Multiple sequence alignment - TraesCS3A01G268800

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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 TraesCS3A01G268800 chr3A 100.000 4739 0 0 1 4739 495075818 495071080 0.000000e+00 8752.0
1 TraesCS3A01G268800 chr3A 96.616 916 22 4 1 914 495075551 495076459 0.000000e+00 1511.0
2 TraesCS3A01G268800 chr3D 89.665 3309 252 37 906 4144 373603564 373600276 0.000000e+00 4133.0
3 TraesCS3A01G268800 chr3D 91.707 410 20 3 4341 4739 373599403 373598997 1.490000e-154 556.0
4 TraesCS3A01G268800 chr3D 79.517 786 122 23 1372 2130 593688216 593688989 1.510000e-144 523.0
5 TraesCS3A01G268800 chr3D 94.787 211 9 2 4140 4350 373600022 373599814 1.270000e-85 327.0
6 TraesCS3A01G268800 chr3D 77.515 169 25 11 4575 4739 598188426 598188585 6.530000e-14 89.8
7 TraesCS3A01G268800 chr3D 84.416 77 9 3 4664 4739 598183435 598183509 6.580000e-09 73.1
8 TraesCS3A01G268800 chr3B 88.788 3398 272 45 906 4217 487443484 487440110 0.000000e+00 4063.0
9 TraesCS3A01G268800 chr3B 94.819 579 19 4 4171 4739 487440103 487439526 0.000000e+00 893.0
10 TraesCS3A01G268800 chr7B 77.977 1058 158 39 1074 2109 518463533 518464537 1.140000e-165 593.0
11 TraesCS3A01G268800 chr7B 89.222 167 9 2 4205 4362 726940742 726940576 2.890000e-47 200.0
12 TraesCS3A01G268800 chr7B 76.987 239 44 11 233 467 633009260 633009029 4.980000e-25 126.0
13 TraesCS3A01G268800 chr7A 77.705 1072 162 41 1074 2122 556557604 556558621 6.830000e-163 584.0
14 TraesCS3A01G268800 chr7A 78.378 333 45 14 366 673 511470073 511469743 1.740000e-44 191.0
15 TraesCS3A01G268800 chr7D 91.029 379 21 7 4373 4739 72123392 72123769 2.550000e-137 499.0
16 TraesCS3A01G268800 chr7D 87.582 153 15 2 4019 4168 72122695 72122846 1.750000e-39 174.0
17 TraesCS3A01G268800 chr7D 85.057 174 23 3 4185 4356 72122833 72123005 1.750000e-39 174.0
18 TraesCS3A01G268800 chr7D 89.147 129 11 2 4019 4144 540791384 540791256 1.770000e-34 158.0
19 TraesCS3A01G268800 chr7D 77.536 138 18 10 4610 4739 58737722 58737590 2.370000e-08 71.3
20 TraesCS3A01G268800 chr6D 77.403 593 80 26 127 670 28664177 28664764 2.140000e-78 303.0
21 TraesCS3A01G268800 chr6D 82.051 234 22 10 276 496 384280053 384279827 1.050000e-41 182.0
22 TraesCS3A01G268800 chr4A 76.152 499 75 22 127 591 618170108 618170596 6.170000e-54 222.0
23 TraesCS3A01G268800 chr2B 83.568 213 20 8 4536 4734 776403816 776404027 8.100000e-43 185.0
24 TraesCS3A01G268800 chr5D 77.054 353 50 23 127 469 377952027 377952358 1.750000e-39 174.0
25 TraesCS3A01G268800 chr5D 80.882 204 31 8 4539 4739 27988402 27988600 2.280000e-33 154.0
26 TraesCS3A01G268800 chr2A 75.325 462 56 28 4305 4739 759303247 759302817 8.160000e-38 169.0
27 TraesCS3A01G268800 chr2A 75.510 343 60 17 136 469 678977113 678976786 3.820000e-31 147.0
28 TraesCS3A01G268800 chr1B 91.429 70 6 0 4670 4739 553133717 553133786 3.900000e-16 97.1
29 TraesCS3A01G268800 chr1A 97.500 40 1 0 552 591 20886685 20886724 8.510000e-08 69.4
30 TraesCS3A01G268800 chr1A 100.000 28 0 0 3912 3939 573927909 573927936 9.000000e-03 52.8


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 TraesCS3A01G268800 chr3A 495071080 495075818 4738 True 8752.000000 8752 100.000000 1 4739 1 chr3A.!!$R1 4738
1 TraesCS3A01G268800 chr3A 495075551 495076459 908 False 1511.000000 1511 96.616000 1 914 1 chr3A.!!$F1 913
2 TraesCS3A01G268800 chr3D 373598997 373603564 4567 True 1672.000000 4133 92.053000 906 4739 3 chr3D.!!$R1 3833
3 TraesCS3A01G268800 chr3D 593688216 593688989 773 False 523.000000 523 79.517000 1372 2130 1 chr3D.!!$F1 758
4 TraesCS3A01G268800 chr3B 487439526 487443484 3958 True 2478.000000 4063 91.803500 906 4739 2 chr3B.!!$R1 3833
5 TraesCS3A01G268800 chr7B 518463533 518464537 1004 False 593.000000 593 77.977000 1074 2109 1 chr7B.!!$F1 1035
6 TraesCS3A01G268800 chr7A 556557604 556558621 1017 False 584.000000 584 77.705000 1074 2122 1 chr7A.!!$F1 1048
7 TraesCS3A01G268800 chr7D 72122695 72123769 1074 False 282.333333 499 87.889333 4019 4739 3 chr7D.!!$F1 720
8 TraesCS3A01G268800 chr6D 28664177 28664764 587 False 303.000000 303 77.403000 127 670 1 chr6D.!!$F1 543

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
865 917 1.685765 CATCCGGGACAGGGTCTCA 60.686 63.158 0.00 0.0 31.52 3.27 F
2435 2552 0.106369 ATCGGTCCGGTGATGGTCTA 60.106 55.000 12.29 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 2602 0.033504 TCCTGCTTCGTGTCAACCTC 59.966 55.0 0.00 0.0 0.0 3.85 R
3794 3925 0.031857 TTGGAACCAGCGCATTGTTG 59.968 50.0 11.47 0.0 0.0 3.33 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
133 134 3.190849 TCCGAGAGCGTACGACCG 61.191 66.667 21.65 14.73 35.23 4.79
431 463 2.223641 CCATGGAGGCACATCAAATTCG 60.224 50.000 5.56 0.00 0.00 3.34
764 816 5.631026 AGATTGAATCGTGATTTGGAAACG 58.369 37.500 0.00 0.00 38.64 3.60
865 917 1.685765 CATCCGGGACAGGGTCTCA 60.686 63.158 0.00 0.00 31.52 3.27
950 1010 7.763172 GCTACTGGCATTATATAGACACATC 57.237 40.000 0.00 0.00 41.35 3.06
953 1013 6.159293 ACTGGCATTATATAGACACATCACG 58.841 40.000 0.00 0.00 0.00 4.35
1052 1115 0.321122 CTCTGCCTCCTTTTGCTCGT 60.321 55.000 0.00 0.00 0.00 4.18
1216 1297 1.301716 GACAGCTTGTTCTCCGCCA 60.302 57.895 0.00 0.00 0.00 5.69
1220 1301 2.342279 CTTGTTCTCCGCCACCGA 59.658 61.111 0.00 0.00 36.29 4.69
1311 1392 2.340078 GCTCTCGTGCACCTCACA 59.660 61.111 12.15 0.00 45.92 3.58
1312 1393 1.735920 GCTCTCGTGCACCTCACAG 60.736 63.158 12.15 1.49 45.92 3.66
1313 1394 1.735920 CTCTCGTGCACCTCACAGC 60.736 63.158 12.15 0.00 45.92 4.40
1385 1469 2.816083 CCGCCGCAATTACACCGA 60.816 61.111 0.00 0.00 0.00 4.69
1387 1471 2.384309 CGCCGCAATTACACCGACA 61.384 57.895 0.00 0.00 0.00 4.35
1451 1535 0.390340 TCACTCGAACTCTGCATGGC 60.390 55.000 0.00 0.00 0.00 4.40
1603 1690 2.771762 GGGCCATCCAGCTCCTCT 60.772 66.667 4.39 0.00 35.00 3.69
1894 2005 0.741221 GAGGCGCCGATTCTTCAACT 60.741 55.000 23.20 0.00 0.00 3.16
1898 2009 2.004583 CGCCGATTCTTCAACTACCA 57.995 50.000 0.00 0.00 0.00 3.25
1899 2010 1.927174 CGCCGATTCTTCAACTACCAG 59.073 52.381 0.00 0.00 0.00 4.00
2050 2161 1.541310 AAAGGACGAGTGCGGGATCA 61.541 55.000 0.00 0.00 43.17 2.92
2123 2234 1.937546 GCCGGGATGCTTTGGAACTG 61.938 60.000 2.18 0.00 0.00 3.16
2126 2237 1.467920 GGGATGCTTTGGAACTGGAG 58.532 55.000 0.00 0.00 0.00 3.86
2203 2314 0.566136 CGACAACGGATTCATCGACG 59.434 55.000 0.00 0.00 34.77 5.12
2259 2370 6.158175 GATGTGAAGTACAGCTACAACAAG 57.842 41.667 0.00 0.00 43.80 3.16
2265 2376 4.734917 AGTACAGCTACAACAAGACGATC 58.265 43.478 0.00 0.00 0.00 3.69
2270 2381 3.258372 AGCTACAACAAGACGATCCTTGA 59.742 43.478 15.93 0.00 44.66 3.02
2271 2382 3.614616 GCTACAACAAGACGATCCTTGAG 59.385 47.826 15.93 10.98 44.66 3.02
2273 2384 2.368875 ACAACAAGACGATCCTTGAGGT 59.631 45.455 15.93 10.94 44.66 3.85
2277 2388 1.153349 GACGATCCTTGAGGTGGCC 60.153 63.158 0.00 0.00 36.34 5.36
2295 2409 2.424956 GGCCAAGAAGCATTACCTGAAG 59.575 50.000 0.00 0.00 0.00 3.02
2296 2410 3.347216 GCCAAGAAGCATTACCTGAAGA 58.653 45.455 0.00 0.00 0.00 2.87
2303 2417 6.112058 AGAAGCATTACCTGAAGATCAAGAC 58.888 40.000 0.00 0.00 0.00 3.01
2305 2419 4.160439 AGCATTACCTGAAGATCAAGACGA 59.840 41.667 0.00 0.00 0.00 4.20
2319 2433 2.675348 CAAGACGAAGAAGATCAAGGGC 59.325 50.000 0.00 0.00 0.00 5.19
2323 2437 1.134965 CGAAGAAGATCAAGGGCTCGT 60.135 52.381 0.00 0.00 0.00 4.18
2324 2438 2.675317 CGAAGAAGATCAAGGGCTCGTT 60.675 50.000 0.00 0.00 0.00 3.85
2326 2440 1.208293 AGAAGATCAAGGGCTCGTTCC 59.792 52.381 0.00 0.00 0.00 3.62
2337 2454 3.076278 TCGTTCCCGGCCGGTAAT 61.076 61.111 40.52 0.00 33.95 1.89
2356 2473 6.158598 GGTAATTACACTTACCACGACTTCA 58.841 40.000 17.16 0.00 46.62 3.02
2357 2474 6.815142 GGTAATTACACTTACCACGACTTCAT 59.185 38.462 17.16 0.00 46.62 2.57
2359 2476 2.413837 ACACTTACCACGACTTCATGC 58.586 47.619 0.00 0.00 0.00 4.06
2363 2480 3.244078 ACTTACCACGACTTCATGCTTCA 60.244 43.478 0.00 0.00 0.00 3.02
2364 2481 1.800805 ACCACGACTTCATGCTTCAG 58.199 50.000 0.00 0.00 0.00 3.02
2369 2486 4.237724 CACGACTTCATGCTTCAGTTCTA 58.762 43.478 0.00 0.00 0.00 2.10
2372 2489 3.589988 ACTTCATGCTTCAGTTCTACGG 58.410 45.455 0.00 0.00 0.00 4.02
2374 2491 2.176045 TCATGCTTCAGTTCTACGGGA 58.824 47.619 0.00 0.00 0.00 5.14
2375 2492 2.166459 TCATGCTTCAGTTCTACGGGAG 59.834 50.000 0.00 0.00 0.00 4.30
2376 2493 1.919240 TGCTTCAGTTCTACGGGAGA 58.081 50.000 0.00 0.00 0.00 3.71
2378 2495 2.631062 TGCTTCAGTTCTACGGGAGAAA 59.369 45.455 3.76 0.00 45.90 2.52
2380 2497 3.306156 GCTTCAGTTCTACGGGAGAAACT 60.306 47.826 3.76 2.01 45.90 2.66
2381 2498 4.487019 CTTCAGTTCTACGGGAGAAACTC 58.513 47.826 3.76 0.00 45.90 3.01
2387 2504 3.702048 CGGGAGAAACTCGGGGCA 61.702 66.667 0.00 0.00 39.03 5.36
2388 2505 2.998949 GGGAGAAACTCGGGGCAT 59.001 61.111 0.00 0.00 0.00 4.40
2389 2506 1.452108 GGGAGAAACTCGGGGCATG 60.452 63.158 0.00 0.00 0.00 4.06
2390 2507 1.452108 GGAGAAACTCGGGGCATGG 60.452 63.158 0.00 0.00 0.00 3.66
2391 2508 2.044946 AGAAACTCGGGGCATGGC 60.045 61.111 11.56 11.56 0.00 4.40
2409 2526 1.348775 GCCATGGAGAAGCCTACCCT 61.349 60.000 18.40 0.00 37.63 4.34
2412 2529 1.134280 CATGGAGAAGCCTACCCTGTG 60.134 57.143 0.00 0.00 37.63 3.66
2413 2530 0.909610 TGGAGAAGCCTACCCTGTGG 60.910 60.000 0.00 0.00 37.63 4.17
2422 2539 0.462047 CTACCCTGTGGCAATCGGTC 60.462 60.000 4.09 0.00 33.59 4.79
2435 2552 0.106369 ATCGGTCCGGTGATGGTCTA 60.106 55.000 12.29 0.00 0.00 2.59
2443 2560 1.820483 CGGTGATGGTCTACGGGGATA 60.820 57.143 0.00 0.00 0.00 2.59
2451 2568 2.525877 TACGGGGATAGGCTGGCC 60.526 66.667 3.00 3.00 0.00 5.36
2463 2580 4.514577 CTGGCCGCCGACGATTCT 62.515 66.667 4.58 0.00 43.93 2.40
2464 2581 4.508128 TGGCCGCCGACGATTCTC 62.508 66.667 4.58 0.00 43.93 2.87
2469 2586 1.368255 CGCCGACGATTCTCTCTCG 60.368 63.158 0.00 0.00 43.93 4.04
2471 2588 1.368255 CCGACGATTCTCTCTCGCG 60.368 63.158 0.00 0.00 39.71 5.87
2473 2590 1.763200 CGACGATTCTCTCTCGCGGA 61.763 60.000 6.13 1.01 39.71 5.54
2474 2591 0.377554 GACGATTCTCTCTCGCGGAA 59.622 55.000 6.13 0.93 39.71 4.30
2477 2594 1.777101 GATTCTCTCTCGCGGAATGG 58.223 55.000 6.13 0.00 30.98 3.16
2481 2598 2.202932 CTCTCGCGGAATGGGGTG 60.203 66.667 6.13 0.00 0.00 4.61
2482 2599 4.467084 TCTCGCGGAATGGGGTGC 62.467 66.667 6.13 0.00 0.00 5.01
2483 2600 4.473520 CTCGCGGAATGGGGTGCT 62.474 66.667 6.13 0.00 0.00 4.40
2484 2601 3.976701 CTCGCGGAATGGGGTGCTT 62.977 63.158 6.13 0.00 0.00 3.91
2485 2602 3.814268 CGCGGAATGGGGTGCTTG 61.814 66.667 0.00 0.00 0.00 4.01
2486 2603 2.361104 GCGGAATGGGGTGCTTGA 60.361 61.111 0.00 0.00 0.00 3.02
2487 2604 2.409870 GCGGAATGGGGTGCTTGAG 61.410 63.158 0.00 0.00 0.00 3.02
2502 2619 1.528586 CTTGAGGTTGACACGAAGCAG 59.471 52.381 0.00 0.00 0.00 4.24
2530 2647 5.998553 TGCTAAGTGTCAGCTACGATATAC 58.001 41.667 0.00 0.00 39.83 1.47
2531 2648 5.529800 TGCTAAGTGTCAGCTACGATATACA 59.470 40.000 0.00 0.00 39.83 2.29
2532 2649 6.206829 TGCTAAGTGTCAGCTACGATATACAT 59.793 38.462 0.00 0.00 39.83 2.29
2550 2667 4.508551 ACATTATCATGCTCCACCTGAA 57.491 40.909 0.00 0.00 33.05 3.02
2553 2670 0.106819 ATCATGCTCCACCTGAAGGC 60.107 55.000 0.00 0.00 39.32 4.35
2577 2694 3.307906 CCTCCCACGAACCGGTCA 61.308 66.667 8.04 0.00 0.00 4.02
2583 2700 0.528924 CCACGAACCGGTCATACTCA 59.471 55.000 8.04 0.00 0.00 3.41
2584 2701 1.469251 CCACGAACCGGTCATACTCAG 60.469 57.143 8.04 0.52 0.00 3.35
2588 2705 3.128242 ACGAACCGGTCATACTCAGTTAG 59.872 47.826 8.04 0.00 0.00 2.34
2589 2706 3.445857 GAACCGGTCATACTCAGTTAGC 58.554 50.000 8.04 0.00 0.00 3.09
2591 2708 2.032620 CCGGTCATACTCAGTTAGCCT 58.967 52.381 0.00 0.00 0.00 4.58
2593 2710 3.491104 CCGGTCATACTCAGTTAGCCTTC 60.491 52.174 0.00 0.00 0.00 3.46
2594 2711 3.130516 CGGTCATACTCAGTTAGCCTTCA 59.869 47.826 0.00 0.00 0.00 3.02
2596 2713 4.081642 GGTCATACTCAGTTAGCCTTCACA 60.082 45.833 0.00 0.00 0.00 3.58
2597 2714 5.479306 GTCATACTCAGTTAGCCTTCACAA 58.521 41.667 0.00 0.00 0.00 3.33
2598 2715 5.932303 GTCATACTCAGTTAGCCTTCACAAA 59.068 40.000 0.00 0.00 0.00 2.83
2601 2727 2.480419 CTCAGTTAGCCTTCACAAACGG 59.520 50.000 0.00 0.00 0.00 4.44
2637 2763 2.222027 GGCGTTTATGATCCCAAGAGG 58.778 52.381 0.00 0.00 0.00 3.69
2658 2784 1.221566 CATCCTGTGCATGGTCGGA 59.778 57.895 8.29 2.48 0.00 4.55
2688 2814 2.081212 CAACGACTCGACCGACTGC 61.081 63.158 5.20 0.00 0.00 4.40
2694 2820 0.670546 ACTCGACCGACTGCCAAATG 60.671 55.000 0.00 0.00 0.00 2.32
2748 2877 4.338710 GGTAAGGGGCACGGCACA 62.339 66.667 0.00 0.00 30.93 4.57
2784 2913 0.452184 TCAGAGACAAGTCCGATCGC 59.548 55.000 10.32 0.00 0.00 4.58
2789 2918 1.822990 AGACAAGTCCGATCGCCTTTA 59.177 47.619 10.32 0.00 0.00 1.85
2940 3069 0.250513 AGATCCTCCGCACCAAGAAC 59.749 55.000 0.00 0.00 0.00 3.01
3006 3135 3.760035 ACGCTGGGCTACCTCACG 61.760 66.667 0.00 0.00 37.76 4.35
3093 3222 2.811317 GACTGGCGCGAGGTGAAG 60.811 66.667 23.76 4.16 0.00 3.02
3196 3325 4.680237 CGGCGGACCAGAGCAACA 62.680 66.667 0.00 0.00 34.57 3.33
3247 3376 1.607509 GGATCGTGCTGCAGATATGCT 60.608 52.381 20.43 2.08 35.49 3.79
3435 3566 0.248661 AGATCATCCTGAACGCGTCG 60.249 55.000 14.44 3.94 0.00 5.12
3453 3584 3.706373 TTGGCAGGCTCCGGACTC 61.706 66.667 0.00 0.00 0.00 3.36
3507 3638 3.014538 ATGACCCGGGTGATGCCA 61.015 61.111 36.01 23.44 39.65 4.92
3729 3860 2.683768 GGTGGGTATGAGATGGTCTCT 58.316 52.381 8.30 0.00 43.73 3.10
3794 3925 2.202570 CGTGGTCGTCGATGGGAC 60.203 66.667 4.48 5.30 42.48 4.46
3852 3985 3.508845 AAGCAAAGTAAAGCTCCCTCA 57.491 42.857 0.00 0.00 40.90 3.86
3859 4013 6.127619 GCAAAGTAAAGCTCCCTCATGTTTAT 60.128 38.462 0.00 0.00 0.00 1.40
3868 4022 5.367945 TCCCTCATGTTTATGGAGTTACC 57.632 43.478 0.00 0.00 34.97 2.85
3910 4072 9.472361 TCGATTTAGACTTAGTTATATGTTGCC 57.528 33.333 0.00 0.00 0.00 4.52
4025 4208 6.110707 GGTTAAGTTTCAATCGATGGGACTA 58.889 40.000 0.00 0.00 0.00 2.59
4032 4215 2.552743 CAATCGATGGGACTAGCTACGA 59.447 50.000 0.00 3.28 0.00 3.43
4039 4222 2.688446 TGGGACTAGCTACGAGTCAATG 59.312 50.000 15.32 0.00 44.34 2.82
4065 4250 8.626526 GGACTTAAATAAGTTTTTGGTCAGTCA 58.373 33.333 7.23 0.00 45.84 3.41
4145 4591 3.862877 TTCTGGCCATGCATGTACTAT 57.137 42.857 24.58 0.00 0.00 2.12
4359 5468 6.331170 ACATGCATACAATACATATACGCG 57.669 37.500 3.53 3.53 0.00 6.01
4364 5473 6.020201 TGCATACAATACATATACGCGCATAC 60.020 38.462 5.73 0.00 0.00 2.39
4475 5766 5.988287 TGGATTAGTGACATCAGCATTACA 58.012 37.500 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 3.885521 CCGAGAGCGTACGACCCC 61.886 72.222 21.65 0.11 35.23 4.95
313 330 3.793144 GAAGAGCTGTTGCGGCGG 61.793 66.667 9.78 0.00 45.42 6.13
431 463 3.202906 TCATACAAGATGCGGCCTAAAC 58.797 45.455 0.00 0.00 0.00 2.01
496 537 7.675161 TGAGTCAATCATCACTTTCCCTATA 57.325 36.000 0.00 0.00 31.12 1.31
497 538 6.566079 TGAGTCAATCATCACTTTCCCTAT 57.434 37.500 0.00 0.00 31.12 2.57
498 539 6.013379 AGTTGAGTCAATCATCACTTTCCCTA 60.013 38.462 9.18 0.00 37.89 3.53
627 679 4.812476 CAACGCCGATGCTCCCGA 62.812 66.667 0.00 0.00 34.43 5.14
764 816 3.400054 CTCGTTCCCCACCTCCCC 61.400 72.222 0.00 0.00 0.00 4.81
803 855 2.049063 GCAGCAACCGTCTCGTCT 60.049 61.111 0.00 0.00 0.00 4.18
852 904 0.970937 TGATCGTGAGACCCTGTCCC 60.971 60.000 0.00 0.00 46.97 4.46
858 910 0.247736 ACAAGCTGATCGTGAGACCC 59.752 55.000 0.00 0.00 46.97 4.46
865 917 1.738099 GGTCGCACAAGCTGATCGT 60.738 57.895 0.00 0.00 39.10 3.73
950 1010 2.809861 ATCAAGGGTGAGCCTGCGTG 62.810 60.000 2.92 0.00 37.14 5.34
953 1013 4.232310 GATCAAGGGTGAGCCTGC 57.768 61.111 2.92 0.00 37.14 4.85
1109 1184 3.359523 TGTAGCGGTCGTCAGCGT 61.360 61.111 0.00 0.00 45.59 5.07
1142 1217 3.176924 AGAAGCTGGTGAGTAAGAGGA 57.823 47.619 0.00 0.00 0.00 3.71
1198 1279 1.301716 TGGCGGAGAACAAGCTGTC 60.302 57.895 0.00 0.00 0.00 3.51
1216 1297 1.948145 GTAGAGGTCATCATCGTCGGT 59.052 52.381 0.00 0.00 0.00 4.69
1220 1301 0.669077 GCCGTAGAGGTCATCATCGT 59.331 55.000 0.00 0.00 43.70 3.73
1311 1392 4.990910 AGGGTGAGGGTGGCAGCT 62.991 66.667 17.16 2.35 34.39 4.24
1312 1393 4.416738 GAGGGTGAGGGTGGCAGC 62.417 72.222 8.47 8.47 0.00 5.25
1313 1394 2.930019 TGAGGGTGAGGGTGGCAG 60.930 66.667 0.00 0.00 0.00 4.85
1385 1469 1.229529 AAGGAGATGGACCCGGTGT 60.230 57.895 0.00 0.00 0.00 4.16
1387 1471 2.058595 CGAAGGAGATGGACCCGGT 61.059 63.158 0.00 0.00 0.00 5.28
1391 1475 0.747852 GAGGACGAAGGAGATGGACC 59.252 60.000 0.00 0.00 0.00 4.46
1530 1614 4.753662 TCGGTGAGGGAGGGACGG 62.754 72.222 0.00 0.00 0.00 4.79
1894 2005 0.107831 AAGAAGCGGTGTTGCTGGTA 59.892 50.000 0.00 0.00 46.60 3.25
1899 2010 3.432186 ACCAAGAAGCGGTGTTGC 58.568 55.556 4.78 0.00 34.69 4.17
2032 2143 1.949847 CTGATCCCGCACTCGTCCTT 61.950 60.000 0.00 0.00 0.00 3.36
2035 2146 1.739338 ATCCTGATCCCGCACTCGTC 61.739 60.000 0.00 0.00 0.00 4.20
2123 2234 2.722201 CCAGTACCCGTCTGGCTCC 61.722 68.421 0.00 0.00 44.46 4.70
2146 2257 1.924335 CTGTTGTCACACCGTCGTG 59.076 57.895 0.00 0.00 46.11 4.35
2154 2265 1.949133 GCTCGACGCTGTTGTCACA 60.949 57.895 0.00 0.00 38.84 3.58
2188 2299 1.625616 GTGACGTCGATGAATCCGTT 58.374 50.000 12.58 0.00 33.03 4.44
2203 2314 0.663568 CTTCTGTGGTCGTCGGTGAC 60.664 60.000 0.00 0.01 38.17 3.67
2257 2368 0.250513 GCCACCTCAAGGATCGTCTT 59.749 55.000 2.30 0.00 38.94 3.01
2259 2370 1.153349 GGCCACCTCAAGGATCGTC 60.153 63.158 2.30 0.00 38.94 4.20
2265 2376 1.246737 GCTTCTTGGCCACCTCAAGG 61.247 60.000 3.88 0.00 41.23 3.61
2270 2381 1.616994 GGTAATGCTTCTTGGCCACCT 60.617 52.381 3.88 0.00 0.00 4.00
2271 2382 0.817654 GGTAATGCTTCTTGGCCACC 59.182 55.000 3.88 0.00 0.00 4.61
2273 2384 1.354031 TCAGGTAATGCTTCTTGGCCA 59.646 47.619 0.00 0.00 0.00 5.36
2277 2388 6.596888 TCTTGATCTTCAGGTAATGCTTCTTG 59.403 38.462 0.00 0.00 0.00 3.02
2295 2409 4.808364 CCCTTGATCTTCTTCGTCTTGATC 59.192 45.833 0.00 0.00 35.44 2.92
2296 2410 4.764172 CCCTTGATCTTCTTCGTCTTGAT 58.236 43.478 0.00 0.00 0.00 2.57
2303 2417 1.134965 ACGAGCCCTTGATCTTCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
2305 2419 2.355209 GGAACGAGCCCTTGATCTTCTT 60.355 50.000 0.00 0.00 0.00 2.52
2323 2437 0.107752 GTGTAATTACCGGCCGGGAA 60.108 55.000 42.83 42.83 43.18 3.97
2324 2438 0.977108 AGTGTAATTACCGGCCGGGA 60.977 55.000 44.99 38.84 39.97 5.14
2326 2440 2.204237 GTAAGTGTAATTACCGGCCGG 58.796 52.381 42.17 42.17 42.03 6.13
2334 2451 6.311935 GCATGAAGTCGTGGTAAGTGTAATTA 59.688 38.462 0.00 0.00 33.60 1.40
2337 2454 3.991773 GCATGAAGTCGTGGTAAGTGTAA 59.008 43.478 0.00 0.00 33.60 2.41
2348 2465 3.393089 AGAACTGAAGCATGAAGTCGT 57.607 42.857 0.00 0.00 0.00 4.34
2349 2466 3.301906 CGTAGAACTGAAGCATGAAGTCG 59.698 47.826 0.00 0.00 0.00 4.18
2356 2473 2.457598 TCTCCCGTAGAACTGAAGCAT 58.542 47.619 0.00 0.00 0.00 3.79
2357 2474 1.919240 TCTCCCGTAGAACTGAAGCA 58.081 50.000 0.00 0.00 0.00 3.91
2359 2476 4.487019 GAGTTTCTCCCGTAGAACTGAAG 58.513 47.826 0.00 0.00 44.02 3.02
2363 2480 1.817447 CCGAGTTTCTCCCGTAGAACT 59.183 52.381 0.00 0.00 44.02 3.01
2364 2481 1.135170 CCCGAGTTTCTCCCGTAGAAC 60.135 57.143 0.00 0.00 44.02 3.01
2369 2486 3.703127 GCCCCGAGTTTCTCCCGT 61.703 66.667 0.00 0.00 0.00 5.28
2372 2489 1.452108 CCATGCCCCGAGTTTCTCC 60.452 63.158 0.00 0.00 0.00 3.71
2374 2491 2.044946 GCCATGCCCCGAGTTTCT 60.045 61.111 0.00 0.00 0.00 2.52
2375 2492 3.140814 GGCCATGCCCCGAGTTTC 61.141 66.667 0.00 0.00 44.06 2.78
2386 2503 3.851955 GGCTTCTCCATGGCCATG 58.148 61.111 34.82 34.82 44.69 3.66
2389 2506 1.149401 GGTAGGCTTCTCCATGGCC 59.851 63.158 6.96 4.07 45.57 5.36
2390 2507 1.149401 GGGTAGGCTTCTCCATGGC 59.851 63.158 6.96 0.00 37.29 4.40
2391 2508 0.471617 CAGGGTAGGCTTCTCCATGG 59.528 60.000 4.97 4.97 37.29 3.66
2392 2509 1.134280 CACAGGGTAGGCTTCTCCATG 60.134 57.143 13.28 13.28 38.70 3.66
2393 2510 1.207791 CACAGGGTAGGCTTCTCCAT 58.792 55.000 0.00 0.00 37.29 3.41
2394 2511 0.909610 CCACAGGGTAGGCTTCTCCA 60.910 60.000 0.00 0.00 37.29 3.86
2404 2521 1.600107 GACCGATTGCCACAGGGTA 59.400 57.895 0.00 0.00 36.17 3.69
2409 2526 3.632080 ACCGGACCGATTGCCACA 61.632 61.111 17.49 0.00 0.00 4.17
2412 2529 2.180204 CATCACCGGACCGATTGCC 61.180 63.158 17.49 0.00 0.00 4.52
2413 2530 2.180204 CCATCACCGGACCGATTGC 61.180 63.158 17.49 0.00 0.00 3.56
2422 2539 2.792947 CCCCGTAGACCATCACCGG 61.793 68.421 0.00 0.00 38.39 5.28
2451 2568 1.368255 CGAGAGAGAATCGTCGGCG 60.368 63.158 1.15 1.15 41.03 6.46
2463 2580 2.363795 ACCCCATTCCGCGAGAGA 60.364 61.111 8.23 0.00 0.00 3.10
2464 2581 2.202932 CACCCCATTCCGCGAGAG 60.203 66.667 8.23 0.00 0.00 3.20
2469 2586 2.361104 TCAAGCACCCCATTCCGC 60.361 61.111 0.00 0.00 0.00 5.54
2471 2588 0.251787 AACCTCAAGCACCCCATTCC 60.252 55.000 0.00 0.00 0.00 3.01
2473 2590 0.482446 TCAACCTCAAGCACCCCATT 59.518 50.000 0.00 0.00 0.00 3.16
2474 2591 0.251341 GTCAACCTCAAGCACCCCAT 60.251 55.000 0.00 0.00 0.00 4.00
2477 2594 1.507141 CGTGTCAACCTCAAGCACCC 61.507 60.000 0.00 0.00 0.00 4.61
2481 2598 0.235926 GCTTCGTGTCAACCTCAAGC 59.764 55.000 0.00 0.00 0.00 4.01
2482 2599 1.528586 CTGCTTCGTGTCAACCTCAAG 59.471 52.381 0.00 0.00 0.00 3.02
2483 2600 1.581934 CTGCTTCGTGTCAACCTCAA 58.418 50.000 0.00 0.00 0.00 3.02
2484 2601 0.249868 CCTGCTTCGTGTCAACCTCA 60.250 55.000 0.00 0.00 0.00 3.86
2485 2602 0.033504 TCCTGCTTCGTGTCAACCTC 59.966 55.000 0.00 0.00 0.00 3.85
2486 2603 0.687354 ATCCTGCTTCGTGTCAACCT 59.313 50.000 0.00 0.00 0.00 3.50
2487 2604 1.079503 GATCCTGCTTCGTGTCAACC 58.920 55.000 0.00 0.00 0.00 3.77
2502 2619 2.977772 AGCTGACACTTAGCAGATCC 57.022 50.000 0.00 0.00 43.53 3.36
2511 2628 8.793592 TGATAATGTATATCGTAGCTGACACTT 58.206 33.333 0.00 0.00 0.00 3.16
2513 2630 9.014533 CATGATAATGTATATCGTAGCTGACAC 57.985 37.037 0.00 0.00 0.00 3.67
2530 2647 3.819337 CCTTCAGGTGGAGCATGATAATG 59.181 47.826 0.00 0.00 37.76 1.90
2531 2648 3.749954 GCCTTCAGGTGGAGCATGATAAT 60.750 47.826 0.00 0.00 37.76 1.28
2532 2649 2.421952 GCCTTCAGGTGGAGCATGATAA 60.422 50.000 0.00 0.00 37.76 1.75
2536 2653 1.030488 CAGCCTTCAGGTGGAGCATG 61.030 60.000 0.00 0.00 40.44 4.06
2561 2678 0.179119 GTATGACCGGTTCGTGGGAG 60.179 60.000 9.42 0.00 0.00 4.30
2565 2682 1.201647 ACTGAGTATGACCGGTTCGTG 59.798 52.381 9.42 1.50 0.00 4.35
2571 2688 2.032620 AGGCTAACTGAGTATGACCGG 58.967 52.381 0.00 0.00 0.00 5.28
2572 2689 3.130516 TGAAGGCTAACTGAGTATGACCG 59.869 47.826 0.00 0.00 0.00 4.79
2577 2694 4.929808 CGTTTGTGAAGGCTAACTGAGTAT 59.070 41.667 0.00 0.00 0.00 2.12
2583 2700 1.235724 GCCGTTTGTGAAGGCTAACT 58.764 50.000 0.00 0.00 46.83 2.24
2584 2701 3.767287 GCCGTTTGTGAAGGCTAAC 57.233 52.632 0.00 0.00 46.83 2.34
2588 2705 0.454452 GATTCGCCGTTTGTGAAGGC 60.454 55.000 0.00 0.00 46.03 4.35
2589 2706 1.128692 GAGATTCGCCGTTTGTGAAGG 59.871 52.381 0.00 0.00 46.03 3.46
2591 2708 1.798223 CTGAGATTCGCCGTTTGTGAA 59.202 47.619 0.00 0.00 46.82 3.18
2593 2710 0.179215 GCTGAGATTCGCCGTTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
2594 2711 0.602638 TGCTGAGATTCGCCGTTTGT 60.603 50.000 0.00 0.00 0.00 2.83
2596 2713 0.037326 TCTGCTGAGATTCGCCGTTT 60.037 50.000 0.00 0.00 0.00 3.60
2597 2714 0.459237 CTCTGCTGAGATTCGCCGTT 60.459 55.000 15.04 0.00 42.73 4.44
2598 2715 1.140589 CTCTGCTGAGATTCGCCGT 59.859 57.895 15.04 0.00 42.73 5.68
2601 2727 1.886777 GCCCTCTGCTGAGATTCGC 60.887 63.158 21.10 12.62 42.73 4.70
2675 2801 0.670546 CATTTGGCAGTCGGTCGAGT 60.671 55.000 0.00 0.00 0.00 4.18
2688 2814 5.998189 AACTTCACAGTGACCAGCATTTGG 61.998 45.833 1.52 0.00 42.64 3.28
2694 2820 0.861837 CGAACTTCACAGTGACCAGC 59.138 55.000 1.52 0.00 31.60 4.85
2700 2826 0.951040 GGGAGGCGAACTTCACAGTG 60.951 60.000 0.00 0.00 31.60 3.66
2703 2829 0.250295 CAAGGGAGGCGAACTTCACA 60.250 55.000 0.00 0.00 0.00 3.58
2747 2876 1.483827 TGAGGCTGCTGATTACTCCTG 59.516 52.381 0.00 0.00 0.00 3.86
2748 2877 1.761784 CTGAGGCTGCTGATTACTCCT 59.238 52.381 0.00 0.00 0.00 3.69
2751 2880 2.430332 GTCTCTGAGGCTGCTGATTACT 59.570 50.000 1.15 0.00 0.00 2.24
2829 2958 2.047179 GCCTCCGACACTTGGTCC 60.047 66.667 0.00 0.00 43.95 4.46
3006 3135 1.347817 CGAAGTTGAGCACGAGAGGC 61.348 60.000 0.00 0.00 0.00 4.70
3061 3190 0.240145 CAGTCGCTCGTCCAGTACAA 59.760 55.000 0.00 0.00 0.00 2.41
3093 3222 2.592308 GCCCTCATCACCACCTCC 59.408 66.667 0.00 0.00 0.00 4.30
3247 3376 2.736995 GAGCACGTACAGCGGCAA 60.737 61.111 1.45 0.00 46.52 4.52
3384 3513 0.324368 AGCCGTCCAGTATCAGACCA 60.324 55.000 0.00 0.00 0.00 4.02
3435 3566 3.959991 GAGTCCGGAGCCTGCCAAC 62.960 68.421 3.06 0.00 0.00 3.77
3535 3666 0.317436 CTCATGCTCGGCTCGTAGAC 60.317 60.000 0.00 0.00 0.00 2.59
3701 3832 1.499438 TCTCATACCCACCGGATCTCT 59.501 52.381 9.46 0.00 0.00 3.10
3708 3839 1.341531 GAGACCATCTCATACCCACCG 59.658 57.143 0.87 0.00 42.90 4.94
3729 3860 4.811969 TCCCGTTTTCTGTTAGATGCTA 57.188 40.909 0.00 0.00 0.00 3.49
3794 3925 0.031857 TTGGAACCAGCGCATTGTTG 59.968 50.000 11.47 0.00 0.00 3.33
3852 3985 8.644374 TTTAGCTTTGGTAACTCCATAAACAT 57.356 30.769 0.00 0.00 46.60 2.71
3859 4013 7.630082 ACTGATATTTAGCTTTGGTAACTCCA 58.370 34.615 0.00 0.00 45.60 3.86
3907 4069 3.358707 ACGAATATAACATCGACGGCA 57.641 42.857 11.44 0.00 41.43 5.69
3910 4072 8.656774 AAGATCTTACGAATATAACATCGACG 57.343 34.615 6.06 0.00 41.43 5.12
3994 4171 7.308589 CCATCGATTGAAACTTAACCAAGTCTT 60.309 37.037 0.00 0.00 44.41 3.01
4009 4186 3.004419 CGTAGCTAGTCCCATCGATTGAA 59.996 47.826 0.00 0.00 0.00 2.69
4013 4190 2.224572 ACTCGTAGCTAGTCCCATCGAT 60.225 50.000 0.00 0.00 0.00 3.59
4039 4222 8.626526 TGACTGACCAAAAACTTATTTAAGTCC 58.373 33.333 3.58 0.00 45.17 3.85
4065 4250 6.377996 TCAATCGAAATGATTCAGGGTCAATT 59.622 34.615 0.00 0.00 45.59 2.32
4128 4316 4.141505 ACTTACATAGTACATGCATGGCCA 60.142 41.667 29.41 8.56 34.56 5.36
4228 4725 4.814147 TGCACGATCTTCATCTATCATCC 58.186 43.478 0.00 0.00 0.00 3.51
4359 5468 7.937387 TTTCGATATATACGTACGTGTATGC 57.063 36.000 34.27 26.57 35.85 3.14
4364 5473 7.269084 ACGGAATTTTCGATATATACGTACGTG 59.731 37.037 30.25 12.03 0.00 4.49
4446 5737 5.471116 TGCTGATGTCACTAATCCATTATGC 59.529 40.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.