Multiple sequence alignment - TraesCS3D01G280700

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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 TraesCS3D01G280700 chr3D 100.000 4339 0 0 1 4339 388534098 388538436 0.000000e+00 8013.0
1 TraesCS3D01G280700 chr3D 95.108 1206 58 1 3134 4339 456085815 456084611 0.000000e+00 1899.0
2 TraesCS3D01G280700 chr3D 93.318 853 50 6 2295 3140 605968448 605967596 0.000000e+00 1253.0
3 TraesCS3D01G280700 chr7B 89.318 2696 210 39 1680 4339 48888982 48891635 0.000000e+00 3312.0
4 TraesCS3D01G280700 chr7B 93.059 850 55 4 2295 3140 648021837 648020988 0.000000e+00 1240.0
5 TraesCS3D01G280700 chr7B 76.382 199 39 7 175 369 500169851 500169657 2.760000e-17 100.0
6 TraesCS3D01G280700 chr3B 92.162 1480 92 14 1680 3140 217386978 217385504 0.000000e+00 2069.0
7 TraesCS3D01G280700 chr3B 90.114 1497 102 15 1680 3140 217316029 217314543 0.000000e+00 1903.0
8 TraesCS3D01G280700 chr3B 94.606 1205 65 0 3134 4338 217385474 217384270 0.000000e+00 1866.0
9 TraesCS3D01G280700 chr3B 94.362 1206 68 0 3134 4339 173150424 173151629 0.000000e+00 1851.0
10 TraesCS3D01G280700 chr3B 91.039 982 29 22 1 958 505835935 505836881 0.000000e+00 1271.0
11 TraesCS3D01G280700 chr3B 93.311 598 14 4 1082 1658 505837397 505837989 0.000000e+00 859.0
12 TraesCS3D01G280700 chr3B 95.588 136 6 0 944 1079 505836896 505837031 7.310000e-53 219.0
13 TraesCS3D01G280700 chr3B 80.749 187 28 8 173 355 799860393 799860575 5.850000e-29 139.0
14 TraesCS3D01G280700 chr4D 91.369 1483 71 14 1675 3140 445341672 445343114 0.000000e+00 1977.0
15 TraesCS3D01G280700 chr4D 96.339 1120 37 1 3134 4249 445343144 445344263 0.000000e+00 1838.0
16 TraesCS3D01G280700 chr4D 86.635 853 73 15 1680 2518 471331306 471332131 0.000000e+00 905.0
17 TraesCS3D01G280700 chr5D 89.973 1506 104 16 1680 3140 447760675 447759172 0.000000e+00 1901.0
18 TraesCS3D01G280700 chr5D 94.671 1201 63 1 3139 4339 362181108 362179909 0.000000e+00 1862.0
19 TraesCS3D01G280700 chr5D 84.930 856 85 18 1680 2524 362182640 362181818 0.000000e+00 826.0
20 TraesCS3D01G280700 chr5D 77.895 190 38 4 168 355 461440621 461440808 9.860000e-22 115.0
21 TraesCS3D01G280700 chr5D 77.720 193 34 9 171 357 352219446 352219257 4.590000e-20 110.0
22 TraesCS3D01G280700 chr5D 84.167 120 12 4 235 354 409339567 409339679 4.590000e-20 110.0
23 TraesCS3D01G280700 chr5D 91.892 74 4 2 165 237 353478312 353478240 7.680000e-18 102.0
24 TraesCS3D01G280700 chr5B 90.101 1485 108 23 1677 3140 34285663 34284197 0.000000e+00 1892.0
25 TraesCS3D01G280700 chr5B 89.669 1510 107 22 1677 3140 272744423 272745929 0.000000e+00 1879.0
26 TraesCS3D01G280700 chr5B 77.720 193 34 9 171 357 416850934 416851123 4.590000e-20 110.0
27 TraesCS3D01G280700 chr5B 91.667 72 4 2 167 237 417438706 417438636 9.930000e-17 99.0
28 TraesCS3D01G280700 chr1B 89.205 1510 111 19 1677 3140 672800270 672801773 0.000000e+00 1838.0
29 TraesCS3D01G280700 chr1B 89.493 809 51 16 1679 2472 282313604 282312815 0.000000e+00 992.0
30 TraesCS3D01G280700 chr1B 80.000 200 33 7 160 355 627928854 627929050 1.630000e-29 141.0
31 TraesCS3D01G280700 chr6B 94.196 1206 66 2 3134 4339 68422830 68421629 0.000000e+00 1836.0
32 TraesCS3D01G280700 chr6B 92.832 851 56 5 2295 3140 704056432 704057282 0.000000e+00 1229.0
33 TraesCS3D01G280700 chr1A 93.833 1200 74 0 3140 4339 535101801 535100602 0.000000e+00 1807.0
34 TraesCS3D01G280700 chr1A 81.818 187 28 6 172 355 550314016 550314199 7.520000e-33 152.0
35 TraesCS3D01G280700 chr4B 93.284 1206 79 2 3134 4339 135202222 135201019 0.000000e+00 1777.0
36 TraesCS3D01G280700 chr2A 87.108 1497 147 25 1680 3140 411115086 411116572 0.000000e+00 1653.0
37 TraesCS3D01G280700 chr2A 89.390 1263 89 10 1880 3132 776057924 776056697 0.000000e+00 1548.0
38 TraesCS3D01G280700 chr2A 80.697 373 54 5 1679 2042 775079145 775078782 1.540000e-69 274.0
39 TraesCS3D01G280700 chr2A 82.258 248 43 1 1680 1927 202066044 202065798 3.400000e-51 213.0
40 TraesCS3D01G280700 chr2A 80.242 248 49 0 1680 1927 470628502 470628749 2.060000e-43 187.0
41 TraesCS3D01G280700 chr2A 80.400 250 44 5 1680 1927 131898134 131898380 7.410000e-43 185.0
42 TraesCS3D01G280700 chr7D 91.919 1089 48 5 2054 3140 167579562 167580612 0.000000e+00 1487.0
43 TraesCS3D01G280700 chr7D 94.947 475 20 3 1944 2415 579943130 579943603 0.000000e+00 741.0
44 TraesCS3D01G280700 chr7D 75.879 199 40 7 175 369 475873995 475873801 1.280000e-15 95.3
45 TraesCS3D01G280700 chr3A 88.227 739 41 25 160 870 509798732 509799452 0.000000e+00 841.0
46 TraesCS3D01G280700 chr3A 83.607 488 29 22 1061 1522 509799544 509800006 1.120000e-110 411.0
47 TraesCS3D01G280700 chr3A 93.407 91 5 1 1 91 509798611 509798700 2.720000e-27 134.0
48 TraesCS3D01G280700 chr3A 97.727 44 1 0 937 980 509799487 509799530 4.650000e-10 76.8
49 TraesCS3D01G280700 chr4A 80.978 184 35 0 172 355 19622312 19622495 3.500000e-31 147.0
50 TraesCS3D01G280700 chr1D 82.286 175 25 6 172 343 457851867 457852038 3.500000e-31 147.0
51 TraesCS3D01G280700 chr5A 78.723 188 36 4 168 353 581487921 581488106 5.890000e-24 122.0
52 TraesCS3D01G280700 chr5A 84.298 121 11 5 235 354 520529270 520529383 1.280000e-20 111.0
53 TraesCS3D01G280700 chr7A 76.263 198 39 7 172 365 520060392 520060585 9.930000e-17 99.0
54 TraesCS3D01G280700 chr2D 89.041 73 8 0 165 237 512043043 512043115 1.660000e-14 91.6


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 TraesCS3D01G280700 chr3D 388534098 388538436 4338 False 8013.0 8013 100.000000 1 4339 1 chr3D.!!$F1 4338
1 TraesCS3D01G280700 chr3D 456084611 456085815 1204 True 1899.0 1899 95.108000 3134 4339 1 chr3D.!!$R1 1205
2 TraesCS3D01G280700 chr3D 605967596 605968448 852 True 1253.0 1253 93.318000 2295 3140 1 chr3D.!!$R2 845
3 TraesCS3D01G280700 chr7B 48888982 48891635 2653 False 3312.0 3312 89.318000 1680 4339 1 chr7B.!!$F1 2659
4 TraesCS3D01G280700 chr7B 648020988 648021837 849 True 1240.0 1240 93.059000 2295 3140 1 chr7B.!!$R2 845
5 TraesCS3D01G280700 chr3B 217384270 217386978 2708 True 1967.5 2069 93.384000 1680 4338 2 chr3B.!!$R2 2658
6 TraesCS3D01G280700 chr3B 217314543 217316029 1486 True 1903.0 1903 90.114000 1680 3140 1 chr3B.!!$R1 1460
7 TraesCS3D01G280700 chr3B 173150424 173151629 1205 False 1851.0 1851 94.362000 3134 4339 1 chr3B.!!$F1 1205
8 TraesCS3D01G280700 chr3B 505835935 505837989 2054 False 783.0 1271 93.312667 1 1658 3 chr3B.!!$F3 1657
9 TraesCS3D01G280700 chr4D 445341672 445344263 2591 False 1907.5 1977 93.854000 1675 4249 2 chr4D.!!$F2 2574
10 TraesCS3D01G280700 chr4D 471331306 471332131 825 False 905.0 905 86.635000 1680 2518 1 chr4D.!!$F1 838
11 TraesCS3D01G280700 chr5D 447759172 447760675 1503 True 1901.0 1901 89.973000 1680 3140 1 chr5D.!!$R3 1460
12 TraesCS3D01G280700 chr5D 362179909 362182640 2731 True 1344.0 1862 89.800500 1680 4339 2 chr5D.!!$R4 2659
13 TraesCS3D01G280700 chr5B 34284197 34285663 1466 True 1892.0 1892 90.101000 1677 3140 1 chr5B.!!$R1 1463
14 TraesCS3D01G280700 chr5B 272744423 272745929 1506 False 1879.0 1879 89.669000 1677 3140 1 chr5B.!!$F1 1463
15 TraesCS3D01G280700 chr1B 672800270 672801773 1503 False 1838.0 1838 89.205000 1677 3140 1 chr1B.!!$F2 1463
16 TraesCS3D01G280700 chr1B 282312815 282313604 789 True 992.0 992 89.493000 1679 2472 1 chr1B.!!$R1 793
17 TraesCS3D01G280700 chr6B 68421629 68422830 1201 True 1836.0 1836 94.196000 3134 4339 1 chr6B.!!$R1 1205
18 TraesCS3D01G280700 chr6B 704056432 704057282 850 False 1229.0 1229 92.832000 2295 3140 1 chr6B.!!$F1 845
19 TraesCS3D01G280700 chr1A 535100602 535101801 1199 True 1807.0 1807 93.833000 3140 4339 1 chr1A.!!$R1 1199
20 TraesCS3D01G280700 chr4B 135201019 135202222 1203 True 1777.0 1777 93.284000 3134 4339 1 chr4B.!!$R1 1205
21 TraesCS3D01G280700 chr2A 411115086 411116572 1486 False 1653.0 1653 87.108000 1680 3140 1 chr2A.!!$F2 1460
22 TraesCS3D01G280700 chr2A 776056697 776057924 1227 True 1548.0 1548 89.390000 1880 3132 1 chr2A.!!$R3 1252
23 TraesCS3D01G280700 chr7D 167579562 167580612 1050 False 1487.0 1487 91.919000 2054 3140 1 chr7D.!!$F1 1086
24 TraesCS3D01G280700 chr3A 509798611 509800006 1395 False 365.7 841 90.742000 1 1522 4 chr3A.!!$F1 1521

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
643 681 0.178947 GATGGGGTGTTGGGGTTCAA 60.179 55.0 0.0 0.0 0.00 2.69 F
1652 2110 0.253044 TCATGCCGGGAAAGGAGAAG 59.747 55.0 0.0 0.0 0.00 2.85 F
1659 2117 0.322906 GGGAAAGGAGAAGGCAGTGG 60.323 60.0 0.0 0.0 0.00 4.00 F
1661 2119 0.962855 GAAAGGAGAAGGCAGTGGGC 60.963 60.0 0.0 0.0 43.74 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2358 0.591170 GCACATTACAAGTGTGGCGT 59.409 50.000 8.17 0.0 45.39 5.68 R
3233 3920 1.284982 CGTTCTTGCCTGTGGAGTCG 61.285 60.000 0.00 0.0 0.00 4.18 R
3281 3968 1.609072 CTCCATCCGCTATCGAAGACA 59.391 52.381 0.00 0.0 42.51 3.41 R
4021 4709 6.899393 AACATTAGCACAATCAAGAAGGAA 57.101 33.333 0.00 0.0 0.00 3.36 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
41 42 0.875059 CCTTGCGAAAACCCTGAGAC 59.125 55.000 0.00 0.00 0.00 3.36
76 82 1.672737 CGAGCAGGTATGAGCACAACA 60.673 52.381 0.00 0.00 0.00 3.33
78 84 2.813754 GAGCAGGTATGAGCACAACAAA 59.186 45.455 0.00 0.00 0.00 2.83
79 85 2.554032 AGCAGGTATGAGCACAACAAAC 59.446 45.455 0.00 0.00 0.00 2.93
82 88 3.565482 CAGGTATGAGCACAACAAACACT 59.435 43.478 0.00 0.00 0.00 3.55
83 89 3.815401 AGGTATGAGCACAACAAACACTC 59.185 43.478 0.00 0.00 0.00 3.51
84 90 3.363970 GGTATGAGCACAACAAACACTCG 60.364 47.826 0.00 0.00 0.00 4.18
85 91 2.017138 TGAGCACAACAAACACTCGA 57.983 45.000 0.00 0.00 0.00 4.04
86 92 1.933181 TGAGCACAACAAACACTCGAG 59.067 47.619 11.84 11.84 0.00 4.04
87 93 2.201732 GAGCACAACAAACACTCGAGA 58.798 47.619 21.68 0.00 0.00 4.04
88 94 2.205074 AGCACAACAAACACTCGAGAG 58.795 47.619 21.68 14.72 0.00 3.20
89 95 1.333258 GCACAACAAACACTCGAGAGC 60.333 52.381 21.68 3.31 0.00 4.09
90 96 2.205074 CACAACAAACACTCGAGAGCT 58.795 47.619 21.68 0.00 0.00 4.09
91 97 3.381045 CACAACAAACACTCGAGAGCTA 58.619 45.455 21.68 0.00 0.00 3.32
92 98 3.426859 CACAACAAACACTCGAGAGCTAG 59.573 47.826 21.68 8.34 0.00 3.42
93 99 2.355717 ACAAACACTCGAGAGCTAGC 57.644 50.000 21.68 6.62 0.00 3.42
94 100 1.067495 ACAAACACTCGAGAGCTAGCC 60.067 52.381 21.68 2.81 0.00 3.93
119 125 0.315568 CCGGAGCAGAGTAGGCATAC 59.684 60.000 0.00 0.00 0.00 2.39
495 526 3.056393 TCCTTCCTATACCAACGTGTGTG 60.056 47.826 0.00 0.00 0.00 3.82
496 527 3.306502 CCTTCCTATACCAACGTGTGTGT 60.307 47.826 0.00 0.00 0.00 3.72
497 528 3.306917 TCCTATACCAACGTGTGTGTG 57.693 47.619 0.00 0.00 0.00 3.82
498 529 1.730064 CCTATACCAACGTGTGTGTGC 59.270 52.381 0.00 0.00 0.00 4.57
547 578 4.644103 GGTGACGCTTTATACTAGGTGA 57.356 45.455 0.00 0.00 0.00 4.02
548 579 4.608951 GGTGACGCTTTATACTAGGTGAG 58.391 47.826 0.00 0.00 0.00 3.51
549 580 4.337555 GGTGACGCTTTATACTAGGTGAGA 59.662 45.833 0.00 0.00 0.00 3.27
555 587 7.479150 ACGCTTTATACTAGGTGAGAAAGTAC 58.521 38.462 0.00 0.00 0.00 2.73
567 603 5.163405 GGTGAGAAAGTACATATCTGCCTCA 60.163 44.000 0.00 0.00 0.00 3.86
568 604 5.751028 GTGAGAAAGTACATATCTGCCTCAC 59.249 44.000 0.00 0.00 37.66 3.51
569 605 5.163405 TGAGAAAGTACATATCTGCCTCACC 60.163 44.000 0.00 0.00 0.00 4.02
570 606 4.101741 AGAAAGTACATATCTGCCTCACCC 59.898 45.833 0.00 0.00 0.00 4.61
571 607 2.330216 AGTACATATCTGCCTCACCCC 58.670 52.381 0.00 0.00 0.00 4.95
643 681 0.178947 GATGGGGTGTTGGGGTTCAA 60.179 55.000 0.00 0.00 0.00 2.69
691 729 1.078709 CGATTTGCTCGGTGATGTGT 58.921 50.000 0.00 0.00 43.82 3.72
693 731 1.398390 GATTTGCTCGGTGATGTGTCC 59.602 52.381 0.00 0.00 0.00 4.02
822 861 4.467062 GCTCAAAAGCGCTCGGCC 62.467 66.667 12.06 0.00 45.17 6.13
897 937 3.181483 GGAAATGGTGCATGGTTGAGATC 60.181 47.826 0.00 0.00 0.00 2.75
899 939 2.118313 TGGTGCATGGTTGAGATCAG 57.882 50.000 0.00 0.00 0.00 2.90
900 940 1.629861 TGGTGCATGGTTGAGATCAGA 59.370 47.619 0.00 0.00 0.00 3.27
901 941 2.240414 TGGTGCATGGTTGAGATCAGAT 59.760 45.455 0.00 0.00 0.00 2.90
902 942 2.877168 GGTGCATGGTTGAGATCAGATC 59.123 50.000 1.64 1.64 0.00 2.75
904 944 3.311871 GTGCATGGTTGAGATCAGATCAC 59.688 47.826 13.14 7.03 0.00 3.06
908 948 1.202580 GGTTGAGATCAGATCACCGGG 60.203 57.143 13.14 0.00 0.00 5.73
910 950 1.403814 TGAGATCAGATCACCGGGAC 58.596 55.000 13.14 0.00 0.00 4.46
1010 1081 1.787012 CTTGGCAGCATGTTGAAACC 58.213 50.000 14.38 5.77 39.31 3.27
1036 1107 2.525368 GGTGGAACAGGCCTAAAATGT 58.475 47.619 3.98 0.00 41.80 2.71
1056 1127 1.082756 CACGCTCTCAACGTTTGGC 60.083 57.895 0.00 0.00 42.96 4.52
1079 1150 1.686052 TCCGCTTTGCTGTGGATTTTT 59.314 42.857 3.73 0.00 41.18 1.94
1146 1582 0.327924 TCCACGACTGAATGGCCAAT 59.672 50.000 10.96 0.00 35.81 3.16
1260 1700 1.004918 CTTTCGTCCCGAGCCAACT 60.005 57.895 0.00 0.00 37.14 3.16
1307 1748 2.776526 AGGGTGGCACCTTGTGGA 60.777 61.111 33.87 0.00 37.69 4.02
1515 1973 1.517276 CGACCAATTCATCTCGCGTAC 59.483 52.381 5.77 0.00 0.00 3.67
1597 2055 4.357947 GCCGCACTGAGTCGGTGA 62.358 66.667 31.93 0.00 46.79 4.02
1611 2069 7.657761 ACTGAGTCGGTGATTTTATATTGATCC 59.342 37.037 3.08 0.00 0.00 3.36
1612 2070 6.645003 TGAGTCGGTGATTTTATATTGATCCG 59.355 38.462 0.00 0.00 37.29 4.18
1652 2110 0.253044 TCATGCCGGGAAAGGAGAAG 59.747 55.000 0.00 0.00 0.00 2.85
1658 2116 0.674895 CGGGAAAGGAGAAGGCAGTG 60.675 60.000 0.00 0.00 0.00 3.66
1659 2117 0.322906 GGGAAAGGAGAAGGCAGTGG 60.323 60.000 0.00 0.00 0.00 4.00
1660 2118 0.322906 GGAAAGGAGAAGGCAGTGGG 60.323 60.000 0.00 0.00 0.00 4.61
1661 2119 0.962855 GAAAGGAGAAGGCAGTGGGC 60.963 60.000 0.00 0.00 43.74 5.36
1780 2238 4.858680 TTGTGTGGCGCCCGACAA 62.859 61.111 27.71 27.71 33.39 3.18
2069 2561 6.267242 CACATCCCTCTCAGATCTGAAGATTA 59.733 42.308 25.09 12.04 39.39 1.75
2113 2605 5.745988 ATCCCTCCTACTAGGTAAACTCA 57.254 43.478 1.83 0.00 36.53 3.41
2200 2701 5.541868 TGGAACCCTTGATTTGCTTGATTTA 59.458 36.000 0.00 0.00 0.00 1.40
2256 2757 4.682860 ACCGTAGTGTTGTTCATTAGTTCG 59.317 41.667 0.00 0.00 0.00 3.95
2296 2797 9.802039 TTGTTAGTGAAACCCTAGATTGTTTAT 57.198 29.630 0.00 0.00 37.80 1.40
2360 2891 9.950496 AACTATGAAATGTTGAGTTCTGTAGAT 57.050 29.630 0.00 0.00 0.00 1.98
2614 3253 4.427394 GCTTCTCGACGATGCCAT 57.573 55.556 0.00 0.00 36.95 4.40
2655 3294 4.838152 TGATGCGCGAGAAGGGGC 62.838 66.667 12.10 0.00 45.18 5.80
2720 3365 4.590647 TGGTTGAAATTGACATGCCCTAAA 59.409 37.500 0.00 0.00 0.00 1.85
2823 3471 1.138247 GAGCGGTACACACCCTACG 59.862 63.158 0.00 0.00 42.43 3.51
2860 3508 1.002624 TCCCGTGGATTCAGTTGGC 60.003 57.895 0.00 0.00 0.00 4.52
2866 3514 2.054453 GGATTCAGTTGGCCAGCCC 61.054 63.158 16.95 6.00 34.56 5.19
2965 3613 2.501610 GACTGGGGAGATGACCGC 59.498 66.667 0.00 0.00 42.15 5.68
3017 3665 2.520982 CCTATCGACGGGAGGCCA 60.521 66.667 5.01 0.00 0.00 5.36
3038 3686 3.990469 CACTATGTATGAGCACCGATTCC 59.010 47.826 0.00 0.00 0.00 3.01
3233 3920 2.224209 TGTCTCGAGGACTTTGTTTCCC 60.224 50.000 13.56 0.00 44.74 3.97
3281 3968 1.598130 GTGGCTGAAGGCGTTGACT 60.598 57.895 0.00 0.00 44.42 3.41
3374 4061 7.077605 TGTTTTGCTATCAAGTCATTTCTTCG 58.922 34.615 0.00 0.00 33.12 3.79
4021 4709 3.059884 CGTATTGACTAAGCATCGCCAT 58.940 45.455 0.00 0.00 0.00 4.40
4233 4925 7.360113 ACCTACAATGGTTTCTTGAAAATGT 57.640 32.000 0.00 4.51 36.89 2.71
4323 5015 2.831685 TCGAAGTGGCAGTACAACAT 57.168 45.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.599792 CTCGCCGTTGCTGCTTTGG 62.600 63.158 0.00 0.53 34.43 3.28
76 82 0.171455 CGGCTAGCTCTCGAGTGTTT 59.829 55.000 15.72 5.69 0.00 2.83
78 84 2.766400 GCGGCTAGCTCTCGAGTGT 61.766 63.158 15.72 3.81 44.04 3.55
79 85 2.025441 GCGGCTAGCTCTCGAGTG 59.975 66.667 15.72 11.53 44.04 3.51
89 95 4.577246 GCTCCGGTCAGCGGCTAG 62.577 72.222 11.45 4.83 0.00 3.42
93 99 4.504916 CTCTGCTCCGGTCAGCGG 62.505 72.222 16.14 16.14 45.90 5.52
94 100 2.329678 CTACTCTGCTCCGGTCAGCG 62.330 65.000 17.63 15.04 42.92 5.18
100 106 0.315568 GTATGCCTACTCTGCTCCGG 59.684 60.000 0.00 0.00 0.00 5.14
161 167 1.165270 ACACCTACGTACGTACCCAC 58.835 55.000 23.60 0.00 0.00 4.61
162 168 1.539388 CAACACCTACGTACGTACCCA 59.461 52.381 23.60 6.22 0.00 4.51
163 169 1.810151 TCAACACCTACGTACGTACCC 59.190 52.381 23.60 0.00 0.00 3.69
164 170 2.729156 GCTCAACACCTACGTACGTACC 60.729 54.545 23.60 2.84 0.00 3.34
165 171 2.160417 AGCTCAACACCTACGTACGTAC 59.840 50.000 23.60 15.90 0.00 3.67
416 425 1.436983 GGCTTCCTTATCCGGTTGCG 61.437 60.000 0.00 0.00 0.00 4.85
417 426 1.436983 CGGCTTCCTTATCCGGTTGC 61.437 60.000 0.00 0.00 39.52 4.17
482 510 2.526993 GCGCACACACACGTTGGTA 61.527 57.895 0.30 0.00 0.00 3.25
483 511 3.871574 GCGCACACACACGTTGGT 61.872 61.111 0.30 0.00 0.00 3.67
498 529 2.495551 GAAATATCTGCGCGCGCG 60.496 61.111 45.73 45.73 45.51 6.86
540 571 6.266558 AGGCAGATATGTACTTTCTCACCTAG 59.733 42.308 0.00 0.00 0.00 3.02
541 572 6.136857 AGGCAGATATGTACTTTCTCACCTA 58.863 40.000 0.00 0.00 0.00 3.08
544 575 5.751028 GTGAGGCAGATATGTACTTTCTCAC 59.249 44.000 0.00 0.00 37.50 3.51
545 576 5.163405 GGTGAGGCAGATATGTACTTTCTCA 60.163 44.000 0.00 0.00 0.00 3.27
546 577 5.293560 GGTGAGGCAGATATGTACTTTCTC 58.706 45.833 0.00 0.00 0.00 2.87
547 578 4.101741 GGGTGAGGCAGATATGTACTTTCT 59.898 45.833 0.00 0.00 0.00 2.52
548 579 4.381411 GGGTGAGGCAGATATGTACTTTC 58.619 47.826 0.00 0.00 0.00 2.62
549 580 3.136626 GGGGTGAGGCAGATATGTACTTT 59.863 47.826 0.00 0.00 0.00 2.66
555 587 1.302033 GCGGGGTGAGGCAGATATG 60.302 63.158 0.00 0.00 0.00 1.78
619 656 1.304381 CCCAACACCCCATCACCTG 60.304 63.158 0.00 0.00 0.00 4.00
822 861 2.223572 ACTGCACGCTGAAAAGGAAAAG 60.224 45.455 2.69 0.00 0.00 2.27
908 948 0.248377 GCATTTGAGCAGCATCCGTC 60.248 55.000 0.00 0.00 0.00 4.79
910 950 1.298116 CGCATTTGAGCAGCATCCG 60.298 57.895 0.00 0.00 0.00 4.18
911 951 0.171903 AACGCATTTGAGCAGCATCC 59.828 50.000 0.00 0.00 0.00 3.51
912 952 1.265568 CAACGCATTTGAGCAGCATC 58.734 50.000 0.00 0.00 37.39 3.91
913 953 0.108992 CCAACGCATTTGAGCAGCAT 60.109 50.000 0.00 0.00 37.39 3.79
914 954 1.286570 CCAACGCATTTGAGCAGCA 59.713 52.632 0.00 0.00 37.39 4.41
980 1051 3.564345 CTGCCAAGCTGCTCCCACT 62.564 63.158 1.00 0.00 0.00 4.00
981 1052 3.060615 CTGCCAAGCTGCTCCCAC 61.061 66.667 1.00 0.00 0.00 4.61
1010 1081 2.674380 GCCTGTTCCACCCTGCAG 60.674 66.667 6.78 6.78 0.00 4.41
1036 1107 1.493772 CCAAACGTTGAGAGCGTGTA 58.506 50.000 0.00 0.00 42.10 2.90
1056 1127 0.962356 ATCCACAGCAAAGCGGAAGG 60.962 55.000 0.00 0.00 0.00 3.46
1079 1150 2.038659 CCCCTTCTTGTTTGAGGCAAA 58.961 47.619 0.00 0.00 0.00 3.68
1080 1151 1.703411 CCCCTTCTTGTTTGAGGCAA 58.297 50.000 0.00 0.00 0.00 4.52
1081 1152 0.827507 GCCCCTTCTTGTTTGAGGCA 60.828 55.000 0.00 0.00 38.79 4.75
1082 1153 1.866853 CGCCCCTTCTTGTTTGAGGC 61.867 60.000 0.00 0.00 35.55 4.70
1086 1521 2.650778 GGCGCCCCTTCTTGTTTG 59.349 61.111 18.11 0.00 0.00 2.93
1113 1548 2.029290 GTCGTGGAAGCCTTGAAGAGTA 60.029 50.000 0.00 0.00 0.00 2.59
1146 1582 1.601162 GGTGACACGAAGAGCAACGTA 60.601 52.381 0.00 0.00 40.76 3.57
1260 1700 1.378378 TCCGCTTTGGATCAAGGCA 59.622 52.632 13.57 0.00 44.80 4.75
1307 1748 2.433145 CGTGACAGCGGCTGTGAT 60.433 61.111 37.72 15.94 45.44 3.06
1413 1855 2.127758 GCAGCGGACAAAACGACG 60.128 61.111 0.00 0.00 0.00 5.12
1554 2012 1.725665 CTGCAATCGCTGGTGGATG 59.274 57.895 0.00 0.00 39.64 3.51
1576 2034 2.701780 CCGACTCAGTGCGGCTAGT 61.702 63.158 0.00 0.00 41.17 2.57
1611 2069 2.290093 GGTGGGTTCGATCTAGTACTCG 59.710 54.545 0.00 0.00 36.25 4.18
1612 2070 3.553904 AGGTGGGTTCGATCTAGTACTC 58.446 50.000 0.00 0.00 0.00 2.59
1672 2130 3.803082 TGATTTCTGCCGCAGCGC 61.803 61.111 15.98 0.00 44.31 5.92
1673 2131 1.985447 ATGTGATTTCTGCCGCAGCG 61.985 55.000 15.98 8.18 44.31 5.18
1674 2132 1.016627 TATGTGATTTCTGCCGCAGC 58.983 50.000 15.98 2.13 40.48 5.25
1675 2133 3.976793 AATATGTGATTTCTGCCGCAG 57.023 42.857 14.62 14.62 0.00 5.18
1811 2269 1.154205 GCATGCGACGCCTAAGACAT 61.154 55.000 18.69 0.00 0.00 3.06
1898 2358 0.591170 GCACATTACAAGTGTGGCGT 59.409 50.000 8.17 0.00 45.39 5.68
1936 2404 1.631072 CCGATGCGCTTAAGTCACG 59.369 57.895 9.73 0.52 0.00 4.35
2069 2561 1.889829 GGAGATCGAATCCACGGATCT 59.110 52.381 13.65 2.65 36.79 2.75
2113 2605 3.561528 GGAGGAAAAGAAAGGGAACGGAT 60.562 47.826 0.00 0.00 0.00 4.18
2200 2701 8.982723 ACTATGACTACACATCCTAAATCAAGT 58.017 33.333 0.00 0.00 0.00 3.16
2613 3252 1.452145 GCCCGGTGTTGTGTGTCAAT 61.452 55.000 0.00 0.00 38.38 2.57
2614 3253 2.115911 GCCCGGTGTTGTGTGTCAA 61.116 57.895 0.00 0.00 0.00 3.18
2698 3338 4.799564 TTAGGGCATGTCAATTTCAACC 57.200 40.909 0.00 0.00 0.00 3.77
2720 3365 8.715191 TCTGCAAAAACAAGTAATGACAAATT 57.285 26.923 0.00 0.00 0.00 1.82
2866 3514 3.851845 TTGAGGTTCGGCGTGGACG 62.852 63.158 6.85 0.00 43.27 4.79
3017 3665 3.305403 CGGAATCGGTGCTCATACATAGT 60.305 47.826 0.00 0.00 0.00 2.12
3093 3741 3.012959 TCTCCCTCCTCTACATCAACCTT 59.987 47.826 0.00 0.00 0.00 3.50
3148 3835 2.525075 TGGCATCCACAGGGCAAA 59.475 55.556 0.00 0.00 35.67 3.68
3233 3920 1.284982 CGTTCTTGCCTGTGGAGTCG 61.285 60.000 0.00 0.00 0.00 4.18
3281 3968 1.609072 CTCCATCCGCTATCGAAGACA 59.391 52.381 0.00 0.00 42.51 3.41
4021 4709 6.899393 AACATTAGCACAATCAAGAAGGAA 57.101 33.333 0.00 0.00 0.00 3.36
4122 4814 3.058501 CACACAAAGATTGAACCGGGTAC 60.059 47.826 6.32 0.00 0.00 3.34
4233 4925 1.538204 GCGGGCATATCTCAACTCGAA 60.538 52.381 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.