Multiple sequence alignment - TraesCS5B01G050500

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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 TraesCS5B01G050500 chr5B 100.000 2611 0 0 1 2611 55494080 55491470 0.000000e+00 4822.0
1 TraesCS5B01G050500 chr7A 89.762 1680 138 15 179 1844 75125806 75127465 0.000000e+00 2119.0
2 TraesCS5B01G050500 chr7A 88.816 304 31 2 1907 2210 75127613 75127913 1.140000e-98 370.0
3 TraesCS5B01G050500 chr7A 84.150 347 33 9 2200 2526 75127933 75128277 1.510000e-82 316.0
4 TraesCS5B01G050500 chr7A 90.164 183 17 1 1 183 75085396 75085577 1.210000e-58 237.0
5 TraesCS5B01G050500 chr2B 93.636 1320 60 10 532 1847 706191093 706189794 0.000000e+00 1951.0
6 TraesCS5B01G050500 chr2B 95.688 487 18 2 1 485 706191584 706191099 0.000000e+00 780.0
7 TraesCS5B01G050500 chr2B 86.047 258 12 10 2278 2516 706176879 706176627 3.330000e-64 255.0
8 TraesCS5B01G050500 chr2B 96.825 63 2 0 1844 1906 706184260 706184198 3.550000e-19 106.0
9 TraesCS5B01G050500 chr2B 96.774 62 1 1 2149 2210 706184027 706183967 4.600000e-18 102.0
10 TraesCS5B01G050500 chr1A 95.461 749 28 3 413 1155 590714258 590713510 0.000000e+00 1190.0
11 TraesCS5B01G050500 chr1A 92.992 371 13 7 1844 2210 590713064 590712703 1.780000e-146 529.0
12 TraesCS5B01G050500 chr1A 90.778 347 11 10 2200 2526 590712680 590712335 6.630000e-121 444.0
13 TraesCS5B01G050500 chr1A 89.231 325 16 3 1373 1694 590713514 590713206 3.150000e-104 388.0
14 TraesCS5B01G050500 chr1A 97.895 95 2 0 1753 1847 590713208 590713114 5.780000e-37 165.0
15 TraesCS5B01G050500 chr1D 77.284 405 73 13 236 624 412176371 412176772 1.220000e-53 220.0
16 TraesCS5B01G050500 chr3B 77.099 393 76 11 238 620 819939539 819939151 5.660000e-52 215.0
17 TraesCS5B01G050500 chr3B 75.342 219 39 12 1639 1847 43897800 43897587 9.950000e-15 91.6
18 TraesCS5B01G050500 chr3B 75.342 219 39 12 1639 1847 44004188 44003975 9.950000e-15 91.6
19 TraesCS5B01G050500 chr2A 76.263 396 82 8 238 623 676230522 676230915 1.580000e-47 200.0
20 TraesCS5B01G050500 chr6B 74.623 398 91 7 238 626 643631678 643632074 1.610000e-37 167.0
21 TraesCS5B01G050500 chr7D 86.517 89 12 0 1756 1844 14240287 14240375 5.950000e-17 99.0
22 TraesCS5B01G050500 chr5A 85.393 89 13 0 1756 1844 512583906 512583818 2.770000e-15 93.5
23 TraesCS5B01G050500 chr4A 85.393 89 13 0 1756 1844 702011456 702011368 2.770000e-15 93.5
24 TraesCS5B01G050500 chr4A 75.225 222 40 12 1633 1844 689633491 689633707 9.950000e-15 91.6
25 TraesCS5B01G050500 chr4A 91.304 46 4 0 2563 2608 695876703 695876658 2.170000e-06 63.9
26 TraesCS5B01G050500 chr4A 92.683 41 3 0 2563 2603 695812276 695812236 2.810000e-05 60.2
27 TraesCS5B01G050500 chr4B 95.918 49 2 0 2563 2611 468062662 468062614 2.150000e-11 80.5
28 TraesCS5B01G050500 chr3A 93.878 49 3 0 2563 2611 642016577 642016529 1.000000e-09 75.0


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 TraesCS5B01G050500 chr5B 55491470 55494080 2610 True 4822.0 4822 100.0000 1 2611 1 chr5B.!!$R1 2610
1 TraesCS5B01G050500 chr7A 75125806 75128277 2471 False 935.0 2119 87.5760 179 2526 3 chr7A.!!$F2 2347
2 TraesCS5B01G050500 chr2B 706189794 706191584 1790 True 1365.5 1951 94.6620 1 1847 2 chr2B.!!$R3 1846
3 TraesCS5B01G050500 chr1A 590712335 590714258 1923 True 543.2 1190 93.2714 413 2526 5 chr1A.!!$R1 2113

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
514 517 0.247814 GCGCGGATCACATGTTGAAG 60.248 55.0 8.83 0.0 37.92 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1729 0.179012 GTTCGTGGTTTCTTGGGGGA 60.179 55.0 0.0 0.0 0.0 4.81 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
22 23 5.673337 TCAACTTAGTGCAATTCTGTGAC 57.327 39.130 0.00 0.00 0.00 3.67
23 24 5.122519 TCAACTTAGTGCAATTCTGTGACA 58.877 37.500 0.00 0.00 0.00 3.58
78 79 7.331934 TCTGATCTGTGTAAGCAAACTGATTAC 59.668 37.037 7.65 7.65 46.16 1.89
91 92 5.695851 AACTGATTACAACTGGCAGAAAG 57.304 39.130 23.66 12.43 0.00 2.62
97 98 2.301346 ACAACTGGCAGAAAGAACAGG 58.699 47.619 23.66 1.95 35.34 4.00
114 115 3.966154 ACAGGCATTAGACGATTCGTAG 58.034 45.455 12.40 1.66 41.37 3.51
128 129 6.870517 ACGATTCGTAGTGTTGAACTAAAAC 58.129 36.000 10.53 0.00 43.08 2.43
310 311 3.416156 AGTGACTTCCAAGCTGAATTCC 58.584 45.455 2.27 0.00 0.00 3.01
355 358 1.415672 AAGACGAGTTTGGGAGGGCA 61.416 55.000 0.00 0.00 0.00 5.36
411 414 4.408182 AGCACCCATACATGACTTAGAC 57.592 45.455 0.00 0.00 0.00 2.59
460 463 7.264947 CAAAACCATACTTGAAAGGTGTTCTT 58.735 34.615 0.00 0.00 37.28 2.52
485 488 3.374745 GCCAAGATGACAAACACACAAG 58.625 45.455 0.00 0.00 0.00 3.16
486 489 3.066621 GCCAAGATGACAAACACACAAGA 59.933 43.478 0.00 0.00 0.00 3.02
489 492 5.392919 CCAAGATGACAAACACACAAGACAA 60.393 40.000 0.00 0.00 0.00 3.18
491 494 3.463533 TGACAAACACACAAGACAACG 57.536 42.857 0.00 0.00 0.00 4.10
492 495 3.067833 TGACAAACACACAAGACAACGA 58.932 40.909 0.00 0.00 0.00 3.85
493 496 3.124466 TGACAAACACACAAGACAACGAG 59.876 43.478 0.00 0.00 0.00 4.18
494 497 3.331150 ACAAACACACAAGACAACGAGA 58.669 40.909 0.00 0.00 0.00 4.04
495 498 3.370978 ACAAACACACAAGACAACGAGAG 59.629 43.478 0.00 0.00 0.00 3.20
496 499 1.571919 ACACACAAGACAACGAGAGC 58.428 50.000 0.00 0.00 0.00 4.09
497 500 0.504384 CACACAAGACAACGAGAGCG 59.496 55.000 0.00 0.00 44.79 5.03
498 501 1.215655 ACACAAGACAACGAGAGCGC 61.216 55.000 0.00 0.00 42.48 5.92
499 502 2.016704 ACAAGACAACGAGAGCGCG 61.017 57.895 0.00 0.00 42.48 6.86
500 503 2.430921 AAGACAACGAGAGCGCGG 60.431 61.111 8.83 0.00 42.48 6.46
501 504 2.916052 AAGACAACGAGAGCGCGGA 61.916 57.895 8.83 0.00 42.48 5.54
502 505 2.202623 GACAACGAGAGCGCGGAT 60.203 61.111 8.83 0.00 42.48 4.18
503 506 2.202623 ACAACGAGAGCGCGGATC 60.203 61.111 8.83 0.00 42.48 3.36
504 507 2.202610 CAACGAGAGCGCGGATCA 60.203 61.111 8.83 0.00 42.48 2.92
505 508 2.202623 AACGAGAGCGCGGATCAC 60.203 61.111 8.83 0.00 42.48 3.06
506 509 2.989881 AACGAGAGCGCGGATCACA 61.990 57.895 8.83 0.00 42.48 3.58
507 510 2.026734 CGAGAGCGCGGATCACAT 59.973 61.111 8.83 0.00 0.00 3.21
508 511 2.298629 CGAGAGCGCGGATCACATG 61.299 63.158 8.83 0.00 0.00 3.21
509 512 1.227089 GAGAGCGCGGATCACATGT 60.227 57.895 8.83 0.00 0.00 3.21
510 513 0.807667 GAGAGCGCGGATCACATGTT 60.808 55.000 8.83 0.00 0.00 2.71
511 514 1.086067 AGAGCGCGGATCACATGTTG 61.086 55.000 8.83 0.00 0.00 3.33
512 515 1.079197 AGCGCGGATCACATGTTGA 60.079 52.632 8.83 0.00 39.11 3.18
513 516 0.673333 AGCGCGGATCACATGTTGAA 60.673 50.000 8.83 0.00 37.92 2.69
514 517 0.247814 GCGCGGATCACATGTTGAAG 60.248 55.000 8.83 0.00 37.92 3.02
515 518 1.358877 CGCGGATCACATGTTGAAGA 58.641 50.000 0.00 0.00 37.92 2.87
516 519 1.061131 CGCGGATCACATGTTGAAGAC 59.939 52.381 0.00 0.00 37.92 3.01
517 520 2.076100 GCGGATCACATGTTGAAGACA 58.924 47.619 0.00 0.00 43.71 3.41
519 522 3.242543 GCGGATCACATGTTGAAGACATC 60.243 47.826 0.00 0.00 45.88 3.06
520 523 4.186926 CGGATCACATGTTGAAGACATCT 58.813 43.478 0.00 0.00 45.88 2.90
521 524 4.269603 CGGATCACATGTTGAAGACATCTC 59.730 45.833 0.00 0.00 45.88 2.75
522 525 4.574013 GGATCACATGTTGAAGACATCTCC 59.426 45.833 0.00 0.00 45.88 3.71
523 526 4.897509 TCACATGTTGAAGACATCTCCT 57.102 40.909 0.00 0.00 45.88 3.69
524 527 4.572909 TCACATGTTGAAGACATCTCCTG 58.427 43.478 0.00 0.00 45.88 3.86
525 528 3.126514 CACATGTTGAAGACATCTCCTGC 59.873 47.826 0.00 0.00 45.88 4.85
526 529 3.008813 ACATGTTGAAGACATCTCCTGCT 59.991 43.478 0.00 0.00 45.88 4.24
527 530 4.223700 ACATGTTGAAGACATCTCCTGCTA 59.776 41.667 0.00 0.00 45.88 3.49
528 531 4.462508 TGTTGAAGACATCTCCTGCTAG 57.537 45.455 0.00 0.00 32.00 3.42
529 532 3.194062 GTTGAAGACATCTCCTGCTAGC 58.806 50.000 8.10 8.10 0.00 3.42
530 533 1.759445 TGAAGACATCTCCTGCTAGCC 59.241 52.381 13.29 0.00 0.00 3.93
673 717 3.441500 TCAGACACTAGCTCTCCTTCA 57.558 47.619 0.00 0.00 0.00 3.02
687 731 2.368875 CTCCTTCACACCACTACCAAGT 59.631 50.000 0.00 0.00 35.91 3.16
701 745 7.236225 ACCACTACCAAGTACCTACTTTTGTAT 59.764 37.037 0.00 0.00 43.57 2.29
858 904 3.004752 AGGAATGGCTACAATGTCACC 57.995 47.619 0.00 0.00 0.00 4.02
912 958 5.750650 ACAAACAATAATGCAGCAAAAAGC 58.249 33.333 0.00 0.00 46.19 3.51
980 1026 2.810274 AGTCAGAGTTTACGTGCGAGTA 59.190 45.455 0.00 0.00 0.00 2.59
1000 1046 3.610040 ATGGACAATTCGAGCACACTA 57.390 42.857 0.00 0.00 0.00 2.74
1085 1135 6.603095 AGCTTTGTTGTTAAGAGATTTAGCG 58.397 36.000 0.00 0.00 0.00 4.26
1117 1167 4.674281 AATTGAGGTCGGAGAAGATACC 57.326 45.455 0.00 0.00 39.69 2.73
1211 1262 0.768622 TGAAACGGTGGACCAAGGAT 59.231 50.000 0.00 0.00 35.14 3.24
1377 1429 1.608055 TGTGTTTGCTGGTCTGGATG 58.392 50.000 0.00 0.00 0.00 3.51
1418 1470 4.187694 CACCATTAGCAGAGAAGAGGAAC 58.812 47.826 0.00 0.00 0.00 3.62
1429 1481 1.878088 GAAGAGGAACGGTTTGGGTTC 59.122 52.381 0.00 0.00 42.32 3.62
1437 1489 1.452801 GGTTTGGGTTCCGAGGACA 59.547 57.895 0.00 0.00 0.00 4.02
1599 1657 0.318955 CAGCAAGGGAAAACGCCTTG 60.319 55.000 12.79 12.79 42.42 3.61
1614 1672 1.423395 CCTTGCGAGTGTCTGAGAAC 58.577 55.000 0.00 0.00 0.00 3.01
1619 1677 0.169230 CGAGTGTCTGAGAACGAGGG 59.831 60.000 0.00 0.00 0.00 4.30
1671 1729 4.115199 GCCCGGACAGGAGGCATT 62.115 66.667 0.73 0.00 46.34 3.56
1875 1989 1.815613 TGTTCCGGCCATACAATGTTG 59.184 47.619 2.24 0.00 0.00 3.33
1923 2070 5.197224 TGAATCTTCATGGGTTGATCCTT 57.803 39.130 0.00 0.00 33.34 3.36
1971 2118 1.772182 CGATACTTCTCCATCGTGCC 58.228 55.000 0.00 0.00 39.30 5.01
1977 2124 0.828022 TTCTCCATCGTGCCGGTTAT 59.172 50.000 1.90 0.00 0.00 1.89
2026 2173 1.576618 CGCGCACCGTGTTATTTCG 60.577 57.895 8.75 0.00 32.40 3.46
2033 2180 4.201353 CGCACCGTGTTATTTCGAAATTTG 60.201 41.667 27.10 12.90 0.00 2.32
2038 2185 7.799447 CACCGTGTTATTTCGAAATTTGAACTA 59.201 33.333 27.10 13.36 0.00 2.24
2058 2205 7.383029 TGAACTACTGGTTGAGTAAATGTAACG 59.617 37.037 0.00 0.00 36.69 3.18
2088 2235 2.836187 GGTAGTTGGGGTGGCACCA 61.836 63.158 35.69 16.03 41.02 4.17
2103 2250 5.049749 GGTGGCACCATGTTATTTCAAAAAC 60.050 40.000 31.26 0.00 38.42 2.43
2121 2268 0.396435 ACTGAACTGCCGGTTGATGA 59.604 50.000 1.90 0.00 38.41 2.92
2216 2399 2.579738 GGAGGTCTGAAGGCGGTC 59.420 66.667 0.00 0.00 0.00 4.79
2221 2404 3.760035 TCTGAAGGCGGTCGCTCC 61.760 66.667 15.04 5.47 41.60 4.70
2263 2446 3.007614 AGGTACGACTGCTTGTGGTAATT 59.992 43.478 6.80 0.00 40.59 1.40
2275 2458 6.491745 TGCTTGTGGTAATTGTTTCCTTATGA 59.508 34.615 0.00 0.00 0.00 2.15
2379 2562 0.595095 GTGGAGCAGGAACAAGCAAG 59.405 55.000 0.00 0.00 34.11 4.01
2442 2645 2.008268 ATAGGTGGACGGCCGTTACG 62.008 60.000 34.65 4.69 36.79 3.18
2443 2646 4.054825 GGTGGACGGCCGTTACGA 62.055 66.667 34.65 15.46 36.79 3.43
2526 2729 1.138247 GGTCCGCACCTACAGTACG 59.862 63.158 0.00 0.00 40.00 3.67
2527 2730 1.515736 GTCCGCACCTACAGTACGC 60.516 63.158 0.00 0.00 33.67 4.42
2528 2731 2.578713 CCGCACCTACAGTACGCG 60.579 66.667 3.53 3.53 39.79 6.01
2529 2732 2.578713 CGCACCTACAGTACGCGG 60.579 66.667 12.47 0.00 37.27 6.46
2530 2733 2.202703 GCACCTACAGTACGCGGG 60.203 66.667 12.47 1.69 0.00 6.13
2531 2734 2.202703 CACCTACAGTACGCGGGC 60.203 66.667 12.47 1.85 0.00 6.13
2532 2735 3.455469 ACCTACAGTACGCGGGCC 61.455 66.667 12.47 0.00 0.00 5.80
2533 2736 3.145551 CCTACAGTACGCGGGCCT 61.146 66.667 12.47 0.00 0.00 5.19
2534 2737 2.104331 CTACAGTACGCGGGCCTG 59.896 66.667 12.47 15.33 0.00 4.85
2535 2738 3.426117 CTACAGTACGCGGGCCTGG 62.426 68.421 15.02 6.08 0.00 4.45
2547 2750 2.280079 GCCTGGGCTGGCCTTATT 59.720 61.111 21.72 0.00 46.82 1.40
2548 2751 1.381735 GCCTGGGCTGGCCTTATTT 60.382 57.895 21.72 0.00 46.82 1.40
2549 2752 0.977627 GCCTGGGCTGGCCTTATTTT 60.978 55.000 21.72 0.00 46.82 1.82
2550 2753 1.687996 GCCTGGGCTGGCCTTATTTTA 60.688 52.381 21.72 0.00 46.82 1.52
2551 2754 2.310538 CCTGGGCTGGCCTTATTTTAG 58.689 52.381 21.72 8.09 36.10 1.85
2552 2755 2.358195 CCTGGGCTGGCCTTATTTTAGT 60.358 50.000 21.72 0.00 36.10 2.24
2553 2756 3.117663 CCTGGGCTGGCCTTATTTTAGTA 60.118 47.826 21.72 0.00 36.10 1.82
2554 2757 3.883489 CTGGGCTGGCCTTATTTTAGTAC 59.117 47.826 21.72 0.00 36.10 2.73
2555 2758 2.876550 GGGCTGGCCTTATTTTAGTACG 59.123 50.000 13.80 0.00 36.10 3.67
2556 2759 3.432608 GGGCTGGCCTTATTTTAGTACGA 60.433 47.826 13.80 0.00 36.10 3.43
2557 2760 4.386711 GGCTGGCCTTATTTTAGTACGAT 58.613 43.478 3.32 0.00 0.00 3.73
2558 2761 5.511888 GGGCTGGCCTTATTTTAGTACGATA 60.512 44.000 13.80 0.00 36.10 2.92
2559 2762 6.171213 GGCTGGCCTTATTTTAGTACGATAT 58.829 40.000 3.32 0.00 0.00 1.63
2560 2763 7.325694 GGCTGGCCTTATTTTAGTACGATATA 58.674 38.462 3.32 0.00 0.00 0.86
2561 2764 7.277319 GGCTGGCCTTATTTTAGTACGATATAC 59.723 40.741 3.32 0.00 0.00 1.47
2562 2765 7.816031 GCTGGCCTTATTTTAGTACGATATACA 59.184 37.037 3.32 0.00 0.00 2.29
2563 2766 9.871238 CTGGCCTTATTTTAGTACGATATACAT 57.129 33.333 3.32 0.00 0.00 2.29
2584 2787 9.878599 ATACATTTAAAGACATTATAACTGCGC 57.121 29.630 0.00 0.00 0.00 6.09
2585 2788 7.757526 ACATTTAAAGACATTATAACTGCGCA 58.242 30.769 10.98 10.98 0.00 6.09
2586 2789 7.910162 ACATTTAAAGACATTATAACTGCGCAG 59.090 33.333 34.89 34.89 0.00 5.18
2587 2790 6.978343 TTAAAGACATTATAACTGCGCAGT 57.022 33.333 36.44 36.44 44.94 4.40
2597 2800 1.797025 ACTGCGCAGTTTTCCTACTC 58.203 50.000 36.44 0.00 38.83 2.59
2598 2801 1.344763 ACTGCGCAGTTTTCCTACTCT 59.655 47.619 36.44 10.21 38.83 3.24
2599 2802 1.996191 CTGCGCAGTTTTCCTACTCTC 59.004 52.381 29.24 0.00 0.00 3.20
2600 2803 1.618837 TGCGCAGTTTTCCTACTCTCT 59.381 47.619 5.66 0.00 0.00 3.10
2601 2804 2.263945 GCGCAGTTTTCCTACTCTCTC 58.736 52.381 0.30 0.00 0.00 3.20
2602 2805 2.352814 GCGCAGTTTTCCTACTCTCTCA 60.353 50.000 0.30 0.00 0.00 3.27
2603 2806 3.246619 CGCAGTTTTCCTACTCTCTCAC 58.753 50.000 0.00 0.00 0.00 3.51
2604 2807 3.246619 GCAGTTTTCCTACTCTCTCACG 58.753 50.000 0.00 0.00 0.00 4.35
2605 2808 3.246619 CAGTTTTCCTACTCTCTCACGC 58.753 50.000 0.00 0.00 0.00 5.34
2606 2809 2.231721 AGTTTTCCTACTCTCTCACGCC 59.768 50.000 0.00 0.00 0.00 5.68
2607 2810 1.919240 TTTCCTACTCTCTCACGCCA 58.081 50.000 0.00 0.00 0.00 5.69
2608 2811 1.174783 TTCCTACTCTCTCACGCCAC 58.825 55.000 0.00 0.00 0.00 5.01
2609 2812 0.328592 TCCTACTCTCTCACGCCACT 59.671 55.000 0.00 0.00 0.00 4.00
2610 2813 1.178276 CCTACTCTCTCACGCCACTT 58.822 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.898320 TCATACTGTCACAGAATTGCACT 58.102 39.130 13.14 0.00 35.18 4.40
22 23 8.554528 CATGGTTCTGCTAACTAATTCATACTG 58.445 37.037 3.13 0.00 0.00 2.74
23 24 7.716998 CCATGGTTCTGCTAACTAATTCATACT 59.283 37.037 2.57 0.00 0.00 2.12
78 79 1.000938 GCCTGTTCTTTCTGCCAGTTG 60.001 52.381 0.00 0.00 0.00 3.16
83 84 3.127721 GTCTAATGCCTGTTCTTTCTGCC 59.872 47.826 0.00 0.00 0.00 4.85
91 92 3.187700 ACGAATCGTCTAATGCCTGTTC 58.812 45.455 0.96 0.00 33.69 3.18
97 98 4.796830 TCAACACTACGAATCGTCTAATGC 59.203 41.667 13.00 0.00 41.54 3.56
114 115 6.759827 TCAGTCCAGTAGTTTTAGTTCAACAC 59.240 38.462 0.00 0.00 0.00 3.32
128 129 9.613428 TCCAAAAATACATATTCAGTCCAGTAG 57.387 33.333 0.00 0.00 0.00 2.57
355 358 3.590630 ACTTATCCAGCAGCATATCCCAT 59.409 43.478 0.00 0.00 0.00 4.00
411 414 4.572389 CCCACTTCATTCTGATTTCGTAGG 59.428 45.833 0.00 0.00 0.00 3.18
460 463 1.028130 TGTTTGTCATCTTGGCGCAA 58.972 45.000 10.83 0.00 0.00 4.85
485 488 2.202623 ATCCGCGCTCTCGTTGTC 60.203 61.111 5.56 0.00 38.14 3.18
486 489 2.202623 GATCCGCGCTCTCGTTGT 60.203 61.111 5.56 0.00 38.14 3.32
489 492 2.775856 ATGTGATCCGCGCTCTCGT 61.776 57.895 5.56 0.00 38.14 4.18
491 494 0.807667 AACATGTGATCCGCGCTCTC 60.808 55.000 5.56 1.07 0.00 3.20
492 495 1.086067 CAACATGTGATCCGCGCTCT 61.086 55.000 5.56 0.00 0.00 4.09
493 496 1.083806 TCAACATGTGATCCGCGCTC 61.084 55.000 5.56 0.00 0.00 5.03
494 497 0.673333 TTCAACATGTGATCCGCGCT 60.673 50.000 5.56 0.00 35.70 5.92
495 498 0.247814 CTTCAACATGTGATCCGCGC 60.248 55.000 0.00 0.00 35.70 6.86
496 499 1.061131 GTCTTCAACATGTGATCCGCG 59.939 52.381 0.00 0.00 35.70 6.46
497 500 2.076100 TGTCTTCAACATGTGATCCGC 58.924 47.619 0.00 0.00 35.70 5.54
507 510 3.368843 GCTAGCAGGAGATGTCTTCAACA 60.369 47.826 10.63 0.00 43.51 3.33
508 511 3.194062 GCTAGCAGGAGATGTCTTCAAC 58.806 50.000 10.63 0.00 0.00 3.18
509 512 2.169352 GGCTAGCAGGAGATGTCTTCAA 59.831 50.000 18.24 0.00 0.00 2.69
510 513 1.759445 GGCTAGCAGGAGATGTCTTCA 59.241 52.381 18.24 0.00 0.00 3.02
511 514 1.069978 GGGCTAGCAGGAGATGTCTTC 59.930 57.143 18.24 0.00 0.00 2.87
512 515 1.127343 GGGCTAGCAGGAGATGTCTT 58.873 55.000 18.24 0.00 0.00 3.01
513 516 1.112315 CGGGCTAGCAGGAGATGTCT 61.112 60.000 18.24 0.00 0.00 3.41
514 517 1.109920 TCGGGCTAGCAGGAGATGTC 61.110 60.000 18.24 0.00 0.00 3.06
515 518 0.470833 ATCGGGCTAGCAGGAGATGT 60.471 55.000 18.24 0.00 0.00 3.06
516 519 0.037512 CATCGGGCTAGCAGGAGATG 60.038 60.000 18.24 18.82 0.00 2.90
517 520 1.825281 GCATCGGGCTAGCAGGAGAT 61.825 60.000 18.24 11.75 40.25 2.75
518 521 2.502492 GCATCGGGCTAGCAGGAGA 61.502 63.158 18.24 9.90 40.25 3.71
519 522 2.030262 GCATCGGGCTAGCAGGAG 59.970 66.667 18.24 4.36 40.25 3.69
520 523 2.763710 TGCATCGGGCTAGCAGGA 60.764 61.111 18.24 13.13 45.15 3.86
521 524 2.590007 GTGCATCGGGCTAGCAGG 60.590 66.667 18.24 7.52 45.15 4.85
522 525 0.816825 AATGTGCATCGGGCTAGCAG 60.817 55.000 18.24 10.13 45.15 4.24
523 526 0.394216 AAATGTGCATCGGGCTAGCA 60.394 50.000 18.24 0.00 45.15 3.49
524 527 0.740737 AAAATGTGCATCGGGCTAGC 59.259 50.000 6.04 6.04 45.15 3.42
525 528 1.003545 CGAAAATGTGCATCGGGCTAG 60.004 52.381 0.00 0.00 45.15 3.42
526 529 1.013596 CGAAAATGTGCATCGGGCTA 58.986 50.000 0.00 0.00 45.15 3.93
527 530 0.960364 ACGAAAATGTGCATCGGGCT 60.960 50.000 11.03 0.00 45.15 5.19
528 531 0.109319 AACGAAAATGTGCATCGGGC 60.109 50.000 11.03 0.00 40.71 6.13
529 532 2.223249 CCTAACGAAAATGTGCATCGGG 60.223 50.000 11.03 0.00 40.71 5.14
530 533 2.791158 GCCTAACGAAAATGTGCATCGG 60.791 50.000 11.03 0.00 40.71 4.18
673 717 4.123729 AGTAGGTACTTGGTAGTGGTGT 57.876 45.455 0.00 0.00 41.75 4.16
707 751 7.806487 CACAGAGTTCTGATGTTTTAGTACGTA 59.194 37.037 15.63 0.00 46.59 3.57
709 755 6.861572 TCACAGAGTTCTGATGTTTTAGTACG 59.138 38.462 15.63 0.00 46.59 3.67
858 904 3.146066 CCTCCTCATCTTCTCTACCTCG 58.854 54.545 0.00 0.00 0.00 4.63
912 958 2.414481 CACAACTCTGCTCCATTTCTCG 59.586 50.000 0.00 0.00 0.00 4.04
980 1026 2.479566 AGTGTGCTCGAATTGTCCAT 57.520 45.000 0.00 0.00 0.00 3.41
1000 1046 2.492088 GCACATGGCAGCATATCATCAT 59.508 45.455 0.00 0.00 43.97 2.45
1085 1135 4.758165 TCCGACCTCAATTTCAAACTAACC 59.242 41.667 0.00 0.00 0.00 2.85
1117 1167 5.278604 CCAGGAGAACAAGGTTTTAAAACG 58.721 41.667 21.58 12.46 39.77 3.60
1337 1389 5.014858 ACATCCTTGAATGATTCTGCACTT 58.985 37.500 6.73 0.00 0.00 3.16
1353 1405 2.233271 CAGACCAGCAAACACATCCTT 58.767 47.619 0.00 0.00 0.00 3.36
1429 1481 1.600636 TTTGCCAAGCTGTCCTCGG 60.601 57.895 0.00 0.00 0.00 4.63
1468 1520 1.642762 AGGCAACCTCTCCATTTCCAT 59.357 47.619 0.00 0.00 37.17 3.41
1502 1554 3.580022 CACTATCCCTATGGTCAGCATCA 59.420 47.826 0.00 0.00 0.00 3.07
1599 1657 0.455295 CCTCGTTCTCAGACACTCGC 60.455 60.000 0.00 0.00 0.00 5.03
1604 1662 1.464734 CTAGCCCTCGTTCTCAGACA 58.535 55.000 0.00 0.00 0.00 3.41
1614 1672 2.054232 TCTACAGAACCTAGCCCTCG 57.946 55.000 0.00 0.00 0.00 4.63
1619 1677 1.831736 TGGCCTTCTACAGAACCTAGC 59.168 52.381 3.32 0.00 0.00 3.42
1668 1726 0.887933 CGTGGTTTCTTGGGGGAATG 59.112 55.000 0.00 0.00 0.00 2.67
1671 1729 0.179012 GTTCGTGGTTTCTTGGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
1844 1905 3.904717 TGGCCGGAACATAACCATTATT 58.095 40.909 5.05 0.00 0.00 1.40
1875 1989 8.462016 AGTCATTTTTAAGATGCAGATAACCAC 58.538 33.333 0.00 0.00 0.00 4.16
1923 2070 3.981071 ACAAGCAAGGATAGCACTGTA 57.019 42.857 0.00 0.00 31.29 2.74
2033 2180 7.383300 ACGTTACATTTACTCAACCAGTAGTTC 59.617 37.037 0.00 0.00 38.90 3.01
2038 2185 5.603596 TCACGTTACATTTACTCAACCAGT 58.396 37.500 0.00 0.00 39.41 4.00
2058 2205 3.056035 CCCCAACTACCTGTCTTACTCAC 60.056 52.174 0.00 0.00 0.00 3.51
2088 2235 6.420604 CGGCAGTTCAGTTTTTGAAATAACAT 59.579 34.615 0.00 0.00 46.85 2.71
2103 2250 1.742761 ATCATCAACCGGCAGTTCAG 58.257 50.000 0.00 0.00 36.18 3.02
2121 2268 3.048600 TGCTGAAGCCAGGAAGGTATAT 58.951 45.455 0.00 0.00 37.82 0.86
2221 2404 0.788391 GAAACTATAATCCGCCGCCG 59.212 55.000 0.00 0.00 0.00 6.46
2263 2446 7.327214 AGCAACAAAACTTTCATAAGGAAACA 58.673 30.769 0.00 0.00 40.51 2.83
2275 2458 3.342719 CCAACCCAAGCAACAAAACTTT 58.657 40.909 0.00 0.00 0.00 2.66
2423 2606 1.818555 GTAACGGCCGTCCACCTAT 59.181 57.895 34.29 17.06 0.00 2.57
2428 2631 2.259204 CTTCGTAACGGCCGTCCA 59.741 61.111 34.29 20.32 0.00 4.02
2442 2645 1.430228 GTCTCCTCGCTCGGTCTTC 59.570 63.158 0.00 0.00 0.00 2.87
2443 2646 2.400158 CGTCTCCTCGCTCGGTCTT 61.400 63.158 0.00 0.00 0.00 3.01
2531 2734 2.310538 CTAAAATAAGGCCAGCCCAGG 58.689 52.381 5.01 0.00 36.58 4.45
2532 2735 3.018423 ACTAAAATAAGGCCAGCCCAG 57.982 47.619 5.01 0.00 36.58 4.45
2533 2736 3.683281 CGTACTAAAATAAGGCCAGCCCA 60.683 47.826 5.01 0.00 36.58 5.36
2534 2737 2.876550 CGTACTAAAATAAGGCCAGCCC 59.123 50.000 5.01 0.00 36.58 5.19
2535 2738 3.800531 TCGTACTAAAATAAGGCCAGCC 58.199 45.455 5.01 0.00 0.00 4.85
2536 2739 7.816031 TGTATATCGTACTAAAATAAGGCCAGC 59.184 37.037 5.01 0.00 0.00 4.85
2537 2740 9.871238 ATGTATATCGTACTAAAATAAGGCCAG 57.129 33.333 5.01 0.00 0.00 4.85
2558 2761 9.878599 GCGCAGTTATAATGTCTTTAAATGTAT 57.121 29.630 0.30 0.00 0.00 2.29
2559 2762 8.884726 TGCGCAGTTATAATGTCTTTAAATGTA 58.115 29.630 5.66 0.00 0.00 2.29
2560 2763 7.757526 TGCGCAGTTATAATGTCTTTAAATGT 58.242 30.769 5.66 0.00 0.00 2.71
2561 2764 7.910162 ACTGCGCAGTTATAATGTCTTTAAATG 59.090 33.333 36.44 7.40 38.83 2.32
2562 2765 7.985476 ACTGCGCAGTTATAATGTCTTTAAAT 58.015 30.769 36.44 7.98 38.83 1.40
2563 2766 7.372451 ACTGCGCAGTTATAATGTCTTTAAA 57.628 32.000 36.44 0.00 38.83 1.52
2564 2767 6.978343 ACTGCGCAGTTATAATGTCTTTAA 57.022 33.333 36.44 0.00 38.83 1.52
2578 2781 1.344763 AGAGTAGGAAAACTGCGCAGT 59.655 47.619 36.44 36.44 44.94 4.40
2579 2782 1.996191 GAGAGTAGGAAAACTGCGCAG 59.004 52.381 34.89 34.89 36.85 5.18
2580 2783 1.618837 AGAGAGTAGGAAAACTGCGCA 59.381 47.619 10.98 10.98 36.85 6.09
2581 2784 2.263945 GAGAGAGTAGGAAAACTGCGC 58.736 52.381 0.00 0.00 36.85 6.09
2582 2785 3.246619 GTGAGAGAGTAGGAAAACTGCG 58.753 50.000 0.00 0.00 36.85 5.18
2583 2786 3.246619 CGTGAGAGAGTAGGAAAACTGC 58.753 50.000 0.00 0.00 0.00 4.40
2584 2787 3.246619 GCGTGAGAGAGTAGGAAAACTG 58.753 50.000 0.00 0.00 0.00 3.16
2585 2788 2.231721 GGCGTGAGAGAGTAGGAAAACT 59.768 50.000 0.00 0.00 0.00 2.66
2586 2789 2.029290 TGGCGTGAGAGAGTAGGAAAAC 60.029 50.000 0.00 0.00 0.00 2.43
2587 2790 2.029290 GTGGCGTGAGAGAGTAGGAAAA 60.029 50.000 0.00 0.00 0.00 2.29
2588 2791 1.544691 GTGGCGTGAGAGAGTAGGAAA 59.455 52.381 0.00 0.00 0.00 3.13
2589 2792 1.174783 GTGGCGTGAGAGAGTAGGAA 58.825 55.000 0.00 0.00 0.00 3.36
2590 2793 0.328592 AGTGGCGTGAGAGAGTAGGA 59.671 55.000 0.00 0.00 0.00 2.94
2591 2794 1.178276 AAGTGGCGTGAGAGAGTAGG 58.822 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.