Multiple sequence alignment - TraesCS7D01G524600

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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 TraesCS7D01G524600 chr7D 100.000 3118 0 0 1 3118 620474493 620477610 0.000000e+00 5758.0
1 TraesCS7D01G524600 chr7D 91.055 559 46 2 1574 2128 620282139 620282697 0.000000e+00 752.0
2 TraesCS7D01G524600 chr7D 86.471 510 57 8 998 1501 620281539 620282042 1.630000e-152 549.0
3 TraesCS7D01G524600 chr7B 94.407 1341 64 7 954 2294 716132708 716134037 0.000000e+00 2050.0
4 TraesCS7D01G524600 chr7B 92.560 914 36 14 1 896 716131790 716132689 0.000000e+00 1282.0
5 TraesCS7D01G524600 chr7B 91.351 555 39 5 1574 2122 716041890 716042441 0.000000e+00 750.0
6 TraesCS7D01G524600 chr7B 84.190 506 60 8 1000 1495 716041324 716041819 1.010000e-129 473.0
7 TraesCS7D01G524600 chr7B 100.000 44 0 0 896 939 696148559 696148516 7.170000e-12 82.4
8 TraesCS7D01G524600 chr7B 100.000 43 0 0 897 939 654494844 654494886 2.580000e-11 80.5
9 TraesCS7D01G524600 chr7B 100.000 43 0 0 897 939 654509026 654509068 2.580000e-11 80.5
10 TraesCS7D01G524600 chr7B 100.000 43 0 0 897 939 654785974 654786016 2.580000e-11 80.5
11 TraesCS7D01G524600 chr7A 85.652 1150 120 25 998 2122 714617905 714616776 0.000000e+00 1168.0
12 TraesCS7D01G524600 chr7A 74.725 182 32 8 1132 1309 735108747 735108576 5.580000e-08 69.4
13 TraesCS7D01G524600 chr6B 88.903 775 62 7 3 753 718274625 718275399 0.000000e+00 933.0
14 TraesCS7D01G524600 chr6B 95.918 49 2 0 891 939 699140390 699140438 2.580000e-11 80.5
15 TraesCS7D01G524600 chr3A 86.705 692 72 18 2439 3115 699841825 699841139 0.000000e+00 750.0
16 TraesCS7D01G524600 chr4D 85.734 715 87 12 2408 3112 111143139 111143848 0.000000e+00 741.0
17 TraesCS7D01G524600 chr4D 85.556 90 11 2 1243 1330 502489024 502489113 3.310000e-15 93.5
18 TraesCS7D01G524600 chr4A 84.807 724 91 15 2408 3118 465773404 465772687 0.000000e+00 710.0
19 TraesCS7D01G524600 chr5A 84.732 727 89 18 2407 3118 156950431 156951150 0.000000e+00 708.0
20 TraesCS7D01G524600 chr5A 85.590 687 86 10 2407 3083 635550931 635550248 0.000000e+00 708.0
21 TraesCS7D01G524600 chr5A 83.333 102 15 2 1230 1330 685793483 685793583 3.310000e-15 93.5
22 TraesCS7D01G524600 chr5D 84.605 721 90 16 2408 3118 548970505 548969796 0.000000e+00 697.0
23 TraesCS7D01G524600 chr5D 85.147 680 86 12 2408 3075 486744261 486743585 0.000000e+00 682.0
24 TraesCS7D01G524600 chr5D 83.079 721 110 10 2407 3118 133671343 133672060 0.000000e+00 645.0
25 TraesCS7D01G524600 chr5D 89.588 461 38 2 1 460 528220774 528221225 7.500000e-161 577.0
26 TraesCS7D01G524600 chr2B 83.671 741 97 16 2399 3118 637898421 637897684 0.000000e+00 676.0
27 TraesCS7D01G524600 chr3D 83.471 726 94 20 2407 3118 36630598 36629885 0.000000e+00 652.0
28 TraesCS7D01G524600 chr3D 81.250 208 27 7 1132 1339 469805183 469804988 1.160000e-34 158.0
29 TraesCS7D01G524600 chr3D 79.500 200 30 6 1132 1331 493036731 493036543 7.020000e-27 132.0
30 TraesCS7D01G524600 chr4B 100.000 44 0 0 895 938 615140431 615140388 7.170000e-12 82.4
31 TraesCS7D01G524600 chr4B 97.826 46 1 0 894 939 88423361 88423406 2.580000e-11 80.5
32 TraesCS7D01G524600 chrUn 100.000 43 0 0 897 939 278315470 278315512 2.580000e-11 80.5
33 TraesCS7D01G524600 chr1B 100.000 43 0 0 897 939 15386190 15386232 2.580000e-11 80.5
34 TraesCS7D01G524600 chr3B 75.796 157 26 5 1129 1283 508757348 508757494 5.580000e-08 69.4


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 TraesCS7D01G524600 chr7D 620474493 620477610 3117 False 5758.0 5758 100.0000 1 3118 1 chr7D.!!$F1 3117
1 TraesCS7D01G524600 chr7D 620281539 620282697 1158 False 650.5 752 88.7630 998 2128 2 chr7D.!!$F2 1130
2 TraesCS7D01G524600 chr7B 716131790 716134037 2247 False 1666.0 2050 93.4835 1 2294 2 chr7B.!!$F5 2293
3 TraesCS7D01G524600 chr7B 716041324 716042441 1117 False 611.5 750 87.7705 1000 2122 2 chr7B.!!$F4 1122
4 TraesCS7D01G524600 chr7A 714616776 714617905 1129 True 1168.0 1168 85.6520 998 2122 1 chr7A.!!$R1 1124
5 TraesCS7D01G524600 chr6B 718274625 718275399 774 False 933.0 933 88.9030 3 753 1 chr6B.!!$F2 750
6 TraesCS7D01G524600 chr3A 699841139 699841825 686 True 750.0 750 86.7050 2439 3115 1 chr3A.!!$R1 676
7 TraesCS7D01G524600 chr4D 111143139 111143848 709 False 741.0 741 85.7340 2408 3112 1 chr4D.!!$F1 704
8 TraesCS7D01G524600 chr4A 465772687 465773404 717 True 710.0 710 84.8070 2408 3118 1 chr4A.!!$R1 710
9 TraesCS7D01G524600 chr5A 156950431 156951150 719 False 708.0 708 84.7320 2407 3118 1 chr5A.!!$F1 711
10 TraesCS7D01G524600 chr5A 635550248 635550931 683 True 708.0 708 85.5900 2407 3083 1 chr5A.!!$R1 676
11 TraesCS7D01G524600 chr5D 548969796 548970505 709 True 697.0 697 84.6050 2408 3118 1 chr5D.!!$R2 710
12 TraesCS7D01G524600 chr5D 486743585 486744261 676 True 682.0 682 85.1470 2408 3075 1 chr5D.!!$R1 667
13 TraesCS7D01G524600 chr5D 133671343 133672060 717 False 645.0 645 83.0790 2407 3118 1 chr5D.!!$F1 711
14 TraesCS7D01G524600 chr2B 637897684 637898421 737 True 676.0 676 83.6710 2399 3118 1 chr2B.!!$R1 719
15 TraesCS7D01G524600 chr3D 36629885 36630598 713 True 652.0 652 83.4710 2407 3118 1 chr3D.!!$R1 711

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
970 996 0.24746 CTGACCACTGAAGATCGGCA 59.753 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 2727 1.068333 CCCGTCTTTCTTTCGTACCGA 60.068 52.381 0.0 0.0 0.0 4.69 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
93 97 7.264294 ACAATCCTATTTCTTCTCCTCTTGT 57.736 36.000 0.00 0.00 0.00 3.16
226 238 0.759346 ACCAGGTTCGCTTCAAGAGT 59.241 50.000 0.00 0.00 0.00 3.24
233 245 4.705507 AGGTTCGCTTCAAGAGTATAGTCA 59.294 41.667 10.21 0.00 0.00 3.41
262 274 6.212993 TGATCTAGAGGCTGCATCTGAATATT 59.787 38.462 25.39 7.08 0.00 1.28
306 318 0.752743 AAGTTGCTGCTGAAGTGGCA 60.753 50.000 0.00 0.00 38.10 4.92
325 338 3.002553 GGCATTTTCTTTTTGCACCACAG 59.997 43.478 0.00 0.00 38.12 3.66
337 350 1.792949 GCACCACAGTTTGAGAGTACG 59.207 52.381 0.00 0.00 0.00 3.67
665 678 1.283321 GGTCCAGAAAAGCCCAGATCT 59.717 52.381 0.00 0.00 0.00 2.75
666 679 2.363683 GTCCAGAAAAGCCCAGATCTG 58.636 52.381 16.24 16.24 39.16 2.90
667 680 1.101331 CCAGAAAAGCCCAGATCTGC 58.899 55.000 17.76 7.09 38.34 4.26
803 829 1.659954 GATGAGCTCGCGTGCTAGG 60.660 63.158 32.83 6.62 44.17 3.02
804 830 3.781770 ATGAGCTCGCGTGCTAGGC 62.782 63.158 32.83 21.65 44.17 3.93
805 831 4.498520 GAGCTCGCGTGCTAGGCA 62.499 66.667 32.83 0.00 44.17 4.75
806 832 4.504916 AGCTCGCGTGCTAGGCAG 62.505 66.667 31.99 8.40 42.10 4.85
818 844 2.275318 GCTAGGCAGCTACTCAACTTG 58.725 52.381 0.00 0.00 44.93 3.16
828 854 6.102663 CAGCTACTCAACTTGCTGTTATACT 58.897 40.000 0.00 0.00 45.31 2.12
831 857 7.122948 AGCTACTCAACTTGCTGTTATACTAGT 59.877 37.037 0.00 0.00 37.07 2.57
838 864 9.343103 CAACTTGCTGTTATACTAGTATATCCG 57.657 37.037 20.67 16.78 37.07 4.18
839 865 8.859236 ACTTGCTGTTATACTAGTATATCCGA 57.141 34.615 20.67 5.81 0.00 4.55
840 866 8.728833 ACTTGCTGTTATACTAGTATATCCGAC 58.271 37.037 20.67 16.19 0.00 4.79
841 867 8.625786 TTGCTGTTATACTAGTATATCCGACA 57.374 34.615 20.67 19.10 0.00 4.35
842 868 8.803397 TGCTGTTATACTAGTATATCCGACAT 57.197 34.615 20.67 0.00 0.00 3.06
843 869 9.895138 TGCTGTTATACTAGTATATCCGACATA 57.105 33.333 20.67 11.92 0.00 2.29
896 922 4.767578 AGAATGGATCAGAAGCTTGCTA 57.232 40.909 2.10 0.00 0.00 3.49
897 923 4.450053 AGAATGGATCAGAAGCTTGCTAC 58.550 43.478 2.10 0.00 0.00 3.58
899 925 1.908619 TGGATCAGAAGCTTGCTACCA 59.091 47.619 2.10 4.27 0.00 3.25
900 926 2.305635 TGGATCAGAAGCTTGCTACCAA 59.694 45.455 2.10 0.00 0.00 3.67
951 977 5.851047 AAATTACAATTGCTGAAGCTTGC 57.149 34.783 2.10 1.98 42.66 4.01
952 978 4.796038 ATTACAATTGCTGAAGCTTGCT 57.204 36.364 2.10 0.00 42.66 3.91
957 983 0.466007 TTGCTGAAGCTTGCTGACCA 60.466 50.000 2.10 0.00 42.66 4.02
965 991 1.350351 AGCTTGCTGACCACTGAAGAT 59.650 47.619 0.00 0.00 0.00 2.40
970 996 0.247460 CTGACCACTGAAGATCGGCA 59.753 55.000 0.00 0.00 0.00 5.69
980 1006 4.838152 GATCGGCAGGGCTCGCAA 62.838 66.667 2.96 0.00 0.00 4.85
1071 1097 4.624364 CACAGGGTCGTGCTGGCA 62.624 66.667 0.00 0.00 0.00 4.92
1221 1247 2.438795 GAGGAGCCGGAGTCGTCT 60.439 66.667 5.05 0.00 33.95 4.18
1228 1254 2.338015 CCGGAGTCGTCTTTCGGGA 61.338 63.158 14.12 0.00 40.32 5.14
1371 1406 3.699894 CGGGAGCAGCAGGTGAGT 61.700 66.667 3.02 0.00 0.00 3.41
1374 1409 2.267324 GAGCAGCAGGTGAGTCCC 59.733 66.667 3.02 0.00 36.75 4.46
1545 1580 4.669700 TGCTTCAGTTACTACAGTAGGGA 58.330 43.478 12.42 0.00 0.00 4.20
1549 1584 7.104290 GCTTCAGTTACTACAGTAGGGATTTT 58.896 38.462 12.42 0.00 0.00 1.82
1550 1585 7.606839 GCTTCAGTTACTACAGTAGGGATTTTT 59.393 37.037 12.42 0.00 0.00 1.94
1566 1601 1.229428 TTTTCTGCGCTCACTCCTTG 58.771 50.000 9.73 0.00 0.00 3.61
1568 1603 2.357881 CTGCGCTCACTCCTTGCA 60.358 61.111 9.73 0.00 0.00 4.08
1572 1644 2.758089 CGCTCACTCCTTGCATGCC 61.758 63.158 16.68 0.00 0.00 4.40
1653 1725 1.530771 GGCATGGACATGGAGAGCT 59.469 57.895 13.63 0.00 39.16 4.09
1680 1752 3.233259 TTCGCGCTGGATGTGGTGA 62.233 57.895 5.56 0.00 0.00 4.02
2140 2215 2.531206 GAGCTCGAATACTGCTTTCGT 58.469 47.619 0.00 0.00 44.69 3.85
2183 2258 4.266976 CGGTCGTATCTCACACAATAAACC 59.733 45.833 0.00 0.00 0.00 3.27
2190 2265 6.609237 ATCTCACACAATAAACCATGATCG 57.391 37.500 0.00 0.00 0.00 3.69
2221 2296 2.455557 TCAAATGTCCATTTCGGCCAT 58.544 42.857 2.24 0.00 38.84 4.40
2222 2297 2.166050 TCAAATGTCCATTTCGGCCATG 59.834 45.455 2.24 0.00 38.84 3.66
2223 2298 2.142356 AATGTCCATTTCGGCCATGA 57.858 45.000 2.24 0.00 33.14 3.07
2224 2299 2.369983 ATGTCCATTTCGGCCATGAT 57.630 45.000 2.24 0.00 33.14 2.45
2225 2300 1.679139 TGTCCATTTCGGCCATGATC 58.321 50.000 2.24 0.00 33.14 2.92
2226 2301 0.588252 GTCCATTTCGGCCATGATCG 59.412 55.000 2.24 0.00 33.14 3.69
2228 2303 1.134250 TCCATTTCGGCCATGATCGAA 60.134 47.619 15.55 15.55 42.56 3.71
2270 2345 5.165961 TCGAGATCCAAGGAATTTCACTT 57.834 39.130 0.00 0.00 0.00 3.16
2271 2346 5.560724 TCGAGATCCAAGGAATTTCACTTT 58.439 37.500 0.00 0.00 0.00 2.66
2272 2347 6.003950 TCGAGATCCAAGGAATTTCACTTTT 58.996 36.000 0.00 0.00 0.00 2.27
2273 2348 6.490040 TCGAGATCCAAGGAATTTCACTTTTT 59.510 34.615 0.00 0.00 0.00 1.94
2297 2372 8.467402 TTTTTAAACACATGACGACATTTTGT 57.533 26.923 0.00 2.08 33.90 2.83
2298 2373 8.467402 TTTTAAACACATGACGACATTTTGTT 57.533 26.923 14.74 14.74 39.67 2.83
2299 2374 9.569167 TTTTAAACACATGACGACATTTTGTTA 57.431 25.926 18.49 7.38 38.31 2.41
2300 2375 8.549777 TTAAACACATGACGACATTTTGTTAC 57.450 30.769 18.49 0.00 38.31 2.50
2301 2376 5.743026 ACACATGACGACATTTTGTTACA 57.257 34.783 0.00 0.00 34.15 2.41
2302 2377 6.312399 ACACATGACGACATTTTGTTACAT 57.688 33.333 0.00 0.00 34.15 2.29
2303 2378 7.428282 ACACATGACGACATTTTGTTACATA 57.572 32.000 0.00 0.00 34.15 2.29
2304 2379 7.295201 ACACATGACGACATTTTGTTACATAC 58.705 34.615 0.00 0.00 34.15 2.39
2305 2380 6.740905 CACATGACGACATTTTGTTACATACC 59.259 38.462 0.00 0.00 34.15 2.73
2306 2381 6.428465 ACATGACGACATTTTGTTACATACCA 59.572 34.615 0.00 0.00 34.15 3.25
2307 2382 6.862711 TGACGACATTTTGTTACATACCAA 57.137 33.333 0.00 0.00 0.00 3.67
2308 2383 7.260558 TGACGACATTTTGTTACATACCAAA 57.739 32.000 0.00 0.00 0.00 3.28
2309 2384 7.704271 TGACGACATTTTGTTACATACCAAAA 58.296 30.769 0.00 0.00 0.00 2.44
2310 2385 8.353684 TGACGACATTTTGTTACATACCAAAAT 58.646 29.630 4.90 4.90 37.62 1.82
2376 2451 6.976934 AGGGCTCTTTTGAAATTTTACTGA 57.023 33.333 0.00 0.00 0.00 3.41
2377 2452 7.360113 AGGGCTCTTTTGAAATTTTACTGAA 57.640 32.000 0.00 0.00 0.00 3.02
2378 2453 7.791029 AGGGCTCTTTTGAAATTTTACTGAAA 58.209 30.769 0.00 0.00 0.00 2.69
2379 2454 8.264347 AGGGCTCTTTTGAAATTTTACTGAAAA 58.736 29.630 0.00 0.00 38.87 2.29
2380 2455 8.551205 GGGCTCTTTTGAAATTTTACTGAAAAG 58.449 33.333 0.00 0.00 37.94 2.27
2381 2456 9.098355 GGCTCTTTTGAAATTTTACTGAAAAGT 57.902 29.630 0.00 0.00 37.94 2.66
2389 2464 9.191479 TGAAATTTTACTGAAAAGTAAGGACCA 57.809 29.630 0.00 0.00 37.94 4.02
2391 2466 9.811995 AAATTTTACTGAAAAGTAAGGACCAAC 57.188 29.630 0.00 0.00 37.94 3.77
2392 2467 7.941431 TTTTACTGAAAAGTAAGGACCAACA 57.059 32.000 0.00 0.00 35.91 3.33
2393 2468 8.528044 TTTTACTGAAAAGTAAGGACCAACAT 57.472 30.769 0.00 0.00 35.91 2.71
2394 2469 7.739498 TTACTGAAAAGTAAGGACCAACATC 57.261 36.000 0.00 0.00 31.45 3.06
2395 2470 5.690865 ACTGAAAAGTAAGGACCAACATCA 58.309 37.500 0.00 0.00 0.00 3.07
2396 2471 6.306987 ACTGAAAAGTAAGGACCAACATCAT 58.693 36.000 0.00 0.00 0.00 2.45
2397 2472 6.777580 ACTGAAAAGTAAGGACCAACATCATT 59.222 34.615 0.00 0.00 0.00 2.57
2433 2508 1.135859 CAAGAGAGTTCATGCGTTGCC 60.136 52.381 0.00 0.00 0.00 4.52
2436 2511 0.534877 AGAGTTCATGCGTTGCCACA 60.535 50.000 0.00 0.00 0.00 4.17
2437 2512 0.523072 GAGTTCATGCGTTGCCACAT 59.477 50.000 0.00 0.00 0.00 3.21
2446 2523 2.035704 TGCGTTGCCACATGAGAAAAAT 59.964 40.909 0.00 0.00 0.00 1.82
2447 2524 3.254411 TGCGTTGCCACATGAGAAAAATA 59.746 39.130 0.00 0.00 0.00 1.40
2487 2568 5.221925 ACACAATAACCATGACTCAAGACCT 60.222 40.000 0.00 0.00 0.00 3.85
2488 2569 5.707298 CACAATAACCATGACTCAAGACCTT 59.293 40.000 0.00 0.00 0.00 3.50
2537 2619 5.533903 ACATGACATCTTATCATTCTTGCCC 59.466 40.000 0.00 0.00 34.49 5.36
2545 2627 5.997746 TCTTATCATTCTTGCCCTTTATCCG 59.002 40.000 0.00 0.00 0.00 4.18
2581 2664 2.611751 CGACGGAAATGCATGGTCATAA 59.388 45.455 0.00 0.00 0.00 1.90
2593 2676 6.767456 TGCATGGTCATAAATGGTTTCTTTT 58.233 32.000 0.00 0.00 0.00 2.27
2641 2727 6.649973 TGTTCATTTTCAATTTGAATCGGCAT 59.350 30.769 12.39 0.00 36.11 4.40
2747 2836 8.496707 AACATCATATTCAGATTATGCGCATA 57.503 30.769 25.78 25.78 0.00 3.14
2844 2935 5.591877 GCATCTGAATCTGTCCCTAAACAAT 59.408 40.000 0.00 0.00 0.00 2.71
3044 3158 5.458595 ACCAAAATCTCAGGGAGTTTTCTT 58.541 37.500 0.00 0.00 39.74 2.52
3057 3173 7.276438 CAGGGAGTTTTCTTCAAAAAGTGAAAG 59.724 37.037 0.00 0.00 45.67 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 238 6.071672 GCAGCCTCTAGATCAACATGACTATA 60.072 42.308 0.00 0.00 0.00 1.31
233 245 3.647113 AGATGCAGCCTCTAGATCAACAT 59.353 43.478 0.00 0.00 0.00 2.71
286 298 0.039708 GCCACTTCAGCAGCAACTTC 60.040 55.000 0.00 0.00 0.00 3.01
306 318 5.936956 TCAAACTGTGGTGCAAAAAGAAAAT 59.063 32.000 0.00 0.00 0.00 1.82
325 338 3.123621 CCATCTTGCACGTACTCTCAAAC 59.876 47.826 0.00 0.00 0.00 2.93
337 350 1.156736 ACGCACTAACCATCTTGCAC 58.843 50.000 0.00 0.00 34.49 4.57
578 591 1.129064 GAACGTCTCGGTCTCTGTCTC 59.871 57.143 0.00 0.00 40.75 3.36
588 601 4.243270 AGTCCTATTTTTGAACGTCTCGG 58.757 43.478 0.00 0.00 0.00 4.63
698 724 7.205297 TCCTATGGAGCTAACGTTAATTACAC 58.795 38.462 9.68 0.00 0.00 2.90
759 785 3.839293 CTCCTGTCTCAACGAGTAAAGG 58.161 50.000 0.00 0.00 0.00 3.11
771 797 2.093553 AGCTCATCTTTGCTCCTGTCTC 60.094 50.000 0.00 0.00 33.90 3.36
805 831 6.287589 AGTATAACAGCAAGTTGAGTAGCT 57.712 37.500 7.16 0.00 41.50 3.32
806 832 7.259161 ACTAGTATAACAGCAAGTTGAGTAGC 58.741 38.462 7.16 0.00 41.50 3.58
813 839 9.293404 TCGGATATACTAGTATAACAGCAAGTT 57.707 33.333 23.14 6.63 44.27 2.66
814 840 8.728833 GTCGGATATACTAGTATAACAGCAAGT 58.271 37.037 23.14 7.27 32.39 3.16
815 841 8.727910 TGTCGGATATACTAGTATAACAGCAAG 58.272 37.037 23.14 12.18 32.39 4.01
816 842 8.625786 TGTCGGATATACTAGTATAACAGCAA 57.374 34.615 23.14 11.60 32.39 3.91
845 871 9.569122 AAATGGTGCGGTTAAAATATAGAGTAT 57.431 29.630 0.00 0.00 0.00 2.12
846 872 8.832521 CAAATGGTGCGGTTAAAATATAGAGTA 58.167 33.333 0.00 0.00 0.00 2.59
847 873 7.681065 GCAAATGGTGCGGTTAAAATATAGAGT 60.681 37.037 0.00 0.00 45.10 3.24
848 874 6.636850 GCAAATGGTGCGGTTAAAATATAGAG 59.363 38.462 0.00 0.00 45.10 2.43
849 875 6.500041 GCAAATGGTGCGGTTAAAATATAGA 58.500 36.000 0.00 0.00 45.10 1.98
850 876 6.747659 GCAAATGGTGCGGTTAAAATATAG 57.252 37.500 0.00 0.00 45.10 1.31
927 953 6.484308 AGCAAGCTTCAGCAATTGTAATTTTT 59.516 30.769 11.00 0.00 45.16 1.94
928 954 5.993441 AGCAAGCTTCAGCAATTGTAATTTT 59.007 32.000 11.00 0.00 45.16 1.82
929 955 5.407387 CAGCAAGCTTCAGCAATTGTAATTT 59.593 36.000 11.00 0.00 45.16 1.82
930 956 4.927425 CAGCAAGCTTCAGCAATTGTAATT 59.073 37.500 11.00 0.00 45.16 1.40
931 957 4.219070 TCAGCAAGCTTCAGCAATTGTAAT 59.781 37.500 11.00 0.00 45.16 1.89
932 958 3.569277 TCAGCAAGCTTCAGCAATTGTAA 59.431 39.130 11.00 0.00 45.16 2.41
933 959 3.058016 GTCAGCAAGCTTCAGCAATTGTA 60.058 43.478 11.00 0.00 45.16 2.41
934 960 1.958579 TCAGCAAGCTTCAGCAATTGT 59.041 42.857 11.00 0.00 45.16 2.71
935 961 2.325761 GTCAGCAAGCTTCAGCAATTG 58.674 47.619 11.00 0.00 45.16 2.32
936 962 1.271656 GGTCAGCAAGCTTCAGCAATT 59.728 47.619 11.00 0.00 45.16 2.32
937 963 0.886563 GGTCAGCAAGCTTCAGCAAT 59.113 50.000 11.00 0.00 45.16 3.56
938 964 0.466007 TGGTCAGCAAGCTTCAGCAA 60.466 50.000 11.00 0.00 45.16 3.91
939 965 1.148949 TGGTCAGCAAGCTTCAGCA 59.851 52.632 11.00 2.42 45.16 4.41
940 966 0.888285 AGTGGTCAGCAAGCTTCAGC 60.888 55.000 0.00 0.00 42.49 4.26
941 967 0.873054 CAGTGGTCAGCAAGCTTCAG 59.127 55.000 0.00 0.00 0.00 3.02
942 968 0.469494 TCAGTGGTCAGCAAGCTTCA 59.531 50.000 0.00 0.00 0.00 3.02
943 969 1.534595 CTTCAGTGGTCAGCAAGCTTC 59.465 52.381 0.00 0.00 0.00 3.86
944 970 1.141657 TCTTCAGTGGTCAGCAAGCTT 59.858 47.619 0.00 0.00 0.00 3.74
945 971 0.761187 TCTTCAGTGGTCAGCAAGCT 59.239 50.000 0.00 0.00 0.00 3.74
946 972 1.736681 GATCTTCAGTGGTCAGCAAGC 59.263 52.381 0.00 0.00 0.00 4.01
947 973 1.998315 CGATCTTCAGTGGTCAGCAAG 59.002 52.381 0.00 0.00 0.00 4.01
948 974 1.338105 CCGATCTTCAGTGGTCAGCAA 60.338 52.381 0.00 0.00 0.00 3.91
949 975 0.247460 CCGATCTTCAGTGGTCAGCA 59.753 55.000 0.00 0.00 0.00 4.41
950 976 1.086634 GCCGATCTTCAGTGGTCAGC 61.087 60.000 0.00 0.00 0.00 4.26
951 977 0.247460 TGCCGATCTTCAGTGGTCAG 59.753 55.000 0.00 0.00 0.00 3.51
952 978 0.247460 CTGCCGATCTTCAGTGGTCA 59.753 55.000 0.00 0.00 0.00 4.02
957 983 1.965754 GAGCCCTGCCGATCTTCAGT 61.966 60.000 9.33 0.00 0.00 3.41
970 996 1.152963 AAACAGTGTTGCGAGCCCT 60.153 52.632 9.79 0.00 0.00 5.19
1228 1254 3.660724 CCAGATCCCGGGGATGTT 58.339 61.111 32.87 17.55 43.27 2.71
1354 1389 3.655810 GACTCACCTGCTGCTCCCG 62.656 68.421 0.00 0.00 0.00 5.14
1371 1406 1.667154 CGTCGAAGCTCATCTGGGGA 61.667 60.000 0.00 0.00 0.00 4.81
1374 1409 1.880340 GCCGTCGAAGCTCATCTGG 60.880 63.158 0.00 0.00 0.00 3.86
1545 1580 2.191128 AGGAGTGAGCGCAGAAAAAT 57.809 45.000 11.47 0.00 0.00 1.82
1549 1584 1.669115 GCAAGGAGTGAGCGCAGAA 60.669 57.895 11.47 0.00 0.00 3.02
1550 1585 2.047844 GCAAGGAGTGAGCGCAGA 60.048 61.111 11.47 0.00 0.00 4.26
1572 1644 2.825836 GTCGAAGCCTGGCATGGG 60.826 66.667 22.65 7.07 0.00 4.00
1638 1710 0.545171 CACCAGCTCTCCATGTCCAT 59.455 55.000 0.00 0.00 0.00 3.41
1639 1711 1.985614 CACCAGCTCTCCATGTCCA 59.014 57.895 0.00 0.00 0.00 4.02
1640 1712 1.451028 GCACCAGCTCTCCATGTCC 60.451 63.158 0.00 0.00 37.91 4.02
1642 1714 2.673523 GGCACCAGCTCTCCATGT 59.326 61.111 0.00 0.00 41.70 3.21
1858 1930 4.711949 CCCTGAACGGCAGCAGCT 62.712 66.667 0.00 0.00 43.50 4.24
1949 2021 4.382320 GCCACCAGGTCGGCGTAA 62.382 66.667 14.96 0.00 38.82 3.18
2167 2242 6.348498 TCGATCATGGTTTATTGTGTGAGAT 58.652 36.000 0.00 0.00 0.00 2.75
2171 2246 5.972973 CCATTCGATCATGGTTTATTGTGTG 59.027 40.000 7.82 0.00 39.26 3.82
2183 2258 2.291365 TGAAGCCACCATTCGATCATG 58.709 47.619 0.00 0.00 0.00 3.07
2190 2265 2.562298 TGGACATTTGAAGCCACCATTC 59.438 45.455 0.00 0.00 0.00 2.67
2231 2306 7.547722 TGGATCTCGATCGAGTTCAAATAAAAA 59.452 33.333 37.73 21.70 40.72 1.94
2240 2315 2.619177 TCCTTGGATCTCGATCGAGTTC 59.381 50.000 36.68 34.93 42.49 3.01
2272 2347 8.467402 ACAAAATGTCGTCATGTGTTTAAAAA 57.533 26.923 0.00 0.00 32.66 1.94
2273 2348 8.467402 AACAAAATGTCGTCATGTGTTTAAAA 57.533 26.923 14.77 0.00 38.66 1.52
2274 2349 9.011407 GTAACAAAATGTCGTCATGTGTTTAAA 57.989 29.630 21.24 8.65 40.43 1.52
2275 2350 8.182227 TGTAACAAAATGTCGTCATGTGTTTAA 58.818 29.630 21.24 12.44 40.43 1.52
2276 2351 7.694886 TGTAACAAAATGTCGTCATGTGTTTA 58.305 30.769 21.24 13.06 40.43 2.01
2277 2352 6.556212 TGTAACAAAATGTCGTCATGTGTTT 58.444 32.000 21.24 7.35 40.43 2.83
2278 2353 6.125327 TGTAACAAAATGTCGTCATGTGTT 57.875 33.333 20.44 20.44 41.59 3.32
2279 2354 5.743026 TGTAACAAAATGTCGTCATGTGT 57.257 34.783 0.00 1.55 35.80 3.72
2280 2355 6.740905 GGTATGTAACAAAATGTCGTCATGTG 59.259 38.462 0.00 0.94 34.19 3.21
2281 2356 6.428465 TGGTATGTAACAAAATGTCGTCATGT 59.572 34.615 0.00 0.00 34.19 3.21
2282 2357 6.836953 TGGTATGTAACAAAATGTCGTCATG 58.163 36.000 0.00 0.00 34.19 3.07
2283 2358 7.441890 TTGGTATGTAACAAAATGTCGTCAT 57.558 32.000 0.00 0.00 35.59 3.06
2284 2359 6.862711 TTGGTATGTAACAAAATGTCGTCA 57.137 33.333 0.00 0.00 0.00 4.35
2350 2425 9.088987 TCAGTAAAATTTCAAAAGAGCCCTTAT 57.911 29.630 0.00 0.00 31.15 1.73
2351 2426 8.472007 TCAGTAAAATTTCAAAAGAGCCCTTA 57.528 30.769 0.00 0.00 31.15 2.69
2352 2427 7.360113 TCAGTAAAATTTCAAAAGAGCCCTT 57.640 32.000 0.00 0.00 0.00 3.95
2353 2428 6.976934 TCAGTAAAATTTCAAAAGAGCCCT 57.023 33.333 0.00 0.00 0.00 5.19
2354 2429 8.432110 TTTTCAGTAAAATTTCAAAAGAGCCC 57.568 30.769 0.00 0.00 29.59 5.19
2355 2430 9.098355 ACTTTTCAGTAAAATTTCAAAAGAGCC 57.902 29.630 17.37 0.00 35.39 4.70
2363 2438 9.191479 TGGTCCTTACTTTTCAGTAAAATTTCA 57.809 29.630 0.00 0.00 43.57 2.69
2365 2440 9.811995 GTTGGTCCTTACTTTTCAGTAAAATTT 57.188 29.630 0.00 0.00 43.57 1.82
2366 2441 8.973182 TGTTGGTCCTTACTTTTCAGTAAAATT 58.027 29.630 0.00 0.00 43.57 1.82
2367 2442 8.528044 TGTTGGTCCTTACTTTTCAGTAAAAT 57.472 30.769 0.00 0.00 43.57 1.82
2368 2443 7.941431 TGTTGGTCCTTACTTTTCAGTAAAA 57.059 32.000 0.00 0.00 43.57 1.52
2369 2444 7.776030 TGATGTTGGTCCTTACTTTTCAGTAAA 59.224 33.333 0.00 0.00 43.57 2.01
2370 2445 7.284074 TGATGTTGGTCCTTACTTTTCAGTAA 58.716 34.615 0.00 0.00 42.27 2.24
2371 2446 6.833041 TGATGTTGGTCCTTACTTTTCAGTA 58.167 36.000 0.00 0.00 34.06 2.74
2372 2447 5.690865 TGATGTTGGTCCTTACTTTTCAGT 58.309 37.500 0.00 0.00 36.99 3.41
2373 2448 6.824305 ATGATGTTGGTCCTTACTTTTCAG 57.176 37.500 0.00 0.00 0.00 3.02
2374 2449 7.595819 AAATGATGTTGGTCCTTACTTTTCA 57.404 32.000 0.00 0.00 0.00 2.69
2375 2450 8.887036 AAAAATGATGTTGGTCCTTACTTTTC 57.113 30.769 0.00 0.00 0.00 2.29
2397 2472 9.216117 GAACTCTCTTGCTAGTAACCATAAAAA 57.784 33.333 0.00 0.00 0.00 1.94
2404 2479 4.568760 GCATGAACTCTCTTGCTAGTAACC 59.431 45.833 0.00 0.00 45.07 2.85
2405 2480 4.266502 CGCATGAACTCTCTTGCTAGTAAC 59.733 45.833 0.00 0.00 45.87 2.50
2416 2491 2.543578 TGGCAACGCATGAACTCTC 58.456 52.632 0.00 0.00 42.51 3.20
2433 2508 6.468956 GCGTGTGGTATTATTTTTCTCATGTG 59.531 38.462 0.00 0.00 0.00 3.21
2436 2511 5.067283 GGGCGTGTGGTATTATTTTTCTCAT 59.933 40.000 0.00 0.00 0.00 2.90
2437 2512 4.396790 GGGCGTGTGGTATTATTTTTCTCA 59.603 41.667 0.00 0.00 0.00 3.27
2446 2523 2.566279 TGTGTTAGGGCGTGTGGTATTA 59.434 45.455 0.00 0.00 0.00 0.98
2447 2524 1.348366 TGTGTTAGGGCGTGTGGTATT 59.652 47.619 0.00 0.00 0.00 1.89
2487 2568 9.983024 TTGAAATAAAGGACATGGACCTATTAA 57.017 29.630 12.86 2.67 36.67 1.40
2488 2569 9.403583 GTTGAAATAAAGGACATGGACCTATTA 57.596 33.333 12.86 12.80 36.67 0.98
2529 2611 3.504520 GTGAAACGGATAAAGGGCAAGAA 59.495 43.478 0.00 0.00 0.00 2.52
2537 2619 2.671396 CGGGAGTGTGAAACGGATAAAG 59.329 50.000 0.00 0.00 42.39 1.85
2545 2627 2.029964 TCGGCGGGAGTGTGAAAC 59.970 61.111 7.21 0.00 37.35 2.78
2567 2650 6.549433 AGAAACCATTTATGACCATGCATT 57.451 33.333 0.00 0.00 0.00 3.56
2612 2698 9.138062 CCGATTCAAATTGAAAATGAACACATA 57.862 29.630 12.75 0.00 40.12 2.29
2614 2700 6.073873 GCCGATTCAAATTGAAAATGAACACA 60.074 34.615 12.75 0.00 40.12 3.72
2641 2727 1.068333 CCCGTCTTTCTTTCGTACCGA 60.068 52.381 0.00 0.00 0.00 4.69
2726 2812 9.387257 AGAAATATGCGCATAATCTGAATATGA 57.613 29.630 31.82 13.72 33.49 2.15
2770 2859 9.758651 AAACCCTAACTCAAATTTTAACATGTC 57.241 29.630 0.00 0.00 0.00 3.06
3036 3141 8.902540 AAACCTTTCACTTTTTGAAGAAAACT 57.097 26.923 0.00 0.00 45.22 2.66


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

AutoCloner maintained by Alex Coulton.