.062138 CCCAATTTCGACACAAATTTGATACTG 59.938 37.037 24.64 14.10 34.37 2.74
2745 2885 5.866633 GCCCAATTTCGACACAAATTTGATA 59.133 36.000 24.64 2.36 34.37 2.15
2747 2887 4.054671 GCCCAATTTCGACACAAATTTGA 58.945 39.130 24.64 0.36 34.37 2.69
2816 2957 7.939039 ACCAGAATCACAAGATCAACTTCTAAA 59.061 33.333 0.00 0.00 36.61 1.85
2817 2958 7.388776 CACCAGAATCACAAGATCAACTTCTAA 59.611 37.037 0.00 0.00 36.61 2.10
2818 2959 6.875726 CACCAGAATCACAAGATCAACTTCTA 59.124 38.462 0.00 0.00 36.61 2.10
2824 2965 5.702670 GTCTTCACCAGAATCACAAGATCAA 59.297 40.000 0.00 0.00 31.90 2.57
2910 3054 1.627864 GCCCCTTCTTTGCCAAAGTA 58.372 50.000 16.33 6.70 39.52 2.24
2965 3109 5.696270 GGAAAATTACAAAAAGCCTGTGAGG 59.304 40.000 0.00 0.00 38.80 3.86
3009 3153 7.393515 ACTCCATCAAACCCATACTTTAGTTTC 59.606 37.037 0.00 0.00 30.27 2.78
3072 3219 2.540931 CACCACAAAGCAATGCAAGAAC 59.459 45.455 8.35 0.00 0.00 3.01
3079 3226 3.149196 AGAGTACCACCACAAAGCAATG 58.851 45.455 0.00 0.00 0.00 2.82
3109 3259 3.117888 GGAGCACTCCCCTAATCAATCAA 60.118 47.826 5.30 0.00 43.94 2.57
3223 3379 7.177744 CAGTGGTTTACCCTATTTAACAATGGT 59.822 37.037 0.00 0.00 34.29 3.55
3234 3390 2.916934 TGAAGCCAGTGGTTTACCCTAT 59.083 45.455 11.70 0.00 34.29 2.57
3239 3395 3.380320 ACAAGTTGAAGCCAGTGGTTTAC 59.620 43.478 11.70 7.36 30.94 2.01
3262 3418 6.086222 CACAGTGCACCTGATTAACAAATAC 58.914 40.000 14.63 0.00 44.49 1.89


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

AutoCloner maintained by Alex Coulton.