Multiple sequence alignment - TraesCS5B01G456400

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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 TraesCS5B01G456400 chr5B 100.000 3332 0 0 1 3332 631462714 631466045 0.000000e+00 6154.0
1 TraesCS5B01G456400 chr5B 91.768 2806 133 47 1 2761 626336308 626339060 0.000000e+00 3812.0
2 TraesCS5B01G456400 chr5B 84.022 363 30 10 2759 3096 626339187 626339546 1.150000e-84 324.0
3 TraesCS5B01G456400 chr5B 93.252 163 8 2 2946 3108 626350768 626350927 1.550000e-58 237.0
4 TraesCS5B01G456400 chr5B 73.717 487 83 37 1560 2043 79805253 79804809 7.450000e-32 148.0
5 TraesCS5B01G456400 chr5B 87.000 100 13 0 1945 2044 115419192 115419291 2.720000e-21 113.0
6 TraesCS5B01G456400 chr5D 90.604 2916 165 45 1 2859 502594532 502597395 0.000000e+00 3766.0
7 TraesCS5B01G456400 chr5D 85.849 106 15 0 1945 2050 106520267 106520162 2.720000e-21 113.0
8 TraesCS5B01G456400 chr5A 89.910 2339 128 61 663 2968 631329134 631331397 0.000000e+00 2913.0
9 TraesCS5B01G456400 chr5A 79.538 303 23 25 3054 3321 631331596 631331894 2.640000e-41 180.0
10 TraesCS5B01G456400 chr5A 87.000 100 13 0 1945 2044 109966829 109966928 2.720000e-21 113.0
11 TraesCS5B01G456400 chr4D 82.567 413 23 21 1019 1427 344359697 344360064 5.360000e-83 318.0
12 TraesCS5B01G456400 chr7A 83.534 249 32 9 2357 2598 136805055 136804809 1.200000e-54 224.0
13 TraesCS5B01G456400 chr3D 86.598 97 13 0 1936 2032 17843166 17843262 1.260000e-19 108.0
14 TraesCS5B01G456400 chrUn 83.036 112 19 0 1936 2047 37382230 37382119 5.880000e-18 102.0
15 TraesCS5B01G456400 chr6D 96.970 33 1 0 1310 1342 457644689 457644721 4.640000e-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 TraesCS5B01G456400 chr5B 631462714 631466045 3331 False 6154.0 6154 100.000 1 3332 1 chr5B.!!$F3 3331
1 TraesCS5B01G456400 chr5B 626336308 626339546 3238 False 2068.0 3812 87.895 1 3096 2 chr5B.!!$F4 3095
2 TraesCS5B01G456400 chr5D 502594532 502597395 2863 False 3766.0 3766 90.604 1 2859 1 chr5D.!!$F1 2858
3 TraesCS5B01G456400 chr5A 631329134 631331894 2760 False 1546.5 2913 84.724 663 3321 2 chr5A.!!$F2 2658

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
223 227 0.234625 TGTTCGCGTTCACTCATTGC 59.765 50.0 5.77 0.0 0.0 3.56 F
333 342 0.531532 CATCACTCATCCTCCCGTGC 60.532 60.0 0.00 0.0 0.0 5.34 F
334 343 1.690219 ATCACTCATCCTCCCGTGCC 61.690 60.0 0.00 0.0 0.0 5.01 F
628 645 1.908340 GCTCCTCACCTCACCATGCT 61.908 60.0 0.00 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1857 1.978580 ACGAAGATGTTGGAGGAGGTT 59.021 47.619 0.00 0.0 0.00 3.50 R
2308 2353 1.355720 AGAGGAATCCTTGTGGTTGGG 59.644 52.381 2.09 0.0 31.76 4.12 R
2322 2367 4.889409 AGTGCAATTCAAAGTCAAGAGGAA 59.111 37.500 0.00 0.0 0.00 3.36 R
2382 2446 0.035881 CTTCAGCCAGGAAGTCAGCA 59.964 55.000 0.00 0.0 39.51 4.41 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
23 24 3.071479 ACGTTGCTGGTACAACTTATGG 58.929 45.455 5.92 0.00 46.21 2.74
35 36 6.884836 GGTACAACTTATGGATCTTTCAACCT 59.115 38.462 0.00 0.00 0.00 3.50
74 78 3.459063 CTTCCCCGTCGAGTCCCC 61.459 72.222 0.00 0.00 0.00 4.81
88 92 2.360726 CCCCACGCCTAACCAACC 60.361 66.667 0.00 0.00 0.00 3.77
140 144 1.983224 CTTGCTCTCCTTTCCGGGA 59.017 57.895 0.00 0.00 0.00 5.14
210 214 6.062021 CGTTAAAATTTCCAAATGTGTTCGC 58.938 36.000 0.00 0.00 0.00 4.70
223 227 0.234625 TGTTCGCGTTCACTCATTGC 59.765 50.000 5.77 0.00 0.00 3.56
224 228 0.234625 GTTCGCGTTCACTCATTGCA 59.765 50.000 5.77 0.00 0.00 4.08
225 229 0.234625 TTCGCGTTCACTCATTGCAC 59.765 50.000 5.77 0.00 0.00 4.57
227 231 1.154413 GCGTTCACTCATTGCACCG 60.154 57.895 0.00 0.00 0.00 4.94
228 232 1.841663 GCGTTCACTCATTGCACCGT 61.842 55.000 0.00 0.00 0.00 4.83
243 249 2.494918 CGTCCCATCCTGGTCGAC 59.505 66.667 7.13 7.13 35.89 4.20
265 271 6.295719 ACCGGAATTTCAGATACAGTAACT 57.704 37.500 9.46 0.00 0.00 2.24
311 317 2.416747 TCCTTCAATCACACTCGCTTG 58.583 47.619 0.00 0.00 0.00 4.01
312 318 1.135859 CCTTCAATCACACTCGCTTGC 60.136 52.381 0.00 0.00 0.00 4.01
333 342 0.531532 CATCACTCATCCTCCCGTGC 60.532 60.000 0.00 0.00 0.00 5.34
334 343 1.690219 ATCACTCATCCTCCCGTGCC 61.690 60.000 0.00 0.00 0.00 5.01
335 344 3.461773 ACTCATCCTCCCGTGCCG 61.462 66.667 0.00 0.00 0.00 5.69
336 345 3.461773 CTCATCCTCCCGTGCCGT 61.462 66.667 0.00 0.00 0.00 5.68
337 346 3.723235 CTCATCCTCCCGTGCCGTG 62.723 68.421 0.00 0.00 0.00 4.94
338 347 4.082523 CATCCTCCCGTGCCGTGT 62.083 66.667 0.00 0.00 0.00 4.49
433 442 8.068380 GCTAAATCCGGATAGTTTATTGACAAC 58.932 37.037 19.48 0.00 0.00 3.32
452 461 4.825085 ACAACAACTTCGAAACCATACCAT 59.175 37.500 0.00 0.00 0.00 3.55
454 463 5.371115 ACAACTTCGAAACCATACCATTG 57.629 39.130 0.00 0.00 0.00 2.82
485 494 5.028549 AGTTATGGATCATTCGAGCACTT 57.971 39.130 0.00 0.00 0.00 3.16
512 521 2.544685 CATCCTCATTGTCCGACTCAC 58.455 52.381 0.00 0.00 0.00 3.51
574 583 2.494918 CCTTACCAGCGACCTCCG 59.505 66.667 0.00 0.00 42.21 4.63
628 645 1.908340 GCTCCTCACCTCACCATGCT 61.908 60.000 0.00 0.00 0.00 3.79
709 726 1.971695 GCGGAAACACAAGGGGGAG 60.972 63.158 0.00 0.00 0.00 4.30
733 751 4.640771 AAGTCCATTGTACACATGGAGT 57.359 40.909 26.60 26.20 46.82 3.85
1812 1857 4.041917 GTGGTCCACCGCGACGTA 62.042 66.667 8.23 0.00 39.43 3.57
2308 2353 4.796314 GGATGATCCCTGAGCTGC 57.204 61.111 0.00 0.00 0.00 5.25
2322 2367 1.607467 GCTGCCCAACCACAAGGAT 60.607 57.895 0.00 0.00 38.69 3.24
2337 2382 5.065914 CACAAGGATTCCTCTTGACTTTGA 58.934 41.667 5.48 0.00 42.94 2.69
2345 2390 4.464008 TCCTCTTGACTTTGAATTGCACT 58.536 39.130 0.00 0.00 0.00 4.40
2347 2392 3.968649 TCTTGACTTTGAATTGCACTGC 58.031 40.909 0.00 0.00 0.00 4.40
2348 2393 3.380954 TCTTGACTTTGAATTGCACTGCA 59.619 39.130 0.00 0.00 36.47 4.41
2352 2416 4.053295 GACTTTGAATTGCACTGCACAAT 58.947 39.130 2.26 0.00 38.71 2.71
2353 2417 4.053295 ACTTTGAATTGCACTGCACAATC 58.947 39.130 2.26 3.28 38.71 2.67
2371 2435 1.348064 TCTCTCGGGTTGTTGATGGT 58.652 50.000 0.00 0.00 0.00 3.55
2372 2436 1.275291 TCTCTCGGGTTGTTGATGGTC 59.725 52.381 0.00 0.00 0.00 4.02
2374 2438 0.320421 CTCGGGTTGTTGATGGTCGT 60.320 55.000 0.00 0.00 0.00 4.34
2376 2440 0.882927 CGGGTTGTTGATGGTCGTGT 60.883 55.000 0.00 0.00 0.00 4.49
2378 2442 1.265905 GGGTTGTTGATGGTCGTGTTC 59.734 52.381 0.00 0.00 0.00 3.18
2382 2446 2.857483 TGTTGATGGTCGTGTTCCAAT 58.143 42.857 0.00 0.00 38.52 3.16
2383 2447 2.551887 TGTTGATGGTCGTGTTCCAATG 59.448 45.455 0.00 0.00 38.52 2.82
2390 2454 1.873591 GTCGTGTTCCAATGCTGACTT 59.126 47.619 0.00 0.00 0.00 3.01
2392 2458 1.197721 CGTGTTCCAATGCTGACTTCC 59.802 52.381 0.00 0.00 0.00 3.46
2400 2466 0.694771 ATGCTGACTTCCTGGCTGAA 59.305 50.000 0.00 0.00 0.00 3.02
2401 2467 0.035881 TGCTGACTTCCTGGCTGAAG 59.964 55.000 13.46 13.46 45.79 3.02
2408 2474 0.323725 TTCCTGGCTGAAGGATTGGC 60.324 55.000 4.50 0.00 45.84 4.52
2409 2475 1.000521 CCTGGCTGAAGGATTGGCA 60.001 57.895 0.00 0.00 40.02 4.92
2410 2476 0.396695 CCTGGCTGAAGGATTGGCAT 60.397 55.000 0.00 0.00 40.02 4.40
2413 2479 1.063492 TGGCTGAAGGATTGGCATCAT 60.063 47.619 0.00 0.00 0.00 2.45
2414 2480 1.612463 GGCTGAAGGATTGGCATCATC 59.388 52.381 0.00 0.00 0.00 2.92
2415 2481 1.612463 GCTGAAGGATTGGCATCATCC 59.388 52.381 9.75 9.75 34.77 3.51
2416 2482 2.752154 GCTGAAGGATTGGCATCATCCT 60.752 50.000 13.81 13.81 46.06 3.24
2417 2483 3.147629 CTGAAGGATTGGCATCATCCTC 58.852 50.000 18.65 13.19 43.53 3.71
2443 2513 3.275088 TCGAAGACGAGTGCTCCC 58.725 61.111 0.00 0.00 43.81 4.30
2445 2515 1.137825 CGAAGACGAGTGCTCCCTC 59.862 63.158 0.00 0.00 42.66 4.30
2446 2516 1.587043 CGAAGACGAGTGCTCCCTCA 61.587 60.000 0.00 0.00 42.66 3.86
2447 2517 0.820871 GAAGACGAGTGCTCCCTCAT 59.179 55.000 0.00 0.00 0.00 2.90
2448 2518 0.534412 AAGACGAGTGCTCCCTCATG 59.466 55.000 0.00 0.00 0.00 3.07
2456 2526 1.150081 GCTCCCTCATGGTGGATGG 59.850 63.158 7.15 0.00 34.77 3.51
2458 2528 1.308128 TCCCTCATGGTGGATGGCT 60.308 57.895 7.15 0.00 34.77 4.75
2479 2549 2.169978 TGGATGGCAGATCTGTTCAGAG 59.830 50.000 23.38 0.00 0.00 3.35
2541 2621 2.887783 GAGATCAATCAGCGGTAGGAGA 59.112 50.000 0.00 0.00 0.00 3.71
2567 2647 6.974932 ACTGTGACAGTAATATGAGCTTTG 57.025 37.500 17.91 0.00 43.46 2.77
2568 2648 5.352569 ACTGTGACAGTAATATGAGCTTTGC 59.647 40.000 17.91 0.00 43.46 3.68
2607 2688 2.548875 CTCAAGGAGTAGCATGAGCAC 58.451 52.381 0.00 0.00 45.49 4.40
2608 2689 2.168106 CTCAAGGAGTAGCATGAGCACT 59.832 50.000 0.00 0.00 45.49 4.40
2609 2690 2.093816 TCAAGGAGTAGCATGAGCACTG 60.094 50.000 0.00 0.00 45.49 3.66
2610 2691 1.857965 AGGAGTAGCATGAGCACTGA 58.142 50.000 0.00 0.00 45.49 3.41
2611 2692 1.755959 AGGAGTAGCATGAGCACTGAG 59.244 52.381 0.00 0.00 45.49 3.35
2612 2693 1.569708 GAGTAGCATGAGCACTGAGC 58.430 55.000 0.00 0.00 45.49 4.26
2724 2806 5.065218 CCAGTCAATATGAACACCTGTAAGC 59.935 44.000 0.00 0.00 0.00 3.09
2753 2835 8.488764 GTTCTGTAGTCAAGAAACTGATGTTAC 58.511 37.037 0.00 0.00 34.96 2.50
2841 3058 4.505808 CATGATGGTGCATATCCTCTCTC 58.494 47.826 10.33 0.00 0.00 3.20
2876 3098 4.280929 GGCCAGGAAAATGTTCAGTACTTT 59.719 41.667 0.00 0.00 35.25 2.66
2879 3101 6.438763 CCAGGAAAATGTTCAGTACTTTGTC 58.561 40.000 0.00 0.00 35.25 3.18
2881 3103 6.039270 CAGGAAAATGTTCAGTACTTTGTCCA 59.961 38.462 13.60 0.00 44.89 4.02
2882 3104 6.263168 AGGAAAATGTTCAGTACTTTGTCCAG 59.737 38.462 13.60 0.00 44.89 3.86
2883 3105 6.262273 GGAAAATGTTCAGTACTTTGTCCAGA 59.738 38.462 8.14 0.00 43.24 3.86
2884 3106 7.201785 GGAAAATGTTCAGTACTTTGTCCAGAA 60.202 37.037 8.14 0.00 43.24 3.02
2885 3107 7.639113 AAATGTTCAGTACTTTGTCCAGAAA 57.361 32.000 0.00 0.00 0.00 2.52
2886 3108 7.823745 AATGTTCAGTACTTTGTCCAGAAAT 57.176 32.000 0.00 0.00 0.00 2.17
2887 3109 8.918202 AATGTTCAGTACTTTGTCCAGAAATA 57.082 30.769 0.00 0.00 0.00 1.40
2888 3110 7.724305 TGTTCAGTACTTTGTCCAGAAATAC 57.276 36.000 0.00 0.00 0.00 1.89
2890 3112 7.990886 TGTTCAGTACTTTGTCCAGAAATACTT 59.009 33.333 0.00 0.00 0.00 2.24
2891 3113 7.962964 TCAGTACTTTGTCCAGAAATACTTG 57.037 36.000 0.00 0.00 0.00 3.16
2905 3139 9.965824 CCAGAAATACTTGTTGAAATACTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
2921 3164 3.009916 ACTTGTTGGAGAATGGATGCTCT 59.990 43.478 0.00 0.00 0.00 4.09
2935 3178 3.623060 GGATGCTCTGCAAGTATTTTCGA 59.377 43.478 0.00 0.00 43.62 3.71
2949 3194 0.883833 TTTCGACGGAGGGAGTACAC 59.116 55.000 0.00 0.00 0.00 2.90
2975 3220 6.210796 TCTTTCTCTGTGCATGTTGATTTTG 58.789 36.000 0.00 0.00 0.00 2.44
3024 3269 3.877508 AGTTTAATTATGTGCCTCCTCGC 59.122 43.478 0.00 0.00 0.00 5.03
3049 3294 2.662637 CACATATGTTTGGTTGCTTGCG 59.337 45.455 5.37 0.00 0.00 4.85
3064 3489 0.944311 TTGCGAGCGACAAACCTCTC 60.944 55.000 0.00 0.00 0.00 3.20
3099 3524 9.708092 AACTAACACTAGTTACCAATTCTCTTC 57.292 33.333 0.00 0.00 44.85 2.87
3114 3539 7.925483 CCAATTCTCTTCTGAACCTCTATACTG 59.075 40.741 0.00 0.00 0.00 2.74
3115 3540 8.474025 CAATTCTCTTCTGAACCTCTATACTGT 58.526 37.037 0.00 0.00 0.00 3.55
3116 3541 7.633193 TTCTCTTCTGAACCTCTATACTGTC 57.367 40.000 0.00 0.00 0.00 3.51
3118 3543 7.175797 TCTCTTCTGAACCTCTATACTGTCAA 58.824 38.462 0.00 0.00 0.00 3.18
3119 3544 7.670140 TCTCTTCTGAACCTCTATACTGTCAAA 59.330 37.037 0.00 0.00 0.00 2.69
3120 3545 8.367660 TCTTCTGAACCTCTATACTGTCAAAT 57.632 34.615 0.00 0.00 0.00 2.32
3122 3547 9.522804 CTTCTGAACCTCTATACTGTCAAATAC 57.477 37.037 0.00 0.00 0.00 1.89
3123 3548 8.589701 TCTGAACCTCTATACTGTCAAATACA 57.410 34.615 0.00 0.00 36.42 2.29
3125 3550 9.823647 CTGAACCTCTATACTGTCAAATACAAT 57.176 33.333 0.00 0.00 37.74 2.71
3183 3627 6.718454 TGGTTATACCTAGTCTAATCCCTTCG 59.282 42.308 0.00 0.00 39.58 3.79
3188 3632 8.773033 ATACCTAGTCTAATCCCTTCGTTTTA 57.227 34.615 0.00 0.00 0.00 1.52
3189 3633 6.871844 ACCTAGTCTAATCCCTTCGTTTTAC 58.128 40.000 0.00 0.00 0.00 2.01
3191 3635 7.147932 ACCTAGTCTAATCCCTTCGTTTTACTC 60.148 40.741 0.00 0.00 0.00 2.59
3192 3636 5.975282 AGTCTAATCCCTTCGTTTTACTCC 58.025 41.667 0.00 0.00 0.00 3.85
3193 3637 4.802563 GTCTAATCCCTTCGTTTTACTCCG 59.197 45.833 0.00 0.00 0.00 4.63
3195 3639 0.680618 TCCCTTCGTTTTACTCCGCA 59.319 50.000 0.00 0.00 0.00 5.69
3196 3640 1.276989 TCCCTTCGTTTTACTCCGCAT 59.723 47.619 0.00 0.00 0.00 4.73
3197 3641 2.496871 TCCCTTCGTTTTACTCCGCATA 59.503 45.455 0.00 0.00 0.00 3.14
3198 3642 3.133362 TCCCTTCGTTTTACTCCGCATAT 59.867 43.478 0.00 0.00 0.00 1.78
3201 3645 5.176958 CCCTTCGTTTTACTCCGCATATTAG 59.823 44.000 0.00 0.00 0.00 1.73
3202 3646 5.333111 CCTTCGTTTTACTCCGCATATTAGC 60.333 44.000 0.00 0.00 0.00 3.09
3280 3733 9.357652 GAACATGCAGTATACAAAATCAACATT 57.642 29.630 5.50 0.00 0.00 2.71
3284 3737 8.741101 TGCAGTATACAAAATCAACATTGAAC 57.259 30.769 5.50 0.00 41.13 3.18
3298 3756 9.631257 ATCAACATTGAACATATAAGATGACCA 57.369 29.630 0.00 0.00 41.13 4.02
3309 3767 9.256228 ACATATAAGATGACCATATACCGTCTT 57.744 33.333 0.00 0.00 38.97 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.435686 AGATCCATAAGTTGTACCAGCAA 57.564 39.130 0.00 0.00 0.00 3.91
7 8 5.880332 TGAAAGATCCATAAGTTGTACCAGC 59.120 40.000 0.00 0.00 0.00 4.85
15 16 8.164070 AGTGTAAGGTTGAAAGATCCATAAGTT 58.836 33.333 0.00 0.00 0.00 2.66
23 24 6.043854 AGAGGAGTGTAAGGTTGAAAGATC 57.956 41.667 0.00 0.00 0.00 2.75
35 36 2.185387 GGGTAGCCAAGAGGAGTGTAA 58.815 52.381 5.96 0.00 36.89 2.41
74 78 1.338674 TGATGAGGTTGGTTAGGCGTG 60.339 52.381 0.00 0.00 0.00 5.34
140 144 4.163078 CCCTTCTCCATATGTCTCACAAGT 59.837 45.833 1.24 0.00 0.00 3.16
200 204 1.577468 TGAGTGAACGCGAACACATT 58.423 45.000 29.16 17.23 39.18 2.71
210 214 0.163788 GACGGTGCAATGAGTGAACG 59.836 55.000 0.00 0.00 36.49 3.95
243 249 7.611213 AAAGTTACTGTATCTGAAATTCCGG 57.389 36.000 0.00 0.00 0.00 5.14
265 271 2.432510 ACGCCCCTTGTTCAAATCAAAA 59.567 40.909 0.00 0.00 0.00 2.44
311 317 1.596477 GGGAGGATGAGTGATGCGC 60.596 63.158 0.00 0.00 0.00 6.09
312 318 1.300465 CGGGAGGATGAGTGATGCG 60.300 63.158 0.00 0.00 0.00 4.73
333 342 4.095610 GTGTCTCACAAAAGAAAACACGG 58.904 43.478 0.00 0.00 34.08 4.94
334 343 4.717991 TGTGTCTCACAAAAGAAAACACG 58.282 39.130 0.00 0.00 41.69 4.49
433 442 4.082787 AGCAATGGTATGGTTTCGAAGTTG 60.083 41.667 0.00 0.00 0.00 3.16
452 461 0.245266 TCCATAACTCGTGCGAGCAA 59.755 50.000 19.86 9.72 45.54 3.91
454 463 1.132588 GATCCATAACTCGTGCGAGC 58.867 55.000 19.86 0.00 45.54 5.03
485 494 2.408565 GGACAATGAGGATGGGAGGTA 58.591 52.381 0.00 0.00 0.00 3.08
512 521 0.976073 TTGTAGGCCGAGAAGGGAGG 60.976 60.000 0.00 0.00 41.48 4.30
616 625 4.052518 GGGGCAGCATGGTGAGGT 62.053 66.667 28.34 0.00 35.86 3.85
628 645 1.493854 ATTGTAGGGTTGACGGGGCA 61.494 55.000 0.00 0.00 0.00 5.36
709 726 4.331968 TCCATGTGTACAATGGACTTTCC 58.668 43.478 24.19 1.92 39.36 3.13
733 751 8.786826 ACGAACATATCTGGAAATTTCAACTA 57.213 30.769 19.49 6.09 0.00 2.24
859 884 4.648626 TGCTGCAGTGGCCACTCC 62.649 66.667 35.79 28.41 40.20 3.85
860 885 3.054503 CTGCTGCAGTGGCCACTC 61.055 66.667 35.79 27.33 40.20 3.51
861 886 3.124051 TTCTGCTGCAGTGGCCACT 62.124 57.895 33.20 33.20 43.61 4.00
862 887 2.595463 TTCTGCTGCAGTGGCCAC 60.595 61.111 29.22 29.22 40.13 5.01
1812 1857 1.978580 ACGAAGATGTTGGAGGAGGTT 59.021 47.619 0.00 0.00 0.00 3.50
2296 2341 2.679716 GTTGGGCAGCTCAGGGAT 59.320 61.111 0.00 0.00 0.00 3.85
2301 2346 1.529010 CTTGTGGTTGGGCAGCTCA 60.529 57.895 0.00 0.00 0.00 4.26
2308 2353 1.355720 AGAGGAATCCTTGTGGTTGGG 59.644 52.381 2.09 0.00 31.76 4.12
2322 2367 4.889409 AGTGCAATTCAAAGTCAAGAGGAA 59.111 37.500 0.00 0.00 0.00 3.36
2337 2382 2.161012 CGAGAGATTGTGCAGTGCAATT 59.839 45.455 21.67 7.44 41.47 2.32
2345 2390 0.396435 ACAACCCGAGAGATTGTGCA 59.604 50.000 0.00 0.00 35.28 4.57
2347 2392 2.766313 TCAACAACCCGAGAGATTGTG 58.234 47.619 0.00 0.00 36.69 3.33
2348 2393 3.338249 CATCAACAACCCGAGAGATTGT 58.662 45.455 0.00 0.00 38.18 2.71
2352 2416 1.275291 GACCATCAACAACCCGAGAGA 59.725 52.381 0.00 0.00 0.00 3.10
2353 2417 1.726853 GACCATCAACAACCCGAGAG 58.273 55.000 0.00 0.00 0.00 3.20
2371 2435 2.143122 GAAGTCAGCATTGGAACACGA 58.857 47.619 0.00 0.00 39.29 4.35
2372 2436 1.197721 GGAAGTCAGCATTGGAACACG 59.802 52.381 0.00 0.00 39.29 4.49
2374 2438 2.507484 CAGGAAGTCAGCATTGGAACA 58.493 47.619 0.00 0.00 0.00 3.18
2376 2440 1.887956 GCCAGGAAGTCAGCATTGGAA 60.888 52.381 0.00 0.00 0.00 3.53
2378 2442 0.323178 AGCCAGGAAGTCAGCATTGG 60.323 55.000 0.00 0.00 0.00 3.16
2382 2446 0.035881 CTTCAGCCAGGAAGTCAGCA 59.964 55.000 0.00 0.00 39.51 4.41
2383 2447 0.676151 CCTTCAGCCAGGAAGTCAGC 60.676 60.000 8.89 0.00 42.14 4.26
2392 2458 1.030457 GATGCCAATCCTTCAGCCAG 58.970 55.000 0.00 0.00 0.00 4.85
2400 2466 1.202903 GCAGAGGATGATGCCAATCCT 60.203 52.381 10.76 10.76 46.69 3.24
2401 2467 1.245732 GCAGAGGATGATGCCAATCC 58.754 55.000 2.01 2.01 36.41 3.01
2408 2474 3.200483 TCGACAAATGCAGAGGATGATG 58.800 45.455 0.00 0.00 0.00 3.07
2409 2475 3.548745 TCGACAAATGCAGAGGATGAT 57.451 42.857 0.00 0.00 0.00 2.45
2410 2476 3.055891 TCTTCGACAAATGCAGAGGATGA 60.056 43.478 0.00 0.00 0.00 2.92
2413 2479 2.688507 GTCTTCGACAAATGCAGAGGA 58.311 47.619 0.00 0.00 32.09 3.71
2414 2480 1.391485 CGTCTTCGACAAATGCAGAGG 59.609 52.381 0.00 0.00 39.71 3.69
2415 2481 2.328473 TCGTCTTCGACAAATGCAGAG 58.672 47.619 0.00 0.00 41.35 3.35
2416 2482 2.288213 ACTCGTCTTCGACAAATGCAGA 60.288 45.455 0.00 0.00 41.35 4.26
2417 2483 2.061773 ACTCGTCTTCGACAAATGCAG 58.938 47.619 0.00 0.00 41.35 4.41
2440 2510 1.308128 AGCCATCCACCATGAGGGA 60.308 57.895 7.63 7.63 38.47 4.20
2441 2511 1.152819 CAGCCATCCACCATGAGGG 60.153 63.158 0.00 0.00 44.81 4.30
2443 2513 0.477204 ATCCAGCCATCCACCATGAG 59.523 55.000 0.00 0.00 33.80 2.90
2445 2515 0.826256 CCATCCAGCCATCCACCATG 60.826 60.000 0.00 0.00 0.00 3.66
2446 2516 1.540166 CCATCCAGCCATCCACCAT 59.460 57.895 0.00 0.00 0.00 3.55
2447 2517 3.009275 CCATCCAGCCATCCACCA 58.991 61.111 0.00 0.00 0.00 4.17
2448 2518 2.520260 GCCATCCAGCCATCCACC 60.520 66.667 0.00 0.00 0.00 4.61
2456 2526 1.307097 GAACAGATCTGCCATCCAGC 58.693 55.000 22.83 0.00 41.50 4.85
2458 2528 2.169978 CTCTGAACAGATCTGCCATCCA 59.830 50.000 22.83 11.73 36.76 3.41
2467 2537 2.115595 CGCGACATCTCTGAACAGATC 58.884 52.381 0.00 0.00 36.76 2.75
2479 2549 0.804933 GTACCTTGGGTCGCGACATC 60.805 60.000 37.26 28.05 37.09 3.06
2531 2611 2.426024 TGTCACAGTATTCTCCTACCGC 59.574 50.000 0.00 0.00 0.00 5.68
2541 2621 9.102757 CAAAGCTCATATTACTGTCACAGTATT 57.897 33.333 18.54 16.57 44.85 1.89
2566 2646 2.016318 CTCACAGAACCAACACAAGCA 58.984 47.619 0.00 0.00 0.00 3.91
2567 2647 1.268743 GCTCACAGAACCAACACAAGC 60.269 52.381 0.00 0.00 0.00 4.01
2568 2648 2.289002 GAGCTCACAGAACCAACACAAG 59.711 50.000 9.40 0.00 0.00 3.16
2620 2701 2.990642 GCCAAACACAAAAGGCAGG 58.009 52.632 0.00 0.00 46.26 4.85
2665 2746 7.942990 ACTAAGAATCCTCCTCTTATGTTACG 58.057 38.462 0.00 0.00 35.40 3.18
2724 2806 5.601662 TCAGTTTCTTGACTACAGAACCAG 58.398 41.667 0.00 0.00 0.00 4.00
2753 2835 2.604855 GGATGCCTGTCTCATACGTACG 60.605 54.545 15.01 15.01 0.00 3.67
2841 3058 1.691196 TCCTGGCCAAGTCAACTTTG 58.309 50.000 7.01 0.00 33.11 2.77
2876 3098 8.918202 AGTATTTCAACAAGTATTTCTGGACA 57.082 30.769 0.00 0.00 0.00 4.02
2879 3101 9.965824 AACAAGTATTTCAACAAGTATTTCTGG 57.034 29.630 0.00 0.00 0.00 3.86
2881 3103 9.965824 CCAACAAGTATTTCAACAAGTATTTCT 57.034 29.630 0.00 0.00 0.00 2.52
2882 3104 9.959749 TCCAACAAGTATTTCAACAAGTATTTC 57.040 29.630 0.00 0.00 0.00 2.17
2883 3105 9.965824 CTCCAACAAGTATTTCAACAAGTATTT 57.034 29.630 0.00 0.00 0.00 1.40
2884 3106 9.349713 TCTCCAACAAGTATTTCAACAAGTATT 57.650 29.630 0.00 0.00 0.00 1.89
2885 3107 8.918202 TCTCCAACAAGTATTTCAACAAGTAT 57.082 30.769 0.00 0.00 0.00 2.12
2886 3108 8.740123 TTCTCCAACAAGTATTTCAACAAGTA 57.260 30.769 0.00 0.00 0.00 2.24
2887 3109 7.639113 TTCTCCAACAAGTATTTCAACAAGT 57.361 32.000 0.00 0.00 0.00 3.16
2888 3110 7.596248 CCATTCTCCAACAAGTATTTCAACAAG 59.404 37.037 0.00 0.00 0.00 3.16
2890 3112 6.775142 TCCATTCTCCAACAAGTATTTCAACA 59.225 34.615 0.00 0.00 0.00 3.33
2891 3113 7.214467 TCCATTCTCCAACAAGTATTTCAAC 57.786 36.000 0.00 0.00 0.00 3.18
2905 3139 0.913924 TGCAGAGCATCCATTCTCCA 59.086 50.000 0.00 0.00 33.66 3.86
2906 3140 1.948145 CTTGCAGAGCATCCATTCTCC 59.052 52.381 0.00 0.00 38.76 3.71
2921 3164 2.343101 CCTCCGTCGAAAATACTTGCA 58.657 47.619 0.00 0.00 0.00 4.08
2935 3178 2.305858 AAGAAGTGTACTCCCTCCGT 57.694 50.000 0.00 0.00 0.00 4.69
2949 3194 5.624344 ATCAACATGCACAGAGAAAGAAG 57.376 39.130 0.00 0.00 0.00 2.85
2991 3236 6.826741 GCACATAATTAAACTCCAAGTAGGGA 59.173 38.462 0.00 0.00 38.24 4.20
2992 3237 6.039382 GGCACATAATTAAACTCCAAGTAGGG 59.961 42.308 0.00 0.00 38.24 3.53
3024 3269 5.107375 GCAAGCAACCAAACATATGTGAAAG 60.107 40.000 9.63 1.65 0.00 2.62
3049 3294 3.701241 CTCTATGAGAGGTTTGTCGCTC 58.299 50.000 0.00 0.00 38.67 5.03
3064 3489 8.033038 TGGTAACTAGTGTTAGTTTGCTCTATG 58.967 37.037 0.00 0.00 45.57 2.23
3099 3524 9.823647 ATTGTATTTGACAGTATAGAGGTTCAG 57.176 33.333 0.00 0.00 39.88 3.02
3122 3547 8.685427 TCCAATGATGTTCATTTGGTAGTATTG 58.315 33.333 12.87 0.00 44.03 1.90
3123 3548 8.821686 TCCAATGATGTTCATTTGGTAGTATT 57.178 30.769 12.87 0.00 44.03 1.89
3125 3550 8.224389 CATCCAATGATGTTCATTTGGTAGTA 57.776 34.615 12.87 0.00 44.03 1.82
3126 3551 7.104043 CATCCAATGATGTTCATTTGGTAGT 57.896 36.000 12.87 3.02 44.03 2.73
3166 3610 7.110043 AGTAAAACGAAGGGATTAGACTAGG 57.890 40.000 0.00 0.00 0.00 3.02
3169 3613 5.393896 CGGAGTAAAACGAAGGGATTAGACT 60.394 44.000 0.00 0.00 0.00 3.24
3170 3614 4.802563 CGGAGTAAAACGAAGGGATTAGAC 59.197 45.833 0.00 0.00 0.00 2.59
3171 3615 4.678840 GCGGAGTAAAACGAAGGGATTAGA 60.679 45.833 0.00 0.00 0.00 2.10
3172 3616 3.554731 GCGGAGTAAAACGAAGGGATTAG 59.445 47.826 0.00 0.00 0.00 1.73
3183 3627 6.258068 AGACAAGCTAATATGCGGAGTAAAAC 59.742 38.462 0.00 0.00 38.13 2.43
3188 3632 3.384789 TCAGACAAGCTAATATGCGGAGT 59.615 43.478 0.00 0.00 38.13 3.85
3189 3633 3.982475 TCAGACAAGCTAATATGCGGAG 58.018 45.455 0.00 0.00 38.13 4.63
3191 3635 4.122776 ACTTCAGACAAGCTAATATGCGG 58.877 43.478 0.00 0.00 38.13 5.69
3192 3636 4.805719 TGACTTCAGACAAGCTAATATGCG 59.194 41.667 0.00 0.00 38.13 4.73
3193 3637 6.668541 TTGACTTCAGACAAGCTAATATGC 57.331 37.500 0.00 0.00 0.00 3.14
3201 3645 8.186821 AGCATATAAATTTGACTTCAGACAAGC 58.813 33.333 0.00 0.00 32.04 4.01
3252 3703 8.522003 TGTTGATTTTGTATACTGCATGTTCAT 58.478 29.630 4.17 0.00 0.00 2.57
3254 3705 8.915871 ATGTTGATTTTGTATACTGCATGTTC 57.084 30.769 4.17 0.00 0.00 3.18
3256 3707 8.522003 TCAATGTTGATTTTGTATACTGCATGT 58.478 29.630 4.17 0.00 31.01 3.21
3257 3708 8.914328 TCAATGTTGATTTTGTATACTGCATG 57.086 30.769 4.17 0.00 31.01 4.06
3258 3709 9.357652 GTTCAATGTTGATTTTGTATACTGCAT 57.642 29.630 4.17 0.00 37.00 3.96
3260 3711 8.741101 TGTTCAATGTTGATTTTGTATACTGC 57.259 30.769 4.17 0.00 37.00 4.40
3272 3725 9.631257 TGGTCATCTTATATGTTCAATGTTGAT 57.369 29.630 0.00 0.00 37.00 2.57
3280 3733 9.031537 ACGGTATATGGTCATCTTATATGTTCA 57.968 33.333 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.