Multiple sequence alignment - TraesCS5B01G112200

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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 TraesCS5B01G112200 chr5B 100.000 4299 0 0 1 4299 173854704 173859002 0.000000e+00 7939.0
1 TraesCS5B01G112200 chr5D 91.725 1861 112 24 3 1836 174830527 174828682 0.000000e+00 2545.0
2 TraesCS5B01G112200 chr5D 91.193 1056 46 18 2673 3682 174827883 174826829 0.000000e+00 1391.0
3 TraesCS5B01G112200 chr5D 92.458 769 27 6 1962 2730 174828680 174827943 0.000000e+00 1070.0
4 TraesCS5B01G112200 chr5D 93.059 389 22 4 3911 4299 174825855 174825472 8.070000e-157 564.0
5 TraesCS5B01G112200 chr5D 85.957 235 28 3 3820 4052 57846054 57846285 3.320000e-61 246.0
6 TraesCS5B01G112200 chr5D 84.681 235 31 3 3819 4051 478443041 478443272 3.340000e-56 230.0
7 TraesCS5B01G112200 chr5A 93.072 1761 70 14 1847 3579 167116754 167118490 0.000000e+00 2529.0
8 TraesCS5B01G112200 chr5A 93.706 1128 49 10 754 1869 167115417 167116534 0.000000e+00 1670.0
9 TraesCS5B01G112200 chr5A 92.285 674 38 4 93 753 167114376 167115048 0.000000e+00 944.0
10 TraesCS5B01G112200 chr5A 90.933 386 32 3 3818 4200 167119094 167119479 2.290000e-142 516.0
11 TraesCS5B01G112200 chr5A 95.187 187 9 0 2725 2911 167116759 167116573 3.250000e-76 296.0
12 TraesCS5B01G112200 chr5A 91.391 151 7 3 4149 4299 167119476 167119620 7.290000e-48 202.0
13 TraesCS5B01G112200 chr5A 90.909 110 10 0 2 111 167072261 167072370 9.630000e-32 148.0
14 TraesCS5B01G112200 chr2B 82.908 392 61 6 2148 2536 158621926 158622314 8.850000e-92 348.0
15 TraesCS5B01G112200 chr2B 100.000 38 0 0 996 1033 158621337 158621374 2.140000e-08 71.3
16 TraesCS5B01G112200 chr3D 87.234 235 24 4 3819 4051 482488081 482487851 3.300000e-66 263.0
17 TraesCS5B01G112200 chr3D 86.207 232 27 3 3820 4049 492119806 492119578 3.320000e-61 246.0
18 TraesCS5B01G112200 chr3B 85.169 236 31 2 3819 4051 679195462 679195228 5.560000e-59 239.0
19 TraesCS5B01G112200 chr3B 82.403 233 25 8 4080 4299 597428325 597428096 5.680000e-44 189.0
20 TraesCS5B01G112200 chr1D 85.000 240 31 3 3820 4057 1531914 1531678 5.560000e-59 239.0
21 TraesCS5B01G112200 chr4B 85.281 231 28 4 3821 4049 633785331 633785557 2.580000e-57 233.0
22 TraesCS5B01G112200 chr2D 81.974 233 26 6 4080 4299 469106391 469106620 2.640000e-42 183.0
23 TraesCS5B01G112200 chr2D 97.368 38 1 0 996 1033 108924862 108924899 9.980000e-07 65.8
24 TraesCS5B01G112200 chr2A 82.222 225 22 9 4089 4299 404906500 404906280 1.230000e-40 178.0
25 TraesCS5B01G112200 chr1A 81.545 233 27 6 4080 4299 461965248 461965477 1.230000e-40 178.0
26 TraesCS5B01G112200 chr1A 81.116 233 28 6 4080 4299 35558571 35558800 5.720000e-39 172.0
27 TraesCS5B01G112200 chrUn 87.179 156 17 1 4144 4299 96554466 96554314 1.590000e-39 174.0
28 TraesCS5B01G112200 chr1B 81.116 233 28 6 4080 4299 470720613 470720384 5.720000e-39 172.0


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 TraesCS5B01G112200 chr5B 173854704 173859002 4298 False 7939.00 7939 100.00000 1 4299 1 chr5B.!!$F1 4298
1 TraesCS5B01G112200 chr5D 174825472 174830527 5055 True 1392.50 2545 92.10875 3 4299 4 chr5D.!!$R1 4296
2 TraesCS5B01G112200 chr5A 167114376 167119620 5244 False 1172.20 2529 92.27740 93 4299 5 chr5A.!!$F2 4206
3 TraesCS5B01G112200 chr2B 158621337 158622314 977 False 209.65 348 91.45400 996 2536 2 chr2B.!!$F1 1540

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
193 195 0.254747 TAAATCGACCTTGCCCCTGG 59.745 55.0 0.0 0.0 0.0 4.45 F
1058 1450 0.396417 CCACGATCCTCCTGTCTCCT 60.396 60.0 0.0 0.0 0.0 3.69 F
1995 2648 0.037790 TTGCCCGCTTTTAATGCACC 60.038 50.0 0.0 0.0 0.0 5.01 F
1999 2652 0.173255 CCGCTTTTAATGCACCTGGG 59.827 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2648 0.394762 ACATGTGCCACTATGCCCAG 60.395 55.000 0.00 0.0 0.00 4.45 R
1999 2652 0.734889 GACCACATGTGCCACTATGC 59.265 55.000 20.81 0.0 0.00 3.14 R
3107 3877 1.136891 GCCAACCCTGCAATATGGTTC 59.863 52.381 6.63 0.0 40.31 3.62 R
3587 4445 2.027561 CCCCGTTGGAATAGACAACTCA 60.028 50.000 6.72 0.0 44.49 3.41 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
43 44 1.146930 ATCGCATGGCCGTCAATCT 59.853 52.632 0.00 0.00 0.00 2.40
63 64 0.321298 ACAAAGCTCGCCATAACCGT 60.321 50.000 0.00 0.00 0.00 4.83
67 68 1.944676 GCTCGCCATAACCGTCTCG 60.945 63.158 0.00 0.00 0.00 4.04
73 74 1.067582 CATAACCGTCTCGAGGGCC 59.932 63.158 13.56 0.00 39.85 5.80
184 186 4.589908 ACCTTTTGCAGATAAATCGACCT 58.410 39.130 0.00 0.00 0.00 3.85
193 195 0.254747 TAAATCGACCTTGCCCCTGG 59.745 55.000 0.00 0.00 0.00 4.45
207 209 2.480555 CTGGCGCATCGTTGGTTC 59.519 61.111 10.83 0.00 0.00 3.62
252 254 3.371063 ATCGCGTGACCTCACCGT 61.371 61.111 5.77 0.00 43.66 4.83
371 384 1.705997 AACCTCACCTCAACCGGCTT 61.706 55.000 0.00 0.00 0.00 4.35
413 426 7.241663 TCTTACGGACACATGCAATATTTAC 57.758 36.000 0.00 0.00 0.00 2.01
416 429 6.509418 ACGGACACATGCAATATTTACTTT 57.491 33.333 0.00 0.00 0.00 2.66
452 468 8.192774 TCTCATCCATGTCAAAAATTTATGAGC 58.807 33.333 13.39 0.00 38.32 4.26
513 531 3.311990 TCAGGACATGGCAGTCTATGAT 58.688 45.455 0.00 0.00 38.57 2.45
604 622 9.337091 CCAAAACGTGTTATATTTAGAAACAGG 57.663 33.333 0.00 6.50 42.01 4.00
752 1139 9.457436 TTTGAGGGGATACTGAACTATTTTTAC 57.543 33.333 0.00 0.00 0.00 2.01
825 1216 0.667993 CCACACACACACATTGGACC 59.332 55.000 0.00 0.00 0.00 4.46
850 1241 3.351416 GCCCAACGAACGACCCAC 61.351 66.667 0.14 0.00 0.00 4.61
859 1250 1.792993 CGAACGACCCACACTCGATAC 60.793 57.143 0.00 0.00 35.08 2.24
1058 1450 0.396417 CCACGATCCTCCTGTCTCCT 60.396 60.000 0.00 0.00 0.00 3.69
1084 1476 2.067766 CTCTTGTGCTCTCTGCTCAAC 58.932 52.381 0.00 0.00 46.19 3.18
1316 1713 2.743928 CGTTGCTGTGAGGGGAGC 60.744 66.667 0.00 0.00 35.65 4.70
1356 1753 1.134487 CATGATTTGCGTCGGCGTT 59.866 52.632 12.58 0.00 44.10 4.84
1357 1754 0.454285 CATGATTTGCGTCGGCGTTT 60.454 50.000 12.58 0.00 44.10 3.60
1401 1798 6.017192 GGTTTGTTTGCATAAGATTTTTGGCT 60.017 34.615 0.00 0.00 0.00 4.75
1434 1832 2.758979 GGAGTACCTGGATTTGAGTCGA 59.241 50.000 0.00 0.00 0.00 4.20
1435 1833 3.194968 GGAGTACCTGGATTTGAGTCGAA 59.805 47.826 0.00 0.00 0.00 3.71
1533 1931 2.226674 CTCTGTCAGTACGCTCAGTTGA 59.773 50.000 0.00 0.00 0.00 3.18
1540 1938 4.700692 TCAGTACGCTCAGTTGATAGTCTT 59.299 41.667 0.00 0.00 0.00 3.01
1715 2124 1.003580 TGGTTCTTCATGTGGGAGCTC 59.996 52.381 4.71 4.71 0.00 4.09
1732 2141 6.558775 TGGGAGCTCTGAATTTGGTATATACT 59.441 38.462 14.64 0.00 0.00 2.12
1733 2142 7.733047 TGGGAGCTCTGAATTTGGTATATACTA 59.267 37.037 14.64 3.71 0.00 1.82
1735 2144 9.593134 GGAGCTCTGAATTTGGTATATACTATG 57.407 37.037 14.64 0.00 0.00 2.23
1736 2145 9.092876 GAGCTCTGAATTTGGTATATACTATGC 57.907 37.037 12.54 4.12 0.00 3.14
1737 2146 8.043710 AGCTCTGAATTTGGTATATACTATGCC 58.956 37.037 12.54 0.00 0.00 4.40
1738 2147 7.824289 GCTCTGAATTTGGTATATACTATGCCA 59.176 37.037 12.54 0.46 31.92 4.92
1767 2176 8.970859 CTAGAATAGTCCCAGAAATGATGTTT 57.029 34.615 0.00 0.00 32.85 2.83
1832 2241 7.269477 AGCCTAGATGTTGCATATTCTTTTC 57.731 36.000 0.00 0.00 0.00 2.29
1837 2246 5.355071 AGATGTTGCATATTCTTTTCTGCGA 59.645 36.000 0.00 0.00 37.44 5.10
1840 2249 5.163824 TGTTGCATATTCTTTTCTGCGAGAG 60.164 40.000 0.00 0.00 37.44 3.20
1865 2274 9.494271 AGCATGTAATTCATACTACATACAAGG 57.506 33.333 0.00 0.00 36.77 3.61
1869 2278 9.607988 TGTAATTCATACTACATACAAGGGTTG 57.392 33.333 0.00 0.00 35.42 3.77
1875 2528 4.662278 ACTACATACAAGGGTTGTGCATT 58.338 39.130 2.50 0.00 45.03 3.56
1886 2539 5.296748 AGGGTTGTGCATTTATTTGTTCAC 58.703 37.500 0.00 0.00 0.00 3.18
1981 2634 9.248291 CTTGTGAATGTGTTATTATAATTGCCC 57.752 33.333 2.68 0.00 0.00 5.36
1995 2648 0.037790 TTGCCCGCTTTTAATGCACC 60.038 50.000 0.00 0.00 0.00 5.01
1999 2652 0.173255 CCGCTTTTAATGCACCTGGG 59.827 55.000 0.00 0.00 0.00 4.45
2010 2663 1.750399 CACCTGGGCATAGTGGCAC 60.750 63.158 10.29 10.29 45.76 5.01
2027 2680 0.961019 CACATGTGGTCCCACTTTGG 59.039 55.000 18.51 6.81 46.30 3.28
2036 2689 1.077265 CCCACTTTGGACCTGGCAT 59.923 57.895 0.00 0.00 40.96 4.40
2102 2755 3.841643 CAACTCATGCCTTGTTTCCATC 58.158 45.455 0.00 0.00 0.00 3.51
2235 2888 2.200081 AGCTGGTTGGTGAGTATGGAT 58.800 47.619 0.00 0.00 0.00 3.41
2583 3236 3.597255 TGCATGTTTTGGCATATGGTTG 58.403 40.909 4.56 0.00 34.58 3.77
2631 3284 8.860088 AGAAATCTAAATGGTTTGCACTAGTTT 58.140 29.630 0.00 0.00 0.00 2.66
2635 3288 7.422399 TCTAAATGGTTTGCACTAGTTTGTTC 58.578 34.615 0.00 0.00 0.00 3.18
2641 3294 7.721402 TGGTTTGCACTAGTTTGTTCAATATT 58.279 30.769 0.00 0.00 0.00 1.28
2650 3303 8.545472 ACTAGTTTGTTCAATATTGGCTACCTA 58.455 33.333 15.36 8.08 0.00 3.08
2668 3321 6.320672 GCTACCTAATACTGGTCTGTTACTGA 59.679 42.308 0.00 0.00 38.88 3.41
2671 3324 8.147244 ACCTAATACTGGTCTGTTACTGATTT 57.853 34.615 0.00 0.00 31.03 2.17
2696 3349 9.681692 TTTTACATGCATCTATGAATTACATGC 57.318 29.630 0.00 0.00 39.77 4.06
2708 3361 3.862877 ATTACATGCTGGCCTGATACA 57.137 42.857 14.77 2.15 0.00 2.29
2801 3571 9.950496 ATGAAATCTACTGTACTTTCAATCACT 57.050 29.630 17.70 5.68 40.03 3.41
2819 3589 2.932614 CACTGCACTGCCTATCTTGTAC 59.067 50.000 0.00 0.00 0.00 2.90
2822 3592 2.304470 TGCACTGCCTATCTTGTACCAA 59.696 45.455 0.00 0.00 0.00 3.67
2849 3619 4.957954 ACATGTTTATGGTCTGATTGCCAT 59.042 37.500 0.00 4.04 46.24 4.40
2910 3680 8.813951 GGTAGGTTGTATATCTTGCTAATACCT 58.186 37.037 0.00 0.00 36.36 3.08
2914 3684 8.368668 GGTTGTATATCTTGCTAATACCTCACT 58.631 37.037 0.00 0.00 0.00 3.41
2952 3722 6.706270 TGAACCTGTTTTCTGTAACTGAGATC 59.294 38.462 0.00 0.00 0.00 2.75
2970 3740 9.896645 ACTGAGATCATGTCAATATTGTTAGTT 57.103 29.630 14.97 0.00 0.00 2.24
3073 3843 3.508793 CCATGAATGTTCCTGCTTGTTCT 59.491 43.478 0.00 0.00 0.00 3.01
3087 3857 6.395426 TGCTTGTTCTCTTTGTGAATGAAT 57.605 33.333 0.00 0.00 0.00 2.57
3467 4254 5.296813 AGCTATTTGGTCGTGATGTTTTC 57.703 39.130 0.00 0.00 0.00 2.29
3525 4312 3.522759 TGGGGTGGTTGTCTGATAGTTA 58.477 45.455 0.00 0.00 0.00 2.24
3587 4445 6.211184 TGATCTATTTGCTGGTTTGTTTCCAT 59.789 34.615 0.00 0.00 34.26 3.41
3598 4456 6.068010 TGGTTTGTTTCCATGAGTTGTCTAT 58.932 36.000 0.00 0.00 0.00 1.98
3620 4478 3.112263 TCCAACGGGGATCAATACTCTT 58.888 45.455 0.00 0.00 42.15 2.85
3622 4480 4.717778 TCCAACGGGGATCAATACTCTTTA 59.282 41.667 0.00 0.00 42.15 1.85
3623 4481 5.057149 CCAACGGGGATCAATACTCTTTAG 58.943 45.833 0.00 0.00 40.01 1.85
3624 4482 4.338379 ACGGGGATCAATACTCTTTAGC 57.662 45.455 0.00 0.00 0.00 3.09
3625 4483 3.967987 ACGGGGATCAATACTCTTTAGCT 59.032 43.478 0.00 0.00 0.00 3.32
3628 4486 6.102663 CGGGGATCAATACTCTTTAGCTATG 58.897 44.000 0.00 0.00 0.00 2.23
3629 4487 5.877564 GGGGATCAATACTCTTTAGCTATGC 59.122 44.000 0.00 0.00 0.00 3.14
3630 4488 5.578727 GGGATCAATACTCTTTAGCTATGCG 59.421 44.000 0.00 0.00 0.00 4.73
3631 4489 6.159988 GGATCAATACTCTTTAGCTATGCGT 58.840 40.000 0.00 0.00 0.00 5.24
3637 4511 9.459640 CAATACTCTTTAGCTATGCGTAAGTTA 57.540 33.333 0.00 0.00 41.68 2.24
3675 4549 0.177141 GCAACCACGTGCCCTAGATA 59.823 55.000 10.91 0.00 38.66 1.98
3682 4556 3.069016 CCACGTGCCCTAGATACATACAA 59.931 47.826 10.91 0.00 0.00 2.41
3683 4557 4.049186 CACGTGCCCTAGATACATACAAC 58.951 47.826 0.82 0.00 0.00 3.32
3684 4558 3.069158 ACGTGCCCTAGATACATACAACC 59.931 47.826 0.00 0.00 0.00 3.77
3685 4559 3.069016 CGTGCCCTAGATACATACAACCA 59.931 47.826 0.00 0.00 0.00 3.67
3686 4560 4.262463 CGTGCCCTAGATACATACAACCAT 60.262 45.833 0.00 0.00 0.00 3.55
3688 4562 6.351033 CGTGCCCTAGATACATACAACCATAT 60.351 42.308 0.00 0.00 0.00 1.78
3689 4563 7.042335 GTGCCCTAGATACATACAACCATATC 58.958 42.308 0.00 0.00 0.00 1.63
3690 4564 6.728632 TGCCCTAGATACATACAACCATATCA 59.271 38.462 0.00 0.00 0.00 2.15
3692 4566 8.100791 GCCCTAGATACATACAACCATATCAAA 58.899 37.037 0.00 0.00 0.00 2.69
3730 4613 5.801350 TCTTTGATTCGTAGGATTGCAAG 57.199 39.130 4.94 0.00 0.00 4.01
3738 4621 4.491676 TCGTAGGATTGCAAGAACTACAC 58.508 43.478 24.99 11.77 35.05 2.90
3740 4623 3.788227 AGGATTGCAAGAACTACACCA 57.212 42.857 4.94 0.00 0.00 4.17
3741 4624 4.307032 AGGATTGCAAGAACTACACCAT 57.693 40.909 4.94 0.00 0.00 3.55
3742 4625 4.012374 AGGATTGCAAGAACTACACCATG 58.988 43.478 4.94 0.00 0.00 3.66
3743 4626 3.758554 GGATTGCAAGAACTACACCATGT 59.241 43.478 4.94 0.00 0.00 3.21
3745 4628 2.412870 TGCAAGAACTACACCATGTCG 58.587 47.619 0.00 0.00 0.00 4.35
3750 4894 5.466819 CAAGAACTACACCATGTCGAGTTA 58.533 41.667 0.00 0.00 31.45 2.24
3756 4900 2.103432 ACACCATGTCGAGTTACCACAA 59.897 45.455 0.00 0.00 0.00 3.33
3775 4919 5.452496 CCACAACCATACAACCACATCAAAA 60.452 40.000 0.00 0.00 0.00 2.44
3999 5974 5.975693 ATGCAGGAAAAATTTCTACGGAA 57.024 34.783 5.91 0.00 37.35 4.30
4005 5980 8.406297 GCAGGAAAAATTTCTACGGAATCTAAT 58.594 33.333 5.91 0.00 37.35 1.73
4006 5981 9.722056 CAGGAAAAATTTCTACGGAATCTAATG 57.278 33.333 5.91 0.00 37.35 1.90
4040 6015 9.595823 AATCCTATGAAAATGCTTTGAATCAAG 57.404 29.630 0.00 0.00 0.00 3.02
4075 6050 7.777095 AGAAGTTCTTCACATATCTACTCACC 58.223 38.462 13.85 0.00 0.00 4.02
4113 6088 0.108186 TCATGACGGCTCTTGCGATT 60.108 50.000 0.00 0.00 40.82 3.34
4126 6101 0.808125 TGCGATTTTGGGATTGTCGG 59.192 50.000 0.00 0.00 33.26 4.79
4136 6111 1.407437 GGGATTGTCGGCAAGATGAGT 60.407 52.381 9.01 0.00 38.10 3.41
4141 6116 3.371102 TGTCGGCAAGATGAGTATAGC 57.629 47.619 0.00 0.00 0.00 2.97
4192 6215 2.134789 ACATCCCAAAGGTCATCAGC 57.865 50.000 0.00 0.00 0.00 4.26
4196 6219 4.660303 ACATCCCAAAGGTCATCAGCTATA 59.340 41.667 0.00 0.00 0.00 1.31
4197 6220 5.311649 ACATCCCAAAGGTCATCAGCTATAT 59.688 40.000 0.00 0.00 0.00 0.86
4198 6221 5.489792 TCCCAAAGGTCATCAGCTATATC 57.510 43.478 0.00 0.00 0.00 1.63
4238 6264 0.674895 ACATCACAAGAGCTTCGGCC 60.675 55.000 0.00 0.00 43.01 6.13
4239 6265 0.674581 CATCACAAGAGCTTCGGCCA 60.675 55.000 2.24 0.00 43.01 5.36
4240 6266 0.674895 ATCACAAGAGCTTCGGCCAC 60.675 55.000 2.24 0.00 43.01 5.01
4247 6273 0.881118 GAGCTTCGGCCACAATTTGA 59.119 50.000 2.24 0.00 43.01 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.710902 CGCATGGTGAGACCTCCGA 61.711 63.158 0.00 0.00 39.58 4.55
1 2 2.202797 CGCATGGTGAGACCTCCG 60.203 66.667 0.00 0.00 39.58 4.63
34 35 1.324736 GCGAGCTTTGTAGATTGACGG 59.675 52.381 0.00 0.00 0.00 4.79
38 39 4.260784 GGTTATGGCGAGCTTTGTAGATTG 60.261 45.833 0.00 0.00 0.00 2.67
43 44 1.066716 ACGGTTATGGCGAGCTTTGTA 60.067 47.619 0.00 0.00 0.00 2.41
140 142 5.069251 GGTAGTACTAGCAGACATGGACAAT 59.931 44.000 23.85 0.00 34.00 2.71
148 150 4.282449 TGCAAAAGGTAGTACTAGCAGACA 59.718 41.667 28.68 17.71 36.11 3.41
155 157 8.689061 TCGATTTATCTGCAAAAGGTAGTACTA 58.311 33.333 0.00 0.00 0.00 1.82
193 195 4.811761 GGCGAACCAACGATGCGC 62.812 66.667 0.00 0.00 46.20 6.09
320 333 0.383124 GTTCACGTGTTGAAGCTCGC 60.383 55.000 16.51 0.00 45.23 5.03
361 374 3.249189 AGCCCTCAAGCCGGTTGA 61.249 61.111 12.29 12.29 43.26 3.18
386 399 0.391130 TGCATGTGTCCGTAAGAGGC 60.391 55.000 0.00 0.00 43.02 4.70
513 531 1.340991 GGTGGTAGGTACCCTCACGTA 60.341 57.143 8.74 0.00 45.87 3.57
723 742 8.581253 AAATAGTTCAGTATCCCCTCAAAAAG 57.419 34.615 0.00 0.00 0.00 2.27
752 1139 3.057609 GCAGCGTAGTTATTTTTGCGTTG 59.942 43.478 0.00 0.00 36.89 4.10
825 1216 2.036571 GTTCGTTGGGCCCGTTAGG 61.037 63.158 19.37 10.90 39.47 2.69
971 1362 3.024356 TCTCCTCTCTCCCCCGCT 61.024 66.667 0.00 0.00 0.00 5.52
973 1364 1.150536 CTCTCTCCTCTCTCCCCCG 59.849 68.421 0.00 0.00 0.00 5.73
974 1365 1.152546 GCTCTCTCCTCTCTCCCCC 60.153 68.421 0.00 0.00 0.00 5.40
976 1367 3.421567 GAGCTCTCTCCTCTCTCCC 57.578 63.158 6.43 0.00 33.19 4.30
1058 1450 2.451490 CAGAGAGCACAAGAGGGTAGA 58.549 52.381 0.00 0.00 0.00 2.59
1206 1601 1.227205 GATCCCTGAGCTCTGCGTG 60.227 63.158 16.19 6.04 0.00 5.34
1220 1615 0.461961 ACGCCACAGCTAAGAGATCC 59.538 55.000 0.00 0.00 36.60 3.36
1316 1713 1.134788 ACTCGCTAATCAACCTTCCCG 60.135 52.381 0.00 0.00 0.00 5.14
1356 1753 2.416747 CTCTCATCTCACAACGGCAAA 58.583 47.619 0.00 0.00 0.00 3.68
1357 1754 1.338105 CCTCTCATCTCACAACGGCAA 60.338 52.381 0.00 0.00 0.00 4.52
1368 1765 6.240894 TCTTATGCAAACAAACCTCTCATCT 58.759 36.000 0.00 0.00 0.00 2.90
1434 1832 1.001641 GCAGTCCTCATGCCAGGTT 60.002 57.895 0.65 0.00 37.73 3.50
1435 1833 2.673523 GCAGTCCTCATGCCAGGT 59.326 61.111 0.65 0.00 37.73 4.00
1715 2124 7.882791 TGGTGGCATAGTATATACCAAATTCAG 59.117 37.037 9.32 0.00 35.45 3.02
1732 2141 3.901844 GGGACTATTCTAGTGGTGGCATA 59.098 47.826 0.00 0.00 39.59 3.14
1733 2142 2.706190 GGGACTATTCTAGTGGTGGCAT 59.294 50.000 0.00 0.00 39.59 4.40
1735 2144 2.103263 CTGGGACTATTCTAGTGGTGGC 59.897 54.545 0.00 0.00 39.59 5.01
1736 2145 3.643237 TCTGGGACTATTCTAGTGGTGG 58.357 50.000 0.00 0.00 39.59 4.61
1737 2146 5.677319 TTTCTGGGACTATTCTAGTGGTG 57.323 43.478 0.00 0.00 39.59 4.17
1738 2147 5.964477 TCATTTCTGGGACTATTCTAGTGGT 59.036 40.000 0.00 0.00 39.59 4.16
1753 2162 4.873817 TGAAGCACAAACATCATTTCTGG 58.126 39.130 0.00 0.00 0.00 3.86
1767 2176 2.025981 AGTGGCTCCATTATGAAGCACA 60.026 45.455 5.68 0.00 0.00 4.57
1840 2249 8.721478 CCCTTGTATGTAGTATGAATTACATGC 58.279 37.037 7.25 6.59 38.54 4.06
1865 2274 6.592166 CATGTGAACAAATAAATGCACAACC 58.408 36.000 0.00 0.00 39.36 3.77
1869 2278 6.470557 AAGCATGTGAACAAATAAATGCAC 57.529 33.333 8.03 0.00 42.17 4.57
1937 2590 5.465390 TCACAAGTTTCTGGTCGTAATCAAG 59.535 40.000 0.00 0.00 0.00 3.02
1944 2597 3.312421 CACATTCACAAGTTTCTGGTCGT 59.688 43.478 0.00 0.00 0.00 4.34
1981 2634 0.458370 GCCCAGGTGCATTAAAAGCG 60.458 55.000 0.00 0.00 33.85 4.68
1995 2648 0.394762 ACATGTGCCACTATGCCCAG 60.395 55.000 0.00 0.00 0.00 4.45
1999 2652 0.734889 GACCACATGTGCCACTATGC 59.265 55.000 20.81 0.00 0.00 3.14
2027 2680 1.336125 GCATAGAGCAAATGCCAGGTC 59.664 52.381 0.94 0.00 43.17 3.85
2235 2888 2.253758 GCTCACGCTTGCACCTCAA 61.254 57.895 0.00 0.00 0.00 3.02
2631 3284 7.936847 CCAGTATTAGGTAGCCAATATTGAACA 59.063 37.037 17.23 0.00 30.19 3.18
2635 3288 7.604164 CAGACCAGTATTAGGTAGCCAATATTG 59.396 40.741 8.58 8.58 40.09 1.90
2641 3294 3.990369 ACAGACCAGTATTAGGTAGCCA 58.010 45.455 0.00 0.00 40.09 4.75
2650 3303 9.787435 TGTAAAAATCAGTAACAGACCAGTATT 57.213 29.630 0.00 0.00 0.00 1.89
2708 3361 6.594788 AAAATTCAGACATGCATGTAACCT 57.405 33.333 31.45 21.22 41.95 3.50
2796 3566 2.238144 ACAAGATAGGCAGTGCAGTGAT 59.762 45.455 25.76 14.53 0.00 3.06
2801 3571 1.905894 TGGTACAAGATAGGCAGTGCA 59.094 47.619 18.61 0.00 31.92 4.57
2819 3589 4.158209 TCAGACCATAAACATGTGCATTGG 59.842 41.667 0.00 7.44 0.00 3.16
2822 3592 5.680408 GCAATCAGACCATAAACATGTGCAT 60.680 40.000 0.00 0.00 0.00 3.96
2849 3619 6.986250 TGTTGCCACAAATACAATATTGACA 58.014 32.000 22.16 9.42 0.00 3.58
2910 3680 5.239306 CAGGTTCAACATCTTTGCTTAGTGA 59.761 40.000 0.00 0.00 0.00 3.41
2914 3684 6.463995 AAACAGGTTCAACATCTTTGCTTA 57.536 33.333 0.00 0.00 0.00 3.09
2970 3740 8.247562 ACAAACAGTATAACACAAGAAGCAAAA 58.752 29.630 0.00 0.00 0.00 2.44
3107 3877 1.136891 GCCAACCCTGCAATATGGTTC 59.863 52.381 6.63 0.00 40.31 3.62
3283 4053 3.796111 AGTTCCTCATTCCTCTTCCTCA 58.204 45.455 0.00 0.00 0.00 3.86
3467 4254 3.639094 AGGAGAATTCCAGGTCATAGTCG 59.361 47.826 0.65 0.00 46.64 4.18
3525 4312 6.708949 TCGTTTACTAAGTTGATTCCTTTGCT 59.291 34.615 0.00 0.00 0.00 3.91
3554 4408 8.299570 CAAACCAGCAAATAGATCACTAAAGTT 58.700 33.333 0.00 0.00 32.04 2.66
3560 4418 6.294731 GGAAACAAACCAGCAAATAGATCACT 60.295 38.462 0.00 0.00 0.00 3.41
3561 4419 5.863935 GGAAACAAACCAGCAAATAGATCAC 59.136 40.000 0.00 0.00 0.00 3.06
3587 4445 2.027561 CCCCGTTGGAATAGACAACTCA 60.028 50.000 6.72 0.00 44.49 3.41
3616 4474 8.913656 GGTATTAACTTACGCATAGCTAAAGAG 58.086 37.037 8.73 4.35 0.00 2.85
3620 4478 8.945481 TTTGGTATTAACTTACGCATAGCTAA 57.055 30.769 0.00 0.00 0.00 3.09
3622 4480 7.334921 TGTTTTGGTATTAACTTACGCATAGCT 59.665 33.333 0.00 0.00 0.00 3.32
3623 4481 7.465989 TGTTTTGGTATTAACTTACGCATAGC 58.534 34.615 0.00 0.00 0.00 2.97
3624 4482 9.646336 GATGTTTTGGTATTAACTTACGCATAG 57.354 33.333 0.00 0.00 0.00 2.23
3625 4483 8.614346 GGATGTTTTGGTATTAACTTACGCATA 58.386 33.333 0.00 0.00 0.00 3.14
3628 4486 6.844254 TGGATGTTTTGGTATTAACTTACGC 58.156 36.000 0.00 0.00 0.00 4.42
3629 4487 9.120422 GTTTGGATGTTTTGGTATTAACTTACG 57.880 33.333 0.00 0.00 0.00 3.18
3630 4488 9.120422 CGTTTGGATGTTTTGGTATTAACTTAC 57.880 33.333 0.00 0.00 0.00 2.34
3631 4489 7.808856 GCGTTTGGATGTTTTGGTATTAACTTA 59.191 33.333 0.00 0.00 0.00 2.24
3637 4511 4.592485 TGCGTTTGGATGTTTTGGTATT 57.408 36.364 0.00 0.00 0.00 1.89
3697 4571 7.720515 TCCTACGAATCAAAGAAACCCTAAAAA 59.279 33.333 0.00 0.00 0.00 1.94
3700 4574 6.363167 TCCTACGAATCAAAGAAACCCTAA 57.637 37.500 0.00 0.00 0.00 2.69
3701 4575 6.555463 ATCCTACGAATCAAAGAAACCCTA 57.445 37.500 0.00 0.00 0.00 3.53
3703 4577 5.676331 GCAATCCTACGAATCAAAGAAACCC 60.676 44.000 0.00 0.00 0.00 4.11
3705 4579 5.938322 TGCAATCCTACGAATCAAAGAAAC 58.062 37.500 0.00 0.00 0.00 2.78
3706 4580 6.429692 TCTTGCAATCCTACGAATCAAAGAAA 59.570 34.615 0.00 0.00 0.00 2.52
3707 4581 5.937540 TCTTGCAATCCTACGAATCAAAGAA 59.062 36.000 0.00 0.00 0.00 2.52
3709 4583 5.801350 TCTTGCAATCCTACGAATCAAAG 57.199 39.130 0.00 0.00 0.00 2.77
3711 4585 5.245531 AGTTCTTGCAATCCTACGAATCAA 58.754 37.500 0.00 0.00 0.00 2.57
3730 4613 4.171754 GGTAACTCGACATGGTGTAGTTC 58.828 47.826 0.00 0.00 32.98 3.01
3738 4621 2.073816 GGTTGTGGTAACTCGACATGG 58.926 52.381 0.00 0.00 44.60 3.66
3740 4623 3.695830 ATGGTTGTGGTAACTCGACAT 57.304 42.857 2.76 0.00 44.60 3.06
3741 4624 3.321396 TGTATGGTTGTGGTAACTCGACA 59.679 43.478 2.76 0.00 44.60 4.35
3742 4625 3.916761 TGTATGGTTGTGGTAACTCGAC 58.083 45.455 0.00 0.00 42.55 4.20
3743 4626 4.309099 GTTGTATGGTTGTGGTAACTCGA 58.691 43.478 0.00 0.00 37.61 4.04
3745 4628 4.214758 GTGGTTGTATGGTTGTGGTAACTC 59.785 45.833 0.00 0.00 37.61 3.01
3750 4894 2.738587 TGTGGTTGTATGGTTGTGGT 57.261 45.000 0.00 0.00 0.00 4.16
3784 4928 8.402798 TGTAATCCTACAAATCAAAGAAGCAA 57.597 30.769 0.00 0.00 35.03 3.91
3785 4929 7.994425 TGTAATCCTACAAATCAAAGAAGCA 57.006 32.000 0.00 0.00 35.03 3.91
3865 5072 6.611236 TCCAACCTCTTTGAAGAAATCCTTTT 59.389 34.615 0.00 0.00 37.39 2.27
3967 5942 9.921637 AGAAATTTTTCCTGCATTAATCGTTTA 57.078 25.926 0.00 0.00 37.92 2.01
3974 5949 7.455641 TCCGTAGAAATTTTTCCTGCATTAA 57.544 32.000 0.00 0.00 37.92 1.40
3975 5950 7.455641 TTCCGTAGAAATTTTTCCTGCATTA 57.544 32.000 0.00 0.00 37.92 1.90
3983 5958 9.788960 AAGCATTAGATTCCGTAGAAATTTTTC 57.211 29.630 0.00 0.00 35.09 2.29
4005 5980 9.723601 AAGCATTTTCATAGGATTTTTAAAGCA 57.276 25.926 0.00 0.00 0.00 3.91
4040 6015 2.572104 TGAAGAACTTCTAAGGGCCTCC 59.428 50.000 6.46 0.00 40.14 4.30
4075 6050 6.018016 GTCATGAAACTTTTTGAACCCATTGG 60.018 38.462 0.00 0.00 37.80 3.16
4087 6062 3.550842 GCAAGAGCCGTCATGAAACTTTT 60.551 43.478 0.00 0.00 33.58 2.27
4113 6088 1.818060 CATCTTGCCGACAATCCCAAA 59.182 47.619 0.00 0.00 34.61 3.28
4159 6182 5.512942 TTGGGATGTAGTCTCCAATTTGA 57.487 39.130 0.00 0.00 34.35 2.69
4192 6215 8.019656 TGGTGGAGATGATGATGATGATATAG 57.980 38.462 0.00 0.00 0.00 1.31
4196 6219 5.578157 TTGGTGGAGATGATGATGATGAT 57.422 39.130 0.00 0.00 0.00 2.45
4197 6220 5.128205 GTTTGGTGGAGATGATGATGATGA 58.872 41.667 0.00 0.00 0.00 2.92
4198 6221 4.885325 TGTTTGGTGGAGATGATGATGATG 59.115 41.667 0.00 0.00 0.00 3.07
4238 6264 6.514947 TCTCAAAGATGGGTTTCAAATTGTG 58.485 36.000 0.00 0.00 0.00 3.33
4239 6265 6.324770 ACTCTCAAAGATGGGTTTCAAATTGT 59.675 34.615 0.00 0.00 0.00 2.71
4240 6266 6.643770 CACTCTCAAAGATGGGTTTCAAATTG 59.356 38.462 0.00 0.00 0.00 2.32
4247 6273 3.884037 ACCACTCTCAAAGATGGGTTT 57.116 42.857 0.00 0.00 36.47 3.27


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

AutoCloner maintained by Alex Coulton.