Multiple sequence alignment - TraesCS5B01G375100

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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 TraesCS5B01G375100 chr5B 100.000 2992 0 0 1 2992 552563076 552566067 0.000000e+00 5526.0
1 TraesCS5B01G375100 chr5B 84.528 1060 109 27 966 2003 75812006 75810980 0.000000e+00 998.0
2 TraesCS5B01G375100 chr5D 92.213 3018 178 25 3 2990 452363382 452366372 0.000000e+00 4218.0
3 TraesCS5B01G375100 chr5D 84.448 1106 112 30 966 2054 70521729 70520667 0.000000e+00 1035.0
4 TraesCS5B01G375100 chr5D 90.446 157 13 2 731 886 70528455 70528300 3.910000e-49 206.0
5 TraesCS5B01G375100 chr5A 92.902 1423 71 18 625 2025 571304018 571305432 0.000000e+00 2041.0
6 TraesCS5B01G375100 chr5A 84.358 1106 112 27 966 2054 60414467 60413406 0.000000e+00 1027.0
7 TraesCS5B01G375100 chr5A 91.083 157 12 2 731 887 60437064 60436910 8.400000e-51 211.0
8 TraesCS5B01G375100 chr5A 81.013 79 11 4 2453 2528 104146287 104146364 3.220000e-05 60.2
9 TraesCS5B01G375100 chr6B 84.629 566 81 6 2 565 200782667 200783228 2.610000e-155 558.0
10 TraesCS5B01G375100 chr6D 84.397 564 83 5 2 563 111625660 111626220 1.570000e-152 549.0
11 TraesCS5B01G375100 chr3D 85.300 517 74 2 49 565 283615613 283615099 1.580000e-147 532.0
12 TraesCS5B01G375100 chr3D 77.108 166 28 8 2370 2528 541199536 541199698 1.480000e-13 87.9
13 TraesCS5B01G375100 chr2D 84.087 553 83 5 16 565 423281959 423282509 2.040000e-146 529.0
14 TraesCS5B01G375100 chr2D 75.381 394 78 9 2588 2978 466797931 466797554 3.970000e-39 172.0
15 TraesCS5B01G375100 chr2D 88.333 60 7 0 2489 2548 38680295 38680354 4.140000e-09 73.1
16 TraesCS5B01G375100 chr2D 84.722 72 9 2 2478 2548 40852611 40852681 1.490000e-08 71.3
17 TraesCS5B01G375100 chr6A 82.109 626 88 15 1 619 136229599 136228991 5.720000e-142 514.0
18 TraesCS5B01G375100 chr6A 87.831 189 20 2 1149 1336 104399235 104399421 5.020000e-53 219.0
19 TraesCS5B01G375100 chr4B 84.526 517 74 6 2 516 484781216 484781728 9.570000e-140 507.0
20 TraesCS5B01G375100 chr3A 83.591 518 83 2 49 565 371161498 371160982 4.480000e-133 484.0
21 TraesCS5B01G375100 chr1A 80.851 564 80 7 2 564 463457486 463456950 4.610000e-113 418.0
22 TraesCS5B01G375100 chr2B 76.752 585 92 34 18 582 368384284 368384844 1.360000e-73 287.0
23 TraesCS5B01G375100 chr2B 72.123 617 105 42 1251 1850 648653646 648653080 1.130000e-24 124.0
24 TraesCS5B01G375100 chr2B 78.182 165 30 4 2366 2525 107567448 107567611 1.900000e-17 100.0
25 TraesCS5B01G375100 chr2B 72.901 262 63 7 52 311 332336821 332336566 1.910000e-12 84.2
26 TraesCS5B01G375100 chr2B 89.091 55 6 0 2490 2544 67425665 67425719 5.350000e-08 69.4
27 TraesCS5B01G375100 chr4A 92.973 185 12 1 1179 1363 688857688 688857505 4.920000e-68 268.0
28 TraesCS5B01G375100 chr7D 82.069 145 22 4 1802 1944 428952610 428952752 1.460000e-23 121.0
29 TraesCS5B01G375100 chr7D 74.459 231 44 10 2410 2635 510585198 510585418 5.310000e-13 86.1
30 TraesCS5B01G375100 chr7B 82.069 145 22 4 1802 1944 446665463 446665605 1.460000e-23 121.0
31 TraesCS5B01G375100 chr7A 82.069 145 22 4 1802 1944 503052290 503052148 1.460000e-23 121.0
32 TraesCS5B01G375100 chr1D 81.250 144 25 2 1802 1944 283617795 283617937 6.780000e-22 115.0
33 TraesCS5B01G375100 chr1D 81.013 79 11 3 2453 2528 335406309 335406386 3.220000e-05 60.2


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 TraesCS5B01G375100 chr5B 552563076 552566067 2991 False 5526 5526 100.000 1 2992 1 chr5B.!!$F1 2991
1 TraesCS5B01G375100 chr5B 75810980 75812006 1026 True 998 998 84.528 966 2003 1 chr5B.!!$R1 1037
2 TraesCS5B01G375100 chr5D 452363382 452366372 2990 False 4218 4218 92.213 3 2990 1 chr5D.!!$F1 2987
3 TraesCS5B01G375100 chr5D 70520667 70521729 1062 True 1035 1035 84.448 966 2054 1 chr5D.!!$R1 1088
4 TraesCS5B01G375100 chr5A 571304018 571305432 1414 False 2041 2041 92.902 625 2025 1 chr5A.!!$F2 1400
5 TraesCS5B01G375100 chr5A 60413406 60414467 1061 True 1027 1027 84.358 966 2054 1 chr5A.!!$R1 1088
6 TraesCS5B01G375100 chr6B 200782667 200783228 561 False 558 558 84.629 2 565 1 chr6B.!!$F1 563
7 TraesCS5B01G375100 chr6D 111625660 111626220 560 False 549 549 84.397 2 563 1 chr6D.!!$F1 561
8 TraesCS5B01G375100 chr3D 283615099 283615613 514 True 532 532 85.300 49 565 1 chr3D.!!$R1 516
9 TraesCS5B01G375100 chr2D 423281959 423282509 550 False 529 529 84.087 16 565 1 chr2D.!!$F3 549
10 TraesCS5B01G375100 chr6A 136228991 136229599 608 True 514 514 82.109 1 619 1 chr6A.!!$R1 618
11 TraesCS5B01G375100 chr4B 484781216 484781728 512 False 507 507 84.526 2 516 1 chr4B.!!$F1 514
12 TraesCS5B01G375100 chr3A 371160982 371161498 516 True 484 484 83.591 49 565 1 chr3A.!!$R1 516
13 TraesCS5B01G375100 chr1A 463456950 463457486 536 True 418 418 80.851 2 564 1 chr1A.!!$R1 562
14 TraesCS5B01G375100 chr2B 368384284 368384844 560 False 287 287 76.752 18 582 1 chr2B.!!$F3 564

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
614 634 0.169009 GATTTGTCAACTCCGGCTGC 59.831 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2297 2369 0.034477 CCGCCCTAGATTTGGGTTGT 60.034 55.0 0.0 0.0 46.22 3.32 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
37 38 3.379445 GGAGGCGAAGGACCGACA 61.379 66.667 0.00 0.00 40.72 4.35
165 169 1.292223 CAAGACCATGTCGTCCGGT 59.708 57.895 0.00 0.00 37.67 5.28
200 204 1.095600 TCGTCATCTCTGGTTCCTCG 58.904 55.000 0.00 0.00 0.00 4.63
221 228 1.068541 CGACGATGACAGGTCTGACAA 60.069 52.381 10.38 0.00 38.57 3.18
226 233 1.048601 TGACAGGTCTGACAACTCCC 58.951 55.000 10.38 0.00 32.80 4.30
258 270 1.733402 CTCCTGCCGCAGACTCCTAG 61.733 65.000 22.35 3.10 32.44 3.02
263 275 0.820074 GCCGCAGACTCCTAGAGCTA 60.820 60.000 0.00 0.00 32.04 3.32
264 276 1.904287 CCGCAGACTCCTAGAGCTAT 58.096 55.000 0.00 0.00 32.04 2.97
266 278 2.499197 CGCAGACTCCTAGAGCTATGA 58.501 52.381 0.00 0.00 32.04 2.15
311 323 0.603975 GCGAGGAAGTGGTGAAGCTT 60.604 55.000 0.00 0.00 0.00 3.74
378 391 2.858344 GTCGGATCGTTGAACTATGTGG 59.142 50.000 0.00 0.00 0.00 4.17
398 411 1.065709 GCTTCCCCGTTTGGTGATCTA 60.066 52.381 0.00 0.00 0.00 1.98
402 415 2.841266 TCCCCGTTTGGTGATCTATTGA 59.159 45.455 0.00 0.00 0.00 2.57
425 438 5.393124 AGTGATGTTTATGTGAATTGTGCG 58.607 37.500 0.00 0.00 0.00 5.34
459 472 5.260140 CAGTTTGTACGTTCGTTTCATGTT 58.740 37.500 2.62 0.00 0.00 2.71
550 568 2.882403 TATGCGGGTGTGGAGGCCTA 62.882 60.000 4.42 0.00 0.00 3.93
566 584 2.172717 GGCCTAGATTTAGGGAGTGCAA 59.827 50.000 11.14 0.00 45.66 4.08
591 611 1.598962 TCCGCGGACGTATAGGAGG 60.599 63.158 27.28 0.00 37.70 4.30
592 612 1.895707 CCGCGGACGTATAGGAGGT 60.896 63.158 24.07 0.00 37.70 3.85
601 621 4.341520 GGACGTATAGGAGGTCAGATTTGT 59.658 45.833 0.00 0.00 43.45 2.83
614 634 0.169009 GATTTGTCAACTCCGGCTGC 59.831 55.000 0.00 0.00 0.00 5.25
657 683 2.126071 CGTTCACGGTCCGCTGAT 60.126 61.111 12.28 0.00 35.37 2.90
669 696 2.103263 GTCCGCTGATATTTGAGGGTCT 59.897 50.000 0.00 0.00 0.00 3.85
681 708 9.125026 GATATTTGAGGGTCTGATTTTGTGTAT 57.875 33.333 0.00 0.00 0.00 2.29
683 710 5.762179 TGAGGGTCTGATTTTGTGTATCT 57.238 39.130 0.00 0.00 0.00 1.98
684 711 5.491070 TGAGGGTCTGATTTTGTGTATCTG 58.509 41.667 0.00 0.00 0.00 2.90
685 712 5.248248 TGAGGGTCTGATTTTGTGTATCTGA 59.752 40.000 0.00 0.00 0.00 3.27
711 738 8.849543 TGAGTATAATAAACTACTCTGGGGTT 57.150 34.615 10.16 0.00 42.75 4.11
884 918 3.434309 CAAAGTCCAACCCATTCCTGAT 58.566 45.455 0.00 0.00 0.00 2.90
901 935 5.316167 TCCTGATATCAGTGCTTTGTGTTT 58.684 37.500 27.03 0.00 42.27 2.83
1488 1538 1.416401 ACTTCACCAAGCCTTCGAAGA 59.584 47.619 26.61 0.70 37.20 2.87
1739 1798 3.283684 CGCAAGCACCGGGTGAAA 61.284 61.111 30.65 0.00 35.23 2.69
2036 2101 1.276421 AGGACTGGATGTGTTCTTCCG 59.724 52.381 0.00 0.00 39.75 4.30
2054 2119 3.519579 TCCGTTTGTTCTTTGTACACGA 58.480 40.909 0.00 0.00 0.00 4.35
2082 2147 4.455533 CACATGCATGTACACCACTAACTT 59.544 41.667 30.92 1.21 39.39 2.66
2083 2148 4.695455 ACATGCATGTACACCACTAACTTC 59.305 41.667 30.50 0.00 39.68 3.01
2084 2149 3.322369 TGCATGTACACCACTAACTTCG 58.678 45.455 0.00 0.00 0.00 3.79
2087 2153 4.630069 GCATGTACACCACTAACTTCGAAT 59.370 41.667 0.00 0.00 0.00 3.34
2092 2158 6.539464 TGTACACCACTAACTTCGAATTTTGT 59.461 34.615 6.04 7.69 0.00 2.83
2100 2166 8.318167 CACTAACTTCGAATTTTGTTTTTGGAC 58.682 33.333 11.47 0.00 0.00 4.02
2145 2217 1.491670 ATGCAGTATACTTGCGCGAG 58.508 50.000 23.34 23.34 0.00 5.03
2157 2229 1.629013 TGCGCGAGAAACATAGTGAG 58.371 50.000 12.10 0.00 0.00 3.51
2189 2261 1.757118 CCGGAAGTCTCAAGCATCCTA 59.243 52.381 0.00 0.00 0.00 2.94
2190 2262 2.366916 CCGGAAGTCTCAAGCATCCTAT 59.633 50.000 0.00 0.00 0.00 2.57
2191 2263 3.574396 CCGGAAGTCTCAAGCATCCTATA 59.426 47.826 0.00 0.00 0.00 1.31
2202 2274 2.766828 AGCATCCTATATAAGTCCGGGC 59.233 50.000 0.00 0.00 0.00 6.13
2222 2294 1.745827 CGGACGGCCCAATCACTAATT 60.746 52.381 0.00 0.00 34.14 1.40
2247 2319 3.481112 AAAAACTCAACCGACACACAC 57.519 42.857 0.00 0.00 0.00 3.82
2272 2344 3.013921 TCAATAACCGGCCTCAAATGTC 58.986 45.455 0.00 0.00 0.00 3.06
2279 2351 1.611673 CGGCCTCAAATGTCCAGACTT 60.612 52.381 0.00 0.00 0.00 3.01
2281 2353 3.682718 CGGCCTCAAATGTCCAGACTTAT 60.683 47.826 0.00 0.00 0.00 1.73
2288 2360 1.557099 TGTCCAGACTTATCGGCACT 58.443 50.000 0.00 0.00 0.00 4.40
2297 2369 5.416013 CAGACTTATCGGCACTCCTCATATA 59.584 44.000 0.00 0.00 0.00 0.86
2300 2372 5.538813 ACTTATCGGCACTCCTCATATACAA 59.461 40.000 0.00 0.00 0.00 2.41
2348 2420 4.024545 GGGCGGGTTTCGGAAGGA 62.025 66.667 0.00 0.00 39.69 3.36
2349 2421 2.032987 GGCGGGTTTCGGAAGGAA 59.967 61.111 0.00 0.00 39.69 3.36
2355 2427 3.015516 GTTTCGGAAGGAACTGGCA 57.984 52.632 0.00 0.00 46.27 4.92
2360 2432 2.054453 GGAAGGAACTGGCATGCCC 61.054 63.158 33.44 17.84 40.86 5.36
2364 2436 3.134127 GAACTGGCATGCCCGGAC 61.134 66.667 33.44 20.18 43.17 4.79
2386 2458 0.174845 GTCCGTCATGTTGGATCCGA 59.825 55.000 7.39 1.27 36.48 4.55
2390 2462 0.810031 GTCATGTTGGATCCGACCCG 60.810 60.000 26.50 18.02 0.00 5.28
2391 2463 1.220749 CATGTTGGATCCGACCCGT 59.779 57.895 26.50 11.89 0.00 5.28
2404 2476 4.047125 CCCGTGATGGCCCACCTT 62.047 66.667 0.00 0.00 36.63 3.50
2425 2497 4.166246 TGACTCCACATATAGTCGTCCT 57.834 45.455 0.00 0.00 44.14 3.85
2472 2544 2.125753 CACTCCACTCAGCTCCGC 60.126 66.667 0.00 0.00 0.00 5.54
2473 2545 3.386237 ACTCCACTCAGCTCCGCC 61.386 66.667 0.00 0.00 0.00 6.13
2474 2546 4.154347 CTCCACTCAGCTCCGCCC 62.154 72.222 0.00 0.00 0.00 6.13
2475 2547 4.704103 TCCACTCAGCTCCGCCCT 62.704 66.667 0.00 0.00 0.00 5.19
2497 2570 2.022240 GCTCCCTTTCGGCGATCTCT 62.022 60.000 11.76 0.00 0.00 3.10
2553 2626 2.039418 CCGACCACTCCTAATCCATCA 58.961 52.381 0.00 0.00 0.00 3.07
2560 2633 4.147321 CACTCCTAATCCATCAATTGGGG 58.853 47.826 5.42 8.10 46.45 4.96
2561 2634 3.160269 CTCCTAATCCATCAATTGGGGC 58.840 50.000 5.42 0.00 46.45 5.80
2562 2635 2.517553 TCCTAATCCATCAATTGGGGCA 59.482 45.455 5.42 0.00 46.45 5.36
2563 2636 3.142597 TCCTAATCCATCAATTGGGGCAT 59.857 43.478 5.42 3.28 46.45 4.40
2564 2637 3.512724 CCTAATCCATCAATTGGGGCATC 59.487 47.826 5.42 0.00 46.45 3.91
2565 2638 2.779429 ATCCATCAATTGGGGCATCA 57.221 45.000 5.42 0.00 46.45 3.07
2566 2639 2.779429 TCCATCAATTGGGGCATCAT 57.221 45.000 5.42 0.00 46.45 2.45
2567 2640 3.049108 TCCATCAATTGGGGCATCATT 57.951 42.857 5.42 0.00 46.45 2.57
2573 2646 2.436542 CAATTGGGGCATCATTCCATGT 59.563 45.455 0.00 0.00 0.00 3.21
2574 2647 3.616343 ATTGGGGCATCATTCCATGTA 57.384 42.857 0.00 0.00 0.00 2.29
2607 2680 3.047877 GGAGGTTGTGGCCGTTCG 61.048 66.667 0.00 0.00 0.00 3.95
2647 2720 3.444805 GAGGAGTGCGCTCGACCT 61.445 66.667 23.35 23.35 42.53 3.85
2706 2779 3.001902 AACAAGCGCTCGGATCCGA 62.002 57.895 33.55 33.55 46.87 4.55
2708 2781 4.554363 AAGCGCTCGGATCCGACG 62.554 66.667 34.55 34.55 44.01 5.12
2736 2809 1.880340 GCTCGAGGTCCATCTTGCG 60.880 63.158 15.58 0.00 0.00 4.85
2746 2819 1.821332 CATCTTGCGCCCCTTCTCC 60.821 63.158 4.18 0.00 0.00 3.71
2785 2858 2.541466 GGCTATAGGGATAGGTGTGCT 58.459 52.381 1.04 0.00 36.32 4.40
2788 2861 0.969894 ATAGGGATAGGTGTGCTCGC 59.030 55.000 0.00 0.00 0.00 5.03
2789 2862 0.106167 TAGGGATAGGTGTGCTCGCT 60.106 55.000 0.00 0.00 36.35 4.93
2849 2935 2.994995 TGTCGATGTGGCGGAGGT 60.995 61.111 0.00 0.00 0.00 3.85
2878 2965 1.375268 GCTGCCGCAGAAGAGAAGT 60.375 57.895 24.80 0.00 32.44 3.01
2882 2969 1.285578 GCCGCAGAAGAGAAGTCATC 58.714 55.000 0.00 0.00 0.00 2.92
2890 2977 0.811915 AGAGAAGTCATCCGTGTCCG 59.188 55.000 0.00 0.00 0.00 4.79
2917 3005 0.598065 ACAAGCGGCAAAGGATGAAC 59.402 50.000 1.45 0.00 0.00 3.18
2922 3010 0.950836 CGGCAAAGGATGAACACACA 59.049 50.000 0.00 0.00 0.00 3.72
2945 3033 0.818296 CCTCGTCCGAGAACAATCCT 59.182 55.000 17.73 0.00 44.53 3.24
2950 3038 1.815421 CCGAGAACAATCCTGGGCG 60.815 63.158 0.00 0.00 0.00 6.13
2954 3042 1.749258 GAACAATCCTGGGCGGTCC 60.749 63.158 0.00 0.00 0.00 4.46
2967 3055 2.510906 GGTCCGTGCCATAGCCAT 59.489 61.111 0.00 0.00 38.69 4.40
2973 3061 1.230635 CGTGCCATAGCCATACTGCC 61.231 60.000 0.00 0.00 38.69 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.737008 GGAGTTGTCGGTCCTTCGC 60.737 63.158 0.00 0.00 0.00 4.70
37 38 1.697432 TGGTGTTGATCCTTCGGAGTT 59.303 47.619 0.00 0.00 34.05 3.01
72 74 1.376543 CACTCGGATTGCTCAATGCT 58.623 50.000 11.35 0.00 43.37 3.79
143 146 1.403647 CGGACGACATGGTCTTGCTTA 60.404 52.381 0.00 0.00 37.12 3.09
154 158 0.816018 TTGCAAACACCGGACGACAT 60.816 50.000 9.46 0.00 0.00 3.06
155 159 1.433053 CTTGCAAACACCGGACGACA 61.433 55.000 9.46 0.00 0.00 4.35
165 169 1.804151 GACGATGTAGCCTTGCAAACA 59.196 47.619 0.00 1.87 32.88 2.83
200 204 0.798771 GTCAGACCTGTCATCGTCGC 60.799 60.000 0.00 0.00 34.10 5.19
258 270 1.442857 CCGATCGCCGTCATAGCTC 60.443 63.158 10.32 0.00 36.31 4.09
263 275 2.417516 CCTTCCGATCGCCGTCAT 59.582 61.111 10.32 0.00 36.31 3.06
264 276 3.833645 CCCTTCCGATCGCCGTCA 61.834 66.667 10.32 0.00 36.31 4.35
284 296 3.710722 ACTTCCTCGCCAGCCCTG 61.711 66.667 0.00 0.00 0.00 4.45
311 323 6.143915 ACTAGATTATAAACAGGAGAGGGCA 58.856 40.000 0.00 0.00 0.00 5.36
378 391 0.322546 AGATCACCAAACGGGGAAGC 60.323 55.000 0.00 0.00 40.18 3.86
398 411 7.543172 GCACAATTCACATAAACATCACTCAAT 59.457 33.333 0.00 0.00 0.00 2.57
402 415 5.181056 TCGCACAATTCACATAAACATCACT 59.819 36.000 0.00 0.00 0.00 3.41
425 438 4.122046 ACGTACAAACTGGTACCAAACTC 58.878 43.478 17.11 2.48 40.37 3.01
459 472 6.989437 GTAGATCACGAAACGATCAAAATCA 58.011 36.000 0.00 0.00 41.49 2.57
520 538 4.563374 CCACACCCGCATATCTCATATTCA 60.563 45.833 0.00 0.00 0.00 2.57
550 568 2.619074 GCACCTTGCACTCCCTAAATCT 60.619 50.000 0.00 0.00 44.26 2.40
591 611 1.464997 GCCGGAGTTGACAAATCTGAC 59.535 52.381 22.72 10.19 0.00 3.51
592 612 1.347707 AGCCGGAGTTGACAAATCTGA 59.652 47.619 22.72 0.00 0.00 3.27
601 621 1.078918 CATCTGCAGCCGGAGTTGA 60.079 57.895 9.47 0.00 33.40 3.18
642 662 2.093921 TCAAATATCAGCGGACCGTGAA 60.094 45.455 16.73 9.06 0.00 3.18
657 683 8.328758 AGATACACAAAATCAGACCCTCAAATA 58.671 33.333 0.00 0.00 0.00 1.40
683 710 9.090103 CCCCAGAGTAGTTTATTATACTCATCA 57.910 37.037 13.22 0.00 46.79 3.07
684 711 9.091220 ACCCCAGAGTAGTTTATTATACTCATC 57.909 37.037 13.22 0.65 46.79 2.92
685 712 9.448587 AACCCCAGAGTAGTTTATTATACTCAT 57.551 33.333 13.22 0.00 46.79 2.90
711 738 2.224523 CCTAGTTCCAACAACTGCCTCA 60.225 50.000 0.00 0.00 0.00 3.86
884 918 6.272318 CAAAAGGAAACACAAAGCACTGATA 58.728 36.000 0.00 0.00 0.00 2.15
901 935 2.825532 GGATTGGTTAGCAGCAAAAGGA 59.174 45.455 0.00 0.00 43.52 3.36
1622 1678 1.481819 GCTGTTGCTTGCGTTTGGTG 61.482 55.000 0.00 0.00 36.03 4.17
2036 2101 4.870221 AGGTCGTGTACAAAGAACAAAC 57.130 40.909 16.83 1.63 0.00 2.93
2054 2119 2.304470 TGGTGTACATGCATGTGTAGGT 59.696 45.455 36.72 15.60 41.89 3.08
2082 2147 7.891183 TTTGAAGTCCAAAAACAAAATTCGA 57.109 28.000 0.00 0.00 41.43 3.71
2083 2148 9.553418 AAATTTGAAGTCCAAAAACAAAATTCG 57.447 25.926 0.00 0.00 46.64 3.34
2145 2217 5.461737 GCTGTAGATGCTCTCACTATGTTTC 59.538 44.000 0.00 0.00 0.00 2.78
2157 2229 0.461961 ACTTCCGGCTGTAGATGCTC 59.538 55.000 0.00 0.00 0.00 4.26
2169 2241 0.539051 AGGATGCTTGAGACTTCCGG 59.461 55.000 0.00 0.00 36.67 5.14
2202 2274 0.179056 ATTAGTGATTGGGCCGTCCG 60.179 55.000 0.00 0.00 38.76 4.79
2241 2313 0.442310 CGGTTATTGAGGCGTGTGTG 59.558 55.000 0.00 0.00 0.00 3.82
2272 2344 1.067821 GAGGAGTGCCGATAAGTCTGG 59.932 57.143 0.00 0.00 39.96 3.86
2279 2351 4.219944 GGTTGTATATGAGGAGTGCCGATA 59.780 45.833 0.00 0.00 39.96 2.92
2281 2353 2.364324 GGTTGTATATGAGGAGTGCCGA 59.636 50.000 0.00 0.00 39.96 5.54
2288 2360 6.272324 CCCTAGATTTGGGTTGTATATGAGGA 59.728 42.308 0.00 0.00 39.82 3.71
2297 2369 0.034477 CCGCCCTAGATTTGGGTTGT 60.034 55.000 0.00 0.00 46.22 3.32
2300 2372 3.331293 CCCGCCCTAGATTTGGGT 58.669 61.111 0.00 0.00 46.22 4.51
2336 2408 0.536460 TGCCAGTTCCTTCCGAAACC 60.536 55.000 0.00 0.00 30.39 3.27
2337 2409 1.200020 CATGCCAGTTCCTTCCGAAAC 59.800 52.381 0.00 0.00 30.39 2.78
2338 2410 1.533625 CATGCCAGTTCCTTCCGAAA 58.466 50.000 0.00 0.00 30.39 3.46
2339 2411 0.960364 GCATGCCAGTTCCTTCCGAA 60.960 55.000 6.36 0.00 0.00 4.30
2340 2412 1.377202 GCATGCCAGTTCCTTCCGA 60.377 57.895 6.36 0.00 0.00 4.55
2341 2413 2.409870 GGCATGCCAGTTCCTTCCG 61.410 63.158 32.08 0.00 35.81 4.30
2342 2414 2.054453 GGGCATGCCAGTTCCTTCC 61.054 63.158 36.56 13.39 37.98 3.46
2343 2415 2.409870 CGGGCATGCCAGTTCCTTC 61.410 63.158 36.56 16.45 37.98 3.46
2344 2416 2.361610 CGGGCATGCCAGTTCCTT 60.362 61.111 36.56 0.00 37.98 3.36
2345 2417 4.431131 CCGGGCATGCCAGTTCCT 62.431 66.667 36.56 0.00 37.98 3.36
2346 2418 4.424711 TCCGGGCATGCCAGTTCC 62.425 66.667 36.56 18.67 37.98 3.62
2347 2419 3.134127 GTCCGGGCATGCCAGTTC 61.134 66.667 36.56 22.56 37.98 3.01
2364 2436 1.752501 GATCCAACATGACGGACGCG 61.753 60.000 3.53 3.53 33.05 6.01
2375 2447 1.261938 ATCACGGGTCGGATCCAACA 61.262 55.000 13.41 0.00 0.00 3.33
2378 2450 2.431454 CCATCACGGGTCGGATCCA 61.431 63.158 13.41 0.00 0.00 3.41
2390 2462 0.678048 GAGTCAAGGTGGGCCATCAC 60.678 60.000 21.02 8.72 37.19 3.06
2391 2463 1.685224 GAGTCAAGGTGGGCCATCA 59.315 57.895 21.02 0.00 37.19 3.07
2404 2476 4.135306 GAGGACGACTATATGTGGAGTCA 58.865 47.826 4.64 0.00 41.87 3.41
2425 2497 1.326951 TTGATCCGGTGAGCGGATGA 61.327 55.000 38.86 30.14 45.20 2.92
2439 2511 0.321653 AGTGGAGTGCCGGTTTGATC 60.322 55.000 1.90 0.00 36.79 2.92
2446 2518 3.302347 GAGTGGAGTGGAGTGCCGG 62.302 68.421 0.00 0.00 36.79 6.13
2565 2638 2.022035 TGACCTCCTCCCTACATGGAAT 60.022 50.000 0.00 0.00 38.35 3.01
2566 2639 1.364678 TGACCTCCTCCCTACATGGAA 59.635 52.381 0.00 0.00 38.35 3.53
2567 2640 1.015609 TGACCTCCTCCCTACATGGA 58.984 55.000 0.00 0.00 38.35 3.41
2573 2646 0.254154 TCCTCCTGACCTCCTCCCTA 60.254 60.000 0.00 0.00 0.00 3.53
2574 2647 1.547755 TCCTCCTGACCTCCTCCCT 60.548 63.158 0.00 0.00 0.00 4.20
2630 2703 2.054140 CTAGGTCGAGCGCACTCCTC 62.054 65.000 11.47 0.00 40.03 3.71
2647 2720 3.238788 TGCCAGATCGAATCCTACCTA 57.761 47.619 0.00 0.00 0.00 3.08
2706 2779 2.363795 TCGAGCTTCCATCCCCGT 60.364 61.111 0.00 0.00 0.00 5.28
2708 2781 2.034048 GACCTCGAGCTTCCATCCCC 62.034 65.000 6.99 0.00 0.00 4.81
2712 2785 2.922162 ATGGACCTCGAGCTTCCAT 58.078 52.632 28.58 28.58 43.47 3.41
2746 2819 0.172803 CCTTGTACTCCTTCGGACCG 59.827 60.000 7.84 7.84 0.00 4.79
2752 2825 3.579151 CCCTATAGCCCTTGTACTCCTTC 59.421 52.174 0.00 0.00 0.00 3.46
2753 2826 3.209152 TCCCTATAGCCCTTGTACTCCTT 59.791 47.826 0.00 0.00 0.00 3.36
2767 2840 2.164624 GCGAGCACACCTATCCCTATAG 59.835 54.545 0.00 0.00 35.73 1.31
2785 2858 3.466836 CCCATCTGCTTATTTACAGCGA 58.533 45.455 0.00 0.00 40.45 4.93
2788 2861 3.809832 CGTCCCCATCTGCTTATTTACAG 59.190 47.826 0.00 0.00 35.15 2.74
2789 2862 3.433031 CCGTCCCCATCTGCTTATTTACA 60.433 47.826 0.00 0.00 0.00 2.41
2860 2946 1.357991 GACTTCTCTTCTGCGGCAGC 61.358 60.000 24.78 0.31 45.41 5.25
2864 2950 1.800655 CGGATGACTTCTCTTCTGCGG 60.801 57.143 0.00 0.00 0.00 5.69
2882 2969 3.118454 GTGGTGATGCGGACACGG 61.118 66.667 0.00 0.00 41.36 4.94
2890 2977 2.419057 TTTGCCGCTTGTGGTGATGC 62.419 55.000 2.01 0.00 0.00 3.91
2931 3019 1.602237 GCCCAGGATTGTTCTCGGA 59.398 57.895 0.00 0.00 0.00 4.55
2950 3038 0.602905 GTATGGCTATGGCACGGACC 60.603 60.000 2.58 0.00 41.84 4.46
2954 3042 2.238353 GCAGTATGGCTATGGCACG 58.762 57.895 2.58 0.00 41.84 5.34


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

AutoCloner maintained by Alex Coulton.