Multiple sequence alignment - TraesCS5B01G176700

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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 TraesCS5B01G176700 chr5B 100.000 2882 0 0 1 2882 322857931 322860812 0.000000e+00 5323.0
1 TraesCS5B01G176700 chr5B 100.000 62 0 0 2374 2435 322860245 322860306 6.530000e-22 115.0
2 TraesCS5B01G176700 chr5B 100.000 62 0 0 2315 2376 322860304 322860365 6.530000e-22 115.0
3 TraesCS5B01G176700 chr5D 93.792 2078 97 18 312 2372 285246970 285249032 0.000000e+00 3094.0
4 TraesCS5B01G176700 chr5D 91.406 512 34 8 2375 2882 285248975 285249480 0.000000e+00 693.0
5 TraesCS5B01G176700 chr5D 94.298 228 7 1 1 222 285246615 285246842 7.650000e-91 344.0
6 TraesCS5B01G176700 chr5D 100.000 30 0 0 786 815 113391895 113391866 4.010000e-04 56.5
7 TraesCS5B01G176700 chr5A 94.139 1672 85 9 339 2003 377119163 377120828 0.000000e+00 2532.0
8 TraesCS5B01G176700 chr5A 90.643 513 33 11 2375 2882 377121164 377121666 0.000000e+00 667.0
9 TraesCS5B01G176700 chr5A 85.644 613 45 18 1 574 377118746 377119354 3.180000e-169 604.0
10 TraesCS5B01G176700 chr5A 94.488 381 8 4 1996 2372 377120851 377121222 2.490000e-160 575.0
11 TraesCS5B01G176700 chr3D 96.552 58 0 2 775 831 252334793 252334849 8.500000e-16 95.3
12 TraesCS5B01G176700 chr3D 100.000 45 0 0 2209 2253 64483310 64483354 1.840000e-12 84.2
13 TraesCS5B01G176700 chr3B 96.491 57 2 0 775 831 313808026 313808082 8.500000e-16 95.3
14 TraesCS5B01G176700 chr3A 100.000 51 0 0 781 831 332220139 332220089 8.500000e-16 95.3
15 TraesCS5B01G176700 chr1B 96.429 56 2 0 2207 2262 6423519 6423574 3.060000e-15 93.5
16 TraesCS5B01G176700 chr6D 98.039 51 1 0 781 831 52724695 52724645 3.960000e-14 89.8
17 TraesCS5B01G176700 chr6B 98.039 51 1 0 781 831 119849607 119849557 3.960000e-14 89.8
18 TraesCS5B01G176700 chr6B 94.340 53 2 1 2212 2264 23292012 23292063 2.380000e-11 80.5
19 TraesCS5B01G176700 chr6A 98.039 51 1 0 781 831 63610635 63610585 3.960000e-14 89.8
20 TraesCS5B01G176700 chr4D 94.828 58 2 1 2206 2263 362116459 362116515 3.960000e-14 89.8
21 TraesCS5B01G176700 chr7B 94.231 52 3 0 2209 2260 382279298 382279247 2.380000e-11 80.5
22 TraesCS5B01G176700 chr7A 91.228 57 3 2 2206 2262 678142675 678142729 3.080000e-10 76.8
23 TraesCS5B01G176700 chr1A 91.071 56 5 0 2209 2264 564146593 564146538 3.080000e-10 76.8


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 TraesCS5B01G176700 chr5B 322857931 322860812 2881 False 1851.0 5323 100.000000 1 2882 3 chr5B.!!$F1 2881
1 TraesCS5B01G176700 chr5D 285246615 285249480 2865 False 1377.0 3094 93.165333 1 2882 3 chr5D.!!$F1 2881
2 TraesCS5B01G176700 chr5A 377118746 377121666 2920 False 1094.5 2532 91.228500 1 2882 4 chr5A.!!$F1 2881

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
64 65 0.391661 GCCACAGAAGATTCCGAGCA 60.392 55.0 0.0 0.0 0.0 4.26 F
1405 1514 0.324552 TGATTTCCATGCCCCACCAG 60.325 55.0 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
1611 1730 0.877743 GTTGCTGGCTCTGGTTCTTC 59.122 55.0 0.0 0.0 0.0 2.87 R
2619 2778 0.613260 AGAGTTGGCGTGCATTAGGA 59.387 50.0 0.0 0.0 0.0 2.94 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
64 65 0.391661 GCCACAGAAGATTCCGAGCA 60.392 55.000 0.00 0.00 0.00 4.26
67 68 1.728971 CACAGAAGATTCCGAGCACAC 59.271 52.381 0.00 0.00 0.00 3.82
117 127 3.056179 CACCACCACCATTACCAATTTCC 60.056 47.826 0.00 0.00 0.00 3.13
119 129 3.447229 CCACCACCATTACCAATTTCCTC 59.553 47.826 0.00 0.00 0.00 3.71
123 133 1.333619 CCATTACCAATTTCCTCCGCG 59.666 52.381 0.00 0.00 0.00 6.46
227 237 2.522503 AGCTCCCTTGCTGGCAAA 59.477 55.556 9.32 0.00 42.33 3.68
229 239 2.202395 GCTCCCTTGCTGGCAAACA 61.202 57.895 9.32 0.00 35.33 2.83
254 289 0.871057 GCAGAGCACAGTCTGTTTCC 59.129 55.000 1.67 0.00 45.07 3.13
283 319 3.000819 TAGCCCGTCCACAGTGGG 61.001 66.667 20.14 4.41 46.22 4.61
292 338 1.833934 CCACAGTGGGCAAAAGCCT 60.834 57.895 12.40 0.00 32.67 4.58
364 419 2.037641 GGCTCTGCCCAAATTTGTTTCT 59.962 45.455 16.73 0.00 44.06 2.52
368 423 1.270041 TGCCCAAATTTGTTTCTCCGC 60.270 47.619 16.73 7.02 0.00 5.54
423 478 4.886755 TTCTCCCCTCATCATCCATTTT 57.113 40.909 0.00 0.00 0.00 1.82
453 553 3.949842 GCTCTGCCAAAAATTCCTTCT 57.050 42.857 0.00 0.00 0.00 2.85
456 556 3.165071 TCTGCCAAAAATTCCTTCTCCC 58.835 45.455 0.00 0.00 0.00 4.30
460 560 3.429410 GCCAAAAATTCCTTCTCCCATCG 60.429 47.826 0.00 0.00 0.00 3.84
498 598 1.475682 CTCTGCCAAAATTCCCTCTGC 59.524 52.381 0.00 0.00 0.00 4.26
500 600 1.203994 CTGCCAAAATTCCCTCTGCAG 59.796 52.381 7.63 7.63 38.78 4.41
505 605 3.305608 CCAAAATTCCCTCTGCAGTTCAC 60.306 47.826 14.67 0.00 0.00 3.18
508 608 0.687354 TTCCCTCTGCAGTTCACTCC 59.313 55.000 14.67 0.00 0.00 3.85
511 611 1.406614 CCCTCTGCAGTTCACTCCATC 60.407 57.143 14.67 0.00 0.00 3.51
545 645 2.527497 TCTGCCCAAATTTGATCTGCA 58.473 42.857 19.86 18.40 0.00 4.41
546 646 2.231964 TCTGCCCAAATTTGATCTGCAC 59.768 45.455 19.86 1.69 0.00 4.57
568 668 1.202348 CGTTTCATTTCCAAGGGGAGC 59.798 52.381 0.00 0.00 46.01 4.70
638 739 4.925068 ACTTGCATCTGAAAACAGAACAC 58.075 39.130 4.09 0.00 34.56 3.32
643 744 4.715896 CATCTGAAAACAGAACACATCGG 58.284 43.478 4.09 0.00 34.56 4.18
696 799 7.445121 AGTCTGTTGTGTTCTTGATGATAGAA 58.555 34.615 0.00 0.00 0.00 2.10
734 840 1.537202 GATGTTGTTGCTGGTCCTGTC 59.463 52.381 0.00 0.00 0.00 3.51
953 1060 8.967664 TGTTACAAGGTGTGTTTTTATACTCT 57.032 30.769 0.00 0.00 41.98 3.24
1047 1154 2.685380 CAAGGGACCCGGAGCTCT 60.685 66.667 14.64 0.00 0.00 4.09
1217 1325 8.170061 ACCCTTCCAAGCATGCTATTTATATAA 58.830 33.333 23.00 6.33 0.00 0.98
1332 1440 5.296531 ACCCAAGCATGTGAAAACAAAAATC 59.703 36.000 0.00 0.00 0.00 2.17
1349 1458 1.379527 ATCGATGAAAACGAAGGCCC 58.620 50.000 0.00 0.00 46.41 5.80
1350 1459 1.017177 TCGATGAAAACGAAGGCCCG 61.017 55.000 0.00 0.00 38.51 6.13
1405 1514 0.324552 TGATTTCCATGCCCCACCAG 60.325 55.000 0.00 0.00 0.00 4.00
1546 1664 6.884280 AGAAAACCTAACAAGAACATGAGG 57.116 37.500 0.00 0.00 0.00 3.86
1626 1745 0.324285 AGCTGAAGAACCAGAGCCAG 59.676 55.000 0.00 0.00 36.29 4.85
1630 1749 0.877743 GAAGAACCAGAGCCAGCAAC 59.122 55.000 0.00 0.00 0.00 4.17
1634 1753 0.250640 AACCAGAGCCAGCAACTGAG 60.251 55.000 15.07 9.53 32.44 3.35
1671 1790 1.333636 CCACCCAAAACCTTGTGGCA 61.334 55.000 0.00 0.00 41.55 4.92
1774 1893 2.226200 TGCATGAACTCAATCACCAACG 59.774 45.455 0.00 0.00 30.82 4.10
1776 1895 1.234821 TGAACTCAATCACCAACGCC 58.765 50.000 0.00 0.00 0.00 5.68
1884 2006 2.615986 TGTACCAGTGCTTCTAGGGA 57.384 50.000 0.00 0.00 0.00 4.20
1885 2007 2.897350 TGTACCAGTGCTTCTAGGGAA 58.103 47.619 0.00 0.00 0.00 3.97
1931 2053 0.683973 CATAGCTGGTAGGGCCTCTG 59.316 60.000 10.74 1.38 38.35 3.35
2213 2369 5.152623 TCTTCATGTACTCCCTGACTTTG 57.847 43.478 0.00 0.00 0.00 2.77
2285 2441 4.742012 TCCGCCTAGATCCTTCTCTTATT 58.258 43.478 0.00 0.00 33.17 1.40
2314 2470 4.658901 TGTCTCTTTTCCTCTTGGTTAGGT 59.341 41.667 0.00 0.00 35.48 3.08
2367 2524 3.190744 GTGAAGCTAGGTAGGTTTTTGCC 59.809 47.826 0.00 0.00 43.36 4.52
2368 2525 3.181438 TGAAGCTAGGTAGGTTTTTGCCA 60.181 43.478 0.00 0.00 43.36 4.92
2369 2526 3.739401 AGCTAGGTAGGTTTTTGCCAT 57.261 42.857 0.00 0.00 0.00 4.40
2370 2527 4.855298 AGCTAGGTAGGTTTTTGCCATA 57.145 40.909 0.00 0.00 0.00 2.74
2371 2528 5.187621 AGCTAGGTAGGTTTTTGCCATAA 57.812 39.130 0.00 0.00 0.00 1.90
2372 2529 5.766590 AGCTAGGTAGGTTTTTGCCATAAT 58.233 37.500 0.00 0.00 0.00 1.28
2373 2530 6.194967 AGCTAGGTAGGTTTTTGCCATAATT 58.805 36.000 0.00 0.00 0.00 1.40
2374 2531 6.667848 AGCTAGGTAGGTTTTTGCCATAATTT 59.332 34.615 0.00 0.00 0.00 1.82
2375 2532 6.978659 GCTAGGTAGGTTTTTGCCATAATTTC 59.021 38.462 0.00 0.00 0.00 2.17
2376 2533 6.926630 AGGTAGGTTTTTGCCATAATTTCA 57.073 33.333 0.00 0.00 0.00 2.69
2377 2534 7.309770 AGGTAGGTTTTTGCCATAATTTCAA 57.690 32.000 0.00 0.00 0.00 2.69
2378 2535 7.386059 AGGTAGGTTTTTGCCATAATTTCAAG 58.614 34.615 0.00 0.00 0.00 3.02
2379 2536 7.016170 AGGTAGGTTTTTGCCATAATTTCAAGT 59.984 33.333 0.00 0.00 0.00 3.16
2380 2537 8.308207 GGTAGGTTTTTGCCATAATTTCAAGTA 58.692 33.333 0.00 0.00 0.00 2.24
2381 2538 9.869757 GTAGGTTTTTGCCATAATTTCAAGTAT 57.130 29.630 0.00 0.00 0.00 2.12
2399 2556 6.879962 CAAGTATTGTGCTCCAACATTTTTG 58.120 36.000 0.00 0.00 42.34 2.44
2400 2557 6.403866 AGTATTGTGCTCCAACATTTTTGA 57.596 33.333 0.00 0.00 35.44 2.69
2401 2558 6.449698 AGTATTGTGCTCCAACATTTTTGAG 58.550 36.000 0.00 0.00 35.44 3.02
2402 2559 4.998671 TTGTGCTCCAACATTTTTGAGA 57.001 36.364 0.00 0.00 27.72 3.27
2403 2560 5.534207 TTGTGCTCCAACATTTTTGAGAT 57.466 34.783 0.00 0.00 27.72 2.75
2404 2561 4.873817 TGTGCTCCAACATTTTTGAGATG 58.126 39.130 0.00 0.00 27.72 2.90
2405 2562 4.341806 TGTGCTCCAACATTTTTGAGATGT 59.658 37.500 0.00 0.00 39.31 3.06
2406 2563 4.682860 GTGCTCCAACATTTTTGAGATGTG 59.317 41.667 0.00 0.00 37.76 3.21
2407 2564 4.583907 TGCTCCAACATTTTTGAGATGTGA 59.416 37.500 0.00 0.00 37.76 3.58
2408 2565 5.068855 TGCTCCAACATTTTTGAGATGTGAA 59.931 36.000 0.00 0.00 37.76 3.18
2409 2566 5.632347 GCTCCAACATTTTTGAGATGTGAAG 59.368 40.000 0.00 0.00 37.76 3.02
2410 2567 5.531634 TCCAACATTTTTGAGATGTGAAGC 58.468 37.500 0.00 0.00 37.76 3.86
2411 2568 5.302568 TCCAACATTTTTGAGATGTGAAGCT 59.697 36.000 0.00 0.00 37.76 3.74
2412 2569 6.489700 TCCAACATTTTTGAGATGTGAAGCTA 59.510 34.615 0.00 0.00 37.76 3.32
2413 2570 6.805271 CCAACATTTTTGAGATGTGAAGCTAG 59.195 38.462 0.00 0.00 37.76 3.42
2414 2571 6.506500 ACATTTTTGAGATGTGAAGCTAGG 57.493 37.500 0.00 0.00 36.43 3.02
2415 2572 6.006449 ACATTTTTGAGATGTGAAGCTAGGT 58.994 36.000 0.00 0.00 36.43 3.08
2416 2573 7.168219 ACATTTTTGAGATGTGAAGCTAGGTA 58.832 34.615 0.00 0.00 36.43 3.08
2417 2574 7.335422 ACATTTTTGAGATGTGAAGCTAGGTAG 59.665 37.037 0.00 0.00 36.43 3.18
2418 2575 5.344743 TTTGAGATGTGAAGCTAGGTAGG 57.655 43.478 0.00 0.00 0.00 3.18
2419 2576 3.982516 TGAGATGTGAAGCTAGGTAGGT 58.017 45.455 0.00 0.00 35.17 3.08
2420 2577 4.353777 TGAGATGTGAAGCTAGGTAGGTT 58.646 43.478 1.08 1.08 45.70 3.50
2421 2578 4.777896 TGAGATGTGAAGCTAGGTAGGTTT 59.222 41.667 0.00 0.00 43.36 3.27
2422 2579 5.248477 TGAGATGTGAAGCTAGGTAGGTTTT 59.752 40.000 0.00 0.00 43.36 2.43
2423 2580 6.128138 AGATGTGAAGCTAGGTAGGTTTTT 57.872 37.500 0.00 0.00 43.36 1.94
2424 2581 5.940470 AGATGTGAAGCTAGGTAGGTTTTTG 59.060 40.000 0.00 0.00 43.36 2.44
2431 2588 5.766590 AGCTAGGTAGGTTTTTGCCATAAT 58.233 37.500 0.00 0.00 0.00 1.28
2434 2591 6.978659 GCTAGGTAGGTTTTTGCCATAATTTC 59.021 38.462 0.00 0.00 0.00 2.17
2457 2614 8.579850 TTCTATTTTGCAGATTGGTGTAGATT 57.420 30.769 0.00 0.00 0.00 2.40
2459 2616 8.461222 TCTATTTTGCAGATTGGTGTAGATTTG 58.539 33.333 0.00 0.00 0.00 2.32
2463 2621 5.754782 TGCAGATTGGTGTAGATTTGGTAT 58.245 37.500 0.00 0.00 0.00 2.73
2472 2630 7.573710 TGGTGTAGATTTGGTATAGAAGCATT 58.426 34.615 0.00 0.00 35.03 3.56
2473 2631 7.498900 TGGTGTAGATTTGGTATAGAAGCATTG 59.501 37.037 0.00 0.00 35.03 2.82
2474 2632 7.355778 GTGTAGATTTGGTATAGAAGCATTGC 58.644 38.462 0.00 0.00 35.03 3.56
2477 2635 6.799512 AGATTTGGTATAGAAGCATTGCAAC 58.200 36.000 11.91 4.27 35.03 4.17
2478 2636 5.973899 TTTGGTATAGAAGCATTGCAACA 57.026 34.783 11.91 0.00 35.03 3.33
2479 2637 6.528537 TTTGGTATAGAAGCATTGCAACAT 57.471 33.333 11.91 1.27 35.03 2.71
2519 2677 7.537649 GTCGAATATTACTCTATTGTCATCGCA 59.462 37.037 0.00 0.00 0.00 5.10
2529 2687 1.246649 TGTCATCGCAACAAGGCAAT 58.753 45.000 0.00 0.00 0.00 3.56
2538 2696 2.029649 GCAACAAGGCAATGTGACTCAT 60.030 45.455 0.00 0.00 31.94 2.90
2556 2714 4.397417 ACTCATGAAAGAAGTATGCAAGCC 59.603 41.667 0.00 0.00 0.00 4.35
2630 2789 9.950680 ATAAATTCACTAAATTCCTAATGCACG 57.049 29.630 0.00 0.00 36.54 5.34
2636 2795 2.128771 ATTCCTAATGCACGCCAACT 57.871 45.000 0.00 0.00 0.00 3.16
2637 2796 1.448985 TTCCTAATGCACGCCAACTC 58.551 50.000 0.00 0.00 0.00 3.01
2638 2797 0.613260 TCCTAATGCACGCCAACTCT 59.387 50.000 0.00 0.00 0.00 3.24
2653 2812 4.275936 GCCAACTCTTGTGTAAATGTGAGT 59.724 41.667 0.00 0.00 36.49 3.41
2659 2818 6.096673 TCTTGTGTAAATGTGAGTGCTAGA 57.903 37.500 0.00 0.00 0.00 2.43
2766 2925 5.899120 TGTACAGAGCCTCAACTTACTAG 57.101 43.478 0.00 0.00 0.00 2.57
2770 2929 5.326069 ACAGAGCCTCAACTTACTAGAGAA 58.674 41.667 0.00 0.00 0.00 2.87
2829 2989 0.481128 GGGGAGGGAAACAAAGTCCA 59.519 55.000 0.00 0.00 36.83 4.02
2856 3016 3.915437 AACAGGATAAAGCACAAACCG 57.085 42.857 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.338200 GGTGTGCTCGGAATCTTCTGT 60.338 52.381 0.00 0.00 35.11 3.41
64 65 1.299976 GAAAGGGATGGCGAGGTGT 59.700 57.895 0.00 0.00 0.00 4.16
67 68 1.452108 GGTGAAAGGGATGGCGAGG 60.452 63.158 0.00 0.00 0.00 4.63
117 127 0.917259 CGAGAGAAACAATCGCGGAG 59.083 55.000 6.13 0.00 36.50 4.63
123 133 4.638963 CGGTTTTAGCGAGAGAAACAATC 58.361 43.478 0.00 0.00 42.41 2.67
222 232 1.874562 CTCTGCTCTGCTGTTTGCC 59.125 57.895 0.00 0.00 42.00 4.52
224 234 0.237761 GTGCTCTGCTCTGCTGTTTG 59.762 55.000 0.00 0.00 0.00 2.93
225 235 0.179037 TGTGCTCTGCTCTGCTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
226 236 0.603172 CTGTGCTCTGCTCTGCTGTT 60.603 55.000 0.00 0.00 0.00 3.16
227 237 1.004799 CTGTGCTCTGCTCTGCTGT 60.005 57.895 0.00 0.00 0.00 4.40
229 239 1.186917 AGACTGTGCTCTGCTCTGCT 61.187 55.000 0.00 0.00 0.00 4.24
230 240 1.015085 CAGACTGTGCTCTGCTCTGC 61.015 60.000 0.00 0.00 31.57 4.26
231 241 0.317799 ACAGACTGTGCTCTGCTCTG 59.682 55.000 7.47 16.15 41.38 3.35
232 242 1.047002 AACAGACTGTGCTCTGCTCT 58.953 50.000 9.33 0.00 41.38 4.09
233 243 1.797635 GAAACAGACTGTGCTCTGCTC 59.202 52.381 9.33 0.00 41.38 4.26
283 319 2.151049 CTGAGGTGGCAGGCTTTTGC 62.151 60.000 0.00 0.67 46.64 3.68
292 338 1.304381 GGATTTGGCTGAGGTGGCA 60.304 57.895 0.00 0.00 40.80 4.92
359 414 2.356069 GGAAATGGATGAGCGGAGAAAC 59.644 50.000 0.00 0.00 0.00 2.78
360 415 2.026356 TGGAAATGGATGAGCGGAGAAA 60.026 45.455 0.00 0.00 0.00 2.52
364 419 0.181114 CCTGGAAATGGATGAGCGGA 59.819 55.000 0.00 0.00 0.00 5.54
368 423 1.144503 CCTCCCCTGGAAATGGATGAG 59.855 57.143 0.00 0.00 0.00 2.90
453 553 0.546122 CCTGGAAATGGACGATGGGA 59.454 55.000 0.00 0.00 0.00 4.37
456 556 0.546122 TCCCCTGGAAATGGACGATG 59.454 55.000 0.00 0.00 0.00 3.84
460 560 1.076705 GCCTCCCCTGGAAATGGAC 60.077 63.158 0.00 0.00 0.00 4.02
498 598 2.355513 CCCTTGGAGATGGAGTGAACTG 60.356 54.545 0.00 0.00 0.00 3.16
500 600 1.065126 CCCCTTGGAGATGGAGTGAAC 60.065 57.143 0.00 0.00 0.00 3.18
531 631 3.302365 AACGGGTGCAGATCAAATTTG 57.698 42.857 12.15 12.15 0.00 2.32
545 645 1.627864 CCCTTGGAAATGAAACGGGT 58.372 50.000 0.00 0.00 0.00 5.28
546 646 0.894835 CCCCTTGGAAATGAAACGGG 59.105 55.000 0.00 0.00 0.00 5.28
589 690 4.339247 GGTGCTGTGTGGCAAGAAATATAT 59.661 41.667 0.00 0.00 44.18 0.86
590 691 3.694072 GGTGCTGTGTGGCAAGAAATATA 59.306 43.478 0.00 0.00 44.18 0.86
638 739 5.410067 ACCTTGCAAATGAAATTACCGATG 58.590 37.500 0.00 0.00 33.67 3.84
696 799 1.211969 CTACACGTGCTACTGCGGT 59.788 57.895 17.22 2.42 43.34 5.68
872 978 9.357161 AGCTAGCTTGATTATGTTACTAGTAGT 57.643 33.333 12.68 8.14 0.00 2.73
953 1060 7.708322 CAGCAGTTTCACTTGCTCTTATATCTA 59.292 37.037 0.00 0.00 32.84 1.98
1047 1154 1.686325 GGCAATCCTCAGCGGACCTA 61.686 60.000 0.00 0.00 46.80 3.08
1056 1163 2.285368 AGGTCCGGGCAATCCTCA 60.285 61.111 9.07 0.00 0.00 3.86
1217 1325 6.331369 ACAAACTTTATGCTTATGTGCACT 57.669 33.333 19.41 6.22 46.33 4.40
1296 1404 1.246056 GCTTGGGTGCATGCTCTCAA 61.246 55.000 28.09 28.09 0.00 3.02
1308 1416 3.902881 TTTGTTTTCACATGCTTGGGT 57.097 38.095 1.28 0.00 31.06 4.51
1332 1440 1.423845 CGGGCCTTCGTTTTCATCG 59.576 57.895 0.84 0.00 0.00 3.84
1349 1458 2.799412 GTCTGAGCAGATATTTCAGGCG 59.201 50.000 3.19 0.00 39.97 5.52
1350 1459 3.801698 TGTCTGAGCAGATATTTCAGGC 58.198 45.455 3.19 0.00 42.40 4.85
1353 1462 7.692460 ATGTTTTGTCTGAGCAGATATTTCA 57.308 32.000 3.19 2.62 39.97 2.69
1405 1514 0.989602 AGTGTTAGGTAGGGGGCAAC 59.010 55.000 0.00 0.00 0.00 4.17
1578 1696 8.043710 TCCACCTGTTTTTGTCACAAAAATATT 58.956 29.630 27.01 13.96 32.55 1.28
1585 1704 4.019858 TGATCCACCTGTTTTTGTCACAA 58.980 39.130 0.00 0.00 0.00 3.33
1611 1730 0.877743 GTTGCTGGCTCTGGTTCTTC 59.122 55.000 0.00 0.00 0.00 2.87
1634 1753 2.756691 TCATGCCCAGCACCATGC 60.757 61.111 0.00 0.00 43.04 4.06
1671 1790 0.882042 CCGAGTTCTGTGCTTGCAGT 60.882 55.000 0.00 0.00 37.70 4.40
1884 2006 6.251471 ACATCAACCATCCATTCTTCTTCTT 58.749 36.000 0.00 0.00 0.00 2.52
1885 2007 5.824421 ACATCAACCATCCATTCTTCTTCT 58.176 37.500 0.00 0.00 0.00 2.85
1886 2008 6.071728 ACAACATCAACCATCCATTCTTCTTC 60.072 38.462 0.00 0.00 0.00 2.87
1931 2053 2.191128 ACAGAACCTGATGCCTTCAC 57.809 50.000 0.45 0.00 35.18 3.18
2213 2369 7.903431 CCAAAATAAGTGTCGCTGATTTAGTAC 59.097 37.037 8.84 0.00 37.29 2.73
2285 2441 1.412710 AGAGGAAAAGAGACACGTGCA 59.587 47.619 17.22 0.00 0.00 4.57
2314 2470 6.403866 AAATGTTGGAGCACAATACTTGAA 57.596 33.333 0.00 0.00 41.95 2.69
2367 2524 8.028354 TGTTGGAGCACAATACTTGAAATTATG 58.972 33.333 0.00 0.00 41.95 1.90
2368 2525 8.121305 TGTTGGAGCACAATACTTGAAATTAT 57.879 30.769 0.00 0.00 41.95 1.28
2369 2526 7.517614 TGTTGGAGCACAATACTTGAAATTA 57.482 32.000 0.00 0.00 41.95 1.40
2370 2527 6.403866 TGTTGGAGCACAATACTTGAAATT 57.596 33.333 0.00 0.00 41.95 1.82
2371 2528 6.594788 ATGTTGGAGCACAATACTTGAAAT 57.405 33.333 0.00 0.00 41.95 2.17
2372 2529 6.403866 AATGTTGGAGCACAATACTTGAAA 57.596 33.333 0.00 0.00 41.95 2.69
2373 2530 6.403866 AAATGTTGGAGCACAATACTTGAA 57.596 33.333 0.00 0.00 41.95 2.69
2374 2531 6.403866 AAAATGTTGGAGCACAATACTTGA 57.596 33.333 0.00 0.00 41.95 3.02
2375 2532 6.700960 TCAAAAATGTTGGAGCACAATACTTG 59.299 34.615 0.00 1.73 41.95 3.16
2376 2533 6.815089 TCAAAAATGTTGGAGCACAATACTT 58.185 32.000 0.00 0.00 41.95 2.24
2377 2534 6.265196 TCTCAAAAATGTTGGAGCACAATACT 59.735 34.615 0.00 0.00 41.95 2.12
2378 2535 6.446318 TCTCAAAAATGTTGGAGCACAATAC 58.554 36.000 0.00 0.00 41.95 1.89
2379 2536 6.647334 TCTCAAAAATGTTGGAGCACAATA 57.353 33.333 0.00 0.00 41.95 1.90
2380 2537 5.534207 TCTCAAAAATGTTGGAGCACAAT 57.466 34.783 0.00 0.00 41.95 2.71
2381 2538 4.998671 TCTCAAAAATGTTGGAGCACAA 57.001 36.364 0.00 0.00 35.07 3.33
2382 2539 4.341806 ACATCTCAAAAATGTTGGAGCACA 59.658 37.500 0.00 0.00 35.07 4.57
2383 2540 4.682860 CACATCTCAAAAATGTTGGAGCAC 59.317 41.667 0.00 0.00 35.07 4.40
2384 2541 4.583907 TCACATCTCAAAAATGTTGGAGCA 59.416 37.500 0.00 0.00 35.07 4.26
2385 2542 5.125100 TCACATCTCAAAAATGTTGGAGC 57.875 39.130 0.00 0.00 35.07 4.70
2386 2543 5.632347 GCTTCACATCTCAAAAATGTTGGAG 59.368 40.000 0.00 0.00 36.27 3.86
2387 2544 5.302568 AGCTTCACATCTCAAAAATGTTGGA 59.697 36.000 0.00 0.00 35.19 3.53
2388 2545 5.535333 AGCTTCACATCTCAAAAATGTTGG 58.465 37.500 0.00 0.00 35.19 3.77
2389 2546 6.805271 CCTAGCTTCACATCTCAAAAATGTTG 59.195 38.462 0.00 0.00 35.19 3.33
2390 2547 6.491403 ACCTAGCTTCACATCTCAAAAATGTT 59.509 34.615 0.00 0.00 35.19 2.71
2391 2548 6.006449 ACCTAGCTTCACATCTCAAAAATGT 58.994 36.000 0.00 0.00 37.85 2.71
2392 2549 6.506500 ACCTAGCTTCACATCTCAAAAATG 57.493 37.500 0.00 0.00 0.00 2.32
2393 2550 6.825721 CCTACCTAGCTTCACATCTCAAAAAT 59.174 38.462 0.00 0.00 0.00 1.82
2394 2551 6.173339 CCTACCTAGCTTCACATCTCAAAAA 58.827 40.000 0.00 0.00 0.00 1.94
2395 2552 5.248477 ACCTACCTAGCTTCACATCTCAAAA 59.752 40.000 0.00 0.00 0.00 2.44
2396 2553 4.777896 ACCTACCTAGCTTCACATCTCAAA 59.222 41.667 0.00 0.00 0.00 2.69
2397 2554 4.353777 ACCTACCTAGCTTCACATCTCAA 58.646 43.478 0.00 0.00 0.00 3.02
2398 2555 3.982516 ACCTACCTAGCTTCACATCTCA 58.017 45.455 0.00 0.00 0.00 3.27
2399 2556 5.346181 AAACCTACCTAGCTTCACATCTC 57.654 43.478 0.00 0.00 0.00 2.75
2400 2557 5.763876 AAAACCTACCTAGCTTCACATCT 57.236 39.130 0.00 0.00 0.00 2.90
2401 2558 5.392057 GCAAAAACCTACCTAGCTTCACATC 60.392 44.000 0.00 0.00 0.00 3.06
2402 2559 4.459337 GCAAAAACCTACCTAGCTTCACAT 59.541 41.667 0.00 0.00 0.00 3.21
2403 2560 3.818773 GCAAAAACCTACCTAGCTTCACA 59.181 43.478 0.00 0.00 0.00 3.58
2404 2561 3.190744 GGCAAAAACCTACCTAGCTTCAC 59.809 47.826 0.00 0.00 0.00 3.18
2405 2562 3.181438 TGGCAAAAACCTACCTAGCTTCA 60.181 43.478 0.00 0.00 0.00 3.02
2406 2563 3.418047 TGGCAAAAACCTACCTAGCTTC 58.582 45.455 0.00 0.00 0.00 3.86
2407 2564 3.518992 TGGCAAAAACCTACCTAGCTT 57.481 42.857 0.00 0.00 0.00 3.74
2408 2565 3.739401 ATGGCAAAAACCTACCTAGCT 57.261 42.857 0.00 0.00 0.00 3.32
2409 2566 6.465439 AATTATGGCAAAAACCTACCTAGC 57.535 37.500 0.00 0.00 0.00 3.42
2410 2567 8.293699 AGAAATTATGGCAAAAACCTACCTAG 57.706 34.615 0.00 0.00 0.00 3.02
2411 2568 9.930158 ATAGAAATTATGGCAAAAACCTACCTA 57.070 29.630 0.00 0.00 0.00 3.08
2412 2569 8.838649 ATAGAAATTATGGCAAAAACCTACCT 57.161 30.769 0.00 0.00 0.00 3.08
2413 2570 9.884636 AAATAGAAATTATGGCAAAAACCTACC 57.115 29.630 0.00 0.00 0.00 3.18
2416 2573 8.729756 GCAAAATAGAAATTATGGCAAAAACCT 58.270 29.630 0.00 0.00 0.00 3.50
2417 2574 8.510505 TGCAAAATAGAAATTATGGCAAAAACC 58.489 29.630 0.00 0.00 0.00 3.27
2418 2575 9.545611 CTGCAAAATAGAAATTATGGCAAAAAC 57.454 29.630 0.00 0.00 30.20 2.43
2419 2576 9.499479 TCTGCAAAATAGAAATTATGGCAAAAA 57.501 25.926 0.00 0.00 30.20 1.94
2420 2577 9.669887 ATCTGCAAAATAGAAATTATGGCAAAA 57.330 25.926 0.00 0.00 30.20 2.44
2421 2578 9.669887 AATCTGCAAAATAGAAATTATGGCAAA 57.330 25.926 0.00 0.00 30.20 3.68
2422 2579 9.100554 CAATCTGCAAAATAGAAATTATGGCAA 57.899 29.630 0.00 0.00 30.20 4.52
2423 2580 7.711772 CCAATCTGCAAAATAGAAATTATGGCA 59.288 33.333 0.00 0.00 0.00 4.92
2424 2581 7.712205 ACCAATCTGCAAAATAGAAATTATGGC 59.288 33.333 0.00 0.00 0.00 4.40
2431 2588 7.994425 TCTACACCAATCTGCAAAATAGAAA 57.006 32.000 0.00 0.00 0.00 2.52
2434 2591 7.703621 CCAAATCTACACCAATCTGCAAAATAG 59.296 37.037 0.00 0.00 0.00 1.73
2457 2614 6.528537 AATGTTGCAATGCTTCTATACCAA 57.471 33.333 6.82 0.00 0.00 3.67
2459 2616 7.165812 CGTAAAATGTTGCAATGCTTCTATACC 59.834 37.037 6.82 0.00 0.00 2.73
2463 2621 5.182190 TCCGTAAAATGTTGCAATGCTTCTA 59.818 36.000 6.82 0.00 0.00 2.10
2472 2630 6.073167 TCGACTTTTATCCGTAAAATGTTGCA 60.073 34.615 0.00 0.00 38.66 4.08
2473 2631 6.308675 TCGACTTTTATCCGTAAAATGTTGC 58.691 36.000 0.00 0.00 38.66 4.17
2474 2632 8.889849 ATTCGACTTTTATCCGTAAAATGTTG 57.110 30.769 0.00 0.00 38.66 3.33
2503 2661 3.935203 CCTTGTTGCGATGACAATAGAGT 59.065 43.478 0.00 0.00 36.51 3.24
2519 2677 3.489355 TCATGAGTCACATTGCCTTGTT 58.511 40.909 0.00 0.00 37.07 2.83
2529 2687 5.550290 TGCATACTTCTTTCATGAGTCACA 58.450 37.500 0.00 0.00 0.00 3.58
2538 2696 4.019792 TCTGGCTTGCATACTTCTTTCA 57.980 40.909 0.00 0.00 0.00 2.69
2582 2740 2.490902 GGATTTATTCCCGGCCTCCATT 60.491 50.000 0.00 0.00 38.75 3.16
2619 2778 0.613260 AGAGTTGGCGTGCATTAGGA 59.387 50.000 0.00 0.00 0.00 2.94
2630 2789 4.275936 ACTCACATTTACACAAGAGTTGGC 59.724 41.667 0.00 0.00 32.88 4.52
2636 2795 6.096673 TCTAGCACTCACATTTACACAAGA 57.903 37.500 0.00 0.00 0.00 3.02
2637 2796 6.785488 TTCTAGCACTCACATTTACACAAG 57.215 37.500 0.00 0.00 0.00 3.16
2638 2797 7.744087 AATTCTAGCACTCACATTTACACAA 57.256 32.000 0.00 0.00 0.00 3.33
2653 2812 6.073447 TCCATTAGGGTTCAAATTCTAGCA 57.927 37.500 0.00 0.00 38.11 3.49
2659 2818 6.542370 CGACAGTATCCATTAGGGTTCAAATT 59.458 38.462 0.00 0.00 38.11 1.82
2766 2925 4.460382 TCATGAGGATTTTGCAAGGTTCTC 59.540 41.667 12.29 12.29 0.00 2.87
2770 2929 4.340381 GCTATCATGAGGATTTTGCAAGGT 59.660 41.667 0.09 0.00 37.44 3.50
2829 2989 2.562738 GTGCTTTATCCTGTTTTGGCCT 59.437 45.455 3.32 0.00 0.00 5.19
2856 3016 4.039730 TCTTGCATGCTCTATCCTTAGGTC 59.960 45.833 20.33 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.