Multiple sequence alignment - TraesCS4A01G053700

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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 TraesCS4A01G053700 chr4A 100.000 4788 0 0 1 4788 45335385 45340172 0 8842
1 TraesCS4A01G053700 chr4D 94.405 2663 108 18 43 2681 419315885 419313240 0 4054
2 TraesCS4A01G053700 chr4D 95.198 2124 80 9 2676 4788 419313212 419311100 0 3338
3 TraesCS4A01G053700 chr4B 91.705 1977 103 21 16 1977 517276415 517274485 0 2686
4 TraesCS4A01G053700 chr4B 93.706 1287 52 13 3515 4788 517267279 517266009 0 1901
5 TraesCS4A01G053700 chr4B 96.247 826 31 0 2676 3501 517273771 517272946 0 1354
6 TraesCS4A01G053700 chr4B 90.365 685 60 3 2003 2681 517274489 517273805 0 894


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 TraesCS4A01G053700 chr4A 45335385 45340172 4787 False 8842.000000 8842 100.000000 1 4788 1 chr4A.!!$F1 4787
1 TraesCS4A01G053700 chr4D 419311100 419315885 4785 True 3696.000000 4054 94.801500 43 4788 2 chr4D.!!$R1 4745
2 TraesCS4A01G053700 chr4B 517266009 517267279 1270 True 1901.000000 1901 93.706000 3515 4788 1 chr4B.!!$R1 1273
3 TraesCS4A01G053700 chr4B 517272946 517276415 3469 True 1644.666667 2686 92.772333 16 3501 3 chr4B.!!$R2 3485

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
725 740 0.818938 TCGATGCCAGTAAGCGGTTA 59.181 50.000 2.26 2.26 34.65 2.85 F
1569 1593 0.539986 TTCCAGCGGAGTACCCAATC 59.460 55.000 0.00 0.00 31.21 2.67 F
2359 2389 1.071471 CTGAACTCCCCGTTGCTGT 59.929 57.895 0.00 0.00 35.56 4.40 F
2491 2521 1.216122 GAAGACATCCGAGCAGATGC 58.784 55.000 10.34 0.00 46.29 3.91 F
2683 2752 2.245438 CTTCAAGGGCCTCCGGAGTC 62.245 65.000 29.25 18.21 38.33 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2635 2665 0.399233 AGCTCCCATGTCCTCCCTAC 60.399 60.000 0.00 0.0 0.00 3.18 R
2638 2668 1.059006 ATGAGCTCCCATGTCCTCCC 61.059 60.000 12.15 0.0 0.00 4.30 R
3660 3729 0.110056 GCCACAAGAGATGCAACACG 60.110 55.000 0.00 0.0 0.00 4.49 R
3677 3746 1.132453 GGGCAAATGTTACTTCTCGCC 59.868 52.381 0.00 0.0 37.57 5.54 R
4188 4261 1.271325 TGGACGGCATGACTTGAATGT 60.271 47.619 0.00 0.0 0.00 2.71 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
41 42 8.603242 GTTGGATCAACTCTTTTGTTCTACTA 57.397 34.615 0.00 0.00 40.73 1.82
66 67 5.290493 AGACATGGACAGTTGAACTTGTA 57.710 39.130 0.00 0.00 0.00 2.41
68 69 6.299141 AGACATGGACAGTTGAACTTGTAAT 58.701 36.000 0.00 0.00 0.00 1.89
179 187 8.017946 GCCAATATCTTTATGATCGTCCTTTTC 58.982 37.037 0.00 0.00 36.65 2.29
238 253 4.154195 GCTGGTACAATAACAGTTGGTGAG 59.846 45.833 3.00 0.00 45.27 3.51
294 309 8.058847 AGGATGGGCACTTTATTGTTCTTTATA 58.941 33.333 0.00 0.00 0.00 0.98
349 364 6.819649 ACATTATTGATGCCAAAATGACCTTG 59.180 34.615 0.64 0.00 39.47 3.61
379 394 6.207691 TGCACTTTCAGGCCTATTATTTTC 57.792 37.500 3.98 0.00 0.00 2.29
467 482 6.610020 TCTCGATATCTTCTTTTGGGAGGTAA 59.390 38.462 0.34 0.00 0.00 2.85
468 483 7.290248 TCTCGATATCTTCTTTTGGGAGGTAAT 59.710 37.037 0.34 0.00 0.00 1.89
469 484 7.217200 TCGATATCTTCTTTTGGGAGGTAATG 58.783 38.462 0.34 0.00 0.00 1.90
470 485 6.073003 CGATATCTTCTTTTGGGAGGTAATGC 60.073 42.308 0.34 0.00 0.00 3.56
471 486 4.657814 TCTTCTTTTGGGAGGTAATGCT 57.342 40.909 0.00 0.00 0.00 3.79
472 487 5.772393 TCTTCTTTTGGGAGGTAATGCTA 57.228 39.130 0.00 0.00 0.00 3.49
473 488 5.497474 TCTTCTTTTGGGAGGTAATGCTAC 58.503 41.667 0.00 0.00 0.00 3.58
505 520 3.581024 TGTGACGGCGTTTTATCTAGT 57.419 42.857 16.19 0.00 0.00 2.57
519 534 8.709646 CGTTTTATCTAGTTTGTGCTTAAGACT 58.290 33.333 6.67 2.78 0.00 3.24
595 610 6.408869 AGAATTTCCATTTGCCTTGTTATGG 58.591 36.000 0.00 0.00 39.09 2.74
638 653 3.889538 AGCAGCAGCATATCAATTGTCAT 59.110 39.130 3.17 0.00 45.49 3.06
679 694 8.265055 TGAAAGTTAATAACTAGGATGAGGTGG 58.735 37.037 6.04 0.00 41.91 4.61
725 740 0.818938 TCGATGCCAGTAAGCGGTTA 59.181 50.000 2.26 2.26 34.65 2.85
863 884 8.415950 TTGTGTGGTTATTTAAGTGATTGGAT 57.584 30.769 0.00 0.00 0.00 3.41
864 885 8.415950 TGTGTGGTTATTTAAGTGATTGGATT 57.584 30.769 0.00 0.00 0.00 3.01
1047 1071 3.383185 AGACAAGCACTATCTCAGCTACC 59.617 47.826 0.00 0.00 37.70 3.18
1347 1371 5.251764 AGGATGTCAGGAACAGAAGAAATG 58.748 41.667 0.00 0.00 42.37 2.32
1428 1452 4.877378 AAATCAGCAAATTTGAGAGGCA 57.123 36.364 22.31 0.00 0.00 4.75
1432 1456 2.555325 CAGCAAATTTGAGAGGCACTGA 59.445 45.455 22.31 0.00 41.55 3.41
1523 1547 4.344679 AGAAAGAAACATCCAATGGTTGCA 59.655 37.500 10.08 0.00 41.00 4.08
1544 1568 2.093447 ACAGAGGACTTTGGCTAATCCG 60.093 50.000 0.00 0.00 37.80 4.18
1569 1593 0.539986 TTCCAGCGGAGTACCCAATC 59.460 55.000 0.00 0.00 31.21 2.67
1595 1619 2.625695 AAAAAGCAGCAATGCCAGTT 57.374 40.000 0.00 0.00 34.90 3.16
1607 1631 2.642154 TGCCAGTTAAGGGTTCGAAA 57.358 45.000 0.00 0.00 0.00 3.46
1621 1645 3.691609 GGTTCGAAATTGCCAGAGAAGAT 59.308 43.478 0.00 0.00 0.00 2.40
1654 1678 3.176924 AGCTAGAACTGTGGAGAAGGA 57.823 47.619 0.00 0.00 0.00 3.36
1658 1682 1.341531 AGAACTGTGGAGAAGGACACG 59.658 52.381 0.00 0.00 40.39 4.49
1714 1738 6.366604 GCTTCACTTCCTACTAAACTCAACTC 59.633 42.308 0.00 0.00 0.00 3.01
1828 1852 3.130869 CCAGCAATTATTACTGGCAAGCA 59.869 43.478 10.88 0.00 44.16 3.91
1862 1886 4.238514 CTGGTAAGACTGGAAGAAGTTCG 58.761 47.826 0.00 0.00 37.43 3.95
1889 1913 3.428045 GGTCCAGCAATGCAAGTATCAAC 60.428 47.826 8.35 0.00 0.00 3.18
1949 1973 4.394920 TCCATTGAAGACGAGTTTATTGCC 59.605 41.667 0.00 0.00 0.00 4.52
2118 2142 6.574759 TCAGATGATGACTTGGACATGTCCT 61.575 44.000 37.92 23.25 40.89 3.85
2214 2244 1.593787 CATCTGGTGGAGTCAGCGT 59.406 57.895 0.00 0.00 43.77 5.07
2260 2290 6.364706 GCCACAGAATATGTAGAAGAATCTCG 59.635 42.308 0.00 0.00 41.41 4.04
2269 2299 1.135257 AGAAGAATCTCGACCAGCACG 60.135 52.381 0.00 0.00 0.00 5.34
2302 2332 8.367660 ACAAGTAGATTCAGTTTAGAGGATGA 57.632 34.615 0.00 0.00 0.00 2.92
2306 2336 9.647918 AGTAGATTCAGTTTAGAGGATGATGTA 57.352 33.333 0.00 0.00 0.00 2.29
2311 2341 5.363868 TCAGTTTAGAGGATGATGTAGTGGG 59.636 44.000 0.00 0.00 0.00 4.61
2327 2357 3.944087 AGTGGGAAGTAATGAAGTGAGC 58.056 45.455 0.00 0.00 0.00 4.26
2359 2389 1.071471 CTGAACTCCCCGTTGCTGT 59.929 57.895 0.00 0.00 35.56 4.40
2389 2419 4.720090 CAGCGATCATTTGATAATCAGGC 58.280 43.478 0.00 0.00 34.37 4.85
2415 2445 6.014156 ACTCAAGACTATGCTCAGTAAACCTT 60.014 38.462 0.00 0.00 0.00 3.50
2417 2447 7.321153 TCAAGACTATGCTCAGTAAACCTTAC 58.679 38.462 0.00 0.00 0.00 2.34
2435 2465 2.533266 ACCTAGAGCATATGCAACCG 57.467 50.000 28.62 14.00 45.16 4.44
2491 2521 1.216122 GAAGACATCCGAGCAGATGC 58.784 55.000 10.34 0.00 46.29 3.91
2520 2550 3.003480 CTCTGCCAGCTACCTAAACAAC 58.997 50.000 0.00 0.00 0.00 3.32
2522 2552 2.744202 CTGCCAGCTACCTAAACAACTG 59.256 50.000 0.00 0.00 0.00 3.16
2557 2587 8.080417 GCAAAATGCAGATGTATATGATTCTGT 58.920 33.333 0.00 0.00 44.26 3.41
2576 2606 7.476540 TTCTGTATTAGCTGAAAGTACCTCA 57.523 36.000 0.00 0.00 35.30 3.86
2578 2608 6.890268 TCTGTATTAGCTGAAAGTACCTCAGA 59.110 38.462 21.22 6.02 42.51 3.27
2580 2610 7.548097 TGTATTAGCTGAAAGTACCTCAGAAG 58.452 38.462 21.22 2.52 42.51 2.85
2582 2612 4.965200 AGCTGAAAGTACCTCAGAAGTT 57.035 40.909 21.22 5.57 42.51 2.66
2605 2635 3.777106 AGCTGATGGAGTGAAAGTCAA 57.223 42.857 0.00 0.00 38.29 3.18
2635 2665 5.406780 GTGTGGAGTCTGTAATCACTGAAAG 59.593 44.000 0.00 0.00 42.29 2.62
2678 2708 2.269241 GACCTTCAAGGGCCTCCG 59.731 66.667 6.46 0.47 37.46 4.63
2683 2752 2.245438 CTTCAAGGGCCTCCGGAGTC 62.245 65.000 29.25 18.21 38.33 3.36
2690 2759 2.960688 GCCTCCGGAGTCTTGCCTT 61.961 63.158 29.25 0.00 0.00 4.35
2749 2818 3.365264 GCTGCTGAAATTGACGATGTTGA 60.365 43.478 0.00 0.00 0.00 3.18
2790 2859 9.031360 CATCTCATTGCCAATCAATTTTAGAAG 57.969 33.333 0.00 0.00 42.48 2.85
2798 2867 7.037438 GCCAATCAATTTTAGAAGCTTCATCA 58.963 34.615 27.57 10.05 0.00 3.07
2811 2880 5.426689 AGCTTCATCAGATGGTGAACTTA 57.573 39.130 10.67 0.00 39.19 2.24
2812 2881 5.181748 AGCTTCATCAGATGGTGAACTTAC 58.818 41.667 10.67 0.00 39.19 2.34
2823 2892 3.071479 GGTGAACTTACGGAGCAATCAA 58.929 45.455 0.00 0.00 0.00 2.57
2836 2905 4.378874 GGAGCAATCAAAGTCTGTGCTAAC 60.379 45.833 0.00 0.00 45.24 2.34
2854 2923 9.719355 TGTGCTAACTGATTCTAATCTACAAAA 57.281 29.630 4.45 0.00 36.39 2.44
2884 2953 5.415701 AGTTAGCAAGTGTCCATAACAATGG 59.584 40.000 0.00 0.00 40.31 3.16
2886 2955 2.493278 GCAAGTGTCCATAACAATGGCT 59.507 45.455 0.00 0.00 46.95 4.75
2890 2959 3.010584 AGTGTCCATAACAATGGCTCCTT 59.989 43.478 0.00 0.00 40.31 3.36
2891 2960 3.378427 GTGTCCATAACAATGGCTCCTTC 59.622 47.826 0.00 0.00 40.31 3.46
2892 2961 2.952310 GTCCATAACAATGGCTCCTTCC 59.048 50.000 0.00 0.00 41.43 3.46
2957 3026 7.429374 AGTGGAAGAACTATCAGATGATGAA 57.571 36.000 5.58 0.00 42.53 2.57
3044 3113 4.460948 AGCAATCAACCCAAATGATGAC 57.539 40.909 0.00 0.00 37.58 3.06
3158 3227 5.567430 AGGGGTAAAATTGTAGAACTCACC 58.433 41.667 0.00 0.00 0.00 4.02
3250 3319 4.534103 AGGTCAGCTAGTGAGAAGGATTTT 59.466 41.667 0.00 0.00 35.13 1.82
3344 3413 6.072508 GGCATCAAGATACACAAGACAAGAAA 60.073 38.462 0.00 0.00 0.00 2.52
3446 3515 3.685139 TTGGTTGGTGCTTTTGAAACA 57.315 38.095 0.00 0.00 0.00 2.83
3554 3623 5.483937 ACGGGATGAGCCATTGTAGATTATA 59.516 40.000 0.00 0.00 38.95 0.98
3660 3729 8.669243 AGTGAAGAGTATTTTTGTATAGCTTGC 58.331 33.333 0.00 0.00 0.00 4.01
3677 3746 3.373020 GCGTGTTGCATCTCTTGTG 57.627 52.632 0.00 0.00 45.45 3.33
3827 3896 4.141846 TGTGCTTTTGTTGGCTTGGATTTA 60.142 37.500 0.00 0.00 0.00 1.40
3828 3897 4.211164 GTGCTTTTGTTGGCTTGGATTTAC 59.789 41.667 0.00 0.00 0.00 2.01
3966 4039 0.391263 GGGGAGCTCCTAAACGTGTG 60.391 60.000 31.36 0.00 35.95 3.82
4032 4105 4.466827 AGATGCATGCACAGATAATTCCA 58.533 39.130 25.37 0.00 0.00 3.53
4067 4140 3.888930 TCATCCACACCCTTCAAACTTTC 59.111 43.478 0.00 0.00 0.00 2.62
4135 4208 8.807118 ACTCTACACTCTTATCACTCATCAAAA 58.193 33.333 0.00 0.00 0.00 2.44
4188 4261 5.675684 TGGCTGTTGTGAGACTTATATCA 57.324 39.130 0.00 0.00 0.00 2.15
4199 4272 8.932945 GTGAGACTTATATCACATTCAAGTCA 57.067 34.615 13.46 0.00 44.86 3.41
4200 4273 9.539825 GTGAGACTTATATCACATTCAAGTCAT 57.460 33.333 13.46 1.58 44.86 3.06
4206 4279 2.076100 TCACATTCAAGTCATGCCGTC 58.924 47.619 0.00 0.00 0.00 4.79
4399 4472 4.365514 TTTCCTGATTGTACTCTGCCAA 57.634 40.909 0.00 0.00 0.00 4.52
4473 4546 4.023291 GTTCCTTCAGCCCCATCATTTTA 58.977 43.478 0.00 0.00 0.00 1.52
4520 4593 7.876582 TCATGATAATGATTTGGTTTTGCACAA 59.123 29.630 0.00 0.00 0.00 3.33
4532 4605 9.566432 TTTGGTTTTGCACAAAAGGATTATTAT 57.434 25.926 8.73 0.00 40.53 1.28
4754 4836 4.212636 CCTAAATTCGGCGGTTATGTTAGG 59.787 45.833 7.21 11.77 32.71 2.69
4761 4843 2.159000 GGCGGTTATGTTAGGTGTAGCT 60.159 50.000 0.00 0.00 0.00 3.32
4774 4856 7.339212 TGTTAGGTGTAGCTGCATCAAATAATT 59.661 33.333 17.82 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.300792 TGATCCAACTCCAAAAACCAACTAC 59.699 40.000 0.00 0.00 0.00 2.73
1 2 5.450453 TGATCCAACTCCAAAAACCAACTA 58.550 37.500 0.00 0.00 0.00 2.24
2 3 4.285863 TGATCCAACTCCAAAAACCAACT 58.714 39.130 0.00 0.00 0.00 3.16
3 4 4.664150 TGATCCAACTCCAAAAACCAAC 57.336 40.909 0.00 0.00 0.00 3.77
4 5 5.017294 GTTGATCCAACTCCAAAAACCAA 57.983 39.130 2.85 0.00 40.73 3.67
5 6 4.664150 GTTGATCCAACTCCAAAAACCA 57.336 40.909 2.85 0.00 40.73 3.67
35 36 8.467598 GTTCAACTGTCCATGTCTAATAGTAGA 58.532 37.037 0.00 0.00 33.77 2.59
39 40 7.604164 ACAAGTTCAACTGTCCATGTCTAATAG 59.396 37.037 0.00 0.00 0.00 1.73
41 42 6.299141 ACAAGTTCAACTGTCCATGTCTAAT 58.701 36.000 0.00 0.00 0.00 1.73
66 67 8.773033 ATATAACAGAAGGGCAATCAAGAATT 57.227 30.769 0.00 0.00 0.00 2.17
68 69 7.345691 TGATATAACAGAAGGGCAATCAAGAA 58.654 34.615 0.00 0.00 0.00 2.52
154 162 9.277783 AGAAAAGGACGATCATAAAGATATTGG 57.722 33.333 0.00 0.00 37.00 3.16
238 253 8.159344 ACTAGCTTGCACTATCATTTATTTCC 57.841 34.615 0.00 0.00 0.00 3.13
312 327 7.040271 TGGCATCAATAATGTCAATATCCACTG 60.040 37.037 0.00 0.00 46.79 3.66
349 364 1.527433 GCCTGAAAGTGCAAGGGGAC 61.527 60.000 3.61 0.00 35.26 4.46
379 394 2.435372 TCCAAATCCAATTCCCGAGG 57.565 50.000 0.00 0.00 0.00 4.63
411 426 6.558771 TGTTCACACCTCTGACAATAATTG 57.441 37.500 0.00 0.00 0.00 2.32
416 431 3.006859 TCGATGTTCACACCTCTGACAAT 59.993 43.478 0.00 0.00 0.00 2.71
467 482 2.103771 CACATGAGTAGCAGGGTAGCAT 59.896 50.000 0.00 0.00 36.85 3.79
468 483 1.482182 CACATGAGTAGCAGGGTAGCA 59.518 52.381 0.00 0.00 36.85 3.49
469 484 1.757118 TCACATGAGTAGCAGGGTAGC 59.243 52.381 0.00 0.00 31.20 3.58
470 485 2.223595 CGTCACATGAGTAGCAGGGTAG 60.224 54.545 0.00 0.00 31.20 3.18
471 486 1.749063 CGTCACATGAGTAGCAGGGTA 59.251 52.381 0.00 0.00 31.20 3.69
472 487 0.532573 CGTCACATGAGTAGCAGGGT 59.467 55.000 0.00 0.00 31.20 4.34
473 488 0.179100 CCGTCACATGAGTAGCAGGG 60.179 60.000 0.00 0.00 31.20 4.45
474 489 0.807667 GCCGTCACATGAGTAGCAGG 60.808 60.000 0.00 0.00 0.00 4.85
475 490 1.142185 CGCCGTCACATGAGTAGCAG 61.142 60.000 0.00 0.00 0.00 4.24
595 610 1.067974 GTTGTTGGGGGCAAACAGTAC 59.932 52.381 0.00 0.00 38.67 2.73
708 723 1.138266 TCCTAACCGCTTACTGGCATC 59.862 52.381 0.00 0.00 0.00 3.91
725 740 1.730501 CATGTGTGCGAGTTGATCCT 58.269 50.000 0.00 0.00 0.00 3.24
787 802 2.017782 CTGCACGCTCTAGAGTAAGGA 58.982 52.381 20.75 10.72 0.00 3.36
863 884 4.085357 AGCATCACAGAACTGTACCAAA 57.915 40.909 7.15 0.00 42.83 3.28
864 885 3.769739 AGCATCACAGAACTGTACCAA 57.230 42.857 7.15 0.00 42.83 3.67
921 945 3.576078 ACCACATCCAAAGAGTCAACA 57.424 42.857 0.00 0.00 0.00 3.33
1047 1071 3.917760 GGACATCGAGGCCTCCCG 61.918 72.222 27.20 17.37 44.70 5.14
1145 1169 0.377554 AGCGTGATACCGTCTTCTCG 59.622 55.000 0.00 0.00 33.37 4.04
1347 1371 8.396390 TGATATACTCGACTTGACTAGTGAAAC 58.604 37.037 0.00 0.00 37.17 2.78
1428 1452 3.244561 ACCAAGTGTTCCGATGATTCAGT 60.245 43.478 0.00 0.00 0.00 3.41
1432 1456 2.618045 GGGACCAAGTGTTCCGATGATT 60.618 50.000 0.00 0.00 31.15 2.57
1523 1547 2.093447 CGGATTAGCCAAAGTCCTCTGT 60.093 50.000 0.00 0.00 35.94 3.41
1544 1568 2.797074 GTACTCCGCTGGAATACCTC 57.203 55.000 5.31 0.00 29.30 3.85
1595 1619 3.008594 TCTCTGGCAATTTCGAACCCTTA 59.991 43.478 0.00 0.00 0.00 2.69
1607 1631 3.433314 CCTGCAGTATCTTCTCTGGCAAT 60.433 47.826 13.81 0.00 32.94 3.56
1621 1645 4.997395 CAGTTCTAGCTTTTTCCTGCAGTA 59.003 41.667 13.81 0.00 0.00 2.74
1654 1678 1.151777 CGGTTGCTTGACAGTCGTGT 61.152 55.000 0.00 0.00 40.71 4.49
1658 1682 2.480845 ACTAACGGTTGCTTGACAGTC 58.519 47.619 3.07 0.00 0.00 3.51
1714 1738 6.591834 AGATGACACAGGAACTTTCTTAATCG 59.408 38.462 0.00 0.00 34.60 3.34
1828 1852 4.997395 CAGTCTTACCAGTATTGCTTGTGT 59.003 41.667 0.00 0.00 0.00 3.72
1862 1886 1.404391 CTTGCATTGCTGGACCTCATC 59.596 52.381 10.49 0.00 0.00 2.92
1889 1913 1.448540 ATCTGAGCGTTCCTTGCCG 60.449 57.895 0.00 0.00 0.00 5.69
1949 1973 8.944029 ACATCATCTTCTTGTAATTCAACAGAG 58.056 33.333 0.00 0.00 32.18 3.35
2118 2142 3.701040 TCAGATTGGACAGACGATGATGA 59.299 43.478 0.00 0.00 0.00 2.92
2214 2244 5.118990 GGCATGTGAAGATAGTTCTGCTAA 58.881 41.667 0.00 0.00 32.72 3.09
2260 2290 3.181500 ACTTGTTTCTTTTCGTGCTGGTC 60.181 43.478 0.00 0.00 0.00 4.02
2302 2332 6.620877 TCACTTCATTACTTCCCACTACAT 57.379 37.500 0.00 0.00 0.00 2.29
2306 2336 3.617531 CGCTCACTTCATTACTTCCCACT 60.618 47.826 0.00 0.00 0.00 4.00
2311 2341 3.994392 TGGTTCGCTCACTTCATTACTTC 59.006 43.478 0.00 0.00 0.00 3.01
2327 2357 2.996621 GAGTTCAGAGACCAATGGTTCG 59.003 50.000 6.30 3.83 35.25 3.95
2359 2389 4.437772 TCAAATGATCGCTGCAATTCAA 57.562 36.364 0.00 0.00 0.00 2.69
2371 2401 6.872628 TGAGTGCCTGATTATCAAATGATC 57.127 37.500 0.00 0.00 36.05 2.92
2389 2419 5.578727 GGTTTACTGAGCATAGTCTTGAGTG 59.421 44.000 0.00 0.00 32.19 3.51
2415 2445 2.299013 CCGGTTGCATATGCTCTAGGTA 59.701 50.000 27.13 3.32 42.66 3.08
2417 2447 1.344438 TCCGGTTGCATATGCTCTAGG 59.656 52.381 27.13 22.72 42.66 3.02
2435 2465 6.219473 TCGATTATCAGCAGAATTCTTCTCC 58.781 40.000 4.86 0.00 38.11 3.71
2447 2477 2.860136 CGTTGAAGCTCGATTATCAGCA 59.140 45.455 15.19 0.00 38.18 4.41
2448 2478 2.219674 CCGTTGAAGCTCGATTATCAGC 59.780 50.000 8.03 8.03 35.73 4.26
2451 2481 4.299155 TCATCCGTTGAAGCTCGATTATC 58.701 43.478 0.00 0.00 0.00 1.75
2454 2484 2.672961 TCATCCGTTGAAGCTCGATT 57.327 45.000 0.00 0.00 0.00 3.34
2455 2485 2.672961 TTCATCCGTTGAAGCTCGAT 57.327 45.000 0.00 0.00 39.44 3.59
2520 2550 1.415374 GCATTTTGCACAGCTGTCAG 58.585 50.000 18.64 8.25 44.26 3.51
2557 2587 7.719871 ACTTCTGAGGTACTTTCAGCTAATA 57.280 36.000 17.65 3.80 41.55 0.98
2562 2592 4.632153 TCAACTTCTGAGGTACTTTCAGC 58.368 43.478 17.65 0.00 41.55 4.26
2572 2602 3.008330 CCATCAGCTTCAACTTCTGAGG 58.992 50.000 0.00 0.00 39.82 3.86
2576 2606 3.326006 TCACTCCATCAGCTTCAACTTCT 59.674 43.478 0.00 0.00 0.00 2.85
2578 2608 3.777106 TCACTCCATCAGCTTCAACTT 57.223 42.857 0.00 0.00 0.00 2.66
2580 2610 3.817647 ACTTTCACTCCATCAGCTTCAAC 59.182 43.478 0.00 0.00 0.00 3.18
2582 2612 3.071457 TGACTTTCACTCCATCAGCTTCA 59.929 43.478 0.00 0.00 0.00 3.02
2605 2635 4.711846 TGATTACAGACTCCACACTAGCAT 59.288 41.667 0.00 0.00 0.00 3.79
2635 2665 0.399233 AGCTCCCATGTCCTCCCTAC 60.399 60.000 0.00 0.00 0.00 3.18
2638 2668 1.059006 ATGAGCTCCCATGTCCTCCC 61.059 60.000 12.15 0.00 0.00 4.30
2678 2708 1.200948 GTGCAATCAAGGCAAGACTCC 59.799 52.381 0.00 0.00 43.91 3.85
2683 2752 2.163010 CCTGTAGTGCAATCAAGGCAAG 59.837 50.000 0.00 0.00 43.91 4.01
2790 2859 4.033358 CGTAAGTTCACCATCTGATGAAGC 59.967 45.833 18.92 6.35 35.55 3.86
2798 2867 1.899814 TGCTCCGTAAGTTCACCATCT 59.100 47.619 0.00 0.00 0.00 2.90
2811 2880 2.146342 CACAGACTTTGATTGCTCCGT 58.854 47.619 0.00 0.00 0.00 4.69
2812 2881 1.135859 GCACAGACTTTGATTGCTCCG 60.136 52.381 0.00 0.00 0.00 4.63
2823 2892 7.846066 AGATTAGAATCAGTTAGCACAGACTT 58.154 34.615 5.11 0.00 37.89 3.01
2854 2923 4.558226 TGGACACTTGCTAACTCATCAT 57.442 40.909 0.00 0.00 0.00 2.45
2855 2924 4.558226 ATGGACACTTGCTAACTCATCA 57.442 40.909 0.00 0.00 0.00 3.07
2891 2960 5.710513 TTGATTTCAGTTCATCCTGTTGG 57.289 39.130 0.00 0.00 34.02 3.77
2892 2961 6.916440 TCATTGATTTCAGTTCATCCTGTTG 58.084 36.000 0.00 0.00 34.02 3.33
2999 3068 4.940046 TCTCCTTCATCTTCTGCATCAAAC 59.060 41.667 0.00 0.00 0.00 2.93
3158 3227 1.153168 CGGGCCATTACTGTCTGGG 60.153 63.158 4.39 0.45 32.90 4.45
3250 3319 9.627123 CACCATTATTTCTGGTATTCCTCTTAA 57.373 33.333 0.00 0.00 45.23 1.85
3344 3413 1.072159 GAATAGCCCCTGCGCATCT 59.928 57.895 12.24 8.69 44.33 2.90
3446 3515 2.379972 CCGTCCTGGAGAAGTATCACT 58.620 52.381 0.00 0.00 42.00 3.41
3503 3572 7.362401 GCCTTTTCATCTTCATCTTGAGCTAAA 60.362 37.037 0.00 0.00 0.00 1.85
3554 3623 4.570772 GGCGATTCCGTAATATGTGCATAT 59.429 41.667 0.31 0.31 38.24 1.78
3564 3633 5.124776 TGAGAAAATTTGGCGATTCCGTAAT 59.875 36.000 0.00 0.00 37.80 1.89
3660 3729 0.110056 GCCACAAGAGATGCAACACG 60.110 55.000 0.00 0.00 0.00 4.49
3675 3744 2.414161 GGCAAATGTTACTTCTCGCCAC 60.414 50.000 0.00 0.00 38.20 5.01
3677 3746 1.132453 GGGCAAATGTTACTTCTCGCC 59.868 52.381 0.00 0.00 37.57 5.54
3827 3896 9.355215 CAACACTCTTGTATTATAGAACTTCGT 57.645 33.333 0.00 0.00 33.55 3.85
3828 3897 8.808529 CCAACACTCTTGTATTATAGAACTTCG 58.191 37.037 0.00 0.00 33.55 3.79
3966 4039 5.851047 AAGAAAATAAGCATTGCAACAGC 57.149 34.783 15.79 15.79 0.00 4.40
4015 4088 5.766670 AGTACCATGGAATTATCTGTGCATG 59.233 40.000 21.47 0.00 0.00 4.06
4032 4105 4.949856 GGTGTGGATGATGAAAAGTACCAT 59.050 41.667 0.00 0.00 0.00 3.55
4067 4140 7.500720 TGCATTGTATCAGGATCAACATAAG 57.499 36.000 0.00 0.00 0.00 1.73
4161 4234 3.045601 AGTCTCACAACAGCCATGTAC 57.954 47.619 0.00 0.00 39.29 2.90
4188 4261 1.271325 TGGACGGCATGACTTGAATGT 60.271 47.619 0.00 0.00 0.00 2.71
4199 4272 1.529226 TGAAACGAAATGGACGGCAT 58.471 45.000 0.00 0.00 34.93 4.40
4200 4273 1.309950 TTGAAACGAAATGGACGGCA 58.690 45.000 0.00 0.00 34.93 5.69
4206 4279 9.796062 CATTCTACAAAATTTGAAACGAAATGG 57.204 29.630 13.19 0.00 0.00 3.16
4358 4431 7.330208 CAGGAAATGACAAGGATCAACAAAATC 59.670 37.037 0.00 0.00 30.82 2.17
4399 4472 3.748568 GGACAGAAAGAGAGCGAAACAAT 59.251 43.478 0.00 0.00 0.00 2.71
4473 4546 9.346005 TCATGATTCATGATGCAATTAGTTACT 57.654 29.630 22.47 0.00 44.60 2.24
4520 4593 5.327737 TTGCGGGGGTATAATAATCCTTT 57.672 39.130 0.00 0.00 0.00 3.11
4754 4836 6.728200 TGCTAATTATTTGATGCAGCTACAC 58.272 36.000 2.53 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.