Multiple sequence alignment - TraesCS3D01G322800

Loading Multiple Alignment...

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 TraesCS3D01G322800 chr3D 100.000 3210 0 0 1 3210 435664971 435661762 0.000000e+00 5928
1 TraesCS3D01G322800 chr3D 98.529 544 7 1 1 543 435677726 435677183 0.000000e+00 959
2 TraesCS3D01G322800 chr3D 97.806 547 11 1 1 546 478103191 478102645 0.000000e+00 942
3 TraesCS3D01G322800 chr3D 94.382 89 5 0 2440 2528 336539177 336539265 1.550000e-28 137
4 TraesCS3D01G322800 chr3B 94.585 1902 54 23 551 2440 571759487 571757623 0.000000e+00 2896
5 TraesCS3D01G322800 chr3B 86.824 721 46 24 2525 3210 571757617 571756911 0.000000e+00 760
6 TraesCS3D01G322800 chr3B 93.478 92 6 0 2439 2530 678709875 678709784 1.550000e-28 137
7 TraesCS3D01G322800 chr3A 94.901 1412 28 12 873 2260 574459723 574458332 0.000000e+00 2169
8 TraesCS3D01G322800 chr3A 87.368 380 23 10 2846 3210 574457675 574457306 2.300000e-111 412
9 TraesCS3D01G322800 chr3A 87.006 354 17 13 2525 2849 574458090 574457737 3.910000e-99 372
10 TraesCS3D01G322800 chr3A 94.839 155 4 2 2287 2437 574458249 574458095 4.140000e-59 239
11 TraesCS3D01G322800 chr3A 95.876 97 1 3 719 812 574459831 574459735 1.540000e-33 154
12 TraesCS3D01G322800 chr7D 98.529 544 7 1 1 543 196267465 196268008 0.000000e+00 959
13 TraesCS3D01G322800 chr7D 98.529 544 7 1 1 543 196279997 196280540 0.000000e+00 959
14 TraesCS3D01G322800 chr7D 98.346 544 8 1 1 543 196254762 196254219 0.000000e+00 953
15 TraesCS3D01G322800 chr7D 77.717 184 29 11 1321 1495 410906265 410906085 5.670000e-18 102
16 TraesCS3D01G322800 chr5D 97.978 544 9 2 1 543 85048638 85048096 0.000000e+00 942
17 TraesCS3D01G322800 chr5D 97.978 544 10 1 1 543 377781800 377781257 0.000000e+00 942
18 TraesCS3D01G322800 chr5D 96.471 85 3 0 2443 2527 519201525 519201441 1.200000e-29 141
19 TraesCS3D01G322800 chr5D 95.349 86 4 0 2443 2528 545281894 545281809 1.550000e-28 137
20 TraesCS3D01G322800 chr4D 97.978 544 10 1 1 543 79416137 79416680 0.000000e+00 942
21 TraesCS3D01G322800 chr4D 97.978 544 10 1 1 543 79428878 79429421 0.000000e+00 942
22 TraesCS3D01G322800 chr5A 94.624 93 4 1 2436 2527 41431254 41431162 3.340000e-30 143
23 TraesCS3D01G322800 chr6D 94.318 88 5 0 2440 2527 95294992 95294905 5.590000e-28 135
24 TraesCS3D01G322800 chr4B 94.318 88 5 0 2440 2527 507357685 507357772 5.590000e-28 135
25 TraesCS3D01G322800 chr2D 91.667 96 6 2 2440 2533 278358782 278358687 7.230000e-27 132
26 TraesCS3D01G322800 chr2D 92.222 90 7 0 2442 2531 201441654 201441565 9.350000e-26 128
27 TraesCS3D01G322800 chr7B 76.812 207 32 13 1300 1495 424645227 424645428 5.670000e-18 102


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 TraesCS3D01G322800 chr3D 435661762 435664971 3209 True 5928.0 5928 100.0000 1 3210 1 chr3D.!!$R1 3209
1 TraesCS3D01G322800 chr3D 435677183 435677726 543 True 959.0 959 98.5290 1 543 1 chr3D.!!$R2 542
2 TraesCS3D01G322800 chr3D 478102645 478103191 546 True 942.0 942 97.8060 1 546 1 chr3D.!!$R3 545
3 TraesCS3D01G322800 chr3B 571756911 571759487 2576 True 1828.0 2896 90.7045 551 3210 2 chr3B.!!$R2 2659
4 TraesCS3D01G322800 chr3A 574457306 574459831 2525 True 669.2 2169 91.9980 719 3210 5 chr3A.!!$R1 2491
5 TraesCS3D01G322800 chr7D 196267465 196268008 543 False 959.0 959 98.5290 1 543 1 chr7D.!!$F1 542
6 TraesCS3D01G322800 chr7D 196279997 196280540 543 False 959.0 959 98.5290 1 543 1 chr7D.!!$F2 542
7 TraesCS3D01G322800 chr7D 196254219 196254762 543 True 953.0 953 98.3460 1 543 1 chr7D.!!$R1 542
8 TraesCS3D01G322800 chr5D 85048096 85048638 542 True 942.0 942 97.9780 1 543 1 chr5D.!!$R1 542
9 TraesCS3D01G322800 chr5D 377781257 377781800 543 True 942.0 942 97.9780 1 543 1 chr5D.!!$R2 542
10 TraesCS3D01G322800 chr4D 79416137 79416680 543 False 942.0 942 97.9780 1 543 1 chr4D.!!$F1 542
11 TraesCS3D01G322800 chr4D 79428878 79429421 543 False 942.0 942 97.9780 1 543 1 chr4D.!!$F2 542

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
546 548 0.035820 GCCATTTACTCCGACACCCA 60.036 55.000 0.0 0.0 0.0 4.51 F
549 551 1.278127 CATTTACTCCGACACCCACCT 59.722 52.381 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 2016 0.388907 GCACGTACTCGCCAAGGTAA 60.389 55.0 0.0 0.0 41.18 2.85 R
2440 2544 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.0 0.0 0.0 0.00 2.90 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
32 33 1.272536 TGCTTCGAGGAAGGGAGTAGT 60.273 52.381 0.00 0.00 39.76 2.73
437 438 0.905809 TTTAGTGGTAGCCGGCCAGA 60.906 55.000 26.15 5.89 36.57 3.86
543 545 0.719465 CGTGCCATTTACTCCGACAC 59.281 55.000 0.00 0.00 0.00 3.67
546 548 0.035820 GCCATTTACTCCGACACCCA 60.036 55.000 0.00 0.00 0.00 4.51
547 549 1.734163 CCATTTACTCCGACACCCAC 58.266 55.000 0.00 0.00 0.00 4.61
548 550 1.677820 CCATTTACTCCGACACCCACC 60.678 57.143 0.00 0.00 0.00 4.61
549 551 1.278127 CATTTACTCCGACACCCACCT 59.722 52.381 0.00 0.00 0.00 4.00
599 601 7.173032 GGACCTTAGGGAATCTTTTTGAGTAA 58.827 38.462 2.32 0.00 36.25 2.24
648 651 6.457159 TTTTCAGGTAGGGGTCATAGAAAA 57.543 37.500 0.00 0.00 33.05 2.29
652 655 3.071167 AGGTAGGGGTCATAGAAAATCGC 59.929 47.826 0.00 0.00 0.00 4.58
709 712 4.394078 CGTCGAAGTCACCCGCGA 62.394 66.667 8.23 0.00 0.00 5.87
873 880 3.331630 CCACGCGCGTACACAACA 61.332 61.111 37.24 0.00 0.00 3.33
875 882 3.684315 ACGCGCGTACACAACACG 61.684 61.111 37.08 0.26 42.24 4.49
942 953 1.774856 CACCTATCCCTTCCCCGATTT 59.225 52.381 0.00 0.00 0.00 2.17
945 956 2.644798 CCTATCCCTTCCCCGATTTGAT 59.355 50.000 0.00 0.00 0.00 2.57
946 957 3.074538 CCTATCCCTTCCCCGATTTGATT 59.925 47.826 0.00 0.00 0.00 2.57
947 958 2.435372 TCCCTTCCCCGATTTGATTG 57.565 50.000 0.00 0.00 0.00 2.67
948 959 1.919654 TCCCTTCCCCGATTTGATTGA 59.080 47.619 0.00 0.00 0.00 2.57
949 960 2.092429 TCCCTTCCCCGATTTGATTGAG 60.092 50.000 0.00 0.00 0.00 3.02
950 961 2.357154 CCCTTCCCCGATTTGATTGAGT 60.357 50.000 0.00 0.00 0.00 3.41
951 962 3.356290 CCTTCCCCGATTTGATTGAGTT 58.644 45.455 0.00 0.00 0.00 3.01
2101 2134 1.202855 AGCTGTGCTGTTGGATCTTGT 60.203 47.619 0.00 0.00 37.57 3.16
2189 2222 7.484959 GCTTGCCTGTTGTAATCTGTAATTAAC 59.515 37.037 0.00 0.00 0.00 2.01
2437 2541 4.033587 TGTCGTGACACTTAGAAAAGCAAC 59.966 41.667 3.68 0.00 36.21 4.17
2440 2544 4.024048 CGTGACACTTAGAAAAGCAACCAT 60.024 41.667 3.68 0.00 36.05 3.55
2441 2545 5.215160 GTGACACTTAGAAAAGCAACCATG 58.785 41.667 0.00 0.00 36.05 3.66
2442 2546 4.887071 TGACACTTAGAAAAGCAACCATGT 59.113 37.500 0.00 0.00 36.05 3.21
2443 2547 6.017440 GTGACACTTAGAAAAGCAACCATGTA 60.017 38.462 0.00 0.00 36.05 2.29
2444 2548 6.017440 TGACACTTAGAAAAGCAACCATGTAC 60.017 38.462 0.00 0.00 36.05 2.90
2445 2549 6.062095 ACACTTAGAAAAGCAACCATGTACT 58.938 36.000 0.00 0.00 36.05 2.73
2446 2550 6.204882 ACACTTAGAAAAGCAACCATGTACTC 59.795 38.462 0.00 0.00 36.05 2.59
2447 2551 5.705905 ACTTAGAAAAGCAACCATGTACTCC 59.294 40.000 0.00 0.00 36.05 3.85
2448 2552 3.421844 AGAAAAGCAACCATGTACTCCC 58.578 45.455 0.00 0.00 0.00 4.30
2449 2553 3.074538 AGAAAAGCAACCATGTACTCCCT 59.925 43.478 0.00 0.00 0.00 4.20
2450 2554 2.789409 AAGCAACCATGTACTCCCTC 57.211 50.000 0.00 0.00 0.00 4.30
2451 2555 0.912486 AGCAACCATGTACTCCCTCC 59.088 55.000 0.00 0.00 0.00 4.30
2452 2556 0.462047 GCAACCATGTACTCCCTCCG 60.462 60.000 0.00 0.00 0.00 4.63
2453 2557 0.902531 CAACCATGTACTCCCTCCGT 59.097 55.000 0.00 0.00 0.00 4.69
2454 2558 1.134788 CAACCATGTACTCCCTCCGTC 60.135 57.143 0.00 0.00 0.00 4.79
2455 2559 0.686769 ACCATGTACTCCCTCCGTCC 60.687 60.000 0.00 0.00 0.00 4.79
2456 2560 1.400530 CCATGTACTCCCTCCGTCCC 61.401 65.000 0.00 0.00 0.00 4.46
2457 2561 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2458 2562 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
2459 2563 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
2460 2564 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
2461 2565 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
2462 2566 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
2463 2567 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2464 2568 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2465 2569 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2466 2570 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2467 2571 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2468 2572 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2469 2573 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2470 2574 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2471 2575 5.184479 CCTCCGTCCCATAATATAAGAACGA 59.816 44.000 0.00 0.00 0.00 3.85
2472 2576 6.127423 CCTCCGTCCCATAATATAAGAACGAT 60.127 42.308 0.00 0.00 0.00 3.73
2473 2577 7.235935 TCCGTCCCATAATATAAGAACGATT 57.764 36.000 0.00 0.00 0.00 3.34
2474 2578 7.673180 TCCGTCCCATAATATAAGAACGATTT 58.327 34.615 0.00 0.00 0.00 2.17
2475 2579 8.152246 TCCGTCCCATAATATAAGAACGATTTT 58.848 33.333 0.00 0.00 0.00 1.82
2476 2580 8.227791 CCGTCCCATAATATAAGAACGATTTTG 58.772 37.037 0.00 0.00 0.00 2.44
2477 2581 8.227791 CGTCCCATAATATAAGAACGATTTTGG 58.772 37.037 0.00 0.00 33.76 3.28
2478 2582 8.021396 GTCCCATAATATAAGAACGATTTTGGC 58.979 37.037 0.00 0.00 33.06 4.52
2479 2583 7.721842 TCCCATAATATAAGAACGATTTTGGCA 59.278 33.333 0.00 0.00 33.06 4.92
2480 2584 7.807907 CCCATAATATAAGAACGATTTTGGCAC 59.192 37.037 0.00 0.00 33.06 5.01
2481 2585 8.567948 CCATAATATAAGAACGATTTTGGCACT 58.432 33.333 0.00 0.00 29.03 4.40
2484 2588 8.500753 AATATAAGAACGATTTTGGCACTACA 57.499 30.769 0.00 0.00 0.00 2.74
2485 2589 4.483476 AAGAACGATTTTGGCACTACAC 57.517 40.909 0.00 0.00 0.00 2.90
2486 2590 3.740115 AGAACGATTTTGGCACTACACT 58.260 40.909 0.00 0.00 0.00 3.55
2487 2591 4.890088 AGAACGATTTTGGCACTACACTA 58.110 39.130 0.00 0.00 0.00 2.74
2488 2592 4.929808 AGAACGATTTTGGCACTACACTAG 59.070 41.667 0.00 0.00 0.00 2.57
2489 2593 4.267349 ACGATTTTGGCACTACACTAGT 57.733 40.909 0.00 0.00 40.28 2.57
2517 2621 7.513371 AAAAACGTTCTTATATTGTGGGACA 57.487 32.000 0.00 0.00 0.00 4.02
2518 2622 6.737254 AAACGTTCTTATATTGTGGGACAG 57.263 37.500 0.00 0.00 41.80 3.51
2519 2623 5.670792 ACGTTCTTATATTGTGGGACAGA 57.329 39.130 0.00 0.00 41.80 3.41
2520 2624 5.661458 ACGTTCTTATATTGTGGGACAGAG 58.339 41.667 0.00 0.00 41.80 3.35
2521 2625 5.050490 CGTTCTTATATTGTGGGACAGAGG 58.950 45.833 0.00 0.00 41.80 3.69
2522 2626 5.395324 CGTTCTTATATTGTGGGACAGAGGT 60.395 44.000 0.00 0.00 41.80 3.85
2523 2627 6.183360 CGTTCTTATATTGTGGGACAGAGGTA 60.183 42.308 0.00 0.00 41.80 3.08
2694 2800 6.156256 ACTGGTCCTGTTATGCACTTCTATAA 59.844 38.462 0.00 0.00 0.00 0.98
2708 2814 8.046708 TGCACTTCTATAATTTAGGCAGAGAAA 58.953 33.333 0.00 0.00 0.00 2.52
2779 2912 5.185828 GGGTAAAATTTGAGGAAGAGTGCAT 59.814 40.000 0.00 0.00 0.00 3.96
2780 2913 6.095377 GGTAAAATTTGAGGAAGAGTGCATG 58.905 40.000 0.00 0.00 0.00 4.06
2849 2982 8.322906 TGTGTTGGAATATGTTTCTGAAGTAG 57.677 34.615 0.00 0.00 0.00 2.57
2854 3052 8.322906 TGGAATATGTTTCTGAAGTAGTTGTG 57.677 34.615 0.00 0.00 0.00 3.33
2879 3077 9.126151 TGAAAATCAGTATGTTCCTGTTTTGTA 57.874 29.630 0.00 0.00 34.03 2.41
2908 3119 8.918202 ACATTGTTTCTTTACCAGTGATCTTA 57.082 30.769 0.00 0.00 0.00 2.10
2969 3182 7.633789 ACCATTAGAAGTCATCCTTGTTATGT 58.366 34.615 0.00 0.00 33.78 2.29
3029 3242 1.661112 GAATGCACGCTCTCTTGTACC 59.339 52.381 0.00 0.00 0.00 3.34
3053 3266 5.909054 CGTGCTAGTAAAATATGCCATGTTG 59.091 40.000 0.00 0.00 0.00 3.33
3071 3284 3.194542 TGTTGCCAGTTTGTTGCTTACTT 59.805 39.130 0.00 0.00 0.00 2.24
3086 3299 7.538334 TGTTGCTTACTTGATTGAATTGAATCG 59.462 33.333 12.17 2.79 35.43 3.34
3128 3341 5.841810 TGCTGTTTCTAGGATTTGTTTTGG 58.158 37.500 0.00 0.00 0.00 3.28
3134 3347 7.123547 TGTTTCTAGGATTTGTTTTGGTCTGTT 59.876 33.333 0.00 0.00 0.00 3.16
3141 3354 7.123547 AGGATTTGTTTTGGTCTGTTGAAACTA 59.876 33.333 0.00 0.00 34.12 2.24
3142 3355 7.762159 GGATTTGTTTTGGTCTGTTGAAACTAA 59.238 33.333 0.00 0.00 33.64 2.24
3178 3391 6.484643 TCAATATGATGTCTTCTTGCCTTAGC 59.515 38.462 0.00 0.00 40.48 3.09
3190 3403 5.009631 TCTTGCCTTAGCTTGCAGAAATTA 58.990 37.500 0.00 0.00 38.95 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
437 438 1.181098 AAGCATTTGTGCCGCCTTCT 61.181 50.000 0.00 0.00 34.90 2.85
447 448 2.309613 TCAAGCACTCCAAGCATTTGT 58.690 42.857 0.00 0.00 32.21 2.83
652 655 4.514577 CACGTGGGGGCGCTCTAG 62.515 72.222 7.48 0.00 34.88 2.43
767 771 2.945440 GCTTGGGCTCATGTGGTAATCA 60.945 50.000 0.92 0.00 35.22 2.57
865 869 0.931202 CGTGTCGAGCGTGTTGTGTA 60.931 55.000 0.00 0.00 0.00 2.90
866 870 2.228241 CGTGTCGAGCGTGTTGTGT 61.228 57.895 0.00 0.00 0.00 3.72
875 882 3.718210 GATGGACCCCGTGTCGAGC 62.718 68.421 0.00 0.00 45.46 5.03
942 953 0.389817 CGTCGGGCTCAACTCAATCA 60.390 55.000 0.00 0.00 0.00 2.57
945 956 2.357034 GCGTCGGGCTCAACTCAA 60.357 61.111 0.00 0.00 39.11 3.02
946 957 4.373116 GGCGTCGGGCTCAACTCA 62.373 66.667 0.00 0.00 42.94 3.41
1015 1026 1.091537 TCCGGCGATTGATTTGGTTC 58.908 50.000 9.30 0.00 0.00 3.62
1278 1308 2.839754 AGGAACTGGTAGGCGAAGAGC 61.840 57.143 0.00 0.00 41.83 4.09
1492 1522 1.313812 ATGAGGAGGACGACGGTGAC 61.314 60.000 0.00 0.00 0.00 3.67
1728 1758 3.672781 CGAAGTAGGAGAAAACGAGGACC 60.673 52.174 0.00 0.00 0.00 4.46
1986 2016 0.388907 GCACGTACTCGCCAAGGTAA 60.389 55.000 0.00 0.00 41.18 2.85
2101 2134 3.334583 ACGCCATGCTCTTCTTTAGAA 57.665 42.857 0.00 0.00 30.91 2.10
2189 2222 4.137849 CAGTCCATACTGCGCATTATTG 57.862 45.455 16.73 13.81 46.28 1.90
2285 2385 5.221803 ACCATGAGCCAAGAATGATAGGTAG 60.222 44.000 0.00 0.00 0.00 3.18
2289 2389 6.204301 CACTAACCATGAGCCAAGAATGATAG 59.796 42.308 0.00 0.00 0.00 2.08
2437 2541 1.400530 GGGACGGAGGGAGTACATGG 61.401 65.000 0.00 0.00 0.00 3.66
2440 2544 0.928505 TATGGGACGGAGGGAGTACA 59.071 55.000 0.00 0.00 0.00 2.90
2441 2545 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2442 2546 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2443 2547 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2444 2548 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2445 2549 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2446 2550 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2447 2551 5.184479 TCGTTCTTATATTATGGGACGGAGG 59.816 44.000 10.35 0.00 0.00 4.30
2448 2552 6.263516 TCGTTCTTATATTATGGGACGGAG 57.736 41.667 10.35 0.00 0.00 4.63
2449 2553 6.845758 ATCGTTCTTATATTATGGGACGGA 57.154 37.500 10.35 2.35 0.00 4.69
2450 2554 7.900782 AAATCGTTCTTATATTATGGGACGG 57.099 36.000 10.35 0.00 0.00 4.79
2451 2555 8.227791 CCAAAATCGTTCTTATATTATGGGACG 58.772 37.037 6.17 6.17 0.00 4.79
2452 2556 8.021396 GCCAAAATCGTTCTTATATTATGGGAC 58.979 37.037 0.00 0.00 0.00 4.46
2453 2557 7.721842 TGCCAAAATCGTTCTTATATTATGGGA 59.278 33.333 0.00 0.00 0.00 4.37
2454 2558 7.807907 GTGCCAAAATCGTTCTTATATTATGGG 59.192 37.037 0.00 0.00 0.00 4.00
2455 2559 8.567948 AGTGCCAAAATCGTTCTTATATTATGG 58.432 33.333 0.00 0.00 0.00 2.74
2458 2562 9.602568 TGTAGTGCCAAAATCGTTCTTATATTA 57.397 29.630 0.00 0.00 0.00 0.98
2459 2563 8.395633 GTGTAGTGCCAAAATCGTTCTTATATT 58.604 33.333 0.00 0.00 0.00 1.28
2460 2564 7.769044 AGTGTAGTGCCAAAATCGTTCTTATAT 59.231 33.333 0.00 0.00 0.00 0.86
2461 2565 7.101054 AGTGTAGTGCCAAAATCGTTCTTATA 58.899 34.615 0.00 0.00 0.00 0.98
2462 2566 5.938125 AGTGTAGTGCCAAAATCGTTCTTAT 59.062 36.000 0.00 0.00 0.00 1.73
2463 2567 5.302360 AGTGTAGTGCCAAAATCGTTCTTA 58.698 37.500 0.00 0.00 0.00 2.10
2464 2568 4.134563 AGTGTAGTGCCAAAATCGTTCTT 58.865 39.130 0.00 0.00 0.00 2.52
2465 2569 3.740115 AGTGTAGTGCCAAAATCGTTCT 58.260 40.909 0.00 0.00 0.00 3.01
2466 2570 4.689345 ACTAGTGTAGTGCCAAAATCGTTC 59.311 41.667 0.00 0.00 37.69 3.95
2467 2571 4.638304 ACTAGTGTAGTGCCAAAATCGTT 58.362 39.130 0.00 0.00 37.69 3.85
2468 2572 4.267349 ACTAGTGTAGTGCCAAAATCGT 57.733 40.909 0.00 0.00 37.69 3.73
2493 2597 7.446013 TCTGTCCCACAATATAAGAACGTTTTT 59.554 33.333 9.22 9.22 0.00 1.94
2494 2598 6.938030 TCTGTCCCACAATATAAGAACGTTTT 59.062 34.615 0.46 0.00 0.00 2.43
2495 2599 6.469410 TCTGTCCCACAATATAAGAACGTTT 58.531 36.000 0.46 0.00 0.00 3.60
2496 2600 6.045072 TCTGTCCCACAATATAAGAACGTT 57.955 37.500 0.00 0.00 0.00 3.99
2497 2601 5.395324 CCTCTGTCCCACAATATAAGAACGT 60.395 44.000 0.00 0.00 0.00 3.99
2498 2602 5.050490 CCTCTGTCCCACAATATAAGAACG 58.950 45.833 0.00 0.00 0.00 3.95
2499 2603 5.990668 ACCTCTGTCCCACAATATAAGAAC 58.009 41.667 0.00 0.00 0.00 3.01
2500 2604 6.901300 ACTACCTCTGTCCCACAATATAAGAA 59.099 38.462 0.00 0.00 0.00 2.52
2501 2605 6.441222 ACTACCTCTGTCCCACAATATAAGA 58.559 40.000 0.00 0.00 0.00 2.10
2502 2606 6.732896 ACTACCTCTGTCCCACAATATAAG 57.267 41.667 0.00 0.00 0.00 1.73
2503 2607 7.589081 TCTACTACCTCTGTCCCACAATATAA 58.411 38.462 0.00 0.00 0.00 0.98
2504 2608 7.157947 TCTACTACCTCTGTCCCACAATATA 57.842 40.000 0.00 0.00 0.00 0.86
2505 2609 6.027025 TCTACTACCTCTGTCCCACAATAT 57.973 41.667 0.00 0.00 0.00 1.28
2506 2610 5.461516 TCTACTACCTCTGTCCCACAATA 57.538 43.478 0.00 0.00 0.00 1.90
2507 2611 4.332683 TCTACTACCTCTGTCCCACAAT 57.667 45.455 0.00 0.00 0.00 2.71
2508 2612 3.820195 TCTACTACCTCTGTCCCACAA 57.180 47.619 0.00 0.00 0.00 3.33
2509 2613 3.820195 TTCTACTACCTCTGTCCCACA 57.180 47.619 0.00 0.00 0.00 4.17
2510 2614 4.710375 TCAATTCTACTACCTCTGTCCCAC 59.290 45.833 0.00 0.00 0.00 4.61
2511 2615 4.942944 TCAATTCTACTACCTCTGTCCCA 58.057 43.478 0.00 0.00 0.00 4.37
2512 2616 5.598830 TCATCAATTCTACTACCTCTGTCCC 59.401 44.000 0.00 0.00 0.00 4.46
2513 2617 6.716934 TCATCAATTCTACTACCTCTGTCC 57.283 41.667 0.00 0.00 0.00 4.02
2514 2618 7.865385 GTCATCATCAATTCTACTACCTCTGTC 59.135 40.741 0.00 0.00 0.00 3.51
2515 2619 7.563188 AGTCATCATCAATTCTACTACCTCTGT 59.437 37.037 0.00 0.00 0.00 3.41
2516 2620 7.866898 CAGTCATCATCAATTCTACTACCTCTG 59.133 40.741 0.00 0.00 0.00 3.35
2517 2621 7.563188 ACAGTCATCATCAATTCTACTACCTCT 59.437 37.037 0.00 0.00 0.00 3.69
2518 2622 7.721402 ACAGTCATCATCAATTCTACTACCTC 58.279 38.462 0.00 0.00 0.00 3.85
2519 2623 7.469318 CGACAGTCATCATCAATTCTACTACCT 60.469 40.741 0.41 0.00 0.00 3.08
2520 2624 6.638873 CGACAGTCATCATCAATTCTACTACC 59.361 42.308 0.41 0.00 0.00 3.18
2521 2625 7.166638 CACGACAGTCATCATCAATTCTACTAC 59.833 40.741 0.41 0.00 0.00 2.73
2522 2626 7.067008 TCACGACAGTCATCATCAATTCTACTA 59.933 37.037 0.41 0.00 0.00 1.82
2523 2627 6.038985 CACGACAGTCATCATCAATTCTACT 58.961 40.000 0.41 0.00 0.00 2.57
2780 2913 5.594317 AGGAATGCATCAGTAATGGTTTACC 59.406 40.000 0.00 0.00 38.81 2.85
2849 2982 6.970484 ACAGGAACATACTGATTTTCACAAC 58.030 36.000 0.00 0.00 39.24 3.32
2854 3052 9.959749 TTACAAAACAGGAACATACTGATTTTC 57.040 29.630 0.00 0.00 38.40 2.29
3029 3242 5.673337 ACATGGCATATTTTACTAGCACG 57.327 39.130 0.00 0.00 0.00 5.34
3053 3266 3.708563 TCAAGTAAGCAACAAACTGGC 57.291 42.857 0.00 0.00 0.00 4.85
3093 3306 9.760926 ATCCTAGAAACAGCATATATCTAGACA 57.239 33.333 9.15 0.00 41.22 3.41
3109 3322 7.039313 ACAGACCAAAACAAATCCTAGAAAC 57.961 36.000 0.00 0.00 0.00 2.78
3114 3327 7.123547 AGTTTCAACAGACCAAAACAAATCCTA 59.876 33.333 0.00 0.00 34.76 2.94
3121 3334 7.397892 TCATTAGTTTCAACAGACCAAAACA 57.602 32.000 0.00 0.00 34.76 2.83
3122 3335 8.188139 TCTTCATTAGTTTCAACAGACCAAAAC 58.812 33.333 0.00 0.00 32.97 2.43
3123 3336 8.287439 TCTTCATTAGTTTCAACAGACCAAAA 57.713 30.769 0.00 0.00 0.00 2.44
3158 3371 4.500499 AGCTAAGGCAAGAAGACATCAT 57.500 40.909 0.00 0.00 41.70 2.45
3167 3380 2.566833 TTCTGCAAGCTAAGGCAAGA 57.433 45.000 8.69 6.20 39.93 3.02
3168 3381 3.863142 ATTTCTGCAAGCTAAGGCAAG 57.137 42.857 8.69 4.37 39.93 4.01
3169 3382 5.243730 AGTTAATTTCTGCAAGCTAAGGCAA 59.756 36.000 8.69 0.00 39.93 4.52
3170 3383 4.766891 AGTTAATTTCTGCAAGCTAAGGCA 59.233 37.500 7.33 7.33 41.70 4.75
3171 3384 5.316327 AGTTAATTTCTGCAAGCTAAGGC 57.684 39.130 0.00 0.00 39.06 4.35
3178 3391 7.329226 CCATGTAACCAAGTTAATTTCTGCAAG 59.671 37.037 0.00 0.00 29.42 4.01


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

AutoCloner maintained by Alex Coulton.