Multiple sequence alignment - TraesCS2B01G313000

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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 TraesCS2B01G313000 chr2B 100.000 3214 0 0 1 3214 448476589 448479802 0.000000e+00 5936
1 TraesCS2B01G313000 chr2D 92.257 2583 128 31 654 3213 377055478 377058011 0.000000e+00 3596
2 TraesCS2B01G313000 chr2A 95.172 1947 66 14 654 2576 510947944 510949886 0.000000e+00 3049
3 TraesCS2B01G313000 chr2A 91.037 569 49 1 87 653 721962979 721962411 0.000000e+00 767
4 TraesCS2B01G313000 chr2A 89.474 570 41 8 2567 3131 510951228 510951783 0.000000e+00 702
5 TraesCS2B01G313000 chr5B 96.989 465 13 1 1 464 43834902 43835366 0.000000e+00 780
6 TraesCS2B01G313000 chr3B 82.957 575 83 8 87 653 684099870 684099303 3.700000e-139 505
7 TraesCS2B01G313000 chr5A 94.953 317 16 0 87 403 636433978 636434294 6.190000e-137 497
8 TraesCS2B01G313000 chr5A 87.843 255 27 3 400 653 636440184 636440435 2.420000e-76 296
9 TraesCS2B01G313000 chr6B 79.021 572 76 23 87 651 163959207 163958673 5.100000e-93 351


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 TraesCS2B01G313000 chr2B 448476589 448479802 3213 False 5936.0 5936 100.000 1 3214 1 chr2B.!!$F1 3213
1 TraesCS2B01G313000 chr2D 377055478 377058011 2533 False 3596.0 3596 92.257 654 3213 1 chr2D.!!$F1 2559
2 TraesCS2B01G313000 chr2A 510947944 510951783 3839 False 1875.5 3049 92.323 654 3131 2 chr2A.!!$F1 2477
3 TraesCS2B01G313000 chr2A 721962411 721962979 568 True 767.0 767 91.037 87 653 1 chr2A.!!$R1 566
4 TraesCS2B01G313000 chr3B 684099303 684099870 567 True 505.0 505 82.957 87 653 1 chr3B.!!$R1 566
5 TraesCS2B01G313000 chr6B 163958673 163959207 534 True 351.0 351 79.021 87 651 1 chr6B.!!$R1 564

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
78 79 0.320334 TCTGCGGCAATCGTTCAAGA 60.320 50.0 3.44 0.0 41.72 3.02 F
1157 1168 0.252197 GGGTTCTGTTCGGGTATGCT 59.748 55.0 0.00 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1947 0.468400 AGAGCTCGTATCCCCTGTCC 60.468 60.0 8.37 0.0 0.0 4.02 R
3100 4509 0.415429 TCTCCCAGCTCCCTCTTTCT 59.585 55.0 0.00 0.0 0.0 2.52 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
50 51 9.525826 AAGATTTTCTTGACCTCATTATGAACT 57.474 29.630 0.00 0.00 34.98 3.01
51 52 9.525826 AGATTTTCTTGACCTCATTATGAACTT 57.474 29.630 0.00 0.00 0.00 2.66
55 56 9.965824 TTTCTTGACCTCATTATGAACTTTTTC 57.034 29.630 0.00 0.00 0.00 2.29
56 57 8.924511 TCTTGACCTCATTATGAACTTTTTCT 57.075 30.769 0.00 0.00 32.36 2.52
57 58 9.354673 TCTTGACCTCATTATGAACTTTTTCTT 57.645 29.630 0.00 0.00 32.36 2.52
63 64 9.727627 CCTCATTATGAACTTTTTCTTATCTGC 57.272 33.333 0.00 0.00 32.36 4.26
64 65 9.430838 CTCATTATGAACTTTTTCTTATCTGCG 57.569 33.333 0.00 0.00 32.36 5.18
65 66 8.397906 TCATTATGAACTTTTTCTTATCTGCGG 58.602 33.333 0.00 0.00 32.36 5.69
66 67 4.419522 TGAACTTTTTCTTATCTGCGGC 57.580 40.909 0.00 0.00 32.36 6.53
67 68 3.818210 TGAACTTTTTCTTATCTGCGGCA 59.182 39.130 1.29 1.29 32.36 5.69
68 69 4.277174 TGAACTTTTTCTTATCTGCGGCAA 59.723 37.500 3.44 0.00 32.36 4.52
69 70 5.048083 TGAACTTTTTCTTATCTGCGGCAAT 60.048 36.000 3.44 3.65 32.36 3.56
70 71 4.986622 ACTTTTTCTTATCTGCGGCAATC 58.013 39.130 3.44 0.00 0.00 2.67
71 72 3.673746 TTTTCTTATCTGCGGCAATCG 57.326 42.857 3.44 0.00 42.76 3.34
72 73 2.309528 TTCTTATCTGCGGCAATCGT 57.690 45.000 3.44 0.00 41.72 3.73
73 74 2.309528 TCTTATCTGCGGCAATCGTT 57.690 45.000 3.44 0.00 41.72 3.85
74 75 2.201732 TCTTATCTGCGGCAATCGTTC 58.798 47.619 3.44 0.00 41.72 3.95
75 76 1.933181 CTTATCTGCGGCAATCGTTCA 59.067 47.619 3.44 0.00 41.72 3.18
76 77 2.017138 TATCTGCGGCAATCGTTCAA 57.983 45.000 3.44 0.00 41.72 2.69
77 78 0.729116 ATCTGCGGCAATCGTTCAAG 59.271 50.000 3.44 0.00 41.72 3.02
78 79 0.320334 TCTGCGGCAATCGTTCAAGA 60.320 50.000 3.44 0.00 41.72 3.02
79 80 0.516877 CTGCGGCAATCGTTCAAGAA 59.483 50.000 3.44 0.00 41.72 2.52
80 81 1.131126 CTGCGGCAATCGTTCAAGAAT 59.869 47.619 3.44 0.00 41.72 2.40
81 82 1.539388 TGCGGCAATCGTTCAAGAATT 59.461 42.857 0.00 0.00 41.72 2.17
82 83 2.030363 TGCGGCAATCGTTCAAGAATTT 60.030 40.909 0.00 0.00 41.72 1.82
83 84 3.189495 TGCGGCAATCGTTCAAGAATTTA 59.811 39.130 0.00 0.00 41.72 1.40
84 85 4.142491 TGCGGCAATCGTTCAAGAATTTAT 60.142 37.500 0.00 0.00 41.72 1.40
85 86 4.798387 GCGGCAATCGTTCAAGAATTTATT 59.202 37.500 0.00 0.00 41.72 1.40
125 126 7.310664 AGAAGTTCAACGATATCGACTGTAAA 58.689 34.615 30.75 14.59 43.02 2.01
192 194 6.041637 TCCTACGGAATAAATATGCACTCACT 59.958 38.462 0.00 0.00 0.00 3.41
213 215 7.963981 TCACTATCTGAATAAAGAAAGCAACG 58.036 34.615 0.00 0.00 0.00 4.10
252 254 1.090052 GGCGGCGTTGAATCTTAGCT 61.090 55.000 9.37 0.00 0.00 3.32
361 363 2.859404 TGTGGAGATAGAGGGAAGAGGA 59.141 50.000 0.00 0.00 0.00 3.71
385 390 1.610554 GCAGCGGGGTAGGAGTTGTA 61.611 60.000 0.00 0.00 0.00 2.41
403 408 3.491342 TGTACTGAAGAGAGCTCACACT 58.509 45.455 17.77 9.29 0.00 3.55
404 409 4.652822 TGTACTGAAGAGAGCTCACACTA 58.347 43.478 17.77 0.00 0.00 2.74
421 426 5.361571 TCACACTATCCTAAATCGCTTGGTA 59.638 40.000 0.00 0.00 0.00 3.25
432 439 1.258445 CGCTTGGTACAGAGAGGGGT 61.258 60.000 0.00 0.00 42.39 4.95
458 465 4.593634 TCAGAGAGATAGGTACAGATCGGA 59.406 45.833 0.00 0.00 0.00 4.55
474 482 1.351017 TCGGAACAGAGCAAAGGGAAT 59.649 47.619 0.00 0.00 0.00 3.01
509 519 2.541588 CGGAAGGACTTTTGTGCAGTTG 60.542 50.000 0.00 0.00 43.65 3.16
512 522 1.678101 AGGACTTTTGTGCAGTTGAGC 59.322 47.619 0.00 0.00 43.65 4.26
526 536 2.024414 GTTGAGCCACTTGACAAGGTT 58.976 47.619 19.16 1.31 0.00 3.50
547 557 5.048573 GGTTCATTGTGTAAAATGTACCCGT 60.049 40.000 10.76 0.00 45.31 5.28
562 572 1.070758 ACCCGTAGCCAGCTTATGATG 59.929 52.381 0.00 0.00 0.00 3.07
569 579 2.440627 AGCCAGCTTATGATGACATCCA 59.559 45.455 12.90 1.88 37.87 3.41
749 759 4.385643 CCCATGACCCACTAATCATTGACT 60.386 45.833 0.00 0.00 33.18 3.41
914 924 0.606673 GAGGGGCGGCCATTATCTTC 60.607 60.000 30.95 9.56 0.00 2.87
1014 1024 0.881796 TCACGATGTCTGTCGAGCTT 59.118 50.000 3.09 0.00 44.06 3.74
1017 1027 1.131504 ACGATGTCTGTCGAGCTTCTC 59.868 52.381 3.09 0.00 44.06 2.87
1157 1168 0.252197 GGGTTCTGTTCGGGTATGCT 59.748 55.000 0.00 0.00 0.00 3.79
1343 1354 5.069914 TGCTAGAATTAGGATTTAGGACGCA 59.930 40.000 0.00 0.00 0.00 5.24
1422 1443 5.104735 ACTTCTTGAGATACTGGGATGGAAC 60.105 44.000 0.00 0.00 0.00 3.62
1448 1469 2.433970 GGCTAGAGATCTTGGTCTTGCT 59.566 50.000 13.12 0.24 40.21 3.91
1649 1670 3.961477 TGTCTGACAAACCATTTCGTG 57.039 42.857 8.27 0.00 0.00 4.35
1651 1672 5.990399 TTGTCTGACAAACCATTTCGTGGG 61.990 45.833 20.14 0.00 41.95 4.61
1671 1693 1.000955 GGTCGCAGGATTCCGATGTAT 59.999 52.381 0.00 0.00 35.76 2.29
1695 1717 0.398318 AAGTCAAGCTCGCCTTCCTT 59.602 50.000 0.00 0.00 0.00 3.36
1713 1735 2.108970 CTTGTCTACCTCTGGTACCCC 58.891 57.143 10.07 0.00 37.09 4.95
1925 1947 4.918583 GTCTTCTACCTCAAGAACTTCACG 59.081 45.833 0.00 0.00 31.60 4.35
2034 2056 5.106317 GGATACCATTTTTCTGTCGCTTTGA 60.106 40.000 0.00 0.00 0.00 2.69
2050 2073 4.886971 GCTTTGATAGCTAACTGTGTTCG 58.113 43.478 0.00 0.00 46.77 3.95
2061 2084 5.808540 GCTAACTGTGTTCGGATGTTACATA 59.191 40.000 0.00 0.00 0.00 2.29
2064 2087 6.222038 ACTGTGTTCGGATGTTACATATCT 57.778 37.500 0.00 0.00 0.00 1.98
2109 2132 1.540707 AGAGGTTCTTCTCGTTCCGAC 59.459 52.381 0.00 0.00 38.71 4.79
2110 2133 1.268899 GAGGTTCTTCTCGTTCCGACA 59.731 52.381 0.00 0.00 0.00 4.35
2137 2160 3.141488 GGAGAGGCCGAGCTTCGA 61.141 66.667 0.00 0.00 43.74 3.71
2218 2241 1.600663 CGGTGCTGATTACTAGCGGAG 60.601 57.143 0.00 0.00 44.01 4.63
2390 2425 8.701908 ATGTTCAGGCTGATTATCACAAATAT 57.298 30.769 19.50 1.33 0.00 1.28
2391 2426 9.797642 ATGTTCAGGCTGATTATCACAAATATA 57.202 29.630 19.50 0.00 0.00 0.86
2397 2432 8.571336 AGGCTGATTATCACAAATATAGTTTGC 58.429 33.333 0.00 0.00 32.93 3.68
2440 2476 8.085909 ACTTTACTTTTATTTTTCGACCATGGG 58.914 33.333 18.09 0.00 0.00 4.00
2539 2575 7.832769 TGAAAAACTAAAAGCTACACCAAAGT 58.167 30.769 0.00 0.00 0.00 2.66
2580 3967 4.040095 TCAAATTCCACCAATTGCATCACA 59.960 37.500 0.00 0.00 34.69 3.58
2582 3969 3.383620 TTCCACCAATTGCATCACAAC 57.616 42.857 0.00 0.00 42.27 3.32
2616 4003 9.416794 CATGTATATGGTAGAAAAGCAGAGTAG 57.583 37.037 0.00 0.00 39.39 2.57
2665 4052 4.479786 AAGGGAGAAGATCAGTACTTGC 57.520 45.455 0.00 0.00 0.00 4.01
2666 4053 3.445008 AGGGAGAAGATCAGTACTTGCA 58.555 45.455 0.00 0.00 0.00 4.08
2667 4054 3.450457 AGGGAGAAGATCAGTACTTGCAG 59.550 47.826 0.00 0.00 0.00 4.41
2668 4055 3.196685 GGGAGAAGATCAGTACTTGCAGT 59.803 47.826 0.00 0.00 0.00 4.40
2692 4079 1.202313 GCACAGGCTAGACTAACCTCG 60.202 57.143 0.00 1.61 36.96 4.63
2702 4093 2.830321 AGACTAACCTCGAACCGGAAAT 59.170 45.455 9.46 0.00 0.00 2.17
2750 4141 6.655078 ATCTGCAAAGGTTTGAATAGTTGT 57.345 33.333 6.63 0.00 40.55 3.32
2844 4241 5.375417 AATGCAGACGAATTGAATTGTCA 57.625 34.783 16.78 4.30 33.83 3.58
2949 4346 1.228124 AGCTACAAAGGCACGCCAA 60.228 52.632 11.35 0.00 38.92 4.52
2951 4348 0.663269 GCTACAAAGGCACGCCAAAC 60.663 55.000 11.35 0.00 38.92 2.93
2956 4353 1.040339 AAAGGCACGCCAAACCAGAA 61.040 50.000 11.35 0.00 38.92 3.02
2976 4373 5.296283 CAGAAATGGAGCTAGGAGACATTTG 59.704 44.000 5.76 0.00 40.60 2.32
3041 4450 2.608546 GCACACAAAGCAAGCATGAAAA 59.391 40.909 0.00 0.00 0.00 2.29
3043 4452 4.580528 CACACAAAGCAAGCATGAAAAAC 58.419 39.130 0.00 0.00 0.00 2.43
3044 4453 4.330620 CACACAAAGCAAGCATGAAAAACT 59.669 37.500 0.00 0.00 0.00 2.66
3046 4455 6.035866 CACACAAAGCAAGCATGAAAAACTTA 59.964 34.615 0.00 0.00 0.00 2.24
3047 4456 6.256321 ACACAAAGCAAGCATGAAAAACTTAG 59.744 34.615 0.00 0.00 0.00 2.18
3048 4457 5.754890 ACAAAGCAAGCATGAAAAACTTAGG 59.245 36.000 0.00 0.00 0.00 2.69
3049 4458 5.535753 AAGCAAGCATGAAAAACTTAGGT 57.464 34.783 0.00 0.00 0.00 3.08
3050 4459 6.648879 AAGCAAGCATGAAAAACTTAGGTA 57.351 33.333 0.00 0.00 0.00 3.08
3051 4460 6.648879 AGCAAGCATGAAAAACTTAGGTAA 57.351 33.333 0.00 0.00 0.00 2.85
3052 4461 7.049799 AGCAAGCATGAAAAACTTAGGTAAA 57.950 32.000 0.00 0.00 0.00 2.01
3053 4462 7.147976 AGCAAGCATGAAAAACTTAGGTAAAG 58.852 34.615 0.00 0.00 41.33 1.85
3054 4463 7.014230 AGCAAGCATGAAAAACTTAGGTAAAGA 59.986 33.333 0.00 0.00 38.67 2.52
3055 4464 7.814587 GCAAGCATGAAAAACTTAGGTAAAGAT 59.185 33.333 0.00 0.00 38.67 2.40
3056 4465 9.346725 CAAGCATGAAAAACTTAGGTAAAGATC 57.653 33.333 0.00 0.00 38.67 2.75
3057 4466 8.056407 AGCATGAAAAACTTAGGTAAAGATCC 57.944 34.615 0.00 0.00 38.67 3.36
3064 4473 5.595257 ACTTAGGTAAAGATCCGGAGTTC 57.405 43.478 11.34 3.08 38.67 3.01
3100 4509 0.885196 GCAAATACACCGGCAAGGAA 59.115 50.000 0.00 0.00 45.00 3.36
3103 4512 2.817258 CAAATACACCGGCAAGGAAGAA 59.183 45.455 0.00 0.00 45.00 2.52
3104 4513 2.871096 ATACACCGGCAAGGAAGAAA 57.129 45.000 0.00 0.00 45.00 2.52
3105 4514 2.178912 TACACCGGCAAGGAAGAAAG 57.821 50.000 0.00 0.00 45.00 2.62
3106 4515 0.472471 ACACCGGCAAGGAAGAAAGA 59.528 50.000 0.00 0.00 45.00 2.52
3111 4520 1.677217 CGGCAAGGAAGAAAGAGGGAG 60.677 57.143 0.00 0.00 0.00 4.30
3114 4523 2.709213 CAAGGAAGAAAGAGGGAGCTG 58.291 52.381 0.00 0.00 0.00 4.24
3145 4554 3.585289 TCATGGTAAACTTGGTGGCTAGA 59.415 43.478 0.00 0.00 0.00 2.43
3163 4572 6.708054 TGGCTAGAGTTCTAGTTATACGTACC 59.292 42.308 15.54 7.18 45.85 3.34
3169 4578 6.109359 AGTTCTAGTTATACGTACCGTCAGT 58.891 40.000 0.00 0.00 41.54 3.41
3172 4581 8.552034 GTTCTAGTTATACGTACCGTCAGTTAT 58.448 37.037 0.00 0.00 41.54 1.89
3182 4591 2.028385 ACCGTCAGTTATGTGTTCTCCC 60.028 50.000 0.00 0.00 0.00 4.30
3203 4612 4.523173 CCCCCGCGTGATCATATATATAGT 59.477 45.833 4.92 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 9.525826 AGTTCATAATGAGGTCAAGAAAATCTT 57.474 29.630 0.00 0.00 37.14 2.40
25 26 9.525826 AAGTTCATAATGAGGTCAAGAAAATCT 57.474 29.630 0.00 0.00 0.00 2.40
29 30 9.965824 GAAAAAGTTCATAATGAGGTCAAGAAA 57.034 29.630 0.00 0.00 33.61 2.52
30 31 9.354673 AGAAAAAGTTCATAATGAGGTCAAGAA 57.645 29.630 0.00 0.00 36.09 2.52
31 32 8.924511 AGAAAAAGTTCATAATGAGGTCAAGA 57.075 30.769 0.00 0.00 36.09 3.02
37 38 9.727627 GCAGATAAGAAAAAGTTCATAATGAGG 57.272 33.333 0.00 0.00 36.09 3.86
38 39 9.430838 CGCAGATAAGAAAAAGTTCATAATGAG 57.569 33.333 0.00 0.00 36.09 2.90
39 40 8.397906 CCGCAGATAAGAAAAAGTTCATAATGA 58.602 33.333 0.00 0.00 36.09 2.57
40 41 7.166473 GCCGCAGATAAGAAAAAGTTCATAATG 59.834 37.037 0.00 0.00 36.09 1.90
41 42 7.148086 TGCCGCAGATAAGAAAAAGTTCATAAT 60.148 33.333 0.00 0.00 36.09 1.28
42 43 6.150307 TGCCGCAGATAAGAAAAAGTTCATAA 59.850 34.615 0.00 0.00 36.09 1.90
43 44 5.645929 TGCCGCAGATAAGAAAAAGTTCATA 59.354 36.000 0.00 0.00 36.09 2.15
44 45 4.458989 TGCCGCAGATAAGAAAAAGTTCAT 59.541 37.500 0.00 0.00 36.09 2.57
45 46 3.818210 TGCCGCAGATAAGAAAAAGTTCA 59.182 39.130 0.00 0.00 36.09 3.18
46 47 4.419522 TGCCGCAGATAAGAAAAAGTTC 57.580 40.909 0.00 0.00 0.00 3.01
47 48 4.846779 TTGCCGCAGATAAGAAAAAGTT 57.153 36.364 0.00 0.00 0.00 2.66
48 49 4.437390 CGATTGCCGCAGATAAGAAAAAGT 60.437 41.667 0.00 0.00 0.00 2.66
49 50 4.031028 CGATTGCCGCAGATAAGAAAAAG 58.969 43.478 0.00 0.00 0.00 2.27
50 51 3.438781 ACGATTGCCGCAGATAAGAAAAA 59.561 39.130 0.00 0.00 43.32 1.94
51 52 3.006940 ACGATTGCCGCAGATAAGAAAA 58.993 40.909 0.00 0.00 43.32 2.29
52 53 2.627945 ACGATTGCCGCAGATAAGAAA 58.372 42.857 0.00 0.00 43.32 2.52
53 54 2.309528 ACGATTGCCGCAGATAAGAA 57.690 45.000 0.00 0.00 43.32 2.52
54 55 2.201732 GAACGATTGCCGCAGATAAGA 58.798 47.619 0.00 0.00 43.32 2.10
55 56 1.933181 TGAACGATTGCCGCAGATAAG 59.067 47.619 0.00 0.00 43.32 1.73
56 57 2.017138 TGAACGATTGCCGCAGATAA 57.983 45.000 0.00 0.00 43.32 1.75
57 58 1.933181 CTTGAACGATTGCCGCAGATA 59.067 47.619 0.00 0.00 43.32 1.98
58 59 0.729116 CTTGAACGATTGCCGCAGAT 59.271 50.000 0.00 0.00 43.32 2.90
59 60 0.320334 TCTTGAACGATTGCCGCAGA 60.320 50.000 0.00 0.00 43.32 4.26
60 61 0.516877 TTCTTGAACGATTGCCGCAG 59.483 50.000 0.00 0.00 43.32 5.18
61 62 1.164411 ATTCTTGAACGATTGCCGCA 58.836 45.000 0.00 0.00 43.32 5.69
62 63 2.262572 AATTCTTGAACGATTGCCGC 57.737 45.000 0.00 0.00 43.32 6.53
63 64 5.229887 CCAATAAATTCTTGAACGATTGCCG 59.770 40.000 0.00 0.00 45.44 5.69
64 65 5.005682 GCCAATAAATTCTTGAACGATTGCC 59.994 40.000 0.00 0.00 0.00 4.52
65 66 5.807011 AGCCAATAAATTCTTGAACGATTGC 59.193 36.000 0.00 0.00 0.00 3.56
66 67 7.028962 TGAGCCAATAAATTCTTGAACGATTG 58.971 34.615 0.00 0.00 0.00 2.67
67 68 7.156876 TGAGCCAATAAATTCTTGAACGATT 57.843 32.000 0.00 0.00 0.00 3.34
68 69 6.757897 TGAGCCAATAAATTCTTGAACGAT 57.242 33.333 0.00 0.00 0.00 3.73
69 70 6.374053 TCATGAGCCAATAAATTCTTGAACGA 59.626 34.615 0.00 0.00 0.00 3.85
70 71 6.554419 TCATGAGCCAATAAATTCTTGAACG 58.446 36.000 0.00 0.00 0.00 3.95
71 72 8.937634 ATTCATGAGCCAATAAATTCTTGAAC 57.062 30.769 0.00 0.00 36.89 3.18
73 74 8.344831 CGTATTCATGAGCCAATAAATTCTTGA 58.655 33.333 0.00 0.00 0.00 3.02
74 75 8.344831 TCGTATTCATGAGCCAATAAATTCTTG 58.655 33.333 0.00 0.00 0.00 3.02
75 76 8.450578 TCGTATTCATGAGCCAATAAATTCTT 57.549 30.769 0.00 0.00 0.00 2.52
76 77 7.933577 TCTCGTATTCATGAGCCAATAAATTCT 59.066 33.333 0.00 0.00 37.66 2.40
77 78 8.087982 TCTCGTATTCATGAGCCAATAAATTC 57.912 34.615 0.00 0.00 37.66 2.17
78 79 8.450578 TTCTCGTATTCATGAGCCAATAAATT 57.549 30.769 0.00 0.00 37.66 1.82
79 80 7.716998 ACTTCTCGTATTCATGAGCCAATAAAT 59.283 33.333 0.00 0.00 37.66 1.40
80 81 7.047891 ACTTCTCGTATTCATGAGCCAATAAA 58.952 34.615 0.00 0.00 37.66 1.40
81 82 6.582636 ACTTCTCGTATTCATGAGCCAATAA 58.417 36.000 0.00 0.00 37.66 1.40
82 83 6.161855 ACTTCTCGTATTCATGAGCCAATA 57.838 37.500 0.00 0.00 37.66 1.90
83 84 5.028549 ACTTCTCGTATTCATGAGCCAAT 57.971 39.130 0.00 0.00 37.66 3.16
84 85 4.471904 ACTTCTCGTATTCATGAGCCAA 57.528 40.909 0.00 0.00 37.66 4.52
85 86 4.081697 TGAACTTCTCGTATTCATGAGCCA 60.082 41.667 0.00 0.00 37.66 4.75
125 126 9.751542 CTAAGAATAATCGTTCCTGATTACTGT 57.248 33.333 0.00 0.00 42.04 3.55
192 194 6.675486 GCTGCGTTGCTTTCTTTATTCAGATA 60.675 38.462 0.00 0.00 0.00 1.98
213 215 3.429881 GCCACAAATTTCTAACAAGCTGC 59.570 43.478 0.00 0.00 0.00 5.25
361 363 0.394352 CTCCTACCCCGCTGCAAATT 60.394 55.000 0.00 0.00 0.00 1.82
385 390 3.699038 GGATAGTGTGAGCTCTCTTCAGT 59.301 47.826 16.19 13.16 0.00 3.41
403 408 5.831525 TCTCTGTACCAAGCGATTTAGGATA 59.168 40.000 0.00 0.00 0.00 2.59
404 409 4.649674 TCTCTGTACCAAGCGATTTAGGAT 59.350 41.667 0.00 0.00 0.00 3.24
432 439 6.227522 CGATCTGTACCTATCTCTCTGAGAA 58.772 44.000 8.95 0.83 42.27 2.87
458 465 3.416156 GTCTCATTCCCTTTGCTCTGTT 58.584 45.455 0.00 0.00 0.00 3.16
509 519 1.967319 TGAACCTTGTCAAGTGGCTC 58.033 50.000 11.61 0.21 0.00 4.70
512 522 3.381272 ACACAATGAACCTTGTCAAGTGG 59.619 43.478 11.61 0.67 39.77 4.00
526 536 5.352016 GCTACGGGTACATTTTACACAATGA 59.648 40.000 0.00 0.00 37.55 2.57
547 557 3.647590 TGGATGTCATCATAAGCTGGCTA 59.352 43.478 14.72 0.00 34.06 3.93
562 572 3.008485 GGGGAATAGATGGACTGGATGTC 59.992 52.174 0.00 0.00 44.63 3.06
569 579 3.254960 CTGGATGGGGAATAGATGGACT 58.745 50.000 0.00 0.00 0.00 3.85
596 606 2.271800 CCAGTACACCAAGCGATTCTC 58.728 52.381 0.00 0.00 0.00 2.87
606 616 0.767998 TTGATGCACCCAGTACACCA 59.232 50.000 0.00 0.00 0.00 4.17
749 759 2.203084 TTTCGGCTCCGTTGTGCA 60.203 55.556 8.28 0.00 40.74 4.57
807 817 2.093921 GGAGAAGACAGGTGGTTAGCTC 60.094 54.545 0.00 0.00 30.85 4.09
914 924 4.193826 TCTTGATGAGTTCTCGGAAAGG 57.806 45.455 0.00 0.00 0.00 3.11
992 1002 1.401670 GCTCGACAGACATCGTGAAGT 60.402 52.381 1.78 0.00 42.80 3.01
1014 1024 4.022589 ACTTACGTGAGGAATTTCGTGAGA 60.023 41.667 12.41 0.00 40.51 3.27
1017 1027 3.122948 CCACTTACGTGAGGAATTTCGTG 59.877 47.826 12.41 0.00 43.97 4.35
1157 1168 2.125310 CACTCCAACGCCGGCATA 60.125 61.111 28.98 5.06 0.00 3.14
1343 1354 0.686789 GCCCCCAAATTGCTGAAAGT 59.313 50.000 0.00 0.00 35.30 2.66
1422 1443 3.450457 AGACCAAGATCTCTAGCCAGTTG 59.550 47.826 0.00 0.00 0.00 3.16
1448 1469 2.493035 TGCTGAAATTCGTCAAGCTCA 58.507 42.857 4.97 0.00 0.00 4.26
1649 1670 3.467226 TCGGAATCCTGCGACCCC 61.467 66.667 0.00 0.00 40.84 4.95
1671 1693 3.334583 AAGGCGAGCTTGACTTCATAA 57.665 42.857 17.05 0.00 28.57 1.90
1713 1735 1.202879 TGGCAACTTACCCTTGTCTGG 60.203 52.381 0.00 0.00 37.61 3.86
1925 1947 0.468400 AGAGCTCGTATCCCCTGTCC 60.468 60.000 8.37 0.00 0.00 4.02
2034 2056 4.737855 ACATCCGAACACAGTTAGCTAT 57.262 40.909 0.00 0.00 0.00 2.97
2048 2071 4.783764 ATCGCAGATATGTAACATCCGA 57.216 40.909 0.00 0.00 45.12 4.55
2049 2072 5.845985 AAATCGCAGATATGTAACATCCG 57.154 39.130 0.00 0.00 45.12 4.18
2050 2073 6.959361 ACAAAATCGCAGATATGTAACATCC 58.041 36.000 0.00 0.00 45.12 3.51
2061 2084 3.311106 CAGCACAAACAAAATCGCAGAT 58.689 40.909 0.00 0.00 45.12 2.90
2064 2087 1.135915 ACCAGCACAAACAAAATCGCA 59.864 42.857 0.00 0.00 0.00 5.10
2109 2132 3.522731 CCTCTCCGCTCGGTCCTG 61.523 72.222 8.28 0.00 36.47 3.86
2218 2241 1.400737 ACCACGACCATCCTAGCTAC 58.599 55.000 0.00 0.00 0.00 3.58
2414 2449 8.085909 CCCATGGTCGAAAAATAAAAGTAAAGT 58.914 33.333 11.73 0.00 0.00 2.66
2415 2450 8.085909 ACCCATGGTCGAAAAATAAAAGTAAAG 58.914 33.333 11.73 0.00 0.00 1.85
2419 2454 6.413783 AACCCATGGTCGAAAAATAAAAGT 57.586 33.333 11.73 0.00 33.12 2.66
2420 2455 7.095397 GGAAAACCCATGGTCGAAAAATAAAAG 60.095 37.037 11.73 0.00 33.12 2.27
2440 2476 7.147983 TGGTGTACCAGCATAAATATGGAAAAC 60.148 37.037 0.00 0.00 42.01 2.43
2490 2526 4.671377 TGTTCTATCGCAATGATTTTGCC 58.329 39.130 4.86 0.00 42.10 4.52
2539 2575 7.492669 GGAATTTGAGACAACGATTCTAGATCA 59.507 37.037 0.00 0.00 0.00 2.92
2554 2590 4.255833 TGCAATTGGTGGAATTTGAGAC 57.744 40.909 7.72 0.00 31.41 3.36
2646 4033 3.791245 CTGCAAGTACTGATCTTCTCCC 58.209 50.000 0.00 0.00 0.00 4.30
2665 4052 1.274728 AGTCTAGCCTGTGCAAGACTG 59.725 52.381 14.21 0.00 41.13 3.51
2666 4053 1.638529 AGTCTAGCCTGTGCAAGACT 58.361 50.000 10.09 10.09 41.13 3.24
2667 4054 3.254892 GTTAGTCTAGCCTGTGCAAGAC 58.745 50.000 5.94 5.94 41.13 3.01
2668 4055 2.233922 GGTTAGTCTAGCCTGTGCAAGA 59.766 50.000 5.53 0.00 41.13 3.02
2692 4079 3.181500 GCAGGTATGTTCATTTCCGGTTC 60.181 47.826 0.00 0.00 0.00 3.62
2702 4093 5.129320 AGTCTATCATGTGCAGGTATGTTCA 59.871 40.000 0.00 0.00 0.00 3.18
2773 4164 9.802039 AATGTGTTCAAGGGTCTACTATTTTTA 57.198 29.630 0.00 0.00 0.00 1.52
2949 4346 3.198853 GTCTCCTAGCTCCATTTCTGGTT 59.801 47.826 0.00 0.00 43.61 3.67
2951 4348 2.768527 TGTCTCCTAGCTCCATTTCTGG 59.231 50.000 0.00 0.00 44.64 3.86
2956 4353 4.851639 ACAAATGTCTCCTAGCTCCATT 57.148 40.909 0.00 0.00 0.00 3.16
2976 4373 3.307242 GCTCGAGATATGTTGTGTGGAAC 59.693 47.826 18.75 0.00 37.35 3.62
3041 4450 5.105023 GGAACTCCGGATCTTTACCTAAGTT 60.105 44.000 3.57 0.00 34.74 2.66
3043 4452 4.404715 TGGAACTCCGGATCTTTACCTAAG 59.595 45.833 3.57 0.00 39.43 2.18
3044 4453 4.161001 GTGGAACTCCGGATCTTTACCTAA 59.839 45.833 3.57 0.00 39.43 2.69
3046 4455 2.500504 GTGGAACTCCGGATCTTTACCT 59.499 50.000 3.57 0.00 39.43 3.08
3047 4456 2.419713 GGTGGAACTCCGGATCTTTACC 60.420 54.545 3.57 8.11 39.43 2.85
3048 4457 2.419713 GGGTGGAACTCCGGATCTTTAC 60.420 54.545 3.57 0.00 44.02 2.01
3049 4458 1.835531 GGGTGGAACTCCGGATCTTTA 59.164 52.381 3.57 0.00 44.02 1.85
3050 4459 0.618981 GGGTGGAACTCCGGATCTTT 59.381 55.000 3.57 0.00 44.02 2.52
3051 4460 0.546747 TGGGTGGAACTCCGGATCTT 60.547 55.000 3.57 0.00 44.02 2.40
3052 4461 1.080354 TGGGTGGAACTCCGGATCT 59.920 57.895 3.57 0.00 44.02 2.75
3053 4462 1.221021 GTGGGTGGAACTCCGGATC 59.779 63.158 3.57 0.00 44.02 3.36
3054 4463 2.298661 GGTGGGTGGAACTCCGGAT 61.299 63.158 3.57 0.00 44.02 4.18
3055 4464 2.926242 GGTGGGTGGAACTCCGGA 60.926 66.667 2.93 2.93 44.02 5.14
3056 4465 2.928396 AGGTGGGTGGAACTCCGG 60.928 66.667 0.00 0.00 44.02 5.14
3057 4466 1.481056 AAGAGGTGGGTGGAACTCCG 61.481 60.000 0.00 0.00 44.02 4.63
3100 4509 0.415429 TCTCCCAGCTCCCTCTTTCT 59.585 55.000 0.00 0.00 0.00 2.52
3103 4512 1.684049 CGTCTCCCAGCTCCCTCTT 60.684 63.158 0.00 0.00 0.00 2.85
3104 4513 1.943730 ATCGTCTCCCAGCTCCCTCT 61.944 60.000 0.00 0.00 0.00 3.69
3105 4514 1.456705 ATCGTCTCCCAGCTCCCTC 60.457 63.158 0.00 0.00 0.00 4.30
3106 4515 1.456705 GATCGTCTCCCAGCTCCCT 60.457 63.158 0.00 0.00 0.00 4.20
3111 4520 1.040646 TACCATGATCGTCTCCCAGC 58.959 55.000 0.00 0.00 0.00 4.85
3114 4523 3.821421 AGTTTACCATGATCGTCTCCC 57.179 47.619 0.00 0.00 0.00 4.30
3163 4572 2.618053 GGGGAGAACACATAACTGACG 58.382 52.381 0.00 0.00 0.00 4.35
3169 4578 1.219664 CGCGGGGGAGAACACATAA 59.780 57.895 0.00 0.00 0.00 1.90
3172 4581 4.308458 CACGCGGGGGAGAACACA 62.308 66.667 12.47 0.00 0.00 3.72
3182 4591 6.561737 AGACTATATATATGATCACGCGGG 57.438 41.667 12.47 6.51 0.00 6.13


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

AutoCloner maintained by Alex Coulton.