Multiple sequence alignment - TraesCS6D01G285400

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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 TraesCS6D01G285400 chr6D 100.000 6026 0 0 1 6026 393651122 393657147 0.000000e+00 11129.0
1 TraesCS6D01G285400 chr6B 94.716 2971 108 19 1 2946 588831262 588834208 0.000000e+00 4571.0
2 TraesCS6D01G285400 chr6B 95.152 1980 80 10 3450 5423 588834657 588836626 0.000000e+00 3110.0
3 TraesCS6D01G285400 chr6B 92.074 757 36 9 5255 6003 588905962 588906702 0.000000e+00 1044.0
4 TraesCS6D01G285400 chr6B 93.598 328 17 3 3126 3450 588834288 588834614 2.520000e-133 486.0
5 TraesCS6D01G285400 chr6B 98.113 53 1 0 2163 2215 8403634 8403582 6.430000e-15 93.5
6 TraesCS6D01G285400 chr6A 93.384 1965 71 23 3440 5393 540045897 540047813 0.000000e+00 2854.0
7 TraesCS6D01G285400 chr6A 94.258 1428 69 8 745 2167 540042827 540044246 0.000000e+00 2170.0
8 TraesCS6D01G285400 chr6A 92.072 719 29 8 9 713 540042120 540042824 0.000000e+00 987.0
9 TraesCS6D01G285400 chr6A 91.876 677 22 9 5335 6003 540048030 540048681 0.000000e+00 915.0
10 TraesCS6D01G285400 chr6A 93.688 602 34 4 2647 3246 540044705 540045304 0.000000e+00 898.0
11 TraesCS6D01G285400 chr6A 92.043 465 34 3 2227 2690 540044245 540044707 0.000000e+00 651.0
12 TraesCS6D01G285400 chr6A 90.698 215 19 1 3236 3450 540045641 540045854 9.890000e-73 285.0
13 TraesCS6D01G285400 chr6A 90.732 205 15 3 5111 5314 540047841 540048042 2.770000e-68 270.0
14 TraesCS6D01G285400 chr1D 85.782 211 27 2 4972 5179 408251607 408251397 2.830000e-53 220.0
15 TraesCS6D01G285400 chr1D 89.928 139 12 2 5223 5360 408251388 408251251 1.730000e-40 178.0
16 TraesCS6D01G285400 chr1A 84.977 213 29 2 4970 5179 504252651 504252439 4.730000e-51 213.0
17 TraesCS6D01G285400 chr1A 94.828 58 3 0 2158 2215 558377637 558377580 2.310000e-14 91.6
18 TraesCS6D01G285400 chr1A 87.013 77 4 2 2158 2228 66895531 66895607 1.390000e-11 82.4
19 TraesCS6D01G285400 chr2A 89.928 139 12 2 5223 5360 40831948 40832085 1.730000e-40 178.0
20 TraesCS6D01G285400 chr2A 96.552 58 2 0 2158 2215 367831954 367832011 4.970000e-16 97.1
21 TraesCS6D01G285400 chr2A 100.000 52 0 0 2164 2215 478110585 478110534 4.970000e-16 97.1
22 TraesCS6D01G285400 chr5A 86.325 117 15 1 4029 4144 646004266 646004382 6.340000e-25 126.0
23 TraesCS6D01G285400 chr4A 85.246 122 7 5 4028 4138 195968437 195968558 1.370000e-21 115.0
24 TraesCS6D01G285400 chr4B 83.607 122 9 5 4028 4138 364042714 364042835 2.970000e-18 104.0
25 TraesCS6D01G285400 chr7A 96.552 58 2 0 2158 2215 721264939 721264996 4.970000e-16 97.1
26 TraesCS6D01G285400 chr5D 88.000 75 7 2 4034 4106 1328104 1328030 2.990000e-13 87.9
27 TraesCS6D01G285400 chr2B 93.443 61 1 2 2155 2215 716971376 716971433 2.990000e-13 87.9
28 TraesCS6D01G285400 chr2B 87.838 74 7 2 4034 4105 369214137 369214064 1.080000e-12 86.1
29 TraesCS6D01G285400 chr1B 92.063 63 3 2 2154 2215 529474285 529474346 2.990000e-13 87.9
30 TraesCS6D01G285400 chr3B 87.838 74 7 2 4034 4105 638815361 638815434 1.080000e-12 86.1
31 TraesCS6D01G285400 chr3B 84.337 83 11 2 4034 4114 379021718 379021636 5.010000e-11 80.5


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 TraesCS6D01G285400 chr6D 393651122 393657147 6025 False 11129.000000 11129 100.000000 1 6026 1 chr6D.!!$F1 6025
1 TraesCS6D01G285400 chr6B 588831262 588836626 5364 False 2722.333333 4571 94.488667 1 5423 3 chr6B.!!$F2 5422
2 TraesCS6D01G285400 chr6B 588905962 588906702 740 False 1044.000000 1044 92.074000 5255 6003 1 chr6B.!!$F1 748
3 TraesCS6D01G285400 chr6A 540042120 540048681 6561 False 1128.750000 2854 92.343875 9 6003 8 chr6A.!!$F1 5994

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
93 95 0.453793 ATCTTCTCTCCACACTCGCG 59.546 55.000 0.00 0.0 0.00 5.87 F
1209 1242 0.167470 CCAACGATGCAAGCACTCAG 59.833 55.000 0.00 0.0 0.00 3.35 F
1218 1251 1.065564 GCAAGCACTCAGAAGGGAGAT 60.066 52.381 0.00 0.0 38.30 2.75 F
1383 1416 1.145738 ACTGTGCCAGAAAATGAGGGT 59.854 47.619 8.91 0.0 35.18 4.34 F
2726 2807 1.341531 GTGGGGTGTGAGATCCTATCG 59.658 57.143 0.00 0.0 0.00 2.92 F
3465 3950 0.034896 AACTGGTTCTGGCACTACCG 59.965 55.000 8.32 6.3 43.94 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1251 0.610174 GATCAGTGCCACTGGACTCA 59.390 55.000 23.85 5.32 45.94 3.41 R
2894 2976 1.012486 GTCCGGTTTGTGTCTAGGCG 61.012 60.000 0.00 0.00 0.00 5.52 R
3038 3120 2.958355 CCAGGTTGACAAACAGGACATT 59.042 45.455 8.97 0.00 38.10 2.71 R
3365 3795 1.340795 ACCTACCTACACTCCTGGACG 60.341 57.143 0.00 0.00 0.00 4.79 R
3953 4444 0.321298 ACTGAAGCACCGCCGTATTT 60.321 50.000 0.00 0.00 0.00 1.40 R
5349 6125 0.034670 AGAAGCTGGCTCATGGGAAC 60.035 55.000 0.00 0.00 0.00 3.62 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
56 57 1.521010 CGCACTCTCAGCCCTCATG 60.521 63.158 0.00 0.00 0.00 3.07
93 95 0.453793 ATCTTCTCTCCACACTCGCG 59.546 55.000 0.00 0.00 0.00 5.87
94 96 0.605589 TCTTCTCTCCACACTCGCGA 60.606 55.000 9.26 9.26 0.00 5.87
231 233 1.361204 ACTCCCACATCACCACATCA 58.639 50.000 0.00 0.00 0.00 3.07
284 288 9.620660 CCCCATTTATATTAATAAAACGAGCAC 57.379 33.333 0.00 0.00 40.16 4.40
331 335 3.884318 TGGTGTAGTGCTGCCAGA 58.116 55.556 0.00 0.00 0.00 3.86
431 445 1.487231 CGCGAGATAAAATCCGCCG 59.513 57.895 0.00 0.00 42.16 6.46
432 446 1.860078 GCGAGATAAAATCCGCCGG 59.140 57.895 0.00 0.00 40.56 6.13
433 447 0.599204 GCGAGATAAAATCCGCCGGA 60.599 55.000 8.97 8.97 40.56 5.14
435 449 1.509703 GAGATAAAATCCGCCGGACC 58.490 55.000 8.62 0.00 32.98 4.46
454 470 2.513897 CCGCGATTTCCCCCACTC 60.514 66.667 8.23 0.00 0.00 3.51
660 689 6.030228 CCGTTGATAGATTTTTCCAGCTTTC 58.970 40.000 0.00 0.00 0.00 2.62
720 749 7.063898 GGATATTTCTTCTTTTGCTTTCTTGGC 59.936 37.037 0.00 0.00 0.00 4.52
724 753 1.277495 CTTTTGCTTTCTTGGCCGCG 61.277 55.000 0.00 0.00 0.00 6.46
909 939 2.079925 GTTTGGGATGCTCTGTGTCTC 58.920 52.381 0.00 0.00 0.00 3.36
1137 1170 3.167485 TCTGAATTCCTTGCCTGCAATT 58.833 40.909 4.84 0.00 35.20 2.32
1171 1204 1.609061 CGGAGATTGGTGTCTTGCACT 60.609 52.381 0.00 0.00 46.86 4.40
1173 1206 2.498167 GAGATTGGTGTCTTGCACTGT 58.502 47.619 0.00 0.00 46.86 3.55
1209 1242 0.167470 CCAACGATGCAAGCACTCAG 59.833 55.000 0.00 0.00 0.00 3.35
1218 1251 1.065564 GCAAGCACTCAGAAGGGAGAT 60.066 52.381 0.00 0.00 38.30 2.75
1263 1296 1.490574 AGGTCCCGAAGAATGAGGAG 58.509 55.000 0.00 0.00 0.00 3.69
1274 1307 4.500499 AGAATGAGGAGGTTGATGAAGG 57.500 45.455 0.00 0.00 0.00 3.46
1326 1359 2.504367 CACTCGGTTGACCCTTTGAAT 58.496 47.619 0.00 0.00 0.00 2.57
1383 1416 1.145738 ACTGTGCCAGAAAATGAGGGT 59.854 47.619 8.91 0.00 35.18 4.34
1443 1476 4.836125 TCTCAGCATTGTCAAAAAGGAC 57.164 40.909 0.00 0.00 38.29 3.85
1490 1523 2.107041 AATCCTGTGACGGTTGCGGA 62.107 55.000 0.00 0.00 0.00 5.54
1609 1642 3.525268 AAGCTTGGTTTTGTGTTCCTG 57.475 42.857 0.00 0.00 0.00 3.86
1681 1714 8.725405 TTAACTAAACAAATCATAGATGGCGA 57.275 30.769 0.00 0.00 0.00 5.54
1843 1876 9.383519 CTAAGGGGCAGTTATATACATTGTATG 57.616 37.037 17.68 4.39 0.00 2.39
1852 1885 7.598869 AGTTATATACATTGTATGTCTGTGCCG 59.401 37.037 17.68 0.00 43.67 5.69
1856 1889 2.760634 TTGTATGTCTGTGCCGTGAT 57.239 45.000 0.00 0.00 0.00 3.06
1911 1944 3.673809 CGGTTTATGCTTATAGCCTCGTC 59.326 47.826 0.00 0.00 41.51 4.20
2059 2093 5.096521 TGATGGAGACCTTGCTATATGGAT 58.903 41.667 0.00 0.00 0.00 3.41
2113 2147 7.201661 CGGCTGGCTAATAGTTAAACAAATACA 60.202 37.037 0.00 0.00 0.00 2.29
2172 2206 7.177921 CCGGAAGTATCATAAATACTACCTCCA 59.822 40.741 0.00 0.00 32.51 3.86
2288 2324 6.401153 GGAAGATTGTGTCTCACGTGTTTATC 60.401 42.308 16.51 9.72 37.14 1.75
2381 2418 4.146564 TGTGTCAGCAAGGTAGTACTGTA 58.853 43.478 5.39 0.00 0.00 2.74
2504 2541 3.758554 GTGCTGACATTACATTCTTGGGT 59.241 43.478 0.00 0.00 0.00 4.51
2515 2552 5.743636 ACATTCTTGGGTTGCATTAATGT 57.256 34.783 16.61 0.00 32.73 2.71
2544 2583 7.453126 TCCTTTATTTAACCAATCTCCAGCAAA 59.547 33.333 0.00 0.00 0.00 3.68
2546 2585 9.143631 CTTTATTTAACCAATCTCCAGCAAAAG 57.856 33.333 0.00 0.00 0.00 2.27
2547 2586 4.519540 TTAACCAATCTCCAGCAAAAGC 57.480 40.909 0.00 0.00 0.00 3.51
2726 2807 1.341531 GTGGGGTGTGAGATCCTATCG 59.658 57.143 0.00 0.00 0.00 2.92
2763 2844 6.599638 GCAGAGGTACCTATTGAATTTGACTT 59.400 38.462 23.52 0.00 0.00 3.01
2784 2865 6.987386 ACTTATCTTCTATTCGACATGAGGG 58.013 40.000 0.00 0.00 0.00 4.30
2790 2871 6.485984 TCTTCTATTCGACATGAGGGTAGTAC 59.514 42.308 0.00 0.00 0.00 2.73
2808 2890 5.252969 AGTACATTATGCATTGTGCCTTG 57.747 39.130 13.21 1.23 44.23 3.61
2894 2976 3.946126 GAAAGCTGGGGCCTGGGAC 62.946 68.421 0.84 0.00 39.73 4.46
2964 3046 1.523758 CGCTACCAAGTTGGCTTCTT 58.476 50.000 22.25 4.45 42.67 2.52
2978 3060 5.125100 TGGCTTCTTGCTTTACAAAGATG 57.875 39.130 5.89 0.00 42.39 2.90
3038 3120 4.842531 TTGCATGAGGACAGGAAGAATA 57.157 40.909 0.00 0.00 0.00 1.75
3076 3159 6.043938 TCAACCTGGACTTCCATAAGTTTACT 59.956 38.462 0.00 0.00 46.09 2.24
3096 3179 8.523464 GTTTACTGTAAGAATTTGCATTATGCG 58.477 33.333 12.78 0.00 42.12 4.73
3117 3200 3.063997 CGTTATGGCTTTAGGAGTGCTTG 59.936 47.826 0.00 0.00 0.00 4.01
3118 3201 2.887151 ATGGCTTTAGGAGTGCTTGT 57.113 45.000 0.00 0.00 0.00 3.16
3132 3215 6.030228 GGAGTGCTTGTTTTGCTAACATATC 58.970 40.000 5.93 1.07 0.00 1.63
3365 3795 4.423625 ACTATGTTGCCTCTTACATCCC 57.576 45.455 0.00 0.00 36.46 3.85
3404 3834 0.108585 TTGGCAGTGTGTCTCCCTTC 59.891 55.000 0.00 0.00 0.00 3.46
3465 3950 0.034896 AACTGGTTCTGGCACTACCG 59.965 55.000 8.32 6.30 43.94 4.02
3518 4003 2.440247 CTGTTTGGATCCCGCCCC 60.440 66.667 9.90 0.00 0.00 5.80
3519 4004 4.055227 TGTTTGGATCCCGCCCCC 62.055 66.667 9.90 0.00 0.00 5.40
3645 4130 5.591067 CCAATATTTTGGCATGGCTTCAAAT 59.409 36.000 21.08 20.64 45.71 2.32
3671 4156 0.609131 CTTCCAACCAAGTGGCCGAT 60.609 55.000 0.00 0.00 38.68 4.18
3693 4178 0.605319 CCCTAGCAGTCAACGCCAAA 60.605 55.000 0.00 0.00 0.00 3.28
3712 4197 1.462731 ATTTTTGGTGCGGCAGCTCA 61.463 50.000 29.51 15.68 45.42 4.26
3713 4198 2.074230 TTTTTGGTGCGGCAGCTCAG 62.074 55.000 29.51 0.00 45.42 3.35
3730 4215 3.181475 GCTCAGGACTATGATCCAAACGA 60.181 47.826 0.00 0.00 41.73 3.85
3784 4269 9.575868 TCTCTTAGCAAGTATAACATACTAGCT 57.424 33.333 0.00 0.00 0.00 3.32
3953 4444 2.762887 TGGTTTCTTGCAATGGTGTTCA 59.237 40.909 0.00 0.00 0.00 3.18
4106 4598 1.153449 TAAGCGCACGCCTAGCATT 60.153 52.632 11.47 0.71 43.17 3.56
4155 4647 0.327000 AGGGCCTAAGGATCTGTGCT 60.327 55.000 2.82 0.00 0.00 4.40
4282 4774 7.435068 TGGACTAAATACAAAGCTGAACTTC 57.565 36.000 0.00 0.00 37.75 3.01
4285 4777 7.387948 GGACTAAATACAAAGCTGAACTTCTCA 59.612 37.037 0.00 0.00 37.75 3.27
4441 4934 6.413783 TGTGTGACATACTTGAGAAGGTAA 57.586 37.500 3.87 0.00 0.00 2.85
4442 4935 6.822442 TGTGTGACATACTTGAGAAGGTAAA 58.178 36.000 3.87 0.00 0.00 2.01
4598 5093 4.450976 GTGGCCTCCTTTTCATTTTGTTT 58.549 39.130 3.32 0.00 0.00 2.83
4613 5108 9.818796 TTCATTTTGTTTAGCTTGTTCAAAAAC 57.181 25.926 16.43 9.71 39.95 2.43
4633 5128 9.150348 CAAAAACCTAGCTTTTCTTCTTCAAAA 57.850 29.630 0.00 0.00 0.00 2.44
4655 5150 5.679734 ACAGCTCAAAACTCACATGTAAG 57.320 39.130 0.00 0.00 0.00 2.34
4772 5267 4.156455 ACGATGCACATCCCTAATTCTT 57.844 40.909 5.09 0.00 34.40 2.52
4773 5268 3.879295 ACGATGCACATCCCTAATTCTTG 59.121 43.478 5.09 0.00 34.40 3.02
4929 5426 1.647346 TCGAGATACGCGGCAAAAAT 58.353 45.000 12.47 0.00 42.26 1.82
5038 5535 3.565902 GCCAGAATAGTACCTGATTTGGC 59.434 47.826 15.17 15.17 41.34 4.52
5126 5623 1.221414 GTCGCAGCCTGTCATTATCC 58.779 55.000 0.00 0.00 0.00 2.59
5288 5786 7.660112 TGTTGCTTCATTTCACATGTCTAAAT 58.340 30.769 0.00 2.51 0.00 1.40
5370 6146 0.254178 TCCCATGAGCCAGCTTCTTC 59.746 55.000 0.00 0.00 0.00 2.87
5527 6309 4.818546 GTCCAGATTCATACAACCATCCAG 59.181 45.833 0.00 0.00 0.00 3.86
5528 6310 3.567164 CCAGATTCATACAACCATCCAGC 59.433 47.826 0.00 0.00 0.00 4.85
5529 6311 4.201657 CAGATTCATACAACCATCCAGCA 58.798 43.478 0.00 0.00 0.00 4.41
5623 6407 1.381872 CCCCTCGACCTGGTCTGAT 60.382 63.158 23.49 0.00 0.00 2.90
5868 6652 0.890683 CCTCCAAAATTGAGCGCCTT 59.109 50.000 2.29 0.00 0.00 4.35
5870 6654 1.270550 CTCCAAAATTGAGCGCCTTGT 59.729 47.619 2.29 0.00 0.00 3.16
5972 6756 6.093404 TGAACAACAAAAACGATGCTAAACA 58.907 32.000 0.00 0.00 0.00 2.83
5997 6781 5.853282 CGAAATTGAAAACATCTCTGGTGTC 59.147 40.000 0.00 0.00 0.00 3.67
6003 6787 5.417266 TGAAAACATCTCTGGTGTCAACAAA 59.583 36.000 0.00 0.00 33.21 2.83
6004 6788 5.913137 AAACATCTCTGGTGTCAACAAAA 57.087 34.783 0.00 0.00 0.00 2.44
6005 6789 5.913137 AACATCTCTGGTGTCAACAAAAA 57.087 34.783 0.00 0.00 0.00 1.94
6025 6809 5.745653 AAAAGATGCTAAACGCGAAATTG 57.254 34.783 15.93 0.00 43.27 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.064581 GGATGTACGGTGGGGAGCT 61.065 63.158 0.00 0.00 0.00 4.09
93 95 2.096417 CGTGGACGGAGAAAAATGTGTC 60.096 50.000 0.00 0.00 35.37 3.67
94 96 1.871039 CGTGGACGGAGAAAAATGTGT 59.129 47.619 0.00 0.00 35.37 3.72
154 156 4.106925 GGAGGAGCCTGGCAGTGG 62.107 72.222 22.65 0.28 0.00 4.00
155 157 3.324930 TGGAGGAGCCTGGCAGTG 61.325 66.667 22.65 6.19 37.63 3.66
156 158 3.007920 CTGGAGGAGCCTGGCAGT 61.008 66.667 22.65 4.07 37.63 4.40
157 159 4.486503 GCTGGAGGAGCCTGGCAG 62.487 72.222 22.65 7.75 42.54 4.85
231 233 3.266772 TGCTGGTGATAGAAAATGGAGGT 59.733 43.478 0.00 0.00 0.00 3.85
316 320 0.875059 GGTTTCTGGCAGCACTACAC 59.125 55.000 10.34 0.00 0.00 2.90
331 335 1.302511 CTACCACCTGCAGCGGTTT 60.303 57.895 25.67 9.35 34.29 3.27
349 353 6.442112 GGATATTTGCTGGATCTTTTACTGC 58.558 40.000 0.00 0.00 0.00 4.40
350 354 6.483307 TCGGATATTTGCTGGATCTTTTACTG 59.517 38.462 0.00 0.00 0.00 2.74
431 445 4.870012 GGGAAATCGCGGGGGTCC 62.870 72.222 6.13 8.38 0.00 4.46
432 446 4.870012 GGGGAAATCGCGGGGGTC 62.870 72.222 6.13 0.00 0.00 4.46
454 470 2.875485 TCGAGAGAGGAAACGCGG 59.125 61.111 12.47 0.00 34.84 6.46
1110 1143 4.736759 GCAGGCAAGGAATTCAGATTGATG 60.737 45.833 16.86 14.71 0.00 3.07
1171 1204 2.052779 CCTCTGACTCCACTGCACA 58.947 57.895 0.00 0.00 0.00 4.57
1173 1206 2.587247 GGCCTCTGACTCCACTGCA 61.587 63.158 0.00 0.00 0.00 4.41
1209 1242 1.484240 CCACTGGACTCATCTCCCTTC 59.516 57.143 0.00 0.00 0.00 3.46
1218 1251 0.610174 GATCAGTGCCACTGGACTCA 59.390 55.000 23.85 5.32 45.94 3.41
1263 1296 3.503748 CCTGAACTTCACCTTCATCAACC 59.496 47.826 0.00 0.00 0.00 3.77
1274 1307 0.819259 TGCACAGGCCTGAACTTCAC 60.819 55.000 39.19 18.24 40.13 3.18
1326 1359 2.499205 CCGGCATGGTTCTCGCTA 59.501 61.111 0.00 0.00 0.00 4.26
1383 1416 2.245438 TATCGCCACCATCCGCACAA 62.245 55.000 0.00 0.00 0.00 3.33
1443 1476 5.641209 AGAATCAACAATTTCCTCAGACTCG 59.359 40.000 0.00 0.00 0.00 4.18
1490 1523 3.437344 GGTGCCCTTCTCCTCTCTATACT 60.437 52.174 0.00 0.00 0.00 2.12
1681 1714 7.331687 GCACAATTGATTAAGTTTGGTAAGCAT 59.668 33.333 13.59 0.00 27.84 3.79
1843 1876 3.062639 CACAAATAGATCACGGCACAGAC 59.937 47.826 0.00 0.00 0.00 3.51
1852 1885 9.941664 CAAATGTATCCTTCACAAATAGATCAC 57.058 33.333 0.00 0.00 0.00 3.06
1856 1889 9.685276 ATCACAAATGTATCCTTCACAAATAGA 57.315 29.630 0.00 0.00 0.00 1.98
1884 1917 3.316868 GGCTATAAGCATAAACCGCCAAA 59.683 43.478 0.78 0.00 44.75 3.28
1911 1944 1.876714 CTACAATGGACCGCCGACG 60.877 63.158 0.00 0.00 36.79 5.12
1958 1991 2.952293 GCTGTGGCTCTCTCCTGCA 61.952 63.158 0.00 0.00 35.22 4.41
2020 2053 7.365652 GGTCTCCATCAATAGGGAAAGTAAGAA 60.366 40.741 0.00 0.00 34.53 2.52
2059 2093 8.883954 TTGCACATCATAAATTTTCTTTGTGA 57.116 26.923 19.58 3.78 36.26 3.58
2073 2107 1.948834 CCAGCCGAATTGCACATCATA 59.051 47.619 0.00 0.00 0.00 2.15
2113 2147 5.370875 ACTATACGTCCTACTCTGTCCTT 57.629 43.478 0.00 0.00 0.00 3.36
2205 2239 1.746220 CTCCCTCCGTCTTGACACTAG 59.254 57.143 1.59 0.00 0.00 2.57
2260 2296 4.021456 ACACGTGAGACACAATCTTCCATA 60.021 41.667 25.01 0.00 38.00 2.74
2381 2418 2.078849 TCGTGACATGCAGAAACGAT 57.921 45.000 11.27 0.00 38.26 3.73
2515 2552 9.131791 GCTGGAGATTGGTTAAATAAAGGATAA 57.868 33.333 0.00 0.00 0.00 1.75
2636 2676 2.006888 ACGCACGGATACAATTCCTTG 58.993 47.619 0.00 0.00 37.92 3.61
2732 2813 1.806496 ATAGGTACCTCTGCATGGCA 58.194 50.000 20.32 0.00 36.92 4.92
2763 2844 7.232188 ACTACCCTCATGTCGAATAGAAGATA 58.768 38.462 0.00 0.00 0.00 1.98
2894 2976 1.012486 GTCCGGTTTGTGTCTAGGCG 61.012 60.000 0.00 0.00 0.00 5.52
3038 3120 2.958355 CCAGGTTGACAAACAGGACATT 59.042 45.455 8.97 0.00 38.10 2.71
3076 3159 7.647318 CCATAACGCATAATGCAAATTCTTACA 59.353 33.333 0.00 0.00 45.36 2.41
3096 3179 4.010349 ACAAGCACTCCTAAAGCCATAAC 58.990 43.478 0.00 0.00 0.00 1.89
3117 3200 7.989826 ACTCCAGAATGATATGTTAGCAAAAC 58.010 34.615 0.00 0.00 39.69 2.43
3118 3201 8.579850 AACTCCAGAATGATATGTTAGCAAAA 57.420 30.769 0.00 0.00 39.69 2.44
3132 3215 3.221771 TGGGACACAAAACTCCAGAATG 58.778 45.455 0.00 0.00 0.00 2.67
3206 3289 6.037786 TCTTCGACCAGTAAATCAGTGAAT 57.962 37.500 0.00 0.00 0.00 2.57
3349 3779 1.653151 GACGGGATGTAAGAGGCAAC 58.347 55.000 0.00 0.00 0.00 4.17
3365 3795 1.340795 ACCTACCTACACTCCTGGACG 60.341 57.143 0.00 0.00 0.00 4.79
3438 3871 3.821033 GTGCCAGAACCAGTTAAGTTCAT 59.179 43.478 8.33 0.00 44.91 2.57
3465 3950 1.006878 ACAGGAGGGACAGGGTAGTAC 59.993 57.143 0.00 0.00 0.00 2.73
3577 4062 2.123897 AGCGGGCAAAACACTGGT 60.124 55.556 0.00 0.00 0.00 4.00
3650 4135 1.832167 GGCCACTTGGTTGGAAGCA 60.832 57.895 0.00 0.00 39.24 3.91
3671 4156 2.571757 CGTTGACTGCTAGGGCGA 59.428 61.111 0.00 0.00 42.25 5.54
3693 4178 1.290009 GAGCTGCCGCACCAAAAAT 59.710 52.632 2.05 0.00 39.10 1.82
3712 4197 2.434702 GGGTCGTTTGGATCATAGTCCT 59.565 50.000 0.00 0.00 39.12 3.85
3713 4198 2.484947 GGGGTCGTTTGGATCATAGTCC 60.485 54.545 0.00 0.00 38.81 3.85
3730 4215 5.396436 CGTCCAAGACATAGATTTAAGGGGT 60.396 44.000 0.00 0.00 32.09 4.95
3953 4444 0.321298 ACTGAAGCACCGCCGTATTT 60.321 50.000 0.00 0.00 0.00 1.40
4155 4647 7.257790 TGGAGAGAAAACAATCAGATCCTAA 57.742 36.000 0.00 0.00 0.00 2.69
4296 4789 3.929610 CGGTGGAAGCAAAAACAAGAAAA 59.070 39.130 0.00 0.00 0.00 2.29
4534 5027 1.003355 CGCCCCTCTTGAGAAGCAA 60.003 57.895 0.00 0.00 34.73 3.91
4598 5093 6.709018 AAAGCTAGGTTTTTGAACAAGCTA 57.291 33.333 14.07 3.39 40.41 3.32
4613 5108 5.917447 GCTGTTTTGAAGAAGAAAAGCTAGG 59.083 40.000 0.00 0.00 0.00 3.02
4633 5128 4.023707 GCTTACATGTGAGTTTTGAGCTGT 60.024 41.667 17.93 0.00 0.00 4.40
4663 5158 4.378774 CATCTTTCTGCCTCCTGTCATAG 58.621 47.826 0.00 0.00 0.00 2.23
4664 5159 3.135348 CCATCTTTCTGCCTCCTGTCATA 59.865 47.826 0.00 0.00 0.00 2.15
4665 5160 2.092538 CCATCTTTCTGCCTCCTGTCAT 60.093 50.000 0.00 0.00 0.00 3.06
4666 5161 1.280133 CCATCTTTCTGCCTCCTGTCA 59.720 52.381 0.00 0.00 0.00 3.58
4772 5267 0.620556 GATGAGAGTTCAAGGGGGCA 59.379 55.000 0.00 0.00 36.78 5.36
4773 5268 0.620556 TGATGAGAGTTCAAGGGGGC 59.379 55.000 0.00 0.00 36.78 5.80
4929 5426 0.393132 TGTCAAAGTTGGTCACCGCA 60.393 50.000 0.00 0.00 0.00 5.69
5038 5535 7.857389 CCAACCAAATCTGTTCAATATACGATG 59.143 37.037 0.00 0.00 0.00 3.84
5126 5623 3.451526 TCTGAAGAATCATACAGCAGCG 58.548 45.455 0.00 0.00 34.37 5.18
5288 5786 7.820648 ACTTAGAAGTAAAACGTATTCTCCGA 58.179 34.615 0.00 0.00 37.52 4.55
5349 6125 0.034670 AGAAGCTGGCTCATGGGAAC 60.035 55.000 0.00 0.00 0.00 3.62
5393 6169 0.387622 CAGCACTGGCAAATGAACGG 60.388 55.000 2.71 0.00 44.61 4.44
5623 6407 6.480763 TCAGTGCCTTTAATGTAGGAATTGA 58.519 36.000 0.00 0.00 35.36 2.57
5802 6586 1.873903 GCTGAACGAGAACTGGAAGCA 60.874 52.381 0.00 0.00 37.60 3.91
5868 6652 7.064134 CACTCACAGTTTAAGACTACAAACACA 59.936 37.037 12.61 0.00 36.65 3.72
5870 6654 7.324935 TCACTCACAGTTTAAGACTACAAACA 58.675 34.615 12.61 0.00 36.65 2.83
5961 6745 6.141527 TGTTTTCAATTTCGTGTTTAGCATCG 59.858 34.615 0.00 0.00 0.00 3.84
5972 6756 5.299279 ACACCAGAGATGTTTTCAATTTCGT 59.701 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.