Multiple sequence alignment - TraesCS5D01G239500

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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 TraesCS5D01G239500 chr5D 100.000 5576 0 0 1 5576 347436705 347442280 0.000000e+00 10298.0
1 TraesCS5D01G239500 chr5D 89.109 101 10 1 2518 2618 434318227 434318128 2.110000e-24 124.0
2 TraesCS5D01G239500 chr5B 95.818 2678 61 17 2836 5487 403713019 403710367 0.000000e+00 4277.0
3 TraesCS5D01G239500 chr5B 95.208 1106 40 8 1443 2540 403714399 403713299 0.000000e+00 1736.0
4 TraesCS5D01G239500 chr5B 93.540 1130 46 11 173 1286 403716311 403715193 0.000000e+00 1657.0
5 TraesCS5D01G239500 chr5B 97.183 213 6 0 2640 2852 403713247 403713035 1.480000e-95 361.0
6 TraesCS5D01G239500 chr5B 95.699 93 4 0 5484 5576 403710262 403710170 3.480000e-32 150.0
7 TraesCS5D01G239500 chr5A 94.623 2399 88 20 173 2548 444540393 444538013 0.000000e+00 3677.0
8 TraesCS5D01G239500 chr5A 95.409 1895 65 12 3693 5576 444536620 444534737 0.000000e+00 2998.0
9 TraesCS5D01G239500 chr5A 94.304 1071 21 9 2640 3697 444537964 444536921 0.000000e+00 1604.0
10 TraesCS5D01G239500 chr5A 94.366 142 7 1 2 142 444540517 444540376 3.380000e-52 217.0
11 TraesCS5D01G239500 chr3B 97.500 80 2 0 2540 2619 707421676 707421597 2.710000e-28 137.0
12 TraesCS5D01G239500 chr2B 98.701 77 1 0 2542 2618 659492960 659492884 2.710000e-28 137.0
13 TraesCS5D01G239500 chr2B 87.037 54 5 2 2332 2385 556687149 556687200 6.030000e-05 60.2
14 TraesCS5D01G239500 chr4D 96.296 81 3 0 2538 2618 477898786 477898866 3.500000e-27 134.0
15 TraesCS5D01G239500 chr1B 96.341 82 2 1 2538 2618 329484783 329484864 3.500000e-27 134.0
16 TraesCS5D01G239500 chr1B 89.899 99 7 3 2522 2618 586298529 586298626 2.110000e-24 124.0
17 TraesCS5D01G239500 chr1B 91.667 48 2 2 2332 2379 171032872 171032917 1.300000e-06 65.8
18 TraesCS5D01G239500 chr6B 95.238 84 3 1 2535 2618 11189804 11189886 1.260000e-26 132.0
19 TraesCS5D01G239500 chr3D 98.611 72 1 0 2547 2618 288436906 288436835 1.630000e-25 128.0
20 TraesCS5D01G239500 chr4A 90.426 94 9 0 2525 2618 617898106 617898199 2.110000e-24 124.0
21 TraesCS5D01G239500 chr4A 95.349 43 1 1 2332 2374 562284096 562284055 3.610000e-07 67.6
22 TraesCS5D01G239500 chr2D 89.091 55 4 2 2332 2385 109070239 109070292 3.610000e-07 67.6
23 TraesCS5D01G239500 chr7D 84.127 63 6 4 2332 2393 465340526 465340585 2.170000e-04 58.4
24 TraesCS5D01G239500 chr7D 85.714 56 5 3 2332 2386 9150471 9150418 7.800000e-04 56.5


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 TraesCS5D01G239500 chr5D 347436705 347442280 5575 False 10298.0 10298 100.0000 1 5576 1 chr5D.!!$F1 5575
1 TraesCS5D01G239500 chr5B 403710170 403716311 6141 True 1636.2 4277 95.4896 173 5576 5 chr5B.!!$R1 5403
2 TraesCS5D01G239500 chr5A 444534737 444540517 5780 True 2124.0 3677 94.6755 2 5576 4 chr5A.!!$R1 5574

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
791 794 1.000486 AGGCGTCTTGCTCCTAGGA 60.000 57.895 11.98 11.98 45.43 2.94 F
2069 2749 0.179000 CCTTCCGACCATTCCCTGAG 59.821 60.000 0.00 0.00 0.00 3.35 F
2544 3234 1.077005 AGAGAGAGGTCAGGCTCTGTT 59.923 52.381 0.00 0.00 41.33 3.16 F
3304 4043 0.179043 TTTACTTGCCGGCTGTCACA 60.179 50.000 29.70 8.88 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2689 3379 1.067213 CGGGGTGCAAATTAAAGGTGG 60.067 52.381 0.00 0.0 0.0 4.61 R
3281 4020 0.666374 ACAGCCGGCAAGTAAAACAC 59.334 50.000 31.54 0.0 0.0 3.32 R
4258 5308 0.951558 AACACCTGCGGAACATTCAC 59.048 50.000 0.00 0.0 0.0 3.18 R
4879 5937 1.140161 CATCCATTGCCCACTTGCG 59.860 57.895 0.00 0.0 0.0 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
28 29 8.704849 ATGTAACTACATCTCAAGCTCTAGAT 57.295 34.615 5.20 5.20 42.96 1.98
94 96 8.206325 ACAGATAAGATGCTCAAAACATACTG 57.794 34.615 0.00 0.00 0.00 2.74
99 101 6.882610 AGATGCTCAAAACATACTGACAAA 57.117 33.333 0.00 0.00 0.00 2.83
139 141 9.769677 AAATGGGATTCATGATGATATGATTCT 57.230 29.630 0.00 0.00 37.49 2.40
140 142 9.769677 AATGGGATTCATGATGATATGATTCTT 57.230 29.630 0.00 0.00 37.49 2.52
141 143 9.769677 ATGGGATTCATGATGATATGATTCTTT 57.230 29.630 0.00 0.00 37.49 2.52
142 144 9.596308 TGGGATTCATGATGATATGATTCTTTT 57.404 29.630 0.00 0.00 37.49 2.27
209 211 1.901591 AAGCACCATGTTCTCCACTG 58.098 50.000 0.00 0.00 0.00 3.66
337 339 6.680874 ACCAGACTATCGAAACTACTAGTG 57.319 41.667 5.39 0.00 0.00 2.74
380 382 1.459592 GGTTGATCTGACGTGAAACCG 59.540 52.381 0.00 0.00 0.00 4.44
509 511 1.131883 CAAGCTCAAATCAGAAGGCCG 59.868 52.381 0.00 0.00 0.00 6.13
538 540 1.129998 GCGATATGGATCATGTGCTGC 59.870 52.381 0.00 0.00 31.78 5.25
553 555 3.345737 CTGCAAGCTATCGTTCCGA 57.654 52.632 0.00 0.00 41.13 4.55
787 790 3.764466 CGGAGGCGTCTTGCTCCT 61.764 66.667 6.34 0.00 45.43 3.69
788 791 2.415608 CGGAGGCGTCTTGCTCCTA 61.416 63.158 6.34 0.00 45.43 2.94
789 792 1.439644 GGAGGCGTCTTGCTCCTAG 59.560 63.158 6.34 0.00 45.43 3.02
790 793 1.439644 GAGGCGTCTTGCTCCTAGG 59.560 63.158 0.82 0.82 45.43 3.02
791 794 1.000486 AGGCGTCTTGCTCCTAGGA 60.000 57.895 11.98 11.98 45.43 2.94
792 795 1.040339 AGGCGTCTTGCTCCTAGGAG 61.040 60.000 31.35 31.35 45.43 3.69
804 807 2.832733 CTCCTAGGAGAAAAGAACGGGT 59.167 50.000 31.97 0.00 44.53 5.28
807 810 2.256117 AGGAGAAAAGAACGGGTGTG 57.744 50.000 0.00 0.00 0.00 3.82
821 824 1.408702 GGGTGTGTGTCACTTTGCAAT 59.591 47.619 0.00 0.00 45.50 3.56
831 834 1.415659 CACTTTGCAATTTGGACCCCA 59.584 47.619 0.00 0.00 0.00 4.96
975 993 1.375853 GCGAGCAGAGAGAGCAGAGA 61.376 60.000 0.00 0.00 0.00 3.10
1081 1099 1.515020 CTCCTCCTCTCCAAGCACG 59.485 63.158 0.00 0.00 0.00 5.34
1236 1254 1.277579 TATCCTACAACAACCCGCCA 58.722 50.000 0.00 0.00 0.00 5.69
1348 1394 7.080724 GTGCAGAATTTAGGTTCTTGAAAGAG 58.919 38.462 0.00 0.00 36.33 2.85
1409 2086 4.362279 CATCAATAGAAAAATGTGGCCGG 58.638 43.478 0.00 0.00 0.00 6.13
1422 2099 2.258286 GCCGGTGCATTGGTGAAC 59.742 61.111 1.90 0.00 37.47 3.18
1423 2100 2.268076 GCCGGTGCATTGGTGAACT 61.268 57.895 1.90 0.00 34.05 3.01
1505 2182 6.176183 ACTGTGAATATTCCTGTCTTTCTGG 58.824 40.000 12.90 0.00 36.63 3.86
1574 2251 2.125673 ATTCGAACGAGTGGCCCG 60.126 61.111 0.00 0.00 0.00 6.13
1618 2295 0.668535 GGGAGTGGCAAACTGTTGTC 59.331 55.000 0.00 0.00 40.07 3.18
1751 2431 3.057876 TGCAGTTTTAGGCATGGTTAACG 60.058 43.478 0.00 0.00 34.58 3.18
1908 2588 7.504574 TCGGACAACTGTATGGATCTATTCTTA 59.495 37.037 0.00 0.00 0.00 2.10
1911 2591 9.685828 GACAACTGTATGGATCTATTCTTACTC 57.314 37.037 0.00 0.00 0.00 2.59
1940 2620 7.732996 ACTTTTTCTGGTAGTGTGTACATACT 58.267 34.615 25.81 25.81 36.69 2.12
1971 2651 9.374838 GATGGATATTGCCCATTTCAAAATATC 57.625 33.333 0.00 0.00 43.96 1.63
2069 2749 0.179000 CCTTCCGACCATTCCCTGAG 59.821 60.000 0.00 0.00 0.00 3.35
2079 2759 2.776536 CCATTCCCTGAGGATGTCTTCT 59.223 50.000 0.00 0.00 43.54 2.85
2096 2776 3.056821 TCTTCTGTTACGGTCAGGACATG 60.057 47.826 1.41 0.00 34.15 3.21
2173 2854 7.119699 TGGTGCATTCTTTCTTGTAGACTAATG 59.880 37.037 0.00 0.00 0.00 1.90
2243 2924 9.462606 AGTTTCCTTGTAACTATGAATTTAGGG 57.537 33.333 0.00 0.00 34.22 3.53
2370 3060 4.993905 AGGCTTTGTTGTTGTTGAAGTAC 58.006 39.130 0.00 0.00 0.00 2.73
2371 3061 4.461081 AGGCTTTGTTGTTGTTGAAGTACA 59.539 37.500 0.00 0.00 0.00 2.90
2544 3234 1.077005 AGAGAGAGGTCAGGCTCTGTT 59.923 52.381 0.00 0.00 41.33 3.16
2548 3238 4.211920 AGAGAGGTCAGGCTCTGTTATAC 58.788 47.826 0.00 0.00 39.86 1.47
2549 3239 4.079443 AGAGAGGTCAGGCTCTGTTATACT 60.079 45.833 0.00 0.00 39.86 2.12
2551 3241 3.301274 AGGTCAGGCTCTGTTATACTCC 58.699 50.000 2.68 0.00 32.61 3.85
2552 3242 2.365941 GGTCAGGCTCTGTTATACTCCC 59.634 54.545 2.68 0.00 32.61 4.30
2554 3244 3.319689 GTCAGGCTCTGTTATACTCCCTC 59.680 52.174 2.68 0.00 32.61 4.30
2555 3245 2.630580 CAGGCTCTGTTATACTCCCTCC 59.369 54.545 0.00 0.00 0.00 4.30
2556 3246 2.247635 AGGCTCTGTTATACTCCCTCCA 59.752 50.000 0.00 0.00 0.00 3.86
2557 3247 3.116551 AGGCTCTGTTATACTCCCTCCAT 60.117 47.826 0.00 0.00 0.00 3.41
2558 3248 3.648545 GGCTCTGTTATACTCCCTCCATT 59.351 47.826 0.00 0.00 0.00 3.16
2559 3249 4.262678 GGCTCTGTTATACTCCCTCCATTC 60.263 50.000 0.00 0.00 0.00 2.67
2560 3250 4.262678 GCTCTGTTATACTCCCTCCATTCC 60.263 50.000 0.00 0.00 0.00 3.01
2561 3251 5.151454 CTCTGTTATACTCCCTCCATTCCT 58.849 45.833 0.00 0.00 0.00 3.36
2563 3253 6.689561 TCTGTTATACTCCCTCCATTCCTAA 58.310 40.000 0.00 0.00 0.00 2.69
2565 3255 7.794683 TCTGTTATACTCCCTCCATTCCTAAAT 59.205 37.037 0.00 0.00 0.00 1.40
2566 3256 9.101325 CTGTTATACTCCCTCCATTCCTAAATA 57.899 37.037 0.00 0.00 0.00 1.40
2572 3262 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
2573 3263 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
2575 3265 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
2577 3267 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
2593 3283 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2595 3285 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2596 3286 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2597 3287 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2598 3288 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2599 3289 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
2600 3290 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
2601 3291 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
2603 3293 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2604 3294 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2605 3295 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2606 3296 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2607 3297 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2608 3298 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
2609 3299 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2610 3300 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2611 3301 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2612 3302 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
2613 3303 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
2614 3304 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
2615 3305 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2616 3306 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2617 3307 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2618 3308 5.109903 ACTACATACGGAGCAAAATGAGTC 58.890 41.667 0.00 0.00 0.00 3.36
2619 3309 4.207891 ACATACGGAGCAAAATGAGTCT 57.792 40.909 0.00 0.00 0.00 3.24
2620 3310 4.579869 ACATACGGAGCAAAATGAGTCTT 58.420 39.130 0.00 0.00 0.00 3.01
2621 3311 5.003804 ACATACGGAGCAAAATGAGTCTTT 58.996 37.500 0.00 0.00 0.00 2.52
2622 3312 6.170506 ACATACGGAGCAAAATGAGTCTTTA 58.829 36.000 0.00 0.00 0.00 1.85
2623 3313 6.092259 ACATACGGAGCAAAATGAGTCTTTAC 59.908 38.462 0.00 0.00 0.00 2.01
2624 3314 4.385825 ACGGAGCAAAATGAGTCTTTACA 58.614 39.130 0.00 0.00 0.00 2.41
2625 3315 4.452455 ACGGAGCAAAATGAGTCTTTACAG 59.548 41.667 0.00 0.00 0.00 2.74
2626 3316 4.690748 CGGAGCAAAATGAGTCTTTACAGA 59.309 41.667 0.00 0.00 0.00 3.41
2689 3379 6.126568 GACTTACACTAGTCTGACTCCATC 57.873 45.833 14.62 0.00 41.07 3.51
2973 3702 9.193806 TCCTATACTTTGGAGTTAGTACGAAAT 57.806 33.333 0.00 0.00 37.33 2.17
3219 3957 4.690748 TCTTTGTTATTGCAGAAGGACTCG 59.309 41.667 0.00 0.00 0.00 4.18
3281 4020 4.569966 CAGGTAGCATCTCACTAGCTTTTG 59.430 45.833 0.00 0.00 43.97 2.44
3302 4041 0.948678 GTTTTACTTGCCGGCTGTCA 59.051 50.000 29.70 14.94 0.00 3.58
3303 4042 0.948678 TTTTACTTGCCGGCTGTCAC 59.051 50.000 29.70 0.00 0.00 3.67
3304 4043 0.179043 TTTACTTGCCGGCTGTCACA 60.179 50.000 29.70 8.88 0.00 3.58
3305 4044 0.882927 TTACTTGCCGGCTGTCACAC 60.883 55.000 29.70 0.00 0.00 3.82
3657 4400 9.271828 GATTCAAAACTAATGTGGAAAACCAAT 57.728 29.630 0.00 0.00 0.00 3.16
3722 4770 3.056891 CCGACAAACTTTGCCATATGGTT 60.057 43.478 22.79 6.18 37.57 3.67
3735 4783 4.261322 GCCATATGGTTCATGTTGCTGTAG 60.261 45.833 22.79 0.00 37.57 2.74
3959 5008 4.081309 TGAATTAGTTCCCAGTTAGTCCCG 60.081 45.833 0.00 0.00 33.26 5.14
3994 5044 7.235812 GGATCAGATTAGGTGGTAGTTATCCTT 59.764 40.741 0.00 0.00 0.00 3.36
3997 5047 9.670442 TCAGATTAGGTGGTAGTTATCCTTATT 57.330 33.333 0.00 0.00 0.00 1.40
4692 5746 6.634837 CGACTGCTTAGTGTATGATCTTACTG 59.365 42.308 17.02 6.28 0.00 2.74
4771 5825 5.193679 GGTTCTTTCCATACTACTGCCAAT 58.806 41.667 0.00 0.00 0.00 3.16
4774 5828 6.313519 TCTTTCCATACTACTGCCAATCTT 57.686 37.500 0.00 0.00 0.00 2.40
4790 5844 4.475944 CAATCTTCGTGGTGGAAAATGTC 58.524 43.478 0.00 0.00 0.00 3.06
4834 5888 6.935741 ACGGTTATTGCTATAAGAAATGCA 57.064 33.333 0.56 0.00 0.00 3.96
4849 5903 7.661127 AAGAAATGCATTGTACTTGTACGTA 57.339 32.000 13.82 0.00 0.00 3.57
4869 5923 1.891150 AGCTTTCAGGTTGGCTCAATG 59.109 47.619 0.00 0.00 0.00 2.82
4879 5937 3.379688 GGTTGGCTCAATGATTCTTCCTC 59.620 47.826 0.00 0.00 0.00 3.71
5063 6125 2.219458 CATGCTCTGGCTTGTCCTATG 58.781 52.381 0.00 0.00 38.36 2.23
5159 6221 1.598701 GGCCAGTCCATTTCAGCCAC 61.599 60.000 0.00 0.00 40.20 5.01
5160 6222 0.895100 GCCAGTCCATTTCAGCCACA 60.895 55.000 0.00 0.00 0.00 4.17
5161 6223 0.883833 CCAGTCCATTTCAGCCACAC 59.116 55.000 0.00 0.00 0.00 3.82
5324 6389 9.435688 GTTGTAGGAAAAGGAATGCATAAAAAT 57.564 29.630 0.00 0.00 0.00 1.82
5459 6524 9.358872 GTTAAGATGAAATGGTCAAATTTCCTC 57.641 33.333 7.08 6.91 43.13 3.71
5461 6526 7.401955 AGATGAAATGGTCAAATTTCCTCTC 57.598 36.000 10.01 4.74 42.75 3.20
5481 6546 4.991056 TCTCACATTTCACAGTAACTCAGC 59.009 41.667 0.00 0.00 0.00 4.26
5490 6663 7.462571 TTCACAGTAACTCAGCAAGTATCTA 57.537 36.000 0.00 0.00 37.17 1.98
5547 6720 1.344953 TGTAAGCTCCCCGATGGCAT 61.345 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.799534 GTGCATGTTCGCTGGCAATC 60.800 55.000 0.00 0.00 38.10 2.67
28 29 1.525718 ATGTGCATGTTCGCTGGCAA 61.526 50.000 0.00 0.00 38.10 4.52
83 85 9.528018 AACCTAATGTTTTGTCAGTATGTTTTG 57.472 29.630 0.00 0.00 32.37 2.44
94 96 8.145122 TCCCATTTTGTAACCTAATGTTTTGTC 58.855 33.333 0.00 0.00 38.42 3.18
99 101 8.429237 TGAATCCCATTTTGTAACCTAATGTT 57.571 30.769 0.00 0.00 41.11 2.71
170 172 9.837525 GGTGCTTAAAGAATCATATCATCATTC 57.162 33.333 0.00 0.00 0.00 2.67
171 173 9.358406 TGGTGCTTAAAGAATCATATCATCATT 57.642 29.630 0.00 0.00 0.00 2.57
183 185 5.183904 GTGGAGAACATGGTGCTTAAAGAAT 59.816 40.000 0.00 0.00 0.00 2.40
209 211 2.018542 TGTTAGACTTGTATGCGGCC 57.981 50.000 0.00 0.00 0.00 6.13
337 339 6.541641 ACCTTCAGAGCTTGATGATAATTGTC 59.458 38.462 11.01 0.00 35.27 3.18
380 382 4.965119 AAATTTGGCTGACGTTAGGATC 57.035 40.909 9.62 0.00 0.00 3.36
553 555 4.082523 CACACGCCCCTCCGTCAT 62.083 66.667 0.00 0.00 39.83 3.06
777 780 4.810191 TCTTTTCTCCTAGGAGCAAGAC 57.190 45.455 31.00 0.00 41.71 3.01
780 783 3.306780 CCGTTCTTTTCTCCTAGGAGCAA 60.307 47.826 30.99 24.88 41.71 3.91
781 784 2.233922 CCGTTCTTTTCTCCTAGGAGCA 59.766 50.000 30.99 20.33 41.71 4.26
782 785 2.418884 CCCGTTCTTTTCTCCTAGGAGC 60.419 54.545 30.99 15.59 41.71 4.70
783 786 2.832733 ACCCGTTCTTTTCTCCTAGGAG 59.167 50.000 30.15 30.15 43.21 3.69
785 788 2.302157 ACACCCGTTCTTTTCTCCTAGG 59.698 50.000 0.82 0.82 0.00 3.02
786 789 3.244112 ACACACCCGTTCTTTTCTCCTAG 60.244 47.826 0.00 0.00 0.00 3.02
787 790 2.701951 ACACACCCGTTCTTTTCTCCTA 59.298 45.455 0.00 0.00 0.00 2.94
788 791 1.489230 ACACACCCGTTCTTTTCTCCT 59.511 47.619 0.00 0.00 0.00 3.69
789 792 1.602377 CACACACCCGTTCTTTTCTCC 59.398 52.381 0.00 0.00 0.00 3.71
790 793 2.285977 ACACACACCCGTTCTTTTCTC 58.714 47.619 0.00 0.00 0.00 2.87
791 794 2.285977 GACACACACCCGTTCTTTTCT 58.714 47.619 0.00 0.00 0.00 2.52
792 795 2.011222 TGACACACACCCGTTCTTTTC 58.989 47.619 0.00 0.00 0.00 2.29
804 807 3.194329 TCCAAATTGCAAAGTGACACACA 59.806 39.130 1.71 0.00 36.74 3.72
807 810 3.123050 GGTCCAAATTGCAAAGTGACAC 58.877 45.455 1.71 0.00 0.00 3.67
821 824 3.327172 TGTCGTATAACTTGGGGTCCAAA 59.673 43.478 0.84 0.00 43.44 3.28
831 834 8.445493 CCCTTTCGTTTATTTGTCGTATAACTT 58.555 33.333 0.00 0.00 0.00 2.66
1085 1103 1.989508 CTTGGGGTGGGAAATGGCC 60.990 63.158 0.00 0.00 0.00 5.36
1348 1394 6.531240 TCAAATTTCAACACAAGTTCTTCTGC 59.469 34.615 0.00 0.00 35.28 4.26
1409 2086 5.824904 AGATTGATAGTTCACCAATGCAC 57.175 39.130 0.00 0.00 31.40 4.57
1505 2182 0.242017 GATTGTCAGCAGGGCAACAC 59.758 55.000 0.00 0.00 39.74 3.32
1574 2251 1.595382 CATCCCATCGGCGAAGGAC 60.595 63.158 30.69 0.00 0.00 3.85
1679 2356 7.020010 GCATGCATATACAAAGATACTTCTGC 58.980 38.462 14.21 0.00 30.72 4.26
1680 2357 8.228464 CAGCATGCATATACAAAGATACTTCTG 58.772 37.037 21.98 0.00 30.72 3.02
1908 2588 6.157211 CACACTACCAGAAAAAGTATCGAGT 58.843 40.000 0.00 0.00 0.00 4.18
1911 2591 6.864685 TGTACACACTACCAGAAAAAGTATCG 59.135 38.462 0.00 0.00 0.00 2.92
1940 2620 6.380414 TGAAATGGGCAATATCCATCCTTTA 58.620 36.000 0.00 0.00 43.61 1.85
2069 2749 3.512680 CTGACCGTAACAGAAGACATCC 58.487 50.000 0.00 0.00 37.54 3.51
2079 2759 3.096852 AGATCATGTCCTGACCGTAACA 58.903 45.455 0.00 0.00 36.48 2.41
2173 2854 4.142600 ACAGCACTTCTGACAGTTGAAAAC 60.143 41.667 1.59 0.00 46.23 2.43
2243 2924 5.166398 CAGCATTCATGAAAAAGAGGAACC 58.834 41.667 13.09 0.00 0.00 3.62
2370 3060 9.258826 TGAAAGGTCAAAATTACAATGTCAATG 57.741 29.630 0.00 0.00 0.00 2.82
2371 3061 9.480053 CTGAAAGGTCAAAATTACAATGTCAAT 57.520 29.630 0.00 0.00 31.88 2.57
2548 3238 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
2549 3239 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
2551 3241 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
2570 3260 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
2572 3262 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
2573 3263 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
2575 3265 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
2577 3267 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2578 3268 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2579 3269 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2581 3271 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2582 3272 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2583 3273 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2585 3275 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
2586 3276 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
2588 3278 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2589 3279 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2592 3282 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2593 3283 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2595 3285 5.086104 ACTCATTTTGCTCCGTATGTAGT 57.914 39.130 0.00 0.00 0.00 2.73
2596 3286 5.352284 AGACTCATTTTGCTCCGTATGTAG 58.648 41.667 0.00 0.00 0.00 2.74
2597 3287 5.339008 AGACTCATTTTGCTCCGTATGTA 57.661 39.130 0.00 0.00 0.00 2.29
2598 3288 4.207891 AGACTCATTTTGCTCCGTATGT 57.792 40.909 0.00 0.00 0.00 2.29
2599 3289 5.551760 AAAGACTCATTTTGCTCCGTATG 57.448 39.130 0.00 0.00 0.00 2.39
2600 3290 6.170506 TGTAAAGACTCATTTTGCTCCGTAT 58.829 36.000 0.00 0.00 0.00 3.06
2601 3291 5.543714 TGTAAAGACTCATTTTGCTCCGTA 58.456 37.500 0.00 0.00 0.00 4.02
2602 3292 4.385825 TGTAAAGACTCATTTTGCTCCGT 58.614 39.130 0.00 0.00 0.00 4.69
2603 3293 4.690748 TCTGTAAAGACTCATTTTGCTCCG 59.309 41.667 0.00 0.00 0.00 4.63
2604 3294 5.703130 AGTCTGTAAAGACTCATTTTGCTCC 59.297 40.000 9.98 0.00 45.09 4.70
2605 3295 6.793492 AGTCTGTAAAGACTCATTTTGCTC 57.207 37.500 9.98 0.00 45.09 4.26
2625 3315 5.415077 TGTAAGGAGCAGACTAGTGTAAGTC 59.585 44.000 0.00 0.00 45.20 3.01
2626 3316 5.183522 GTGTAAGGAGCAGACTAGTGTAAGT 59.816 44.000 0.00 0.00 0.00 2.24
2627 3317 5.416326 AGTGTAAGGAGCAGACTAGTGTAAG 59.584 44.000 0.00 0.00 0.00 2.34
2628 3318 5.322754 AGTGTAAGGAGCAGACTAGTGTAA 58.677 41.667 0.00 0.00 0.00 2.41
2629 3319 4.919793 AGTGTAAGGAGCAGACTAGTGTA 58.080 43.478 0.00 0.00 0.00 2.90
2630 3320 3.768878 AGTGTAAGGAGCAGACTAGTGT 58.231 45.455 0.00 0.00 0.00 3.55
2631 3321 4.461081 AGAAGTGTAAGGAGCAGACTAGTG 59.539 45.833 0.00 0.00 0.00 2.74
2632 3322 4.461081 CAGAAGTGTAAGGAGCAGACTAGT 59.539 45.833 0.00 0.00 0.00 2.57
2633 3323 4.461081 ACAGAAGTGTAAGGAGCAGACTAG 59.539 45.833 0.00 0.00 34.05 2.57
2634 3324 4.408276 ACAGAAGTGTAAGGAGCAGACTA 58.592 43.478 0.00 0.00 34.05 2.59
2635 3325 3.235200 ACAGAAGTGTAAGGAGCAGACT 58.765 45.455 0.00 0.00 34.05 3.24
2636 3326 3.005897 TGACAGAAGTGTAAGGAGCAGAC 59.994 47.826 0.00 0.00 36.88 3.51
2637 3327 3.005897 GTGACAGAAGTGTAAGGAGCAGA 59.994 47.826 0.00 0.00 36.88 4.26
2638 3328 3.321497 GTGACAGAAGTGTAAGGAGCAG 58.679 50.000 0.00 0.00 36.88 4.24
2689 3379 1.067213 CGGGGTGCAAATTAAAGGTGG 60.067 52.381 0.00 0.00 0.00 4.61
2973 3702 9.127006 CAAATGTATCGTTTGATTTGACAATCA 57.873 29.630 8.24 0.00 45.96 2.57
2989 3718 4.183865 TCTCTGTTCTGGCAAATGTATCG 58.816 43.478 0.00 0.00 0.00 2.92
3054 3783 4.151121 TCAGAGAAATCAATTGCCAACCA 58.849 39.130 0.00 0.00 0.00 3.67
3115 3844 9.627395 GCAGTAGTTGTACAACATATAGGATAG 57.373 37.037 33.93 16.08 43.47 2.08
3116 3845 9.138596 TGCAGTAGTTGTACAACATATAGGATA 57.861 33.333 33.93 16.27 43.47 2.59
3117 3846 8.018537 TGCAGTAGTTGTACAACATATAGGAT 57.981 34.615 33.93 17.18 43.47 3.24
3118 3847 7.123697 ACTGCAGTAGTTGTACAACATATAGGA 59.876 37.037 33.93 20.98 43.47 2.94
3206 3944 2.159819 GACCAGCGAGTCCTTCTGCA 62.160 60.000 0.00 0.00 0.00 4.41
3219 3957 0.881796 GTGGCAGTAAAAGGACCAGC 59.118 55.000 0.00 0.00 0.00 4.85
3281 4020 0.666374 ACAGCCGGCAAGTAAAACAC 59.334 50.000 31.54 0.00 0.00 3.32
3302 4041 9.686683 AATAAATAAAGTTCTGATAGCTGGTGT 57.313 29.630 0.00 0.00 0.00 4.16
3657 4400 5.701750 CACAGATGGCAAAAATGGAATTCAA 59.298 36.000 7.93 0.00 33.67 2.69
3722 4770 1.408683 GCATCCCCTACAGCAACATGA 60.409 52.381 0.00 0.00 0.00 3.07
3735 4783 2.757099 CCCAACAGCAGCATCCCC 60.757 66.667 0.00 0.00 0.00 4.81
3959 5008 6.271159 ACCACCTAATCTGATCCCTAAGATTC 59.729 42.308 8.79 0.00 41.20 2.52
3994 5044 9.791820 CAGCTGATGTTGAATATTGTTCAAATA 57.208 29.630 8.42 4.00 39.76 1.40
3997 5047 7.218228 ACAGCTGATGTTGAATATTGTTCAA 57.782 32.000 23.35 4.64 39.96 2.69
4258 5308 0.951558 AACACCTGCGGAACATTCAC 59.048 50.000 0.00 0.00 0.00 3.18
4692 5746 1.333619 CATACATTGCGTGCCTTACCC 59.666 52.381 0.00 0.00 0.00 3.69
4753 5807 5.116180 CGAAGATTGGCAGTAGTATGGAAA 58.884 41.667 0.00 0.00 0.00 3.13
4756 5810 3.804325 CACGAAGATTGGCAGTAGTATGG 59.196 47.826 0.00 0.00 0.00 2.74
4771 5825 2.500229 GGACATTTTCCACCACGAAGA 58.500 47.619 0.00 0.00 45.10 2.87
4807 5861 9.329913 GCATTTCTTATAGCAATAACCGTATTG 57.670 33.333 2.71 2.71 46.44 1.90
4834 5888 5.867716 CCTGAAAGCTACGTACAAGTACAAT 59.132 40.000 10.63 1.17 35.87 2.71
4849 5903 1.891150 CATTGAGCCAACCTGAAAGCT 59.109 47.619 0.00 0.00 38.56 3.74
4869 5923 1.373570 CCCACTTGCGAGGAAGAATC 58.626 55.000 11.24 0.00 0.00 2.52
4879 5937 1.140161 CATCCATTGCCCACTTGCG 59.860 57.895 0.00 0.00 0.00 4.85
5324 6389 8.485392 AGAAAGGAAATGAAAAATCAACTCCAA 58.515 29.630 10.42 0.00 30.94 3.53
5459 6524 4.751600 TGCTGAGTTACTGTGAAATGTGAG 59.248 41.667 0.00 0.00 0.00 3.51
5461 6526 5.008019 ACTTGCTGAGTTACTGTGAAATGTG 59.992 40.000 0.00 0.00 33.92 3.21
5537 6710 2.809706 CCAAAGCATGCCATCGGG 59.190 61.111 15.66 5.56 37.18 5.14
5547 6720 1.140452 TGGAAATTTGCAGCCAAAGCA 59.860 42.857 8.47 0.00 43.60 3.91


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

AutoCloner maintained by Alex Coulton.