Multiple sequence alignment - TraesCS2D01G417700

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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 TraesCS2D01G417700 chr2D 100.000 3028 0 0 1 3028 531927734 531930761 0.000000e+00 5592.0
1 TraesCS2D01G417700 chr2D 79.389 131 25 2 62 191 562031944 562032073 1.160000e-14 91.6
2 TraesCS2D01G417700 chr2A 89.743 2642 134 60 462 3028 676381583 676384162 0.000000e+00 3251.0
3 TraesCS2D01G417700 chr2B 88.004 1142 54 23 665 1791 631721419 631722492 0.000000e+00 1273.0
4 TraesCS2D01G417700 chr2B 93.301 612 26 7 1841 2447 631722502 631723103 0.000000e+00 889.0
5 TraesCS2D01G417700 chr2B 93.793 580 30 3 2453 3028 631723282 631723859 0.000000e+00 867.0
6 TraesCS2D01G417700 chr2B 91.429 420 25 5 1 410 631702753 631703171 1.580000e-157 566.0
7 TraesCS2D01G417700 chr2B 88.987 227 16 3 445 664 631703168 631703392 3.850000e-69 272.0
8 TraesCS2D01G417700 chr2B 80.153 131 24 2 62 191 577284728 577284857 2.480000e-16 97.1
9 TraesCS2D01G417700 chr3B 82.927 123 17 4 72 191 536991082 536991203 1.150000e-19 108.0
10 TraesCS2D01G417700 chr3A 80.741 135 22 4 62 194 117059180 117059048 5.340000e-18 102.0
11 TraesCS2D01G417700 chr7D 79.851 134 25 2 62 194 186594809 186594677 2.480000e-16 97.1
12 TraesCS2D01G417700 chr6B 80.303 132 22 4 62 191 517071150 517071279 2.480000e-16 97.1
13 TraesCS2D01G417700 chr6A 79.389 131 25 2 62 191 570781014 570781143 1.160000e-14 91.6
14 TraesCS2D01G417700 chr3D 79.104 134 26 2 62 194 281055184 281055052 1.160000e-14 91.6
15 TraesCS2D01G417700 chr7A 85.915 71 1 3 1140 1201 538819758 538819688 1.950000e-07 67.6
16 TraesCS2D01G417700 chr7A 84.507 71 2 5 1140 1201 538807613 538807543 9.060000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G417700 chr2D 531927734 531930761 3027 False 5592.000000 5592 100.000000 1 3028 1 chr2D.!!$F1 3027
1 TraesCS2D01G417700 chr2A 676381583 676384162 2579 False 3251.000000 3251 89.743000 462 3028 1 chr2A.!!$F1 2566
2 TraesCS2D01G417700 chr2B 631721419 631723859 2440 False 1009.666667 1273 91.699333 665 3028 3 chr2B.!!$F3 2363
3 TraesCS2D01G417700 chr2B 631702753 631703392 639 False 419.000000 566 90.208000 1 664 2 chr2B.!!$F2 663

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
411 422 0.031178 AACCGAACGCTCGTACTGTT 59.969 50.0 7.52 1.35 43.87 3.16 F
412 423 0.031178 ACCGAACGCTCGTACTGTTT 59.969 50.0 7.52 0.00 43.87 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1872 0.116143 ACAGAAGGGAGGTCTCTGCT 59.884 55.0 0.0 0.0 32.16 4.24 R
2248 2341 2.256117 ACCAGCTTGTCACCTTGTAC 57.744 50.0 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
154 165 4.370094 TCCTACGTGGGGTTGTTTAATT 57.630 40.909 18.84 0.00 36.20 1.40
157 168 1.267533 ACGTGGGGTTGTTTAATTCGC 59.732 47.619 0.00 0.00 0.00 4.70
167 178 7.306953 GGGTTGTTTAATTCGCAGTATTACAA 58.693 34.615 0.00 0.00 0.00 2.41
174 185 5.947228 ATTCGCAGTATTACAATCCATGG 57.053 39.130 4.97 4.97 0.00 3.66
177 188 5.056480 TCGCAGTATTACAATCCATGGAAG 58.944 41.667 20.67 16.85 34.61 3.46
204 215 3.306364 CCTTAGGATACAGGGCATCTTCG 60.306 52.174 0.00 0.00 41.41 3.79
247 258 4.574599 AATTTGGCGCATTCTAATCCTC 57.425 40.909 10.83 0.00 0.00 3.71
287 298 6.061022 TGACTTGGCTGATTTGTAGGATTA 57.939 37.500 0.00 0.00 0.00 1.75
368 379 6.121776 TCATCCACTACAACCTAATGTGTT 57.878 37.500 0.00 0.00 34.75 3.32
377 388 9.662947 ACTACAACCTAATGTGTTTAATCCTAC 57.337 33.333 0.00 0.00 34.75 3.18
381 392 8.508875 CAACCTAATGTGTTTAATCCTACGTTT 58.491 33.333 0.00 0.00 0.00 3.60
394 405 2.034076 CTACGTTTTTCTGCGCACAAC 58.966 47.619 5.66 6.47 0.00 3.32
396 407 1.528248 CGTTTTTCTGCGCACAACCG 61.528 55.000 5.66 0.00 0.00 4.44
409 420 0.662374 ACAACCGAACGCTCGTACTG 60.662 55.000 7.52 3.98 43.87 2.74
410 421 0.662374 CAACCGAACGCTCGTACTGT 60.662 55.000 7.52 0.00 43.87 3.55
411 422 0.031178 AACCGAACGCTCGTACTGTT 59.969 50.000 7.52 1.35 43.87 3.16
412 423 0.031178 ACCGAACGCTCGTACTGTTT 59.969 50.000 7.52 0.00 43.87 2.83
413 424 1.134226 CCGAACGCTCGTACTGTTTT 58.866 50.000 7.52 0.00 43.87 2.43
414 425 1.136721 CCGAACGCTCGTACTGTTTTG 60.137 52.381 7.52 0.00 43.87 2.44
415 426 1.519758 CGAACGCTCGTACTGTTTTGT 59.480 47.619 0.00 0.00 40.33 2.83
416 427 2.655577 CGAACGCTCGTACTGTTTTGTG 60.656 50.000 0.00 0.00 40.33 3.33
417 428 2.212869 ACGCTCGTACTGTTTTGTGA 57.787 45.000 0.00 0.00 0.00 3.58
418 429 2.542597 ACGCTCGTACTGTTTTGTGAA 58.457 42.857 0.00 0.00 0.00 3.18
419 430 2.283351 ACGCTCGTACTGTTTTGTGAAC 59.717 45.455 0.00 0.00 0.00 3.18
420 431 2.348218 CGCTCGTACTGTTTTGTGAACC 60.348 50.000 0.00 0.00 0.00 3.62
421 432 2.870411 GCTCGTACTGTTTTGTGAACCT 59.130 45.455 0.00 0.00 0.00 3.50
422 433 4.053295 GCTCGTACTGTTTTGTGAACCTA 58.947 43.478 0.00 0.00 0.00 3.08
423 434 4.689345 GCTCGTACTGTTTTGTGAACCTAT 59.311 41.667 0.00 0.00 0.00 2.57
424 435 5.178809 GCTCGTACTGTTTTGTGAACCTATT 59.821 40.000 0.00 0.00 0.00 1.73
425 436 6.366877 GCTCGTACTGTTTTGTGAACCTATTA 59.633 38.462 0.00 0.00 0.00 0.98
426 437 7.095523 GCTCGTACTGTTTTGTGAACCTATTAA 60.096 37.037 0.00 0.00 0.00 1.40
427 438 8.659925 TCGTACTGTTTTGTGAACCTATTAAA 57.340 30.769 0.00 0.00 0.00 1.52
428 439 8.550376 TCGTACTGTTTTGTGAACCTATTAAAC 58.450 33.333 0.00 0.00 0.00 2.01
429 440 7.528182 CGTACTGTTTTGTGAACCTATTAAACG 59.472 37.037 0.00 0.00 0.00 3.60
430 441 6.731164 ACTGTTTTGTGAACCTATTAAACGG 58.269 36.000 0.00 0.00 37.68 4.44
431 442 5.521544 TGTTTTGTGAACCTATTAAACGGC 58.478 37.500 0.00 0.00 0.00 5.68
432 443 4.769859 TTTGTGAACCTATTAAACGGCC 57.230 40.909 0.00 0.00 0.00 6.13
433 444 2.713877 TGTGAACCTATTAAACGGCCC 58.286 47.619 0.00 0.00 0.00 5.80
434 445 1.667212 GTGAACCTATTAAACGGCCCG 59.333 52.381 0.00 0.00 0.00 6.13
435 446 0.659427 GAACCTATTAAACGGCCCGC 59.341 55.000 1.23 0.00 0.00 6.13
436 447 0.253894 AACCTATTAAACGGCCCGCT 59.746 50.000 1.23 0.00 0.00 5.52
437 448 1.122227 ACCTATTAAACGGCCCGCTA 58.878 50.000 1.23 0.00 0.00 4.26
438 449 1.485895 ACCTATTAAACGGCCCGCTAA 59.514 47.619 1.23 1.25 0.00 3.09
439 450 2.093021 ACCTATTAAACGGCCCGCTAAA 60.093 45.455 1.23 0.00 0.00 1.85
440 451 2.546789 CCTATTAAACGGCCCGCTAAAG 59.453 50.000 1.23 2.61 0.00 1.85
441 452 1.385528 ATTAAACGGCCCGCTAAAGG 58.614 50.000 1.23 0.00 0.00 3.11
457 468 1.755393 AAGGCAACGGAACCGAGTCT 61.755 55.000 20.14 14.54 46.39 3.24
477 488 3.747976 GTGGCATGTTGACCGGGC 61.748 66.667 6.32 1.57 0.00 6.13
485 496 0.327924 TGTTGACCGGGCATCATCTT 59.672 50.000 17.36 0.00 0.00 2.40
506 517 1.751351 CAAGTCCGCTAGATCCTGACA 59.249 52.381 0.00 0.00 0.00 3.58
518 529 4.099633 AGATCCTGACATTGTCCTCTTCA 58.900 43.478 14.05 0.00 0.00 3.02
522 533 3.193263 CTGACATTGTCCTCTTCATCCG 58.807 50.000 14.05 0.00 0.00 4.18
576 590 0.734889 GCCATATGCACACCACACTC 59.265 55.000 0.00 0.00 40.77 3.51
608 623 0.608130 ATACTCTGCACAAGCCGACA 59.392 50.000 0.00 0.00 41.13 4.35
725 759 3.630312 GCCACGCCTAGAATATTTCCAAA 59.370 43.478 0.00 0.00 0.00 3.28
726 760 4.097286 GCCACGCCTAGAATATTTCCAAAA 59.903 41.667 0.00 0.00 0.00 2.44
765 799 4.059459 CGCGCGCGTTCAGAAGTT 62.059 61.111 42.49 0.00 34.35 2.66
789 823 3.526360 AATTAGGAGGAGGGAGGGAAA 57.474 47.619 0.00 0.00 0.00 3.13
790 824 3.526360 ATTAGGAGGAGGGAGGGAAAA 57.474 47.619 0.00 0.00 0.00 2.29
823 860 2.484203 GACGACGAGGAGGAACCG 59.516 66.667 0.00 0.00 44.74 4.44
827 864 0.731855 CGACGAGGAGGAACCGAAAC 60.732 60.000 0.00 0.00 44.74 2.78
842 882 2.545952 CCGAAACAGCAGCCGTCTATAT 60.546 50.000 0.00 0.00 0.00 0.86
859 899 7.742019 GTCTATATGTGACGCGATTAATCAT 57.258 36.000 15.93 10.67 0.00 2.45
860 900 7.604386 GTCTATATGTGACGCGATTAATCATG 58.396 38.462 15.93 8.98 0.00 3.07
1045 1087 3.364366 CGGAAGAACACATCTCACAAAGC 60.364 47.826 0.00 0.00 37.42 3.51
1054 1096 3.248602 ACATCTCACAAAGCGAAGTTCAC 59.751 43.478 3.32 0.00 0.00 3.18
1080 1122 1.862123 CGCAGTGTAGTGTTGCCAG 59.138 57.895 0.00 0.00 34.42 4.85
1081 1123 1.568612 CGCAGTGTAGTGTTGCCAGG 61.569 60.000 0.00 0.00 34.42 4.45
1082 1124 1.856265 GCAGTGTAGTGTTGCCAGGC 61.856 60.000 3.66 3.66 31.79 4.85
1083 1125 0.534877 CAGTGTAGTGTTGCCAGGCA 60.535 55.000 11.22 11.22 36.47 4.75
1092 1134 3.790416 TTGCCAGGCACACTCCACC 62.790 63.158 15.89 0.00 38.71 4.61
1540 1596 2.433662 TGCCTGCATGCATACCTAAA 57.566 45.000 22.97 0.00 36.04 1.85
1555 1611 6.537660 GCATACCTAAATCCATTACCCGTATC 59.462 42.308 0.00 0.00 0.00 2.24
1564 1620 3.318017 CATTACCCGTATCAGTAGCTGC 58.682 50.000 0.00 0.00 0.00 5.25
1566 1622 1.486211 ACCCGTATCAGTAGCTGCTT 58.514 50.000 7.79 0.00 0.00 3.91
1568 1624 1.212616 CCGTATCAGTAGCTGCTTGC 58.787 55.000 7.79 1.21 43.29 4.01
1576 1632 0.179936 GTAGCTGCTTGCCTGATCCT 59.820 55.000 7.79 0.00 44.23 3.24
1703 1765 0.249784 ATACAGCTGCTCGCCATCAG 60.250 55.000 15.27 0.00 40.39 2.90
1704 1766 1.322538 TACAGCTGCTCGCCATCAGA 61.323 55.000 15.27 0.00 40.39 3.27
1705 1767 1.227586 CAGCTGCTCGCCATCAGAT 60.228 57.895 0.00 0.00 40.39 2.90
1706 1768 1.069427 AGCTGCTCGCCATCAGATC 59.931 57.895 0.00 0.00 40.39 2.75
1707 1769 1.227468 GCTGCTCGCCATCAGATCA 60.227 57.895 0.00 0.00 32.26 2.92
1776 1844 1.269723 TCGCTCAGTTACCAGTCAGTG 59.730 52.381 0.00 0.00 0.00 3.66
1791 1859 6.377327 CAGTCAGTGGATTTACTTTGTTGT 57.623 37.500 0.00 0.00 0.00 3.32
1793 1861 6.692681 CAGTCAGTGGATTTACTTTGTTGTTG 59.307 38.462 0.00 0.00 0.00 3.33
1797 1865 6.019640 CAGTGGATTTACTTTGTTGTTGCTTG 60.020 38.462 0.00 0.00 0.00 4.01
1802 1870 7.384932 GGATTTACTTTGTTGTTGCTTGCTTAT 59.615 33.333 0.00 0.00 0.00 1.73
1803 1871 8.661352 ATTTACTTTGTTGTTGCTTGCTTATT 57.339 26.923 0.00 0.00 0.00 1.40
1804 1872 9.757227 ATTTACTTTGTTGTTGCTTGCTTATTA 57.243 25.926 0.00 0.00 0.00 0.98
1817 1885 3.394674 GCTTATTAGCAGAGACCTCCC 57.605 52.381 0.00 0.00 46.95 4.30
1818 1886 2.969262 GCTTATTAGCAGAGACCTCCCT 59.031 50.000 0.00 0.00 46.95 4.20
1819 1887 3.389656 GCTTATTAGCAGAGACCTCCCTT 59.610 47.826 0.00 0.00 46.95 3.95
1834 1902 3.763897 CCTCCCTTCTGTAATTTGTTGGG 59.236 47.826 0.00 0.00 34.98 4.12
1862 1930 7.639039 TGAATTGGATATGTGCGAGTTATTTC 58.361 34.615 0.00 0.00 0.00 2.17
1868 1936 2.499197 TGTGCGAGTTATTTCCAGCAA 58.501 42.857 0.00 0.00 36.32 3.91
1880 1948 7.668052 AGTTATTTCCAGCAACCAGTACATTTA 59.332 33.333 0.00 0.00 0.00 1.40
1882 1950 6.909550 TTTCCAGCAACCAGTACATTTATT 57.090 33.333 0.00 0.00 0.00 1.40
1989 2059 0.251341 AGGGTGCCAAATGTCAGACC 60.251 55.000 0.00 0.00 0.00 3.85
2041 2111 4.207019 GGCAAACATAATAAATGCGTGCTC 59.793 41.667 11.14 0.00 37.88 4.26
2096 2166 4.873746 ATGCCGTGAGCTGTACTATAAT 57.126 40.909 0.00 0.00 44.23 1.28
2102 2172 5.048643 CCGTGAGCTGTACTATAATAGCACT 60.049 44.000 0.00 0.00 38.59 4.40
2141 2212 6.980051 ACCAAACTAATACGGAAAAGCTAG 57.020 37.500 0.00 0.00 0.00 3.42
2248 2341 4.322080 TCAACCAACAGACAGACAGTAG 57.678 45.455 0.00 0.00 0.00 2.57
2249 2342 3.704566 TCAACCAACAGACAGACAGTAGT 59.295 43.478 0.00 0.00 0.00 2.73
2250 2343 4.891168 TCAACCAACAGACAGACAGTAGTA 59.109 41.667 0.00 0.00 0.00 1.82
2384 2480 8.794553 CGTATTTACAGAGACATATTCCCTACT 58.205 37.037 0.00 0.00 0.00 2.57
2439 2535 0.539518 TGTGCAATCGCCCTAGCTAA 59.460 50.000 0.00 0.00 37.32 3.09
2440 2536 1.065782 TGTGCAATCGCCCTAGCTAAA 60.066 47.619 0.00 0.00 37.32 1.85
2441 2537 1.599542 GTGCAATCGCCCTAGCTAAAG 59.400 52.381 0.00 0.00 37.32 1.85
2442 2538 1.209504 TGCAATCGCCCTAGCTAAAGT 59.790 47.619 0.00 0.00 37.32 2.66
2444 2540 3.118555 TGCAATCGCCCTAGCTAAAGTTA 60.119 43.478 0.00 0.00 37.32 2.24
2446 2542 5.221561 TGCAATCGCCCTAGCTAAAGTTATA 60.222 40.000 0.00 0.00 37.32 0.98
2447 2543 5.120363 GCAATCGCCCTAGCTAAAGTTATAC 59.880 44.000 0.00 0.00 36.60 1.47
2448 2544 4.494350 TCGCCCTAGCTAAAGTTATACG 57.506 45.455 0.00 0.00 36.60 3.06
2449 2545 3.254166 TCGCCCTAGCTAAAGTTATACGG 59.746 47.826 0.00 0.00 36.60 4.02
2450 2546 3.324117 GCCCTAGCTAAAGTTATACGGC 58.676 50.000 0.00 0.00 35.50 5.68
2456 2728 5.105834 AGCTAAAGTTATACGGCGAGTAG 57.894 43.478 16.62 3.97 38.94 2.57
2513 2785 3.044059 GACTTCCACATGCTGCCGC 62.044 63.158 0.00 0.00 0.00 6.53
2561 2833 4.221422 GCCTGCGCCTCGTCCATA 62.221 66.667 4.18 0.00 0.00 2.74
2581 2853 2.742116 GGCCATCCTTACCCTCGCA 61.742 63.158 0.00 0.00 0.00 5.10
2593 2865 1.446792 CCTCGCAAGACGCAGACAT 60.447 57.895 0.00 0.00 45.01 3.06
2609 2881 2.179547 CATCGCGCCAACCATAGCA 61.180 57.895 0.00 0.00 0.00 3.49
2762 3034 1.081242 GTCGTTGAGCGGGTCGTAA 60.081 57.895 2.41 0.00 41.72 3.18
2807 3079 0.815213 GCCAATGCTGGACTATGCGA 60.815 55.000 0.00 0.00 46.92 5.10
2901 3173 1.266989 CCGCCTGACAAAAGAAAGGAC 59.733 52.381 0.00 0.00 30.92 3.85
2908 3180 5.468746 CCTGACAAAAGAAAGGACGATTACA 59.531 40.000 0.00 0.00 30.92 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.650972 AGTTACATACTGGGCCAAGAAA 57.349 40.909 16.25 1.04 35.19 2.52
32 33 5.765576 TTAGTTACATACTGGGCCAAGAA 57.234 39.130 16.25 0.00 37.73 2.52
34 35 5.063880 GGATTAGTTACATACTGGGCCAAG 58.936 45.833 8.04 5.25 37.73 3.61
36 37 4.303794 AGGATTAGTTACATACTGGGCCA 58.696 43.478 5.85 5.85 37.73 5.36
37 38 4.262938 GGAGGATTAGTTACATACTGGGCC 60.263 50.000 0.00 0.00 37.73 5.80
38 39 4.347000 TGGAGGATTAGTTACATACTGGGC 59.653 45.833 0.00 0.00 37.73 5.36
39 40 6.688073 ATGGAGGATTAGTTACATACTGGG 57.312 41.667 0.00 0.00 37.73 4.45
106 117 3.856900 TCCCGATGATTAGAATCCTCCA 58.143 45.455 0.00 0.00 34.50 3.86
138 149 1.267261 TGCGAATTAAACAACCCCACG 59.733 47.619 0.00 0.00 0.00 4.94
154 165 4.681074 TCCATGGATTGTAATACTGCGA 57.319 40.909 11.44 0.00 0.00 5.10
174 185 4.882427 GCCCTGTATCCTAAGGAAAACTTC 59.118 45.833 0.00 0.00 40.64 3.01
177 188 4.230745 TGCCCTGTATCCTAAGGAAAAC 57.769 45.455 0.00 0.00 34.34 2.43
184 195 3.572642 TCGAAGATGCCCTGTATCCTAA 58.427 45.455 0.00 0.00 0.00 2.69
265 276 5.880332 TGTAATCCTACAAATCAGCCAAGTC 59.120 40.000 0.00 0.00 35.03 3.01
344 355 6.313519 ACACATTAGGTTGTAGTGGATGAT 57.686 37.500 0.00 0.00 34.65 2.45
349 360 7.610305 AGGATTAAACACATTAGGTTGTAGTGG 59.390 37.037 0.00 0.00 34.65 4.00
368 379 3.747010 TGCGCAGAAAAACGTAGGATTAA 59.253 39.130 5.66 0.00 0.00 1.40
377 388 1.528248 CGGTTGTGCGCAGAAAAACG 61.528 55.000 22.60 20.70 0.00 3.60
381 392 1.353804 GTTCGGTTGTGCGCAGAAA 59.646 52.632 22.60 11.59 0.00 2.52
396 407 2.536803 TCACAAAACAGTACGAGCGTTC 59.463 45.455 0.00 0.00 0.00 3.95
409 420 4.919168 GGCCGTTTAATAGGTTCACAAAAC 59.081 41.667 0.00 0.00 0.00 2.43
410 421 4.022155 GGGCCGTTTAATAGGTTCACAAAA 60.022 41.667 0.00 0.00 0.00 2.44
411 422 3.506844 GGGCCGTTTAATAGGTTCACAAA 59.493 43.478 0.00 0.00 0.00 2.83
412 423 3.083293 GGGCCGTTTAATAGGTTCACAA 58.917 45.455 0.00 0.00 0.00 3.33
413 424 2.713877 GGGCCGTTTAATAGGTTCACA 58.286 47.619 0.00 0.00 0.00 3.58
414 425 1.667212 CGGGCCGTTTAATAGGTTCAC 59.333 52.381 19.97 0.00 0.00 3.18
415 426 2.013058 GCGGGCCGTTTAATAGGTTCA 61.013 52.381 28.82 0.00 0.00 3.18
416 427 0.659427 GCGGGCCGTTTAATAGGTTC 59.341 55.000 28.82 1.40 0.00 3.62
417 428 0.253894 AGCGGGCCGTTTAATAGGTT 59.746 50.000 28.82 0.00 0.00 3.50
418 429 1.122227 TAGCGGGCCGTTTAATAGGT 58.878 50.000 28.82 4.12 0.00 3.08
419 430 2.243602 TTAGCGGGCCGTTTAATAGG 57.756 50.000 28.82 0.00 0.00 2.57
420 431 2.546789 CCTTTAGCGGGCCGTTTAATAG 59.453 50.000 28.82 20.83 0.00 1.73
421 432 2.563702 CCTTTAGCGGGCCGTTTAATA 58.436 47.619 28.82 14.55 0.00 0.98
422 433 1.385528 CCTTTAGCGGGCCGTTTAAT 58.614 50.000 28.82 11.08 0.00 1.40
423 434 1.307355 GCCTTTAGCGGGCCGTTTAA 61.307 55.000 28.82 20.52 43.49 1.52
424 435 1.746239 GCCTTTAGCGGGCCGTTTA 60.746 57.895 28.82 13.43 43.49 2.01
425 436 3.060000 GCCTTTAGCGGGCCGTTT 61.060 61.111 28.82 18.46 43.49 3.60
434 445 0.952010 TCGGTTCCGTTGCCTTTAGC 60.952 55.000 11.04 0.00 44.14 3.09
435 446 1.076332 CTCGGTTCCGTTGCCTTTAG 58.924 55.000 11.04 0.00 0.00 1.85
436 447 0.393820 ACTCGGTTCCGTTGCCTTTA 59.606 50.000 11.04 0.00 0.00 1.85
437 448 0.883370 GACTCGGTTCCGTTGCCTTT 60.883 55.000 11.04 0.00 0.00 3.11
438 449 1.301479 GACTCGGTTCCGTTGCCTT 60.301 57.895 11.04 0.00 0.00 4.35
439 450 1.755393 AAGACTCGGTTCCGTTGCCT 61.755 55.000 11.04 1.38 0.00 4.75
440 451 0.883370 AAAGACTCGGTTCCGTTGCC 60.883 55.000 11.04 0.00 0.00 4.52
441 452 0.234884 CAAAGACTCGGTTCCGTTGC 59.765 55.000 11.04 2.22 0.00 4.17
442 453 1.260561 CACAAAGACTCGGTTCCGTTG 59.739 52.381 11.04 9.88 0.00 4.10
443 454 1.578583 CACAAAGACTCGGTTCCGTT 58.421 50.000 11.04 0.00 0.00 4.44
444 455 0.249741 CCACAAAGACTCGGTTCCGT 60.250 55.000 11.04 0.00 0.00 4.69
445 456 1.566018 GCCACAAAGACTCGGTTCCG 61.566 60.000 4.74 4.74 0.00 4.30
446 457 0.534203 TGCCACAAAGACTCGGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
450 461 1.069022 CAACATGCCACAAAGACTCGG 60.069 52.381 0.00 0.00 0.00 4.63
457 468 1.459455 CCCGGTCAACATGCCACAAA 61.459 55.000 0.00 0.00 0.00 2.83
477 488 4.313277 TCTAGCGGACTTGAAGATGATG 57.687 45.455 0.00 0.00 0.00 3.07
485 496 2.025155 GTCAGGATCTAGCGGACTTGA 58.975 52.381 0.00 0.00 32.12 3.02
506 517 1.825474 ACGTCGGATGAAGAGGACAAT 59.175 47.619 3.82 0.00 0.00 2.71
518 529 3.868757 TCTTCTTCAATCACGTCGGAT 57.131 42.857 0.00 0.00 0.00 4.18
522 533 4.143221 GCACTCTTCTTCTTCAATCACGTC 60.143 45.833 0.00 0.00 0.00 4.34
576 590 1.065928 GAGTATGCGGGTGTCTCGG 59.934 63.158 0.00 0.00 0.00 4.63
608 623 2.430367 GTCCTTCGGCCCAACAGT 59.570 61.111 0.00 0.00 0.00 3.55
666 688 2.292103 GCTCACAGACTTAGCCTCTG 57.708 55.000 0.00 0.00 40.97 3.35
765 799 2.679082 CCTCCCTCCTCCTAATTTCGA 58.321 52.381 0.00 0.00 0.00 3.71
789 823 1.937899 CGTCCAGAACAAGAAACCGTT 59.062 47.619 0.00 0.00 0.00 4.44
790 824 1.137479 TCGTCCAGAACAAGAAACCGT 59.863 47.619 0.00 0.00 0.00 4.83
823 860 3.246226 CACATATAGACGGCTGCTGTTTC 59.754 47.826 16.36 3.77 0.00 2.78
827 864 2.398498 GTCACATATAGACGGCTGCTG 58.602 52.381 0.00 6.98 0.00 4.41
842 882 2.030335 GTGCATGATTAATCGCGTCACA 59.970 45.455 5.77 0.00 0.00 3.58
994 1036 4.514401 CCCTGCGGTTTATATAATCCTCC 58.486 47.826 16.90 10.30 0.00 4.30
1045 1087 2.171940 GCGCTGCTGTGAACTTCG 59.828 61.111 8.49 0.00 0.00 3.79
1054 1096 3.846590 CTACACTGCGCGCTGCTG 61.847 66.667 33.78 29.32 46.63 4.41
1092 1134 1.172180 ATGCCACCCACGAAACACAG 61.172 55.000 0.00 0.00 0.00 3.66
1243 1287 3.397613 GAGGGTAGGCCTGCTGCTG 62.398 68.421 21.02 0.00 40.92 4.41
1293 1346 2.813200 GGCTGGTAGTAGTCGGCC 59.187 66.667 7.34 7.34 46.54 6.13
1540 1596 4.220821 CAGCTACTGATACGGGTAATGGAT 59.779 45.833 0.00 0.00 32.44 3.41
1555 1611 1.297664 GATCAGGCAAGCAGCTACTG 58.702 55.000 13.05 13.05 44.79 2.74
1564 1620 4.148128 ACATACAGAAGGATCAGGCAAG 57.852 45.455 0.00 0.00 0.00 4.01
1566 1622 4.574674 AAACATACAGAAGGATCAGGCA 57.425 40.909 0.00 0.00 0.00 4.75
1568 1624 6.824305 AACAAAACATACAGAAGGATCAGG 57.176 37.500 0.00 0.00 0.00 3.86
1576 1632 9.868277 AGATCAAAACAAACAAAACATACAGAA 57.132 25.926 0.00 0.00 0.00 3.02
1703 1765 2.083774 TGTGCCAAGGAAACGATGATC 58.916 47.619 0.00 0.00 0.00 2.92
1704 1766 2.198827 TGTGCCAAGGAAACGATGAT 57.801 45.000 0.00 0.00 0.00 2.45
1705 1767 1.606668 GTTGTGCCAAGGAAACGATGA 59.393 47.619 0.00 0.00 0.00 2.92
1706 1768 1.608590 AGTTGTGCCAAGGAAACGATG 59.391 47.619 0.00 0.00 0.00 3.84
1707 1769 1.981256 AGTTGTGCCAAGGAAACGAT 58.019 45.000 0.00 0.00 0.00 3.73
1724 1786 7.615365 TGATACAGAATTAAGCCAAATCCAAGT 59.385 33.333 0.00 0.00 0.00 3.16
1776 1844 5.049828 AGCAAGCAACAACAAAGTAAATCC 58.950 37.500 0.00 0.00 0.00 3.01
1802 1870 2.225394 ACAGAAGGGAGGTCTCTGCTAA 60.225 50.000 0.00 0.00 32.16 3.09
1803 1871 1.359474 ACAGAAGGGAGGTCTCTGCTA 59.641 52.381 0.00 0.00 32.16 3.49
1804 1872 0.116143 ACAGAAGGGAGGTCTCTGCT 59.884 55.000 0.00 0.00 32.16 4.24
1806 1874 5.181748 CAAATTACAGAAGGGAGGTCTCTG 58.818 45.833 0.00 0.00 34.85 3.35
1808 1876 5.167303 ACAAATTACAGAAGGGAGGTCTC 57.833 43.478 0.00 0.00 0.00 3.36
1809 1877 5.316987 CAACAAATTACAGAAGGGAGGTCT 58.683 41.667 0.00 0.00 0.00 3.85
1810 1878 4.459337 CCAACAAATTACAGAAGGGAGGTC 59.541 45.833 0.00 0.00 0.00 3.85
1811 1879 4.407365 CCAACAAATTACAGAAGGGAGGT 58.593 43.478 0.00 0.00 0.00 3.85
1812 1880 3.763897 CCCAACAAATTACAGAAGGGAGG 59.236 47.826 0.00 0.00 37.22 4.30
1814 1882 3.161866 GCCCAACAAATTACAGAAGGGA 58.838 45.455 0.00 0.00 37.22 4.20
1815 1883 2.896685 TGCCCAACAAATTACAGAAGGG 59.103 45.455 0.00 0.00 38.10 3.95
1816 1884 4.220382 TCATGCCCAACAAATTACAGAAGG 59.780 41.667 0.00 0.00 0.00 3.46
1817 1885 5.389859 TCATGCCCAACAAATTACAGAAG 57.610 39.130 0.00 0.00 0.00 2.85
1818 1886 5.798125 TTCATGCCCAACAAATTACAGAA 57.202 34.783 0.00 0.00 0.00 3.02
1819 1887 5.999205 ATTCATGCCCAACAAATTACAGA 57.001 34.783 0.00 0.00 0.00 3.41
1834 1902 3.251729 ACTCGCACATATCCAATTCATGC 59.748 43.478 0.00 0.00 0.00 4.06
1862 1930 5.066505 GGAGAATAAATGTACTGGTTGCTGG 59.933 44.000 0.00 0.00 0.00 4.85
1868 1936 7.016153 TCAACTGGAGAATAAATGTACTGGT 57.984 36.000 0.00 0.00 0.00 4.00
1882 1950 7.688325 GCAATGGCAAAAACTCAACTGGAGA 62.688 44.000 0.00 0.00 42.52 3.71
1928 1996 2.481952 GTGACATCTGAGGAACAGCAAC 59.518 50.000 0.00 0.00 45.38 4.17
1941 2009 3.067106 CGTAGGTTGCTTTGTGACATCT 58.933 45.455 0.00 0.00 0.00 2.90
1989 2059 4.407365 ACCTATGGACAAACAAAAGAGGG 58.593 43.478 0.00 0.00 0.00 4.30
2041 2111 9.651718 GCTGTAAGTATCGAATATTTCCAAAAG 57.348 33.333 0.00 0.00 35.30 2.27
2096 2166 8.715190 TGGTTATTATGTCAGGTATAGTGCTA 57.285 34.615 0.00 0.00 0.00 3.49
2141 2212 3.998341 TCCTGTGTTGCTACCGATTTAAC 59.002 43.478 0.00 0.00 0.00 2.01
2177 2266 4.331968 CTTGTTTAGGTCCAAGCCATACA 58.668 43.478 0.00 0.00 32.46 2.29
2248 2341 2.256117 ACCAGCTTGTCACCTTGTAC 57.744 50.000 0.00 0.00 0.00 2.90
2249 2342 4.564821 GGATTACCAGCTTGTCACCTTGTA 60.565 45.833 0.00 0.00 35.97 2.41
2250 2343 3.412386 GATTACCAGCTTGTCACCTTGT 58.588 45.455 0.00 0.00 0.00 3.16
2439 2535 1.339291 GGCCTACTCGCCGTATAACTT 59.661 52.381 0.00 0.00 39.64 2.66
2440 2536 0.957362 GGCCTACTCGCCGTATAACT 59.043 55.000 0.00 0.00 39.64 2.24
2441 2537 3.486285 GGCCTACTCGCCGTATAAC 57.514 57.895 0.00 0.00 39.64 1.89
2449 2545 0.528470 CTAGCTATGGGCCTACTCGC 59.472 60.000 4.53 0.00 43.05 5.03
2450 2546 0.528470 GCTAGCTATGGGCCTACTCG 59.472 60.000 7.70 0.00 43.05 4.18
2456 2728 2.432123 GGTGGCTAGCTATGGGCC 59.568 66.667 15.72 14.13 45.45 5.80
2593 2865 2.511373 CTGCTATGGTTGGCGCGA 60.511 61.111 12.10 0.00 30.65 5.87
2642 2914 1.967066 GAGATCATCTCCCACACCGAT 59.033 52.381 2.84 0.00 37.55 4.18
2762 3034 1.149854 GGGTGAACCTGACCCGTTT 59.850 57.895 0.00 0.00 43.87 3.60
2831 3103 3.695606 GCTGCTGACCACCGAGGA 61.696 66.667 0.00 0.00 41.22 3.71
2901 3173 5.621422 CACTGTGGAAAATGAGTGTAATCG 58.379 41.667 0.00 0.00 32.74 3.34
2908 3180 6.350445 GGAAATATGCACTGTGGAAAATGAGT 60.350 38.462 5.98 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.