Multiple sequence alignment - TraesCS3B01G054300

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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 TraesCS3B01G054300 chr3B 100.000 3089 0 0 1 3089 28083494 28080406 0.000000e+00 5705.0
1 TraesCS3B01G054300 chr3B 92.424 2376 106 30 14 2331 12402268 12399909 0.000000e+00 3323.0
2 TraesCS3B01G054300 chr3B 81.695 1180 151 38 971 2095 12181780 12180611 0.000000e+00 922.0
3 TraesCS3B01G054300 chr3B 82.624 282 38 3 2574 2855 544115603 544115333 3.980000e-59 239.0
4 TraesCS3B01G054300 chrUn 89.739 2339 164 39 1 2282 35453393 35451074 0.000000e+00 2920.0
5 TraesCS3B01G054300 chrUn 81.046 1166 159 40 973 2086 35795027 35796182 0.000000e+00 872.0
6 TraesCS3B01G054300 chrUn 86.851 289 31 2 2799 3083 115882931 115883216 1.790000e-82 316.0
7 TraesCS3B01G054300 chrUn 85.238 210 23 6 1818 2019 395714880 395715089 3.120000e-50 209.0
8 TraesCS3B01G054300 chrUn 82.278 237 32 5 2567 2803 115873999 115874225 2.430000e-46 196.0
9 TraesCS3B01G054300 chr3D 88.365 2398 158 59 1 2337 5608105 5610442 0.000000e+00 2771.0
10 TraesCS3B01G054300 chr3D 79.304 1121 177 29 1001 2097 29309160 29308071 0.000000e+00 734.0
11 TraesCS3B01G054300 chr3D 83.014 783 117 12 1326 2095 5681050 5680271 0.000000e+00 695.0
12 TraesCS3B01G054300 chr3D 98.276 58 0 1 2514 2571 5610594 5610650 1.960000e-17 100.0
13 TraesCS3B01G054300 chr3A 88.564 1574 119 25 795 2338 15781036 15779494 0.000000e+00 1853.0
14 TraesCS3B01G054300 chr3A 87.106 1427 116 27 785 2177 17258738 17257346 0.000000e+00 1554.0
15 TraesCS3B01G054300 chr3A 85.349 1133 141 11 905 2021 11629290 11628167 0.000000e+00 1149.0
16 TraesCS3B01G054300 chr3A 84.408 1148 137 22 962 2090 15695341 15694217 0.000000e+00 1090.0
17 TraesCS3B01G054300 chr3A 93.117 523 30 4 2567 3089 715691817 715692333 0.000000e+00 761.0
18 TraesCS3B01G054300 chr3A 89.888 178 16 2 2157 2332 15778293 15778116 8.620000e-56 228.0
19 TraesCS3B01G054300 chr3A 87.079 178 19 4 2177 2352 15776694 15776519 6.760000e-47 198.0
20 TraesCS3B01G054300 chr3A 93.548 62 0 1 2514 2571 15776517 15776456 4.240000e-14 89.8
21 TraesCS3B01G054300 chr7B 99.235 523 3 1 2568 3089 41200517 41199995 0.000000e+00 942.0
22 TraesCS3B01G054300 chr7B 82.986 288 38 3 2568 2855 329210504 329210228 1.840000e-62 250.0
23 TraesCS3B01G054300 chr7B 100.000 34 0 0 2567 2600 686842538 686842505 2.570000e-06 63.9
24 TraesCS3B01G054300 chr5A 97.358 530 13 1 2561 3089 457836690 457836161 0.000000e+00 900.0
25 TraesCS3B01G054300 chr5A 94.837 523 23 2 2567 3089 22992184 22992702 0.000000e+00 813.0
26 TraesCS3B01G054300 chr7A 94.073 523 26 3 2567 3089 473948165 473948682 0.000000e+00 789.0
27 TraesCS3B01G054300 chr7A 91.765 170 10 3 2352 2517 34363999 34363830 1.850000e-57 233.0
28 TraesCS3B01G054300 chr6D 94.152 171 8 1 2346 2514 87478204 87478374 3.060000e-65 259.0
29 TraesCS3B01G054300 chr2B 83.391 289 37 3 2567 2855 21217586 21217863 1.100000e-64 257.0
30 TraesCS3B01G054300 chr2B 88.333 60 6 1 2568 2626 735521766 735521825 1.540000e-08 71.3
31 TraesCS3B01G054300 chr7D 92.771 166 9 2 2353 2515 552951678 552951513 1.430000e-58 237.0
32 TraesCS3B01G054300 chr6B 91.860 172 10 3 2345 2514 521034407 521034576 1.430000e-58 237.0
33 TraesCS3B01G054300 chr5D 91.813 171 10 3 2353 2519 189021914 189021744 5.150000e-58 235.0
34 TraesCS3B01G054300 chr5D 90.230 174 14 2 2353 2523 42949724 42949551 1.110000e-54 224.0
35 TraesCS3B01G054300 chr5B 91.813 171 10 3 2352 2518 541610181 541610351 5.150000e-58 235.0
36 TraesCS3B01G054300 chr5B 83.146 267 34 3 2589 2855 589821151 589821406 1.850000e-57 233.0
37 TraesCS3B01G054300 chr4A 90.698 172 12 3 2348 2515 428284289 428284118 3.100000e-55 226.0
38 TraesCS3B01G054300 chr4D 89.444 180 14 4 2348 2522 28983050 28982871 4.010000e-54 222.0
39 TraesCS3B01G054300 chr4D 87.097 62 6 2 2567 2627 422933593 422933533 5.530000e-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 TraesCS3B01G054300 chr3B 28080406 28083494 3088 True 5705.0 5705 100.00000 1 3089 1 chr3B.!!$R3 3088
1 TraesCS3B01G054300 chr3B 12399909 12402268 2359 True 3323.0 3323 92.42400 14 2331 1 chr3B.!!$R2 2317
2 TraesCS3B01G054300 chr3B 12180611 12181780 1169 True 922.0 922 81.69500 971 2095 1 chr3B.!!$R1 1124
3 TraesCS3B01G054300 chrUn 35451074 35453393 2319 True 2920.0 2920 89.73900 1 2282 1 chrUn.!!$R1 2281
4 TraesCS3B01G054300 chrUn 35795027 35796182 1155 False 872.0 872 81.04600 973 2086 1 chrUn.!!$F1 1113
5 TraesCS3B01G054300 chr3D 5608105 5610650 2545 False 1435.5 2771 93.32050 1 2571 2 chr3D.!!$F1 2570
6 TraesCS3B01G054300 chr3D 29308071 29309160 1089 True 734.0 734 79.30400 1001 2097 1 chr3D.!!$R2 1096
7 TraesCS3B01G054300 chr3D 5680271 5681050 779 True 695.0 695 83.01400 1326 2095 1 chr3D.!!$R1 769
8 TraesCS3B01G054300 chr3A 17257346 17258738 1392 True 1554.0 1554 87.10600 785 2177 1 chr3A.!!$R3 1392
9 TraesCS3B01G054300 chr3A 11628167 11629290 1123 True 1149.0 1149 85.34900 905 2021 1 chr3A.!!$R1 1116
10 TraesCS3B01G054300 chr3A 15694217 15695341 1124 True 1090.0 1090 84.40800 962 2090 1 chr3A.!!$R2 1128
11 TraesCS3B01G054300 chr3A 715691817 715692333 516 False 761.0 761 93.11700 2567 3089 1 chr3A.!!$F1 522
12 TraesCS3B01G054300 chr3A 15776456 15781036 4580 True 592.2 1853 89.76975 795 2571 4 chr3A.!!$R4 1776
13 TraesCS3B01G054300 chr7B 41199995 41200517 522 True 942.0 942 99.23500 2568 3089 1 chr7B.!!$R1 521
14 TraesCS3B01G054300 chr5A 457836161 457836690 529 True 900.0 900 97.35800 2561 3089 1 chr5A.!!$R1 528
15 TraesCS3B01G054300 chr5A 22992184 22992702 518 False 813.0 813 94.83700 2567 3089 1 chr5A.!!$F1 522
16 TraesCS3B01G054300 chr7A 473948165 473948682 517 False 789.0 789 94.07300 2567 3089 1 chr7A.!!$F1 522

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
829 860 1.271379 GGCTGTGTGTGGAATAGTGGT 60.271 52.381 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2113 2301 0.394938 TCGGTAAGCTTCAACTGCCA 59.605 50.0 0.0 0.0 0.0 4.92 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
254 261 7.715267 TGACAATTAGGGAATTAGGGGATTA 57.285 36.000 0.00 0.00 33.33 1.75
295 302 7.927629 TGAATATTCATGGAAAAATAGCCTTGC 59.072 33.333 14.23 0.00 31.01 4.01
332 341 7.541162 TCTTGAATGCTCCTAATCATGTTTTG 58.459 34.615 0.00 0.00 0.00 2.44
363 373 5.667539 TTCGGGATTTTCCAATAATTGCA 57.332 34.783 0.00 0.00 38.64 4.08
452 462 7.647715 TCATCTTTCACGTCTTTTCATTTTTCC 59.352 33.333 0.00 0.00 0.00 3.13
474 484 8.990163 TTCCTTATTTCTTTGTTAACCAGACT 57.010 30.769 2.48 0.00 0.00 3.24
485 495 2.972505 CCAGACTGCCGCGTGTTT 60.973 61.111 4.92 0.00 0.00 2.83
503 513 5.387649 CGTGTTTAAAACTATCGTCGCTTCA 60.388 40.000 0.00 0.00 0.00 3.02
680 708 1.978617 GGGCACTGGGACAATGTGG 60.979 63.158 0.00 0.00 38.13 4.17
736 764 5.222463 TGGCAGGTATATCATGTACTCCCTA 60.222 44.000 0.00 0.00 0.00 3.53
744 772 2.585900 TCATGTACTCCCTACCTCCAGT 59.414 50.000 0.00 0.00 0.00 4.00
758 786 6.890814 CCTACCTCCAGTCCGTAATATAAGAT 59.109 42.308 0.00 0.00 0.00 2.40
760 788 6.312529 ACCTCCAGTCCGTAATATAAGATCA 58.687 40.000 0.00 0.00 0.00 2.92
783 811 2.717580 TTCACACTGGTGCGTAGTAG 57.282 50.000 0.17 0.00 44.87 2.57
811 842 2.355010 TACTCGGTTACTCTAGGGGC 57.645 55.000 0.00 0.00 0.00 5.80
829 860 1.271379 GGCTGTGTGTGGAATAGTGGT 60.271 52.381 0.00 0.00 0.00 4.16
891 939 3.276857 TGAAGCAAGCATCTCAATCTCC 58.723 45.455 0.00 0.00 0.00 3.71
916 964 3.458163 TACCGGCCGAGCTCCTTG 61.458 66.667 30.73 9.82 0.00 3.61
1222 1306 1.336795 TGAAGATCGACATGTGCGTGT 60.337 47.619 1.15 0.00 34.39 4.49
1300 1396 1.270839 TGCTCCCTTCCTTCTTTCGTG 60.271 52.381 0.00 0.00 0.00 4.35
1303 1399 1.160137 CCCTTCCTTCTTTCGTGCAG 58.840 55.000 0.00 0.00 0.00 4.41
1319 1441 2.786578 GTGCAGACTCGATCGATTCTTC 59.213 50.000 29.06 25.41 32.86 2.87
1776 1918 2.645510 CGTGTTCGTGCTCACCGTC 61.646 63.158 0.00 0.00 0.00 4.79
2065 2246 4.492160 TCAGCGTCCGCATCGACC 62.492 66.667 14.70 0.00 44.88 4.79
2242 3846 7.066307 TGCCAAGTCATAATTATCTGAGCTA 57.934 36.000 0.00 0.00 0.00 3.32
2255 3862 8.985315 ATTATCTGAGCTAAAATGGATGTGAA 57.015 30.769 0.00 0.00 0.00 3.18
2325 3938 5.172591 CGCATGCTATTGAACACATCATTTC 59.827 40.000 17.13 0.00 38.03 2.17
2352 5542 5.352700 TTCCTTTTGGGGGCATCATATAT 57.647 39.130 0.00 0.00 40.87 0.86
2353 5543 6.476409 TTCCTTTTGGGGGCATCATATATA 57.524 37.500 0.00 0.00 40.87 0.86
2354 5544 5.826643 TCCTTTTGGGGGCATCATATATAC 58.173 41.667 0.00 0.00 40.87 1.47
2355 5545 5.555542 TCCTTTTGGGGGCATCATATATACT 59.444 40.000 0.00 0.00 40.87 2.12
2356 5546 5.888161 CCTTTTGGGGGCATCATATATACTC 59.112 44.000 0.00 0.00 35.46 2.59
2357 5547 5.450818 TTTGGGGGCATCATATATACTCC 57.549 43.478 0.00 0.00 0.00 3.85
2358 5548 3.393687 TGGGGGCATCATATATACTCCC 58.606 50.000 5.57 5.57 0.00 4.30
2359 5549 3.015158 TGGGGGCATCATATATACTCCCT 59.985 47.826 11.49 0.00 33.89 4.20
2360 5550 3.392616 GGGGGCATCATATATACTCCCTG 59.607 52.174 5.35 0.00 33.89 4.45
2361 5551 4.040755 GGGGCATCATATATACTCCCTGT 58.959 47.826 9.84 0.00 32.98 4.00
2362 5552 4.475016 GGGGCATCATATATACTCCCTGTT 59.525 45.833 9.84 0.00 32.98 3.16
2363 5553 5.396884 GGGGCATCATATATACTCCCTGTTC 60.397 48.000 9.84 0.00 32.98 3.18
2364 5554 5.396884 GGGCATCATATATACTCCCTGTTCC 60.397 48.000 0.00 0.00 0.00 3.62
2365 5555 5.426833 GGCATCATATATACTCCCTGTTCCT 59.573 44.000 0.00 0.00 0.00 3.36
2366 5556 6.611642 GGCATCATATATACTCCCTGTTCCTA 59.388 42.308 0.00 0.00 0.00 2.94
2367 5557 7.125811 GGCATCATATATACTCCCTGTTCCTAA 59.874 40.741 0.00 0.00 0.00 2.69
2368 5558 8.540388 GCATCATATATACTCCCTGTTCCTAAA 58.460 37.037 0.00 0.00 0.00 1.85
2377 5567 9.900112 ATACTCCCTGTTCCTAAATATAAGTCT 57.100 33.333 0.00 0.00 0.00 3.24
2378 5568 8.625467 ACTCCCTGTTCCTAAATATAAGTCTT 57.375 34.615 0.00 0.00 0.00 3.01
2379 5569 9.059023 ACTCCCTGTTCCTAAATATAAGTCTTT 57.941 33.333 0.00 0.00 0.00 2.52
2380 5570 9.549078 CTCCCTGTTCCTAAATATAAGTCTTTC 57.451 37.037 0.00 0.00 0.00 2.62
2381 5571 9.280456 TCCCTGTTCCTAAATATAAGTCTTTCT 57.720 33.333 0.00 0.00 0.00 2.52
2422 5612 9.734620 ATGATTACATACGGAACAAAATGAATG 57.265 29.630 0.00 0.00 34.71 2.67
2423 5613 8.951243 TGATTACATACGGAACAAAATGAATGA 58.049 29.630 0.00 0.00 0.00 2.57
2424 5614 9.781834 GATTACATACGGAACAAAATGAATGAA 57.218 29.630 0.00 0.00 0.00 2.57
2426 5616 9.781834 TTACATACGGAACAAAATGAATGAATC 57.218 29.630 0.00 0.00 0.00 2.52
2427 5617 8.055279 ACATACGGAACAAAATGAATGAATCT 57.945 30.769 0.00 0.00 0.00 2.40
2428 5618 9.173021 ACATACGGAACAAAATGAATGAATCTA 57.827 29.630 0.00 0.00 0.00 1.98
2429 5619 9.438291 CATACGGAACAAAATGAATGAATCTAC 57.562 33.333 0.00 0.00 0.00 2.59
2430 5620 7.447374 ACGGAACAAAATGAATGAATCTACA 57.553 32.000 0.00 0.00 0.00 2.74
2431 5621 7.305474 ACGGAACAAAATGAATGAATCTACAC 58.695 34.615 0.00 0.00 0.00 2.90
2432 5622 7.174946 ACGGAACAAAATGAATGAATCTACACT 59.825 33.333 0.00 0.00 0.00 3.55
2433 5623 7.693951 CGGAACAAAATGAATGAATCTACACTC 59.306 37.037 0.00 0.00 0.00 3.51
2434 5624 8.734386 GGAACAAAATGAATGAATCTACACTCT 58.266 33.333 0.00 0.00 0.00 3.24
2473 5663 9.220635 CATACATTCGTATGTTGTTACCATTTG 57.779 33.333 13.12 0.00 46.70 2.32
2474 5664 7.441890 ACATTCGTATGTTGTTACCATTTGA 57.558 32.000 1.31 0.00 42.29 2.69
2475 5665 7.877003 ACATTCGTATGTTGTTACCATTTGAA 58.123 30.769 1.31 0.00 42.29 2.69
2476 5666 8.353684 ACATTCGTATGTTGTTACCATTTGAAA 58.646 29.630 1.31 0.00 42.29 2.69
2477 5667 9.352784 CATTCGTATGTTGTTACCATTTGAAAT 57.647 29.630 0.00 0.00 0.00 2.17
2478 5668 8.735303 TTCGTATGTTGTTACCATTTGAAATG 57.265 30.769 10.84 10.84 0.00 2.32
2479 5669 7.877003 TCGTATGTTGTTACCATTTGAAATGT 58.123 30.769 15.93 7.49 0.00 2.71
2480 5670 8.018520 TCGTATGTTGTTACCATTTGAAATGTC 58.981 33.333 15.93 5.28 0.00 3.06
2481 5671 8.020819 CGTATGTTGTTACCATTTGAAATGTCT 58.979 33.333 15.93 4.25 0.00 3.41
2492 5682 9.533253 ACCATTTGAAATGTCTAAAAAGACTTG 57.467 29.630 15.93 0.00 39.41 3.16
2493 5683 8.490355 CCATTTGAAATGTCTAAAAAGACTTGC 58.510 33.333 15.93 0.00 39.41 4.01
2494 5684 9.033481 CATTTGAAATGTCTAAAAAGACTTGCA 57.967 29.630 9.67 0.00 39.41 4.08
2495 5685 9.768662 ATTTGAAATGTCTAAAAAGACTTGCAT 57.231 25.926 7.04 0.00 39.41 3.96
2496 5686 9.598517 TTTGAAATGTCTAAAAAGACTTGCATT 57.401 25.926 7.04 0.00 39.41 3.56
2497 5687 9.598517 TTGAAATGTCTAAAAAGACTTGCATTT 57.401 25.926 7.04 0.00 39.41 2.32
2500 5690 9.696917 AAATGTCTAAAAAGACTTGCATTTAGG 57.303 29.630 12.84 0.00 39.41 2.69
2501 5691 8.635765 ATGTCTAAAAAGACTTGCATTTAGGA 57.364 30.769 12.84 4.03 39.41 2.94
2502 5692 8.458573 TGTCTAAAAAGACTTGCATTTAGGAA 57.541 30.769 12.84 2.72 39.41 3.36
2503 5693 8.349983 TGTCTAAAAAGACTTGCATTTAGGAAC 58.650 33.333 12.84 7.39 39.41 3.62
2504 5694 7.534239 GTCTAAAAAGACTTGCATTTAGGAACG 59.466 37.037 12.84 0.00 36.48 3.95
2505 5695 4.766404 AAAGACTTGCATTTAGGAACGG 57.234 40.909 0.00 0.00 0.00 4.44
2506 5696 3.695830 AGACTTGCATTTAGGAACGGA 57.304 42.857 0.00 0.00 0.00 4.69
2507 5697 3.600388 AGACTTGCATTTAGGAACGGAG 58.400 45.455 0.00 0.00 0.00 4.63
2508 5698 2.678336 GACTTGCATTTAGGAACGGAGG 59.322 50.000 0.00 0.00 0.00 4.30
2509 5699 2.017049 CTTGCATTTAGGAACGGAGGG 58.983 52.381 0.00 0.00 0.00 4.30
2510 5700 1.281419 TGCATTTAGGAACGGAGGGA 58.719 50.000 0.00 0.00 0.00 4.20
2511 5701 1.209504 TGCATTTAGGAACGGAGGGAG 59.790 52.381 0.00 0.00 0.00 4.30
2512 5702 1.209747 GCATTTAGGAACGGAGGGAGT 59.790 52.381 0.00 0.00 0.00 3.85
2977 6172 4.473520 CGCCGCCCCTGATTCTGT 62.474 66.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.337578 AGGTTGTAACATGCAAAAACACT 57.662 34.783 0.00 0.00 0.00 3.55
281 288 5.803967 CAGTCATGAAGCAAGGCTATTTTTC 59.196 40.000 0.00 0.00 38.25 2.29
295 302 5.391736 GGAGCATTCAAGAACAGTCATGAAG 60.392 44.000 0.00 0.00 42.86 3.02
332 341 5.952526 TGGAAAATCCCGAAAAAGTAGAC 57.047 39.130 0.00 0.00 35.03 2.59
434 444 9.463443 AGAAATAAGGAAAAATGAAAAGACGTG 57.537 29.630 0.00 0.00 0.00 4.49
452 462 7.084486 GGCAGTCTGGTTAACAAAGAAATAAG 58.916 38.462 8.10 1.26 0.00 1.73
474 484 2.159814 CGATAGTTTTAAACACGCGGCA 60.160 45.455 12.47 0.00 0.00 5.69
503 513 1.991121 TCGAGGCGGTATTACTGGAT 58.009 50.000 4.85 0.00 0.00 3.41
646 661 5.360714 CCAGTGCCCATATCAAATTGTACTT 59.639 40.000 0.00 0.00 0.00 2.24
648 663 4.037923 CCCAGTGCCCATATCAAATTGTAC 59.962 45.833 0.00 0.00 0.00 2.90
654 682 1.638070 TGTCCCAGTGCCCATATCAAA 59.362 47.619 0.00 0.00 0.00 2.69
680 708 7.278646 GCTTTTTATTGGTGAAAATGGGAGATC 59.721 37.037 0.00 0.00 0.00 2.75
716 744 6.297712 GGAGGTAGGGAGTACATGATATACCT 60.298 46.154 0.00 11.85 43.34 3.08
720 748 5.076598 ACTGGAGGTAGGGAGTACATGATAT 59.923 44.000 0.00 0.00 32.62 1.63
736 764 6.312529 TGATCTTATATTACGGACTGGAGGT 58.687 40.000 0.00 0.00 0.00 3.85
758 786 2.020720 ACGCACCAGTGTGAAAAATGA 58.979 42.857 17.68 0.00 45.76 2.57
760 788 3.211045 ACTACGCACCAGTGTGAAAAAT 58.789 40.909 17.68 0.00 45.76 1.82
783 811 7.277319 CCCTAGAGTAACCGAGTAAATGTTTTC 59.723 40.741 0.00 0.00 0.00 2.29
811 842 4.690748 CACTTACCACTATTCCACACACAG 59.309 45.833 0.00 0.00 0.00 3.66
829 860 3.072468 CCCGCGTCCCTCCACTTA 61.072 66.667 4.92 0.00 0.00 2.24
916 964 4.699522 AGCAAACGGGGCGAGGAC 62.700 66.667 0.00 0.00 36.08 3.85
1222 1306 4.704833 GCAGAGCGGGCAGTGGAA 62.705 66.667 0.00 0.00 0.00 3.53
1300 1396 2.389998 GGAAGAATCGATCGAGTCTGC 58.610 52.381 39.03 36.94 46.92 4.26
1303 1399 2.860582 GCAGGGAAGAATCGATCGAGTC 60.861 54.545 32.03 32.03 39.24 3.36
1319 1441 0.180642 AGATCAGCACATCTGCAGGG 59.819 55.000 15.13 9.34 46.97 4.45
2065 2246 2.892425 GGACCAAGGCGCGATCTG 60.892 66.667 12.10 1.95 0.00 2.90
2113 2301 0.394938 TCGGTAAGCTTCAACTGCCA 59.605 50.000 0.00 0.00 0.00 4.92
2114 2302 1.079503 CTCGGTAAGCTTCAACTGCC 58.920 55.000 0.00 0.00 0.00 4.85
2115 2303 2.080286 TCTCGGTAAGCTTCAACTGC 57.920 50.000 0.00 0.00 0.00 4.40
2325 3938 0.766288 TGCCCCCAAAAGGAAAAGGG 60.766 55.000 0.00 0.00 41.12 3.95
2352 5542 9.725206 AAGACTTATATTTAGGAACAGGGAGTA 57.275 33.333 0.00 0.00 0.00 2.59
2353 5543 8.625467 AAGACTTATATTTAGGAACAGGGAGT 57.375 34.615 0.00 0.00 0.00 3.85
2354 5544 9.549078 GAAAGACTTATATTTAGGAACAGGGAG 57.451 37.037 0.00 0.00 0.00 4.30
2355 5545 9.280456 AGAAAGACTTATATTTAGGAACAGGGA 57.720 33.333 0.00 0.00 0.00 4.20
2396 5586 9.734620 CATTCATTTTGTTCCGTATGTAATCAT 57.265 29.630 0.00 0.00 38.00 2.45
2397 5587 8.951243 TCATTCATTTTGTTCCGTATGTAATCA 58.049 29.630 0.00 0.00 0.00 2.57
2398 5588 9.781834 TTCATTCATTTTGTTCCGTATGTAATC 57.218 29.630 0.00 0.00 0.00 1.75
2400 5590 9.781834 GATTCATTCATTTTGTTCCGTATGTAA 57.218 29.630 0.00 0.00 0.00 2.41
2401 5591 9.173021 AGATTCATTCATTTTGTTCCGTATGTA 57.827 29.630 0.00 0.00 0.00 2.29
2402 5592 8.055279 AGATTCATTCATTTTGTTCCGTATGT 57.945 30.769 0.00 0.00 0.00 2.29
2403 5593 9.438291 GTAGATTCATTCATTTTGTTCCGTATG 57.562 33.333 0.00 0.00 0.00 2.39
2404 5594 9.173021 TGTAGATTCATTCATTTTGTTCCGTAT 57.827 29.630 0.00 0.00 0.00 3.06
2405 5595 8.447833 GTGTAGATTCATTCATTTTGTTCCGTA 58.552 33.333 0.00 0.00 0.00 4.02
2406 5596 7.174946 AGTGTAGATTCATTCATTTTGTTCCGT 59.825 33.333 0.00 0.00 0.00 4.69
2407 5597 7.530010 AGTGTAGATTCATTCATTTTGTTCCG 58.470 34.615 0.00 0.00 0.00 4.30
2408 5598 8.734386 AGAGTGTAGATTCATTCATTTTGTTCC 58.266 33.333 0.00 0.00 0.00 3.62
2466 5656 9.533253 CAAGTCTTTTTAGACATTTCAAATGGT 57.467 29.630 14.70 4.00 41.02 3.55
2467 5657 8.490355 GCAAGTCTTTTTAGACATTTCAAATGG 58.510 33.333 14.70 0.00 41.02 3.16
2468 5658 9.033481 TGCAAGTCTTTTTAGACATTTCAAATG 57.967 29.630 8.67 8.67 41.02 2.32
2469 5659 9.768662 ATGCAAGTCTTTTTAGACATTTCAAAT 57.231 25.926 7.92 0.00 41.02 2.32
2470 5660 9.598517 AATGCAAGTCTTTTTAGACATTTCAAA 57.401 25.926 7.92 0.00 41.02 2.69
2471 5661 9.598517 AAATGCAAGTCTTTTTAGACATTTCAA 57.401 25.926 7.92 0.00 41.02 2.69
2474 5664 9.696917 CCTAAATGCAAGTCTTTTTAGACATTT 57.303 29.630 14.10 0.00 41.02 2.32
2475 5665 9.077885 TCCTAAATGCAAGTCTTTTTAGACATT 57.922 29.630 14.10 0.00 41.02 2.71
2476 5666 8.635765 TCCTAAATGCAAGTCTTTTTAGACAT 57.364 30.769 14.10 0.00 41.02 3.06
2477 5667 8.349983 GTTCCTAAATGCAAGTCTTTTTAGACA 58.650 33.333 14.10 1.66 41.02 3.41
2478 5668 7.534239 CGTTCCTAAATGCAAGTCTTTTTAGAC 59.466 37.037 14.10 6.82 39.00 2.59
2479 5669 7.308348 CCGTTCCTAAATGCAAGTCTTTTTAGA 60.308 37.037 14.10 1.97 0.00 2.10
2480 5670 6.801862 CCGTTCCTAAATGCAAGTCTTTTTAG 59.198 38.462 7.85 7.85 0.00 1.85
2481 5671 6.487331 TCCGTTCCTAAATGCAAGTCTTTTTA 59.513 34.615 0.00 0.00 0.00 1.52
2482 5672 5.300792 TCCGTTCCTAAATGCAAGTCTTTTT 59.699 36.000 0.00 0.00 0.00 1.94
2483 5673 4.825085 TCCGTTCCTAAATGCAAGTCTTTT 59.175 37.500 0.00 0.00 0.00 2.27
2484 5674 4.394729 TCCGTTCCTAAATGCAAGTCTTT 58.605 39.130 0.00 0.00 0.00 2.52
2485 5675 4.003648 CTCCGTTCCTAAATGCAAGTCTT 58.996 43.478 0.00 0.00 0.00 3.01
2486 5676 3.600388 CTCCGTTCCTAAATGCAAGTCT 58.400 45.455 0.00 0.00 0.00 3.24
2487 5677 2.678336 CCTCCGTTCCTAAATGCAAGTC 59.322 50.000 0.00 0.00 0.00 3.01
2488 5678 2.618045 CCCTCCGTTCCTAAATGCAAGT 60.618 50.000 0.00 0.00 0.00 3.16
2489 5679 2.017049 CCCTCCGTTCCTAAATGCAAG 58.983 52.381 0.00 0.00 0.00 4.01
2490 5680 1.631388 TCCCTCCGTTCCTAAATGCAA 59.369 47.619 0.00 0.00 0.00 4.08
2491 5681 1.209504 CTCCCTCCGTTCCTAAATGCA 59.790 52.381 0.00 0.00 0.00 3.96
2492 5682 1.209747 ACTCCCTCCGTTCCTAAATGC 59.790 52.381 0.00 0.00 0.00 3.56
2493 5683 4.957684 ATACTCCCTCCGTTCCTAAATG 57.042 45.455 0.00 0.00 0.00 2.32
2494 5684 5.666265 AGAAATACTCCCTCCGTTCCTAAAT 59.334 40.000 0.00 0.00 0.00 1.40
2495 5685 5.028131 AGAAATACTCCCTCCGTTCCTAAA 58.972 41.667 0.00 0.00 0.00 1.85
2496 5686 4.617593 AGAAATACTCCCTCCGTTCCTAA 58.382 43.478 0.00 0.00 0.00 2.69
2497 5687 4.079327 AGAGAAATACTCCCTCCGTTCCTA 60.079 45.833 0.00 0.00 45.96 2.94
2498 5688 3.032459 GAGAAATACTCCCTCCGTTCCT 58.968 50.000 0.00 0.00 39.53 3.36
2499 5689 3.032459 AGAGAAATACTCCCTCCGTTCC 58.968 50.000 0.00 0.00 45.96 3.62
2500 5690 4.037803 GGTAGAGAAATACTCCCTCCGTTC 59.962 50.000 0.00 0.00 45.96 3.95
2501 5691 3.959449 GGTAGAGAAATACTCCCTCCGTT 59.041 47.826 0.00 0.00 45.96 4.44
2502 5692 3.204831 AGGTAGAGAAATACTCCCTCCGT 59.795 47.826 0.00 0.00 45.96 4.69
2503 5693 3.834938 AGGTAGAGAAATACTCCCTCCG 58.165 50.000 0.00 0.00 45.96 4.63
2504 5694 5.078949 GGTAGGTAGAGAAATACTCCCTCC 58.921 50.000 0.00 0.00 45.96 4.30
2505 5695 4.761227 CGGTAGGTAGAGAAATACTCCCTC 59.239 50.000 0.00 0.00 45.96 4.30
2506 5696 4.727677 CGGTAGGTAGAGAAATACTCCCT 58.272 47.826 0.00 0.00 45.96 4.20
2507 5697 3.255395 GCGGTAGGTAGAGAAATACTCCC 59.745 52.174 0.00 0.00 45.96 4.30
2508 5698 3.887716 TGCGGTAGGTAGAGAAATACTCC 59.112 47.826 0.00 0.00 45.96 3.85
2509 5699 4.554330 CGTGCGGTAGGTAGAGAAATACTC 60.554 50.000 0.00 0.00 45.22 2.59
2510 5700 3.314635 CGTGCGGTAGGTAGAGAAATACT 59.685 47.826 0.00 0.00 0.00 2.12
2511 5701 3.313526 TCGTGCGGTAGGTAGAGAAATAC 59.686 47.826 0.00 0.00 0.00 1.89
2512 5702 3.544684 TCGTGCGGTAGGTAGAGAAATA 58.455 45.455 0.00 0.00 0.00 1.40
2647 5842 2.092592 GGGACGGGGACTTATTTGTCAT 60.093 50.000 0.00 0.00 38.61 3.06


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

AutoCloner maintained by Alex Coulton.