Multiple sequence alignment - TraesCS3D01G390400

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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 TraesCS3D01G390400 chr3D 100.000 2791 0 0 1 2791 505403616 505406406 0.000000e+00 5155.0
1 TraesCS3D01G390400 chr3B 93.628 1491 48 18 785 2248 667173442 667174912 0.000000e+00 2183.0
2 TraesCS3D01G390400 chr3B 93.089 492 18 8 1 477 667172746 667173236 0.000000e+00 706.0
3 TraesCS3D01G390400 chr3B 92.537 469 29 2 2329 2791 667174911 667175379 0.000000e+00 667.0
4 TraesCS3D01G390400 chr3B 92.857 56 4 0 674 729 667173326 667173381 6.410000e-12 82.4
5 TraesCS3D01G390400 chr3B 96.970 33 0 1 662 694 667173281 667173312 1.000000e-03 54.7
6 TraesCS3D01G390400 chr3A 95.887 1094 35 9 681 1769 643545417 643546505 0.000000e+00 1762.0
7 TraesCS3D01G390400 chr3A 90.457 503 22 7 1760 2248 643546842 643547332 8.430000e-180 640.0
8 TraesCS3D01G390400 chr3A 92.308 286 12 4 1 279 643544868 643545150 5.600000e-107 398.0
9 TraesCS3D01G390400 chr3A 96.104 154 5 1 499 652 643545267 643545419 1.660000e-62 250.0
10 TraesCS3D01G390400 chr3A 85.328 259 15 12 2542 2788 643547531 643547778 2.150000e-61 246.0
11 TraesCS3D01G390400 chr3A 97.368 76 1 1 403 477 643545202 643545277 8.110000e-26 128.0
12 TraesCS3D01G390400 chr3A 98.529 68 1 0 324 391 643545147 643545214 1.360000e-23 121.0
13 TraesCS3D01G390400 chr7D 90.426 94 7 2 2239 2331 103820529 103820621 3.780000e-24 122.0
14 TraesCS3D01G390400 chr7A 88.764 89 9 1 2246 2333 40538244 40538156 1.060000e-19 108.0
15 TraesCS3D01G390400 chr4A 88.764 89 9 1 2246 2333 647209304 647209392 1.060000e-19 108.0
16 TraesCS3D01G390400 chr5D 88.636 88 8 2 2246 2331 498655283 498655370 3.800000e-19 106.0
17 TraesCS3D01G390400 chr5D 87.640 89 9 2 2245 2332 122198429 122198516 4.920000e-18 102.0
18 TraesCS3D01G390400 chr2B 88.636 88 9 1 2247 2333 90009490 90009403 3.800000e-19 106.0
19 TraesCS3D01G390400 chr1A 87.500 88 10 1 2247 2333 251695701 251695788 1.770000e-17 100.0
20 TraesCS3D01G390400 chr5A 85.567 97 10 3 2246 2338 476958894 476958990 6.360000e-17 99.0
21 TraesCS3D01G390400 chr5A 86.517 89 11 1 2245 2332 134085972 134086060 2.290000e-16 97.1


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 TraesCS3D01G390400 chr3D 505403616 505406406 2790 False 5155.000000 5155 100.000000 1 2791 1 chr3D.!!$F1 2790
1 TraesCS3D01G390400 chr3B 667172746 667175379 2633 False 738.620000 2183 93.816200 1 2791 5 chr3B.!!$F1 2790
2 TraesCS3D01G390400 chr3A 643544868 643547778 2910 False 506.428571 1762 93.711571 1 2788 7 chr3A.!!$F1 2787

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
699 718 0.985549 GTCTAGCGCAGTTTGTCTCG 59.014 55.0 11.47 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2459 0.315706 GCTCTACCGCTGTACGTACG 60.316 60.0 20.18 15.01 41.42 3.67 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
123 125 5.070580 TGGTGTTAATGTTAAAACCCCCAAG 59.929 40.000 17.93 0.00 46.18 3.61
132 136 4.603535 ACCCCCAAGGCTGTGCAC 62.604 66.667 10.75 10.75 40.58 4.57
135 139 1.074775 CCCCAAGGCTGTGCACTTA 59.925 57.895 19.41 0.00 0.00 2.24
254 263 6.224584 ACTAGCTCTGTACCTGTTTTTCTTC 58.775 40.000 0.00 0.00 0.00 2.87
263 272 3.633986 ACCTGTTTTTCTTCTCTTGCCTG 59.366 43.478 0.00 0.00 0.00 4.85
291 300 8.175925 TGAATTCAATGGTGTGATACTGAAAA 57.824 30.769 5.45 0.00 28.65 2.29
305 314 9.387123 GTGATACTGAAAACTCTTGTGATTTTC 57.613 33.333 0.00 0.00 40.93 2.29
313 322 7.587037 AAACTCTTGTGATTTTCTGAATGGA 57.413 32.000 0.00 0.00 0.00 3.41
319 328 9.130661 TCTTGTGATTTTCTGAATGGAGTTAAA 57.869 29.630 0.00 0.00 0.00 1.52
477 493 5.774690 TCCCTGAAAAGTTATGTCAAGCAAT 59.225 36.000 0.00 0.00 0.00 3.56
478 494 6.267471 TCCCTGAAAAGTTATGTCAAGCAATT 59.733 34.615 0.00 0.00 0.00 2.32
479 495 6.930722 CCCTGAAAAGTTATGTCAAGCAATTT 59.069 34.615 0.00 0.00 0.00 1.82
480 496 7.442062 CCCTGAAAAGTTATGTCAAGCAATTTT 59.558 33.333 0.00 0.00 0.00 1.82
481 497 8.829612 CCTGAAAAGTTATGTCAAGCAATTTTT 58.170 29.630 0.00 0.00 0.00 1.94
505 521 9.875675 TTTTGTTTTGTTTTTGAGAATGTCAAG 57.124 25.926 0.00 0.00 46.09 3.02
506 522 7.059448 TGTTTTGTTTTTGAGAATGTCAAGC 57.941 32.000 0.00 0.00 46.09 4.01
507 523 6.648310 TGTTTTGTTTTTGAGAATGTCAAGCA 59.352 30.769 0.00 0.00 46.09 3.91
508 524 7.172190 TGTTTTGTTTTTGAGAATGTCAAGCAA 59.828 29.630 0.00 0.00 46.09 3.91
509 525 7.664082 TTTGTTTTTGAGAATGTCAAGCAAA 57.336 28.000 11.95 11.95 46.09 3.68
512 528 8.266392 TGTTTTTGAGAATGTCAAGCAAAAAT 57.734 26.923 12.87 0.00 46.09 1.82
519 535 9.248291 TGAGAATGTCAAGCAAAAATTTAGAAC 57.752 29.630 0.00 0.00 29.64 3.01
520 536 8.285776 AGAATGTCAAGCAAAAATTTAGAACG 57.714 30.769 0.00 0.00 0.00 3.95
631 650 6.772360 AGAGTTAGGTTTACTGTAGCTACC 57.228 41.667 21.01 6.44 0.00 3.18
632 651 5.655974 AGAGTTAGGTTTACTGTAGCTACCC 59.344 44.000 21.01 13.18 0.00 3.69
652 671 5.036916 ACCCTAACATCCCTTGATAAGTCA 58.963 41.667 0.00 0.00 0.00 3.41
653 672 5.131142 ACCCTAACATCCCTTGATAAGTCAG 59.869 44.000 0.00 0.00 35.39 3.51
654 673 5.455326 CCCTAACATCCCTTGATAAGTCAGG 60.455 48.000 0.00 0.00 35.39 3.86
655 674 5.366768 CCTAACATCCCTTGATAAGTCAGGA 59.633 44.000 0.00 0.00 34.36 3.86
656 675 5.983333 AACATCCCTTGATAAGTCAGGAT 57.017 39.130 0.00 0.00 39.00 3.24
657 676 5.559148 ACATCCCTTGATAAGTCAGGATC 57.441 43.478 0.00 0.00 37.33 3.36
658 677 5.222870 ACATCCCTTGATAAGTCAGGATCT 58.777 41.667 0.00 0.00 37.33 2.75
659 678 5.306678 ACATCCCTTGATAAGTCAGGATCTC 59.693 44.000 0.00 0.00 37.33 2.75
660 679 3.891977 TCCCTTGATAAGTCAGGATCTCG 59.108 47.826 0.00 0.00 33.56 4.04
661 680 3.639094 CCCTTGATAAGTCAGGATCTCGT 59.361 47.826 0.00 0.00 33.56 4.18
662 681 4.100189 CCCTTGATAAGTCAGGATCTCGTT 59.900 45.833 0.00 0.00 33.56 3.85
663 682 5.285651 CCTTGATAAGTCAGGATCTCGTTC 58.714 45.833 0.00 0.00 33.56 3.95
664 683 4.920640 TGATAAGTCAGGATCTCGTTCC 57.079 45.455 0.00 0.00 35.90 3.62
665 684 4.278310 TGATAAGTCAGGATCTCGTTCCA 58.722 43.478 0.00 0.00 38.32 3.53
666 685 4.895889 TGATAAGTCAGGATCTCGTTCCAT 59.104 41.667 0.00 0.00 38.32 3.41
667 686 5.363868 TGATAAGTCAGGATCTCGTTCCATT 59.636 40.000 0.00 0.00 38.32 3.16
668 687 4.559862 AAGTCAGGATCTCGTTCCATTT 57.440 40.909 0.00 0.00 38.32 2.32
669 688 4.559862 AGTCAGGATCTCGTTCCATTTT 57.440 40.909 0.00 0.00 38.32 1.82
670 689 4.911390 AGTCAGGATCTCGTTCCATTTTT 58.089 39.130 0.00 0.00 38.32 1.94
672 691 6.653989 AGTCAGGATCTCGTTCCATTTTTAT 58.346 36.000 0.00 0.00 38.32 1.40
682 701 7.118680 TCTCGTTCCATTTTTATAGTGGTTGTC 59.881 37.037 0.00 0.00 34.61 3.18
697 716 2.135933 GTTGTCTAGCGCAGTTTGTCT 58.864 47.619 11.47 0.00 0.00 3.41
699 718 0.985549 GTCTAGCGCAGTTTGTCTCG 59.014 55.000 11.47 0.00 0.00 4.04
747 797 4.322080 TGCAGAGGATTTGGTCGTATAG 57.678 45.455 0.00 0.00 0.00 1.31
748 798 3.958147 TGCAGAGGATTTGGTCGTATAGA 59.042 43.478 0.00 0.00 0.00 1.98
753 803 6.263392 CAGAGGATTTGGTCGTATAGAGAGAA 59.737 42.308 0.00 0.00 0.00 2.87
754 804 7.007723 AGAGGATTTGGTCGTATAGAGAGAAT 58.992 38.462 0.00 0.00 0.00 2.40
811 861 4.916983 TTTTGATCTGGTCACACTTTGG 57.083 40.909 0.00 0.00 36.32 3.28
1030 1085 3.774766 AGAGTGCAGTAGAGAGAGAGAGA 59.225 47.826 0.00 0.00 0.00 3.10
1031 1086 4.122776 GAGTGCAGTAGAGAGAGAGAGAG 58.877 52.174 0.00 0.00 0.00 3.20
1032 1087 3.774766 AGTGCAGTAGAGAGAGAGAGAGA 59.225 47.826 0.00 0.00 0.00 3.10
1033 1088 4.122776 GTGCAGTAGAGAGAGAGAGAGAG 58.877 52.174 0.00 0.00 0.00 3.20
1044 1099 4.567385 GAGAGAGGGAGCAGCGCG 62.567 72.222 0.00 0.00 34.07 6.86
1726 1791 5.048507 GTCCCTGTGAATACGGAAATAGTC 58.951 45.833 0.00 0.00 35.05 2.59
1753 1818 2.479566 ACTGCCACACTGTTATCCTG 57.520 50.000 0.00 0.00 0.00 3.86
1790 2201 2.017049 GAACAAAGGCAGTGTGTGTCT 58.983 47.619 0.00 0.00 45.84 3.41
2004 2426 3.270877 ACACAGGTTATCCGAGAAATGC 58.729 45.455 0.00 0.00 39.05 3.56
2014 2436 1.667724 CCGAGAAATGCTTACTGGCAG 59.332 52.381 14.16 14.16 45.75 4.85
2020 2442 5.509498 AGAAATGCTTACTGGCAGGATAAA 58.491 37.500 20.34 6.57 45.75 1.40
2037 2459 4.329256 GGATAAACTTGAACCAGCGTAGTC 59.671 45.833 0.00 0.00 0.00 2.59
2079 2504 5.355350 GCTTTATTTATCTCTGCCACAGTGT 59.645 40.000 0.00 0.00 32.61 3.55
2080 2505 6.457528 GCTTTATTTATCTCTGCCACAGTGTC 60.458 42.308 0.00 0.00 32.61 3.67
2133 2559 5.771666 ACACACAATCAATGAATCTGGAGTT 59.228 36.000 0.00 0.00 0.00 3.01
2143 2569 0.257039 ATCTGGAGTTGGATGTGCCC 59.743 55.000 0.00 0.00 34.97 5.36
2248 2686 5.124776 AGCTCAGCTCGGACAGATATTATAC 59.875 44.000 0.00 0.00 30.62 1.47
2249 2687 5.124776 GCTCAGCTCGGACAGATATTATACT 59.875 44.000 0.00 0.00 0.00 2.12
2250 2688 6.676943 GCTCAGCTCGGACAGATATTATACTC 60.677 46.154 0.00 0.00 0.00 2.59
2251 2689 5.648526 TCAGCTCGGACAGATATTATACTCC 59.351 44.000 0.00 0.00 0.00 3.85
2252 2690 4.951094 AGCTCGGACAGATATTATACTCCC 59.049 45.833 0.00 0.00 0.00 4.30
2253 2691 4.951094 GCTCGGACAGATATTATACTCCCT 59.049 45.833 0.00 0.00 0.00 4.20
2254 2692 5.066764 GCTCGGACAGATATTATACTCCCTC 59.933 48.000 0.00 0.00 0.00 4.30
2255 2693 5.183969 TCGGACAGATATTATACTCCCTCG 58.816 45.833 0.00 0.00 0.00 4.63
2256 2694 4.335874 CGGACAGATATTATACTCCCTCGG 59.664 50.000 0.00 0.00 0.00 4.63
2257 2695 5.262804 GGACAGATATTATACTCCCTCGGT 58.737 45.833 0.00 0.00 0.00 4.69
2258 2696 5.357596 GGACAGATATTATACTCCCTCGGTC 59.642 48.000 0.00 0.00 0.00 4.79
2259 2697 5.262804 ACAGATATTATACTCCCTCGGTCC 58.737 45.833 0.00 0.00 0.00 4.46
2260 2698 5.222275 ACAGATATTATACTCCCTCGGTCCA 60.222 44.000 0.00 0.00 0.00 4.02
2261 2699 5.894393 CAGATATTATACTCCCTCGGTCCAT 59.106 44.000 0.00 0.00 0.00 3.41
2262 2700 7.061054 CAGATATTATACTCCCTCGGTCCATA 58.939 42.308 0.00 0.00 0.00 2.74
2263 2701 7.560262 CAGATATTATACTCCCTCGGTCCATAA 59.440 40.741 0.00 0.00 0.00 1.90
2264 2702 8.290277 AGATATTATACTCCCTCGGTCCATAAT 58.710 37.037 0.00 0.00 0.00 1.28
2265 2703 9.584008 GATATTATACTCCCTCGGTCCATAATA 57.416 37.037 0.00 0.00 0.00 0.98
2268 2706 9.947189 ATTATACTCCCTCGGTCCATAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
2269 2707 9.947189 TTATACTCCCTCGGTCCATAATATAAT 57.053 33.333 0.00 0.00 0.00 1.28
2272 2710 8.251383 ACTCCCTCGGTCCATAATATAATATG 57.749 38.462 1.35 1.35 33.85 1.78
2273 2711 7.844779 ACTCCCTCGGTCCATAATATAATATGT 59.155 37.037 6.98 0.00 32.48 2.29
2274 2712 8.618240 TCCCTCGGTCCATAATATAATATGTT 57.382 34.615 6.98 0.00 32.48 2.71
2275 2713 9.053472 TCCCTCGGTCCATAATATAATATGTTT 57.947 33.333 6.98 0.00 32.48 2.83
2276 2714 9.681062 CCCTCGGTCCATAATATAATATGTTTT 57.319 33.333 6.98 0.00 32.48 2.43
2305 2743 9.900264 CAAGCTAAAACAGTTTGTAAAAACATC 57.100 29.630 11.11 0.00 39.80 3.06
2306 2744 9.869757 AAGCTAAAACAGTTTGTAAAAACATCT 57.130 25.926 11.11 0.00 35.20 2.90
2307 2745 9.869757 AGCTAAAACAGTTTGTAAAAACATCTT 57.130 25.926 11.11 1.85 35.20 2.40
2323 2761 8.848474 AAAACATCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
2324 2762 6.546428 ACATCTTATATTATGGGACGGAGG 57.454 41.667 0.00 0.00 0.00 4.30
2325 2763 5.425539 ACATCTTATATTATGGGACGGAGGG 59.574 44.000 0.00 0.00 0.00 4.30
2326 2764 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2327 2765 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2328 2766 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2329 2767 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2334 2772 1.557832 TGGGACGGAGGGAGTATTTTG 59.442 52.381 0.00 0.00 0.00 2.44
2404 2843 2.095853 ACACACGTTCAGCTGTTCAAAG 59.904 45.455 14.67 5.83 0.00 2.77
2415 2854 6.656902 TCAGCTGTTCAAAGGATATGAAGAT 58.343 36.000 14.67 0.00 37.46 2.40
2471 2918 7.316544 AGATGAATACCGTTTTACATGGTTC 57.683 36.000 0.00 0.00 42.98 3.62
2534 2998 3.265791 CTGGCTCTTGGTCTTGTATCAC 58.734 50.000 0.00 0.00 0.00 3.06
2540 3004 6.283694 GCTCTTGGTCTTGTATCACATCATA 58.716 40.000 0.00 0.00 0.00 2.15
2541 3005 6.201806 GCTCTTGGTCTTGTATCACATCATAC 59.798 42.308 0.00 0.00 0.00 2.39
2543 3007 4.944048 TGGTCTTGTATCACATCATACGG 58.056 43.478 0.00 0.00 32.61 4.02
2550 3014 1.153188 CACATCATACGGGCTGCCA 60.153 57.895 22.05 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 5.481105 ACACCAATAAAAACGAGTATCCGA 58.519 37.500 0.00 0.00 0.00 4.55
123 125 5.873179 TTTAACAGTATAAGTGCACAGCC 57.127 39.130 21.04 1.69 0.00 4.85
156 160 4.148128 AGATTTATGGAGCCAGACACAG 57.852 45.455 0.00 0.00 0.00 3.66
254 263 3.928727 TTGAATTCAAGCAGGCAAGAG 57.071 42.857 16.91 0.00 0.00 2.85
263 272 6.032094 CAGTATCACACCATTGAATTCAAGC 58.968 40.000 24.17 6.16 39.47 4.01
291 300 6.302269 ACTCCATTCAGAAAATCACAAGAGT 58.698 36.000 0.00 0.00 0.00 3.24
305 314 7.710907 TCGATACCAGATTTTAACTCCATTCAG 59.289 37.037 0.00 0.00 0.00 3.02
319 328 9.326413 CTAACAGGTAAATTTCGATACCAGATT 57.674 33.333 13.92 8.06 35.15 2.40
395 404 2.318578 CAAACGTGCAACATCATGTCC 58.681 47.619 0.00 0.00 35.32 4.02
396 405 2.318578 CCAAACGTGCAACATCATGTC 58.681 47.619 0.00 0.00 35.32 3.06
397 406 1.602668 GCCAAACGTGCAACATCATGT 60.603 47.619 0.00 0.00 37.78 3.21
398 407 1.062258 GCCAAACGTGCAACATCATG 58.938 50.000 0.00 0.00 35.74 3.07
400 409 0.672889 ATGCCAAACGTGCAACATCA 59.327 45.000 2.95 0.00 42.92 3.07
401 410 1.062258 CATGCCAAACGTGCAACATC 58.938 50.000 2.95 0.00 42.92 3.06
479 495 9.875675 CTTGACATTCTCAAAAACAAAACAAAA 57.124 25.926 0.00 0.00 38.47 2.44
480 496 8.014517 GCTTGACATTCTCAAAAACAAAACAAA 58.985 29.630 0.00 0.00 38.47 2.83
481 497 7.172190 TGCTTGACATTCTCAAAAACAAAACAA 59.828 29.630 0.00 0.00 38.47 2.83
482 498 6.648310 TGCTTGACATTCTCAAAAACAAAACA 59.352 30.769 0.00 0.00 38.47 2.83
483 499 7.059448 TGCTTGACATTCTCAAAAACAAAAC 57.941 32.000 0.00 0.00 38.47 2.43
484 500 7.664082 TTGCTTGACATTCTCAAAAACAAAA 57.336 28.000 0.00 0.00 38.47 2.44
485 501 7.664082 TTTGCTTGACATTCTCAAAAACAAA 57.336 28.000 0.00 0.00 38.47 2.83
486 502 7.664082 TTTTGCTTGACATTCTCAAAAACAA 57.336 28.000 0.00 0.00 38.47 2.83
487 503 7.664082 TTTTTGCTTGACATTCTCAAAAACA 57.336 28.000 6.97 0.00 39.90 2.83
488 504 9.558648 AAATTTTTGCTTGACATTCTCAAAAAC 57.441 25.926 11.68 0.00 44.25 2.43
491 507 9.814899 TCTAAATTTTTGCTTGACATTCTCAAA 57.185 25.926 0.00 0.00 38.47 2.69
492 508 9.814899 TTCTAAATTTTTGCTTGACATTCTCAA 57.185 25.926 0.00 0.00 36.46 3.02
493 509 9.248291 GTTCTAAATTTTTGCTTGACATTCTCA 57.752 29.630 0.00 0.00 0.00 3.27
494 510 8.420189 CGTTCTAAATTTTTGCTTGACATTCTC 58.580 33.333 0.00 0.00 0.00 2.87
495 511 8.134895 TCGTTCTAAATTTTTGCTTGACATTCT 58.865 29.630 0.00 0.00 0.00 2.40
496 512 8.280909 TCGTTCTAAATTTTTGCTTGACATTC 57.719 30.769 0.00 0.00 0.00 2.67
497 513 8.134895 TCTCGTTCTAAATTTTTGCTTGACATT 58.865 29.630 0.00 0.00 0.00 2.71
498 514 7.648142 TCTCGTTCTAAATTTTTGCTTGACAT 58.352 30.769 0.00 0.00 0.00 3.06
499 515 7.022055 TCTCGTTCTAAATTTTTGCTTGACA 57.978 32.000 0.00 0.00 0.00 3.58
500 516 7.908193 TTCTCGTTCTAAATTTTTGCTTGAC 57.092 32.000 0.00 0.00 0.00 3.18
501 517 8.188139 AGTTTCTCGTTCTAAATTTTTGCTTGA 58.812 29.630 0.00 0.00 0.00 3.02
502 518 8.340230 AGTTTCTCGTTCTAAATTTTTGCTTG 57.660 30.769 0.00 0.00 0.00 4.01
503 519 8.188139 TGAGTTTCTCGTTCTAAATTTTTGCTT 58.812 29.630 0.00 0.00 32.35 3.91
504 520 7.644157 GTGAGTTTCTCGTTCTAAATTTTTGCT 59.356 33.333 0.00 0.00 32.35 3.91
505 521 7.356476 CGTGAGTTTCTCGTTCTAAATTTTTGC 60.356 37.037 0.00 0.00 32.35 3.68
506 522 7.111593 CCGTGAGTTTCTCGTTCTAAATTTTTG 59.888 37.037 0.00 0.00 32.17 2.44
507 523 7.130269 CCGTGAGTTTCTCGTTCTAAATTTTT 58.870 34.615 0.00 0.00 32.17 1.94
508 524 6.293244 CCCGTGAGTTTCTCGTTCTAAATTTT 60.293 38.462 0.00 0.00 32.17 1.82
509 525 5.178809 CCCGTGAGTTTCTCGTTCTAAATTT 59.821 40.000 0.00 0.00 32.17 1.82
512 528 3.318839 TCCCGTGAGTTTCTCGTTCTAAA 59.681 43.478 0.79 0.00 32.17 1.85
519 535 2.363788 TCATTCCCGTGAGTTTCTCG 57.636 50.000 0.00 0.00 32.35 4.04
520 536 4.065789 ACTTTCATTCCCGTGAGTTTCTC 58.934 43.478 0.00 0.00 0.00 2.87
631 650 5.366768 TCCTGACTTATCAAGGGATGTTAGG 59.633 44.000 0.00 0.00 35.87 2.69
632 651 6.485830 TCCTGACTTATCAAGGGATGTTAG 57.514 41.667 0.00 0.00 33.30 2.34
652 671 6.992715 CCACTATAAAAATGGAACGAGATCCT 59.007 38.462 0.00 0.00 40.35 3.24
653 672 6.766467 ACCACTATAAAAATGGAACGAGATCC 59.234 38.462 0.00 0.00 40.10 3.36
654 673 7.787725 ACCACTATAAAAATGGAACGAGATC 57.212 36.000 0.00 0.00 36.94 2.75
655 674 7.610305 ACAACCACTATAAAAATGGAACGAGAT 59.390 33.333 0.00 0.00 36.94 2.75
656 675 6.938030 ACAACCACTATAAAAATGGAACGAGA 59.062 34.615 0.00 0.00 36.94 4.04
657 676 7.119262 AGACAACCACTATAAAAATGGAACGAG 59.881 37.037 0.00 0.00 36.94 4.18
658 677 6.938030 AGACAACCACTATAAAAATGGAACGA 59.062 34.615 0.00 0.00 36.94 3.85
659 678 7.141100 AGACAACCACTATAAAAATGGAACG 57.859 36.000 0.00 0.00 36.94 3.95
660 679 8.182227 GCTAGACAACCACTATAAAAATGGAAC 58.818 37.037 0.00 0.00 36.94 3.62
661 680 7.065324 CGCTAGACAACCACTATAAAAATGGAA 59.935 37.037 0.00 0.00 36.94 3.53
662 681 6.537301 CGCTAGACAACCACTATAAAAATGGA 59.463 38.462 0.00 0.00 36.94 3.41
663 682 6.715464 CGCTAGACAACCACTATAAAAATGG 58.285 40.000 0.00 0.00 39.57 3.16
664 683 6.183360 TGCGCTAGACAACCACTATAAAAATG 60.183 38.462 9.73 0.00 0.00 2.32
665 684 5.878116 TGCGCTAGACAACCACTATAAAAAT 59.122 36.000 9.73 0.00 0.00 1.82
666 685 5.239351 TGCGCTAGACAACCACTATAAAAA 58.761 37.500 9.73 0.00 0.00 1.94
667 686 4.823157 TGCGCTAGACAACCACTATAAAA 58.177 39.130 9.73 0.00 0.00 1.52
668 687 4.081862 ACTGCGCTAGACAACCACTATAAA 60.082 41.667 9.73 0.00 0.00 1.40
669 688 3.446161 ACTGCGCTAGACAACCACTATAA 59.554 43.478 9.73 0.00 0.00 0.98
670 689 3.021695 ACTGCGCTAGACAACCACTATA 58.978 45.455 9.73 0.00 0.00 1.31
672 691 1.254026 ACTGCGCTAGACAACCACTA 58.746 50.000 9.73 0.00 0.00 2.74
682 701 0.388649 ACCGAGACAAACTGCGCTAG 60.389 55.000 9.73 7.16 0.00 3.42
699 718 2.202892 GATCTTGGCCGTCCGACC 60.203 66.667 0.00 0.00 34.14 4.79
761 811 5.654650 AGGAAATACGTGCCATTTTATCCAA 59.345 36.000 0.00 0.00 0.00 3.53
764 814 5.507315 CCCAGGAAATACGTGCCATTTTATC 60.507 44.000 0.00 0.00 33.64 1.75
822 872 6.857964 CAGTCAAAACATGTTGTCATCTTACC 59.142 38.462 12.82 0.00 31.15 2.85
1359 1414 2.394912 CTCCTCGTCGTCGTCGTC 59.605 66.667 11.41 0.00 38.33 4.20
1360 1415 3.117171 CCTCCTCGTCGTCGTCGT 61.117 66.667 11.41 0.00 38.33 4.34
1361 1416 2.800581 CTCCTCCTCGTCGTCGTCG 61.801 68.421 5.50 5.50 38.33 5.12
1646 1711 9.525409 AGACAAACAATCATCAAGAAAGAAAAG 57.475 29.630 0.00 0.00 0.00 2.27
1726 1791 1.003580 ACAGTGTGGCAGTAATCTGGG 59.996 52.381 0.00 0.00 41.57 4.45
1790 2201 5.163405 GCTCCTATTACTGACAAGATCACCA 60.163 44.000 0.00 0.00 32.37 4.17
2004 2426 5.123979 GGTTCAAGTTTATCCTGCCAGTAAG 59.876 44.000 0.00 0.00 0.00 2.34
2014 2436 4.251268 ACTACGCTGGTTCAAGTTTATCC 58.749 43.478 0.00 0.00 0.00 2.59
2020 2442 0.672342 ACGACTACGCTGGTTCAAGT 59.328 50.000 0.00 0.00 43.96 3.16
2037 2459 0.315706 GCTCTACCGCTGTACGTACG 60.316 60.000 20.18 15.01 41.42 3.67
2048 2473 5.635700 GGCAGAGATAAATAAAGCTCTACCG 59.364 44.000 0.00 0.00 36.06 4.02
2143 2569 2.901840 ATAACGCATGCAGGCCCG 60.902 61.111 18.98 7.27 0.00 6.13
2248 2686 8.251383 ACATATTATATTATGGACCGAGGGAG 57.749 38.462 15.60 0.00 34.50 4.30
2249 2687 8.618240 AACATATTATATTATGGACCGAGGGA 57.382 34.615 15.60 0.00 34.50 4.20
2250 2688 9.681062 AAAACATATTATATTATGGACCGAGGG 57.319 33.333 15.60 0.00 34.50 4.30
2277 2715 9.909644 TGTTTTTACAAACTGTTTTAGCTTGTA 57.090 25.926 2.41 0.00 42.34 2.41
2278 2716 8.819643 TGTTTTTACAAACTGTTTTAGCTTGT 57.180 26.923 2.41 0.90 45.17 3.16
2279 2717 9.900264 GATGTTTTTACAAACTGTTTTAGCTTG 57.100 29.630 2.41 0.00 42.61 4.01
2280 2718 9.869757 AGATGTTTTTACAAACTGTTTTAGCTT 57.130 25.926 2.41 0.00 42.61 3.74
2281 2719 9.869757 AAGATGTTTTTACAAACTGTTTTAGCT 57.130 25.926 2.41 0.00 42.61 3.32
2297 2735 9.284968 CTCCGTCCCATAATATAAGATGTTTTT 57.715 33.333 0.00 0.00 0.00 1.94
2298 2736 7.883311 CCTCCGTCCCATAATATAAGATGTTTT 59.117 37.037 0.00 0.00 0.00 2.43
2299 2737 7.394816 CCTCCGTCCCATAATATAAGATGTTT 58.605 38.462 0.00 0.00 0.00 2.83
2300 2738 6.070194 CCCTCCGTCCCATAATATAAGATGTT 60.070 42.308 0.00 0.00 0.00 2.71
2301 2739 5.425539 CCCTCCGTCCCATAATATAAGATGT 59.574 44.000 0.00 0.00 0.00 3.06
2302 2740 5.661312 TCCCTCCGTCCCATAATATAAGATG 59.339 44.000 0.00 0.00 0.00 2.90
2303 2741 5.850278 TCCCTCCGTCCCATAATATAAGAT 58.150 41.667 0.00 0.00 0.00 2.40
2304 2742 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2305 2743 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2306 2744 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2307 2745 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2308 2746 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2309 2747 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2310 2748 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2311 2749 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2312 2750 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
2313 2751 2.172717 CAAAATACTCCCTCCGTCCCAT 59.827 50.000 0.00 0.00 0.00 4.00
2314 2752 1.557832 CAAAATACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
2315 2753 1.746171 GCAAAATACTCCCTCCGTCCC 60.746 57.143 0.00 0.00 0.00 4.46
2316 2754 1.065709 TGCAAAATACTCCCTCCGTCC 60.066 52.381 0.00 0.00 0.00 4.79
2317 2755 2.396590 TGCAAAATACTCCCTCCGTC 57.603 50.000 0.00 0.00 0.00 4.79
2318 2756 2.039879 AGTTGCAAAATACTCCCTCCGT 59.960 45.455 0.00 0.00 0.00 4.69
2319 2757 2.420022 CAGTTGCAAAATACTCCCTCCG 59.580 50.000 0.00 0.00 0.00 4.63
2320 2758 3.686016 TCAGTTGCAAAATACTCCCTCC 58.314 45.455 0.00 0.00 0.00 4.30
2321 2759 3.127721 GCTCAGTTGCAAAATACTCCCTC 59.872 47.826 0.00 0.00 0.00 4.30
2322 2760 3.084786 GCTCAGTTGCAAAATACTCCCT 58.915 45.455 0.00 0.00 0.00 4.20
2323 2761 2.159517 CGCTCAGTTGCAAAATACTCCC 60.160 50.000 0.00 0.00 0.00 4.30
2324 2762 2.742053 TCGCTCAGTTGCAAAATACTCC 59.258 45.455 0.00 0.00 0.00 3.85
2325 2763 3.679980 TCTCGCTCAGTTGCAAAATACTC 59.320 43.478 0.00 0.00 0.00 2.59
2326 2764 3.433615 GTCTCGCTCAGTTGCAAAATACT 59.566 43.478 0.00 0.00 0.00 2.12
2327 2765 3.186409 TGTCTCGCTCAGTTGCAAAATAC 59.814 43.478 0.00 0.00 0.00 1.89
2328 2766 3.398406 TGTCTCGCTCAGTTGCAAAATA 58.602 40.909 0.00 0.00 0.00 1.40
2329 2767 2.221169 TGTCTCGCTCAGTTGCAAAAT 58.779 42.857 0.00 0.00 0.00 1.82
2334 2772 0.441533 CACATGTCTCGCTCAGTTGC 59.558 55.000 0.00 0.00 0.00 4.17
2404 2843 8.087982 TCACGATTTTGCTTATCTTCATATCC 57.912 34.615 0.00 0.00 0.00 2.59
2415 2854 4.094146 TCGATTGCATCACGATTTTGCTTA 59.906 37.500 6.35 0.00 37.28 3.09
2437 2876 6.839820 AACGGTATTCATCTTCGGTAATTC 57.160 37.500 0.00 0.00 0.00 2.17
2445 2892 7.316544 ACCATGTAAAACGGTATTCATCTTC 57.683 36.000 0.00 0.00 0.00 2.87
2534 2998 1.146930 AGTGGCAGCCCGTATGATG 59.853 57.895 9.64 0.00 0.00 3.07
2710 3180 2.700773 GGACGCCTTTGGGATGCAC 61.701 63.158 0.00 0.00 33.58 4.57


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

AutoCloner maintained by Alex Coulton.