Multiple sequence alignment - TraesCS5A01G311500

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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 TraesCS5A01G311500 chr5A 100.000 2717 0 0 1 2717 523135705 523138421 0.000000e+00 5018
1 TraesCS5A01G311500 chr5A 76.600 1500 230 70 800 2235 523449892 523451334 0.000000e+00 713
2 TraesCS5A01G311500 chr5A 84.270 356 48 7 1066 1414 522066673 522067027 9.320000e-90 340
3 TraesCS5A01G311500 chr5B 92.132 2542 148 21 10 2532 493673070 493675578 0.000000e+00 3539
4 TraesCS5A01G311500 chr5B 80.130 926 142 21 798 1715 493931210 493932101 0.000000e+00 652
5 TraesCS5A01G311500 chr5B 84.857 350 51 2 1066 1414 492619520 492619868 4.300000e-93 351
6 TraesCS5A01G311500 chr5D 90.692 2471 165 30 76 2532 411195821 411198240 0.000000e+00 3229
7 TraesCS5A01G311500 chr5D 80.238 926 139 25 800 1715 411627435 411628326 0.000000e+00 656
8 TraesCS5A01G311500 chr5D 85.429 350 48 3 1066 1414 410444225 410444572 7.150000e-96 361
9 TraesCS5A01G311500 chr5D 83.095 349 57 2 1067 1414 411785487 411785140 1.570000e-82 316


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 TraesCS5A01G311500 chr5A 523135705 523138421 2716 False 5018 5018 100.000 1 2717 1 chr5A.!!$F2 2716
1 TraesCS5A01G311500 chr5A 523449892 523451334 1442 False 713 713 76.600 800 2235 1 chr5A.!!$F3 1435
2 TraesCS5A01G311500 chr5B 493673070 493675578 2508 False 3539 3539 92.132 10 2532 1 chr5B.!!$F2 2522
3 TraesCS5A01G311500 chr5B 493931210 493932101 891 False 652 652 80.130 798 1715 1 chr5B.!!$F3 917
4 TraesCS5A01G311500 chr5D 411195821 411198240 2419 False 3229 3229 90.692 76 2532 1 chr5D.!!$F2 2456
5 TraesCS5A01G311500 chr5D 411627435 411628326 891 False 656 656 80.238 800 1715 1 chr5D.!!$F3 915

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
344 357 0.178992 TGAAAACTGGTGAGCTGGGG 60.179 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2117 0.911769 AGGCCACATCTTCCGAATCA 59.088 50.0 5.01 0.0 0.0 2.57 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
23 24 3.120889 CGATGTGGCTAATACTTCGCATG 60.121 47.826 0.00 0.00 38.35 4.06
25 26 4.071961 TGTGGCTAATACTTCGCATGAT 57.928 40.909 0.00 0.00 0.00 2.45
27 28 3.187227 GTGGCTAATACTTCGCATGATGG 59.813 47.826 0.00 0.00 0.00 3.51
30 31 4.083802 GGCTAATACTTCGCATGATGGTTC 60.084 45.833 0.00 0.00 0.00 3.62
31 32 4.376413 GCTAATACTTCGCATGATGGTTCG 60.376 45.833 0.00 0.00 0.00 3.95
42 43 0.676782 GATGGTTCGGGTTGTGGGAG 60.677 60.000 0.00 0.00 0.00 4.30
58 59 3.364277 GAGACGCCTCCAATACCAC 57.636 57.895 0.00 0.00 33.30 4.16
65 66 1.734163 CCTCCAATACCACGGACAAC 58.266 55.000 0.00 0.00 0.00 3.32
94 104 6.036300 CGTACTAATAAACGCCTCCATTTTGA 59.964 38.462 0.00 0.00 31.66 2.69
98 108 2.368655 AACGCCTCCATTTTGAATGC 57.631 45.000 0.00 0.00 0.00 3.56
104 114 1.483415 CTCCATTTTGAATGCCAGGGG 59.517 52.381 0.00 0.00 0.00 4.79
141 151 2.320681 AGGTATCCGCCCTGCTAATA 57.679 50.000 0.00 0.00 0.00 0.98
143 153 2.302157 AGGTATCCGCCCTGCTAATAAC 59.698 50.000 0.00 0.00 0.00 1.89
158 171 7.011482 CCTGCTAATAACAGTATGAAACACTCC 59.989 40.741 0.00 0.00 39.69 3.85
166 179 7.440523 ACAGTATGAAACACTCCTTGATTTC 57.559 36.000 0.00 0.00 39.69 2.17
173 186 6.488683 TGAAACACTCCTTGATTTCCGTATTT 59.511 34.615 0.00 0.00 31.39 1.40
175 188 4.941873 ACACTCCTTGATTTCCGTATTTCC 59.058 41.667 0.00 0.00 0.00 3.13
185 198 3.788333 TCCGTATTTCCTAACTGGTCG 57.212 47.619 0.00 0.00 37.07 4.79
255 268 3.999001 CACTCACTTTGCATAGAGCTCAA 59.001 43.478 17.77 0.00 45.94 3.02
259 272 5.494724 TCACTTTGCATAGAGCTCAATCTT 58.505 37.500 17.77 0.00 45.94 2.40
262 275 5.942236 ACTTTGCATAGAGCTCAATCTTTCA 59.058 36.000 17.77 1.35 45.94 2.69
274 287 3.184379 TCAATCTTTCAGAAGTGAACGCG 59.816 43.478 3.53 3.53 42.60 6.01
279 292 0.319469 TCAGAAGTGAACGCGCATCA 60.319 50.000 5.73 8.84 0.00 3.07
286 299 1.328680 GTGAACGCGCATCATCAGAAT 59.671 47.619 16.83 0.00 0.00 2.40
288 301 2.419673 TGAACGCGCATCATCAGAATTT 59.580 40.909 5.73 0.00 0.00 1.82
318 331 6.808008 AAAATCAAGGATAGTGTGAGTGTG 57.192 37.500 0.00 0.00 0.00 3.82
321 334 4.407365 TCAAGGATAGTGTGAGTGTGAGA 58.593 43.478 0.00 0.00 0.00 3.27
329 342 4.832248 AGTGTGAGTGTGAGAACTTGAAA 58.168 39.130 0.00 0.00 0.00 2.69
330 343 5.245531 AGTGTGAGTGTGAGAACTTGAAAA 58.754 37.500 0.00 0.00 0.00 2.29
331 344 5.122396 AGTGTGAGTGTGAGAACTTGAAAAC 59.878 40.000 0.00 0.00 0.00 2.43
333 346 5.122239 TGTGAGTGTGAGAACTTGAAAACTG 59.878 40.000 0.00 0.00 0.00 3.16
337 350 4.394920 GTGTGAGAACTTGAAAACTGGTGA 59.605 41.667 0.00 0.00 0.00 4.02
344 357 0.178992 TGAAAACTGGTGAGCTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
353 366 1.407437 GGTGAGCTGGGGATAACACTG 60.407 57.143 0.00 0.00 0.00 3.66
355 368 1.278985 TGAGCTGGGGATAACACTGTG 59.721 52.381 6.19 6.19 0.00 3.66
360 373 0.462047 GGGGATAACACTGTGCTCGG 60.462 60.000 7.90 0.00 0.00 4.63
380 393 2.612212 GGCCATCTACGGTTGTAATGTG 59.388 50.000 0.00 0.00 0.00 3.21
383 396 3.938963 CCATCTACGGTTGTAATGTGCTT 59.061 43.478 0.00 0.00 0.00 3.91
385 398 4.260139 TCTACGGTTGTAATGTGCTTGA 57.740 40.909 0.00 0.00 0.00 3.02
410 423 4.483476 AAAATGTGGTACTTGTCTTCGC 57.517 40.909 0.00 0.00 0.00 4.70
411 424 2.831685 ATGTGGTACTTGTCTTCGCA 57.168 45.000 0.00 0.00 0.00 5.10
412 425 1.860676 TGTGGTACTTGTCTTCGCAC 58.139 50.000 0.00 0.00 0.00 5.34
433 446 5.096169 CACAGAAGTACATAACACGAGGAG 58.904 45.833 0.00 0.00 0.00 3.69
441 454 2.736144 TAACACGAGGAGAATGCGTT 57.264 45.000 0.00 0.00 35.90 4.84
501 514 6.463995 TTATCAGTTTCAAGCAACACCTTT 57.536 33.333 0.00 0.00 0.00 3.11
507 520 1.403679 TCAAGCAACACCTTTTCACGG 59.596 47.619 0.00 0.00 0.00 4.94
650 665 2.344500 CTTCCCCACACCGCGTAA 59.656 61.111 4.92 0.00 0.00 3.18
651 666 1.740296 CTTCCCCACACCGCGTAAG 60.740 63.158 4.92 0.00 43.44 2.34
691 706 6.821160 TCAATCGCTGGAGAACAACATATAAA 59.179 34.615 0.00 0.00 0.00 1.40
739 754 1.669779 CAGCCTGCTGTTTGCTAGATC 59.330 52.381 10.97 0.00 43.37 2.75
773 788 1.947678 GCCCCAACTGTCAGTCTCATG 60.948 57.143 5.82 0.50 0.00 3.07
885 900 2.037136 GCAGCGCACTCCACAAGAT 61.037 57.895 11.47 0.00 0.00 2.40
892 907 2.926200 CGCACTCCACAAGATACTCAAG 59.074 50.000 0.00 0.00 0.00 3.02
908 923 3.073062 ACTCAAGCATAACCAACACTCCT 59.927 43.478 0.00 0.00 0.00 3.69
909 924 4.074970 CTCAAGCATAACCAACACTCCTT 58.925 43.478 0.00 0.00 0.00 3.36
997 1014 1.374252 CACCGACCACCTGCAGTAC 60.374 63.158 13.81 0.00 0.00 2.73
1292 1312 1.366366 CCCCGTGTCTCAACTTCGT 59.634 57.895 0.00 0.00 0.00 3.85
1535 1558 1.154225 CTGGCGACGGAATGTTTGC 60.154 57.895 0.00 0.00 39.98 3.68
1823 1883 5.191727 ACCCATCAAATCCTGTGACATAA 57.808 39.130 0.00 0.00 0.00 1.90
1982 2048 4.862574 GCTTCATGTGTCGTGACTATAACA 59.137 41.667 1.23 0.00 0.00 2.41
2043 2114 2.263227 CGTGGTCCATGTACGCCA 59.737 61.111 2.56 0.00 0.00 5.69
2044 2115 1.374885 CGTGGTCCATGTACGCCAA 60.375 57.895 2.56 0.00 32.26 4.52
2045 2116 0.742990 CGTGGTCCATGTACGCCAAT 60.743 55.000 2.56 0.00 32.26 3.16
2046 2117 1.459450 GTGGTCCATGTACGCCAATT 58.541 50.000 0.00 0.00 32.26 2.32
2071 2142 0.179034 GGAAGATGTGGCCTAGGCAG 60.179 60.000 34.09 0.00 44.11 4.85
2125 2217 3.432326 CCCTGGGATCTTTTTCTAGTCCG 60.432 52.174 7.01 0.00 0.00 4.79
2208 2300 1.643868 GAATCGCGTGGCCAACATGA 61.644 55.000 7.24 3.44 38.41 3.07
2247 2339 2.940410 TGTGTCACGAACCTTTTTCCTC 59.060 45.455 0.00 0.00 0.00 3.71
2256 2349 3.532641 ACCTTTTTCCTCTTGGAGCAT 57.467 42.857 0.00 0.00 44.24 3.79
2365 2458 2.355197 GCTTTGTTTTGCCTTTGTGGT 58.645 42.857 0.00 0.00 38.35 4.16
2374 2467 0.385390 GCCTTTGTGGTGAACTGGTG 59.615 55.000 0.00 0.00 38.35 4.17
2433 2526 6.753279 CACATATTCATGGGTTGATGTCAAAC 59.247 38.462 2.17 2.17 42.60 2.93
2434 2527 6.436847 ACATATTCATGGGTTGATGTCAAACA 59.563 34.615 12.40 8.14 45.01 2.83
2435 2528 7.124599 ACATATTCATGGGTTGATGTCAAACAT 59.875 33.333 12.40 9.82 45.01 2.71
2440 2533 7.377398 TCATGGGTTGATGTCAAACATAAAAG 58.623 34.615 12.40 3.09 45.01 2.27
2476 2569 1.358787 TCATGGGTTTCCTGATGCCTT 59.641 47.619 0.00 0.00 0.00 4.35
2493 2586 1.884579 CCTTTGTGAAGACTGCTGCAT 59.115 47.619 1.31 0.00 34.71 3.96
2494 2587 2.351447 CCTTTGTGAAGACTGCTGCATG 60.351 50.000 1.31 0.00 34.71 4.06
2495 2588 0.594602 TTGTGAAGACTGCTGCATGC 59.405 50.000 11.82 11.82 43.25 4.06
2496 2589 5.396328 CTTTGTGAAGACTGCTGCATGCA 62.396 47.826 21.29 21.29 41.46 3.96
2528 2621 1.136305 GGTGCATAGTGACGGAGCTAA 59.864 52.381 0.00 0.00 0.00 3.09
2532 2625 2.855187 GCATAGTGACGGAGCTAAGACG 60.855 54.545 0.00 0.00 0.00 4.18
2533 2626 0.731417 TAGTGACGGAGCTAAGACGC 59.269 55.000 0.00 0.00 0.00 5.19
2534 2627 1.868251 GTGACGGAGCTAAGACGCG 60.868 63.158 3.53 3.53 34.40 6.01
2535 2628 2.330372 TGACGGAGCTAAGACGCGT 61.330 57.895 13.85 13.85 34.40 6.01
2536 2629 1.868251 GACGGAGCTAAGACGCGTG 60.868 63.158 20.70 2.28 34.40 5.34
2537 2630 2.178521 CGGAGCTAAGACGCGTGT 59.821 61.111 20.70 11.10 34.40 4.49
2538 2631 2.152699 CGGAGCTAAGACGCGTGTG 61.153 63.158 20.70 2.05 34.40 3.82
2539 2632 1.080705 GGAGCTAAGACGCGTGTGT 60.081 57.895 20.70 0.00 34.40 3.72
2540 2633 1.344942 GGAGCTAAGACGCGTGTGTG 61.345 60.000 20.70 10.74 34.40 3.82
2541 2634 0.663568 GAGCTAAGACGCGTGTGTGT 60.664 55.000 20.70 0.00 42.75 3.72
2542 2635 0.939577 AGCTAAGACGCGTGTGTGTG 60.940 55.000 20.70 5.10 39.39 3.82
2543 2636 1.886861 GCTAAGACGCGTGTGTGTGG 61.887 60.000 20.70 0.00 39.39 4.17
2544 2637 0.318360 CTAAGACGCGTGTGTGTGGA 60.318 55.000 20.70 0.00 39.39 4.02
2545 2638 0.315886 TAAGACGCGTGTGTGTGGAT 59.684 50.000 20.70 0.00 39.39 3.41
2546 2639 0.944311 AAGACGCGTGTGTGTGGATC 60.944 55.000 20.70 0.00 39.39 3.36
2547 2640 1.372997 GACGCGTGTGTGTGGATCT 60.373 57.895 20.70 0.00 39.39 2.75
2548 2641 1.344942 GACGCGTGTGTGTGGATCTC 61.345 60.000 20.70 0.00 39.39 2.75
2549 2642 1.372872 CGCGTGTGTGTGGATCTCA 60.373 57.895 0.00 0.00 0.00 3.27
2550 2643 1.617755 CGCGTGTGTGTGGATCTCAC 61.618 60.000 0.00 12.30 46.23 3.51
2551 2644 0.319900 GCGTGTGTGTGGATCTCACT 60.320 55.000 17.36 0.00 46.20 3.41
2552 2645 1.422388 CGTGTGTGTGGATCTCACTG 58.578 55.000 17.36 6.37 46.20 3.66
2553 2646 1.800805 GTGTGTGTGGATCTCACTGG 58.199 55.000 17.36 0.00 46.20 4.00
2554 2647 1.070758 GTGTGTGTGGATCTCACTGGT 59.929 52.381 17.36 0.00 46.20 4.00
2555 2648 1.768275 TGTGTGTGGATCTCACTGGTT 59.232 47.619 17.36 0.00 46.20 3.67
2556 2649 2.146342 GTGTGTGGATCTCACTGGTTG 58.854 52.381 17.36 0.00 46.20 3.77
2557 2650 1.768275 TGTGTGGATCTCACTGGTTGT 59.232 47.619 17.36 0.00 46.20 3.32
2558 2651 2.172505 TGTGTGGATCTCACTGGTTGTT 59.827 45.455 17.36 0.00 46.20 2.83
2559 2652 3.214328 GTGTGGATCTCACTGGTTGTTT 58.786 45.455 13.32 0.00 46.20 2.83
2560 2653 4.141597 TGTGTGGATCTCACTGGTTGTTTA 60.142 41.667 17.36 0.00 46.20 2.01
2561 2654 4.452455 GTGTGGATCTCACTGGTTGTTTAG 59.548 45.833 13.32 0.00 46.20 1.85
2562 2655 4.003648 GTGGATCTCACTGGTTGTTTAGG 58.996 47.826 6.98 0.00 42.86 2.69
2563 2656 3.010420 GGATCTCACTGGTTGTTTAGGC 58.990 50.000 0.00 0.00 0.00 3.93
2564 2657 3.307762 GGATCTCACTGGTTGTTTAGGCT 60.308 47.826 0.00 0.00 0.00 4.58
2565 2658 3.126001 TCTCACTGGTTGTTTAGGCTG 57.874 47.619 0.00 0.00 0.00 4.85
2566 2659 2.154462 CTCACTGGTTGTTTAGGCTGG 58.846 52.381 0.00 0.00 0.00 4.85
2567 2660 1.493022 TCACTGGTTGTTTAGGCTGGT 59.507 47.619 0.00 0.00 0.00 4.00
2568 2661 2.092103 TCACTGGTTGTTTAGGCTGGTT 60.092 45.455 0.00 0.00 0.00 3.67
2569 2662 2.034558 CACTGGTTGTTTAGGCTGGTTG 59.965 50.000 0.00 0.00 0.00 3.77
2570 2663 1.000274 CTGGTTGTTTAGGCTGGTTGC 60.000 52.381 0.00 0.00 41.94 4.17
2571 2664 1.036707 GGTTGTTTAGGCTGGTTGCA 58.963 50.000 0.00 0.00 45.15 4.08
2572 2665 1.000274 GGTTGTTTAGGCTGGTTGCAG 60.000 52.381 0.00 0.00 45.15 4.41
2573 2666 1.681264 GTTGTTTAGGCTGGTTGCAGT 59.319 47.619 0.00 0.00 45.15 4.40
2574 2667 1.317613 TGTTTAGGCTGGTTGCAGTG 58.682 50.000 0.00 0.00 45.15 3.66
2575 2668 0.598065 GTTTAGGCTGGTTGCAGTGG 59.402 55.000 0.00 0.00 45.15 4.00
2576 2669 0.539438 TTTAGGCTGGTTGCAGTGGG 60.539 55.000 0.00 0.00 45.15 4.61
2577 2670 2.424842 TTAGGCTGGTTGCAGTGGGG 62.425 60.000 0.00 0.00 45.15 4.96
2578 2671 4.603535 GGCTGGTTGCAGTGGGGT 62.604 66.667 0.00 0.00 45.15 4.95
2579 2672 2.434331 GCTGGTTGCAGTGGGGTA 59.566 61.111 0.00 0.00 42.31 3.69
2580 2673 1.000896 GCTGGTTGCAGTGGGGTAT 60.001 57.895 0.00 0.00 42.31 2.73
2581 2674 0.611896 GCTGGTTGCAGTGGGGTATT 60.612 55.000 0.00 0.00 42.31 1.89
2582 2675 1.340600 GCTGGTTGCAGTGGGGTATTA 60.341 52.381 0.00 0.00 42.31 0.98
2583 2676 2.686715 GCTGGTTGCAGTGGGGTATTAT 60.687 50.000 0.00 0.00 42.31 1.28
2584 2677 3.434453 GCTGGTTGCAGTGGGGTATTATA 60.434 47.826 0.00 0.00 42.31 0.98
2585 2678 4.749785 GCTGGTTGCAGTGGGGTATTATAT 60.750 45.833 0.00 0.00 42.31 0.86
2586 2679 5.514136 GCTGGTTGCAGTGGGGTATTATATA 60.514 44.000 0.00 0.00 42.31 0.86
2587 2680 5.871834 TGGTTGCAGTGGGGTATTATATAC 58.128 41.667 0.00 0.00 0.00 1.47
2588 2681 5.609284 TGGTTGCAGTGGGGTATTATATACT 59.391 40.000 0.00 0.00 0.00 2.12
2589 2682 6.171213 GGTTGCAGTGGGGTATTATATACTC 58.829 44.000 0.00 0.00 0.00 2.59
2590 2683 5.654603 TGCAGTGGGGTATTATATACTCG 57.345 43.478 0.00 0.00 0.00 4.18
2591 2684 5.081728 TGCAGTGGGGTATTATATACTCGT 58.918 41.667 0.00 0.00 0.00 4.18
2592 2685 6.247676 TGCAGTGGGGTATTATATACTCGTA 58.752 40.000 0.00 0.00 0.00 3.43
2593 2686 6.893554 TGCAGTGGGGTATTATATACTCGTAT 59.106 38.462 0.00 0.00 0.00 3.06
2594 2687 7.398047 TGCAGTGGGGTATTATATACTCGTATT 59.602 37.037 0.00 0.00 0.00 1.89
2595 2688 8.255905 GCAGTGGGGTATTATATACTCGTATTT 58.744 37.037 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.792949 GCGAAGTATTAGCCACATCGG 59.207 52.381 2.87 0.00 41.08 4.18
1 2 2.469826 TGCGAAGTATTAGCCACATCG 58.530 47.619 0.00 0.00 46.68 3.84
2 3 4.058124 TCATGCGAAGTATTAGCCACATC 58.942 43.478 0.00 0.00 46.68 3.06
3 4 4.071961 TCATGCGAAGTATTAGCCACAT 57.928 40.909 0.00 0.00 46.68 3.21
4 5 3.535280 TCATGCGAAGTATTAGCCACA 57.465 42.857 0.00 0.00 46.68 4.17
5 6 3.187227 CCATCATGCGAAGTATTAGCCAC 59.813 47.826 0.00 0.00 46.68 5.01
6 7 3.181455 ACCATCATGCGAAGTATTAGCCA 60.181 43.478 0.00 0.00 46.68 4.75
7 8 3.403038 ACCATCATGCGAAGTATTAGCC 58.597 45.455 0.00 0.00 46.68 3.93
23 24 0.676782 CTCCCACAACCCGAACCATC 60.677 60.000 0.00 0.00 0.00 3.51
25 26 1.766864 TCTCCCACAACCCGAACCA 60.767 57.895 0.00 0.00 0.00 3.67
27 28 1.666872 CGTCTCCCACAACCCGAAC 60.667 63.158 0.00 0.00 0.00 3.95
31 32 3.607370 GAGGCGTCTCCCACAACCC 62.607 68.421 5.50 0.00 34.01 4.11
42 43 1.520787 CCGTGGTATTGGAGGCGTC 60.521 63.158 0.00 0.00 0.00 5.19
58 59 5.495412 CGTTTATTAGTACGAACGTTGTCCG 60.495 44.000 5.00 5.84 40.03 4.79
65 66 3.483558 GGAGGCGTTTATTAGTACGAACG 59.516 47.826 13.27 13.27 45.39 3.95
68 69 4.924305 ATGGAGGCGTTTATTAGTACGA 57.076 40.909 0.00 0.00 40.03 3.43
69 70 5.978934 AAATGGAGGCGTTTATTAGTACG 57.021 39.130 0.00 0.00 40.55 3.67
71 72 7.925043 TTCAAAATGGAGGCGTTTATTAGTA 57.075 32.000 0.00 0.00 0.00 1.82
72 73 6.827586 TTCAAAATGGAGGCGTTTATTAGT 57.172 33.333 0.00 0.00 0.00 2.24
73 74 6.198966 GCATTCAAAATGGAGGCGTTTATTAG 59.801 38.462 2.17 0.00 0.00 1.73
94 104 3.473113 AACATTTAGACCCCTGGCATT 57.527 42.857 0.00 0.00 0.00 3.56
98 108 3.739401 AGGAAACATTTAGACCCCTGG 57.261 47.619 0.00 0.00 0.00 4.45
141 151 7.040409 GGAAATCAAGGAGTGTTTCATACTGTT 60.040 37.037 0.00 0.00 32.96 3.16
143 153 6.402550 CGGAAATCAAGGAGTGTTTCATACTG 60.403 42.308 0.00 0.00 32.96 2.74
158 171 6.598064 ACCAGTTAGGAAATACGGAAATCAAG 59.402 38.462 0.00 0.00 41.22 3.02
166 179 2.199236 GCGACCAGTTAGGAAATACGG 58.801 52.381 0.00 0.00 41.22 4.02
173 186 1.940883 ATTCGCGCGACCAGTTAGGA 61.941 55.000 35.02 15.47 41.22 2.94
175 188 0.800683 TCATTCGCGCGACCAGTTAG 60.801 55.000 35.02 16.44 0.00 2.34
185 198 5.116377 TGTTTACTTTCATTTTCATTCGCGC 59.884 36.000 0.00 0.00 0.00 6.86
220 233 6.073276 TGCAAAGTGAGTGTTGTATGTACATC 60.073 38.462 12.68 5.06 35.89 3.06
223 236 5.666969 TGCAAAGTGAGTGTTGTATGTAC 57.333 39.130 0.00 0.00 0.00 2.90
224 237 7.382898 TCTATGCAAAGTGAGTGTTGTATGTA 58.617 34.615 0.00 0.00 33.06 2.29
232 245 3.007290 TGAGCTCTATGCAAAGTGAGTGT 59.993 43.478 16.19 0.00 45.94 3.55
235 248 5.117584 AGATTGAGCTCTATGCAAAGTGAG 58.882 41.667 15.60 0.00 45.94 3.51
239 252 6.315642 TCTGAAAGATTGAGCTCTATGCAAAG 59.684 38.462 15.60 6.73 41.05 2.77
255 268 1.461127 GCGCGTTCACTTCTGAAAGAT 59.539 47.619 8.43 0.00 46.36 2.40
259 272 0.790207 GATGCGCGTTCACTTCTGAA 59.210 50.000 8.43 0.00 33.76 3.02
262 275 1.002366 GATGATGCGCGTTCACTTCT 58.998 50.000 14.20 0.00 0.00 2.85
295 308 6.533730 TCACACTCACACTATCCTTGATTTT 58.466 36.000 0.00 0.00 0.00 1.82
308 321 5.122396 AGTTTTCAAGTTCTCACACTCACAC 59.878 40.000 0.00 0.00 0.00 3.82
311 324 4.635765 CCAGTTTTCAAGTTCTCACACTCA 59.364 41.667 0.00 0.00 0.00 3.41
315 328 4.584874 TCACCAGTTTTCAAGTTCTCACA 58.415 39.130 0.00 0.00 0.00 3.58
316 329 4.496507 GCTCACCAGTTTTCAAGTTCTCAC 60.497 45.833 0.00 0.00 0.00 3.51
317 330 3.627577 GCTCACCAGTTTTCAAGTTCTCA 59.372 43.478 0.00 0.00 0.00 3.27
318 331 3.879892 AGCTCACCAGTTTTCAAGTTCTC 59.120 43.478 0.00 0.00 0.00 2.87
321 334 2.689983 CCAGCTCACCAGTTTTCAAGTT 59.310 45.455 0.00 0.00 0.00 2.66
329 342 1.282157 GTTATCCCCAGCTCACCAGTT 59.718 52.381 0.00 0.00 0.00 3.16
330 343 0.912486 GTTATCCCCAGCTCACCAGT 59.088 55.000 0.00 0.00 0.00 4.00
331 344 0.911769 TGTTATCCCCAGCTCACCAG 59.088 55.000 0.00 0.00 0.00 4.00
333 346 0.912486 AGTGTTATCCCCAGCTCACC 59.088 55.000 0.00 0.00 0.00 4.02
337 350 0.035056 GCACAGTGTTATCCCCAGCT 60.035 55.000 1.61 0.00 0.00 4.24
344 357 0.391130 TGGCCGAGCACAGTGTTATC 60.391 55.000 1.61 0.00 0.00 1.75
353 366 2.279517 CCGTAGATGGCCGAGCAC 60.280 66.667 0.00 0.00 0.00 4.40
355 368 1.883084 CAACCGTAGATGGCCGAGC 60.883 63.158 0.00 0.00 0.00 5.03
360 373 2.031683 GCACATTACAACCGTAGATGGC 59.968 50.000 0.00 0.00 0.00 4.40
410 423 5.055642 TCCTCGTGTTATGTACTTCTGTG 57.944 43.478 0.00 0.00 0.00 3.66
411 424 5.008331 TCTCCTCGTGTTATGTACTTCTGT 58.992 41.667 0.00 0.00 0.00 3.41
412 425 5.562506 TCTCCTCGTGTTATGTACTTCTG 57.437 43.478 0.00 0.00 0.00 3.02
433 446 2.414161 GCCTTGGACAAGTAACGCATTC 60.414 50.000 10.81 0.00 36.72 2.67
501 514 0.037447 TCATGGATTGGCACCGTGAA 59.963 50.000 14.71 1.83 46.30 3.18
507 520 2.309764 GACGCGTCATGGATTGGCAC 62.310 60.000 33.09 1.78 0.00 5.01
511 524 1.078709 AAGTGACGCGTCATGGATTG 58.921 50.000 40.84 0.00 42.18 2.67
691 706 2.126888 CGCATTTTTCTGCCGCGT 60.127 55.556 4.92 0.00 40.99 6.01
885 900 4.286032 AGGAGTGTTGGTTATGCTTGAGTA 59.714 41.667 0.00 0.00 0.00 2.59
892 907 3.610911 AGCTAAGGAGTGTTGGTTATGC 58.389 45.455 0.00 0.00 0.00 3.14
997 1014 1.077501 AGCCGGTCATGTCCATTGG 60.078 57.895 9.71 0.00 0.00 3.16
1074 1094 3.887335 GAACTTGGTACGCCCGGCA 62.887 63.158 10.77 0.00 35.15 5.69
1083 1103 1.336517 CGCGTCTCCTTGAACTTGGTA 60.337 52.381 0.00 0.00 0.00 3.25
1292 1312 3.760035 GGAGCCAAGCGGAGTCGA 61.760 66.667 0.00 0.00 39.00 4.20
1451 1471 3.941836 GCGCGGATTGGCTACAGC 61.942 66.667 8.83 0.00 41.14 4.40
1509 1529 1.601419 TTCCGTCGCCAGAAGGTAGG 61.601 60.000 0.86 0.00 44.76 3.18
1558 1581 4.122776 GACATATCCAGCTCGAACATGTT 58.877 43.478 11.78 11.78 0.00 2.71
1823 1883 1.139058 AGAACTCCGTCTGTTTGCAGT 59.861 47.619 0.00 0.00 43.05 4.40
2002 2072 7.604164 ACGTCTCTCTGATTAACAAATTGATGT 59.396 33.333 0.00 0.00 34.24 3.06
2005 2075 6.368791 CCACGTCTCTCTGATTAACAAATTGA 59.631 38.462 0.00 0.00 0.00 2.57
2043 2114 2.689983 GGCCACATCTTCCGAATCAATT 59.310 45.455 0.00 0.00 0.00 2.32
2044 2115 2.092212 AGGCCACATCTTCCGAATCAAT 60.092 45.455 5.01 0.00 0.00 2.57
2045 2116 1.281867 AGGCCACATCTTCCGAATCAA 59.718 47.619 5.01 0.00 0.00 2.57
2046 2117 0.911769 AGGCCACATCTTCCGAATCA 59.088 50.000 5.01 0.00 0.00 2.57
2208 2300 6.594744 TGACACATCACCTATATGCATCTTT 58.405 36.000 0.19 0.00 0.00 2.52
2235 2327 3.312736 TGCTCCAAGAGGAAAAAGGTT 57.687 42.857 0.00 0.00 45.19 3.50
2273 2366 6.223852 CACACTAGTCATTTCCACAGTTACT 58.776 40.000 0.00 0.00 0.00 2.24
2276 2369 3.815401 GCACACTAGTCATTTCCACAGTT 59.185 43.478 0.00 0.00 0.00 3.16
2286 2379 5.649395 ACAATTATTGCAGCACACTAGTCAT 59.351 36.000 4.68 0.00 0.00 3.06
2365 2458 3.226777 CAACCCATTTACCACCAGTTCA 58.773 45.455 0.00 0.00 0.00 3.18
2374 2467 5.891551 AGGAACATGATACAACCCATTTACC 59.108 40.000 0.00 0.00 0.00 2.85
2447 2540 2.028203 AGGAAACCCATGAAATTTGGCG 60.028 45.455 0.00 0.00 32.60 5.69
2448 2541 3.007831 TCAGGAAACCCATGAAATTTGGC 59.992 43.478 0.00 0.00 32.60 4.52
2449 2542 4.888326 TCAGGAAACCCATGAAATTTGG 57.112 40.909 0.00 0.00 0.00 3.28
2452 2545 3.198417 GGCATCAGGAAACCCATGAAATT 59.802 43.478 0.00 0.00 0.00 1.82
2476 2569 0.594602 GCATGCAGCAGTCTTCACAA 59.405 50.000 14.21 0.00 44.79 3.33
2528 2621 1.372997 GATCCACACACACGCGTCT 60.373 57.895 9.86 0.00 0.00 4.18
2532 2625 2.153913 GTGAGATCCACACACACGC 58.846 57.895 13.46 0.00 45.03 5.34
2540 2633 4.003648 CCTAAACAACCAGTGAGATCCAC 58.996 47.826 6.29 6.29 46.03 4.02
2541 2634 3.559171 GCCTAAACAACCAGTGAGATCCA 60.559 47.826 0.00 0.00 0.00 3.41
2542 2635 3.010420 GCCTAAACAACCAGTGAGATCC 58.990 50.000 0.00 0.00 0.00 3.36
2543 2636 3.686726 CAGCCTAAACAACCAGTGAGATC 59.313 47.826 0.00 0.00 0.00 2.75
2544 2637 3.560025 CCAGCCTAAACAACCAGTGAGAT 60.560 47.826 0.00 0.00 0.00 2.75
2545 2638 2.224523 CCAGCCTAAACAACCAGTGAGA 60.225 50.000 0.00 0.00 0.00 3.27
2546 2639 2.154462 CCAGCCTAAACAACCAGTGAG 58.846 52.381 0.00 0.00 0.00 3.51
2547 2640 1.493022 ACCAGCCTAAACAACCAGTGA 59.507 47.619 0.00 0.00 0.00 3.41
2548 2641 1.981256 ACCAGCCTAAACAACCAGTG 58.019 50.000 0.00 0.00 0.00 3.66
2549 2642 2.306847 CAACCAGCCTAAACAACCAGT 58.693 47.619 0.00 0.00 0.00 4.00
2550 2643 1.000274 GCAACCAGCCTAAACAACCAG 60.000 52.381 0.00 0.00 37.23 4.00
2551 2644 1.036707 GCAACCAGCCTAAACAACCA 58.963 50.000 0.00 0.00 37.23 3.67
2552 2645 1.000274 CTGCAACCAGCCTAAACAACC 60.000 52.381 0.00 0.00 44.83 3.77
2553 2646 1.681264 ACTGCAACCAGCCTAAACAAC 59.319 47.619 0.00 0.00 43.02 3.32
2554 2647 1.680735 CACTGCAACCAGCCTAAACAA 59.319 47.619 0.00 0.00 43.02 2.83
2555 2648 1.317613 CACTGCAACCAGCCTAAACA 58.682 50.000 0.00 0.00 43.02 2.83
2556 2649 0.598065 CCACTGCAACCAGCCTAAAC 59.402 55.000 0.00 0.00 43.02 2.01
2557 2650 0.539438 CCCACTGCAACCAGCCTAAA 60.539 55.000 0.00 0.00 43.02 1.85
2558 2651 1.074775 CCCACTGCAACCAGCCTAA 59.925 57.895 0.00 0.00 43.02 2.69
2559 2652 2.756400 CCCACTGCAACCAGCCTA 59.244 61.111 0.00 0.00 43.02 3.93
2560 2653 4.290622 CCCCACTGCAACCAGCCT 62.291 66.667 0.00 0.00 43.02 4.58
2561 2654 2.499303 ATACCCCACTGCAACCAGCC 62.499 60.000 0.00 0.00 43.02 4.85
2562 2655 0.611896 AATACCCCACTGCAACCAGC 60.612 55.000 0.00 0.00 43.02 4.85
2563 2656 2.799126 TAATACCCCACTGCAACCAG 57.201 50.000 0.00 0.00 44.80 4.00
2564 2657 5.609284 AGTATATAATACCCCACTGCAACCA 59.391 40.000 0.00 0.00 0.00 3.67
2565 2658 6.123045 AGTATATAATACCCCACTGCAACC 57.877 41.667 0.00 0.00 0.00 3.77
2566 2659 5.867716 CGAGTATATAATACCCCACTGCAAC 59.132 44.000 0.00 0.00 0.00 4.17
2567 2660 5.541101 ACGAGTATATAATACCCCACTGCAA 59.459 40.000 0.00 0.00 0.00 4.08
2568 2661 5.081728 ACGAGTATATAATACCCCACTGCA 58.918 41.667 0.00 0.00 0.00 4.41
2569 2662 5.656213 ACGAGTATATAATACCCCACTGC 57.344 43.478 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.