Multiple sequence alignment - TraesCS3B01G441600

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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 TraesCS3B01G441600 chr3B 100.000 4030 0 0 1 4030 681097302 681101331 0.000000e+00 7443.0
1 TraesCS3B01G441600 chr3B 95.312 64 3 0 2414 2477 55770390 55770327 7.130000e-18 102.0
2 TraesCS3B01G441600 chr3B 85.263 95 6 4 2381 2473 531401374 531401462 1.540000e-14 91.6
3 TraesCS3B01G441600 chr3D 93.867 2397 104 21 2 2386 517274052 517276417 0.000000e+00 3572.0
4 TraesCS3B01G441600 chr3D 95.866 895 30 3 2470 3357 517276416 517277310 0.000000e+00 1441.0
5 TraesCS3B01G441600 chr3D 94.737 551 27 1 3480 4030 517278574 517279122 0.000000e+00 856.0
6 TraesCS3B01G441600 chr3D 94.378 249 11 2 3361 3609 517278324 517278569 2.940000e-101 379.0
7 TraesCS3B01G441600 chr3A 93.552 2404 107 28 4 2383 653240885 653243264 0.000000e+00 3537.0
8 TraesCS3B01G441600 chr3A 94.723 1573 66 9 2469 4030 653243265 653244831 0.000000e+00 2429.0
9 TraesCS3B01G441600 chr5D 90.110 91 4 2 2388 2473 7627239 7627149 3.290000e-21 113.0
10 TraesCS3B01G441600 chr5D 92.683 41 3 0 2377 2417 372452954 372452914 4.350000e-05 60.2
11 TraesCS3B01G441600 chr6D 95.522 67 1 2 2415 2480 42565320 42565385 5.510000e-19 106.0
12 TraesCS3B01G441600 chr4A 92.958 71 2 1 2415 2485 731368205 731368272 2.560000e-17 100.0
13 TraesCS3B01G441600 chr2B 91.781 73 3 3 2415 2485 639288134 639288205 9.220000e-17 99.0
14 TraesCS3B01G441600 chr2B 100.000 34 0 0 2384 2417 493983902 493983935 3.360000e-06 63.9
15 TraesCS3B01G441600 chr1B 92.754 69 3 2 2415 2482 488538994 488538927 9.220000e-17 99.0
16 TraesCS3B01G441600 chr2D 91.549 71 5 1 2415 2485 240791079 240791010 3.320000e-16 97.1
17 TraesCS3B01G441600 chr1D 84.615 91 10 4 2382 2471 493948373 493948460 2.000000e-13 87.9
18 TraesCS3B01G441600 chr6A 93.617 47 2 1 2371 2417 442254553 442254508 7.230000e-08 69.4
19 TraesCS3B01G441600 chr5B 97.500 40 1 0 2370 2409 442819601 442819562 7.230000e-08 69.4
20 TraesCS3B01G441600 chr1A 97.368 38 1 0 2377 2414 127116382 127116419 9.350000e-07 65.8
21 TraesCS3B01G441600 chr6B 100.000 31 0 0 2384 2414 21080094 21080124 1.560000e-04 58.4


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 TraesCS3B01G441600 chr3B 681097302 681101331 4029 False 7443 7443 100.0000 1 4030 1 chr3B.!!$F2 4029
1 TraesCS3B01G441600 chr3D 517274052 517279122 5070 False 1562 3572 94.7120 2 4030 4 chr3D.!!$F1 4028
2 TraesCS3B01G441600 chr3A 653240885 653244831 3946 False 2983 3537 94.1375 4 4030 2 chr3A.!!$F1 4026

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
451 468 0.232303 GTCTCCGCGTTTCTTGTGTG 59.768 55.0 4.92 0.0 0.00 3.82 F
1249 1286 0.111061 AACACCCTGCTCTGATGCAA 59.889 50.0 0.00 0.0 42.83 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2248 0.824109 TCACCATACGAAGGAGCTGG 59.176 55.0 0.0 0.0 0.00 4.85 R
3113 3158 0.322975 TCAGCCAAGAACTCCTCTGC 59.677 55.0 0.0 0.0 33.37 4.26 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
85 86 1.806623 CGTGTAGGGTCAAGCTATGGC 60.807 57.143 0.00 0.00 39.06 4.40
141 143 3.006677 GGCCCTTGGAGTGCCATA 58.993 61.111 0.00 0.00 45.46 2.74
148 150 1.945394 CTTGGAGTGCCATAGTGATGC 59.055 52.381 0.00 0.00 45.46 3.91
163 165 0.692419 GATGCTCAGAGGGGAAGGGA 60.692 60.000 0.00 0.00 0.00 4.20
177 186 3.116091 AGGGAAGCACCTTGTGTTG 57.884 52.632 0.00 0.00 37.69 3.33
178 187 0.550914 AGGGAAGCACCTTGTGTTGA 59.449 50.000 0.00 0.00 37.69 3.18
179 188 1.145738 AGGGAAGCACCTTGTGTTGAT 59.854 47.619 0.00 0.00 37.69 2.57
180 189 1.270550 GGGAAGCACCTTGTGTTGATG 59.729 52.381 0.00 0.00 38.98 3.07
181 190 1.336240 GGAAGCACCTTGTGTTGATGC 60.336 52.381 0.00 0.00 35.75 3.91
182 191 1.337703 GAAGCACCTTGTGTTGATGCA 59.662 47.619 0.00 0.00 38.79 3.96
196 205 7.604549 TGTGTTGATGCAATAGTTCATGATTT 58.395 30.769 0.00 0.00 0.00 2.17
225 234 1.205179 TCAATTGACATGCCATGTGCC 59.795 47.619 16.43 2.04 45.03 5.01
231 240 0.754217 ACATGCCATGTGCCCTGATC 60.754 55.000 10.06 0.00 43.01 2.92
262 271 9.965824 TGAATACTTCCAAGATTTCTGTTTTTC 57.034 29.630 0.00 0.00 0.00 2.29
341 357 5.899299 AGCAAGATTTGTGCAGATTTATCC 58.101 37.500 0.00 0.00 44.74 2.59
351 367 5.882557 TGTGCAGATTTATCCTCTTCTTTCC 59.117 40.000 0.00 0.00 0.00 3.13
451 468 0.232303 GTCTCCGCGTTTCTTGTGTG 59.768 55.000 4.92 0.00 0.00 3.82
465 494 8.548721 CGTTTCTTGTGTGTTAGTCTAAGATTT 58.451 33.333 0.00 0.00 0.00 2.17
556 585 1.955778 TCGGTGGTCAAGTCTTCGTTA 59.044 47.619 0.00 0.00 0.00 3.18
557 586 2.030540 TCGGTGGTCAAGTCTTCGTTAG 60.031 50.000 0.00 0.00 0.00 2.34
577 606 7.874016 TCGTTAGAAGTTAGGCAGTATTTTTCA 59.126 33.333 0.00 0.00 0.00 2.69
579 608 9.216117 GTTAGAAGTTAGGCAGTATTTTTCAGA 57.784 33.333 0.00 0.00 0.00 3.27
638 667 6.144402 CCACTTGCTAGTTGCTAAATGTTTTG 59.856 38.462 0.00 0.00 43.37 2.44
640 670 6.918022 ACTTGCTAGTTGCTAAATGTTTTGTC 59.082 34.615 0.00 0.00 43.37 3.18
667 697 8.687824 AAAATAACTTGCAACATGCTATACAC 57.312 30.769 0.00 0.00 45.31 2.90
668 698 7.630242 AATAACTTGCAACATGCTATACACT 57.370 32.000 0.00 0.00 45.31 3.55
697 728 4.404073 AGCTCCATCAGTTAACTAGTGAGG 59.596 45.833 8.04 4.48 39.51 3.86
744 775 6.850555 ACGAGACTATGACCTTAGTTTGTAC 58.149 40.000 0.00 0.00 32.59 2.90
745 776 6.432162 ACGAGACTATGACCTTAGTTTGTACA 59.568 38.462 0.00 0.00 32.59 2.90
746 777 6.967767 CGAGACTATGACCTTAGTTTGTACAG 59.032 42.308 0.00 0.00 32.59 2.74
747 778 7.361885 CGAGACTATGACCTTAGTTTGTACAGT 60.362 40.741 0.00 0.00 32.59 3.55
748 779 7.603651 AGACTATGACCTTAGTTTGTACAGTG 58.396 38.462 0.00 0.00 32.59 3.66
817 848 6.124340 ACAGGAACATCATCAAATAGCATCA 58.876 36.000 0.00 0.00 0.00 3.07
839 870 9.599866 CATCATGTATTCCTGTTAACAAGTAGA 57.400 33.333 10.03 1.80 0.00 2.59
882 913 9.440773 CATTGTTATTTAGATAGGCTGCTGATA 57.559 33.333 0.00 0.00 0.00 2.15
891 926 3.258971 AGGCTGCTGATACTTGTCTTC 57.741 47.619 0.00 0.00 0.00 2.87
915 950 4.018490 TGTAGGCATCACAGAAATTGCAT 58.982 39.130 0.00 0.00 36.82 3.96
935 972 5.105392 TGCATTGGGTTGGATTTAATCTGAC 60.105 40.000 4.87 4.24 0.00 3.51
1041 1078 0.248012 ACCCATCAACGACATACGCA 59.752 50.000 0.00 0.00 46.94 5.24
1212 1249 5.477984 TGCTGCATTTCAGAACTCCTTTTAT 59.522 36.000 0.00 0.00 45.72 1.40
1249 1286 0.111061 AACACCCTGCTCTGATGCAA 59.889 50.000 0.00 0.00 42.83 4.08
1300 1337 3.070302 GTCTCAACAGAACTCCCAGTCTT 59.930 47.826 0.00 0.00 0.00 3.01
1353 1390 6.295249 AGTAGAGTTCGATGATGAGATCAGA 58.705 40.000 0.00 0.00 43.53 3.27
1425 1462 1.988293 TGTTCGAAATTTCCCAGGCA 58.012 45.000 12.54 2.69 0.00 4.75
1638 1675 2.415010 CTCCGGCAGATGGTCTCG 59.585 66.667 0.00 0.00 0.00 4.04
1767 1804 2.398588 CCTCCAACCCTGTATCAGCTA 58.601 52.381 0.00 0.00 0.00 3.32
1857 1894 2.656947 TACTTGAAGCCTGCAAAGGT 57.343 45.000 0.00 0.00 0.00 3.50
1925 1962 5.406780 GCCAGTATATTACACTGATGCAGTC 59.593 44.000 3.65 0.00 43.43 3.51
1992 2029 2.094545 TGTGGATGATCACGAGACAGTG 60.095 50.000 0.00 0.00 43.11 3.66
2032 2069 1.228552 AAGGTCATTGGGCAACGCT 60.229 52.632 0.00 0.00 37.60 5.07
2055 2092 1.004440 GAAGCTTGCGGAGGACTGT 60.004 57.895 2.10 0.00 0.00 3.55
2211 2248 0.921347 CGATCATGAACGAACGGGAC 59.079 55.000 19.51 0.00 0.00 4.46
2313 2350 7.121315 GCTCCATTTCAGACAAGGTTAGTTATT 59.879 37.037 0.00 0.00 0.00 1.40
2386 2423 6.987404 GGATAGTTTCTCCACATCCTTTCTAC 59.013 42.308 0.00 0.00 33.74 2.59
2387 2424 7.147637 GGATAGTTTCTCCACATCCTTTCTACT 60.148 40.741 0.00 0.00 33.74 2.57
2389 2426 5.046231 AGTTTCTCCACATCCTTTCTACTCC 60.046 44.000 0.00 0.00 0.00 3.85
2390 2427 3.375699 TCTCCACATCCTTTCTACTCCC 58.624 50.000 0.00 0.00 0.00 4.30
2392 2429 3.375699 TCCACATCCTTTCTACTCCCTC 58.624 50.000 0.00 0.00 0.00 4.30
2393 2430 3.012959 TCCACATCCTTTCTACTCCCTCT 59.987 47.826 0.00 0.00 0.00 3.69
2394 2431 3.133721 CCACATCCTTTCTACTCCCTCTG 59.866 52.174 0.00 0.00 0.00 3.35
2396 2433 4.223923 CACATCCTTTCTACTCCCTCTGTT 59.776 45.833 0.00 0.00 0.00 3.16
2397 2434 4.468153 ACATCCTTTCTACTCCCTCTGTTC 59.532 45.833 0.00 0.00 0.00 3.18
2398 2435 3.442076 TCCTTTCTACTCCCTCTGTTCC 58.558 50.000 0.00 0.00 0.00 3.62
2399 2436 3.077695 TCCTTTCTACTCCCTCTGTTCCT 59.922 47.826 0.00 0.00 0.00 3.36
2400 2437 4.294168 TCCTTTCTACTCCCTCTGTTCCTA 59.706 45.833 0.00 0.00 0.00 2.94
2401 2438 5.024118 CCTTTCTACTCCCTCTGTTCCTAA 58.976 45.833 0.00 0.00 0.00 2.69
2402 2439 5.484290 CCTTTCTACTCCCTCTGTTCCTAAA 59.516 44.000 0.00 0.00 0.00 1.85
2403 2440 6.157123 CCTTTCTACTCCCTCTGTTCCTAAAT 59.843 42.308 0.00 0.00 0.00 1.40
2404 2441 7.311360 CCTTTCTACTCCCTCTGTTCCTAAATT 60.311 40.741 0.00 0.00 0.00 1.82
2405 2442 7.569599 TTCTACTCCCTCTGTTCCTAAATTT 57.430 36.000 0.00 0.00 0.00 1.82
2406 2443 8.674925 TTCTACTCCCTCTGTTCCTAAATTTA 57.325 34.615 0.00 0.00 0.00 1.40
2407 2444 8.674925 TCTACTCCCTCTGTTCCTAAATTTAA 57.325 34.615 0.00 0.00 0.00 1.52
2408 2445 8.759782 TCTACTCCCTCTGTTCCTAAATTTAAG 58.240 37.037 0.00 0.00 0.00 1.85
2409 2446 7.331089 ACTCCCTCTGTTCCTAAATTTAAGT 57.669 36.000 0.00 0.00 0.00 2.24
2410 2447 7.395617 ACTCCCTCTGTTCCTAAATTTAAGTC 58.604 38.462 0.00 0.00 0.00 3.01
2411 2448 7.237887 ACTCCCTCTGTTCCTAAATTTAAGTCT 59.762 37.037 0.00 0.00 0.00 3.24
2412 2449 7.985589 TCCCTCTGTTCCTAAATTTAAGTCTT 58.014 34.615 0.00 0.00 0.00 3.01
2413 2450 8.445588 TCCCTCTGTTCCTAAATTTAAGTCTTT 58.554 33.333 0.00 0.00 0.00 2.52
2414 2451 8.515414 CCCTCTGTTCCTAAATTTAAGTCTTTG 58.485 37.037 0.00 0.00 0.00 2.77
2415 2452 9.067986 CCTCTGTTCCTAAATTTAAGTCTTTGT 57.932 33.333 0.00 0.00 0.00 2.83
2422 2459 9.802039 TCCTAAATTTAAGTCTTTGTATGTGGT 57.198 29.630 0.00 0.00 0.00 4.16
2425 2462 8.472007 AAATTTAAGTCTTTGTATGTGGTCCA 57.528 30.769 0.00 0.00 0.00 4.02
2426 2463 8.650143 AATTTAAGTCTTTGTATGTGGTCCAT 57.350 30.769 0.00 0.00 37.58 3.41
2427 2464 9.747898 AATTTAAGTCTTTGTATGTGGTCCATA 57.252 29.630 0.00 0.00 34.86 2.74
2428 2465 8.786826 TTTAAGTCTTTGTATGTGGTCCATAG 57.213 34.615 0.00 0.00 36.71 2.23
2429 2466 6.374417 AAGTCTTTGTATGTGGTCCATAGT 57.626 37.500 0.00 0.00 36.71 2.12
2430 2467 5.734720 AGTCTTTGTATGTGGTCCATAGTG 58.265 41.667 0.00 0.00 36.71 2.74
2431 2468 4.876107 GTCTTTGTATGTGGTCCATAGTGG 59.124 45.833 0.00 0.00 36.71 4.00
2432 2469 4.780554 TCTTTGTATGTGGTCCATAGTGGA 59.219 41.667 0.00 0.00 45.98 4.02
2446 2483 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
2447 2484 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
2448 2485 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
2449 2486 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
2465 2502 9.907229 ACAAAGACTTATATTTAGGAAAGGAGG 57.093 33.333 0.00 0.00 0.00 4.30
2466 2503 9.343539 CAAAGACTTATATTTAGGAAAGGAGGG 57.656 37.037 0.00 0.00 0.00 4.30
2467 2504 8.871570 AAGACTTATATTTAGGAAAGGAGGGA 57.128 34.615 0.00 0.00 0.00 4.20
2468 2505 8.499288 AGACTTATATTTAGGAAAGGAGGGAG 57.501 38.462 0.00 0.00 0.00 4.30
2469 2506 8.074991 AGACTTATATTTAGGAAAGGAGGGAGT 58.925 37.037 0.00 0.00 0.00 3.85
2470 2507 9.377238 GACTTATATTTAGGAAAGGAGGGAGTA 57.623 37.037 0.00 0.00 0.00 2.59
2471 2508 9.382307 ACTTATATTTAGGAAAGGAGGGAGTAG 57.618 37.037 0.00 0.00 0.00 2.57
2472 2509 9.603189 CTTATATTTAGGAAAGGAGGGAGTAGA 57.397 37.037 0.00 0.00 0.00 2.59
2473 2510 7.859026 ATATTTAGGAAAGGAGGGAGTAGAC 57.141 40.000 0.00 0.00 0.00 2.59
2474 2511 4.687262 TTAGGAAAGGAGGGAGTAGACA 57.313 45.455 0.00 0.00 0.00 3.41
2475 2512 2.822697 AGGAAAGGAGGGAGTAGACAC 58.177 52.381 0.00 0.00 0.00 3.67
2476 2513 2.384029 AGGAAAGGAGGGAGTAGACACT 59.616 50.000 0.00 0.00 37.87 3.55
2511 2548 8.816894 TCCTTTGTAGATTCTGTCTATTGACTT 58.183 33.333 8.74 0.00 41.33 3.01
2512 2549 8.877779 CCTTTGTAGATTCTGTCTATTGACTTG 58.122 37.037 8.74 2.41 41.33 3.16
2513 2550 9.645059 CTTTGTAGATTCTGTCTATTGACTTGA 57.355 33.333 8.74 4.56 41.33 3.02
2606 2645 5.662674 ATGACTACTACTCCGCTCTTTTT 57.337 39.130 0.00 0.00 0.00 1.94
2717 2756 2.859273 CTTGCGAAGGCCCTGATCGT 62.859 60.000 16.14 0.00 38.75 3.73
2766 2805 7.272037 TCTCTACTCATACGTCATGCAAATA 57.728 36.000 0.00 0.00 34.35 1.40
2773 2818 7.334421 ACTCATACGTCATGCAAATACTTCTTT 59.666 33.333 0.00 0.00 34.35 2.52
2855 2900 2.813754 CGAAGTTGCTGGAAAATGGAGA 59.186 45.455 0.00 0.00 0.00 3.71
2906 2951 0.243636 GCCCATTTAGCAGCAACGTT 59.756 50.000 0.00 0.00 0.00 3.99
2914 2959 0.530744 AGCAGCAACGTTATCGGAGA 59.469 50.000 0.00 0.00 45.75 3.71
2915 2960 0.924090 GCAGCAACGTTATCGGAGAG 59.076 55.000 0.00 0.00 43.63 3.20
2957 3002 2.614829 ACTGCGACAGGTACAAGTTT 57.385 45.000 10.80 0.00 35.51 2.66
3039 3084 0.175760 GTGGCAATAGGTCGAGCTCA 59.824 55.000 22.33 9.71 0.00 4.26
3113 3158 3.489568 GGTTGTAAAAAGGGTGTGAACCG 60.490 47.826 0.00 0.00 0.00 4.44
3115 3160 1.677052 GTAAAAAGGGTGTGAACCGCA 59.323 47.619 0.00 0.00 0.00 5.69
3348 3397 2.113860 TGGGAACTAGAACATGCAGC 57.886 50.000 0.00 0.00 0.00 5.25
3425 4484 6.267471 ACTTGCAAAAGTCCATCCAGATTTTA 59.733 34.615 0.00 0.00 0.00 1.52
3426 4485 6.662865 TGCAAAAGTCCATCCAGATTTTAA 57.337 33.333 0.00 0.00 0.00 1.52
3609 4801 8.600668 ACACACATATGCTCTCCAGATATATTT 58.399 33.333 1.58 0.00 0.00 1.40
3912 5104 3.761657 TGCATGCAAAGATTTCGATGAC 58.238 40.909 20.30 0.00 0.00 3.06
3928 5120 0.537143 TGACCCAATGACACACAGGC 60.537 55.000 0.00 0.00 0.00 4.85
3935 5127 3.986006 GACACACAGGCGGTCCGA 61.986 66.667 17.49 0.00 37.47 4.55
3951 5143 3.621715 GGTCCGATTGACAATCTGTTACC 59.378 47.826 22.54 18.77 46.38 2.85
3960 5152 4.937620 TGACAATCTGTTACCTCTGCATTC 59.062 41.667 0.00 0.00 0.00 2.67
3963 5155 5.189736 ACAATCTGTTACCTCTGCATTCCTA 59.810 40.000 0.00 0.00 0.00 2.94
3987 5179 0.586319 TGCGAAGGCTTGAACTTTCG 59.414 50.000 3.46 0.42 40.82 3.46
3989 5181 0.110192 CGAAGGCTTGAACTTTCGGC 60.110 55.000 3.46 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.431942 CCGACCAGACGAAACCGG 60.432 66.667 0.00 0.00 35.09 5.28
85 86 0.320374 TCTACACGCAACCCCAAGAG 59.680 55.000 0.00 0.00 0.00 2.85
128 129 4.296310 GAGCATCACTATGGCACTCCAAG 61.296 52.174 0.00 0.00 39.95 3.61
129 130 2.420547 GAGCATCACTATGGCACTCCAA 60.421 50.000 0.00 0.00 39.95 3.53
130 131 1.139654 GAGCATCACTATGGCACTCCA 59.860 52.381 0.00 0.00 40.57 3.86
131 132 1.139654 TGAGCATCACTATGGCACTCC 59.860 52.381 0.00 0.00 42.56 3.85
132 133 2.102084 TCTGAGCATCACTATGGCACTC 59.898 50.000 0.00 0.00 42.56 3.51
133 134 2.102757 CTCTGAGCATCACTATGGCACT 59.897 50.000 0.00 0.00 42.56 4.40
141 143 1.202330 CTTCCCCTCTGAGCATCACT 58.798 55.000 0.00 0.00 42.56 3.41
148 150 0.911525 TGCTTCCCTTCCCCTCTGAG 60.912 60.000 0.00 0.00 0.00 3.35
163 165 1.401761 TGCATCAACACAAGGTGCTT 58.598 45.000 0.00 0.00 36.98 3.91
217 226 1.954382 CATTCTGATCAGGGCACATGG 59.046 52.381 22.42 0.00 0.00 3.66
262 271 5.751990 GCTCAAATCTATTGGGATGCAAAAG 59.248 40.000 0.00 0.00 0.00 2.27
341 357 2.159043 TGCTATGCTCGGGAAAGAAGAG 60.159 50.000 0.00 0.00 35.28 2.85
351 367 5.237815 TCCTAAATAACATGCTATGCTCGG 58.762 41.667 0.00 0.00 0.00 4.63
556 585 7.224297 TGTCTGAAAAATACTGCCTAACTTCT 58.776 34.615 0.00 0.00 0.00 2.85
557 586 7.435068 TGTCTGAAAAATACTGCCTAACTTC 57.565 36.000 0.00 0.00 0.00 3.01
667 697 5.837437 AGTTAACTGATGGAGCTCGAATAG 58.163 41.667 7.48 9.10 0.00 1.73
668 698 5.854010 AGTTAACTGATGGAGCTCGAATA 57.146 39.130 7.48 0.00 0.00 1.75
697 728 6.018994 CGTACCTAACAAGTAATCCAATCAGC 60.019 42.308 0.00 0.00 0.00 4.26
744 775 4.754618 TGTTCACATACCTAACTTGCACTG 59.245 41.667 0.00 0.00 0.00 3.66
745 776 4.968259 TGTTCACATACCTAACTTGCACT 58.032 39.130 0.00 0.00 0.00 4.40
746 777 4.154195 CCTGTTCACATACCTAACTTGCAC 59.846 45.833 0.00 0.00 0.00 4.57
747 778 4.323417 CCTGTTCACATACCTAACTTGCA 58.677 43.478 0.00 0.00 0.00 4.08
748 779 3.689649 CCCTGTTCACATACCTAACTTGC 59.310 47.826 0.00 0.00 0.00 4.01
811 842 6.886459 ACTTGTTAACAGGAATACATGATGCT 59.114 34.615 23.06 0.00 0.00 3.79
817 848 7.852263 AGCTCTACTTGTTAACAGGAATACAT 58.148 34.615 23.06 3.40 0.00 2.29
870 901 4.026744 AGAAGACAAGTATCAGCAGCCTA 58.973 43.478 0.00 0.00 0.00 3.93
882 913 4.202357 TGTGATGCCTACAAGAAGACAAGT 60.202 41.667 0.00 0.00 0.00 3.16
891 926 4.082625 TGCAATTTCTGTGATGCCTACAAG 60.083 41.667 0.00 0.00 38.00 3.16
915 950 4.658063 ACGTCAGATTAAATCCAACCCAA 58.342 39.130 0.00 0.00 0.00 4.12
935 972 2.739379 GAGGCCTTCTTTCTTCAGAACG 59.261 50.000 6.77 0.00 33.13 3.95
1026 1063 8.534333 AAATATTATCTGCGTATGTCGTTGAT 57.466 30.769 0.00 0.00 42.13 2.57
1065 1102 3.283684 TTTGAGTTGGGTGCGCCG 61.284 61.111 10.86 0.00 34.97 6.46
1197 1234 6.121776 TGCTGGTTATAAAAGGAGTTCTGA 57.878 37.500 0.00 0.00 0.00 3.27
1212 1249 3.813166 GTGTTAGTGAAGCTTGCTGGTTA 59.187 43.478 2.10 0.00 36.40 2.85
1300 1337 8.774546 AGTCCAGAACTCTGATTATCTGATAA 57.225 34.615 12.17 12.17 46.59 1.75
1425 1462 3.021695 CCATTCATCACTGATGCAACCT 58.978 45.455 13.46 0.00 39.63 3.50
1578 1615 4.025647 GCTTCATCTACGTTGTATTCAGCC 60.026 45.833 0.00 0.00 0.00 4.85
1587 1624 1.394917 GCCTGTGCTTCATCTACGTTG 59.605 52.381 0.00 0.00 33.53 4.10
1767 1804 4.464951 TCAAAGAGGATTTGCATTGCTGAT 59.535 37.500 10.49 3.72 0.00 2.90
1925 1962 7.062605 GTGGTTTGTTTGCATCATCTTTCATAG 59.937 37.037 0.00 0.00 0.00 2.23
1992 2029 1.893919 GACCTCCCACAGTCCTCTGC 61.894 65.000 0.00 0.00 44.77 4.26
2004 2041 1.065126 CCAATGACCTTCAGACCTCCC 60.065 57.143 0.00 0.00 0.00 4.30
2032 2069 1.003355 CCTCCGCAAGCTTCTCCAA 60.003 57.895 0.00 0.00 0.00 3.53
2055 2092 4.949856 GCCCTGAACTCAAAAGATATTCCA 59.050 41.667 0.00 0.00 0.00 3.53
2211 2248 0.824109 TCACCATACGAAGGAGCTGG 59.176 55.000 0.00 0.00 0.00 4.85
2313 2350 5.534278 TGCCGCAATAGAATTGGATAATGAA 59.466 36.000 0.00 0.00 0.00 2.57
2386 2423 7.625469 AGACTTAAATTTAGGAACAGAGGGAG 58.375 38.462 13.73 0.00 0.00 4.30
2387 2424 7.569599 AGACTTAAATTTAGGAACAGAGGGA 57.430 36.000 13.73 0.00 0.00 4.20
2389 2426 9.067986 ACAAAGACTTAAATTTAGGAACAGAGG 57.932 33.333 13.73 1.06 0.00 3.69
2396 2433 9.802039 ACCACATACAAAGACTTAAATTTAGGA 57.198 29.630 13.73 0.00 0.00 2.94
2399 2436 9.575868 TGGACCACATACAAAGACTTAAATTTA 57.424 29.630 0.00 0.00 0.00 1.40
2400 2437 8.472007 TGGACCACATACAAAGACTTAAATTT 57.528 30.769 0.00 0.00 0.00 1.82
2401 2438 8.650143 ATGGACCACATACAAAGACTTAAATT 57.350 30.769 0.00 0.00 38.26 1.82
2402 2439 9.396022 CTATGGACCACATACAAAGACTTAAAT 57.604 33.333 0.00 0.00 41.03 1.40
2403 2440 8.380099 ACTATGGACCACATACAAAGACTTAAA 58.620 33.333 0.00 0.00 41.03 1.52
2404 2441 7.822334 CACTATGGACCACATACAAAGACTTAA 59.178 37.037 0.00 0.00 41.03 1.85
2405 2442 7.327975 CACTATGGACCACATACAAAGACTTA 58.672 38.462 0.00 0.00 41.03 2.24
2406 2443 6.173339 CACTATGGACCACATACAAAGACTT 58.827 40.000 0.00 0.00 41.03 3.01
2407 2444 5.338381 CCACTATGGACCACATACAAAGACT 60.338 44.000 0.00 0.00 40.96 3.24
2408 2445 4.876107 CCACTATGGACCACATACAAAGAC 59.124 45.833 0.00 0.00 40.96 3.01
2409 2446 4.780554 TCCACTATGGACCACATACAAAGA 59.219 41.667 0.00 0.00 42.67 2.52
2410 2447 5.097742 TCCACTATGGACCACATACAAAG 57.902 43.478 0.00 0.00 42.67 2.77
2422 2459 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
2423 2460 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
2439 2476 9.907229 CCTCCTTTCCTAAATATAAGTCTTTGT 57.093 33.333 0.00 0.00 0.00 2.83
2440 2477 9.343539 CCCTCCTTTCCTAAATATAAGTCTTTG 57.656 37.037 0.00 0.00 0.00 2.77
2441 2478 9.292751 TCCCTCCTTTCCTAAATATAAGTCTTT 57.707 33.333 0.00 0.00 0.00 2.52
2442 2479 8.871570 TCCCTCCTTTCCTAAATATAAGTCTT 57.128 34.615 0.00 0.00 0.00 3.01
2443 2480 8.074991 ACTCCCTCCTTTCCTAAATATAAGTCT 58.925 37.037 0.00 0.00 0.00 3.24
2444 2481 8.265108 ACTCCCTCCTTTCCTAAATATAAGTC 57.735 38.462 0.00 0.00 0.00 3.01
2445 2482 9.382307 CTACTCCCTCCTTTCCTAAATATAAGT 57.618 37.037 0.00 0.00 0.00 2.24
2446 2483 9.603189 TCTACTCCCTCCTTTCCTAAATATAAG 57.397 37.037 0.00 0.00 0.00 1.73
2447 2484 9.377238 GTCTACTCCCTCCTTTCCTAAATATAA 57.623 37.037 0.00 0.00 0.00 0.98
2448 2485 8.517047 TGTCTACTCCCTCCTTTCCTAAATATA 58.483 37.037 0.00 0.00 0.00 0.86
2449 2486 7.290481 GTGTCTACTCCCTCCTTTCCTAAATAT 59.710 40.741 0.00 0.00 0.00 1.28
2450 2487 6.610425 GTGTCTACTCCCTCCTTTCCTAAATA 59.390 42.308 0.00 0.00 0.00 1.40
2451 2488 5.425862 GTGTCTACTCCCTCCTTTCCTAAAT 59.574 44.000 0.00 0.00 0.00 1.40
2452 2489 4.776308 GTGTCTACTCCCTCCTTTCCTAAA 59.224 45.833 0.00 0.00 0.00 1.85
2453 2490 4.045590 AGTGTCTACTCCCTCCTTTCCTAA 59.954 45.833 0.00 0.00 28.79 2.69
2454 2491 3.596956 AGTGTCTACTCCCTCCTTTCCTA 59.403 47.826 0.00 0.00 28.79 2.94
2455 2492 2.384029 AGTGTCTACTCCCTCCTTTCCT 59.616 50.000 0.00 0.00 28.79 3.36
2456 2493 2.822697 AGTGTCTACTCCCTCCTTTCC 58.177 52.381 0.00 0.00 28.79 3.13
2457 2494 7.657023 TTATTAGTGTCTACTCCCTCCTTTC 57.343 40.000 0.00 0.00 38.36 2.62
2458 2495 7.624077 ACATTATTAGTGTCTACTCCCTCCTTT 59.376 37.037 0.00 0.00 38.36 3.11
2459 2496 7.133483 ACATTATTAGTGTCTACTCCCTCCTT 58.867 38.462 0.00 0.00 38.36 3.36
2460 2497 6.684538 ACATTATTAGTGTCTACTCCCTCCT 58.315 40.000 0.00 0.00 38.36 3.69
2461 2498 6.980416 ACATTATTAGTGTCTACTCCCTCC 57.020 41.667 0.00 0.00 38.36 4.30
2462 2499 7.288158 AGGAACATTATTAGTGTCTACTCCCTC 59.712 40.741 4.87 0.00 38.36 4.30
2463 2500 7.133483 AGGAACATTATTAGTGTCTACTCCCT 58.867 38.462 4.87 0.00 38.36 4.20
2464 2501 7.362802 AGGAACATTATTAGTGTCTACTCCC 57.637 40.000 4.87 0.00 38.36 4.30
2465 2502 9.099454 CAAAGGAACATTATTAGTGTCTACTCC 57.901 37.037 0.00 0.00 38.36 3.85
2466 2503 9.654663 ACAAAGGAACATTATTAGTGTCTACTC 57.345 33.333 0.00 0.00 38.36 2.59
2511 2548 2.306847 GGCAGTGGGAAGAAAAACTCA 58.693 47.619 0.00 0.00 0.00 3.41
2512 2549 1.266989 CGGCAGTGGGAAGAAAAACTC 59.733 52.381 0.00 0.00 0.00 3.01
2513 2550 1.133915 TCGGCAGTGGGAAGAAAAACT 60.134 47.619 0.00 0.00 0.00 2.66
2518 2557 2.347490 GCTCGGCAGTGGGAAGAA 59.653 61.111 0.00 0.00 0.00 2.52
2606 2645 1.202639 AGTGTTGCGTCCAGTGAATCA 60.203 47.619 0.00 0.00 0.00 2.57
2717 2756 4.160439 CAGCACTAGAATTACCTCTCCACA 59.840 45.833 0.00 0.00 0.00 4.17
2855 2900 0.529337 CAGCCATCGTCATTCTCGCT 60.529 55.000 0.00 0.00 0.00 4.93
2906 2951 3.375610 GCAGCGATCTTATCTCTCCGATA 59.624 47.826 0.00 0.00 33.48 2.92
2914 2959 2.437200 GCTCAGCAGCGATCTTATCT 57.563 50.000 0.00 0.00 35.39 1.98
2957 3002 2.042762 CCCCCATGGTCCTCCTCA 59.957 66.667 11.73 0.00 34.23 3.86
3039 3084 2.162681 GCTAATGCAACCCAAGTCAGT 58.837 47.619 0.00 0.00 39.41 3.41
3113 3158 0.322975 TCAGCCAAGAACTCCTCTGC 59.677 55.000 0.00 0.00 33.37 4.26
3115 3160 2.831565 AGATCAGCCAAGAACTCCTCT 58.168 47.619 0.00 0.00 35.13 3.69
3348 3397 6.959639 ACCTGTGGCCAAACTTATATATTG 57.040 37.500 7.24 0.00 0.00 1.90
3425 4484 9.561069 CTGCCAACTACTCTATTGGTTATAATT 57.439 33.333 5.01 0.00 46.07 1.40
3426 4485 7.661847 GCTGCCAACTACTCTATTGGTTATAAT 59.338 37.037 5.01 0.00 46.07 1.28
3609 4801 7.282224 AGTGTTGTCAGCTAAATTACTTCAACA 59.718 33.333 0.00 0.00 36.60 3.33
3656 4848 4.819105 AGACAAATATGGTCCGTGAAGA 57.181 40.909 0.00 0.00 35.89 2.87
3912 5104 2.334946 CCGCCTGTGTGTCATTGGG 61.335 63.158 0.00 0.00 0.00 4.12
3928 5120 2.010145 ACAGATTGTCAATCGGACCG 57.990 50.000 26.23 7.84 46.38 4.79
3935 5127 4.910195 TGCAGAGGTAACAGATTGTCAAT 58.090 39.130 0.00 0.00 41.41 2.57
3960 5152 0.734889 CAAGCCTTCGCATGGTTAGG 59.265 55.000 0.00 0.00 37.52 2.69
3963 5155 0.598065 GTTCAAGCCTTCGCATGGTT 59.402 50.000 0.00 0.00 34.44 3.67
3987 5179 4.583871 AGCCAATATCTATAAGCACTGCC 58.416 43.478 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.