Multiple sequence alignment - TraesCS1D01G006900

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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 TraesCS1D01G006900 chr1D 100.000 2638 0 0 1 2638 3451071 3453708 0.000000e+00 4872
1 TraesCS1D01G006900 chr1D 98.220 337 6 0 1 337 4979988 4979652 8.130000e-165 590
2 TraesCS1D01G006900 chr1D 87.871 371 33 8 1 366 3380896 3381259 2.430000e-115 425
3 TraesCS1D01G006900 chr1D 88.636 88 10 0 417 504 4979653 4979566 9.980000e-20 108
4 TraesCS1D01G006900 chr1B 88.064 2128 194 29 526 2638 22275190 22273108 0.000000e+00 2468
5 TraesCS1D01G006900 chr1B 88.773 2022 174 24 629 2638 17254479 17256459 0.000000e+00 2427
6 TraesCS1D01G006900 chr1B 89.738 1832 141 17 1 1821 7363710 7365505 0.000000e+00 2298
7 TraesCS1D01G006900 chr1B 90.596 1308 99 16 548 1849 7553172 7551883 0.000000e+00 1712
8 TraesCS1D01G006900 chr1B 90.291 1308 102 17 548 1849 7544640 7543352 0.000000e+00 1688
9 TraesCS1D01G006900 chr1B 90.061 1308 105 17 548 1849 7548902 7547614 0.000000e+00 1672
10 TraesCS1D01G006900 chr1B 88.556 1101 88 15 1105 2200 6575039 6573972 0.000000e+00 1301
11 TraesCS1D01G006900 chr1B 82.930 826 101 17 1823 2638 7547553 7546758 0.000000e+00 708
12 TraesCS1D01G006900 chr1B 82.896 801 92 17 1848 2638 7543269 7542504 0.000000e+00 678
13 TraesCS1D01G006900 chr1B 83.466 756 88 13 1887 2638 7366011 7366733 0.000000e+00 669
14 TraesCS1D01G006900 chr1B 77.718 929 123 55 823 1707 7304676 7305564 2.360000e-135 492
15 TraesCS1D01G006900 chr1B 87.829 304 34 2 1 304 7406784 7407084 1.160000e-93 353
16 TraesCS1D01G006900 chr1B 91.129 124 8 3 978 1100 6579029 6578908 5.840000e-37 165
17 TraesCS1D01G006900 chr1B 92.708 96 6 1 1 95 6801736 6801641 1.270000e-28 137
18 TraesCS1D01G006900 chr1B 89.623 106 11 0 819 924 6579155 6579050 4.580000e-28 135
19 TraesCS1D01G006900 chr1B 77.253 233 37 13 1 229 629794854 629795074 3.570000e-24 122
20 TraesCS1D01G006900 chr1B 89.412 85 2 1 548 625 17254354 17254438 1.670000e-17 100
21 TraesCS1D01G006900 chr1B 86.022 93 13 0 452 544 22332846 22332754 1.670000e-17 100
22 TraesCS1D01G006900 chr1A 90.508 1791 134 17 1 1774 6024464 6022693 0.000000e+00 2333
23 TraesCS1D01G006900 chr1A 92.708 96 6 1 1 95 4692350 4692445 1.270000e-28 137


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 TraesCS1D01G006900 chr1D 3451071 3453708 2637 False 4872.000000 4872 100.000000 1 2638 1 chr1D.!!$F2 2637
1 TraesCS1D01G006900 chr1B 22273108 22275190 2082 True 2468.000000 2468 88.064000 526 2638 1 chr1B.!!$R2 2112
2 TraesCS1D01G006900 chr1B 7363710 7366733 3023 False 1483.500000 2298 86.602000 1 2638 2 chr1B.!!$F4 2637
3 TraesCS1D01G006900 chr1B 7542504 7553172 10668 True 1291.600000 1712 87.354800 548 2638 5 chr1B.!!$R5 2090
4 TraesCS1D01G006900 chr1B 17254354 17256459 2105 False 1263.500000 2427 89.092500 548 2638 2 chr1B.!!$F5 2090
5 TraesCS1D01G006900 chr1B 6573972 6579155 5183 True 533.666667 1301 89.769333 819 2200 3 chr1B.!!$R4 1381
6 TraesCS1D01G006900 chr1B 7304676 7305564 888 False 492.000000 492 77.718000 823 1707 1 chr1B.!!$F1 884
7 TraesCS1D01G006900 chr1A 6022693 6024464 1771 True 2333.000000 2333 90.508000 1 1774 1 chr1A.!!$R1 1773

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
971 1036 0.39034 GCTGACAGATGAAGGTGCGA 60.39 55.0 6.65 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 11263 0.107703 GAGCATGGTGATGAACGGGA 60.108 55.0 0.0 0.0 0.0 5.14 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
25 26 1.269936 ACCAGACATTTGCAAAGCAGC 60.270 47.619 18.19 6.97 40.61 5.25
45 46 4.277515 GCCATGGCTACTAAGATCATGA 57.722 45.455 29.98 0.00 37.75 3.07
48 49 5.353678 GCCATGGCTACTAAGATCATGATTC 59.646 44.000 29.98 3.48 37.75 2.52
60 61 5.613329 AGATCATGATTCTGCTTCTTCTCC 58.387 41.667 10.14 0.00 0.00 3.71
61 62 4.831674 TCATGATTCTGCTTCTTCTCCA 57.168 40.909 0.00 0.00 0.00 3.86
73 74 2.733956 TCTTCTCCAGCTCCTCTCTTC 58.266 52.381 0.00 0.00 0.00 2.87
85 86 2.099405 CCTCTCTTCTCAGAGTCCACC 58.901 57.143 0.00 0.00 46.24 4.61
90 91 0.836400 TTCTCAGAGTCCACCACCCC 60.836 60.000 0.00 0.00 0.00 4.95
91 92 1.229336 CTCAGAGTCCACCACCCCT 60.229 63.158 0.00 0.00 0.00 4.79
92 93 0.838122 CTCAGAGTCCACCACCCCTT 60.838 60.000 0.00 0.00 0.00 3.95
93 94 0.490017 TCAGAGTCCACCACCCCTTA 59.510 55.000 0.00 0.00 0.00 2.69
94 95 0.613777 CAGAGTCCACCACCCCTTAC 59.386 60.000 0.00 0.00 0.00 2.34
95 96 0.492276 AGAGTCCACCACCCCTTACT 59.508 55.000 0.00 0.00 0.00 2.24
96 97 1.132495 AGAGTCCACCACCCCTTACTT 60.132 52.381 0.00 0.00 0.00 2.24
97 98 1.703513 GAGTCCACCACCCCTTACTTT 59.296 52.381 0.00 0.00 0.00 2.66
98 99 1.703513 AGTCCACCACCCCTTACTTTC 59.296 52.381 0.00 0.00 0.00 2.62
99 100 1.422402 GTCCACCACCCCTTACTTTCA 59.578 52.381 0.00 0.00 0.00 2.69
100 101 2.136863 TCCACCACCCCTTACTTTCAA 58.863 47.619 0.00 0.00 0.00 2.69
101 102 2.158579 TCCACCACCCCTTACTTTCAAC 60.159 50.000 0.00 0.00 0.00 3.18
102 103 2.235891 CACCACCCCTTACTTTCAACC 58.764 52.381 0.00 0.00 0.00 3.77
103 104 2.141067 ACCACCCCTTACTTTCAACCT 58.859 47.619 0.00 0.00 0.00 3.50
104 105 2.516702 ACCACCCCTTACTTTCAACCTT 59.483 45.455 0.00 0.00 0.00 3.50
105 106 3.154710 CCACCCCTTACTTTCAACCTTC 58.845 50.000 0.00 0.00 0.00 3.46
110 111 4.278419 CCCCTTACTTTCAACCTTCACAAG 59.722 45.833 0.00 0.00 0.00 3.16
126 127 1.407258 ACAAGCAGAGTATCGAGGAGC 59.593 52.381 0.00 0.00 42.67 4.70
132 133 1.944024 AGAGTATCGAGGAGCTTCACG 59.056 52.381 5.36 5.36 42.67 4.35
162 163 2.034221 GGGCGTTGGCTCCTTTCT 59.966 61.111 0.00 0.00 39.81 2.52
167 168 1.604604 CGTTGGCTCCTTTCTTTCCA 58.395 50.000 0.00 0.00 0.00 3.53
169 170 1.270826 GTTGGCTCCTTTCTTTCCAGC 59.729 52.381 0.00 0.00 0.00 4.85
229 232 1.752694 AGCAGGCTCTCGTCTCCTC 60.753 63.158 0.00 0.00 0.00 3.71
230 233 1.752694 GCAGGCTCTCGTCTCCTCT 60.753 63.158 0.00 0.00 0.00 3.69
241 244 5.117584 TCTCGTCTCCTCTATGACTACAAC 58.882 45.833 0.00 0.00 0.00 3.32
292 295 1.895238 CCATGAAGGCCAAAGCTGG 59.105 57.895 5.01 0.67 46.65 4.85
330 333 1.096386 CGTAGGTGAGGAGGAGGTCG 61.096 65.000 0.00 0.00 0.00 4.79
331 334 0.752376 GTAGGTGAGGAGGAGGTCGG 60.752 65.000 0.00 0.00 0.00 4.79
335 338 1.000771 TGAGGAGGAGGTCGGTGAG 60.001 63.158 0.00 0.00 0.00 3.51
352 355 2.439883 GTACGGCGAGGAGGAGGT 60.440 66.667 16.62 0.00 0.00 3.85
405 409 1.674441 CATGATGGAGCAATTGAGCGT 59.326 47.619 10.34 0.00 40.15 5.07
420 424 3.059884 TGAGCGTTGACATCTCTGTTTC 58.940 45.455 0.00 0.00 35.14 2.78
426 430 1.338105 TGACATCTCTGTTTCGCCAGG 60.338 52.381 0.00 0.00 35.14 4.45
427 431 0.687354 ACATCTCTGTTTCGCCAGGT 59.313 50.000 0.00 0.00 33.14 4.00
466 470 0.542702 CCCCAAAGCTCCCATGTGTT 60.543 55.000 0.00 0.00 0.00 3.32
483 487 7.397970 CCATGTGTTTGTCATTTGTTTGTTAC 58.602 34.615 0.00 0.00 0.00 2.50
484 488 7.277539 CCATGTGTTTGTCATTTGTTTGTTACT 59.722 33.333 0.00 0.00 0.00 2.24
645 698 6.616017 ACATGAGTGTATACATATCTCGCTG 58.384 40.000 9.18 13.45 36.63 5.18
668 721 5.816258 TGTTTATATTTGTGGGCAATGCATG 59.184 36.000 7.79 0.00 34.18 4.06
689 742 5.994887 TGTATGTACGTGCTTCTTTTTGT 57.005 34.783 4.97 0.00 0.00 2.83
752 805 3.429272 CGGTGGCCACTAATTAAGACGTA 60.429 47.826 33.91 0.00 0.00 3.57
769 822 3.321497 ACGTAAGAAGAGAAGCAAGCAG 58.679 45.455 0.00 0.00 43.62 4.24
971 1036 0.390340 GCTGACAGATGAAGGTGCGA 60.390 55.000 6.65 0.00 0.00 5.10
1014 1081 8.466798 GTCACTGGGTGCTTATAAATAACAATT 58.533 33.333 0.00 0.00 32.98 2.32
1116 5059 0.537188 ACCCACTCTCACTAATGCCG 59.463 55.000 0.00 0.00 0.00 5.69
1125 5068 1.075542 CACTAATGCCGTCAAAGCGA 58.924 50.000 0.00 0.00 0.00 4.93
1493 5458 2.016961 CGACTGCAACAGCAAGTGT 58.983 52.632 0.00 0.00 43.24 3.55
1521 5486 3.308053 CACCTGCGTGTGAAGAATATCAG 59.692 47.826 0.00 0.00 38.55 2.90
1557 5523 0.250295 TTCGGTTGAGCCTCTTGGTG 60.250 55.000 0.00 0.00 35.27 4.17
1563 5529 3.412386 GTTGAGCCTCTTGGTGTGTATT 58.588 45.455 0.00 0.00 35.27 1.89
1596 5565 5.282055 ACCTATGGTATGATATGGATGCG 57.718 43.478 0.00 0.00 32.11 4.73
1618 5587 4.082787 CGGCCTGTGATTGTCATAAAGTTT 60.083 41.667 0.00 0.00 0.00 2.66
1672 5644 8.504815 GTTGTATCTTTTCTTTACTCCTTGTCC 58.495 37.037 0.00 0.00 0.00 4.02
1719 5696 9.101655 CTTGATGGTAATTTTCATTGGAAATCC 57.898 33.333 3.37 2.87 42.31 3.01
1720 5697 7.264221 TGATGGTAATTTTCATTGGAAATCCG 58.736 34.615 3.37 0.00 42.31 4.18
1725 5702 4.839668 TTTTCATTGGAAATCCGAACGT 57.160 36.364 0.00 0.00 42.31 3.99
1797 5775 1.625511 AAGACGTACTCCCTCCGTTT 58.374 50.000 0.00 0.00 34.51 3.60
1801 5779 1.000171 ACGTACTCCCTCCGTTTCAAC 60.000 52.381 0.00 0.00 0.00 3.18
1900 10707 1.350193 CTGTTGCTACCACTACTGCG 58.650 55.000 0.00 0.00 0.00 5.18
1901 10708 0.669318 TGTTGCTACCACTACTGCGC 60.669 55.000 0.00 0.00 0.00 6.09
1917 10724 2.023318 CGCCACTACTAGCGCTACT 58.977 57.895 14.45 7.48 46.50 2.57
1935 10742 5.463392 CGCTACTAGTACCATTACGACTACA 59.537 44.000 0.00 0.00 32.93 2.74
1943 10750 3.123804 CCATTACGACTACAGCCATCAC 58.876 50.000 0.00 0.00 0.00 3.06
1944 10751 2.554806 TTACGACTACAGCCATCACG 57.445 50.000 0.00 0.00 0.00 4.35
1980 10787 8.718734 ACTACCTAAATTTTCGTGAAACAGATC 58.281 33.333 0.00 0.00 35.74 2.75
2029 10855 0.601046 CTGCGGCTCTCACTTGTTCA 60.601 55.000 0.00 0.00 0.00 3.18
2037 10863 3.434984 GCTCTCACTTGTTCATGGACTTC 59.565 47.826 5.55 0.00 0.00 3.01
2044 10870 3.126001 TGTTCATGGACTTCTCACCAC 57.874 47.619 5.55 0.00 39.06 4.16
2045 10871 2.705658 TGTTCATGGACTTCTCACCACT 59.294 45.455 5.55 0.00 39.06 4.00
2046 10872 3.136443 TGTTCATGGACTTCTCACCACTT 59.864 43.478 5.55 0.00 39.06 3.16
2047 10873 3.407424 TCATGGACTTCTCACCACTTG 57.593 47.619 0.00 0.00 39.06 3.16
2048 10874 1.808945 CATGGACTTCTCACCACTTGC 59.191 52.381 0.00 0.00 39.06 4.01
2049 10875 0.249868 TGGACTTCTCACCACTTGCG 60.250 55.000 0.00 0.00 0.00 4.85
2050 10876 0.249911 GGACTTCTCACCACTTGCGT 60.250 55.000 0.00 0.00 0.00 5.24
2051 10877 1.000506 GGACTTCTCACCACTTGCGTA 59.999 52.381 0.00 0.00 0.00 4.42
2052 10878 2.547218 GGACTTCTCACCACTTGCGTAA 60.547 50.000 0.00 0.00 0.00 3.18
2053 10879 3.326747 GACTTCTCACCACTTGCGTAAT 58.673 45.455 0.00 0.00 0.00 1.89
2127 10953 8.367156 ACTTTTTGTATAGGTGGTACGAAACTA 58.633 33.333 0.00 0.00 35.96 2.24
2162 10988 2.359850 GCCACATGGTTCCGCAGA 60.360 61.111 0.00 0.00 37.57 4.26
2163 10989 2.401766 GCCACATGGTTCCGCAGAG 61.402 63.158 0.00 0.00 37.57 3.35
2175 11001 3.885724 TCCGCAGAGTAATCACATGAA 57.114 42.857 0.00 0.00 0.00 2.57
2176 11002 3.521560 TCCGCAGAGTAATCACATGAAC 58.478 45.455 0.00 0.00 0.00 3.18
2200 11032 8.620533 ACGAAAAGAGCTTAATTTGCATATTC 57.379 30.769 5.60 0.00 0.00 1.75
2235 11067 0.402504 TACCACTCGGCATTTTGGGT 59.597 50.000 0.00 0.00 34.57 4.51
2278 11110 1.079057 GGACGCTCCTGGGAAACTC 60.079 63.158 0.00 0.00 32.53 3.01
2310 11142 0.954452 CAGCCGCTTCCAAAAGAACT 59.046 50.000 0.00 0.00 34.14 3.01
2332 11164 2.034221 GCCACCACCAGAACCCTC 59.966 66.667 0.00 0.00 0.00 4.30
2333 11165 2.529744 GCCACCACCAGAACCCTCT 61.530 63.158 0.00 0.00 0.00 3.69
2343 11175 3.959991 GAACCCTCTCTGCCGCCAC 62.960 68.421 0.00 0.00 0.00 5.01
2371 11206 4.402528 CCAATGGCGGACGGTGGA 62.403 66.667 0.00 0.00 0.00 4.02
2401 11236 1.076923 GCCCGTACTCCCTCTCTCA 60.077 63.158 0.00 0.00 0.00 3.27
2424 11259 1.284785 CTCCCAACCTTCCATGGCTTA 59.715 52.381 6.96 0.00 35.28 3.09
2426 11261 2.034124 CCCAACCTTCCATGGCTTATG 58.966 52.381 6.96 2.19 35.28 1.90
2428 11263 3.099141 CCAACCTTCCATGGCTTATGTT 58.901 45.455 6.96 3.10 34.87 2.71
2436 11271 2.364632 CATGGCTTATGTTCCCGTTCA 58.635 47.619 0.00 0.00 31.92 3.18
2440 11275 2.354821 GGCTTATGTTCCCGTTCATCAC 59.645 50.000 0.00 0.00 0.00 3.06
2445 11280 0.451783 GTTCCCGTTCATCACCATGC 59.548 55.000 0.00 0.00 0.00 4.06
2448 11283 0.107508 CCCGTTCATCACCATGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
2458 11293 3.580039 TCACCATGCTCTGATCCAGATA 58.420 45.455 0.00 0.00 39.92 1.98
2464 11299 5.421374 CCATGCTCTGATCCAGATATAGTGA 59.579 44.000 0.00 0.00 39.92 3.41
2473 11308 5.339423 TCCAGATATAGTGACCAGATCCA 57.661 43.478 0.00 0.00 0.00 3.41
2479 11314 8.373981 CAGATATAGTGACCAGATCCATTTTCT 58.626 37.037 0.00 0.00 0.00 2.52
2485 11320 5.292101 GTGACCAGATCCATTTTCTTCGTAG 59.708 44.000 0.00 0.00 0.00 3.51
2507 15596 1.342496 CTTAGCGGCATCCATGAGAGA 59.658 52.381 1.45 0.00 0.00 3.10
2510 15599 1.300465 CGGCATCCATGAGAGACCG 60.300 63.158 0.00 4.00 39.64 4.79
2538 15627 1.133009 CCTAGAGCCCATCACTAGGGT 60.133 57.143 0.00 0.00 46.28 4.34
2547 15636 3.557898 CCCATCACTAGGGTCATATGCAC 60.558 52.174 0.00 0.00 41.61 4.57
2560 15649 2.877097 TATGCACATGAGGGTTGTGT 57.123 45.000 0.00 0.00 44.96 3.72
2570 15659 1.541588 GAGGGTTGTGTTGGAGATTGC 59.458 52.381 0.00 0.00 0.00 3.56
2610 15700 3.550992 CCGCGTCCGTCCAAATCG 61.551 66.667 4.92 0.00 0.00 3.34
2619 15709 1.212751 GTCCAAATCGGGCAGCAAC 59.787 57.895 0.00 0.00 40.18 4.17
2633 15723 2.072298 CAGCAACTGGTTGAGCTAGTC 58.928 52.381 16.41 0.00 42.93 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.730064 CATGGCTGCTTTGCAAATGTC 59.270 47.619 13.23 8.32 38.41 3.06
25 26 6.594547 CAGAATCATGATCTTAGTAGCCATGG 59.405 42.308 9.06 7.63 35.13 3.66
45 46 2.093021 GGAGCTGGAGAAGAAGCAGAAT 60.093 50.000 0.00 0.00 42.06 2.40
48 49 0.903942 AGGAGCTGGAGAAGAAGCAG 59.096 55.000 0.00 0.00 42.06 4.24
60 61 2.684881 GACTCTGAGAAGAGAGGAGCTG 59.315 54.545 12.44 0.00 43.42 4.24
61 62 2.357154 GGACTCTGAGAAGAGAGGAGCT 60.357 54.545 12.44 0.00 43.42 4.09
73 74 0.838122 AAGGGGTGGTGGACTCTGAG 60.838 60.000 2.45 2.45 0.00 3.35
85 86 3.568430 GTGAAGGTTGAAAGTAAGGGGTG 59.432 47.826 0.00 0.00 0.00 4.61
90 91 5.296780 TCTGCTTGTGAAGGTTGAAAGTAAG 59.703 40.000 0.00 0.00 0.00 2.34
91 92 5.189928 TCTGCTTGTGAAGGTTGAAAGTAA 58.810 37.500 0.00 0.00 0.00 2.24
92 93 4.776349 TCTGCTTGTGAAGGTTGAAAGTA 58.224 39.130 0.00 0.00 0.00 2.24
93 94 3.620488 TCTGCTTGTGAAGGTTGAAAGT 58.380 40.909 0.00 0.00 0.00 2.66
94 95 3.629398 ACTCTGCTTGTGAAGGTTGAAAG 59.371 43.478 0.00 0.00 0.00 2.62
95 96 3.620488 ACTCTGCTTGTGAAGGTTGAAA 58.380 40.909 0.00 0.00 0.00 2.69
96 97 3.281727 ACTCTGCTTGTGAAGGTTGAA 57.718 42.857 0.00 0.00 0.00 2.69
97 98 4.569943 GATACTCTGCTTGTGAAGGTTGA 58.430 43.478 0.00 0.00 0.00 3.18
98 99 3.369147 CGATACTCTGCTTGTGAAGGTTG 59.631 47.826 0.00 0.00 0.00 3.77
99 100 3.258372 TCGATACTCTGCTTGTGAAGGTT 59.742 43.478 0.00 0.00 0.00 3.50
100 101 2.826128 TCGATACTCTGCTTGTGAAGGT 59.174 45.455 0.00 0.00 0.00 3.50
101 102 3.443037 CTCGATACTCTGCTTGTGAAGG 58.557 50.000 0.00 0.00 0.00 3.46
102 103 3.129462 TCCTCGATACTCTGCTTGTGAAG 59.871 47.826 0.00 0.00 0.00 3.02
103 104 3.089284 TCCTCGATACTCTGCTTGTGAA 58.911 45.455 0.00 0.00 0.00 3.18
104 105 2.685388 CTCCTCGATACTCTGCTTGTGA 59.315 50.000 0.00 0.00 0.00 3.58
105 106 2.797792 GCTCCTCGATACTCTGCTTGTG 60.798 54.545 0.00 0.00 0.00 3.33
110 111 1.678627 TGAAGCTCCTCGATACTCTGC 59.321 52.381 0.00 0.00 0.00 4.26
126 127 1.746727 CGCTCCATCGCTTCGTGAAG 61.747 60.000 5.24 5.24 41.24 3.02
159 160 0.105224 TGACGAACCGCTGGAAAGAA 59.895 50.000 1.50 0.00 0.00 2.52
162 163 1.301401 CCTGACGAACCGCTGGAAA 60.301 57.895 1.50 0.00 0.00 3.13
221 224 3.002451 CCGTTGTAGTCATAGAGGAGACG 59.998 52.174 0.00 0.00 39.67 4.18
229 232 2.096980 TCGTCTGCCGTTGTAGTCATAG 59.903 50.000 0.00 0.00 37.94 2.23
230 233 2.086094 TCGTCTGCCGTTGTAGTCATA 58.914 47.619 0.00 0.00 37.94 2.15
305 308 2.034532 TCCTCACCTACGCCGTGA 59.965 61.111 0.00 0.60 37.91 4.35
330 333 2.772691 CCTCCTCGCCGTACTCACC 61.773 68.421 0.00 0.00 0.00 4.02
331 334 1.716826 CTCCTCCTCGCCGTACTCAC 61.717 65.000 0.00 0.00 0.00 3.51
335 338 2.439883 ACCTCCTCCTCGCCGTAC 60.440 66.667 0.00 0.00 0.00 3.67
352 355 1.692749 GGTAGGTGATGCAGGGGGA 60.693 63.158 0.00 0.00 0.00 4.81
405 409 2.416747 CTGGCGAAACAGAGATGTCAA 58.583 47.619 0.00 0.00 40.97 3.18
420 424 2.362397 AGACATCACTATACACCTGGCG 59.638 50.000 0.00 0.00 0.00 5.69
426 430 7.959175 TGGGGTAATTAGACATCACTATACAC 58.041 38.462 0.00 0.00 0.00 2.90
427 431 8.555896 TTGGGGTAATTAGACATCACTATACA 57.444 34.615 0.00 0.00 0.00 2.29
466 470 5.654650 AGGACCAGTAACAAACAAATGACAA 59.345 36.000 0.00 0.00 0.00 3.18
483 487 2.768527 TGCTCTAAGGATGAAGGACCAG 59.231 50.000 0.00 0.00 0.00 4.00
484 488 2.832838 TGCTCTAAGGATGAAGGACCA 58.167 47.619 0.00 0.00 0.00 4.02
514 518 1.602323 GCCCGGATTTGGTGTGTGA 60.602 57.895 0.73 0.00 0.00 3.58
576 580 1.165907 AGACAACACATGTGCCACCG 61.166 55.000 25.68 11.69 44.12 4.94
645 698 5.816777 ACATGCATTGCCCACAAATATAAAC 59.183 36.000 6.12 0.00 39.77 2.01
668 721 7.305763 CCAAAACAAAAAGAAGCACGTACATAC 60.306 37.037 0.00 0.00 0.00 2.39
689 742 0.110678 TGTGACCATACCGCCCAAAA 59.889 50.000 0.00 0.00 0.00 2.44
752 805 1.073603 AGCCTGCTTGCTTCTCTTCTT 59.926 47.619 0.00 0.00 38.85 2.52
991 1058 7.124147 AGCAATTGTTATTTATAAGCACCCAGT 59.876 33.333 7.40 0.00 0.00 4.00
1014 1081 5.491635 TGTGCATATAAAAACGCATAGCA 57.508 34.783 0.00 0.00 36.64 3.49
1125 5068 4.760047 GACAGCGGCGATGGTGGT 62.760 66.667 29.60 8.04 41.54 4.16
1421 5386 1.443872 CGCGCACGAAGAACTACCT 60.444 57.895 8.75 0.00 43.93 3.08
1521 5486 1.669795 CGAACCATTTGCCTTTCTGCC 60.670 52.381 0.00 0.00 0.00 4.85
1557 5523 6.618811 CCATAGGTAGATGGTACGAATACAC 58.381 44.000 0.00 0.00 41.42 2.90
1586 5555 0.694771 ATCACAGGCCGCATCCATAT 59.305 50.000 0.00 0.00 0.00 1.78
1596 5565 5.391312 AAACTTTATGACAATCACAGGCC 57.609 39.130 0.00 0.00 0.00 5.19
1618 5587 9.635404 TCTTTATTTGACAGGAAGAAAAGGTAA 57.365 29.630 0.00 0.00 0.00 2.85
1712 5689 1.792006 ACAGACACGTTCGGATTTCC 58.208 50.000 0.00 0.00 0.00 3.13
1719 5696 8.729529 AATATATCTCATTACAGACACGTTCG 57.270 34.615 0.00 0.00 0.00 3.95
1782 5760 1.000060 TGTTGAAACGGAGGGAGTACG 60.000 52.381 0.00 0.00 0.00 3.67
1784 5762 4.081309 CCTTATGTTGAAACGGAGGGAGTA 60.081 45.833 0.00 0.00 0.00 2.59
1797 5775 8.141298 TCATTCACTACTAACCCTTATGTTGA 57.859 34.615 0.00 0.00 0.00 3.18
1860 10191 2.479560 GCGGTAGCACCATCATTTTTCC 60.480 50.000 6.21 0.00 44.35 3.13
1900 10707 2.973419 CTAGTAGCGCTAGTAGTGGC 57.027 55.000 35.81 17.96 41.68 5.01
1917 10724 4.525996 TGGCTGTAGTCGTAATGGTACTA 58.474 43.478 0.00 0.00 0.00 1.82
1919 10726 3.788333 TGGCTGTAGTCGTAATGGTAC 57.212 47.619 0.00 0.00 0.00 3.34
1925 10732 2.086094 TCGTGATGGCTGTAGTCGTAA 58.914 47.619 0.00 0.00 0.00 3.18
1935 10742 2.347490 GTGGTGGTCGTGATGGCT 59.653 61.111 0.00 0.00 0.00 4.75
1943 10750 1.259609 TTAGGTAGTGGTGGTGGTCG 58.740 55.000 0.00 0.00 0.00 4.79
1944 10751 3.994931 ATTTAGGTAGTGGTGGTGGTC 57.005 47.619 0.00 0.00 0.00 4.02
2029 10855 1.609061 CGCAAGTGGTGAGAAGTCCAT 60.609 52.381 0.00 0.00 36.09 3.41
2096 10922 9.206870 TCGTACCACCTATACAAAAAGTAAAAG 57.793 33.333 0.00 0.00 36.05 2.27
2102 10928 7.662604 AGTTTCGTACCACCTATACAAAAAG 57.337 36.000 0.00 0.00 0.00 2.27
2111 10937 9.590451 CTTGAATATTTAGTTTCGTACCACCTA 57.410 33.333 0.00 0.00 0.00 3.08
2112 10938 8.098912 ACTTGAATATTTAGTTTCGTACCACCT 58.901 33.333 0.00 0.00 0.00 4.00
2113 10939 8.260270 ACTTGAATATTTAGTTTCGTACCACC 57.740 34.615 0.00 0.00 0.00 4.61
2119 10945 9.367444 CCAGTCTACTTGAATATTTAGTTTCGT 57.633 33.333 8.82 0.00 0.00 3.85
2127 10953 5.815581 TGTGGCCAGTCTACTTGAATATTT 58.184 37.500 5.11 0.00 0.00 1.40
2142 10968 3.443045 GCGGAACCATGTGGCCAG 61.443 66.667 5.11 0.00 39.32 4.85
2162 10988 5.934625 AGCTCTTTTCGTTCATGTGATTACT 59.065 36.000 0.00 0.00 0.00 2.24
2163 10989 6.170675 AGCTCTTTTCGTTCATGTGATTAC 57.829 37.500 0.00 0.00 0.00 1.89
2175 11001 8.462016 AGAATATGCAAATTAAGCTCTTTTCGT 58.538 29.630 0.00 0.00 0.00 3.85
2176 11002 8.847444 AGAATATGCAAATTAAGCTCTTTTCG 57.153 30.769 0.00 0.00 0.00 3.46
2200 11032 7.628794 GCCGAGTGGTATCATAGGAACTAATAG 60.629 44.444 0.00 0.00 40.72 1.73
2211 11043 4.133820 CCAAAATGCCGAGTGGTATCATA 58.866 43.478 0.00 0.00 40.01 2.15
2235 11067 0.536460 GGTCGGGCAAGTTTCCTTCA 60.536 55.000 0.00 0.00 0.00 3.02
2298 11130 1.460273 GGCCGCCAGTTCTTTTGGAA 61.460 55.000 3.91 0.00 37.96 3.53
2299 11131 1.901464 GGCCGCCAGTTCTTTTGGA 60.901 57.895 3.91 0.00 37.96 3.53
2343 11175 2.106683 GCCATTGGACGTTCTCCCG 61.107 63.158 6.95 0.00 38.49 5.14
2390 11225 1.075600 GGGAGGGTGAGAGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
2391 11226 1.452226 TTGGGAGGGTGAGAGAGGGA 61.452 60.000 0.00 0.00 0.00 4.20
2394 11229 0.252467 AGGTTGGGAGGGTGAGAGAG 60.252 60.000 0.00 0.00 0.00 3.20
2401 11236 1.509548 CCATGGAAGGTTGGGAGGGT 61.510 60.000 5.56 0.00 0.00 4.34
2424 11259 2.368439 CATGGTGATGAACGGGAACAT 58.632 47.619 0.00 0.00 0.00 2.71
2426 11261 0.451783 GCATGGTGATGAACGGGAAC 59.548 55.000 0.00 0.00 0.00 3.62
2428 11263 0.107703 GAGCATGGTGATGAACGGGA 60.108 55.000 0.00 0.00 0.00 5.14
2436 11271 2.405559 TCTGGATCAGAGCATGGTGAT 58.594 47.619 0.00 0.00 35.39 3.06
2440 11275 5.421374 TCACTATATCTGGATCAGAGCATGG 59.579 44.000 3.94 4.58 44.08 3.66
2445 11280 6.244654 TCTGGTCACTATATCTGGATCAGAG 58.755 44.000 8.52 0.00 44.08 3.35
2448 11283 5.954752 GGATCTGGTCACTATATCTGGATCA 59.045 44.000 0.00 0.00 31.68 2.92
2458 11293 6.051717 CGAAGAAAATGGATCTGGTCACTAT 58.948 40.000 0.00 0.00 0.00 2.12
2464 11299 4.192317 GCTACGAAGAAAATGGATCTGGT 58.808 43.478 0.00 0.00 0.00 4.00
2473 11308 3.195661 CCGCTAAGGCTACGAAGAAAAT 58.804 45.455 6.13 0.00 36.09 1.82
2507 15596 1.404843 GGCTCTAGGATCAAGTCGGT 58.595 55.000 0.00 0.00 0.00 4.69
2510 15599 2.968574 TGATGGGCTCTAGGATCAAGTC 59.031 50.000 0.00 0.00 0.00 3.01
2538 15627 3.281158 CACAACCCTCATGTGCATATGA 58.719 45.455 22.82 22.82 41.42 2.15
2547 15636 2.566833 TCTCCAACACAACCCTCATG 57.433 50.000 0.00 0.00 0.00 3.07
2570 15659 1.372087 GCCACAAATGCGAGAGGGAG 61.372 60.000 0.00 0.00 0.00 4.30
2602 15692 1.074775 AGTTGCTGCCCGATTTGGA 59.925 52.632 0.00 0.00 42.00 3.53
2606 15696 1.228552 AACCAGTTGCTGCCCGATT 60.229 52.632 0.00 0.00 0.00 3.34
2610 15700 2.924105 GCTCAACCAGTTGCTGCCC 61.924 63.158 5.63 0.00 40.24 5.36


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

AutoCloner maintained by Alex Coulton.